Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001679.1 Hibiscus syriacus cultivar Beakdansim tig00003357_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: 79969
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.34
Found at i:9568 original size:27 final size:27
Alignment explanation
Indices: 9537--9590 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
9527 ATCTTGTGAT
9537 TATTTGGTCTCCACATTGCTTGAATAG
1 TATTTGGTCTCCACATTGCTTGAATAG
9564 TATTTGGTCTCCACATTGCTTGAATAG
1 TATTTGGTCTCCACATTGCTTGAATAG
9591 GAACGGTTCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.22, C:0.19, G:0.19, T:0.41
Consensus pattern (27 bp):
TATTTGGTCTCCACATTGCTTGAATAG
Found at i:12667 original size:21 final size:21
Alignment explanation
Indices: 12642--12705 Score: 101
Period size: 21 Copynumber: 3.0 Consensus size: 21
12632 CATCAGAGTC
* *
12642 TTTGTTGAAGCCATGAAATCT
1 TTTGTCGAGGCCATGAAATCT
12663 TTTGTCGAGGCCATGAAATCT
1 TTTGTCGAGGCCATGAAATCT
*
12684 TTTGTCGAGGCCATGAATTCT
1 TTTGTCGAGGCCATGAAATCT
12705 T
1 T
12706 GCAATGAAAC
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 40 1.00
ACGTcount: A:0.23, C:0.17, G:0.22, T:0.38
Consensus pattern (21 bp):
TTTGTCGAGGCCATGAAATCT
Found at i:21861 original size:16 final size:16
Alignment explanation
Indices: 21820--21866 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
21810 ACTTTGATAA
*
21820 CATTTCTTTCTTTCA-T
1 CATTTCTTTC-TTAATT
*
21836 C-TTTCATTCTTAATT
1 CATTTCTTTCTTAATT
21851 CATTTCTTTCTTAATT
1 CATTTCTTTCTTAATT
21867 TTATAACTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
14 3 0.12
15 9 0.35
16 14 0.54
ACGTcount: A:0.17, C:0.21, G:0.00, T:0.62
Consensus pattern (16 bp):
CATTTCTTTCTTAATT
Found at i:24980 original size:24 final size:24
Alignment explanation
Indices: 24953--25002 Score: 84
Period size: 24 Copynumber: 2.1 Consensus size: 24
24943 GCATGACATT
24953 TGTACATAGATGTTT-TATACATCA
1 TGTACATAGAT-TTTCTATACATCA
24977 TGTACATAGATTTTCTATACATCA
1 TGTACATAGATTTTCTATACATCA
25001 TG
1 TG
25003 AGGAAGACTT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
23 3 0.12
24 22 0.88
ACGTcount: A:0.32, C:0.14, G:0.12, T:0.42
Consensus pattern (24 bp):
TGTACATAGATTTTCTATACATCA
Found at i:29452 original size:44 final size:46
Alignment explanation
Indices: 29331--29457 Score: 161
Period size: 48 Copynumber: 2.8 Consensus size: 46
29321 TATAAAATCT
*
29331 CTTACCATTT-ATCCCATAAGCTCGTAAGCTTATTTTACCAAAATA
1 CTTACCATTTAATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
* *
29376 CTTACCATTTAAAATTCCATAAGCTCGTAAGCTTATTTTTCCAATATA
1 CTTACCATTT--AATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
* * *
29424 CTTGCCA-TT-ATTCCGTAAGCTCATAAGCTTATTT
1 CTTACCATTTAATTCCATAAGCTCGTAAGCTTATTT
29458 GCATGGTTAC
Statistics
Matches: 73, Mismatches: 6, Indels: 7
0.85 0.07 0.08
Matches are distributed among these distances:
44 23 0.32
45 10 0.14
47 2 0.03
48 38 0.52
ACGTcount: A:0.31, C:0.23, G:0.08, T:0.39
Consensus pattern (46 bp):
CTTACCATTTAATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
Found at i:29529 original size:15 final size:15
Alignment explanation
Indices: 29509--29540 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
29499 CAATAAACCG
29509 TAGACAATAGACCAA
1 TAGACAATAGACCAA
*
29524 TAGACAATAGCCCAA
1 TAGACAATAGACCAA
29539 TA
1 TA
29541 TAACACCCTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.50, C:0.22, G:0.12, T:0.16
Consensus pattern (15 bp):
TAGACAATAGACCAA
Found at i:33740 original size:31 final size:30
Alignment explanation
Indices: 33675--33742 Score: 82
Period size: 30 Copynumber: 2.2 Consensus size: 30
33665 TTTAGTGAGT
* ** *
33675 GACCAAATTATAAATTTTTTAAAGTTAAGT
1 GACCAAAGTATAAATTTTGAAAAGTTAAGG
*
33705 GACCAAAGTATAAATTTTAGAAAAGTTTAGG
1 GACCAAAGTATAAATTTT-GAAAAGTTAAGG
33736 GACCAAA
1 GACCAAA
33743 ATGGTAATTT
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
30 17 0.53
31 15 0.47
ACGTcount: A:0.46, C:0.09, G:0.15, T:0.31
Consensus pattern (30 bp):
GACCAAAGTATAAATTTTGAAAAGTTAAGG
Found at i:35349 original size:24 final size:24
Alignment explanation
Indices: 35322--35370 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
35312 TGCATGACAT
*
35322 TGTACATAGATGTTTTATACATCA
1 TGTACATAGATGTTCTATACATCA
35346 TGTACATAGATGTTCTATACATCA
1 TGTACATAGATGTTCTATACATCA
35370 T
1 T
35371 CAGGAGGACT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.33, C:0.14, G:0.12, T:0.41
Consensus pattern (24 bp):
TGTACATAGATGTTCTATACATCA
Found at i:36624 original size:24 final size:24
Alignment explanation
Indices: 36588--36637 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 24
36578 AGTTGAGTTT
**
36588 TTATCGATCGATCTTGTTTAGTGA
1 TTATCGATCGATCCAGTTTAGTGA
* *
36612 TTATCTATTGATCCAGTTTAGTGA
1 TTATCGATCGATCCAGTTTAGTGA
36636 TT
1 TT
36638 CTTGCACTCC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.22, C:0.12, G:0.18, T:0.48
Consensus pattern (24 bp):
TTATCGATCGATCCAGTTTAGTGA
Found at i:36791 original size:24 final size:24
Alignment explanation
Indices: 36764--36818 Score: 58
Period size: 24 Copynumber: 2.3 Consensus size: 24
36754 TCATTCATGC
* *
36764 ACTCCTGTATTAGTACCTTTGGGT
1 ACTCCTGTATTAGTACATTTGGAT
* *
36788 ACT-CTAGTGTTAGTACATTTGTAT
1 ACTCCT-GTATTAGTACATTTGGAT
36812 ACTCCTG
1 ACTCCTG
36819 GCACTATATG
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
23 2 0.08
24 21 0.84
25 2 0.08
ACGTcount: A:0.20, C:0.20, G:0.18, T:0.42
Consensus pattern (24 bp):
ACTCCTGTATTAGTACATTTGGAT
Found at i:37510 original size:17 final size:17
Alignment explanation
Indices: 37488--37526 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
37478 ATGTTATAGA
*
37488 AAAATAAAAATGATAAT
1 AAAATAAAAATCATAAT
* *
37505 AAAATAAATATCATTAT
1 AAAATAAAAATCATAAT
37522 AAAAT
1 AAAAT
37527 TAAAGGGAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.67, C:0.03, G:0.03, T:0.28
Consensus pattern (17 bp):
AAAATAAAAATCATAAT
Found at i:38385 original size:174 final size:175
Alignment explanation
Indices: 38092--38410 Score: 516
Period size: 174 Copynumber: 1.8 Consensus size: 175
38082 CGTTTTACCA
* * * * *
38092 TTCAAACTTAAATAGGTATTATTTTAATTTGAAATTATACAAAAGTATATAATTATCTTTAATAT
1 TTCAAACCTAAAAAGATATTATTTTAATTTGAAATTACACAAAAATATATAATTATCTTTAATAT
* * *
38157 TCAAAGTTAAAAAAGATAACAAATACCTTTATAAATTGACATATTCATAGAGTAATTATCCTACT
66 TCAAAATTAAAAAAGATAACAAATACCTTTATAAATTGACATATTAAAAGAGTAATTATCCTACT
*
38222 AATATTCAAATTAAATAATATATTTAATTTGCATTGGTCAAAAGG
131 AATAGTCAAATTAAATAATATATTTAATTTGCATTGGTCAAAAGG
38267 TTCAAACCTAAAAAGATATTATTTTAATTTGAAA-TACACAAAAATATATAATTATCTTTTAATA
1 TTCAAACCTAAAAAGATATTATTTTAATTTGAAATTACACAAAAATATATAATTATC-TTTAATA
* *
38331 TTCAAAATT-AAAAAGATAACAAATACCTTTTTAAATTGACTTATTAAAAGAGTAATTATCCTAC
65 TTCAAAATTAAAAAAGATAACAAATACCTTTATAAATTGACATATTAAAAGAGTAATTATCCTAC
38395 TAATAGTCAAATTAAA
130 TAATAGTCAAATTAAA
38411 AATTAAATTA
Statistics
Matches: 132, Mismatches: 11, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
174 86 0.65
175 46 0.35
ACGTcount: A:0.46, C:0.10, G:0.07, T:0.37
Consensus pattern (175 bp):
TTCAAACCTAAAAAGATATTATTTTAATTTGAAATTACACAAAAATATATAATTATCTTTAATAT
TCAAAATTAAAAAAGATAACAAATACCTTTATAAATTGACATATTAAAAGAGTAATTATCCTACT
AATAGTCAAATTAAATAATATATTTAATTTGCATTGGTCAAAAGG
Found at i:41322 original size:50 final size:50
Alignment explanation
Indices: 41262--41365 Score: 181
Period size: 50 Copynumber: 2.1 Consensus size: 50
41252 TGATCCACGC
*
41262 TATAGTTGTTTATCTGACACATGGAGTATAGCGTGGTACAGGGGGCGCGA
1 TATAGCTGTTTATCTGACACATGGAGTATAGCGTGGTACAGGGGGCGCGA
* *
41312 TATAGCTGTTTATCTGACACGTGGGGTATAGCGTGGTACAGGGGGCGCGA
1 TATAGCTGTTTATCTGACACATGGAGTATAGCGTGGTACAGGGGGCGCGA
41362 TATA
1 TATA
41366 CCTTTAATTA
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
50 51 1.00
ACGTcount: A:0.23, C:0.14, G:0.35, T:0.28
Consensus pattern (50 bp):
TATAGCTGTTTATCTGACACATGGAGTATAGCGTGGTACAGGGGGCGCGA
Found at i:41524 original size:17 final size:18
Alignment explanation
Indices: 41488--41528 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
41478 ATATTATGTA
*
41488 TTTAATTTATTTAAGCAT
1 TTTACTTTATTTAAGCAT
*
41506 TTTACTTTATTTAA-TAT
1 TTTACTTTATTTAAGCAT
41523 TTTACT
1 TTTACT
41529 AATATAGTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 8 0.38
18 13 0.62
ACGTcount: A:0.29, C:0.07, G:0.02, T:0.61
Consensus pattern (18 bp):
TTTACTTTATTTAAGCAT
Found at i:43833 original size:35 final size:33
Alignment explanation
Indices: 43794--43878 Score: 91
Period size: 35 Copynumber: 2.5 Consensus size: 33
43784 GTATTTCAGT
43794 TAATTTTGTT-TATTACCATTTAATATCAGTTATTG
1 TAATTTTGTTATATTACCATTTAAT-TC--TTATTG
*
43829 TAATTTGGTTATCATTTACCATTTAATTCTTATTG
1 TAATTTTGTTAT-A-TTACCATTTAATTCTTATTG
* *
43864 TAAGTTTGTTGTATT
1 TAATTTTGTTATATT
43879 TAAAATTATA
Statistics
Matches: 43, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
33 2 0.05
34 1 0.02
35 24 0.56
36 1 0.02
37 3 0.07
38 12 0.28
ACGTcount: A:0.26, C:0.08, G:0.11, T:0.55
Consensus pattern (33 bp):
TAATTTTGTTATATTACCATTTAATTCTTATTG
Found at i:47214 original size:13 final size:12
Alignment explanation
Indices: 47181--47214 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
47171 AATAAGTATA
*
47181 ATAAAAAAATTT
1 ATAACAAAATTT
47193 ATAACAAAATTT
1 ATAACAAAATTT
47205 ATAACGAAAA
1 ATAAC-AAAA
47215 ATCGCACGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 16 0.80
13 4 0.20
ACGTcount: A:0.65, C:0.06, G:0.03, T:0.26
Consensus pattern (12 bp):
ATAACAAAATTT
Found at i:48906 original size:191 final size:190
Alignment explanation
Indices: 48573--48920 Score: 522
Period size: 191 Copynumber: 1.8 Consensus size: 190
48563 CTTAAATAGG
* *
48573 TATTATTTTAATTTGAAATATACAAAAGTATATAATTATCTTTAATATTCAAAGTTAGAAAGATA
1 TATTATTTTAATTTGAAATATACAAAAGTATATAATTATCTTTAATATTCAAAATTAAAAAGAT-
** * *
48638 AAAAAAATATTTTTTTAAATTGATATATTCAAATAATAATTATCCTACTAATATTCAAAATAAAT
65 AAAAAAATACATTTTTAAATTGATATATTAAAAGAATAATTATCCTACTAATATTCAAAATAAAT
*
48703 AATATATTTAATTTGCAATGGTCAAAATGTAATCTTCTTTTACTATTCAGACTTAAACATA
130 AATATATTTAATTTGCAATAGTCAAAATGTAATCTTCTTTTACTATTCAGACTTAAACATA
*
48764 TATTATTTTAATTTGAAATATACAAAAGTATATACTTATCTTTTAATATTCAAAATTAAAAAGAT
1 TATTATTTTAATTTGAAATATACAAAAGTATATAATTATC-TTTAATATTCAAAATTAAAAAGAT
* * *
48829 -AACAAATACATTTTTAAATTGACT-TATTAAAAGAGTAATTATCCTACTAATATTCAAATTAAA
65 AAAAAAATACATTTTTAAATTGA-TATATTAAAAGAATAATTATCCTACTAATATTCAAAATAAA
*
48892 -AATTATCTTTTAATTTGCAATAGTCAAAA
129 TAA-TAT-ATTTAATTTGCAATAGTCAAAA
48921 ACACCATGAA
Statistics
Matches: 141, Mismatches: 12, Indels: 8
0.88 0.07 0.05
Matches are distributed among these distances:
189 2 0.01
190 57 0.40
191 60 0.43
192 22 0.16
ACGTcount: A:0.45, C:0.09, G:0.05, T:0.41
Consensus pattern (190 bp):
TATTATTTTAATTTGAAATATACAAAAGTATATAATTATCTTTAATATTCAAAATTAAAAAGATA
AAAAAATACATTTTTAAATTGATATATTAAAAGAATAATTATCCTACTAATATTCAAAATAAATA
ATATATTTAATTTGCAATAGTCAAAATGTAATCTTCTTTTACTATTCAGACTTAAACATA
Found at i:52207 original size:29 final size:29
Alignment explanation
Indices: 52165--52267 Score: 131
Period size: 31 Copynumber: 3.5 Consensus size: 29
52155 CATATATCAC
*
52165 AAATAAGTACCTAAAGTATTTTTTGGTCG
1 AAATAAGTACCTAAAGTATTTTTTGGTCA
*
52194 AAATGAGTACCTAAAGTTATCTTTTTGGTCA
1 AAATAAGTACCTAAAG-TAT-TTTTTGGTCA
52225 AAATAAGTACCTAAAGTATTTTATT--TCA
1 AAATAAGTACCTAAAGTATTTT-TTGGTCA
52253 AAAT-AGATACCTAAA
1 AAATAAG-TACCTAAA
52268 CTATACAACT
Statistics
Matches: 67, Mismatches: 3, Indels: 9
0.85 0.04 0.11
Matches are distributed among these distances:
27 2 0.03
28 15 0.22
29 18 0.27
30 8 0.12
31 24 0.36
ACGTcount: A:0.40, C:0.12, G:0.13, T:0.36
Consensus pattern (29 bp):
AAATAAGTACCTAAAGTATTTTTTGGTCA
Found at i:52401 original size:29 final size:28
Alignment explanation
Indices: 52354--52451 Score: 81
Period size: 29 Copynumber: 3.3 Consensus size: 28
52344 AAAAAAATTG
* *
52354 AATACTTTAGGTACTTATTTTGAACAAAA
1 AATACTTTAGGCACCTATTTT-AACAAAA
*
52383 AATACTTTAGGCGCCTATTTTAACCAAAA
1 AATACTTTAGGCACCTATTTTAA-CAAAA
* * *
52412 ATATAACTGTAGGTACTTA-TTTAGACAAAAA
1 A-AT-ACTTTAGGCACCTATTTTA-AC-AAAA
52443 AATACTTTA
1 AATACTTTA
52452 TGTACTTAAA
Statistics
Matches: 56, Mismatches: 8, Indels: 10
0.76 0.11 0.14
Matches are distributed among these distances:
28 2 0.04
29 29 0.52
30 9 0.16
31 16 0.29
ACGTcount: A:0.42, C:0.13, G:0.10, T:0.35
Consensus pattern (28 bp):
AATACTTTAGGCACCTATTTTAACAAAA
Found at i:52457 original size:29 final size:29
Alignment explanation
Indices: 52323--52459 Score: 100
Period size: 31 Copynumber: 4.6 Consensus size: 29
52313 TTAATTTAAG
** *
52323 AATACTTTAGGTACTTAGATA-AAAAAAA
1 AATACTTTAGGTACTTATTTAGACAAAAA
*
52351 TTGAATACTTTAGGTACTTATTTTGA-ACAAAA
1 ---AATACTTTAGGTACTTATTTAGACA-AAAA
** *
52383 AATACTTTAGGCGCCTATTTTA-ACCAAAAA
1 AATACTTTAGGTACTTA-TTTAGA-CAAAAA
* *
52413 TATAACTGTAGGTACTTATTTAGACAAAAA
1 AAT-ACTTTAGGTACTTATTTAGACAAAAA
*
52443 AATACTTTATGTACTTA
1 AATACTTTAGGTACTTA
52460 AATAAAAATA
Statistics
Matches: 84, Mismatches: 15, Indels: 16
0.73 0.13 0.14
Matches are distributed among these distances:
29 27 0.32
30 21 0.25
31 31 0.37
32 5 0.06
ACGTcount: A:0.42, C:0.12, G:0.11, T:0.35
Consensus pattern (29 bp):
AATACTTTAGGTACTTATTTAGACAAAAA
Found at i:53108 original size:57 final size:57
Alignment explanation
Indices: 53039--53149 Score: 152
Period size: 57 Copynumber: 1.9 Consensus size: 57
53029 GATAAAATTA
* * **
53039 TAACATAAGATTACCGCATATAGAGAT-ATTATTATTTATTTGCATGCAGGAAGACCC
1 TAACATAAGATTACCCCATATAGAGATAATT-TTATATACATGCATGCAGGAAGACCC
* *
53096 TAACATAAGATTACCCCATATGGAGATAATTTTATATGCATGCATGCAGGAAGA
1 TAACATAAGATTACCCCATATAGAGATAATTTTATATACATGCATGCAGGAAGA
53150 TCCTCTTCGA
Statistics
Matches: 47, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
57 44 0.94
58 3 0.06
ACGTcount: A:0.38, C:0.15, G:0.17, T:0.30
Consensus pattern (57 bp):
TAACATAAGATTACCCCATATAGAGATAATTTTATATACATGCATGCAGGAAGACCC
Found at i:53777 original size:14 final size:14
Alignment explanation
Indices: 53760--53788 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
53750 TTTTTATATA
53760 TTTTTGTTTTTCTT
1 TTTTTGTTTTTCTT
53774 TTTTTGTTTTTCTT
1 TTTTTGTTTTTCTT
53788 T
1 T
53789 CATTTTAGTT
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:0.00, C:0.07, G:0.07, T:0.86
Consensus pattern (14 bp):
TTTTTGTTTTTCTT
Found at i:54620 original size:3 final size:3
Alignment explanation
Indices: 54602--54648 Score: 53
Period size: 3 Copynumber: 15.7 Consensus size: 3
54592 TCTATAAAAA
*
54602 TAT TAT TAAT TA- TAT TAT TA- TGT TAT TAT TATT TAT TAT TAT TAT
1 TAT TAT T-AT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT
54647 TA
1 TA
54649 ATTACTTACT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
2 3 0.08
3 29 0.76
4 6 0.16
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:54640 original size:13 final size:13
Alignment explanation
Indices: 54602--54652 Score: 68
Period size: 13 Copynumber: 3.9 Consensus size: 13
54592 TCTATAAAAA
54602 TATTATTAATTA-
1 TATTATTAATTAT
*
54614 TATTATTATGTTAT
1 TATTATTA-ATTAT
*
54628 TATTATTTATTAT
1 TATTATTAATTAT
54641 TATTATTAATTA
1 TATTATTAATTA
54653 CTTACTTTTT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
12 8 0.24
13 18 0.55
14 7 0.21
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (13 bp):
TATTATTAATTAT
Found at i:54856 original size:60 final size:60
Alignment explanation
Indices: 54762--54890 Score: 215
Period size: 60 Copynumber: 2.1 Consensus size: 60
54752 CCTATCAACG
* * *
54762 CCATGCCCTGTCACAGGAGATCATTCCCCATCCACCAACTGTCTACAATAGCCAACCCCA
1 CCATGCCCTGCCACAGGAGACCATTCCCCATCCACCAACTGTCTACAACAGCCAACCCCA
54822 CCATGCCCTGCCACAGGAGACCATT-CCCAGTCCACCAACTGTCTACAACAGCCAACCCCA
1 CCATGCCCTGCCACAGGAGACCATTCCCCA-TCCACCAACTGTCTACAACAGCCAACCCCA
54882 CCATGCCCT
1 CCATGCCCT
54891 ACCATCTCAA
Statistics
Matches: 65, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
59 4 0.06
60 61 0.94
ACGTcount: A:0.27, C:0.44, G:0.12, T:0.16
Consensus pattern (60 bp):
CCATGCCCTGCCACAGGAGACCATTCCCCATCCACCAACTGTCTACAACAGCCAACCCCA
Found at i:59869 original size:30 final size:31
Alignment explanation
Indices: 59830--59888 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
59820 TGTAGAGATC
* *
59830 AAAAGAAGCAAAG-AGAAAATAAGCAAAGAG
1 AAAAGAAGCAAAGCAAAAAAAAAGCAAAGAG
*
59860 AAAATAAGCAAAGCAAAAAAAAAGCAAAG
1 AAAAGAAGCAAAGCAAAAAAAAAGCAAAG
59889 CAAAAGGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
30 12 0.48
31 13 0.52
ACGTcount: A:0.69, C:0.08, G:0.19, T:0.03
Consensus pattern (31 bp):
AAAAGAAGCAAAGCAAAAAAAAAGCAAAGAG
Found at i:59893 original size:15 final size:15
Alignment explanation
Indices: 59830--59888 Score: 82
Period size: 15 Copynumber: 3.9 Consensus size: 15
59820 TGTAGAGATC
*
59830 AAAAGAAGCAAAGAG
1 AAAATAAGCAAAGAG
59845 AAAATAAGCAAAGAG
1 AAAATAAGCAAAGAG
*
59860 AAAATAAGCAAAGCAA
1 AAAATAAGCAAAG-AG
*
59876 AAAAAAAGCAAAG
1 AAAATAAGCAAAG
59889 CAAAAGGAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
15 27 0.68
16 13 0.32
ACGTcount: A:0.69, C:0.08, G:0.19, T:0.03
Consensus pattern (15 bp):
AAAATAAGCAAAGAG
Found at i:61172 original size:24 final size:24
Alignment explanation
Indices: 61140--61187 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
61130 CTCGCGTGAG
61140 ATAGTTTTATCTAAAAACAAATTT
1 ATAGTTTTATCTAAAAACAAATTT
61164 ATAGTTTTATCTAAAAACAAATTT
1 ATAGTTTTATCTAAAAACAAATTT
61188 TGTCTCGCAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.46, C:0.08, G:0.04, T:0.42
Consensus pattern (24 bp):
ATAGTTTTATCTAAAAACAAATTT
Found at i:61309 original size:36 final size:36
Alignment explanation
Indices: 61262--61375 Score: 131
Period size: 36 Copynumber: 3.2 Consensus size: 36
61252 GATACAAATT
* **
61262 TTGAGTTTGTTTCACTTGAAACAAA-GTTGATCTCAC
1 TTGAGATTGTTTCACTCAAAACAAACGTTG-TCTCAC
** *
61298 TTGAGATTGTTTTTCTCAAAACAAACTTTGTCTCAC
1 TTGAGATTGTTTCACTCAAAACAAACGTTGTCTCAC
** *
61334 TTGAGATTGTTTTTCTCAAAACAAACTTTGTCTCAC
1 TTGAGATTGTTTCACTCAAAACAAACGTTGTCTCAC
61370 TTGAGA
1 TTGAGA
61376 CAGTCTTCCT
Statistics
Matches: 71, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
36 68 0.96
37 3 0.04
ACGTcount: A:0.28, C:0.18, G:0.14, T:0.40
Consensus pattern (36 bp):
TTGAGATTGTTTCACTCAAAACAAACGTTGTCTCAC
Found at i:61394 original size:36 final size:36
Alignment explanation
Indices: 61292--61399 Score: 126
Period size: 36 Copynumber: 3.0 Consensus size: 36
61282 ACAAAGTTGA
** * *
61292 TCTCACTTGAGATTGTTTTTCTCAAAACAAACTTTG
1 TCTCACTTGAGACAGTCTTCCTCAAAACAAACTTTG
** * *
61328 TCTCACTTGAGATTGTTTTTCTCAAAACAAACTTTG
1 TCTCACTTGAGACAGTCTTCCTCAAAACAAACTTTG
* *
61364 TCTCACTTGAGACAGTCTTCCTTAAGACAAACTTTG
1 TCTCACTTGAGACAGTCTTCCTCAAAACAAACTTTG
61400 AAATTGTTTC
Statistics
Matches: 66, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 66 1.00
ACGTcount: A:0.28, C:0.21, G:0.12, T:0.39
Consensus pattern (36 bp):
TCTCACTTGAGACAGTCTTCCTCAAAACAAACTTTG
Found at i:61511 original size:66 final size:65
Alignment explanation
Indices: 61407--61575 Score: 191
Period size: 66 Copynumber: 2.6 Consensus size: 65
61397 TTGAAATTGT
* * * * **
61407 TTCTCTTGAAA-A--ATCTTTGAGTTTGTTTCCCTAGAAACAAGTTTTGTCTCCCTTGAGACATT
1 TTCTCTTGAAACACCATATTTGAGTTCGTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGC
* * *
61469 TTCTCTTGAAACACCCATATTTGAGATCGTTTCCCTTTAAACAAATTTTGTCTCTCTTGAGACAG
1 TTCTCTTGAAACA-CCATATTTGAGTTCGTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAG
61534 C
65 C
* * * *
61535 TTCTCTTGAAGCATCATCTTTGAGTTGGTTTCCCTTGAAAC
1 TTCTCTTGAAACACCATATTTGAGTTCGTTTCCCTTGAAAC
61576 CATTATCCCT
Statistics
Matches: 88, Mismatches: 15, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
62 11 0.12
63 1 0.01
65 23 0.26
66 53 0.60
ACGTcount: A:0.24, C:0.22, G:0.14, T:0.40
Consensus pattern (65 bp):
TTCTCTTGAAACACCATATTTGAGTTCGTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGC
Found at i:61819 original size:131 final size:129
Alignment explanation
Indices: 61580--61936 Score: 392
Period size: 131 Copynumber: 2.7 Consensus size: 129
61570 TGAAACCATT
* * * *
61580 ATCCCTAAAGATGGCATGCCATCCACATCATGTAGGAACCGTGTCATCCCCCGACCAGACCTCCT
1 ATCCCTAAAGATGGCATG-CATCCTCATCATGTAGGAACTGTGTCATCCACCGACCAAACCTCCT
* * * * * * * *
61645 CATCATGTAAGAGATGTGTCACCCTTAAATAAGCAGTCGTCCTTATCACGTAGGAGCTGTGTTAT
65 CATCACGTAGGAG-TGTGTCACCCTTAGATAACCAGTCATCCTTATCACGTAAGAACCGTGTTAT
61710 C
129 C
* * * * *
61711 ATCCCTAAAGTTGGCATGTCATCCTCATCATGTAGAAACTATGTCATCCACCAACCATACCTCCT
1 ATCCCTAAAGATGGCATG-CATCCTCATCATGTAGGAACTGTGTCATCCACCGACCAAACCTCCT
* *
61776 CATCACGTAGGAGTCGTGTCACCCCTAGATAACCAGTCATCCTTATCGCGTAAGAACCGTGTTAT
65 CATCACGTAGGAGT-GTGTCACCCTTAGATAACCAGTCATCCTTATCACGTAAGAACCGTGTTAT
61841 C
129 C
* * * * * * *
61842 ACCACCTAAAAATGGCTTGCAGTCCTCGTCGCT-TAGGAATTGTGTCATCCACCGACCAAATCTC
1 ATC-CCTAAAGATGGCATGCA-TCCTCATC-ATGTAGGAACTGTGTCATCCACCGACCAAACCTC
*
61906 CTTATCACGTAGGAGTTGTGTCACCCTTAGA
63 CTCATCACGTAGGAG-TGTGTCACCCTTAGA
61937 CGACCAAAAA
Statistics
Matches: 188, Mismatches: 33, Indels: 9
0.82 0.14 0.04
Matches are distributed among these distances:
130 1 0.01
131 114 0.61
132 71 0.38
133 2 0.01
ACGTcount: A:0.27, C:0.29, G:0.18, T:0.26
Consensus pattern (129 bp):
ATCCCTAAAGATGGCATGCATCCTCATCATGTAGGAACTGTGTCATCCACCGACCAAACCTCCTC
ATCACGTAGGAGTGTGTCACCCTTAGATAACCAGTCATCCTTATCACGTAAGAACCGTGTTATC
Found at i:62146 original size:3 final size:3
Alignment explanation
Indices: 62128--62177 Score: 50
Period size: 3 Copynumber: 16.7 Consensus size: 3
62118 TCAACAAAAA
*
62128 TAT TAT TAAT TA- TAT TAT TA- TGT TAT TAT TAT TAAT TAT TAT TAT
1 TAT TAT T-AT TAT TAT TAT TAT TAT TAT TAT TAT T-AT TAT TAT TAT
*
62173 GAT TA
1 TAT TA
62178 ATTACTTACT
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
2 3 0.08
3 30 0.77
4 6 0.15
ACGTcount: A:0.36, C:0.00, G:0.04, T:0.60
Consensus pattern (3 bp):
TAT
Found at i:62156 original size:11 final size:10
Alignment explanation
Indices: 62128--62170 Score: 50
Period size: 11 Copynumber: 4.0 Consensus size: 10
62118 TCAACAAAAA
62128 TATTATTAATT
1 TATTATT-ATT
62139 ATATTATTATGT
1 -TATTATTAT-T
62151 TATTATTATT
1 TATTATTATT
*
62161 AATTATTATT
1 TATTATTATT
62171 ATGATTAATT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
10 10 0.34
11 11 0.38
12 8 0.28
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (10 bp):
TATTATTATT
Found at i:62169 original size:16 final size:16
Alignment explanation
Indices: 62129--62181 Score: 56
Period size: 16 Copynumber: 3.2 Consensus size: 16
62119 CAACAAAAAT
62129 ATTATTAATTA-TATT-
1 ATTATT-ATTATTATTA
62144 ATTATGTTATTATTATTA
1 ATTA--TTATTATTATTA
*
62162 ATTATTATTATGATTA
1 ATTATTATTATTATTA
62178 ATTA
1 ATTA
62182 CTTACTTTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
15 4 0.12
16 19 0.58
17 6 0.18
18 4 0.12
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (16 bp):
ATTATTATTATTATTA
Found at i:62181 original size:13 final size:12
Alignment explanation
Indices: 62140--62177 Score: 51
Period size: 13 Copynumber: 3.2 Consensus size: 12
62130 TTATTAATTA
62140 TATTATTATG-T
1 TATTATTATGAT
*
62151 TATTATTATTAAT
1 TATTATTA-TGAT
62164 TATTATTATGAT
1 TATTATTATGAT
62176 TA
1 TA
62178 ATTACTTACT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
11 8 0.35
12 6 0.26
13 9 0.39
ACGTcount: A:0.34, C:0.00, G:0.05, T:0.61
Consensus pattern (12 bp):
TATTATTATGAT
Found at i:66185 original size:13 final size:13
Alignment explanation
Indices: 66163--66192 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
66153 ACTAAACACC
66163 TTTC-ACATACCT
1 TTTCAACATACCT
66175 TTTCAACATACCT
1 TTTCAACATACCT
66188 TTTCA
1 TTTCA
66193 TCTTTGGCCA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 4 0.24
13 13 0.76
ACGTcount: A:0.27, C:0.30, G:0.00, T:0.43
Consensus pattern (13 bp):
TTTCAACATACCT
Found at i:68935 original size:15 final size:15
Alignment explanation
Indices: 68900--68928 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
68890 GTGCTTCAAC
68900 TTCTTT-CTTTTCTT
1 TTCTTTGCTTTTCTT
68914 TTCTTTGCTTTTCTT
1 TTCTTTGCTTTTCTT
68929 CTTTTTGAGT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.00, C:0.21, G:0.03, T:0.76
Consensus pattern (15 bp):
TTCTTTGCTTTTCTT
Found at i:73612 original size:22 final size:23
Alignment explanation
Indices: 73559--73616 Score: 73
Period size: 23 Copynumber: 2.6 Consensus size: 23
73549 AGTTTACTTA
*
73559 TATGACACATTTTCATATGCCTT
1 TATGACACGTTTTCATATGCCTT
* * *
73582 TATGACACGTTTTCTTCTGTCTT
1 TATGACACGTTTTCATATGCCTT
73605 T-TGACACGTTTT
1 TATGACACGTTTT
73617 TAGGTCATTT
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
22 11 0.35
23 20 0.65
ACGTcount: A:0.19, C:0.21, G:0.12, T:0.48
Consensus pattern (23 bp):
TATGACACGTTTTCATATGCCTT
Found at i:77452 original size:19 final size:19
Alignment explanation
Indices: 77428--77464 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
77418 ATGACCAACA
*
77428 AAATCGCAATGCGATCTCT
1 AAATCGCAACGCGATCTCT
77447 AAATCGCAACGCGATCTC
1 AAATCGCAACGCGATCTC
77465 CAGTATCGCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.32, C:0.30, G:0.16, T:0.22
Consensus pattern (19 bp):
AAATCGCAACGCGATCTCT
Found at i:77517 original size:20 final size:20
Alignment explanation
Indices: 77494--77602 Score: 148
Period size: 20 Copynumber: 5.4 Consensus size: 20
77484 CCAAATTCGT
*
77494 AACGCGATTTTGACTATCGC
1 AACGCGATTCTGACTATCGC
77514 AACGCGATTCTGACTATCGC
1 AACGCGATTCTGACTATCGC
* **
77534 AACGTGATAAT-ACATAATCGC
1 AACGCGATTCTGAC-T-ATCGC
77555 AACGCGATTCTGACTATCGC
1 AACGCGATTCTGACTATCGC
*
77575 AACGCGATTTTGACTATCGC
1 AACGCGATTCTGACTATCGC
77595 AACGCGAT
1 AACGCGAT
77603 AATACAAAAA
Statistics
Matches: 78, Mismatches: 8, Indels: 6
0.85 0.09 0.07
Matches are distributed among these distances:
19 2 0.03
20 60 0.77
21 14 0.18
22 2 0.03
ACGTcount: A:0.29, C:0.26, G:0.19, T:0.26
Consensus pattern (20 bp):
AACGCGATTCTGACTATCGC
Found at i:77576 original size:61 final size:62
Alignment explanation
Indices: 77494--77625 Score: 212
Period size: 61 Copynumber: 2.1 Consensus size: 62
77484 CCAAATTCGT
* * *
77494 AACGCGATTTTGACTATCGCAACGCGATTCTGACTATCGCAACGTGATAATAC-ATAATCGC
1 AACGCGATTCTGACTATCGCAACGCGATTCTGACTATCGCAACGCGATAATACAAAAATCGC
*
77555 AACGCGATTCTGACTATCGCAACGCGATTTTGACTATCGCAACGCGATAATACAAAAATCGC
1 AACGCGATTCTGACTATCGCAACGCGATTCTGACTATCGCAACGCGATAATACAAAAATCGC
*
77617 AATGCGATT
1 AACGCGATT
77626 TTCAAAGCGC
Statistics
Matches: 65, Mismatches: 5, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
61 50 0.77
62 15 0.23
ACGTcount: A:0.33, C:0.24, G:0.18, T:0.25
Consensus pattern (62 bp):
AACGCGATTCTGACTATCGCAACGCGATTCTGACTATCGCAACGCGATAATACAAAAATCGC
Found at i:77799 original size:22 final size:22
Alignment explanation
Indices: 77774--77815 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
77764 GCGACATCTG
77774 TCCCCATCTCCGACGAAATCCA
1 TCCCCATCTCCGACGAAATCCA
77796 TCCCCATCTCCGACGAAATC
1 TCCCCATCTCCGACGAAATC
77816 TGTCTATCTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.26, C:0.45, G:0.10, T:0.19
Consensus pattern (22 bp):
TCCCCATCTCCGACGAAATCCA
Found at i:78214 original size:20 final size:20
Alignment explanation
Indices: 78189--78305 Score: 86
Period size: 20 Copynumber: 6.2 Consensus size: 20
78179 AAAATCGCAA
78189 CGATAGTCAAATTCGCGTTG
1 CGATAGTCAAATTCGCGTTG
** *
78209 CGATAGTCATTTTCGTGTTG
1 CGATAGTCAAATTCGCGTTG
** * *
78229 CGATTTTC-ATTTTGCGTTG
1 CGATAGTCAAATTCGCGTTG
*
78248 CGAT--T---A-TCTCGTTG
1 CGATAGTCAAATTCGCGTTG
78262 CGATAGTCAAATTCGCGTTG
1 CGATAGTCAAATTCGCGTTG
** *
78282 CGATAGTCATTTTCGTGTTG
1 CGATAGTCAAATTCGCGTTG
78302 CGAT
1 CGAT
78306 TTTAAGTTTT
Statistics
Matches: 76, Mismatches: 15, Indels: 12
0.74 0.15 0.12
Matches are distributed among these distances:
14 10 0.13
16 1 0.01
17 1 0.01
19 13 0.17
20 51 0.67
ACGTcount: A:0.18, C:0.18, G:0.24, T:0.40
Consensus pattern (20 bp):
CGATAGTCAAATTCGCGTTG
Found at i:78284 original size:53 final size:54
Alignment explanation
Indices: 78204--78306 Score: 145
Period size: 53 Copynumber: 1.9 Consensus size: 54
78194 GTCAAATTCG
** * **
78204 CGTTGCGATAGTCATTTTCGTGTTGCGATTTTCATTTT-GCGTTGCGATTATCT
1 CGTTGCGATAGTCAAATTCGCGTTGCGATAGTCATTTTCGCGTTGCGATTATCT
*
78257 CGTTGCGATAGTCAAATTCGCGTTGCGATAGTCATTTTCGTGTTGCGATT
1 CGTTGCGATAGTCAAATTCGCGTTGCGATAGTCATTTTCGCGTTGCGATT
78307 TTAAGTTTTA
Statistics
Matches: 43, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
53 33 0.77
54 10 0.23
ACGTcount: A:0.16, C:0.17, G:0.24, T:0.43
Consensus pattern (54 bp):
CGTTGCGATAGTCAAATTCGCGTTGCGATAGTCATTTTCGCGTTGCGATTATCT
Found at i:78327 original size:73 final size:73
Alignment explanation
Indices: 78189--78327 Score: 208
Period size: 73 Copynumber: 1.9 Consensus size: 73
78179 AAAATCGCAA
* * ***
78189 CGATAGTCAAATTCGCGTTGCGATAGTCATTTTCGTGTTGCGATTTTCATTTTGCGTTGCGATTA
1 CGATAGTCAAATTCGCGTTGCGATAGTCATTTTCGTGTTGCGATTTTAATTTTGAGAAACGATTA
78254 TCTCGTTG
66 TCTCGTTG
*
78262 CGATAGTCAAATTCGCGTTGCGATAGTCATTTTCGTGTTGCGATTTTAAGTTTT-AGAAACTATT
1 CGATAGTCAAATTCGCGTTGCGATAGTCATTTTCGTGTTGCGATTTTAA-TTTTGAGAAACGATT
78326 AT
65 AT
78328 TATTCTGCAA
Statistics
Matches: 59, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
73 55 0.93
74 4 0.07
ACGTcount: A:0.21, C:0.16, G:0.22, T:0.42
Consensus pattern (73 bp):
CGATAGTCAAATTCGCGTTGCGATAGTCATTTTCGTGTTGCGATTTTAATTTTGAGAAACGATTA
TCTCGTTG
Done.