Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000731.1 Hibiscus syriacus cultivar Beakdansim tig00001418_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: 166303
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 2
Found at i:2370 original size:17 final size:16
Alignment explanation
Indices: 2332--2385 Score: 67
Period size: 17 Copynumber: 3.4 Consensus size: 16
2322 TATTTCACTG
2332 AAAAAAATGAAAAAGA
1 AAAAAAATGAAAAAGA
*
2348 CTAAAAAATGAAAAATGA
1 -AAAAAAATGAAAAA-GA
2366 AAAAAAA-G-AAAAGA
1 AAAAAAATGAAAAAGA
2380 AAAAAA
1 AAAAAA
2386 TAAAAGGAGG
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
14 8 0.24
15 4 0.12
16 1 0.03
17 19 0.56
18 2 0.06
ACGTcount: A:0.80, C:0.02, G:0.11, T:0.07
Consensus pattern (16 bp):
AAAAAAATGAAAAAGA
Found at i:3626 original size:41 final size:42
Alignment explanation
Indices: 3517--3870 Score: 295
Period size: 46 Copynumber: 7.9 Consensus size: 42
3507 TCAACTCCCC
3517 AGATCTGATATTCCCTTCAGAGTAAGTGGAACAGGTCTCTCTCTCA
1 AGATCTGATATTCCCTTCAGAGTAAGTGGAACAGG--TCT-TC-CA
* * * *
3563 AGATTTGATATTCCCTTTAGAGTAAGTGGAACAAGTCTGCC-
1 AGATCTGATATTCCCTTCAGAGTAAGTGGAACAGGTCTTCCA
*
3604 AGATCTGATATTCCCTTCAGAGTAAGCGGAACAGGTCTCTCTTCTCAA
1 AGATCTGATATTCCCTTCAGAGTAAGTGGAACAGG----TCTTC-C-A
* **
3652 AGATTTGATATTCCCTTCAGAGTAAGTGGAACAAATCTATCTTCTCCA
1 AGATCTGATATTCCCTTCAGAGTAAGTGGAAC--A--GGTC-T-TCCA
*
3700 AGATCTGATATT-CCTTCAGAGTAAGCGGAACAGGTCTCTCTTCTCA
1 AGATCTGATATTCCCTTCAGAGTAAGTGGAACAGG----TCTTC-CA
* *
3746 AGAT-TGATATTCCCTTCAGAGTAAGTGGAACAAGTCTACC-
1 AGATCTGATATTCCCTTCAGAGTAAGTGGAACAGGTCTTCCA
*
3786 AGATCTGACATTCCCTTCAGAGTAAGTGGAACAGGTCTCTTTTTCCA
1 AGATCTGATATTCCCTTCAGAGTAAGTGGAACAGG--TC---TTCCA
* * *
3833 TGATTTGATATTCCCTTCAGAAG-AAGCGGAACAGGTCT
1 AGATCTGATATTCCCTTCAG-AGTAAGTGGAACAGGTCT
3871 CTCTTTTCCA
Statistics
Matches: 254, Mismatches: 27, Indels: 58
0.75 0.08 0.17
Matches are distributed among these distances:
40 4 0.02
41 60 0.24
42 6 0.02
43 3 0.01
44 3 0.01
45 16 0.06
46 63 0.25
47 48 0.19
48 46 0.18
49 2 0.01
50 3 0.01
ACGTcount: A:0.28, C:0.22, G:0.19, T:0.31
Consensus pattern (42 bp):
AGATCTGATATTCCCTTCAGAGTAAGTGGAACAGGTCTTCCA
Found at i:3742 original size:47 final size:48
Alignment explanation
Indices: 3604--3896 Score: 331
Period size: 48 Copynumber: 6.3 Consensus size: 48
3594 CAAGTCTGCC
*
3604 AGATCTGATATTCCCTTCAGAGTAAGCGGAACAGGTCTCTCTTCTCAA
1 AGATCTGATATTCCCTTCAGAGTAAGCGGAACAGGTCTCTCTTCTCCA
* * ** *
3652 AGATTTGATATTCCCTTCAGAGTAAGTGGAACAAATCTATCTTCTCCA
1 AGATCTGATATTCCCTTCAGAGTAAGCGGAACAGGTCTCTCTTCTCCA
3700 AGATCTGATATT-CCTTCAGAGTAAGCGGAACAGGTCTCTCTTCT-CA
1 AGATCTGATATTCCCTTCAGAGTAAGCGGAACAGGTCTCTCTTCTCCA
* * *
3746 AGAT-TGATATTCCCTTCAGAGTAAGTGGAACAAG----TC-T-ACC-
1 AGATCTGATATTCCCTTCAGAGTAAGCGGAACAGGTCTCTCTTCTCCA
* * *
3786 AGATCTGACATTCCCTTCAGAGTAAGTGGAACAGGTCTCT-TTTTCCA
1 AGATCTGATATTCCCTTCAGAGTAAGCGGAACAGGTCTCTCTTCTCCA
* * *
3833 TGATTTGATATTCCCTTCAGAAG-AAGCGGAACAGGTCTCTCTTTTCCA
1 AGATCTGATATTCCCTTCAG-AGTAAGCGGAACAGGTCTCTCTTCTCCA
* * *
3881 AGGTTTGGTATTCCCT
1 AGATCTGATATTCCCT
3897 GTGACAGCGG
Statistics
Matches: 209, Mismatches: 24, Indels: 24
0.81 0.09 0.09
Matches are distributed among these distances:
40 4 0.02
41 30 0.14
42 2 0.01
45 9 0.04
46 28 0.13
47 61 0.29
48 75 0.36
ACGTcount: A:0.27, C:0.23, G:0.19, T:0.32
Consensus pattern (48 bp):
AGATCTGATATTCCCTTCAGAGTAAGCGGAACAGGTCTCTCTTCTCCA
Found at i:3825 original size:182 final size:182
Alignment explanation
Indices: 3517--3853 Score: 570
Period size: 182 Copynumber: 1.9 Consensus size: 182
3507 TCAACTCCCC
* *
3517 AGATCTGATATTCCCTTCAGAGTAAGTGGAACAGGTCTCTCTCTCAAGATTTGATATTCCCTTTA
1 AGATCTGATATTCCCTTCAGAGTAAGCGGAACAGGTCTCTCTCTCAAGATTTGATATTCCCTTCA
* *
3582 GAGTAAGTGGAACAAGTCTGCCAGATCTGATATTCCCTTCAGAGTAAGCGGAACAGGTCTCTCTT
66 GAGTAAGTGGAACAAGTCTACCAGATCTGACATTCCCTTCAGAGTAAGCGGAACAGGTCTCT-TT
3647 CTCAAAGATTTGATATTCCCTTCAGAGTAAGTGGAACAAATCTATCTTCTCCA
130 CTCAAAGATTTGATATTCCCTTCAGAGTAAGTGGAACAAATCTATCTTCTCCA
3700 AGATCTGATATT-CCTTCAGAGTAAGCGGAACAGGTCTCTCTTCTCAAGA-TTGATATTCCCTTC
1 AGATCTGATATTCCCTTCAGAGTAAGCGGAACAGGTCTCTC-TCTCAAGATTTGATATTCCCTTC
*
3763 AGAGTAAGTGGAACAAGTCTACCAGATCTGACATTCCCTTCAGAGTAAGTGGAACAGGTCTCTTT
65 AGAGTAAGTGGAACAAGTCTACCAGATCTGACATTCCCTTCAGAGTAAGCGGAACAGGTCTCTTT
* * *
3828 TTCCATGATTTGATATTCCCTTCAGA
130 CTCAAAGATTTGATATTCCCTTCAGA
3854 AGAAGCGGAA
Statistics
Matches: 145, Mismatches: 8, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
181 25 0.17
182 100 0.69
183 20 0.14
ACGTcount: A:0.28, C:0.22, G:0.19, T:0.31
Consensus pattern (182 bp):
AGATCTGATATTCCCTTCAGAGTAAGCGGAACAGGTCTCTCTCTCAAGATTTGATATTCCCTTCA
GAGTAAGTGGAACAAGTCTACCAGATCTGACATTCCCTTCAGAGTAAGCGGAACAGGTCTCTTTC
TCAAAGATTTGATATTCCCTTCAGAGTAAGTGGAACAAATCTATCTTCTCCA
Found at i:4135 original size:3 final size:3
Alignment explanation
Indices: 4127--4167 Score: 57
Period size: 3 Copynumber: 13.7 Consensus size: 3
4117 CATCTCGTTC
*
4127 TTA TTA TTA TTA -TA TGTA TTA TTA TTA TTA TTA ATA TTA TT
1 TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA TTA TT
4168 TTACATATTT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
2 2 0.06
3 29 0.85
4 3 0.09
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:4175 original size:12 final size:12
Alignment explanation
Indices: 4127--4176 Score: 50
Period size: 12 Copynumber: 4.2 Consensus size: 12
4117 CATCTCGTTC
*
4127 TTATTATTATTA
1 TTATTATTAATA
*
4139 -TATGTATTATTA
1 TTAT-TATTAATA
4151 TTATTATTAATA
1 TTATTATTAATA
4163 TTATT-TTACATA
1 TTATTATTA-ATA
4175 TT
1 TT
4177 TGGCAGGCTT
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
11 6 0.18
12 25 0.74
13 3 0.09
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.62
Consensus pattern (12 bp):
TTATTATTAATA
Found at i:7877 original size:20 final size:19
Alignment explanation
Indices: 7822--7892 Score: 67
Period size: 20 Copynumber: 3.7 Consensus size: 19
7812 CCTATATATA
*
7822 TTTTTAATTATATT-TTAT
1 TTTTTATTTATATTATTAT
*
7840 TTATTTATTTACTA-TATTCCT
1 TT-TTTATTTA-TATTATT-AT
7861 TTTTTATTTATATTATTA-
1 TTTTTATTTATATTATTAT
7879 TTTTTATTATATAT
1 TTTTTATT-TATAT
7893 CTTATATCAT
Statistics
Matches: 44, Mismatches: 3, Indels: 11
0.76 0.05 0.19
Matches are distributed among these distances:
18 10 0.23
19 15 0.34
20 16 0.36
21 3 0.07
ACGTcount: A:0.27, C:0.04, G:0.00, T:0.69
Consensus pattern (19 bp):
TTTTTATTTATATTATTAT
Found at i:7886 original size:12 final size:12
Alignment explanation
Indices: 7864--7911 Score: 51
Period size: 12 Copynumber: 3.8 Consensus size: 12
7854 TATTCCTTTT
7864 TTATTTATATTA
1 TTATTTATATTA
*
7876 TTATTTTTATTA
1 TTATTTATATTA
*
7888 TATATCTTATATCA
1 T-TAT-TTATATTA
*
7902 TTATATATAT
1 TTATTTATAT
7912 ACATGTATAG
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
12 17 0.57
13 6 0.20
14 7 0.23
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.62
Consensus pattern (12 bp):
TTATTTATATTA
Found at i:8074 original size:26 final size:25
Alignment explanation
Indices: 8022--8113 Score: 71
Period size: 26 Copynumber: 3.6 Consensus size: 25
8012 TCTATTTTTG
8022 TTTTTATTTATTTATATATATTATA
1 TTTTTATTTATTTATATATATTATA
* * * *
8047 TTTTTACTTTATTTTTATTTTTTCTA
1 TTTTTA-TTTATTTATATATATTATA
* *
8073 TTATTATTTTTCTTA-ATATCATATATA
1 TTTTTATTTAT-TTATATAT-AT-TATA
*
8100 TCTTTATTT-TTTAT
1 TTTTTATTTATTTAT
8114 TTGTTTTACT
Statistics
Matches: 50, Mismatches: 12, Indels: 9
0.70 0.17 0.13
Matches are distributed among these distances:
25 16 0.32
26 24 0.48
27 10 0.20
ACGTcount: A:0.25, C:0.05, G:0.00, T:0.70
Consensus pattern (25 bp):
TTTTTATTTATTTATATATATTATA
Found at i:8218 original size:18 final size:17
Alignment explanation
Indices: 8195--8228 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
8185 ATTTTTATTC
8195 CTTTTTAATTTCTTTTAT
1 CTTTTT-ATTTCTTTTAT
*
8213 CTTTTTATTTTTTTTA
1 CTTTTTATTTCTTTTA
8229 CTCCATTAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.15, C:0.09, G:0.00, T:0.76
Consensus pattern (17 bp):
CTTTTTATTTCTTTTAT
Found at i:8292 original size:18 final size:17
Alignment explanation
Indices: 8263--8307 Score: 54
Period size: 19 Copynumber: 2.5 Consensus size: 17
8253 TGTGTCTTTG
*
8263 TTTTTTAATATTTTATTCA
1 TTTTTTTAT-TTTTATT-A
8282 TTTTGTTTATTTTTATTA
1 TTTT-TTTATTTTTATTA
8300 TTTTTTTA
1 TTTTTTTA
8308 CGTGTTTTGT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
17 4 0.17
18 5 0.21
19 11 0.46
20 4 0.17
ACGTcount: A:0.20, C:0.02, G:0.02, T:0.76
Consensus pattern (17 bp):
TTTTTTTATTTTTATTA
Found at i:10258 original size:27 final size:26
Alignment explanation
Indices: 10213--10263 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 26
10203 ACATTTCATG
*
10213 CATTTTTGCATTTTGCATATACATTT
1 CATTTTTGCATTTTGCATAAACATTT
10239 CATTTTTAAGCATTTT-CATAAACAT
1 CATTTTT--GCATTTTGCATAAACAT
10264 GAAATTTCTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
26 7 0.32
27 8 0.36
28 7 0.32
ACGTcount: A:0.29, C:0.16, G:0.06, T:0.49
Consensus pattern (26 bp):
CATTTTTGCATTTTGCATAAACATTT
Found at i:12718 original size:110 final size:106
Alignment explanation
Indices: 12509--12775 Score: 304
Period size: 110 Copynumber: 2.5 Consensus size: 106
12499 ACGAAAGGGC
** * *
12509 TTCCCAGTT-TCAGAGCCAATTTCAACTTCACAGTGAGGGATATTGGACTCAAGACAACACAAGC
1 TTCCCAGTTCT-AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCGAGACAACACAAGC
* * *
12573 TCAAATTCATAACGAAGGGGTGACTGATTGTCAACAAACAACT
65 TCAAATTCACAACGAAGGGGCGACTGACTGTCAACAAACAA-T
* * * * *
12616 TT-TCAGTTTCATTTAGAGTCAATTTTAACTTCACAACGAAGGATATTGAACTCGAGACAACAGA
1 TTCCCAG-TTC---TAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCGAGACAACACA
* * * *
12680 AGCTCAACTTCACAGCGAAGGGGCGGCTGGCTGTCAACAAACAAT
62 AGCTCAAATTCACAACGAAGGGGCGACTGACTGTCAACAAACAAT
* *
12725 TTCCCAGTTCTAGAGCCAATTTCAACTTCACGACGGAGGATATTGGACTCG
1 TTCCCAGTTCTAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCG
12776 GAACAATACT
Statistics
Matches: 132, Mismatches: 22, Indels: 13
0.79 0.13 0.08
Matches are distributed among these distances:
106 39 0.30
107 4 0.03
109 6 0.05
110 82 0.62
111 1 0.01
ACGTcount: A:0.33, C:0.22, G:0.20, T:0.25
Consensus pattern (106 bp):
TTCCCAGTTCTAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCGAGACAACACAAGCT
CAAATTCACAACGAAGGGGCGACTGACTGTCAACAAACAAT
Found at i:14144 original size:20 final size:18
Alignment explanation
Indices: 14119--14201 Score: 60
Period size: 20 Copynumber: 4.3 Consensus size: 18
14109 ATATTCCTTT
14119 TTTTTATTCATATTATATTA
1 TTTTTATT-ATA-TATATTA
14139 TTTTTATTATATATATCT-
1 TTTTTATTATATATAT-TA
* *
14157 TATATCATTATATATATATA
1 T-TTTTATTATATATAT-TA
* *
14177 TATATATATATATATATTAA
1 TTTTTAT-TATATATATT-A
14197 TTTTT
1 TTTTT
14202 CTCCATTTAC
Statistics
Matches: 49, Mismatches: 9, Indels: 10
0.72 0.13 0.15
Matches are distributed among these distances:
18 6 0.12
19 21 0.43
20 22 0.45
ACGTcount: A:0.36, C:0.04, G:0.00, T:0.60
Consensus pattern (18 bp):
TTTTTATTATATATATTA
Found at i:14153 original size:2 final size:2
Alignment explanation
Indices: 14146--14193 Score: 64
Period size: 2 Copynumber: 24.5 Consensus size: 2
14136 TTATTTTTAT
*
14146 TA TA TA TA TC T- TA TA TCA T- TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA
14187 TA TA TA T
1 TA TA TA T
14194 TAATTTTTCT
Statistics
Matches: 42, Mismatches: 1, Indels: 6
0.86 0.02 0.12
Matches are distributed among these distances:
1 2 0.05
2 38 0.90
3 2 0.05
ACGTcount: A:0.44, C:0.04, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:14159 original size:14 final size:15
Alignment explanation
Indices: 14128--14195 Score: 68
Period size: 14 Copynumber: 4.4 Consensus size: 15
14118 TTTTTTATTC
*
14128 ATATTATAT-TATTT
1 ATATTATATATATAT
*
14142 TTATTATATATATCTTAT
1 ATATTATATATA---TAT
14160 ATCATTATATATATAT
1 AT-ATTATATATATAT
14176 ATA-TATATATATAT
1 ATATTATATATATAT
14190 ATATTA
1 ATATTA
14196 ATTTTTCTCC
Statistics
Matches: 45, Mismatches: 3, Indels: 11
0.76 0.05 0.19
Matches are distributed among these distances:
14 22 0.49
15 5 0.11
16 5 0.11
18 3 0.07
19 10 0.22
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (15 bp):
ATATTATATATATAT
Found at i:14237 original size:17 final size:17
Alignment explanation
Indices: 14217--14276 Score: 57
Period size: 17 Copynumber: 3.2 Consensus size: 17
14207 TTTACTATGT
14217 ATATATATTTTTTCTTA
1 ATATATATTTTTTCTTA
* *
14234 ATATTATATTTTATACGTTTTT
1 ATA-TATATTTT-T---TCTTA
14256 ATATATATTTTTTCTTA
1 ATATATATTTTTTCTTA
14273 ATAT
1 ATAT
14277 TCTATTTTTA
Statistics
Matches: 34, Mismatches: 4, Indels: 10
0.71 0.08 0.21
Matches are distributed among these distances:
17 10 0.29
18 8 0.24
19 1 0.03
20 1 0.03
21 8 0.24
22 6 0.18
ACGTcount: A:0.30, C:0.05, G:0.02, T:0.63
Consensus pattern (17 bp):
ATATATATTTTTTCTTA
Found at i:14302 original size:2 final size:2
Alignment explanation
Indices: 14295--14327 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
14285 TATTTTTATT
14295 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
14328 TTATTTTATT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:14303 original size:40 final size:39
Alignment explanation
Indices: 14216--14299 Score: 129
Period size: 39 Copynumber: 2.2 Consensus size: 39
14206 ATTTACTATG
14216 TATATATATTTTTTCTTAATATTATATTTTATACGTTTT
1 TATATATATTTTTTCTTAATATTATATTTTATACGTTTT
*
14255 TATATATATTTTTTCTTAATATTCTATTTT-TA--TTTT
1 TATATATATTTTTTCTTAATATTATATTTTATACGTTTT
*
14291 TATTTATAT
1 TATATATAT
14300 ATATATATAT
Statistics
Matches: 43, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
36 12 0.28
38 2 0.05
39 29 0.67
ACGTcount: A:0.27, C:0.05, G:0.01, T:0.67
Consensus pattern (39 bp):
TATATATATTTTTTCTTAATATTATATTTTATACGTTTT
Found at i:14385 original size:36 final size:36
Alignment explanation
Indices: 14348--14428 Score: 103
Period size: 36 Copynumber: 2.2 Consensus size: 36
14338 TTTTCTGTTA
14348 TTGTTTT-CTTAATATTATGTATATCT-TTATTTTTTAT
1 TTGTTTTACTTAATATTA--TATATCTATTA-TTTTTAT
* *
14385 TTGTTTTACTTAGTATTATATATTTATTATTTTTAT
1 TTGTTTTACTTAATATTATATATCTATTATTTTTAT
14421 TTGTTTTA
1 TTGTTTTA
14429 GTAAATACTA
Statistics
Matches: 40, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
36 21 0.52
37 10 0.25
38 9 0.22
ACGTcount: A:0.22, C:0.04, G:0.06, T:0.68
Consensus pattern (36 bp):
TTGTTTTACTTAATATTATATATCTATTATTTTTAT
Found at i:14498 original size:17 final size:18
Alignment explanation
Indices: 14466--14500 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
14456 ATTTTTATTT
14466 CTTTTTAATTTCTTTTAC
1 CTTTTTAATTTCTTTTAC
*
14484 CTTTTTTATTT-TTTTAC
1 CTTTTTAATTTCTTTTAC
14501 TCCATTAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.14, C:0.14, G:0.00, T:0.71
Consensus pattern (18 bp):
CTTTTTAATTTCTTTTAC
Found at i:14578 original size:11 final size:11
Alignment explanation
Indices: 14562--14587 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
14552 ATTTTGTTTA
14562 TTTTTATTATT
1 TTTTTATTATT
14573 TTTTTATTATT
1 TTTTTATTATT
14584 TTTT
1 TTTT
14588 ACGTGTTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (11 bp):
TTTTTATTATT
Found at i:14585 original size:19 final size:20
Alignment explanation
Indices: 14543--14624 Score: 57
Period size: 19 Copynumber: 4.2 Consensus size: 20
14533 GTTTTTTAAC
*
14543 ATTTTATTCATTTTGTTTA-T
1 ATTTTATT-ATTTTATTTATT
14563 -TTTTATTATTTT-TTTATT
1 ATTTTATTATTTTATTTATT
*
14581 ATTTT-TTACGTGTTTTTTTATT
1 ATTTTATTA--T-TTTATTTATT
* *
14603 -TTTTCTTGTTTTATTTATT
1 ATTTTATTATTTTATTTATT
14622 ATT
1 ATT
14625 CTCACTTTTG
Statistics
Matches: 52, Mismatches: 2, Indels: 16
0.74 0.03 0.23
Matches are distributed among these distances:
17 4 0.08
18 9 0.17
19 20 0.38
20 4 0.08
21 7 0.13
22 8 0.15
ACGTcount: A:0.16, C:0.04, G:0.05, T:0.76
Consensus pattern (20 bp):
ATTTTATTATTTTATTTATT
Found at i:14605 original size:9 final size:9
Alignment explanation
Indices: 14552--14621 Score: 52
Period size: 9 Copynumber: 7.3 Consensus size: 9
14542 CATTTTATTC
*
14552 ATTTTGTTT
1 ATTTTTTTT
*
14561 ATTTTTATT
1 ATTTTTTTT
14570 A-TTTTTTT
1 ATTTTTTTT
14578 ATTATTTTTT
1 ATT-TTTTTT
14588 ACGTGTTTTTTT
1 A--T-TTTTTTT
14600 ATTTTTTCTT
1 ATTTTTT-TT
* *
14610 GTTTTATTT
1 ATTTTTTTT
14619 ATT
1 ATT
14622 ATTCTCACTT
Statistics
Matches: 49, Mismatches: 6, Indels: 12
0.73 0.09 0.18
Matches are distributed among these distances:
8 7 0.14
9 18 0.37
10 15 0.31
12 8 0.16
13 1 0.02
ACGTcount: A:0.14, C:0.03, G:0.06, T:0.77
Consensus pattern (9 bp):
ATTTTTTTT
Found at i:14612 original size:18 final size:19
Alignment explanation
Indices: 14573--14621 Score: 64
Period size: 19 Copynumber: 2.5 Consensus size: 19
14563 TTTTATTATT
14573 TTTTTATTATTTTTTACGTG
1 TTTTT-TTATTTTTTACGTG
*
14593 TTTTTTTATTTTTT-CTTG
1 TTTTTTTATTTTTTACGTG
14611 TTTTATTTATT
1 TTTT-TTTATT
14622 ATTCTCACTT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
18 7 0.26
19 15 0.56
20 5 0.19
ACGTcount: A:0.12, C:0.04, G:0.06, T:0.78
Consensus pattern (19 bp):
TTTTTTTATTTTTTACGTG
Found at i:14623 original size:22 final size:21
Alignment explanation
Indices: 14562--14624 Score: 60
Period size: 20 Copynumber: 3.0 Consensus size: 21
14552 ATTTTGTTTA
* *
14562 TTTTTATTATTTTTTTATTAT
1 TTTTTCTTGTTTTTTTATTAT
*
14583 TTTTTAC--GTGTTTTT-TTAT
1 TTTTT-CTTGTTTTTTTATTAT
14602 TTTTTCTTGTTTTATTTATTAT
1 TTTTTCTTGTTTT-TTTATTAT
14624 T
1 T
14625 CTCACTTTTG
Statistics
Matches: 33, Mismatches: 4, Indels: 9
0.72 0.09 0.20
Matches are distributed among these distances:
18 1 0.03
19 9 0.27
20 10 0.30
21 8 0.24
22 5 0.15
ACGTcount: A:0.14, C:0.03, G:0.05, T:0.78
Consensus pattern (21 bp):
TTTTTCTTGTTTTTTTATTAT
Found at i:15142 original size:40 final size:40
Alignment explanation
Indices: 15087--15168 Score: 164
Period size: 40 Copynumber: 2.0 Consensus size: 40
15077 AATCTGGAGC
15087 GTTTATGTAGAACATTTGACATGGAAAGACCAAATTAGAG
1 GTTTATGTAGAACATTTGACATGGAAAGACCAAATTAGAG
15127 GTTTATGTAGAACATTTGACATGGAAAGACCAAATTAGAG
1 GTTTATGTAGAACATTTGACATGGAAAGACCAAATTAGAG
15167 GT
1 GT
15169 GAGCAAAACT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 42 1.00
ACGTcount: A:0.39, C:0.10, G:0.23, T:0.28
Consensus pattern (40 bp):
GTTTATGTAGAACATTTGACATGGAAAGACCAAATTAGAG
Found at i:15354 original size:2 final size:2
Alignment explanation
Indices: 15349--15393 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
15339 AAAAATATGA
15349 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
15391 AT A
1 AT A
15394 ATTATAGAAA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:20458 original size:23 final size:24
Alignment explanation
Indices: 20432--20477 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 24
20422 TATTTTTTAA
20432 ATTTAAAAAAAAT-AAAATAAAAT
1 ATTTAAAAAAAATAAAAATAAAAT
**
20455 ATTTTTAAAAAATAAAAATAAAA
1 ATTTAAAAAAAATAAAAATAAAA
20478 AATATTTTCT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 11 0.55
24 9 0.45
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (24 bp):
ATTTAAAAAAAATAAAAATAAAAT
Found at i:20471 original size:32 final size:32
Alignment explanation
Indices: 20417--20481 Score: 78
Period size: 32 Copynumber: 2.0 Consensus size: 32
20407 TTATTAATCA
* **
20417 AAAAGTATTTTTTAAATTTAAAAAAAATAAAAT
1 AAAAGTATTTTTAAAAAATAAAAAAAA-AAAAT
*
20450 AAAA-TATTTTTAAAAAATAAAAATAAAAAAT
1 AAAAGTATTTTTAAAAAATAAAAAAAAAAAAT
20481 A
1 A
20482 TTTTCTAGAA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
31 6 0.21
32 18 0.64
33 4 0.14
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (32 bp):
AAAAGTATTTTTAAAAAATAAAAAAAAAAAAT
Found at i:24587 original size:95 final size:93
Alignment explanation
Indices: 24399--24635 Score: 287
Period size: 95 Copynumber: 2.5 Consensus size: 93
24389 ATTGGTGTAC
* * * * *
24399 AATTT-TTTTTAAGAAAATAATTTCAAATTAGATCAATTTTGTTTCAATTGCAAAAAATTAAAAA
1 AATTTGTTTTT-AGAAAACAATCTCAAATGAGATCAATTTTGTTTCAAGTGAAAAAAATTAAAAA
24463 AATTTCGAAAACTGTCTCAAGCAAGACGA
65 AATTTCGAAAACTGTCTCAAGCAAGACGA
* *
24492 AATTTGTTTTTAGGAAAACAATCTCAAGTGAGATCAATTTTGTTTCAAGTGTAAAAAAATTCAAA
1 AATTTGTTTTTA-GAAAACAATCTCAAATGAGATCAATTTTGTTTCAAGTG-AAAAAAATTAAAA
** * * *
24557 ATTTTTTGAAAATTGTCTTAAGCAAGACGA
64 AAATTTCGAAAACTGTCTCAAGCAAGACGA
* * * *
24587 AATTTGTTTTGAGAGGAACAATCTCAATTGGGATCAATTTTGTTTCAAG
1 AATTTGTTTTTAGA-AAACAATCTCAAATGAGATCAATTTTGTTTCAAG
24636 AAATACTATT
Statistics
Matches: 124, Mismatches: 16, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
93 6 0.05
94 40 0.32
95 78 0.63
ACGTcount: A:0.40, C:0.10, G:0.14, T:0.36
Consensus pattern (93 bp):
AATTTGTTTTTAGAAAACAATCTCAAATGAGATCAATTTTGTTTCAAGTGAAAAAAATTAAAAAA
ATTTCGAAAACTGTCTCAAGCAAGACGA
Found at i:26899 original size:3 final size:3
Alignment explanation
Indices: 26893--26949 Score: 55
Period size: 3 Copynumber: 18.7 Consensus size: 3
26883 AGGTTCTAAT
* *
26893 TTA TTA TTAA CTTA TTA TTA TTTA TTA TTA TTA TTA TTA -TA CTA ATA
1 TTA TTA TT-A -TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA
26940 TTA TT- TTA TT
1 TTA TTA TTA TT
26950 TTCATATTAC
Statistics
Matches: 47, Mismatches: 2, Indels: 10
0.80 0.03 0.17
Matches are distributed among these distances:
2 4 0.09
3 36 0.77
4 5 0.11
5 2 0.04
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:28701 original size:6 final size:6
Alignment explanation
Indices: 28692--28754 Score: 65
Period size: 6 Copynumber: 9.8 Consensus size: 6
28682 AATAATGGTA
28692 ATTTTT ATTTTT ATAATATTT CA-TTTT ATTTTT ATTTTT ATTTTT AATTTTT
1 ATTTTT ATTTTT AT--T-TTT -ATTTTT ATTTTT ATTTTT ATTTTT -ATTTTT
*
28744 ATTTTC ATTTT
1 ATTTTT ATTTT
28755 GTTTTATTTA
Statistics
Matches: 50, Mismatches: 1, Indels: 12
0.79 0.02 0.19
Matches are distributed among these distances:
5 1 0.02
6 37 0.74
7 7 0.14
8 1 0.02
9 3 0.06
10 1 0.02
ACGTcount: A:0.22, C:0.03, G:0.00, T:0.75
Consensus pattern (6 bp):
ATTTTT
Found at i:28743 original size:19 final size:18
Alignment explanation
Indices: 28710--28754 Score: 65
Period size: 19 Copynumber: 2.5 Consensus size: 18
28700 TTTTATAATA
28710 TTTCA-TTTTATTTTTAT
1 TTTCATTTTTATTTTTAT
*
28727 TTTTATTTTTAATTTTTAT
1 TTTCATTTTT-ATTTTTAT
28746 TTTCATTTT
1 TTTCATTTT
28755 GTTTTATTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 4 0.17
18 4 0.17
19 16 0.67
ACGTcount: A:0.18, C:0.04, G:0.00, T:0.78
Consensus pattern (18 bp):
TTTCATTTTTATTTTTAT
Found at i:29004 original size:19 final size:18
Alignment explanation
Indices: 28959--29004 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 18
28949 ATTTTCTTTT
*
28959 AATAATTAATATAGAATA
1 AATAATTAATATACAATA
*
28977 AATCAATTAATATTCAATA
1 AAT-AATTAATATACAATA
28996 AATAGATTA
1 AATA-ATTA
29005 TAATTTAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 4 0.17
19 20 0.83
ACGTcount: A:0.57, C:0.04, G:0.04, T:0.35
Consensus pattern (18 bp):
AATAATTAATATACAATA
Found at i:29344 original size:13 final size:14
Alignment explanation
Indices: 29317--29345 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
29307 ATAATTATTT
29317 TTTTAAAATAATTG
1 TTTTAAAATAATTG
29331 TTTTAAAA-AATTG
1 TTTTAAAATAATTG
29344 TT
1 TT
29346 ATGACAATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.47
14 8 0.53
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.52
Consensus pattern (14 bp):
TTTTAAAATAATTG
Found at i:29694 original size:37 final size:37
Alignment explanation
Indices: 29600--29704 Score: 120
Period size: 37 Copynumber: 2.8 Consensus size: 37
29590 CATTTTCGTC
29600 CTACTAGGATTTAAACTCCTAAAAATAGGATAAAATT
1 CTACTAGGATTTAAACTCCTAAAAATAGGATAAAATT
* ** * * * *
29637 TTGTTAGGATTCAAACTCCTAAAAATATGATAGAGTT
1 CTACTAGGATTTAAACTCCTAAAAATAGGATAAAATT
* * *
29674 CTACTAAGATTTAAATTCCTAAAGATAGGAT
1 CTACTAGGATTTAAACTCCTAAAAATAGGAT
29705 CCACAAGCAC
Statistics
Matches: 53, Mismatches: 15, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
37 53 1.00
ACGTcount: A:0.42, C:0.12, G:0.13, T:0.32
Consensus pattern (37 bp):
CTACTAGGATTTAAACTCCTAAAAATAGGATAAAATT
Found at i:30178 original size:22 final size:22
Alignment explanation
Indices: 30125--30178 Score: 58
Period size: 22 Copynumber: 2.5 Consensus size: 22
30115 TTTTCAATTG
*
30125 ATTTTTTATACTATATATTATT
1 ATTTATTATACTATATATTATT
*
30147 A-TTATCTATAC-ATATATTTTTT
1 ATTTAT-TATACTATATA-TTATT
30169 ATTTATTATA
1 ATTTATTATA
30179 TTCATTGGTT
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
21 8 0.30
22 15 0.56
23 4 0.15
ACGTcount: A:0.33, C:0.06, G:0.00, T:0.61
Consensus pattern (22 bp):
ATTTATTATACTATATATTATT
Found at i:30211 original size:2 final size:2
Alignment explanation
Indices: 30195--30235 Score: 66
Period size: 2 Copynumber: 21.0 Consensus size: 2
30185 GGTTATATTT
*
30195 TA TA TA TT TA T- TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
30236 CTTTTTTTAA
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (2 bp):
TA
Found at i:30319 original size:2 final size:2
Alignment explanation
Indices: 30314--30372 Score: 118
Period size: 2 Copynumber: 29.5 Consensus size: 2
30304 ACTTTATCAT
30314 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
30356 TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA T
30373 GTATGTATGT
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 57 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:30494 original size:18 final size:19
Alignment explanation
Indices: 30468--30503 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
30458 GTTTTGGTTT
*
30468 TTTTTATATTA-TATTATA
1 TTTTCATATTACTATTATA
30486 TTTTCATATTACTATTAT
1 TTTTCATATTACTATTAT
30504 TATTGTTATG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.31, C:0.06, G:0.00, T:0.64
Consensus pattern (19 bp):
TTTTCATATTACTATTATA
Found at i:30547 original size:2 final size:2
Alignment explanation
Indices: 30540--30582 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
30530 TTTACTCATT
30540 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
30582 T
1 T
30583 TTCATTTATT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:30607 original size:16 final size:16
Alignment explanation
Indices: 30580--30664 Score: 50
Period size: 16 Copynumber: 5.1 Consensus size: 16
30570 TATATATATA
30580 TATTTCATTTATTCATT
1 TATTT-ATTTATTCATT
*
30597 TATTTATTTATTTTTCCTTT
1 TATTTATTTA---TT-CATT
* *
30617 TATTTATTT-TTTACT
1 TATTTATTTATTCATT
*
30632 TATTT-TATTCTTCATT
1 TATTTAT-TTATTCATT
30648 T-TTTCATTTATTCATT
1 TATTT-ATTTATTCATT
30664 T
1 T
30665 TTCCCTCTGA
Statistics
Matches: 53, Mismatches: 7, Indels: 17
0.69 0.09 0.22
Matches are distributed among these distances:
14 1 0.02
15 11 0.21
16 21 0.40
17 6 0.11
19 2 0.04
20 12 0.23
ACGTcount: A:0.19, C:0.11, G:0.00, T:0.71
Consensus pattern (16 bp):
TATTTATTTATTCATT
Found at i:35122 original size:183 final size:183
Alignment explanation
Indices: 34587--35123 Score: 914
Period size: 183 Copynumber: 2.9 Consensus size: 183
34577 ATTAAATCCG
*
34587 TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGTAAACTCGAAAGCCCTGGCTTTATGA
1 TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
*
34652 ATAGATTATGTTCAAACTATGACACTACTCGGACACTTGGCAATTCGGTGTTTGCTCCACTGCTT
66 ATAGATTATGTTCAAACTATGACACTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTGCTT
* *
34717 TTGTCAGGCCAAAGACTTTGTGATAAGATGAACCCTTCAATGATTTGTCACTC
131 TTGTCAGGCCAAAGACTTTGTGATGAGATGAACCCTTCAGTGATTTGTCACTC
34770 TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
1 TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
34835 ATAGATTATGTTCAAACTATGACACTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTGCTT
66 ATAGATTATGTTCAAACTATGACACTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTGCTT
* *
34900 TTGTCAGGCCAAAGACTTTGTGATGAGACGAACCCTTCAGTGATTTGTCCCTC
131 TTGTCAGGCCAAAGACTTTGTGATGAGATGAACCCTTCAGTGATTTGTCACTC
** * *
34953 TAAAGCTGAGCTATTCCACTAAGATAATTAGTTATAGAGGAAACTCGAAACCCCTGGCTTTATGA
1 TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
* ** * *
35018 ATATATTACATTCAAA-TCATGACATTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCATTGCT
66 ATAGATTATGTTCAAACT-ATGACACTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTGCT
*
35082 TTTGTCAGGTCAAAGACTTTGTGATGAGATGAACCCTTCAGT
130 TTTGTCAGGCCAAAGACTTTGTGATGAGATGAACCCTTCAGT
35124 TAAACCTGAT
Statistics
Matches: 336, Mismatches: 17, Indels: 2
0.95 0.05 0.01
Matches are distributed among these distances:
182 1 0.00
183 335 1.00
ACGTcount: A:0.28, C:0.21, G:0.20, T:0.31
Consensus pattern (183 bp):
TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
ATAGATTATGTTCAAACTATGACACTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTGCTT
TTGTCAGGCCAAAGACTTTGTGATGAGATGAACCCTTCAGTGATTTGTCACTC
Found at i:36300 original size:36 final size:36
Alignment explanation
Indices: 36260--36376 Score: 99
Period size: 36 Copynumber: 3.1 Consensus size: 36
36250 ATACTTTGTC
36260 TCACTTGAGACTGTTTTTCTCGAAAGAAGATTTATT
1 TCACTTGAGACTGTTTTTCTCGAAAGAAGATTTATT
** * ** * * *
36296 TCACTCAAGATTGTTTTTCTTAAAACAAGATTTGTC
1 TCACTTGAGACTGTTTTTCTCGAAAGAAGATTTATT
* * *
36332 TCGCTTGAGACCGTTTTCACTCGAAAGAAGGCATTTCATT
1 TCACTTGAGACTGTTTT-TCTCGAAAGAA-G-ATTT-ATT
36372 TCACT
1 TCACT
36377 CAAGGCTGTT
Statistics
Matches: 57, Mismatches: 20, Indels: 4
0.70 0.25 0.05
Matches are distributed among these distances:
36 40 0.70
37 7 0.12
38 1 0.02
39 4 0.07
40 5 0.09
ACGTcount: A:0.27, C:0.19, G:0.15, T:0.38
Consensus pattern (36 bp):
TCACTTGAGACTGTTTTTCTCGAAAGAAGATTTATT
Found at i:36310 original size:72 final size:75
Alignment explanation
Indices: 36219--36393 Score: 209
Period size: 72 Copynumber: 2.4 Consensus size: 75
36209 ATGCAGATGA
* * * * *
36219 TTATCTCACTCAA-ATTTGTTTTTCTTAAAGCATA-CTTTGTCTCACTTGAGACTGTTTT-TCTC
1 TTATTTCACTCAAGA-TTGTTTTTCTTAAAACA-AGATTTGTCTCACTTGAGACCGTTTTCACTC
36281 GAAAGAA-G-AT
64 GAAAGAAGGCAT
*
36291 TTATTTCACTCAAGATTGTTTTTCTTAAAACAAGATTTGTCTCGCTTGAGACCGTTTTCACTCGA
1 TTATTTCACTCAAGATTGTTTTTCTTAAAACAAGATTTGTCTCACTTGAGACCGTTTTCACTCGA
36356 AAGAAGGCAT
66 AAGAAGGCAT
**
36366 TTCATTTCACTCAAGGCTGTTTTT-TTAA
1 TT-ATTTCACTCAAGATTGTTTTTCTTAA
36394 GAAGATTTTA
Statistics
Matches: 89, Mismatches: 8, Indels: 9
0.84 0.08 0.08
Matches are distributed among these distances:
71 1 0.01
72 49 0.55
73 11 0.12
74 1 0.01
75 8 0.09
76 19 0.21
ACGTcount: A:0.26, C:0.18, G:0.14, T:0.42
Consensus pattern (75 bp):
TTATTTCACTCAAGATTGTTTTTCTTAAAACAAGATTTGTCTCACTTGAGACCGTTTTCACTCGA
AAGAAGGCAT
Found at i:36428 original size:73 final size:72
Alignment explanation
Indices: 36235--36430 Score: 177
Period size: 72 Copynumber: 2.7 Consensus size: 72
36225 CACTCAAATT
* * * * *
36235 TGTTTTTCTTAAAGCATA-CTTTGTCTCACTTGAGACTGTTTT-TCTCGAAAGAAGATTTATTTC
1 TGTTTTTCTTAAA-CA-AGATTTATCTCGCTTGAGACAGTTTTCACTCGAAAGAAGATTTATTTC
*
36298 ACTCAAGAT
64 ACTCAAGAC
* *
36307 TGTTTTTCTTAAAACAAGATTTGTCTCGCTTGAGACCGTTTTCACTCGAAAGAAGGCATTTCATT
1 TGTTTTTCTT-AAACAAGATTTATCTCGCTTGAGACAGTTTTCACTCGAAAGAA-G-ATTT-ATT
*
36372 TCACTCAAGGC
62 TCACTCAAGAC
* * * *
36383 TGTTTTT-TT-AAGAAGATTTTATCTTGCTTGAGATAG-TTTCCCTCGAAA
1 TGTTTTTCTTAAACAAGA-TTTATCTCGCTTGAGACAGTTTTCACTCGAAA
36431 CAGAAAATTT
Statistics
Matches: 105, Mismatches: 12, Indels: 13
0.81 0.09 0.10
Matches are distributed among these distances:
71 1 0.01
72 33 0.31
73 30 0.29
74 16 0.15
75 6 0.06
76 19 0.18
ACGTcount: A:0.26, C:0.17, G:0.16, T:0.41
Consensus pattern (72 bp):
TGTTTTTCTTAAACAAGATTTATCTCGCTTGAGACAGTTTTCACTCGAAAGAAGATTTATTTCAC
TCAAGAC
Found at i:36544 original size:39 final size:39
Alignment explanation
Indices: 36487--36561 Score: 98
Period size: 39 Copynumber: 1.9 Consensus size: 39
36477 CCTTGAAATT
* *
36487 AATTTTTTCTCTCCTGAGATAGTTTCCCTCGAAACAGAA
1 AATTTTGTCTCTCCTGAGACAGTTTCCCTCGAAACAGAA
* *
36526 AATTTTGTCTC-CCTTGAGACAGTTTCTCTTGAAACA
1 AATTTTGTCTCTCC-TGAGACAGTTTCCCTCGAAACA
36562 TAAACATTGA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
38 2 0.06
39 29 0.94
ACGTcount: A:0.27, C:0.23, G:0.13, T:0.37
Consensus pattern (39 bp):
AATTTTGTCTCTCCTGAGACAGTTTCCCTCGAAACAGAA
Found at i:36732 original size:36 final size:36
Alignment explanation
Indices: 36679--36754 Score: 109
Period size: 36 Copynumber: 2.1 Consensus size: 36
36669 ATTGAAAACA
* *
36679 TTTCCCTTGAAATGAATTTTATCTCGCTTGAGATAG
1 TTTCCCTTGAAATGAATTTTATCTCCCTTGAGACAG
*
36715 TTTCCCTTG-AATCGAATTTTGTCTCCCTTGAGACAG
1 TTTCCCTTGAAAT-GAATTTTATCTCCCTTGAGACAG
36751 TTTC
1 TTTC
36755 TCTCCAAACA
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
35 3 0.08
36 33 0.92
ACGTcount: A:0.21, C:0.21, G:0.16, T:0.42
Consensus pattern (36 bp):
TTTCCCTTGAAATGAATTTTATCTCCCTTGAGACAG
Found at i:36768 original size:101 final size:103
Alignment explanation
Indices: 36464--36779 Score: 485
Period size: 102 Copynumber: 3.1 Consensus size: 103
36454 ATAGTTTCTC
* *
36464 TTGAAAACATTTCCCTTGAAATTAATTTTTTCTCTCCTGAGATAGTTTCCCTCGAAACAGAAAAT
1 TTGAAAACATTTCCCTTGAAATGAATTTTTTCTCTCTTGAGATAGTTTCCCTCGAAACAG-AAAT
36529 TTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACA
65 TTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACA
*
36568 TTGAAAACATTTCCCTTGAAATG-ATTTTTTTTCTCTTGAGATAGTTTCCCTCGAAACAGAAATT
1 TTGAAAACATTTCCCTTGAAATGAATTTTTTCTCTCTTGAGATAGTTTCCCTCGAAACAGAAATT
* * *
36632 TTATCTCCCTTGAGACAATTTCTCTTGAAATATAAACA
66 TTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACA
* * * *
36670 TTGAAAACATTTCCCTTGAAATGAATTTTATCTCGCTTGAGATAGTTTCCCTTGAATC-G-AATT
1 TTGAAAACATTTCCCTTGAAATGAATTTTTTCTCTCTTGAGATAGTTTCCCTCGAAACAGAAATT
** *
36733 TTGTCTCCCTTGAGACAGTTTCTCTCCAAACATAAACT
66 TTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACA
36771 TTGAAAACA
1 TTGAAAACA
36780 ATTTAACGAA
Statistics
Matches: 194, Mismatches: 17, Indels: 5
0.90 0.08 0.02
Matches are distributed among these distances:
101 45 0.23
102 64 0.33
103 63 0.32
104 22 0.11
ACGTcount: A:0.31, C:0.20, G:0.12, T:0.37
Consensus pattern (103 bp):
TTGAAAACATTTCCCTTGAAATGAATTTTTTCTCTCTTGAGATAGTTTCCCTCGAAACAGAAATT
TTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACA
Found at i:37151 original size:105 final size:105
Alignment explanation
Indices: 36954--37583 Score: 853
Period size: 105 Copynumber: 6.0 Consensus size: 105
36944 ATATCGTGAC
* * * * *
36954 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGA-CGACTGGTTGTCAACAAACAACTTCT
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCG-CTGCTTGTCAA-AAACAACTTCC
37018 CAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
64 CAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* *
37060 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAATAACAACTTCTCA
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAAAAACAACTTCCCA
37125 ATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 ATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * *
37165 ACTTCAGTCAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCA
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAAAAACAACTTCCCA
*
37230 ATCTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 ATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* *
37270 ACTCCAGACAACGCAAGTTCAACTTCACGATGAAGGGACCGCTGCTTGTCAACAACAACTTCCCA
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAAAAACAACTTCCCA
*
37335 ATCTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 ATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * *
37375 ACTCCAGACAACGCAAGTTCAAC-TCTATGACGAAGGGACCGCTGCTTGTCAATAA-AA-TT-TC
1 ACTCCAGACAACGCAAGTTCAACTTC-ACGACGAAGGGACCGCTGCTTGTCAAAAACAACTTCCC
* * *
37436 -A-TTCAGAGTC-ATTTCAACTTCACAGCGAAGGATATTGA
65 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* ** * * * ** * *
37474 AATTGAGACAACACAAGTTCAACTTCACAATGAAGGGATGGCTGGTTGTCAACAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAA-AAACAACTTCCC
** * * *
37539 GGTTCCAGAGCCAATTTCAACTTCACGACGGAGGATATTGG
65 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
37580 ACTC
1 ACTC
37584 GGAACAATGC
Statistics
Matches: 472, Mismatches: 42, Indels: 20
0.88 0.08 0.04
Matches are distributed among these distances:
99 65 0.14
100 11 0.02
101 3 0.01
102 3 0.01
103 3 0.01
104 4 0.01
105 310 0.66
106 71 0.15
107 2 0.00
ACGTcount: A:0.34, C:0.26, G:0.18, T:0.23
Consensus pattern (105 bp):
ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAAAAACAACTTCCCA
ATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
Found at i:38179 original size:37 final size:37
Alignment explanation
Indices: 38126--38230 Score: 138
Period size: 37 Copynumber: 2.8 Consensus size: 37
38116 CATTTTCGTC
38126 CTACTAGGATTCAAACTCCTAAAAATAGGATAAAATT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAAAATT
* * * *
38163 TTGCTAGGATTCAAACTCCTAAAAATAGGATAGAGTT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAAAATT
* * * *
38200 CTACTAAGATTTAAATTCCTAAAGATAGGAT
1 CTACTAGGATTCAAACTCCTAAAAATAGGAT
38231 CCACAAGCAC
Statistics
Matches: 58, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
37 58 1.00
ACGTcount: A:0.42, C:0.14, G:0.14, T:0.30
Consensus pattern (37 bp):
CTACTAGGATTCAAACTCCTAAAAATAGGATAAAATT
Found at i:39018 original size:18 final size:19
Alignment explanation
Indices: 38992--39027 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
38982 TTTTTGGTTT
*
38992 TTTTTATATTA-TATTATA
1 TTTTCATATTACTATTATA
39010 TTTTCATATTACTATTAT
1 TTTTCATATTACTATTAT
39028 TATTGTTATG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.31, C:0.06, G:0.00, T:0.64
Consensus pattern (19 bp):
TTTTCATATTACTATTATA
Found at i:39098 original size:4 final size:4
Alignment explanation
Indices: 39091--39136 Score: 60
Period size: 4 Copynumber: 11.8 Consensus size: 4
39081 ATATTAATAT
*
39091 TTTA TTTA TTTA TTTA TTT- TTTCT TTTA TTTA TTT- TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTT-A TTTA TTTA TTTA TTTA TTTA TTT
39137 TTATTCTTCA
Statistics
Matches: 38, Mismatches: 1, Indels: 6
0.84 0.02 0.13
Matches are distributed among these distances:
3 6 0.16
4 29 0.76
5 3 0.08
ACGTcount: A:0.17, C:0.02, G:0.00, T:0.80
Consensus pattern (4 bp):
TTTA
Found at i:40195 original size:31 final size:31
Alignment explanation
Indices: 40155--40218 Score: 110
Period size: 31 Copynumber: 2.1 Consensus size: 31
40145 AAAACATACT
* *
40155 ATATGATTATTTTCGTTTTTATTTAATTAAG
1 ATATAATTATTTTAGTTTTTATTTAATTAAG
40186 ATATAATTATTTTAGTTTTTATTTAATTAAG
1 ATATAATTATTTTAGTTTTTATTTAATTAAG
40217 AT
1 AT
40219 GTGATCACCA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.33, C:0.02, G:0.08, T:0.58
Consensus pattern (31 bp):
ATATAATTATTTTAGTTTTTATTTAATTAAG
Found at i:40495 original size:25 final size:26
Alignment explanation
Indices: 40458--40506 Score: 75
Period size: 25 Copynumber: 1.9 Consensus size: 26
40448 AAAAATAATT
40458 TTTTTAAATTAAGTTAATAATAAAATA
1 TTTTTAAATTAAGTTAAT-ATAAAATA
40485 TTTTT-AA-TAAGTTAATATAAAA
1 TTTTTAAATTAAGTTAATATAAAA
40507 AACATTTCTT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 6 0.27
25 9 0.41
26 2 0.09
27 5 0.23
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.45
Consensus pattern (26 bp):
TTTTTAAATTAAGTTAATATAAAATA
Found at i:40507 original size:25 final size:25
Alignment explanation
Indices: 40458--40538 Score: 69
Period size: 26 Copynumber: 3.1 Consensus size: 25
40448 AAAAATAATT
40458 TTTTTAAATTAAGTTAATA-ATAAAATA
1 TTTTT-AA-TAAGTTAATATA-AAAATA
*
40485 TTTTTAATAAGTTAATATAAAAAACA
1 TTTTTAATAAGTTAATAT-AAAAATA
40511 TTTCTT-A-AAGTTAACATATAAAAATA
1 TTT-TTAATAAGTT-A-ATATAAAAATA
40537 TT
1 TT
40539 ATAAATGATA
Statistics
Matches: 47, Mismatches: 2, Indels: 11
0.78 0.03 0.18
Matches are distributed among these distances:
25 15 0.32
26 20 0.43
27 12 0.26
ACGTcount: A:0.51, C:0.04, G:0.04, T:0.42
Consensus pattern (25 bp):
TTTTTAATAAGTTAATATAAAAATA
Found at i:40518 original size:27 final size:25
Alignment explanation
Indices: 40467--40534 Score: 68
Period size: 25 Copynumber: 2.7 Consensus size: 25
40457 TTTTTTAAAT
* *
40467 TAAGTTAATA-ATAAAATATTTTTAA
1 TAAGTTAATATAAAAAACATTTTT-A
40492 TAAGTTAATATAAAAAACATTTCTTA
1 TAAGTTAATATAAAAAACATTT-TTA
*
40518 -AAGTTAACATATAAAAA
1 TAAGTTAATATA-AAAAA
40535 TATTATAAAT
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
25 20 0.54
26 15 0.41
27 2 0.05
ACGTcount: A:0.54, C:0.04, G:0.04, T:0.37
Consensus pattern (25 bp):
TAAGTTAATATAAAAAACATTTTTA
Found at i:46619 original size:15 final size:16
Alignment explanation
Indices: 46591--46620 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
46581 AAACAAAAAT
46591 AAATAAATACAATGAC
1 AAATAAATACAATGAC
46607 AAATAAA-ACAATGA
1 AAATAAATACAATGA
46621 AACCATGATA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.67, C:0.10, G:0.07, T:0.17
Consensus pattern (16 bp):
AAATAAATACAATGAC
Found at i:47777 original size:24 final size:24
Alignment explanation
Indices: 47750--47801 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
47740 AACGGATATA
*
47750 TCAAAAATCAAAACATAAATCAGG
1 TCAAAAATCAAAACAGAAATCAGG
** * *
47774 TCAAGTATCATATCAGAAATCAGG
1 TCAAAAATCAAAACAGAAATCAGG
47798 TCAA
1 TCAA
47802 GTAACAGATC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.50, C:0.17, G:0.12, T:0.21
Consensus pattern (24 bp):
TCAAAAATCAAAACAGAAATCAGG
Found at i:47802 original size:24 final size:24
Alignment explanation
Indices: 47770--47888 Score: 161
Period size: 24 Copynumber: 5.0 Consensus size: 24
47760 AAACATAAAT
*
47770 CAGGTCAAGTATCATATCAGAAAT-
1 CAGGTCAAGTATCAGATCAG-AATC
*
47794 CAGGTCAAGTAACAGATCAGAATC
1 CAGGTCAAGTATCAGATCAGAATC
*
47818 CAAGTCAAGTATCAGATCAGAATC
1 CAGGTCAAGTATCAGATCAGAATC
*
47842 CATGTC-AGATATCAGATCAGAATC
1 CAGGTCAAG-TATCAGATCAGAATC
*
47866 CATGTCAAGTATCAGATCAGAAT
1 CAGGTCAAGTATCAGATCAGAAT
47889 TCAAATCGAA
Statistics
Matches: 87, Mismatches: 5, Indels: 6
0.89 0.05 0.06
Matches are distributed among these distances:
23 5 0.06
24 80 0.92
25 2 0.02
ACGTcount: A:0.40, C:0.19, G:0.18, T:0.23
Consensus pattern (24 bp):
CAGGTCAAGTATCAGATCAGAATC
Found at i:47904 original size:48 final size:48
Alignment explanation
Indices: 47806--47906 Score: 141
Period size: 48 Copynumber: 2.1 Consensus size: 48
47796 GGTCAAGTAA
** *
47806 CAGATCAGAATCCAAGTCAAGTATCAGATCAGAATCCATGTCAGATAT
1 CAGATCAGAATCCAAGTCAAGTATCAGATCAGAATCCAAATCAGAAAT
* *
47854 CAGATCAGAATCCATGTCAAGTATCAGATCAGAATTCAAATC-GAAAAT
1 CAGATCAGAATCCAAGTCAAGTATCAGATCAGAATCCAAATCAG-AAAT
47902 CAGAT
1 CAGAT
47907 AAAATATTCA
Statistics
Matches: 47, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
47 1 0.02
48 46 0.98
ACGTcount: A:0.42, C:0.20, G:0.16, T:0.23
Consensus pattern (48 bp):
CAGATCAGAATCCAAGTCAAGTATCAGATCAGAATCCAAATCAGAAAT
Found at i:50371 original size:7 final size:7
Alignment explanation
Indices: 50359--50420 Score: 88
Period size: 7 Copynumber: 8.4 Consensus size: 7
50349 TGGTCAACGC
50359 CGGTCAA
1 CGGTCAA
50366 CGGTCAA
1 CGGTCAA
*
50373 TGGGTCAA
1 -CGGTCAA
50381 CGGTCAA
1 CGGTCAA
50388 CGGGTCAA
1 C-GGTCAA
50396 CGGTCAA
1 CGGTCAA
50403 CGGGTCAA
1 C-GGTCAA
50411 CGGTCAA
1 CGGTCAA
50418 CGG
1 CGG
50421 GTCGGGTCGA
Statistics
Matches: 50, Mismatches: 2, Indels: 6
0.86 0.03 0.10
Matches are distributed among these distances:
7 30 0.60
8 20 0.40
ACGTcount: A:0.26, C:0.26, G:0.34, T:0.15
Consensus pattern (7 bp):
CGGTCAA
Found at i:50380 original size:15 final size:15
Alignment explanation
Indices: 50350--50423 Score: 121
Period size: 15 Copynumber: 4.8 Consensus size: 15
50340 GGTCAACAGT
50350 GGTCAACGCCGGTCAAC
1 GGTCAACG--GGTCAAC
*
50367 GGTCAATGGGTCAAC
1 GGTCAACGGGTCAAC
50382 GGTCAACGGGTCAAC
1 GGTCAACGGGTCAAC
50397 GGTCAACGGGTCAAC
1 GGTCAACGGGTCAAC
50412 GGTCAACGGGTC
1 GGTCAACGGGTC
50424 GGGTCGATTC
Statistics
Matches: 55, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
15 48 0.87
17 7 0.13
ACGTcount: A:0.24, C:0.27, G:0.34, T:0.15
Consensus pattern (15 bp):
GGTCAACGGGTCAAC
Found at i:50451 original size:14 final size:13
Alignment explanation
Indices: 50432--50465 Score: 59
Period size: 13 Copynumber: 2.5 Consensus size: 13
50422 TCGGGTCGAT
50432 TCGGGTCAACGGGG
1 TCGGGTCAAC-GGG
50446 TCGGGTCAACGGG
1 TCGGGTCAACGGG
50459 TCGGGTC
1 TCGGGTC
50466 GGGTTGTGAC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 10 0.50
14 10 0.50
ACGTcount: A:0.12, C:0.24, G:0.47, T:0.18
Consensus pattern (13 bp):
TCGGGTCAACGGG
Found at i:53621 original size:2 final size:2
Alignment explanation
Indices: 53614--53643 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
53604 CTACACAATA
53614 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
53644 GAATAAATTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:53771 original size:25 final size:25
Alignment explanation
Indices: 53728--53776 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
53718 ATTAATTACT
*
53728 AATATTATCGATTTATAACAAAATA
1 AATATTATCGATATATAACAAAATA
* *
53753 AATATTATTGATATGTAACAAAAT
1 AATATTATCGATATATAACAAAAT
53777 GGTCATCCTG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.51, C:0.06, G:0.06, T:0.37
Consensus pattern (25 bp):
AATATTATCGATATATAACAAAATA
Found at i:56680 original size:43 final size:43
Alignment explanation
Indices: 56594--56812 Score: 187
Period size: 42 Copynumber: 5.1 Consensus size: 43
56584 ATATAAAAAT
* * * * *
56594 GCCGCAAAATGTCAAGTTCTCTAGCGGCGTTTTTGCCA-A-AAAC
1 GCCGCAAAAGGTC-AGATCTATAGCGGCATTTTTG-GATACAAAC
* * *
56637 GCCGCAAAAGGGT-AGATATATAGCGGCGTTGTTGGATACAAAC
1 GCCGCAAAA-GGTCAGATCTATAGCGGCATTTTTGGATACAAAC
** * *
56680 GCCGCAAAAGGTCAAGATCTATAGCGG-ATTTTTTAAAAAAAAC
1 GCCGCAAAAGGTC-AGATCTATAGCGGCATTTTTGGATACAAAC
* * *
56723 GCCGCAAGAGGTCAGATCTATAGCGGTA-TTTTGGACACAAAC
1 GCCGCAAAAGGTCAGATCTATAGCGGCATTTTTGGATACAAAC
* * * * *
56765 GCTGCAAAATGTCATATCTATAGCGGCGTTTTTGGATATAAAC
1 GCCGCAAAAGGTCAGATCTATAGCGGCATTTTTGGATACAAAC
56808 GCCGC
1 GCCGC
56813 TAATTACCAT
Statistics
Matches: 142, Mismatches: 27, Indels: 14
0.78 0.15 0.08
Matches are distributed among these distances:
41 1 0.01
42 66 0.46
43 61 0.43
44 14 0.10
ACGTcount: A:0.32, C:0.20, G:0.24, T:0.24
Consensus pattern (43 bp):
GCCGCAAAAGGTCAGATCTATAGCGGCATTTTTGGATACAAAC
Found at i:56745 original size:86 final size:85
Alignment explanation
Indices: 56594--56797 Score: 232
Period size: 86 Copynumber: 2.4 Consensus size: 85
56584 ATATAAAAAT
* * * ***
56594 GCCGCAAAATGTCAAGTTCTCTAGCGGCGTTTTTGCCAAAAACGCCGCAAAAGGGTAGATATATA
1 GCCGCAAAATGTCAAGATCTATAGCGGAGTTTTTAAAAAAAACGCCGCAAAAGGGTAGATATATA
* *
56659 GCGGCGTTGTTGGATACAAAC
66 GCGGCATT-TTGGACACAAAC
* * * *
56680 GCCGCAAAAGGTCAAGATCTATAGCGGATTTTTTAAAAAAAACGCCGCAAGA-GGTCAGATCTAT
1 GCCGCAAAATGTCAAGATCTATAGCGGAGTTTTTAAAAAAAACGCCGCAAAAGGGT-AGATATAT
*
56744 AGCGGTATTTTGGACACAAAC
65 AGCGGCATTTTGGACACAAAC
* * *
56765 GCTGCAAAATGTC-ATATCTATAGCGGCGTTTTT
1 GCCGCAAAATGTCAAGATCTATAGCGGAGTTTTT
56798 GGATATAAAC
Statistics
Matches: 99, Mismatches: 18, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
84 17 0.17
85 25 0.25
86 57 0.58
ACGTcount: A:0.32, C:0.20, G:0.24, T:0.25
Consensus pattern (85 bp):
GCCGCAAAATGTCAAGATCTATAGCGGAGTTTTTAAAAAAAACGCCGCAAAAGGGTAGATATATA
GCGGCATTTTGGACACAAAC
Found at i:56765 original size:42 final size:42
Alignment explanation
Indices: 56633--56812 Score: 168
Period size: 43 Copynumber: 4.2 Consensus size: 42
56623 TTTTTGCCAA
* **
56633 AAACGCCGCAAAAGGGT-AGATATATAGCGGCGTTGTTGGATAC
1 AAACGCCGCAAAA-GGTCAGATCTATAGCGGTATT-TTGGATAC
** * *
56676 AAACGCCGCAAAAGGTCAAGATCTATAGCGG-ATTTTTTAAAAA
1 AAACGCCGCAAAAGGTC-AGATCTATAGCGGTA-TTTTGGATAC
* *
56719 AAACGCCGCAAGAGGTCAGATCTATAGCGGTATTTTGGACAC
1 AAACGCCGCAAAAGGTCAGATCTATAGCGGTATTTTGGATAC
* * * *
56761 AAACGCTGCAAAATGTCATATCTATAGCGGCGT-TTTTGGATAT
1 AAACGCCGCAAAAGGTCAGATCTATAGC-G-GTATTTTGGATAC
56804 AAACGCCGC
1 AAACGCCGC
56813 TAATTACCAT
Statistics
Matches: 113, Mismatches: 18, Indels: 12
0.79 0.13 0.08
Matches are distributed among these distances:
42 46 0.41
43 51 0.45
44 16 0.14
ACGTcount: A:0.34, C:0.19, G:0.24, T:0.23
Consensus pattern (42 bp):
AAACGCCGCAAAAGGTCAGATCTATAGCGGTATTTTGGATAC
Found at i:57480 original size:2 final size:2
Alignment explanation
Indices: 57473--57539 Score: 134
Period size: 2 Copynumber: 33.5 Consensus size: 2
57463 GAATCAAGCG
57473 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
57515 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 A
57540 GGATAGTGGA
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 65 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:59341 original size:2 final size:2
Alignment explanation
Indices: 59334--59388 Score: 110
Period size: 2 Copynumber: 27.5 Consensus size: 2
59324 TCAGAATTAG
59334 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
59376 TA TA TA TA TA TA T
1 TA TA TA TA TA TA T
59389 CAATTTTATT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:68851 original size:3 final size:3
Alignment explanation
Indices: 68839--68908 Score: 88
Period size: 3 Copynumber: 23.0 Consensus size: 3
68829 TAAATATTAT
* *
68839 TAA TAA -AA TAA TAA TAA TAA TAA TAA TAA TTA TAA TTA TAA TAA TAAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA
*
68887 TGA TAA TAA TAAA TAA TAA TAA
1 TAA TAA TAA T-AA TAA TAA TAA
68909 AACAAACTCA
Statistics
Matches: 58, Mismatches: 6, Indels: 6
0.83 0.09 0.09
Matches are distributed among these distances:
2 2 0.03
3 50 0.86
4 6 0.10
ACGTcount: A:0.64, C:0.00, G:0.01, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:71695 original size:44 final size:44
Alignment explanation
Indices: 71502--71755 Score: 195
Period size: 44 Copynumber: 5.8 Consensus size: 44
71492 CATTTGATTG
* * * * *
71502 TGTTGATCCATCTCCTTCTGTAATGGAATCTAACAAAAGAGAAA
1 TGTTGATCCAACTCCTTATGTGATGGAATCGAACAAAAGAGTAA
* * * * * * * *
71546 TATTGATTCAACTCCTTATATGATGGAATCCAACGAAATAATGA
1 TGTTGATCCAACTCCTTATGTGATGGAATCGAACAAAAGAGTAA
* * * * * * *
71590 TGATGATCCAACTTCTTATATGATAGAATCTAGCAAAA-ACGGAA
1 TGTTGATCCAACTCCTTATGTGATGGAATCGAACAAAAGA-GTAA
** *
71634 TGTTGATCCGTCTCCTTCTGTGATGGAATCGAACAAAAGAGTAA
1 TGTTGATCCAACTCCTTATGTGATGGAATCGAACAAAAGAGTAA
* * * * * * *
71678 TGTTGATCCAAATCCTTCTGTGATGAAATTGAGCTAAATAGTAA
1 TGTTGATCCAACTCCTTATGTGATGGAATCGAACAAAAGAGTAA
* * *
71722 TGTTGATCTAACTCCATATGTAATGGAATCGAAC
1 TGTTGATCCAACTCCTTATGTGATGGAATCGAAC
71756 CTTTAAAAAT
Statistics
Matches: 159, Mismatches: 49, Indels: 4
0.75 0.23 0.02
Matches are distributed among these distances:
43 1 0.01
44 157 0.99
45 1 0.01
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.31
Consensus pattern (44 bp):
TGTTGATCCAACTCCTTATGTGATGGAATCGAACAAAAGAGTAA
Found at i:71751 original size:132 final size:132
Alignment explanation
Indices: 71502--71751 Score: 293
Period size: 132 Copynumber: 1.9 Consensus size: 132
71492 CATTTGATTG
* * *
71502 TGTTGATCCATCTCCTTCTGTAATGGAATCTAACAAAAGAGAAATATTGATTCAACTCCTTATAT
1 TGTTGATCCATCTCCTTCTGTAATGGAATCGAACAAAAGAGAAATATTGATCCAAATCCTTATAT
* * * * *
71567 GATGGAATCCAACGAAATAATGATGATGATCCAACTTCTTATATGATAGAATCTAGCAAAAACGG
66 GATGAAATCCAACGAAATAATAATGATGATCCAACTCCATATATAATAGAATCTAGCAAAAACGG
71632 AA
131 AA
* * * * * *
71634 TGTTGATCCGTCTCCTTCTGTGATGGAATCGAACAAAAGAGTAATGTTGATCCAAATCCTTCTGT
1 TGTTGATCCATCTCCTTCTGTAATGGAATCGAACAAAAGAGAAATATTGATCCAAATCCTTATAT
** * * * * * * *
71699 GATGAAATTGAGCTAAATAGTAATGTTGATCTAACTCCATATGTAATGGAATC
66 GATGAAATCCAACGAAATAATAATGATGATCCAACTCCATATATAATAGAATC
71752 GAACCTTTAA
Statistics
Matches: 95, Mismatches: 23, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
132 95 1.00
ACGTcount: A:0.35, C:0.16, G:0.17, T:0.31
Consensus pattern (132 bp):
TGTTGATCCATCTCCTTCTGTAATGGAATCGAACAAAAGAGAAATATTGATCCAAATCCTTATAT
GATGAAATCCAACGAAATAATAATGATGATCCAACTCCATATATAATAGAATCTAGCAAAAACGG
AA
Found at i:71895 original size:20 final size:20
Alignment explanation
Indices: 71851--71899 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
71841 CATCATGCTT
*
71851 GGAGGTCTTATAGATGTCCC
1 GGAGGTCTTATAGATGGCCC
* *
71871 AGAGGTCTTATAGATGGCTC
1 GGAGGTCTTATAGATGGCCC
71891 GGAGGTCTT
1 GGAGGTCTT
71900 GTCATCTTGC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.20, C:0.16, G:0.33, T:0.31
Consensus pattern (20 bp):
GGAGGTCTTATAGATGGCCC
Found at i:76924 original size:19 final size:19
Alignment explanation
Indices: 76900--76958 Score: 65
Period size: 19 Copynumber: 3.4 Consensus size: 19
76890 TGTCATTGTA
76900 TGAGTGTTGCATTTTGAGG
1 TGAGTGTTGCATTTTGAGG
*
76919 TGAGTG-T-CA--TTG-TG
1 TGAGTGTTGCATTTTGAGG
*
76933 TGAGTGTTGCATTTTGAGT
1 TGAGTGTTGCATTTTGAGG
76952 TGAGTGT
1 TGAGTGT
76959 CATTTTTAGA
Statistics
Matches: 32, Mismatches: 3, Indels: 10
0.71 0.07 0.22
Matches are distributed among these distances:
14 7 0.22
15 4 0.12
16 2 0.06
17 2 0.06
18 4 0.12
19 13 0.41
ACGTcount: A:0.15, C:0.05, G:0.36, T:0.44
Consensus pattern (19 bp):
TGAGTGTTGCATTTTGAGG
Found at i:76930 original size:33 final size:33
Alignment explanation
Indices: 76888--76962 Score: 132
Period size: 33 Copynumber: 2.3 Consensus size: 33
76878 TCGAGAAGTA
76888 AGTGTCATTGTATGAGTGTTGCATTTTGAGGTG
1 AGTGTCATTGTATGAGTGTTGCATTTTGAGGTG
* *
76921 AGTGTCATTGTGTGAGTGTTGCATTTTGAGTTG
1 AGTGTCATTGTATGAGTGTTGCATTTTGAGGTG
76954 AGTGTCATT
1 AGTGTCATT
76963 TTTAGAGCAT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 40 1.00
ACGTcount: A:0.17, C:0.07, G:0.32, T:0.44
Consensus pattern (33 bp):
AGTGTCATTGTATGAGTGTTGCATTTTGAGGTG
Found at i:76950 original size:14 final size:14
Alignment explanation
Indices: 76900--76951 Score: 50
Period size: 14 Copynumber: 3.4 Consensus size: 14
76890 TGTCATTGTA
76900 TGAGTGTTGCATTT
1 TGAGTGTTGCATTT
*
76914 TGAGGTGAGTGTCATTGT
1 TGA-GTG-TTG-CATT-T
76932 GTGAGTGTTGCATTT
1 -TGAGTGTTGCATTT
76947 TGAGT
1 TGAGT
76952 TGAGTGTCAT
Statistics
Matches: 31, Mismatches: 2, Indels: 10
0.72 0.05 0.23
Matches are distributed among these distances:
14 8 0.26
15 4 0.13
16 6 0.19
17 6 0.19
18 4 0.13
19 3 0.10
ACGTcount: A:0.15, C:0.06, G:0.35, T:0.44
Consensus pattern (14 bp):
TGAGTGTTGCATTT
Found at i:76964 original size:17 final size:16
Alignment explanation
Indices: 76888--76964 Score: 54
Period size: 19 Copynumber: 4.7 Consensus size: 16
76878 TCGAGAAGTA
*
76888 AGTGTCATTGT-A-TG
1 AGTGTCATTTTGAGTG
76902 AGTGTTGCATTTTGAGGTG
1 AGTG-T-CATTTTGA-GTG
*
76921 AGTGTCA--TTGTGTG
1 AGTGTCATTTTGAGTG
76935 AGTGTTGCATTTTGAGTTG
1 AGTG-T-CATTTTGAG-TG
76954 AGTGTCATTTT
1 AGTGTCATTTT
76965 TAGAGCATCC
Statistics
Matches: 50, Mismatches: 3, Indels: 17
0.71 0.04 0.24
Matches are distributed among these distances:
14 11 0.22
15 5 0.10
16 7 0.14
17 9 0.18
18 6 0.12
19 12 0.24
ACGTcount: A:0.17, C:0.06, G:0.31, T:0.45
Consensus pattern (16 bp):
AGTGTCATTTTGAGTG
Found at i:78305 original size:9 final size:9
Alignment explanation
Indices: 78277--78341 Score: 55
Period size: 9 Copynumber: 7.1 Consensus size: 9
78267 TCGAACCTAA
78277 AATAA-AAT
1 AATAATAAT
*
78285 AA-AATAAA
1 AATAATAAT
78293 AATAATAAT
1 AATAATAAT
78302 AATAATAAT
1 AATAATAAT
*
78311 -ATATTTAAT
1 AATA-ATAAT
78320 ATATAATATAT
1 A-ATAATA-AT
78331 AATATATAAT
1 AATA-ATAAT
78341 A
1 A
78342 TATATTTAAA
Statistics
Matches: 46, Mismatches: 4, Indels: 12
0.74 0.06 0.19
Matches are distributed among these distances:
7 2 0.04
8 9 0.20
9 18 0.39
10 8 0.17
11 9 0.20
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (9 bp):
AATAATAAT
Found at i:78326 original size:7 final size:7
Alignment explanation
Indices: 78294--78363 Score: 76
Period size: 7 Copynumber: 10.3 Consensus size: 7
78284 TAAAATAAAA
78294 ATAATA-
1 ATAATAT
78300 ATAATA-
1 ATAATAT
78306 ATAATAT
1 ATAATAT
78313 ATTTAATAT
1 A--TAATAT
78322 ATAATAT
1 ATAATAT
78329 ATAATAT
1 ATAATAT
78336 ATAATAT
1 ATAATAT
*
78343 AT-ATTT
1 ATAATAT
*
78349 A-AAAAT
1 ATAATAT
78355 ATAATAT
1 ATAATAT
78362 AT
1 AT
78364 TTTAATAAAA
Statistics
Matches: 55, Mismatches: 4, Indels: 9
0.81 0.06 0.13
Matches are distributed among these distances:
6 19 0.35
7 29 0.53
9 7 0.13
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (7 bp):
ATAATAT
Found at i:78340 original size:21 final size:21
Alignment explanation
Indices: 78294--78363 Score: 76
Period size: 19 Copynumber: 3.4 Consensus size: 21
78284 TAAAATAAAA
78294 ATAATA-ATAATA-ATAATAT
1 ATAATATATAATATATAATAT
78313 ATTTAATATATAATATATAATAT
1 A--TAATATATAATATATAATAT
* *
78336 ATAATATAT-ATTTA-AAAAT
1 ATAATATATAATATATAATAT
78355 ATAATATAT
1 ATAATATAT
78364 TTTAATAAAA
Statistics
Matches: 45, Mismatches: 2, Indels: 8
0.82 0.04 0.15
Matches are distributed among these distances:
19 14 0.31
20 4 0.09
21 13 0.29
22 6 0.13
23 8 0.18
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (21 bp):
ATAATATATAATATATAATAT
Found at i:78379 original size:33 final size:31
Alignment explanation
Indices: 78284--78379 Score: 95
Period size: 33 Copynumber: 3.0 Consensus size: 31
78274 TAAAATAAAA
*
78284 TAAAATA-AAAATAATAATAATAATAATATATT
1 TAAAATATAATAT-ATAATAATAA-AATATATT
* *
78316 TAATATATAATATATAATATATAATATATATT
1 TAAAATATAATATATAATA-ATAAAATATATT
**
78348 TAAAAATATAATATATTTTAATAAAACTATAT
1 T-AAAATATAATATATAATAATAAAA-TATAT
78380 ATGTTTTTCA
Statistics
Matches: 53, Mismatches: 7, Indels: 7
0.79 0.10 0.10
Matches are distributed among these distances:
32 25 0.47
33 28 0.53
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.41
Consensus pattern (31 bp):
TAAAATATAATATATAATAATAAAATATATT
Found at i:78381 original size:20 final size:21
Alignment explanation
Indices: 78334--78407 Score: 73
Period size: 21 Copynumber: 3.6 Consensus size: 21
78324 AATATATAAT
*
78334 ATATAATATATATT--TAAAA
1 ATATAATATATTTTAATAAAA
78353 ATATAATATATTTTAATAAAA
1 ATATAATATATTTTAATAAAA
* * * *
78374 CTAT-ATATGTTTTTCAGAAAA
1 ATATAATAT-ATTTTAATAAAA
78395 ATATAATATATTT
1 ATATAATATATTT
78408 CAAATATATA
Statistics
Matches: 44, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
19 13 0.30
20 4 0.09
21 23 0.52
22 4 0.09
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.45
Consensus pattern (21 bp):
ATATAATATATTTTAATAAAA
Found at i:78424 original size:19 final size:20
Alignment explanation
Indices: 78334--78424 Score: 66
Period size: 19 Copynumber: 4.6 Consensus size: 20
78324 AATATATAAT
78334 ATATAATATATATTT-A-AAA
1 ATAT-ATATATATTTCAGAAA
* *
78353 ATATA-ATATATTTTAATAAA
1 ATATATATATA-TTTCAGAAA
* *
78373 ACTATATATGTTTTTCAGAAA
1 A-TATATATATATTTCAGAAA
*
78394 A-ATATAATATATTTCA-AAT
1 ATATAT-ATATATTTCAGAAA
78413 ATATATATATAT
1 ATATATATATAT
78425 ATATATCAAA
Statistics
Matches: 58, Mismatches: 7, Indels: 14
0.73 0.09 0.18
Matches are distributed among these distances:
17 5 0.09
18 4 0.07
19 18 0.31
20 16 0.28
21 12 0.21
22 3 0.05
ACGTcount: A:0.51, C:0.03, G:0.02, T:0.44
Consensus pattern (20 bp):
ATATATATATATTTCAGAAA
Found at i:78426 original size:21 final size:21
Alignment explanation
Indices: 78331--78467 Score: 71
Period size: 20 Copynumber: 6.8 Consensus size: 21
78321 TATAATATAT
78331 AATATATA-ATATATATTT-A
1 AATATATATATATATATTTCA
*
78350 AA-A-ATATA-ATATATTT-T
1 AATATATATATATATATTTCA
* * *
78367 AATAAAACTATATATGTTTTTCA
1 AAT-ATA-TATATATATATTTCA
*
78390 GAA-AAATATA-ATATATTTCA
1 -AATATATATATATATATTTCA
78410 AATATATATATATATATATATCA
1 AATATATATATATATAT-T-TCA
* *
78433 AACT-TATATTTATGT-TTTCA
1 AA-TATATATATATATATTTCA
*
78453 AAAATATATA-ATATA
1 AATATATATATATATA
78468 CATATTTTCA
Statistics
Matches: 91, Mismatches: 12, Indels: 29
0.69 0.09 0.22
Matches are distributed among these distances:
17 13 0.14
18 2 0.02
19 8 0.09
20 25 0.27
21 15 0.16
22 11 0.12
23 14 0.15
24 3 0.03
ACGTcount: A:0.50, C:0.04, G:0.02, T:0.44
Consensus pattern (21 bp):
AATATATATATATATATTTCA
Found at i:78436 original size:61 final size:62
Alignment explanation
Indices: 78331--78467 Score: 158
Period size: 61 Copynumber: 2.2 Consensus size: 62
78321 TATAATATAT
* *
78331 AATATATAATATATATTTAAAAATATAATATATTTTAATAAAAC-TATA-TATGTTTTTCAGAA
1 AATATATAATATATATTCAAAAATATAATATATTATAATAAAACTTATATTATG-TTTTCA-AA
* *
78393 AA-ATATAATATAT-TTCAAATATAT-ATATATATATATATCAAACTTATATTTATGTTTTCAAA
1 AATATATAATATATATTCAAAAATATAATATAT-TATA-ATAAAACTTATA-TTATGTTTTCAAA
78455 AATATATAATATA
1 AATATATAATATA
78468 CATATTTTCA
Statistics
Matches: 65, Mismatches: 4, Indels: 11
0.81 0.05 0.14
Matches are distributed among these distances:
59 6 0.09
60 12 0.18
61 17 0.26
62 10 0.15
63 16 0.25
64 4 0.06
ACGTcount: A:0.50, C:0.04, G:0.02, T:0.44
Consensus pattern (62 bp):
AATATATAATATATATTCAAAAATATAATATATTATAATAAAACTTATATTATGTTTTCAAA
Found at i:79762 original size:23 final size:21
Alignment explanation
Indices: 79732--79774 Score: 59
Period size: 23 Copynumber: 2.0 Consensus size: 21
79722 AAACCAACAT
*
79732 AGAATTTTGAAATGAAAGTGTCA
1 AGAATTTT-AAAGGAAA-TGTCA
79755 AGAATTTTAAAGGAAATGTC
1 AGAATTTTAAAGGAAATGTC
79775 GATTGTCACT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 4 0.21
22 7 0.37
23 8 0.42
ACGTcount: A:0.44, C:0.05, G:0.21, T:0.30
Consensus pattern (21 bp):
AGAATTTTAAAGGAAATGTCA
Found at i:80246 original size:17 final size:16
Alignment explanation
Indices: 80215--80250 Score: 54
Period size: 17 Copynumber: 2.2 Consensus size: 16
80205 CCACCAAACA
80215 CTCTTCCTTTTCTTCT
1 CTCTTCCTTTTCTTCT
*
80231 CTCTTTCTTCTTCTTCT
1 CTCTTCCTT-TTCTTCT
80248 CTC
1 CTC
80251 ACTTCAAAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 8 0.44
17 10 0.56
ACGTcount: A:0.00, C:0.39, G:0.00, T:0.61
Consensus pattern (16 bp):
CTCTTCCTTTTCTTCT
Found at i:81379 original size:2 final size:2
Alignment explanation
Indices: 81368--81419 Score: 97
Period size: 2 Copynumber: 26.5 Consensus size: 2
81358 GAATAAAATG
81368 TA TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
81409 TA TA TA TA TA T
1 TA TA TA TA TA T
81420 GTCGAATTTA
Statistics
Matches: 49, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 48 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:87504 original size:8 final size:8
Alignment explanation
Indices: 87489--87518 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
87479 GAGGGGCCCA
87489 AGAATACT
1 AGAATACT
*
87497 ATAATACT
1 AGAATACT
87505 AGAATACT
1 AGAATACT
87513 AGAATA
1 AGAATA
87519 TCTTCTAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.53, C:0.10, G:0.10, T:0.27
Consensus pattern (8 bp):
AGAATACT
Found at i:91817 original size:19 final size:21
Alignment explanation
Indices: 91795--91838 Score: 67
Period size: 19 Copynumber: 2.2 Consensus size: 21
91785 TTTACATTAT
91795 AATATTA-TCTAAAA-TATAA
1 AATATTAGTCTAAAATTATAA
91814 AATA-TAGTCTAAAATTATAA
1 AATATTAGTCTAAAATTATAA
91834 AATAT
1 AATAT
91839 ATTTATAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
18 2 0.09
19 11 0.50
20 9 0.41
ACGTcount: A:0.57, C:0.05, G:0.02, T:0.36
Consensus pattern (21 bp):
AATATTAGTCTAAAATTATAA
Found at i:91834 original size:20 final size:19
Alignment explanation
Indices: 91790--91840 Score: 70
Period size: 20 Copynumber: 2.7 Consensus size: 19
91780 TTATTTTTAC
*
91790 ATTATAATAT-TATCTAAA
1 ATTATAAAATATATCTAAA
91808 A-TATAAAATATAGTCTAAA
1 ATTATAAAATATA-TCTAAA
91827 ATTATAAAATATAT
1 ATTATAAAATATAT
91841 TTATAATATT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
17 7 0.24
18 3 0.10
19 8 0.28
20 11 0.38
ACGTcount: A:0.55, C:0.04, G:0.02, T:0.39
Consensus pattern (19 bp):
ATTATAAAATATATCTAAA
Found at i:93151 original size:21 final size:21
Alignment explanation
Indices: 93127--93189 Score: 126
Period size: 21 Copynumber: 3.0 Consensus size: 21
93117 ACATTAAGTC
93127 GACAAACACATTAATCTCCAT
1 GACAAACACATTAATCTCCAT
93148 GACAAACACATTAATCTCCAT
1 GACAAACACATTAATCTCCAT
93169 GACAAACACATTAATCTCCAT
1 GACAAACACATTAATCTCCAT
93190 CCATTTCCAA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 42 1.00
ACGTcount: A:0.43, C:0.29, G:0.05, T:0.24
Consensus pattern (21 bp):
GACAAACACATTAATCTCCAT
Found at i:95215 original size:446 final size:442
Alignment explanation
Indices: 94382--95277 Score: 1467
Period size: 446 Copynumber: 2.0 Consensus size: 442
94372 CGTAAAAAAA
*
94382 CTTGAATCGTTAAAGTATCGACTATCAATGTTGTTGGAACCATTAACCTACTCAATATACAATGT
1 CTTGAATCATTAAAGTATCGACTATCAATGTTGTTGGAACCATTAACCTACTCAATATACAATGT
94447 TGAGGATGATGGTGATGTGGACATGATGGTCGATTCCCACTTGCAGTATTCATTAGAAGAGGCCT
66 TGAGGATGATGGTGATGTGGACATGATGGTCGATTCCCACTTGCAGTATTCATTAGAAGAGGCCT
* *
94512 TTGAGTTATATATAATTTTTTCTAATGATAATGATTCTACCAGTGTCCCGAGAGATGAACAAATT
131 TTGAGTTATATACAATTTTTTCTAATGAGAATGATTCTACCAGTGTCCCGAGAGATGAACAAATT
*
94577 TTGACTTGGATTCTAATTTCAATATGACAGCTAATTTAGGAAATGACTTCAACTTATTAAGTATA
196 TTGACTTGGATTCTAATTTCAATATGAAAGCTAATTTAGGAAATGACTTCAACTTATTAAGTATA
94642 CAAAGTACACGAAATGACTTGAGTGCATCATCACCTTCGATGCCAAGGCATTCTTACATAGCTAG
261 CAAAGTACACGAAATGACTTGAGTGCATCATCACCTTCGATGCCAAGGCA-T-TTAC--AGCTAG
94707 CTTTGAATTTGACCTAAGTATACACGGTATTTGTGTGGAATGTCATCTTCTCAGCAAGACATTAA
322 CTTTGAATTTGACCTAAGTATACACGGTATTTGTGTGGAATGTCATCTTCTCAGCAAGACATTAA
** *
94772 GTGGCAAGACCATGAAGCTTTTAACTCGTTCGATGATTTCTCATCTAGACGATATT
387 GTGAAAAGACCATGAAGCTTTTAACTCGTTCGATGATTTCTCATCTAGACAATATT
* *
94828 CTTGAATCATTAAAGTATTGACTATCGATGTTGTTGGAACCATTAACCTACTCAATATACAATGT
1 CTTGAATCATTAAAGTATCGACTATCAATGTTGTTGGAACCATTAACCTACTCAATATACAATGT
94893 TGAGGATGATGGTGATGTGGACATGATGGTCGATTCCCACTTGCAGTATTCATTAGAAGAGGCCT
66 TGAGGATGATGGTGATGTGGACATGATGGTCGATTCCCACTTGCAGTATTCATTAGAAGAGGCCT
* *
94958 TTGAGTTATATGCAATTTTTTCTAATGAGAATGATTCTACCAGTGTCCCGAATTAGAGATGAATA
131 TTGAGTTATATACAATTTTTTCTAATGAGAATGATTCTACCAGTGTCCCG----AGAGATGAACA
* * *
95023 AATTTTGACTTGGATTTTAATGTTCACAATCTGAAAGCTAATTTAGGTAATGACTTCAACTTATT
192 AATTTTGACTTGGATTCTAAT-TT--CAATATGAAAGCTAATTTAGGAAATGACTTCAACTTATT
* * * *
95088 AAGTATATAAAGTACATGAAATGACTTGTGTGCATCATCATCTTCGATGCCAAGGCA-TT-C-GC
254 AAGTATACAAAGTACACGAAATGACTTGAGTGCATCATCACCTTCGATGCCAAGGCATTTACAGC
*
95150 TA-CTTTGACTTTGACCTAAGTATACACGGTATTTGTGTGGAACTGTCATCTTCTCAGCAAGACA
319 TAGCTTTGAATTTGACCTAAGTATACACGGTATTTGTGTGGAA-TGTCATCTTCTCAGCAAGACA
* *
95214 TTAGGTGAAAAGACCATGAAGCTTTTTACTCGTTCGATGATTTCTCATCTAGACAATATT
383 TTAAGTGAAAAGACCATGAAGCTTTTAACTCGTTCGATGATTTCTCATCTAGACAATATT
95274 CTTG
1 CTTG
95278 TGCTGGTGCT
Statistics
Matches: 421, Mismatches: 21, Indels: 16
0.92 0.05 0.03
Matches are distributed among these distances:
445 39 0.09
446 258 0.61
449 1 0.00
450 32 0.08
451 2 0.00
453 89 0.21
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.34
Consensus pattern (442 bp):
CTTGAATCATTAAAGTATCGACTATCAATGTTGTTGGAACCATTAACCTACTCAATATACAATGT
TGAGGATGATGGTGATGTGGACATGATGGTCGATTCCCACTTGCAGTATTCATTAGAAGAGGCCT
TTGAGTTATATACAATTTTTTCTAATGAGAATGATTCTACCAGTGTCCCGAGAGATGAACAAATT
TTGACTTGGATTCTAATTTCAATATGAAAGCTAATTTAGGAAATGACTTCAACTTATTAAGTATA
CAAAGTACACGAAATGACTTGAGTGCATCATCACCTTCGATGCCAAGGCATTTACAGCTAGCTTT
GAATTTGACCTAAGTATACACGGTATTTGTGTGGAATGTCATCTTCTCAGCAAGACATTAAGTGA
AAAGACCATGAAGCTTTTAACTCGTTCGATGATTTCTCATCTAGACAATATT
Found at i:101096 original size:16 final size:16
Alignment explanation
Indices: 101075--101109 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
101065 GTCCTAGGGT
101075 TTCACAAAAGTAGAGA
1 TTCACAAAAGTAGAGA
101091 TTCACAAAAGTAGAGA
1 TTCACAAAAGTAGAGA
101107 TTC
1 TTC
101110 CCTAGATTCC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.46, C:0.14, G:0.17, T:0.23
Consensus pattern (16 bp):
TTCACAAAAGTAGAGA
Found at i:108034 original size:20 final size:20
Alignment explanation
Indices: 108009--108047 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
107999 TGCATCAGGG
108009 TCTTTGTAGAAGCCATAAAA
1 TCTTTGTAGAAGCCATAAAA
*
108029 TCTTTGTCGAAGCCATAAA
1 TCTTTGTAGAAGCCATAAA
108048 TTCCAACAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.36, C:0.18, G:0.15, T:0.31
Consensus pattern (20 bp):
TCTTTGTAGAAGCCATAAAA
Found at i:111041 original size:10 final size:10
Alignment explanation
Indices: 111026--111050 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
111016 CAAATATAAC
111026 CTAAATGCAA
1 CTAAATGCAA
111036 CTAAATGCAA
1 CTAAATGCAA
111046 CTAAA
1 CTAAA
111051 ATATTGTGCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.52, C:0.20, G:0.08, T:0.20
Consensus pattern (10 bp):
CTAAATGCAA
Found at i:115279 original size:15 final size:16
Alignment explanation
Indices: 115252--115281 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
115242 TCTAACTTAA
115252 TTCTTTTTCAATCATT
1 TTCTTTTTCAATCATT
115268 TTCTTTTT-AATCAT
1 TTCTTTTTCAATCAT
115282 CAATGGCTTC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.20, C:0.17, G:0.00, T:0.63
Consensus pattern (16 bp):
TTCTTTTTCAATCATT
Found at i:116356 original size:14 final size:13
Alignment explanation
Indices: 116326--116373 Score: 51
Period size: 13 Copynumber: 3.5 Consensus size: 13
116316 CATTCATAAT
*
116326 AAACAAACAAACCA
1 AAACAAAC-ATCCA
116340 AAATCAAACATCCA
1 AAA-CAAACATCCA
*
116354 AAACAAATATCCA
1 AAACAAACATCCA
*
116367 AACCAAA
1 AAACAAA
116374 TATTCAAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
13 15 0.50
14 10 0.33
15 5 0.17
ACGTcount: A:0.65, C:0.27, G:0.00, T:0.08
Consensus pattern (13 bp):
AAACAAACATCCA
Found at i:116365 original size:13 final size:13
Alignment explanation
Indices: 116337--116382 Score: 56
Period size: 13 Copynumber: 3.5 Consensus size: 13
116327 AACAAACAAA
*
116337 CCAAAATCAAACAT
1 CCAAAA-CAAATAT
116351 CCAAAACAAATAT
1 CCAAAACAAATAT
*
116364 CCAAACCAAATAT
1 CCAAAACAAATAT
*
116377 TCAAAA
1 CCAAAA
116383 TCCATCCAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
13 22 0.79
14 6 0.21
ACGTcount: A:0.59, C:0.26, G:0.00, T:0.15
Consensus pattern (13 bp):
CCAAAACAAATAT
Found at i:118317 original size:20 final size:20
Alignment explanation
Indices: 118279--118317 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
118269 AAACCCGACT
* *
118279 AGGGGTATCGGTACCCATTG
1 AGGGGTATCGATACACATTG
118299 AGGGGTATCGATACACATT
1 AGGGGTATCGATACACATT
118318 CAAGGAGGGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.26, C:0.18, G:0.31, T:0.26
Consensus pattern (20 bp):
AGGGGTATCGATACACATTG
Found at i:122521 original size:20 final size:20
Alignment explanation
Indices: 122478--122514 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
122468 TCTAACTCTT
*
122478 TTTTCAACATTTCATTTTGA
1 TTTTCAAAATTTCATTTTGA
122498 TTTTCAAAATTT-ATTTT
1 TTTTCAAAATTTCATTTT
122515 AGCTTTTAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
19 5 0.31
20 11 0.69
ACGTcount: A:0.27, C:0.11, G:0.03, T:0.59
Consensus pattern (20 bp):
TTTTCAAAATTTCATTTTGA
Found at i:124274 original size:13 final size:13
Alignment explanation
Indices: 124256--124281 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
124246 AAATGTTAAG
124256 ATCTTAAAATTCA
1 ATCTTAAAATTCA
124269 ATCTTAAAATTCA
1 ATCTTAAAATTCA
124282 TTAACACTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.15, G:0.00, T:0.38
Consensus pattern (13 bp):
ATCTTAAAATTCA
Found at i:134861 original size:10 final size:10
Alignment explanation
Indices: 134846--134870 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
134836 CAAATATAAC
134846 CTAAATGCAA
1 CTAAATGCAA
134856 CTAAATGCAA
1 CTAAATGCAA
134866 CTAAA
1 CTAAA
134871 ATATTGTGCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.52, C:0.20, G:0.08, T:0.20
Consensus pattern (10 bp):
CTAAATGCAA
Found at i:135731 original size:20 final size:20
Alignment explanation
Indices: 135688--135731 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
135678 AGGGGTATCG
* *
135688 ATACTCATGGCCTGGTTTCG
1 ATACTCATGGCCTGGTCTCA
**
135708 ATACTCATGGGGTGGTCTCA
1 ATACTCATGGCCTGGTCTCA
135728 ATAC
1 ATAC
135732 CGATGACAAG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.20, C:0.23, G:0.25, T:0.32
Consensus pattern (20 bp):
ATACTCATGGCCTGGTCTCA
Found at i:135831 original size:21 final size:21
Alignment explanation
Indices: 135807--135920 Score: 210
Period size: 21 Copynumber: 5.4 Consensus size: 21
135797 AGGGGTAGAT
135807 TATCGATACTCCCCATAAGAG
1 TATCGATACTCCCCATAAGAG
*
135828 TATCGATATTCCCCATAAGAG
1 TATCGATACTCCCCATAAGAG
135849 TATCGATACTCCCCATAAGAG
1 TATCGATACTCCCCATAAGAG
*
135870 TATCGATACTCCCTATAAGAG
1 TATCGATACTCCCCATAAGAG
135891 TATCGATACTCCCCATAAGAG
1 TATCGATACTCCCCATAAGAG
135912 TATCGATAC
1 TATCGATAC
135921 CAAGACATTT
Statistics
Matches: 89, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 89 1.00
ACGTcount: A:0.33, C:0.26, G:0.14, T:0.26
Consensus pattern (21 bp):
TATCGATACTCCCCATAAGAG
Found at i:138169 original size:41 final size:41
Alignment explanation
Indices: 138124--138255 Score: 119
Period size: 41 Copynumber: 3.2 Consensus size: 41
138114 CTGGTTCTCC
138124 CCATGCATACGAGCCATACGAGTGCGAGCCATGCGAGGTGG
1 CCATGCATACGAGCCATACGAGTGCGAGCCATGCGAGGTGG
* * *** **
138165 CCATGCAGT--G-G-AATAGAGAGGTCGTTCTCCCCATGCGAGGTCC
1 CCATGCA-TACGAGCCATA-CGA-GT-G--CGAGCCATGCGAGGTGG
138208 CCATGCATACGAGCCATACGAGTGCGAGCCATGCGAGGTGG
1 CCATGCATACGAGCCATACGAGTGCGAGCCATGCGAGGTGG
138249 CCATGCA
1 CCATGCA
138256 GTGGAATAGA
Statistics
Matches: 67, Mismatches: 14, Indels: 20
0.66 0.14 0.20
Matches are distributed among these distances:
38 3 0.04
39 3 0.04
40 3 0.04
41 27 0.40
42 2 0.03
43 20 0.30
44 3 0.04
45 3 0.04
46 3 0.04
ACGTcount: A:0.23, C:0.28, G:0.32, T:0.17
Consensus pattern (41 bp):
CCATGCATACGAGCCATACGAGTGCGAGCCATGCGAGGTGG
Found at i:138270 original size:55 final size:55
Alignment explanation
Indices: 138210--138320 Score: 222
Period size: 55 Copynumber: 2.0 Consensus size: 55
138200 CGAGGTCCCC
138210 ATGCATACGAGCCATACGAGTGCGAGCCATGCGAGGTGGCCATGCAGTGGAATAG
1 ATGCATACGAGCCATACGAGTGCGAGCCATGCGAGGTGGCCATGCAGTGGAATAG
138265 ATGCATACGAGCCATACGAGTGCGAGCCATGCGAGGTGGCCATGCAGTGGAATAG
1 ATGCATACGAGCCATACGAGTGCGAGCCATGCGAGGTGGCCATGCAGTGGAATAG
138320 A
1 A
138321 GAGGTCGTTC
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
55 56 1.00
ACGTcount: A:0.28, C:0.22, G:0.34, T:0.16
Consensus pattern (55 bp):
ATGCATACGAGCCATACGAGTGCGAGCCATGCGAGGTGGCCATGCAGTGGAATAG
Found at i:138376 original size:15 final size:15
Alignment explanation
Indices: 138356--138424 Score: 58
Period size: 15 Copynumber: 4.9 Consensus size: 15
138346 CCCATGCATA
*
138356 CGAGCCATACGAGTG
1 CGAGCCATGCGAGTG
138371 CGAGCCATGCGAG-G
1 CGAGCCATGCGAGTG
* *
138385 TC--CCCATGC-A-TA
1 -CGAGCCATGCGAGTG
*
138397 CGAGCCATACGAGTG
1 CGAGCCATGCGAGTG
138412 CGAGCCATGCGAG
1 CGAGCCATGCGAG
138425 GTGGCATGCA
Statistics
Matches: 41, Mismatches: 7, Indels: 12
0.68 0.12 0.20
Matches are distributed among these distances:
11 1 0.02
12 1 0.02
13 11 0.27
14 2 0.05
15 26 0.63
ACGTcount: A:0.25, C:0.30, G:0.32, T:0.13
Consensus pattern (15 bp):
CGAGCCATGCGAGTG
Found at i:138387 original size:41 final size:41
Alignment explanation
Indices: 138334--138426 Score: 186
Period size: 41 Copynumber: 2.3 Consensus size: 41
138324 GTCGTTCTCC
138334 CCATGCGAGGTCCCCATGCATACGAGCCATACGAGTGCGAG
1 CCATGCGAGGTCCCCATGCATACGAGCCATACGAGTGCGAG
138375 CCATGCGAGGTCCCCATGCATACGAGCCATACGAGTGCGAG
1 CCATGCGAGGTCCCCATGCATACGAGCCATACGAGTGCGAG
138416 CCATGCGAGGT
1 CCATGCGAGGT
138427 GGCATGCAGT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.24, C:0.31, G:0.30, T:0.15
Consensus pattern (41 bp):
CCATGCGAGGTCCCCATGCATACGAGCCATACGAGTGCGAG
Found at i:138481 original size:29 final size:29
Alignment explanation
Indices: 138448--138557 Score: 220
Period size: 29 Copynumber: 3.8 Consensus size: 29
138438 GAATAGGGTG
138448 TAGGTCGCCATGTAGTCCCGGCGACCTTA
1 TAGGTCGCCATGTAGTCCCGGCGACCTTA
138477 TAGGTCGCCATGTAGTCCCGGCGACCTTA
1 TAGGTCGCCATGTAGTCCCGGCGACCTTA
138506 TAGGTCGCCATGTAGTCCCGGCGACCTTA
1 TAGGTCGCCATGTAGTCCCGGCGACCTTA
138535 TAGGTCGCCATGTAGTCCCGGCG
1 TAGGTCGCCATGTAGTCCCGGCG
138558 CCATTCCCAT
Statistics
Matches: 81, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 81 1.00
ACGTcount: A:0.16, C:0.31, G:0.29, T:0.24
Consensus pattern (29 bp):
TAGGTCGCCATGTAGTCCCGGCGACCTTA
Found at i:138628 original size:27 final size:23
Alignment explanation
Indices: 138563--138622 Score: 120
Period size: 23 Copynumber: 2.6 Consensus size: 23
138553 CGGCGCCATT
138563 CCCATCATCCATTCACATGCAGC
1 CCCATCATCCATTCACATGCAGC
138586 CCCATCATCCATTCACATGCAGC
1 CCCATCATCCATTCACATGCAGC
138609 CCCATCATCCATTC
1 CCCATCATCCATTC
138623 CTTCACGTGT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.25, C:0.45, G:0.07, T:0.23
Consensus pattern (23 bp):
CCCATCATCCATTCACATGCAGC
Found at i:138761 original size:25 final size:25
Alignment explanation
Indices: 138733--138784 Score: 86
Period size: 25 Copynumber: 2.1 Consensus size: 25
138723 TGTACAATTA
*
138733 TTGGTGAAATAATTAAGGCAGTCGG
1 TTGGTGAAATAATTAAGGCAGCCGG
*
138758 TTGGTGAAATAATTGAGGCAGCCGG
1 TTGGTGAAATAATTAAGGCAGCCGG
138783 TT
1 TT
138785 ATAAAAGAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.29, C:0.10, G:0.33, T:0.29
Consensus pattern (25 bp):
TTGGTGAAATAATTAAGGCAGCCGG
Found at i:138855 original size:4 final size:4
Alignment explanation
Indices: 138846--138903 Score: 53
Period size: 4 Copynumber: 14.0 Consensus size: 4
138836 ATTGCCATCG
** **
138846 AGAA AGAA AGAA AGGG AGAA AGGAA AGAA AGAA AGAA AGGG AGAA AGGAA
1 AGAA AGAA AGAA AGAA AGAA A-GAA AGAA AGAA AGAA AGAA AGAA A-GAA
*
138896 AGTA AGAA
1 AGAA AGAA
138904 GAATTCGAAA
Statistics
Matches: 42, Mismatches: 10, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
4 34 0.81
5 8 0.19
ACGTcount: A:0.64, C:0.00, G:0.34, T:0.02
Consensus pattern (4 bp):
AGAA
Found at i:138873 original size:17 final size:16
Alignment explanation
Indices: 138845--138876 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
138835 GATTGCCATC
138845 GAGAAAGAAAGAAAGG
1 GAGAAAGAAAGAAAGG
138861 GAGAAAGGAAAGAAAG
1 GAGAAA-GAAAGAAAG
138877 AAAGAAAGGG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.62, C:0.00, G:0.38, T:0.00
Consensus pattern (16 bp):
GAGAAAGAAAGAAAGG
Found at i:138874 original size:25 final size:25
Alignment explanation
Indices: 138846--138903 Score: 107
Period size: 25 Copynumber: 2.3 Consensus size: 25
138836 ATTGCCATCG
138846 AGAAAGAAAGAAAGGGAGAAAGGAA
1 AGAAAGAAAGAAAGGGAGAAAGGAA
138871 AGAAAGAAAGAAAGGGAGAAAGGAA
1 AGAAAGAAAGAAAGGGAGAAAGGAA
*
138896 AGTAAGAA
1 AGAAAGAA
138904 GAATTCGAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.64, C:0.00, G:0.34, T:0.02
Consensus pattern (25 bp):
AGAAAGAAAGAAAGGGAGAAAGGAA
Found at i:139169 original size:45 final size:47
Alignment explanation
Indices: 139107--139197 Score: 134
Period size: 45 Copynumber: 2.0 Consensus size: 47
139097 TTATATAGTT
139107 AAAAAATAATTAATTAGTTTGTATT-GTT-AATAGTT-AGTTATATA
1 AAAAAATAATTAATTAGTTTGTATTAGTTAAATAGTTAAGTTATATA
* *
139151 AAAAAATTATTTAATTAGTTTGTGTTAGTTAAATAGTTAAGTTATAT
1 AAAAAA-TAATTAATTAGTTTGTATTAGTTAAATAGTTAAGTTATAT
139198 TTGTTTGTTG
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
44 6 0.15
45 17 0.41
46 3 0.07
47 7 0.17
48 8 0.20
ACGTcount: A:0.42, C:0.00, G:0.12, T:0.46
Consensus pattern (47 bp):
AAAAAATAATTAATTAGTTTGTATTAGTTAAATAGTTAAGTTATATA
Found at i:141579 original size:17 final size:17
Alignment explanation
Indices: 141557--141589 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
141547 CAATGATTTT
*
141557 TAGTATCAAATCATTAC
1 TAGTATCAAATAATTAC
141574 TAGTATCAAATAATTA
1 TAGTATCAAATAATTA
141590 GATATTTAGT
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:0.45, C:0.12, G:0.06, T:0.36
Consensus pattern (17 bp):
TAGTATCAAATAATTAC
Done.