Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005243.1 Hibiscus syriacus cultivar Beakdansim tig00011866_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: 75449
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:7357 original size:14 final size:15
Alignment explanation
Indices: 7340--7369 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
7330 AGGAAGAATG
7340 ATTTTATAG-AGAAA
1 ATTTTATAGCAGAAA
7354 ATTTTATAGCAGAAA
1 ATTTTATAGCAGAAA
7369 A
1 A
7370 AGTAAAACAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.60
15 6 0.40
ACGTcount: A:0.50, C:0.03, G:0.13, T:0.33
Consensus pattern (15 bp):
ATTTTATAGCAGAAA
Found at i:7511 original size:14 final size:14
Alignment explanation
Indices: 7487--7539 Score: 61
Period size: 14 Copynumber: 3.8 Consensus size: 14
7477 CGTTTTGTTA
*
7487 TAAATCCTAAATCG
1 TAAACCCTAAATCG
* *
7501 TAAACCTTAAATTG
1 TAAACCCTAAATCG
*
7515 TAAACCCTAAATTG
1 TAAACCCTAAATCG
*
7529 TGAACCCTAAA
1 TAAACCCTAAA
7540 CACTAACCCC
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 34 1.00
ACGTcount: A:0.43, C:0.21, G:0.08, T:0.28
Consensus pattern (14 bp):
TAAACCCTAAATCG
Found at i:7656 original size:2 final size:2
Alignment explanation
Indices: 7614--7638 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
7604 AAAAAACAAC
7614 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
7639 AAGTAAATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:7728 original size:7 final size:7
Alignment explanation
Indices: 7713--7778 Score: 69
Period size: 7 Copynumber: 9.4 Consensus size: 7
7703 TATGTTTATA
*
7713 TAAATCC
1 TAAACCC
7720 TAAACCC
1 TAAACCC
7727 TAAACCC
1 TAAACCC
7734 TAAACCC
1 TAAACCC
**
7741 TAAACTT
1 TAAACCC
*
7748 TAAACCA
1 TAAACCC
*
7755 TAAACAC
1 TAAACCC
**
7762 TAAACTA
1 TAAACCC
7769 TAAACCC
1 TAAACCC
7776 TAA
1 TAA
7779 TATAAATAGA
Statistics
Matches: 48, Mismatches: 11, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
7 48 1.00
ACGTcount: A:0.48, C:0.30, G:0.00, T:0.21
Consensus pattern (7 bp):
TAAACCC
Found at i:7742 original size:21 final size:21
Alignment explanation
Indices: 7713--7778 Score: 78
Period size: 21 Copynumber: 3.1 Consensus size: 21
7703 TATGTTTATA
* **
7713 TAAATCCTAAACCCTAAACCC
1 TAAACCCTAAACTATAAACCC
* *
7734 TAAACCCTAAACTTTAAACCA
1 TAAACCCTAAACTATAAACCC
*
7755 TAAACACTAAACTATAAACCC
1 TAAACCCTAAACTATAAACCC
7776 TAA
1 TAA
7779 TATAAATAGA
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 38 1.00
ACGTcount: A:0.48, C:0.30, G:0.00, T:0.21
Consensus pattern (21 bp):
TAAACCCTAAACTATAAACCC
Found at i:8613 original size:24 final size:23
Alignment explanation
Indices: 8586--8634 Score: 80
Period size: 24 Copynumber: 2.1 Consensus size: 23
8576 CATATAAACC
8586 ATGTATAGTATATATAAACTATAT
1 ATGTATAGTATATATAAA-TATAT
*
8610 ATGTATAGTATATATATATATAT
1 ATGTATAGTATATATAAATATAT
8633 AT
1 AT
8635 AAACTATATA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 7 0.29
24 17 0.71
ACGTcount: A:0.45, C:0.02, G:0.08, T:0.45
Consensus pattern (23 bp):
ATGTATAGTATATATAAATATAT
Found at i:8729 original size:7 final size:7
Alignment explanation
Indices: 8719--8785 Score: 55
Period size: 7 Copynumber: 9.7 Consensus size: 7
8709 TAGTTTATAG
8719 AAACCCT
1 AAACCCT
8726 AAACCCT
1 AAACCCT
* *
8733 AAATCAT
1 AAACCCT
**
8740 AATTCCT
1 AAACCCT
**
8747 AAACTTT
1 AAACCCT
8754 AAA-CCT
1 AAACCCT
8760 AAACCCT
1 AAACCCT
*
8767 AAACACT
1 AAACCCT
*
8774 AAACCAT
1 AAACCCT
8781 AAACC
1 AAACC
8786 ATAATGTAAA
Statistics
Matches: 46, Mismatches: 13, Indels: 2
0.75 0.21 0.03
Matches are distributed among these distances:
6 4 0.09
7 42 0.91
ACGTcount: A:0.48, C:0.31, G:0.00, T:0.21
Consensus pattern (7 bp):
AAACCCT
Found at i:8769 original size:20 final size:21
Alignment explanation
Indices: 8719--8785 Score: 73
Period size: 21 Copynumber: 3.2 Consensus size: 21
8709 TAGTTTATAG
* *
8719 AAACCCTAAACCCTAAATCAT
1 AAACCCTAAACACTAAACCAT
** **
8740 AATTCCTAAACTTTAAACC-T
1 AAACCCTAAACACTAAACCAT
8760 AAACCCTAAACACTAAACCAT
1 AAACCCTAAACACTAAACCAT
8781 AAACC
1 AAACC
8786 ATAATGTAAA
Statistics
Matches: 36, Mismatches: 9, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
20 16 0.44
21 20 0.56
ACGTcount: A:0.48, C:0.31, G:0.00, T:0.21
Consensus pattern (21 bp):
AAACCCTAAACACTAAACCAT
Found at i:8969 original size:14 final size:14
Alignment explanation
Indices: 8950--8996 Score: 50
Period size: 14 Copynumber: 3.7 Consensus size: 14
8940 ATTTTTTCTT
8950 TATATAAATTAAAC
1 TATATAAATTAAAC
8964 TATAT-AATT----
1 TATATAAATTAAAC
8973 TATATAAATTAAAC
1 TATATAAATTAAAC
*
8987 TATATTAATT
1 TATATAAATT
8997 TTCCTTTGCA
Statistics
Matches: 27, Mismatches: 1, Indels: 10
0.71 0.03 0.26
Matches are distributed among these distances:
9 5 0.19
10 4 0.15
13 4 0.15
14 14 0.52
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (14 bp):
TATATAAATTAAAC
Found at i:8975 original size:23 final size:24
Alignment explanation
Indices: 8948--8997 Score: 93
Period size: 23 Copynumber: 2.1 Consensus size: 24
8938 TTATTTTTTC
8948 TTTATATAAATTAAACTATA-TAA
1 TTTATATAAATTAAACTATATTAA
8971 TTTATATAAATTAAACTATATTAA
1 TTTATATAAATTAAACTATATTAA
8995 TTT
1 TTT
8998 TCCTTTGCAT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 20 0.77
24 6 0.23
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (24 bp):
TTTATATAAATTAAACTATATTAA
Found at i:9062 original size:22 final size:24
Alignment explanation
Indices: 9019--9070 Score: 81
Period size: 22 Copynumber: 2.2 Consensus size: 24
9009 ATTAGTCATG
9019 TTTTATCTAATTTACATTAAATAA
1 TTTTATCTAATTTACATTAAATAA
*
9043 TTTTAT-TAATTT-TATTAAATAA
1 TTTTATCTAATTTACATTAAATAA
9065 TTTTAT
1 TTTTAT
9071 ATTATAGGTC
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
22 15 0.56
23 6 0.22
24 6 0.22
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.58
Consensus pattern (24 bp):
TTTTATCTAATTTACATTAAATAA
Found at i:9287 original size:16 final size:16
Alignment explanation
Indices: 9266--9320 Score: 83
Period size: 16 Copynumber: 3.4 Consensus size: 16
9256 CGGATCATTT
*
9266 ACAGGTCAGGTTAAAA
1 ACAGGTCAGGTTGAAA
9282 ACAGGTCAGGTTGAAA
1 ACAGGTCAGGTTGAAA
* *
9298 ACATGTTAGGTTGAAA
1 ACAGGTCAGGTTGAAA
9314 ACAGGTC
1 ACAGGTC
9321 GGGTAATACC
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 34 1.00
ACGTcount: A:0.38, C:0.13, G:0.27, T:0.22
Consensus pattern (16 bp):
ACAGGTCAGGTTGAAA
Found at i:10822 original size:33 final size:33
Alignment explanation
Indices: 10747--10822 Score: 91
Period size: 33 Copynumber: 2.3 Consensus size: 33
10737 TACTAGGACT
**
10747 AAATAAT-TTTGTCACAATTTATTATTGTGAAA
1 AAATAATATTTGTCACAATTTATTATAATGAAA
* * *
10779 AAATATTATTTGTCACAATTTTTTATAATGAGA
1 AAATAATATTTGTCACAATTTATTATAATGAAA
*
10812 AATTAATATTT
1 AAATAATATTT
10823 ATTATAAATT
Statistics
Matches: 36, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
32 6 0.17
33 30 0.83
ACGTcount: A:0.41, C:0.05, G:0.08, T:0.46
Consensus pattern (33 bp):
AAATAATATTTGTCACAATTTATTATAATGAAA
Found at i:11122 original size:195 final size:196
Alignment explanation
Indices: 10743--11148 Score: 548
Period size: 195 Copynumber: 2.1 Consensus size: 196
10733 TTTTTACTAG
* * *
10743 GACTAAATAATTTTGTCACAATTTATTATTGTGAAAAAATATTATTTGTCACAATTTTTTATAAT
1 GACTAAATAAATTTGTCACAATTGATTATTGTGAAAAAATATTATTTGTCACAACTTTTTATAAT
* *
10808 GAGAAATTAATATTTATTATAAATTGTTATTTTGATTAAATAAATTTGTCAAAAGTTGTTATTTT
66 GAGAAATTAATATTTATTATAAATTGTTATTATAATT--ATAAATTTGTCAAAAGTTGTTATTTT
* * *
10873 GAGAAAATGTTGTGACGAAATAAATTTTACATAAATTTTTATTTTAATTAAATTTAATATGTTAT
129 GAGAAAATATTGTGACGAAATAAATTTGACATAAATTTTTATTTTAACTAAATTTAATATGTTAT
10938 TGT
194 TGT
* * * * *
10941 GACTAAATAAATTTGTTATAATTGATTATTGTG-AAAAATATTATTTTTCATAACTTTTTATATT
1 GACTAAATAAATTTGTCACAATTGATTATTGTGAAAAAATATTATTTGTCACAACTTTTTATAAT
* * *
11005 GAGAAATTAATATTTATTATAATTTGTTATTATAACTT-TAAATTTGTCATAATTTGTTATTTTG
66 GAGAAATTAATATTTATTATAAATTGTTATTATAA-TTATAAATTTGTCAAAAGTTGTTATTTTG
* * * *
11069 ATAAAATATT-TAGACTAAATAAATTTGACATAATTTTTTATTTTAACTAAATTTAATTTGTTAT
130 AGAAAATATTGT-GACGAAATAAATTTGACATAAATTTTTATTTTAACTAAATTTAATATGTTAT
*
11133 TTT
194 TGT
* *
11136 GTCTATATAAATT
1 GACTAAATAAATT
11149 ATCATAATTT
Statistics
Matches: 183, Mismatches: 23, Indels: 7
0.86 0.11 0.03
Matches are distributed among these distances:
194 1 0.01
195 92 0.50
197 59 0.32
198 31 0.17
ACGTcount: A:0.38, C:0.04, G:0.09, T:0.49
Consensus pattern (196 bp):
GACTAAATAAATTTGTCACAATTGATTATTGTGAAAAAATATTATTTGTCACAACTTTTTATAAT
GAGAAATTAATATTTATTATAAATTGTTATTATAATTATAAATTTGTCAAAAGTTGTTATTTTGA
GAAAATATTGTGACGAAATAAATTTGACATAAATTTTTATTTTAACTAAATTTAATATGTTATTG
T
Found at i:11158 original size:31 final size:31
Alignment explanation
Indices: 11122--11186 Score: 121
Period size: 31 Copynumber: 2.1 Consensus size: 31
11112 TAACTAAATT
*
11122 TAATTTGTTATTTTGTCTATATAAATTATCA
1 TAATTTGTTATTTTGTCTAAATAAATTATCA
11153 TAATTTGTTATTTTGTCTAAATAAATTATCA
1 TAATTTGTTATTTTGTCTAAATAAATTATCA
11184 TAA
1 TAA
11187 ATTATCTTTC
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.35, C:0.06, G:0.06, T:0.52
Consensus pattern (31 bp):
TAATTTGTTATTTTGTCTAAATAAATTATCA
Found at i:13108 original size:2 final size:2
Alignment explanation
Indices: 13101--13139 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
13091 TAAATCTTAT
13101 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
13140 TATTTTTATT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:13292 original size:15 final size:14
Alignment explanation
Indices: 13260--13318 Score: 55
Period size: 15 Copynumber: 4.0 Consensus size: 14
13250 ATCATTATTG
*
13260 TTTTTTATATTTTAT
1 TTTTTTATA-TATAT
*
13275 TTTATTATATATAT
1 TTTTTTATATATAT
* *
13289 TTTTCTTATGTACAT
1 TTTT-TTATATATAT
13304 TTTTTGTATATATAT
1 TTTTT-TATATATAT
13319 ATATATTATT
Statistics
Matches: 35, Mismatches: 7, Indels: 4
0.76 0.15 0.09
Matches are distributed among these distances:
14 8 0.23
15 27 0.77
ACGTcount: A:0.25, C:0.03, G:0.03, T:0.68
Consensus pattern (14 bp):
TTTTTTATATATAT
Found at i:13342 original size:15 final size:14
Alignment explanation
Indices: 13322--13357 Score: 54
Period size: 15 Copynumber: 2.5 Consensus size: 14
13312 TATATATATA
13322 TATTATTATTTTCAT
1 TATTATTATTTT-AT
13337 TATTATTATTTTAT
1 TATTATTATTTTAT
*
13351 TACTATT
1 TATTATT
13358 TTTACTATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
14 8 0.40
15 12 0.60
ACGTcount: A:0.28, C:0.06, G:0.00, T:0.67
Consensus pattern (14 bp):
TATTATTATTTTAT
Found at i:13639 original size:49 final size:48
Alignment explanation
Indices: 13586--13679 Score: 127
Period size: 49 Copynumber: 1.9 Consensus size: 48
13576 TACTTTTATT
*
13586 TTTTTTATCTAT-ATTTTCCTTGTTTTATTTACTTTTTATCTTTACTCCG
1 TTTTTT-TCTATCATTTTACTTGTTTTATTTACTTTTTAT-TTTACTCCG
* * *
13635 TTTTTTTCTCTCATTTTATTTGTTTTATTTATTTTTTATTTTACT
1 TTTTTTTCTATCATTTTACTTGTTTTATTTACTTTTTATTTTACT
13680 TTCTTCATTT
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
48 10 0.25
49 30 0.75
ACGTcount: A:0.14, C:0.13, G:0.03, T:0.70
Consensus pattern (48 bp):
TTTTTTTCTATCATTTTACTTGTTTTATTTACTTTTTATTTTACTCCG
Found at i:14615 original size:4 final size:4
Alignment explanation
Indices: 14606--14632 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
14596 TTTCCTTATT
14606 TTTC TTTC TTTC TTTC TTTC TTTC TTT
1 TTTC TTTC TTTC TTTC TTTC TTTC TTT
14633 TGTCATTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTC
Found at i:18824 original size:110 final size:110
Alignment explanation
Indices: 18635--19358 Score: 988
Period size: 110 Copynumber: 6.7 Consensus size: 110
18625 TGATGGTTGT
* * *
18635 TCAACTTCAAAGCGAAGGGGCGA----CTATCAACAAACAACTTTTTAGTTTCATTCAGAGTCAA
1 TCAACTTCACAGCGAAGGGGCGACTGGCTGTCAACAAACAACTTTTCAGTTTCATTCAGAGTCAA
18696 TTTCAACTTCACAGTGAAGGATATTGGACTCGAGACAACACAAGC
66 TTTCAACTTCACAGTGAAGGATATTGGACTCGAGACAACACAAGC
* *
18741 TCAACTTCACAGCGAAGGGGCGACTGGCTGTCAATAAATAACTTTTCAGTTTCATTCAGAGTCAA
1 TCAACTTCACAGCGAAGGGGCGACTGGCTGTCAACAAACAACTTTTCAGTTTCATTCAGAGTCAA
*
18806 TTTCAACTTCACAATGAAGGATATTGGACTCGAGACAACACAAGC
66 TTTCAACTTCACAGTGAAGGATATTGGACTCGAGACAACACAAGC
* * * * * * *
18851 TCAACTTTACAGCGAAGGGGTGACTGGCTATTAATAAACAACTTTTCAGTTTCAGTCATAGTCAA
1 TCAACTTCACAGCGAAGGGGCGACTGGCTGTCAACAAACAACTTTTCAGTTTCATTCAGAGTCAA
* * *
18916 TTTCAACTTCACAGCGAAGGATATTAGACTCGAGAAAACACAAGC
66 TTTCAACTTCACAGTGAAGGATATTGGACTCGAGACAACACAAGC
* * * *
18961 TCAACTTCACAGCAAAGGGGCAACTGACTGTCAACAAACAACTTTTCAGTTTCATTGAGAGTCAA
1 TCAACTTCACAGCGAAGGGGCGACTGGCTGTCAACAAACAACTTTTCAGTTTCATTCAGAGTCAA
*
19026 TTTCAACTTCACAGTGAATGATATTGGACTCGAGACAACACAAGC
66 TTTCAACTTCACAGTGAAGGATATTGGACTCGAGACAACACAAGC
* *
19071 TCAACTTCATAGCGAAGGGGCGACTGACTGTCAAC--A-AAC--TTCAGTTTCATTCAGAGTCAA
1 TCAACTTCACAGCGAAGGGGCGACTGGCTGTCAACAAACAACTTTTCAGTTTCATTCAGAGTCAA
* **
19131 TTTCAACTTCACAGCGAAATATATTGGACTCGAGACAACACAAGC
66 TTTCAACTTCACAGTGAAGGATATTGGACTCGAGACAACACAAGC
* ** *
19176 TCAACTTCATAGCGAAAAGGCGACTGGCTGTCAATAAACAACTTTTCAGTTTCATTCAGAGTCAA
1 TCAACTTCACAGCGAAGGGGCGACTGGCTGTCAACAAACAACTTTTCAGTTTCATTCAGAGTCAA
** * *
19241 TTTCAACTTCACAGTGAAAAATATTAGACTCGAGACAACTCAAGC
66 TTTCAACTTCACAGTGAAGGATATTGGACTCGAGACAACACAAGC
* ** * * *
19286 TCAACTTCACAGTGAATAGGTGATTGGCTGTCAACAAACAACTTTCCAG-TT--TT-AGAGTCAA
1 TCAACTTCACAGCGAAGGGGCGACTGGCTGTCAACAAACAACTTTTCAGTTTCATTCAGAGTCAA
*
19347 TTTAAACTTCAC
66 TTTCAACTTCAC
19359 GGCGAATGAC
Statistics
Matches: 554, Mismatches: 55, Indels: 18
0.88 0.09 0.03
Matches are distributed among these distances:
105 93 0.17
106 41 0.07
107 6 0.01
108 4 0.01
109 2 0.00
110 408 0.74
ACGTcount: A:0.35, C:0.22, G:0.17, T:0.26
Consensus pattern (110 bp):
TCAACTTCACAGCGAAGGGGCGACTGGCTGTCAACAAACAACTTTTCAGTTTCATTCAGAGTCAA
TTTCAACTTCACAGTGAAGGATATTGGACTCGAGACAACACAAGC
Found at i:19595 original size:85 final size:83
Alignment explanation
Indices: 19494--19859 Score: 380
Period size: 85 Copynumber: 4.4 Consensus size: 83
19484 GGAATCATGC
* * * * *
19494 CCACCAAAGGCCTTCGAGTTCGACTATGCTCAGCTCCAAGGTACATTATTTGTAGCATAACTTAA
1 CCACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAA
19559 GTCGAGAAGGGTTATCTG
66 GTCGAGAAGGGTTATCTG
* *
19577 CCAACCAAAAGACCTTCGAGTTCGACTACGCTCAGCT-CAAGGGCACATCATTTGCAGTATAGCT
1 CC-ACC-AAAGACCTTCGAGTTCGACTACGCTCAGCTCCAA-GGCACATCATTTGCAGCATAACT
19641 TAAGTCGAGAAGGGTTATCTG
63 TAAGTCGAGAAGGGTTATCTG
* * * * * * *
19662 ---CCAAAGACCCTCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTACAGCATAACTCA
1 CCACCAAAGACCTTCGAGTTCGACTACGCTCAGC-TCCAAGGCACATCATTTGCAGCATAACTTA
* *
19724 AGGCTAGAAGGGTTATCTG
65 AGTCGAGAAGGGTTATCTG
* * * ** *
19743 TCACCAAAAGACCTTCGAGTTTGACTACGCTCAGCTCCAAGGGACATCATTTGCAATATAGCTTA
1 CCACC-AAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTA
* *
19808 AGTCAAGAAGGGCTATCTG
65 AGTCGAGAAGGGTTATCTG
* * ** * *
19827 TCAACCGAAGACCTTTAAGTTCGATTACACTCA
1 -CCACCAAAGACCTTCGAGTTCGACTACGCTCA
19860 ACTCAGAGGC
Statistics
Matches: 232, Mismatches: 41, Indels: 19
0.79 0.14 0.07
Matches are distributed among these distances:
80 26 0.11
81 41 0.18
82 1 0.00
83 2 0.01
84 67 0.29
85 95 0.41
ACGTcount: A:0.30, C:0.25, G:0.20, T:0.25
Consensus pattern (83 bp):
CCACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAA
GTCGAGAAGGGTTATCTG
Found at i:19779 original size:165 final size:167
Alignment explanation
Indices: 19547--19911 Score: 470
Period size: 165 Copynumber: 2.2 Consensus size: 167
19537 CATTATTTGT
* * *
19547 AGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAAGACCTTCGAGTTCGACTACGCTCAG
1 AGCATAACTCAAGGCAAGAAGGGTTATCTGCCAACCAAAAGACCTTCGAGTTCGACTACGCTCAG
* * * *
19612 CT-CAAGGGCACATCATTTGCAGTATAGCTTAAGTCGAGAAGGGTTATCTG-CCAAAGACCCTCG
66 CTCCAAGGG-ACATCATTTGCAATATAGCTTAAGTCAAGAAGGGCTATCTGACCAAAGACCCTCA
* * *
19675 AGTTCGATTACACTCAGCTTC-GAGGGCACATC-ATTTAC
130 AGTTCGATTACACTCAAC-TCAGA-GGCAAACCAATTTAC
* * *
19713 AGCATAACTCAAGGCTAGAAGGGTTATCTGTC-ACCAAAAGACCTTCGAGTTTGACTACGCTCAG
1 AGCATAACTCAAGGCAAGAAGGGTTATCTGCCAACCAAAAGACCTTCGAGTTCGACTACGCTCAG
* *
19777 CTCCAAGGGACATCATTTGCAATATAGCTTAAGTCAAGAAGGGCTATCTGTCAACCGAAGACCTT
66 CTCCAAGGGACATCATTTGCAATATAGCTTAAGTCAAGAAGGGCTATCTG---ACCAAAGACCCT
*
19842 TAAGTTCGATTACACTCAACTCAGAGGCAAACCAAATTTAC
128 CAAGTTCGATTACACTCAACTCAGAGGCAAACC-AATTTAC
* *
19883 AGAATAACTCAAGGCAAGAAGGGCTATCT
1 AGCATAACTCAAGGCAAGAAGGGTTATCT
19912 ATAAAAAAAA
Statistics
Matches: 173, Mismatches: 18, Indels: 12
0.85 0.09 0.06
Matches are distributed among these distances:
165 71 0.41
166 34 0.20
168 8 0.05
169 28 0.16
170 32 0.18
ACGTcount: A:0.32, C:0.24, G:0.21, T:0.24
Consensus pattern (167 bp):
AGCATAACTCAAGGCAAGAAGGGTTATCTGCCAACCAAAAGACCTTCGAGTTCGACTACGCTCAG
CTCCAAGGGACATCATTTGCAATATAGCTTAAGTCAAGAAGGGCTATCTGACCAAAGACCCTCAA
GTTCGATTACACTCAACTCAGAGGCAAACCAATTTAC
Found at i:22749 original size:23 final size:24
Alignment explanation
Indices: 22717--22761 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
22707 CATTTAAATC
22717 TTATTATTTATATA-TATATTTAA
1 TTATTATTTATATACTATATTTAA
* *
22740 TTATTTTTTATTTACTATATTT
1 TTATTATTTATATACTATATTT
22762 TTCTATTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 12 0.63
24 7 0.37
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (24 bp):
TTATTATTTATATACTATATTTAA
Found at i:22751 original size:15 final size:17
Alignment explanation
Indices: 22733--22769 Score: 51
Period size: 15 Copynumber: 2.3 Consensus size: 17
22723 TTTATATATA
22733 TATTTAAT-TATTTTT-
1 TATTTAATATATTTTTC
*
22748 TATTTACTATATTTTTC
1 TATTTAATATATTTTTC
22765 TATTT
1 TATTT
22770 TTGGTTTATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
15 7 0.37
16 7 0.37
17 5 0.26
ACGTcount: A:0.24, C:0.05, G:0.00, T:0.70
Consensus pattern (17 bp):
TATTTAATATATTTTTC
Found at i:22824 original size:2 final size:2
Alignment explanation
Indices: 22819--22845 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
22809 TATTTTTTAT
22819 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
22846 TACTCATATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:22883 original size:12 final size:12
Alignment explanation
Indices: 22868--22996 Score: 62
Period size: 14 Copynumber: 9.5 Consensus size: 12
22858 TTTTCATCAT
22868 TATTATTTTTTA
1 TATTATTTTTTA
22880 TATTTTATTTTATTA
1 TA--TTATTTT-TTA
22895 TATATATTTTCTTA
1 TAT-TATTTT-TTA
*
22909 TGTATATTTTTTTGTA
1 --TAT-TATTTTT-TA
22925 TATATATTTTTTA
1 TAT-TATTTTTTA
*
22938 T-TTGATATTTTATT
1 TATT-AT-TTTT-TA
*
22952 TATTATTTTTCA
1 TATTATTTTTTA
22964 TTATTATTATTTTAA
1 -TATTATT-TTTT-A
* *
22979 TACTATTTTTTC
1 TATTATTTTTTA
22991 TATTAT
1 TATTAT
22997 CATTATAACT
Statistics
Matches: 93, Mismatches: 10, Indels: 28
0.71 0.08 0.21
Matches are distributed among these distances:
11 1 0.01
12 10 0.11
13 23 0.25
14 39 0.42
15 9 0.10
16 11 0.12
ACGTcount: A:0.26, C:0.03, G:0.02, T:0.69
Consensus pattern (12 bp):
TATTATTTTTTA
Found at i:22889 original size:14 final size:14
Alignment explanation
Indices: 22873--22976 Score: 70
Period size: 16 Copynumber: 7.0 Consensus size: 14
22863 ATCATTATTA
22873 TTTT-TTATATTTT
1 TTTTATTATATTTT
22886 ATTTTATTATATATATT
1 -TTTTATTATAT-T-TT
22903 TTCTTATGTATATTTT
1 TT-TTAT-TATATTTT
22919 TTTGTATATATATTTT
1 TTT-TAT-TATATTTT
*
22935 TTATT-TGATATTTT
1 TT-TTATTATATTTT
*
22949 ATTTATTAT-TTTT
1 TTTTATTATATTTT
**
22962 CATTATTATTATTTT
1 TTTTATTA-TATTTT
22977 AATACTATTT
Statistics
Matches: 74, Mismatches: 6, Indels: 19
0.75 0.06 0.19
Matches are distributed among these distances:
13 12 0.16
14 16 0.22
15 12 0.16
16 21 0.28
17 8 0.11
18 5 0.07
ACGTcount: A:0.24, C:0.02, G:0.03, T:0.71
Consensus pattern (14 bp):
TTTTATTATATTTT
Found at i:23325 original size:21 final size:20
Alignment explanation
Indices: 23284--23326 Score: 50
Period size: 21 Copynumber: 2.1 Consensus size: 20
23274 TTTTCTCTCA
* *
23284 TTTTATTTATTTTATTTATT
1 TTTTATTTACTTTATTCATT
*
23304 TTTTAATTTACTTTCTTCATT
1 TTTT-ATTTACTTTATTCATT
23325 TT
1 TT
23327 ATTTTATTAC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 4 0.21
21 15 0.79
ACGTcount: A:0.19, C:0.07, G:0.00, T:0.74
Consensus pattern (20 bp):
TTTTATTTACTTTATTCATT
Found at i:28391 original size:2 final size:2
Alignment explanation
Indices: 28384--28414 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
28374 TCAATCTACA
28384 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
28415 ATTTACGAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:28611 original size:13 final size:13
Alignment explanation
Indices: 28595--28636 Score: 66
Period size: 13 Copynumber: 3.2 Consensus size: 13
28585 AATGAATGTT
28595 ATAAATGTGCGTC
1 ATAAATGTGCGTC
*
28608 ATAAATGTGTGTC
1 ATAAATGTGCGTC
*
28621 ATAAATGCGCGTC
1 ATAAATGTGCGTC
28634 ATA
1 ATA
28637 GATTTGTGAC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.33, C:0.14, G:0.21, T:0.31
Consensus pattern (13 bp):
ATAAATGTGCGTC
Found at i:28614 original size:26 final size:26
Alignment explanation
Indices: 28585--28636 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
28575 AATGACGCTT
* *
28585 AATGAATGTTATAAATGTGCGTCATA
1 AATGAATGTCATAAATGCGCGTCATA
**
28611 AATGTGTGTCATAAATGCGCGTCATA
1 AATGAATGTCATAAATGCGCGTCATA
28637 GATTTGTGAC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.35, C:0.12, G:0.21, T:0.33
Consensus pattern (26 bp):
AATGAATGTCATAAATGCGCGTCATA
Found at i:37468 original size:20 final size:20
Alignment explanation
Indices: 37439--37493 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 20
37429 ACGCACTATA
* * *
37439 AGTTTAGAAACTTTAGGCAT
1 AGTTTTGAAACTTTAGGAAG
*
37459 AGTTTTGAAACTTTAGTAAG
1 AGTTTTGAAACTTTAGGAAG
37479 AGTTTTGAAACTTTA
1 AGTTTTGAAACTTTA
37494 AAACACACTA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.35, C:0.07, G:0.18, T:0.40
Consensus pattern (20 bp):
AGTTTTGAAACTTTAGGAAG
Found at i:39544 original size:18 final size:18
Alignment explanation
Indices: 39521--39563 Score: 86
Period size: 18 Copynumber: 2.4 Consensus size: 18
39511 CATAATTGTA
39521 CTCCCTTAGGTATGAGAC
1 CTCCCTTAGGTATGAGAC
39539 CTCCCTTAGGTATGAGAC
1 CTCCCTTAGGTATGAGAC
39557 CTCCCTT
1 CTCCCTT
39564 TCCTCTAGCG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.19, C:0.33, G:0.19, T:0.30
Consensus pattern (18 bp):
CTCCCTTAGGTATGAGAC
Found at i:44962 original size:16 final size:15
Alignment explanation
Indices: 44938--44984 Score: 67
Period size: 16 Copynumber: 3.0 Consensus size: 15
44928 CGTATTAAAA
44938 TTAAAATAAATTAAT
1 TTAAAATAAATTAAT
44953 TTAAATATAAATTAAT
1 TTAAA-ATAAATTAAT
*
44969 TAAAAAGTAAATTAAT
1 TTAAAA-TAAATTAAT
44985 AATTTTATTA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
15 6 0.21
16 23 0.79
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (15 bp):
TTAAAATAAATTAAT
Found at i:46244 original size:23 final size:23
Alignment explanation
Indices: 46218--46261 Score: 88
Period size: 23 Copynumber: 1.9 Consensus size: 23
46208 TTTCGACCAC
46218 TGTCAATATTTAATTCTGGCTAA
1 TGTCAATATTTAATTCTGGCTAA
46241 TGTCAATATTTAATTCTGGCT
1 TGTCAATATTTAATTCTGGCT
46262 CCGGTCGTGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.27, C:0.14, G:0.14, T:0.45
Consensus pattern (23 bp):
TGTCAATATTTAATTCTGGCTAA
Found at i:46335 original size:16 final size:17
Alignment explanation
Indices: 46314--46352 Score: 62
Period size: 16 Copynumber: 2.4 Consensus size: 17
46304 GTTTTCATTT
*
46314 CAAATAAGTTC-AACCG
1 CAAATAAGTTCAAACCC
46330 CAAATAAGTTCAAACCC
1 CAAATAAGTTCAAACCC
46347 CAAATA
1 CAAATA
46353 GAAAATTCCA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
16 11 0.52
17 10 0.48
ACGTcount: A:0.49, C:0.26, G:0.08, T:0.18
Consensus pattern (17 bp):
CAAATAAGTTCAAACCC
Found at i:48585 original size:27 final size:28
Alignment explanation
Indices: 48528--48585 Score: 68
Period size: 29 Copynumber: 2.1 Consensus size: 28
48518 AGAGGTGCAC
48528 AAAAAATCCGAATATCCGATTTTGGGTAA
1 AAAAAATCCGAATATCCGATTTTGGG-AA
*
48557 AAAATATCCGAA-A-CCAGATTTT-GGAA
1 AAAAAATCCGAATATCC-GATTTTGGGAA
48583 AAA
1 AAA
48586 CTAGTTTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
26 5 0.19
27 4 0.15
28 7 0.26
29 11 0.41
ACGTcount: A:0.47, C:0.14, G:0.16, T:0.24
Consensus pattern (28 bp):
AAAAAATCCGAATATCCGATTTTGGGAA
Found at i:48684 original size:24 final size:25
Alignment explanation
Indices: 48657--48718 Score: 90
Period size: 27 Copynumber: 2.4 Consensus size: 25
48647 AAATTGAACG
48657 ACCGGTTTTTTT-ACCGGATTAAAA
1 ACCGGTTTTTTTAACCGGATTAAAA
48681 ACCGGTTTTTTTCAAACCGGATTAAAA
1 ACCGGTTTTTTT--AACCGGATTAAAA
*
48708 ACTGGTTTTTT
1 ACCGGTTTTTT
48719 ATCCGAAAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
24 12 0.35
27 22 0.65
ACGTcount: A:0.27, C:0.16, G:0.16, T:0.40
Consensus pattern (25 bp):
ACCGGTTTTTTTAACCGGATTAAAA
Found at i:52768 original size:17 final size:17
Alignment explanation
Indices: 52743--52782 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
52733 ATATGTTGTT
*
52743 CATTAAAGCATGCATTG
1 CATTTAAGCATGCATTG
* *
52760 CATTTAAGCATGTATTT
1 CATTTAAGCATGCATTG
52777 CATTTA
1 CATTTA
52783 GGGAAGTAGT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.33, C:0.15, G:0.12, T:0.40
Consensus pattern (17 bp):
CATTTAAGCATGCATTG
Found at i:52809 original size:17 final size:17
Alignment explanation
Indices: 52789--52847 Score: 50
Period size: 17 Copynumber: 3.5 Consensus size: 17
52779 TTTAGGGAAG
52789 TAGTTCATTTATGCATC
1 TAGTTCATTTATGCATC
* *
52806 TAGTT-ATTTAAT-AAAC
1 TAGTTCATTT-ATGCATC
* * *
52822 TACTTCATTCATGCATT
1 TAGTTCATTTATGCATC
52839 TAGTTCATT
1 TAGTTCATT
52848 GAATAATGTT
Statistics
Matches: 31, Mismatches: 8, Indels: 6
0.69 0.18 0.13
Matches are distributed among these distances:
16 12 0.39
17 19 0.61
ACGTcount: A:0.29, C:0.15, G:0.08, T:0.47
Consensus pattern (17 bp):
TAGTTCATTTATGCATC
Found at i:56518 original size:17 final size:17
Alignment explanation
Indices: 56498--56556 Score: 50
Period size: 17 Copynumber: 3.5 Consensus size: 17
56488 TTTAGGGAAG
56498 TAGTTCATTTATGCATC
1 TAGTTCATTTATGCATC
* *
56515 TAGTT-ATTTAAT-AAAC
1 TAGTTCATTT-ATGCATC
* * *
56531 TACTTCATTCATGCATT
1 TAGTTCATTTATGCATC
56548 TAGTTCATT
1 TAGTTCATT
56557 GAATAATGTT
Statistics
Matches: 31, Mismatches: 8, Indels: 6
0.69 0.18 0.13
Matches are distributed among these distances:
16 12 0.39
17 19 0.61
ACGTcount: A:0.29, C:0.15, G:0.08, T:0.47
Consensus pattern (17 bp):
TAGTTCATTTATGCATC
Found at i:59099 original size:62 final size:61
Alignment explanation
Indices: 58976--59159 Score: 146
Period size: 62 Copynumber: 3.0 Consensus size: 61
58966 TCGCAATGCG
* ** * * ** * *
58976 ATTTCAAATTCGCAACACGAACTCCAATTTCGCAA-TAC-AGTTTCCAAATTCGCAACGCGA
1 ATTTCGAATTCGCAACACGATGTCAAATTTCGCAACT-CGATTTTTGAATTTCGCAACACGA
*
59036 ATTTGGAATTCGCAACAC-ATAAGTCAAATTT-GCAACTCGA-TTTTGACAATTTCGCAACACGA
1 ATTTCGAATTCGCAACACGAT--GTCAAATTTCGCAACTCGATTTTTG--AATTTCGCAACACGA
*** * *
59098 ATTTCTTTTTCGCAACACGATTTTAAATTTCGCAACTCGATTTTTGAATTT-GCAACACGA
1 ATTTCGAATTCGCAACACGATGTCAAATTTCGCAACTCGATTTTTGAATTTCGCAACACGA
59158 AT
1 AT
59160 CTTCTCCGTA
Statistics
Matches: 100, Mismatches: 15, Indels: 18
0.75 0.11 0.14
Matches are distributed among these distances:
59 1 0.01
60 35 0.35
61 21 0.21
62 36 0.36
63 7 0.07
ACGTcount: A:0.33, C:0.23, G:0.12, T:0.32
Consensus pattern (61 bp):
ATTTCGAATTCGCAACACGATGTCAAATTTCGCAACTCGATTTTTGAATTTCGCAACACGA
Found at i:59110 original size:20 final size:20
Alignment explanation
Indices: 59085--59243 Score: 100
Period size: 20 Copynumber: 8.1 Consensus size: 20
59075 ATTTTGACAA
59085 TTTCGCAACACGAATTTCTT
1 TTTCGCAACACGAATTTCTT
* ***
59105 TTTCGCAACACGATTTTAAA
1 TTTCGCAACACGAATTTCTT
*
59125 TTTCGCAACTCG-ATTT-TT
1 TTTCGCAACACGAATTTCTT
59143 GAATTT-GCAACACGAA--TCTT
1 ---TTTCGCAACACGAATTTCTT
* * * *
59163 CTCCGTAACTA-GATTTTCTT
1 TTTCGCAAC-ACGAATTTCTT
*
59183 TTTCGCAACACCAATTTCTT
1 TTTCGCAACACGAATTTCTT
* *
59203 ATTT-GCAACTCGATTTTCTT
1 -TTTCGCAACACGAATTTCTT
*
59223 TTTTGCAACACGAATTT-TT
1 TTTCGCAACACGAATTTCTT
59242 TT
1 TT
59244 GGGTATATAA
Statistics
Matches: 104, Mismatches: 23, Indels: 25
0.68 0.15 0.16
Matches are distributed among these distances:
17 1 0.01
18 6 0.06
19 13 0.12
20 77 0.74
21 7 0.07
ACGTcount: A:0.25, C:0.22, G:0.10, T:0.43
Consensus pattern (20 bp):
TTTCGCAACACGAATTTCTT
Found at i:59153 original size:40 final size:43
Alignment explanation
Indices: 59062--59157 Score: 114
Period size: 40 Copynumber: 2.3 Consensus size: 43
59052 ACATAAGTCA
*
59062 AATTTGCAACTCGATTTTGACAATTTCGCAACACGAATTTCTT
1 AATTTGCAACACGATTTTGACAATTTCGCAACACGAATTTCTT
*
59105 --TTTCGCAACACGATTTT-A-AATTTCGCAACTCG-ATTT-TT
1 AATTT-GCAACACGATTTTGACAATTTCGCAACACGAATTTCTT
59143 GAATTTGCAACACGA
1 -AATTTGCAACACGA
59158 ATCTTCTCCG
Statistics
Matches: 47, Mismatches: 2, Indels: 11
0.78 0.03 0.18
Matches are distributed among these distances:
38 2 0.04
39 4 0.09
40 22 0.47
41 7 0.15
42 12 0.26
ACGTcount: A:0.30, C:0.21, G:0.12, T:0.36
Consensus pattern (43 bp):
AATTTGCAACACGATTTTGACAATTTCGCAACACGAATTTCTT
Found at i:60036 original size:12 final size:12
Alignment explanation
Indices: 60003--60030 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
59993 ACCACATTTC
60003 CAATACCAAACA
1 CAATACCAAACA
60015 CAATACCAAACA
1 CAATACCAAACA
60027 CAAT
1 CAAT
60031 CTCAAAATCC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.57, C:0.32, G:0.00, T:0.11
Consensus pattern (12 bp):
CAATACCAAACA
Found at i:62853 original size:20 final size:19
Alignment explanation
Indices: 62811--62859 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
62801 ACTCAAATTT
* *
62811 GCAACGCGAAAATAAAATC
1 GCAACGCGATATTAAAATC
*
62830 GCAACTCGATATTAAAATTC
1 GCAACGCGATATTAAAA-TC
62850 GCAACGCGAT
1 GCAACGCGAT
62860 TTTCGTGTTA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
19 14 0.56
20 11 0.44
ACGTcount: A:0.43, C:0.22, G:0.16, T:0.18
Consensus pattern (19 bp):
GCAACGCGATATTAAAATC
Found at i:62893 original size:20 final size:20
Alignment explanation
Indices: 62856--62923 Score: 73
Period size: 20 Copynumber: 3.4 Consensus size: 20
62846 ATTCGCAACG
** *
62856 CGATTTTCGTGTTACGAATT
1 CGATTTTCGCATTGCGAATT
* **
62876 TGATTTTCGCATTGCGAAAC
1 CGATTTTCGCATTGCGAATT
*
62896 CGATTTTCGCGTTGCGAATT
1 CGATTTTCGCATTGCGAATT
62916 CGATTTTC
1 CGATTTTC
62924 TTAAACGTAT
Statistics
Matches: 38, Mismatches: 10, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
20 38 1.00
ACGTcount: A:0.19, C:0.19, G:0.21, T:0.41
Consensus pattern (20 bp):
CGATTTTCGCATTGCGAATT
Found at i:64485 original size:21 final size:21
Alignment explanation
Indices: 64459--64598 Score: 108
Period size: 21 Copynumber: 6.7 Consensus size: 21
64449 AGTATGGAAT
*
64459 GTGGATCCTGAACGATAGGAG
1 GTGGATCCTGAACGATGGGAG
*
64480 GTGGATCTTGAACGATGGGAAG
1 GTGGATCCTGAACGATGGG-AG
** *
64502 G-GCTTCTTGAACGATGGGAG
1 GTGGATCCTGAACGATGGGAG
* * * *
64522 G-GGCCTCTTGAATGATGGAAG
1 GTGG-ATCCTGAACGATGGGAG
*
64543 G-GG-TCTCTTGAACGATGAGAG
1 GTGGATC-C-TGAACGATGGGAG
* *
64564 GTGAATCCTGAACAATGGGAG
1 GTGGATCCTGAACGATGGGAG
64585 GTGGATCCTGAACG
1 GTGGATCCTGAACG
64599 GCTGTAGGTG
Statistics
Matches: 96, Mismatches: 17, Indels: 12
0.77 0.14 0.10
Matches are distributed among these distances:
19 2 0.02
20 4 0.04
21 83 0.86
22 5 0.05
23 2 0.02
ACGTcount: A:0.26, C:0.14, G:0.38, T:0.22
Consensus pattern (21 bp):
GTGGATCCTGAACGATGGGAG
Found at i:64531 original size:42 final size:42
Alignment explanation
Indices: 64467--64581 Score: 126
Period size: 42 Copynumber: 2.7 Consensus size: 42
64457 ATGTGGATCC
*
64467 TGAACGATAGGAGGTGGATCTTGAACGATGGGAAGGGCT-TCT
1 TGAACGATGGGAGGTGGATCTTGAACGAT-GGAAGGGCTCTCT
* * *
64509 TGAACGATGGGAGG-GGCCTCTTGAATGATGGAAGGGGTCTCT
1 TGAACGATGGGAGGTGG-ATCTTGAACGATGGAAGGGCTCTCT
* * * *
64551 TGAACGATGAGAGGTGAATCCTGAACAATGG
1 TGAACGATGGGAGGTGGATCTTGAACGATGG
64582 GAGGTGGATC
Statistics
Matches: 60, Mismatches: 10, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
41 10 0.17
42 49 0.82
43 1 0.02
ACGTcount: A:0.27, C:0.13, G:0.37, T:0.23
Consensus pattern (42 bp):
TGAACGATGGGAGGTGGATCTTGAACGATGGAAGGGCTCTCT
Found at i:64996 original size:21 final size:21
Alignment explanation
Indices: 64911--64997 Score: 52
Period size: 21 Copynumber: 4.1 Consensus size: 21
64901 TAGAGCACCG
* * **
64911 ACCTCATCACATAAAGAAGCT
1 ACCTCACCACGTAAAGACCCT
*
64932 ACCTCACCACGTAAAGCACCAT
1 ACCTCACCACGTAAAG-ACCCT
** * * *
64954 -TGTCATCATGTAAA-ACAACT
1 ACCTCACCACGTAAAGAC-CCT
64974 ACCTCACCACGTAAAGACCCT
1 ACCTCACCACGTAAAGACCCT
64995 ACC
1 ACC
64998 GTATCACGCC
Statistics
Matches: 46, Mismatches: 16, Indels: 8
0.66 0.23 0.11
Matches are distributed among these distances:
19 2 0.04
20 1 0.02
21 39 0.85
22 4 0.09
ACGTcount: A:0.38, C:0.34, G:0.09, T:0.18
Consensus pattern (21 bp):
ACCTCACCACGTAAAGACCCT
Found at i:64997 original size:63 final size:63
Alignment explanation
Indices: 64911--65030 Score: 143
Period size: 63 Copynumber: 1.9 Consensus size: 63
64901 TAGAGCACCG
* * * *
64911 ACCTCATCACATAAAGAAGCTACC-TCACCACGTAAAGCACCATTGTCATCATGTAAAACAACT
1 ACCTCACCACATAAAGAACCTACCGT-ACCACGCAAAGCACCATTGTCATCACGTAAAACAACT
* * * * *
64974 ACCTCACCACGTAAAGACCCTACCGTATCACGCCATGCACCATTGTCATCACGTAAA
1 ACCTCACCACATAAAGAACCTACCGTACCACGCAAAGCACCATTGTCATCACGTAAA
65031 GTATTGACCT
Statistics
Matches: 47, Mismatches: 9, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
63 46 0.98
64 1 0.02
ACGTcount: A:0.36, C:0.33, G:0.11, T:0.20
Consensus pattern (63 bp):
ACCTCACCACATAAAGAACCTACCGTACCACGCAAAGCACCATTGTCATCACGTAAAACAACT
Found at i:65263 original size:42 final size:41
Alignment explanation
Indices: 65165--65309 Score: 177
Period size: 42 Copynumber: 3.5 Consensus size: 41
65155 GTGATGGAAT
* *
65165 AGGTGATGGATCTCGGTGTCGAGGTGTATAGTCGGCT-A-G
1 AGGTGATGGATCTCGGTGTCGAGGTGTAGAATCGGCTGATG
* * *
65204 AGGTGATGGCTCTCGGTGTCGAGGTATAGAATCGGCTGGATC
1 AGGTGATGGATCTCGGTGTCGAGGTGTAGAATCGGCT-GATG
* * * *
65246 AGGTGATGAATCTCGGTGTCGAAGTGGAGAATCGACTCGATG
1 AGGTGATGGATCTCGGTGTCGAGGTGTAGAATCGGCT-GATG
65288 AGGTGATGGATCTCGGTGTCGA
1 AGGTGATGGATCTCGGTGTCGA
65310 ATTGAAAAAT
Statistics
Matches: 89, Mismatches: 14, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
39 33 0.37
41 1 0.01
42 55 0.62
ACGTcount: A:0.21, C:0.14, G:0.39, T:0.26
Consensus pattern (41 bp):
AGGTGATGGATCTCGGTGTCGAGGTGTAGAATCGGCTGATG
Found at i:65310 original size:42 final size:42
Alignment explanation
Indices: 65165--65330 Score: 176
Period size: 42 Copynumber: 4.0 Consensus size: 42
65155 GTGATGGAAT
* * * *
65165 AGGTGATGGATCTCGGTGTCGAGGTGTATAGTCGGCT--A-G
1 AGGTGATGGATCTCGGTGTCGAAGTGTAGAATCGACTCGATG
* * * * * *
65204 AGGTGATGGCTCTCGGTGTCGAGGTATAGAATCGGCTGGATC
1 AGGTGATGGATCTCGGTGTCGAAGTGTAGAATCGACTCGATG
* *
65246 AGGTGATGAATCTCGGTGTCGAAGTGGAGAATCGACTCGATG
1 AGGTGATGGATCTCGGTGTCGAAGTGTAGAATCGACTCGATG
* * *
65288 AGGTGATGGATCTCGGTGTCGAATTGAAAAATCGACTCGATG
1 AGGTGATGGATCTCGGTGTCGAAGTGTAGAATCGACTCGATG
65330 A
1 A
65331 AAATGTGGGG
Statistics
Matches: 107, Mismatches: 17, Indels: 3
0.84 0.13 0.02
Matches are distributed among these distances:
39 33 0.31
41 1 0.01
42 73 0.68
ACGTcount: A:0.23, C:0.14, G:0.36, T:0.26
Consensus pattern (42 bp):
AGGTGATGGATCTCGGTGTCGAAGTGTAGAATCGACTCGATG
Found at i:66893 original size:14 final size:15
Alignment explanation
Indices: 66876--66908 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
66866 CTTGAAAATG
66876 AAATTTGCAACAC-A
1 AAATTTGCAACACGA
*
66890 AAATTTGTAACACGA
1 AAATTTGCAACACGA
66905 AAAT
1 AAAT
66909 CGAAACGCGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 12 0.71
15 5 0.29
ACGTcount: A:0.52, C:0.15, G:0.09, T:0.24
Consensus pattern (15 bp):
AAATTTGCAACACGA
Found at i:66954 original size:19 final size:19
Alignment explanation
Indices: 66904--66970 Score: 73
Period size: 20 Copynumber: 3.4 Consensus size: 19
66894 TTGTAACACG
*
66904 AAAATCGAAACGCGAAAAT
1 AAAATCGCAACGCGAAAAT
* *
66923 AAAATTTGCAACGTGAAAAT
1 AAAA-TCGCAACGCGAAAAT
66943 AAAATCGCAACGC-AAAACCT
1 AAAATCGCAACGCGAAAA--T
66963 AAAATCGC
1 AAAATCGC
66971 GTTGCGATTT
Statistics
Matches: 40, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
18 4 0.10
19 11 0.28
20 25 0.62
ACGTcount: A:0.52, C:0.19, G:0.13, T:0.15
Consensus pattern (19 bp):
AAAATCGCAACGCGAAAAT
Found at i:67002 original size:20 final size:20
Alignment explanation
Indices: 66977--67015 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
66967 TCGCGTTGCG
66977 ATTTTCGTGTTGCGAATTTC
1 ATTTTCGTGTTGCGAATTTC
*
66997 ATTTTCGTGTTGCGGATTT
1 ATTTTCGTGTTGCGAATTT
67016 AAGTTTTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.13, C:0.13, G:0.23, T:0.51
Consensus pattern (20 bp):
ATTTTCGTGTTGCGAATTTC
Found at i:67474 original size:20 final size:20
Alignment explanation
Indices: 67449--67504 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
67439 ATTTACATTT
* *
67449 GTGTTGCGAAATTAATATTC
1 GTGTTGCGAAAATAAAATTC
*
67469 GTGTTGTGAAAATAAAATTC
1 GTGTTGCGAAAATAAAATTC
*
67489 GCGTTGCGAAAATAAA
1 GTGTTGCGAAAATAAA
67505 CGCGCTTTGC
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.38, C:0.09, G:0.21, T:0.32
Consensus pattern (20 bp):
GTGTTGCGAAAATAAAATTC
Found at i:74661 original size:20 final size:20
Alignment explanation
Indices: 74638--74687 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
74628 CAGTCCTCTG
*
74638 GTATGGAGACCAGTCTTTCA
1 GTATGGAGACCAGTCTTCCA
** *
74658 GTATATAGATCAGTCTTCCA
1 GTATGGAGACCAGTCTTCCA
74678 GTATGGAGAC
1 GTATGGAGAC
74688 TAGTGGTCTT
Statistics
Matches: 23, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.28, C:0.18, G:0.24, T:0.30
Consensus pattern (20 bp):
GTATGGAGACCAGTCTTCCA
Found at i:74851 original size:20 final size:20
Alignment explanation
Indices: 74800--74853 Score: 65
Period size: 20 Copynumber: 2.7 Consensus size: 20
74790 TAGAACAAGA
* *
74800 ACAATGTCGATACTGTTCAT
1 ACAATATCGACACTGTTCAT
*
74820 AC-ATCATTGACACTGTTCAT
1 ACAAT-ATCGACACTGTTCAT
74840 ACAATATCGACACT
1 ACAATATCGACACT
74854 ATCGCTCAGA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
19 2 0.07
20 24 0.86
21 2 0.07
ACGTcount: A:0.33, C:0.24, G:0.11, T:0.31
Consensus pattern (20 bp):
ACAATATCGACACTGTTCAT
Done.