Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001883.1 Hibiscus syriacus cultivar Beakdansim tig00003824_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: 94701
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.33
Found at i:2151 original size:22 final size:22
Alignment explanation
Indices: 2126--2189 Score: 76
Period size: 22 Copynumber: 2.9 Consensus size: 22
2116 AAAAAATAAA
2126 AAATGAACATATAAGGAACGCT
1 AAATGAACATATAAGGAACGCT
* * *
2148 AAATAAACACTA-AACGAATGCT
1 AAATGAACA-TATAAGGAACGCT
2170 AAATGAACATATAAGCGAAC
1 AAATGAACATATAAG-GAAC
2190 ATGTAACAAA
Statistics
Matches: 33, Mismatches: 6, Indels: 5
0.75 0.14 0.11
Matches are distributed among these distances:
21 2 0.06
22 26 0.79
23 5 0.15
ACGTcount: A:0.53, C:0.16, G:0.14, T:0.17
Consensus pattern (22 bp):
AAATGAACATATAAGGAACGCT
Found at i:3587 original size:2 final size:2
Alignment explanation
Indices: 3580--3623 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
3570 CAATTATAAA
3580 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
3622 AT
1 AT
3624 TTCTGATAAA
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:11079 original size:27 final size:25
Alignment explanation
Indices: 11019--11089 Score: 85
Period size: 26 Copynumber: 2.8 Consensus size: 25
11009 TTTTAATTTT
11019 AATATTAATTTTTTAA-A-TAAATTA
1 AATATTAA-TTTTTAATATTAAATTA
*
11043 AATATTAATTTTTAATATTATATTA
1 AATATTAATTTTTAATATTAAATTA
11068 TAGATATTAA-TTTTAATATTAA
1 -A-ATATTAATTTTTAATATTAA
11090 TTTTTTAAAT
Statistics
Matches: 41, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
23 7 0.17
24 9 0.22
25 6 0.15
26 12 0.29
27 7 0.17
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.52
Consensus pattern (25 bp):
AATATTAATTTTTAATATTAAATTA
Found at i:11088 original size:12 final size:12
Alignment explanation
Indices: 10979--11093 Score: 87
Period size: 12 Copynumber: 9.4 Consensus size: 12
10969 CTTCACAAAG
10979 ATTTT-ATATTTA
1 ATTTTAATA-TTA
10991 ATTTT-ATATT-
1 ATTTTAATATTA
* *
11001 ATATTTGATTTTA
1 AT-TTTAATATTA
11014 ATTTTAATATTA
1 ATTTTAATATTA
11026 ATTTTTTAA-A-TA
1 A--TTTTAATATTA
* *
11038 AATTAAATATTA
1 ATTTTAATATTA
11050 ATTTTTAATATTA
1 A-TTTTAATATTA
*
11063 TATTATAGATATTA
1 -ATTTTA-ATATTA
11077 ATTTTAATATTA
1 ATTTTAATATTA
11089 ATTTT
1 ATTTT
11094 TTAAATTTAT
Statistics
Matches: 84, Mismatches: 9, Indels: 20
0.74 0.08 0.18
Matches are distributed among these distances:
10 6 0.07
11 6 0.07
12 38 0.45
13 21 0.25
14 13 0.15
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (12 bp):
ATTTTAATATTA
Found at i:11105 original size:13 final size:14
Alignment explanation
Indices: 11015--11106 Score: 67
Period size: 13 Copynumber: 7.1 Consensus size: 14
11005 TTGATTTTAA
11015 TTTTAATATTAATT
1 TTTTAATATTAATT
11029 TTTTAA-A-TAA--
1 TTTTAATATTAATT
* *
11039 ATTAAATATTAA-T
1 TTTTAATATTAATT
*
11052 TTTTAATATT-ATA
1 TTTTAATATTAATT
*
11065 TTATAGATATTAA--
1 TTTTA-ATATTAATT
11078 TTTTAATATTAATT
1 TTTTAATATTAATT
*
11092 TTTTAA-ATTTATT
1 TTTTAATATTAATT
11105 TT
1 TT
11107 ATATCATATA
Statistics
Matches: 62, Mismatches: 8, Indels: 17
0.71 0.09 0.20
Matches are distributed among these distances:
10 4 0.06
11 1 0.02
12 14 0.23
13 25 0.40
14 17 0.27
15 1 0.02
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.59
Consensus pattern (14 bp):
TTTTAATATTAATT
Found at i:11138 original size:20 final size:20
Alignment explanation
Indices: 11094--11163 Score: 69
Period size: 18 Copynumber: 3.6 Consensus size: 20
11084 TATTAATTTT
11094 TTAAATTTATTTTATATCA-TA
1 TTAAA-TTATTTTATAT-ATTA
11115 -TAAATTATTTTATATATTA
1 TTAAATTATTTTATATATTA
11134 TTAAA--ATTTTATAT-TTA
1 TTAAATTATTTTATATATTA
*
11151 TTTTAATTATTTT
1 -TTAAATTATTTT
11164 GATTTAAGTT
Statistics
Matches: 43, Mismatches: 1, Indels: 11
0.78 0.02 0.20
Matches are distributed among these distances:
17 3 0.07
18 14 0.33
19 13 0.30
20 13 0.30
ACGTcount: A:0.37, C:0.01, G:0.00, T:0.61
Consensus pattern (20 bp):
TTAAATTATTTTATATATTA
Found at i:11140 original size:21 final size:21
Alignment explanation
Indices: 11094--11141 Score: 57
Period size: 19 Copynumber: 2.4 Consensus size: 21
11084 TATTAATTTT
*
11094 TTAAATTTATTTTATATCATA
1 TTAAAATTATTTTATATCATA
11115 -T-AAATTATTTTATAT-ATTA
1 TTAAAATTATTTTATATCA-TA
11134 TTAAAATT
1 TTAAAATT
11142 TTATATTTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 6
0.77 0.03 0.20
Matches are distributed among these distances:
18 1 0.04
19 15 0.65
20 2 0.09
21 5 0.22
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (21 bp):
TTAAAATTATTTTATATCATA
Found at i:11650 original size:17 final size:17
Alignment explanation
Indices: 11628--11674 Score: 94
Period size: 17 Copynumber: 2.8 Consensus size: 17
11618 GTTTAAAAAA
11628 TCAGTTTATTTTATATT
1 TCAGTTTATTTTATATT
11645 TCAGTTTATTTTATATT
1 TCAGTTTATTTTATATT
11662 TCAGTTTATTTTA
1 TCAGTTTATTTTA
11675 GCAGTCTGCA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 30 1.00
ACGTcount: A:0.23, C:0.06, G:0.06, T:0.64
Consensus pattern (17 bp):
TCAGTTTATTTTATATT
Found at i:16535 original size:23 final size:23
Alignment explanation
Indices: 16509--16560 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 23
16499 GATTAAAAAA
16509 TATTATAAATAT-TAATTATATAT
1 TATTATAAATATATAATTA-ATAT
* * *
16532 TATTATTATTATATCATTAATAT
1 TATTATAAATATATAATTAATAT
16555 TATTAT
1 TATTAT
16561 TACATTTTGT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 20 0.80
24 5 0.20
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (23 bp):
TATTATAAATATATAATTAATAT
Found at i:16541 original size:20 final size:21
Alignment explanation
Indices: 16508--16562 Score: 60
Period size: 20 Copynumber: 2.7 Consensus size: 21
16498 GGATTAAAAA
* * *
16508 ATATTATAAATATTA-ATTAT
1 ATATTATTATTATTATATCAT
16528 ATATTATTATTATTATATCAT
1 ATATTATTATTATTATATCAT
*
16549 -TAATATTATTATTA
1 ATATTATTATTATTA
16563 CATTTTGTTG
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
20 26 0.87
21 4 0.13
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.55
Consensus pattern (21 bp):
ATATTATTATTATTATATCAT
Found at i:16550 original size:17 final size:16
Alignment explanation
Indices: 16516--16560 Score: 63
Period size: 17 Copynumber: 2.7 Consensus size: 16
16506 AAATATTATA
16516 AATATTAATTATATATT
1 AATATT-ATTATATATT
*
16533 ATTATTATTATATCATT
1 AATATTATTATAT-ATT
16550 AATATTATTAT
1 AATATTATTAT
16561 TACATTTTGT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 7 0.28
17 18 0.72
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (16 bp):
AATATTATTATATATT
Found at i:16566 original size:17 final size:16
Alignment explanation
Indices: 16516--16566 Score: 57
Period size: 17 Copynumber: 3.0 Consensus size: 16
16506 AAATATTATA
*
16516 AATATTAATTATATATT
1 AATATT-ATTATACATT
*
16533 ATTATTATTATATCATT
1 AATATTATTATA-CATT
16550 AATATTATTATTACATT
1 AATATTATTA-TACATT
16567 TTGTTGCAGG
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
16 6 0.21
17 21 0.72
18 2 0.07
ACGTcount: A:0.41, C:0.04, G:0.00, T:0.55
Consensus pattern (16 bp):
AATATTATTATACATT
Found at i:21033 original size:6 final size:6
Alignment explanation
Indices: 21022--21056 Score: 52
Period size: 6 Copynumber: 5.5 Consensus size: 6
21012 ATCGATACCT
21022 TTTGCA TTTGCA TTTGCA TTTGCA TCTTTGCA TTT
1 TTTGCA TTTGCA TTTGCA TTTGCA --TTTGCA TTT
21057 TTACGTTTGT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
6 21 0.78
8 6 0.22
ACGTcount: A:0.14, C:0.17, G:0.14, T:0.54
Consensus pattern (6 bp):
TTTGCA
Found at i:26162 original size:53 final size:54
Alignment explanation
Indices: 26079--26220 Score: 137
Period size: 54 Copynumber: 2.6 Consensus size: 54
26069 TGTGTTTTTC
* * * * *
26079 AGAAACTAAGTCCGATTTTTTAGAAGTTTCTTGATCA-TTTCAAATGA-GTTTTCAG
1 AGAAACTAAGT-CTAATTTTCAAAAGTTTCTTGATCATTTTCAAAT-ATGTTTT-AA
* *
26134 AGAAA-TAAGTCTAATTTTCAAAAGTTTCTCGATGATTTTCAAATATGTTTTAA
1 AGAAACTAAGTCTAATTTTCAAAAGTTTCTTGATCATTTTCAAATATGTTTTAA
* * **
26187 AGAAACTAAGTTTGATTTTCGGAAGTTTCTTGAT
1 AGAAACTAAGTCTAATTTTCAAAAGTTTCTTGAT
26221 GAATTTCGAA
Statistics
Matches: 72, Mismatches: 12, Indels: 7
0.79 0.13 0.08
Matches are distributed among these distances:
53 26 0.36
54 41 0.57
55 5 0.07
ACGTcount: A:0.33, C:0.11, G:0.15, T:0.41
Consensus pattern (54 bp):
AGAAACTAAGTCTAATTTTCAAAAGTTTCTTGATCATTTTCAAATATGTTTTAA
Found at i:26222 original size:54 final size:53
Alignment explanation
Indices: 26095--26227 Score: 144
Period size: 54 Copynumber: 2.5 Consensus size: 53
26085 TAAGTCCGAT
* * *
26095 TTTTTAGAAGTTTCTTGATCATTTCAAATGAGTTTTCAGAGAAATAAGTCTAA
1 TTTTCAGAAGTTTCTTGATGATTTCAAATGAGTTTTCAAAGAAATAAGTCTAA
* * * *
26148 TTTTCAAAAGTTTCTCGATGATTTTCAAAT-ATGTTTT-AAAGAAACTAAGTTTGA
1 TTTTCAGAAGTTTCTTGATGA-TTTCAAATGA-GTTTTCAAAGAAA-TAAGTCTAA
*
26202 TTTTCGGAAGTTTCTTGATGAATTTC
1 TTTTCAGAAGTTTCTTGATG-ATTTC
26228 GAAGAAATTA
Statistics
Matches: 66, Mismatches: 10, Indels: 7
0.80 0.12 0.08
Matches are distributed among these distances:
53 24 0.36
54 41 0.62
55 1 0.02
ACGTcount: A:0.32, C:0.10, G:0.15, T:0.44
Consensus pattern (53 bp):
TTTTCAGAAGTTTCTTGATGATTTCAAATGAGTTTTCAAAGAAATAAGTCTAA
Found at i:26352 original size:90 final size:92
Alignment explanation
Indices: 26249--26443 Score: 333
Period size: 91 Copynumber: 2.2 Consensus size: 92
26239 CCCTAATTTT
**
26249 TAGGATGTTTTCAAATGAGATTTAAGAAACTAAGCCTTC-GGGGGTTTCTTGATTTGTAAGTTTT
1 TAGGATGTTTTCAAATGAGATTTAAGAAACTAAGCCTTCAGGGGGTTTCTTGATTTGTAAGTCCT
* *
26313 TCGGGCCATTCATAAGACCTTCAGTGC
66 TCGGGCAATCCATAAGACCTTCAGTGC
26340 -AGGATGTTTTCAAATGAGATTTAAGAAACTAAGCCTTCAGGGGGTTTCTTGATTTGTAAGTCCT
1 TAGGATGTTTTCAAATGAGATTTAAGAAACTAAGCCTTCAGGGGGTTTCTTGATTTGTAAGTCCT
26404 TCGGGCAATCCATAAGACCTTCAGTGC
66 TCGGGCAATCCATAAGACCTTCAGTGC
26431 TA-GATGTTTTCAA
1 TAGGATGTTTTCAA
26444 TATTTCTGTT
Statistics
Matches: 98, Mismatches: 4, Indels: 4
0.92 0.04 0.04
Matches are distributed among these distances:
90 38 0.39
91 59 0.60
92 1 0.01
ACGTcount: A:0.27, C:0.16, G:0.23, T:0.35
Consensus pattern (92 bp):
TAGGATGTTTTCAAATGAGATTTAAGAAACTAAGCCTTCAGGGGGTTTCTTGATTTGTAAGTCCT
TCGGGCAATCCATAAGACCTTCAGTGC
Found at i:26699 original size:136 final size:136
Alignment explanation
Indices: 26455--26805 Score: 560
Period size: 136 Copynumber: 2.6 Consensus size: 136
26445 ATTTCTGTTG
* * *
26455 CTCGATTCACGATATTTTGAATCAGTGACGACTCGCTTG-AGGAATTGACATTTCCAATGGAGAG
1 CTCGATTCACGATATTTCGAATCAGTGACGTCTCGCTTGAAGG-ATTGACATTTTCAATGGAGAG
*
26519 TTTATAATGAGAAGAACTCATCCGAAAGAGGGAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAA
65 TTCATAATGAGAAGAACTCATCCGAAAGAGGGAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAA
26584 CCTATCA
130 CCTATCA
* *
26591 CTCGATTCACGACATTTCGAATCAGTGACGTCTCGCTTGAACGATTGACATTTTCAATGGAGAGT
1 CTCGATTCACGATATTTCGAATCAGTGACGTCTCGCTTGAAGGATTGACATTTTCAATGGAGAGT
* * * * *
26656 TCATAGTGAGAAGAACTCATCTGACAGAGGGAGAAGAAGTTCATAATGAGAAGAGTTTGTTCGAC
66 TCATAATGAGAAGAACTCATCCGAAAGAGGGAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAAC
26721 CTATCA
131 CTATCA
* * *
26727 CTCGATTCACGATATTTCGAATCAGTGACGTCTCGTTTGAGGGATCGACATTTTCAATGGAGAGT
1 CTCGATTCACGATATTTCGAATCAGTGACGTCTCGCTTGAAGGATTGACATTTTCAATGGAGAGT
26792 TCATAATGAGAAGA
66 TCATAATGAGAAGA
26806 GCTTGTTCGA
Statistics
Matches: 197, Mismatches: 17, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
136 195 0.99
137 2 0.01
ACGTcount: A:0.32, C:0.17, G:0.23, T:0.28
Consensus pattern (136 bp):
CTCGATTCACGATATTTCGAATCAGTGACGTCTCGCTTGAAGGATTGACATTTTCAATGGAGAGT
TCATAATGAGAAGAACTCATCCGAAAGAGGGAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAAC
CTATCA
Found at i:26863 original size:96 final size:96
Alignment explanation
Indices: 26693--26901 Score: 337
Period size: 96 Copynumber: 2.2 Consensus size: 96
26683 AGGGAGAAGA
* * *
26693 AGTTCATAATGAGAAGAGTTTGTTCGACCTATCACTCGATTCACGATATTTCGAATCAGTGACGT
1 AGTTCATAATGAGAAGAGCTTGTTCGACCTATCACTCGATTCACGACATTTCGAATCAGTGACGC
* *
26758 CTCGTTTGAGGGATCGACATTTTCAATGGAG
66 CTCGCTTGAGGGATCGACATTTCCAATGGAG
* *
26789 AGTTCATAATGAGAAGAGCTTGTTCGATCTATCACTCTATTCACGACATTTCGAATCAGTGACGC
1 AGTTCATAATGAGAAGAGCTTGTTCGACCTATCACTCGATTCACGACATTTCGAATCAGTGACGC
* *
26854 CTCGCTTGAGGGATTGACATTTCCAATTGAG
66 CTCGCTTGAGGGATCGACATTTCCAATGGAG
26885 AGTTCATAATGAGAAGA
1 AGTTCATAATGAGAAGA
26902 ACTCATCCGA
Statistics
Matches: 104, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
96 104 1.00
ACGTcount: A:0.29, C:0.18, G:0.22, T:0.31
Consensus pattern (96 bp):
AGTTCATAATGAGAAGAGCTTGTTCGACCTATCACTCGATTCACGACATTTCGAATCAGTGACGC
CTCGCTTGAGGGATCGACATTTCCAATGGAG
Found at i:26963 original size:232 final size:232
Alignment explanation
Indices: 26557--27037 Score: 782
Period size: 232 Copynumber: 2.1 Consensus size: 232
26547 AGGGAGAAGA
*
26557 AGTTCATAATGAGAAGAGCTTGTTCAACCTATCACTCGATTCACGACATTTCGAATCAGTGACGT
1 AGTTCATAATGAGAAGAGCTTGTTCAACCTATCACTCGATTCACGACATTTCGAATCAGTGACGC
* * *
26622 CTCGCTTGAACGATTGACATTTTCAATGGAGAGTTCATAGTGAGAAGAACTCATCTGACAGAGGG
66 CTCGCTTGAACGATTGACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGACAGAGGG
** *
26687 AGAAGAAGTTCATAATGAGAAGAGTTTGTTCGACCTATCACTCGATTCACGATATTTCGAATCAG
131 AGAAGAAGTTCATAATGAGAAGAACTTGTTCGACCTATCACTCGATTCACGACATTTCGAATCAG
* * *
26752 TGACGTCTCGTTTGAGGGATCGACATTTTCAATGGAG
196 TGACGCCTCGCTTGAGGGATCGACATTTCCAATGGAG
* * *
26789 AGTTCATAATGAGAAGAGCTTGTTCGATCTATCACTCTATTCACGACATTTCGAATCAGTGACGC
1 AGTTCATAATGAGAAGAGCTTGTTCAACCTATCACTCGATTCACGACATTTCGAATCAGTGACGC
** *
26854 CTCGCTTGAGGGATTGACATTTCCAATTGAGAGTTCATAATGAGAAGAACTCATCCGACAGAGGG
66 CTCGCTTGAACGATTGACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGACAGAGGG
* * *
26919 AGAAGAAGTTCATAATGAGAAGAACTTGTTCTACCTATCACTCGATTCACGGCATTTTGAATCAG
131 AGAAGAAGTTCATAATGAGAAGAACTTGTTCGACCTATCACTCGATTCACGACATTTCGAATCAG
*
26984 TGACGCCTCGCTTGAGGGATTGACATTTCCAATGGAG
196 TGACGCCTCGCTTGAGGGATCGACATTTCCAATGGAG
27021 AGTTCATAATGAGAAGA
1 AGTTCATAATGAGAAGA
27038 ACTCATCTGA
Statistics
Matches: 229, Mismatches: 20, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
232 229 1.00
ACGTcount: A:0.31, C:0.19, G:0.23, T:0.28
Consensus pattern (232 bp):
AGTTCATAATGAGAAGAGCTTGTTCAACCTATCACTCGATTCACGACATTTCGAATCAGTGACGC
CTCGCTTGAACGATTGACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGACAGAGGG
AGAAGAAGTTCATAATGAGAAGAACTTGTTCGACCTATCACTCGATTCACGACATTTCGAATCAG
TGACGCCTCGCTTGAGGGATCGACATTTCCAATGGAG
Found at i:27033 original size:136 final size:136
Alignment explanation
Indices: 26789--27217 Score: 654
Period size: 136 Copynumber: 3.2 Consensus size: 136
26779 TTCAATGGAG
* * * * *
26789 AGTTCATAATGAGAAGAGCTTGTTCGATCTATCACTCTATTCACGACATTTCGAATCAGTGACGC
1 AGTTCATAATGAGAAGAACTTGTTCGACCTATCACTCAATTCACGGCATTTTGAATCAGTGACGC
*
26854 CTCGCTTGAGGGATTGACATTTCCAATTGAGAGTTCATAATGAGAAGAACTCATCCGACAGAGGG
66 CTCGCTTGAGGGATTGACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGACAGAGGG
26919 AGAAGA
131 AGAAGA
* *
26925 AGTTCATAATGAGAAGAACTTGTTCTACCTATCACTCGATTCACGGCATTTTGAATCAGTGACGC
1 AGTTCATAATGAGAAGAACTTGTTCGACCTATCACTCAATTCACGGCATTTTGAATCAGTGACGC
*
26990 CTCGCTTGAGGGATTGACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCTGACAGAGGG
66 CTCGCTTGAGGGATTGACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGACAGAGGG
*
27055 GGAAGA
131 AGAAGA
*
27061 AGTTCATAATGAGTAA-AGA-TTGTTCGACCTATCACTCAATTCATGGCATTTTGAATCAGTGAC
1 AGTTCATAATGAG-AAGA-ACTTGTTCGACCTATCACTCAATTCACGGCATTTTGAATCAGTGAC
** * *
27124 ATCTCACTTGAGGGATTGACATTTCCAATGAAGAGTTCATAATGAGAAGAACTCATCC-A-A-AG
64 GCCTCGCTTGAGGGATTGACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGACAGAG
*
27186 AGA-AAGA
129 GGAGAAGA
27193 AGTTCATAATGAGAAGAACTTGTTC
1 AGTTCATAATGAGAAGAACTTGTTC
27218 AATCCAACAC
Statistics
Matches: 270, Mismatches: 19, Indels: 12
0.90 0.06 0.04
Matches are distributed among these distances:
131 3 0.01
132 24 0.09
133 3 0.01
134 1 0.00
135 1 0.00
136 235 0.87
137 3 0.01
ACGTcount: A:0.33, C:0.18, G:0.22, T:0.27
Consensus pattern (136 bp):
AGTTCATAATGAGAAGAACTTGTTCGACCTATCACTCAATTCACGGCATTTTGAATCAGTGACGC
CTCGCTTGAGGGATTGACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGACAGAGGG
AGAAGA
Found at i:27137 original size:368 final size:368
Alignment explanation
Indices: 26459--27173 Score: 1153
Period size: 368 Copynumber: 1.9 Consensus size: 368
26449 CTGTTGCTCG
* * *
26459 ATTCACGATATTTTGAATCAGTGACGACTCGCTTGAGGAATTGACATTTCCAATGGAGAGTTTAT
1 ATTCACGACATTTCGAATCAGTGACGACTCGCTTGAGGAATTGACATTTCCAATGGAGAGTTCAT
*
26524 AATGAGAAGAACTCATCCGAAAGAGGGAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTAT
66 AATGAGAAGAACTCATCCGAAAGAGGGAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTAT
* *
26589 CACTCGATTCACGACATTTCGAATCAGTGACGTCTCGCTTGAACGATTGACATTTTCAATGGAGA
131 CACTCGATTCACGACATTTCGAATCAGTGACGCCTCGCTTGAACGATTGACATTTCCAATGGAGA
* *
26654 GTTCATAGTGAGAAGAACTCATCTGACAGAGGGAGAAGAAGTTCATAATGAGAAGAGTTTGTTCG
196 GTTCATAATGAGAAGAACTCATCTGACAGAGGGAGAAGAAGTTCATAATGAGAAGAGATTGTTCG
* * * ** *
26719 ACCTATCACTCGATTCACGATATTTCGAATCAGTGACGTCTCGTTTGAGGGATCGACATTTTCAA
261 ACCTATCACTCAATTCACGACATTTCGAATCAGTGACATCTCACTTGAGGGATCGACATTTCCAA
*
26784 TGGAGAGTTCATAATGAGAAGAGCTTGTTCGATCTATCACTCT
326 TGAAGAGTTCATAATGAGAAGAGCTTGTTCGATCTATCACTCT
* * *
26827 ATTCACGACATTTCGAATCAGTGACGCCTCGCTTGAGGGATTGACATTTCCAATTGAGAGTTCAT
1 ATTCACGACATTTCGAATCAGTGACGACTCGCTTGAGGAATTGACATTTCCAATGGAGAGTTCAT
* *
26892 AATGAGAAGAACTCATCCGACAGAGGGAGAAGAAGTTCATAATGAGAAGAACTTGTTCTACCTAT
66 AATGAGAAGAACTCATCCGAAAGAGGGAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTAT
* * **
26957 CACTCGATTCACGGCATTTTGAATCAGTGACGCCTCGCTTGAGGGATTGACATTTCCAATGGAGA
131 CACTCGATTCACGACATTTCGAATCAGTGACGCCTCGCTTGAACGATTGACATTTCCAATGGAGA
*
27022 GTTCATAATGAGAAGAACTCATCTGACAGAGGGGGAAGAAGTTCATAATGAGTAA-AGATTGTTC
196 GTTCATAATGAGAAGAACTCATCTGACAGAGGGAGAAGAAGTTCATAATGAG-AAGAGATTGTTC
* * * *
27086 GACCTATCACTCAATTCATGGCATTTTGAATCAGTGACATCTCACTTGAGGGATTGACATTTCCA
260 GACCTATCACTCAATTCACGACATTTCGAATCAGTGACATCTCACTTGAGGGATCGACATTTCCA
27151 ATGAAGAGTTCATAATGAGAAGA
325 ATGAAGAGTTCATAATGAGAAGA
27174 ACTCATCCAA
Statistics
Matches: 317, Mismatches: 29, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
368 315 0.99
369 2 0.01
ACGTcount: A:0.32, C:0.17, G:0.23, T:0.28
Consensus pattern (368 bp):
ATTCACGACATTTCGAATCAGTGACGACTCGCTTGAGGAATTGACATTTCCAATGGAGAGTTCAT
AATGAGAAGAACTCATCCGAAAGAGGGAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTAT
CACTCGATTCACGACATTTCGAATCAGTGACGCCTCGCTTGAACGATTGACATTTCCAATGGAGA
GTTCATAATGAGAAGAACTCATCTGACAGAGGGAGAAGAAGTTCATAATGAGAAGAGATTGTTCG
ACCTATCACTCAATTCACGACATTTCGAATCAGTGACATCTCACTTGAGGGATCGACATTTCCAA
TGAAGAGTTCATAATGAGAAGAGCTTGTTCGATCTATCACTCT
Found at i:27206 original size:18 final size:18
Alignment explanation
Indices: 27157--27207 Score: 52
Period size: 18 Copynumber: 2.8 Consensus size: 18
27147 TCCAATGAAG
27157 AGTTCATAATGAG-AAGA
1 AGTTCATAATGAGAAAGA
* *
27174 A-CTCATCCAAAGAGAAAGA
1 AGTTCAT--AATGAGAAAGA
27193 AGTTCATAATGAGAA
1 AGTTCATAATGAGAA
27208 GAACTTGTTC
Statistics
Matches: 26, Mismatches: 4, Indels: 7
0.70 0.11 0.19
Matches are distributed among these distances:
16 4 0.15
17 1 0.04
18 12 0.46
19 5 0.19
20 4 0.15
ACGTcount: A:0.49, C:0.12, G:0.20, T:0.20
Consensus pattern (18 bp):
AGTTCATAATGAGAAAGA
Found at i:27407 original size:3 final size:3
Alignment explanation
Indices: 27399--27437 Score: 51
Period size: 3 Copynumber: 12.7 Consensus size: 3
27389 ATTAATGATA
* *
27399 TAT TAT TAT TAT TAT TAT ATAT CAT TAA TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT -TAT TAT TAT TAT TAT TAT TA
27438 CATTTTATTG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
3 28 0.90
4 3 0.10
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (3 bp):
TAT
Found at i:27420 original size:19 final size:19
Alignment explanation
Indices: 27386--27435 Score: 64
Period size: 19 Copynumber: 2.6 Consensus size: 19
27376 AAATATTATA
* *
27386 AATATTAATGATATATTATT
1 AATATT-ATTATATATCATT
*
27406 ATTATTATTATATATCATT
1 AATATTATTATATATCATT
27425 AATATTATTAT
1 AATATTATTAT
27436 TACATTTTAT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
19 21 0.81
20 5 0.19
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.54
Consensus pattern (19 bp):
AATATTATTATATATCATT
Found at i:29435 original size:8 final size:8
Alignment explanation
Indices: 29422--29460 Score: 51
Period size: 8 Copynumber: 4.8 Consensus size: 8
29412 ATGTGAATAT
29422 TTTTATTA
1 TTTTATTA
29430 TTTTATTA
1 TTTTATTA
**
29438 TTCAATATA
1 TTTTAT-TA
29447 TTTTATTA
1 TTTTATTA
29455 TTTTAT
1 TTTTAT
29461 GTAAAGGATA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
8 20 0.77
9 6 0.23
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.69
Consensus pattern (8 bp):
TTTTATTA
Found at i:32000 original size:25 final size:25
Alignment explanation
Indices: 31972--32022 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
31962 AAGAATGGAC
31972 ATTACAGGAATATGATTGTAGAAAG
1 ATTACAGGAATATGATTGTAGAAAG
31997 ATTACAGGAATATGATTGTAGAAAG
1 ATTACAGGAATATGATTGTAGAAAG
32022 A
1 A
32023 ACAAAAAAGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.45, C:0.04, G:0.24, T:0.27
Consensus pattern (25 bp):
ATTACAGGAATATGATTGTAGAAAG
Found at i:36561 original size:29 final size:29
Alignment explanation
Indices: 36527--36585 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
36517 CCTAAATTAA
36527 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
36556 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
36585 T
1 T
36586 AGGTGAAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.24, C:0.14, G:0.14, T:0.49
Consensus pattern (29 bp):
TTTGATGTCATTGCTTACATCAATTTAGT
Found at i:41217 original size:29 final size:29
Alignment explanation
Indices: 41183--41241 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
41173 CCTAAATTAA
*
41183 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATATCATTGCTTACATCAATTTAGT
41212 TTTGATATCATTGCTTACATCAATTTAGT
1 TTTGATATCATTGCTTACATCAATTTAGT
41241 T
1 T
41242 AGGTGAAAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.25, C:0.14, G:0.12, T:0.49
Consensus pattern (29 bp):
TTTGATATCATTGCTTACATCAATTTAGT
Found at i:43153 original size:3 final size:3
Alignment explanation
Indices: 43145--43199 Score: 103
Period size: 3 Copynumber: 18.7 Consensus size: 3
43135 TTCAAAATTA
43145 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
43193 A-T ATT AT
1 ATT ATT AT
43200 AGTACATATT
Statistics
Matches: 51, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.04
3 49 0.96
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:43574 original size:39 final size:40
Alignment explanation
Indices: 43501--43576 Score: 136
Period size: 40 Copynumber: 1.9 Consensus size: 40
43491 AAAAAGAAGA
43501 TTTTTTTGTTAAAAATAACAATTGAAGTTAACATAGGCAT
1 TTTTTTTGTTAAAAATAACAATTGAAGTTAACATAGGCAT
*
43541 TTTTTTTGTTAAAAATAAGAATTGAAGTT-ACATAGG
1 TTTTTTTGTTAAAAATAACAATTGAAGTTAACATAGG
43577 TATTCCATAG
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
39 7 0.20
40 28 0.80
ACGTcount: A:0.39, C:0.05, G:0.14, T:0.41
Consensus pattern (40 bp):
TTTTTTTGTTAAAAATAACAATTGAAGTTAACATAGGCAT
Found at i:43593 original size:40 final size:40
Alignment explanation
Indices: 43506--43594 Score: 101
Period size: 40 Copynumber: 2.2 Consensus size: 40
43496 GAAGATTTTT
* **
43506 TTGTTAAAAATAACAATTGAAGTTAACATAGGCATTTTTT
1 TTGTTAAAAATAACAATTGAAGTTAACATAGGCATTATAG
* *
43546 TTGTTAAAAATAAGAATTGAAGTT-ACATAGGTATTCCATAG
1 TTGTTAAAAATAACAATTGAAGTTAACATAGGCATT--ATAG
43587 TT-TTAAAA
1 TTGTTAAAA
43595 GAGGGTAAGA
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
39 10 0.24
40 29 0.69
41 3 0.07
ACGTcount: A:0.42, C:0.07, G:0.13, T:0.38
Consensus pattern (40 bp):
TTGTTAAAAATAACAATTGAAGTTAACATAGGCATTATAG
Found at i:44252 original size:28 final size:28
Alignment explanation
Indices: 44212--44284 Score: 128
Period size: 28 Copynumber: 2.6 Consensus size: 28
44202 ATTTTGAATT
*
44212 TGTGAAATTTTTACCTATCTTTATAATA
1 TGTGATATTTTTACCTATCTTTATAATA
*
44240 TGTGATATTTTTACCTATCTTTATAATT
1 TGTGATATTTTTACCTATCTTTATAATA
44268 TGTGATATTTTTACCTA
1 TGTGATATTTTTACCTA
44285 AATTTTGTTA
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 43 1.00
ACGTcount: A:0.27, C:0.11, G:0.08, T:0.53
Consensus pattern (28 bp):
TGTGATATTTTTACCTATCTTTATAATA
Found at i:44522 original size:31 final size:32
Alignment explanation
Indices: 44482--44554 Score: 114
Period size: 31 Copynumber: 2.3 Consensus size: 32
44472 TTATTTTGAC
44482 CACTCAACTTTAC-TTTTAATTTTGTTTTAGT
1 CACTCAACTTTACTTTTTAATTTTGTTTTAGT
* *
44513 CACTAAAC-TTACTTTTTATTTTTGTTTTAGT
1 CACTCAACTTTACTTTTTAATTTTGTTTTAGT
44544 CACTCAACTTT
1 CACTCAACTTT
44555 TAAAAAAAAT
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
30 4 0.11
31 31 0.84
32 2 0.05
ACGTcount: A:0.23, C:0.18, G:0.05, T:0.53
Consensus pattern (32 bp):
CACTCAACTTTACTTTTTAATTTTGTTTTAGT
Found at i:45271 original size:16 final size:18
Alignment explanation
Indices: 45250--45294 Score: 58
Period size: 20 Copynumber: 2.5 Consensus size: 18
45240 AACATTCTCA
45250 GTAATCTTATT-CC-CTG
1 GTAATCTTATTCCCACTG
45266 GTAATCTTACATTCCCACTG
1 GTAATCTT--ATTCCCACTG
45286 GTAATCTTA
1 GTAATCTTA
45295 CATTCCGTGA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
16 8 0.32
18 4 0.16
19 2 0.08
20 11 0.44
ACGTcount: A:0.24, C:0.24, G:0.11, T:0.40
Consensus pattern (18 bp):
GTAATCTTATTCCCACTG
Found at i:45288 original size:20 final size:20
Alignment explanation
Indices: 45263--45300 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
45253 ATCTTATTCC
45263 CTGGTAATCTTACATTCCCA
1 CTGGTAATCTTACATTCCCA
45283 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
45301 GTGAACCAAA
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:0.24, C:0.29, G:0.11, T:0.37
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCA
Found at i:46016 original size:20 final size:21
Alignment explanation
Indices: 45978--46019 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
45968 CTTTTAAATA
* *
45978 TTATTTTAAAAATTGATTTTT
1 TTATTTGAAAAAATGATTTTT
45999 TTATTTGAAAAAAT-ATTTTT
1 TTATTTGAAAAAATGATTTTT
46019 T
1 T
46020 ATAAATATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 7 0.37
21 12 0.63
ACGTcount: A:0.36, C:0.00, G:0.05, T:0.60
Consensus pattern (21 bp):
TTATTTGAAAAAATGATTTTT
Found at i:51405 original size:26 final size:26
Alignment explanation
Indices: 51349--51413 Score: 69
Period size: 26 Copynumber: 2.5 Consensus size: 26
51339 TTCATCACTC
* *
51349 ATAAATTTTTATAAGTTTATATCTAT
1 ATAAAATTTTATAAATTTATATCTAT
* *
51375 TTAAAATTTTATAAATTTATCCTCTA-
1 ATAAAATTTTATAAATTTAT-ATCTAT
*
51401 ATAAAAATTTATA
1 ATAAAATTTTATA
51414 TGTATGTTCC
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
26 28 0.88
27 4 0.12
ACGTcount: A:0.43, C:0.06, G:0.02, T:0.49
Consensus pattern (26 bp):
ATAAAATTTTATAAATTTATATCTAT
Found at i:52091 original size:12 final size:12
Alignment explanation
Indices: 52074--52098 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
52064 AATGCACTCC
52074 CAAGATTAATTG
1 CAAGATTAATTG
52086 CAAGATTAATTG
1 CAAGATTAATTG
52098 C
1 C
52099 TCAAATAGGG
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:0.40, C:0.12, G:0.16, T:0.32
Consensus pattern (12 bp):
CAAGATTAATTG
Found at i:52171 original size:29 final size:29
Alignment explanation
Indices: 52129--52185 Score: 105
Period size: 29 Copynumber: 2.0 Consensus size: 29
52119 AGTGTTGGCC
*
52129 GTAGGTCGCCATGCACTCCGGGCGACCTT
1 GTAGGTCGCCATGCACTCCAGGCGACCTT
52158 GTAGGTCGCCATGCACTCCAGGCGACCT
1 GTAGGTCGCCATGCACTCCAGGCGACCT
52186 ACCCTTGCTC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.16, C:0.35, G:0.30, T:0.19
Consensus pattern (29 bp):
GTAGGTCGCCATGCACTCCAGGCGACCTT
Found at i:52326 original size:29 final size:29
Alignment explanation
Indices: 52244--52328 Score: 134
Period size: 29 Copynumber: 2.9 Consensus size: 29
52234 TCCCAACACA
* * *
52244 TAGGTCGCCATGCCCTCAAGGCGAACTTG
1 TAGGTCGCCATGCACTCCAGGCGACCTTG
*
52273 TAGGTCGCCATGCACTCCGGGCGACCTTG
1 TAGGTCGCCATGCACTCCAGGCGACCTTG
52302 TAGGTCGCCATGCACTCCAGGCGACCT
1 TAGGTCGCCATGCACTCCAGGCGACCT
52329 ACCCTTGCTC
Statistics
Matches: 51, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 51 1.00
ACGTcount: A:0.18, C:0.34, G:0.28, T:0.20
Consensus pattern (29 bp):
TAGGTCGCCATGCACTCCAGGCGACCTTG
Found at i:52387 original size:143 final size:143
Alignment explanation
Indices: 52129--52442 Score: 619
Period size: 143 Copynumber: 2.2 Consensus size: 143
52119 AGTGTTGGCC
52129 GTAGGTCGCCATGCACTCCGGGCGACCTTGTAGGTCGCCATGCACTCCAGGCGACCTACCCTTGC
1 GTAGGTCGCCATGCACTCCGGGCGACCTTGTAGGTCGCCATGCACTCCAGGCGACCTACCCTTGC
52194 TCAAACAGAGAGAATGAATGTGTTGCATGGCACATGCACATCCCAACACATAGGTCGCCATGCCC
66 TCAAACAGAGAGAATGAATGTGTTGCATGGCACATGCACATCCCAACACATAGGTCGCCATGCCC
52259 TCAAGGCGAACTT
131 TCAAGGCGAACTT
52272 GTAGGTCGCCATGCACTCCGGGCGACCTTGTAGGTCGCCATGCACTCCAGGCGACCTACCCTTGC
1 GTAGGTCGCCATGCACTCCGGGCGACCTTGTAGGTCGCCATGCACTCCAGGCGACCTACCCTTGC
52337 TCAAACAGAGAGAATGAATGTGTTGCATGGCACATGCACATCCCAACACATAGGTCGCCATGCCC
66 TCAAACAGAGAGAATGAATGTGTTGCATGGCACATGCACATCCCAACACATAGGTCGCCATGCCC
*
52402 TCAAGGCGACCTT
131 TCAAGGCGAACTT
52415 GTAGGTCGCCATGCACTCCGGGCGACCT
1 GTAGGTCGCCATGCACTCCGGGCGACCT
52443 ACCCTAGTCG
Statistics
Matches: 170, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
143 170 1.00
ACGTcount: A:0.23, C:0.32, G:0.25, T:0.19
Consensus pattern (143 bp):
GTAGGTCGCCATGCACTCCGGGCGACCTTGTAGGTCGCCATGCACTCCAGGCGACCTACCCTTGC
TCAAACAGAGAGAATGAATGTGTTGCATGGCACATGCACATCCCAACACATAGGTCGCCATGCCC
TCAAGGCGAACTT
Found at i:52420 original size:29 final size:29
Alignment explanation
Indices: 52387--52442 Score: 85
Period size: 29 Copynumber: 1.9 Consensus size: 29
52377 TCCCAACACA
*
52387 TAGGTCGCCATGCCCTCAAGGCGACCTTG
1 TAGGTCGCCATGCACTCAAGGCGACCTTG
**
52416 TAGGTCGCCATGCACTCCGGGCGACCT
1 TAGGTCGCCATGCACTCAAGGCGACCT
52443 ACCCTAGTCG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.16, C:0.36, G:0.29, T:0.20
Consensus pattern (29 bp):
TAGGTCGCCATGCACTCAAGGCGACCTTG
Found at i:52500 original size:14 final size:14
Alignment explanation
Indices: 52478--52510 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
52468 CCTCGGATAG
*
52478 CTCGTTCGGATGGC
1 CTCGGTCGGATGGC
52492 CTCGGTCGGATGGC
1 CTCGGTCGGATGGC
52506 CTCGG
1 CTCGG
52511 ATGCTCTCGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.06, C:0.30, G:0.39, T:0.24
Consensus pattern (14 bp):
CTCGGTCGGATGGC
Found at i:52510 original size:10 final size:10
Alignment explanation
Indices: 52497--52573 Score: 88
Period size: 10 Copynumber: 7.7 Consensus size: 10
52487 ATGGCCTCGG
52497 TCGGATGGCC
1 TCGGATGGCC
52507 TCGGAT-GCTC
1 TCGGATGGC-C
52517 TCGGATGGCC
1 TCGGATGGCC
52527 TCGGAT-GCTC
1 TCGGATGGC-C
52537 TCGGATGGCC
1 TCGGATGGCC
*
52547 TCAGAT-GCTC
1 TCGGATGGC-C
52557 TCGGATGGCC
1 TCGGATGGCC
*
52567 TCAGATG
1 TCGGATG
52574 CTCAGCGTGT
Statistics
Matches: 58, Mismatches: 3, Indels: 12
0.79 0.04 0.16
Matches are distributed among these distances:
9 6 0.10
10 46 0.79
11 6 0.10
ACGTcount: A:0.13, C:0.29, G:0.34, T:0.25
Consensus pattern (10 bp):
TCGGATGGCC
Found at i:52522 original size:20 final size:20
Alignment explanation
Indices: 52497--52576 Score: 142
Period size: 20 Copynumber: 4.0 Consensus size: 20
52487 ATGGCCTCGG
*
52497 TCGGATGGCCTCGGATGCTC
1 TCGGATGGCCTCAGATGCTC
*
52517 TCGGATGGCCTCGGATGCTC
1 TCGGATGGCCTCAGATGCTC
52537 TCGGATGGCCTCAGATGCTC
1 TCGGATGGCCTCAGATGCTC
52557 TCGGATGGCCTCAGATGCTC
1 TCGGATGGCCTCAGATGCTC
52577 AGCGTGTTGG
Statistics
Matches: 59, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
20 59 1.00
ACGTcount: A:0.12, C:0.30, G:0.33, T:0.25
Consensus pattern (20 bp):
TCGGATGGCCTCAGATGCTC
Found at i:54081 original size:21 final size:22
Alignment explanation
Indices: 54055--54112 Score: 64
Period size: 21 Copynumber: 2.6 Consensus size: 22
54045 ATTTGAGGAC
54055 TTATTTATTTTTAAAA-ATAAA
1 TTATTTATTTTTAAAATATAAA
**
54076 TTATTTAAATTTAAAATATAAA
1 TTATTTATTTTTAAAATATAAA
*
54098 TATAATTTTTTTTTA
1 T-T-ATTTATTTTTA
54113 TATATTCGAT
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
21 14 0.48
22 6 0.21
23 1 0.03
24 8 0.28
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (22 bp):
TTATTTATTTTTAAAATATAAA
Found at i:66423 original size:13 final size:13
Alignment explanation
Indices: 66405--66433 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
66395 TAAATGATTT
66405 AAAGTAAGCATTA
1 AAAGTAAGCATTA
66418 AAAGTAAGCATTA
1 AAAGTAAGCATTA
66431 AAA
1 AAA
66434 TGCTCTAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.59, C:0.07, G:0.14, T:0.21
Consensus pattern (13 bp):
AAAGTAAGCATTA
Found at i:67708 original size:23 final size:23
Alignment explanation
Indices: 67682--67726 Score: 90
Period size: 23 Copynumber: 2.0 Consensus size: 23
67672 CTGAATTATT
67682 TACCACTTCAACCAATTCCTTAG
1 TACCACTTCAACCAATTCCTTAG
67705 TACCACTTCAACCAATTCCTTA
1 TACCACTTCAACCAATTCCTTA
67727 TTATGAAACA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.31, C:0.36, G:0.02, T:0.31
Consensus pattern (23 bp):
TACCACTTCAACCAATTCCTTAG
Found at i:77455 original size:24 final size:24
Alignment explanation
Indices: 77428--77479 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
77418 AACGGATATA
*
77428 TCAAAAATCAAAACATAAATCAGG
1 TCAAAAATCAAAACAGAAATCAGG
** * *
77452 TCAAGTATCATATCAGAAATCAGG
1 TCAAAAATCAAAACAGAAATCAGG
77476 TCAA
1 TCAA
77480 GTAACAGATC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.50, C:0.17, G:0.12, T:0.21
Consensus pattern (24 bp):
TCAAAAATCAAAACAGAAATCAGG
Found at i:77480 original size:24 final size:24
Alignment explanation
Indices: 77448--77566 Score: 143
Period size: 24 Copynumber: 5.0 Consensus size: 24
77438 AAACATAAAT
*
77448 CAGGTCAAGTATCATATCAGAAAT-
1 CAGGTCAAGTATCAGATCAG-AATC
*
77472 CAGGTCAAGTAACAGATCAGAATC
1 CAGGTCAAGTATCAGATCAGAATC
* *
77496 CAAGTTAAGTATCAGATCAGAATC
1 CAGGTCAAGTATCAGATCAGAATC
* *
77520 CATGTC-AGATATCATATCAGAATC
1 CAGGTCAAG-TATCAGATCAGAATC
*
77544 CATGTCAAGTATCAGATCAGAAT
1 CAGGTCAAGTATCAGATCAGAAT
77567 TCAAATCGAA
Statistics
Matches: 83, Mismatches: 9, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
23 5 0.06
24 76 0.92
25 2 0.02
ACGTcount: A:0.40, C:0.18, G:0.17, T:0.24
Consensus pattern (24 bp):
CAGGTCAAGTATCAGATCAGAATC
Found at i:79876 original size:3 final size:3
Alignment explanation
Indices: 79868--79897 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
79858 CCATTATATC
79868 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
79898 CGGAAGCTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:89308 original size:21 final size:20
Alignment explanation
Indices: 89251--89311 Score: 61
Period size: 21 Copynumber: 3.0 Consensus size: 20
89241 CAGACTTATT
*
89251 GAAAATAAAA-GAAACAAAA
1 GAAAATAAAATGAAATAAAA
** *
89270 GAAAATAAATATTTAATATAA
1 GAAAATAAA-ATGAAATAAAA
89291 GAAAATAAAATGACAATAAAA
1 GAAAATAAAATGA-AATAAAA
89312 AATATCGACG
Statistics
Matches: 32, Mismatches: 7, Indels: 4
0.74 0.16 0.09
Matches are distributed among these distances:
19 9 0.28
20 3 0.09
21 20 0.62
ACGTcount: A:0.70, C:0.03, G:0.08, T:0.18
Consensus pattern (20 bp):
GAAAATAAAATGAAATAAAA
Found at i:89353 original size:84 final size:85
Alignment explanation
Indices: 89253--89424 Score: 269
Period size: 84 Copynumber: 2.0 Consensus size: 85
89243 GACTTATTGA
* * *
89253 AAATAAAAGAAACAAAAGAAAATAAATATTTAATATAAGAAAATAAAATGACAATAAAAAATA-T
1 AAATAAAAGAAACAAAAGAAAATAAAGATGTAATATAAGAAAATAAAAAGACAATAAAAAATACT
89317 CGACGATCGACAA-CTAACATT
66 -GACGATCGACAATC-AACATT
*
89338 AAATAATA-AAACAAAAGAAAATAAAGATGTAATATAAGAAAATAAAAAGACAATAAAAAATACT
1 AAATAAAAGAAACAAAAGAAAATAAAGATGTAATATAAGAAAATAAAAAGACAATAAAAAATACT
89402 GACGATCGACAATCAACATT
66 GACGATCGACAATCAACATT
89422 AAA
1 AAA
89425 GTTAGTGTCG
Statistics
Matches: 81, Mismatches: 4, Indels: 5
0.90 0.04 0.06
Matches are distributed among these distances:
84 72 0.89
85 9 0.11
ACGTcount: A:0.63, C:0.09, G:0.09, T:0.19
Consensus pattern (85 bp):
AAATAAAAGAAACAAAAGAAAATAAAGATGTAATATAAGAAAATAAAAAGACAATAAAAAATACT
GACGATCGACAATCAACATT
Found at i:89398 original size:39 final size:39
Alignment explanation
Indices: 89251--89399 Score: 101
Period size: 39 Copynumber: 3.6 Consensus size: 39
89241 CAGACTTATT
* * *
89251 GAAAATAAAAGAAACAAAAGAAAATAAATATTTAATATAA
1 GAAAATAAAA-AGACAAAAGAAAATAAAGATGTAATATAA
* *
89291 GAAAATAAAATGACAATAA-AAAATATCGACGATCG-ACA-ACTAA
1 GAAAATAAAAAGACAA-AAGAAAATA---AAGAT-GTA-ATA-TAA
*
89334 CATTAAATAATAAA-ACAAAAGAAAATAAAGATGTAATATAA
1 GA--AAATAA-AAAGACAAAAGAAAATAAAGATGTAATATAA
89375 GAAAATAAAAAGACAATAA-AAAATA
1 GAAAATAAAAAGACAA-AAGAAAATA
89400 CTGACGATCG
Statistics
Matches: 85, Mismatches: 9, Indels: 31
0.68 0.07 0.25
Matches are distributed among these distances:
38 3 0.04
39 26 0.31
40 14 0.16
41 6 0.07
42 11 0.13
43 5 0.06
44 2 0.02
45 16 0.19
46 2 0.02
ACGTcount: A:0.66, C:0.07, G:0.09, T:0.18
Consensus pattern (39 bp):
GAAAATAAAAAGACAAAAGAAAATAAAGATGTAATATAA
Found at i:89555 original size:2 final size:2
Alignment explanation
Indices: 89548--89581 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
89538 ATCAATTACA
89548 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
89582 TGAATTTGAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:90527 original size:24 final size:24
Alignment explanation
Indices: 90500--90575 Score: 82
Period size: 24 Copynumber: 3.2 Consensus size: 24
90490 TATATCAAAA
90500 ATCAAAACATAAAT-CAGGTCAAGT
1 ATCAAAACA-AAATCCAGGTCAAGT
* *
90524 ATCATATCAAAATCCAGGTCAAGT
1 ATCAAAACAAAATCCAGGTCAAGT
* * * *
90548 ATCAGATCAGAATCCAAGTCAAGT
1 ATCAAAACAAAATCCAGGTCAAGT
90572 ATCA
1 ATCA
90576 GATCAGAATC
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
23 4 0.09
24 42 0.91
ACGTcount: A:0.45, C:0.20, G:0.13, T:0.22
Consensus pattern (24 bp):
ATCAAAACAAAATCCAGGTCAAGT
Found at i:90576 original size:24 final size:24
Alignment explanation
Indices: 90517--90632 Score: 146
Period size: 24 Copynumber: 4.8 Consensus size: 24
90507 CATAAATCAG
* *
90517 GTCAAGTATCATATCAAAATCCAG
1 GTCAAGTATCATATCAGAATCCAA
*
90541 GTCAAGTATCAGATCAGAATCCAA
1 GTCAAGTATCATATCAGAATCCAA
*
90565 GTCAAGTATCAGATCAGAAT-CAA
1 GTCAAGTATCATATCAGAATCCAA
*
90588 TGTC-AGATATCATATCAGAATCCAT
1 -GTCAAG-TATCATATCAGAATCCAA
*
90613 GTCAAGTATCATACCAGAAT
1 GTCAAGTATCATATCAGAAT
90633 TCAAATCGAA
Statistics
Matches: 82, Mismatches: 6, Indels: 8
0.85 0.06 0.08
Matches are distributed among these distances:
23 5 0.06
24 73 0.89
25 4 0.05
ACGTcount: A:0.41, C:0.20, G:0.15, T:0.25
Consensus pattern (24 bp):
GTCAAGTATCATATCAGAATCCAA
Found at i:93036 original size:18 final size:18
Alignment explanation
Indices: 93013--93048 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
93003 TACTCGGTCA
*
93013 AAACGGGTCGGGTCGGGT
1 AAACGGGACGGGTCGGGT
93031 AAACGGGACGGGTCGGGT
1 AAACGGGACGGGTCGGGT
93049 TGGAACCGGT
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:0.19, C:0.17, G:0.50, T:0.14
Consensus pattern (18 bp):
AAACGGGACGGGTCGGGT
Done.