Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008830.1 Hibiscus syriacus cultivar Beakdansim tig00112021_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: 78713
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:1300 original size:63 final size:64
Alignment explanation
Indices: 1228--1382 Score: 197
Period size: 63 Copynumber: 2.4 Consensus size: 64
1218 ACCAAGTGTG
* * *
1228 CATCGATGCATGAAATGCATTCGATGTTTGAAAAATAGCCTGA-TGCATTGATGCATGG-CTGTA
1 CATCGATGCATGAAATGCATTCGATGTTTG-AAAATAGCCAGAGTGCATCGATGCATGGACAGTA
* ** * *
1291 CATCGATGCATCAAATGCATTCGATGTTTGAAAATATTCAGAGTGCATCGATGCATGGAGAGTG
1 CATCGATGCATGAAATGCATTCGATGTTTGAAAATAGCCAGAGTGCATCGATGCATGGACAGTA
* *
1355 CATCGGTGCATGGAATGCATTCGATGTT
1 CATCGATGCATGAAATGCATTCGATGTT
1383 CAATTAATTC
Statistics
Matches: 79, Mismatches: 11, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
62 9 0.11
63 43 0.54
64 27 0.34
ACGTcount: A:0.29, C:0.16, G:0.25, T:0.30
Consensus pattern (64 bp):
CATCGATGCATGAAATGCATTCGATGTTTGAAAATAGCCAGAGTGCATCGATGCATGGACAGTA
Found at i:1354 original size:19 final size:19
Alignment explanation
Indices: 1330--1380 Score: 70
Period size: 19 Copynumber: 2.7 Consensus size: 19
1320 GAAAATATTC
1330 AGAGTGCATCGATGCATGG
1 AGAGTGCATCGATGCATGG
*
1349 AGAGTGCATCGGTGCATGG
1 AGAGTGCATCGATGCATGG
1368 A-A-TGCATTCGATG
1 AGAGTGCA-TCGATG
1381 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:2056 original size:18 final size:18
Alignment explanation
Indices: 2030--2064 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
2020 TCTCTTAAGG
2030 GTGTCGTATAAGAGAAAC
1 GTGTCGTATAAGAGAAAC
* *
2048 GTGTTGTATGAGAGAAA
1 GTGTCGTATAAGAGAAA
2065 GGTGCAATTG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.37, C:0.06, G:0.31, T:0.26
Consensus pattern (18 bp):
GTGTCGTATAAGAGAAAC
Found at i:4276 original size:19 final size:19
Alignment explanation
Indices: 4254--4293 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
4244 AATGGAGCAT
4254 ATGAGAACGTGAGGAGAAG
1 ATGAGAACGTGAGGAGAAG
* *
4273 ATGAGAATGTGAGGAGCAG
1 ATGAGAACGTGAGGAGAAG
4292 AT
1 AT
4294 TTATCTAGCC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.40, C:0.05, G:0.40, T:0.15
Consensus pattern (19 bp):
ATGAGAACGTGAGGAGAAG
Found at i:5473 original size:21 final size:19
Alignment explanation
Indices: 5445--5490 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 19
5435 TCATTGAATC
5445 ATTA-TTCTTAGCTCCTTAAT
1 ATTAGTTCTTAGCT--TTAAT
5465 ATTAGTTCTTAGCTTTAAT
1 ATTAGTTCTTAGCTTTAAT
5484 ACTTAGT
1 A-TTAGT
5491 AGGATTAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 6 0.25
20 9 0.38
21 9 0.38
ACGTcount: A:0.26, C:0.15, G:0.09, T:0.50
Consensus pattern (19 bp):
ATTAGTTCTTAGCTTTAAT
Found at i:10529 original size:14 final size:14
Alignment explanation
Indices: 10512--10539 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
10502 TAATATATTC
10512 AAAATAAAAATAAT
1 AAAATAAAAATAAT
10526 AAAATAAAAATAAT
1 AAAATAAAAATAAT
10540 TATTTTGGCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (14 bp):
AAAATAAAAATAAT
Found at i:11681 original size:187 final size:187
Alignment explanation
Indices: 11356--11710 Score: 649
Period size: 187 Copynumber: 1.9 Consensus size: 187
11346 AAAAAAACAG
*
11356 TTTATAATTAATTTAAATAATATATAATTATAAAATAAAAATTTTATATAAATTTTTTAATTAAT
1 TTTACAATTAATTTAAATAATATATAATTATAAAATAAAAATTTTATATAAATTTTTTAATTAAT
*
11421 TAATATTGATTTAGGTTTAAAAGTTATTGGATCTTAAATTATTAATTGAGTTTTAAATGGTTTGG
66 TAATATTGATTTAGGTTTAAAAGTTATTGGATCTTAAATTATTAATTGAGTTTTAAATAGTTTGG
* **
11486 GTTGAGTCCATATTTTATATATAATATATTTAATATTTTTTTAATTCAGAAAATTAA
131 GCTGAGTCCATATGCTATATATAATATATTTAATATTTTTTTAATTCAGAAAATTAA
11543 TTTACAATTAATTTAAATAATATATAATTATAAAATAAAAATTTTATATAAATTTTTTAATTAAT
1 TTTACAATTAATTTAAATAATATATAATTATAAAATAAAAATTTTATATAAATTTTTTAATTAAT
11608 TAATATTGATTTAGGTTTAAAAGTTATTGGATCTTAAATTATTAATTG-GATTTTAAATAGTTTG
66 TAATATTGATTTAGGTTTAAAAGTTATTGGATCTTAAATTATTAATTGAG-TTTTAAATAGTTTG
11672 GGCTGAGTCCATATGCTATATATAATATATTTAATATTT
130 GGCTGAGTCCATATGCTATATATAATATATTTAATATTT
11711 AAAATTTTAT
Statistics
Matches: 162, Mismatches: 5, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
186 1 0.01
187 161 0.99
ACGTcount: A:0.41, C:0.03, G:0.09, T:0.48
Consensus pattern (187 bp):
TTTACAATTAATTTAAATAATATATAATTATAAAATAAAAATTTTATATAAATTTTTTAATTAAT
TAATATTGATTTAGGTTTAAAAGTTATTGGATCTTAAATTATTAATTGAGTTTTAAATAGTTTGG
GCTGAGTCCATATGCTATATATAATATATTTAATATTTTTTTAATTCAGAAAATTAA
Found at i:30397 original size:17 final size:18
Alignment explanation
Indices: 30375--30408 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
30365 TCAACCGGTC
30375 CGGTTC-GAACGGTTCAA
1 CGGTTCTGAACGGTTCAA
*
30392 CGGTTCTGACCGGTTCA
1 CGGTTCTGAACGGTTCA
30409 CTAATAACGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.18, C:0.26, G:0.29, T:0.26
Consensus pattern (18 bp):
CGGTTCTGAACGGTTCAA
Found at i:31532 original size:50 final size:50
Alignment explanation
Indices: 31464--31588 Score: 164
Period size: 50 Copynumber: 2.5 Consensus size: 50
31454 GTAAAGCGTT
*
31464 CCCCTGAACCGCGCTATACGCTGATTTGGCGCCACGTAGGTATAGCGCGC
1 CCCCTGATCCGCGCTATACGCTGATTTGGCGCCACGTAGGTATAGCGCGC
* * * * * *
31514 CCCTTG-TCTCGCGATATACGGTGATTTGGCGCTACGTGGGTATAGCGTGC
1 CCCCTGATC-CGCGCTATACGCTGATTTGGCGCCACGTAGGTATAGCGCGC
31564 CCCCTGATCCGCGCTATAC-CTGATT
1 CCCCTGATCCGCGCTATACGCTGATT
31589 ATCTGACACG
Statistics
Matches: 63, Mismatches: 10, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
49 6 0.10
50 55 0.87
51 2 0.03
ACGTcount: A:0.16, C:0.31, G:0.27, T:0.26
Consensus pattern (50 bp):
CCCCTGATCCGCGCTATACGCTGATTTGGCGCCACGTAGGTATAGCGCGC
Found at i:31727 original size:10 final size:10
Alignment explanation
Indices: 31709--31747 Score: 69
Period size: 10 Copynumber: 3.9 Consensus size: 10
31699 TCACACCAAA
31709 TTCTCTCAAT
1 TTCTCTCAAT
*
31719 TTCTTTCAAT
1 TTCTCTCAAT
31729 TTCTCTCAAT
1 TTCTCTCAAT
31739 TTCTCTCAA
1 TTCTCTCAA
31748 ATACTCTCTC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
10 27 1.00
ACGTcount: A:0.21, C:0.28, G:0.00, T:0.51
Consensus pattern (10 bp):
TTCTCTCAAT
Found at i:31754 original size:20 final size:20
Alignment explanation
Indices: 31705--31755 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
31695 TTTTTCACAC
*
31705 CAAATTCTCTCAATTTCTTT
1 CAAATTCTCTCAATTTCTCT
*
31725 CAATTTCTCTCAATTTCTCT
1 CAAATTCTCTCAATTTCTCT
*
31745 CAAATACTCTC
1 CAAATTCTCTC
31756 TCTTTTTAAG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.25, C:0.29, G:0.00, T:0.45
Consensus pattern (20 bp):
CAAATTCTCTCAATTTCTCT
Found at i:31834 original size:17 final size:18
Alignment explanation
Indices: 31797--31837 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
31787 ATATTATGTA
*
31797 TTTAATTTATTTAAGTAT
1 TTTACTTTATTTAAGTAT
31815 TTTACTTTATTTAA-TAT
1 TTTACTTTATTTAAGTAT
31832 TTTACT
1 TTTACT
31838 AATATAATTC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 9 0.41
18 13 0.59
ACGTcount: A:0.29, C:0.05, G:0.02, T:0.63
Consensus pattern (18 bp):
TTTACTTTATTTAAGTAT
Found at i:32101 original size:111 final size:111
Alignment explanation
Indices: 31907--32120 Score: 428
Period size: 111 Copynumber: 1.9 Consensus size: 111
31897 ATATATATCT
31907 ACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAATAATTAGT
1 ACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAATAATTAGT
31972 TGATTTATTTAATGCATGATTATTAGATTAAGAATTAAATATCTCG
66 TGATTTATTTAATGCATGATTATTAGATTAAGAATTAAATATCTCG
32018 ACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAATAATTAGT
1 ACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAATAATTAGT
32083 TGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
66 TGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
32121 TTTTTGTAAT
Statistics
Matches: 103, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
111 103 1.00
ACGTcount: A:0.36, C:0.07, G:0.12, T:0.44
Consensus pattern (111 bp):
ACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAATAATTAGT
TGATTTATTTAATGCATGATTATTAGATTAAGAATTAAATATCTCG
Found at i:34026 original size:15 final size:15
Alignment explanation
Indices: 34006--34036 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
33996 CAGGACGACA
34006 ACGACGATGATGATG
1 ACGACGATGATGATG
*
34021 ACGACGATGGTGATG
1 ACGACGATGATGATG
34036 A
1 A
34037 TGATGACAGC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.32, C:0.13, G:0.35, T:0.19
Consensus pattern (15 bp):
ACGACGATGATGATG
Found at i:36558 original size:18 final size:18
Alignment explanation
Indices: 36522--36555 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
36512 TATTCATATT
*
36522 TTTATTTTTTCTTTTAAC
1 TTTATTTTTTCTTTAAAC
36540 TTTATTTTTT-TTTAAA
1 TTTATTTTTTCTTTAAA
36556 ACTATGAAGG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.21, C:0.06, G:0.00, T:0.74
Consensus pattern (18 bp):
TTTATTTTTTCTTTAAAC
Found at i:36961 original size:23 final size:23
Alignment explanation
Indices: 36930--36973 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
36920 AGTATAATAC
* *
36930 TATATTAGGTAGCGTTTATATAA
1 TATAATAGGTAGCGCTTATATAA
36953 TATAATAGGTAGCGCTTATAT
1 TATAATAGGTAGCGCTTATAT
36974 TGACCTATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.34, C:0.07, G:0.18, T:0.41
Consensus pattern (23 bp):
TATAATAGGTAGCGCTTATATAA
Found at i:37903 original size:182 final size:181
Alignment explanation
Indices: 37590--38041 Score: 685
Period size: 182 Copynumber: 2.5 Consensus size: 181
37580 CACTTTTTAC
* * * *
37590 TACCAGTTTTGTCCTTTTGAGATCGATTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGA
1 TACCTGTTTTGTCATTTAGAGACCGATTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGA
* ** *
37655 TACATTTTTATAAAGTACCGACACTTTATTAACGTTATAACTTCTTTTCTTTTAAATTCTAAAAG
66 TACATTTTTATAAAGTATCGACACTTTATTAACACTATAACTTCTTTTCTTTTAAATTCCAAAAG
*
37720 TGTCGATACTTATAATAAAATATCGACACTATCAACATATTCGGTAGC-TCTT
131 TGTCGATACTTATAAT-AAATATCGACACTATCAACATATCCGGTAGCGT-TT
*
37772 TACC-GATTTTGTCATTTCGAGACCGATTTTGTCATATTTTTACCTGTTATATTGTTATGGATCG
1 TACCTG-TTTTGTCATTTAGAGACCGATTTTGTCATATTTTTACCTGTTATATTGTTATGGATCG
* * *
37836 ATATATTTTTATAAAGTATCAACACTTTATTAGCACTATAACTTCTTTTCTTTTAAATTCCAAAA
65 ATACATTTTTATAAAGTATCGACACTTTATTAACACTATAACTTCTTTTCTTTTAAATTCCAAAA
*
37901 GTGTCGATACTTATAATAAGTATCGACACTATCAACATATCCGGTAGCGTTT
130 GTGTCGATACTTATAATAAATATCGACACTATCAACATATCCGGTAGCGTTT
* * * * *
37953 TACCTGTTTTGTCATTTATAGACCAATTTTGTCAT-TTTTTACTTGTTTTATTGTTATGGATTGA
1 TACCTGTTTTGTCATTTAGAGACCGATTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGA
38017 TACATTTTTATAAAGTATCGACACT
66 TACATTTTTATAAAGTATCGACACT
38042 ATCAACATAT
Statistics
Matches: 247, Mismatches: 20, Indels: 8
0.90 0.07 0.03
Matches are distributed among these distances:
180 49 0.20
181 62 0.25
182 136 0.55
ACGTcount: A:0.28, C:0.15, G:0.12, T:0.44
Consensus pattern (181 bp):
TACCTGTTTTGTCATTTAGAGACCGATTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGA
TACATTTTTATAAAGTATCGACACTTTATTAACACTATAACTTCTTTTCTTTTAAATTCCAAAAG
TGTCGATACTTATAATAAATATCGACACTATCAACATATCCGGTAGCGTTT
Found at i:38191 original size:111 final size:112
Alignment explanation
Indices: 37918--38514 Score: 984
Period size: 111 Copynumber: 5.4 Consensus size: 112
37908 TACTTATAAT
* * * **
37918 AAGTATCGACACTATCAACATATCCGGTAGCGTTTTACCTGTTTTGTCATTTATAGACCAATTTT
1 AAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGTTTT
* * *
37983 GTCA-TTTTTTACTTGTTTTATTGTTATGGATTGATACATTTTTATA
66 GTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATA
* * * *
38029 AAGTATCGACACTATCAACATATCCGTTAGCGCTTTACCTGTTTTGTCATTTATAGATCGGTTTT
1 AAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGTTTT
* *
38094 GTCATTTTTTTACATGTTATATTGTTATGGATCGATACAATTTTATA
66 GTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATA
*
38141 AAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTATTTT-TCATTTATAGACCGGTTTT
1 AAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGTTTT
* *
38205 TTCATTTTTTTACCTGTTATATTGTTATGGATCGATACAATTTTATA
66 GTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATA
*
38252 AATTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTT-TCATTTATAGACCGGTTTT
1 AAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGTTTT
38316 GTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATA
66 GTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATA
*
38363 AAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACATGTTTTGTCATTTATAGACCGGTTTT
1 AAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGTTTT
* *
38428 GTCATTTTTTTACCTGTTATATTGTTATGGATTGATATATTTTTATA
66 GTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATA
38475 AAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCT
1 AAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCT
38515 AGGGGTGTTC
Statistics
Matches: 459, Mismatches: 25, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
111 277 0.60
112 182 0.40
ACGTcount: A:0.25, C:0.16, G:0.14, T:0.45
Consensus pattern (112 bp):
AAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGTTTT
GTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATA
Found at i:38415 original size:223 final size:224
Alignment explanation
Indices: 37918--38514 Score: 993
Period size: 223 Copynumber: 2.7 Consensus size: 224
37908 TACTTATAAT
* * * **
37918 AAGTATCGACACTATCAACATATCCGGTAGCGTTTTACCTGTTTTGTCATTTATAGACCAATTTT
1 AAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGTTTT
* * *
37983 GTCA-TTTTTTACTTGTTTTATTGTTATGGATTGATACATTTTTATAAAGTATCGACACTATCAA
66 GTCATTTTTTTACCTGTTATATTGTTATGGATTGATACATTTTTATAAAGTATCGACACTTTCAA
* * *
38047 CATATCCGTTAGCGCTTTACCTGTTTTGTCATTTATAGATCGGTTTTGTCATTTTTTTACATGTT
131 TATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGTTTTGTCATTTTTTTACATGTT
38112 ATATTGTTATGGATCGATACAATTTTATA
196 ATATTGTTATGGATCGATACAATTTTATA
*
38141 AAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTATTTT-TCATTTATAGACCGGTTTT
1 AAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGTTTT
* * * *
38205 TTCATTTTTTTACCTGTTATATTGTTATGGATCGATACAATTTTATAAATTATCGACACTTTCAA
66 GTCATTTTTTTACCTGTTATATTGTTATGGATTGATACATTTTTATAAAGTATCGACACTTTCAA
*
38270 TATATCCGGTAGCGCTTTACCTGTTTT-TCATTTATAGACCGGTTTTGTCATTTTTTTACCTGTT
131 TATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGTTTTGTCATTTTTTTACATGTT
*
38334 ATATTGTTATGGATCGATACATTTTTATA
196 ATATTGTTATGGATCGATACAATTTTATA
*
38363 AAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACATGTTTTGTCATTTATAGACCGGTTTT
1 AAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGTTTT
*
38428 GTCATTTTTTTACCTGTTATATTGTTATGGATTGATATATTTTTATAAAGTATCGACACTTTCAA
66 GTCATTTTTTTACCTGTTATATTGTTATGGATTGATACATTTTTATAAAGTATCGACACTTTCAA
38493 TATATCCGGTAGCGCTTTACCT
131 TATATCCGGTAGCGCTTTACCT
38515 AGGGGTGTTC
Statistics
Matches: 347, Mismatches: 25, Indels: 4
0.92 0.07 0.01
Matches are distributed among these distances:
222 126 0.36
223 221 0.64
ACGTcount: A:0.25, C:0.16, G:0.14, T:0.45
Consensus pattern (224 bp):
AAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGTTTT
GTCATTTTTTTACCTGTTATATTGTTATGGATTGATACATTTTTATAAAGTATCGACACTTTCAA
TATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGTTTTGTCATTTTTTTACATGTT
ATATTGTTATGGATCGATACAATTTTATA
Found at i:39014 original size:184 final size:184
Alignment explanation
Indices: 38696--39083 Score: 661
Period size: 184 Copynumber: 2.1 Consensus size: 184
38686 ATTAAATTTT
* * *
38696 AAATTTTAAATATATTATATATAACATATGGGCTCAGCCCAAACCATTTAAAACCCAATTAATAA
1 AAATATTAAATATATTATATATAACATATAGGCTAAGCCCAAACCATTTAAAACCCAATTAATAA
*
38761 TTTAAGATCTAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAAATTATATAAAATTT
66 TTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAAATTATATAAAATTT
*
38826 TTATTTTATAATTATATATTATTTAAATTAATTGTAAACTATTTTTTAATTAAA
131 TTATTTTATAATTATATATTATTTAAATTAATTATAAACTATTTTTTAATTAAA
*
38880 AAATATTATATATATTATATATAACATATAGGCTAAGCCCAAACCATTTAAAACCCAATTAATAA
1 AAATATTAAATATATTATATATAACATATAGGCTAAGCCCAAACCATTTAAAACCCAATTAATAA
* * *
38945 TTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAATTTATCTGAAATTT
66 TTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAAATTATATAAAATTT
*
39010 TTATTTTATAATTATATATTATTTAAATTAATTATAAACTTTTTTTTAATTAAA
131 TTATTTTATAATTATATATTATTTAAATTAATTATAAACTATTTTTTAATTAAA
* *
39064 AAATATTTAAT-TTTTATATA
1 AAATATTAAATATATTATATA
39084 AATTAGGAAA
Statistics
Matches: 191, Mismatches: 13, Indels: 1
0.93 0.06 0.00
Matches are distributed among these distances:
183 8 0.04
184 183 0.96
ACGTcount: A:0.46, C:0.09, G:0.03, T:0.42
Consensus pattern (184 bp):
AAATATTAAATATATTATATATAACATATAGGCTAAGCCCAAACCATTTAAAACCCAATTAATAA
TTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAAATTATATAAAATTT
TTATTTTATAATTATATATTATTTAAATTAATTATAAACTATTTTTTAATTAAA
Found at i:39230 original size:15 final size:15
Alignment explanation
Indices: 39210--39238 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
39200 AAAAAAAGTT
39210 TGGTTAATTCGGTTA
1 TGGTTAATTCGGTTA
39225 TGGTTAATTCGGTT
1 TGGTTAATTCGGTT
39239 CGGTTCGGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.17, C:0.07, G:0.28, T:0.48
Consensus pattern (15 bp):
TGGTTAATTCGGTTA
Found at i:40242 original size:3 final size:3
Alignment explanation
Indices: 40234--40322 Score: 178
Period size: 3 Copynumber: 29.7 Consensus size: 3
40224 TTTACAAAGA
40234 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
40282 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
40323 AGTAAAAGCA
Statistics
Matches: 86, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 86 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:45326 original size:20 final size:21
Alignment explanation
Indices: 45272--45334 Score: 65
Period size: 20 Copynumber: 2.9 Consensus size: 21
45262 GATTCCCCTG
45272 TGGGGGGAATCGGTTCCCCTTCAA
1 TGGGGGG-ATCGGTT-CCC-TCAA
* *
45296 AGGGGGAATCGGTTCCCTC-A
1 TGGGGGGATCGGTTCCCTCAA
*
45316 TGGGGGGATCGATTCCCTC
1 TGGGGGGATCGGTTCCCTC
45335 TGCACCAAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
20 17 0.50
21 2 0.06
22 3 0.09
23 7 0.21
24 5 0.15
ACGTcount: A:0.16, C:0.25, G:0.35, T:0.24
Consensus pattern (21 bp):
TGGGGGGATCGGTTCCCTCAA
Found at i:49180 original size:22 final size:21
Alignment explanation
Indices: 49138--49177 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
49128 GAGTTTGTTT
*
49138 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
49159 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
49178 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:57100 original size:29 final size:29
Alignment explanation
Indices: 57037--57203 Score: 127
Period size: 30 Copynumber: 5.6 Consensus size: 29
57027 AAAATAACAA
* * ***
57037 AAACTGAAAGGACTAAAATAGAAAAAACCT
1 AAACTTAAGGGACTAAAATA-AAAAAATAG
* *
57067 AAACTTAAGAGATTAAAATAAAAAAATAG
1 AAACTTAAGGGACTAAAATAAAAAAATAG
* * *
57096 AAACTTAAGGGACTAAAACAACAAAAACAT
1 AAACTTAAGGGACTAAAATAA-AAAAATAG
* * *
57126 ATAGTTAAGGGACTAAAATCATAAAAATAG
1 AAACTTAAGGGACTAAAAT-AAAAAAATAG
* * ** *
57156 AAACTTAAGGGGCTAAATTAGTAAAAACCAA
1 AAACTTAAGGGACTAAAATA--AAAAAATAG
57187 AAACTTAAGGGACTAAA
1 AAACTTAAGGGACTAAA
57204 TAGTAAATAA
Statistics
Matches: 106, Mismatches: 27, Indels: 7
0.76 0.19 0.05
Matches are distributed among these distances:
29 25 0.24
30 59 0.56
31 22 0.21
ACGTcount: A:0.57, C:0.11, G:0.14, T:0.18
Consensus pattern (29 bp):
AAACTTAAGGGACTAAAATAAAAAAATAG
Found at i:57109 original size:59 final size:60
Alignment explanation
Indices: 57037--57203 Score: 176
Period size: 59 Copynumber: 2.8 Consensus size: 60
57027 AAAATAACAA
* * *
57037 AAACTGAAAGGACTAAAATAGAAAAAACCTAAACTTAAGAGATTAAAAT-AAAAAAATAG
1 AAACTTAAGGGACTAAAATAGAAAAAACCTAAACTTAAGAGACTAAAATCAAAAAAATAG
* * * * * *
57096 AAACTTAAGGGACTAAAACA-ACAAAAACATATAGTTAAGGGACTAAAATCATAAAAATAG
1 AAACTTAAGGGACTAAAATAGA-AAAAACCTAAACTTAAGAGACTAAAATCAAAAAAATAG
* * * * *
57156 AAACTTAAGGGGCTAAATTAGTAAAAACCAAAAACTTAAGGGACTAAA
1 AAACTTAAGGGACTAAAATAGAAAAAACC-TAAACTTAAGAGACTAAA
57204 TAGTAAATAA
Statistics
Matches: 87, Mismatches: 17, Indels: 6
0.79 0.15 0.05
Matches are distributed among these distances:
58 1 0.01
59 39 0.45
60 32 0.37
61 15 0.17
ACGTcount: A:0.57, C:0.11, G:0.14, T:0.18
Consensus pattern (60 bp):
AAACTTAAGGGACTAAAATAGAAAAAACCTAAACTTAAGAGACTAAAATCAAAAAAATAG
Found at i:58895 original size:3 final size:3
Alignment explanation
Indices: 58887--58928 Score: 52
Period size: 3 Copynumber: 14.3 Consensus size: 3
58877 AAAATAACAA
*
58887 AAT AAT AAT AAT AA- ACAT AAT AAT AAT AAT AA- ATT AAT AAT A
1 AAT AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT A
58929 TTTTTAGTAG
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
2 2 0.06
3 31 0.91
4 1 0.03
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:58903 original size:18 final size:18
Alignment explanation
Indices: 58882--58919 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
58872 AATTAAAAAT
58882 AACAAAATAATAATAATA
1 AACAAAATAATAATAATA
*
58900 AACATAATAATAATAATA
1 AACAAAATAATAATAATA
58918 AA
1 AA
58920 TTAATAATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.71, C:0.05, G:0.00, T:0.24
Consensus pattern (18 bp):
AACAAAATAATAATAATA
Found at i:60490 original size:20 final size:20
Alignment explanation
Indices: 60454--60492 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
60444 CTCTAAATCA
*
60454 TTTTCAAAATTTCATTTTGG
1 TTTTCAAAATTCCATTTTGG
60474 TTTTCAAAA-TCCAATTTTG
1 TTTTCAAAATTCC-ATTTTG
60493 CTTTCAATAG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 2 0.12
20 15 0.88
ACGTcount: A:0.28, C:0.13, G:0.08, T:0.51
Consensus pattern (20 bp):
TTTTCAAAATTCCATTTTGG
Found at i:61762 original size:31 final size:31
Alignment explanation
Indices: 61719--61781 Score: 108
Period size: 31 Copynumber: 2.0 Consensus size: 31
61709 GTATCGATAC
*
61719 TACCTTTGTTATTTTTAAATCAACTAGTCGT
1 TACCTTTGTTATTTTTAAATCAACTAGCCGT
*
61750 TACCTTTTTTATTTTTAAATCAACTAGCCGT
1 TACCTTTGTTATTTTTAAATCAACTAGCCGT
61781 T
1 T
61782 GGGGCCTGAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.25, C:0.17, G:0.08, T:0.49
Consensus pattern (31 bp):
TACCTTTGTTATTTTTAAATCAACTAGCCGT
Found at i:63508 original size:18 final size:18
Alignment explanation
Indices: 63487--63521 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
63477 ACACTTACCA
63487 CGATAACACCACTTGTCG
1 CGATAACACCACTTGTCG
*
63505 CGATAACATCACTTGTC
1 CGATAACACCACTTGTC
63522 ACGGCAACTC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.29, C:0.31, G:0.14, T:0.26
Consensus pattern (18 bp):
CGATAACACCACTTGTCG
Found at i:64551 original size:27 final size:27
Alignment explanation
Indices: 64484--64538 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 27
64474 ATGTCCTCCA
*
64484 CCGTATCCTCCACCTCCACTACCGTAT
1 CCGTATCCTCCACCTCCACCACCGTAT
64511 CCGTATCCTCCACCTCCACCACCGTAT
1 CCGTATCCTCCACCTCCACCACCGTAT
64538 C
1 C
64539 ATTTATGCCC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.18, C:0.51, G:0.07, T:0.24
Consensus pattern (27 bp):
CCGTATCCTCCACCTCCACCACCGTAT
Found at i:64642 original size:18 final size:18
Alignment explanation
Indices: 64582--64642 Score: 50
Period size: 18 Copynumber: 3.2 Consensus size: 18
64572 TACTGGAACT
* * *
64582 TCCATGTCTATCGCATCC
1 TCCATGTTTACCGTATCC
* *
64600 TCCATGTTTACCACCATATCT
1 TCCATGTTT---ACCGTATCC
64621 TCCATGTTTACCGTATCC
1 TCCATGTTTACCGTATCC
64639 TCCA
1 TCCA
64643 CCATAACCGT
Statistics
Matches: 33, Mismatches: 7, Indels: 6
0.72 0.15 0.13
Matches are distributed among these distances:
18 19 0.58
21 14 0.42
ACGTcount: A:0.20, C:0.36, G:0.08, T:0.36
Consensus pattern (18 bp):
TCCATGTTTACCGTATCC
Found at i:75075 original size:14 final size:13
Alignment explanation
Indices: 75037--75077 Score: 64
Period size: 13 Copynumber: 3.1 Consensus size: 13
75027 ACTTGACCGA
75037 ATCCGATTACCCG
1 ATCCGATTACCCG
*
75050 ATCTGATTACCCG
1 ATCCGATTACCCG
75063 ATCCGATTTACCCG
1 ATCCGA-TTACCCG
75077 A
1 A
75078 CCCAATACTT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
13 17 0.68
14 8 0.32
ACGTcount: A:0.24, C:0.34, G:0.15, T:0.27
Consensus pattern (13 bp):
ATCCGATTACCCG
Found at i:75556 original size:23 final size:22
Alignment explanation
Indices: 75481--75556 Score: 62
Period size: 23 Copynumber: 3.2 Consensus size: 22
75471 AAAAAATTAG
*
75481 ATTTATAATAAAAATAATAGAA
1 ATTTATAATAAAAATAATATAA
* * * *
75503 AATAACTAAAAAAGAAATAATATTAT
1 ATTTA-T-AATAA-AAATAATA-TAA
75529 ATTTATAATAAAAATAATATAA
1 ATTTATAATAAAAATAATATAA
75551 AGTTTA
1 A-TTTA
75557 CTTATGTTAC
Statistics
Matches: 40, Mismatches: 9, Indels: 9
0.69 0.16 0.16
Matches are distributed among these distances:
22 6 0.15
23 13 0.32
24 8 0.20
25 9 0.22
26 4 0.10
ACGTcount: A:0.62, C:0.01, G:0.04, T:0.33
Consensus pattern (22 bp):
ATTTATAATAAAAATAATATAA
Done.