Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009206.1 Hibiscus syriacus cultivar Beakdansim tig00112792_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: 160838
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:12413 original size:3 final size:3
Alignment explanation
Indices: 12396--12468 Score: 87
Period size: 3 Copynumber: 25.0 Consensus size: 3
12386 TATATATATT
* * *
12396 TAA T-A TAA T-A TAA TAA TAA TAA TAT TTA TAA TAA TTA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* *
12442 TAA TAA TAA TTA TAA TTA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA
12469 ATAAATTAAT
Statistics
Matches: 58, Mismatches: 10, Indels: 4
0.81 0.14 0.06
Matches are distributed among these distances:
2 4 0.07
3 54 0.93
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (3 bp):
TAA
Found at i:12462 original size:21 final size:21
Alignment explanation
Indices: 12396--12468 Score: 96
Period size: 21 Copynumber: 3.6 Consensus size: 21
12386 TATATATATT
*
12396 TAAT-ATAAT-ATAATAATAA
1 TAATAATAATAATAATTATAA
* *
12415 TAATATTTATAATAATTATAA
1 TAATAATAATAATAATTATAA
12436 TAATAATAATAATAATTATAA
1 TAATAATAATAATAATTATAA
*
12457 TTATAATAATAA
1 TAATAATAATAA
12469 ATAAATTAAT
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
19 4 0.09
20 3 0.07
21 39 0.85
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (21 bp):
TAATAATAATAATAATTATAA
Found at i:16723 original size:30 final size:30
Alignment explanation
Indices: 16687--16819 Score: 239
Period size: 30 Copynumber: 4.4 Consensus size: 30
16677 TCCGAAGGAC
16687 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
16717 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
*
16747 CTATCAAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
16777 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
* *
16807 CTGTCCATAGGTC
1 CTATCCAGAGGTC
16820 CCGAAGAACC
Statistics
Matches: 99, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 99 1.00
ACGTcount: A:0.32, C:0.23, G:0.20, T:0.24
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCCTCGGTAA
Found at i:16836 original size:30 final size:30
Alignment explanation
Indices: 16793--16886 Score: 89
Period size: 31 Copynumber: 3.1 Consensus size: 30
16783 AGAGGTCATA
* * *
16793 AAGATCCTCGGTAACTGTCCATAGGTCCCG
1 AAGAACCTAGGTAACTGTCCATATGTCCCG
* * *
16823 AAGAACCTAGGTAAACTATCCATATGTTCCT
1 AAGAACCTAGGT-AACTGTCCATATGTCCCG
* * *
16854 TAGAACATAGGTATACTGTCCATATGTCTCG
1 AAGAACCTAGGTA-ACTGTCCATATGTCCCG
16885 AA
1 AA
16887 AGACATAGGT
Statistics
Matches: 49, Mismatches: 13, Indels: 3
0.75 0.20 0.05
Matches are distributed among these distances:
30 11 0.22
31 38 0.78
ACGTcount: A:0.31, C:0.23, G:0.18, T:0.28
Consensus pattern (30 bp):
AAGAACCTAGGTAACTGTCCATATGTCCCG
Found at i:16836 original size:60 final size:60
Alignment explanation
Indices: 16687--16844 Score: 217
Period size: 60 Copynumber: 2.6 Consensus size: 60
16677 TCCGAAGGAC
* *
16687 CTATCCAGAGGTCATAAAGATCCTCGGTAACTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCAAGAGGTCACAAAGATCCTCGGTAACTATCCAGAGGTCATAAAGATCCTCGGTAA
*
16747 CTATCAAGAGGTCATAAAGATCCTCGGTAACTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCAAGAGGTCACAAAGATCCTCGGTAACTATCCAGAGGTCATAAAGATCCTCGGTAA
* * * * * * *
16807 CTGTCCATAGGTCCCGAAGAACCTAGGTAAACTATCCA
1 CTATCAAGAGGTCACAAAGATCCTCGGT-AACTATCCA
16845 TATGTTCCTT
Statistics
Matches: 88, Mismatches: 9, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
60 79 0.90
61 9 0.10
ACGTcount: A:0.34, C:0.24, G:0.20, T:0.23
Consensus pattern (60 bp):
CTATCAAGAGGTCACAAAGATCCTCGGTAACTATCCAGAGGTCATAAAGATCCTCGGTAA
Found at i:16893 original size:31 final size:30
Alignment explanation
Indices: 16802--16897 Score: 88
Period size: 31 Copynumber: 3.1 Consensus size: 30
16792 AAAGATCCTC
* * *
16802 GGTAACTGTCCATAGGTCCCGAAGAACCTA
1 GGTAACTGTCCATATGTCTCGAAGAACATA
* **
16832 GGTAAACTATCCATATGT-TCCTTAGAACATA
1 GGT-AACTGTCCATATGTCT-CGAAGAACATA
16863 GGTATACTGTCCATATGTCTCGAA-AGACATA
1 GGTA-ACTGTCCATATGTCTCGAAGA-ACATA
16894 GGTA
1 GGTA
16898 GTTCTTTGAC
Statistics
Matches: 52, Mismatches: 9, Indels: 9
0.74 0.13 0.13
Matches are distributed among these distances:
30 5 0.10
31 46 0.88
32 1 0.02
ACGTcount: A:0.32, C:0.21, G:0.20, T:0.27
Consensus pattern (30 bp):
GGTAACTGTCCATATGTCTCGAAGAACATA
Found at i:18108 original size:63 final size:63
Alignment explanation
Indices: 17952--18112 Score: 189
Period size: 64 Copynumber: 2.5 Consensus size: 63
17942 TCTTTAGCAT
* * * * * * *
17952 GTGCATCGATGCAGTACCCGTGCATCGATGCACAAATCACCTTCGATGTTTTCATTTTAAGGG
1 GTGCATCGATGCACTTCCTGTGCATCGATACACAAATCACATTCGATGTTTCCATTTTAAGAG
* * ** *
18015 GATGCATCGATGCAC-TCCTTATGCATCGATACACCAATTGCATTCGATGTTTCCATTTTAATAG
1 G-TGCATCGATGCACTTCC-TGTGCATCGATACACAAATCACATTCGATGTTTCCATTTTAAGAG
18079 GTGCATCGATGCACTTCCTGTGCATCGATACACA
1 GTGCATCGATGCACTTCCTGTGCATCGATACACA
18113 CTGAACAATT
Statistics
Matches: 81, Mismatches: 14, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
63 30 0.37
64 51 0.63
ACGTcount: A:0.25, C:0.25, G:0.19, T:0.31
Consensus pattern (63 bp):
GTGCATCGATGCACTTCCTGTGCATCGATACACAAATCACATTCGATGTTTCCATTTTAAGAG
Found at i:19057 original size:21 final size:21
Alignment explanation
Indices: 19015--19057 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
19005 TTTATGGGCT
* *
19015 AGGGGAATCGGTACCCATTCA
1 AGGGGAATCGATACCCACTCA
* *
19036 AGGGGAATCGATCCCCCCTCA
1 AGGGGAATCGATACCCACTCA
19057 A
1 A
19058 ACGAGTATGA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.28, C:0.30, G:0.26, T:0.16
Consensus pattern (21 bp):
AGGGGAATCGATACCCACTCA
Found at i:19110 original size:20 final size:20
Alignment explanation
Indices: 19085--19123 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
19075 GAATGCTAGA
*
19085 GGGGAATCGATACCCCCATG
1 GGGGAACCGATACCCCCATG
*
19105 GGGGAACCGATTCCCCCAT
1 GGGGAACCGATACCCCCAT
19124 AATGAAAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.23, C:0.33, G:0.28, T:0.15
Consensus pattern (20 bp):
GGGGAACCGATACCCCCATG
Found at i:19988 original size:31 final size:30
Alignment explanation
Indices: 19950--20044 Score: 79
Period size: 31 Copynumber: 3.1 Consensus size: 30
19940 GTCAAAGAAC
19950 TACCTATGTCTTTCGAGACATATGGACAGT
1 TACCTATGTCTTTCGAGACATATGGACAGT
*** *
19980 ATACCTATGTTCTAAGGA-ACATATGGATAGTT
1 -TACCTATG-TCTTTCGAGACATATGGACAG-T
* *
20012 TACCTAGGT-TCTTCGGGAC-TATGGACAGT
1 TACCTATGTCT-TTCGAGACATATGGACAGT
20041 TACC
1 TACC
20045 GAGGATCTTT
Statistics
Matches: 50, Mismatches: 10, Indels: 10
0.71 0.14 0.14
Matches are distributed among these distances:
29 6 0.12
30 10 0.20
31 28 0.56
32 6 0.12
ACGTcount: A:0.27, C:0.19, G:0.21, T:0.33
Consensus pattern (30 bp):
TACCTATGTCTTTCGAGACATATGGACAGT
Found at i:20073 original size:30 final size:30
Alignment explanation
Indices: 20033--20206 Score: 321
Period size: 30 Copynumber: 5.8 Consensus size: 30
20023 TTCGGGACTA
*
20033 TGGACAGTTACCGAGGATCTTTATGACCTC
1 TGGATAGTTACCGAGGATCTTTATGACCTC
20063 TGGATAGTTACCGAGGATCTTTATGACCTC
1 TGGATAGTTACCGAGGATCTTTATGACCTC
*
20093 TGGATAGTTACCGAGGATCTTTATGACCTA
1 TGGATAGTTACCGAGGATCTTTATGACCTC
20123 TGGATAGTTACCGAGGATCTTTATGACCTC
1 TGGATAGTTACCGAGGATCTTTATGACCTC
20153 TGGATAGTTACCGAGGATCTTTATGACCTC
1 TGGATAGTTACCGAGGATCTTTATGACCTC
*
20183 TGGATAGTTACCGAAGATCTTTAT
1 TGGATAGTTACCGAGGATCTTTAT
20207 AGGTCCTTCG
Statistics
Matches: 140, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 140 1.00
ACGTcount: A:0.25, C:0.19, G:0.23, T:0.33
Consensus pattern (30 bp):
TGGATAGTTACCGAGGATCTTTATGACCTC
Found at i:22330 original size:36 final size:36
Alignment explanation
Indices: 22283--22352 Score: 106
Period size: 36 Copynumber: 1.9 Consensus size: 36
22273 AGGGTTCTAC
22283 GTGGTCCTTCGGGACACAGTGGTCCT-TCGGGACATA
1 GTGGTCCTTCGGGACACAGTGGTCCTGT-GGGACATA
* *
22319 GTGGTCCTTCGGGATATAGTGGTCCTGTGGGACA
1 GTGGTCCTTCGGGACACAGTGGTCCTGTGGGACA
22353 AATTCTATGG
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
36 30 0.97
37 1 0.03
ACGTcount: A:0.16, C:0.21, G:0.36, T:0.27
Consensus pattern (36 bp):
GTGGTCCTTCGGGACACAGTGGTCCTGTGGGACATA
Found at i:22350 original size:18 final size:18
Alignment explanation
Indices: 22283--22344 Score: 106
Period size: 18 Copynumber: 3.4 Consensus size: 18
22273 AGGGTTCTAC
*
22283 GTGGTCCTTCGGGACACA
1 GTGGTCCTTCGGGACATA
22301 GTGGTCCTTCGGGACATA
1 GTGGTCCTTCGGGACATA
*
22319 GTGGTCCTTCGGGATATA
1 GTGGTCCTTCGGGACATA
22337 GTGGTCCT
1 GTGGTCCT
22345 GTGGGACAAA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 42 1.00
ACGTcount: A:0.15, C:0.23, G:0.34, T:0.29
Consensus pattern (18 bp):
GTGGTCCTTCGGGACATA
Found at i:23123 original size:51 final size:51
Alignment explanation
Indices: 23066--23173 Score: 180
Period size: 51 Copynumber: 2.1 Consensus size: 51
23056 GTTAAAGAAT
* * *
23066 TACTTTATAGAATAGAAGTTTTAAATTTTTTATGGTTTTTATAAAATTATA
1 TACTTTATAGAATAGAAGTTTTAAATTTTCTATGGATTTTATAAAAGTATA
*
23117 TGCTTTATAGAATAGAAGTTTTAAATTTTCTATGGATTTTATAAAAGTATA
1 TACTTTATAGAATAGAAGTTTTAAATTTTCTATGGATTTTATAAAAGTATA
23168 TACTTT
1 TACTTT
23174 GACTGATCAA
Statistics
Matches: 52, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
51 52 1.00
ACGTcount: A:0.36, C:0.04, G:0.11, T:0.49
Consensus pattern (51 bp):
TACTTTATAGAATAGAAGTTTTAAATTTTCTATGGATTTTATAAAAGTATA
Found at i:29484 original size:20 final size:21
Alignment explanation
Indices: 29450--29489 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
29440 AAATAATCTA
29450 AAATAAATAATTTTAATTTTT
1 AAATAAATAATTTTAATTTTT
*
29471 AAATTAATAA-TTTAATTTT
1 AAATAAATAATTTTAATTTT
29490 GATTTAGTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (21 bp):
AAATAAATAATTTTAATTTTT
Found at i:36045 original size:28 final size:29
Alignment explanation
Indices: 35990--36057 Score: 93
Period size: 28 Copynumber: 2.3 Consensus size: 29
35980 ATATAAGAAA
35990 GGTGTCTAACATATGTTTTCGATTTCAGTTT
1 GGTGTCT-A-ATATGTTTTCGATTTCAGTTT
*
36021 GGTGTCTAATATTTTTTCG-TTTCAGTTT
1 GGTGTCTAATATGTTTTCGATTTCAGTTT
*
36049 GGTATCTAA
1 GGTGTCTAA
36058 CGTTTCATTC
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
28 17 0.49
29 10 0.29
30 1 0.03
31 7 0.20
ACGTcount: A:0.19, C:0.12, G:0.19, T:0.50
Consensus pattern (29 bp):
GGTGTCTAATATGTTTTCGATTTCAGTTT
Found at i:37597 original size:20 final size:20
Alignment explanation
Indices: 37572--37616 Score: 81
Period size: 20 Copynumber: 2.2 Consensus size: 20
37562 TGAGGCATAT
37572 GTGCCCAGTTGGCTACTGAA
1 GTGCCCAGTTGGCTACTGAA
*
37592 GTGCCCAGTTGGCTATTGAA
1 GTGCCCAGTTGGCTACTGAA
37612 GTGCC
1 GTGCC
37617 TTGGCACTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.18, C:0.24, G:0.31, T:0.27
Consensus pattern (20 bp):
GTGCCCAGTTGGCTACTGAA
Found at i:37903 original size:20 final size:20
Alignment explanation
Indices: 37864--37909 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
37854 CTGTGGGTAC
*
37864 CGATACTGACCCTTCAGTAT
1 CGATACTGAACCTTCAGTAT
* **
37884 TGATACTGAACCTTTGGTAT
1 CGATACTGAACCTTCAGTAT
37904 CGATAC
1 CGATAC
37910 CCACCTGCTG
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.26, C:0.24, G:0.17, T:0.33
Consensus pattern (20 bp):
CGATACTGAACCTTCAGTAT
Found at i:49267 original size:87 final size:82
Alignment explanation
Indices: 49063--49365 Score: 308
Period size: 76 Copynumber: 3.7 Consensus size: 82
49053 CCATACAGTA
*
49063 TTATCGAAGAAGAAGAGTGATAAATCAG----CCATACACATATTCTCAATTTATCATGC-TTGC
1 TTATCGAAGAAGAAGAGTGATAAATCAGCCACCCATACATATATTCTCAATTTATC-TGCATTGC
* *
49123 ATGCATAAGTTCATATTG
65 ATGCATAAATTCATAGTG
* * *
49141 TTATTGGAGAAGAAGAGTGATAAATCAGTCACCCATACATATATTCTCAAATTATCATGCTTGCA
1 TTATCGAAGAAGAAGAGTGATAAATCAGCCACCCATACATATATTCTC-AATT-T-AT-C-TGCA
49206 TTGCATGCATAAATTCATAGTG
61 TTGCATGCATAAATTCATAGTG
* *
49228 TTATCGAAGTAG-AGAGTGATAAATCAGCCACCCCGTACATATATTCTCAATTTA--T-CA-TGC
1 TTATCGAAGAAGAAGAGTGATAAATCAGCCA-CCCATACATATATTCTCAATTTATCTGCATTGC
* * *
49288 ATACATACA-T-ACAGTG
65 ATGCATAAATTCATAGTG
* * *
49304 TTATCAAAGAAG-AGAGTGACAAATCAGTCACCCCATACATATATTCTCAATTTATCATGCAT
1 TTATCGAAGAAGAAGAGTGATAAATCAGCCA-CCCATACATATATTCTCAATTTATC-TGCAT
49366 ACACACATGC
Statistics
Matches: 191, Mismatches: 19, Indels: 27
0.81 0.08 0.11
Matches are distributed among these distances:
76 54 0.28
77 1 0.01
78 36 0.19
79 3 0.02
80 3 0.02
82 15 0.08
83 4 0.02
84 2 0.01
85 3 0.02
86 25 0.13
87 45 0.24
ACGTcount: A:0.36, C:0.18, G:0.15, T:0.31
Consensus pattern (82 bp):
TTATCGAAGAAGAAGAGTGATAAATCAGCCACCCATACATATATTCTCAATTTATCTGCATTGCA
TGCATAAATTCATAGTG
Found at i:49411 original size:76 final size:76
Alignment explanation
Indices: 49224--49404 Score: 272
Period size: 76 Copynumber: 2.4 Consensus size: 76
49214 ATAAATTCAT
* * * *
49224 AGTGTTATCGAAGTAGAGAGTGATAAATCAGCCACCCCGTACATATATTCTCAATTTATCATGCA
1 AGTGTTATCGAAGAAGAGAGTGACAAATCAGTCACCCCATACATATATTCTCAATTTATCATGCA
*
49289 TACATACATAC
66 TACACACATAC
*
49300 AGTGTTATCAAAGAAGAGAGTGACAAATCAGTCACCCCATACATATATTCTCAATTTATCATGCA
1 AGTGTTATCGAAGAAGAGAGTGACAAATCAGTCACCCCATACATATATTCTCAATTTATCATGCA
*
49365 TACACACATGC
66 TACACACATAC
* * *
49376 AGTGTTGTCGAAGAAAAGAGTGAGAAATC
1 AGTGTTATCGAAGAAGAGAGTGACAAATC
49405 GATCACCTCG
Statistics
Matches: 94, Mismatches: 11, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
76 94 1.00
ACGTcount: A:0.38, C:0.19, G:0.17, T:0.27
Consensus pattern (76 bp):
AGTGTTATCGAAGAAGAGAGTGACAAATCAGTCACCCCATACATATATTCTCAATTTATCATGCA
TACACACATAC
Found at i:54380 original size:16 final size:16
Alignment explanation
Indices: 54362--54402 Score: 64
Period size: 16 Copynumber: 2.5 Consensus size: 16
54352 TATTCTTTCA
54362 TTTATTTTTAATTTTAT
1 TTTA-TTTTAATTTTAT
54379 TTTATTTTAATTTTAT
1 TTTATTTTAATTTTAT
*
54395 TTTGTTTT
1 TTTATTTT
54403 TTAGGGAACT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
16 19 0.83
17 4 0.17
ACGTcount: A:0.20, C:0.00, G:0.02, T:0.78
Consensus pattern (16 bp):
TTTATTTTAATTTTAT
Found at i:63690 original size:10 final size:11
Alignment explanation
Indices: 63675--63709 Score: 54
Period size: 10 Copynumber: 3.2 Consensus size: 11
63665 ATAGTTATTA
63675 ATAATTAAATT
1 ATAATTAAATT
63686 A-AATTAAATT
1 ATAATTAAATT
63696 ATAATTATAATT
1 ATAATTA-AATT
63708 AT
1 AT
63710 GAAAAAAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 10 0.45
11 6 0.27
12 6 0.27
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (11 bp):
ATAATTAAATT
Found at i:64007 original size:29 final size:29
Alignment explanation
Indices: 63935--64011 Score: 77
Period size: 29 Copynumber: 2.7 Consensus size: 29
63925 GTAAATGAGT
*
63935 TTAATTGATTTTTTTA-ATAAGTTTGAGGGC
1 TTAATT-ATTTTTTTATA-AAGTTTGAGGAC
* *
63965 TTAATTAATATTTTATAAAGTTTGAGGAC
1 TTAATTATTTTTTTATAAAGTTTGAGGAC
**
63994 TTGTTTATTTTTTT-TAAA
1 TTAATTATTTTTTTATAAA
64012 ATTAAGATAT
Statistics
Matches: 39, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
28 4 0.10
29 28 0.72
30 7 0.18
ACGTcount: A:0.30, C:0.03, G:0.14, T:0.53
Consensus pattern (29 bp):
TTAATTATTTTTTTATAAAGTTTGAGGAC
Found at i:64161 original size:30 final size:31
Alignment explanation
Indices: 64104--64161 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 31
64094 ATTAAATTAT
*
64104 TAAAAAAATAGTTTAAGTACCACATTGAATG
1 TAAAAAAATAGTTTAAGGACCACATTGAATG
* *
64135 TAAAAAAA-AGTTTAGGGACCATATTGA
1 TAAAAAAATAGTTTAAGGACCACATTGA
64162 TTTTTTTTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
30 16 0.67
31 8 0.33
ACGTcount: A:0.48, C:0.09, G:0.16, T:0.28
Consensus pattern (31 bp):
TAAAAAAATAGTTTAAGGACCACATTGAATG
Found at i:68070 original size:11 final size:11
Alignment explanation
Indices: 68054--68078 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
68044 CCAATACACA
68054 ATATTTTCTTG
1 ATATTTTCTTG
68065 ATATTTTCTTG
1 ATATTTTCTTG
68076 ATA
1 ATA
68079 AATACCCTAT
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:0.24, C:0.08, G:0.08, T:0.60
Consensus pattern (11 bp):
ATATTTTCTTG
Found at i:70142 original size:2 final size:2
Alignment explanation
Indices: 70135--70193 Score: 56
Period size: 2 Copynumber: 32.0 Consensus size: 2
70125 TCCTTCAACT
* * *
70135 TA TA TA TA TA TA TA TA TA T- TA TA AA T- TA TA AA T- TA TA AA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
70174 T- TA T- TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA
70194 GGGACGCAGT
Statistics
Matches: 46, Mismatches: 6, Indels: 10
0.74 0.10 0.16
Matches are distributed among these distances:
1 5 0.11
2 41 0.89
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:70162 original size:7 final size:7
Alignment explanation
Indices: 70147--70177 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
70137 TATATATATA
*
70147 TATATAT
1 TATAAAT
70154 TATAAAT
1 TATAAAT
70161 TATAAAT
1 TATAAAT
70168 TATAAAT
1 TATAAAT
70175 TAT
1 TAT
70178 TATATATATA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (7 bp):
TATAAAT
Found at i:70350 original size:32 final size:32
Alignment explanation
Indices: 70314--70380 Score: 125
Period size: 32 Copynumber: 2.1 Consensus size: 32
70304 TATTTTGCCT
*
70314 CCTCATTTTCTATGGTTAATTATACTTTGTCC
1 CCTCATTTTCTATGATTAATTATACTTTGTCC
70346 CCTCATTTTCTATGATTAATTATACTTTGTCC
1 CCTCATTTTCTATGATTAATTATACTTTGTCC
70378 CCT
1 CCT
70381 TAAGTTTGAA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.19, C:0.24, G:0.07, T:0.49
Consensus pattern (32 bp):
CCTCATTTTCTATGATTAATTATACTTTGTCC
Found at i:70913 original size:2 final size:2
Alignment explanation
Indices: 70906--70946 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
70896 GGTCTGAGAC
70906 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
70947 CGAATCTCCA
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 37 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:73501 original size:17 final size:17
Alignment explanation
Indices: 73475--73523 Score: 55
Period size: 17 Copynumber: 2.9 Consensus size: 17
73465 TATATTAATT
*
73475 TTTTAAAATAATATATA
1 TTTTATAATAATATATA
* *
73492 TTTTATAATAATTTTTA
1 TTTTATAATAATATATA
73509 TATTT-TAATAATATA
1 T-TTTATAATAATATA
73524 AAAATAAAAT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
17 23 0.88
18 3 0.12
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
TTTTATAATAATATATA
Found at i:73552 original size:2 final size:2
Alignment explanation
Indices: 73541--73577 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
73531 AATTCTTAAA
73541 AT AT -T 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
73578 TAATCAGGTC
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:78570 original size:24 final size:24
Alignment explanation
Indices: 78515--78560 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
78505 AAAGTTGATA
* * *
78515 AAATGCTTTTAGTTCATTTAATTG
1 AAATGATTTTAATTCACTTAATTG
78539 AAATGATTTTAATTCACTTAAT
1 AAATGATTTTAATTCACTTAAT
78561 CTGACAGATT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.35, C:0.09, G:0.09, T:0.48
Consensus pattern (24 bp):
AAATGATTTTAATTCACTTAATTG
Found at i:84828 original size:2 final size:2
Alignment explanation
Indices: 84823--84849 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
84813 TAAAAAAAAC
84823 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
84850 AATCGATCTA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:96475 original size:34 final size:34
Alignment explanation
Indices: 96433--96557 Score: 111
Period size: 34 Copynumber: 3.8 Consensus size: 34
96423 TTCGTCATAC
*
96433 TAGGATTCAAATTCCTAAAAATAGGATAGAATTT
1 TAGGATTCAAACTCCTAAAAATAGGATAGAATTT
* *
96467 TAGGATTCAAACTCCTAAAGATATGATAGAATTTT
1 TAGGATTCAAACTCCTAAAAATAGGATAGAA-TTT
*
96502 GCTAGGATT-----T--AAAAAATAGGATAGAATTT
1 --TAGGATTCAAACTCCTAAAAATAGGATAGAATTT
* * *
96531 TATGATTTAAACTCCTAAAGATAGGAT
1 TAGGATTCAAACTCCTAAAAATAGGAT
96558 CCACAAGCAC
Statistics
Matches: 72, Mismatches: 9, Indels: 20
0.71 0.09 0.20
Matches are distributed among these distances:
27 6 0.08
29 3 0.04
30 13 0.18
32 2 0.03
34 38 0.53
35 3 0.04
37 7 0.10
ACGTcount: A:0.42, C:0.09, G:0.16, T:0.33
Consensus pattern (34 bp):
TAGGATTCAAACTCCTAAAAATAGGATAGAATTT
Found at i:96953 original size:18 final size:17
Alignment explanation
Indices: 96914--96956 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
96904 ATTATATGGA
96914 TATT-TTATTCATTTAT
1 TATTATTATTCATTTAT
*
96930 TTTTATTATTCATGTTAT
1 TATTATTATTCAT-TTAT
96948 TATTATTAT
1 TATTATTAT
96957 ATGTATATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 3 0.13
17 8 0.35
18 12 0.52
ACGTcount: A:0.26, C:0.05, G:0.02, T:0.67
Consensus pattern (17 bp):
TATTATTATTCATTTAT
Found at i:98678 original size:5 final size:5
Alignment explanation
Indices: 98668--98700 Score: 66
Period size: 5 Copynumber: 6.6 Consensus size: 5
98658 TCTTTTCATC
98668 TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTT
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTT
98701 CATCACTTGC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 28 1.00
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTAT
Found at i:100041 original size:8 final size:8
Alignment explanation
Indices: 100028--100066 Score: 53
Period size: 8 Copynumber: 5.0 Consensus size: 8
100018 GAACATTTCA
*
100028 TGCATTCT
1 TGCATTTT
100036 TGCA-TTT
1 TGCATTTT
100043 TGCATTTT
1 TGCATTTT
*
100051 TGCCTTTT
1 TGCATTTT
100059 TGCATTTT
1 TGCATTTT
100067 CATCTACATT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
7 6 0.22
8 21 0.78
ACGTcount: A:0.10, C:0.18, G:0.13, T:0.59
Consensus pattern (8 bp):
TGCATTTT
Found at i:101218 original size:12 final size:11
Alignment explanation
Indices: 101185--101232 Score: 51
Period size: 12 Copynumber: 4.1 Consensus size: 11
101175 AATCAAGAAC
101185 AAAAAAGAAAAG
1 AAAAAA-AAAAG
**
101197 AAGCAAAAAAG
1 AAAAAAAAAAG
101208 CAAAAAAAAAAG
1 -AAAAAAAAAAG
101220 AAAAAGAAAAAG
1 AAAAA-AAAAAG
101232 A
1 A
101233 GAAACAATAA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
11 10 0.33
12 20 0.67
ACGTcount: A:0.81, C:0.04, G:0.15, T:0.00
Consensus pattern (11 bp):
AAAAAAAAAAG
Found at i:101223 original size:8 final size:8
Alignment explanation
Indices: 101185--101278 Score: 64
Period size: 8 Copynumber: 11.5 Consensus size: 8
101175 AATCAAGAAC
101185 AAAAAAGA
1 AAAAAAGA
* *
101193 AAAGAAGC
1 AAAAAAGA
101201 AAAAAAGCA
1 AAAAAAG-A
*
101210 AAAAAAAA
1 AAAAAAGA
101218 AGAAAAAGA
1 A-AAAAAGA
*
101227 AAAAGAG-
1 AAAAAAGA
* *
101234 AAACAATA
1 AAAAAAGA
*
101242 ACAAAAGA
1 AAAAAAGA
101250 AAAAAAGA
1 AAAAAAGA
* **
101258 GCAAAAATC
1 -AAAAAAGA
101267 AAAAAAGA
1 AAAAAAGA
101275 AAAA
1 AAAA
101279 GGGACAAAAA
Statistics
Matches: 62, Mismatches: 20, Indels: 8
0.69 0.22 0.09
Matches are distributed among these distances:
7 4 0.06
8 40 0.65
9 18 0.29
ACGTcount: A:0.79, C:0.06, G:0.13, T:0.02
Consensus pattern (8 bp):
AAAAAAGA
Found at i:101247 original size:23 final size:23
Alignment explanation
Indices: 101220--101288 Score: 70
Period size: 25 Copynumber: 2.9 Consensus size: 23
101210 AAAAAAAAAG
101220 AAAAAGAAAAAGAG-AAACAAT-A
1 AAAAAGAAAAAGAGCAAA-AATCA
101242 ACAAAAGAAAAAAAGAGCAAAAATCA
1 A-AAAAG--AAAAAGAGCAAAAATCA
*
101268 AAAAAGAAAAAGGGACAAAAA
1 AAAAAGAAAAAGAG-CAAAAA
101289 GCACATGCAA
Statistics
Matches: 40, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
22 1 0.03
23 12 0.30
24 6 0.15
25 16 0.40
26 5 0.12
ACGTcount: A:0.75, C:0.07, G:0.14, T:0.03
Consensus pattern (23 bp):
AAAAAGAAAAAGAGCAAAAATCA
Found at i:101254 original size:25 final size:25
Alignment explanation
Indices: 101226--101278 Score: 74
Period size: 25 Copynumber: 2.1 Consensus size: 25
101216 AAAGAAAAAG
101226 AAAAAGAG-AAACAAT-AACAAAAGAA
1 AAAAAGAGCAAA-AATCAA-AAAAGAA
101251 AAAAAGAGCAAAAATCAAAAAAGAA
1 AAAAAGAGCAAAAATCAAAAAAGAA
101276 AAA
1 AAA
101279 GGGACAAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
25 21 0.81
26 5 0.19
ACGTcount: A:0.77, C:0.08, G:0.11, T:0.04
Consensus pattern (25 bp):
AAAAAGAGCAAAAATCAAAAAAGAA
Found at i:101942 original size:22 final size:22
Alignment explanation
Indices: 101915--101985 Score: 115
Period size: 22 Copynumber: 3.2 Consensus size: 22
101905 CCATCAATCT
* *
101915 TTTGAGCATCCAATGTAAAACC
1 TTTGAGCATCAAATGTCAAACC
101937 TTTGAGCATCAAATGTCAAACC
1 TTTGAGCATCAAATGTCAAACC
*
101959 TTTGAGCATCAAATGCCAAACC
1 TTTGAGCATCAAATGTCAAACC
101981 TTTGA
1 TTTGA
101986 CCAAACATAA
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 46 1.00
ACGTcount: A:0.35, C:0.23, G:0.14, T:0.28
Consensus pattern (22 bp):
TTTGAGCATCAAATGTCAAACC
Found at i:102946 original size:36 final size:36
Alignment explanation
Indices: 102903--103184 Score: 312
Period size: 36 Copynumber: 8.0 Consensus size: 36
102893 ACTAGAAGAG
102903 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
*
102939 TTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAA
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
* * *
102975 TTTCGTCTATCTTGAGACAGTTTCCCTTGAAATAAA
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
103011 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
* * * * *
103047 ------ATAT-TTGA-ATATGTTTTCTTTGAAACAAA
1 TTTTGTCTCTCTTGAGACA-GTTTCCCTTGAAACAAA
* * ** * *
103076 TTTCGTCTCCCTTGAGACAGTTTCTTTTGGAACTAAG
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAAC-AAA
* *
103113 TTTTGTCTCTCTTGAGACAGTTTCTCTTGAAA-TAA
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
*
103148 TTTTCGTCTATCTTGAGACAGTTTCCCTTGAAACAAA
1 TTTT-GTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
103185 ATCTTTGAAT
Statistics
Matches: 204, Mismatches: 30, Indels: 23
0.79 0.12 0.09
Matches are distributed among these distances:
28 2 0.01
29 19 0.09
30 2 0.01
35 6 0.03
36 141 0.69
37 34 0.17
ACGTcount: A:0.26, C:0.19, G:0.14, T:0.41
Consensus pattern (36 bp):
TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
Found at i:102946 original size:71 final size:73
Alignment explanation
Indices: 102861--103184 Score: 239
Period size: 72 Copynumber: 4.6 Consensus size: 73
102851 GTTTTTCTTA
* * * * * *
102861 AAACAAGA-TTTGTCTCGCTTGAGACCGTTTTCACTAG-AA-GAGTTTTGTCTCTCTTGAGACAG
1 AAACAA-ATTTTGTCTCTCTTGAGACAGTTTTCACTAGAAACAAATTTCGTCTATCTTGAGACAG
102923 TTTCCCTTG
65 TTTCCCTTG
* *
102932 AAACAAATTTTGTCTCTCTTGAGACAG-TTTCTCTTGAAACAAATTTCGTCTATCTTGAGACAGT
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTTCACTAGAAACAAATTTCGTCTATCTTGAGACAGT
102996 TTCCCTTG
66 TTCCCTTG
* * * * *
103004 AAATAAATTTTGTCTCTCTTGAGACAG-TTTCCCTTGAAACAAA------ATAT-TTGA-ATATG
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTTCACTAGAAACAAATTTCGTCTATCTTGAGACA-G
* *
103060 TTTTCTTTG
65 TTTCCCTTG
* * ** * * * * *
103069 AAACAAATTTCGTCTCCCTTGAGACAG-TTTCTTTTGGAACTAAGTTTTGTCTCTCTTGAGACAG
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTTCACTAGAAAC-AAATTTCGTCTATCTTGAGACAG
*
103133 TTTCTCTTG
65 TTTCCCTTG
* * * *
103142 AAA-TAATTTTCGTCTATCTTGAGACAG-TTTCCCTTGAAACAAA
1 AAACAAATTTT-GTCTCTCTTGAGACAGTTTTCACTAGAAACAAA
103185 ATCTTTGAAT
Statistics
Matches: 204, Mismatches: 35, Indels: 27
0.77 0.13 0.10
Matches are distributed among these distances:
64 2 0.01
65 46 0.23
66 5 0.02
70 8 0.04
71 25 0.12
72 78 0.38
73 38 0.19
74 2 0.01
ACGTcount: A:0.27, C:0.19, G:0.15, T:0.39
Consensus pattern (73 bp):
AAACAAATTTTGTCTCTCTTGAGACAGTTTTCACTAGAAACAAATTTCGTCTATCTTGAGACAGT
TTCCCTTG
Found at i:103144 original size:102 final size:102
Alignment explanation
Indices: 102959--103144 Score: 293
Period size: 102 Copynumber: 1.8 Consensus size: 102
102949 CTTGAGACAG
*
102959 TTTCTCTTGAAACAAATTTCGTCTATCTTGAGACAGTTTCCCTTGAAATAAATTTTGTCTCTCTT
1 TTTCTCTTGAAACAAATTTCGTCTACCTTGAGACAGTTTCCCTTGAAATAAATTTTGTCTCTCTT
103024 GAGACAGTTTCCCTTGAAACAAAATATTTGAATATGT
66 GAGACAGTTTCCCTTGAAACAAAATATTTGAATATGT
* ** * *
103061 TTTCT-TTGAAACAAATTTCGTCTCCCTTGAGACAGTTTCTTTTGGAACTAAGTTTTGTCTCTCT
1 TTTCTCTTGAAACAAATTTCGTCTACCTTGAGACAGTTTCCCTT-GAAATAAATTTTGTCTCTCT
*
103125 TGAGACAGTTTCTCTTGAAA
65 TGAGACAGTTTCCCTTGAAA
103145 TAATTTTCGT
Statistics
Matches: 76, Mismatches: 7, Indels: 2
0.89 0.08 0.02
Matches are distributed among these distances:
101 34 0.45
102 42 0.55
ACGTcount: A:0.26, C:0.18, G:0.14, T:0.41
Consensus pattern (102 bp):
TTTCTCTTGAAACAAATTTCGTCTACCTTGAGACAGTTTCCCTTGAAATAAATTTTGTCTCTCTT
GAGACAGTTTCCCTTGAAACAAAATATTTGAATATGT
Found at i:103176 original size:138 final size:137
Alignment explanation
Indices: 102923--103247 Score: 463
Period size: 138 Copynumber: 2.4 Consensus size: 137
102913 CTTGAGACAG
*
102923 TTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAATTTCGTCTATCTT
1 TTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACAAATTTCGTCTATCTT
*
102988 GAGACAGTTTCCCTTGAAATAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATATTT
66 GAGACAGTTTCCCTTGAAATAAATTTTGTCTATCTTGAGACAGTTTCCCTTGAAACAAAATATTT
*
103053 GAATATG
131 GAATATA
* * * * * * * *
103060 TTTTCTTTGAAACAAATTTCGTCTCCCTTGAGACAGTTTCTTTTGGAACTAAGTTTTGTCTCTCT
1 TTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAAC-AAATTTCGTCTATCT
* *
103125 TGAGACAGTTTCTCTTGAAAT-AATTTTCGTCTATCTTGAGACAGTTTCCCTTGAAACAAAATCT
65 TGAGACAGTTTCCCTTGAAATAAATTTT-GTCTATCTTGAGACAGTTTCCCTTGAAACAAAATAT
*
103189 TTGAATTTA
129 TTGAATATA
* * * *
103198 TTTCCCCTAAAACAAATTTTGTCTCCCTTGAGACAATTACTCTTGAAACA
1 TTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACA
103248 CAAAATCTTC
Statistics
Matches: 163, Mismatches: 23, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
137 50 0.31
138 113 0.69
ACGTcount: A:0.28, C:0.20, G:0.13, T:0.40
Consensus pattern (137 bp):
TTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACAAATTTCGTCTATCTT
GAGACAGTTTCCCTTGAAATAAATTTTGTCTATCTTGAGACAGTTTCCCTTGAAACAAAATATTT
GAATATA
Found at i:103266 original size:67 final size:66
Alignment explanation
Indices: 103144--103299 Score: 197
Period size: 67 Copynumber: 2.3 Consensus size: 66
103134 TTCTCTTGAA
** * * **
103144 ATAATTTTCGTCTATCTTGAGACAGTTTCCCTTGAAACAAAATCTTTGAATTTATTTCCCCTAAA
1 ATAATTTT-GTCTCCCTTGAGACAATTACCCTTGAAACAAAATCTTCAAATTTATTTCCCCTAAA
103209 AC
65 AC
* *
103211 A-AATTTTGTCTCCCTTGAGACAATTACTCTTGAAACACAAAATCTTCAAATTTATTTCCCTTAA
1 ATAATTTTGTCTCCCTTGAGACAATTACCCTTG-AA-ACAAAATCTTCAAATTTATTTCCCCTAA
103275 AAC
64 AAC
*
103278 ATAATTTTGTTTCCCTTGAGAC
1 ATAATTTTGTCTCCCTTGAGAC
103300 CGTTTCTCAT
Statistics
Matches: 77, Mismatches: 9, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
65 20 0.26
66 8 0.10
67 30 0.39
68 19 0.25
ACGTcount: A:0.32, C:0.21, G:0.08, T:0.38
Consensus pattern (66 bp):
ATAATTTTGTCTCCCTTGAGACAATTACCCTTGAAACAAAATCTTCAAATTTATTTCCCCTAAAA
C
Found at i:104152 original size:105 final size:105
Alignment explanation
Indices: 103920--104685 Score: 1096
Period size: 105 Copynumber: 7.3 Consensus size: 105
103910 GCCATCTGCG
* * * * * *
103920 ATTTCAACTCCACGACGGAGGATATCGTGGCACTCGAGACAACACAAGTTCAACTTCACAACGAA
1 ATTTCAACTTCACAACGAAGGATAT--TGG-ACTCCAGACAACGCAAGTTCAACTTCACGACGAA
* * *
103985 GGGACGGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGACA
63 GGGACCGCTGCTTGTCAAC-AACAACTTCTCAATTTCAGAGCCA
* * *
104029 ATTTCAACTTCACAACGAAGGATATTAGACACTAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
* *
104094 ACCGCTGCCTGTCAACAACAACTTATCAATTTCAGAGCCA
66 ACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGAGCCA
104134 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
*
104199 ACCGCTGCTTGTCAACAACAACTTCTCAATTCCAGAGCCA
66 ACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGAGCCA
* *
104239 ATTTTAACTTCACAACGAAGGATATTGGACTTCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
* *
104304 ACCGCTGCTTGTCAACAACAACTTCCCAATCTCAGAGCCA
66 ACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGAGCCA
*
104344 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAATGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
* *
104409 ACCGCTGCTTGTCAACAACAACTTCCCAATCTCAGAGCCA
66 ACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGAGCCA
*
104449 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACAACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
* **
104514 ACCGCTGCTTGTCAA-AA-AAATT-TC-A-TTCAGATTCA
66 ACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGAGCCA
* * *
104549 ATTTCAACTTCACAACGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
* * * ** *
104614 ACGGCTGGTTGTCAACAAACAA-TTTTCCGGTTCCAGAGCCA
66 ACCGCTGCTTGTCAAC-AACAACTTCT-CAATTTCAGAGCCA
*
104655 ATTTCAACTTCACGAC-AGAGGATATTGGACT
1 ATTTCAACTTCACAACGA-AGGATATTGGACT
104686 TGGAACAATG
Statistics
Matches: 606, Mismatches: 43, Indels: 19
0.91 0.06 0.03
Matches are distributed among these distances:
100 83 0.14
101 1 0.00
102 5 0.01
103 7 0.01
104 3 0.00
105 402 0.66
106 81 0.13
107 2 0.00
109 22 0.04
ACGTcount: A:0.34, C:0.26, G:0.18, T:0.22
Consensus pattern (105 bp):
ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
ACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGAGCCA
Found at i:105277 original size:34 final size:34
Alignment explanation
Indices: 105234--105358 Score: 111
Period size: 34 Copynumber: 3.8 Consensus size: 34
105224 TTCGTCCTAC
105234 TAGGATTCAAACTCCTAAAAATAGGATAGAATTT
1 TAGGATTCAAACTCCTAAAAATAGGATAGAATTT
* * *
105268 TAGGATTCAAACTTCTAAAGATATGATAGAATTTT
1 TAGGATTCAAACTCCTAAAAATAGGATAGAA-TTT
*
105303 GCTAGGATTC--A-----AAAAATAGGATATAATTT
1 --TAGGATTCAAACTCCTAAAAATAGGATAGAATTT
* * *
105332 TATGATTTAAACTCCTAAAGATAGGAT
1 TAGGATTCAAACTCCTAAAAATAGGAT
105359 CCACAAGCAC
Statistics
Matches: 72, Mismatches: 9, Indels: 20
0.71 0.09 0.20
Matches are distributed among these distances:
27 6 0.08
29 4 0.06
30 12 0.17
34 38 0.53
35 4 0.06
37 8 0.11
ACGTcount: A:0.42, C:0.10, G:0.15, T:0.33
Consensus pattern (34 bp):
TAGGATTCAAACTCCTAAAAATAGGATAGAATTT
Found at i:105754 original size:18 final size:17
Alignment explanation
Indices: 105715--105757 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
105705 ATTATATGGA
105715 TATT-TTATTCATTTAT
1 TATTATTATTCATTTAT
*
105731 TTTTATTATTCATGTTAT
1 TATTATTATTCAT-TTAT
105749 TATTATTAT
1 TATTATTAT
105758 ATGTATATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 3 0.13
17 8 0.35
18 12 0.52
ACGTcount: A:0.26, C:0.05, G:0.02, T:0.67
Consensus pattern (17 bp):
TATTATTATTCATTTAT
Found at i:107163 original size:36 final size:36
Alignment explanation
Indices: 107106--107206 Score: 130
Period size: 37 Copynumber: 2.8 Consensus size: 36
107096 TTTTGTCCTA
*
107106 CTAGGATTCAAACTCTTAAAAATAGGATAGAATTCTG
1 CTAGGATTC-AACTCCTAAAAATAGGATAGAATTCTG
*
107143 CTAGGATTCAACTCCTAAAAATAGGATAGAATTTTG
1 CTAGGATTCAACTCCTAAAAATAGGATAGAATTCTG
** * *
107179 CTATGTTTTAAACTCCTAAAGATAGGAT
1 CTA-GGATTCAACTCCTAAAAATAGGAT
107207 CCACAAGCAC
Statistics
Matches: 57, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
36 28 0.49
37 29 0.51
ACGTcount: A:0.39, C:0.14, G:0.16, T:0.32
Consensus pattern (36 bp):
CTAGGATTCAACTCCTAAAAATAGGATAGAATTCTG
Found at i:107204 original size:37 final size:36
Alignment explanation
Indices: 107106--107206 Score: 130
Period size: 36 Copynumber: 2.8 Consensus size: 36
107096 TTTTGTCCTA
*
107106 CTAGGATTCAAACTCTTAAAAATAGGATAGAATTCTG
1 CTAGGATT-AAACTCCTAAAAATAGGATAGAATTCTG
* *
107143 CTAGGATTCAACTCCTAAAAATAGGATAGAATTTTG
1 CTAGGATTAAACTCCTAAAAATAGGATAGAATTCTG
** *
107179 CTATGTTTTAAACTCCTAAAGATAGGAT
1 CTA-GGATTAAACTCCTAAAAATAGGAT
107207 CCACAAGCAC
Statistics
Matches: 56, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
36 28 0.50
37 28 0.50
ACGTcount: A:0.39, C:0.14, G:0.16, T:0.32
Consensus pattern (36 bp):
CTAGGATTAAACTCCTAAAAATAGGATAGAATTCTG
Found at i:107637 original size:11 final size:11
Alignment explanation
Indices: 107617--107700 Score: 55
Period size: 11 Copynumber: 7.3 Consensus size: 11
107607 TTAATTATTT
*
107617 TTATTCTAATA
1 TTATTTTAATA
*
107628 TTATTTTAATG
1 TTATTTTAATA
107639 TT-TTTTAA-A
1 TTATTTTAATA
*
107648 GTTATTATATATA
1 -TTATTTTA-ATA
107661 TATATTTATAACTA
1 T-TATTT-TAA-TA
*
107675 TTATATTTATTA
1 TTAT-TTTAATA
*
107687 TTATTTTACTA
1 TTATTTTAATA
107698 TTA
1 TTA
107701 ACGTATATAA
Statistics
Matches: 58, Mismatches: 7, Indels: 16
0.72 0.09 0.20
Matches are distributed among these distances:
10 8 0.14
11 24 0.41
12 8 0.14
13 11 0.19
14 7 0.12
ACGTcount: A:0.35, C:0.04, G:0.02, T:0.60
Consensus pattern (11 bp):
TTATTTTAATA
Found at i:107691 original size:15 final size:15
Alignment explanation
Indices: 107649--107691 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 15
107639 TTTTTTAAAG
107649 TTATTATATATATATAT
1 TTATTAT-TAT-TATAT
* *
107666 TTATAACTATTATAT
1 TTATTATTATTATAT
107681 TTATTATTATT
1 TTATTATTATT
107692 TTACTATTAA
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
15 14 0.64
16 3 0.14
17 5 0.23
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.60
Consensus pattern (15 bp):
TTATTATTATTATAT
Found at i:107919 original size:21 final size:24
Alignment explanation
Indices: 107871--107919 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
107861 TGTATTTATA
* *
107871 TTATTACATTATTATTATTTTACT
1 TTATTAAATTATTATTATTTTACG
107895 TTATTAAATTATT-TT-TTTT-CG
1 TTATTAAATTATTATTATTTTACG
107916 TTAT
1 TTAT
107920 AATATTTATT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
21 5 0.22
22 4 0.17
23 2 0.09
24 12 0.52
ACGTcount: A:0.27, C:0.06, G:0.02, T:0.65
Consensus pattern (24 bp):
TTATTAAATTATTATTATTTTACG
Found at i:111275 original size:27 final size:27
Alignment explanation
Indices: 111241--111299 Score: 68
Period size: 27 Copynumber: 2.2 Consensus size: 27
111231 GGGTAAAAAG
*
111241 AAAAAAGAA-AAGAAGCAAAAAAGGAA-
1 AAAAAAGAACAA-AAACAAAAAAGGAAC
*
111267 AAAACAAGAACAAAAATAAAAAAGGAAC
1 AAAA-AAGAACAAAAACAAAAAAGGAAC
111295 AAAAA
1 AAAAA
111300 GCACATGCAA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
26 4 0.14
27 18 0.64
28 6 0.21
ACGTcount: A:0.78, C:0.07, G:0.14, T:0.02
Consensus pattern (27 bp):
AAAAAAGAACAAAAACAAAAAAGGAAC
Found at i:112875 original size:36 final size:36
Alignment explanation
Indices: 112832--113110 Score: 279
Period size: 36 Copynumber: 7.9 Consensus size: 36
112822 ACTAGAAGAG
*
112832 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
1 TTTTGTCTATCTTGAGACAGTTTCCCTTGAAACAAA
*
112868 TTTTGTCTATCTTGAGACAGTTTCTCTTGAAACAAA
1 TTTTGTCTATCTTGAGACAGTTTCCCTTGAAACAAA
* *
112904 TTTCGTCTATCTTGAGACAGTTTCCCTTGAAATAAA
1 TTTTGTCTATCTTGAGACAGTTTCCCTTGAAACAAA
* *
112940 TTTTTTTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
1 -TTTTGTCTATCTTGAGACAGTTTCCCTTGAAACAAA
* * * *
112977 ------ATAT-TTGA-ATATGTTTTCTTTGAAACAAA
1 TTTTGTCTATCTTGAGACA-GTTTCCCTTGAAACAAA
* ** ** * *
113006 TTTCGTCTCCCTTGAGACAGTTTCTTTTGGAACTAAG
1 TTTTGTCTATCTTGAGACAGTTTCCCTTGAAAC-AAA
* *
113043 TTTTGTCTCTCTTGAGACAGTTTCTCTTGAAAC-AA
1 TTTTGTCTATCTTGAGACAGTTTCCCTTGAAACAAA
*
113078 TTTTCGTCTATCTTGAGACAGTTTCCCTAGAAA
1 TTTT-GTCTATCTTGAGACAGTTTCCCTTGAAA
113111 TAAAATCTTT
Statistics
Matches: 201, Mismatches: 30, Indels: 24
0.79 0.12 0.09
Matches are distributed among these distances:
28 2 0.01
29 19 0.09
30 2 0.01
35 6 0.03
36 107 0.53
37 65 0.32
ACGTcount: A:0.26, C:0.19, G:0.14, T:0.41
Consensus pattern (36 bp):
TTTTGTCTATCTTGAGACAGTTTCCCTTGAAACAAA
Found at i:112875 original size:71 final size:73
Alignment explanation
Indices: 112790--113110 Score: 224
Period size: 73 Copynumber: 4.5 Consensus size: 73
112780 GTTTTTCTTA
* * * * * *
112790 AAACAAGA-TTTGTCTCGCTTGAGACCGTTTTCACTAG-AA-GAGTTTTGTCTCTCTTGAGACAG
1 AAACAA-ATTTTGTCTCTCTTGAGACAGTTTTCACTAGAAACAAATTTCGTCTATCTTGAGACAG
112852 TTTCCCTTG
65 TTTCCCTTG
* * *
112861 AAACAAATTTTGTCTATCTTGAGACAG-TTTCTCTTGAAACAAATTTCGTCTATCTTGAGACAGT
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTTCACTAGAAACAAATTTCGTCTATCTTGAGACAGT
112925 TTCCCTTG
66 TTCCCTTG
* * * * * *
112933 AAATAAATTTTTTTCTCTCTTGAGACAG-TTTCCCTTGAAACAAA------ATAT-TTGA-ATAT
1 AAACAAA-TTTTGTCTCTCTTGAGACAGTTTTCACTAGAAACAAATTTCGTCTATCTTGAGACA-
* *
112989 GTTTTCTTTG
64 GTTTCCCTTG
* * ** * * * * *
112999 AAACAAATTTCGTCTCCCTTGAGACAG-TTTCTTTTGGAACTAAGTTTTGTCTCTCTTGAGACAG
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTTCACTAGAAAC-AAATTTCGTCTATCTTGAGACAG
*
113063 TTTCTCTTG
65 TTTCCCTTG
* *
113072 AAAC-AATTTTCGTCTATCTTGAGACAG-TTTCCCTAGAAA
1 AAACAAATTTT-GTCTCTCTTGAGACAGTTTTCACTAGAAA
113111 TAAAATCTTT
Statistics
Matches: 197, Mismatches: 38, Indels: 28
0.75 0.14 0.11
Matches are distributed among these distances:
65 29 0.15
66 20 0.10
67 3 0.02
70 8 0.04
71 24 0.12
72 41 0.21
73 70 0.36
74 2 0.01
ACGTcount: A:0.26, C:0.19, G:0.15, T:0.40
Consensus pattern (73 bp):
AAACAAATTTTGTCTCTCTTGAGACAGTTTTCACTAGAAACAAATTTCGTCTATCTTGAGACAGT
TTCCCTTG
Found at i:112918 original size:21 final size:20
Alignment explanation
Indices: 112857--112918 Score: 53
Period size: 21 Copynumber: 3.2 Consensus size: 20
112847 GACAGTTTCC
112857 CTTGAAACAAATTTTGTCTAT
1 CTTGAAACAAA-TTTGTCTAT
* *
112878 CTTGAGAC--AGTT-TC--T
1 CTTGAAACAAATTTGTCTAT
112893 CTTGAAACAAATTTCGTCTAT
1 CTTGAAACAAATTT-GTCTAT
112914 CTTGA
1 CTTGA
112919 GACAGTTTCC
Statistics
Matches: 31, Mismatches: 4, Indels: 12
0.66 0.09 0.26
Matches are distributed among these distances:
15 8 0.26
17 5 0.16
18 2 0.06
19 3 0.10
21 13 0.42
ACGTcount: A:0.29, C:0.18, G:0.13, T:0.40
Consensus pattern (20 bp):
CTTGAAACAAATTTGTCTAT
Found at i:113028 original size:102 final size:103
Alignment explanation
Indices: 112830--113077 Score: 297
Period size: 102 Copynumber: 2.4 Consensus size: 103
112820 TCACTAGAAG
* *
112830 AGTTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTATCTTGAGACA-G-TTTCT
1 AGTTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA------ATAT-TTGA-ATATGTTTTCT
*
112893 CTTGAAACAAATTTCGTCTATCTTGAGACAGTTTCCCTT-GAAATAA
58 CTTGAAACAAATTTCGTCTACCTTGAGACAGTTTCCCTTGGAAAT-A
* *
112939 ATTTTTTTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATATTTGAATATGTTTTCT-TTGAAAC
1 AGTTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATATTTGAATATGTTTTCTCTTGAAAC
* ** *
113003 AAATTTCGTCTCCCTTGAGACAGTTTCTTTTGGAACTA
66 AAATTTCGTCTACCTTGAGACAGTTTCCCTTGGAAATA
*
113041 AGTTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAA
1 AGTTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAA
113078 TTTTCGTCTA
Statistics
Matches: 124, Mismatches: 12, Indels: 13
0.83 0.08 0.09
Matches are distributed among these distances:
101 2 0.02
102 74 0.60
103 12 0.10
109 36 0.29
ACGTcount: A:0.26, C:0.19, G:0.14, T:0.41
Consensus pattern (103 bp):
AGTTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATATTTGAATATGTTTTCTCTTGAAAC
AAATTTCGTCTACCTTGAGACAGTTTCCCTTGGAAATA
Found at i:113057 original size:37 final size:36
Alignment explanation
Indices: 112991--113102 Score: 147
Period size: 37 Copynumber: 3.1 Consensus size: 36
112981 TTGAATATGT
* *
112991 TTTCT-TTGAAACAAATTTCGTCTCCCTTGAGACAG
1 TTTCTCTTGAAACAATTTTCGTCTCTCTTGAGACAG
* *
113026 TTTCTTTTGGAACTAAGTTTT-GTCTCTCTTGAGACAG
1 TTTCTCTTGAAAC-AA-TTTTCGTCTCTCTTGAGACAG
*
113063 TTTCTCTTGAAACAATTTTCGTCTATCTTGAGACAG
1 TTTCTCTTGAAACAATTTTCGTCTCTCTTGAGACAG
113099 TTTC
1 TTTC
113103 CCTAGAAATA
Statistics
Matches: 67, Mismatches: 6, Indels: 7
0.84 0.08 0.09
Matches are distributed among these distances:
35 9 0.13
36 27 0.40
37 28 0.42
38 3 0.04
ACGTcount: A:0.22, C:0.20, G:0.15, T:0.43
Consensus pattern (36 bp):
TTTCTCTTGAAACAATTTTCGTCTCTCTTGAGACAG
Found at i:113116 original size:138 final size:138
Alignment explanation
Indices: 112852--113177 Score: 429
Period size: 138 Copynumber: 2.4 Consensus size: 138
112842 CTTGAGACAG
**
112852 TTTCCCTTGAAACAAATTTTGTCTATCTTGAGACAGTTTCTCTTGAAACAAATTTCGTCTATCTT
1 TTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACAAATTTCGTCTATCTT
** * *
112917 GAGACAGTTTCCCTTGAAATAAATTTTTTTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATATT
66 GAGACAGTTTCCCTTGAAATAAATTTTCGTCTATCTTGAGACAGTTTCCCTAGAAACAAAATATT
*
112982 TGAATATG
131 TGAATATA
* * * * * * * *
112990 TTTTCTTTGAAACAAATTTCGTCTCCCTTGAGACAGTTTCTTTTGGAACTAAGTTTTGTCTCTCT
1 TTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAAC-AAATTTCGTCTATCT
* * * *
113055 TGAGACAGTTTCTCTTGAAA-CAATTTTCGTCTATCTTGAGACAGTTTCCCTAGAAATAAAATCT
65 TGAGACAGTTTCCCTTGAAATAAATTTTCGTCTATCTTGAGACAGTTTCCCTAGAAACAAAATAT
*
113119 TTGAATTTA
130 TTGAATATA
* * *
113128 TTTCCCCTAAAACAAATTTTGTCTCCCTTGAGACAGTTACTCTTGAAACA
1 TTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACA
113178 CAAAATCTTC
Statistics
Matches: 159, Mismatches: 28, Indels: 3
0.84 0.15 0.02
Matches are distributed among these distances:
137 1 0.01
138 127 0.80
139 31 0.19
ACGTcount: A:0.28, C:0.19, G:0.13, T:0.40
Consensus pattern (138 bp):
TTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACAAATTTCGTCTATCTT
GAGACAGTTTCCCTTGAAATAAATTTTCGTCTATCTTGAGACAGTTTCCCTAGAAACAAAATATT
TGAATATA
Found at i:114010 original size:106 final size:105
Alignment explanation
Indices: 113850--114303 Score: 515
Period size: 106 Copynumber: 4.3 Consensus size: 105
113840 GCCATCCGCG
* * *
113850 ATTTCAACTCCACGACGGAGGATATCGTGGCACTCGAGACAACACAAGTTCAACTTCACAACGAA
1 ATTTCAACTTCACAACGAAGGATAT--TGG-ACTCGAGACAACACAAGTTCAACTTCACAACGAA
* * *
113915 GGGACGACTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCA
63 GGGACGGCTGATTGTCAAC-AACAATTTCTCAATTTCAGAGCCA
* * * *
113959 ATTTCAACTTCACAATGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAACGAAGGG
* * *
114024 ACCGCTGCTTGTCAACAACAATTTTTCAAATTTCAGAGCCA
66 ACGGCTGATTGTCAACAACAATTTCTC-AATTTCAGAGCCA
* *
114065 ATTTCAACTTCACAGCGAAGGATATTGGACTCGAGAAAACACAAGTTCAACTTCACAACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAACGAAGGG
* * * *
114130 ATGGCTGATTGTCAACAA-GATTT-T---GTTCAGAGTCA
66 ACGGCTGATTGTCAACAACAATTTCTCAATTTCAGAGCCA
* * * * *
114165 ATTTCAACTTCACAGCGAAGGATATTAGACTCGAGACAGCACAAGCTCAACTTCACAGCGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAACGAAGGG
* * * ** * *
114230 GCGGCTGACTGTCAACAAACAATTTCCCGGTTCCAGAACCA
66 ACGGCTGATTGTCAAC-AACAATTTCTCAATTTCAGAGCCA
*
114271 ATTTCAACTTCACAGC-AGAGGATATTGGACTCG
1 ATTTCAACTTCACAACGA-AGGATATTGGACTCG
114304 GAACAATATT
Statistics
Matches: 298, Mismatches: 39, Indels: 19
0.84 0.11 0.05
Matches are distributed among these distances:
100 82 0.28
101 2 0.01
102 4 0.01
104 1 0.00
105 14 0.05
106 171 0.57
107 3 0.01
109 21 0.07
ACGTcount: A:0.34, C:0.24, G:0.20, T:0.22
Consensus pattern (105 bp):
ATTTCAACTTCACAACGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAACGAAGGG
ACGGCTGATTGTCAACAACAATTTCTCAATTTCAGAGCCA
Found at i:114245 original size:206 final size:210
Alignment explanation
Indices: 113850--114303 Score: 532
Period size: 206 Copynumber: 2.2 Consensus size: 210
113840 GCCATCCGCG
* * *
113850 ATTTCAACTCCAC-GACGGAGGATATCGTGGCACTCGAGACAACACAAGTTCAACTTCACAACGA
1 ATTTCAACTTCACAG-CGAAGGATAT--TGG-ACTCGAGAAAACACAAGTTCAACTTCACAACGA
* *
113914 AGGGACGACTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAATGAAG
62 AGGGACGACTGATTGTCAACAAACAACTTCT--ATTTCAGAGCCAATTTCAACTTCACAACGAAG
* * *
113979 GATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAAC-AAC
125 GATATTAGACTCCAGACAACACAAGCTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAAAC
* * *
114043 AATTTTTCAAATTTCAGAGCCA
190 AA-TTTCCAAATTCCAGAACCA
114065 ATTTCAACTTCACAGCGAAGGATATTGGACTCGAGAAAACACAAGTTCAACTTCACAACGAAGGG
1 ATTTCAACTTCACAGCGAAGGATATTGGACTCGAGAAAACACAAGTTCAACTTCACAACGAAGGG
* * * * *
114130 ATGGCTGATTGTCAAC-AA-GA-TT-T-TGTTCAGAGTCAATTTCAACTTCACAGCGAAGGATAT
66 ACGACTGATTGTCAACAAACAACTTCTAT-TTCAGAGCCAATTTCAACTTCACAACGAAGGATAT
* * * *
114190 TAGACTCGAGACAGCACAAGCTCAACTTCAC-AGCGAAGGGGCGGCTGAC-TGTCAACAAACAAT
130 TAGACTCCAGACAACACAAGCTCAACTTCACGA-CGAAGGGACCGCTG-CTTGTCAACAAACAAT
***
114253 TTCCCGGTTCCAGAACCA
193 TTCCAAATTCCAGAACCA
114271 ATTTCAACTTCACAGC-AGAGGATATTGGACTCG
1 ATTTCAACTTCACAGCGA-AGGATATTGGACTCG
114304 GAACAATATT
Statistics
Matches: 210, Mismatches: 23, Indels: 21
0.83 0.09 0.08
Matches are distributed among these distances:
205 3 0.01
206 121 0.58
207 6 0.03
208 1 0.00
209 2 0.01
210 1 0.00
211 2 0.01
212 49 0.23
213 3 0.01
215 21 0.10
216 1 0.00
ACGTcount: A:0.34, C:0.24, G:0.20, T:0.22
Consensus pattern (210 bp):
ATTTCAACTTCACAGCGAAGGATATTGGACTCGAGAAAACACAAGTTCAACTTCACAACGAAGGG
ACGACTGATTGTCAACAAACAACTTCTATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATT
AGACTCCAGACAACACAAGCTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAAACAATTTC
CAAATTCCAGAACCA
Found at i:114821 original size:36 final size:37
Alignment explanation
Indices: 114764--114833 Score: 117
Period size: 36 Copynumber: 1.9 Consensus size: 37
114754 TTTTGTCCTA
114764 CTAGGATTCAAACTCTCAAAAATAGGATAGAATTCTG
1 CTAGGATTCAAACTCTCAAAAATAGGATAGAATTCTG
114801 CTAGGATTC-AACTC-CTAAAAATAGGATAGAATT
1 CTAGGATTCAAACTCTC-AAAAATAGGATAGAATT
114834 TTACTATGTT
Statistics
Matches: 32, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
35 1 0.03
36 22 0.69
37 9 0.28
ACGTcount: A:0.41, C:0.16, G:0.16, T:0.27
Consensus pattern (37 bp):
CTAGGATTCAAACTCTCAAAAATAGGATAGAATTCTG
Found at i:115295 original size:11 final size:11
Alignment explanation
Indices: 115275--115360 Score: 50
Period size: 11 Copynumber: 7.3 Consensus size: 11
115265 TTAATTATTT
*
115275 TTATTCTAATA
1 TTATTTTAATA
*
115286 TTATTTTAATG
1 TTATTTTAATA
115297 TT-TTTTAA-A
1 TTATTTTAATA
115306 GTTATTATATATATA
1 -TTATT-T-TA-ATA
115321 TATATTTATAACTA
1 T-TATTT-TAA-TA
*
115335 TTATATTTATTA
1 TTAT-TTTAATA
*
115347 TTATTTTACTA
1 TTATTTTAATA
115358 TTA
1 TTA
115361 ACGTATATAA
Statistics
Matches: 61, Mismatches: 5, Indels: 18
0.73 0.06 0.21
Matches are distributed among these distances:
10 8 0.13
11 22 0.36
12 7 0.11
13 8 0.13
14 11 0.18
15 5 0.08
ACGTcount: A:0.35, C:0.03, G:0.02, T:0.59
Consensus pattern (11 bp):
TTATTTTAATA
Found at i:115550 original size:16 final size:16
Alignment explanation
Indices: 115529--115562 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
115519 CATGTATTTA
115529 TATTATATTACATTAT
1 TATTATATTACATTAT
* *
115545 TATTATTTTACTTTAT
1 TATTATATTACATTAT
115561 TA
1 TA
115563 AATTATTTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.32, C:0.06, G:0.00, T:0.62
Consensus pattern (16 bp):
TATTATATTACATTAT
Found at i:118240 original size:22 final size:22
Alignment explanation
Indices: 118215--118275 Score: 68
Period size: 22 Copynumber: 2.8 Consensus size: 22
118205 CAACACATGG
118215 AAGTGCCTTAGCACTGGCACAA
1 AAGTGCCTTAGCACTGGCACAA
* * ***
118237 AAGTGCATTCGCACTAATACAA
1 AAGTGCCTTAGCACTGGCACAA
*
118259 AAGTGCCTTAACACTGG
1 AAGTGCCTTAGCACTGG
118276 GGAGAGAATC
Statistics
Matches: 29, Mismatches: 10, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.34, C:0.25, G:0.20, T:0.21
Consensus pattern (22 bp):
AAGTGCCTTAGCACTGGCACAA
Found at i:145188 original size:19 final size:18
Alignment explanation
Indices: 145164--145200 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
145154 TAAATAAGGA
*
145164 CGTATTTTGTAACATATGT
1 CGTATTTTATAAC-TATGT
145183 CGTATTTTATAACTATGT
1 CGTATTTTATAACTATGT
145201 TATTGTTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.27, C:0.11, G:0.14, T:0.49
Consensus pattern (18 bp):
CGTATTTTATAACTATGT
Found at i:147332 original size:40 final size:38
Alignment explanation
Indices: 147286--147367 Score: 105
Period size: 38 Copynumber: 2.1 Consensus size: 38
147276 TTCATGCATA
147286 TAAATGATGTATTATGATCTTATATG-A-TTTCAATAAGTTT
1 TAAATGATGTA-TATGA---TATATGAATTTTCAATAAGTTT
*
147326 TAAATGATGTATATGATATTTGAATTTTCAATAAGTTT
1 TAAATGATGTATATGATATATGAATTTTCAATAAGTTT
147364 TAAA
1 TAAA
147368 GCGTCAAATG
Statistics
Matches: 39, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
36 5 0.13
37 1 0.03
38 17 0.44
39 5 0.13
40 11 0.28
ACGTcount: A:0.38, C:0.04, G:0.12, T:0.46
Consensus pattern (38 bp):
TAAATGATGTATATGATATATGAATTTTCAATAAGTTT
Found at i:147717 original size:25 final size:26
Alignment explanation
Indices: 147688--147745 Score: 68
Period size: 26 Copynumber: 2.3 Consensus size: 26
147678 AATAAAACCT
147688 TAAATTTAGA-TT-AAAA-TTAAAAAA
1 TAAATTTA-ATTTAAAAATTTAAAAAA
*
147712 TCAAATTTAATTTAAAAATTTTAAAAA
1 T-AAATTTAATTTAAAAATTTAAAAAA
147739 TAAATTT
1 TAAATTT
147746 CAAGAACAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
24 2 0.07
25 9 0.31
26 10 0.34
27 8 0.28
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.40
Consensus pattern (26 bp):
TAAATTTAATTTAAAAATTTAAAAAA
Found at i:154616 original size:49 final size:48
Alignment explanation
Indices: 154562--154704 Score: 164
Period size: 49 Copynumber: 2.9 Consensus size: 48
154552 TTTTCTTCCC
* *
154562 TTTTTTATTTTTCAATTTAGAGCGCCCTTTCGGGTTTTCACCCTAAATA
1 TTTTTT-TTTTTCAACTTAGAGCGCCCTTTCGGGTTTTCACCCTAAACA
*
154611 TTTTTTTTACTTCAACTTA-AGGCGCCCTTTCGGGTTTTCACCCTAAACA
1 TTTTTTTT-TTTCAACTTAGA-GCGCCCTTTCGGGTTTTCACCCTAAACA
* * * * *
154660 TTTTTTTGCTTT-AACTTAGGGAGCACTTTCAGGTTTTCACCCTAA
1 TTTTTTT-TTTTCAACTTAGAGCGCCCTTTCGGGTTTTCACCCTAA
154705 GCAAAGTATT
Statistics
Matches: 81, Mismatches: 9, Indels: 9
0.82 0.09 0.09
Matches are distributed among these distances:
48 31 0.38
49 50 0.62
ACGTcount: A:0.20, C:0.22, G:0.13, T:0.44
Consensus pattern (48 bp):
TTTTTTTTTTTCAACTTAGAGCGCCCTTTCGGGTTTTCACCCTAAACA
Found at i:154617 original size:50 final size:49
Alignment explanation
Indices: 154583--154704 Score: 174
Period size: 48 Copynumber: 2.5 Consensus size: 49
154573 TCAATTTAGA
*
154583 GCGCCCTTTCGGGTTTTCACCCTAAATATTTTTTTTACTTCAACTTAAG
1 GCGCCCTTTCGGGTTTTCACCCTAAACATTTTTTTTACTTCAACTTAAG
* * *
154632 GCGCCCTTTCGGGTTTTCACCCTAAACA-TTTTTTTGCTTTAACTTAGG
1 GCGCCCTTTCGGGTTTTCACCCTAAACATTTTTTTTACTTCAACTTAAG
* * *
154680 GAGCACTTTCAGGTTTTCACCCTAA
1 GCGCCCTTTCGGGTTTTCACCCTAA
154705 GCAAAGTATT
Statistics
Matches: 66, Mismatches: 7, Indels: 1
0.89 0.09 0.01
Matches are distributed among these distances:
48 39 0.59
49 27 0.41
ACGTcount: A:0.20, C:0.25, G:0.15, T:0.40
Consensus pattern (49 bp):
GCGCCCTTTCGGGTTTTCACCCTAAACATTTTTTTTACTTCAACTTAAG
Found at i:157480 original size:19 final size:19
Alignment explanation
Indices: 157456--157493 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
157446 TCCCTTACTA
157456 GAGATAGCGTAGGGCACCT
1 GAGATAGCGTAGGGCACCT
*
157475 GAGATAGTGTAGGGCACCT
1 GAGATAGCGTAGGGCACCT
157494 TAGTAGACTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.26, C:0.18, G:0.37, T:0.18
Consensus pattern (19 bp):
GAGATAGCGTAGGGCACCT
Done.