Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002582.1 Hibiscus syriacus cultivar Beakdansim tig00005228_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: 124688
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.32
Found at i:102 original size:42 final size:43
Alignment explanation
Indices: 43--126 Score: 118
Period size: 42 Copynumber: 2.0 Consensus size: 43
33 ATAAATATTA
*
43 ATTAATAATTTGATATTTTTAATTATTTATTA-AAAATTAATAG
1 ATTAATAATTTGATATTTTT-ATTATCTATTAGAAAATTAATAG
* *
86 ATTATTAATTT-ATATTTTTATTATCTATTAGTAAATTAATA
1 ATTAATAATTTGATATTTTTATTATCTATTAGAAAATTAATA
127 ATTTTATGAA
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
41 10 0.27
42 17 0.46
43 10 0.27
ACGTcount: A:0.42, C:0.01, G:0.04, T:0.54
Consensus pattern (43 bp):
ATTAATAATTTGATATTTTTATTATCTATTAGAAAATTAATAG
Found at i:3834 original size:11 final size:11
Alignment explanation
Indices: 3820--3844 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
3810 ACTTTTCAAG
3820 TTCTTTTATTT
1 TTCTTTTATTT
3831 TTCTTTTATTT
1 TTCTTTTATTT
3842 TTC
1 TTC
3845 AATATGCTAA
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:0.08, C:0.12, G:0.00, T:0.80
Consensus pattern (11 bp):
TTCTTTTATTT
Found at i:8682 original size:20 final size:21
Alignment explanation
Indices: 8643--8687 Score: 65
Period size: 20 Copynumber: 2.1 Consensus size: 21
8633 AGTTGTGGTT
8643 AAAATAAAAATAAGAATTAAATA
1 AAAATAAAAAT-A-AATTAAATA
8666 AAAATAAAAAT-AATTAAATA
1 AAAATAAAAATAAATTAAATA
8686 AA
1 AA
8688 CAAATTAAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 11 0.50
23 11 0.50
ACGTcount: A:0.76, C:0.00, G:0.02, T:0.22
Consensus pattern (21 bp):
AAAATAAAAATAAATTAAATA
Found at i:9428 original size:74 final size:75
Alignment explanation
Indices: 9350--9495 Score: 224
Period size: 75 Copynumber: 2.0 Consensus size: 75
9340 TTCTAAATCC
*
9350 TAATTAAAATACT-AAAACTATTTAAACTAAAATACAAAGATAAAGATAAAAT-ATAAAAATAAT
1 TAATTAAAATACTAAAAACTATTTAAACTAAAATAAAAAGATAAA-ATAAAATGATAAAAATAAT
9413 ATCCTAAAAAT
65 ATCCTAAAAAT
* * * *
9424 TAATTAAAATACTAAAAACTATTTAAACTAAAATAAAAAGATAAAATATAATGTTTAAAATATTA
1 TAATTAAAATACTAAAAACTATTTAAACTAAAATAAAAAGATAAAATAAAATGATAAAAATAATA
9489 TCCTAAA
66 TCCTAAA
9496 TTTGAGTTTA
Statistics
Matches: 65, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
74 19 0.29
75 46 0.71
ACGTcount: A:0.60, C:0.08, G:0.03, T:0.29
Consensus pattern (75 bp):
TAATTAAAATACTAAAAACTATTTAAACTAAAATAAAAAGATAAAATAAAATGATAAAAATAATA
TCCTAAAAAT
Found at i:11344 original size:19 final size:20
Alignment explanation
Indices: 11308--11346 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
11298 AAAGTTCGCT
* *
11308 AAAAAAATAAAACGAAAATA
1 AAAAAAACAAAACAAAAATA
11328 AAAAAAACAAAA-AAAAATA
1 AAAAAAACAAAACAAAAATA
11347 TAACGAAATG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.85, C:0.05, G:0.03, T:0.08
Consensus pattern (20 bp):
AAAAAAACAAAACAAAAATA
Found at i:13065 original size:129 final size:130
Alignment explanation
Indices: 12834--13087 Score: 483
Period size: 129 Copynumber: 2.0 Consensus size: 130
12824 ATTTCCAAGT
12834 TAAATTCCTGTAAAAGCAGGATCCACCGGATAAGCCTTGGTTTTACTTCCTTTTTGCTCATCAAA
1 TAAATTCCTGTAAAAGCAGGATCCACCGGATAAGCCTTGGTTTTACTTCCTTTTTGCTCATCAAA
12899 TACCTTATAGTTGCATGATAAGAAAAAACAGTAATTTTAGTACCAAGCAAATAGGATCTACCGGA
66 TACCTTATAGTTGCATGATAAGAAAAAACAGTAATTTTAGTACCAAGCAAATAGGATCTACCGGA
*
12964 TAAATTCCTGTAAAAGCAGGATCCACCGGATAAGCTTTGGTTTTACTT-CTTTTTGCTCATCAAA
1 TAAATTCCTGTAAAAGCAGGATCCACCGGATAAGCCTTGGTTTTACTTCCTTTTTGCTCATCAAA
*
13028 TACCTTATAGTTGCATGATAAGAAAAAACAGTAATTTTAGTACCAGGCAAATAGGATCTA
66 TACCTTATAGTTGCATGATAAGAAAAAACAGTAATTTTAGTACCAAGCAAATAGGATCTA
13088 AATTTTTCTA
Statistics
Matches: 122, Mismatches: 2, Indels: 1
0.98 0.02 0.01
Matches are distributed among these distances:
129 75 0.61
130 47 0.39
ACGTcount: A:0.35, C:0.18, G:0.16, T:0.31
Consensus pattern (130 bp):
TAAATTCCTGTAAAAGCAGGATCCACCGGATAAGCCTTGGTTTTACTTCCTTTTTGCTCATCAAA
TACCTTATAGTTGCATGATAAGAAAAAACAGTAATTTTAGTACCAAGCAAATAGGATCTACCGGA
Found at i:17165 original size:18 final size:18
Alignment explanation
Indices: 17144--17178 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
17134 GTTGTGGTTA
17144 AAATAAAA-AATAAGAATT
1 AAATAAAAGAA-AAGAATT
17162 AAATAAAAGAAAAGAAT
1 AAATAAAAGAAAAGAAT
17179 AATTAAATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.74, C:0.00, G:0.09, T:0.17
Consensus pattern (18 bp):
AAATAAAAGAAAAGAATT
Found at i:17933 original size:75 final size:76
Alignment explanation
Indices: 17854--18001 Score: 228
Period size: 76 Copynumber: 2.0 Consensus size: 76
17844 ATCTAAATCC
*
17854 TAATTAAAATACT-AAAATCTATTTAAACTAAAATACAAAGATAAAGATAAAAT-ATAAAAATAA
1 TAATTAAAATACTAAAAACCTATTTAAACTAAAATACAAAGATAAA-ATAAAATGATAAAAATAA
17917 TATCCTAAAAAT
65 TATCCTAAAAAT
* * * *
17929 TAATTAAAATACTAAAAACCTATTTAAACTAAAATACAAAGATAAAATATAATGTTTAAAATATT
1 TAATTAAAATACTAAAAACCTATTTAAACTAAAATACAAAGATAAAATAAAATGATAAAAATAAT
17994 ATCCTAAA
66 ATCCTAAA
18002 TTTGAGTTTA
Statistics
Matches: 66, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
75 19 0.29
76 47 0.71
ACGTcount: A:0.59, C:0.09, G:0.03, T:0.30
Consensus pattern (76 bp):
TAATTAAAATACTAAAAACCTATTTAAACTAAAATACAAAGATAAAATAAAATGATAAAAATAAT
ATCCTAAAAAT
Found at i:24173 original size:35 final size:35
Alignment explanation
Indices: 24110--24245 Score: 170
Period size: 35 Copynumber: 3.9 Consensus size: 35
24100 TGAATAAGAA
*
24110 GAACGAAAGGAAGCAT---CACTTTCGATTCAAGT
1 GAACGGAAGGAAGCATCGGCACTTTCGATTCAAGT
* * *
24142 GAACGGATGGAAGCATCGGTACTTTCGATTCAAGAA
1 GAACGGAAGGAAGCATCGGCACTTTCGATTCAAG-T
*
24178 GAACGGAAGGAAGCATGGGCACTTTCGATTCAAGT
1 GAACGGAAGGAAGCATCGGCACTTTCGATTCAAGT
* **
24213 GAACGGAAGGAAGTATCAACACTTTCGATTCAA
1 GAACGGAAGGAAGCATCGGCACTTTCGATTCAA
24246 TTGTTCATCT
Statistics
Matches: 88, Mismatches: 12, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
32 14 0.16
35 43 0.49
36 31 0.35
ACGTcount: A:0.35, C:0.18, G:0.26, T:0.21
Consensus pattern (35 bp):
GAACGGAAGGAAGCATCGGCACTTTCGATTCAAGT
Found at i:24218 original size:71 final size:68
Alignment explanation
Indices: 24105--24245 Score: 201
Period size: 71 Copynumber: 2.0 Consensus size: 68
24095 GAAGGTGAAT
* ***
24105 AAGAAGAACGAAAGGAAGCATCACTTTCGATTCAAGTGAACGGATGGAAGCATCGGTACTTTCGA
1 AAGAAGAACGAAAGGAAGCATCACTTTCGATTCAAGTGAACGGAAGGAAGCATCAACACTTTCGA
24170 TTC
66 TTC
* *
24173 AAGAAGAACGGAAGGAAGCATGGGCACTTTCGATTCAAGTGAACGGAAGGAAGTATCAACACTTT
1 AAGAAGAACGAAAGGAAGCAT---CACTTTCGATTCAAGTGAACGGAAGGAAGCATCAACACTTT
24238 CGATTC
63 CGATTC
24244 AA
1 AA
24246 TTGTTCATCT
Statistics
Matches: 64, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
68 20 0.31
71 44 0.69
ACGTcount: A:0.37, C:0.17, G:0.26, T:0.21
Consensus pattern (68 bp):
AAGAAGAACGAAAGGAAGCATCACTTTCGATTCAAGTGAACGGAAGGAAGCATCAACACTTTCGA
TTC
Found at i:28900 original size:23 final size:22
Alignment explanation
Indices: 28849--28891 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 22
28839 AAAAATATTC
28849 AAATAAAATCTTAAATAATAGA
1 AAATAAAATCTTAAATAATAGA
28871 AAGATAAAAT-TCTAAATAATA
1 AA-ATAAAATCT-TAAATAATA
28892 AATTAATAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
22 3 0.16
23 16 0.84
ACGTcount: A:0.63, C:0.05, G:0.05, T:0.28
Consensus pattern (22 bp):
AAATAAAATCTTAAATAATAGA
Found at i:29773 original size:19 final size:19
Alignment explanation
Indices: 29746--29782 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
29736 TCAAACCTTT
29746 TTTCTTTTTTC-TTTTTTC
1 TTTCTTTTTTCATTTTTTC
29764 TTTCTGTTTTTCATTTTTT
1 TTTCT-TTTTTCATTTTTT
29783 TCTAGTGTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 5 0.29
19 6 0.35
20 6 0.35
ACGTcount: A:0.03, C:0.14, G:0.03, T:0.81
Consensus pattern (19 bp):
TTTCTTTTTTCATTTTTTC
Found at i:29781 original size:7 final size:7
Alignment explanation
Indices: 29742--29766 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
29732 TTTTTCAAAC
29742 CTTTTTT
1 CTTTTTT
29749 CTTTTTT
1 CTTTTTT
29756 CTTTTTT
1 CTTTTTT
29763 CTTT
1 CTTT
29767 CTGTTTTTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (7 bp):
CTTTTTT
Found at i:31876 original size:21 final size:21
Alignment explanation
Indices: 31824--31894 Score: 76
Period size: 20 Copynumber: 3.5 Consensus size: 21
31814 TTTCTAGCTC
* *
31824 AAAGGATTGATCCC-TT-ACT
1 AAAGGATCGACCCCTTTGACT
*
31843 AAGAGGATTGACCCCTTTGACT
1 AA-AGGATCGACCCCTTTGACT
*
31865 AAAGGATCGACCCCTTTGA-A
1 AAAGGATCGACCCCTTTGACT
31885 AAAGGATCGA
1 AAAGGATCGA
31895 TCTCTTGGAT
Statistics
Matches: 46, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
19 2 0.04
20 21 0.46
21 18 0.39
22 5 0.11
ACGTcount: A:0.34, C:0.21, G:0.21, T:0.24
Consensus pattern (21 bp):
AAAGGATCGACCCCTTTGACT
Found at i:31890 original size:20 final size:21
Alignment explanation
Indices: 31846--31894 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
31836 CCTTACTAAG
* *
31846 AGGATTGACCCCTTTGACTAA
1 AGGATCGACCCCTTTGACAAA
31867 AGGATCGACCCCTTTGA-AAA
1 AGGATCGACCCCTTTGACAAA
31887 AGGATCGA
1 AGGATCGA
31895 TCTCTTGGAT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
20 10 0.38
21 16 0.62
ACGTcount: A:0.33, C:0.22, G:0.22, T:0.22
Consensus pattern (21 bp):
AGGATCGACCCCTTTGACAAA
Found at i:33223 original size:15 final size:15
Alignment explanation
Indices: 33203--33246 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
33193 AGTTGATGGT
*
33203 AGAAGAGGATGAGAA
1 AGAAGAGGAAGAGAA
** *
33218 AGAAGAATAAAAGAA
1 AGAAGAGGAAGAGAA
33233 AGAAGAGGAAGAGA
1 AGAAGAGGAAGAGA
33247 GAAAACAAAA
Statistics
Matches: 22, Mismatches: 7, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.61, C:0.00, G:0.34, T:0.05
Consensus pattern (15 bp):
AGAAGAGGAAGAGAA
Found at i:34293 original size:2 final size:2
Alignment explanation
Indices: 34286--34342 Score: 114
Period size: 2 Copynumber: 28.5 Consensus size: 2
34276 GTCTGTGTAG
34286 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
34328 AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT A
34343 ACACGGAAGC
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 55 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:36845 original size:19 final size:18
Alignment explanation
Indices: 36797--36845 Score: 53
Period size: 18 Copynumber: 2.6 Consensus size: 18
36787 TCTATTTTAT
*
36797 TATTAACTTAATTTAAAAA
1 TATTATCTT-ATTTAAAAA
* *
36816 TATTTTTTTATTTAAAAA
1 TATTATCTTATTTAAAAA
36834 TATGTATCTTAT
1 TAT-TATCTTAT
36846 GCTAAAATTT
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
18 12 0.50
19 12 0.50
ACGTcount: A:0.41, C:0.04, G:0.02, T:0.53
Consensus pattern (18 bp):
TATTATCTTATTTAAAAA
Found at i:40094 original size:30 final size:30
Alignment explanation
Indices: 40058--40118 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
40048 ATATATTAAA
40058 ATACTTCAATTTAAGTTAAATTTTATTTAG
1 ATACTTCAATTTAAGTTAAATTTTATTTAG
40088 ATACTTCAATTTAAGTTAAATTTTATTTAG
1 ATACTTCAATTTAAGTTAAATTTTATTTAG
40118 A
1 A
40119 CGATGACATC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.38, C:0.07, G:0.07, T:0.49
Consensus pattern (30 bp):
ATACTTCAATTTAAGTTAAATTTTATTTAG
Found at i:45559 original size:238 final size:238
Alignment explanation
Indices: 45141--45616 Score: 835
Period size: 238 Copynumber: 2.0 Consensus size: 238
45131 GCTAACAAAC
* ** *
45141 TTACATTACTAATCAATTTGAACAACTTGCAACAAAAACAATATACTTTGTCTGCATTTTTGGAA
1 TTACATTACTAATCAATTTAAACAACTTGCAACAAAAACAATATACTTTGTCAACATTTTTAGAA
*
45206 TAAACTAACCATTTTCTATCACTAGTCTCACCATTGCTCAACTTTCTAGAATAACATTCATATGA
66 TAAACTAACCATTTTCTATCACTAGTCTCACCATTGATCAACTTTCTAGAATAACATTCATATGA
* *
45271 GAAATGTCTATAATATTTATCAACAGGAAATTCAATATCCATTTCTCTTATGGGCCCTTTTTTAA
131 GAAATGTCTATAATATTTATCAACAGGAAATTCAAGATCCATTTCTCTTATGGGCCCTTTTTCAA
*
45336 CAAATATATCCCTCGCATTATTGTCAAGATTCTCCTAATTTAT
196 CAAATATATCCCTCGCATTATTGTCAAGATTCTCCCAATTTAT
*
45379 TTACATTACTAATCGATTTAAACAACTTGCAACAAAAACAATATACTTTGTCAACATTTTTAGAA
1 TTACATTACTAATCAATTTAAACAACTTGCAACAAAAACAATATACTTTGTCAACATTTTTAGAA
45444 TAAACTAACCATTTTCTATCACTAGTCTCACCATTGATCAACTTTCTAGAATAACATTCATATGA
66 TAAACTAACCATTTTCTATCACTAGTCTCACCATTGATCAACTTTCTAGAATAACATTCATATGA
* * *
45509 GAAATGTCTATAATATTTATCAATAGGAAATTCAAGATTCATTTCTCTTATGGGTCCTTTTTCAA
131 GAAATGTCTATAATATTTATCAACAGGAAATTCAAGATCCATTTCTCTTATGGGCCCTTTTTCAA
*
45574 CTAATATATCCCTCGCATTATTGTCAAGATTCTCCCAATTTAT
196 CAAATATATCCCTCGCATTATTGTCAAGATTCTCCCAATTTAT
45617 AGGATCATAT
Statistics
Matches: 225, Mismatches: 13, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
238 225 1.00
ACGTcount: A:0.35, C:0.20, G:0.08, T:0.37
Consensus pattern (238 bp):
TTACATTACTAATCAATTTAAACAACTTGCAACAAAAACAATATACTTTGTCAACATTTTTAGAA
TAAACTAACCATTTTCTATCACTAGTCTCACCATTGATCAACTTTCTAGAATAACATTCATATGA
GAAATGTCTATAATATTTATCAACAGGAAATTCAAGATCCATTTCTCTTATGGGCCCTTTTTCAA
CAAATATATCCCTCGCATTATTGTCAAGATTCTCCCAATTTAT
Found at i:54113 original size:3 final size:3
Alignment explanation
Indices: 54105--54138 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
54095 TTTAAATCAG
54105 CTA CTA CTA CTA CTA CTA CTA CTA CTA CTA CTA C
1 CTA CTA CTA CTA CTA CTA CTA CTA CTA CTA CTA C
54139 ACTGATACAG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.32, C:0.35, G:0.00, T:0.32
Consensus pattern (3 bp):
CTA
Found at i:57638 original size:245 final size:244
Alignment explanation
Indices: 57199--57684 Score: 776
Period size: 245 Copynumber: 2.0 Consensus size: 244
57189 CACTGAACCA
*
57199 CTTATCTACTCTTAACATATACAAATAAATAGCAATATCCAAGTTCCAGAGAAGAACTAGGGATG
1 CTTATCTACTCTTAACATATACAAATAAATAGCAATATCCAAGTTCCAGAGAACAACTAGGGATG
* **
57264 AAGTTGATAGTAAGAATTTTATGTTGCCGAGGCATAAGTTTGTTGCTGTCATTGAAGAACACATT
66 AAGTTGATAGTAAGAATTTTATGTTGCCGAGACATAAGTTTGTTGCTAACATTGAAGAACACATT
* *
57329 ATAGTATTTGCAAAAAAATGAATCCTATTGCCAGTCACTTCCTCAAGCATGATCTGGAAAATATA
131 ATAGTATTTGCAAAAAAATGAATCCTATTGCCAGTCACTTCCTCAAGAATGATATGGAAAATATA
* * *
57394 AAGGTACACCAGATCCTACGCTTACTAGGTTTGAGTCGGGACAGAAACTG
196 AAGGTAC-CCAGATCCTACACTTACTAGGCTTGAGTCAGGACAGAAACTG
* *
57444 CTTATCTACTTTTAACATATACAAATAAATAGCAATATCCAAGTTCCAGAGAACAACTAGTGATG
1 CTTATCTACTCTTAACATATACAAATAAATAGCAATATCCAAGTTCCAGAGAACAACTAGGGATG
* *
57509 AAGTTGATAGTAAGAATTTTAATGTTG-TGAGACATAAGTTTGTTGCTAACATTGTAGAACACAT
66 AAGTTGATAGTAAGAATTTT-ATGTTGCCGAGACATAAGTTTGTTGCTAACATTGAAGAACACAT
* * * * *
57573 TATGGTATTTGCAAACAATTGAATCCTATTGCCAGTCACTTCCTGAAGAATGATATGGCAAATAT
130 TATAGTATTTGCAAAAAAATGAATCCTATTGCCAGTCACTTCCTCAAGAATGATATGGAAAATAT
*
57638 AGAGGTACCCAGATCCTACACTTACTAGGCTTGAGTCAGGACAGAAA
195 AAAGGTACCCAGATCCTACACTTACTAGGCTTGAGTCAGGACAGAAA
57685 GGTAATAGTA
Statistics
Matches: 221, Mismatches: 19, Indels: 3
0.91 0.08 0.01
Matches are distributed among these distances:
244 36 0.16
245 179 0.81
246 6 0.03
ACGTcount: A:0.36, C:0.17, G:0.18, T:0.29
Consensus pattern (244 bp):
CTTATCTACTCTTAACATATACAAATAAATAGCAATATCCAAGTTCCAGAGAACAACTAGGGATG
AAGTTGATAGTAAGAATTTTATGTTGCCGAGACATAAGTTTGTTGCTAACATTGAAGAACACATT
ATAGTATTTGCAAAAAAATGAATCCTATTGCCAGTCACTTCCTCAAGAATGATATGGAAAATATA
AAGGTACCCAGATCCTACACTTACTAGGCTTGAGTCAGGACAGAAACTG
Found at i:61039 original size:23 final size:23
Alignment explanation
Indices: 61013--61081 Score: 93
Period size: 23 Copynumber: 3.0 Consensus size: 23
61003 CACCACAGCT
* *
61013 CGTATAATTGTACCGAAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
*
61036 CGTAGAATTGCACCGGAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
* *
61059 CGTAGAATTGCAACGTAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
61082 TATAATAATG
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 41 1.00
ACGTcount: A:0.29, C:0.23, G:0.26, T:0.22
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCA
Found at i:62677 original size:20 final size:22
Alignment explanation
Indices: 62614--62692 Score: 135
Period size: 22 Copynumber: 3.7 Consensus size: 22
62604 CGTTTGAGGG
*
62614 GGGTATCGATTCCCCATTGAAT
1 GGGTACCGATTCCCCATTGAAT
62636 GGGTACCGATTCCCCATTGAAT
1 GGGTACCGATTCCCCATTGAAT
62658 GGGTACCGATT-CCC-TTGAAT
1 GGGTACCGATTCCCCATTGAAT
62678 GGGTACCGATTCCCC
1 GGGTACCGATTCCCC
62693 TTGCCCAGAA
Statistics
Matches: 55, Mismatches: 1, Indels: 3
0.93 0.02 0.05
Matches are distributed among these distances:
20 17 0.31
21 6 0.11
22 32 0.58
ACGTcount: A:0.20, C:0.28, G:0.24, T:0.28
Consensus pattern (22 bp):
GGGTACCGATTCCCCATTGAAT
Found at i:66105 original size:23 final size:23
Alignment explanation
Indices: 66079--66147 Score: 93
Period size: 23 Copynumber: 3.0 Consensus size: 23
66069 CACCACAGCT
*
66079 CGTATAATTGCACCGAAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
* * *
66102 CGTAGAATTGCACTGGAGTGCCG
1 CGTAGAATTGCACCGAAGTGCCA
*
66125 CGTAGAATTGCACCGTAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
66148 TATAATAATG
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.26, C:0.25, G:0.28, T:0.22
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCA
Found at i:66334 original size:103 final size:103
Alignment explanation
Indices: 66163--66375 Score: 363
Period size: 103 Copynumber: 2.1 Consensus size: 103
66153 TAATGTCCAT
* * * * *
66163 AAGGACCACATATCATTCCTTAATAATCATATACATATACTAGGGATCAAGTATGTGTCTCACTA
1 AAGGACTACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
*
66228 GACTTCACACATGTTCTAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
*
66266 AAGGACTACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACTACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
66331 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66369 AAGGACT
1 AAGGACT
66376 GCGTAGACCC
Statistics
Matches: 103, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
103 103 1.00
ACGTcount: A:0.36, C:0.22, G:0.14, T:0.28
Consensus pattern (103 bp):
AAGGACTACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:67214 original size:20 final size:20
Alignment explanation
Indices: 67191--67236 Score: 92
Period size: 20 Copynumber: 2.3 Consensus size: 20
67181 CTCTTTATAA
67191 ACATCTATTTCTATTTCCCT
1 ACATCTATTTCTATTTCCCT
67211 ACATCTATTTCTATTTCCCT
1 ACATCTATTTCTATTTCCCT
67231 ACATCT
1 ACATCT
67237 CTCGACTTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.22, C:0.30, G:0.00, T:0.48
Consensus pattern (20 bp):
ACATCTATTTCTATTTCCCT
Found at i:67776 original size:22 final size:22
Alignment explanation
Indices: 67751--67809 Score: 100
Period size: 22 Copynumber: 2.7 Consensus size: 22
67741 GTTTGAGGGG
* *
67751 GGGTATCGGTTCCCCATTGAAT
1 GGGTACCGATTCCCCATTGAAT
67773 GGGTACCGATTCCCCATTGAAT
1 GGGTACCGATTCCCCATTGAAT
67795 GGGTACCGATTCCCC
1 GGGTACCGATTCCCC
67810 TTGCCCAGAA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 35 1.00
ACGTcount: A:0.19, C:0.29, G:0.25, T:0.27
Consensus pattern (22 bp):
GGGTACCGATTCCCCATTGAAT
Found at i:68632 original size:17 final size:17
Alignment explanation
Indices: 68607--68647 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
68597 TTAAATTCAT
68607 ATTTAAAATTT-TAAATA
1 ATTTAAAATTTATAAA-A
*
68624 ATTTTAAATTTATAAAA
1 ATTTAAAATTTATAAAA
68641 A-TTAAAA
1 ATTTAAAA
68648 AAATTAAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
16 5 0.24
17 12 0.57
18 4 0.19
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
ATTTAAAATTTATAAAA
Found at i:69412 original size:31 final size:30
Alignment explanation
Indices: 69330--69412 Score: 76
Period size: 30 Copynumber: 2.7 Consensus size: 30
69320 GCGTCACACG
* * *
69330 TGGACATACCACGTCAGCATTTAGTATACG
1 TGGACATGCCACGTCAGCATCTAGTATACA
* * * * * *
69360 TGAATATGCCACATCATCATCTATTATGATA
1 TGGACATGCCACGTCAGCATCTAGTAT-ACA
69391 TGGACATGCCACGTCAGCATCT
1 TGGACATGCCACGTCAGCATCT
69413 CACTCCACAT
Statistics
Matches: 39, Mismatches: 13, Indels: 1
0.74 0.25 0.02
Matches are distributed among these distances:
30 20 0.51
31 19 0.49
ACGTcount: A:0.30, C:0.24, G:0.17, T:0.29
Consensus pattern (30 bp):
TGGACATGCCACGTCAGCATCTAGTATACA
Found at i:72909 original size:102 final size:103
Alignment explanation
Indices: 72695--72915 Score: 250
Period size: 102 Copynumber: 2.2 Consensus size: 103
72685 AGTAGCCAAT
* * * *
72695 TTTGGTATCGATACTCATAAGAGTATCAATACCTATGGTAGTGTATCGATACTCCTAGTAGGGGT
1 TTTGGTATCGATACTCATAAGAGTATCAATACCTAGGGTAGGGTATCGATACTCCTAGGAGGAGT
* * * *
72760 ATCGATACTAAGGTATTTTTCAAAACATCGAATGTAAT
66 ATCAATACTAAGATATTTTTCAAAACATCGAATATAAA
** * * * * *
72798 TTTAATATCGGTACT-GTATGAGTATCGATA-CTAAGGGTAGGGTATCGATACTCTTAGGAGGAG
1 TTTGGTATCGATACTCATAAGAGTATCAATACCT-AGGGTAGGGTATCGATACTCCTAGGAGGAG
* *
72861 TATCAATACTAA-ATTTTTTTCTGAAACATCGAATATAAA
65 TATCAATACTAAGATATTTTTC-AAAACATCGAATATAAA
72900 TTTGGTATCGATACTC
1 TTTGGTATCGATACTC
72916 GAGGAAGTAT
Statistics
Matches: 95, Mismatches: 20, Indels: 6
0.79 0.17 0.05
Matches are distributed among these distances:
101 9 0.09
102 74 0.78
103 12 0.13
ACGTcount: A:0.32, C:0.14, G:0.19, T:0.35
Consensus pattern (103 bp):
TTTGGTATCGATACTCATAAGAGTATCAATACCTAGGGTAGGGTATCGATACTCCTAGGAGGAGT
ATCAATACTAAGATATTTTTCAAAACATCGAATATAAA
Found at i:74340 original size:19 final size:20
Alignment explanation
Indices: 74311--74348 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
74301 AGAAATTTAT
74311 TGAAGGTGCATCGATGCATA
1 TGAAGGTGCATCGATGCATA
74331 TGAA-GTGCATCGATGCAT
1 TGAAGGTGCATCGATGCAT
74349 TAATTTAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.29, C:0.16, G:0.29, T:0.26
Consensus pattern (20 bp):
TGAAGGTGCATCGATGCATA
Found at i:74387 original size:63 final size:61
Alignment explanation
Indices: 74316--74474 Score: 205
Period size: 63 Copynumber: 2.5 Consensus size: 61
74306 TTTATTGAAG
* * * *
74316 GTGCATCGATGCATATGAAGTGCATCGATGCATTAATTTAA-ATACA-AACATCGAATGTCGTCA
1 GTGCATCGATGCATA-GGAGTGCATCGATGCATT--TTTAATA-AAAGAACATCGAATGCCCTCA
74379 GTGCATCGATGCATAAGGAGTGCATCGATGCATTTTTAATAAAATGAACATCGAATGCCCTCA
1 GTGCATCGATGCAT-AGGAGTGCATCGATGCATTTTTAATAAAA-GAACATCGAATGCCCTCA
74442 GTGCATCGATGCATCAGGAGTGCATCGATGCAT
1 GTGCATCGATGCAT-AGGAGTGCATCGATGCAT
74475 GCCTCCATTA
Statistics
Matches: 87, Mismatches: 5, Indels: 8
0.87 0.05 0.08
Matches are distributed among these distances:
61 7 0.08
62 1 0.01
63 78 0.90
64 1 0.01
ACGTcount: A:0.32, C:0.19, G:0.22, T:0.27
Consensus pattern (61 bp):
GTGCATCGATGCATAGGAGTGCATCGATGCATTTTTAATAAAAGAACATCGAATGCCCTCA
Found at i:75108 original size:149 final size:149
Alignment explanation
Indices: 74930--75391 Score: 829
Period size: 149 Copynumber: 3.1 Consensus size: 149
74920 GGGTAGAGGG
*
74930 TCTACGCAGTCCTTCGGGATATATATATATTCTGTGGAACATGTGTGAAGTCTTGTAAGACACAT
1 TCTACGCGGTCCTTCGGGATATATATATATTCTGTGGAACATGTGTGAAGTCTTGTAAGACACAT
74995 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTATGGACATTATTA
66 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTATGGACATTATTA
75060 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
*
75079 TCTACGCGGTCCTTCGGGATATATATATATTCTATGGAACATGTGTGAAGTCTTGTAAGACACAT
1 TCTACGCGGTCCTTCGGGATATATATATATTCTGTGGAACATGTGTGAAGTCTTGTAAGACACAT
* *
75144 ACTTGATCCCTAGTATATGTATATGGTTCTTAAGGAATGATATGTGGTTCTTATGGACATTATTA
66 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTATGGACATTATTA
*
75209 TATGGCACTACGGTGTAAT
131 TATGGCACTACGGTGCAAT
75228 TCTACGCGGTCCTTC--GATATATATATATTCTGTGGAACATGTGTGAAGTCTTGTAAGACACAT
1 TCTACGCGGTCCTTCGGGATATATATATATTCTGTGGAACATGTGTGAAGTCTTGTAAGACACAT
*
75291 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTATGGATATTATTA
66 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTATGGACATTATTA
*
75356 TATGGCATTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
* *
75375 TCTACGTGGTACTTCGG
1 TCTACGCGGTCCTTCGG
75392 TGCAATTATA
Statistics
Matches: 298, Mismatches: 13, Indels: 4
0.95 0.04 0.01
Matches are distributed among these distances:
147 139 0.47
149 159 0.53
ACGTcount: A:0.27, C:0.15, G:0.21, T:0.37
Consensus pattern (149 bp):
TCTACGCGGTCCTTCGGGATATATATATATTCTGTGGAACATGTGTGAAGTCTTGTAAGACACAT
ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTATGGACATTATTA
TATGGCACTACGGTGCAAT
Found at i:81535 original size:19 final size:20
Alignment explanation
Indices: 81506--81543 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
81496 AAAAATTTGT
*
81506 TGAAGGTGCATTGATGCATA
1 TGAAGGTGCATCGATGCATA
81526 TGAA-GTGCATCGATGCAT
1 TGAAGGTGCATCGATGCAT
81544 TAATTTAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.29, C:0.13, G:0.29, T:0.29
Consensus pattern (20 bp):
TGAAGGTGCATCGATGCATA
Found at i:81585 original size:63 final size:62
Alignment explanation
Indices: 81511--81669 Score: 194
Period size: 63 Copynumber: 2.5 Consensus size: 62
81501 TTTGTTGAAG
* * * * *
81511 GTGCATTGATGCATATGAAGTGCATCGATGCATTAAT-TTAAATACAAACATCGAATGTCGTCA
1 GTGCATCGATGCATA-GGAGTGCATCGATGCATTAATAATAAA-ACAAACATCGAATGCCCTCA
** **
81574 GTGCATCGATGCATAAGGAGTGCATCGATGCATTTCTAATAAAATGAACATCGAATGCCCTCA
1 GTGCATCGATGCAT-AGGAGTGCATCGATGCATTAATAATAAAACAAACATCGAATGCCCTCA
81637 GTGCATCGATGCATCAGGAGTGCATCGATGCAT
1 GTGCATCGATGCAT-AGGAGTGCATCGATGCAT
81670 GCCTCCATTA
Statistics
Matches: 84, Mismatches: 10, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
63 79 0.94
64 5 0.06
ACGTcount: A:0.32, C:0.19, G:0.22, T:0.27
Consensus pattern (62 bp):
GTGCATCGATGCATAGGAGTGCATCGATGCATTAATAATAAAACAAACATCGAATGCCCTCA
Found at i:82565 original size:149 final size:149
Alignment explanation
Indices: 82125--82567 Score: 832
Period size: 149 Copynumber: 3.0 Consensus size: 149
82115 GGGTAGAGGG
*
82125 TCTACGCGGTCCTTCAGGATATATATATATTCTGTGGAACATGTGTGAAGTCTTGTAAGACACAT
1 TCTACGCGGTCCTTCGGGATATATATATATTCTGTGGAACATGTGTGAAGTCTTGTAAGACACAT
*
82190 ACTTGATCCCTAGTATATGTACATGATTCTTAAGGAATGATATGTGGTCCTTATGGACATTATTA
66 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTATGGACATTATTA
*
82255 TATGGCACTACGATGCAAT
131 TATGGCACTACGGTGCAAT
82274 TCTACGCGGTCCTTCGGGATATATATATATTCTGTGGAACATGTGTGAAGTCTTGTAAGACACAT
1 TCTACGCGGTCCTTCGGGATATATATATATTCTGTGGAACATGTGTGAAGTCTTGTAAGACACAT
82339 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTATGGACATTATTA
66 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTATGGACATTATTA
*
82404 TATGGAACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
* *
82423 TCTACACGGTCCTTCGGGATATATATATATTCTGTGGAATATGTGTGAAGTCTTGTAAGACACAT
1 TCTACGCGGTCCTTCGGGATATATATATATTCTGTGGAACATGTGTGAAGTCTTGTAAGACACAT
82488 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTATGGACATTATTA
66 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTATGGACATTATTA
82553 TATGGCACTACGGTG
131 TATGGCACTACGGTG
82568 ACAGCATAGT
Statistics
Matches: 287, Mismatches: 7, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
149 287 1.00
ACGTcount: A:0.28, C:0.15, G:0.21, T:0.36
Consensus pattern (149 bp):
TCTACGCGGTCCTTCGGGATATATATATATTCTGTGGAACATGTGTGAAGTCTTGTAAGACACAT
ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTATGGACATTATTA
TATGGCACTACGGTGCAAT
Found at i:83521 original size:13 final size:13
Alignment explanation
Indices: 83503--83534 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
83493 TTTTATGAAT
83503 AGTGAACAATAAC
1 AGTGAACAATAAC
83516 AGTGAACAATAAC
1 AGTGAACAATAAC
83529 AGTGAA
1 AGTGAA
83535 TAGTACCCAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.53, C:0.12, G:0.19, T:0.16
Consensus pattern (13 bp):
AGTGAACAATAAC
Found at i:84072 original size:46 final size:45
Alignment explanation
Indices: 83948--84100 Score: 236
Period size: 45 Copynumber: 3.4 Consensus size: 45
83938 TTCAAAATAT
* *
83948 TTACCATTTATCCCATAAGCTCGTAAGCTTATTTTACTAACATAC
1 TTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAACATAC
83993 TTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAACATAC
1 TTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAACATAC
* * *
84038 TTACCACTTATTCCCATAAGCTCGTAAGCTTATTTTACCAATACAC
1 TTACCATTTATT-CCATAAGCTCGTAAGCTTATTTTACCAACATAC
*
84084 TTGCCA-TTATTCCATAA
1 TTACCATTTATTCCATAA
84101 CCATATACCA
Statistics
Matches: 101, Mismatches: 6, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
44 6 0.06
45 59 0.58
46 36 0.36
ACGTcount: A:0.31, C:0.25, G:0.07, T:0.37
Consensus pattern (45 bp):
TTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAACATAC
Found at i:84289 original size:61 final size:61
Alignment explanation
Indices: 84182--84296 Score: 169
Period size: 61 Copynumber: 1.9 Consensus size: 61
84172 GTAGTGCTAA
* *
84182 ACCTGCACTAAGCTTACACCATAGTGCTAATCCGGACAATACACATAAGGTCGTGCCCACC
1 ACCTACACTAAGCTTACACCATAGTGCTAATCCGGACAATACACATAAAGTCGTGCCCACC
* * *
84243 ACCTACACTAAGCTTACGCTATAGTGCTAATCCGGAC-ATGATACATAAAGTCGT
1 ACCTACACTAAGCTTACACCATAGTGCTAATCCGGACAAT-ACACATAAAGTCGT
84297 ATCCACCTTT
Statistics
Matches: 48, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
60 2 0.04
61 46 0.96
ACGTcount: A:0.32, C:0.29, G:0.17, T:0.23
Consensus pattern (61 bp):
ACCTACACTAAGCTTACACCATAGTGCTAATCCGGACAATACACATAAAGTCGTGCCCACC
Found at i:86923 original size:31 final size:31
Alignment explanation
Indices: 86888--86967 Score: 99
Period size: 34 Copynumber: 2.5 Consensus size: 31
86878 TTCAACATCC
86888 AAGTGACCAAAACTTAATAAAACAATAACAT
1 AAGTGACCAAAACTTAATAAAACAATAACAT
** *
86919 AAGTGATAAAAAAAACTTAATAAAACGATAACAT
1 AAGTG---ACCAAAACTTAATAAAACAATAACAT
86953 -AGTGACCAAAACTTA
1 AAGTGACCAAAACTTA
86968 TGTTTTTAAA
Statistics
Matches: 41, Mismatches: 5, Indels: 7
0.77 0.09 0.13
Matches are distributed among these distances:
30 9 0.22
31 5 0.12
33 4 0.10
34 23 0.56
ACGTcount: A:0.57, C:0.14, G:0.09, T:0.20
Consensus pattern (31 bp):
AAGTGACCAAAACTTAATAAAACAATAACAT
Found at i:87846 original size:93 final size:94
Alignment explanation
Indices: 87688--87875 Score: 265
Period size: 93 Copynumber: 2.0 Consensus size: 94
87678 GTAAATGACA
* * * * *
87688 ATGATTTATGTTTTGAATGAAAAATTAAAGGTTTATTTATTTCACGGGAAACATATTTCGGAAAA
1 ATGATTCACGTTTTGAATGAAAAATTAAAGGTTTATTTATTTAACGGAAAACATATTTCGAAAAA
87753 TGAATCTT-GTAAAATTAA-TATATTTCTT
66 TGAAT-TTCGTAAAATTAATTATATTTCTT
* *
87781 ATGATTCACGTTTTGAATGAAAAATTAAAGGTTTGTTTGTTTAACGGAAAACATATTAT-GAAAA
1 ATGATTCACGTTTTGAATGAAAAATTAAAGGTTTATTTATTTAACGGAAAACATATT-TCGAAAA
*
87845 ATGACTTTCGTAAAATTAATTATATTTCTT
65 ATGAATTTCGTAAAATTAATTATATTTCTT
87875 A
1 A
87876 AAAATATTTT
Statistics
Matches: 84, Mismatches: 8, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
92 2 0.02
93 70 0.83
94 12 0.14
ACGTcount: A:0.38, C:0.07, G:0.14, T:0.41
Consensus pattern (94 bp):
ATGATTCACGTTTTGAATGAAAAATTAAAGGTTTATTTATTTAACGGAAAACATATTTCGAAAAA
TGAATTTCGTAAAATTAATTATATTTCTT
Found at i:88112 original size:29 final size:34
Alignment explanation
Indices: 88080--88152 Score: 86
Period size: 33 Copynumber: 2.3 Consensus size: 34
88070 TATTATTATT
88080 AAAATATTATAG-CTA-TA-ATTTTA-T-AAATA
1 AAAATATTATAGACTATTATATTTTATTAAAATA
*
88109 AAAATATTA-AGATTATTATATTTTATTAAAATA
1 AAAATATTATAGACTATTATATTTTATTAAAATA
*
88142 AAATTATTATA
1 AAAATATTATA
88153 AATTATATTA
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
28 2 0.06
29 11 0.31
30 2 0.06
31 6 0.17
32 1 0.03
33 13 0.36
34 1 0.03
ACGTcount: A:0.52, C:0.01, G:0.03, T:0.44
Consensus pattern (34 bp):
AAAATATTATAGACTATTATATTTTATTAAAATA
Found at i:88169 original size:38 final size:37
Alignment explanation
Indices: 88130--88235 Score: 106
Period size: 42 Copynumber: 2.7 Consensus size: 37
88120 ATTATTATAT
88130 TTTATTAAAATAAAATTATTATAAATTATATTAATTA
1 TTTATTAAAATAAAATTATTATAAATTATATTAATTA
* * *
88167 TTTACTAAAATAAGAATAATATATTTTTAATTATATTAATTA
1 TTTATTAAAAT---AA-AAT-TATTATAAATTATATTAATTA
* *
88209 CTTATT-AAATAATATTATTATTAAATT
1 TTTATTAAAATAAAATTATTA-TAAATT
88236 TTTGATAAAT
Statistics
Matches: 55, Mismatches: 8, Indels: 12
0.73 0.11 0.16
Matches are distributed among these distances:
36 4 0.07
37 17 0.31
38 2 0.04
40 2 0.04
41 7 0.13
42 23 0.42
ACGTcount: A:0.48, C:0.02, G:0.01, T:0.49
Consensus pattern (37 bp):
TTTATTAAAATAAAATTATTATAAATTATATTAATTA
Found at i:88392 original size:14 final size:14
Alignment explanation
Indices: 88373--88417 Score: 56
Period size: 14 Copynumber: 3.1 Consensus size: 14
88363 TATTTGAATA
88373 ATTTATTAAATATT
1 ATTTATTAAATATT
*
88387 ATTTATATCAATATT
1 ATTTAT-TAAATATT
88402 A-TTATTCAAATATT
1 ATTTATT-AAATATT
88416 AT
1 AT
88418 AATTATAATG
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
13 1 0.04
14 17 0.65
15 8 0.31
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.53
Consensus pattern (14 bp):
ATTTATTAAATATT
Found at i:88542 original size:38 final size:37
Alignment explanation
Indices: 88448--88557 Score: 102
Period size: 38 Copynumber: 2.9 Consensus size: 37
88438 ATATTAAGAT
88448 TATTATATT-TTATTAAAGTAA-AAT-TATTATAAATTA
1 TATTA-ATTATTATTAAA-TAATAATATATTATAAATTA
* ** * *
88484 TATTAATTAATAAAATAATAATAATATATTTTTAATTA
1 TATTAATTATTATTA-AATAATAATATATTATAAATTA
88522 TATTAATTACTTATTAAATAATAATATTATTA-AAAT
1 TATTAATTA-TTATTAAATAATAATA-TATTATAAAT
88558 ATTAAACAAT
Statistics
Matches: 58, Mismatches: 10, Indels: 10
0.74 0.13 0.13
Matches are distributed among these distances:
35 3 0.05
36 11 0.19
37 5 0.09
38 32 0.55
39 7 0.12
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.48
Consensus pattern (37 bp):
TATTAATTATTATTAAATAATAATATATTATAAATTA
Found at i:88827 original size:14 final size:14
Alignment explanation
Indices: 88756--88851 Score: 61
Period size: 14 Copynumber: 6.8 Consensus size: 14
88746 TAATTATATT
* *
88756 ATTATAATATTATAT
1 ATTATAATAATA-AA
*
88771 ATTATAATAATATA
1 ATTATAATAATAAA
*
88785 ATTATAACAATAAA
1 ATTATAATAATAAA
* * *
88799 AATATTAT-ATTAA
1 ATTATAATAATAAA
*
88812 ATTATATTAATAAA
1 ATTATAATAATAAA
* *
88826 ATTTTCAATAATTATA
1 ATTAT-AATAA-TAAA
88842 ATT-TAATAAT
1 ATTATAATAAT
88852 TAATATTTTT
Statistics
Matches: 62, Mismatches: 16, Indels: 8
0.72 0.19 0.09
Matches are distributed among these distances:
13 10 0.16
14 30 0.48
15 16 0.26
16 6 0.10
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (14 bp):
ATTATAATAATAAA
Found at i:89492 original size:2 final size:2
Alignment explanation
Indices: 89485--89510 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
89475 AGATATGTTC
89485 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
89511 CTTTTGTTTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:91363 original size:5 final size:5
Alignment explanation
Indices: 91353--91381 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
91343 AATTCCACTT
91353 TCACC TCACC TCACC TCACC TCACC TCAC
1 TCACC TCACC TCACC TCACC TCACC TCAC
91382 TCCACAAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.21, C:0.59, G:0.00, T:0.21
Consensus pattern (5 bp):
TCACC
Found at i:98051 original size:18 final size:18
Alignment explanation
Indices: 98027--98062 Score: 65
Period size: 17 Copynumber: 2.1 Consensus size: 18
98017 TACTTGAATT
98027 TAAAAAAATCA-GAAAAA
1 TAAAAAAATCAGGAAAAA
98044 TAAAAAAATCAGGAAAAA
1 TAAAAAAATCAGGAAAAA
98062 T
1 T
98063 TACAAACAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 11 0.61
18 7 0.39
ACGTcount: A:0.72, C:0.06, G:0.08, T:0.14
Consensus pattern (18 bp):
TAAAAAAATCAGGAAAAA
Found at i:98315 original size:13 final size:13
Alignment explanation
Indices: 98297--98329 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
98287 CATAGTTGAA
98297 CAGTCTTCATATG
1 CAGTCTTCATATG
98310 CAGTCTTCATATG
1 CAGTCTTCATATG
98323 CACGTCT
1 CA-GTCT
98330 GTAATGGGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 15 0.79
14 4 0.21
ACGTcount: A:0.21, C:0.27, G:0.15, T:0.36
Consensus pattern (13 bp):
CAGTCTTCATATG
Found at i:99416 original size:21 final size:21
Alignment explanation
Indices: 99386--99426 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
99376 TCATGAATAG
*
99386 TGCTATAGTGCATCGATGCAT
1 TGCTACAGTGCATCGATGCAT
* *
99407 TGCTACAGTGCCTCTATGCA
1 TGCTACAGTGCATCGATGCA
99427 CCAAAATTTC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.22, C:0.24, G:0.22, T:0.32
Consensus pattern (21 bp):
TGCTACAGTGCATCGATGCAT
Found at i:100019 original size:23 final size:25
Alignment explanation
Indices: 99967--100020 Score: 62
Period size: 23 Copynumber: 2.3 Consensus size: 25
99957 TATCATATAA
*
99967 TCATATACTTATCGTTTATACAAAT
1 TCATATACTTATCGTTAATACAAAT
99992 T-ATATACTTCAT-G-TAATAC-AAT
1 TCATATACTT-ATCGTTAATACAAAT
100014 TCATATA
1 TCATATA
100021 ACTAAAACAT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
22 4 0.15
23 10 0.38
24 9 0.35
25 3 0.12
ACGTcount: A:0.39, C:0.15, G:0.04, T:0.43
Consensus pattern (25 bp):
TCATATACTTATCGTTAATACAAAT
Found at i:104009 original size:15 final size:17
Alignment explanation
Indices: 103978--104010 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 17
103968 ATGTATTTTT
103978 ATCTATCTTGTAATTTA
1 ATCTATCTTGTAATTTA
103995 ATCTA-CTTG-AATTTA
1 ATCTATCTTGTAATTTA
104010 A
1 A
104011 AAAAAATCAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.44
16 4 0.25
17 5 0.31
ACGTcount: A:0.33, C:0.12, G:0.06, T:0.48
Consensus pattern (17 bp):
ATCTATCTTGTAATTTA
Found at i:104978 original size:42 final size:42
Alignment explanation
Indices: 104911--104993 Score: 112
Period size: 42 Copynumber: 2.0 Consensus size: 42
104901 TGTATCCAAC
* * * *
104911 ATGGTGTACATGTTTTGTATTTTAGGGTCTAAAGTAGACAAT
1 ATGGTGTACATATTTTGCATCTTAGGGTCTAAAGTAAACAAT
* *
104953 ATGGTGTATATATTTTGCATCTTAGGGTTTAAAGTAAACAA
1 ATGGTGTACATATTTTGCATCTTAGGGTCTAAAGTAAACAA
104994 CGTGGTCTAA
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
42 35 1.00
ACGTcount: A:0.31, C:0.07, G:0.22, T:0.40
Consensus pattern (42 bp):
ATGGTGTACATATTTTGCATCTTAGGGTCTAAAGTAAACAAT
Found at i:114665 original size:6 final size:7
Alignment explanation
Indices: 114649--114673 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
114639 AACTGCCTCC
114649 TTTTTAT
1 TTTTTAT
114656 TTTTTAT
1 TTTTTAT
114663 TTTTTAT
1 TTTTTAT
114670 TTTT
1 TTTT
114674 CAAGGGTTGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (7 bp):
TTTTTAT
Found at i:117981 original size:31 final size:31
Alignment explanation
Indices: 117946--118012 Score: 100
Period size: 31 Copynumber: 2.2 Consensus size: 31
117936 TAAAACTTGT
117946 AATATAATCCC-CTAACATTTAGTCCATTTGC
1 AATATAATCCCTC-AACATTTAGTCCATTTGC
**
117977 AATATGGTCCCTCAACATTTAGTCCATTTGC
1 AATATAATCCCTCAACATTTAGTCCATTTGC
118008 AATAT
1 AATAT
118013 GGTCCCGATG
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
31 32 0.97
32 1 0.03
ACGTcount: A:0.31, C:0.24, G:0.09, T:0.36
Consensus pattern (31 bp):
AATATAATCCCTCAACATTTAGTCCATTTGC
Found at i:118013 original size:31 final size:30
Alignment explanation
Indices: 117955--118018 Score: 119
Period size: 31 Copynumber: 2.1 Consensus size: 30
117945 TAATATAATC
117955 CCCTAACATTTAGTCCATTTGCAATATGGT
1 CCCTAACATTTAGTCCATTTGCAATATGGT
117985 CCCTCAACATTTAGTCCATTTGCAATATGGT
1 CCCT-AACATTTAGTCCATTTGCAATATGGT
118016 CCC
1 CCC
118019 GATGTAACTG
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
30 4 0.12
31 29 0.88
ACGTcount: A:0.25, C:0.28, G:0.12, T:0.34
Consensus pattern (30 bp):
CCCTAACATTTAGTCCATTTGCAATATGGT
Found at i:118660 original size:2 final size:2
Alignment explanation
Indices: 118653--118686 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
118643 GTTGTAACTT
118653 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
118687 AAATTTTAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:120079 original size:16 final size:17
Alignment explanation
Indices: 120042--120081 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
120032 TAAATATTAA
*
120042 AAAATATAATGATTATTT
1 AAAAT-TAATCATTATTT
120060 AAAATTAATCATTA-TT
1 AAAATTAATCATTATTT
120076 AAAATT
1 AAAATT
120082 TAATTATAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 8 0.38
17 8 0.38
18 5 0.24
ACGTcount: A:0.53, C:0.03, G:0.03, T:0.42
Consensus pattern (17 bp):
AAAATTAATCATTATTT
Found at i:120084 original size:17 final size:18
Alignment explanation
Indices: 120042--120085 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 18
120032 TAAATATTAA
* *
120042 AAAATATAATGATTATTT
1 AAAATTTAATCATTATTT
120060 AAAA-TTAATCATTA-TT
1 AAAATTTAATCATTATTT
120076 AAAATTTAAT
1 AAAATTTAAT
120086 TATAATTGAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
16 6 0.26
17 13 0.57
18 4 0.17
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.43
Consensus pattern (18 bp):
AAAATTTAATCATTATTT
Found at i:120249 original size:31 final size:31
Alignment explanation
Indices: 120202--120272 Score: 108
Period size: 31 Copynumber: 2.3 Consensus size: 31
120192 TTAAAACTTG
* *
120202 CAATATAGT-CCCCAACATTTAGTCCGTTTA
1 CAATATGGTCCCCCAACATTAAGTCCGTTTA
*
120232 CAATATGGTCCCCCAACATTAAGTCCGTTTG
1 CAATATGGTCCCCCAACATTAAGTCCGTTTA
120263 CAATATGGTC
1 CAATATGGTC
120273 TCCAATTTAA
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
30 8 0.22
31 29 0.78
ACGTcount: A:0.28, C:0.27, G:0.14, T:0.31
Consensus pattern (31 bp):
CAATATGGTCCCCCAACATTAAGTCCGTTTA
Done.