Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005223.1 Hibiscus syriacus cultivar Beakdansim tig00011824_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: 548742
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
File 3 of 3
Found at i:352907 original size:3 final size:3
Alignment explanation
Indices: 352899--353001 Score: 106
Period size: 3 Copynumber: 35.0 Consensus size: 3
352889 GCCTATTTTG
* * *
352899 TAA TAA TAA TATT TAT TAA TAA TAA AAA TAAA TAA TAA T-A TAA TAA
1 TAA TAA TAA TA-A TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA
*
352945 TAA TAA TAA TAA TAA TAA TAA -AA AAA TAA -AA TAA -AA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* *
352990 TAG TAA AAA TAA
1 TAA TAA TAA TAA
353002 AACAAATGGA
Statistics
Matches: 85, Mismatches: 9, Indels: 12
0.80 0.08 0.11
Matches are distributed among these distances:
2 8 0.09
3 72 0.85
4 5 0.06
ACGTcount: A:0.68, C:0.00, G:0.01, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:352967 original size:42 final size:39
Alignment explanation
Indices: 352900--353001 Score: 125
Period size: 39 Copynumber: 2.6 Consensus size: 39
352890 CCTATTTTGT
* * * *
352900 AATAATAATATTTATTAATAATAA-AAATAAATAATAATAT
1 AATAATAATA-ATAATAATAATAATAAAAAAATAA-AATAA
352940 AATAATAATAATAATAATAATAATAAAAAAATAAAATAA
1 AATAATAATAATAATAATAATAATAAAAAAATAAAATAA
* *
352979 AATAATAATAATAGTAAAAATAA
1 AATAATAATAATAATAATAATAA
353002 AACAAATGGA
Statistics
Matches: 55, Mismatches: 6, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
39 36 0.65
40 19 0.35
ACGTcount: A:0.69, C:0.00, G:0.01, T:0.30
Consensus pattern (39 bp):
AATAATAATAATAATAATAATAATAAAAAAATAAAATAA
Found at i:353002 original size:36 final size:37
Alignment explanation
Indices: 352900--353008 Score: 132
Period size: 36 Copynumber: 2.9 Consensus size: 37
352890 CCTATTTTGT
* * *
352900 AATAATAATATTTATTAATAATAAAAAT-AAATAATAA
1 AATAATAATA-ATAATAATAATAAAAATAAAAAAATAA
* *
352937 TATAATAATAATAATAATAATAATAATAAAAAAATAA
1 AATAATAATAATAATAATAATAAAAATAAAAAAATAA
*
352974 AATAA-AATAATAATAATAGTAAAAATAAAACAAAT
1 AATAATAATAATAATAATAATAAAAATAAAA-AAAT
353009 GGATGGAAAA
Statistics
Matches: 62, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
36 37 0.60
37 25 0.40
ACGTcount: A:0.69, C:0.01, G:0.01, T:0.29
Consensus pattern (37 bp):
AATAATAATAATAATAATAATAAAAATAAAAAAATAA
Found at i:353683 original size:123 final size:123
Alignment explanation
Indices: 353384--354161 Score: 1247
Period size: 123 Copynumber: 6.3 Consensus size: 123
353374 AAGTCGAACA
* * * * * * * * *
353384 AGTTATTCTCATTATGAACTT--TCTGGAAACGTGGATGTTCATCTATCTTCTTATGTGATAGAA
1 AGTTCTTCTCATTATGAACTTCCTCTGGAAATGTTGATGCTGATCTATCTCCTTCTGTGACAGAG
* * * * * *
353447 TCGAGCAAAAGGTTGAATAAATTCTTCTCATTATGAACTTCTTGTTCTTATTCAGATG
66 TCAAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATG
* *
353505 ATAAGTTCTTCTCATTATGAACTTTCTCTGGAAATGTTGATGCTGATCTATCTCCTTATGTGACA
1 ---AGTTCTTCTCATTATGAACTTCCTCTGGAAATGTTGATGCTGATCTATCTCCTTCTGTGACA
*
353570 GAGTCAAGCAAAAGGTTGAACAAGTTCTTTTCATTATGAACTTCTTCTTCCTCTTCAGATG
63 GAGTCAAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATG
353631 AGTTCTTCTCATTATGAACTTCCTCTGGAAATGTTGATGCTGATCTATCTCCTTCTGTGACAGAG
1 AGTTCTTCTCATTATGAACTTCCTCTGGAAATGTTGATGCTGATCTATCTCCTTCTGTGACAGAG
*
353696 TCAAGCAAAAGGTTGAACAAGTTCTTCTCATTATAAACTTCTTCTTCCTCTTCAGATG
66 TCAAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATG
353754 AGTTCTTCTCATTATGAACTTCCTCTGGAAATGTTGATGCTGATCTATCTCCTTCTGTGACAGAG
1 AGTTCTTCTCATTATGAACTTCCTCTGGAAATGTTGATGCTGATCTATCTCCTTCTGTGACAGAG
*
353819 TCAAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTATTCTTCCTTCTTCAGATG
66 TCAAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCC-TCTTCAGATG
* * *
353878 AGTTCTTCTCATTATGAACTCCCTCTGGAAATATTGATGCTGATCTATCTCATTCTGTGACAGAG
1 AGTTCTTCTCATTATGAACTTCCTCTGGAAATGTTGATGCTGATCTATCTCCTTCTGTGACAGAG
*
353943 TCAAGCAAAAGGTTGAATAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATG
66 TCAAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATG
354001 AGTTCTTCTCATTATGAACTTCCTCTGGAAATGTTGATGCTGATCTATCTCCTTCTGTGACAGAG
1 AGTTCTTCTCATTATGAACTTCCTCTGGAAATGTTGATGCTGATCTATCTCCTTCTGTGACAGAG
*
354066 TCAAGCAAAAGGTTGAACAAGTTCTTCTCATTATGGACTTCTTCTTCCTTCTTCAGATG
66 TCAAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCC-TCTTCAGATG
* *
354125 AGTTCTTCTCATTATGAACTCCCTCTGG-CATGTTGAT
1 AGTTCTTCTCATTATGAACTTCCTCTGGAAATGTTGAT
354162 CCATTGAGTG
Statistics
Matches: 617, Mismatches: 33, Indels: 9
0.94 0.05 0.01
Matches are distributed among these distances:
123 356 0.58
124 175 0.28
126 86 0.14
ACGTcount: A:0.25, C:0.20, G:0.16, T:0.38
Consensus pattern (123 bp):
AGTTCTTCTCATTATGAACTTCCTCTGGAAATGTTGATGCTGATCTATCTCCTTCTGTGACAGAG
TCAAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATG
Found at i:353984 original size:247 final size:246
Alignment explanation
Indices: 353384--354161 Score: 1258
Period size: 247 Copynumber: 3.2 Consensus size: 246
353374 AAGTCGAACA
* * * * * * * * *
353384 AGTTATTCTCATTATGAACT--TTCTGGAAACGTGGATGTTCATCTATCTTCTTATGTGATAGAA
1 AGTTCTTCTCATTATGAACTCCCTCTGGAAATGTTGATGCTGATCTATC-TCTTCTGTGACAGAG
* * * * *
353447 TCGAGCAAAAGGTTGAATAAATTCTTCTCATTATGAACTTCTTGTTCTTATTCAGATGATAAGTT
65 TCAAGCAAAAGGTTGAATAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATG---AGTT
* *
353512 CTTCTCATTATGAACTTTCTCTGGAAATGTTGATGCTGATCTATCTCCTTATGTGACAGAGTCAA
127 CTTCTCATTATGAACTTCCTCTGGAAATGTTGATGCTGATCTATCTCCTTCTGTGACAGAGTCAA
*
353577 GCAAAAGGTTGAACAAGTTCTTTTCATTATGAACTTCTTCTTCC-TCTTCAGATG
192 GCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATG
*
353631 AGTTCTTCTCATTATGAACTTCCTCTGGAAATGTTGATGCTGATCTATCTCCTTCTGTGACAGAG
1 AGTTCTTCTCATTATGAACTCCCTCTGGAAATGTTGATGCTGATCTATCT-CTTCTGTGACAGAG
* *
353696 TCAAGCAAAAGGTTGAACAAGTTCTTCTCATTATAAACTTCTTCTTCCTCTTCAGATGAGTTCTT
65 TCAAGCAAAAGGTTGAATAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTT
353761 CTCATTATGAACTTCCTCTGGAAATGTTGATGCTGATCTATCTCCTTCTGTGACAGAGTCAAGCA
130 CTCATTATGAACTTCCTCTGGAAATGTTGATGCTGATCTATCTCCTTCTGTGACAGAGTCAAGCA
*
353826 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTATTCTTCCTTCTTCAGATG
195 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATG
*
353878 AGTTCTTCTCATTATGAACTCCCTCTGGAAATATTGATGCTGATCTATCTCATTCTGTGACAGAG
1 AGTTCTTCTCATTATGAACTCCCTCTGGAAATGTTGATGCTGATCTATCTC-TTCTGTGACAGAG
353943 TCAAGCAAAAGGTTGAATAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTT
65 TCAAGCAAAAGGTTGAATAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTT
354008 CTCATTATGAACTTCCTCTGGAAATGTTGATGCTGATCTATCTCCTTCTGTGACAGAGTCAAGCA
130 CTCATTATGAACTTCCTCTGGAAATGTTGATGCTGATCTATCTCCTTCTGTGACAGAGTCAAGCA
*
354073 AAAGGTTGAACAAGTTCTTCTCATTATGGACTTCTTCTTCCTTCTTCAGATG
195 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATG
*
354125 AGTTCTTCTCATTATGAACTCCCTCTGG-CATGTTGAT
1 AGTTCTTCTCATTATGAACTCCCTCTGGAAATGTTGAT
354162 CCATTGAGTG
Statistics
Matches: 498, Mismatches: 28, Indels: 11
0.93 0.05 0.02
Matches are distributed among these distances:
246 117 0.23
247 296 0.59
248 1 0.00
249 84 0.17
ACGTcount: A:0.25, C:0.20, G:0.16, T:0.38
Consensus pattern (246 bp):
AGTTCTTCTCATTATGAACTCCCTCTGGAAATGTTGATGCTGATCTATCTCTTCTGTGACAGAGT
CAAGCAAAAGGTTGAATAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTC
TCATTATGAACTTCCTCTGGAAATGTTGATGCTGATCTATCTCCTTCTGTGACAGAGTCAAGCAA
AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATG
Found at i:354070 original size:370 final size:371
Alignment explanation
Indices: 353384--354161 Score: 1260
Period size: 370 Copynumber: 2.1 Consensus size: 371
353374 AAGTCGAACA
* * * * * *
353384 AGTTATTCTCATTATGAACTT--TCTGGAAACGTGGATGTTCATCTATCTTCTTATGTGATAGAA
1 AGTTCTTCTCATTATGAACTTCCTCTGGAAATGTTGATGCTCATCTATCTCCTTATGTGACAGAA
* * * *
353447 TCGAGCAAAAGGTTGAATAAATTCTTCTCATTATGAACTTCTTGTTCTTATTCAGATGATAAGTT
66 TCAAGCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTATTCTTCTTATTCAGATG--AAGTT
** * *
353512 CTTCTCATTATGAACTTTCTCTGGAAATGTTGATGCTGATCTATCTCCTTATGTGACAGAGTCAA
129 CTTCTCATTATGAACTCCCTCTGGAAATATTGATGCTGATCTATCTCATTATGTGACAGAGTCAA
*
353577 GCAAAAGGTTGAACAAGTTCTTTTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCA
194 GCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCA
353642 TTATGAACTTCCTCTGGAAATGTTGATGCTGATCTATCTCCTTCTGTGACAGAGTCAAGCAAAAG
259 TTATGAACTTCCTCTGGAAATGTTGATGCTGATCTATCTCCTTCTGTGACAGAGTCAAGCAAAAG
353707 GTTGAACAAGTTCTTCTCATTATAAACTTCTTCTTCC-TCTTCAGATG
324 GTTGAACAAGTTCTTCTCATTATAAACTTCTTCTTCCTTCTTCAGATG
* * *
353754 AGTTCTTCTCATTATGAACTTCCTCTGGAAATGTTGATGCTGATCTATCTCCTTCTGTGACAGAG
1 AGTTCTTCTCATTATGAACTTCCTCTGGAAATGTTGATGCTCATCTATCTCCTTATGTGACAGAA
* *
353819 TCAAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTATTCTTCCTTCTTCAGATG-AGTTC
66 TCAAGCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTATTCTT-CTTATTCAGATGAAGTTC
*
353883 TTCTCATTATGAACTCCCTCTGGAAATATTGATGCTGATCTATCTCATTCTGTGACAGAGTCAAG
130 TTCTCATTATGAACTCCCTCTGGAAATATTGATGCTGATCTATCTCATTATGTGACAGAGTCAAG
*
353948 CAAAAGGTTGAATAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCAT
195 CAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCAT
354013 TATGAACTTCCTCTGGAAATGTTGATGCTGATCTATCTCCTTCTGTGACAGAGTCAAGCAAAAGG
260 TATGAACTTCCTCTGGAAATGTTGATGCTGATCTATCTCCTTCTGTGACAGAGTCAAGCAAAAGG
**
354078 TTGAACAAGTTCTTCTCATTATGGACTTCTTCTTCCTTCTTCAGATG
325 TTGAACAAGTTCTTCTCATTATAAACTTCTTCTTCCTTCTTCAGATG
* *
354125 AGTTCTTCTCATTATGAACTCCCTCTGG-CATGTTGAT
1 AGTTCTTCTCATTATGAACTTCCTCTGGAAATGTTGAT
354162 CCATTGAGTG
Statistics
Matches: 378, Mismatches: 26, Indels: 8
0.92 0.06 0.02
Matches are distributed among these distances:
370 255 0.67
371 37 0.10
372 75 0.20
373 11 0.03
ACGTcount: A:0.25, C:0.20, G:0.16, T:0.38
Consensus pattern (371 bp):
AGTTCTTCTCATTATGAACTTCCTCTGGAAATGTTGATGCTCATCTATCTCCTTATGTGACAGAA
TCAAGCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTATTCTTCTTATTCAGATGAAGTTCT
TCTCATTATGAACTCCCTCTGGAAATATTGATGCTGATCTATCTCATTATGTGACAGAGTCAAGC
AAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATT
ATGAACTTCCTCTGGAAATGTTGATGCTGATCTATCTCCTTCTGTGACAGAGTCAAGCAAAAGGT
TGAACAAGTTCTTCTCATTATAAACTTCTTCTTCCTTCTTCAGATG
Found at i:354598 original size:22 final size:22
Alignment explanation
Indices: 354543--354600 Score: 98
Period size: 22 Copynumber: 2.6 Consensus size: 22
354533 AATAGAGCCT
* *
354543 TCATCTTTGAAAAGGGAATCTA
1 TCATCTTTGAAGAGAGAATCTA
354565 TCATCTTTGAAGAGAGAATCTA
1 TCATCTTTGAAGAGAGAATCTA
354587 TCATCTTTGAAGAG
1 TCATCTTTGAAGAG
354601 CATAAATGCA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 34 1.00
ACGTcount: A:0.34, C:0.14, G:0.19, T:0.33
Consensus pattern (22 bp):
TCATCTTTGAAGAGAGAATCTA
Found at i:358670 original size:33 final size:33
Alignment explanation
Indices: 358628--358694 Score: 100
Period size: 33 Copynumber: 2.0 Consensus size: 33
358618 TTGAAGGAAG
**
358628 GGTTGTTATGCTCATCT-GATGGAGATACTTCTT
1 GGTTGTTATGCTCATCTCG-TAAAGATACTTCTT
358661 GGTTGTTATGCTCATCTCGTAAAGATACTTCTT
1 GGTTGTTATGCTCATCTCGTAAAGATACTTCTT
358694 G
1 G
358695 TTTCCAGACT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
33 30 0.97
34 1 0.03
ACGTcount: A:0.19, C:0.16, G:0.22, T:0.42
Consensus pattern (33 bp):
GGTTGTTATGCTCATCTCGTAAAGATACTTCTT
Found at i:359226 original size:8 final size:9
Alignment explanation
Indices: 359188--359231 Score: 54
Period size: 9 Copynumber: 4.9 Consensus size: 9
359178 CTTGGTTCAA
359188 TTTTTTTCC
1 TTTTTTTCC
359197 TTTTTTTCC
1 TTTTTTTCC
*
359206 -ATTTTTCC
1 TTTTTTTCC
*
359214 ATTTTTTTCT
1 -TTTTTTTCC
359224 TTTTTTTC
1 TTTTTTTC
359232 AAGTATAATA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
8 7 0.23
9 17 0.57
10 6 0.20
ACGTcount: A:0.05, C:0.18, G:0.00, T:0.77
Consensus pattern (9 bp):
TTTTTTTCC
Found at i:361746 original size:43 final size:44
Alignment explanation
Indices: 361663--361749 Score: 115
Period size: 43 Copynumber: 2.0 Consensus size: 44
361653 CTGTGCATCA
* *
361663 AACAAAACTTTTACATGTAGGAGACAACTTTCAGTTCTAACTTC
1 AACAAAACTTTTACATATAGGAGACAACTTTCACTTCTAACTTC
* *
361707 AACAAAAC-TTTACATATAGGGGATAACTTTC-CTTCCTAACTTC
1 AACAAAACTTTTACATATAGGAGACAACTTTCACTT-CTAACTTC
361750 TCTAAAGCCA
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
42 2 0.05
43 28 0.74
44 8 0.21
ACGTcount: A:0.36, C:0.22, G:0.10, T:0.32
Consensus pattern (44 bp):
AACAAAACTTTTACATATAGGAGACAACTTTCACTTCTAACTTC
Found at i:364097 original size:2 final size:2
Alignment explanation
Indices: 364090--364120 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
364080 ATTTAAACCA
364090 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 A
364121 ATAAAAATAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:365534 original size:3 final size:3
Alignment explanation
Indices: 365526--365628 Score: 90
Period size: 3 Copynumber: 35.0 Consensus size: 3
365516 GCCTGTTTTG
* * * *
365526 TAA TAA TAA TATT TAT TAA TAA TAA AAA TAAA TAA TAA T-A TAT TAA
1 TAA TAA TAA TA-A TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA
365572 TAA TAA TAA TAA TAA TAA TAA -ACA -AA TAA -AA TAA -AA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA
* *
365614 TAA TAG TAA AAA TAA
1 TAA TAA TAA TAA TAA
365629 AACAAATGGA
Statistics
Matches: 83, Mismatches: 10, Indels: 14
0.78 0.09 0.13
Matches are distributed among these distances:
2 8 0.10
3 70 0.84
4 5 0.06
ACGTcount: A:0.66, C:0.01, G:0.01, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:365559 original size:29 final size:26
Alignment explanation
Indices: 365527--365618 Score: 105
Period size: 27 Copynumber: 3.5 Consensus size: 26
365517 CCTGTTTTGT
*
365527 AATAATAAT-ATTTATTAATAATAAA
1 AATAATAATAATATATTAATAATAAA
*
365552 AATAAATAATAATATATTAATAATAAT
1 AAT-AATAATAATATATTAATAATAAA
* ** *
365579 AATAATAATAATAAACAAATAAAATAA
1 AATAATAATAATATATTAATAATA-AA
365606 AATAATAATAATA
1 AATAATAATAATA
365619 GTAAAAATAA
Statistics
Matches: 57, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
25 3 0.05
26 23 0.40
27 31 0.54
ACGTcount: A:0.66, C:0.01, G:0.00, T:0.33
Consensus pattern (26 bp):
AATAATAATAATATATTAATAATAAA
Found at i:365586 original size:36 final size:36
Alignment explanation
Indices: 365542--365635 Score: 118
Period size: 36 Copynumber: 2.6 Consensus size: 36
365532 TAATATTTAT
* * *
365542 TAATAATAAAAATAAA-TAATAATATATTAATAATAA
1 TAATAATAAAAATAAACAAATAAAATA-AAATAATAA
*
365578 TAATAATAATAATAAACAAATAAAATAAAATAATAA
1 TAATAATAAAAATAAACAAATAAAATAAAATAATAA
*
365614 TAATAGTAAAAATAAAACAAAT
1 TAATAATAAAAAT-AAACAAAT
365636 GGATGGAAAA
Statistics
Matches: 50, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
36 34 0.68
37 16 0.32
ACGTcount: A:0.69, C:0.02, G:0.01, T:0.28
Consensus pattern (36 bp):
TAATAATAAAAATAAACAAATAAAATAAAATAATAA
Found at i:369043 original size:30 final size:30
Alignment explanation
Indices: 368977--369047 Score: 97
Period size: 30 Copynumber: 2.4 Consensus size: 30
368967 TTTATAATTA
*
368977 TGAATTAATTAAAATCTAATTTAATTATTC
1 TGAATTAAATAAAATCTAATTTAATTATTC
** * *
369007 CAAATTAAATAAAATCTTATTTAATTATTT
1 TGAATTAAATAAAATCTAATTTAATTATTC
369037 TGAATTAAATA
1 TGAATTAAATA
369048 TTCATTAAAA
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.46, C:0.06, G:0.03, T:0.45
Consensus pattern (30 bp):
TGAATTAAATAAAATCTAATTTAATTATTC
Found at i:382892 original size:21 final size:21
Alignment explanation
Indices: 382868--382912 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
382858 TTTTTTACTG
* *
382868 TGGTTTTGAAATCCCC-TAAGA
1 TGGTTTT-AAAACCCCATAAAA
382889 TGGTTTTAAAACCCCATAAAA
1 TGGTTTTAAAACCCCATAAAA
382910 TGG
1 TGG
382913 CCATTTTGGT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 7 0.33
21 14 0.67
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Consensus pattern (21 bp):
TGGTTTTAAAACCCCATAAAA
Found at i:384511 original size:65 final size:64
Alignment explanation
Indices: 384403--384555 Score: 193
Period size: 65 Copynumber: 2.4 Consensus size: 64
384393 CCCTAATTCA
* * * * * *
384403 AATGCATTTTGTGTACCGATCCACAGCCATGCATCGATACACTCCT-GATTTTATTGAAACATTG
1 AATGTATTTTATGTACCGATGCACAACCATGCATCGATACACTCCTGGATCTT-TTGAAACATCG
*
384467 AATGTATTTTATGTACCGATGCACATACCATGCATCGATACACTCCTGGCTCTTTTGAAACATCG
1 AATGTATTTTATGTACCGATGCACA-ACCATGCATCGATACACTCCTGGATCTTTTGAAACATCG
*
384532 AATGTA-ATTAGTGTACCGATGCAC
1 AATGTATTTTA-TGTACCGATGCAC
384556 CCCAAGTGTA
Statistics
Matches: 78, Mismatches: 8, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
64 25 0.32
65 49 0.63
66 4 0.05
ACGTcount: A:0.29, C:0.23, G:0.16, T:0.32
Consensus pattern (64 bp):
AATGTATTTTATGTACCGATGCACAACCATGCATCGATACACTCCTGGATCTTTTGAAACATCG
Found at i:391251 original size:29 final size:28
Alignment explanation
Indices: 391219--391300 Score: 84
Period size: 29 Copynumber: 3.0 Consensus size: 28
391209 GTGTTTAAAC
* *
391219 ATTTTGAATATTTGGCTTT-GTTTGTTTGG
1 ATTTTGAATATTTAG-TTTGGATTGTTT-G
391248 ATTTTGAATATTTAGTTTGGATTGTTTG
1 ATTTTGAATATTTAGTTTGGATTGTTTG
391276 -TTTTGAATATGTT--TTTGGA-TGTTTG
1 ATTTTGAATAT-TTAGTTTGGATTGTTTG
391301 GTTTGTTTGA
Statistics
Matches: 49, Mismatches: 2, Indels: 8
0.83 0.03 0.14
Matches are distributed among these distances:
25 6 0.12
26 6 0.12
27 10 0.20
28 6 0.12
29 21 0.43
ACGTcount: A:0.17, C:0.01, G:0.23, T:0.59
Consensus pattern (28 bp):
ATTTTGAATATTTAGTTTGGATTGTTTG
Found at i:391304 original size:26 final size:27
Alignment explanation
Indices: 391240--391304 Score: 82
Period size: 26 Copynumber: 2.4 Consensus size: 27
391230 TTGGCTTTGT
391240 TTGTTTGGATTTTGAATATTTAGTTTGGA
1 TTGTTTGG-TTTTGAATATTTA-TTTGGA
391269 TTGTTT-GTTTTGAATATGTT-TTTGGA
1 TTGTTTGGTTTTGAATAT-TTATTTGGA
391295 -TGTTTGGTTT
1 TTGTTTGGTTT
391305 GTTTGAATGA
Statistics
Matches: 34, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
25 5 0.15
26 10 0.29
27 10 0.29
28 3 0.09
29 6 0.18
ACGTcount: A:0.15, C:0.00, G:0.25, T:0.60
Consensus pattern (27 bp):
TTGTTTGGTTTTGAATATTTATTTGGA
Found at i:391305 original size:25 final size:26
Alignment explanation
Indices: 391240--391305 Score: 73
Period size: 25 Copynumber: 2.5 Consensus size: 26
391230 TTGGCTTTGT
391240 TTGTTTGGATTTTGAATATTTAGTTTGGA
1 TTGTTTGG--TTTGAATATTTA-TTTGGA
*
391269 TTGTTTGTTTTGAATATGTT-TTTGGA
1 TTGTTTGGTTTGAATAT-TTATTTGGA
391295 -TGTTTGGTTTG
1 TTGTTTGGTTTG
391306 TTTGAATGAT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
25 10 0.29
26 6 0.18
27 9 0.26
28 2 0.06
29 7 0.21
ACGTcount: A:0.15, C:0.00, G:0.26, T:0.59
Consensus pattern (26 bp):
TTGTTTGGTTTGAATATTTATTTGGA
Found at i:392063 original size:65 final size:65
Alignment explanation
Indices: 391981--392107 Score: 168
Period size: 65 Copynumber: 2.0 Consensus size: 65
391971 GTGTACCGAT
* * *
391981 CCATGAATCGATGCACTCCT-GATTTTATTGAAACATCAAATGCATTTTA-TGTACCGATGCACA
1 CCATGAATCGATACACTCCTGGATCTT-TTGAAACATCAAATGCA-ATTAGTGTACCGATGCACA
392044 TA
64 TA
* * *
392046 CCATGCATCGATACACTCCTGGCTCTTTTGAAACATCAAATGTAATTAGTGTACCGATGCAC
1 CCATGAATCGATACACTCCTGGATCTTTTGAAACATCAAATGCAATTAGTGTACCGATGCAC
392108 CTATGCTCCC
Statistics
Matches: 54, Mismatches: 6, Indels: 4
0.84 0.09 0.06
Matches are distributed among these distances:
64 3 0.06
65 47 0.87
66 4 0.07
ACGTcount: A:0.31, C:0.24, G:0.15, T:0.31
Consensus pattern (65 bp):
CCATGAATCGATACACTCCTGGATCTTTTGAAACATCAAATGCAATTAGTGTACCGATGCACATA
Found at i:397359 original size:24 final size:25
Alignment explanation
Indices: 397323--397372 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 25
397313 GTTGTAACCA
*
397323 GACTCTAGATTTGCTTTGTAATTGG
1 GACTCCAGATTTGCTTTGTAATTGG
* *
397348 GACTCCAG-TTTGTTTTGTATTTGG
1 GACTCCAGATTTGCTTTGTAATTGG
397372 G
1 G
397373 CCCCGATTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
24 15 0.68
25 7 0.32
ACGTcount: A:0.16, C:0.12, G:0.26, T:0.46
Consensus pattern (25 bp):
GACTCCAGATTTGCTTTGTAATTGG
Found at i:398453 original size:47 final size:45
Alignment explanation
Indices: 398372--398498 Score: 157
Period size: 47 Copynumber: 2.8 Consensus size: 45
398362 ATATAAAATC
* * *
398372 ACTTACCATTTATCCCAGAAGCTCGTAAGATTATTTTTCCAATAT
1 ACTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTTCCAATAT
*
398417 ACTTACCATTTAAATTCCATAAGCTCGTAAGCTTATTTTTTCAATAT
1 ACTTACCATTT--ATTCCATAAGCTCGTAAGCTTATTTTTCCAATAT
* * * *
398464 ACTTGCCA-TTATTGCGTAAGCTCATAAGCTTATTT
1 ACTTACCATTTATTCCATAAGCTCGTAAGCTTATTT
398499 GCATGGTTAC
Statistics
Matches: 72, Mismatches: 8, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
44 22 0.31
45 11 0.15
46 2 0.03
47 37 0.51
ACGTcount: A:0.30, C:0.20, G:0.09, T:0.40
Consensus pattern (45 bp):
ACTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTTCCAATAT
Found at i:398660 original size:40 final size:40
Alignment explanation
Indices: 398603--398684 Score: 155
Period size: 40 Copynumber: 2.0 Consensus size: 40
398593 ACCGTAGTGC
398603 TACACATAAGGTCGTGCCCACCATATACACTGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACTGAAGTGTAT
*
398643 TACACATAAGGTTGTGCCCACCATATACACTGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACTGAAGTGTAT
398683 TA
1 TA
398685 TAAACCTGCA
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.33, C:0.23, G:0.17, T:0.27
Consensus pattern (40 bp):
TACACATAAGGTCGTGCCCACCATATACACTGAAGTGTAT
Found at i:402559 original size:20 final size:20
Alignment explanation
Indices: 402536--402578 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
402526 TTTTTTTTCA
402536 TCTCTCATTCTTTTTCTCTT
1 TCTCTCATTCTTTTTCTCTT
** *
402556 TCTCTTTTTCTTTTTCTTTT
1 TCTCTCATTCTTTTTCTCTT
402576 TCT
1 TCT
402579 TTTTATATTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.02, C:0.26, G:0.00, T:0.72
Consensus pattern (20 bp):
TCTCTCATTCTTTTTCTCTT
Found at i:402581 original size:6 final size:6
Alignment explanation
Indices: 402543--402658 Score: 92
Period size: 6 Copynumber: 18.8 Consensus size: 6
402533 TCATCTCTCA
* *
402543 TTCTTT TTCTCTT TCTCTTT TTCTTT TTCTTT TTCTTT TT-ATA TT-TTT
1 TTCTTT TTCT-TT T-TCTTT TTCTTT TTCTTT TTCTTT TTCTTT TTCTTT
* * * * * *
402591 TTCTTC TTCTTC TTCTTC TTCTTT TTCATT TTCATT TTCATT TTCATTTT
1 TTCTTT TTCTTT TTCTTT TTCTTT TTCTTT TTCTTT TTCTTT TTC--TTT
*
402641 ATTATTT TTCTTT TTCTT
1 -TTCTTT TTCTTT TTCTT
402659 ATATAATATA
Statistics
Matches: 94, Mismatches: 10, Indels: 12
0.81 0.09 0.10
Matches are distributed among these distances:
5 6 0.06
6 72 0.77
7 9 0.10
8 5 0.05
9 2 0.02
ACGTcount: A:0.07, C:0.18, G:0.00, T:0.75
Consensus pattern (6 bp):
TTCTTT
Found at i:402590 original size:40 final size:40
Alignment explanation
Indices: 402546--402622 Score: 102
Period size: 40 Copynumber: 1.9 Consensus size: 40
402536 TCTCTCATTC
* * *
402546 TTTTTCTCTT-TCTCTTTTTCTTTTTCTTTTTCTTTTTATA
1 TTTTTCTCTTCT-TCTTCTTCTTCTTCTTTTTCATTTTATA
*
402586 TTTTTTTCTTCTTCTTCTTCTTCTTCTTTTTCATTTT
1 TTTTTCTCTTCTTCTTCTTCTTCTTCTTTTTCATTTT
402623 CATTTTCATT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
40 31 0.97
41 1 0.03
ACGTcount: A:0.04, C:0.19, G:0.00, T:0.77
Consensus pattern (40 bp):
TTTTTCTCTTCTTCTTCTTCTTCTTCTTTTTCATTTTATA
Found at i:405392 original size:47 final size:45
Alignment explanation
Indices: 405320--405492 Score: 231
Period size: 47 Copynumber: 3.8 Consensus size: 45
405310 TATAAAATCT
* * * *
405320 CTTACCATTTATCCCATAAGTTCGTAAGCTTATTTTACCAAAATA
1 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTTCCAATATA
405365 CTTACCATTTAAATTCCATAAGCTCGTAAGCTTATTTTTCCAATATA
1 CTTACCATTT--ATTCCATAAGCTCGTAAGCTTATTTTTCCAATATA
* *
405412 CTTACTATTTAAATTTCATAAGCTCGTAAGCTTATTTTTCCAATATA
1 CTTACCATTT--ATTCCATAAGCTCGTAAGCTTATTTTTCCAATATA
* *
405459 CTTGCCA-TTATTCCATAAGCTCATAAGCTTATTT
1 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTT
405493 GCATGGTTAC
Statistics
Matches: 116, Mismatches: 10, Indels: 5
0.89 0.08 0.04
Matches are distributed among these distances:
44 23 0.20
45 10 0.09
46 2 0.02
47 81 0.70
ACGTcount: A:0.31, C:0.21, G:0.07, T:0.41
Consensus pattern (45 bp):
CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTTCCAATATA
Found at i:407971 original size:81 final size:82
Alignment explanation
Indices: 407832--408362 Score: 661
Period size: 82 Copynumber: 6.5 Consensus size: 82
407822 GGGTATTACA
* * **
407832 ATATGTTCCTCTTTTTTGGGTAGTCAGATCAATTTTGGAAGATGAGTTTGCTATTCTATTCATTC
1 ATATGTTCCTCTTTTTCGGGTAGTCAGATCAATTTTGGAAGACGAGTTTGCTCCTCTATTCATTC
407897 A-GGGAGATCAGACTTG
66 AGGGGAGATCAGACTTG
* * *
407913 ATATGTTCCTCTTTTTCGGGTAGTCAGATCAATTTTGGAAGGCGGGTTTTCTCCTCTATTCATTC
1 ATATGTTCCTCTTTTTCGGGTAGTCAGATCAATTTTGGAAGACGAGTTTGCTCCTCTATTCATTC
407978 AGGGGAGATCAGACTTG
66 AGGGGAGATCAGACTTG
* * *
407995 ATATGTTCCTTTTTTCTCGGGTAGTCAGATCAATTTTGGAAGATGAGTCTGCTCCTCTATTCATT
1 ATATGTTCCTCTTTT-TCGGGTAGTCAGATCAATTTTGGAAGACGAGTTTGCTCCTCTATTCATT
* *
408060 CAGGGGAGATTAAACTTG
65 CAGGGGAGATCAGACTTG
* *
408078 ATATGTTCCTCTTTTTCGGGTAGTTAGATCAATTTTGGAAGAC-AGTTCTGCTCCTCTATTCTTT
1 ATATGTTCCTCTTTTTCGGGTAGTCAGATCAATTTTGGAAGACGAGTT-TGCTCCTCTATTCATT
*
408142 CAGGGGGGATCAGACTTG
65 CAGGGGAGATCAGACTTG
* * *
408160 ATTTGTTCCT-TTTTT-GGGTA---AGATCAATTTTGGAAGACGTA-TTTGCTCCACTAGTCATT
1 ATATGTTCCTCTTTTTCGGGTAGTCAGATCAATTTTGGAAGACG-AGTTTGCTCCTCTATTCATT
* *
408219 CAGGGGTGATCAGAATTG
65 CAGGGGAGATCAGACTTG
* ** * * *
408237 ATATGTTCCTCTTTTTTGGGTAGTCAGATTTATTTTGGAAGAC-AGGTTTGCT-TTACTCTTCTT
1 ATATGTTCCTCTTTTTCGGGTAGTCAGATCAATTTTGGAAGACGA-GTTTGCTCCT-CTATTCAT
* * *
408300 TTA-GGGAGATAAGACTCG
64 TCAGGGGAGATCAGACTTG
* *
408318 ATATGTTCCTCTTTTTTGGGTAGTCAGATCAATTTTGGAAAACGA
1 ATATGTTCCTCTTTTTCGGGTAGTCAGATCAATTTTGGAAGACGA
408363 TTATATTCCA
Statistics
Matches: 391, Mismatches: 45, Indels: 27
0.84 0.10 0.06
Matches are distributed among these distances:
77 56 0.14
78 7 0.02
79 6 0.02
80 6 0.02
81 118 0.30
82 124 0.32
83 74 0.19
ACGTcount: A:0.22, C:0.16, G:0.23, T:0.40
Consensus pattern (82 bp):
ATATGTTCCTCTTTTTCGGGTAGTCAGATCAATTTTGGAAGACGAGTTTGCTCCTCTATTCATTC
AGGGGAGATCAGACTTG
Found at i:408397 original size:81 final size:81
Alignment explanation
Indices: 407832--408384 Score: 570
Period size: 81 Copynumber: 6.8 Consensus size: 81
407822 GGGTATTACA
* * ***
407832 ATATGTTCCTCTTTTTTGGGTAGTCAGATCAATTTTGGAAGATGAGTTTGCTATTCTATTCATTC
1 ATATGTTCCTCTTTTTTGGGTAGTCAGATCAATTTTGGAAGACGA-TTTGTTCCACTATTCATTC
407897 A-GGGAGATCAGACTTG
65 AGGGGAGATCAGACTTG
* * * *
407913 ATATGTTCCTCTTTTTCGGGTAGTCAGATCAATTTTGGAAGGCGGGTTT-TCTCCTCTATTCATT
1 ATATGTTCCTCTTTTTTGGGTAGTCAGATCAATTTTGGAAGAC-GATTTGT-TCCACTATTCATT
407977 CAGGGGAGATCAGACTTG
64 CAGGGGAGATCAGACTTG
* * * *
407995 ATATGTTCCT-TTTTTCTCGGGTAGTCAGATCAATTTTGGAAGATGAGTCTGCTCCTCTATTCAT
1 ATATGTTCCTCTTTTT-T-GGGTAGTCAGATCAATTTTGGAAGACGA-TTTGTTCCACTATTCAT
* *
408059 TCAGGGGAGATTAAACTTG
63 TCAGGGGAGATCAGACTTG
* * * * *
408078 ATATGTTCCTCTTTTTCGGGTAGTTAGATCAATTTTGGAAGAC-AGTTCTGCTCCTCTATTCTTT
1 ATATGTTCCTCTTTTTTGGGTAGTCAGATCAATTTTGGAAGACGA-TT-TGTTCCACTATTCATT
*
408142 CAGGGGGGATCAGACTTG
64 CAGGGGAGATCAGACTTG
* * *
408160 ATTTGTT-C-CTTTTTTGGGTA---AGATCAATTTTGGAAGACGTATTTGCTCCACTAGTCATTC
1 ATATGTTCCTCTTTTTTGGGTAGTCAGATCAATTTTGGAAGACG-ATTTGTTCCACTATTCATTC
* *
408220 AGGGGTGATCAGAATTG
65 AGGGGAGATCAGACTTG
** * * * *
408237 ATATGTTCCTCTTTTTTGGGTAGTCAGATTTATTTTGGAAGACAGGTTTGCTT-TACTCTTCTTT
1 ATATGTTCCTCTTTTTTGGGTAGTCAGATCAATTTTGGAAGAC-GATTTG-TTCCACTATTCATT
* * *
408301 TA-GGGAGATAAGACTCG
64 CAGGGGAGATCAGACTTG
* * * *
408318 ATATGTTCCTCTTTTTTGGGTAGTCAGATCAATTTTGGAAAACGATTATATTCCACTCTTCTTTC
1 ATATGTTCCTCTTTTTTGGGTAGTCAGATCAATTTTGGAAGACGATT-TGTTCCACTATTCATTC
408383 AG
65 AG
408385 AGAGATAAGA
Statistics
Matches: 400, Mismatches: 51, Indels: 41
0.81 0.10 0.08
Matches are distributed among these distances:
77 53 0.13
78 3 0.01
79 13 0.03
80 16 0.04
81 128 0.32
82 115 0.29
83 67 0.17
84 5 0.01
ACGTcount: A:0.22, C:0.16, G:0.22, T:0.40
Consensus pattern (81 bp):
ATATGTTCCTCTTTTTTGGGTAGTCAGATCAATTTTGGAAGACGATTTGTTCCACTATTCATTCA
GGGGAGATCAGACTTG
Found at i:408445 original size:55 final size:55
Alignment explanation
Indices: 408369--408496 Score: 148
Period size: 55 Copynumber: 2.3 Consensus size: 55
408359 ACGATTATAT
* * * * * * *
408369 TCCACTCTTCTTTCAGAGAGATAAGACTCAAGAAATATTTGGAAGACGGGTCTGC
1 TCCACTGTTCGTTCAGGGAGATAAGACTAAAAAAAGATTTGGAAAACGGGTCTGC
* * * *
408424 TCCATTTTTCGTTCAGGGAGATAAGACTAAAAAAAGCTTTGGAAAATGGGTCTGC
1 TCCACTGTTCGTTCAGGGAGATAAGACTAAAAAAAGATTTGGAAAACGGGTCTGC
*
408479 TCCACTGTTCTTTCAGGG
1 TCCACTGTTCGTTCAGGG
408497 GGAGATCAGA
Statistics
Matches: 60, Mismatches: 13, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
55 60 1.00
ACGTcount: A:0.29, C:0.19, G:0.23, T:0.30
Consensus pattern (55 bp):
TCCACTGTTCGTTCAGGGAGATAAGACTAAAAAAAGATTTGGAAAACGGGTCTGC
Found at i:408679 original size:89 final size:90
Alignment explanation
Indices: 408495--408687 Score: 264
Period size: 89 Copynumber: 2.2 Consensus size: 90
408485 GTTCTTTCAG
* * * * *
408495 GGGGAGATCAGACTTGAGGATTGATTTTCTTCGCTTCTTCTTTAGGAAGGCCAAATCTGAAATAA
1 GGGGAGATCAGACTAGAGGATTGATTTGCTTCACTACTTCTTTAGGAAGACCAAATCTGAAATAA
*
408560 GAAGAATTTATTCCACTACACTTTC
66 GAAGAATTGATTCCACTACACTTTC
*
408585 AGGGAGATCAGACTAGA-GATTGATTTGCTTCACTACTTCTTTAGGAAGACCAAATCTGAAATAA
1 GGGGAGATCAGACTAGAGGATTGATTTGCTTCACTACTTCTTTAGGAAGACCAAATCTGAAATAA
* * * *
408649 GAAGAATCTGCTT-CTCTACTCTTTT
66 GAAGAAT-TGATTCCACTACACTTTC
408674 GGGGAGATCAGACT
1 GGGGAGATCAGACT
408688 CATGATCTTT
Statistics
Matches: 90, Mismatches: 12, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
89 72 0.80
90 18 0.20
ACGTcount: A:0.30, C:0.18, G:0.21, T:0.32
Consensus pattern (90 bp):
GGGGAGATCAGACTAGAGGATTGATTTGCTTCACTACTTCTTTAGGAAGACCAAATCTGAAATAA
GAAGAATTGATTCCACTACACTTTC
Found at i:408879 original size:62 final size:62
Alignment explanation
Indices: 408782--409315 Score: 494
Period size: 62 Copynumber: 8.6 Consensus size: 62
408772 GTCAAAAAAA
* * * * *
408782 TGACTTCTCTTTACGAGGAAGTCAAGGATTGACTCTACTGGGGAGTCAGGGATAATAAAGGT
1 TGACTTCTCTTCACGAGGAAATCAAGGATTGACTCTACTAGGGAGTCAGAGATAACAAAGGT
* * * *
408844 TGACTTCTCTTCACAAGGAAATCAAGGATTGACTCTACTGGGGAGTCAGAAATAACAAATGT
1 TGACTTCTCTTCACGAGGAAATCAAGGATTGACTCTACTAGGGAGTCAGAGATAACAAAGGT
* *
408906 TGACTTATCTTCATGA-GAAAGTCAAGGATTGACTCTACTA-GGAGTCAG-GAGTAACAAAGGT
1 TGACTTCTCTTCACGAGGAAA-TCAAGGATTGACTCTACTAGGGAGTCAGAGA-TAACAAAGGT
* * * * * * **
408967 TGACTTCTCTTCATGAGGAAATCAAAGATTGACTCTGCTAGGGAGTTATAGATAAAAAAAAT
1 TGACTTCTCTTCACGAGGAAATCAAGGATTGACTCTACTAGGGAGTCAGAGATAACAAAGGT
* * * * * * **
409029 TGACTTCTCTTCATGAGGAAATCAAAGATTGACTCTGCTAGGGAGTTATAGATAAAAAAAAT
1 TGACTTCTCTTCACGAGGAAATCAAGGATTGACTCTACTAGGGAGTCAGAGATAACAAAGGT
* * * *
409091 TGACTTCTCTTCATG-CGAAAGTCAAGGATCGACTCTACTGGGGAGTCAG-GAATAACAAAGGT
1 TGACTTCTCTTCACGAGGAAA-TCAAGGATTGACTCTACTAGGGAGTCAGAG-ATAACAAAGGT
* * * * *
409153 TGGCTTCTCTTCACGAGGAAGTCAAGGATTGACTCTTCTAAGGAGTCA-AGAGTAACAAAGTT
1 TGACTTCTCTTCACGAGGAAATCAAGGATTGACTCTACTAGGGAGTCAGAGA-TAACAAAGGT
* * *
409215 TGAATTCTCTTCATGA-GAAAGTCAAGGATTAACTCCT-CTTCATGAGGAAGTCA-AGGATAACA
1 TGACTTCTCTTCACGAGGAAA-TCAAGGATTGACT-CTAC-T-A-G-GG-AGTCAGA-GATAACA
*
409277 AAGAT
58 AAGGT
* * *
409282 TAACTTCTCTTTACGAGG-AATCAAGGATTTACTC
1 TGACTTCTCTTCACGAGGAAATCAAGGATTGACTC
409316 CTCTTCACGA
Statistics
Matches: 401, Mismatches: 52, Indels: 35
0.82 0.11 0.07
Matches are distributed among these distances:
60 1 0.00
61 62 0.15
62 282 0.70
63 8 0.02
64 1 0.00
65 1 0.00
66 14 0.03
67 29 0.07
68 3 0.01
ACGTcount: A:0.34, C:0.16, G:0.22, T:0.28
Consensus pattern (62 bp):
TGACTTCTCTTCACGAGGAAATCAAGGATTGACTCTACTAGGGAGTCAGAGATAACAAAGGT
Found at i:408998 original size:29 final size:29
Alignment explanation
Indices: 408960--409062 Score: 77
Period size: 29 Copynumber: 3.4 Consensus size: 29
408950 TCAGGAGTAA
*
408960 CAAAGGTTGACTTCTCTTCATGAGGAAAT
1 CAAAGATTGACTTCTCTTCATGAGGAAAT
* *
408989 CAAAGATTGAC-TCTGC-T-AGGGAGTTATAGAT
1 CAAAGATTGACTTCT-CTTCA-TGAG-GA-A-AT
* *
409020 AAAAAAAATTGACTTCTCTTCATGAGGAAAT
1 --CAAAGATTGACTTCTCTTCATGAGGAAAT
409051 CAAAGATTGACT
1 CAAAGATTGACT
409063 CTGCTAGGGA
Statistics
Matches: 55, Mismatches: 9, Indels: 20
0.65 0.11 0.24
Matches are distributed among these distances:
27 1 0.02
28 7 0.13
29 22 0.40
30 1 0.02
31 4 0.07
32 1 0.02
33 11 0.20
34 7 0.13
35 1 0.02
ACGTcount: A:0.37, C:0.15, G:0.19, T:0.29
Consensus pattern (29 bp):
CAAAGATTGACTTCTCTTCATGAGGAAAT
Found at i:409096 original size:185 final size:185
Alignment explanation
Indices: 408782--409249 Score: 580
Period size: 185 Copynumber: 2.5 Consensus size: 185
408772 GTCAAAAAAA
* * * * *
408782 TGACTTCTCTTTACGAGGAAGTCAAGGATTGACTCTACTGGGGAGTCAGGGATAATAAAGGTTGA
1 TGACTTCTCTTCACGAGGAAGTCAAGGATTGACTCTACTAGGGAGTCA-AGATAAAAAAGATTGA
** * * **
408847 CTTCTCTTCACAAGGAAATCAAGGATTGACTCTACTGGGGAGTCAGAAATAACAAATGTTGACTT
65 CTTCTCTTCATGAGGAAATCAAGGATTGACTCTACTAGGGAGTCAGAAATAAAAAAAATTGACTT
* *
408912 ATCTTCATGAGAAAGTCAAGGATTGACTCTACT-AGGAGTCAGGAGTAACAAAGGT
130 ATCTTCATGAGAAAGTCAAGGATCGACTCTACTGAGGAGTCAGGAATAACAAAGGT
* * * * * *
408967 TGACTTCTCTTCATGAGGAAATCAAAGATTGACTCTGCTAGGGAGTTATAGATAAAAAAAATTGA
1 TGACTTCTCTTCACGAGGAAGTCAAGGATTGACTCTACTAGGGAGTCA-AGATAAAAAAGATTGA
* * * * *
409032 CTTCTCTTCATGAGGAAATCAAAGATTGACTCTGCTAGGGAGTTATAGATAAAAAAAATTGACTT
65 CTTCTCTTCATGAGGAAATCAAGGATTGACTCTACTAGGGAGTCAGAAATAAAAAAAATTGACTT
* * *
409097 CTCTTCATGCGAAAGTCAAGGATCGACTCTACTGGGGAGTCAGGAATAACAAAGGT
130 ATCTTCATGAGAAAGTCAAGGATCGACTCTACTGAGGAGTCAGGAATAACAAAGGT
* * * * *
409153 TGGCTTCTCTTCACGAGGAAGTCAAGGATTGACTCTTCTAAGGAGTCAAGAGTAACAAAGTTTGA
1 TGACTTCTCTTCACGAGGAAGTCAAGGATTGACTCTACTAGGGAGTCAAGA-TAAAAAAGATTGA
* *
409218 ATTCTCTTCATGA-GAAAGTCAAGGATTAACTC
65 CTTCTCTTCATGAGGAAA-TCAAGGATTGACTC
409250 CTCTTCATGA
Statistics
Matches: 239, Mismatches: 41, Indels: 5
0.84 0.14 0.02
Matches are distributed among these distances:
185 144 0.60
186 95 0.40
ACGTcount: A:0.34, C:0.16, G:0.23, T:0.27
Consensus pattern (185 bp):
TGACTTCTCTTCACGAGGAAGTCAAGGATTGACTCTACTAGGGAGTCAAGATAAAAAAGATTGAC
TTCTCTTCATGAGGAAATCAAGGATTGACTCTACTAGGGAGTCAGAAATAAAAAAAATTGACTTA
TCTTCATGAGAAAGTCAAGGATCGACTCTACTGAGGAGTCAGGAATAACAAAGGT
Found at i:409411 original size:29 final size:29
Alignment explanation
Indices: 409369--409432 Score: 94
Period size: 29 Copynumber: 2.2 Consensus size: 29
409359 GGTTAACAAA
*
409369 GATTGACTTCTCTTCACGA-GGAAGTCAAG
1 GATTGAATTCTCTTCACGAGGGAA-TCAAG
*
409398 GATTGAATTCTCTTCATGAGGGAATCAAG
1 GATTGAATTCTCTTCACGAGGGAATCAAG
409427 GATTGA
1 GATTGA
409433 CTCTACTAGA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
29 28 0.88
30 4 0.12
ACGTcount: A:0.30, C:0.16, G:0.25, T:0.30
Consensus pattern (29 bp):
GATTGAATTCTCTTCACGAGGGAATCAAG
Found at i:409439 original size:91 final size:91
Alignment explanation
Indices: 409263--409488 Score: 269
Period size: 91 Copynumber: 2.5 Consensus size: 91
409253 TTCATGAGGA
* * *
409263 AGTCAAGG-ATAACAAAGATTAACTTCTCTTTACGAGGAA-TCAAGGATTTACTCCTCTTCACGA
1 AGTC-AGGAATAACAAAGATTAACTTCTCTTCACGAGGAAGTCAAGGATTGAATCCTCTTCACGA
* * *
409326 GGAAGTTAAGAATTGACTCTACTGGGG
65 GGAAGTCAAGAATTGACTCTACTAGAG
* ** * * *
409353 TGTCAGGGTTAACAAAGATTGACTTCTCTTCACGAGGAAGTCAAGGATTGAATTCTCTTCATGAG
1 AGTCAGGAATAACAAAGATTAACTTCTCTTCACGAGGAAGTCAAGGATTGAATCCTCTTCACGA-
*
409418 GGAA-TCAAGGATTGACTCTACTAGAG
65 GGAAGTCAAGAATTGACTCTACTAGAG
* * *
409444 AGTCAGGAATAACAAAGATTAACTTATCTTCATGAGAAAGTCAAG
1 AGTCAGGAATAACAAAGATTAACTTCTCTTCACGAGGAAGTCAAG
409489 TTGAAATTTC
Statistics
Matches: 114, Mismatches: 19, Indels: 5
0.83 0.14 0.04
Matches are distributed among these distances:
89 3 0.03
90 31 0.27
91 76 0.67
92 4 0.04
ACGTcount: A:0.35, C:0.16, G:0.22, T:0.27
Consensus pattern (91 bp):
AGTCAGGAATAACAAAGATTAACTTCTCTTCACGAGGAAGTCAAGGATTGAATCCTCTTCACGAG
GAAGTCAAGAATTGACTCTACTAGAG
Found at i:412660 original size:31 final size:31
Alignment explanation
Indices: 412622--412825 Score: 291
Period size: 31 Copynumber: 6.5 Consensus size: 31
412612 TATAATAATA
* *
412622 TGTCCATATGTCCCGAATAACATAGGTAAAT
1 TGTCCATATGTCCCGAAGAACATAGGTAAAC
* *
412653 TGTCCATATATCCCAAAGAACATAGGTAAAC
1 TGTCCATATGTCCCGAAGAACATAGGTAAAC
*
412684 TGTCCATATGTCCCGAAGAACATAGGTAAAA
1 TGTCCATATGTCCCGAAGAACATAGGTAAAC
412715 TGTCCATATGTCCCGAAGAACATAGGTAAAC
1 TGTCCATATGTCCCGAAGAACATAGGTAAAC
* *
412746 TGTCCATATGTCCCAAATAACATAGGTAAAC
1 TGTCCATATGTCCCGAAGAACATAGGTAAAC
* * * *
412777 TATCCATATATCCCGAAGAACATAGATAATAA
1 TGTCCATATGTCCCGAAGAACATAGGTAA-AC
*
412809 TGTCCATATATCCCGAA
1 TGTCCATATGTCCCGAA
412826 AGACATAAGT
Statistics
Matches: 155, Mismatches: 17, Indels: 1
0.90 0.10 0.01
Matches are distributed among these distances:
31 138 0.89
32 17 0.11
ACGTcount: A:0.39, C:0.22, G:0.15, T:0.25
Consensus pattern (31 bp):
TGTCCATATGTCCCGAAGAACATAGGTAAAC
Found at i:412783 original size:93 final size:94
Alignment explanation
Indices: 412616--412825 Score: 334
Period size: 93 Copynumber: 2.3 Consensus size: 94
412606 AGCTCATATA
* *
412616 ATAAT-ATGTCCATATGTCCCGAATAACATAGGTAAATTGTCCATATATCCCAAAGAACATAGGT
1 ATAATAATGTCCATATGTCCCGAAGAACATAGGTAAACTGTCCATATATCCCAAAGAACATAGGT
* *
412680 AAACTGTCCATATGTCCCGAAGAACATAG
66 AAACTATCCATATATCCCGAAGAACATAG
* * *
412709 GTAA-AATGTCCATATGTCCCGAAGAACATAGGTAAACTGTCCATATGTCCCAAATAACATAGGT
1 ATAATAATGTCCATATGTCCCGAAGAACATAGGTAAACTGTCCATATATCCCAAAGAACATAGGT
412773 AAACTATCCATATATCCCGAAGAACATAG
66 AAACTATCCATATATCCCGAAGAACATAG
*
412802 ATAATAATGTCCATATATCCCGAA
1 ATAATAATGTCCATATGTCCCGAA
412826 AGACATAAGT
Statistics
Matches: 106, Mismatches: 9, Indels: 3
0.90 0.08 0.03
Matches are distributed among these distances:
93 88 0.83
94 18 0.17
ACGTcount: A:0.40, C:0.21, G:0.14, T:0.25
Consensus pattern (94 bp):
ATAATAATGTCCATATGTCCCGAAGAACATAGGTAAACTGTCCATATATCCCAAAGAACATAGGT
AAACTATCCATATATCCCGAAGAACATAG
Found at i:421631 original size:2 final size:2
Alignment explanation
Indices: 421588--421617 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
421578 ATTATTATTA
421588 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
421618 TTTTGGATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:435850 original size:3 final size:3
Alignment explanation
Indices: 435842--435910 Score: 70
Period size: 3 Copynumber: 23.3 Consensus size: 3
435832 CTACCAAAAA
*
435842 TAT TAT TA- TAT TA- TATT TAT TAT TAT TAT TAA TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT TAT TAT
** * *
435886 TAT GGT TAT TTT TAT TAA TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT T
435911 TACATTTTTT
Statistics
Matches: 53, Mismatches: 10, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
2 4 0.08
3 47 0.89
4 2 0.04
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:436093 original size:98 final size:98
Alignment explanation
Indices: 435968--436161 Score: 307
Period size: 98 Copynumber: 2.0 Consensus size: 98
435958 AAGCCCAATT
*
435968 GGCCCAGCTAACCTACCCAATCTTGGTTACAACTCAAACCCGAACCAATTGGAATCCAAAGCAGA
1 GGCCCAGCTAACCTACCCAATCCTGGTTACAACTCAAACCCGAACCAATTGGAATCCAAAGCAGA
436033 CCCAAGATCAAACCCATCAGCAAAACCCGAATC
66 CCCAAGATCAAACCCATCAGCAAAACCCGAATC
* * * * * *
436066 GGCCCAGCTATCCTACCCAATCCTGGTTACAACTTAAACCCGACCCAATTGGAATCTAGAGTAGA
1 GGCCCAGCTAACCTACCCAATCCTGGTTACAACTCAAACCCGAACCAATTGGAATCCAAAGCAGA
* *
436131 CTCGAGATCAAACCCATCAGCAAAACCCGAA
66 CCCAAGATCAAACCCATCAGCAAAACCCGAA
436162 CTGACCCAGC
Statistics
Matches: 87, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
98 87 1.00
ACGTcount: A:0.36, C:0.34, G:0.14, T:0.16
Consensus pattern (98 bp):
GGCCCAGCTAACCTACCCAATCCTGGTTACAACTCAAACCCGAACCAATTGGAATCCAAAGCAGA
CCCAAGATCAAACCCATCAGCAAAACCCGAATC
Found at i:437487 original size:30 final size:30
Alignment explanation
Indices: 437426--437487 Score: 72
Period size: 30 Copynumber: 2.1 Consensus size: 30
437416 TCATTAAAAA
* **
437426 TTCTATTTTTGATCTTTTAGACCTTTGAGT
1 TTCTATTTTTGATATTTTAGACCTTCAAGT
*
437456 TTCTATTTTT-ACTATTTTAGTCCTTCAAGT
1 TTCTATTTTTGA-TATTTTAGACCTTCAAGT
437486 TT
1 TT
437488 ATGTTTTCCC
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
29 1 0.04
30 26 0.96
ACGTcount: A:0.18, C:0.15, G:0.10, T:0.58
Consensus pattern (30 bp):
TTCTATTTTTGATATTTTAGACCTTCAAGT
Found at i:437795 original size:5 final size:5
Alignment explanation
Indices: 437785--437820 Score: 54
Period size: 5 Copynumber: 7.0 Consensus size: 5
437775 ATTTTTGCAC
*
437785 TTTTA TTTTA TTTCA TTTTA TTTTA TTTTA TCTTTA
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA T-TTTA
437821 CAAAAATTGG
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
5 24 0.86
6 4 0.14
ACGTcount: A:0.19, C:0.06, G:0.00, T:0.75
Consensus pattern (5 bp):
TTTTA
Found at i:443019 original size:4 final size:4
Alignment explanation
Indices: 443002--443190 Score: 215
Period size: 4 Copynumber: 48.2 Consensus size: 4
442992 ATCGAGAAAA
* *
443002 ACAT ACAT ATAT ACAT ACAT ACAT ACAT ACAT ACAC ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
*
443050 ACAT ACAT ACAT ACAT --AT ACAT ACAC ACAT ACAT ACAT AC-- ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
* * * * * *
443094 ACAT GCAT ACAT GCAT ACAT GCAT ACAT GCAT ACAT GCAT ACAT GCAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
* * * * * *
443142 ACAT GCAT ACAT GCAT ACAT GCAT ACAT GCAT ACAT GCAT ACAT GCAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
443190 A
1 A
443191 GTTGGCTAAA
Statistics
Matches: 151, Mismatches: 30, Indels: 8
0.80 0.16 0.04
Matches are distributed among these distances:
2 4 0.03
4 147 0.97
ACGTcount: A:0.44, C:0.25, G:0.06, T:0.24
Consensus pattern (4 bp):
ACAT
Found at i:444002 original size:51 final size:52
Alignment explanation
Indices: 443941--444061 Score: 131
Period size: 51 Copynumber: 2.3 Consensus size: 52
443931 AATCTGTGAG
* *
443941 TTTGTTTCTCTT-A-ACAAAATCATCTTTGAGTTTATTTCTTTAAAAAC-AAAT
1 TTTGTCTCTCTTGAGAC-AAATCAT-TTTGAGTCTATTTCTTTAAAAACAAAAT
* * * **
443992 TTTGTCTCTCTTGAGACAATTTATTTTGAGTCTGTTTCTTTGGAAACAAAAT
1 TTTGTCTCTCTTGAGACAAATCATTTTGAGTCTATTTCTTTAAAAACAAAAT
*
444044 TTTATCTCTCTTGAGACA
1 TTTGTCTCTCTTGAGACA
444062 GTTTATTTTG
Statistics
Matches: 59, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
51 30 0.51
52 27 0.46
53 2 0.03
ACGTcount: A:0.28, C:0.15, G:0.11, T:0.46
Consensus pattern (52 bp):
TTTGTCTCTCTTGAGACAAATCATTTTGAGTCTATTTCTTTAAAAACAAAAT
Found at i:444061 original size:52 final size:51
Alignment explanation
Indices: 443965--444073 Score: 155
Period size: 52 Copynumber: 2.1 Consensus size: 51
443955 CAAAATCATC
* *
443965 TTTGAGTTTATTTCTTTAAAAACAAATTTTGTCTCTCTTGAGACAATTTAT
1 TTTGAGTCTATTTCTTTAAAAACAAATTTTATCTCTCTTGAGACAATTTAT
* ** *
444016 TTTGAGTCTGTTTCTTTGGAAACAAAATTTTATCTCTCTTGAGACAGTTTAT
1 TTTGAGTCTATTTCTTTAAAAAC-AAATTTTATCTCTCTTGAGACAATTTAT
444068 TTTGAG
1 TTTGAG
444074 AAAAATCTTT
Statistics
Matches: 51, Mismatches: 6, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
51 19 0.37
52 32 0.63
ACGTcount: A:0.27, C:0.12, G:0.14, T:0.48
Consensus pattern (51 bp):
TTTGAGTCTATTTCTTTAAAAACAAATTTTATCTCTCTTGAGACAATTTAT
Found at i:444792 original size:15 final size:14
Alignment explanation
Indices: 444752--444794 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 14
444742 CTACCAAAAA
*
444752 TATTATATTATTAT
1 TATTATATTATTTT
*
444766 TATTATGGTTATTTT
1 TATTAT-ATTATTTT
444781 TATTAATATTATTT
1 TATT-ATATTATTT
444795 ACATTTTTTG
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
14 6 0.25
15 16 0.67
16 2 0.08
ACGTcount: A:0.30, C:0.00, G:0.05, T:0.65
Consensus pattern (14 bp):
TATTATATTATTTT
Found at i:448961 original size:14 final size:14
Alignment explanation
Indices: 448942--448969 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
448932 TTTAACATAA
448942 TATCATCACTAACT
1 TATCATCACTAACT
448956 TATCATCACTAACT
1 TATCATCACTAACT
448970 AAAGTTTTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.29, G:0.00, T:0.36
Consensus pattern (14 bp):
TATCATCACTAACT
Found at i:452902 original size:2 final size:2
Alignment explanation
Indices: 452891--452925 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
452881 CATGTTGAAC
452891 AT AT -T 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
452926 GACAGATCTG
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:453674 original size:3 final size:3
Alignment explanation
Indices: 453668--453704 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
453658 TTGTTATTAT
453668 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
453705 TACAATTAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:457231 original size:28 final size:28
Alignment explanation
Indices: 457191--457246 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
457181 TCGTATTCAC
457191 AAGTTGTCTGGAGACACCAAGGAAATGG
1 AAGTTGTCTGGAGACACCAAGGAAATGG
457219 AAGTTGTCTGGAGACACCAAGGAAATGG
1 AAGTTGTCTGGAGACACCAAGGAAATGG
457247 TGACAACTGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.36, C:0.14, G:0.32, T:0.18
Consensus pattern (28 bp):
AAGTTGTCTGGAGACACCAAGGAAATGG
Found at i:461401 original size:15 final size:15
Alignment explanation
Indices: 461383--461416 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
461373 GAGGGTATAA
461383 TAGTCCTTCAGGACG
1 TAGTCCTTCAGGACG
* *
461398 TAGTCCTTCGGGATG
1 TAGTCCTTCAGGACG
461413 TAGT
1 TAGT
461417 GGTCCTACGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.18, C:0.21, G:0.29, T:0.32
Consensus pattern (15 bp):
TAGTCCTTCAGGACG
Found at i:468121 original size:15 final size:15
Alignment explanation
Indices: 468103--468137 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
468093 CGAGGGTATA
468103 ATAGTCCTTCGGGAT
1 ATAGTCCTTCGGGAT
468118 ATAGTCCTTCGGGAT
1 ATAGTCCTTCGGGAT
*
468133 GTAGT
1 ATAGT
468138 GGTCCTACGG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.20, C:0.17, G:0.29, T:0.34
Consensus pattern (15 bp):
ATAGTCCTTCGGGAT
Found at i:469055 original size:75 final size:75
Alignment explanation
Indices: 468949--469096 Score: 224
Period size: 75 Copynumber: 2.0 Consensus size: 75
468939 TTATATATAC
* * * * *
468949 AATAAAGCTTGAGTTGTCCCTCTAAAGCAATTGGTTAATCGCCCTGGCTTTATGGGTAATATTCA
1 AATAAAGCTTAAGTTGTCCCCCTAAAACAATTGGTTAATCGCCCTGACTTTATGGATAATATTCA
469014 GATAGCCTAT
66 GATAGCCTAT
* *
469024 AATATAGCTTAAGTTTTCCCCCTAAAACAATTGGTTAATCGCCCTGACTTTATGGATAATATTCA
1 AATAAAGCTTAAGTTGTCCCCCTAAAACAATTGGTTAATCGCCCTGACTTTATGGATAATATTCA
*
469089 GCTAGCCT
66 GATAGCCT
469097 GTTATACTAT
Statistics
Matches: 65, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
75 65 1.00
ACGTcount: A:0.29, C:0.20, G:0.17, T:0.34
Consensus pattern (75 bp):
AATAAAGCTTAAGTTGTCCCCCTAAAACAATTGGTTAATCGCCCTGACTTTATGGATAATATTCA
GATAGCCTAT
Found at i:471147 original size:22 final size:22
Alignment explanation
Indices: 471089--471150 Score: 79
Period size: 22 Copynumber: 2.8 Consensus size: 22
471079 ATCTACATTC
* * * *
471089 TTCAAAGATGACAGATTCTCTT
1 TTCAAAGATGAAAGCTTTTATT
*
471111 TTCAAATATGAAAGCTTTTATT
1 TTCAAAGATGAAAGCTTTTATT
471133 TTCAAAGATGAAAGCTTT
1 TTCAAAGATGAAAGCTTT
471151 ATTGGATTTC
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 34 1.00
ACGTcount: A:0.35, C:0.13, G:0.13, T:0.39
Consensus pattern (22 bp):
TTCAAAGATGAAAGCTTTTATT
Found at i:472242 original size:222 final size:221
Alignment explanation
Indices: 471836--473642 Score: 2628
Period size: 222 Copynumber: 8.1 Consensus size: 221
471826 CCCTAATTTG
* * * *
471836 TAAATCCTCAGGGTCATCTGTAAGACTTTCGAGCAAGATGATAAGACCTTCGGGCCATCAATAAG
1 TAAATCCTCCGGGTCATCTGTAAGCCTTTCGAGCAAGATGATAAGACCTCCGGGCCATCCATAAG
* * *
471901 ACCATCGGGCAAGATGTTTTCAAATGAAATTTTGGAAACTAAGCCTTTCAGGGGTTTCTTAATAA
66 ACCTTCGGGC-AGATGTTTTCAAATGAGATTTTGGAAACTAAGCCTTTCAGGGGTTTCTTAATTA
* ** *
471966 TCTCAAAAGAGTTGTTAATGGAAGCTAAGCCTTTTAAGGGGTTCTTTGACAACCAAGAAACTAAG
130 TCTCAATAGAGTTGTTAAAAGAAGCTAAGCCTTTTAAGGGGTTCCTTGACAACCAAGAAACTAAG
472031 CTTGATTTTCAAGGGTTTCTTGATGTT
195 CTTGATTTTCAAGGGTTTCTTGATGTT
* * *
472058 TAATTCCTCCGGGTCATCTGTAAGCCTTTCTAGCAAGATGATAAGACCTCCGGGCCATCCGTAAG
1 TAAATCCTCCGGGTCATCTGTAAGCCTTTCGAGCAAGATGATAAGACCTCCGGGCCATCCATAAG
* * * *
472123 ACCTTCGTGCAGTATGTTTTCAAATGAGATTTTGAAAACCAAGCCTTTGAGGGGTTTCTTAATTA
66 ACCTTCGGGCAG-ATGTTTTCAAATGAGATTTTGGAAACTAAGCCTTTCAGGGGTTTCTTAATTA
*
472188 TCTCAATAGAGTTGTTAAAAGAAGCTAAGCCTTTTAAGGGGTTCCTTAACAACCAAGAAACTAAG
130 TCTCAATAGAGTTGTTAAAAGAAGCTAAGCCTTTTAAGGGGTTCCTTGACAACCAAGAAACTAAG
*
472253 CTTGATTTTTAAGGGTTT-TCTGATGTT
195 CTTGATTTTCAAGGGTTTCT-TGATGTT
* * * ** *
472280 TAAATCCTTCGAGTCATCTGTAAGCCTTTCAAGCAAGATGATAAGACCTCCAAGCCATCAATAAG
1 TAAATCCTCCGGGTCATCTGTAAGCCTTTCGAGCAAGATGATAAGACCTCCGGGCCATCCATAAG
* *
472345 GCCTTCGGGCAAGATGTTTTCAAATGAGATTTTGGAAAATAAGCCTTTCAGGGGTTTCTTAATTA
66 ACCTTCGGGC-AGATGTTTTCAAATGAGATTTTGGAAACTAAGCCTTTCAGGGGTTTCTTAATTA
* * *
472410 TCTTAATAGAGTTGTTAAAAGAAGCTAAGCTTTTTAAGGGGTTCCTTGACAACCATGAAACTAAG
130 TCTCAATAGAGTTGTTAAAAGAAGCTAAGCCTTTTAAGGGGTTCCTTGACAACCAAGAAACTAAG
*
472475 CTTAATTTTCAAGGGTTTCTTGATGTT
195 CTTGATTTTCAAGGGTTTCTTGATGTT
* * * * * *
472502 TAAATCCTCTGGGTCATCTATAAGCCTTTCTAGCAAGATGATAAGACCTTCGAGCCATCCTTAAG
1 TAAATCCTCCGGGTCATCTGTAAGCCTTTCGAGCAAGATGATAAGACCTCCGGGCCATCCATAAG
* * * *
472567 ACCTTCAGGAAGGATGTTTTCAAATGATATTTTGGAAACTAAGCCTTTCAGTGGTTTCTTAATTA
66 ACCTTCGGGCA-GATGTTTTCAAATGAGATTTTGGAAACTAAGCCTTTCAGGGGTTTCTTAATTA
* * *
472632 TCTCAATAGAGTTGTT-AAAGAAAGCTAAGCCTTTTAAGGGGTTTCTTGAAAAACAAGAAACTAA
130 TCTCAATAGAGTTGTTAAAAG-AAGCTAAGCCTTTTAAGGGGTTCCTTGACAACCAAGAAACTAA
*
472696 GCTTGATTTTCAAGGGTTTCTTAATGTT
194 GCTTGATTTTCAAGGGTTTCTTGATGTT
* * ** * *
472724 TAAATCCTCCGGGTCATCTGTAAGTCTTTCAAAAAAGATGATAAGACCTTCAGGCCATCCATAAG
1 TAAATCCTCCGGGTCATCTGTAAGCCTTTCGAGCAAGATGATAAGACCTCCGGGCCATCCATAAG
* * * *
472789 ACCTTCGAGCATGATGTTTTCAAATGAGATTTTGGAAAGTAAGCTTTTCAGGGGTTTCATAATTA
66 ACCTTCGGGCA-GATGTTTTCAAATGAGATTTTGGAAACTAAGCCTTTCAGGGGTTTCTTAATTA
* * * * *
472854 TCTCAAAAGATTTGTTAAAGGAATCTAAGCCTTTTAAGGGGTTCCTTGATAACCAAGAAACTAAG
130 TCTCAATAGAGTTGTTAAAAGAAGCTAAGCCTTTTAAGGGGTTCCTTGACAACCAAGAAACTAAG
*
472919 CTTGATTTTCAAGGGTTTCTTTATGTT
195 CTTGATTTTCAAGGGTTTCTTGATGTT
* * * * *
472946 TAAATCCTCTGGGTCATCTATAAGCCTTTCGAACAAGATGATAAGACCTCCGAGCCATCTATAAG
1 TAAATCCTCCGGGTCATCTGTAAGCCTTTCGAGCAAGATGATAAGACCTCCGGGCCATCCATAAG
* *
473011 ACCTTCGGGCAGAATGTTTTCAAATGAGATTTTGGAAACTAAGCCTTTCCGGGGTTTCGTAATTA
66 ACCTTCGGGCAG-ATGTTTTCAAATGAGATTTTGGAAACTAAGCCTTTCAGGGGTTTCTTAATTA
* * * *
473076 TCCCAATAGAGTTATTTAAAGAAGCTAAGACTTTTAAGGGGTTCCTTGACAACCAAGAAACTAAG
130 TCTCAATAGAGTTGTTAAAAGAAGCTAAGCCTTTTAAGGGGTTCCTTGACAACCAAGAAACTAAG
*
473141 CTTTATTTTCAAGGGTTTCTTGATGTT
195 CTTGATTTTCAAGGGTTTCTTGATGTT
* *
473168 TAAATCCTACGGGTCATCTGTAAGCCTTTCGAGCAAGATGATAAGACCTCCGGGCCATCTATAAG
1 TAAATCCTCCGGGTCATCTGTAAGCCTTTCGAGCAAGATGATAAGACCTCCGGGCCATCCATAAG
** *
473233 ACCTTCAGGTAAGATGTTTTCAAATGAGATTTTGGAAACTAAGCCTTTCAGGGATTTCTTAATTA
66 ACCTTC-GGGCAGATGTTTTCAAATGAGATTTTGGAAACTAAGCCTTTCAGGGGTTTCTTAATTA
* * * *
473298 TCGCAAAAGAGTTGTTAAAGGAAGCTAAGCCTTTTAAGGGGTTTCTTGACAACCAAGAAACTAAG
130 TCTCAATAGAGTTGTTAAAAGAAGCTAAGCCTTTTAAGGGGTTCCTTGACAACCAAGAAACTAAG
473363 CTTGATTTTCAAGGGTTTCTTGATGTT
195 CTTGATTTTCAAGGGTTTCTTGATGTT
** * *
473390 TAAATCCTCTAGGTCATCTGTAAGCCTTTCGAGAAAGATGATAAGACCTCTGGGCCATCCATAAG
1 TAAATCCTCCGGGTCATCTGTAAGCCTTTCGAGCAAGATGATAAGACCTCCGGGCCATCCATAAG
* *
473455 ACCTTTGGGCAGGATGTTTTCAAATGAGATTTTTGGAAACTAAGCCTTTCAGGGATTTCTTAATT
66 ACCTTCGGGCA-GATGTTTTCAAATGAGA-TTTTGGAAACTAAGCCTTTCAGGGGTTTCTTAATT
* * * * *
473520 TTCTCAATAGAGTTGTTAAAGGAATCTAAGTCTTTTAAGGGGTTCCTTGACAACCAAGAAATTAA
129 ATCTCAATAGAGTTGTTAAAAGAAGCTAAGCCTTTTAAGGGGTTCCTTGACAACCAAGAAACTAA
**
473585 GCTTTCTTTTCAAGGGTTTCTTGATGTT
194 GCTTGATTTTCAAGGGTTTCTTGATGTT
*
473613 TAAATCCTCCGGGTCATCTGTAAGCTTTTC
1 TAAATCCTCCGGGTCATCTGTAAGCCTTTC
473643 CCTTCGGGCA
Statistics
Matches: 1421, Mismatches: 153, Indels: 21
0.89 0.10 0.01
Matches are distributed among these distances:
221 12 0.01
222 1253 0.88
223 156 0.11
ACGTcount: A:0.30, C:0.17, G:0.20, T:0.33
Consensus pattern (221 bp):
TAAATCCTCCGGGTCATCTGTAAGCCTTTCGAGCAAGATGATAAGACCTCCGGGCCATCCATAAG
ACCTTCGGGCAGATGTTTTCAAATGAGATTTTGGAAACTAAGCCTTTCAGGGGTTTCTTAATTAT
CTCAATAGAGTTGTTAAAAGAAGCTAAGCCTTTTAAGGGGTTCCTTGACAACCAAGAAACTAAGC
TTGATTTTCAAGGGTTTCTTGATGTT
Found at i:473799 original size:186 final size:185
Alignment explanation
Indices: 473456--474015 Score: 870
Period size: 186 Copynumber: 3.0 Consensus size: 185
473446 ATCCATAAGA
* *
473456 CCTTTGGGCAGGATGTTTTCAAATGAGATTTTTGGAAACTAAGCCTTTCAGGGATTTCTTAATTT
1 CCTTCGGGCAGGATGTTTTCAAATGAGA-TTTTGGAAACTAAGCCTTTCAGGG-TTTCTTAATTA
* * * *
473521 TCTCAATAGAGTTGTTAAAGGAATCTAAGTCTTTTAAGGGGTTCCTTGACAACCAAGAAATTAAG
64 TCTCAAAAGAGTTGTTAAAGGAAGCTAAGTCTTTTAAGGGGTTCCTTAACAACCAAGAAACTAAG
** *
473586 CTTTCTTTTCAAGGGTTTCTTGATGTTTAAATCCTCCGGGTCATCTGTAAGCTTTTC
129 CTTGATTTTCAAGGGTTTCTTGATGTTTAAATCCTTCGGGTCATCTGTAAGCTTTTC
* *
473643 CCTTCGGGCAAGATATTTTCAAATGAGATTTTGGAAACTAAGCCTTTCAGGAGTTTCTTAATTAT
1 CCTTCGGGCAGGATGTTTTCAAATGAGATTTTGGAAACTAAGCCTTTCAGG-GTTTCTTAATTAT
** *
473708 CTCAAAATTGTTGTTAAAGAAAGCTAAGTCTTTTAAGGGGTTCCTTAACAACCAAGAAACTAAGC
65 CTCAAAAGAGTTGTTAAAGGAAGCTAAGTCTTTTAAGGGGTTCCTTAACAACCAAGAAACTAAGC
473773 TTGATTTTCAAGGGTTTCTTGATGTTTAAATCCTTCGGGTCATCTGTAAGCCTTTT-
130 TTGATTTTCAAGGGTTTCTTGATGTTTAAATCCTTCGGGTCATCTGTAAG-CTTTTC
*
473829 CCTTCGGGCAGGATGTTTTCAAATGAGATTTTGGAAACTAAGCCTTTCAGGGGTTTCTTAACTAT
1 CCTTCGGGCAGGATGTTTTCAAATGAGATTTTGGAAACTAAGCCTTTCA-GGGTTTCTTAATTAT
* *
473894 CTCAAAAGAGTTGTTAAAGGAAGCTAAGCCTTTTAAGGGGTTCCTTAACAACCAAGAAACTAATC
65 CTCAAAAGAGTTGTTAAAGGAAGCTAAGTCTTTTAAGGGGTTCCTTAACAACCAAGAAACTAAGC
* * * *
473959 TTGATTTTATAAGGGTTTCTTGATGTTTAAATCCTTCGGGTTATCTATAAGCCTTTC
130 TTGATTTT-CAAGGGTTTCTTGATGTTTAAATCCTTCGGGTCATCTGTAAGCTTTTC
474016 GAGTAAGATG
Statistics
Matches: 342, Mismatches: 26, Indels: 10
0.90 0.07 0.03
Matches are distributed among these distances:
186 270 0.79
187 72 0.21
ACGTcount: A:0.28, C:0.16, G:0.19, T:0.37
Consensus pattern (185 bp):
CCTTCGGGCAGGATGTTTTCAAATGAGATTTTGGAAACTAAGCCTTTCAGGGTTTCTTAATTATC
TCAAAAGAGTTGTTAAAGGAAGCTAAGTCTTTTAAGGGGTTCCTTAACAACCAAGAAACTAAGCT
TGATTTTCAAGGGTTTCTTGATGTTTAAATCCTTCGGGTCATCTGTAAGCTTTTC
Found at i:480192 original size:11 final size:11
Alignment explanation
Indices: 480172--480214 Score: 50
Period size: 11 Copynumber: 3.7 Consensus size: 11
480162 TTTGCCCTAT
*
480172 TTTTATTTATCA
1 TTTTA-TTATTA
480184 TTTTATTATTA
1 TTTTATTATTA
*
480195 TTATATTATTA
1 TTTTATTATTA
480206 TTATTATTA
1 TT-TTATTA
480215 AAAAATAATA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
11 17 0.63
12 10 0.37
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.67
Consensus pattern (11 bp):
TTTTATTATTA
Found at i:480194 original size:3 final size:3
Alignment explanation
Indices: 480186--480214 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
480176 ATTTATCATT
480186 TTA TTA TTA TTA -TA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
480215 AAAAATAATA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.08
3 23 0.92
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:480203 original size:14 final size:14
Alignment explanation
Indices: 480186--480212 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
480176 ATTTATCATT
480186 TTATTATTATTATA
1 TTATTATTATTATA
480200 TTATTATTATTAT
1 TTATTATTATTAT
480213 TAAAAAATAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (14 bp):
TTATTATTATTATA
Found at i:483472 original size:27 final size:27
Alignment explanation
Indices: 483407--483485 Score: 79
Period size: 27 Copynumber: 2.9 Consensus size: 27
483397 CTTTTAAGTA
*
483407 ATTAAAATAAATTGTTAATAAATAAATT
1 ATTAAAATAAAATGTTAAT-AATAAATT
*** *
483435 ATTTTTA-AAAATGTTAATATTAAATT
1 ATTAAAATAAAATGTTAATAATAAATT
*
483461 ATTAAAATAAAATGTAAATACATAA
1 ATTAAAATAAAATGTTAATA-ATAA
483486 TAGAGTGGAG
Statistics
Matches: 39, Mismatches: 10, Indels: 4
0.74 0.19 0.08
Matches are distributed among these distances:
26 11 0.28
27 21 0.54
28 7 0.18
ACGTcount: A:0.56, C:0.01, G:0.04, T:0.39
Consensus pattern (27 bp):
ATTAAAATAAAATGTTAATAATAAATT
Found at i:484761 original size:387 final size:384
Alignment explanation
Indices: 484019--484836 Score: 1126
Period size: 387 Copynumber: 2.1 Consensus size: 384
484009 AGAAAACATT
* * * *
484019 TTTTAAATATACATTAGTGTTTTCTAAACGCACTTTTAGCT-AAAAAGTCTGTTTTGACCGCTAC
1 TTTTCAATATACATTAGTGTTTTCTAAACGAATTTTTAGCTAAAAAACTCTGTTTTGACCGCTAC
484083 ACCAAACAGGACCTAAATCATATATTTACAATTTAATACATTTTTTTCAAGAAATATTAGTTATG
66 ACCAAACAGGACCTAAATCATATATTTACAATTTAATACATTTTTTTCAAGAAATATTAGTTATG
* * * *
484148 GAATATTTGCTGTATTAGCGTTGAAAACCGATGGGGGGTTTCTCTTTCTTTTACATAGCCGAGGT
131 GAATATTTACTGTATTAGCGTTGAAAACCGATGGGGGGTTTCTCTTTCTTTTACACAGCAGAGGA
* * *
484213 GTTTAATTATTTGCTTTTTGCATGCATGCTATTTGGAAATGAAACCACCATTTTCATAATAATTA
196 GTTTAATTATTTGCTTTTTGCATACATGCTATTTAGAAACGAAACCACCATTTTCATAATAATTA
* * * *
484278 TTTTTAATATTTTACCCATCTGATATTGATTTTGCAGTTAAAACAGAATGTTTAACTAACAGTGT
261 TTTTTAATACTTTACCCATCTGATATTGATTTTACAGTCAAAACAGAATGTTTAACTAAAAGTGT
* * * **
484343 GTTTAGAAAGCATTTTTCAAAACCCATTAGTGCTTTCTAAACAAACTTTTCTGCCGCAA
326 ATTTAGAAAACATTTTTCAAAACACATTAGTGCTTTCTAAACAAACTTTTCCACCGCAA
* *
484402 TTTTCAATATACATTAGTGCTTTCTAAACGAATTTTTAGCTAAAAAACT-TGTTTTGACCGTTAC
1 TTTTCAATATACATTAGTGTTTTCTAAACGAATTTTTAGCTAAAAAACTCTGTTTTGACCGCTAC
*
484466 ACCAAGCAGGACCTAAATCATATATTTACAATTTAATACATTTTTTTTCAAGAAATATAAGTTAG
66 ACCAAACAGGACCTAAATCATATATTTACAATTTAATACA-TTTTTTTCAAG-AA-AT-A-TTAG
*
484531 TTATGGAATCTTTACTGTATTAGCGTTGAAAACCGAT-GGGGGTTTCTCTTTCTTTTACACAGCA
126 TTATGGAATATTTACTGTATTAGCGTTGAAAACCGATGGGGGGTTTCTCTTTCTTTTACACAGCA
* * *
484595 GATGAGTTTAATTATTTGCTTTTTGCATACATGCTATTTAGAAACGAAACCACCGTTTTCATGAT
191 GAGGAGTTTAATTATTTGCTTTTTGCATACATGCTATTTAGAAACGAAACCACCATTTTCATAAT
* * * * * * * * *
484660 AA-T-TTTTTAATACTTTACTCGTTTGGTATTGATTTTACGGTCAAAACATATTTTTTTAAGTTA
256 AATTATTTTTAATACTTTACCCATCTGATATTGATTTTACAGTCAAAACAGA-ATGTTTAA-CTA
* * * **
484723 AAAGTGTATTTAGAAAACATTTTTCAATATACATTAGTGCTTTTTAAACGTACTTTTCCACCGCA
319 AAAGTGTATTTAGAAAACATTTTTCAAAACACATTAGTGCTTTCTAAACAAACTTTTCCACCGCA
484788 A
384 A
*
484789 TTTTCAATATATATATTAGTGTTTTCTAAAC-ACATTTTTAGCTAAAAA
1 TTTTC-A-ATATACATTAGTGTTTTCTAAACGA-ATTTTTAGCTAAAAA
484837 TCCATTTTGA
Statistics
Matches: 381, Mismatches: 43, Indels: 16
0.87 0.10 0.04
Matches are distributed among these distances:
383 90 0.24
384 17 0.04
385 40 0.10
386 9 0.02
387 148 0.39
388 41 0.11
389 36 0.09
ACGTcount: A:0.32, C:0.15, G:0.13, T:0.40
Consensus pattern (384 bp):
TTTTCAATATACATTAGTGTTTTCTAAACGAATTTTTAGCTAAAAAACTCTGTTTTGACCGCTAC
ACCAAACAGGACCTAAATCATATATTTACAATTTAATACATTTTTTTCAAGAAATATTAGTTATG
GAATATTTACTGTATTAGCGTTGAAAACCGATGGGGGGTTTCTCTTTCTTTTACACAGCAGAGGA
GTTTAATTATTTGCTTTTTGCATACATGCTATTTAGAAACGAAACCACCATTTTCATAATAATTA
TTTTTAATACTTTACCCATCTGATATTGATTTTACAGTCAAAACAGAATGTTTAACTAAAAGTGT
ATTTAGAAAACATTTTTCAAAACACATTAGTGCTTTCTAAACAAACTTTTCCACCGCAA
Found at i:484880 original size:2 final size:2
Alignment explanation
Indices: 484873--484914 Score: 66
Period size: 2 Copynumber: 21.0 Consensus size: 2
484863 GACCTAAATC
* *
484873 AT AT AT AT AT AT AT AT AT AT AT GT GT 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
484915 TCAATTTAAT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (2 bp):
AT
Found at i:485780 original size:33 final size:33
Alignment explanation
Indices: 485743--485807 Score: 85
Period size: 33 Copynumber: 2.0 Consensus size: 33
485733 GTTTGTGTAG
* *
485743 GTTCGTTTATGTTCATTTATTGTGTTCTTTTAT
1 GTTCGTTTACGTTCATTTATTGTGTTCGTTTAT
** *
485776 GTTCGTTTACGTTTGTTTATTTTGTTCGTTTA
1 GTTCGTTTACGTTCATTTATTGTGTTCGTTTA
485808 CATCAGTTCA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
33 27 1.00
ACGTcount: A:0.11, C:0.09, G:0.17, T:0.63
Consensus pattern (33 bp):
GTTCGTTTACGTTCATTTATTGTGTTCGTTTAT
Found at i:485820 original size:23 final size:24
Alignment explanation
Indices: 485766--485829 Score: 76
Period size: 23 Copynumber: 2.7 Consensus size: 24
485756 CATTTATTGT
* * **
485766 GTTCTTTTATGTTCGTTTACGTTT
1 GTTCATTTATGTTCGTTTACATCA
*
485790 GTTTATTT-TGTTCGTTTACATCA
1 GTTCATTTATGTTCGTTTACATCA
485813 GTTCATTTATGTTCGTT
1 GTTCATTTATGTTCGTT
485830 CATTTGATTT
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
23 19 0.58
24 14 0.42
ACGTcount: A:0.12, C:0.12, G:0.16, T:0.59
Consensus pattern (24 bp):
GTTCATTTATGTTCGTTTACATCA
Found at i:491213 original size:32 final size:32
Alignment explanation
Indices: 491177--491238 Score: 106
Period size: 32 Copynumber: 1.9 Consensus size: 32
491167 GGTTAAATGA
* *
491177 AAGGAGTTTGTTGTGTAAGAGATTGAAGATAT
1 AAGGAGTCTGTTATGTAAGAGATTGAAGATAT
491209 AAGGAGTCTGTTATGTAAGAGATTGAAGAT
1 AAGGAGTCTGTTATGTAAGAGATTGAAGAT
491239 GATGTGCACA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.35, C:0.02, G:0.31, T:0.32
Consensus pattern (32 bp):
AAGGAGTCTGTTATGTAAGAGATTGAAGATAT
Found at i:496622 original size:76 final size:71
Alignment explanation
Indices: 496497--496716 Score: 242
Period size: 76 Copynumber: 3.0 Consensus size: 71
496487 TAAACTCAAG
* * * ** *
496497 TTTAGGATAATATTTTAAAAATTATATTTTATATTTGTATTTTAATTTAAATAGGTTTTAGTATT
1 TTTAGAATATTATTTTAAATATTAT-TTTT-T-TAGGTATTTTAGTTTAAATA-GTTTTAGTATT
*
496562 TTAATTAAGT
62 TTAATTAAGA
* * *
496572 TTTAGGATATTATTTTTATATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATATGTTTTAGTAT
1 TTTAGAATATTA-TTTTAAATATTA--TTT-TTTTAGGTATTTTAGTTTAAATA-GTTTTAGTAT
*
496637 TTTAATTAGGA
61 TTTAATTAAGA
*
496648 TTTAGAATATTATTTTAAATATTATTTTTTTAGGTATTTTAGTTTAAATAGTTTTAAGTGTTTTA
1 TTTAGAATATTATTTTAAATATTATTTTTTTAGGTATTTTAGTTTAAATAGTTTT-AGTATTTTA
496713 ATTA
65 ATTA
496717 GTATTTAAGA
Statistics
Matches: 126, Mismatches: 14, Indels: 13
0.82 0.09 0.08
Matches are distributed among these distances:
71 5 0.04
72 35 0.28
73 3 0.02
75 21 0.17
76 56 0.44
77 3 0.02
78 3 0.02
ACGTcount: A:0.31, C:0.00, G:0.11, T:0.57
Consensus pattern (71 bp):
TTTAGAATATTATTTTAAATATTATTTTTTTAGGTATTTTAGTTTAAATAGTTTTAGTATTTTAA
TTAAGA
Found at i:496744 original size:21 final size:20
Alignment explanation
Indices: 496690--496744 Score: 60
Period size: 21 Copynumber: 2.8 Consensus size: 20
496680 GGTATTTTAG
*
496690 TTTAAATAG-TTTTAAGTGT
1 TTTAATTAGTTTTTAAGTGT
*
496709 TTTAATTAGTATTTAAGATGT
1 TTTAATTAGTTTTTAAG-TGT
496730 TTTAACTT-GTTTTTA
1 TTTAA-TTAGTTTTTA
496745 GTAATATGAA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
19 8 0.27
20 6 0.20
21 14 0.47
22 2 0.07
ACGTcount: A:0.29, C:0.02, G:0.13, T:0.56
Consensus pattern (20 bp):
TTTAATTAGTTTTTAAGTGT
Found at i:497336 original size:18 final size:18
Alignment explanation
Indices: 497313--497355 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
497303 TTTTAATTTG
*
497313 TTTATTTAATTATTTTCT
1 TTTATTTAATTATTATCT
*
497331 TTTATTTAATTCTTATCT
1 TTTATTTAATTATTATCT
497349 TTTATTT
1 TTTATTT
497356 TAAAAATAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.21, C:0.07, G:0.00, T:0.72
Consensus pattern (18 bp):
TTTATTTAATTATTATCT
Found at i:497417 original size:15 final size:16
Alignment explanation
Indices: 497379--497420 Score: 61
Period size: 15 Copynumber: 2.8 Consensus size: 16
497369 TAAAAACTCC
497379 CTTTTA-TATTTATTA
1 CTTTTACTATTTATTA
*
497394 CTATTACTATTTATTA
1 CTTTTACTATTTATTA
497410 -TTTTACTATTT
1 CTTTTACTATTT
497421 TTCCTTTTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
15 15 0.62
16 9 0.38
ACGTcount: A:0.26, C:0.10, G:0.00, T:0.64
Consensus pattern (16 bp):
CTTTTACTATTTATTA
Found at i:497428 original size:15 final size:16
Alignment explanation
Indices: 497378--497428 Score: 54
Period size: 15 Copynumber: 3.4 Consensus size: 16
497368 TTAAAAACTC
497378 CCTTTTA-TATTTATT
1 CCTTTTACTATTTATT
* *
497393 ACTATTACTATTTATT
1 CCTTTTACTATTTATT
*
497409 -ATTTTACTATTT-TT
1 CCTTTTACTATTTATT
497423 CCTTTT
1 CCTTTT
497429 TATAATTATT
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
14 2 0.07
15 19 0.66
16 8 0.28
ACGTcount: A:0.22, C:0.14, G:0.00, T:0.65
Consensus pattern (16 bp):
CCTTTTACTATTTATT
Found at i:502974 original size:33 final size:33
Alignment explanation
Indices: 502911--502974 Score: 76
Period size: 33 Copynumber: 1.9 Consensus size: 33
502901 AGACAACCCA
***
502911 TTTCGTTCTATTTTTTATTTAATTTCATTTTAT
1 TTTCGTTCTATTTTTTAGCAAATTTCATTTTAT
*
502944 TTTCGTTTTATTTTTTAGCAAACTTT-ATTTT
1 TTTCGTTCTATTTTTTAGCAAA-TTTCATTTT
502975 CATTCTATTT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
33 23 0.88
34 3 0.12
ACGTcount: A:0.19, C:0.09, G:0.05, T:0.67
Consensus pattern (33 bp):
TTTCGTTCTATTTTTTAGCAAATTTCATTTTAT
Found at i:502992 original size:5 final size:5
Alignment explanation
Indices: 502967--503019 Score: 54
Period size: 5 Copynumber: 10.6 Consensus size: 5
502957 TTTAGCAAAC
* * * *
502967 TTTAT TTTCAT TCTA- TTTAT TTTAT TTTAT TTTAA TTAAT TTTAT TCTAT
1 TTTAT TTT-AT TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT
503017 TTT
1 TTT
503020 TCTCTGAACA
Statistics
Matches: 38, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
4 3 0.08
5 31 0.82
6 4 0.11
ACGTcount: A:0.23, C:0.06, G:0.00, T:0.72
Consensus pattern (5 bp):
TTTAT
Found at i:506892 original size:21 final size:21
Alignment explanation
Indices: 506837--506900 Score: 74
Period size: 21 Copynumber: 3.0 Consensus size: 21
506827 ATTCCCCTGT
506837 GGGGGGGAATCGGTTCCCCTTCA
1 GGGGGGGAATCGGTT-CCC-TCA
**
506860 AAGGGGGAATCGGTTCCCTCA
1 GGGGGGGAATCGGTTCCCTCA
* *
506881 GGGGGGGGATCGATTCCCTC
1 GGGGGGGAATCGGTTCCCTC
506901 TGCACCAAAA
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
21 19 0.54
22 3 0.09
23 13 0.37
ACGTcount: A:0.16, C:0.25, G:0.39, T:0.20
Consensus pattern (21 bp):
GGGGGGGAATCGGTTCCCTCA
Found at i:510412 original size:22 final size:21
Alignment explanation
Indices: 510370--510409 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
510360 GAGTTTGTTT
*
510370 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
510391 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
510410 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:514210 original size:76 final size:71
Alignment explanation
Indices: 514125--514314 Score: 238
Period size: 76 Copynumber: 2.6 Consensus size: 71
514115 TTTTATCTTT
* * * *
514125 GTATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAAGTTTTAGGATATTATTTTTATATTTTAT
1 GTATTTTAGTTTAAATA-GTTTTAGTATTTTAATTAAGATTTAGAATATTA-TTTTAAATATTA-
*
514190 CTTTGTTTTAG
63 -TTTG-TTTAA
*
514201 GTATTTTAGTTTAAATATGTTTTAGTATTTTAATTATGATTTAGAATATTATTTTAAATATTATT
1 GTATTTTAGTTTAAATA-GTTTTAGTATTTTAATTAAGATTTAGAATATTATTTTAAATATTATT
514266 TGTTTAA
65 TGTTTAA
* *
514273 GTATTTTAGTTTAAATAGTTTTAAGT-GTTTAATTAGGATTTA
1 GTATTTTAGTTTAAATAGTTTT-AGTATTTTAATTAAGATTTA
514315 AGATGTTTTA
Statistics
Matches: 104, Mismatches: 9, Indels: 7
0.87 0.08 0.06
Matches are distributed among these distances:
71 19 0.18
72 24 0.23
73 4 0.04
75 10 0.10
76 47 0.45
ACGTcount: A:0.30, C:0.01, G:0.13, T:0.57
Consensus pattern (71 bp):
GTATTTTAGTTTAAATAGTTTTAGTATTTTAATTAAGATTTAGAATATTATTTTAAATATTATTT
GTTTAA
Found at i:514286 original size:14 final size:15
Alignment explanation
Indices: 514247--514289 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
514237 TGATTTAGAA
*
514247 TATTATTTTAAATAT
1 TATTAGTTTAAATAT
* *
514262 TATTTGTTTAAGTAT
1 TATTAGTTTAAATAT
514277 T-TTAGTTTAAATA
1 TATTAGTTTAAATA
514290 GTTTTAAGTG
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
14 10 0.43
15 13 0.57
ACGTcount: A:0.35, C:0.00, G:0.07, T:0.58
Consensus pattern (15 bp):
TATTAGTTTAAATAT
Found at i:514294 original size:15 final size:14
Alignment explanation
Indices: 514253--514295 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 14
514243 AGAATATTAT
*
514253 TTTAAATATTATTTG
1 TTTAAATATT-TTAG
*
514268 TTTAAGTATTTTAG
1 TTTAAATATTTTAG
514282 TTTAAATAGTTTTA
1 TTTAAATA-TTTTA
514296 AGTGTTTAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
14 10 0.42
15 14 0.58
ACGTcount: A:0.33, C:0.00, G:0.09, T:0.58
Consensus pattern (14 bp):
TTTAAATATTTTAG
Found at i:514931 original size:18 final size:18
Alignment explanation
Indices: 514908--514949 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
514898 TTTAATTTGC
*
514908 TTATTTAATTATTTTCTT
1 TTATTTAATTATTATCTT
*
514926 TTATTTAATTCTTATCTT
1 TTATTTAATTATTATCTT
514944 TTATTT
1 TTATTT
514950 TAAAAACAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.21, C:0.07, G:0.00, T:0.71
Consensus pattern (18 bp):
TTATTTAATTATTATCTT
Found at i:515040 original size:18 final size:18
Alignment explanation
Indices: 514995--515046 Score: 52
Period size: 18 Copynumber: 2.9 Consensus size: 18
514985 TTACTATTAA
* *
514995 TATTTATTATTTTATTAT
1 TATTTATTTTTTTATAAT
*
515013 T-TTTCCTTTTTTTATAAT
1 TATTT-ATTTTTTTATAAT
*
515031 TATTTATTTTATTATA
1 TATTTATTTTTTTATA
515047 CCTTTTATAC
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
17 3 0.11
18 21 0.78
19 3 0.11
ACGTcount: A:0.25, C:0.04, G:0.00, T:0.71
Consensus pattern (18 bp):
TATTTATTTTTTTATAAT
Found at i:516550 original size:2 final size:2
Alignment explanation
Indices: 516545--516576 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
516535 TATTATTTTA
516545 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
516577 TATTGTCGAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:521877 original size:20 final size:20
Alignment explanation
Indices: 521852--522033 Score: 168
Period size: 20 Copynumber: 8.7 Consensus size: 20
521842 TTTTCCTAAT
*
521852 TCGCAATGCGAATACGTAGA
1 TCGCAATGCGAATACGTAAA
521872 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
* *
521892 TCGCAACGCGATTAAC-TAAA
1 TCGCAATGCGAAT-ACGTAAA
* *
521912 TCGCAATGCGAATTGTGATTTTCATAAT
1 TCGCAATGCGAA---T-A----CGTAAA
*
521940 TCGCAATGTGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
* * *
521960 TCGCAACGCGATTAAGTAAA
1 TCGCAATGCGAATACGTAAA
* *
521980 TCGCAATGCGAATTAGGAAAA
1 TCGCAATGCGAA-TACGTAAA
522001 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
522021 TCGCAATGCGAAT
1 TCGCAATGCGAAT
522034 CTGACTATCG
Statistics
Matches: 132, Mismatches: 20, Indels: 20
0.77 0.12 0.12
Matches are distributed among these distances:
20 93 0.70
21 20 0.15
23 2 0.02
24 1 0.01
25 1 0.01
27 1 0.01
28 14 0.11
ACGTcount: A:0.37, C:0.19, G:0.20, T:0.24
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:521946 original size:88 final size:89
Alignment explanation
Indices: 521840--522013 Score: 251
Period size: 88 Copynumber: 2.0 Consensus size: 89
521830 TTCGCGTTAC
* * * *
521840 GATTTTCCTAATTCGCAATGCGAATACGTAGATCGCAATGCGAATACGTAAATCGCAACGCG-AT
1 GATTTTCATAATTCGCAATGCGAATACGTAAATCGCAACGCGAATAAGTAAATCGCAACGCGAAT
*
521904 TAACTAAATCGCAATGCGAATTGT
66 TAACAAAATCGCAATGCGAATTGT
* * *
521928 GATTTTCATAATTCGCAATGTGAATACGTAAATCGCAACGCGATTAAGTAAATCGCAATGCGAAT
1 GATTTTCATAATTCGCAATGCGAATACGTAAATCGCAACGCGAATAAGTAAATCGCAACGCGAAT
**
521993 TAGGAAAATCGCAATGCGAAT
66 TAACAAAATCGCAATGCGAAT
522014 ACGTAAATCG
Statistics
Matches: 75, Mismatches: 10, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
88 55 0.73
89 20 0.27
ACGTcount: A:0.36, C:0.18, G:0.20, T:0.26
Consensus pattern (89 bp):
GATTTTCATAATTCGCAATGCGAATACGTAAATCGCAACGCGAATAAGTAAATCGCAACGCGAAT
TAACAAAATCGCAATGCGAATTGT
Found at i:522005 original size:41 final size:41
Alignment explanation
Indices: 521940--522033 Score: 127
Period size: 41 Copynumber: 2.3 Consensus size: 41
521930 TTTTCATAAT
* * *
521940 TCGCAATGTGAA-TACGTAAATCGCAACGCGATTAAGTAAA
1 TCGCAATGCGAATTACGAAAATCGCAACGCGAATAAGTAAA
* * *
521980 TCGCAATGCGAATTAGGAAAATCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATTACGAAAATCGCAACGCGAATAAGTAAA
522021 TCGCAATGCGAAT
1 TCGCAATGCGAAT
522034 CTGACTATCG
Statistics
Matches: 47, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
40 11 0.23
41 36 0.77
ACGTcount: A:0.39, C:0.18, G:0.21, T:0.21
Consensus pattern (41 bp):
TCGCAATGCGAATTACGAAAATCGCAACGCGAATAAGTAAA
Found at i:522625 original size:19 final size:20
Alignment explanation
Indices: 522580--522628 Score: 73
Period size: 19 Copynumber: 2.5 Consensus size: 20
522570 TTCGAGAATA
522580 AAAATCGCAACGCGGAAATG
1 AAAATCGCAACGCGGAAATG
**
522600 ACTATCGCAACGC-GAAATG
1 AAAATCGCAACGCGGAAATG
522619 AAAATCGCAA
1 AAAATCGCAA
522629 TGAGAGAATC
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
19 14 0.56
20 11 0.44
ACGTcount: A:0.45, C:0.22, G:0.20, T:0.12
Consensus pattern (20 bp):
AAAATCGCAACGCGGAAATG
Found at i:522734 original size:20 final size:19
Alignment explanation
Indices: 522656--522759 Score: 74
Period size: 19 Copynumber: 5.6 Consensus size: 19
522646 GAAACCAAAA
* **
522656 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATAGTCATT
522675 TCGCGTTGCGAT--TC---
1 TCGCGTTGCGATAGTCATT
* **
522689 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATAGTCATT
522708 TCGCGTTGCGATAGTCATT
1 TCGCGTTGCGATAGTCATT
**
522727 TCCGCGTTGCGATTTTCATT
1 T-CGCGTTGCGATAGTCATT
*
522747 CTCTCGTTGCGAT
1 -TCGCGTTGCGAT
522760 TTTCATTTCA
Statistics
Matches: 70, Mismatches: 8, Indels: 13
0.77 0.09 0.14
Matches are distributed among these distances:
14 11 0.16
16 2 0.03
17 2 0.03
19 28 0.40
20 26 0.37
21 1 0.01
ACGTcount: A:0.12, C:0.24, G:0.21, T:0.43
Consensus pattern (19 bp):
TCGCGTTGCGATAGTCATT
Found at i:522760 original size:20 final size:19
Alignment explanation
Indices: 522656--522768 Score: 128
Period size: 20 Copynumber: 6.1 Consensus size: 19
522646 GAAACCAAAA
*
522656 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
522675 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
522689 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
522708 TCGCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
522727 TCCGCGTTGCGATTTTCATT
1 T-CGCGTTGCGATTTTCATT
*
522747 CTCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
522767 TC
1 TC
522769 AACCAAAAGA
Statistics
Matches: 79, Mismatches: 8, Indels: 14
0.78 0.08 0.14
Matches are distributed among these distances:
14 10 0.13
16 3 0.04
17 3 0.04
19 29 0.37
20 33 0.42
21 1 0.01
ACGTcount: A:0.12, C:0.24, G:0.19, T:0.45
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:522766 original size:40 final size:39
Alignment explanation
Indices: 522661--522768 Score: 129
Period size: 33 Copynumber: 2.9 Consensus size: 39
522651 CAAAATCGCA
*
522661 TTGCGATTTTCATTTCGCGTTGCGAT--TC---T-CTCG
1 TTGCGATTTTCATTTCGCGTTGCGATAGTCATTTCCGCG
522694 TTGCGATTTTCATTTCGCGTTGCGATAGTCATTTCCGCG
1 TTGCGATTTTCATTTCGCGTTGCGATAGTCATTTCCGCG
* **
522733 TTGCGATTTTCATTCTCTCGTTGCGATTTTCATTTC
1 TTGCGATTTTCATT-TCGCGTTGCGATAGTCATTTC
522769 AACCAAAAGA
Statistics
Matches: 64, Mismatches: 4, Indels: 7
0.85 0.05 0.09
Matches are distributed among these distances:
33 26 0.41
35 2 0.03
38 1 0.02
39 17 0.27
40 18 0.28
ACGTcount: A:0.11, C:0.23, G:0.19, T:0.46
Consensus pattern (39 bp):
TTGCGATTTTCATTTCGCGTTGCGATAGTCATTTCCGCG
Found at i:524847 original size:20 final size:20
Alignment explanation
Indices: 524822--525014 Score: 246
Period size: 20 Copynumber: 9.7 Consensus size: 20
524812 CGATTTAGGA
524822 AAATCGCAATGCGGTTACGT
1 AAATCGCAATGCGGTTACGT
524842 AAATCGCAATGCGGTTACGT
1 AAATCGCAATGCGGTTACGT
*
524862 AAATCGCAATGCGGTTACAT
1 AAATCGCAATGCGGTTACGT
524882 AAATCGCAATGCGGTTACGT
1 AAATCGCAATGCGGTTACGT
524902 AAATCGCAATGCGGTTACGT
1 AAATCGCAATGCGGTTACGT
** * *
524922 AAATCGCAATGCAAATTATGA
1 AAATCGCAATGC-GGTTACGT
*
524943 AAATCGCAATGCGATTACGT
1 AAATCGCAATGCGGTTACGT
* **
524963 AAATTGCAATGCGAATACGT
1 AAATCGCAATGCGGTTACGT
* *
524983 -AATCGCAATGTGATTTACGT
1 AAATCGCAATGCG-GTTACGT
*
525003 -AATCGCATTGCG
1 AAATCGCAATGCG
525015 ATTTTCCTAA
Statistics
Matches: 154, Mismatches: 17, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
19 10 0.06
20 128 0.83
21 16 0.10
ACGTcount: A:0.34, C:0.19, G:0.22, T:0.26
Consensus pattern (20 bp):
AAATCGCAATGCGGTTACGT
Found at i:525017 original size:20 final size:20
Alignment explanation
Indices: 524823--525160 Score: 213
Period size: 20 Copynumber: 16.7 Consensus size: 20
524813 GATTTAGGAA
*
524823 AATCGCAATGCG-GTTACGT
1 AATCGCAATGCGATTTACGT
*
524842 AAATCGCAATGCG-GTTACGT
1 -AATCGCAATGCGATTTACGT
* *
524862 AAATCGCAATGCG-GTTACAT
1 -AATCGCAATGCGATTTACGT
*
524882 AAATCGCAATGCG-GTTACGT
1 -AATCGCAATGCGATTTACGT
*
524902 AAATCGCAATGCG-GTTACGT
1 -AATCGCAATGCGATTTACGT
* * * *
524922 AAATCGCAATGCAAATTATGAA
1 -AATCGCAATGCGATTTACG-T
524944 AATCGCAATGCGA-TTACGT
1 AATCGCAATGCGATTTACGT
* *
524963 AAATTGCAATGCGA-ATACGT
1 -AATCGCAATGCGATTTACGT
*
524983 AATCGCAATGTGATTTACGT
1 AATCGCAATGCGATTTACGT
* * *
525003 AATCGCATTGCGATTTTCCT
1 AATCGCAATGCGATTTACGT
* *
525023 AATTTGCATTGCGATTTACGT
1 AA-TCGCAATGCGATTTACGT
* * *
525044 AATCGCATTGCGATTTTCCT
1 AATCGCAATGCGATTTACGT
*
525064 AATTCGCATTGCGATTTACGT
1 AA-TCGCAATGCGATTTACGT
* * * *
525085 AATCTCATTGTGATTTAAGT
1 AATCGCAATGCGATTTACGT
* * * * *
525105 ATTCGCATTGCGAATTAGGAA
1 AATCGCAATGCGATTTACG-T
* ** *
525126 AATCGCAACGCGAATTTGGGA
1 AATCGCAATGCG-ATTTACGT
525147 AATCGCAATGCGAT
1 AATCGCAATGCGAT
525161 AGTCAGAATC
Statistics
Matches: 269, Mismatches: 41, Indels: 16
0.83 0.13 0.05
Matches are distributed among these distances:
19 11 0.04
20 181 0.67
21 72 0.27
22 5 0.02
ACGTcount: A:0.31, C:0.18, G:0.21, T:0.30
Consensus pattern (20 bp):
AATCGCAATGCGATTTACGT
Found at i:525033 original size:21 final size:21
Alignment explanation
Indices: 525005--525080 Score: 118
Period size: 21 Copynumber: 3.7 Consensus size: 21
524995 ATTTACGTAA
525005 TCGCATTGCGATTTTCCTAAT
1 TCGCATTGCGATTTTCCTAAT
* * *
525026 TTGCATTGCGATTTACGTAA-
1 TCGCATTGCGATTTTCCTAAT
525046 TCGCATTGCGATTTTCCTAAT
1 TCGCATTGCGATTTTCCTAAT
525067 TCGCATTGCGATTT
1 TCGCATTGCGATTT
525081 ACGTAATCTC
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
20 17 0.35
21 31 0.65
ACGTcount: A:0.20, C:0.21, G:0.17, T:0.42
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCTAAT
Found at i:525039 original size:41 final size:41
Alignment explanation
Indices: 524985--525117 Score: 187
Period size: 41 Copynumber: 3.3 Consensus size: 41
524975 GAATACGTAA
* *
524985 TCGCAATGTGATTTACGTAATCGCATTGCGATTTTCCTAAT
1 TCGCATTGCGATTTACGTAATCGCATTGCGATTTTCCTAAT
*
525026 TTGCATTGCGATTTACGTAATCGCATTGCGATTTTCCTAAT
1 TCGCATTGCGATTTACGTAATCGCATTGCGATTTTCCTAAT
* * ***
525067 TCGCATTGCGATTTACGTAATCTCATTGTGATTTAAGT-AT
1 TCGCATTGCGATTTACGTAATCGCATTGCGATTTTCCTAAT
525107 TCGCATTGCGA
1 TCGCATTGCGA
525118 ATTAGGAAAA
Statistics
Matches: 83, Mismatches: 9, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
40 13 0.16
41 70 0.84
ACGTcount: A:0.23, C:0.19, G:0.18, T:0.40
Consensus pattern (41 bp):
TCGCATTGCGATTTACGTAATCGCATTGCGATTTTCCTAAT
Found at i:525059 original size:61 final size:61
Alignment explanation
Indices: 524944--525117 Score: 192
Period size: 61 Copynumber: 2.9 Consensus size: 61
524934 AAATTATGAA
* * * * * * *
524944 AATCGCAATGCGA-TTACGTAAATTGCAATGCGA-ATACGTAATCGCAATGTGATTTACGT
1 AATCGCATTGCGATTTACGTAATTTGCATTGCGATTTACGTAATCGCATTGCGATTTACCT
* * *
525003 AATCGCATTGCGATTTTCCTAATTTGCATTGCGATTTACGTAATCGCATTGCGATTTTCCT
1 AATCGCATTGCGATTTACGTAATTTGCATTGCGATTTACGTAATCGCATTGCGATTTACCT
* * * *
525064 AATTCGCATTGCGATTTACGTAATCT-CATTGTGATTTAAGTATTCGCATTGCGA
1 AA-TCGCATTGCGATTTACGTAATTTGCATTGCGATTTACGTAATCGCATTGCGA
525118 ATTAGGAAAA
Statistics
Matches: 96, Mismatches: 16, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
59 12 0.12
60 16 0.17
61 48 0.50
62 20 0.21
ACGTcount: A:0.27, C:0.18, G:0.18, T:0.36
Consensus pattern (61 bp):
AATCGCATTGCGATTTACGTAATTTGCATTGCGATTTACGTAATCGCATTGCGATTTACCT
Found at i:525132 original size:21 final size:21
Alignment explanation
Indices: 525107--525159 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
525097 ATTTAAGTAT
*
525107 TCGCATTGCGAATTAGGAAAA
1 TCGCAATGCGAATTAGGAAAA
* * *
525128 TCGCAACGCGAATTTGGGAAA
1 TCGCAATGCGAATTAGGAAAA
525149 TCGCAATGCGA
1 TCGCAATGCGA
525160 TAGTCAGAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.34, C:0.19, G:0.26, T:0.21
Consensus pattern (21 bp):
TCGCAATGCGAATTAGGAAAA
Found at i:530227 original size:26 final size:26
Alignment explanation
Indices: 530191--530244 Score: 90
Period size: 26 Copynumber: 2.1 Consensus size: 26
530181 ACCGAAGTGC
*
530191 TAATACACATAATGTCATGCCCACCA
1 TAATACACATAAGGTCATGCCCACCA
*
530217 TAATACACATAAGGTCGTGCCCACCA
1 TAATACACATAAGGTCATGCCCACCA
530243 TA
1 TA
530245 TGTACTTAGG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.37, C:0.30, G:0.11, T:0.22
Consensus pattern (26 bp):
TAATACACATAAGGTCATGCCCACCA
Found at i:537725 original size:21 final size:20
Alignment explanation
Indices: 537667--537726 Score: 61
Period size: 21 Copynumber: 2.9 Consensus size: 20
537657 ATTTTGGTGC
537667 AGAGGGAATCGATCCCCCCA
1 AGAGGGAATCGATCCCCCCA
*
537687 TGAGGGAA-CTGATTCCCCCCA
1 AGAGGGAATC-GA-TCCCCCCA
537708 CAG-GGGAATCGATACCCCC
1 -AGAGGGAATCGAT-CCCCC
537727 TAGGGTTCTG
Statistics
Matches: 33, Mismatches: 2, Indels: 9
0.75 0.05 0.20
Matches are distributed among these distances:
19 1 0.03
20 10 0.30
21 20 0.61
22 2 0.06
ACGTcount: A:0.27, C:0.35, G:0.25, T:0.13
Consensus pattern (20 bp):
AGAGGGAATCGATCCCCCCA
Found at i:542250 original size:13 final size:12
Alignment explanation
Indices: 542216--542241 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
542206 GATAACTCTA
542216 TTTAAAAAATAG
1 TTTAAAAAATAG
542228 TTTAAAAAATAG
1 TTTAAAAAATAG
542240 TT
1 TT
542242 GTACAAAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.54, C:0.00, G:0.08, T:0.38
Consensus pattern (12 bp):
TTTAAAAAATAG
Found at i:542518 original size:21 final size:21
Alignment explanation
Indices: 542493--542533 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
542483 TCGATATTGT
542493 CATTTTATTAT-TTTTAAAATA
1 CATTTT-TTATATTTTAAAATA
*
542514 CATTTTTTTTATTTTAAAAT
1 CATTTTTTATATTTTAAAAT
542534 TTCAATAAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 3 0.17
21 15 0.83
ACGTcount: A:0.34, C:0.05, G:0.00, T:0.61
Consensus pattern (21 bp):
CATTTTTTATATTTTAAAATA
Found at i:546417 original size:19 final size:19
Alignment explanation
Indices: 546393--546467 Score: 123
Period size: 19 Copynumber: 3.9 Consensus size: 19
546383 ATGACCAATA
* *
546393 AAATCGTAATGCGATCTTT
1 AAATCGTAACGCGATCTCT
*
546412 AAATCGCAACGCGATCTCT
1 AAATCGTAACGCGATCTCT
546431 AAATCGTAACGCGATCTCT
1 AAATCGTAACGCGATCTCT
546450 AAATCGTAACGCGATCTC
1 AAATCGTAACGCGATCTC
546468 CAGTATCGCA
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 52 1.00
ACGTcount: A:0.32, C:0.25, G:0.16, T:0.27
Consensus pattern (19 bp):
AAATCGTAACGCGATCTCT
Found at i:546516 original size:20 final size:20
Alignment explanation
Indices: 546493--546666 Score: 131
Period size: 20 Copynumber: 8.6 Consensus size: 20
546483 GTTTTCAAAT
*
546493 TCGCAACGCGATTTTGACAA
1 TCGCAACGCGATTCTGACAA
* * *
546513 TCGCAATGCGAATATGTA-AA
1 TCGCAACGCGATTCTG-ACAA
* *
546533 TCGCAACGCAATTCTGACTA
1 TCGCAACGCGATTCTGACAA
**
546553 TCGCAACGCGATAAT-ACATAA
1 TCGCAACGCGATTCTGAC--AA
*
546574 TCGCAACGCGATTCTGACCA
1 TCGCAACGCGATTCTGACAA
546594 TCGCAACGCGATTCTGATC-A
1 TCGCAACGCGATTCTGA-CAA
* **
546614 TCGCAACGTGATAAT-ACATAA
1 TCGCAACGCGATTCTGAC--AA
* * *
546635 TCGCAATGCTATTCTGACTA
1 TCGCAACGCGATTCTGACAA
546655 TCGCAACGCGAT
1 TCGCAACGCGAT
546667 AATACAAATC
Statistics
Matches: 118, Mismatches: 26, Indels: 20
0.72 0.16 0.12
Matches are distributed among these distances:
18 1 0.01
19 4 0.03
20 82 0.69
21 27 0.23
22 4 0.03
ACGTcount: A:0.32, C:0.26, G:0.18, T:0.24
Consensus pattern (20 bp):
TCGCAACGCGATTCTGACAA
Found at i:546638 original size:41 final size:40
Alignment explanation
Indices: 546593--546687 Score: 129
Period size: 41 Copynumber: 2.4 Consensus size: 40
546583 GATTCTGACC
* *
546593 ATCGCAACGCGATTCTGA-TCATCGCAACGTGATAATACATA
1 ATCGCAATGCGATTCTGACT-ATCGCAACGCGATAATACA-A
*
546634 ATCGCAATGCTATTCTGACTATCGCAACGCGATAATACAA
1 ATCGCAATGCGATTCTGACTATCGCAACGCGATAATACAA
*
546674 ATCTCAATGCGATT
1 ATCGCAATGCGATT
546688 TTCAAAGAGC
Statistics
Matches: 48, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
40 13 0.27
41 34 0.71
42 1 0.02
ACGTcount: A:0.34, C:0.24, G:0.16, T:0.26
Consensus pattern (40 bp):
ATCGCAATGCGATTCTGACTATCGCAACGCGATAATACAA
Found at i:546664 original size:61 final size:61
Alignment explanation
Indices: 546532--546666 Score: 209
Period size: 61 Copynumber: 2.2 Consensus size: 61
546522 GAATATGTAA
*
546532 ATCGCAACGCAATTCTGACTATCGCAACGCGATAATACATAATCGCAACGCGATTCTGACC
1 ATCGCAACGCGATTCTGACTATCGCAACGCGATAATACATAATCGCAACGCGATTCTGACC
* * * *
546593 ATCGCAACGCGATTCTGA-TCATCGCAACGTGATAATACATAATCGCAATGCTATTCTGACT
1 ATCGCAACGCGATTCTGACT-ATCGCAACGCGATAATACATAATCGCAACGCGATTCTGACC
546654 ATCGCAACGCGAT
1 ATCGCAACGCGAT
546667 AATACAAATC
Statistics
Matches: 68, Mismatches: 5, Indels: 2
0.91 0.07 0.03
Matches are distributed among these distances:
60 1 0.01
61 67 0.99
ACGTcount: A:0.32, C:0.27, G:0.17, T:0.24
Consensus pattern (61 bp):
ATCGCAACGCGATTCTGACTATCGCAACGCGATAATACATAATCGCAACGCGATTCTGACC
Found at i:546856 original size:22 final size:22
Alignment explanation
Indices: 546831--546877 Score: 94
Period size: 22 Copynumber: 2.1 Consensus size: 22
546821 CTACGGCGAC
546831 ATCCGTCCCCATCTCCGACGAA
1 ATCCGTCCCCATCTCCGACGAA
546853 ATCCGTCCCCATCTCCGACGAA
1 ATCCGTCCCCATCTCCGACGAA
546875 ATC
1 ATC
546878 AGTCTATCTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.23, C:0.45, G:0.13, T:0.19
Consensus pattern (22 bp):
ATCCGTCCCCATCTCCGACGAA
Found at i:547281 original size:20 final size:20
Alignment explanation
Indices: 547256--547372 Score: 68
Period size: 20 Copynumber: 6.2 Consensus size: 20
547246 AAAATCGCAA
547256 CGATAGTCAAATTCGCGTTG
1 CGATAGTCAAATTCGCGTTG
** **
547276 CGATAGTCATTTTCATGTTG
1 CGATAGTCAAATTCGCGTTG
** *
547296 CGATTTTC-ATTTCGCGTTG
1 CGATAGTCAAATTCGCGTTG
* *
547315 CGAT--T---A-TCTCGTTA
1 CGATAGTCAAATTCGCGTTG
547329 CGATAGTCAAATTCGCGTTG
1 CGATAGTCAAATTCGCGTTG
* ** *
547349 CGATAATCATTTTCGTGTTG
1 CGATAGTCAAATTCGCGTTG
547369 CGAT
1 CGAT
547373 TTTAAGTTTC
Statistics
Matches: 73, Mismatches: 18, Indels: 12
0.71 0.17 0.12
Matches are distributed among these distances:
14 10 0.14
16 1 0.01
17 1 0.01
19 13 0.18
20 48 0.66
ACGTcount: A:0.21, C:0.19, G:0.21, T:0.39
Consensus pattern (20 bp):
CGATAGTCAAATTCGCGTTG
Found at i:547394 original size:73 final size:73
Alignment explanation
Indices: 547255--547394 Score: 192
Period size: 73 Copynumber: 1.9 Consensus size: 73
547245 GAAAATCGCA
* * * ***
547255 ACGATAGTCAAATTCGCGTTGCGATAGTCATTTTCATGTTGCGATTTTCATTTCGCGTTGCGATT
1 ACGATAGTCAAATTCGCGTTGCGATAATCATTTTCATGTTGCGATTTTAATTTCGAGAAACGATT
547320 ATCTCGTT
66 ATCTCGTT
* *
547328 ACGATAGTCAAATTCGCGTTGCGATAATCATTTTCGTGTTGCGATTTTAAGTTTC-AGAAACTAT
1 ACGATAGTCAAATTCGCGTTGCGATAATCATTTTCATGTTGCGATTTTAA-TTTCGAGAAACGAT
547392 TAT
65 TAT
547395 TCTTCTGCAA
Statistics
Matches: 58, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
73 54 0.93
74 4 0.07
ACGTcount: A:0.24, C:0.17, G:0.19, T:0.40
Consensus pattern (73 bp):
ACGATAGTCAAATTCGCGTTGCGATAATCATTTTCATGTTGCGATTTTAATTTCGAGAAACGATT
ATCTCGTT
Done.