Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006320.1 Hibiscus syriacus cultivar Beakdansim tig00015100_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: 89180
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:1396 original size:20 final size:19
Alignment explanation
Indices: 1373--1412 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
1363 TCTGAAACTT
1373 AAAATCGTAACACGAAAATG
1 AAAATCG-AACACGAAAATG
*
1393 AAAATCGCACACGAAAATG
1 AAAATCGAACACGAAAATG
1412 A
1 A
1413 CTATCGCAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 12 0.63
20 7 0.37
ACGTcount: A:0.55, C:0.17, G:0.15, T:0.12
Consensus pattern (19 bp):
AAAATCGAACACGAAAATG
Found at i:1418 original size:19 final size:19
Alignment explanation
Indices: 1382--1440 Score: 64
Period size: 19 Copynumber: 3.1 Consensus size: 19
1372 TAAAATCGTA
**
1382 ACACGAAAATGAAAATCGC
1 ACACGAAAATGACTATCGC
1401 ACACGAAAATGACTATCGC
1 ACACGAAAATGACTATCGC
* **
1420 AACGCGAATTTGACTATCGC
1 -ACACGAAAATGACTATCGC
1440 A
1 A
1441 ACGCGAAACT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
19 18 0.53
20 16 0.47
ACGTcount: A:0.42, C:0.24, G:0.17, T:0.17
Consensus pattern (19 bp):
ACACGAAAATGACTATCGC
Found at i:1433 original size:20 final size:20
Alignment explanation
Indices: 1410--1447 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
1400 CACACGAAAA
1410 TGACTATCGCAACGCGAATT
1 TGACTATCGCAACGCGAATT
1430 TGACTATCGCAACGCGAA
1 TGACTATCGCAACGCGAA
1448 ACTAAAATCG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.32, C:0.26, G:0.21, T:0.21
Consensus pattern (20 bp):
TGACTATCGCAACGCGAATT
Found at i:2086 original size:20 final size:20
Alignment explanation
Indices: 2060--2197 Score: 154
Period size: 20 Copynumber: 6.9 Consensus size: 20
2050 ACGCTTTGAA
2060 AATCGCATTGCGATAGTCAG
1 AATCGCATTGCGATAGTCAG
*
2080 CATCGCATTGCGATAGTCA-
1 AATCGCATTGCGATAGTCAG
* *
2099 ACATCGCGTTGCGACAGTCAG
1 A-ATCGCATTGCGATAGTCAG
*
2120 AATCGCGTTGCGATAGTCAG
1 AATCGCATTGCGATAGTCAG
* *
2140 AATCGCGTTGCGATAGTCAT
1 AATCGCATTGCGATAGTCAG
* * *
2160 ACTCGCATTGCGAT-TTACAT
1 AATCGCATTGCGATAGT-CAG
*
2180 ATTCGCATTGCGATAGTC
1 AATCGCATTGCGATAGTC
2198 GAAAAATCGC
Statistics
Matches: 103, Mismatches: 11, Indels: 8
0.84 0.09 0.07
Matches are distributed among these distances:
19 1 0.01
20 100 0.97
21 2 0.02
ACGTcount: A:0.25, C:0.23, G:0.24, T:0.28
Consensus pattern (20 bp):
AATCGCATTGCGATAGTCAG
Found at i:2197 original size:60 final size:60
Alignment explanation
Indices: 2060--2172 Score: 174
Period size: 60 Copynumber: 1.9 Consensus size: 60
2050 ACGCTTTGAA
* *
2060 AATCGCATTGCGATAGTCAGCATCGCATTGCGATAGTCAACATCGCGTTGCGACAGTCAG
1 AATCGCATTGCGATAGTCAGAATCGCATTGCGATAGTCAACATCGCATTGCGACAGTCAG
* *
2120 AATCGCGTTGCGATAGTCAGAATCGCGTTGCGATAGTCATAC-TCGCATTGCGA
1 AATCGCATTGCGATAGTCAGAATCGCATTGCGATAGTCA-ACATCGCATTGCGA
2173 TTTACATATT
Statistics
Matches: 48, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
60 46 0.96
61 2 0.04
ACGTcount: A:0.26, C:0.24, G:0.26, T:0.25
Consensus pattern (60 bp):
AATCGCATTGCGATAGTCAGAATCGCATTGCGATAGTCAACATCGCATTGCGACAGTCAG
Found at i:2214 original size:22 final size:22
Alignment explanation
Indices: 2189--2240 Score: 52
Period size: 21 Copynumber: 2.4 Consensus size: 22
2179 TATTCGCATT
2189 GCGATAGTCGAAAAATCGCAAC
1 GCGATAGTCGAAAAATCGCAAC
* * * * *
2211 GCGA-ATTTGGAAAATTGCAAT
1 GCGATAGTCGAAAAATCGCAAC
2232 GCGATAGTC
1 GCGATAGTC
2241 AGAATCGTGT
Statistics
Matches: 22, Mismatches: 7, Indels: 2
0.71 0.23 0.06
Matches are distributed among these distances:
21 16 0.73
22 6 0.27
ACGTcount: A:0.37, C:0.17, G:0.25, T:0.21
Consensus pattern (22 bp):
GCGATAGTCGAAAAATCGCAAC
Found at i:2427 original size:16 final size:16
Alignment explanation
Indices: 2408--2440 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
2398 CTCTAACTGT
*
2408 TACGATGTTGACGTGG
1 TACGATGCTGACGTGG
2424 TACGATGCTGACGTGG
1 TACGATGCTGACGTGG
2440 T
1 T
2441 GATCCACATC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.18, C:0.15, G:0.36, T:0.30
Consensus pattern (16 bp):
TACGATGCTGACGTGG
Found at i:5252 original size:19 final size:21
Alignment explanation
Indices: 5228--5268 Score: 59
Period size: 19 Copynumber: 2.0 Consensus size: 21
5218 ATCCAACGAG
5228 GAAGAAAAATGA-A-AAAGCA
1 GAAGAAAAATGAGATAAAGCA
*
5247 GAAGAAGAATGAGATAAAGCA
1 GAAGAAAAATGAGATAAAGCA
5268 G
1 G
5269 GAGACAACAC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 11 0.58
20 1 0.05
21 7 0.37
ACGTcount: A:0.61, C:0.05, G:0.27, T:0.07
Consensus pattern (21 bp):
GAAGAAAAATGAGATAAAGCA
Found at i:9780 original size:36 final size:36
Alignment explanation
Indices: 9726--9978 Score: 176
Period size: 37 Copynumber: 7.2 Consensus size: 36
9716 TAATTCACTC
9726 AAAACAAAGTTTTGTCTCTCTTGAGACAGTTTTTCTT
1 AAAACAAA-TTTTGTCTCTCTTGAGACAGTTTTTCTT
*
9763 AAAACAAATTTTGTCTCTCTTGAGACA-TTTTTTTT
1 AAAACAAATTTTGTCTCTCTTGAGACAGTTTTTCTT
9798 AAAAAACAAATTTTGTCTCTCTTGAGACAGTTTCTT-TT
1 --AAAACAAATTTTGTCTCTCTTGAGACAGTTT-TTCTT
* **
9836 GAAACAAA-----AATCT-TTGA-ATC--TATTTTCTTT
1 AAAACAAATTTTGTCTCTCTTGAGA-CAGT-TTTTC-TT
* * *
9866 TAAACAAATTTCGTCTCCCTTGAGACAGTTTCTT-TT
1 AAAACAAATTTTGTCTCTCTTGAGACAGTTT-TTCTT
** * *
9902 GGAACTAAGTTTTGTCTCTC---AGACAGTTTTCCTT
1 AAAAC-AAATTTTGTCTCTCTTGAGACAGTTTTTCTT
* * *
9936 AAAACAAAGTTTTGTCTCCCTTGAGATAGTTTCTCTT
1 AAAACAAA-TTTTGTCTCTCTTGAGACAGTTTTTCTT
*
9973 GAAACA
1 AAAACA
9979 CCAATGTCGC
Statistics
Matches: 170, Mismatches: 22, Indels: 48
0.71 0.09 0.20
Matches are distributed among these distances:
28 3 0.02
29 3 0.02
30 14 0.08
31 3 0.02
33 3 0.02
34 24 0.14
35 9 0.05
36 36 0.21
37 65 0.38
38 8 0.05
39 2 0.01
ACGTcount: A:0.29, C:0.17, G:0.12, T:0.42
Consensus pattern (36 bp):
AAAACAAATTTTGTCTCTCTTGAGACAGTTTTTCTT
Found at i:10369 original size:12 final size:12
Alignment explanation
Indices: 10335--10402 Score: 66
Period size: 12 Copynumber: 5.7 Consensus size: 12
10325 AAAAATGAAA
*
10335 AAATGAAAAAAT
1 AAATAAAAAAAT
* *
10347 GAAGAATAAAAAT
1 AAATAA-AAAAAT
*
10360 AAGTAAAAAAAT
1 AAATAAAAAAAT
*
10372 AAA-AAGAAAAT
1 AAATAAAAAAAT
*
10383 AAATAAATAAAT
1 AAATAAAAAAAT
10395 AAATAAAA
1 AAATAAAA
10403 TATTAAAATA
Statistics
Matches: 43, Mismatches: 11, Indels: 4
0.74 0.19 0.07
Matches are distributed among these distances:
11 10 0.23
12 24 0.56
13 9 0.21
ACGTcount: A:0.76, C:0.00, G:0.07, T:0.16
Consensus pattern (12 bp):
AAATAAAAAAAT
Found at i:10376 original size:8 final size:8
Alignment explanation
Indices: 10324--10404 Score: 58
Period size: 8 Copynumber: 10.0 Consensus size: 8
10314 GTGTTAGAGG
*
10324 AAAAAATG
1 AAAAAATA
*
10332 AAAAAATG
1 AAAAAATA
10340 AAAAAAT-
1 AAAAAATA
* *
10347 GAAGAATA
1 AAAAAATA
10355 AAAATAAGTA
1 AAAA-AA-TA
10365 AAAAAATA
1 AAAAAATA
*
10373 AAAAGA-A
1 AAAAAATA
*
10380 AATAAATA
1 AAAAAATA
*
10388 AATAAATA
1 AAAAAATA
10396 AATAAAATA
1 AA-AAAATA
10405 TTAAAATATA
Statistics
Matches: 60, Mismatches: 8, Indels: 9
0.78 0.10 0.12
Matches are distributed among these distances:
7 10 0.17
8 35 0.58
9 9 0.15
10 6 0.10
ACGTcount: A:0.77, C:0.00, G:0.07, T:0.16
Consensus pattern (8 bp):
AAAAAATA
Found at i:10378 original size:27 final size:27
Alignment explanation
Indices: 10348--10402 Score: 76
Period size: 27 Copynumber: 2.0 Consensus size: 27
10338 TGAAAAAATG
*
10348 AAGAATAA-AAATAAGTAAAAAAATAAA
1 AAGAA-AATAAATAAATAAAAAAATAAA
*
10375 AAGAAAATAAATAAATAAATAAATAAA
1 AAGAAAATAAATAAATAAAAAAATAAA
10402 A
1 A
10403 TATTAAAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 2 0.08
27 23 0.92
ACGTcount: A:0.78, C:0.00, G:0.05, T:0.16
Consensus pattern (27 bp):
AAGAAAATAAATAAATAAAAAAATAAA
Found at i:10388 original size:4 final size:4
Alignment explanation
Indices: 10356--10401 Score: 51
Period size: 4 Copynumber: 11.8 Consensus size: 4
10346 TGAAGAATAA
* *
10356 AAAT AAGT AAAA AAAT AAA- AAGA- AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AA-AT AAAT AAAT AAAT AAAT AAAT AAA
10402 ATATTAAAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
3 3 0.08
4 33 0.92
ACGTcount: A:0.78, C:0.00, G:0.04, T:0.17
Consensus pattern (4 bp):
AAAT
Found at i:12322 original size:106 final size:106
Alignment explanation
Indices: 11997--13477 Score: 2106
Period size: 106 Copynumber: 14.0 Consensus size: 106
11987 GCATTGTTCT
* * *
11997 GAGTCCAATATTCTCCG-TCGTGAAGTTGAAATTGGCTCTGGAACTATGA-AA-TTGTTTGTTGA
1 GAGTCCAATATCCTTCGCT-GTGAAGTTGAAATTGGCTCT-GAAAT-TGAGAAGTTGTTTGTTGA
* * * * *
12059 CAACCAACCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTC
63 CAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
12103 GAGTCTAATATCCTTCGTTGTGAAGTTGAAATTGACTCTG-AA-TGA-AA--T-TTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
* * * * * *
12162 TCAGCCGCCCCTTCGTCGTGAAGTTGAGCTTGTGTTGCCTTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTC-TG
* * ** *
12204 G-GTTCAAGATCCTTCGCTGAAAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
* *
12268 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * * * *
12309 GAGTCAAATATCCTACACTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
*
12374 CCAGCGATCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
** * * * *
12415 GAGTCCAATATCCTTCATTGTGAAGTTGAAATTGGATCTAAAATTGATAAGGTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
12480 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
12521 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
* * *
12586 CCAGCAGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
12627 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTATTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
* *
12692 CCAGCGGTCCCTTCCTCGTGAAGTTGAACTTGCGTTGTCTA
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
**
12733 GAGTCCAATATCCTTCATTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
12798 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
12839 GAGTCCAAAATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
* *
12904 CCAGCGGTCCCTTCGTTGTGAAGTTGAACTTGCGTTGTATG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
12945 GAGTCCAATATCCTTTGCTGTGAAGTTTAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
*
13010 CCAGCGGTCCCTTCGTCGTGAAGTTAAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
13051 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGAAAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
13116 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
13157 GAGTCCAATATCCTTCGCTTTGAAGTTGAAATTGGCTCTGAAATTG-GAAAGTTGTTTATTGACA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAG-AAGTTGTTTGTTGACA
* * *
13221 ACCAACGATCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCTG
65 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
13263 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGATCTGAAATTGGGAAATTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
* *
13328 CCAACGGTCCCTTAGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
13369 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCCGAAATTG-GAAAATTG-TTGTTGACA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAG-AAGTTGTTTGTTGACA
* * * * * *
13432 ACCAGCCGTCCCTTCATTGTAAAGTTGAACTTGTGTTGTCTT
65 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
13474 GAGT
1 GAGT
13478 GGCATGATAT
Statistics
Matches: 1243, Mismatches: 120, Indels: 25
0.90 0.09 0.02
Matches are distributed among these distances:
100 75 0.06
101 5 0.00
102 8 0.01
103 2 0.00
104 1 0.00
105 52 0.04
106 1098 0.88
107 2 0.00
ACGTcount: A:0.24, C:0.18, G:0.24, T:0.34
Consensus pattern (106 bp):
GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:14319 original size:22 final size:22
Alignment explanation
Indices: 14293--14369 Score: 136
Period size: 22 Copynumber: 3.5 Consensus size: 22
14283 TTATGTTTGG
14293 TCAAAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
14315 TCAAAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
*
14337 TCATAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
*
14359 TCAACGGTTTG
1 TCAAAGGTTTG
14370 ATGGGTAGCT
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 52 1.00
ACGTcount: A:0.21, C:0.14, G:0.27, T:0.38
Consensus pattern (22 bp):
TCAAAGGTTTGGCATTTGATGC
Found at i:15001 original size:20 final size:18
Alignment explanation
Indices: 14974--15037 Score: 76
Period size: 20 Copynumber: 3.4 Consensus size: 18
14964 TTTTTGTCCC
14974 TTTTTCTTTTTTATTTTTG
1 TTTTTCTTTTTT-TTTTTG
14993 TTCTTTCTTTTTTTCTTTTG
1 TT-TTTCTTTTTTT-TTTTG
* *
15013 TTTCTCTTTTTTCTTTT-
1 TTTTTCTTTTTTTTTTTG
15030 TTTTTCTT
1 TTTTTCTT
15038 GATTGGATCT
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
17 7 0.17
18 4 0.10
19 12 0.30
20 17 0.43
ACGTcount: A:0.02, C:0.12, G:0.03, T:0.83
Consensus pattern (18 bp):
TTTTTCTTTTTTTTTTTG
Found at i:15011 original size:26 final size:25
Alignment explanation
Indices: 14973--15034 Score: 70
Period size: 26 Copynumber: 2.4 Consensus size: 25
14963 CTTTTTGTCC
* *
14973 CTTTTTCTTTTTTATTTTTGTTCTTT
1 CTTTTT-TTTTTTATTTCTCTTCTTT
* *
14999 CTTTTTTTCTTTTGTTTCTCTTTTTT
1 CTTTTTTT-TTTTATTTCTCTTCTTT
15025 CTTTTTTTTT
1 CTTTTTTTTT
15035 CTTGATTGGA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
25 4 0.13
26 27 0.87
ACGTcount: A:0.02, C:0.13, G:0.03, T:0.82
Consensus pattern (25 bp):
CTTTTTTTTTTTATTTCTCTTCTTT
Found at i:15022 original size:18 final size:17
Alignment explanation
Indices: 14996--15029 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
14986 ATTTTTGTTC
14996 TTTCTTTTTTTCTTTTG
1 TTTCTTTTTTTCTTTTG
15013 TTTCTCTTTTTTCTTTT
1 TTTCT-TTTTTTCTTTT
15030 TTTTTCTTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.00, C:0.15, G:0.03, T:0.82
Consensus pattern (17 bp):
TTTCTTTTTTTCTTTTG
Found at i:15030 original size:19 final size:18
Alignment explanation
Indices: 14978--15036 Score: 64
Period size: 19 Copynumber: 3.1 Consensus size: 18
14968 TGTCCCTTTT
*
14978 TCTTTTTTATTTTTGTTCTT
1 TCTTTTTT-TTTTTGTT-TC
14998 TCTTTTTTTCTTTTGTTTC
1 TCTTTTTTT-TTTTGTTTC
*
15017 TCTTTTTTCTTTTTTTTTC
1 TCTTTTTT-TTTTTGTTTC
15036 T
1 T
15037 TGATTGGATC
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
19 19 0.54
20 16 0.46
ACGTcount: A:0.02, C:0.14, G:0.03, T:0.81
Consensus pattern (18 bp):
TCTTTTTTTTTTTGTTTC
Found at i:16212 original size:8 final size:8
Alignment explanation
Indices: 16199--16234 Score: 56
Period size: 8 Copynumber: 4.6 Consensus size: 8
16189 GTAGATGAAG
16199 ATGCAAAA
1 ATGCAAAA
16207 ATGCAAAA
1 ATGCAAAA
16215 ATGC-AAA
1 ATGCAAAA
*
16222 ATGCAAGA
1 ATGCAAAA
16230 ATGCA
1 ATGCA
16235 TGAAATGTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
7 7 0.27
8 19 0.73
ACGTcount: A:0.56, C:0.14, G:0.17, T:0.14
Consensus pattern (8 bp):
ATGCAAAA
Found at i:16224 original size:15 final size:15
Alignment explanation
Indices: 16199--16234 Score: 54
Period size: 15 Copynumber: 2.3 Consensus size: 15
16189 GTAGATGAAG
16199 ATGCAAAAATGCAAAA
1 ATGC-AAAATGCAAAA
*
16215 ATGCAAAATGCAAGA
1 ATGCAAAATGCAAAA
16230 ATGCA
1 ATGCA
16235 TGAAATGTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 15 0.79
16 4 0.21
ACGTcount: A:0.56, C:0.14, G:0.17, T:0.14
Consensus pattern (15 bp):
ATGCAAAATGCAAAA
Found at i:19495 original size:8 final size:8
Alignment explanation
Indices: 19482--19515 Score: 68
Period size: 8 Copynumber: 4.2 Consensus size: 8
19472 GTGTTAGAGA
19482 AAAAAATG
1 AAAAAATG
19490 AAAAAATG
1 AAAAAATG
19498 AAAAAATG
1 AAAAAATG
19506 AAAAAATG
1 AAAAAATG
19514 AA
1 AA
19516 GAATAAAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 26 1.00
ACGTcount: A:0.76, C:0.00, G:0.12, T:0.12
Consensus pattern (8 bp):
AAAAAATG
Found at i:19526 original size:6 final size:6
Alignment explanation
Indices: 19507--19559 Score: 63
Period size: 6 Copynumber: 8.5 Consensus size: 6
19497 GAAAAAATGA
*
19507 AAAAAT GAAGAAT AAAAAT AAGTAAA- AAAAAT AAAAAT AAAAAT AAAAAT
1 AAAAAT -AAAAAT AAAAAT AA--AAAT AAAAAT AAAAAT AAAAAT AAAAAT
19557 AAA
1 AAA
19560 TAAATAAATA
Statistics
Matches: 41, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
5 3 0.07
6 28 0.68
7 7 0.17
8 3 0.07
ACGTcount: A:0.79, C:0.00, G:0.06, T:0.15
Consensus pattern (6 bp):
AAAAAT
Found at i:19534 original size:10 final size:10
Alignment explanation
Indices: 19517--19571 Score: 62
Period size: 10 Copynumber: 5.6 Consensus size: 10
19507 AAAAATGAAG
19517 AATAAAAATA
1 AATAAAAATA
*
19527 AGTAAAAA-A
1 AATAAAAATA
19536 AATAAAAATAAA
1 AATAAAAAT--A
19548 AATAAAAATA
1 AATAAAAATA
19558 AAT--AAATA
1 AATAAAAATA
19566 AATAAA
1 AATAAA
19572 TGAAATATAA
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
8 8 0.21
9 8 0.21
10 12 0.32
12 10 0.26
ACGTcount: A:0.80, C:0.00, G:0.02, T:0.18
Consensus pattern (10 bp):
AATAAAAATA
Found at i:19552 original size:31 final size:31
Alignment explanation
Indices: 19493--19571 Score: 88
Period size: 31 Copynumber: 2.5 Consensus size: 31
19483 AAAAATGAAA
* *
19493 AAATGAAAAAATGAAAAAATGAAGAATAAAAAT
1 AAATAAAAAAAT--AAAAATGAAAAATAAAAAT
*
19526 AAGTAAAAAAAATAAAAAT-AAAAATAAAAAT
1 AAAT-AAAAAAATAAAAATGAAAAATAAAAAT
*
19557 AAATAAATAAATAAA
1 AAATAAAAAAATAAA
19572 TGAAATATAA
Statistics
Matches: 40, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
30 10 0.25
31 14 0.35
32 6 0.15
33 3 0.08
34 7 0.17
ACGTcount: A:0.77, C:0.00, G:0.06, T:0.16
Consensus pattern (31 bp):
AAATAAAAAAATAAAAATGAAAAATAAAAAT
Found at i:19722 original size:29 final size:30
Alignment explanation
Indices: 19656--19722 Score: 75
Period size: 29 Copynumber: 2.3 Consensus size: 30
19646 GTAATATGAC
*
19656 AATAT-AATATAATATAAATAAAAAAACCA
1 AATATAAAAATAATATAAATAAAAAAACCA
* * * *
19685 AAAACAAAAATAA-ATAAATATATAAACCA
1 AATATAAAAATAATATAAATAAAAAAACCA
19714 AATATAAAA
1 AATATAAAA
19723 GTATACATAT
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
29 24 0.80
30 6 0.20
ACGTcount: A:0.72, C:0.07, G:0.00, T:0.21
Consensus pattern (30 bp):
AATATAAAAATAATATAAATAAAAAAACCA
Found at i:19876 original size:2 final size:2
Alignment explanation
Indices: 19869--19899 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
19859 ATATTTTAAA
*
19869 AT AT AT AT AT AT AC AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
19900 ATAATAATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:20505 original size:37 final size:37
Alignment explanation
Indices: 20459--20560 Score: 141
Period size: 37 Copynumber: 2.8 Consensus size: 37
20449 CTTGTGGATC
* * *
20459 CTATCTTTAGGAGTTTAAATCATAGTAGAACTCTATA
1 CTATTTTTAGGAGTTTGAATCCTAGTAGAACTCTATA
* * * *
20496 CTATTTTTAGGAGTTTGAATCCTAGCAAAATTCTATC
1 CTATTTTTAGGAGTTTGAATCCTAGTAGAACTCTATA
20533 CTATTTTTAGGAGTTTGAATCCTAGTAG
1 CTATTTTTAGGAGTTTGAATCCTAGTAG
20561 GACGAAAAGG
Statistics
Matches: 56, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
37 56 1.00
ACGTcount: A:0.30, C:0.14, G:0.16, T:0.40
Consensus pattern (37 bp):
CTATTTTTAGGAGTTTGAATCCTAGTAGAACTCTATA
Found at i:20719 original size:27 final size:27
Alignment explanation
Indices: 20681--20737 Score: 98
Period size: 27 Copynumber: 2.1 Consensus size: 27
20671 CTGGAAACAC
20681 AAAAAACCTTTG-AAATCGTTTCTCTTG
1 AAAAAACCTTTGAAAAT-GTTTCTCTTG
20708 AAAAAACCTTTGAAAATGTTTCTCTTG
1 AAAAAACCTTTGAAAATGTTTCTCTTG
20735 AAA
1 AAA
20738 CACAAAGACC
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
27 25 0.86
28 4 0.14
ACGTcount: A:0.39, C:0.16, G:0.11, T:0.35
Consensus pattern (27 bp):
AAAAAACCTTTGAAAATGTTTCTCTTG
Found at i:20885 original size:84 final size:84
Alignment explanation
Indices: 20740--20986 Score: 352
Period size: 84 Copynumber: 2.9 Consensus size: 84
20730 TCTTGAAACA
* * * *
20740 CAAAGACCTTAGAGTTCGACTACGCTCAGCTCCAAGGCACATTATTTGCAGCATAGCTCAAGGCT
1 CAAAGACCTTCGAGTTCGACTACGTTCAGCTCCAAGGCACATCATTTGCAGCATAACTCAAGGCT
20805 AGAAGGGTTATCTGCC-AC
66 AGAAGGGTTATCTGCCAAC
* * *
20823 CAAAAGACCTTCGAGTTTGACTACGTTCAGCTCCAAGGCATATCATTTGCAGCATAATTCAAGGC
1 C-AAAGACCTTCGAGTTCGACTACGTTCAGCTCCAAGGCACATCATTTGCAGCATAACTCAAGGC
20888 TAGAAGGGTTATCTGCCAAC
65 TAGAAGGGTTATCTGCCAAC
* * * * * **
20908 CAAAGACCTTCGAGTTCGATTACATTCAGCTCAAATGCACATCATTTACAGCATAACTCAAGGGA
1 CAAAGACCTTCGAGTTCGACTACGTTCAGCTCCAAGGCACATCATTTGCAGCATAACTCAAGGCT
20973 AGAAGGGTTATCTG
66 AGAAGGGTTATCTG
20987 TCATTAAAAT
Statistics
Matches: 145, Mismatches: 17, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
83 1 0.01
84 141 0.97
85 3 0.02
ACGTcount: A:0.31, C:0.24, G:0.20, T:0.25
Consensus pattern (84 bp):
CAAAGACCTTCGAGTTCGACTACGTTCAGCTCCAAGGCACATCATTTGCAGCATAACTCAAGGCT
AGAAGGGTTATCTGCCAAC
Found at i:21577 original size:3 final size:3
Alignment explanation
Indices: 21569--21614 Score: 65
Period size: 3 Copynumber: 15.0 Consensus size: 3
21559 ATTTATTTAT
* *
21569 TTA TTA TTA TTA TTA TTA GTA TTA TTA TTTA TTA GTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA
21615 ATAATATTTT
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
3 35 0.92
4 3 0.08
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:21622 original size:28 final size:28
Alignment explanation
Indices: 21565--21622 Score: 89
Period size: 28 Copynumber: 2.1 Consensus size: 28
21555 TGGAATTTAT
* * *
21565 TTATTTATTATTATTATTATTAGTATTA
1 TTATTTATTAGTATTATTATTAATAATA
21593 TTATTTATTAGTATTATTATTAATAATA
1 TTATTTATTAGTATTATTATTAATAATA
21621 TT
1 TT
21623 TTTTTATTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.62
Consensus pattern (28 bp):
TTATTTATTAGTATTATTATTAATAATA
Found at i:24029 original size:20 final size:20
Alignment explanation
Indices: 23992--24030 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
23982 TATCAAGTAG
* * *
23992 AAGCAAGCAATATCAAACAA
1 AAGCAAACAACATAAAACAA
24012 AAGCAAACAACATAAAACA
1 AAGCAAACAACATAAAACA
24031 GAATAAAGCA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.64, C:0.21, G:0.08, T:0.08
Consensus pattern (20 bp):
AAGCAAACAACATAAAACAA
Found at i:32413 original size:18 final size:18
Alignment explanation
Indices: 32392--32591 Score: 126
Period size: 18 Copynumber: 11.1 Consensus size: 18
32382 AATAAATTAA
32392 TATATAGTTTATATATAC
1 TATATAGTTTATATATAC
32410 TATATAGTTTATATATAC
1 TATATAGTTTATATATAC
* *
32428 TA-AT-G--AACTATATAA
1 TATATAGTTTA-TATATAC
*
32443 TATATAGTTTGTATATAC
1 TATATAGTTTATATATAC
* * *
32461 CATATACTATATAGGTTATA-
1 TATATAGTTTATA---TATAC
* ** *
32481 TATACTAATGAACTATATAA
1 TATA-TAGTTTA-TATATAC
32501 TATATAGTTTATATATAC
1 TATATAGTTTATATATAC
** *
32519 TA-AT-GAACTATATATAA
1 TATATAG-TTTATATATAC
*
32536 TGTATAGTTTATATATAC
1 TATATAGTTTATATATAC
* * **
32554 GATATAGTCTATATATGT
1 TATATAGTTTATATATAC
32572 TATATAGTTTATATATAC
1 TATATAGTTTATATATAC
32590 TA
1 TA
32592 ATAAACTATA
Statistics
Matches: 135, Mismatches: 33, Indels: 28
0.69 0.17 0.14
Matches are distributed among these distances:
14 1 0.01
15 8 0.06
16 4 0.03
17 14 0.10
18 82 0.61
19 9 0.07
20 7 0.05
21 8 0.06
22 2 0.01
ACGTcount: A:0.41, C:0.07, G:0.08, T:0.45
Consensus pattern (18 bp):
TATATAGTTTATATATAC
Found at i:32423 original size:51 final size:51
Alignment explanation
Indices: 32366--32533 Score: 135
Period size: 51 Copynumber: 3.1 Consensus size: 51
32356 TTTCAATTAA
*
32366 TATATATGTTTATATTAATAAATTAATATATAGTTTATATATACTATATAG
1 TATATATGTTTATATTAATAAATTAATATATAGTTTATATATACTATATAC
* * * * * * *
32417 TTTATATATACTA-ATGAACTATA-TAATATATAGTTTGTATATACCATATAC
1 TATATATGT-TTATATTAA-TAAATTAATATATAGTTTATATATACTATATAC
*
32468 TATATAGGTTATATATACTAATGAACTATATAATATATAGTTTATATATACTA-ATGAAC
1 TATATATGTT-TATAT--TAAT-AA--AT-TAATATATAGTTTATATATACTATAT--AC
32527 TATATAT
1 TATATAT
32534 AATGTATAGT
Statistics
Matches: 87, Mismatches: 17, Indels: 18
0.71 0.14 0.15
Matches are distributed among these distances:
51 44 0.51
52 7 0.08
53 1 0.01
54 3 0.03
56 1 0.01
57 2 0.02
58 21 0.24
59 8 0.09
ACGTcount: A:0.43, C:0.06, G:0.07, T:0.45
Consensus pattern (51 bp):
TATATATGTTTATATTAATAAATTAATATATAGTTTATATATACTATATAC
Found at i:32447 original size:33 final size:33
Alignment explanation
Indices: 32403--32615 Score: 219
Period size: 33 Copynumber: 6.5 Consensus size: 33
32393 ATATAGTTTA
*
32403 TATATACTATATAGTTTATATATACTAATGAAC
1 TATATAATATATAGTTTATATATACTAATGAAC
*
32436 TATATAATATATAGTTTGTATATAC-------C
1 TATATAATATATAGTTTATATATACTAATGAAC
* *
32462 -ATATACTATATAGGTTATATATACTAATGAAC
1 TATATAATATATAGTTTATATATACTAATGAAC
32494 TATATAATATATAGTTTATATATACTAATGAAC
1 TATATAATATATAGTTTATATATACTAATGAAC
* * *
32527 TATATATAATGTATAGTTTATATATACGATAT-AGTC
1 --TATATAATATATAGTTTATATATACTA-ATGA-AC
* *
32563 TATATATGTTATATAGTTTATATATACTAATAAAC
1 TATATA--ATATATAGTTTATATATACTAATGAAC
*
32598 TATATAATGTATAGTTTA
1 TATATAATATATAGTTTA
32616 GGGTTTAGGA
Statistics
Matches: 149, Mismatches: 16, Indels: 30
0.76 0.08 0.15
Matches are distributed among these distances:
25 21 0.14
26 1 0.01
32 1 0.01
33 63 0.42
34 6 0.04
35 35 0.23
36 22 0.15
ACGTcount: A:0.42, C:0.07, G:0.08, T:0.44
Consensus pattern (33 bp):
TATATAATATATAGTTTATATATACTAATGAAC
Found at i:32480 original size:58 final size:58
Alignment explanation
Indices: 32404--32518 Score: 212
Period size: 58 Copynumber: 2.0 Consensus size: 58
32394 TATAGTTTAT
* *
32404 ATATACTATATAGTTTATATATACTAATGAACTATATAATATATAGTTTGTATATACC
1 ATATACTATATAGGTTATATATACTAATGAACTATATAATATATAGTTTATATATACC
32462 ATATACTATATAGGTTATATATACTAATGAACTATATAATATATAGTTTATATATAC
1 ATATACTATATAGGTTATATATACTAATGAACTATATAATATATAGTTTATATATAC
32519 TAATGAACTA
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
58 55 1.00
ACGTcount: A:0.43, C:0.08, G:0.07, T:0.43
Consensus pattern (58 bp):
ATATACTATATAGGTTATATATACTAATGAACTATATAATATATAGTTTATATATACC
Found at i:32499 original size:17 final size:17
Alignment explanation
Indices: 32477--32534 Score: 59
Period size: 17 Copynumber: 3.5 Consensus size: 17
32467 CTATATAGGT
32477 TATATATACTAATGAAC
1 TATATATACTAATGAAC
**
32494 TATATA-A-TATAT-AGTT
1 TATATATACTA-ATGA-AC
32510 TATATATACTAATGAAC
1 TATATATACTAATGAAC
32527 TATATATA
1 TATATATA
32535 ATGTATAGTT
Statistics
Matches: 32, Mismatches: 4, Indels: 10
0.70 0.09 0.22
Matches are distributed among these distances:
15 3 0.09
16 9 0.28
17 17 0.53
18 3 0.09
ACGTcount: A:0.47, C:0.07, G:0.05, T:0.41
Consensus pattern (17 bp):
TATATATACTAATGAAC
Found at i:32505 original size:91 final size:93
Alignment explanation
Indices: 32403--32577 Score: 273
Period size: 91 Copynumber: 1.9 Consensus size: 93
32393 ATATAGTTTA
* *
32403 TATATACTATATAGTTTATATATACTAATGAAC-TATATAATATATAGTTTGTATATACCATATA
1 TATATAATATATAGTTTATATATACTAATGAACATATATAATATATAGTTTATATATACCATATA
32467 -CTATATAGGTTATATATACTAATGAAC
66 GCTATATAGGTTATATATACTAATGAAC
* *
32494 TATATAATATATAGTTTATATATACTAATGAACTATATATAATGTATAGTTTATATATACGATAT
1 TATATAATATATAGTTTATATATACTAATGAAC-ATATATAATATATAGTTTATATATACCATAT
*
32559 AGTCTATATATGTTATATA
65 AG-CTATATAGGTTATATA
32578 GTTTATATAT
Statistics
Matches: 75, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
91 32 0.43
93 28 0.37
95 15 0.20
ACGTcount: A:0.42, C:0.07, G:0.08, T:0.43
Consensus pattern (93 bp):
TATATAATATATAGTTTATATATACTAATGAACATATATAATATATAGTTTATATATACCATATA
GCTATATAGGTTATATATACTAATGAAC
Found at i:32660 original size:162 final size:161
Alignment explanation
Indices: 32393--32685 Score: 369
Period size: 162 Copynumber: 1.8 Consensus size: 161
32383 ATAAATTAAT
* * *
32393 ATATAGTTTATATATACTATATAGTTTATATATACTAATGAACTATATAATATATAGTTTGTATA
1 ATATAGTCTATATATACTATATAGTTTATATATACTAATAAACTATATAATATATAGTTTGGATA
32458 TACCATATACTATATAGGTTATATATACTAATGAACTATATA-ATATATAGTTTATATATACTAA
66 TACCATATACTATATAGGTTATATATAC-AATGAACTATATAGATATATAGTTTATATATA-TAA
32522 TGAACTATATATAATGTATAGTTTATATATACG
129 TGAACTATATATAATGTATAGTTTATATATACG
** * *
32555 ATATAGTCTATATATGTTATATAGTTTATATATACTAATAAACTATATAATGTATAGTTTAGGGT
1 ATATAGTCTATATATACTATATAGTTTATATATACTAATAAACTATATAATATATAGTTT-GGAT
* ** * * * *
32620 TTAGGATTTTA-TATATA-GTTCATATGTA-AATTATACTATATAGTATATATAGTTTATCTATA
65 ATACCA-TATACTATATAGGTT-ATATATACAATGA-ACTATATAG-ATATATAGTTTATATATA
32682 TAAT
126 TAAT
32686 ATATAGTATA
Statistics
Matches: 111, Mismatches: 14, Indels: 11
0.82 0.10 0.08
Matches are distributed among these distances:
161 4 0.04
162 66 0.59
163 21 0.19
164 20 0.18
ACGTcount: A:0.40, C:0.06, G:0.09, T:0.45
Consensus pattern (161 bp):
ATATAGTCTATATATACTATATAGTTTATATATACTAATAAACTATATAATATATAGTTTGGATA
TACCATATACTATATAGGTTATATATACAATGAACTATATAGATATATAGTTTATATATATAATG
AACTATATATAATGTATAGTTTATATATACG
Found at i:32687 original size:20 final size:20
Alignment explanation
Indices: 32651--32723 Score: 69
Period size: 20 Copynumber: 3.6 Consensus size: 20
32641 ATATGTAAAT
32651 TATA-CTATATAGTATATATAG
1 TATATCTATATA--ATATATAG
*
32672 TTTATCTATATAATATATAG
1 TATATCTATATAATATATAG
**
32692 TATATGAATATAA-ACTATAG
1 TATATCTATATAATA-TATAG
*
32712 TATATATATATA
1 TATATCTATATA
32724 GGTCATATGT
Statistics
Matches: 44, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
19 1 0.02
20 33 0.75
21 3 0.07
22 7 0.16
ACGTcount: A:0.45, C:0.04, G:0.07, T:0.44
Consensus pattern (20 bp):
TATATCTATATAATATATAG
Found at i:32737 original size:31 final size:30
Alignment explanation
Indices: 32702--32827 Score: 117
Period size: 31 Copynumber: 4.4 Consensus size: 30
32692 TATATGAATA
32702 TAAACTATAGTATATATATATAGGTCATATG
1 TAAACTATAGTATATATATATA-GTCATATG
*
32733 TAAACTATA-TA-GTATATA-A---ATA--
1 TAAACTATAGTATATATATATAGTCATATG
*
32755 TCAACTATAGTATATATATAT-GTCATATG
1 TAAACTATAGTATATATATATAGTCATATG
* *
32784 TAAAGTATATAGTTTATATATATAGTTCATATG
1 TAAA--CTATAGTATATATATATAG-TCATATG
32817 TAAACTATAGT
1 TAAACTATAGT
32828 TCATATGTAA
Statistics
Matches: 76, Mismatches: 7, Indels: 24
0.71 0.07 0.22
Matches are distributed among these distances:
22 8 0.11
23 2 0.03
24 9 0.12
27 3 0.04
28 1 0.01
29 9 0.12
30 2 0.03
31 30 0.39
32 1 0.01
33 11 0.14
ACGTcount: A:0.43, C:0.06, G:0.10, T:0.40
Consensus pattern (30 bp):
TAAACTATAGTATATATATATAGTCATATG
Found at i:32749 original size:18 final size:19
Alignment explanation
Indices: 32718--32905 Score: 63
Period size: 18 Copynumber: 10.2 Consensus size: 19
32708 ATAGTATATA
32718 TATATAGGTCATATGTAAAC
1 TATATA-GTCATATGTAAAC
32738 TATATAGT-ATA--TAAA-
1 TATATAGTCATATGTAAAC
* *
32753 TATCA-ACT-ATA-GTATA-
1 TAT-ATAGTCATATGTAAAC
*
32769 TATATATGTCATATGTAAAG
1 TATATA-GTCATATGTAAAC
*
32789 TATATAG---T-T-TATA-
1 TATATAGTCATATGTAAAC
32802 TATATAGTTCATATGTAAAC
1 TATATAG-TCATATGTAAAC
*
32822 --TATAGTTCATATGTAAATAT
1 TATATAG-TCATATGT-AA-AC
*
32842 TAACTATAGTTTATATGTAAAC
1 T-A-TATAG-TCATATGTAAAC
32864 TATAGTTAGT-ATA--TAAAC
1 TATA--TAGTCATATGTAAAC
*
32882 TATATAGTTTATATGTAAAC
1 TATATAG-TCATATGTAAAC
32902 TATA
1 TATA
32906 GTTCATATAT
Statistics
Matches: 133, Mismatches: 9, Indels: 52
0.69 0.05 0.27
Matches are distributed among these distances:
13 7 0.05
14 3 0.02
15 10 0.08
16 16 0.12
17 3 0.02
18 33 0.25
19 12 0.09
20 27 0.20
21 2 0.02
22 5 0.04
23 2 0.02
24 13 0.10
ACGTcount: A:0.42, C:0.06, G:0.10, T:0.41
Consensus pattern (19 bp):
TATATAGTCATATGTAAAC
Found at i:32793 original size:51 final size:52
Alignment explanation
Indices: 32685--32807 Score: 185
Period size: 53 Copynumber: 2.4 Consensus size: 52
32675 ATCTATATAA
*
32685 TATATAGTATATGAATATAAACTATAGTATATATATATAGGTCATATGTAAAC
1 TATATAGTATATAAATATAAACTATAGTATATATATATA-GTCATATGTAAAC
* *
32738 TATATAGTATATAAATATCAACTATAGTATATATATAT-GTCATATGTAAAG
1 TATATAGTATATAAATATAAACTATAGTATATATATATAGTCATATGTAAAC
* *
32789 TATATAGTTTATATATATA
1 TATATAGTATATAAATATA
32808 GTTCATATGT
Statistics
Matches: 64, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
51 28 0.44
53 36 0.56
ACGTcount: A:0.45, C:0.05, G:0.10, T:0.41
Consensus pattern (52 bp):
TATATAGTATATAAATATAAACTATAGTATATATATATAGTCATATGTAAAC
Found at i:32897 original size:38 final size:38
Alignment explanation
Indices: 32802--32918 Score: 155
Period size: 38 Copynumber: 3.0 Consensus size: 38
32792 ATAGTTTATA
* * *
32802 TATATAGTTCATATGTAAACTATAGTTCATATGTAAATAT
1 TATATAGTTTATATGTAAACTATAGTTCATATAT-AA-AC
32842 TAACTATAGTTTATATGTAAACTATAGTT-AGTATATAAAC
1 T-A-TATAGTTTATATGTAAACTATAGTTCA-TATATAAAC
32882 TATATAGTTTATATGTAAACTATAGTTCATATATAAA
1 TATATAGTTTATATGTAAACTATAGTTCATATATAAA
32919 TATGAACCTT
Statistics
Matches: 70, Mismatches: 3, Indels: 10
0.84 0.04 0.12
Matches are distributed among these distances:
38 33 0.47
39 2 0.03
40 3 0.04
41 4 0.06
42 28 0.40
ACGTcount: A:0.42, C:0.07, G:0.09, T:0.42
Consensus pattern (38 bp):
TATATAGTTTATATGTAAACTATAGTTCATATATAAAC
Found at i:32906 original size:18 final size:18
Alignment explanation
Indices: 32804--32918 Score: 106
Period size: 18 Copynumber: 5.9 Consensus size: 18
32794 AGTTTATATA
32804 TATAGTTCATATGTAAAC
1 TATAGTTCATATGTAAAC
32822 TATAGTTCATATGTAAATATTAAC
1 TATAGTTCATATG----TA--AAC
*
32846 TATAGTTTATATGTAAAC
1 TATAGTTCATATGTAAAC
*
32864 TATAGTT-AGTATATAAAC
1 TATAGTTCA-TATGTAAAC
*
32882 TATATAGTTTATATGTAAAC
1 --TATAGTTCATATGTAAAC
*
32902 TATAGTTCATATATAAA
1 TATAGTTCATATGTAAA
32919 TATGAACCTT
Statistics
Matches: 82, Mismatches: 5, Indels: 20
0.77 0.05 0.19
Matches are distributed among these distances:
17 1 0.01
18 46 0.56
20 17 0.21
21 1 0.01
22 2 0.02
24 15 0.18
ACGTcount: A:0.42, C:0.07, G:0.10, T:0.42
Consensus pattern (18 bp):
TATAGTTCATATGTAAAC
Found at i:32999 original size:33 final size:33
Alignment explanation
Indices: 32944--33028 Score: 104
Period size: 33 Copynumber: 2.7 Consensus size: 33
32934 ATACATATTT
* *
32944 ATATATATAGT-T-TATATGTAAACTATAGTTC
1 ATATATATAGTATATAAATATAAACTATAGTTC
*
32975 ATATATATAGTATATAAATATAAACTATAGTTT
1 ATATATATAGTATATAAATATAAACTATAGTTC
* *
33008 ATATAAATATTATA-AAATATA
1 ATATATATAGTATATAAATATA
33029 GTATATAAAT
Statistics
Matches: 47, Mismatches: 5, Indels: 3
0.85 0.09 0.05
Matches are distributed among these distances:
31 11 0.23
32 8 0.17
33 28 0.60
ACGTcount: A:0.48, C:0.04, G:0.06, T:0.42
Consensus pattern (33 bp):
ATATATATAGTATATAAATATAAACTATAGTTC
Found at i:33003 original size:20 final size:20
Alignment explanation
Indices: 32979--33052 Score: 85
Period size: 20 Copynumber: 3.5 Consensus size: 20
32969 TAGTTCATAT
32979 ATATAGTATATAAATATAAA
1 ATATAGTATATAAATATAAA
*
32999 CTATAGTTTATATAAATATTATAAA
1 ATATAG--TATAT-AA-A-TATAAA
33024 ATATAGTATATAAATATAAA
1 ATATAGTATATAAATATAAA
*
33044 TTATAGTAT
1 ATATAGTAT
33053 GTAGTTTATA
Statistics
Matches: 46, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
20 19 0.41
21 1 0.02
22 7 0.15
23 7 0.15
24 1 0.02
25 11 0.24
ACGTcount: A:0.53, C:0.01, G:0.05, T:0.41
Consensus pattern (20 bp):
ATATAGTATATAAATATAAA
Found at i:33011 original size:31 final size:30
Alignment explanation
Indices: 32942--33012 Score: 90
Period size: 31 Copynumber: 2.3 Consensus size: 30
32932 ATATACATAT
* *
32942 TTATATATATAGTTTATATGTAAACTATAG
1 TTATATATATAGTTTAAATATAAACTATAG
32972 TTCATATATATAGTATATAAATATAAACTATAG
1 TT-ATATATATAGT-T-TAAATATAAACTATAG
33005 TT-TATATA
1 TTATATATA
33013 AATATTATAA
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
30 2 0.06
31 17 0.47
32 1 0.03
33 16 0.44
ACGTcount: A:0.44, C:0.04, G:0.07, T:0.45
Consensus pattern (30 bp):
TTATATATATAGTTTAAATATAAACTATAG
Found at i:33028 original size:25 final size:25
Alignment explanation
Indices: 32993--33069 Score: 75
Period size: 25 Copynumber: 3.0 Consensus size: 25
32983 AGTATATAAA
*
32993 TATAAACTATAGTTTATATAAATAT
1 TATAAAATATAGTTTATATAAATAT
*
33018 TATAAAATATAGTATATA-AATATAAAT
1 TATAAAATATAGTTTATATAA-AT--AT
** *
33045 TATAGTATGTAGTTTATATAAATAT
1 TATAAAATATAGTTTATATAAATAT
33070 AAATATAAAC
Statistics
Matches: 42, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
24 2 0.05
25 20 0.48
27 18 0.43
28 2 0.05
ACGTcount: A:0.49, C:0.01, G:0.06, T:0.43
Consensus pattern (25 bp):
TATAAAATATAGTTTATATAAATAT
Found at i:33040 original size:29 final size:30
Alignment explanation
Indices: 33008--33075 Score: 79
Period size: 29 Copynumber: 2.3 Consensus size: 30
32998 ACTATAGTTT
33008 ATATAAATATTATAAAATATAG-TATATAA
1 ATATAAATATTATAAAATATAGTTATATAA
** *
33037 ATAT-AA-ATTATAGTATGTAGTTTATATAA
1 ATATAAATATTATAAAATATAG-TTATATAA
33066 ATATAAATAT
1 ATATAAATAT
33076 AAACCTTAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
27 11 0.34
28 2 0.06
29 15 0.47
30 2 0.06
31 2 0.06
ACGTcount: A:0.53, C:0.00, G:0.06, T:0.41
Consensus pattern (30 bp):
ATATAAATATTATAAAATATAGTTATATAA
Found at i:33058 original size:103 final size:99
Alignment explanation
Indices: 32846--33063 Score: 228
Period size: 103 Copynumber: 2.1 Consensus size: 99
32836 AAATATTAAC
*
32846 TATAGTTTATATGTAAACTATAGTTAGTATATAAACTATATAGTTTATATGTAAACTATAGTTCA
1 TATAGTTTATATGTAAACTATAGTTAGTATATAAACTATATA---TATATATAAACTATAGTT-A
** *
32911 TATATAAATATGAACCTTAGTATATACATATTTATATA
62 TATATAAATATGAAAATTAGTATATAAATATTTATATA
* *
32949 TATAGTTTATATGTAAACTATAGTTCA-TATATATAGTATATA-A-ATATAAACTATAGTT-TAT
1 TATAGTTTATATGTAAACTATAGTT-AGTATATAAACTATATATATATATAAACTATAGTTATAT
*
33010 ATAAATATTATAAAATATAGTATATAAATATAAATTATAGTA
65 ATAAATA-T-GAAAAT-TAGTATATAAATAT---TTATA-TA
*
33052 TGTAGTTTATAT
1 TATAGTTTATAT
33064 AAATATAAAT
Statistics
Matches: 99, Mismatches: 8, Indels: 16
0.80 0.07 0.13
Matches are distributed among these distances:
96 10 0.10
97 1 0.01
98 17 0.17
99 14 0.14
102 5 0.05
103 51 0.52
104 1 0.01
ACGTcount: A:0.44, C:0.05, G:0.08, T:0.43
Consensus pattern (99 bp):
TATAGTTTATATGTAAACTATAGTTAGTATATAAACTATATATATATATAAACTATAGTTATATA
TAAATATGAAAATTAGTATATAAATATTTATATA
Found at i:33144 original size:22 final size:22
Alignment explanation
Indices: 33103--33166 Score: 83
Period size: 22 Copynumber: 2.8 Consensus size: 22
33093 CCCTAAACAC
* *
33103 TAAACCATATAATATATATATATA
1 TAAACTATATAATTTATAT-TA-A
*
33127 TAAACTATATAGTTTATATTAA
1 TAAACTATATAATTTATATTAA
33149 TAAACTATATAATTTATA
1 TAAACTATATAATTTATA
33167 CAATATATAT
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
22 18 0.50
23 2 0.06
24 16 0.44
ACGTcount: A:0.50, C:0.06, G:0.02, T:0.42
Consensus pattern (22 bp):
TAAACTATATAATTTATATTAA
Found at i:33245 original size:9 final size:10
Alignment explanation
Indices: 33169--33248 Score: 51
Period size: 9 Copynumber: 7.8 Consensus size: 10
33159 AATTTATACA
33169 ATATAT-ATT
1 ATATATAATT
*
33178 ATTTATAATT
1 ATATATAATT
*
33188 ATACATAATAT
1 ATATATAAT-T
33199 ATAAATATAAATT
1 AT--ATAT-AATT
*
33212 GTATAGT--TT
1 ATATA-TAATT
33221 ATATATAATT
1 ATATATAATT
33231 CATATATAATT
1 -ATATATAATT
33242 -TATATAA
1 ATATATAA
33249 ACTATGTAGT
Statistics
Matches: 56, Mismatches: 6, Indels: 18
0.70 0.08 0.22
Matches are distributed among these distances:
8 1 0.02
9 18 0.32
10 12 0.21
11 16 0.29
12 1 0.02
13 5 0.09
14 3 0.05
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (10 bp):
ATATATAATT
Found at i:33259 original size:40 final size:40
Alignment explanation
Indices: 33114--33272 Score: 125
Period size: 40 Copynumber: 4.0 Consensus size: 40
33104 AAACCATATA
* **
33114 ATATAT-ATATATATAAACTATATAGTTTATAT-TAATAA
1 ATATATAATTTATATAAACTATATAGTTTATATATAATTC
* *
33152 ACTATATAATTTATA-CAA-TATATA--TTATTTATAATT-
1 A-TATATAATTTATATAAACTATATAGTTTATATATAATTC
* * *
33188 ATACATAATATATAAATATAAATTGTATAGTTTATATATAATTC
1 ATATATAAT-T-T--ATATAAACTATATAGTTTATATATAATTC
* * *
33232 ATATATAATTTATATAAACTATGTAGTTTCTATATAGTTC
1 ATATATAATTTATATAAACTATATAGTTTATATATAATTC
33272 A
1 A
33273 ATAGTTCATA
Statistics
Matches: 95, Mismatches: 14, Indels: 22
0.73 0.11 0.17
Matches are distributed among these distances:
35 7 0.07
36 7 0.07
37 5 0.05
38 7 0.07
39 10 0.11
40 33 0.35
41 5 0.05
42 1 0.01
43 12 0.13
44 8 0.08
ACGTcount: A:0.45, C:0.05, G:0.04, T:0.46
Consensus pattern (40 bp):
ATATATAATTTATATAAACTATATAGTTTATATATAATTC
Found at i:33335 original size:27 final size:28
Alignment explanation
Indices: 33292--33407 Score: 86
Period size: 27 Copynumber: 4.4 Consensus size: 28
33282 ATATAAACTT
* * **
33292 TATAGTATTATAGTTTATGCATGGTATA
1 TATAGTATTATACTTTATACATAATATA
33320 TATAGT-TTATACTTTATACATAATATA
1 TATAGTATTATACTTTATACATAATATA
* *
33347 TATA-TA-TATA-TATATATAT-ATATA
1 TATAGTATTATACTTTATACATAATATA
* *
33371 TATA-TATATATA-TATATATATATATATA
1 TATAGTAT-TATACTTTATACATA-ATATA
33399 TATA-TATTA
1 TATAGTATTA
33408 GTTGTTTTAT
Statistics
Matches: 77, Mismatches: 6, Indels: 11
0.82 0.06 0.12
Matches are distributed among these distances:
24 11 0.14
25 7 0.09
26 18 0.23
27 23 0.30
28 18 0.23
ACGTcount: A:0.43, C:0.03, G:0.05, T:0.49
Consensus pattern (28 bp):
TATAGTATTATACTTTATACATAATATA
Found at i:33349 original size:2 final size:2
Alignment explanation
Indices: 33342--33405 Score: 128
Period size: 2 Copynumber: 32.0 Consensus size: 2
33332 TTTATACATA
33342 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
33384 AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT
33406 TAGTTGTTTT
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 62 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:33788 original size:209 final size:213
Alignment explanation
Indices: 33428--34240 Score: 1177
Period size: 209 Copynumber: 3.8 Consensus size: 213
33418 TTTTTTCTCA
* * *
33428 ACTTATTACTTATTTCTATTTATT-AATTGGTCCATAACTTTTTAAATGAATATAATTTAGTA-T
1 ACTTATTACTTATTTATATTT-TTAAATTGGCCCATAACTTTTTAAATGGATATAATTTAGTACT
* *
33491 ATTTTTGTATTAATTTCAACCTCAAAATTTAAAATTATTTCGATTTGATCCCT-T-T-TGTGTTA
65 -TTTTTGTATTAATTTCAACCTCACAATTTAAAATTATTTCGATTTGATCCCTATATGTGTGTTG
* *
33553 TTTAATATATTTAAATTTTTATTTGTAATTT-GTATTTTTTCAATTTAGTCCTCCAAATTTTATT
129 TTTAATATATTTAAATTTTTATTTGTAATTTCATATTTGTTCAATTTAGTCCTCCAAATTTTATT
*
33617 TGCACCTGAAATTGACCCAT
194 TGCATCTGAAATTGACCCAT
* *
33637 ACTTATTACTTATTTATATTTTTAAATTGGCCCGTAACTTTTTAAATGGGTATAATTTAGTACTT
1 ACTTATTACTTATTTATATTTTTAAATTGGCCCATAACTTTTTAAATGGATATAATTTAGTACTT
*
33702 TTTTGTATTAATTTCAACCTCA-AAGTTTAAAATTATTTTGATTTGATCCCT-T-T-TGTGTTGT
66 TTTTGTATTAATTTCAACCTCACAA-TTTAAAATTATTTCGATTTGATCCCTATATGTGTGTTGT
*
33763 TTAATATATTTAAAATTTTATTTGTAATTTCATATTTGTTCAATTTAGTCCTCCAAATTTTATTT
130 TTAATATATTTAAATTTTTATTTGTAATTTCATATTTGTTCAATTTAGTCCTCCAAATTTTATTT
33828 GCATCTGAAATTGACCCAT
195 GCATCTGAAATTGACCCAT
* * *
33847 ACTTATTACTTATTTCTATTTTTAAATTGACACATAAC-TTTTAAATAGG-TATAATTTAGTAC-
1 ACTTATTACTTATTTATATTTTTAAATTGGCCCATAACTTTTTAAAT-GGATATAATTTAGTACT
*
33909 TTTTTGTATTAATTTCAACATCACAATTTAAAATTATTTCGATTTGATCCCTAATCAATGTGTGT
65 TTTTTGTATTAATTTCAACCTCACAATTTAAAATTATTTCGATTTGATCCCT-AT--ATGTGTGT
*
33974 TGTTTAATTTATTTAAATTTTTATTTGTAATTTCATATTTGTTCAATTTAGTCCTCCAAATTTTA
127 TGTTTAATATATTTAAATTTTTATTTGTAATTTCATATTTGTTCAATTTAGTCCTCCAAATTTTA
* * *
34039 TTTGCATATGAAATTGATCAAT
192 TTTGCATCTGAAATTGACCCAT
* * *
34061 ACTTATTACTTAATTCTAT-TTTTTTATTTGGCCCATAACTTTTTAAATGGATATAATTTAGTAT
1 ACTTATTACTT-ATT-TATATTTTTAAATTGGCCCATAACTTTTTAAATGGATATAATTTAGTAC
* * *
34125 TTTTTTGTATTAATTTCAACCTCACAACTTAAAATTATTTCAAGTTGATCCCTCATCAATGTGTG
64 TTTTTTGTATTAATTTCAACCTCACAATTTAAAATTATTTCGATTTGATCCCT-AT--ATGTGTG
*
34190 TTGTTTAATTTATTTAAATTTTTATTTGTAATTTCATATTTGTTCAATTTA
126 TTGTTTAATATATTTAAATTTTTATTTGTAATTTCATATTTGTTCAATTTA
34241 ATTCTTAAAT
Statistics
Matches: 554, Mismatches: 33, Indels: 26
0.90 0.05 0.04
Matches are distributed among these distances:
208 51 0.09
209 163 0.29
210 88 0.16
213 1 0.00
214 98 0.18
215 21 0.04
216 22 0.04
217 110 0.20
ACGTcount: A:0.30, C:0.12, G:0.08, T:0.50
Consensus pattern (213 bp):
ACTTATTACTTATTTATATTTTTAAATTGGCCCATAACTTTTTAAATGGATATAATTTAGTACTT
TTTTGTATTAATTTCAACCTCACAATTTAAAATTATTTCGATTTGATCCCTATATGTGTGTTGTT
TAATATATTTAAATTTTTATTTGTAATTTCATATTTGTTCAATTTAGTCCTCCAAATTTTATTTG
CATCTGAAATTGACCCAT
Found at i:51534 original size:21 final size:22
Alignment explanation
Indices: 51483--51534 Score: 56
Period size: 21 Copynumber: 2.5 Consensus size: 22
51473 CAGTTTGCGA
51483 TTTTTT-TTTTCATGTATTGTT
1 TTTTTTATTTTCATGTATTGTT
**
51504 TTTTACATTTT-ATGTATT-TT
1 TTTTTTATTTTCATGTATTGTT
51524 CTTTTTTATTT
1 -TTTTTTATTT
51535 ATATATATAT
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
20 2 0.08
21 19 0.76
22 4 0.16
ACGTcount: A:0.13, C:0.06, G:0.06, T:0.75
Consensus pattern (22 bp):
TTTTTTATTTTCATGTATTGTT
Found at i:51539 original size:2 final size:2
Alignment explanation
Indices: 51534--51570 Score: 51
Period size: 2 Copynumber: 19.5 Consensus size: 2
51524 CTTTTTTATT
*
51534 TA TA TA TA TA TA TA T- TA GA T- TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
51571 TAATTTTTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
1 2 0.06
2 29 0.94
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (2 bp):
TA
Found at i:51607 original size:36 final size:36
Alignment explanation
Indices: 51562--51634 Score: 85
Period size: 36 Copynumber: 2.0 Consensus size: 36
51552 ATTATATATA
* *
51562 TATATATATTAATT-TTTATTATCTATTTTATTAATT
1 TATACATATTAATTATTTATTATAT-TTTTATTAATT
* * *
51598 TATACATATTTATTATTTTTTATATTTTTATTTATT
1 TATACATATTAATTATTTATTATATTTTTATTAATT
51634 T
1 T
51635 TATTTATATA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
36 23 0.74
37 8 0.26
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.67
Consensus pattern (36 bp):
TATACATATTAATTATTTATTATATTTTTATTAATT
Found at i:51627 original size:18 final size:18
Alignment explanation
Indices: 51587--51637 Score: 57
Period size: 18 Copynumber: 2.8 Consensus size: 18
51577 TTATTATCTA
*
51587 TTTTATTAATTTATACAT
1 TTTTATTATTTTATACAT
* * *
51605 ATTTATTATTTTTTATAT
1 TTTTATTATTTTATACAT
51623 TTTTATTTATTTTAT
1 TTTTA-TTATTTTAT
51638 TTATATACAT
Statistics
Matches: 26, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
18 18 0.69
19 8 0.31
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (18 bp):
TTTTATTATTTTATACAT
Found at i:51768 original size:53 final size:52
Alignment explanation
Indices: 51710--51829 Score: 131
Period size: 53 Copynumber: 2.3 Consensus size: 52
51700 CCCTCTTGCA
51710 TTTATTTATTTATTTACTATGTATATATTATT-TTTATCATTATT-T-TCTAGTAT
1 TTTATTTATTTATTTACT-TGTATATATT-TTATTTAT--TTATTATGTCTAGTAT
* * **
51763 TTTATTTATTTTATTTTCTTTTATATATTTTATTTATTTATTATGTCTTTTAT
1 TTTATTTA-TTTATTTACTTGTATATATTTTATTTATTTATTATGTCTAGTAT
51816 TTT-TTTATTTATTT
1 TTTATTTATTTATTT
51830 TTCTTTTCGT
Statistics
Matches: 59, Mismatches: 4, Indels: 10
0.81 0.05 0.14
Matches are distributed among these distances:
51 12 0.20
52 7 0.12
53 31 0.53
54 9 0.15
ACGTcount: A:0.23, C:0.04, G:0.03, T:0.71
Consensus pattern (52 bp):
TTTATTTATTTATTTACTTGTATATATTTTATTTATTTATTATGTCTAGTAT
Found at i:51774 original size:9 final size:9
Alignment explanation
Indices: 51760--51830 Score: 72
Period size: 9 Copynumber: 7.7 Consensus size: 9
51750 TATTTTCTAG
51760 TATTTTATT
1 TATTTTATT
51769 TATTTTATTT
1 TATTTTA-TT
* *
51779 TCTTTTATA
1 TATTTTATT
51788 TATTTTATT
1 TATTTTATT
*
51797 TATTTATTATG
1 TA-TT-TTATT
*
51808 TCTTTTATT
1 TATTTTATT
51817 T-TTTTATT
1 TATTTTATT
51825 TATTTT
1 TATTTT
51831 TCTTTTCGTT
Statistics
Matches: 51, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
8 8 0.16
9 26 0.51
10 12 0.24
11 5 0.10
ACGTcount: A:0.20, C:0.03, G:0.01, T:0.76
Consensus pattern (9 bp):
TATTTTATT
Found at i:51794 original size:28 final size:29
Alignment explanation
Indices: 51760--51830 Score: 103
Period size: 28 Copynumber: 2.5 Consensus size: 29
51750 TATTTTCTAG
51760 TATTTTATTTATTTTATT-T-TCTTTTAT
1 TATTTTATTTATTTTATTATGTCTTTTAT
51787 ATATTTTATTTA-TTTATTATGTCTTTTAT
1 -TATTTTATTTATTTTATTATGTCTTTTAT
*
51816 TTTTTTATTTATTTT
1 TATTTTATTTATTTT
51831 TCTTTTCGTT
Statistics
Matches: 39, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
27 6 0.15
28 22 0.56
29 11 0.28
ACGTcount: A:0.20, C:0.03, G:0.01, T:0.76
Consensus pattern (29 bp):
TATTTTATTTATTTTATTATGTCTTTTAT
Found at i:54901 original size:22 final size:20
Alignment explanation
Indices: 54860--54910 Score: 57
Period size: 22 Copynumber: 2.5 Consensus size: 20
54850 TTTTTAAAAT
* *
54860 TTATTTTATATAATTGTTTA
1 TTATATTATATAATTATTTA
54880 TTATATTATATTATATTATTTA
1 TTATATTATA-TA-ATTATTTA
*
54902 ATATATTAT
1 TTATATTAT
54911 TGTCGAGCAC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
20 9 0.35
21 2 0.08
22 15 0.58
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (20 bp):
TTATATTATATAATTATTTA
Found at i:56732 original size:15 final size:15
Alignment explanation
Indices: 56712--56741 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
56702 TAATTATATG
56712 TTTAGTACTTTATAA
1 TTTAGTACTTTATAA
*
56727 TTTAGTATTTTATAA
1 TTTAGTACTTTATAA
56742 ATTAATTTAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.33, C:0.03, G:0.07, T:0.57
Consensus pattern (15 bp):
TTTAGTACTTTATAA
Found at i:58245 original size:2 final size:2
Alignment explanation
Indices: 58238--58306 Score: 138
Period size: 2 Copynumber: 34.5 Consensus size: 2
58228 GTTATTAAAG
58238 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
58280 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
58307 AGGTATAGAC
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 67 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:59034 original size:3 final size:3
Alignment explanation
Indices: 59018--59061 Score: 52
Period size: 3 Copynumber: 14.0 Consensus size: 3
59008 TATATACATG
* *
59018 TTA TTA TAA ATA TTA TTTA TTA TTA TTA TTA TTTA TTA TTA TTA
1 TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA -TTA TTA TTA TTA
59062 ATTCTATTAA
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
3 29 0.83
4 6 0.17
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:59044 original size:13 final size:13
Alignment explanation
Indices: 59028--59079 Score: 54
Period size: 13 Copynumber: 3.8 Consensus size: 13
59018 TTATTATAAA
59028 TATTATT-TATTAT
1 TATTATTAT-TTAT
59041 TATTATTATTTAT
1 TATTATTATTTAT
59054 TATTATTAATTCTAT
1 TATTATT-ATT-TAT
59069 TAATT-TTATTT
1 T-ATTATTATTT
59080 TTACAGGCCC
Statistics
Matches: 35, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
13 19 0.54
14 7 0.20
15 6 0.17
16 3 0.09
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (13 bp):
TATTATTATTTAT
Found at i:59057 original size:16 final size:16
Alignment explanation
Indices: 59018--59061 Score: 70
Period size: 16 Copynumber: 2.8 Consensus size: 16
59008 TATATACATG
* *
59018 TTATTATAAATATTAT
1 TTATTATTATTATTAT
59034 TTATTATTATTATTAT
1 TTATTATTATTATTAT
59050 TTATTATTATTA
1 TTATTATTATTA
59062 ATTCTATTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (16 bp):
TTATTATTATTATTAT
Found at i:60341 original size:23 final size:25
Alignment explanation
Indices: 60314--60360 Score: 64
Period size: 23 Copynumber: 2.0 Consensus size: 25
60304 AGGTTCACCA
60314 ATTATT-TTTGTTTTT-TTT-ATTTT
1 ATTATTCTTT-TTTTTCTTTCATTTT
60337 ATTATTCTTTTTTTTCTTTCATTT
1 ATTATTCTTTTTTTTCTTTCATTT
60361 ATTTAACATT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
23 11 0.52
24 6 0.29
25 4 0.19
ACGTcount: A:0.13, C:0.06, G:0.02, T:0.79
Consensus pattern (25 bp):
ATTATTCTTTTTTTTCTTTCATTTT
Found at i:64228 original size:106 final size:106
Alignment explanation
Indices: 64043--65028 Score: 1711
Period size: 106 Copynumber: 9.3 Consensus size: 106
64033 ATTTTGCTCG
* *
64043 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTTCAGACAACGCAAGTTCAACTTCACGA
1 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
* * *
64108 CGAAGGGACCGCTGGTTGTTAATAAACAATTTCCCAATTTC
66 CGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTC
*
64149 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACGCAAGTTCAACTTCACGA
1 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
* *
64214 CGAAGGGACCGCTGGTTGTCAAAAAATAACTTCCCAATTTC
66 CGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTC
*
64255 AGAGCTAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
1 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
* *
64320 CGAAGGGACCGCTGGTTGTCAACAAATAATTTCCCAATTTC
66 CGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTC
*
64361 AGAGCCAATTTCAACTTCACAGCAAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
1 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
* *
64426 CGAAGGGACCGCTAGTTGTCAACAAACAACTTCTCAATTTC
66 CGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTC
*
64467 AGAGCCAATTTCAACTTCACAGCGAAGGATATTAGACTCCAGACAACGCAAGTTCAACTTCACGA
1 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
*
64532 CGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAATTTC
66 CGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTC
64573 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
1 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
* * *
64638 TGAAGGGACCACTGGTTGTCAACAAACAACTTCTCAATTTC
66 CGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTC
64679 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
1 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
* * *
64744 CGAAGGAACAGCTGGTTGTCAACAAACAACTTCTCAATTTC
66 CGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTC
64785 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
1 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
*
64850 CGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTC
66 CGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTC
*
64891 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGCTCAACTTCACGA
1 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
* * *
64956 CGAAGGGACCGCTGGTTGTCAATAAATAATTTCCCAATTTC
66 CGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTC
* *
64997 AGAGCCAATTTCAACTTCACAACGAAAGATAT
1 AGAGCCAATTTCAACTTCACAGCGAAGGATAT
65029 CGTGCCCAAT
Statistics
Matches: 840, Mismatches: 40, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
106 840 1.00
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.22
Consensus pattern (106 bp):
AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
CGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTC
Found at i:69280 original size:31 final size:32
Alignment explanation
Indices: 69244--69306 Score: 103
Period size: 31 Copynumber: 2.0 Consensus size: 32
69234 AAATTGAAGT
69244 TTAACAATACAT-AATCAAACCTAAAAA-AAAA
1 TTAACAATACATAAAT-AAACCTAAAAATAAAA
69275 TTAACAATACATAAATAAACCTAAAAATAAAA
1 TTAACAATACATAAATAAACCTAAAAATAAAA
69307 AATTAATAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
31 23 0.77
32 7 0.23
ACGTcount: A:0.65, C:0.14, G:0.00, T:0.21
Consensus pattern (32 bp):
TTAACAATACATAAATAAACCTAAAAATAAAA
Found at i:69799 original size:18 final size:18
Alignment explanation
Indices: 69778--69820 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
69768 GTTGTTTTAA
*
69778 AAATAAAAGATAAGAATT
1 AAATAAAAGAAAAGAATT
*
69796 AAATAAAAGAAAATAATT
1 AAATAAAAGAAAAGAATT
*
69814 AATTAAA
1 AAATAAA
69821 TAATTTAAAG
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:0.70, C:0.00, G:0.07, T:0.23
Consensus pattern (18 bp):
AAATAAAAGAAAAGAATT
Found at i:71180 original size:42 final size:41
Alignment explanation
Indices: 71093--71189 Score: 115
Period size: 42 Copynumber: 2.3 Consensus size: 41
71083 CGTTTGTGAC
* ** *
71093 ATAAACGCCGCAATAGTGTGTCCCTTAGTGGCATTTTTGTA
1 ATAAACGCCGTAATAGAATGTCCCTTAGTGGCATTTTTATA
* *
71134 ATAAACGCCGTAATAGAATAGTTCCTTTGTGGCATTTTTA-A
1 ATAAACGCCGTAATAGAAT-GTCCCTTAGTGGCATTTTTATA
71175 TATAAACGCCGTAAT
1 -ATAAACGCCGTAAT
71190 TGTCCTTTAA
Statistics
Matches: 48, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
41 17 0.35
42 31 0.65
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.34
Consensus pattern (41 bp):
ATAAACGCCGTAATAGAATGTCCCTTAGTGGCATTTTTATA
Found at i:78581 original size:21 final size:21
Alignment explanation
Indices: 78563--78655 Score: 91
Period size: 21 Copynumber: 4.3 Consensus size: 21
78553 CAAGGGAAAT
78563 AGAGAGAGCAGCAGCGGAAGC
1 AGAGAGAGCAGCAGCGGAAGC
**
78584 AGCTAGAGCAGCAGCGGAAGC
1 AGAGAGAGCAGCAGCGGAAGC
*
78605 AGAGAGAGAAGCAGCGGCACCA-C
1 AGAGAGAGCAGCAGCGG-A--AGC
* *
78628 AGAGAGAGGCAGCGGCAGAA-C
1 AGAGAGA-GCAGCAGCGGAAGC
78649 AGAGAGA
1 AGAGAGA
78656 AGTAATATAT
Statistics
Matches: 60, Mismatches: 8, Indels: 8
0.79 0.11 0.11
Matches are distributed among these distances:
21 42 0.70
22 1 0.02
23 9 0.15
24 8 0.13
ACGTcount: A:0.39, C:0.20, G:0.40, T:0.01
Consensus pattern (21 bp):
AGAGAGAGCAGCAGCGGAAGC
Found at i:79073 original size:43 final size:43
Alignment explanation
Indices: 79012--79134 Score: 133
Period size: 43 Copynumber: 2.8 Consensus size: 43
79002 TTTGTGAAGA
* * *
79012 AAACGCCGCTAAACATCAACGA-CTATTGCGGTGTTTGT-CTGCC
1 AAACGCCGCTAAATATCAAC-ACCTATTGCGGCGTTT-TAATGCC
* * *
79055 AAATGCCGTTAAATATCAACACCTATTGCGGCGTTTTAATGCT
1 AAACGCCGCTAAATATCAACACCTATTGCGGCGTTTTAATGCC
* *
79098 AAACGCCGCTAAATATCAATACCTTTTTGCGGCGTTT
1 AAACGCCGCTAAATATCAACACC-TATTGCGGCGTTT
79135 GTTGAACAAT
Statistics
Matches: 67, Mismatches: 10, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
42 2 0.03
43 53 0.79
44 12 0.18
ACGTcount: A:0.28, C:0.24, G:0.18, T:0.30
Consensus pattern (43 bp):
AAACGCCGCTAAATATCAACACCTATTGCGGCGTTTTAATGCC
Found at i:80941 original size:17 final size:16
Alignment explanation
Indices: 80910--80943 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
80900 CACGTGAGGA
80910 TTATTTTCTTCTTATT
1 TTATTTTCTTCTTATT
*
80926 TTATTTATCTTTTTATT
1 TTATTT-TCTTCTTATT
80943 T
1 T
80944 ACTATTTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.15, C:0.09, G:0.00, T:0.76
Consensus pattern (16 bp):
TTATTTTCTTCTTATT
Done.