Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001459.1 Hibiscus syriacus cultivar Beakdansim tig00002821_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: 118778
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.32
Found at i:4761 original size:54 final size:54
Alignment explanation
Indices: 4648--5039 Score: 550
Period size: 54 Copynumber: 7.4 Consensus size: 54
4638 TTACCAAATA
*
4648 GGCACTAAGTGTGCAA-TCACGGAATTCATCATAT-ATGATGAACAACCGTTTC
1 GGCACTAAGTGTGCAATTCACGGAATTCATCATATGTTGATGAACAACCGTTTC
* * *
4700 GGTACTAAGTGTGTAATTCACGGAATTCATCATATGTTGATGAACAACTGTTTC
1 GGCACTAAGTGTGCAATTCACGGAATTCATCATATGTTGATGAACAACCGTTTC
* * *
4754 AGCACTAAGTGTGCAATTCATGAAATTCATCATATGTTGATGAACAACCGTTTC
1 GGCACTAAGTGTGCAATTCACGGAATTCATCATATGTTGATGAACAACCGTTTC
* * *
4808 GGCAGTAAGTGTACAATTCATGGAATTCATCATATGTTGATGAACAACCGTTTC
1 GGCACTAAGTGTGCAATTCACGGAATTCATCATATGTTGATGAACAACCGTTTC
** * *
4862 AACACTAAGTGTGCAATTCACAGAATTCATCATATG-T--TGAACAACCGTTTT
1 GGCACTAAGTGTGCAATTCACGGAATTCATCATATGTTGATGAACAACCGTTTC
* *
4913 GGCACTGAA-TGTGCAATTCACGGAATTCATCCTATGTTGATGAACAACCATTTC
1 GGCACT-AAGTGTGCAATTCACGGAATTCATCATATGTTGATGAACAACCGTTTC
* *
4967 GGCACTATGTGTACAATTCACGGAATTCATCATATG-T--TGAACAACCGTTTC
1 GGCACTAAGTGTGCAATTCACGGAATTCATCATATGTTGATGAACAACCGTTTC
5018 GGCACTAAGTGTGCAATTCACG
1 GGCACTAAGTGTGCAATTCACG
5040 AAATGTTAGA
Statistics
Matches: 300, Mismatches: 33, Indels: 15
0.86 0.09 0.04
Matches are distributed among these distances:
51 75 0.25
52 17 0.06
53 21 0.07
54 187 0.62
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Consensus pattern (54 bp):
GGCACTAAGTGTGCAATTCACGGAATTCATCATATGTTGATGAACAACCGTTTC
Found at i:4973 original size:105 final size:105
Alignment explanation
Indices: 4649--5039 Score: 561
Period size: 105 Copynumber: 3.7 Consensus size: 105
4639 TACCAAATAG
* *
4649 GCACTAAGTGTGCAA-TCACGGAATTCATCATATATGATGAACAACCGTTTCGGTACTAAGTGTG
1 GCACTAAGTGTGCAATTCACGGAATTCATC--ATATGTTGAACAACCGTTTCGGCACTAAGTGTG
* *
4713 TAATTCACGGAATTCATCATATGTTGATGAACAACTGTTTCA
64 CAATTCACGGAATTCATCATATGTTGATGAACAACCGTTTCA
* * *
4755 GCACTAAGTGTGCAATTCATGAAATTCATCATATGTTGATGAACAACCGTTTCGGCAGTAAGTGT
1 GCACTAAGTGTGCAATTCACGGAATTCATCATATG-T--TGAACAACCGTTTCGGCACTAAGTGT
* *
4820 ACAATTCATGGAATTCATCATATGTTGATGAACAACCGTTTCA
63 GCAATTCACGGAATTCATCATATGTTGATGAACAACCGTTTCA
* * *
4863 ACACTAAGTGTGCAATTCACAGAATTCATCATATGTTGAACAACCGTTTTGGCACTGAA-TGTGC
1 GCACTAAGTGTGCAATTCACGGAATTCATCATATGTTGAACAACCGTTTCGGCACT-AAGTGTGC
* * *
4927 AATTCACGGAATTCATCCTATGTTGATGAACAACCATTTCG
65 AATTCACGGAATTCATCATATGTTGATGAACAACCGTTTCA
* *
4968 GCACTATGTGTACAATTCACGGAATTCATCATATGTTGAACAACCGTTTCGGCACTAAGTGTGCA
1 GCACTAAGTGTGCAATTCACGGAATTCATCATATGTTGAACAACCGTTTCGGCACTAAGTGTGCA
5033 ATTCACG
66 ATTCACG
5040 AAATGTTAGA
Statistics
Matches: 254, Mismatches: 25, Indels: 13
0.87 0.09 0.04
Matches are distributed among these distances:
104 2 0.01
105 128 0.50
106 17 0.07
107 13 0.05
108 94 0.37
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.31
Consensus pattern (105 bp):
GCACTAAGTGTGCAATTCACGGAATTCATCATATGTTGAACAACCGTTTCGGCACTAAGTGTGCA
ATTCACGGAATTCATCATATGTTGATGAACAACCGTTTCA
Found at i:9601 original size:19 final size:19
Alignment explanation
Indices: 9579--9616 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
9569 ATTAAGGTAC
9579 TTCGATCAGATCGAGGTGA
1 TTCGATCAGATCGAGGTGA
9598 TTCGATCAGATCGAGGTGA
1 TTCGATCAGATCGAGGTGA
9617 AGAATACTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.26, C:0.16, G:0.32, T:0.26
Consensus pattern (19 bp):
TTCGATCAGATCGAGGTGA
Found at i:13887 original size:46 final size:46
Alignment explanation
Indices: 13834--14066 Score: 358
Period size: 46 Copynumber: 5.1 Consensus size: 46
13824 GGATAACACT
* **
13834 AATGTATAACAATGCATAATTGTTATGAAAGGATGCCATAAATGAA
1 AATGTATAACAGTGCATAATTGGCATGAAAGGATGCCATAAATGAA
*
13880 AATGTATAACAGTGCATAATTGGCATGAAAGGATGTCATAAATGAA
1 AATGTATAACAGTGCATAATTGGCATGAAAGGATGCCATAAATGAA
**
13926 AATGTATAACAGTGCATAATTGGCATGAAAGGATGATATAAATGAA
1 AATGTATAACAGTGCATAATTGGCATGAAAGGATGCCATAAATGAA
* * * *
13972 AATGTATAACAGTGCGTAATTAGCATGAAATGATGTCATAAATGAA
1 AATGTATAACAGTGCATAATTGGCATGAAAGGATGCCATAAATGAA
* *
14018 AATTTATAACAGTGCATAATTGGCATGAAAGGATGCCACAAATGAA
1 AATGTATAACAGTGCATAATTGGCATGAAAGGATGCCATAAATGAA
14064 AAT
1 AAT
14067 ACATAGTGGT
Statistics
Matches: 170, Mismatches: 17, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
46 170 1.00
ACGTcount: A:0.45, C:0.09, G:0.20, T:0.27
Consensus pattern (46 bp):
AATGTATAACAGTGCATAATTGGCATGAAAGGATGCCATAAATGAA
Found at i:19315 original size:55 final size:55
Alignment explanation
Indices: 19233--19761 Score: 643
Period size: 55 Copynumber: 9.7 Consensus size: 55
19223 ATTACCAAAT
* * * * *
19233 AGGCACTAAGTGTGC-ATTCCACGGAATTCATCAT-ATGTGGATGAATAACTGTTTC
1 AGGCACTATGTGTGCAAATCCACGGAATTCATCATGA-GTTGATGAATAACCG-TAC
* * *
19288 -GGCATTAAGTGTGCAAATCCACAGAATTCATCATGAGTTGATGAATAACCGTAC
1 AGGCACTATGTGTGCAAATCCACGGAATTCATCATGAGTTGATGAATAACCGTAC
* * *
19342 ATGCACTATGTGTGTAAATCCATGGAATTCATCATGAGTTGATGAATAACCGTAC
1 AGGCACTATGTGTGCAAATCCACGGAATTCATCATGAGTTGATGAATAACCGTAC
* * *
19397 ATGCACTATGTGTGCAAATCCACGTAATTCATCATGAGTTGATTAATAACCGTAC
1 AGGCACTATGTGTGCAAATCCACGGAATTCATCATGAGTTGATGAATAACCGTAC
* ** *
19452 AGGCACTATATGTGCAAATCCAATGAATTCATCATGAGTTGATGAATAACAGTAC
1 AGGCACTATGTGTGCAAATCCACGGAATTCATCATGAGTTGATGAATAACCGTAC
** *** *
19507 AAACACTATGTGTGCAAATCCATATAATTCATCATGAGTTGATGAATAACAGTAC
1 AGGCACTATGTGTGCAAATCCACGGAATTCATCATGAGTTGATGAATAACCGTAC
** * * * *
19562 ATTCACTATGTGTGCAAATCCATGGAATTCATCATGAGTTAATGAATAACCATAT
1 AGGCACTATGTGTGCAAATCCACGGAATTCATCATGAGTTGATGAATAACCGTAC
* * * *
19617 AGACACTATGTGTGCAAATCCACGAAATTCATCATGAGTTAATGAATAACCGTAT
1 AGGCACTATGTGTGCAAATCCACGGAATTCATCATGAGTTGATGAATAACCGTAC
* * *
19672 AGGCTCTATGTGTGCAAATCCACGGAATTCATCATGAGTTGATGAATAACCATAT
1 AGGCACTATGTGTGCAAATCCACGGAATTCATCATGAGTTGATGAATAACCGTAC
* * * *
19727 AGGCACGATGTGTGC-AACCCCCGAAATTCATCATG
1 AGGCACTATGTGTGCAAATCCACGGAATTCATCATG
19762 GGTAAATGAA
Statistics
Matches: 419, Mismatches: 52, Indels: 7
0.88 0.11 0.01
Matches are distributed among these distances:
54 32 0.08
55 386 0.92
56 1 0.00
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.29
Consensus pattern (55 bp):
AGGCACTATGTGTGCAAATCCACGGAATTCATCATGAGTTGATGAATAACCGTAC
Found at i:20103 original size:45 final size:45
Alignment explanation
Indices: 20034--20158 Score: 223
Period size: 45 Copynumber: 2.8 Consensus size: 45
20024 GATCGATAGC
*
20034 AATGCATAATGGTGTATAAAAGGCATGAAAGGATGCCATAAATGA
1 AATGTATAATGGTGTATAAAAGGCATGAAAGGATGCCATAAATGA
*
20079 AATGTATAATGATGTATAAAAGGCATGAAAGGATGCCATAAATGA
1 AATGTATAATGGTGTATAAAAGGCATGAAAGGATGCCATAAATGA
*
20124 AATGTATAATGGTGTATAAAAGGCATAAAAGGATG
1 AATGTATAATGGTGTATAAAAGGCATGAAAGGATG
20159 TATAAACAAA
Statistics
Matches: 76, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
45 76 1.00
ACGTcount: A:0.46, C:0.06, G:0.24, T:0.24
Consensus pattern (45 bp):
AATGTATAATGGTGTATAAAAGGCATGAAAGGATGCCATAAATGA
Found at i:21671 original size:23 final size:21
Alignment explanation
Indices: 21645--21688 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 21
21635 CTGTGTAATT
21645 TAAAAATATTTCTTTATTCTAAA
1 TAAAAATATTT-TTTA-TCTAAA
*
21668 TAAATATATTTTTTATCTAAA
1 TAAAAATATTTTTTATCTAAA
21689 ACACAAAACT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 6 0.30
22 4 0.20
23 10 0.50
ACGTcount: A:0.43, C:0.07, G:0.00, T:0.50
Consensus pattern (21 bp):
TAAAAATATTTTTTATCTAAA
Found at i:21672 original size:21 final size:21
Alignment explanation
Indices: 21648--21688 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
21638 TGTAATTTAA
21648 AAATAT-TTCTTTATTCTAAAT
1 AAATATATTCTTTA-TCTAAAT
*
21669 AAATATATTTTTTATCTAAA
1 AAATATATTCTTTATCTAAA
21689 ACACAAAACT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.41, C:0.07, G:0.00, T:0.51
Consensus pattern (21 bp):
AAATATATTCTTTATCTAAAT
Found at i:22202 original size:13 final size:13
Alignment explanation
Indices: 22184--22241 Score: 64
Period size: 13 Copynumber: 4.5 Consensus size: 13
22174 ATTTAAGAAC
22184 TTTCATATTTCAT
1 TTTCATATTTCAT
* * *
22197 TTTCATCTTTTAC
1 TTTCATATTTCAT
22210 TTTCATA-TTCAT
1 TTTCATATTTCAT
* *
22222 TTTCACATTTTAT
1 TTTCATATTTCAT
22235 TTTCATA
1 TTTCATA
22242 ACCAGTACTT
Statistics
Matches: 35, Mismatches: 9, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
12 9 0.26
13 26 0.74
ACGTcount: A:0.22, C:0.17, G:0.00, T:0.60
Consensus pattern (13 bp):
TTTCATATTTCAT
Found at i:22215 original size:19 final size:19
Alignment explanation
Indices: 22184--22240 Score: 62
Period size: 19 Copynumber: 3.0 Consensus size: 19
22174 ATTTAAGAAC
*
22184 TTTCATATTTCATTTTCAT
1 TTTCACATTTCATTTTCAT
* *
22203 CTTTTAC-TTTCATATTCAT
1 -TTTCACATTTCATTTTCAT
*
22222 TTTCACATTTTATTTTCAT
1 TTTCACATTTCATTTTCAT
22241 AACCAGTACT
Statistics
Matches: 30, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
18 5 0.17
19 21 0.70
20 4 0.13
ACGTcount: A:0.21, C:0.18, G:0.00, T:0.61
Consensus pattern (19 bp):
TTTCACATTTCATTTTCAT
Found at i:22226 original size:25 final size:26
Alignment explanation
Indices: 22182--22241 Score: 88
Period size: 25 Copynumber: 2.3 Consensus size: 26
22172 ACATTTAAGA
22182 ACTTTCATATTTCATTTTCATC-TTTT
1 ACTTTCATATTTCATTTTCA-CATTTT
22208 ACTTTCATA-TTCATTTTCACATTTT
1 ACTTTCATATTTCATTTTCACATTTT
*
22233 ATTTTCATA
1 ACTTTCATA
22242 ACCAGTACTT
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
24 1 0.03
25 22 0.69
26 9 0.28
ACGTcount: A:0.23, C:0.18, G:0.00, T:0.58
Consensus pattern (26 bp):
ACTTTCATATTTCATTTTCACATTTT
Found at i:22336 original size:19 final size:19
Alignment explanation
Indices: 22272--22391 Score: 81
Period size: 19 Copynumber: 6.6 Consensus size: 19
22262 GAATTCATTC
* *
22272 TCAAATTCAAAACCT-ATT
1 TCAAATTCATAACTTAATT
* * *
22290 TCCATATTCAAAACTTACTT
1 T-CAAATTCATAACTTAATT
* *
22310 TTAGATTCATAACTTAATT
1 TCAAATTCATAACTTAATT
22329 TCAAATTC---A--TAATT
1 TCAAATTCATAACTTAATT
*
22343 TCAAATTCATAGCTTAATT
1 TCAAATTCATAACTTAATT
* * *
22362 TCATATTTATAGCTTAATT
1 TCAAATTCATAACTTAATT
*
22381 TCATATTCATA
1 TCAAATTCATA
22392 GGCCAATGCA
Statistics
Matches: 82, Mismatches: 13, Indels: 13
0.76 0.12 0.12
Matches are distributed among these distances:
14 13 0.16
16 1 0.01
18 1 0.01
19 64 0.78
20 3 0.04
ACGTcount: A:0.38, C:0.17, G:0.03, T:0.43
Consensus pattern (19 bp):
TCAAATTCATAACTTAATT
Found at i:22343 original size:14 final size:14
Alignment explanation
Indices: 22324--22353 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
22314 ATTCATAACT
22324 TAATTTCAAATTCA
1 TAATTTCAAATTCA
22338 TAATTTCAAATTCA
1 TAATTTCAAATTCA
22352 TA
1 TA
22354 GCTTAATTTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.43, C:0.13, G:0.00, T:0.43
Consensus pattern (14 bp):
TAATTTCAAATTCA
Found at i:22392 original size:19 final size:19
Alignment explanation
Indices: 22338--22392 Score: 92
Period size: 19 Copynumber: 2.9 Consensus size: 19
22328 TTCAAATTCA
*
22338 TAATTTCAAATTCATAGCT
1 TAATTTCATATTCATAGCT
*
22357 TAATTTCATATTTATAGCT
1 TAATTTCATATTCATAGCT
22376 TAATTTCATATTCATAG
1 TAATTTCATATTCATAG
22393 GCCAATGCAT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 33 1.00
ACGTcount: A:0.35, C:0.13, G:0.05, T:0.47
Consensus pattern (19 bp):
TAATTTCATATTCATAGCT
Found at i:26840 original size:35 final size:36
Alignment explanation
Indices: 26794--26864 Score: 126
Period size: 35 Copynumber: 2.0 Consensus size: 36
26784 CAAAATCGTC
26794 ATTTCCAATACTAGTGGGATAACCTAATTT-AGCAT
1 ATTTCCAATACTAGTGGGATAACCTAATTTGAGCAT
*
26829 ATTTCTAATACTAGTGGGATAACCTAATTTGAGCAT
1 ATTTCCAATACTAGTGGGATAACCTAATTTGAGCAT
26865 TATCAATATT
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
35 29 0.85
36 5 0.15
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.35
Consensus pattern (36 bp):
ATTTCCAATACTAGTGGGATAACCTAATTTGAGCAT
Found at i:44411 original size:18 final size:18
Alignment explanation
Indices: 44388--44440 Score: 79
Period size: 18 Copynumber: 2.9 Consensus size: 18
44378 AGGGATAATC
44388 AGTGGTCCTTCGGGACAT
1 AGTGGTCCTTCGGGACAT
* *
44406 AGTGGTTCTTCGGGATAT
1 AGTGGTCCTTCGGGACAT
*
44424 AGTGGTCCTTTGGGACA
1 AGTGGTCCTTCGGGACA
44441 AATTCTATGC
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.17, C:0.17, G:0.34, T:0.32
Consensus pattern (18 bp):
AGTGGTCCTTCGGGACAT
Found at i:45780 original size:25 final size:26
Alignment explanation
Indices: 45752--45814 Score: 74
Period size: 29 Copynumber: 2.3 Consensus size: 26
45742 ATAATACCCC
45752 AAATTTTGA-TTAGTGACCAAAATAT
1 AAATTTTGAGTTAGTGACCAAAATAT
*
45777 AAATTTTGAAAGTTTAGTGACCAAAGTAT
1 AAATTTTG--AG-TTAGTGACCAAAATAT
*
45806 AAAGTTTGA
1 AAATTTTGA
45815 AAAAGTTTAA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
25 8 0.25
27 2 0.06
29 22 0.69
ACGTcount: A:0.43, C:0.06, G:0.16, T:0.35
Consensus pattern (26 bp):
AAATTTTGAGTTAGTGACCAAAATAT
Found at i:45823 original size:31 final size:29
Alignment explanation
Indices: 45761--45834 Score: 96
Period size: 29 Copynumber: 2.5 Consensus size: 29
45751 CAAATTTTGA
* *
45761 TTAGTGACCAAAATATAAATTTTGAAAGT
1 TTAGTGACCAAAGTATAAAGTTTGAAAGT
45790 TTAGTGACCAAAGTATAAAGTTTGAAAAAGT
1 TTAGTGACCAAAGTATAAAGTTTG--AAAGT
45821 TTAAG-GACCAAAGT
1 TT-AGTGACCAAAGT
45835 CTAATTTTTA
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
29 22 0.55
31 16 0.40
32 2 0.05
ACGTcount: A:0.45, C:0.08, G:0.18, T:0.30
Consensus pattern (29 bp):
TTAGTGACCAAAGTATAAAGTTTGAAAGT
Found at i:51847 original size:35 final size:35
Alignment explanation
Indices: 51800--51878 Score: 133
Period size: 35 Copynumber: 2.3 Consensus size: 35
51790 GAATACTGGG
*
51800 TGACATTTATATTGTCCTT-CTTCAGATTAGCAACT
1 TGACATTCATATTGT-CTTGCTTCAGATTAGCAACT
51835 TGACATTCATATTGTCTTGCTTCAGATTAGCAACT
1 TGACATTCATATTGTCTTGCTTCAGATTAGCAACT
51870 TGACATTCA
1 TGACATTCA
51879 ATCCCAAACA
Statistics
Matches: 42, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
34 3 0.07
35 39 0.93
ACGTcount: A:0.27, C:0.20, G:0.13, T:0.41
Consensus pattern (35 bp):
TGACATTCATATTGTCTTGCTTCAGATTAGCAACT
Found at i:55404 original size:29 final size:29
Alignment explanation
Indices: 55344--55412 Score: 95
Period size: 29 Copynumber: 2.3 Consensus size: 29
55334 TATTTATTTT
*
55344 TTTTATTATATTTTATTATTACTATAATAA
1 TTTTATTAT-TATTATTATTACTATAATAA
*
55374 TTTTATTATTATTATTATTATTA-AATAAA
1 TTTTATTATTATTATTATTACTATAAT-AA
55403 TTTTATTATT
1 TTTTATTATT
55413 TCAGATCCAA
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
28 3 0.08
29 24 0.67
30 9 0.25
ACGTcount: A:0.36, C:0.01, G:0.00, T:0.62
Consensus pattern (29 bp):
TTTTATTATTATTATTATTACTATAATAA
Found at i:55412 original size:3 final size:3
Alignment explanation
Indices: 55325--55396 Score: 60
Period size: 3 Copynumber: 24.3 Consensus size: 3
55315 TCCATTACTC
* * * *
55325 ATT ATTT ATT ATTT ATT TTT TTT ATT A-T ATT -TT ATT ATT ACT ATA
1 ATT A-TT ATT A-TT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
*
55370 ATA ATT -TT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT A
55397 AATAAATTTT
Statistics
Matches: 58, Mismatches: 6, Indels: 10
0.78 0.08 0.14
Matches are distributed among these distances:
2 6 0.10
3 46 0.79
4 6 0.10
ACGTcount: A:0.32, C:0.01, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:56854 original size:16 final size:17
Alignment explanation
Indices: 56835--56868 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
56825 ATTTATTCAT
*
56835 TGTTTAA-TTTTTTTTA
1 TGTTTAACTTTTTATTA
56851 TGTTTAACTTTTTATTA
1 TGTTTAACTTTTTATTA
56868 T
1 T
56869 TACTATTATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.21, C:0.03, G:0.06, T:0.71
Consensus pattern (17 bp):
TGTTTAACTTTTTATTA
Found at i:61994 original size:16 final size:15
Alignment explanation
Indices: 61973--62010 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
61963 ATATACTCAA
*
61973 AAAAAAAGGAAAAAGG
1 AAAAAAA-GAAAAAAG
61989 AAAAAAAGAAAAAAG
1 AAAAAAAGAAAAAAG
62004 AAAAAAA
1 AAAAAAA
62011 ATTGAATCAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
15 14 0.67
16 7 0.33
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (15 bp):
AAAAAAAGAAAAAAG
Found at i:62011 original size:16 final size:16
Alignment explanation
Indices: 61972--62011 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
61962 CATATACTCA
*
61972 AAAAAAAAGGAAAAAG
1 AAAAAAAAGAAAAAAG
*
61988 GAAAAAAAGAAAAAAG
1 AAAAAAAAGAAAAAAG
62004 AAAAAAAA
1 AAAAAAAA
62012 TTGAATCATG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (16 bp):
AAAAAAAAGAAAAAAG
Found at i:67422 original size:113 final size:113
Alignment explanation
Indices: 67224--67774 Score: 810
Period size: 113 Copynumber: 4.9 Consensus size: 113
67214 GATTCAAATC
* * * * *
67224 CATCATTCAATGGATCAACATT-TCTGGAAGAGTTCATAATGAGAAGAACTCATCTGAAGAAAAA
1 CATCATTCGATGGATCAACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAAGA
*
67288 AGAAGAAGTTCATAATGAGAAGAACTTGTCCAACTTTTCGCTTGAATT
66 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTCGCTTGAATT
*
67336 CATCATTCGATGGATCAACATTGCCAGGTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAAGA
1 CATCATTCGATGGATCAACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAAGA
* * * *
67401 AGAAGAAGTTCATAATAAGAAGAACTTGTTCAAATTTTTGCTTAAATT
66 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTCGCTTGAATT
* * *
67449 CATCATTCGATGGATCATCATTGCCAGGTAGAGTTCATAATGAGAAGAACTCATTTGAAGAAGGA
1 CATCATTCGATGGATCAACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAAGA
67514 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTCGCTTGAATT
66 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTCGCTTGAATT
* * *
67562 CATCATTCGATGGATCAGCATTGCCAGGTCGAGTTCATAATGAGAAGAACTCATCTGAATAAAGA
1 CATCATTCGATGGATCAACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAAGA
* *
67627 AGAAGAAGTTCATAATGAGAAGAACGTT-TTCAACTTTT-TCTCGAATT
66 AGAAGAAGTTCATAATGAGAAGAAC-TTGTTCAACTTTTCGCTTGAATT
* * * * *
67674 CATCACTCGATGGTTCAACTTTTCCAGAG-AGAGTTCATTATGAGAAGAACTCATCTGAAG-AAG
1 CATCATTCGATGGATCAACATTGCCAG-GTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAAG
67737 --GAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTT
65 AAGAAGAAGTTCATAATGAGAAGAACTTGTTCAA-CTTTT
67775 GCATGATTCT
Statistics
Matches: 400, Mismatches: 34, Indels: 12
0.90 0.08 0.03
Matches are distributed among these distances:
108 2 0.00
109 29 0.07
110 5 0.01
111 3 0.01
112 78 0.19
113 281 0.70
114 2 0.00
ACGTcount: A:0.37, C:0.15, G:0.19, T:0.28
Consensus pattern (113 bp):
CATCATTCGATGGATCAACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAAGA
AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTCGCTTGAATT
Found at i:67986 original size:20 final size:19
Alignment explanation
Indices: 67926--67986 Score: 54
Period size: 20 Copynumber: 3.2 Consensus size: 19
67916 AGTGGAAGAG
67926 TTCATAATGAGAAGAATTA
1 TTCATAATGAGAAGAATTA
* ** *
67945 GTCCCAAAGAAGAAGAA-T-
1 TTCATAATG-AGAAGAATTA
67963 TTCATAATGAGAAGAACTTA
1 TTCATAATGAGAAGAA-TTA
67983 TTCA
1 TTCA
67987 ACATTTTTAT
Statistics
Matches: 30, Mismatches: 8, Indels: 7
0.67 0.18 0.16
Matches are distributed among these distances:
17 7 0.23
18 5 0.17
19 7 0.23
20 11 0.37
ACGTcount: A:0.46, C:0.11, G:0.16, T:0.26
Consensus pattern (19 bp):
TTCATAATGAGAAGAATTA
Found at i:68143 original size:16 final size:14
Alignment explanation
Indices: 68122--68160 Score: 53
Period size: 16 Copynumber: 2.7 Consensus size: 14
68112 CCATTACTCA
68122 TTATTTATTATTTATT
1 TTATTTATTA--TATT
68138 TTATTTATTATATT
1 TTATTTATTATATT
68152 TTA-TTATTA
1 TTATTTATTA
68161 CTATAATAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 6 0.26
14 7 0.30
16 10 0.43
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (14 bp):
TTATTTATTATATT
Found at i:68158 original size:13 final size:13
Alignment explanation
Indices: 68125--68160 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
68115 TTACTCATTA
68125 TTTATTATT-TAT
1 TTTATTATTATAT
68137 TTTATTTATTATAT
1 TTTA-TTATTATAT
68151 TTTATTATTA
1 TTTATTATTA
68161 CTATAATAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 4 0.18
13 11 0.50
14 7 0.32
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (13 bp):
TTTATTATTATAT
Found at i:68200 original size:29 final size:29
Alignment explanation
Indices: 68141--68208 Score: 93
Period size: 29 Copynumber: 2.3 Consensus size: 29
68131 ATTTATTTTA
*
68141 TTTATTATATTTTATTATTACTATAATAAT
1 TTTATTAT-TATTATTATTACTATAATAAT
*
68171 TTTATTATTATTATTATTATTA-AATAAAT
1 TTTATTATTATTATTATTACTATAAT-AAT
68200 TTTATTATT
1 TTTATTATT
68209 TCAGATCCAA
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
28 3 0.09
29 24 0.69
30 8 0.23
ACGTcount: A:0.37, C:0.01, G:0.00, T:0.62
Consensus pattern (29 bp):
TTTATTATTATTATTATTACTATAATAAT
Found at i:68208 original size:3 final size:3
Alignment explanation
Indices: 68121--68192 Score: 62
Period size: 3 Copynumber: 24.3 Consensus size: 3
68111 TCCATTACTC
* *
68121 ATT ATTT ATT ATTT ATT -TT ATTT ATT A-T ATT -TT ATT ATT ACT ATA
1 ATT A-TT ATT A-TT ATT ATT A-TT ATT ATT ATT ATT ATT ATT ATT ATT
*
68166 ATA ATT -TT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT A
68193 AATAAATTTT
Statistics
Matches: 58, Mismatches: 4, Indels: 14
0.76 0.05 0.18
Matches are distributed among these distances:
2 8 0.14
3 41 0.71
4 9 0.16
ACGTcount: A:0.33, C:0.01, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:69605 original size:10 final size:10
Alignment explanation
Indices: 69569--69598 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
69559 CTAGTTTTAA
*
69569 TATTTTAATT
1 TATTTTTATT
69579 TATTTTTATT
1 TATTTTTATT
69589 TATTTTTATT
1 TATTTTTATT
69599 GTTTTTTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (10 bp):
TATTTTTATT
Found at i:69658 original size:14 final size:14
Alignment explanation
Indices: 69639--69667 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
69629 ATTTATTCAT
69639 TGTTTAATTTTTTA
1 TGTTTAATTTTTTA
69653 TGTTTAATTTTTTA
1 TGTTTAATTTTTTA
69667 T
1 T
69668 TATTACTATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.21, C:0.00, G:0.07, T:0.72
Consensus pattern (14 bp):
TGTTTAATTTTTTA
Found at i:71887 original size:16 final size:16
Alignment explanation
Indices: 71866--71899 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
71856 TTACTATTTA
71866 TGTGAATAGTAAAATT
1 TGTGAATAGTAAAATT
71882 TGTGAATAGTAAAATT
1 TGTGAATAGTAAAATT
71898 TG
1 TG
71900 CTCTGCGATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.41, C:0.00, G:0.21, T:0.38
Consensus pattern (16 bp):
TGTGAATAGTAAAATT
Found at i:72679 original size:14 final size:15
Alignment explanation
Indices: 72650--72687 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
72640 TGGCCGATCG
*
72650 AAATCTAGAACGGGA
1 AAATCAAGAACGGGA
72665 AAATCAAGAAC-GGA
1 AAATCAAGAACGGGA
*
72679 AAATAAAGA
1 AAATCAAGA
72688 TTTTAACTGT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 11 0.52
15 10 0.48
ACGTcount: A:0.58, C:0.11, G:0.21, T:0.11
Consensus pattern (15 bp):
AAATCAAGAACGGGA
Found at i:87120 original size:48 final size:50
Alignment explanation
Indices: 87006--87130 Score: 164
Period size: 48 Copynumber: 2.5 Consensus size: 50
86996 TATACTACTT
* * *
87006 ACACCAGTGTAAGTATGTGTTAAGTGCTACACCCTTTTATTTTATTCAGTT
1 ACACCAGTGTAAGTATGTGTTAAGTGCTACA-CCTTTTATTTAATTCACTC
* * *
87057 ACATCGGTGTAAGTATGTGTTAAGTGCTGCA-CTTTT-TTTAATTCACTC
1 ACACCAGTGTAAGTATGTGTTAAGTGCTACACCTTTTATTTAATTCACTC
*
87105 ACACCAGTGTAAGTATATGTTAAGTG
1 ACACCAGTGTAAGTATGTGTTAAGTG
87131 TTAAACACTT
Statistics
Matches: 65, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
48 32 0.49
49 5 0.08
51 28 0.43
ACGTcount: A:0.26, C:0.16, G:0.18, T:0.39
Consensus pattern (50 bp):
ACACCAGTGTAAGTATGTGTTAAGTGCTACACCTTTTATTTAATTCACTC
Found at i:88599 original size:20 final size:20
Alignment explanation
Indices: 88574--88623 Score: 100
Period size: 20 Copynumber: 2.5 Consensus size: 20
88564 TGTAACTCTG
88574 GTATCGATACCACCCCAAGA
1 GTATCGATACCACCCCAAGA
88594 GTATCGATACCACCCCAAGA
1 GTATCGATACCACCCCAAGA
88614 GTATCGATAC
1 GTATCGATAC
88624 TTGACCTACA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.34, C:0.32, G:0.16, T:0.18
Consensus pattern (20 bp):
GTATCGATACCACCCCAAGA
Found at i:101787 original size:19 final size:21
Alignment explanation
Indices: 101763--101802 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
101753 GCAAAACAAA
101763 AAGAT-AACT-ATTAAATAAC
1 AAGATAAACTAATTAAATAAC
101782 AAGATAAACTAAATTAAATAA
1 AAGATAAACT-AATTAAATAA
101803 ATAAAGACTA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 5 0.28
20 4 0.22
22 9 0.50
ACGTcount: A:0.62, C:0.07, G:0.05, T:0.25
Consensus pattern (21 bp):
AAGATAAACTAATTAAATAAC
Found at i:105876 original size:26 final size:26
Alignment explanation
Indices: 105810--105869 Score: 79
Period size: 26 Copynumber: 2.3 Consensus size: 26
105800 TGAAAGAGCT
*
105810 AATAAAT-ATATTCTAATAAAAGAGGA
1 AATAAATCAT-TTTTAATAAAAGAGGA
105836 AATAAATCATTTTTAATAAAAGA-GA
1 AATAAATCATTTTTAATAAAAGAGGA
105861 AATTAAATC
1 AA-TAAATC
105870 TCTTTTATAT
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
25 4 0.13
26 25 0.81
27 2 0.06
ACGTcount: A:0.57, C:0.05, G:0.08, T:0.30
Consensus pattern (26 bp):
AATAAATCATTTTTAATAAAAGAGGA
Found at i:111206 original size:65 final size:63
Alignment explanation
Indices: 111134--111293 Score: 198
Period size: 65 Copynumber: 2.5 Consensus size: 63
111124 AATTAAATTG
* * *
111134 AACATCGAATGCATTTCATGCATCGATGCACA-TACCATGCATCGATGCACT-GAGGTTTTTATG
1 AACATCGAATGCATTTGATGCATCGATGCACAGT--CATGCATCGATGCACTCGAGATATTT-TG
111197 AA
63 -A
* *
111199 AACATCGAATGCATTTGATGCATCGATGCACCAGTCATGCATCGATGGACTCTAGATATTTTGA
1 AACATCGAATGCATTTGATGCATCGATGCA-CAGTCATGCATCGATGCACTCGAGATATTTTGA
* *
111263 AACATCGAATGCACTTGATGCATCAATGCAC
1 AACATCGAATGCATTTGATGCATCGATGCAC
111294 TCTTAGTGCA
Statistics
Matches: 85, Mismatches: 7, Indels: 8
0.85 0.07 0.08
Matches are distributed among these distances:
63 1 0.01
64 29 0.34
65 46 0.54
66 8 0.09
67 1 0.01
ACGTcount: A:0.31, C:0.22, G:0.19, T:0.28
Consensus pattern (63 bp):
AACATCGAATGCATTTGATGCATCGATGCACAGTCATGCATCGATGCACTCGAGATATTTTGA
Done.