Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold385
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: 592280
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.32
Warning! 29825 characters in sequence are not A, C, G, or T
File 2 of 2
Found at i:347450 original size:44 final size:44
Alignment explanation
Indices: 347383--347498 Score: 153
Period size: 44 Copynumber: 2.6 Consensus size: 44
347373 CATTCAGTCT
*
347383 GCTCCACTGCAACTTTAGGGAGATAAGACT-TGTAACTTTAATCC
1 GCTCCACTGCAACTTCAGGGAGATAAGACTAT-TAACTTTAATCC
* * * ** *
347427 GCTCCACTGCAACCTCAGAGAGATAGGACTATTGGCTTTAATCT
1 GCTCCACTGCAACTTCAGGGAGATAAGACTATTAACTTTAATCC
347471 GCTCCACTGCAACTTCAGGGAGATAAGA
1 GCTCCACTGCAACTTCAGGGAGATAAGA
347499 TTCGCCATGT
Statistics
Matches: 61, Mismatches: 10, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
44 60 0.98
45 1 0.02
ACGTcount: A:0.29, C:0.24, G:0.21, T:0.26
Consensus pattern (44 bp):
GCTCCACTGCAACTTCAGGGAGATAAGACTATTAACTTTAATCC
Found at i:369057 original size:138 final size:138
Alignment explanation
Indices: 368705--369125 Score: 641
Period size: 138 Copynumber: 3.1 Consensus size: 138
368695 TAGAAAAAGA
* *
368705 AATTATATTCTTTCCAAAAGAATATTAATTTCTATGCCTTTTATATTTTGCCCGAAATTAATTAA
1 AATTATATTCTTTCCAAAAGAATATTAATTTCTATGCCTTTTATATTTTGGCTGAAATTAATTAA
* * *
368770 TATAATTATTTATATTAATAAATTCAGTAAAATATATACAATTAATATTTTGTGTGAATCAAATA
66 TATAATTATTTATATTAATAAATTCGGTAAAATATATACAATTAATATTTTGTATGAATCAAATT
368835 CATA-ATT
131 CATATATT
* * * * *
368842 AATTATATTCTTTCCAAAAGAATATTAATGTCTATGTCTTCTATATTTT-GATCAAAATTAATTA
1 AATTATATTCTTTCCAAAAGAATATTAATTTCTATGCCTTTTATATTTTGGCT-GAAATTAATTA
* * **
368906 ATATAATTGTTTATATTAATAAATTCGGTGAAATATATACAATTAATATTTTACATGAATCAAAT
65 ATATAATTATTTATATTAATAAATTCGGTAAAATATATACAATTAATATTTTGTATGAATCAAAT
368971 TCATATATT
130 TCATATATT
* * *
368980 AATTATATTCTTTCCAAAAGAATATTAATTT-TCAAGGCTTTTATATTTTGGCTGAAAGTAATTA
1 AATTATATTCTTTCCAAAAGAATATTAATTTCT-ATGCCTTTTATATTTTGGCTGAAATTAATTA
*
369044 ATATAACTATTTATATTAATAAATTCGGTAAAATATATACAATTAATATTTTGTATGAATCAAAT
65 ATATAATTATTTATATTAATAAATTCGGTAAAATATATACAATTAATATTTTGTATGAATCAAAT
369109 TCATATATT
130 TCATATATT
369118 AATTATAT
1 AATTATAT
369126 CTATATTCTC
Statistics
Matches: 254, Mismatches: 26, Indels: 7
0.89 0.09 0.02
Matches are distributed among these distances:
137 120 0.47
138 132 0.52
139 2 0.01
ACGTcount: A:0.41, C:0.09, G:0.07, T:0.44
Consensus pattern (138 bp):
AATTATATTCTTTCCAAAAGAATATTAATTTCTATGCCTTTTATATTTTGGCTGAAATTAATTAA
TATAATTATTTATATTAATAAATTCGGTAAAATATATACAATTAATATTTTGTATGAATCAAATT
CATATATT
Found at i:369194 original size:13 final size:13
Alignment explanation
Indices: 369176--369204 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
369166 TGTGTTTAAT
369176 ATTTAACTATCAA
1 ATTTAACTATCAA
369189 ATTTAACTATCAA
1 ATTTAACTATCAA
369202 ATT
1 ATT
369205 AAGTTAATTC
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:0.45, C:0.14, G:0.00, T:0.41
Consensus pattern (13 bp):
ATTTAACTATCAA
Found at i:380563 original size:17 final size:17
Alignment explanation
Indices: 380524--380568 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 17
380514 TAAAAAAGTG
* *
380524 ATAAAAAAAGTACAGAAA
1 ATAAGAAAA-TACAAAAA
380542 A-AAGAAAATACAAAAA
1 ATAAGAAAATACAAAAA
380558 ATAAGAAAATA
1 ATAAGAAAATA
380569 TTATGTGGAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
16 8 0.33
17 15 0.62
18 1 0.04
ACGTcount: A:0.76, C:0.04, G:0.09, T:0.11
Consensus pattern (17 bp):
ATAAGAAAATACAAAAA
Found at i:386132 original size:43 final size:43
Alignment explanation
Indices: 386084--386213 Score: 112
Period size: 40 Copynumber: 3.1 Consensus size: 43
386074 TGTGTTGAAA
386084 GTAATACTAAGATTGGTTTGATTAGTGTATGTTTTTTTATATT
1 GTAATACTAAGATTGGTTTGATTAGTGTATGTTTTTTTATATT
* * * * *** * *
386127 GTAATAAT-A-ATTTGTAT-ATTTAAG-ATAT-AACTTTGA-A-A
1 GTAATACTAAGATTGGTTTGA-TT-AGTGTATGTTTTTTTATATT
386165 GTAATACTAAGATTGGTTTGATTAGTGTATGTTTTTTTATATT
1 GTAATACTAAGATTGGTTTGATTAGTGTATGTTTTTTTATATT
386208 GTAATA
1 GTAATA
386214 ATAATTTGTA
Statistics
Matches: 60, Mismatches: 18, Indels: 18
0.62 0.19 0.19
Matches are distributed among these distances:
38 7 0.12
39 4 0.07
40 16 0.27
41 16 0.27
42 4 0.07
43 13 0.22
ACGTcount: A:0.32, C:0.02, G:0.16, T:0.49
Consensus pattern (43 bp):
GTAATACTAAGATTGGTTTGATTAGTGTATGTTTTTTTATATT
Found at i:386203 original size:81 final size:81
Alignment explanation
Indices: 386078--386244 Score: 334
Period size: 81 Copynumber: 2.1 Consensus size: 81
386068 TAGATTTGTG
386078 TTGAAAGTAATACTAAGATTGGTTTGATTAGTGTATGTTTTTTTATATTGTAATAATAATTTGTA
1 TTGAAAGTAATACTAAGATTGGTTTGATTAGTGTATGTTTTTTTATATTGTAATAATAATTTGTA
386143 TATTTAAGATATAACT
66 TATTTAAGATATAACT
386159 TTGAAAGTAATACTAAGATTGGTTTGATTAGTGTATGTTTTTTTATATTGTAATAATAATTTGTA
1 TTGAAAGTAATACTAAGATTGGTTTGATTAGTGTATGTTTTTTTATATTGTAATAATAATTTGTA
386224 TATTTAAGATATAACT
66 TATTTAAGATATAACT
386240 TTGAA
1 TTGAA
386245 CATTATATTT
Statistics
Matches: 86, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
81 86 1.00
ACGTcount: A:0.35, C:0.02, G:0.15, T:0.48
Consensus pattern (81 bp):
TTGAAAGTAATACTAAGATTGGTTTGATTAGTGTATGTTTTTTTATATTGTAATAATAATTTGTA
TATTTAAGATATAACT
Found at i:386263 original size:19 final size:20
Alignment explanation
Indices: 386239--386279 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
386229 AAGATATAAC
*
386239 TTTGAA-CATTATATTTTTG
1 TTTGAATCATTATATTTGTG
*
386258 TTTGAATGATTATATTTGTG
1 TTTGAATCATTATATTTGTG
386278 TT
1 TT
386280 GAAAGTAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 6 0.32
20 13 0.68
ACGTcount: A:0.24, C:0.02, G:0.15, T:0.59
Consensus pattern (20 bp):
TTTGAATCATTATATTTGTG
Found at i:395172 original size:27 final size:26
Alignment explanation
Indices: 395143--395195 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 26
395133 AATTTTTAAA
395143 TTTTTAACAGTAAATTGAATTAAAATATT
1 TTTTTAA-A-TAAATTGAATTAAAATA-T
*
395172 TTTTTAAATTAATTGAATTAAAAT
1 TTTTTAAATAAATTGAATTAAAAT
395196 TTATATGTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
27 15 0.65
28 1 0.04
29 7 0.30
ACGTcount: A:0.45, C:0.02, G:0.06, T:0.47
Consensus pattern (26 bp):
TTTTTAAATAAATTGAATTAAAATAT
Found at i:396186 original size:3 final size:3
Alignment explanation
Indices: 396178--396206 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
396168 CACATGTTTC
396178 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
396207 GCAACTTAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:398927 original size:9 final size:10
Alignment explanation
Indices: 398915--399008 Score: 70
Period size: 9 Copynumber: 9.6 Consensus size: 10
398905 CAAAAAAATA
398915 AAAAATTA-T
1 AAAAATTATT
*
398924 AAAAAATATTT
1 AAAAATTA-TT
* *
398935 AGAAGTTATT
1 AAAAATTATT
* *
398945 AATAATT-GT
1 AAAAATTATT
398954 AAAAA-TATT
1 AAAAATTATT
398963 AAAAA-TATT
1 AAAAATTATT
*
398972 AAAAATTAAT
1 AAAAATTATT
*
398982 AAGAATTACTT
1 AAAAATTA-TT
*
398993 AAAATTTATT
1 AAAAATTATT
399003 AAAAAT
1 AAAAAT
399009 CACATTTATA
Statistics
Matches: 64, Mismatches: 16, Indels: 9
0.72 0.18 0.10
Matches are distributed among these distances:
8 1 0.02
9 27 0.42
10 23 0.36
11 13 0.20
ACGTcount: A:0.59, C:0.01, G:0.04, T:0.36
Consensus pattern (10 bp):
AAAAATTATT
Found at i:399432 original size:13 final size:13
Alignment explanation
Indices: 399414--399438 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
399404 ATTAGATTTT
399414 AACTAAGAAAATG
1 AACTAAGAAAATG
399427 AACTAAGAAAAT
1 AACTAAGAAAAT
399439 TAAAAGGTAA
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:0.64, C:0.08, G:0.12, T:0.16
Consensus pattern (13 bp):
AACTAAGAAAATG
Found at i:403819 original size:25 final size:26
Alignment explanation
Indices: 403791--403844 Score: 76
Period size: 25 Copynumber: 2.1 Consensus size: 26
403781 CAATTAGTAT
*
403791 AAAATATT-AATAATTCAAT-AAATTG
1 AAAA-ATTAAATAATTAAATAAAATTG
403816 AAAAATTAAATAATTAAATAAAATTG
1 AAAAATTAAATAATTAAATAAAATTG
403842 AAA
1 AAA
403845 TTAGGAGAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
24 3 0.12
25 14 0.54
26 9 0.35
ACGTcount: A:0.63, C:0.02, G:0.04, T:0.31
Consensus pattern (26 bp):
AAAAATTAAATAATTAAATAAAATTG
Found at i:407389 original size:27 final size:27
Alignment explanation
Indices: 407329--407394 Score: 98
Period size: 27 Copynumber: 2.4 Consensus size: 27
407319 ACATTTTGTA
*
407329 AGCCTTTGTGACGAACTCTGAAAGAAT
1 AGCCTTTGTGGCGAACTCTGAAAGAAT
*
407356 AGGCTTTGTGGCGAACTCTGAAAGAACT
1 AGCCTTTGTGGCGAACTCTGAAAGAA-T
407384 -GCCTTTGTGGC
1 AGCCTTTGTGGC
407395 ATACCTAGAT
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
27 34 0.97
28 1 0.03
ACGTcount: A:0.26, C:0.20, G:0.27, T:0.27
Consensus pattern (27 bp):
AGCCTTTGTGGCGAACTCTGAAAGAAT
Found at i:408782 original size:10 final size:11
Alignment explanation
Indices: 408751--408799 Score: 57
Period size: 10 Copynumber: 4.5 Consensus size: 11
408741 GTGTATTTGA
408751 AATTTTTAATACT
1 AATTTTT-A-ACT
408764 AATTTTTAACT
1 AATTTTTAACT
*
408775 AA-TTTTAAGT
1 AATTTTTAACT
408785 AATTTTTAA-T
1 AATTTTTAACT
408795 AATTT
1 AATTT
408800 GCCTCAAATT
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
10 15 0.44
11 11 0.32
12 1 0.03
13 7 0.21
ACGTcount: A:0.39, C:0.04, G:0.02, T:0.55
Consensus pattern (11 bp):
AATTTTTAACT
Found at i:413791 original size:38 final size:38
Alignment explanation
Indices: 413740--413818 Score: 158
Period size: 38 Copynumber: 2.1 Consensus size: 38
413730 AGTAGAAAAG
413740 TATATTTTATATTTTACTTAATTGGTACAAAATTCCAA
1 TATATTTTATATTTTACTTAATTGGTACAAAATTCCAA
413778 TATATTTTATATTTTACTTAATTGGTACAAAATTCCAA
1 TATATTTTATATTTTACTTAATTGGTACAAAATTCCAA
413816 TAT
1 TAT
413819 TTTAAATTGG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 41 1.00
ACGTcount: A:0.37, C:0.10, G:0.05, T:0.48
Consensus pattern (38 bp):
TATATTTTATATTTTACTTAATTGGTACAAAATTCCAA
Found at i:418022 original size:4 final size:4
Alignment explanation
Indices: 418013--419364 Score: 2704
Period size: 4 Copynumber: 338.0 Consensus size: 4
418003 TAAAAGAACA
418013 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
418061 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
418109 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
418157 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
418205 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
418253 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
418301 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
418349 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
418397 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
418445 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
418493 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
418541 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
418589 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
418637 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
418685 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
418733 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
418781 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
418829 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
418877 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
418925 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
418973 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
419021 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
419069 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
419117 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
419165 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
419213 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
419261 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
419309 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
419357 TATG TATG
1 TATG TATG
419365 ATCTAGTTTT
Statistics
Matches: 1348, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 1348 1.00
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.50
Consensus pattern (4 bp):
TATG
Found at i:425520 original size:13 final size:13
Alignment explanation
Indices: 425502--425564 Score: 72
Period size: 13 Copynumber: 4.8 Consensus size: 13
425492 TTTAAACCAA
425502 ACTTTTCAAAAGC
1 ACTTTTCAAAAGC
*
425515 AGTTTTCAAAAGC
1 ACTTTTCAAAAGC
* ** *
425528 ACTTTTCCACTGT
1 ACTTTTCAAAAGC
*
425541 ACTTTTCAAAAGT
1 ACTTTTCAAAAGC
425554 ACTTTTCAAAA
1 ACTTTTCAAAA
425565 ACAATGAAGA
Statistics
Matches: 41, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
13 41 1.00
ACGTcount: A:0.35, C:0.21, G:0.08, T:0.37
Consensus pattern (13 bp):
ACTTTTCAAAAGC
Found at i:430189 original size:15 final size:15
Alignment explanation
Indices: 430169--430220 Score: 52
Period size: 15 Copynumber: 3.5 Consensus size: 15
430159 CATAATTTTT
430169 TTTTAAAAAATATTA
1 TTTTAAAAAATATTA
*
430184 TTTTAAAAACATA-AA
1 TTTTAAAAA-ATATTA
** *
430199 AATTAAAAAATATTT
1 TTTTAAAAAATATTA
430214 TTTTAAA
1 TTTTAAA
430221 TAAAAATATA
Statistics
Matches: 28, Mismatches: 7, Indels: 4
0.72 0.18 0.10
Matches are distributed among these distances:
14 3 0.11
15 22 0.79
16 3 0.11
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (15 bp):
TTTTAAAAAATATTA
Found at i:431861 original size:7 final size:8
Alignment explanation
Indices: 431837--431894 Score: 52
Period size: 9 Copynumber: 7.5 Consensus size: 8
431827 AATAATTCTA
*
431837 AAAAATAT
1 AAAATTAT
431845 AAAA-T-T
1 AAAATTAT
431851 AAAATTA-
1 AAAATTAT
*
431858 AAAATTAG
1 AAAATTAT
431866 AAAATATAT
1 AAAAT-TAT
431875 AAAATATAT
1 AAAAT-TAT
431884 AAAATT-T
1 AAAATTAT
431891 AAAA
1 AAAA
431895 AAAAAGAGAA
Statistics
Matches: 45, Mismatches: 1, Indels: 9
0.82 0.02 0.16
Matches are distributed among these distances:
6 5 0.11
7 14 0.31
8 10 0.22
9 16 0.36
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (8 bp):
AAAATTAT
Found at i:431878 original size:9 final size:9
Alignment explanation
Indices: 431820--431888 Score: 51
Period size: 9 Copynumber: 8.1 Consensus size: 9
431810 ATTTCTAGTT
431820 TATATAAAA
1 TATATAAAA
*
431829 TAATTCTAAAA
1 T-A-TATAAAA
*
431840 AATAT-AAA
1 TATATAAAA
431848 -AT-TAAAA
1 TATATAAAA
431855 T-TA-AAAA
1 TATATAAAA
*
431862 T-TAGAAAA
1 TATATAAAA
431870 TATATAAAA
1 TATATAAAA
431879 TATATAAAA
1 TATATAAAA
431888 T
1 T
431889 TTAAAAAAAA
Statistics
Matches: 49, Mismatches: 4, Indels: 14
0.73 0.06 0.21
Matches are distributed among these distances:
6 1 0.02
7 13 0.27
8 8 0.16
9 19 0.39
10 2 0.04
11 6 0.12
ACGTcount: A:0.65, C:0.01, G:0.01, T:0.32
Consensus pattern (9 bp):
TATATAAAA
Found at i:436710 original size:87 final size:83
Alignment explanation
Indices: 436574--436774 Score: 224
Period size: 87 Copynumber: 2.4 Consensus size: 83
436564 ACAAAATTTT
* * * ** * *
436574 AAATTGAATAAAATCTGTTCCGAGATTTATTCCCGTCGTTTAACAAATTTTATTTCATCTTTGAT
1 AAATTAAATAAAATCTGTTTCGGGATTTATTCCCCCCGTTCAACAAATTTTATTCCA--TTT--T
* *
436639 TTTATTTCCAAACAAG-TATTA
62 TTTATTGCCAAACAAGAAATTA
*
436660 AAATTAAAATAAAATCTGTTTCGGGATTTATTCCCCCCGTTCAACGAATTTTATTCCATTTTTTT
1 AAATT-AAATAAAATCTGTTTCGGGATTTATTCCCCCCGTTCAACAAATTTTATTCCATTTTTTT
* **
436725 GTTGCCAAATGAGAAATTA
65 ATTGCCAAACAAGAAATTA
*
436744 AAATTAAATAAAATCTGTTTTGGGATTTATT
1 AAATTAAATAAAATCTGTTTCGGGATTTATT
436775 TCTGTCACTT
Statistics
Matches: 99, Mismatches: 14, Indels: 7
0.82 0.12 0.06
Matches are distributed among these distances:
83 38 0.38
84 9 0.09
85 3 0.03
86 5 0.05
87 44 0.44
ACGTcount: A:0.33, C:0.14, G:0.11, T:0.42
Consensus pattern (83 bp):
AAATTAAATAAAATCTGTTTCGGGATTTATTCCCCCCGTTCAACAAATTTTATTCCATTTTTTTA
TTGCCAAACAAGAAATTA
Found at i:440387 original size:27 final size:27
Alignment explanation
Indices: 440357--440417 Score: 113
Period size: 27 Copynumber: 2.3 Consensus size: 27
440347 TAACAACTTG
440357 GTTTTTGTTTGTATGAATGATTTGCAT
1 GTTTTTGTTTGTATGAATGATTTGCAT
*
440384 GTTTTCGTTTGTATGAATGATTTGCAT
1 GTTTTTGTTTGTATGAATGATTTGCAT
440411 GTTTTTG
1 GTTTTTG
440418 CAGATACGCA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.16, C:0.05, G:0.23, T:0.56
Consensus pattern (27 bp):
GTTTTTGTTTGTATGAATGATTTGCAT
Found at i:454492 original size:24 final size:24
Alignment explanation
Indices: 454445--454503 Score: 64
Period size: 24 Copynumber: 2.5 Consensus size: 24
454435 CTCTTGTACA
*
454445 CATCTTTATCTCAATCATCATTTT
1 CATCTTTATCTCAACCATCATTTT
* * * *
454469 TATCTTTATCTCCACCCTCGTTTT
1 CATCTTTATCTCAACCATCATTTT
*
454493 CATCTTCATCT
1 CATCTTTATCT
454504 TCATCGCCTT
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.19, C:0.31, G:0.02, T:0.49
Consensus pattern (24 bp):
CATCTTTATCTCAACCATCATTTT
Found at i:460445 original size:19 final size:20
Alignment explanation
Indices: 460421--460462 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
460411 AAATTAATAT
*
460421 ATTTTT-ATTTATATTTTGA
1 ATTTTTAATTAATATTTTGA
*
460440 ATTTTTAATTAATTTTTTGA
1 ATTTTTAATTAATATTTTGA
460460 ATT
1 ATT
460463 GATCAGATCG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 6 0.30
20 14 0.70
ACGTcount: A:0.29, C:0.00, G:0.05, T:0.67
Consensus pattern (20 bp):
ATTTTTAATTAATATTTTGA
Found at i:460804 original size:5 final size:5
Alignment explanation
Indices: 460788--460869 Score: 53
Period size: 5 Copynumber: 16.0 Consensus size: 5
460778 CATGATACTT
* *
460788 TTAAA TTAAAA TTAAA TTAAA TTAAA TTATAA --AAA -TGAA TTTAA TTAAA
1 TTAAA TT-AAA TTAAA TTAAA TTAAA TTA-AA TTAAA TTAAA TTAAA TTAAA
* * *
460837 TTAAA CTATAAA GATGAA TTTAA TTAAA TTAAA
1 TTAAA -T-TAAA -TTAAA TTAAA TTAAA TTAAA
460870 CTTTTCAATT
Statistics
Matches: 62, Mismatches: 9, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
3 2 0.03
4 3 0.05
5 42 0.68
6 11 0.18
7 4 0.06
ACGTcount: A:0.57, C:0.01, G:0.04, T:0.38
Consensus pattern (5 bp):
TTAAA
Found at i:460833 original size:28 final size:28
Alignment explanation
Indices: 460797--460871 Score: 123
Period size: 28 Copynumber: 2.7 Consensus size: 28
460787 TTTAAATTAA
* *
460797 AATTAAATTAAATTAAATTATAAAAATG
1 AATTTAATTAAATTAAACTATAAAAATG
*
460825 AATTTAATTAAATTAAACTATAAAGATG
1 AATTTAATTAAATTAAACTATAAAAATG
460853 AATTTAATTAAATTAAACT
1 AATTTAATTAAATTAAACT
460872 TTTCAATTTT
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 44 1.00
ACGTcount: A:0.56, C:0.03, G:0.04, T:0.37
Consensus pattern (28 bp):
AATTTAATTAAATTAAACTATAAAAATG
Found at i:476726 original size:13 final size:13
Alignment explanation
Indices: 476708--476732 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
476698 AAAAAAAAAT
476708 CATATCTTTTAAC
1 CATATCTTTTAAC
476721 CATATCTTTTAA
1 CATATCTTTTAA
476733 GGTTAAAATT
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:0.20, G:0.00, T:0.48
Consensus pattern (13 bp):
CATATCTTTTAAC
Found at i:476801 original size:16 final size:16
Alignment explanation
Indices: 476777--476809 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
476767 TTCGCTGTAT
*
476777 TGGAGTAGAGGCGTAA
1 TGGAATAGAGGCGTAA
476793 TGGAATAGAGGCGTAA
1 TGGAATAGAGGCGTAA
476809 T
1 T
476810 AGCAATTCAA
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:0.33, C:0.06, G:0.39, T:0.21
Consensus pattern (16 bp):
TGGAATAGAGGCGTAA
Found at i:477050 original size:18 final size:17
Alignment explanation
Indices: 477029--477063 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
477019 TTATTATTAA
*
477029 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
477047 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
477064 TCTTAATAAT
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:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:477350 original size:18 final size:17
Alignment explanation
Indices: 477329--477363 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
477319 TTATTATTAA
*
477329 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
477347 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
477364 TCTTAATAAT
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:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:477383 original size:16 final size:16
Alignment explanation
Indices: 477362--477404 Score: 70
Period size: 16 Copynumber: 2.8 Consensus size: 16
477352 ATTTAATAAA
*
477362 ATTCTTAATAATCAAT
1 ATTCTTAATAACCAAT
477378 ATTCTTAATAACCAAT
1 ATTCTTAATAACCAAT
477394 ATTCTT-ATAAC
1 ATTCTTAATAAC
477405 AAAAATTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
15 5 0.19
16 21 0.81
ACGTcount: A:0.42, C:0.16, G:0.00, T:0.42
Consensus pattern (16 bp):
ATTCTTAATAACCAAT
Found at i:480259 original size:10 final size:9
Alignment explanation
Indices: 480184--480285 Score: 64
Period size: 10 Copynumber: 10.9 Consensus size: 9
480174 ATATCATTGC
480184 AAAATTATAA
1 AAAATTAT-A
480194 AAAATTATA
1 AAAATTATA
*
480203 AAATTTCATA
1 AAAATT-ATA
480213 AAAGATTATA
1 AAA-ATTATA
* *
480223 AAAA-CATT
1 AAAATTATA
**
480231 GCAATTATTA
1 AAAATTA-TA
480241 AAAATTATA
1 AAAATTATA
480250 AAAATATATA
1 AAAAT-TATA
* *
480260 AAAGTGCA-A
1 AAAAT-TATA
480269 AAAATTATA
1 AAAATTATA
*
480278 AATATTAT
1 AAAATTAT
480286 TTAAAAAAAC
Statistics
Matches: 70, Mismatches: 16, Indels: 13
0.71 0.16 0.13
Matches are distributed among these distances:
8 5 0.07
9 28 0.40
10 35 0.50
11 2 0.03
ACGTcount: A:0.60, C:0.04, G:0.04, T:0.32
Consensus pattern (9 bp):
AAAATTATA
Found at i:487988 original size:25 final size:25
Alignment explanation
Indices: 487960--488071 Score: 142
Period size: 25 Copynumber: 4.5 Consensus size: 25
487950 CAGCTCATAT
* *
487960 GAGCTTACTGATTTGTAGCTCGTGA
1 GAGCTTACCGATTTGCAGCTCGTGA
487985 GAGCTTACCGATTTGCCA-CTCGTGA
1 GAGCTTACCGATTTG-CAGCTCGTGA
*
488010 GAGCTTACCGATTTGCAGTTCGTGA
1 GAGCTTACCGATTTGCAGCTCGTGA
488035 GAGCTTA-CGATTCT-CAGCTCGT-A
1 GAGCTTACCGATT-TGCAGCTCGTGA
488058 TGAGCTTACCGATT
1 -GAGCTTACCGATT
488072 CACAACTGGC
Statistics
Matches: 78, Mismatches: 4, Indels: 10
0.85 0.04 0.11
Matches are distributed among these distances:
23 1 0.01
24 21 0.27
25 55 0.71
26 1 0.01
ACGTcount: A:0.21, C:0.22, G:0.25, T:0.32
Consensus pattern (25 bp):
GAGCTTACCGATTTGCAGCTCGTGA
Found at i:488298 original size:30 final size:30
Alignment explanation
Indices: 488259--488319 Score: 74
Period size: 31 Copynumber: 2.0 Consensus size: 30
488249 TACATGAAAT
488259 ACATGGAAAT-GAT-ATTACATGATATATTGAA
1 ACATGGAAATGGATGA-TACATG-TATA-TGAA
488290 ACAT-GAAATGGATGATACATGTATATGAA
1 ACATGGAAATGGATGATACATGTATATGAA
488319 A
1 A
488320 TTTGCTTAGT
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
29 5 0.18
30 9 0.32
31 13 0.46
32 1 0.04
ACGTcount: A:0.46, C:0.07, G:0.18, T:0.30
Consensus pattern (30 bp):
ACATGGAAATGGATGATACATGTATATGAA
Found at i:494167 original size:9 final size:9
Alignment explanation
Indices: 494150--494229 Score: 117
Period size: 9 Copynumber: 8.9 Consensus size: 9
494140 TATAAATAGT
494150 GGTTAATTC
1 GGTTAATTC
*
494159 GGGTAATTC
1 GGTTAATTC
494168 GGTTAATTC
1 GGTTAATTC
494177 TGG-TAATTC
1 -GGTTAATTC
*
494186 GGGTAATTC
1 GGTTAATTC
494195 GGTTAATTC
1 GGTTAATTC
*
494204 GGATAATTC
1 GGTTAATTC
494213 GGTTAATTC
1 GGTTAATTC
494222 GGTTAATT
1 GGTTAATT
494230 TTTAACCAAA
Statistics
Matches: 64, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
8 2 0.03
9 60 0.94
10 2 0.03
ACGTcount: A:0.24, C:0.10, G:0.25, T:0.41
Consensus pattern (9 bp):
GGTTAATTC
Found at i:494183 original size:27 final size:27
Alignment explanation
Indices: 494153--494229 Score: 129
Period size: 27 Copynumber: 2.9 Consensus size: 27
494143 AAATAGTGGT
494153 TAATTCGGGTAATTCGGTTAATTCTGG-
1 TAATTCGGGTAATTCGGTTAATTC-GGA
494180 TAATTCGGGTAATTCGGTTAATTCGGA
1 TAATTCGGGTAATTCGGTTAATTCGGA
*
494207 TAATTCGGTTAATTCGGTTAATT
1 TAATTCGGGTAATTCGGTTAATT
494230 TTTAACCAAA
Statistics
Matches: 48, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
26 2 0.04
27 46 0.96
ACGTcount: A:0.25, C:0.10, G:0.23, T:0.42
Consensus pattern (27 bp):
TAATTCGGGTAATTCGGTTAATTCGGA
Found at i:496695 original size:12 final size:12
Alignment explanation
Indices: 496678--496702 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
496668 GGCCTAGAAT
496678 CTCTATTGCACA
1 CTCTATTGCACA
496690 CTCTATTGCACA
1 CTCTATTGCACA
496702 C
1 C
496703 CCATGAGACA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.36, G:0.08, T:0.32
Consensus pattern (12 bp):
CTCTATTGCACA
Found at i:498120 original size:2 final size:2
Alignment explanation
Indices: 498113--498140 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
498103 AACAGAAAAC
498113 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
498141 CATGTACCTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:511471 original size:16 final size:16
Alignment explanation
Indices: 511450--511487 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
511440 TTGATTTGCT
*
511450 ATTACACCTCTATTCC
1 ATTACACCTCTAATCC
511466 ATTACACCTCTAATCC
1 ATTACACCTCTAATCC
*
511482 AATACA
1 ATTACA
511488 GCGAACCAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.34, C:0.34, G:0.00, T:0.32
Consensus pattern (16 bp):
ATTACACCTCTAATCC
Found at i:527274 original size:23 final size:23
Alignment explanation
Indices: 527234--527369 Score: 66
Period size: 23 Copynumber: 5.8 Consensus size: 23
527224 AATGCTGTCC
* * *
527234 AATTTTGTATACACGTGCTGTTA
1 AATTTTGTGTATAAGTGCTGTTA
*
527257 AATTTTGTGTATAAGTGCTGTCCA
1 AATTTTGTGTATAAGTGCTGT-TA
* *
527281 AA--TTG-GTATATGTATGCTGCCTA
1 AATTTTGTGTATAAG--TGCTG-TTA
* * **
527304 ATTTTTAGTGAATCAA-TGCTGTCC
1 AATTTT-GTGTAT-AAGTGCTGTTA
* *
527328 AATTTTGTATACACA-TGCTGTTA
1 AATTTTGTGTATA-AGTGCTGTTA
527351 AATTTTGTGTATAAGTGCT
1 AATTTTGTGTATAAGTGCT
527370 ATCCAAATTG
Statistics
Matches: 81, Mismatches: 21, Indels: 22
0.65 0.17 0.18
Matches are distributed among these distances:
21 6 0.07
22 5 0.06
23 50 0.62
24 8 0.10
25 7 0.09
26 1 0.01
27 3 0.04
28 1 0.01
ACGTcount: A:0.26, C:0.12, G:0.18, T:0.43
Consensus pattern (23 bp):
AATTTTGTGTATAAGTGCTGTTA
Found at i:527324 original size:94 final size:94
Alignment explanation
Indices: 527199--527570 Score: 564
Period size: 94 Copynumber: 3.9 Consensus size: 94
527189 TTGATGTATT
*
527199 TATGCTGCCTAATTTTTGGTGAATCAATGCTGTCCAATTTTGTATACACGTGCTGTTAAATTTTG
1 TATGCTGCCTAATTTTTGGTGAATCAATGCTGTCCAATTTTGTATACACATGCTGTTAAATTTTG
527264 TGTATAAGTGCTGTCCAAATTGGTATATG
66 TGTATAAGTGCTGTCCAAATTGGTATATG
*
527293 TATGCTGCCTAATTTTTAGTGAATCAATGCTGTCCAATTTTGTATACACATGCTGTTAAATTTTG
1 TATGCTGCCTAATTTTTGGTGAATCAATGCTGTCCAATTTTGTATACACATGCTGTTAAATTTTG
*
527358 TGTATAAGTGCTATCCAAATTGGTATATG
66 TGTATAAGTGCTGTCCAAATTGGTATATG
* * *
527387 TATGATGCCCAAATTTTTGGTGAATCAGTGCTGTCCAATTTTGTATACACATGCTGTTAAATTTT
1 TATGCTG-CCTAATTTTTGGTGAATCAATGCTGTCCAATTTTGTATACACATGCTGTTAAATTTT
527452 GTGTATAAGTGCTGTCCAAATTGGTATATG
65 GTGTATAAGTGCTGTCCAAATTGGTATATG
* ** * * * *
527482 TATGCTGCCTAATTTTGGGTGAAAAAAAAATGCTGTCCAATTTTGTATATATATGCTGCTCAATT
1 TATGCTGCCTAATTTTTGGTG---AATCAATGCTGTCCAATTTTGTATACACATGCTG-TTAAAT
*
527547 TTTGATGTATAAGAGCTGTCCAAA
62 TTTG-TGTATAAGTGCTGTCCAAA
527571 CAGGGTAGAT
Statistics
Matches: 253, Mismatches: 19, Indels: 7
0.91 0.07 0.03
Matches are distributed among these distances:
94 109 0.43
95 89 0.35
97 29 0.11
98 8 0.03
99 18 0.07
ACGTcount: A:0.27, C:0.14, G:0.19, T:0.40
Consensus pattern (94 bp):
TATGCTGCCTAATTTTTGGTGAATCAATGCTGTCCAATTTTGTATACACATGCTGTTAAATTTTG
TGTATAAGTGCTGTCCAAATTGGTATATG
Found at i:527443 original size:23 final size:23
Alignment explanation
Indices: 527413--527479 Score: 64
Period size: 23 Copynumber: 2.9 Consensus size: 23
527403 TTGGTGAATC
527413 AGTGCTGTCCAATTTTGTATACA
1 AGTGCTGTCCAATTTTGTATACA
** * *
527436 CA-TGCTGTTAAATTTTGTGTATA
1 -AGTGCTGTCCAATTTTGTATACA
* *
527459 AGTGCTGTCCAAATTGGTATA
1 AGTGCTGTCCAATTTTGTATA
527480 TGTATGCTGC
Statistics
Matches: 33, Mismatches: 9, Indels: 3
0.73 0.20 0.07
Matches are distributed among these distances:
22 1 0.03
23 31 0.94
24 1 0.03
ACGTcount: A:0.27, C:0.13, G:0.19, T:0.40
Consensus pattern (23 bp):
AGTGCTGTCCAATTTTGTATACA
Found at i:536072 original size:37 final size:36
Alignment explanation
Indices: 536022--536106 Score: 100
Period size: 36 Copynumber: 2.3 Consensus size: 36
536012 CAATCTGTGC
* * *
536022 AAAAATAAGAAAGAAGAATTTAAATC-TAATAATAAGT
1 AAAAATAAGAAAG-AGAATTGAAATCGAAATAACAA-T
* *
536059 AAAAATAATAAAGATAATTGAAATCGAAATAACAAT
1 AAAAATAAGAAAGAGAATTGAAATCGAAATAACAAT
536095 AAAAATAAGAAA
1 AAAAATAAGAAA
536107 AAATGAAATT
Statistics
Matches: 41, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
36 22 0.54
37 19 0.46
ACGTcount: A:0.66, C:0.04, G:0.09, T:0.21
Consensus pattern (36 bp):
AAAAATAAGAAAGAGAATTGAAATCGAAATAACAAT
Found at i:537260 original size:21 final size:20
Alignment explanation
Indices: 537230--537269 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 20
537220 TAATAATATT
537230 AAATTTTTTT-ATTTATTTAA
1 AAATTTTTTTAATTT-TTTAA
537250 AAATATTTTTTAATTTTTTA
1 AAAT-TTTTTTAATTTTTTA
537270 TACATTCTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 4 0.22
21 10 0.56
22 4 0.22
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (20 bp):
AAATTTTTTTAATTTTTTAA
Found at i:540573 original size:19 final size:19
Alignment explanation
Indices: 540551--540590 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
540541 ATTAATCTTG
* *
540551 ATCAAGTAAATTTAAATTA
1 ATCAAATAAATTAAAATTA
*
540570 ATCAAATTAATTAAAATTA
1 ATCAAATAAATTAAAATTA
540589 AT
1 AT
540591 TTGATATTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.55, C:0.05, G:0.03, T:0.38
Consensus pattern (19 bp):
ATCAAATAAATTAAAATTA
Found at i:541090 original size:25 final size:26
Alignment explanation
Indices: 541036--541096 Score: 65
Period size: 25 Copynumber: 2.4 Consensus size: 26
541026 TAAATTAAAT
*
541036 TTAATACTT-ATATTAATAGTATTTTA
1 TTAATA-TTAATATTAATAGTATTATA
*
541062 TTAAT-TTAATATTAA-AGTGATTATC
1 TTAATATTAATATTAATAGT-ATTATA
541087 TTAATATTAA
1 TTAATATTAA
541097 ATTTAATTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
24 5 0.17
25 16 0.53
26 9 0.30
ACGTcount: A:0.41, C:0.03, G:0.05, T:0.51
Consensus pattern (26 bp):
TTAATATTAATATTAATAGTATTATA
Found at i:543789 original size:285 final size:285
Alignment explanation
Indices: 543272--543840 Score: 996
Period size: 285 Copynumber: 2.0 Consensus size: 285
543262 AGCACTTGAT
* * *
543272 CTATTGTAATCTCACTTTTTGTTCTGGGGCCTTCAAAAGTTGGTATTTATACCATCTAATTGATT
1 CTATTGCAATCTCACTTTTTGTTCTAGGGCCTTCAAAAGCTGGTATTTATACCATCTAATTGATT
*
543337 TCCAACCGTTGTGGTTGTTGATGAATTAAATAGAGTCGTTGGGGATGAAAATGACATATCATTAA
66 TCCAACCGTTGTGGTTGTTGAGGAATTAAATAGAGTCGTTGGGGATGAAAATGACATATCATTAA
* *
543402 ATTCATTTGCAACAAAAGGTATCGATACTTTTTCTATGTGTATCGATACTATTAGCATTTAATAC
131 ATTCACTTGCAACAAAAGGTATCGATACTTTTTCTATGTGTATCGATACTATTAGAATTTAATAC
* **
543467 ATGATTCAGTGACTGTTAAAGTTAATTTACAACGATACCAAAGGCATTTTATCGATACCTCGTAA
196 ATGATTCAATGACTGTTAAAGTTAATTTACAACGATACCAAAGAAATTTTATCGATACCTCGTAA
543532 AAGGTATCAATACTTTTTGAAAAGA
261 AAGGTATCAATACTTTTTGAAAAGA
* *
543557 CTATTGCAATCTCACTTTTTGTTGTAGGGCCTTCAAAAGCTGGTATTTATACCCTCTAATTGATT
1 CTATTGCAATCTCACTTTTTGTTCTAGGGCCTTCAAAAGCTGGTATTTATACCATCTAATTGATT
* *
543622 TTCAACCGTTGTGGTTGTTGAGGAATTGAATAGAGTCGTTGGGGATGAAAAT-ACCATATCATTA
66 TCCAACCGTTGTGGTTGTTGAGGAATTAAATAGAGTCGTTGGGGATGAAAATGA-CATATCATTA
543686 AATTCACTTGCAACAAAAGGTATCGATACTTTTTCTATGTGTATCGATACTATTAGAATTTAATA
130 AATTCACTTGCAACAAAAGGTATCGATACTTTTTCTATGTGTATCGATACTATTAGAATTTAATA
543751 CATGATTCAATGACTGTTAAAGTTAATTTACAACGATACCAAAGAAATTTTATCGATACCTCGTA
195 CATGATTCAATGACTGTTAAAGTTAATTTACAACGATACCAAAGAAATTTTATCGATACCTCGTA
*
543816 AAAGGTATCAGTACTTTTTGAAAAG
260 AAAGGTATCAATACTTTTTGAAAAG
543841 GTATCGATAC
Statistics
Matches: 269, Mismatches: 14, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
284 1 0.00
285 268 1.00
ACGTcount: A:0.32, C:0.15, G:0.17, T:0.36
Consensus pattern (285 bp):
CTATTGCAATCTCACTTTTTGTTCTAGGGCCTTCAAAAGCTGGTATTTATACCATCTAATTGATT
TCCAACCGTTGTGGTTGTTGAGGAATTAAATAGAGTCGTTGGGGATGAAAATGACATATCATTAA
ATTCACTTGCAACAAAAGGTATCGATACTTTTTCTATGTGTATCGATACTATTAGAATTTAATAC
ATGATTCAATGACTGTTAAAGTTAATTTACAACGATACCAAAGAAATTTTATCGATACCTCGTAA
AAGGTATCAATACTTTTTGAAAAGA
Found at i:543839 original size:21 final size:21
Alignment explanation
Indices: 543815--543856 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
543805 GATACCTCGT
543815 AAAAGGTATC-AGTACTTTTTG
1 AAAAGGTATCGA-TACTTTTTG
543836 AAAAGGTATCGATACTTTTTG
1 AAAAGGTATCGATACTTTTTG
543857 TGATTGTTTG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 19 0.95
22 1 0.05
ACGTcount: A:0.33, C:0.10, G:0.19, T:0.38
Consensus pattern (21 bp):
AAAAGGTATCGATACTTTTTG
Found at i:543958 original size:20 final size:20
Alignment explanation
Indices: 543933--543975 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
543923 AAAATACAAT
543933 AGGTATCAATACTTTTTGAA
1 AGGTATCAATACTTTTTGAA
* *
543953 AGGTATCGATACTTTTTGTA
1 AGGTATCAATACTTTTTGAA
543973 AGG
1 AGG
543976 AGCAGTTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.30, C:0.09, G:0.21, T:0.40
Consensus pattern (20 bp):
AGGTATCAATACTTTTTGAA
Found at i:552914 original size:94 final size:94
Alignment explanation
Indices: 552753--552943 Score: 382
Period size: 94 Copynumber: 2.0 Consensus size: 94
552743 GGGACAACTT
552753 AGCTAAGTGTTCCTTTAGAAAAGCTAGTCAAGCAAGAAGGTGTTGTAACACATCAGTCACAAAAC
1 AGCTAAGTGTTCCTTTAGAAAAGCTAGTCAAGCAAGAAGGTGTTGTAACACATCAGTCACAAAAC
552818 CTTGATAAACTTCGAGTAATGATAACCTA
66 CTTGATAAACTTCGAGTAATGATAACCTA
552847 AGCTAAGTGTTCCTTTAGAAAAGCTAGTCAAGCAAGAAGGTGTTGTAACACATCAGTCACAAAAC
1 AGCTAAGTGTTCCTTTAGAAAAGCTAGTCAAGCAAGAAGGTGTTGTAACACATCAGTCACAAAAC
552912 CTTGATAAACTTCGAGTAATGATAACCTA
66 CTTGATAAACTTCGAGTAATGATAACCTA
552941 AGC
1 AGC
552944 GAGATCATTC
Statistics
Matches: 97, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
94 97 1.00
ACGTcount: A:0.38, C:0.18, G:0.18, T:0.25
Consensus pattern (94 bp):
AGCTAAGTGTTCCTTTAGAAAAGCTAGTCAAGCAAGAAGGTGTTGTAACACATCAGTCACAAAAC
CTTGATAAACTTCGAGTAATGATAACCTA
Found at i:553142 original size:46 final size:46
Alignment explanation
Indices: 553075--553445 Score: 218
Period size: 46 Copynumber: 8.5 Consensus size: 46
553065 TACAGGTCTG
* * * * *
553075 ATCTCCCTGAGATTACAGTGGAGTAGACCGAAGAATTTCAAATCTC
1 ATCTCCCTGAGATTACAGTGGAGCAGACTGAAGAATTCCAGATCTT
* * *
553121 ATCTCCCTGAGGTTACAGTGGAGCAGATTGAAG----CCAGATATT
1 ATCTCCCTGAGATTACAGTGGAGCAGACTGAAGAATTCCAGATCTT
*
553163 ATCTCCCTGAGATTACAGTGGAGCAGACTGAAGAATTGCAGATCTT
1 ATCTCCCTGAGATTACAGTGGAGCAGACTGAAGAATTCCAGATCTT
** * *
553209 ATCTCCCTGAGATTACAACGGAGCAGA-TCGAAG-A---CACTATCCT
1 ATCTCCCTGAGATTACAGTGGAGCAGACT-GAAGAATTCCA-GATCTT
* * * *
553252 ATCTCTCTGAGATTACAGTGGAGCGGA-T-TA-AA----GGATCTT
1 ATCTCCCTGAGATTACAGTGGAGCAGACTGAAGAATTCCAGATCTT
* * * * ** * * *
553291 ATATCTCT-AAAGTTACAGTAGAGTGGA-T--TGTA-T-CAGGTCTT
1 ATCTCCCTGAGA-TTACAGTGGAGCAGACTGAAGAATTCCAGATCTT
*
553332 ATCTCCCTGAGATTACAGTGGAGCAGACTGAAGAATTGCAGATCTT
1 ATCTCCCTGAGATTACAGTGGAGCAGACTGAAGAATTCCAGATCTT
** * * *
553378 ATCTCCCTGAGATTACAACGGAGCAGA-TCAAAGATAGT--A-ATCCT
1 ATCTCCCTGAGATTACAGTGGAGCAGACT-GAAGA-ATTCCAGATCTT
*
553422 ATCTCCTTGAGATTACAGTGGAGC
1 ATCTCCCTGAGATTACAGTGGAGC
553446 GGATTAAAGG
Statistics
Matches: 257, Mismatches: 49, Indels: 40
0.74 0.14 0.12
Matches are distributed among these distances:
38 2 0.01
39 26 0.10
41 25 0.10
42 41 0.16
43 28 0.11
44 27 0.11
45 5 0.02
46 101 0.39
47 2 0.01
ACGTcount: A:0.31, C:0.20, G:0.22, T:0.27
Consensus pattern (46 bp):
ATCTCCCTGAGATTACAGTGGAGCAGACTGAAGAATTCCAGATCTT
Found at i:553344 original size:80 final size:79
Alignment explanation
Indices: 553251--553534 Score: 234
Period size: 80 Copynumber: 3.4 Consensus size: 79
553241 GACACTATCC
* * *
553251 TATCTCTCTGAGATTACAGTGGAGCGGATTAAAGGATCTTATATCTCTAAAGTTACAGTAGAGTG
1 TATCTCCCTGAGATTACAGTGGAGCAGATTAAAGGATCTTATCTCTCT-AAGTTACAGTAGAGTG
*
553316 GATTGTATCAGGTCT
65 GATAGTATCAGGTCT
* * *
553331 TATCTCCCTGAGATTACAGTGGAGCAGACTGAAGAATTGCAGATCTTATCTCCCTGAGATTACAA
1 TATCTCCCTGAGATTACAGTGGAGCAGA-T-TA-AA--G--GATCTTATCTCTCTAAG-TTAC-A
* * *
553396 CGGAGCAGATCAAAGATAGTA--A--TCC
57 -GTAG-AG-T---GGATAGTATCAGGTCT
* * *
553421 TATCTCCTTGAGATTACAGTGGAGCGGATTAAAGGATCTTATCTCTCTGAAGTTATAGTAGAGTG
1 TATCTCCCTGAGATTACAGTGGAGCAGATTAAAGGATCTTATCTCTCT-AAGTTACAGTAGAGTG
*
553486 GATCGTATCAGGTCT
65 GATAGTATCAGGTCT
* * *
553501 TATCTCCCTGAGCTTACAGCGGAGCAGATCAAAG
1 TATCTCCCTGAGATTACAGTGGAGCAGATTAAAG
553535 ATAGTAATCT
Statistics
Matches: 159, Mismatches: 25, Indels: 40
0.71 0.11 0.18
Matches are distributed among these distances:
76 6 0.04
78 1 0.01
79 1 0.01
80 59 0.37
81 4 0.03
82 2 0.01
83 18 0.11
84 2 0.01
85 2 0.01
86 2 0.01
87 18 0.11
88 2 0.01
89 4 0.03
90 30 0.19
91 1 0.01
92 1 0.01
94 6 0.04
ACGTcount: A:0.30, C:0.18, G:0.23, T:0.29
Consensus pattern (79 bp):
TATCTCCCTGAGATTACAGTGGAGCAGATTAAAGGATCTTATCTCTCTAAGTTACAGTAGAGTGG
ATAGTATCAGGTCT
Found at i:553445 original size:44 final size:44
Alignment explanation
Indices: 553075--553617 Score: 262
Period size: 44 Copynumber: 12.6 Consensus size: 44
553065 TACAGGTCTG
* * * * *
553075 ATCTCCCTGAGATTACAGTGGAGTAGACCGAAGA-ATTTCAAATCTC
1 ATCTCCCTGAGATTACAGTGGAGCAGATCAAAGATA-GT--AATCTT
* ** ** *
553121 ATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGCCAG--ATATT
1 ATCTCCCTGAGATTACAGTGGAGCAGATCAAAGATAGTAATCTT
* * *
553163 ATCTCCCTGAGATTACAGTGGAGCAGA-CTGAAGAATTGCAGATCTT
1 ATCTCCCTGAGATTACAGTGGAGCAGATC-AAAG-ATAGTA-ATCTT
** * * * *
553209 ATCTCCCTGAGATTACAACGGAGCAGATCGAAGACACT-ATCCT
1 ATCTCCCTGAGATTACAGTGGAGCAGATCAAAGATAGTAATCTT
* * *
553252 ATCTCTCTGAGATTACAGTGGAGCGGATTAAAG---G--ATCTT
1 ATCTCCCTGAGATTACAGTGGAGCAGATCAAAGATAGTAATCTT
* * * * ** * *
553291 ATATCTCT-AAAGTTACAGTAGAGTGGAT---TG-TA-TCAGGTCTT
1 ATCTCCCTGAGA-TTACAGTGGAGCAGATCAAAGATAGT-A-ATCTT
* * *
553332 ATCTCCCTGAGATTACAGTGGAGCAGA-CTGAAGAATTGCAGATCTT
1 ATCTCCCTGAGATTACAGTGGAGCAGATC-AAAG-ATAGTA-ATCTT
** *
553378 ATCTCCCTGAGATTACAACGGAGCAGATCAAAGATAGTAATCCT
1 ATCTCCCTGAGATTACAGTGGAGCAGATCAAAGATAGTAATCTT
* * *
553422 ATCTCCTTGAGATTACAGTGGAGCGGATTAAAG---G--ATCTT
1 ATCTCCCTGAGATTACAGTGGAGCAGATCAAAGATAGTAATCTT
* * * ** *
553461 ATCTCTCTGA-AGTTATAGTAGAGTGGATC---G-TA-TCAGGTCTT
1 ATCTCCCTGAGA-TTACAGTGGAGCAGATCAAAGATAGT-A-ATCTT
* *
553502 ATCTCCCTGAGCTTACAGCGGAGCAGATCAAAGATAGTAATCTT
1 ATCTCCCTGAGATTACAGTGGAGCAGATCAAAGATAGTAATCTT
* * * * *
553546 ATCTTCCTGAGATTACAGCGGAGCAGATCAGAGCTAGTAATCCT
1 ATCTCCCTGAGATTACAGTGGAGCAGATCAAAGATAGTAATCTT
553590 ATCTCCCTGA-AGTTACAGTGGAGCAGAT
1 ATCTCCCTGAGA-TTACAGTGGAGCAGAT
553618 TAAAACCACA
Statistics
Matches: 381, Mismatches: 79, Indels: 76
0.71 0.15 0.14
Matches are distributed among these distances:
36 2 0.01
38 3 0.01
39 50 0.13
41 48 0.13
42 35 0.09
43 33 0.09
44 101 0.27
45 8 0.02
46 98 0.26
47 3 0.01
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.27
Consensus pattern (44 bp):
ATCTCCCTGAGATTACAGTGGAGCAGATCAAAGATAGTAATCTT
Found at i:553456 original size:170 final size:170
Alignment explanation
Indices: 553161--553682 Score: 723
Period size: 170 Copynumber: 3.1 Consensus size: 170
553151 AAGCCAGATA
553161 TTATCTCCCTGAGATTACAGTGGAGCAGACTGAAGAATTGCAGATCTTATCTCCCTGAGATTACA
1 TTATCTCCCTGAGATTACAGTGGAGCAGACTGAAGAATTGCAGATCTTATCTCCCTGAGATTACA
* * *
553226 ACGGAGCAGATCGAAGACACT-ATCCTATCT-CTCTGAGATTACAGTGGAGCGGATTAAAGGATC
66 ACGGAGCAGATCAAAGATAGTAATCCTATCTCCT-TGAGATTACAGTGGAGCGGATTAAAGGATC
* * *
553289 TTATATCTCTAAAGTTACAGTAGAGTGGATTGTATCAGGTC
130 TTATCTCTCTGAAGTTACAGTAGAGTGGATCGTATCAGGTC
553330 TTATCTCCCTGAGATTACAGTGGAGCAGACTGAAGAATTGCAGATCTTATCTCCCTGAGATTACA
1 TTATCTCCCTGAGATTACAGTGGAGCAGACTGAAGAATTGCAGATCTTATCTCCCTGAGATTACA
553395 ACGGAGCAGATCAAAGATAGTAATCCTATCTCCTTGAGATTACAGTGGAGCGGATTAAAGGATCT
66 ACGGAGCAGATCAAAGATAGTAATCCTATCTCCTTGAGATTACAGTGGAGCGGATTAAAGGATCT
*
553460 TATCTCTCTGAAGTTATAGTAGAGTGGATCGTATCAGGTC
131 TATCTCTCTGAAGTTACAGTAGAGTGGATCGTATCAGGTC
* * * * * *
553500 TTATCTCCCTGAGCTTACAGCGGAGCAGA-TCAA-AGATAGTA-ATCTTATCTTCCTGAGATTAC
1 TTATCTCCCTGAGATTACAGTGGAGCAGACTGAAGA-ATTGCAGATCTTATCTCCCTGAGATTAC
* * * * *
553562 AGCGGAGCAGATCAGAGCTAGTAATCCTATCTCCCTGA-AGTTACAGTGGAGCAGATTAAAACCA
65 AACGGAGCAGATCAAAGATAGTAATCCTATCTCCTTGAGA-TTACAGTGGAGCGGATT--AA--A
* * * *
553626 CAGATCTTATCTCTCTGAGGTTACAGTAGGGTGGATCGTATCAGGCC
125 -GGATCTTATCTCTCTGAAGTTACAGTAGAGTGGATCGTATCAGGTC
*
553673 TTATATCCCT
1 TTATCTCCCT
553683 AATGTTGCAG
Statistics
Matches: 320, Mismatches: 24, Indels: 14
0.89 0.07 0.04
Matches are distributed among these distances:
167 1 0.00
168 71 0.22
169 90 0.28
170 105 0.33
171 2 0.01
172 1 0.00
173 50 0.16
ACGTcount: A:0.30, C:0.20, G:0.22, T:0.28
Consensus pattern (170 bp):
TTATCTCCCTGAGATTACAGTGGAGCAGACTGAAGAATTGCAGATCTTATCTCCCTGAGATTACA
ACGGAGCAGATCAAAGATAGTAATCCTATCTCCTTGAGATTACAGTGGAGCGGATTAAAGGATCT
TATCTCTCTGAAGTTACAGTAGAGTGGATCGTATCAGGTC
Found at i:553610 original size:124 final size:121
Alignment explanation
Indices: 553374--553611 Score: 284
Period size: 124 Copynumber: 1.9 Consensus size: 121
553364 GAATTGCAGA
553374 TCTTATCTCCCTGAGATTACAACGGAGCAGATCAAAGATAGTAATCCTATCTCCTTGAGATTACA
1 TCTTATCTCCCTGAGATTACAACGGAGCAGATCAAAGATAGTAATCCTATCTCCTTGAGATTACA
* * * * * * *
553439 GTGGAGCGGATTAAAGGATCTTATCTCTCTGAAGTTATAGTAGAGTGGATCGTATCAGG
66 GCGGAGCAGATCAAAGAATCCTATCTCCCTGAAG-T-TA-TACAGTGGATCGTATCAGG
* * *
553498 TCTTATCTCCCTGAGCTTACAGCGGAGCAGATCAAAGATAGTAATCTTATCTTCC-TGAGATTAC
1 TCTTATCTCCCTGAGATTACAACGGAGCAGATCAAAGATAGTAATCCTATC-TCCTTGAGATTAC
553562 AGCGGAGCAGATCAGAGCTAGTAATCCTATCTCCCTGAAG-T-TACAGTGGA
65 AGCGGAGCAGATCA-A---AG-AATCCTATCTCCCTGAAGTTATACAGTGGA
553612 GCAGATTAAA
Statistics
Matches: 98, Mismatches: 10, Indels: 12
0.82 0.08 0.10
Matches are distributed among these distances:
124 76 0.78
125 4 0.04
126 1 0.01
128 2 0.02
129 15 0.15
ACGTcount: A:0.29, C:0.20, G:0.22, T:0.29
Consensus pattern (121 bp):
TCTTATCTCCCTGAGATTACAACGGAGCAGATCAAAGATAGTAATCCTATCTCCTTGAGATTACA
GCGGAGCAGATCAAAGAATCCTATCTCCCTGAAGTTATACAGTGGATCGTATCAGG
Found at i:555133 original size:29 final size:28
Alignment explanation
Indices: 555100--555164 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 28
555090 TAGTCCCTTT
* *
555100 CATTTTATTTTTCTTTCAATTTCGCCCTA
1 CATTTTATTTTTATTTCAATTTAGCCC-A
*
555129 CATTTTCATTTTTATTTCGATTTAGCCCA
1 CATTTT-ATTTTTATTTCAATTTAGCCCA
*
555158 TATTTTA
1 CATTTTA
555165 GCAATTTTAT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
28 1 0.03
29 12 0.39
30 18 0.58
ACGTcount: A:0.20, C:0.20, G:0.05, T:0.55
Consensus pattern (28 bp):
CATTTTATTTTTATTTCAATTTAGCCCA
Found at i:570989 original size:38 final size:40
Alignment explanation
Indices: 570938--571019 Score: 105
Period size: 38 Copynumber: 2.1 Consensus size: 40
570928 CACCGTCAAT
* * *
570938 AGAAGCTCATAAGAGCTGGTCCTCCCGAA-CATGCC-AAC
1 AGAAGCTCATAAGAGCTGATCCACCCGAATCACGCCAAAC
* *
570976 AGAAGCTCGTAAGAGTTGATCCACCCGAATCACGCCAAAC
1 AGAAGCTCATAAGAGCTGATCCACCCGAATCACGCCAAAC
571016 AGAA
1 AGAA
571020 AGTATAACAT
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
38 25 0.68
39 5 0.14
40 7 0.19
ACGTcount: A:0.35, C:0.29, G:0.21, T:0.15
Consensus pattern (40 bp):
AGAAGCTCATAAGAGCTGATCCACCCGAATCACGCCAAAC
Found at i:576914 original size:23 final size:23
Alignment explanation
Indices: 576882--576925 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
576872 GCCATAGATG
*
576882 TAATATCCCGAAAATTACTACTA
1 TAATACCCCGAAAATTACTACTA
576905 TAATACCCCGAAAATTACTAC
1 TAATACCCCGAAAATTACTAC
576926 AGTAAGAAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.43, C:0.25, G:0.05, T:0.27
Consensus pattern (23 bp):
TAATACCCCGAAAATTACTACTA
Found at i:580377 original size:25 final size:25
Alignment explanation
Indices: 580349--580409 Score: 77
Period size: 25 Copynumber: 2.4 Consensus size: 25
580339 TGATAAAAAA
* *
580349 TAAGCTCCTCCAAGCTAAATAGCGG
1 TAAGCTCATACAAGCTAAATAGCGG
* * *
580374 TAAGCTCATACAAGCTGAGTATCGG
1 TAAGCTCATACAAGCTAAATAGCGG
580399 TAAGCTCATAC
1 TAAGCTCATAC
580410 TGGAATTGGT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 31 1.00
ACGTcount: A:0.33, C:0.25, G:0.20, T:0.23
Consensus pattern (25 bp):
TAAGCTCATACAAGCTAAATAGCGG
Found at i:583684 original size:25 final size:24
Alignment explanation
Indices: 583646--583697 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 24
583636 AAGTTCAAGT
*
583646 GAGCCATATTAGGA-AGCTCACAAA
1 GAGCCATATCAGGACA-CTCACAAA
*
583670 GAGCCTATATCAGGACACTCATAAA
1 GAGCC-ATATCAGGACACTCACAAA
583695 GAG
1 GAG
583698 TTGCGGTATG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 5 0.21
25 18 0.75
26 1 0.04
ACGTcount: A:0.40, C:0.21, G:0.21, T:0.17
Consensus pattern (24 bp):
GAGCCATATCAGGACACTCACAAA
Done.