Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000439.1 Hibiscus syriacus cultivar Beakdansim tig00000803_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: 75042
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:11738 original size:45 final size:46
Alignment explanation
Indices: 11689--11776 Score: 142
Period size: 45 Copynumber: 1.9 Consensus size: 46
11679 GAACATCGAA
* *
11689 TGCATTTTATGCATCGATGCAC-ATACCATGCATCGATGCACTTAG
1 TGCATTTGATGCATCGATGCACAAGACCATGCATCGATGCACTTAG
*
11734 TGCATTTGATGCATCGATGCACAAGACCATGCATTGATGCACT
1 TGCATTTGATGCATCGATGCACAAGACCATGCATCGATGCACT
11777 CAGGCTATTT
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
45 21 0.54
46 18 0.46
ACGTcount: A:0.27, C:0.24, G:0.19, T:0.30
Consensus pattern (46 bp):
TGCATTTGATGCATCGATGCACAAGACCATGCATCGATGCACTTAG
Found at i:12811 original size:37 final size:37
Alignment explanation
Indices: 12761--12835 Score: 141
Period size: 37 Copynumber: 2.0 Consensus size: 37
12751 ACTCGAGATC
*
12761 GATTTGCTTCACTACTCTTTGGTGAAGGCTTAGGATG
1 GATTTGCTTCACTACTCTTCGGTGAAGGCTTAGGATG
12798 GATTTGCTTCACTACTCTTCGGTGAAGGCTTAGGATG
1 GATTTGCTTCACTACTCTTCGGTGAAGGCTTAGGATG
12835 G
1 G
12836 CTTGGATGAC
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.19, C:0.17, G:0.28, T:0.36
Consensus pattern (37 bp):
GATTTGCTTCACTACTCTTCGGTGAAGGCTTAGGATG
Found at i:13012 original size:42 final size:41
Alignment explanation
Indices: 12888--13016 Score: 154
Period size: 42 Copynumber: 3.1 Consensus size: 41
12878 AGAACTTATG
* * * *
12888 GATGACCCGAAGGATTTATCATCTTGCTCAAAAGA-TTCACA
1 GATGACCCAAAGGATTTATCATCATGCTCGAAAGACTT-ACT
*
12929 AATGACCCGAAA-GATTTAATCATCATGCTCGAAAGACTTACT
1 GATGACCC-AAAGGATTT-ATCATCATGCTCGAAAGACTTACT
*
12971 GATGACCCAAAGGATTTCATTATCATGCTCGAAAGACTTACT
1 GATGACCCAAAGGATTT-ATCATCATGCTCGAAAGACTTACT
13013 GATG
1 GATG
13017 GCACTTACTG
Statistics
Matches: 76, Mismatches: 8, Indels: 7
0.84 0.09 0.08
Matches are distributed among these distances:
41 15 0.20
42 59 0.78
43 2 0.03
ACGTcount: A:0.35, C:0.21, G:0.17, T:0.27
Consensus pattern (41 bp):
GATGACCCAAAGGATTTATCATCATGCTCGAAAGACTTACT
Found at i:13024 original size:13 final size:13
Alignment explanation
Indices: 13006--13030 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
12996 TGCTCGAAAG
13006 ACTTACTGATGGC
1 ACTTACTGATGGC
13019 ACTTACTGATGG
1 ACTTACTGATGG
13031 ATTTGCTTCA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.20, G:0.24, T:0.32
Consensus pattern (13 bp):
ACTTACTGATGGC
Found at i:16420 original size:40 final size:39
Alignment explanation
Indices: 16331--16431 Score: 134
Period size: 40 Copynumber: 2.6 Consensus size: 39
16321 AAATCCAGAA
*
16331 CCCC-AGGGGGGTATCGATTCCCCTATGGGGAATCGGTT
1 CCCCTAGGGGGGTATCGATTCCCCTAGGGGGAATCGGTT
* *
16369 CCCCTAGGGGGGAATCGGTTCCCCTAGGGGGGAATCGGTT
1 CCCCTAGGGGGGTATCGATTCCCCTA-GGGGGAATCGGTT
*
16409 -CCCTCATGGGGGTATCGATTCCC
1 CCCCT-AGGGGGGTATCGATTCCC
16432 TCTGCACCAA
Statistics
Matches: 54, Mismatches: 6, Indels: 4
0.84 0.09 0.06
Matches are distributed among these distances:
38 4 0.07
39 23 0.43
40 27 0.50
ACGTcount: A:0.15, C:0.28, G:0.35, T:0.23
Consensus pattern (39 bp):
CCCCTAGGGGGGTATCGATTCCCCTAGGGGGAATCGGTT
Found at i:16433 original size:20 final size:20
Alignment explanation
Indices: 16331--16411 Score: 121
Period size: 20 Copynumber: 4.2 Consensus size: 20
16321 AAATCCAGAA
* *
16331 CCCC-AGGGGGGTATCGATT
1 CCCCTAGGGGGGAATCGGTT
*
16350 CCCCTA-TGGGGAATCGGTT
1 CCCCTAGGGGGGAATCGGTT
16369 CCCCTAGGGGGGAATCGGTT
1 CCCCTAGGGGGGAATCGGTT
16389 CCCCTAGGGGGGAATCGGTT
1 CCCCTAGGGGGGAATCGGTT
16409 CCC
1 CCC
16412 TCATGGGGGT
Statistics
Matches: 56, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
19 20 0.36
20 36 0.64
ACGTcount: A:0.15, C:0.28, G:0.36, T:0.21
Consensus pattern (20 bp):
CCCCTAGGGGGGAATCGGTT
Found at i:20276 original size:22 final size:21
Alignment explanation
Indices: 20234--20273 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
20224 GAGTTTATTT
*
20234 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
20255 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
20274 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:22605 original size:13 final size:13
Alignment explanation
Indices: 22587--22611 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
22577 TGCTCGAAAG
22587 ACTTACTGATGGC
1 ACTTACTGATGGC
22600 ACTTACTGATGG
1 ACTTACTGATGG
22612 GTTTGCTTCA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.20, G:0.24, T:0.32
Consensus pattern (13 bp):
ACTTACTGATGGC
Found at i:22713 original size:42 final size:42
Alignment explanation
Indices: 22654--22734 Score: 126
Period size: 42 Copynumber: 1.9 Consensus size: 42
22644 AAATTACCCA
* *
22654 AAGGATTTAATCATCATGCTCGAAAGACCTACTGATGGCCCG
1 AAGGACTTAATCATCATGCTCGAAAAACCTACTGATGGCCCG
* *
22696 AAGGACTTCATCATCATGCTCGAAAAACTTACTGATGGC
1 AAGGACTTAATCATCATGCTCGAAAAACCTACTGATGGC
22735 ACTTACTGAT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 35 1.00
ACGTcount: A:0.32, C:0.23, G:0.20, T:0.25
Consensus pattern (42 bp):
AAGGACTTAATCATCATGCTCGAAAAACCTACTGATGGCCCG
Found at i:22740 original size:13 final size:13
Alignment explanation
Indices: 22722--22746 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
22712 TGCTCGAAAA
22722 ACTTACTGATGGC
1 ACTTACTGATGGC
22735 ACTTACTGATGG
1 ACTTACTGATGG
22747 GTTTGCTTCA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.20, G:0.24, T:0.32
Consensus pattern (13 bp):
ACTTACTGATGGC
Found at i:22798 original size:135 final size:135
Alignment explanation
Indices: 22551--22869 Score: 496
Period size: 135 Copynumber: 2.4 Consensus size: 135
22541 CAACACTTAT
* *
22551 TGATAGCCCGAAGGACTTCAACATCATGCTCGAAAGACTTACTGATGGCACTTACTGATGGGTTT
1 TGATGGCCCGAAGGACTTCAACATCATGCTCGAAAAACTTACTGATGGCACTTACTGATGGGTTT
* * *
22616 GCTTCACTACTCTTCCGTGAAGGCTTACAAATTACCCAAAGGATTTAATCATCATGCTCGAAAGA
66 GCTTCACTACTCTTCCATGAAGGCTTACAAATTACCCAAAGGATTTAATCATAATACTCGAAAGA
22681 CCTAC
131 CCTAC
*
22686 TGATGGCCCGAAGGACTTCATCATCATGCTCGAAAAACTTACTGATGGCACTTACTGATGGGTTT
1 TGATGGCCCGAAGGACTTCAACATCATGCTCGAAAAACTTACTGATGGCACTTACTGATGGGTTT
* * *
22751 GCTTCACTACTCTTCCATGAATGCTTGCAAATTACCCGAAGGATTTAATCATAATACTCGAAAGA
66 GCTTCACTACTCTTCCATGAAGGCTTACAAATTACCCAAAGGATTTAATCATAATACTCGAAAGA
*
22816 CTTAC
131 CCTAC
* * * *
22821 TGATGGCCCTAAGGA-TTTAAGCATCATGCTCGAAATACTTATTGATGGC
1 TGATGGCCCGAAGGACTTCAA-CATCATGCTCGAAAAACTTACTGATGGC
22870 CCGAATGACT
Statistics
Matches: 168, Mismatches: 15, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
134 3 0.02
135 165 0.98
ACGTcount: A:0.29, C:0.23, G:0.19, T:0.29
Consensus pattern (135 bp):
TGATGGCCCGAAGGACTTCAACATCATGCTCGAAAAACTTACTGATGGCACTTACTGATGGGTTT
GCTTCACTACTCTTCCATGAAGGCTTACAAATTACCCAAAGGATTTAATCATAATACTCGAAAGA
CCTAC
Found at i:22853 original size:42 final size:42
Alignment explanation
Indices: 22789--22871 Score: 121
Period size: 42 Copynumber: 2.0 Consensus size: 42
22779 AAATTACCCG
*
22789 AAGGATTTAATCATAATACTCGAAAGACTTACTGATGGCCCT
1 AAGGATTTAAGCATAATACTCGAAAGACTTACTGATGGCCCT
* * * *
22831 AAGGATTTAAGCATCATGCTCGAAATACTTATTGATGGCCC
1 AAGGATTTAAGCATAATACTCGAAAGACTTACTGATGGCCC
22872 GAATGACTTA
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 36 1.00
ACGTcount: A:0.34, C:0.19, G:0.18, T:0.29
Consensus pattern (42 bp):
AAGGATTTAAGCATAATACTCGAAAGACTTACTGATGGCCCT
Found at i:27096 original size:48 final size:47
Alignment explanation
Indices: 27043--27208 Score: 196
Period size: 44 Copynumber: 3.6 Consensus size: 47
27033 CACAAAAAAT
* * *
27043 CCTAACCACATGATATCTAATTCGCATGCTTGTTCAAGAAAAAATAAA
1 CCTAACCGCATGATTTCTAGTTCGCATGCTTGTTC-AGAAAAAATAAA
* *
27091 CCTAACCGCATGATTTCTAGTTCGCATACATGTTC--AAAAAA-AAA
1 CCTAACCGCATGATTTCTAGTTCGCATGCTTGTTCAGAAAAAATAAA
* * * * *
27135 CTTAATCGTATGATTTCTAGTTTGCTTGCTTGTTC-GAGAAAAATAAA
1 CCTAACCGCATGATTTCTAGTTCGCATGCTTGTTCAGA-AAAAATAAA
27182 CCTAACCGCATGATTTCTAGTTCGCAT
1 CCTAACCGCATGATTTCTAGTTCGCAT
27209 ACATTTATTC
Statistics
Matches: 98, Mismatches: 17, Indels: 7
0.80 0.14 0.06
Matches are distributed among these distances:
44 31 0.32
45 7 0.07
46 5 0.05
47 25 0.26
48 30 0.31
ACGTcount: A:0.34, C:0.20, G:0.13, T:0.32
Consensus pattern (47 bp):
CCTAACCGCATGATTTCTAGTTCGCATGCTTGTTCAGAAAAAATAAA
Found at i:27663 original size:13 final size:13
Alignment explanation
Indices: 27645--27669 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
27635 AGGAAAAGAG
27645 AAAAACACACAAT
1 AAAAACACACAAT
27658 AAAAACACACAA
1 AAAAACACACAA
27670 AATCAATTCC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.72, C:0.24, G:0.00, T:0.04
Consensus pattern (13 bp):
AAAAACACACAAT
Found at i:30353 original size:3 final size:3
Alignment explanation
Indices: 30340--30371 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
30330 TAAACAGTAT
30340 TAA TAA T-A TAA TAA TAA T-A TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
30372 TATATCCCGG
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
2 4 0.15
3 23 0.85
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:30356 original size:11 final size:11
Alignment explanation
Indices: 30340--30369 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
30330 TAAACAGTAT
30340 TAATAATATAA
1 TAATAATATAA
30351 TAATAATATAA
1 TAATAATATAA
30362 TAATAATA
1 TAATAATA
30370 ATTATATCCC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (11 bp):
TAATAATATAA
Found at i:32293 original size:28 final size:28
Alignment explanation
Indices: 32241--32336 Score: 140
Period size: 28 Copynumber: 3.4 Consensus size: 28
32231 TGGGTTCGGG
*
32241 TCGGGTCGGG-TTTTTTAAGTTTGATAT
1 TCGGGTCGGGTTTTTTTAAGTGTGATAT
*
32268 TCGGGTCGGGTTTTTTTAAATGTGATAT
1 TCGGGTCGGGTTTTTTTAAGTGTGATAT
*
32296 TCGGGTTGGGTTTTTTTTAAGTGTGATAT
1 TCGGGTCGGG-TTTTTTTAAGTGTGATAT
*
32325 TTGGGTCGGGTT
1 TCGGGTCGGGTT
32337 CGGGTTTAGG
Statistics
Matches: 61, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
27 10 0.16
28 26 0.43
29 25 0.41
ACGTcount: A:0.14, C:0.06, G:0.32, T:0.48
Consensus pattern (28 bp):
TCGGGTCGGGTTTTTTTAAGTGTGATAT
Found at i:32310 original size:29 final size:29
Alignment explanation
Indices: 32241--32336 Score: 135
Period size: 29 Copynumber: 3.4 Consensus size: 29
32231 TGGGTTCGGG
*
32241 TCGGGTCGGG--TTTTTTAAGTTTGATAT
1 TCGGGTCGGGTTTTTTTTAAGTGTGATAT
*
32268 TCGGGTCGGG-TTTTTTTAAATGTGATAT
1 TCGGGTCGGGTTTTTTTTAAGTGTGATAT
*
32296 TCGGGTTGGGTTTTTTTTAAGTGTGATAT
1 TCGGGTCGGGTTTTTTTTAAGTGTGATAT
*
32325 TTGGGTCGGGTT
1 TCGGGTCGGGTT
32337 CGGGTTTAGG
Statistics
Matches: 61, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
27 10 0.16
28 24 0.39
29 27 0.44
ACGTcount: A:0.14, C:0.06, G:0.32, T:0.48
Consensus pattern (29 bp):
TCGGGTCGGGTTTTTTTTAAGTGTGATAT
Found at i:35327 original size:45 final size:45
Alignment explanation
Indices: 35259--35348 Score: 144
Period size: 45 Copynumber: 2.0 Consensus size: 45
35249 TTAGCAAAGC
* *
35259 ATAGAATAGCGAGGTTGTATTTGTAAACTAGTCGCAGCTAGTGTT
1 ATAGAATAGCGAAGTTGTATTTGTAAACTAGCCGCAGCTAGTGTT
* *
35304 ATAGAATAGCGAAGTTGTGTTTGTAAACTAGCCGCGGCTAGTGTT
1 ATAGAATAGCGAAGTTGTATTTGTAAACTAGCCGCAGCTAGTGTT
35349 GTAGTATTAC
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 41 1.00
ACGTcount: A:0.28, C:0.12, G:0.28, T:0.32
Consensus pattern (45 bp):
ATAGAATAGCGAAGTTGTATTTGTAAACTAGCCGCAGCTAGTGTT
Found at i:35897 original size:23 final size:23
Alignment explanation
Indices: 35871--35937 Score: 66
Period size: 23 Copynumber: 3.0 Consensus size: 23
35861 GTTGTATTTG
35871 TAAACTAGCCACAGCTAGTGTTA
1 TAAACTAGCCACAGCTAGTGTTA
* * * *
35894 TAAAATAGCGA-AG-TTGTGTTTG
1 TAAACTAGCCACAGCTAGTG-TTA
*
35916 TAAACTAGCCGCAGCTAGTGTT
1 TAAACTAGCCACAGCTAGTGTT
35938 GTAGTATTTC
Statistics
Matches: 33, Mismatches: 8, Indels: 6
0.70 0.17 0.13
Matches are distributed among these distances:
21 4 0.12
22 12 0.36
23 13 0.39
24 4 0.12
ACGTcount: A:0.31, C:0.16, G:0.22, T:0.30
Consensus pattern (23 bp):
TAAACTAGCCACAGCTAGTGTTA
Found at i:35916 original size:45 final size:45
Alignment explanation
Indices: 35852--35937 Score: 154
Period size: 45 Copynumber: 1.9 Consensus size: 45
35842 CAAAGCATAG
35852 AATAGCGAAGTTGTATTTGTAAACTAGCCACAGCTAGTGTTATAA
1 AATAGCGAAGTTGTATTTGTAAACTAGCCACAGCTAGTGTTATAA
* *
35897 AATAGCGAAGTTGTGTTTGTAAACTAGCCGCAGCTAGTGTT
1 AATAGCGAAGTTGTATTTGTAAACTAGCCACAGCTAGTGTT
35938 GTAGTATTTC
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
45 39 1.00
ACGTcount: A:0.31, C:0.14, G:0.23, T:0.31
Consensus pattern (45 bp):
AATAGCGAAGTTGTATTTGTAAACTAGCCACAGCTAGTGTTATAA
Found at i:35924 original size:22 final size:22
Alignment explanation
Indices: 35854--35924 Score: 72
Period size: 22 Copynumber: 3.2 Consensus size: 22
35844 AAGCATAGAA
*
35854 TAGCGAAGTTGTATTTGTAAAC
1 TAGCGAAGTTGTGTTTGTAAAC
* * * *
35876 TAGCCACAGCTAGTG-TTATAAAA
1 TAGCGA-AG-TTGTGTTTGTAAAC
35899 TAGCGAAGTTGTGTTTGTAAAC
1 TAGCGAAGTTGTGTTTGTAAAC
35921 TAGC
1 TAGC
35925 CGCAGCTAGT
Statistics
Matches: 37, Mismatches: 9, Indels: 6
0.71 0.17 0.12
Matches are distributed among these distances:
21 4 0.11
22 17 0.46
23 13 0.35
24 3 0.08
ACGTcount: A:0.32, C:0.13, G:0.23, T:0.32
Consensus pattern (22 bp):
TAGCGAAGTTGTGTTTGTAAAC
Found at i:36252 original size:589 final size:589
Alignment explanation
Indices: 35131--36311 Score: 2121
Period size: 589 Copynumber: 2.0 Consensus size: 589
35121 GTTTATTACA
*
35131 TCTATATATACGGGTGTTCTAGTTTAGTTTAATATATGAACACAAGTGAGAAAAATGAAGGTTTA
1 TCTATATATACGGGTGTTCTAGTTTAGTTTAATATATGAACACAAGTGAGAAAAATGAAGGCTTA
* *
35196 GAAAAGCCAGAATGAATAATAATTTAGCAAAGCTATTAGAGAGAGGGTAAAGCTTAGCAAAGCAT
66 GAAAAGCCAGAATGAATAATAATTTAGCAAAGCTATTAAAGAGAGGCTAAAGCTTAGCAAAGCAT
* * * *
35261 AGAATAGCGAGGTTGTATTTGTAAACTAGTCGCAGCTAGTGTTATAGAATAGCGAAGTTGTGTTT
131 AGAATAGCGAAGTTGTATTTGTAAACTAGCCACAGCTAGTGTTATAAAATAGCGAAGTTGTGTTT
*
35326 GTAAACTAGCCGCGGCTAGTGTTGTAGTATTACAGTATTGTAATATTGGGGTAACGTCGTTGTAA
196 GTAAACTAGCCGCAGCTAGTGTTGTAGTATTACAGTATTGTAATATTGGGGTAACGTCGTTGTAA
35391 CGTATTTTGCCTCATATTAATAATATTTCGAGTTTTATAAATTATCGAGTGCCCACCTACGCTTC
261 CGTATTTTGCCTCATATTAATAATATTTCGAGTTTTATAAATTATCGAGTGCCCACCTACGCTTC
* *
35456 CAGCAAGTGGTCTCAGAGCTTGGTTCGAGTTTAACGTGGTGGAGAAGATGACCAACATGATTCAA
326 CAACAAGTGGCCTCAGAGCTTGGTTCGAGTTTAACGTGGTGGAGAAGATGACCAACATGATTCAA
*
35521 CCACAAATCTCGAGATTGACAAAGACAAATTATGGCAATTGGAGTATTCAAATGAAGGTGTTACT
391 CCACAAATCTCGAGATTGACAAAGACAAATTATGGCAATTGGAGTATTCAAATGAAGGCGTTACT
* *
35586 AGGCTCCCAAGATTGTTGGGATATCATCGAGAATGGTTACACCGAGCCTGAAAATGCAGCAGCAG
456 AGGCTCCCAAGATTGTTGGGATATCATCGAGAATGGTTACACCGAGCCTGAAAACGCAGCAACAG
* *
35651 AAGCAGTCCTTACTAATGAAGAAAAGAAGATACTGAAGGAATCCCGGAAAAAAGATAAAAGAGCG
521 AAGCAATCCTTACTAATGAAGAAAAGAAGATACTGAAGGAATCACGGAAAAAAGATAAAAGAGCG
35716 TTGT
586 TTGT
35720 TCTATATATACGGGTGTTCTAGTTTAGTTTAATATATGAACACAAGTGAGAAAAATGAAGGCTTA
1 TCTATATATACGGGTGTTCTAGTTTAGTTTAATATATGAACACAAGTGAGAAAAATGAAGGCTTA
*
35785 GAAAAGCCAGAATGAATAATAATTTAGCAAAGCTATTAAAGATAGGCTAAAGCTTAGCAAAGCAT
66 GAAAAGCCAGAATGAATAATAATTTAGCAAAGCTATTAAAGAGAGGCTAAAGCTTAGCAAAGCAT
35850 AGAATAGCGAAGTTGTATTTGTAAACTAGCCACAGCTAGTGTTATAAAATAGCGAAGTTGTGTTT
131 AGAATAGCGAAGTTGTATTTGTAAACTAGCCACAGCTAGTGTTATAAAATAGCGAAGTTGTGTTT
*
35915 GTAAACTAGCCGCAGCTAGTGTTGTAGTATTTCAGTATTGTAATATTGGGGTAACGTCGTTGTAA
196 GTAAACTAGCCGCAGCTAGTGTTGTAGTATTACAGTATTGTAATATTGGGGTAACGTCGTTGTAA
* * * *
35980 CGTATTTTGCCTCGTATTAATAATATTTTGAGTTTTATAAATTATTGAGTGTCCACCTACGCTTC
261 CGTATTTTGCCTCATATTAATAATATTTCGAGTTTTATAAATTATCGAGTGCCCACCTACGCTTC
36045 CAACAAGTGGCCTCAGAGCTTGGTTCGAGTTTAACGTGGTGGAGAAGATGACCAACATGATTCAA
326 CAACAAGTGGCCTCAGAGCTTGGTTCGAGTTTAACGTGGTGGAGAAGATGACCAACATGATTCAA
36110 CCACAAATCTCGAGATTGACAAAGACAAATTATGGCAATTGGAGTATTCAAATGAAGGCGTTACT
391 CCACAAATCTCGAGATTGACAAAGACAAATTATGGCAATTGGAGTATTCAAATGAAGGCGTTACT
*
36175 AGGCTGCCAAGATTGTTGGGATATCATCGA-AGATGGTTACACCGAGCCTGAAAACGCAGCAACA
456 AGGCTCCCAAGATTGTTGGGATATCATCGAGA-ATGGTTACACCGAGCCTGAAAACGCAGCAACA
* * *
36239 GAAGCAATCCTTACTAATGAAGAAAAGAAGATATTGAAGGAATCACGGGAAAAAGATAAAAGAGT
520 GAAGCAATCCTTACTAATGAAGAAAAGAAGATACTGAAGGAATCACGGAAAAAAGATAAAAGAGC
36304 GTTGT
585 GTTGT
36309 TCT
1 TCT
36312 TTATTTTTCA
Statistics
Matches: 566, Mismatches: 25, Indels: 2
0.95 0.04 0.00
Matches are distributed among these distances:
588 1 0.00
589 565 1.00
ACGTcount: A:0.35, C:0.14, G:0.23, T:0.28
Consensus pattern (589 bp):
TCTATATATACGGGTGTTCTAGTTTAGTTTAATATATGAACACAAGTGAGAAAAATGAAGGCTTA
GAAAAGCCAGAATGAATAATAATTTAGCAAAGCTATTAAAGAGAGGCTAAAGCTTAGCAAAGCAT
AGAATAGCGAAGTTGTATTTGTAAACTAGCCACAGCTAGTGTTATAAAATAGCGAAGTTGTGTTT
GTAAACTAGCCGCAGCTAGTGTTGTAGTATTACAGTATTGTAATATTGGGGTAACGTCGTTGTAA
CGTATTTTGCCTCATATTAATAATATTTCGAGTTTTATAAATTATCGAGTGCCCACCTACGCTTC
CAACAAGTGGCCTCAGAGCTTGGTTCGAGTTTAACGTGGTGGAGAAGATGACCAACATGATTCAA
CCACAAATCTCGAGATTGACAAAGACAAATTATGGCAATTGGAGTATTCAAATGAAGGCGTTACT
AGGCTCCCAAGATTGTTGGGATATCATCGAGAATGGTTACACCGAGCCTGAAAACGCAGCAACAG
AAGCAATCCTTACTAATGAAGAAAAGAAGATACTGAAGGAATCACGGAAAAAAGATAAAAGAGCG
TTGT
Found at i:37003 original size:45 final size:45
Alignment explanation
Indices: 36922--37008 Score: 120
Period size: 45 Copynumber: 1.9 Consensus size: 45
36912 TTAGCAAAGC
* * *
36922 ATAGAATAGCGAAGTTATGTTTGTAAACTAGCCGTAGCTAGTGTT
1 ATAGAATAGCGAAGTTATATTTATAAAATAGCCGTAGCTAGTGTT
* * *
36967 ATAGAATAGTGAAGTTGTATTTATAAAATAGTCGTAGCTAGT
1 ATAGAATAGCGAAGTTATATTTATAAAATAGCCGTAGCTAGT
37009 ATTGTAGTAT
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
45 36 1.00
ACGTcount: A:0.34, C:0.08, G:0.23, T:0.34
Consensus pattern (45 bp):
ATAGAATAGCGAAGTTATATTTATAAAATAGCCGTAGCTAGTGTT
Found at i:44420 original size:3 final size:3
Alignment explanation
Indices: 44412--44445 Score: 59
Period size: 3 Copynumber: 11.0 Consensus size: 3
44402 CTACACTTGA
44412 TAT TAT TAT TAT TAT TAT TAT TAT TATT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT
44446 ATGGACTGAT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 27 0.90
4 3 0.10
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:45970 original size:30 final size:30
Alignment explanation
Indices: 45935--46038 Score: 136
Period size: 30 Copynumber: 3.5 Consensus size: 30
45925 ACCCAAGGAC
* *
45935 CCCGAGAAGAAACCGGAAAAGCCTAAAGAG
1 CCCGAGAAGAAACCGGAAAAACCTAAAGAA
*
45965 GCCGAGAAGAAACCGGAAAAACCTAAAGAA
1 CCCGAGAAGAAACCGGAAAAACCTAAAGAA
* * *
45995 CCCGAGAAGAAACCCGAGAAACCGAAAGAA
1 CCCGAGAAGAAACCGGAAAAACCTAAAGAA
* *
46025 CCTGAAAAGAAACC
1 CCCGAGAAGAAACC
46039 CGAGAAGCCT
Statistics
Matches: 65, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 65 1.00
ACGTcount: A:0.50, C:0.24, G:0.23, T:0.03
Consensus pattern (30 bp):
CCCGAGAAGAAACCGGAAAAACCTAAAGAA
Found at i:46039 original size:30 final size:30
Alignment explanation
Indices: 45941--46063 Score: 115
Period size: 30 Copynumber: 4.1 Consensus size: 30
45931 GGACCCCGAG
* * *
45941 AAGAAACCGGA-AAAGCCTAAAGAGGCC-GAG
1 AAGAAACCCGAGAAA-CCTAAAGA-ACCTGAA
* * * *
45971 AAGAAACCGGAAAAACCTAAAGAACCCGAG
1 AAGAAACCCGAGAAACCTAAAGAACCTGAA
*
46001 AAGAAACCCGAGAAACCGAAAGAACCTGAA
1 AAGAAACCCGAGAAACCTAAAGAACCTGAA
* * *
46031 AAGAAACCCGAGAAGCCTAAGGAGCCTGAA
1 AAGAAACCCGAGAAACCTAAAGAACCTGAA
46061 AAG
1 AAG
46064 CCCAAAGAAT
Statistics
Matches: 81, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
29 2 0.02
30 76 0.94
31 3 0.04
ACGTcount: A:0.50, C:0.22, G:0.24, T:0.04
Consensus pattern (30 bp):
AAGAAACCCGAGAAACCTAAAGAACCTGAA
Found at i:46050 original size:60 final size:60
Alignment explanation
Indices: 45935--46050 Score: 137
Period size: 60 Copynumber: 1.9 Consensus size: 60
45925 ACCCAAGGAC
* * * * *
45935 CCCGAGAAGAAACCGGAAAAGCCTAAAGAGGCCGAGAAGAAACCGGAAAAACCTAAAGAA
1 CCCGAGAAGAAACCCGAAAAGCCGAAAGAGACCGAAAAGAAACCCGAAAAACCTAAAGAA
* *
45995 CCCGAGAAGAAACCCGAGAAA-CCGAAAGA-ACCTGAAAAGAAACCCGAGAAGCCTAA
1 CCCGAGAAGAAACCCGA-AAAGCCGAAAGAGACC-GAAAAGAAACCCGAAAAACCTAA
46051 GGAGCCTGAA
Statistics
Matches: 47, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
59 2 0.04
60 42 0.89
61 3 0.06
ACGTcount: A:0.49, C:0.24, G:0.23, T:0.03
Consensus pattern (60 bp):
CCCGAGAAGAAACCCGAAAAGCCGAAAGAGACCGAAAAGAAACCCGAAAAACCTAAAGAA
Found at i:46864 original size:2 final size:2
Alignment explanation
Indices: 46857--46886 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
46847 ATTCAATCAA
46857 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
46887 GTTGTCGATG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:54639 original size:27 final size:27
Alignment explanation
Indices: 54600--54664 Score: 112
Period size: 27 Copynumber: 2.4 Consensus size: 27
54590 ATAGAACGGG
*
54600 CAACTAAAAAACCCTTTGTACCTGTTT
1 CAACCAAAAAACCCTTTGTACCTGTTT
*
54627 CAACCAAACAACCCTTTGTACCTGTTT
1 CAACCAAAAAACCCTTTGTACCTGTTT
54654 CAACCAAAAAA
1 CAACCAAAAAA
54665 AAGTCAAGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.38, C:0.29, G:0.06, T:0.26
Consensus pattern (27 bp):
CAACCAAAAAACCCTTTGTACCTGTTT
Found at i:54931 original size:33 final size:33
Alignment explanation
Indices: 54888--54968 Score: 87
Period size: 33 Copynumber: 2.4 Consensus size: 33
54878 AAAAATTTGG
*
54888 ATATAAAAAATATAT-AATAATAATAATAAGTAAAA
1 ATAT-AAAAATATATCAATAATAAAAAT-A-TAAAA
*
54923 AT-TAAAAATAT-TCATTAATAAAAATATAAAA
1 ATATAAAAATATATCAATAATAAAAATATAAAA
54954 ATATAAAAATTATAT
1 ATATAAAAA-TATAT
54969 TTAAATATGT
Statistics
Matches: 40, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
31 7 0.17
32 8 0.20
33 21 0.52
34 2 0.05
35 2 0.05
ACGTcount: A:0.65, C:0.01, G:0.01, T:0.32
Consensus pattern (33 bp):
ATATAAAAATATATCAATAATAAAAATATAAAA
Found at i:54932 original size:23 final size:24
Alignment explanation
Indices: 54893--54956 Score: 69
Period size: 24 Copynumber: 2.6 Consensus size: 24
54883 TTTGGATATA
54893 AAAAATATATAATAATAAT-AATAAGT
1 AAAAATATA-AA-AATAATCAATAA-T
* *
54919 AAAAAT-TAAAAATATTCATTAAT
1 AAAAATATAAAAATAATCAATAAT
54942 AAAAATATAAAAATA
1 AAAAATATAAAAATA
54957 TAAAAATTAT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
23 12 0.35
24 14 0.41
25 2 0.06
26 6 0.18
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.30
Consensus pattern (24 bp):
AAAAATATAAAAATAATCAATAAT
Found at i:65061 original size:16 final size:16
Alignment explanation
Indices: 65031--65061 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
65021 AAAACTCGAA
*
65031 TCGAACTCGAAAAAAC
1 TCGAACTCAAAAAAAC
65047 TCGAACTCAAAAAAA
1 TCGAACTCAAAAAAA
65062 ATCCAGAAGC
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:0.55, C:0.23, G:0.10, T:0.13
Consensus pattern (16 bp):
TCGAACTCAAAAAAAC
Found at i:65083 original size:11 final size:11
Alignment explanation
Indices: 65067--65110 Score: 52
Period size: 11 Copynumber: 3.8 Consensus size: 11
65057 AAAAAATCCA
65067 GAAGCTCAATT
1 GAAGCTCAATT
65078 GAAGCTCAATACT
1 GAAGCTCAAT--T
* *
65091 CAAGCTCGATT
1 GAAGCTCAATT
65102 GAAGCTCAA
1 GAAGCTCAA
65111 GACTCGAGCT
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
11 18 0.67
13 9 0.33
ACGTcount: A:0.36, C:0.23, G:0.18, T:0.23
Consensus pattern (11 bp):
GAAGCTCAATT
Found at i:65102 original size:24 final size:24
Alignment explanation
Indices: 65068--65134 Score: 107
Period size: 24 Copynumber: 2.8 Consensus size: 24
65058 AAAAATCCAG
* *
65068 AAGCTCAATTGAAGCTCAATACTC
1 AAGCTCGATTGAAGCTCAAGACTC
65092 AAGCTCGATTGAAGCTCAAGACTC
1 AAGCTCGATTGAAGCTCAAGACTC
*
65116 GAGCTCGATTGAAGCTCAA
1 AAGCTCGATTGAAGCTCAA
65135 ATTTGAGCTC
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 40 1.00
ACGTcount: A:0.34, C:0.24, G:0.19, T:0.22
Consensus pattern (24 bp):
AAGCTCGATTGAAGCTCAAGACTC
Found at i:68306 original size:2 final size:2
Alignment explanation
Indices: 68294--68359 Score: 118
Period size: 2 Copynumber: 34.0 Consensus size: 2
68284 AACGGAACTA
68294 AT AT A- AT AT AT AT A- 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
68334 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
68360 GTTGGGGTAA
Statistics
Matches: 62, Mismatches: 0, Indels: 4
0.94 0.00 0.06
Matches are distributed among these distances:
1 2 0.03
2 60 0.97
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:74133 original size:113 final size:114
Alignment explanation
Indices: 73915--74145 Score: 299
Period size: 113 Copynumber: 2.0 Consensus size: 114
73905 ACTTTTGACT
* * *
73915 ATGTATTCATTTTTAAATTAATTTTTTGAATGCTATTTATTTAATATGATATAAAATAAAAAAAA
1 ATGTATTCATTTTAAAATTAATATTTTGAATGCAATTTATTTAATATGATATAAAAT-AAAAAAA
* * * *
73980 GGTTTGAATGTAATATTGGCATAATGAAATAGTATCTAATGTTTGACAAA
65 GGTTTGAATGTAATAATGGCATAATGAAAAAATATATAATGTTTGACAAA
* * *
74030 ATGTATTCA-TTTAAAATTAA-ATTTTGAATGCAATTTTTTTAATATGATAT-AAAT-CATAAAG
1 ATGTATTCATTTTAAAATTAATATTTTGAATGCAATTTATTTAATATGATATAAAATAAAAAAAG
*
74091 GTTTGAATGTAAAATAATGGCATGATGAAAAAATAGTATAATGTTTGACAAA
66 GTTTGAATGT--AATAATGGCATAATGAAAAAATA-TATAATGTTTGACAAA
74143 ATG
1 ATG
74146 ATTAACTTTT
Statistics
Matches: 102, Mismatches: 11, Indels: 8
0.84 0.09 0.07
Matches are distributed among these distances:
110 15 0.15
112 23 0.23
113 45 0.44
114 10 0.10
115 9 0.09
ACGTcount: A:0.43, C:0.04, G:0.13, T:0.40
Consensus pattern (114 bp):
ATGTATTCATTTTAAAATTAATATTTTGAATGCAATTTATTTAATATGATATAAAATAAAAAAAG
GTTTGAATGTAATAATGGCATAATGAAAAAATATATAATGTTTGACAAA
Done.