Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006643.1 Hibiscus syriacus cultivar Beakdansim tig00016358_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: 94563
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Found at i:10305 original size:20 final size:20
Alignment explanation
Indices: 10282--10319 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
10272 ATAAATGAAT
10282 GAACATAAACGAACGAACAC
1 GAACATAAACGAACGAACAC
* *
10302 GAACGTAAATGAACGAAC
1 GAACATAAACGAACGAAC
10320 GAGACCTATG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.53, C:0.21, G:0.18, T:0.08
Consensus pattern (20 bp):
GAACATAAACGAACGAACAC
Found at i:16522 original size:18 final size:18
Alignment explanation
Indices: 16490--16525 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
16480 ACTCGAAGCC
**
16490 TGAGCCTTTTGAATGGCT
1 TGAGCCTTTCCAATGGCT
16508 TGAGCCTTTCCAATGGCT
1 TGAGCCTTTCCAATGGCT
16526 AGAGTGATCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.17, C:0.22, G:0.25, T:0.36
Consensus pattern (18 bp):
TGAGCCTTTCCAATGGCT
Found at i:17881 original size:55 final size:55
Alignment explanation
Indices: 17797--17939 Score: 193
Period size: 55 Copynumber: 2.6 Consensus size: 55
17787 ATTGTATGAG
*
17797 TGTGTATCGGTACGCTGAGGAGTGTATCGATATC-CTCAAAACATCGAATGT-C-ATT
1 TGTGTATCGGTACACTGAGGAGTGTATCGATA-CACTCAAAACATCG-A-GTACTATT
* *
17852 TGTGTATTGGTACACTGAGGAGTGTATCGATACATTCAAAACATCGAGTACTATT
1 TGTGTATCGGTACACTGAGGAGTGTATCGATACACTCAAAACATCGAGTACTATT
* *
17907 TGTGTATCGGTACACTGGGGAGTGTATTGATAC
1 TGTGTATCGGTACACTGAGGAGTGTATCGATAC
17940 TCCCAAGTAG
Statistics
Matches: 79, Mismatches: 6, Indels: 6
0.87 0.07 0.07
Matches are distributed among these distances:
53 2 0.03
54 3 0.04
55 74 0.94
ACGTcount: A:0.27, C:0.15, G:0.25, T:0.32
Consensus pattern (55 bp):
TGTGTATCGGTACACTGAGGAGTGTATCGATACACTCAAAACATCGAGTACTATT
Found at i:18444 original size:15 final size:16
Alignment explanation
Indices: 18418--18448 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
18408 TTGCTTGTAT
18418 TACATGTTATGTGATA
1 TACATGTTATGTGATA
18434 TACAT-TTATGTGATA
1 TACATGTTATGTGATA
18449 ATGGTCTATG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.67
16 5 0.33
ACGTcount: A:0.32, C:0.06, G:0.16, T:0.45
Consensus pattern (16 bp):
TACATGTTATGTGATA
Found at i:19127 original size:2 final size:2
Alignment explanation
Indices: 19120--19145 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
19110 CAGCTTAAGC
19120 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
19146 ATCAATTGGC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:20192 original size:64 final size:64
Alignment explanation
Indices: 20124--20264 Score: 178
Period size: 64 Copynumber: 2.2 Consensus size: 64
20114 GAACACTTGA
* *
20124 TGCATCGGTGCACCAAG-TGTGCATCGATGCATGAAATGCATTCGATG-TTTGAAAATAGCCTGA
1 TGCATCGATGCA--AAGCTGTGCATCGATGCATCAAATGCATTCGATGTTTTGAAAATAGCCTGA
20187 T
64 T
* ** * *
20188 TGCATCGATGCATAGCTTGTGCATCGATGCATCAAATGCATTCGATGTTTTGAAAATATTCAGAG
1 TGCATCGATGCAAAGC-TGTGCATCGATGCATCAAATGCATTCGATGTTTTGAAAATAGCCTGAT
20253 TGCATCGATGCA
1 TGCATCGATGCA
20265 TGGAGAATGC
Statistics
Matches: 67, Mismatches: 7, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
62 2 0.03
64 40 0.60
65 25 0.37
ACGTcount: A:0.28, C:0.18, G:0.23, T:0.30
Consensus pattern (64 bp):
TGCATCGATGCAAAGCTGTGCATCGATGCATCAAATGCATTCGATGTTTTGAAAATAGCCTGAT
Found at i:20276 original size:65 final size:65
Alignment explanation
Indices: 20143--20302 Score: 196
Period size: 65 Copynumber: 2.5 Consensus size: 65
20133 GCACCAAGTG
* * ****
20143 TGCATCGATGCATGAAATGCATTCGATG-TTTGAAAATAGCCTGATTGCATCGATGCATAGCTTG
1 TGCATCGATGCATGAAATGCATTCGATGTTTTGAAAATAGCCAGAGTGCATCGATGCATAGAGAA
* ** *
20207 TGCATCGATGCATCAAATGCATTCGATGTTTTGAAAATATTCAGAGTGCATCGATGCATGGAGAA
1 TGCATCGATGCATGAAATGCATTCGATGTTTTGAAAATAGCCAGAGTGCATCGATGCATAGAGAA
* * *
20272 TGCATCGGTACATGGAATGCATTCGATGTTT
1 TGCATCGATGCATGAAATGCATTCGATGTTT
20303 CAATTAATTC
Statistics
Matches: 81, Mismatches: 14, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
64 27 0.33
65 54 0.67
ACGTcount: A:0.29, C:0.16, G:0.24, T:0.31
Consensus pattern (65 bp):
TGCATCGATGCATGAAATGCATTCGATGTTTTGAAAATAGCCAGAGTGCATCGATGCATAGAGAA
Found at i:20542 original size:20 final size:21
Alignment explanation
Indices: 20519--20558 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
20509 GAATCGAATA
20519 TAAAAT-TGTAAAA-TCATTTG
1 TAAAATCT-TAAAATTCATTTG
20539 TAAAATCTTAAAATTCATTT
1 TAAAATCTTAAAATTCATTT
20559 AACTTAATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.45, C:0.07, G:0.05, T:0.42
Consensus pattern (21 bp):
TAAAATCTTAAAATTCATTTG
Found at i:20882 original size:65 final size:63
Alignment explanation
Indices: 20813--20998 Score: 214
Period size: 65 Copynumber: 2.9 Consensus size: 63
20803 AATTAAATTG
* *
20813 AACATCGAATGCATTTTATGCATCGATGCACATACCATGCACCGATGCACTGAGGAT-TTTATGA
1 AACATCGAATGCATTTGATGCATCGATGCACAT-CCATGCACCGATGCACTAAGGATATTT-TG-
20877 A
63 A
* * ** *
20878 AACATCGAATGCATTTGATGCATCGATGCACCAGCCATGCATCGATGCACTCTGGCTATTTTGA
1 AACATCGAATGCATTTGATGCATCGATGCA-CATCCATGCACCGATGCACTAAGGATATTTTGA
* * *
20942 AACATCGAATGCACTTGATGCATCGATTCAC-TCTTAGTGCACCGATGCACTAAGGAT
1 AACATCGAATGCATTTGATGCATCGATGCACATC-CA-TGCACCGATGCACTAAGGAT
20999 CCAACGGTCA
Statistics
Matches: 103, Mismatches: 14, Indels: 9
0.82 0.11 0.07
Matches are distributed among these distances:
62 1 0.01
63 2 0.02
64 45 0.44
65 50 0.49
66 5 0.05
ACGTcount: A:0.30, C:0.24, G:0.19, T:0.27
Consensus pattern (63 bp):
AACATCGAATGCATTTGATGCATCGATGCACATCCATGCACCGATGCACTAAGGATATTTTGA
Found at i:22218 original size:26 final size:27
Alignment explanation
Indices: 22170--22220 Score: 68
Period size: 26 Copynumber: 1.9 Consensus size: 27
22160 GTTAATAATT
* * *
22170 ATCAAATAAATTTTGGTTTGATTAACG
1 ATCAAATAAATTTCGATTCGATTAACG
22197 ATCAAAT-AATTTCGATTCGATTAA
1 ATCAAATAAATTTCGATTCGATTAA
22221 TGTTAAAGAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 14 0.67
27 7 0.33
ACGTcount: A:0.39, C:0.10, G:0.12, T:0.39
Consensus pattern (27 bp):
ATCAAATAAATTTCGATTCGATTAACG
Found at i:22318 original size:93 final size:94
Alignment explanation
Indices: 22159--22383 Score: 382
Period size: 93 Copynumber: 2.4 Consensus size: 94
22149 ATTAACTGTT
* *
22159 GGTTAATAATTATCAAATAAATTTTGGTTTGATTAACGATCAAATAATTTCGATTCGATTAATGT
1 GGTTAATAATTTTCAAATAAATTTTGGTTCGATTAACGATCAAATAATTTCGATTCGATTAATGT
* *
22224 TAAAGAAAAAA-ATTGGTTAATTTGGTTC
66 TAAAGAAAAAATATCGGTTAATTGGGTTC
*
22252 GGTTAATAATTTTCAAATAAATTTTGGTTCGATTAAC-AGTCAAATAATTTCGGTTCGATTAATG
1 GGTTAATAATTTTCAAATAAATTTTGGTTCGATTAACGA-TCAAATAATTTCGATTCGATTAATG
22316 TTAAAGAAAAAATATCGGTTAATTGGGTTC
65 TTAAAGAAAAAATATCGGTTAATTGGGTTC
22346 GGTTAATAATTTTCAAATAAATTTTGGTTCGATTAACG
1 GGTTAATAATTTTCAAATAAATTTTGGTTCGATTAACG
22384 GTTAAGGAAA
Statistics
Matches: 124, Mismatches: 5, Indels: 4
0.93 0.04 0.03
Matches are distributed among these distances:
92 1 0.01
93 71 0.57
94 52 0.42
ACGTcount: A:0.37, C:0.08, G:0.16, T:0.40
Consensus pattern (94 bp):
GGTTAATAATTTTCAAATAAATTTTGGTTCGATTAACGATCAAATAATTTCGATTCGATTAATGT
TAAAGAAAAAATATCGGTTAATTGGGTTC
Found at i:22375 original size:68 final size:65
Alignment explanation
Indices: 22291--22454 Score: 197
Period size: 66 Copynumber: 2.5 Consensus size: 65
22281 CGATTAACAG
*
22291 TCAAAT-AATTTCGGTTCGATTAATGTTAAAGAAAAAAT-ATCGGTTAATTGGGTTCGGTTAATA
1 TCAAATAAATTTCGGTTCGATTAATGTTAAAGAAAAAATAAT---TT-ATTGGATTCGGTTAATA
22354 ATTT
62 ATTT
* * * **
22358 TCAAATAAATTTTGGTTCGATTAACGGTTAAGGAAAAAATAATTTATTTTATTCGGTTAATAATT
1 TCAAATAAATTTCGGTTCGATTAA-TGTTAAAGAAAAAATAATTTATTGGATTCGGTTAATAATT
22423 T
65 T
* *
22424 TCAAATAAATTTCGATTCGATTAATGGTAAA
1 TCAAATAAATTTCGGTTCGATTAATGTTAAA
22455 ATAATTTCGG
Statistics
Matches: 83, Mismatches: 11, Indels: 8
0.81 0.11 0.08
Matches are distributed among these distances:
65 4 0.05
66 40 0.48
67 8 0.10
68 16 0.19
69 13 0.16
70 2 0.02
ACGTcount: A:0.38, C:0.07, G:0.15, T:0.40
Consensus pattern (65 bp):
TCAAATAAATTTCGGTTCGATTAATGTTAAAGAAAAAATAATTTATTGGATTCGGTTAATAATTT
Found at i:22481 original size:27 final size:27
Alignment explanation
Indices: 22426--22477 Score: 88
Period size: 26 Copynumber: 2.0 Consensus size: 27
22416 AATAATTTTC
22426 AAATAAATTTCGATTCGATTAATGGTA
1 AAATAAATTTCGATTCGATTAATGGTA
*
22453 AAAT-AATTTCGGTTCGATTAATGGT
1 AAATAAATTTCGATTCGATTAATGGT
22478 TAAAGAAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
26 20 0.83
27 4 0.17
ACGTcount: A:0.37, C:0.08, G:0.17, T:0.38
Consensus pattern (27 bp):
AAATAAATTTCGATTCGATTAATGGTA
Found at i:22509 original size:161 final size:159
Alignment explanation
Indices: 22198--22659 Score: 671
Period size: 160 Copynumber: 2.9 Consensus size: 159
22188 TGATTAACGA
* * **
22198 TCAAAT-AATTTCGATTCGATT-AATGTTAAAGAAAAA-AATTGGTTAATTTGGTTCGGTTAATA
1 TCAAATAAATTTCGGTTCGATTAAAGGTTAAAGAAAAATAA-T--TT-ATTTTATTCGGTTAATA
* *
22260 ATTTTCAAATAAATTTTGGTTCGATTAACAGTCAAATAATTTCGGTTCGATTAAT-GTTAAAGAA
62 ATTTTCAAATAAATTTCGGTTCGATTAACGGTCAAATAATTTCGGTTCGATTAATGGTTAAAGAA
22324 AAAATATCGGTTAATTGGGTTCGGTTAATAATTT
127 AAAA-ATCGGTTAATTGGGTTCGGTTAATAATTT
* * *
22358 TCAAATAAATTTTGGTTCGATTAACGGTTAAGGAAAAAATAATTTATTTTATTCGGTTAATAATT
1 TCAAATAAATTTCGGTTCGATTAAAGGTTAAAG-AAAAATAATTTATTTTATTCGGTTAATAATT
* * *
22423 TTCAAATAAATTTCGATTCGATTAATGGTAAAATAATTTCGGTTCGATTAATGGTTAAAGAAAAA
65 TTCAAATAAATTTCGGTTCGATTAACGGTCAAATAATTTCGGTTCGATTAATGGTTAAAGAAAAA
* *
22488 CAATCGGTTGATTTGGTTCGGTTAATAATTT
130 -AATCGGTTAATTGGGTTCGGTTAATAATTT
22519 TCAAATAAATTTCGGTTCGATTAAAGGTTAAAGAAAAATAATTTATTTTATTCGGTTAATAATTT
1 TCAAATAAATTTCGGTTCGATTAAAGGTTAAAGAAAAATAATTTATTTTATTCGGTTAATAATTT
* * *
22584 TCAAATAAATTTGGGTTCGATTAACGGTCAAATAATTTTGGTTCGGTTAATGGTTAAAGAAAAAA
66 TCAAATAAATTTCGGTTCGATTAACGGTCAAATAATTTCGGTTCGATTAATGGTTAAAGAAAAAA
22649 ATTCGGTTAAT
131 A-TCGGTTAAT
22660 AATTTTCAAA
Statistics
Matches: 271, Mismatches: 24, Indels: 14
0.88 0.08 0.05
Matches are distributed among these distances:
159 2 0.01
160 169 0.62
161 84 0.31
162 8 0.03
163 6 0.02
164 2 0.01
ACGTcount: A:0.37, C:0.07, G:0.16, T:0.39
Consensus pattern (159 bp):
TCAAATAAATTTCGGTTCGATTAAAGGTTAAAGAAAAATAATTTATTTTATTCGGTTAATAATTT
TCAAATAAATTTCGGTTCGATTAACGGTCAAATAATTTCGGTTCGATTAATGGTTAAAGAAAAAA
ATCGGTTAATTGGGTTCGGTTAATAATTT
Found at i:22601 original size:65 final size:67
Alignment explanation
Indices: 22453--22607 Score: 226
Period size: 65 Copynumber: 2.3 Consensus size: 67
22443 ATTAATGGTA
* *
22453 AAAT-AATTTCGGTTCGATTAATGGTTAAAGAAAAACAATCGGTTGATTTGGTTCGGTTAATAAT
1 AAATAAATTTCGGTTCGATTAAAGGTTAAAGAAAAACAAT--GTTGATTTGATTCGGTTAATAAT
22517 TTTC
64 TTTC
* *
22521 AAATAAATTTCGGTTCGATTAAAGGTTAAAGAAAAATAAT-TT-ATTTTATTCGGTTAATAATTT
1 AAATAAATTTCGGTTCGATTAAAGGTTAAAGAAAAACAATGTTGATTTGATTCGGTTAATAATTT
22584 TC
66 TC
*
22586 AAATAAATTTGGGTTCGATTAA
1 AAATAAATTTCGGTTCGATTAA
22608 CGGTCAAATA
Statistics
Matches: 81, Mismatches: 5, Indels: 5
0.89 0.05 0.05
Matches are distributed among these distances:
65 42 0.52
66 2 0.02
68 4 0.05
69 33 0.41
ACGTcount: A:0.37, C:0.07, G:0.16, T:0.39
Consensus pattern (67 bp):
AAATAAATTTCGGTTCGATTAAAGGTTAAAGAAAAACAATGTTGATTTGATTCGGTTAATAATTT
TC
Found at i:22601 original size:95 final size:90
Alignment explanation
Indices: 22519--22968 Score: 460
Period size: 95 Copynumber: 5.0 Consensus size: 90
22509 TTAATAATTT
*
22519 TCAAATAAATTTCGGTTCGATTAAAGGTTAAAGAAAAATAATTTATTTTATTCGGTTAATAATTT
1 TCAAAT-AATTTTGGTTCGATT-AAGGTTAAAGAAAAATAATTTATTTTATTCGGTTAATAATTT
*
22584 TCAAATAAATTTGGGTTCGATTAACGG
64 TCAAATAAATTTCGGTTCGATTAACGG
*
22611 TCAAATAATTTTGGTTCGGTTAATGGTTAAAG--AAA-AA---A----ATTCGGTTAATAATTTT
1 TCAAATAATTTTGGTTCGATTAA-GGTTAAAGAAAAATAATTTATTTTATTCGGTTAATAATTTT
* *
22666 CAAATAAATTTTGGTTCGATTGACGG
65 CAAATAAATTTCGGTTCGATTAACGG
* * *
22692 TCAAATAATTTTGGTTCGATTAATGTTAAAGAAAAAAAATTTGATTAATTTGGTTCGGTTAATAA
1 TCAAATAATTTTGGTTCGATTAAGGTTAAAGAAAAATAATTT-A-T--TTT-ATTCGGTTAATAA
22757 TTTTCAAATAAATTTCGGTTCGATTAACGG
61 TTTTCAAATAAATTTCGGTTCGATTAACGG
* ** * **
22787 TCAAATAATTTTGGTTCGATTAATGTT--A-AAAAATCGGTTAATTTGGTTCGGTTAATAATTTT
1 TCAAATAATTTTGGTTCGATTAAGGTTAAAGAAAAAT-AATTTATTTTATTCGGTTAATAATTTT
*
22849 CAAATAAATTTCGGTTCGATTAACGA
65 CAAATAAATTTCGGTTCGATTAACGG
** * ** **
22875 TCAAATAATTTCAGTTTGATTATTGTTAAAGAAAAA-AATTTCGGTTAATTTGGTTCGGTTAATA
1 TCAAATAATTTTGGTTCGATTAAGGTTAAAGAAAAATAA--T---TT-ATTTTATTCGGTTAATA
*
22939 ATTTTCAAATAAATTTCGATTCGATTAACG
60 ATTTTCAAATAAATTTCGGTTCGATTAACG
22969 ATTAAAGAAA
Statistics
Matches: 309, Mismatches: 23, Indels: 49
0.81 0.06 0.13
Matches are distributed among these distances:
80 7 0.02
81 63 0.20
82 3 0.01
83 2 0.01
85 1 0.00
87 1 0.00
88 67 0.22
89 5 0.02
90 3 0.01
91 28 0.09
92 12 0.04
93 3 0.01
94 1 0.00
95 113 0.37
ACGTcount: A:0.36, C:0.08, G:0.16, T:0.40
Consensus pattern (90 bp):
TCAAATAATTTTGGTTCGATTAAGGTTAAAGAAAAATAATTTATTTTATTCGGTTAATAATTTTC
AAATAAATTTCGGTTCGATTAACGG
Found at i:22614 original size:27 final size:27
Alignment explanation
Indices: 22584--22714 Score: 99
Period size: 26 Copynumber: 4.9 Consensus size: 27
22574 TTAATAATTT
*
22584 TCAAATAAATTTGGGTTCGATTAACGG
1 TCAAATAAATTTTGGTTCGATTAACGG
* *
22611 TCAAAT-AATTTTGGTTCGGTTAATGG
1 TCAAATAAATTTTGGTTCGATTAACGG
* * * * * ***
22637 TTAAAGAAAAAAATTCGGTT--AATAATTT
1 -T-CA-AATAAATTTTGGTTCGATTAACGG
*
22665 TCAAATAAATTTTGGTTCGATTGACGG
1 TCAAATAAATTTTGGTTCGATTAACGG
22692 TCAAAT-AATTTTGGTTCGATTAA
1 TCAAATAAATTTTGGTTCGATTAA
22715 TGTTAAAGAA
Statistics
Matches: 77, Mismatches: 21, Indels: 13
0.69 0.19 0.12
Matches are distributed among these distances:
25 11 0.14
26 34 0.44
27 17 0.22
28 5 0.06
29 2 0.03
30 8 0.10
ACGTcount: A:0.35, C:0.08, G:0.18, T:0.38
Consensus pattern (27 bp):
TCAAATAAATTTTGGTTCGATTAACGG
Found at i:22730 original size:81 final size:81
Alignment explanation
Indices: 22568--22923 Score: 320
Period size: 81 Copynumber: 4.1 Consensus size: 81
22558 AATTTATTTT
* *
22568 ATTCGGTTAATAATTTTCAAATAAATTTGGGTTCGATTAACGGTCAAATAATTTTGGTTCGGTTA
1 ATTCGGTTAATAATTTTCAAATAAATTTTGGTTCGATTAACGGTCAAATAATTTTGGTTCGATTA
22633 ATGGTTAAAG-AAAAAA
66 AT-GTTAAAGAAAAAAA
*
22649 ATTCGGTTAATAATTTTCAAATAAATTTTGGTTCGATTGACGGTCAAATAATTTTGGTTCGATTA
1 ATTCGGTTAATAATTTTCAAATAAATTTTGGTTCGATTAACGGTCAAATAATTTTGGTTCGATTA
22714 ATGTTAAAGAAAAAAA
66 ATGTTAAAGAAAAAAA
* * ** *
22730 ATTTGATTAATTTGGTTCGGTTAATAATTTTCAAATAAATTTCGGTTCGATTAACGGTCAAATAA
1 ATTCGGTTAA--TAATT---TTCA-AA---T-AAAT---TTT-GGTTCGATTAACGGTCAAATAA
**
22795 TTTTGGTTCGATTAATGTTAAA-AAATCGGTTAA
52 TTTTGGTTCGATTAATGTTAAAGAAA----AAAA
* * * * ** *
22828 TTTGGTTCGGTTAATAATTTTCAAATAAATTTCGGTTCGATTAACGATCAAATAATTTCAGTTTG
1 ATTCG----GTTAATAATTTTCAAATAAATTTTGGTTCGATTAACGGTCAAATAATTTTGGTTCG
*
22893 ATTATTGTTAAAGAAAAAAA
62 ATTAATGTTAAAGAAAAAAA
*
22913 TTTCGGTTAAT
1 ATTCGGTTAAT
22924 TTGGTTCGGT
Statistics
Matches: 225, Mismatches: 26, Indels: 48
0.75 0.09 0.16
Matches are distributed among these distances:
80 7 0.03
81 84 0.37
83 3 0.01
85 6 0.03
86 3 0.01
87 2 0.01
88 39 0.17
89 5 0.02
90 1 0.00
91 4 0.02
92 4 0.02
93 1 0.00
94 6 0.03
95 43 0.19
96 2 0.01
97 3 0.01
98 5 0.02
100 3 0.01
102 4 0.02
ACGTcount: A:0.36, C:0.08, G:0.16, T:0.40
Consensus pattern (81 bp):
ATTCGGTTAATAATTTTCAAATAAATTTTGGTTCGATTAACGGTCAAATAATTTTGGTTCGATTA
ATGTTAAAGAAAAAAA
Found at i:22969 original size:95 final size:95
Alignment explanation
Indices: 22650--22970 Score: 487
Period size: 95 Copynumber: 3.5 Consensus size: 95
22640 AAGAAAAAAA
* * *
22650 TTCGGTTAATAATTTTCAAATAAATTTTGGTTCGATTGACGGTCAAATAATTTTGGTTCGATTAA
1 TTCGGTTAATAATTTTCAAATAAATTTCGGTTCGATTAACGATCAAATAATTTTGGTTCGATTAA
*
22715 TGTTAAAGAAAAAAAATTT-GATTAATTTGG
66 TGTTAAAG-AAAAAAATTTCGGTTAATTTGG
*
22745 TTCGGTTAATAATTTTCAAATAAATTTCGGTTCGATTAACGGTCAAATAATTTTGGTTCGATTAA
1 TTCGGTTAATAATTTTCAAATAAATTTCGGTTCGATTAACGATCAAATAATTTTGGTTCGATTAA
22810 TGTT-----AAAAAA--TCGGTTAATTTGG
66 TGTTAAAGAAAAAAATTTCGGTTAATTTGG
** * *
22833 TTCGGTTAATAATTTTCAAATAAATTTCGGTTCGATTAACGATCAAATAATTTCAGTTTGATTAT
1 TTCGGTTAATAATTTTCAAATAAATTTCGGTTCGATTAACGATCAAATAATTTTGGTTCGATTAA
22898 TGTTAAAGAAAAAAATTTCGGTTAATTTGG
66 TGTTAAAGAAAAAAATTTCGGTTAATTTGG
*
22928 TTCGGTTAATAATTTTCAAATAAATTTCGATTCGATTAACGAT
1 TTCGGTTAATAATTTTCAAATAAATTTCGGTTCGATTAACGAT
22971 TAAAGAAACT
Statistics
Matches: 209, Mismatches: 9, Indels: 16
0.89 0.04 0.07
Matches are distributed among these distances:
87 1 0.00
88 74 0.35
89 6 0.03
93 6 0.03
95 122 0.58
ACGTcount: A:0.35, C:0.08, G:0.16, T:0.41
Consensus pattern (95 bp):
TTCGGTTAATAATTTTCAAATAAATTTCGGTTCGATTAACGATCAAATAATTTTGGTTCGATTAA
TGTTAAAGAAAAAAATTTCGGTTAATTTGG
Found at i:24304 original size:2 final size:2
Alignment explanation
Indices: 24293--24322 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
24283 TCCTATAGTT
24293 TA TA -A 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 T
24323 TAACATTGTT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:25926 original size:5 final size:5
Alignment explanation
Indices: 25916--26014 Score: 180
Period size: 5 Copynumber: 19.4 Consensus size: 5
25906 GAATACTTAC
25916 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA
1 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA
25966 ATATA ATATA ATATA ATATA ATATAA TATATA ATATA ATATA ATATA AT
1 ATATA ATATA ATATA ATATA ATAT-A -ATATA ATATA ATATA ATATA AT
26015 GTGAGGGAAT
Statistics
Matches: 92, Mismatches: 0, Indels: 4
0.96 0.00 0.04
Matches are distributed among these distances:
5 86 0.93
6 2 0.02
7 4 0.04
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
ATATA
Found at i:27567 original size:38 final size:36
Alignment explanation
Indices: 27518--27597 Score: 124
Period size: 38 Copynumber: 2.2 Consensus size: 36
27508 TCGGGTCGGG
27518 TATATATATTTAAATTAAATATATAAATATTATATA
1 TATATATATTTAAATTAAATATATAAATATTATATA
* *
27554 TATATATTAATTTAAATTAAATTTATTAATATTATATA
1 TATATA-T-ATTTAAATTAAATATATAAATATTATATA
27592 TATATA
1 TATATA
27598 ATTATTTTTA
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
36 6 0.15
37 1 0.03
38 33 0.82
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (36 bp):
TATATATATTTAAATTAAATATATAAATATTATATA
Found at i:27582 original size:19 final size:19
Alignment explanation
Indices: 27525--27583 Score: 66
Period size: 19 Copynumber: 3.1 Consensus size: 19
27515 GGGTATATAT
*
27525 ATTTAAATTAAATATATAA
1 ATTTAAATTAAATATATTA
* *
27544 ATATTATA-TATATATATTA
1 AT-TTAAATTAAATATATTA
*
27563 ATTTAAATTAAATTTATTA
1 ATTTAAATTAAATATATTA
27582 AT
1 AT
27584 ATTATATATA
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
18 4 0.12
19 24 0.75
20 4 0.12
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (19 bp):
ATTTAAATTAAATATATTA
Found at i:27728 original size:30 final size:30
Alignment explanation
Indices: 27660--27729 Score: 97
Period size: 30 Copynumber: 2.3 Consensus size: 30
27650 ACCAAACCCG
27660 TCCCCGTCCCCGTTTAACATAAACATTTTT
1 TCCCCGTCCCCGTTTAACATAAACATTTTT
* * *
27690 TTCTCGTCCCCGTTTAGCATAAACGA-TTTT
1 TCCCCGTCCCCGTTTAACATAAAC-ATTTTT
27720 TCCCCGTCCC
1 TCCCCGTCCC
27730 TATTTAATTC
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
30 33 0.97
31 1 0.03
ACGTcount: A:0.19, C:0.36, G:0.10, T:0.36
Consensus pattern (30 bp):
TCCCCGTCCCCGTTTAACATAAACATTTTT
Found at i:28689 original size:37 final size:37
Alignment explanation
Indices: 28613--28689 Score: 93
Period size: 37 Copynumber: 2.1 Consensus size: 37
28603 TTTTTATATT
*
28613 TTTAATTTTGTAAAAAAAATTATATAAATATTATGAA
1 TTTAATTTTGTAAAAAAAATTATATAAATATTATCAA
* * * *
28650 TTTATTTTTTTAAAGAAAA-TATATAAATATTTTACAA
1 TTTAATTTTGTAAAAAAAATTATATAAATATTAT-CAA
28687 TTT
1 TTT
28690 GTAATATTAT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
36 13 0.38
37 21 0.62
ACGTcount: A:0.47, C:0.01, G:0.04, T:0.48
Consensus pattern (37 bp):
TTTAATTTTGTAAAAAAAATTATATAAATATTATCAA
Found at i:28951 original size:20 final size:20
Alignment explanation
Indices: 28920--28966 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
28910 CATGAAATGT
* *
28920 AAGATTATCAGTTAGAATAA
1 AAGATTACCAGTGAGAATAA
*
28940 AATATTACCAGTGAGAATAA
1 AAGATTACCAGTGAGAATAA
28960 AAGATTA
1 AAGATTA
28967 TCAAGGAATA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.51, C:0.06, G:0.15, T:0.28
Consensus pattern (20 bp):
AAGATTACCAGTGAGAATAA
Found at i:29199 original size:36 final size:38
Alignment explanation
Indices: 29126--29200 Score: 93
Period size: 37 Copynumber: 2.0 Consensus size: 38
29116 GTTGGAAAAT
* *
29126 ATTTATATATTTTCTTTAAAAAAATTTAAATTCATAAA
1 ATTTATATATTTTCTTTAAAAAAATTAAAAATCATAAA
*
29164 ATTTATATAATTTT-TTT-ACAAAATTAAAAAT-ATAAA
1 ATTTATAT-ATTTTCTTTAAAAAAATTAAAAATCATAAA
29200 A
1 A
29201 ATGTTTAATG
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
36 6 0.18
37 11 0.33
38 11 0.33
39 5 0.15
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (38 bp):
ATTTATATATTTTCTTTAAAAAAATTAAAAATCATAAA
Found at i:29855 original size:22 final size:23
Alignment explanation
Indices: 29813--29870 Score: 57
Period size: 22 Copynumber: 2.6 Consensus size: 23
29803 ATACAATAAA
29813 TAATATTATTTATCATAAAAT-T
1 TAATATTATTTATCATAAAATAT
* *
29835 TAATATTA-TTATTATTTAAATAT
1 TAATATTATTTATCA-TAAAATAT
* *
29858 TAAAATAATTTAT
1 TAATATTATTTAT
29871 TTATTAATTT
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
21 5 0.17
22 13 0.45
23 7 0.24
24 4 0.14
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.52
Consensus pattern (23 bp):
TAATATTATTTATCATAAAATAT
Found at i:29948 original size:31 final size:29
Alignment explanation
Indices: 29872--30010 Score: 72
Period size: 31 Copynumber: 4.7 Consensus size: 29
29862 ATAATTTATT
*
29872 TATTAAT-TTTATAATTTTATTAATAAAAA
1 TATTAATAATTAT-ATTTTATTAATAAAAA
*
29901 TATTAATATTGGTATATTTTATTGAAATAAAAA
1 TATTAATAAT--TATATTTTATT--AATAAAAA
* * *
29934 TATT-ATAAATTATATTAATTATTTATTAAAG
1 TATTAAT-AATTATATT--TTATTAATAAAAA
* * * * *
29965 TAATAGT-GTTATATTATATT-TTAAAAA
1 TATTAATAATTATATTTTATTAATAAAAA
29992 TATTAAT-ATGTATATTTTA
1 TATTAATAAT-TATATTTTA
30011 AATATATTTA
Statistics
Matches: 85, Mismatches: 15, Indels: 21
0.70 0.12 0.17
Matches are distributed among these distances:
27 10 0.12
28 12 0.14
29 7 0.08
30 9 0.11
31 22 0.26
32 6 0.07
33 19 0.22
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (29 bp):
TATTAATAATTATATTTTATTAATAAAAA
Found at i:30008 original size:23 final size:22
Alignment explanation
Indices: 29975--30018 Score: 70
Period size: 23 Copynumber: 2.0 Consensus size: 22
29965 TAATAGTGTT
29975 ATATTATATTTTAAAAATATTA
1 ATATTATATTTTAAAAATATTA
*
29997 ATATGTATATTTTAAATATATT
1 ATAT-TATATTTTAAAAATATT
30019 TATTAAAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 4 0.20
23 16 0.80
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (22 bp):
ATATTATATTTTAAAAATATTA
Found at i:30032 original size:11 final size:12
Alignment explanation
Indices: 29928--30062 Score: 56
Period size: 11 Copynumber: 11.8 Consensus size: 12
29918 TTTATTGAAA
*
29928 TAAAAATATTA-
1 TAAATATATTAT
29939 TAAAT-TA-TAT
1 TAAATATATTAT
*
29949 TAATTAT-TTAT
1 TAAATATATTAT
* *
29960 TAAAGTAATAGTGT
1 TAAA-T-ATATTAT
*
29974 TATATTATATT-T
1 TA-AATATATTAT
* *
29986 TAAAAATATTAA
1 TAAATATATTAT
**
29998 TATGTATATT-T
1 TAAATATATTAT
30009 TAAATATATTTAT
1 TAAATATA-TTAT
30022 TAAA-ATATTAT
1 TAAATATATTAT
*
30033 TAGAT-TATTA-
1 TAAATATATTAT
* *
30043 TATAT-TAATAT
1 TAAATATATTAT
30054 TAAATATAT
1 TAAATATAT
30063 AAATAATATT
Statistics
Matches: 90, Mismatches: 21, Indels: 25
0.66 0.15 0.18
Matches are distributed among these distances:
9 2 0.02
10 14 0.16
11 39 0.43
12 18 0.20
13 11 0.12
14 5 0.06
15 1 0.01
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.50
Consensus pattern (12 bp):
TAAATATATTAT
Found at i:30075 original size:21 final size:21
Alignment explanation
Indices: 30018--30102 Score: 56
Period size: 21 Copynumber: 4.2 Consensus size: 21
30008 TTAAATATAT
*
30018 TTATT-AA-AATATTATTAGA
1 TTATTAAATAATATTATTAAA
* * *
30037 TTATTATATATTAATATTAAA
1 TTATTAAATAATATTATTAAA
*
30058 -TATATAAATAATATTATT-CA
1 TTAT-TAAATAATATTATTAAA
*
30078 TTATT-AATAAT-TTAATAATA
1 TTATTAAATAATATTATTAA-A
30098 TTATT
1 TTATT
30103 TCTATGATTA
Statistics
Matches: 50, Mismatches: 10, Indels: 11
0.70 0.14 0.15
Matches are distributed among these distances:
18 4 0.08
19 11 0.22
20 12 0.24
21 23 0.46
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.51
Consensus pattern (21 bp):
TTATTAAATAATATTATTAAA
Found at i:30262 original size:21 final size:21
Alignment explanation
Indices: 30204--30265 Score: 56
Period size: 23 Copynumber: 2.8 Consensus size: 21
30194 TGATTATTTT
30204 AATATAATATTAAA-ATTATAA
1 AATATAAT-TTAAATATTATAA
*
30225 AATTATATATTAGAAATATTA-ATA
1 AA-TATA-ATT-TAAATATTATA-A
30249 AATATAATTTAAATATT
1 AATATAATTTAAATATT
30266 TCAATAATTG
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
21 9 0.26
22 8 0.24
23 10 0.29
24 7 0.21
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (21 bp):
AATATAATTTAAATATTATAA
Found at i:30265 original size:30 final size:30
Alignment explanation
Indices: 30209--30265 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 30
30199 ATTTTAATAT
* *
30209 AATATTAAAATTATAAAATTATATATTAGA
1 AATATTAAAAATATAAAATTAAATATTAGA
*
30239 AATATTAATAAATAT-AATTTAAATATT
1 AATATTAA-AAATATAAAATTAAATATT
30266 TCAATAATTG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
30 18 0.78
31 5 0.22
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (30 bp):
AATATTAAAAATATAAAATTAAATATTAGA
Found at i:31615 original size:18 final size:18
Alignment explanation
Indices: 31584--31630 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 18
31574 ATCCTAGAAA
*
31584 ATTATATAATTAATAATAAT
1 ATTATATTA-TAAT-ATAAT
*
31604 TTTA-ATTATAATATAAT
1 ATTATATTATAATATAAT
31621 ATTATATTAT
1 ATTATATTAT
31631 GATGAATTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
17 8 0.35
18 9 0.39
19 3 0.13
20 3 0.13
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
ATTATATTATAATATAAT
Found at i:32191 original size:39 final size:39
Alignment explanation
Indices: 32148--32253 Score: 119
Period size: 39 Copynumber: 2.7 Consensus size: 39
32138 TATAATCCTC
* *
32148 AAATTATTTCACTCTAACGTTCTAAATTCCTAATTTATT
1 AAATTATTTCACTCTAACATTCTAAATTCATAATTTATT
* * *
32187 AAATT-TTATCAC-CATAATATTCGAAATTCATAATTTCTT
1 AAATTATT-TCACTC-TAACATTCTAAATTCATAATTTATT
32226 AAATTATTTCACAT-TAACATTCTAAATT
1 AAATTATTTCAC-TCTAACATTCTAAATT
32254 GTTTTTAAAA
Statistics
Matches: 55, Mismatches: 7, Indels: 10
0.76 0.10 0.14
Matches are distributed among these distances:
38 3 0.05
39 50 0.91
40 2 0.04
ACGTcount: A:0.38, C:0.16, G:0.02, T:0.44
Consensus pattern (39 bp):
AAATTATTTCACTCTAACATTCTAAATTCATAATTTATT
Found at i:32429 original size:17 final size:16
Alignment explanation
Indices: 32407--32442 Score: 54
Period size: 17 Copynumber: 2.2 Consensus size: 16
32397 TCAATTTTTT
32407 ATATATATTTAAAAATA
1 ATATATATTTAAAAA-A
*
32424 ATATATTTTTAAAAAA
1 ATATATATTTAAAAAA
32440 ATA
1 ATA
32443 AAAAATATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 4 0.22
17 14 0.78
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
ATATATATTTAAAAAA
Found at i:37405 original size:29 final size:30
Alignment explanation
Indices: 37372--37433 Score: 108
Period size: 30 Copynumber: 2.1 Consensus size: 30
37362 ACTTAATAAA
37372 ACAATATCATA-AATCAAGAGACCATTTAT
1 ACAATATCATATAATCAAGAGACCATTTAT
*
37401 ACAATATCATATAGTCAAGAGACCATTTAT
1 ACAATATCATATAATCAAGAGACCATTTAT
37431 ACA
1 ACA
37434 CTTTACCCTT
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
29 11 0.35
30 20 0.65
ACGTcount: A:0.47, C:0.18, G:0.08, T:0.27
Consensus pattern (30 bp):
ACAATATCATATAATCAAGAGACCATTTAT
Found at i:42609 original size:18 final size:18
Alignment explanation
Indices: 42569--42610 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
42559 TTCAAACATT
**
42569 ATTGCACCTAATTTTGTT
1 ATTGCACCTAATTTTGAC
*
42587 GTTGCACCTAATTTTGAC
1 ATTGCACCTAATTTTGAC
42605 ATTGCA
1 ATTGCA
42611 ATATTAGGTG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.24, C:0.19, G:0.14, T:0.43
Consensus pattern (18 bp):
ATTGCACCTAATTTTGAC
Found at i:47533 original size:10 final size:10
Alignment explanation
Indices: 47518--47542 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
47508 TCGAATTCGC
47518 GGTCGGAGGA
1 GGTCGGAGGA
47528 GGTCGGAGGA
1 GGTCGGAGGA
47538 GGTCG
1 GGTCG
47543 TTTCTTTAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.16, C:0.12, G:0.60, T:0.12
Consensus pattern (10 bp):
GGTCGGAGGA
Found at i:56514 original size:34 final size:33
Alignment explanation
Indices: 56433--56514 Score: 96
Period size: 33 Copynumber: 2.5 Consensus size: 33
56423 AAAAATAAAT
* *
56433 CAACGTATTTGAGTCATATTAAAACCCTAAAAC
1 CAACATATTTGAGTCATATTAAAACACTAAAAC
*
56466 CAACATATTTGAGTC-TGATTGAAACACTAAAAC
1 CAACATATTTGAGTCAT-ATTAAAACACTAAAAC
56499 CGAAGCAT-TTTGAGTC
1 C-AA-CATATTTGAGTC
56515 CATGTAGGAC
Statistics
Matches: 43, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
32 1 0.02
33 29 0.67
34 10 0.23
35 3 0.07
ACGTcount: A:0.39, C:0.20, G:0.13, T:0.28
Consensus pattern (33 bp):
CAACATATTTGAGTCATATTAAAACACTAAAAC
Found at i:56815 original size:20 final size:20
Alignment explanation
Indices: 56787--56829 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
56777 ACTTATTCTT
*
56787 TTTATTTTAT-TTTTTATTTA
1 TTTACTTTATATTTTT-TTTA
56807 TTTACTTTATATTTTTTTTA
1 TTTACTTTATATTTTTTTTA
56827 TTT
1 TTT
56830 TCTCCTAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 16 0.76
21 5 0.24
ACGTcount: A:0.19, C:0.02, G:0.00, T:0.79
Consensus pattern (20 bp):
TTTACTTTATATTTTTTTTA
Found at i:56879 original size:4 final size:4
Alignment explanation
Indices: 56870--56919 Score: 50
Period size: 4 Copynumber: 12.2 Consensus size: 4
56860 TACATTGTTA
*
56870 TATT TATT TATT TATT TATT TCATT T-TT TATT AATAT TA-T TATAT TATT
1 TATT TATT TATT TATT TATT T-ATT TATT TATT TAT-T TATT TAT-T TATT
56919 T
1 T
56920 TTTTTATTAT
Statistics
Matches: 39, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
3 6 0.15
4 23 0.59
5 10 0.26
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (4 bp):
TATT
Found at i:56907 original size:26 final size:24
Alignment explanation
Indices: 56878--56931 Score: 58
Period size: 24 Copynumber: 2.2 Consensus size: 24
56868 TATATTTATT
56878 TATTTATT-TATTTCATTTTTTATTAA
1 TATTTATTATA-TT-ATTTTTT-TTAA
*
56904 TA-TTATTATATTATTTTTTTTAT
1 TATTTATTATATTATTTTTTTTAA
56927 TATTT
1 TATTT
56932 GTTTCTCATG
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
23 5 0.20
24 9 0.36
25 7 0.28
26 4 0.16
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.72
Consensus pattern (24 bp):
TATTTATTATATTATTTTTTTTAA
Found at i:58128 original size:16 final size:16
Alignment explanation
Indices: 58098--58128 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
58088 TTGAAACTCA
*
58098 ACTCGAACTCGAAAAG
1 ACTCGAACTCAAAAAG
58114 ACTCGAACTCAAAAA
1 ACTCGAACTCAAAAA
58129 AAAAATTGAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.48, C:0.26, G:0.13, T:0.13
Consensus pattern (16 bp):
ACTCGAACTCAAAAAG
Found at i:58172 original size:23 final size:23
Alignment explanation
Indices: 58139--58199 Score: 86
Period size: 23 Copynumber: 2.7 Consensus size: 23
58129 AAAAATTGAA
*
58139 GAGCTCAATTCAAGCTCAATTTT
1 GAGCTCGATTCAAGCTCAATTTT
* *
58162 GAGCTCGATTCAAGTTCGATTTT
1 GAGCTCGATTCAAGCTCAATTTT
*
58185 GAGCTCGTTTCAAGC
1 GAGCTCGATTCAAGC
58200 CACTAGCCTA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.25, C:0.21, G:0.20, T:0.34
Consensus pattern (23 bp):
GAGCTCGATTCAAGCTCAATTTT
Found at i:59726 original size:21 final size:21
Alignment explanation
Indices: 59680--59840 Score: 66
Period size: 21 Copynumber: 7.7 Consensus size: 21
59670 TATAATTGGA
* *
59680 TTAAGAGTTTAGGGTTT-ATGT
1 TTAA-AGTTTAGGTTTTAAGGT
59701 CTTAAAGTTTAGGTTTTAAGGT
1 -TTAAAGTTTAGGTTTTAAGGT
* *** *
59723 TTAAAATTTATAATTTAGGGT
1 TTAAAGTTTAGGTTTTAAGGT
* * *
59744 TTGAAAATTAAGG-TTTATGGT
1 TT-AAAGTTTAGGTTTTAAGGT
*
59765 TTATAGTTTATGGTTTT-AGGT
1 TTAAAGTTTA-GGTTTTAAGGT
* * *
59786 TT-GAGTTT-GGGTTTAGGGT
1 TTAAAGTTTAGGTTTTAAGGT
* *
59805 TTATAGTTTAGAG-ATTAA-GT
1 TTAAAGTTTAG-GTTTTAAGGT
*
59825 TTTAAGTTTAAGGTTT
1 TTAAAGTTT-AGGTTT
59841 AGAGTGTAAT
Statistics
Matches: 105, Mismatches: 24, Indels: 21
0.70 0.16 0.14
Matches are distributed among these distances:
18 5 0.05
19 5 0.05
20 25 0.24
21 52 0.50
22 18 0.17
ACGTcount: A:0.27, C:0.01, G:0.24, T:0.48
Consensus pattern (21 bp):
TTAAAGTTTAGGTTTTAAGGT
Found at i:59833 original size:40 final size:41
Alignment explanation
Indices: 59751--59842 Score: 107
Period size: 40 Copynumber: 2.3 Consensus size: 41
59741 GGTTTGAAAA
* * * *
59751 TTAAGGTTTATGGTTTATAGTTTATGGTTTTAGGTTTGAGT
1 TTAAGGTTTAGGGTTTATAGTTTATGGATTAAGGTTTAAGT
* *
59792 TT-GGGTTTAGGGTTTATAGTTTA-GAGATTAAGTTTTAAGT
1 TTAAGGTTTAGGGTTTATAGTTTATG-GATTAAGGTTTAAGT
59832 TTAAGGTTTAG
1 TTAAGGTTTAG
59843 AGTGTAATCT
Statistics
Matches: 42, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
39 1 0.02
40 32 0.76
41 9 0.21
ACGTcount: A:0.23, C:0.00, G:0.27, T:0.50
Consensus pattern (41 bp):
TTAAGGTTTAGGGTTTATAGTTTATGGATTAAGGTTTAAGT
Found at i:60959 original size:309 final size:307
Alignment explanation
Indices: 60393--60972 Score: 937
Period size: 309 Copynumber: 1.9 Consensus size: 307
60383 GGAAATAGAC
* * * * *
60393 GATTCCAATCTTCATTAACAACTATTCGATCCAGCCTTTTCGAGATACCTCCACGATACCAAGTA
1 GATTCCAATCTTCATTAACAACCATCCGATCCAGCCTTCTCGAGATACCCCCAAGATACCAAGTA
* * *
60458 AACTGCGGACCTTTGAATCCAAGGTGCATAAGATTACGATAGTCCATAAAGCTCTGGAACATAGA
66 AACTGCAGACCTTTGAATCCAAGGTCCATAAGATTACGATAGTCCATAAAACTCTGGAACATAGA
*
60523 GCAACCTTTGCCACGTTAAAATCCACCCGACTTCTCAGTACTCGAAAGAATGGCATTAAAATCAC
131 GAAACCTTTGCCACGTTAAAATCCACCCGACTTCTCAGTACTCGAAAGAATGGCATTAAAATCAC
* * *
60588 CCGCCATAACCCAAGGGGTACTAGCCGGTCTTGCAACAGCACTAAGATTACTCCATAGAGATAAA
196 CCACCATAACCCAAGGGGTACTAGCCGGTCTTGCAACAACACTAAGATTACTCCAAAGAGATAAA
60653 CGCTTCTTCTTATCCGGGCTACCATATACAACCATTAACAACCATAT
261 CGCTTCTTCTTATCCGGGCTACCATATACAACCATTAACAACCATAT
* *
60700 GATTGCAATCTTTATTAACAACCATCCGATCCAGCCTTCTCGAGATACCCCCAAGATACCAAGTA
1 GATTCCAATCTTCATTAACAACCATCCGATCCAGCCTTCTCGAGATACCCCCAAGATACCAAGTA
*
60765 AACTGCAGACCCCTTTGAATCCAAGGTCCATAAGATTATGATAGTCCATAAAACTCTGGAACATA
66 AACTGCAGA--CCTTTGAATCCAAGGTCCATAAGATTACGATAGTCCATAAAACTCTGGAACATA
* * *
60830 GGGAAACCTTTGCCACGTTGAACTCCACCCGACTTCTCAGTACGT-GAAAGAATGGCATTAAAAT
129 GAGAAACCTTTGCCACGTTAAAATCCACCCGACTTCTCAGTAC-TCGAAAGAATGGCATTAAAAT
* * *
60894 CACCCATCATAACCCAAGGGGTACTAGCCGGTCTTGCAACAACAGTAAGATTACTCTAAAGAGAT
193 CACCCACCATAACCCAAGGGGTACTAGCCGGTCTTGCAACAACACTAAGATTACTCCAAAGAGAT
60959 AAACGCTTCTTCTT
258 AAACGCTTCTTCTT
60973 GTATGGTCTA
Statistics
Matches: 249, Mismatches: 21, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
307 66 0.27
309 182 0.73
310 1 0.00
ACGTcount: A:0.33, C:0.27, G:0.16, T:0.24
Consensus pattern (307 bp):
GATTCCAATCTTCATTAACAACCATCCGATCCAGCCTTCTCGAGATACCCCCAAGATACCAAGTA
AACTGCAGACCTTTGAATCCAAGGTCCATAAGATTACGATAGTCCATAAAACTCTGGAACATAGA
GAAACCTTTGCCACGTTAAAATCCACCCGACTTCTCAGTACTCGAAAGAATGGCATTAAAATCAC
CCACCATAACCCAAGGGGTACTAGCCGGTCTTGCAACAACACTAAGATTACTCCAAAGAGATAAA
CGCTTCTTCTTATCCGGGCTACCATATACAACCATTAACAACCATAT
Found at i:63410 original size:23 final size:23
Alignment explanation
Indices: 63384--63433 Score: 82
Period size: 23 Copynumber: 2.2 Consensus size: 23
63374 TTGGTTCTAT
* *
63384 CTAATCTGTTAACATTCCTATTA
1 CTAAGCTGTAAACATTCCTATTA
63407 CTAAGCTGTAAACATTCCTATTA
1 CTAAGCTGTAAACATTCCTATTA
63430 CTAA
1 CTAA
63434 ACTGAATTTC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.34, C:0.22, G:0.06, T:0.38
Consensus pattern (23 bp):
CTAAGCTGTAAACATTCCTATTA
Found at i:65267 original size:17 final size:17
Alignment explanation
Indices: 65247--65299 Score: 70
Period size: 17 Copynumber: 3.1 Consensus size: 17
65237 TTAATAAAGT
*
65247 TAGTTCATTAATTACAC
1 TAGTTCATTAATTAAAC
* *
65264 TAGTTCATTCATCAAAC
1 TAGTTCATTAATTAAAC
*
65281 TAGTTCATTTATTAAAC
1 TAGTTCATTAATTAAAC
65298 TA
1 TA
65300 ACTCTTAATT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 31 1.00
ACGTcount: A:0.36, C:0.17, G:0.06, T:0.42
Consensus pattern (17 bp):
TAGTTCATTAATTAAAC
Found at i:66191 original size:21 final size:21
Alignment explanation
Indices: 66167--66216 Score: 100
Period size: 21 Copynumber: 2.4 Consensus size: 21
66157 GTGGGTCACG
66167 TTCCATCTACTTCCACTTCGA
1 TTCCATCTACTTCCACTTCGA
66188 TTCCATCTACTTCCACTTCGA
1 TTCCATCTACTTCCACTTCGA
66209 TTCCATCT
1 TTCCATCT
66217 CTTTATATTG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.18, C:0.38, G:0.04, T:0.40
Consensus pattern (21 bp):
TTCCATCTACTTCCACTTCGA
Found at i:72013 original size:24 final size:25
Alignment explanation
Indices: 71966--72015 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 25
71956 TATTAACTTA
*
71966 ATTTAAAAATATTTTATTTTTATGTTC
1 ATTTAAAAATA--TTATTTATATGTTC
71993 ATTTAAAAATA-TATTTATATGTT
1 ATTTAAAAATATTATTTATATGTT
72016 AAAATTTATT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
24 11 0.50
27 11 0.50
ACGTcount: A:0.38, C:0.02, G:0.04, T:0.56
Consensus pattern (25 bp):
ATTTAAAAATATTATTTATATGTTC
Found at i:73330 original size:15 final size:15
Alignment explanation
Indices: 73305--73351 Score: 58
Period size: 15 Copynumber: 3.0 Consensus size: 15
73295 TTCACCTCGA
73305 AAAATTATAAATAATT
1 AAAA-TATAAATAATT
* *
73321 AATATATAAATATTT
1 AAAATATAAATAATT
73336 AAAATATAAAATAATT
1 AAAATAT-AAATAATT
73352 TTAATTATTC
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
15 16 0.62
16 10 0.38
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (15 bp):
AAAATATAAATAATT
Found at i:78454 original size:29 final size:29
Alignment explanation
Indices: 78365--78454 Score: 69
Period size: 29 Copynumber: 3.0 Consensus size: 29
78355 AACCAAAATG
*
78365 TTTTACTTCAATTTTATATAATTTGACCA
1 TTTTACTTCAATTTTATATAATTTGATCA
* * * *
78394 CTTTACTATGCTTAAATTT-GA-CATTT-AGTCA
1 TTTTACT-T-C--AATTTTATATAATTTGA-TCA
78425 TTTTACTTCAATTTTATATAATTTGATCA
1 TTTTACTTCAATTTTATATAATTTGATCA
78454 T
1 T
78455 CTAGTATATT
Statistics
Matches: 44, Mismatches: 9, Indels: 16
0.64 0.13 0.23
Matches are distributed among these distances:
27 5 0.11
28 1 0.02
29 15 0.34
30 4 0.09
31 13 0.30
32 1 0.02
33 5 0.11
ACGTcount: A:0.30, C:0.13, G:0.06, T:0.51
Consensus pattern (29 bp):
TTTTACTTCAATTTTATATAATTTGATCA
Found at i:79871 original size:24 final size:21
Alignment explanation
Indices: 79827--79867 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
79817 ATAAAAAAAT
79827 TACATAAAATATTATTATTTA
1 TACATAAAATATTATTATTTA
*
79848 TACATAAAATATTAATATTT
1 TACATAAAATATTATTATTT
79868 TTTAACATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (21 bp):
TACATAAAATATTATTATTTA
Found at i:80394 original size:60 final size:59
Alignment explanation
Indices: 80274--80405 Score: 142
Period size: 60 Copynumber: 2.2 Consensus size: 59
80264 AATTTAAGGT
*
80274 AAAA-TATATAAATAGTCCCCAATTATAAAGTATTGCTTTGTCGAATCCTCTAAATATTA
1 AAAATTATA-AAATAGTCCCCAATTATAAAGTATTGCTTTGTCGAATCCTATAAATATTA
* * * * * * *
80333 AAAGTTATAAAATGGTCCCTCAATTATAAAGTGTTGCTTTGTTGAGTCACTAT-ATTTTTA
1 AAAATTATAAAATAGTCCC-CAATTATAAAGTATTGCTTTGTCGAATC-CTATAAATATTA
*
80393 AAAATTACAAAAT
1 AAAATTATAAAAT
80406 TATCACCCAA
Statistics
Matches: 60, Mismatches: 10, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
59 12 0.20
60 45 0.75
61 3 0.05
ACGTcount: A:0.39, C:0.13, G:0.11, T:0.37
Consensus pattern (59 bp):
AAAATTATAAAATAGTCCCCAATTATAAAGTATTGCTTTGTCGAATCCTATAAATATTA
Found at i:82129 original size:18 final size:18
Alignment explanation
Indices: 82108--82153 Score: 92
Period size: 18 Copynumber: 2.6 Consensus size: 18
82098 TTTTATGTAG
82108 GGGACGAATTTAAACTTA
1 GGGACGAATTTAAACTTA
82126 GGGACGAATTTAAACTTA
1 GGGACGAATTTAAACTTA
82144 GGGACGAATT
1 GGGACGAATT
82154 AAAATTATAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.37, C:0.11, G:0.26, T:0.26
Consensus pattern (18 bp):
GGGACGAATTTAAACTTA
Found at i:87294 original size:54 final size:54
Alignment explanation
Indices: 87212--87321 Score: 220
Period size: 54 Copynumber: 2.0 Consensus size: 54
87202 TAGAAATATT
87212 AGCTATGTGCAGGGACGGACGTAAGATTTTATTCTAGGGTAATTTATAAAATTA
1 AGCTATGTGCAGGGACGGACGTAAGATTTTATTCTAGGGTAATTTATAAAATTA
87266 AGCTATGTGCAGGGACGGACGTAAGATTTTATTCTAGGGTAATTTATAAAATTA
1 AGCTATGTGCAGGGACGGACGTAAGATTTTATTCTAGGGTAATTTATAAAATTA
87320 AG
1 AG
87322 GGGGGAAATA
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 56 1.00
ACGTcount: A:0.34, C:0.09, G:0.25, T:0.33
Consensus pattern (54 bp):
AGCTATGTGCAGGGACGGACGTAAGATTTTATTCTAGGGTAATTTATAAAATTA
Found at i:92889 original size:12 final size:12
Alignment explanation
Indices: 92872--92915 Score: 88
Period size: 12 Copynumber: 3.7 Consensus size: 12
92862 CAATCCAGGC
92872 GACATACGGGGT
1 GACATACGGGGT
92884 GACATACGGGGT
1 GACATACGGGGT
92896 GACATACGGGGT
1 GACATACGGGGT
92908 GACATACG
1 GACATACG
92916 AGCCATACGA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 32 1.00
ACGTcount: A:0.27, C:0.18, G:0.39, T:0.16
Consensus pattern (12 bp):
GACATACGGGGT
Found at i:93091 original size:29 final size:29
Alignment explanation
Indices: 92984--93081 Score: 153
Period size: 29 Copynumber: 3.4 Consensus size: 29
92974 AGGAATAGAG
92984 AGGTCGCCATGCAGCCTAGGCGACCTTGT
1 AGGTCGCCATGCAGCCTAGGCGACCTTGT
93013 AGGTCGCCATGCAGCCTAGGCGACCTTGT
1 AGGTCGCCATGCAGCCTAGGCGACCTTGT
* * *
93042 AGGTCGCCGTGTAGTCC-CGGCGACCTTGT
1 AGGTCGCCATGCAG-CCTAGGCGACCTTGT
93071 AGGTCGCCATG
1 AGGTCGCCATG
93082 TAGTCCCGGC
Statistics
Matches: 64, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
29 62 0.97
30 2 0.03
ACGTcount: A:0.15, C:0.31, G:0.33, T:0.21
Consensus pattern (29 bp):
AGGTCGCCATGCAGCCTAGGCGACCTTGT
Found at i:93369 original size:23 final size:23
Alignment explanation
Indices: 93341--93386 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
93331 AAAAGAAAGA
93341 AAGAAAGGGAGAAGAGATTGCAG
1 AAGAAAGGGAGAAGAGATTGCAG
**
93364 AAGAAAGTTAGAAGAGATTGCAG
1 AAGAAAGGGAGAAGAGATTGCAG
93387 CCGAGAAAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.48, C:0.04, G:0.35, T:0.13
Consensus pattern (23 bp):
AAGAAAGGGAGAAGAGATTGCAG
Found at i:93401 original size:25 final size:23
Alignment explanation
Indices: 93341--93401 Score: 59
Period size: 23 Copynumber: 2.6 Consensus size: 23
93331 AAAAGAAAGA
**
93341 AAGAAAGGGAGAAGAGATTGCAG
1 AAGAAAGAAAGAAGAGATTGCAG
**
93364 AAGAAAGTTAGAAGAGATTGCAG
1 AAGAAAGAAAGAAGAGATTGCAG
*
93387 CCGAGAAAGAAAGAA
1 --AAGAAAGAAAGAA
93402 AGGGAGAAAG
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
23 21 0.68
25 10 0.32
ACGTcount: A:0.51, C:0.07, G:0.33, T:0.10
Consensus pattern (23 bp):
AAGAAAGAAAGAAGAGATTGCAG
Found at i:93415 original size:21 final size:21
Alignment explanation
Indices: 93391--93443 Score: 97
Period size: 21 Copynumber: 2.5 Consensus size: 21
93381 TTGCAGCCGA
93391 GAAAGAAAGAAAGGGAGAAAG
1 GAAAGAAAGAAAGGGAGAAAG
93412 GAAAGAAAGAAAGGGAGAAAG
1 GAAAGAAAGAAAGGGAGAAAG
*
93433 GAAAGTAAGAA
1 GAAAGAAAGAA
93444 GAAGAAAGGG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.62, C:0.00, G:0.36, T:0.02
Consensus pattern (21 bp):
GAAAGAAAGAAAGGGAGAAAG
Found at i:93437 original size:17 final size:16
Alignment explanation
Indices: 93389--93420 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
93379 GATTGCAGCC
93389 GAGAAAGAAAGAAAGG
1 GAGAAAGAAAGAAAGG
93405 GAGAAAGGAAAGAAAG
1 GAGAAA-GAAAGAAAG
93421 AAAGGGAGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.62, C:0.00, G:0.38, T:0.00
Consensus pattern (16 bp):
GAGAAAGAAAGAAAGG
Found at i:93682 original size:44 final size:47
Alignment explanation
Indices: 93643--93732 Score: 132
Period size: 45 Copynumber: 2.0 Consensus size: 47
93633 AGTTATAGTT
*
93643 AAAAA-TAATTAATTAGTTTGT-TTTGTT-AATAGTTAGTTATATAA
1 AAAAATTAATTAATTAGTTTGTGTTAGTTAAATAGTTAGTTATATAA
*
93687 AAAAATTATTTAATTAGTTTGTGTTAGTTAAATAGTTAAGTTATAT
1 AAAAATTAATTAATTAGTTTGTGTTAGTTAAATAGTT-AGTTATAT
93733 TTGTTTGTTG
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
44 5 0.12
45 15 0.38
46 5 0.12
47 7 0.17
48 8 0.20
ACGTcount: A:0.40, C:0.00, G:0.12, T:0.48
Consensus pattern (47 bp):
AAAAATTAATTAATTAGTTTGTGTTAGTTAAATAGTTAGTTATATAA
Found at i:93708 original size:40 final size:38
Alignment explanation
Indices: 93604--93708 Score: 95
Period size: 41 Copynumber: 2.6 Consensus size: 38
93594 TACATAAATT
93604 AAAAATTATTTAATTAGTATATGTTTGATAGTTATAGTTAA
1 AAAAATTATTTAATTAGT-T-TGTTTGATAGTTATAG-TAA
* * * *
93645 AAATAATTAATTAGTTTGTTTTGTTAATAGTTAGTTATA-TAA
1 AAA-AATTATTTAATTAG-TTTGTT--T-GATAGTTATAGTAA
93687 AAAAATTATTTAATTAGTTTGT
1 AAAAATTATTTAATTAGTTTGT
93709 GTTAGTTAAA
Statistics
Matches: 52, Mismatches: 7, Indels: 11
0.74 0.10 0.16
Matches are distributed among these distances:
40 5 0.10
41 18 0.35
42 18 0.35
43 2 0.04
44 9 0.17
ACGTcount: A:0.40, C:0.00, G:0.11, T:0.49
Consensus pattern (38 bp):
AAAAATTATTTAATTAGTTTGTTTGATAGTTATAGTAA
Found at i:93923 original size:16 final size:16
Alignment explanation
Indices: 93891--93937 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
93881 TTTAAAAAGT
*
93891 TTAGTTTGTTAGT-TTA
1 TTAGTTTATTA-TATTA
93907 TTAGTTTATTATATTA
1 TTAGTTTATTATATTA
*
93923 TAAG-TTATTATATTA
1 TTAGTTTATTATATTA
93938 AAGTTTAGTG
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
15 12 0.43
16 16 0.57
ACGTcount: A:0.30, C:0.00, G:0.11, T:0.60
Consensus pattern (16 bp):
TTAGTTTATTATATTA
Found at i:93932 original size:15 final size:14
Alignment explanation
Indices: 93912--93942 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
93902 GTTTATTAGT
93912 TTATTATATTATAAG
1 TTATTATATTA-AAG
93927 TTATTATATTAAAG
1 TTATTATATTAAAG
93941 TT
1 TT
93943 TAGTGTTGTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.31
15 11 0.69
ACGTcount: A:0.39, C:0.00, G:0.06, T:0.55
Consensus pattern (14 bp):
TTATTATATTAAAG
Done.