Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007955.1 Hibiscus syriacus cultivar Beakdansim tig00110382_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: 136692
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:335 original size:196 final size:195
Alignment explanation
Indices: 1--438 Score: 783
Period size: 196 Copynumber: 2.2 Consensus size: 195
1 TTCATTCTGG-AAAAAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTC
1 TTCATTCTGGAAAAAAAATATCGA-ACAAACTATATTAGTGTCGACACATTATTTAGACTTATTC
*
65 TCTCATAAAACCGGTATATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGG
65 TCTCATAAAACCGGTATATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGG
130 TTCGATGATTTTGGGATCGACACTTTTTATATATGGATCGACACTTTATTGATGCACCTTGTAAA
130 TTCGATGATTTTGGGATCGACACTTTTTATATATGGATCGACACTTTATTGATGCACCTTGT-AA
195 AA
194 AA
197 TTCATTCTGGAAAAAAAAATATCG-ACAAACTATATTAGTGTCGACACATTATTTAGACTTATTC
1 TTCATTCTGG-AAAAAAAATATCGAACAAACTATATTAGTGTCGACACATTATTTAGACTTATTC
261 TCTCATAAAACCGGTATAATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGG
65 TCTCATAAAACCGGTAT-ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGG
*
326 G-TCGATGATTTTGGGATCGACACTTTTTATATATGGATCGCCACTTTATTGATGCACCTTGTAA
129 GTTCGATGATTTTGGGATCGACACTTTTTATATATGGATCGACACTTTATTGATGCACCTTGTAA
390 AA
194 AA
*
392 TTCATTCTGGAAAAAAAATATCGACACAAACTATATTAGTATCGACA
1 TTCATTCTGGAAAAAAAATATCGA-ACAAACTATATTAGTGTCGACA
439 TGACCCTTAA
Statistics
Matches: 234, Mismatches: 3, Indels: 10
0.95 0.01 0.04
Matches are distributed among these distances:
194 13 0.06
195 14 0.06
196 148 0.63
197 47 0.20
198 12 0.05
ACGTcount: A:0.35, C:0.16, G:0.14, T:0.36
Consensus pattern (195 bp):
TTCATTCTGGAAAAAAAATATCGAACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCT
CTCATAAAACCGGTATATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGT
TCGATGATTTTGGGATCGACACTTTTTATATATGGATCGACACTTTATTGATGCACCTTGTAAAA
Found at i:546 original size:19 final size:19
Alignment explanation
Indices: 519--582 Score: 110
Period size: 19 Copynumber: 3.4 Consensus size: 19
509 TATTCACATA
*
519 AAAAATATAAATCGTATAC
1 AAAATTATAAATCGTATAC
538 AAAATTATAAATCGTATAC
1 AAAATTATAAATCGTATAC
*
557 AAAATTATAAATCTTATAC
1 AAAATTATAAATCGTATAC
576 AAAATTA
1 AAAATTA
583 ACTCGACATT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 43 1.00
ACGTcount: A:0.56, C:0.09, G:0.03, T:0.31
Consensus pattern (19 bp):
AAAATTATAAATCGTATAC
Found at i:2405 original size:33 final size:33
Alignment explanation
Indices: 2368--2433 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
2358 CATCTTAATA
*
2368 TCACCCCTTAACACCGAAACTTCTTTCACCACT
1 TCACCCCTCAACACCGAAACTTCTTTCACCACT
***
2401 TCACCCCTCAACACCTCTACTTCTTTCACCACT
1 TCACCCCTCAACACCGAAACTTCTTTCACCACT
2434 CCATCTATTT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.24, C:0.45, G:0.02, T:0.29
Consensus pattern (33 bp):
TCACCCCTCAACACCGAAACTTCTTTCACCACT
Found at i:4768 original size:21 final size:20
Alignment explanation
Indices: 4721--4768 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
4711 TCCGGTATCA
*
4721 TTTTACCGTTTTTATCATTT
1 TTTTACCGGTTTTATCATTT
**
4741 TGATACCGGTTTTATCATATT
1 TTTTACCGGTTTTATCAT-TT
4762 TTTTACC
1 TTTTACC
4769 TGTTATATCG
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
20 15 0.68
21 7 0.32
ACGTcount: A:0.19, C:0.17, G:0.08, T:0.56
Consensus pattern (20 bp):
TTTTACCGGTTTTATCATTT
Found at i:4912 original size:20 final size:20
Alignment explanation
Indices: 4885--4931 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
4875 ACACTTTTAA
4885 TTTTACCGGTTTTATCAT-T
1 TTTTACCGGTTTTATCATAT
4904 TTGTTACCGGTTTTATCATAT
1 TT-TTACCGGTTTTATCATAT
4925 TTTTACC
1 TTTTACC
4932 TGGTATATCG
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
19 2 0.08
20 21 0.81
21 3 0.12
ACGTcount: A:0.17, C:0.17, G:0.11, T:0.55
Consensus pattern (20 bp):
TTTTACCGGTTTTATCATAT
Found at i:5423 original size:227 final size:227
Alignment explanation
Indices: 4996--5442 Score: 781
Period size: 228 Copynumber: 2.0 Consensus size: 227
4986 TTAAAACTGC
*
4996 TTTTAAAGTTATGTAATTTATGTTTCAATTTATTTAATAGTGTTTTATGTTTTCCACCTACAATA
1 TTTTAAAGTTATGTAATTTATGTTTCAATTTATTTAATAGTGTTTCATGTTTTCCACCTACAATA
**
5061 TTAATTTAATAATTTAATTTACACAAATTTTATTTGATTGTTTTGATATTTTATAAAATATTATT
66 TTAATTTAATAATTTAATTTACACAAAAATTATTTGATTGTTTTGATATTTTATAAAATATTATT
* *
5126 TAGAATTTAAATTTAACAATATTAACCAAATATAATAATAAATATGTTTTCAACAGTGAAATAAG
131 TAGAATTTAAATTTAACAATATTAACCAAAGATAATAATAAATATATTTTCAACAGTGAAATAAG
*
5191 TATGGACACTTTTATAAAAATGATATATACTT
196 TATGGACACTTTTATAAAAAGGATATATACTT
5223 TTTTGAAAGTTATGTAATTTATGTTTCAATTT-TTTAATAGTGTTTCATGTTTTCCACCTACAAT
1 TTTT-AAAGTTATGTAATTTATGTTTCAATTTATTTAATAGTGTTTCATGTTTTCCACCTACAAT
*
5287 ATTAATTTAATAATTTCATTTACACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATATTA
65 ATTAATTTAATAATTTAATTTACAC-AAAAATTATTTGATTGTTTTGATATTTTATAAAATATTA
* *
5352 TTTAGATTTTAAATTTAACAATATTAACTAAAGATAATAATAAATATATTTTC-ACAGTGAAATA
129 TTTAGAATTTAAATTTAACAATATTAACCAAAGATAATAATAAATATATTTTCAACAGTGAAATA
5416 AGTATGGACACTTTTATAAAAAGGATA
194 AGTATGGACACTTTTATAAAAAGGATA
5443 GATAATTTAC
Statistics
Matches: 209, Mismatches: 9, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
227 96 0.46
228 113 0.54
ACGTcount: A:0.39, C:0.07, G:0.08, T:0.45
Consensus pattern (227 bp):
TTTTAAAGTTATGTAATTTATGTTTCAATTTATTTAATAGTGTTTCATGTTTTCCACCTACAATA
TTAATTTAATAATTTAATTTACACAAAAATTATTTGATTGTTTTGATATTTTATAAAATATTATT
TAGAATTTAAATTTAACAATATTAACCAAAGATAATAATAAATATATTTTCAACAGTGAAATAAG
TATGGACACTTTTATAAAAAGGATATATACTT
Found at i:20317 original size:61 final size:61
Alignment explanation
Indices: 20222--20362 Score: 255
Period size: 61 Copynumber: 2.3 Consensus size: 61
20212 CTATTTATTA
*
20222 TTAAAGGAGAAGAAAAACTTGAAAATCTTGAGTGAGATGCATACAATATGTGTATCAGCTT
1 TTAAAGGAGAAGAAAAACTGGAAAATCTTGAGTGAGATGCATACAATATGTGTATCAGCTT
* *
20283 TTAAAGGAGAAGAAAAACTGGAATATCTTGAGTGAGATGTATACAATATGTGTATCAGCTT
1 TTAAAGGAGAAGAAAAACTGGAAAATCTTGAGTGAGATGCATACAATATGTGTATCAGCTT
20344 TTAAAGGAGAAGAAAAACT
1 TTAAAGGAGAAGAAAAACT
20363 TGATACCATT
Statistics
Matches: 77, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
61 77 1.00
ACGTcount: A:0.43, C:0.09, G:0.22, T:0.27
Consensus pattern (61 bp):
TTAAAGGAGAAGAAAAACTGGAAAATCTTGAGTGAGATGCATACAATATGTGTATCAGCTT
Found at i:22972 original size:15 final size:16
Alignment explanation
Indices: 22952--22986 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
22942 TAATAGTTAA
22952 ATTTTAAA-ATAAAAT
1 ATTTTAAACATAAAAT
*
22967 ATTTTAAACATTAAAT
1 ATTTTAAACATAAAAT
22983 ATTT
1 ATTT
22987 GATTAATAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 8 0.44
16 10 0.56
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (16 bp):
ATTTTAAACATAAAAT
Found at i:23008 original size:13 final size:13
Alignment explanation
Indices: 22990--23016 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
22980 AATATTTGAT
22990 TAATAATTTTTTA
1 TAATAATTTTTTA
23003 TAATAATTTTTTA
1 TAATAATTTTTTA
23016 T
1 T
23017 GTTTTATATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (13 bp):
TAATAATTTTTTA
Found at i:23363 original size:32 final size:33
Alignment explanation
Indices: 23324--23394 Score: 92
Period size: 32 Copynumber: 2.2 Consensus size: 33
23314 AATATGAATA
* *
23324 TTTAAAAAATTTAGTAGAGTC-AAATTA-AATTT
1 TTTAAAAAAATT-GAAGAGTCTAAATTATAATTT
*
23356 TTTAAAAAAATTGAAGGGTCTAAATTATAATTT
1 TTTAAAAAAATTGAAGAGTCTAAATTATAATTT
23389 TTTAAA
1 TTTAAA
23395 TTTGGAGGGG
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
31 6 0.18
32 17 0.50
33 11 0.32
ACGTcount: A:0.46, C:0.03, G:0.10, T:0.41
Consensus pattern (33 bp):
TTTAAAAAAATTGAAGAGTCTAAATTATAATTT
Found at i:23774 original size:78 final size:77
Alignment explanation
Indices: 23675--23818 Score: 200
Period size: 78 Copynumber: 1.9 Consensus size: 77
23665 TATATTATCA
* ** * * *
23675 AAAATTTTAATATTTTTGGTAAAGTATTA-CATAAAATATTATTTTTTTATTATAAATTTTAATA
1 AAAATTTTAATATTTTCGGTAAAACATTATC-TAAAATATTATTTTTTTACTAAAAATATTAATA
23739 TTGCGCGTTATTT
65 TTGCGCGTTATTT
*
23752 AAAATGTTTAATATTTTCGGTAAAACGTTATCTAAAATATTATTTTTTTACTAAAAATATTAATA
1 AAAAT-TTTAATATTTTCGGTAAAACATTATCTAAAATATTATTTTTTTACTAAAAATATTAATA
23817 TT
65 TT
23819 AGACGCTACT
Statistics
Matches: 58, Mismatches: 7, Indels: 3
0.85 0.10 0.04
Matches are distributed among these distances:
77 5 0.09
78 52 0.90
79 1 0.02
ACGTcount: A:0.39, C:0.05, G:0.07, T:0.49
Consensus pattern (77 bp):
AAAATTTTAATATTTTCGGTAAAACATTATCTAAAATATTATTTTTTTACTAAAAATATTAATAT
TGCGCGTTATTT
Found at i:24120 original size:20 final size:20
Alignment explanation
Indices: 24095--24167 Score: 112
Period size: 20 Copynumber: 3.6 Consensus size: 20
24085 CTATCGCAAA
24095 TTCGCGTTGCGATTTTTCAT
1 TTCGCGTTGCGATTTTTCAT
* *
24115 TTCGCGTTGCGATTTTCCAG
1 TTCGCGTTGCGATTTTTCAT
24135 TTCGCGTTGCGA-TTTTCTAT
1 TTCGCGTTGCGATTTTTC-AT
24155 TTCGCGTTGCGAT
1 TTCGCGTTGCGAT
24168 AGTTGAAAAT
Statistics
Matches: 47, Mismatches: 4, Indels: 3
0.87 0.07 0.06
Matches are distributed among these distances:
19 4 0.09
20 43 0.91
ACGTcount: A:0.10, C:0.22, G:0.23, T:0.45
Consensus pattern (20 bp):
TTCGCGTTGCGATTTTTCAT
Found at i:24192 original size:41 final size:41
Alignment explanation
Indices: 24091--24192 Score: 118
Period size: 40 Copynumber: 2.5 Consensus size: 41
24081 TCCACTATCG
* *
24091 CAAATTCGCGTTGCGATTTT-TCATTTCGCGTTGCGATTTT
1 CAAAATCGCGTTGCGATTTTCTCATTTCGCGTTGCGATGTT
* **
24131 CCAGTTCGCGTTGCGATTTTCT-ATTTCGCGTTGCGATAGTT
1 CAAAATCGCGTTGCGATTTTCTCATTTCGCGTTGCGAT-GTT
* *
24172 GAAAATCGCGTTACGATTTTC
1 CAAAATCGCGTTGCGATTTTC
24193 CAAATTCGTT
Statistics
Matches: 52, Mismatches: 8, Indels: 3
0.83 0.13 0.05
Matches are distributed among these distances:
40 33 0.63
41 19 0.37
ACGTcount: A:0.17, C:0.21, G:0.22, T:0.41
Consensus pattern (41 bp):
CAAAATCGCGTTGCGATTTTCTCATTTCGCGTTGCGATGTT
Found at i:24341 original size:6 final size:6
Alignment explanation
Indices: 24330--24387 Score: 81
Period size: 6 Copynumber: 10.5 Consensus size: 6
24320 AACACGTATT
24330 ACCACG ACCACG ACCACG ACCACG ACCACG A-CACG A-CACG ACC-CG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
24375 ACC-CG ACC-CG ACC
1 ACCACG ACCACG ACC
24388 CGAGACGAAC
Statistics
Matches: 51, Mismatches: 0, Indels: 3
0.94 0.00 0.06
Matches are distributed among these distances:
5 25 0.49
6 26 0.51
ACGTcount: A:0.31, C:0.52, G:0.17, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:24387 original size:5 final size:5
Alignment explanation
Indices: 24334--24390 Score: 60
Period size: 5 Copynumber: 10.6 Consensus size: 5
24324 CGTATTACCA
* *
24334 CGACC ACGACC ACGACC ACGACC ACGACA CGACA CGACC CGACC CGACC
1 CGACC -CGACC -CGACC -CGACC -CGACC CGACC CGACC CGACC CGACC
24383 CGACC CGA
1 CGACC CGA
24391 GACGAACGGC
Statistics
Matches: 49, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
5 27 0.55
6 22 0.45
ACGTcount: A:0.30, C:0.51, G:0.19, T:0.00
Consensus pattern (5 bp):
CGACC
Found at i:24881 original size:6 final size:6
Alignment explanation
Indices: 24872--24904 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
24862 GTCCGTCTCG
24872 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
24905 AATGGTAATG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.00, C:0.15, G:0.52, T:0.33
Consensus pattern (6 bp):
GGTCGT
Found at i:24910 original size:6 final size:6
Alignment explanation
Indices: 24901--24925 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
24891 GTCGTGGTCG
24901 TGGTAA TGGTAA TGGTAA TGGTAA T
1 TGGTAA TGGTAA TGGTAA TGGTAA T
24926 ACGTGGATAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.32, T:0.36
Consensus pattern (6 bp):
TGGTAA
Found at i:24910 original size:18 final size:18
Alignment explanation
Indices: 24872--24910 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
24862 GTCCGTCTCG
**
24872 GGTCGTGGTCGTGGTCGT
1 GGTCGTGGTCGTGGTAAT
24890 GGTCGTGGTCGTGGTAAT
1 GGTCGTGGTCGTGGTAAT
24908 GGT
1 GGT
24911 AATGGTAATG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.05, C:0.13, G:0.49, T:0.33
Consensus pattern (18 bp):
GGTCGTGGTCGTGGTAAT
Found at i:25046 original size:22 final size:22
Alignment explanation
Indices: 25018--25070 Score: 88
Period size: 22 Copynumber: 2.4 Consensus size: 22
25008 AATTTGGAAA
25018 ATCGCAACGACAACTGTAGACT
1 ATCGCAACGACAACTGTAGACT
* *
25040 ATCGCAACAACAATTGTAGACT
1 ATCGCAACGACAACTGTAGACT
25062 ATCGCAACG
1 ATCGCAACG
25071 CGAAATGGAA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.38, C:0.26, G:0.17, T:0.19
Consensus pattern (22 bp):
ATCGCAACGACAACTGTAGACT
Found at i:32327 original size:10 final size:10
Alignment explanation
Indices: 32314--32379 Score: 51
Period size: 10 Copynumber: 5.8 Consensus size: 10
32304 GAACGTTTGG
32314 TTATGTTCGT
1 TTATGTTCGT
32324 TTATGTTCGTT
1 TTATGTTCG-T
*
32335 CAGTTATATTCGT
1 ---TTATGTTCGT
32348 TTATGTTCGTT
1 TTATGTTCG-T
32359 CGATTATGTTCGT
1 ---TTATGTTCGT
32372 TTATGTTC
1 TTATGTTC
32380 ATTCATTTAT
Statistics
Matches: 46, Mismatches: 2, Indels: 16
0.72 0.03 0.25
Matches are distributed among these distances:
10 25 0.54
11 2 0.04
13 2 0.04
14 17 0.37
ACGTcount: A:0.14, C:0.12, G:0.18, T:0.56
Consensus pattern (10 bp):
TTATGTTCGT
Found at i:32389 original size:24 final size:23
Alignment explanation
Indices: 32314--32392 Score: 113
Period size: 24 Copynumber: 3.3 Consensus size: 23
32304 GAACGTTTGG
32314 TTATGTTCGTTTATGTTCGTTCA
1 TTATGTTCGTTTATGTTCGTTCA
*
32337 GTTATATTCGTTTATGTTCGTTCGA
1 -TTATGTTCGTTTATGTTCGTTC-A
*
32362 TTATGTTCGTTTATGTTCATTCA
1 TTATGTTCGTTTATGTTCGTTCA
32385 TTTATGTT
1 -TTATGTT
32393 TAACCCAATC
Statistics
Matches: 50, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
23 1 0.02
24 48 0.96
25 1 0.02
ACGTcount: A:0.15, C:0.11, G:0.16, T:0.57
Consensus pattern (23 bp):
TTATGTTCGTTTATGTTCGTTCA
Found at i:33491 original size:16 final size:16
Alignment explanation
Indices: 33470--33506 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
33460 GTCTCCAACA
*
33470 TTTATGTTCGTGTTTG
1 TTTATGTTCATGTTTG
33486 TTTATGTTCATGTTTG
1 TTTATGTTCATGTTTG
33502 TTTAT
1 TTTAT
33507 TTATTAAATG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.11, C:0.05, G:0.19, T:0.65
Consensus pattern (16 bp):
TTTATGTTCATGTTTG
Found at i:46731 original size:16 final size:16
Alignment explanation
Indices: 46708--46751 Score: 56
Period size: 15 Copynumber: 2.9 Consensus size: 16
46698 GGTGTGCAAA
46708 TCCGGGTACTCGGATT
1 TCCGGGTACTCGGATT
* *
46724 TTCGGGTA-TCCGATT
1 TCCGGGTACTCGGATT
46739 TCCGGGTAC-CGGA
1 TCCGGGTACTCGGA
46752 ACTTCTGGGT
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
15 16 0.70
16 7 0.30
ACGTcount: A:0.14, C:0.25, G:0.32, T:0.30
Consensus pattern (16 bp):
TCCGGGTACTCGGATT
Found at i:51600 original size:30 final size:30
Alignment explanation
Indices: 51564--51629 Score: 96
Period size: 30 Copynumber: 2.2 Consensus size: 30
51554 AGTGAACTGG
*
51564 CGGTTCAAACCGGTTTTGCCGGTTTTCAGC
1 CGGTTCAAACCGGTTTTACCGGTTTTCAGC
**
51594 CGGTTCACCCCGGTTTTACCGGTTTTCAGC
1 CGGTTCAAACCGGTTTTACCGGTTTTCAGC
*
51624 CTGTTC
1 CGGTTC
51630 TTCTAGTTCT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.11, C:0.30, G:0.24, T:0.35
Consensus pattern (30 bp):
CGGTTCAAACCGGTTTTACCGGTTTTCAGC
Found at i:52616 original size:14 final size:14
Alignment explanation
Indices: 52597--52623 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
52587 ACAAAAGTTT
52597 TGATCAAACAATTA
1 TGATCAAACAATTA
52611 TGATCAAACAATT
1 TGATCAAACAATT
52624 GATTTCCCTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.48, C:0.15, G:0.07, T:0.30
Consensus pattern (14 bp):
TGATCAAACAATTA
Found at i:52780 original size:14 final size:14
Alignment explanation
Indices: 52761--52788 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
52751 CCAAAAGTTT
52761 TGATCAAACAATTG
1 TGATCAAACAATTG
52775 TGATCAAACAATTG
1 TGATCAAACAATTG
52789 ATTTCCCTTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.14, G:0.14, T:0.29
Consensus pattern (14 bp):
TGATCAAACAATTG
Found at i:52782 original size:164 final size:165
Alignment explanation
Indices: 52443--52817 Score: 599
Period size: 164 Copynumber: 2.3 Consensus size: 165
52433 ACAAAAGTTT
*
52443 TGATCAAACAATTGATTTCCCTGCCCGCCAATCTCGCGCCCCCGCCAGTCTCTGATATCGATATA
1 TGATCAAACAATTGATTTCCCTGCCCGCCAATCTCACG--CCC-CCAGTCTCTGATATCGATATA
* * * *
52508 ATTGATGATGATGTTCAACGAGGTAATGTCAATAGTTTAATATCAATTGTTTTCTCTGATCGGGT
63 ATTAATGATGATGTTCAACGAGGTAATGTCAATAGATTAATATCAATTGATTTCTCTGATCGGGG
52573 AATCGAATTAGCGAACAAAAGTTTTGATCAAACAATTA
128 AATCGAATTAGCGAACAAAAGTTTTGATCAAACAATTA
* * *
52611 TGATCAAACAATTGATTTCCCTGCCCACCAATCTCACGCCCCCAGTCTCTGATATTGATATAGTT
1 TGATCAAACAATTGATTTCCCTGCCCGCCAATCTCACGCCCCCAGTCTCTGATATCGATATAATT
* *
52676 AATGGTGATGTTCAACGAGGTAATGTCAATGGATTAATATCAATTGATTTCT-TGATCGGGGAAT
66 AATGATGATGTTCAACGAGGTAATGTCAATAGATTAATATCAATTGATTTCTCTGATCGGGGAAT
* *
52740 CGAATTAGCGACCAAAAGTTTTGATCAAACAATTG
131 CGAATTAGCGAACAAAAGTTTTGATCAAACAATTA
*
52775 TGATCAAACAATTGATTTCCCTTCCCGCCAATCTCACGCCCCC
1 TGATCAAACAATTGATTTCCCTGCCCGCCAATCTCACGCCCCC
52818 GCTAGTCTCG
Statistics
Matches: 193, Mismatches: 14, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
164 85 0.44
165 69 0.36
166 3 0.02
168 36 0.19
ACGTcount: A:0.30, C:0.23, G:0.17, T:0.31
Consensus pattern (165 bp):
TGATCAAACAATTGATTTCCCTGCCCGCCAATCTCACGCCCCCAGTCTCTGATATCGATATAATT
AATGATGATGTTCAACGAGGTAATGTCAATAGATTAATATCAATTGATTTCTCTGATCGGGGAAT
CGAATTAGCGAACAAAAGTTTTGATCAAACAATTA
Found at i:56471 original size:21 final size:20
Alignment explanation
Indices: 56431--56472 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
56421 CCAACTTACA
*
56431 ATGCATTATGAACCATTATT
1 ATGCATTATCAACCATTATT
*
56451 ATGCATTATACAACTATTATT
1 ATGCATTAT-CAACCATTATT
56472 A
1 A
56473 GTTGTATGAC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.38, C:0.14, G:0.07, T:0.40
Consensus pattern (20 bp):
ATGCATTATCAACCATTATT
Found at i:61181 original size:21 final size:20
Alignment explanation
Indices: 61141--61182 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
61131 CCAACTTACA
*
61141 ATGCATTATGAACCATTATT
1 ATGCATTATCAACCATTATT
*
61161 ATGCATTATACAACTATTATT
1 ATGCATTAT-CAACCATTATT
61182 A
1 A
61183 GTTGTATGAC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.38, C:0.14, G:0.07, T:0.40
Consensus pattern (20 bp):
ATGCATTATCAACCATTATT
Found at i:75174 original size:25 final size:25
Alignment explanation
Indices: 75146--75206 Score: 70
Period size: 25 Copynumber: 2.4 Consensus size: 25
75136 TAACTGCAAA
**
75146 AAAATAAAATATTTAAATAAATAAT
1 AAAATAAAATAAATAAATAAATAAT
*
75171 AAAA-AAAATTAAATAATTAAATAAT
1 AAAATAAAA-TAAATAAATAAATAAT
*
75196 TAAATAAAATA
1 AAAATAAAATA
75207 CTAACAAATA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
24 4 0.13
25 22 0.73
26 4 0.13
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (25 bp):
AAAATAAAATAAATAAATAAATAAT
Found at i:75184 original size:29 final size:30
Alignment explanation
Indices: 75143--75204 Score: 90
Period size: 29 Copynumber: 2.1 Consensus size: 30
75133 TTATAACTGC
*
75143 AAAAAAATAAAATATTTAAATAAAT-AATA
1 AAAAAAATAAAATAATTAAATAAATAAATA
* *
75172 AAAAAAATTAAATAATTAAATAATTAAATA
1 AAAAAAATAAAATAATTAAATAAATAAATA
75202 AAA
1 AAA
75205 TACTAACAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
29 22 0.76
30 7 0.24
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (30 bp):
AAAAAAATAAAATAATTAAATAAATAAATA
Found at i:75190 original size:8 final size:8
Alignment explanation
Indices: 75152--75202 Score: 54
Period size: 8 Copynumber: 6.8 Consensus size: 8
75142 CAAAAAAATA
*
75152 AAATATTT
1 AAATAATT
*
75160 AAATAAAT
1 AAATAATT
75168 -AATAA--
1 AAATAATT
*
75173 AAAAAATT
1 AAATAATT
75181 AAATAATT
1 AAATAATT
75189 AAATAATT
1 AAATAATT
75197 AAATAA
1 AAATAA
75203 AATACTAACA
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
6 4 0.11
7 5 0.14
8 27 0.75
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (8 bp):
AAATAATT
Found at i:75200 original size:21 final size:20
Alignment explanation
Indices: 75152--75206 Score: 55
Period size: 21 Copynumber: 2.9 Consensus size: 20
75142 CAAAAAAATA
*
75152 AAATATTTAAA-TAAATAAT
1 AAATAATTAAATTAAATAAT
75171 AAA-AA--AAATTAAATAATT
1 AAATAATTAAATTAAATAA-T
*
75189 AAATAATTAAATAAAATA
1 AAATAATTAAATTAAATA
75207 CTAACAAATA
Statistics
Matches: 29, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
16 3 0.10
17 7 0.24
18 5 0.17
19 5 0.17
21 9 0.31
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (20 bp):
AAATAATTAAATTAAATAAT
Found at i:75220 original size:38 final size:37
Alignment explanation
Indices: 75152--75223 Score: 99
Period size: 38 Copynumber: 1.9 Consensus size: 37
75142 CAAAAAAATA
*
75152 AAATATTTAAATAAATAATAAAAAAAATTAAATAATT
1 AAATAATTAAATAAATAATAAAAAAAATTAAATAATT
* * *
75189 AAATAATTAAATAAAATACTAACAAATATTAAATA
1 AAATAATTAAAT-AAATAATAAAAAAAATTAAATA
75224 TAACAAAATA
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
37 11 0.37
38 19 0.63
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.31
Consensus pattern (37 bp):
AAATAATTAAATAAATAATAAAAAAAATTAAATAATT
Found at i:75283 original size:10 final size:10
Alignment explanation
Indices: 75268--75302 Score: 61
Period size: 10 Copynumber: 3.5 Consensus size: 10
75258 AGGTTTGGTT
*
75268 TTTGAGAGAA
1 TTTGAGAGGA
75278 TTTGAGAGGA
1 TTTGAGAGGA
75288 TTTGAGAGGA
1 TTTGAGAGGA
75298 TTTGA
1 TTTGA
75303 TGTGGTGAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
10 24 1.00
ACGTcount: A:0.31, C:0.00, G:0.34, T:0.34
Consensus pattern (10 bp):
TTTGAGAGGA
Found at i:77093 original size:17 final size:17
Alignment explanation
Indices: 77038--77094 Score: 50
Period size: 17 Copynumber: 3.5 Consensus size: 17
77028 CATAAAACTT
77038 AATATTATTATT-TTAA
1 AATATTATTATTATTAA
* *
77054 AA-A-TATTA-GAATAA
1 AATATTATTATTATTAA
*
77068 ATTATTTATTATTATTAA
1 AATA-TTATTATTATTAA
77086 AATATTATT
1 AATATTATT
77095 TCTATACCAA
Statistics
Matches: 30, Mismatches: 6, Indels: 9
0.67 0.13 0.20
Matches are distributed among these distances:
14 9 0.30
15 2 0.07
16 2 0.07
17 10 0.33
18 7 0.23
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (17 bp):
AATATTATTATTATTAA
Found at i:77741 original size:48 final size:49
Alignment explanation
Indices: 77642--77744 Score: 127
Period size: 48 Copynumber: 2.1 Consensus size: 49
77632 ACTTTTCATC
* * * ** * *
77642 TAACTTGCATTAGTGGCACATTTTCTGCCAAAATGCATTGTTGGTCATT
1 TAACTTGCATTAGTGACACACTTTATGCCAAAATGCACCGTTAGACATT
*
77691 TAACTTGCATTAGTGACAC-CTTTATGCCAAAATGCACCGTTAGACTTT
1 TAACTTGCATTAGTGACACACTTTATGCCAAAATGCACCGTTAGACATT
77739 TAACTT
1 TAACTT
77745 TTCATCTAAC
Statistics
Matches: 46, Mismatches: 8, Indels: 1
0.84 0.15 0.02
Matches are distributed among these distances:
48 28 0.61
49 18 0.39
ACGTcount: A:0.27, C:0.20, G:0.16, T:0.37
Consensus pattern (49 bp):
TAACTTGCATTAGTGACACACTTTATGCCAAAATGCACCGTTAGACATT
Found at i:77791 original size:60 final size:60
Alignment explanation
Indices: 77686--77931 Score: 348
Period size: 60 Copynumber: 4.1 Consensus size: 60
77676 GCATTGTTGG
* * * **
77686 TCATTTAACTTGCATTAGTGACACCTTTATGCCAAAATGCACCGTTAGACTTTTAACTTT
1 TCATCTAACTTGCATTAGTGGCACCTTTCTGCCAAAATGCACCGTTAGACACTTAACTTT
* * * ** *
77746 TCATCTAACATGCATTAGTGGCACCTTTCTGCCAAAATGCTCCGTTGGGTATTTAACTTT
1 TCATCTAACTTGCATTAGTGGCACCTTTCTGCCAAAATGCACCGTTAGACACTTAACTTT
* *
77806 TCATCTAACTTGCATTAGTGGCACCTTTCTGCCAAAATGCACGGTTATACACTTAACTTT
1 TCATCTAACTTGCATTAGTGGCACCTTTCTGCCAAAATGCACCGTTAGACACTTAACTTT
* * *
77866 TCATCTAACTTGCATTAGTGGCACATTTCTGCCAAAATGCACAGTTAGGCACTTAACTTT
1 TCATCTAACTTGCATTAGTGGCACCTTTCTGCCAAAATGCACCGTTAGACACTTAACTTT
77926 TCATCT
1 TCATCT
77932 TAGAGCAGTT
Statistics
Matches: 165, Mismatches: 21, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
60 165 1.00
ACGTcount: A:0.26, C:0.24, G:0.14, T:0.36
Consensus pattern (60 bp):
TCATCTAACTTGCATTAGTGGCACCTTTCTGCCAAAATGCACCGTTAGACACTTAACTTT
Found at i:79573 original size:22 final size:23
Alignment explanation
Indices: 79548--79592 Score: 65
Period size: 24 Copynumber: 2.0 Consensus size: 23
79538 TAAAAGTAAT
*
79548 AGTATTA-TATTATATTTTAAAA
1 AGTATTAGTAATATATTTTAAAA
79570 AGTATTAGTTAATATATTTTAAA
1 AGTATTAG-TAATATATTTTAAA
79593 TATTTTTATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 7 0.35
24 13 0.65
ACGTcount: A:0.44, C:0.00, G:0.07, T:0.49
Consensus pattern (23 bp):
AGTATTAGTAATATATTTTAAAA
Found at i:79586 original size:29 final size:30
Alignment explanation
Indices: 79521--79587 Score: 77
Period size: 28 Copynumber: 2.3 Consensus size: 30
79511 AATATTATAA
79521 AATATATTAATTATTTATAAAAGTAATAGT
1 AATATATTAATTATTTATAAAAGTAATAGT
* *
79551 ATTATATT-A-TATTT-TAAAAAGTATTAGTT
1 AATATATTAATTATTTAT-AAAAGTAATAG-T
79580 AATATATT
1 AATATATT
79588 TTAAATATTT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
27 1 0.03
28 15 0.47
29 9 0.28
30 7 0.22
ACGTcount: A:0.46, C:0.00, G:0.06, T:0.48
Consensus pattern (30 bp):
AATATATTAATTATTTATAAAAGTAATAGT
Found at i:79609 original size:23 final size:24
Alignment explanation
Indices: 79559--79610 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
79549 GTATTATATT
*
79559 ATATTTTAAAAAGTATTAGTTAAT
1 ATATTTTAAAAAGTATTAGTTAAA
* * *
79583 ATATTTTAAATATTTTTA-TTAAA
1 ATATTTTAAAAAGTATTAGTTAAA
79606 ATATT
1 ATATT
79611 ATTAGATTAT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
23 9 0.38
24 15 0.62
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.52
Consensus pattern (24 bp):
ATATTTTAAAAAGTATTAGTTAAA
Found at i:79748 original size:21 final size:21
Alignment explanation
Indices: 79688--79748 Score: 52
Period size: 21 Copynumber: 2.9 Consensus size: 21
79678 TTTCTATGAA
*
79688 ATTAATAAATAATATAA-ATTTT
1 ATTAA-AAA-AATATAATATATT
* ** *
79710 ATTAATAATTTATTATATATT
1 ATTAAAAAAATATAATATATT
79731 ATTAAAAAAATATAATAT
1 ATTAAAAAAATATAATAT
79749 CTTACATTAT
Statistics
Matches: 29, Mismatches: 9, Indels: 3
0.71 0.22 0.07
Matches are distributed among these distances:
20 4 0.14
21 20 0.69
22 5 0.17
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (21 bp):
ATTAAAAAAATATAATATATT
Found at i:91894 original size:2 final size:2
Alignment explanation
Indices: 91889--91924 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
91879 TTTTAAAGAA
91889 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
91925 TCCAACTTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:92155 original size:13 final size:13
Alignment explanation
Indices: 92137--92166 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
92127 GACAAACTCC
92137 TAATATTTATATA
1 TAATATTTATATA
92150 TAATATTTATATA
1 TAATATTTATATA
92163 TAAT
1 TAAT
92167 GACGGTCTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (13 bp):
TAATATTTATATA
Found at i:92248 original size:15 final size:16
Alignment explanation
Indices: 92230--92271 Score: 50
Period size: 15 Copynumber: 2.6 Consensus size: 16
92220 AACATTCAAA
*
92230 ATATTTTTATT-TTAT
1 ATATTTTTATTAATAT
92245 ATATTTTATATTAATAT
1 ATATTTT-TATTAATAT
92262 ATTATTTTTA
1 A-TATTTTTA
92272 GTATCATTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
15 7 0.30
16 4 0.17
17 6 0.26
18 6 0.26
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (16 bp):
ATATTTTTATTAATAT
Found at i:92299 original size:29 final size:28
Alignment explanation
Indices: 92238--92299 Score: 72
Period size: 29 Copynumber: 2.2 Consensus size: 28
92228 AAATATTTTT
* *
92238 ATTTTATATATTTTATATTAATATATTA
1 ATTTTATATATTTTATATAAAAATATTA
*
92266 TTTTTAGTATCATTTTA-ATAAAAATATTA
1 ATTTTA-TAT-ATTTTATATAAAAATATTA
92295 ATTTT
1 ATTTT
92300 TAAATTATGT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
28 5 0.18
29 17 0.61
30 6 0.21
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.58
Consensus pattern (28 bp):
ATTTTATATATTTTATATAAAAATATTA
Found at i:92418 original size:20 final size:20
Alignment explanation
Indices: 92390--92428 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
92380 ATAAATTTAT
92390 TTTAATAATA-TATTTAATAA
1 TTTAATAATACTA-TTAATAA
*
92410 TTTATTAATACTATTAATA
1 TTTAATAATACTATTAATA
92429 TTATTTGTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 15 0.88
21 2 0.12
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (20 bp):
TTTAATAATACTATTAATAA
Found at i:92533 original size:7 final size:8
Alignment explanation
Indices: 92511--92552 Score: 50
Period size: 8 Copynumber: 5.2 Consensus size: 8
92501 ATAATATTCT
92511 TATTTTAA
1 TATTTTAA
92519 TATTTTAA
1 TATTTTAA
92527 T-TTTTAA
1 TATTTTAA
* *
92534 TAATATTAT
1 T-ATTTTAA
92543 TATTTTAA
1 TATTTTAA
92551 TA
1 TA
92553 AGTAATTAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
7 7 0.25
8 16 0.57
9 5 0.18
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (8 bp):
TATTTTAA
Found at i:92539 original size:37 final size:38
Alignment explanation
Indices: 92497--92610 Score: 95
Period size: 37 Copynumber: 3.1 Consensus size: 38
92487 CCTTAAAATG
*
92497 TAATATAATATTCTTATTTTAATA-T-TTTAATTT-TTAA
1 TAATAT-ATA-TCTTATTTTAATAGTAATTAATTTATTAA
92534 TAATAT-TA--TTATTTTAATAAGTAATTAATTTAATTAA
1 TAATATATATCTTATTTTAAT-AGTAATTAATTT-ATTAA
92571 TAATATATTACTCTTATTTTAATA--AA-TAATTTA-TAA
1 TAATATA-TA-TCTTATTTTAATAGTAATTAATTTATTAA
92607 TAAT
1 TAAT
92611 TTTATTTCAA
Statistics
Matches: 66, Mismatches: 1, Indels: 21
0.75 0.01 0.24
Matches are distributed among these distances:
32 10 0.15
33 1 0.02
34 1 0.02
35 9 0.14
36 7 0.11
37 17 0.26
38 6 0.09
39 4 0.06
41 1 0.02
42 10 0.15
ACGTcount: A:0.43, C:0.03, G:0.01, T:0.54
Consensus pattern (38 bp):
TAATATATATCTTATTTTAATAGTAATTAATTTATTAA
Found at i:92580 original size:20 final size:18
Alignment explanation
Indices: 92516--92580 Score: 64
Period size: 20 Copynumber: 3.6 Consensus size: 18
92506 ATTCTTATTT
*
92516 TAATATTTTAATTTTTAA
1 TAATATATTAATTTTTAA
92534 TAATATTATT-A-TTTTAA
1 TAATA-TATTAATTTTTAA
92551 TAAGTA-ATTAATTTAATTAA
1 TAA-TATATTAATTT--TTAA
92571 TAATATATTA
1 TAATATATTA
92581 CTCTTATTTT
Statistics
Matches: 39, Mismatches: 1, Indels: 12
0.75 0.02 0.23
Matches are distributed among these distances:
16 3 0.08
17 10 0.26
18 10 0.26
19 5 0.13
20 11 0.28
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.54
Consensus pattern (18 bp):
TAATATATTAATTTTTAA
Found at i:92656 original size:30 final size:34
Alignment explanation
Indices: 92604--92665 Score: 87
Period size: 32 Copynumber: 1.9 Consensus size: 34
92594 AAATAATTTA
92604 TAATAATTTTATTTCAATAAAA-TATA-ATAGTAT
1 TAATAATTTTATTT-AATAAAATTATATATAGTAT
92637 TAAT-ATTTTATTT-ATAAAATTATATATAG
1 TAATAATTTTATTTAATAAAATTATATATAG
92666 AATATTTTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
30 6 0.22
31 4 0.15
32 13 0.48
33 4 0.15
ACGTcount: A:0.47, C:0.02, G:0.03, T:0.48
Consensus pattern (34 bp):
TAATAATTTTATTTAATAAAATTATATATAGTAT
Found at i:103437 original size:19 final size:20
Alignment explanation
Indices: 103375--103442 Score: 70
Period size: 19 Copynumber: 3.5 Consensus size: 20
103365 AAAAATAGCT
103375 TAAA-TATAAAATAAGTGCC
1 TAAACTATAAAATAAGTGCC
* * *
103394 TAAACTGCTAAAA-AAATGACT
1 TAAACT-ATAAAATAAGTG-CC
103415 TAAA-TATAAAATAAGTGCC
1 TAAACTATAAAATAAGTGCC
103434 TAAACTATA
1 TAAACTATA
103443 GTGTTTTTTA
Statistics
Matches: 38, Mismatches: 6, Indels: 9
0.72 0.11 0.17
Matches are distributed among these distances:
19 14 0.37
20 14 0.37
21 10 0.26
ACGTcount: A:0.53, C:0.12, G:0.09, T:0.26
Consensus pattern (20 bp):
TAAACTATAAAATAAGTGCC
Found at i:109384 original size:18 final size:16
Alignment explanation
Indices: 109353--109386 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 16
109343 ATAAAACATC
109353 ATATATTATTTTTAAT
1 ATATATTATTTTTAAT
109369 ATATATCTATTATTTAAT
1 ATATAT-TATT-TTTAAT
109387 TAATAAAAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.38
17 4 0.25
18 6 0.38
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (16 bp):
ATATATTATTTTTAAT
Found at i:114332 original size:30 final size:30
Alignment explanation
Indices: 114298--114399 Score: 118
Period size: 30 Copynumber: 3.4 Consensus size: 30
114288 ATAATTTATG
*
114298 TAAAATGGATTACCTGAAAACTGTTTTACT
1 TAAAATGAATTACCTGAAAACTGTTTTACT
* *
114328 TAAAATGAATTACGTGAAAATTGTTTTA-T
1 TAAAATGAATTACCTGAAAACTGTTTTACT
* * * *
114357 ATGAAATAAATTACCT-AAAACTGCTTTACG
1 -TAAAATGAATTACCTGAAAACTGTTTTACT
114387 TAAAATGAATTAC
1 TAAAATGAATTAC
114400 ATTTTACGGG
Statistics
Matches: 59, Mismatches: 11, Indels: 5
0.79 0.15 0.07
Matches are distributed among these distances:
29 22 0.37
30 37 0.63
ACGTcount: A:0.42, C:0.11, G:0.12, T:0.35
Consensus pattern (30 bp):
TAAAATGAATTACCTGAAAACTGTTTTACT
Found at i:114348 original size:59 final size:59
Alignment explanation
Indices: 114284--114399 Score: 144
Period size: 59 Copynumber: 2.0 Consensus size: 59
114274 TGATTTTCTG
* ** * *
114284 GAAAA-TAATTTATGTAAAATGGATTACCTGAAAACTGTTTTACTTAAAATGAATTACGT
1 GAAAATTAATTTATATAAAATAAATTACCT-AAAACTGCTTTACGTAAAATGAATTACGT
** *
114343 GAAAATTGTTTTATATGAAATAAATTACCTAAAACTGCTTTACGTAAAATGAATTAC
1 GAAAATTAATTTATATAAAATAAATTACCTAAAACTGCTTTACGTAAAATGAATTAC
114400 ATTTTACGGG
Statistics
Matches: 48, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
59 30 0.62
60 18 0.38
ACGTcount: A:0.43, C:0.09, G:0.12, T:0.35
Consensus pattern (59 bp):
GAAAATTAATTTATATAAAATAAATTACCTAAAACTGCTTTACGTAAAATGAATTACGT
Found at i:115121 original size:42 final size:42
Alignment explanation
Indices: 115069--115149 Score: 108
Period size: 42 Copynumber: 1.9 Consensus size: 42
115059 ATTACATTGG
* * *
115069 TAAAATCAATTAAAACTATCAAACACTGGAAAATGTTTTCCA
1 TAAAACCAATTAAAACTATCAAACACTGAAAAATATTTTCCA
** *
115111 TAAAACCAATTGCAGCTATCAAACACTGAAAAATATTTT
1 TAAAACCAATTAAAACTATCAAACACTGAAAAATATTTT
115150 TCGAAAAATA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
42 33 1.00
ACGTcount: A:0.47, C:0.17, G:0.07, T:0.28
Consensus pattern (42 bp):
TAAAACCAATTAAAACTATCAAACACTGAAAAATATTTTCCA
Found at i:125550 original size:15 final size:15
Alignment explanation
Indices: 125532--125561 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
125522 GCACCTTTAC
125532 CTGGTCTTTCAGCAA
1 CTGGTCTTTCAGCAA
125547 CTGGTCTTTCAGCAA
1 CTGGTCTTTCAGCAA
125562 TTGACCTTTT
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:0.27, G:0.20, T:0.33
Consensus pattern (15 bp):
CTGGTCTTTCAGCAA
Found at i:131418 original size:2 final size:2
Alignment explanation
Indices: 131413--131449 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
131403 ACATACACAT
131413 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
131450 TCAAAACCAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:136541 original size:31 final size:31
Alignment explanation
Indices: 136505--136580 Score: 107
Period size: 31 Copynumber: 2.5 Consensus size: 31
136495 TAAAAAAATG
* *
136505 AGATATTGTCACTTTCATTTTTATTTAATTA
1 AGATATAGTCACTTTCATTTTTATATAATTA
*
136536 AGATATAGTCACTTTCGTTTTTATATAATTA
1 AGATATAGTCACTTTCATTTTTATATAATTA
* *
136567 AGATGTGGTCACTT
1 AGATATAGTCACTT
136581 CGAGTTAACT
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 40 1.00
ACGTcount: A:0.29, C:0.11, G:0.12, T:0.49
Consensus pattern (31 bp):
AGATATAGTCACTTTCATTTTTATATAATTA
Done.