Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004526.1 Hibiscus syriacus cultivar Beakdansim tig00009989_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: 127759
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:391 original size:14 final size:14
Alignment explanation
Indices: 372--415 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
362 ACCTTCATTC
372 TACTTCCATTACCA
1 TACTTCCATTACCA
386 TACTT-CA-T-CC-
1 TACTTCCATTACCA
396 TACTTCCATTACCA
1 TACTTCCATTACCA
*
410 TGCTTC
1 TACTTC
416 ATCATTTCCT
Statistics
Matches: 25, Mismatches: 1, Indels: 8
0.74 0.03 0.24
Matches are distributed among these distances:
10 5 0.20
11 4 0.16
12 2 0.08
13 4 0.16
14 10 0.40
ACGTcount: A:0.23, C:0.36, G:0.02, T:0.39
Consensus pattern (14 bp):
TACTTCCATTACCA
Found at i:391 original size:24 final size:24
Alignment explanation
Indices: 364--418 Score: 92
Period size: 24 Copynumber: 2.3 Consensus size: 24
354 TATCCATCAC
*
364 CTTCATTCTACTTCCATTACCATA
1 CTTCATCCTACTTCCATTACCATA
*
388 CTTCATCCTACTTCCATTACCATG
1 CTTCATCCTACTTCCATTACCATA
412 CTTCATC
1 CTTCATC
419 ATTTCCTTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.22, C:0.36, G:0.02, T:0.40
Consensus pattern (24 bp):
CTTCATCCTACTTCCATTACCATA
Found at i:5070 original size:22 final size:21
Alignment explanation
Indices: 5014--5070 Score: 51
Period size: 22 Copynumber: 2.6 Consensus size: 21
5004 AATAAATAAT
* * *
5014 ATTATTTATCATAAAACTTAAT
1 ATTATTTAT-TTAAAAATTAAA
*
5036 ATTATTATTTTTAAAATATTAAA
1 ATTATT-TATTTAAAA-ATTAAA
5059 ATTATTTATTTA
1 ATTATTTATTTA
5071 TTATTAAAAT
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
22 16 0.57
23 12 0.43
ACGTcount: A:0.44, C:0.04, G:0.00, T:0.53
Consensus pattern (21 bp):
ATTATTTATTTAAAAATTAAA
Found at i:5232 original size:12 final size:12
Alignment explanation
Indices: 5187--5262 Score: 59
Period size: 11 Copynumber: 6.4 Consensus size: 12
5177 AGTGTTATAT
5187 TATATT-TTAAA
1 TATATTATTAAA
* * *
5198 AATATTAAT-AG
1 TATATTATTAAA
5209 TATATT-TTAAA
1 TATATTATTAAA
*
5220 TATCTTATTAAA
1 TATATTATTAAA
*
5232 TATATTATTATTA
1 TATATTATTA-AA
*
5245 TATTAATATTAAA
1 TA-TATTATTAAA
5258 TATAT
1 TATAT
5263 AATAATATTA
Statistics
Matches: 48, Mismatches: 12, Indels: 9
0.70 0.17 0.13
Matches are distributed among these distances:
10 1 0.02
11 17 0.35
12 17 0.35
13 6 0.12
14 7 0.15
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.51
Consensus pattern (12 bp):
TATATTATTAAA
Found at i:5255 original size:17 final size:18
Alignment explanation
Indices: 5233--5274 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
5223 CTTATTAAAT
*
5233 ATATTATTAT-TATATTA
1 ATATTATTATATATAATA
*
5250 ATATTA-AATATATAATA
1 ATATTATTATATATAATA
5267 ATATTATT
1 ATATTATT
5275 CATTGTTAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 3
0.77 0.12 0.12
Matches are distributed among these distances:
16 2 0.10
17 18 0.90
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (18 bp):
ATATTATTATATATAATA
Found at i:5445 original size:21 final size:21
Alignment explanation
Indices: 5402--5459 Score: 61
Period size: 21 Copynumber: 2.9 Consensus size: 21
5392 ATTTATTATA
*
5402 ATATTA-AAATA-TAAT-ATT
1 ATATTATAAATATTAATAAAT
5420 ATATTATAAATATTAATAAAT
1 ATATTATAAATATTAATAAAT
*
5441 ATATT-TTAATATTTAATAA
1 ATATTATAAATA-TTAATAA
5460 TTAATATTTG
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
18 6 0.18
19 5 0.15
20 9 0.26
21 14 0.41
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (21 bp):
ATATTATAAATATTAATAAAT
Found at i:5446 original size:51 final size:50
Alignment explanation
Indices: 5330--5438 Score: 116
Period size: 51 Copynumber: 2.2 Consensus size: 50
5320 AATAAATTTA
* *
5330 ATTAATAATT-TATTATATATAAAATAAAAATATAATCTTATATTATTATG
1 ATTAATAATTAT-TTATATATAAAATAAAAATATAATATTATATTATAATG
* * *
5380 ATATAATTGATTATTTAT-TATAATATTAAAATATAATATTATATTATAAAT-
1 AT-TAA-TAATTATTTATATATAAAATAAAAATATAATATTATATTAT-AATG
5431 ATTAATAA
1 ATTAATAA
5439 ATATATTTTA
Statistics
Matches: 49, Mismatches: 6, Indels: 9
0.77 0.09 0.14
Matches are distributed among these distances:
49 2 0.04
50 5 0.10
51 31 0.63
52 10 0.20
53 1 0.02
ACGTcount: A:0.50, C:0.01, G:0.02, T:0.47
Consensus pattern (50 bp):
ATTAATAATTATTTATATATAAAATAAAAATATAATATTATATTATAATG
Found at i:8449 original size:19 final size:19
Alignment explanation
Indices: 8425--8465 Score: 82
Period size: 19 Copynumber: 2.2 Consensus size: 19
8415 TGGCTATTCA
8425 TGAATTGTTTTGGGGGTTT
1 TGAATTGTTTTGGGGGTTT
8444 TGAATTGTTTTGGGGGTTT
1 TGAATTGTTTTGGGGGTTT
8463 TGA
1 TGA
8466 TTATGGCGGC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.12, C:0.00, G:0.37, T:0.51
Consensus pattern (19 bp):
TGAATTGTTTTGGGGGTTT
Found at i:12106 original size:17 final size:18
Alignment explanation
Indices: 12070--12110 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
12060 ATATTATGTA
*
12070 TTTAATTTATTTAAGCAT
1 TTTACTTTATTTAAGCAT
*
12088 TTTACTTTATTTAA-TAT
1 TTTACTTTATTTAAGCAT
12105 TTTACT
1 TTTACT
12111 AATATAATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 8 0.38
18 13 0.62
ACGTcount: A:0.29, C:0.07, G:0.02, T:0.61
Consensus pattern (18 bp):
TTTACTTTATTTAAGCAT
Found at i:13815 original size:18 final size:18
Alignment explanation
Indices: 13792--13831 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
13782 ACAGCAGCCA
*
13792 CCGCAGCCATTTATGATG
1 CCGCAGCCATATATGATG
13810 CCGCAGCCATATATGATG
1 CCGCAGCCATATATGATG
13828 CCGC
1 CCGC
13832 CGCCTTTCCA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.23, C:0.33, G:0.23, T:0.23
Consensus pattern (18 bp):
CCGCAGCCATATATGATG
Found at i:14394 original size:26 final size:24
Alignment explanation
Indices: 14323--14395 Score: 71
Period size: 26 Copynumber: 3.0 Consensus size: 24
14313 TTATATTTGT
14323 ATTTACTTTATTTTGTTAAATTGTA
1 ATTTACTTTATTTTGTTAAATT-TA
**
14348 ATTT--TTTATTATT-TTTCATTTA
1 ATTTACTTTATT-TTGTTAAATTTA
14370 ATACTTACTTTATTTTGTTAAATTTA
1 AT--TTACTTTATTTTGTTAAATTTA
14396 TTGGACTTTT
Statistics
Matches: 38, Mismatches: 4, Indels: 11
0.72 0.08 0.21
Matches are distributed among these distances:
22 4 0.11
23 11 0.29
24 4 0.11
25 6 0.16
26 13 0.34
ACGTcount: A:0.27, C:0.05, G:0.04, T:0.63
Consensus pattern (24 bp):
ATTTACTTTATTTTGTTAAATTTA
Found at i:22581 original size:2 final size:2
Alignment explanation
Indices: 22574--22673 Score: 79
Period size: 2 Copynumber: 53.5 Consensus size: 2
22564 AAATAATTTA
* * *
22574 AT AT AT AT AT AT AT AT AT -T AT AT TT GT AT AA AT AT AT A- AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * *
22614 AT AT AT -T AT -T TT A- AT AT -T TT TT AT AT AA 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
*
22652 A- AT AT AT AT AT AT AT AT TT AT A
1 AT AT AT AT AT AT AT AT AT AT AT A
22674 ATTTCTGGGG
Statistics
Matches: 80, Mismatches: 11, Indels: 14
0.76 0.10 0.13
Matches are distributed among these distances:
1 7 0.09
2 73 0.91
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.53
Consensus pattern (2 bp):
AT
Found at i:22603 original size:23 final size:23
Alignment explanation
Indices: 22575--22620 Score: 65
Period size: 25 Copynumber: 1.9 Consensus size: 23
22565 AATAATTTAA
*
22575 TATATATATATATATATTATATTTG
1 TATAAATATATA-ATA-TATATTTG
22600 TATAAATATATAATATATATT
1 TATAAATATATAATATATATT
22621 ATTTTAATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 3 0.15
25 11 0.55
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (23 bp):
TATAAATATATAATATATATTTG
Found at i:22656 original size:17 final size:17
Alignment explanation
Indices: 22636--22668 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
22626 AATATTTTTT
22636 ATATAAATATATATATA
1 ATATAAATATATATATA
*
22653 ATATATATATATATAT
1 ATATAAATATATATAT
22669 TTATAATTTC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (17 bp):
ATATAAATATATATATA
Found at i:23300 original size:55 final size:55
Alignment explanation
Indices: 23235--23344 Score: 220
Period size: 55 Copynumber: 2.0 Consensus size: 55
23225 TAAATAACAA
23235 AAAATATAATAAAGATAATAATAATTTTTTTATCATTTCATCTGTAAATATTCAT
1 AAAATATAATAAAGATAATAATAATTTTTTTATCATTTCATCTGTAAATATTCAT
23290 AAAATATAATAAAGATAATAATAATTTTTTTATCATTTCATCTGTAAATATTCAT
1 AAAATATAATAAAGATAATAATAATTTTTTTATCATTTCATCTGTAAATATTCAT
23345 TGAATACATT
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
55 55 1.00
ACGTcount: A:0.45, C:0.07, G:0.04, T:0.44
Consensus pattern (55 bp):
AAAATATAATAAAGATAATAATAATTTTTTTATCATTTCATCTGTAAATATTCAT
Found at i:32288 original size:3 final size:3
Alignment explanation
Indices: 32251--32313 Score: 58
Period size: 3 Copynumber: 21.7 Consensus size: 3
32241 TCTATTGTTT
* * * *
32251 TTA TTA TAA TAA TTA TAA TTA TAA TTA TT- TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* *
32298 TTA ATA TAA TT- TTA TT
1 TTA TTA TTA TTA TTA TT
32314 TATTTTACAG
Statistics
Matches: 48, Mismatches: 10, Indels: 4
0.77 0.16 0.06
Matches are distributed among these distances:
2 4 0.08
3 44 0.92
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (3 bp):
TTA
Found at i:32291 original size:20 final size:20
Alignment explanation
Indices: 32262--32320 Score: 59
Period size: 20 Copynumber: 3.0 Consensus size: 20
32252 TATTATAATA
32262 ATTATAATTATAATTATTTT
1 ATTATAATTATAATTATTTT
* *
32282 ATTATTATTATTATTA--TT
1 ATTATAATTATAATTATTTT
* * *
32300 AATATAATTTTATTTATTTT
1 ATTATAATTATAATTATTTT
32320 A
1 A
32321 CAGGCCCAAA
Statistics
Matches: 30, Mismatches: 7, Indels: 4
0.73 0.17 0.10
Matches are distributed among these distances:
18 13 0.43
20 17 0.57
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (20 bp):
ATTATAATTATAATTATTTT
Found at i:32294 original size:29 final size:29
Alignment explanation
Indices: 32249--32313 Score: 78
Period size: 29 Copynumber: 2.2 Consensus size: 29
32239 GTTCTATTGT
*
32249 TTTTATTATAATAATTATAATT-ATAATTA
1 TTTTATTATAATAATTATAATTAAT-ATAA
* * *
32278 TTTTATTATTATTATTATTATTAATATAA
1 TTTTATTATAATAATTATAATTAATATAA
32307 TTTTATT
1 TTTTATT
32314 TATTTTACAG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
29 29 0.94
30 2 0.06
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (29 bp):
TTTTATTATAATAATTATAATTAATATAA
Found at i:33852 original size:44 final size:44
Alignment explanation
Indices: 33795--33944 Score: 132
Period size: 50 Copynumber: 3.3 Consensus size: 44
33785 ATAAATTCTT
33795 TATTTT-TTATTAATTCGTTTACTTTTATTATACTTATCCATGG
1 TATTTTATTATTAATTCGTTTACTTTTATTATACTTATCCATGG
* * * *
33838 TATTTTATTATTAATATAACGTTAAGTGTGTTAATTAATA-TAAATCC-T-T
1 TATTTTATTATTAAT-T--CGTTTACT-T-TT-ATT-ATACT-TATCCATGG
*
33887 TATTTATTTTATTAATT-GTTTACTTTTA-TATACTTATCCATGG
1 TATTT-TATTATTAATTCGTTTACTTTTATTATACTTATCCATGG
33930 TATTTTATTATTAAT
1 TATTTTATTATTAAT
33945 ATAACGTTAA
Statistics
Matches: 84, Mismatches: 10, Indels: 27
0.69 0.08 0.22
Matches are distributed among these distances:
41 7 0.08
42 12 0.14
43 12 0.14
44 10 0.12
45 2 0.02
46 5 0.06
47 6 0.07
48 1 0.01
49 8 0.10
50 14 0.17
51 7 0.08
ACGTcount: A:0.29, C:0.08, G:0.07, T:0.56
Consensus pattern (44 bp):
TATTTTATTATTAATTCGTTTACTTTTATTATACTTATCCATGG
Found at i:33888 original size:92 final size:93
Alignment explanation
Indices: 33775--33961 Score: 326
Period size: 92 Copynumber: 2.0 Consensus size: 93
33765 TATATAGATA
*
33775 TTAATTAAATATAAATTCTTTA-TT-TTTTATTAATTCGTTTACTTTTATTATACTTATCCATGG
1 TTAATTAAATATAAATCCTTTATTTATTTTATTAATT-GTTTACTTTTA-TATACTTATCCATGG
33838 TATTTTATTATTAATATAACGTTAAGTGTG
64 TATTTTATTATTAATATAACGTTAAGTGTG
33868 TTAATT-AATATAAATCCTTTATTTATTTTATTAATTGTTTACTTTTATATACTTATCCATGGTA
1 TTAATTAAATATAAATCCTTTATTTATTTTATTAATTGTTTACTTTTATATACTTATCCATGGTA
33932 TTTTATTATTAATATAACGTTAAGTGTG
66 TTTTATTATTAATATAACGTTAAGTGTG
33960 TT
1 TT
33962 TATATTGTAG
Statistics
Matches: 91, Mismatches: 1, Indels: 5
0.94 0.01 0.05
Matches are distributed among these distances:
92 61 0.67
93 19 0.21
94 11 0.12
ACGTcount: A:0.31, C:0.07, G:0.07, T:0.54
Consensus pattern (93 bp):
TTAATTAAATATAAATCCTTTATTTATTTTATTAATTGTTTACTTTTATATACTTATCCATGGTA
TTTTATTATTAATATAACGTTAAGTGTG
Found at i:34004 original size:24 final size:24
Alignment explanation
Indices: 33977--34027 Score: 61
Period size: 24 Copynumber: 2.1 Consensus size: 24
33967 TGTAGTTTTA
33977 ATTTTATTTAGT-TATTATTTCATT
1 ATTTTATTT-GTATATTATTTCATT
*
34001 A-TTTATTTGTAATATTATTTTATT
1 ATTTTATTTGT-ATATTATTTCATT
34025 ATT
1 ATT
34028 ATTTTTAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
22 2 0.09
23 7 0.30
24 13 0.57
25 1 0.04
ACGTcount: A:0.27, C:0.02, G:0.04, T:0.67
Consensus pattern (24 bp):
ATTTTATTTGTATATTATTTCATT
Found at i:34018 original size:12 final size:11
Alignment explanation
Indices: 33989--34077 Score: 67
Period size: 12 Copynumber: 7.9 Consensus size: 11
33979 TTTATTTAGT
* *
33989 TATTATTTCAT
1 TATTATTTTAA
34000 TATTTATTTGTAA
1 TA-TTATTT-TAA
*
34013 TATTATTTTAT
1 TATTATTTTAA
34024 TATTATTTTTAA
1 TATTA-TTTTAA
34036 TA-TATTTTAA
1 TATTATTTTAA
*
34046 TTATTACTTT-A
1 -TATTATTTTAA
*
34057 -ATTATTATTAT
1 TATTATT-TTAA
34068 TATTATTTTA
1 TATTATTTTA
34078 TCTTAGTCTT
Statistics
Matches: 63, Mismatches: 7, Indels: 16
0.73 0.08 0.19
Matches are distributed among these distances:
9 5 0.08
10 8 0.13
11 17 0.27
12 30 0.48
13 3 0.05
ACGTcount: A:0.31, C:0.02, G:0.01, T:0.65
Consensus pattern (11 bp):
TATTATTTTAA
Found at i:34026 original size:3 final size:3
Alignment explanation
Indices: 34013--34078 Score: 52
Period size: 3 Copynumber: 23.0 Consensus size: 3
34003 TTATTTGTAA
* *
34013 TAT TAT T-T TAT TAT TAT TTT TAA TA- TAT T-T TAAT TAT TACT T-T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T-AT TAT TA-T TAT
*
34056 AAT TAT TAT TAT TAT TAT T-T TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT
34079 CTTAGTCTTA
Statistics
Matches: 51, Mismatches: 5, Indels: 14
0.73 0.07 0.20
Matches are distributed among these distances:
2 9 0.18
3 38 0.75
4 4 0.08
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:34027 original size:35 final size:33
Alignment explanation
Indices: 33972--34077 Score: 103
Period size: 35 Copynumber: 3.2 Consensus size: 33
33962 TATATTGTAG
*
33972 TTTTAATTTTA-TTTAGTTATTATTTCATTATTTA
1 TTTTAATATTATTTTA-TTATTATTT-ATTATTTA
*
34006 TTTGTAATATTATTTTATTATTATTT-TTAATATA
1 TTT-TAATATTATTTTATTATTATTTATT-ATTTA
*
34040 TTTTAATTATTACTTTAATTATTA-TTATTA-TTA
1 TTTTAA-TATTA-TTTTATTATTATTTATTATTTA
34073 TTTTA
1 TTTTA
34078 TCTTAGTCTT
Statistics
Matches: 62, Mismatches: 4, Indels: 13
0.78 0.05 0.16
Matches are distributed among these distances:
33 12 0.19
34 18 0.29
35 28 0.45
36 4 0.06
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.66
Consensus pattern (33 bp):
TTTTAATATTATTTTATTATTATTTATTATTTA
Found at i:34500 original size:127 final size:125
Alignment explanation
Indices: 34272--34502 Score: 311
Period size: 127 Copynumber: 1.8 Consensus size: 125
34262 ATCATATTTA
* * * * *
34272 TATTTATATGTTTTTTAATATTAAGAAATGTGCTGTCTTAAAGCACATAGAAGTCCTTTTCTGAT
1 TATTTATATATTTTTTAATATGAAGAAAAGAGCTGTCTTAAAGCACATAGAAGTCATTTTCTGAT
34337 ATTCAAATAATAAATATCTTACTTTTATAAATTATATCTACTTTTAAATAAATGTTTTAAT
66 ATTCAAATAATAAATATCTTAC-TTTATAAATTATATCTACTTTTAAATAAATGTTTTAAT
* * *
34398 TATTTATTTATTTTTTAATATCGAAGAAAAGAGCTGTCTTAAGGCACCTAGAAGTCATTTTCTGA
1 TATTTATATATTTTTTAATAT-GAAGAAAAGAGCTGTCTTAAAGCACATAGAAGTCATTTTCTGA
* *
34463 TATTTCTAAATAAATAAATATTTTA-TTTATATATATATAT
65 TA-TTC-AAAT-AATAAATATCTTACTTTATAAAT-TATAT
34503 AAATTAATAT
Statistics
Matches: 90, Mismatches: 10, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
126 19 0.21
127 39 0.43
128 11 0.12
129 9 0.10
130 12 0.13
ACGTcount: A:0.37, C:0.09, G:0.09, T:0.45
Consensus pattern (125 bp):
TATTTATATATTTTTTAATATGAAGAAAAGAGCTGTCTTAAAGCACATAGAAGTCATTTTCTGAT
ATTCAAATAATAAATATCTTACTTTATAAATTATATCTACTTTTAAATAAATGTTTTAAT
Found at i:36688 original size:27 final size:27
Alignment explanation
Indices: 36652--36711 Score: 86
Period size: 27 Copynumber: 2.3 Consensus size: 27
36642 CATTCACATA
36652 TTTACATTTGCATTTACATTTGCATTT
1 TTTACATTTGCATTTACATTTGCATTT
* * *
36679 TTTACGTTTGTATTTACATTTTCA-TT
1 TTTACATTTGCATTTACATTTGCATTT
36705 TTTACAT
1 TTTACAT
36712 AATTACATTT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
26 8 0.28
27 21 0.72
ACGTcount: A:0.22, C:0.13, G:0.07, T:0.58
Consensus pattern (27 bp):
TTTACATTTGCATTTACATTTGCATTT
Found at i:36705 original size:12 final size:12
Alignment explanation
Indices: 36651--36678 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
36641 ACATTCACAT
36651 ATTTACATTTGC
1 ATTTACATTTGC
36663 ATTTACATTTGC
1 ATTTACATTTGC
36675 ATTT
1 ATTT
36679 TTTACGTTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.25, C:0.14, G:0.07, T:0.54
Consensus pattern (12 bp):
ATTTACATTTGC
Found at i:38643 original size:14 final size:13
Alignment explanation
Indices: 38621--38683 Score: 63
Period size: 13 Copynumber: 4.6 Consensus size: 13
38611 AAAGAAAGAG
38621 AAGGAAAAAAGAAA
1 AAGGAAAAAA-AAA
38635 AAGGGAAAAAAAAAA
1 AA-GG-AAAAAAAAA
**
38650 AAAAAAAAAAAAA
1 AAGGAAAAAAAAA
**
38663 AAAAAAAAAAAAA
1 AAGGAAAAAAAAA
38676 AAGGAAAA
1 AAGGAAAA
38684 TTGAATCAAG
Statistics
Matches: 43, Mismatches: 4, Indels: 5
0.83 0.08 0.10
Matches are distributed among these distances:
13 28 0.65
14 2 0.05
15 7 0.16
16 6 0.14
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (13 bp):
AAGGAAAAAAAAA
Found at i:38643 original size:15 final size:14
Alignment explanation
Indices: 38623--38683 Score: 54
Period size: 14 Copynumber: 4.4 Consensus size: 14
38613 AGAAAGAGAA
38623 GGAAAAAAGAAAAAG
1 GGAAAAAA-AAAAAG
38638 GGAAAAAAAAAAA-
1 GGAAAAAAAAAAAG
* *
38651 -AAAAAAAAAAAAA
1 GGAAAAAAAAAAAG
** *
38664 AAAAAAAAAAAAAA
1 GGAAAAAAAAAAAG
38678 GGAAAA
1 GGAAAA
38684 TTGAATCAAG
Statistics
Matches: 41, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
12 11 0.27
14 22 0.54
15 8 0.20
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (14 bp):
GGAAAAAAAAAAAG
Found at i:38644 original size:1 final size:1
Alignment explanation
Indices: 38640--38677 Score: 76
Period size: 1 Copynumber: 38.0 Consensus size: 1
38630 AGAAAAAGGG
38640 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
38678 GGAAAATTGA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 37 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:44367 original size:112 final size:112
Alignment explanation
Indices: 43982--44386 Score: 559
Period size: 112 Copynumber: 3.6 Consensus size: 112
43972 TAGCAAAGAT
* * * **
43982 TTAAATCCATCACTTGATGGATCAATATTTCCAGA-AGTGTTCATAATGAGAAGAACTCATCTGA
1 TTAAATTCATCACTTGATGGATTAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
* * *
44046 AGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTTAACCTTTTGC
66 AGAAGG-AGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
* ** * *
44094 TCAAATTCATCACTTGATGGACCACCATTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTGA
1 TTAAATTCATCACTTGATGGATTAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
44159 AG-AGGAGAAAGAAATTCATAAT--GAAGAATTTGTTCAACC-TTTGC
66 AGAAGGAG-AAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
* * * *
44203 CTGAATTCATCACTTGATGGATTAACTTTTCCAGAGGAAGTTCATAATGAGAAGAACTCATCTGA
1 TTAAATTCATCACTTGATGGATTAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
44268 AGAAGGAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
66 AGAAGGAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
* ** * *
44315 TTTAATTCATCACCCGATGGATTAGCATTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
1 TTAAATTCATCACTTGATGGATTAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
44380 AGAAGGA
66 AGAAGGA
44387 AGATGAAGTT
Statistics
Matches: 259, Mismatches: 28, Indels: 12
0.87 0.09 0.04
Matches are distributed among these distances:
109 77 0.30
110 20 0.08
111 19 0.07
112 115 0.44
113 28 0.11
ACGTcount: A:0.38, C:0.15, G:0.19, T:0.28
Consensus pattern (112 bp):
TTAAATTCATCACTTGATGGATTAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
AGAAGGAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
Found at i:44399 original size:24 final size:24
Alignment explanation
Indices: 44372--44423 Score: 95
Period size: 24 Copynumber: 2.2 Consensus size: 24
44362 TGAGAAGAAC
*
44372 TCATCTGAAGAAGGAAGATGAAGT
1 TCATCTGAAGAAGGAAGATAAAGT
44396 TCATCTGAAGAAGGAAGATAAAGT
1 TCATCTGAAGAAGGAAGATAAAGT
44420 TCAT
1 TCAT
44424 AATGAGAAGA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.42, C:0.10, G:0.25, T:0.23
Consensus pattern (24 bp):
TCATCTGAAGAAGGAAGATAAAGT
Found at i:44407 original size:221 final size:221
Alignment explanation
Indices: 43989--44910 Score: 670
Period size: 221 Copynumber: 4.0 Consensus size: 221
43979 GATTTAAATC
*
43989 CATCACTTGATGGATCAATATTTCCAGAAGTGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
1 CATCACTTGATGGATCAATATTTCCAGAAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
* * **
44054 GAAGAAGTTCATAATGAGAAGAACTTGTTTAACCTTTTGCTCAAATTCATCACTTGATGGACCAC
66 GAAGAAATTCATAATGAGAAGAACTTGTTCAACCTTTTGCTCAAATTCATCACCCGATGGACCAC
* *
44119 CATTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTGAAGAGGAGAAAGAAATTCATAATGAA
131 CATTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAGGAGAAAGAAATTCATAATGAA
44184 GAATTTGTTCAACCTTTGCCTGAATT
196 GAATTTGTTCAACCTTTGCCTGAATT
* *
44210 CATCACTTGATGGATTAACT-TTTCCAGAGGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGG
1 CATCACTTGATGGATCAA-TATTTCCAGAAG-AGTTCATAATGAGAAGAACTCATCTGAAGAAGG
* ** **
44274 -AGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTTTAATTCATCACCCGATGGATT
64 AAGAAGAAATTCATAATGAGAAGAACTTGTTCAACCTTTTGCTCAAATTCATCACCCGATGGACC
* * *
44338 AGCATTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA-AGATGAAGTTCATCT
129 ACCATTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG-AGGAGA-AAGAAATTCA--T
** * ** **
44402 GAA-GAAGGAAGATAAAGTTCATA-ATGAG-AAGAACTT
190 -AATGAA-G-A-AT-TTGTTCA-ACCTTTGCCTGAA-TT
** * ** * ** * * * *
44438 GTTCAACCTTTTGCTCAAATCCATCACTTGATGGATCAACATTTCCAGAAGTGTTCATAATGATA
1 CATC-A-C--TTGAT-GGATCAAT-A-TT--TCCA-GAAGAGTT-CATAA-TG------A-G--A
* * *
44503 AGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTTAACCTTTTGCTCGA
45 AGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAACTTGTTCAACCTTTTGCTCAA
** * * * * * * * *
44568 ATTCATCACTTGATAGATCAACATTTCTAGAGAAAGTTCATAATGAGACGAACTTATCTAAAGAG
110 ATTCATCACCCGATGGACCACCATTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAG
44633 GA-AGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCCTGAATT
175 GAGA-AAGAAATTCATAAT--GAAGAATTTGTTCAACC-TTTGCCTGAATT
* * * *
44683 CATCACTTGATGAATTAACT-TTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTGAAG-AGG
1 CATCACTTGATGGATCAA-TATTTCCAGA-AGAGTTCATAATGAGAAGAACTCATCTGAAGAAGG
* * * * ** ***
44746 AAGAAGAAGTTCAT-A--AGAAGAATTTGTTCAACCTTTGTTTGACTC-TATCACAGAAGGAGAT
64 AAGAAGAAATTCATAATGAGAAGAACTTGTTCAACC--T-TTTG-CTCAAAT-TCATCACCCGAT
* * * * **
44807 AGATCAACATTTCCAGA-AGTGTTCATAATGAGAAGAACTCATCTGAAGAAGGAG-AAGAAATTC
124 GGACCACCATTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG-AGGAGAAAGAAATTC
*
44870 ATAATGAGAAGAATTTGTTCAACC-TTGCCTTAATT
188 ATAAT--GAAGAATTTGTTCAACCTTTGCCTGAATT
*
44905 TATCAC
1 CATCAC
44911 ATATGAAGTT
Statistics
Matches: 558, Mismatches: 92, Indels: 101
0.74 0.12 0.13
Matches are distributed among these distances:
221 139 0.25
222 60 0.11
223 2 0.00
224 86 0.15
225 47 0.08
226 1 0.00
227 6 0.01
228 12 0.02
229 2 0.00
230 1 0.00
232 5 0.01
233 3 0.01
234 2 0.00
235 7 0.01
236 6 0.01
237 5 0.01
238 7 0.01
239 2 0.00
240 4 0.01
241 5 0.01
243 2 0.00
244 6 0.01
245 11 0.02
246 6 0.01
247 1 0.00
248 37 0.07
249 93 0.17
ACGTcount: A:0.38, C:0.15, G:0.19, T:0.28
Consensus pattern (221 bp):
CATCACTTGATGGATCAATATTTCCAGAAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
GAAGAAATTCATAATGAGAAGAACTTGTTCAACCTTTTGCTCAAATTCATCACCCGATGGACCAC
CATTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAGGAGAAAGAAATTCATAATGAA
GAATTTGTTCAACCTTTGCCTGAATT
Found at i:44434 original size:27 final size:24
Alignment explanation
Indices: 44372--44432 Score: 79
Period size: 24 Copynumber: 2.5 Consensus size: 24
44362 TGAGAAGAAC
* *
44372 TCATCTGAAGAAGGAAGATGAAGT
1 TCATATGAAGAAGGAAGATAAAGT
*
44396 TCATCTGAAGAAGGAAGATAAAGT
1 TCATATGAAGAAGGAAGATAAAGT
44420 TCATAATG-AGAAG
1 TCAT-ATGAAGAAG
44433 AACTTGTTCA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
24 32 0.94
25 2 0.06
ACGTcount: A:0.44, C:0.08, G:0.26, T:0.21
Consensus pattern (24 bp):
TCATATGAAGAAGGAAGATAAAGT
Found at i:44531 original size:136 final size:136
Alignment explanation
Indices: 44252--44535 Score: 394
Period size: 137 Copynumber: 2.1 Consensus size: 136
44242 GTTCATAATG
* *
44252 AGAAGAA-CTCATCTGAAGAAGGAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCT
1 AGAAGAAGTTCATCTGAAGAAGGAGAAGAAATTCATAATGAGAAGAACTTGTTCAACCTTTTGCT
** * * *
44316 TTAATTCATCACCCGATGGATTAGCATTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAA
66 CAAATCCATCACCCGATGGATCAACATTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAA
44381 GAAGGA
131 GAAGGA
* *
44387 AGATGAAGTTCATCTGAAGAAGGAAGATA-AAGTTCATAATGAGAAGAACTTGTTCAACCTTTTG
1 AGAAGAAGTTCATCTGAAGAAGG-AGA-AGAAATTCATAATGAGAAGAACTTGTTCAACCTTTTG
** * ** *
44451 CTCAAATCCATCACTTGATGGATCAACATTTCCAGA-AGTGTTCATAATGATAAGAACTCATCTG
64 CTCAAATCCATCACCCGATGGATCAACATTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTG
44515 AAGAAGGA
129 AAGAAGGA
44523 AGAAGAAGTTCAT
1 AGAAGAAGTTCAT
44536 AATGAGAAGA
Statistics
Matches: 130, Mismatches: 16, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
135 6 0.05
136 59 0.45
137 64 0.49
138 1 0.01
ACGTcount: A:0.39, C:0.15, G:0.20, T:0.26
Consensus pattern (136 bp):
AGAAGAAGTTCATCTGAAGAAGGAGAAGAAATTCATAATGAGAAGAACTTGTTCAACCTTTTGCT
CAAATCCATCACCCGATGGATCAACATTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAA
GAAGGA
Found at i:44593 original size:112 final size:113
Alignment explanation
Indices: 44396--44895 Score: 603
Period size: 112 Copynumber: 4.5 Consensus size: 113
44386 AAGATGAAGT
* * *
44396 TCATCTGAAGAAGGAAGATA-AAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTCAAATCC
1 TCATCTGAAGAAGGAAGA-AGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCGAATTC
* ** *
44460 ATCACTTGATGGATCAACATTTCCAGA-AGTGTTCATAATGATAAGAAC
65 ATCACTTGATAGATCAACATTTCCAGAGAAAGTTCATAATGAGAAGAAC
* *
44508 TCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTTAACCTTTTGCTCGAATTCA
1 TCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCGAATTCA
* *
44573 TCACTTGATAGATCAACATTTCTAGAGAAAGTTCATAATGAGACGAAC
66 TCACTTGATAGATCAACATTTCCAGAGAAAGTTCATAATGAGAAGAAC
* * *
44621 TTATCTAAAG-AGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC-CTGAATTC
1 TCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC-GAATTC
* *
44684 ATCACTTGAT-GAATTAACTTTTCCAGAGAAAGTTCATAATGAGAAGAAC
65 ATCACTTGATAG-ATCAACATTTCCAGAGAAAGTTCATAATGAGAAGAAC
* * * *
44733 TTATCTGAAG-AGGAAGAAGAAGTTCAT-A--AGAAGAATTTGTTCAACC-TTTGTTTG-ACTCT
1 TCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCGAATTC-
** **
44792 ATCACAGAAGGAGATAGATCAACATTTCCAGA-AGTGTTCATAATGAGAAGAAC
65 ATCAC-----TTGATAGATCAACATTTCCAGAGAAAGTTCATAATGAGAAGAAC
*
44845 TCATCTGAAGAAGG-AGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTT
1 TCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTT
44896 GCCTTAATTT
Statistics
Matches: 340, Mismatches: 31, Indels: 30
0.85 0.08 0.07
Matches are distributed among these distances:
107 3 0.01
108 10 0.03
109 18 0.05
111 4 0.01
112 240 0.71
113 45 0.13
114 1 0.00
115 18 0.05
116 1 0.00
ACGTcount: A:0.39, C:0.14, G:0.18, T:0.29
Consensus pattern (113 bp):
TCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCGAATTCA
TCACTTGATAGATCAACATTTCCAGAGAAAGTTCATAATGAGAAGAAC
Found at i:44716 original size:361 final size:357
Alignment explanation
Indices: 44030--44759 Score: 1067
Period size: 361 Copynumber: 2.0 Consensus size: 357
44020 GTTCATAATG
* *
44030 AGAAGAA-CTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTTAACCTTTTGC
1 AGAAGAAGTTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGC
* * *
44094 TCAAATTCATCACTTGATGGACCACCATTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTGA
66 TCAAATCCATCACTTGATGGACCAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
* *
44159 AGAGGAGAAAGAAATTCATAATGAAGAATTTGTTCAACCTTTGCCTGAATTCATCACTTGATGGA
131 AGAGGAGAAAGAAATTCATAATGAAGAACTTGTTCAACCTTTGCCTGAATTCATCACTTGATAGA
* * * *
44224 TTAACTTTTCCAGAGGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAGAAGAAATTCATAA
196 TCAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTAAAGAAGGAGAAGAAATTCATAA
* * * *
44289 TGAGAAGAATTTGTTCAACCTTTTGCTTTAATTCATCACCCGATGGATTAGCATTGCCAGAGAAA
261 TGAGAAGAATTTGTTCAACCTTTTGCCTGAATTCATCACCCGATGAATTAACATTGCCAGAGAAA
44354 GTTCATAATGAGAAGAACTCATCTGAAGAAGGA
326 GTTCATAATGAGAAGAACTCATCTGAAG-AGGA
*
44387 AGATGAAGTTCATCTGAAGAAGGAAGATA-AAGTTCATAATGAGAAGAACTTGTTCAACCTTTTG
1 AGAAGAAGTTCATCTGAAGAAGGAAGA-AGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTG
* ** *
44451 CTCAAATCCATCACTTGATGGATCAACATTTCCAGA-AGTGTTCATAATGATAAGAACTCATCTG
65 CTCAAATCCATCACTTGATGGACCAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTG
* *
44515 AAGAAGGA-AGAAGAAGTTCATAATGAGAAGAACTTGTTTAACCTTTTG-CTCGAATTCATCACT
130 AAG-AGGAGA-AAGAAATTCATAAT--GAAGAACTTGTTCAACC-TTTGCCT-GAATTCATCACT
* * *
44578 TGATAGATCAACATTTCTAGAGAAAGTTCATAATGAGACGAACTTATCTAAAG-AGGAAGAAGAA
189 TGATAGATCAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTAAAGAAGG-AGAAGAA
** * *
44642 ATTCATAATGAGAAGAATTTGTTCAACCTTTTGCCTGAATTCATCACTTGATGAATTAACTTTTC
253 ATTCATAATGAGAAGAATTTGTTCAACCTTTTGCCTGAATTCATCACCCGATGAATTAACATTGC
*
44707 CAGAGAAAGTTCATAATGAGAAGAACTTATCTGAAGAGGA
318 CAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAGGA
44747 AGAAGAAGTTCAT
1 AGAAGAAGTTCAT
44760 AAGAAGAATT
Statistics
Matches: 333, Mismatches: 31, Indels: 15
0.88 0.08 0.04
Matches are distributed among these distances:
357 34 0.10
358 102 0.31
359 1 0.00
360 36 0.11
361 160 0.48
ACGTcount: A:0.38, C:0.15, G:0.19, T:0.28
Consensus pattern (357 bp):
AGAAGAAGTTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGC
TCAAATCCATCACTTGATGGACCAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
AGAGGAGAAAGAAATTCATAATGAAGAACTTGTTCAACCTTTGCCTGAATTCATCACTTGATAGA
TCAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTAAAGAAGGAGAAGAAATTCATAA
TGAGAAGAATTTGTTCAACCTTTTGCCTGAATTCATCACCCGATGAATTAACATTGCCAGAGAAA
GTTCATAATGAGAAGAACTCATCTGAAGAGGA
Found at i:46847 original size:90 final size:96
Alignment explanation
Indices: 46693--46882 Score: 329
Period size: 90 Copynumber: 2.0 Consensus size: 96
46683 ATTATAGATA
46693 TTAATTAAATATAAATCTCTTTTATTTATTTATTAATTCGTTTACTTTTATTATACTTATCCATG
1 TTAATTAAATATAAATCTCTTTTATTTATTTATTAATTCGTTTACTTTTATTATACTTATCCATG
46758 GTA-TT-TTATT-ATATAACGTTAAGTGTGT
66 GTATTTATTATTAATATAACGTTAAGTGTGT
46786 TTAATT-AATATAAATCTCTTTTA-TTATTTATTAATTCG-TTACTTTTATTATACTTATCCATG
1 TTAATTAAATATAAATCTCTTTTATTTATTTATTAATTCGTTTACTTTTATTATACTTATCCATG
46848 GTATTTTATTATTAATATAACGTTAAGTGTGT
66 GTA-TTTATTATTAATATAACGTTAAGTGTGT
46880 TTA
1 TTA
46883 TTGTAGTGTA
Statistics
Matches: 93, Mismatches: 0, Indels: 7
0.93 0.00 0.07
Matches are distributed among these distances:
90 27 0.29
91 15 0.16
92 19 0.20
93 11 0.12
94 21 0.23
ACGTcount: A:0.31, C:0.08, G:0.07, T:0.54
Consensus pattern (96 bp):
TTAATTAAATATAAATCTCTTTTATTTATTTATTAATTCGTTTACTTTTATTATACTTATCCATG
GTATTTATTATTAATATAACGTTAAGTGTGT
Found at i:46943 original size:11 final size:11
Alignment explanation
Indices: 46927--46991 Score: 78
Period size: 11 Copynumber: 5.8 Consensus size: 11
46917 TATTTATTTG
46927 TATTATTTTAT
1 TATTATTTTAT
46938 TATTATTTT-T
1 TATTATTTTAT
*
46948 AATATATTTTAAT
1 TAT-TATTTT-AT
* *
46961 TATTACTTAAT
1 TATTATTTTAT
46972 TATTATTTTAT
1 TATTATTTTAT
46983 TATTATTTT
1 TATTATTTT
46992 TATCTTAGTC
Statistics
Matches: 45, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
10 3 0.07
11 35 0.78
12 4 0.09
13 3 0.07
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.68
Consensus pattern (11 bp):
TATTATTTTAT
Found at i:46990 original size:34 final size:33
Alignment explanation
Indices: 46891--46991 Score: 86
Period size: 34 Copynumber: 3.0 Consensus size: 33
46881 TATTGTAGTG
* *
46891 TAATT-TTATTTAGTTATTTATTTCATTATTTATTT
1 TAATTATTA-TTAATTA-TTATTTTATTA-TTATTT
*
46926 GT-ATTATT-TT-ATTATTATTTT-TAATATATTT
1 -TAATTATTATTAATTATTATTTTATTAT-TATTT
46957 TAATTATTACTTAATTATTATTTTATTATTATTT
1 TAATTATTA-TTAATTATTATTTTATTATTATTT
46991 T
1 T
46992 TATCTTAGTC
Statistics
Matches: 54, Mismatches: 4, Indels: 16
0.73 0.05 0.22
Matches are distributed among these distances:
30 2 0.04
31 13 0.24
32 6 0.11
33 5 0.09
34 19 0.35
35 6 0.11
36 3 0.06
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.67
Consensus pattern (33 bp):
TAATTATTATTAATTATTATTTTATTATTATTT
Found at i:47424 original size:25 final size:23
Alignment explanation
Indices: 47391--47443 Score: 61
Period size: 23 Copynumber: 2.2 Consensus size: 23
47381 ATATTTTCTA
*
47391 AATAAATAAATATTTTATTTATAAT
1 AATAAAT-AATATTTT-TTCATAAT
*
47416 AATATATAATATTTTTTCATAAT
1 AATAAATAATATTTTTTCATAAT
*
47439 TATAA
1 AATAA
47444 TTTTGAAATA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
23 10 0.42
24 8 0.33
25 6 0.25
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (23 bp):
AATAAATAATATTTTTTCATAAT
Found at i:64149 original size:39 final size:39
Alignment explanation
Indices: 64073--64156 Score: 107
Period size: 39 Copynumber: 2.2 Consensus size: 39
64063 CCAAAGCTCA
* * * *
64073 TCTTAGCCTGAGCACGAAGTAGAGGTGCCTACGGTAAGG
1 TCTTAGCCTGAGCACAAAGCAGAGGAGCCTACAGTAAGG
*
64112 TCTTAGCCTGAGCACAAAGCAG-GAGAGCCTGCAGTAAGG
1 TCTTAGCCTGAGCACAAAGCAGAG-GAGCCTACAGTAAGG
64151 TCTTAG
1 TCTTAG
64157 TAGTCCTAGA
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
38 1 0.03
39 38 0.97
ACGTcount: A:0.27, C:0.21, G:0.31, T:0.20
Consensus pattern (39 bp):
TCTTAGCCTGAGCACAAAGCAGAGGAGCCTACAGTAAGG
Found at i:65905 original size:18 final size:18
Alignment explanation
Indices: 65882--65924 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
65872 TCTTAAAATA
65882 AGTCAACACCCGGTCAAC
1 AGTCAACACCCGGTCAAC
***
65900 AGTCAACGGTCGGTCAAC
1 AGTCAACACCCGGTCAAC
65918 AGTCAAC
1 AGTCAAC
65925 GGACAATCAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.33, C:0.33, G:0.21, T:0.14
Consensus pattern (18 bp):
AGTCAACACCCGGTCAAC
Found at i:65925 original size:18 final size:18
Alignment explanation
Indices: 65892--65926 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
65882 AGTCAACACC
65892 CGGTCAACAGTCAACGGT
1 CGGTCAACAGTCAACGGT
65910 CGGTCAACAGTCAACGG
1 CGGTCAACAGTCAACGG
65927 ACAATCAAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.29, C:0.29, G:0.29, T:0.14
Consensus pattern (18 bp):
CGGTCAACAGTCAACGGT
Found at i:65934 original size:18 final size:18
Alignment explanation
Indices: 65895--65934 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
65885 CAACACCCGG
* **
65895 TCAACAGTCAACGGTCGG
1 TCAACAGTCAACGGACAA
65913 TCAACAGTCAACGGACAA
1 TCAACAGTCAACGGACAA
65931 TCAA
1 TCAA
65935 AGGTCAACTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.38, C:0.28, G:0.20, T:0.15
Consensus pattern (18 bp):
TCAACAGTCAACGGACAA
Found at i:67439 original size:20 final size:20
Alignment explanation
Indices: 67416--67508 Score: 116
Period size: 20 Copynumber: 4.7 Consensus size: 20
67406 GTTTTCAGAT
*
67416 TCGCAATGCGATTTTGACTA
1 TCGCAATGCGATTCTGACTA
* * *
67436 TCGCAATGCGAATATGTA-AA
1 TCGCAATGCGATTCTG-ACTA
*
67456 TCGCAACGCGATTCTGACTA
1 TCGCAATGCGATTCTGACTA
*
67476 TCGCAACGCGATTCTGACTA
1 TCGCAATGCGATTCTGACTA
67496 TCGCAATGCGATT
1 TCGCAATGCGATT
67509 TTCCAAATTT
Statistics
Matches: 63, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
19 1 0.02
20 61 0.97
21 1 0.02
ACGTcount: A:0.28, C:0.24, G:0.20, T:0.28
Consensus pattern (20 bp):
TCGCAATGCGATTCTGACTA
Found at i:67547 original size:19 final size:20
Alignment explanation
Indices: 67523--67563 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 20
67513 AAATTTACGT
67523 TAGTCCAAATT-CGTTGCGA
1 TAGTCCAAATTACGTTGCGA
*
67542 TAGTCCAAGTTCACGTTGCGA
1 TAGTCCAAATT-ACGTTGCGA
67563 T
1 T
67564 TTTTTAAGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 10 0.53
21 9 0.47
ACGTcount: A:0.24, C:0.22, G:0.22, T:0.32
Consensus pattern (20 bp):
TAGTCCAAATTACGTTGCGA
Found at i:68005 original size:19 final size:20
Alignment explanation
Indices: 67973--68015 Score: 70
Period size: 19 Copynumber: 2.2 Consensus size: 20
67963 ACAACACGTT
*
67973 TTTTAAACTCTCGCAACACA
1 TTTTAAACTATCGCAACACA
67993 TTTT-AACTATCGCAACACA
1 TTTTAAACTATCGCAACACA
68012 TTTT
1 TTTT
68016 TCAAAATCGT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 18 0.82
20 4 0.18
ACGTcount: A:0.33, C:0.26, G:0.05, T:0.37
Consensus pattern (20 bp):
TTTTAAACTATCGCAACACA
Found at i:70580 original size:3 final size:3
Alignment explanation
Indices: 70572--70605 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
70562 CACATCCTAC
70572 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
70606 TAACTTATCA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TCT
Found at i:77259 original size:18 final size:19
Alignment explanation
Indices: 77224--77259 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
77214 AAATGAAGAT
77224 TTTCAAAGATTTAGGTTTA
1 TTTCAAAGATTTAGGTTTA
*
77243 TTTCAAA-ATTTATGTTT
1 TTTCAAAGATTTAGGTTT
77260 TCTTTTTAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.31, C:0.06, G:0.11, T:0.53
Consensus pattern (19 bp):
TTTCAAAGATTTAGGTTTA
Found at i:77618 original size:20 final size:20
Alignment explanation
Indices: 77593--77634 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
77583 TATAAAAATA
77593 AATGTATGAACTTTGTCTTG
1 AATGTATGAACTTTGTCTTG
77613 AATGTATGAACTTTGTCTTG
1 AATGTATGAACTTTGTCTTG
77633 AA
1 AA
77635 AAACATTTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.29, C:0.10, G:0.19, T:0.43
Consensus pattern (20 bp):
AATGTATGAACTTTGTCTTG
Found at i:77827 original size:19 final size:19
Alignment explanation
Indices: 77798--77837 Score: 64
Period size: 19 Copynumber: 2.1 Consensus size: 19
77788 TTTTTTTTTC
77798 ATTTTTCATTAAAAAATAAT
1 ATTTTTCATTAAAAAA-AAT
77818 ATTTTT-ATTAAAAAAAAT
1 ATTTTTCATTAAAAAAAAT
77836 AT
1 AT
77838 AACGGTAGCC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 5 0.25
19 9 0.45
20 6 0.30
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.45
Consensus pattern (19 bp):
ATTTTTCATTAAAAAAAAT
Found at i:79078 original size:53 final size:53
Alignment explanation
Indices: 78998--79101 Score: 208
Period size: 53 Copynumber: 2.0 Consensus size: 53
78988 TATAAATGCA
78998 ATGAACGCGTTGACCGGGTAGTGGCACAAATAATAAATAACTCAATGGAGACT
1 ATGAACGCGTTGACCGGGTAGTGGCACAAATAATAAATAACTCAATGGAGACT
79051 ATGAACGCGTTGACCGGGTAGTGGCACAAATAATAAATAACTCAATGGAGA
1 ATGAACGCGTTGACCGGGTAGTGGCACAAATAATAAATAACTCAATGGAGA
79102 TTAGGGTTTA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 51 1.00
ACGTcount: A:0.38, C:0.16, G:0.25, T:0.20
Consensus pattern (53 bp):
ATGAACGCGTTGACCGGGTAGTGGCACAAATAATAAATAACTCAATGGAGACT
Found at i:79477 original size:35 final size:35
Alignment explanation
Indices: 79422--79493 Score: 117
Period size: 35 Copynumber: 2.1 Consensus size: 35
79412 GAGTCGAATA
* *
79422 TCAAGTAGTTTGTTTTGGCTCGTTAATAACTCGAG
1 TCAAGTAGTTCGTTTCGGCTCGTTAATAACTCGAG
*
79457 TCAAGTAGTTCGTTTCGGCTCGTTAATAATTCGAG
1 TCAAGTAGTTCGTTTCGGCTCGTTAATAACTCGAG
79492 TC
1 TC
79494 GAGTTCGAGT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.22, C:0.17, G:0.22, T:0.39
Consensus pattern (35 bp):
TCAAGTAGTTCGTTTCGGCTCGTTAATAACTCGAG
Found at i:81168 original size:60 final size:60
Alignment explanation
Indices: 81033--81168 Score: 150
Period size: 60 Copynumber: 2.3 Consensus size: 60
81023 TGGTCGAGTA
* * * *
81033 ACCATTTTGTAACTTTTAATAGTCGATGAACTCAACAAAATAATGTCATATAGTCTAAAG
1 ACCATTTTATAATTTTTAATAGTCGATGAACTCAACAAAATAACGTCATATAGTCGAAAG
* * * * * *
81093 ACTATTTTATAATTTTTAATAGTTGATGAACTCAACAAAGTAGCGT-ATTATATTCGAAGG
1 ACCATTTTATAATTTTTAATAGTCGATGAACTCAACAAAATAACGTCA-TATAGTCGAAAG
81153 ACCA-TTTATATATTTT
1 ACCATTTTATA-ATTTT
81169 ACCTAAATAT
Statistics
Matches: 63, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
59 7 0.11
60 56 0.89
ACGTcount: A:0.38, C:0.12, G:0.12, T:0.38
Consensus pattern (60 bp):
ACCATTTTATAATTTTTAATAGTCGATGAACTCAACAAAATAACGTCATATAGTCGAAAG
Found at i:101795 original size:23 final size:20
Alignment explanation
Indices: 101764--101820 Score: 51
Period size: 20 Copynumber: 2.7 Consensus size: 20
101754 CTATGAGATT
*
101764 TATCTCGAATGACCACTATGAAA
1 TATCCCGAATGACCAC--TG-AA
* * *
101787 TATCCCGAAGGATCACTGTA
1 TATCCCGAATGACCACTGAA
101807 TATCCCGAATGACC
1 TATCCCGAATGACC
101821 GCGTAGACCC
Statistics
Matches: 28, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
20 13 0.46
21 2 0.07
23 13 0.46
ACGTcount: A:0.33, C:0.26, G:0.16, T:0.25
Consensus pattern (20 bp):
TATCCCGAATGACCACTGAA
Found at i:124982 original size:16 final size:17
Alignment explanation
Indices: 124958--124990 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
124948 TTCTCTTAAA
*
124958 GTTTTGGAT-AAAATGG
1 GTTTCGGATCAAAATGG
124974 GTTTCGGATCAAAATGG
1 GTTTCGGATCAAAATGG
124991 TGTAGCTGGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.30, C:0.06, G:0.30, T:0.33
Consensus pattern (17 bp):
GTTTCGGATCAAAATGG
Done.