Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007889.1 Hibiscus syriacus cultivar Beakdansim tig00110271_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: 1663484
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 9
Found at i:412253 original size:20 final size:20
Alignment explanation
Indices: 412228--412295 Score: 57
Period size: 20 Copynumber: 3.4 Consensus size: 20
412218 CCCGATTCGA
412228 TCCGTTTATCGTAATTAAGC
1 TCCGTTTATCGTAATTAAGC
* *** * *
412248 TCCGTTTTTCACCCGATT-CGA
1 TCCGTTTAT--CGTAATTAAGC
412269 TCCGTTTATCGTAATTAAGC
1 TCCGTTTATCGTAATTAAGC
412289 TCCGTTT
1 TCCGTTT
412296 TTAATATAAT
Statistics
Matches: 33, Mismatches: 12, Indels: 6
0.65 0.24 0.12
Matches are distributed among these distances:
19 4 0.12
20 16 0.48
21 9 0.27
22 4 0.12
ACGTcount: A:0.19, C:0.25, G:0.15, T:0.41
Consensus pattern (20 bp):
TCCGTTTATCGTAATTAAGC
Found at i:412260 original size:41 final size:41
Alignment explanation
Indices: 412215--412297 Score: 166
Period size: 41 Copynumber: 2.0 Consensus size: 41
412205 CACTGATTTA
412215 TCACCCGATTCGATCCGTTTATCGTAATTAAGCTCCGTTTT
1 TCACCCGATTCGATCCGTTTATCGTAATTAAGCTCCGTTTT
412256 TCACCCGATTCGATCCGTTTATCGTAATTAAGCTCCGTTTT
1 TCACCCGATTCGATCCGTTTATCGTAATTAAGCTCCGTTTT
412297 T
1 T
412298 AATATAATTT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 42 1.00
ACGTcount: A:0.19, C:0.27, G:0.14, T:0.40
Consensus pattern (41 bp):
TCACCCGATTCGATCCGTTTATCGTAATTAAGCTCCGTTTT
Found at i:414898 original size:63 final size:63
Alignment explanation
Indices: 414796--414919 Score: 142
Period size: 63 Copynumber: 2.0 Consensus size: 63
414786 CTAATGTGAC
* * ** * *
414796 TCTTAGGTAGGCTCTGCGGCCCTGAGATCATTCTCGGGTAGGCCCTGCGACCCTAAGATGTGG
1 TCTTAGGTAGGCCCTACGGCCCCAAAATCATTCTCGGGTAGGCCCTGAGACCCTAAGATGTGG
* * * *
414859 TCTTAGGTAGGCCCTACGGCCCCAAAATC-TATCTTGGGTAGGCTCTTAGGCCCTAAGATGT
1 TCTTAGGTAGGCCCTACGGCCCCAAAATCAT-TCTCGGGTAGGCCCTGAGACCCTAAGATGT
414920 TCCCTTAGGT
Statistics
Matches: 50, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
62 1 0.02
63 49 0.98
ACGTcount: A:0.19, C:0.27, G:0.28, T:0.27
Consensus pattern (63 bp):
TCTTAGGTAGGCCCTACGGCCCCAAAATCATTCTCGGGTAGGCCCTGAGACCCTAAGATGTGG
Found at i:417364 original size:304 final size:307
Alignment explanation
Indices: 416812--417419 Score: 1033
Period size: 304 Copynumber: 2.0 Consensus size: 307
416802 GAGAGTGGGC
* *
416812 ATAGTCTGGGTGATAATTTAGTAATTAATTTATGTTTAGGTGTTATTTGTGTAAAATCCGGGTGT
1 ATAGTCTGGGTGATAATCTAGTAATTAATTTATGTTTAGGTGCTATTTGTGTAAAATCCGGGTGT
*
416877 TAGATTGGTAAATCTTTACAGAATGTGGCTAATTTGGTAATTAATTTATGTTAGGGTGATATTTG
66 TAGATTGGTAAATATTTACAGAATGTGGCTAATTTGGTAATTAATTTATGTTAGGGTGATATTTG
*
416942 TGTAAAATGGTCGACTGTTGACCGTTGACCGGCGTTGACCACTGTTGACAAAAACTTTGACTGGC
131 TGTAAAATGGTCGACTGTTGACCGTTGACCGGCGTTGACCACTATTGACAAAAACTTTGACTGGC
*
417007 TTTGACCGGGCATTAAACGACCATTGACTTTGACCGAGTATACCTATCCTGACATTTTTCGCCGT
196 TTTGACCGGGCATTAAACGACCATTGACTTTGACCGAGTATACCTATCCTGACATTTTTCGACGT
* * *
417072 TCTAAATCCAATTTCGCAGTCTGTTTTTCGAAATTTGAACCCGATCG
261 TCCAAATCCAATTCCGCAATCTGTTTTTCGAAATTTGAACCCGATCG
*
417119 ATAGTCTGGGTGATAATCTAGTAATTAATTTATGTTTGGGTGCTA-TTGTGTAAAATCC-GGTGT
1 ATAGTCTGGGTGATAATCTAGTAATTAATTTATGTTTAGGTGCTATTTGTGTAAAATCCGGGTGT
*
417182 TAGATTGGTAAATATTTACAGAATGTGGCTAATTTGGTAATTAA-TTCTGTTAGGGTGATATTTG
66 TAGATTGGTAAATATTTACAGAATGTGGCTAATTTGGTAATTAATTTATGTTAGGGTGATATTTG
* * *
417246 TGTAAAATGGTCGACTGTTGACCGTTGACCGTCGTTGATCACTATTGACCAAAACTTTGACTGGC
131 TGTAAAATGGTCGACTGTTGACCGTTGACCGGCGTTGACCACTATTGACAAAAACTTTGACTGGC
* * *
417311 TTTGACCGGGCATTAAACGATCTTTGACTTTGATCGAGTATACCTATCCTGACATTTTTCGACGT
196 TTTGACCGGGCATTAAACGACCATTGACTTTGACCGAGTATACCTATCCTGACATTTTTCGACGT
* *
417376 TCCAAATCCAATTCCGCAATTTGTTTTTTGAAATTTGAACCCGA
261 TCCAAATCCAATTCCGCAATCTGTTTTTCGAAATTTGAACCCGA
417420 AGGCCTCGAA
Statistics
Matches: 283, Mismatches: 18, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
304 180 0.64
305 48 0.17
306 13 0.05
307 42 0.15
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.37
Consensus pattern (307 bp):
ATAGTCTGGGTGATAATCTAGTAATTAATTTATGTTTAGGTGCTATTTGTGTAAAATCCGGGTGT
TAGATTGGTAAATATTTACAGAATGTGGCTAATTTGGTAATTAATTTATGTTAGGGTGATATTTG
TGTAAAATGGTCGACTGTTGACCGTTGACCGGCGTTGACCACTATTGACAAAAACTTTGACTGGC
TTTGACCGGGCATTAAACGACCATTGACTTTGACCGAGTATACCTATCCTGACATTTTTCGACGT
TCCAAATCCAATTCCGCAATCTGTTTTTCGAAATTTGAACCCGATCG
Found at i:422359 original size:31 final size:31
Alignment explanation
Indices: 422319--422424 Score: 90
Period size: 31 Copynumber: 3.4 Consensus size: 31
422309 CTAATGTGAC
* *
422319 TCTTAGGTAGGCTCTACGGCCCTAAGATCAT
1 TCTTGGGTAGGCCCTACGGCCCTAAGATCAT
* * * * *
422350 TCTCGGGTAGGCCCTGCGGCGCTAATATGTAT
1 TCTTGGGTAGGCCCTACGGCCCTAAGAT-CAT
* *
422382 TCTTAGGTAGGCCCCACGGCCCTGAA-ATC-T
1 TCTTGGGTAGGCCCTACGGCCCT-AAGATCAT
422412 ATCTTGGGTAGGC
1 -TCTTGGGTAGGC
422425 TTTCAGGCCC
Statistics
Matches: 58, Mismatches: 14, Indels: 6
0.74 0.18 0.08
Matches are distributed among these distances:
30 1 0.02
31 33 0.57
32 22 0.38
33 2 0.03
ACGTcount: A:0.19, C:0.26, G:0.27, T:0.27
Consensus pattern (31 bp):
TCTTGGGTAGGCCCTACGGCCCTAAGATCAT
Found at i:422391 original size:32 final size:31
Alignment explanation
Indices: 422319--422404 Score: 91
Period size: 31 Copynumber: 2.7 Consensus size: 31
422309 CTAATGTGAC
*
422319 TCTTAGGTAGGCTCTACGGCCCTAAGATCAT
1 TCTTAGGTAGGCCCTACGGCCCTAAGATCAT
** * * * *
422350 TCTCGGGTAGGCCCTGCGGCGCTAATATGTAT
1 TCTTAGGTAGGCCCTACGGCCCTAAGAT-CAT
*
422382 TCTTAGGTAGGCCCCACGGCCCT
1 TCTTAGGTAGGCCCTACGGCCCT
422405 GAAATCTATC
Statistics
Matches: 42, Mismatches: 12, Indels: 1
0.76 0.22 0.02
Matches are distributed among these distances:
31 22 0.52
32 20 0.48
ACGTcount: A:0.17, C:0.29, G:0.27, T:0.27
Consensus pattern (31 bp):
TCTTAGGTAGGCCCTACGGCCCTAAGATCAT
Found at i:427242 original size:12 final size:12
Alignment explanation
Indices: 427183--427240 Score: 89
Period size: 12 Copynumber: 4.8 Consensus size: 12
427173 ACTATACGGT
427183 ATGAACAGTATC
1 ATGAACAGTATC
427195 ATGAACAGTATC
1 ATGAACAGTATC
*
427207 ATGAACAATATC
1 ATGAACAGTATC
*
427219 ATGAACAGTACC
1 ATGAACAGTATC
*
427231 GTGAACAGTA
1 ATGAACAGTA
427241 CCAAATGTTA
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 42 1.00
ACGTcount: A:0.43, C:0.17, G:0.17, T:0.22
Consensus pattern (12 bp):
ATGAACAGTATC
Found at i:427309 original size:20 final size:21
Alignment explanation
Indices: 427273--427311 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
427263 TTGCTTCAGG
*
427273 GGTATCGATACCCCTGCTATA
1 GGTACCGATACCCCTGCTATA
427294 GGTACCGATA-CCCTGCTA
1 GGTACCGATACCCCTGCTA
427312 CAGTACTGCT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.23, C:0.31, G:0.21, T:0.26
Consensus pattern (21 bp):
GGTACCGATACCCCTGCTATA
Found at i:427737 original size:25 final size:26
Alignment explanation
Indices: 427694--427746 Score: 65
Period size: 25 Copynumber: 2.1 Consensus size: 26
427684 TGTAATATAG
427694 TTCATATAACTAGAAACAT-ATATCCT
1 TTCATATAACTAGAAACATGA-ATCCT
* *
427720 TTCATATAATTA-ATACATGAATCCT
1 TTCATATAACTAGAAACATGAATCCT
427745 TT
1 TT
427747 AATTTATTTC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 12 0.50
26 12 0.50
ACGTcount: A:0.40, C:0.17, G:0.04, T:0.40
Consensus pattern (26 bp):
TTCATATAACTAGAAACATGAATCCT
Found at i:427932 original size:23 final size:23
Alignment explanation
Indices: 427905--427952 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
427895 GTCCCACTAG
427905 GGGCATATGAAATTTGTCCCGAA
1 GGGCATATGAAATTTGTCCCGAA
427928 GGGCATATGAAATTTGTCCCGAA
1 GGGCATATGAAATTTGTCCCGAA
427951 GG
1 GG
427953 ACCTATGTAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.29, C:0.17, G:0.29, T:0.25
Consensus pattern (23 bp):
GGGCATATGAAATTTGTCCCGAA
Found at i:427959 original size:23 final size:23
Alignment explanation
Indices: 427908--427959 Score: 86
Period size: 23 Copynumber: 2.3 Consensus size: 23
427898 CCACTAGGGG
*
427908 CATATGAAATTTGTCCCGAAGGG
1 CATATGAAATTTGTCCCGAAGGA
427931 CATATGAAATTTGTCCCGAAGGA
1 CATATGAAATTTGTCCCGAAGGA
*
427954 CCTATG
1 CATATG
427960 TAGCTGTCCA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.31, C:0.19, G:0.23, T:0.27
Consensus pattern (23 bp):
CATATGAAATTTGTCCCGAAGGA
Found at i:427998 original size:31 final size:31
Alignment explanation
Indices: 427963--428021 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
427953 ACCTATGTAG
*
427963 CTGTCCATATGTTTCGAAGAACATAGGTGAA
1 CTGTCCATATGTTCCGAAGAACATAGGTGAA
*
427994 CTGTCCATATGTTCCGTAGAACATAGGT
1 CTGTCCATATGTTCCGAAGAACATAGGT
428022 AACCCTCGAC
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:0.29, C:0.19, G:0.22, T:0.31
Consensus pattern (31 bp):
CTGTCCATATGTTCCGAAGAACATAGGTGAA
Found at i:431198 original size:64 final size:65
Alignment explanation
Indices: 431038--431198 Score: 207
Period size: 65 Copynumber: 2.5 Consensus size: 65
431028 GAATAAATTG
* * * * * *
431038 AACATCGAATGCAGTTTATGCATCGATGCACTCTCTATGCATCGATGCACTTAGGTTTTAATGAA
1 AACATCGAATGCATTTTATGCATCGATGCACACACCATGCATCGATGCACTTAGGTCTTAATCAA
* *
431103 AACATTGAATGCATTTTATGCATCGATGCACACACCATGCATCGATGCACTTAGG-CTTATTCAA
1 AACATCGAATGCATTTTATGCATCGATGCACACACCATGCATCGATGCACTTAGGTCTTAATCAA
* * * *
431167 AACATCAAATACATTTTATGTATCAATGCACA
1 AACATCGAATGCATTTTATGCATCGATGCACA
431199 TTTAGTGCAC
Statistics
Matches: 83, Mismatches: 13, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
64 33 0.40
65 50 0.60
ACGTcount: A:0.33, C:0.21, G:0.15, T:0.31
Consensus pattern (65 bp):
AACATCGAATGCATTTTATGCATCGATGCACACACCATGCATCGATGCACTTAGGTCTTAATCAA
Found at i:436686 original size:23 final size:21
Alignment explanation
Indices: 436631--436695 Score: 76
Period size: 21 Copynumber: 3.0 Consensus size: 21
436621 CGATGTATCC
*
436631 CTTTGAATGTGCATCGATACA
1 CTTTGAATGTGCATCGATGCA
* * *
436652 CTATGAAGGTGCACCGATGCA
1 CTTTGAATGTGCATCGATGCA
436673 CTCCTTGAATGTGCATCGATGCA
1 CT--TTGAATGTGCATCGATGCA
436696 TCCGTCGGGT
Statistics
Matches: 35, Mismatches: 7, Indels: 2
0.80 0.16 0.05
Matches are distributed among these distances:
21 19 0.54
23 16 0.46
ACGTcount: A:0.26, C:0.23, G:0.23, T:0.28
Consensus pattern (21 bp):
CTTTGAATGTGCATCGATGCA
Found at i:439155 original size:46 final size:45
Alignment explanation
Indices: 439103--439201 Score: 144
Period size: 45 Copynumber: 2.2 Consensus size: 45
439093 TCTCCATTCT
* *
439103 TCGATGCACTCAGGTTTTAATGAAAACATCGAATGCATTTTATGCA
1 TCGATGCACTCAGG-ATTAATCAAAACATCGAATGCATTTTATGCA
* *
439149 TCGATGCACTTAGGATTATTCAAAACATCGAATGCATTTTATGCA
1 TCGATGCACTCAGGATTAATCAAAACATCGAATGCATTTTATGCA
*
439194 CCGATGCA
1 TCGATGCA
439202 AACTTAGTGC
Statistics
Matches: 48, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
45 35 0.73
46 13 0.27
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.31
Consensus pattern (45 bp):
TCGATGCACTCAGGATTAATCAAAACATCGAATGCATTTTATGCA
Found at i:456891 original size:41 final size:40
Alignment explanation
Indices: 456837--457152 Score: 280
Period size: 41 Copynumber: 7.7 Consensus size: 40
456827 GGTTCATCGA
*
456837 TAGTGGCGTTTTT-TCAACAAACGCCGCAAAAGAGTAGTACTT
1 TAGTGGCGTTTTTAT--ACAAACGCCGCTAAAGA-TAGTACTT
*
456879 TAGTGGCGTTTTTATACAAACGCCGCTAAAGACTAGTAATT
1 TAGTGGCGTTTTTATACAAACGCCGCTAAAGA-TAGTACTT
* * *
456920 TAGTGGCATTTTTATACAAACGCCGTTATAGAATTA-TACTT
1 TAGTGGCGTTTTTATACAAACGCCGCTAAAG-A-TAGTACTT
* * * *
456961 TAATGGCGTTTTTATACAAACGCCGTTATACACAT-GTACTA
1 TAGTGGCGTTTTTATACAAACGCCGCTA-A-AGATAGTACTT
*
457002 TAGTGGCGTTTTTATACAAACACCGCTAAAGACTCA-TACTT
1 TAGTGGCGTTTTTATACAAACGCCGCTAAAGA-T-AGTACTT
* ** *
457043 TAGTGGCATTTTTATACAAATTCCGCTAAAGATGCGTACTT
1 TAGTGGCGTTTTTATACAAACGCCGCTAAAGAT-AGTACTT
* * * * * * *
457084 TAGTGGCATTTTTATTCAAACGCCGTTATACACTTGTACTA
1 TAGTGGCGTTTTTATACAAACGCCGCTAAAGA-TAGTACTT
*
457125 TAGTGGCGTTTGTGTTTACAAACGCCGC
1 TAGTGGCGTTT-T-TATACAAACGCCGC
457153 AAGTTTACAA
Statistics
Matches: 227, Mismatches: 35, Indels: 23
0.80 0.12 0.08
Matches are distributed among these distances:
39 2 0.01
40 3 0.01
41 190 0.84
42 19 0.08
43 13 0.06
ACGTcount: A:0.29, C:0.19, G:0.18, T:0.34
Consensus pattern (40 bp):
TAGTGGCGTTTTTATACAAACGCCGCTAAAGATAGTACTT
Found at i:456973 original size:123 final size:124
Alignment explanation
Indices: 456840--457135 Score: 336
Period size: 123 Copynumber: 2.4 Consensus size: 124
456830 TCATCGATAG
* * *
456840 TGGCGTTTTTTCA-ACAAACGCCG-CA-AAAGAGTAGTACTTTAGTGGCGTTTTTATACAAACGC
1 TGGCGTTTTTT-ATACAAACGCCGTCATAAACA-T-GTACTATAGTGGCGTTTTTATACAAACAC
456902 CGCTAAAGACT-AGTAATTTAGTGGCATTTTTATACAAACGCCGTTATAGAATTATACTTTAA
63 CGCTAAAGACTCA-TAATTTAGTGGCATTTTTATACAAACGCCGTTATAGAATTATACTTTAA
* *
456964 TGGCG-TTTTTATACAAACGCCGTTATACACATGTACTATAGTGGCGTTTTTATACAAACACCGC
1 TGGCGTTTTTTATACAAACGCCGTCATAAACATGTACTATAGTGGCGTTTTTATACAAACACCGC
* ** * * ** *
457028 TAAAGACTCATACTTTAGTGGCATTTTTATACAAATTCCGCTAAAG-ATGCGTACTTTAG
66 TAAAGACTCATAATTTAGTGGCATTTTTATACAAACGCCGTTATAGAAT-TATACTTTAA
* * * * *
457087 TGGC-ATTTTTATTCAAACGCCGTTATACACTTGTACTATAGTGGCGTTT
1 TGGCGTTTTTTATACAAACGCCGTCATAAACATGTACTATAGTGGCGTTT
457136 GTGTTTACAA
Statistics
Matches: 151, Mismatches: 15, Indels: 13
0.84 0.08 0.07
Matches are distributed among these distances:
122 3 0.02
123 137 0.91
124 8 0.05
125 3 0.02
ACGTcount: A:0.30, C:0.18, G:0.17, T:0.35
Consensus pattern (124 bp):
TGGCGTTTTTTATACAAACGCCGTCATAAACATGTACTATAGTGGCGTTTTTATACAAACACCGC
TAAAGACTCATAATTTAGTGGCATTTTTATACAAACGCCGTTATAGAATTATACTTTAA
Found at i:460502 original size:43 final size:43
Alignment explanation
Indices: 460429--460695 Score: 228
Period size: 43 Copynumber: 6.2 Consensus size: 43
460419 AAGGTAATTA
* * *
460429 GCGGCGTTTGTA-TCCAAAAATGCCGCTATAGGTCTGACTTTTT
1 GCGGCGTTTG-AGTTCAAAAACGCCGCTATAGGTCTGACCTTTT
* *
460472 GCGGCGTTTGAGTTCACAAACGCCGTTATAGGTCTGACCTTTT
1 GCGGCGTTTGAGTTCAAAAACGCCGCTATAGGTCTGACCTTTT
* * *
460515 GCGGCGTTTGTGTCCAAAAACGCCGTTATAGGTCTGACCTTTT
1 GCGGCGTTTGAGTTCAAAAACGCCGCTATAGGTCTGACCTTTT
* * *
460558 GCGGCGTTT--GTTCTAAAAACGCCGCTAT-GTTTCATAACTTTTT
1 GCGGCGTTTGAGTTC-AAAAACGCCGCTATAG-GTC-TGACCTTTT
* * * *
460601 GCGGCGTTT-A-TTCCAAAAACGCCGATATAGATATCGACCTTTA
1 GCGGCGTTTGAGTT-CAAAAACGCCGCTATAGGTCT-GACCTTTT
* * *
460644 GCGGCGTTT--GTTCAAAAAACGCCG-TAATAGATATTGACCTATT
1 GCGGCGTTTGAGTTC-AAAAACGCCGCT-ATAGGT-CTGACCTTTT
460687 GCGGCGTTT
1 GCGGCGTTT
460696 TTTGTTCTCA
Statistics
Matches: 190, Mismatches: 22, Indels: 24
0.81 0.09 0.10
Matches are distributed among these distances:
41 4 0.02
42 19 0.10
43 164 0.86
44 3 0.02
ACGTcount: A:0.22, C:0.22, G:0.23, T:0.33
Consensus pattern (43 bp):
GCGGCGTTTGAGTTCAAAAACGCCGCTATAGGTCTGACCTTTT
Found at i:460601 original size:86 final size:83
Alignment explanation
Indices: 460429--460667 Score: 273
Period size: 86 Copynumber: 2.8 Consensus size: 83
460419 AAGGTAATTA
* * * *
460429 GCGGCGTTTGTATCCAAAAATGCCGCTATAGGTCTGACTTTTTGCGGCGTTTGAGTTCACAAACG
1 GCGGCGTTTGT-TCCAAAAACGCCGATATAGGTCTGACCTTTTGCGGCGTTT--GTTCAAAAACG
* *
460494 CCGTTATAGGTCTGACCTTTT
63 CCGCTATAGGTCTAACCTTTT
*
460515 GCGGCGTTTGTGTCCAAAAACGCCGTTATAGGTCTGACCTTTTGCGGCGTTTGTTCTAAAAACGC
1 GCGGCGTTTGT-TCCAAAAACGCCGATATAGGTCTGACCTTTTGCGGCGTTTGTTC-AAAAACGC
* *
460580 CGCTAT-GTTTCATAACTTTTT
64 CGCTATAG-GTC-TAACCTTTT
* * * *
460601 GCGGCGTTTATTCCAAAAACGCCGATATAGATATCGACCTTTAGCGGCGTTTGTTCAAAAAACGC
1 GCGGCGTTTGTTCCAAAAACGCCGATATAGGTCT-GACCTTTTGCGGCGTTTGTTC-AAAAACGC
460666 CG
64 CG
460668 TAATAGATAT
Statistics
Matches: 134, Mismatches: 15, Indels: 8
0.85 0.10 0.05
Matches are distributed among these distances:
84 5 0.04
85 34 0.25
86 95 0.71
ACGTcount: A:0.22, C:0.23, G:0.23, T:0.32
Consensus pattern (83 bp):
GCGGCGTTTGTTCCAAAAACGCCGATATAGGTCTGACCTTTTGCGGCGTTTGTTCAAAAACGCCG
CTATAGGTCTAACCTTTT
Found at i:460682 original size:129 final size:129
Alignment explanation
Indices: 460429--460695 Score: 328
Period size: 129 Copynumber: 2.1 Consensus size: 129
460419 AAGGTAATTA
* * *
460429 GCGGCGTTTGTATCCAAAAATGCCGCTATAGGTCTGACTTTTTGCGGCGTTTGAGTTCACAAACG
1 GCGGCGTTTGTATCCAAAAACGCCGCTATAGGTCTAACTTTTTGCGGCGTTTGAGTTCAAAAACG
* * * * * * * *
460494 CCGTTATAGGTCTGACCTTTTGCGGCGTTTGTGTCCAAAAACGCCGTTATAGGTCTGACCTTTT
66 CCGATATAGATATGACCTTTAGCGGCGTTTGTGTCAAAAAACGCCGTAATAGATCTGACCTATT
* *
460558 GCGGCGTTTGT-TCTAAAAACGCCGCTAT-GTTTCATAACTTTTTGCGGCGTTT-A-TTCCAAAA
1 GCGGCGTTTGTATCCAAAAACGCCGCTATAG-GTC-TAACTTTTTGCGGCGTTTGAGTT-CAAAA
*
460619 ACGCCGATATAGATATCGACCTTTAGCGGCGTTTGT-TCAAAAAACGCCGTAATAGATATTGACC
63 ACGCCGATATAGATAT-GACCTTTAGCGGCGTTTGTGTCAAAAAACGCCGTAATAGAT-CTGACC
460683 TATT
126 TATT
460687 GCGGCGTTT
1 GCGGCGTTT
460696 TTTGTTCTCA
Statistics
Matches: 119, Mismatches: 14, Indels: 10
0.83 0.10 0.07
Matches are distributed among these distances:
127 3 0.03
128 53 0.45
129 63 0.53
ACGTcount: A:0.22, C:0.22, G:0.23, T:0.33
Consensus pattern (129 bp):
GCGGCGTTTGTATCCAAAAACGCCGCTATAGGTCTAACTTTTTGCGGCGTTTGAGTTCAAAAACG
CCGATATAGATATGACCTTTAGCGGCGTTTGTGTCAAAAAACGCCGTAATAGATCTGACCTATT
Found at i:460689 original size:86 final size:82
Alignment explanation
Indices: 460429--460695 Score: 268
Period size: 86 Copynumber: 3.1 Consensus size: 82
460419 AAGGTAATTA
* * * *
460429 GCGGCGTTTGTATCCAAAAATGCCGCTATAGGTCTGACTTTTTGCGGCGTTTGAGTTCACAAACG
1 GCGGCGTTTGTATCCAAAAACGCCGATATAGGTCTGACCTTTTGCGGCGTTT--GTTCAAAAACG
*
460494 CCGTTATAGGTCTGACCTTTT
64 CCG-TATA-GTTTGACCTTTT
* *
460515 GCGGCGTTTGTGTCCAAAAACGCCGTTATAGGTCTGACCTTTTGCGGCGTTTGTTCTAAAAACGC
1 GCGGCGTTTGTATCCAAAAACGCCGATATAGGTCTGACCTTTTGCGGCGTTTGTTC-AAAAACGC
* *
460580 CGCTAT-GTTTCATAACTTTTT
65 CG-TATAG-TT--TGACCTTTT
* * * *
460601 GCGGCGTTTAT-TCCAAAAACGCCGATATAGATATCGACCTTTAGCGGCGTTTGTTCAAAAAACG
1 GCGGCGTTTGTATCCAAAAACGCCGATATAGGTCT-GACCTTTTGCGGCGTTTGTTC-AAAAACG
*
460665 CCGTAATAGATATTGACCTATT
64 CCGT-ATAG-T-TTGACCTTTT
460687 GCGGCGTTT
1 GCGGCGTTT
460696 TTTGTTCTCA
Statistics
Matches: 154, Mismatches: 19, Indels: 16
0.81 0.10 0.08
Matches are distributed among these distances:
83 1 0.01
84 5 0.03
85 33 0.21
86 112 0.73
87 2 0.01
88 1 0.01
ACGTcount: A:0.22, C:0.22, G:0.23, T:0.33
Consensus pattern (82 bp):
GCGGCGTTTGTATCCAAAAACGCCGATATAGGTCTGACCTTTTGCGGCGTTTGTTCAAAAACGCC
GTATAGTTTGACCTTTT
Found at i:463325 original size:60 final size:59
Alignment explanation
Indices: 463202--463332 Score: 156
Period size: 60 Copynumber: 2.2 Consensus size: 59
463192 AATAGTCGGT
* * *
463202 GACCATTTTGTAACTTTTAATAGTCGAGATACTCAACAAAGCAACTCCCTATAGTCAGGG
1 GACCATTTTGTAACTTTTAATAGTCGAGAGACTCAACAAA-CAACTCCCTATAATCAGAG
* * * * *
463262 GACCATTTTGTAACTTTTAATAGTTGAGGGACTCAACAAA-ATAGTATCCTATAATTAGAG
1 GACCATTTTGTAACTTTTAATAGTCGAGAGACTCAACAAACA-ACT-CCCTATAATCAGAG
463322 GACCATTTTGT
1 GACCATTTTGT
463333 GTACTTTATC
Statistics
Matches: 61, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
58 1 0.02
59 2 0.03
60 58 0.95
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.32
Consensus pattern (59 bp):
GACCATTTTGTAACTTTTAATAGTCGAGAGACTCAACAAACAACTCCCTATAATCAGAG
Found at i:476691 original size:3 final size:3
Alignment explanation
Indices: 476685--476735 Score: 59
Period size: 3 Copynumber: 17.0 Consensus size: 3
476675 CATTTAAATT
* **
476685 TTA TTA TTA TTA TTA -AA TTTA TTA TTA TTA AAA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA
476730 TTA TTA
1 TTA TTA
476736 ATATATATAT
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
2 1 0.03
3 38 0.95
4 1 0.03
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:476707 original size:18 final size:18
Alignment explanation
Indices: 476678--476732 Score: 80
Period size: 18 Copynumber: 3.2 Consensus size: 18
476668 TTTTTTTCAT
476678 TTAAATTTTATTATTATTA
1 TTAAA-TTTATTATTATTA
476697 TTAAATTTATTATTATTA
1 TTAAATTTATTATTATTA
476715 --AAA-TTATTATTATTA
1 TTAAATTTATTATTATTA
476730 TTA
1 TTA
476733 TTAATATATA
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
15 12 0.35
16 3 0.09
17 1 0.03
18 13 0.38
19 5 0.15
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (18 bp):
TTAAATTTATTATTATTA
Found at i:476708 original size:15 final size:15
Alignment explanation
Indices: 476687--476729 Score: 77
Period size: 15 Copynumber: 2.9 Consensus size: 15
476677 TTTAAATTTT
476687 ATTATTATTATTAAA
1 ATTATTATTATTAAA
*
476702 TTTATTATTATTAAA
1 ATTATTATTATTAAA
476717 ATTATTATTATTA
1 ATTATTATTATTA
476730 TTATTAATAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 26 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (15 bp):
ATTATTATTATTAAA
Found at i:476806 original size:21 final size:21
Alignment explanation
Indices: 476769--476808 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
476759 AAAGGACCCG
*
476769 GAGGCCCGTTTTACAAATCTA
1 GAGGCCCGTTATACAAATCTA
476790 GAGGCCCGGTTAT-CAAATC
1 GAGGCCC-GTTATACAAATC
476809 CCAAGCCCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.28, C:0.25, G:0.23, T:0.25
Consensus pattern (21 bp):
GAGGCCCGTTATACAAATCTA
Found at i:480972 original size:21 final size:21
Alignment explanation
Indices: 480948--480987 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
480938 CTTTTCATAC
480948 ATGCATTTACATTTTGTATCT
1 ATGCATTTACATTTTGTATCT
*
480969 ATGCATTTTCATTTTGTAT
1 ATGCATTTACATTTTGTAT
480988 TTTTACTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.23, C:0.12, G:0.10, T:0.55
Consensus pattern (21 bp):
ATGCATTTACATTTTGTATCT
Found at i:483551 original size:15 final size:16
Alignment explanation
Indices: 483526--483559 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
483516 CTCATCCAAC
483526 AAAGAAAGAAAAAAGA
1 AAAGAAAGAAAAAAGA
*
483542 AAAG-AAGAAAAAGGA
1 AAAGAAAGAAAAAAGA
483557 AAA
1 AAA
483560 TTGAATCAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 13 0.76
16 4 0.24
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (16 bp):
AAAGAAAGAAAAAAGA
Found at i:484142 original size:80 final size:80
Alignment explanation
Indices: 483975--484134 Score: 320
Period size: 80 Copynumber: 2.0 Consensus size: 80
483965 AATGCATGAT
483975 ATGAAAAATGATAAAGTGGGGGTTCAAGATGTAAATTTTTAAATAACATCTTGAAACCAAAGGAG
1 ATGAAAAATGATAAAGTGGGGGTTCAAGATGTAAATTTTTAAATAACATCTTGAAACCAAAGGAG
484040 GATTCCAGTTGAAAA
66 GATTCCAGTTGAAAA
484055 ATGAAAAATGATAAAGTGGGGGTTCAAGATGTAAATTTTTAAATAACATCTTGAAACCAAAGGAG
1 ATGAAAAATGATAAAGTGGGGGTTCAAGATGTAAATTTTTAAATAACATCTTGAAACCAAAGGAG
484120 GATTCCAGTTGAAAA
66 GATTCCAGTTGAAAA
484135 CCTAAAAAAG
Statistics
Matches: 80, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
80 80 1.00
ACGTcount: A:0.44, C:0.09, G:0.21, T:0.26
Consensus pattern (80 bp):
ATGAAAAATGATAAAGTGGGGGTTCAAGATGTAAATTTTTAAATAACATCTTGAAACCAAAGGAG
GATTCCAGTTGAAAA
Found at i:486297 original size:115 final size:114
Alignment explanation
Indices: 485894--486348 Score: 750
Period size: 114 Copynumber: 4.0 Consensus size: 114
485884 AAGTGCCATG
* *
485894 TGCTCATAGTAGAAATAAGAAGACTCAATAGCATCTTATGGAAGTGTTCTTTGAGTTATCTGATC
1 TGCTCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
485959 TGATTTGGTATGAACTCCAAAATCAATCATTGGATTTGAAAGATGAATT
66 TGATTTGGTATGAACTCCAAAATCAATCATTGGATTTGAAAGATGAATT
* *
486008 TGCTCATAGTAGAAATAAGAAGACCCAATAGTATCTTCTGAAAGTGTTCTTTGAGTTATCTGATC
1 TGCTCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
486073 TGATTTGGTATGAACTCCAAAATCAATCATTGGATTTGAAAGATGAATT
66 TGATTTGGTATGAACTCCAAAATCAATCATTGGATTTGAAAGATGAATT
** *
486122 TGCTCATAGTAGAAATAAGAAGACCCAATAATATCTTCTGGAAGTGTTCTTTGAATTATCTGATC
1 TGCTCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
*
486187 TGATTTGGTATGAACTCCAAAATTAATCATTGGATTTGAAAGATGAATTT
66 TGATTTGGTATGAACTCCAAAATCAATCATTGGATTTGAAAGATGAA-TT
*
486237 TGCTCATAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
1 TGCTCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
* * * * * *
486302 TGATTCGGTAGGAACCCCAGAA-CTGATCATTGGAATTGAAAGATGAA
66 TGATTTGGTATGAACTCCAAAATC-AATCATTGGATTTGAAAGATGAA
486349 CTGCATGGTC
Statistics
Matches: 320, Mismatches: 19, Indels: 3
0.94 0.06 0.01
Matches are distributed among these distances:
114 218 0.68
115 102 0.32
ACGTcount: A:0.34, C:0.13, G:0.20, T:0.33
Consensus pattern (114 bp):
TGCTCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
TGATTTGGTATGAACTCCAAAATCAATCATTGGATTTGAAAGATGAATT
Found at i:487577 original size:74 final size:75
Alignment explanation
Indices: 487485--487656 Score: 231
Period size: 74 Copynumber: 2.3 Consensus size: 75
487475 ATTAACAAGA
* * *
487485 AGCAAATATTGGGGCATGCTGAAAACCCTTTTCAAACAGAATCAGAAATGTTGAAATATTCTGAA
1 AGCAAATGTTGGGGCATGCTGAAAACCCATTTCAAACAGAATCAGAAATGTTGAAACATTCTGAA
*
487550 TA-TT-TATC
66 CACTTGTATC
* * * *
487558 AGCAAAATGTTGGGGCATGCTGAAAACCCATTTCAATCAGAATCAGAACTGTTGATACATTTTGA
1 AGC-AAATGTTGGGGCATGCTGAAAACCCATTTCAAACAGAATCAGAAATGTTGAAACATTCTGA
*
487623 ACACTTGTATT
65 ACACTTGTATC
*
487634 AGCCAATGTTGGGGCATGCTGAA
1 AGCAAATGTTGGGGCATGCTGAA
487657 GGCCCACAAT
Statistics
Matches: 86, Mismatches: 10, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
73 3 0.03
74 56 0.65
75 21 0.24
76 6 0.07
ACGTcount: A:0.35, C:0.16, G:0.20, T:0.29
Consensus pattern (75 bp):
AGCAAATGTTGGGGCATGCTGAAAACCCATTTCAAACAGAATCAGAAATGTTGAAACATTCTGAA
CACTTGTATC
Found at i:489024 original size:22 final size:22
Alignment explanation
Indices: 488995--489049 Score: 92
Period size: 22 Copynumber: 2.5 Consensus size: 22
488985 ATCTACACTC
*
488995 TTCAAAGATGATAGGTTCTCTT
1 TTCAAAGATGATAGATTCTCTT
*
489017 TTTAAAGATGATAGATTCTCTT
1 TTCAAAGATGATAGATTCTCTT
489039 TTCAAAGATGA
1 TTCAAAGATGA
489050 AAGCTTTATG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.33, C:0.11, G:0.16, T:0.40
Consensus pattern (22 bp):
TTCAAAGATGATAGATTCTCTT
Found at i:489826 original size:76 final size:76
Alignment explanation
Indices: 489727--490825 Score: 2063
Period size: 76 Copynumber: 14.5 Consensus size: 76
489717 CTATTTCCCA
*
489727 CATCTGTACGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
489792 AGCCTTCGGGT
66 AGCCTTAGGGT
489803 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
489868 AGCCTTAGGGT
66 AGCCTTAGGGT
489879 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
489944 AGCCTTAGGGT
66 AGCCTTAGGGT
489955 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
490020 AGCCTTCGGGT
66 AGCCTTAGGGT
*
490031 CATTTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
490096 AGCCTTCGGGT
66 AGCCTTAGGGT
490107 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
490172 AGCCTTAGGGT
66 AGCCTTAGGGT
490183 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
490248 AGCCTTAGGGT
66 AGCCTTAGGGT
*
490259 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAATCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
490324 AGCCTTAGGGC
66 AGCCTTAGGGT
*
490335 CATCTGTAAGTCCTTCAGTGAATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
490400 AGCCTTAGGGT
66 AGCCTTAGGGT
490411 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
490476 AGCCTTAGGGT
66 AGCCTTAGGGT
490487 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
490552 AGCCTTAGGGT
66 AGCCTTAGGGT
490563 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
490628 AGCCTTAGGGT
66 AGCCTTAGGGT
*
490639 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
490704 AGCCTTAGGGT
66 AGCCTTAGGGT
*
490715 CATATGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
490780 AGCCTTCGGGT
66 AGCCTTAGGGT
* * * *
490791 CATCTGTAAGCCCTTTAGTGCATGATATTTTCAAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAA
490826 CATTTCCATC
Statistics
Matches: 1002, Mismatches: 21, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
76 1002 1.00
ACGTcount: A:0.22, C:0.20, G:0.22, T:0.36
Consensus pattern (76 bp):
CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
AGCCTTAGGGT
Found at i:490960 original size:3 final size:3
Alignment explanation
Indices: 490952--491000 Score: 55
Period size: 3 Copynumber: 16.3 Consensus size: 3
490942 CATTTAAATT
* **
490952 TTA TTA TTA TTA TTA -AA TTTA TTA TTA TTA AAA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA
490997 TTA T
1 TTA T
491001 ATATATATAT
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
2 1 0.03
3 36 0.95
4 1 0.03
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:490974 original size:18 final size:18
Alignment explanation
Indices: 490945--490999 Score: 80
Period size: 18 Copynumber: 3.2 Consensus size: 18
490935 ATTTTTTCAT
490945 TTAAATTTTATTATTATTA
1 TTAAA-TTTATTATTATTA
490964 TTAAATTTATTATTATTA
1 TTAAATTTATTATTATTA
490982 --AAA-TTATTATTATTA
1 TTAAATTTATTATTATTA
490997 TTA
1 TTA
491000 TATATATATA
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
15 12 0.35
16 3 0.09
17 1 0.03
18 13 0.38
19 5 0.15
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (18 bp):
TTAAATTTATTATTATTA
Found at i:490975 original size:15 final size:15
Alignment explanation
Indices: 490954--490996 Score: 77
Period size: 15 Copynumber: 2.9 Consensus size: 15
490944 TTTAAATTTT
490954 ATTATTATTATTAAA
1 ATTATTATTATTAAA
*
490969 TTTATTATTATTAAA
1 ATTATTATTATTAAA
490984 ATTATTATTATTA
1 ATTATTATTATTA
490997 TTATATATAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 26 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (15 bp):
ATTATTATTATTAAA
Found at i:491067 original size:21 final size:21
Alignment explanation
Indices: 491030--491069 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
491020 AAAGGACCCG
*
491030 GAGGCCCGTTTTACAAATCTA
1 GAGGCCCGTTATACAAATCTA
491051 GAGGCCCGGTTAT-CAAATC
1 GAGGCCC-GTTATACAAATC
491070 CCAAGCCCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.28, C:0.25, G:0.23, T:0.25
Consensus pattern (21 bp):
GAGGCCCGTTATACAAATCTA
Found at i:495127 original size:32 final size:33
Alignment explanation
Indices: 495081--495142 Score: 90
Period size: 32 Copynumber: 1.9 Consensus size: 33
495071 AAGAAAATGG
* *
495081 GAAAGTTATTCCCTATATGT-AAAGTTTTGACT
1 GAAAGTTATCCCCTACATGTAAAAGTTTTGACT
*
495113 GAAAGTTGTCCCCTACATGTAAAAGTTTTG
1 GAAAGTTATCCCCTACATGTAAAAGTTTTG
495143 TTTGATGTAC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
32 17 0.65
33 9 0.35
ACGTcount: A:0.31, C:0.15, G:0.18, T:0.37
Consensus pattern (33 bp):
GAAAGTTATCCCCTACATGTAAAAGTTTTGACT
Found at i:497825 original size:15 final size:16
Alignment explanation
Indices: 497800--497833 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
497790 CTCATCCAAC
497800 AAAGAAAGAAAAAAGA
1 AAAGAAAGAAAAAAGA
*
497816 AAAG-AAGAAAAAGGA
1 AAAGAAAGAAAAAAGA
497831 AAA
1 AAA
497834 TTGAATCAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 13 0.76
16 4 0.24
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (16 bp):
AAAGAAAGAAAAAAGA
Found at i:500489 original size:115 final size:114
Alignment explanation
Indices: 500087--500540 Score: 750
Period size: 114 Copynumber: 4.0 Consensus size: 114
500077 AAGTGCCATG
* *
500087 TGCTCATAGTAGAAATAAGAAGACTCAATAGCATCTTATGGAAGTGTTCTTTGAGTTATCTGATC
1 TGCTCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
500152 TGATTTGGTATGAACTCC-AAATCAATCATTGGATTTGAAAGATGAATT
66 TGATTTGGTATGAACTCCAAAATCAATCATTGGATTTGAAAGATGAATT
*
500200 TGCTCATAGTAGAAATAAGAAGACCCAATAGTATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
1 TGCTCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
500265 TGATTTGGTATGAACTCCAAAATCAATCATTGGATTTGAAAGATGAATT
66 TGATTTGGTATGAACTCCAAAATCAATCATTGGATTTGAAAGATGAATT
** *
500314 TGCTCATAGTAGAAATAAGAAGACCCAATAATATCTTCTGGAAGTGTTCTTTGAATTATCTGATC
1 TGCTCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
*
500379 TGATTTGGTATGAACTCCAAAATTAATCATTGGATTTGAAAGATGAATTT
66 TGATTTGGTATGAACTCCAAAATCAATCATTGGATTTGAAAGATGAA-TT
*
500429 TGCTCATAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
1 TGCTCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
* * * * * *
500494 TGATTCGGTAGGAACCCCAGAA-CTGATCATTGGAATTGAAAGATGAA
66 TGATTTGGTATGAACTCCAAAATC-AATCATTGGATTTGAAAGATGAA
500541 CTGCATGGTC
Statistics
Matches: 321, Mismatches: 17, Indels: 4
0.94 0.05 0.01
Matches are distributed among these distances:
113 80 0.25
114 139 0.43
115 102 0.32
ACGTcount: A:0.33, C:0.13, G:0.20, T:0.33
Consensus pattern (114 bp):
TGCTCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
TGATTTGGTATGAACTCCAAAATCAATCATTGGATTTGAAAGATGAATT
Found at i:500525 original size:229 final size:227
Alignment explanation
Indices: 500087--500540 Score: 748
Period size: 229 Copynumber: 2.0 Consensus size: 227
500077 AAGTGCCATG
* * *
500087 TGCTCATAGTAGAAATAAGAAGACTCAATAGCATCTTATGGAAGTGTTCTTTGAGTTATCTGATC
1 TGCTCATAGTAGAAATAAGAAGACCCAATAACATCTTATGGAAGTGTTCTTTGAATTATCTGATC
500152 TGATTTGGTATGAACTCCAAATCAATCATTGGATTTGAAAGATGAATTTGCTCATAGTAGAAATA
66 TGATTTGGTATGAACTCCAAATCAATCATTGGATTTGAAAGATGAATTTGCTCATAGTAGAAATA
* * * *
500217 AGAAGACCCAATAGTATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTTGGTATGAACTC
131 AGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTCGGTAGGAACCC
*
500282 CAAAATCAATCATTGGATTTGAAAGATGAATT
196 CAAAATCAATCATTGGAATTGAAAGATGAATT
* *
500314 TGCTCATAGTAGAAATAAGAAGACCCAATAATATCTTCTGGAAGTGTTCTTTGAATTATCTGATC
1 TGCTCATAGTAGAAATAAGAAGACCCAATAACATCTTATGGAAGTGTTCTTTGAATTATCTGATC
*
500379 TGATTTGGTATGAACTCCAAAATTAATCATTGGATTTGAAAGATGAATTTTGCTCATAGTAGAAA
66 TGATTTGGTATGAACTCC-AAATCAATCATTGGATTTGAAAGATGAA-TTTGCTCATAGTAGAAA
*
500444 TAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTCGGTAGGAAC
129 TAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTCGGTAGGAAC
* *
500509 CCCAGAA-CTGATCATTGGAATTGAAAGATGAA
194 CCCAAAATC-AATCATTGGAATTGAAAGATGAA
500541 CTGCATGGTC
Statistics
Matches: 210, Mismatches: 14, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
227 78 0.37
228 28 0.13
229 104 0.50
ACGTcount: A:0.33, C:0.13, G:0.20, T:0.33
Consensus pattern (227 bp):
TGCTCATAGTAGAAATAAGAAGACCCAATAACATCTTATGGAAGTGTTCTTTGAATTATCTGATC
TGATTTGGTATGAACTCCAAATCAATCATTGGATTTGAAAGATGAATTTGCTCATAGTAGAAATA
AGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTCGGTAGGAACCC
CAAAATCAATCATTGGAATTGAAAGATGAATT
Found at i:501769 original size:74 final size:75
Alignment explanation
Indices: 501677--501848 Score: 231
Period size: 74 Copynumber: 2.3 Consensus size: 75
501667 ATTAACAAGA
* * *
501677 AGCAAATATTGGGGCATGCTGAAAACCCTTTTCAAACAGAATCAGAAATGTTGAAATATTCTGAA
1 AGCAAATGTTGGGGCATGCTGAAAACCCATTTCAAACAGAATCAGAAATGTTGAAACATTCTGAA
*
501742 TA-TT-TATC
66 CACTTGTATC
* * * *
501750 AGCAAAATGTTGGGGCATGCTGAAAACCCATTTCAATCAGAATCAGAACTGTTGATACATTTTGA
1 AGC-AAATGTTGGGGCATGCTGAAAACCCATTTCAAACAGAATCAGAAATGTTGAAACATTCTGA
*
501815 ACACTTGTATT
65 ACACTTGTATC
*
501826 AGCCAATGTTGGGGCATGCTGAA
1 AGCAAATGTTGGGGCATGCTGAA
501849 GGCCCACAAT
Statistics
Matches: 86, Mismatches: 10, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
73 3 0.03
74 56 0.65
75 21 0.24
76 6 0.07
ACGTcount: A:0.35, C:0.16, G:0.20, T:0.29
Consensus pattern (75 bp):
AGCAAATGTTGGGGCATGCTGAAAACCCATTTCAAACAGAATCAGAAATGTTGAAACATTCTGAA
CACTTGTATC
Found at i:503215 original size:22 final size:22
Alignment explanation
Indices: 503186--503240 Score: 92
Period size: 22 Copynumber: 2.5 Consensus size: 22
503176 ATCTACACTC
*
503186 TTCAAAGATGATAGGTTCTCTT
1 TTCAAAGATGATAGATTCTCTT
*
503208 TTTAAAGATGATAGATTCTCTT
1 TTCAAAGATGATAGATTCTCTT
503230 TTCAAAGATGA
1 TTCAAAGATGA
503241 AAGCTTTATG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.33, C:0.11, G:0.16, T:0.40
Consensus pattern (22 bp):
TTCAAAGATGATAGATTCTCTT
Found at i:504077 original size:76 final size:76
Alignment explanation
Indices: 503917--505011 Score: 2036
Period size: 76 Copynumber: 14.5 Consensus size: 76
503907 CTATTTCCCA
*
503917 CATCTGTACGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTC-GGAGC-TTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
503980 AGCCTTCGGGT
66 AGCCTTAGGGT
503991 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
504056 AGCCTTAGGGT
66 AGCCTTAGGGT
504067 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
504132 AGCCTTAGGGT
66 AGCCTTAGGGT
504143 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
504208 AGCCTTCGGGT
66 AGCCTTAGGGT
*
504219 CATTTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
504284 AGCCTTCGGGT
66 AGCCTTAGGGT
504295 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
504360 AGCCTTAGGGT
66 AGCCTTAGGGT
504371 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
504436 AGCCTTAGGGT
66 AGCCTTAGGGT
*
504447 CATCTATAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
504512 AGCCTTAGGGC
66 AGCCTTAGGGT
*
504523 CATCTGTAAGTCCTTCAGTGAATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
504588 AGCCTTAGGGT
66 AGCCTTAGGGT
504599 CATCTGTAAGTCCTTCAGTGCATGATGTTTCC-AAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
504663 AGCCTTAGGGT
66 AGCCTTAGGGT
504674 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
504739 AGCCTTAGGGT
66 AGCCTTAGGGT
504750 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
504815 AGCCTTAGGGT
66 AGCCTTAGGGT
*
504826 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTTC-A
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
504890 AGCCTTAGGGT
66 AGCCTTAGGGT
504901 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
504966 AGCCTTCGGGT
66 AGCCTTAGGGT
* * * *
504977 CATCTGTAAGCCCTTTAGTGCATGATATTTTCAAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAA
505012 CATTTCCATC
Statistics
Matches: 998, Mismatches: 19, Indels: 6
0.98 0.02 0.01
Matches are distributed among these distances:
74 42 0.04
75 154 0.15
76 802 0.80
ACGTcount: A:0.22, C:0.20, G:0.22, T:0.36
Consensus pattern (76 bp):
CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
AGCCTTAGGGT
Found at i:505156 original size:15 final size:15
Alignment explanation
Indices: 505138--505180 Score: 77
Period size: 15 Copynumber: 2.9 Consensus size: 15
505128 CATTTAAATT
505138 TTTATTATTATTAAA
1 TTTATTATTATTAAA
505153 TTTATTATTATTAAA
1 TTTATTATTATTAAA
*
505168 ATTATTATTATTA
1 TTTATTATTATTA
505181 TTATATATAT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (15 bp):
TTTATTATTATTAAA
Found at i:505251 original size:21 final size:21
Alignment explanation
Indices: 505214--505253 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
505204 AAAGGACCCG
*
505214 GAGGCCCGTTTTACAAATCTA
1 GAGGCCCGTTATACAAATCTA
505235 GAGGCCCGGTTAT-CAAATC
1 GAGGCCC-GTTATACAAATC
505254 CCAAGCCCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.28, C:0.25, G:0.23, T:0.25
Consensus pattern (21 bp):
GAGGCCCGTTATACAAATCTA
Found at i:508765 original size:34 final size:34
Alignment explanation
Indices: 508715--508783 Score: 104
Period size: 34 Copynumber: 2.0 Consensus size: 34
508705 AATTAGAAAC
* *
508715 AAAATGAAAAAGAAAGAAGAGAAAACA-AAACAA
1 AAAATGAAAAACAAAGAAAAGAAAACACAAACAA
508748 AAAAGTGAAAAACAAAGAAAAGAAAACACAAACAA
1 AAAA-TGAAAAACAAAGAAAAGAAAACACAAACAA
508783 A
1 A
508784 GAAAAAAGAG
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
33 4 0.12
34 21 0.66
35 7 0.22
ACGTcount: A:0.75, C:0.09, G:0.13, T:0.03
Consensus pattern (34 bp):
AAAATGAAAAACAAAGAAAAGAAAACACAAACAA
Found at i:508772 original size:15 final size:14
Alignment explanation
Indices: 508741--508789 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 14
508731 AAGAGAAAAC
*
508741 AAAACAAAAAAGTGA
1 AAAACAAAAAA-AGA
508756 AAAACAAAGAAAAGA
1 AAAACAAA-AAAAGA
*
508771 AAACACAAACAAAGA
1 AAA-ACAAAAAAAGA
508786 AAAA
1 AAAA
508790 AGAGAGGAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
14 1 0.03
15 21 0.70
16 8 0.27
ACGTcount: A:0.78, C:0.10, G:0.10, T:0.02
Consensus pattern (14 bp):
AAAACAAAAAAAGA
Found at i:510033 original size:4 final size:4
Alignment explanation
Indices: 509740--510016 Score: 297
Period size: 4 Copynumber: 69.5 Consensus size: 4
509730 TAATAATATA
* * * ** * *
509740 GATG GATG GATA GATG GACG GACG GACA GACG GATG GATG GATG GATC
1 GATG GATG GATG GATG GATG GATG GATG GATG GATG GATG GATG GATG
* * * * *
509788 GATA GATG GATG GATG GATG GATC AATA GATG GATG GATG GATG GATC
1 GATG GATG GATG GATG GATG GATG GATG GATG GATG GATG GATG GATG
* * * * * * *
509836 GATA GATA G-TG GATA GATA GATG GATG GATG GATG GAGG GAGG GACG
1 GATG GATG GATG GATG GATG GATG GATG GATG GATG GATG GATG GATG
* * * *
509883 GATG GATG GATG GACG GATG GAAT- GACG GACG GATG GACG GATG GATG
1 GATG GATG GATG GATG GATG G-ATG GATG GATG GATG GATG GATG GATG
509931 GATG GATG GATG GATG GATG GATG GATG GATG GATG GATG GATG GATG
1 GATG GATG GATG GATG GATG GATG GATG GATG GATG GATG GATG GATG
* * *
509979 GATG GACG GATG GACG GATG GATG GACG GATG GATG GA
1 GATG GATG GATG GATG GATG GATG GATG GATG GATG GA
510017 CAGATGGACG
Statistics
Matches: 236, Mismatches: 34, Indels: 6
0.86 0.12 0.02
Matches are distributed among these distances:
3 3 0.01
4 231 0.98
5 2 0.01
ACGTcount: A:0.29, C:0.05, G:0.46, T:0.20
Consensus pattern (4 bp):
GATG
Found at i:510065 original size:2 final size:2
Alignment explanation
Indices: 510060--510089 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
510050 ATAGTTTTGA
510060 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
510090 TTGAAAACAT
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:510074 original size:22 final size:22
Alignment explanation
Indices: 510046--510176 Score: 63
Period size: 22 Copynumber: 5.7 Consensus size: 22
510036 ACAGACAGAC
510046 ATATATAGTTTTGAATATATAT
1 ATATATAGTTTTGAATATATAT
*
510068 ATATATA--TAT-ATATATATAT
1 ATATATAGTTTTGA-ATATATAT
* * *
510088 ATTTGAAAACATTTTGAAAACTATATAT
1 ATAT--ATA-GTTTTG--AA-TATATAT
* *
510116 AATATATAGTTTTTGAAAATATTT
1 -ATATATAG-TTTTGAATATATAT
* * *
510140 TTAAATCA-TTTTGAAAATATAT
1 ATATAT-AGTTTTGAATATATAT
510162 ATATATAGTTTTGAA
1 ATATATAGTTTTGAA
510177 ACGTTTCTGA
Statistics
Matches: 81, Mismatches: 14, Indels: 28
0.66 0.11 0.23
Matches are distributed among these distances:
19 1 0.01
20 13 0.16
21 1 0.01
22 33 0.41
23 4 0.05
24 6 0.07
25 4 0.05
27 8 0.10
28 8 0.10
29 3 0.04
ACGTcount: A:0.44, C:0.02, G:0.07, T:0.47
Consensus pattern (22 bp):
ATATATAGTTTTGAATATATAT
Found at i:510177 original size:22 final size:22
Alignment explanation
Indices: 510110--510177 Score: 75
Period size: 22 Copynumber: 3.0 Consensus size: 22
510100 TTTGAAAACT
510110 ATATATAATATATAGTTTTTGAAA
1 ATATAT-ATATATAG-TTTTGAAA
* * *
510134 ATATTTTTAAATCA-TTTTGAAA
1 ATATATATATAT-AGTTTTGAAA
510156 ATATATATATATAGTTTTGAAA
1 ATATATATATATAGTTTTGAAA
510178 CGTTTCTGAA
Statistics
Matches: 36, Mismatches: 6, Indels: 6
0.75 0.12 0.12
Matches are distributed among these distances:
21 1 0.03
22 25 0.69
23 4 0.11
24 6 0.17
ACGTcount: A:0.44, C:0.01, G:0.07, T:0.47
Consensus pattern (22 bp):
ATATATATATATAGTTTTGAAA
Found at i:510188 original size:33 final size:33
Alignment explanation
Indices: 510147--510307 Score: 141
Period size: 35 Copynumber: 4.8 Consensus size: 33
510137 TTTTTAAATC
510147 ATTTTGAAAATATATATATATAGTTTTGAAAC-
1 ATTTTGAAAATATATATATATAGTTTTGAAACA
* * * **
510179 GTTTCTGAAAATGTATATAATATAATTTTG--ATT
1 ATTT-TGAAAATATATAT-ATATAGTTTTGAAACA
* * *
510212 TTTTTTAAAATATATAT-TATAGTTTTAAAAACA
1 ATTTTGAAAATATATATATATAGTTTT-GAAACA
*
510245 ATTTTGAAAATATATATTATATGGTTTTGAAAACA
1 ATTTTGAAAATATATA-TATATAGTTTTG-AAACA
* *
510280 ATTTTTAAAATCATATATATATATTTTT
1 ATTTTGAAAAT-ATATATATATAGTTTT
510308 AATATAATTT
Statistics
Matches: 101, Mismatches: 18, Indels: 17
0.74 0.13 0.12
Matches are distributed among these distances:
30 8 0.08
32 15 0.15
33 30 0.30
34 11 0.11
35 32 0.32
36 5 0.05
ACGTcount: A:0.42, C:0.03, G:0.07, T:0.48
Consensus pattern (33 bp):
ATTTTGAAAATATATATATATAGTTTTGAAACA
Found at i:510320 original size:35 final size:32
Alignment explanation
Indices: 510212--510321 Score: 105
Period size: 35 Copynumber: 3.2 Consensus size: 32
510202 AATTTTGATT
*
510212 TTTTTTAAAATATATATTATAGTTTTAAAAACA
1 TTTTTTAAAATATATATTATATTTTTAAAAA-A
* *
510245 ATTTTGAAAATATATATTATATGGTTTTGAAAACAA
1 TTTTTTAAAATATATATTATAT--TTTT-AAAA-AA
*
510281 -TTTTTAAAATCATATATATATATTTTTAATATAA
1 TTTTTTAAAAT-ATATAT-TATATTTTTAA-AAAA
510315 TTTTTTA
1 TTTTTTA
510322 TTTTTATTAT
Statistics
Matches: 64, Mismatches: 5, Indels: 14
0.77 0.06 0.17
Matches are distributed among these distances:
33 19 0.30
34 4 0.06
35 24 0.38
36 11 0.17
37 6 0.09
ACGTcount: A:0.43, C:0.03, G:0.05, T:0.50
Consensus pattern (32 bp):
TTTTTTAAAATATATATTATATTTTTAAAAAA
Found at i:510325 original size:19 final size:19
Alignment explanation
Indices: 510301--510338 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
510291 CATATATATA
510301 TATTTTTAATATAATTTTT
1 TATTTTTAATATAATTTTT
*
510320 TATTTTTATTATAATTTTT
1 TATTTTTAATATAATTTTT
510339 ATTATTATTT
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:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (19 bp):
TATTTTTAATATAATTTTT
Found at i:510336 original size:12 final size:12
Alignment explanation
Indices: 510321--510354 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
510311 ATAATTTTTT
510321 ATTTTTATTATA
1 ATTTTTATTATA
*
510333 ATTTTTATTATT
1 ATTTTTATTATA
510345 A-TTTTATTAT
1 ATTTTTATTAT
510355 CTTATTAGTA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
11 9 0.43
12 12 0.57
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (12 bp):
ATTTTTATTATA
Found at i:510337 original size:18 final size:19
Alignment explanation
Indices: 510301--510347 Score: 69
Period size: 18 Copynumber: 2.5 Consensus size: 19
510291 CATATATATA
*
510301 TATTTTTAATATAATTTTT
1 TATTTTTATTATAATTTTT
510320 TATTTTTATTATAA-TTTT
1 TATTTTTATTATAATTTTT
*
510338 TATTATTATT
1 TATTTTTATT
510348 TTATTATCTT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
18 13 0.50
19 13 0.50
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (19 bp):
TATTTTTATTATAATTTTT
Found at i:510360 original size:31 final size:31
Alignment explanation
Indices: 510297--510375 Score: 81
Period size: 31 Copynumber: 2.5 Consensus size: 31
510287 AAATCATATA
* * *
510297 TATATATTTTTAATATAATTTTTTATTTTTAT
1 TATA-ATTTTTATTATTATTTTTTATTCTTAT
510329 TATAATTTTTATTATTATTTTATTA-TCTTAT
1 TATAATTTTTATTATTATTTT-TTATTCTTAT
*
510360 TAGT-ATTTTTTTTATT
1 TA-TAATTTTTATTATT
510376 TTATTTAAAG
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
31 33 0.80
32 8 0.20
ACGTcount: A:0.28, C:0.01, G:0.01, T:0.70
Consensus pattern (31 bp):
TATAATTTTTATTATTATTTTTTATTCTTAT
Found at i:510580 original size:19 final size:20
Alignment explanation
Indices: 510544--510594 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
510534 TGACCCAATC
510544 CAACGGCCAGAAAGCGATCT
1 CAACGGCCAGAAAGCGATCT
*
510564 CAACGGCCAG-GAGCGATCT
1 CAACGGCCAGAAAGCGATCT
*
510583 CAACGGCTAGAA
1 CAACGGCCAGAA
510595 GCACCACGCG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
19 17 0.63
20 10 0.37
ACGTcount: A:0.33, C:0.29, G:0.27, T:0.10
Consensus pattern (20 bp):
CAACGGCCAGAAAGCGATCT
Found at i:511444 original size:18 final size:18
Alignment explanation
Indices: 511421--511455 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
511411 GATCCTTTAA
*
511421 ATTTTTACTTATTTTTTT
1 ATTTTTACATATTTTTTT
*
511439 ATTTTTTCATATTTTTT
1 ATTTTTACATATTTTTT
511456 ATTGATTTTA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.17, C:0.06, G:0.00, T:0.77
Consensus pattern (18 bp):
ATTTTTACATATTTTTTT
Found at i:511553 original size:12 final size:13
Alignment explanation
Indices: 511531--511578 Score: 53
Period size: 13 Copynumber: 3.7 Consensus size: 13
511521 GAACATTTTC
511531 TTCATTTTTTCTT
1 TTCATTTTTTCTT
511544 TTCA-TTTTTCTT
1 TTCATTTTTTCTT
**
511556 AACATTTTTTCTT
1 TTCATTTTTTCTT
*
511569 CTCAATTTTT
1 TTC-ATTTTT
511579 ATTTATTTAT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
12 10 0.34
13 13 0.45
14 6 0.21
ACGTcount: A:0.15, C:0.17, G:0.00, T:0.69
Consensus pattern (13 bp):
TTCATTTTTTCTT
Found at i:511567 original size:25 final size:24
Alignment explanation
Indices: 511526--511578 Score: 72
Period size: 25 Copynumber: 2.2 Consensus size: 24
511516 AGACCGAACA
*
511526 TTTTCTTCATTTTTTCTTTTC-AT
1 TTTTCTTCATTTTTTCTTCTCAAT
511549 TTTTCTTAACATTTTTTCTTCTCAAT
1 TTTTCTT--CATTTTTTCTTCTCAAT
511575 TTTT
1 TTTT
511579 ATTTATTTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
23 7 0.27
25 13 0.50
26 6 0.23
ACGTcount: A:0.13, C:0.17, G:0.00, T:0.70
Consensus pattern (24 bp):
TTTTCTTCATTTTTTCTTCTCAAT
Found at i:514764 original size:126 final size:126
Alignment explanation
Indices: 514539--514790 Score: 495
Period size: 126 Copynumber: 2.0 Consensus size: 126
514529 CTTATTTTAG
*
514539 GAATCAAAGAATGAAAGAATTTTATAAAACATTGCCCCTTAATTCAGGCTCACAATTGAATCGAA
1 GAATCAAAGAATGAAAGAATTTTATAAAACATTGCCCCTTAATTCAGGCTCACAATCGAATCGAA
514604 TTATAAACATGAGTTCACAAAATATCAAAAGAATCAATAGCTCTCTAATGTTTTCAAAGTT
66 TTATAAACATGAGTTCACAAAATATCAAAAGAATCAATAGCTCTCTAATGTTTTCAAAGTT
514665 GAATCAAAGAATGAAAGAATTTTATAAAACATTGCCCCTTAATTCAGGCTCACAATCGAATCGAA
1 GAATCAAAGAATGAAAGAATTTTATAAAACATTGCCCCTTAATTCAGGCTCACAATCGAATCGAA
514730 TTATAAACATGAGTTCACAAAATATCAAAAGAATCAATAGCTCTCTAATGTTTTCAAAGTT
66 TTATAAACATGAGTTCACAAAATATCAAAAGAATCAATAGCTCTCTAATGTTTTCAAAGTT
514791 ATAGCTCTTT
Statistics
Matches: 125, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
126 125 1.00
ACGTcount: A:0.43, C:0.16, G:0.12, T:0.29
Consensus pattern (126 bp):
GAATCAAAGAATGAAAGAATTTTATAAAACATTGCCCCTTAATTCAGGCTCACAATCGAATCGAA
TTATAAACATGAGTTCACAAAATATCAAAAGAATCAATAGCTCTCTAATGTTTTCAAAGTT
Found at i:528501 original size:7 final size:7
Alignment explanation
Indices: 528489--528559 Score: 142
Period size: 7 Copynumber: 10.1 Consensus size: 7
528479 AAGTGTATTT
528489 TTTCGCA
1 TTTCGCA
528496 TTTCGCA
1 TTTCGCA
528503 TTTCGCA
1 TTTCGCA
528510 TTTCGCA
1 TTTCGCA
528517 TTTCGCA
1 TTTCGCA
528524 TTTCGCA
1 TTTCGCA
528531 TTTCGCA
1 TTTCGCA
528538 TTTCGCA
1 TTTCGCA
528545 TTTCGCA
1 TTTCGCA
528552 TTTCGCA
1 TTTCGCA
528559 T
1 T
528560 CTTAATGTTT
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 64 1.00
ACGTcount: A:0.14, C:0.28, G:0.14, T:0.44
Consensus pattern (7 bp):
TTTCGCA
Found at i:531204 original size:20 final size:20
Alignment explanation
Indices: 531179--531311 Score: 203
Period size: 20 Copynumber: 6.7 Consensus size: 20
531169 TTTTCCTAAT
531179 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
*
531199 TCGCAATGCGAATATGTAAA
1 TCGCAATGCGAATACGTAAA
* *
531219 TCGTAATACGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
531239 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
* *
531259 TCACAATGCGAATACATAAA
1 TCGCAATGCGAATACGTAAA
*
531279 TCGCAATGCGAATATGTAAA
1 TCGCAATGCGAATACGTAAA
*
531299 TCGCAACGCGAAT
1 TCGCAATGCGAAT
531312 CTGACTATCG
Statistics
Matches: 101, Mismatches: 12, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 101 1.00
ACGTcount: A:0.41, C:0.19, G:0.18, T:0.22
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:531532 original size:22 final size:22
Alignment explanation
Indices: 531507--531572 Score: 105
Period size: 22 Copynumber: 3.0 Consensus size: 22
531497 GGCAACATCC
531507 GTCCCCATCTCCGACGAAATCA
1 GTCCCCATCTCCGACGAAATCA
*
531529 GTCCCCATCTCCGACGATATCA
1 GTCCCCATCTCCGACGAAATCA
* *
531551 GTCTCCATCTCCGGCGAAATCA
1 GTCCCCATCTCCGACGAAATCA
531573 TTCACGATCA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 40 1.00
ACGTcount: A:0.24, C:0.39, G:0.15, T:0.21
Consensus pattern (22 bp):
GTCCCCATCTCCGACGAAATCA
Found at i:533972 original size:14 final size:15
Alignment explanation
Indices: 533940--533973 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 15
533930 AATGCGAAAT
533940 GAAAATCGCAACAAC
1 GAAAATCGCAACAAC
533955 -AAAATCGCAAC-AC
1 GAAAATCGCAACAAC
533968 GAAAAT
1 GAAAAT
533974 GACTATCGCA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
13 2 0.11
14 16 0.89
ACGTcount: A:0.56, C:0.24, G:0.12, T:0.09
Consensus pattern (15 bp):
GAAAATCGCAACAAC
Found at i:534051 original size:20 final size:20
Alignment explanation
Indices: 533848--534050 Score: 200
Period size: 20 Copynumber: 10.8 Consensus size: 20
533838 AGAATAGTTT
533848 ACTATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
* *
533868 ACTATCGCAACGCAAAAATG
1 ACTATCGCAATGCGAAAATG
*
533888 ACTATCGCAACGCGAAAATG
1 ACTATCGCAATGCGAAAATG
* *
533908 ACTATCGTAA--CG-AGA-G
1 ACTATCGCAATGCGAAAATG
533924 A--ATCGCAATGCG-AAATG
1 ACTATCGCAATGCGAAAATG
**
533941 AAAATCGCAA--C-AACAA--
1 ACTATCGCAATGCGAA-AATG
**
533957 A--ATCGCAACACGAAAATG
1 ACTATCGCAATGCGAAAATG
533975 ACTATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
533995 ACTATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
**
534015 ACTATCGCAATGCGAATTTG
1 ACTATCGCAATGCGAAAATG
534035 ACTATCGCAATGCGAA
1 ACTATCGCAATGCGAA
534051 TGAAAATCGC
Statistics
Matches: 158, Mismatches: 11, Indels: 28
0.80 0.06 0.14
Matches are distributed among these distances:
14 13 0.08
16 10 0.06
17 8 0.05
18 5 0.03
19 7 0.04
20 115 0.73
ACGTcount: A:0.42, C:0.22, G:0.19, T:0.18
Consensus pattern (20 bp):
ACTATCGCAATGCGAAAATG
Found at i:534122 original size:20 final size:20
Alignment explanation
Indices: 534074--534161 Score: 104
Period size: 20 Copynumber: 4.3 Consensus size: 20
534064 GCGATTCTCG
*
534074 TTGCGATAATCAAATTCGCA
1 TTGCGATAGTCAAATTCGCA
534094 TTGCGATAGTCAAATTCGCA
1 TTGCGATAGTCAAATTCGCA
** *
534114 TTGCGATAGTCATTTTCCGCG
1 TTGCGATAGTCAAATT-CGCA
** *
534135 TTGCGATAGTCATTTTCGCG
1 TTGCGATAGTCAAATTCGCA
534155 TTGCGAT
1 TTGCGAT
534162 TTTAAGTTTC
Statistics
Matches: 63, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
20 44 0.70
21 19 0.30
ACGTcount: A:0.23, C:0.20, G:0.22, T:0.35
Consensus pattern (20 bp):
TTGCGATAGTCAAATTCGCA
Found at i:536030 original size:100 final size:100
Alignment explanation
Indices: 535897--536096 Score: 368
Period size: 100 Copynumber: 2.0 Consensus size: 100
535887 TGGTTTGAAA
535897 ATGTTTGGTTTAAGTAGCTAGAATTCAATAATTTGTTGTTTGTAGG-TTTAGATGTGTAGAAAGT
1 ATGTTTGGTTTAAGTAGCTAGAATTCAATAATTTGTTGTTTGTAGGTTTTAGATGTGTAGAAAGT
535961 GTTGTTGATTCAATATTTGGTTTCTGCAGGTTAATCC
66 GTTGTTGATTC-A-ATTTGGTTTCTGCAGGTTAATCC
535998 ATGTTTGG-TTAAGTAGCTAGAATTCAATAATTTGTTGTTTGTAGGTTTTAGATGTGTAGAAAGT
1 ATGTTTGGTTTAAGTAGCTAGAATTCAATAATTTGTTGTTTGTAGGTTTTAGATGTGTAGAAAGT
536062 GTTGTTGATTCAATTTGGTTTCTGCAGGTTAATCC
66 GTTGTTGATTCAATTTGGTTTCTGCAGGTTAATCC
536097 TGAAGTGAGC
Statistics
Matches: 98, Mismatches: 0, Indels: 4
0.96 0.00 0.04
Matches are distributed among these distances:
99 23 0.23
100 38 0.39
101 37 0.38
ACGTcount: A:0.24, C:0.07, G:0.24, T:0.45
Consensus pattern (100 bp):
ATGTTTGGTTTAAGTAGCTAGAATTCAATAATTTGTTGTTTGTAGGTTTTAGATGTGTAGAAAGT
GTTGTTGATTCAATTTGGTTTCTGCAGGTTAATCC
Found at i:536465 original size:20 final size:20
Alignment explanation
Indices: 536438--536531 Score: 145
Period size: 20 Copynumber: 4.7 Consensus size: 20
536428 GCGATTCTCT
536438 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTTCCG
* *
536458 CATTGCGATAGTCAATTCCG
1 CGTTGCGATAGTCATTTCCG
536478 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTTCCG
*
536498 TGTTGCGATAGTCATATT-CG
1 CGTTGCGATAGTCAT-TTCCG
536518 CGTTGCGATAGTCA
1 CGTTGCGATAGTCA
536532 AATGAATGTC
Statistics
Matches: 67, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
20 65 0.97
21 2 0.03
ACGTcount: A:0.19, C:0.22, G:0.24, T:0.34
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTCCG
Found at i:538960 original size:24 final size:24
Alignment explanation
Indices: 538926--538979 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
538916 TCTAAAAATC
538926 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
538950 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
538974 ATCAAA
1 ATCAAA
538980 TTTCGAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:538993 original size:24 final size:24
Alignment explanation
Indices: 538926--538993 Score: 64
Period size: 24 Copynumber: 2.8 Consensus size: 24
538916 TCTAAAAATC
* * *
538926 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
** *
538950 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
* *
538974 ATCAAATTTCGAATACTGAC
1 ATCAAAGTCCGAATACTGAC
538994 TAGTACTCAC
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.18, T:0.24
Consensus pattern (24 bp):
ATCAAAGTCCGAATACTGACCAAG
Found at i:539839 original size:20 final size:20
Alignment explanation
Indices: 539814--539900 Score: 156
Period size: 20 Copynumber: 4.3 Consensus size: 20
539804 AAATTCAGTA
539814 TTGCGATAGTCAGAATCTCG
1 TTGCGATAGTCAGAATCTCG
539834 TTGCGATAGTCAGAATCTCG
1 TTGCGATAGTCAGAATCTCG
539854 TTGCGATAGTCAGAATCTCG
1 TTGCGATAGTCAGAATCTCG
* *
539874 TTGCGATAGTCAGATTCACG
1 TTGCGATAGTCAGAATCTCG
539894 TTGCGAT
1 TTGCGAT
539901 TTACATATTC
Statistics
Matches: 65, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 65 1.00
ACGTcount: A:0.24, C:0.20, G:0.25, T:0.31
Consensus pattern (20 bp):
TTGCGATAGTCAGAATCTCG
Found at i:539910 original size:20 final size:20
Alignment explanation
Indices: 539894--540043 Score: 230
Period size: 20 Copynumber: 7.5 Consensus size: 20
539884 CAGATTCACG
*
539894 TTGCGATTTACATATTCGCA
1 TTGCGATTTACGTATTCGCA
*
539914 TTGCGATTTACGTATCCGCA
1 TTGCGATTTACGTATTCGCA
539934 TTGCGATTTACGTA-TCTGCA
1 TTGCGATTTACGTATTC-GCA
* * *
539954 TTGTGATTTACATATCCGCA
1 TTGCGATTTACGTATTCGCA
*
539974 TTGCGATTTACGTATCCGCA
1 TTGCGATTTACGTATTCGCA
539994 TTGCGATTTACGTATTCGCA
1 TTGCGATTTACGTATTCGCA
540014 TTGCGATTTACGTATTCGCA
1 TTGCGATTTACGTATTCGCA
540034 TTGCGATTTA
1 TTGCGATTTA
540044 GGAAAATCGC
Statistics
Matches: 119, Mismatches: 9, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
19 1 0.01
20 117 0.98
21 1 0.01
ACGTcount: A:0.21, C:0.21, G:0.19, T:0.39
Consensus pattern (20 bp):
TTGCGATTTACGTATTCGCA
Found at i:540060 original size:21 final size:20
Alignment explanation
Indices: 540036--540082 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 20
540026 TATTCGCATT
540036 GCGATTTAGGAAAATCGCAAC
1 GCGATTT-GGAAAATCGCAAC
*
540057 GCGAATTTGGAAAATCGCAAT
1 GCG-ATTTGGAAAATCGCAAC
540078 GCGAT
1 GCGAT
540083 AGTCAGAATC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
20 2 0.08
21 18 0.75
22 4 0.17
ACGTcount: A:0.36, C:0.17, G:0.26, T:0.21
Consensus pattern (20 bp):
GCGATTTGGAAAATCGCAAC
Found at i:545704 original size:11 final size:11
Alignment explanation
Indices: 545688--545712 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
545678 AATATCATCC
545688 TTTTTTTCTTT
1 TTTTTTTCTTT
545699 TTTTTTTCTTT
1 TTTTTTTCTTT
545710 TTT
1 TTT
545713 CCATTTAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (11 bp):
TTTTTTTCTTT
Found at i:546842 original size:3 final size:3
Alignment explanation
Indices: 546821--546870 Score: 66
Period size: 3 Copynumber: 16.7 Consensus size: 3
546811 GTATCCTGCA
* *
546821 AAT AATT AAT AAC AAT AAT AAT AAT AA- AAT AAT AAT AAT AAT AAA
1 AAT AA-T AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
546866 AAT AA
1 AAT AA
546871 AGATGGGTCC
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
2 2 0.05
3 36 0.88
4 3 0.07
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.28
Consensus pattern (3 bp):
AAT
Found at i:546853 original size:14 final size:15
Alignment explanation
Indices: 546821--546861 Score: 66
Period size: 14 Copynumber: 2.7 Consensus size: 15
546811 GTATCCTGCA
546821 AATAATTAATAACAAT
1 AATAA-TAATAACAAT
546837 AATAATAATAA-AAT
1 AATAATAATAACAAT
546851 AATAATAATAA
1 AATAATAATAA
546862 TAAAAATAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
14 14 0.56
15 6 0.24
16 5 0.20
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.29
Consensus pattern (15 bp):
AATAATAATAACAAT
Found at i:546854 original size:23 final size:23
Alignment explanation
Indices: 546827--546871 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
546817 TGCAAATAAT
*
546827 TAATAACAATAATAATAATAAAA
1 TAATAACAATAATAAAAATAAAA
*
546850 TAATAATAATAATAAAAATAAA
1 TAATAACAATAATAAAAATAAA
546872 GATGGGTCCG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (23 bp):
TAATAACAATAATAAAAATAAAA
Found at i:546856 original size:17 final size:17
Alignment explanation
Indices: 546834--546866 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
546824 AATTAATAAC
546834 AATAATAATAATAAAAT
1 AATAATAATAATAAAAT
546851 AATAATAATAATAAAA
1 AATAATAATAATAAAA
546867 ATAAAGATGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (17 bp):
AATAATAATAATAAAAT
Found at i:548427 original size:33 final size:33
Alignment explanation
Indices: 548367--548430 Score: 92
Period size: 33 Copynumber: 1.9 Consensus size: 33
548357 TCACATATAA
* ** *
548367 CAGATTTGTCTTCCCTTGTTTCGTCACCTATTT
1 CAGATTTGTCTTCCCCTACTTCATCACCTATTT
548400 CAGATTTGTCTTCCCCTACTTCATCACCTAT
1 CAGATTTGTCTTCCCCTACTTCATCACCTAT
548431 GACATATTTG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 27 1.00
ACGTcount: A:0.16, C:0.31, G:0.09, T:0.44
Consensus pattern (33 bp):
CAGATTTGTCTTCCCCTACTTCATCACCTATTT
Found at i:548440 original size:33 final size:33
Alignment explanation
Indices: 548357--548440 Score: 87
Period size: 33 Copynumber: 2.5 Consensus size: 33
548347 TTATGTTAAG
* * * ** *
548357 TCACATATAACAGATTTGTCTTCCCTTGTTTCG
1 TCACCTATGACAGATTTGTCTTCCCCTACTTCA
**
548390 TCACCTATTTCAGATTTGTCTTCCCCTACTTCA
1 TCACCTATGACAGATTTGTCTTCCCCTACTTCA
*
548423 TCACCTATGACATATTTG
1 TCACCTATGACAGATTTG
548441 CTTTCACCAA
Statistics
Matches: 41, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
33 41 1.00
ACGTcount: A:0.21, C:0.27, G:0.10, T:0.42
Consensus pattern (33 bp):
TCACCTATGACAGATTTGTCTTCCCCTACTTCA
Found at i:548712 original size:27 final size:28
Alignment explanation
Indices: 548678--548732 Score: 94
Period size: 27 Copynumber: 2.0 Consensus size: 28
548668 TTTACCACCT
*
548678 CACTCAATGTTTTGTTTCTT-CACCTCA
1 CACTCAATGTTTTATTTCTTCCACCTCA
548705 CACTCAATGTTTTATTTCTTCCACCTCA
1 CACTCAATGTTTTATTTCTTCCACCTCA
548733 AAGTTTGTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
27 19 0.73
28 7 0.27
ACGTcount: A:0.20, C:0.31, G:0.05, T:0.44
Consensus pattern (28 bp):
CACTCAATGTTTTATTTCTTCCACCTCA
Found at i:549971 original size:10 final size:10
Alignment explanation
Indices: 549942--550010 Score: 63
Period size: 10 Copynumber: 7.1 Consensus size: 10
549932 GCTGCTGGAA
549942 AACCGGTTTG
1 AACCGGTTTG
*
549952 -ACCAGTTTTG
1 AACC-GGTTTG
549962 AACCGGTTTG
1 AACCGGTTTG
* *
549972 -ATCGGTCTG
1 AACCGGTTTG
549981 AACCGGTTTG
1 AACCGGTTTG
*
549991 -ACCGGTCTG
1 AACCGGTTTG
*
550000 AACCGGGTTG
1 AACCGGTTTG
550010 A
1 A
550011 CCCGACCCGA
Statistics
Matches: 46, Mismatches: 9, Indels: 8
0.73 0.14 0.13
Matches are distributed among these distances:
9 18 0.39
10 25 0.54
11 3 0.07
ACGTcount: A:0.19, C:0.22, G:0.30, T:0.29
Consensus pattern (10 bp):
AACCGGTTTG
Found at i:549984 original size:19 final size:19
Alignment explanation
Indices: 549942--550012 Score: 97
Period size: 19 Copynumber: 3.7 Consensus size: 19
549932 GCTGCTGGAA
* *
549942 AACCGGTTTGACCAGTTTTG
1 AACCGGTTTGACC-GGTCTG
*
549962 AACCGGTTTGATCGGTCTG
1 AACCGGTTTGACCGGTCTG
549981 AACCGGTTTGACCGGTCTG
1 AACCGGTTTGACCGGTCTG
*
550000 AACCGGGTTGACC
1 AACCGGTTTGACC
550013 CGACCCGACT
Statistics
Matches: 46, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
19 34 0.74
20 12 0.26
ACGTcount: A:0.18, C:0.24, G:0.30, T:0.28
Consensus pattern (19 bp):
AACCGGTTTGACCGGTCTG
Found at i:550028 original size:17 final size:17
Alignment explanation
Indices: 550006--550072 Score: 116
Period size: 17 Copynumber: 3.9 Consensus size: 17
549996 TCTGAACCGG
550006 GTTGACCCGACCCGACT
1 GTTGACCCGACCCGACT
550023 GTTGACCCGACCCGACT
1 GTTGACCCGACCCGACT
* *
550040 GTTGACCTGACCCGAAT
1 GTTGACCCGACCCGACT
550057 GTTGACCCGACCCGAC
1 GTTGACCCGACCCGAC
550073 CGTTTACCGT
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 46 1.00
ACGTcount: A:0.19, C:0.39, G:0.24, T:0.18
Consensus pattern (17 bp):
GTTGACCCGACCCGACT
Found at i:550096 original size:13 final size:13
Alignment explanation
Indices: 550078--550131 Score: 63
Period size: 13 Copynumber: 4.2 Consensus size: 13
550068 CCGACCGTTT
*
550078 ACCGTTAACTGTG
1 ACCGTTGACTGTG
* * *
550091 ACCGTTGGCCGTT
1 ACCGTTGACTGTG
550104 ACCGTTGACTGTG
1 ACCGTTGACTGTG
*
550117 ACCGTTGACCGTG
1 ACCGTTGACTGTG
550130 AC
1 AC
550132 TTTCTTTGAC
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
13 33 1.00
ACGTcount: A:0.17, C:0.28, G:0.28, T:0.28
Consensus pattern (13 bp):
ACCGTTGACTGTG
Found at i:550106 original size:26 final size:26
Alignment explanation
Indices: 550070--550128 Score: 91
Period size: 26 Copynumber: 2.2 Consensus size: 26
550060 GACCCGACCC
550070 GACCGTTTACCGTTAACTGTGACCGTT
1 GACCG-TTACCGTTAACTGTGACCGTT
* *
550097 GGCCGTTACCGTTGACTGTGACCGTT
1 GACCGTTACCGTTAACTGTGACCGTT
550123 GACCGT
1 GACCGT
550129 GACTTTCTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
26 25 0.86
27 4 0.14
ACGTcount: A:0.15, C:0.27, G:0.27, T:0.31
Consensus pattern (26 bp):
GACCGTTACCGTTAACTGTGACCGTT
Found at i:550127 original size:7 final size:7
Alignment explanation
Indices: 550070--550128 Score: 52
Period size: 7 Copynumber: 8.9 Consensus size: 7
550060 GACCCGACCC
550070 GACCGTT
1 GACCGTT
*
550077 TACCGTT
1 GACCGTT
* *
550084 AACTG-T
1 GACCGTT
550090 GACCGTT
1 GACCGTT
*
550097 GGCCGTT
1 GACCGTT
550104 -ACCGTT
1 GACCGTT
*
550110 GACTG-T
1 GACCGTT
550116 GACCGTT
1 GACCGTT
550123 GACCGT
1 GACCGT
550129 GACTTTCTTT
Statistics
Matches: 40, Mismatches: 9, Indels: 6
0.73 0.16 0.11
Matches are distributed among these distances:
6 14 0.35
7 26 0.65
ACGTcount: A:0.15, C:0.27, G:0.27, T:0.31
Consensus pattern (7 bp):
GACCGTT
Found at i:553671 original size:18 final size:20
Alignment explanation
Indices: 553629--553679 Score: 63
Period size: 18 Copynumber: 2.6 Consensus size: 20
553619 GCTGCTGGAA
*
553629 AACCGGTTTTGACCAGTTTTG
1 AACCGG-TTTGACCAGTTCTG
553650 AACCGGTTTGACC-G-TCTG
1 AACCGGTTTGACCAGTTCTG
553668 AACCGG-TTGACC
1 AACCGGTTTGACC
553680 CGACCCGACT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
17 6 0.21
18 9 0.31
19 1 0.03
20 7 0.24
21 6 0.21
ACGTcount: A:0.20, C:0.25, G:0.25, T:0.29
Consensus pattern (20 bp):
AACCGGTTTGACCAGTTCTG
Found at i:553694 original size:17 final size:17
Alignment explanation
Indices: 553673--553736 Score: 101
Period size: 17 Copynumber: 3.8 Consensus size: 17
553663 GTCTGAACCG
553673 GTTGACCCGACCCGACT
1 GTTGACCCGACCCGACT
*
553690 ATTGACCCGACCCGACT
1 GTTGACCCGACCCGACT
*
553707 GTTGACCCGACCCGAAT
1 GTTGACCCGACCCGACT
*
553724 GTTGGCCCGACCC
1 GTTGACCCGACCC
553737 AACCGTGACC
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 43 1.00
ACGTcount: A:0.19, C:0.41, G:0.23, T:0.17
Consensus pattern (17 bp):
GTTGACCCGACCCGACT
Found at i:553772 original size:7 final size:7
Alignment explanation
Indices: 553738--553799 Score: 58
Period size: 7 Copynumber: 9.3 Consensus size: 7
553728 GCCCGACCCA
553738 ACCG-TG
1 ACCGTTG
*
553744 ACCATTG
1 ACCGTTG
*
553751 ACCGTTA
1 ACCGTTG
*
553758 ACTG-TG
1 ACCGTTG
553764 ACCGTTG
1 ACCGTTG
553771 ACCGTTG
1 ACCGTTG
*
553778 ACTG-TG
1 ACCGTTG
*
553784 ACCGTTA
1 ACCGTTG
553791 ACCGTTG
1 ACCGTTG
553798 AC
1 AC
553800 TTTCTTTGAC
Statistics
Matches: 43, Mismatches: 10, Indels: 5
0.74 0.17 0.09
Matches are distributed among these distances:
6 12 0.28
7 31 0.72
ACGTcount: A:0.21, C:0.27, G:0.24, T:0.27
Consensus pattern (7 bp):
ACCGTTG
Found at i:553797 original size:20 final size:20
Alignment explanation
Indices: 553741--553800 Score: 93
Period size: 20 Copynumber: 3.0 Consensus size: 20
553731 CGACCCAACC
* *
553741 GTGACCATTGACCGTTAACT
1 GTGACCGTTGACCGTTGACT
553761 GTGACCGTTGACCGTTGACT
1 GTGACCGTTGACCGTTGACT
*
553781 GTGACCGTTAACCGTTGACT
1 GTGACCGTTGACCGTTGACT
553801 TTCTTTGACC
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
20 37 1.00
ACGTcount: A:0.20, C:0.25, G:0.25, T:0.30
Consensus pattern (20 bp):
GTGACCGTTGACCGTTGACT
Found at i:554730 original size:32 final size:31
Alignment explanation
Indices: 554657--554733 Score: 82
Period size: 31 Copynumber: 2.5 Consensus size: 31
554647 CTAATGTGAC
* * *
554657 TCTTAGGTAGGCTCTGTGGCCCTGAGATCAT
1 TCTTAGGTAGGCCCTGCGGCCCTAAGATCAT
** **
554688 TCTCGGGTAGGCCCTGCGGCCCTAAGATGTGT
1 TCTTAGGTAGGCCCTGCGGCCCTAAGAT-CAT
554720 TCTTAGGTAGGCCC
1 TCTTAGGTAGGCCC
554734 ACACGCCCGA
Statistics
Matches: 36, Mismatches: 9, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
31 23 0.64
32 13 0.36
ACGTcount: A:0.14, C:0.26, G:0.31, T:0.29
Consensus pattern (31 bp):
TCTTAGGTAGGCCCTGCGGCCCTAAGATCAT
Found at i:556049 original size:20 final size:20
Alignment explanation
Indices: 556024--556094 Score: 67
Period size: 20 Copynumber: 3.5 Consensus size: 20
556014 GGATGAACAA
556024 TATCGATACT-A-GTGAAGAAG
1 TATCGATACTGATGTGAAG--G
556044 TATCGATACTGATGTGAAGG
1 TATCGATACTGATGTGAAGG
** *
556064 TATCGATACCAAGGAT-AAGG
1 TATCGATACTGATG-TGAAGG
556084 TATCGATACTG
1 TATCGATACTG
556095 TAAGTAAAGT
Statistics
Matches: 43, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
20 35 0.81
21 2 0.05
22 6 0.14
ACGTcount: A:0.35, C:0.13, G:0.25, T:0.27
Consensus pattern (20 bp):
TATCGATACTGATGTGAAGG
Found at i:556993 original size:23 final size:23
Alignment explanation
Indices: 556962--557031 Score: 81
Period size: 23 Copynumber: 3.0 Consensus size: 23
556952 AGTCGAGGGT
*
556962 TCTATGTGGTCATTCGAGACAAA
1 TCTAAGTGGTCATTCGAGACAAA
* *
556985 TCTAAGTGGTCCTTCTG-GATAAA
1 TCTAAGTGGTCATTC-GAGACAAA
557008 TCTATA-TGGTCATTCGAGACAAA
1 TCTA-AGTGGTCATTCGAGACAAA
557031 T
1 T
557032 ATGTGGCACT
Statistics
Matches: 39, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
22 1 0.03
23 36 0.92
24 2 0.05
ACGTcount: A:0.30, C:0.17, G:0.20, T:0.33
Consensus pattern (23 bp):
TCTAAGTGGTCATTCGAGACAAA
Found at i:559653 original size:22 final size:22
Alignment explanation
Indices: 559623--559672 Score: 82
Period size: 22 Copynumber: 2.2 Consensus size: 22
559613 ATTTAGTGTT
559623 TAAACAAACGATATTCATAGTTA
1 TAAA-AAACGATATTCATAGTTA
*
559646 TAAAAAACGATATTTATAGTTA
1 TAAAAAACGATATTCATAGTTA
559668 TAAAA
1 TAAAA
559673 TATTTTTCCT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
22 22 0.85
23 4 0.15
ACGTcount: A:0.52, C:0.08, G:0.08, T:0.32
Consensus pattern (22 bp):
TAAAAAACGATATTCATAGTTA
Found at i:563329 original size:2 final size:2
Alignment explanation
Indices: 563324--563354 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
563314 AATAACATTA
563324 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
563355 CACTATGATT
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:564107 original size:21 final size:21
Alignment explanation
Indices: 564082--564122 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
564072 TATATAAATC
* *
564082 AATATTATACACTAATTACAT
1 AATATCATACACTAAATACAT
*
564103 AATATCATACATTAAATACA
1 AATATCATACACTAAATACA
564123 ATATATAAGA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.51, C:0.15, G:0.00, T:0.34
Consensus pattern (21 bp):
AATATCATACACTAAATACAT
Found at i:564128 original size:21 final size:20
Alignment explanation
Indices: 564076--564129 Score: 51
Period size: 21 Copynumber: 2.8 Consensus size: 20
564066 TTATAATATA
564076 TAAAT-CAATAT-TATACAC
1 TAAATACAATATATATACAC
* *
564094 TAATTAC-ATAATATCATACAT
1 TAAATACAAT-ATAT-ATACAC
564115 TAAATACAATATATA
1 TAAATACAATATATA
564130 AGAGTCATAA
Statistics
Matches: 28, Mismatches: 3, Indels: 8
0.72 0.08 0.21
Matches are distributed among these distances:
18 6 0.21
19 3 0.11
20 2 0.07
21 15 0.54
22 2 0.07
ACGTcount: A:0.52, C:0.13, G:0.00, T:0.35
Consensus pattern (20 bp):
TAAATACAATATATATACAC
Found at i:573084 original size:24 final size:24
Alignment explanation
Indices: 573057--573132 Score: 89
Period size: 24 Copynumber: 3.2 Consensus size: 24
573047 ATTTGAATTC
573057 TGTTATGATACCTGACATGGATTA
1 TGTTATGATACCTGACATGGATTA
* * * *
573081 TGTTCTAATACCTGACTTGGATTC
1 TGTTATGATACCTGACATGGATTA
** *
573105 TGTTATGATATATGACCTGGATTA
1 TGTTATGATACCTGACATGGATTA
573129 TGTT
1 TGTT
573133 TTGAATTTTG
Statistics
Matches: 42, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 42 1.00
ACGTcount: A:0.25, C:0.13, G:0.20, T:0.42
Consensus pattern (24 bp):
TGTTATGATACCTGACATGGATTA
Found at i:575962 original size:21 final size:21
Alignment explanation
Indices: 575934--575973 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
575924 CAAGCTTAAC
575934 TTTCAAATCAAT-ATTTTATT
1 TTTCAAATCAATGATTTTATT
*
575954 TTTCTAAATCATTGATTTTA
1 TTTC-AAATCAATGATTTTA
575974 ACTTTTGAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 4 0.24
21 7 0.41
22 6 0.35
ACGTcount: A:0.33, C:0.10, G:0.03, T:0.55
Consensus pattern (21 bp):
TTTCAAATCAATGATTTTATT
Found at i:576549 original size:15 final size:14
Alignment explanation
Indices: 576529--576581 Score: 52
Period size: 15 Copynumber: 3.6 Consensus size: 14
576519 GCCTACCTCA
576529 TTCTTCTTTTCTTCC
1 TTCTTCTTTTCTT-C
*
576544 TTCTTCTTGTCTTTC
1 TTCTTCTTTTC-TTC
* *
576559 TTTTTCTTTATCATC
1 TTCTTCTTT-TCTTC
576574 TTCTTCTT
1 TTCTTCTT
576582 CTTTCACCAT
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
15 27 0.87
16 4 0.13
ACGTcount: A:0.04, C:0.26, G:0.02, T:0.68
Consensus pattern (14 bp):
TTCTTCTTTTCTTC
Found at i:577975 original size:20 final size:21
Alignment explanation
Indices: 577945--577984 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
577935 AGCGATTGGG
*
577945 GCCTGATGGTATTGATACTAT
1 GCCTGATGGTATCGATACTAT
577966 GCCT-ATGGTATCGATACTA
1 GCCTGATGGTATCGATACTA
577985 CTTTACAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.25, C:0.17, G:0.23, T:0.35
Consensus pattern (21 bp):
GCCTGATGGTATCGATACTAT
Found at i:578242 original size:26 final size:28
Alignment explanation
Indices: 578181--578242 Score: 65
Period size: 31 Copynumber: 2.2 Consensus size: 28
578171 GAGTATTGCT
* *
578181 GAGCTCGACTCGACTCGAAAACTTTGAAAT
1 GAGCTCGACTCGACTCGAAAACTTCG--AC
578211 GAAGCTCGACTCGACTCGAAAAC-TCG-C
1 G-AGCTCGACTCGACTCGAAAACTTCGAC
578238 GAGCT
1 GAGCT
578243 TAAAATTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
26 4 0.14
27 1 0.03
30 3 0.10
31 21 0.72
ACGTcount: A:0.31, C:0.27, G:0.23, T:0.19
Consensus pattern (28 bp):
GAGCTCGACTCGACTCGAAAACTTCGAC
Found at i:578550 original size:11 final size:11
Alignment explanation
Indices: 578536--578590 Score: 78
Period size: 11 Copynumber: 5.0 Consensus size: 11
578526 TCGTTAAGAA
578536 CTCGAGTCGAG
1 CTCGAGTCGAG
578547 CTCGAGTCGAG
1 CTCGAGTCGAG
578558 -TCGAGCTCGAG
1 CTCGAG-TCGAG
578569 -TCGAGTCTGAG
1 CTCGAGTC-GAG
578580 CTCGAGTCGAG
1 CTCGAGTCGAG
578591 TCCATTCGAT
Statistics
Matches: 41, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
10 7 0.17
11 27 0.66
12 7 0.17
ACGTcount: A:0.18, C:0.25, G:0.36, T:0.20
Consensus pattern (11 bp):
CTCGAGTCGAG
Found at i:578556 original size:5 final size:5
Alignment explanation
Indices: 578537--578592 Score: 76
Period size: 5 Copynumber: 10.4 Consensus size: 5
578527 CGTTAAGAAC
578537 TCGAG TCGAG CTCGAG TCGAG TCGAG CTCGAG TCGAG TCTGAG CTCGAG
1 TCGAG TCGAG -TCGAG TCGAG TCGAG -TCGAG TCGAG TC-GAG -TCGAG
578586 TCGAG TC
1 TCGAG TC
578593 CATTCGATCT
Statistics
Matches: 47, Mismatches: 0, Indels: 8
0.85 0.00 0.15
Matches are distributed among these distances:
5 29 0.62
6 16 0.34
7 2 0.04
ACGTcount: A:0.18, C:0.25, G:0.36, T:0.21
Consensus pattern (5 bp):
TCGAG
Found at i:578558 original size:16 final size:16
Alignment explanation
Indices: 578537--578592 Score: 103
Period size: 16 Copynumber: 3.4 Consensus size: 16
578527 CGTTAAGAAC
578537 TCGAGTCGAGCTCGAG
1 TCGAGTCGAGCTCGAG
578553 TCGAGTCGAGCTCGAG
1 TCGAGTCGAGCTCGAG
578569 TCGAGTCTGAGCTCGAG
1 TCGAGTC-GAGCTCGAG
578586 TCGAGTC
1 TCGAGTC
578593 CATTCGATCT
Statistics
Matches: 39, Mismatches: 0, Indels: 1
0.98 0.00 0.03
Matches are distributed among these distances:
16 23 0.59
17 16 0.41
ACGTcount: A:0.18, C:0.25, G:0.36, T:0.21
Consensus pattern (16 bp):
TCGAGTCGAGCTCGAG
Found at i:579622 original size:2 final size:2
Alignment explanation
Indices: 579611--580087 Score: 128
Period size: 2 Copynumber: 237.0 Consensus size: 2
579601 TTGAAACAAT
579611 TA TA -A 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
* * *
579652 TA T- TT TA TT TA TA TA CTA TA TA TGA -A CTA TA TA T- TA TG TA
1 TA TA TA TA TA TA TA TA -TA TA TA T-A TA -TA TA TA TA TA TA TA
* * * * * *
579692 TA AA CTA TA TA GTT TA T- TA AA AA CTA TA T- TT TA TA TA TA AA
1 TA TA -TA TA TA -TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA
* * *
579733 GTA TA TA TA TA TA TA TT TA T- TA TA TA CTA TA TA TA AA T- TG TA
1 -TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA
* * * * *
579775 TA TA TA T- TA TG TA TA -A AA TA TA TA TA CCA TG TA TA AA CTA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA -TA TA
* *
579817 TA GTT TA TA TA TGA -A CTA T- TGA -A CTA TA TA TA AA T- TA TA TA
1 TA -TA TA TA TA T-A TA -TA TA T-A TA -TA TA TA TA TA TA TA TA TA
* * *
579858 GTT TA TA TA TA AA T- TA TA TA TGA -A T- TA TA TA TA AA CTA TA
1 -TA TA TA TA TA TA TA TA TA TA T-A TA TA TA TA TA TA TA -TA TA
* * *
579898 CA -A CT- TT TA TA TA TA TA TA TA TA TA T- TA TG TA TGA T- TA TA
1 TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA
* * * *
579938 AA T- TA TA TA TA T- TA TG TA TA AA T- TA TA TA GTT 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
* * *
579978 AA CTA TA TA GTA TA TA GA TA -A TA GTA TA TA AA CTA TA TA T- TA
1 TA -TA TA TA -TA TA TA TA TA TA TA -TA TA TA TA -TA TA TA TA TA
* * * * *
580020 CA TA TGA -A CTA TA TG TA TA AA CTA TA TA AA CTA TA TA TA TA AA
1 TA TA T-A TA -TA TA TA TA TA TA -TA TA TA TA -TA TA TA TA TA TA
* *
580063 CTA TG TA AA CTA TA TA -A TA TA TA TA
1 -TA TA TA TA -TA TA TA TA TA TA TA TA
580088 GTTTAGTAGT
Statistics
Matches: 346, Mismatches: 70, Indels: 118
0.65 0.13 0.22
Matches are distributed among these distances:
1 28 0.08
2 284 0.82
3 34 0.10
ACGTcount: A:0.46, C:0.04, G:0.05, T:0.45
Consensus pattern (2 bp):
TA
Found at i:579845 original size:116 final size:114
Alignment explanation
Indices: 579618--579878 Score: 271
Period size: 116 Copynumber: 2.3 Consensus size: 114
579608 AATTATAATA
* * * *
579618 TATATATATATATATATATATATATATATATATATATTTTATTTATATACTATATATGAACTATA
1 TATATATATATATATATATATATATATATATATAAATTGTA-TTATATACTATATATAAAATATA
* **
579683 TATTATGTATAAACTATATAGTTTATTAAAAACTATATTTTATATATAAAG
65 TATCATGTATAAACTATATAGTTTATTAAAAAC-ATATTGAATATATAAAG
* * *
579734 TATATATATATATATTTAT-TATATACTATATATAAATTGTA-TATATATTATGTATAAAATATA
1 TATATATATATATATATATATATATA-TATATATAAATTGTATTATATACTATATATAAAATATA
** *
579797 TATACCATGTATAAACTATATAGTTTATATATGAAC-TATTGAACTATATATAAA
65 TAT--CATGTATAAACTATATAGTTTAT-TAAAAACATATTGAA-TATATA-AAG
* *
579851 T-TATATAGTTTATATATAAAT-TATATAT
1 TATATATA-TATATATATATATATATATAT
579879 GAATTATATA
Statistics
Matches: 121, Mismatches: 16, Indels: 16
0.79 0.10 0.10
Matches are distributed among these distances:
114 21 0.17
115 11 0.09
116 68 0.56
117 20 0.17
118 1 0.01
ACGTcount: A:0.45, C:0.04, G:0.04, T:0.47
Consensus pattern (114 bp):
TATATATATATATATATATATATATATATATATAAATTGTATTATATACTATATATAAAATATAT
ATCATGTATAAACTATATAGTTTATTAAAAACATATTGAATATATAAAG
Found at i:579877 original size:13 final size:11
Alignment explanation
Indices: 579841--579986 Score: 78
Period size: 11 Copynumber: 13.5 Consensus size: 11
579831 ACTATTGAAC
579841 TATATATAAAT
1 TATATATAAAT
579852 TATATAGT---T
1 TATATA-TAAAT
579861 TATATATAAAT
1 TATATATAAAT
*
579872 TATATATGAAT
1 TATATATAAAT
579883 TATATATAAA-
1 TATATATAAAT
* * *
579893 -CTATACAACT
1 TATATATAAAT
* *
579903 TTTATATATAT
1 TATATATAAAT
*
579914 ATATATATATTAT
1 -TATATATA-AAT
579927 GTATGATTATAAAT
1 -TAT-A-TATAAAT
579941 TATATAT--AT
1 TATATATAAAT
*
579950 TATGTATAAAT
1 TATATATAAAT
579961 TATATAGT---T
1 TATATA-TAAAT
*
579970 TATATATAAAC
1 TATATATAAAT
579981 TATATA
1 TATATA
579987 GTATATAGAT
Statistics
Matches: 104, Mismatches: 15, Indels: 32
0.69 0.10 0.21
Matches are distributed among these distances:
8 2 0.02
9 28 0.27
11 48 0.46
12 10 0.10
13 9 0.09
14 3 0.03
15 4 0.04
ACGTcount: A:0.46, C:0.03, G:0.04, T:0.47
Consensus pattern (11 bp):
TATATATAAAT
Found at i:579942 original size:17 final size:16
Alignment explanation
Indices: 579907--579952 Score: 56
Period size: 17 Copynumber: 2.8 Consensus size: 16
579897 ACAACTTTTA
*
579907 TATATATATATATATAT
1 TATATATAT-TATAAAT
*
579924 TATGTATGATTATAAAT
1 TATATAT-ATTATAAAT
579941 TATATATATTAT
1 TATATATATTAT
579953 GTATAAATTA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
16 5 0.20
17 18 0.72
18 2 0.08
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.52
Consensus pattern (16 bp):
TATATATATTATAAAT
Found at i:580164 original size:15 final size:15
Alignment explanation
Indices: 580133--580218 Score: 75
Period size: 15 Copynumber: 5.3 Consensus size: 15
580123 ATTAATGAAC
*
580133 TATATAAACTATTTA
1 TATATAAACTATATA
*
580148 TATAGTATA-TATATA
1 TATA-TAAACTATATA
580163 TATATAAACTATATA
1 TATATAAACTATATA
580178 TATATAAAAACTATAATTTA
1 TATAT--AAACTAT-A--TA
*
580198 TATCTAAACTATATA
1 TATATAAACTATATA
580213 CTATAT
1 -TATAT
580219 TTGATAATTA
Statistics
Matches: 58, Mismatches: 5, Indels: 15
0.74 0.06 0.19
Matches are distributed among these distances:
14 3 0.05
15 26 0.45
16 7 0.12
17 8 0.14
18 8 0.14
20 6 0.10
ACGTcount: A:0.49, C:0.07, G:0.01, T:0.43
Consensus pattern (15 bp):
TATATAAACTATATA
Found at i:580168 original size:17 final size:17
Alignment explanation
Indices: 580155--580218 Score: 83
Period size: 17 Copynumber: 3.6 Consensus size: 17
580145 TTATATAGTA
580155 TATATATATATATAAAC
1 TATATATATATATAAAC
*
580172 TATATATATATAAAAAC
1 TATATATATATATAAAC
* *
580189 TATAATTTATATCTAAAC
1 TAT-ATATATATATAAAC
580207 TATATACTATAT
1 TATATA-TATAT
580219 TTGATAATTA
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
17 21 0.52
18 19 0.47
ACGTcount: A:0.50, C:0.08, G:0.00, T:0.42
Consensus pattern (17 bp):
TATATATATATATAAAC
Found at i:580624 original size:18 final size:18
Alignment explanation
Indices: 580603--580641 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
580593 AATTTTTTTT
*
580603 ATATAATAATCATAA-TTA
1 ATATAAAAATC-TAATTTA
580621 ATATAAAAATCTAATTTA
1 ATATAAAAATCTAATTTA
580639 ATA
1 ATA
580642 ATTTCAATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 3 0.16
18 16 0.84
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.38
Consensus pattern (18 bp):
ATATAAAAATCTAATTTA
Found at i:580755 original size:15 final size:17
Alignment explanation
Indices: 580730--580773 Score: 56
Period size: 15 Copynumber: 2.7 Consensus size: 17
580720 AAAAGTTTTG
*
580730 AATATATTTATAAA-AT
1 AATAAATTTATAAATAT
580746 AA-AAATTTATAAATAT
1 AATAAATTTATAAATAT
*
580762 AATAAATATATA
1 AATAAATTTATA
580774 TTAATTGAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 10 0.42
16 6 0.25
17 8 0.33
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (17 bp):
AATAAATTTATAAATAT
Found at i:584281 original size:27 final size:27
Alignment explanation
Indices: 584250--584303 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
584240 TAATCCCTAA
584250 CCCTCGCGCATCCATTCCCAAATCCTC
1 CCCTCGCGCATCCATTCCCAAATCCTC
*** *
584277 CCCTCGCTTGTCCATTCCCAACTCCTC
1 CCCTCGCGCATCCATTCCCAAATCCTC
584304 ATCTCTTCGC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.15, C:0.52, G:0.07, T:0.26
Consensus pattern (27 bp):
CCCTCGCGCATCCATTCCCAAATCCTC
Found at i:590369 original size:6 final size:6
Alignment explanation
Indices: 590351--590386 Score: 56
Period size: 6 Copynumber: 6.2 Consensus size: 6
590341 TTGGATCCAT
*
590351 ACCCTA A-CCTA ACCCTA ACCCTA ACCCTA ACTCTA A
1 ACCCTA ACCCTA ACCCTA ACCCTA ACCCTA ACCCTA A
590387 AGATATCATT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
5 5 0.18
6 23 0.82
ACGTcount: A:0.36, C:0.44, G:0.00, T:0.19
Consensus pattern (6 bp):
ACCCTA
Found at i:599637 original size:42 final size:42
Alignment explanation
Indices: 599577--599690 Score: 151
Period size: 42 Copynumber: 2.7 Consensus size: 42
599567 AAGGTTTTCT
*
599577 TGATGAGTAAGTCTTTCAGGCCATC-AGTAAGTCTTTCGAGCA
1 TGATGAGTAAGTCCTTCAGGCCATCTA-TAAGTCTTTCGAGCA
*
599619 TGATGCGTAAGTCCTTCAGGCCATCTATAAGTCTTTCGAGCA
1 TGATGAGTAAGTCCTTCAGGCCATCTATAAGTCTTTCGAGCA
* * **
599661 AGATGA-TAAGACCTTTGGGCCATCTATAAG
1 TGATGAGTAAGTCCTTCAGGCCATCTATAAG
599691 ACCTTCGTGC
Statistics
Matches: 64, Mismatches: 7, Indels: 3
0.86 0.09 0.04
Matches are distributed among these distances:
41 21 0.33
42 42 0.66
43 1 0.02
ACGTcount: A:0.27, C:0.20, G:0.23, T:0.30
Consensus pattern (42 bp):
TGATGAGTAAGTCCTTCAGGCCATCTATAAGTCTTTCGAGCA
Done.