Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008550.1 Hibiscus syriacus cultivar Beakdansim tig00111445_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: 1154708
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
File 2 of 6
Found at i:180934 original size:18 final size:18
Alignment explanation
Indices: 180911--180946 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
180901 AAGCAAAAGG
*
180911 AAATCAAAATCGCAATCA
1 AAATCAAAATCCCAATCA
180929 AAATCAAAATCCCAATCA
1 AAATCAAAATCCCAATCA
180947 CAACCGGCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.56, C:0.25, G:0.03, T:0.17
Consensus pattern (18 bp):
AAATCAAAATCCCAATCA
Found at i:181322 original size:20 final size:20
Alignment explanation
Indices: 181270--181330 Score: 70
Period size: 20 Copynumber: 3.0 Consensus size: 20
181260 AATAAGCGTT
181270 GCGATAGTCAAATTCGCAAC
1 GCGATAGTCAAATTCGCAAC
* * * *
181290 GAGAAAGAT-AAATTTGGAAC
1 GCGATAG-TCAAATTCGCAAC
181310 GCGATAGTCAAATTCGCAAC
1 GCGATAGTCAAATTCGCAAC
181330 G
1 G
181331 TGAAATCGCA
Statistics
Matches: 31, Mismatches: 8, Indels: 4
0.72 0.19 0.09
Matches are distributed among these distances:
19 1 0.03
20 29 0.94
21 1 0.03
ACGTcount: A:0.39, C:0.18, G:0.23, T:0.20
Consensus pattern (20 bp):
GCGATAGTCAAATTCGCAAC
Found at i:181368 original size:20 final size:20
Alignment explanation
Indices: 181345--181394 Score: 91
Period size: 20 Copynumber: 2.5 Consensus size: 20
181335 ATCGCAAACT
181345 GAATTTGACTTTCGCGTTAC
1 GAATTTGACTTTCGCGTTAC
*
181365 GAATTTGACTTTCGCGTTGC
1 GAATTTGACTTTCGCGTTAC
181385 GAATTTGACT
1 GAATTTGACT
181395 ATCACAACGC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.20, C:0.18, G:0.22, T:0.40
Consensus pattern (20 bp):
GAATTTGACTTTCGCGTTAC
Found at i:181433 original size:20 final size:20
Alignment explanation
Indices: 181408--181449 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
181398 ACAACGCTTA
*
181408 TTTCGCGTTGTAAATTTACC
1 TTTCGCGTTGCAAATTTACC
*
181428 TTTCGCGTTGCGAATTTACC
1 TTTCGCGTTGCAAATTTACC
181448 TT
1 TT
181450 CAACAGGTCT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.17, C:0.21, G:0.17, T:0.45
Consensus pattern (20 bp):
TTTCGCGTTGCAAATTTACC
Found at i:181979 original size:39 final size:39
Alignment explanation
Indices: 181936--182022 Score: 147
Period size: 39 Copynumber: 2.2 Consensus size: 39
181926 TCCGATGCTC
* *
181936 ATCAAAATCCAAAGCTCATATGGTGTCAAGCAAAAGGAA
1 ATCAAAATCCAAAGCTCATATGGTGCCAAGAAAAAGGAA
*
181975 ATCAAAATCCAAATCTCATATGGTGCCAAGAAAAAGGAA
1 ATCAAAATCCAAAGCTCATATGGTGCCAAGAAAAAGGAA
182014 ATCAAAATC
1 ATCAAAATC
182023 TACAACTTGA
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
39 45 1.00
ACGTcount: A:0.48, C:0.18, G:0.15, T:0.18
Consensus pattern (39 bp):
ATCAAAATCCAAAGCTCATATGGTGCCAAGAAAAAGGAA
Found at i:182294 original size:20 final size:20
Alignment explanation
Indices: 182269--182311 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
182259 AACCGAAAAC
* *
182269 CGCGTTGCGAATTTGACTTT
1 CGCGTTGCAAATTTGACTAT
182289 CGCGTTGCAAATTTGACTAT
1 CGCGTTGCAAATTTGACTAT
182309 CGC
1 CGC
182312 AACGCTTATT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.19, C:0.23, G:0.23, T:0.35
Consensus pattern (20 bp):
CGCGTTGCAAATTTGACTAT
Found at i:186369 original size:20 final size:20
Alignment explanation
Indices: 186344--186428 Score: 77
Period size: 20 Copynumber: 4.2 Consensus size: 20
186334 GCATAAAAAC
186344 ATTTGACTTTCGCGTTGCGA
1 ATTTGACTTTCGCGTTGCGA
*
186364 ATTTGAC-TTCTGTGTTGCG-
1 ATTTGACTTTC-GCGTTGCGA
* ***
186383 ATTT-ACAAATTCGCAACGCGA
1 ATTTGAC--TTTCGCGTTGCGA
186404 ATTTGACTTTCGCGTTGCGA
1 ATTTGACTTTCGCGTTGCGA
186424 ATTTG
1 ATTTG
186429 GAAAATTGCA
Statistics
Matches: 50, Mismatches: 9, Indels: 12
0.70 0.13 0.17
Matches are distributed among these distances:
18 2 0.04
19 7 0.14
20 32 0.64
21 7 0.14
22 2 0.04
ACGTcount: A:0.20, C:0.19, G:0.22, T:0.39
Consensus pattern (20 bp):
ATTTGACTTTCGCGTTGCGA
Found at i:186407 original size:40 final size:40
Alignment explanation
Indices: 186360--186449 Score: 114
Period size: 41 Copynumber: 2.2 Consensus size: 40
186350 CTTTCGCGTT
*
186360 GCGAATTTGAC-TTCTGTGTTGCG-ATTT-ACAAATTCGCAAC
1 GCGAATTTGACTTTC-GCGTTGCGAATTTGA-AAATT-GCAAC
186400 GCGAATTTGACTTTCGCGTTGCGAATTTGGAAAATTGCAAC
1 GCGAATTTGACTTTCGCGTTGCGAATTT-GAAAATTGCAAC
186441 GCGAATTTG
1 GCGAATTTG
186450 GAAAATCGAA
Statistics
Matches: 45, Mismatches: 1, Indels: 7
0.85 0.02 0.13
Matches are distributed among these distances:
40 18 0.40
41 21 0.47
42 5 0.11
43 1 0.02
ACGTcount: A:0.26, C:0.18, G:0.23, T:0.33
Consensus pattern (40 bp):
GCGAATTTGACTTTCGCGTTGCGAATTTGAAAATTGCAAC
Found at i:186465 original size:21 final size:21
Alignment explanation
Indices: 186419--186465 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
186409 ACTTTCGCGT
* *
186419 TGCGAATTTGGAAAATTGCAA
1 TGCGAATTTGGAAAATCGAAA
*
186440 CGCGAATTTGGAAAATCGAAA
1 TGCGAATTTGGAAAATCGAAA
186461 TGCGA
1 TGCGA
186466 TTTACATATT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.38, C:0.13, G:0.26, T:0.23
Consensus pattern (21 bp):
TGCGAATTTGGAAAATCGAAA
Found at i:187766 original size:20 final size:20
Alignment explanation
Indices: 187743--187867 Score: 130
Period size: 20 Copynumber: 6.2 Consensus size: 20
187733 TGCGATTTTC
187743 CAAATTCGCAACGCGAAAGT
1 CAAATTCGCAACGCGAAAGT
*
187763 CAAATTCGCAACGCAAAAGT
1 CAAATTCGCAACGCGAAAGT
* *** *
187783 CAAATTCACGTTGCGAATTTGT
1 CAAATTCGCAACGCGAA--AGT
*
187805 -AAA-TCGCAACAC-AGAAGT
1 CAAATTCGCAACGCGA-AAGT
*
187823 CAAATTCGCAACGCGATAGT
1 CAAATTCGCAACGCGAAAGT
187843 CAAATTCGCAACGCGAAAGT
1 CAAATTCGCAACGCGAAAGT
187863 CAAAT
1 CAAAT
187868 GTTTTTACGC
Statistics
Matches: 83, Mismatches: 16, Indels: 12
0.75 0.14 0.11
Matches are distributed among these distances:
18 2 0.02
19 4 0.05
20 71 0.86
21 4 0.05
22 2 0.02
ACGTcount: A:0.40, C:0.23, G:0.18, T:0.19
Consensus pattern (20 bp):
CAAATTCGCAACGCGAAAGT
Found at i:188386 original size:20 final size:20
Alignment explanation
Indices: 188345--188386 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
188335 GAAACTAAAA
* * *
188345 TCGCGTTGCGATTTTCATTT
1 TCGCGTTGCGAATTTAAGTT
188365 TCGCGTTGCGAATTTAAGTT
1 TCGCGTTGCGAATTTAAGTT
188385 TC
1 TC
188387 AGAAACTTAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.14, C:0.19, G:0.21, T:0.45
Consensus pattern (20 bp):
TCGCGTTGCGAATTTAAGTT
Found at i:190411 original size:42 final size:42
Alignment explanation
Indices: 190364--190482 Score: 107
Period size: 42 Copynumber: 2.8 Consensus size: 42
190354 GATGTACCTA
* *
190364 TCATCATTCAAGAGGCGCC-TCCTATCGTTCAAGAGACCCCTC
1 TCATCATTCAAGAGGC-CCTTCCCACCGTTCAAGAGACCCCTC
* * * *
190406 TCATCA-TCGAAAAAGCCCTTCCCACCGTTCAAGAGGCCCCTG
1 TCATCATTC-AAGAGGCCCTTCCCACCGTTCAAGAGACCCCTC
* ** * *
190448 TCATCGTTCAAGAGGTACTGCCCGCCGTTCAAGAG
1 TCATCATTCAAGAGGCCCTTCCCACCGTTCAAGAG
190483 CCCAATTCAC
Statistics
Matches: 61, Mismatches: 13, Indels: 6
0.76 0.16 0.08
Matches are distributed among these distances:
41 4 0.07
42 55 0.90
43 2 0.03
ACGTcount: A:0.24, C:0.34, G:0.19, T:0.22
Consensus pattern (42 bp):
TCATCATTCAAGAGGCCCTTCCCACCGTTCAAGAGACCCCTC
Found at i:191903 original size:14 final size:14
Alignment explanation
Indices: 191884--191951 Score: 73
Period size: 14 Copynumber: 4.9 Consensus size: 14
191874 TTTTGATTAA
191884 TTGATTTGTAAAAG
1 TTGATTTGTAAAAG
** *
191898 TTGATTTGTTTAAT
1 TTGATTTGTAAAAG
191912 TTGATTTGTAAAAG
1 TTGATTTGTAAAAG
* ** *
191926 TTTATTTGTTTAAT
1 TTGATTTGTAAAAG
191940 TTGATTTGTAAA
1 TTGATTTGTAAA
191952 TAAGAATTAT
Statistics
Matches: 41, Mismatches: 13, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
14 41 1.00
ACGTcount: A:0.29, C:0.00, G:0.16, T:0.54
Consensus pattern (14 bp):
TTGATTTGTAAAAG
Found at i:191921 original size:28 final size:28
Alignment explanation
Indices: 191875--191951 Score: 129
Period size: 28 Copynumber: 2.8 Consensus size: 28
191865 AGATTTATTT
*
191875 TTTGATTAA-TTGATTTGTAAAAGTTGA
1 TTTGTTTAATTTGATTTGTAAAAGTTGA
*
191902 TTTGTTTAATTTGATTTGTAAAAGTTTA
1 TTTGTTTAATTTGATTTGTAAAAGTTGA
191930 TTTGTTTAATTTGATTTGTAAA
1 TTTGTTTAATTTGATTTGTAAA
191952 TAAGAATTAT
Statistics
Matches: 47, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
27 8 0.17
28 39 0.83
ACGTcount: A:0.30, C:0.00, G:0.16, T:0.55
Consensus pattern (28 bp):
TTTGTTTAATTTGATTTGTAAAAGTTGA
Found at i:192143 original size:20 final size:20
Alignment explanation
Indices: 192118--192171 Score: 99
Period size: 20 Copynumber: 2.7 Consensus size: 20
192108 GATTTTAGGT
192118 TTGCGAATTTGACTTTCGCG
1 TTGCGAATTTGACTTTCGCG
*
192138 TTGCGAATTTGACTTTTGCG
1 TTGCGAATTTGACTTTCGCG
192158 TTGCGAATTTGACT
1 TTGCGAATTTGACT
192172 ATCGTAACAC
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:0.17, C:0.17, G:0.24, T:0.43
Consensus pattern (20 bp):
TTGCGAATTTGACTTTCGCG
Found at i:192442 original size:39 final size:39
Alignment explanation
Indices: 192388--192474 Score: 149
Period size: 39 Copynumber: 2.2 Consensus size: 39
192378 TCAAGTTGTA
192388 GATTTTGATTTCCTTTTGCTTGGA-ACCATATGAGATTTG
1 GATTTTGATTTCCTTTTGCTT-GACACCATATGAGATTTG
*
192427 GATTTTGATTTCCTTTTGCTTGACACCATATGAGCTTTG
1 GATTTTGATTTCCTTTTGCTTGACACCATATGAGATTTG
192466 GATTTTGAT
1 GATTTTGAT
192475 GATCATCGGA
Statistics
Matches: 46, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
38 2 0.04
39 44 0.96
ACGTcount: A:0.20, C:0.14, G:0.20, T:0.47
Consensus pattern (39 bp):
GATTTTGATTTCCTTTTGCTTGACACCATATGAGATTTG
Found at i:192881 original size:25 final size:25
Alignment explanation
Indices: 192847--192896 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
192837 ATTATTTTTC
*
192847 CAAATAATGTACCCATAACAATGTT
1 CAAATAATGTACCCACAACAATGTT
192872 CAAATAATGTACCCACAACAATGTT
1 CAAATAATGTACCCACAACAATGTT
192897 TAATTGATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.44, C:0.22, G:0.08, T:0.26
Consensus pattern (25 bp):
CAAATAATGTACCCACAACAATGTT
Found at i:192964 original size:20 final size:20
Alignment explanation
Indices: 192936--192988 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
192926 GCATTATGTT
* * *
192936 AAAGGTAAATTCGCAACGCG
1 AAAGTTAAATTCGCAACACA
192956 AAAGTTAAATTCGCAACACA
1 AAAGTTAAATTCGCAACACA
*
192976 AAAGTCAAATTCG
1 AAAGTTAAATTCG
192989 GTTTGCGATT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.45, C:0.19, G:0.17, T:0.19
Consensus pattern (20 bp):
AAAGTTAAATTCGCAACACA
Found at i:193355 original size:18 final size:18
Alignment explanation
Indices: 193332--193367 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
193322 AAGCCGGTTG
*
193332 TGATTGGGATTTTGATTT
1 TGATTGCGATTTTGATTT
193350 TGATTGCGATTTTGATTT
1 TGATTGCGATTTTGATTT
193368 CCTTTTGCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.17, C:0.03, G:0.25, T:0.56
Consensus pattern (18 bp):
TGATTGCGATTTTGATTT
Found at i:194690 original size:23 final size:22
Alignment explanation
Indices: 194664--194732 Score: 66
Period size: 23 Copynumber: 3.0 Consensus size: 22
194654 CACCACAGCT
*
194664 CATATAATTGCACCTAAGTGCCA
1 CATAGAATTGCACC-AAGTGCCA
* * *
194687 CATAGAATTACACCGGAGTGCCG
1 CATAGAATTGCACC-AAGTGCCA
*
194710 CGTAGAATTGCACCATAGTGCCA
1 CATAGAATTGCACCA-AGTGCCA
194733 TATAATAATG
Statistics
Matches: 36, Mismatches: 9, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.32, C:0.26, G:0.20, T:0.22
Consensus pattern (22 bp):
CATAGAATTGCACCAAGTGCCA
Found at i:194876 original size:103 final size:103
Alignment explanation
Indices: 194751--194965 Score: 376
Period size: 103 Copynumber: 2.1 Consensus size: 103
194741 TGTCCATAAG
194751 GACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCAGAC
1 GACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCAGAC
*
194816 ATCACACATGTTCTAAAGAATACATATATGTCCCGAAA
66 ATCACACATGTTCCAAAGAATACATATATGTCCCGAAA
* * *
194854 GACCACATATCATTCCTTAAGAATCGTATACATCTGCCAAGGATCCAGTATGTGTCTCACCAGAC
1 GACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCAGAC
* *
194919 CTCACACATGTTCCAAAGAATACATATATGTCCCGAAG
66 ATCACACATGTTCCAAAGAATACATATATGTCCCGAAA
194957 GACCACATA
1 GACCACATA
194966 GACCCTCTAC
Statistics
Matches: 106, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
103 106 1.00
ACGTcount: A:0.36, C:0.26, G:0.13, T:0.25
Consensus pattern (103 bp):
GACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCAGAC
ATCACACATGTTCCAAAGAATACATATATGTCCCGAAA
Found at i:195559 original size:64 final size:63
Alignment explanation
Indices: 195450--195586 Score: 159
Period size: 64 Copynumber: 2.1 Consensus size: 63
195440 TACACCATGA
* * * *
195450 ATCGATGCATAAATCCTATTCGATGTTTGTATTTAATGGGGATGCATCGATGCACTCCTTATGC
1 ATCGATGCATAAATCCTATTAGATGTTTCTATTTAAT-GGAATGCATCGATGCACTCCATATGC
* * * * *
195514 ATCGATGCATAAATCCTATTAGATGTTTTCTTTTTAAAT-TAATGCATCGATGCGCTGCATGTGC
1 ATCGATGCATAAATCCTATTAGATG-TTTCTATTT-AATGGAATGCATCGATGCACTCCATATGC
195578 ATCGATGCA
1 ATCGATGCA
195587 CCTTACACAA
Statistics
Matches: 62, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
64 52 0.84
65 7 0.11
66 3 0.05
ACGTcount: A:0.26, C:0.18, G:0.19, T:0.36
Consensus pattern (63 bp):
ATCGATGCATAAATCCTATTAGATGTTTCTATTTAATGGAATGCATCGATGCACTCCATATGC
Found at i:201693 original size:23 final size:23
Alignment explanation
Indices: 201667--201730 Score: 78
Period size: 23 Copynumber: 2.8 Consensus size: 23
201657 CAGCTCATAT
*
201667 AATTGCACCTAAGTGCCACTTAG
1 AATTGCACCTAAGTGCCACGTAG
*
201690 AATTGCACC-AGAGTGCCGCGTAG
1 AATTGCACCTA-AGTGCCACGTAG
201713 AATTGCACCGT-AGTGCCA
1 AATTGCACC-TAAGTGCCA
201731 TATAATAATG
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
22 1 0.03
23 34 0.97
ACGTcount: A:0.28, C:0.27, G:0.23, T:0.22
Consensus pattern (23 bp):
AATTGCACCTAAGTGCCACGTAG
Found at i:201866 original size:103 final size:103
Alignment explanation
Indices: 201750--201963 Score: 392
Period size: 103 Copynumber: 2.1 Consensus size: 103
201740 GTCCATAAGG
201750 ACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTAACCAGACC
1 ACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTAACCAGACC
*
201815 TCACACATGTTCCAAAGAATATATATATGTCCCGAAGA
66 TCACACATGTTCCAAAGAATACATATATGTCCCGAAGA
* *
201853 ACCACATATCATTCCTTAAGAATCATATACATATGTCAAGGATCAAGTATGTGTCTCACCAGACC
1 ACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTAACCAGACC
*
201918 TCACACATGTTCCAAAGAATACATATATGTCCCGAAGG
66 TCACACATGTTCCAAAGAATACATATATGTCCCGAAGA
201956 ACCACATA
1 ACCACATA
201964 GACCCTCTAC
Statistics
Matches: 107, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
103 107 1.00
ACGTcount: A:0.37, C:0.24, G:0.13, T:0.26
Consensus pattern (103 bp):
ACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTAACCAGACC
TCACACATGTTCCAAAGAATACATATATGTCCCGAAGA
Found at i:203408 original size:27 final size:27
Alignment explanation
Indices: 203370--203447 Score: 108
Period size: 27 Copynumber: 3.0 Consensus size: 27
203360 GAATGGATGT
203370 TCAAAATCCGAGTATTGACCAAGATCA
1 TCAAAATCCGAGTATTGACCAAGATCA
203397 TCAAAATCCGAGTATTGACCAAG---A
1 TCAAAATCCGAGTATTGACCAAGATCA
* * *
203421 TCAAATTCCGGGTATTAACCAAGATCA
1 TCAAAATCCGAGTATTGACCAAGATCA
203448 AATTTCGAAT
Statistics
Matches: 45, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
24 21 0.47
27 24 0.53
ACGTcount: A:0.40, C:0.22, G:0.15, T:0.23
Consensus pattern (27 bp):
TCAAAATCCGAGTATTGACCAAGATCA
Found at i:203430 original size:24 final size:24
Alignment explanation
Indices: 203370--203449 Score: 106
Period size: 24 Copynumber: 3.2 Consensus size: 24
203360 GAATGGATGT
203370 TCAAAATCCGAGTATTGACCAAGATCA
1 TCAAAATCCGAGTATTGACCAAG---A
203397 TCAAAATCCGAGTATTGACCAAGA
1 TCAAAATCCGAGTATTGACCAAGA
* * *
203421 TCAAATTCCGGGTATTAACCAAGA
1 TCAAAATCCGAGTATTGACCAAGA
203445 TCAAA
1 TCAAA
203450 TTTCGAATAC
Statistics
Matches: 50, Mismatches: 3, Indels: 3
0.89 0.05 0.05
Matches are distributed among these distances:
24 27 0.54
27 23 0.46
ACGTcount: A:0.41, C:0.21, G:0.15, T:0.23
Consensus pattern (24 bp):
TCAAAATCCGAGTATTGACCAAGA
Found at i:203463 original size:24 final size:24
Alignment explanation
Indices: 203396--203463 Score: 64
Period size: 24 Copynumber: 2.8 Consensus size: 24
203386 GACCAAGATC
* * * *
203396 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAATTCCGAATACTAACCAAG
** *
203420 ATCAAATTCCGGGTATTAACCAAG
1 ATCAAATTCCGAATACTAACCAAG
*
203444 ATCAAATTTCGAATACTAAC
1 ATCAAATTCCGAATACTAAC
203464 TAGTACTCAC
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.41, C:0.21, G:0.13, T:0.25
Consensus pattern (24 bp):
ATCAAATTCCGAATACTAACCAAG
Found at i:210177 original size:15 final size:15
Alignment explanation
Indices: 210153--210225 Score: 96
Period size: 15 Copynumber: 4.9 Consensus size: 15
210143 TTGGTTTTCC
210153 GGAAAATGAATTACT
1 GGAAAATGAATTACT
**
210168 GGAATTTGAATTACT
1 GGAAAATGAATTACT
210183 GGAAAATGAATTACT
1 GGAAAATGAATTACT
*
210198 -GAAATTTGAATT-CT
1 GGAAA-ATGAATTACT
210212 GGAAAATGAATTAC
1 GGAAAATGAATTAC
210226 ATTTCTGGAA
Statistics
Matches: 49, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
14 12 0.24
15 37 0.76
ACGTcount: A:0.42, C:0.07, G:0.19, T:0.32
Consensus pattern (15 bp):
GGAAAATGAATTACT
Found at i:210221 original size:21 final size:22
Alignment explanation
Indices: 210195--210243 Score: 57
Period size: 20 Copynumber: 2.3 Consensus size: 22
210185 AAAATGAATT
**
210195 ACTGAAATTTGAATTCTGGAAA
1 ACTGAAATTACAATTCTGGAAA
*
210217 A-TG-AATTACATTTCTGGAAA
1 ACTGAAATTACAATTCTGGAAA
210237 ACTGAAA
1 ACTGAAA
210244 AACGTTTTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 4
0.76 0.10 0.14
Matches are distributed among these distances:
20 15 0.68
21 4 0.18
22 3 0.14
ACGTcount: A:0.43, C:0.10, G:0.16, T:0.31
Consensus pattern (22 bp):
ACTGAAATTACAATTCTGGAAA
Found at i:210223 original size:29 final size:30
Alignment explanation
Indices: 210153--210225 Score: 130
Period size: 30 Copynumber: 2.5 Consensus size: 30
210143 TTGGTTTTCC
*
210153 GGAAAATGAATTACTGGAATTTGAATTACT
1 GGAAAATGAATTACTGAAATTTGAATTACT
210183 GGAAAATGAATTACTGAAATTTGAATT-CT
1 GGAAAATGAATTACTGAAATTTGAATTACT
210212 GGAAAATGAATTAC
1 GGAAAATGAATTAC
210226 ATTTCTGGAA
Statistics
Matches: 42, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
29 16 0.38
30 26 0.62
ACGTcount: A:0.42, C:0.07, G:0.19, T:0.32
Consensus pattern (30 bp):
GGAAAATGAATTACTGAAATTTGAATTACT
Found at i:210620 original size:28 final size:27
Alignment explanation
Indices: 210565--210642 Score: 79
Period size: 28 Copynumber: 2.7 Consensus size: 27
210555 TTTACTAAAA
*
210565 TATTATTTAAATATATAAATAATATTAT
1 TATTA-TTAAATATATAAAAAATATTAT
210593 TCATTATTAAATATATAAAAAAATTTATTAT
1 T-ATTATTAAATATAT-AAAAAA--TATTAT
210624 ATATTATTAAA-ATA-AAAAA
1 -TATTATTAAATATATAAAAA
210643 TATAATATCT
Statistics
Matches: 44, Mismatches: 1, Indels: 10
0.80 0.02 0.18
Matches are distributed among these distances:
28 16 0.36
29 9 0.20
30 3 0.07
31 15 0.34
32 1 0.02
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.44
Consensus pattern (27 bp):
TATTATTAAATATATAAAAAATATTAT
Found at i:210737 original size:50 final size:52
Alignment explanation
Indices: 210622--210737 Score: 150
Period size: 50 Copynumber: 2.2 Consensus size: 52
210612 AAAATTTATT
*
210622 ATATATTATTAAAATAAAAAATATAATATCTTATATTATTATAATATAATTGA
1 ATATATTATTAAAATAAAAAATATAATA-CTTATATTATTATAATATAATTAA
* *
210675 TTATATTATTAAACT-AAAAATATAATA-TTATATTATTATAAATATTAA-TAA
1 ATATATTATTAAAATAAAAAATATAATACTTATATTATTAT-AATA-TAATTAA
210726 ATATATT-TTAAA
1 ATATATTATTAAA
210738 TATTTTAATA
Statistics
Matches: 57, Mismatches: 4, Indels: 7
0.84 0.06 0.10
Matches are distributed among these distances:
50 17 0.30
51 12 0.21
52 15 0.26
53 13 0.23
ACGTcount: A:0.53, C:0.02, G:0.01, T:0.45
Consensus pattern (52 bp):
ATATATTATTAAAATAAAAAATATAATACTTATATTATTATAATATAATTAA
Found at i:210977 original size:42 final size:42
Alignment explanation
Indices: 210930--211031 Score: 152
Period size: 42 Copynumber: 2.4 Consensus size: 42
210920 ATAAATTACG
* *
210930 TTCCGAAAAACAAATTACGTGAAAC-AAACACGGGAAAACATT
1 TTCCGAAAAACGAATTACGTGAAACAAAAC-CGGAAAAACATT
210972 TTCCGAAAAACGAATTACGTGAAACAAAACCGGAAAAACATT
1 TTCCGAAAAACGAATTACGTGAAACAAAACCGGAAAAACATT
**
211014 TTCTAAAAAACGAATTAC
1 TTCCGAAAAACGAATTAC
211032 ATTAAATAAA
Statistics
Matches: 55, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
42 51 0.93
43 4 0.07
ACGTcount: A:0.50, C:0.19, G:0.13, T:0.19
Consensus pattern (42 bp):
TTCCGAAAAACGAATTACGTGAAACAAAACCGGAAAAACATT
Found at i:213260 original size:20 final size:20
Alignment explanation
Indices: 213233--213284 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
213223 AACGCGATCT
213233 CCAGAATCGCAAATCAGTTC
1 CCAGAATCGCAAATCAGTTC
*
213253 CCATAATCGCAAATCAGTTC
1 CCAGAATCGCAAATCAGTTC
213273 CCAGAATCGCAA
1 CCAGAATCGCAA
213285 TGTGATAGTA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.37, C:0.31, G:0.13, T:0.19
Consensus pattern (20 bp):
CCAGAATCGCAAATCAGTTC
Found at i:213360 original size:22 final size:20
Alignment explanation
Indices: 213319--213371 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
213309 AATTTTCCAT
213319 AATCGCAACGCGAATATAAA
1 AATCGCAACGCGAATATAAA
* *
213339 AATCGCAACGCGAACATATA
1 AATCGCAACGCGAATATAAA
* *
213359 AATTGCAATGCGA
1 AATCGCAACGCGA
213372 TTCTGACTAT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.45, C:0.21, G:0.17, T:0.17
Consensus pattern (20 bp):
AATCGCAACGCGAATATAAA
Found at i:213424 original size:20 final size:20
Alignment explanation
Indices: 213380--213587 Score: 164
Period size: 20 Copynumber: 10.3 Consensus size: 20
213370 GATTCTGACT
213380 ATCGCAACGAGTATCCGTAAA
1 ATCGCAACGAGTATCCGT-AA
* *
213401 ATCGTAACGTGTATCCGTAA
1 ATCGCAACGAGTATCCGTAA
* *
213421 ATCGCAACGAGAATACGTAA
1 ATCGCAACGAGTATCCGTAA
* * **
213441 ATCGTAACGTGTATATGTAA
1 ATCGCAACGAGTATCCGTAA
** *
213461 ATCGCAACGACAATACGTAA
1 ATCGCAACGAGTATCCGTAA
* *
213481 ATCGCAATGCGTATCCGTAA
1 ATCGCAACGAGTATCCGTAA
* *
213501 ATCGCAATGCGTATCCGTAA
1 ATCGCAACGAGTATCCGTAA
* * * *
213521 ATCGCAATGCGAATACGTAA
1 ATCGCAACGAGTATCCGTAA
* * * *
213541 ATCGCAATGCGAATACGTAA
1 ATCGCAACGAGTATCCGTAA
* * * *
213561 ATCGCAATGCGAATACGTAA
1 ATCGCAACGAGTATCCGTAA
213581 ATCGCAA
1 ATCGCAA
213588 TGCGAATCTG
Statistics
Matches: 165, Mismatches: 22, Indels: 1
0.88 0.12 0.01
Matches are distributed among these distances:
20 149 0.90
21 16 0.10
ACGTcount: A:0.38, C:0.21, G:0.19, T:0.22
Consensus pattern (20 bp):
ATCGCAACGAGTATCCGTAA
Found at i:213454 original size:40 final size:40
Alignment explanation
Indices: 213380--213604 Score: 218
Period size: 40 Copynumber: 5.6 Consensus size: 40
213370 GATTCTGACT
* * * * *
213380 ATCGCAACGAGTATCCGTAAAATCGTAACGTGTATCCGTAA
1 ATCGCAACGAGAATACGT-AAATCGCAACGCGTATACGTAA
* * *
213421 ATCGCAACGAGAATACGTAAATCGTAACGTGTATATGTAA
1 ATCGCAACGAGAATACGTAAATCGCAACGCGTATACGTAA
* * *
213461 ATCGCAACGACAATACGTAAATCGCAATGCGTATCCGTAA
1 ATCGCAACGAGAATACGTAAATCGCAACGCGTATACGTAA
* * * * * *
213501 ATCGCAATGCGTATCCGTAAATCGCAATGCGAATACGTAA
1 ATCGCAACGAGAATACGTAAATCGCAACGCGTATACGTAA
* * * *
213541 ATCGCAATGCGAATACGTAAATCGCAATGCGAATACGTAA
1 ATCGCAACGAGAATACGTAAATCGCAACGCGTATACGTAA
* *
213581 ATCGCAATGCGAAT-CTGTAAATCG
1 ATCGCAACGAGAATAC-GTAAATCG
213605 TAACAAGATT
Statistics
Matches: 164, Mismatches: 19, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
39 1 0.01
40 147 0.90
41 16 0.10
ACGTcount: A:0.37, C:0.21, G:0.20, T:0.23
Consensus pattern (40 bp):
ATCGCAACGAGAATACGTAAATCGCAACGCGTATACGTAA
Found at i:213480 original size:60 final size:60
Alignment explanation
Indices: 213380--213604 Score: 238
Period size: 60 Copynumber: 3.7 Consensus size: 60
213370 GATTCTGACT
* * * * * * * * *
213380 ATCGCAACGAGTATCCGTAAAATCGTAACGTGTATCCGTAAATCGCAACGAGAATACGTAA
1 ATCGCAATGCGTATACGT-AAATCGCAACGCGAATACGTAAATCGCAATGCGAATACGTAA
* * * * * *
213441 ATCGTAACGTGTATATGTAAATCGCAACGAC-AATACGTAAATCGCAATGCGTATCCGTAA
1 ATCGCAATGCGTATACGTAAATCGCAACG-CGAATACGTAAATCGCAATGCGAATACGTAA
* *
213501 ATCGCAATGCGTATCCGTAAATCGCAATGCGAATACGTAAATCGCAATGCGAATACGTAA
1 ATCGCAATGCGTATACGTAAATCGCAACGCGAATACGTAAATCGCAATGCGAATACGTAA
* *
213561 ATCGCAATGCGAATACGTAAATCGCAATGCGAAT-CTGTAAATCG
1 ATCGCAATGCGTATACGTAAATCGCAACGCGAATAC-GTAAATCG
213605 TAACAAGATT
Statistics
Matches: 139, Mismatches: 22, Indels: 7
0.83 0.13 0.04
Matches are distributed among these distances:
59 2 0.01
60 123 0.88
61 14 0.10
ACGTcount: A:0.37, C:0.21, G:0.20, T:0.23
Consensus pattern (60 bp):
ATCGCAATGCGTATACGTAAATCGCAACGCGAATACGTAAATCGCAATGCGAATACGTAA
Found at i:213588 original size:20 final size:20
Alignment explanation
Indices: 213416--213604 Score: 238
Period size: 20 Copynumber: 9.4 Consensus size: 20
213406 AACGTGTATC
* *
213416 CGTAAATCGCAACGAGAATA
1 CGTAAATCGCAATGCGAATA
* * * *
213436 CGTAAATCGTAACGTGTATA
1 CGTAAATCGCAATGCGAATA
* *
213456 TGTAAATCGCAACGAC-AATA
1 CGTAAATCGCAATG-CGAATA
* *
213476 CGTAAATCGCAATGCGTATC
1 CGTAAATCGCAATGCGAATA
* *
213496 CGTAAATCGCAATGCGTATC
1 CGTAAATCGCAATGCGAATA
213516 CGTAAATCGCAATGCGAATA
1 CGTAAATCGCAATGCGAATA
213536 CGTAAATCGCAATGCGAATA
1 CGTAAATCGCAATGCGAATA
213556 CGTAAATCGCAATGCGAATA
1 CGTAAATCGCAATGCGAATA
213576 CGTAAATCGCAATGCGAAT-
1 CGTAAATCGCAATGCGAATA
213595 CTGTAAATCG
1 C-GTAAATCG
213605 TAACAAGATT
Statistics
Matches: 153, Mismatches: 13, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
19 2 0.01
20 151 0.99
ACGTcount: A:0.38, C:0.21, G:0.20, T:0.22
Consensus pattern (20 bp):
CGTAAATCGCAATGCGAATA
Found at i:214496 original size:24 final size:24
Alignment explanation
Indices: 214469--214522 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
214459 GTATTCGAAA
214469 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
214493 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
214517 TTTGAT
1 TTTGAT
214523 GATTTTTCAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:217015 original size:20 final size:19
Alignment explanation
Indices: 216979--217046 Score: 91
Period size: 19 Copynumber: 3.5 Consensus size: 19
216969 GCAACGAGAT
*
216979 AATCGCAATGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
216998 AATCGCAACGCGGAAATGAC
1 AATCGCAACGC-GAAATGAA
* *
217018 TATCGCAATGCGAAATGAA
1 AATCGCAACGCGAAATGAA
217037 AATCGCAACG
1 AATCGCAACG
217047 AGGGAATCGC
Statistics
Matches: 41, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
19 25 0.61
20 16 0.39
ACGTcount: A:0.43, C:0.21, G:0.22, T:0.15
Consensus pattern (19 bp):
AATCGCAACGCGAAATGAA
Found at i:217034 original size:39 final size:33
Alignment explanation
Indices: 216966--217079 Score: 138
Period size: 33 Copynumber: 3.3 Consensus size: 33
216956 GGAAATTACT
**
216966 ATCGCAACGAGATAATCGCAATGCGAAATGAAA
1 ATCGCAACGAGGGAATCGCAATGCGAAATGAAA
*
216999 ATCGCAACGCGGAAATGACTATCGCAATGCGAAATGAAA
1 ATCGCAACGAGG----GA--ATCGCAATGCGAAATGAAA
217038 ATCGCAACGAGGGAATCGCAATGCGAAATGAAA
1 ATCGCAACGAGGGAATCGCAATGCGAAATGAAA
*
217071 ATTGCAACG
1 ATCGCAACG
217080 TGAATTTAGT
Statistics
Matches: 70, Mismatches: 5, Indels: 12
0.80 0.06 0.14
Matches are distributed among these distances:
33 37 0.53
35 2 0.03
37 1 0.01
39 30 0.43
ACGTcount: A:0.42, C:0.19, G:0.24, T:0.15
Consensus pattern (33 bp):
ATCGCAACGAGGGAATCGCAATGCGAAATGAAA
Found at i:217062 original size:72 final size:73
Alignment explanation
Indices: 216939--217079 Score: 203
Period size: 72 Copynumber: 1.9 Consensus size: 73
216929 TGGGACTCTT
* * ** *
216939 AATGTCTATCGCAACGCGGAAATTACTATCGCAACGAGATAATCGCAATGCGAAATGAAAATCGC
1 AATGACTATCGCAACGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGC
217004 AACGCGGA
66 AACGCGGA
* * *
217012 AATGACTATCGCAATGC-GAAATGAAAATCGCAACGAGGGAATCGCAATGCGAAATGAAAATTGC
1 AATGACTATCGCAACGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGC
217076 AACG
66 AACG
217080 TGAATTTAGT
Statistics
Matches: 60, Mismatches: 8, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
72 45 0.75
73 15 0.25
ACGTcount: A:0.40, C:0.20, G:0.23, T:0.17
Consensus pattern (73 bp):
AATGACTATCGCAACGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGC
AACGCGGA
Found at i:217157 original size:20 final size:19
Alignment explanation
Indices: 217129--217231 Score: 64
Period size: 19 Copynumber: 5.9 Consensus size: 19
217119 CAACGTGAAA
*
217129 ATCGTAATGCGGAAATGACT
1 ATCGCAATGC-GAAATGACT
**
217149 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGACT
*
217168 ATCGCAA--CGAGA-GA--
1 ATCGCAATGCGAAATGACT
**
217182 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGACT
*
217201 ATCGCAA--CGAGA-GA--
1 ATCGCAATGCGAAATGACT
217215 ATCGCAATGCGAAATGA
1 ATCGCAATGCGAAATGA
217232 AAATCGCAAC
Statistics
Matches: 68, Mismatches: 7, Indels: 19
0.72 0.07 0.20
Matches are distributed among these distances:
14 14 0.21
16 12 0.18
17 12 0.18
19 21 0.31
20 9 0.13
ACGTcount: A:0.43, C:0.17, G:0.24, T:0.16
Consensus pattern (19 bp):
ATCGCAATGCGAAATGACT
Found at i:217167 original size:53 final size:52
Alignment explanation
Indices: 217108--217207 Score: 146
Period size: 53 Copynumber: 1.9 Consensus size: 52
217098 GCAATTTTAG
* * **
217108 AATGAAAATCGCAACGTGAAAATCGTAATGCGGAAATGACTATCGCAATGCGA
1 AATGAAAATCGCAACGAGAAAATCGCAATGC-GAAATGAAAATCGCAATGCGA
*
217161 AATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAA
1 AATGAAAATCGCAACGAGAAAATCGCAATGCGAAATGAAAATCGCAA
217208 CGAGAGAATC
Statistics
Matches: 42, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
52 14 0.33
53 28 0.67
ACGTcount: A:0.45, C:0.17, G:0.22, T:0.16
Consensus pattern (52 bp):
AATGAAAATCGCAACGAGAAAATCGCAATGCGAAATGAAAATCGCAATGCGA
Found at i:217186 original size:14 final size:14
Alignment explanation
Indices: 217167--217254 Score: 59
Period size: 14 Copynumber: 5.6 Consensus size: 14
217157 GCGAAATGAA
217167 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
217181 AATCGCAATGCGAAATGAA
1 AATCGCAA--CG--A-GAG
217200 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
217214 AATCGCAATGCGAAATGAA
1 AATCGCAA--CG--A-GAG
*
217233 AATCGCAACGAGGG
1 AATCGCAACGAGAG
217247 AATCGCAA
1 AATCGCAA
217255 TGCGAAATGA
Statistics
Matches: 59, Mismatches: 5, Indels: 20
0.70 0.06 0.24
Matches are distributed among these distances:
14 27 0.46
15 2 0.03
16 4 0.07
17 4 0.07
18 2 0.03
19 20 0.34
ACGTcount: A:0.44, C:0.19, G:0.25, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:217188 original size:33 final size:33
Alignment explanation
Indices: 217149--217275 Score: 245
Period size: 33 Copynumber: 3.8 Consensus size: 33
217139 GGAAATGACT
217149 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
217182 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
217215 ATCGCAATGCGAAATGAAAATCGCAACGAGGGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
217248 ATCGCAATGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
217276 CGAATTTAGT
Statistics
Matches: 93, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
33 93 1.00
ACGTcount: A:0.44, C:0.19, G:0.24, T:0.13
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:217310 original size:19 final size:19
Alignment explanation
Indices: 217275--217337 Score: 99
Period size: 19 Copynumber: 3.3 Consensus size: 19
217265 AAATCGCAAC
*
217275 GCGAATTTAGTTTCGCGTT
1 GCGATTTTAGTTTCGCGTT
217294 GCGATTTTAGTTTCGCGTT
1 GCGATTTTAGTTTCGCGTT
* *
217313 GCGATTTTAATTTCGCATT
1 GCGATTTTAGTTTCGCGTT
217332 GCGATT
1 GCGATT
217338 CTCTCGTTGC
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 41 1.00
ACGTcount: A:0.16, C:0.16, G:0.24, T:0.44
Consensus pattern (19 bp):
GCGATTTTAGTTTCGCGTT
Found at i:217368 original size:19 final size:19
Alignment explanation
Indices: 217285--217369 Score: 83
Period size: 19 Copynumber: 4.7 Consensus size: 19
217275 GCGAATTTAG
*
217285 TTTCGCGTTGCGATTTT-A
1 TTTCGCATTGCGATTTTCA
* *
217303 GTTTCGCGTTGCGATTTTAA
1 -TTTCGCATTGCGATTTTCA
217323 TTTCGCATTGCGA--TTC-
1 TTTCGCATTGCGATTTTCA
*
217339 TCTCG--TTGCGATTTTCA
1 TTTCGCATTGCGATTTTCA
217356 TTTCGCATTGCGAT
1 TTTCGCATTGCGAT
217370 AGTCATTTTT
Statistics
Matches: 56, Mismatches: 4, Indels: 12
0.78 0.06 0.17
Matches are distributed among these distances:
14 6 0.11
16 7 0.12
17 6 0.11
19 36 0.64
20 1 0.02
ACGTcount: A:0.13, C:0.20, G:0.21, T:0.46
Consensus pattern (19 bp):
TTTCGCATTGCGATTTTCA
Found at i:218924 original size:42 final size:42
Alignment explanation
Indices: 218848--218970 Score: 115
Period size: 42 Copynumber: 2.9 Consensus size: 42
218838 GTGAATCGGG
* ** *
218848 CTCTTGAATGGTGGGA-GGGACCTCTTC-AACAATGACAGTGGC
1 CTCTTGAACGGTGGGAGGGGA-CTC-TCGAGGAATGACAGGGGC
*
218890 CTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGACAGGGGC
* * * * * *
218932 CTCTTCAACGATAGGAGTGGACTCTTGAGGGATGACAGG
1 CTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGACAGG
218971 CGAGTCGGGC
Statistics
Matches: 67, Mismatches: 12, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
41 2 0.03
42 61 0.91
43 4 0.06
ACGTcount: A:0.24, C:0.19, G:0.36, T:0.22
Consensus pattern (42 bp):
CTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGACAGGGGC
Found at i:220981 original size:20 final size:20
Alignment explanation
Indices: 220937--220982 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
220927 CTTTTGGTTG
220937 AAATGAAAATCACAACGAGA
1 AAATGAAAATCACAACGAGA
* * *
220957 GAATGAAAATCGCAACGCGA
1 AAATGAAAATCACAACGAGA
220977 AAATGA
1 AAATGA
220983 CTATCGCAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.54, C:0.15, G:0.20, T:0.11
Consensus pattern (20 bp):
AAATGAAAATCACAACGAGA
Found at i:221058 original size:19 final size:20
Alignment explanation
Indices: 221036--221146 Score: 83
Period size: 20 Copynumber: 5.8 Consensus size: 20
221026 GCGATTTTGG
221036 TTTCGTGTTGCGATTTTCA-
1 TTTCGTGTTGCGATTTTCAT
**
221055 TTTCGCATTGCGA--TTC--
1 TTTCGTGTTGCGATTTTCAT
* *
221071 TCTC--GTTGCGATTTTTACT
1 TTTCGTGTTGCGATTTTCA-T
* * **
221090 TCTCGCGTTGCGATAGTCAT
1 TTTCGTGTTGCGATTTTCAT
221110 TTTCGTGTTGCGATTTTCAT
1 TTTCGTGTTGCGATTTTCAT
*
221130 TTTCATGTTGCGATTTT
1 TTTCGTGTTGCGATTTT
221147 AAGTTTAGAA
Statistics
Matches: 72, Mismatches: 13, Indels: 13
0.73 0.13 0.13
Matches are distributed among these distances:
14 6 0.08
16 5 0.07
17 3 0.04
19 15 0.21
20 33 0.46
21 10 0.14
ACGTcount: A:0.12, C:0.19, G:0.20, T:0.50
Consensus pattern (20 bp):
TTTCGTGTTGCGATTTTCAT
Found at i:221733 original size:20 final size:20
Alignment explanation
Indices: 221708--221880 Score: 195
Period size: 20 Copynumber: 8.6 Consensus size: 20
221698 CTTTAAAAAT
221708 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
221728 CGCGTTGCGATTTTACGTAT-
1 CGCGTTGCGA-TTTACGGATA
*
221748 TGTCGTTGCGATTTACGGATA
1 CG-CGTTGCGATTTACGGATA
* * *
221769 CGCATTGCGATTTACGTATT
1 CGCGTTGCGATTTACGGATA
* **
221789 CTCGTTGCGATTTACAAATA
1 CGCGTTGCGATTTACGGATA
* *
221809 CGCGTTGCGATTTACGTATT
1 CGCGTTGCGATTTACGGATA
*
221829 CTCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
221849 CGCGTTGTGATTTTACGGATA
1 CGCGTTGCGA-TTTACGGATA
*
221870 CTCGTTGCGAT
1 CGCGTTGCGAT
221881 AGTCAGAATC
Statistics
Matches: 126, Mismatches: 23, Indels: 8
0.80 0.15 0.05
Matches are distributed among these distances:
20 91 0.72
21 35 0.28
ACGTcount: A:0.19, C:0.19, G:0.25, T:0.37
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:221794 original size:40 final size:41
Alignment explanation
Indices: 221710--221880 Score: 265
Period size: 40 Copynumber: 4.2 Consensus size: 41
221700 TTAAAAATCG
*
221710 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTGT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
*
221751 CGTTGCGATTTACGGATACGCATTGCGA-TTTACGTATTCT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
**
221791 CGTTGCGATTTACAAATACGCGTTGCGA-TTTACGTATTCT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
* * *
221831 CGTTGCGATTTACGGATACGCGTTGTGATTTTACGGATACT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
221872 CGTTGCGAT
1 CGTTGCGAT
221881 AGTCAGAATC
Statistics
Matches: 119, Mismatches: 10, Indels: 2
0.91 0.08 0.02
Matches are distributed among these distances:
40 73 0.61
41 46 0.39
ACGTcount: A:0.19, C:0.19, G:0.25, T:0.37
Consensus pattern (41 bp):
CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
Found at i:221894 original size:81 final size:80
Alignment explanation
Indices: 221710--221900 Score: 251
Period size: 81 Copynumber: 2.4 Consensus size: 80
221700 TTAAAAATCG
* ** *
221710 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTGTCGTTGCGATTTACGGATACGCATT
1 CGTTGCGATGTACAAATACGCGTTGCGA-TTTACGTATTCTCGTTGCGATTTACGGATACGCATT
* *
221775 GCGATTTACGTATTCT
65 GCGATTTACGGATACT
* *
221791 CGTTGCGATTTACAAATACGCGTTGCGATTTACGTATTCTCGTTGCGATTTACGGATACGCGTTG
1 CGTTGCGATGTACAAATACGCGTTGCGATTTACGTATTCTCGTTGCGATTTACGGATACGCATTG
*
221856 TGATTTTACGGATACT
66 CGA-TTTACGGATACT
221872 CGTTGCGATAGT-CAGAAT-CGCGTTGCGAT
1 CGTTGCGAT-GTACA-AATACGCGTTGCGAT
221901 AGTCAGAATC
Statistics
Matches: 99, Mismatches: 8, Indels: 6
0.88 0.07 0.05
Matches are distributed among these distances:
80 37 0.37
81 58 0.59
82 4 0.04
ACGTcount: A:0.20, C:0.19, G:0.25, T:0.36
Consensus pattern (80 bp):
CGTTGCGATGTACAAATACGCGTTGCGATTTACGTATTCTCGTTGCGATTTACGGATACGCATTG
CGATTTACGGATACT
Found at i:221896 original size:101 final size:100
Alignment explanation
Indices: 221699--221923 Score: 235
Period size: 101 Copynumber: 2.2 Consensus size: 100
221689 ATAATGGCGC
* * *
221699 TTTAAAAATCGCGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTGTCGTTGCGATTTAC
1 TTTACAAATCGCGTTGCGATTTACGGATACGCGTTGCGATTTTACGGATCGTCGTTGCGATTTAC
* * *
221764 GGATACGCATTGCGATTTACGTATTCTCGTTGCGA
66 GGATACGCATTGCGATTCACGTAATCGCGTTGCGA
* * * *
221799 TTTACAAATACGCGTTGCGATTTACGTATTCTCGTTGCGA-TTTACGGATACG-CGTTGTGATTT
1 TTTACAAAT-CGCGTTGCGATTTACGGATACGCGTTGCGATTTTACGGAT-CGTCGTTGCGA-TT
* *
221862 TACGGATACTCGTTGCGATAGTCA-G-AATCGCGTTGCGA
63 TACGGATACGCATTGCGAT--TCACGTAATCGCGTTGCGA
*
221900 TAGT-CAGAATCGCGTTGCGATTTA
1 T-TTACA-AATCGCGTTGCGATTTA
221924 TATGTTCGCG
Statistics
Matches: 105, Mismatches: 13, Indels: 13
0.80 0.10 0.10
Matches are distributed among these distances:
100 23 0.22
101 75 0.71
102 5 0.05
103 2 0.02
ACGTcount: A:0.22, C:0.18, G:0.24, T:0.36
Consensus pattern (100 bp):
TTTACAAATCGCGTTGCGATTTACGGATACGCGTTGCGATTTTACGGATCGTCGTTGCGATTTAC
GGATACGCATTGCGATTCACGTAATCGCGTTGCGA
Found at i:221897 original size:20 final size:20
Alignment explanation
Indices: 221872--221920 Score: 98
Period size: 20 Copynumber: 2.5 Consensus size: 20
221862 TACGGATACT
221872 CGTTGCGATAGTCAGAATCG
1 CGTTGCGATAGTCAGAATCG
221892 CGTTGCGATAGTCAGAATCG
1 CGTTGCGATAGTCAGAATCG
221912 CGTTGCGAT
1 CGTTGCGAT
221921 TTATATGTTC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.22, C:0.20, G:0.31, T:0.27
Consensus pattern (20 bp):
CGTTGCGATAGTCAGAATCG
Found at i:221932 original size:20 final size:20
Alignment explanation
Indices: 221909--221961 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
221899 ATAGTCAGAA
*
221909 TCGCGTTGCGATTTATATGT
1 TCGCGTTGCGATTTATATAT
* *
221929 TCGCGTTACGATTTTTATAT
1 TCGCGTTGCGATTTATATAT
*
221949 TTGCGTTGCGATT
1 TCGCGTTGCGATT
221962 ATGAAAAATC
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.15, C:0.15, G:0.23, T:0.47
Consensus pattern (20 bp):
TCGCGTTGCGATTTATATAT
Found at i:221934 original size:121 final size:121
Alignment explanation
Indices: 221710--221942 Score: 267
Period size: 121 Copynumber: 1.9 Consensus size: 121
221700 TTAAAAATCG
* ** * *
221710 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTGTCGTTGCGATTTACGGATACGCATT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGGATACTCGTTGCGATTCACGAATACGCATT
* * * *
221775 GCGATTTACGTATTCTCGTTGCGATTTACAAATACGCGTTGCGATTTACGTATTCT
66 GCGATTCACGTAATCGCGTTGCGATTTACAAATACGCGTTACGATTTACGTATTCT
* *
221831 CGTTGCGATTTACGGATACGCGTTGTGATTTTACGGATACTCGTTGCGATAGTCA-GAAT-CGCG
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGGATACTCGTTGCGAT--TCACGAATACGCA
* ** *
221894 TTGCGATAGTCA-G-AATCGCGTTGCGATTTATATGTTCGCGTTACGATTT
64 TTGCGAT--TCACGTAATCGCGTTGCGATTTACAAATACGCGTTACGATTT
221943 TTATATTTGC
Statistics
Matches: 93, Mismatches: 15, Indels: 8
0.80 0.13 0.07
Matches are distributed among these distances:
121 85 0.91
122 4 0.04
123 4 0.04
ACGTcount: A:0.20, C:0.18, G:0.25, T:0.36
Consensus pattern (121 bp):
CGTTGCGATTTACGGATACGCGTTGCGATTTTACGGATACTCGTTGCGATTCACGAATACGCATT
GCGATTCACGTAATCGCGTTGCGATTTACAAATACGCGTTACGATTTACGTATTCT
Found at i:222060 original size:20 final size:19
Alignment explanation
Indices: 222011--222064 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 19
222001 ATTCTTCATA
222011 ATCGCGTTGCGATTCTGGG
1 ATCGCGTTGCGATTCTGGG
* **
222030 AACTGATTTGCGATTCTGGAG
1 ATC-GCGTTGCGATTCTGG-G
222051 ATCGCGTTGCGATT
1 ATCGCGTTGCGATT
222065 TTTATTTCGC
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
19 2 0.07
20 22 0.81
21 3 0.11
ACGTcount: A:0.17, C:0.19, G:0.31, T:0.33
Consensus pattern (19 bp):
ATCGCGTTGCGATTCTGGG
Found at i:222392 original size:60 final size:61
Alignment explanation
Indices: 222245--222398 Score: 188
Period size: 60 Copynumber: 2.6 Consensus size: 61
222235 GCATCACGTG
* * * * *
222245 TCCCTAAACTATAACCTTTATTTTAAAATAGT-CTATAAACTTTTAAATATTTTAATTTCA
1 TCCCTAAACTATGACCTTTATTCTAAATTAGTCCTATAAACTTTTAAACATTTCAATTTCA
* *
222305 TCCTTAAACTATGA-CTATTATTCTAAATTAGTCCT-TAAACTTTTTAACATTTCAATTTCA
1 TCCCTAAACTATGACCT-TTATTCTAAATTAGTCCTATAAACTTTTAAACATTTCAATTTCA
* * *
222365 TCCCCAAACTATGACCTTCATTCTAAATTGGTCC
1 TCCCTAAACTATGACCTTTATTCTAAATTAGTCC
222399 CCAGACTATT
Statistics
Matches: 80, Mismatches: 11, Indels: 6
0.82 0.11 0.06
Matches are distributed among these distances:
59 2 0.03
60 74 0.93
61 4 0.05
ACGTcount: A:0.34, C:0.20, G:0.04, T:0.42
Consensus pattern (61 bp):
TCCCTAAACTATGACCTTTATTCTAAATTAGTCCTATAAACTTTTAAACATTTCAATTTCA
Found at i:222433 original size:60 final size:60
Alignment explanation
Indices: 222281--222436 Score: 154
Period size: 60 Copynumber: 2.6 Consensus size: 60
222271 AATAGTCTAT
* * * ** * **
222281 AAACTTTTAAATATTTTAATTTCATCCTTAAACTATGACTATTATTCTAAATTAGTCCTT
1 AAACTTTTGAACATTTCAATTTCATCCCCAAACTATGACTATCATTCTAAATTAGTCCCC
* *
222341 AAACTTTTTAACATTTCAATTTCATCCCCAAACTATGACCT-TCATTCTAAATTGGTCCCC
1 AAACTTTTGAACATTTCAATTTCATCCCCAAACTATGA-CTATCATTCTAAATTAGTCCCC
* * * *
222401 AGACTATTTGAACATTTCTATTTTAT-CTCAAACTAT
1 AAACT-TTTGAACATTTCAATTTCATCCCCAAACTAT
222437 ACATATACGC
Statistics
Matches: 80, Mismatches: 14, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
60 61 0.76
61 19 0.24
ACGTcount: A:0.33, C:0.21, G:0.04, T:0.42
Consensus pattern (60 bp):
AAACTTTTGAACATTTCAATTTCATCCCCAAACTATGACTATCATTCTAAATTAGTCCCC
Found at i:222578 original size:60 final size:60
Alignment explanation
Indices: 222498--222659 Score: 218
Period size: 60 Copynumber: 2.7 Consensus size: 60
222488 ATTAAAATGA
* *
222498 TCAAAATTTTAAGGAATAATTTGAAATGAGAGTTATAGTTTGAGGATAAAATT-ATAATAT
1 TCAAAAGTTTAAGGAATAATTTAAAATGAGAGTTATAGTTTGAGGATAAAATTGA-AATAT
* * * * * *
222558 TCAAAAGTTTAGGGACTAATTTAAAATAAGAATTGTAGTTTGAGGATGAAATTGAAATAT
1 TCAAAAGTTTAAGGAATAATTTAAAATGAGAGTTATAGTTTGAGGATAAAATTGAAATAT
* *
222618 TCAAAAGTTTAAGGATTAATTTAAAATGAAAGTTATAGTTTG
1 TCAAAAGTTTAAGGAATAATTTAAAATGAGAGTTATAGTTTG
222660 GGGACATATG
Statistics
Matches: 87, Mismatches: 14, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
60 86 0.99
61 1 0.01
ACGTcount: A:0.44, C:0.02, G:0.18, T:0.36
Consensus pattern (60 bp):
TCAAAAGTTTAAGGAATAATTTAAAATGAGAGTTATAGTTTGAGGATAAAATTGAAATAT
Found at i:222644 original size:29 final size:29
Alignment explanation
Indices: 222534--222644 Score: 71
Period size: 29 Copynumber: 3.8 Consensus size: 29
222524 TGAGAGTTAT
* * *
222534 AGTTTGAGGATAAAATTATAATATTCAAA
1 AGTTTAAGGATTAAATTAAAATATTCAAA
* * * ** *
222563 AGTTTAGGGACTAATTTAAAATA-AGAATTGT
1 AGTTTAAGGATTAAATTAAAATATTCAA---A
* * *
222594 AGTTTGAGGATGAAATTGAAATATTCAAA
1 AGTTTAAGGATTAAATTAAAATATTCAAA
*
222623 AGTTTAAGGATTAATTTAAAAT
1 AGTTTAAGGATTAAATTAAAAT
222645 GAAAGTTATA
Statistics
Matches: 56, Mismatches: 22, Indels: 8
0.65 0.26 0.09
Matches are distributed among these distances:
28 2 0.04
29 35 0.62
31 17 0.30
32 2 0.04
ACGTcount: A:0.45, C:0.03, G:0.17, T:0.35
Consensus pattern (29 bp):
AGTTTAAGGATTAAATTAAAATATTCAAA
Found at i:224958 original size:18 final size:18
Alignment explanation
Indices: 224931--224968 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
224921 GCCTCGTGAA
224931 AAACGATCCCTGCTAGAG
1 AAACGATCCCTGCTAGAG
*
224949 AAACGTTCCCTGCTAGAG
1 AAACGATCCCTGCTAGAG
224967 AA
1 AA
224969 TTTGCCGTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.34, C:0.26, G:0.21, T:0.18
Consensus pattern (18 bp):
AAACGATCCCTGCTAGAG
Found at i:230205 original size:58 final size:59
Alignment explanation
Indices: 230143--230254 Score: 147
Period size: 60 Copynumber: 1.9 Consensus size: 59
230133 GGAAGATTAA
* * *
230143 AAAGTTTGA-GGATCAATTTAGAAT-GAGTCATAGTTTGGGGATGAAATTAAAAATATGC
1 AAAGTTTAAGGGAT-AAATTAGAATAGAGTCATAGTTTGAGGATGAAATTAAAAATATGC
* *
230201 AAAGTTTAAGGGATAAATTAGAGTGAGAGTCATAGTTTGAGGATTAAATTAAAA
1 AAAGTTTAAGGGATAAATTAGAAT-AGAGTCATAGTTTGAGGATGAAATTAAAA
230255 TATTTAAAAG
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
58 16 0.35
59 4 0.09
60 26 0.57
ACGTcount: A:0.42, C:0.04, G:0.24, T:0.30
Consensus pattern (59 bp):
AAAGTTTAAGGGATAAATTAGAATAGAGTCATAGTTTGAGGATGAAATTAAAAATATGC
Found at i:231095 original size:2 final size:2
Alignment explanation
Indices: 231088--231135 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
231078 TCTAATTAGA
231088 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
231130 AT AT AT
1 AT AT AT
231136 GCTTGCGTGC
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:243841 original size:21 final size:21
Alignment explanation
Indices: 243815--243859 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
243805 GATTTCTAGG
* *
243815 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
243836 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
243857 CAA
1 CAA
243860 ACGAACAAGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:245603 original size:23 final size:22
Alignment explanation
Indices: 245544--245610 Score: 116
Period size: 22 Copynumber: 3.0 Consensus size: 22
245534 TATGGACATC
*
245544 ATTCTACGGGCACTACGGTGCA
1 ATTCTACGGGCACTTCGGTGCA
245566 ATTCTACGGGCACTTCGGTGCA
1 ATTCTACGGGCACTTCGGTGCA
245588 ATTCTACGGGGCACTTCGGTGCA
1 ATTCTAC-GGGCACTTCGGTGCA
245611 TTTATACGAG
Statistics
Matches: 43, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
22 28 0.65
23 15 0.35
ACGTcount: A:0.19, C:0.27, G:0.28, T:0.25
Consensus pattern (22 bp):
ATTCTACGGGCACTTCGGTGCA
Found at i:248766 original size:21 final size:21
Alignment explanation
Indices: 248740--248784 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
248730 GATTTCTGGG
* *
248740 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
248761 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
248782 CAA
1 CAA
248785 ACGAACAAGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:249175 original size:26 final size:24
Alignment explanation
Indices: 249120--249178 Score: 68
Period size: 24 Copynumber: 2.5 Consensus size: 24
249110 CTATGTTAGA
*
249120 ATGCATGAATATATGATTATATGT
1 ATGCATGAATACATGATTATATGT
*
249144 AT--ATGAATGACATGAATTGTATGT
1 ATGCATGAAT-ACATG-ATTATATGT
249168 ATGCATGAATA
1 ATGCATGAATA
249179 TATGTGTTGA
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
22 6 0.21
23 4 0.14
24 12 0.41
25 1 0.03
26 6 0.21
ACGTcount: A:0.39, C:0.05, G:0.19, T:0.37
Consensus pattern (24 bp):
ATGCATGAATACATGATTATATGT
Found at i:250532 original size:23 final size:22
Alignment explanation
Indices: 250473--250539 Score: 116
Period size: 22 Copynumber: 3.0 Consensus size: 22
250463 TATGGACATC
*
250473 ATTCTACGGGCACTACGGTGCA
1 ATTCTACGGGCACTTCGGTGCA
250495 ATTCTACGGGCACTTCGGTGCA
1 ATTCTACGGGCACTTCGGTGCA
250517 ATTCTACGGGGCACTTCGGTGCA
1 ATTCTAC-GGGCACTTCGGTGCA
250540 TTTATACGAG
Statistics
Matches: 43, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
22 28 0.65
23 15 0.35
ACGTcount: A:0.19, C:0.27, G:0.28, T:0.25
Consensus pattern (22 bp):
ATTCTACGGGCACTTCGGTGCA
Found at i:251491 original size:29 final size:30
Alignment explanation
Indices: 251422--251491 Score: 106
Period size: 29 Copynumber: 2.4 Consensus size: 30
251412 TTCAGTTCAG
*
251422 TTAATCGAACCAAAATTTATTTGAAAATTA
1 TTAATCGAACCAAAATTAATTTGAAAATTA
*
251452 TTAATCAAACC-AAATTAATTTGAAAATTA
1 TTAATCGAACCAAAATTAATTTGAAAATTA
*
251481 TTAACCGAACC
1 TTAATCGAACC
251492 GAACTAACCG
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
29 26 0.72
30 10 0.28
ACGTcount: A:0.47, C:0.14, G:0.06, T:0.33
Consensus pattern (30 bp):
TTAATCGAACCAAAATTAATTTGAAAATTA
Found at i:251565 original size:137 final size:136
Alignment explanation
Indices: 251397--251896 Score: 614
Period size: 137 Copynumber: 3.7 Consensus size: 136
251387 GGTTAAAGAA
* ** * * *
251397 AAAATATTCAGTTAATTCAGTTCAGTTAATCGAACCAAAATTTATTTGAAAATTATTAATCAAAC
1 AAAA-ATTCGGTTAATTTGGTTCGGTTAATCGAACCAAAATTTATTTGAAAATTATTAACCGAAC
* * *
251462 CAAATTAATTTGAAAATTATTAACCGAACCGAACTAACCGAATATTTTTGAAA-ATTAACTAAAT
65 CAAATTAATTTGAAAATTATTAACCGAACCGAATTAACAG-AT-TTTTT-AAATATTAACTGAAT
251526 TAATCGAAGC
127 TAATCGAAGC
*
251536 AAAAA-TCGGTTAATTTGGTTTGGTTAATCGAACCAAAATTTATTTGAAAATTATTAACCGAACC
1 AAAAATTCGGTTAATTTGGTTCGGTTAATCGAACCAAAATTTATTTGAAAATTATTAACCGAACC
* * *
251600 TAATTAATTTGAAAATTATTAACCGAACCGAATTAACTGATTTTTTTAAACTATTAACCGAATTA
66 AAATTAATTTGAAAATTATTAACCGAACCGAATTAACAGA-TTTTTTAAA-TATTAACTGAATTA
*
251665 AACGAAGC
129 ATCGAAGC
* * *
251673 AAAAATTCGGTTAATTCGGTTCGATTAATCGAACCAAAATTTATTTGAAAATTATTAACTGAACC
1 AAAAATTCGGTTAATTTGGTTCGGTTAATCGAACCAAAATTTATTTGAAAATTATTAACCGAACC
* * *
251738 AAATTATTTTGAAAATTATTAACTGAACCGAATTAACAGATTTTTTAAATTATTAATTGAATTAA
66 AAATTAATTTGAAAATTATTAACCGAACCGAATTAACAGATTTTTTAAA-TATTAACTGAATTAA
*
251803 TCGAAGA
130 TCGAAGC
* **
251810 AAAAATTTGGTTAACCT-GTTCGG-T--T--------AATTTATTTGAAAATTATTAACCGAACC
1 AAAAATTCGGTTAATTTGGTTCGGTTAATCGAACCAAAATTTATTTGAAAATTATTAACCGAACC
*
251863 AAATTAATTTGAAAATTATTAACCAAACCGAATT
66 AAATTAATTTGAAAATTATTAACCGAACCGAATT
251897 TTTTCTTTAA
Statistics
Matches: 322, Mismatches: 35, Indels: 22
0.85 0.09 0.06
Matches are distributed among these distances:
125 58 0.18
133 1 0.00
135 4 0.01
136 11 0.03
137 152 0.47
138 92 0.29
139 4 0.01
ACGTcount: A:0.43, C:0.12, G:0.10, T:0.35
Consensus pattern (136 bp):
AAAAATTCGGTTAATTTGGTTCGGTTAATCGAACCAAAATTTATTTGAAAATTATTAACCGAACC
AAATTAATTTGAAAATTATTAACCGAACCGAATTAACAGATTTTTTAAATATTAACTGAATTAAT
CGAAGC
Found at i:251598 original size:30 final size:29
Alignment explanation
Indices: 251559--251635 Score: 109
Period size: 29 Copynumber: 2.6 Consensus size: 29
251549 TTTGGTTTGG
* *
251559 TTAATCGAACCAAAATTTATTTGAAAATTA
1 TTAACCGAACC-AAATTAATTTGAAAATTA
*
251589 TTAACCGAACCTAATTAATTTGAAAATTA
1 TTAACCGAACCAAATTAATTTGAAAATTA
*
251618 TTAACCGAACCGAATTAA
1 TTAACCGAACCAAATTAA
251636 CTGATTTTTT
Statistics
Matches: 43, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
29 33 0.77
30 10 0.23
ACGTcount: A:0.45, C:0.14, G:0.08, T:0.32
Consensus pattern (29 bp):
TTAACCGAACCAAATTAATTTGAAAATTA
Found at i:251604 original size:29 final size:29
Alignment explanation
Indices: 251572--251635 Score: 110
Period size: 29 Copynumber: 2.2 Consensus size: 29
251562 ATCGAACCAA
* *
251572 AATTTATTTGAAAATTATTAACCGAACCT
1 AATTAATTTGAAAATTATTAACCGAACCG
251601 AATTAATTTGAAAATTATTAACCGAACCG
1 AATTAATTTGAAAATTATTAACCGAACCG
251630 AATTAA
1 AATTAA
251636 CTGATTTTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.45, C:0.12, G:0.08, T:0.34
Consensus pattern (29 bp):
AATTAATTTGAAAATTATTAACCGAACCG
Found at i:251743 original size:17 final size:17
Alignment explanation
Indices: 251721--251772 Score: 51
Period size: 17 Copynumber: 3.4 Consensus size: 17
251711 ATTTATTTGA
251721 AAATTATTAACTGAACC
1 AAATTATTAACTGAACC
*
251738 AAATTATT--TTG-A--
1 AAATTATTAACTGAACC
251750 AAATTATTAACTGAACC
1 AAATTATTAACTGAACC
*
251767 GAATTA
1 AAATTA
251773 ACAGATTTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 10
0.68 0.08 0.25
Matches are distributed among these distances:
12 8 0.30
14 3 0.11
15 3 0.11
17 13 0.48
ACGTcount: A:0.46, C:0.12, G:0.08, T:0.35
Consensus pattern (17 bp):
AAATTATTAACTGAACC
Found at i:251751 original size:29 final size:30
Alignment explanation
Indices: 251703--251772 Score: 108
Period size: 29 Copynumber: 2.4 Consensus size: 30
251693 TCGATTAATC
251703 GAACCAAAATT-TATTTGAAAATTATTAACT
1 GAACC-AAATTATATTTGAAAATTATTAACT
251733 GAACCAAATTAT-TTTGAAAATTATTAACT
1 GAACCAAATTATATTTGAAAATTATTAACT
*
251762 GAACCGAATTA
1 GAACCAAATTA
251773 ACAGATTTTT
Statistics
Matches: 38, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
29 32 0.84
30 6 0.16
ACGTcount: A:0.46, C:0.11, G:0.09, T:0.34
Consensus pattern (30 bp):
GAACCAAATTATATTTGAAAATTATTAACT
Found at i:251872 original size:29 final size:29
Alignment explanation
Indices: 251835--251950 Score: 117
Period size: 29 Copynumber: 4.0 Consensus size: 29
251825 CTGTTCGGTT
251835 AATTTATTTGAAAATTATTAACCGAACCA
1 AATTTATTTGAAAATTATTAACCGAACCA
* * *
251864 AATTAATTTGAAAATTATTAACCAAACCG
1 AATTTATTTGAAAATTATTAACCGAACCA
*** *** *
251893 AATTT-TTTCTTTAACCGTTAATCGAACCAA
1 AATTTATTT-GAAAATTATTAACCGAACC-A
251923 AATTTATTTGAAAATTATTAACCGAACC
1 AATTTATTTGAAAATTATTAACCGAACC
251951 GAACAAATTT
Statistics
Matches: 64, Mismatches: 20, Indels: 5
0.72 0.22 0.06
Matches are distributed among these distances:
28 3 0.05
29 41 0.64
30 17 0.27
31 3 0.05
ACGTcount: A:0.42, C:0.16, G:0.07, T:0.35
Consensus pattern (29 bp):
AATTTATTTGAAAATTATTAACCGAACCA
Found at i:254677 original size:29 final size:30
Alignment explanation
Indices: 254610--254686 Score: 84
Period size: 30 Copynumber: 2.6 Consensus size: 30
254600 AAATTAACGG
* * *
254610 TCGGTGGTTTGATTGAATCAATTAAATAGT
1 TCGGTGGTCTGATTGATTAAATTAAATAGT
* *
254640 TGGGTGGTCTGATTGATTAAATTGAA-AGT
1 TCGGTGGTCTGATTGATTAAATTAAATAGT
**
254669 TCGGTGGTCACATTGATT
1 TCGGTGGTCTGATTGATT
254687 TTTGACCATA
Statistics
Matches: 39, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
29 18 0.46
30 21 0.54
ACGTcount: A:0.26, C:0.08, G:0.27, T:0.39
Consensus pattern (30 bp):
TCGGTGGTCTGATTGATTAAATTAAATAGT
Found at i:262860 original size:13 final size:12
Alignment explanation
Indices: 262837--262869 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
262827 TTGGTCATCC
262837 ATTTATTATTTA
1 ATTTATTATTTA
262849 ATTTATTTATTTA
1 ATTTA-TTATTTA
262862 A-TTATTAT
1 ATTTATTAT
262870 AAGTTTAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
11 4 0.20
12 8 0.40
13 8 0.40
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (12 bp):
ATTTATTATTTA
Found at i:265017 original size:2 final size:2
Alignment explanation
Indices: 265010--265050 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
265000 ATGCATATCA
265010 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
265051 GTTGTACCAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:272710 original size:6 final size:6
Alignment explanation
Indices: 272699--272749 Score: 102
Period size: 6 Copynumber: 8.5 Consensus size: 6
272689 TGGATAAATG
272699 CATCTA CATCTA CATCTA CATCTA CATCTA CATCTA CATCTA CATCTA
1 CATCTA CATCTA CATCTA CATCTA CATCTA CATCTA CATCTA CATCTA
272747 CAT
1 CAT
272750 ATTGTTTCTT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 45 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (6 bp):
CATCTA
Found at i:283696 original size:32 final size:32
Alignment explanation
Indices: 283660--283723 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
283650 TTTGTGGGTC
283660 TTAAACTCTCCCTTGAAGGGCATAGAGTTTAG
1 TTAAACTCTCCCTTGAAGGGCATAGAGTTTAG
283692 TTAAACTCTCCCTTGAAGGGCATAGAGTTTAG
1 TTAAACTCTCCCTTGAAGGGCATAGAGTTTAG
283724 ACCTTGCCTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.28, C:0.19, G:0.22, T:0.31
Consensus pattern (32 bp):
TTAAACTCTCCCTTGAAGGGCATAGAGTTTAG
Found at i:286157 original size:24 final size:24
Alignment explanation
Indices: 286130--286180 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
286120 CGGATTTAAC
* * *
286130 AAAAATAGTTACAGCAACGTCTAT
1 AAAAACAGTTACAACAACGGCTAT
*
286154 AAAAGCAGTTACAACAACGGCTAT
1 AAAAACAGTTACAACAACGGCTAT
286178 AAA
1 AAA
286181 CTGATATATG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.49, C:0.18, G:0.14, T:0.20
Consensus pattern (24 bp):
AAAAACAGTTACAACAACGGCTAT
Found at i:287956 original size:24 final size:24
Alignment explanation
Indices: 287924--287983 Score: 111
Period size: 24 Copynumber: 2.5 Consensus size: 24
287914 AGGTGAAGAT
287924 GGTGGTGATGATGGTGAAGGTGGA
1 GGTGGTGATGATGGTGAAGGTGGA
287948 GGTGGTGATGATGGTGAAGGTGGA
1 GGTGGTGATGATGGTGAAGGTGGA
*
287972 GGTGGTAATGAT
1 GGTGGTGATGAT
287984 AGAGGTGGAG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 35 1.00
ACGTcount: A:0.22, C:0.00, G:0.52, T:0.27
Consensus pattern (24 bp):
GGTGGTGATGATGGTGAAGGTGGA
Found at i:288006 original size:24 final size:24
Alignment explanation
Indices: 287924--288006 Score: 84
Period size: 24 Copynumber: 3.6 Consensus size: 24
287914 AGGTGAAGAT
* *
287924 GGTGGTGATGATGGTGAAGGTGGA
1 GGTGGTGAAGATGATGAAGGTGGA
* *
287948 GGTGGTGATGATGGTGAAGGTGGA
1 GGTGGTGAAGATGATGAAGGTGGA
287972 GGTGGT--A-ATGAT-AGAGGTGGA
1 GGTGGTGAAGATGATGA-AGGTGGA
*
287993 GATGGTGAAGATGA
1 GGTGGTGAAGATGA
288007 AGATGAAGCA
Statistics
Matches: 52, Mismatches: 3, Indels: 8
0.83 0.05 0.13
Matches are distributed among these distances:
20 1 0.02
21 16 0.31
23 1 0.02
24 34 0.65
ACGTcount: A:0.25, C:0.00, G:0.51, T:0.24
Consensus pattern (24 bp):
GGTGGTGAAGATGATGAAGGTGGA
Found at i:289923 original size:24 final size:24
Alignment explanation
Indices: 289887--289939 Score: 88
Period size: 24 Copynumber: 2.2 Consensus size: 24
289877 TGAGAGACTA
* *
289887 CAGAAAATTGAGGAATTTGAGGTG
1 CAGAAAATAGAGGAAATTGAGGTG
289911 CAGAAAATAGAGGAAATTGAGGTG
1 CAGAAAATAGAGGAAATTGAGGTG
289935 CAGAA
1 CAGAA
289940 CATGTATAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.43, C:0.06, G:0.32, T:0.19
Consensus pattern (24 bp):
CAGAAAATAGAGGAAATTGAGGTG
Found at i:291730 original size:23 final size:23
Alignment explanation
Indices: 291702--291745 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
291692 TAACAAAAAT
*
291702 AGTTACAGCAACGGCTATAAAGC
1 AGTTACAACAACGGCTATAAAGC
*
291725 AGTTACAACAATGGCTATAAA
1 AGTTACAACAACGGCTATAAA
291746 ACTGATATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.43, C:0.18, G:0.18, T:0.20
Consensus pattern (23 bp):
AGTTACAACAACGGCTATAAAGC
Found at i:302106 original size:26 final size:25
Alignment explanation
Indices: 302051--302100 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
302041 TTTTGAGTGT
302051 ATTATTTGAATATTTTTTTCAACAA
1 ATTATTTGAATATTTTTTTCAACAA
302076 ATTATTTGAATATTTTTTTCAACAA
1 ATTATTTGAATATTTTTTTCAACAA
302101 TGTTATATCC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.36, C:0.08, G:0.04, T:0.52
Consensus pattern (25 bp):
ATTATTTGAATATTTTTTTCAACAA
Found at i:303203 original size:20 final size:20
Alignment explanation
Indices: 303178--303363 Score: 195
Period size: 20 Copynumber: 9.5 Consensus size: 20
303168 GATTTTCCAT
* *
303178 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGAATACGTA
*
303198 AATCGCAATGCG-A-A--TA
1 AATCGCAACGCGAATACGTA
*
303214 AATCGCAACGAGAATACGTA
1 AATCGCAACGCGAATACGTA
*
303234 AATCGCAACGCGTAT-CTGTA
1 AATCGCAACGCGAATAC-GTA
*
303254 AATCGCAACGAGAATACGTA
1 AATCGCAACGCGAATACGTA
* * *
303274 AATCGCAATGCAAATCCGTA
1 AATCGCAACGCGAATACGTA
* *
303294 AATCGCAATGCAAATACGTA
1 AATCGCAACGCGAATACGTA
*
303314 AATCGCAATGCGAATACGTA
1 AATCGCAACGCGAATACGTA
*
303334 AATCGCAATGCGAAT-CTGTA
1 AATCGCAACGCGAATAC-GTA
303354 AATCGCAACG
1 AATCGCAACG
303364 AGATTCTGAC
Statistics
Matches: 144, Mismatches: 15, Indels: 14
0.83 0.09 0.08
Matches are distributed among these distances:
16 11 0.08
17 1 0.01
18 2 0.01
19 3 0.02
20 126 0.88
21 1 0.01
ACGTcount: A:0.41, C:0.22, G:0.19, T:0.19
Consensus pattern (20 bp):
AATCGCAACGCGAATACGTA
Found at i:304243 original size:24 final size:24
Alignment explanation
Indices: 304216--304269 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
304206 GTATTCGAAA
304216 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
304240 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
304264 TTTGAT
1 TTTGAT
304270 GATTTTTCAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:305576 original size:19 final size:19
Alignment explanation
Indices: 305512--305601 Score: 99
Period size: 20 Copynumber: 4.6 Consensus size: 19
305502 TCTTTTGGTT
* *
305512 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCACAACGC
*
305531 GAGAATGAAAATCGCAACGC
1 GA-AATGAAAATCACAACGC
**
305551 GGAAATGACTATCACAACGC
1 -GAAATGAAAATCACAACGC
*
305571 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCACAACGC
*
305590 GAAATTAAAATC
1 GAAATGAAAATC
305602 GCAATGAGAG
Statistics
Matches: 61, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
19 29 0.48
20 30 0.49
21 2 0.03
ACGTcount: A:0.48, C:0.19, G:0.20, T:0.13
Consensus pattern (19 bp):
GAAATGAAAATCACAACGC
Found at i:305602 original size:19 final size:19
Alignment explanation
Indices: 305512--305643 Score: 139
Period size: 19 Copynumber: 7.1 Consensus size: 19
305502 TCTTTTGGTT
*
305512 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
305531 GAGAATGAAAATCGCAACGC
1 GA-AATGAAAATCGCAACGC
** *
305551 GGAAATGACTATCACAACGC
1 -GAAATGAAAATCGCAACGC
305571 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
* *
305590 GAAATTAAAATCGCAA--T
1 GAAATGAAAATCGCAACGC
*
305607 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
305623 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
305642 GA
1 GA
305644 TTTTGGTTTC
Statistics
Matches: 92, Mismatches: 14, Indels: 14
0.77 0.12 0.12
Matches are distributed among these distances:
14 9 0.10
15 1 0.01
16 1 0.01
17 1 0.01
18 1 0.01
19 47 0.51
20 30 0.33
21 2 0.02
ACGTcount: A:0.46, C:0.19, G:0.22, T:0.13
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:305687 original size:33 final size:34
Alignment explanation
Indices: 305650--305731 Score: 121
Period size: 33 Copynumber: 2.4 Consensus size: 34
305640 GCGATTTTGG
**
305650 TTTCGTGTTGCGATTCTCTCGTTGCAATTTTCA-
1 TTTCGTGTTGCGATTCTCTCGTTGCAATAGTCAT
* *
305683 TTTCGCGTTGCGATTCTCTCGTTGCGATAGTCAT
1 TTTCGTGTTGCGATTCTCTCGTTGCAATAGTCAT
305717 TTTCGTGTTGCGATT
1 TTTCGTGTTGCGATT
305732 TTCATTTTCA
Statistics
Matches: 43, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
33 29 0.67
34 14 0.33
ACGTcount: A:0.11, C:0.21, G:0.22, T:0.46
Consensus pattern (34 bp):
TTTCGTGTTGCGATTCTCTCGTTGCAATAGTCAT
Found at i:305728 original size:20 final size:20
Alignment explanation
Indices: 305703--305747 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
305693 CGATTCTCTC
*
305703 GTTGCGATAGTCATTTTCGT
1 GTTGCGATAGTCATTTTCAT
**
305723 GTTGCGATTTTCATTTTCAT
1 GTTGCGATAGTCATTTTCAT
305743 GTTGC
1 GTTGC
305748 ATTTTAAGTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.13, C:0.16, G:0.22, T:0.49
Consensus pattern (20 bp):
GTTGCGATAGTCATTTTCAT
Found at i:306406 original size:40 final size:40
Alignment explanation
Indices: 306316--306522 Score: 263
Period size: 40 Copynumber: 5.1 Consensus size: 40
306306 TTAAAAATTG
* *
306316 CGTTGCGATTTACGGATATGCGTTGCGATTTTACGTATT-T
1 CGTTGCGATTTACGGATACGCGTTGC-AATTTACGTATTCT
* * *
306356 GCATTTCGATTTACGGATACGCATTGCAATTTACGTATTCT
1 -CGTTGCGATTTACGGATACGCGTTGCAATTTACGTATTCT
* * *
306397 CGTTGCGATTTACAGATACGCGTTACGATTTACGTATTCT
1 CGTTGCGATTTACGGATACGCGTTGCAATTTACGTATTCT
* *
306437 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTAT
1 CGTTGCGATTTACGGATACGCGTTGC-AATTTACGTATTCT
* * *
306478 CGTTGCGATTTACGGATACGCGTTGCGATTTACGGATACT
1 CGTTGCGATTTACGGATACGCGTTGCAATTTACGTATTCT
306518 CGTTG
1 CGTTG
306523 TGATAGTCAG
Statistics
Matches: 143, Mismatches: 21, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
40 83 0.58
41 60 0.42
ACGTcount: A:0.20, C:0.18, G:0.23, T:0.38
Consensus pattern (40 bp):
CGTTGCGATTTACGGATACGCGTTGCAATTTACGTATTCT
Found at i:306516 original size:20 final size:20
Alignment explanation
Indices: 306315--306522 Score: 211
Period size: 20 Copynumber: 10.3 Consensus size: 20
306305 TTTAAAAATT
*
306315 GCGTTGCGATTTACGGATAT
1 GCGTTGCGATTTACGGATAC
* **
306335 GCGTTGCGATTTTACGTATTT
1 GCGTTGCGA-TTTACGGATAC
* *
306356 GCATTTCGATTTACGGATAC
1 GCGTTGCGATTTACGGATAC
* * * *
306376 GCATTGCAATTTACGTATTC
1 GCGTTGCGATTTACGGATAC
* *
306396 TCGTTGCGATTTACAGATAC
1 GCGTTGCGATTTACGGATAC
* * *
306416 GCGTTACGATTTACGTATTC
1 GCGTTGCGATTTACGGATAC
*
306436 TCGTTGCGATTTACGGATAC
1 GCGTTGCGATTTACGGATAC
*
306456 GCGTTGCGATTTTACGTATTA-
1 GCGTTGCGA-TTTACGGA-TAC
*
306477 TCGTTGCGATTTACGGATAC
1 GCGTTGCGATTTACGGATAC
306497 GCGTTGCGATTTACGGATAC
1 GCGTTGCGATTTACGGATAC
*
306517 TCGTTG
1 GCGTTG
306523 TGATAGTCAG
Statistics
Matches: 152, Mismatches: 32, Indels: 8
0.79 0.17 0.04
Matches are distributed among these distances:
19 2 0.01
20 117 0.77
21 31 0.20
22 2 0.01
ACGTcount: A:0.20, C:0.18, G:0.24, T:0.38
Consensus pattern (20 bp):
GCGTTGCGATTTACGGATAC
Found at i:306540 original size:81 final size:81
Alignment explanation
Indices: 306316--306548 Score: 231
Period size: 81 Copynumber: 2.9 Consensus size: 81
306306 TTAAAAATTG
* * * * * * * * * *
306316 CGTTGCGATTTACGGATATGCGTTGCGATTTTACGTAT-TTGCATTTCGATTTACGGATACGCAT
1 CGTTGCGATTTACAGATACGCGTTACGA-TTTACGGATACT-CGTTGCGATTCACGAATACGCGT
* *
306380 TGC-AATTTACGTATTCT
64 TGCGATTTTACGTATTAT
* * * *
306397 CGTTGCGATTTACAGATACGCGTTACGATTTACGTATTCTCGTTGCGATTTACGGATACGCGTTG
1 CGTTGCGATTTACAGATACGCGTTACGATTTACGGATACTCGTTGCGATTCACGAATACGCGTTG
306462 CGATTTTACGTATTAT
66 CGATTTTACGTATTAT
* * *
306478 CGTTGCGATTTACGGATACGCGTTGCGATTTACGGATACTCGTTGTGATAGTCA-GAAT-CGCGT
1 CGTTGCGATTTACAGATACGCGTTACGATTTACGGATACTCGTTGCGAT--TCACGAATACGCGT
306541 TGCGATTT
64 TGCGATTT
306549 ATATGTTCGC
Statistics
Matches: 132, Mismatches: 16, Indels: 8
0.85 0.10 0.05
Matches are distributed among these distances:
80 32 0.24
81 95 0.72
82 3 0.02
83 2 0.02
ACGTcount: A:0.21, C:0.18, G:0.24, T:0.38
Consensus pattern (81 bp):
CGTTGCGATTTACAGATACGCGTTACGATTTACGGATACTCGTTGCGATTCACGAATACGCGTTG
CGATTTTACGTATTAT
Found at i:306540 original size:121 final size:121
Alignment explanation
Indices: 306315--306587 Score: 336
Period size: 121 Copynumber: 2.3 Consensus size: 121
306305 TTTAAAAATT
* *
306315 GCGTTGCGATTTACGGATATGCGTTGCGATTTTACGTATTTGCATTTCGATTTACGGATACGCAT
1 GCGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTTGCATTGCGATTTACGGATACGCAT
* * * *
306380 TGCAATTTACGTATTCTCGTTGCGATTTACAGATACGCGTTACGATTTACGTATTC
66 TGCAATTTACGGATACTCGTTGCGATGTACAGATACGCGTTACGATTTACATATTC
* * *
306436 TCGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTAT-CGTTGCGATTTACGGATACGCG
1 GCGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATT-TGCATTGCGATTTACGGATACGCA
* * * * *
306500 TTGCGATTTACGGATACTCGTTGTGATAGT-CAGA-ATCGCGTTGCGATTTATATGTTC
65 TTGCAATTTACGGATACTCGTTGCGAT-GTACAGATA-CGCGTTACGATTTACATATTC
* ** *
306557 GCGTTGCGATTTTCATATTCGCGTTGCGATT
1 GCGTTGCGATTTACGGATACGCGTTGCGATT
306588 ATGGAAAATC
Statistics
Matches: 130, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
120 1 0.01
121 127 0.98
122 2 0.02
ACGTcount: A:0.20, C:0.18, G:0.24, T:0.38
Consensus pattern (121 bp):
GCGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTTGCATTGCGATTTACGGATACGCAT
TGCAATTTACGGATACTCGTTGCGATGTACAGATACGCGTTACGATTTACATATTC
Found at i:306558 original size:20 final size:20
Alignment explanation
Indices: 306535--306587 Score: 81
Period size: 20 Copynumber: 2.6 Consensus size: 20
306525 ATAGTCAGAA
*
306535 TCGCGTTGCGATTTAT-ATGT
1 TCGCGTTGCGATTT-TCATAT
306555 TCGCGTTGCGATTTTCATAT
1 TCGCGTTGCGATTTTCATAT
306575 TCGCGTTGCGATT
1 TCGCGTTGCGATT
306588 ATGGAAAATC
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 1 0.03
20 30 0.97
ACGTcount: A:0.13, C:0.19, G:0.25, T:0.43
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCATAT
Found at i:308347 original size:15 final size:15
Alignment explanation
Indices: 308323--308378 Score: 78
Period size: 15 Copynumber: 3.8 Consensus size: 15
308313 GTATTACTAA
*
308323 ATTAATTTATAAAAT
1 ATTAAATTATAAAAT
*
308338 ATTAAATTATAGAAT
1 ATTAAATTATAAAAT
*
308353 ATTAAATTATAGAAT
1 ATTAAATTATAAAAT
308368 ATTAAA-TATAA
1 ATTAAATTATAA
308379 TTATAAATTA
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
14 4 0.11
15 34 0.89
ACGTcount: A:0.55, C:0.00, G:0.04, T:0.41
Consensus pattern (15 bp):
ATTAAATTATAAAAT
Found at i:308856 original size:60 final size:61
Alignment explanation
Indices: 308752--308873 Score: 165
Period size: 60 Copynumber: 2.0 Consensus size: 61
308742 TTTAATTTAA
* * *
308752 TAAAATTTTCATCCAATCGAATGGTGCCACATGTCACCAATTGAATGGATAGAAAATAAAT
1 TAAAATTTTCATCCAATCAAATGGTACCACATGTCACCAATTGAATGAATAGAAAATAAAT
* * * * *
308813 TAAATTTTTCATCCAATCAAATGGTATC-CGTTTCACCAATTGAATGAATATAAAATAAAT
1 TAAAATTTTCATCCAATCAAATGGTACCACATGTCACCAATTGAATGAATAGAAAATAAAT
308873 T
1 T
308874 GAATCAGTAA
Statistics
Matches: 53, Mismatches: 8, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
60 29 0.55
61 24 0.45
ACGTcount: A:0.41, C:0.16, G:0.11, T:0.32
Consensus pattern (61 bp):
TAAAATTTTCATCCAATCAAATGGTACCACATGTCACCAATTGAATGAATAGAAAATAAAT
Found at i:310297 original size:16 final size:16
Alignment explanation
Indices: 310276--310317 Score: 68
Period size: 16 Copynumber: 2.6 Consensus size: 16
310266 TTTTATAAAT
310276 GATGCTCATCATTAAC
1 GATGCTCATCATTAAC
310292 GATGCTCATCATTAAC
1 GATGCTCATCATTAAC
310308 -AGTGCTCATC
1 GA-TGCTCATC
310318 CGTGCTCGTC
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
15 1 0.04
16 24 0.96
ACGTcount: A:0.29, C:0.26, G:0.14, T:0.31
Consensus pattern (16 bp):
GATGCTCATCATTAAC
Found at i:320837 original size:50 final size:50
Alignment explanation
Indices: 320704--320850 Score: 203
Period size: 50 Copynumber: 3.0 Consensus size: 50
320694 GGTTCCACGC
* * * *
320704 ATCTCCAGAATATTCCATAAGATTCCACACTCTTCCACAAGC-TCT-TAC
1 ATCTCCAGAATATTCCAGAGGATTCCACACTCTTCCACAAGCTTCTAGAG
* *
320752 A-CTCCAGAA-ATTCTAGAGGATTTCACACTCTTCCACAAGCTTCTAGAG
1 ATCTCCAGAATATTCCAGAGGATTCCACACTCTTCCACAAGCTTCTAGAG
*
320800 ATCTCCATAATATTCCAGAGGATTCCACACTCTTCCACAAGCTTCTAGAG
1 ATCTCCAGAATATTCCAGAGGATTCCACACTCTTCCACAAGCTTCTAGAG
320850 A
1 A
320851 GTTCTACACT
Statistics
Matches: 86, Mismatches: 9, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
46 27 0.31
47 11 0.13
48 3 0.03
49 7 0.08
50 38 0.44
ACGTcount: A:0.31, C:0.30, G:0.11, T:0.28
Consensus pattern (50 bp):
ATCTCCAGAATATTCCAGAGGATTCCACACTCTTCCACAAGCTTCTAGAG
Found at i:327541 original size:187 final size:186
Alignment explanation
Indices: 327214--327601 Score: 726
Period size: 187 Copynumber: 2.1 Consensus size: 186
327204 TGGAAGCATC
*
327214 ATCATTGGTAA-AAATACAGCAGAAAGCAACTCCCATCCATTGACTATCATTCCGAATATTGAAA
1 ATCATTGGTAACTAATACAGCAGAAAGCAACTCCCATCCATTGACTATCATTCCGAATATTGAAA
327278 GGCAGTGGTATCCTGATTGAGGACTCAACTCTCTGATGGCTGAACCATTCGGATTTCACTTCCAG
66 GGCAGTGGTATCCTGATTGAGGACTCAAC-CTCTGATGGCTGAACCATTCGGATTTCACTTCCAG
327343 GAATAAAACGCTAAATATTTTTCTTGCGTTTGCAAATACCTGGAAAATTAAACAGCT
130 GAATAAAACGCTAAATATTTTTCTTGCGTTTGCAAATACCTGGAAAATTAAACAGCT
327400 ATCATTGGTAACTAATACAGCAGAAAGCAACTCCCATCCATTGACTATCATTCCGAATATTGAAA
1 ATCATTGGTAACTAATACAGCAGAAAGCAACTCCCATCCATTGACTATCATTCCGAATATTGAAA
327465 GGCAGTGGTATCCTGATTGAGGACTCAA-CTCTGATGGCTGAACCATTCTGGGATTTCACTTCCA
66 GGCAGTGGTATCCTGATTGAGGACTCAACCTCTGATGGCTGAACCATTC--GGATTTCACTTCCA
327529 GGAATAAAACGCTAAATATTTTTCTTGCGTTTGCAAATACCTGGAAAATTAAACAGCT
129 GGAATAAAACGCTAAATATTTTTCTTGCGTTTGCAAATACCTGGAAAATTAAACAGCT
327587 ATCATTGGTAACTAA
1 ATCATTGGTAACTAA
327602 AACCATAAAT
Statistics
Matches: 198, Mismatches: 1, Indels: 5
0.97 0.00 0.02
Matches are distributed among these distances:
185 20 0.10
186 11 0.06
187 167 0.84
ACGTcount: A:0.33, C:0.21, G:0.17, T:0.29
Consensus pattern (186 bp):
ATCATTGGTAACTAATACAGCAGAAAGCAACTCCCATCCATTGACTATCATTCCGAATATTGAAA
GGCAGTGGTATCCTGATTGAGGACTCAACCTCTGATGGCTGAACCATTCGGATTTCACTTCCAGG
AATAAAACGCTAAATATTTTTCTTGCGTTTGCAAATACCTGGAAAATTAAACAGCT
Found at i:331159 original size:32 final size:31
Alignment explanation
Indices: 331123--331199 Score: 82
Period size: 31 Copynumber: 2.5 Consensus size: 31
331113 CGGGGCCATG
* *
331123 GGGCCTACCTAAGAACACATCTTAGGGCCGCA
1 GGGCCTACCTAAGAA-ACATCTCAAGGCCGCA
** **
331155 GGGCCTACCCGAGAATGATCTCAAGGCCGCA
1 GGGCCTACCTAAGAAACATCTCAAGGCCGCA
*
331186 GAGCCTACCTAAGA
1 GGGCCTACCTAAGA
331200 GTCACATTAG
Statistics
Matches: 36, Mismatches: 9, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
31 23 0.64
32 13 0.36
ACGTcount: A:0.29, C:0.31, G:0.26, T:0.14
Consensus pattern (31 bp):
GGGCCTACCTAAGAAACATCTCAAGGCCGCA
Found at i:332902 original size:27 final size:28
Alignment explanation
Indices: 332864--332918 Score: 103
Period size: 27 Copynumber: 2.0 Consensus size: 28
332854 AAAGATAGGA
332864 TCCCAACAATCAAATCA-TAATTTATCG
1 TCCCAACAATCAAATCAGTAATTTATCG
332891 TCCCAACAATCAAATCAGTAATTTATCG
1 TCCCAACAATCAAATCAGTAATTTATCG
332919 ATTTAAAAAC
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
27 17 0.63
28 10 0.37
ACGTcount: A:0.40, C:0.25, G:0.05, T:0.29
Consensus pattern (28 bp):
TCCCAACAATCAAATCAGTAATTTATCG
Found at i:347750 original size:58 final size:56
Alignment explanation
Indices: 347673--347792 Score: 134
Period size: 58 Copynumber: 2.1 Consensus size: 56
347663 TCATTATGCA
* * *
347673 ATATTTAAATTTCATTTTAGTCCTTCCACTATAAAAATAAATATTTTAGTCCTTTATT
1 ATATTTAAATTTCATTTTAGTCCATCCACTATAAAAAGAAACATTTTAGTCC-TTA-T
* * * * *
347731 ATATTTAGATGTTCA-TTTAGTTCATCTACTATAAAAAGGAGCATTTTAGTCCTTAT
1 ATATTTAAAT-TTCATTTTAGTCCATCCACTATAAAAAGAAACATTTTAGTCCTTAT
347787 ATATTT
1 ATATTT
347793 GAAGGTCCTT
Statistics
Matches: 53, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
56 7 0.13
57 3 0.06
58 39 0.74
59 4 0.08
ACGTcount: A:0.33, C:0.12, G:0.07, T:0.47
Consensus pattern (56 bp):
ATATTTAAATTTCATTTTAGTCCATCCACTATAAAAAGAAACATTTTAGTCCTTAT
Found at i:348383 original size:20 final size:20
Alignment explanation
Indices: 348369--348409 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
348359 CTCCAATTTT
348369 GCAACTCAGTTTCCAAATTC
1 GCAACTCAGTTTCCAAATTC
348389 GCAACTCAGTTTCCAAATTC
1 GCAACTCAGTTTCCAAATTC
348409 G
1 G
348410 TAACGTGAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.29, C:0.29, G:0.12, T:0.29
Consensus pattern (20 bp):
GCAACTCAGTTTCCAAATTC
Found at i:348473 original size:20 final size:20
Alignment explanation
Indices: 348448--348494 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
348438 TTTTCTGAAT
348448 TCGCAACGCGAATCTGTAAA
1 TCGCAACGCGAATCTGTAAA
* *
348468 TCGCAACGTGAATCTGTAAT
1 TCGCAACGCGAATCTGTAAA
348488 TCGCAAC
1 TCGCAAC
348495 ACAGAAGTCA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.32, C:0.26, G:0.19, T:0.23
Consensus pattern (20 bp):
TCGCAACGCGAATCTGTAAA
Found at i:349087 original size:20 final size:20
Alignment explanation
Indices: 349042--349090 Score: 89
Period size: 20 Copynumber: 2.5 Consensus size: 20
349032 ACTTAAATTT
*
349042 GCAACACGAAAATGAAAATC
1 GCAACGCGAAAATGAAAATC
349062 GCAACGCGAAAATGAAAATC
1 GCAACGCGAAAATGAAAATC
349082 GCAACGCGA
1 GCAACGCGA
349091 TTTTAGTTTC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.49, C:0.22, G:0.20, T:0.08
Consensus pattern (20 bp):
GCAACGCGAAAATGAAAATC
Found at i:357169 original size:64 final size:64
Alignment explanation
Indices: 357033--357157 Score: 162
Period size: 64 Copynumber: 2.0 Consensus size: 64
357023 TAAAATAAAG
* * ** *
357033 ACATCGAATGCAATTCGTGCATCGATGCATAAGTAGTGCATCGATACATCCCATTAATAGTGAA
1 ACATCGAATGCAATTCGTACATCGATGCATAAGGAGTGCATCGATACATCCCAGCAATAATGAA
* **
357097 ACATCGAATGCAA-TCGGTATATCGATGCATAAGGAGTGCATCGATGTATCCCAGCAATAAT
1 ACATCGAATGCAATTC-GTACATCGATGCATAAGGAGTGCATCGATACATCCCAGCAATAAT
357158 ACTACATCGA
Statistics
Matches: 52, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
63 2 0.04
64 50 0.96
ACGTcount: A:0.34, C:0.20, G:0.20, T:0.26
Consensus pattern (64 bp):
ACATCGAATGCAATTCGTACATCGATGCATAAGGAGTGCATCGATACATCCCAGCAATAATGAA
Found at i:357530 original size:24 final size:24
Alignment explanation
Indices: 357503--357575 Score: 71
Period size: 24 Copynumber: 3.1 Consensus size: 24
357493 ACATGCATAA
*
357503 GATATAT-ATATGTTCATGTGATAT
1 GATATATGATATG-ACATGTGATAT
*
357527 GATATGTGATATGACATGTGATAT
1 GATATATGATATGACATGTGATAT
* *
357551 GAGAACATGATATGA-A-GTGATAT
1 GA-TATATGATATGACATGTGATAT
357574 GA
1 GA
357576 GATACATGAT
Statistics
Matches: 42, Mismatches: 5, Indels: 5
0.81 0.10 0.10
Matches are distributed among these distances:
23 9 0.21
24 19 0.45
25 14 0.33
ACGTcount: A:0.37, C:0.04, G:0.23, T:0.36
Consensus pattern (24 bp):
GATATATGATATGACATGTGATAT
Found at i:357535 original size:12 final size:12
Alignment explanation
Indices: 357517--357552 Score: 63
Period size: 12 Copynumber: 3.0 Consensus size: 12
357507 TATATATGTT
357517 CATGTGATATGA
1 CATGTGATATGA
*
357529 TATGTGATATGA
1 CATGTGATATGA
357541 CATGTGATATGA
1 CATGTGATATGA
357553 GAACATGATA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.33, C:0.06, G:0.25, T:0.36
Consensus pattern (12 bp):
CATGTGATATGA
Found at i:357574 original size:23 final size:26
Alignment explanation
Indices: 357517--357585 Score: 85
Period size: 24 Copynumber: 2.8 Consensus size: 26
357507 TATATATGTT
**
357517 CATGTGATAT--GATATGTGATATGA
1 CATGTGATATGAGATACATGATATGA
357541 CATGTGATATGAGA-ACATGATATGA
1 CATGTGATATGAGATACATGATATGA
357566 -A-GTGATATGAGATACATGAT
1 CATGTGATATGAGATACATGAT
357586 CACAAGAGAA
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
23 11 0.28
24 18 0.45
25 9 0.22
26 2 0.05
ACGTcount: A:0.38, C:0.06, G:0.25, T:0.32
Consensus pattern (26 bp):
CATGTGATATGAGATACATGATATGA
Found at i:364114 original size:64 final size:63
Alignment explanation
Indices: 364046--364222 Score: 187
Period size: 64 Copynumber: 2.8 Consensus size: 63
364036 TAAAATAAAG
** *
364046 ACATCGAATACAATTCGCGCATCGATGCATAAGTAGTGCATCGATGCATCCCATTAATAGTGA-A
1 ACATCGAATACAATTCG-GCATCGATGCATAAGTAGTGCATCGATGCATCCCAGCAATAAT-ACA
* * * *
364110 ACATCGAATGCAA-TCGGTATATCGATGCATAAGGAGTGCATCGATGCATCCCAGCAATAATACT
1 ACATCGAATACAATTCGG--CATCGATGCATAAGTAGTGCATCGATGCATCCCAGCAATAATACA
* ** * *
364174 ACATCGAATACCATTTATGCACCGATGCATCAGTAGTGCATCGATGCAT
1 ACATCGAATA-CAATTCGGCATCGATGCATAAGTAGTGCATCGATGCAT
364223 ACCTTCATTA
Statistics
Matches: 93, Mismatches: 15, Indels: 10
0.79 0.13 0.08
Matches are distributed among these distances:
62 1 0.01
63 4 0.04
64 84 0.90
65 2 0.02
66 2 0.02
ACGTcount: A:0.33, C:0.23, G:0.19, T:0.25
Consensus pattern (63 bp):
ACATCGAATACAATTCGGCATCGATGCATAAGTAGTGCATCGATGCATCCCAGCAATAATACA
Found at i:370886 original size:20 final size:20
Alignment explanation
Indices: 370835--370889 Score: 92
Period size: 20 Copynumber: 2.7 Consensus size: 20
370825 TTTGAAACTT
*
370835 AAATTCGCAACACGAAAATGA
1 AAATT-GCAACGCGAAAATGA
370856 AAATTGCAACGCGAAAATGA
1 AAATTGCAACGCGAAAATGA
370876 AAATTGCAACGCGA
1 AAATTGCAACGCGA
370890 TTTTAGTTTC
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
20 28 0.85
21 5 0.15
ACGTcount: A:0.49, C:0.18, G:0.18, T:0.15
Consensus pattern (20 bp):
AAATTGCAACGCGAAAATGA
Found at i:373635 original size:172 final size:172
Alignment explanation
Indices: 373349--373690 Score: 675
Period size: 172 Copynumber: 2.0 Consensus size: 172
373339 ATTACTTGTT
373349 AAAGATGGTTTTACTCGGATGGATGACCTCAATGTTGTCCGAGTATGCCTTTTATTACTTTTGCA
1 AAAGATGGTTTTACTCGGATGGATGACCTCAATGTTGTCCGAGTATGCCTTTTATTACTTTTGCA
373414 TGCCGACTTTTTAGGCAAAGAGGCCAGACAACCTATTTATGATGACCTAATATTATTGGTAGAGG
66 TGCCGACTTTTTAGGCAAAGAGGCCAGACAACCTATTTATGATGACCTAATATTATTGGTAGAGG
373479 ACCTAAATGCATAGAACGTGTTTCCGTGGGGTTCATATATGG
131 ACCTAAATGCATAGAACGTGTTTCCGTGGGGTTCATATATGG
373521 AAAGATGGTTTTACTCGGATGGATGACCTCAATGTTGTCCGAGTATGCCTTTTATTACTTTTGCA
1 AAAGATGGTTTTACTCGGATGGATGACCTCAATGTTGTCCGAGTATGCCTTTTATTACTTTTGCA
*
373586 TGCCGACTTTTTAGGCAAAGAGGCCAGACAACCTATTTATGATGACCTAATATTATTTGTAGAGG
66 TGCCGACTTTTTAGGCAAAGAGGCCAGACAACCTATTTATGATGACCTAATATTATTGGTAGAGG
373651 ACCTAAATGCATAGAACGTGTTTCCGTGGGGTTCATATAT
131 ACCTAAATGCATAGAACGTGTTTCCGTGGGGTTCATATAT
373691 ATGGAAAGCT
Statistics
Matches: 169, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
172 169 1.00
ACGTcount: A:0.27, C:0.17, G:0.23, T:0.34
Consensus pattern (172 bp):
AAAGATGGTTTTACTCGGATGGATGACCTCAATGTTGTCCGAGTATGCCTTTTATTACTTTTGCA
TGCCGACTTTTTAGGCAAAGAGGCCAGACAACCTATTTATGATGACCTAATATTATTGGTAGAGG
ACCTAAATGCATAGAACGTGTTTCCGTGGGGTTCATATATGG
Found at i:374287 original size:42 final size:42
Alignment explanation
Indices: 374193--374291 Score: 117
Period size: 42 Copynumber: 2.4 Consensus size: 42
374183 CCCCCCACTT
* * * ** *
374193 CGAGAGCCATCACATGATCGAGCCGATTCTACAGCTTGACAC
1 CGAGAGCCATCACCTGATCGAGCCGATTATACACCTCCACAA
* * *
374235 CCATAACCATCACCTGATCGAGCCGATTATACACCTCCACAA
1 CGAGAGCCATCACCTGATCGAGCCGATTATACACCTCCACAA
374277 CGAGAGCCATCACCT
1 CGAGAGCCATCACCT
374292 ATTCCATCAC
Statistics
Matches: 45, Mismatches: 12, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
42 45 1.00
ACGTcount: A:0.30, C:0.35, G:0.16, T:0.18
Consensus pattern (42 bp):
CGAGAGCCATCACCTGATCGAGCCGATTATACACCTCCACAA
Done.