Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001279.1 Hibiscus syriacus cultivar Beakdansim tig00002511_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: 6984689
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 23 of 29
Found at i:5353810 original size:21 final size:19
Alignment explanation
Indices: 5353772--5353817 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 19
5353762 AATTAATCAT
5353772 ACTAAGTATTAAAGCTAAGA
1 ACTAA-TATTAAAGCTAAGA
5353792 ACTAATATTAAGGAGCTAAGA
1 ACTAATATTAA--AGCTAAGA
5353813 A-TAAT
1 ACTAAT
5353818 GATTCAATGA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 6 0.25
20 9 0.38
21 9 0.38
ACGTcount: A:0.50, C:0.09, G:0.15, T:0.26
Consensus pattern (19 bp):
ACTAATATTAAAGCTAAGA
Found at i:5357688 original size:2 final size:2
Alignment explanation
Indices: 5357681--5357713 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
5357671 ACTTGAAAAT
5357681 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
5357714 CTTATAACTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5358602 original size:5 final size:6
Alignment explanation
Indices: 5358587--5358611 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
5358577 TTCGCTTCAT
5358587 TTTTTA TTTTTA TTTTTA TTTTTA T
1 TTTTTA TTTTTA TTTTTA TTTTTA T
5358612 CCTTAATTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (6 bp):
TTTTTA
Found at i:5365924 original size:15 final size:15
Alignment explanation
Indices: 5365900--5365933 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
5365890 AACCCGACCC
*
5365900 GACCCGTTGACCGTT
1 GACCCATTGACCGTT
*
5365915 GACCCATTGACTGTT
1 GACCCATTGACCGTT
5365930 GACC
1 GACC
5365934 GGCGTTGACC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.18, C:0.32, G:0.24, T:0.26
Consensus pattern (15 bp):
GACCCATTGACCGTT
Found at i:5368416 original size:24 final size:24
Alignment explanation
Indices: 5368396--5368476 Score: 117
Period size: 24 Copynumber: 3.4 Consensus size: 24
5368386 ATAATACCTT
*
5368396 ACCTGGATTCTGATCGGATACTTG
1 ACCTGGATTTTGATCGGATACTTG
* * *
5368420 ACCTTGATTTTGATTGAATACTTG
1 ACCTGGATTTTGATCGGATACTTG
*
5368444 ACCTGGATTTTGATCTGATACTTG
1 ACCTGGATTTTGATCGGATACTTG
5368468 ACCTGGATT
1 ACCTGGATT
5368477 ATGTTATGAT
Statistics
Matches: 49, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 49 1.00
ACGTcount: A:0.22, C:0.17, G:0.21, T:0.40
Consensus pattern (24 bp):
ACCTGGATTTTGATCGGATACTTG
Found at i:5368492 original size:24 final size:24
Alignment explanation
Indices: 5368396--5368486 Score: 94
Period size: 24 Copynumber: 3.8 Consensus size: 24
5368386 ATAATACCTT
* **
5368396 ACCTGGATTCTGATCGGATACTTG
1 ACCTGGATTATGATATGATACTTG
* *
5368420 ACCTTGATTTTGAT-TGAATACTTG
1 ACCTGGATTATGATATG-ATACTTG
* *
5368444 ACCTGGATTTTGATCTGATACTTG
1 ACCTGGATTATGATATGATACTTG
*
5368468 ACCTGGATTATGTTATGAT
1 ACCTGGATTATGATATGAT
5368487 TTTTGATATA
Statistics
Matches: 58, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
23 1 0.02
24 55 0.95
25 2 0.03
ACGTcount: A:0.23, C:0.15, G:0.21, T:0.41
Consensus pattern (24 bp):
ACCTGGATTATGATATGATACTTG
Found at i:5378339 original size:103 final size:103
Alignment explanation
Indices: 5378150--5378367 Score: 373
Period size: 103 Copynumber: 2.1 Consensus size: 103
5378140 GTCGAGGGTC
* *
5378150 TATGCGGTCTTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
* *
5378215 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
* *
5378253 TATGTGGTCCTTCGGTACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACATATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
*
5378318 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
5378356 TATGTGGTCCTT
1 TATGTGGTCCTT
5378368 ATGGACATTA
Statistics
Matches: 108, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
103 108 1.00
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.38
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
Found at i:5378417 original size:23 final size:23
Alignment explanation
Indices: 5378383--5378451 Score: 111
Period size: 23 Copynumber: 3.0 Consensus size: 23
5378373 CATTATTATA
5378383 TGGCACTACGGTGCAATTCTACG
1 TGGCACTACGGTGCAATTCTACG
*
5378406 TGGCACTCCGGTGCAATTCTACG
1 TGGCACTACGGTGCAATTCTACG
* *
5378429 TGGCACTTCGGTGCAATTATACG
1 TGGCACTACGGTGCAATTCTACG
5378452 AGCTGTGGTG
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 43 1.00
ACGTcount: A:0.20, C:0.26, G:0.26, T:0.28
Consensus pattern (23 bp):
TGGCACTACGGTGCAATTCTACG
Found at i:5382209 original size:31 final size:30
Alignment explanation
Indices: 5382160--5382219 Score: 77
Period size: 31 Copynumber: 2.0 Consensus size: 30
5382150 TTATATAAGC
*
5382160 TATGTGATACAATGATGGAACATGATATGTT
1 TATGTGATACAAGGATGGAA-ATGATATGTT
*
5382191 TATGTGATA-AAGGTATGGAAATTATATGT
1 TATGTGATACAAGG-ATGGAAATGATATGT
5382220 CTATACAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
30 11 0.42
31 15 0.58
ACGTcount: A:0.37, C:0.03, G:0.23, T:0.37
Consensus pattern (30 bp):
TATGTGATACAAGGATGGAAATGATATGTT
Found at i:5382502 original size:46 final size:46
Alignment explanation
Indices: 5382442--5382533 Score: 157
Period size: 46 Copynumber: 2.0 Consensus size: 46
5382432 CAATCTTATA
5382442 TGGCACTACGGTGCAATTCTACATGGCACTTCGGTGCAATTATACG
1 TGGCACTACGGTGCAATTCTACATGGCACTTCGGTGCAATTATACG
* * *
5382488 TGGCACTTCGGTGCAATTCTACGTGGCACTTCGGTGCATTTATACG
1 TGGCACTACGGTGCAATTCTACATGGCACTTCGGTGCAATTATACG
5382534 AGCTGTGGTG
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
46 43 1.00
ACGTcount: A:0.21, C:0.24, G:0.25, T:0.30
Consensus pattern (46 bp):
TGGCACTACGGTGCAATTCTACATGGCACTTCGGTGCAATTATACG
Found at i:5382533 original size:23 final size:23
Alignment explanation
Indices: 5382442--5382533 Score: 139
Period size: 23 Copynumber: 4.0 Consensus size: 23
5382432 CAATCTTATA
* * *
5382442 TGGCACTACGGTGCAATTCTACA
1 TGGCACTTCGGTGCAATTATACG
5382465 TGGCACTTCGGTGCAATTATACG
1 TGGCACTTCGGTGCAATTATACG
*
5382488 TGGCACTTCGGTGCAATTCTACG
1 TGGCACTTCGGTGCAATTATACG
*
5382511 TGGCACTTCGGTGCATTTATACG
1 TGGCACTTCGGTGCAATTATACG
5382534 AGCTGTGGTG
Statistics
Matches: 63, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 63 1.00
ACGTcount: A:0.21, C:0.24, G:0.25, T:0.30
Consensus pattern (23 bp):
TGGCACTTCGGTGCAATTATACG
Found at i:5387139 original size:23 final size:25
Alignment explanation
Indices: 5387082--5387139 Score: 59
Period size: 23 Copynumber: 2.4 Consensus size: 25
5387072 TCGTTACTCT
5387082 AATCCGCTAAAGCCCTAAATTTTTA
1 AATCCGCTAAAGCCCTAAATTTTTA
** * *
5387107 AA-CCTATAAA-CCTTAATTTTTTA
1 AATCCGCTAAAGCCCTAAATTTTTA
5387130 AATCC-CTAAA
1 AATCCGCTAAA
5387140 TTATTATATT
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
23 17 0.63
24 8 0.30
25 2 0.07
ACGTcount: A:0.40, C:0.22, G:0.03, T:0.34
Consensus pattern (25 bp):
AATCCGCTAAAGCCCTAAATTTTTA
Found at i:5393376 original size:17 final size:18
Alignment explanation
Indices: 5393339--5393387 Score: 64
Period size: 17 Copynumber: 2.7 Consensus size: 18
5393329 TAATCATTAT
5393339 AAAAAAATTAGTTTTGATGA
1 AAAAAAATTA--TTTGATGA
5393359 AAAAAAATTATTTG-TGA
1 AAAAAAATTATTTGATGA
*
5393376 AAGAAAATTATT
1 AAAAAAATTATT
5393388 AGTTAATATA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
17 14 0.50
18 4 0.14
20 10 0.36
ACGTcount: A:0.53, C:0.00, G:0.12, T:0.35
Consensus pattern (18 bp):
AAAAAAATTATTTGATGA
Found at i:5395888 original size:22 final size:22
Alignment explanation
Indices: 5395839--5395890 Score: 79
Period size: 22 Copynumber: 2.4 Consensus size: 22
5395829 GGTGGGATGG
*
5395839 TGTGGGTGGCCTGATGCACCGG
1 TGTGGGTGGCCTGATGCACCGC
5395861 TGTGGGTGGCCTGATGCACCAGC
1 TGTGGGTGGCCTGATGCACC-GC
5395884 T-TGGGTG
1 TGTGGGTG
5395891 CCATGAACGG
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
22 26 0.93
23 2 0.07
ACGTcount: A:0.10, C:0.21, G:0.44, T:0.25
Consensus pattern (22 bp):
TGTGGGTGGCCTGATGCACCGC
Found at i:5395890 original size:28 final size:22
Alignment explanation
Indices: 5395837--5395880 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
5395827 GGGGTGGGAT
5395837 GGTGTGGGTGGCCTGATGCACC
1 GGTGTGGGTGGCCTGATGCACC
5395859 GGTGTGGGTGGCCTGATGCACC
1 GGTGTGGGTGGCCTGATGCACC
5395881 AGCTTGGGTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.09, C:0.23, G:0.45, T:0.23
Consensus pattern (22 bp):
GGTGTGGGTGGCCTGATGCACC
Found at i:5398185 original size:3 final size:3
Alignment explanation
Indices: 5398177--5398393 Score: 291
Period size: 3 Copynumber: 72.7 Consensus size: 3
5398167 TTATTTATTA
*
5398177 AAT AAT AAT AAT AAT AAT ATAT AAT ATT ATAT AAT AAT AAT AAAT ATAT
1 AAT AAT AAT AAT AAT AAT A-AT AAT AAT A-AT AAT AAT AAT -AAT A-AT
* * *
5398226 AAT AAT AAT AAT AAT AAT AA- AAA AAT AAT AAT AAT AAT GAT AAT GAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
*
5398273 AAT AAT AAT -AT AAT AAT AAT AAT AAT AAT AAT GAT AAT AAT AAT -AT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * *
5398319 AAT AAT AAT -AT AAT AAT AAT AAT -AT AAT GAT AAT GAT AAT ATT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
5398365 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
5398394 AATGGATAAA
Statistics
Matches: 190, Mismatches: 15, Indels: 18
0.85 0.07 0.08
Matches are distributed among these distances:
2 10 0.05
3 169 0.89
4 11 0.06
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (3 bp):
AAT
Found at i:5398996 original size:114 final size:114
Alignment explanation
Indices: 5398644--5399426 Score: 1212
Period size: 114 Copynumber: 6.7 Consensus size: 114
5398634 GCTCTTGATG
*
5398644 AGTTCTTCTCATTATGAACTTTTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTAC-
1 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTT-CT
* * * * *
5398708 CTGGTAATGTTGATCCATCAA-ATGATGGATTCAAACAAAAGGTTGAACA
65 CTGGAAATGATGATCCATCAATTTGATGAATTCAAGCAAAAGGTTGAACA
5398757 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGACGAATTCTTCTCATTATGAACTCT
1 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGA-G--TTCTTCTCATTATGAACT-T
* *
5398822 TCTTCTGGAAATGATGATCCATCAATTTGATGAATTCAGGTAAAAGGTTGAACA
62 TC-TCTGGAAATGATGATCCATCAATTTGATGAATTCAAGCAAAAGGTTGAACA
*
5398876 AATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTC
1 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTC
*
5398941 TGGAAACGATGATCCATCAATTTGATGAATTCAAGCAAAAGGTTGAACA
66 TGGAAATGATGATCCATCAATTTGATGAATTCAAGCAAAAGGTTGAACA
*
5398990 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTC
1 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTC
* * * * *
5399055 TGGAAAAGAATAATCCATCAA-GTGATGAATTTAAACAAAAGGTTGAACA
66 TGGAAATG-ATGATCCATCAATTTGATGAATTCAAGCAAAAGGTTGAACA
5399104 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGACGAATTCTTCTCATTATGAACTTC
1 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGA-G--TTCTTCTCATTATGAACTT-
* *
5399169 TCTTCTGGAAATGATGATCCATCAATTTGATGAATTCAGGTAAAAGGTTGAACA
62 TC-TCTGGAAATGATGATCCATCAATTTGATGAATTCAAGCAAAAGGTTGAACA
*
5399223 AATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTC
1 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTC
*
5399288 TGGAAACGATGATCCATCAATTTGATGAATTCAAGCAAAAGGTTGAACA
66 TGGAAATGATGATCCATCAATTTGATGAATTCAAGCAAAAGGTTGAACA
5399337 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGACGAATTCTTCTCATTATGAACTCT
1 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGA-G--TTCTTCTCATTATGAACT-T
5399402 TCTTCTGGAAATGATGATCCATCAA
62 TC-TCTGGAAATGATGATCCATCAA
5399427 ATGATAGATT
Statistics
Matches: 618, Mismatches: 33, Indels: 32
0.90 0.05 0.05
Matches are distributed among these distances:
113 40 0.06
114 273 0.44
115 18 0.03
116 56 0.09
117 38 0.06
118 37 0.06
119 156 0.25
ACGTcount: A:0.28, C:0.20, G:0.13, T:0.38
Consensus pattern (114 bp):
AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTC
TGGAAATGATGATCCATCAATTTGATGAATTCAAGCAAAAGGTTGAACA
Found at i:5399187 original size:233 final size:228
Alignment explanation
Indices: 5398644--5399426 Score: 1212
Period size: 233 Copynumber: 3.4 Consensus size: 228
5398634 GCTCTTGATG
*
5398644 AGTTCTTCTCATTATGAACTTTTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTAC-
1 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTT-CT
* * * * *
5398708 CTGGTAATGTTGATCCATCAA-ATGATGGATTCAAACAAAAGGTTGAACAAGTTCTTCTCATTAT
65 CTGGAAATGATGATCCATCAATTTGATGAATTCAAGCAAAAGGTTGAACAAGTTCTTCTCATTAT
*
5398772 GAACTTCTTCTTCCTTCTTCAGATGACGAATTCTTCTCATTATGAACTCTTCTTCTGGAAATGAT
130 GAACTTCTTCTTCCTTCTTCAGATGA-G--TTCTTCTCATTATGAAC-CTTC-TCTGGAAAAGAT
* *
5398837 GATCCATCAATTTGATGAATTCAGGTAAAAGGTTGAACA
190 GATCCATCAATTTGATGAATTCAAGCAAAAGGTTGAACA
*
5398876 AATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTC
1 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTC
*
5398941 TGGAAACGATGATCCATCAATTTGATGAATTCAAGCAAAAGGTTGAACAAGTTCTTCTCATTATG
66 TGGAAATGATGATCCATCAATTTGATGAATTCAAGCAAAAGGTTGAACAAGTTCTTCTCATTATG
*
5399006 AACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTGGAAAAGAATAATCC
131 AACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTGGAAAAG-ATGATCC
* * *
5399071 ATCAA-GTGATGAATTTAAACAAAAGGTTGAACA
195 ATCAATTTGATGAATTCAAGCAAAAGGTTGAACA
5399104 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGACGAATTCTTCTCATTATGAACTTC
1 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGA-G--TTCTTCTCATTATGAACTT-
* * *
5399169 TCTTCTGGAAATGATGATCCATCAATTTGATGAATTCAGGTAAAAGGTTGAACAAATTCTTCTCA
62 TC-TCTGGAAATGATGATCCATCAATTTGATGAATTCAAGCAAAAGGTTGAACAAGTTCTTCTCA
* *
5399234 TTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAACGATG
126 TTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTGGAAAAGATG
5399299 ATCCATCAATTTGATGAATTCAAGCAAAAGGTTGAACA
191 ATCCATCAATTTGATGAATTCAAGCAAAAGGTTGAACA
5399337 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGACGAATTCTTCTCATTATGAACTCT
1 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGA-G--TTCTTCTCATTATGAACT-T
5399402 TCTTCTGGAAATGATGATCCATCAA
62 TC-TCTGGAAATGATGATCCATCAA
5399427 ATGATAGATT
Statistics
Matches: 515, Mismatches: 26, Indels: 19
0.92 0.05 0.03
Matches are distributed among these distances:
228 72 0.14
229 16 0.03
230 17 0.03
231 20 0.04
232 92 0.18
233 297 0.58
234 1 0.00
ACGTcount: A:0.28, C:0.20, G:0.13, T:0.38
Consensus pattern (228 bp):
AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTC
TGGAAATGATGATCCATCAATTTGATGAATTCAAGCAAAAGGTTGAACAAGTTCTTCTCATTATG
AACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTGGAAAAGATGATCCA
TCAATTTGATGAATTCAAGCAAAAGGTTGAACA
Found at i:5399278 original size:347 final size:346
Alignment explanation
Indices: 5398644--5399431 Score: 1409
Period size: 347 Copynumber: 2.3 Consensus size: 346
5398634 GCTCTTGATG
* *
5398644 AGTTCTTCTCATTATGAACTTTTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTAC-
1 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTT-CT
* * *
5398708 CTGGTAATGTTGATCCATCAAATGATGGATTCAAACAAAAGGTTGAACAAGTTCTTCTCATTATG
65 CTGGAAATGATGATCCATCAAATGATGAATTCAAACAAAAGGTTGAACAAGTTCTTCTCATTATG
5398773 AACTTCTTCTTCCTTCTTCAGATGACGAATTCTTCTCATTATGAACTCTTCTTCTGGAAATGATG
130 AACTTCTTCTTCCTTCTTCAGATGACGAATTCTTCTCATTATGAACTCTTCTTCTGGAAATGATG
5398838 ATCCATCAATTTGATGAATTCAGGTAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTT
195 ATCCATCAATTTGATGAATTCAGGTAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTT
5398903 CCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAACGATGATCCATCAATTTGATG
260 CCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAACGATGATCCATCAATTTGATG
5398968 AATTCAAGCAAAAGGTTGAACA
325 AATTCAAGCAAAAGGTTGAACA
5398990 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTC
1 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTC
* * * *
5399055 TGGAAAAGAATAATCCATCAAGTGATGAATTTAAACAAAAGGTTGAACAAGTTCTTCTCATTATG
66 TGGAAATG-ATGATCCATCAAATGATGAATTCAAACAAAAGGTTGAACAAGTTCTTCTCATTATG
5399120 AACTTCTTCTTCCTTCTTCAGATGACGAATTCTTCTCATTATGAACT-TCTCTTCTGGAAATGAT
130 AACTTCTTCTTCCTTCTTCAGATGACGAATTCTTCTCATTATGAACTCT-TCTTCTGGAAATGAT
5399184 GATCCATCAATTTGATGAATTCAGGTAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCT
194 GATCCATCAATTTGATGAATTCAGGTAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCT
5399249 TCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAACGATGATCCATCAATTTGAT
259 TCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAACGATGATCCATCAATTTGAT
5399314 GAATTCAAGCAAAAGGTTGAACA
324 GAATTCAAGCAAAAGGTTGAACA
5399337 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGACGAATTCTTCTCATTATGAACTCT
1 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGA-G--TTCTTCTCATTATGAAC-CT
5399402 TCTTCTGGAAATGATGATCCATCAAATGAT
62 TC-TCTGGAAATGATGATCCATCAAATGAT
5399432 AGATTTGAAT
Statistics
Matches: 422, Mismatches: 12, Indels: 11
0.95 0.03 0.02
Matches are distributed among these distances:
345 1 0.00
346 68 0.16
347 307 0.73
348 1 0.00
350 17 0.04
351 19 0.05
352 9 0.02
ACGTcount: A:0.28, C:0.20, G:0.13, T:0.38
Consensus pattern (346 bp):
AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTC
TGGAAATGATGATCCATCAAATGATGAATTCAAACAAAAGGTTGAACAAGTTCTTCTCATTATGA
ACTTCTTCTTCCTTCTTCAGATGACGAATTCTTCTCATTATGAACTCTTCTTCTGGAAATGATGA
TCCATCAATTTGATGAATTCAGGTAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTC
CTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAACGATGATCCATCAATTTGATGA
ATTCAAGCAAAAGGTTGAACA
Found at i:5400161 original size:52 final size:52
Alignment explanation
Indices: 5400056--5401053 Score: 1833
Period size: 52 Copynumber: 19.2 Consensus size: 52
5400046 TCTAAACTCA
* * *
5400056 ATGCT-TGATTCTGTCTAATCAGATCAGAT-ATTCAAAGAACACTTCCAGAAG
1 ATGCTATG-TTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAG
*
5400107 ATGCTATGTTCTGTCCAAACAGATCAGATAACTCAAAGAACACTTCCAGAAG
1 ATGCTATGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAG
5400159 ATGCTATGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAG
1 ATGCTATGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAG
5400211 ATGCTATGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAG
1 ATGCTATGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAG
5400263 ATGCTATGTTCTGTCC-ACCAGATCAGATAACTCAAAGAACACTTCCAGAAG
1 ATGCTATGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAG
5400314 ATGCTATGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAG
1 ATGCTATGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAG
5400366 ATGCTATGTTCTGTCC-ACCAGATCAGATAACTCAAAGAACACTTCCAGAAG
1 ATGCTATGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAG
5400417 ATGCTATGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAG
1 ATGCTATGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAG
*
5400469 ATGCTATGTTCTGTCCAACCAGATCAGATAACTCAAAGAACGCTTCCAGAAG
1 ATGCTATGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAG
5400521 ATGCTATGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAG
1 ATGCTATGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAG
5400573 ATGCTATGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAG
1 ATGCTATGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAG
* * *
5400625 ATGCTATGTTTTTTTTCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAG
1 ATGCTATG-TTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAG
5400678 ATGCTATGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAG
1 ATGCTATGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAG
5400730 ATGCTATGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAG
1 ATGCTATGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAG
*
5400782 ATGCTATGTTCTGTCCAACCAGATCAGATAACTCAAAGAACGCTTCCAGAAG
1 ATGCTATGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAG
5400834 ATGCTATGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAG
1 ATGCTATGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAG
* * *
5400886 ATGCTATGTTTTTTTTCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAG
1 ATGCTATG-TTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAG
5400939 ATGCTATGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAG
1 ATGCTATGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAG
5400991 ATGCTATGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAG
1 ATGCTATGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAG
5401043 ATGCTATGTTC
1 ATGCTATGTTC
5401054 ACATTCATTT
Statistics
Matches: 921, Mismatches: 20, Indels: 11
0.97 0.02 0.01
Matches are distributed among these distances:
51 126 0.14
52 697 0.76
53 98 0.11
ACGTcount: A:0.36, C:0.24, G:0.15, T:0.24
Consensus pattern (52 bp):
ATGCTATGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAG
Found at i:5400767 original size:261 final size:260
Alignment explanation
Indices: 5400056--5401053 Score: 1833
Period size: 261 Copynumber: 3.8 Consensus size: 260
5400046 TCTAAACTCA
* * * *
5400056 ATGCT-TGATTCTGTCTAATCAGATCAGAT-ATTCAAAGAACACTTCCAGAAGATGCTATGTTCT
1 ATGCTATG-TTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTTT
* * *
5400119 GTCCAAACAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAACCAGATC
65 TTTCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAACCAGATC
5400184 AGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAACCAGATCAGATAACTCAAAG
130 AGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAACCAGATCAGATAACTCAAAG
5400249 AACACTTCCAGAAGATGCTATGTTCTGTCC-ACCAGATCAGATAACTCAAAGAACACTTCCAGAA
195 AACACTTCCAGAAGATGCTATGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAA
5400313 G
260 G
*
5400314 ATGCTATGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATG-TTCT
1 ATGCTATGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTTTT
* *
5400378 GTCCACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAACCAGATCA
66 TTCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAACCAGATCA
5400443 GATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAACCAGATCAGATAACTCAAAGA
131 GATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAACCAGATCAGATAACTCAAAGA
*
5400508 ACGCTTCCAGAAGATGCTATGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAG
196 ACACTTCCAGAAGATGCTATGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAG
5400573 ATGCTATGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTTTT
1 ATGCTATGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATG-TTTT
5400638 TTTCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAACCAGATC
65 TTTCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAACCAGATC
5400703 AGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAACCAGATCAGATAACTCAAAG
130 AGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAACCAGATCAGATAACTCAAAG
*
5400768 AACACTTCCAGAAGATGCTATGTTCTGTCCAACCAGATCAGATAACTCAAAGAACGCTTCCAGAA
195 AACACTTCCAGAAGATGCTATGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAA
5400833 G
260 G
5400834 ATGCTATGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTTTT
1 ATGCTATGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATG-TTTT
5400899 TTTCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAACCAGATC
65 TTTCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAACCAGATC
5400964 AGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAACCAGATCAGATAACTCAAAG
130 AGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAACCAGATCAGATAACTCAAAG
5401029 AACACTTCCAGAAGATGCTATGTTC
195 AACACTTCCAGAAGATGCTATGTTC
5401054 ACATTCATTT
Statistics
Matches: 719, Mismatches: 16, Indels: 7
0.97 0.02 0.01
Matches are distributed among these distances:
258 179 0.25
259 126 0.18
261 414 0.58
ACGTcount: A:0.36, C:0.24, G:0.15, T:0.24
Consensus pattern (260 bp):
ATGCTATGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTTTT
TTCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAACCAGATCA
GATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAACCAGATCAGATAACTCAAAGA
ACACTTCCAGAAGATGCTATGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAG
Found at i:5412350 original size:13 final size:15
Alignment explanation
Indices: 5412328--5412364 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
5412318 TTTGACATAA
5412328 AAAT-AAATAC-TG-
1 AAATAAAATACTTGC
5412340 AAATAAAATACTTGC
1 AAATAAAATACTTGC
5412355 AAATAAAATA
1 AAATAAAATA
5412365 AAACATATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 4 0.18
13 6 0.27
14 2 0.09
15 10 0.45
ACGTcount: A:0.62, C:0.08, G:0.05, T:0.24
Consensus pattern (15 bp):
AAATAAAATACTTGC
Found at i:5413185 original size:20 final size:21
Alignment explanation
Indices: 5413162--5413208 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
5413152 AAATTATTTA
5413162 AATATATAA-ACAATTAAAAC
1 AATATATAATACAATTAAAAC
* *
5413182 AATA-AAAATACAATTAGAAC
1 AATATATAATACAATTAAAAC
5413202 AATATAT
1 AATATAT
5413209 TTAAAAGTGG
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
19 3 0.14
20 18 0.82
21 1 0.05
ACGTcount: A:0.64, C:0.09, G:0.02, T:0.26
Consensus pattern (21 bp):
AATATATAATACAATTAAAAC
Found at i:5414138 original size:33 final size:35
Alignment explanation
Indices: 5414073--5414144 Score: 89
Period size: 35 Copynumber: 2.1 Consensus size: 35
5414063 GTTGTTGTAT
5414073 TTCTCCCTCTGTTTTTTTTGTTGTTGGCTGTCTCGG
1 TTCTCCCTCTGTTTTTTTTGTTGTTGGCTGTCTC-G
*
5414109 TTCTTCCTCT-TTTTTTTTGTT-TCT-G-TGTCTCG
1 TTCTCCCTCTGTTTTTTTTGTTGT-TGGCTGTCTCG
5414141 TTCT
1 TTCT
5414145 GTCTCTCTCC
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
32 5 0.15
33 6 0.18
34 2 0.06
35 12 0.35
36 9 0.26
ACGTcount: A:0.00, C:0.22, G:0.17, T:0.61
Consensus pattern (35 bp):
TTCTCCCTCTGTTTTTTTTGTTGTTGGCTGTCTCG
Found at i:5414532 original size:3 final size:3
Alignment explanation
Indices: 5414524--5414772 Score: 372
Period size: 3 Copynumber: 82.0 Consensus size: 3
5414514 AATTATTTAT
* *
5414524 TAA TAA TAAA TAA TAA TAA TATA TAA TAT TAA TAA TAA TAA TAAA TAC
1 TAA TAA T-AA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA T-AA TAA
*
5414572 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA AAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * *
5414620 TAA TGA TAA TGA TAA TAA TAA TAT TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* *
5414668 TGA TAA TAA TAA TAT TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * *
5414716 TAA TGA TAA TGA TAA TAA TAA TAT TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
5414764 TAA TAA TAA
1 TAA TAA TAA
5414773 AATGGATAAA
Statistics
Matches: 221, Mismatches: 22, Indels: 6
0.89 0.09 0.02
Matches are distributed among these distances:
3 212 0.96
4 9 0.04
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:5415417 original size:23 final size:23
Alignment explanation
Indices: 5415387--5415430 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
5415377 AGTAAAACGC
5415387 GGATCACCATCCACGCCTTCCTA
1 GGATCACCATCCACGCCTTCCTA
* *
5415410 GGATCACCATTCGCGCCTTCC
1 GGATCACCATCCACGCCTTCC
5415431 ATTATTTCCT
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:0.18, C:0.43, G:0.16, T:0.23
Consensus pattern (23 bp):
GGATCACCATCCACGCCTTCCTA
Found at i:5421916 original size:21 final size:22
Alignment explanation
Indices: 5421890--5421931 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
5421880 TAATGAGTTC
5421890 GTATATAAAT-AAT-TTTTTTAA
1 GTATAT-AATGAATATTTTTTAA
5421911 GTATATAATGAATATTTTTTA
1 GTATATAATGAATATTTTTTA
5421932 CACTGAATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 3 0.16
21 9 0.47
22 7 0.37
ACGTcount: A:0.40, C:0.00, G:0.07, T:0.52
Consensus pattern (22 bp):
GTATATAATGAATATTTTTTAA
Found at i:5425218 original size:12 final size:12
Alignment explanation
Indices: 5425201--5425227 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
5425191 ACAGCAATAC
5425201 TTAGGACTAAAA
1 TTAGGACTAAAA
5425213 TTAGGACTAAAA
1 TTAGGACTAAAA
5425225 TTA
1 TTA
5425228 AACGCACTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.48, C:0.07, G:0.15, T:0.30
Consensus pattern (12 bp):
TTAGGACTAAAA
Found at i:5435729 original size:44 final size:42
Alignment explanation
Indices: 5435649--5435750 Score: 125
Period size: 44 Copynumber: 2.4 Consensus size: 42
5435639 ATAAAAAGAC
* *
5435649 AAATAAATAAATAAATAAAATACACTAAAATTAAAAGAGAAAAA
1 AAATGAATAACTAAATAAAATACACTAAAATTAAAAG-G-AAAA
* *
5435693 AAATGAATAACTAAATAAAA-ATACTAAAATTAAAAAGGAACA
1 AAATGAATAACTAAATAAAATACACTAAAATT-AAAAGGAAAA
*
5435735 AAATGACTAACTAAAT
1 AAATGAATAACTAAAT
5435751 TGAAATAAAT
Statistics
Matches: 52, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
42 18 0.35
43 11 0.21
44 23 0.44
ACGTcount: A:0.68, C:0.07, G:0.06, T:0.20
Consensus pattern (42 bp):
AAATGAATAACTAAATAAAATACACTAAAATTAAAAGGAAAA
Found at i:5435748 original size:42 final size:44
Alignment explanation
Indices: 5435649--5435750 Score: 136
Period size: 42 Copynumber: 2.4 Consensus size: 44
5435639 ATAAAAAGAC
* *
5435649 AAATAAATAAATAAATAAAATACACTAAAATTAAAAGAGAAAAA
1 AAATGAATAACTAAATAAAATACACTAAAATTAAAAGAGAAAAA
* * *
5435693 AAATGAATAACTAAATAAAA-ATACTAAAATTAAAA-AGGAACA
1 AAATGAATAACTAAATAAAATACACTAAAATTAAAAGAGAAAAA
*
5435735 AAATGACTAACTAAAT
1 AAATGAATAACTAAAT
5435751 TGAAATAAAT
Statistics
Matches: 52, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
42 20 0.38
43 14 0.27
44 18 0.35
ACGTcount: A:0.68, C:0.07, G:0.06, T:0.20
Consensus pattern (44 bp):
AAATGAATAACTAAATAAAATACACTAAAATTAAAAGAGAAAAA
Found at i:5447983 original size:31 final size:31
Alignment explanation
Indices: 5447945--5448004 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
5447935 ATTACACGAT
**
5447945 TTTTATTTAGGATTTAAGATTTATAATTTTA
1 TTTTATTTAAAATTTAAGATTTATAATTTTA
*
5447976 TTTTATTTAAAATTTAAGATTTGTAATTT
1 TTTTATTTAAAATTTAAGATTTATAATTT
5448005 AACAAGATTA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.33, C:0.00, G:0.08, T:0.58
Consensus pattern (31 bp):
TTTTATTTAAAATTTAAGATTTATAATTTTA
Found at i:5476337 original size:2 final size:2
Alignment explanation
Indices: 5476330--5476361 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
5476320 ATTAATTTAA
5476330 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
5476362 TTAAATGTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5476507 original size:24 final size:24
Alignment explanation
Indices: 5476480--5476550 Score: 124
Period size: 24 Copynumber: 3.0 Consensus size: 24
5476470 TTTATTAGTT
5476480 TAATTTAATATATAAAATTATTAA
1 TAATTTAATATATAAAATTATTAA
5476504 TAATTTAATATATAAAATTATTAA
1 TAATTTAATATATAAAATTATTAA
* *
5476528 TAATTAAATATATAATATTATTA
1 TAATTTAATATATAAAATTATTA
5476551 TATATAAAAA
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 45 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (24 bp):
TAATTTAATATATAAAATTATTAA
Found at i:5476863 original size:21 final size:22
Alignment explanation
Indices: 5476834--5476880 Score: 71
Period size: 21 Copynumber: 2.2 Consensus size: 22
5476824 ATTCTGACTA
5476834 TCGCATTGCGATTTTCC-AAAT
1 TCGCATTGCGATTTTCCGAAAT
*
5476855 TCGCGTTGCGATTTTCCGAAA-
1 TCGCATTGCGATTTTCCGAAAT
5476876 TCGCA
1 TCGCA
5476881 ATGCAAATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 20 0.87
22 3 0.13
ACGTcount: A:0.21, C:0.26, G:0.19, T:0.34
Consensus pattern (22 bp):
TCGCATTGCGATTTTCCGAAAT
Found at i:5476911 original size:20 final size:19
Alignment explanation
Indices: 5476872--5476925 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 19
5476862 GCGATTTTCC
*
5476872 GAAATCGCAATGCAAATAT
1 GAAATCGCAATGCGAATAT
*
5476891 GTAAATCGCAATGCGATTAT
1 G-AAATCGCAATGCGAATAT
*
5476911 GACTATCGCAATGCG
1 GA-AATCGCAATGCG
5476926 CTTCTGACTA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
19 2 0.07
20 28 0.93
ACGTcount: A:0.37, C:0.19, G:0.20, T:0.24
Consensus pattern (19 bp):
GAAATCGCAATGCGAATAT
Found at i:5476933 original size:20 final size:20
Alignment explanation
Indices: 5476895--5477023 Score: 150
Period size: 20 Copynumber: 6.4 Consensus size: 20
5476885 AAATATGTAA
* *
5476895 ATCGCAATGCGATTATGACT
1 ATCGCAACGCGATTCTGACT
* *
5476915 ATCGCAATGCGCTTCTGACT
1 ATCGCAACGCGATTCTGACT
* *
5476935 ATCGCAACGCAAATTCTGATT
1 ATCGCAACGC-GATTCTGACT
* *
5476956 ATCGCAACGAGATTTTGACT
1 ATCGCAACGCGATTCTGACT
*
5476976 ATCGCAACGAGATTCTGACT
1 ATCGCAACGCGATTCTGACT
*
5476996 ATCACAACGCGATTCTGACT
1 ATCGCAACGCGATTCTGACT
*
5477016 GTCGCAAC
1 ATCGCAAC
5477024 ACTGAATTTC
Statistics
Matches: 93, Mismatches: 15, Indels: 2
0.85 0.14 0.02
Matches are distributed among these distances:
20 77 0.83
21 16 0.17
ACGTcount: A:0.29, C:0.26, G:0.19, T:0.27
Consensus pattern (20 bp):
ATCGCAACGCGATTCTGACT
Found at i:5476976 original size:61 final size:60
Alignment explanation
Indices: 5476895--5477023 Score: 159
Period size: 61 Copynumber: 2.1 Consensus size: 60
5476885 AAATATGTAA
* * * * * * *
5476895 ATCGCAATGCGATTATGACTATCGCAATGCGCTTCTGACTATCGCAACGCAAATTCTGATT
1 ATCGCAACGAGATTATGACTATCGCAACGAGATTCTGACTATCACAACGC-AATTCTGACT
* *
5476956 ATCGCAACGAGATTTTGACTATCGCAACGAGATTCTGACTATCACAACGCGATTCTGACT
1 ATCGCAACGAGATTATGACTATCGCAACGAGATTCTGACTATCACAACGCAATTCTGACT
*
5477016 GTCGCAAC
1 ATCGCAAC
5477024 ACTGAATTTC
Statistics
Matches: 58, Mismatches: 10, Indels: 1
0.84 0.14 0.01
Matches are distributed among these distances:
60 15 0.26
61 43 0.74
ACGTcount: A:0.29, C:0.26, G:0.19, T:0.27
Consensus pattern (60 bp):
ATCGCAACGAGATTATGACTATCGCAACGAGATTCTGACTATCACAACGCAATTCTGACT
Found at i:5480388 original size:20 final size:20
Alignment explanation
Indices: 5480363--5480602 Score: 218
Period size: 20 Copynumber: 12.7 Consensus size: 20
5480353 TTACACATTC
*
5480363 ATTTGAATATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
* *
5480383 ATTTGACTATCGTAATGCGA
1 ATTTGACTATCGCAACGCGA
5480403 ATTTGACTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
5480423 ATTTGACTATCGCAA--CGA
1 ATTTGACTATCGCAACGCGA
**
5480441 A----AAAATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
*
5480457 ATTTAACTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
**
5480477 ATTTGACTATCGCAACAAGA
1 ATTTGACTATCGCAACGCGA
*
5480497 ATTTGACTATCGCAACGTGA
1 ATTTGACTATCGCAACGCGA
* * * *
5480517 ATTTGATTATCACAACGGGT
1 ATTTGACTATCGCAACGCGA
* *
5480537 ATTCGACTATCGCAACGAGA
1 ATTTGACTATCGCAACGCGA
* *
5480557 A----A--ATCGCAAAGCGT
1 ATTTGACTATCGCAACGCGA
*
5480571 ATTAGACTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
*
5480591 A-TTGACTTTCGC
1 ATTTGACTATCGC
5480603 GTTGCGATTT
Statistics
Matches: 178, Mismatches: 30, Indels: 25
0.76 0.13 0.11
Matches are distributed among these distances:
14 18 0.10
16 5 0.03
18 5 0.03
19 9 0.05
20 141 0.79
ACGTcount: A:0.34, C:0.22, G:0.19, T:0.25
Consensus pattern (20 bp):
ATTTGACTATCGCAACGCGA
Found at i:5480492 original size:74 final size:74
Alignment explanation
Indices: 5480371--5480513 Score: 241
Period size: 74 Copynumber: 1.9 Consensus size: 74
5480361 TCATTTGAAT
* * * **
5480371 ATCGCAACGCGAATTTGACTATCGTAATGCGAATTTGACTATCGCAACGCGAATTTGACTATCGC
1 ATCGCAACGCGAATTTAACTATCGCAACGCGAATTTGACTATCGCAACAAGAATTTGACTATCGC
5480436 AACGAAAAA
66 AACGAAAAA
5480445 ATCGCAACGCGAATTTAACTATCGCAACGCGAATTTGACTATCGCAACAAGAATTTGACTATCGC
1 ATCGCAACGCGAATTTAACTATCGCAACGCGAATTTGACTATCGCAACAAGAATTTGACTATCGC
5480510 AACG
66 AACG
5480514 TGAATTTGAT
Statistics
Matches: 64, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
74 64 1.00
ACGTcount: A:0.35, C:0.23, G:0.18, T:0.24
Consensus pattern (74 bp):
ATCGCAACGCGAATTTAACTATCGCAACGCGAATTTGACTATCGCAACAAGAATTTGACTATCGC
AACGAAAAA
Found at i:5480563 original size:114 final size:114
Alignment explanation
Indices: 5480363--5480602 Score: 322
Period size: 114 Copynumber: 2.1 Consensus size: 114
5480353 TTACACATTC
* ** * * * *
5480363 ATTTGAATATCGCAACGCGAATTTGACTATCGTAATGCGAATTTGACTATCGCAACGCGAATTTG
1 ATTTGACTATCGCAACAAGAATTTGACTATCGCAACGCGAATTTGACTATCACAACGCGAATTCG
*
5480428 ACTATCGCAACGAAAAAATCGCAACGCGAATTTA-ACTATCGCAACGCGA
66 ACTATCGCAACGAAAAAATCGCAAAGCGAA-TTAGACTATCGCAACGCGA
* * * *
5480477 ATTTGACTATCGCAACAAGAATTTGACTATCGCAACGTGAATTTGATTATCACAACGGGTATTCG
1 ATTTGACTATCGCAACAAGAATTTGACTATCGCAACGCGAATTTGACTATCACAACGCGAATTCG
* *
5480542 ACTATCGCAACGAGAAAATCGCAAAGCGTATTAGACTATCGCAACGCGA
66 ACTATCGCAACGAAAAAATCGCAAAGCGAATTAGACTATCGCAACGCGA
*
5480591 A-TTGACTTTCGC
1 ATTTGACTATCGC
5480603 GTTGCGATTT
Statistics
Matches: 110, Mismatches: 15, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
113 13 0.12
114 97 0.88
ACGTcount: A:0.34, C:0.22, G:0.19, T:0.25
Consensus pattern (114 bp):
ATTTGACTATCGCAACAAGAATTTGACTATCGCAACGCGAATTTGACTATCACAACGCGAATTCG
ACTATCGCAACGAAAAAATCGCAAAGCGAATTAGACTATCGCAACGCGA
Found at i:5480621 original size:20 final size:20
Alignment explanation
Indices: 5480596--5480634 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
5480586 CGCGAATTGA
*
5480596 CTTTCGCGTTGCGATTTTGG
1 CTTTCGCATTGCGATTTTGG
5480616 CTTTCGCATTGCGATTTTG
1 CTTTCGCATTGCGATTTTG
5480635 AGTTTAGCGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.08, C:0.21, G:0.26, T:0.46
Consensus pattern (20 bp):
CTTTCGCATTGCGATTTTGG
Found at i:5482309 original size:64 final size:64
Alignment explanation
Indices: 5482254--5482420 Score: 217
Period size: 65 Copynumber: 2.6 Consensus size: 64
5482244 CGGTGCACCA
*
5482254 AGTGTGCATCGATGCATGAAATGCATTCGATGTTTCAAAATAGCCTGAGTGCATCGATGCATGG
1 AGTGTGCATCGATGCATGAAATGCATTCGATGTTTCAAAATAGCCAGAGTGCATCGATGCATGG
** * * **
5482318 CTTGTGCATCGATGCATCAAATGCATTCGATGTTTTGAAAATATTCAGAGTGCATCGATGCATGG
1 AGTGTGCATCGATGCATGAAATGCATTCGATG-TTTCAAAATAGCCAGAGTGCATCGATGCATGG
** * * *
5482383 AGAATGCATCGGTGCATGGAATGCATTTGATGTTTCAA
1 AGTGTGCATCGATGCATGAAATGCATTCGATGTTTCAA
5482421 TTAATTCACT
Statistics
Matches: 86, Mismatches: 16, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
64 34 0.40
65 52 0.60
ACGTcount: A:0.28, C:0.16, G:0.25, T:0.31
Consensus pattern (64 bp):
AGTGTGCATCGATGCATGAAATGCATTCGATGTTTCAAAATAGCCAGAGTGCATCGATGCATGG
Found at i:5482399 original size:65 final size:62
Alignment explanation
Indices: 5482258--5482466 Score: 195
Period size: 65 Copynumber: 3.2 Consensus size: 62
5482248 GCACCAAGTG
* ** * *
5482258 TGCATCGATGCATGAAATGCATTCGATGTTTCAAAATAGCCTGAGTGCATCGATGCATGGCTTG-
1 TGCATCGATGCATCAAATGCATTCGATGTTT-AAAATATTCAGAGTGCATCGATGCATGG--AGA
5482322 TGCATCGATGCATCAAATGCATTCGATGTTTTGAAAATATTCAGAGTGCATCGATGCATGGAGAA
1 TGCATCGATGCATCAAATGCATTCGATG-TTT-AAAATATTCAGAGTGCATCGATGCATGGAG-A
* ** * * * * * *
5482387 TGCATCGGTGCATGGAATGCATTTGATGTTTCAATTAATTCACTAATGCATCGATGCATGGTTGA
1 TGCATCGATGCATCAAATGCATTCGATGTTTAAAAT-ATTCA-GAGTGCATCGATGCATGG-AGA
*
5482452 TGCATCGGTGCATCA
1 TGCATCGATGCATCA
5482467 CCTCAAATAA
Statistics
Matches: 122, Mismatches: 17, Indels: 11
0.81 0.11 0.07
Matches are distributed among these distances:
63 4 0.03
64 35 0.29
65 82 0.67
66 1 0.01
ACGTcount: A:0.28, C:0.17, G:0.24, T:0.31
Consensus pattern (62 bp):
TGCATCGATGCATCAAATGCATTCGATGTTTAAAATATTCAGAGTGCATCGATGCATGGAGA
Found at i:5482657 original size:20 final size:21
Alignment explanation
Indices: 5482634--5482673 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
5482624 GAATCGAATA
5482634 TAAAAT-TGTAAAA-TCATTTG
1 TAAAATCT-TAAAATTCATTTG
5482654 TAAAATCTTAAAATTCATTT
1 TAAAATCTTAAAATTCATTT
5482674 AACTTAATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.45, C:0.07, G:0.05, T:0.42
Consensus pattern (21 bp):
TAAAATCTTAAAATTCATTTG
Found at i:5485018 original size:20 final size:20
Alignment explanation
Indices: 5484993--5485046 Score: 65
Period size: 20 Copynumber: 2.7 Consensus size: 20
5484983 AACCCGACGG
*
5484993 ATGCATCGGTGCATGGTCT-T
1 ATGCATCGGTGCATGGT-TAA
* *
5485013 ATGCATCGATGCATTGTTAA
1 ATGCATCGGTGCATGGTTAA
5485033 ATGCATCGGTGCAT
1 ATGCATCGGTGCAT
5485047 AAAGCACAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
19 1 0.03
20 28 0.97
ACGTcount: A:0.22, C:0.19, G:0.26, T:0.33
Consensus pattern (20 bp):
ATGCATCGGTGCATGGTTAA
Found at i:5488897 original size:22 final size:21
Alignment explanation
Indices: 5488855--5488894 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
5488845 GAGTTTGTTT
*
5488855 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
5488876 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
5488895 ACAGTTTATC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:5490894 original size:64 final size:64
Alignment explanation
Indices: 5490841--5491004 Score: 229
Period size: 65 Copynumber: 2.5 Consensus size: 64
5490831 CGGTGCACCA
*
5490841 AGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAATAGCCTGAGTGCATCGATGCATGG
1 AGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAATAGCCAGAGTGCATCGATGCATGG
** * **
5490905 CTTGTGCATCGATGCATCAAATGCATTCGATGTTTTGAAAATATTCAGAGTGCATCGATGCATGG
1 AGTGTGCATCGATGCATGAAATGCATTCGATG-TTTGAAAATAGCCAGAGTGCATCGATGCATGG
** * *
5490970 AGAATGCATCGGTGCATGGAATGCATTCGATGTTT
1 AGTGTGCATCGATGCATGAAATGCATTCGATGTTT
5491005 CAATTAATTC
Statistics
Matches: 86, Mismatches: 13, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
64 32 0.37
65 54 0.63
ACGTcount: A:0.27, C:0.16, G:0.26, T:0.30
Consensus pattern (64 bp):
AGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAATAGCCAGAGTGCATCGATGCATGG
Found at i:5490993 original size:17 final size:19
Alignment explanation
Indices: 5490955--5491001 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
5490945 ATATTCAGAG
5490955 TGCATCGATGCATGGAGAA
1 TGCATCGATGCATGGAGAA
*
5490974 TGCATCGGTGCAT-G-GAA
1 TGCATCGATGCATGGAGAA
5490991 TGCATTCGATG
1 TGCA-TCGATG
5491002 TTTCAATTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 7 0.28
18 6 0.24
19 12 0.48
ACGTcount: A:0.26, C:0.17, G:0.32, T:0.26
Consensus pattern (19 bp):
TGCATCGATGCATGGAGAA
Found at i:5491024 original size:65 final size:62
Alignment explanation
Indices: 5490845--5491051 Score: 204
Period size: 65 Copynumber: 3.2 Consensus size: 62
5490835 GCACCAAGTG
* *
5490845 TGCATCGATGCATGAAATGCATTCGATGTTTGAAAATAGC-CTGAGTGCATCGATGCATGGCTTG
1 TGCATCGATGCATGAAATGCATTCGATGTTTGAAAAT-TCACT-AGTGCATCGATGCATGG--AG
5490909 -
62 A
* *
5490909 TGCATCGATGCATCAAATGCATTCGATGTTTTGAAAATATTCA-GAGTGCATCGATGCATGGAGA
1 TGCATCGATGCATGAAATGCATTCGATG-TTTG-AAA-ATTCACTAGTGCATCGATGCATGGAG-
5490973 A
62 A
* * * * *
5490974 TGCATCGGTGCATGGAATGCATTCGATGTTTCAATTAATTCACTAATGCATCGATGCATGGTTGA
1 TGCATCGATGCATGAAATGCATTCGATGTTTGAA--AATTCACTAGTGCATCGATGCATGG-AGA
*
5491039 TGCATCGGTGCAT
1 TGCATCGATGCAT
5491052 CACCTCAAAT
Statistics
Matches: 122, Mismatches: 11, Indels: 19
0.80 0.07 0.12
Matches are distributed among these distances:
63 3 0.02
64 35 0.29
65 77 0.63
66 5 0.04
67 2 0.02
ACGTcount: A:0.28, C:0.17, G:0.25, T:0.31
Consensus pattern (62 bp):
TGCATCGATGCATGAAATGCATTCGATGTTTGAAAATTCACTAGTGCATCGATGCATGGAGA
Found at i:5491244 original size:20 final size:21
Alignment explanation
Indices: 5491221--5491260 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
5491211 GAATCGAATA
5491221 TAAAAT-TGTAAAA-TCATTTG
1 TAAAATCT-TAAAATTCATTTG
5491241 TAAAATCTTAAAATTCATTT
1 TAAAATCTTAAAATTCATTT
5491261 AACTTAATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.45, C:0.07, G:0.05, T:0.42
Consensus pattern (21 bp):
TAAAATCTTAAAATTCATTTG
Found at i:5492045 original size:21 final size:18
Alignment explanation
Indices: 5492021--5492065 Score: 54
Period size: 21 Copynumber: 2.3 Consensus size: 18
5492011 GAACGGTGGG
5492021 AGGGGACTCTTGAGGGATGAT
1 AGGGGACTCTTGA---ATGAT
*
5492042 AGGGGCCTCTTGAATGAT
1 AGGGGACTCTTGAATGAT
5492060 AGGGGA
1 AGGGGA
5492066 GGCCTCTTGA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
18 10 0.45
21 12 0.55
ACGTcount: A:0.24, C:0.11, G:0.42, T:0.22
Consensus pattern (18 bp):
AGGGGACTCTTGAATGAT
Found at i:5492595 original size:18 final size:18
Alignment explanation
Indices: 5492572--5492638 Score: 80
Period size: 20 Copynumber: 3.5 Consensus size: 18
5492562 AAAACTTAAA
*
5492572 ATCGCAACACGAATGACT
1 ATCGCAACGCGAATGACT
5492590 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCG--AATGACT
5492610 ATCGCAACGCGAATTTGACT
1 ATCGCAACGCGAA--TGACT
*
5492630 ATCTCAACG
1 ATCGCAACG
5492639 AGAGAATCGC
Statistics
Matches: 43, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
18 12 0.28
20 31 0.72
ACGTcount: A:0.36, C:0.27, G:0.18, T:0.19
Consensus pattern (18 bp):
ATCGCAACGCGAATGACT
Found at i:5492608 original size:20 final size:20
Alignment explanation
Indices: 5492583--5492638 Score: 85
Period size: 20 Copynumber: 2.8 Consensus size: 20
5492573 TCGCAACACG
5492583 AATGACTATCGCAACGCGAA
1 AATGACTATCGCAACGCGAA
5492603 AATGACTATCGCAACGCGAA
1 AATGACTATCGCAACGCGAA
** *
5492623 TTTGACTATCTCAACG
1 AATGACTATCGCAACG
5492639 AGAGAATCGC
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.36, C:0.25, G:0.18, T:0.21
Consensus pattern (20 bp):
AATGACTATCGCAACGCGAA
Found at i:5492708 original size:20 final size:20
Alignment explanation
Indices: 5492683--5492724 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
5492673 GATTCTTTCA
5492683 TTGCGATAGTCAAATTCGCG
1 TTGCGATAGTCAAATTCGCG
**
5492703 TTGCGATAGTCATTTTCGCG
1 TTGCGATAGTCAAATTCGCG
5492723 TT
1 TT
5492725 ACGAAAGTAA
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:0.19, C:0.19, G:0.24, T:0.38
Consensus pattern (20 bp):
TTGCGATAGTCAAATTCGCG
Found at i:5494546 original size:20 final size:20
Alignment explanation
Indices: 5494523--5494629 Score: 110
Period size: 20 Copynumber: 5.5 Consensus size: 20
5494513 TTTGAAACTT
*
5494523 AAAATCGCAACACGAAAATG
1 AAAATCGCAACGCGAAAATG
*
5494543 AAAATCGCAACACGAAAATG
1 AAAATCGCAACGCGAAAATG
** **
5494563 ACTATCGCAACGCGAATTTG
1 AAAATCGCAACGCGAAAATG
** *
5494583 ACTATCGTAACGCG-AAATG
1 AAAATCGCAACGCGAAAATG
*
5494602 AAAATCGCAACGCGAAACT-
1 AAAATCGCAACGCGAAAATG
5494621 AAAATCGCA
1 AAAATCGCA
5494630 TTGCGATTCT
Statistics
Matches: 74, Mismatches: 12, Indels: 3
0.83 0.13 0.03
Matches are distributed among these distances:
19 23 0.31
20 51 0.69
ACGTcount: A:0.46, C:0.22, G:0.17, T:0.15
Consensus pattern (20 bp):
AAAATCGCAACGCGAAAATG
Found at i:5495632 original size:20 final size:20
Alignment explanation
Indices: 5495607--5495656 Score: 100
Period size: 20 Copynumber: 2.5 Consensus size: 20
5495597 TAAAAAGTAA
5495607 AAATTATATTTTATATTTTT
1 AAATTATATTTTATATTTTT
5495627 AAATTATATTTTATATTTTT
1 AAATTATATTTTATATTTTT
5495647 AAATTATATT
1 AAATTATATT
5495657 GATTCCTTAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (20 bp):
AAATTATATTTTATATTTTT
Found at i:5498665 original size:15 final size:17
Alignment explanation
Indices: 5498627--5498665 Score: 55
Period size: 15 Copynumber: 2.4 Consensus size: 17
5498617 AGATTGTCAG
5498627 TGGGAATATAGATTACT
1 TGGGAATATAGATTACT
*
5498644 AGGGAATA-AGATTA-T
1 TGGGAATATAGATTACT
5498659 TGGGAAT
1 TGGGAAT
5498666 GTTATATTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
15 7 0.35
16 6 0.30
17 7 0.35
ACGTcount: A:0.38, C:0.03, G:0.28, T:0.31
Consensus pattern (17 bp):
TGGGAATATAGATTACT
Found at i:5498871 original size:36 final size:38
Alignment explanation
Indices: 5498798--5498872 Score: 93
Period size: 36 Copynumber: 2.0 Consensus size: 38
5498788 GTTAGAAAAT
* *
5498798 ATTTATATATTTTTTTTTAAAAAAATTAAATTCATAAA
1 ATTTATATATATTTTTTTAAAAAAATTAAAATCATAAA
*
5498836 ATTTATATA-ATTTTTTT-ACAAAATTAAAAAT-ATAAA
1 ATTTATATATATTTTTTTAAAAAAATT-AAAATCATAAA
5498872 A
1 A
5498873 AGGTTTAATG
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
36 13 0.39
37 11 0.33
38 9 0.27
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.47
Consensus pattern (38 bp):
ATTTATATATATTTTTTTAAAAAAATTAAAATCATAAA
Found at i:5502706 original size:42 final size:42
Alignment explanation
Indices: 5502632--5502740 Score: 186
Period size: 42 Copynumber: 2.6 Consensus size: 42
5502622 TTACTCATAA
*
5502632 TTGTGACGA-AAATATTTTT-TCACTAGTCTTAGTTGGTGAT
1 TTGTGACGACAATTATTTTTGTCACTAGTCTTAGTTGGTGAT
5502672 TTGTGACGACAATTATTTTTGTCACTAGTCTTAGTTGGTGAT
1 TTGTGACGACAATTATTTTTGTCACTAGTCTTAGTTGGTGAT
*
5502714 TTGTGATGACAATTATTTTTGTCACTA
1 TTGTGACGACAATTATTTTTGTCACTA
5502741 TTGAAGTGAA
Statistics
Matches: 65, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
40 9 0.14
41 9 0.14
42 47 0.72
ACGTcount: A:0.24, C:0.11, G:0.19, T:0.46
Consensus pattern (42 bp):
TTGTGACGACAATTATTTTTGTCACTAGTCTTAGTTGGTGAT
Found at i:5503636 original size:23 final size:23
Alignment explanation
Indices: 5503610--5503670 Score: 77
Period size: 23 Copynumber: 2.7 Consensus size: 23
5503600 CACCACAGCT
*
5503610 CGTATAAATGCACCGAAGTACCA
1 CGTAAAAATGCACCGAAGTACCA
* * *
5503633 CGTAGAATTGCACCGAAGTACCG
1 CGTAAAAATGCACCGAAGTACCA
*
5503656 CATAAAAATGCACCG
1 CGTAAAAATGCACCG
5503671 TAGTGCCATA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.38, C:0.26, G:0.20, T:0.16
Consensus pattern (23 bp):
CGTAAAAATGCACCGAAGTACCA
Found at i:5510872 original size:24 final size:24
Alignment explanation
Indices: 5510844--5510895 Score: 104
Period size: 24 Copynumber: 2.2 Consensus size: 24
5510834 TATTGATGAC
5510844 ATATAAAGTGATCAATAGTATTTG
1 ATATAAAGTGATCAATAGTATTTG
5510868 ATATAAAGTGATCAATAGTATTTG
1 ATATAAAGTGATCAATAGTATTTG
5510892 ATAT
1 ATAT
5510896 TTGTTATGCC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.42, C:0.04, G:0.15, T:0.38
Consensus pattern (24 bp):
ATATAAAGTGATCAATAGTATTTG
Found at i:5517037 original size:24 final size:24
Alignment explanation
Indices: 5517009--5517060 Score: 104
Period size: 24 Copynumber: 2.2 Consensus size: 24
5516999 TATTGATGAC
5517009 ATATAAAGTGATCAATAGTATTTG
1 ATATAAAGTGATCAATAGTATTTG
5517033 ATATAAAGTGATCAATAGTATTTG
1 ATATAAAGTGATCAATAGTATTTG
5517057 ATAT
1 ATAT
5517061 TTGTTATGCC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.42, C:0.04, G:0.15, T:0.38
Consensus pattern (24 bp):
ATATAAAGTGATCAATAGTATTTG
Found at i:5522772 original size:24 final size:25
Alignment explanation
Indices: 5522724--5522772 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 25
5522714 AAAATTATAT
* * *
5522724 TAAAATTTTAGGGGGTGCGATATTA
1 TAAAATCTTAGGGGGTGCAAAATTA
5522749 TAAAATCTTA-GGGGTGCAAAATTA
1 TAAAATCTTAGGGGGTGCAAAATTA
5522773 AATAATTCAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
24 12 0.57
25 9 0.43
ACGTcount: A:0.37, C:0.06, G:0.24, T:0.33
Consensus pattern (25 bp):
TAAAATCTTAGGGGGTGCAAAATTA
Found at i:5525345 original size:14 final size:14
Alignment explanation
Indices: 5525326--5525352 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
5525316 TTTTAATTTT
5525326 GAGTTATTTGAGTC
1 GAGTTATTTGAGTC
5525340 GAGTTATTTGAGT
1 GAGTTATTTGAGT
5525353 TAACTTGAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.22, C:0.04, G:0.30, T:0.44
Consensus pattern (14 bp):
GAGTTATTTGAGTC
Found at i:5525892 original size:157 final size:157
Alignment explanation
Indices: 5525474--5526031 Score: 687
Period size: 157 Copynumber: 3.5 Consensus size: 157
5525464 TAGTCATTGC
* * * * * *
5525474 TTTCATTATTTCTTCAA-TTCATCATTTATTTTAAGTTTGTTTTTACCGAATTTGATCTACATGC
1 TTTCCTTATTTCTTTAACTTCATC-CTTATTTTAAGTTTGTTTTTACCAAATTTGAACCACATGC
* * *
5525538 TCCTAAACCATTATAGAATACATATGTACTTTCAATTCCACTTTTTGATAAC-AATTTTCTATTT
65 TCATAAACCATCATAGAATACATATGTACTTTCAATTCCTCTTTTTGATAACAAATTTTCTATTT
*
5525602 TTCAATTTAGCCCCTCAATTTTTTATAA
130 TTCAATTTAGTCCCTCAATTTTTTATAA
* * * *
5525630 TTTCCTTATTTTTTTCAA-TTCTTCCTTTATTTTAAGTCTCTTTTTTTACCAAATTTGAAACACA
1 TTTCCTTATTTCTTT-AACTTCATCC-TTATTTTAAGT-T-TGTTTTTACCAAATTTGAACCACA
* * * * *
5525694 TGCTCCTAAACCATCGA-AAAATACATATGTACTTTCCATTCCTTTTTTTGATAACAAATTTTAT
62 TGCTCATAAACCATC-ATAGAATACATATGTACTTTCAATTCCTCTTTTTGATAACAAATTTTCT
*
5525758 ATTTTTCAATTTAGTCCCTCAATTTTTTATAG
126 ATTTTTCAATTTAGTCCCTCAATTTTTTATAA
* * *
5525790 TTTCTTTGTTTCTTTAACTT-ATCCTATATTTTAAGTATGTTTTTACCAAATTTGAACCACATGC
1 TTTCCTTATTTCTTTAACTTCATCCT-TATTTTAAGTTTGTTTTTACCAAATTTGAACCACATGC
*
5525854 TCATAAATCATCATAGAATACATATGTACTTTCAATTCCTCTTTTTGATAACAAATTTTCTATTT
65 TCATAAACCATCATAGAATACATATGTACTTTCAATTCCTCTTTTTGATAACAAATTTTCTA-TT
*
5525919 TTTTAATTTAGTCCCTCAATTTTTTATAA
129 TTTCAATTTAGTCCCTCAATTTTTTATAA
* * * * ** *
5525948 TTTCCTTATTTC-TTCACTTCATTCTTATTTTAAAATTTTTTTTTACCAAATTTGAGTCACATTC
1 TTTCCTTATTTCTTTAACTTCATCCTTATTTT-AAGTTTGTTTTTACCAAATTTGAACCACATGC
* *
5526012 TCATATACCATAATAGAATA
65 TCATAAACCATCATAGAATA
5526032 TCCACGTAAC
Statistics
Matches: 344, Mismatches: 46, Indels: 22
0.83 0.11 0.05
Matches are distributed among these distances:
156 13 0.04
157 109 0.32
158 88 0.26
159 82 0.24
160 52 0.15
ACGTcount: A:0.28, C:0.18, G:0.05, T:0.49
Consensus pattern (157 bp):
TTTCCTTATTTCTTTAACTTCATCCTTATTTTAAGTTTGTTTTTACCAAATTTGAACCACATGCT
CATAAACCATCATAGAATACATATGTACTTTCAATTCCTCTTTTTGATAACAAATTTTCTATTTT
TCAATTTAGTCCCTCAATTTTTTATAA
Found at i:5527492 original size:24 final size:24
Alignment explanation
Indices: 5527444--5527492 Score: 57
Period size: 24 Copynumber: 2.0 Consensus size: 24
5527434 TTTAAAAATG
*
5527444 ATTAACCGGTATTGGTTAACCGTT
1 ATTAACCGGTATTGGTTAACAGTT
5527468 ATTAA-CGGT-TTGGTTACACAAGTT
1 ATTAACCGGTATTGGTTA-AC-AGTT
5527492 A
1 A
5527493 ACCTGTAACC
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
22 7 0.32
23 6 0.27
24 9 0.41
ACGTcount: A:0.29, C:0.14, G:0.20, T:0.37
Consensus pattern (24 bp):
ATTAACCGGTATTGGTTAACAGTT
Found at i:5527736 original size:17 final size:17
Alignment explanation
Indices: 5527714--5527749 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
5527704 TTTCAAAGAT
5527714 AATCTTTAGTAAACATA
1 AATCTTTAGTAAACATA
5527731 AATCTTTAGTAAACATA
1 AATCTTTAGTAAACATA
5527748 AA
1 AA
5527750 ATAAACTTCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.50, C:0.11, G:0.06, T:0.33
Consensus pattern (17 bp):
AATCTTTAGTAAACATA
Found at i:5530112 original size:46 final size:46
Alignment explanation
Indices: 5530045--5530424 Score: 627
Period size: 46 Copynumber: 8.3 Consensus size: 46
5530035 TTACTCATTA
*
5530045 ATTTCATTTATGGCATACTTTCATGCCTTAATGCATCATTTCATGC
1 ATTTCATTTATGGCATCCTTTCATGCCTTAATGCATCATTTCATGC
*
5530091 ATTTCATTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGC
1 ATTTCATTTATGGCATCCTTTCATGCCTTAATGCATCATTTCATGC
* *
5530137 ATTTCATTTATGTCATCCTTTCATACCTTAATGCATCATTT-ATGC
1 ATTTCATTTATGGCATCCTTTCATGCCTTAATGCATCATTTCATGC
* *
5530182 ATTTCATATATGACATCCTTTCATGCCTTAATGCATCATTTCATGC
1 ATTTCATTTATGGCATCCTTTCATGCCTTAATGCATCATTTCATGC
* *
5530228 ATTTCATTTATGACATCCTTTCATGCTTTAATGCATCATTTCATGC
1 ATTTCATTTATGGCATCCTTTCATGCCTTAATGCATCATTTCATGC
* * *
5530274 ATTTCATTTATGGTATCATTTCATGCCTTAATGCATCCTTTCATGC
1 ATTTCATTTATGGCATCCTTTCATGCCTTAATGCATCATTTCATGC
* *
5530320 ATTTCATTTATGACATCCTTTCACGCCTTAATGCATCATTTCATGC
1 ATTTCATTTATGGCATCCTTTCATGCCTTAATGCATCATTTCATGC
*
5530366 ATTTTATTTATGGCATCCTTTCATGCCTTAATGCATCATTTCATGC
1 ATTTCATTTATGGCATCCTTTCATGCCTTAATGCATCATTTCATGC
5530412 ATTTCATTTATGG
1 ATTTCATTTATGG
5530425 ATTCATTTTA
Statistics
Matches: 309, Mismatches: 24, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
45 42 0.14
46 267 0.86
ACGTcount: A:0.23, C:0.23, G:0.10, T:0.44
Consensus pattern (46 bp):
ATTTCATTTATGGCATCCTTTCATGCCTTAATGCATCATTTCATGC
Found at i:5530353 original size:183 final size:184
Alignment explanation
Indices: 5530045--5530423 Score: 652
Period size: 183 Copynumber: 2.1 Consensus size: 184
5530035 TTACTCATTA
* *
5530045 ATTTCATTTATGGCATACTTTCATGCCTTAATGCATCATTTCATGCATTTCATTTATGGCATCCT
1 ATTTCATTTATGACATACTTTCATGCCTTAATGCATCATTTCATGCATTTCATTTATGGCATCAT
* *
5530110 TTCATGCCTTAATGCATCCTTTCATGCATTTCATTTATGTCATCCTTTCATACCTTAATGCATCA
66 TTCATGCCTTAATGCATCCTTTCATGCATTTCATTTATGACATCCTTTCACACCTTAATGCATCA
5530175 TTT-ATGCATTTCATATATGACATCCTTTCATGCCTTAATGCATCATTTCATGC
131 TTTCATGCATTTCATATATGACATCCTTTCATGCCTTAATGCATCATTTCATGC
* * *
5530228 ATTTCATTTATGACATCCTTTCATGCTTTAATGCATCATTTCATGCATTTCATTTATGGTATCAT
1 ATTTCATTTATGACATACTTTCATGCCTTAATGCATCATTTCATGCATTTCATTTATGGCATCAT
*
5530293 TTCATGCCTTAATGCATCCTTTCATGCATTTCATTTATGACATCCTTTCACGCCTTAATGCATCA
66 TTCATGCCTTAATGCATCCTTTCATGCATTTCATTTATGACATCCTTTCACACCTTAATGCATCA
* * *
5530358 TTTCATGCATTTTATTTATGGCATCCTTTCATGCCTTAATGCATCATTTCATGC
131 TTTCATGCATTTCATATATGACATCCTTTCATGCCTTAATGCATCATTTCATGC
5530412 ATTTCATTTATG
1 ATTTCATTTATG
5530424 GATTCATTTT
Statistics
Matches: 184, Mismatches: 11, Indels: 1
0.94 0.06 0.01
Matches are distributed among these distances:
183 125 0.68
184 59 0.32
ACGTcount: A:0.23, C:0.23, G:0.09, T:0.45
Consensus pattern (184 bp):
ATTTCATTTATGACATACTTTCATGCCTTAATGCATCATTTCATGCATTTCATTTATGGCATCAT
TTCATGCCTTAATGCATCCTTTCATGCATTTCATTTATGACATCCTTTCACACCTTAATGCATCA
TTTCATGCATTTCATATATGACATCCTTTCATGCCTTAATGCATCATTTCATGC
Found at i:5531483 original size:17 final size:17
Alignment explanation
Indices: 5531460--5531505 Score: 83
Period size: 17 Copynumber: 2.7 Consensus size: 17
5531450 TTAATCCTTC
5531460 CTTAATCTTACATATCA
1 CTTAATCTTACATATCA
*
5531477 TTTAATCTTACATATCA
1 CTTAATCTTACATATCA
5531494 CTTAATCTTACA
1 CTTAATCTTACA
5531506 AGAGCAACCC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.35, C:0.22, G:0.00, T:0.43
Consensus pattern (17 bp):
CTTAATCTTACATATCA
Found at i:5538899 original size:20 final size:20
Alignment explanation
Indices: 5538870--5538912 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
5538860 ATTCCACCAC
*
5538870 ATGCAACTATATGCTCCTAA
1 ATGCAACTATATGATCCTAA
*
5538890 ATGCATCTATATGATCCTAA
1 ATGCAACTATATGATCCTAA
5538910 ATG
1 ATG
5538913 GGCTATTAGG
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:0.35, C:0.21, G:0.12, T:0.33
Consensus pattern (20 bp):
ATGCAACTATATGATCCTAA
Found at i:5539007 original size:20 final size:20
Alignment explanation
Indices: 5538979--5539057 Score: 68
Period size: 20 Copynumber: 3.6 Consensus size: 20
5538969 GAGTTACCAA
*
5538979 CATCCTTTCATGCCTTAATG
1 CATCATTTCATGCCTTAATG
**
5538999 CATCATTTCATGTATTTTATTTATGG
1 CATCATTTCATG--CCTTA---AT-G
*
5539025 CATCATTTCATTCCTTAATG
1 CATCATTTCATGCCTTAATG
5539045 CATCATTTCATGC
1 CATCATTTCATGC
5539058 ATTTCATTTA
Statistics
Matches: 46, Mismatches: 7, Indels: 12
0.71 0.11 0.18
Matches are distributed among these distances:
20 24 0.52
21 2 0.04
22 3 0.07
24 3 0.07
25 2 0.04
26 12 0.26
ACGTcount: A:0.23, C:0.23, G:0.09, T:0.46
Consensus pattern (20 bp):
CATCATTTCATGCCTTAATG
Found at i:5539034 original size:26 final size:26
Alignment explanation
Indices: 5538998--5539074 Score: 76
Period size: 26 Copynumber: 3.2 Consensus size: 26
5538988 ATGCCTTAAT
* *
5538998 GCATCATTTCATGTATTTTATTTATG
1 GCATCATTTCATGCATTTCATTTATG
* *
5539024 GCATCA-TT--T-CA-TTCCTTAAT-
1 GCATCATTTCATGCATTTCATTTATG
5539044 GCATCATTTCATGCATTTCATTTATG
1 GCATCATTTCATGCATTTCATTTATG
5539070 GCATC
1 GCATC
5539075 CATCTGTGCC
Statistics
Matches: 39, Mismatches: 6, Indels: 12
0.68 0.11 0.21
Matches are distributed among these distances:
20 6 0.15
21 8 0.21
22 1 0.03
23 2 0.05
24 2 0.05
25 9 0.23
26 11 0.28
ACGTcount: A:0.23, C:0.19, G:0.10, T:0.47
Consensus pattern (26 bp):
GCATCATTTCATGCATTTCATTTATG
Found at i:5539051 original size:46 final size:46
Alignment explanation
Indices: 5538979--5539129 Score: 205
Period size: 46 Copynumber: 3.3 Consensus size: 46
5538969 GAGTTACCAA
* * *
5538979 CATCCTTTCATGCCTTAATGCATCATTTCATGTATTTTATTTATGG
1 CATCATTTCATGCCTTAATGCATCATTTCATGCATTTCATTTATGG
*
5539025 CATCATTTCATTCCTTAATGCATCATTTCATGCATTTCATTTATGG
1 CATCATTTCATGCCTTAATGCATCATTTCATGCATTTCATTTATGG
* * * *
5539071 CATCCATCT-GTGCCTTAATGCATTATTTCATGCATTTCATTTATGT
1 CAT-CATTTCATGCCTTAATGCATCATTTCATGCATTTCATTTATGG
*
5539117 CATCCTTTCATGC
1 CATCATTTCATGC
5539130 ATTTCATTTA
Statistics
Matches: 91, Mismatches: 12, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
45 3 0.03
46 84 0.92
47 4 0.04
ACGTcount: A:0.22, C:0.23, G:0.10, T:0.46
Consensus pattern (46 bp):
CATCATTTCATGCCTTAATGCATCATTTCATGCATTTCATTTATGG
Found at i:5539132 original size:26 final size:25
Alignment explanation
Indices: 5539042--5539238 Score: 130
Period size: 26 Copynumber: 8.1 Consensus size: 25
5539032 TCATTCCTTA
*
5539042 ATGCATCATTTCATGCATTTCATTT
1 ATGCATCCTTTCATGCATTTCATTT
* * * *
5539067 ATGGCATCC-ATC-TG---TGCCTTA
1 AT-GCATCCTTTCATGCATTTCATTT
**
5539088 ATGCATTATTTCATGCATTTCATTT
1 ATGCATCCTTTCATGCATTTCATTT
5539113 ATGTCATCCTTTCATGCATTTCATTT
1 ATG-CATCCTTTCATGCATTTCATTT
** *
5539139 ATGGCATCCTTTCAT--ACCTCCTTT
1 AT-GCATCCTTTCATGCATTTCATTT
*
5539163 CAATGCATACTTTCATGCATTTCATTT
1 --ATGCATCCTTTCATGCATTTCATTT
* * *
5539190 ATGGTATCATTTCATGC----CA-TA
1 AT-GCATCCTTTCATGCATTTCATTT
5539211 ATGCATCCTTTCATGCATTTCATTT
1 ATGCATCCTTTCATGCATTTCATTT
5539236 ATG
1 ATG
5539239 GATTCGTTTT
Statistics
Matches: 127, Mismatches: 27, Indels: 36
0.67 0.14 0.19
Matches are distributed among these distances:
20 16 0.13
21 11 0.09
22 4 0.03
24 10 0.08
25 28 0.22
26 51 0.40
27 7 0.06
ACGTcount: A:0.22, C:0.23, G:0.10, T:0.45
Consensus pattern (25 bp):
ATGCATCCTTTCATGCATTTCATTT
Found at i:5539187 original size:77 final size:73
Alignment explanation
Indices: 5539045--5539206 Score: 206
Period size: 77 Copynumber: 2.2 Consensus size: 73
5539035 TTCCTTAATG
*
5539045 CATCATTTCATGCATTTCATTTATGGCATCCATCTGTGCCTTAATGCATTATTTCATGCATTTCA
1 CATCATTTCATGCATTTCATTTATGGCATCCATCTCTGCCTTAATGCATTATTTCATGCATTTCA
5539110 TTTAT-GT
66 TTTATGGT
* *
5539117 CATCCTTTCATGCATTTCATTTATGGCATCCTTTCATACCT-CCTTTCAATGCA-TACTTTCATG
1 CATCATTTCATGCATTTCATTTATGGCATCC-ATC-T--CTGCC-TT-AATGCATTA-TTTCATG
5539180 CATTTCATTTATGGT
59 CATTTCATTTATGGT
5539195 -ATCATTTCATGC
1 CATCATTTCATGC
5539207 CATAATGCAT
Statistics
Matches: 78, Mismatches: 4, Indels: 11
0.84 0.04 0.12
Matches are distributed among these distances:
72 30 0.38
73 2 0.03
74 1 0.01
75 2 0.03
76 5 0.06
77 36 0.46
78 2 0.03
ACGTcount: A:0.22, C:0.23, G:0.10, T:0.45
Consensus pattern (73 bp):
CATCATTTCATGCATTTCATTTATGGCATCCATCTCTGCCTTAATGCATTATTTCATGCATTTCA
TTTATGGT
Found at i:5539213 original size:123 final size:118
Alignment explanation
Indices: 5538999--5539238 Score: 313
Period size: 123 Copynumber: 2.0 Consensus size: 118
5538989 TGCCTTAATG
* *
5538999 CATCATTTCATGTATTTTATTTATGGCATCATTTCATTCCTTAATGCATCATTTCATGCATTTCA
1 CATCATTTCATGCATTTCATTTATGGCATCATTTCATTCCTTAATGCATCATTTCATGCATTTCA
* * *
5539064 TTTATGGCATCCATCTGTGCCTTAATGCATTATTTCATGCATTTCATTTATGT
66 TTTATGGCATCCATCTATGCCATAATGCATCATTTCATGCATTTCATTTATGT
* *
5539117 CATCCTTTCATGCATTTCATTTATGGCATCCTTTCATACCTCCTTTCAATGCAT-ACTTTCATGC
1 CATCATTTCATGCATTTCATTTATGGCATCATTTCAT---TCC-TT-AATGCATCA-TTTCATGC
* * *
5539181 ATTTCATTTATGGTAT-CATTTCATGCCATAATGCATCCTTTCATGCATTTCATTTATG
60 ATTTCATTTATGGCATCCATCT-ATGCCATAATGCATCATTTCATGCATTTCATTTATG
5539239 GATTCGTTTT
Statistics
Matches: 105, Mismatches: 10, Indels: 9
0.85 0.08 0.07
Matches are distributed among these distances:
118 33 0.31
121 3 0.03
122 7 0.07
123 62 0.59
ACGTcount: A:0.23, C:0.22, G:0.10, T:0.46
Consensus pattern (118 bp):
CATCATTTCATGCATTTCATTTATGGCATCATTTCATTCCTTAATGCATCATTTCATGCATTTCA
TTTATGGCATCCATCTATGCCATAATGCATCATTTCATGCATTTCATTTATGT
Found at i:5539214 original size:46 final size:49
Alignment explanation
Indices: 5539121--5539239 Score: 154
Period size: 51 Copynumber: 2.4 Consensus size: 49
5539111 TTATGTCATC
* * *
5539121 CTTTCATGCATTTCATTTATGGCATCCTTTCATACCTCCTTTCAATGCATA
1 CTTTCATGCATTTCATTTATGGCATCATTTCAT--CGCCTATCAATGCATA
* *
5539172 CTTTCATGCATTTCATTTATGGTATCATTTCAT-GCC-AT-AATGCATC
1 CTTTCATGCATTTCATTTATGGCATCATTTCATCGCCTATCAATGCATA
5539218 CTTTCATGCATTTCATTTATGG
1 CTTTCATGCATTTCATTTATGG
5539240 ATTCGTTTTA
Statistics
Matches: 63, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
46 29 0.46
47 1 0.02
48 2 0.03
51 31 0.49
ACGTcount: A:0.22, C:0.24, G:0.10, T:0.45
Consensus pattern (49 bp):
CTTTCATGCATTTCATTTATGGCATCATTTCATCGCCTATCAATGCATA
Found at i:5549458 original size:117 final size:117
Alignment explanation
Indices: 5549247--5549764 Score: 761
Period size: 117 Copynumber: 4.4 Consensus size: 117
5549237 TTCAGGCTCT
* * * * *
5549247 TTTGTTGTGTGCTCAGGGTAAGTCCTTACTGGTGTGCAGGTAGGTGTATGGTTCTGGGGTACCTA
1 TTTGCTGTGTGCTTAGGGTAAGTCTTTACTGGTGTGCAGGTGGGTGTATGGTTCTGGGGAACCTA
5549312 CACATTGTAGTGAGTGGAGTGACTGGATGGGGAAGTTATTACTACAGACTCC
66 CACATTGTAGTGAGTGGAGTGACTGGATGGGGAAGTTATTACTACAGACTCC
*
5549364 TTTGCTGTGTGCTTAGGGTAAGTCTTTACTGGTGTGCAGGTGGGTGTATGGTTCTGGGGAACTTA
1 TTTGCTGTGTGCTTAGGGTAAGTCTTTACTGGTGTGCAGGTGGGTGTATGGTTCTGGGGAACCTA
**
5549429 CACATTGTAGTGAGTGGAGTGACTGGATGGGGAAGTTATTACTGTAGACTCC
66 CACATTGTAGTGAGTGGAGTGACTGGATGGGGAAGTTATTACTACAGACTCC
* *
5549481 TTTACTGTGTGCTTAGGGTAAGTCTTTACTGGTGTACAGGTGGGTGTATGGTTCTGGGGAACCTA
1 TTTGCTGTGTGCTTAGGGTAAGTCTTTACTGGTGTGCAGGTGGGTGTATGGTTCTGGGGAACCTA
*
5549546 CACATTGTAGTGAGTGGAGTGACTGGATGGGGAAGTTATTACTGCAGACTCC
66 CACATTGTAGTGAGTGGAGTGACTGGATGGGGAAGTTATTACTACAGACTCC
* * ** *
5549598 TTTGCTGTGTGCTTAGGGTAAGTCTTTACTGTTGTGCAGGTGGGTGTATAGTTCTAAGGAACTTA
1 TTTGCTGTGTGCTTAGGGTAAGTCTTTACTGGTGTGCAGGTGGGTGTATGGTTCTGGGGAACCTA
* ** * * * *
5549663 CACATTTTAGTGA-TGGAAACGACTGGATGGAGACGTTATTTCTACAGGCTCC
66 CACATTGTAGTGAGTGG-AGTGACTGGATGGGGAAGTTATTACTACAGACTCC
** * *
5549715 TCAGCT-TCGTGCTTAGGGTAAGTCCTTACTGGTGTGTAGGTGGGTGTATG
1 TTTGCTGT-GTGCTTAGGGTAAGTCTTTACTGGTGTGCAGGTGGGTGTATG
5549765 TTTCGGGAAA
Statistics
Matches: 366, Mismatches: 33, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
116 4 0.01
117 362 0.99
ACGTcount: A:0.20, C:0.14, G:0.33, T:0.34
Consensus pattern (117 bp):
TTTGCTGTGTGCTTAGGGTAAGTCTTTACTGGTGTGCAGGTGGGTGTATGGTTCTGGGGAACCTA
CACATTGTAGTGAGTGGAGTGACTGGATGGGGAAGTTATTACTACAGACTCC
Found at i:5556895 original size:21 final size:21
Alignment explanation
Indices: 5556871--5556920 Score: 91
Period size: 21 Copynumber: 2.4 Consensus size: 21
5556861 GTCCAAAGAA
*
5556871 GCATGTATTATGGACTTTGGT
1 GCATGTATTATGGACTCTGGT
5556892 GCATGTATTATGGACTCTGGT
1 GCATGTATTATGGACTCTGGT
5556913 GCATGTAT
1 GCATGTAT
5556921 CATTCACCCA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.20, C:0.12, G:0.28, T:0.40
Consensus pattern (21 bp):
GCATGTATTATGGACTCTGGT
Found at i:5557416 original size:9 final size:9
Alignment explanation
Indices: 5557402--5557428 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
5557392 AAGTATGGGT
5557402 AGAAATATC
1 AGAAATATC
5557411 AGAAATATC
1 AGAAATATC
5557420 AGAAATATC
1 AGAAATATC
5557429 CGAGTTATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.56, C:0.11, G:0.11, T:0.22
Consensus pattern (9 bp):
AGAAATATC
Found at i:5560054 original size:22 final size:22
Alignment explanation
Indices: 5560026--5560072 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
5560016 TCGTTTTCAA
*
5560026 TTTTTTGAAATTTTGGCTTTTT
1 TTTTTTGAAATTTTGCCTTTTT
***
5560048 TTTTTTGTTTTTTTGCCTTTTT
1 TTTTTTGAAATTTTGCCTTTTT
5560070 TTT
1 TTT
5560073 GAAAAAAATA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.06, C:0.06, G:0.11, T:0.77
Consensus pattern (22 bp):
TTTTTTGAAATTTTGCCTTTTT
Found at i:5561821 original size:117 final size:117
Alignment explanation
Indices: 5561614--5562360 Score: 1201
Period size: 117 Copynumber: 6.5 Consensus size: 117
5561604 GTATTTCAGG
* * *
5561614 CTCCTTTGCTGTGTGCTCAGGGTAAGTCCTTACTGGTGTGCAGGTAGGTGTATGGTTCTGGGGAA
1 CTCCTTTGCTGTGTGCTTAGGGTAAGTCTTTACTGGTGTGCAGGTGGGTGTATGGTTCTGGGGAA
*
5561679 CCTACACATTGTAGTGAGTGAAGTGACTGGATGGGGAAGTTATTACTGCAGA
66 CCTACACATTGTAGTGAGTGGAGTGACTGGATGGGGAAGTTATTACTGCAGA
*
5561731 CTCCTTTGCTGTGTGCTTAGGGTAAGTCTTTACTGGTGTGCAGTTGGGTGTATGGTTCTGGGGAA
1 CTCCTTTGCTGTGTGCTTAGGGTAAGTCTTTACTGGTGTGCAGGTGGGTGTATGGTTCTGGGGAA
*
5561796 CCTACACATTGTAGTGAGTGGAGTGACTGGATGGGGAAGTTATTACTACAGA
66 CCTACACATTGTAGTGAGTGGAGTGACTGGATGGGGAAGTTATTACTGCAGA
*
5561848 CTCCTTTGCTGTGTGCTTAGGGTAAGTCTTTACTGGTGTGCAGGTGGGTGTATGGTTATGGGGAA
1 CTCCTTTGCTGTGTGCTTAGGGTAAGTCTTTACTGGTGTGCAGGTGGGTGTATGGTTCTGGGGAA
5561913 CCTACACATTGTAGTGAGTGGAGTGACTGGATGGGGAAGTTATTACTGCAGA
66 CCTACACATTGTAGTGAGTGGAGTGACTGGATGGGGAAGTTATTACTGCAGA
5561965 ---C--T-C---GTGCTTAGGGTAAGTCTTTACTGGTGTGCAGGTGGGTGTATGGTTCTGGGGAA
1 CTCCTTTGCTGTGTGCTTAGGGTAAGTCTTTACTGGTGTGCAGGTGGGTGTATGGTTCTGGGGAA
* *
5562021 CCTACACATTGTAGTGAGTGGAGTGACTGGATAGGGAAGTTATTACTACAGA
66 CCTACACATTGTAGTGAGTGGAGTGACTGGATGGGGAAGTTATTACTGCAGA
5562073 CTCCTTTGCTGTGTGCTTAGGGTAAGTCTTTACTGGTGTGCAGGTGGGTGTATGGTTCTGGGGAA
1 CTCCTTTGCTGTGTGCTTAGGGTAAGTCTTTACTGGTGTGCAGGTGGGTGTATGGTTCTGGGGAA
5562138 CCTACACATTGTAGTGAGTGGAGTGACTGGATGGGGAAGTTATTACTGCAGA
66 CCTACACATTGTAGTGAGTGGAGTGACTGGATGGGGAAGTTATTACTGCAGA
* * *
5562190 CTCCTTTGCTGTGTGCTTAGAGTAAGTCTTTACTGGTGTGCAGGTGGGTATATGGTTCTGAGGAA
1 CTCCTTTGCTGTGTGCTTAGGGTAAGTCTTTACTGGTGTGCAGGTGGGTGTATGGTTCTGGGGAA
* ** * * *
5562255 CTTACACATTGTAGTGA-TGGAAACGACTGGATGGAGACGTTATTACTGCAGG
66 CCTACACATTGTAGTGAGTGG-AGTGACTGGATGGGGAAGTTATTACTGCAGA
** * *
5562307 CTCCTCAGCT-TCGTGCTTAGGGTAAGTCCTTACTGGTGTGCATGTGGGTGTATG
1 CTCCTTTGCTGT-GTGCTTAGGGTAAGTCTTTACTGGTGTGCAGGTGGGTGTATG
5562361 TTTCGGGAAA
Statistics
Matches: 590, Mismatches: 29, Indels: 22
0.92 0.05 0.03
Matches are distributed among these distances:
108 102 0.17
111 2 0.00
112 1 0.00
113 1 0.00
114 2 0.00
116 4 0.01
117 478 0.81
ACGTcount: A:0.20, C:0.14, G:0.33, T:0.32
Consensus pattern (117 bp):
CTCCTTTGCTGTGTGCTTAGGGTAAGTCTTTACTGGTGTGCAGGTGGGTGTATGGTTCTGGGGAA
CCTACACATTGTAGTGAGTGGAGTGACTGGATGGGGAAGTTATTACTGCAGA
Found at i:5562263 original size:342 final size:346
Alignment explanation
Indices: 5561626--5562360 Score: 1219
Period size: 342 Copynumber: 2.1 Consensus size: 346
5561616 CCTTTGCTGT
* *
5561626 GTGCTCAGGGTAAGTCCTTACTGGTGTGCAGGTAGGTGTATGGTTCTGGGGAACCTACACATTGT
1 GTGCTTAGGGTAAGTCCTTACTGGTGTGCAGGTGGGTGTATGGTTCTGGGGAACCTACACATTGT
* *
5561691 AGTGAGTGAAGTGACTGGATGGGGAAGTTATTACTGCAGACTCCTTTGCTGTGTGCTTAGGGTAA
66 AGTGAGTGAAGTGACTGGATAGGGAAGTTATTACTACAGACTCCTTTGCTGTGTGCTTAGGGTAA
*
5561756 GTCTTTACTGGTGTGCAGTTGGGTGTATGGTTCTGGGGAACCTACACATTGTAGTGAGTGGAGTG
131 GTCTTTACTGGTGTGCAGGTGGGTGTATGGTTCTGGGGAACCTACACATTGTAGTGAGTGGAGTG
*
5561821 ACTGGATGGGGAAGTTATTACTACAGACTCCTTTGCTGTGTGCTTAGGGTAAGTCTTTACTGGTG
196 ACTGGATGGGGAAGTTATTACTACAGACTCCTTTGCTGTGTGCTTAGAGTAAGTCTTTACTGGTG
* * ** *
5561886 TGCAGGTGGGTGTATGGTTATGGGGAACCTACACATTGTAGTGAGTGG-AGTGACTGGATGGGGA
261 TGCAGGTGGGTATATGGTTATGAGGAACCTACACATTGTAGTGA-TGGAAACGACTGGATGGAGA
5561950 AGTTATTACTGCA-G-A-C-TC
325 AGTTATTACTGCAGGCAGCTTC
*
5561968 GTGCTTAGGGTAAGTCTTTACTGGTGTGCAGGTGGGTGTATGGTTCTGGGGAACCTACACATTGT
1 GTGCTTAGGGTAAGTCCTTACTGGTGTGCAGGTGGGTGTATGGTTCTGGGGAACCTACACATTGT
*
5562033 AGTGAGTGGAGTGACTGGATAGGGAAGTTATTACTACAGACTCCTTTGCTGTGTGCTTAGGGTAA
66 AGTGAGTGAAGTGACTGGATAGGGAAGTTATTACTACAGACTCCTTTGCTGTGTGCTTAGGGTAA
5562098 GTCTTTACTGGTGTGCAGGTGGGTGTATGGTTCTGGGGAACCTACACATTGTAGTGAGTGGAGTG
131 GTCTTTACTGGTGTGCAGGTGGGTGTATGGTTCTGGGGAACCTACACATTGTAGTGAGTGGAGTG
*
5562163 ACTGGATGGGGAAGTTATTACTGCAGACTCCTTTGCTGTGTGCTTAGAGTAAGTCTTTACTGGTG
196 ACTGGATGGGGAAGTTATTACTACAGACTCCTTTGCTGTGTGCTTAGAGTAAGTCTTTACTGGTG
* * *
5562228 TGCAGGTGGGTATATGGTTCTGAGGAACTTACACATTGTAGTGATGGAAACGACTGGATGGAGAC
261 TGCAGGTGGGTATATGGTTATGAGGAACCTACACATTGTAGTGATGGAAACGACTGGATGGAGAA
5562293 GTTATTACTGCAGGCTCCTCAGCTTC
326 GTTATTACTGCAGG-----CAGCTTC
*
5562319 GTGCTTAGGGTAAGTCCTTACTGGTGTGCATGTGGGTGTATG
1 GTGCTTAGGGTAAGTCCTTACTGGTGTGCAGGTGGGTGTATG
5562361 TTTCGGGAAA
Statistics
Matches: 364, Mismatches: 19, Indels: 11
0.92 0.05 0.03
Matches are distributed among these distances:
341 3 0.01
342 316 0.87
343 1 0.00
349 1 0.00
350 1 0.00
351 42 0.12
ACGTcount: A:0.20, C:0.14, G:0.34, T:0.32
Consensus pattern (346 bp):
GTGCTTAGGGTAAGTCCTTACTGGTGTGCAGGTGGGTGTATGGTTCTGGGGAACCTACACATTGT
AGTGAGTGAAGTGACTGGATAGGGAAGTTATTACTACAGACTCCTTTGCTGTGTGCTTAGGGTAA
GTCTTTACTGGTGTGCAGGTGGGTGTATGGTTCTGGGGAACCTACACATTGTAGTGAGTGGAGTG
ACTGGATGGGGAAGTTATTACTACAGACTCCTTTGCTGTGTGCTTAGAGTAAGTCTTTACTGGTG
TGCAGGTGGGTATATGGTTATGAGGAACCTACACATTGTAGTGATGGAAACGACTGGATGGAGAA
GTTATTACTGCAGGCAGCTTC
Found at i:5565291 original size:20 final size:20
Alignment explanation
Indices: 5565263--5565387 Score: 79
Period size: 20 Copynumber: 5.7 Consensus size: 20
5565253 GAGTTATCAA
*
5565263 CATCCTTTCATGCCTTAATG
1 CATCATTTCATGCCTTAATG
*
5565283 CATCATTTCATGCATTTCATTTATG
1 CATCATTTCATGC----C-TTAATG
*
5565308 CCATCCTTTCATGCCTTAATG
1 -CATCATTTCATGCCTTAATG
* * *
5565329 AATCATTTTATGCATTTCATTTATAG
1 CATCATTTCATGC----C-TTAAT-G
*
5565355 CATCCTTTCATGCCTTAATG
1 CATCATTTCATGCCTTAATG
5565375 CATCATTTCATGC
1 CATCATTTCATGC
5565388 ATTTGATTTT
Statistics
Matches: 80, Mismatches: 13, Indels: 24
0.68 0.11 0.21
Matches are distributed among these distances:
20 35 0.44
21 9 0.11
22 2 0.03
24 2 0.03
25 9 0.11
26 23 0.29
ACGTcount: A:0.23, C:0.25, G:0.09, T:0.43
Consensus pattern (20 bp):
CATCATTTCATGCCTTAATG
Found at i:5565473 original size:20 final size:20
Alignment explanation
Indices: 5565448--5565526 Score: 59
Period size: 20 Copynumber: 3.6 Consensus size: 20
5565438 CATTTATGGA
5565448 ATCATTTCATGCCTTAATGC
1 ATCATTTCATGCCTTAATGC
*
5565468 ATCATTTTCATGCATTTCATTTATGTC
1 ATCA-TTTCATGC----C-TTAATG-C
* *
5565495 ATCCTTTTATGCCTTAATGC
1 ATCATTTCATGCCTTAATGC
*
5565515 ATCATTTAATGC
1 ATCATTTCATGC
5565527 ATTTCATTTA
Statistics
Matches: 46, Mismatches: 6, Indels: 14
0.70 0.09 0.21
Matches are distributed among these distances:
20 15 0.33
21 13 0.28
22 1 0.02
25 1 0.02
26 12 0.26
27 4 0.09
ACGTcount: A:0.24, C:0.22, G:0.09, T:0.46
Consensus pattern (20 bp):
ATCATTTCATGCCTTAATGC
Found at i:5565549 original size:46 final size:45
Alignment explanation
Indices: 5565263--5565538 Score: 399
Period size: 46 Copynumber: 6.0 Consensus size: 45
5565253 GAGTTATCAA
5565263 CATCCTTTCATGCCTTAATGCATCATTTCATGCATTTCATTTATG
1 CATCCTTTCATGCCTTAATGCATCATTTCATGCATTTCATTTATG
* *
5565308 CCATCCTTTCATGCCTTAATGAATCATTTTATGCATTTCATTTATAG
1 -CATCCTTTCATGCCTTAATGCATCATTTCATGCATTTCATTTAT-G
* *
5565355 CATCCTTTCATGCCTTAATGCATCATTTCATGCATTTGATTTTTG
1 CATCCTTTCATGCCTTAATGCATCATTTCATGCATTTCATTTATG
* * *
5565400 AAATCCTTTCATGCCTTAATGCATCCTTTCATGTATTTCATTTATGG
1 -CATCCTTTCATGCCTTAATGCATCATTTCATGCATTTCATTTAT-G
* *
5565447 AATCATTTCATGCCTTAATGCATCATTTTCATGCATTTCATTTATG
1 CATCCTTTCATGCCTTAATGCATCA-TTTCATGCATTTCATTTATG
* *
5565493 TCATCCTTTTATGCCTTAATGCATCATTTAATGCATTTCATTTATG
1 -CATCCTTTCATGCCTTAATGCATCATTTCATGCATTTCATTTATG
5565539 GATTCGTTTT
Statistics
Matches: 207, Mismatches: 18, Indels: 10
0.88 0.08 0.04
Matches are distributed among these distances:
45 1 0.00
46 164 0.79
47 42 0.20
ACGTcount: A:0.24, C:0.21, G:0.09, T:0.46
Consensus pattern (45 bp):
CATCCTTTCATGCCTTAATGCATCATTTCATGCATTTCATTTATG
Found at i:5576304 original size:19 final size:21
Alignment explanation
Indices: 5576282--5576328 Score: 64
Period size: 20 Copynumber: 2.4 Consensus size: 21
5576272 GATATTTTTA
*
5576282 TTCTTTAA-TTCTTT-TATAT
1 TTCTTTAACATCTTTATATAT
5576301 TTCTTTAACATCTTTATATAT
1 TTCTTTAACATCTTTATATAT
5576322 TT-TTTAA
1 TTCTTTAA
5576329 ATAAAATATT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
19 8 0.32
20 10 0.40
21 7 0.28
ACGTcount: A:0.26, C:0.11, G:0.00, T:0.64
Consensus pattern (21 bp):
TTCTTTAACATCTTTATATAT
Found at i:5586209 original size:19 final size:20
Alignment explanation
Indices: 5586173--5586211 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
5586163 ATGACTATTT
5586173 TATCTGATTTGGAATGTTTC
1 TATCTGATTTGGAATGTTTC
5586193 TATCTG-TTT-GAATTGTTTC
1 TATCTGATTTGGAA-TGTTTC
5586212 CCTATGATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 3 0.17
19 9 0.50
20 6 0.33
ACGTcount: A:0.18, C:0.10, G:0.18, T:0.54
Consensus pattern (20 bp):
TATCTGATTTGGAATGTTTC
Found at i:5586468 original size:35 final size:36
Alignment explanation
Indices: 5586406--5586475 Score: 108
Period size: 35 Copynumber: 2.0 Consensus size: 36
5586396 AAGTCTCTGC
5586406 AGGTTCAACTCGGACCAAGCTGGTAATTCCTTATAT
1 AGGTTCAACTCGGACCAAGCTGGTAATTCCTTATAT
*
5586442 AGGTTCAACATC-GATCAA-CTGGTAATTCCTTATA
1 AGGTTCAAC-TCGGACCAAGCTGGTAATTCCTTATA
5586476 GACCTAAGGC
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
35 16 0.50
36 14 0.44
37 2 0.06
ACGTcount: A:0.30, C:0.21, G:0.17, T:0.31
Consensus pattern (36 bp):
AGGTTCAACTCGGACCAAGCTGGTAATTCCTTATAT
Found at i:5586734 original size:35 final size:35
Alignment explanation
Indices: 5586688--5586758 Score: 133
Period size: 35 Copynumber: 2.0 Consensus size: 35
5586678 TGGCACCTAC
*
5586688 GCCTTTTGGGCCTAGGATAAGTTTTTATGGATGCA
1 GCCTTTTGGGCCTAGGATAAGTTCTTATGGATGCA
5586723 GCCTTTTGGGCCTAGGATAAGTTCTTATGGATGCA
1 GCCTTTTGGGCCTAGGATAAGTTCTTATGGATGCA
5586758 G
1 G
5586759 TTCTTGGGAA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.20, C:0.15, G:0.30, T:0.35
Consensus pattern (35 bp):
GCCTTTTGGGCCTAGGATAAGTTCTTATGGATGCA
Found at i:5587748 original size:2 final size:2
Alignment explanation
Indices: 5587741--5587774 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
5587731 CGCCTTTTAA
5587741 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
5587775 CACATGGACA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5588586 original size:16 final size:17
Alignment explanation
Indices: 5588554--5588592 Score: 62
Period size: 16 Copynumber: 2.3 Consensus size: 17
5588544 AAATATTTTT
5588554 AAATCTTAAAATATATAA
1 AAAT-TTAAAATATATAA
5588572 AAATTTAAAAT-TATAA
1 AAATTTAAAATATATAA
5588588 AAATT
1 AAATT
5588593 GTTATTTGGT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 10 0.48
17 7 0.33
18 4 0.19
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.36
Consensus pattern (17 bp):
AAATTTAAAATATATAA
Found at i:5588658 original size:16 final size:15
Alignment explanation
Indices: 5588606--5588661 Score: 60
Period size: 14 Copynumber: 3.6 Consensus size: 15
5588596 ATTTGGTTAA
5588606 ATTTTAAAATAATAATT
1 ATTTTAAAA-AAT-ATT
*
5588623 CTTTTAAAAAA-ATT
1 ATTTTAAAAAATATT
*
5588637 AGTTTAAAAAATATTT
1 ATTTTAAAAAATA-TT
5588653 ATTTTAAAA
1 ATTTTAAAA
5588662 TATAAAAATA
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
14 12 0.36
15 1 0.03
16 12 0.36
17 8 0.24
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (15 bp):
ATTTTAAAAAATATT
Found at i:5588973 original size:12 final size:12
Alignment explanation
Indices: 5588956--5588981 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
5588946 ACAATTGAGC
5588956 ATAGTGTTGTAA
1 ATAGTGTTGTAA
5588968 ATAGTGTTGTAA
1 ATAGTGTTGTAA
5588980 AT
1 AT
5588982 CCCTTTGTTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.35, C:0.00, G:0.23, T:0.42
Consensus pattern (12 bp):
ATAGTGTTGTAA
Found at i:5589083 original size:30 final size:32
Alignment explanation
Indices: 5589026--5589084 Score: 77
Period size: 32 Copynumber: 1.9 Consensus size: 32
5589016 GAATTTTGAA
**
5589026 TTTTTTAAAATAATTATGTAATGTTTTAGATT
1 TTTTTTAAAATAATTATGTAACATTTTAGATT
*
5589058 TTTTTTAAAAT-TTTA-GTAACATTTTAG
1 TTTTTTAAAATAATTATGTAACATTTTAG
5589085 TATCTTTCTA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 10 0.42
31 3 0.12
32 11 0.46
ACGTcount: A:0.34, C:0.02, G:0.08, T:0.56
Consensus pattern (32 bp):
TTTTTTAAAATAATTATGTAACATTTTAGATT
Found at i:5590639 original size:22 final size:22
Alignment explanation
Indices: 5590614--5590663 Score: 57
Period size: 22 Copynumber: 2.2 Consensus size: 22
5590604 AAATACATAA
*
5590614 TTATATGATTTTAAAAAT-ATTT
1 TTATAT-ATTATAAAAATAATTT
*
5590636 TTATAATATTATAAATATAATTT
1 TTAT-ATATTATAAAAATAATTT
5590659 TTATA
1 TTATA
5590664 AATATTTCAT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
22 14 0.58
23 10 0.42
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (22 bp):
TTATATATTATAAAAATAATTT
Found at i:5590970 original size:124 final size:124
Alignment explanation
Indices: 5590826--5591069 Score: 479
Period size: 124 Copynumber: 2.0 Consensus size: 124
5590816 AAGCTTTCAG
5590826 TCATTAATTTAAAGTATTTCATATTTGAATCTTATAATCATAAAAAATATTGATTTTGTGATGAT
1 TCATTAATTTAAAGTATTTCATATTTGAATCTTATAATCATAAAAAATATTGATTTTGTGATGAT
5590891 GTCATTATATAAGTTAAATATAAAATGTGGTGAAATTTACACAAACAACTAGCTATCGA
66 GTCATTATATAAGTTAAATATAAAATGTGGTGAAATTTACACAAACAACTAGCTATCGA
5590950 TCATTAATTTAAAGTATTTCATATTTGAATCTTATAATCATAAAAAATATTGATTTTGTGATGAT
1 TCATTAATTTAAAGTATTTCATATTTGAATCTTATAATCATAAAAAATATTGATTTTGTGATGAT
*
5591015 TTCATTATATAAGTTAAATATAAAATGTGGTGAAATTTACACAAACAACTAGCTA
66 GTCATTATATAAGTTAAATATAAAATGTGGTGAAATTTACACAAACAACTAGCTA
5591070 AGCTTAATGA
Statistics
Matches: 119, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
124 119 1.00
ACGTcount: A:0.41, C:0.09, G:0.11, T:0.39
Consensus pattern (124 bp):
TCATTAATTTAAAGTATTTCATATTTGAATCTTATAATCATAAAAAATATTGATTTTGTGATGAT
GTCATTATATAAGTTAAATATAAAATGTGGTGAAATTTACACAAACAACTAGCTATCGA
Found at i:5592158 original size:27 final size:26
Alignment explanation
Indices: 5592114--5592190 Score: 97
Period size: 27 Copynumber: 3.0 Consensus size: 26
5592104 TTTTAGTTCC
*
5592114 AATAAAAGAGCTATTAAATCTCTTTTA
1 AATAAAAGAGC-AATAAATCTCTTTTA
5592141 AATAAAAGAGGCAATAAATCTCTTTT-
1 AATAAAAGA-GCAATAAATCTCTTTTA
*
5592167 ACTAAAAGA--AATAAATCTCTTTTA
1 AATAAAAGAGCAATAAATCTCTTTTA
5592191 TCTTTATCCT
Statistics
Matches: 46, Mismatches: 2, Indels: 7
0.84 0.04 0.13
Matches are distributed among these distances:
23 14 0.30
26 8 0.17
27 22 0.48
28 2 0.04
ACGTcount: A:0.47, C:0.12, G:0.08, T:0.34
Consensus pattern (26 bp):
AATAAAAGAGCAATAAATCTCTTTTA
Found at i:5597723 original size:27 final size:27
Alignment explanation
Indices: 5597679--5597732 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
5597669 TTTTAATTCC
* *
5597679 AATAAAAGAGCTATTAAATCTCTTTTA
1 AATAAAAGAGCTAATAAATCTATTTTA
*
5597706 AATAAAAGAGGTAATAAATCTATTTTA
1 AATAAAAGAGCTAATAAATCTATTTTA
5597733 TCTTTATCCT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.48, C:0.07, G:0.09, T:0.35
Consensus pattern (27 bp):
AATAAAAGAGCTAATAAATCTATTTTA
Found at i:5608885 original size:22 final size:21
Alignment explanation
Indices: 5608852--5608927 Score: 66
Period size: 22 Copynumber: 3.6 Consensus size: 21
5608842 AGTGCTATCA
*
5608852 ATAAGTCTTTCGAGCATGATG
1 ATAAGTCCTTCGAGCATGATG
* *
5608873 ATGAAGTCCTTCGGGCCATCA-G
1 AT-AAGTCCTTCGAG-CATGATG
*
5608895 -TAAGTCTTTCGAGCATGATG
1 ATAAGTCCTTCGAGCATGATG
*
5608915 ATTAAATCCTTCG
1 A-TAAGTCCTTCG
5608928 GGTAATTTGT
Statistics
Matches: 42, Mismatches: 8, Indels: 9
0.71 0.14 0.15
Matches are distributed among these distances:
19 4 0.10
20 11 0.26
21 3 0.07
22 20 0.48
23 4 0.10
ACGTcount: A:0.26, C:0.20, G:0.22, T:0.32
Consensus pattern (21 bp):
ATAAGTCCTTCGAGCATGATG
Found at i:5608912 original size:42 final size:42
Alignment explanation
Indices: 5608848--5609235 Score: 411
Period size: 42 Copynumber: 9.4 Consensus size: 42
5608838 AGTAAGTGCT
* *
5608848 ATCAATAAGTCTTTCGAGCATGATGATGAAGTCCTTCGGGCC
1 ATCAGTAAGTCTTTCGAGCATGATGATGAAATCCTTCGGGCC
* **
5608890 ATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTA
1 ATCAGTAAGTCTTTCGAGCATGATGATGAAATCCTTCGGGCC
** * * * * *
5608932 ATTTGTAAG-CCTTC-ACCGAAGA-GTAGTG-AAGCCAAT----CC
1 ATCAGTAAGTCTTTCGAGC-ATGATG-A-TGAAATCC-TTCGGGCC
* * **
5608970 ATCAGTAAGTCTTTCGAGCATGAAGATTAAATCCTTCGGGTA
1 ATCAGTAAGTCTTTCGAGCATGATGATGAAATCCTTCGGGCC
*
5609012 ATCAG-AAGTCTTTCGAGCATGATGATGAAGTCCTTCGGGCC
1 ATCAGTAAGTCTTTCGAGCATGATGATGAAATCCTTCGGGCC
* *
5609053 ATCAGTAAGTCTTTCGAGCATGATGATTAAGTCCTTCGGGCC
1 ATCAGTAAGTCTTTCGAGCATGATGATGAAATCCTTCGGGCC
*
5609095 ATCAGTAAGTCTTTCGAGCATGATGATGAAATCCTTCAGGCC
1 ATCAGTAAGTCTTTCGAGCATGATGATGAAATCCTTCGGGCC
* *
5609137 ATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGACC
1 ATCAGTAAGTCTTTCGAGCATGATGATGAAATCCTTCGGGCC
* * * *
5609179 ATCAGTAAGTTTTTCGGGCAAGATGAT-AAATCCTTCGGGTC
1 ATCAGTAAGTCTTTCGAGCATGATGATGAAATCCTTCGGGCC
*
5609220 ATCCA-TAAGTCCTTCG
1 AT-CAGTAAGTCTTTCG
5609236 GGTAGGATGT
Statistics
Matches: 288, Mismatches: 44, Indels: 29
0.80 0.12 0.08
Matches are distributed among these distances:
38 9 0.03
39 12 0.04
40 6 0.02
41 71 0.25
42 190 0.66
ACGTcount: A:0.28, C:0.21, G:0.22, T:0.30
Consensus pattern (42 bp):
ATCAGTAAGTCTTTCGAGCATGATGATGAAATCCTTCGGGCC
Found at i:5609068 original size:20 final size:20
Alignment explanation
Indices: 5609039--5609237 Score: 84
Period size: 20 Copynumber: 9.6 Consensus size: 20
5609029 CATGATGATG
5609039 AAGTCCTTCGGGCCATCAGT
1 AAGTCCTTCGGGCCATCAGT
* * *
5609059 AAGTCTTTCGAG-CATGATGATT
1 AAGTCCTTCGGGCCATCA-G--T
5609081 AAGTCCTTCGGGCCATCAGT
1 AAGTCCTTCGGGCCATCAGT
* * *
5609101 AAGTCTTTCGAG-CATGATGAT
1 AAGTCCTTCGGGCCATCA-G-T
* *
5609122 GAAATCCTTCAGGCCATCAGT
1 -AAGTCCTTCGGGCCATCAGT
* * *
5609143 AAGTCTTTCGAG-CATGATGATT
1 AAGTCCTTCGGGCCATCA-G--T
* *
5609165 AAATCCTTCGGACCATCAGT
1 AAGTCCTTCGGGCCATCAGT
** **
5609185 AAGTTTTTCGGG-CAAGATGAT
1 AAGTCCTTCGGGCCATCA-G-T
* *
5609206 AAATCCTTCGGGTCATCCA-T
1 AAGTCCTTCGGGCCAT-CAGT
5609226 AAGTCCTTCGGG
1 AAGTCCTTCGGG
5609238 TAGGATGTTT
Statistics
Matches: 127, Mismatches: 36, Indels: 32
0.65 0.18 0.16
Matches are distributed among these distances:
19 15 0.12
20 54 0.43
21 12 0.09
22 33 0.26
23 13 0.10
ACGTcount: A:0.26, C:0.22, G:0.23, T:0.30
Consensus pattern (20 bp):
AAGTCCTTCGGGCCATCAGT
Found at i:5609785 original size:53 final size:53
Alignment explanation
Indices: 5609633--5609787 Score: 202
Period size: 53 Copynumber: 2.9 Consensus size: 53
5609623 ATAATCACAC
* * * *
5609633 CAGAAGATTGTTCAAGTTCTACTCCCTGAAGTAAGAGGGAGCAAACCCGTAGA
1 CAGAAAATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGA
* * *
5609686 CAGAAAATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGTGAACCTGTAGG
1 CAGAAAATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGA
* * * **
5609739 CATAATATTGTTCGAGTTCTACTCCTTGAAGCAAGAATGAGCGAACCCG
1 CAGAAAATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCG
5609788 CTGGTTGAAG
Statistics
Matches: 88, Mismatches: 14, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
53 88 1.00
ACGTcount: A:0.32, C:0.21, G:0.25, T:0.23
Consensus pattern (53 bp):
CAGAAAATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGA
Found at i:5615595 original size:25 final size:25
Alignment explanation
Indices: 5615567--5615627 Score: 113
Period size: 25 Copynumber: 2.4 Consensus size: 25
5615557 TAACTACTAA
5615567 CATACTAACATTTTATTTTATTGTT
1 CATACTAACATTTTATTTTATTGTT
5615592 CATACTAACATTTTATTTTATTGTT
1 CATACTAACATTTTATTTTATTGTT
*
5615617 CATAATAACAT
1 CATACTAACAT
5615628 ACTAACATTT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 35 1.00
ACGTcount: A:0.33, C:0.13, G:0.03, T:0.51
Consensus pattern (25 bp):
CATACTAACATTTTATTTTATTGTT
Found at i:5615598 original size:33 final size:33
Alignment explanation
Indices: 5615564--5615826 Score: 283
Period size: 33 Copynumber: 8.5 Consensus size: 33
5615554 ATTTAACTAC
5615564 TAACATACTAACATTTTATTTTATTG----T--
1 TAACATACTAACATTTTATTTTATTGTTTATAA
*
5615591 T--CATACTAACATTTTATTTTATTGTTCATAA
1 TAACATACTAACATTTTATTTTATTGTTTATAA
* *
5615622 TAACATACTAACATTTTATTTGATTGTTTGTAA
1 TAACATACTAACATTTTATTTTATTGTTTATAA
* * *
5615655 TAATATAATAAC-TTTTATTTTATTGTTTATAC
1 TAACATACTAACATTTTATTTTATTGTTTATAA
5615687 TAACATACTAACATTTTATTTTATTG----T--
1 TAACATACTAACATTTTATTTTATTGTTTATAA
*
5615714 T--CATACTAACATTTTATTTTATTGTTCATAA
1 TAACATACTAACATTTTATTTTATTGTTTATAA
* *
5615745 TAACATACTAACATTTTATTTGATTGTTTGTAA
1 TAACATACTAACATTTTATTTTATTGTTTATAA
* * *
5615778 TAATATAATAAC-TTTTATTTTATTGTTTATAC
1 TAACATACTAACATTTTATTTTATTGTTTATAA
*
5615810 TAACTTACTAACATTTT
1 TAACATACTAACATTTT
5615827 TTATTTGTTC
Statistics
Matches: 197, Mismatches: 21, Indels: 30
0.79 0.08 0.12
Matches are distributed among these distances:
25 46 0.23
27 2 0.01
29 3 0.02
31 2 0.01
32 53 0.27
33 91 0.46
ACGTcount: A:0.33, C:0.10, G:0.05, T:0.52
Consensus pattern (33 bp):
TAACATACTAACATTTTATTTTATTGTTTATAA
Found at i:5615676 original size:65 final size:65
Alignment explanation
Indices: 5615597--5615826 Score: 321
Period size: 65 Copynumber: 3.6 Consensus size: 65
5615587 TTGTTCATAC
5615597 TAACATTTTATTTTATTGTTCATAATAACATACTAACATTTTATTTGATTGTTTGTAATAATATA
1 TAAC-TTTTATTTTATTGTTCATAATAACATACTAACATTTTATTTGATTGTTTGTAATAATATA
5615662 A
65 A
* * * * *
5615663 TAACTTTTATTTTATTGTTTATACTAACATACTAACATTTTATTTTATTG--T-TCAT-A-CTAA
1 TAACTTTTATTTTATTGTTCATAATAACATACTAACATTTTATTTGATTGTTTGTAATAATATAA
*
5615723 -CA-TTTTATTTTATTGTTCATAATAACATACTAACATTTTATTTGATTGTTTGTAATAATATAA
1 TAACTTTTATTTTATTGTTCATAATAACATACTAACATTTTATTTGATTGTTTGTAATAATATAA
* * *
5615786 TAACTTTTATTTTATTGTTTATACTAACTTACTAACATTTT
1 TAACTTTTATTTTATTGTTCATAATAACATACTAACATTTT
5615827 TTATTTGTTC
Statistics
Matches: 142, Mismatches: 15, Indels: 15
0.83 0.09 0.09
Matches are distributed among these distances:
58 43 0.30
59 1 0.01
60 4 0.03
61 4 0.03
62 4 0.03
63 4 0.03
64 1 0.01
65 77 0.54
66 4 0.03
ACGTcount: A:0.33, C:0.10, G:0.05, T:0.52
Consensus pattern (65 bp):
TAACTTTTATTTTATTGTTCATAATAACATACTAACATTTTATTTGATTGTTTGTAATAATATAA
Found at i:5615698 original size:123 final size:123
Alignment explanation
Indices: 5615561--5615826 Score: 523
Period size: 123 Copynumber: 2.2 Consensus size: 123
5615551 TGAATTTAAC
5615561 TACTAACATACTAACATTTTATTTTATTGTTCATACTAACATTTTATTTTATTGTTCATAATAAC
1 TACTAACATACTAACATTTTATTTTATTGTTCATACTAACATTTTATTTTATTGTTCATAATAAC
5615626 ATACTAACATTTTATTTGATTGTTTGTAATAATATAATAACTTTTATTTTATTGTTTA
66 ATACTAACATTTTATTTGATTGTTTGTAATAATATAATAACTTTTATTTTATTGTTTA
5615684 TACTAACATACTAACATTTTATTTTATTGTTCATACTAACATTTTATTTTATTGTTCATAATAAC
1 TACTAACATACTAACATTTTATTTTATTGTTCATACTAACATTTTATTTTATTGTTCATAATAAC
5615749 ATACTAACATTTTATTTGATTGTTTGTAATAATATAATAACTTTTATTTTATTGTTTA
66 ATACTAACATTTTATTTGATTGTTTGTAATAATATAATAACTTTTATTTTATTGTTTA
*
5615807 TACTAACTTACTAACATTTT
1 TACTAACATACTAACATTTT
5615827 TTATTTGTTC
Statistics
Matches: 142, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
123 142 1.00
ACGTcount: A:0.33, C:0.11, G:0.05, T:0.52
Consensus pattern (123 bp):
TACTAACATACTAACATTTTATTTTATTGTTCATACTAACATTTTATTTTATTGTTCATAATAAC
ATACTAACATTTTATTTGATTGTTTGTAATAATATAATAACTTTTATTTTATTGTTTA
Found at i:5615722 original size:25 final size:25
Alignment explanation
Indices: 5615690--5615750 Score: 113
Period size: 25 Copynumber: 2.4 Consensus size: 25
5615680 TTTATACTAA
5615690 CATACTAACATTTTATTTTATTGTT
1 CATACTAACATTTTATTTTATTGTT
5615715 CATACTAACATTTTATTTTATTGTT
1 CATACTAACATTTTATTTTATTGTT
*
5615740 CATAATAACAT
1 CATACTAACAT
5615751 ACTAACATTT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 35 1.00
ACGTcount: A:0.33, C:0.13, G:0.03, T:0.51
Consensus pattern (25 bp):
CATACTAACATTTTATTTTATTGTT
Found at i:5615794 original size:90 final size:90
Alignment explanation
Indices: 5615625--5615813 Score: 263
Period size: 90 Copynumber: 2.1 Consensus size: 90
5615615 TTCATAATAA
** * * *
5615625 CATACTAACATTTTATTTGATTGTTTGTAATAATATAATAACTTTTATTTTATTGTTTATACTAA
1 CATACTAACATTTTATTTGATTGTTCATAATAACATAATAACTTTTATTTGATTGTTTATAATAA
*
5615690 CATACTAACATTTTATTTTATTGTT
66 CATAATAACATTTTATTTTATTGTT
* * *
5615715 CATACTAACATTTTATTTTATTGTTCATAATAACATACTAACATTTTATTTGATTGTTTGTAATA
1 CATACTAACATTTTATTTGATTGTTCATAATAACATAATAAC-TTTTATTTGATTGTTTATAATA
*
5615780 ATATAATAAC-TTTTATTTTATTGTT
65 ACATAATAACATTTTATTTTATTGTT
*
5615805 TATACTAAC
1 CATACTAAC
5615814 TTACTAACAT
Statistics
Matches: 87, Mismatches: 11, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
90 60 0.69
91 27 0.31
ACGTcount: A:0.33, C:0.10, G:0.05, T:0.52
Consensus pattern (90 bp):
CATACTAACATTTTATTTGATTGTTCATAATAACATAATAACTTTTATTTGATTGTTTATAATAA
CATAATAACATTTTATTTTATTGTT
Found at i:5616101 original size:28 final size:29
Alignment explanation
Indices: 5616044--5616104 Score: 74
Period size: 28 Copynumber: 2.1 Consensus size: 29
5616034 ATATTTTATT
*
5616044 TTTTAGTCCCTTTAATTTCATGCATTTTA
1 TTTTAGTCCCTTTAATTTCATGCATCTTA
5616073 TTTTAGT-CCTTTAATGTTCCA-GCA-CTTA
1 TTTTAGTCCCTTTAAT-TT-CATGCATCTTA
5616101 TTTT
1 TTTT
5616105 TTTGTGTTCT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
28 15 0.52
29 12 0.41
30 2 0.07
ACGTcount: A:0.20, C:0.18, G:0.08, T:0.54
Consensus pattern (29 bp):
TTTTAGTCCCTTTAATTTCATGCATCTTA
Found at i:5616105 original size:29 final size:28
Alignment explanation
Indices: 5616043--5616105 Score: 67
Period size: 29 Copynumber: 2.2 Consensus size: 28
5616033 AATATTTTAT
*
5616043 TTTTTAGTCCCTTTAATTTCATGCATTT
1 TTTTTAGTCCCTTTAATTTCATGCATTA
5616071 TATTTTAGT-CCTTTAATGTTCCA-GCACTTA
1 T-TTTTAGTCCCTTTAAT-TT-CATGCA-TTA
5616101 TTTTT
1 TTTTT
5616106 TTGTGTTCTC
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
28 9 0.30
29 16 0.53
30 5 0.17
ACGTcount: A:0.19, C:0.17, G:0.08, T:0.56
Consensus pattern (28 bp):
TTTTTAGTCCCTTTAATTTCATGCATTA
Found at i:5616856 original size:13 final size:13
Alignment explanation
Indices: 5616838--5616864 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
5616828 ACTTTTTATC
5616838 TTTAAAATTATTT
1 TTTAAAATTATTT
5616851 TTTAAAATTATTT
1 TTTAAAATTATTT
5616864 T
1 T
5616865 AGAAGATGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (13 bp):
TTTAAAATTATTT
Found at i:5618497 original size:21 final size:21
Alignment explanation
Indices: 5618473--5618534 Score: 106
Period size: 21 Copynumber: 3.0 Consensus size: 21
5618463 TACCATTATC
5618473 TAATAAATAACTTTTTATATT
1 TAATAAATAACTTTTTATATT
*
5618494 TAATAAATATCTTTTTATATT
1 TAATAAATAACTTTTTATATT
*
5618515 TAATAAATAACTTTTCATAT
1 TAATAAATAACTTTTTATAT
5618535 AAATAACTCT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 38 1.00
ACGTcount: A:0.42, C:0.06, G:0.00, T:0.52
Consensus pattern (21 bp):
TAATAAATAACTTTTTATATT
Found at i:5628782 original size:62 final size:62
Alignment explanation
Indices: 5628629--5629118 Score: 583
Period size: 62 Copynumber: 7.9 Consensus size: 62
5628619 TCTTGTGTCC
* * * *
5628629 TAGAATCAATCCTTGACTTCCTCATGAAGAGAAGTCAACTTTTGTTATTTCTGACT-TCCAG
1 TAGAGTCAATCCTTGACTTCCTCGTGAAGAGAAGTCAACATTTGTTATTTCTGACTCCCCAG
* * * * *
5628690 TAGATTCAATCCTTGACTTCCTCATAAAGAGAAGTCAACCTTTGTTATTTTTGACTCCCCAG
1 TAGAGTCAATCCTTGACTTCCTCGTGAAGAGAAGTCAACATTTGTTATTTCTGACTCCCCAG
* * * *
5628752 TAGAGTCAATCCTTGATTTCCTCGTGAAGAGAAGTCAACATTTATTATTTGTGACTCCCTAG
1 TAGAGTCAATCCTTGACTTCCTCGTGAAGAGAAGTCAACATTTGTTATTTCTGACTCCCCAG
* ** * * * * * * * *
5628814 TAGAGTTAATATTTGACTTCCTCTTAAAGAGAAGTTAACCTTTATTATTTTTTACT-CCTAGG
1 TAGAGTCAATCCTTGACTTCCTCGTGAAGAGAAGTCAACATTTGTTATTTCTGACTCCCCA-G
* * **
5628876 TAGAGTCAATCATTGACTTCCTCGTGAAGAGAAGTAAACATTTGTTATTTCTGACTCCTTAG
1 TAGAGTCAATCCTTGACTTCCTCGTGAAGAGAAGTCAACATTTGTTATTTCTGACTCCCCAG
* ** * *
5628938 TAGAGTCAATCATTGACTTCCTCGTGAAGAGAAGTCAACATTTGTTATTTCTGACAACTCAA
1 TAGAGTCAATCCTTGACTTCCTCGTGAAGAGAAGTCAACATTTGTTATTTCTGACTCCCCAG
* * *
5629000 TAGAGTCAATCTTTGACTCCCTCGTGAAGAGAAGTCAACATTTGTTATTCCTGACT-CCCAG
1 TAGAGTCAATCCTTGACTTCCTCGTGAAGAGAAGTCAACATTTGTTATTTCTGACTCCCCAG
* * *
5629061 TAGAGTCAAAT-TTTGACTTCCTCGTGAAGAGAAGTCAACCTTTATTATTTCTGACTCC
1 TAGAGTC-AATCCTTGACTTCCTCGTGAAGAGAAGTCAACATTTGTTATTTCTGACTCC
5629119 TCAGAGGAAC
Statistics
Matches: 375, Mismatches: 49, Indels: 9
0.87 0.11 0.02
Matches are distributed among these distances:
61 107 0.29
62 265 0.71
63 3 0.01
ACGTcount: A:0.28, C:0.20, G:0.16, T:0.36
Consensus pattern (62 bp):
TAGAGTCAATCCTTGACTTCCTCGTGAAGAGAAGTCAACATTTGTTATTTCTGACTCCCCAG
Found at i:5629353 original size:36 final size:36
Alignment explanation
Indices: 5629301--5629830 Score: 719
Period size: 36 Copynumber: 14.7 Consensus size: 36
5629291 TATTTCAAAT
*
5629301 TTAGCCTCCACAGAAGAGTAGTGAAGCAAAGCAATC
1 TTAGCCTCCACGGAAGAGTAGTGAAGCAAAGCAATC
*
5629337 TTAGCCTCCACGGAAGAGTAGTGAAGCAAAGCCATC
1 TTAGCCTCCACGGAAGAGTAGTGAAGCAAAGCAATC
5629373 TTAGCCTCCACGGAAGAGTAGTGAAGCAAAGCAATC
1 TTAGCCTCCACGGAAGAGTAGTGAAGCAAAGCAATC
*
5629409 TTAGCCTCCACGGAAGAGTAGTGAAGTAAAGTC-ATC
1 TTAGCCTCCACGGAAGAGTAGTGAAGCAAAG-CAATC
* * *
5629445 TTAGCCTCCAAGGAAGAGTAGTGAAGAAAAACAATC
1 TTAGCCTCCACGGAAGAGTAGTGAAGCAAAGCAATC
5629481 TTAGCCTCCACGGAAGAGTAGTGAAGCAAAGCAATC
1 TTAGCCTCCACGGAAGAGTAGTGAAGCAAAGCAATC
** * *
5629517 TTAGCCTCCTTGGAAGAGTAGTAAAGCAAAGTC-ATT
1 TTAGCCTCCACGGAAGAGTAGTGAAGCAAAG-CAATC
*
5629553 TTAGCCTCCACGGAAGAGTAGTGAAACAAAGCAATC
1 TTAGCCTCCACGGAAGAGTAGTGAAGCAAAGCAATC
* * * * *
5629589 TTAGCATCCGCGGAATAGAAGTGAAGTAAAGTC-ATC
1 TTAGCCTCCACGGAAGAGTAGTGAAGCAAAG-CAATC
*
5629625 TTAGCCTCCACGGAAGAGTAGTGAACCAAAGCAATC
1 TTAGCCTCCACGGAAGAGTAGTGAAGCAAAGCAATC
* * * * *
5629661 TTATCATCCACGAAAGACTAGTGAAGCAAAGCCATC
1 TTAGCCTCCACGGAAGAGTAGTGAAGCAAAGCAATC
* *
5629697 TTAGCCTCCATGGAAGAGTAGTGAAGTAAAGCAATC
1 TTAGCCTCCACGGAAGAGTAGTGAAGCAAAGCAATC
* *
5629733 TTAGCCTCCACGGAAGAGGT-GTGAAGTAAATTC-ATC
1 TTAGCCTCCACGGAAGA-GTAGTGAAGCAAA-GCAATC
* * *
5629769 TTAGCCTTCACGGAAGATTAGTGAAGCAAAGCCATC
1 TTAGCCTCCACGGAAGAGTAGTGAAGCAAAGCAATC
5629805 TTAGCCTCCACGGAAGAGTAGTGAAG
1 TTAGCCTCCACGGAAGAGTAGTGAAG
5629831 TAAACCATCA
Statistics
Matches: 432, Mismatches: 52, Indels: 20
0.86 0.10 0.04
Matches are distributed among these distances:
35 5 0.01
36 421 0.97
37 6 0.01
ACGTcount: A:0.36, C:0.21, G:0.24, T:0.20
Consensus pattern (36 bp):
TTAGCCTCCACGGAAGAGTAGTGAAGCAAAGCAATC
Found at i:5630052 original size:3 final size:3
Alignment explanation
Indices: 5630034--5630074 Score: 57
Period size: 3 Copynumber: 13.7 Consensus size: 3
5630024 TTTCGTCCCG
*
5630034 TAT TTT TAT ATAT TAT TAT TAT TAT TAT TA- TAT TAT TAT TA
1 TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
5630075 CAAATAATAC
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
2 2 0.06
3 29 0.85
4 3 0.09
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:5631261 original size:20 final size:22
Alignment explanation
Indices: 5631216--5631273 Score: 75
Period size: 20 Copynumber: 2.6 Consensus size: 22
5631206 TGCAGGGCTG
5631216 TGCATCGATGCACATGTTAAAGAA
1 TGCATCGATGCAC-TGTT-AAGAA
5631240 TGCATCGATGCACTG-T-AGAA
1 TGCATCGATGCACTGTTAAGAA
*
5631260 TGTATCGATGCACT
1 TGCATCGATGCACT
5631274 TCAAAGGGAA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
20 17 0.52
22 1 0.03
23 2 0.06
24 13 0.39
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.28
Consensus pattern (22 bp):
TGCATCGATGCACTGTTAAGAA
Found at i:5639149 original size:22 final size:21
Alignment explanation
Indices: 5639107--5639146 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
5639097 GAGTTTATTT
*
5639107 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
5639128 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
5639147 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:5641289 original size:65 final size:63
Alignment explanation
Indices: 5641095--5641300 Score: 206
Period size: 65 Copynumber: 3.2 Consensus size: 63
5641085 CTAAGAGTGT
* * * *
5641095 ATCGATGCATCAAGTGCATTCGATGTTTCA-AAATAGC-CAAAGTGCATCGATGTATGGCTGGTG
1 ATCGATGCATCAAATGCATTCGATGTTTCATAAA-ATCTC--AGTGCATCGATGCATGGTTGGTG
5641158 C
63 C
*
5641159 ATCGATGCATCAAATGCATTCGATGTTTTCATAAAATCCTCAGTGCATCGGTGCATGGTAT-GTG
1 ATCGATGCATCAAATGCATTCGATG-TTTCATAAAAT-CTCAGTGCATCGATGCATGGT-TGGTG
5641223 C
63 C
* **
5641224 ATCGATGCATGAAATGCATTCGATG-TTCAATTTAAT-TCATGGTGCATCGATGCATGGATTGGT
1 ATCGATGCATCAAATGCATTCGATGTTTC-ATAAAATCTCA--GTGCATCGATGCATGG-TTGGT
5641287 GC
62 GC
*
5641289 ATCGGTGCATCA
1 ATCGATGCATCA
5641301 CTCTGAAAAA
Statistics
Matches: 121, Mismatches: 11, Indels: 19
0.80 0.07 0.13
Matches are distributed among these distances:
62 3 0.02
63 3 0.02
64 45 0.37
65 64 0.53
66 5 0.04
67 1 0.01
ACGTcount: A:0.27, C:0.18, G:0.24, T:0.31
Consensus pattern (63 bp):
ATCGATGCATCAAATGCATTCGATGTTTCATAAAATCTCAGTGCATCGATGCATGGTTGGTGC
Done.