Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003341.1 Hibiscus syriacus cultivar Beakdansim tig00007031_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: 141700
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:1947 original size:42 final size:42
Alignment explanation
Indices: 1815--1947 Score: 123
Period size: 41 Copynumber: 3.2 Consensus size: 42
1805 CTATTCTACT
* * * *
1815 GCGGTGTTTATTACGAAAACACCACTAAGGGACACAC-TATT-
1 GCGGCGTTTATTACAAAAACACCACTAAAGTACA-ACTTATTA
* * *
1856 GCGGTGTTTATTACAAAAA-GCCACTAAATTACAACTCTATTA
1 GCGGCGTTTATTACAAAAACACCACTAAAGTACAACT-TATTA
* *
1898 -CGACGTTTATGT-CAAAAACACCACTAAAGTACAACTTTTTA
1 GCGGCGTTTAT-TACAAAAACACCACTAAAGTACAACTTATTA
1939 GCGGCGTTT
1 GCGGCGTTT
1948 GGTAACAAAC
Statistics
Matches: 75, Mismatches: 11, Indels: 11
0.77 0.11 0.11
Matches are distributed among these distances:
39 2 0.03
40 10 0.13
41 40 0.53
42 23 0.31
ACGTcount: A:0.35, C:0.21, G:0.16, T:0.29
Consensus pattern (42 bp):
GCGGCGTTTATTACAAAAACACCACTAAAGTACAACTTATTA
Found at i:2169 original size:132 final size:132
Alignment explanation
Indices: 1885--2124 Score: 345
Period size: 132 Copynumber: 1.8 Consensus size: 132
1875 GCCACTAAAT
* *
1885 TACAACTCTATTACGACGTTTATGTCAAAAACACCACTAAAGTACAACTTTTTAGCGGCGTTTGG
1 TACAACTATATTACGGCGTTTATGTCAAAAACACCACTAAAGTACAACTTTTTAGCGGCGTTTGG
* * * *
1950 TAACAAACGCCACTAAATTTAGAGTATTTTAGGCGTTTGCTTAAAAACGCCGTTATAAATAATAA
66 TAACAAACGCCACTAAATTAAGAGTATTTTAGGCGTTTGATTAAAAACGCCGTGAAAAATAATAA
2015 TA
131 TA
* * ** *
2017 TACAACTCTATTACGGCGTTTATGTCAAAAACGCCTTTAAAGTACAACTTTTTAGCGGCGTTTGT
1 TACAACTATATTACGGCGTTTATGTCAAAAACACCACTAAAGTACAACTTTTTAGCGGCGTTTGG
* * *
2082 TACCAAACGCTACTAAATTAAGAGTATTTTGCGGCGTTTGATT
66 TAACAAACGCCACTAAATTAAGAGTATTTT-AGGCGTTTGATT
2125 GCGGCGGGTG
Statistics
Matches: 97, Mismatches: 10, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
132 87 0.90
133 10 0.10
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Consensus pattern (132 bp):
TACAACTATATTACGGCGTTTATGTCAAAAACACCACTAAAGTACAACTTTTTAGCGGCGTTTGG
TAACAAACGCCACTAAATTAAGAGTATTTTAGGCGTTTGATTAAAAACGCCGTGAAAAATAATAA
TA
Found at i:3496 original size:41 final size:40
Alignment explanation
Indices: 3452--3614 Score: 172
Period size: 40 Copynumber: 4.0 Consensus size: 40
3442 GCATTTATAA
*
3452 AAAAAACGCCACTATTGATT-ACACTATTATGGCGTTTGTT
1 AAAAAACGCCACTATTGATTAACACTATTACGGCGTTT-TT
* *
3492 AAAAAACGCTACTATTGATTAAAACTATTACGGCGTTTTT
1 AAAAAACGCCACTATTGATTAACACTATTACGGCGTTTTT
* *
3532 CTAAAAACGCCACTAGTGATTAACACTATT--GTGCGTTTGTCT
1 -AAAAAACGCCACTATTGATTAACACTATTACG-GCGTTT-T-T
* * * *
3574 -AAAAACACCACTATTTATTATCACTATTGCGGCGTTTTT
1 AAAAAACGCCACTATTGATTAACACTATTACGGCGTTTTT
3613 AA
1 AA
3615 GAATAAATGC
Statistics
Matches: 104, Mismatches: 11, Indels: 16
0.79 0.08 0.12
Matches are distributed among these distances:
39 2 0.02
40 53 0.51
41 47 0.45
42 2 0.02
ACGTcount: A:0.33, C:0.18, G:0.13, T:0.35
Consensus pattern (40 bp):
AAAAAACGCCACTATTGATTAACACTATTACGGCGTTTTT
Found at i:3538 original size:81 final size:81
Alignment explanation
Indices: 3453--3612 Score: 218
Period size: 81 Copynumber: 2.0 Consensus size: 81
3443 CATTTATAAA
*
3453 AAAAACGCCACTATTGATT-ACACTATTATGGCGTTTGT-TAAAAA-ACGCTACTATTGATTAAA
1 AAAAACGCCACTAGTGATTAACACTATTAT-GCGTTTGTCTAAAAACAC-C-ACTATTGATTAAA
3515 ACTATTACGGCGTTTTTCT
63 ACTATTACGGCGTTTTTCT
* * **
3534 AAAAACGCCACTAGTGATTAACACTATTGTGCGTTTGTCTAAAAACACCACTATTTATTATCACT
1 AAAAACGCCACTAGTGATTAACACTATTATGCGTTTGTCTAAAAACACCACTATTGATTAAAACT
*
3599 ATTGCGGCGTTTTT
66 ATTACGGCGTTTTT
3613 AAGAATAAAT
Statistics
Matches: 70, Mismatches: 6, Indels: 6
0.85 0.07 0.07
Matches are distributed among these distances:
81 52 0.74
82 16 0.23
83 2 0.03
ACGTcount: A:0.32, C:0.19, G:0.14, T:0.36
Consensus pattern (81 bp):
AAAAACGCCACTAGTGATTAACACTATTATGCGTTTGTCTAAAAACACCACTATTGATTAAAACT
ATTACGGCGTTTTTCT
Found at i:3685 original size:42 final size:40
Alignment explanation
Indices: 3638--3776 Score: 117
Period size: 42 Copynumber: 3.4 Consensus size: 40
3628 TATATGTGTA
3638 ATCTATTGCGTCGTTTGTGGTATAAACGCCGCTAATTTACC
1 ATCTATTGCG-CGTTTGTGGTATAAACGCCGCTAATTTACC
* *
3679 GATCTATTGCG-GATTT-TGGCTA-AAACTCCACTATATGTTA--
1 -ATCTATTGCGCG-TTTGTGG-TATAAACGCCGCTA-AT-TTACC
* *
3719 ATATATTGCAGCGTTTGCGGTATAAACGCCGCTAATTTACC
1 ATCTATTGC-GCGTTTGTGGTATAAACGCCGCTAATTTACC
*
3760 ACTCTATTACGACGTTT
1 A-TCTATTGCG-CGTTT
3777 TGTAAAAAAA
Statistics
Matches: 77, Mismatches: 8, Indels: 24
0.71 0.07 0.22
Matches are distributed among these distances:
39 11 0.14
40 21 0.27
41 21 0.27
42 24 0.31
ACGTcount: A:0.25, C:0.21, G:0.18, T:0.36
Consensus pattern (40 bp):
ATCTATTGCGCGTTTGTGGTATAAACGCCGCTAATTTACC
Found at i:3939 original size:23 final size:22
Alignment explanation
Indices: 3913--3957 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 22
3903 ACGTGTTATA
3913 TTTTAATTTTTGTGGCGTTTTCT
1 TTTTAATTTTTGT-GCGTTTTCT
3936 TTTTAATTTTTGTGCGTTTTCT
1 TTTTAATTTTTGTGCGTTTTCT
3958 CCATATTTCG
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
22 9 0.41
23 13 0.59
ACGTcount: A:0.09, C:0.09, G:0.16, T:0.67
Consensus pattern (22 bp):
TTTTAATTTTTGTGCGTTTTCT
Found at i:5909 original size:15 final size:15
Alignment explanation
Indices: 5878--5908 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
5868 TTAGAAAAAG
5878 TTAAAAGTATTATTT
1 TTAAAAGTATTATTT
5893 TTAAAA-TATTATTT
1 TTAAAAGTATTATTT
5907 TT
1 TT
5909 TTTCTAAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.62
15 6 0.38
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (15 bp):
TTAAAAGTATTATTT
Found at i:6176 original size:32 final size:33
Alignment explanation
Indices: 6130--6193 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 33
6120 TATCTCAATT
*
6130 TTATCATTCACTCTAAGTTAACTTTA-GGATTC
1 TTATAATTCACTCTAAGTTAACTTTACGGATTC
*
6162 TTATAATTCGCTCTAAGTTAACTTTACGGATT
1 TTATAATTCACTCTAAGTTAACTTTACGGATT
6194 TATGGGTGAT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 24 0.83
33 5 0.17
ACGTcount: A:0.28, C:0.17, G:0.11, T:0.44
Consensus pattern (33 bp):
TTATAATTCACTCTAAGTTAACTTTACGGATTC
Found at i:7794 original size:15 final size:16
Alignment explanation
Indices: 7774--7813 Score: 66
Period size: 15 Copynumber: 2.6 Consensus size: 16
7764 TGGCACCGAA
7774 AGCCGAGAAGAAA-CC
1 AGCCGAGAAGAAAGCC
7789 AGCCGAGAA-AAAGCC
1 AGCCGAGAAGAAAGCC
7804 AGCCGAGAAG
1 AGCCGAGAAG
7814 GCCCCAGCTG
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 3 0.13
15 20 0.87
ACGTcount: A:0.45, C:0.25, G:0.30, T:0.00
Consensus pattern (16 bp):
AGCCGAGAAGAAAGCC
Found at i:8933 original size:18 final size:19
Alignment explanation
Indices: 8900--8935 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
8890 AATTTTATTT
*
8900 AAGTTTTTTTATAATTTTG
1 AAGTATTTTTATAATTTTG
8919 AAGTATTTTTA-AATTTT
1 AAGTATTTTTATAATTTT
8936 ATTAATGTTC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 6 0.38
19 10 0.62
ACGTcount: A:0.31, C:0.00, G:0.08, T:0.61
Consensus pattern (19 bp):
AAGTATTTTTATAATTTTG
Found at i:14649 original size:23 final size:23
Alignment explanation
Indices: 14623--14670 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
14613 ATTAAGTACA
*
14623 ATAACATAATAGGTAACGCTTAT
1 ATAACATAATAGGTAACACTTAT
** *
14646 ATAATGTAATAGGTAGCACTTAT
1 ATAACATAATAGGTAACACTTAT
14669 AT
1 AT
14671 TGACTTATTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.42, C:0.10, G:0.15, T:0.33
Consensus pattern (23 bp):
ATAACATAATAGGTAACACTTAT
Found at i:15098 original size:200 final size:198
Alignment explanation
Indices: 14717--15194 Score: 597
Period size: 200 Copynumber: 2.4 Consensus size: 198
14707 ATAACATTAC
* ** *
14717 AAATTTACCTATTACATTATAATTATCGGTTTCGATGTTTTTTTGATTGATACAATTT--TAAAT
1 AAATTTA-CTATTACATTATAATTATCGGTTTCGATGTTTATGAGATTGATAC-TTTTAATAAAT
* * *
14780 GTATCGACACTTTATATATACACCTCGTTGGGCATTCATTCTGGAAAAAAGTATTGACACAAACT
64 GTATCGACACTTTATACATACACCTCGTTGGGCATTCATTATGGAAAAAAGTATCGACACAAACT
* * * * *
14845 TAAAAAGTATTAATACATTATTTAGACATATTTTCTCATAAAACCAGTATATTTCTATCGGGTAC
129 TAAAAAGTATCAATACATTATCTAGACATATTTTCTCATAAAACCAATATATTTATATCAGGTAC
14910 ATTGT
194 ATTGT
* * *
14915 AAATTTACATATCACATTGTAATTATCGGTTTCGATGTTTATGAGATCGATACTTTTAATAAATG
1 AAATTTAC-TATTACATTATAATTATCGGTTTCGATGTTTATGAGATTGATACTTTTAATAAATG
* * * * *
14980 TATCGACACTTTATGCGTGCA-CTCCGTTTGGCATTCATTATGGACAAAAAGTATCGACACAAAT
65 TATCGACACTTTATACATACACCT-CGTTGGGCATTCATTATGGA-AAAAAGTATCGACACAAAC
* * * * * * *
15044 TTAAATAGTGTCGATACTTTATGCT-GACCTATTTTCTCATAAAACCAATATATTTATATTAGTT
128 TTAAAAAGTATCAATACATTAT-CTAGACATATTTTCTCATAAAACCAATATATTTATATCAGGT
15108 ACATTGT
192 ACATTGT
*
15115 AAATTTATCTATTACATTATAATTATCGGTTTCGATG-TAATTGAGATTGATACTTTTAATAAAT
1 AAATTTA-CTATTACATTATAATTATCGGTTTCGATGTTTA-TGAGATTGATACTTTTAATAAAT
15179 GTATCGACACTTTATA
64 GTATCGACACTTTATA
15195 TTCTAGACAA
Statistics
Matches: 240, Mismatches: 32, Indels: 14
0.84 0.11 0.05
Matches are distributed among these distances:
197 4 0.02
198 47 0.20
199 43 0.18
200 144 0.60
201 2 0.01
ACGTcount: A:0.34, C:0.14, G:0.12, T:0.40
Consensus pattern (198 bp):
AAATTTACTATTACATTATAATTATCGGTTTCGATGTTTATGAGATTGATACTTTTAATAAATGT
ATCGACACTTTATACATACACCTCGTTGGGCATTCATTATGGAAAAAAGTATCGACACAAACTTA
AAAAGTATCAATACATTATCTAGACATATTTTCTCATAAAACCAATATATTTATATCAGGTACAT
TGT
Found at i:19209 original size:199 final size:199
Alignment explanation
Indices: 18869--19635 Score: 1062
Period size: 199 Copynumber: 3.8 Consensus size: 199
18859 GCGTAATTTA
* * * **
18869 AAAATGTATCGACATAAATTT-AAAAGTGTCGATACACTATGTTAACCTATTTTCTCATAAAGCC
1 AAAATGTATCGACACAAATTTAAAAAGTGTCGATACATTATGTT-ACCTATTTGCTCATAAAATC
18933 GGTATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTTTCGGTTTCGATGTTT
65 GGTATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTTTCGGTTTCGATGTTT
*
18998 TTTGGATCGATACTTTTTATAAATGTATCGACACTTTATGCGTGCACCCCGTTTTGCATTCATTA
130 TTTGGATCGATACTTTTTATAAATGTATCGACACTTTATGCGTGCACCCCGTTTAGCATTCATTA
19063 TGGAC
195 TGGAC
*
19068 AAAATGTATCGACACAAATCTAAAAAGTGTCGATACATTATGTTCACCTATTTGCTCATAAAA-C
1 AAAATGTATCGACACAAATTTAAAAAGTGTCGATACATTATGTT-ACCTATTTGCTCATAAAATC
* * ** *
19132 GATATACTTATACATGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATG-TT
65 GGTATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTTTCGGTTTCGATGTTT
* *
19196 TTTGAGATCGATACTTTTTAAAAATGTATCGACACTTTATGCGTGCACCCCGTTTGGCATTCATT
130 TTTG-GATCGATACTTTTTATAAATGTATCGACACTTTATGCGTGCACCCCGTTTAGCATTCATT
*
19261 ATGGAA
194 ATGGAC
* * * *
19267 AAAATGTATCAACACAAATTTAAACAGAGTCGATACATTATGTATACCTATTTTCTCATAAAATC
1 AAAATGTATCGACACAAATTTAAAAAGTGTCGATACATTATGT-TACCTATTTGCTCATAAAATC
* *
19332 GGTATATTTATATCGGTTACATTGTATATTTACCTATTACATTATAATTTTCGGTTTCGATGTTT
65 GGTATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTTTCGGTTTCGATGTTT
** * * * * * * **
19397 TTTGGATCGATACAATTT-TAAATGTATCGACACTTTTATGCATGAAGCTCGTTGAGCA--AAGG
130 TTTGGATCGATACTTTTTATAAATGTATCGACAC-TTTATGCGTGCACCCCGTTTAGCATTCATT
* *
19459 CTCGAAC
194 AT-GGAC
* * * * *
19466 AAAAAGTATCGACTCAAATTTAAAAGGTGTCGATACTTTATGCTGACCTATTTGCTCATAAAATC
1 AAAATGTATCGACACAAATTTAAAAAGTGTCGATACATTATG-TTACCTATTTGCTCATAAAATC
*
19531 GGTATATTTATACCGGTCACATTGTAAATTTACCTATTACATTATAATTTTCGGTTTCGATGTTT
65 GGTATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTTTCGGTTTCGATGTTT
19596 TTTGGATCGATA-TCTTTTATAAATGTATCGACACTTTATG
130 TTTGGATCGATACT-TTTTATAAATGTATCGACACTTTATG
19636 GGAAACTTTA
Statistics
Matches: 503, Mismatches: 55, Indels: 20
0.87 0.10 0.03
Matches are distributed among these distances:
198 8 0.02
199 349 0.69
200 140 0.28
201 6 0.01
ACGTcount: A:0.31, C:0.16, G:0.14, T:0.39
Consensus pattern (199 bp):
AAAATGTATCGACACAAATTTAAAAAGTGTCGATACATTATGTTACCTATTTGCTCATAAAATCG
GTATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTTTCGGTTTCGATGTTTT
TTGGATCGATACTTTTTATAAATGTATCGACACTTTATGCGTGCACCCCGTTTAGCATTCATTAT
GGAC
Found at i:19606 original size:399 final size:397
Alignment explanation
Indices: 18868--19635 Score: 1114
Period size: 399 Copynumber: 1.9 Consensus size: 397
18858 CGCGTAATTT
* * * *
18868 AAAAATGTATCGACATAAATTTAAAAGTGTCGATACACTATGTTAACCTATTTTCTCATAAAGCC
1 AAAAATGTATCAACACAAATTTAAAAGAGTCGATACACTATGTTAACCTATTTTCTCATAAAACC
18933 GGTATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTTTCGGTTTCGATGTTT
66 GGTATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTTTCGGTTTCGATGTTT
** * * ** * **
18998 TTTGGATCGATACTTTTTATAAATGTATCGACACTTTATGCGTGCACCCCGTTTTGCATTCATTA
131 TTTGGATCGATACAATTTATAAATGTATCGACACTTTATGCATGAACCCCGTTGAGCA-TAAGGA
* * *
19063 TGGACAAAATGTATCGACACAAATCTAAAAAGTGTCGATACATTATGTTCACCTATTTGCTCATA
195 TGAACAAAAAGTATCGACACAAATCTAAAAAGTGTCGATACATTATGCTCACCTATTTGCTCATA
* *
19128 AAACGATATACTTATACATGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGAT
260 AAACGATATACTTATACAGGTCACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGAT
19193 GTTTTTGAGATCGATA-CTTTTTAAAAATGTATCGACACTTTATGCGTGCACCCCGTTTGGCATT
325 GTTTTTGAGATCGATATC-TTTTAAAAATGTATCGACACTTTATGCGTGCACCCCGTTTGGCATT
19257 CATTATGGA
389 CATTATGGA
*
19266 AAAAATGTATCAACACAAATTTAAACAGAGTCGATACATTATG-TATACCTATTTTCTCATAAAA
1 AAAAATGTATCAACACAAATTTAAA-AGAGTCGATACACTATGTTA-ACCTATTTTCTCATAAAA
* * *
19330 TCGGTATATTTATATCGGTTACATTGTATATTTACCTATTACATTATAATTTTCGGTTTCGATGT
64 CCGGTATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTTTCGGTTTCGATGT
* *
19395 TTTTTGGATCGATACAATTT-TAAATGTATCGACACTTTTATGCATGAAGCTCGTTGAGCA-AAG
129 TTTTTGGATCGATACAATTTATAAATGTATCGACAC-TTTATGCATGAACCCCGTTGAGCATAAG
* * * * * *
19458 GCTCGAACAAAAAGTATCGACTCAAATTTAAAAGGTGTCGATACTTTATGCTGACCTATTTGCTC
193 GAT-GAACAAAAAGTATCGACACAAATCTAAAAAGTGTCGATACATTATGCTCACCTATTTGCTC
* * * *
19523 ATAAAATCGGTATATTTATACCGGTCACATTGTAAATTTACCTATTACATTATAATTTTCGGTTT
257 ATAAAA-CGATATACTTATACAGGTCACATTGTAAATTTACCTATTACATTATAATTATCGGTTT
*
19588 CGATGTTTTTTG-GATCGATATCTTTTATAAATGTATCGACACTTTATG
321 CGATG-TTTTTGAGATCGATATCTTTTAAAAATGTATCGACACTTTATG
19636 GGAAACTTTA
Statistics
Matches: 328, Mismatches: 35, Indels: 13
0.87 0.09 0.03
Matches are distributed among these distances:
397 2 0.01
398 99 0.30
399 220 0.67
400 7 0.02
ACGTcount: A:0.31, C:0.16, G:0.14, T:0.39
Consensus pattern (397 bp):
AAAAATGTATCAACACAAATTTAAAAGAGTCGATACACTATGTTAACCTATTTTCTCATAAAACC
GGTATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTTTCGGTTTCGATGTTT
TTTGGATCGATACAATTTATAAATGTATCGACACTTTATGCATGAACCCCGTTGAGCATAAGGAT
GAACAAAAAGTATCGACACAAATCTAAAAAGTGTCGATACATTATGCTCACCTATTTGCTCATAA
AACGATATACTTATACAGGTCACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATG
TTTTTGAGATCGATATCTTTTAAAAATGTATCGACACTTTATGCGTGCACCCCGTTTGGCATTCA
TTATGGA
Found at i:19894 original size:18 final size:18
Alignment explanation
Indices: 19871--19907 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
19861 TGAAATTTAT
19871 ATTGAAATTCAAAATCAA
1 ATTGAAATTCAAAATCAA
* *
19889 ATTGAAATTGAAATTCAA
1 ATTGAAATTCAAAATCAA
19907 A
1 A
19908 CTCCAATTAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.54, C:0.08, G:0.08, T:0.30
Consensus pattern (18 bp):
ATTGAAATTCAAAATCAA
Found at i:22432 original size:15 final size:15
Alignment explanation
Indices: 22412--22440 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
22402 AAGAGGTTGT
22412 GGTTGAGAAGAGCTG
1 GGTTGAGAAGAGCTG
22427 GGTTGAGAAGAGCT
1 GGTTGAGAAGAGCT
22441 TTGAGAAAGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.28, C:0.07, G:0.45, T:0.21
Consensus pattern (15 bp):
GGTTGAGAAGAGCTG
Found at i:22875 original size:21 final size:21
Alignment explanation
Indices: 22849--22900 Score: 95
Period size: 21 Copynumber: 2.5 Consensus size: 21
22839 TGTTTTTGGG
*
22849 ATCGACACTTTTTAGAAATGT
1 ATCGACACTTTTTAAAAATGT
22870 ATCGACACTTTTTAAAAATGT
1 ATCGACACTTTTTAAAAATGT
22891 ATCGACACTT
1 ATCGACACTT
22901 AATGGGTGCA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.35, C:0.17, G:0.12, T:0.37
Consensus pattern (21 bp):
ATCGACACTTTTTAAAAATGT
Found at i:23541 original size:387 final size:395
Alignment explanation
Indices: 22870--23887 Score: 1315
Period size: 389 Copynumber: 2.6 Consensus size: 395
22860 TTAGAAATGT
* * * * * * * *
22870 ATCGACACTTTTTAAAAATGTATCGACACTTAATGGGTGCACCCTTTT-AGCATTCC-TTCTAGA
1 ATCGACACTTTTTAAAAATATATCAACACTTTATGCGTTCACCATTTTGGGCA-TCCATTCTGGA
* * * * * * * *
22933 CAAAAAGTATCGACA-CAAATTCTATAAGTGTCGATACATTTTCTAGACCTATTCTCGCATAAAA
65 AAAAAAGTATCAACACCAATTTC-AAAAGTGTCGATACATTATATAGACATATTCT----TACAA
22997 CCAGTATATTTATACCAGTTACATTGAAAAATTACCTATTACATTATAATCATGGGTTTCGATGT
125 CCA--ATA-TTATA-CAGTTACATTGAAAAATTACCTATTACATTATAATCATGGGTTTCGATGT
* * *
23062 TTATGGGATCTATACTTTTTATAAATGTTTCGACACTTTATGTGTGCACCATTTTTTTGGGCATT
186 TTATGGGATCGATACTTTTTATAAATGTATCGACACTTTATGCGTGCACCATTTTTTTGGGCATT
* *
23127 CGTTATGGACAAAAGGTATCGACACAAAATTAAAAAGTGTCGATACATTATGTAGACCTA-TCTC
251 CATTATGGACAAAAGGTATCGACACAAAATTAAAAAGTGTCAATACATTATGTAGACCTATTCTC
* *
23191 ACATAATACCGATAAATTTATACTGGTTACATTACAAAATTACCTATTACATTATAATTAT-GGG
316 ACATAAAACCGATAAATTTATACCGGTTACATTACAAAATTACCTATTACATTATAATTATGGGG
*
23255 TTCAATGTCTTTGGG
381 TTCAATGTCTCTGGG
* *
23270 ATCGACACTTTTTAAAAATGTATCAACACTTTATGCGTTCACCATTTTGGGCATTCATTCTGGAA
1 ATCGACACTTTTTAAAAATATATCAACACTTTATGCGTTCACCATTTTGGGCATCCATTCTGGAA
* *
23335 AAAAAGTATCAACACCAATTTCAAATGTGTCGATACATTATATAGACCTATTC-T-C-A-C-ATA
66 AAAAAGTATCAACACCAATTTCAAAAGTGTCGATACATTATATAGACATATTCTTACAACCAATA
* * * *
23395 -TAT-CGGTTACATTGAAAAAGTACCTATTACATTATAATCATGAGTTTCGATGTTTCTGGGATC
131 TTATACAGTTACATTGAAAAATTACCTATTACATTATAATCATGGGTTTCGATGTTTATGGGATC
* *
23458 GATACTTTTTTATAAATGTATCGACACTTTATGCGTGCACGATTTTTTTGGGCATTCATTCTGGA
196 GATAC-TTTTTATAAATGTATCGACACTTTATGCGTGCACCATTTTTTTGGGCATTCATTATGGA
* *
23523 CAAAATGTATCGACACAAAATTAAAAAGTGTCAATACATTATGTAGACCTATTCTCATATAAAAC
260 CAAAAGGTATCGACACAAAATTAAAAAGTGTCAATACATTATGTAGACCTATTCTCACATAAAAC
* * * *
23588 CGATATATTTATACCGGTTACATTACAAAATTATCTATTATATTATAATTATGGGGTTCGATGTC
325 CGATAAATTTATACCGGTTACATTACAAAATTACCTATTACATTATAATTATGGGGTTCAATGTC
23653 TCTGGG
390 TCTGGG
* * * * *
23659 ATCGACACTTTTTATAAATATATCGACACTTTATGCGTTCACCATTTTGTGTATCCATTCTGGAC
1 ATCGACACTTTTTAAAAATATATCAACACTTTATGCGTTCACCATTTTGGGCATCCATTCTGGAA
* *
23724 AAAAAGTATCGACACCAATTTCAAAAGTGTCGATACATTATGTAGACATATTCTTACATAAAACC
66 AAAAAGTATCAACACCAATTTCAAAAGTGTCGATACATTATATAGACATATTCTTAC----AACC
* *
23789 AATATATTTATACCAGTTATATT-ACAAAATTACCTATTACATTATAATTATGGGTTTCGATGTT
127 -A-ATA-TTATA-CAGTTACATTGA-AAAATTACCTATTACATTATAATCATGGGTTTCGATGTT
*
23853 TTTGGGATCGATACTTTTTATAAATGTATCGACAC
187 TATGGGATCGATACTTTTTATAAATGTATCGACAC
23888 ATCTGCTTAC
Statistics
Matches: 543, Mismatches: 53, Indels: 41
0.85 0.08 0.06
Matches are distributed among these distances:
386 60 0.11
387 103 0.19
388 62 0.11
389 123 0.23
390 4 0.01
391 1 0.00
393 1 0.00
394 1 0.00
396 2 0.00
397 1 0.00
400 48 0.09
401 49 0.09
402 9 0.02
403 22 0.04
404 57 0.10
ACGTcount: A:0.33, C:0.17, G:0.14, T:0.36
Consensus pattern (395 bp):
ATCGACACTTTTTAAAAATATATCAACACTTTATGCGTTCACCATTTTGGGCATCCATTCTGGAA
AAAAAGTATCAACACCAATTTCAAAAGTGTCGATACATTATATAGACATATTCTTACAACCAATA
TTATACAGTTACATTGAAAAATTACCTATTACATTATAATCATGGGTTTCGATGTTTATGGGATC
GATACTTTTTATAAATGTATCGACACTTTATGCGTGCACCATTTTTTTGGGCATTCATTATGGAC
AAAAGGTATCGACACAAAATTAAAAAGTGTCAATACATTATGTAGACCTATTCTCACATAAAACC
GATAAATTTATACCGGTTACATTACAAAATTACCTATTACATTATAATTATGGGGTTCAATGTCT
CTGGG
Found at i:23562 original size:189 final size:184
Alignment explanation
Indices: 23215--23579 Score: 491
Period size: 189 Copynumber: 2.0 Consensus size: 184
23205 AATTTATACT
* *
23215 GGTTACATTACAAAATTACCTATTACATTATAATTATGGGTTCAATGTCTTTGGGATCGACACTT
1 GGTTACATTACAAAAGTACCTATTACATTATAATCATGGGTTCAATGTCTTTGGGATCGACACTT
*
23280 TTTAAAAATGTATCAACACTTTATGCGTTCACCATTTTGGGCATTCATTCTGGAAAAAAAGTATC
66 TTTAAAAATGTATCAACACTTTATGCGTGCACCATTTTGGGCATTCATTCTGGAAAAAAAGTATC
* * * * *
23345 AACACCAATTTCAAATGTGTCGATACATTATATAGACCTATTCTCACATATATC
131 AACACAAAATTAAAAAGTGTCAATACATTATATAGACCTATTCTCACATATATC
* * *
23399 GGTTACATTGA-AAAAGTACCTATTACATTATAATCATGAGTTTCGATGT-TTCTGGGATCGATA
1 GGTTACATT-ACAAAAGTACCTATTACATTATAATCATG-GGTTCAATGTCTT-TGGGATCGACA
* * * *
23462 CTTTTTTATAAATGTATCGACACTTTATGCGTGCACGATTTTTTTGGGCATTCATTCTGGACAAA
63 C-TTTTTAAAAATGTATCAACACTTTATGCGTGCACCA---TTTTGGGCATTCATTCTGGAAAAA
* * *
23527 ATGTATCGACACAAAATTAAAAAGTGTCAATACATTATGTAGACCTATTCTCA
124 AAGTATCAACACAAAATTAAAAAGTGTCAATACATTATATAGACCTATTCTCA
23580 TATAAAACCG
Statistics
Matches: 156, Mismatches: 18, Indels: 9
0.85 0.10 0.05
Matches are distributed among these distances:
184 36 0.23
185 20 0.13
186 32 0.21
189 68 0.44
ACGTcount: A:0.33, C:0.17, G:0.14, T:0.36
Consensus pattern (184 bp):
GGTTACATTACAAAAGTACCTATTACATTATAATCATGGGTTCAATGTCTTTGGGATCGACACTT
TTTAAAAATGTATCAACACTTTATGCGTGCACCATTTTGGGCATTCATTCTGGAAAAAAAGTATC
AACACAAAATTAAAAAGTGTCAATACATTATATAGACCTATTCTCACATATATC
Found at i:23766 original size:200 final size:201
Alignment explanation
Indices: 23393--23887 Score: 697
Period size: 200 Copynumber: 2.5 Consensus size: 201
23383 TATTCTCACA
* * * *
23393 TATATCGGTTACATTGA-AAAAGTACCTATTACATTATAATCATGAGTTTCGATGTTTCTGGGAT
1 TATACCGGTTACATT-ACAAAATTACCTATTACATTATAATTATGGGTTTCGATGTTTCTGGGAT
* *
23457 CGATACTTTTTTATAAATGTATCGACACTTTATGCGTGCACGATTTTTTTGGGCATTCATTCTGG
65 CGATAC-TTTTTATAAATGTATCGACACTTTATGCGTGCACCA--TTTTTGGGCATCCATTCTGG
* * *
23522 ACAAAATGTATCGACACAAAATTAAAAAGTGTCAATACATTATGTAGACCTATTCTCATATAAAA
127 ACAAAAAGTATCGACACAAAATTAAAAAGTGTCAATACATTATGTAGACATATTCTCACATAAAA
*
23587 CCGATATATT
192 CCAATATATT
* * * *
23597 TATACCGGTTACATTACAAAATTATCTATTATATTATAATTATGGGGTTCGATGTCTCTGGGATC
1 TATACCGGTTACATTACAAAATTACCTATTACATTATAATTATGGGTTTCGATGTTTCTGGGATC
* * * * *
23662 GACACTTTTTATAAATATATCGACACTTTATGCGTTCACCA-TTTTGTGTATCCATTCTGGACAA
66 GATACTTTTTATAAATGTATCGACACTTTATGCGTGCACCATTTTTGGGCATCCATTCTGGACAA
* * * * *
23726 AAAGTATCGACACCAATTTCAAAAGTGTCGATACATTATGTAGACATATTCTTACATAAAACCAA
131 AAAGTATCGACACAAAATTAAAAAGTGTCAATACATTATGTAGACATATTCTCACATAAAACCAA
23791 TATATT
196 TATATT
* * *
23797 TATACCAGTTATATTACAAAATTACCTATTACATTATAATTATGGGTTTCGATGTTTTTGGGATC
1 TATACCGGTTACATTACAAAATTACCTATTACATTATAATTATGGGTTTCGATGTTTCTGGGATC
23862 GATACTTTTTATAAATGTATCGACAC
66 GATACTTTTTATAAATGTATCGACAC
23888 ATCTGCTTAC
Statistics
Matches: 257, Mismatches: 33, Indels: 6
0.87 0.11 0.02
Matches are distributed among these distances:
200 164 0.64
203 34 0.13
204 59 0.23
ACGTcount: A:0.33, C:0.16, G:0.14, T:0.38
Consensus pattern (201 bp):
TATACCGGTTACATTACAAAATTACCTATTACATTATAATTATGGGTTTCGATGTTTCTGGGATC
GATACTTTTTATAAATGTATCGACACTTTATGCGTGCACCATTTTTGGGCATCCATTCTGGACAA
AAAGTATCGACACAAAATTAAAAAGTGTCAATACATTATGTAGACATATTCTCACATAAAACCAA
TATATT
Found at i:25271 original size:29 final size:29
Alignment explanation
Indices: 25234--25315 Score: 128
Period size: 29 Copynumber: 2.8 Consensus size: 29
25224 CAAACTAATT
* *
25234 GATGCCATTACTTACATCATTTAATTAAA
1 GATGTCATTGCTTACATCATTTAATTAAA
*
25263 GATGTCATTGCTTACATCATTTAATTAAT
1 GATGTCATTGCTTACATCATTTAATTAAA
25292 GATGTCATTGCTTACATCAATTTA
1 GATGTCATTGCTTACATC-ATTTA
25316 GTTAGGTGAG
Statistics
Matches: 49, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
29 44 0.90
30 5 0.10
ACGTcount: A:0.33, C:0.16, G:0.10, T:0.41
Consensus pattern (29 bp):
GATGTCATTGCTTACATCATTTAATTAAA
Found at i:26627 original size:15 final size:15
Alignment explanation
Indices: 26604--26633 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
26594 ACGAGGCTGG
26604 AATTACAACAATAAC
1 AATTACAACAATAAC
*
26619 AATTCCAACAATAAC
1 AATTACAACAATAAC
26634 TATGAGAAAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.57, C:0.23, G:0.00, T:0.20
Consensus pattern (15 bp):
AATTACAACAATAAC
Found at i:30034 original size:29 final size:29
Alignment explanation
Indices: 29999--30080 Score: 137
Period size: 29 Copynumber: 2.8 Consensus size: 29
29989 AAACTAAATT
*
29999 GATGTCATTACTTACATCATTTAATTAAA
1 GATGTCATTGCTTACATCATTTAATTAAA
*
30028 GATGTCATTGCTTACATCATTTAATTAAT
1 GATGTCATTGCTTACATCATTTAATTAAA
30057 GATGTCATTGCTTACATCAATTTA
1 GATGTCATTGCTTACATC-ATTTA
30081 GTTAGGTGAG
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
29 45 0.90
30 5 0.10
ACGTcount: A:0.33, C:0.15, G:0.10, T:0.43
Consensus pattern (29 bp):
GATGTCATTGCTTACATCATTTAATTAAA
Found at i:30713 original size:132 final size:133
Alignment explanation
Indices: 30472--30819 Score: 379
Period size: 132 Copynumber: 2.6 Consensus size: 133
30462 CTACACTGTC
* *
30472 GCCAAGAGAAATAAATATG-AACCC-TATCTCCATTGG-ACCCAATGCTCGC-ACGTTAAATCAG
1 GCCAAGAGAAACAAATA-GAAACCCTTATCTCCATTGGTACCC-ATGCTCGCAACG-TAAACCAG
* * *
30533 CAGTCGACTATCGGACCACTGCCCGTTTCGTTCAGATCGACAGGGAACAACTCAAATCCGACACC
63 CAGTCGACTGTCGGACCATTGCCAGTTTCGTTCAGATCGACAGGGAACAACTCAAATCCGACACC
**
30598 AATTAG
128 AACAAG
* *
30604 GCCAAGAGAAACAAATAGAAACCCTTAT-TCCATTGGTACCCGTGCTCGCAACGTAGACCAGCAG
1 GCCAAGAGAAACAAATAGAAACCCTTATCTCCATTGGTACCCATGCTCGCAACGTAAACCAGCAG
* * ** **
30668 TCGACTGTCCGACCATTGCCATTTTCGTTCCA-ATCGA-AGGTGAACAACTGGAATCCGACGTCA
66 TCGACTGTCGGACCATTGCCAGTTTCGTT-CAGATCGACAGG-GAACAACTCAAATCCGACACCA
*
30731 CCAAG
129 ACAAG
* * * * * * * *
30736 GCTAAGACAAACAAATATAAACCCTT-TCTCCATTGGTGCCAATGCTCACAACTTAAACCAGCGG
1 GCCAAGAGAAACAAATAGAAACCCTTATCTCCATTGGTACCCATGCTCGCAACGTAAACCAGCAG
30800 TCGACTGTCGGACCATTGCC
66 TCGACTGTCGGACCATTGCC
30820 TCTTTCTTTC
Statistics
Matches: 182, Mismatches: 27, Indels: 14
0.82 0.12 0.06
Matches are distributed among these distances:
131 5 0.03
132 165 0.91
133 12 0.07
ACGTcount: A:0.31, C:0.29, G:0.19, T:0.21
Consensus pattern (133 bp):
GCCAAGAGAAACAAATAGAAACCCTTATCTCCATTGGTACCCATGCTCGCAACGTAAACCAGCAG
TCGACTGTCGGACCATTGCCAGTTTCGTTCAGATCGACAGGGAACAACTCAAATCCGACACCAAC
AAG
Found at i:31122 original size:127 final size:127
Alignment explanation
Indices: 30896--31145 Score: 446
Period size: 127 Copynumber: 2.0 Consensus size: 127
30886 AGGGCAGTAG
* * * *
30896 TCAATTGTGGGACCGCTGCCGTCTACGGGGATTAGGAGCAACTCGATTCCGACAGCGTCTATAAG
1 TCAATTGTCGGACCGCTGCCGTCTACGGGGATTAGGAGCAACTCGATTCCGACAACGTCAACAAG
*
30961 AGTTTGTGTTGTGCCGCCGATGATGAGGGTGCAAGTGCAACAGTCCCGCGTTGAGCCAGCAA
66 AGTTTGTGTTGTGCCGCAGATGATGAGGGTGCAAGTGCAACAGTCCCGCGTTGAGCCAGCAA
31023 TCAATTGTCGGACCGCTGCCGTCTACGGGGATTAGGAGCAACTCGATTCCGACAACGTCAACAAG
1 TCAATTGTCGGACCGCTGCCGTCTACGGGGATTAGGAGCAACTCGATTCCGACAACGTCAACAAG
*
31088 AGTTTGTGTTGTGCCGCAGATGATGAGGGTGCAAGTGCAACAGTCCTGCGTTGAGCCA
66 AGTTTGTGTTGTGCCGCAGATGATGAGGGTGCAAGTGCAACAGTCCCGCGTTGAGCCA
31146 TTCACAAGGC
Statistics
Matches: 117, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
127 117 1.00
ACGTcount: A:0.23, C:0.24, G:0.31, T:0.23
Consensus pattern (127 bp):
TCAATTGTCGGACCGCTGCCGTCTACGGGGATTAGGAGCAACTCGATTCCGACAACGTCAACAAG
AGTTTGTGTTGTGCCGCAGATGATGAGGGTGCAAGTGCAACAGTCCCGCGTTGAGCCAGCAA
Found at i:31755 original size:127 final size:127
Alignment explanation
Indices: 31529--31780 Score: 441
Period size: 127 Copynumber: 2.0 Consensus size: 127
31519 TTAGGGCAGC
* * *
31529 AGTCAATTGTGGGACCGCTGCCGTCTACGGGGATTAGGAGCAACTCGATTCCGATAGCGTTAACA
1 AGTCAATTGTGGGACCGCTGCCGTCTACGGGGATTAGGAGCAACTCGATTCCGACAACGTCAACA
* * *
31594 AGAGTTTGTTTTGTGCCGCAGATGATGAGGGTGCAAGTGCAACAATCCCGCGTTGAGCCAGT
66 AGAGTTTGTGTTGTGCCACAGATGACGAGGGTGCAAGTGCAACAATCCCGCGTTGAGCCAGT
31656 AGTCAATTGTGGGACCGCTGCCGTCTACGGGGATTAGGAGCAACTCGATTCCGACAACGTCAACA
1 AGTCAATTGTGGGACCGCTGCCGTCTACGGGGATTAGGAGCAACTCGATTCCGACAACGTCAACA
*
31721 AGAGTTTGTGTTGTGCCACAGATGACGAGGGTGCAAGTGCAACAGTCCCGCGTTGAGCCA
66 AGAGTTTGTGTTGTGCCACAGATGACGAGGGTGCAAGTGCAACAATCCCGCGTTGAGCCA
31781 TTCACAAGGC
Statistics
Matches: 118, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
127 118 1.00
ACGTcount: A:0.24, C:0.23, G:0.31, T:0.23
Consensus pattern (127 bp):
AGTCAATTGTGGGACCGCTGCCGTCTACGGGGATTAGGAGCAACTCGATTCCGACAACGTCAACA
AGAGTTTGTGTTGTGCCACAGATGACGAGGGTGCAAGTGCAACAATCCCGCGTTGAGCCAGT
Found at i:33612 original size:23 final size:24
Alignment explanation
Indices: 33579--33624 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 24
33569 GTTAATAAAA
*
33579 TCGATATAATTATATATTTTATCC
1 TCGATATAATTATATATTCTATCC
33603 TCGAT-TAATTATATATTCTATC
1 TCGATATAATTATATATTCTATC
33625 AATATATCTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 16 0.76
24 5 0.24
ACGTcount: A:0.33, C:0.13, G:0.04, T:0.50
Consensus pattern (24 bp):
TCGATATAATTATATATTCTATCC
Found at i:33824 original size:11 final size:12
Alignment explanation
Indices: 33803--33856 Score: 51
Period size: 11 Copynumber: 4.6 Consensus size: 12
33793 GTCCGGATTA
33803 TAAATATTATAT
1 TAAATATTATAT
33815 TAAA-ATTATAT
1 TAAATATTATAT
*
33826 T-ATTATTAT-T
1 TAAATATTATAT
*
33836 ATAACTATTATAT
1 -TAAATATTATAT
33849 TATAATAT
1 TA-AATAT
33857 ATTATTATTA
Statistics
Matches: 34, Mismatches: 3, Indels: 9
0.74 0.07 0.20
Matches are distributed among these distances:
10 2 0.06
11 14 0.41
12 13 0.38
13 5 0.15
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (12 bp):
TAAATATTATAT
Found at i:33831 original size:3 final size:3
Alignment explanation
Indices: 33819--33875 Score: 55
Period size: 3 Copynumber: 19.3 Consensus size: 3
33809 TTATATTAAA
* * *
33819 ATT A-T ATT ATT ATT ATT ATA ACT ATT A-T ATT ATA ATAT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT-T ATT ATT
*
33863 ATT ACT ATT ATT A
1 ATT ATT ATT ATT A
33876 ATGTTACATA
Statistics
Matches: 43, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
2 4 0.09
3 37 0.86
4 2 0.05
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.56
Consensus pattern (3 bp):
ATT
Found at i:33839 original size:34 final size:33
Alignment explanation
Indices: 33799--33866 Score: 109
Period size: 34 Copynumber: 2.0 Consensus size: 33
33789 TTTTGTCCGG
33799 ATTATAAATATTATATTAAAATTATATTATTATT
1 ATTATAAATATTATATTAAAA-TATATTATTATT
* *
33833 ATTATAACTATTATATTATAATATATTATTATT
1 ATTATAAATATTATATTAAAATATATTATTATT
33866 A
1 A
33867 CTATTATTAA
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
33 13 0.41
34 19 0.59
ACGTcount: A:0.46, C:0.01, G:0.00, T:0.53
Consensus pattern (33 bp):
ATTATAAATATTATATTAAAATATATTATTATT
Found at i:35184 original size:29 final size:29
Alignment explanation
Indices: 35152--35213 Score: 106
Period size: 29 Copynumber: 2.1 Consensus size: 29
35142 GTTTAATATA
35152 ATTTAGTTTGTATTCACGTGTCCATTAGC
1 ATTTAGTTTGTATTCACGTGTCCATTAGC
* *
35181 ATTTTGTTTGTATTCATGTGTCCATTAGC
1 ATTTAGTTTGTATTCACGTGTCCATTAGC
35210 ATTT
1 ATTT
35214 GAGTCATATT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.19, C:0.15, G:0.16, T:0.50
Consensus pattern (29 bp):
ATTTAGTTTGTATTCACGTGTCCATTAGC
Found at i:35223 original size:29 final size:29
Alignment explanation
Indices: 35162--35224 Score: 74
Period size: 29 Copynumber: 2.2 Consensus size: 29
35152 ATTTAGTTTG
* **
35162 TATTCACGTGTCCATTAGCATTTTGTTTG
1 TATTCACGTGTCCATTAGCATTTTGGTCA
*
35191 TATTCATGTGTCCATTAGCA-TTTGAGTCA
1 TATTCACGTGTCCATTAGCATTTTG-GTCA
35220 TATTC
1 TATTC
35225 GTGTACTACA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
28 4 0.14
29 25 0.86
ACGTcount: A:0.21, C:0.17, G:0.16, T:0.46
Consensus pattern (29 bp):
TATTCACGTGTCCATTAGCATTTTGGTCA
Found at i:38103 original size:26 final size:25
Alignment explanation
Indices: 38051--38103 Score: 70
Period size: 26 Copynumber: 2.1 Consensus size: 25
38041 CTTTACCCTC
*
38051 TCTCTCATAGCTTTGCTAAGCTATT
1 TCTCTCATAGCTTTGCTAAACTATT
* *
38076 TCTCGTCATTGCTTTGCTAAACTTTT
1 TCTC-TCATAGCTTTGCTAAACTATT
38102 TC
1 TC
38104 ATTCTCTAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
25 4 0.17
26 20 0.83
ACGTcount: A:0.17, C:0.25, G:0.11, T:0.47
Consensus pattern (25 bp):
TCTCTCATAGCTTTGCTAAACTATT
Found at i:40202 original size:14 final size:16
Alignment explanation
Indices: 40171--40203 Score: 52
Period size: 14 Copynumber: 2.2 Consensus size: 16
40161 TCTATTTTAC
40171 ATTTTATAAAACTATA
1 ATTTTATAAAACTATA
40187 ATTTT-TAAAA-TATA
1 ATTTTATAAAACTATA
40201 ATT
1 ATT
40204 AATAAATTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 7 0.41
15 5 0.29
16 5 0.29
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (16 bp):
ATTTTATAAAACTATA
Found at i:40351 original size:21 final size:21
Alignment explanation
Indices: 40310--40351 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
40300 AGTACAATAG
*
40310 ATAAAATTGTTTATTTCTTTA
1 ATAAAATTGTTTATATCTTTA
*
40331 ATAAAAGTTTTTTATAT-TTTA
1 ATAAAA-TTGTTTATATCTTTA
40352 TTATAATTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.36, C:0.02, G:0.05, T:0.57
Consensus pattern (21 bp):
ATAAAATTGTTTATATCTTTA
Found at i:40706 original size:3 final size:3
Alignment explanation
Indices: 40698--40735 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
40688 TTGACCTACT
40698 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
40736 TACGATGAGA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:41310 original size:3 final size:3
Alignment explanation
Indices: 41304--41343 Score: 64
Period size: 3 Copynumber: 13.7 Consensus size: 3
41294 GTCAAAAAAA
*
41304 TAT TAT TA- AAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
41344 ATACAAATTT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
2 1 0.03
3 33 0.97
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:42066 original size:3 final size:3
Alignment explanation
Indices: 42058--42091 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
42048 TCTTTGAATC
42058 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
42092 TGTTATTTTC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:43349 original size:28 final size:29
Alignment explanation
Indices: 43317--43377 Score: 81
Period size: 29 Copynumber: 2.1 Consensus size: 29
43307 TTATTTTCAT
43317 TTAAATGTATGTTT-TTTTA-TTTAATCCC
1 TTAAAT-TATGTTTGTTTTATTTTAATCCC
* *
43345 TTAAATTTTGTTTGTTTTATTTTAATCCT
1 TTAAATTATGTTTGTTTTATTTTAATCCC
43374 TTAA
1 TTAA
43378 GTTCATATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
27 6 0.21
28 11 0.38
29 12 0.41
ACGTcount: A:0.25, C:0.08, G:0.07, T:0.61
Consensus pattern (29 bp):
TTAAATTATGTTTGTTTTATTTTAATCCC
Found at i:48033 original size:18 final size:18
Alignment explanation
Indices: 48012--48054 Score: 86
Period size: 18 Copynumber: 2.4 Consensus size: 18
48002 AGAAATTGGA
48012 AGAAATGGTAAAATCAGT
1 AGAAATGGTAAAATCAGT
48030 AGAAATGGTAAAATCAGT
1 AGAAATGGTAAAATCAGT
48048 AGAAATG
1 AGAAATG
48055 ATTGAACCGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.51, C:0.05, G:0.23, T:0.21
Consensus pattern (18 bp):
AGAAATGGTAAAATCAGT
Found at i:53645 original size:25 final size:23
Alignment explanation
Indices: 53606--53684 Score: 90
Period size: 23 Copynumber: 3.4 Consensus size: 23
53596 ATTATGCTTG
* *
53606 AAGAAAAAAAAGAAACAAATAAA
1 AAGAAAAAAAAGAAAAAAAGAAA
53629 AAGAAAACAAAACGAAAAAAAGAAA
1 AAGAAAA-AAAA-GAAAAAAAGAAA
53654 AAGAAAAAAAATG-AAAAAAGAAA
1 AAGAAAAAAAA-GAAAAAAAGAAA
*
53677 TA-AAAAAA
1 AAGAAAAAA
53685 TGAAAAGAGA
Statistics
Matches: 50, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
22 6 0.12
23 18 0.36
24 9 0.18
25 17 0.34
ACGTcount: A:0.82, C:0.04, G:0.10, T:0.04
Consensus pattern (23 bp):
AAGAAAAAAAAGAAAAAAAGAAA
Found at i:53670 original size:35 final size:34
Alignment explanation
Indices: 53610--53698 Score: 92
Period size: 35 Copynumber: 2.6 Consensus size: 34
53600 TGCTTGAAGA
* * *
53610 AAAAAAAGAAACA-AATAAAAAGAAAACAA-AACG
1 AAAAAAAGAAAAAGAAAAAAAAGAAAA-AAGAAAG
*
53643 AAAAAAAGAAAAAGAAAAAAAATGAAAAAAGAAAT
1 AAAAAAAGAAAAAGAAAAAAAA-GAAAAAAGAAAG
53678 AAAAAAATGAAAAGAGAAAAA
1 AAAAAAA-GAAAA-AGAAAAA
53699 TGAGGGTTTG
Statistics
Matches: 47, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
33 12 0.26
34 9 0.19
35 14 0.30
36 5 0.11
37 7 0.15
ACGTcount: A:0.81, C:0.03, G:0.11, T:0.04
Consensus pattern (34 bp):
AAAAAAAGAAAAAGAAAAAAAAGAAAAAAGAAAG
Found at i:53683 original size:20 final size:20
Alignment explanation
Indices: 53658--53696 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
53648 AAGAAAAAGA
53658 AAAAAAATGAAAAAAGAAAT
1 AAAAAAATGAAAAAAGAAAT
*
53678 AAAAAAATGAAAAGAGAAA
1 AAAAAAATGAAAAAAGAAA
53697 AATGAGGGTT
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:0.79, C:0.00, G:0.13, T:0.08
Consensus pattern (20 bp):
AAAAAAATGAAAAAAGAAAT
Found at i:53690 original size:8 final size:7
Alignment explanation
Indices: 53611--53698 Score: 52
Period size: 7 Copynumber: 11.7 Consensus size: 7
53601 GCTTGAAGAA
53611 AAAAAAG
1 AAAAAAG
*
53618 AAACAAAT
1 AAA-AAAG
*
53626 AAAAAGAA
1 AAAAA-AG
53634 AACAAAACG
1 AA-AAAA-G
53643 AAAAAAAG
1 -AAAAAAG
*
53651 AAAAAGAA
1 AAAAA-AG
53659 AAAAAATG
1 AAAAAA-G
53667 AAAAAAG
1 AAAAAAG
*
53674 AAATAA-
1 AAAAAAG
*
53680 AAAAATG
1 AAAAAAG
*
53687 AAAAGAG
1 AAAAAAG
53694 AAAAA
1 AAAAA
53699 TGAGGGTTTG
Statistics
Matches: 62, Mismatches: 11, Indels: 16
0.70 0.12 0.18
Matches are distributed among these distances:
6 4 0.06
7 26 0.42
8 23 0.37
9 7 0.11
10 2 0.03
ACGTcount: A:0.81, C:0.03, G:0.11, T:0.05
Consensus pattern (7 bp):
AAAAAAG
Found at i:54943 original size:91 final size:91
Alignment explanation
Indices: 54788--54959 Score: 283
Period size: 91 Copynumber: 1.9 Consensus size: 91
54778 AAAGAGATGG
* *
54788 ATCAACATTTCCAATGGAGAGTTCATAATAAGAAGAACTCATCCAATGAGAGAGAATAAGTTCAT
1 ATCAACATTTCCAATGGAGAGCTCATAATAAGAAGAACTCATCCAATGAGAGAGAAGAAGTTCAT
54853 AATGAGAAGAACTTGTCCAACTTCGC
66 AATGAGAAGAACTTGTCCAACTTCGC
* *
54879 ATCAACATTTTCAATGGAGAGCTCATAATGAGAAGAACTCATCCAATGAG-GAAGAAGAAGTTCA
1 ATCAACATTTCCAATGGAGAGCTCATAATAAGAAGAACTCATCCAATGAGAG-AGAAGAAGTTCA
*
54943 TAATGAGAAGAGCTTGT
65 TAATGAGAAGAACTTGT
54960 TCGACCTATC
Statistics
Matches: 75, Mismatches: 5, Indels: 2
0.91 0.06 0.02
Matches are distributed among these distances:
90 1 0.01
91 74 0.99
ACGTcount: A:0.41, C:0.16, G:0.20, T:0.24
Consensus pattern (91 bp):
ATCAACATTTCCAATGGAGAGCTCATAATAAGAAGAACTCATCCAATGAGAGAGAAGAAGTTCAT
AATGAGAAGAACTTGTCCAACTTCGC
Found at i:55110 original size:331 final size:332
Alignment explanation
Indices: 54551--55292 Score: 1057
Period size: 331 Copynumber: 2.2 Consensus size: 332
54541 GGTGAACCAG
* *
54551 CATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGAAAGAGGTAGAAGAAGTTCATAATG
1 CATTTTCAATGGAGAGTTCATAATGAGAAGAACTCATCC-AAAGAGGAAGAAGAAGTTCATAATG
* * *
54616 AGAAGAGCCTATTCGACCTATCACTAGATTCACATCATTTCGAATTAGTGACACCTCGCTTGAGG
65 AGAAGAGCTTGTTCGACCTATCACTAGATTCACATCATTTCGAATCAGTGACACCTCGCTTGAGG
* *
54681 GATTGACATTTTTCAGAAGAGTTCATAATGAGAAGAACTCGTCCTAAAGGAGAAAGTTCATAATG
130 GATTGACATTTTCCAAAAGAGTTCATAATGAGAAGAACTCGTCCTAAAGGAGAAAGTTCATAATG
* *
54746 AGAAGAACTTGTTCCTTTCAAGTCCATCACAGAAAGAGATGGA-TCAACATTTCCAATGGAGAGT
195 AAAAGAACTTGTTCCTTTCAAGTCCACCACAGAAAGAGAT-GACTCAACATTTCCAATGGAGAGT
* * *
54810 TCATAATAAGAAGAACTCATCCAATGA-GAGAGAATAAGTTCATAATGAGAAGAACTTGTCCAA-
259 TCATAATAAGAAGAACTCATCCAACGAGGA-AGAAGAAGTTCATAATGAGAAGAACATGTCCAAC
54873 CTTCGCATCAA
323 CTT-GCATCAA
* *
54884 CATTTTCAATGGAGAGCTCATAATGAGAAGAACTCATCCAATGAGGAAGAAGAAGTTCATAATGA
1 CATTTTCAATGGAGAGTTCATAATGAGAAGAACTCATCCAAAGAGGAAGAAGAAGTTCATAATGA
* *
54949 GAAGAGCTTGTTCGACCTATCACTCGATTCACGA-CATTTCGAATCAGTGACGCCTCG-TTAGAG
66 GAAGAGCTTGTTCGACCTATCACTAGATTCAC-ATCATTTCGAATCAGTGACACCTCGCTT-GAG
* *
55012 GGATTGATA-TTTCCAAAAGAGTTCATAATGAGAAGAACTCGTCTTAAAGGAGAAAGTTCATAAT
129 GGATTGACATTTTCCAAAAGAGTTCATAATGAGAAGAACTCGTCCTAAAGGAGAAAGTTCATAAT
* * ** * *
55076 GAAAAGAACTTGTTCCTTTCAAGTCCACCACAGAAATAGGTGACTCAACATTTTTAGTTGAGAGT
194 GAAAAGAACTTGTTCCTTTCAAGTCCACCACAGAAAGAGATGACTCAACATTTCCAATGGAGAGT
* *
55141 TCATAATGAGAAGAACTCATCCAACGAGGAAGAAGAAGTTCATAATGAGAAGAACATGTTCAACC
259 TCATAATAAGAAGAACTCATCCAACGAGGAAGAAGAAGTTCATAATGAGAAGAACATGTCCAACC
* *
55206 TTGTATCAG
324 TTGCATCAA
* * * * * *
55215 TA-TTTCCAGGGAAGAGTTCATCATAAGAAGAACTCATCTAAAGAGGAAGAAGAAGTTCATAATG
1 CATTTTCAATGG-AGAGTTCATAATGAGAAGAACTCATCCAAAGAGGAAGAAGAAGTTCATAATG
*
55279 AGAAGAACTTGTTC
65 AGAAGAGCTTGTTC
55293 AATCCAATGC
Statistics
Matches: 366, Mismatches: 37, Indels: 14
0.88 0.09 0.03
Matches are distributed among these distances:
330 9 0.02
331 229 0.63
332 90 0.25
333 38 0.10
ACGTcount: A:0.38, C:0.17, G:0.20, T:0.25
Consensus pattern (332 bp):
CATTTTCAATGGAGAGTTCATAATGAGAAGAACTCATCCAAAGAGGAAGAAGAAGTTCATAATGA
GAAGAGCTTGTTCGACCTATCACTAGATTCACATCATTTCGAATCAGTGACACCTCGCTTGAGGG
ATTGACATTTTCCAAAAGAGTTCATAATGAGAAGAACTCGTCCTAAAGGAGAAAGTTCATAATGA
AAAGAACTTGTTCCTTTCAAGTCCACCACAGAAAGAGATGACTCAACATTTCCAATGGAGAGTTC
ATAATAAGAAGAACTCATCCAACGAGGAAGAAGAAGTTCATAATGAGAAGAACATGTCCAACCTT
GCATCAA
Found at i:55201 original size:20 final size:20
Alignment explanation
Indices: 55139--55202 Score: 51
Period size: 20 Copynumber: 3.2 Consensus size: 20
55129 TTAGTTGAGA
55139 GTTCATAATGAGAAGAAC-T
1 GTTCATAATGAGAAGAACAT
** * * * *
55158 CATC-CAACGAGGAAGAAGAA
1 GTTCATAATGA-GAAGAACAT
55178 GTTCATAATGAGAAGAACAT
1 GTTCATAATGAGAAGAACAT
55198 GTTCA
1 GTTCA
55203 ACCTTGTATC
Statistics
Matches: 30, Mismatches: 12, Indels: 5
0.64 0.26 0.11
Matches are distributed among these distances:
18 4 0.13
19 8 0.27
20 14 0.47
21 4 0.13
ACGTcount: A:0.44, C:0.14, G:0.22, T:0.20
Consensus pattern (20 bp):
GTTCATAATGAGAAGAACAT
Found at i:55462 original size:3 final size:3
Alignment explanation
Indices: 55456--55498 Score: 70
Period size: 3 Copynumber: 14.7 Consensus size: 3
55446 GTCAAAAAAA
*
55456 TAT TAT TA- AAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
55499 ATACAAATTT
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
2 1 0.03
3 36 0.97
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:58145 original size:14 final size:14
Alignment explanation
Indices: 58102--58162 Score: 52
Period size: 14 Copynumber: 4.4 Consensus size: 14
58092 TGTTTCGTTG
*
58102 AAAATATTTTT-TA
1 AAAATATTTTTCGA
* *
58115 GAAAATGTTTTTGGA
1 -AAAATATTTTTCGA
58130 AAAATATTTTTCGA
1 AAAATATTTTTCGA
* *
58144 AAAATGTTTCTCGA
1 AAAATATTTTTCGA
*
58158 TAAAT
1 AAAAT
58163 GAATTACATT
Statistics
Matches: 39, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
14 38 0.97
15 1 0.03
ACGTcount: A:0.41, C:0.05, G:0.11, T:0.43
Consensus pattern (14 bp):
AAAATATTTTTCGA
Found at i:58162 original size:28 final size:28
Alignment explanation
Indices: 58102--58162 Score: 70
Period size: 28 Copynumber: 2.2 Consensus size: 28
58092 TGTTTCGTTG
* * *
58102 AAAATATTTTTTAGAAAATGTTTTTGGA
1 AAAATATTTTTGAGAAAATGTTTCTCGA
58130 AAAATATTTTTCGA-AAAATGTTTCTCGA
1 AAAATATTTTT-GAGAAAATGTTTCTCGA
*
58158 TAAAT
1 AAAAT
58163 GAATTACATT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
28 27 0.96
29 1 0.04
ACGTcount: A:0.41, C:0.05, G:0.11, T:0.43
Consensus pattern (28 bp):
AAAATATTTTTGAGAAAATGTTTCTCGA
Found at i:58163 original size:14 final size:14
Alignment explanation
Indices: 58116--58163 Score: 60
Period size: 14 Copynumber: 3.4 Consensus size: 14
58106 TATTTTTTAG
*
58116 AAAATGTTTTTGGA
1 AAAATGTTTTTCGA
*
58130 AAAATATTTTTCGA
1 AAAATGTTTTTCGA
*
58144 AAAATGTTTCTCGA
1 AAAATGTTTTTCGA
*
58158 TAAATG
1 AAAATG
58164 AATTACATTT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 29 1.00
ACGTcount: A:0.40, C:0.06, G:0.15, T:0.40
Consensus pattern (14 bp):
AAAATGTTTTTCGA
Found at i:58196 original size:15 final size:14
Alignment explanation
Indices: 58168--58202 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
58158 TAAATGAATT
58168 ACATTTTCTGAAAA
1 ACATTTTCTGAAAA
*
58182 ACATTTTTTGAAAA
1 ACATTTTCTGAAAA
*
58196 ACGTTTT
1 ACATTTT
58203 ACGATGTTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.37, C:0.11, G:0.09, T:0.43
Consensus pattern (14 bp):
ACATTTTCTGAAAA
Found at i:58493 original size:23 final size:23
Alignment explanation
Indices: 58464--58508 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
58454 AGTGTTATAT
58464 TATATTTTAAAAATATTAATTAG
1 TATATTTTAAAAATATTAATTAG
* *
58487 TATATTTTAAATATATTTATTA
1 TATATTTTAAAAATATTAATTA
58509 AAGTATTATT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.53
Consensus pattern (23 bp):
TATATTTTAAAAATATTAATTAG
Found at i:58515 original size:23 final size:22
Alignment explanation
Indices: 58465--58545 Score: 71
Period size: 23 Copynumber: 3.7 Consensus size: 22
58455 GTGTTATATT
* * *
58465 ATATTTTAAAAATATTAATTAGT
1 ATATTTTAAATATATTTATTA-A
58488 ATATTTTAAATATATTTATTAA
1 ATATTTTAAATATATTTATTAA
58510 AGTATTATTAAAT-TATTATATT-A
1 A-TATT-TTAAATATATT-TATTAA
58533 ATA--TTAAATATAT
1 ATATTTTAAATATAT
58546 AAACAATATT
Statistics
Matches: 51, Mismatches: 3, Indels: 11
0.78 0.05 0.17
Matches are distributed among these distances:
19 6 0.12
20 3 0.06
22 3 0.06
23 29 0.57
24 10 0.20
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (22 bp):
ATATTTTAAATATATTTATTAA
Found at i:58604 original size:50 final size:51
Alignment explanation
Indices: 58550--58669 Score: 115
Period size: 54 Copynumber: 2.3 Consensus size: 51
58540 ATATATAAAC
*
58550 AATATTATTCATTATTA-ATAATTTATTATACATTATTA-AA-A-TAAAAATAT
1 AATATTATT-ATTATTATATAATTGATTAT--ATTATTATAATATTAAAAATAT
* *
58600 AATATCTTATATTATTAATATATAATTGATTATTTTATTATAATATTAAAAATAT
1 AATA---T-TATTATTATTATATAATTGATTATATTATTATAATATTAAAAATAT
58655 AATATTA-TATTATTA
1 AATATTATTATTATTA
58670 GAAATATTAG
Statistics
Matches: 58, Mismatches: 4, Indels: 16
0.74 0.05 0.21
Matches are distributed among these distances:
50 11 0.19
51 2 0.03
52 7 0.12
53 9 0.16
54 16 0.28
55 13 0.22
ACGTcount: A:0.47, C:0.03, G:0.01, T:0.49
Consensus pattern (51 bp):
AATATTATTATTATTATATAATTGATTATATTATTATAATATTAAAAATAT
Found at i:58662 original size:22 final size:22
Alignment explanation
Indices: 58635--58676 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
58625 TTGATTATTT
58635 TATTATAATATTAAAAATATAA
1 TATTATAATATTAAAAATATAA
* *
58657 TATTATATTATTAGAAATAT
1 TATTATAATATTAAAAATAT
58677 TAGTAAATAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.45
Consensus pattern (22 bp):
TATTATAATATTAAAAATATAA
Found at i:68997 original size:33 final size:33
Alignment explanation
Indices: 68955--69021 Score: 125
Period size: 33 Copynumber: 2.0 Consensus size: 33
68945 AGCTTCAGAG
68955 ATAGATTTAGAGCTGGACCCCACATTAATTTTC
1 ATAGATTTAGAGCTGGACCCCACATTAATTTTC
*
68988 ATAGATTTAGAGCTGGATCCCACATTAATTTTC
1 ATAGATTTAGAGCTGGACCCCACATTAATTTTC
69021 A
1 A
69022 CTTTAAACGA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.31, C:0.19, G:0.15, T:0.34
Consensus pattern (33 bp):
ATAGATTTAGAGCTGGACCCCACATTAATTTTC
Found at i:78494 original size:32 final size:31
Alignment explanation
Indices: 78457--78533 Score: 84
Period size: 31 Copynumber: 2.5 Consensus size: 31
78447 CGGGGTCGTG
*
78457 GGGCCTACCTAAGAACACATCTTAGGGCCGCA
1 GGGCCTACCTAAGAA-ACATCTCAGGGCCGCA
* **
78489 GGGCCTAACC-GAGAATGATCTCAGGGCCGCA
1 GGGCCT-ACCTAAGAAACATCTCAGGGCCGCA
*
78520 GAGCCTACCTAAGA
1 GGGCCTACCTAAGA
78534 GTCACATTAG
Statistics
Matches: 37, Mismatches: 6, Indels: 5
0.77 0.12 0.10
Matches are distributed among these distances:
30 3 0.08
31 21 0.57
32 10 0.27
33 3 0.08
ACGTcount: A:0.29, C:0.30, G:0.27, T:0.14
Consensus pattern (31 bp):
GGGCCTACCTAAGAAACATCTCAGGGCCGCA
Found at i:83423 original size:20 final size:20
Alignment explanation
Indices: 83329--83697 Score: 458
Period size: 20 Copynumber: 18.4 Consensus size: 20
83319 GATTTTCCAT
* ** *
83329 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
83349 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
83369 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
83389 AATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
**
83409 AATCGCAACGCGTATGGGTA
1 AATCGCAACGCGTATCCGTA
*
83429 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
83449 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
83469 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* *
83489 AACCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
83509 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
83529 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
83549 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
83569 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
83589 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
83609 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
83629 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
83649 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
83669 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
83689 AATCACAAC
1 AATCGCAAC
83698 ACTGAAATTT
Statistics
Matches: 305, Mismatches: 36, Indels: 16
0.85 0.10 0.04
Matches are distributed among these distances:
19 3 0.01
20 299 0.98
21 3 0.01
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.20
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:84419 original size:24 final size:24
Alignment explanation
Indices: 84380--84426 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
84370 AAATTTGGTC
84380 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
84404 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
84427 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:84618 original size:12 final size:12
Alignment explanation
Indices: 84601--84625 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
84591 ATATAATCCT
84601 GAAGAAGAAAAA
1 GAAGAAGAAAAA
84613 GAAGAAGAAAAA
1 GAAGAAGAAAAA
84625 G
1 G
84626 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:86931 original size:19 final size:19
Alignment explanation
Indices: 86909--87229 Score: 369
Period size: 19 Copynumber: 18.4 Consensus size: 19
86899 CGGAAAATAC
*
86909 AATCGCAACGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
86928 AATCCCAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
86942 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
*
86962 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
86976 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
86995 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
87014 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
87028 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
87047 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
87066 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
87085 AATCGCAA--CGACA-G--
1 AATCGCAATGCGAAATGAA
*
87099 AATCGCAATGCGAAATTAA
1 AATCGCAATGCGAAATGAA
87118 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
87137 AATCGCAA--CGAAA-G--
1 AATCGCAATGCGAAATGAA
87151 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
87170 AATCGCAA--CGAAA-G--
1 AATCGCAATGCGAAATGAA
87184 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
87203 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
87222 AATCGCAA
1 AATCGCAA
87230 CGAGATAATC
Statistics
Matches: 261, Mismatches: 10, Indels: 62
0.78 0.03 0.19
Matches are distributed among these distances:
14 56 0.21
15 2 0.01
16 22 0.08
17 20 0.08
18 3 0.01
19 145 0.56
20 13 0.05
ACGTcount: A:0.47, C:0.18, G:0.21, T:0.14
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:86996 original size:33 final size:33
Alignment explanation
Indices: 86909--87210 Score: 243
Period size: 33 Copynumber: 8.8 Consensus size: 33
86899 CGGAAAATAC
* *
86909 AATCGCAACGCGAAATGAAAATCCCAAC-ATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGA-GAA
*
86942 AATCGCAATGCGGAAATGAAAATCGCAACGAGAG
1 AATCGCAATGC-GAAATGAAAATCGCAACGAGAA
86976 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAA--CG--A-GAA
*
87014 AATCGCAA--CG--A-GAGAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAA--CG--A-GAA
87047 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAA--CG--A-GAA
* *
87085 AATCGCAA--CGACA-G--AATCGCAATGCGAAATTAA
1 AATCGCAATGCGAAATGAAAATCGCAA--CG--A-GAA
87118 AATCGCAATGCGAAATGAAAATCGCAACGA-AA
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAA
87150 GAATCGCAATGCGAAATGAAAATCGCAACGA-AA
1 -AATCGCAATGCGAAATGAAAATCGCAACGAGAA
87183 GAATCGCAATGCGAAATGAAAATCGCAA
1 -AATCGCAATGCGAAATGAAAATCGCAA
87211 TGCGAAATGA
Statistics
Matches: 242, Mismatches: 9, Indels: 36
0.84 0.03 0.13
Matches are distributed among these distances:
32 2 0.01
33 141 0.58
34 31 0.13
35 10 0.04
36 9 0.04
37 2 0.01
38 47 0.19
ACGTcount: A:0.47, C:0.19, G:0.21, T:0.14
Consensus pattern (33 bp):
AATCGCAATGCGAAATGAAAATCGCAACGAGAA
Found at i:87156 original size:14 final size:14
Alignment explanation
Indices: 87137--87191 Score: 65
Period size: 14 Copynumber: 3.6 Consensus size: 14
87127 GCGAAATGAA
87137 AATCGCAACGAAAG
1 AATCGCAACGAAAG
87151 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
87168 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
87184 AATCGCAA
1 AATCGCAA
87192 TGCGAAATGA
Statistics
Matches: 36, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
14 16 0.44
16 6 0.17
17 6 0.17
19 8 0.22
ACGTcount: A:0.49, C:0.20, G:0.20, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:87267 original size:52 final size:52
Alignment explanation
Indices: 86937--87251 Score: 412
Period size: 52 Copynumber: 6.0 Consensus size: 52
86927 AAATCCCAAC
86937 ATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
86990 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
* * * *
87042 ATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGA-AAT-GAAAAT-CGCA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCG-CAATGCGAA
* * *
87092 ACGACAGAATCGCAATGCGAAATTAAAATCGCAATGCGAAATGAAAATCGCAA--CGAA
1 ATGA-A-AATCGCAATGCGAAATGAAAATCGCAA--CG--A-GAGAATCGCAATGCGAA
*
87149 A-G--AATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
*
87198 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGATAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
87250 AT
1 AT
87252 TATAAACGCA
Statistics
Matches: 232, Mismatches: 15, Indels: 31
0.83 0.05 0.11
Matches are distributed among these distances:
47 9 0.04
48 1 0.00
49 5 0.02
50 10 0.04
51 7 0.03
52 170 0.73
53 16 0.07
54 1 0.00
56 1 0.00
57 6 0.03
58 5 0.02
59 1 0.00
ACGTcount: A:0.47, C:0.17, G:0.22, T:0.14
Consensus pattern (52 bp):
ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
Found at i:87348 original size:19 final size:19
Alignment explanation
Indices: 87258--87340 Score: 113
Period size: 20 Copynumber: 4.6 Consensus size: 19
87248 AAATTATAAA
87258 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
87277 CCGCATTGCGATTTTCATTT
1 -CGCATTGCGATTTTCATTT
*
87297 CGCATTGCGA--TTC-TCT
1 CGCATTGCGATTTTCATTT
87313 CG--TTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
87330 CGCATTGCGAT
1 CGCATTGCGAT
87341 AGTCATTTTT
Statistics
Matches: 56, Mismatches: 2, Indels: 11
0.81 0.03 0.16
Matches are distributed among these distances:
14 6 0.11
16 7 0.12
17 7 0.12
19 17 0.30
20 19 0.34
ACGTcount: A:0.14, C:0.24, G:0.18, T:0.43
Consensus pattern (19 bp):
CGCATTGCGATTTTCATTT
Found at i:87466 original size:14 final size:14
Alignment explanation
Indices: 87447--87483 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
87437 CATCAATTAC
87447 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
87461 ACAAATCATCTTTT
1 ACAAATCAACTTTT
87475 ACAAATCAA
1 ACAAATCAA
87484 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:89483 original size:14 final size:14
Alignment explanation
Indices: 89464--89520 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
89454 GCGAAATGAA
*
89464 AATCGCAACGACAG
1 AATCGCAACGAAAG
89478 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
89495 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
89511 AATCGCAACG
1 AATCGCAACG
89521 CGAAATGAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 18 0.49
16 5 0.14
17 6 0.16
19 8 0.22
ACGTcount: A:0.46, C:0.23, G:0.21, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:89491 original size:33 final size:33
Alignment explanation
Indices: 89445--89537 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
89435 GCGAAACCAA
*
89445 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
*
89478 AATCGCAATGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
89511 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
89538 TGCGATTTTG
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.47, C:0.22, G:0.20, T:0.11
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:89502 original size:19 final size:19
Alignment explanation
Indices: 89408--89542 Score: 128
Period size: 19 Copynumber: 7.6 Consensus size: 19
89398 TAGTTTACTT
* *
89408 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
**
89428 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
89447 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
89466 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
89480 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
89499 TCGCAA--CGAAA-G--AA
1 TCGCAACGCGAAATGAAAA
89513 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
89532 TCGCAATGCGA
1 TCGCAACGCGA
89543 TTTTGGTTTC
Statistics
Matches: 97, Mismatches: 8, Indels: 21
0.77 0.06 0.17
Matches are distributed among these distances:
14 16 0.16
16 11 0.11
17 11 0.11
19 47 0.48
20 12 0.12
ACGTcount: A:0.46, C:0.24, G:0.19, T:0.11
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:89560 original size:19 final size:19
Alignment explanation
Indices: 89538--89666 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
89528 AAAATCGCAA
89538 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
89557 TGCGATCTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
89571 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
89590 TGCGATTCT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
**
89604 TGCGATTTTCATTTCGCGT
1 TGCGATTTTGGTTTCGCGT
89623 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
89642 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT-GGTTTCGCGT
89662 TGCGA
1 TGCGA
89667 AAGTAAACTA
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 22 0.24
15 1 0.01
16 2 0.02
17 2 0.02
18 2 0.02
19 48 0.53
20 13 0.14
ACGTcount: A:0.09, C:0.17, G:0.29, T:0.46
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:89580 original size:33 final size:33
Alignment explanation
Indices: 89538--89629 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 33
89528 AAAATCGCAA
89538 TGCGATTTTGGTTTCGCGTTGCGA-TCTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTC-TGTCGT
89571 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
**
89604 TGCGATTTTCATTTCGCGTTGCGATT
1 TGCGATTTTGGTTTCGCGTTGCGATT
89630 TTGGTTTCGC
Statistics
Matches: 56, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
33 54 0.96
34 2 0.04
ACGTcount: A:0.08, C:0.18, G:0.28, T:0.46
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
Found at i:89857 original size:93 final size:93
Alignment explanation
Indices: 89698--90163 Score: 909
Period size: 93 Copynumber: 5.0 Consensus size: 93
89688 GCAAATTGAA
89698 ACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTA
1 ACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTA
89763 GCAGAATTGGCAGCAACCGAACAAATTT
66 GCAGAATTGGCAGCAACCGAACAAATTT
89791 ACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTA
1 ACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTA
89856 GCAGAATTGGCAGCAACCGAACAAATTT
66 GCAGAATTGGCAGCAACCGAACAAATTT
89884 ACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTA
1 ACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTA
89949 GCAGAATTGGCAGCAACCGAACAAATTT
66 GCAGAATTGGCAGCAACCGAACAAATTT
89977 ACTTTCAACCAAAAGACAAAACAAAGACAAATA-TA-TTCACAGTGTTAAAGAATACACAGTTTA
1 ACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTA
90040 GCAGAATTGGCAGCAACCGAACAAATTT
66 GCAGAATTGGCAGCAACCGAACAAATTT
90068 ACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTA
1 ACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTA
*
90133 GCAGAATTGGCAGCAACCGAATAAATTT
66 GCAGAATTGGCAGCAACCGAACAAATTT
90161 ACT
1 ACT
90164 AAGCAATCTA
Statistics
Matches: 370, Mismatches: 1, Indels: 4
0.99 0.00 0.01
Matches are distributed among these distances:
91 89 0.24
92 4 0.01
93 277 0.75
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (93 bp):
ACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTA
GCAGAATTGGCAGCAACCGAACAAATTT
Found at i:90137 original size:184 final size:186
Alignment explanation
Indices: 89698--90163 Score: 909
Period size: 184 Copynumber: 2.5 Consensus size: 186
89688 GCAAATTGAA
89698 ACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTA
1 ACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTA
89763 GCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAT
66 GCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAT
89828 TTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAATTT
131 TTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAATTT
89884 ACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTA
1 ACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTA
89949 GCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA-TA-
66 GCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAT
90012 TTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAATTT
131 TTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAATTT
90068 ACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTA
1 ACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTA
*
90133 GCAGAATTGGCAGCAACCGAATAAATTTACT
66 GCAGAATTGGCAGCAACCGAACAAATTTACT
90164 AAGCAATCTA
Statistics
Matches: 279, Mismatches: 1, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
184 151 0.54
185 2 0.01
186 126 0.45
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (186 bp):
ACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTA
GCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAT
TTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAATTT
Found at i:91889 original size:14 final size:14
Alignment explanation
Indices: 91870--91959 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
91860 TTGAAATGAA
91870 AATCGCAACGAGAG
1 AATCGCAACGAGAG
91884 AATCGCAACACGAGATG
1 AATCGC-A-ACGAGA-G
91901 ACAATCGCAACGAGAG
1 --AATCGCAACGAGAG
*
91917 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
91936 AATCGCAACGAGAG
1 AATCGCAACGAGAG
91950 AATCGCAACG
1 AATCGCAACG
91960 CGAAATGAAA
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
14 26 0.41
15 2 0.03
16 9 0.14
17 9 0.14
18 2 0.03
19 16 0.25
ACGTcount: A:0.43, C:0.23, G:0.24, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:91907 original size:33 final size:33
Alignment explanation
Indices: 91862--91976 Score: 203
Period size: 33 Copynumber: 3.5 Consensus size: 33
91852 TCTTTTGGTT
*
91862 GAAATGAAAATCGCAACGAGAGAATCGCAACAC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
* *
91895 GAGATGACAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
91928 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
91961 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
91977 TGCGATTTTG
Statistics
Matches: 77, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 77 1.00
ACGTcount: A:0.46, C:0.21, G:0.23, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:91908 original size:19 final size:18
Alignment explanation
Indices: 91869--91976 Score: 69
Period size: 19 Copynumber: 6.5 Consensus size: 18
91859 GTTGAAATGA
91869 AAATCGC-A-ACGAGA-G
1 AAATCGCAACACGAGATG
91884 -AATCGCAACACGAGATG
1 AAATCGCAACACGAGATG
91901 ACAATCGC-A-ACGAGA-G
1 A-AATCGCAACACGAGATG
* *
91917 -AATCGCAACGCGAAATG
1 AAATCGCAACACGAGATG
91934 AAAATCGC-A-ACGAGA-G
1 -AAATCGCAACACGAGATG
* *
91950 -AATCGCAACGCGAAATG
1 AAATCGCAACACGAGATG
91967 AAAATCGCAA
1 -AAATCGCAA
91977 TGCGATTTTG
Statistics
Matches: 72, Mismatches: 6, Indels: 26
0.69 0.06 0.25
Matches are distributed among these distances:
14 18 0.25
15 3 0.04
16 16 0.22
17 13 0.18
18 2 0.03
19 20 0.28
ACGTcount: A:0.45, C:0.22, G:0.23, T:0.09
Consensus pattern (18 bp):
AAATCGCAACACGAGATG
Found at i:91981 original size:19 final size:19
Alignment explanation
Indices: 91917--91981 Score: 77
Period size: 19 Copynumber: 3.7 Consensus size: 19
91907 GCAACGAGAG
91917 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
91936 AATCGCAA--CG--A-GAG
1 AATCGCAACGCGAAATGAA
91950 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
91969 AATCGCAATGCGA
1 AATCGCAACGCGA
91982 TTTTGGTTTC
Statistics
Matches: 38, Mismatches: 3, Indels: 10
0.75 0.06 0.20
Matches are distributed among these distances:
14 10 0.26
15 1 0.03
16 2 0.05
17 2 0.05
18 1 0.03
19 22 0.58
ACGTcount: A:0.45, C:0.22, G:0.23, T:0.11
Consensus pattern (19 bp):
AATCGCAACGCGAAATGAA
Found at i:92012 original size:14 final size:14
Alignment explanation
Indices: 91993--92047 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
91983 TTTGGTTTCG
91993 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
92007 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
92026 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
92040 CGTTGCGA
1 CGTTGCGA
92048 CAGTCATTCT
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
16 3 0.09
17 3 0.09
19 10 0.29
ACGTcount: A:0.09, C:0.25, G:0.24, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:92025 original size:33 final size:33
Alignment explanation
Indices: 91977--92047 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
91967 AAAATCGCAA
**
91977 TGCGATTTTGGTTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
92010 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
92043 TGCGA
1 TGCGA
92048 CAGTCATTCT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.08, C:0.23, G:0.25, T:0.44
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
Found at i:92055 original size:33 final size:33
Alignment explanation
Indices: 91988--92069 Score: 119
Period size: 33 Copynumber: 2.5 Consensus size: 33
91978 GCGATTTTGG
***
91988 TTTCGCGTTGCGATTCTCTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
92021 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
1 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
*
92054 TTCTCTCGTTGCGATT
1 TT-TCGCGTTGCGATT
92070 TTCATTTATC
Statistics
Matches: 44, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
33 32 0.73
34 12 0.27
ACGTcount: A:0.10, C:0.26, G:0.22, T:0.43
Consensus pattern (33 bp):
TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
Found at i:92074 original size:20 final size:20
Alignment explanation
Indices: 92000--92088 Score: 75
Period size: 20 Copynumber: 4.8 Consensus size: 20
91990 TCGCGTTGCG
92000 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
*
92020 ATT-TCGCGTTGCG------
1 ATTCTCTCGTTGCGATTTTC
***
92033 ATTCTCTCGTTGCGACAGTC
1 ATTCTCTCGTTGCGATTTTC
92053 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
*
92073 ATTTATCTCGTTGCGA
1 A-TTCTCTCGTTGCGA
92089 CTCTTCTGCA
Statistics
Matches: 55, Mismatches: 6, Indels: 15
0.72 0.08 0.20
Matches are distributed among these distances:
13 3 0.05
14 9 0.16
19 9 0.16
20 21 0.38
21 13 0.24
ACGTcount: A:0.12, C:0.25, G:0.19, T:0.44
Consensus pattern (20 bp):
ATTCTCTCGTTGCGATTTTC
Found at i:92210 original size:33 final size:33
Alignment explanation
Indices: 92168--92238 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
92158 AATACTAACT
*
92168 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
* *
92201 TGAAAATCGCAACGACAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
92234 TGAAA
1 TGAAA
92239 TCTAAGTGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.48, C:0.18, G:0.23, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGACAGAATAGCAACGCGAAA
Found at i:92472 original size:22 final size:22
Alignment explanation
Indices: 92420--92474 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 22
92410 TGGTTGTGAG
**
92420 GGATTTCACCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
* **
92442 CGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
92464 GGATTTCTTCG
1 GGATTTCTTCG
92475 CCGTAGAGAG
Statistics
Matches: 25, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.22, C:0.18, G:0.36, T:0.24
Consensus pattern (22 bp):
GGATTTCTTCGGAGATGGGGAC
Found at i:92645 original size:20 final size:20
Alignment explanation
Indices: 92620--92812 Score: 219
Period size: 20 Copynumber: 9.6 Consensus size: 20
92610 CTTTAAATAT
92620 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
92640 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
92662 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
92681 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* **
92701 CGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
92721 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
92741 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
92761 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
92781 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
92801 CGCGTTGCGATT
1 CGCGTTGCGATT
92813 ATGGAAAATC
Statistics
Matches: 146, Mismatches: 22, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
19 2 0.01
20 127 0.87
21 15 0.10
22 2 0.01
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.35
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:92807 original size:60 final size:60
Alignment explanation
Indices: 92620--92812 Score: 251
Period size: 60 Copynumber: 3.2 Consensus size: 60
92610 CTTTAAATAT
**
92620 CGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTATCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGA-TTTATGTATTCGCGTTGCGATTTACGGATA
* * *** *
92681 CGCGTTGCGATATACGGATACGCATTGCGATTTACCCATACGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
* * * ** *
92741 CACGTTGCGATTTACGGATACGCGTTGCGATTTATGTGTTCGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
92801 CGCGTTGCGATT
1 CGCGTTGCGATT
92813 ATGGAAAATC
Statistics
Matches: 111, Mismatches: 21, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
60 83 0.75
61 28 0.25
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.35
Consensus pattern (60 bp):
CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
Found at i:92893 original size:20 final size:20
Alignment explanation
Indices: 92868--92919 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
92858 AAGAATCGCG
*
92868 TTGCGATTTTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
92888 TTGCGATTCTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
92908 TTGCGATTCTGG
1 TTGCGATTCTGG
92920 GGATCGCGTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.21, C:0.13, G:0.27, T:0.38
Consensus pattern (20 bp):
TTGCGATTCTGGAAACTGAT
Found at i:93639 original size:4 final size:4
Alignment explanation
Indices: 93630--93662 Score: 66
Period size: 4 Copynumber: 8.2 Consensus size: 4
93620 TTTTTATAAC
93630 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT A
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT A
93663 TATATATATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 29 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AAAT
Found at i:93667 original size:2 final size:2
Alignment explanation
Indices: 93660--93685 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
93650 AAATAAATAA
93660 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
93686 TGCTACATGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:98275 original size:16 final size:16
Alignment explanation
Indices: 98251--98281 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
98241 TTTGAGTTTT
*
98251 ATTTGGGGGTTATGAG
1 ATTTAGGGGTTATGAG
98267 ATTTAGGGGTTATGA
1 ATTTAGGGGTTATGA
98282 AAAATTATGG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.23, C:0.00, G:0.39, T:0.39
Consensus pattern (16 bp):
ATTTAGGGGTTATGAG
Found at i:98893 original size:105 final size:105
Alignment explanation
Indices: 98744--99121 Score: 580
Period size: 105 Copynumber: 3.6 Consensus size: 105
98734 TCATTTTGTT
* * * * *
98744 GGATGAGTTCTTCTCATTATGAAATCTTCTAGAAATTTTTATTCACCTCATTCTGGGGTGAATTT
1 GGATGAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGATTCACCTCTTTCTGGGGTGAATTT
* *
98809 CAAAGGAACATGCTCTTCTCATTACGAACCTTCTCCTTTA
66 GAAAGGAACAAGCTCTTCTCATTACGAACCTTCTCCTTTA
98849 GGATGAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGATTCACCTCTTTCTGGGGTGAATTT
1 GGATGAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGATTCACCTCTTTCTGGGGTGAATTT
* *
98914 GAAAGGAACACGCTCTTGTCATTACGAACCTTCTCCTTTA
66 GAAAGGAACAAGCTCTTCTCATTACGAACCTTCTCCTTTA
* * *
98954 GGACGAGTTCTTCTCATTATGAACTCTTTTGGAAATGTTGATTCACATCTTTCTGGGGTGAATTT
1 GGATGAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGATTCACCTCTTTCTGGGGTGAATTT
*
99019 GAAAGGAAAAAGCTCTTCTCATTACGAACCTTCTCCTTTA
66 GAAAGGAACAAGCTCTTCTCATTACGAACCTTCTCCTTTA
* * * *
99059 GGATGAGTTCTTCTCATTATAAACTCTTTTGTAAATATTGATTCACCT-TCTTCT-GGGTGAATT
1 GGATGAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGATTCACCTCT-TTCTGGGGTGAATT
99122 ATAGTTGTTG
Statistics
Matches: 253, Mismatches: 19, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
104 10 0.04
105 243 0.96
ACGTcount: A:0.25, C:0.20, G:0.17, T:0.39
Consensus pattern (105 bp):
GGATGAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGATTCACCTCTTTCTGGGGTGAATTT
GAAAGGAACAAGCTCTTCTCATTACGAACCTTCTCCTTTA
Found at i:100021 original size:6 final size:6
Alignment explanation
Indices: 100010--100133 Score: 58
Period size: 6 Copynumber: 20.3 Consensus size: 6
100000 TCTCGAACCC
* * *
100010 TCTTTT TC-TTT TCATTTT TTTATTT TTTTATT TCTTTCT T-TTTT TCATTT
1 TCTTTT TCTTTT TC-TTTT TCT-TTT TCTT-TT TCTTT-T TCTTTT TCTTTT
* * * * * * **
100060 TCATTT TCATTT TCATTT TCATTT TCATTT TCATTT TCATTTT T-TCAT
1 TCTTTT TCTTTT TCTTTT TCTTTT TCTTTT TCTTTT TC-TTTT TCTTTT
*
100108 TCTTTT T-TTTT TCAATTT TCTTTT TC
1 TCTTTT TCTTTT TC-TTTT TCTTTT TC
100134 ACTTTTTCAT
Statistics
Matches: 98, Mismatches: 10, Indels: 20
0.77 0.08 0.16
Matches are distributed among these distances:
5 15 0.15
6 57 0.58
7 26 0.27
ACGTcount: A:0.11, C:0.15, G:0.00, T:0.74
Consensus pattern (6 bp):
TCTTTT
Found at i:100034 original size:8 final size:8
Alignment explanation
Indices: 100018--100060 Score: 50
Period size: 8 Copynumber: 5.2 Consensus size: 8
100008 CCTCTTTTTC
*
100018 TTTTCATT
1 TTTTTATT
100026 TTTTTATT
1 TTTTTATT
100034 TTTTTATT
1 TTTTTATT
* *
100042 TCTTTCTT
1 TTTTTATT
100050 TTTTTCATT
1 TTTTT-ATT
100059 TT
1 TT
100061 CATTTTCATT
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
8 25 0.86
9 4 0.14
ACGTcount: A:0.09, C:0.09, G:0.00, T:0.81
Consensus pattern (8 bp):
TTTTTATT
Found at i:100061 original size:18 final size:18
Alignment explanation
Indices: 100051--100102 Score: 104
Period size: 18 Copynumber: 2.9 Consensus size: 18
100041 TTCTTTCTTT
100051 TTTTCATTTTCATTTTCA
1 TTTTCATTTTCATTTTCA
100069 TTTTCATTTTCATTTTCA
1 TTTTCATTTTCATTTTCA
100087 TTTTCATTTTCATTTT
1 TTTTCATTTTCATTTT
100103 TTCATTCTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 34 1.00
ACGTcount: A:0.15, C:0.15, G:0.00, T:0.69
Consensus pattern (18 bp):
TTTTCATTTTCATTTTCA
Found at i:100066 original size:12 final size:12
Alignment explanation
Indices: 100051--100102 Score: 104
Period size: 12 Copynumber: 4.3 Consensus size: 12
100041 TTCTTTCTTT
100051 TTTTCATTTTCA
1 TTTTCATTTTCA
100063 TTTTCATTTTCA
1 TTTTCATTTTCA
100075 TTTTCATTTTCA
1 TTTTCATTTTCA
100087 TTTTCATTTTCA
1 TTTTCATTTTCA
100099 TTTT
1 TTTT
100103 TTCATTCTTT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 40 1.00
ACGTcount: A:0.15, C:0.15, G:0.00, T:0.69
Consensus pattern (12 bp):
TTTTCATTTTCA
Found at i:106925 original size:12 final size:12
Alignment explanation
Indices: 106908--106934 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
106898 TGCTGACACA
106908 TGCATGAGATTG
1 TGCATGAGATTG
106920 TGCATGAGATTG
1 TGCATGAGATTG
106932 TGC
1 TGC
106935 TTCTTGAGGT
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:0.22, C:0.11, G:0.33, T:0.33
Consensus pattern (12 bp):
TGCATGAGATTG
Found at i:109364 original size:17 final size:17
Alignment explanation
Indices: 109342--109391 Score: 54
Period size: 17 Copynumber: 3.1 Consensus size: 17
109332 AAATTCTTCT
109342 AACATTCATAGAAACCA
1 AACATTCATAGAAACCA
*
109359 AACA-T--T-GATACTCA
1 AACATTCATAGAAAC-CA
109373 AACATTCATAGAAACCA
1 AACATTCATAGAAACCA
109390 AA
1 AA
109392 ACATGAATAA
Statistics
Matches: 26, Mismatches: 2, Indels: 10
0.68 0.05 0.26
Matches are distributed among these distances:
13 4 0.15
14 7 0.27
15 1 0.04
16 1 0.04
17 9 0.35
18 4 0.15
ACGTcount: A:0.52, C:0.22, G:0.06, T:0.20
Consensus pattern (17 bp):
AACATTCATAGAAACCA
Found at i:113209 original size:23 final size:23
Alignment explanation
Indices: 113191--113251 Score: 97
Period size: 23 Copynumber: 2.7 Consensus size: 23
113181 CTCGTATAAA
113191 TGCACCGAAGTGCCACGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
*
113214 TGCACCGAAGTGCCGCGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
113237 TGCACC-ATAGTGCCA
1 TGCACCGA-AGTGCCA
113252 TATAAGATTG
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
22 1 0.03
23 34 0.97
ACGTcount: A:0.28, C:0.28, G:0.26, T:0.18
Consensus pattern (23 bp):
TGCACCGAAGTGCCACGTAGAAT
Found at i:113508 original size:30 final size:31
Alignment explanation
Indices: 113474--113534 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 31
113464 TATTGTATAG
113474 ACATATAAT-TTCCAT-ACCTTTATCACATAA
1 ACATATAATGTTCCATCA-CTTTATCACATAA
*
113504 ACATATCATGTTCCATCACTTTATCACATAA
1 ACATATAATGTTCCATCACTTTATCACATAA
113535 CTTATATAAC
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
30 8 0.29
31 19 0.68
32 1 0.04
ACGTcount: A:0.38, C:0.25, G:0.02, T:0.36
Consensus pattern (31 bp):
ACATATAATGTTCCATCACTTTATCACATAA
Found at i:120403 original size:30 final size:31
Alignment explanation
Indices: 120369--120429 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 31
120359 TATTGTATAT
120369 ACATATAAT-TTCCAT-ACCTTTATCACATAA
1 ACATATAATGTTCCATCA-CTTTATCACATAA
*
120399 ACATATCATGTTCCATCACTTTATCACATAA
1 ACATATAATGTTCCATCACTTTATCACATAA
120430 CTTATATAAC
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
30 8 0.29
31 19 0.68
32 1 0.04
ACGTcount: A:0.38, C:0.25, G:0.02, T:0.36
Consensus pattern (31 bp):
ACATATAATGTTCCATCACTTTATCACATAA
Found at i:121929 original size:2 final size:2
Alignment explanation
Indices: 121874--121913 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
121864 TATTTTTTTA
121874 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
121914 GGATGGATGG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:121935 original size:20 final size:22
Alignment explanation
Indices: 121902--121941 Score: 57
Period size: 20 Copynumber: 1.9 Consensus size: 22
121892 ATATATATAT
121902 ATATATATATATGGATGGATGG
1 ATATATATATATGGATGGATGG
*
121924 ATATAT-TA-ATGGGTGGAT
1 ATATATATATATGGATGGAT
121942 AGATGTTGCG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 9 0.53
21 2 0.12
22 6 0.35
ACGTcount: A:0.35, C:0.00, G:0.28, T:0.38
Consensus pattern (22 bp):
ATATATATATATGGATGGATGG
Found at i:131343 original size:16 final size:17
Alignment explanation
Indices: 131322--131373 Score: 58
Period size: 15 Copynumber: 3.2 Consensus size: 17
131312 TTTTCAATTT
131322 AATTACT-TAACTTTCA
1 AATTACTCTAACTTTCA
131338 AATTACTCCTAA-TTT--
1 AATTACT-CTAACTTTCA
*
131353 AATCACTCTAACTTTCA
1 AATTACTCTAACTTTCA
131370 AATT
1 AATT
131374 TAATTTTTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 9
0.73 0.05 0.22
Matches are distributed among these distances:
14 4 0.14
15 9 0.31
16 7 0.24
17 6 0.21
18 3 0.10
ACGTcount: A:0.37, C:0.21, G:0.00, T:0.42
Consensus pattern (17 bp):
AATTACTCTAACTTTCA
Found at i:132563 original size:47 final size:48
Alignment explanation
Indices: 132490--132580 Score: 107
Period size: 47 Copynumber: 1.9 Consensus size: 48
132480 TAAATTATAA
* *
132490 ATTTTACTATTTAAATTTCTTCTTATT-TCTATTTT-GTTTTTTTTTTC
1 ATTTTACTATTGAAATTTCTTCTTATTCT-TATTTTAGTTATTTTTTTC
* *
132537 ATTTTATTATTGAATTTTCTAT-TTATTCTTATTTTAGTTATTTT
1 ATTTTACTATTGAAATTTCT-TCTTATTCTTATTTTAGTTATTTT
132581 GTCTTTGGAC
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
47 28 0.76
48 9 0.24
ACGTcount: A:0.20, C:0.08, G:0.03, T:0.69
Consensus pattern (48 bp):
ATTTTACTATTGAAATTTCTTCTTATTCTTATTTTAGTTATTTTTTTC
Found at i:132744 original size:91 final size:92
Alignment explanation
Indices: 132646--132831 Score: 277
Period size: 91 Copynumber: 2.0 Consensus size: 92
132636 AAATAATATC
* * * *
132646 ATAATTTTCTTTATTTTTTTAT-TAAAAAGATCTTAGTTTTATATTCTCTCTGATTTCTTTCAAA
1 ATAATTTTCTTTA-TTTTTTATGAAAAAAAATCTTAGTTCTATACTCTCTCTGATTTCTTTCAAA
132710 TCTCAATTATAAAGGGATA-AAAAAAAG
65 TCTCAATTATAAAGGGATAGAAAAAAAG
* *
132737 ATAATTTTCTTTATTTTTTATGAAAAAAAATCTTAGTTCTATACTCTCTTTGGTTTCTTTCAAAT
1 ATAATTTTCTTTATTTTTTATGAAAAAAAATCTTAGTTCTATACTCTCTCTGATTTCTTTCAAAT
* *
132802 CTCAATTGTAAAGGGATAGAAAAGAAG
66 CTCAATTATAAAGGGATAGAAAAAAAG
132829 ATA
1 ATA
132832 GTGAGCTATA
Statistics
Matches: 85, Mismatches: 8, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
90 8 0.09
91 67 0.79
92 10 0.12
ACGTcount: A:0.36, C:0.10, G:0.10, T:0.44
Consensus pattern (92 bp):
ATAATTTTCTTTATTTTTTATGAAAAAAAATCTTAGTTCTATACTCTCTCTGATTTCTTTCAAAT
CTCAATTATAAAGGGATAGAAAAAAAG
Found at i:139021 original size:20 final size:20
Alignment explanation
Indices: 138996--139034 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
138986 GTTATAACTT
138996 TTTA-TTATATAAATAGATTG
1 TTTATTTATA-AAATAGATTG
*
139016 TTTATTTTTAAAATAGATT
1 TTTATTTATAAAATAGATT
139035 CAAATCCATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.38, C:0.00, G:0.08, T:0.54
Consensus pattern (20 bp):
TTTATTTATAAAATAGATTG
Found at i:140386 original size:114 final size:112
Alignment explanation
Indices: 140208--140431 Score: 394
Period size: 114 Copynumber: 2.0 Consensus size: 112
140198 TTATAAATAT
*
140208 GTGTGTATGTATTGGAACTATCCAGATTCTTTTTTTTGTAACTTTTGATGCAATGTCTTGTATAA
1 GTGTGTATGTATTAGAACTATCCAGATTCTTTTTTTTGTAACTTTTGATGCAATGTCTTGTATAA
* *
140273 CTTCAAGGTTACATGACTACTCAATAGATATTAGTTGCTTTCTATAC
66 CTTCAAGGTTACATGACTACTCAATACACATTAGTTGCTTTCTATAC
140320 GTGTGTATGTATTAGAACTATCCAGATTCTTTTTTTTTTGTAACTTTTGATGCAATGTCTTGTAT
1 GTGTGTATGTATTAGAACTATCCAGATTC--TTTTTTTTGTAACTTTTGATGCAATGTCTTGTAT
*
140385 AACTTCAAGGTTACATGACTACTCAATACACATTAGTTTCTTTCTAT
64 AACTTCAAGGTTACATGACTACTCAATACACATTAGTTGCTTTCTAT
140432 GTTGGTTTTC
Statistics
Matches: 106, Mismatches: 4, Indels: 2
0.95 0.04 0.02
Matches are distributed among these distances:
112 28 0.26
114 78 0.74
ACGTcount: A:0.26, C:0.15, G:0.15, T:0.45
Consensus pattern (112 bp):
GTGTGTATGTATTAGAACTATCCAGATTCTTTTTTTTGTAACTTTTGATGCAATGTCTTGTATAA
CTTCAAGGTTACATGACTACTCAATACACATTAGTTGCTTTCTATAC
Done.