Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002844.1 Hibiscus syriacus cultivar Beakdansim tig00005856_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: 1090609
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 5
Found at i:467198 original size:20 final size:20
Alignment explanation
Indices: 467148--467214 Score: 82
Period size: 20 Copynumber: 3.4 Consensus size: 20
467138 TAGTTTACTT
*
467148 TCGCAACACGAAAATGACTA
1 TCGCAACGCGAAAATGACTA
*
467168 TCGCAACGCGAAAATGGCTA
1 TCGCAACGCGAAAATGACTA
* **
467188 TCGCAATGCG-AAATGAAAA
1 TCGCAACGCGAAAATGACTA
467207 TCGCAACG
1 TCGCAACG
467215 ACAAAATCGC
Statistics
Matches: 40, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
19 13 0.32
20 27 0.68
ACGTcount: A:0.40, C:0.24, G:0.21, T:0.15
Consensus pattern (20 bp):
TCGCAACGCGAAAATGACTA
Found at i:467209 original size:19 final size:19
Alignment explanation
Indices: 467187--467268 Score: 104
Period size: 19 Copynumber: 4.6 Consensus size: 19
467177 GAAAATGGCT
467187 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
467206 ATCGCAA--CG--A-CAAA
1 ATCGCAATGCGAAATGAAA
467220 ATCGCAATGCGAAATG-AA
1 ATCGCAATGCGAAATGAAA
*
467238 ATCGCAACGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
467257 ATCGCAATGCGA
1 ATCGCAATGCGA
467269 TTTGTGTTTC
Statistics
Matches: 53, Mismatches: 4, Indels: 12
0.77 0.06 0.17
Matches are distributed among these distances:
14 10 0.19
15 1 0.02
16 2 0.04
17 2 0.04
18 18 0.34
19 20 0.38
ACGTcount: A:0.45, C:0.21, G:0.21, T:0.13
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:467299 original size:14 final size:14
Alignment explanation
Indices: 467280--467337 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
467270 TTGTGTTTCG
467280 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
467294 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
467310 CGCATTGCGATTTTGT
1 CG--TTGCGATTTTGT
467326 CGTTGCGATTTT
1 CGTTGCGATTTT
467338 CATTTCGCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.10, C:0.17, G:0.24, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:467318 original size:32 final size:33
Alignment explanation
Indices: 467275--467350 Score: 136
Period size: 32 Copynumber: 2.3 Consensus size: 33
467265 GCGATTTGTG
*
467275 TTTCGCGTTGCGATTTTGTCGTTGCGA-TTTCA
1 TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
467307 TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
1 TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
467340 TTTCGCATTGC
1 TTTCGCATTGC
467351 AATAGCCATT
Statistics
Matches: 42, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
32 26 0.62
33 16 0.38
ACGTcount: A:0.11, C:0.20, G:0.22, T:0.47
Consensus pattern (33 bp):
TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
Found at i:467360 original size:19 final size:20
Alignment explanation
Indices: 467338--467381 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
467328 TTGCGATTTT
467338 CATTTC-GCATTGCAATAGC
1 CATTTCTGCATTGCAATAGC
* * *
467357 CATTTCTGCGTTGCGATAGT
1 CATTTCTGCATTGCAATAGC
467377 CATTT
1 CATTT
467382 TCACGTTGCG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 6 0.29
20 15 0.71
ACGTcount: A:0.20, C:0.23, G:0.18, T:0.39
Consensus pattern (20 bp):
CATTTCTGCATTGCAATAGC
Found at i:469280 original size:14 final size:14
Alignment explanation
Indices: 469261--469296 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
469251 ATTGTTTAAT
469261 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
469275 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
469289 TGATTTGT
1 TGATTTGT
469297 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:469404 original size:20 final size:20
Alignment explanation
Indices: 469379--469416 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
469369 ATGTTGAAGG
469379 CAAAACAGACTATCGCAACA
1 CAAAACAGACTATCGCAACA
*
469399 CAAAACTGACTATCGCAA
1 CAAAACAGACTATCGCAA
469417 TGAGAGAATC
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:0.47, C:0.29, G:0.11, T:0.13
Consensus pattern (20 bp):
CAAAACAGACTATCGCAACA
Found at i:469447 original size:19 final size:17
Alignment explanation
Indices: 469423--469468 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 17
469413 GCAATGAGAG
469423 AATCGCAATGCGAAATGAA
1 AATCGCAATGCG-AA-GAA
469442 AATCGCAA--CG-AGAA
1 AATCGCAATGCGAAGAA
469456 AATCGCAATGCGA
1 AATCGCAATGCGA
469469 TTTTCATTTC
Statistics
Matches: 24, Mismatches: 0, Indels: 8
0.75 0.00 0.25
Matches are distributed among these distances:
14 11 0.46
15 1 0.04
16 2 0.08
17 2 0.08
19 8 0.33
ACGTcount: A:0.46, C:0.20, G:0.22, T:0.13
Consensus pattern (17 bp):
AATCGCAATGCGAAGAA
Found at i:469501 original size:33 final size:33
Alignment explanation
Indices: 469473--469554 Score: 146
Period size: 33 Copynumber: 2.5 Consensus size: 33
469463 ATGCGATTTT
*
469473 CATTTCGCATTGCGATTTTGTCGTTGCGATAGC
1 CATTTCGCATTGCGATTTTCTCGTTGCGATAGC
469506 CATTTCGCATTGCGATTTTCTCGTTGCGATAGC
1 CATTTCGCATTGCGATTTTCTCGTTGCGATAGC
*
469539 CATTTCGCGTTGCGAT
1 CATTTCGCATTGCGAT
469555 AGCCATTTTC
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 47 1.00
ACGTcount: A:0.15, C:0.23, G:0.23, T:0.39
Consensus pattern (33 bp):
CATTTCGCATTGCGATTTTCTCGTTGCGATAGC
Found at i:469520 original size:19 final size:19
Alignment explanation
Indices: 469494--469596 Score: 135
Period size: 20 Copynumber: 5.6 Consensus size: 19
469484 GCGATTTTGT
469494 CGTTGCGATAGCCATTTCG
1 CGTTGCGATAGCCATTTCG
* *
469513 CATTGCGAT-----TTTCT
1 CGTTGCGATAGCCATTTCG
469527 CGTTGCGATAGCCATTTCG
1 CGTTGCGATAGCCATTTCG
469546 CGTTGCGATAGCCATTTTCG
1 CGTTGCGATAGCCA-TTTCG
469566 CGTTGCGATAGCCATTTTCG
1 CGTTGCGATAGCCA-TTTCG
469586 CGTTGCGATAG
1 CGTTGCGATAG
469597 TCAAATGAAT
Statistics
Matches: 74, Mismatches: 4, Indels: 11
0.83 0.04 0.12
Matches are distributed among these distances:
14 12 0.16
19 26 0.35
20 36 0.49
ACGTcount: A:0.16, C:0.24, G:0.25, T:0.35
Consensus pattern (19 bp):
CGTTGCGATAGCCATTTCG
Found at i:469566 original size:20 final size:20
Alignment explanation
Indices: 469520--469596 Score: 138
Period size: 20 Copynumber: 3.9 Consensus size: 20
469510 TCGCATTGCG
*
469520 ATTTTCTCGTTGCGATAGCC
1 ATTTTCGCGTTGCGATAGCC
469540 A-TTTCGCGTTGCGATAGCC
1 ATTTTCGCGTTGCGATAGCC
469559 ATTTTCGCGTTGCGATAGCC
1 ATTTTCGCGTTGCGATAGCC
469579 ATTTTCGCGTTGCGATAG
1 ATTTTCGCGTTGCGATAG
469597 TCAAATGAAT
Statistics
Matches: 55, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
19 18 0.33
20 37 0.67
ACGTcount: A:0.16, C:0.23, G:0.25, T:0.36
Consensus pattern (20 bp):
ATTTTCGCGTTGCGATAGCC
Found at i:469834 original size:20 final size:20
Alignment explanation
Indices: 469809--469859 Score: 93
Period size: 20 Copynumber: 2.5 Consensus size: 20
469799 AAATGATTGC
*
469809 CTTTCGCAACGCGATTTTGA
1 CTTTCGCAACGCGATTCTGA
469829 CTTTCGCAACGCGATTCTGA
1 CTTTCGCAACGCGATTCTGA
469849 CTTTCGCAACG
1 CTTTCGCAACG
469860 AGATAATACA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.20, C:0.29, G:0.20, T:0.31
Consensus pattern (20 bp):
CTTTCGCAACGCGATTCTGA
Found at i:470638 original size:24 final size:24
Alignment explanation
Indices: 470604--470657 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
470594 GTATTCGAAA
*
470604 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATACCCGGAC
* *
470628 TTTGATATTGGTCAATACTCGGAT
1 TTTGATATTGGTCAATACCCGGAC
470652 TTTGAT
1 TTTGAT
470658 GATGTTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.22, C:0.17, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATATTGGTCAATACCCGGAC
Found at i:473175 original size:19 final size:19
Alignment explanation
Indices: 473153--473250 Score: 63
Period size: 19 Copynumber: 5.7 Consensus size: 19
473143 GGAAATTACT
473153 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
* *
473172 ATCGCAA--CG--CT-AAT
1 ATCGCAATGCGAAATGAAA
*
473186 TTCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
**
473205 ATCGCAA--CG--A-GGGA
1 ATCGCAATGCGAAATGAAA
*
473219 ATCGCAATGAGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
473238 ATCGCAACGCGAA
1 ATCGCAATGCGAA
473251 TTTAATTTCG
Statistics
Matches: 56, Mismatches: 13, Indels: 20
0.63 0.15 0.22
Matches are distributed among these distances:
14 17 0.30
15 2 0.04
16 3 0.05
17 4 0.07
18 2 0.04
19 28 0.50
ACGTcount: A:0.43, C:0.19, G:0.22, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:473196 original size:33 final size:33
Alignment explanation
Indices: 473154--473253 Score: 141
Period size: 33 Copynumber: 3.0 Consensus size: 33
473144 GAAATTACTA
*
473154 TCGCAATGCGAAATGAAAATCGCAACGCTAATT
1 TCGCAATGCGAAATGAAAATCGCAACGCGAATT
*
473187 TCGCAATGCGAAATGAAAATCGCAACGAGGGAA--
1 TCGCAATGCGAAATGAAAATCGCAAC--GCGAATT
*
473220 TCGCAATGAGAAATGAAAATCGCAACGCGAATT
1 TCGCAATGCGAAATGAAAATCGCAACGCGAATT
473253 T
1 T
473254 AATTTCGCGT
Statistics
Matches: 59, Mismatches: 4, Indels: 8
0.83 0.06 0.11
Matches are distributed among these distances:
31 4 0.07
33 52 0.88
35 3 0.05
ACGTcount: A:0.41, C:0.19, G:0.22, T:0.18
Consensus pattern (33 bp):
TCGCAATGCGAAATGAAAATCGCAACGCGAATT
Found at i:473428 original size:14 final size:14
Alignment explanation
Indices: 473409--473445 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
473399 CATCAATTAA
473409 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
473423 ACAAATCACCTTTT
1 ACAAATCAACTTTT
473437 ACAAATCAA
1 ACAAATCAA
473446 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:474869 original size:21 final size:21
Alignment explanation
Indices: 474803--474869 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
474793 GTGAATCGGG
*
474803 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * ** * *
474823 CCTCTTCAACGATGACAGTGGC
1 -CTCTTGAACGGTGGGAGGGGA
474845 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
474866 CTCT
1 CTCT
474870 CGAGGAATGA
Statistics
Matches: 32, Mismatches: 13, Indels: 2
0.68 0.28 0.04
Matches are distributed among these distances:
21 30 0.94
22 2 0.06
ACGTcount: A:0.19, C:0.21, G:0.36, T:0.24
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGA
Found at i:474888 original size:42 final size:41
Alignment explanation
Indices: 474803--474925 Score: 113
Period size: 42 Copynumber: 2.9 Consensus size: 41
474793 GTGAATCGGG
* * * *
474803 CTCTTGAATGGTGGGA-GGGACCTCTTCAACGATGACAGTGGC
1 CTCTTGAACGGTGGGAGGGGA-CTC-TCGAGGATGACAGGGGC
*
474845 CTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGAGGGGACTCTCGAGG-ATGACAGGGGC
* * * * *
474887 CTCTTCAACGATAGGAGTGGACTCTTGAGGGATGACAGG
1 CTCTTGAACGGTGGGAGGGGACTCTCGA-GGATGACAGG
474926 CGAGTCGGGC
Statistics
Matches: 67, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
41 4 0.06
42 57 0.85
43 6 0.09
ACGTcount: A:0.23, C:0.19, G:0.37, T:0.22
Consensus pattern (41 bp):
CTCTTGAACGGTGGGAGGGGACTCTCGAGGATGACAGGGGC
Found at i:475324 original size:92 final size:90
Alignment explanation
Indices: 475144--475329 Score: 275
Period size: 92 Copynumber: 2.0 Consensus size: 90
475134 ATTTCAAACT
*
475144 TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTTTAGC
1 TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTT--A-AATAAACAGTTTAGC
475209 AGAATTGGCAGCAACCGAATAAATTTAC
63 AGAATTGGCAGCAACCGAATAAATTTAC
*
475237 TTCAACCAAAAGACAAAACAAAAAAGACAAATACTAACTTCACAGTGTT-AATAAACAGTTTAGG
1 TTCAACCAAAAGACAAAAC---AAAGACAAATACTAACTTCACAGTGTTAAATAAACAGTTTAGC
**
475301 AGTTTTGGCAGCAACCGAATAAATTTAC
63 AGAATTGGCAGCAACCGAATAAATTTAC
475329 T
1 T
475330 AAGCAATCTA
Statistics
Matches: 86, Mismatches: 4, Indels: 7
0.89 0.04 0.07
Matches are distributed among these distances:
92 40 0.47
93 19 0.22
96 27 0.31
ACGTcount: A:0.47, C:0.18, G:0.13, T:0.22
Consensus pattern (90 bp):
TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAATAAACAGTTTAGCAGA
ATTGGCAGCAACCGAATAAATTTAC
Found at i:477103 original size:33 final size:33
Alignment explanation
Indices: 477046--477144 Score: 162
Period size: 33 Copynumber: 3.0 Consensus size: 33
477036 ACGAGATAAT
477046 GAGAATCGCAACGCGGAAATGACTATCGCAACGA
1 GAGAATCGCAACGC-GAAATGACTATCGCAACGA
*
477080 GAGAATCGCAACGCGAAATGACTATCGCGACGA
1 GAGAATCGCAACGCGAAATGACTATCGCAACGA
**
477113 GAGAATCGCAACGCGAAATGAAAATCGCAACG
1 GAGAATCGCAACGCGAAATGACTATCGCAACG
477145 CGAAATAAAA
Statistics
Matches: 61, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
33 47 0.77
34 14 0.23
ACGTcount: A:0.39, C:0.23, G:0.26, T:0.11
Consensus pattern (33 bp):
GAGAATCGCAACGCGAAATGACTATCGCAACGA
Found at i:477138 original size:19 final size:19
Alignment explanation
Indices: 477021--477185 Score: 143
Period size: 19 Copynumber: 9.1 Consensus size: 19
477011 TCTTTTGGTT
*
477021 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
*
477040 GATAATGAGAATCGCAACGC
1 GA-AATGAAAATCGCAACGC
**
477060 GGAAATGACTATCGCAA--C
1 -GAAATGAAAATCGCAACGC
*
477078 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
** *
477094 GAAATGACTATCGCGA--C
1 GAAATGAAAATCGCAACGC
*
477111 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
477127 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
477146 GAAATAAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
477165 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
477184 GA
1 GA
477186 TTTTGGTTTC
Statistics
Matches: 118, Mismatches: 16, Indels: 24
0.75 0.10 0.15
Matches are distributed among these distances:
14 17 0.14
15 2 0.02
16 4 0.03
17 3 0.03
18 3 0.03
19 60 0.51
20 27 0.23
21 2 0.02
ACGTcount: A:0.44, C:0.21, G:0.24, T:0.12
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:477763 original size:20 final size:20
Alignment explanation
Indices: 477738--477790 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
477728 GCGCTATGTA
477738 AATCGCGTTGCGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
477758 AATCGCGTTGCGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
* *
477778 TATCTCGTTGCGA
1 AATCGCGTTGCGA
477791 TTTTGTATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (20 bp):
AATCGCGTTGCGAAAGTCAG
Found at i:477824 original size:20 final size:20
Alignment explanation
Indices: 477799--477852 Score: 99
Period size: 20 Copynumber: 2.7 Consensus size: 20
477789 GATTTTGTAT
477799 TATCGCATTGCGATAGTAAG
1 TATCGCATTGCGATAGTAAG
*
477819 TATCGCATTGCGATAGTCAG
1 TATCGCATTGCGATAGTAAG
477839 TATCGCATTGCGAT
1 TATCGCATTGCGAT
477853 TTTCCCAATT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.31
Consensus pattern (20 bp):
TATCGCATTGCGATAGTAAG
Found at i:477837 original size:61 final size:61
Alignment explanation
Indices: 477739--477855 Score: 162
Period size: 61 Copynumber: 1.9 Consensus size: 61
477729 CGCTATGTAA
* * * * *
477739 ATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGTATCTCGTTGCGATTTTGTATT
1 ATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTGTATT
* * *
477800 ATCGCATTGCGATAGTAAGTATCGCATTGCGATAGTCAGTATCGCATTGCGATTTT
1 ATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTT
477856 CCCAATTCGC
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
61 48 1.00
ACGTcount: A:0.24, C:0.18, G:0.25, T:0.33
Consensus pattern (61 bp):
ATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTGTATT
Found at i:477871 original size:61 final size:61
Alignment explanation
Indices: 477739--477873 Score: 155
Period size: 61 Copynumber: 2.2 Consensus size: 61
477729 CGCTATGTAA
* * * * * ** *
477739 ATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGTATCTCGTTGCGATTTTGTATT
1 ATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTCCAAT
* * *
477800 ATCGCATTGCGATAGTAAGTATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCCCAAT
1 ATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTT-CCAAT
477862 -TCGCGTTGCGAT
1 ATCGCGTTGCGAT
477874 TTACTTATTC
Statistics
Matches: 61, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
61 59 0.97
62 2 0.03
ACGTcount: A:0.23, C:0.20, G:0.24, T:0.33
Consensus pattern (61 bp):
ATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTCCAAT
Found at i:478501 original size:29 final size:29
Alignment explanation
Indices: 478459--478530 Score: 144
Period size: 29 Copynumber: 2.5 Consensus size: 29
478449 ACAAGACTCT
478459 ATAGTCGAAGGACTATTTTGTAATTTTTA
1 ATAGTCGAAGGACTATTTTGTAATTTTTA
478488 ATAGTCGAAGGACTATTTTGTAATTTTTA
1 ATAGTCGAAGGACTATTTTGTAATTTTTA
478517 ATAGTCGAAGGACT
1 ATAGTCGAAGGACT
478531 TGATAAAGCA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 43 1.00
ACGTcount: A:0.32, C:0.08, G:0.19, T:0.40
Consensus pattern (29 bp):
ATAGTCGAAGGACTATTTTGTAATTTTTA
Found at i:483863 original size:37 final size:39
Alignment explanation
Indices: 483815--484102 Score: 421
Period size: 37 Copynumber: 7.6 Consensus size: 39
483805 CATATAACGC
*
483815 ATATAATATATAGTTATGAAAACATTTTTTTGAAAATAT
1 ATATAATATATAGTTTTGAAAACATTTTTTTGAAAATAT
* **
483854 ATATAATATATAGTTTT-AAAA-ATATTTTTGAAAACGT
1 ATATAATATATAGTTTTGAAAACATTTTTTTGAAAATAT
*
483891 ATATAATATGTAGTTTTGAAAACA--TTTTTGAAAATAT
1 ATATAATATATAGTTTTGAAAACATTTTTTTGAAAATAT
*
483928 ATATAATATATAGTTTTGAAAACATTTTTTCGAAAATAT
1 ATATAATATATAGTTTTGAAAACATTTTTTTGAAAATAT
*
483967 ATATAATATATAGTTTTG-AAA-ATATTTTTG-AAATAT
1 ATATAATATATAGTTTTGAAAACATTTTTTTGAAAATAT
*
484003 ATATAATATATAGTTTTAAAAACATTTTTTTTGAAAATAT
1 ATATAATATATAGTTTTGAAAACA-TTTTTTTGAAAATAT
* *
484043 ATATAATATATAGTTTTGAAAACA-TTTTTCGAATATAT
1 ATATAATATATAGTTTTGAAAACATTTTTTTGAAAATAT
484081 ATATAATATATAGTTTTGAAAA
1 ATATAATATATAGTTTTGAAAA
484103 ACGTATATAA
Statistics
Matches: 225, Mismatches: 16, Indels: 17
0.87 0.06 0.07
Matches are distributed among these distances:
36 23 0.10
37 73 0.32
38 46 0.20
39 54 0.24
40 29 0.13
ACGTcount: A:0.45, C:0.03, G:0.08, T:0.44
Consensus pattern (39 bp):
ATATAATATATAGTTTTGAAAACATTTTTTTGAAAATAT
Found at i:483911 original size:76 final size:76
Alignment explanation
Indices: 483815--484102 Score: 415
Period size: 76 Copynumber: 3.8 Consensus size: 76
483805 CATATAACGC
*
483815 ATATAATATATAGTTATGAAAACATTTTTTTGAAAATATATATAATATATAGTTTT-AAAA-ATA
1 ATATAATATATAGTTTTGAAAACA-TTTTTTGAAAATATATATAATATATAGTTTTGAAAACAT-
*
483878 TTTTTGAAAACGT
64 TTTTTGAAAACAT
*
483891 ATATAATATGTAGTTTTGAAAACA-TTTTTGAAAATATATATAATATATAGTTTTGAAAACATTT
1 ATATAATATATAGTTTTGAAAACATTTTTTGAAAATATATATAATATATAGTTTTGAAAACATTT
*
483955 TTTCGAAAATAT
66 TTT-GAAAACAT
* *
483967 ATATAATATATAGTTTTGAAAATA-TTTTTG-AAATATATATAATATATAGTTTTAAAAACATTT
1 ATATAATATATAGTTTTGAAAACATTTTTTGAAAATATATATAATATATAGTTTTGAAAACA--T
*
484030 TTTTTGAAAATAT
64 TTTTTGAAAACAT
* *
484043 ATATAATATATAGTTTTGAAAACATTTTTCGAATATATATATAATATATAGTTTTGAAAA
1 ATATAATATATAGTTTTGAAAACATTTTTTGAAAATATATATAATATATAGTTTTGAAAA
484103 ACGTATATAA
Statistics
Matches: 194, Mismatches: 11, Indels: 12
0.89 0.05 0.06
Matches are distributed among these distances:
74 30 0.15
75 38 0.20
76 89 0.46
77 11 0.06
78 26 0.13
ACGTcount: A:0.45, C:0.03, G:0.08, T:0.44
Consensus pattern (76 bp):
ATATAATATATAGTTTTGAAAACATTTTTTGAAAATATATATAATATATAGTTTTGAAAACATTT
TTTGAAAACAT
Found at i:484174 original size:21 final size:19
Alignment explanation
Indices: 484150--484194 Score: 54
Period size: 21 Copynumber: 2.3 Consensus size: 19
484140 TAGAACACAT
*
484150 TTTATATTATATAGTTTTTTA
1 TTTATATTATAT--TTATTTA
*
484171 TTTACATTATATTTATTTA
1 TTTATATTATATTTATTTA
484190 TTTAT
1 TTTAT
484195 TTTGTTTATT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
19 10 0.48
21 11 0.52
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.67
Consensus pattern (19 bp):
TTTATATTATATTTATTTA
Found at i:492490 original size:34 final size:33
Alignment explanation
Indices: 492451--492521 Score: 97
Period size: 34 Copynumber: 2.1 Consensus size: 33
492441 TTTTGTAAAG
*
492451 GGGAAAGGTTCTAGCTTAACCCGTGTAAAATCTA
1 GGGAAAGGTTCTAGCTTAACCCGTG-AAAAACTA
* * *
492485 GGGAAATGTTCTAGTTTATCCCGTGAAAAACTA
1 GGGAAAGGTTCTAGCTTAACCCGTGAAAAACTA
492518 GGGA
1 GGGA
492522 GTTGTAAAGG
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
33 11 0.33
34 22 0.67
ACGTcount: A:0.32, C:0.15, G:0.25, T:0.27
Consensus pattern (33 bp):
GGGAAAGGTTCTAGCTTAACCCGTGAAAAACTA
Found at i:493102 original size:22 final size:22
Alignment explanation
Indices: 493022--493108 Score: 77
Period size: 22 Copynumber: 4.0 Consensus size: 22
493012 GTTTCTTCCT
* *
493022 ATTTTATTTTATTTTC-TTTTAA
1 ATTTAATTTTA-TTTCATTTTGA
* * *
493044 ATTTAATTTTCTTTCATTCTGT
1 ATTTAATTTTATTTCATTTTGA
* * *
493066 ACTTCATTTTATTTCCTTTTGA
1 ATTTAATTTTATTTCATTTTGA
*
493088 ATTTAATTTTCTTTCATTTTG
1 ATTTAATTTTATTTCATTTTG
493109 TGTGGGATAT
Statistics
Matches: 49, Mismatches: 15, Indels: 2
0.74 0.23 0.03
Matches are distributed among these distances:
21 4 0.08
22 45 0.92
ACGTcount: A:0.20, C:0.11, G:0.03, T:0.66
Consensus pattern (22 bp):
ATTTAATTTTATTTCATTTTGA
Found at i:498067 original size:36 final size:37
Alignment explanation
Indices: 498002--498272 Score: 209
Period size: 36 Copynumber: 7.6 Consensus size: 37
497992 ACATATAACG
* *
498002 TATATAATATATATTTTTG--AA-TTTGTTTTGAAAATA
1 TATATAATATATAGTTTTGAAAACATT-TTTTG-AAATA
*
498038 TATAAT-ATATAG--TTTTGAAAACATTTTTTGAAAATA
1 TAT-ATAATATATAGTTTTGAAAACATTTTTTG-AAATA
498074 TATATAAATATATAGTTTTGAAAACA-TTTTTGAAA-A
1 TATAT-AATATATAGTTTTGAAAACATTTTTTGAAATA
* * * **
498110 TATAT-ATATA-A----T--ATATAGTTTTGAAAATA
1 TATATAATATATAGTTTTGAAAACATTTTTTGAAATA
* ** *
498139 TATATAATATATAGTTTTGGAAACATTTTTCAAAAATG
1 TATATAATATATAGTTTTGAAAACATTTTT-TGAAATA
*
498177 TATATAATATATAGTTTTAAAAACA-TTTTTGAAATA
1 TATATAATATATAGTTTTGAAAACATTTTTTGAAATA
**
498213 TATATAATATATAGTTTTGAAAA-ATATTTCAGAAATA
1 TATATAATATATAGTTTTGAAAACAT-TTTTTGAAATA
*
498250 TATACAATATATAGTTTTGAAAA
1 TATATAATATATAGTTTTGAAAA
498273 GCGTATATAA
Statistics
Matches: 193, Mismatches: 21, Indels: 41
0.76 0.08 0.16
Matches are distributed among these distances:
27 3 0.02
28 7 0.04
29 7 0.04
30 5 0.03
31 1 0.01
33 1 0.01
34 10 0.05
35 4 0.02
36 56 0.29
37 54 0.28
38 34 0.18
39 11 0.06
ACGTcount: A:0.45, C:0.03, G:0.08, T:0.44
Consensus pattern (37 bp):
TATATAATATATAGTTTTGAAAACATTTTTTGAAATA
Found at i:498104 original size:38 final size:37
Alignment explanation
Indices: 498002--498272 Score: 277
Period size: 38 Copynumber: 7.6 Consensus size: 37
497992 ACATATAACG
* **
498002 TATATAATATATATTTTTG--AATTTGTTTTGAAAATA
1 TATATAATATATAGTTTTGAAAACAT-TTTTGAAAATA
498038 TAT--AATATATAGTTTTGAAAACATTTTTTGAAAATA
1 TATATAATATATAGTTTTGAAAACA-TTTTTGAAAATA
498074 TATATAAATATATAGTTTTGAAAACATTTTTGAAAATA
1 TATAT-AATATATAGTTTTGAAAACATTTTTGAAAATA
* *
498112 TATAT-ATA-ATA----T----ATAGTTTTGAAAATA
1 TATATAATATATAGTTTTGAAAACATTTTTGAAAATA
* * *
498139 TATATAATATATAGTTTTGGAAACATTTTTCAAAAATG
1 TATATAATATATAGTTTTGAAAACATTTTT-GAAAATA
*
498177 TATATAATATATAGTTTTAAAAACATTTTTG-AAATA
1 TATATAATATATAGTTTTGAAAACATTTTTGAAAATA
* *
498213 TATATAATATATAGTTTTGAAAA-ATATTTCAGAAATA
1 TATATAATATATAGTTTTGAAAACATTTTTGA-AAATA
*
498250 TATACAATATATAGTTTTGAAAA
1 TATATAATATATAGTTTTGAAAA
498273 GCGTATATAA
Statistics
Matches: 199, Mismatches: 17, Indels: 37
0.79 0.07 0.15
Matches are distributed among these distances:
27 18 0.09
28 3 0.02
29 3 0.02
31 1 0.01
33 1 0.01
34 13 0.07
35 8 0.04
36 48 0.24
37 34 0.17
38 50 0.25
39 20 0.10
ACGTcount: A:0.45, C:0.03, G:0.08, T:0.44
Consensus pattern (37 bp):
TATATAATATATAGTTTTGAAAACATTTTTGAAAATA
Found at i:498113 original size:65 final size:64
Alignment explanation
Indices: 498055--498199 Score: 186
Period size: 64 Copynumber: 2.3 Consensus size: 64
498045 TATAGTTTTG
* *
498055 AAAACAT-TTTTTGAAAATATATATAAATATATAGTTTTGAAAACATTTTTGAAAATATATATAT
1 AAAACATAGTTTTGAAAATATATAT-AATATATAGTTTTGAAAACATTTTTCAAAATATATATAT
* * * *
498119 AATATATAGTTTTGAAAATATATATAATATATAGTTTTGGAAACATTTTTCAAAA-ATGTATAT
1 AAAACATAGTTTTGAAAATATATATAATATATAGTTTTGAAAACATTTTTCAAAATATATATAT
* * *
498182 AATATATAGTTTTAAAAA
1 AAAACATAGTTTTGAAAA
498200 CATTTTTGAA
Statistics
Matches: 73, Mismatches: 7, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
63 24 0.33
64 33 0.45
65 16 0.22
ACGTcount: A:0.48, C:0.03, G:0.08, T:0.42
Consensus pattern (64 bp):
AAAACATAGTTTTGAAAATATATATAATATATAGTTTTGAAAACATTTTTCAAAATATATATAT
Found at i:498145 original size:25 final size:27
Alignment explanation
Indices: 498101--498157 Score: 100
Period size: 25 Copynumber: 2.2 Consensus size: 27
498091 TTGAAAACAT
498101 TTTTGAAAATATATATATAATATATAG
1 TTTTGAAAATATATATATAATATATAG
498128 TTTTG-AAA-ATATATATAATATATAG
1 TTTTGAAAATATATATATAATATATAG
498153 TTTTG
1 TTTTG
498158 GAAACATTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
25 22 0.73
26 3 0.10
27 5 0.17
ACGTcount: A:0.44, C:0.00, G:0.09, T:0.47
Consensus pattern (27 bp):
TTTTGAAAATATATATATAATATATAG
Found at i:498248 original size:37 final size:37
Alignment explanation
Indices: 498134--498272 Score: 190
Period size: 37 Copynumber: 3.8 Consensus size: 37
498124 ATAGTTTTGA
* * *
498134 AAATATATATAATATATAGTTTTGGAAACATTTTTCAA
1 AAATATATATAATATATAGTTTT-GAAAAATATTTCAG
* * **
498172 AAATGTATATAATATATAGTTTT-AAAAACATTTTTG
1 AAATATATATAATATATAGTTTTGAAAAATATTTCAG
498208 AAATATATATAATATATAGTTTTGAAAAATATTTCAG
1 AAATATATATAATATATAGTTTTGAAAAATATTTCAG
*
498245 AAATATATACAATATATAGTTTTGAAAA
1 AAATATATATAATATATAGTTTTGAAAA
498273 GCGTATATAA
Statistics
Matches: 88, Mismatches: 12, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
36 29 0.33
37 37 0.42
38 22 0.25
ACGTcount: A:0.47, C:0.04, G:0.08, T:0.41
Consensus pattern (37 bp):
AAATATATATAATATATAGTTTTGAAAAATATTTCAG
Found at i:498376 original size:23 final size:25
Alignment explanation
Indices: 498333--498383 Score: 70
Period size: 23 Copynumber: 2.1 Consensus size: 25
498323 TTATATAGTT
*
498333 TTTTATTTACATTATATTTATTTCG
1 TTTTAATTACATTATATTTATTTCG
*
498358 TTTTAATTA-ATTA-ATTTATTTTG
1 TTTTAATTACATTATATTTATTTCG
498381 TTT
1 TTT
498384 ATTTTTTTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 12 0.50
24 4 0.17
25 8 0.33
ACGTcount: A:0.25, C:0.04, G:0.04, T:0.67
Consensus pattern (25 bp):
TTTTAATTACATTATATTTATTTCG
Found at i:499618 original size:15 final size:15
Alignment explanation
Indices: 499598--499628 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
499588 CGATCAATGG
499598 TAAGTACCAAGAAAT
1 TAAGTACCAAGAAAT
499613 TAAGTACCAAGAAAT
1 TAAGTACCAAGAAAT
499628 T
1 T
499629 CTAATCGAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.52, C:0.13, G:0.13, T:0.23
Consensus pattern (15 bp):
TAAGTACCAAGAAAT
Found at i:501964 original size:20 final size:19
Alignment explanation
Indices: 501935--501976 Score: 50
Period size: 20 Copynumber: 2.2 Consensus size: 19
501925 CCGAGTCAGT
501935 CTTGAACTGAACT-GTTGACC
1 CTTGAACTG-ACTCGTTG-CC
*
501955 CTTGACCTGACTCGTTGCC
1 CTTGAACTGACTCGTTGCC
501974 CTT
1 CTT
501977 TGTCTTTGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
19 8 0.40
20 12 0.60
ACGTcount: A:0.17, C:0.31, G:0.19, T:0.33
Consensus pattern (19 bp):
CTTGAACTGACTCGTTGCC
Found at i:507011 original size:24 final size:24
Alignment explanation
Indices: 506921--507016 Score: 57
Period size: 24 Copynumber: 3.8 Consensus size: 24
506911 TCTGTTAAGT
*
506921 TCCTCTTCAGAGGTTAACTCGGGA
1 TCCTCTTCAGAGGTTAACTCAGGA
* * * * *
506945 TCCTCTTCTGAAGTCTAATTTTTGTAGAGT
1 TCCTCTTCAGAGGT-TAA---CT-CAG-GA
* *
506975 TCCTTTTCGGAGGTTAACTCAGGA
1 TCCTCTTCAGAGGTTAACTCAGGA
*
506999 TCCTCTTCAGAGGGTAAC
1 TCCTCTTCAGAGGTTAAC
507017 ATTCTTATCA
Statistics
Matches: 51, Mismatches: 15, Indels: 12
0.65 0.19 0.15
Matches are distributed among these distances:
24 28 0.55
25 5 0.10
26 1 0.02
28 1 0.02
29 4 0.08
30 12 0.24
ACGTcount: A:0.21, C:0.22, G:0.22, T:0.35
Consensus pattern (24 bp):
TCCTCTTCAGAGGTTAACTCAGGA
Found at i:509448 original size:30 final size:30
Alignment explanation
Indices: 509407--509467 Score: 88
Period size: 30 Copynumber: 2.0 Consensus size: 30
509397 ATCCCAAAGG
509407 ACCTATCCATATGTTC-CGAAGAACATAGGT
1 ACCTATCCATATG-TCACGAAGAACATAGGT
* *
509437 ACCTGTCCATATGTCACGAAGGACATAGGT
1 ACCTATCCATATGTCACGAAGAACATAGGT
509467 A
1 A
509468 ACCCTCGACT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 2 0.07
30 26 0.93
ACGTcount: A:0.33, C:0.23, G:0.20, T:0.25
Consensus pattern (30 bp):
ACCTATCCATATGTCACGAAGAACATAGGT
Found at i:510664 original size:11 final size:11
Alignment explanation
Indices: 510648--510672 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
510638 TAACTTTAAC
510648 TAATAACCAGT
1 TAATAACCAGT
510659 TAATAACCAGT
1 TAATAACCAGT
510670 TAA
1 TAA
510673 CAACAAACTC
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:0.48, C:0.16, G:0.08, T:0.28
Consensus pattern (11 bp):
TAATAACCAGT
Found at i:534269 original size:22 final size:22
Alignment explanation
Indices: 534241--534285 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
534231 TAACTTTTGC
534241 CCTCGTAGTAGATTTAATTTAT
1 CCTCGTAGTAGATTTAATTTAT
534263 CCTCGTAGTAGATTTAATTTAT
1 CCTCGTAGTAGATTTAATTTAT
534285 C
1 C
534286 ACTTTCACCC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.27, C:0.16, G:0.13, T:0.44
Consensus pattern (22 bp):
CCTCGTAGTAGATTTAATTTAT
Found at i:534983 original size:38 final size:37
Alignment explanation
Indices: 534906--534993 Score: 106
Period size: 37 Copynumber: 2.4 Consensus size: 37
534896 CCCGACCCGA
* *
534906 TCGGGTCGGATTTTTTTAAAAAAATTTCGGGTTCGGG
1 TCGGGTCGGGTTTTTTTAAAAAAATTTCGGGTTCAGG
** *
534943 TCGGGTCGGGTTTTTTTAAATGTACTGTTCGGG-TCAGG
1 TCGGGTCGGGTTTTTTTAAA-AAAAT-TTCGGGTTCAGG
534981 TCGGGTCGGGTTT
1 TCGGGTCGGGTTT
534994 AGGGTGAAAA
Statistics
Matches: 44, Mismatches: 5, Indels: 3
0.85 0.10 0.06
Matches are distributed among these distances:
37 19 0.43
38 19 0.43
39 6 0.14
ACGTcount: A:0.15, C:0.12, G:0.34, T:0.39
Consensus pattern (37 bp):
TCGGGTCGGGTTTTTTTAAAAAAATTTCGGGTTCAGG
Found at i:535583 original size:3 final size:3
Alignment explanation
Indices: 535575--535607 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
535565 ATCACAACTT
535575 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
535608 AAACAAGAAC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:536359 original size:3 final size:3
Alignment explanation
Indices: 536351--536403 Score: 106
Period size: 3 Copynumber: 17.7 Consensus size: 3
536341 ATTCTCTCTC
536351 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
536399 TTA TT
1 TTA TT
536404 TTGTTGCCAG
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 50 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:539451 original size:176 final size:177
Alignment explanation
Indices: 539154--539510 Score: 662
Period size: 176 Copynumber: 2.0 Consensus size: 177
539144 CAGCACGGCC
539154 TACTGCCTTACAACTGCTAGATCACCCCTTCATTCGTGACCAAGCAACAACAAGAGTTGCTAACA
1 TACTGCCTTACAACTGCTAGATCACCCCTTCATTCGTGACCAAG--ACAACAAGAGTTGCTAACA
539219 TAAGCATAACCAAGGATGCATTTCCTTACACTTTTGATGGAAGCCGCACTCCGGTATATATTCTT
64 TAAGCATAACCAAGGATGCATTTCCTTACACTTTTGATGGAAGCCGCACTCCGGTATATATTCTT
* *
539284 AAGATGATTTTTATTACTCCTATTGCATAGACTTTGACTTGCATACATT
129 AAGATAATTTTTATTACTCCTATTGAATAGACTTTGACTTGCATACATT
*
539333 TACTGCCTTACAACTGCTAGATCACCCCTTCATTCTTGACCAAG-CAACAAGAGTTGCTAACATA
1 TACTGCCTTACAACTGCTAGATCACCCCTTCATTCGTGACCAAGACAACAAGAGTTGCTAACATA
539397 AGCATAACCAAGGATGCATTTCCTTACACTTTTGATGGAAGCCGCACTCCGGTATATATTCTTAA
66 AGCATAACCAAGGATGCATTTCCTTACACTTTTGATGGAAGCCGCACTCCGGTATATATTCTTAA
539462 GATAATTTTTATTACTCCTATTGAATAGACTTTGACTTGCATACATT
131 GATAATTTTTATTACTCCTATTGAATAGACTTTGACTTGCATACATT
539509 TA
1 TA
539511 ACGTAGACTT
Statistics
Matches: 175, Mismatches: 3, Indels: 3
0.97 0.02 0.02
Matches are distributed among these distances:
176 132 0.75
179 43 0.25
ACGTcount: A:0.30, C:0.24, G:0.14, T:0.32
Consensus pattern (177 bp):
TACTGCCTTACAACTGCTAGATCACCCCTTCATTCGTGACCAAGACAACAAGAGTTGCTAACATA
AGCATAACCAAGGATGCATTTCCTTACACTTTTGATGGAAGCCGCACTCCGGTATATATTCTTAA
GATAATTTTTATTACTCCTATTGAATAGACTTTGACTTGCATACATT
Found at i:542155 original size:29 final size:26
Alignment explanation
Indices: 542123--542187 Score: 71
Period size: 26 Copynumber: 2.5 Consensus size: 26
542113 AAATGGAGGA
*
542123 AAAAATAAATAAGTA-AAGAGTAATAAA
1 AAAAATAAATAA-TAGAAGAGT-ATAAG
542150 AGAAAATAAA-AATAGAAGAGTATAAG
1 A-AAAATAAATAATAGAAGAGTATAAG
*
542176 AATAATAAATAA
1 AAAAATAAATAA
542188 AATACATGTA
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
25 7 0.21
26 9 0.27
27 9 0.27
28 8 0.24
ACGTcount: A:0.69, C:0.00, G:0.12, T:0.18
Consensus pattern (26 bp):
AAAAATAAATAATAGAAGAGTATAAG
Found at i:542415 original size:14 final size:14
Alignment explanation
Indices: 542398--542450 Score: 65
Period size: 14 Copynumber: 3.9 Consensus size: 14
542388 AATATTTTAA
542398 AAAAAATAATAAAT
1 AAAAAATAATAAAT
542412 AAAAAA-AATAAA-
1 AAAAAATAATAAAT
*
542424 AAAAATATAATATAT
1 AAAAA-ATAATAAAT
*
542439 AAAATATAATAA
1 AAAAAATAATAA
542451 TAATAATGAA
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
12 5 0.15
13 7 0.21
14 17 0.52
15 4 0.12
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (14 bp):
AAAAAATAATAAAT
Found at i:542429 original size:25 final size:26
Alignment explanation
Indices: 542395--542457 Score: 76
Period size: 25 Copynumber: 2.5 Consensus size: 26
542385 TAAAATATTT
542395 TAAAAAAAATAATAA-ATAAAAAAAA
1 TAAAAAAAATAATAATATAAAAAAAA
* *
542420 TAAAAAAAAT-ATAATATATAAAATA
1 TAAAAAAAATAATAATATAAAAAAAA
* *
542445 TAATAATAATAAT
1 TAAAAAAAATAAT
542458 GAAGTATATA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
24 4 0.12
25 26 0.81
26 2 0.06
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (26 bp):
TAAAAAAAATAATAATATAAAAAAAA
Found at i:542455 original size:20 final size:20
Alignment explanation
Indices: 542418--542478 Score: 65
Period size: 20 Copynumber: 3.2 Consensus size: 20
542408 AAATAAAAAA
* *
542418 AATAAAAAAAATATAAT-AT
1 AATAAAATATATATAATAAT
542437 -ATAAAATATA-ATAATAAT
1 AATAAAATATATATAATAAT
* *
542455 AATGAAGTATATATAATAAT
1 AATAAAATATATATAATAAT
542475 AATA
1 AATA
542479 GTAAGGAAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 5
0.77 0.11 0.11
Matches are distributed among these distances:
17 5 0.15
18 10 0.29
19 8 0.24
20 11 0.32
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.31
Consensus pattern (20 bp):
AATAAAATATATATAATAAT
Found at i:542846 original size:12 final size:12
Alignment explanation
Indices: 542799--542848 Score: 55
Period size: 13 Copynumber: 3.9 Consensus size: 12
542789 TTCTTGTTTC
*
542799 TCTTTTTTATTT
1 TCTTTTTTTTTT
*
542811 TCTCTTTGTTTTT
1 TCT-TTTTTTTTT
542824 TCATTTGTTTTTTT
1 TC-TTT-TTTTTTT
542838 TCTTTTTTTTT
1 TCTTTTTTTTT
542849 GTTATGATTG
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
12 9 0.28
13 14 0.44
14 9 0.28
ACGTcount: A:0.04, C:0.10, G:0.04, T:0.82
Consensus pattern (12 bp):
TCTTTTTTTTTT
Found at i:543709 original size:10 final size:10
Alignment explanation
Indices: 543694--543731 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
543684 ACCCGTTGAC
*
543694 CGTTGACCGG
1 CGTTGACCGA
543704 CGTTGACCGA
1 CGTTGACCGA
543714 CGTTGACC-A
1 CGTTGACCGA
543723 CTGTTGACC
1 C-GTTGACC
543732 AAAACTTTGA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
9 2 0.08
10 24 0.92
ACGTcount: A:0.16, C:0.32, G:0.29, T:0.24
Consensus pattern (10 bp):
CGTTGACCGA
Found at i:545050 original size:18 final size:18
Alignment explanation
Indices: 545024--545058 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
545014 TCGAAAGGAC
*
545024 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
545042 TGAATTAAATAATAAGA
1 TGAAGTAAATAATAAGA
545059 CCGGATGGAA
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:0.54, C:0.00, G:0.17, T:0.29
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:546197 original size:24 final size:24
Alignment explanation
Indices: 546170--546278 Score: 123
Period size: 24 Copynumber: 4.5 Consensus size: 24
546160 AATTATTTTA
*
546170 TCTGATTTCCGA-CTTGAATTCTGT
1 TCTGATTTCTGATC-TGAATTCTGT
* * *
546194 TCTGA-TACATTACCTGAATTCTGT
1 TCTGATTTC-TGATCTGAATTCTGT
*
546218 TCTGATTTCTGATCTGGATTCTGT
1 TCTGATTTCTGATCTGAATTCTGT
*
546242 TCTGATATCTGATCTGAATTCTGT
1 TCTGATTTCTGATCTGAATTCTGT
*
546266 TTTGATTTCTGAT
1 TCTGATTTCTGAT
546279 ATATCCGTTT
Statistics
Matches: 71, Mismatches: 11, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
23 2 0.03
24 66 0.93
25 3 0.04
ACGTcount: A:0.18, C:0.17, G:0.17, T:0.48
Consensus pattern (24 bp):
TCTGATTTCTGATCTGAATTCTGT
Found at i:546222 original size:12 final size:12
Alignment explanation
Indices: 546207--546276 Score: 70
Period size: 12 Copynumber: 5.8 Consensus size: 12
546197 GATACATTAC
546207 CTGAATTCTGTT
1 CTGAATTCTGTT
* *
546219 CTGATTTCTGAT
1 CTGAATTCTGTT
*
546231 CTGGATTCTGTT
1 CTGAATTCTGTT
*
546243 CTG-ATATCTGAT
1 CTGAAT-TCTGTT
546255 CTGAATTCTGTT
1 CTGAATTCTGTT
* *
546267 TTGATTTCTG
1 CTGAATTCTG
546277 ATATATCCGT
Statistics
Matches: 47, Mismatches: 9, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
11 2 0.04
12 43 0.91
13 2 0.04
ACGTcount: A:0.16, C:0.16, G:0.19, T:0.50
Consensus pattern (12 bp):
CTGAATTCTGTT
Found at i:546275 original size:48 final size:48
Alignment explanation
Indices: 546170--546278 Score: 141
Period size: 48 Copynumber: 2.3 Consensus size: 48
546160 AATTATTTTA
* * *
546170 TCTGATTTCCGA-CTTGAATTCTGTTCTGATACATTACCTGAATTCTGT
1 TCTGATTTCTGATC-TGGATTCTGTTCTGATACATGACCTGAATTCTGT
*
546218 TCTGATTTCTGATCTGGATTCTGTTCTGATATC-TGATCTGAATTCTGT
1 TCTGATTTCTGATCTGGATTCTGTTCTGATA-CATGACCTGAATTCTGT
*
546266 TTTGATTTCTGAT
1 TCTGATTTCTGAT
546279 ATATCCGTTT
Statistics
Matches: 54, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
48 52 0.96
49 2 0.04
ACGTcount: A:0.18, C:0.17, G:0.17, T:0.48
Consensus pattern (48 bp):
TCTGATTTCTGATCTGGATTCTGTTCTGATACATGACCTGAATTCTGT
Found at i:549387 original size:13 final size:13
Alignment explanation
Indices: 549369--549393 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
549359 TCACTTAAAA
549369 CGGGTTTAGAGCT
1 CGGGTTTAGAGCT
549382 CGGGTTTAGAGC
1 CGGGTTTAGAGC
549394 CTTAGATGAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.16, G:0.40, T:0.28
Consensus pattern (13 bp):
CGGGTTTAGAGCT
Found at i:550094 original size:9 final size:9
Alignment explanation
Indices: 550076--550266 Score: 62
Period size: 9 Copynumber: 20.8 Consensus size: 9
550066 CATAATAAAC
550076 AAAT-AAAT
1 AAATAAAAT
550084 AAATAAAAT
1 AAATAAAAT
*
550093 AAGA-AGAA-
1 AA-ATAAAAT
550101 AAATACAAAT
1 AAATA-AAAT
*
550111 AAATAAAAC
1 AAATAAAAT
* *
550120 AAATGTAAAG
1 AAAT-AAAAT
550130 AAGATAAAA-
1 AA-ATAAAAT
550139 AAATAAAA-
1 AAATAAAAT
550147 AAATAAAGAT
1 AAATAAA-AT
* *
550157 AAGGTATAA-
1 AA-ATAAAAT
550166 AAATAAAAAT
1 AAAT-AAAAT
* **
550176 GAAATAGAGG
1 -AAATAAAAT
550186 AAA-AAAAT
1 AAATAAAAT
**
550194 AAA-AAGGGT
1 AAATAA-AAT
550203 AAATAGAAAT
1 AAATA-AAAT
550213 AAATAAAAT
1 AAATAAAAT
550222 AGAATAATAAT
1 A-AATAA-AAT
*
550233 -AATACTAAT
1 AAATA-AAAT
550242 -AATAATAAT
1 AAATAA-AAT
550251 -AATAACAAT
1 AAATAA-AAT
550260 AAATAAA
1 AAATAAA
550267 GAGTAATAAA
Statistics
Matches: 139, Mismatches: 23, Indels: 41
0.68 0.11 0.20
Matches are distributed among these distances:
7 1 0.01
8 28 0.20
9 61 0.44
10 36 0.26
11 13 0.09
ACGTcount: A:0.70, C:0.02, G:0.09, T:0.19
Consensus pattern (9 bp):
AAATAAAAT
Found at i:550109 original size:31 final size:30
Alignment explanation
Indices: 550072--550159 Score: 90
Period size: 31 Copynumber: 2.8 Consensus size: 30
550062 TATACATAAT
550072 AAACAAATAAATAAATAAAATAAGAAGAAA
1 AAACAAATAAATAAATAAAATAAGAAGAAA
*
550102 AATACAAATAAATAAA-ACAAATGTAAAGAAGATA
1 AA-ACAAATAAATAAATA-AAA--T-AAGAAGAAA
*
550136 AAA-AAATAAAAAAATAAAGATAAG
1 AAACAAATAAATAAATAAA-ATAAG
550160 GTATAAAAAT
Statistics
Matches: 49, Mismatches: 2, Indels: 14
0.75 0.03 0.22
Matches are distributed among these distances:
30 6 0.12
31 17 0.35
32 12 0.24
33 4 0.08
34 10 0.20
ACGTcount: A:0.74, C:0.03, G:0.08, T:0.15
Consensus pattern (30 bp):
AAACAAATAAATAAATAAAATAAGAAGAAA
Found at i:550148 original size:7 final size:8
Alignment explanation
Indices: 550069--550153 Score: 62
Period size: 8 Copynumber: 9.8 Consensus size: 8
550059 ATATATACAT
*
550069 AATAAACA
1 AATAAAAA
*
550077 AATAAATA
1 AATAAAAA
*
550085 AATAAAAT
1 AATAAAAA
*
550093 AAGAAGAAA
1 AATAA-AAA
550102 AATACAAATA
1 AATA-AAA-A
550112 AATAAAACA
1 AATAAAA-A
550121 AATGTAAAGAA
1 AA--TAAA-AA
*
550132 GATAAAAA
1 AATAAAAA
550140 AATAAAAA
1 AATAAAAA
550148 AATAAA
1 AATAAA
550154 GATAAGGTAT
Statistics
Matches: 62, Mismatches: 9, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
8 32 0.52
9 17 0.27
10 6 0.10
11 6 0.10
12 1 0.02
ACGTcount: A:0.75, C:0.04, G:0.06, T:0.15
Consensus pattern (8 bp):
AATAAAAA
Found at i:550232 original size:3 final size:3
Alignment explanation
Indices: 550224--550261 Score: 58
Period size: 3 Copynumber: 12.7 Consensus size: 3
550214 AATAAAATAG
* *
550224 AAT AAT AAT AAT ACT AAT AAT AAT AAT AAT AAC AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
550262 ATAAAGAGTA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.66, C:0.05, G:0.00, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:550286 original size:24 final size:25
Alignment explanation
Indices: 550242--550315 Score: 71
Period size: 24 Copynumber: 3.0 Consensus size: 25
550232 TAATACTAAT
* *
550242 AATAATAATAATAACAATAAATAAAG
1 AATAATAA-AAGAATAATAAATAAAG
*
550268 AGTAATAAAAGAA-AATAAA-AATAG
1 AATAATAAAAGAATAATAAATAA-AG
* *
550292 AATGATATAAGAATAATAAATAAA
1 AATAATAAAAGAATAATAAATAAA
550316 ATATATGTAT
Statistics
Matches: 40, Mismatches: 5, Indels: 7
0.77 0.10 0.13
Matches are distributed among these distances:
23 2 0.05
24 18 0.45
25 11 0.28
26 9 0.22
ACGTcount: A:0.69, C:0.01, G:0.08, T:0.22
Consensus pattern (25 bp):
AATAATAAAAGAATAATAAATAAAG
Found at i:550389 original size:2 final size:2
Alignment explanation
Indices: 550384--550409 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
550374 GGAAAAAATG
550384 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
550410 ATAGTAATAC
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):
TA
Found at i:550557 original size:15 final size:17
Alignment explanation
Indices: 550521--550571 Score: 61
Period size: 17 Copynumber: 3.0 Consensus size: 17
550511 ATAAAATGTT
550521 TTAAAAAAAATAATAAA
1 TTAAAAAAAATAATAAA
*
550538 TTAAAAAAGATAA-AAA
1 TTAAAAAAAATAATAAA
550554 -TAAAATAAAATATATAAA
1 TTAAAA-AAAATA-ATAAA
550572 ATATAATAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
15 5 0.17
16 8 0.28
17 13 0.45
18 3 0.10
ACGTcount: A:0.75, C:0.00, G:0.02, T:0.24
Consensus pattern (17 bp):
TTAAAAAAAATAATAAA
Found at i:550557 original size:20 final size:20
Alignment explanation
Indices: 550532--550583 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
550522 TAAAAAAAAT
*
550532 AATAAATTAAAAAAGATAAA
1 AATAAAATAAAAAAGATAAA
* *
550552 AATAAAATAAAATATATAAA
1 AATAAAATAAAAAAGATAAA
550572 ATATAATAATAA
1 A-ATAA-AATAA
550584 TAATTAAGTA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
20 18 0.67
21 4 0.15
22 5 0.19
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.25
Consensus pattern (20 bp):
AATAAAATAAAAAAGATAAA
Found at i:550570 original size:14 final size:14
Alignment explanation
Indices: 550553--550608 Score: 51
Period size: 14 Copynumber: 3.9 Consensus size: 14
550543 AAAGATAAAA
550553 ATAAAATAAAATAT
1 ATAAAATAAAATAT
*
550567 ATAAAATATAATA-
1 ATAAAATAAAATAT
* *
550580 ATAATAATTAAGTAT
1 ATAA-AATAAAATAT
*
550595 ATATAATAATAATA
1 ATAAAATAA-AATA
550609 GTAAGGAAAA
Statistics
Matches: 32, Mismatches: 7, Indels: 5
0.73 0.16 0.11
Matches are distributed among these distances:
13 4 0.12
14 22 0.69
15 6 0.19
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (14 bp):
ATAAAATAAAATAT
Found at i:550585 original size:20 final size:19
Alignment explanation
Indices: 550550--550608 Score: 66
Period size: 19 Copynumber: 3.1 Consensus size: 19
550540 AAAAAAGATA
*
550550 AAAATAAAATAA-AATATAT
1 AAAATATAATAATAATA-AT
550569 AAAATATAATAATAATAAT
1 AAAATATAATAATAATAAT
* *
550588 TAAGTATATATAATAATAAT
1 AAAATATA-ATAATAATAAT
550608 A
1 A
550609 GTAAGGAAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
19 19 0.56
20 15 0.44
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (19 bp):
AAAATATAATAATAATAAT
Found at i:551023 original size:37 final size:37
Alignment explanation
Indices: 550973--551084 Score: 188
Period size: 37 Copynumber: 3.0 Consensus size: 37
550963 ATGTTTATAG
550973 ATCCTATTTTTAGGAGTTTGAATCATAGTAAAACTCT
1 ATCCTATTTTTAGGAGTTTGAATCATAGTAAAACTCT
551010 ATCCTATTTTTAGGAGTTTGAATCATAGTAAAACTCT
1 ATCCTATTTTTAGGAGTTTGAATCATAGTAAAACTCT
* * * *
551047 ATCATATTTTTAAGAGTTTAAATCTTAGTAAAACTCT
1 ATCCTATTTTTAGGAGTTTGAATCATAGTAAAACTCT
551084 A
1 A
551085 ACGTTATATT
Statistics
Matches: 71, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 71 1.00
ACGTcount: A:0.35, C:0.12, G:0.12, T:0.41
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTGAATCATAGTAAAACTCT
Found at i:563845 original size:23 final size:23
Alignment explanation
Indices: 563789--563850 Score: 70
Period size: 23 Copynumber: 2.7 Consensus size: 23
563779 CATTTTATAT
*
563789 GGAACTTCGGTGCAATCCTACGT
1 GGAACTTCGGTGCAATCCTACGC
* * * * *
563812 GGCACTACGGTGCATTTCTATGC
1 GGAACTTCGGTGCAATCCTACGC
563835 GGAACTTCGGTGCAAT
1 GGAACTTCGGTGCAAT
563851 TATACGATCT
Statistics
Matches: 30, Mismatches: 9, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.21, C:0.24, G:0.27, T:0.27
Consensus pattern (23 bp):
GGAACTTCGGTGCAATCCTACGC
Found at i:568838 original size:4 final size:5
Alignment explanation
Indices: 568825--568896 Score: 78
Period size: 5 Copynumber: 14.4 Consensus size: 5
568815 AAACAAAAGT
**
568825 AATAA AAT-A AATAA AATAA AATAA AA-AA CCTAA AA-AA AATAA AATAA
1 AATAA AATAA AATAA AATAA AATAA AATAA AATAA AATAA AATAA AATAA
568872 AATAA TGGAATAA AATAA AATAA AA
1 AATAA ---AATAA AATAA AATAA AA
568897 AAGATACAAA
Statistics
Matches: 57, Mismatches: 4, Indels: 12
0.78 0.05 0.16
Matches are distributed among these distances:
4 10 0.18
5 42 0.74
8 5 0.09
ACGTcount: A:0.76, C:0.03, G:0.03, T:0.18
Consensus pattern (5 bp):
AATAA
Found at i:568858 original size:23 final size:21
Alignment explanation
Indices: 568814--568898 Score: 89
Period size: 23 Copynumber: 3.8 Consensus size: 21
568804 ATGTCAAAAC
*
568814 AAAACAAAAGTAATAAAATAAAT
1 AAAATAAAA-TAA-AAAATAAAT
*
568837 AAAATAAAATAAAAAACCTAAAA
1 AAAATAAAATAAAAAA--TAAAT
*
568860 AAAATAAAATAAAATAATGGAAT
1 AAAATAAAATAAAA-AAT-AAAT
568883 AAAATAAAATAAAAAA
1 AAAATAAAATAAAAAA
568899 GATACAAAAA
Statistics
Matches: 54, Mismatches: 4, Indels: 9
0.81 0.06 0.13
Matches are distributed among these distances:
21 4 0.07
22 6 0.11
23 42 0.78
24 2 0.04
ACGTcount: A:0.76, C:0.04, G:0.04, T:0.16
Consensus pattern (21 bp):
AAAATAAAATAAAAAATAAAT
Found at i:568891 original size:28 final size:27
Alignment explanation
Indices: 568825--568938 Score: 85
Period size: 28 Copynumber: 4.1 Consensus size: 27
568815 AAACAAAAGT
568825 AATAAAAT-AAATAAAATAAAATAAAA
1 AATAAAATAAAATAAAATAAAATAAAA
**
568851 AACCTAAAA-AAAATAAAATAAAATAATGG
1 AA--TAAAATAAAATAAAATAAAATAA-AA
*
568880 AATAAAATAAAATAAAA-AAGATACAAA
1 AATAAAATAAAATAAAATAAAATA-AAA
* *
568907 AACCAAAA-AAGAA-AAAAGAAAAATAAAA
1 AA-TAAAATAA-AATAAAA-TAAAATAAAA
568935 AATA
1 AATA
568939 TATAAAAAGG
Statistics
Matches: 70, Mismatches: 8, Indels: 19
0.72 0.08 0.20
Matches are distributed among these distances:
26 2 0.03
27 19 0.27
28 42 0.60
29 7 0.10
ACGTcount: A:0.77, C:0.04, G:0.04, T:0.14
Consensus pattern (27 bp):
AATAAAATAAAATAAAATAAAATAAAA
Found at i:569187 original size:2 final size:2
Alignment explanation
Indices: 569182--569234 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
569172 GAAAAAAATA
569182 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
569224 AT AT AT AT AT A
1 AT AT AT AT AT A
569235 AATGTTAAAT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:575664 original size:7 final size:7
Alignment explanation
Indices: 575655--575691 Score: 58
Period size: 7 Copynumber: 5.4 Consensus size: 7
575645 GATCCTAACT
*
575655 TATCACT
1 TATCACA
575662 TAT-ACA
1 TATCACA
575668 TATCACA
1 TATCACA
575675 TATCACA
1 TATCACA
575682 TATCACA
1 TATCACA
575689 TAT
1 TAT
575692 ATCATTTCAC
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
6 5 0.18
7 23 0.82
ACGTcount: A:0.41, C:0.24, G:0.00, T:0.35
Consensus pattern (7 bp):
TATCACA
Found at i:575684 original size:14 final size:13
Alignment explanation
Indices: 575655--575702 Score: 60
Period size: 14 Copynumber: 3.5 Consensus size: 13
575645 GATCCTAACT
*
575655 TATCACTTATACA
1 TATCACATATACA
575668 TATCACATATCACA
1 TATCACATAT-ACA
575682 TATCACATATATCA
1 TATCACATATA-CA
*
575696 TTTCACA
1 TATCACA
575703 GGAAACACAC
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
13 10 0.32
14 21 0.68
ACGTcount: A:0.40, C:0.25, G:0.00, T:0.35
Consensus pattern (13 bp):
TATCACATATACA
Found at i:575880 original size:18 final size:18
Alignment explanation
Indices: 575853--575900 Score: 69
Period size: 18 Copynumber: 2.7 Consensus size: 18
575843 AGAATTTGTA
*
575853 CCGTATGACCACTATATC
1 CCGTAGGACCACTATATC
* *
575871 TCGTAGGACCACTATGTC
1 CCGTAGGACCACTATATC
575889 CCGTAGGACCAC
1 CCGTAGGACCAC
575901 GTAGAACACA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.25, C:0.33, G:0.19, T:0.23
Consensus pattern (18 bp):
CCGTAGGACCACTATATC
Found at i:575952 original size:46 final size:46
Alignment explanation
Indices: 575874--575999 Score: 207
Period size: 46 Copynumber: 2.7 Consensus size: 46
575864 CTATATCTCG
*
575874 TAGGACCACTATGTCCCGTAGGACCACGTAGAACACATATGTCCCA
1 TAGGACCACTATGTCCCGTAGGACCACATAGAACACATATGTCCCA
* * *
575920 TAGGGCCACTATGTCCCGTAGGACCATATAGAACACATATGTCCCG
1 TAGGACCACTATGTCCCGTAGGACCACATAGAACACATATGTCCCA
*
575966 TAGGACCACTATGTCCCGTAGGACCACGTAGAAC
1 TAGGACCACTATGTCCCGTAGGACCACATAGAAC
576000 CCTCGACTCT
Statistics
Matches: 73, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
46 73 1.00
ACGTcount: A:0.29, C:0.29, G:0.21, T:0.20
Consensus pattern (46 bp):
TAGGACCACTATGTCCCGTAGGACCACATAGAACACATATGTCCCA
Found at i:575980 original size:18 final size:18
Alignment explanation
Indices: 575957--575992 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
575947 ATAGAACACA
575957 TATGTCCCGTAGGACCAC
1 TATGTCCCGTAGGACCAC
575975 TATGTCCCGTAGGACCAC
1 TATGTCCCGTAGGACCAC
575993 GTAGAACCCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.22, C:0.33, G:0.22, T:0.22
Consensus pattern (18 bp):
TATGTCCCGTAGGACCAC
Found at i:576532 original size:25 final size:25
Alignment explanation
Indices: 576504--576553 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
576494 TTTAGCACCA
*
576504 TATCACTACATGTTTATGCTTCAGT
1 TATCACTACATATTTATGCTTCAGT
*
576529 TATCACTATATATTTATGCTTCAGT
1 TATCACTACATATTTATGCTTCAGT
576554 ACCCCTGATC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.26, C:0.18, G:0.10, T:0.46
Consensus pattern (25 bp):
TATCACTACATATTTATGCTTCAGT
Found at i:579957 original size:46 final size:46
Alignment explanation
Indices: 579900--580028 Score: 231
Period size: 46 Copynumber: 2.8 Consensus size: 46
579890 GCGTAGAATT
*
579900 TGTCCCGTAGGACCACTATGTCCCATAGGACCACATAGAACACATA
1 TGTCCCATAGGACCACTATGTCCCATAGGACCACATAGAACACATA
*
579946 TGTCCCATAGGACCACTATGTCCCGTAGGACCACATAGAACACATA
1 TGTCCCATAGGACCACTATGTCCCATAGGACCACATAGAACACATA
*
579992 TGTCCTATAGGACCACTATGTCCCATAGGACCACATA
1 TGTCCCATAGGACCACTATGTCCCATAGGACCACATA
580029 AAACCCTCGA
Statistics
Matches: 79, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
46 79 1.00
ACGTcount: A:0.32, C:0.30, G:0.17, T:0.21
Consensus pattern (46 bp):
TGTCCCATAGGACCACTATGTCCCATAGGACCACATAGAACACATA
Found at i:579965 original size:18 final size:18
Alignment explanation
Indices: 579944--580025 Score: 65
Period size: 18 Copynumber: 5.0 Consensus size: 18
579934 ATAGAACACA
579944 TATGTCCCATAGGACCAC
1 TATGTCCCATAGGACCAC
*
579962 TATGTCCCGTAGGA-C-C
1 TATGTCCCATAGGACCAC
*
579978 -A-----CATA-GAACAC
1 TATGTCCCATAGGACCAC
*
579989 ATATGTCCTATAGGACCAC
1 -TATGTCCCATAGGACCAC
580008 TATGTCCCATAGGACCAC
1 TATGTCCCATAGGACCAC
580026 ATAAAACCCT
Statistics
Matches: 49, Mismatches: 5, Indels: 20
0.66 0.07 0.27
Matches are distributed among these distances:
9 2 0.04
10 4 0.08
11 1 0.02
13 1 0.02
15 1 0.02
16 1 0.02
17 1 0.02
18 33 0.67
19 5 0.10
ACGTcount: A:0.30, C:0.30, G:0.17, T:0.22
Consensus pattern (18 bp):
TATGTCCCATAGGACCAC
Found at i:582547 original size:20 final size:20
Alignment explanation
Indices: 582522--582562 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
582512 TATCCATTGT
*
582522 GAGTGTTTTGGAGCCGTTGG
1 GAGTGTTTTAGAGCCGTTGG
582542 GAGTGTTTTAGAGCCGTTGG
1 GAGTGTTTTAGAGCCGTTGG
582562 G
1 G
582563 GATCAATTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.12, C:0.10, G:0.44, T:0.34
Consensus pattern (20 bp):
GAGTGTTTTAGAGCCGTTGG
Found at i:585121 original size:18 final size:20
Alignment explanation
Indices: 585085--585133 Score: 57
Period size: 18 Copynumber: 2.5 Consensus size: 20
585075 CCTAAATTTG
* *
585085 GTATCAATACTCAAGC-A-A
1 GTATCGATACTCAACCAAGA
*
585103 GTATCGATACTCATCCAAGA
1 GTATCGATACTCAACCAAGA
585123 GTATCGATACT
1 GTATCGATACT
585134 ACCTTACCCA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
18 13 0.50
19 1 0.04
20 12 0.46
ACGTcount: A:0.37, C:0.22, G:0.14, T:0.27
Consensus pattern (20 bp):
GTATCGATACTCAACCAAGA
Found at i:589378 original size:20 final size:20
Alignment explanation
Indices: 589353--589421 Score: 138
Period size: 20 Copynumber: 3.5 Consensus size: 20
589343 ATGTGAGTAG
589353 TATCGATACTCTACTTGCAA
1 TATCGATACTCTACTTGCAA
589373 TATCGATACTCTACTTGCAA
1 TATCGATACTCTACTTGCAA
589393 TATCGATACTCTACTTGCAA
1 TATCGATACTCTACTTGCAA
589413 TATCGATAC
1 TATCGATAC
589422 CCCTAAGGTT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 49 1.00
ACGTcount: A:0.30, C:0.25, G:0.10, T:0.35
Consensus pattern (20 bp):
TATCGATACTCTACTTGCAA
Found at i:594571 original size:25 final size:23
Alignment explanation
Indices: 594537--594584 Score: 69
Period size: 25 Copynumber: 2.0 Consensus size: 23
594527 ATTTGAGTAT
594537 ATTTTTAAGTGGTGTAAATATAATA
1 ATTTTTAAGT-GTGTAAAT-TAATA
*
594562 ATTTTTAAGTGTGTATATTAATA
1 ATTTTTAAGTGTGTAAATTAATA
594585 CATGATAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 5 0.23
24 7 0.32
25 10 0.45
ACGTcount: A:0.38, C:0.00, G:0.15, T:0.48
Consensus pattern (23 bp):
ATTTTTAAGTGTGTAAATTAATA
Found at i:595345 original size:20 final size:20
Alignment explanation
Indices: 595320--595424 Score: 142
Period size: 20 Copynumber: 5.3 Consensus size: 20
595310 TACATTGGGC
*
595320 TATGAATATGAAAGTAAAGT
1 TATGAATCTGAAAGTAAAGT
*
595340 TATGAATCTGAAAGTAAAGC
1 TATGAATCTGAAAGTAAAGT
* *
595360 TATGAATATGAAAGTATAGT
1 TATGAATCTGAAAGTAAAGT
*
595380 TATGAATCTGAAAGTAAAGC
1 TATGAATCTGAAAGTAAAGT
*
595400 TATGAATCTTAAA-TAAA-T
1 TATGAATCTGAAAGTAAAGT
595418 TATGAAT
1 TATGAAT
595425 TTGGAAAGTT
Statistics
Matches: 75, Mismatches: 10, Indels: 2
0.86 0.11 0.02
Matches are distributed among these distances:
18 7 0.09
19 4 0.05
20 64 0.85
ACGTcount: A:0.47, C:0.05, G:0.17, T:0.31
Consensus pattern (20 bp):
TATGAATCTGAAAGTAAAGT
Found at i:595373 original size:40 final size:40
Alignment explanation
Indices: 595318--595433 Score: 173
Period size: 40 Copynumber: 2.9 Consensus size: 40
595308 TATACATTGG
595318 GCTATGAATATGAAAGTAAAGTTATGAATCTGAAAGTAAA
1 GCTATGAATATGAAAGTAAAGTTATGAATCTGAAAGTAAA
*
595358 GCTATGAATATGAAAGTATAGTTATGAATCTGAAAGTAAA
1 GCTATGAATATGAAAGTAAAGTTATGAATCTGAAAGTAAA
* * *
595398 GCTATGAATCTTAAA-TAAA-TTATGAATTTGGAAAGT
1 GCTATGAATATGAAAGTAAAGTTATGAATCT-GAAAGT
595434 TCTGAATCTG
Statistics
Matches: 70, Mismatches: 5, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
38 9 0.13
39 9 0.13
40 52 0.74
ACGTcount: A:0.45, C:0.05, G:0.19, T:0.31
Consensus pattern (40 bp):
GCTATGAATATGAAAGTAAAGTTATGAATCTGAAAGTAAA
Found at i:595397 original size:60 final size:59
Alignment explanation
Indices: 595320--595433 Score: 158
Period size: 60 Copynumber: 1.9 Consensus size: 59
595310 TACATTGGGC
*
595320 TATGAATATGAAAGTAAAGTTATGAATCTGAAAGTAAAGCTATGAATAT-GAAAGTATAGT
1 TATGAATATGAAAGTAAAGCTATGAATCTGAAA-TAAA-CTATGAATATGGAAAGTATAGT
* * * *
595380 TATGAATCTGAAAGTAAAGCTATGAATCTTAAATAAATTATGAATTTGGAAAGT
1 TATGAATATGAAAGTAAAGCTATGAATCTGAAATAAACTATGAATATGGAAAGT
595434 TCTGAATCTG
Statistics
Matches: 48, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
58 8 0.17
59 10 0.21
60 30 0.62
ACGTcount: A:0.46, C:0.04, G:0.18, T:0.32
Consensus pattern (59 bp):
TATGAATATGAAAGTAAAGCTATGAATCTGAAATAAACTATGAATATGGAAAGTATAGT
Found at i:598111 original size:24 final size:25
Alignment explanation
Indices: 598082--598145 Score: 62
Period size: 24 Copynumber: 2.6 Consensus size: 25
598072 AGCTTAAGTT
598082 CAAATATAATATAGTACTA-CAAAC
1 CAAATATAATATAGTACTATCAAAC
** *
598106 CAAATACCATAT-GTCCTATCAAAC
1 CAAATATAATATAGTACTATCAAAC
*
598130 CATCATATAATA-AGTA
1 CA-AATATAATATAGTA
598146 AATACATGTC
Statistics
Matches: 30, Mismatches: 7, Indels: 5
0.71 0.17 0.12
Matches are distributed among these distances:
23 5 0.17
24 17 0.57
25 8 0.27
ACGTcount: A:0.48, C:0.20, G:0.05, T:0.27
Consensus pattern (25 bp):
CAAATATAATATAGTACTATCAAAC
Found at i:598367 original size:26 final size:27
Alignment explanation
Indices: 598333--598384 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 27
598323 GAGGCATATT
598333 AAAACATAAGTAT-TTCATATAAAATC
1 AAAACATAAGTATATTCATATAAAATC
* * *
598359 AAAATATAAGTTTATTCGTATAAAAT
1 AAAACATAAGTATATTCATATAAAAT
598385 ATATTAACGC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 11 0.50
27 11 0.50
ACGTcount: A:0.52, C:0.08, G:0.06, T:0.35
Consensus pattern (27 bp):
AAAACATAAGTATATTCATATAAAATC
Found at i:602230 original size:2 final size:2
Alignment explanation
Indices: 602223--602266 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
602213 AAACATGATA
602223 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
602265 AT
1 AT
602267 GTTTTTGTAA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:602730 original size:23 final size:23
Alignment explanation
Indices: 602696--602763 Score: 75
Period size: 23 Copynumber: 3.0 Consensus size: 23
602686 ACCTGGTAAT
*
602696 GGCACTTTGGTGCATTTCTACGC
1 GGCACTTAGGTGCATTTCTACGC
* * *
602719 GGCAC-TACGGTGCAATTCTATGT
1 GGCACTTA-GGTGCATTTCTACGC
*
602742 GGCACTTAGGTGCATTTATACG
1 GGCACTTAGGTGCATTTCTACG
602764 AGCTGTGGTG
Statistics
Matches: 36, Mismatches: 7, Indels: 4
0.77 0.15 0.09
Matches are distributed among these distances:
22 1 0.03
23 33 0.92
24 2 0.06
ACGTcount: A:0.19, C:0.22, G:0.26, T:0.32
Consensus pattern (23 bp):
GGCACTTAGGTGCATTTCTACGC
Found at i:606240 original size:19 final size:20
Alignment explanation
Indices: 606197--606242 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
606187 TACTCTACTG
* * *
606197 GAAATTAATGTTAGAGTGTT
1 GAAATTGATGTTAGAATGAT
606217 GAAATTGATGTTAGAAT-AT
1 GAAATTGATGTTAGAATGAT
606236 GAAATTG
1 GAAATTG
606243 GATCATTTTG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 8 0.35
20 15 0.65
ACGTcount: A:0.39, C:0.00, G:0.24, T:0.37
Consensus pattern (20 bp):
GAAATTGATGTTAGAATGAT
Found at i:608123 original size:28 final size:27
Alignment explanation
Indices: 608092--608151 Score: 66
Period size: 27 Copynumber: 2.2 Consensus size: 27
608082 ATATAGTTAT
*
608092 TAAATTAAAAAAATAGAAATACAGTGAG
1 TAAATTAAAAAAATA-AAATACACTGAG
* * * *
608120 TAAAATAAGATAATAAAATTCACTGAG
1 TAAATTAAAAAAATAAAATACACTGAG
608147 TAAAT
1 TAAAT
608152 GTATAATTTA
Statistics
Matches: 26, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
27 14 0.54
28 12 0.46
ACGTcount: A:0.58, C:0.05, G:0.12, T:0.25
Consensus pattern (27 bp):
TAAATTAAAAAAATAAAATACACTGAG
Found at i:615305 original size:23 final size:23
Alignment explanation
Indices: 615270--615326 Score: 87
Period size: 23 Copynumber: 2.5 Consensus size: 23
615260 ATTAAGTACA
* *
615270 ATAACATATTAGGTAGCGCTTAT
1 ATAATATAATAGGTAGCGCTTAT
615293 ATAATATAATAGGTAGCGCTTAT
1 ATAATATAATAGGTAGCGCTTAT
*
615316 ATAATAAAATA
1 ATAATATAATA
615327 AGCATTTAAC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.44, C:0.09, G:0.14, T:0.33
Consensus pattern (23 bp):
ATAATATAATAGGTAGCGCTTAT
Found at i:615390 original size:87 final size:87
Alignment explanation
Indices: 615242--615404 Score: 272
Period size: 87 Copynumber: 1.9 Consensus size: 87
615232 TATGTTATAT
* *
615242 CATTTAACCGGAAATATTATTAAGTACAATAACATATTAGGTAGCGCTTATATAATATAATAGGT
1 CATTTAACCAGAAATATTATCAAGTACAATAACATATTAGGTAGCGCTTATATAATATAATAGGT
615307 AGCGCTTATATAATAAAATAAG
66 AGCGCTTATATAATAAAATAAG
* * * *
615329 CATTTAACCAGAAATATTATCAAGTACAATAACATATTAGGTAGTGTTTATATTATGTAATAGGT
1 CATTTAACCAGAAATATTATCAAGTACAATAACATATTAGGTAGCGCTTATATAATATAATAGGT
615394 AGCGCTTATAT
66 AGCGCTTATAT
615405 TGACCTATTT
Statistics
Matches: 70, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
87 70 1.00
ACGTcount: A:0.41, C:0.10, G:0.14, T:0.34
Consensus pattern (87 bp):
CATTTAACCAGAAATATTATCAAGTACAATAACATATTAGGTAGCGCTTATATAATATAATAGGT
AGCGCTTATATAATAAAATAAG
Found at i:616065 original size:201 final size:197
Alignment explanation
Indices: 615399--616123 Score: 891
Period size: 197 Copynumber: 3.6 Consensus size: 197
615389 TAGGTAGCGC
* * * * *
615399 TTATATTGACCTATTTTATAAGTAAACCCGGTATATTTATACCGGTAACATTGCAAATTTACCTA
1 TTATGTTGACCTATTTTCTAA-TAAAACCGGTATATTTATACCGGTTACATTGTAAATTTACCTA
* * *
615464 TTACATTATAATTATCGGTTTCGATGTTTTTTGGATCGATACAATTTT--AAATGTATTGACACT
65 TTACATTATAATTATCGGTTTCGATATTTTTGGGATCGATAC--TTTTAAAAATGTATCGACACT
* * *
615527 TTATGCGTGCACCTCGTTAGGTATTCATTCTGGA-AACAAGTATCGACACAAACTTAAAGAGTGT
128 TTATGCGTGCACCTCGTTTGGCATTCATTATGGACAA-AAGTATCGACACAAACTTAAA-AGTGT
615591 CGATACA
191 CGATACA
* * *
615598 TTAT-TTAGACCTATTTTTTCATAAAATCGGTATATTGCTAT-CCGG-TACATTGTAAATTTACC
1 TTATGTT-GACCTATTTTCTAATAAAACCGGTATATT--TATACCGGTTACATTGTAAATTTACC
* *
615660 TATCACATTGTAATTATCGGTTTCG--ATTTTTGGGATCGATACTTTTAATAAATGTATCGACAC
63 TATTACATTATAATTATCGGTTTCGATATTTTTGGGATCGATACTTTTAA-AAATGTATCGACAC
* * *
615723 TTTATGCGTGCACC-CGTTTGGCATTCATTATGGACAAAATGTATCAATACAAATTTAATAAGTG
127 TTTATGCGTGCACCTCGTTTGGCATTCATTATGGACAAAA-GTATCGACACAAACTTAA-AAGTG
*
615787 TCGATACT
190 TCGATACA
* * * * *
615795 TTATGATGACATATTTTCTCATAAAACCGGTATATTTATACCGATTACATTGTAAATTTTACATA
1 TTATGTTGACCTATTTTCTAATAAAACCGGTATATTTATACCGGTTACATTGTAAA-TTTACCTA
*
615860 TTACATTATAATTATCGGTTTCGAT-TTTATTGGGATCGATACTTTTAATAATTGTATCGACACT
65 TTACATTATAATTATCGGTTTCGATATTT-TTGGGATCGATACTTTTAA-AAATGTATCGACACT
*
615924 TTATGCGTACACCTCGTTTGGGCATTCATTATGGACAATAAGTATCGACACAAA-TTACACAAGT
128 TTATGCGTGCACCTCGTTT-GGCATTCATTATGGACAA-AAGTATCGACACAAACTTA-A-AAGT
615988 GTCGATACA
189 GTCGATACA
* * *
615997 TTATGTTGACTTATTTTCTAAT-TAACCGGTATATTTATACCGGTTACATTGTTAATTTTACCTA
1 TTATGTTGACCTATTTTCTAATAAAACCGGTATATTTATACCGGTTACATTG-TAAATTTACCTA
*
616061 TTACATTATAATTATTGGTTTCGATATTTTTTGGG-TCGATACTTTTAGAAAATGTATCGACAC
65 TTACATTATAATTATCGGTTTCGATA-TTTTTGGGATCGATACTTTTA-AAAATGTATCGACAC
616124 ATATTTAGGT
Statistics
Matches: 461, Mismatches: 41, Indels: 46
0.84 0.07 0.08
Matches are distributed among these distances:
194 4 0.01
195 3 0.01
196 37 0.08
197 96 0.21
198 83 0.18
199 23 0.05
200 49 0.11
201 91 0.20
202 70 0.15
203 5 0.01
ACGTcount: A:0.31, C:0.15, G:0.14, T:0.40
Consensus pattern (197 bp):
TTATGTTGACCTATTTTCTAATAAAACCGGTATATTTATACCGGTTACATTGTAAATTTACCTAT
TACATTATAATTATCGGTTTCGATATTTTTGGGATCGATACTTTTAAAAATGTATCGACACTTTA
TGCGTGCACCTCGTTTGGCATTCATTATGGACAAAAGTATCGACACAAACTTAAAAGTGTCGATA
CA
Found at i:619000 original size:121 final size:121
Alignment explanation
Indices: 618775--618992 Score: 384
Period size: 121 Copynumber: 1.8 Consensus size: 121
618765 AATAATGGTT
**
618775 GGAATCAGTTATGTAACTGGGATTATCCTGGTTAATCATGTTGACTGCATAGCCAATAAAACCTG
1 GGAATCAGTTATGTAACTGGGATTATCCAAGTTAATCATGTTGACTGCATAGCCAATAAAACCTG
618840 GGAGTCCAAATGGTAAGCTAGGATATGGTAAGGCAAGCTTCTCCGCAATCATGGCC
66 GGAGTCCAAATGGTAAGCTAGGATATGGTAAGGCAAGCTTCTCCGCAATCATGGCC
*
618896 GGAATCAGTTCTGTAACTGGGATTATCCAAGTTAATCATGTTGACTGCATAGCCAATAAAACCTG
1 GGAATCAGTTATGTAACTGGGATTATCCAAGTTAATCATGTTGACTGCATAGCCAATAAAACCTG
*
618961 TGAGTCCAAATGGTAAGCTAGGA-ATTGGTAAG
66 GGAGTCCAAATGGTAAGCTAGGATA-TGGTAAG
618993 TTAAGCTTTT
Statistics
Matches: 92, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
120 1 0.01
121 91 0.99
ACGTcount: A:0.31, C:0.17, G:0.24, T:0.27
Consensus pattern (121 bp):
GGAATCAGTTATGTAACTGGGATTATCCAAGTTAATCATGTTGACTGCATAGCCAATAAAACCTG
GGAGTCCAAATGGTAAGCTAGGATATGGTAAGGCAAGCTTCTCCGCAATCATGGCC
Found at i:621048 original size:201 final size:199
Alignment explanation
Indices: 620340--621509 Score: 1413
Period size: 200 Copynumber: 5.8 Consensus size: 199
620330 CGTTATTTAC
* * ** * *
620340 AAGTATCGACACAAA-TCTAAAACGTGTCGATATATTATGTTCACCTATTTTCTCATAAAACCGG
1 AAGTATCGACACAAATTCCAAAA-GTGTCGATACATTATGTAGACCTATTCTCACATAAAACCGG
*
620404 TACATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATGGTTTT
65 TATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGAT-GTTTT
* * *
620469 GGGATCGATACTTTTTACAAAATGTATCGACACTTTATGTGTGTAACCC-TTTTGGCATTCATTT
129 GGGATCGATACTTTTTA-AAAATGTATCGACACTTTATGGGTG-CACCCTTTTTGGCATTCATTC
620533 TGGACAAA
192 TGGACAAA
* * ** * *
620541 AAGTATCGACACAAA-TCTAAAATGTGTCGATACATTGTGTTCACCTATTTTAACATAAAACCGG
1 AAGTATCGACACAAATTCCAAAA-GTGTCGATACATTATGTAGACCTATTCTCACATAAAACCGG
620605 TATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATGTTTTT
65 TATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATG-TTTT
* * ** * * *
620670 GGGATCGATACATTTTATAAATGTATCGACACTTTATTCGTTCACCCTTTTGGGCATTCATTTTG
129 GGGATCGATACTTTTTAAAAATGTATCGACACTTTATGGGTGCACCCTTTTTGGCATTCATTCTG
620735 GACAAA
194 GACAAA
* * * *
620741 AAGTATCGACACAACATT-AAAAAGTGTCGACACATTATGTAGACATATTCTCACTTAAAACCGG
1 AAGTATCGACACAA-ATTCCAAAAGTGTCGATACATTATGTAGACCTATTCTCACATAAAACCGG
* * ** * * *
620805 TATATTTATACCGATTATATTACAAAATTACCTATTACATTATATTTATGGGTTTCGATGTTTTA
65 TATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATGTTTT-
* *
620870 GGGATCGATACTTTTTAAAAATGTATCGACACTTTATGGGTGCACCCTTTTTGG-ATTTTCCTTG
129 GGGATCGATACTTTTTAAAAATGTATCGACACTTTATGGGTGCACCCTTTTTGGCA--TTCATTC
*
620934 TGGACCAA
192 TGGACAAA
* * ** * * * **
620942 AAGTATCGACACAAATTCCACAAGTGTCGATACATTATGTATATGTATTTTCTCAAAAAATTGGT
1 AAGTATCGACACAAATTCCAAAAGTGTCGATACATTATGTAGACCTATTCTCACATAAAACCGGT
* * *
621007 TTATTTATACCAGTTACATTGTAAATTTACCTATTACATTATAAATATCGGTTTCGATGTTTCTG
66 ATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATGTTT-TG
* * * * * * * * *
621072 GGATTGATACTTTTTATAAATGTATCAACACTCTATGCGTTCACCATTTTGGGCATTCATTCTAG
130 GGATCGATACTTTTTAAAAATGTATCGACACTTTATGGGTGCACCCTTTTTGGCATTCATTCTGG
621137 ACAAA
195 ACAAA
* *
621142 AATTATCGACACAACATT-CAAAAGTGTCGACACATTATGTAGACCTATTCTCACATAAAACCGG
1 AAGTATCGACACAA-ATTCCAAAAGTGTCGATACATTATGTAGACCTATTCTCACATAAAACCGG
* * ** *
621206 TATATTTATACCGTTTATATTACAAAATTACCTATTACATTATAATTAT-GAGTTTCGATGTTTT
65 TATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATCG-GTTTCGATGTTTT
* * *
621270 GGGATCGATACTTTTTAAACATGTATCTACACTTTATGGGTGCA-CCTTTTTGGGCATTCCTTCT
129 GGGATCGATACTTTTTAAAAATGTATCGACACTTTATGGGTGCACCCTTTTT-GGCATTCATTCT
621334 GGACAAA
193 GGACAAA
* * * * * *
621341 TAGTATCGACACAAATTCCAGAAGTGTCGATATATTATGTAGACCTATTCTCTCTTAAAACTGGT
1 AAGTATCGACACAAATTCCAAAAGTGTCGATACATTATGTAGACCTATTCTCACATAAAACCGGT
* * * *
621406 TTAGTTATACCGGTTACATTGTAAATTTACCTATTACAATATATTTAT-GGATTTCGATGTTTCT
66 ATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATCGG-TTTCGATGTTT-T
* *
621470 GGGATCGATACTTTTTAAAACTGTATCGACAGTTTATGGG
129 GGGATCGATACTTTTTAAAAATGTATCGACACTTTATGGG
621510 AAACTTTAAG
Statistics
Matches: 830, Mismatches: 123, Indels: 33
0.84 0.12 0.03
Matches are distributed among these distances:
198 9 0.01
199 169 0.20
200 345 0.42
201 304 0.37
202 3 0.00
ACGTcount: A:0.31, C:0.16, G:0.14, T:0.38
Consensus pattern (199 bp):
AAGTATCGACACAAATTCCAAAAGTGTCGATACATTATGTAGACCTATTCTCACATAAAACCGGT
ATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATGTTTTGG
GATCGATACTTTTTAAAAATGTATCGACACTTTATGGGTGCACCCTTTTTGGCATTCATTCTGGA
CAAA
Found at i:621089 original size:401 final size:398
Alignment explanation
Indices: 620340--621507 Score: 1605
Period size: 401 Copynumber: 2.9 Consensus size: 398
620330 CGTTATTTAC
* * * ** * *
620340 AAGTATCGACACAA-ATCTAAAACGTGTCGATATATTATGTTCACCTATTTTCTCATAAAACCGG
1 AAGTATCGACACAACAT-TAAAAAGTGTCGACACATTATGTAGACCTATTCTCACATAAAACCGG
* * * ** * *
620404 TACATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATGGTTTT
65 TATATTTATACCGATTATATTACAAAATTACCTATTACATTATAATTATGGGTTTCGAT-GTTTT
* * * *
620469 GGGATCGATACTTTTTACAAAATGTATCGACACTTTATGTGTGTAACCC-TTTTGGCATTCATTT
129 GGGATCGATACTTTTTA-AAAATGTATCGACACTTTATGGGTG-CACCCTTTTTGG-ATTCCTTC
* * * **
620533 TGGACAAAAAGTATCGACACAAA-TCTAAAATGTGTCGATACATTGTGT-TCACCTATTTTAACA
191 TGGACCAAAAGTATCGACACAAATTCCAAAA-GTGTCGATACATTATGTAT-ACCTATTTTCTCA
* *
620596 TAAAACCGGTATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTC
254 TAAAACTGGTTTATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTC
* * * *
620661 GATGTTTTTGGGATCGATACATTTTATAAATGTATCGACACTTTATTCGTTCACCCTTTTGGGCA
319 GATGTTTCTGGGATCGATACTTTTTATAAATGTATCGACACTTTATGCGTTCACCATTTTGGGCA
* *
620726 TTCATTTTGGACAAA
384 TTCATTCTAGACAAA
* *
620741 AAGTATCGACACAACATTAAAAAGTGTCGACACATTATGTAGACATATTCTCACTTAAAACCGGT
1 AAGTATCGACACAACATTAAAAAGTGTCGACACATTATGTAGACCTATTCTCACATAAAACCGGT
*
620806 ATATTTATACCGATTATATTACAAAATTACCTATTACATTATATTTATGGGTTTCGATGTTTTAG
66 ATATTTATACCGATTATATTACAAAATTACCTATTACATTATAATTATGGGTTTCGATGTTTT-G
*
620871 GGATCGATACTTTTTAAAAATGTATCGACACTTTATGGGTGCACCCTTTTTGGATTTTCCTTGTG
130 GGATCGATACTTTTTAAAAATGTATCGACACTTTATGGGTGCACCCTTTTTGGA--TTCCTTCTG
* ** *
620936 GACCAAAAGTATCGACACAAATTCCACAAGTGTCGATACATTATGTATATGTATTTTCTCAAAAA
193 GACCAAAAGTATCGACACAAATTCCAAAAGTGTCGATACATTATGTATACCTATTTTCTCATAAA
* * *
621001 ATTGGTTTATTTATACCAGTTACATTGTAAATTTACCTATTACATTATAAATATCGGTTTCGATG
258 ACTGGTTTATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATG
* * *
621066 TTTCTGGGATTGATACTTTTTATAAATGTATCAACACTCTATGCGTTCACCATTTTGGGCATTCA
323 TTTCTGGGATCGATACTTTTTATAAATGTATCGACACTTTATGCGTTCACCATTTTGGGCATTCA
621131 TTCTAGACAAA
388 TTCTAGACAAA
* *
621142 AATTATCGACACAACATTCAAAAGTGTCGACACATTATGTAGACCTATTCTCACATAAAACCGGT
1 AAGTATCGACACAACATTAAAAAGTGTCGACACATTATGTAGACCTATTCTCACATAAAACCGGT
* *
621207 ATATTTATACCGTTTATATTACAAAATTACCTATTACATTATAATTATGAGTTTCGATGTTTTGG
66 ATATTTATACCGATTATATTACAAAATTACCTATTACATTATAATTATGGGTTTCGATGTTTTGG
* *
621272 GATCGATACTTTTTAAACATGTATCTACACTTTATGGGTGCA-CCTTTTTGGGCATTCCTTCTGG
131 GATCGATACTTTTTAAAAATGTATCGACACTTTATGGGTGCACCCTTTTT-GG-ATTCCTTCTGG
* * * * *
621336 A-CAAATAGTATCGACACAAATTCCAGAAGTGTCGATATATTATGTAGACCTATTCTCTCTTAAA
194 ACCAAA-AGTATCGACACAAATTCCAAAAGTGTCGATACATTATGTATACCTATTTTCTCATAAA
* * *
621400 ACTGGTTTAGTTATACCGGTTACATTGTAAATTTACCTATTACAATATATTTAT-GGATTTCGAT
258 ACTGGTTTATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATCGG-TTTCGAT
*
621464 GTTTCTGGGATCGATACTTTTTA-AAACTGTATCGACAGTTTATG
322 GTTTCTGGGATCGATACTTTTTATAAA-TGTATCGACACTTTATG
621508 GGAAACTTTA
Statistics
Matches: 683, Mismatches: 72, Indels: 26
0.87 0.09 0.03
Matches are distributed among these distances:
398 9 0.01
399 163 0.24
400 79 0.12
401 424 0.62
402 8 0.01
ACGTcount: A:0.31, C:0.17, G:0.14, T:0.38
Consensus pattern (398 bp):
AAGTATCGACACAACATTAAAAAGTGTCGACACATTATGTAGACCTATTCTCACATAAAACCGGT
ATATTTATACCGATTATATTACAAAATTACCTATTACATTATAATTATGGGTTTCGATGTTTTGG
GATCGATACTTTTTAAAAATGTATCGACACTTTATGGGTGCACCCTTTTTGGATTCCTTCTGGAC
CAAAAGTATCGACACAAATTCCAAAAGTGTCGATACATTATGTATACCTATTTTCTCATAAAACT
GGTTTATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATGTTT
CTGGGATCGATACTTTTTATAAATGTATCGACACTTTATGCGTTCACCATTTTGGGCATTCATTC
TAGACAAA
Found at i:624723 original size:200 final size:200
Alignment explanation
Indices: 624372--625532 Score: 1422
Period size: 200 Copynumber: 5.8 Consensus size: 200
624362 ATTTAAAATG
* * * * *
624372 GTATCGACACAAATTTAACAATTGTAGATACTTTATG-ATGACCTATTTTCTCATAAAACCGGTA
1 GTATCGACACAAATTAAACAAGTGTCGATACATTATGTA-GACCTATTCTCTCATAAAACCGGTA
* * * * *
624436 TATTTATACCGCTTACATTGGAAATTTACCTATTACATTATAATTATCGGTTTCGATGTTTTTGG
65 TATTTATACCGGTTACATTGAAAAATTACCTATTACATTATAATTATGGGTTTCGATGTTTCTGG
*
624501 GATCGACACTTTTTAA-AAATGTATCGACACTTTATGTGTGCAACCCTTTT-GGCATTCCTTCTG
130 GATCGACAC-TTTTAATAAATGTATCGACACTTTATGCGTGC-ACCCTTTTGGGCATTCCTTCTG
624564 GACAAAAA
193 GACAAAAA
**
624572 GTATCGACACAAATTCCACAAGTGTCGATACATGT-TGTAGACCTATTCTCTCATAAAACCGGTA
1 GTATCGACACAAATTAAACAAGTGTCGATACAT-TATGTAGACCTATTCTCTCATAAAACCGGTA
* * * *
624636 TAGTTATACCGGTTACATTGTAAATTTACCTATTACATTATATTTATGGGTTTCGATGTTTCTGG
65 TATTTATACCGGTTACATTGAAAAATTACCTATTACATTATAATTATGGGTTTCGATGTTTCTGG
* * * * * ** *
624701 TATCGACACTTTCAATAAATGTATCGACACTTTATGCGTTCATCATTTTGGGCATTAATTTTGGA
130 GATCGACACTTTTAATAAATGTATCGACACTTTATGCGTGCACCCTTTTGGGCATTCCTTCTGGA
*
624766 CAAAAG
195 CAAAAA
* * *
624772 GTATCGACACAAAATAAAAAAGTGTCGATACATTATGTAGACATATTCTCAT-ATAAAACCGGTA
1 GTATCGACACAAATTAAACAAGTGTCGATACATTATGTAGACCTATTCTC-TCATAAAACCGGTA
* * * * * * * *
624836 TATTTGTACAGATTATATTAAAAAATTACATATTACATTATAATTATGAGTTTCGATGTTTTTGG
65 TATTTATACCGGTTACATTGAAAAATTACCTATTACATTATAATTATGGGTTTCGATGTTTCTGG
* *
624901 GATCGACACTTTTTATAAATGTATCGACACTTAATG-GTGCACCCTTTTTGGGCATTCCTTCTGG
130 GATCGACACTTTTAATAAATGTATCGACACTTTATGCGTGCACCC-TTTTGGGCATTCCTTCTGG
*
624965 ACCAAAA
194 ACAAAAA
*
624972 GTATCGACACAAATTACACAAGTGTCGATACA-TATTGTAGACCTATTCTCTCATAAAACCGGTA
1 GTATCGACACAAATTAAACAAGTGTCGATACATTA-TGTAGACCTATTCTCTCATAAAACCGGTA
* *
625036 TATGTATACCGGTTACATTGAAAAATTACCTATTACATTATAATTATGGGTTTTGATGTTTCTGG
65 TATTTATACCGGTTACATTGAAAAATTACCTATTACATTATAATTATGGGTTTCGATGTTTCTGG
* * * * *
625101 GATCGATACTTGTTTATAAATGGATCGACACTTTTTGCGTGCACCCTTTTTGGGCAATCCTTCTG
130 GATCGACACTT-TTAATAAATGTATCGACACTTTATGCGTGCACCC-TTTTGGGCATTCCTTCTG
*
625166 GACAAACA
193 GACAAAAA
* ** ** *
625174 GTATCAACACAAATTCCAGTAGTGTCGATACATTATGTAGACCTATTCTCTCATAAAACCGGTTT
1 GTATCGACACAAATTAAACAAGTGTCGATACATTATGTAGACCTATTCTCTCATAAAACCGGTAT
* * * * * * * *
625239 AGTTATATCGGTAACATTGTAAATTTACCTATTACATTATATTTACGGGTTTCTATGTTTCTGGG
66 ATTTATACCGGTTACATTGAAAAATTACCTATTACATTATAATTATGGGTTTCGATGTTTCTGGG
* * * * *** **
625304 ATCGACACTTTCAATAAATATGTCGACACTTTATGCGTTCATAATTTTGGGCATTAATTCTGGAC
131 ATCGACACTTTTAATAAATGTATCGACACTTTATGCGTGCACCCTTTTGGGCATTCCTTCTGGAC
625369 AAAAA
196 AAAAA
* * * * *
625374 GTATCGACACATTATGAAA-AAGTGTTGATACATTATGTAGACCTATTCTCACATAAAACCGTTA
1 GTATCGACACA-AATTAAACAAGTGTCGATACATTATGTAGACCTATTCTCTCATAAAACCGGTA
* * *
625438 TATTTATACCTGTTATATT-ACAAAATTACCTATTACATTATAATTATGGGTTTCGATGTTTTTG
65 TATTTATACCGGTTACATTGA-AAAATTACCTATTACATTATAATTATGGGTTTCGATGTTTCTG
* *
625502 GGATCGATACTTTTTATAAATGTATCGACAC
129 GGATCGACACTTTTAATAAATGTATCGACAC
625533 ATATGCTTAC
Statistics
Matches: 819, Mismatches: 128, Indels: 28
0.84 0.13 0.03
Matches are distributed among these distances:
199 20 0.02
200 592 0.72
201 52 0.06
202 153 0.19
203 2 0.00
ACGTcount: A:0.31, C:0.17, G:0.15, T:0.37
Consensus pattern (200 bp):
GTATCGACACAAATTAAACAAGTGTCGATACATTATGTAGACCTATTCTCTCATAAAACCGGTAT
ATTTATACCGGTTACATTGAAAAATTACCTATTACATTATAATTATGGGTTTCGATGTTTCTGGG
ATCGACACTTTTAATAAATGTATCGACACTTTATGCGTGCACCCTTTTGGGCATTCCTTCTGGAC
AAAAA
Found at i:625395 original size:21 final size:21
Alignment explanation
Indices: 625369--625410 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
625359 AATTCTGGAC
625369 AAAAAGTATCGACACATTATG
1 AAAAAGTATCGACACATTATG
* * *
625390 AAAAAGTGTTGATACATTATG
1 AAAAAGTATCGACACATTATG
625411 TAGACCTATT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.45, C:0.10, G:0.17, T:0.29
Consensus pattern (21 bp):
AAAAAGTATCGACACATTATG
Found at i:625516 original size:602 final size:600
Alignment explanation
Indices: 624372--625532 Score: 1803
Period size: 602 Copynumber: 1.9 Consensus size: 600
624362 ATTTAAAATG
* *
624372 GTATCGACACAAATTTAACAATTGTAGATACTTTATGATGACCTATTTTCTCATAAAACCGGTAT
1 GTATCGACACAAATTTAACAAGTGTAGATACTTTATGATGACCTATTCTCTCATAAAACCGGTAT
* * * *
624437 ATTTATACCGCTTACATTGGAAATTTACCTATTACATTATAATTATCGGTTTCGATGTTTTTGGG
66 ATGTATACCGCTTACATTGAAAAATTACCTATTACATTATAATTATCGGTTTCGATGTTTCTGGG
* * *
624502 ATCGACACTTTTTAAAAATGTATCGACACTTTATGTGTGCAACCCTTTTGGCATTCCTTCTGGAC
131 ATCGACACTTTTTAAAAATGGATCGACACTTTATGCGTGCAACCCTTTTGGCAATCCTTCTGGAC
*
624567 AAAAAGTATCGACACAAATTCCACAAGTGTCGATACATGTTGTAGACCTATTCTCTCATAAAACC
196 AAAAAGTATCAACACAAATTCCACAAGTGTCGATACATGTTGTAGACCTATTCTCTCATAAAACC
* *
624632 GGTATAGTTATACCGGTTACATTGTAAATTTACCTATTACATTATATTTATGGGTTTCGATGTTT
261 GGTATAGTTATACCGGTAACATTGTAAATTTACCTATTACATTATATTTACGGGTTTCGATGTTT
* * * *
624697 CTGGTATCGACACTTTCAATAAATGTATCGACACTTTATGCGTTCATCATTTTGGGCATTAATTT
326 CTGGGATCGACACTTTCAATAAATATATCGACACTTTATGCGTTCATAATTTTGGGCATTAATTC
* *
624762 TGGACAAAAGGTATCGACACAAAATAAAAAAGTGTCGATACATTATGTAGACATATTCTCATATA
391 TGGACAAAAAGTATCGACACAAAATAAAAAAGTGTCGATACATTATGTAGACATATTCTCACATA
*
624827 AAACCGGTATATTTGTACAGATTATATTAAAAAATTACATATTACATTATAATTATGAGTTTCGA
456 AAACCGGTATATTTATACAGATTATATTAAAAAATTACATATTACATTATAATTATGAGTTTCGA
624892 TGTTTTTGGGATCGACACTTTTTATAAATGTATCGACACTTAATGGTGCACCCTTTTTGGGCATT
521 TGTTTTTGGGATCGACACTTTTTATAAATGTATCGACACTTAATGGTGCACCCTTTTTGGGCATT
624957 CCTTCTGGACCAAAA
586 CCTTCTGGACCAAAA
* *
624972 GTATCGACACAAA-TTACACAAGTGTCGATAC-ATATTG-TAGACCTATTCTCTCATAAAACCGG
1 GTATCGACACAAATTTA-ACAAGTGTAGATACTTTA-TGAT-GACCTATTCTCTCATAAAACCGG
* * *
625034 TATATGTATACCGGTTACATTGAAAAATTACCTATTACATTATAATTATGGGTTTTGATGTTTCT
63 TATATGTATACCGCTTACATTGAAAAATTACCTATTACATTATAATTATCGGTTTCGATGTTTCT
* * *
625099 GGGATCGATACTTGTTTATAAATGGATCGACACTTTTTGCGTGC-ACCCTTTTTGGGCAATCCTT
128 GGGATCGACACTT-TTTAAAAATGGATCGACACTTTATGCGTGCAACCC-TTTT-GGCAATCCTT
* **
625163 CTGGACAAACAGTATCAACACAAATTCCAGTAGTGTCGATACAT-TATGTAGACCTATTCTCTCA
190 CTGGACAAAAAGTATCAACACAAATTCCACAAGTGTCGATACATGT-TGTAGACCTATTCTCTCA
* *
625227 TAAAACCGGTTTAGTTATATCGGTAACATTGTAAATTTACCTATTACATTATATTTACGGGTTTC
254 TAAAACCGGTATAGTTATACCGGTAACATTGTAAATTTACCTATTACATTATATTTACGGGTTTC
* *
625292 TATGTTTCTGGGATCGACACTTTCAATAAATATGTCGACACTTTATGCGTTCATAATTTTGGGCA
319 GATGTTTCTGGGATCGACACTTTCAATAAATATATCGACACTTTATGCGTTCATAATTTTGGGCA
** * * *
625357 TTAATTCTGGACAAAAAGTATCGACACATTATGAAAAAGTGTTGATACATTATGTAGACCTATTC
384 TTAATTCTGGACAAAAAGTATCGACACAAAATAAAAAAGTGTCGATACATTATGTAGACATATTC
* * * *
625422 TCACATAAAACCGTTATATTTATACCTG-TTATATTACAAAATTACCTATTACATTATAATTATG
449 TCACATAAAACCGGTATATTTATA-CAGATTATATTAAAAAATTACATATTACATTATAATTATG
* *
625486 GGTTTCGATGTTTTTGGGATCGATACTTTTTATAAATGTATCGACAC
513 AGTTTCGATGTTTTTGGGATCGACACTTTTTATAAATGTATCGACAC
625533 ATATGCTTAC
Statistics
Matches: 508, Mismatches: 45, Indels: 14
0.90 0.08 0.02
Matches are distributed among these distances:
599 6 0.01
600 123 0.24
601 31 0.06
602 346 0.68
603 2 0.00
ACGTcount: A:0.31, C:0.17, G:0.15, T:0.37
Consensus pattern (600 bp):
GTATCGACACAAATTTAACAAGTGTAGATACTTTATGATGACCTATTCTCTCATAAAACCGGTAT
ATGTATACCGCTTACATTGAAAAATTACCTATTACATTATAATTATCGGTTTCGATGTTTCTGGG
ATCGACACTTTTTAAAAATGGATCGACACTTTATGCGTGCAACCCTTTTGGCAATCCTTCTGGAC
AAAAAGTATCAACACAAATTCCACAAGTGTCGATACATGTTGTAGACCTATTCTCTCATAAAACC
GGTATAGTTATACCGGTAACATTGTAAATTTACCTATTACATTATATTTACGGGTTTCGATGTTT
CTGGGATCGACACTTTCAATAAATATATCGACACTTTATGCGTTCATAATTTTGGGCATTAATTC
TGGACAAAAAGTATCGACACAAAATAAAAAAGTGTCGATACATTATGTAGACATATTCTCACATA
AAACCGGTATATTTATACAGATTATATTAAAAAATTACATATTACATTATAATTATGAGTTTCGA
TGTTTTTGGGATCGACACTTTTTATAAATGTATCGACACTTAATGGTGCACCCTTTTTGGGCATT
CCTTCTGGACCAAAA
Found at i:625906 original size:19 final size:19
Alignment explanation
Indices: 625882--625930 Score: 89
Period size: 19 Copynumber: 2.6 Consensus size: 19
625872 TTAAATCCAC
625882 ATACAAAATTATAAATCGT
1 ATACAAAATTATAAATCGT
*
625901 ATACAAAATTATAAATCTT
1 ATACAAAATTATAAATCGT
625920 ATACAAAATTA
1 ATACAAAATTA
625931 ACTCTACATT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.55, C:0.10, G:0.02, T:0.33
Consensus pattern (19 bp):
ATACAAAATTATAAATCGT
Found at i:629317 original size:18 final size:18
Alignment explanation
Indices: 629294--629362 Score: 111
Period size: 18 Copynumber: 3.8 Consensus size: 18
629284 ATTTCCTCCA
629294 TCTTTTCTTCTTCATTCC
1 TCTTTTCTTCTTCATTCC
*
629312 TCTTTTCTTCTTCCTTCC
1 TCTTTTCTTCTTCATTCC
* *
629330 TCTTTTCTTCTTCCTCCC
1 TCTTTTCTTCTTCATTCC
629348 TCTTTTCTTCTTCAT
1 TCTTTTCTTCTTCAT
629363 ATTTTTTTAG
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 48 1.00
ACGTcount: A:0.03, C:0.36, G:0.00, T:0.61
Consensus pattern (18 bp):
TCTTTTCTTCTTCATTCC
Found at i:629334 original size:36 final size:36
Alignment explanation
Indices: 629286--629360 Score: 116
Period size: 36 Copynumber: 2.1 Consensus size: 36
629276 TCCTCCTCAT
*
629286 TTCCTCCATCTTTTCTTCTTCATTCCTCTTTTCTTC
1 TTCCTCCATCTTTTCTTCTTCATCCCTCTTTTCTTC
*
629322 TTCCTTCC-TCTTTTCTTCTTCCTCCCTCTTTTCTTC
1 TTCC-TCCATCTTTTCTTCTTCATCCCTCTTTTCTTC
629358 TTC
1 TTC
629361 ATATTTTTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
36 33 0.92
37 3 0.08
ACGTcount: A:0.03, C:0.39, G:0.00, T:0.59
Consensus pattern (36 bp):
TTCCTCCATCTTTTCTTCTTCATCCCTCTTTTCTTC
Found at i:637657 original size:8 final size:8
Alignment explanation
Indices: 637641--637682 Score: 50
Period size: 8 Copynumber: 5.2 Consensus size: 8
637631 TGTTTCAACA
637641 TTTTGGAT
1 TTTTGGAT
*
637649 TTTTTGAT
1 TTTTGGAT
637657 TTTGTGGAT
1 TTT-TGGAT
*
637666 TGTTGGA-
1 TTTTGGAT
637673 TTTTGGAT
1 TTTTGGAT
637681 TT
1 TT
637683 ATGAATGGTG
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
7 6 0.21
8 16 0.57
9 6 0.21
ACGTcount: A:0.12, C:0.00, G:0.26, T:0.62
Consensus pattern (8 bp):
TTTTGGAT
Found at i:637666 original size:17 final size:17
Alignment explanation
Indices: 637644--637677 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
637634 TTCAACATTT
* *
637644 TGGATTTTTTGATTTTG
1 TGGATTGTTGGATTTTG
637661 TGGATTGTTGGATTTTG
1 TGGATTGTTGGATTTTG
637678 GATTTATGAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.12, C:0.00, G:0.29, T:0.59
Consensus pattern (17 bp):
TGGATTGTTGGATTTTG
Found at i:639351 original size:15 final size:15
Alignment explanation
Indices: 639331--639361 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
639321 TCTGTTTTCT
*
639331 CTCACCGTCATCCCC
1 CTCACCATCATCCCC
639346 CTCACCATCATCCCC
1 CTCACCATCATCCCC
639361 C
1 C
639362 AATACAACCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.16, C:0.61, G:0.03, T:0.19
Consensus pattern (15 bp):
CTCACCATCATCCCC
Found at i:639672 original size:22 final size:23
Alignment explanation
Indices: 639644--639701 Score: 64
Period size: 24 Copynumber: 2.5 Consensus size: 23
639634 AACCTGTATT
*
639644 TATAATAAAAT-TTATAATTTTA
1 TATAATAAAATACTATAATTTTA
* *
639666 TATAATAACTATACTATCATTTTA
1 TATAATAA-AATACTATAATTTTA
*
639690 TATAAAAAAATA
1 TATAATAAAATA
639702 AAAACGTTCT
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
22 8 0.28
23 5 0.17
24 16 0.55
ACGTcount: A:0.52, C:0.05, G:0.00, T:0.43
Consensus pattern (23 bp):
TATAATAAAATACTATAATTTTA
Found at i:642118 original size:181 final size:180
Alignment explanation
Indices: 641656--642145 Score: 705
Period size: 180 Copynumber: 2.7 Consensus size: 180
641646 TACGCGTACT
*
641656 TATTAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCAGTTTTGTCATTTAGAGACCG
1 TATTAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCGGTTTTGTCATTTAGAGACCG
* * * *
641721 GTTTTGTCATATTTTTACCTATTATATCGTTATCGATCAATACATATTTATAAAGTATCGACACT
66 GTTTTGTCATATTTTTACCTATTATATCGTTGTGGATCGATACATATTTATAAAGTATCGACATT
641786 TTATAAGCGCTAAAACTGCTTCTCTTTTAAATTCACAGTGTCGATACTTA
131 TTATAAGCGCTAAAACTGCTTCTCTTTTAAATTCACAGTGTCGATACTTA
* * * * *
641836 TATTGAAGTATCGACACTTTCAATATATCCGGTCGCTCTATACCAGG-TTTGTCCTTTAGAGACC
1 TATTAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACC-GGTTTTGTCATTTAGAGACC
* * *
641900 GATTTTGTCATATTTTTACATGTTATATCGTTGTGGATCGATACATATTTATAAAGTATCGACAT
65 GGTTTTGTCATATTTTTACCTATTATATCGTTGTGGATCGATACATATTTATAAAGTATCGACAT
* *
641965 TTTATAGGCGCTAAAACTGTTTCTCTTTTAAATT-ACAATGTGTCGATACTTA
130 TTTATAAGCGCTAAAACTGCTTCTCTTTTAAATTCAC-A-GTGTCGATACTTA
* * * *
642017 TATTAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCGGTTTTGTCTTTTCGTGACTG
1 TATTAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCGGTTTTGTCATTTAGAGACCG
* * * * * * *
642082 GTTCTGTCATATTTTTTCCTCTTATATTGATGTGGATCGATATATTTTTATAAAGTATCGACAT
66 GTTTTGTCATATTTTTACCTATTATATCGTTGTGGATCGATACATATTTATAAAGTATCGACAT
642146 AAACCGACAA
Statistics
Matches: 274, Mismatches: 32, Indels: 7
0.88 0.10 0.02
Matches are distributed among these distances:
179 2 0.01
180 149 0.54
181 123 0.45
ACGTcount: A:0.27, C:0.17, G:0.15, T:0.41
Consensus pattern (180 bp):
TATTAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCGGTTTTGTCATTTAGAGACCG
GTTTTGTCATATTTTTACCTATTATATCGTTGTGGATCGATACATATTTATAAAGTATCGACATT
TTATAAGCGCTAAAACTGCTTCTCTTTTAAATTCACAGTGTCGATACTTA
Found at i:651595 original size:18 final size:17
Alignment explanation
Indices: 651554--651598 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
651544 AAATATTCAC
*
651554 CTAAAAAAAAGAAAATA
1 CTAAAAATAAGAAAATA
* *
651571 ATTAAAATAAGAAAAGTA
1 CTAAAAATAAGAAAA-TA
651589 CTAAAAATAA
1 CTAAAAATAA
651599 AATAAATAAA
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
17 12 0.55
18 10 0.45
ACGTcount: A:0.71, C:0.04, G:0.07, T:0.18
Consensus pattern (17 bp):
CTAAAAATAAGAAAATA
Found at i:657202 original size:19 final size:19
Alignment explanation
Indices: 657175--657219 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
657165 AAAAACCGAT
657175 AAACCGAACCGAACCAAAA
1 AAACCGAACCGAACCAAAA
* *
657194 AACCCGAACCGATCCAAAA
1 AAACCGAACCGAACCAAAA
657213 AAACCGA
1 AAACCGA
657220 TTTCAGTTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.53, C:0.33, G:0.11, T:0.02
Consensus pattern (19 bp):
AAACCGAACCGAACCAAAA
Found at i:662301 original size:20 final size:20
Alignment explanation
Indices: 662276--662317 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
662266 CTTCTACTAT
*
662276 TCTAAGACATGATATTGAAG
1 TCTAAGACATGATACTGAAG
662296 TCTAAGACATGATACTGAAG
1 TCTAAGACATGATACTGAAG
662316 TC
1 TC
662318 ATGTCATATT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.38, C:0.14, G:0.19, T:0.29
Consensus pattern (20 bp):
TCTAAGACATGATACTGAAG
Found at i:663500 original size:81 final size:81
Alignment explanation
Indices: 663361--664243 Score: 1223
Period size: 81 Copynumber: 10.9 Consensus size: 81
663351 ACAATTAGTA
* * * * *
663361 TTTTACTCAAAGGTATTTAACCTTTCATCTAACAGGCATAATTGACA-CTTTTTCGTCAAATGCA
1 TTTTACTCAACGGTACTTAACCATTCATCTAACTGGCATAATTGACACCTTTCT-GTCAAATGCA
663425 CAGCTAGGCCATTAATC
65 CAGCTAGGCCATTAATC
* * *
663442 TTTTACTCAACGGTAATTAATCATTCATCTAACTGGCATAATTGACACATTTCTGTCAAATGCAC
1 TTTTACTCAACGGTACTTAACCATTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCAC
* * *
663507 AACCAGGCCATTAATA
66 AGCTAGGCCATTAATC
* *
663523 TTTTACTCAACGGTACTTAACCGTTCATCTAACTGGCATAATTAACACCTTTCTGTCAAATGCAC
1 TTTTACTCAACGGTACTTAACCATTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCAC
* *
663588 AGCTAGACCACTAATC
66 AGCTAGGCCATTAATC
* * * * *
663604 TTTTACTCAACGGTACTTAATCGTTCATCTAACTGACATAATTGACACATTTCTATCAAATGCAC
1 TTTTACTCAACGGTACTTAACCATTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCAC
*
663669 AACTAGGCCATTAATC
66 AGCTAGGCCATTAATC
* * * * * *
663685 TTTTACTCAATGGTACTTAATCATTCATCTAACTAGCATAATTGACACATTTCTATCAAATGCAT
1 TTTTACTCAACGGTACTTAACCATTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCAC
*
663750 AGCTAGGCTATTAATC
66 AGCTAGGCCATTAATC
*
663766 TTTTACTCAACGGTACTTAACCATTCATCTAACTGGCATAATTGACACCTTTATGTCAAATGCAC
1 TTTTACTCAACGGTACTTAACCATTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCAC
*
663831 AACTAGGCCATTAATC
66 AGCTAGGCCATTAATC
* *
663847 TTTTACTCAACGGTACTTAACCGTTCATCTTACT-GCATAATTGACACCTTTCTGTCAAATGCAC
1 TTTTACTCAACGGTACTTAACCATTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCAC
663911 AGCTAGGCCATTAATC
66 AGCTAGGCCATTAATC
* * * * * *
663927 TTTAACTCAACAGTACTTAACCGTTCATCTAACTGACATAATTGAAACCTTTCTGTCAAATGCAT
1 TTTTACTCAACGGTACTTAACCATTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCAC
663992 AGCTAGGCCATTAATC
66 AGCTAGGCCATTAATC
** * *
664008 TTTTACTCAACAATACTTAACCATTCATCTAACTGGCATAATTGACTCCTTTCTATCAAATGCAC
1 TTTTACTCAACGGTACTTAACCATTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCAC
* * *
664073 AACTATGACATTAATC
66 AGCTAGGCCATTAATC
* * *
664089 TTTTACTCAACGATACTTAA-CAGTTCATCTAACTGGCATAATTGACACCTTTCTATCAAATGTA
1 TTTTACTCAACGGTACTTAACCA-TTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCA
* *
664153 CAACTAGGCCATTAATA
65 CAGCTAGGCCATTAATC
* * * * *
664170 TTTTACTCAACGGTACTTTACCGTTCATCTAACTGGCATAATTGACACATTTTTGTCAAATGCAT
1 TTTTACTCAACGGTACTTAACCATTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCAC
*
664235 AGTTAGGCC
66 AGCTAGGCC
664244 TCAAAGGCAC
Statistics
Matches: 717, Mismatches: 81, Indels: 8
0.89 0.10 0.01
Matches are distributed among these distances:
80 77 0.11
81 635 0.89
82 5 0.01
ACGTcount: A:0.32, C:0.23, G:0.11, T:0.34
Consensus pattern (81 bp):
TTTTACTCAACGGTACTTAACCATTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCAC
AGCTAGGCCATTAATC
Found at i:664284 original size:68 final size:68
Alignment explanation
Indices: 664193--664351 Score: 255
Period size: 68 Copynumber: 2.3 Consensus size: 68
664183 TACTTTACCG
* *
664193 TTCATCTAACTGGCATAATTGACACATTTTTGTCAAATGCATAGTTAGGCCTCAAAGGCACTTAG
1 TTCATCTAACTTGCATAATTGACACATTTCTGTCAAATGCATAGTTAGGCCTCAAAGGCACTTAG
664258 CAT
66 CAT
* * *
664261 TTCATCTAACTTGCATCATTGACACCTTTCTGTCAAATGCATAGTTAGGCCTCTAAGGCACTTAG
1 TTCATCTAACTTGCATAATTGACACATTTCTGTCAAATGCATAGTTAGGCCTCAAAGGCACTTAG
*
664326 CCT
66 CAT
*
664329 TTCATCTAACTTGCATGATTGAC
1 TTCATCTAACTTGCATAATTGAC
664352 TCTGTAATCA
Statistics
Matches: 84, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
68 84 1.00
ACGTcount: A:0.28, C:0.23, G:0.15, T:0.34
Consensus pattern (68 bp):
TTCATCTAACTTGCATAATTGACACATTTCTGTCAAATGCATAGTTAGGCCTCAAAGGCACTTAG
CAT
Found at i:664875 original size:36 final size:36
Alignment explanation
Indices: 664828--664898 Score: 142
Period size: 36 Copynumber: 2.0 Consensus size: 36
664818 ATAGAGAAGA
664828 AAACTTTTACCTTAGCCCGAGTGATTGTTTTTCGTC
1 AAACTTTTACCTTAGCCCGAGTGATTGTTTTTCGTC
664864 AAACTTTTACCTTAGCCCGAGTGATTGTTTTTCGT
1 AAACTTTTACCTTAGCCCGAGTGATTGTTTTTCGT
664899 TGGAATAGGT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.20, C:0.21, G:0.17, T:0.42
Consensus pattern (36 bp):
AAACTTTTACCTTAGCCCGAGTGATTGTTTTTCGTC
Found at i:665820 original size:23 final size:23
Alignment explanation
Indices: 665794--665838 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
665784 TTGTTTTTTT
* *
665794 AATTATATTTTTGTTAATATTTA
1 AATTATAATTTGGTTAATATTTA
*
665817 AATTATAATTTGGTTACTATTT
1 AATTATAATTTGGTTAATATTT
665839 TTATTTTATT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.33, C:0.02, G:0.07, T:0.58
Consensus pattern (23 bp):
AATTATAATTTGGTTAATATTTA
Found at i:665847 original size:5 final size:5
Alignment explanation
Indices: 665837--665879 Score: 54
Period size: 5 Copynumber: 8.8 Consensus size: 5
665827 TGGTTACTAT
*
665837 TTTTA TTTTA TTTTA TTTTA TTTT- TATTA TTTTCA -TTTA TTTT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTT-A TTTTA TTTT
665880 TCAATACTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
4 4 0.12
5 28 0.85
6 1 0.03
ACGTcount: A:0.19, C:0.02, G:0.00, T:0.79
Consensus pattern (5 bp):
TTTTA
Done.