Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008200.1 Hibiscus syriacus cultivar Beakdansim tig00110820_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: 59290
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:5457 original size:22 final size:21
Alignment explanation
Indices: 5409--5492 Score: 80
Period size: 21 Copynumber: 3.9 Consensus size: 21
5399 TTTTGGTGCA
5409 GAGGGAATCGATTCCTCCCCCT
1 GAGGGAATCGATTCC-CCCCCT
**
5431 GAGGGAATCGATTCCCCCTTT
1 GAGGGAATCGATTCCCCCCCT
* *
5452 GAAGGGGAACCGATTCCCCCCACA
1 G-A-GGGAATCGATTCCCCCC-CT
*
5476 G-GGGAATCGATACCCCC
1 GAGGGAATCGATTCCCCC
5493 TGGGGATCTG
Statistics
Matches: 51, Mismatches: 8, Indels: 7
0.77 0.12 0.11
Matches are distributed among these distances:
21 19 0.37
22 16 0.31
23 15 0.29
24 1 0.02
ACGTcount: A:0.23, C:0.35, G:0.25, T:0.18
Consensus pattern (21 bp):
GAGGGAATCGATTCCCCCCCT
Found at i:12332 original size:2 final size:2
Alignment explanation
Indices: 12325--12392 Score: 136
Period size: 2 Copynumber: 34.0 Consensus size: 2
12315 TTAATTGATA
12325 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
12367 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
12393 GAATTGTGTA
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 66 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:15861 original size:34 final size:34
Alignment explanation
Indices: 15818--15934 Score: 131
Period size: 34 Copynumber: 3.6 Consensus size: 34
15808 TTCGTCCTAC
15818 TAGGATTCAAACTCCTAAAAATATGATAGAATTT
1 TAGGATTCAAACTCCTAAAAATATGATAGAATTT
*
15852 TAGGATTCAAACTCCTAAAGATATGATAGAATTTT
1 TAGGATTCAAACTCCTAAAAATATGATAGAA-TTT
15887 GCTAGGATTC--A-----AAAAATATGATAGAATTT
1 --TAGGATTCAAACTCCTAAAAATATGATAGAATTT
* *
15916 TATGATTTAAACTCCTAAA
1 TAGGATTCAAACTCCTAAA
15935 GATAGGATCC
Statistics
Matches: 69, Mismatches: 4, Indels: 20
0.74 0.04 0.22
Matches are distributed among these distances:
27 6 0.09
29 4 0.06
30 14 0.20
34 33 0.48
35 4 0.06
37 8 0.12
ACGTcount: A:0.43, C:0.11, G:0.13, T:0.33
Consensus pattern (34 bp):
TAGGATTCAAACTCCTAAAAATATGATAGAATTT
Found at i:16242 original size:23 final size:22
Alignment explanation
Indices: 16211--16272 Score: 58
Period size: 23 Copynumber: 2.8 Consensus size: 22
16201 CTTTTCTTTT
16211 TTTTCATGTAATATTTTTTTTAC
1 TTTT-ATGTAATATTTTTTTTAC
*
16234 ATTTTATGT-ATTTTCTTTTTTAC
1 -TTTTATGTAATATT-TTTTTTAC
16257 -TTTA-GTATATATTTTT
1 TTTTATGTA-ATATTTTT
16273 ATTTTTTTAG
Statistics
Matches: 33, Mismatches: 2, Indels: 9
0.75 0.05 0.20
Matches are distributed among these distances:
20 2 0.06
21 7 0.21
22 8 0.24
23 12 0.36
24 4 0.12
ACGTcount: A:0.21, C:0.06, G:0.05, T:0.68
Consensus pattern (22 bp):
TTTTATGTAATATTTTTTTTAC
Found at i:16269 original size:24 final size:23
Alignment explanation
Indices: 16226--16271 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 23
16216 ATGTAATATT
*
16226 TTTTTTACATTTTATGTATTTTC
1 TTTTTTACATTTTATATATTTTC
16249 TTTTTTAC-TTTAGTATATATTTT
1 TTTTTTACATTT--TATATATTTT
16272 TATTTTTTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 3 0.15
23 8 0.40
24 9 0.45
ACGTcount: A:0.20, C:0.07, G:0.04, T:0.70
Consensus pattern (23 bp):
TTTTTTACATTTTATATATTTTC
Found at i:16342 original size:21 final size:21
Alignment explanation
Indices: 16287--16342 Score: 53
Period size: 21 Copynumber: 2.7 Consensus size: 21
16277 TTTTAGATTA
* * *
16287 TATATATAAATATATTATTTT
1 TATATATATATTTATTAATTT
16308 TAT-TATCAGT-TTTATTAATTT
1 TATATAT-A-TATTTATTAATTT
16329 TATATATATATTTA
1 TATATATATATTTA
16343 CTTTTTATTT
Statistics
Matches: 28, Mismatches: 3, Indels: 8
0.72 0.08 0.21
Matches are distributed among these distances:
20 4 0.14
21 21 0.75
22 3 0.11
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.59
Consensus pattern (21 bp):
TATATATATATTTATTAATTT
Found at i:16401 original size:29 final size:27
Alignment explanation
Indices: 16329--16433 Score: 94
Period size: 28 Copynumber: 3.9 Consensus size: 27
16319 TTATTAATTT
16329 TATATATATATTTACTTTTTATTTTTTA
1 TATATATATATTTA-TTTTTATTTTTTA
16357 TATATATATATATTATTTTTACTTTTTTA
1 TATATATATAT-TTATTTTTA-TTTTTTA
*
16386 T-TAT-TAT-TTTATTTATT-TGTTTTA
1 TATATATATATTTATTT-TTATTTTTTA
* * * *
16410 TTTCTATAT-TTTCTTTTTCTTTTT
1 TATATATATATTTATTTTTATTTTT
16434 CTTCTTTTTC
Statistics
Matches: 67, Mismatches: 4, Indels: 14
0.79 0.05 0.16
Matches are distributed among these distances:
24 7 0.10
25 10 0.15
26 16 0.24
27 3 0.04
28 20 0.30
29 11 0.16
ACGTcount: A:0.23, C:0.05, G:0.01, T:0.71
Consensus pattern (27 bp):
TATATATATATTTATTTTTATTTTTTA
Found at i:16421 original size:13 final size:13
Alignment explanation
Indices: 16325--16421 Score: 56
Period size: 13 Copynumber: 7.4 Consensus size: 13
16315 AGTTTTATTA
*
16325 ATTTTATATATAT
1 ATTTTATTTATAT
*
16338 A-TTTACTTTTTAT
1 ATTTTA-TTTATAT
*
16351 TTTTTATATATATAT
1 ATTTTAT-T-TATAT
* *
16366 ATATTATTTTTACT
1 ATTTTATTTATA-T
*
16380 TTTTTA-TTAT-T
1 ATTTTATTTATAT
*
16391 ATTTTATTTATTT
1 ATTTTATTTATAT
* *
16404 GTTTTATTTCTAT
1 ATTTTATTTATAT
16417 ATTTT
1 ATTTT
16422 CTTTTTCTTT
Statistics
Matches: 62, Mismatches: 15, Indels: 14
0.68 0.16 0.15
Matches are distributed among these distances:
11 6 0.10
12 8 0.13
13 28 0.45
14 11 0.18
15 9 0.15
ACGTcount: A:0.26, C:0.03, G:0.01, T:0.70
Consensus pattern (13 bp):
ATTTTATTTATAT
Found at i:16570 original size:15 final size:15
Alignment explanation
Indices: 16552--16581 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
16542 TATTTATTTC
16552 TTACCTTTTTATCTA
1 TTACCTTTTTATCTA
16567 TTACCTTTTTATCTA
1 TTACCTTTTTATCTA
16582 ACATGGTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.20, C:0.20, G:0.00, T:0.60
Consensus pattern (15 bp):
TTACCTTTTTATCTA
Found at i:20801 original size:183 final size:183
Alignment explanation
Indices: 20485--20834 Score: 619
Period size: 183 Copynumber: 1.9 Consensus size: 183
20475 ATTAAATCCG
*
20485 TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
1 TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTAGCTTTATGA
** * *
20550 ATAGATTATGTTCAAACTATGACACTGCTCGGACACTTGGCAATTCAGTGTTTGCTCCACTGCTT
66 ATAGATTACATTCAAACCATGACACTGCTCGGACACTTGGCAATTCAGTGTTTGCTCCACTACTT
20615 TTGTCAGGCCAAAGACTTTGTGATGAGACGAACCCTTCAGTGATTTGTCCCTC
131 TTGTCAGGCCAAAGACTTTGTGATGAGACGAACCCTTCAGTGATTTGTCCCTC
20668 TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTAGCTTTATGA
1 TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTAGCTTTATGA
* * *
20733 ATAGATTACATTCAAACCATGACATTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCATTACTT
66 ATAGATTACATTCAAACCATGACACTGCTCGGACACTTGGCAATTCAGTGTTTGCTCCACTACTT
*
20798 TTGTCAGGCCAAAGACTTTGTGATGAGATGAACCCTT
131 TTGTCAGGCCAAAGACTTTGTGATGAGACGAACCCTT
20835 TAGTTAAACC
Statistics
Matches: 158, Mismatches: 9, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
183 158 1.00
ACGTcount: A:0.28, C:0.21, G:0.21, T:0.30
Consensus pattern (183 bp):
TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTAGCTTTATGA
ATAGATTACATTCAAACCATGACACTGCTCGGACACTTGGCAATTCAGTGTTTGCTCCACTACTT
TTGTCAGGCCAAAGACTTTGTGATGAGACGAACCCTTCAGTGATTTGTCCCTC
Found at i:22189 original size:37 final size:37
Alignment explanation
Indices: 22122--22208 Score: 122
Period size: 37 Copynumber: 2.4 Consensus size: 37
22112 ATTGAAAACA
** * *
22122 TTTCCCTTGAAA-TGAATTTTGTCTCTCTTGAGATAG
1 TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAG
22158 TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAG
1 TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAG
*
22195 TTTCTCTTGAAACA
1 TTTCCCTTGAAACA
22209 TAAACATTGA
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
36 12 0.27
37 33 0.73
ACGTcount: A:0.25, C:0.21, G:0.14, T:0.40
Consensus pattern (37 bp):
TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAG
Found at i:22211 original size:102 final size:102
Alignment explanation
Indices: 22033--22337 Score: 504
Period size: 102 Copynumber: 3.0 Consensus size: 102
22023 TTAAAACAAG
* * * *
22033 ATTTTATCTCGCTTGAGATAGTTTCCCTCGAAACAGAAAGTTTTGTCTCACTTGAGACAGTTTCT
1 ATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACA-AAA-TTTTGTCTCCCTTGAGACAGTTTCT
*
22098 CTTTAAACATAAACATTGAAAACATTTCCCTTGAAATGA
64 CTTGAAACATAAACATTGAAAACATTTCCCTTGAAATGA
22137 ATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCT
1 ATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCT
22202 TGAAACATAAACATTGAAAACATTTCCCTTGAAATGA
66 TGAAACATAAACATTGAAAACATTTCCCTTGAAATGA
* *
22239 ATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAAC-AAATTTTGTCTCCTTTGAGACAGTTTCTAT
1 ATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCT
*
22303 TGAAACATAAACTTTGAAAACAGTTTCCCTTGAAA
66 TGAAACATAAACATTGAAAACA-TTTCCCTTGAAA
22338 CAAAATCTTT
Statistics
Matches: 192, Mismatches: 8, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
101 49 0.26
102 108 0.56
103 3 0.02
104 32 0.17
ACGTcount: A:0.30, C:0.19, G:0.13, T:0.37
Consensus pattern (102 bp):
ATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCT
TGAAACATAAACATTGAAAACATTTCCCTTGAAATGA
Found at i:22271 original size:36 final size:36
Alignment explanation
Indices: 22224--22478 Score: 118
Period size: 36 Copynumber: 7.4 Consensus size: 36
22214 ATTGAAAACA
** *
22224 TTTCCCTTGAAATGAATTTTGTCT-CTCTTGAGATAG
1 TTTCCCTTGAAACAAATTTTGTCTCCT-TTGAGACAG
22260 TTTCCCTTGAAACAAATTTTGTCTCCTTTGAGACAG
1 TTTCCCTTGAAACAAATTTTGTCTCCTTTGAGACAG
** * *
22296 TTTCTATTGAAACATAA--------ACTTTGAAAACAG
1 TTTCCCTTGAAACA-AATTTTGTCTCCTTTG-AGACAG
* *
22326 TTTCCCTTGAAACAAA------AT-CTTTGA-ATATG
1 TTTCCCTTGAAACAAATTTTGTCTCCTTTGAGACA-G
* * *
22355 TTTTACATT-AAACAAATTTCGTCT-CTCTTGAGACAG
1 -TTTCCCTTGAAACAAATTTTGTCTCCT-TTGAGACAG
* *
22391 TTTCTCTTGAAACAAATTTTGTCT-CTCTTAAGACATG
1 TTTCCCTTGAAACAAATTTTGTCTCCT-TTGAGACA-G
** * *
22428 TTTTTCTTAAAACAAAATTTTGTCTCCCTTGAGACAG
1 TTTCCCTTGAAAC-AAATTTTGTCTCCTTTGAGACAG
*
22465 TTTCTCTTGAAACA
1 TTTCCCTTGAAACA
22479 TCAATCCTTG
Statistics
Matches: 175, Mismatches: 25, Indels: 38
0.74 0.11 0.16
Matches are distributed among these distances:
28 2 0.01
29 16 0.09
30 28 0.16
35 8 0.05
36 72 0.41
37 30 0.17
38 18 0.10
39 1 0.01
ACGTcount: A:0.30, C:0.18, G:0.12, T:0.40
Consensus pattern (36 bp):
TTTCCCTTGAAACAAATTTTGTCTCCTTTGAGACAG
Found at i:22327 original size:30 final size:30
Alignment explanation
Indices: 22292--22350 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
22282 CTCCTTTGAG
*
22292 ACAGTTTCTATTGAAACATAAA-CTTTGAAA
1 ACAGTTTCCATTGAAACA-AAATCTTTGAAA
*
22322 ACAGTTTCCCTTGAAACAAAATCTTTGAA
1 ACAGTTTCCATTGAAACAAAATCTTTGAA
22351 TATGTTTTAC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 3 0.12
30 23 0.88
ACGTcount: A:0.41, C:0.17, G:0.10, T:0.32
Consensus pattern (30 bp):
ACAGTTTCCATTGAAACAAAATCTTTGAAA
Found at i:22446 original size:38 final size:36
Alignment explanation
Indices: 22364--22478 Score: 167
Period size: 36 Copynumber: 3.1 Consensus size: 36
22354 GTTTTACATT
*
22364 AAACAAATTTCGTCTCTCTTGAGACAGTTTCTCTTG
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTG
* * *
22400 AAACAAATTTTGTCTCTCTTAAGACATGTTTTTCTTA
1 AAACAAATTTTGTCTCTCTTGAGACA-GTTTCTCTTG
*
22437 AAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTG
1 AAAC-AAATTTTGTCTCTCTTGAGACAGTTTCTCTTG
22474 AAACA
1 AAACA
22479 TCAATCCTTG
Statistics
Matches: 69, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
36 25 0.36
37 24 0.35
38 20 0.29
ACGTcount: A:0.30, C:0.20, G:0.11, T:0.39
Consensus pattern (36 bp):
AAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTG
Found at i:22583 original size:33 final size:33
Alignment explanation
Indices: 22519--22633 Score: 162
Period size: 33 Copynumber: 3.5 Consensus size: 33
22509 CCATGATACA
22519 GTTTCTCTTGAAACACAAAAAGAAACCTTTGAAATT
1 GTTTCTCTTGAAACAC--AAA-AAACCTTTGAAATT
*
22555 GTTTCTCTTGAAACACAAAAAACCTTTGAAAAT
1 GTTTCTCTTGAAACACAAAAAACCTTTGAAATT
*
22588 GTTTCTCTTGAAACAC--AAAACCTTTGAGATT
1 GTTTCTCTTGAAACACAAAAAACCTTTGAAATT
*
22619 GTTTCCCTTGAAACA
1 GTTTCTCTTGAAACA
22634 AATTTCGTCT
Statistics
Matches: 75, Mismatches: 4, Indels: 5
0.89 0.05 0.06
Matches are distributed among these distances:
31 27 0.36
33 29 0.39
34 3 0.04
36 16 0.21
ACGTcount: A:0.37, C:0.19, G:0.11, T:0.32
Consensus pattern (33 bp):
GTTTCTCTTGAAACACAAAAAACCTTTGAAATT
Found at i:22680 original size:67 final size:67
Alignment explanation
Indices: 22588--22773 Score: 255
Period size: 67 Copynumber: 2.7 Consensus size: 67
22578 CTTTGAAAAT
*
22588 GTTTCTCTTGAAACACAAAACCTTTGAGATTGTTTCCCTTGAAACAAATTTCGTCTCCCTTGAGA
1 GTTTCTCTTGAAACACAAAATCTTTGAGATTGTTTCCCTTGAAACAAATTTCGTCTCCCTTGAGA
22653 CA
66 CA
* * * * *
22655 GTTTCTCTTGAAACACAAAATCTTTGAGTTTATTTCCCTTAAAACAAATTTTGTCTCCCTTGAGG
1 GTTTCTCTTGAAACACAAAATCTTTGAGATTGTTTCCCTTGAAACAAATTTCGTCTCCCTTGAGA
*
22720 CC
66 CA
* * * *
22722 GTTTCTCATGAAACAACATATATCTTTAAGATTGTTTCCCTTGAAACGAATT
1 GTTTCTCTTGAAAC-ACA-AAATCTTTGAGATTGTTTCCCTTGAAACAAATT
22774 CTGTCTTTTT
Statistics
Matches: 103, Mismatches: 14, Indels: 2
0.87 0.12 0.02
Matches are distributed among these distances:
67 73 0.71
68 3 0.03
69 27 0.26
ACGTcount: A:0.29, C:0.22, G:0.12, T:0.37
Consensus pattern (67 bp):
GTTTCTCTTGAAACACAAAATCTTTGAGATTGTTTCCCTTGAAACAAATTTCGTCTCCCTTGAGA
CA
Found at i:23828 original size:34 final size:34
Alignment explanation
Indices: 23785--23908 Score: 127
Period size: 34 Copynumber: 3.8 Consensus size: 34
23775 TCGTCCTACC
23785 AGGATTCAAACTCCTAAAAATAGGATAGAATTTT
1 AGGATTCAAACTCCTAAAAATAGGATAGAATTTT
* *
23819 AGGATTCAAACTCCTAAAGATATGATAGAATTTTGCT
1 AGGATTCAAACTCCTAAAAATAGGATAGAA-TTT--T
23856 AGGATTC--A-----AAAAATAGGATAGAATTTT
1 AGGATTCAAACTCCTAAAAATAGGATAGAATTTT
* * *
23883 ATGATTTAAACTCCTAAAGATAGGAT
1 AGGATTCAAACTCCTAAAAATAGGAT
23909 CCACAAGCAC
Statistics
Matches: 73, Mismatches: 7, Indels: 20
0.73 0.07 0.20
Matches are distributed among these distances:
27 6 0.08
29 4 0.05
30 13 0.18
34 38 0.52
35 4 0.05
37 8 0.11
ACGTcount: A:0.43, C:0.10, G:0.16, T:0.31
Consensus pattern (34 bp):
AGGATTCAAACTCCTAAAAATAGGATAGAATTTT
Found at i:24224 original size:24 final size:23
Alignment explanation
Indices: 24181--24226 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 23
24171 CATGTAATAT
*
24181 TTTTTTACATTTTATGTATTTTC
1 TTTTTTACATTTTATATATTTTC
24204 TTTTTTAC-TTTAGTATATATTTT
1 TTTTTTACATTT--TATATATTTT
24227 TATTTTTTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 3 0.15
23 8 0.40
24 9 0.45
ACGTcount: A:0.20, C:0.07, G:0.04, T:0.70
Consensus pattern (23 bp):
TTTTTTACATTTTATATATTTTC
Found at i:24289 original size:2 final size:2
Alignment explanation
Indices: 24282--24308 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
24272 TTTATTAATT
24282 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 T
24309 TTACTTTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:24334 original size:30 final size:29
Alignment explanation
Indices: 24298--24383 Score: 95
Period size: 30 Copynumber: 2.8 Consensus size: 29
24288 TATATATATA
24298 TATATATATATTTACTTTTTTATTTTTTAT
1 TATATATATATTTA-TTTTTTATTTTTTAT
24328 TATATATATATATTA-TTTTTACTTTTTTAT
1 TATATATATAT-TTATTTTTTA-TTTTTTAT
*
24358 TAT-TATTTTATTTATTTGTTTTATTT
1 TATATA-TATATTTA-TT-TTTTATTT
24384 CTATATTTTT
Statistics
Matches: 49, Mismatches: 1, Indels: 11
0.80 0.02 0.18
Matches are distributed among these distances:
29 11 0.22
30 26 0.53
31 7 0.14
32 5 0.10
ACGTcount: A:0.26, C:0.02, G:0.01, T:0.71
Consensus pattern (29 bp):
TATATATATATTTATTTTTTATTTTTTAT
Found at i:24337 original size:32 final size:31
Alignment explanation
Indices: 24296--24383 Score: 103
Period size: 32 Copynumber: 2.8 Consensus size: 31
24286 TATATATATA
24296 TATATATATATATTTACTTTTTTATTTTTTAT
1 TATATATATATATTTA-TTTTTTATTTTTTAT
24328 TATATATATATA-TTA-TTTTTACTTTTTTAT
1 TATATATATATATTTATTTTTTA-TTTTTTAT
*
24358 TAT-TAT-TTTATTTATTTGTTTTATTT
1 TATATATATATATTTA-TT-TTTTATTT
24384 CTATATTTTT
Statistics
Matches: 50, Mismatches: 1, Indels: 11
0.81 0.02 0.18
Matches are distributed among these distances:
28 3 0.06
29 12 0.24
30 11 0.22
31 7 0.14
32 17 0.34
ACGTcount: A:0.26, C:0.02, G:0.01, T:0.70
Consensus pattern (31 bp):
TATATATATATATTTATTTTTTATTTTTTAT
Found at i:24390 original size:21 final size:21
Alignment explanation
Indices: 24366--24406 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
24356 ATTATTATTT
*
24366 TATTTATTTGTTTTATTTCTA
1 TATTTATTTCTTTTATTTCTA
* *
24387 TATTTTTTTCTTTTTTTTCT
1 TATTTATTTCTTTTATTTCT
24407 TTTTCTTCTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.12, C:0.07, G:0.02, T:0.78
Consensus pattern (21 bp):
TATTTATTTCTTTTATTTCTA
Found at i:24409 original size:15 final size:15
Alignment explanation
Indices: 24391--24423 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
24381 TTTCTATATT
*
24391 TTTTTCTTTTTTTTC
1 TTTTTCTTCTTTTTC
24406 TTTTTCTTCTTTTTC
1 TTTTTCTTCTTTTTC
24421 TTT
1 TTT
24424 ATTTTTTATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (15 bp):
TTTTTCTTCTTTTTC
Found at i:24547 original size:15 final size:15
Alignment explanation
Indices: 24529--24558 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
24519 TATTTATTTC
24529 TTACCTTTTTATCTA
1 TTACCTTTTTATCTA
24544 TTACCTTTTTATCTA
1 TTACCTTTTTATCTA
24559 ACATGGTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.20, C:0.20, G:0.00, T:0.60
Consensus pattern (15 bp):
TTACCTTTTTATCTA
Found at i:30495 original size:2 final size:2
Alignment explanation
Indices: 30488--30519 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
30478 ATACATAGTT
30488 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
30520 AAAGAGGTGC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:34347 original size:21 final size:20
Alignment explanation
Indices: 34261--34418 Score: 86
Period size: 21 Copynumber: 7.8 Consensus size: 20
34251 AAATGACCAA
**
34261 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
* ***
34280 AAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** *
34300 CAGAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
34320 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * *
34341 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
34362 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
34382 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
34403 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
34419 ACACATAAAT
Statistics
Matches: 104, Mismatches: 29, Indels: 11
0.72 0.20 0.08
Matches are distributed among these distances:
19 16 0.15
20 41 0.39
21 47 0.45
ACGTcount: A:0.39, C:0.25, G:0.17, T:0.19
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:34409 original size:20 final size:20
Alignment explanation
Indices: 34385--34578 Score: 210
Period size: 20 Copynumber: 9.7 Consensus size: 20
34375 CGATTTTCCA
** *
34385 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGAATCCGT
*
34405 AAATCGCAACGCGAA-CACAT
1 AAATCGCAACGCGAATC-CGT
*
34425 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGAATCCGT
* *
34445 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGAATCCGT
* **
34465 AAATCGCAACGCGTATGGGT
1 AAATCGCAACGCGAATCCGT
* *
34485 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGAATCCGT
* *
34505 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGAATCCGT
* *
34525 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGAATCCGT
**
34545 AAATCGCAACGATAATCCGT
1 AAATCGCAACGCGAATCCGT
34565 AAATCGCAACGCGA
1 AAATCGCAACGCGA
34579 TATTTAAAGC
Statistics
Matches: 149, Mismatches: 23, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
20 148 0.99
21 1 0.01
ACGTcount: A:0.36, C:0.25, G:0.20, T:0.19
Consensus pattern (20 bp):
AAATCGCAACGCGAATCCGT
Found at i:34998 original size:33 final size:33
Alignment explanation
Indices: 34959--35029 Score: 106
Period size: 33 Copynumber: 2.2 Consensus size: 33
34949 TTCACTTAGA
* *
34959 TTTCATTTCGCGTTACGATTCTGTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTCCGAT
* *
34992 TTTCATTTCGCGTTGCTATTCTCTCGTTCCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTCCGAT
35025 TTTCA
1 TTTCA
35030 AGTTAGTATT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.11, C:0.24, G:0.17, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTCCGAT
Found at i:35166 original size:41 final size:38
Alignment explanation
Indices: 35102--35218 Score: 136
Period size: 41 Copynumber: 3.1 Consensus size: 38
35092 TTCAATTTGC
* *
35102 AGAAGAGTCGCAACGAGATAAATGAAAATCGCAACGAG
1 AGAATAGTCGCAACGAGAGAAATGAAAATCGCAACGAG
*
35140 AGAATGACTGTCGCAACGAGAGAAATGACAATCGCAACGAG
1 AGAAT-A--GTCGCAACGAGAGAAATGAAAATCGCAACGAG
*
35181 AG-A-A-TCGCAAC--GCGAAATGAAAATCGCAACGAG
1 AGAATAGTCGCAACGAGAGAAATGAAAATCGCAACGAG
35214 AGAAT
1 AGAAT
35219 CGCAACGCGA
Statistics
Matches: 69, Mismatches: 5, Indels: 13
0.79 0.06 0.15
Matches are distributed among these distances:
33 22 0.32
34 1 0.01
35 7 0.10
38 5 0.07
39 1 0.01
40 1 0.01
41 32 0.46
ACGTcount: A:0.45, C:0.18, G:0.26, T:0.11
Consensus pattern (38 bp):
AGAATAGTCGCAACGAGAGAAATGAAAATCGCAACGAG
Found at i:35182 original size:21 final size:21
Alignment explanation
Indices: 35109--35184 Score: 109
Period size: 21 Copynumber: 3.7 Consensus size: 21
35099 TGCAGAAGAG
* *
35109 TCGCAACGAGATAAATGAAAA
1 TCGCAACGAGAGAAATGACAA
**
35130 TCGCAACGAGAG-AATGACTG
1 TCGCAACGAGAGAAATGACAA
35150 TCGCAACGAGAGAAATGACAA
1 TCGCAACGAGAGAAATGACAA
35171 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
35185 TCGCAACGCG
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
20 17 0.35
21 31 0.65
ACGTcount: A:0.45, C:0.18, G:0.25, T:0.12
Consensus pattern (21 bp):
TCGCAACGAGAGAAATGACAA
Found at i:35188 original size:14 final size:14
Alignment explanation
Indices: 35169--35225 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
35159 GAGAAATGAC
35169 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
35183 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
35202 AATCGCAACGAGAG
1 AATCGCAACGAGAG
35216 AATCGCAACG
1 AATCGCAACG
35226 CGAAACCAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.28
ACGTcount: A:0.44, C:0.23, G:0.25, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:35206 original size:33 final size:33
Alignment explanation
Indices: 35161--35241 Score: 135
Period size: 33 Copynumber: 2.5 Consensus size: 33
35151 CGCAACGAGA
*
35161 GAAATGACAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
35194 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
**
35227 GAAACCAAAATCGCA
1 GAAATGAAAATCGCA
35242 TTGCGATTTT
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 45 1.00
ACGTcount: A:0.46, C:0.23, G:0.22, T:0.09
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:35259 original size:19 final size:19
Alignment explanation
Indices: 35237--35334 Score: 72
Period size: 19 Copynumber: 5.7 Consensus size: 19
35227 GAAACCAAAA
*
35237 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
35256 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* *
35270 TCTCGTTGCGATTGTCATT
1 TCGCGTTGCGATTTTCATT
35289 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* * *
35303 TCTCGTTGCGATTGTCATC
1 TCGCGTTGCGATTTTCATT
35322 TCGCGTTGCGATT
1 TCGCGTTGCGATT
35335 CTCTCGTTGC
Statistics
Matches: 61, Mismatches: 8, Indels: 20
0.69 0.09 0.22
Matches are distributed among these distances:
14 20 0.33
16 4 0.07
17 5 0.08
19 32 0.52
ACGTcount: A:0.10, C:0.24, G:0.23, T:0.42
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:35278 original size:14 final size:14
Alignment explanation
Indices: 35259--35362 Score: 109
Period size: 14 Copynumber: 6.7 Consensus size: 14
35249 TTTCATTTCG
35259 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
35273 CGTTGCGATTGTCATTTCG
1 CGTTGCGA-T-TC---TCT
35292 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
35306 CGTTGCGATTGTCATCT
1 CGTTGCGA-T-TC-TCT
35323 CGCGTTGCGATTCTCT
1 --CGTTGCGATTCTCT
35339 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
35353 CGTTGCGATT
1 CGTTGCGATT
35363 TTCATTTCAA
Statistics
Matches: 78, Mismatches: 2, Indels: 20
0.78 0.02 0.20
Matches are distributed among these distances:
14 42 0.54
15 2 0.03
16 7 0.09
17 7 0.09
18 2 0.03
19 18 0.23
ACGTcount: A:0.09, C:0.26, G:0.24, T:0.41
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:35288 original size:33 final size:33
Alignment explanation
Indices: 35242--35348 Score: 196
Period size: 33 Copynumber: 3.2 Consensus size: 33
35232 CAAAATCGCA
*
35242 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTGTCATTTCGCGTTGCGATTCTCTCG
35275 TTGCGATTGTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTGTCATTTCGCGTTGCGATTCTCTCG
*
35308 TTGCGATTGTCATCTCGCGTTGCGATTCTCTCG
1 TTGCGATTGTCATTTCGCGTTGCGATTCTCTCG
35341 TTGCGATT
1 TTGCGATT
35349 CTCTCGTTGC
Statistics
Matches: 72, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 72 1.00
ACGTcount: A:0.09, C:0.24, G:0.23, T:0.43
Consensus pattern (33 bp):
TTGCGATTGTCATTTCGCGTTGCGATTCTCTCG
Found at i:37228 original size:93 final size:93
Alignment explanation
Indices: 37069--37542 Score: 921
Period size: 93 Copynumber: 5.1 Consensus size: 93
37059 TAGATTGCTT
*
37069 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
37134 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
37162 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
37227 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
37255 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
37320 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
* *
37348 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTATATTCTATAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
37413 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
37441 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
37506 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
37534 AGTAAATTT
1 AGTAAATTT
37543 ATCCATTCAA
Statistics
Matches: 376, Mismatches: 5, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
93 376 1.00
ACGTcount: A:0.23, C:0.13, G:0.19, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:37626 original size:19 final size:19
Alignment explanation
Indices: 37586--37714 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
37576 TAGTTTACTT
* *
37586 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
37606 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
**
37625 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
*
37644 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAACCAAAA
37658 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
*
37677 TCGCAA--CG--A-CAAGA
1 TCGCAACGCGAAACCAAAA
37691 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
37710 TCGCA
1 TCGCA
37715 TTGCGATTTT
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 19 0.21
15 2 0.02
16 4 0.04
17 4 0.04
18 2 0.02
19 46 0.51
20 13 0.14
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:37665 original size:33 final size:32
Alignment explanation
Indices: 37622--37714 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 32
37612 CGCGAAACCA
**
37622 AAATCGCAACGCGAAATGAAAATCGCAACGAC
1 AAATCGCAACGCGAAACCAAAATCGCAACGAC
37654 AGAATCGCAACGCGAAACCAAAATCGCAACGAC
1 A-AATCGCAACGCGAAACCAAAATCGCAACGAC
37687 AAGATCGCAACGCGAAACCAAAATCGCA
1 AA-ATCGCAACGCGAAACCAAAATCGCA
37715 TTGCGATTTT
Statistics
Matches: 57, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
32 2 0.04
33 55 0.96
ACGTcount: A:0.46, C:0.28, G:0.18, T:0.08
Consensus pattern (32 bp):
AAATCGCAACGCGAAACCAAAATCGCAACGAC
Found at i:37712 original size:52 final size:52
Alignment explanation
Indices: 37586--37714 Score: 140
Period size: 52 Copynumber: 2.5 Consensus size: 52
37576 TAGTTTACTT
**
37586 TCGCAACACGAAACTTAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
1 TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
* * *
37638 T-G-AAAATCGCAACGACAGAATCGCAACGCGAAACCAAAATCGCAACGAC-AAGA
1 TCGCAACA-CGAAAC-ACAAAATCGCAACGCGAAACCAAAATCGCAACG-CGAA-A
*
37691 TCGCAACGCGAAAC-CAAAATCGCA
1 TCGCAACACGAAACACAAAATCGCA
37715 TTGCGATTTT
Statistics
Matches: 62, Mismatches: 9, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
50 3 0.05
51 6 0.10
52 42 0.68
53 3 0.05
54 6 0.10
55 2 0.03
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (52 bp):
TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
Found at i:37732 original size:19 final size:19
Alignment explanation
Indices: 37710--37844 Score: 128
Period size: 19 Copynumber: 7.6 Consensus size: 19
37700 GAAACCAAAA
*
37710 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
37729 TCGCGTTGCGA--TTC-TT
1 TCGCGTTGCGATTTTCATT
37745 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
37762 TCGCATTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
37778 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
37795 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
*
37814 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
37834 TCGTGTTGCGA
1 TCGCGTTGCGA
37845 AAGTAAACTA
Statistics
Matches: 95, Mismatches: 10, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 15 0.16
16 11 0.12
17 11 0.12
19 46 0.48
20 12 0.13
ACGTcount: A:0.11, C:0.19, G:0.24, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:37751 original size:14 final size:14
Alignment explanation
Indices: 37732--37788 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
37722 TTTCATTTCG
37732 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
37746 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TTT
*
37763 CGCATTGCGATTCTGT
1 CG--TTGCGATTCTTT
37779 CGTTGCGATT
1 CGTTGCGATT
37789 TTCATTTCGC
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 16 0.43
16 7 0.19
17 8 0.22
19 6 0.16
ACGTcount: A:0.11, C:0.21, G:0.23, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:37757 original size:33 final size:33
Alignment explanation
Indices: 37715--37807 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
37705 CAAAATCGCA
*
37715 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
*
37748 TTGCGATTTTCATTTCGCATTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
37781 TTGCGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
37808 TTGGTTTCGC
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.11, C:0.20, G:0.22, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
Found at i:39789 original size:14 final size:14
Alignment explanation
Indices: 39770--39805 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
39760 ATTGTTTAAT
39770 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
39784 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
39798 TGATTTGT
1 TGATTTGT
39806 GTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:39936 original size:19 final size:19
Alignment explanation
Indices: 39912--40009 Score: 143
Period size: 19 Copynumber: 5.4 Consensus size: 19
39902 AAAATTGACT
39912 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
39931 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
39950 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
39964 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
39983 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
40003 ATCGCAA
1 ATCGCAA
40010 CGAGAGAATC
Statistics
Matches: 71, Mismatches: 2, Indels: 11
0.85 0.02 0.13
Matches are distributed among these distances:
14 10 0.14
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 39 0.55
20 16 0.23
ACGTcount: A:0.46, C:0.17, G:0.22, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:40041 original size:53 final size:53
Alignment explanation
Indices: 39912--40028 Score: 227
Period size: 53 Copynumber: 2.2 Consensus size: 53
39902 AAAATTGACT
39912 ATCGCAATGCGAAATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
39964 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
40017 ATCGCAATGCGA
1 ATCGCAATGCGA
40029 TTTTCATTTC
Statistics
Matches: 64, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
52 29 0.45
53 35 0.55
ACGTcount: A:0.44, C:0.18, G:0.24, T:0.14
Consensus pattern (53 bp):
ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
Found at i:42361 original size:12 final size:12
Alignment explanation
Indices: 42344--42368 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
42334 TCTTCGGGGA
42344 CTTTTTCTTCTT
1 CTTTTTCTTCTT
42356 CTTTTTCTTCTT
1 CTTTTTCTTCTT
42368 C
1 C
42369 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:42576 original size:24 final size:24
Alignment explanation
Indices: 42542--42588 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
42532 CTGAAACATC
42542 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
42566 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
42589 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:43520 original size:20 final size:20
Alignment explanation
Indices: 43270--43519 Score: 261
Period size: 20 Copynumber: 12.5 Consensus size: 20
43260 AAATTTCAGT
* * *
43270 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
43290 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
* *
43310 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
43330 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
* *
43350 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
*
43370 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
43390 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATTCGC
* **
43410 ATTGCGATTTACCCATAT-GC
1 GTTGCGATTTACGGAT-TCGC
*
43430 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
*
43450 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
*
43470 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATTCGC
* **
43490 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATTCGC
43510 GTTGCGATTT
1 GTTGCGATTT
43520 TGGAAAATCG
Statistics
Matches: 198, Mismatches: 28, Indels: 8
0.85 0.12 0.03
Matches are distributed among these distances:
20 197 0.99
21 1 0.01
ACGTcount: A:0.19, C:0.18, G:0.25, T:0.38
Consensus pattern (20 bp):
GTTGCGATTTACGGATTCGC
Found at i:43536 original size:21 final size:21
Alignment explanation
Indices: 43506--43588 Score: 78
Period size: 21 Copynumber: 4.0 Consensus size: 21
43496 ATTTTCATAT
*
43506 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTTGGAAAA
* * * **
43527 TCGCAATGCGAATTTGTACTA
1 TCGCATTGCGATTTTGGAAAA
*
43548 TCGCATTGCGATTTT-CAAGAA
1 TCGCATTGCGATTTTGGAA-AA
*
43569 TCGCGTTGCGATTTTGGAAA
1 TCGCATTGCGATTTTGGAAA
43589 CTGATTTGCG
Statistics
Matches: 47, Mismatches: 13, Indels: 4
0.73 0.20 0.06
Matches are distributed among these distances:
20 1 0.02
21 44 0.94
22 2 0.04
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTTGGAAAA
Found at i:43579 original size:42 final size:43
Alignment explanation
Indices: 43486--43584 Score: 100
Period size: 42 Copynumber: 2.4 Consensus size: 43
43476 ATTTATGTGT
* *
43486 TCGCGTTGCG-ATTT-TCATATTCGCGTTGCGATTTTGGAAAA
1 TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
**
43527 TCGCAATGCGAATTTGT-ACTA-TCGCATTGCGATTTT-CAAGAA
1 TCGCGTTGCGAATTTGTCA-TATTCGCATTGCGATTTTGCAA-AA
*
43569 TCGCGTTGCGATTTTG
1 TCGCGTTGCGAATTTG
43585 GAAACTGATT
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
41 10 0.21
42 34 0.72
43 3 0.06
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.37
Consensus pattern (43 bp):
TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
Found at i:51321 original size:23 final size:24
Alignment explanation
Indices: 51286--51344 Score: 70
Period size: 24 Copynumber: 2.5 Consensus size: 24
51276 ATTGATAATA
*
51286 AAAATTTA-CTTTT-AAAAT-TTT
1 AAAATTTATTTTTTCAAAATGTTT
*
51307 ATAAATTTATTTTTTCTAAATGTTT
1 A-AAATTTATTTTTTCAAAATGTTT
51332 AAAATTTATTTTT
1 AAAATTTATTTTT
51345 GTAACATAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
21 1 0.03
22 7 0.22
23 4 0.12
24 16 0.50
25 4 0.12
ACGTcount: A:0.37, C:0.03, G:0.02, T:0.58
Consensus pattern (24 bp):
AAAATTTATTTTTTCAAAATGTTT
Found at i:52024 original size:18 final size:18
Alignment explanation
Indices: 52001--52036 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
51991 GAAATGAAAT
* *
52001 ATTATAGTATTAAATAAA
1 ATTATAGAATAAAATAAA
52019 ATTATAGAATAAAATAAA
1 ATTATAGAATAAAATAAA
52037 TAATACTAGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.61, C:0.00, G:0.06, T:0.33
Consensus pattern (18 bp):
ATTATAGAATAAAATAAA
Found at i:53757 original size:3 final size:3
Alignment explanation
Indices: 53749--53782 Score: 54
Period size: 3 Copynumber: 12.0 Consensus size: 3
53739 TATTTTATGA
53749 AAT AAT AAT -AT AAT -AT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
53783 TTGACCCCAC
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
2 4 0.14
3 25 0.86
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
AAT
Found at i:54476 original size:19 final size:20
Alignment explanation
Indices: 54433--54473 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
54423 CTTATTGTAC
54433 TTAAAAATATTTTTACGTTT
1 TTAAAAATATTTTTACGTTT
* *
54453 TTAAAATTATTTTTATGTTT
1 TTAAAAATATTTTTACGTTT
54473 T
1 T
54474 AAATAAATAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.32, C:0.02, G:0.05, T:0.61
Consensus pattern (20 bp):
TTAAAAATATTTTTACGTTT
Found at i:55908 original size:35 final size:35
Alignment explanation
Indices: 55838--55910 Score: 103
Period size: 35 Copynumber: 2.1 Consensus size: 35
55828 AAATAATTTG
* *
55838 AAAATGTTTTTTAAAGTTTGGTAAAGTTTCTTTGA
1 AAAATGTTTTTCAAAGTTTGGTAAAGTTTCGTTGA
*
55873 AAAATGTTTTTCAAAGTTTGGTATATGTTT-GTTGA
1 AAAATGTTTTTCAAAGTTTGGTA-AAGTTTCGTTGA
55908 AAA
1 AAA
55911 TATGGGTAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
35 29 0.85
36 5 0.15
ACGTcount: A:0.33, C:0.03, G:0.18, T:0.47
Consensus pattern (35 bp):
AAAATGTTTTTCAAAGTTTGGTAAAGTTTCGTTGA
Found at i:57550 original size:24 final size:22
Alignment explanation
Indices: 57508--57555 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 22
57498 TATGAGCGAG
57508 AAAGGGATAAGACACTTTTGTCA
1 AAAGGGATAAGACACTTTTG-CA
* *
57531 AAAGGGATGAAGATAGTTTTGCA
1 AAAGGGAT-AAGACACTTTTGCA
57554 AA
1 AA
57556 GATTGGCAAG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 12 0.55
24 10 0.45
ACGTcount: A:0.42, C:0.08, G:0.25, T:0.25
Consensus pattern (22 bp):
AAAGGGATAAGACACTTTTGCA
Done.