Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007535.1 Hibiscus syriacus cultivar Beakdansim tig00021081_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: 62581
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:591 original size:2 final size:2
Alignment explanation
Indices: 584--621 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
574 TATTGAAGAT
584 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
622 AATAAAAGAG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:4207 original size:15 final size:15
Alignment explanation
Indices: 4187--4232 Score: 83
Period size: 15 Copynumber: 3.1 Consensus size: 15
4177 TTCAACTATA
*
4187 CCATCAGTTTTCTTC
1 CCATCAATTTTCTTC
4202 CCATCAATTTTCTTC
1 CCATCAATTTTCTTC
4217 CCATCAATTTTCTTC
1 CCATCAATTTTCTTC
4232 C
1 C
4233 TCTGTCTAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
15 30 1.00
ACGTcount: A:0.17, C:0.35, G:0.02, T:0.46
Consensus pattern (15 bp):
CCATCAATTTTCTTC
Found at i:8455 original size:17 final size:17
Alignment explanation
Indices: 8433--8472 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
8423 ACGGTTGACT
**
8433 GTTGACCATTGACTTGC
1 GTTGACCATTGACCGGC
*
8450 GTTGACCGTTGACCGGC
1 GTTGACCATTGACCGGC
8467 GTTGAC
1 GTTGAC
8473 TATAGTTGAC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.15, C:0.25, G:0.30, T:0.30
Consensus pattern (17 bp):
GTTGACCATTGACCGGC
Found at i:12528 original size:8 final size:8
Alignment explanation
Indices: 12515--12540 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
12505 AAAAAGGATT
12515 AAATTGTA
1 AAATTGTA
12523 AAATTGTA
1 AAATTGTA
12531 AAATTGTA
1 AAATTGTA
12539 AA
1 AA
12541 GTTGGTAGAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.54, C:0.00, G:0.12, T:0.35
Consensus pattern (8 bp):
AAATTGTA
Found at i:13309 original size:17 final size:17
Alignment explanation
Indices: 13287--13328 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
13277 GACTATTAAC
**
13287 CGTTGACTGTTGACTTG
1 CGTTGACTGTTGACCGG
*
13304 CGTTGACCGTTGACCGG
1 CGTTGACTGTTGACCGG
13321 CGTTGACT
1 CGTTGACT
13329 ACAGATGATC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.12, C:0.24, G:0.31, T:0.33
Consensus pattern (17 bp):
CGTTGACTGTTGACCGG
Found at i:14998 original size:18 final size:19
Alignment explanation
Indices: 14977--15023 Score: 62
Period size: 18 Copynumber: 2.6 Consensus size: 19
14967 GTAAAAATAT
*
14977 ATTAAAAT-AATAAAAGTG
1 ATTAAAATAAATAAAAGTA
14995 ATT-AAATAAATAAAAGTA
1 ATTAAAATAAATAAAAGTA
*
15013 ATTAAAGTAAA
1 ATTAAAATAAA
15024 AATAAGAAGA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 4 0.16
18 15 0.60
19 6 0.24
ACGTcount: A:0.64, C:0.00, G:0.09, T:0.28
Consensus pattern (19 bp):
ATTAAAATAAATAAAAGTA
Found at i:15648 original size:24 final size:24
Alignment explanation
Indices: 15621--15685 Score: 96
Period size: 23 Copynumber: 2.7 Consensus size: 24
15611 TCGTGAAAAT
15621 AAAAGAAAAAGGGAAAAAAACTTG
1 AAAAGAAAAAGGGAAAAAAACTTG
*
15645 AAAAGAAAAA-GAAAAAAAACTTG
1 AAAAGAAAAAGGGAAAAAAACTTG
*
15668 AAAAGTAAAAAGAGAAAA
1 AAAAG-AAAAAGGGAAAA
15686 CTTTATTAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
23 17 0.47
24 15 0.42
25 4 0.11
ACGTcount: A:0.72, C:0.03, G:0.17, T:0.08
Consensus pattern (24 bp):
AAAAGAAAAAGGGAAAAAAACTTG
Found at i:15660 original size:23 final size:23
Alignment explanation
Indices: 15621--15685 Score: 94
Period size: 24 Copynumber: 2.7 Consensus size: 23
15611 TCGTGAAAAT
*
15621 AAAAGAAAAAGGGAAAAAAACTTG
1 AAAAGAAAAA-GAAAAAAAACTTG
15645 AAAAGAAAAAGAAAAAAAACTTG
1 AAAAGAAAAAGAAAAAAAACTTG
*
15668 AAAAGTAAAAAGAGAAAA
1 AAAAG-AAAAAGAAAAAA
15686 CTTTATTAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
23 17 0.45
24 21 0.55
ACGTcount: A:0.72, C:0.03, G:0.17, T:0.08
Consensus pattern (23 bp):
AAAAGAAAAAGAAAAAAAACTTG
Found at i:16741 original size:22 final size:22
Alignment explanation
Indices: 16690--16752 Score: 60
Period size: 22 Copynumber: 2.9 Consensus size: 22
16680 ATTTTTCTTC
* *
16690 CTTTTTTTCACACTTTTATTGT
1 CTTTTTTTCACATTTTTTTTGT
16712 -TTTGTTTTC-CATTTTTTTATGT
1 CTTT-TTTTCACATTTTTTT-TGT
*
16734 CTTTTTTTCTC-TTTTTTTT
1 CTTTTTTTCACATTTTTTTT
16753 CTAACATCAT
Statistics
Matches: 35, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
21 11 0.31
22 20 0.57
23 4 0.11
ACGTcount: A:0.08, C:0.14, G:0.05, T:0.73
Consensus pattern (22 bp):
CTTTTTTTCACATTTTTTTTGT
Found at i:22845 original size:31 final size:31
Alignment explanation
Indices: 22810--22877 Score: 75
Period size: 32 Copynumber: 2.2 Consensus size: 31
22800 TAGGCTCTAC
* * *
22810 GGCCCTGAGATCA-TTCTCGGGTAGGCCCTGT
1 GGCCCTAAGAT-AGTTCTCAGGTAGGCCCCGT
*
22841 GGCCCTAAGATATGTTCTTAGGTAGGCCCCGT
1 GGCCCTAAGATA-GTTCTCAGGTAGGCCCCGT
22873 GGCCC
1 GGCCC
22878 CGAACTTTCT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
30 1 0.03
31 10 0.32
32 20 0.65
ACGTcount: A:0.15, C:0.29, G:0.31, T:0.25
Consensus pattern (31 bp):
GGCCCTAAGATAGTTCTCAGGTAGGCCCCGT
Found at i:24995 original size:17 final size:17
Alignment explanation
Indices: 24975--25015 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
24965 GTGTAAAACG
* *
24975 GTTGATTGTTAACCTGC
1 GTTGACTGTTAACCGGC
*
24992 GTTGACTGTTCACCGGC
1 GTTGACTGTTAACCGGC
25009 GTTGACT
1 GTTGACT
25016 ACAATTGACC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.15, C:0.22, G:0.27, T:0.37
Consensus pattern (17 bp):
GTTGACTGTTAACCGGC
Found at i:26705 original size:19 final size:21
Alignment explanation
Indices: 26664--26706 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
26654 AATAATTCAG
*
26664 GAAAACGTCCGAATTACACTA
1 GAAAACGTCCGAAGTACACTA
26685 GAAAAC-TCCGAAGTA-ACTA
1 GAAAACGTCCGAAGTACACTA
26704 GAA
1 GAA
26707 TTGACTTGAC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 7 0.33
20 8 0.38
21 6 0.29
ACGTcount: A:0.47, C:0.21, G:0.16, T:0.16
Consensus pattern (21 bp):
GAAAACGTCCGAAGTACACTA
Found at i:29486 original size:22 final size:22
Alignment explanation
Indices: 29427--29493 Score: 80
Period size: 22 Copynumber: 3.0 Consensus size: 22
29417 AAATAAATCA
* *
29427 AGACAATATAATTAAACACATT
1 AGACAATATAATTAAAAAAATT
* *
29449 ATTGAAAAAATAATTAAAAAAATT
1 A--GACAATATAATTAAAAAAATT
29473 AGACAATATAATTAAAAAAAT
1 AGACAATATAATTAAAAAAAT
29494 AAATTACTAT
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
22 19 0.51
24 18 0.49
ACGTcount: A:0.63, C:0.06, G:0.04, T:0.27
Consensus pattern (22 bp):
AGACAATATAATTAAAAAAATT
Found at i:30925 original size:301 final size:300
Alignment explanation
Indices: 30388--31356 Score: 1417
Period size: 301 Copynumber: 3.2 Consensus size: 300
30378 TAAACCGCTG
* * * * *
30388 GGAATGATACCATAAATCTGGTTCCCATACAAC-CTTAATTCTTTCAATTTAGAAAGGTTATCAA
1 GGAATGCTACCAGAAATCTGGTTCCCAT-CCACGCTTAATACTTGCAATTTAGAAAGGTTATCAA
* * * * * * * *
30452 ATGTTCTCGACTTTAAATTGCCTACAGTGGGATTGTTAATTATAAAATAACTTTTATCTAATGAA
65 ATATTTTCGACTCTAGATGGCCTGCAGTGAGATTGTTAATTATAAAACAACTTTTATCTAATGAA
* * * *
30517 AATAAAAGAGAACGGAATGCAAATGAGG-AATTATTTACCTTTGAAATTGTTGAAACCAAGATAC
130 AATAAAAGAGAACGAAATGCAAATGTGGAAATT-TTTACCTTTGAAGTTGTTGTAACCAAGATAC
* ** *
30581 AAATATTGGAGCATTTTCAAATTTCCGATTTCTATAGGTATACTTCCTTCCATAGAGTTGTTCCA
194 AAAGATTGGAGCATAGTCAAATTTCCGATTTCTATAGGTATACTTTCTTCCATAGAGTTGTTCCA
* *
30646 CAATGA-AATATACCTCAACTCTTTGCACTTGTATAAACTACC
259 CAGTGATAA-ATACCTTAACTCTTTGCACTTGTATAAACTACC
* * * * *
30688 AGGAATGCTACCAGAAATCTGATTACCATCCAAC-CTTAA-ACCTTGCAAATTAGAAAGGCTGTC
1 -GGAATGCTACCAGAAATCTGGTTCCCATCC-ACGCTTAATA-CTTGCAATTTAGAAAGGTTATC
* *
30751 AAATATTTTGGACTCTAGATGGCCTGCAGCGAGATTGTTAATTATAAAACAACTTTTATCTAATG
63 AAATATTTTCGACTCTAGATGGCCTGCAGTGAGATTGTTAATTATAAAACAACTTTTATCTAATG
30816 AAAATAAAAGAGAACGAAATGCAAATGTGGAAATTTTTACCTTTGAAGTTGTTGTAACCAAGATA
128 AAAATAAAAGAGAACGAAATGCAAATGTGGAAATTTTTACCTTTGAAGTTGTTGTAACCAAGATA
* *
30881 CAAAGATTGGAGCATAGTCAAATTTTCGATTTCTATAAGTATACTTTCTTCCATAGAGTTGTTCC
193 CAAAGATTGGAGCATAGTCAAATTTCCGATTTCTATAGGTATACTTTCTTCCATAGAGTTGTTCC
30946 ACAGTGATAAATACCTTAACTCTTTGCACTTGTATAAACTACC
258 ACAGTGATAAATACCTTAACTCTTTGCACTTGTATAAACTACC
* * * *
30989 GGAAATGCTACCAGTATTCTGGTTCCCCTCCGCGCTTAATACTTGCAATTTAGAAAGGTTATCAA
1 GG-AATGCTACCAGAAATCTGGTTCCCATCCACGCTTAATACTTGCAATTTAGAAAGGTTATCAA
* *
31054 ATATTTTCAACTCTAGATGGCCTGCAGTGAGATTGTTAATTATAAAACAACTTTTATATAATGAA
65 ATATTTTCGACTCTAGATGGCCTGCAGTGAGATTGTTAATTATAAAACAACTTTTATCTAATGAA
* *
31119 AATAAAAGATAACGAAATGCAAATGTGGAAATTTTTACATTTGAAGTTGTTGTAACCAAGATACA
130 AATAAAAGAGAACGAAATGCAAATGTGGAAATTTTTACCTTTGAAGTTGTTGTAACCAAGATACA
*
31184 AAGATTGGAGCATAGTCAAATTTCCGATTTGTATAGGTATACTTTCTTCCATAGAGTTGTTCCAC
195 AAGATTGGAGCATAGTCAAATTTCCGATTTCTATAGGTATACTTTCTTCCATAGAGTTGTTCCAC
* *
31249 AGTGATAAATACCTTAACTCTTTCCACTTGTATAAACTATCG
260 AGTGATAAATACCTTAACTCTTTGCACTTGTATAAACTA-CC
* * *
31291 GGAATGCTACCAGTATTCTGGTTCCCCTCCACGCTTAATACTTGCAATTTAGAAAGGTTATCAAA
1 GGAATGCTACCAGAAATCTGGTTCCCATCCACGCTTAATACTTGCAATTTAGAAAGGTTATCAAA
31356 T
66 T
31357 TATTCAAACC
Statistics
Matches: 607, Mismatches: 53, Indels: 16
0.90 0.08 0.02
Matches are distributed among these distances:
300 4 0.01
301 593 0.98
302 10 0.02
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.33
Consensus pattern (300 bp):
GGAATGCTACCAGAAATCTGGTTCCCATCCACGCTTAATACTTGCAATTTAGAAAGGTTATCAAA
TATTTTCGACTCTAGATGGCCTGCAGTGAGATTGTTAATTATAAAACAACTTTTATCTAATGAAA
ATAAAAGAGAACGAAATGCAAATGTGGAAATTTTTACCTTTGAAGTTGTTGTAACCAAGATACAA
AGATTGGAGCATAGTCAAATTTCCGATTTCTATAGGTATACTTTCTTCCATAGAGTTGTTCCACA
GTGATAAATACCTTAACTCTTTGCACTTGTATAAACTACC
Found at i:31499 original size:18 final size:19
Alignment explanation
Indices: 31476--31512 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
31466 TAGTTTATAA
31476 TTTTAATC-AAAATTTTAT
1 TTTTAATCTAAAATTTTAT
*
31494 TTTTAATCTATAATTTTAT
1 TTTTAATCTAAAATTTTAT
31513 GATTCTAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.35, C:0.05, G:0.00, T:0.59
Consensus pattern (19 bp):
TTTTAATCTAAAATTTTAT
Found at i:32061 original size:3 final size:3
Alignment explanation
Indices: 32049--32108 Score: 72
Period size: 3 Copynumber: 20.7 Consensus size: 3
32039 AAATCTACCC
32049 TTA TTA -TA TTA TTA TTA TTA TTA TTA TTA TTA -TA TT- TATA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA
* *
32092 TAA ATA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TT
32109 TAAAACCATC
Statistics
Matches: 49, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
2 5 0.10
3 43 0.88
4 1 0.02
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:33304 original size:110 final size:110
Alignment explanation
Indices: 33098--33297 Score: 282
Period size: 110 Copynumber: 1.8 Consensus size: 110
33088 GCCCTAAACG
* **
33098 TTTAGCGTGTTTTTGCAATTTGGTCACATGTAGGGACCAAAACTGCTATTTTTCCTTTTCTGTGC
1 TTTAGCGTGTATTTGCAATTTGGTCACATGTAGGGACCAAAACTGCTATTTCCCCTTTTCTGTGC
*
33163 GTGTCTTTTATTTTTTTGGGTTATTCATGTTTTAGTCTATATTAT
66 ATGTCTTTTATTTTTTTGGGTTATTCATGTTTTAGTCTATATTAT
* * *
33208 TTTAGCGTGTATTTGCATTTTGGTCACATGTAGGG-CTTAAAATTG-TAATTTCCCCTTTTCT-T
1 TTTAGCGTGTATTTGCAATTTGGTCACATGTAGGGAC-CAAAACTGCT-ATTTCCCCTTTTCTGT
33270 GCATGT-TTTTATTTATTTTGGGTTATTC
64 GCATGTCTTTTATTT-TTTTGGGTTATTC
33298 TCTGTTTGGT
Statistics
Matches: 80, Mismatches: 7, Indels: 7
0.85 0.07 0.07
Matches are distributed among these distances:
108 8 0.10
109 21 0.26
110 51 0.64
ACGTcount: A:0.17, C:0.14, G:0.18, T:0.51
Consensus pattern (110 bp):
TTTAGCGTGTATTTGCAATTTGGTCACATGTAGGGACCAAAACTGCTATTTCCCCTTTTCTGTGC
ATGTCTTTTATTTTTTTGGGTTATTCATGTTTTAGTCTATATTAT
Found at i:41817 original size:54 final size:53
Alignment explanation
Indices: 41758--42058 Score: 168
Period size: 56 Copynumber: 5.5 Consensus size: 53
41748 GCGGTTTTTT
41758 AGAAACTATAACTAATTTTAAGGGGTTTCTTGATAATTTT-AAATGAGTTTTTAA
1 AGAAACTA-AACTAATTTT-AGGGGTTTCTTGATAATTTTCAAATGAGTTTTTAA
* ** ** * **
41812 AGAAACTAAGTCTGCTTTTTAGAAGCTTCTTGACGATTTTCAAATGAGTTTTTAA
1 AGAAACTAA-ACT-AATTTTAGGGGTTTCTTGATAATTTTCAAATGAGTTTTTAA
* * * * *
41867 AGAAGCTAAA-T--TTTTAGGTGTTTCTTGATGATTTTTTCCAATGA-ATTTTAA
1 AGAAACTAAACTAATTTTAGGGGTTTCTTGAT-A-ATTTTCAAATGAGTTTTTAA
* * * * *
41918 AGAAGCTAAACCTAATTTTCAGGGGTTTCTTGGTGATTATTTCCAATGA-ATTTTAA
1 AGAAACTAAA-CTAATTTT-AGGGGTTTCTTGAT-AAT-TTTCAAATGAGTTTTTAA
* * * * * *
41974 AGAAGCTAAGCCTGATTTTCAAGGGTTTCTTGATGATTATTTCCAAAT-AATTTTTAA
1 AGAAACTAA-ACTAATTTT-AGGGGTTTCTTGAT-A--ATTTTCAAATGAGTTTTTAA
* *
42031 AGAAGCTAAGCCTAATTTTA-GGGTTTCT
1 AGAAACTAA-ACTAATTTTAGGGGTTTCT
42059 CGATGATAAC
Statistics
Matches: 203, Mismatches: 29, Indels: 29
0.78 0.11 0.11
Matches are distributed among these distances:
50 14 0.07
51 16 0.08
52 10 0.05
53 3 0.01
54 25 0.12
55 40 0.20
56 64 0.32
57 30 0.15
58 1 0.00
ACGTcount: A:0.32, C:0.11, G:0.17, T:0.41
Consensus pattern (53 bp):
AGAAACTAAACTAATTTTAGGGGTTTCTTGATAATTTTCAAATGAGTTTTTAA
Found at i:41955 original size:56 final size:55
Alignment explanation
Indices: 41861--42065 Score: 260
Period size: 56 Copynumber: 3.8 Consensus size: 55
41851 TCAAATGAGT
* *
41861 TTTTAAAGAAGCTAAA--T--TTTTAGGTGTTTCTTGATGATTTTTTCCAATGAA
1 TTTTAAAGAAGCTAAACCTAATTTTAGGGGTTTCTTGATGATTATTTCCAATGAA
*
41912 TTTTAAAGAAGCTAAACCTAATTTTCAGGGGTTTCTTGGTGATTATTTCCAATGAA
1 TTTTAAAGAAGCTAAACCTAATTTT-AGGGGTTTCTTGATGATTATTTCCAATGAA
* * *
41968 TTTTAAAGAAGCTAAGCCTGATTTTCAAGGGTTTCTTGATGATTATTTCCAAAT-AA
1 TTTTAAAGAAGCTAAACCTAATTTT-AGGGGTTTCTTGATGATTATTTCC-AATGAA
* *
42024 TTTTTAAAGAAGCTAAGCCTAATTTTA-GGGTTTCTCGATGAT
1 -TTTTAAAGAAGCTAAACCTAATTTTAGGGGTTTCTTGATGAT
42066 AACTGTAAAA
Statistics
Matches: 138, Mismatches: 9, Indels: 10
0.88 0.06 0.06
Matches are distributed among these distances:
51 16 0.12
53 1 0.01
55 18 0.13
56 76 0.55
57 27 0.20
ACGTcount: A:0.30, C:0.11, G:0.17, T:0.41
Consensus pattern (55 bp):
TTTTAAAGAAGCTAAACCTAATTTTAGGGGTTTCTTGATGATTATTTCCAATGAA
Found at i:42079 original size:57 final size:56
Alignment explanation
Indices: 41910--42116 Score: 177
Period size: 56 Copynumber: 3.7 Consensus size: 56
41900 TTTTCCAATG
* * * * * * *** *
41910 AATTTTAAAGAAGCTAAACCTAATTTTCAGGGGTTTCTTGGTGATTATT-TCCAATG
1 AATTTTAAAGAAGCTAAGCCTGATTTT-AAGGGTTTCTCGATGATAATTAAAAAATA
* * ***
41966 AATTTTAAAGAAGCTAAGCCTGATTTTCAAGGGTTTCTTGATGATTATTTCCAAATA
1 AATTTTAAAGAAGCTAAGCCTGATTTT-AAGGGTTTCTCGATGATAATTAAAAAATA
* *
42023 ATTTTTAAAGAAGCTAAGCCTAATTTT-AGGGTTTCTCGATGATAACTGTAAAAAATA
1 AATTTTAAAGAAGCTAAGCCTGATTTTAAGGGTTTCTCGATGATAA-T-TAAAAAATA
* *
42080 AATTTT-AAGAAACTAAGCTTGATTTTCAAGGGTTTCT
1 AATTTTAAAGAAGCTAAGCCTGATTTT-AAGGGTTTCT
42117 TGATTTGTAA
Statistics
Matches: 128, Mismatches: 18, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
55 16 0.12
56 63 0.49
57 40 0.31
58 9 0.07
ACGTcount: A:0.34, C:0.12, G:0.16, T:0.38
Consensus pattern (56 bp):
AATTTTAAAGAAGCTAAGCCTGATTTTAAGGGTTTCTCGATGATAATTAAAAAATA
Found at i:42096 original size:113 final size:112
Alignment explanation
Indices: 41886--42120 Score: 298
Period size: 113 Copynumber: 2.1 Consensus size: 112
41876 ATTTTTAGGT
* * *
41886 GTTTCTTGATGATTTTTTCCAATGAATTTTAAAGAAGCTAAACCTAATTTTCAGGGGTTTCTTGG
1 GTTTCTTGATGATTATTTCCAATGAATTTTAAAGAAGCTAAACCTAATTTTCAGGGGTTTCTCGA
* *** * *
41951 TGATTATTTCCAATGAATTTTAAAGAAGCTAAGCCTGATTTTCAAGG
66 TGATAATTAAAAATAAATTTTAAAGAAACTAAGCCTGATTTTCAAGG
*
41998 GTTTCTTGATGATTATTTCCAAAT-AATTTTTAAAGAAGCTAAGCCTAATTTT-A-GGGTTTCTC
1 GTTTCTTGATGATTATTTCC-AATGAA-TTTTAAAGAAGCTAAACCTAATTTTCAGGGGTTTCTC
*
42060 GATGATAACTGTAAAAAATAAATTTT-AAGAAACTAAGCTTGATTTTCAAGG
64 GATGATAA-T-T-AAAAATAAATTTTAAAGAAACTAAGCCTGATTTTCAAGG
42111 GTTTCTTGAT
1 GTTTCTTGAT
42121 TTGTAAGTCC
Statistics
Matches: 107, Mismatches: 11, Indels: 9
0.84 0.09 0.07
Matches are distributed among these distances:
111 14 0.13
112 23 0.21
113 61 0.57
114 9 0.08
ACGTcount: A:0.32, C:0.11, G:0.17, T:0.40
Consensus pattern (112 bp):
GTTTCTTGATGATTATTTCCAATGAATTTTAAAGAAGCTAAACCTAATTTTCAGGGGTTTCTCGA
TGATAATTAAAAATAAATTTTAAAGAAACTAAGCCTGATTTTCAAGG
Found at i:42539 original size:240 final size:240
Alignment explanation
Indices: 42123--43328 Score: 1715
Period size: 240 Copynumber: 5.0 Consensus size: 240
42113 TTCTTGATTT
* * *
42123 GTAAGTCCTTTGGGCCATCAATAAGTCTTTCGAGCATGATGTTTAAATCCTTCGGGTCATCTATA
1 GTAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGTTTAAATCCTTTGGGTCATCTATA
* * * * *
42188 AGTTTTTCGAGCAAGATGATAAGTTCTTCAGGA-TATCCATAAGACCTTCGGGTAGAATGTTTTC
66 AGTCTTTCGAGCAAGATGATAAGTCCTTC-GGACCATCCATAAGACCTTCGGGTAGGATGTCTTC
*
42252 ACATGATTTTTGAAAAATGAGAAAGCGATTACCAAAGTTTCTCATTCAAATCTTTTATGAAAACT
130 ACATGATTTTTGAAAAATGAGAAAGCGATTTCCAAAGTTTCTCATTCAAATCTTTTATGAAAACT
* *
42317 GACATTTCTGAAAAGTAAGAAAATGATTACCAAAGTTTCTTACTTA
195 GACATTTCTGAAAAGTAAGAAAACGATTTCCAAAGTTTCTTACTTA
* * * *
42363 GTAAGTCCTTCGGGTCATCAGTAAGTCTTTTGATCATGATGTTTAAAT-CTTTCAGGTCATCTAT
1 GTAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGTTTAAATCCTTT-GGGTCATCTAT
* *
42427 AAGTCTTTCGAGCAAGATGATAAGTCCTTCGGACCATCCATAAGACCTTCGTGTAGGATTTCTTC
65 AAGTCTTTCGAGCAAGATGATAAGTCCTTCGGACCATCCATAAGACCTTCGGGTAGGATGTCTTC
* * * *
42492 ACATGATTTTCGAAAAATGAGAAAGTGATTTCCAAAGTTTTTCATTCAAATCTTTTATGAAAATT
130 ACATGATTTTTGAAAAATGAGAAAGCGATTTCCAAAGTTTCTCATTCAAATCTTTTATGAAAACT
* * *
42557 GACATTTCTGGAAAGTAAGAAAACGATTTCCAAAGTTTTTTATTTA
195 GACATTTCTGAAAAGTAAGAAAACGATTTCCAAAGTTTCTTACTTA
* * *
42603 GTAAGTCCTAT-GGGCCATCAGTAAGTATTTTGAGCATGATGTTTAAATCCTTTGGGTCATCTCT
1 GTAAGTCCT-TCGGGCCATCAGTAAGTCTTTCGAGCATGATGTTTAAATCCTTTGGGTCATCTAT
*
42667 AAGTCTTTCGAGCAAGATGATAAGTCCTTCGGGCCATCCATAAGACCTTCGGGTAGGATGTCTTC
65 AAGTCTTTCGAGCAAGATGATAAGTCCTTCGGACCATCCATAAGACCTTCGGGTAGGATGTCTTC
* * * *
42732 ACATGATTTTTGAAAAATGAGAAAGGGATTTCCAAAGTTTCTCATTCAAATATTTTCTGAAAATT
130 ACATGATTTTTGAAAAATGAGAAAGCGATTTCCAAAGTTTCTCATTCAAATCTTTTATGAAAACT
* *
42797 G-CATTTCTGAAAAGTAAGAGAACGATTTCAAAAGTTTCTTACTTA
195 GACATTTCTGAAAAGTAAGAAAACGATTTCCAAAGTTTCTTACTTA
* * *
42842 GTAAGTCCTTCGGGCCATCAGCAAGTCTTTCAAGCATGAT-TTTAAATCCTTTGGGTCATTTATA
1 GTAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGTTTAAATCCTTTGGGTCATCTATA
* * * * * * **
42906 AGTCTTTTGAACAAGATTATAAGTCCTTCGGGCCATCCATAAAACCTTCGGGCAGGATGTAATCA
66 AGTCTTTCGAGCAAGATGATAAGTCCTTCGGACCATCCATAAGACCTTCGGGTAGGATGTCTTCA
* * *
42971 CATGATTTTTGAAAAATGAGAAAGCGATTTCCAATGTTTCTCATTCAAATATTTTTTGAAAACTG
131 CATGATTTTTGAAAAATGAGAAAGCGATTTCCAAAGTTTCTCATTCAAATCTTTTATGAAAACTG
* *
43036 ACATTTTTGAAAAGTAAGAAAACGATTTCCAAAGTTTCTTATTTA
196 ACATTTCTGAAAAGTAAGAAAACGATTTCCAAAGTTTCTTACTTA
* * * *
43081 GTATGTCCTTTGGGCCATCAGTAAGTCTCTCGAGCATGATGTTTAAATCCTTTGGG-CTATTTAT
1 GTAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGTTTAAATCCTTTGGGTC-ATCTAT
* * * *
43145 AAGTCTTTCGAACAAGATGATAAATCCTTC-GAGCCATCCATAAGACCTTCGGGCAGAATGTCTT
65 AAGTCTTTCGAGCAAGATGATAAGTCCTTCGGA-CCATCCATAAGACCTTCGGGTAGGATGTCTT
* ** * * * * *
43209 CAGACAATTTTCGAAAAATGATAAAGCGATTTCCAAAGTTTCTCATTTAAATCTTTTCTTAAAAC
129 CACATGATTTTTGAAAAATGAGAAAGCGATTTCCAAAGTTTCTCATTCAAATCTTTTATGAAAAC
*
43274 TGACATTTCTGAAAAGTAAGAAAATGATTTCCAAAGTTTCTTACTTA
194 TGACATTTCTGAAAAGTAAGAAAACGATTTCCAAAGTTTCTTACTTA
43321 GTAAGTCC
1 GTAAGTCC
43329 AAAGAGCGAG
Statistics
Matches: 867, Mismatches: 90, Indels: 18
0.89 0.09 0.02
Matches are distributed among these distances:
238 142 0.16
239 156 0.18
240 564 0.65
241 5 0.01
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.35
Consensus pattern (240 bp):
GTAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGTTTAAATCCTTTGGGTCATCTATA
AGTCTTTCGAGCAAGATGATAAGTCCTTCGGACCATCCATAAGACCTTCGGGTAGGATGTCTTCA
CATGATTTTTGAAAAATGAGAAAGCGATTTCCAAAGTTTCTCATTCAAATCTTTTATGAAAACTG
ACATTTCTGAAAAGTAAGAAAACGATTTCCAAAGTTTCTTACTTA
Found at i:43082 original size:478 final size:480
Alignment explanation
Indices: 42111--43328 Score: 1807
Period size: 478 Copynumber: 2.5 Consensus size: 480
42101 ATTTTCAAGG
*
42111 GTTTCTTGATTT-GTAAGTCCTTTGGGCCATCAATAAGTCTTTCGAGCATGATGTTTAAATCCTT
1 GTTTCTT-ATTTAGTAAGTCCTTTGGGCCATCAGTAAGTCTTTCGAGCATGATGTTTAAATCCTT
* * * * **
42175 CGGGTCATCTATAAGTTTTTCGAGCAAGATGATAAGTTCTTCAGGATATCCATAAGACCTTCGGG
65 TGGGTCATCTATAAGTCTTTCGAGCAAGATGATAAGTCCTTCGGGCCATCCATAAGACCTTCGGG
* *
42240 TAGAATGTTTTCACATGATTTTTGAAAAATGAGAAAGCGATTACCAAAGTTTCTCATTCAAATCT
130 TAGAATGTCTTCACATGATTTTTGAAAAATGAGAAAGCGATTTCCAAAGTTTCTCATTCAAATCT
* *
42305 TTTATGAAAACTGACATTTCTGAAAAGTAAGAAAATGATTACCAAAGTTTCTTACTTAGTAAGTC
195 TTTCTGAAAACTGACATTTCTGAAAAGTAAGAAAATGATTTCCAAAGTTTCTTACTTAGTAAGTC
* * ** *
42370 CTTCGGGTCATCAGTAAGTCTTTTGATCATGATGTTTAAATCTTTCAGGTCATCTATAAGTCTTT
260 CTTCGGGCCATCAGCAAGTCTTTCAAGCATGATGTTTAAATCTTTCAGGTCATCTATAAGTCTTT
* * * * * **
42435 CGAGCAAGATGATAAGTCCTTCGGACCATCCATAAGACCTTCGTGTAGGATTTCTTCACATGATT
325 CGAACAAGATGATAAGTCCTTCGGACCATCCATAAAACCTTCGGGCAGGATGTAATCACATGATT
* * * *
42500 TTCGAAAAATGAGAAAGTGATTTCCAAAGTTTTTCATTCAAATCTTTTATGAAAATTGACATTTC
390 TTCGAAAAATGAGAAAGCGATTTCCAAAGTTTCTCATTCAAATATTTTATGAAAACTGACATTTC
*
42565 TGGAAAGTAAGAAAACGATTTCCAAA
455 TGAAAAGTAAGAAAACGATTTCCAAA
* * * *
42591 GTTTTTTATTTAGTAAGTCCTATGGGCCATCAGTAAGTATTTTGAGCATGATGTTTAAATCCTTT
1 GTTTCTTATTTAGTAAGTCCTTTGGGCCATCAGTAAGTCTTTCGAGCATGATGTTTAAATCCTTT
*
42656 GGGTCATCTCTAAGTCTTTCGAGCAAGATGATAAGTCCTTCGGGCCATCCATAAGACCTTCGGGT
66 GGGTCATCTATAAGTCTTTCGAGCAAGATGATAAGTCCTTCGGGCCATCCATAAGACCTTCGGGT
* * *
42721 AGGATGTCTTCACATGATTTTTGAAAAATGAGAAAGGGATTTCCAAAGTTTCTCATTCAAATATT
131 AGAATGTCTTCACATGATTTTTGAAAAATGAGAAAGCGATTTCCAAAGTTTCTCATTCAAATCTT
* * * *
42786 TTCTGAAAATTG-CATTTCTGAAAAGTAAGAGAACGATTTCAAAAGTTTCTTACTTAGTAAGTCC
196 TTCTGAAAACTGACATTTCTGAAAAGTAAGAAAATGATTTCCAAAGTTTCTTACTTAGTAAGTCC
* *
42850 TTCGGGCCATCAGCAAGTCTTTCAAGCATGAT-TTTAAATCCTTT-GGGTCATTTATAAGTCTTT
261 TTCGGGCCATCAGCAAGTCTTTCAAGCATGATGTTTAAAT-CTTTCAGGTCATCTATAAGTCTTT
* * *
42913 TGAACAAGATTATAAGTCCTTCGGGCCATCCATAAAACCTTCGGGCAGGATGTAATCACATGATT
325 CGAACAAGATGATAAGTCCTTCGGACCATCCATAAAACCTTCGGGCAGGATGTAATCACATGATT
* * * *
42978 TTTGAAAAATGAGAAAGCGATTTCCAATGTTTCTCATTCAAATATTTTTTGAAAACTGACATTTT
390 TTCGAAAAATGAGAAAGCGATTTCCAAAGTTTCTCATTCAAATATTTTATGAAAACTGACATTTC
43043 TGAAAAGTAAGAAAACGATTTCCAAA
455 TGAAAAGTAAGAAAACGATTTCCAAA
* *
43069 GTTTCTTATTTAGTATGTCCTTTGGGCCATCAGTAAGTCTCTCGAGCATGATGTTTAAATCCTTT
1 GTTTCTTATTTAGTAAGTCCTTTGGGCCATCAGTAAGTCTTTCGAGCATGATGTTTAAATCCTTT
* * * *
43134 GGG-CTATTTATAAGTCTTTCGAACAAGATGATAAATCCTTCGAGCCATCCATAAGACCTTCGGG
66 GGGTC-ATCTATAAGTCTTTCGAGCAAGATGATAAGTCCTTCGGGCCATCCATAAGACCTTCGGG
* * ** * * *
43198 CAGAATGTCTTCAGACAATTTTCGAAAAATGATAAAGCGATTTCCAAAGTTTCTCATTTAAATCT
130 TAGAATGTCTTCACATGATTTTTGAAAAATGAGAAAGCGATTTCCAAAGTTTCTCATTCAAATCT
*
43263 TTTCTTAAAACTGACATTTCTGAAAAGTAAGAAAATGATTTCCAAAGTTTCTTACTTAGTAAGTC
195 TTTCTGAAAACTGACATTTCTGAAAAGTAAGAAAATGATTTCCAAAGTTTCTTACTTAGTAAGTC
43328 C
260 C
43329 AAAGAGCGAG
Statistics
Matches: 659, Mismatches: 75, Indels: 9
0.89 0.10 0.01
Matches are distributed among these distances:
477 1 0.00
478 343 0.52
479 132 0.20
480 183 0.28
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.35
Consensus pattern (480 bp):
GTTTCTTATTTAGTAAGTCCTTTGGGCCATCAGTAAGTCTTTCGAGCATGATGTTTAAATCCTTT
GGGTCATCTATAAGTCTTTCGAGCAAGATGATAAGTCCTTCGGGCCATCCATAAGACCTTCGGGT
AGAATGTCTTCACATGATTTTTGAAAAATGAGAAAGCGATTTCCAAAGTTTCTCATTCAAATCTT
TTCTGAAAACTGACATTTCTGAAAAGTAAGAAAATGATTTCCAAAGTTTCTTACTTAGTAAGTCC
TTCGGGCCATCAGCAAGTCTTTCAAGCATGATGTTTAAATCTTTCAGGTCATCTATAAGTCTTTC
GAACAAGATGATAAGTCCTTCGGACCATCCATAAAACCTTCGGGCAGGATGTAATCACATGATTT
TCGAAAAATGAGAAAGCGATTTCCAAAGTTTCTCATTCAAATATTTTATGAAAACTGACATTTCT
GAAAAGTAAGAAAACGATTTCCAAA
Found at i:44241 original size:14 final size:15
Alignment explanation
Indices: 44208--44247 Score: 55
Period size: 14 Copynumber: 2.7 Consensus size: 15
44198 AACTCACCAA
*
44208 AGTCAACTCGGACTG
1 AGTCAACTCGTACTG
*
44223 AGTCAACTCGTTC-G
1 AGTCAACTCGTACTG
44237 AGTCAACTCGT
1 AGTCAACTCGT
44248 CGAAGTCGAC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 12 0.52
15 11 0.48
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.25
Consensus pattern (15 bp):
AGTCAACTCGTACTG
Found at i:44494 original size:21 final size:21
Alignment explanation
Indices: 44468--44509 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
44458 TTAAACATTA
*
44468 TTAAAATTTTAAAAAAATATT
1 TTAAAATTATAAAAAAATATT
*
44489 TTAAAATTATAAATAAATATT
1 TTAAAATTATAAAAAAATATT
44510 ATTTATTGTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (21 bp):
TTAAAATTATAAAAAAATATT
Found at i:54833 original size:20 final size:18
Alignment explanation
Indices: 54810--54928 Score: 64
Period size: 17 Copynumber: 6.4 Consensus size: 18
54800 GAAGAGATAT
*
54810 AGAAAAAAATAGACACAAAA
1 AGAAAAAAATA-A-AAAAAA
* *
54830 AGAAAGAAA-AAAGAAAA
1 AGAAAAAAATAAAAAAAA
54847 AGAAAAAAATATAGAAAAAA
1 AGAAAAAAATA-A-AAAAAA
* **
54867 AG-AAAAAAGAGGAAAAA
1 AGAAAAAAATAAAAAAAA
* *
54884 GGAAAAAAACACAAAAAAA
1 AGAAAAAAATA-AAAAAAA
* * *
54903 GAGAAAAGAA-AGAAAAGA
1 -AGAAAAAAATAAAAAAAA
54921 AGAAAAAA
1 AGAAAAAA
54929 TTTGATCAAA
Statistics
Matches: 77, Mismatches: 16, Indels: 15
0.71 0.15 0.14
Matches are distributed among these distances:
17 26 0.34
18 14 0.18
19 15 0.19
20 22 0.29
ACGTcount: A:0.78, C:0.03, G:0.16, T:0.03
Consensus pattern (18 bp):
AGAAAAAAATAAAAAAAA
Found at i:54848 original size:17 final size:17
Alignment explanation
Indices: 54826--54927 Score: 67
Period size: 17 Copynumber: 6.3 Consensus size: 17
54816 AAATAGACAC
54826 AAAAAGAAAGAAAAAAG
1 AAAAAGAAAGAAAAAAG
54843 AAAAAGAAA-AAAATATAG
1 AAAAAGAAAGAAAA-A-AG
54861 -AAAA-AAAGAAAAAAG
1 AAAAAGAAAGAAAAAAG
** *
54876 AGGAA-AAAG-GAAAA-
1 AAAAAGAAAGAAAAAAG
* * *
54890 AAACACAAA-AAAAGAG
1 AAAAAGAAAGAAAAAAG
54906 -AAAAGAAAGAAAAGAAG
1 AAAAAGAAAGAAAA-AAG
54923 AAAAA
1 AAAAA
54928 ATTTGATCAA
Statistics
Matches: 64, Mismatches: 11, Indels: 19
0.68 0.12 0.20
Matches are distributed among these distances:
14 2 0.03
15 18 0.28
16 18 0.28
17 20 0.31
18 6 0.09
ACGTcount: A:0.79, C:0.02, G:0.17, T:0.02
Consensus pattern (17 bp):
AAAAAGAAAGAAAAAAG
Found at i:54851 original size:37 final size:36
Alignment explanation
Indices: 54810--54928 Score: 123
Period size: 37 Copynumber: 3.2 Consensus size: 36
54800 GAAGAGATAT
* *
54810 AGAAAAAAATAGACACAAAAAGAAAGAAAAAAGAAAA
1 AGAAAAAAATACACAAAAAAAGAAA-AAAAAAGAAAA
* * * *
54847 AGAAAAAAATATAGAAAAAAAGAAAAAAGAGGAAAA
1 AGAAAAAAATACACAAAAAAAGAAAAAAAAAGAAAA
* *
54883 AGGAAAAAA-ACACAAAAAAAGAGAAAAGAAAGAAAAGA
1 AGAAAAAAATACACAAAAAAAGA-AAAAAAAAG-AAA-A
54921 AGAAAAAA
1 AGAAAAAA
54929 TTTGATCAAA
Statistics
Matches: 67, Mismatches: 12, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
35 11 0.16
36 23 0.34
37 25 0.37
38 8 0.12
ACGTcount: A:0.78, C:0.03, G:0.16, T:0.03
Consensus pattern (36 bp):
AGAAAAAAATACACAAAAAAAGAAAAAAAAAGAAAA
Found at i:55016 original size:10 final size:11
Alignment explanation
Indices: 54990--55014 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
54980 ATGAAACACC
54990 AAAAGAAAATA
1 AAAAGAAAATA
55001 AAAAGAAAATA
1 AAAAGAAAATA
55012 AAA
1 AAA
55015 GACACACAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.84, C:0.00, G:0.08, T:0.08
Consensus pattern (11 bp):
AAAAGAAAATA
Found at i:56968 original size:52 final size:52
Alignment explanation
Indices: 56811--56978 Score: 178
Period size: 52 Copynumber: 3.1 Consensus size: 52
56801 CCAAACAATA
* * * *
56811 TGATGTTTTCAAATGAGTTTTTACAAACTAA-TCTTGATTTTCAGGGGTTTCTT
1 TGATGTTTTCAAATTAATTTTTAGAAACTAAGCCTT-ATTTTCAGGGGTTTC-T
* * *
56864 GATGATGATTTTC-AATTAATTTCTTAAAAGAAGCTAAGCCTAATTTTTAGGGGTTTCT
1 --TGATG-TTTTCAAATTAATTT-TT---AGAAACTAAGCCTTATTTTCAGGGGTTTCT
56922 TGATGTTTTCAAATTAATTTTTAGAAACTAAGCCTTATTTTCAGGGGTTTCT
1 TGATGTTTTCAAATTAATTTTTAGAAACTAAGCCTTATTTTCAGGGGTTTCT
56974 TGATG
1 TGATG
56979 ATTATCTCCA
Statistics
Matches: 96, Mismatches: 10, Indels: 17
0.78 0.08 0.14
Matches are distributed among these distances:
52 32 0.33
55 19 0.20
56 21 0.22
58 1 0.01
59 21 0.22
60 2 0.02
ACGTcount: A:0.27, C:0.11, G:0.17, T:0.45
Consensus pattern (52 bp):
TGATGTTTTCAAATTAATTTTTAGAAACTAAGCCTTATTTTCAGGGGTTTCT
Found at i:57187 original size:41 final size:42
Alignment explanation
Indices: 57081--57187 Score: 128
Period size: 42 Copynumber: 2.6 Consensus size: 42
57071 TCTTGAAGAG
* *
57081 TAAGTCCTTCGGGCCAT-CAGTAAGTCTTTCGAGCTAGATGCT
1 TAAGTCCTTCGGGCCATCCA-TAAGTCTTTCGAGCAAGATGCA
* * * * *
57123 TAAATCCTTTGGGTCATCTATAAGTCTTTCTAGCAAGATG-A
1 TAAGTCCTTCGGGCCATCCATAAGTCTTTCGAGCAAGATGCA
57164 TAAGTCCTTCGGGCCATCCATAAG
1 TAAGTCCTTCGGGCCATCCATAAG
57188 ACCTTCGAAC
Statistics
Matches: 53, Mismatches: 11, Indels: 3
0.79 0.16 0.04
Matches are distributed among these distances:
41 20 0.38
42 32 0.60
43 1 0.02
ACGTcount: A:0.25, C:0.22, G:0.21, T:0.32
Consensus pattern (42 bp):
TAAGTCCTTCGGGCCATCCATAAGTCTTTCGAGCAAGATGCA
Found at i:57312 original size:39 final size:38
Alignment explanation
Indices: 57269--57470 Score: 189
Period size: 39 Copynumber: 5.4 Consensus size: 38
57259 TGAGGGATCA
*
57269 ACATCTAGCTTGAGATAGTTTCACTCGAAACATAAGATT
1 ACATCTCGCTTGAGATAGTTTCACTCGAAACA-AAGATT
* **
57308 ACATCTCGCTTGAGATAATTTCACTC-AAA-AAATTTT
1 ACATCTCGCTTGAGATAGTTTCACTCGAAACAAAGATT
** * *
57344 TTATCTCGCTTGAGATAGCTTCACTCGAAACATGAGATT
1 ACATCTCGCTTGAGATAGTTTCACTCGAAACA-AAGATT
* * *
57383 ACATCTCGTTTGAGATAATTTCATTCGAAACAAA-ATT
1 ACATCTCGCTTGAGATAGTTTCACTCGAAACAAAGATT
** * *
57420 TTATCTC-ATTTAGATAGTTTCACTCGAAACAAAAGATT
1 ACATCTCGCTTGAGATAGTTTCACTCGAAAC-AAAGATT
* *
57458 -TATCTCACTTGAG
1 ACATCTCGCTTGAG
57471 TCATTTTTCT
Statistics
Matches: 131, Mismatches: 26, Indels: 13
0.77 0.15 0.08
Matches are distributed among these distances:
36 45 0.34
37 21 0.16
38 12 0.09
39 53 0.40
ACGTcount: A:0.34, C:0.18, G:0.13, T:0.35
Consensus pattern (38 bp):
ACATCTCGCTTGAGATAGTTTCACTCGAAACAAAGATT
Found at i:57399 original size:75 final size:76
Alignment explanation
Indices: 57271--57470 Score: 264
Period size: 75 Copynumber: 2.7 Consensus size: 76
57261 AGGGATCAAC
*
57271 ATCTAGCTTGAGATAGTTTCACTCGAAACATAAGATTACATCTCGCTTGAGATAATTTCACTC-A
1 ATCTCGCTTGAGATAGTTTCACTCGAAACATAAGATTACATCTCGCTTGAGATAATTTCACTCGA
*
57335 AA-AAATTTTTT
66 AACAAA-ATTTT
* * * *
57346 ATCTCGCTTGAGATAGCTTCACTCGAAACATGAGATTACATCTCGTTTGAGATAATTTCATTCGA
1 ATCTCGCTTGAGATAGTTTCACTCGAAACATAAGATTACATCTCGCTTGAGATAATTTCACTCGA
57411 AACAAAATTTT
66 AACAAAATTTT
* * * * *
57422 ATCTC-ATTTAGATAGTTTCACTCGAAACAAAAGATT-TATCTCACTTGAG
1 ATCTCGCTTGAGATAGTTTCACTCGAAACATAAGATTACATCTCGCTTGAG
57471 TCATTTTTCT
Statistics
Matches: 109, Mismatches: 14, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
74 10 0.09
75 84 0.77
76 12 0.11
77 3 0.03
ACGTcount: A:0.34, C:0.18, G:0.13, T:0.35
Consensus pattern (76 bp):
ATCTCGCTTGAGATAGTTTCACTCGAAACATAAGATTACATCTCGCTTGAGATAATTTCACTCGA
AACAAAATTTT
Found at i:57441 original size:36 final size:38
Alignment explanation
Indices: 57278--57470 Score: 160
Period size: 36 Copynumber: 5.1 Consensus size: 38
57268 AACATCTAGC
* * * **
57278 TTGAGATAGTTTCACTCGAAACATAAGATTACATCTCGC
1 TTGAGATAATTTCACTCGAAACAAAAGATT-TATCTCAT
*** **
57317 TTGAGATAATTTCACTC-AAA-AAATTTTTTATCTCGC
1 TTGAGATAATTTCACTCGAAACAAAAGATTTATCTCAT
** ** * *
57353 TTGAGATAGCTTCACTCGAAACATGAGATTACATCTCGT
1 TTGAGATAATTTCACTCGAAACAAAAGATT-TATCTCAT
* *
57392 TTGAGATAATTTCATTCGAAACAAAA-TTTTATCTCAT
1 TTGAGATAATTTCACTCGAAACAAAAGATTTATCTCAT
* *
57429 TT-AGATAGTTTCACTCGAAACAAAAGATTTATCTCAC
1 TTGAGATAATTTCACTCGAAACAAAAGATTTATCTCAT
57466 TTGAG
1 TTGAG
57471 TCATTTTTCT
Statistics
Matches: 122, Mismatches: 27, Indels: 11
0.76 0.17 0.07
Matches are distributed among these distances:
36 43 0.35
37 26 0.21
38 10 0.08
39 43 0.35
ACGTcount: A:0.34, C:0.18, G:0.13, T:0.35
Consensus pattern (38 bp):
TTGAGATAATTTCACTCGAAACAAAAGATTTATCTCAT
Found at i:61151 original size:47 final size:49
Alignment explanation
Indices: 61056--61154 Score: 157
Period size: 47 Copynumber: 2.1 Consensus size: 49
61046 AAAAGCTAAA
*
61056 ATAAATTAAGACAATATAATTAAAAAATTTAATGGAAATATATATTTTT
1 ATAAATTAAGACAATATAATTAAAAAATTCAATGGAAATATATATTTTT
* *
61105 ATAAATTAAGACAATATAA-TAAAAAA-TCAATGGAAATATCTCTTTTT
1 ATAAATTAAGACAATATAATTAAAAAATTCAATGGAAATATATATTTTT
61152 ATA
1 ATA
61155 TTTAAATACA
Statistics
Matches: 47, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
47 21 0.45
48 7 0.15
49 19 0.40
ACGTcount: A:0.53, C:0.05, G:0.06, T:0.36
Consensus pattern (49 bp):
ATAAATTAAGACAATATAATTAAAAAATTCAATGGAAATATATATTTTT
Done.