Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006504.1 Hibiscus syriacus cultivar Beakdansim tig00015828_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: 50552
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Found at i:4534 original size:19 final size:19
Alignment explanation
Indices: 4510--4560 Score: 70
Period size: 19 Copynumber: 2.7 Consensus size: 19
4500 GAAAATATTC
4510 AGAGTGCATCGATGCATGG
1 AGAGTGCATCGATGCATGG
*
4529 AGAGTGCATCGGTGCATGG
1 AGAGTGCATCGATGCATGG
4548 A-A-TGCATTCGATG
1 AGAGTGCA-TCGATG
4561 TTCAATTAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
17 4 0.14
18 6 0.21
19 19 0.66
ACGTcount: A:0.25, C:0.16, G:0.35, T:0.24
Consensus pattern (19 bp):
AGAGTGCATCGATGCATGG
Found at i:4602 original size:65 final size:64
Alignment explanation
Indices: 4404--4610 Score: 219
Period size: 65 Copynumber: 3.2 Consensus size: 64
4394 GCACCAAGTG
* * * *
4404 TGCATCGGTGCATGAAATGCATTCGATGTTTGAAAAATAGCCTGGTGCATCGATGCAT-GTCTTG
1 TGCATCGGTGCATGAAATGCATTCGATGTTTGAAAAAT-TCATGATGCATCGATGCATGGAC-TG
4468 -
64 A
* *
4468 TGCATCGATGCATCAAATGCATTCGATGTTTTGAAAATATTCA-GAGTGCATCGATGCATGGA--
1 TGCATCGGTGCATGAAATGCATTCGATG-TTTGAAAA-ATTCATGA-TGCATCGATGCATGGACT
4530 GA
63 GA
* * *
4532 GTGCATCGGTGCATGGAATGCATTCGATG-TTCAATTAATTCATCGATGCATCGATGCATGGACT
1 -TGCATCGGTGCATGAAATGCATTCGATGTTTGAA-AAATTCAT-GATGCATCGATGCATGGACT
4596 GA
63 GA
4598 TGCATCGGTGCAT
1 TGCATCGGTGCAT
4611 ACCTTTGAAT
Statistics
Matches: 121, Mismatches: 11, Indels: 21
0.79 0.07 0.14
Matches are distributed among these distances:
63 10 0.08
64 44 0.36
65 62 0.51
66 5 0.04
ACGTcount: A:0.27, C:0.17, G:0.26, T:0.30
Consensus pattern (64 bp):
TGCATCGGTGCATGAAATGCATTCGATGTTTGAAAAATTCATGATGCATCGATGCATGGACTGA
Found at i:9394 original size:19 final size:19
Alignment explanation
Indices: 9370--9420 Score: 84
Period size: 19 Copynumber: 2.7 Consensus size: 19
9360 GGAACACTTA
*
9370 GTGCATCGGTGCACCAAGT
1 GTGCATCGATGCACCAAGT
9389 GTGCATCGATGCACCAAGT
1 GTGCATCGATGCACCAAGT
*
9408 GTGTATCGATGCA
1 GTGCATCGATGCA
9421 TAAAATGCAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.24, C:0.24, G:0.29, T:0.24
Consensus pattern (19 bp):
GTGCATCGATGCACCAAGT
Found at i:9491 original size:64 final size:64
Alignment explanation
Indices: 9412--9566 Score: 186
Period size: 64 Copynumber: 2.4 Consensus size: 64
9402 CCAAGTGTGT
* ** * * ***
9412 ATCGATGCATAAAATGCATTCGATGTTTGAA-AATAACCTGAGTGCATCGATGCATTGCTTGTGC
1 ATCGATGCATGAAATGCATTCGATGTTTGAATAA-AACCCAAGTGCATCGATACATAGAGAGTGC
* * * *
9476 ATTGATGCATGAAATGCATTCTATGTTTTAATAAAACCCAAGTGTATCGATACATAGAGAGTGC
1 ATCGATGCATGAAATGCATTCGATGTTTGAATAAAACCCAAGTGCATCGATACATAGAGAGTGC
9540 ATCGATGCATGAAATGCATTCGATGTT
1 ATCGATGCATGAAATGCATTCGATGTT
9567 CAATTTATTC
Statistics
Matches: 76, Mismatches: 14, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
64 74 0.97
65 2 0.03
ACGTcount: A:0.32, C:0.15, G:0.21, T:0.32
Consensus pattern (64 bp):
ATCGATGCATGAAATGCATTCGATGTTTGAATAAAACCCAAGTGCATCGATACATAGAGAGTGC
Found at i:11736 original size:219 final size:219
Alignment explanation
Indices: 11357--11787 Score: 700
Period size: 219 Copynumber: 2.0 Consensus size: 219
11347 CCACCCTAGT
11357 GGTGGTGGTGCAGGATTCACCCATAACAGAGGTGAGACTGGTGGCTATGGAGGAGGCGGCGTACA
1 GGTGGTGGTGCAGGATTCACCCATAACAGAGGTGAGACTGGTGGCTATGGAGGAGGCGGCGTACA
* * * * **
11422 TGACGCCAGCTGTGGGTACCCCACAGAAGATATTGGGACTGGGTATTACTCGGGCGGGCAGGTTA
66 TGACGCCAACAGTGGGTACCCCACAGAAGATACTGGGACTGGGTATGACTCGGGAAGGCAGGTTA
*
11487 GGGCGGATGAAAATATGAATATGGGGTATGGTGGAGAAACAGGGGGTGGATTAGGTTATTCAACA
131 GGGCGGATGAAAATATGAATATGGGGTATGGTGGAGAAACAGAGGGTGGATTAGGTTATTCAACA
*
11552 ACTGGGGGAAACATTGGAGGGGCA
196 ACCGGGGGAAACATTGGAGGGGCA
* * *
11576 GGTGGTGGTGCTGGATTCACCCATAACAGAGGTGAGACTGGTGGCTATGGAGGCGGCGGCGTATA
1 GGTGGTGGTGCAGGATTCACCCATAACAGAGGTGAGACTGGTGGCTATGGAGGAGGCGGCGTACA
* * *
11641 TGACGCCAACAGTGGGTACTCCACAGCAGATACTGGGACTGGGTATGACTTGGGAAGGCAGGTTA
66 TGACGCCAACAGTGGGTACCCCACAGAAGATACTGGGACTGGGTATGACTCGGGAAGGCAGGTTA
* * *
11706 GGTCGGATGAAAATATGAATATGGGGTATGGTGGAGACACAGAGGGTGGATTGGGTTATTCAACA
131 GGGCGGATGAAAATATGAATATGGGGTATGGTGGAGAAACAGAGGGTGGATTAGGTTATTCAACA
*
11771 ACCGGGGGAAGCATTGG
196 ACCGGGGGAAACATTGG
11788 TGGGACATGG
Statistics
Matches: 194, Mismatches: 18, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
219 194 1.00
ACGTcount: A:0.26, C:0.15, G:0.39, T:0.21
Consensus pattern (219 bp):
GGTGGTGGTGCAGGATTCACCCATAACAGAGGTGAGACTGGTGGCTATGGAGGAGGCGGCGTACA
TGACGCCAACAGTGGGTACCCCACAGAAGATACTGGGACTGGGTATGACTCGGGAAGGCAGGTTA
GGGCGGATGAAAATATGAATATGGGGTATGGTGGAGAAACAGAGGGTGGATTAGGTTATTCAACA
ACCGGGGGAAACATTGGAGGGGCA
Found at i:12322 original size:38 final size:35
Alignment explanation
Indices: 12218--12392 Score: 171
Period size: 38 Copynumber: 4.9 Consensus size: 35
12208 AAAACAATTT
* * *
12218 TTTTAGTTTTATAATT-AAAAAATACGAAAATCAA
1 TTTTAGTGTTATAATTGAAAAAATATGAAAATAAA
12252 TTTTAGT-TTCATAATTGAAAAAAATACT-AAAATAAAAA
1 TTTTAGTGTT-ATAATTG-AAAAAATA-TGAAAAT--AAA
*
12290 TATTTAGTGTTATAATTGAAAAAATATGAAAATTAA
1 T-TTTAGTGTTATAATTGAAAAAATATGAAAATAAA
12326 TTTTAGTGTTATAATTGAAAAAATTACT-AAAATCAAAA
1 TTTTAGTGTTATAATTGAAAAAA-TA-TGAAAAT--AAA
* *
12364 TTTTATTGTTCTAATTGAAAAAAT-TGAAA
1 TTTTAGTGTTATAATTGAAAAAATATGAAA
12393 GTTTAATAAT
Statistics
Matches: 121, Mismatches: 6, Indels: 26
0.79 0.04 0.17
Matches are distributed among these distances:
33 2 0.02
34 13 0.11
35 23 0.19
36 26 0.21
37 3 0.02
38 39 0.32
39 13 0.11
40 2 0.02
ACGTcount: A:0.50, C:0.04, G:0.08, T:0.38
Consensus pattern (35 bp):
TTTTAGTGTTATAATTGAAAAAATATGAAAATAAA
Found at i:12399 original size:73 final size:74
Alignment explanation
Indices: 12219--12392 Score: 248
Period size: 74 Copynumber: 2.4 Consensus size: 74
12209 AAACAATTTT
* * *
12219 TTTAGTTTTATAATT-AAAAAATACGAAAATCAATTTTAGTTTCATAATTGAAAAAAATACTAAA
1 TTTAGTGTTATAATTGAAAAAATATGAAAATTAATTTTAGTTTCATAATTGAAAAAAATACTAAA
12283 ATAAAAATA
66 ATAAAAATA
*
12292 TTTAGTGTTATAATTGAAAAAATATGAAAATTAATTTTAGTGTT-ATAATTGAAAAAATTACTAA
1 TTTAGTGTTATAATTGAAAAAATATGAAAATTAATTTTAGT-TTCATAATTGAAAAAAATACTAA
*
12356 AATCAAAAT-
65 AATAAAAATA
* *
12365 TTTATTGTTCTAATTGAAAAAAT-TGAAA
1 TTTAGTGTTATAATTGAAAAAATATGAAA
12393 GTTTAATAAT
Statistics
Matches: 92, Mismatches: 7, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
72 5 0.05
73 35 0.38
74 50 0.54
75 2 0.02
ACGTcount: A:0.50, C:0.04, G:0.08, T:0.38
Consensus pattern (74 bp):
TTTAGTGTTATAATTGAAAAAATATGAAAATTAATTTTAGTTTCATAATTGAAAAAAATACTAAA
ATAAAAATA
Found at i:12836 original size:17 final size:15
Alignment explanation
Indices: 12814--12861 Score: 53
Period size: 14 Copynumber: 3.0 Consensus size: 15
12804 CAATCATCGA
12814 TATTTTTTTAGTCTTTT
1 TATTTTTTTA-T-TTTT
12831 TATTTTTTCTTATTTTT
1 TA-TTTTT-TTATTTTT
12848 TA-TTTTTTATTTTT
1 TATTTTTTTATTTTT
12862 AATAAGCTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
14 8 0.28
15 4 0.14
17 8 0.28
18 6 0.21
19 3 0.10
ACGTcount: A:0.12, C:0.04, G:0.02, T:0.81
Consensus pattern (15 bp):
TATTTTTTTATTTTT
Found at i:14504 original size:13 final size:14
Alignment explanation
Indices: 14474--14511 Score: 69
Period size: 13 Copynumber: 2.8 Consensus size: 14
14464 TCAACTCGTC
14474 TGACTTTGACCTGT
1 TGACTTTGACCTGT
14488 TGACTTTGACC-GT
1 TGACTTTGACCTGT
14501 TGACTTTGACC
1 TGACTTTGACC
14512 CAAAAAGTCA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
13 13 0.54
14 11 0.46
ACGTcount: A:0.16, C:0.24, G:0.21, T:0.39
Consensus pattern (14 bp):
TGACTTTGACCTGT
Found at i:17738 original size:20 final size:22
Alignment explanation
Indices: 17689--17746 Score: 75
Period size: 20 Copynumber: 2.6 Consensus size: 22
17679 GCATGGGTAG
17689 TGCATCGATGCACATGTTAAAGAA
1 TGCATCGATGCAC-TGTT-AAGAA
*
17713 TGCATCGATGCACTG-T-AGAT
1 TGCATCGATGCACTGTTAAGAA
17733 TGCATCGATGCACT
1 TGCATCGATGCACT
17747 TCAAGGGGAA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
20 17 0.52
22 1 0.03
23 2 0.06
24 13 0.39
ACGTcount: A:0.29, C:0.21, G:0.22, T:0.28
Consensus pattern (22 bp):
TGCATCGATGCACTGTTAAGAA
Found at i:20163 original size:34 final size:33
Alignment explanation
Indices: 20125--20231 Score: 112
Period size: 34 Copynumber: 3.3 Consensus size: 33
20115 AGAACATTTC
20125 CATTTCATATCAAACTTGTACCTTTCACTTTATT
1 CATTTCATATCAAAC-TGTACCTTTCACTTTATT
* * *
20159 CATTTCATAGC--A-TGTATCATTCACTTTATT
1 CATTTCATATCAAACTGTACCTTTCACTTTATT
* * *
20189 CATTTCACATCAAACATGTGCCTTTCATTTTATT
1 CATTTCATATCAAAC-TGTACCTTTCACTTTATT
*
20223 CTTTTCATA
1 CATTTCATA
20232 GCCCATTGTA
Statistics
Matches: 58, Mismatches: 11, Indels: 8
0.75 0.14 0.10
Matches are distributed among these distances:
30 25 0.43
32 2 0.03
34 31 0.53
ACGTcount: A:0.26, C:0.22, G:0.05, T:0.47
Consensus pattern (33 bp):
CATTTCATATCAAACTGTACCTTTCACTTTATT
Found at i:20396 original size:48 final size:48
Alignment explanation
Indices: 20339--20548 Score: 249
Period size: 48 Copynumber: 4.4 Consensus size: 48
20329 TACAATTGAA
* * * *
20339 AGCAGCACCACCTTCACACATACGTCAGATGTGCTAGTTATCATTAAT
1 AGCAGCACCACCGTCACACAGACGTCAGACGTGCTAATTATCATTAAT
* * * * * *
20387 AGCATCACCATCATCACACAGATGTCAGACGTGCTAGTTATCGTTAAT
1 AGCAGCACCACCGTCACACAGACGTCAGACGTGCTAATTATCATTAAT
* ** *
20435 AGTAGCACCATAGTCACACAGACGTCAAACGTGCTAATTATCATTAAT
1 AGCAGCACCACCGTCACACAGACGTCAGACGTGCTAATTATCATTAAT
* * * *
20483 AGCATCACCACCGTTACACAGACGTCAGACGTGCTAATTATCTTTGAT
1 AGCAGCACCACCGTCACACAGACGTCAGACGTGCTAATTATCATTAAT
*
20531 AGTAGCACCACCGTCACA
1 AGCAGCACCACCGTCACA
20549 AAAGTGACGT
Statistics
Matches: 136, Mismatches: 26, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
48 136 1.00
ACGTcount: A:0.32, C:0.27, G:0.16, T:0.25
Consensus pattern (48 bp):
AGCAGCACCACCGTCACACAGACGTCAGACGTGCTAATTATCATTAAT
Found at i:20547 original size:96 final size:96
Alignment explanation
Indices: 20342--20548 Score: 288
Period size: 96 Copynumber: 2.2 Consensus size: 96
20332 AATTGAAAGC
* * * * * *
20342 AGCACCACCTTCACACATACGTCAGATGTGCTAGTTATCATTAATAGCATCACCATCATCACACA
1 AGCACCACCGTCACACAGACGTCAAACGTGCTAATTATCATTAATAGCATCACCACCATCACACA
* *
20407 GATGTCAGACGTGCTAGTTATCGTTAATAGT
66 GACGTCAGACGTGCTAATTATCGTTAATAGT
** * *
20438 AGCACCATAGTCACACAGACGTCAAACGTGCTAATTATCATTAATAGCATCACCACCGTTACACA
1 AGCACCACCGTCACACAGACGTCAAACGTGCTAATTATCATTAATAGCATCACCACCATCACACA
* *
20503 GACGTCAGACGTGCTAATTATCTTTGATAGT
66 GACGTCAGACGTGCTAATTATCGTTAATAGT
20534 AGCACCACCGTCACA
1 AGCACCACCGTCACA
20549 AAAGTGACGT
Statistics
Matches: 95, Mismatches: 16, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
96 95 1.00
ACGTcount: A:0.32, C:0.27, G:0.15, T:0.26
Consensus pattern (96 bp):
AGCACCACCGTCACACAGACGTCAAACGTGCTAATTATCATTAATAGCATCACCACCATCACACA
GACGTCAGACGTGCTAATTATCGTTAATAGT
Found at i:22586 original size:15 final size:15
Alignment explanation
Indices: 22552--22599 Score: 60
Period size: 15 Copynumber: 3.0 Consensus size: 15
22542 CCTTTTTCAT
22552 ATTATATTATATTGTAA
1 ATTATATTA-ATT-TAA
22569 ATTATATTAATTTAA
1 ATTATATTAATTTAA
*
22584 ATTATTTTAAATTTAA
1 ATTATATT-AATTTAA
22600 TGATACTTCA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
15 10 0.34
16 10 0.34
17 9 0.31
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
ATTATATTAATTTAA
Found at i:24164 original size:19 final size:19
Alignment explanation
Indices: 24142--24179 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
24132 ATCGATTGTT
* *
24142 TAAAATTTTTACCGTTTTC
1 TAAAATTTTAACCGGTTTC
24161 TAAAATTTTAACCGGTTTC
1 TAAAATTTTAACCGGTTTC
24180 GACAACAAAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.29, C:0.16, G:0.08, T:0.47
Consensus pattern (19 bp):
TAAAATTTTAACCGGTTTC
Found at i:26257 original size:64 final size:62
Alignment explanation
Indices: 26173--26376 Score: 182
Period size: 64 Copynumber: 3.2 Consensus size: 62
26163 CATTCATAAG
*
26173 TGCATCGATGCATTCC-TTTAAAAGAAGAACATCGAATGCCTTTGATGCATCGATGCATAGCTAA
1 TGCATCGATGCA-TCCTTTTAAAAGAAGAACATCGAATGCATTT-ATGCATCGATGCATAG-TAA
* * **
26237 TGCATCGATGCATCCTTTTAAAATAATAGAACATCAAATGCAAGTAGTGCATCGATGCATAAGGT
1 TGCATCGATGCATCCTTTTAAAA-GA-AGAACATCGAATGCATTTA-TGCATCGATGCAT-A-GT
26302 -A
61 AA
* * * *
26303 TGCATCGATGCAT-CTCATTAATAAGGA-AACATCGAATGCATTTTATGCACCGATGCACAAGTA
1 TGCATCGATGCATCCT-TTTAA-AAGAAGAACATCGAATGCA-TTTATGCATCGATGCA-TAGTA
*
26366 G
62 A
26367 TGCATCGATG
1 TGCATCGATG
26377 TATACCTTCA
Statistics
Matches: 115, Mismatches: 14, Indels: 22
0.76 0.09 0.15
Matches are distributed among these distances:
63 5 0.04
64 53 0.46
65 7 0.06
66 45 0.39
67 4 0.03
68 1 0.01
ACGTcount: A:0.34, C:0.19, G:0.19, T:0.27
Consensus pattern (62 bp):
TGCATCGATGCATCCTTTTAAAAGAAGAACATCGAATGCATTTATGCATCGATGCATAGTAA
Found at i:26290 original size:66 final size:62
Alignment explanation
Indices: 26150--26316 Score: 165
Period size: 66 Copynumber: 2.5 Consensus size: 62
26140 TCTAGACAAG
* * * * **
26150 GTGCATCGATGCACATTCATAAGTGCATCGATGCATTCCTTTAAAAGAAGAACATCGAATGCCTT
1 GTGCATCGATGCATA-GC-TAA-TGCATCGATGCA-TCCTTTAAAAAAAGAACATCAAATGCAGT
*
26215 T
62 A
26216 GATGCATCGATGCATAGCTAATGCATCGATGCATCCTTTTAAAATAATAGAACATCAAATGCAAG
1 G-TGCATCGATGCATAGCTAATGCATCGATGCATCC-TTTAAAA-AA-AGAACATCAAATGC-AG
26281 TA
61 TA
*
26283 GTGCATCGATGCATAAGGT-ATGCATCGATGCATC
1 GTGCATCGATGCAT-AGCTAATGCATCGATGCATC
26317 TCATTAATAA
Statistics
Matches: 87, Mismatches: 8, Indels: 12
0.81 0.07 0.11
Matches are distributed among these distances:
63 3 0.03
64 19 0.22
65 4 0.05
66 43 0.49
67 18 0.21
ACGTcount: A:0.34, C:0.20, G:0.19, T:0.28
Consensus pattern (62 bp):
GTGCATCGATGCATAGCTAATGCATCGATGCATCCTTTAAAAAAAGAACATCAAATGCAGTA
Found at i:27109 original size:30 final size:30
Alignment explanation
Indices: 27058--27121 Score: 76
Period size: 30 Copynumber: 2.1 Consensus size: 30
27048 AAGGAACATA
* *
27058 TGGATAGTTGCCGAGGATCTTTATGACCTC
1 TGGATAGTTACCGAGGATCTTTATAACCTC
* *
27088 TGGATAGTTACC-AGGGTTCTTTGTAACCTC
1 TGGATAGTTACCGA-GGATCTTTATAACCTC
27118 TGGA
1 TGGA
27122 CAGGTCCTTC
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
29 1 0.03
30 28 0.97
ACGTcount: A:0.20, C:0.19, G:0.27, T:0.34
Consensus pattern (30 bp):
TGGATAGTTACCGAGGATCTTTATAACCTC
Found at i:30063 original size:20 final size:20
Alignment explanation
Indices: 30026--30063 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
30016 AATCGTTTGT
*
30026 TTAAATTTTTTACCATTTTC
1 TTAAATTTTTAACCATTTTC
30046 TTAAA-TTTTAACCGATTT
1 TTAAATTTTTAACC-ATTT
30064 AGAAATTGTA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 7 0.44
20 9 0.56
ACGTcount: A:0.29, C:0.13, G:0.03, T:0.55
Consensus pattern (20 bp):
TTAAATTTTTAACCATTTTC
Found at i:31408 original size:6 final size:6
Alignment explanation
Indices: 31397--31435 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
31387 ATTTATATTG
* * *
31397 AAATTC AAATTC AAACTC AAATTG AAATTT AAATTC AAA
1 AAATTC AAATTC AAATTC AAATTC AAATTC AAATTC AAA
31436 CTCCAATTAA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.54, C:0.13, G:0.03, T:0.31
Consensus pattern (6 bp):
AAATTC
Found at i:31416 original size:12 final size:12
Alignment explanation
Indices: 31401--31443 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
31391 ATATTGAAAT
31401 TCAAATTCAAAC
1 TCAAATTCAAAC
* *
31413 TCAAATTGAAAT
1 TCAAATTCAAAC
*
31425 TTAAATTCAAAC
1 TCAAATTCAAAC
*
31437 TCCAATT
1 TCAAATT
31444 AAAAATGAAA
Statistics
Matches: 24, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.47, C:0.19, G:0.02, T:0.33
Consensus pattern (12 bp):
TCAAATTCAAAC
Found at i:31420 original size:24 final size:24
Alignment explanation
Indices: 31393--31443 Score: 84
Period size: 24 Copynumber: 2.1 Consensus size: 24
31383 CAAAATTTAT
31393 ATTGAAATTCAAATTCAAACTCAA
1 ATTGAAATTCAAATTCAAACTCAA
* *
31417 ATTGAAATTTAAATTCAAACTCCA
1 ATTGAAATTCAAATTCAAACTCAA
31441 ATT
1 ATT
31444 AAAAATGAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.47, C:0.16, G:0.04, T:0.33
Consensus pattern (24 bp):
ATTGAAATTCAAATTCAAACTCAA
Found at i:31454 original size:24 final size:24
Alignment explanation
Indices: 31403--31454 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
31393 ATTGAAATTC
* * *
31403 AAATTCAAACTCAAATTGAAATTT
1 AAATTCAAACTCAAATTAAAAATG
*
31427 AAATTCAAACTCCAATTAAAAATG
1 AAATTCAAACTCAAATTAAAAATG
31451 AAAT
1 AAAT
31455 GAACATGAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.54, C:0.13, G:0.04, T:0.29
Consensus pattern (24 bp):
AAATTCAAACTCAAATTAAAAATG
Found at i:34024 original size:18 final size:17
Alignment explanation
Indices: 34003--34080 Score: 79
Period size: 18 Copynumber: 4.4 Consensus size: 17
33993 TGATTTGGTC
34003 AGAAGAAGAGATTGGTTG
1 AGAAGAAGAG-TTGGTTG
*
34021 AGAAGAAG-GTTGTCGTTA
1 AGAAGAAGAGTTG--GTTG
34039 AGAAGAAGAGCTTGGTTG
1 AGAAGAAGAG-TTGGTTG
34057 AGAAGAAG-GTTGTCGTTG
1 AGAAGAAGAGTTG--GTTG
34075 AGAAGA
1 AGAAGA
34081 CCCGCACCTC
Statistics
Matches: 52, Mismatches: 2, Indels: 12
0.79 0.03 0.18
Matches are distributed among these distances:
16 6 0.12
17 2 0.04
18 40 0.77
19 1 0.02
20 3 0.06
ACGTcount: A:0.36, C:0.04, G:0.37, T:0.23
Consensus pattern (17 bp):
AGAAGAAGAGTTGGTTG
Found at i:34054 original size:36 final size:36
Alignment explanation
Indices: 34003--34080 Score: 138
Period size: 36 Copynumber: 2.2 Consensus size: 36
33993 TGATTTGGTC
34003 AGAAGAAGAGATTGGTTGAGAAGAAGGTTGTCGTTA
1 AGAAGAAGAGATTGGTTGAGAAGAAGGTTGTCGTTA
* *
34039 AGAAGAAGAGCTTGGTTGAGAAGAAGGTTGTCGTTG
1 AGAAGAAGAGATTGGTTGAGAAGAAGGTTGTCGTTA
34075 AGAAGA
1 AGAAGA
34081 CCCGCACCTC
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 40 1.00
ACGTcount: A:0.36, C:0.04, G:0.37, T:0.23
Consensus pattern (36 bp):
AGAAGAAGAGATTGGTTGAGAAGAAGGTTGTCGTTA
Found at i:34699 original size:201 final size:200
Alignment explanation
Indices: 34369--35306 Score: 1382
Period size: 201 Copynumber: 4.7 Consensus size: 200
34359 TTAAAACATT
* **
34369 GTATCGATACATTATGTTTACCTATTCTCTCATTAAACCGGTATATTTTTACCAGTTACATTGTA
1 GTATCGATACATTATGTTTACCTATTCTCTCATTAAACCGATATATTTTTACTGGTTACATTGTA
* * *
34434 AATTTACCTATTACTTTATAATAATCGGTTTTGATGTTTTAAGGATCGATACTTAATAAAAAATG
66 AATTTACCTATTACTTTATAATAATCGGTTTCGATGTTTTGAGGATCGATACTTTAT-AAAAATG
* * *
34499 TATCGACACTTTATGTGTGCATCTCGTTTGGCATTCATTCTGGACAAAAAGTATCGATACAATTT
130 TATCGACACTTTATGCGTACATCTCGTTTGGCAATCATTCTGGACAAAAAGTATCGATACAATTT
34564 AAAAAA
195 AAAAAA
* *
34570 GTATCGATACATTATGTTTACCTATTCTTTCATTAAACCAATATATTTTTACTGGTTACATTGTA
1 GTATCGATACATTATGTTTACCTATTCTCTCATTAAACCGATATATTTTTACTGGTTACATTGT-
*
34635 AAATTTACCTATTACTTTATAATAATCGGTTTCGATGTTTTGATGATCGATACTTTATAAAAATG
65 AAATTTACCTATTACTTTATAATAATCGGTTTCGATGTTTTGAGGATCGATACTTTATAAAAATG
34700 TATCGACACTTTATGCGTACATCTCGTTTGGCAATCATTCTGGACAAAAAGTATCGATACAATTT
130 TATCGACACTTTATGCGTACATCTCGTTTGGCAATCATTCTGGACAAAAAGTATCGATACAATTT
34765 AAAAAAA
195 -AAAAAA
* * * *
34772 ATATCGATACATTATGTTTACCTTTTCT-TCCATTAAACCGGTATATTTTTACCGGTTACATTGT
1 GTATCGATACATTATGTTTACCTATTCTCT-CATTAAACCGATATATTTTTACTGGTTACATTGT
* * * **
34836 AAATTTACATATTACTTTATAATAATAGGTTTTGACATTTTGAGGATCGATACTTTATAAAAATG
65 AAATTTACCTATTACTTTATAATAATCGGTTTCGATGTTTTGAGGATCGATACTTTATAAAAATG
* * * * * * * *
34901 TATCAACACTTTATGCGTGCATCTCGTTTGACATTCATTTTGGACAAAAAGTTTCAATACCATTT
130 TATCGACACTTTATGCGTACATCTCGTTTGGCAATCATTCTGGACAAAAAGTATCGATA-CAATT
34966 TAAAAAA
194 TAAAAAA
* *
34973 GTATCGATACATTATGTTTACCTATTCTCTCATTAAATCGATATATTTTTACCT-GTTACATTCT
1 GTATCGATACATTATGTTTACCTATTCTCTCATTAAACCGATATATTTTTA-CTGGTTACATTGT
* * * * * *
35037 AAATTTACCTATTACTTTATAATAATCAGTTTCGATATTTTTAGGATAGATACTTAATATAAATG
65 AAATTTACCTATTACTTTATAATAATCGGTTTCGATGTTTTGAGGATCGATACTTTATAAAAATG
* * * *
35102 TATTGCCACTTTATGCATACATCTCGTTTGGAAATCATTCTGGACAAAAAGTATCGATACAATTT
130 TATCGACACTTTATGCGTACATCTCGTTTGGCAATCATTCTGGACAAAAAGTATCGATACAATTT
35167 -AAAAA
195 AAAAAA
*
35172 GTATCGATACATTATGTTTACCTATTCTCTCATTAAACTGATATATTTTTA-TCGGTTACATTGT
1 GTATCGATACATTATGTTTACCTATTCTCTCATTAAACCGATATATTTTTACT-GGTTACATTGT
*
35236 AAATTTACCTATTACTTTATAATAATCAGTTTCGATGTTTTGAGGATCGATAC-TTATAATAAAT
65 AAATTTACCTATTACTTTATAATAATCGGTTTCGATGTTTTGAGGATCGATACTTTATAA-AAAT
35300 GTATCGA
129 GTATCGA
35307 TACCTCTAGT
Statistics
Matches: 660, Mismatches: 68, Indels: 20
0.88 0.09 0.03
Matches are distributed among these distances:
197 1 0.00
198 4 0.01
199 122 0.18
200 5 0.01
201 404 0.61
202 124 0.19
ACGTcount: A:0.33, C:0.15, G:0.12, T:0.41
Consensus pattern (200 bp):
GTATCGATACATTATGTTTACCTATTCTCTCATTAAACCGATATATTTTTACTGGTTACATTGTA
AATTTACCTATTACTTTATAATAATCGGTTTCGATGTTTTGAGGATCGATACTTTATAAAAATGT
ATCGACACTTTATGCGTACATCTCGTTTGGCAATCATTCTGGACAAAAAGTATCGATACAATTTA
AAAAA
Found at i:40215 original size:20 final size:21
Alignment explanation
Indices: 40190--40239 Score: 59
Period size: 22 Copynumber: 2.4 Consensus size: 21
40180 ACAACCTGCA
*
40190 TTTATAATTAA-AT-TTATCAT
1 TTTATAAATAATATATTAT-AT
40210 TTTATATAATAATATATTATAT
1 TTTATA-AATAATATATTATAT
40232 TTTATAAA
1 TTTATAAA
40240 AAACAAAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
20 6 0.23
21 6 0.23
22 10 0.38
23 4 0.15
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (21 bp):
TTTATAAATAATATATTATAT
Found at i:42502 original size:180 final size:181
Alignment explanation
Indices: 42215--42647 Score: 592
Period size: 180 Copynumber: 2.4 Consensus size: 181
42205 TCCGGTATCA
* * *
42215 CTTTACCGGTTTTTTCATAATGAAACC-TTTTATCATACTTTTACCTGTTATATTGTTACATATC
1 CTTTACCGGTTTTGTCATAATGAAACCGTTTTGTCATACTTTTACCTGATATATTGTTACA-ATC
* *
42279 GATACATATTTATAAAATATCGATACTTTATAGGCGCTATTAATGATTTTCTTTAAAATTCTATA
65 GATACATATTTATAAAATATCGATACTTTATAGGCGCTATTAATGATTTTCTTTAAAAATCCATA
* * *
42344 AGTATCGATAATTATTTGAATGGAATCGATACCTTCAACATATCTACTAGTG
130 AGTATCGATAATTATTTGAATGGAATCGATACATTCAACATATCCACTAGCG
*
42396 CTTTACCGGTTTTGTCATAATGAAACCGGTTTTGTCATA-TTTTACCTGCTATATTGTTAC-ATC
1 CTTTACCGGTTTTGTCATAATGAAACC-GTTTTGTCATACTTTTACCTGATATATTGTTACAATC
* * * *
42459 GATACATGTTTATAAAGTATCGATACTTTATAGGCTCTATTAATGCTTTTCTTTAAAAATCCATA
65 GATACATATTTATAAAATATCGATACTTTATAGGCGCTATTAATGATTTTCTTTAAAAATCCATA
* * **
42524 AGTATCGATACTTATTTGAATGTAATCGATACATTCAACATATCCGGTAGCG
130 AGTATCGATAATTATTTGAATGGAATCGATACATTCAACATATCCACTAGCG
* * * **
42576 CTTTA-CGGTTTTGTCATATTG-AA--GTTATGTCATATTTTTACCTGATATATTGTTATGTATC
1 CTTTACCGGTTTTGTCATAATGAAACCGTTTTGTCATACTTTTACCTGATATATTGTTA-CAATC
42637 GATACATATTT
65 GATACATATTT
42648 GAATGGTATC
Statistics
Matches: 226, Mismatches: 21, Indels: 13
0.87 0.08 0.05
Matches are distributed among these distances:
175 10 0.04
176 19 0.08
178 15 0.07
179 15 0.07
180 112 0.50
181 26 0.12
182 20 0.09
183 9 0.04
ACGTcount: A:0.30, C:0.15, G:0.12, T:0.43
Consensus pattern (181 bp):
CTTTACCGGTTTTGTCATAATGAAACCGTTTTGTCATACTTTTACCTGATATATTGTTACAATCG
ATACATATTTATAAAATATCGATACTTTATAGGCGCTATTAATGATTTTCTTTAAAAATCCATAA
GTATCGATAATTATTTGAATGGAATCGATACATTCAACATATCCACTAGCG
Found at i:43958 original size:18 final size:18
Alignment explanation
Indices: 43927--43974 Score: 59
Period size: 16 Copynumber: 2.8 Consensus size: 18
43917 GGTGCGTTTT
43927 AGGTA-GGTTAGGTT-AG
1 AGGTATGGTTAGGTTAAG
43943 AGGTATGGTGTAGGTTAAG
1 AGGTATGGT-TAGGTTAAG
43962 AGG-ATGG-TAGGTT
1 AGGTATGGTTAGGTT
43975 TTCAGTCGTG
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
16 11 0.38
17 3 0.10
18 10 0.34
19 5 0.17
ACGTcount: A:0.25, C:0.00, G:0.44, T:0.31
Consensus pattern (18 bp):
AGGTATGGTTAGGTTAAG
Done.