Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005349.1 Hibiscus syriacus cultivar Beakdansim tig00012136_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: 1796274
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
File 2 of 8
Found at i:269183 original size:37 final size:37
Alignment explanation
Indices: 269131--269209 Score: 131
Period size: 37 Copynumber: 2.1 Consensus size: 37
269121 TTTTGTTCGG
*
269131 GTCGGGTCGGGTTTTTTAAGTGTGATATTCGGGTCGA
1 GTCGGATCGGGTTTTTTAAGTGTGATATTCGGGTCGA
* *
269168 GTCGGATCGGTTTTTTTAAGTGTGATATTCGGGTCGG
1 GTCGGATCGGGTTTTTTAAGTGTGATATTCGGGTCGA
269205 GTCGG
1 GTCGG
269210 GTCGAGTTCG
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
37 39 1.00
ACGTcount: A:0.13, C:0.11, G:0.38, T:0.38
Consensus pattern (37 bp):
GTCGGATCGGGTTTTTTAAGTGTGATATTCGGGTCGA
Found at i:274081 original size:26 final size:28
Alignment explanation
Indices: 274021--274082 Score: 74
Period size: 31 Copynumber: 2.2 Consensus size: 28
274011 GAGTATTGCT
*
274021 GAGCTCGACTCGACTCGAAAACTCTGAAATG
1 GAGCTCGACTCGACTCGAAAACTCTG--A-C
274052 GAGCTCGACTCGACTCGAAAACTC-G-C
1 GAGCTCGACTCGACTCGAAAACTCTGAC
274078 GAGCT
1 GAGCT
274083 TAAAATTTTC
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
26 5 0.17
30 1 0.03
31 24 0.80
ACGTcount: A:0.29, C:0.29, G:0.24, T:0.18
Consensus pattern (28 bp):
GAGCTCGACTCGACTCGAAAACTCTGAC
Found at i:274719 original size:121 final size:122
Alignment explanation
Indices: 274504--274743 Score: 419
Period size: 121 Copynumber: 2.0 Consensus size: 122
274494 TCCCTAATGG
** *
274504 TACATATGGAGATTATGGTACCAAACTACCAATGGCCATACAATGGCCGTAGCCCTCCGACATTC
1 TACATATGGAGATTATGGTACCAAACTACCAATGGCCATACAATGAACGTAGCCCTCCAACATTC
274569 TGCTAAATCCAACTCGCTACTTTCACATAGTTCAATCTGAGACTTCCAAGTTGGCCA
66 TGCTAAATCCAACTCGCTACTTTCACATAGTTCAATCTGAGACTTCCAAGTTGGCCA
* * *
274626 TACATATGTAGATTATGGTACGAAACTACCATTGG-CATACAATGAACGTAGCCCTCCAACATTC
1 TACATATGGAGATTATGGTACCAAACTACCAATGGCCATACAATGAACGTAGCCCTCCAACATTC
274690 TGCTAAATCCAACTCGCTACTTTCACATAGTTCAATCTGAGACTTCCAAGTTGG
66 TGCTAAATCCAACTCGCTACTTTCACATAGTTCAATCTGAGACTTCCAAGTTGG
274744 ACTCTTTAAG
Statistics
Matches: 112, Mismatches: 6, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
121 80 0.71
122 32 0.29
ACGTcount: A:0.30, C:0.26, G:0.16, T:0.28
Consensus pattern (122 bp):
TACATATGGAGATTATGGTACCAAACTACCAATGGCCATACAATGAACGTAGCCCTCCAACATTC
TGCTAAATCCAACTCGCTACTTTCACATAGTTCAATCTGAGACTTCCAAGTTGGCCA
Found at i:289878 original size:10 final size:10
Alignment explanation
Indices: 289863--289930 Score: 64
Period size: 10 Copynumber: 6.1 Consensus size: 10
289853 TTTTTGTGTG
289863 TGTTCGTTTA
1 TGTTCGTTTA
289873 TGTTCGTTTA
1 TGTTCGTTTA
289883 TTGTGTTCGTTTA
1 ---TGTTCGTTTA
*
289896 TGTTCGTTCGTTCG
1 TGTTCG-T--TT-A
289910 TGTTCGTTTA
1 TGTTCGTTTA
289920 TGTTCGTTTA
1 TGTTCGTTTA
289930 T
1 T
289931 TTATTAAATG
Statistics
Matches: 49, Mismatches: 2, Indels: 14
0.75 0.03 0.22
Matches are distributed among these distances:
10 27 0.55
11 3 0.06
13 13 0.27
14 6 0.12
ACGTcount: A:0.07, C:0.12, G:0.22, T:0.59
Consensus pattern (10 bp):
TGTTCGTTTA
Found at i:289887 original size:23 final size:23
Alignment explanation
Indices: 289861--289931 Score: 115
Period size: 23 Copynumber: 3.0 Consensus size: 23
289851 GTTTTTTGTG
289861 TGTGTTCGTTTATGTTCGTTTAT
1 TGTGTTCGTTTATGTTCGTTTAT
**
289884 TGTGTTCGTTTATGTTCGTTCGT
1 TGTGTTCGTTTATGTTCGTTTAT
289907 TCGTGTTCGTTTATGTTCGTTTAT
1 T-GTGTTCGTTTATGTTCGTTTAT
289931 T
1 T
289932 TATTAAATGA
Statistics
Matches: 43, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
23 22 0.51
24 21 0.49
ACGTcount: A:0.07, C:0.11, G:0.23, T:0.59
Consensus pattern (23 bp):
TGTGTTCGTTTATGTTCGTTTAT
Found at i:290019 original size:16 final size:16
Alignment explanation
Indices: 289998--290028 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
289988 AAAAATTTTA
289998 TTCGTTTATATTCGTG
1 TTCGTTTATATTCGTG
*
290014 TTCGTTTATGTTCGT
1 TTCGTTTATATTCGT
290029 TTATTTATTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.10, C:0.13, G:0.19, T:0.58
Consensus pattern (16 bp):
TTCGTTTATATTCGTG
Found at i:297068 original size:43 final size:43
Alignment explanation
Indices: 297007--297256 Score: 376
Period size: 43 Copynumber: 5.8 Consensus size: 43
296997 GTAAAAACGA
* * *
297007 TAAGGTCTTACCCTTGCACATAGCAAAAGAACCTAGGGAAACTG
1 TAAGG-CTTACCCTTGCACACAGCAAAGGAACCTGGGGAAACTG
* * *
297051 TAAGGTTTACCCTTGCACACAACAAAGTAACCTGGGGAAACTG
1 TAAGGCTTACCCTTGCACACAGCAAAGGAACCTGGGGAAACTG
* *
297094 TAAGGCTTACCCTTGCATATAGCAAAGGAACCTGGGGAAACTG
1 TAAGGCTTACCCTTGCACACAGCAAAGGAACCTGGGGAAACTG
* *
297137 TAAGGCTTACCCTTGCACATAGCAAAGGAACCTGAGGAAACTG
1 TAAGGCTTACCCTTGCACACAGCAAAGGAACCTGGGGAAACTG
*
297180 TAAGGCTTACCCTTGCACACATC-AAGGAAACCTGGGGAAACTG
1 TAAGGCTTACCCTTGCACACAGCAAAGG-AACCTGGGGAAACTG
297223 TAAGGCTTACCCTTGCACACAGCAAAGGAACCTG
1 TAAGGCTTACCCTTGCACACAGCAAAGGAACCTG
297257 TGGTAACGGT
Statistics
Matches: 187, Mismatches: 17, Indels: 5
0.89 0.08 0.02
Matches are distributed among these distances:
42 4 0.02
43 174 0.93
44 9 0.05
ACGTcount: A:0.34, C:0.24, G:0.22, T:0.20
Consensus pattern (43 bp):
TAAGGCTTACCCTTGCACACAGCAAAGGAACCTGGGGAAACTG
Found at i:297247 original size:129 final size:130
Alignment explanation
Indices: 297007--297256 Score: 414
Period size: 129 Copynumber: 1.9 Consensus size: 130
296997 GTAAAAACGA
*
297007 TAAGGTCTTACCCTTGCACATAGCAAAAGAACCTAGGGAAACTGTAAGGTTTACCCTTGCACACA
1 TAAGGTCTTACCCTTGCACATAGCAAAAGAACCTAGGGAAACTGTAAGGCTTACCCTTGCACACA
* * *
297072 ACAAAGTAACCTGGGGAAACTGTAAGGCTTACCCTTGCATATAGCAAAGGAACCTGGGGAAACTG
66 ACAAAGAAACCTGGGGAAACTGTAAGGCTTACCCTTGCACACAGCAAAGGAACCTGGGGAAACTG
*
297137 TAAGG-CTTACCCTTGCACATAGCAAAGGAACCT-GAGGAAACTGTAAGGCTTACCCTTGCACAC
1 TAAGGTCTTACCCTTGCACATAGCAAAAGAACCTAG-GGAAACTGTAAGGCTTACCCTTGCACAC
* *
297200 ATCAAGGAAACCTGGGGAAACTGTAAGGCTTACCCTTGCACACAGCAAAGGAACCTG
65 AACAAAGAAACCTGGGGAAACTGTAAGGCTTACCCTTGCACACAGCAAAGGAACCTG
297257 TGGTAACGGT
Statistics
Matches: 112, Mismatches: 7, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
128 1 0.01
129 106 0.95
130 5 0.04
ACGTcount: A:0.34, C:0.24, G:0.22, T:0.20
Consensus pattern (130 bp):
TAAGGTCTTACCCTTGCACATAGCAAAAGAACCTAGGGAAACTGTAAGGCTTACCCTTGCACACA
ACAAAGAAACCTGGGGAAACTGTAAGGCTTACCCTTGCACACAGCAAAGGAACCTGGGGAAACTG
Found at i:301254 original size:64 final size:63
Alignment explanation
Indices: 301169--301353 Score: 191
Period size: 64 Copynumber: 2.9 Consensus size: 63
301159 GCACTACTTG
* *
301169 TGCATCGGTGCATAAAATGCATTCAATGTTTTCTTATTAATGAGATGCATCGATGCA-T-GCCTT
1 TGCATCGATGCATAAAATGCATTCGATGTTTTCTTATTAA-GAGATGCATCGATGCATTAG-C-T
301232 A
63 A
* * * *
301233 TGCATCGATGCACT-AATTGCATTCGATGTTCTATTATTAAAAGGATGCATCGATGCATTAGCTA
1 TGCATCGATGCA-TAAAATGCATTCGATGTTTTCTTATTAAGA-GATGCATCGATGCATTAGCTA
* *
301297 TGCATCGATGCATCAAAGGCATTCGATGTTCTTCTT-TTAA-AGGAATGCATCGATGCA
1 TGCATCGATGCATAAAATGCATTCGATGTT-TTCTTATTAAGA-G-ATGCATCGATGCA
301354 CTTATGAATG
Statistics
Matches: 104, Mismatches: 10, Indels: 14
0.81 0.08 0.11
Matches are distributed among these distances:
63 5 0.05
64 92 0.88
65 6 0.06
66 1 0.01
ACGTcount: A:0.29, C:0.18, G:0.19, T:0.34
Consensus pattern (63 bp):
TGCATCGATGCATAAAATGCATTCGATGTTTTCTTATTAAGAGATGCATCGATGCATTAGCTA
Found at i:305403 original size:64 final size:64
Alignment explanation
Indices: 305293--305504 Score: 202
Period size: 64 Copynumber: 3.3 Consensus size: 64
305283 TCTTTCAATG
* * * * *
305293 AAGGTATGCATCGATGCACTACTTGTGCATCGGTGCATAAAATGCATTCAATGTTTTTTTATTAA
1 AAGG-ATGCATCGATGCACTGCTTATGCATCGATGCATAAAATGCATTCAATGTTCTATTATTAA
* * *
305358 TTA-GATGCATCGATGCA-TGCCTTATGCATCGATGCACT-AATTGCATTCGATGTTCTATTATT
1 -AAGGATGCATCGATGCACTG-CTTATGCATCGATGCA-TAAAATGCATTCAATGTTCTATTATT
305420 AA
63 AA
* * * * *
305422 AAGGATGCATCGATGCATTAGC-TATGCATCGATGCATCAAAGGCATTCGATGTTCT-TCT-TTT
1 AAGGATGCATCGATGCACT-GCTTATGCATCGATGCATAAAATGCATTCAATGTTCTAT-TATTA
305484 A
64 A
305485 AAGGAATGCATCGATGCACT
1 AAGG-ATGCATCGATGCACT
305505 TATGAATGTG
Statistics
Matches: 125, Mismatches: 13, Indels: 18
0.80 0.08 0.12
Matches are distributed among these distances:
63 11 0.09
64 108 0.86
65 4 0.03
66 2 0.02
ACGTcount: A:0.28, C:0.18, G:0.19, T:0.34
Consensus pattern (64 bp):
AAGGATGCATCGATGCACTGCTTATGCATCGATGCATAAAATGCATTCAATGTTCTATTATTAA
Found at i:308770 original size:30 final size:30
Alignment explanation
Indices: 308734--308797 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 30
308724 GAAGGACCTG
* *
308734 TCCAGAGGTTACAAAGAACCTCGGTAACTA
1 TCCAGAGGTCACAAAGAACCTCGGAAACTA
* * *
308764 TCCAGAGGTCATAAAGATCCTCGGAAACTG
1 TCCAGAGGTCACAAAGAACCTCGGAAACTA
308794 TCCA
1 TCCA
308798 TATGTTCCTT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.34, C:0.25, G:0.20, T:0.20
Consensus pattern (30 bp):
TCCAGAGGTCACAAAGAACCTCGGAAACTA
Found at i:309504 original size:64 final size:64
Alignment explanation
Indices: 309392--309603 Score: 184
Period size: 64 Copynumber: 3.3 Consensus size: 64
309382 TCTTTCAATG
* * * * *
309392 AAGGTATGCATCGATGCACTACTTGTGCATCGGTGCATAAAATGCATTCAATGTTTTCTTATT-A
1 AAGG-ATGCATCGATGCACTGCTTATGCATCGATGCATAAAATGCATTCAATGTTCTATTATTAA
* * * *
309456 ATGAGATGCATCGATGCA-TGCCTTATGCATCGATGCACT-AATTTCATTCGATGTTCTATTATT
1 AAG-GATGCATCGATGCACTG-CTTATGCATCGATGCA-TAAAATGCATTCAATGTTCTATTATT
309519 AA
63 AA
* * * * * *
309521 AAGGATGCATCAATGCATTAGC-TATGCATCGATGCATCAAAGGCATTCGATGTTCT-TCT-TTT
1 AAGGATGCATCGATGCACT-GCTTATGCATCGATGCATAAAATGCATTCAATGTTCTAT-TATTA
309583 A
64 A
309584 AAGGAATGCATCGATGCACT
1 AAGG-ATGCATCGATGCACT
309604 TATGAATGTG
Statistics
Matches: 122, Mismatches: 17, Indels: 18
0.78 0.11 0.11
Matches are distributed among these distances:
63 10 0.08
64 104 0.85
65 7 0.06
66 1 0.01
ACGTcount: A:0.29, C:0.18, G:0.19, T:0.34
Consensus pattern (64 bp):
AAGGATGCATCGATGCACTGCTTATGCATCGATGCATAAAATGCATTCAATGTTCTATTATTAA
Found at i:312736 original size:30 final size:30
Alignment explanation
Indices: 312700--312763 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 30
312690 GAAGGACCTG
* *
312700 TCCAGAGGTTACAAAGAACCTCGGTAACTA
1 TCCAGAGGTCACAAAGAACCTCGGCAACTA
* * *
312730 TCCAGAGGTCATAAAGATCCTCGGCAACTG
1 TCCAGAGGTCACAAAGAACCTCGGCAACTA
312760 TCCA
1 TCCA
312764 TATGTTCCTT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.33, C:0.27, G:0.20, T:0.20
Consensus pattern (30 bp):
TCCAGAGGTCACAAAGAACCTCGGCAACTA
Found at i:313560 original size:64 final size:62
Alignment explanation
Indices: 313444--313614 Score: 168
Period size: 64 Copynumber: 2.7 Consensus size: 62
313434 TCGGTGCATA
* * * *
313444 AAATGCATTCAATGTTTTCTTATTAATGAGATGCATCGATGCATGCCTTATGCATCGATGCA-C
1 AAATGCATTCGATGTTCT-TTATTAAAG-GATGCATCGATGCATGCCTTATGCATCGATACATC
*
313507 TAATTGCATTCGATGTTCTATTATTAAAAGGATGCATCGATGCATTAG-C-TATGCATCGATACA
1 -AAATGCATTCGATGTTCT-TTATT-AAAGGATGCATCGATGCA-T-GCCTTATGCATCGATACA
313570 TC
61 TC
* * *
313572 AAAGGAATTCGATGTTCTTCTTTTAAAGGAATGCATCGATGCA
1 AAATGCATTCGATGTTCTT-TATTAAAGG-ATGCATCGATGCA
313615 CTTATGAATG
Statistics
Matches: 91, Mismatches: 10, Indels: 12
0.81 0.09 0.11
Matches are distributed among these distances:
63 6 0.07
64 78 0.86
65 6 0.07
66 1 0.01
ACGTcount: A:0.30, C:0.17, G:0.18, T:0.35
Consensus pattern (62 bp):
AAATGCATTCGATGTTCTTTATTAAAGGATGCATCGATGCATGCCTTATGCATCGATACATC
Found at i:314479 original size:14 final size:14
Alignment explanation
Indices: 314460--314487 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
314450 TTATGGTCAA
314460 CAATGGTCAACGAT
1 CAATGGTCAACGAT
314474 CAATGGTCAACGAT
1 CAATGGTCAACGAT
314488 TTTATACAAA
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:0.21, G:0.21, T:0.21
Consensus pattern (14 bp):
CAATGGTCAACGAT
Found at i:316743 original size:2 final size:2
Alignment explanation
Indices: 316736--316789 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
316726 ATCTTACTTA
316736 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
316778 AT AT AT AT AT AT
1 AT AT AT AT AT AT
316790 TGTACATGAT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:324401 original size:17 final size:17
Alignment explanation
Indices: 324357--324400 Score: 72
Period size: 17 Copynumber: 2.6 Consensus size: 17
324347 ATGATTTGGA
324357 ATTAGAGTTTTCAAAGT
1 ATTAGAGTTTTCAAAGT
324374 ATTAGAGTTTTCAAAGT
1 ATTAGAGTTTTCAAAGT
*
324391 -TTTGAGTTTT
1 ATTAGAGTTTT
324401 TTTATTTAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
16 9 0.35
17 17 0.65
ACGTcount: A:0.30, C:0.05, G:0.18, T:0.48
Consensus pattern (17 bp):
ATTAGAGTTTTCAAAGT
Found at i:326822 original size:18 final size:19
Alignment explanation
Indices: 326799--326836 Score: 69
Period size: 18 Copynumber: 2.1 Consensus size: 19
326789 GTCTCATTCG
326799 ATTTGAAATAAGAGT-TCA
1 ATTTGAAATAAGAGTCTCA
326817 ATTTGAAATAAGAGTCTCA
1 ATTTGAAATAAGAGTCTCA
326836 A
1 A
326837 ATTTTGTTCA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 15 0.79
19 4 0.21
ACGTcount: A:0.45, C:0.08, G:0.16, T:0.32
Consensus pattern (19 bp):
ATTTGAAATAAGAGTCTCA
Found at i:327049 original size:20 final size:20
Alignment explanation
Indices: 327024--327064 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
327014 CTCTTTAATC
327024 ATTGAGGTCGCTGATACTCA
1 ATTGAGGTCGCTGATACTCA
327044 ATTGAGGTCGCTGATACTCA
1 ATTGAGGTCGCTGATACTCA
327064 A
1 A
327065 ATCCGGAATC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.27, C:0.20, G:0.24, T:0.29
Consensus pattern (20 bp):
ATTGAGGTCGCTGATACTCA
Found at i:327171 original size:23 final size:22
Alignment explanation
Indices: 327144--327205 Score: 63
Period size: 23 Copynumber: 2.8 Consensus size: 22
327134 CACTTTTAAC
327144 ATTTATATTATAATATTATATAT
1 ATTTATATTAT-ATATTATATAT
* * *
327167 ATTTAATTTTTTATATGATATAT
1 ATTT-ATATTATATATTATATAT
*
327190 A-TTATATAATATATTA
1 ATTTATATTATATATTA
327206 AAAATAAACT
Statistics
Matches: 31, Mismatches: 7, Indels: 4
0.74 0.17 0.10
Matches are distributed among these distances:
21 9 0.29
22 2 0.06
23 15 0.48
24 5 0.16
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (22 bp):
ATTTATATTATATATTATATAT
Found at i:329553 original size:2 final size:2
Alignment explanation
Indices: 329546--329572 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
329536 TGTTGATTAC
329546 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 A
329573 ATGTATGGTG
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:337197 original size:3 final size:3
Alignment explanation
Indices: 337189--337266 Score: 156
Period size: 3 Copynumber: 26.0 Consensus size: 3
337179 ACATAGGAAC
337189 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
337237 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
337267 ATGTACTTTA
Statistics
Matches: 75, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 75 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:344083 original size:20 final size:20
Alignment explanation
Indices: 344054--344091 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
344044 TTTCAAAGGG
344054 ATGCACCGATGCACCAATCC
1 ATGCACCGATGCACCAATCC
*
344074 ATGCATCGATGCACCAAT
1 ATGCACCGATGCACCAAT
344092 GAATAAATTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.32, C:0.34, G:0.16, T:0.18
Consensus pattern (20 bp):
ATGCACCGATGCACCAATCC
Found at i:352420 original size:2 final size:2
Alignment explanation
Indices: 352413--352442 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
352403 CAGCTTAAGC
352413 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
352443 ATCAATTGGC
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):
TA
Found at i:352902 original size:20 final size:20
Alignment explanation
Indices: 352873--352910 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
352863 TTTCAAAGGG
352873 ATGCACCGATGCACCAATCC
1 ATGCACCGATGCACCAATCC
*
352893 ATGCATCGATGCACCAAT
1 ATGCACCGATGCACCAAT
352911 GAATAAATTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.32, C:0.34, G:0.16, T:0.18
Consensus pattern (20 bp):
ATGCACCGATGCACCAATCC
Found at i:353684 original size:20 final size:20
Alignment explanation
Indices: 353655--353692 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
353645 TTTCAAAGGG
353655 ATGCACCGATGCACCAATCC
1 ATGCACCGATGCACCAATCC
*
353675 ATGCATCGATGCACCAAT
1 ATGCACCGATGCACCAAT
353693 GAATAAATTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.32, C:0.34, G:0.16, T:0.18
Consensus pattern (20 bp):
ATGCACCGATGCACCAATCC
Found at i:353793 original size:18 final size:18
Alignment explanation
Indices: 353770--353815 Score: 85
Period size: 18 Copynumber: 2.6 Consensus size: 18
353760 TTAATGAAAA
353770 CATCGAATGCATTTTATG
1 CATCGAATGCATTTTATG
353788 CATCGAATGCATTTTATG
1 CATCGAATGCATTTTATG
353806 CATCG-ATGCA
1 CATCGAATGCA
353816 CATACCATGC
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
17 5 0.18
18 23 0.82
ACGTcount: A:0.28, C:0.20, G:0.17, T:0.35
Consensus pattern (18 bp):
CATCGAATGCATTTTATG
Found at i:353806 original size:83 final size:82
Alignment explanation
Indices: 353705--353899 Score: 252
Period size: 83 Copynumber: 2.4 Consensus size: 82
353695 ATAAATTGAA
* * * * *
353705 CATCGAATGCATTCTATGCATTGATGCAC-TCTCCATGCATCGATGCACT-TGGGTTTTAATGAA
1 CATCGAATGCATTCTATGCATCGATGCACAT-ACCATGCACCGATGCACTGTGGCTTTT--TCAA
353768 AACATCGAATGCATTTTATG
63 AACATCGAATGCATTTTATG
*
353788 CATCGAATGCATTTTATGCATCGATGCACATACCATGCACCGATGCACTGTGGCTTTTTCAAAAC
1 CATCGAATGCATTCTATGCATCGATGCACATACCATGCACCGATGCACTGTGGCTTTTTCAAAAC
353853 ATCGAATGCATTTTATG
66 ATCGAATGCATTTTATG
* *
353870 CATCG-ATGCATACTTAGTGCACCGATGCAC
1 CATCGAATGCATTC-TA-TGCATCGATGCAC
353900 TAAGTGTTCC
Statistics
Matches: 99, Mismatches: 9, Indels: 8
0.85 0.08 0.07
Matches are distributed among these distances:
81 6 0.06
82 30 0.30
83 55 0.56
84 8 0.08
ACGTcount: A:0.28, C:0.23, G:0.18, T:0.31
Consensus pattern (82 bp):
CATCGAATGCATTCTATGCATCGATGCACATACCATGCACCGATGCACTGTGGCTTTTTCAAAAC
ATCGAATGCATTTTATG
Found at i:356786 original size:2 final size:2
Alignment explanation
Indices: 356779--356813 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
356769 TGAGAAACCA
* *
356779 TC TC TC TC TC TC TC TT TC TC TC TC TC TC TC CC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
356814 TCTAATTTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:362509 original size:397 final size:396
Alignment explanation
Indices: 361747--362541 Score: 1310
Period size: 397 Copynumber: 2.0 Consensus size: 396
361737 AAAGATGTAG
361747 TGATATCACATTCTGAAGGAACACTTTTCTTTTTCATTTAAAATTATAAGTATTTCTATTTTGGT
1 TGATATCACATTCTGAAGGAACACTTTTCTTTTTCATTTAAAATTATAAGTATTTCTATTTTGGT
361812 CGTTTGTACTGGTCGATTCCCCCTCCCCCCTTTTCTACAATTTCCCATTCAGAAATCTTTTCATT
66 CGTTTGTACTGGTCGATTCCCCCTCCCCCCTTTTCTACAATTTCCCATTCAGAAATCTTTTCATT
* * *
361877 TTAAAACCATATTAAGGTTATTAGACTGTAAGGAGTAACCCTAATTGCATGAGTAAAACTGTTTA
131 TTAAAACCATATTAAGGTTATTACACTGTAACGAGTAACCCTAATTGCATGAGTAAAACTATTTA
*
361942 TAACATGAATTGAGTAAAGGTGCGTTTATTTTTCTATCTTCTTATTTTTTCAGGTAGAGTCAGGT
196 TAACATGAATTGAGTAAAGGTGCGTTTATTTTTCTATCTTCTTATTTTTTCAGGTAGAATCAGGT
362007 ATAAATTTGCATCATTTTGGAACAGGAACCACACAGTACGAGCATTATAGCGTGCAACAAAAAAC
261 ATAAATTTGCATCATTTTGGAACAGGAACCACACAGTACGAGCATTATAGCGTGCAACAAAAAAC
****
362072 CACCATGCAATGTTGGAAGCTGAGAAGGTTTTTTTTTTTTTGCATGTTCTCCATGTGATCTATTA
326 CACCATGCAATGTTGGAAGCTGAGAAGGTAAGGTTTTTTTTGCATGTTCTCCATGTGATCTATTA
362137 CTTATT
391 CTTATT
* *
362143 TGAT-TCACATTCTGAAGGAACACTCTTCTTTTTTTCATTTAAAATTATACGTATTTCTATTTTG
1 TGATATCACATTCTGAAGGAACACT-TT-TCTTTTTCATTTAAAATTATAAGTATTTCTATTTTG
*
362207 GTCGTTTGTACTGGTCGATTCCCCCCTCCCCCCTTTT-TACAGTTTCCCATTCAGAAATCTTTTC
64 GTCGTTTGTACTGGTCGATT-CCCCCTCCCCCCTTTTCTACAATTTCCCATTCAGAAATCTTTTC
* * *
362271 ATTTTAAAACCATATTAAGGTTATTACATTGTAACGAGTAACCCTAATTGCATGAGTGAGACTAT
128 ATTTTAAAACCATATTAAGGTTATTACACTGTAACGAGTAACCCTAATTGCATGAGTAAAACTAT
* *
362336 TTATAACATGAATTGGGTAAAGGTGTGTTTATTTTTCTATCTTCTTATTTTTTTTCAGGTAGAAT
193 TTATAACATGAATTGAGTAAAGGTGCGTTTATTTTTCTATCTTCTTA--TTTTTTCAGGTAGAAT
362401 CAGGTATAAATTTGCATCATTTTGGAACAGGAACCACACAGTACGAGCATTATAGCGTGCAACAA
256 CAGGTATAAATTTGCATCATTTTGGAACAGGAACCACACAGTACGAGCATTATAGCGTGCAAC-A
*
362466 AAAAACCACCATGCAATGTTGGAAGCTGAGAA-G-AAGGTTTTTTTTTTTTGCATGTTCTCCCTG
320 AAAAACCACCATGCAATGTTGGAAGCTGAGAAGGTAAGG----TTTTTTTTGCATGTTCTCCATG
*
362529 TGATCTGTTACTT
381 TGATCTATTACTT
362542 CTTATTTGAT
Statistics
Matches: 371, Mismatches: 18, Indels: 14
0.92 0.04 0.03
Matches are distributed among these distances:
395 20 0.05
396 6 0.02
397 184 0.50
398 16 0.04
399 79 0.21
400 33 0.09
402 33 0.09
ACGTcount: A:0.28, C:0.18, G:0.16, T:0.39
Consensus pattern (396 bp):
TGATATCACATTCTGAAGGAACACTTTTCTTTTTCATTTAAAATTATAAGTATTTCTATTTTGGT
CGTTTGTACTGGTCGATTCCCCCTCCCCCCTTTTCTACAATTTCCCATTCAGAAATCTTTTCATT
TTAAAACCATATTAAGGTTATTACACTGTAACGAGTAACCCTAATTGCATGAGTAAAACTATTTA
TAACATGAATTGAGTAAAGGTGCGTTTATTTTTCTATCTTCTTATTTTTTCAGGTAGAATCAGGT
ATAAATTTGCATCATTTTGGAACAGGAACCACACAGTACGAGCATTATAGCGTGCAACAAAAAAC
CACCATGCAATGTTGGAAGCTGAGAAGGTAAGGTTTTTTTTGCATGTTCTCCATGTGATCTATTA
CTTATT
Found at i:375413 original size:10 final size:10
Alignment explanation
Indices: 375398--375465 Score: 64
Period size: 10 Copynumber: 6.1 Consensus size: 10
375388 TTTTTGTGTG
375398 TGTTCGTTTA
1 TGTTCGTTTA
375408 TGTTCGTTTA
1 TGTTCGTTTA
375418 TTGTGTTCGTTTA
1 ---TGTTCGTTTA
*
375431 TGTTCGTTCGTTCG
1 TGTTCG-T--TT-A
375445 TGTTCGTTTA
1 TGTTCGTTTA
375455 TGTTCGTTTA
1 TGTTCGTTTA
375465 T
1 T
375466 TTATTAAATG
Statistics
Matches: 49, Mismatches: 2, Indels: 14
0.75 0.03 0.22
Matches are distributed among these distances:
10 27 0.55
11 3 0.06
13 13 0.27
14 6 0.12
ACGTcount: A:0.07, C:0.12, G:0.22, T:0.59
Consensus pattern (10 bp):
TGTTCGTTTA
Found at i:375422 original size:23 final size:23
Alignment explanation
Indices: 375396--375466 Score: 115
Period size: 23 Copynumber: 3.0 Consensus size: 23
375386 GTTTTTTGTG
375396 TGTGTTCGTTTATGTTCGTTTAT
1 TGTGTTCGTTTATGTTCGTTTAT
**
375419 TGTGTTCGTTTATGTTCGTTCGT
1 TGTGTTCGTTTATGTTCGTTTAT
375442 TCGTGTTCGTTTATGTTCGTTTAT
1 T-GTGTTCGTTTATGTTCGTTTAT
375466 T
1 T
375467 TATTAAATGA
Statistics
Matches: 43, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
23 22 0.51
24 21 0.49
ACGTcount: A:0.07, C:0.11, G:0.23, T:0.59
Consensus pattern (23 bp):
TGTGTTCGTTTATGTTCGTTTAT
Found at i:375552 original size:16 final size:16
Alignment explanation
Indices: 375531--375563 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
375521 AAAAAAATTT
375531 TGTTCGTTTATATTCG
1 TGTTCGTTTATATTCG
*
375547 TGTTCGTTTATGTTCG
1 TGTTCGTTTATATTCG
375563 T
1 T
375564 TTATTTATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.09, C:0.12, G:0.21, T:0.58
Consensus pattern (16 bp):
TGTTCGTTTATATTCG
Found at i:377125 original size:35 final size:36
Alignment explanation
Indices: 377079--377152 Score: 141
Period size: 36 Copynumber: 2.1 Consensus size: 36
377069 TCTTTAGAAG
377079 CATGAGACTCAAT-AAATAGTGTTATAGTCGAAAAT
1 CATGAGACTCAATAAAATAGTGTTATAGTCGAAAAT
377114 CATGAGACTCAATAAAATAGTGTTATAGTCGAAAAT
1 CATGAGACTCAATAAAATAGTGTTATAGTCGAAAAT
377150 CAT
1 CAT
377153 TTATATACTT
Statistics
Matches: 38, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
35 13 0.34
36 25 0.66
ACGTcount: A:0.43, C:0.12, G:0.16, T:0.28
Consensus pattern (36 bp):
CATGAGACTCAATAAAATAGTGTTATAGTCGAAAAT
Found at i:377714 original size:41 final size:41
Alignment explanation
Indices: 377449--377698 Score: 430
Period size: 41 Copynumber: 6.1 Consensus size: 41
377439 ATTTCGCGTT
377449 GCGATTTTCCAGATTCGCATTGCGATAGT-CAAAATCGCAAC
1 GCGATTTT-CAGATTCGCATTGCGATAGTCCAAAATCGCAAC
377490 GCGATTTTCAGATTCGCATTGCGATAGTCCAAAATCGCAAC
1 GCGATTTTCAGATTCGCATTGCGATAGTCCAAAATCGCAAC
377531 GCGATTTTCAGATTCGCATTGCGATAGTCCAAAATCGCAAC
1 GCGATTTTCAGATTCGCATTGCGATAGTCCAAAATCGCAAC
* * **
377572 GCGGTTTTAAGATTCGCATTGCGATAGTATAAAATCGCAAC
1 GCGATTTTCAGATTCGCATTGCGATAGTCCAAAATCGCAAC
377613 GCGATTTTCAGATTCGCATTGCGATAGTCCAAAATCGCAAC
1 GCGATTTTCAGATTCGCATTGCGATAGTCCAAAATCGCAAC
**
377654 GCGATTTTCAGATTCGCATTGCGATAGTTGAAAATCGCAAC
1 GCGATTTTCAGATTCGCATTGCGATAGTCCAAAATCGCAAC
377695 GCGA
1 GCGA
377699 CTGGTGGTAT
Statistics
Matches: 198, Mismatches: 10, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
40 20 0.10
41 178 0.90
ACGTcount: A:0.30, C:0.22, G:0.21, T:0.27
Consensus pattern (41 bp):
GCGATTTTCAGATTCGCATTGCGATAGTCCAAAATCGCAAC
Found at i:377788 original size:6 final size:6
Alignment explanation
Indices: 377777--377801 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
377767 GACACGTATT
377777 ACCACG ACCACG ACCACG ACCACG A
1 ACCACG ACCACG ACCACG ACCACG A
377802 TATTATTATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.36, C:0.48, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:381470 original size:29 final size:29
Alignment explanation
Indices: 381436--381494 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
381426 CCTAAATTAA
381436 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
381465 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
381494 T
1 T
381495 AGGTGAAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.24, C:0.14, G:0.14, T:0.49
Consensus pattern (29 bp):
TTTGATGTCATTGCTTACATCAATTTAGT
Found at i:384421 original size:10 final size:10
Alignment explanation
Indices: 384406--384473 Score: 64
Period size: 10 Copynumber: 6.1 Consensus size: 10
384396 TTTTTGTGTG
384406 TGTTCGTTTA
1 TGTTCGTTTA
384416 TGTTCGTTTA
1 TGTTCGTTTA
384426 TTGTGTTCGTTTA
1 ---TGTTCGTTTA
*
384439 TGTTCGTTCGTTCG
1 TGTTCG-T--TT-A
384453 TGTTCGTTTA
1 TGTTCGTTTA
384463 TGTTCGTTTA
1 TGTTCGTTTA
384473 T
1 T
384474 TTATTAAATG
Statistics
Matches: 49, Mismatches: 2, Indels: 14
0.75 0.03 0.22
Matches are distributed among these distances:
10 27 0.55
11 3 0.06
13 13 0.27
14 6 0.12
ACGTcount: A:0.07, C:0.12, G:0.22, T:0.59
Consensus pattern (10 bp):
TGTTCGTTTA
Found at i:384430 original size:23 final size:23
Alignment explanation
Indices: 384404--384474 Score: 115
Period size: 23 Copynumber: 3.0 Consensus size: 23
384394 GTTTTTTGTG
384404 TGTGTTCGTTTATGTTCGTTTAT
1 TGTGTTCGTTTATGTTCGTTTAT
**
384427 TGTGTTCGTTTATGTTCGTTCGT
1 TGTGTTCGTTTATGTTCGTTTAT
384450 TCGTGTTCGTTTATGTTCGTTTAT
1 T-GTGTTCGTTTATGTTCGTTTAT
384474 T
1 T
384475 TATTAAATGA
Statistics
Matches: 43, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
23 22 0.51
24 21 0.49
ACGTcount: A:0.07, C:0.11, G:0.23, T:0.59
Consensus pattern (23 bp):
TGTGTTCGTTTATGTTCGTTTAT
Found at i:384560 original size:16 final size:16
Alignment explanation
Indices: 384539--384571 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
384529 AAAAAAATTT
384539 TGTTCGTTTATATTCG
1 TGTTCGTTTATATTCG
*
384555 TGTTCGTTTATGTTCG
1 TGTTCGTTTATATTCG
384571 T
1 T
384572 TTATTTATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.09, C:0.12, G:0.21, T:0.58
Consensus pattern (16 bp):
TGTTCGTTTATATTCG
Found at i:390558 original size:19 final size:19
Alignment explanation
Indices: 390534--390571 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
390524 AACCCCTAAG
390534 TTAATTTTAAGGGCTTAAA
1 TTAATTTTAAGGGCTTAAA
*
390553 TTAATTTTAAGTGCTTAAA
1 TTAATTTTAAGGGCTTAAA
390572 GAATTTGTAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.37, C:0.05, G:0.13, T:0.45
Consensus pattern (19 bp):
TTAATTTTAAGGGCTTAAA
Found at i:391787 original size:20 final size:19
Alignment explanation
Indices: 391753--391792 Score: 62
Period size: 20 Copynumber: 2.1 Consensus size: 19
391743 AAATCTAGAC
391753 TAATTGAGTAATAAAATAA
1 TAATTGAGTAATAAAATAA
*
391772 TAATTGAAGTAGTAAAATAA
1 TAATTG-AGTAATAAAATAA
391792 T
1 T
391793 TATTAAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 6 0.32
20 13 0.68
ACGTcount: A:0.55, C:0.00, G:0.12, T:0.33
Consensus pattern (19 bp):
TAATTGAGTAATAAAATAA
Found at i:394152 original size:32 final size:32
Alignment explanation
Indices: 394116--394179 Score: 119
Period size: 32 Copynumber: 2.0 Consensus size: 32
394106 AAAAGAGAAG
394116 AGGTGAATCATACCTAGAGCATTAGGGAGAGT
1 AGGTGAATCATACCTAGAGCATTAGGGAGAGT
*
394148 AGGTGAATCATACCTATAGCATTAGGGAGAGT
1 AGGTGAATCATACCTAGAGCATTAGGGAGAGT
394180 CTAAGGTAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.34, C:0.12, G:0.30, T:0.23
Consensus pattern (32 bp):
AGGTGAATCATACCTAGAGCATTAGGGAGAGT
Found at i:397253 original size:61 final size:61
Alignment explanation
Indices: 397141--397255 Score: 167
Period size: 61 Copynumber: 1.9 Consensus size: 61
397131 GTAGTGCTAA
* *
397141 ACCTGCACTAAGCTTACGCCATAATGCTAATCCGGATATGACACATAAGGTCGTGCCCACC
1 ACCTACACTAAGCTTACGCCATAATGCTAATCCGGACATGACACATAAGGTCGTGCCCACC
* * * * *
397202 ACCTACACTAAGCTTATGCTATAGTGCTAATCCGGACATGATACATTAGGTCGT
1 ACCTACACTAAGCTTACGCCATAATGCTAATCCGGACATGACACATAAGGTCGT
397256 ATCCACCTTC
Statistics
Matches: 47, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
61 47 1.00
ACGTcount: A:0.30, C:0.27, G:0.18, T:0.25
Consensus pattern (61 bp):
ACCTACACTAAGCTTACGCCATAATGCTAATCCGGACATGACACATAAGGTCGTGCCCACC
Found at i:400569 original size:60 final size:60
Alignment explanation
Indices: 400501--400613 Score: 163
Period size: 60 Copynumber: 1.9 Consensus size: 60
400491 ATTCTCCCCT
* ** * *
400501 GACTATAGGGTGATGTTTCGTTGAGTCTTTCGACTATTAAAAGTTATAAAATGATTTTTC
1 GACTATAGGGTGATGTTTCGTTCAGTCCCTCGACTATCAAAAGTTACAAAATGATTTTTC
* *
400561 GACTATAGGGTGTTGTTTTGTTCAGTCCCTCGACTATCAAAAGTTACAAAATG
1 GACTATAGGGTGATGTTTCGTTCAGTCCCTCGACTATCAAAAGTTACAAAATG
400614 GTTATCCAAC
Statistics
Matches: 46, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
60 46 1.00
ACGTcount: A:0.28, C:0.13, G:0.20, T:0.38
Consensus pattern (60 bp):
GACTATAGGGTGATGTTTCGTTCAGTCCCTCGACTATCAAAAGTTACAAAATGATTTTTC
Found at i:400626 original size:60 final size:60
Alignment explanation
Indices: 400502--400626 Score: 151
Period size: 60 Copynumber: 2.1 Consensus size: 60
400492 TTCTCCCCTG
* ** * * * * *
400502 ACTATAGGGTGATGTTTCGTTGAGTCTTTCGACTATTAAAAGTTATAAAATGATTTTTCG
1 ACTATAGGGTGATGTTTCGTTCAGTCCCTCGACTATCAAAAGTTACAAAATGATTATCCA
* * *
400562 ACTATAGGGTGTTGTTTTGTTCAGTCCCTCGACTATCAAAAGTTACAAAATGGTTATCCA
1 ACTATAGGGTGATGTTTCGTTCAGTCCCTCGACTATCAAAAGTTACAAAATGATTATCCA
400622 ACTAT
1 ACTAT
400627 TTAGTATGTT
Statistics
Matches: 54, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
60 54 1.00
ACGTcount: A:0.29, C:0.14, G:0.18, T:0.38
Consensus pattern (60 bp):
ACTATAGGGTGATGTTTCGTTCAGTCCCTCGACTATCAAAAGTTACAAAATGATTATCCA
Found at i:401041 original size:2 final size:2
Alignment explanation
Indices: 401034--401059 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
401024 TGTATGGCAA
401034 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
401060 GACCAATCAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:404424 original size:149 final size:149
Alignment explanation
Indices: 404154--404456 Score: 597
Period size: 149 Copynumber: 2.0 Consensus size: 149
404144 ATCTTTGACT
*
404154 TTTATTGACACTCATTGTTACAGGTTGTCCTTTATAATTTTGGTTGCTGTTACCTTCTTTGGAGC
1 TTTATTAACACTCATTGTTACAGGTTGTCCTTTATAATTTTGGTTGCTGTTACCTTCTTTGGAGC
404219 ATTGAGTTCTCTCATTTTGGTTCTTAGAACCAGAAAGTACTACAGAGGCCATATATACAAGAAAT
66 ATTGAGTTCTCTCATTTTGGTTCTTAGAACCAGAAAGTACTACAGAGGCCATATATACAAGAAAT
404284 ACAGAGAAAATACAGAGAG
131 ACAGAGAAAATACAGAGAG
404303 TTTATTAACACTCATTGTTACAGGTTGTCCTTTATAATTTTGGTTGCTGTTACCTTCTTTGGAGC
1 TTTATTAACACTCATTGTTACAGGTTGTCCTTTATAATTTTGGTTGCTGTTACCTTCTTTGGAGC
404368 ATTGAGTTCTCTCATTTTGGTTCTTAGAACCAGAAAGTACTACAGAGGCCATATATACAAGAAAT
66 ATTGAGTTCTCTCATTTTGGTTCTTAGAACCAGAAAGTACTACAGAGGCCATATATACAAGAAAT
404433 ACAGAGAAAATACAGAGAG
131 ACAGAGAAAATACAGAGAG
404452 TTTAT
1 TTTAT
404457 GAGCACCCAA
Statistics
Matches: 153, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
149 153 1.00
ACGTcount: A:0.30, C:0.16, G:0.18, T:0.36
Consensus pattern (149 bp):
TTTATTAACACTCATTGTTACAGGTTGTCCTTTATAATTTTGGTTGCTGTTACCTTCTTTGGAGC
ATTGAGTTCTCTCATTTTGGTTCTTAGAACCAGAAAGTACTACAGAGGCCATATATACAAGAAAT
ACAGAGAAAATACAGAGAG
Found at i:406029 original size:3 final size:3
Alignment explanation
Indices: 406021--406063 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
406011 AACAAGTTGC
406021 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
406064 GTGGACAGTT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:406165 original size:3 final size:3
Alignment explanation
Indices: 406157--406187 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
406147 AACAAGTTGC
406157 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
406188 GTGGACAGTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:407617 original size:13 final size:14
Alignment explanation
Indices: 407599--407641 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
407589 GCAAACGAAT
407599 ATAAACGAACAC-A
1 ATAAACGAACACAA
*
407612 ATAAACAAACACAA
1 ATAAACGAACACAA
* *
407626 ATGAACGAACATAA
1 ATAAACGAACACAA
407640 AT
1 AT
407642 GAAAATATAT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
13 11 0.44
14 14 0.56
ACGTcount: A:0.63, C:0.19, G:0.07, T:0.12
Consensus pattern (14 bp):
ATAAACGAACACAA
Found at i:407833 original size:20 final size:20
Alignment explanation
Indices: 407820--407875 Score: 58
Period size: 24 Copynumber: 2.6 Consensus size: 20
407810 AACATAAATG
*
407820 AACGCACATAAACAAACATA
1 AACGAACATAAACAAACATA
*
407840 AACGAACATAAATGAACGAACATA
1 AACGAACAT--A--AACAAACATA
407864 AACGAACATAAA
1 AACGAACATAAA
407876 TGAACGAACA
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
20 10 0.33
22 2 0.07
24 18 0.60
ACGTcount: A:0.61, C:0.20, G:0.09, T:0.11
Consensus pattern (20 bp):
AACGAACATAAACAAACATA
Found at i:407847 original size:14 final size:15
Alignment explanation
Indices: 407844--407889 Score: 51
Period size: 14 Copynumber: 3.2 Consensus size: 15
407834 AACATAAACG
* *
407844 AACATAAATGAAC-G
1 AACATAAACGAACAT
407858 AACATAAACGAACAT
1 AACATAAACGAACAT
*
407873 AA-ATGAACGAACAT
1 AACATAAACGAACAT
407887 AAC
1 AAC
407890 GAACATAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
14 25 0.93
15 2 0.07
ACGTcount: A:0.59, C:0.17, G:0.11, T:0.13
Consensus pattern (15 bp):
AACATAAACGAACAT
Found at i:407849 original size:34 final size:34
Alignment explanation
Indices: 407810--407898 Score: 119
Period size: 34 Copynumber: 2.6 Consensus size: 34
407800 TATTAGGCTA
*
407810 AACATAAATGAACGCACATAAACAAACATAAACG
1 AACATAAATGAACGAACATAAACAAACATAAACG
* *
407844 AACATAAATGAACGAACATAAACGAACATAAATG
1 AACATAAATGAACGAACATAAACAAACATAAACG
*
407878 AACGA-ACAT-AACGAACATAAA
1 AAC-ATAAATGAACGAACATAAA
407899 TGTATGAACA
Statistics
Matches: 50, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
33 12 0.24
34 37 0.74
35 1 0.02
ACGTcount: A:0.60, C:0.18, G:0.10, T:0.12
Consensus pattern (34 bp):
AACATAAATGAACGAACATAAACAAACATAAACG
Found at i:407856 original size:10 final size:10
Alignment explanation
Indices: 407820--407898 Score: 61
Period size: 10 Copynumber: 7.2 Consensus size: 10
407810 AACATAAATG
*
407820 AACGCACATA
1 AACGAACATA
*
407830 AACAAACATA
1 AACGAACATA
407840 AACGAACATAAA
1 AACGAACAT--A
407852 TGAACGAACATA
1 --AACGAACATA
407864 AACGAACATAAA
1 AACGAACAT--A
407876 TGAACGAACAT-
1 --AACGAACATA
407887 AACGAACATA
1 AACGAACATA
407897 AA
1 AA
407899 TGTATGAACA
Statistics
Matches: 57, Mismatches: 3, Indels: 18
0.73 0.04 0.23
Matches are distributed among these distances:
9 9 0.16
10 27 0.47
12 3 0.05
14 18 0.32
ACGTcount: A:0.59, C:0.19, G:0.10, T:0.11
Consensus pattern (10 bp):
AACGAACATA
Found at i:407861 original size:24 final size:24
Alignment explanation
Indices: 407834--407920 Score: 140
Period size: 24 Copynumber: 3.7 Consensus size: 24
407824 CACATAAACA
407834 AACATAAACGAACATAAATGAACG
1 AACATAAACGAACATAAATGAACG
407858 AACATAAACGAACATAAATGAACG
1 AACATAAACGAACATAAATGAACG
* *
407882 AACAT-AACGAACATAAATGTATG
1 AACATAAACGAACATAAATGAACG
*
407905 AACATAAATGAACATA
1 AACATAAACGAACATA
407921 CTACCGAACG
Statistics
Matches: 59, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
23 21 0.36
24 38 0.64
ACGTcount: A:0.57, C:0.15, G:0.11, T:0.16
Consensus pattern (24 bp):
AACATAAACGAACATAAATGAACG
Found at i:419624 original size:32 final size:32
Alignment explanation
Indices: 419568--419628 Score: 88
Period size: 32 Copynumber: 1.9 Consensus size: 32
419558 GATTTATATA
*
419568 TATATGTATGTATATATTGTATTTGTTGTTTG
1 TATATGTATGTATATATTGAATTTGTTGTTTG
*
419600 TATATGTATGTATGT-TATGAATTTGTTGT
1 TATATGTATGTATATAT-TGAATTTGTTGT
419629 GACAGTATCG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
31 1 0.04
32 25 0.96
ACGTcount: A:0.23, C:0.00, G:0.20, T:0.57
Consensus pattern (32 bp):
TATATGTATGTATATATTGAATTTGTTGTTTG
Found at i:420558 original size:16 final size:18
Alignment explanation
Indices: 420523--420561 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
420513 ACTAGGCTAT
*
420523 TATATATATGTTGATTTA
1 TATATATATGTTGATGTA
420541 TATATATATG-T-ATGTA
1 TATATATATGTTGATGTA
420557 TATAT
1 TATAT
420562 TGTATTTGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 9 0.45
17 1 0.05
18 10 0.50
ACGTcount: A:0.36, C:0.00, G:0.10, T:0.54
Consensus pattern (18 bp):
TATATATATGTTGATGTA
Found at i:420609 original size:32 final size:32
Alignment explanation
Indices: 420545--420611 Score: 82
Period size: 32 Copynumber: 2.1 Consensus size: 32
420535 GATTTATATA
* * *
420545 TATATGTATGTATATATTGTATTTGTTTTTTG
1 TATATGTATGTATATATTGAATTTATTGTTTG
*
420577 TATATGTATGTATGT-TATGAATTTATTGTTTG
1 TATATGTATGTATATAT-TGAATTTATTGTTTG
420609 TAT
1 TAT
420612 GTTATGAATT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
31 1 0.03
32 29 0.97
ACGTcount: A:0.24, C:0.00, G:0.16, T:0.60
Consensus pattern (32 bp):
TATATGTATGTATATATTGAATTTATTGTTTG
Found at i:420611 original size:22 final size:22
Alignment explanation
Indices: 420585--420666 Score: 121
Period size: 22 Copynumber: 3.8 Consensus size: 22
420575 TGTATATGTA
**
420585 TGTATGTTATGAATTTATTGTT
1 TGTATGTTATGAATTTGCTGTT
420607 TGTATGTTATGAATTTGCTGTT
1 TGTATGTTATGAATTTGCTGTT
*
420629 TGTATGTTATGAATTTGCTATT
1 TGTATGTTATGAATTTGCTGTT
*
420651 TG-ATGTTATGTATTTG
1 TGTATGTTATGAATTTG
420667 TTGTGTATGC
Statistics
Matches: 56, Mismatches: 4, Indels: 1
0.92 0.07 0.02
Matches are distributed among these distances:
21 13 0.23
22 43 0.77
ACGTcount: A:0.21, C:0.02, G:0.21, T:0.56
Consensus pattern (22 bp):
TGTATGTTATGAATTTGCTGTT
Found at i:421766 original size:30 final size:30
Alignment explanation
Indices: 421732--421901 Score: 212
Period size: 30 Copynumber: 5.9 Consensus size: 30
421722 TCTTTTTGAT
*
421732 TATGTAAGAAATATTATATGGTTTGTGGTC
1 TATGTTAGAAATATTATATGGTTTGTGGTC
421762 TATGTTAGAAATATTATATGG-TT-T-GTC
1 TATGTTAGAAATATTATATGGTTTGTGGTC
* * *
421789 GATGTTCA-AAACATTATATGGTTTGTGGTT
1 TATGTT-AGAAATATTATATGGTTTGTGGTC
421819 TATGTTAGAAATATTATATGG-TT-T-GTC
1 TATGTTAGAAATATTATATGGTTTGTGGTC
* *
421846 GATGTTCA-AAACATTATATGGTTTGTGGTC
1 TATGTT-AGAAATATTATATGGTTTGTGGTC
421876 TATGTTAGAAATATTATATGGTTTGT
1 TATGTTAGAAATATTATATGGTTTGT
421902 ATTAAAGTTA
Statistics
Matches: 119, Mismatches: 11, Indels: 20
0.79 0.07 0.13
Matches are distributed among these distances:
27 39 0.33
28 8 0.07
29 8 0.07
30 64 0.54
ACGTcount: A:0.29, C:0.05, G:0.21, T:0.45
Consensus pattern (30 bp):
TATGTTAGAAATATTATATGGTTTGTGGTC
Found at i:421804 original size:27 final size:27
Alignment explanation
Indices: 421774--421871 Score: 135
Period size: 27 Copynumber: 3.5 Consensus size: 27
421764 TGTTAGAAAT
421774 ATTATATGGTTTGTCGATGTTCAAAAC
1 ATTATATGGTTTGTCGATGTTCAAAAC
* *
421801 ATTATATGGTTTGTGGTTTATGTT-AGAAAT
1 ATTATATGGTTTGTCG---ATGTTCA-AAAC
421831 ATTATATGGTTTGTCGATGTTCAAAAC
1 ATTATATGGTTTGTCGATGTTCAAAAC
421858 ATTATATGGTTTGT
1 ATTATATGGTTTGT
421872 GGTCTATGTT
Statistics
Matches: 62, Mismatches: 4, Indels: 10
0.82 0.05 0.13
Matches are distributed among these distances:
27 37 0.60
28 1 0.02
29 1 0.02
30 23 0.37
ACGTcount: A:0.28, C:0.06, G:0.20, T:0.46
Consensus pattern (27 bp):
ATTATATGGTTTGTCGATGTTCAAAAC
Found at i:421832 original size:57 final size:57
Alignment explanation
Indices: 421744--421901 Score: 307
Period size: 57 Copynumber: 2.8 Consensus size: 57
421734 TGTAAGAAAT
421744 ATTATATGGTTTGTGGTCTATGTTAGAAATATTATATGGTTTGTCGATGTTCAAAAC
1 ATTATATGGTTTGTGGTCTATGTTAGAAATATTATATGGTTTGTCGATGTTCAAAAC
*
421801 ATTATATGGTTTGTGGTTTATGTTAGAAATATTATATGGTTTGTCGATGTTCAAAAC
1 ATTATATGGTTTGTGGTCTATGTTAGAAATATTATATGGTTTGTCGATGTTCAAAAC
421858 ATTATATGGTTTGTGGTCTATGTTAGAAATATTATATGGTTTGT
1 ATTATATGGTTTGTGGTCTATGTTAGAAATATTATATGGTTTGT
421902 ATTAAAGTTA
Statistics
Matches: 99, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
57 99 1.00
ACGTcount: A:0.27, C:0.05, G:0.22, T:0.46
Consensus pattern (57 bp):
ATTATATGGTTTGTGGTCTATGTTAGAAATATTATATGGTTTGTCGATGTTCAAAAC
Found at i:423260 original size:31 final size:31
Alignment explanation
Indices: 423222--423280 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
423212 AATTGTATGG
*
423222 ATTATTTAAATTTCAATATTGTAAAACTAAA
1 ATTATTTAAATTTCAATATTGCAAAACTAAA
*
423253 ATTATTTAAATTTCAGTATTGCAAAACT
1 ATTATTTAAATTTCAATATTGCAAAACT
423281 CTTTTAAGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.44, C:0.08, G:0.05, T:0.42
Consensus pattern (31 bp):
ATTATTTAAATTTCAATATTGCAAAACTAAA
Found at i:423542 original size:2 final size:2
Alignment explanation
Indices: 423535--423605 Score: 124
Period size: 2 Copynumber: 35.5 Consensus size: 2
423525 TGAGAAACCA
*
423535 TC TC TC TC TC TC TC TC TC TC TC TC TC TT TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
*
423577 TC TC TC TC TC TC TC TC TC TC TC TC CC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
423606 TCTAATTTTT
Statistics
Matches: 65, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 65 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:426782 original size:27 final size:27
Alignment explanation
Indices: 426740--426834 Score: 158
Period size: 27 Copynumber: 3.6 Consensus size: 27
426730 TTGTAGGAAT
426740 TATAGAG--ATGATTTGTTACCATTCC
1 TATAGAGATATGATTTGTTACCATTCC
*
426765 TATAGAGATATGATTTGTTTCCATTCC
1 TATAGAGATATGATTTGTTACCATTCC
426792 TATAGAGATATGATTTGTTACCATTCC
1 TATAGAGATATGATTTGTTACCATTCC
*
426819 TATAGATATATGATTT
1 TATAGAGATATGATTT
426835 TGTAAATAGA
Statistics
Matches: 65, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
25 7 0.11
27 58 0.89
ACGTcount: A:0.29, C:0.13, G:0.15, T:0.43
Consensus pattern (27 bp):
TATAGAGATATGATTTGTTACCATTCC
Found at i:430596 original size:27 final size:27
Alignment explanation
Indices: 430554--430648 Score: 158
Period size: 27 Copynumber: 3.6 Consensus size: 27
430544 GTGTAGGAAT
430554 TATAGAG--ATGATTTGTTACCATTCC
1 TATAGAGATATGATTTGTTACCATTCC
*
430579 TATAGAGATATGATTTGTTTCCATTCC
1 TATAGAGATATGATTTGTTACCATTCC
*
430606 TATAGAGATATGATTTGGTACCATTCC
1 TATAGAGATATGATTTGTTACCATTCC
430633 TATAGAGATATGATTT
1 TATAGAGATATGATTT
430649 TGTAAATAGA
Statistics
Matches: 65, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
25 7 0.11
27 58 0.89
ACGTcount: A:0.29, C:0.13, G:0.17, T:0.41
Consensus pattern (27 bp):
TATAGAGATATGATTTGTTACCATTCC
Found at i:432278 original size:20 final size:20
Alignment explanation
Indices: 432253--432299 Score: 87
Period size: 20 Copynumber: 2.4 Consensus size: 20
432243 TAAAGGTGTG
432253 TTTATTTTTCTATCTTCTTC
1 TTTATTTTTCTATCTTCTTC
432273 TTTATTTTTCTATCTTCTTC
1 TTTATTTTTCTATCTTCTTC
432293 TTT-TTTT
1 TTTATTTT
432300 CAGGTAGAGT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 4 0.15
20 23 0.85
ACGTcount: A:0.09, C:0.17, G:0.00, T:0.74
Consensus pattern (20 bp):
TTTATTTTTCTATCTTCTTC
Found at i:438698 original size:2 final size:2
Alignment explanation
Indices: 438691--438740 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
438681 AATGACAAGT
438691 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
438733 TA TA TA TA
1 TA TA TA TA
438741 ACTTCGAGTC
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:443131 original size:25 final size:25
Alignment explanation
Indices: 443101--443158 Score: 84
Period size: 25 Copynumber: 2.4 Consensus size: 25
443091 TATGAATAGA
443101 TATTTATTTAGATTTTT-TAATTTT
1 TATTTATTTAGATTTTTCTAATTTT
*
443125 TAATTTATTTAGATTTTTCTTATTTT
1 T-ATTTATTTAGATTTTTCTAATTTT
443151 T-TTTATTT
1 TATTTATTT
443159 TTAGCTATTT
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
24 8 0.26
25 16 0.52
26 7 0.23
ACGTcount: A:0.22, C:0.02, G:0.03, T:0.72
Consensus pattern (25 bp):
TATTTATTTAGATTTTTCTAATTTT
Found at i:445821 original size:15 final size:16
Alignment explanation
Indices: 445789--445821 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
445779 TAAAAGTGTT
*
445789 TAAATTATAAAAACAA
1 TAAATAATAAAAACAA
445805 TAAATAATAAAAA-AA
1 TAAATAATAAAAACAA
445820 TA
1 TA
445822 TATCGATTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 4 0.25
16 12 0.75
ACGTcount: A:0.73, C:0.03, G:0.00, T:0.24
Consensus pattern (16 bp):
TAAATAATAAAAACAA
Found at i:454295 original size:65 final size:65
Alignment explanation
Indices: 454172--454333 Score: 179
Period size: 65 Copynumber: 2.5 Consensus size: 65
454162 AATAGACGTG
* * * ** *
454172 GTGCATCGATGCATGGATTA-TGCATCGGTACATTAAATGCATTCGATGTTTCTATTAATTCAAG
1 GTGCATCGATGCATTGACTAGTGCATCGGTACACTAAATGCATTCGATAATTCAATTAATT-AAG
454236 A
65 A
* *
454237 GTGCATCGATGCATTGA-GAGTGCATCGGTACACTAAATGCATTCGA-AATTCAACTTAATTAGG
1 GTGCATCGATGCATTGACTAGTGCATCGGTACACTAAATGCATTCGATAATTCAA-TTAATTAAG
454300 A
65 A
* *
454301 ATGTATCGATGCA-TGAACTAGTGCATCGGTACA
1 GTGCATCGATGCATTG-ACTAGTGCATCGGTACA
454334 TCCCTTTGAA
Statistics
Matches: 83, Mismatches: 10, Indels: 8
0.82 0.10 0.08
Matches are distributed among these distances:
63 2 0.02
64 20 0.24
65 61 0.73
ACGTcount: A:0.31, C:0.17, G:0.22, T:0.31
Consensus pattern (65 bp):
GTGCATCGATGCATTGACTAGTGCATCGGTACACTAAATGCATTCGATAATTCAATTAATTAAGA
Found at i:456942 original size:23 final size:21
Alignment explanation
Indices: 456912--457011 Score: 80
Period size: 23 Copynumber: 4.6 Consensus size: 21
456902 CATGACAGTG
456912 TGCATCGATGCACATTCAAGAAA
1 TGCATCGATGCACATTCAAG--A
*
456935 TGCATCGATGCATC-TTCATGA
1 TGCATCGATGCA-CATTCAAGA
* *
456956 TGTATCGATGTACATTCAAAGGGA
1 TGCATCGATGCACATTC-AA--GA
*
456980 TGCATCGATGCACTATT-TAG-
1 TGCATCGATGCAC-ATTCAAGA
457000 TGCATCGATGCA
1 TGCATCGATGCA
457012 TTATGCACAA
Statistics
Matches: 64, Mismatches: 7, Indels: 15
0.74 0.08 0.17
Matches are distributed among these distances:
20 13 0.20
21 15 0.23
22 1 0.02
23 18 0.28
24 14 0.22
25 3 0.05
ACGTcount: A:0.30, C:0.20, G:0.21, T:0.29
Consensus pattern (21 bp):
TGCATCGATGCACATTCAAGA
Found at i:457007 original size:44 final size:43
Alignment explanation
Indices: 456891--457011 Score: 122
Period size: 44 Copynumber: 2.8 Consensus size: 43
456881 ATCTTGACGG
456891 ATGCATCGATGCATGA--CAGTGTGCATCGATGCACATTCAAGAA
1 ATGCATCGATGCAT-ATTCA-TGTGCATCGATGCACATTCAAGAA
* * * **
456934 ATGCATCGATGCATCTTCATGATGTATCGATGTACATTCAAAGGG
1 ATGCATCGATGCATATTCATG-TGCATCGATGCACATTC-AAGAA
*
456979 ATGCATCGATGCACTATTTA-GTGCATCGATGCA
1 ATGCATCGATGCA-TATTCATGTGCATCGATGCA
457012 TTATGCACAA
Statistics
Matches: 64, Mismatches: 9, Indels: 9
0.78 0.11 0.11
Matches are distributed among these distances:
43 16 0.25
44 27 0.42
45 17 0.27
46 4 0.06
ACGTcount: A:0.30, C:0.20, G:0.22, T:0.28
Consensus pattern (43 bp):
ATGCATCGATGCATATTCATGTGCATCGATGCACATTCAAGAA
Found at i:460697 original size:21 final size:22
Alignment explanation
Indices: 460673--460717 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 22
460663 TAAGTTATGC
**
460673 AAATCAAT-ATTTTTCTTTTCA
1 AAATCAATAATTTTGATTTTCA
*
460694 AAATCATTAATTTTGATTTTCA
1 AAATCAATAATTTTGATTTTCA
460716 AA
1 AA
460718 TCTTTAATCT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 7 0.35
22 13 0.65
ACGTcount: A:0.38, C:0.11, G:0.02, T:0.49
Consensus pattern (22 bp):
AAATCAATAATTTTGATTTTCA
Found at i:462701 original size:18 final size:16
Alignment explanation
Indices: 462641--462717 Score: 59
Period size: 17 Copynumber: 4.6 Consensus size: 16
462631 TAGAAATTAC
462641 AATTAAAAAGATAAA-A
1 AATTAAAAAGA-AAATA
*
462657 GATATAATAAGAGAAAATA
1 AAT-TAA-AA-AGAAAATA
*
462676 ATTTAAAAAAGAAAATGA
1 AATT-AAAAAGAAAAT-A
462694 AATTAAAAAGAAAA-A
1 AATTAAAAAGAAAATA
*
462709 AATCAAAAA
1 AATTAAAAA
462718 TCATAAAAAA
Statistics
Matches: 50, Mismatches: 5, Indels: 13
0.74 0.07 0.19
Matches are distributed among these distances:
15 9 0.18
16 2 0.04
17 20 0.40
18 12 0.24
19 7 0.14
ACGTcount: A:0.71, C:0.01, G:0.09, T:0.18
Consensus pattern (16 bp):
AATTAAAAAGAAAATA
Found at i:465004 original size:2 final size:2
Alignment explanation
Indices: 464997--465022 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
464987 ACACGCCGAA
464997 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
465023 GACTTGTATG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:465884 original size:92 final size:92
Alignment explanation
Indices: 465764--465935 Score: 290
Period size: 92 Copynumber: 1.9 Consensus size: 92
465754 TATGATAGAA
* *
465764 TTGAACCAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCATCATCGAATGAGTTCTTC
1 TTGAACCAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCATCATCGAACGAGTTCTTC
465829 TCATTATGAACTCTCCACTGGAAAATG
66 TCATTATGAACTCTCCACTGGAAAATG
* * * *
465856 TTGATCCAAAGTTGAACAAGTTCTTCTCATTATGAACTTTTTCTCCTTCATCGGACGAGTTCTTC
1 TTGAACCAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCATCATCGAACGAGTTCTTC
465921 TCATTATGAACTCTC
66 TCATTATGAACTCTC
465936 TATTTGAAAT
Statistics
Matches: 74, Mismatches: 6, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
92 74 1.00
ACGTcount: A:0.26, C:0.23, G:0.13, T:0.37
Consensus pattern (92 bp):
TTGAACCAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCATCATCGAACGAGTTCTTC
TCATTATGAACTCTCCACTGGAAAATG
Found at i:466110 original size:91 final size:91
Alignment explanation
Indices: 466001--466268 Score: 398
Period size: 91 Copynumber: 2.9 Consensus size: 91
465991 CGAGTGATAA
* * *
466001 GTCGAACAAGCTCTTCTCATTATGAACCTCTTCTCCCTTGTTGGATGAGTTCTTCTCATTATGAA
1 GTCGAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCGTCGGATGAGTTCTTCTCATTATGAA
**
466066 CTCTCTGCTGGAAATGTTGA-GTCAAG
66 CTCTCCACTGGAAATGTTGATG-CAAG
* *
466092 GTCGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCC-CGTCGGATGAATTCTTCTCATTATGA
1 GTCGAACAAGCTCTTCTCATTATGAACTTCTTC-TCCCTCGTCGGATGAGTTCTTCTCATTATGA
466156 ACTCTCCACTGGAAATGTTGATGCAAG
65 ACTCTCCACTGGAAATGTTGATGCAAG
* * *
466183 GTTGAACAAGCTCTTCTCATTATGAACTTATTCTTCCTCGTCGGATGAGTTCTTCTCATTATGAA
1 GTCGAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCGTCGGATGAGTTCTTCTCATTATGAA
466248 CTCTCCA-TCGGAAATGTTGAT
66 CTCTCCACT-GGAAATGTTGAT
466269 TGGTTTATCT
Statistics
Matches: 161, Mismatches: 12, Indels: 8
0.89 0.07 0.04
Matches are distributed among these distances:
90 4 0.02
91 152 0.94
92 5 0.03
ACGTcount: A:0.23, C:0.23, G:0.17, T:0.37
Consensus pattern (91 bp):
GTCGAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCGTCGGATGAGTTCTTCTCATTATGAA
CTCTCCACTGGAAATGTTGATGCAAG
Found at i:466638 original size:30 final size:30
Alignment explanation
Indices: 466604--466713 Score: 175
Period size: 30 Copynumber: 3.7 Consensus size: 30
466594 AGACAAAATT
* **
466604 TGTTTCAAGGGAAACAATCTCAAAGGTTGG
1 TGTTTCAAGAGAAACTGTCTCAAAGGTTGG
*
466634 TGTTTCAAGAGATACTGTCTCAAAGGTTGG
1 TGTTTCAAGAGAAACTGTCTCAAAGGTTGG
466664 TGTTTCAAGAGAAACTGTCTCAAAGGTTGG
1 TGTTTCAAGAGAAACTGTCTCAAAGGTTGG
*
466694 TGTTTCAAGAGAAACCGTCT
1 TGTTTCAAGAGAAACTGTCT
466714 TAAGAGAGAC
Statistics
Matches: 74, Mismatches: 6, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
30 74 1.00
ACGTcount: A:0.30, C:0.15, G:0.25, T:0.30
Consensus pattern (30 bp):
TGTTTCAAGAGAAACTGTCTCAAAGGTTGG
Found at i:466785 original size:66 final size:65
Alignment explanation
Indices: 466569--466951 Score: 381
Period size: 66 Copynumber: 5.9 Consensus size: 65
466559 AAATTTCTTA
* *
466569 TTTCAAGGGAAAACTGTTTCAAGCA-AGACAAAATTTGTTTCAAGGGAAACAATCTCAAAGGTTG
1 TTTCAAGAG-AAACTGTCTCAAG-AGAGACAAAATTTGTTTCAAGGGAAACAATCTCAAA-GTTG
466633 GTG
63 GTG
* * **
466636 TTTCAAGAGATACTGTCTCAA-AG-G------TTGGTGTTTCAAGAGAAACTGTCTCAAAGGTTG
1 TTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT--TGTTTCAAGGGAAACAATCTCAAA-GTTG
466693 GTG
63 GTG
* * ** *
466696 TTTCAAGAGAAACCGTCTTAAGAGAGACAAAACATGTTTCAAGGGAAACAATCTCAAATGTGGGT
1 TTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACAATCTCAAA-GTTGGT
466761 G
65 G
* * * * * **
466762 TTTCAAGGGAAATTGTCTCAAGAGAGACGAAATTCGTTTCAAGGGAAACGATCTCAAAGATTTTT
1 TTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACAATCTCAAAG-TTGGT
466827 G
65 G
* * * *
466828 TTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTGCAAGAGAAACATAT-TCAAAGATTTT
1 TTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACA-ATCTCAAAG--TTG
466892 GTG
63 GTG
* *
466895 TTTCAAGAGAAACTGTCTCAAGCGAGACAAAATTTGTTTCAAGGGAAACTATCTCAA
1 TTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACAATCTCAA
466952 TAGATACAAA
Statistics
Matches: 259, Mismatches: 42, Indels: 30
0.78 0.13 0.09
Matches are distributed among these distances:
58 2 0.01
60 47 0.18
61 2 0.01
62 1 0.00
64 2 0.01
65 1 0.00
66 139 0.54
67 65 0.25
ACGTcount: A:0.36, C:0.14, G:0.22, T:0.27
Consensus pattern (65 bp):
TTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACAATCTCAAAGTTGGTG
Found at i:466812 original size:21 final size:20
Alignment explanation
Indices: 466770--466812 Score: 50
Period size: 21 Copynumber: 2.1 Consensus size: 20
466760 TGTTTCAAGG
*
466770 GAAATTGTCTCAAGAGAGAC
1 GAAATTGTCTCAAGAGAAAC
* *
466790 GAAATTCGTTTCAAGGGAAAC
1 GAAATT-GTCTCAAGAGAAAC
466811 GA
1 GA
466813 TCTCAAAGAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 6 0.32
21 13 0.68
ACGTcount: A:0.40, C:0.14, G:0.26, T:0.21
Consensus pattern (20 bp):
GAAATTGTCTCAAGAGAAAC
Found at i:466871 original size:36 final size:34
Alignment explanation
Indices: 466824--467012 Score: 172
Period size: 36 Copynumber: 5.4 Consensus size: 34
466814 CTCAAAGATT
466824 TTTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAA
1 TTTGTTTCAAGAGAAACTGTCTCAA--GAGACAAAA
* * **
466860 TTTGTTGCAAGAGAAACATAT-TCAA-AG---ATT
1 TTTGTTTCAAGAGAAAC-TGTCTCAAGAGACAAAA
466890 TTGTGTTTCAAGAGAAACTGTCTCAAGCGAGACAAAA
1 TT-TGTTTCAAGAGAAACTGTCTCAA--GAGACAAAA
* * *
466927 TTTGTTTCAAGGGAAACTATCTCAATAGATACAAAA
1 TTTGTTTCAAGAGAAACTGTCTC-A-AGAGACAAAA
*
466963 TTTGTTTCAAGGGAAACTGTCTCAAGAGACAAAA
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGACAAAA
* *
466997 TTCTATTTCAAAAGAA
1 TT-TGTTTCAAGAGAA
467013 TCAGACTCAT
Statistics
Matches: 125, Mismatches: 16, Indels: 25
0.75 0.10 0.15
Matches are distributed among these distances:
30 5 0.04
31 18 0.14
33 2 0.02
34 13 0.10
35 11 0.09
36 69 0.55
37 6 0.05
38 1 0.01
ACGTcount: A:0.40, C:0.14, G:0.18, T:0.29
Consensus pattern (34 bp):
TTTGTTTCAAGAGAAACTGTCTCAAGAGACAAAA
Found at i:467249 original size:20 final size:21
Alignment explanation
Indices: 467194--467298 Score: 74
Period size: 20 Copynumber: 5.0 Consensus size: 21
467184 GGTCTTATGG
467194 ATGGCCCGAAGGACTTATCAT
1 ATGGCCCGAAGGACTTATCAT
* * * *
467215 CTTGCTCGAAAGACTTAT-AT
1 ATGGCCCGAAGGACTTATCAT
*
467235 ATGGCCCGAAGGACTTACGCAT
1 ATGGCCCGAAGGACTTA-TCAT
* *
467257 CAT-GCTCGAAAGACTTAT--T
1 -ATGGCCCGAAGGACTTATCAT
*
467276 GATGGCCTGAAGGACTTACTCAT
1 -ATGGCCCGAAGGACTTA-TCAT
467299 CAAGAAACCC
Statistics
Matches: 61, Mismatches: 16, Indels: 12
0.69 0.18 0.13
Matches are distributed among these distances:
19 3 0.05
20 26 0.43
21 15 0.25
22 14 0.23
23 3 0.05
ACGTcount: A:0.29, C:0.23, G:0.22, T:0.27
Consensus pattern (21 bp):
ATGGCCCGAAGGACTTATCAT
Found at i:467281 original size:42 final size:42
Alignment explanation
Indices: 467187--467300 Score: 169
Period size: 42 Copynumber: 2.7 Consensus size: 42
467177 ACACAGGGGT
* *
467187 CTTATGGATGGCCCGAAGGACTTA-TCATCTTGCTCGAAAGA
1 CTTATTGATGGCCCGAAGGACTTACTCATCATGCTCGAAAGA
*
467228 CTTATAT-ATGGCCCGAAGGACTTACGCATCATGCTCGAAAGA
1 CTTAT-TGATGGCCCGAAGGACTTACTCATCATGCTCGAAAGA
*
467270 CTTATTGATGGCCTGAAGGACTTACTCATCA
1 CTTATTGATGGCCCGAAGGACTTACTCATCA
467301 AGAAACCCTT
Statistics
Matches: 65, Mismatches: 5, Indels: 5
0.87 0.07 0.07
Matches are distributed among these distances:
41 23 0.35
42 42 0.65
ACGTcount: A:0.28, C:0.23, G:0.22, T:0.27
Consensus pattern (42 bp):
CTTATTGATGGCCCGAAGGACTTACTCATCATGCTCGAAAGA
Found at i:467390 original size:43 final size:43
Alignment explanation
Indices: 467337--467464 Score: 220
Period size: 43 Copynumber: 3.0 Consensus size: 43
467327 TTCTTAGTTG
*
467337 TCATCAAGGAACCCCTACATATCACGTTGGTCCCTCAAGCTTC
1 TCATAAAGGAACCCCTACATATCACGTTGGTCCCTCAAGCTTC
* *
467380 TCATAAAGGAACCCCTACACATCACATTGGTCCCTCAAGCTTC
1 TCATAAAGGAACCCCTACATATCACGTTGGTCCCTCAAGCTTC
*
467423 TCATGAAGGAACCCCTACATATCACGTTGGTCCCTCAAGCTT
1 TCATAAAGGAACCCCTACATATCACGTTGGTCCCTCAAGCTT
467465 AGTTTCTTAT
Statistics
Matches: 79, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 79 1.00
ACGTcount: A:0.27, C:0.34, G:0.14, T:0.25
Consensus pattern (43 bp):
TCATAAAGGAACCCCTACATATCACGTTGGTCCCTCAAGCTTC
Found at i:469445 original size:8 final size:7
Alignment explanation
Indices: 469426--469493 Score: 52
Period size: 8 Copynumber: 9.6 Consensus size: 7
469416 TGGATTTGTT
469426 TTCTTTA
1 TTCTTTA
469433 TTCTTTCA
1 TTCTTT-A
469441 TTCTTT-
1 TTCTTTA
469447 TTCTTT-
1 TTCTTTA
*
469453 TTCTTTC
1 TTCTTTA
469460 TCTCTTT-
1 T-TCTTTA
*
469467 TTCTTTT
1 TTCTTTA
469474 TTCTTTTA
1 TTC-TTTA
*
469482 TTTCTTTT
1 -TTCTTTA
469490 TTCT
1 TTCT
469494 CTGTTTTTCT
Statistics
Matches: 53, Mismatches: 2, Indels: 12
0.79 0.03 0.18
Matches are distributed among these distances:
6 17 0.32
7 15 0.28
8 18 0.34
9 3 0.06
ACGTcount: A:0.04, C:0.19, G:0.00, T:0.76
Consensus pattern (7 bp):
TTCTTTA
Found at i:469452 original size:6 final size:6
Alignment explanation
Indices: 469424--469480 Score: 60
Period size: 6 Copynumber: 8.5 Consensus size: 6
469414 GTTGGATTTG
469424 TTTTCT TTATTCT TTCATTCT TTTTCT TTTTCT TTCTCTCT TTTTCTT
1 TTTTCT TT-TTCT TT--TTCT TTTTCT TTTTCT TT-T-TCT TTTTC-T
469472 TTTTCT TTT
1 TTTTCT TTT
469481 ATTTCTTTTT
Statistics
Matches: 46, Mismatches: 0, Indels: 10
0.82 0.00 0.18
Matches are distributed among these distances:
6 20 0.43
7 14 0.30
8 12 0.26
ACGTcount: A:0.04, C:0.19, G:0.00, T:0.77
Consensus pattern (6 bp):
TTTTCT
Found at i:469456 original size:20 final size:20
Alignment explanation
Indices: 469424--469490 Score: 82
Period size: 21 Copynumber: 3.2 Consensus size: 20
469414 GTTGGATTTG
469424 TTTTCTTTATTCTTTCATTCT
1 TTTTCTTT-TTCTTTCATTCT
469445 TTTTCTTTTTCTTTC-TCTCT
1 TTTTCTTTTTCTTTCAT-TCT
*
469465 TTTTCTTTTTTCTTTTATTTCT
1 TTTTC-TTTTTCTTTCA-TTCT
469487 TTTT
1 TTTT
469491 TCTCTGTTTT
Statistics
Matches: 41, Mismatches: 1, Indels: 7
0.84 0.02 0.14
Matches are distributed among these distances:
19 1 0.02
20 15 0.37
21 17 0.41
22 7 0.17
23 1 0.02
ACGTcount: A:0.04, C:0.18, G:0.00, T:0.78
Consensus pattern (20 bp):
TTTTCTTTTTCTTTCATTCT
Found at i:469479 original size:33 final size:33
Alignment explanation
Indices: 469427--469526 Score: 89
Period size: 33 Copynumber: 2.9 Consensus size: 33
469417 GGATTTGTTT
*
469427 TCTTTATTCTTTCATTCTTTTTCTTTTTCTTTCTC
1 TCTTT-TTCTTT-TTTCTTTTTCTTTTTCTTTCTC
469462 TCTTTTTCTTTTTTCTTTTAT-TTCTTT-TTTCTC
1 TCTTTTTCTTTTTTCTTTT-TCTT-TTTCTTTCTC
* *
469495 TGTTTTTCTCTGTTT-TTTTTCTTATTTTCTTT
1 TCTTTTTCT-TTTTTCTTTTTC-T-TTTTCTTT
469527 TCTTTGCGTT
Statistics
Matches: 55, Mismatches: 3, Indels: 14
0.76 0.04 0.19
Matches are distributed among these distances:
32 1 0.02
33 27 0.49
34 18 0.33
35 9 0.16
ACGTcount: A:0.04, C:0.18, G:0.02, T:0.76
Consensus pattern (33 bp):
TCTTTTTCTTTTTTCTTTTTCTTTTTCTTTCTC
Found at i:469500 original size:9 final size:10
Alignment explanation
Indices: 469487--469511 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
469477 TTTTATTTCT
469487 TTTTTCTCTG
1 TTTTTCTCTG
469497 TTTTTCTCTG
1 TTTTTCTCTG
469507 TTTTT
1 TTTTT
469512 TTTCTTATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.00, C:0.16, G:0.08, T:0.76
Consensus pattern (10 bp):
TTTTTCTCTG
Found at i:469505 original size:41 final size:42
Alignment explanation
Indices: 469424--469527 Score: 103
Period size: 41 Copynumber: 2.6 Consensus size: 42
469414 GTTGGATTTG
* * * *
469424 TTTTCTTTATTCTTTCA-TTC-TTTTTCTTTTTCTTTCTCTC
1 TTTTCTTTTTTCTTTTATTTCTTTTTTCTCTGTCTTTCTCTC
469464 TTTTTCTTTTTTCTTTTATTTCTTTTTTCTCTGT-TTT-TCTC
1 -TTTTCTTTTTTCTTTTATTTCTTTTTTCTCTGTCTTTCTCTC
* *
469505 TGTT-TTTTTTCTTAT-TTTCTTTT
1 TTTTCTTTTTTCTTTTATTTCTTTT
469528 CTTTGCGTTA
Statistics
Matches: 55, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
38 8 0.15
39 10 0.18
40 3 0.05
41 19 0.35
42 6 0.11
43 9 0.16
ACGTcount: A:0.04, C:0.17, G:0.02, T:0.77
Consensus pattern (42 bp):
TTTTCTTTTTTCTTTTATTTCTTTTTTCTCTGTCTTTCTCTC
Found at i:469778 original size:2 final size:2
Alignment explanation
Indices: 469771--469819 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
469761 ACAACAATGG
469771 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
469813 AT AT AT A
1 AT AT AT A
469820 ATGATAAATG
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:472284 original size:18 final size:18
Alignment explanation
Indices: 472244--472285 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
472234 AAATTACATG
**
472244 ATTTTAATAAAATATTTT
1 ATTTTAATAAAATATGAT
472262 ATTTTAATAAAATATCGAT
1 ATTTTAATAAAATAT-GAT
472281 -TTTTA
1 ATTTTA
472286 TGGTCTGTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 20 0.95
19 1 0.05
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.52
Consensus pattern (18 bp):
ATTTTAATAAAATATGAT
Found at i:473629 original size:2 final size:2
Alignment explanation
Indices: 473622--473647 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
473612 AAACACGCCA
473622 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
473648 GGCTTGTATG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:475497 original size:17 final size:17
Alignment explanation
Indices: 475453--475496 Score: 72
Period size: 17 Copynumber: 2.6 Consensus size: 17
475443 AGGATTTGGA
475453 ATTAGAGTTTTCAAAGT
1 ATTAGAGTTTTCAAAGT
475470 ATTAGAGTTTTCAAAGT
1 ATTAGAGTTTTCAAAGT
*
475487 -TTTGAGTTTT
1 ATTAGAGTTTT
475497 TTTATTAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
16 9 0.35
17 17 0.65
ACGTcount: A:0.30, C:0.05, G:0.18, T:0.48
Consensus pattern (17 bp):
ATTAGAGTTTTCAAAGT
Found at i:476590 original size:2 final size:2
Alignment explanation
Indices: 476585--476645 Score: 122
Period size: 2 Copynumber: 30.5 Consensus size: 2
476575 TGATTATTAG
476585 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
476627 AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT A
476646 CACCATGCAG
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 59 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:480046 original size:7 final size:7
Alignment explanation
Indices: 480031--480069 Score: 51
Period size: 7 Copynumber: 5.6 Consensus size: 7
480021 ATTTTAGATC
480031 ATATAAT
1 ATATAAT
*
480038 ATATGAT
1 ATATAAT
* *
480045 ATAGATT
1 ATATAAT
480052 ATATAAT
1 ATATAAT
480059 ATATAAT
1 ATATAAT
480066 ATAT
1 ATAT
480070 TAAAAATAAA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.51, C:0.00, G:0.05, T:0.44
Consensus pattern (7 bp):
ATATAAT
Found at i:480055 original size:21 final size:21
Alignment explanation
Indices: 480025--480068 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
480015 GATCAAATTT
*
480025 TAGATCATATAATATATGATA
1 TAGATCATATAATATATAATA
*
480046 TAGATTATATAATATATAATA
1 TAGATCATATAATATATAATA
480067 TA
1 TA
480069 TTAAAAATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.50, C:0.02, G:0.07, T:0.41
Consensus pattern (21 bp):
TAGATCATATAATATATAATA
Found at i:482399 original size:48 final size:49
Alignment explanation
Indices: 482302--482399 Score: 135
Period size: 48 Copynumber: 2.0 Consensus size: 49
482292 CAATAAGTTT
* * * *
482302 ACATAAAGACAAAAAAAAGTTTGTTACAACAATAAGCACATGATAAAAAA
1 ACATAAAGAC-AAAAAAAGTTAGCTACAACAATAAGCAAATGAGAAAAAA
*
482352 ACATAAAGAC-AAAAAAGTTAGCTACAACAATAAGCAAATGAGGAAAAA
1 ACATAAAGACAAAAAAAGTTAGCTACAACAATAAGCAAATGAGAAAAAA
482400 CATGTTGATT
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
48 33 0.77
50 10 0.23
ACGTcount: A:0.60, C:0.12, G:0.12, T:0.15
Consensus pattern (49 bp):
ACATAAAGACAAAAAAAGTTAGCTACAACAATAAGCAAATGAGAAAAAA
Found at i:483140 original size:48 final size:49
Alignment explanation
Indices: 483043--483140 Score: 135
Period size: 48 Copynumber: 2.0 Consensus size: 49
483033 CAATAAGTTT
* * * *
483043 ACATAAAGACAAAAAAAAGTTTGTTACAACAATAAGCACATGATAAAAAA
1 ACATAAAGAC-AAAAAAAGTTAGCTACAACAATAAGCAAATGAGAAAAAA
*
483093 ACATAAAGAC-AAAAAAGTTAGCTACAACAATAAGCAAATGAGGAAAAA
1 ACATAAAGACAAAAAAAGTTAGCTACAACAATAAGCAAATGAGAAAAAA
483141 CATGTTGATT
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
48 33 0.77
50 10 0.23
ACGTcount: A:0.60, C:0.12, G:0.12, T:0.15
Consensus pattern (49 bp):
ACATAAAGACAAAAAAAGTTAGCTACAACAATAAGCAAATGAGAAAAAA
Found at i:483157 original size:2 final size:2
Alignment explanation
Indices: 483150--483201 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
483140 ACATGTTGAT
483150 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
483192 TA TA TA TA TA
1 TA TA TA TA TA
483202 ATGTATGGTG
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:489052 original size:121 final size:122
Alignment explanation
Indices: 488837--489062 Score: 391
Period size: 121 Copynumber: 1.9 Consensus size: 122
488827 TTTATTATGG
* * **
488837 TACATTTGGAGCTTATGGTACCAAACTACCAATGGCCATACAATGAACGTAGCCCTCTGGCATTC
1 TACATATGGAGATTATGGTACCAAACTACCAATGGCCATACAATGAACGTAGCCCTCCAGCATTC
488902 TGCTAAATCCAACTCGCGACTTTCACATAGTTCAATCTGAGACTTCCAAGTTGGCCA
66 TGCTAAATCCAACTCGCGACTTTCACATAGTTCAATCTGAGACTTCCAAGTTGGCCA
*
488959 TACATATGGAGATTATGGTACCAAACTACTAATGG-CATACAATGAACGTAGCCCTCCAGCATTC
1 TACATATGGAGATTATGGTACCAAACTACCAATGGCCATACAATGAACGTAGCCCTCCAGCATTC
*
489023 TGCTAAATCCAACTCGCTACTTTCACATAGTTCAATCTGA
66 TGCTAAATCCAACTCGCGACTTTCACATAGTTCAATCTGA
489063 TTGTGGCTGG
Statistics
Matches: 98, Mismatches: 6, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
121 66 0.67
122 32 0.33
ACGTcount: A:0.31, C:0.26, G:0.16, T:0.27
Consensus pattern (122 bp):
TACATATGGAGATTATGGTACCAAACTACCAATGGCCATACAATGAACGTAGCCCTCCAGCATTC
TGCTAAATCCAACTCGCGACTTTCACATAGTTCAATCTGAGACTTCCAAGTTGGCCA
Found at i:490087 original size:12 final size:12
Alignment explanation
Indices: 490070--490096 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
490060 TTATTGAAAA
490070 ATATATACTAAT
1 ATATATACTAAT
490082 ATATATACTAAT
1 ATATATACTAAT
490094 ATA
1 ATA
490097 ATTTAATAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.52, C:0.07, G:0.00, T:0.41
Consensus pattern (12 bp):
ATATATACTAAT
Found at i:491832 original size:24 final size:24
Alignment explanation
Indices: 491817--491934 Score: 148
Period size: 24 Copynumber: 4.9 Consensus size: 24
491807 CATAATTCAC
* * *
491817 GTCAGGTATCATATCAAAATCCAG
1 GTCAAGTATCAGATCAAAATCCAT
*
491841 GTCAAGTATCAGATCAAAATCCAA
1 GTCAAGTATCAGATCAAAATCCAT
*
491865 GTCAAGTATCAGATCAGAATCCAT
1 GTCAAGTATCAGATCAAAATCCAT
* *
491889 GTCATA-TATCATATCAGAATCCAT
1 GTCA-AGTATCAGATCAAAATCCAT
491913 GTCAAGTATCAGATCAGAAATC
1 GTCAAGTATCAGATCA-AAATC
491935 AAATAAAAAA
Statistics
Matches: 83, Mismatches: 8, Indels: 5
0.86 0.08 0.05
Matches are distributed among these distances:
23 1 0.01
24 77 0.93
25 5 0.06
ACGTcount: A:0.40, C:0.20, G:0.14, T:0.25
Consensus pattern (24 bp):
GTCAAGTATCAGATCAAAATCCAT
Found at i:491948 original size:72 final size:72
Alignment explanation
Indices: 491796--491948 Score: 182
Period size: 72 Copynumber: 2.1 Consensus size: 72
491786 CGGATATATC
* * * *
491796 AAAAATCAAATCATAATTCACGTCAGGTATCATATCAAAATCCAGGTCAAGTATCAGATCAAAAT
1 AAAAATCAGATCAGAATCCACGTCAGATATCATATCAAAATCCAGGTCAAGTATCAGATCAAAAT
* *
491861 CCAAGTC
66 CCAAATA
** * * * *
491868 AAGTATCAGATCAGAATCCATGTCATATATCATATCAGAATCCATGTCAAGTATCAGATCAGAAA
1 AAAAATCAGATCAGAATCCACGTCAGATATCATATCAAAATCCAGGTCAAGTATCAGATCA-AAA
491933 T-CAAATA
65 TCCAAATA
491940 AAAAATCAG
1 AAAAATCAG
491949 GTAAAATATT
Statistics
Matches: 66, Mismatches: 14, Indels: 2
0.80 0.17 0.02
Matches are distributed among these distances:
72 62 0.94
73 4 0.06
ACGTcount: A:0.45, C:0.19, G:0.12, T:0.24
Consensus pattern (72 bp):
AAAAATCAGATCAGAATCCACGTCAGATATCATATCAAAATCCAGGTCAAGTATCAGATCAAAAT
CCAAATA
Found at i:496710 original size:18 final size:18
Alignment explanation
Indices: 496687--496756 Score: 104
Period size: 18 Copynumber: 3.9 Consensus size: 18
496677 CAAAGTTTTT
496687 GTCAACGGGTCGGGTCGG
1 GTCAACGGGTCGGGTCGG
*
496705 GTCAACGGGTTGGGTCGG
1 GTCAACGGGTCGGGTCGG
* *
496723 GTCAACCGGTCAGGTCGG
1 GTCAACGGGTCGGGTCGG
*
496741 GTAAACGGGTCGGGTC
1 GTCAACGGGTCGGGTC
496757 AGGTTGTAAC
Statistics
Matches: 45, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 45 1.00
ACGTcount: A:0.14, C:0.21, G:0.46, T:0.19
Consensus pattern (18 bp):
GTCAACGGGTCGGGTCGG
Found at i:507045 original size:30 final size:30
Alignment explanation
Indices: 507009--507070 Score: 124
Period size: 30 Copynumber: 2.1 Consensus size: 30
506999 CTCTTTTCGT
507009 TTTTTCTTGCTCTCCAAAATTCATCCCTTC
1 TTTTTCTTGCTCTCCAAAATTCATCCCTTC
507039 TTTTTCTTGCTCTCCAAAATTCATCCCTTC
1 TTTTTCTTGCTCTCCAAAATTCATCCCTTC
507069 TT
1 TT
507071 CGTATCTTCT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.16, C:0.32, G:0.03, T:0.48
Consensus pattern (30 bp):
TTTTTCTTGCTCTCCAAAATTCATCCCTTC
Found at i:510347 original size:39 final size:37
Alignment explanation
Indices: 510270--510359 Score: 94
Period size: 39 Copynumber: 2.3 Consensus size: 37
510260 GCTTAATAAA
510270 ATATAATAATATTATTATAAATATATTAAATAATTTT
1 ATATAATAATATTATTATAAATATATTAAATAATTTT
* *
510307 ATATGATAAT-TTATTTATTAAATGATATTATA-AATCTTT
1 ATATAATAATATTA-TTA-TAAAT-ATATTAAATAAT-TTT
510346 ATATATATATATAT
1 ATATA-ATA-ATAT
510360 ATATACATGA
Statistics
Matches: 43, Mismatches: 3, Indels: 9
0.78 0.05 0.16
Matches are distributed among these distances:
36 3 0.07
37 12 0.28
38 8 0.19
39 14 0.33
40 3 0.07
41 2 0.05
42 1 0.02
ACGTcount: A:0.47, C:0.01, G:0.02, T:0.50
Consensus pattern (37 bp):
ATATAATAATATTATTATAAATATATTAAATAATTTT
Found at i:512784 original size:28 final size:28
Alignment explanation
Indices: 512751--513059 Score: 467
Period size: 28 Copynumber: 10.9 Consensus size: 28
512741 CATTTTTTAA
*
512751 AAATAATTACGAAAATATCACTTTTTCG
1 AAATAATTACCAAAATATCACTTTTTCG
512779 AAATAATTACCAAAATATCACTTTTTCG
1 AAATAATTACCAAAATATCACTTTTTCG
* *
512807 AAATAATTACTAAAATATCACTTTTTTG
1 AAATAATTACCAAAATATCACTTTTTCG
* *
512835 AAATAAGTACCAAAATATCA-ATTTTCG
1 AAATAATTACCAAAATATCACTTTTTCG
*
512862 AAATAATTACTAAAATATCACTTTTTCG
1 AAATAATTACCAAAATATCACTTTTTCG
*
512890 AAATAATGACCAAAATATCACTTTTTCG
1 AAATAATTACCAAAATATCACTTTTTCG
** *
512918 AAATAATTACCACTATATCATTTTTTTCG
1 AAATAATTACCAAAATATCA-CTTTTTCG
512947 AAATAATTACCAAAATATCACTTTTTCG
1 AAATAATTACCAAAATATCACTTTTTCG
*
512975 AAATAATTACCAAAATATCATTTTTTTTTCG
1 AAATAATTACCAAAATATCA---CTTTTTCG
*
513006 AAATAATTACCAAAATAACACTTTTTCG
1 AAATAATTACCAAAATATCACTTTTTCG
513034 AAATAATTACCAAAATATCACTTTTT
1 AAATAATTACCAAAATATCACTTTTT
513060 TTTTCGAAAT
Statistics
Matches: 253, Mismatches: 23, Indels: 10
0.88 0.08 0.03
Matches are distributed among these distances:
27 23 0.09
28 179 0.71
29 25 0.10
31 26 0.10
ACGTcount: A:0.43, C:0.16, G:0.04, T:0.38
Consensus pattern (28 bp):
AAATAATTACCAAAATATCACTTTTTCG
Found at i:513123 original size:29 final size:29
Alignment explanation
Indices: 513067--513162 Score: 129
Period size: 29 Copynumber: 3.3 Consensus size: 29
513057 TTTTTTTCGA
** *
513067 AATATTTACGAAACTAACACCTTCTTAAC
1 AATATTTACGAAACTAACATTTTTTTAAC
* * *
513096 AGTATTTACGAAACTAACTTTTTTTTAAT
1 AATATTTACGAAACTAACATTTTTTTAAC
*
513125 AATATTTACGAAACTTACATTTTTTTAAC
1 AATATTTACGAAACTAACATTTTTTTAAC
513154 AATATTTAC
1 AATATTTAC
513163 AAAAATACCA
Statistics
Matches: 57, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 57 1.00
ACGTcount: A:0.39, C:0.16, G:0.04, T:0.42
Consensus pattern (29 bp):
AATATTTACGAAACTAACATTTTTTTAAC
Found at i:514654 original size:15 final size:16
Alignment explanation
Indices: 514634--514663 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
514624 AATACCTCGT
514634 CCTGATGA-GTAACTA
1 CCTGATGACGTAACTA
514649 CCTGATGACGTAACT
1 CCTGATGACGTAACT
514664 CGAATCAAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.30, C:0.23, G:0.20, T:0.27
Consensus pattern (16 bp):
CCTGATGACGTAACTA
Found at i:517347 original size:28 final size:28
Alignment explanation
Indices: 517271--517552 Score: 346
Period size: 28 Copynumber: 10.2 Consensus size: 28
517261 ACAGTCAACT
* * *
517271 ATTACGAAAATAACACATTTTTTTAAATA
1 ATTACCAAAATATCAC-TTTTTTGAAATA
*
517300 ATTACGAAAATATCAC-TTTTTGAAATA
1 ATTACCAAAATATCACTTTTTTGAAATA
*
517327 ATTACCAAAATATCACTTTTTCGAAATA
1 ATTACCAAAATATCACTTTTTTGAAATA
*
517355 ATTACC--AA-A-CACTTTTTCGAAATA
1 ATTACCAAAATATCACTTTTTTGAAATA
*
517379 ATTACCAAAATATCACTTTTTCGAAATA
1 ATTACCAAAATATCACTTTTTTGAAATA
**
517407 ATTACCACTATATCA-TTTTTTCGAAATA
1 ATTACCAAAATATCACTTTTTT-GAAATA
*
517435 ATTACCAAAATATCACTTTTTTGAATTA
1 ATTACCAAAATATCACTTTTTTGAAATA
*
517463 ATTACCAAAATATCA-TTTTTTCAAAATA
1 ATTACCAAAATATCACTTTTTT-GAAATA
517491 ATTACCAAAATATCA-TTTTTTCGAAATA
1 ATTACCAAAATATCACTTTTTT-GAAATA
*
517519 ACTACCAAAATATCACTTTTTTCGAAATA
1 ATTACCAAAATATCACTTTTTT-GAAATA
*
517548 TTTAC
1 ATTAC
517553 GAAACTAACA
Statistics
Matches: 228, Mismatches: 16, Indels: 18
0.87 0.06 0.07
Matches are distributed among these distances:
24 21 0.09
25 1 0.00
26 4 0.02
27 37 0.16
28 128 0.56
29 37 0.16
ACGTcount: A:0.42, C:0.16, G:0.04, T:0.38
Consensus pattern (28 bp):
ATTACCAAAATATCACTTTTTTGAAATA
Found at i:517493 original size:84 final size:84
Alignment explanation
Indices: 517271--517552 Score: 394
Period size: 84 Copynumber: 3.4 Consensus size: 84
517261 ACAGTCAACT
* * * *
517271 ATTACGAAAATAACACATTTTTTTAAATAATTACGAAAATATCACTTTTT-GAAATAATTACCAA
1 ATTACCAAAATATCAC-TTTTTTGAAATAATTACCAAAATATCACTTTTTCGAAATAATTACCAA
*
517335 AATATCACTTTTTCGAAATA
65 AATATCATTTTTTCGAAATA
* **
517355 ATTACC--AA-A-CACTTTTTCGAAATAATTACCAAAATATCACTTTTTCGAAATAATTACCACT
1 ATTACCAAAATATCACTTTTTTGAAATAATTACCAAAATATCACTTTTTCGAAATAATTACCAAA
517416 ATATCATTTTTTCGAAATA
66 ATATCATTTTTTCGAAATA
* * *
517435 ATTACCAAAATATCACTTTTTTGAATTAATTACCAAAATATCATTTTTTCAAAATAATTACCAAA
1 ATTACCAAAATATCACTTTTTTGAAATAATTACCAAAATATCACTTTTTCGAAATAATTACCAAA
517500 ATATCATTTTTTCGAAATA
66 ATATCATTTTTTCGAAATA
* *
517519 ACTACCAAAATATCACTTTTTTCGAAATATTTAC
1 ATTACCAAAATATCACTTTTTT-GAAATAATTAC
517553 GAAACTAACA
Statistics
Matches: 176, Mismatches: 16, Indels: 11
0.87 0.08 0.05
Matches are distributed among these distances:
79 30 0.17
80 40 0.23
81 1 0.01
82 4 0.02
83 1 0.01
84 91 0.52
85 9 0.05
ACGTcount: A:0.42, C:0.16, G:0.04, T:0.38
Consensus pattern (84 bp):
ATTACCAAAATATCACTTTTTTGAAATAATTACCAAAATATCACTTTTTCGAAATAATTACCAAA
ATATCATTTTTTCGAAATA
Found at i:517588 original size:29 final size:29
Alignment explanation
Indices: 517544--517639 Score: 147
Period size: 29 Copynumber: 3.3 Consensus size: 29
517534 CTTTTTTCGA
** *
517544 AATATTTACGAAACTAACACCTTCTTAAC
1 AATATTTACGAAACTAACATTTTTTTAAC
* *
517573 ACTATTTACGAAACTAACATTTTTTTAAT
1 AATATTTACGAAACTAACATTTTTTTAAC
517602 AATATTTACGAAACTAACATTTTTTTAAC
1 AATATTTACGAAACTAACATTTTTTTAAC
517631 AATATTTAC
1 AATATTTAC
517640 AAAAATACCA
Statistics
Matches: 60, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 60 1.00
ACGTcount: A:0.41, C:0.17, G:0.03, T:0.40
Consensus pattern (29 bp):
AATATTTACGAAACTAACATTTTTTTAAC
Found at i:519123 original size:58 final size:59
Alignment explanation
Indices: 519032--519159 Score: 138
Period size: 59 Copynumber: 2.2 Consensus size: 59
519022 TTGGGTAAAA
* *
519032 TACATAAATGGTCCTCTAACTATATGGTTTTGTTTTATTTAGTCTC-CGACTATT-GCAAGT
1 TACA-AAATGGTCCTCTAACTATATGGTGTTGTTTTATTGAGT-TCACGACTATTAG-AAGT
* * *
519092 TATAAAATGGTCC-CTCACTATA-GAGTGTTGTTTTGTTGAGTTCATCGACTATTAGAAGT
1 TACAAAATGGTCCTCTAACTATATG-GTGTTGTTTTATTGAGTTCA-CGACTATTAGAAGT
519151 TACAAAATG
1 TACAAAATG
519160 ATCTCATGTC
Statistics
Matches: 58, Mismatches: 6, Indels: 9
0.79 0.08 0.12
Matches are distributed among these distances:
57 3 0.05
58 22 0.38
59 29 0.50
60 4 0.07
ACGTcount: A:0.28, C:0.15, G:0.17, T:0.40
Consensus pattern (59 bp):
TACAAAATGGTCCTCTAACTATATGGTGTTGTTTTATTGAGTTCACGACTATTAGAAGT
Found at i:521149 original size:42 final size:43
Alignment explanation
Indices: 521069--521155 Score: 149
Period size: 42 Copynumber: 2.0 Consensus size: 43
521059 CATCCAACCG
* *
521069 AACACACCATATTGTGTAGGTTTCCCCGAACCATACACCCACC
1 AACACACCATAATGTGTAGGTTTCCCAGAACCATACACCCACC
521112 AACACACCATAATGTGTAGG-TTCCCAGAACCATACACCCACC
1 AACACACCATAATGTGTAGGTTTCCCAGAACCATACACCCACC
521154 AA
1 AA
521156 TAAACCAAGT
Statistics
Matches: 42, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
42 23 0.55
43 19 0.45
ACGTcount: A:0.34, C:0.36, G:0.11, T:0.18
Consensus pattern (43 bp):
AACACACCATAATGTGTAGGTTTCCCAGAACCATACACCCACC
Found at i:521330 original size:24 final size:24
Alignment explanation
Indices: 521285--521394 Score: 143
Period size: 24 Copynumber: 4.6 Consensus size: 24
521275 ATCAGGCAAA
* *
521285 TATCATATCAGAAAT-CAGGTCAAG
1 TATCAGATCAG-AATCCATGTCAAG
* *
521309 TAACAGATCAGAATCCAAGTCAAG
1 TATCAGATCAGAATCCATGTCAAG
*
521333 TATCAGATCATAATCCATGTC-AG
1 TATCAGATCAGAATCCATGTCAAG
521356 ATATCAGATCAGAATCCATGTCAAG
1 -TATCAGATCAGAATCCATGTCAAG
521381 TATCAGATCAGAAT
1 TATCAGATCAGAAT
521395 TCAAATCGAA
Statistics
Matches: 76, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
23 5 0.07
24 69 0.91
25 2 0.03
ACGTcount: A:0.41, C:0.19, G:0.15, T:0.25
Consensus pattern (24 bp):
TATCAGATCAGAATCCATGTCAAG
Found at i:521410 original size:48 final size:48
Alignment explanation
Indices: 521312--521412 Score: 132
Period size: 48 Copynumber: 2.1 Consensus size: 48
521302 GGTCAAGTAA
* ** *
521312 CAGATCAGAATCCAAGTCAAGTATCAGATCATAATCCATGTCAGATAT
1 CAGATCAGAATCCAAGTCAAGTATCAGATCAGAATCCAAATCAGAAAT
* *
521360 CAGATCAGAATCCATGTCAAGTATCAGATCAGAATTCAAATC-GAAAAT
1 CAGATCAGAATCCAAGTCAAGTATCAGATCAGAATCCAAATCAG-AAAT
521408 CAGAT
1 CAGAT
521413 AAAATATTCA
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
47 1 0.02
48 45 0.98
ACGTcount: A:0.42, C:0.20, G:0.15, T:0.24
Consensus pattern (48 bp):
CAGATCAGAATCCAAGTCAAGTATCAGATCAGAATCCAAATCAGAAAT
Found at i:523987 original size:8 final size:8
Alignment explanation
Indices: 523912--523969 Score: 52
Period size: 8 Copynumber: 7.5 Consensus size: 8
523902 GGTCAACAAT
523912 GGTCAACG
1 GGTCAACG
523920 CCGGTCAACG
1 --GGTCAACG
*
523930 AGTCAAC-
1 GGTCAACG
523937 GGTCAACG
1 GGTCAACG
*
523945 GGTTAACG
1 GGTCAACG
523953 GGTC--C-
1 GGTCAACG
523958 GGTCAACG
1 GGTCAACG
523966 GGTC
1 GGTC
523970 GGGTCGGGTC
Statistics
Matches: 40, Mismatches: 4, Indels: 10
0.74 0.07 0.19
Matches are distributed among these distances:
5 4 0.10
6 1 0.03
7 7 0.17
8 20 0.50
10 8 0.20
ACGTcount: A:0.22, C:0.28, G:0.34, T:0.16
Consensus pattern (8 bp):
GGTCAACG
Done.