Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002249.1 Hibiscus syriacus cultivar Beakdansim tig00004569_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: 68538
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Found at i:2460 original size:18 final size:19
Alignment explanation
Indices: 2405--2468 Score: 73
Period size: 17 Copynumber: 3.5 Consensus size: 19
2395 CGAAACCGGT
2405 TTTTTCGGTTCGGTTCGGG
1 TTTTTCGGTTCGGTTCGGG
* *
2424 TTTTT---TAACAGTTCGGG
1 TTTTTCGGT-TCGGTTCGGG
2441 TTTTTCGGTTCGGTTC-GG
1 TTTTTCGGTTCGGTTCGGG
2459 TTTTTCGGTT
1 TTTTTCGGTT
2469 TTTCAATGAA
Statistics
Matches: 37, Mismatches: 4, Indels: 9
0.74 0.08 0.18
Matches are distributed among these distances:
16 1 0.03
17 13 0.35
18 12 0.32
19 10 0.27
20 1 0.03
ACGTcount: A:0.05, C:0.14, G:0.30, T:0.52
Consensus pattern (19 bp):
TTTTTCGGTTCGGTTCGGG
Found at i:7955 original size:69 final size:69
Alignment explanation
Indices: 7837--8012 Score: 262
Period size: 69 Copynumber: 2.6 Consensus size: 69
7827 AACTTACACA
* * * * *
7837 AGATTGGATTTCAACTTCATAACGAAGGATATCCAACTCAAATCCAATTTGGTGAAGCAATAAAA
1 AGATTGGATTTCAACTTCACAACGAAGGATATCCAACTAAAAACCAATTTAGTAAAGCAATAAAA
7902 CTCG
66 CTCG
* *
7906 AGATTGGATTTCAACTTCACAACGAAGGATATCCAACTAAAAACTAATTTAGTAAAGCAATACAA
1 AGATTGGATTTCAACTTCACAACGAAGGATATCCAACTAAAAACCAATTTAGTAAAGCAATAAAA
7971 CTCG
66 CTCG
* * *
7975 AGATTGGATTTTAACTTCACAATGAAGTATATCCAACT
1 AGATTGGATTTCAACTTCACAACGAAGGATATCCAACT
8013 CAAAGCTCAA
Statistics
Matches: 97, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
69 97 1.00
ACGTcount: A:0.40, C:0.18, G:0.14, T:0.27
Consensus pattern (69 bp):
AGATTGGATTTCAACTTCACAACGAAGGATATCCAACTAAAAACCAATTTAGTAAAGCAATAAAA
CTCG
Found at i:8276 original size:5 final size:5
Alignment explanation
Indices: 8266--8459 Score: 290
Period size: 5 Copynumber: 38.4 Consensus size: 5
8256 ACAAAAACAG
8266 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
1 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
8316 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
1 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
8366 TATAT TATAT TATAT TAT-T T-TAT TATAT TATAT TATATT ATATAT TATTAT
1 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATA-T -TATAT TA-TAT
8417 TATTAT TATAT TATTAT TATTAT TATTAT TA-AT T-TA- TATAT TA
1 TA-TAT TATAT TA-TAT TA-TAT TA-TAT TATAT TATAT TATAT TA
8460 CAATTATTTT
Statistics
Matches: 180, Mismatches: 0, Indels: 18
0.91 0.00 0.09
Matches are distributed among these distances:
3 2 0.01
4 10 0.06
5 134 0.74
6 30 0.17
7 4 0.02
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (5 bp):
TATAT
Found at i:21536 original size:11 final size:11
Alignment explanation
Indices: 21512--21559 Score: 64
Period size: 10 Copynumber: 4.5 Consensus size: 11
21502 AATGAAAAAG
*
21512 AAAAAAAGAA-
1 AAAAAAGGAAC
21522 AAAAAAGGAAC
1 AAAAAAGGAAC
21533 AAAAAAGGAAC
1 AAAAAAGGAAC
*
21544 AAAAAA-GAAT
1 AAAAAAGGAAC
21554 AAAAAA
1 AAAAAA
21560 AAAAGAAAGA
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
10 18 0.51
11 17 0.49
ACGTcount: A:0.81, C:0.04, G:0.12, T:0.02
Consensus pattern (11 bp):
AAAAAAGGAAC
Found at i:21536 original size:21 final size:21
Alignment explanation
Indices: 21512--21560 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
21502 AATGAAAAAG
21512 AAAAAAAGAA-AAAAAAGGAAC
1 AAAAAAAGAACAAAAAA-GAAC
* *
21533 AAAAAAGGAACAAAAAAGAAT
1 AAAAAAAGAACAAAAAAGAAC
21554 AAAAAAA
1 AAAAAAA
21561 AAAGAAAGAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 18 0.75
22 6 0.25
ACGTcount: A:0.82, C:0.04, G:0.12, T:0.02
Consensus pattern (21 bp):
AAAAAAAGAACAAAAAAGAAC
Found at i:21560 original size:11 final size:10
Alignment explanation
Indices: 21512--21572 Score: 54
Period size: 10 Copynumber: 6.2 Consensus size: 10
21502 AATGAAAAAG
21512 AAAAAAAGAA
1 AAAAAAAGAA
*
21522 AAAAAAGGAA
1 AAAAAAAGAA
*
21532 CAAAAAAGGAA
1 -AAAAAAAGAA
*
21543 CAAAAAAG-A
1 AAAAAAAGAA
*
21552 ATAAAAA-AA
1 AAAAAAAGAA
*
21561 AAAGAAAGAA
1 AAAAAAAGAA
21571 AA
1 AA
21573 TGAGAGTTCA
Statistics
Matches: 41, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
9 12 0.29
10 19 0.46
11 10 0.24
ACGTcount: A:0.82, C:0.03, G:0.13, T:0.02
Consensus pattern (10 bp):
AAAAAAAGAA
Found at i:21572 original size:14 final size:13
Alignment explanation
Indices: 21498--21572 Score: 53
Period size: 14 Copynumber: 5.2 Consensus size: 13
21488 CCTGAAGATG
*
21498 AAAAAATGAAAAA
1 AAAAAAAGAAAAA
21511 GAAAAAAAGAAAAA
1 -AAAAAAAGAAAAA
21525 AAAGGAACAA-AAAAGGA
1 AAA--AA-AAGAAAA--A
21542 ACAAAAAAGAATAAA
1 A-AAAAAAGAA-AAA
*
21557 AAAAAAAGAAAGA
1 AAAAAAAGAAAAA
21570 AAA
1 AAA
21573 TGAGAGTTCA
Statistics
Matches: 51, Mismatches: 2, Indels: 17
0.73 0.03 0.24
Matches are distributed among these distances:
13 8 0.16
14 21 0.41
15 10 0.20
16 6 0.12
17 4 0.08
18 2 0.04
ACGTcount: A:0.81, C:0.03, G:0.13, T:0.03
Consensus pattern (13 bp):
AAAAAAAGAAAAA
Found at i:23054 original size:54 final size:54
Alignment explanation
Indices: 22859--23887 Score: 1154
Period size: 54 Copynumber: 19.5 Consensus size: 54
22849 TAGTGAAGCG
* * *
22859 GAAGAAGATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACTCGTTT
1 GAAGAAGATGTCCGAGTTCTATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTT
* * * *
22913 ---GAAGATGTCCAAGTTCCATACTCCCTAGAGAAAGAGGGAGTGAACCCGTGT
1 GAAGAAGATGTCCGAGTTCTATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTT
** * *
22964 GAAG-TTAT-T-AGAGTTCTATACTTCCT-GAAGAAAGAGGGAGCGAACCCGTTT
1 GAAGAAGATGTCCGAGTTCTATACTCCCTAG-AGAAAGAGGGAGCGAACCCGTTT
23015 GAAGAAGATGTCCGAGTTCTATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTT
1 GAAGAAGATGTCCGAGTTCTATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTT
* * *
23069 ---GAAGATGTCTGAGTTCCATACTCCCTAGAGAAAGAGGGAGCAAACCCG--T
1 GAAGAAGATGTCCGAGTTCTATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTT
* * * ** *
23118 G-CGAAGTTATTGGAGTTCTATACTTCCT-GAAGAAAGAGGGAGCGAACCCGTTT
1 GAAGAAGATGTCCGAGTTCTATACTCCCTAG-AGAAAGAGGGAGCGAACCCGTTT
* *
23171 GAAGAAGATGTCCGAGTTCTATACTTCCT-GAAGAAAGAGGGAGCAAACCCGTTT
1 GAAGAAGATGTCCGAGTTCTATACTCCCTAG-AGAAAGAGGGAGCGAACCCGTTT
* *
23225 GAAGAAGATGTTCGAGTTCCATACTCCCT-GAGGAAAGAGGGAGCGAACCCGTTT
1 GAAGAAGATGTCCGAGTTCTATACTCCCTAGA-GAAAGAGGGAGCGAACCCGTTT
*
23279 GAAGAAGATGTCCGAGTTCTATACTCCCTAGAGAAAGAGGGAGCGAACCCATTT
1 GAAGAAGATGTCCGAGTTCTATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTT
* *
23333 ---GAAGATGTCCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTGT
1 GAAGAAGATGTCCGAGTTCTATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTT
** * * *
23384 GAAG-TTAT-T-GGAGTTCTATACTTCCT-GAAGAAAGAGGGAGCAAACCCGTTT
1 GAAGAAGATGTCCGAGTTCTATACTCCCTAG-AGAAAGAGGGAGCGAACCCGTTT
*
23435 GAAGAAGATGTCTGAGTTCTATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTT
1 GAAGAAGATGTCCGAGTTCTATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTT
* *
23489 ---GAAGATGTCCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTGT
1 GAAGAAGATGTCCGAGTTCTATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTT
** * * *
23540 GAAG-TTAT-T-GGAGTTCTATACTTCCT-GAAGAAAGAGAGAGCGAACCCGTTT
1 GAAGAAGATGTCCGAGTTCTATACTCCCTAG-AGAAAGAGGGAGCGAACCCGTTT
* *
23591 GAAGAAGATGTCCGAGTTCTATACTTCCT-GAAGAAAGAGGGAGCGAACTCGTTT
1 GAAGAAGATGTCCGAGTTCTATACTCCCTAG-AGAAAGAGGGAGCGAACCCGTTT
* *
23645 GAAGAAGATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTT
1 GAAGAAGATGTCCGAGTTCTATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTT
* * * *
23699 GAAGAAGATGTCTGAATTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGATT
1 GAAGAAGATGTCCGAGTTCTATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTT
* * * **
23753 GAAAAAGATGTTCGAGTTCTATACTTCCT-GAAGAAAGAGGGAGCGAACCCGTAA
1 GAAGAAGATGTCCGAGTTCTATACTCCCTAG-AGAAAGAGGGAGCGAACCCGTTT
* * ** * * * **
23807 GAAGACGATTTTTTGAGTTCTATACTTCCT-GAAGAAAGAGGGAGAGAACTCGTAA
1 GAAGAAGA-TGTCCGAGTTCTATACTCCCTAG-AGAAAGAGGGAGCGAACCCGTTT
*
23862 GAAGAAGATGTTCGAG-TCTCATACTC
1 GAAGAAGATGTCCGAGTTCT-ATACTC
23888 TCTGAAAGAA
Statistics
Matches: 843, Mismatches: 97, Indels: 70
0.83 0.10 0.07
Matches are distributed among these distances:
49 1 0.00
50 4 0.00
51 342 0.41
52 9 0.01
53 16 0.02
54 417 0.49
55 54 0.06
ACGTcount: A:0.32, C:0.19, G:0.27, T:0.22
Consensus pattern (54 bp):
GAAGAAGATGTCCGAGTTCTATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTT
Found at i:23143 original size:156 final size:157
Alignment explanation
Indices: 22859--23804 Score: 1213
Period size: 156 Copynumber: 6.0 Consensus size: 157
22849 TAGTGAAGCG
* * ***
22859 GAAGAAGATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACTCGTTTGAAGATGTCCA
1 GAAGAAGATGTCCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTGAAGATGTTGG
* * * * *
22924 AGTTCCATACTCCCTAGAGAAAGAGGGAGTGAACCCG-TG-TGAAGTTATTAGAGTTCTATACTT
66 AGTTCCATACTCCCT-GAGAAAGAGGGAGCGAACCCGTTGAAGAAGATGTTCGAGTTCTATACTT
22987 CCTGAAGAAAGAGGGAGCGAACCCGTTT
130 CCTGAAGAAAGAGGGAGCGAACCCGTTT
*
23015 GAAGAAGATGTCCGAGTTCTATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTGAAGATGTCT-
1 GAAGAAGATGTCCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTGAAGATGT-TG
* * * * *
23079 GAGTTCCATACTCCCTAGAGAAAGAGGGAGCAAACCCG-TG-CGAAGTTATTGGAGTTCTATACT
65 GAGTTCCATACTCCCT-GAGAAAGAGGGAGCGAACCCGTTGAAGAAGATGTTCGAGTTCTATACT
23142 TCCTGAAGAAAGAGGGAGCGAACCCGTTT
129 TCCTGAAGAAAGAGGGAGCGAACCCGTTT
* * *
23171 GAAGAAGATGTCCGAGTTCTATACTTCCT-GAAGAAAGAGGGAGCAAACCCGTTTGAAGAAGATG
1 GAAGAAGATGTCCGAGTTCCATACTCCCTAG-AGAAAGAGGGAGCGAACCCGTTT---GAAGATG
* *
23235 TTCGAGTTCCATACTCCCTGAGGAAAGAGGGAGCGAACCCGTTTGAAGAAGATGTCCGAGTTCTA
62 TTGGAGTTCCATACTCCCTGA-GAAAGAGGGAGCGAACCCG-TTGAAGAAGATGTTCGAGTTCTA
* *
23300 TACTCCCT-AGAGAAAGAGGGAGCGAACCCATTT
125 TACTTCCTGA-AGAAAGAGGGAGCGAACCCGTTT
* * *
23333 ---GAAGATGTCCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTGTGAAGTTATTGG
1 GAAGAAGATGTCCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTGAAGATGTTGG
* * *
23395 AGTTCTATACTTCCTGAAGAAAGAGGGAGCAAACCCGTTTGAAGAAGATG-TCTGAGTTCTATAC
66 AGTTCCATACTCCCTG-AGAAAGAGGGAGCGAACCCG-TTGAAGAAGATGTTC-GAGTTCTATAC
*
23459 TCCCT-AGAGAAAGAGGGAGCGAACCCGTTT
128 TTCCTGA-AGAAAGAGGGAGCGAACCCGTTT
* * *
23489 ---GAAGATGTCCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTGTGAAGTTATTGG
1 GAAGAAGATGTCCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTGAAGATGTTGG
* * * *
23551 AGTTCTATACTTCCTGAAGAAAGAGAGAGCGAACCCGTTTGAAGAAGATGTCCGAGTTCTATACT
66 AGTTCCATACTCCCTG-AGAAAGAGGGAGCGAACCCG-TTGAAGAAGATGTTCGAGTTCTATACT
*
23616 TCCTGAAGAAAGAGGGAGCGAACTCGTTT
129 TCCTGAAGAAAGAGGGAGCGAACCCGTTT
*
23645 GAAGAAGATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTGAAGAAGATGT
1 GAAGAAGATGTCCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTT---GAAGATGT
* *
23710 CT-GAATTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGATTGAAAAAGATGTTCGAGTTCTA
63 -TGGAGTTCCATACTCCCT-GAGAAAGAGGGAGCGAACCCG-TTGAAGAAGATGTTCGAGTTCTA
23774 TACTTCCTGAAGAAAGAGGGAGCGAACCCGT
125 TACTTCCTGAAGAAAGAGGGAGCGAACCCGT
23805 AAGAAGACGA
Statistics
Matches: 718, Mismatches: 48, Indels: 42
0.89 0.06 0.05
Matches are distributed among these distances:
155 2 0.00
156 436 0.61
157 3 0.00
158 3 0.00
159 136 0.19
160 1 0.00
161 3 0.00
162 132 0.18
163 2 0.00
ACGTcount: A:0.32, C:0.19, G:0.27, T:0.22
Consensus pattern (157 bp):
GAAGAAGATGTCCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTGAAGATGTTGG
AGTTCCATACTCCCTGAGAAAGAGGGAGCGAACCCGTTGAAGAAGATGTTCGAGTTCTATACTTC
CTGAAGAAAGAGGGAGCGAACCCGTTT
Found at i:23646 original size:420 final size:420
Alignment explanation
Indices: 22859--23887 Score: 1663
Period size: 420 Copynumber: 2.4 Consensus size: 420
22849 TAGTGAAGCG
* * * *
22859 GAAGAAGATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACTCGTTTGAAGATGTCCA
1 GAAGAAGATGTCCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCATTTGAAGATGTCCG
*
22924 AGTTCCATACTCCCTAGAGAAAGAGGGAGTGAACCCGTGTGAAGTTATTAGAGTTCTATACTTCC
66 AGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTGTGAAGTTATTAGAGTTCTATACTTCC
*
22989 TGAAGAAAGAGGGAGCGAACCCGTTTGAAGAAGATGTCCGAGTTCTATACTCCCTAGAGAAAGAG
131 TGAAGAAAGAGGGAGCAAACCCGTTTGAAGAAGATGTCCGAGTTCTATACTCCCTAGAGAAAGAG
*
23054 GGAGCGAACCCGTTTGAAGATGTCTGAGTTCCATACTCCCTAGAGAAAGAGGGAGCAAACCCGTG
196 GGAGCGAACCCGTTTGAAGATGTCCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCAAACCCGTG
*
23119 CGAAGTTATTGGAGTTCTATACTTCCTGAAGAAAGAGGGAGCGAACCCGTTTGAAGAAGATGTCC
261 CGAAGTTATTGGAGTTCTATACTTCCTGAAGAAAGAGAGAGCGAACCCGTTTGAAGAAGATGTCC
23184 GAGTTCTATACTTCCTGAAGAAAGAGGGAGCAAACCCGTTTGAAGAAGATGTTCGAGTTCCATAC
326 GAGTTCTATACTTCCTGAAGAAAGAGGGAGCAAACCCGTTTGAAGAAGATGTTCGAGTTCCATAC
23249 TCCCT-GAGGAAAGAGGGAGCGAACCCGTTT
391 TCCCTAGA-GAAAGAGGGAGCGAACCCGTTT
*
23279 GAAGAAGATGTCCGAGTTCTATACTCCCTAGAGAAAGAGGGAGCGAACCCATTTGAAGATGTCCG
1 GAAGAAGATGTCCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCATTTGAAGATGTCCG
*
23344 AGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTGTGAAGTTATTGGAGTTCTATACTTCC
66 AGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTGTGAAGTTATTAGAGTTCTATACTTCC
*
23409 TGAAGAAAGAGGGAGCAAACCCGTTTGAAGAAGATGTCTGAGTTCTATACTCCCTAGAGAAAGAG
131 TGAAGAAAGAGGGAGCAAACCCGTTTGAAGAAGATGTCCGAGTTCTATACTCCCTAGAGAAAGAG
*
23474 GGAGCGAACCCGTTTGAAGATGTCCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTG
196 GGAGCGAACCCGTTTGAAGATGTCCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCAAACCCGTG
*
23539 TGAAGTTATTGGAGTTCTATACTTCCTGAAGAAAGAGAGAGCGAACCCGTTTGAAGAAGATGTCC
261 CGAAGTTATTGGAGTTCTATACTTCCTGAAGAAAGAGAGAGCGAACCCGTTTGAAGAAGATGTCC
* *
23604 GAGTTCTATACTTCCTGAAGAAAGAGGGAGCGAACTCGTTTGAAGAAGATGTTCGAGTTCCATAC
326 GAGTTCTATACTTCCTGAAGAAAGAGGGAGCAAACCCGTTTGAAGAAGATGTTCGAGTTCCATAC
23669 TCCCTAGAGAAAGAGGGAGCGAACCCGTTT
391 TCCCTAGAGAAAGAGGGAGCGAACCCGTTT
* *
23699 GAAGAAGATGTCTGAATTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGA-TTGAAAAAGATG
1 GAAGAAGATGTCCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCC-ATTTG---AAGATG
* * * * * * *
23763 TTCGAGTTCTATACTTCCT-GAAGAAAGAGGGAGCGAACCCGTAAGAAGACGATTTTTTGAGTTC
62 TCCGAGTTCCATACTCCCTAG-AGAAAGAGGGAGCGAACCCGT--G-TGAAG-TTATTAGAGTTC
* ** *
23827 TATACTTCCTGAAGAAAGAGGGAG-AGAACTCGTAAGAAGAAGATGTTCGAG-TCTCATACTC
122 TATACTTCCTGAAGAAAGAGGGAGCA-AACCCGTTTGAAGAAGATGTCCGAGTTCT-ATACTC
23888 TCTGAAAGAA
Statistics
Matches: 567, Mismatches: 30, Indels: 17
0.92 0.05 0.03
Matches are distributed among these distances:
420 452 0.80
421 3 0.01
422 1 0.00
423 43 0.08
425 1 0.00
426 7 0.01
427 60 0.11
ACGTcount: A:0.32, C:0.19, G:0.27, T:0.22
Consensus pattern (420 bp):
GAAGAAGATGTCCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCATTTGAAGATGTCCG
AGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTGTGAAGTTATTAGAGTTCTATACTTCC
TGAAGAAAGAGGGAGCAAACCCGTTTGAAGAAGATGTCCGAGTTCTATACTCCCTAGAGAAAGAG
GGAGCGAACCCGTTTGAAGATGTCCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCAAACCCGTG
CGAAGTTATTGGAGTTCTATACTTCCTGAAGAAAGAGAGAGCGAACCCGTTTGAAGAAGATGTCC
GAGTTCTATACTTCCTGAAGAAAGAGGGAGCAAACCCGTTTGAAGAAGATGTTCGAGTTCCATAC
TCCCTAGAGAAAGAGGGAGCGAACCCGTTT
Found at i:23897 original size:55 final size:54
Alignment explanation
Indices: 22859--24223 Score: 838
Period size: 54 Copynumber: 25.6 Consensus size: 54
22849 TAGTGAAGCG
* * *
22859 GAAGAAGATGTTCGAGTTCCATACTCCCT-AGAGAAAGAGGGAGCGAACTCGTTT
1 GAAGAAGATGTTCGAGTT-CATACTCTCTGAAAGAAAGAGGGAGCGAACCCGTTT
* * * * *
22913 ---GAAGATGTCCAAGTTCCATACTCCCT-AGAGAAAGAGGGAGTGAACCCG--T
1 GAAGAAGATGTTCGAGTT-CATACTCTCTGAAAGAAAGAGGGAGCGAACCCGTTT
* * * *
22962 G-TGAAGTTATTAGAGTTCTATACT-TCCTG-AAGAAAGAGGGAGCGAACCCGTTT
1 GAAGAAGATGTTCGAGTTC-ATACTCT-CTGAAAGAAAGAGGGAGCGAACCCGTTT
* * *
23015 GAAGAAGATGTCCGAGTTCTATACTCCCT-AGAGAAAGAGGGAGCGAACCCGTTT
1 GAAGAAGATGTTCGAGTTC-ATACTCTCTGAAAGAAAGAGGGAGCGAACCCGTTT
* * *
23069 ---GAAGATG-TCTGAGTTCCATACTCCCT-AGAGAAAGAGGGAGCAAACCCG--T
1 GAAGAAGATGTTC-GAGTT-CATACTCTCTGAAAGAAAGAGGGAGCGAACCCGTTT
* * * *
23118 G-CGAAGTTATTGGAGTTCTATACT-TCCTG-AAGAAAGAGGGAGCGAACCCGTTT
1 GAAGAAGATGTTCGAGTTC-ATACTCT-CTGAAAGAAAGAGGGAGCGAACCCGTTT
* *
23171 GAAGAAGATGTCCGAGTTCTATACT-TCCTG-AAGAAAGAGGGAGCAAACCCGTTT
1 GAAGAAGATGTTCGAGTTC-ATACTCT-CTGAAAGAAAGAGGGAGCGAACCCGTTT
* *
23225 GAAGAAGATGTTCGAGTTCCATACTCCCTG-AGGAAAGAGGGAGCGAACCCGTTT
1 GAAGAAGATGTTCGAGTT-CATACTCTCTGAAAGAAAGAGGGAGCGAACCCGTTT
* * * *
23279 GAAGAAGATGTCCGAGTTCTATACTCCCT-AGAGAAAGAGGGAGCGAACCCATTT
1 GAAGAAGATGTTCGAGTTC-ATACTCTCTGAAAGAAAGAGGGAGCGAACCCGTTT
* * *
23333 ---GAAGATGTCCGAGTTCCATACTCCCT-AGAGAAAGAGGGAGCGAACCCG--T
1 GAAGAAGATGTTCGAGTT-CATACTCTCTGAAAGAAAGAGGGAGCGAACCCGTTT
* * * * *
23382 G-TGAAGTTATTGGAGTTCTATACT-TCCTG-AAGAAAGAGGGAGCAAACCCGTTT
1 GAAGAAGATGTTCGAGTTC-ATACTCT-CTGAAAGAAAGAGGGAGCGAACCCGTTT
* *
23435 GAAGAAGATG-TCTGAGTTCTATACTCCCT-AGAGAAAGAGGGAGCGAACCCGTTT
1 GAAGAAGATGTTC-GAGTTC-ATACTCTCTGAAAGAAAGAGGGAGCGAACCCGTTT
* * *
23489 ---GAAGATGTCCGAGTTCCATACTCCCT-AGAGAAAGAGGGAGCGAACCCG--T
1 GAAGAAGATGTTCGAGTT-CATACTCTCTGAAAGAAAGAGGGAGCGAACCCGTTT
* * * * *
23538 G-TGAAGTTATTGGAGTTCTATACT-TCCTG-AAGAAAGAGAGAGCGAACCCGTTT
1 GAAGAAGATGTTCGAGTTC-ATACTCT-CTGAAAGAAAGAGGGAGCGAACCCGTTT
* *
23591 GAAGAAGATGTCCGAGTTCTATACT-TCCTG-AAGAAAGAGGGAGCGAACTCGTTT
1 GAAGAAGATGTTCGAGTTC-ATACTCT-CTGAAAGAAAGAGGGAGCGAACCCGTTT
* *
23645 GAAGAAGATGTTCGAGTTCCATACTCCCT-AGAGAAAGAGGGAGCGAACCCGTTT
1 GAAGAAGATGTTCGAGTT-CATACTCTCTGAAAGAAAGAGGGAGCGAACCCGTTT
* * * *
23699 GAAGAAGATG-TCTGAATTCCATACTCCCT-AGAGAAAGAGGGAGCGAACCCGATT
1 GAAGAAGATGTTC-GAGTT-CATACTCTCTGAAAGAAAGAGGGAGCGAACCCGTTT
* **
23753 GAAAAAGATGTTCGAGTTCTATACT-TCCTG-AAGAAAGAGGGAGCGAACCCGTAA
1 GAAGAAGATGTTCGAGTTC-ATACTCT-CTGAAAGAAAGAGGGAGCGAACCCGTTT
* * * * * **
23807 GAAGACGATTTTTTGAGTTCTATACT-TCCTG-AAGAAAGAGGGAGAGAACTCGTAA
1 GAAGAAGA-TGTTCGAGTTC-ATACTCT-CTGAAAGAAAGAGGGAGCGAACCCGTTT
* * * *
23862 GAAGAAGATGTTCGAGTCTCATACTCTCTGAAAG-AATAGGGAAC-AGACACGATT
1 GAAGAAGATGTTCGAGT-TCATACTCTCTGAAAGAAAGAGGGAGCGA-ACCCGTTT
* * * ***
23916 -ATTGAAGATTGTTCGAGTCTCATACTCTCT-AAAGAAATAGGGAACAGACACAATTATT
1 GA-AGAAGA-TGTTCGAGT-TCATACTCTCTGAAAGAAAGAGGGAGC-GA-ACCCGT-TT
* * * * * *
23974 GAAG-A-TTGTTCGAGTCTCATACTCTCTGAAAG-AATAGGGAACAAACACGATT
1 GAAGAAGATGTTCGAGT-TCATACTCTCTGAAAGAAAGAGGGAGCGAACCCGTTT
* * * * ***
24026 -ATTGAAGATTGTTCGAGTCTCATACTCTCTG-AAGGAATAGGGAACAGACACAATTATT
1 GA-AGAAGA-TGTTCGAGT-TCATACTCTCTGAAAGAAAGAGGGAGC-GA-ACCCGT-TT
* * * *
24084 GAAG-A-TTGTTCGAGTCTCATACTCTCTGAAAG-AATAGGGAGCAAACAC-TATT
1 GAAGAAGATGTTCGAGT-TCATACTCTCTGAAAGAAAGAGGGAGCGAACCCGT-TT
* * * * *
24136 -ATTGAAGATTGTTCGAGTCTTATACTCTCT-AAAGAAATAGGGAGC-AGACACGATT
1 GA-AGAAGA-TGTTCGAGT-TCATACTCTCTGAAAGAAAGAGGGAGCGA-ACCCGTTT
* *
24191 -ATTGAAGATTGTTCGAGTCTCGTACTCTCTGAA
1 GA-AGAAGA-TGTTCGAGT-TCATACTCTCTGAA
24224 TGAATAGGGA
Statistics
Matches: 1097, Mismatches: 128, Indels: 170
0.79 0.09 0.12
Matches are distributed among these distances:
49 4 0.00
50 5 0.00
51 322 0.29
52 13 0.01
53 23 0.02
54 455 0.41
55 248 0.23
56 10 0.01
57 9 0.01
58 6 0.01
59 2 0.00
ACGTcount: A:0.33, C:0.18, G:0.25, T:0.24
Consensus pattern (54 bp):
GAAGAAGATGTTCGAGTTCATACTCTCTGAAAGAAAGAGGGAGCGAACCCGTTT
Found at i:24234 original size:55 final size:55
Alignment explanation
Indices: 23865--24233 Score: 600
Period size: 55 Copynumber: 6.7 Consensus size: 55
23855 CTCGTAAGAA
23865 GAAGA-TGTTCGAGTCTCATACTCTCTGAAAGAATAGGGAACAGACACGATTATT
1 GAAGATTGTTCGAGTCTCATACTCTCTGAAAGAATAGGGAACAGACACGATTATT
*
23919 GAAGATTGTTCGAGTCTCATACTCTCT-AAAGAAATAGGGAACAGACACAATTATT
1 GAAGATTGTTCGAGTCTCATACTCTCTGAAAG-AATAGGGAACAGACACGATTATT
*
23974 GAAGATTGTTCGAGTCTCATACTCTCTGAAAGAATAGGGAACAAACACGATTATT
1 GAAGATTGTTCGAGTCTCATACTCTCTGAAAGAATAGGGAACAGACACGATTATT
* *
24029 GAAGATTGTTCGAGTCTCATACTCTCTGAAGGAATAGGGAACAGACACAATTATT
1 GAAGATTGTTCGAGTCTCATACTCTCTGAAAGAATAGGGAACAGACACGATTATT
* * *
24084 GAAGATTGTTCGAGTCTCATACTCTCTGAAAGAATAGGGAGCAAACACTATTATT
1 GAAGATTGTTCGAGTCTCATACTCTCTGAAAGAATAGGGAACAGACACGATTATT
* *
24139 GAAGATTGTTCGAGTCTTATACTCTCT-AAAGAAATAGGGAGCAGACACGATTATT
1 GAAGATTGTTCGAGTCTCATACTCTCTGAAAG-AATAGGGAACAGACACGATTATT
* *
24194 GAAGATTGTTCGAGTCTCGTACTCTCTGAATGAATAGGGA
1 GAAGATTGTTCGAGTCTCATACTCTCTGAAAGAATAGGGA
24234 GTGAACATGT
Statistics
Matches: 294, Mismatches: 16, Indels: 9
0.92 0.05 0.03
Matches are distributed among these distances:
54 13 0.04
55 274 0.93
56 7 0.02
ACGTcount: A:0.35, C:0.16, G:0.21, T:0.28
Consensus pattern (55 bp):
GAAGATTGTTCGAGTCTCATACTCTCTGAAAGAATAGGGAACAGACACGATTATT
Found at i:29584 original size:27 final size:29
Alignment explanation
Indices: 29539--29592 Score: 76
Period size: 27 Copynumber: 1.9 Consensus size: 29
29529 TCTATTTACC
* *
29539 TTAAAATAAAATGACAAGAATCAAAATAT
1 TTAAAATAAAAAGACAAGAATAAAAATAT
29568 TTAAAA-AAAAAGA-AAGAATAAAAAT
1 TTAAAATAAAAAGACAAGAATAAAAAT
29593 CAAATTAACT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 11 0.48
28 6 0.26
29 6 0.26
ACGTcount: A:0.69, C:0.04, G:0.07, T:0.20
Consensus pattern (29 bp):
TTAAAATAAAAAGACAAGAATAAAAATAT
Found at i:33174 original size:74 final size:76
Alignment explanation
Indices: 33072--33270 Score: 260
Period size: 75 Copynumber: 2.6 Consensus size: 76
33062 GACCGTTGAA
* * *
33072 CAGGGGGGAATCGGTACCCCCT-TGGGGGG-ATCGGTTCCCTCCGAGCATACTGGAATTCTCGGA
1 CAGGGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATACTGGAAATCTCGGA
**
33135 ACAAAAATGTT
66 ACAAAAACATT
* * *
33146 TAGGGGGGAATTGGTTCCTCCTAT-GGGGGAATCGGTTCCCTCCGAGCATTCTGGAAATCTCGGA
1 CAGGGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATACTGGAAATCTCGGA
* * *
33210 GCCAAACCATT
66 ACAAAAACATT
*
33221 CAGGGGGGAATCGGTTCCTCCTATGGGGGGGAATCGGTTCCCTCTGAGCA
1 CAGGGGGGAATCGGTTCCTCCTAT-GGGGGGAATCGGTTCCCTCCGAGCA
33271 ATCTGTAATT
Statistics
Matches: 107, Mismatches: 14, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
74 23 0.21
75 61 0.57
77 23 0.21
ACGTcount: A:0.21, C:0.24, G:0.32, T:0.23
Consensus pattern (76 bp):
CAGGGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATACTGGAAATCTCGGA
ACAAAAACATT
Found at i:33906 original size:17 final size:17
Alignment explanation
Indices: 33884--33927 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
33874 TTCATAAATC
33884 CAAAATCCAACAATCCA
1 CAAAATCCAACAATCCA
*
33901 CAAAATCAAACAATCCA
1 CAAAATCCAACAATCCA
33918 -AAATATCCAA
1 CAAA-ATCCAA
33928 AATGTTGAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 3 0.12
17 21 0.88
ACGTcount: A:0.57, C:0.30, G:0.00, T:0.14
Consensus pattern (17 bp):
CAAAATCCAACAATCCA
Found at i:33919 original size:9 final size:8
Alignment explanation
Indices: 33879--33929 Score: 52
Period size: 9 Copynumber: 6.2 Consensus size: 8
33869 CACCATTCAT
33879 AAATCC-A
1 AAATCCAA
33886 AAATCCAA
1 AAATCCAA
*
33894 CAATCCACA
1 AAATCCA-A
33903 AAAT-CAA
1 AAATCCAA
33910 ACAATCCAA
1 A-AATCCAA
33919 AATATCCAA
1 AA-ATCCAA
33928 AA
1 AA
33930 TGTTGAAACA
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
7 8 0.22
8 13 0.35
9 16 0.43
ACGTcount: A:0.59, C:0.27, G:0.00, T:0.14
Consensus pattern (8 bp):
AAATCCAA
Found at i:35886 original size:21 final size:21
Alignment explanation
Indices: 35860--35899 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
35850 CAGAACCCCA
*
35860 GGGGGGTATCGATTCCCCTGT
1 GGGGGGAATCGATTCCCCTGT
*
35881 GGGGGGAATCGGTTCCCCT
1 GGGGGGAATCGATTCCCCT
35900 TCAAAGGGGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.10, C:0.25, G:0.40, T:0.25
Consensus pattern (21 bp):
GGGGGGAATCGATTCCCCTGT
Found at i:35928 original size:20 final size:21
Alignment explanation
Indices: 35882--35942 Score: 79
Period size: 20 Copynumber: 2.9 Consensus size: 21
35872 TTCCCCTGTG
35882 GGGGGAATCGGTTCCCCTTCAAA
1 GGGGGAATCGGTT-CCC-TCAAA
35905 GGGGGAATCGGTTCCCTC-AA
1 GGGGGAATCGGTTCCCTCAAA
* *
35925 GGGGGGATCGATTCCCTC
1 GGGGGAATCGGTTCCCTC
35943 TGCACCAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
20 18 0.50
21 2 0.06
22 3 0.08
23 13 0.36
ACGTcount: A:0.18, C:0.26, G:0.34, T:0.21
Consensus pattern (21 bp):
GGGGGAATCGGTTCCCTCAAA
Found at i:41807 original size:96 final size:98
Alignment explanation
Indices: 41699--41939 Score: 317
Period size: 96 Copynumber: 2.5 Consensus size: 98
41689 CCGTTGAACA
* * *
41699 GGGGGGAATCGGTACCCCCT-TGGGGGGGATCGGTTCCCTCCGAGCATACTGGAATTCTCGGAAC
1 GGGGGGAATCGGTTCCTCCTATGGGGGGGATCGGTTCCCTCCGAGCATACTGGAAATCTCGGAAC
** * * *
41763 AAAAATGTTTAGTGGGGAATCGGTTCCTCCTAT
66 AAAAACATTCAGGGGGGAATCAGTTCCTCCTAT
* * *
41796 -GGGGGAATCGGTTCCTCCTAT-GGGGGAATCGGTTCCCTCCGAGCATTCTGGAAATCTCGGAGC
1 GGGGGGAATCGGTTCCTCCTATGGGGGGGATCGGTTCCCTCCGAGCATACTGGAAATCTCGGAAC
* *
41859 CAAACCATTCAGGGGGGAATCAGTTCCTCCTAT
66 AAAAACATTCAGGGGGGAATCAGTTCCTCCTAT
* *
41892 GGGGGGAATCGGTTCCTCCTATGGGGGGGAATCAGTTCCCTCTGAGCA
1 GGGGGGAATCGGTTCCTCCTATGGGGGGG-ATCGGTTCCCTCCGAGCA
41940 ATCTGTAATT
Statistics
Matches: 124, Mismatches: 16, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
96 81 0.65
97 22 0.18
98 5 0.04
99 16 0.13
ACGTcount: A:0.20, C:0.24, G:0.32, T:0.24
Consensus pattern (98 bp):
GGGGGGAATCGGTTCCTCCTATGGGGGGGATCGGTTCCCTCCGAGCATACTGGAAATCTCGGAAC
AAAAACATTCAGGGGGGAATCAGTTCCTCCTAT
Found at i:41835 original size:22 final size:21
Alignment explanation
Indices: 41776--41831 Score: 112
Period size: 21 Copynumber: 2.7 Consensus size: 21
41766 AATGTTTAGT
41776 GGGGAATCGGTTCCTCCTATG
1 GGGGAATCGGTTCCTCCTATG
41797 GGGGAATCGGTTCCTCCTATG
1 GGGGAATCGGTTCCTCCTATG
41818 GGGGAATCGGTTCC
1 GGGGAATCGGTTCC
41832 CTCCGAGCAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.14, C:0.23, G:0.36, T:0.27
Consensus pattern (21 bp):
GGGGAATCGGTTCCTCCTATG
Found at i:41898 original size:22 final size:23
Alignment explanation
Indices: 41870--41930 Score: 106
Period size: 22 Copynumber: 2.7 Consensus size: 23
41860 AAACCATTCA
41870 GGGGGGAATCAGTTCCTCCTAT-
1 GGGGGGAATCAGTTCCTCCTATG
*
41892 GGGGGGAATCGGTTCCTCCTATG
1 GGGGGGAATCAGTTCCTCCTATG
41915 GGGGGGAATCAGTTCC
1 GGGGGGAATCAGTTCC
41931 CTCTGAGCAA
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
22 21 0.58
23 15 0.42
ACGTcount: A:0.16, C:0.21, G:0.38, T:0.25
Consensus pattern (23 bp):
GGGGGGAATCAGTTCCTCCTATG
Found at i:43079 original size:3 final size:3
Alignment explanation
Indices: 43064--43122 Score: 109
Period size: 3 Copynumber: 19.7 Consensus size: 3
43054 TTGAGCATGC
*
43064 AAT AAT AAC AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
43112 AAT AAT AAT AA
1 AAT AAT AAT AA
43123 AAAAAAAGCA
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 54 1.00
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:45384 original size:25 final size:26
Alignment explanation
Indices: 45351--45415 Score: 71
Period size: 25 Copynumber: 2.5 Consensus size: 26
45341 GCTTTCACAA
45351 AAAATTATTTTAGATATCTA-AATAAAT
1 AAAA-TATTTTA-ATATCTACAATAAAT
* *
45378 -AAATATTTTAAGTATCTACTATAACT
1 AAAATATTTTAA-TATCTACAATAAAT
45404 AAAATATTTTAA
1 AAAATATTTTAA
45416 ATATAAAAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
24 1 0.03
25 13 0.39
26 8 0.24
27 11 0.33
ACGTcount: A:0.49, C:0.06, G:0.03, T:0.42
Consensus pattern (26 bp):
AAAATATTTTAATATCTACAATAAAT
Found at i:47018 original size:2 final size:2
Alignment explanation
Indices: 47011--47063 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
47001 AGTAATATTA
47011 AT AT AT AT AT AT AT AT AT AT AT AT AT AT 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 AT AT AT AT
47053 AT AT AT AT AT A
1 AT AT AT AT AT A
47064 CACTCTTTTT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:48760 original size:16 final size:16
Alignment explanation
Indices: 48735--48802 Score: 68
Period size: 16 Copynumber: 4.3 Consensus size: 16
48725 GATGAAGACT
48735 CAAATCGAAAATAATC
1 CAAATCGAAAATAATC
* *
48751 TAAATTGAAAATAATC
1 CAAATCGAAAATAATC
*
48767 CAAATCGAAAGTAA-C
1 CAAATCGAAAATAATC
* *
48782 TCAAACCG-AAAGAATC
1 -CAAATCGAAAATAATC
48798 CAAAT
1 CAAAT
48803 TTTATTTATC
Statistics
Matches: 41, Mismatches: 9, Indels: 5
0.75 0.16 0.09
Matches are distributed among these distances:
15 9 0.22
16 32 0.78
ACGTcount: A:0.54, C:0.18, G:0.09, T:0.19
Consensus pattern (16 bp):
CAAATCGAAAATAATC
Found at i:53958 original size:22 final size:21
Alignment explanation
Indices: 53930--53975 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
53920 CCAGAAATGT
*
53930 TAAAAAATATTAATGTTTCAGG
1 TAAAAAA-AATAATGTTTCAGG
*
53952 TAAAAAAAATAATGTTTTAGG
1 TAAAAAAAATAATGTTTCAGG
53973 TAA
1 TAA
53976 TTTTTTTACT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 15 0.68
22 7 0.32
ACGTcount: A:0.50, C:0.02, G:0.13, T:0.35
Consensus pattern (21 bp):
TAAAAAAAATAATGTTTCAGG
Found at i:64418 original size:21 final size:20
Alignment explanation
Indices: 64386--64424 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
64376 AACTGCCCAA
64386 TATAGAGGGTATCGGTACTCC
1 TATAGAGGGTATC-GTACTCC
64407 TATAG-GGAGTATCGTACT
1 TATAGAGG-GTATCGTACT
64425 ACCTTTGTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.26, C:0.15, G:0.28, T:0.31
Consensus pattern (20 bp):
TATAGAGGGTATCGTACTCC
Found at i:66331 original size:2 final size:2
Alignment explanation
Indices: 66314--66351 Score: 58
Period size: 2 Copynumber: 18.0 Consensus size: 2
66304 TCTAAACTTG
66314 AT AT GAT AT GAT AT AT AT AT AT AT 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 AT
66352 TCAACAACAA
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
2 30 0.88
3 4 0.12
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.47
Consensus pattern (2 bp):
AT
Done.