Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007867.1 Hibiscus syriacus cultivar Beakdansim tig00110239_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: 3477501
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 18
Found at i:29 original size:18 final size:18
Alignment explanation
Indices: 6--41 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
1 TAGGA
6 CTTGGAGGTGCAGGTTGT
1 CTTGGAGGTGCAGGTTGT
*
24 CTTGGAGGTGTAGGTTGT
1 CTTGGAGGTGCAGGTTGT
42 GACGATGTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.11, C:0.08, G:0.44, T:0.36
Consensus pattern (18 bp):
CTTGGAGGTGCAGGTTGT
Found at i:953 original size:54 final size:53
Alignment explanation
Indices: 875--977 Score: 152
Period size: 54 Copynumber: 1.9 Consensus size: 53
865 CCACCTCCAA
* * *
875 GTTGGAGTTATCTCTGGATATGGAGGTTGTCTTAGAGCCACAAGTTGTGGCAGT
1 GTTGAAGTTATCTCAGGATATGGAGGTTGTCTT-GAACCACAAGTTGTGGCAGT
* *
929 GTTGAAGTTATCTCAGGATGTGGAGGTTGTCTTGAACCGCAAGTTGTGG
1 GTTGAAGTTATCTCAGGATATGGAGGTTGTCTTGAACCACAAGTTGTGG
978 TAAGGTTGGA
Statistics
Matches: 44, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
53 14 0.32
54 30 0.68
ACGTcount: A:0.20, C:0.13, G:0.34, T:0.33
Consensus pattern (53 bp):
GTTGAAGTTATCTCAGGATATGGAGGTTGTCTTGAACCACAAGTTGTGGCAGT
Found at i:1005 original size:53 final size:53
Alignment explanation
Indices: 895--1015 Score: 120
Period size: 53 Copynumber: 2.3 Consensus size: 53
885 TCTCTGGATA
* * * *
895 TGGAGGTTGTCTTAGAGCCACAAGTTGTGGCAGTGTTGAAGTTATCTCAGGATG
1 TGGAGGTTGTCTT-GAACCACAAGTTGTGGAAGTGTTGAAGTTATCTCAGAAGG
* * *
949 TGGAGGTTGTCTTGAACCGCAAGTTGTGGTAAG-GTTGGAGTTATTTCTA-AAGG
1 TGGAGGTTGTCTTGAACCACAAGTTGTGG-AAGTGTTGAAGTTATCTC-AGAAGG
**
1002 TGGAAATTGTCTTG
1 TGGAGGTTGTCTTG
1016 GAGGTGCAGG
Statistics
Matches: 56, Mismatches: 9, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
53 40 0.71
54 16 0.29
ACGTcount: A:0.22, C:0.11, G:0.33, T:0.34
Consensus pattern (53 bp):
TGGAGGTTGTCTTGAACCACAAGTTGTGGAAGTGTTGAAGTTATCTCAGAAGG
Found at i:2548 original size:54 final size:54
Alignment explanation
Indices: 2483--2637 Score: 179
Period size: 54 Copynumber: 2.9 Consensus size: 54
2473 GATTGTGTTG
* **
2483 AGGTTAGAGTTATATT-TAGAGGTGGAAGTTGTCTTGGAGGCGCAGGTTGT-GGC
1 AGGTTAGAGTTAT-TTCTAGAGGTGGAGGTTGTCTTGGAGGCGCAGGTTGTAGAA
* * * * *
2536 AGTGTTAAAGTTATTTCTAGAGGTGGTGGTGGTCTTGAAGGCGCAGATTGTAGAA
1 AG-GTTAGAGTTATTTCTAGAGGTGGAGGTTGTCTTGGAGGCGCAGGTTGTAGAA
* * *
2591 AGGTTGGAGTTATTTCTAAAGGTGGAGGTTGTCTTGGAGGTGCAGGT
1 AGGTTAGAGTTATTTCTAGAGGTGGAGGTTGTCTTGGAGGCGCAGGT
2638 GATGGTGGCA
Statistics
Matches: 83, Mismatches: 16, Indels: 5
0.80 0.15 0.05
Matches are distributed among these distances:
53 4 0.05
54 76 0.92
55 3 0.04
ACGTcount: A:0.22, C:0.07, G:0.38, T:0.33
Consensus pattern (54 bp):
AGGTTAGAGTTATTTCTAGAGGTGGAGGTTGTCTTGGAGGCGCAGGTTGTAGAA
Found at i:7872 original size:21 final size:21
Alignment explanation
Indices: 7822--7923 Score: 179
Period size: 21 Copynumber: 4.9 Consensus size: 21
7812 TGCTGAAGTT
*
7822 ACTGTAGCAGTGCATCGATGC
1 ACTGTAGCAGTACATCGATGC
7843 ACT-TAGCAGTACATCGATGC
1 ACTGTAGCAGTACATCGATGC
7863 ACTGTAGCAGTACATCGATGC
1 ACTGTAGCAGTACATCGATGC
7884 ACTGTAGCAGTACATCGATGC
1 ACTGTAGCAGTACATCGATGC
*
7905 ACTGTAGCAGTATATCGAT
1 ACTGTAGCAGTACATCGAT
7924 ACAATTTATA
Statistics
Matches: 78, Mismatches: 2, Indels: 2
0.95 0.02 0.02
Matches are distributed among these distances:
20 19 0.24
21 59 0.76
ACGTcount: A:0.28, C:0.23, G:0.24, T:0.25
Consensus pattern (21 bp):
ACTGTAGCAGTACATCGATGC
Found at i:11935 original size:53 final size:52
Alignment explanation
Indices: 11824--11940 Score: 128
Period size: 53 Copynumber: 2.2 Consensus size: 52
11814 TCCACCTCCA
* * * *
11824 TGTTGGAGTTATCTCTAGAGGTAGGTTGTCTTGTAAGCGTAGGTTGTAGCGG
1 TGTTGGAGTTATCTCTAGAGGGAGATTGTCTTGGAAGCGCAGGTTGTAGCGG
* * * * *
11876 CGTTGGAGTTATCTTTAGAGTGGAGATTTTCTTGGAGGCGCATGTTGT-GACGG
1 TGTTGGAGTTATCTCTAGAG-GGAGATTGTCTTGGAAGCGCAGGTTGTAG-CGG
11929 TGTTGGAGTTAT
1 TGTTGGAGTTAT
11941 TTCTGAAGGT
Statistics
Matches: 53, Mismatches: 10, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
52 19 0.36
53 34 0.64
ACGTcount: A:0.17, C:0.09, G:0.36, T:0.38
Consensus pattern (52 bp):
TGTTGGAGTTATCTCTAGAGGGAGATTGTCTTGGAAGCGCAGGTTGTAGCGG
Found at i:12365 original size:54 final size:54
Alignment explanation
Indices: 12278--12416 Score: 156
Period size: 54 Copynumber: 2.6 Consensus size: 54
12268 GAATTATCTT
* * * * * **
12278 TGGATGTGGAGGTTATCTTGGAGGCACAGGTTGTAG-CATTGTTGGAGTTATTTC
1 TGGAGGTGGAGGTTGTCTAGGAGGCGCAAGTTGT-GCCAAGGTTGGAGTTATTTC
*
12332 TGGAGGTGGAAGTTGTCTAGGAGGCGCAAGTTGTGCCAAGGTTGGAGTTATTTC
1 TGGAGGTGGAGGTTGTCTAGGAGGCGCAAGTTGTGCCAAGGTTGGAGTTATTTC
* *
12386 TAGAGGTGGAGGTTGTCTTA-GAGGTGCAAGT
1 TGGAGGTGGAGGTTGTC-TAGGAGGCGCAAGT
12417 GGCGACGATA
Statistics
Matches: 72, Mismatches: 11, Indels: 4
0.83 0.13 0.05
Matches are distributed among these distances:
53 1 0.01
54 69 0.96
55 2 0.03
ACGTcount: A:0.20, C:0.09, G:0.38, T:0.32
Consensus pattern (54 bp):
TGGAGGTGGAGGTTGTCTAGGAGGCGCAAGTTGTGCCAAGGTTGGAGTTATTTC
Found at i:12431 original size:54 final size:54
Alignment explanation
Indices: 12319--12432 Score: 131
Period size: 54 Copynumber: 2.1 Consensus size: 54
12309 TGTAGCATTG
* * * * *
12319 TTGGAGTTATTTCTGGAGGTGGAAGTTGTCTAGGAGGCGCAAGTTGTGCCAAGG
1 TTGGAGTTATTTCTAGAGGTGGAAGTTGTCTAGGAGGCGCAAGTGGCGACAAGA
* * * *
12373 TTGGAGTTATTTCTAGAGGTGGAGGTTGTCTTA-GAGGTGCAAGTGGCGACGATA
1 TTGGAGTTATTTCTAGAGGTGGAAGTTGTC-TAGGAGGCGCAAGTGGCGACAAGA
12427 TTGGAG
1 TTGGAG
12433 CTGGAGTTAG
Statistics
Matches: 50, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
54 48 0.96
55 2 0.04
ACGTcount: A:0.21, C:0.10, G:0.39, T:0.31
Consensus pattern (54 bp):
TTGGAGTTATTTCTAGAGGTGGAAGTTGTCTAGGAGGCGCAAGTGGCGACAAGA
Found at i:15178 original size:24 final size:24
Alignment explanation
Indices: 15151--15202 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
15141 ATTTAATCGT
15151 AAGAGTTAAGTGATCCTATTGAGA
1 AAGAGTTAAGTGATCCTATTGAGA
** *
15175 AAGAGTTGGGTGATCTTATTGAGA
1 AAGAGTTAAGTGATCCTATTGAGA
15199 AAGA
1 AAGA
15203 CTTATTGAAC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.37, C:0.06, G:0.29, T:0.29
Consensus pattern (24 bp):
AAGAGTTAAGTGATCCTATTGAGA
Found at i:31628 original size:24 final size:22
Alignment explanation
Indices: 31579--31624 Score: 76
Period size: 22 Copynumber: 2.1 Consensus size: 22
31569 TTTAGTATGG
*
31579 ATTGATTTATTTTAAAATATAT
1 ATTGATTTATTTTAAAAAATAT
31601 ATTGATTTATTTTAAAAAAT-T
1 ATTGATTTATTTTAAAAAATAT
31622 ATT
1 ATT
31625 ATTGTAGTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 4 0.17
22 19 0.83
ACGTcount: A:0.41, C:0.00, G:0.04, T:0.54
Consensus pattern (22 bp):
ATTGATTTATTTTAAAAAATAT
Found at i:32051 original size:24 final size:23
Alignment explanation
Indices: 32020--32067 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 23
32010 ACCGGTTTAA
32020 TTTTCTTT-TATCTTATTTTCTTC
1 TTTTCTTTAT-TCTTATTTTCTTC
*
32043 TTTTACTTTATTCTTTTTTTCTTC
1 TTTT-CTTTATTCTTATTTTCTTC
32067 T
1 T
32068 CCATTTTGTC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
23 4 0.18
24 17 0.77
25 1 0.05
ACGTcount: A:0.08, C:0.17, G:0.00, T:0.75
Consensus pattern (23 bp):
TTTTCTTTATTCTTATTTTCTTC
Found at i:32211 original size:20 final size:20
Alignment explanation
Indices: 32174--32212 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
32164 CCAACAATAT
*
32174 TTATTTTATAAATTTATGAG
1 TTATTTTATAAATATATGAG
* *
32194 TTATTTTGTAGATATATGA
1 TTATTTTATAAATATATGA
32213 TTGTTAGGTA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.33, C:0.00, G:0.13, T:0.54
Consensus pattern (20 bp):
TTATTTTATAAATATATGAG
Found at i:38449 original size:23 final size:23
Alignment explanation
Indices: 38419--38497 Score: 122
Period size: 23 Copynumber: 3.4 Consensus size: 23
38409 GTATAAATGT
38419 ACCGAAGTGCCACGTAGAATTGC
1 ACCGAAGTGCCACGTAGAATTGC
*
38442 ACCGAAGTGCCACGTAGAATTAC
1 ACCGAAGTGCCACGTAGAATTGC
* *
38465 ACCGAAGTGACGCGTAGAATTGC
1 ACCGAAGTGCCACGTAGAATTGC
*
38488 ACCGTAGTGC
1 ACCGAAGTGC
38498 TGTATGAAAT
Statistics
Matches: 50, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 50 1.00
ACGTcount: A:0.30, C:0.25, G:0.27, T:0.18
Consensus pattern (23 bp):
ACCGAAGTGCCACGTAGAATTGC
Found at i:39773 original size:267 final size:266
Alignment explanation
Indices: 39299--39829 Score: 963
Period size: 267 Copynumber: 2.0 Consensus size: 266
39289 TGGTCTTAGG
*
39299 GTATCGGAACCTGTTCATATGATACCGATACCCCTTGCCCAGAACAGGCTTTTCACCCAAAAATT
1 GTATCGGAACCTGTTCATATGATACCGATACCCCTTGCCCAGAACAGACTTTTCACCCAAAAATT
* *
39364 CATCAACACTTCACTGAATTTCATCATATAAAGCTCCTTTCATACCACCATGCTCAACTATAATC
66 CATCAACACTTCACTAAATTTCATCATATAAAGCTCCTTTCATACCACCATGCTCAAATATAATC
*
39429 CCTTTGACTATCATTTCTCTTCTTAACACCTTATAAACTTAACTATCTCATTGCAATTCTTGAAA
131 CCTTTGACTATCATTTCTCTTCTTAACAACTTATAAACTTAACTATCTCATTGCAATTCTTGAAA
*
39494 CTAAGAATTTGACTAAGTTTTCCATGTAATCCAAACTTAGTTCTAACACTTATTATTTCTTGTAC
196 CTAAGAATTTGACTAAGTTTTCCATATAATCCAAACTTAGTTCTAACACTTATTATTTCTTGTAC
39559 ACACTT
261 ACACTT
* * * *
39565 GTATCGGTACTTGTTCATATGATACCGATACCCCTTGCCCATAACAGTATTTTTCACCCAAAAAT
1 GTATCGGAACCTGTTCATATGATACCGATACCCCTTGCCCAGAACAG-ACTTTTCACCCAAAAAT
*
39630 TTATCAACACTTCACTAAATTTCATCATATAAAGCTCCTTTCATACCACCATGCTCAAATATAAT
65 TCATCAACACTTCACTAAATTTCATCATATAAAGCTCCTTTCATACCACCATGCTCAAATATAAT
39695 CCCTTTGACTATCATTTCTCTTCTTAACAACTTATAAACTTAACTATCTCATTGCAATTCTTGAA
130 CCCTTTGACTATCATTTCTCTTCTTAACAACTTATAAACTTAACTATCTCATTGCAATTCTTGAA
39760 ACTAAGAATTTGACTAAGTTTTCCATATAATCCAAACTTAGTTCTAACACTTATTATTTCTTGTA
195 ACTAAGAATTTGACTAAGTTTTCCATATAATCCAAACTTAGTTCTAACACTTATTATTTCTTGTA
39825 CACAC
260 CACAC
39830 CTATTAAAAG
Statistics
Matches: 254, Mismatches: 10, Indels: 1
0.96 0.04 0.00
Matches are distributed among these distances:
266 44 0.17
267 210 0.83
ACGTcount: A:0.32, C:0.25, G:0.08, T:0.36
Consensus pattern (266 bp):
GTATCGGAACCTGTTCATATGATACCGATACCCCTTGCCCAGAACAGACTTTTCACCCAAAAATT
CATCAACACTTCACTAAATTTCATCATATAAAGCTCCTTTCATACCACCATGCTCAAATATAATC
CCTTTGACTATCATTTCTCTTCTTAACAACTTATAAACTTAACTATCTCATTGCAATTCTTGAAA
CTAAGAATTTGACTAAGTTTTCCATATAATCCAAACTTAGTTCTAACACTTATTATTTCTTGTAC
ACACTT
Found at i:44722 original size:23 final size:23
Alignment explanation
Indices: 44696--44753 Score: 71
Period size: 23 Copynumber: 2.5 Consensus size: 23
44686 GTATAAATGT
44696 ACCGAAGTGCCACGTAGAATTGC
1 ACCGAAGTGCCACGTAGAATTGC
** **
44719 ACCGAAGTAACGTGTAGAATTGC
1 ACCGAAGTGCCACGTAGAATTGC
*
44742 ACCGTAGTGCCA
1 ACCGAAGTGCCA
44754 TATGAAATGT
Statistics
Matches: 27, Mismatches: 8, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.31, C:0.24, G:0.26, T:0.19
Consensus pattern (23 bp):
ACCGAAGTGCCACGTAGAATTGC
Found at i:54384 original size:3 final size:3
Alignment explanation
Indices: 54376--54434 Score: 118
Period size: 3 Copynumber: 19.7 Consensus size: 3
54366 CTATGTTGAT
54376 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
54424 ATA ATA ATA AT
1 ATA ATA ATA AT
54435 CTTGTTTCTT
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 56 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:56334 original size:103 final size:104
Alignment explanation
Indices: 56208--56410 Score: 318
Period size: 104 Copynumber: 2.0 Consensus size: 104
56198 GATAAAATAC
* * * *
56208 TTCAGTAAAATCAGTTTATCAAACATG-ATTTAAAAATATGAACACTACCCACATCCGATCACTA
1 TTCAATAAAATCAATTTATCAAACAAGTATTTAAAAATATGAACACTACCCACATCCGATCACCA
*
56272 AAATGTGTAGGTTCTCCAAAACCATACACCCACCTATAA
66 AAATGTGTAGGTTCCCCAAAACCATACACCCACCTATAA
* *
56311 TTCAATAAAATCAATTTATCAAACAAGTTTTTAAAAATATGAACACTACCCCCATCCGATCACCA
1 TTCAATAAAATCAATTTATCAAACAAGTATTTAAAAATATGAACACTACCCACATCCGATCACCA
* *
56376 GAATGTTTAGGTTCCCCAAAACCATACACCCACCT
66 AAATGTGTAGGTTCCCCAAAACCATACACCCACCT
56411 GTATACCCGG
Statistics
Matches: 90, Mismatches: 9, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
103 24 0.27
104 66 0.73
ACGTcount: A:0.40, C:0.26, G:0.08, T:0.26
Consensus pattern (104 bp):
TTCAATAAAATCAATTTATCAAACAAGTATTTAAAAATATGAACACTACCCACATCCGATCACCA
AAATGTGTAGGTTCCCCAAAACCATACACCCACCTATAA
Found at i:56503 original size:39 final size:39
Alignment explanation
Indices: 56445--56661 Score: 287
Period size: 39 Copynumber: 5.6 Consensus size: 39
56435 ACATAGCATA
* *
56445 AGGA-CCTGCGGTAAGGACTTACCGC-GTGTACAAAGCAG
1 AGGAGCCTGCGGTAAGGACTTACC-CTGAGCACAAAGCAG
* *
56483 AGGAGCCTGCAGTAAGGACTTACCCTGTGCACAAAGCAG
1 AGGAGCCTGCGGTAAGGACTTACCCTGAGCACAAAGCAG
*
56522 ATGAGCCTGCGGTAAGGACTTACCCTGAGCACAAAGCCA-
1 AGGAGCCTGCGGTAAGGACTTACCCTGAGCACAAAG-CAG
* *
56561 AAGAGCCTGCGGTAAGGACTTACCCTGAGCACAAAGCCG
1 AGGAGCCTGCGGTAAGGACTTACCCTGAGCACAAAGCAG
* * *
56600 AGGAGCCTGCGGTAAGGACTTACCTTGAGCATAAAGCCG
1 AGGAGCCTGCGGTAAGGACTTACCCTGAGCACAAAGCAG
* *
56639 AGGAGCATGCGATAAGGACTTAC
1 AGGAGCCTGCGGTAAGGACTTAC
56662 AAGTCATAGA
Statistics
Matches: 163, Mismatches: 12, Indels: 7
0.90 0.07 0.04
Matches are distributed among these distances:
38 6 0.04
39 155 0.95
40 2 0.01
ACGTcount: A:0.30, C:0.25, G:0.29, T:0.16
Consensus pattern (39 bp):
AGGAGCCTGCGGTAAGGACTTACCCTGAGCACAAAGCAG
Found at i:57583 original size:11 final size:11
Alignment explanation
Indices: 57561--57590 Score: 51
Period size: 11 Copynumber: 2.6 Consensus size: 11
57551 TCCAAGGGTC
57561 GAAAATATTCTG
1 GAAAA-ATTCTG
57573 GAAAAATTCTG
1 GAAAAATTCTG
57584 GAAAAAT
1 GAAAAAT
57591 GTTTTAAGGG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 13 0.72
12 5 0.28
ACGTcount: A:0.50, C:0.07, G:0.17, T:0.27
Consensus pattern (11 bp):
GAAAAATTCTG
Found at i:60311 original size:103 final size:102
Alignment explanation
Indices: 60194--60391 Score: 290
Period size: 103 Copynumber: 1.9 Consensus size: 102
60184 AAAATACTTT
* * *
60194 AGTAAAATCAGTTTATCAAACATGTTTTAAAAATATGAACACTACCCCCA-TCTGATCGCCATAA
1 AGTAAAATCAGTTTATCAAACATGTTTTAAAAATATGAACAAT-CCCCCATTC-GATCACCAGAA
*
60258 TGTGCAGGTTCCTCAAAACCATACACCCACATATAATTC
64 TGTGCAGGTTCCCCAAAACCATACACCCACATATAATTC
* * **
60297 AGTAAAATCAGTTTATCAAACATGTTTTAAAAATATTAACAATGCCTTATTCGATCACCAGAATG
1 AGTAAAATCAGTTTATCAAACATGTTTTAAAAATATGAACAATCCCCCATTCGATCACCAGAATG
*
60362 TGTAGGTTCCCCAAAACCATACACCCACAT
66 TGCAGGTTCCCCAAAACCATACACCCACAT
60392 GTATACCCAG
Statistics
Matches: 85, Mismatches: 9, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
102 42 0.49
103 43 0.51
ACGTcount: A:0.38, C:0.24, G:0.10, T:0.28
Consensus pattern (102 bp):
AGTAAAATCAGTTTATCAAACATGTTTTAAAAATATGAACAATCCCCCATTCGATCACCAGAATG
TGCAGGTTCCCCAAAACCATACACCCACATATAATTC
Found at i:60495 original size:39 final size:39
Alignment explanation
Indices: 60434--60517 Score: 107
Period size: 39 Copynumber: 2.2 Consensus size: 39
60424 TAAGGACCTA
* *
60434 CGGTAATGACTTACCATCTACACAAAACAGAGGAGCATG
1 CGGTAAGGACTTACCATCTACACAAAACAGAGAAGCATG
* **
60473 CGGTAAGGACTTAACC-TGTACACAAAGTAGAGAAGCATG
1 CGGTAAGGACTT-ACCATCTACACAAAACAGAGAAGCATG
60512 CGGTAA
1 CGGTAA
60518 TAAATTACCC
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
39 36 0.92
40 3 0.08
ACGTcount: A:0.38, C:0.20, G:0.24, T:0.18
Consensus pattern (39 bp):
CGGTAAGGACTTACCATCTACACAAAACAGAGAAGCATG
Found at i:60536 original size:39 final size:39
Alignment explanation
Indices: 60452--60538 Score: 95
Period size: 39 Copynumber: 2.2 Consensus size: 39
60442 ACTTACCATC
** * * *
60452 TACACAAAACAGAGGAGCATGCGGTAAGGACTTAACCTG
1 TACACAAAGTAGAGAAGCATGCGGTAAGAAATTAACCTG
* *
60491 TACACAAAGTAGAGAAGCATGCGGTAATAAATTACCCTG
1 TACACAAAGTAGAGAAGCATGCGGTAAGAAATTAACCTG
60530 -AGCACAAAG
1 TA-CACAAAG
60539 CCGAGGCGTC
Statistics
Matches: 40, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
38 1 0.03
39 39 0.98
ACGTcount: A:0.41, C:0.20, G:0.23, T:0.16
Consensus pattern (39 bp):
TACACAAAGTAGAGAAGCATGCGGTAAGAAATTAACCTG
Found at i:64277 original size:103 final size:103
Alignment explanation
Indices: 64150--64345 Score: 313
Period size: 103 Copynumber: 1.9 Consensus size: 103
64140 AAAGTACTTT
* **
64150 AGTAAAATCAGTTTATCAAACATGTTTTTAAAAATATGAACACT-ACCCCATCTGATCACCAGAA
1 AGTAAAATCAGTTTATAAAACATG-TTTTAAAAATATGAACACTGACCCCATCCAATCACCAGAA
*
64214 TGTGTAGGTTTCCCAAAACCATAAACCCACCTATAATTC
65 TGTGTAGGTTCCCCAAAACCATAAACCCACCTATAATTC
* *
64253 AGTAAAATCAGTTTATAAAACATGTTTTAAAAATATGAACATTGCCCCCATCCAATCACCAGAAT
1 AGTAAAATCAGTTTATAAAACATGTTTTAAAAATATGAACACTGACCCCATCCAATCACCAGAAT
*
64318 GTGTAGGTTCCCCAAAACCATACACCCA
66 GTGTAGGTTCCCCAAAACCATAAACCCA
64346 TATGTATACC
Statistics
Matches: 85, Mismatches: 7, Indels: 2
0.90 0.07 0.02
Matches are distributed among these distances:
102 18 0.21
103 67 0.79
ACGTcount: A:0.39, C:0.24, G:0.10, T:0.27
Consensus pattern (103 bp):
AGTAAAATCAGTTTATAAAACATGTTTTAAAAATATGAACACTGACCCCATCCAATCACCAGAAT
GTGTAGGTTCCCCAAAACCATAAACCCACCTATAATTC
Found at i:64553 original size:39 final size:39
Alignment explanation
Indices: 64391--64600 Score: 156
Period size: 39 Copynumber: 5.4 Consensus size: 39
64381 TGAGGACCTA
* * * *
64391 CGGTAAGGACTTACTCTGTGCACAAAGCAGATGAGCCTG
1 CGGTAAGGACTTACCCTGAGCACAAAGCAGAGGAGCATG
* *
64430 -GGTTAAGGACTTACCCTGTA-CACAAAGCAGGGGATCATG
1 CGG-TAAGGACTTACCCTG-AGCACAAAGCAGAGGAGCATG
* * * * * * * *
64469 TGGTAAGCAATTACCTTGAGCATAAATTC-GAGGAGCCTA
1 CGGTAAGGACTTACCCTGAGCACAAA-GCAGAGGAGCATG
* * * *
64508 CAGTAAGGACTTACCATGAGCACAAAGCCGAGGAGCTTG
1 CGGTAAGGACTTACCCTGAGCACAAAGCAGAGGAGCATG
* * * * *
64547 CGGTAAGTACTTACCCTGAGAAAAAAAGCTGAGAAGCATG
1 CGGTAAGGACTTACCCTGAG-CACAAAGCAGAGGAGCATG
64587 CGGTAAGGACTTAC
1 CGGTAAGGACTTAC
64601 AAGTCATAGA
Statistics
Matches: 131, Mismatches: 33, Indels: 13
0.74 0.19 0.07
Matches are distributed among these distances:
38 4 0.03
39 97 0.74
40 30 0.23
ACGTcount: A:0.33, C:0.20, G:0.27, T:0.20
Consensus pattern (39 bp):
CGGTAAGGACTTACCCTGAGCACAAAGCAGAGGAGCATG
Found at i:65876 original size:18 final size:19
Alignment explanation
Indices: 65853--65896 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 19
65843 TTTGGATCCG
*
65853 AATTTA-ATCAAAATTTTA
1 AATTTAGATAAAAATTTTA
* *
65871 AATTTAGTTAAAAATTTTC
1 AATTTAGATAAAAATTTTA
65890 AATTTAG
1 AATTTAG
65897 TCCTAAAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
18 6 0.27
19 16 0.73
ACGTcount: A:0.45, C:0.05, G:0.05, T:0.45
Consensus pattern (19 bp):
AATTTAGATAAAAATTTTA
Found at i:65886 original size:19 final size:20
Alignment explanation
Indices: 65862--65907 Score: 67
Period size: 19 Copynumber: 2.3 Consensus size: 20
65852 GAATTTAATC
65862 AAAATTTTAAATTTAGT-TA
1 AAAATTTTAAATTTAGTCTA
*
65881 AAAATTTTCAATTTAGTCCTA
1 AAAATTTTAAATTTAGT-CTA
65902 AAAATT
1 AAAATT
65908 AAAAACATTA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 16 0.67
21 8 0.33
ACGTcount: A:0.46, C:0.07, G:0.04, T:0.43
Consensus pattern (20 bp):
AAAATTTTAAATTTAGTCTA
Found at i:66036 original size:59 final size:60
Alignment explanation
Indices: 65940--66089 Score: 194
Period size: 60 Copynumber: 2.5 Consensus size: 60
65930 GGGTGTGACA
** * * * * *
65940 ATTAAAAGTTACAAAATGGACATTCGACTATAGAGTATTGA-TTGTTGAGTCCCTCGGCT
1 ATTAAAAGTTACAAAAAAGTCACTCAACTATAAAGTATTGATTTGTTGAGTCCCTCGACT
* *
65999 ATTAAAAGTTATAAAAAAGTCACTCAACTATAAAGTATTGATTTGTTGAGTCCCTCGATT
1 ATTAAAAGTTACAAAAAAGTCACTCAACTATAAAGTATTGATTTGTTGAGTCCCTCGACT
* *
66059 ATTAAAAGTTACAAAATAGTCACTCGACTAT
1 ATTAAAAGTTACAAAAAAGTCACTCAACTAT
66090 TCATTATATT
Statistics
Matches: 78, Mismatches: 12, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
59 34 0.44
60 44 0.56
ACGTcount: A:0.37, C:0.15, G:0.15, T:0.33
Consensus pattern (60 bp):
ATTAAAAGTTACAAAAAAGTCACTCAACTATAAAGTATTGATTTGTTGAGTCCCTCGACT
Found at i:72079 original size:103 final size:103
Alignment explanation
Indices: 71917--72106 Score: 265
Period size: 103 Copynumber: 1.8 Consensus size: 103
71907 GGAAACCATC
* * * * *
71917 TCAAGCGAGATAAGATTTTTCTTTGAGTGAAATGATCTCAAAGTTTGTATTT-TAGGGAAATTGT
1 TCAAGCGAGATAAAATTTTTCTTTAAGTGAAATGATCTCAAAGTTTGTATTTCAAGGAAAACTGT
71981 CTCAAGCAAGATGAAATTTTGTCTTAAGAGAAGCGATA
66 CTCAAGCAAGATGAAATTTTGTCTTAAGAGAAGCGATA
* *
72019 TCAAGTGAGATAAAATTTTTCTTTTAAGTGAAATGATCTCAAAGTTTGTGTTTCAAGGAAAACTG
1 TCAAGCGAGATAAAATTTTTC-TTTAAGTGAAATGATCTCAAAGTTTGTATTTCAAGGAAAACTG
* * **
72084 TTTCTAGTGAGATGAAATTTTGT
65 TCTCAAGCAAGATGAAATTTTGT
72107 TTCAAGGGAA
Statistics
Matches: 75, Mismatches: 11, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
102 19 0.25
103 29 0.39
104 27 0.36
ACGTcount: A:0.34, C:0.09, G:0.21, T:0.37
Consensus pattern (103 bp):
TCAAGCGAGATAAAATTTTTCTTTAAGTGAAATGATCTCAAAGTTTGTATTTCAAGGAAAACTGT
CTCAAGCAAGATGAAATTTTGTCTTAAGAGAAGCGATA
Found at i:72136 original size:104 final size:102
Alignment explanation
Indices: 71874--72231 Score: 314
Period size: 104 Copynumber: 3.5 Consensus size: 102
71864 TTCCAAGGGG
* * * * * *
71874 AACTATCTCAAGTGAGACGAAA-TCTGTTTCAAGGGAAACCATCTCAAGCGAGATAAGATTTTTC
1 AACTGTCTCAAGTGAGATGAAATTTTGTTTCAAGGGAAACAATCTCAAGTGAGATAAAATTTTTC
* * *
71938 TTTGAGTGAAATGATCTCAAAGTTTGTATTTTAGGGA
66 TTTAAGTGAAATGATCTCAAAGTTTGTATTTAAGGAA
* ** * * * *
71975 AATTGTCTCAAGCAAGATGAAATTTTGTCTT-AAGAGAAGCGATATCAAGTGAGATAAAATTTTT
1 AACTGTCTCAAGTGAGATGAAATTTTGT-TTCAAGGGAAACAATCTCAAGTGAGATAAAATTTTT
*
72039 CTTTTAAGTGAAATGATCTCAAAGTTTGTGTTTCAAGGAA
65 C-TTTAAGTGAAATGATCTCAAAGTTTGTATTT-AAGGAA
* * * * * *
72079 AACTGTTTCTAGTGAGATGAAATTTTGTTTCAAGGGAAATAACCTCAAGTGAGATAAAAAATTTA
1 AACTGTCTCAAGTGAGATGAAATTTTGTTTCAAGGGAAACAATCTCAAGTGAGAT-AAAATTTTT
* * * *
72144 CTTCAAAT-ACAA-CAGTCTCAAAGTTTTTGT-TTTAAGGGA
65 CTTTAAGTGA-AATGA-TCTCAAAG--TTTGTATTTAAGGAA
* * * **
72183 AACTTTCTCAAGTAAGAAGAAA-TTTGTTTCAAGGGAAACTGTCTCAAGT
1 AACTGTCTCAAGTGAGATGAAATTTTGTTTCAAGGGAAACAATCTCAAGT
72232 AAGGCGAAAT
Statistics
Matches: 205, Mismatches: 42, Indels: 18
0.77 0.16 0.07
Matches are distributed among these distances:
101 17 0.08
102 32 0.16
103 58 0.28
104 82 0.40
105 11 0.05
106 5 0.02
ACGTcount: A:0.36, C:0.12, G:0.19, T:0.33
Consensus pattern (102 bp):
AACTGTCTCAAGTGAGATGAAATTTTGTTTCAAGGGAAACAATCTCAAGTGAGATAAAATTTTTC
TTTAAGTGAAATGATCTCAAAGTTTGTATTTAAGGAA
Found at i:72217 original size:36 final size:36
Alignment explanation
Indices: 72169--72256 Score: 122
Period size: 36 Copynumber: 2.4 Consensus size: 36
72159 TCTCAAAGTT
* *
72169 TTTGTTTTAAGGGAAACTTTCTCAAGTAAGAAGAAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGTAAGAAGAAA
**
72205 TTTGTTTCAAGGGAAACTGTCTCAAGTAAGGCGAAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGTAAGAAGAAA
* *
72241 TTTTTTTCGAGGGAAA
1 TTTGTTTCAAGGGAAA
72257 TAATTCTCAA
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 46 1.00
ACGTcount: A:0.34, C:0.10, G:0.23, T:0.33
Consensus pattern (36 bp):
TTTGTTTCAAGGGAAACTGTCTCAAGTAAGAAGAAA
Found at i:84562 original size:14 final size:16
Alignment explanation
Indices: 84543--84574 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
84533 CCCCCTTACT
84543 TTAACA-TT-TCCCCC
1 TTAACACTTCTCCCCC
84557 TTAACACTTCTCCCCC
1 TTAACACTTCTCCCCC
84573 TT
1 TT
84575 TTTGTTAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 6 0.38
15 2 0.12
16 8 0.50
ACGTcount: A:0.19, C:0.44, G:0.00, T:0.38
Consensus pattern (16 bp):
TTAACACTTCTCCCCC
Found at i:90314 original size:27 final size:28
Alignment explanation
Indices: 90284--90352 Score: 97
Period size: 27 Copynumber: 2.5 Consensus size: 28
90274 TATATATATA
*
90284 ATATTTTATA-TTTTTTATATTAATTAT
1 ATATTATATATTTTTTTATATTAATTAT
90311 ATA-TATATATTTTTTTATATTAATTAT
1 ATATTATATATTTTTTTATATTAATTAT
* *
90338 ATATAAAATATTTTT
1 ATATTATATATTTTT
90353 GGGTTTGGGT
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
26 5 0.14
27 23 0.62
28 9 0.24
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (28 bp):
ATATTATATATTTTTTTATATTAATTAT
Found at i:91176 original size:20 final size:20
Alignment explanation
Indices: 91134--91176 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
91124 TTGTTTTTAT
*
91134 TTTTTAATTTCAAAATATTA
1 TTTTTAATTTCAAAATATAA
*
91154 TTTTTATATTTGAAAA-ATAA
1 TTTTTA-ATTTCAAAATATAA
91174 TTT
1 TTT
91177 CTCATAATCT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 12 0.60
21 8 0.40
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (20 bp):
TTTTTAATTTCAAAATATAA
Found at i:93239 original size:19 final size:19
Alignment explanation
Indices: 93210--93268 Score: 59
Period size: 19 Copynumber: 3.1 Consensus size: 19
93200 CTATTTGTTC
* *
93210 AAGATTGCATCGATGCA-T
1 AAGAGTGCATCGATACACT
*
93228 AGAGAGTGCATCGGTACACT
1 A-AGAGTGCATCGATACACT
93248 AAGAGTGCATC-AGTACACT
1 AAGAGTGCATCGA-TACACT
93267 AA
1 AA
93269 ATGGATTTGA
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
18 1 0.03
19 31 0.91
20 2 0.06
ACGTcount: A:0.36, C:0.19, G:0.24, T:0.22
Consensus pattern (19 bp):
AAGAGTGCATCGATACACT
Found at i:105487 original size:15 final size:14
Alignment explanation
Indices: 105465--105500 Score: 54
Period size: 15 Copynumber: 2.5 Consensus size: 14
105455 TCTTTCTTTG
*
105465 GAAAGAAAGTGGAA
1 GAAAGAAAATGGAA
105479 GAGAAGAAAATGGAA
1 GA-AAGAAAATGGAA
105494 GAAAGAA
1 GAAAGAA
105501 GCAGAGGAGT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
14 7 0.35
15 13 0.65
ACGTcount: A:0.61, C:0.00, G:0.33, T:0.06
Consensus pattern (14 bp):
GAAAGAAAATGGAA
Found at i:108295 original size:2 final size:2
Alignment explanation
Indices: 108288--108316 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
108278 AAAATTAGTA
108288 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
108317 AATTTACAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:111351 original size:16 final size:16
Alignment explanation
Indices: 111298--111353 Score: 51
Period size: 16 Copynumber: 3.2 Consensus size: 16
111288 ATTTAAACAT
111298 ATAAAATTAAAATATAA
1 ATAAAATTAAAAT-TAA
111315 ATAAACAATGAGTAAAA-TAA
1 AT-AA-AAT---TAAAATTAA
111335 ATAAAATTAAAATTAA
1 ATAAAATTAAAATTAA
111351 ATA
1 ATA
111354 TAAAAAGTAA
Statistics
Matches: 33, Mismatches: 0, Indels: 13
0.72 0.00 0.28
Matches are distributed among these distances:
15 5 0.15
16 6 0.18
17 2 0.06
18 5 0.15
19 5 0.15
20 5 0.15
22 5 0.15
ACGTcount: A:0.68, C:0.02, G:0.04, T:0.27
Consensus pattern (16 bp):
ATAAAATTAAAATTAA
Found at i:111368 original size:37 final size:37
Alignment explanation
Indices: 111298--111368 Score: 92
Period size: 37 Copynumber: 1.9 Consensus size: 37
111288 ATTTAAACAT
* *
111298 ATAAAATTAAAATATAAATAAACAATGAGTAAAATAA
1 ATAAAATTAAAATATAAATAAAAAATGAATAAAATAA
111335 ATAAAATTAAAAT-TAAATATAAAAA-GTAATAAAA
1 ATAAAATTAAAATATAAATA-AAAAATG-AATAAAA
111369 CTTATAATTA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
36 7 0.23
37 23 0.77
ACGTcount: A:0.69, C:0.01, G:0.04, T:0.25
Consensus pattern (37 bp):
ATAAAATTAAAATATAAATAAAAAATGAATAAAATAA
Found at i:112638 original size:3 final size:3
Alignment explanation
Indices: 112620--112675 Score: 85
Period size: 3 Copynumber: 18.0 Consensus size: 3
112610 TTGTAATATT
*
112620 TAA TAAA TAA TAAA TAA TAT TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA T-AA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
112667 TAA TAA TAA
1 TAA TAA TAA
112676 ATTTAAATTT
Statistics
Matches: 49, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
3 43 0.88
4 6 0.12
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:112861 original size:45 final size:45
Alignment explanation
Indices: 112810--112908 Score: 180
Period size: 45 Copynumber: 2.2 Consensus size: 45
112800 GAAATGTTTG
*
112810 AAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTA
1 AAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTTTTA
*
112855 AAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTTTTG
1 AAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTTTTA
112900 AAAACATCA
1 AAAACATCA
112909 AAAAGCTCCC
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
45 52 1.00
ACGTcount: A:0.38, C:0.20, G:0.20, T:0.21
Consensus pattern (45 bp):
AAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTTTTA
Found at i:112982 original size:76 final size:76
Alignment explanation
Indices: 112856--113264 Score: 694
Period size: 76 Copynumber: 5.4 Consensus size: 76
112846 AAGGTTTTAA
* * *
112856 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
112921 AGGCTTTTTGG
66 AGGCTTTTTGG
* * *
112932 AAACACCATGCACTGTAGGACTTACAGATGACCTTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
112997 AGGCTTTTTGG
66 AGGCTTTTTGG
** * *
113008 AAACATCATGCACTATAGGACTTATAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTTCCGA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
113073 AGGCTTTTTGG
66 AGGCTTTTTGG
*
113084 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCAA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
113149 AGGCTTTTTGG
66 AGGCTTTTTGG
* *
113160 AAACATTATGCACTGCAGGACTTACAGATGGCCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
113225 AGGCTTTTTGG
66 AGGCTTTTTGG
113236 AAA-ATCATGCACTGCAGGACTTACAGATG
1 AAACATCATGCACTGCAGGACTTACAGATG
113265 TAGGAAATAG
Statistics
Matches: 314, Mismatches: 19, Indels: 1
0.94 0.06 0.00
Matches are distributed among these distances:
75 25 0.08
76 289 0.92
ACGTcount: A:0.35, C:0.22, G:0.20, T:0.23
Consensus pattern (76 bp):
AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
AGGCTTTTTGG
Found at i:113965 original size:22 final size:22
Alignment explanation
Indices: 113940--114016 Score: 118
Period size: 22 Copynumber: 3.5 Consensus size: 22
113930 AATAAAGCTT
113940 TCATCTTTGAAAAGAGAATATA
1 TCATCTTTGAAAAGAGAATATA
* *
113962 TCATCTTTAAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATATA
*
113984 TCATCTTTGAAAAGAGAATTTA
1 TCATCTTTGAAAAGAGAATATA
*
114006 TCATTTTTGAA
1 TCATCTTTGAA
114017 GAGTGTAAAT
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 50 1.00
ACGTcount: A:0.42, C:0.10, G:0.12, T:0.36
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATATA
Found at i:115506 original size:74 final size:75
Alignment explanation
Indices: 115357--115533 Score: 241
Period size: 74 Copynumber: 2.4 Consensus size: 75
115347 ACATGATGAT
* * *
115357 ATGGGCCTTCAGCATGTCCCAGCATTTTGCTGATATAAATATTCAGGATACATCAACATTCATGA
1 ATGGGCTTTCAGCATGCCCCAGCATTTTGCTGA-ATAAATATTCAGAATACATCAACATTCATGA
*
115422 TTCTGATTGAA
65 TTCGGATTGAA
**
115433 ATGGGCTTTCAGCATGCCCCAGCATTTTGCTG-ATAAATATTCAGAATATTTCAACATTTC-TGA
1 ATGGGCTTTCAGCATGCCCCAGCATTTTGCTGAATAAATATTCAGAATACATCAACA-TTCATGA
115496 TTCGGATTGAA
65 TTCGGATTGAA
* * *
115507 AAGGGTTTTCAGCATGCCCCAACATTT
1 ATGGGCTTTCAGCATGCCCCAGCATTT
115534 GCTTCTTGTT
Statistics
Matches: 91, Mismatches: 9, Indels: 4
0.88 0.09 0.04
Matches are distributed among these distances:
74 58 0.64
75 3 0.03
76 30 0.33
ACGTcount: A:0.29, C:0.20, G:0.18, T:0.33
Consensus pattern (75 bp):
ATGGGCTTTCAGCATGCCCCAGCATTTTGCTGAATAAATATTCAGAATACATCAACATTCATGAT
TCGGATTGAA
Found at i:118314 original size:7 final size:7
Alignment explanation
Indices: 118302--118355 Score: 74
Period size: 7 Copynumber: 7.7 Consensus size: 7
118292 TTTCTCCCTT
118302 TTTTTTC
1 TTTTTTC
118309 TTTTTTC
1 TTTTTTC
*
118316 TTTTTGC
1 TTTTTTC
*
118323 TTTTAT-
1 TTTTTTC
118329 TTTTTTC
1 TTTTTTC
118336 TTTCTTTC
1 TTT-TTTC
118344 TTTTTTC
1 TTTTTTC
118351 TTTTT
1 TTTTT
118356 ATTGTTGTTG
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
6 5 0.12
7 29 0.71
8 7 0.17
ACGTcount: A:0.02, C:0.13, G:0.02, T:0.83
Consensus pattern (7 bp):
TTTTTTC
Found at i:118343 original size:28 final size:27
Alignment explanation
Indices: 118301--118354 Score: 90
Period size: 28 Copynumber: 2.0 Consensus size: 27
118291 ATTTCTCCCT
118301 TTTTTTTCTTTTTTCTTTTTGCTTTTA
1 TTTTTTTCTTTTTTCTTTTTGCTTTTA
*
118328 TTTTTTTCTTTCTTTCTTTTTTCTTTT
1 TTTTTTTCTTT-TTTCTTTTTGCTTTT
118355 TATTGTTGTT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
27 11 0.44
28 14 0.56
ACGTcount: A:0.02, C:0.13, G:0.02, T:0.83
Consensus pattern (27 bp):
TTTTTTTCTTTTTTCTTTTTGCTTTTA
Found at i:121222 original size:14 final size:15
Alignment explanation
Indices: 121205--121237 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
121195 TAAAATTATG
121205 AATGCAAA-ATGAAA
1 AATGCAAAGATGAAA
*
121219 AATGCAAAGATGCAA
1 AATGCAAAGATGAAA
121234 AATG
1 AATG
121238 AAATGCTATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.58, C:0.09, G:0.18, T:0.15
Consensus pattern (15 bp):
AATGCAAAGATGAAA
Found at i:123371 original size:20 final size:20
Alignment explanation
Indices: 123339--123460 Score: 158
Period size: 20 Copynumber: 6.1 Consensus size: 20
123329 CTATACCTGC
* *
123339 TTCCAAGAATCGCAATGCGA
1 TTCCAAAAATCGCAACGCGA
123359 TT-CAGAAAATCGCAACGCGA
1 TTCCA-AAAATCGCAACGCGA
*
123379 TTCCAAGAATCGCAACGCGA
1 TTCCAAAAATCGCAACGCGA
*
123399 TT-AAGAAAATCGCAACGCGA
1 TTCCA-AAAATCGCAACGCGA
*
123419 TTCCAAGAATCGCAACGCGA
1 TTCCAAAAATCGCAACGCGA
*
123439 TTCCAAGAATCGCAACGCGA
1 TTCCAAAAATCGCAACGCGA
123459 TT
1 TT
123461 AAGAAAATGA
Statistics
Matches: 91, Mismatches: 7, Indels: 8
0.86 0.07 0.08
Matches are distributed among these distances:
19 3 0.03
20 85 0.93
21 3 0.03
ACGTcount: A:0.37, C:0.26, G:0.20, T:0.17
Consensus pattern (20 bp):
TTCCAAAAATCGCAACGCGA
Found at i:123399 original size:40 final size:40
Alignment explanation
Indices: 123339--123460 Score: 201
Period size: 40 Copynumber: 3.0 Consensus size: 40
123329 CTATACCTGC
*
123339 TTCCAAGAATCGCAATGCGATTCAGAAAATCGCAACGCGA
1 TTCCAAGAATCGCAACGCGATTCAGAAAATCGCAACGCGA
*
123379 TTCCAAGAATCGCAACGCGATTAAGAAAATCGCAACGCGA
1 TTCCAAGAATCGCAACGCGATTCAGAAAATCGCAACGCGA
*
123419 TTCCAAGAATCGCAACGCGATTCCA-AGAATCGCAACGCGA
1 TTCCAAGAATCGCAACGCGATT-CAGAAAATCGCAACGCGA
123459 TT
1 TT
123461 AAGAAAATGA
Statistics
Matches: 77, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
40 76 0.99
41 1 0.01
ACGTcount: A:0.37, C:0.26, G:0.20, T:0.17
Consensus pattern (40 bp):
TTCCAAGAATCGCAACGCGATTCAGAAAATCGCAACGCGA
Found at i:123439 original size:60 final size:60
Alignment explanation
Indices: 123346--123468 Score: 212
Period size: 60 Copynumber: 2.0 Consensus size: 60
123336 TGCTTCCAAG
*
123346 AATCGCAATGCGATTCAGAAAATCGCAACGCGATTCCAAGAATCGCAACGCGATTAAGAA
1 AATCGCAACGCGATTCAGAAAATCGCAACGCGATTCCAAGAATCGCAACGCGATTAAGAA
*
123406 AATCGCAACGCGATTCCA-AGAATCGCAACGCGATTCCAAGAATCGCAACGCGATTAAGAA
1 AATCGCAACGCGATT-CAGAAAATCGCAACGCGATTCCAAGAATCGCAACGCGATTAAGAA
123466 AAT
1 AAT
123469 GAGTAAATTC
Statistics
Matches: 60, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
60 58 0.97
61 2 0.03
ACGTcount: A:0.40, C:0.24, G:0.20, T:0.16
Consensus pattern (60 bp):
AATCGCAACGCGATTCAGAAAATCGCAACGCGATTCCAAGAATCGCAACGCGATTAAGAA
Found at i:123580 original size:6 final size:6
Alignment explanation
Indices: 123564--123607 Score: 81
Period size: 6 Copynumber: 7.5 Consensus size: 6
123554 GACACGTATT
123564 ACCAC- ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACC
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACC
123608 CGAGACGAGA
Statistics
Matches: 38, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 5 0.13
6 33 0.87
ACGTcount: A:0.34, C:0.52, G:0.14, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:124112 original size:6 final size:6
Alignment explanation
Indices: 124102--124140 Score: 69
Period size: 6 Copynumber: 6.5 Consensus size: 6
124092 TCTCGTCTCG
*
124102 GGTCGG GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
124141 AATACGTGTC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.00, C:0.15, G:0.54, T:0.31
Consensus pattern (6 bp):
GGTCGT
Found at i:124268 original size:20 final size:20
Alignment explanation
Indices: 124243--124662 Score: 558
Period size: 20 Copynumber: 20.8 Consensus size: 20
124233 CTCATTTTCT
124243 GAATCGCGTTGCGATTCTTG
1 GAATCGCGTTGCGATTCTTG
*
124263 GAATCGCGTTGCGATT-TTCT
1 GAATCGCGTTGCGATTCTT-G
124283 GAATCGCGTTGCGATTCTTG
1 GAATCGCGTTGCGATTCTTG
124303 GAATCGCGTTGCGATTCTTG
1 GAATCGCGTTGCGATTCTTG
124323 GAATCGCGTTGCGATTTTCTT-
1 GAATCGCGTTGCGA--TTCTTG
124344 -AATCGCGTTGCGATTCTTG
1 GAATCGCGTTGCGATTCTTG
124363 GAATCGCGTTGCGATTTTCTT-
1 GAATCGCGTTGCGA--TTCTTG
124384 -AATCGCGTTGCGATTCTTG
1 GAATCGCGTTGCGATTCTTG
*
124403 GAATCGCGTTGCGATT-TTCT
1 GAATCGCGTTGCGATTCTT-G
124423 GAATCGCGTTGCGATTCTTG
1 GAATCGCGTTGCGATTCTTG
124443 GAATCGCGTTGCGATTCTTG
1 GAATCGCGTTGCGATTCTTG
124463 GAATCGCGTTGCGATTCTTG
1 GAATCGCGTTGCGATTCTTG
124483 GAATCGCGTTGCGATTTTCTT-
1 GAATCGCGTTGCGA--TTCTTG
124504 -AATCGCGTTGCGATTCTTG
1 GAATCGCGTTGCGATTCTTG
124523 GAATCGCGTTGCGATTTTCTT-
1 GAATCGCGTTGCGA--TTCTTG
124544 -AATCGCGTTGCGATTCTTG
1 GAATCGCGTTGCGATTCTTG
*
124563 GAATCGCGTTGCGATT-TTCT
1 GAATCGCGTTGCGATTCTT-G
*
124583 GAATCGCATTGCGATTCTTG
1 GAATCGCGTTGCGATTCTTG
124603 GAAGATCGCGTTGCGATTCTCT-
1 G-A-ATCGCGTTGCGATTCT-TG
* *
124625 TAATCGCATTGCGATTCTTG
1 GAATCGCGTTGCGATTCTTG
124645 GAATATCGCGTTGCGATT
1 G-A-ATCGCGTTGCGATT
124663 TTCTTTTGAC
Statistics
Matches: 360, Mismatches: 12, Indels: 54
0.85 0.03 0.13
Matches are distributed among these distances:
18 20 0.06
19 7 0.02
20 275 0.76
21 9 0.03
22 48 0.13
23 1 0.00
ACGTcount: A:0.16, C:0.20, G:0.26, T:0.38
Consensus pattern (20 bp):
GAATCGCGTTGCGATTCTTG
Found at i:124376 original size:80 final size:78
Alignment explanation
Indices: 124243--124667 Score: 631
Period size: 80 Copynumber: 5.3 Consensus size: 78
124233 CTCATTTTCT
*
124243 GAATCGCGTTGCGA--TTCTTGGAATCGCGTTGCGATT-TTCTGAATCGCGTTGCGATTCTTGGA
1 GAATCGCGTTGCGATTTTCTT--AATCGCGTTGCGATTCTT-GGAATCGCGTTGCGATTCTT--A
124305 ATCGCGTTGCGATTCTTG
61 ATCGCGTTGCGATTCTTG
124323 GAATCGCGTTGCGATTTTCTTAATCGCGTTGCGATTCTTGGAATCGCGTTGCGATTTTCTTAATC
1 GAATCGCGTTGCGATTTTCTTAATCGCGTTGCGATTCTTGGAATCGCGTTGCGA--TTCTTAATC
124388 GCGTTGCGATTCTTG
64 GCGTTGCGATTCTTG
*
124403 GAATCGCGTTGCGATTTTCTGAATCGCGTTGCGATTCTTGGAATCGCGTTGCGATTCTTGGAATC
1 GAATCGCGTTGCGATTTTCTTAATCGCGTTGCGATTCTTGGAATCGCGTTGCGATTCTT--AATC
124468 GCGTTGCGATTCTTG
64 GCGTTGCGATTCTTG
124483 GAATCGCGTTGCGATTTTCTTAATCGCGTTGCGATTCTTGGAATCGCGTTGCGATTTTCTTAATC
1 GAATCGCGTTGCGATTTTCTTAATCGCGTTGCGATTCTTGGAATCGCGTTGCGA--TTCTTAATC
124548 GCGTTGCGATTCTTG
64 GCGTTGCGATTCTTG
* *
124563 GAATCGCGTTGCGATTTTCTGAATCGCATTGCGATTCTTGGAAGATCGCGTTGCGATTCTCTTAA
1 GAATCGCGTTGCGATTTTCTTAATCGCGTTGCGATTCTTGG-A-ATCGCGTTGCGA-T-TCTTAA
*
124628 TCGCATTGCGATTCTTG
62 TCGCGTTGCGATTCTTG
124645 GAATATCGCGTTGCGATTTTCTT
1 G-A-ATCGCGTTGCGATTTTCTT
124668 TTGACCGTTG
Statistics
Matches: 324, Mismatches: 7, Indels: 24
0.91 0.02 0.07
Matches are distributed among these distances:
78 5 0.02
80 245 0.76
81 5 0.02
82 50 0.15
83 1 0.00
84 18 0.06
ACGTcount: A:0.16, C:0.20, G:0.26, T:0.38
Consensus pattern (78 bp):
GAATCGCGTTGCGATTTTCTTAATCGCGTTGCGATTCTTGGAATCGCGTTGCGATTCTTAATCGC
GTTGCGATTCTTG
Found at i:124716 original size:20 final size:20
Alignment explanation
Indices: 124236--124743 Score: 476
Period size: 20 Copynumber: 25.2 Consensus size: 20
124226 GAATTTACTC
124236 ATTTTCTGAATCGCGTTGCG
1 ATTTTCTGAATCGCGTTGCG
*
124256 ATTCTT-GGAATCGCGTTGCG
1 ATT-TTCTGAATCGCGTTGCG
124276 ATTTTCTGAATCGCGTTGCG
1 ATTTTCTGAATCGCGTTGCG
*
124296 ATTCTT-GGAATCGCGTTGCG
1 ATT-TTCTGAATCGCGTTGCG
*
124316 ATTCTT-GGAATCGCGTTGCG
1 ATT-TTCTGAATCGCGTTGCG
*
124336 ATTTTCTTAATCGCGTTGCG
1 ATTTTCTGAATCGCGTTGCG
*
124356 ATTCTT-GGAATCGCGTTGCG
1 ATT-TTCTGAATCGCGTTGCG
*
124376 ATTTTCTTAATCGCGTTGCG
1 ATTTTCTGAATCGCGTTGCG
*
124396 ATTCTT-GGAATCGCGTTGCG
1 ATT-TTCTGAATCGCGTTGCG
124416 ATTTTCTGAATCGCGTTGCG
1 ATTTTCTGAATCGCGTTGCG
*
124436 ATTCTT-GGAATCGCGTTGCG
1 ATT-TTCTGAATCGCGTTGCG
*
124456 ATTCTT-GGAATCGCGTTGCG
1 ATT-TTCTGAATCGCGTTGCG
*
124476 ATTCTT-GGAATCGCGTTGCG
1 ATT-TTCTGAATCGCGTTGCG
*
124496 ATTTTCTTAATCGCGTTGCG
1 ATTTTCTGAATCGCGTTGCG
*
124516 ATTCTT-GGAATCGCGTTGCG
1 ATT-TTCTGAATCGCGTTGCG
*
124536 ATTTTCTTAATCGCGTTGCG
1 ATTTTCTGAATCGCGTTGCG
*
124556 ATTCTT-GGAATCGCGTTGCG
1 ATT-TTCTGAATCGCGTTGCG
*
124576 ATTTTCTGAATCGCATTGCG
1 ATTTTCTGAATCGCGTTGCG
*
124596 ATTCTT-GGAAGATCGCGTTGCG
1 ATT-TTCTG-A-ATCGCGTTGCG
* * *
124618 ATTCTCTTAATCGCATTGCG
1 ATTTTCTGAATCGCGTTGCG
*
124638 ATTCTT-GGAATATCGCGTTGCG
1 ATT-TTCTG-A-ATCGCGTTGCG
124660 ATTTTCTTTTG-A-C-CGTTGCG
1 ATTTTC---TGAATCGCGTTGCG
** *
124680 ATTTTCT-TTTCAACGTTGCG
1 ATTTTCTGAATC-GCGTTGCG
*
124700 ATTTTCTAAATCGCGTTGCG
1 ATTTTCTGAATCGCGTTGCG
*
124720 ATTTT-T-ATTTCGCGTTGCG
1 ATTTTCTGA-ATCGCGTTGCG
124739 ATTTT
1 ATTTT
124744 GTTGGTCATT
Statistics
Matches: 418, Mismatches: 39, Indels: 63
0.80 0.08 0.12
Matches are distributed among these distances:
17 1 0.00
18 2 0.00
19 30 0.07
20 331 0.79
21 26 0.06
22 27 0.06
25 1 0.00
ACGTcount: A:0.16, C:0.20, G:0.25, T:0.40
Consensus pattern (20 bp):
ATTTTCTGAATCGCGTTGCG
Found at i:125296 original size:15 final size:16
Alignment explanation
Indices: 125278--125316 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
125268 TTAATACCTG
*
125278 AATAAAAAAT-ATATT
1 AATAAAAAATAATAGT
*
125293 AATATAAAATAATAGT
1 AATAAAAAATAATAGT
125309 AATAAAAA
1 AATAAAAA
125317 TTTGAAAGAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
15 9 0.45
16 11 0.55
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.28
Consensus pattern (16 bp):
AATAAAAAATAATAGT
Found at i:125963 original size:21 final size:22
Alignment explanation
Indices: 125939--125982 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
125929 AAACATTTTC
125939 TTAAGATAATAA-AAATTTATT
1 TTAAGATAATAAGAAATTTATT
* * *
125960 TTAATATAGTAAGATATTTATT
1 TTAAGATAATAAGAAATTTATT
125982 T
1 T
125983 ATTCCAAAGT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 10 0.53
22 9 0.47
ACGTcount: A:0.45, C:0.00, G:0.07, T:0.48
Consensus pattern (22 bp):
TTAAGATAATAAGAAATTTATT
Found at i:127576 original size:3 final size:3
Alignment explanation
Indices: 127558--127640 Score: 123
Period size: 3 Copynumber: 27.0 Consensus size: 3
127548 TTGTAATATT
*
127558 TAA TAAA TAA TAAA TAA TAAA TAA TAT TAA TAA TAA TAA TAA TAA TAA
1 TAA T-AA TAA T-AA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA
127606 TAA TAA TAA TAA T-A TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
127641 ATTTAAATTT
Statistics
Matches: 74, Mismatches: 2, Indels: 8
0.88 0.02 0.10
Matches are distributed among these distances:
2 2 0.03
3 63 0.85
4 9 0.12
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:128021 original size:17 final size:17
Alignment explanation
Indices: 127999--128042 Score: 88
Period size: 17 Copynumber: 2.6 Consensus size: 17
127989 AAAAATGTCG
127999 TATTGATTCTGGGGTCA
1 TATTGATTCTGGGGTCA
128016 TATTGATTCTGGGGTCA
1 TATTGATTCTGGGGTCA
128033 TATTGATTCT
1 TATTGATTCT
128043 TTGGTGCTGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.18, C:0.11, G:0.25, T:0.45
Consensus pattern (17 bp):
TATTGATTCTGGGGTCA
Found at i:128778 original size:19 final size:19
Alignment explanation
Indices: 128754--128797 Score: 88
Period size: 19 Copynumber: 2.3 Consensus size: 19
128744 AGTATGATAC
128754 ATATATTTATTCATTATAT
1 ATATATTTATTCATTATAT
128773 ATATATTTATTCATTATAT
1 ATATATTTATTCATTATAT
128792 ATATAT
1 ATATAT
128798 ATTTTACAGG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.39, C:0.05, G:0.00, T:0.57
Consensus pattern (19 bp):
ATATATTTATTCATTATAT
Found at i:128900 original size:16 final size:16
Alignment explanation
Indices: 128876--128913 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
128866 CCAGGACCCG
*
128876 CGAACCGGTCCAGACC
1 CGAATCGGTCCAGACC
*
128892 CGAATCGGTTCAGACC
1 CGAATCGGTCCAGACC
128908 CGAATC
1 CGAATC
128914 AGCTAGGGTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.26, C:0.37, G:0.24, T:0.13
Consensus pattern (16 bp):
CGAATCGGTCCAGACC
Found at i:129885 original size:2 final size:2
Alignment explanation
Indices: 129872--129926 Score: 92
Period size: 2 Copynumber: 27.5 Consensus size: 2
129862 TATTTAATAC
* *
129872 TA TA TT TA TA TA TA TT TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
129914 TA TA TA TA TA TA T
1 TA TA TA TA TA TA T
129927 TTACTTACTA
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (2 bp):
TA
Found at i:129887 original size:10 final size:10
Alignment explanation
Indices: 129853--129929 Score: 95
Period size: 10 Copynumber: 7.7 Consensus size: 10
129843 TTTCCTTTTG
129853 ATATTTAT-T
1 ATATTTATAT
129862 -TATTTAATACT
1 ATATTT-ATA-T
129873 ATATTTATAT
1 ATATTTATAT
129883 ATATTTATAT
1 ATATTTATAT
*
129893 ATATATATAT
1 ATATTTATAT
*
129903 ATATATATAT
1 ATATTTATAT
*
129913 ATATATATAT
1 ATATTTATAT
129923 ATATTTA
1 ATATTTA
129930 CTTACTATTT
Statistics
Matches: 62, Mismatches: 2, Indels: 7
0.87 0.03 0.10
Matches are distributed among these distances:
8 5 0.08
9 2 0.03
10 46 0.74
11 4 0.06
12 5 0.08
ACGTcount: A:0.43, C:0.01, G:0.00, T:0.56
Consensus pattern (10 bp):
ATATTTATAT
Found at i:130028 original size:9 final size:9
Alignment explanation
Indices: 130004--130083 Score: 63
Period size: 9 Copynumber: 8.1 Consensus size: 9
129994 TATTATTATA
130004 TATTTTATTT
1 TATTTT-TTT
130014 TA-TTTTTT
1 TATTTTTTT
130022 TATTTTTTT
1 TATTTTTTT
130031 TATTTTTCCCTT
1 TATTTTT---TT
130043 TATTATTATTAT
1 TATT-TT-TT-T
*
130055 TATATTTTT
1 TATTTTTTT
*
130064 TATTTATTT
1 TATTTTTTT
130073 TATTTATTTT
1 TATTT-TTTT
130083 T
1 T
130084 TACTATTTTC
Statistics
Matches: 58, Mismatches: 4, Indels: 16
0.74 0.05 0.21
Matches are distributed among these distances:
8 5 0.09
9 29 0.50
10 8 0.14
11 3 0.05
12 10 0.17
13 2 0.03
14 1 0.02
ACGTcount: A:0.19, C:0.04, G:0.00, T:0.78
Consensus pattern (9 bp):
TATTTTTTT
Found at i:130046 original size:46 final size:46
Alignment explanation
Indices: 129993--130083 Score: 128
Period size: 46 Copynumber: 1.9 Consensus size: 46
129983 CCTACTACTA
* * *
129993 TTATTATTATATATTTTATTTTATTTTTTTATTTTTTTTATTTTTCCCT
1 TTATTATTAT-TATTATA-TTT-TTTATTTATTTTATTTATTTTTCCCT
130042 TTATTATTATTATTATATTTTTTATTTATTTTATTTATTTTT
1 TTATTATTATTATTATATTTTTTATTTATTTTATTTATTTTT
130084 TACTATTTTC
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
46 20 0.51
47 3 0.08
48 6 0.15
49 10 0.26
ACGTcount: A:0.21, C:0.03, G:0.00, T:0.76
Consensus pattern (46 bp):
TTATTATTATTATTATATTTTTTATTTATTTTATTTATTTTTCCCT
Found at i:130057 original size:55 final size:58
Alignment explanation
Indices: 129946--130084 Score: 169
Period size: 55 Copynumber: 2.4 Consensus size: 58
129936 ATTTTCACTC
* *
129946 TTTTATTATATATTTTTTATTCTTTTTTGTCTATGTCCCTACTACTATTATTATTATATA
1 TTTTATTTTAT-TTTTTTATT-TTTTTTATCTATGTCCCTACTACTATTATTATTATATA
* * * *
130006 TTTTATTTTATTTTTTTATTTTTTTTAT-T-TTTCCCT-TTATTATTATTATTATATT
1 TTTTATTTTATTTTTTTATTTTTTTTATCTATGTCCCTACTACTATTATTATTATATA
130061 TTTTA-TTTATTTTATTTATTTTTT
1 TTTTATTTTATTTT-TTTATTTTTT
130085 ACTATTTTCT
Statistics
Matches: 72, Mismatches: 6, Indels: 7
0.85 0.07 0.08
Matches are distributed among these distances:
54 8 0.11
55 31 0.43
56 6 0.08
57 1 0.01
58 7 0.10
59 9 0.12
60 10 0.14
ACGTcount: A:0.20, C:0.07, G:0.01, T:0.71
Consensus pattern (58 bp):
TTTTATTTTATTTTTTTATTTTTTTTATCTATGTCCCTACTACTATTATTATTATATA
Found at i:130090 original size:19 final size:20
Alignment explanation
Indices: 129999--130092 Score: 77
Period size: 21 Copynumber: 4.5 Consensus size: 20
129989 ACTATTATTA
*
129999 TTATATATTTTATTTTATTTTT
1 TTAT-TATTTTATTATA-TTTT
*
130021 TTATT-TTTT-TTATTTTTCCCT
1 TTATTATTTTATTATATTT---T
130042 TTATTATTATTATTATATTTT
1 TTATTATT-TTATTATATTTT
130063 TTATTTATTTTATT-TATTTT
1 TTA-TTATTTTATTATATTTT
*
130083 TTACTATTTT
1 TTATTATTTT
130093 CTTTTATTTG
Statistics
Matches: 61, Mismatches: 4, Indels: 17
0.74 0.05 0.21
Matches are distributed among these distances:
18 3 0.05
19 9 0.15
20 13 0.21
21 16 0.26
22 11 0.18
23 2 0.03
24 7 0.11
ACGTcount: A:0.20, C:0.04, G:0.00, T:0.76
Consensus pattern (20 bp):
TTATTATTTTATTATATTTT
Found at i:130474 original size:2 final size:2
Alignment explanation
Indices: 130467--130501 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
130457 ACCTAACGGT
130467 TA 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 TA T
130502 TATTTTTTTC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:130540 original size:14 final size:14
Alignment explanation
Indices: 130523--130549 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
130513 TTTTTATTCG
130523 TTTTTTTCGTTTTA
1 TTTTTTTCGTTTTA
130537 TTTTTTTCGTTTT
1 TTTTTTTCGTTTT
130550 TTATTTCTTT
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:0.04, C:0.07, G:0.07, T:0.81
Consensus pattern (14 bp):
TTTTTTTCGTTTTA
Found at i:130571 original size:34 final size:33
Alignment explanation
Indices: 130501--130574 Score: 98
Period size: 34 Copynumber: 2.2 Consensus size: 33
130491 TATATATATA
*
130501 TTATTTTTTTCTTTTTTATTCGTTTTTTTCGTT
1 TTATTTTTTTCTTTTTTATTCGTTTTTTTCGCT
130534 TTATTTTTTTCGTTTTTTATTTC-TTTTATTT-GCT
1 TTATTTTTTTC-TTTTTTA-TTCGTTTT-TTTCGCT
130568 TTATTTT
1 TTATTTT
130575 ATTTGATTTG
Statistics
Matches: 37, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
33 11 0.30
34 20 0.54
35 6 0.16
ACGTcount: A:0.08, C:0.08, G:0.05, T:0.78
Consensus pattern (33 bp):
TTATTTTTTTCTTTTTTATTCGTTTTTTTCGCT
Found at i:136389 original size:85 final size:83
Alignment explanation
Indices: 136194--136519 Score: 289
Period size: 85 Copynumber: 3.8 Consensus size: 83
136184 TTCTAGCCTA
* * *
136194 TTACAGTATAACTCAAGGACAAAAGGGCTATCTGTCAACCAAAACCTTCAAGTTTGATTACATTC
1 TTACAGCATAACTCAAGG-CAAAAGGGATATCTGTCAA-CAAAACCTTCAAGTTCGATTACATTC
136259 AGCT-AAGGACATATCAAAT
64 AGCTCAAGGACATATCAAAT
* * * * *
136278 TTACAGTATAACTCAAGGCGAGAAGGGATATCTTTCAATAAAGACCTTCCAGTTCGATTACATTC
1 TTACAGCATAACTCAAGGC-AAAAGGGATATCTGTCAACAAA-ACCTTCAAGTTCGATTACATTC
*
136343 AGCTCAAATG-CATATCAAAT
64 AGCTC-AAGGACATATCAAAT
* * * * *
136363 TTACTGCATAACTTAAGGCAATAAGGGTTATCTGTCAACAAATACCTTCAAGTTCGATTCCATTT
1 TTACAGCATAACTCAAGGCAA-AAGGGATATCTGTCAACAAA-ACCTTCAAGTTCGATTACATTC
* * * *
136428 AGCTCGAGGGCATGTGAAAT
64 AGCTCAAGGACATATCAAAT
* * ** * * * * * *
136448 TTACAGCATAGCTTAAATCGAGAAA-AGCTATCTGTCAACAAAAACTATCGAGTTTGATTCCATT
1 TTACAGCATAACTCAAGGC-A-AAAGGGATATCTGTCAACAAAACCT-TCAAGTTCGATTACATT
136512 CAGCTCAA
63 CAGCTCAA
136520 TCACACATCA
Statistics
Matches: 200, Mismatches: 33, Indels: 17
0.80 0.13 0.07
Matches are distributed among these distances:
83 4 0.02
84 63 0.31
85 126 0.63
86 6 0.03
87 1 0.00
ACGTcount: A:0.36, C:0.20, G:0.16, T:0.28
Consensus pattern (83 bp):
TTACAGCATAACTCAAGGCAAAAGGGATATCTGTCAACAAAACCTTCAAGTTCGATTACATTCAG
CTCAAGGACATATCAAAT
Found at i:139558 original size:17 final size:17
Alignment explanation
Indices: 139520--139562 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 17
139510 TTTCTTTTTG
*
139520 ATATTTATTTAATTAAT
1 ATATATATTTAATTAAT
* *
139537 A-ATATATTTTATTTAT
1 ATATATATTTAATTAAT
139553 ATATATATTT
1 ATATATATTT
139563 GCTTACTATT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
16 13 0.59
17 9 0.41
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (17 bp):
ATATATATTTAATTAAT
Found at i:139670 original size:46 final size:47
Alignment explanation
Indices: 139582--139687 Score: 114
Period size: 46 Copynumber: 2.2 Consensus size: 47
139572 TTTCACTCTT
*
139582 TTATTATATATTTTTTATTATTTTTTTGTCTCTGTCCCTATTAT-TA
1 TTATTATATATTTTTTATTATTTTTTTATCTCTGTCCCTATTATATA
139628 TTATTATATATTTTATT-TTATTTTATTTAT-T-T-TCCCCTTATTATATA
1 TTATTATATATTTT-TTATTATTTT-TTTATCTCTGT-CCC-TATTATATA
139675 TATATATATATAT
1 T-TAT-TATATAT
139688 ATATATATGT
Statistics
Matches: 52, Mismatches: 1, Indels: 11
0.81 0.02 0.17
Matches are distributed among these distances:
44 1 0.02
45 4 0.08
46 28 0.54
47 9 0.17
48 3 0.06
49 7 0.13
ACGTcount: A:0.25, C:0.08, G:0.02, T:0.64
Consensus pattern (47 bp):
TTATTATATATTTTTTATTATTTTTTTATCTCTGTCCCTATTATATA
Found at i:139676 original size:2 final size:2
Alignment explanation
Indices: 139669--139695 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
139659 TTCCCCTTAT
139669 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 T
139696 GTTTTGTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:140166 original size:9 final size:9
Alignment explanation
Indices: 140133--140227 Score: 56
Period size: 9 Copynumber: 10.9 Consensus size: 9
140123 GTTTTTGTTT
140133 TTTA-TTTA
1 TTTATTTTA
*
140141 -TTATTTTT
1 TTTATTTTA
*
140149 TTTCCTTTTA
1 TTT-ATTTTA
140159 TTTATTTTA
1 TTTATTTTA
140168 TTTGA-TTTA
1 TTT-ATTTTA
*** *
140177 TTTCCCTAA
1 TTTATTTTA
* *
140186 TTTAGTTAA
1 TTTATTTTA
*
140195 TTTATTTGA
1 TTTATTTTA
140204 -TT-TTTTA
1 TTTATTTTA
140211 TTTATTTTA
1 TTTATTTTA
140220 TTTATTTT
1 TTTATTTT
140228 CTTTTTAATT
Statistics
Matches: 67, Mismatches: 13, Indels: 13
0.72 0.14 0.14
Matches are distributed among these distances:
7 7 0.10
8 7 0.10
9 45 0.67
10 8 0.12
ACGTcount: A:0.20, C:0.05, G:0.03, T:0.72
Consensus pattern (9 bp):
TTTATTTTA
Found at i:140238 original size:21 final size:22
Alignment explanation
Indices: 140186--140239 Score: 62
Period size: 21 Copynumber: 2.6 Consensus size: 22
140176 ATTTCCCTAA
*
140186 TTTAGTTAA-TTTATTTGATTT
1 TTTATTTAATTTTATTTGATTT
140207 TTTATTT-ATTTTATTT-ATTT
1 TTTATTTAATTTTATTTGATTT
140227 TCTT-TTTAATTTT
1 T-TTATTTAATTTT
140240 TGGGATATTT
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
20 9 0.31
21 20 0.69
ACGTcount: A:0.20, C:0.02, G:0.04, T:0.74
Consensus pattern (22 bp):
TTTATTTAATTTTATTTGATTT
Found at i:159157 original size:23 final size:22
Alignment explanation
Indices: 159118--159160 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
159108 TTTGCATAGA
*
159118 ATTTTTATTTAGGATTTTTAAT
1 ATTTTTAATTAGGATTTTTAAT
*
159140 ATTTATTAATTAGTATTTTTA
1 ATTT-TTAATTAGGATTTTTA
159161 GTTTGTTAGA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 4 0.22
23 14 0.78
ACGTcount: A:0.30, C:0.00, G:0.07, T:0.63
Consensus pattern (22 bp):
ATTTTTAATTAGGATTTTTAAT
Found at i:162675 original size:2 final size:2
Alignment explanation
Indices: 162670--162718 Score: 57
Period size: 2 Copynumber: 25.5 Consensus size: 2
162660 TATATTAATT
* * *
162670 TA TA TA TA TA TA TA TA TA TA TA TA TA TA AA T- TA TA TT TA AA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
162711 TA -A TA TA T
1 TA TA TA TA T
162719 TTATTTACTT
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
1 2 0.05
2 37 0.95
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:164781 original size:6 final size:6
Alignment explanation
Indices: 164770--164811 Score: 57
Period size: 6 Copynumber: 6.5 Consensus size: 6
164760 TACTATTTAC
164770 TTTATT TTTATTT TTTATT TATTCATT TTTATT TTTATT TTT
1 TTTATT TTTA-TT TTTATT T-TT-ATT TTTATT TTTATT TTT
164812 TTCTTTATAT
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
6 19 0.58
7 10 0.30
8 4 0.12
ACGTcount: A:0.17, C:0.02, G:0.00, T:0.81
Consensus pattern (6 bp):
TTTATT
Found at i:164799 original size:21 final size:21
Alignment explanation
Indices: 164763--164809 Score: 69
Period size: 20 Copynumber: 2.2 Consensus size: 21
164753 TACTATTTAC
*
164763 TATTTACTTTATTTTTATTTTT
1 TATTTACTTCATTTTTA-TTTT
164785 TATTTA-TTCATTTTTATTTT
1 TATTTACTTCATTTTTATTTT
164805 TATTT
1 TATTT
164810 TTTTCTTTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 9 0.38
21 9 0.38
22 6 0.25
ACGTcount: A:0.19, C:0.04, G:0.00, T:0.77
Consensus pattern (21 bp):
TATTTACTTCATTTTTATTTT
Found at i:164819 original size:12 final size:12
Alignment explanation
Indices: 164770--164811 Score: 57
Period size: 14 Copynumber: 3.2 Consensus size: 12
164760 TACTATTTAC
164770 TTTATTTTTATTT
1 TTTATTTTTA-TT
164783 TTTATTTATTCATT
1 TTTATTT-TT-ATT
164797 TTTATTTTTATT
1 TTTATTTTTATT
164809 TTT
1 TTT
164812 TTCTTTATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
12 6 0.22
13 9 0.33
14 11 0.41
15 1 0.04
ACGTcount: A:0.17, C:0.02, G:0.00, T:0.81
Consensus pattern (12 bp):
TTTATTTTTATT
Found at i:165660 original size:25 final size:25
Alignment explanation
Indices: 165615--165664 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
165605 AAAGCATTCG
*
165615 AACAAAAAAGTAAAATTAAAAATAAC
1 AACAAAAAAG-AAAATAAAAAATAAC
165641 AACAAAAAA-AATAATAAAAAATAA
1 AACAAAAAAGAA-AATAAAAAATAA
165665 AAAATAAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
24 2 0.09
25 11 0.50
26 9 0.41
ACGTcount: A:0.78, C:0.06, G:0.02, T:0.14
Consensus pattern (25 bp):
AACAAAAAAGAAAATAAAAAATAAC
Found at i:168033 original size:19 final size:20
Alignment explanation
Indices: 167989--168065 Score: 79
Period size: 20 Copynumber: 3.8 Consensus size: 20
167979 AGAATGCAAA
167989 AATGGTATCGATACCATA-T
1 AATGGTATCGATACCATAGT
168008 GAA-GGTATCGATACCATAGT
1 -AATGGTATCGATACCATAGT
*
168028 -ATGGTAGTATCGATACCATGGT
1 AAT-G--GTATCGATACCATAGT
*
168050 AAGGGTATCGATACCA
1 AATGGTATCGATACCA
168066 GGTAACATAG
Statistics
Matches: 49, Mismatches: 2, Indels: 12
0.78 0.03 0.19
Matches are distributed among these distances:
18 1 0.02
19 15 0.31
20 16 0.33
22 16 0.33
23 1 0.02
ACGTcount: A:0.34, C:0.16, G:0.23, T:0.27
Consensus pattern (20 bp):
AATGGTATCGATACCATAGT
Found at i:168037 original size:22 final size:20
Alignment explanation
Indices: 167992--168065 Score: 89
Period size: 22 Copynumber: 3.6 Consensus size: 20
167982 ATGCAAAAAT
167992 GGTATCGATACCATA-TGAA-
1 GGTATCGATACCATAGT-AAG
*
168011 GGTATCGATACCATAGTATG
1 GGTATCGATACCATAGTAAG
*
168031 GTAGTATCGATACCATGGTAAG
1 G--GTATCGATACCATAGTAAG
168053 GGTATCGATACCA
1 GGTATCGATACCA
168066 GGTAACATAG
Statistics
Matches: 48, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
19 16 0.33
20 14 0.29
22 18 0.38
ACGTcount: A:0.32, C:0.16, G:0.24, T:0.27
Consensus pattern (20 bp):
GGTATCGATACCATAGTAAG
Found at i:168050 original size:17 final size:18
Alignment explanation
Indices: 167992--168069 Score: 59
Period size: 19 Copynumber: 4.0 Consensus size: 18
167982 ATGCAAAAAT
* *
167992 GGTATCGATACCATATGAA
1 GGTATCGATACCAT-GGTA
*
168011 GGTATCGATACCATAGTA
1 GGTATCGATACCATGGTA
168029 TGGTAGTATCGATACCATGGTAA
1 --G--GTATCGATACCATGGT-A
168052 GGGTATCGATACCA-GGTA
1 -GGTATCGATACCATGGTA
168070 ACATAGAATA
Statistics
Matches: 51, Mismatches: 3, Indels: 11
0.78 0.05 0.17
Matches are distributed among these distances:
18 3 0.06
19 17 0.33
20 13 0.25
22 17 0.33
23 1 0.02
ACGTcount: A:0.32, C:0.15, G:0.26, T:0.27
Consensus pattern (18 bp):
GGTATCGATACCATGGTA
Found at i:168538 original size:54 final size:54
Alignment explanation
Indices: 168480--168831 Score: 503
Period size: 54 Copynumber: 6.6 Consensus size: 54
168470 TTACCAAATA
*
168480 GGCACTAAGTGTGCATTTCACGGAATTCATCATATGTGGATGAATAACCGTTTC
1 GGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTC
** *
168534 GGCACTAAGTGTGCATTTCATAGAATTCATCCTAT-TGG-TTAATAACCGTTAT-
1 GGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTT-TC
* * * *
168586 GGCACTAAGTGTGCATTTCATGGAATCCATCCTATGTGGACGAATAACTGTTTC
1 GGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTC
* * * *
168640 GGTACTAAGTTTACATTTCACGGAATTCATCCTATGTAGATGAATAACCGTTTC
1 GGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTC
* *
168694 GGCACTAAGTGTACATTTCACGGAATTCATCCTATGTGGATGAATAATCGTTTC
1 GGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTC
* * *
168748 GGCACTAAGTGTGCATTTCACGGAATTCATCCTATATAGATGAATAATCGTTTC
1 GGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTC
* *
168802 GGCACTAAGTGTACATTTCACGGGATTCAT
1 GGCACTAAGTGTGCATTTCACGGAATTCAT
168832 AAGAAGTTTA
Statistics
Matches: 268, Mismatches: 26, Indels: 8
0.89 0.09 0.03
Matches are distributed among these distances:
52 44 0.16
53 8 0.03
54 216 0.81
ACGTcount: A:0.28, C:0.19, G:0.20, T:0.33
Consensus pattern (54 bp):
GGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTC
Found at i:174900 original size:20 final size:20
Alignment explanation
Indices: 174875--174912 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
174865 TTTTTCAATC
174875 AGTATCGATACCGAAGGGGG
1 AGTATCGATACCGAAGGGGG
*
174895 AGTATCGATATCGAAGGG
1 AGTATCGATACCGAAGGG
174913 AAGGTATCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.32, C:0.13, G:0.37, T:0.18
Consensus pattern (20 bp):
AGTATCGATACCGAAGGGGG
Found at i:174919 original size:20 final size:20
Alignment explanation
Indices: 174875--174926 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
174865 TTTTTCAATC
*
174875 AGTATCGATACCGAAGGGGG
1 AGTATCGATACCGAAGGGAG
*
174895 AGTATCGATATCGAAGGGA-
1 AGTATCGATACCGAAGGGAG
*
174914 AGGTATCAATACC
1 A-GTATCGATACC
174927 ATTTTGAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
19 1 0.04
20 26 0.96
ACGTcount: A:0.35, C:0.15, G:0.31, T:0.19
Consensus pattern (20 bp):
AGTATCGATACCGAAGGGAG
Found at i:175507 original size:54 final size:54
Alignment explanation
Indices: 175439--175953 Score: 726
Period size: 54 Copynumber: 9.6 Consensus size: 54
175429 TTACCAAATA
* *
175439 GGCATTAAGTGTGCATTTCACGAAATTCATCCTATGTGGATGAATAACCGTTTC
1 GGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTC
* * ** *
175493 AGCACTAGGTGTGCATTTCACAAAATTCATCTTATGTGGATGAATAACCGTTTC
1 GGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTC
* * * *
175547 GACACTAAGTGTGAATTTCACGGAATTCATCCTATGTAGATGAATAATCGTTTC
1 GGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTC
** * *
175601 GATACTATGTGTGCATTTCATGGAATTCATCCTATGTGGATGAATAACCGTTTC
1 GGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTC
* * *
175655 GGCACTAAGTGTGCATTTCACAGAATTCATCCTAT-TGGATTAATAACCGTTTT
1 GGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTC
* *
175708 GGCACTAAGTGTGCATTTCATGGAATTCATCCTATGTGGATGAATAACTGTTTC
1 GGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTC
* * *
175762 GGTACTAAGTGTACATTTCACGGAATTCATCCTATGTAGATGAATAACCGTTTC
1 GGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTC
* * *
175816 GGCACTAAGTGTACATTTCACAGAATTCATCCTATGTGGATGAATAATCGTTTC
1 GGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTC
* * **
175870 GGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTAGATTAATAATTGTTTC
1 GGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTC
* * *
175924 GGCACTAAGGGTACATTTCACGGGATTCAT
1 GGCACTAAGTGTGCATTTCACGGAATTCAT
175954 AAGAAGTTTA
Statistics
Matches: 411, Mismatches: 49, Indels: 2
0.89 0.11 0.00
Matches are distributed among these distances:
53 49 0.12
54 362 0.88
ACGTcount: A:0.28, C:0.18, G:0.20, T:0.34
Consensus pattern (54 bp):
GGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTC
Found at i:175925 original size:269 final size:269
Alignment explanation
Indices: 175439--175953 Score: 771
Period size: 269 Copynumber: 1.9 Consensus size: 269
175429 TTACCAAATA
* *
175439 GGCATTAAGTGTGCATTTCACGAAATTCATCCTATGTGGATGAATAACCGTTTCAGCACTAGGTG
1 GGCACTAAGTGTGCATTTCACGAAATTCATCCTATGTGGATGAATAACCGTTTCAGCACTAAGTG
* * * *
175504 TGCATTTCACAAAATTCATCTTATGTGGATGAATAACCGTTTCGACACTAAGTGTGAATTTCACG
66 TACATTTCACAAAATTCATCCTATGTAGATGAATAACCGTTTCGACACTAAGTGTGAATTTCACA
* * *
175569 GAATTCATCCTATGTAGATGAATAATCGTTTCGATACTATGTGTGCATTTCATGGAATTCATCCT
131 GAATTCATCCTATGTAGATGAATAATCGTTTCGACACTAAGTGTGCATTTCACGGAATTCATCCT
* * *
175634 ATGTGGATGAATAACCGTTTCGGCACTAAGTGTGCATTTCACAGAATTCATCCTATTGGATTAAT
196 ATGTAGATGAATAACCGTTTCGGCACTAAGGGTACATTTCACAGAATTCATCCTATTGGATTAAT
175699 AACCGTTTT
261 AACCGTTTT
* * * * *
175708 GGCACTAAGTGTGCATTTCATGGAATTCATCCTATGTGGATGAATAACTGTTTCGGTACTAAGTG
1 GGCACTAAGTGTGCATTTCACGAAATTCATCCTATGTGGATGAATAACCGTTTCAGCACTAAGTG
** *
175773 TACATTTCACGGAATTCATCCTATGTAGATGAATAACCGTTTCGGCACTAAGTGT-ACATTTCAC
66 TACATTTCACAAAATTCATCCTATGTAGATGAATAACCGTTTCGACACTAAGTGTGA-ATTTCAC
* *
175837 AGAATTCATCCTATGTGGATGAATAATCGTTTCGGCACTAAGTGTGCATTTCACGGAATTCATCC
130 AGAATTCATCCTATGTAGATGAATAATCGTTTCGACACTAAGTGTGCATTTCACGGAATTCATCC
* ** * *
175902 TATGTAGATTAATAATTGTTTCGGCACTAAGGGTACATTTCACGGGATTCAT
195 TATGTAGATGAATAACCGTTTCGGCACTAAGGGTACATTTCACAGAATTCAT
175954 AAGAAGTTTA
Statistics
Matches: 218, Mismatches: 27, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
268 1 0.00
269 217 1.00
ACGTcount: A:0.28, C:0.18, G:0.20, T:0.34
Consensus pattern (269 bp):
GGCACTAAGTGTGCATTTCACGAAATTCATCCTATGTGGATGAATAACCGTTTCAGCACTAAGTG
TACATTTCACAAAATTCATCCTATGTAGATGAATAACCGTTTCGACACTAAGTGTGAATTTCACA
GAATTCATCCTATGTAGATGAATAATCGTTTCGACACTAAGTGTGCATTTCACGGAATTCATCCT
ATGTAGATGAATAACCGTTTCGGCACTAAGGGTACATTTCACAGAATTCATCCTATTGGATTAAT
AACCGTTTT
Found at i:181253 original size:17 final size:18
Alignment explanation
Indices: 181222--181257 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
181212 TTTAAATTTA
*
181222 AGGATGAATTTTTTAAGG
1 AGGATGAATTGTTTAAGG
181240 AGGA-GAATTGTTTAAGG
1 AGGATGAATTGTTTAAGG
181257 A
1 A
181258 CCTTATTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 13 0.76
18 4 0.24
ACGTcount: A:0.36, C:0.00, G:0.31, T:0.33
Consensus pattern (18 bp):
AGGATGAATTGTTTAAGG
Found at i:182037 original size:20 final size:20
Alignment explanation
Indices: 182012--182049 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
182002 TGTTTCAATC
182012 AGTATCGATACCGAAGGGGG
1 AGTATCGATACCGAAGGGGG
182032 AGTATCGATACCGAAGGG
1 AGTATCGATACCGAAGGG
182050 AAGGTATCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.32, C:0.16, G:0.37, T:0.16
Consensus pattern (20 bp):
AGTATCGATACCGAAGGGGG
Found at i:182056 original size:20 final size:20
Alignment explanation
Indices: 182012--182063 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
182002 TGTTTCAATC
*
182012 AGTATCGATACCGAAGGGGG
1 AGTATCGATACCGAAGGGAG
182032 AGTATCGATACCGAAGGGA-
1 AGTATCGATACCGAAGGGAG
*
182051 AGGTATCAATACC
1 A-GTATCGATACC
182064 ATTTTGAAAC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 1 0.03
20 28 0.97
ACGTcount: A:0.35, C:0.17, G:0.31, T:0.17
Consensus pattern (20 bp):
AGTATCGATACCGAAGGGAG
Found at i:182532 original size:2 final size:2
Alignment explanation
Indices: 182525--182568 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
182515 TGCACTAATC
182525 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
182567 AT
1 AT
182569 GCTTGTTTAA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:182668 original size:54 final size:54
Alignment explanation
Indices: 182608--182841 Score: 389
Period size: 54 Copynumber: 4.3 Consensus size: 54
182598 AAATAGGCAT
*
182608 TAAGTGTGCATTTCACAAAATTCATCCTATGTGGATGAATAACCGTTTC-AGCAC
1 TAAGTGTGCATTTCACGAAATTCATCCTATGTGGATGAATAACCGTTTCGA-CAC
182662 TAAGTGTGCATTTCACGAAATTCATCCTATGTGGATGAATAACCGTTTCGACAC
1 TAAGTGTGCATTTCACGAAATTCATCCTATGTGGATGAATAACCGTTTCGACAC
* * * *
182716 TAAGTGTGAATTTCACGGAATTCATCCTATGTAGATGAATAACCGTTTCGGCAC
1 TAAGTGTGCATTTCACGAAATTCATCCTATGTGGATGAATAACCGTTTCGACAC
* *
182770 TAAGTGTGCATTTCATGGAATTCATCCTATGTGGATGAATAACCGTTTCGACAC
1 TAAGTGTGCATTTCACGAAATTCATCCTATGTGGATGAATAACCGTTTCGACAC
182824 TAAGTGTGCATTTCACGA
1 TAAGTGTGCATTTCACGA
182842 GATTTATAGT
Statistics
Matches: 168, Mismatches: 11, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
54 167 0.99
55 1 0.01
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.32
Consensus pattern (54 bp):
TAAGTGTGCATTTCACGAAATTCATCCTATGTGGATGAATAACCGTTTCGACAC
Found at i:183184 original size:21 final size:23
Alignment explanation
Indices: 183140--183184 Score: 58
Period size: 21 Copynumber: 2.0 Consensus size: 23
183130 AAGTTAATGT
* *
183140 ATGTTTTATTATAAGCGAATTAA
1 ATGTTTTATTATAAACGAAATAA
183163 ATGTTTTA-TA-AAACGAAATAA
1 ATGTTTTATTATAAACGAAATAA
183184 A
1 A
183185 ATTTTACGAG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 10 0.50
22 2 0.10
23 8 0.40
ACGTcount: A:0.47, C:0.04, G:0.11, T:0.38
Consensus pattern (23 bp):
ATGTTTTATTATAAACGAAATAA
Found at i:187067 original size:20 final size:20
Alignment explanation
Indices: 187039--187090 Score: 77
Period size: 20 Copynumber: 2.5 Consensus size: 20
187029 ACTCAGTTTC
*
187039 TAAATTCGCAACGTGAATATG
1 TAAA-TCGCAACGCGAATATG
*
187060 TAAATCGCAACGCGAATCTG
1 TAAATCGCAACGCGAATATG
187080 TAAATCGCAAC
1 TAAATCGCAAC
187091 ACATAAGTCA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
20 25 0.86
21 4 0.14
ACGTcount: A:0.38, C:0.21, G:0.17, T:0.23
Consensus pattern (20 bp):
TAAATCGCAACGCGAATATG
Found at i:187121 original size:20 final size:20
Alignment explanation
Indices: 187098--187191 Score: 109
Period size: 20 Copynumber: 4.7 Consensus size: 20
187088 AACACATAAG
* *
187098 TCAAATTCACAACGCGATTT
1 TCAAATTCGCAACTCGATTT
* *
187118 TCAAATTCGCAACACTGAATT
1 TCAAATTCGCAACTC-GATTT
187139 TCAAATTCGCAACTCGA-TT
1 TCAAATTCGCAACTCGATTT
*
187158 TCTGAATTCGCAACTCGATTT
1 TC-AAATTCGCAACTCGATTT
*
187179 TCGAATTCGCAAC
1 TCAAATTCGCAAC
187192 ACGAATTTTA
Statistics
Matches: 66, Mismatches: 5, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
19 4 0.06
20 40 0.61
21 22 0.33
ACGTcount: A:0.32, C:0.26, G:0.12, T:0.31
Consensus pattern (20 bp):
TCAAATTCGCAACTCGATTT
Found at i:187157 original size:41 final size:41
Alignment explanation
Indices: 187098--187200 Score: 111
Period size: 41 Copynumber: 2.5 Consensus size: 41
187088 AACACATAAG
* *
187098 TCAAATTCACAACGCGATTTTC-AAATTCGCAACACTGAATT
1 TCAAATTCGCAACACGATTTTCTAAATTCGCAACAC-GAATT
* * * *
187139 TCAAATTCGCAACTCGA-TTTCTGAATTCGCAACTCGATTT
1 TCAAATTCGCAACACGATTTTCTAAATTCGCAACACGAATT
*
187179 TCGAATTCGCAACACGAATTTT
1 TCAAATTCGCAACACG-ATTTT
187201 AATTTCGTAA
Statistics
Matches: 52, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
40 22 0.42
41 27 0.52
42 3 0.06
ACGTcount: A:0.32, C:0.24, G:0.12, T:0.32
Consensus pattern (41 bp):
TCAAATTCGCAACACGATTTTCTAAATTCGCAACACGAATT
Found at i:187207 original size:20 final size:19
Alignment explanation
Indices: 187101--187204 Score: 84
Period size: 20 Copynumber: 5.2 Consensus size: 19
187091 ACATAAGTCA
* * *
187101 AATTCACAACGCGATTTTCA
1 AATTCGCAACACGATTTT-G
**
187121 AATTCGCAACACTGAATTTCA
1 AATTCGCAACAC-G-ATTTTG
*
187142 AATTCGCAACTCGATTTCTG
1 AATTCGCAACACGATTT-TG
*
187162 AATTCGCAACTCGATTTTCG
1 AATTCGCAACACGATTTT-G
187182 AATTCGCAACACGAATTTT-
1 AATTCGCAACACG-ATTTTG
187201 AATT
1 AATT
187205 TCGTAATAGG
Statistics
Matches: 72, Mismatches: 7, Indels: 11
0.80 0.08 0.12
Matches are distributed among these distances:
19 9 0.12
20 41 0.57
21 18 0.25
22 4 0.06
ACGTcount: A:0.33, C:0.23, G:0.12, T:0.33
Consensus pattern (19 bp):
AATTCGCAACACGATTTTG
Found at i:187403 original size:16 final size:15
Alignment explanation
Indices: 187368--187406 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
187358 TCCCCATCTC
*
187368 TAATTTTTTTTTACA
1 TAATTTTTTTCTACA
*
187383 TAATTTTATTTCTATA
1 TAATTTT-TTTCTACA
187399 TAATTTTT
1 TAATTTTT
187407 CAATGATTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
15 8 0.38
16 13 0.62
ACGTcount: A:0.28, C:0.05, G:0.00, T:0.67
Consensus pattern (15 bp):
TAATTTTTTTCTACA
Found at i:187973 original size:12 final size:12
Alignment explanation
Indices: 187952--187985 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
187942 ACCACATTTC
*
187952 CAATACCAAACA
1 CAATATCAAACA
187964 CAATATCAAACA
1 CAATATCAAACA
*
187976 CAATCTCAAA
1 CAATATCAAA
187986 ACCCACATCC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.56, C:0.29, G:0.00, T:0.15
Consensus pattern (12 bp):
CAATATCAAACA
Found at i:188162 original size:24 final size:24
Alignment explanation
Indices: 188111--188164 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
188101 GTATTCGAAA
* *
188111 TTTGATCTTAGTCAATACCCGTAC
1 TTTGATCTTAGTCAATACCAGAAC
* * *
188135 TTTGATCTTGGTCAATACTAGAAT
1 TTTGATCTTAGTCAATACCAGAAC
188159 TTTGAT
1 TTTGAT
188165 GATGTTTCAG
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.26, C:0.17, G:0.15, T:0.43
Consensus pattern (24 bp):
TTTGATCTTAGTCAATACCAGAAC
Found at i:190458 original size:18 final size:18
Alignment explanation
Indices: 190435--190470 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
190425 AAACAAAAGG
190435 AAATCAAAATCGCAATCA
1 AAATCAAAATCGCAATCA
*
190453 AAATCAAAATCTCAATCA
1 AAATCAAAATCGCAATCA
190471 CAACCGGCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.56, C:0.22, G:0.03, T:0.19
Consensus pattern (18 bp):
AAATCAAAATCGCAATCA
Found at i:191324 original size:24 final size:24
Alignment explanation
Indices: 191297--191348 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
191287 TTTCATATGC
*
191297 AATTGGAGTTTGAATTTAAATTTA
1 AATTGGAGTTTGAATTTAAATATA
** *
191321 AATTTTAGTTTGAATTTCAATATA
1 AATTGGAGTTTGAATTTAAATATA
191345 AATT
1 AATT
191349 TCGGCTCCAC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.38, C:0.02, G:0.12, T:0.48
Consensus pattern (24 bp):
AATTGGAGTTTGAATTTAAATATA
Found at i:191349 original size:24 final size:24
Alignment explanation
Indices: 191303--191349 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
191293 ATGCAATTGG
*
191303 AGTTTGAATTTAAATTTAAATTTT
1 AGTTTGAATTTAAATATAAATTTT
*
191327 AGTTTGAATTTCAATATAAATTT
1 AGTTTGAATTTAAATATAAATTT
191350 CGGCTCCACT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.38, C:0.02, G:0.09, T:0.51
Consensus pattern (24 bp):
AGTTTGAATTTAAATATAAATTTT
Found at i:192519 original size:6 final size:6
Alignment explanation
Indices: 192508--192536 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
192498 AAGCAAAAGG
192508 AAATCA AAATCA AAATCA AAATCA AAATC
1 AAATCA AAATCA AAATCA AAATCA AAATC
192537 CCAATCACAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.66, C:0.17, G:0.00, T:0.17
Consensus pattern (6 bp):
AAATCA
Found at i:192829 original size:20 final size:20
Alignment explanation
Indices: 192804--192869 Score: 87
Period size: 20 Copynumber: 3.3 Consensus size: 20
192794 AAAATCGCAA
192804 TGCGAATTTGACTTTCGCGT
1 TGCGAATTTGACTTTCGCGT
* * **
192824 TACGAATTTGACTATCGCAA
1 TGCGAATTTGACTTTCGCGT
*
192844 CGCGAATTTGACTTTCGCGT
1 TGCGAATTTGACTTTCGCGT
192864 TGCGAA
1 TGCGAA
192870 AGTGTACATT
Statistics
Matches: 36, Mismatches: 10, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.23, C:0.21, G:0.23, T:0.33
Consensus pattern (20 bp):
TGCGAATTTGACTTTCGCGT
Found at i:193001 original size:64 final size:64
Alignment explanation
Indices: 192929--193077 Score: 235
Period size: 64 Copynumber: 2.3 Consensus size: 64
192919 AATTTAAAAC
192929 AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAATAAGAATTATTTACACATCAATTA
1 AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAATAAGAATTATTTACACATCAATTA
* *** * *
192993 AACAAATCAACTTTTACAAATCAATTAAACAATCAAAAAATAATTCTTATTTCCTCATCAATTA
1 AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAATAAGAATTATTTACACATCAATTA
*
193057 AACAAATCAACTTTTAAAAAT
1 AACAAATCAACTTTTACAAAT
193078 ACATAAATTT
Statistics
Matches: 78, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
64 78 1.00
ACGTcount: A:0.52, C:0.17, G:0.01, T:0.30
Consensus pattern (64 bp):
AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAATAAGAATTATTTACACATCAATTA
Found at i:193016 original size:27 final size:26
Alignment explanation
Indices: 192978--193028 Score: 84
Period size: 27 Copynumber: 1.9 Consensus size: 26
192968 ATAAGAATTA
*
192978 TTTACACATCAATTAAACAAATCAACT
1 TTTACAAATCAATTAAAC-AATCAACT
193005 TTTACAAATCAATTAAACAATCAA
1 TTTACAAATCAATTAAACAATCAA
193029 AAAATAATTC
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
26 6 0.26
27 17 0.74
ACGTcount: A:0.51, C:0.20, G:0.00, T:0.29
Consensus pattern (26 bp):
TTTACAAATCAATTAAACAATCAACT
Found at i:194431 original size:21 final size:22
Alignment explanation
Indices: 194402--194468 Score: 59
Period size: 21 Copynumber: 3.2 Consensus size: 22
194392 GTGAATCGGG
*
194402 CTCTCGAACGGTGGGAGA-GAC
1 CTCTTGAACGGTGGGAGAGGAC
* ** *
194423 CTCTTGAACGATGACA-AGGGC
1 CTCTTGAACGGTGGGAGAGGAC
*
194444 CTCTTGAACGGTGGGAG-GGGC
1 CTCTTGAACGGTGGGAGAGGAC
194465 CTCT
1 CTCT
194469 GGAAGGATGA
Statistics
Matches: 36, Mismatches: 8, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
20 1 0.03
21 35 0.97
ACGTcount: A:0.21, C:0.24, G:0.36, T:0.19
Consensus pattern (22 bp):
CTCTTGAACGGTGGGAGAGGAC
Found at i:194521 original size:43 final size:42
Alignment explanation
Indices: 194415--194521 Score: 106
Period size: 43 Copynumber: 2.5 Consensus size: 42
194405 TCGAACGGTG
* * * * * *
194415 GGAGAGACCTCTTGAACGATGACAAGGGCCTCTTGAACGGTG
1 GGAGAGGCATCTTGAACGATGAAAAAGGCCTCTTGAACGATA
* * * *
194457 GGAGGGGCCTCTGGAAGGATGATAAAAGGCCTCTTGAACGATA
1 GGAGAGGCATCTTGAACGATGA-AAAAGGCCTCTTGAACGATA
*
194500 GGAGAGGCATTTTGAACGATGA
1 GGAGAGGCATCTTGAACGATGA
194522 CAGGTGAATC
Statistics
Matches: 51, Mismatches: 13, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
42 18 0.35
43 33 0.65
ACGTcount: A:0.29, C:0.17, G:0.35, T:0.20
Consensus pattern (42 bp):
GGAGAGGCATCTTGAACGATGAAAAAGGCCTCTTGAACGATA
Found at i:194813 original size:21 final size:21
Alignment explanation
Indices: 194789--194847 Score: 109
Period size: 21 Copynumber: 2.8 Consensus size: 21
194779 GTAGAGCGGC
*
194789 TACCTCATCACGTAAAGTAGA
1 TACCTCACCACGTAAAGTAGA
194810 TACCTCACCACGTAAAGTAGA
1 TACCTCACCACGTAAAGTAGA
194831 TACCTCACCACGTAAAG
1 TACCTCACCACGTAAAG
194848 CACCATTGTC
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 37 1.00
ACGTcount: A:0.37, C:0.29, G:0.14, T:0.20
Consensus pattern (21 bp):
TACCTCACCACGTAAAGTAGA
Found at i:194886 original size:21 final size:21
Alignment explanation
Indices: 194862--194905 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
194852 ATTGTCATTG
194862 CGTAAA-ACCTCTACCTCACCA
1 CGTAAAGACC-CTACCTCACCA
* *
194883 CGTAAAGACCGTACCTCATCA
1 CGTAAAGACCCTACCTCACCA
194904 CG
1 CG
194906 CCATGCACTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 17 0.85
22 3 0.15
ACGTcount: A:0.32, C:0.39, G:0.11, T:0.18
Consensus pattern (21 bp):
CGTAAAGACCCTACCTCACCA
Found at i:197121 original size:22 final size:21
Alignment explanation
Indices: 197069--197128 Score: 95
Period size: 20 Copynumber: 2.9 Consensus size: 21
197059 GATTTCTGGG
197069 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAATCGGTACCCATT
197090 CAA-GGGAATCGGTACCCATT
1 CAAGGGGAATCGGTACCCATT
*
197110 CAATGGGGAATCGATACCC
1 CAA-GGGGAATCGGTACCC
197129 CTCAAGCGAA
Statistics
Matches: 36, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
20 20 0.56
21 3 0.08
22 13 0.36
ACGTcount: A:0.30, C:0.25, G:0.27, T:0.18
Consensus pattern (21 bp):
CAAGGGGAATCGGTACCCATT
Found at i:198157 original size:31 final size:31
Alignment explanation
Indices: 198115--198285 Score: 297
Period size: 31 Copynumber: 5.5 Consensus size: 31
198105 AGGGTCGAGG
*
198115 GTTTACATATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
198146 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
198177 GTTTACCTATGTTCTTCGAGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
198208 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
198239 GTTTACCTATGTTCTTCGGTACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* *
198270 GATTACCTAGGTTCTT
1 GTTTACCTATGTTCTT
198286 TGGAATCTAT
Statistics
Matches: 134, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 134 1.00
ACGTcount: A:0.20, C:0.19, G:0.21, T:0.40
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:198807 original size:21 final size:21
Alignment explanation
Indices: 198782--198824 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
198772 AAAGAATATA
198782 TTGTATAA-GCTCTGAATAATT
1 TTGTA-AATGCTCTGAATAATT
* *
198803 TTGTAAATGTTTTGAATAATT
1 TTGTAAATGCTCTGAATAATT
198824 T
1 T
198825 AAATGTTATA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 2 0.11
21 17 0.89
ACGTcount: A:0.33, C:0.05, G:0.14, T:0.49
Consensus pattern (21 bp):
TTGTAAATGCTCTGAATAATT
Found at i:203092 original size:31 final size:31
Alignment explanation
Indices: 203054--203147 Score: 129
Period size: 31 Copynumber: 3.0 Consensus size: 31
203044 AGGGTCGAGG
*
203054 GTTTACCTGTGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
203085 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* *
203116 GATTACCTA-GATTCTTCGGAATC-TATGGACT
1 GTTTACCTATG-TTCTTCGGGA-CATATGGACT
203147 G
1 G
203148 GTCCTTCGGG
Statistics
Matches: 58, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
30 1 0.02
31 56 0.97
32 1 0.02
ACGTcount: A:0.20, C:0.19, G:0.23, T:0.37
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:203652 original size:21 final size:21
Alignment explanation
Indices: 203627--203669 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
203617 AAAGAATATA
203627 TTGTATAA-GCTCTGAATAATT
1 TTGTA-AATGCTCTGAATAATT
* *
203648 TTGTAAATGTTTTGAATAATT
1 TTGTAAATGCTCTGAATAATT
203669 T
1 T
203670 AAATGTTATA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 2 0.11
21 17 0.89
ACGTcount: A:0.33, C:0.05, G:0.14, T:0.49
Consensus pattern (21 bp):
TTGTAAATGCTCTGAATAATT
Found at i:206989 original size:23 final size:22
Alignment explanation
Indices: 206945--206989 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
206935 AATCTCATAG
*
206945 GGGAATCGATTCCCCCACAGGA
1 GGGAATCGATTCCCCCAAAGGA
206967 GGGAATCGATTCCCCCTAAAGGA
1 GGGAATCGATTCCCCC-AAAGGA
206990 AAAATGTGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
22 16 0.76
23 5 0.24
ACGTcount: A:0.29, C:0.29, G:0.27, T:0.16
Consensus pattern (22 bp):
GGGAATCGATTCCCCCAAAGGA
Found at i:207935 original size:31 final size:31
Alignment explanation
Indices: 207897--208052 Score: 251
Period size: 31 Copynumber: 5.0 Consensus size: 31
207887 GGGGTCGAGG
*
207897 GTTTACCTATGTTTTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
207928 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
207959 GTTTACCTATGTTCTTCGGGACATATGAACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
207990 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* * *
208021 GATTACCTAGGTTCTTCGGAATC-TATGGACT
1 GTTTACCTATGTTCTTCGGGA-CATATGGACT
208052 G
1 G
208053 GTCCTTCGGG
Statistics
Matches: 118, Mismatches: 6, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
31 117 0.99
32 1 0.01
ACGTcount: A:0.21, C:0.19, G:0.22, T:0.38
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Done.