Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008361.1 Hibiscus syriacus cultivar Beakdansim tig00111100_pilon, whole genome shotgun sequence
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: 1124086
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 4
Found at i:275065 original size:11 final size:10
Alignment explanation
Indices: 275049--275094 Score: 67
Period size: 11 Copynumber: 4.5 Consensus size: 10
275039 TTGTTATGGT
275049 TTGTTATTAG
1 TTGTTATTAG
275059 CTTGTTATTAG
1 -TTGTTATTAG
275070 TTGTTATTAG
1 TTGTTATTAG
275080 TTTGTTA-TAG
1 -TTGTTATTAG
275090 TTGTT
1 TTGTT
275095 GGTTACTTGG
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
9 5 0.15
10 13 0.38
11 16 0.47
ACGTcount: A:0.17, C:0.02, G:0.20, T:0.61
Consensus pattern (10 bp):
TTGTTATTAG
Found at i:275090 original size:10 final size:11
Alignment explanation
Indices: 275036--275091 Score: 73
Period size: 10 Copynumber: 5.4 Consensus size: 11
275026 TGAATGTTAG
275036 AGTTTGTTA-T
1 AGTTTGTTATT
*
275046 GGTTTGTTATT
1 AGTTTGTTATT
*
275057 AGCTTGTTATT
1 AGTTTGTTATT
275068 AG-TTGTTATT
1 AGTTTGTTATT
275078 AGTTTGTTA-T
1 AGTTTGTTATT
275088 AGTT
1 AGTT
275092 GTTGGTTACT
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
10 23 0.56
11 18 0.44
ACGTcount: A:0.18, C:0.02, G:0.21, T:0.59
Consensus pattern (11 bp):
AGTTTGTTATT
Found at i:277290 original size:14 final size:15
Alignment explanation
Indices: 277268--277298 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
277258 ATCTTTATTT
277268 TTTATTTTTTAAAAA
1 TTTATTTTTTAAAAA
*
277283 TTTATTTTTAAAAAA
1 TTTATTTTTTAAAAA
277298 T
1 T
277299 ATCAATAGTT
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:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (15 bp):
TTTATTTTTTAAAAA
Found at i:298494 original size:57 final size:57
Alignment explanation
Indices: 298406--298522 Score: 234
Period size: 57 Copynumber: 2.1 Consensus size: 57
298396 AGATGGAACC
298406 TCCAGCACCTCTGCAGCAAAACCAAGAATCTGATCCTAGTCCAAGATCTTGTGAAGA
1 TCCAGCACCTCTGCAGCAAAACCAAGAATCTGATCCTAGTCCAAGATCTTGTGAAGA
298463 TCCAGCACCTCTGCAGCAAAACCAAGAATCTGATCCTAGTCCAAGATCTTGTGAAGA
1 TCCAGCACCTCTGCAGCAAAACCAAGAATCTGATCCTAGTCCAAGATCTTGTGAAGA
298520 TCC
1 TCC
298523 TTTAGGTAAT
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
57 60 1.00
ACGTcount: A:0.32, C:0.29, G:0.17, T:0.21
Consensus pattern (57 bp):
TCCAGCACCTCTGCAGCAAAACCAAGAATCTGATCCTAGTCCAAGATCTTGTGAAGA
Found at i:306584 original size:2 final size:2
Alignment explanation
Indices: 306577--306612 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
306567 TTCTCTAATC
306577 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
306613 TCATATTCTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:308967 original size:31 final size:30
Alignment explanation
Indices: 308921--309007 Score: 104
Period size: 31 Copynumber: 2.8 Consensus size: 30
308911 TTCGATAATA
308921 TAATAATTATTTTATAGTA-TTTAGATAAATT
1 TAATAA-TATTTTATAGTATTTTA-ATAAATT
* *
308952 TATTAATAATTTTATAATATTTTAATAAATT
1 TAATAAT-ATTTTATAGTATTTTAATAAATT
*
308983 TAATAAGTATTTTATAGTTTTTTAA
1 TAATAA-TATTTTATAGTATTTTAA
309008 ACTTTATTGA
Statistics
Matches: 48, Mismatches: 5, Indels: 6
0.81 0.08 0.10
Matches are distributed among these distances:
30 1 0.02
31 42 0.88
32 5 0.10
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (30 bp):
TAATAATATTTTATAGTATTTTAATAAATT
Found at i:308978 original size:19 final size:21
Alignment explanation
Indices: 308954--308996 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
308944 GATAAATTTA
*
308954 TTAAT-AATTTTATAA-TATT
1 TTAATAAATTTAATAAGTATT
308973 TTAATAAATTTAATAAGTATT
1 TTAATAAATTTAATAAGTATT
308994 TTA
1 TTA
308997 TAGTTTTTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 5 0.24
20 9 0.43
21 7 0.33
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.53
Consensus pattern (21 bp):
TTAATAAATTTAATAAGTATT
Found at i:312319 original size:18 final size:18
Alignment explanation
Indices: 312296--312358 Score: 101
Period size: 18 Copynumber: 3.5 Consensus size: 18
312286 TAGTATCGAT
312296 GAAGGAAGAAGAACACAA
1 GAAGGAAGAAGAACACAA
*
312314 GAAGGAAGAGGAACACAA
1 GAAGGAAGAAGAACACAA
312332 GAAGGAAGAAGAAC-CAAA
1 GAAGGAAGAAGAACAC-AA
312350 GAAGGAAGA
1 GAAGGAAGA
312359 GGAGGCGAAG
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
17 1 0.02
18 41 0.98
ACGTcount: A:0.59, C:0.10, G:0.32, T:0.00
Consensus pattern (18 bp):
GAAGGAAGAAGAACACAA
Found at i:312337 original size:36 final size:36
Alignment explanation
Indices: 312296--312379 Score: 118
Period size: 36 Copynumber: 2.3 Consensus size: 36
312286 TAGTATCGAT
312296 GAAGGAAGAAGAA-CACAAGAAGGAAGAGGA-ACACAA
1 GAAGGAAGAAGAACCA-AAGAAGGAAGAGGAGAC-CAA
* *
312332 GAAGGAAGAAGAACCAAAGAAGGAAGAGGAGGCGAA
1 GAAGGAAGAAGAACCAAAGAAGGAAGAGGAGACCAA
312368 GAAGGAAGAAGA
1 GAAGGAAGAAGA
312380 GGCCAAGAAA
Statistics
Matches: 44, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
36 41 0.93
37 3 0.07
ACGTcount: A:0.56, C:0.08, G:0.36, T:0.00
Consensus pattern (36 bp):
GAAGGAAGAAGAACCAAAGAAGGAAGAGGAGACCAA
Found at i:312369 original size:18 final size:18
Alignment explanation
Indices: 312296--312388 Score: 84
Period size: 18 Copynumber: 5.2 Consensus size: 18
312286 TAGTATCGAT
*
312296 GAAGGAAGAAGA-ACACAA
1 GAAGGAAGAAGAGGC-CAA
* *
312314 GAAGGAAGAGGA-ACACAA
1 GAAGGAAGAAGAGGC-CAA
*
312332 GAAGGAAGAAGA-ACCAAA
1 GAAGGAAGAAGAGGCC-AA
* *
312350 GAAGGAAGAGGAGGCGAA
1 GAAGGAAGAAGAGGCCAA
312368 GAAGGAAGAAGAGGCCAA
1 GAAGGAAGAAGAGGCCAA
312386 GAA
1 GAA
312389 AGGAGGAGAA
Statistics
Matches: 66, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
17 1 0.02
18 64 0.97
19 1 0.02
ACGTcount: A:0.55, C:0.10, G:0.35, T:0.00
Consensus pattern (18 bp):
GAAGGAAGAAGAGGCCAA
Found at i:318708 original size:3 final size:3
Alignment explanation
Indices: 318702--318775 Score: 141
Period size: 3 Copynumber: 25.0 Consensus size: 3
318692 AGAGGAGGAG
318702 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
318750 GAA GAA GAA GAA GAA GAA G-A GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA
318776 AAAAAAGGGA
Statistics
Matches: 70, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
2 2 0.03
3 68 0.97
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:322406 original size:12 final size:13
Alignment explanation
Indices: 322388--322422 Score: 54
Period size: 12 Copynumber: 2.8 Consensus size: 13
322378 CTATCATAAA
322388 CTATAAAATCTAT
1 CTATAAAATCTAT
322401 -TATAAAATCTAT
1 CTATAAAATCTAT
*
322413 CCATAAAATC
1 CTATAAAATC
322423 GAAAGAAGAG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
12 12 0.60
13 8 0.40
ACGTcount: A:0.49, C:0.17, G:0.00, T:0.34
Consensus pattern (13 bp):
CTATAAAATCTAT
Found at i:325269 original size:41 final size:39
Alignment explanation
Indices: 325182--325262 Score: 105
Period size: 39 Copynumber: 2.1 Consensus size: 39
325172 ACCTTTTTAT
* *
325182 ATTTTAAATTTTGTAAAAAAATATATATAAATTTTATGA
1 ATTTAAAATTTTGTAAAAAAATATATATAAATTTTATCA
325221 ATTTAAAATTTT-TAAAGAAAATATATA-AATATTTT-TCA
1 ATTTAAAATTTTGTAAA-AAAATATATATAA-ATTTTATCA
325259 ATTT
1 ATTT
325263 GTTAAAAAAC
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
38 12 0.32
39 26 0.68
ACGTcount: A:0.48, C:0.01, G:0.04, T:0.47
Consensus pattern (39 bp):
ATTTAAAATTTTGTAAAAAAATATATATAAATTTTATCA
Found at i:325348 original size:29 final size:29
Alignment explanation
Indices: 325315--325418 Score: 82
Period size: 29 Copynumber: 3.3 Consensus size: 29
325305 AGACATTCCA
325315 ATAATCTTTTATTCCTTTAACCAAACACG
1 ATAATCTTTTATTCCTTTAACCAAACACG
** * *
325344 ATAATCTTACATTCCTGCTAAACCAAATATACATTCCA
1 ATAATCTTTTATTCCT--TTAACC--A-A-ACA---CG
*
325382 ATAATCTTTTATTCCTTTAACCAAATACG
1 ATAATCTTTTATTCCTTTAACCAAACACG
325411 ATAATCTT
1 ATAATCTT
325419 ACATTCCTGC
Statistics
Matches: 57, Mismatches: 9, Indels: 18
0.68 0.11 0.21
Matches are distributed among these distances:
29 23 0.40
31 5 0.09
32 2 0.04
33 2 0.04
34 2 0.04
35 3 0.05
36 5 0.09
38 15 0.26
ACGTcount: A:0.37, C:0.23, G:0.03, T:0.38
Consensus pattern (29 bp):
ATAATCTTTTATTCCTTTAACCAAACACG
Found at i:325380 original size:67 final size:67
Alignment explanation
Indices: 325300--325433 Score: 250
Period size: 67 Copynumber: 2.0 Consensus size: 67
325290 ACAATTTGAT
325300 CAAATAGACATTCCAATAATCTTTTATTCCTTTAACCAAACACGATAATCTTACATTCCTGCTAA
1 CAAATAGACATTCCAATAATCTTTTATTCCTTTAACCAAACACGATAATCTTACATTCCTGCTAA
325365 AC
66 AC
* *
325367 CAAATATACATTCCAATAATCTTTTATTCCTTTAACCAAATACGATAATCTTACATTCCTGCTAA
1 CAAATAGACATTCCAATAATCTTTTATTCCTTTAACCAAACACGATAATCTTACATTCCTGCTAA
325432 AC
66 AC
325434 TAACCAAACA
Statistics
Matches: 65, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
67 65 1.00
ACGTcount: A:0.37, C:0.25, G:0.04, T:0.34
Consensus pattern (67 bp):
CAAATAGACATTCCAATAATCTTTTATTCCTTTAACCAAACACGATAATCTTACATTCCTGCTAA
AC
Found at i:325501 original size:20 final size:19
Alignment explanation
Indices: 325471--325512 Score: 75
Period size: 20 Copynumber: 2.2 Consensus size: 19
325461 AGTAATCCTA
325471 TTCTATGGTAATCTTACAT
1 TTCTATGGTAATCTTACAT
325490 TTCTACTGGTAATCTTACAT
1 TTCTA-TGGTAATCTTACAT
325510 TTC
1 TTC
325513 GTGAACCAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 5 0.23
20 17 0.77
ACGTcount: A:0.24, C:0.19, G:0.10, T:0.48
Consensus pattern (19 bp):
TTCTATGGTAATCTTACAT
Found at i:328090 original size:2 final size:2
Alignment explanation
Indices: 328083--328128 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
328073 GTGCTATGTG
328083 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
328125 AT AT
1 AT AT
328129 GAACATATGT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:328711 original size:22 final size:19
Alignment explanation
Indices: 328661--328713 Score: 54
Period size: 18 Copynumber: 2.7 Consensus size: 19
328651 AGGGTATTAT
*
328661 AGTCCTTCGGGACGTAATG
1 AGTCCTTCGGGACATAATG
*
328680 -GTCCTGCGGGACATATATAG
1 AGTCCTTCGGGACATA-AT-G
328700 CAGTCCTTCGGGAC
1 -AGTCCTTCGGGAC
328714 GAATACTGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
18 13 0.48
19 2 0.07
20 1 0.04
22 11 0.41
ACGTcount: A:0.21, C:0.25, G:0.30, T:0.25
Consensus pattern (19 bp):
AGTCCTTCGGGACATAATG
Found at i:329918 original size:43 final size:42
Alignment explanation
Indices: 329811--329918 Score: 162
Period size: 42 Copynumber: 2.5 Consensus size: 42
329801 AAATAAGACA
329811 ATAACACTATTAAGTCTCAATAAGTCTAAAATAAATAACATC
1 ATAACACTATTAAGTCTCAATAAGTCTAAAATAAATAACATC
* * *
329853 ATAACACCATTAAATCTCAATAAGTTTAAAATAAAATAACATC
1 ATAACACTATTAAGTCTCAATAAGTCTAAAAT-AAATAACATC
* *
329896 ATAACACTAATAAGTCTAAATAA
1 ATAACACTATTAAGTCTCAATAA
329919 AATCAACATC
Statistics
Matches: 58, Mismatches: 7, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
42 29 0.50
43 29 0.50
ACGTcount: A:0.53, C:0.16, G:0.04, T:0.28
Consensus pattern (42 bp):
ATAACACTATTAAGTCTCAATAAGTCTAAAATAAATAACATC
Found at i:336000 original size:21 final size:21
Alignment explanation
Indices: 335974--336015 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
335964 TTTGGGTGTA
335974 CGGTGAAAAAACTCAGACCCG
1 CGGTGAAAAAACTCAGACCCG
335995 CGGTGAAAAAACTCAGACCCG
1 CGGTGAAAAAACTCAGACCCG
336016 AGGGTAATAA
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:0.38, C:0.29, G:0.24, T:0.10
Consensus pattern (21 bp):
CGGTGAAAAAACTCAGACCCG
Found at i:336819 original size:2 final size:2
Alignment explanation
Indices: 336814--336896 Score: 166
Period size: 2 Copynumber: 41.5 Consensus size: 2
336804 TTAATCATTA
336814 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
336856 AT AT AT AT 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 AT AT AT AT A
336897 ATGATAATTA
Statistics
Matches: 81, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 81 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:341546 original size:48 final size:48
Alignment explanation
Indices: 341510--341608 Score: 198
Period size: 48 Copynumber: 2.1 Consensus size: 48
341500 TCGTTTCTGT
341510 TTCTACCTTGTCTAGATCTTGTTCCATAATCTCTCTTCTGCTTACTGA
1 TTCTACCTTGTCTAGATCTTGTTCCATAATCTCTCTTCTGCTTACTGA
341558 TTCTACCTTGTCTAGATCTTGTTCCATAATCTCTCTTCTGCTTACTGA
1 TTCTACCTTGTCTAGATCTTGTTCCATAATCTCTCTTCTGCTTACTGA
341606 TTC
1 TTC
341609 CTTCTGCAAT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 51 1.00
ACGTcount: A:0.16, C:0.27, G:0.10, T:0.46
Consensus pattern (48 bp):
TTCTACCTTGTCTAGATCTTGTTCCATAATCTCTCTTCTGCTTACTGA
Found at i:342542 original size:20 final size:20
Alignment explanation
Indices: 342517--342590 Score: 94
Period size: 20 Copynumber: 3.6 Consensus size: 20
342507 TTTTCCCAAT
*
342517 TCGCAATGCGAATAAGTAAA
1 TCGCAACGCGAATAAGTAAA
** *
342537 TCGCAACGCGAATTGGGAAAA
1 TCGCAACGCGAA-TAAGTAAA
*
342558 TCGCAATGCGAATAAGTAAA
1 TCGCAACGCGAATAAGTAAA
342578 TCGCAACGCGAAT
1 TCGCAACGCGAAT
342591 TGGGTACTGA
Statistics
Matches: 44, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.41, C:0.19, G:0.23, T:0.18
Consensus pattern (20 bp):
TCGCAACGCGAATAAGTAAA
Found at i:342562 original size:41 final size:41
Alignment explanation
Indices: 342517--342594 Score: 156
Period size: 41 Copynumber: 1.9 Consensus size: 41
342507 TTTTCCCAAT
342517 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
342558 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGG
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGG
342595 TACTGACTAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 37 1.00
ACGTcount: A:0.38, C:0.18, G:0.26, T:0.18
Consensus pattern (41 bp):
TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
Found at i:342650 original size:20 final size:20
Alignment explanation
Indices: 342625--342697 Score: 110
Period size: 20 Copynumber: 3.6 Consensus size: 20
342615 TAATACAAAA
* *
342625 TCGCAACGAGATACTTACTT
1 TCGCAACGCGATACTGACTT
342645 TCGCAACGCGATACTGACTT
1 TCGCAACGCGATACTGACTT
* *
342665 TCGCAACGTGATTCTGACTT
1 TCGCAACGCGATACTGACTT
342685 TCGCAACGCGATA
1 TCGCAACGCGATA
342698 ATACATAATC
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 47 1.00
ACGTcount: A:0.26, C:0.27, G:0.19, T:0.27
Consensus pattern (20 bp):
TCGCAACGCGATACTGACTT
Found at i:342913 original size:22 final size:22
Alignment explanation
Indices: 342885--342928 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
342875 CACTCTCTCA
342885 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
*
342907 CCCATCTCCGGCGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
342929 TATCTCCATC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.20, C:0.45, G:0.16, T:0.18
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:343243 original size:20 final size:20
Alignment explanation
Indices: 343189--343247 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
343179 GCGATTCTCT
**
343189 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCATTTTCG
343209 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
* **
343229 TGTTGCGATTTTCATTTTC
1 CGTTGCGATAGTCATTTTC
343248 AGAAACTATT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.17, C:0.19, G:0.22, T:0.42
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTTCG
Found at i:344581 original size:18 final size:18
Alignment explanation
Indices: 344560--344604 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
344550 TCCACTTCGG
*
344560 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCACCCA
*
344578 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
344596 GAGCCATCA
1 GAGCCATCA
344605 TCTGATCGAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.27, C:0.44, G:0.16, T:0.13
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:345110 original size:20 final size:20
Alignment explanation
Indices: 345085--345130 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
345075 ATAGTTACTT
345085 TCGCAACAC-GAAAATGACTA
1 TCGCAACACAG-AAATGACTA
* *
345105 TCGCAACGCAGAAATGGCTA
1 TCGCAACACAGAAATGACTA
345125 TCGCAA
1 TCGCAA
345131 TGCGAAATGA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 22 0.96
21 1 0.04
ACGTcount: A:0.39, C:0.26, G:0.20, T:0.15
Consensus pattern (20 bp):
TCGCAACACAGAAATGACTA
Found at i:345139 original size:19 final size:20
Alignment explanation
Indices: 345096--345151 Score: 69
Period size: 20 Copynumber: 2.9 Consensus size: 20
345086 CGCAACACGA
345096 AAATGACTATCGCAACGCAG
1 AAATGACTATCGCAACGCAG
* *
345116 AAATGGCTATCGCAATGC-G
1 AAATGACTATCGCAACGCAG
**
345135 AAATGAAAATCGCAACG
1 AAATGACTATCGCAACG
345152 ACAAAATCGC
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
19 14 0.47
20 16 0.53
ACGTcount: A:0.41, C:0.21, G:0.21, T:0.16
Consensus pattern (20 bp):
AAATGACTATCGCAACGCAG
Found at i:345159 original size:14 final size:14
Alignment explanation
Indices: 345140--345197 Score: 62
Period size: 14 Copynumber: 3.9 Consensus size: 14
345130 ATGCGAAATG
345140 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
345154 AAAATCGCAATGCGAA
1 AAAATCGCAA--CGAC
345170 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
*
345186 AAAATCGTAACG
1 AAAATCGCAACG
345198 CGAAATGAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
14 20 0.54
16 8 0.22
18 9 0.24
ACGTcount: A:0.48, C:0.22, G:0.17, T:0.12
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:345182 original size:32 final size:33
Alignment explanation
Indices: 345124--345214 Score: 157
Period size: 32 Copynumber: 2.8 Consensus size: 33
345114 AGAAATGGCT
345124 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
345157 ATCGCAATGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
* *
345189 ATCGTAACGCGAAATGAAAATCGCAA
1 ATCGCAATGCGAAATGAAAATCGCAA
345215 TGCGATTTGT
Statistics
Matches: 55, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
32 30 0.55
33 25 0.45
ACGTcount: A:0.47, C:0.21, G:0.19, T:0.13
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:345289 original size:19 final size:19
Alignment explanation
Indices: 345226--345348 Score: 105
Period size: 20 Copynumber: 6.7 Consensus size: 19
345216 GCGATTTGTG
345226 TTTCGCGTTGCGA-TTTCA
1 TTTCGCGTTGCGATTTTCA
345244 TTTCGCGTTGCGATTTT--
1 TTTCGCGTTGCGATTTTCA
*
345261 GTT---GTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTCA
* ***
345277 TTTCGCATTGCGATAGCCA
1 TTTCGCGTTGCGATTTTCA
**
345296 TTTCCGCGTTGCGATAGTCA
1 TTT-CGCGTTGCGATTTTCA
*
345316 TTTCGCGTTGCGATTTTAA
1 TTTCGCGTTGCGATTTTCA
*
345335 GTTTCGTGTTGCGA
1 -TTTCGCGTTGCGA
345349 AAGTAAACTA
Statistics
Matches: 85, Mismatches: 12, Indels: 14
0.77 0.11 0.13
Matches are distributed among these distances:
14 11 0.13
16 2 0.02
17 2 0.02
18 13 0.15
19 28 0.33
20 29 0.34
ACGTcount: A:0.13, C:0.20, G:0.24, T:0.43
Consensus pattern (19 bp):
TTTCGCGTTGCGATTTTCA
Found at i:345346 original size:39 final size:37
Alignment explanation
Indices: 345215--345348 Score: 111
Period size: 39 Copynumber: 3.6 Consensus size: 37
345205 AAAATCGCAA
345215 TGCGATTTGT-GTTTCGCGTTGCGATTTCATTTCGCGT
1 TGCGATTT-TAGTTTCGCGTTGCGATTTCATTTCGCGT
*
345252 TGCGATTTT-G-TT---GTTGCGATTTTCATTTCGCAT
1 TGCGATTTTAGTTTCGCGTTGCGA-TTTCATTTCGCGT
*** *
345285 TGCGATAGCCA-TTTCCGCGTTGCGATAGTCATTTCGCGT
1 TGCGAT-TTTAGTTT-CGCGTTGCGAT-TTCATTTCGCGT
*
345324 TGCGATTTTAAGTTTCGTGTTGCGA
1 TGCGATTTT-AGTTTCGCGTTGCGA
345349 AAGTAAACTA
Statistics
Matches: 76, Mismatches: 10, Indels: 20
0.72 0.09 0.19
Matches are distributed among these distances:
32 7 0.09
33 18 0.24
35 4 0.05
36 2 0.03
37 8 0.11
38 1 0.01
39 33 0.43
40 3 0.04
ACGTcount: A:0.13, C:0.19, G:0.25, T:0.43
Consensus pattern (37 bp):
TGCGATTTTAGTTTCGCGTTGCGATTTCATTTCGCGT
Found at i:347348 original size:14 final size:14
Alignment explanation
Indices: 347329--347384 Score: 58
Period size: 14 Copynumber: 3.6 Consensus size: 14
347319 CGAAATGGCT
347329 ATCGCAATGAGAAA
1 ATCGCAATGAGAAA
347343 ATCGCAATGCGAAATGAAA
1 ATCGCAAT--G--A-GAAA
*
347362 ATCGCAACGAGAAA
1 ATCGCAATGAGAAA
347376 ATCGCAATG
1 ATCGCAATG
347385 CGATTTTCAT
Statistics
Matches: 35, Mismatches: 2, Indels: 10
0.74 0.04 0.21
Matches are distributed among these distances:
14 20 0.57
15 1 0.03
16 1 0.03
17 1 0.03
18 1 0.03
19 11 0.31
ACGTcount: A:0.46, C:0.18, G:0.21, T:0.14
Consensus pattern (14 bp):
ATCGCAATGAGAAA
Found at i:347361 original size:19 final size:17
Alignment explanation
Indices: 347338--347387 Score: 61
Period size: 14 Copynumber: 3.0 Consensus size: 17
347328 TATCGCAATG
347338 AGAAAATCGCAATGCGAA
1 AGAAAATCGCAATGCG-A
347356 ATGAAAATCGCAA--CG-
1 A-GAAAATCGCAATGCGA
347371 AGAAAATCGCAATGCGA
1 AGAAAATCGCAATGCGA
347388 TTTTCATTTC
Statistics
Matches: 28, Mismatches: 0, Indels: 9
0.76 0.00 0.24
Matches are distributed among these distances:
14 11 0.39
15 1 0.04
16 2 0.07
17 2 0.07
18 1 0.04
19 11 0.39
ACGTcount: A:0.48, C:0.18, G:0.22, T:0.12
Consensus pattern (17 bp):
AGAAAATCGCAATGCGA
Found at i:347400 original size:33 final size:33
Alignment explanation
Indices: 347310--347387 Score: 111
Period size: 33 Copynumber: 2.4 Consensus size: 33
347300 AAAACAGACT
* *** *
347310 ATCGCAACGCGAAATGGCTATCGCAATGAGAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
347343 ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
347376 ATCGCAATGCGA
1 ATCGCAATGCGA
347388 TTTTCATTTC
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 40 1.00
ACGTcount: A:0.42, C:0.21, G:0.23, T:0.14
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
Found at i:347431 original size:20 final size:20
Alignment explanation
Indices: 347406--347463 Score: 98
Period size: 20 Copynumber: 2.9 Consensus size: 20
347396 TCGCATTGCG
* *
347406 ATTTTCTCGTTGTGATAGCC
1 ATTTTCGCGTTGCGATAGCC
347426 ATTTTCGCGTTGCGATAGCC
1 ATTTTCGCGTTGCGATAGCC
347446 ATTTTCGCGTTGCGATAG
1 ATTTTCGCGTTGCGATAG
347464 TCAAATGAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.16, C:0.21, G:0.24, T:0.40
Consensus pattern (20 bp):
ATTTTCGCGTTGCGATAGCC
Found at i:348519 original size:24 final size:24
Alignment explanation
Indices: 348492--348545 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
348482 GTATTCGAAA
* *
348492 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATACACGGAC
*
348516 TTTGATATTGGTCAATACACGGAT
1 TTTGATATTGGTCAATACACGGAC
348540 TTTGAT
1 TTTGAT
348546 GATATTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.24, C:0.17, G:0.20, T:0.39
Consensus pattern (24 bp):
TTTGATATTGGTCAATACACGGAC
Found at i:348737 original size:12 final size:12
Alignment explanation
Indices: 348720--348744 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
348710 ATATAATCCT
348720 GAAGAAGAAAAA
1 GAAGAAGAAAAA
348732 GAAGAAGAAAAA
1 GAAGAAGAAAAA
348744 G
1 G
348745 TCCCCGAAGA
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:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:350972 original size:21 final size:21
Alignment explanation
Indices: 350943--351023 Score: 65
Period size: 21 Copynumber: 3.9 Consensus size: 21
350933 GAATGGTGGG
*
350943 AGGGACCTCTTCAACGATGAC
1 AGGGGCCTCTTCAACGATGAC
* * * **
350964 AGTGGCCTCTTGAACGGTGGG
1 AGGGGCCTCTTCAACGATGAC
* * *
350985 AGGGGACTC-TCAAGGAATGAT
1 AGGGGCCTCTTCAACG-ATGAC
351006 AGGGGCCTCTTCAACGAT
1 AGGGGCCTCTTCAACGAT
351024 AGGAGTGGAC
Statistics
Matches: 43, Mismatches: 15, Indels: 4
0.69 0.24 0.06
Matches are distributed among these distances:
20 4 0.09
21 34 0.79
22 5 0.12
ACGTcount: A:0.25, C:0.22, G:0.32, T:0.21
Consensus pattern (21 bp):
AGGGGCCTCTTCAACGATGAC
Found at i:351013 original size:42 final size:41
Alignment explanation
Indices: 350928--351036 Score: 112
Period size: 42 Copynumber: 2.6 Consensus size: 41
350918 GTGAATCGGG
* *
350928 CTCTTGAATGGTGGGA-GGGACCTCTTCAACGATGACAGTGGC
1 CTCTTGAACGGTGGGAGGGGA-CTC-TCAACGATGACAGGGGC
* *
350970 CTCTTGAACGGTGGGAGGGGACTCTCAAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGAGGGGACTCTCAACG-ATGACAGGGGC
* * * *
351012 CTCTTCAACGATAGGAGTGGACTCT
1 CTCTTGAACGGTGGGAGGGGACTCT
351037 TGAGGGATGA
Statistics
Matches: 57, Mismatches: 8, Indels: 4
0.83 0.12 0.06
Matches are distributed among these distances:
41 5 0.09
42 48 0.84
43 4 0.07
ACGTcount: A:0.23, C:0.20, G:0.34, T:0.23
Consensus pattern (41 bp):
CTCTTGAACGGTGGGAGGGGACTCTCAACGATGACAGGGGC
Found at i:351444 original size:91 final size:90
Alignment explanation
Indices: 351266--351452 Score: 286
Period size: 91 Copynumber: 2.0 Consensus size: 90
351256 ATATTTCAAA
*
351266 ACTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTTTA
1 ACTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTT--A-AATAAACAGTTTA
*
351331 GCAGAATTGGCAGCAACCGAATAAATTT
63 GCAGAATTGGAAGCAACCGAATAAATTT
*
351359 ACTTCAATCAAAAGACAAAACAAAAAGACAAATACTAACTTCACAGTGTT-AATAAACAGTTTAG
1 ACTTCAACCAAAAGACAAAAC--AAAGACAAATACTAACTTCACAGTGTTAAATAAACAGTTTAG
*
351423 CAGTATTGGAAGCAACCGAATAAATTT
64 CAGAATTGGAAGCAACCGAATAAATTT
351450 ACT
1 ACT
351453 AAGCAATCTA
Statistics
Matches: 88, Mismatches: 4, Indels: 6
0.90 0.04 0.06
Matches are distributed among these distances:
91 41 0.47
93 20 0.23
95 27 0.31
ACGTcount: A:0.48, C:0.18, G:0.12, T:0.22
Consensus pattern (90 bp):
ACTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAATAAACAGTTTAGCA
GAATTGGAAGCAACCGAATAAATTT
Found at i:353028 original size:19 final size:19
Alignment explanation
Indices: 352977--353055 Score: 95
Period size: 19 Copynumber: 4.1 Consensus size: 19
352967 TCTTTTGGTT
*
352977 GAAATGAAAATCGCAAAGA
1 GAAATGAAAATCGCAAAGC
*
352996 GATAATGAGAATCGCAAAGC
1 GA-AATGAAAATCGCAAAGC
** *
353016 GAAATGACTATCGCAACGC
1 GAAATGAAAATCGCAAAGC
*
353035 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAAAGC
353054 GA
1 GA
353056 TTTTGGTTTC
Statistics
Matches: 51, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
19 34 0.67
20 17 0.33
ACGTcount: A:0.47, C:0.16, G:0.23, T:0.14
Consensus pattern (19 bp):
GAAATGAAAATCGCAAAGC
Found at i:353674 original size:20 final size:20
Alignment explanation
Indices: 353649--353701 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
353639 GCGTTATGTA
353649 AATCGCGTTGCGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
353669 AATCGCGTTGCGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
* *
353689 TATCTCGTTGCGA
1 AATCGCGTTGCGA
353702 TTTTGTATTA
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:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (20 bp):
AATCGCGTTGCGAAAGTCAG
Found at i:353735 original size:20 final size:20
Alignment explanation
Indices: 353710--353760 Score: 93
Period size: 20 Copynumber: 2.5 Consensus size: 20
353700 GATTTTGTAT
353710 TATCGCATTGCGATAGTAAG
1 TATCGCATTGCGATAGTAAG
*
353730 TATCGCATTGCGATAGTCAG
1 TATCGCATTGCGATAGTAAG
353750 TATCGCATTGC
1 TATCGCATTGC
353761 AATTTTTCCA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.25, C:0.20, G:0.24, T:0.31
Consensus pattern (20 bp):
TATCGCATTGCGATAGTAAG
Found at i:353766 original size:61 final size:61
Alignment explanation
Indices: 353650--353766 Score: 153
Period size: 61 Copynumber: 1.9 Consensus size: 61
353640 CGTTATGTAA
* * * * * *
353650 ATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGTATCTCGTTGCGATTTTGTATT
1 ATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCAATTTTGTATT
* * *
353711 ATCGCATTGCGATAGTAAGTATCGCATTGCGATAGTCAGTATCGCATTGCAATTTT
1 ATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCAATTTT
353767 TCCAATTCGC
Statistics
Matches: 47, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
61 47 1.00
ACGTcount: A:0.25, C:0.18, G:0.24, T:0.33
Consensus pattern (61 bp):
ATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCAATTTTGTATT
Found at i:353841 original size:21 final size:21
Alignment explanation
Indices: 353801--353841 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
353791 ACTATAGACC
**
353801 ATCGCAACGCGATTTCCAACT
1 ATCGCAACGCGAAATCCAACT
*
353822 ATCGCAACGCGAAATGCAAC
1 ATCGCAACGCGAAATCCAAC
353842 GCGAATTTGC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.34, C:0.32, G:0.17, T:0.17
Consensus pattern (21 bp):
ATCGCAACGCGAAATCCAACT
Found at i:354510 original size:21 final size:21
Alignment explanation
Indices: 354461--354524 Score: 83
Period size: 21 Copynumber: 2.9 Consensus size: 21
354451 AGGTATATTT
* *
354461 TATTTTATTTAATATCTTATTAG
1 TATTTTATTTAAT-TATT-TTAA
354484 TATTTTATTTAATTATTTTAA
1 TATTTTATTTAATTATTTTAA
354505 TATTTTATTTAATTAATTTT
1 TATTTTATTTAATT-ATTTT
354525 TTTTTCTTTT
Statistics
Matches: 38, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
21 17 0.45
22 8 0.21
23 13 0.34
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.66
Consensus pattern (21 bp):
TATTTTATTTAATTATTTTAA
Found at i:359417 original size:66 final size:66
Alignment explanation
Indices: 359341--359473 Score: 266
Period size: 66 Copynumber: 2.0 Consensus size: 66
359331 TATATTGACC
359341 AAAAAAAATTAAGCACCTAAATAGGAAAATAAATGTAGTTTATAATTTTTTTATTAATCTCTTTT
1 AAAAAAAATTAAGCACCTAAATAGGAAAATAAATGTAGTTTATAATTTTTTTATTAATCTCTTTT
359406 T
66 T
359407 AAAAAAAATTAAGCACCTAAATAGGAAAATAAATGTAGTTTATAATTTTTTTATTAATCTCTTTT
1 AAAAAAAATTAAGCACCTAAATAGGAAAATAAATGTAGTTTATAATTTTTTTATTAATCTCTTTT
359472 T
66 T
359473 A
1 A
359474 TATAAATGTA
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
66 67 1.00
ACGTcount: A:0.44, C:0.08, G:0.08, T:0.41
Consensus pattern (66 bp):
AAAAAAAATTAAGCACCTAAATAGGAAAATAAATGTAGTTTATAATTTTTTTATTAATCTCTTTT
T
Found at i:359705 original size:13 final size:13
Alignment explanation
Indices: 359665--359708 Score: 54
Period size: 13 Copynumber: 3.5 Consensus size: 13
359655 TTATAAATTT
359665 TTTAAAATT-TTA
1 TTTAAAATTATTA
* **
359677 TTTAAAATAAAAA
1 TTTAAAATTATTA
359690 TTTAAAATTATTA
1 TTTAAAATTATTA
359703 TTTAAA
1 TTTAAA
359709 GGTTTTTTTA
Statistics
Matches: 25, Mismatches: 6, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
12 8 0.32
13 17 0.68
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
TTTAAAATTATTA
Found at i:361218 original size:20 final size:21
Alignment explanation
Indices: 361181--361220 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
361171 AATTGTTAAT
* *
361181 TATTGATATTCTTTTTTTATA
1 TATTGATATTATTGTTTTATA
361202 TATTG-TATTATTGTTTTAT
1 TATTGATATTATTGTTTTAT
361221 TTTTTATTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.23, C:0.03, G:0.07, T:0.68
Consensus pattern (21 bp):
TATTGATATTATTGTTTTATA
Found at i:363333 original size:15 final size:15
Alignment explanation
Indices: 363304--363332 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
363294 TTTTGTTTGG
363304 AATGTTTTAACTTTT
1 AATGTTTTAACTTTT
363319 AATGTTTTAA-TTTT
1 AATGTTTTAACTTTT
363333 TGATCAAAAC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 4 0.29
15 10 0.71
ACGTcount: A:0.28, C:0.03, G:0.07, T:0.62
Consensus pattern (15 bp):
AATGTTTTAACTTTT
Found at i:387487 original size:175 final size:174
Alignment explanation
Indices: 387196--387545 Score: 691
Period size: 175 Copynumber: 2.0 Consensus size: 174
387186 AATCCCAGCG
387196 ATGGAAGGAGATTGTCCTGTGACTCGTTGTATCATAGTGATTTATCCTCACAGAGATATTCCACA
1 ATGGAAGGAGATTGTCCTGTGACTCGTTGTATCATAGTGATTTATCCTCACAGAGATATTCCACA
387261 GCTTCAATTCGAGGTGATATATTGAAAATGCATCTTATTCATCATGATTCTTTGTTGTTGAAAGG
66 GCTTCAATTCGAGGTGATATATTGAAAATGCATCTTATTCATCATGATTCTTTGTTGTTGAAAGG
387326 CAAAGTAAAAAGGAAAATGTAAAAGACCAAGAACTTGAAAAATTC
131 CAAAGT-AAAAGGAAAATGTAAAAGACCAAGAACTTGAAAAATTC
387371 ATGGAAGGAGATTGTCCTGTGACTCGTTGTATCATAGTGATTTATCCTCACAGAGATATTCCACA
1 ATGGAAGGAGATTGTCCTGTGACTCGTTGTATCATAGTGATTTATCCTCACAGAGATATTCCACA
387436 GCTTCAATTCGAGGTGATATATTGAAAATGCATCTTATTCATCATGATTCTTTGTTGTTGAAAGG
66 GCTTCAATTCGAGGTGATATATTGAAAATGCATCTTATTCATCATGATTCTTTGTTGTTGAAAGG
387501 CAAAGTAAAAGGAAAATGTAAAAGACCAAGAACTTGAAAAATTC
131 CAAAGTAAAAGGAAAATGTAAAAGACCAAGAACTTGAAAAATTC
387545 A
1 A
387546 GAATTTGTAA
Statistics
Matches: 175, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
174 39 0.22
175 136 0.78
ACGTcount: A:0.35, C:0.14, G:0.19, T:0.31
Consensus pattern (174 bp):
ATGGAAGGAGATTGTCCTGTGACTCGTTGTATCATAGTGATTTATCCTCACAGAGATATTCCACA
GCTTCAATTCGAGGTGATATATTGAAAATGCATCTTATTCATCATGATTCTTTGTTGTTGAAAGG
CAAAGTAAAAGGAAAATGTAAAAGACCAAGAACTTGAAAAATTC
Found at i:397390 original size:12 final size:12
Alignment explanation
Indices: 397370--397399 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
397360 ATCATCATCA
*
397370 ATCATAACATAG
1 ATCACAACATAG
397382 ATCACAACATAG
1 ATCACAACATAG
397394 ATCACA
1 ATCACA
397400 TTATCCTTAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.50, C:0.23, G:0.07, T:0.20
Consensus pattern (12 bp):
ATCACAACATAG
Found at i:401118 original size:31 final size:31
Alignment explanation
Indices: 401080--401143 Score: 83
Period size: 31 Copynumber: 2.1 Consensus size: 31
401070 TTTATGATCC
*
401080 CTAACGTTACCGATCCATTCGATTTTAATCT
1 CTAACGTTACCAATCCATTCGATTTTAATCT
* * * *
401111 CTAACGTTACTAATCCGTTTGATTTTAGTCT
1 CTAACGTTACCAATCCATTCGATTTTAATCT
401142 CT
1 CT
401144 CAATCATTAA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.23, C:0.23, G:0.11, T:0.42
Consensus pattern (31 bp):
CTAACGTTACCAATCCATTCGATTTTAATCT
Found at i:406814 original size:7 final size:7
Alignment explanation
Indices: 406802--406843 Score: 75
Period size: 7 Copynumber: 6.0 Consensus size: 7
406792 CTTCACCTTT
406802 CCTTTTC
1 CCTTTTC
406809 CCTTTTC
1 CCTTTTC
*
406816 CCCTTTC
1 CCTTTTC
406823 CCTTTTC
1 CCTTTTC
406830 CCTTTTC
1 CCTTTTC
406837 CCTTTTC
1 CCTTTTC
406844 GTTTCCCTTA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
7 33 1.00
ACGTcount: A:0.00, C:0.45, G:0.00, T:0.55
Consensus pattern (7 bp):
CCTTTTC
Found at i:406828 original size:21 final size:21
Alignment explanation
Indices: 406797--406843 Score: 78
Period size: 21 Copynumber: 2.3 Consensus size: 21
406787 TTCCCCTTCA
406797 CCTTT-CCTTTTCCCTTTTCC
1 CCTTTCCCTTTTCCCTTTTCC
406817 CCTTTCCCTTTTCCCTTTTCC
1 CCTTTCCCTTTTCCCTTTTCC
*
406838 CTTTTC
1 CCTTTC
406844 GTTTCCCTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
20 5 0.20
21 20 0.80
ACGTcount: A:0.00, C:0.45, G:0.00, T:0.55
Consensus pattern (21 bp):
CCTTTCCCTTTTCCCTTTTCC
Found at i:407845 original size:29 final size:29
Alignment explanation
Indices: 407812--407867 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
407802 TCCCAACACA
* *
407812 TAGGTTGCCATGC-CTTCTGGGCGACCTTG
1 TAGGTCGCCATGCAC-TCCGGGCGACCTTG
407841 TAGGTCGCCATGCACTCCGGGCGACCT
1 TAGGTCGCCATGCACTCCGGGCGACCT
407868 ACCCTCGCTC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 23 0.96
30 1 0.04
ACGTcount: A:0.12, C:0.32, G:0.30, T:0.25
Consensus pattern (29 bp):
TAGGTCGCCATGCACTCCGGGCGACCTTG
Found at i:408039 original size:29 final size:29
Alignment explanation
Indices: 408002--408059 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
407992 GCAATCTCTT
* *
408002 GTAGCTCGCCGGGAA-GACATGGCGACCTA
1 GTAGCTCGCCCGAAATG-CATGGCGACCTA
*
408031 GTAGGTCGCCCGAAATGCATGGCGACCTA
1 GTAGCTCGCCCGAAATGCATGGCGACCTA
408060 CGGCCAATAC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 24 0.96
30 1 0.04
ACGTcount: A:0.24, C:0.28, G:0.33, T:0.16
Consensus pattern (29 bp):
GTAGCTCGCCCGAAATGCATGGCGACCTA
Found at i:409144 original size:27 final size:27
Alignment explanation
Indices: 409089--409142 Score: 76
Period size: 25 Copynumber: 2.1 Consensus size: 27
409079 AATAGTTCGG
*
409089 TTCGGTTTGGCTTTAAACGGTTTGATT
1 TTCGGTTCGGCTTTAAACGGTTTGATT
*
409116 TTCGGTTCGG-TTTAAA-GGTTTTATT
1 TTCGGTTCGGCTTTAAACGGTTTGATT
409141 TT
1 TT
409143 TTTTATTCGG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 10 0.40
26 6 0.24
27 9 0.36
ACGTcount: A:0.15, C:0.09, G:0.24, T:0.52
Consensus pattern (27 bp):
TTCGGTTCGGCTTTAAACGGTTTGATT
Found at i:410394 original size:20 final size:20
Alignment explanation
Indices: 410371--410414 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
410361 CCTTGAGCAT
*
410371 AAATCTCTAACCTTAATATC
1 AAATCTCTAACCCTAATATC
* *
410391 AAATCTCTTACCCTAATCTC
1 AAATCTCTAACCCTAATATC
410411 AAAT
1 AAAT
410415 TTATTATAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.39, C:0.27, G:0.00, T:0.34
Consensus pattern (20 bp):
AAATCTCTAACCCTAATATC
Found at i:411546 original size:27 final size:25
Alignment explanation
Indices: 411516--411579 Score: 69
Period size: 27 Copynumber: 2.4 Consensus size: 25
411506 TAAAAAATTT
411516 AAAGATAAATTATATATTTTTAAATGA
1 AAAGATAAA-TA-ATATTTTTAAATGA
411543 AAAGAATTACAA-AATATTTTTAAATGA
1 AAAG-A-TA-AATAATATTTTTAAATGA
411570 AAA-ATAAATA
1 AAAGATAAATA
411580 TTAACCTAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 11
0.75 0.00 0.25
Matches are distributed among these distances:
23 2 0.06
24 3 0.09
25 1 0.03
27 21 0.64
28 2 0.06
29 2 0.06
30 2 0.06
ACGTcount: A:0.58, C:0.02, G:0.06, T:0.34
Consensus pattern (25 bp):
AAAGATAAATAATATTTTTAAATGA
Found at i:420815 original size:13 final size:13
Alignment explanation
Indices: 420797--420821 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
420787 TTAAGTCGAA
420797 TTATTTAAATTTT
1 TTATTTAAATTTT
420810 TTATTTAAATTT
1 TTATTTAAATTT
420822 AATCGAAAAT
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:0.00, G:0.00, T:0.68
Consensus pattern (13 bp):
TTATTTAAATTTT
Found at i:424206 original size:18 final size:18
Alignment explanation
Indices: 424183--424220 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
424173 CCGTAGAGCT
* *
424183 TAAAAATTTATTTTTTTA
1 TAAAAATATATTATTTTA
424201 TAAAAATATATTATTTTA
1 TAAAAATATATTATTTTA
424219 TA
1 TA
424221 CGAATTTGAT
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:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (18 bp):
TAAAAATATATTATTTTA
Found at i:432265 original size:42 final size:42
Alignment explanation
Indices: 432217--432299 Score: 166
Period size: 42 Copynumber: 2.0 Consensus size: 42
432207 TATACATCAT
432217 CCACACGTGTCATGTAAATTGATACATAGATAAACATGCTTC
1 CCACACGTGTCATGTAAATTGATACATAGATAAACATGCTTC
432259 CCACACGTGTCATGTAAATTGATACATAGATAAACATGCTT
1 CCACACGTGTCATGTAAATTGATACATAGATAAACATGCTT
432300 ATGAGATGAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.36, C:0.20, G:0.14, T:0.29
Consensus pattern (42 bp):
CCACACGTGTCATGTAAATTGATACATAGATAAACATGCTTC
Found at i:434943 original size:15 final size:15
Alignment explanation
Indices: 434923--435085 Score: 202
Period size: 15 Copynumber: 10.5 Consensus size: 15
434913 TAATAAGGTT
434923 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
*
434938 ATTTATTATAAAATA
1 ATTTATTTTAAAATA
434953 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
*
434968 ATTTATTATAAAATA
1 ATTTATTTTAAAATA
*
434983 ATTTATTATAAAATA
1 ATTTATTTTAAAATA
*
434998 ATTTATTATAAAATA
1 ATTTATTTTAAAATA
435013 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
* *
435028 AATTATTATAAAATATGGA
1 ATTTATT-TTAAA-AT--A
435047 TTGATTTATTTTAAAATA
1 ---ATTTATTTTAAAATA
435065 ATTTA-TTTAAAATA
1 ATTTATTTTAAAATA
435079 ATTTATT
1 ATTTATT
435086 AGTATGGATT
Statistics
Matches: 132, Mismatches: 8, Indels: 16
0.85 0.05 0.10
Matches are distributed among these distances:
14 14 0.11
15 98 0.74
16 4 0.03
17 2 0.02
18 1 0.01
19 1 0.01
20 2 0.02
21 4 0.03
22 6 0.05
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (15 bp):
ATTTATTTTAAAATA
Found at i:434959 original size:30 final size:30
Alignment explanation
Indices: 434923--435085 Score: 238
Period size: 30 Copynumber: 5.2 Consensus size: 30
434913 TAATAAGGTT
434923 ATTTATTTTAAAATAATTTATTATAAAATA
1 ATTTATTTTAAAATAATTTATTATAAAATA
434953 ATTTATTTTAAAATAATTTATTATAAAATA
1 ATTTATTTTAAAATAATTTATTATAAAATA
*
434983 ATTTATTATAAAATAATTTATTATAAAATA
1 ATTTATTTTAAAATAATTTATTATAAAATA
*
435013 ATTTATTTTAAAATAAATTATTATAAAATATGGA
1 ATTTATTTTAAAATAATTTATTAT-AAA-AT--A
435047 TTGATTTATTTTAAAATAATTTATT-TAAAATA
1 ---ATTTATTTTAAAATAATTTATTATAAAATA
435079 ATTTATT
1 ATTTATT
435086 AGTATGGATT
Statistics
Matches: 122, Mismatches: 4, Indels: 15
0.87 0.03 0.11
Matches are distributed among these distances:
29 7 0.06
30 81 0.66
31 3 0.02
32 3 0.02
34 3 0.02
35 3 0.02
36 1 0.01
37 21 0.17
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (30 bp):
ATTTATTTTAAAATAATTTATTATAAAATA
Found at i:434980 original size:45 final size:45
Alignment explanation
Indices: 434923--435118 Score: 225
Period size: 45 Copynumber: 4.2 Consensus size: 45
434913 TAATAAGGTT
*
434923 ATTTATTTTAAAATAATTTATTATAAAATAATTTATTTTAAAATA
1 ATTTATTATAAAATAATTTATTATAAAATAATTTATTTTAAAATA
*
434968 ATTTATTATAAAATAATTTATTATAAAATAATTTATTATAAAATA
1 ATTTATTATAAAATAATTTATTATAAAATAATTTATTTTAAAATA
* *
435013 ATTTATTTTAAAATAAATTATTATAAAATATGGATTGATTTATTTTAAAATA
1 ATTTATTATAAAATAATTTATTAT-AAA-AT--A---ATTTATTTTAAAATA
* * *
435065 ATTTATT-TAAAATAATTTATTAGTATGGATTGATTTATTTT-AAATA
1 ATTTATTATAAAATAATTTATTA-TA--AAATAATTTATTTTAAAATA
435111 ATTTATTA
1 ATTTATTA
435119 GTATAGATTG
Statistics
Matches: 131, Mismatches: 9, Indels: 20
0.82 0.06 0.12
Matches are distributed among these distances:
45 65 0.50
46 15 0.11
47 11 0.08
49 1 0.01
51 15 0.11
52 23 0.18
53 1 0.01
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (45 bp):
ATTTATTATAAAATAATTTATTATAAAATAATTTATTTTAAAATA
Found at i:435103 original size:32 final size:32
Alignment explanation
Indices: 435065--435283 Score: 179
Period size: 32 Copynumber: 6.4 Consensus size: 32
435055 TTTTAAAATA
*
435065 ATTTATTTAAAATAATTTATTAGTATGGATTG
1 ATTTATTTAAAATAATTTATTAGTATAGATTG
*
435097 ATTTATTTTAAATAATTTATTAGTATAGATTG
1 ATTTATTTAAAATAATTTATTAGTATAGATTG
* * * * *
435129 ATTTATTTTAAAATATGGATTGATTTATTTTA-AATA
1 ATTTA-TTTAAAATA---ATTTA-TTAGTATAGATTG
* * * *
435165 ATTTATTAGTATGGATTGATTTATTTTAAAATATAGATTG
1 ATTTATT--TA--AAATAATTTA--TT--AGTATAGATTG
* *
435205 ATTTATTTTAAATAATTTATTAGTATGGATTG
1 ATTTATTTAAAATAATTTATTAGTATAGATTG
*
435237 ATTTATTTTAAATAATTTATTAGTATAGATTG
1 ATTTATTTAAAATAATTTATTAGTATAGATTG
435269 ATTTATTTTAAAATA
1 ATTTA-TTTAAAATA
435284 TGGATTGATT
Statistics
Matches: 149, Mismatches: 24, Indels: 27
0.75 0.12 0.14
Matches are distributed among these distances:
32 80 0.54
33 16 0.11
34 2 0.01
35 2 0.01
36 22 0.15
37 11 0.07
38 1 0.01
39 6 0.04
40 9 0.06
ACGTcount: A:0.37, C:0.00, G:0.11, T:0.52
Consensus pattern (32 bp):
ATTTATTTAAAATAATTTATTAGTATAGATTG
Found at i:435157 original size:54 final size:54
Alignment explanation
Indices: 435088--435547 Score: 485
Period size: 54 Copynumber: 8.3 Consensus size: 54
435078 AATTTATTAG
*
435088 TATGGATTGATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
435142 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
*
435196 TATAGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTT-AAA
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
* * * * * * ***
435249 TA---ATTTA-TTAGTATAGATTGATTTATTTTAAAATATGGATTGATTTATTATTGTAGTTG
1 TATGGATTGATTTATTTTA-AATAATTTA--TT--AGTATGGATTGATTTA-T-TT-TA-AAA
435308 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
*
435362 TATGGATTGATTTA--TT--AT--TGTAGTT-GTATGGATTGATTTATTTTAAATAATTTATTA
1 TATGGATTGATTTATTTTAAATAATTTA-TTAGTATGGATTGATTTA-TTT---TAA---A--A
*
435419 GTATGGATTGATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAAA
1 -TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
* *
435474 TATGTATTGATTTATTTTAAATAATTTATTTGTATGGATTGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAATAATTTATTAGTAT-G---GATTGATTTATTTTAAAA
435532 TATGGATTGATTTATT
1 TATGGATTGATTTATT
435548 ATTGTAGTTG
Statistics
Matches: 343, Mismatches: 27, Indels: 68
0.78 0.06 0.16
Matches are distributed among these distances:
48 18 0.05
49 11 0.03
50 13 0.04
52 7 0.02
53 5 0.01
54 164 0.48
55 5 0.01
56 4 0.01
57 4 0.01
58 62 0.18
59 2 0.01
60 7 0.02
62 13 0.04
63 11 0.03
64 17 0.05
ACGTcount: A:0.34, C:0.00, G:0.13, T:0.53
Consensus pattern (54 bp):
TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
Found at i:435348 original size:80 final size:80
Alignment explanation
Indices: 435142--435627 Score: 679
Period size: 80 Copynumber: 5.9 Consensus size: 80
435132 TATTTTAAAA
*
435142 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATAGATTGAT
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGAT
*
435207 TTATTTTAAATAATTTA-TTAG
66 TTA--TT--AT--TGTAGTT-G
*
435228 TATGGATTGATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAAATATGGATTGAT
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGAT
435293 TTATTATTGTAGTTG
66 TTATTATTGTAGTTG
435308 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGAT
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGAT
435373 TTATTATTGTAGTTG
66 TTATTATTGTAGTTG
*
435388 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAATAATTTATTAGT
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTT-AA-AA--TA-T-GG
* * * ***
435453 ATAGATTGATTTATTTTA-AAA
60 ATTGATTTA-TTATTGTAGTTG
* *
435474 TATGTATTGATTTATTTTAAATAATTTATTTGTATGGATTGATTGATTTATTTTAAAATATGGAT
1 TATGGATTGATTTATTTTAAATAATTTATTAGTAT-G---GATTGATTTATTTTAAAATATGGAT
435539 TGATTTATTATTGTAGTTG
62 TGATTTATTATTGTAGTTG
*
435558 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATAGATTGAT
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGAT
435623 TTATT
66 TTATT
435628 TTAAATAATT
Statistics
Matches: 364, Mismatches: 23, Indels: 32
0.87 0.05 0.08
Matches are distributed among these distances:
80 166 0.46
81 4 0.01
82 4 0.01
83 8 0.02
84 45 0.12
85 2 0.01
86 109 0.30
87 8 0.02
88 2 0.01
89 2 0.01
90 14 0.04
ACGTcount: A:0.33, C:0.00, G:0.14, T:0.53
Consensus pattern (80 bp):
TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGAT
TTATTATTGTAGTTG
Found at i:435354 original size:18 final size:18
Alignment explanation
Indices: 435331--435378 Score: 51
Period size: 22 Copynumber: 2.4 Consensus size: 18
435321 ATTTTAAATA
*
435331 ATTTATTAGTATGGATTG
1 ATTTATTAATATGGATTG
435349 ATTTATTTTAAAATATGGATTG
1 ATTTA--TT--AATATGGATTG
435371 ATTTATTA
1 ATTTATTA
435379 TTGTAGTTGT
Statistics
Matches: 25, Mismatches: 1, Indels: 8
0.74 0.03 0.24
Matches are distributed among these distances:
18 6 0.24
20 4 0.16
22 15 0.60
ACGTcount: A:0.33, C:0.00, G:0.15, T:0.52
Consensus pattern (18 bp):
ATTTATTAATATGGATTG
Found at i:435428 original size:32 final size:32
Alignment explanation
Indices: 435387--435610 Score: 224
Period size: 32 Copynumber: 7.7 Consensus size: 32
435377 TATTGTAGTT
435387 GTATGGATTGATTTATTTTAAATAATTTATTA
1 GTATGGATTGATTTATTTTAAATAATTTATTA
435419 GTATGGATTGATTTATTTTAAATAATTTATTA
1 GTATGGATTGATTTATTTTAAATAATTTATTA
*
435451 GTATAGATTGATTTATTTT-AA-AA--TA-T-
1 GTATGGATTGATTTATTTTAAATAATTTATTA
*
435477 G--T--ATTGATTTATTTTAAATAATTTATTT
1 GTATGGATTGATTTATTTTAAATAATTTATTA
* *
435505 GTATGGATTGATTGA-TTT--AT--TTTA-AA
1 GTATGGATTGATTTATTTTAAATAATTTATTA
* *
435531 ATATGGATTGATTTA--TT--AT--TGTAGTT-
1 GTATGGATTGATTTATTTTAAATAATTTA-TTA
435557 GTATGGATTGATTTATTTTAAATAATTTATTA
1 GTATGGATTGATTTATTTTAAATAATTTATTA
435589 GTATGGATTGATTTATTTTAAA
1 GTATGGATTGATTTATTTTAAA
435611 ATATAGATTG
Statistics
Matches: 163, Mismatches: 10, Indels: 38
0.77 0.05 0.18
Matches are distributed among these distances:
22 13 0.08
23 2 0.01
24 3 0.02
25 7 0.04
26 30 0.18
27 6 0.04
28 5 0.03
29 2 0.01
30 5 0.03
31 7 0.04
32 83 0.51
ACGTcount: A:0.33, C:0.00, G:0.14, T:0.53
Consensus pattern (32 bp):
GTATGGATTGATTTATTTTAAATAATTTATTA
Found at i:435466 original size:18 final size:18
Alignment explanation
Indices: 435411--435467 Score: 59
Period size: 18 Copynumber: 3.4 Consensus size: 18
435401 ATTTTAAATA
*
435411 ATTTATTAGTATGGATTG
1 ATTTATTAGTATAGATTG
* *
435429 ATTTATT--T-TA-AATA
1 ATTTATTAGTATAGATTG
435443 ATTTATTAGTATAGATTG
1 ATTTATTAGTATAGATTG
435461 ATTTATT
1 ATTTATT
435468 TTAAAATATG
Statistics
Matches: 30, Mismatches: 5, Indels: 8
0.70 0.12 0.19
Matches are distributed among these distances:
14 9 0.30
15 1 0.03
16 2 0.07
17 2 0.07
18 16 0.53
ACGTcount: A:0.33, C:0.00, G:0.12, T:0.54
Consensus pattern (18 bp):
ATTTATTAGTATAGATTG
Found at i:435504 original size:36 final size:36
Alignment explanation
Indices: 435461--435530 Score: 90
Period size: 36 Copynumber: 1.9 Consensus size: 36
435451 GTATAGATTG
435461 ATTTATTT-TA-AAATATGTATTGATTTATTTTAAATA
1 ATTTATTTGTATAAAT-TG-ATTGATTTATTTTAAATA
**
435497 ATTTATTTGTATGGATTGATTGATTTATTTTAAA
1 ATTTATTTGTATAAATTGATTGATTTATTTTAAA
435531 ATATGGATTG
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
36 24 0.80
37 4 0.13
38 2 0.07
ACGTcount: A:0.34, C:0.00, G:0.10, T:0.56
Consensus pattern (36 bp):
ATTTATTTGTATAAATTGATTGATTTATTTTAAATA
Found at i:443859 original size:13 final size:13
Alignment explanation
Indices: 443836--443869 Score: 59
Period size: 13 Copynumber: 2.5 Consensus size: 13
443826 TTTTTTCAAA
443836 AAAACAAAAAAGGC
1 AAAA-AAAAAAGGC
443850 AAAAAAAAAAGGC
1 AAAAAAAAAAGGC
443863 AAAAAAA
1 AAAAAAA
443870 CAAAAAAAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 16 0.80
14 4 0.20
ACGTcount: A:0.79, C:0.09, G:0.12, T:0.00
Consensus pattern (13 bp):
AAAAAAAAAAGGC
Found at i:443895 original size:20 final size:20
Alignment explanation
Indices: 443851--443888 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
443841 AAAAAAGGCA
*
443851 AAAAAAAAAGGCAAAAAAAC
1 AAAAAAAAAGCCAAAAAAAC
*
443871 AAAAAAAGAGCCAAAAAA
1 AAAAAAAAAGCCAAAAAA
443889 GCCAAAATTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.79, C:0.11, G:0.11, T:0.00
Consensus pattern (20 bp):
AAAAAAAAAGCCAAAAAAAC
Found at i:464186 original size:71 final size:71
Alignment explanation
Indices: 464103--464235 Score: 248
Period size: 71 Copynumber: 1.9 Consensus size: 71
464093 GTGATGTTAT
464103 TGTACTAGTTTGTCCTAATATAAACAATTATCCTTTATCATATGTGGCATGCATATATATATATA
1 TGTACTAGTTTGTCCTAATATAAACAATTATCCTTTATCATATGTGGCATGCATATATATATATA
464168 TATATG
66 TATATG
* *
464174 TGTACTAGTTTGTCCTAATATAAGCAATTCTCCTTTATCATATGTGGCATGCATATATATAT
1 TGTACTAGTTTGTCCTAATATAAACAATTATCCTTTATCATATGTGGCATGCATATATATAT
464236 TTATTCATAT
Statistics
Matches: 60, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
71 60 1.00
ACGTcount: A:0.32, C:0.14, G:0.12, T:0.42
Consensus pattern (71 bp):
TGTACTAGTTTGTCCTAATATAAACAATTATCCTTTATCATATGTGGCATGCATATATATATATA
TATATG
Found at i:481529 original size:30 final size:30
Alignment explanation
Indices: 481457--481567 Score: 105
Period size: 30 Copynumber: 3.6 Consensus size: 30
481447 TTTTAAGTTC
* * **
481457 ACCTCTAAATTTTAGATAGAATGCTAATTGG
1 ACCT-TAAACTTTAGATAAAATGCTAATTTA
* * * *
481488 ACCCTAAACTTTGGTTAAAATGCTAATTTT
1 ACCTTAAACTTTAGATAAAATGCTAATTTA
* *
481518 ACCTTACACTTTAGATAAAATACTAATTTA
1 ACCTTAAACTTTAGATAAAATGCTAATTTA
*
481548 ACTCTTAAACTTTAAATAAA
1 AC-CTTAAACTTTAGATAAA
481568 TACCAATTTG
Statistics
Matches: 64, Mismatches: 15, Indels: 2
0.79 0.19 0.02
Matches are distributed among these distances:
30 46 0.72
31 18 0.28
ACGTcount: A:0.40, C:0.15, G:0.08, T:0.37
Consensus pattern (30 bp):
ACCTTAAACTTTAGATAAAATGCTAATTTA
Found at i:481569 original size:30 final size:30
Alignment explanation
Indices: 481503--481576 Score: 87
Period size: 30 Copynumber: 2.5 Consensus size: 30
481493 AAACTTTGGT
* * * *
481503 TAAAATGCTAATTTTACCTTACACTTTAGA
1 TAAAATACTAATTTAACCTTAAACTTTAAA
481533 TAAAATACTAATTTAACTCTTAAACTTTAAA
1 TAAAATACTAATTTAAC-CTTAAACTTTAAA
*
481564 T-AAATACCAATTT
1 TAAAATACTAATTT
481577 GACTGTTGAA
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
30 26 0.68
31 12 0.32
ACGTcount: A:0.43, C:0.15, G:0.03, T:0.39
Consensus pattern (30 bp):
TAAAATACTAATTTAACCTTAAACTTTAAA
Found at i:491832 original size:84 final size:84
Alignment explanation
Indices: 491723--491885 Score: 218
Period size: 84 Copynumber: 1.9 Consensus size: 84
491713 CCATGAAATT
* ** * * *
491723 TCTCCACAATTGTCGAATTCAAAACAATGGTATTTCCATCGTTCTTTTCATGCACCACTGGCATT
1 TCTCCACAATCGTCGAATTCAAAACAATGGTATTTAAATCGTTCTTCTCATGCACCAATGGAATT
491788 GCTACTCCCACTTGCAATC
66 GCTACTCCCACTTGCAATC
* * ** *
491807 TCTCCACAATCGTTGAATTCGAAACAATGGTATTTAAATTTTTCTTCTCATGCACCAATTGAATT
1 TCTCCACAATCGTCGAATTCAAAACAATGGTATTTAAATCGTTCTTCTCATGCACCAATGGAATT
*
491872 GGTACTCCCACTTG
66 GCTACTCCCACTTG
491886 TCTTTCCCCA
Statistics
Matches: 67, Mismatches: 12, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
84 67 1.00
ACGTcount: A:0.26, C:0.26, G:0.12, T:0.35
Consensus pattern (84 bp):
TCTCCACAATCGTCGAATTCAAAACAATGGTATTTAAATCGTTCTTCTCATGCACCAATGGAATT
GCTACTCCCACTTGCAATC
Found at i:496283 original size:20 final size:19
Alignment explanation
Indices: 496258--496297 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
496248 CTCGGTAAGC
496258 TTTCCT-TTCTTTCTTTCTTT
1 TTTCCTGTT-TTTC-TTCTTT
496278 TTTCCTGTTTTTCTTCTTT
1 TTTCCTGTTTTTCTTCTTT
496297 T
1 T
496298 CTGTTTTTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 7 0.37
20 10 0.53
21 2 0.11
ACGTcount: A:0.00, C:0.23, G:0.03, T:0.75
Consensus pattern (19 bp):
TTTCCTGTTTTTCTTCTTT
Found at i:496292 original size:16 final size:16
Alignment explanation
Indices: 496271--496305 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
496261 CCTTTCTTTC
496271 TTTCTT-TTTTCCTGTT
1 TTTCTTCTTTT-CTGTT
496287 TTTCTTCTTTTCTGTT
1 TTTCTTCTTTTCTGTT
496303 TTT
1 TTT
496306 TGTCTCCCCG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 14 0.78
17 4 0.22
ACGTcount: A:0.00, C:0.17, G:0.06, T:0.77
Consensus pattern (16 bp):
TTTCTTCTTTTCTGTT
Found at i:496694 original size:11 final size:11
Alignment explanation
Indices: 496678--496718 Score: 55
Period size: 11 Copynumber: 3.6 Consensus size: 11
496668 AATGGGTTTG
496678 TAATAATTATT
1 TAATAATTATT
* *
496689 TAATAATAATA
1 TAATAATTATT
496700 TAATAATATATT
1 TAATAAT-TATT
496712 TAATAAT
1 TAATAAT
496719 AATAATAATA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
11 16 0.64
12 9 0.36
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (11 bp):
TAATAATTATT
Found at i:496695 original size:3 final size:3
Alignment explanation
Indices: 496689--496748 Score: 56
Period size: 3 Copynumber: 21.0 Consensus size: 3
496679 AATAATTATT
*
496689 TAA TAA TAA T-A TAA TAA T-A TATT TAA TAA TAA TAA TAA TAA -AA
1 TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA
* *
496732 T-T TAA CAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA
496749 ATTTAAATGA
Statistics
Matches: 46, Mismatches: 6, Indels: 10
0.74 0.10 0.16
Matches are distributed among these distances:
2 7 0.15
3 37 0.80
4 2 0.04
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:496743 original size:19 final size:18
Alignment explanation
Indices: 496719--496754 Score: 63
Period size: 19 Copynumber: 1.9 Consensus size: 18
496709 ATTTAATAAT
496719 AATAATAATAAAATTTAAC
1 AATAATAAT-AAATTTAAC
496738 AATAATAATAAATTTAA
1 AATAATAATAAATTTAA
496755 ATGAAAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (18 bp):
AATAATAATAAATTTAAC
Found at i:497037 original size:1 final size:1
Alignment explanation
Indices: 497033--497057 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
497023 TCCCAAAGGC
497033 TTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTT
497058 GGAAACATCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:497177 original size:175 final size:173
Alignment explanation
Indices: 496886--497211 Score: 562
Period size: 175 Copynumber: 1.9 Consensus size: 173
496876 GAAATGTTGA
*
496886 AAACATCATGCACTGAAGGACTTACAGATGACTCGAAGGCATTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCATTGAAAACATCAAAAAGCTCCCGA
* * *
496951 AGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTTGTAAATATCA
66 AGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCATAAGGCTTTTGAAAACATC-
497016 AAAAAACTCCCAAAGGCTTTTTTTTTTTTTTTTTTTTTTTTTGG
130 AAAAAACTCCCAAAGGCTTTTTTTTTTTTTTTTTTTTTTTTTGG
* *
497060 AAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTTGAAAACATCAAAAAGCTCCCG
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGC-ATTGAAAACATCAAAAAGCTCCCG
497125 AAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCATAAGGCTTTTGAAAACATC
65 AAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCATAAGGCTTTTGAAAACATC
* *
497190 AAAAAGCTCCCGAAGGCTTTTT
130 AAAAAACTCCCAAAGGCTTTTT
497212 GGAAACATCA
Statistics
Matches: 143, Mismatches: 8, Indels: 2
0.93 0.05 0.01
Matches are distributed among these distances:
174 58 0.41
175 85 0.59
ACGTcount: A:0.34, C:0.20, G:0.17, T:0.28
Consensus pattern (173 bp):
AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCATTGAAAACATCAAAAAGCTCCCGA
AGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCATAAGGCTTTTGAAAACATCA
AAAAACTCCCAAAGGCTTTTTTTTTTTTTTTTTTTTTTTTTGG
Found at i:497392 original size:76 final size:76
Alignment explanation
Indices: 497053--497622 Score: 1070
Period size: 76 Copynumber: 7.5 Consensus size: 76
497043 TTTTTTTTTT
*
497053 TTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTTGAAAACATCAAAAA
1 TTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGC-TTTGAAAACATCAAAAA
497118 GCTCCCGAAGGC
65 GCTCCCGAAGGC
**
497130 TTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCATAAGGCTTTTGAAAACATCAAAAA
1 TTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGC-TTTGAAAACATCAAAAA
497195 GCTCCCGAAGGC
65 GCTCCCGAAGGC
497207 TTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATC-AAAAG
1 TTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAG
497271 CTCCCGAAGGC
66 CTCCCGAAGGC
497282 TTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAG
1 TTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAG
497347 CTCCCGAAGGC
66 CTCCCGAAGGC
*
497358 TTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGATTTGAAAACATCAAAAAG
1 TTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAG
497423 CTCCCGAAGGC
66 CTCCCGAAGGC
497434 TTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAG
1 TTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAG
497499 CTCCCGAAGGC
66 CTCCCGAAGGC
*
497510 TTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTTTTGAAAACATCAAAAAG
1 TTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAG
497575 CTCCCGAAGGC
66 CTCCCGAAGGC
497586 TTTTTGGAAACATCATGCACTGAAGGACTTACAGATG
1 TTTTTGGAAACATCATGCACTGAAGGACTTACAGATG
497623 TGAGAAATAG
Statistics
Matches: 486, Mismatches: 6, Indels: 3
0.98 0.01 0.01
Matches are distributed among these distances:
75 75 0.15
76 290 0.60
77 121 0.25
ACGTcount: A:0.35, C:0.21, G:0.21, T:0.22
Consensus pattern (76 bp):
TTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAG
CTCCCGAAGGC
Found at i:498767 original size:54 final size:53
Alignment explanation
Indices: 498678--498904 Score: 296
Period size: 54 Copynumber: 4.3 Consensus size: 53
498668 ATAATCACTG
*
498678 GTTCGTAAAACATTTGACAATACATTCATCTTTTCCTGTGGCTTCTGCTCAGAT
1 GTTCGTAAAACATTTGACAACACATTCATC-TTTCCTGTGGCTTCTGCTCAGAT
* * * *
498732 GTTCATAAAACATTTGACCACACATTCATCCTTTCCTGTGGTTTCTGTTCAGAT
1 GTTCGTAAAACATTTGACAACACATTCAT-CTTTCCTGTGGCTTCTGCTCAGAT
* * *
498786 GTTCGTAAAACATTTGACAACACATTCATCATTTCCTGTGGTTTCTGTTTAGAT
1 GTTCGTAAAACATTTGACAACACATTCATC-TTTCCTGTGGCTTCTGCTCAGAT
* ** *
498840 GTTCGTAAAACATTTGACAACATATTCAT-TTTTTTGTGTCTTCTGCTCAGAT
1 GTTCGTAAAACATTTGACAACACATTCATCTTTCCTGTGGCTTCTGCTCAGAT
*
498892 GTTC-TCAAACATT
1 GTTCGTAAAACATT
498905 GAATCTCTTT
Statistics
Matches: 155, Mismatches: 16, Indels: 7
0.87 0.09 0.04
Matches are distributed among these distances:
51 8 0.05
52 21 0.14
53 1 0.01
54 124 0.80
55 1 0.01
ACGTcount: A:0.25, C:0.21, G:0.14, T:0.41
Consensus pattern (53 bp):
GTTCGTAAAACATTTGACAACACATTCATCTTTCCTGTGGCTTCTGCTCAGAT
Found at i:501163 original size:114 final size:114
Alignment explanation
Indices: 500963--501281 Score: 541
Period size: 114 Copynumber: 2.8 Consensus size: 114
500953 ACAATCATGT
* * * * * *
500963 AATTCACCTTTCAATTCCAATGATTGGTTCTGG-GATTCATACCAAACCAGACCAGATAACTTAA
1 AATTCATCTTTCAAATCCAATGATTGATTTTGGAG-TTCATACCAAACCAGATCAGATAACTCAA
*
501027 AGAACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACCATGAGCA
65 AGAACACTTCCAGAAGATGCTATTGAGTCTCCTTATTTCTACCATGAGCA
*
501077 AATTCATCTTTCAAATCTAATGATTGATTTTGGAGTTCATACCAAACCAGATCAGATAACTCAAA
1 AATTCATCTTTCAAATCCAATGATTGATTTTGGAGTTCATACCAAACCAGATCAGATAACTCAAA
*
501142 GAACACTTCCAGAAGATGCTATTGAGTCTCCTTATTTCTACTATGAGCA
66 GAACACTTCCAGAAGATGCTATTGAGTCTCCTTATTTCTACCATGAGCA
501191 AATTCATCTTTCAAATCCAATGATTGATTTTGGAGTTCATACCAAACCAGATCAGATAACTCAAA
1 AATTCATCTTTCAAATCCAATGATTGATTTTGGAGTTCATACCAAACCAGATCAGATAACTCAAA
501256 GAACACTTCCAGAAGATGCTATTGAG
66 GAACACTTCCAGAAGATGCTATTGAG
501282 CACATTATTC
Statistics
Matches: 194, Mismatches: 10, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
114 193 0.99
115 1 0.01
ACGTcount: A:0.34, C:0.21, G:0.14, T:0.30
Consensus pattern (114 bp):
AATTCATCTTTCAAATCCAATGATTGATTTTGGAGTTCATACCAAACCAGATCAGATAACTCAAA
GAACACTTCCAGAAGATGCTATTGAGTCTCCTTATTTCTACCATGAGCA
Found at i:501361 original size:84 final size:84
Alignment explanation
Indices: 501235--501457 Score: 430
Period size: 84 Copynumber: 2.7 Consensus size: 84
501225 GTTCATACCA
501235 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCACATTATTCTTCCAAAT
1 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCACATTATTCTTCCAAAT
501300 TCAATGATTGG-TCTTGTCC
66 TCAATGATTGGTTC-TGTCC
501319 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCACATTATTCTTCCAAAT
1 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCACATTATTCTTCCAAAT
501384 TCAATGATTGGTTCTGTCC
66 TCAATGATTGGTTCTGTCC
501403 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCACATTAT
1 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCACATTAT
501458 ATTTGTTCCA
Statistics
Matches: 138, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
84 136 0.99
85 2 0.01
ACGTcount: A:0.36, C:0.22, G:0.14, T:0.27
Consensus pattern (84 bp):
AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCACATTATTCTTCCAAAT
TCAATGATTGGTTCTGTCC
Found at i:508928 original size:20 final size:21
Alignment explanation
Indices: 508905--508945 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
508895 TATTATATAT
**
508905 ATATTTATGAATAT-ATAAAA
1 ATATTTAACAATATAATAAAA
508925 ATATTTAACAATATAATAAAA
1 ATATTTAACAATATAATAAAA
508946 GAAAAAATTC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.37
Consensus pattern (21 bp):
ATATTTAACAATATAATAAAA
Found at i:509004 original size:19 final size:18
Alignment explanation
Indices: 508959--509011 Score: 65
Period size: 16 Copynumber: 3.0 Consensus size: 18
508949 AAAATTCTAC
* *
508959 TAAAACAATATATTAAA-
1 TAAAACAATAAAATAAAT
508976 -AAAACAATAAAATAAAT
1 TAAAACAATAAAATAAAT
508993 TAAAACATATAAAATAAAT
1 TAAAACA-ATAAAATAAAT
509012 GACTAAATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
16 14 0.45
18 6 0.19
19 11 0.35
ACGTcount: A:0.70, C:0.06, G:0.00, T:0.25
Consensus pattern (18 bp):
TAAAACAATAAAATAAAT
Found at i:509794 original size:20 final size:19
Alignment explanation
Indices: 509769--509808 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
509759 CTCGGTAAGC
509769 TTTCCT-TTCTTTCTTTCTTT
1 TTTCCTGTT-TTTC-TTCTTT
509789 TTTCCTGTTTTTCTTCTTT
1 TTTCCTGTTTTTCTTCTTT
509808 T
1 T
509809 CTGTTTTTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 7 0.37
20 10 0.53
21 2 0.11
ACGTcount: A:0.00, C:0.23, G:0.03, T:0.75
Consensus pattern (19 bp):
TTTCCTGTTTTTCTTCTTT
Found at i:509803 original size:16 final size:16
Alignment explanation
Indices: 509782--509816 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
509772 CCTTTCTTTC
509782 TTTCTT-TTTTCCTGTT
1 TTTCTTCTTTT-CTGTT
509798 TTTCTTCTTTTCTGTT
1 TTTCTTCTTTTCTGTT
509814 TTT
1 TTT
509817 TGTCTCCCCG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 14 0.78
17 4 0.22
ACGTcount: A:0.00, C:0.17, G:0.06, T:0.77
Consensus pattern (16 bp):
TTTCTTCTTTTCTGTT
Found at i:510205 original size:3 final size:3
Alignment explanation
Indices: 510199--510264 Score: 64
Period size: 3 Copynumber: 22.0 Consensus size: 3
510189 AATAATTATT
* *
510199 TAA TAA TAA T-A TAC TAA TAA TAA TATT TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA
* *
510244 TAA -ATT TAA CAA TAA TAA TAA
1 TAA TA-A TAA TAA TAA TAA TAA
510265 ATTTAAATGA
Statistics
Matches: 51, Mismatches: 8, Indels: 8
0.76 0.12 0.12
Matches are distributed among these distances:
2 3 0.06
3 45 0.88
4 3 0.06
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:510228 original size:27 final size:25
Alignment explanation
Indices: 510188--510264 Score: 111
Period size: 24 Copynumber: 3.0 Consensus size: 25
510178 AATGGGTTTG
510188 TAATAATTATTTAATAATAATATACTAA
1 TAATAA-TATTTAATAATAATA-A-TAA
510216 TAATAATATTTAATAATAATAATAA
1 TAATAATATTTAATAATAATAATAA
*
510241 TAATAA-ATTTAACAATAATAATAA
1 TAATAATATTTAATAATAATAATAA
510265 ATTTAAATGA
Statistics
Matches: 48, Mismatches: 1, Indels: 4
0.91 0.02 0.08
Matches are distributed among these distances:
24 17 0.35
25 9 0.19
26 1 0.02
27 15 0.31
28 6 0.12
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (25 bp):
TAATAATATTTAATAATAATAATAA
Found at i:510259 original size:18 final size:18
Alignment explanation
Indices: 510236--510270 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
510226 TAATAATAAT
510236 AATAATAATAAATTTAAC
1 AATAATAATAAATTTAAC
510254 AATAATAATAAATTTAA
1 AATAATAATAAATTTAA
510271 ATGAAAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.34
Consensus pattern (18 bp):
AATAATAATAAATTTAAC
Found at i:511189 original size:24 final size:25
Alignment explanation
Indices: 511147--511199 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 25
511137 ATGTTTAATT
* * *
511147 TATTTTTTATTGTTTTAAATATAAA
1 TATTTTTTATTATTATAAAAATAAA
511172 TATTTTTTA-TATTATAAAAATAAA
1 TATTTTTTATTATTATAAAAATAAA
511196 -ATTT
1 TATTT
511200 AGTACAAAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 4 0.16
24 12 0.48
25 9 0.36
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.57
Consensus pattern (25 bp):
TATTTTTTATTATTATAAAAATAAA
Found at i:512346 original size:182 final size:177
Alignment explanation
Indices: 512039--512489 Score: 600
Period size: 182 Copynumber: 2.5 Consensus size: 177
512029 ACTTTTTTAC
* *
512039 TACCGGTTTTGTCATTTCGAGACCGATTTTGTCATATTTTTACATGTTATATTGTTATGGATTGA
1 TACCGGTTTTGTCATTTCGAGACCGGTTTTGTCATATTTTTACATGTTATATTGTTATGGATCGA
*
512104 TACATTTTTATAAAGTATCGACACTTTATTGGCGCTATAACTTCTTTTCTTTAAAATTCCAAAAG
66 TACATTTTTATAAAGTATCGACACTTTATTAGCGCTATAACTTCTTTTCTTTAAAATTCCAAAAG
* *
512169 TG-TCGATACTTATAATAAAATATCGACACTTTCAACATATCCGGTAGCTCTT
131 TGCT-GATACTTATAATAAAATATCGACACTATCAACATAT-C--T--CGCTT
* * *
512221 TACCGGTTTTGTCATTTCGAGACCGGTTTTGTCATATTTTTACTTGTTATATTATTATAGATCGA
1 TACCGGTTTTGTCATTTCGAGACCGGTTTTGTCATATTTTTACATGTTATATTGTTATGGATCGA
*
512286 TACATTTTTATAAAGTATCGACACTTTATTAGCGCTATAACTT-TTTCTCTTTTAAATTCCAAAA
66 TACATTTTTATAAAGTATCGACACTTTATTAGCGCTATAACTTCTTT-TCTTTAAAATTCCAAAA
* * * *
512350 TTGCTGATACTTATAATAAAGTATCGACACTATCGATATATCTCGCTT
130 GTGCTGATACTTATAATAAAATATCGACACTATCAACATATCTCGCTT
** * ** * * *
512398 TACCTATTTTGTTATTTATAGACCGGTTTTGTCATATTTTTACCTGCTATATTGTTATGGATCAA
1 TACCGGTTTTGTCATTTCGAGACCGGTTTTGTCATATTTTTACATGTTATATTGTTATGGATCGA
* * **
512463 AAAAAATTTATAAAGTATCGACACTTT
66 TACATTTTTATAAAGTATCGACACTTT
512490 CAATATATCC
Statistics
Matches: 240, Mismatches: 27, Indels: 9
0.87 0.10 0.03
Matches are distributed among these distances:
177 82 0.34
179 1 0.00
181 4 0.02
182 152 0.63
183 1 0.00
ACGTcount: A:0.29, C:0.16, G:0.12, T:0.43
Consensus pattern (177 bp):
TACCGGTTTTGTCATTTCGAGACCGGTTTTGTCATATTTTTACATGTTATATTGTTATGGATCGA
TACATTTTTATAAAGTATCGACACTTTATTAGCGCTATAACTTCTTTTCTTTAAAATTCCAAAAG
TGCTGATACTTATAATAAAATATCGACACTATCAACATATCTCGCTT
Found at i:512828 original size:112 final size:112
Alignment explanation
Indices: 512365--513047 Score: 975
Period size: 112 Copynumber: 6.1 Consensus size: 112
512355 GATACTTATA
* * * *
512365 ATAAAGTATCGACACTATCGATATAT-C--T--CGCTTTACCTATTTTGTTATTTATAGACCGGT
1 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
* * * * * **
512425 TTTGTCATATTTTTACCTGCTATATTGTTATGGATCAAAAAAAATTT
66 TTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTT
*
512472 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTG-TTTGTCATTTATAGACCGAT
1 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
*
512536 TTTGTCA-TTTTTTACCTATTATATTGTTATGGATCGATACATTTTT
66 TTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTT
* *
512582 ATAAAGTATCGACACTTTCAATATATTCGGTAGCGCTTTACCTGTTTTGTCATTTACAGACCGGT
1 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
* *
512647 ATTGTCATTTTTTTTTACCTGTTATATTTTTATGGATCGATACATTTTT
66 TTTGTCA--TTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTT
* * * *
512696 ATAAAGTATCAACACTTTCAATATATCCGATAGCGCTTTACCTGTTTTGTCATATATATACCGGT
1 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
* *
512761 TTTGTCATTTTTTTACATGTTATATTGTTATGAATCGATACATTTTT
66 TTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTT
* * *
512808 ATAAAGTATCGACACTTTCAATATATTCGGTAGCGCTTTACATGTTTTGTCATTTATATACCGGT
1 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
* *
512873 TTTGTCATTTTTTTACATGTTATATTATTATGGATCGATACATTTTT
66 TTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTT
* * * *
512920 ATAAAGTATCAATACTTTCAATATATCCGGTAGCGCTTTACCTATTTTGTCTTTTATAGACCGGT
1 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
* * *
512985 TTTGTCATTTTTGTTACCTGTTATATTATTATGGATCAATATATTTTT
66 TTTGTCATTTTT-TTACCTGTTATATTGTTATGGATCGATACATTTTT
513033 ATAAAGTATCGACAC
1 ATAAAGTATCGACAC
513048 AAACCGACAA
Statistics
Matches: 518, Mismatches: 48, Indels: 14
0.89 0.08 0.02
Matches are distributed among these distances:
107 24 0.05
108 1 0.00
110 75 0.14
111 49 0.09
112 222 0.43
113 45 0.09
114 102 0.20
ACGTcount: A:0.27, C:0.15, G:0.13, T:0.45
Consensus pattern (112 bp):
ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
TTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTT
Found at i:513645 original size:50 final size:50
Alignment explanation
Indices: 513560--513668 Score: 146
Period size: 50 Copynumber: 2.2 Consensus size: 50
513550 AGCAGTAAAA
* * *
513560 CGCGCCCCTTGAACTGCGCTATACGCTGATTTGGCGCCACGTGGGTATAG
1 CGCGCCCCTTGAACCGCGATATACGCTGATCTGGCGCCACGTGGGTATAG
** *
513610 CGCGCCCCTTGCCCCGCGATATACGGTGATCTGGCGCCACGTGGGTATAG
1 CGCGCCCCTTGAACCGCGATATACGCTGATCTGGCGCCACGTGGGTATAG
* *
513660 TGCCCCCCT
1 CGCGCCCCT
513669 AGCGCGGATC
Statistics
Matches: 51, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
50 51 1.00
ACGTcount: A:0.14, C:0.35, G:0.29, T:0.22
Consensus pattern (50 bp):
CGCGCCCCTTGAACCGCGATATACGCTGATCTGGCGCCACGTGGGTATAG
Found at i:514073 original size:111 final size:111
Alignment explanation
Indices: 513933--514154 Score: 374
Period size: 111 Copynumber: 2.0 Consensus size: 111
513923 TAGAAATCAT
* *
513933 ATATCTCTACACTTTGCTGATACGGTAACATTTTAAAGTTTTAATTTAATTTATATTA-TTAGTA
1 ATATCTCGACACTTTGCTGATACGGTAACATTTTAAAGTTTTAATTTAATTTAAATTATTTA-TA
* *
513997 ATATTTAGTTGATTTATTTAATGTATGATTATTAGATTAAGAATTAA
65 ATAATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
* *
514044 ATATCTCGACACTTTGTTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTTATAA
1 ATATCTCGACACTTTGCTGATACGGTAACATTTTAAAGTTTTAATTTAATTTAAATTATTTATAA
514109 TAATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
66 TAATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
514155 TTTTTGTAAT
Statistics
Matches: 104, Mismatches: 6, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
111 101 0.97
112 3 0.03
ACGTcount: A:0.36, C:0.07, G:0.11, T:0.47
Consensus pattern (111 bp):
ATATCTCGACACTTTGCTGATACGGTAACATTTTAAAGTTTTAATTTAATTTAAATTATTTATAA
TAATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
Found at i:516035 original size:3 final size:3
Alignment explanation
Indices: 516027--516112 Score: 100
Period size: 3 Copynumber: 28.7 Consensus size: 3
516017 ACCTGCTCAG
** * *
516027 GAC GAC GAC GAC GAC GAC GAC GAC GGT GAC GAC GAC AAC GAC GAT GAC
1 GAC GAC GAC GAC GAC GAC GAC GAC GAC GAC GAC GAC GAC GAC GAC GAC
* * * *
516075 AAT GAC GAC GAC GAC GAT GAT GAC GAC GAC GAC GAC GA
1 GAC GAC GAC GAC GAC GAC GAC GAC GAC GAC GAC GAC GA
516113 TGATGACAGT
Statistics
Matches: 69, Mismatches: 14, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
3 69 1.00
ACGTcount: A:0.35, C:0.27, G:0.33, T:0.06
Consensus pattern (3 bp):
GAC
Found at i:516062 original size:24 final size:24
Alignment explanation
Indices: 516030--516112 Score: 112
Period size: 24 Copynumber: 3.5 Consensus size: 24
516020 TGCTCAGGAC
* *
516030 GACGACGACGACGACGACGACGGT
1 GACGACGACGACGACGATGACGAT
* *
516054 GACGACGACAACGACGATGACAAT
1 GACGACGACGACGACGATGACGAT
* *
516078 GACGACGACGACGATGATGACGAC
1 GACGACGACGACGACGATGACGAT
516102 GACGACGACGA
1 GACGACGACGA
516113 TGATGACAGT
Statistics
Matches: 51, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 51 1.00
ACGTcount: A:0.35, C:0.27, G:0.33, T:0.06
Consensus pattern (24 bp):
GACGACGACGACGACGATGACGAT
Found at i:516116 original size:21 final size:21
Alignment explanation
Indices: 516033--516119 Score: 120
Period size: 21 Copynumber: 4.1 Consensus size: 21
516023 TCAGGACGAC
* *
516033 GACGACGACGACGACGACGGT
1 GACGACGACGACGACGATGAT
* *
516054 GACGACGACAACGACGATGAC
1 GACGACGACGACGACGATGAT
* *
516075 AATGACGACGACGACGATGAT
1 GACGACGACGACGACGATGAT
516096 GACGACGACGACGACGATGAT
1 GACGACGACGACGACGATGAT
516117 GAC
1 GAC
516120 AGTGAGGAGT
Statistics
Matches: 56, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 56 1.00
ACGTcount: A:0.34, C:0.25, G:0.32, T:0.08
Consensus pattern (21 bp):
GACGACGACGACGACGATGAT
Found at i:521302 original size:4 final size:4
Alignment explanation
Indices: 521293--521325 Score: 66
Period size: 4 Copynumber: 8.2 Consensus size: 4
521283 ATAATACTAT
521293 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA T
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA T
521326 ATTTATATAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 29 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTA
Found at i:522584 original size:14 final size:15
Alignment explanation
Indices: 522543--522587 Score: 56
Period size: 18 Copynumber: 2.9 Consensus size: 15
522533 CAAAATATAG
522543 ATATATTTTAACTTGAAA
1 ATATATTTTAA--T-AAA
522561 ATATATTTTAATAAA
1 ATATATTTTAATAAA
522576 ATA-ATTTTAATA
1 ATATATTTTAATA
522588 TTATTTATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
14 9 0.33
15 6 0.22
16 1 0.04
18 11 0.41
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (15 bp):
ATATATTTTAATAAA
Found at i:522710 original size:29 final size:29
Alignment explanation
Indices: 522652--522722 Score: 79
Period size: 29 Copynumber: 2.4 Consensus size: 29
522642 AAAATATATT
* * *
522652 AATATATTTTATTCTTATTTTAATTTTAA
1 AATATATTTTATTCTTATCTTAACTATAA
* *
522681 AATATGTTTTATTTTTATCTTAACTATAAA
1 AATATATTTTATTCTTATCTTAACTAT-AA
*
522711 AAAATATTTTAT
1 AATATATTTTAT
522723 ATTAATTTTA
Statistics
Matches: 34, Mismatches: 7, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
29 22 0.65
30 12 0.35
ACGTcount: A:0.38, C:0.04, G:0.01, T:0.56
Consensus pattern (29 bp):
AATATATTTTATTCTTATCTTAACTATAA
Found at i:523219 original size:20 final size:17
Alignment explanation
Indices: 523194--523249 Score: 58
Period size: 20 Copynumber: 3.1 Consensus size: 17
523184 GTACATTATG
523194 ATTATAAATCATAAAATGAT
1 ATTATAAAT-ATAAAAT--T
523214 ATTATACAATATAAAATT
1 ATTATA-AATATAAAATT
* *
523232 ATTATAAAAATAATATT
1 ATTATAAATATAAAATT
523249 A
1 A
523250 ACATATCAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
17 10 0.30
18 7 0.21
20 13 0.39
21 3 0.09
ACGTcount: A:0.57, C:0.04, G:0.02, T:0.38
Consensus pattern (17 bp):
ATTATAAATATAAAATT
Found at i:523236 original size:18 final size:19
Alignment explanation
Indices: 523194--523239 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 19
523184 GTACATTATG
523194 ATTATAAATCATAAAATGAT
1 ATTATAAATCATAAAAT-AT
523214 ATTATACAAT-ATAAAAT-T
1 ATTATA-AATCATAAAATAT
523232 ATTATAAA
1 ATTATAAA
523240 AATAATATTA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
17 2 0.08
18 7 0.28
20 13 0.52
21 3 0.12
ACGTcount: A:0.57, C:0.04, G:0.02, T:0.37
Consensus pattern (19 bp):
ATTATAAATCATAAAATAT
Found at i:526389 original size:29 final size:30
Alignment explanation
Indices: 526347--526499 Score: 161
Period size: 30 Copynumber: 5.0 Consensus size: 30
526337 ATAGAATCTA
*
526347 TGGTTCTTGTTGTTACAAATTTCAGAC-TT
1 TGGTTCTTGTTGTTACAAATTTCAAACTTT
*
526376 TGGTTCTTGTTGTTGCAAATTTCAAATCTCAAACTTT
1 TGGTTCTTGTTGTT----A---CAAATTTCAAACTTT
526413 TGGTTC---TTGTTACAAATTTCAAACTTT
1 TGGTTCTTGTTGTTACAAATTTCAAACTTT
** *
526440 TGGTTGGTGTTGTTACAAATTTAAAACTTT
1 TGGTTCTTGTTGTTACAAATTTCAAACTTT
*
526470 TGGTTCTTGATGTTACAAATTTCAAACTTT
1 TGGTTCTTGTTGTTACAAATTTCAAACTTT
526500 GGTGATCTAG
Statistics
Matches: 104, Mismatches: 9, Indels: 21
0.78 0.07 0.16
Matches are distributed among these distances:
27 19 0.18
29 14 0.13
30 47 0.45
33 1 0.01
34 5 0.05
36 10 0.10
37 8 0.08
ACGTcount: A:0.25, C:0.13, G:0.15, T:0.47
Consensus pattern (30 bp):
TGGTTCTTGTTGTTACAAATTTCAAACTTT
Found at i:529311 original size:2 final size:2
Alignment explanation
Indices: 529304--529386 Score: 166
Period size: 2 Copynumber: 41.5 Consensus size: 2
529294 AAATTGATAG
529304 TA TA TA TA TA TA TA 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 TA TA TA TA TA TA TA
529346 TA 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 TA T
529387 TTAATGCTAT
Statistics
Matches: 81, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 81 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:534737 original size:15 final size:15
Alignment explanation
Indices: 534696--534738 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
534686 GACTAAATTC
*
534696 TAAAGATTGAAAGTT
1 TAAAGATTGAAAGTG
*
534711 TATAGATT-AAAGTG
1 TAAAGATTGAAAGTG
*
534725 TAAACATTGAAAGT
1 TAAAGATTGAAAGT
534739 TTTGGTGCCT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
14 11 0.48
15 12 0.52
ACGTcount: A:0.47, C:0.02, G:0.19, T:0.33
Consensus pattern (15 bp):
TAAAGATTGAAAGTG
Found at i:540859 original size:24 final size:25
Alignment explanation
Indices: 540805--540851 Score: 87
Period size: 24 Copynumber: 1.9 Consensus size: 25
540795 GCATCGGGAG
540805 CGGCTCTTTTTTGGTAGTCATTACC
1 CGGCTCTTTTTTGGTAGTCATTACC
540830 CGGCTC-TTTTTGGTAGTCATTA
1 CGGCTCTTTTTTGGTAGTCATTA
540852 TCCTGCTCAA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 16 0.73
25 6 0.27
ACGTcount: A:0.13, C:0.21, G:0.21, T:0.45
Consensus pattern (25 bp):
CGGCTCTTTTTTGGTAGTCATTACC
Found at i:541541 original size:75 final size:75
Alignment explanation
Indices: 541418--541568 Score: 284
Period size: 75 Copynumber: 2.0 Consensus size: 75
541408 GATAACATGT
*
541418 ACTCAATCCTCACGCCACATCTTCTGGCATTTCAAGCACTGATAGAATGTCATTGCTGGCTCATC
1 ACTCAATCCTCACGCCACATCTTCTCGCATTTCAAGCACTGATAGAATGTCATTGCTGGCTCATC
541483 AGCTGACCGG
66 AGCTGACCGG
*
541493 ACTCAATCCTCACGCCACATCTTCTCGCATTTCAAGCACTGATAGAATGTCGTTGCTGGCTCATC
1 ACTCAATCCTCACGCCACATCTTCTCGCATTTCAAGCACTGATAGAATGTCATTGCTGGCTCATC
541558 AGCTGACCGG
66 AGCTGACCGG
541568 A
1 A
541569 TCTGCACCTG
Statistics
Matches: 74, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
75 74 1.00
ACGTcount: A:0.24, C:0.31, G:0.19, T:0.26
Consensus pattern (75 bp):
ACTCAATCCTCACGCCACATCTTCTCGCATTTCAAGCACTGATAGAATGTCATTGCTGGCTCATC
AGCTGACCGG
Found at i:547146 original size:2 final size:2
Alignment explanation
Indices: 547139--547165 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
547129 TAATTAATTG
547139 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
547166 CAATGCTGAA
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:550195 original size:2 final size:2
Alignment explanation
Indices: 550183--550218 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
550173 TTGGATCAAC
*
550183 AT AT TT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
550219 TAAATTCTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Done.