Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003379.1 Hibiscus syriacus cultivar Beakdansim tig00007102_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: 78349
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:6345 original size:22 final size:22
Alignment explanation
Indices: 6317--6364 Score: 87
Period size: 22 Copynumber: 2.2 Consensus size: 22
6307 ATTTCATCTT
6317 TAGAGTAGAGATAAAGATACTC
1 TAGAGTAGAGATAAAGATACTC
*
6339 TAGAGTAGAGATGAAGATACTC
1 TAGAGTAGAGATAAAGATACTC
6361 TAGA
1 TAGA
6365 ATAAAGATGA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.44, C:0.08, G:0.25, T:0.23
Consensus pattern (22 bp):
TAGAGTAGAGATAAAGATACTC
Found at i:6372 original size:22 final size:22
Alignment explanation
Indices: 6325--6374 Score: 73
Period size: 22 Copynumber: 2.3 Consensus size: 22
6315 TTTAGAGTAG
* * *
6325 AGATAAAGATACTCTAGAGTAG
1 AGATGAAGATACTCTAGAATAA
6347 AGATGAAGATACTCTAGAATAA
1 AGATGAAGATACTCTAGAATAA
6369 AGATGA
1 AGATGA
6375 GGACGGGAGA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.48, C:0.08, G:0.22, T:0.22
Consensus pattern (22 bp):
AGATGAAGATACTCTAGAATAA
Found at i:7003 original size:2 final size:2
Alignment explanation
Indices: 6996--7030 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
6986 ATGGAGGGAC
6996 AT AT 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 AT AT A
7031 ATAAGTCAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:15030 original size:22 final size:22
Alignment explanation
Indices: 15000--15062 Score: 54
Period size: 24 Copynumber: 2.8 Consensus size: 22
14990 CTTATTTGTT
* **
15000 TTTTTAATAAAAATATTTTAAA
1 TTTTAAATAAAAATATTAAAAA
*
15022 TTTTAAATATAAAAATATCAAAAA
1 TTTT-AA-ATAAAAATATTAAAAA
* *
15046 ATTTAAATATAAATATT
1 TTTTAAATAAAAATATT
15063 CCATTAATTA
Statistics
Matches: 32, Mismatches: 7, Indels: 4
0.74 0.16 0.09
Matches are distributed among these distances:
22 13 0.41
23 3 0.09
24 16 0.50
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.43
Consensus pattern (22 bp):
TTTTAAATAAAAATATTAAAAA
Found at i:15686 original size:31 final size:31
Alignment explanation
Indices: 15651--15710 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
15641 AACTTAAAAG
*
15651 AGTTTTGCAATACTGAAATTGAAATAATTTT
1 AGTTTTACAATACTGAAATTGAAATAATTTT
* *
15682 AGTTTTATAATACTGAAATTTAAATAATT
1 AGTTTTACAATACTGAAATTGAAATAATT
15711 CATACAACTA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.42, C:0.05, G:0.10, T:0.43
Consensus pattern (31 bp):
AGTTTTACAATACTGAAATTGAAATAATTTT
Found at i:15766 original size:22 final size:22
Alignment explanation
Indices: 15734--16032 Score: 481
Period size: 22 Copynumber: 13.6 Consensus size: 22
15724 TAATAATAAT
* *
15734 TTTTTAAATAAATCAATCCAAA
1 TTTTAAAATAAATCAATCCATA
*
15756 ATTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
*
15778 TTTTAAAATAAATCAATCCAAA
1 TTTTAAAATAAATCAATCCATA
* *** *
15800 TTTAAAAATAAATTTTTTCATA
1 TTTTAAAATAAATCAATCCATA
15822 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
*
15844 TTTTAAAATAAATCAATCAATA
1 TTTTAAAATAAATCAATCCATA
15866 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
*
15888 TTTTAAAATAAATCAATCTATA
1 TTTTAAAATAAATCAATCCATA
15910 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
15932 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
15954 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
* *
15976 TTTTAAAATAAATCAATTCATG
1 TTTTAAAATAAATCAATCCATA
15998 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
16020 TTTTAAAATAAAT
1 TTTTAAAATAAAT
16033 TTTAAAATAG
Statistics
Matches: 253, Mismatches: 24, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 253 1.00
ACGTcount: A:0.51, C:0.11, G:0.00, T:0.38
Consensus pattern (22 bp):
TTTTAAAATAAATCAATCCATA
Found at i:16049 original size:11 final size:12
Alignment explanation
Indices: 16019--16058 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
16009 ATCAATCCAT
16019 ATTTTAAAATAA
1 ATTTTAAAATAA
*
16031 ATTTTAAAATAG
1 ATTTTAAAATAA
16043 A-TTT-AAAT-A
1 ATTTTAAAATAA
16052 ATTTTAA
1 ATTTTAA
16059 TGTTCTTTGA
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
9 1 0.04
10 7 0.29
11 4 0.17
12 12 0.50
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.45
Consensus pattern (12 bp):
ATTTTAAAATAA
Found at i:17849 original size:20 final size:20
Alignment explanation
Indices: 17824--17875 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
17814 TAGTTGAAAA
*
17824 TCGCGTTGCGATTTTTCATT
1 TCGCGTTGCGATTTTCCATT
17844 TCGCGTTGCGATTTTCCATT
1 TCGCGTTGCGATTTTCCATT
17864 TCGCGTTGCGAT
1 TCGCGTTGCGAT
17876 AGTCTACAGT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.10, C:0.23, G:0.23, T:0.44
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCCATT
Found at i:18538 original size:21 final size:21
Alignment explanation
Indices: 18512--18560 Score: 73
Period size: 20 Copynumber: 2.4 Consensus size: 21
18502 TCGTGGTCGT
* *
18512 AACGCGATAGTTGAAAATCGC
1 AACGCGATAATGGAAAATCGC
18533 AACGCGA-AATGGAAAATCGC
1 AACGCGATAATGGAAAATCGC
18553 AACGCGAT
1 AACGCGAT
18561 TTTCGCAACG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 18 0.72
21 7 0.28
ACGTcount: A:0.41, C:0.20, G:0.24, T:0.14
Consensus pattern (21 bp):
AACGCGATAATGGAAAATCGC
Found at i:18587 original size:19 final size:19
Alignment explanation
Indices: 18563--18631 Score: 66
Period size: 19 Copynumber: 3.5 Consensus size: 19
18553 AACGCGATTT
18563 TCGCAACGAATTTGGAAAA
1 TCGCAACGAATTTGGAAAA
* * **
18582 TCGCAACGACAACTGTAGACTA
1 TCGCAACG--AA-TTTGGAAAA
*
18604 TCGCAACGAATTTGAAAAA
1 TCGCAACGAATTTGGAAAA
18623 TCGCAACGA
1 TCGCAACGA
18632 CAACTGTAGA
Statistics
Matches: 38, Mismatches: 9, Indels: 6
0.72 0.17 0.11
Matches are distributed among these distances:
19 21 0.55
20 2 0.05
21 2 0.05
22 13 0.34
ACGTcount: A:0.41, C:0.22, G:0.19, T:0.19
Consensus pattern (19 bp):
TCGCAACGAATTTGGAAAA
Found at i:18609 original size:22 final size:22
Alignment explanation
Indices: 18581--18652 Score: 87
Period size: 22 Copynumber: 3.4 Consensus size: 22
18571 AATTTGGAAA
*
18581 ATCGCAACGACAACTGTAGACT
1 ATCGCAACGACAACTGTAGAAT
** *
18603 ATCGCAACGA-ATTTG-A-AAA
1 ATCGCAACGACAACTGTAGAAT
18622 ATCGCAACGACAACTGTAGAAT
1 ATCGCAACGACAACTGTAGAAT
18644 ATCGCAACG
1 ATCGCAACG
18653 CGAAACGAAA
Statistics
Matches: 40, Mismatches: 7, Indels: 6
0.75 0.13 0.11
Matches are distributed among these distances:
19 11 0.28
20 4 0.10
21 4 0.10
22 21 0.52
ACGTcount: A:0.40, C:0.24, G:0.18, T:0.18
Consensus pattern (22 bp):
ATCGCAACGACAACTGTAGAAT
Found at i:18623 original size:41 final size:41
Alignment explanation
Indices: 18563--18652 Score: 162
Period size: 41 Copynumber: 2.2 Consensus size: 41
18553 AACGCGATTT
* *
18563 TCGCAACGAATTTGGAAAATCGCAACGACAACTGTAGACTA
1 TCGCAACGAATTTGAAAAATCGCAACGACAACTGTAGAATA
18604 TCGCAACGAATTTGAAAAATCGCAACGACAACTGTAGAATA
1 TCGCAACGAATTTGAAAAATCGCAACGACAACTGTAGAATA
18645 TCGCAACG
1 TCGCAACG
18653 CGAAACGAAA
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 47 1.00
ACGTcount: A:0.40, C:0.22, G:0.19, T:0.19
Consensus pattern (41 bp):
TCGCAACGAATTTGAAAAATCGCAACGACAACTGTAGAATA
Found at i:18704 original size:21 final size:21
Alignment explanation
Indices: 18643--18704 Score: 63
Period size: 21 Copynumber: 3.0 Consensus size: 21
18633 AACTGTAGAA
* *
18643 TATCGCAACGCGAAACG-AAA
1 TATCGCAACGCGAAATGCAAC
* ** *
18663 AATCGCAACGCGATTTTCAAC
1 TATCGCAACGCGAAATGCAAC
18684 TATCGCAACGCGAAATGCAAC
1 TATCGCAACGCGAAATGCAAC
18705 GCGAATTATC
Statistics
Matches: 31, Mismatches: 10, Indels: 1
0.74 0.24 0.02
Matches are distributed among these distances:
20 12 0.39
21 19 0.61
ACGTcount: A:0.39, C:0.27, G:0.18, T:0.16
Consensus pattern (21 bp):
TATCGCAACGCGAAATGCAAC
Found at i:25340 original size:19 final size:17
Alignment explanation
Indices: 25298--25352 Score: 55
Period size: 17 Copynumber: 3.4 Consensus size: 17
25288 GAAAATATTT
25298 TATATATAAT-T-AATA
1 TATATATAATATAAATA
*
25313 TA-A-AAAATATAAAATA
1 TATATATAATAT-AAATA
25329 TTATATATAATATAAATA
1 -TATATATAATATAAATA
25347 TATATA
1 TATATA
25353 ATCAAGACGG
Statistics
Matches: 32, Mismatches: 2, Indels: 10
0.73 0.05 0.23
Matches are distributed among these distances:
13 4 0.12
14 2 0.06
15 2 0.06
16 4 0.12
17 8 0.25
18 6 0.19
19 6 0.19
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (17 bp):
TATATATAATATAAATA
Found at i:27834 original size:2 final size:2
Alignment explanation
Indices: 27827--27900 Score: 134
Period size: 2 Copynumber: 38.0 Consensus size: 2
27817 AGGGTTCATA
27827 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
27868 AT AT AT AT AT AT AT AT AT A- AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
27901 GGAATTTAAG
Statistics
Matches: 70, Mismatches: 0, Indels: 4
0.95 0.00 0.05
Matches are distributed among these distances:
1 2 0.03
2 68 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:35168 original size:2 final size:2
Alignment explanation
Indices: 35161--35187 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
35151 CCTTTGTACA
35161 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 A
35188 AGGAAGAATT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:35379 original size:3 final size:3
Alignment explanation
Indices: 35371--36463 Score: 1920
Period size: 3 Copynumber: 371.7 Consensus size: 3
35361 CGCCCTTTTC
35371 TAT TAT TAT TA- TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
35418 TAT TAT TAT TAT TAT TA- TAT TAT TAT TAT TAT TAT TAT TAT TAT T-T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
35464 ATAT TAT TAT TAT TAT TAT TAT TAT TAT TA- TAT TAT TAT TAT TAT
1 -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
35509 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
35557 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
35605 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA- TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
35652 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA- TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
35699 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
35747 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA- TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
35794 TAT TAT TAT TAT ATAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
35840 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T-T TAT TAT TAT TAT TA-
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
35886 TAT TAT TAT TA- TAT TAT ATAT TAT TAT TAT TA- TAT TAT TA- TAT
1 TAT TAT TAT TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT
35929 TAT TAT TAT TA- TAT TAT TA- TAT TAT TAT TAT TAT TAT TAT TA- TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
35974 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
36022 TAT TAT TAT TAT T-T TAT TAT TAT TA- TAT TAT TAT TA- TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
36067 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TATT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT
36113 TA- TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
36160 TAT TAT TA- TAT TAT TAT TAT TA- TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
36206 TAT TAT TAT TA- TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
36253 TAT TAT TAT TAT TAT TAT TAT TA- TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
36300 TAT TA- TAT TAT TA- TAT TAT T-T TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
36345 TA- TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
36392 TAT TAT TAT TAT TA- TAT TAT TAT TA- TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
36438 TAT TAT TATT TATT TATT TAT TAT TA
1 TAT TAT TA-T TA-T TA-T TAT TAT TA
36464 GTTTATAAAT
Statistics
Matches: 1056, Mismatches: 0, Indels: 68
0.94 0.00 0.06
Matches are distributed among these distances:
2 57 0.05
3 978 0.93
4 21 0.02
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:42359 original size:29 final size:27
Alignment explanation
Indices: 42316--42382 Score: 71
Period size: 29 Copynumber: 2.4 Consensus size: 27
42306 TGATTGATTC
* *
42316 TTTAAGAAAATTTTAGAGCTTAATTAATT
1 TTTAA-AAAATTTTACAGCCTAATTAA-T
* *
42345 TTTAAAAAATGTTTACATCCTAATTTAT
1 TTTAAAAAAT-TTTACAGCCTAATTAAT
42373 TTTAAAAAAT
1 TTTAAAAAAT
42383 AAATAAATAT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
28 16 0.48
29 17 0.52
ACGTcount: A:0.43, C:0.06, G:0.06, T:0.45
Consensus pattern (27 bp):
TTTAAAAAATTTTACAGCCTAATTAAT
Found at i:43013 original size:59 final size:58
Alignment explanation
Indices: 42902--43074 Score: 154
Period size: 59 Copynumber: 2.9 Consensus size: 58
42892 TGAATTTGGG
* ***
42902 GATGAAATTGAAATATTCAAAAGTTTCAGAA-A-TAATTTAGAATGAGCGTCATAGTTT-A
1 GATGAAATTAAAATA-TCAAAAGTTT-A-AAGACTAATTTAGAATGAAAATCATAGTTTGA
* **
42960 GAATGAATTTGGAATGATCAAAAGTTTAAAGACTAATTTAGAATGAAAATCATAGTTTGA
1 G-ATGAAATTAAAAT-ATCAAAAGTTTAAAGACTAATTTAGAATGAAAATCATAGTTTGA
* * * * *
43020 TGATGAAATTAAAATATTAAAACATTTAAGGACTAATTTAAAATAAAAATCATAG
1 -GATGAAATTAAAATATCAAAA-GTTTAAAGACTAATTTAGAATGAAAATCATAG
43075 ATGAGAGACA
Statistics
Matches: 95, Mismatches: 13, Indels: 12
0.79 0.11 0.10
Matches are distributed among these distances:
57 2 0.02
58 3 0.03
59 49 0.52
60 40 0.42
61 1 0.01
ACGTcount: A:0.47, C:0.06, G:0.15, T:0.32
Consensus pattern (58 bp):
GATGAAATTAAAATATCAAAAGTTTAAAGACTAATTTAGAATGAAAATCATAGTTTGA
Found at i:45200 original size:13 final size:13
Alignment explanation
Indices: 45182--45206 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
45172 CACAATTAAT
45182 TTTATGTTCATTG
1 TTTATGTTCATTG
45195 TTTATGTTCATT
1 TTTATGTTCATT
45207 TACGTTCGTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.08, G:0.12, T:0.64
Consensus pattern (13 bp):
TTTATGTTCATTG
Found at i:49062 original size:2 final size:2
Alignment explanation
Indices: 49055--49093 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
49045 TGGATTTAAA
49055 AT AT AT AT 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 AT AT AT AT A
49094 ATTGTTAGTA
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:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:49634 original size:60 final size:60
Alignment explanation
Indices: 49523--49640 Score: 148
Period size: 60 Copynumber: 2.0 Consensus size: 60
49513 ATATTCGAGT
* ** * *
49523 GATCATTTTGTAACTTTTAATAGTTGAGAGGCTCAATAAAGCAACTCCTTATAATCGATG
1 GATCATTTTGTAACTTTTAATAATCAAGAGACTCAATAAAACAACTCCTTATAATCGATG
* * *
49583 GATCATTTTGTAACTTTTAATAATCAATAGACTCAATAAAATAA-TATCTTATAATCGA
1 GATCATTTTGTAACTTTTAATAATCAAGAGACTCAATAAAACAACT-CCTTATAATCGA
49641 AAAACTATTT
Statistics
Matches: 49, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
59 1 0.02
60 48 0.98
ACGTcount: A:0.38, C:0.14, G:0.12, T:0.36
Consensus pattern (60 bp):
GATCATTTTGTAACTTTTAATAATCAAGAGACTCAATAAAACAACTCCTTATAATCGATG
Found at i:57054 original size:31 final size:31
Alignment explanation
Indices: 57013--57086 Score: 105
Period size: 31 Copynumber: 2.4 Consensus size: 31
57003 ATTTGTACAC
*
57013 TTTTGATCACTTACAG-TATCGTTTTATTAAG
1 TTTTGGTCACTTAC-GTTATCGTTTTATTAAG
*
57044 TTTTGGTCACTTACGTTATTGTTTTATTAAG
1 TTTTGGTCACTTACGTTATCGTTTTATTAAG
*
57075 CTTTGGTCACTT
1 TTTTGGTCACTT
57087 GAACGTTGAA
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
30 1 0.03
31 38 0.97
ACGTcount: A:0.20, C:0.14, G:0.15, T:0.51
Consensus pattern (31 bp):
TTTTGGTCACTTACGTTATCGTTTTATTAAG
Found at i:57883 original size:30 final size:31
Alignment explanation
Indices: 57798--57922 Score: 162
Period size: 31 Copynumber: 4.1 Consensus size: 31
57788 AAGTGATAAG
* * **
57798 AACTTAATAAAACGATAATAAAAGTGACTGA
1 AACTTAATAAAACGATAACATAAGTGACCAA
*
57829 AACATAATAAAACGATAACATAAGTGACCAA
1 AACTTAATAAAACGATAACATAAGTGACCAA
*
57860 AACTTAATAAAA-GATATCATAAGTGACCAA
1 AACTTAATAAAACGATAACATAAGTGACCAA
* * *
57890 AACTTAATAAAATGATAACGTAAGTGGCCAA
1 AACTTAATAAAACGATAACATAAGTGACCAA
57921 AA
1 AA
57923 GTGTACAAAT
Statistics
Matches: 83, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
30 29 0.35
31 54 0.65
ACGTcount: A:0.54, C:0.13, G:0.12, T:0.21
Consensus pattern (31 bp):
AACTTAATAAAACGATAACATAAGTGACCAA
Found at i:57907 original size:61 final size:62
Alignment explanation
Indices: 57798--57922 Score: 164
Period size: 61 Copynumber: 2.0 Consensus size: 62
57788 AAGTGATAAG
**
57798 AACTTAATAAAACGATAATAAAAGTGACTGAAACATAATAAAACGATAACATAAGTGACCAA
1 AACTTAATAAAACGATAATAAAAGTGACCAAAACATAATAAAACGATAACATAAGTGACCAA
* * * * *
57860 AACTTAATAAAA-GAT-ATCATAAGTGACCAAAACTTAATAAAATGATAACGTAAGTGGCCAA
1 AACTTAATAAAACGATAAT-AAAAGTGACCAAAACATAATAAAACGATAACATAAGTGACCAA
57921 AA
1 AA
57923 GTGTACAAAT
Statistics
Matches: 55, Mismatches: 7, Indels: 3
0.85 0.11 0.05
Matches are distributed among these distances:
60 2 0.04
61 41 0.75
62 12 0.22
ACGTcount: A:0.54, C:0.13, G:0.12, T:0.21
Consensus pattern (62 bp):
AACTTAATAAAACGATAATAAAAGTGACCAAAACATAATAAAACGATAACATAAGTGACCAA
Found at i:75160 original size:48 final size:49
Alignment explanation
Indices: 75066--75167 Score: 179
Period size: 48 Copynumber: 2.1 Consensus size: 49
75056 TGTAGTCTAG
75066 GAAACAAAAGAATGGCTTAATCGGGTAAGTTATATTACCGGTTAGTATC
1 GAAACAAAAGAATGGCTTAATCGGGTAAGTTATATTACCGGTTAGTATC
* *
75115 GAAACAAAAGAATGGCTTAATC-GGTAAGTTATGTTATCGGTTAGTATC
1 GAAACAAAAGAATGGCTTAATCGGGTAAGTTATATTACCGGTTAGTATC
75163 GAAAC
1 GAAAC
75168 TGAGGACCGA
Statistics
Matches: 51, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
48 29 0.57
49 22 0.43
ACGTcount: A:0.37, C:0.12, G:0.23, T:0.28
Consensus pattern (49 bp):
GAAACAAAAGAATGGCTTAATCGGGTAAGTTATATTACCGGTTAGTATC
Found at i:78129 original size:242 final size:249
Alignment explanation
Indices: 77703--78343 Score: 747
Period size: 242 Copynumber: 2.6 Consensus size: 249
77693 GGCAACCATA
* * *
77703 TATATACCAAATCTTAAAAGTTTATGCTCTTAACCTA-TTGATGTTGT-GGGAACGCCAAGGCTC
1 TATATACCAAATCGTAAAAGTTTGTGCTCTTAACCTATTTGATTTTGTGGGGAACGCCAA-GCTC
* ** *
77766 CATCAGCTAAAACTTTCATAATACTTTTGCTGCAATCGTTTTTATTTTTTAAAATGATAATATTC
65 CATCAGCTAAAACTTTCATAATACTTTAGCTGCAATCACTTCTATTTTTTAAAATGATAATATTC
*
77831 CAGATTGCAACATGCTTTCTTTGGGGACCATGACATTCTGGACGCAATCTATTCTATTAATACAC
130 CAGATTGCAACATGCATTCTTTGGGGACCATGACATTCTGGACGCAATCTATTCTA-TAATACAC
77896 AAGTAGACATT-AGTCGCAACCTATTT-CTGTT-A-A-A-GCCGTGACACCGTATC
194 AAGTAGACATTAAGTCGCAACCTATTTCCTGTTAACATATGCCGTGACACCGTATC
*
77946 TATATACCAAATCGTAAAAGTTTGTGCTCTTAACCTATTTTATTTTGTGGGGAACGCCAA-CTCC
1 TATATACCAAATCGTAAAAGTTTGTGCTCTTAACCTATTTGATTTTGTGGGGAACGCCAAGCTCC
* *
78010 ATCAGCTAAAAC-TTCATAATACTTTAGAC-GCAGTCACTTCTATTTTTTTAAATGATAATATTC
66 ATCAGCTAAAACTTTCATAATACTTTAG-CTGCAATCACTTCTATTTTTTAAAATGATAATATTC
* * *
78073 CAGATTGCAACATGCATTCTTTGGGGGCCATGACATTCTGGGCGCAATCTATTCTATAATACAGA
130 CAGATTGCAACATGCATTCTTTGGGGACCATGACATTCTGGACGCAATCTATTCTATAATACACA
* * * * ** *
78138 AGTTGACATTACAAGTCGTAACTTATTTCCTTTTGAACCGTGATATTCTGGGGTGACACCTTATC
195 AGTAGACATT--AAGTCGCAACCTATTTCCTGTT-AA-C---ATA---TGCCGTGACACCGTATC
* * * *
78203 TATATACCAAATTGTAAAAGTTTGTGCTCTTAACCTATTTGATTGTCGTGGGGAACACCAATTCT
1 TATATACCAAATCGTAAAAGTTTGTGCTCTTAACCTATTTGATT-TTGTGGGGAACGCCAA-GCT
* * ** * *
78268 CCATCGGCTAAAACTTTCAT-A-A-TTTAGGTGCAATCGTTTTTACTTTTTAAAATGATAATATT
64 CCATCAGCTAAAACTTTCATAATACTTTAGCTGCAATCACTTCTATTTTTTAAAATGATAATATT
*
78330 -C-GATTACAACATGC
129 CCAGATTGCAACATGC
78344 CTTTGG
Statistics
Matches: 340, Mismatches: 34, Indels: 35
0.83 0.08 0.09
Matches are distributed among these distances:
241 17 0.05
242 96 0.28
243 52 0.15
244 21 0.06
245 15 0.04
247 1 0.00
252 1 0.00
253 1 0.00
256 12 0.04
257 56 0.16
258 46 0.14
259 1 0.00
260 16 0.05
261 5 0.01
ACGTcount: A:0.30, C:0.19, G:0.15, T:0.36
Consensus pattern (249 bp):
TATATACCAAATCGTAAAAGTTTGTGCTCTTAACCTATTTGATTTTGTGGGGAACGCCAAGCTCC
ATCAGCTAAAACTTTCATAATACTTTAGCTGCAATCACTTCTATTTTTTAAAATGATAATATTCC
AGATTGCAACATGCATTCTTTGGGGACCATGACATTCTGGACGCAATCTATTCTATAATACACAA
GTAGACATTAAGTCGCAACCTATTTCCTGTTAACATATGCCGTGACACCGTATC
Done.