Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold150
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: 1465027
ACGTcount: A:0.31, C:0.15, G:0.16, T:0.31
Warning! 98465 characters in sequence are not A, C, G, or T
File 3 of 9
Found at i:268882 original size:27 final size:28
Alignment explanation
Indices: 268834--268891 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 28
268824 TTATTTATAA
*
268834 ATATAATTTTAATATATATAAT-TTTTT
1 ATATAATTTTAATAAATATAATATTTTT
268861 ATATAAATTTTAATAAAT-TAATAATTTTT
1 ATAT-AATTTTAATAAATATAAT-ATTTTT
268890 AT
1 AT
268892 TATTTAAATT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
27 8 0.30
28 12 0.44
29 7 0.26
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (28 bp):
ATATAATTTTAATAAATATAATATTTTT
Found at i:268909 original size:29 final size:30
Alignment explanation
Indices: 268834--268926 Score: 90
Period size: 29 Copynumber: 3.2 Consensus size: 30
268824 TTATTTATAA
268834 ATAT-AATTTTAATA-TATATAA-TTTT-TT
1 ATATAAATTTTAATATTA-ATAATTTTTATT
268861 ATATAAATTTTAATAAATTAATAATTTTTATT
1 ATATAAATTTTAAT--ATTAATAATTTTTATT
*
268893 ATTTAAA-TTTAATATTAA-AATATTTTATT
1 ATATAAATTTTAATATTAATAAT-TTTTATT
*
268922 TTATA
1 ATATA
268927 TTAATATTTT
Statistics
Matches: 56, Mismatches: 3, Indels: 12
0.79 0.04 0.17
Matches are distributed among these distances:
27 4 0.07
28 12 0.21
29 15 0.27
30 5 0.09
31 12 0.21
32 8 0.14
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (30 bp):
ATATAAATTTTAATATTAATAATTTTTATT
Found at i:268922 original size:20 final size:20
Alignment explanation
Indices: 268899--268941 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
268889 TATTATTTAA
268899 ATTTAATATTAAAATATTTT
1 ATTTAATATTAAAATATTTT
* * *
268919 ATTTTATATTAATATTTTTT
1 ATTTAATATTAAAATATTTT
268939 ATT
1 ATT
268942 ATATTCATGT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (20 bp):
ATTTAATATTAAAATATTTT
Found at i:268934 original size:18 final size:18
Alignment explanation
Indices: 268877--268946 Score: 62
Period size: 18 Copynumber: 4.2 Consensus size: 18
268867 ATTTTAATAA
*
268877 ATTAATAATTTTTATTAT
1 ATTAATATTTTTTATTAT
**
268895 -TTAA-ATTTAATATTA-
1 ATTAATATTTTTTATTAT
268910 A--AATATTTTATT-TTAT
1 ATTAATATTTT-TTATTAT
268926 ATTAATATTTTTTATTAT
1 ATTAATATTTTTTATTAT
268944 ATT
1 ATT
268947 CATGTTATAT
Statistics
Matches: 40, Mismatches: 5, Indels: 14
0.68 0.08 0.24
Matches are distributed among these distances:
14 2 0.05
15 7 0.17
16 10 0.25
17 6 0.15
18 15 0.38
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (18 bp):
ATTAATATTTTTTATTAT
Found at i:269699 original size:15 final size:15
Alignment explanation
Indices: 269679--269708 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
269669 ATGAATCTGC
269679 TACATGTATGTCTTA
1 TACATGTATGTCTTA
269694 TACATGTATGTCTTA
1 TACATGTATGTCTTA
269709 AAATGCTACA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.27, C:0.13, G:0.13, T:0.47
Consensus pattern (15 bp):
TACATGTATGTCTTA
Found at i:273858 original size:4 final size:4
Alignment explanation
Indices: 273851--273896 Score: 92
Period size: 4 Copynumber: 11.5 Consensus size: 4
273841 GCATTCTTGC
273851 ATCT ATCT ATCT ATCT ATCT ATCT ATCT ATCT ATCT ATCT ATCT AT
1 ATCT ATCT ATCT ATCT ATCT ATCT ATCT ATCT ATCT ATCT ATCT AT
273897 ATATATATAT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 42 1.00
ACGTcount: A:0.26, C:0.24, G:0.00, T:0.50
Consensus pattern (4 bp):
ATCT
Found at i:273901 original size:2 final size:2
Alignment explanation
Indices: 273894--273922 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
273884 TCTATCTATC
273894 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
273923 GCTTTGGATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:276367 original size:29 final size:29
Alignment explanation
Indices: 276325--276382 Score: 107
Period size: 29 Copynumber: 2.0 Consensus size: 29
276315 TTTAAATACT
276325 TATGTGTAACATGAATGTGAAGAGGGCAA
1 TATGTGTAACATGAATGTGAAGAGGGCAA
*
276354 TATGTTTAACATGAATGTGAAGAGGGCAA
1 TATGTGTAACATGAATGTGAAGAGGGCAA
276383 AAAAAAAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.38, C:0.07, G:0.29, T:0.26
Consensus pattern (29 bp):
TATGTGTAACATGAATGTGAAGAGGGCAA
Found at i:282084 original size:36 final size:35
Alignment explanation
Indices: 282026--282102 Score: 86
Period size: 36 Copynumber: 2.1 Consensus size: 35
282016 TTTTCAATTT
*
282026 TAAATATAAAATAATAAAAATATTTTTATAAATA-AA
1 TAAA-ATAAAATAATAAAAATATTATTA-AAATATAA
*
282062 TAAAATAAAAT-ATAAAATAATATTATTAAATTATAA
1 TAAAATAAAATAAT-AAA-AATATTATTAAAATATAA
282098 TAAAA
1 TAAAA
282103 CAATAAACAT
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
34 2 0.06
35 14 0.39
36 20 0.56
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (35 bp):
TAAAATAAAATAATAAAAATATTATTAAAATATAA
Found at i:285777 original size:28 final size:29
Alignment explanation
Indices: 285745--285803 Score: 86
Period size: 28 Copynumber: 2.1 Consensus size: 29
285735 TTGCTAATTT
285745 TATTATTA-TGTTGATATTTTT-AAATTAA
1 TATTATTACT-TTGATATTTTTAAAATTAA
*
285773 TATTATTACTTTGGTATTTTTAAAATTAA
1 TATTATTACTTTGATATTTTTAAAATTAA
285802 TA
1 TA
285804 AAATATTATA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
28 18 0.64
29 10 0.36
ACGTcount: A:0.36, C:0.02, G:0.07, T:0.56
Consensus pattern (29 bp):
TATTATTACTTTGATATTTTTAAAATTAA
Found at i:286143 original size:14 final size:14
Alignment explanation
Indices: 286124--286153 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
286114 TAATTACAAC
286124 TTAAATTAAAAATT
1 TTAAATTAAAAATT
*
286138 TTAAATTAAATATT
1 TTAAATTAAAAATT
286152 TT
1 TT
286154 GAGAATAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
TTAAATTAAAAATT
Found at i:286276 original size:19 final size:19
Alignment explanation
Indices: 286248--286289 Score: 68
Period size: 19 Copynumber: 2.3 Consensus size: 19
286238 TATCATTATA
*
286248 TTTA-TAATAATATTATCT
1 TTTATTAATAATATAATCT
286266 TTTATTAATAATATAATCT
1 TTTATTAATAATATAATCT
286285 TTTAT
1 TTTAT
286290 ATATTTAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 4 0.18
19 18 0.82
ACGTcount: A:0.38, C:0.05, G:0.00, T:0.57
Consensus pattern (19 bp):
TTTATTAATAATATAATCT
Found at i:286584 original size:29 final size:29
Alignment explanation
Indices: 286543--286610 Score: 82
Period size: 29 Copynumber: 2.3 Consensus size: 29
286533 GATTTTTCAC
*
286543 ATTTCAAAATAATAATATTATGATAATTT
1 ATTTCAAAATAATAATATTATAATAATTT
* * * *
286572 ATTTTAAATTAATATTATTTTAATAATTT
1 ATTTCAAAATAATAATATTATAATAATTT
*
286601 ATTTAAAAAT
1 ATTTCAAAAT
286611 TAGGGATACT
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.50
Consensus pattern (29 bp):
ATTTCAAAATAATAATATTATAATAATTT
Found at i:290049 original size:24 final size:24
Alignment explanation
Indices: 290007--290054 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
289997 TTAAATAACA
*
290007 TAATAAACAATATTGAATATTATT
1 TAATAAACAATATTGAATAATATT
*
290031 TAATAAA-AATATTTTAATAATATT
1 TAATAAACAATA-TTGAATAATATT
290055 AAACTTCTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 4 0.19
24 17 0.81
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (24 bp):
TAATAAACAATATTGAATAATATT
Found at i:290369 original size:2 final size:2
Alignment explanation
Indices: 290364--290396 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
290354 TTTTTTTCTA
290364 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
290397 CACACACACA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:290516 original size:3 final size:3
Alignment explanation
Indices: 290508--290554 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
290498 TAGTTTTAAC
290508 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
290555 AAATTAGAAA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:290986 original size:28 final size:30
Alignment explanation
Indices: 290947--291004 Score: 84
Period size: 28 Copynumber: 2.0 Consensus size: 30
290937 ATTTAAATTA
*
290947 AAAACTCAATTT-TTTTT-GTTGACCCAAT
1 AAAACTCAATTTCTTTTTGGTGGACCCAAT
290975 AAAACTCAATTTCCTTTTTGGTGGACCCAA
1 AAAACTCAATTT-CTTTTTGGTGGACCCAA
291005 AATATACAAC
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
28 12 0.46
30 5 0.19
31 9 0.35
ACGTcount: A:0.31, C:0.21, G:0.10, T:0.38
Consensus pattern (30 bp):
AAAACTCAATTTCTTTTTGGTGGACCCAAT
Found at i:291714 original size:18 final size:19
Alignment explanation
Indices: 291679--291714 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
291669 CATCCCTAAC
*
291679 TTTATTTTATAGTTTTAAT
1 TTTATTTTATACTTTTAAT
291698 TTTATTTTA-ACTTTTAA
1 TTTATTTTATACTTTTAA
291715 AAAAATTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.28, C:0.03, G:0.03, T:0.67
Consensus pattern (19 bp):
TTTATTTTATACTTTTAAT
Found at i:292683 original size:2 final size:2
Alignment explanation
Indices: 292676--292716 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
292666 TTTAATTTCT
292676 TC TC TC TC TC TC TC TC 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 TC TC TC TC T
292717 TTTTCTTCTT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:298175 original size:79 final size:79
Alignment explanation
Indices: 298065--298722 Score: 572
Period size: 79 Copynumber: 8.4 Consensus size: 79
298055 ATTTTGGAGG
* * * * * * * *
298065 TAAAACCCGAGGTTTGAGTATTCCCTCGAAAATAACAGGGTTGGAGTATCC-CTGATTATGGAAA
1 TAAAA-CCGGGGTTGGAGTATCCCCTTGAAAATAACGGGGTTAGAGTATCCTC-GATTGTGAAAA
*
298129 ATTGATGTTTTGGAAA
64 ATTGATGTTTTGAAAA
** * **
298145 TAAAACCGGGGTTGGAGTATCCATTTGAAAATAACGGAGTCGGAGTATCCTCGATTGTGAAAAAT
1 TAAAACCGGGGTTGGAGTATCCCCTTGAAAATAACGGGGTTAGAGTATCCTCGATTGTGAAAAAT
*
298210 CGATGTTTTGAAAA
66 TGATGTTTTGAAAA
** ** * * *
298224 TAAAACCGAAGTTGGAGTATCCCCTCAAAAATAACGGGGTTGGAATATTCTCGATTGTGAAAAAT
1 TAAAACCGGGGTTGGAGTATCCCCTTGAAAATAACGGGGTTAGAGTATCCTCGATTGTGAAAAAT
298289 CTG-TGTTTTGAAAA
66 -TGATGTTTTGAAAA
* * * * * * **
298303 TAAAATCGAGGTTAGAGTAT-CCCTTCAGAAATAACGGGGTTGGAGTATCC-CCAGTTGTCTAAA
1 TAAAACCGGGGTTGGAGTATCCCCTTGA-AAATAACGGGGTTAGAGTATCCTCGA-TTGTGAAAA
*
298366 ATCGATGTTTTGAAAA
64 ATTGATGTTTTGAAAA
* * ** * *
298382 TAAAACTGGGGTT---G-A--CCCTCGAAAATAACGGAATTAGAGTATCCCCGATTGTAAAAAAT
1 TAAAACCGGGGTTGGAGTATCCCCTTGAAAATAACGGGGTTAGAGTATCCTCGATTGTGAAAAAT
298441 T-AGTGTTTTGAAAA
66 TGA-TGTTTTGAAAA
* * * * * * * *
298455 TAAAA-CTGGGTTGGAGTATGCACTTGGAAATAATGAGGTTAGAGTATCCCCAATTGTGAAAAAT
1 TAAAACCGGGGTTGGAGTATCCCCTTGAAAATAACGGGGTTAGAGTATCCTCGATTGTGAAAAAT
* * *
298519 TGGTATTTTGGAAA
66 TGATGTTTTGAAAA
* * * * *
298533 TAAAACTGGGGTTGGAGTCTCCCCTTGGAAATAACGGGGTTAGAGTATTCTCGATTATGAAAAA-
1 TAAAACCGGGGTTGGAGTATCCCCTTGAAAATAACGGGGTTAGAGTATCCTCGATTGTGAAAAAT
*
298597 TCAGTGTTTTGAAAA
66 TGA-TGTTTTGAAAA
* * * * * *
298612 T-AAACCAGGGTTGGAGTATCCCTTTGGAAATAATGGGGTTAGAGTATCCTCAATTATGAAAAAT
1 TAAAACCGGGGTTGGAGTATCCCCTTGAAAATAACGGGGTTAGAGTATCCTCGATTGTGAAAAAT
*
298676 CGATGTTTTG-AAA
66 TGATGTTTTGAAAA
* **
298689 TAAAATCGGGGTTGGAGTATCCCCTAAAAAATAA
1 TAAAACCGGGGTTGGAGTATCCCCTTGAAAATAA
298723 AAACATGAAT
Statistics
Matches: 469, Mismatches: 91, Indels: 38
0.78 0.15 0.06
Matches are distributed among these distances:
72 6 0.01
73 44 0.09
74 7 0.01
75 2 0.00
76 2 0.00
77 4 0.01
78 147 0.31
79 250 0.53
80 7 0.01
ACGTcount: A:0.34, C:0.13, G:0.23, T:0.29
Consensus pattern (79 bp):
TAAAACCGGGGTTGGAGTATCCCCTTGAAAATAACGGGGTTAGAGTATCCTCGATTGTGAAAAAT
TGATGTTTTGAAAA
Found at i:298607 original size:230 final size:231
Alignment explanation
Indices: 298171--298615 Score: 499
Period size: 230 Copynumber: 1.9 Consensus size: 231
298161 GTATCCATTT
* * * * *
298171 GAAAATAACGGAGTCGGAGTATCCTCGATTGTGAAAAATCGATGTTTTGAAAATAAAACCGAAGT
1 GAAAATAACGGAATCAGAGTATCCCCGATTGTAAAAAATAGATGTTTTGAAAATAAAACCGAAGT
* * * * * * *
298236 TGGAGTATCCCCTCAAAAATAACGGGGTTGGAATATTCTCGATTGTGAAAAATCTGTGTTTTGAA
66 TGGAGTATCCACTCAAAAATAACGAGGTTAGAATATCCCCAATTGTGAAAAATCTGTATTTTGAA
* * *
298301 AATAAAATCGAGGTTAGAGTATCCCTTCAGAAATAACGGGGTTGGAGTATCCCCAGTTGTCTAAA
131 AATAAAATCGAGGTTAGAGTATCCCTTCAGAAATAACGGGGTTAGAGTATCCCCAGTTATCAAAA
298366 ATCGATGTTTTGAAAATAAAACTGGGGTTGACCCTC
196 ATCGATGTTTTGAAAATAAAACTGGGGTTGACCCTC
* * *
298402 GAAAATAACGGAATTAGAGTATCCCCGATTGTAAAAAATTAG-TGTTTTGAAAATAAAACTG-GG
1 GAAAATAACGGAATCAGAGTATCCCCGATTGTAAAAAA-TAGATGTTTTGAAAATAAAACCGAAG
* *** * *
298465 TTGGAGTATGCACTTGGAAATAATGAGGTTAGAGTATCCCCAATTGTGAAAAAT-TGGTATTTTG
65 TTGGAGTATCCACTCAAAAATAACGAGGTTAGAATATCCCCAATTGTGAAAAATCT-GTATTTTG
* * * * * * *
298529 GAAATAAAA-CTGGGGTTGGAGTCTCCCCTT-GGAAATAACGGGGTTAGAGTATTCTC-GATTAT
129 AAAATAAAATC-GAGGTTAGAGTAT-CCCTTCAGAAATAACGGGGTTAGAGTATCCCCAG-TTAT
*
298591 GAAAAATC-AGTGTTTTGAAAATAAA
191 CAAAAATCGA-TGTTTTGAAAATAAA
298616 CCAGGGTTGG
Statistics
Matches: 176, Mismatches: 32, Indels: 13
0.80 0.14 0.06
Matches are distributed among these distances:
229 4 0.02
230 114 0.65
231 56 0.32
232 2 0.01
ACGTcount: A:0.35, C:0.13, G:0.23, T:0.29
Consensus pattern (231 bp):
GAAAATAACGGAATCAGAGTATCCCCGATTGTAAAAAATAGATGTTTTGAAAATAAAACCGAAGT
TGGAGTATCCACTCAAAAATAACGAGGTTAGAATATCCCCAATTGTGAAAAATCTGTATTTTGAA
AATAAAATCGAGGTTAGAGTATCCCTTCAGAAATAACGGGGTTAGAGTATCCCCAGTTATCAAAA
ATCGATGTTTTGAAAATAAAACTGGGGTTGACCCTC
Found at i:298752 original size:157 final size:157
Alignment explanation
Indices: 298134--298722 Score: 418
Period size: 157 Copynumber: 3.8 Consensus size: 157
298124 GGAAAATTGA
* * * * * * ** * *
298134 TGTTTTGGAAATAAAACCGGGGTTGGAGTATCCATTTGAAAATAACG-GAGTCGGAGTATCCTCG
1 TGTTTTGAAAATAAAA-CAGGGTTGGAGTATGCACTTGGAAATAATGAG-GTTAGAGTATCCCCA
* * * * ** * * *
298198 ATTGTGAAAAATCGATGTTTTGAAAATAAAACCGAAGTTGGAGTATCCCCTCAAAAATAACGGGG
64 ATTATGAAAAATCGATATTTTGGAAATAAAACTGGGGTTGGAGTATCCCCTAAAAAATAACAGGA
* * * *
298263 TTGGA-ATATTCTCGATTG-TGAAAAATCTG
129 ATAGAGA-ATTCTCGA-TGAAGAAAAATCAG
* * * * * *
298292 TGTTTTGAAAATAAAATC-GAGGTTAGAGTAT-CCCTTCAGAAATAACGGGGTTGGAGTATCCCC
1 TGTTTTGAAAATAAAA-CAG-GGTTGGAGTATGCACTT-GGAAATAATGAGGTTAGAGTATCCCC
* * ** * * **
298355 AGTTGTCTAAAATCGATGTTTTGAAAATAAAACTGGGGTT---G-A--CCCTCGAAAATAAC-GG
63 AATTATGAAAAATCGATATTTTGGAAATAAAACTGGGGTTGGAGTATCCCCTAAAAAATAACAGG
* * * * *
298413 AATTAGAGTATCCCCGATTGTA-AAAAATTAG
128 AA-TAGAGAATTCTCGA-TGAAGAAAAATCAG
*
298444 TGTTTTGAAAATAAAACTGGGTTGGAGTATGCACTTGGAAATAATGAGGTTAGAGTATCCCCAAT
1 TGTTTTGAAAATAAAACAGGGTTGGAGTATGCACTTGGAAATAATGAGGTTAGAGTATCCCCAAT
* * * * *** * **
298509 TGTGAAAAATTGGTATTTTGGAAATAAAACTGGGGTTGGAGTCTCCCCTTGGAAATAACGGGGTT
66 TATGAAAAATCGATATTTTGGAAATAAAACTGGGGTTGGAGTATCCCCTAAAAAATAACAGGAAT
* * *
298574 AGAGTATTCTCGATTATGAAAAATCAG
131 AGAGAATTCTCGATGAAGAAAAATCAG
* * * *
298601 TGTTTTGAAAATAAACCAGGGTTGGAGTAT-CCCTTTGGAAATAATGGGGTTAGAGTATCCTCAA
1 TGTTTTGAAAATAAAACAGGGTTGGAGTATGCAC-TTGGAAATAATGAGGTTAGAGTATCCCCAA
*
298665 TTATGAAAAATCGATGTTTT-GAAATAAAA-TCGGGGTTGGAGTATCCCCTAAAAAATAA
65 TTATGAAAAATCGATATTTTGGAAATAAAACT-GGGGTTGGAGTATCCCCTAAAAAATAA
298723 AAACATGAAT
Statistics
Matches: 350, Mismatches: 63, Indels: 38
0.78 0.14 0.08
Matches are distributed among these distances:
151 68 0.19
152 53 0.15
154 2 0.01
155 2 0.01
156 35 0.10
157 108 0.31
158 81 0.23
159 1 0.00
ACGTcount: A:0.35, C:0.13, G:0.23, T:0.29
Consensus pattern (157 bp):
TGTTTTGAAAATAAAACAGGGTTGGAGTATGCACTTGGAAATAATGAGGTTAGAGTATCCCCAAT
TATGAAAAATCGATATTTTGGAAATAAAACTGGGGTTGGAGTATCCCCTAAAAAATAACAGGAAT
AGAGAATTCTCGATGAAGAAAAATCAG
Found at i:299410 original size:11 final size:10
Alignment explanation
Indices: 299386--299411 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
299376 CTCTTTGAGG
299386 AAAAAATTTC
1 AAAAAATTTC
299396 AAAAAATTTC
1 AAAAAATTTC
299406 AAAAAA
1 AAAAAA
299412 CTTGTTTCAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.69, C:0.08, G:0.00, T:0.23
Consensus pattern (10 bp):
AAAAAATTTC
Found at i:301124 original size:20 final size:21
Alignment explanation
Indices: 301099--301157 Score: 66
Period size: 24 Copynumber: 2.7 Consensus size: 21
301089 TAAAACTCAG
* *
301099 AATGTATCGATATAATGAATA
1 AATGTATCGATACAATGAAGA
301120 ATGTATGTATCGATACAATGAAG-
1 A---ATGTATCGATACAATGAAGA
301143 AATGTATCGATACAA
1 AATGTATCGATACAA
301158 ATTATGAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
20 14 0.42
21 1 0.03
23 1 0.03
24 17 0.52
ACGTcount: A:0.44, C:0.08, G:0.17, T:0.31
Consensus pattern (21 bp):
AATGTATCGATACAATGAAGA
Found at i:301132 original size:24 final size:24
Alignment explanation
Indices: 301100--301149 Score: 82
Period size: 24 Copynumber: 2.1 Consensus size: 24
301090 AAAACTCAGA
* *
301100 ATGTATCGATATAATGAATAATGT
1 ATGTATCGATACAATGAAGAATGT
301124 ATGTATCGATACAATGAAGAATGT
1 ATGTATCGATACAATGAAGAATGT
301148 AT
1 AT
301150 CGATACAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.42, C:0.06, G:0.18, T:0.34
Consensus pattern (24 bp):
ATGTATCGATACAATGAAGAATGT
Found at i:302767 original size:27 final size:28
Alignment explanation
Indices: 302735--302790 Score: 71
Period size: 28 Copynumber: 2.0 Consensus size: 28
302725 ACATTTTTTG
*
302735 AATTTTA-AATGAT-TAAATTTTTAATTA
1 AATTTTATAAT-ATGTAAAATTTTAATTA
*
302762 AATTTTATCATATGTAAAATTTTAATTA
1 AATTTTATAATATGTAAAATTTTAATTA
302790 A
1 A
302791 CCCCTTTGGG
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
27 9 0.36
28 16 0.64
ACGTcount: A:0.45, C:0.02, G:0.04, T:0.50
Consensus pattern (28 bp):
AATTTTATAATATGTAAAATTTTAATTA
Found at i:303403 original size:20 final size:20
Alignment explanation
Indices: 303373--303449 Score: 91
Period size: 20 Copynumber: 3.9 Consensus size: 20
303363 TTTTACCCAG
303373 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
* * * *
303393 ATATCTCGATACATGTTTGA
1 ATGTATCGATACATTTTTCA
* *
303413 ATGTATCGATATATTCTTCA
1 ATGTATCGATACATTTTTCA
*
303433 ATGTATTGATACATTTT
1 ATGTATCGATACATTTT
303450 GTCTTTTTAC
Statistics
Matches: 44, Mismatches: 13, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.30, C:0.13, G:0.12, T:0.45
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:303444 original size:40 final size:39
Alignment explanation
Indices: 303373--303450 Score: 102
Period size: 40 Copynumber: 2.0 Consensus size: 39
303363 TTTTACCCAG
* *
303373 ATGTATCGATACATTTTTCAATATCTCGATACATGTTTGA
1 ATGTATCGATACATTCTTCAATATATCGATACAT-TTTGA
* * *
303413 ATGTATCGATATATTCTTCAATGTATTGATACATTTTG
1 ATGTATCGATACATTCTTCAATATATCGATACATTTTG
303451 TCTTTTTACC
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
39 4 0.12
40 29 0.88
ACGTcount: A:0.29, C:0.13, G:0.13, T:0.45
Consensus pattern (39 bp):
ATGTATCGATACATTCTTCAATATATCGATACATTTTGA
Found at i:305771 original size:97 final size:96
Alignment explanation
Indices: 305629--305868 Score: 354
Period size: 97 Copynumber: 2.5 Consensus size: 96
305619 AATTTTATTT
* **
305629 ATCGGAGACACTTCAACATCATTCCTCCGAGGGGATACTCCAACCCCGCTTTTAAACACATAAAA
1 ATCGGGGACACTTCAACCCCATTCCTCCGA-GGGATACTCCAACCCCGCTTTTAAACACATAAAA
*
305694 ATTTAAATTTTATTCTCACTTAAATTGTCATC
65 ATTTAAATTTAATTCTCACTTAAATTGTCATC
* * * *
305726 ATCGGGGACACTTCAACCCCATTCCTTCGAGAGGATACTTCAACCCCGCTTTTAAACGCATCAAA
1 ATCGGGGACACTTCAACCCCATTCCTCCGAG-GGATACTCCAACCCCGCTTTTAAACACATAAAA
305791 ATTTAAATTTAATTCTCACTTAAATTGTCATC
65 ATTTAAATTTAATTCTCACTTAAATTGTCATC
* * *
305823 ATTGGGGACACTCCAACCCCATTCGTCCGAGGAGATACTCCAACCC
1 ATCGGGGACACTTCAACCCCATTCCTCCGAGG-GATACTCCAACCC
305869 TGTTTTTCAA
Statistics
Matches: 128, Mismatches: 13, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
96 2 0.02
97 126 0.98
ACGTcount: A:0.31, C:0.28, G:0.12, T:0.28
Consensus pattern (96 bp):
ATCGGGGACACTTCAACCCCATTCCTCCGAGGGATACTCCAACCCCGCTTTTAAACACATAAAAA
TTTAAATTTAATTCTCACTTAAATTGTCATC
Found at i:308500 original size:29 final size:29
Alignment explanation
Indices: 308418--308532 Score: 124
Period size: 29 Copynumber: 4.0 Consensus size: 29
308408 CTATTTTGAG
*
308418 GTCAAAGTATAATTTTAAAAAGTTCAAGG-
1 GTCAAAGTATAATTTTAAAAAGTT-TAGGA
* *
308447 GTCAATGTACAATTTTAAAAAGTTTAGGA
1 GTCAAAGTATAATTTTAAAAAGTTTAGGA
* *
308476 GTCAAAGTGTAATTTTAAAAAGTTTAGAA
1 GTCAAAGTATAATTTTAAAAAGTTTAGGA
* *** *
308505 ATCAAAACGTAATTTTGAAAAGTTTAGG
1 GTCAAAGTATAATTTTAAAAAGTTTAGG
308533 GATTTAGTAG
Statistics
Matches: 73, Mismatches: 12, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
28 3 0.04
29 70 0.96
ACGTcount: A:0.43, C:0.06, G:0.17, T:0.33
Consensus pattern (29 bp):
GTCAAAGTATAATTTTAAAAAGTTTAGGA
Found at i:309797 original size:42 final size:42
Alignment explanation
Indices: 309750--309839 Score: 171
Period size: 42 Copynumber: 2.1 Consensus size: 42
309740 AAATAAAAGA
*
309750 ATTTAAAATAGTAATATATCAATTATTATGAGAACGAAGGCC
1 ATTTAAAATAGTAATATATCAATGATTATGAGAACGAAGGCC
309792 ATTTAAAATAGTAATATATCAATGATTATGAGAACGAAGGCC
1 ATTTAAAATAGTAATATATCAATGATTATGAGAACGAAGGCC
309834 ATTTAA
1 ATTTAA
309840 GTCATGTTTG
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 47 1.00
ACGTcount: A:0.46, C:0.09, G:0.14, T:0.31
Consensus pattern (42 bp):
ATTTAAAATAGTAATATATCAATGATTATGAGAACGAAGGCC
Found at i:311744 original size:18 final size:19
Alignment explanation
Indices: 311723--311758 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
311713 TATTCATTAT
311723 ATTATTTTTAT-ATTAATA
1 ATTATTTTTATAATTAATA
311741 ATTATTTTTATAATTAAT
1 ATTATTTTTATAATTAAT
311759 TCAAATAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 11 0.65
19 6 0.35
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (19 bp):
ATTATTTTTATAATTAATA
Found at i:313758 original size:19 final size:17
Alignment explanation
Indices: 313714--313773 Score: 63
Period size: 17 Copynumber: 3.5 Consensus size: 17
313704 TATTTAATTT
313714 TAATAAATTTAAA-TAAA
1 TAAT-AATTTAAATTAAA
*
313731 -AATATTTTAATTATTAAA
1 TAATAATTTAA--ATTAAA
313749 TAATAATTTAAATTAAA
1 TAATAATTTAAATTAAA
313766 TAA-AATTT
1 TAATAATTT
313774 TATTCAAAAC
Statistics
Matches: 37, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
15 6 0.16
16 8 0.22
17 10 0.27
18 4 0.11
19 9 0.24
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
TAATAATTTAAATTAAA
Found at i:315348 original size:16 final size:16
Alignment explanation
Indices: 315329--315361 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
315319 TAAACATATA
315329 AAAAAT-TAATAAAAAT
1 AAAAATATAA-AAAAAT
315345 AAAAATATAAAAAAAT
1 AAAAATATAAAAAAAT
315361 A
1 A
315362 TTTTTTATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 13 0.81
17 3 0.19
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (16 bp):
AAAAATATAAAAAAAT
Found at i:318116 original size:2 final size:2
Alignment explanation
Indices: 318111--318148 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
318101 TGGAGAGAAC
*
318111 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA GA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
318149 GACCATTTGT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
TA
Found at i:320884 original size:2 final size:2
Alignment explanation
Indices: 320877--320903 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
320867 TTAAGCCAAT
320877 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
320904 TTATTTATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:321695 original size:13 final size:13
Alignment explanation
Indices: 321677--321705 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
321667 ACTATCAAAC
321677 CCTTCCCTTCCAT
1 CCTTCCCTTCCAT
321690 CCTTCCCTTCCAT
1 CCTTCCCTTCCAT
321703 CCT
1 CCT
321706 ATCTTCAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.07, C:0.55, G:0.00, T:0.38
Consensus pattern (13 bp):
CCTTCCCTTCCAT
Found at i:323110 original size:15 final size:15
Alignment explanation
Indices: 323090--323143 Score: 56
Period size: 15 Copynumber: 3.5 Consensus size: 15
323080 TAAATTTTTA
323090 AATCATTTTAATTTG
1 AATCATTTTAATTTG
*
323105 AATCATTTTAGA-TTC
1 AATCATTTTA-ATTTG
*
323120 AATTATTTTAACTTTG
1 AATCATTTTAA-TTTG
*
323136 GATCATTT
1 AATCATTT
323144 CGGATTCAAG
Statistics
Matches: 31, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
14 1 0.03
15 21 0.68
16 9 0.29
ACGTcount: A:0.31, C:0.09, G:0.07, T:0.52
Consensus pattern (15 bp):
AATCATTTTAATTTG
Found at i:323143 original size:31 final size:30
Alignment explanation
Indices: 323094--323152 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 30
323084 TTTTTAAATC
*
323094 ATTTTAATTTGAATCATTTTAGATTCAATT
1 ATTTTAATTTGAATCATTTCAGATTCAATT
* *
323124 ATTTTAACTTTGGATCATTTCGGATTCAA
1 ATTTTAA-TTTGAATCATTTCAGATTCAA
323153 GTCTATTAGG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
30 7 0.28
31 18 0.72
ACGTcount: A:0.31, C:0.10, G:0.10, T:0.49
Consensus pattern (30 bp):
ATTTTAATTTGAATCATTTCAGATTCAATT
Found at i:323335 original size:16 final size:16
Alignment explanation
Indices: 323314--323347 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
323304 TTAATTGATC
323314 AAGTTAATTCAAATTT
1 AAGTTAATTCAAATTT
* *
323330 AAGTTATTTTAAATTT
1 AAGTTAATTCAAATTT
323346 AA
1 AA
323348 ATTATTTTAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.44, C:0.03, G:0.06, T:0.47
Consensus pattern (16 bp):
AAGTTAATTCAAATTT
Found at i:323352 original size:16 final size:16
Alignment explanation
Indices: 323324--323356 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
323314 AAGTTAATTC
*
323324 AAATTTAAGTTATTTT
1 AAATTTAAATTATTTT
323340 AAATTTAAATTATTTT
1 AAATTTAAATTATTTT
323356 A
1 A
323357 GGTTTGAATC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (16 bp):
AAATTTAAATTATTTT
Found at i:332871 original size:2 final size:2
Alignment explanation
Indices: 332866--332914 Score: 71
Period size: 2 Copynumber: 24.5 Consensus size: 2
332856 TCATATGAGA
* * *
332866 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AA AT GT AT AA AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
332908 AT AT AT A
1 AT AT AT A
332915 CACACATATA
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (2 bp):
AT
Found at i:337740 original size:17 final size:17
Alignment explanation
Indices: 337715--337777 Score: 51
Period size: 17 Copynumber: 3.8 Consensus size: 17
337705 CAAGTTCAGA
*
337715 TTAAAATTATAATATTT
1 TTAATATTATAATATTT
*
337732 TTAATATTA-AAAATTAT
1 TTAATATTATAATATT-T
*
337749 TTTATA-T-TAATATTT
1 TTAATATTATAATATTT
*
337764 ATATATATTATAAT
1 TTA-ATATTATAAT
337778 TAAATTTAAA
Statistics
Matches: 35, Mismatches: 6, Indels: 9
0.70 0.12 0.18
Matches are distributed among these distances:
15 2 0.06
16 14 0.40
17 15 0.43
18 4 0.11
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
TTAATATTATAATATTT
Found at i:337791 original size:33 final size:33
Alignment explanation
Indices: 337724--337802 Score: 81
Period size: 32 Copynumber: 2.4 Consensus size: 33
337714 ATTAAAATTA
* * *
337724 TAATATTTTTA-ATATTAAAAATTATTTTATAT
1 TAATATTTATATATATTAAAAATTAATTTAAAT
*
337756 TAATATTTATATATATT-ATAATTAAATTTAAAT
1 TAATATTTATATATATTAAAAATT-AATTTAAAT
337789 TAAAATATTTATAT
1 T--AATATTTATAT
337803 TGATGATCAC
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
32 15 0.38
33 13 0.33
35 11 0.28
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (33 bp):
TAATATTTATATATATTAAAAATTAATTTAAAT
Found at i:338776 original size:17 final size:16
Alignment explanation
Indices: 338744--338793 Score: 50
Period size: 16 Copynumber: 3.2 Consensus size: 16
338734 AAAATTAATT
338744 TAAATATTAAATAAAA
1 TAAATATTAAATAAAA
338760 TAAATACTT-AATAAAA
1 TAAATA-TTAAATAAAA
* * *
338776 -ATATATTTAATTAAA
1 TAAATATTAAATAAAA
338791 TAA
1 TAA
338794 TATGATTTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
14 2 0.07
15 10 0.36
16 14 0.50
17 2 0.07
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (16 bp):
TAAATATTAAATAAAA
Found at i:338795 original size:17 final size:17
Alignment explanation
Indices: 338747--338801 Score: 53
Period size: 15 Copynumber: 3.4 Consensus size: 17
338737 ATTAATTTAA
* *
338747 ATATTAAATAAAATAA-
1 ATATTTAATTAAATAAT
*
338763 ATACTTAA-TAAA-AAT
1 ATATTTAATTAAATAAT
338778 ATATTTAATTAAATAAT
1 ATATTTAATTAAATAAT
338795 ATGATTT
1 AT-ATTT
338802 TTAATATAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
14 2 0.06
15 10 0.32
16 10 0.32
17 5 0.16
18 4 0.13
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (17 bp):
ATATTTAATTAAATAAT
Found at i:338898 original size:12 final size:11
Alignment explanation
Indices: 338881--338911 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
338871 AATAAGCTTA
*
338881 AATTTTTTTTT
1 AATTTTTTATT
338892 AATTTTTTATT
1 AATTTTTTATT
338903 AATTTTTTA
1 AATTTTTTA
338912 AATTTATAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (11 bp):
AATTTTTTATT
Found at i:338982 original size:18 final size:18
Alignment explanation
Indices: 338959--338996 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
338949 ATAAACTTTT
* *
338959 ATTTAATTATTCGATTTG
1 ATTTAATTATCCAATTTG
338977 ATTTAATTATCCAATTTG
1 ATTTAATTATCCAATTTG
338995 AT
1 AT
338997 ATTTTTTAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.32, C:0.08, G:0.08, T:0.53
Consensus pattern (18 bp):
ATTTAATTATCCAATTTG
Found at i:339426 original size:2 final size:2
Alignment explanation
Indices: 339421--339459 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
339411 ACTTTTTGTC
339421 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
339460 GAAAATTATG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:339705 original size:25 final size:23
Alignment explanation
Indices: 339671--339721 Score: 57
Period size: 23 Copynumber: 2.1 Consensus size: 23
339661 GTAAAATCAT
*
339671 AAAAACTTAATAAGTATACATATAA
1 AAAAACTTAA-AAGTAT-CAAATAA
* *
339696 AAAAATTTAAAATTATCAAATAA
1 AAAAACTTAAAAGTATCAAATAA
339719 AAA
1 AAA
339722 TATCTAACGT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
23 9 0.39
24 5 0.22
25 9 0.39
ACGTcount: A:0.65, C:0.06, G:0.02, T:0.27
Consensus pattern (23 bp):
AAAAACTTAAAAGTATCAAATAA
Found at i:339778 original size:17 final size:17
Alignment explanation
Indices: 339756--339856 Score: 82
Period size: 17 Copynumber: 5.9 Consensus size: 17
339746 AGTCACATTT
339756 ATTATGAAAATTTATGA
1 ATTATGAAAATTTATGA
**
339773 ATTATGAGTATTTAT-A
1 ATTATGAAAATTTATGA
*
339789 TATCAT-AAAGATTTATGA
1 -ATTATGAAA-ATTTATGA
* * *
339807 ATTATAAAAATATATGT
1 ATTATGAAAATTTATGA
*
339824 ATTAT-AAATATTTATAA
1 ATTATGAAA-ATTTATGA
*
339841 ATCATGAAAATTTATG
1 ATTATGAAAATTTATG
339857 TATTTTCAAA
Statistics
Matches: 65, Mismatches: 13, Indels: 12
0.72 0.14 0.13
Matches are distributed among these distances:
16 5 0.08
17 53 0.82
18 7 0.11
ACGTcount: A:0.47, C:0.02, G:0.09, T:0.43
Consensus pattern (17 bp):
ATTATGAAAATTTATGA
Found at i:339828 original size:51 final size:51
Alignment explanation
Indices: 339756--339856 Score: 132
Period size: 51 Copynumber: 2.0 Consensus size: 51
339746 AGTCACATTT
* * * * *
339756 ATTATGAAAATTTATGAATTATGAGTATTTATATATCAT-AAAGATTTATGA
1 ATTATAAAAATATATGAATTATAAATATTTATAAATCATGAAA-ATTTATGA
*
339807 ATTATAAAAATATATGTATTATAAATATTTATAAATCATGAAAATTTATG
1 ATTATAAAAATATATGAATTATAAATATTTATAAATCATGAAAATTTATG
339857 TATTTTCAAA
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
51 40 0.93
52 3 0.07
ACGTcount: A:0.47, C:0.02, G:0.09, T:0.43
Consensus pattern (51 bp):
ATTATAAAAATATATGAATTATAAATATTTATAAATCATGAAAATTTATGA
Found at i:339831 original size:34 final size:33
Alignment explanation
Indices: 339755--339860 Score: 113
Period size: 34 Copynumber: 3.1 Consensus size: 33
339745 AAGTCACATT
** *
339755 TATTATGAAAATTTATGAATTATGAGTATTTATA
1 TATTAT-AAAATTTATGAATTATGAAAATTTATG
* * *
339789 TATCATAAAGATTTATGAATTATAAAAATATATG
1 TATTATAAA-ATTTATGAATTATGAAAATTTATG
* *
339823 TATTATAAATATTTATAAATCATGAAAATTTATG
1 TATTATAAA-ATTTATGAATTATGAAAATTTATG
339857 TATT
1 TATT
339861 TTCAAAGAGT
Statistics
Matches: 59, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
33 3 0.05
34 56 0.95
ACGTcount: A:0.45, C:0.02, G:0.08, T:0.44
Consensus pattern (33 bp):
TATTATAAAATTTATGAATTATGAAAATTTATG
Found at i:340424 original size:15 final size:15
Alignment explanation
Indices: 340400--340439 Score: 62
Period size: 15 Copynumber: 2.7 Consensus size: 15
340390 TAATAAAATC
*
340400 TTAAATTATTTATTA
1 TTAAAATATTTATTA
340415 TTAAAATATTTATTA
1 TTAAAATATTTATTA
*
340430 TTGAAATATT
1 TTAAAATATT
340440 AAAATTAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (15 bp):
TTAAAATATTTATTA
Found at i:343173 original size:201 final size:200
Alignment explanation
Indices: 342829--343230 Score: 651
Period size: 201 Copynumber: 2.0 Consensus size: 200
342819 CAAGTCCAAG
* * *
342829 ACTCATACCAACAGCTGGAACCTGCTTTGCGCTAAAATTTCCTATCAGATTGTCGTATCGTCCAC
1 ACTCATACCAACAGCCGGAACCTGCTTTGCGCCAAAATTTCCTATCAGATTGTCGTATCATCCAC
** * *
342894 TGGCACCAATTGAACCAACTGAATATAAAAAGAGATCGATCATATCATTCAAGGGGCAGATAGAA
66 CAGCACCAACTGAACCAACTGAATATAAAAAGAAATCGATCATATCATTCAAGGGGCAGATAGAA
*
342959 TAAACAACACAATAAAGAAGAGAGTTAAGCCATTGCAATAATTAATGCAGGTTCCATAATTTAAG
131 TAAACAACACAATAAAGAAGAGAGTTAAGCCATTGCAATAATTAATGCAGGTGCCATAATTTAAG
*
343024 GACAA
196 CACAA
* *
343029 ACTCATACCAACGGCCGGAACCTGCTTTGTGCCAAAATTTCCTATCAGATTGTCGTATCATCCAC
1 ACTCATACCAACAGCCGGAACCTGCTTTGCGCCAAAATTTCCTATCAGATTGTCGTATCATCCAC
**
343094 CAGCAGTAACTGAACCAACCTGAATATAAAAAGAAATCGATCATATCATTCAAGGGGCAGATAGA
66 CAGCACCAACTGAACCAA-CTGAATATAAAAAGAAATCGATCATATCATTCAAGGGGCAGATAGA
* * *
343159 ATAAACAACACAATAAAGAAGAGAGTTATGCCATTGCAATAATTAATGCGGGTGCCATATTTTAA
130 ATAAACAACACAATAAAGAAGAGAGTTAAGCCATTGCAATAATTAATGCAGGTGCCATAATTTAA
343224 GCACAA
195 GCACAA
343230 A
1 A
343231 TGTGGATAAA
Statistics
Matches: 185, Mismatches: 16, Indels: 1
0.92 0.08 0.00
Matches are distributed among these distances:
200 73 0.39
201 112 0.61
ACGTcount: A:0.39, C:0.21, G:0.17, T:0.24
Consensus pattern (200 bp):
ACTCATACCAACAGCCGGAACCTGCTTTGCGCCAAAATTTCCTATCAGATTGTCGTATCATCCAC
CAGCACCAACTGAACCAACTGAATATAAAAAGAAATCGATCATATCATTCAAGGGGCAGATAGAA
TAAACAACACAATAAAGAAGAGAGTTAAGCCATTGCAATAATTAATGCAGGTGCCATAATTTAAG
CACAA
Found at i:343669 original size:11 final size:11
Alignment explanation
Indices: 343653--343688 Score: 54
Period size: 11 Copynumber: 3.2 Consensus size: 11
343643 TTATTACATA
343653 TATTTAATATT
1 TATTTAATATT
343664 TATTTAATATT
1 TATTTAATATT
*
343675 AAATTTAATATT
1 -TATTTAATATT
343687 TA
1 TA
343689 AATATATTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
11 12 0.55
12 10 0.45
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (11 bp):
TATTTAATATT
Found at i:345157 original size:19 final size:19
Alignment explanation
Indices: 345129--345176 Score: 62
Period size: 19 Copynumber: 2.6 Consensus size: 19
345119 ATGCCTATTT
*
345129 TTTATTTTTTGA-TTTTAC
1 TTTATTTTTTTAGTTTTAC
*
345147 TTTATTTTTTTAGTTTTGC
1 TTTATTTTTTTAGTTTTAC
*
345166 ATTATTTTTTT
1 TTTATTTTTTT
345177 CGTTAGGCTT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
18 11 0.42
19 15 0.58
ACGTcount: A:0.15, C:0.04, G:0.06, T:0.75
Consensus pattern (19 bp):
TTTATTTTTTTAGTTTTAC
Found at i:350203 original size:15 final size:15
Alignment explanation
Indices: 350183--350212 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
350173 TTCAAACAAG
350183 ATCCCCCCTGTAACT
1 ATCCCCCCTGTAACT
350198 ATCCCCCCTGTAACT
1 ATCCCCCCTGTAACT
350213 GCCTCGCCAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.20, C:0.47, G:0.07, T:0.27
Consensus pattern (15 bp):
ATCCCCCCTGTAACT
Found at i:354782 original size:20 final size:20
Alignment explanation
Indices: 354757--354809 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
354747 GTTGGGCTCA
**
354757 ATGTATCGATACAATTCATT
1 ATGTATCGATACAATTCACC
354777 ATGTATCGATACAATTCACC
1 ATGTATCGATACAATTCACC
354797 ATGTATCGATACA
1 ATGTATCGATACA
354810 TTGTATCGAT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.36, C:0.19, G:0.11, T:0.34
Consensus pattern (20 bp):
ATGTATCGATACAATTCACC
Found at i:354816 original size:13 final size:13
Alignment explanation
Indices: 354798--354822 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
354788 CAATTCACCA
354798 TGTATCGATACAT
1 TGTATCGATACAT
354811 TGTATCGATACA
1 TGTATCGATACA
354823 AAGTGAGTTT
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:355019 original size:20 final size:21
Alignment explanation
Indices: 354996--355036 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
354986 GATACTTTGA
354996 ATTATTTTTAT-TTGAAAAAC
1 ATTATTTTTATCTTGAAAAAC
355016 ATTATTTTTATGCTTGAAAAA
1 ATTATTTTTAT-CTTGAAAAA
355037 ATCTATACTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 11 0.58
22 8 0.42
ACGTcount: A:0.39, C:0.05, G:0.07, T:0.49
Consensus pattern (21 bp):
ATTATTTTTATCTTGAAAAAC
Found at i:355171 original size:50 final size:50
Alignment explanation
Indices: 355112--355212 Score: 166
Period size: 50 Copynumber: 2.0 Consensus size: 50
355102 TATAAGTGAA
*
355112 GAAAACTTATTACGATTTTTCAAAGCATTTTTCGGATTTATTCATACTTT
1 GAAAACTTATTACGATTTTTCAAAACATTTTTCGGATTTATTCATACTTT
* * *
355162 GAAAACTTATTACGGTTTTTCAAAACATTTTTTGGATTTATTCATAGTTT
1 GAAAACTTATTACGATTTTTCAAAACATTTTTCGGATTTATTCATACTTT
355212 G
1 G
355213 TTATATCAAA
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
50 47 1.00
ACGTcount: A:0.30, C:0.12, G:0.12, T:0.47
Consensus pattern (50 bp):
GAAAACTTATTACGATTTTTCAAAACATTTTTCGGATTTATTCATACTTT
Found at i:371996 original size:51 final size:51
Alignment explanation
Indices: 371931--372050 Score: 195
Period size: 51 Copynumber: 2.4 Consensus size: 51
371921 TCAAAAATAA
371931 CGGGGTTGGAGTATCCCCGATTGTGAGAAATCAATATTTTAAAAATAAAAC
1 CGGGGTTGGAGTATCCCCGATTGTGAGAAATCAATATTTTAAAAATAAAAC
* * ** *
371982 CGGGGTTGAAGTATCCCTGATTGTGAGAAATCAATATTTTGGAAATAAAGC
1 CGGGGTTGGAGTATCCCCGATTGTGAGAAATCAATATTTTAAAAATAAAAC
372033 CGGGGTTGGAGTATCCCC
1 CGGGGTTGGAGTATCCCC
372051 TCGAAAATAA
Statistics
Matches: 62, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
51 62 1.00
ACGTcount: A:0.32, C:0.15, G:0.26, T:0.28
Consensus pattern (51 bp):
CGGGGTTGGAGTATCCCCGATTGTGAGAAATCAATATTTTAAAAATAAAAC
Found at i:372107 original size:28 final size:30
Alignment explanation
Indices: 372033--372109 Score: 126
Period size: 28 Copynumber: 2.7 Consensus size: 30
372023 GAAATAAAGC
372033 CGGGGTTGGAGTATCCCC--TCGAAAATAA
1 CGGGGTTGGAGTATCCCCGATCGAAAATAA
372061 CGGGGTTGGAGTATCCCCGAT-G-AAATAA
1 CGGGGTTGGAGTATCCCCGATCGAAAATAA
372089 CGGGGTTGGAGTATCCCCGAT
1 CGGGGTTGGAGTATCCCCGAT
372110 TGTGCAAAAT
Statistics
Matches: 47, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
28 45 0.96
29 1 0.02
30 1 0.02
ACGTcount: A:0.25, C:0.21, G:0.32, T:0.22
Consensus pattern (30 bp):
CGGGGTTGGAGTATCCCCGATCGAAAATAA
Found at i:372186 original size:158 final size:158
Alignment explanation
Indices: 371898--372207 Score: 401
Period size: 158 Copynumber: 2.0 Consensus size: 158
371888 TTTTGGAGAT
371898 AATAACGGGGTTGGAGTATCCCCTCAAAAATAACGGGGTTGGAGTATCCCCGATTGTGAGAAATC
1 AATAACGGGGTTGGAGTATCCCCTCAAAAATAACGGGGTTGGAGTATCCCCGATTGTGAGAAATC
* * *
371963 AATATTTTAAAAATAAAACCGGGGTTGAAGTATCCCTGATTGTGAGAAATCAATATTTTGGAAAT
66 AATATTTTAAAAATAAAACCGGAGTTGAAGTATCCCCGATTGTGAGAAATCAATATTTTAGAAAT
* *
372028 AAAGCCGGGGTTGGAGTATCCCCTCGAA
131 AAAACCGGAGTTGGAGTATCCCCTCGAA
* *
372056 AATAACGGGGTTGGAGTATCCCC-GATGAAATAACGGGGTTGGAGTATCCCCGATTGTGCA-AAA
1 AATAACGGGGTTGGAGTATCCCCTCA-AAAATAACGGGGTTGGAGTATCCCCGATTGTG-AGAAA
* * * ** * * *** *
372119 TTAGTGTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCGATTGTG-GAAAATTGGTGTTTTAGA
64 TCAATATTTTAAAAATAAAACCGGAGTTGAAGTATCCCCGATTGTGAG-AAATCAATATTTTAGA
*
372183 AATAAAATCGGAGTTGGAGTATCCC
128 AATAAAACCGGAGTTGGAGTATCCC
372208 AATTGTAGAA
Statistics
Matches: 130, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
157 2 0.02
158 127 0.98
159 1 0.01
ACGTcount: A:0.32, C:0.15, G:0.26, T:0.27
Consensus pattern (158 bp):
AATAACGGGGTTGGAGTATCCCCTCAAAAATAACGGGGTTGGAGTATCCCCGATTGTGAGAAATC
AATATTTTAAAAATAAAACCGGAGTTGAAGTATCCCCGATTGTGAGAAATCAATATTTTAGAAAT
AAAACCGGAGTTGGAGTATCCCCTCGAA
Found at i:372234 original size:50 final size:50
Alignment explanation
Indices: 372093--372258 Score: 244
Period size: 51 Copynumber: 3.3 Consensus size: 50
372083 AAATAACGGG
* *
372093 GTTGGAGTATCCCCGATTGTGCAAAATTAGTGTTTTGGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTGTG-AAAATTGGTGTTTTAGAAATAAAATCGGA
372144 GTTGGAGTATCCCCGATTGTGGAAAATTGGTGTTTTAGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTGT-GAAAATTGGTGTTTTAGAAATAAAATCGGA
* * * *
372195 GTTGGAGTAT-CCCAATTGTAGAAAATTGGTATTTTAGAAATAAATTCGGG
1 GTTGGAGTATCCCCGATTGT-GAAAATTGGTGTTTTAGAAATAAAATCGGA
372245 GTTGGAGTATCCCC
1 GTTGGAGTATCCCC
372259 TCAGAAATAA
Statistics
Matches: 106, Mismatches: 7, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
50 45 0.42
51 60 0.57
52 1 0.01
ACGTcount: A:0.31, C:0.11, G:0.26, T:0.32
Consensus pattern (50 bp):
GTTGGAGTATCCCCGATTGTGAAAATTGGTGTTTTAGAAATAAAATCGGA
Found at i:372272 original size:28 final size:28
Alignment explanation
Indices: 372241--372309 Score: 95
Period size: 28 Copynumber: 2.5 Consensus size: 28
372231 GAAATAAATT
*
372241 CGGGGTTGGAGTATCCCCTCA-GAAATAA
1 CGGGATTGGAGTATCCCC-CATGAAATAA
*
372269 CGGGATTGGAGTATCCCCGATGAAATAA
1 CGGGATTGGAGTATCCCCCATGAAATAA
*
372297 CGGGATTAGAGTA
1 CGGGATTGGAGTA
372310 CCCTCGATTA
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
27 1 0.03
28 36 0.97
ACGTcount: A:0.30, C:0.17, G:0.30, T:0.22
Consensus pattern (28 bp):
CGGGATTGGAGTATCCCCCATGAAATAA
Found at i:372294 original size:208 final size:209
Alignment explanation
Indices: 371935--372318 Score: 535
Period size: 208 Copynumber: 1.8 Consensus size: 209
371925 AAATAACGGG
*
371935 GTTGGAGTATCCCCGATTGTGAGAAATCAATATTTTAAAAATAAAACCGGGGTTGAAGTATCCCT
1 GTTGGAGTATCCCCGATTGTGAGAAATCAATATTTTAAAAATAAAACCGGAGTTGAAGTATCCCT
* *
372000 GATTGTGAGAAATCAATATTTTGGAAATAAAGCCGGGGTTGGAGTATCCCCTCGAAAATAACGGG
66 AATTGTGAGAAATCAATATTTTAGAAATAAAGCCGGGGTTGGAGTATCCCCTCGAAAATAACGGG
* * *
372065 GTTGGAGTATCCCCGATGAAATAACGGGGTTGGAGTATCCC-CGATTGTGCAAAATTAGTGTTTT
131 ATTGGAGTATCCCCGATGAAATAACGGGATTAGAGTA-CCCTCGATTGTGCAAAATTAGTGTTTT
372129 GGAAATAAAATCGGA
195 GGAAATAAAATCGGA
*** * * * *
372144 GTTGGAGTATCCCCGATTGTG-GAAAATTGGTGTTTTAGAAATAAAATCGGAGTTGGAGTATCCC
1 GTTGGAGTATCCCCGATTGTGAG-AAATCAATATTTTAAAAATAAAACCGGAGTTGAAGTATCCC
*** **
372208 -AATTGT-AGAAAATTGGTATTTTAGAAATAAATTCGGGGTTGGAGTATCCCCTC-AGAAATAAC
65 TAATTGTGAG-AAATCAATATTTTAGAAATAAAGCCGGGGTTGGAGTATCCCCTCGA-AAATAAC
372270 GGGATTGGAGTATCCCCGATGAAATAACGGGATTAGAGTACCCTCGATT
128 GGGATTGGAGTATCCCCGATGAAATAACGGGATTAGAGTACCCTCGATT
372319 ATGAAAAAAT
Statistics
Matches: 153, Mismatches: 18, Indels: 9
0.85 0.10 0.05
Matches are distributed among these distances:
207 6 0.04
208 93 0.61
209 54 0.35
ACGTcount: A:0.32, C:0.14, G:0.26, T:0.28
Consensus pattern (209 bp):
GTTGGAGTATCCCCGATTGTGAGAAATCAATATTTTAAAAATAAAACCGGAGTTGAAGTATCCCT
AATTGTGAGAAATCAATATTTTAGAAATAAAGCCGGGGTTGGAGTATCCCCTCGAAAATAACGGG
ATTGGAGTATCCCCGATGAAATAACGGGATTAGAGTACCCTCGATTGTGCAAAATTAGTGTTTTG
GAAATAAAATCGGA
Found at i:372317 original size:28 final size:28
Alignment explanation
Indices: 372249--372317 Score: 88
Period size: 28 Copynumber: 2.5 Consensus size: 28
372239 TTCGGGGTTG
* *
372249 GAGTATCCCCTCA-GAAATAACGGGATTG
1 GAGTATCCCC-GATGAAATAACGGGATTA
372277 GAGTATCCCCGATGAAATAACGGGATTA
1 GAGTATCCCCGATGAAATAACGGGATTA
372305 GAGTA-CCCTCGAT
1 GAGTATCCC-CGAT
372318 TATGAAAAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
27 4 0.11
28 33 0.89
ACGTcount: A:0.32, C:0.22, G:0.25, T:0.22
Consensus pattern (28 bp):
GAGTATCCCCGATGAAATAACGGGATTA
Found at i:374761 original size:20 final size:20
Alignment explanation
Indices: 374736--374789 Score: 81
Period size: 20 Copynumber: 2.7 Consensus size: 20
374726 AAAATGCCTG
* * *
374736 AATGTATCGATGCATTGTAA
1 AATGTATCGATACAATGCAA
374756 AATGTATCGATACAATGCAA
1 AATGTATCGATACAATGCAA
374776 AATGTATCGATACA
1 AATGTATCGATACA
374790 TCTGGGTAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.41, C:0.13, G:0.17, T:0.30
Consensus pattern (20 bp):
AATGTATCGATACAATGCAA
Found at i:374852 original size:13 final size:13
Alignment explanation
Indices: 374805--374834 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
374795 GTAAACTCAA
374805 AATGTATCGATAC
1 AATGTATCGATAC
374818 AATGTATCGATAC
1 AATGTATCGATAC
374831 AATG
1 AATG
374835 AACAATGTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.40, C:0.13, G:0.17, T:0.30
Consensus pattern (13 bp):
AATGTATCGATAC
Found at i:376476 original size:30 final size:30
Alignment explanation
Indices: 376442--376552 Score: 97
Period size: 30 Copynumber: 3.7 Consensus size: 30
376432 TTTTGCAATC
* *
376442 TAAATTTTAGGTAATTTACTTTATATAATT
1 TAAATTTTATGCAATTTACTTTATATAATT
* *
376472 TAAA-TTTATGCAATTTACTTTCTTACAATT
1 TAAATTTTATGCAATTTACTTT-ATATAATT
* *
376502 T-AATTTTATACAATTTACTTTCT-TGAAATT
1 TAAATTTTATGCAATTTACTTTATAT--AATT
376532 TAAATTTATAT--AATTTACTTT
1 TAAATTT-TATGCAATTTACTTT
376553 CTCACGACTT
Statistics
Matches: 68, Mismatches: 7, Indels: 12
0.78 0.08 0.14
Matches are distributed among these distances:
29 18 0.26
30 42 0.62
31 5 0.07
32 3 0.04
ACGTcount: A:0.35, C:0.08, G:0.04, T:0.53
Consensus pattern (30 bp):
TAAATTTTATGCAATTTACTTTATATAATT
Found at i:376500 original size:15 final size:15
Alignment explanation
Indices: 376482--376643 Score: 89
Period size: 15 Copynumber: 10.7 Consensus size: 15
376472 TAAATTTATG
*
376482 CAATTTACTTTCTTA
1 CAATTTAATTTCTTA
376497 CAATTTAATTT-TATA
1 CAATTTAATTTCT-TA
*
376512 CAATTTACTTTCTTGA
1 CAATTTAATTTCTT-A
*
376528 -AATTTAAATTT-ATA
1 CAATTT-AATTTCTTA
* * *
376542 TAATTTACTTTCTCA
1 CAATTTAATTTCTTA
* * * *
376557 CGACTTAAATTCATA
1 CAATTTAATTTCTTA
*
376572 CAATTTATTTTCTTA
1 CAATTTAATTTCTTA
* *
376587 CGATTTAAATTT-ATA
1 CAATTT-AATTTCTTA
* * *
376602 TAATTTACTTTCTTG
1 CAATTTAATTTCTTA
* *
376617 CAATTTATTTTCTTG
1 CAATTTAATTTCTTA
376632 CAATTTTAATTT
1 CAA-TTTAATTT
376644 ATGCAATATA
Statistics
Matches: 108, Mismatches: 30, Indels: 17
0.70 0.19 0.11
Matches are distributed among these distances:
14 10 0.09
15 81 0.75
16 17 0.16
ACGTcount: A:0.31, C:0.13, G:0.03, T:0.52
Consensus pattern (15 bp):
CAATTTAATTTCTTA
Found at i:376553 original size:30 final size:30
Alignment explanation
Indices: 376454--376623 Score: 200
Period size: 30 Copynumber: 5.7 Consensus size: 30
376444 AATTTTAGGT
* * *
376454 AATTTACTTT-ATATAATTTAAATTTATGC
1 AATTTACTTTCTTACAATTTAAATTTATAC
*
376483 AATTTACTTTCTTACAATTTAATTTTATAC
1 AATTTACTTTCTTACAATTTAAATTTATAC
*
376513 AATTTACTTTCTTGA-AATTTAAATTTATAT
1 AATTTACTTTCTT-ACAATTTAAATTTATAC
* * * *
376543 AATTTACTTTCTCACGACTTAAATTCATAC
1 AATTTACTTTCTTACAATTTAAATTTATAC
* * *
376573 AATTTATTTTCTTACGATTTAAATTTATAT
1 AATTTACTTTCTTACAATTTAAATTTATAC
*
376603 AATTTACTTTCTTGCAATTTA
1 AATTTACTTTCTTACAATTTA
376624 TTTTCTTGCA
Statistics
Matches: 119, Mismatches: 19, Indels: 5
0.83 0.13 0.03
Matches are distributed among these distances:
29 11 0.09
30 107 0.90
31 1 0.01
ACGTcount: A:0.34, C:0.12, G:0.03, T:0.51
Consensus pattern (30 bp):
AATTTACTTTCTTACAATTTAAATTTATAC
Found at i:376649 original size:30 final size:29
Alignment explanation
Indices: 376615--376716 Score: 82
Period size: 30 Copynumber: 3.4 Consensus size: 29
376605 TTTACTTTCT
376615 TGCAATTTATTTTCTTGCAATTTTAATTTA
1 TGCAATTTATTTTC-TGCAATTTTAATTTA
* *** *
376645 TGCAATATACTTTAAGGTAATTTTAA-TTA
1 TGCAATTTA-TTTTCTGCAATTTTAATTTA
* *
376674 TGCACTTTACTTTTGCTGCAA-GTTAATTTA
1 TGCAATTTA-TTTT-CTGCAATTTTAATTTA
*
376704 TGCATTTTATTTT
1 TGCAATTTATTTT
376717 ATTGTATATA
Statistics
Matches: 56, Mismatches: 13, Indels: 7
0.74 0.17 0.09
Matches are distributed among these distances:
29 22 0.39
30 31 0.55
31 3 0.05
ACGTcount: A:0.27, C:0.11, G:0.10, T:0.52
Consensus pattern (29 bp):
TGCAATTTATTTTCTGCAATTTTAATTTA
Found at i:376667 original size:45 final size:45
Alignment explanation
Indices: 376572--376667 Score: 102
Period size: 45 Copynumber: 2.1 Consensus size: 45
376562 TAAATTCATA
* * * ***
376572 CAATTTATTTTCTTACGATTTAAATTTATATAATTTACTTTCTTG
1 CAATTTATTTTCTTACAATTTAAATTTATACAATATACTTTAAGG
* * *
376617 CAATTTATTTTCTTGCAATTTTAATTTATGCAATATACTTTAAGG
1 CAATTTATTTTCTTACAATTTAAATTTATACAATATACTTTAAGG
*
376662 TAATTT
1 CAATTT
376668 TAATTATGCA
Statistics
Matches: 41, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
45 41 1.00
ACGTcount: A:0.30, C:0.10, G:0.06, T:0.53
Consensus pattern (45 bp):
CAATTTATTTTCTTACAATTTAAATTTATACAATATACTTTAAGG
Found at i:379109 original size:13 final size:13
Alignment explanation
Indices: 379091--379116 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
379081 CAATTTTTTG
379091 TGTATCGATACAT
1 TGTATCGATACAT
379104 TGTATCGATACAT
1 TGTATCGATACAT
379117 ACTTGCTGTA
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:379797 original size:21 final size:21
Alignment explanation
Indices: 379756--379799 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
379746 CTCCCCTTTA
* *
379756 TCTCCCCCGTTTATTAATAAT
1 TCTCCCCCGTTAATCAATAAT
379777 TCTCCCCC-TTAATCAAGTAAT
1 TCTCCCCCGTTAATCAA-TAAT
379798 TC
1 TC
379800 ATATAAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.25, C:0.32, G:0.05, T:0.39
Consensus pattern (21 bp):
TCTCCCCCGTTAATCAATAAT
Found at i:379816 original size:25 final size:25
Alignment explanation
Indices: 379788--379839 Score: 95
Period size: 25 Copynumber: 2.1 Consensus size: 25
379778 CTCCCCCTTA
379788 ATCAAGTAATTCATATAAAAAATTT
1 ATCAAGTAATTCATATAAAAAATTT
*
379813 ATCAAGTAATTCATATCAAAAATTT
1 ATCAAGTAATTCATATAAAAAATTT
379838 AT
1 AT
379840 TTGCACATAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.50, C:0.10, G:0.04, T:0.37
Consensus pattern (25 bp):
ATCAAGTAATTCATATAAAAAATTT
Found at i:383689 original size:15 final size:15
Alignment explanation
Indices: 383669--383699 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
383659 ATTTCGTTTG
*
383669 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
383684 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
383699 G
1 G
383700 GACATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:387780 original size:13 final size:13
Alignment explanation
Indices: 387762--387787 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
387752 CAATTTTTTG
387762 TGTATCGATACAT
1 TGTATCGATACAT
387775 TGTATCGATACAT
1 TGTATCGATACAT
387788 ACTTGCTGTA
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:388784 original size:17 final size:17
Alignment explanation
Indices: 388759--388801 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 17
388749 AGTCCGAGCT
388759 CGAAAAAGCCAGAACCC
1 CGAAAAAGCCAGAACCC
* *
388776 CGAATAAGCCCGAA-CC
1 CGAAAAAGCCAGAACCC
*
388792 CGAAAGAGCC
1 CGAAAAAGCC
388802 CAAATCCGAA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
16 10 0.45
17 12 0.55
ACGTcount: A:0.42, C:0.35, G:0.21, T:0.02
Consensus pattern (17 bp):
CGAAAAAGCCAGAACCC
Found at i:388795 original size:16 final size:16
Alignment explanation
Indices: 388735--388795 Score: 59
Period size: 16 Copynumber: 3.8 Consensus size: 16
388725 CCGACCTGAA
*
388735 CCCGAACCCAAATAAG
1 CCCGAACCCGAATAAG
* * * *
388751 TCCGAGCTCGAAAAAG
1 CCCGAACCCGAATAAG
*
388767 CCAGAACCCCGAATAAG
1 CCCGAA-CCCGAATAAG
388784 CCCGAACCCGAA
1 CCCGAACCCGAA
388796 AGAGCCCAAA
Statistics
Matches: 33, Mismatches: 11, Indels: 2
0.72 0.24 0.04
Matches are distributed among these distances:
16 20 0.61
17 13 0.39
ACGTcount: A:0.39, C:0.36, G:0.18, T:0.07
Consensus pattern (16 bp):
CCCGAACCCGAATAAG
Found at i:389735 original size:19 final size:19
Alignment explanation
Indices: 389707--389749 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
389697 ATATCAACAA
* *
389707 ATAA-AAAAATTAATAATT
1 ATAATAAAAATAAATAAGT
389725 ATAATAAAAATAAATAAGT
1 ATAATAAAAATAAATAAGT
389744 ATAATA
1 ATAATA
389750 TTATTATTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 4 0.18
19 18 0.82
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.30
Consensus pattern (19 bp):
ATAATAAAAATAAATAAGT
Found at i:390670 original size:16 final size:15
Alignment explanation
Indices: 390644--390684 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 15
390634 TAGAATAGAG
*
390644 ATTTTTTCTAACAAA
1 ATTTTTTCTAAAAAA
390659 ATTTTTTACTAAAAAA
1 ATTTTTT-CTAAAAAA
390675 ATGTTTTTCT
1 AT-TTTTTCT
390685 CTTGTAGTGA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
15 7 0.30
16 11 0.48
17 5 0.22
ACGTcount: A:0.37, C:0.10, G:0.02, T:0.51
Consensus pattern (15 bp):
ATTTTTTCTAAAAAA
Found at i:397057 original size:51 final size:50
Alignment explanation
Indices: 397000--397144 Score: 220
Period size: 49 Copynumber: 2.9 Consensus size: 50
396990 TTTTAACTAG
* *
397000 ATGTATCGATACATTGAAAAATATTTCGATACATATGGGTAAAAAGACAGA
1 ATGTATCGATACATTGAAAAATGTATCGATACAT-TGGGTAAAAAGACAGA
* *
397051 ATGTATCGATACATTGAAAAATGTATCAATACATTGGGT-AAAAGATAGA
1 ATGTATCGATACATTGAAAAATGTATCGATACATTGGGTAAAAAGACAGA
*
397100 ATATATCGATACATTGAAAAATGTATCGATACATTTGGGTAAAAA
1 ATGTATCGATACATTGAAAAATGTATCGATACA-TTGGGTAAAAA
397145 TGTAACTTTT
Statistics
Matches: 86, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
49 40 0.47
50 11 0.13
51 35 0.41
ACGTcount: A:0.45, C:0.09, G:0.17, T:0.29
Consensus pattern (50 bp):
ATGTATCGATACATTGAAAAATGTATCGATACATTGGGTAAAAAGACAGA
Found at i:397075 original size:20 final size:20
Alignment explanation
Indices: 397050--397134 Score: 80
Period size: 20 Copynumber: 3.8 Consensus size: 20
397040 AAAAAGACAG
397050 AATGTATCGATACATTGAAA
1 AATGTATCGATACATTGAAA
*
397070 AATGTATCAATACATTGGGTAAA
1 AATGTATCGATACATT--G-AAA
397093 AGATAGAATATATCGATACATTGAAA
1 A-AT-G----TATCGATACATTGAAA
397119 AATGTATCGATACATT
1 AATGTATCGATACATT
397135 TGGGTAAAAA
Statistics
Matches: 54, Mismatches: 2, Indels: 18
0.73 0.03 0.24
Matches are distributed among these distances:
20 27 0.50
22 1 0.02
23 4 0.07
24 3 0.06
25 3 0.06
26 4 0.07
27 1 0.02
29 11 0.20
ACGTcount: A:0.45, C:0.09, G:0.15, T:0.31
Consensus pattern (20 bp):
AATGTATCGATACATTGAAA
Found at i:398504 original size:20 final size:20
Alignment explanation
Indices: 398479--398532 Score: 74
Period size: 20 Copynumber: 2.7 Consensus size: 20
398469 GTTACAAGCA
* *
398479 ATGTATCAATACAAT-TCATC
1 ATGTATCGATACAATGT-ACC
398499 ATGTATCGATACAATGTACC
1 ATGTATCGATACAATGTACC
398519 ATGTATCGATACAA
1 ATGTATCGATACAA
398533 ACAGTGGTAG
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
20 30 0.97
21 1 0.03
ACGTcount: A:0.39, C:0.19, G:0.11, T:0.31
Consensus pattern (20 bp):
ATGTATCGATACAATGTACC
Found at i:398606 original size:19 final size:19
Alignment explanation
Indices: 398560--398654 Score: 129
Period size: 19 Copynumber: 4.9 Consensus size: 19
398550 ACTGCTAGTT
*
398560 TCATGTATTGATACAATTG-
1 TCATGTATCGATACAA-TGA
*
398579 TCTATGTATCGATACAATAA
1 TC-ATGTATCGATACAATGA
398599 TCATGTATCGATACAATGA
1 TCATGTATCGATACAATGA
*
398618 TCGTGTATCGATACAATGA
1 TCATGTATCGATACAATGA
*
398637 TCATGTGTCGATACAATG
1 TCATGTATCGATACAATG
398655 TATCGATACA
Statistics
Matches: 68, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
19 53 0.78
20 15 0.22
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.35
Consensus pattern (19 bp):
TCATGTATCGATACAATGA
Found at i:398662 original size:32 final size:34
Alignment explanation
Indices: 398582--398664 Score: 98
Period size: 38 Copynumber: 2.4 Consensus size: 34
398572 ACAATTGTCT
398582 ATGTATCGATACAATAATCATGTATCGATACAATG
1 ATGTATCGATACAATAATCATGTATCGATACAA-G
* *
398617 ATCGTGTATCGATACAATGATCATGTGTCGATAC-A-
1 A---TGTATCGATACAATAATCATGTATCGATACAAG
398652 ATGTATCGATACA
1 ATGTATCGATACA
398665 TCTGGGTGTG
Statistics
Matches: 43, Mismatches: 2, Indels: 9
0.80 0.04 0.17
Matches are distributed among these distances:
32 12 0.28
35 2 0.05
37 1 0.02
38 28 0.65
ACGTcount: A:0.36, C:0.16, G:0.17, T:0.31
Consensus pattern (34 bp):
ATGTATCGATACAATAATCATGTATCGATACAAG
Found at i:404577 original size:79 final size:79
Alignment explanation
Indices: 404485--404670 Score: 234
Period size: 79 Copynumber: 2.4 Consensus size: 79
404475 AGTGTTTTGA
* * * *
404485 AAATGAAATCGGGGTTAAAGTATCCTC-TCGAAAATAACGGGGTTGAAGTATCC-CTGATTGTGA
1 AAATAAAACCGGGGTTAGAGTATCCCCGT-GAAAATAACGGGGTTGAAGTATCCTC-GATTGTGA
404548 AAAATTGATGCTTTAG
64 AAAATTGATGCTTTAG
* *
404564 AAA-AAAGACCGGGGTTGGAGTATCCCCGTGAAAATAACGGGGTTGGAGTATCCTCGATTGTGAA
1 AAATAAA-ACCGGGGTTAGAGTATCCCCGTGAAAATAACGGGGTTGAAGTATCCTCGATTGTGAA
* *
404628 AAATTGGTGTTTTAG
65 AAATTGATGCTTTAG
**
404643 AAATAAAATAGGGGTTAGAGTATCCCCG
1 AAATAAAACCGGGGTTAGAGTATCCCCG
404671 ATTATGAGAA
Statistics
Matches: 92, Mismatches: 11, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
78 2 0.02
79 85 0.92
80 5 0.05
ACGTcount: A:0.33, C:0.13, G:0.27, T:0.27
Consensus pattern (79 bp):
AAATAAAACCGGGGTTAGAGTATCCCCGTGAAAATAACGGGGTTGAAGTATCCTCGATTGTGAAA
AATTGATGCTTTAG
Found at i:404657 original size:130 final size:131
Alignment explanation
Indices: 404523--404812 Score: 376
Period size: 130 Copynumber: 2.2 Consensus size: 131
404513 CGAAAATAAC
* * ** *
404523 GGGGTTGAAGTATCCCTGATTGTGAAAAATTGATGCTTTAGAAA-AAAGACCGGGGTTGGAGTAT
1 GGGGTTGAAGTATCCCCGATTATGAAAAATCAATACTTTAGAAATAAAG-CCGGGGTTGGAGTAT
* *
404587 CCCCGT-GAAAATAACGGGGTTGGAGTATCC-TCGATTGTGAAAA-ATTGGTGTTTTAGAAATAA
65 CCCC-TCGAAAATAACGGGATTGGAGTATCCTTC-ATTGTGAAAAGATTAGTGTTTTAGAAATAA
404649 AATA
128 AATA
* * *
404653 GGGGTT-AGAGTATCCCCGATTATGAGAAATCAATATTTTATAAATAAAGCCGGGGTTGGAGTAT
1 GGGGTTGA-AGTATCCCCGATTATGAAAAATCAATACTTTAGAAATAAAGCCGGGGTTGGAGTAT
*
404717 CCCCTCGGAAATAACGGGATTGGAGTATCCTTCATTGTGAAAAGATTAGTGTTTTAGAAATAAAA
65 CCCCTCGAAAATAACGGGATTGGAGTATCCTTCATTGTGAAAAGATTAGTGTTTTAGAAATAAAA
*
404782 TC
130 TA
* *
404784 GGGGTTGGAGTATCCCCGA-GATGAAAAAT
1 GGGGTTGAAGTATCCCCGATTATGAAAAAT
404813 TTAAAAATTT
Statistics
Matches: 139, Mismatches: 15, Indels: 12
0.84 0.09 0.07
Matches are distributed among these distances:
129 2 0.01
130 93 0.67
131 44 0.32
ACGTcount: A:0.33, C:0.12, G:0.27, T:0.28
Consensus pattern (131 bp):
GGGGTTGAAGTATCCCCGATTATGAAAAATCAATACTTTAGAAATAAAGCCGGGGTTGGAGTATC
CCCTCGAAAATAACGGGATTGGAGTATCCTTCATTGTGAAAAGATTAGTGTTTTAGAAATAAAAT
A
Found at i:406445 original size:20 final size:19
Alignment explanation
Indices: 406420--406493 Score: 85
Period size: 20 Copynumber: 3.7 Consensus size: 19
406410 TTTACCCAGA
*
406420 TGTATCGTTACATTTTGCAT
1 TGTATCGATACATTTT-CAT
*
406440 TGTATCGATACATTGCTCAT
1 TGTATCGATACATT-TTCAT
* *
406460 TGTATCAATACATTTTACAA
1 TGTATCGATACATTTT-CAT
406480 TGTATCGATACATT
1 TGTATCGATACATT
406494 CAGGCATTTT
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
19 1 0.02
20 44 0.96
21 1 0.02
ACGTcount: A:0.28, C:0.16, G:0.12, T:0.43
Consensus pattern (19 bp):
TGTATCGATACATTTTCAT
Found at i:409748 original size:27 final size:27
Alignment explanation
Indices: 409710--409780 Score: 142
Period size: 27 Copynumber: 2.6 Consensus size: 27
409700 GGTTGAAAAC
409710 GGGGTTGGAGTGTCCCCTCGGAGGAAT
1 GGGGTTGGAGTGTCCCCTCGGAGGAAT
409737 GGGGTTGGAGTGTCCCCTCGGAGGAAT
1 GGGGTTGGAGTGTCCCCTCGGAGGAAT
409764 GGGGTTGGAGTGTCCCC
1 GGGGTTGGAGTGTCCCC
409781 GCCGAATAAA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 44 1.00
ACGTcount: A:0.13, C:0.20, G:0.45, T:0.23
Consensus pattern (27 bp):
GGGGTTGGAGTGTCCCCTCGGAGGAAT
Found at i:412013 original size:13 final size:13
Alignment explanation
Indices: 411995--412019 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
411985 ACAGAGATCA
411995 AATGTATCGATAC
1 AATGTATCGATAC
412008 AATGTATCGATA
1 AATGTATCGATA
412020 AATTTGAGTA
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:0.40, C:0.12, G:0.16, T:0.32
Consensus pattern (13 bp):
AATGTATCGATAC
Found at i:412084 original size:13 final size:13
Alignment explanation
Indices: 412066--412117 Score: 50
Period size: 13 Copynumber: 3.5 Consensus size: 13
412056 AGCTTCGTAG
412066 CGATACATTGTAT
1 CGATACATTGTAT
412079 CGATACAAAACTTATGTAT
1 CGATAC---A-TT--GTAT
412098 CGATACATTGTAT
1 CGATACATTGTAT
412111 CGATACA
1 CGATACA
412118 ACACTTATGT
Statistics
Matches: 33, Mismatches: 0, Indels: 12
0.73 0.00 0.27
Matches are distributed among these distances:
13 17 0.52
15 2 0.06
16 2 0.06
17 2 0.06
19 10 0.30
ACGTcount: A:0.37, C:0.17, G:0.13, T:0.33
Consensus pattern (13 bp):
CGATACATTGTAT
Found at i:412098 original size:19 final size:18
Alignment explanation
Indices: 412074--412136 Score: 64
Period size: 19 Copynumber: 3.7 Consensus size: 18
412064 AGCGATACAT
412074 TGTATCGATACAAAACTTA
1 TGTATCGATAC-AAACTTA
412093 TGTATCGATAC--A--T-
1 TGTATCGATACAAACTTA
412106 TGTATCGATACAACACTTA
1 TGTATCGATACAA-ACTTA
*
412125 TGTATCGTTACA
1 TGTATCGATACA
412137 GTTACGGTTT
Statistics
Matches: 37, Mismatches: 1, Indels: 12
0.74 0.02 0.24
Matches are distributed among these distances:
13 11 0.30
14 1 0.03
16 2 0.05
18 1 0.03
19 22 0.59
ACGTcount: A:0.35, C:0.17, G:0.13, T:0.35
Consensus pattern (18 bp):
TGTATCGATACAAACTTA
Found at i:412107 original size:32 final size:32
Alignment explanation
Indices: 412066--412136 Score: 124
Period size: 32 Copynumber: 2.2 Consensus size: 32
412056 AGCTTCGTAG
412066 CGATACATTGTATCGATACAAAACTTATGTAT
1 CGATACATTGTATCGATACAAAACTTATGTAT
*
412098 CGATACATTGTATCGATACAACACTTATGTAT
1 CGATACATTGTATCGATACAAAACTTATGTAT
*
412130 CGTTACA
1 CGATACA
412137 GTTACGGTTT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 37 1.00
ACGTcount: A:0.35, C:0.18, G:0.13, T:0.34
Consensus pattern (32 bp):
CGATACATTGTATCGATACAAAACTTATGTAT
Found at i:412588 original size:51 final size:52
Alignment explanation
Indices: 412528--412642 Score: 128
Period size: 51 Copynumber: 2.2 Consensus size: 52
412518 TATTCCGAAG
* *
412528 GGATACTCCAACCT-TGGTTTTA-TTTCTAAAACACCAATTCCCCACAATAGA
1 GGATACTCCAACCTCCGATTTTATTTTC-AAAACACCAATTCCCCACAATAGA
* *** * *
412579 GGATACTCCAA-CTCCGATTTTATTTTCAAAACACTAATTTTTCACAATCGG
1 GGATACTCCAACCTCCGATTTTATTTTCAAAACACCAATTCCCCACAATAGA
412630 GGATACTCCAACC
1 GGATACTCCAACC
412643 CCATTATTTC
Statistics
Matches: 53, Mismatches: 8, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
50 2 0.04
51 46 0.87
52 5 0.09
ACGTcount: A:0.32, C:0.27, G:0.10, T:0.30
Consensus pattern (52 bp):
GGATACTCCAACCTCCGATTTTATTTTCAAAACACCAATTCCCCACAATAGA
Found at i:412661 original size:28 final size:28
Alignment explanation
Indices: 412625--412726 Score: 143
Period size: 28 Copynumber: 3.6 Consensus size: 28
412615 ATTTTTCACA
*
412625 ATCGGGGATACTCCAACCCCATTATTTC
1 ATCGGGGATACTCCAACCCCGTTATTTC
*
412653 ATCGGGGATGCTCCAACCCCGTTATTTC
1 ATCGGGGATACTCCAACCCCGTTATTTC
* *
412681 ATCGAGGATGCTCCAACCCCGTTATTTCC
1 ATCGGGGATACTCCAACCCCGTTATTT-C
*
412710 A-AGGGGATACTCCAACC
1 ATCGGGGATACTCCAACC
412727 TCGGCTTTAT
Statistics
Matches: 67, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
28 65 0.97
29 2 0.03
ACGTcount: A:0.24, C:0.32, G:0.19, T:0.25
Consensus pattern (28 bp):
ATCGGGGATACTCCAACCCCGTTATTTC
Found at i:412784 original size:79 final size:79
Alignment explanation
Indices: 412681--412855 Score: 235
Period size: 79 Copynumber: 2.2 Consensus size: 79
412671 CCGTTATTTC
* * * *
412681 ATCGAGGATGCTCCAACCCCGTTATTTCCAAGGGGATACTCCAACCTCGGCTTTATTTCTAAAAT
1 ATCGGGGATACTCCAACCCCGTTATTTCCAAGGGGATACTCCAACCCCGGCTTTATTTCTAAAAC
* * * *
412746 ATTAGTT-TCTTATA
66 ACTAATTCTC-CACA
* * *
412760 ATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGGTTTTATTTCTAAAAC
1 ATCGGGGATACTCCAACCCCGTTATTTCCAAGGGGATACTCCAACCCCGGCTTTATTTCTAAAAC
412825 ACTAATTCTCCACA
66 ACTAATTCTCCACA
412839 ATCGGGGATACTCCAAC
1 ATCGGGGATACTCCAAC
412856 TCTGATTTTA
Statistics
Matches: 84, Mismatches: 11, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
79 82 0.98
80 2 0.02
ACGTcount: A:0.27, C:0.27, G:0.16, T:0.30
Consensus pattern (79 bp):
ATCGGGGATACTCCAACCCCGTTATTTCCAAGGGGATACTCCAACCCCGGCTTTATTTCTAAAAC
ACTAATTCTCCACA
Found at i:412867 original size:51 final size:51
Alignment explanation
Indices: 412791--412910 Score: 168
Period size: 51 Copynumber: 2.4 Consensus size: 51
412781 TTATTTTCGA
* * * *
412791 GGGGATACTCCAACCCCGGTTTTATTTCTAAAACACTAATTCTCCACAATC
1 GGGGATACTCCAACTCTGATTTTATTTCCAAAACACTAATTCTCCACAATC
* *
412842 GGGGATACTCCAACTCTGATTTTATTTCCAAAACACTAATTTTTCACAATC
1 GGGGATACTCCAACTCTGATTTTATTTCCAAAACACTAATTCTCCACAATC
* *
412893 GGGGATACTTCAGCTCTG
1 GGGGATACTCCAACTCTG
412911 TTATTTCATC
Statistics
Matches: 61, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
51 61 1.00
ACGTcount: A:0.28, C:0.26, G:0.14, T:0.32
Consensus pattern (51 bp):
GGGGATACTCCAACTCTGATTTTATTTCCAAAACACTAATTCTCCACAATC
Found at i:413000 original size:237 final size:237
Alignment explanation
Indices: 412673--413138 Score: 616
Period size: 237 Copynumber: 2.0 Consensus size: 237
412663 CTCCAACCCC
* * * *
412673 GTTATTTCATCGAGGATGCTCCAACCCCGTTATTTCCAAGGGGATACTCCAACCTCGGCTTTATT
1 GTTATTTCATCGAGGATACTCCAACCCCGTTATTTCCAAGGAGATACTCCAACCCCGACTTTATT
* * * * *
412738 TCTAAAATATTAGTTTCTTATAATCGGGGATACTCCAACCCCGTTATTTTCGA-GGGGATACTCC
66 TCCAAAATATGAGTTTCTCATAATCGGGGATACTCCAACCCCATTATTTTC-ACAGGGATACTCC
*
412802 AACCCCGGTTTTATTTCTAAAACA-CTAATTCTCCACAATCGGGGATACTCCAA-CTCTGATTTT
130 AACCCCGATTTTATTTCTAAAACATC-AATTCTCCACAATCGGGGATACTCCAATCTC-GATTTT
412865 ATTTCCAAAACACTAATTTTTCACAATCGGGGATACTTCAGCTCT
193 ATTTCCAAAACACTAATTTTTCACAATCGGGGATACTTCAGCTCT
* * *
412910 GTTATTTCATCGGGGATACTCTAACCCCGTTATTTCCGAGGAGATACTCCAACCCCGACTTTATT
1 GTTATTTCATCGAGGATACTCCAACCCCGTTATTTCCAAGGAGATACTCCAACCCCGACTTTATT
* *
412975 TCCAAAATACTGA-TTTCTCATAATCGGGGATACTCCAACCCTATTATTTTCACAGGGATATTCC
66 TCCAAAATA-TGAGTTTCTCATAATCGGGGATACTCCAACCCCATTATTTTCACAGGGATACTCC
* * * ** * * * *
413039 AATCCTGATTTTATTTTTAAAGTATCGATTTTCTATAATCGGGGATACTCCAATCTCGATTTTAT
130 AACCCCGATTTTATTTCTAAAACATCAATTCTCCACAATCGGGGATACTCCAATCTCGATTTTAT
* * * *
413104 TTCTAAATCATTGATTTTTCACAATCGGGGATACT
195 TTCCAAAACACTAATTTTTCACAATCGGGGATACT
413139 CCAACCCGTT
Statistics
Matches: 197, Mismatches: 28, Indels: 8
0.85 0.12 0.03
Matches are distributed among these distances:
236 1 0.01
237 190 0.96
238 6 0.03
ACGTcount: A:0.27, C:0.24, G:0.14, T:0.35
Consensus pattern (237 bp):
GTTATTTCATCGAGGATACTCCAACCCCGTTATTTCCAAGGAGATACTCCAACCCCGACTTTATT
TCCAAAATATGAGTTTCTCATAATCGGGGATACTCCAACCCCATTATTTTCACAGGGATACTCCA
ACCCCGATTTTATTTCTAAAACATCAATTCTCCACAATCGGGGATACTCCAATCTCGATTTTATT
TCCAAAACACTAATTTTTCACAATCGGGGATACTTCAGCTCT
Found at i:413001 original size:79 final size:79
Alignment explanation
Indices: 412918--413091 Score: 194
Period size: 79 Copynumber: 2.2 Consensus size: 79
412908 CTGTTATTTC
* *
412918 ATCGGGGATACTCTAACCCCGTTA-TTTC-CGAGGAGATACTCCAACCCCGACTTTATTTCCAAA
1 ATCGGGGATACTCCAACCCCATTATTTTCAC-AGG-GATACTCCAACCCCGACTTTATTTCCAAA
412981 ATA-CTGA-TTTCTCATA
64 ATATC-GATTTTCT-ATA
* * * * * ** *
412997 ATCGGGGATACTCCAACCCTATTATTTTCACAGGGATATTCCAATCCTGATTTTATTTTTAAAGT
1 ATCGGGGATACTCCAACCCCATTATTTTCACAGGGATACTCCAACCCCGACTTTATTTCCAAAAT
413062 ATCGATTTTCTATA
66 ATCGATTTTCTATA
413076 ATCGGGGATACTCCAA
1 ATCGGGGATACTCCAA
413092 TCTCGATTTT
Statistics
Matches: 81, Mismatches: 10, Indels: 8
0.82 0.10 0.08
Matches are distributed among these distances:
79 67 0.83
80 13 0.16
81 1 0.01
ACGTcount: A:0.28, C:0.24, G:0.14, T:0.34
Consensus pattern (79 bp):
ATCGGGGATACTCCAACCCCATTATTTTCACAGGGATACTCCAACCCCGACTTTATTTCCAAAAT
ATCGATTTTCTATA
Found at i:413091 original size:51 final size:51
Alignment explanation
Indices: 413029--413142 Score: 144
Period size: 51 Copynumber: 2.2 Consensus size: 51
413019 TATTTTCACA
* * *
413029 GGGATATTCCAATC-CTGATTTTATTTTTAAAGT-ATCGA-TTTTCTATAATCG
1 GGGATACTCCAATCTC-GATTTTATTTCTAAA-TCATCGATTTTTC-ACAATCG
*
413080 GGGATACTCCAATCTCGATTTTATTTCTAAATCATTGATTTTTCACAATCG
1 GGGATACTCCAATCTCGATTTTATTTCTAAATCATCGATTTTTCACAATCG
413131 GGGATACTCCAA
1 GGGATACTCCAA
413143 CCCGTTATGA
Statistics
Matches: 56, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
50 1 0.02
51 49 0.88
52 6 0.11
ACGTcount: A:0.28, C:0.18, G:0.14, T:0.40
Consensus pattern (51 bp):
GGGATACTCCAATCTCGATTTTATTTCTAAATCATCGATTTTTCACAATCG
Found at i:419314 original size:12 final size:13
Alignment explanation
Indices: 419297--419325 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
419287 TTTCTCTTTC
419297 CTTTC-TTTTCCT
1 CTTTCTTTTTCCT
419309 CTTTCTTTTTCCT
1 CTTTCTTTTTCCT
419322 CTTT
1 CTTT
419326 TCATTTTTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 5 0.31
13 11 0.69
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (13 bp):
CTTTCTTTTTCCT
Found at i:419316 original size:21 final size:21
Alignment explanation
Indices: 419291--419342 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 21
419281 ATTTTTTTTC
*
419291 TCTTTCCTTTCTTTTCCTCTT
1 TCTTTCCTTTCTTTTCATCTT
*
419312 TCTTT--TTCCTCTTTTCATTTT
1 TCTTTCCTT--TCTTTTCATCTT
419333 TCTTTCCTTT
1 TCTTTCCTTT
419343 TTTATCTTCA
Statistics
Matches: 25, Mismatches: 2, Indels: 8
0.71 0.06 0.23
Matches are distributed among these distances:
19 2 0.08
21 21 0.84
23 2 0.08
ACGTcount: A:0.02, C:0.29, G:0.00, T:0.69
Consensus pattern (21 bp):
TCTTTCCTTTCTTTTCATCTT
Found at i:421732 original size:15 final size:16
Alignment explanation
Indices: 421703--421738 Score: 65
Period size: 15 Copynumber: 2.3 Consensus size: 16
421693 TCCAGCAATG
421703 AATAAAACAAAATCAA
1 AATAAAACAAAATCAA
421719 AATAAAAC-AAATCAA
1 AATAAAACAAAATCAA
421734 AATAA
1 AATAA
421739 TCAATATATT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 12 0.60
16 8 0.40
ACGTcount: A:0.75, C:0.11, G:0.00, T:0.14
Consensus pattern (16 bp):
AATAAAACAAAATCAA
Found at i:421920 original size:26 final size:25
Alignment explanation
Indices: 421857--421942 Score: 84
Period size: 26 Copynumber: 3.2 Consensus size: 25
421847 TGTACTATAT
*
421857 TATTTTTTAATTAAATATATTAAAA
1 TATTTTTTAAATAAATATATTAAAA
*
421882 AATTTATTATAAATAAATAT-TTAAATTA
1 TATTT-TT-TAAATAAATATATTAAA--A
421910 TATTTTTTAAATAAATAAGTATCTAAAA
1 TATTTTTTAAATAAAT-A-TAT-TAAAA
421938 TATTT
1 TATTT
421943 AATAAAAATG
Statistics
Matches: 50, Mismatches: 3, Indels: 13
0.76 0.05 0.20
Matches are distributed among these distances:
25 4 0.08
26 16 0.32
27 13 0.26
28 12 0.24
29 1 0.02
30 4 0.08
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.49
Consensus pattern (25 bp):
TATTTTTTAAATAAATATATTAAAA
Found at i:422960 original size:21 final size:21
Alignment explanation
Indices: 422936--422975 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
422926 ATATTTTATT
422936 TAAAT-TTAATTATAAAATATA
1 TAAATATTAATTA-AAAATATA
422957 TAAATATTAATTAAAAATA
1 TAAATATTAATTAAAAATA
422976 ATTTTTAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (21 bp):
TAAATATTAATTAAAAATATA
Found at i:428186 original size:22 final size:22
Alignment explanation
Indices: 428142--428182 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
428132 CAAAACTATT
428142 ATATTAATATTAAAGATATTTA
1 ATATTAATATTAAAGATATTTA
*
428164 ATATTAA-ATTATA-ATATTT
1 ATATTAATATTAAAGATATTT
428183 TTAAAGATCA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 6 0.33
21 5 0.28
22 7 0.39
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (22 bp):
ATATTAATATTAAAGATATTTA
Found at i:429183 original size:16 final size:15
Alignment explanation
Indices: 429150--429206 Score: 55
Period size: 16 Copynumber: 3.8 Consensus size: 15
429140 TTTTTATCAT
*
429150 ATTTTTTAAACAT--
1 ATTTTTTTAACATAA
**
429163 ATTTTTTTAATGTAA
1 ATTTTTTTAACATAA
429178 ACTTTTTTTAACATAA
1 A-TTTTTTTAACATAA
429194 ATTTTTTTCAACA
1 ATTTTTTT-AACA
429207 GACTAAACTA
Statistics
Matches: 35, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
13 10 0.29
15 8 0.23
16 17 0.49
ACGTcount: A:0.35, C:0.09, G:0.02, T:0.54
Consensus pattern (15 bp):
ATTTTTTTAACATAA
Found at i:437578 original size:52 final size:52
Alignment explanation
Indices: 437498--437617 Score: 213
Period size: 52 Copynumber: 2.3 Consensus size: 52
437488 AAAAGTTACT
* *
437498 TGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAGATTTGCC
1 TGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGCC
*
437550 TGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTTGCC
1 TGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGCC
437602 TGCATGTATCGATACA
1 TGCATGTATCGATACA
437618 AAGATCGGTG
Statistics
Matches: 65, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 65 1.00
ACGTcount: A:0.28, C:0.17, G:0.19, T:0.35
Consensus pattern (52 bp):
TGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGCC
Found at i:437630 original size:52 final size:52
Alignment explanation
Indices: 437498--437637 Score: 185
Period size: 52 Copynumber: 2.7 Consensus size: 52
437488 AAAAGTTACT
* *
437498 TGCATGTATCGATACATTTA-ATAGTGTATCGATACATCTGGGCAGATTTGCC
1 TGCATGTATCGATACA-TAAGATAGTGTATCGATACATCTGGGCAAATTTGCC
*** *
437550 TGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTTGCC
1 TGCATGTATCGATACATAAGATAGTGTATCGATACATCTGGGCAAATTTGCC
*
437602 TGCATGTATCGATACA-AAGATCGGTGTATCGATACA
1 TGCATGTATCGATACATAAGAT-AGTGTATCGATACA
437638 ATGTATCGAT
Statistics
Matches: 78, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
51 4 0.05
52 74 0.95
ACGTcount: A:0.29, C:0.17, G:0.20, T:0.34
Consensus pattern (52 bp):
TGCATGTATCGATACATAAGATAGTGTATCGATACATCTGGGCAAATTTGCC
Found at i:437644 original size:13 final size:13
Alignment explanation
Indices: 437626--437650 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
437616 CAAAGATCGG
437626 TGTATCGATACAA
1 TGTATCGATACAA
437639 TGTATCGATACA
1 TGTATCGATACA
437651 TTTGAGTAAT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:437728 original size:33 final size:33
Alignment explanation
Indices: 437691--437757 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
437681 AGTAGCTTAA
437691 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
437724 ATTGTATCGATACAACATTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
437757 A
1 A
437758 AATCGTTGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.34
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:437731 original size:13 final size:13
Alignment explanation
Indices: 437713--437737 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
437703 CAAAAAAATA
437713 TGTATCGATACAT
1 TGTATCGATACAT
437726 TGTATCGATACA
1 TGTATCGATACA
437738 ACATTTTATG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:437907 original size:21 final size:21
Alignment explanation
Indices: 437881--437922 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
437871 ACCCTATCTC
437881 GACTAGGGACGATGGGAAATT
1 GACTAGGGACGATGGGAAATT
437902 GACTAGGGACGATGGGAAATT
1 GACTAGGGACGATGGGAAATT
437923 CGTCCCCACA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.33, C:0.10, G:0.38, T:0.19
Consensus pattern (21 bp):
GACTAGGGACGATGGGAAATT
Found at i:440874 original size:21 final size:21
Alignment explanation
Indices: 440845--440901 Score: 69
Period size: 21 Copynumber: 2.7 Consensus size: 21
440835 GTTAAAAAGT
440845 TATATTTTTTTCATCCAAAAAA
1 TATA-TTTTTTCATCCAAAAAA
**
440867 TATATTTTTTCATCCAACCAA
1 TATATTTTTTCATCCAAAAAA
* *
440888 TGTATTATTTCATC
1 TATATTTTTTCATC
440902 TAAATATACT
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
21 27 0.87
22 4 0.13
ACGTcount: A:0.33, C:0.18, G:0.02, T:0.47
Consensus pattern (21 bp):
TATATTTTTTCATCCAAAAAA
Found at i:444975 original size:20 final size:20
Alignment explanation
Indices: 444950--445023 Score: 91
Period size: 20 Copynumber: 3.8 Consensus size: 20
444940 TAAAAGACAT
444950 AATGTATCGATACATTGAAG
1 AATGTATCGATACATTGAAG
*
444970 AATGTATCGATACATTCATA-
1 AATGTATCGATACATTGA-AG
*
444990 CATGTATCGATACATTG-AG
1 AATGTATCGATACATTGAAG
445009 AAATGTAT-GATACAT
1 -AATGTATCGATACAT
445024 ATGGGTACTT
Statistics
Matches: 47, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
18 1 0.02
19 7 0.15
20 38 0.81
21 1 0.02
ACGTcount: A:0.39, C:0.12, G:0.16, T:0.32
Consensus pattern (20 bp):
AATGTATCGATACATTGAAG
Done.