Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009278.1 Hibiscus syriacus cultivar Beakdansim tig00112961_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: 63324
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.31
Found at i:222 original size:28 final size:28
Alignment explanation
Indices: 182--236 Score: 92
Period size: 28 Copynumber: 2.0 Consensus size: 28
172 GAAAACATAG
* *
182 TTCTGATTTATGGTTTTTGATCTCTGGA
1 TTCTGATATATGGTTTTTGATCACTGGA
210 TTCTGATATATGGTTTTTGATCACTGG
1 TTCTGATATATGGTTTTTGATCACTGG
237 TATATGATTG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.16, C:0.11, G:0.22, T:0.51
Consensus pattern (28 bp):
TTCTGATATATGGTTTTTGATCACTGGA
Found at i:244 original size:28 final size:28
Alignment explanation
Indices: 185--244 Score: 77
Period size: 28 Copynumber: 2.1 Consensus size: 28
175 AACATAGTTC
* * *
185 TGATTTATGGTTTTTGATCTCTGGATTC
1 TGATATATGGTTTTTGATCACTGGATTA
213 TGATATATGGTTTTTGATCACTGG-TATA
1 TGATATATGGTTTTTGATCACTGGAT-TA
241 TGAT
1 TGAT
245 TGGATACATC
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
27 1 0.04
28 27 0.96
ACGTcount: A:0.20, C:0.08, G:0.22, T:0.50
Consensus pattern (28 bp):
TGATATATGGTTTTTGATCACTGGATTA
Found at i:605 original size:17 final size:17
Alignment explanation
Indices: 583--615 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
573 TTTTAAGATT
583 TTATATTCGATTTAATA
1 TTATATTCGATTTAATA
*
600 TTATATTCTATTTAAT
1 TTATATTCGATTTAAT
616 TATTCGAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.33, C:0.06, G:0.03, T:0.58
Consensus pattern (17 bp):
TTATATTCGATTTAATA
Found at i:3503 original size:39 final size:40
Alignment explanation
Indices: 3459--3540 Score: 148
Period size: 40 Copynumber: 2.1 Consensus size: 40
3449 GTATAGGTAC
3459 TATAGGTAATAC-TCTTCCATACAAATAGAAAATGTGTTA
1 TATAGGTAATACATCTTCCATACAAATAGAAAATGTGTTA
*
3498 TATAGGTAATACATCTTCCATACAAATAGAAACTGTGTTA
1 TATAGGTAATACATCTTCCATACAAATAGAAAATGTGTTA
3538 TAT
1 TAT
3541 GTGAAAGAGT
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
39 12 0.29
40 29 0.71
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.34
Consensus pattern (40 bp):
TATAGGTAATACATCTTCCATACAAATAGAAAATGTGTTA
Found at i:6767 original size:16 final size:17
Alignment explanation
Indices: 6735--6767 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
6725 AATAAAATGA
*
6735 ATAAATAAATGATTTTG
1 ATAAAAAAATGATTTTG
6752 ATAAAAAAAT-ATTTTG
1 ATAAAAAAATGATTTTG
6768 GGAGTCGCCA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.52, C:0.00, G:0.09, T:0.39
Consensus pattern (17 bp):
ATAAAAAAATGATTTTG
Found at i:7451 original size:17 final size:18
Alignment explanation
Indices: 7429--7462 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
7419 CTAAAATAAA
7429 AAAATAATAATG-AAAAT
1 AAAATAATAATGTAAAAT
*
7446 AAAATACTAATGTAAAA
1 AAAATAATAATGTAAAA
7463 GTATTGAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.68, C:0.03, G:0.06, T:0.24
Consensus pattern (18 bp):
AAAATAATAATGTAAAAT
Found at i:8719 original size:3 final size:3
Alignment explanation
Indices: 8711--8770 Score: 70
Period size: 3 Copynumber: 20.0 Consensus size: 3
8701 TGTGGGCCTG
*
8711 TAA TAA TAA T-T TAA TTAA TAA TAA TAA TAA TAA TAA TAA GTAA TAA
1 TAA TAA TAA TAA TAA -TAA TAA TAA TAA TAA TAA TAA TAA -TAA TAA
*
8757 -AA TAA TAA GAA TAA
1 TAA TAA TAA TAA TAA
8771 AAAATAAAAA
Statistics
Matches: 49, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
2 3 0.06
3 40 0.82
4 6 0.12
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:8763 original size:15 final size:15
Alignment explanation
Indices: 8727--8777 Score: 72
Period size: 15 Copynumber: 3.5 Consensus size: 15
8717 TAATTTAATT
8727 AATAATAA-TAATAA
1 AATAATAAGTAATAA
8741 TAATAATAAGTAATAA
1 -AATAATAAGTAATAA
8757 AATAATAAG-AATAA
1 AATAATAAGTAATAA
8771 AA-AATAA
1 AATAATAA
8778 AAAATGGATA
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
13 5 0.14
14 7 0.20
15 17 0.49
16 6 0.17
ACGTcount: A:0.71, C:0.00, G:0.04, T:0.25
Consensus pattern (15 bp):
AATAATAAGTAATAA
Found at i:8763 original size:21 final size:21
Alignment explanation
Indices: 8712--8779 Score: 57
Period size: 21 Copynumber: 3.1 Consensus size: 21
8702 GTGGGCCTGT
* *
8712 AATAATAAT-TTAATTAATAA
1 AATAATAATAATAAATAATAA
8732 TAATAATAATAATAATAAGTAATAA
1 -AATAATAATAAT-A-AA-TAATAA
* *
8757 AATAATAAGAATAAAAAATAA
1 AATAATAATAATAAATAATAA
8778 AA
1 AA
8780 AATGGATAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
21 16 0.41
22 3 0.08
23 2 0.05
24 12 0.31
25 6 0.15
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.29
Consensus pattern (21 bp):
AATAATAATAATAAATAATAA
Found at i:18224 original size:15 final size:15
Alignment explanation
Indices: 18204--18250 Score: 51
Period size: 15 Copynumber: 2.9 Consensus size: 15
18194 CGAGTGACGT
18204 TTATATTATATATTA
1 TTATATTATATATTA
18219 TTATATATAATAATATTA
1 TTATAT-T-AT-ATATTA
18237 TTAATATTAT-TATT
1 TT-ATATTATATATT
18251 TACAAAGCAT
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
15 10 0.36
16 1 0.04
17 4 0.14
18 9 0.32
19 4 0.14
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (15 bp):
TTATATTATATATTA
Found at i:18250 original size:12 final size:13
Alignment explanation
Indices: 18207--18249 Score: 54
Period size: 12 Copynumber: 3.5 Consensus size: 13
18197 GTGACGTTTA
*
18207 TATTATATATTAT
1 TATTATATAATAT
*
18220 TA-TATATAATAA
1 TATTATATAATAT
18232 TATTAT-TAATAT
1 TATTATATAATAT
18244 TATTAT
1 TATTAT
18250 TTACAAAGCA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
12 21 0.81
13 5 0.19
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
TATTATATAATAT
Found at i:26581 original size:20 final size:20
Alignment explanation
Indices: 26556--27236 Score: 802
Period size: 20 Copynumber: 34.1 Consensus size: 20
26546 TTTCCCATAA
26556 ATTTGTAAAGCCTCTGGGTC
1 ATTTGTAAAGCCTCTGGGTC
* *
26576 ATTTGTAAAGCCTCCGGGCC
1 ATTTGTAAAGCCTCTGGGTC
* *
26596 ATTTGTAAAGCCTCCGGGTT
1 ATTTGTAAAGCCTCTGGGTC
26616 ATTTGTAAAGCCT-TCGGGTC
1 ATTTGTAAAGCCTCT-GGGTC
* *
26636 ATTTGTAAAGCCTCCGAGTC
1 ATTTGTAAAGCCTCTGGGTC
* *
26656 AATTGTAAAGCCTCTAGGTC
1 ATTTGTAAAGCCTCTGGGTC
*
26676 ATTTGTAAAGCCTCCGGGTC
1 ATTTGTAAAGCCTCTGGGTC
26696 ATTTGTAAAGCGCTC-GGGTC
1 ATTTGTAAAGC-CTCTGGGTC
26716 ATTTGTAAAGCGCTC-GGGTC
1 ATTTGTAAAGC-CTCTGGGTC
*
26736 ATTTGTATAGCCTCTGGGTC
1 ATTTGTAAAGCCTCTGGGTC
26756 ATTTGTAAAGCC-CTCGGGTC
1 ATTTGTAAAGCCTCT-GGGTC
**
26776 ATTTGTAAAGCCTCCAGGTC
1 ATTTGTAAAGCCTCTGGGTC
*
26796 ATTTGTAAAGCCTCCGGGTC
1 ATTTGTAAAGCCTCTGGGTC
*
26816 ATTTGTAAAGCCTCCGGGTC
1 ATTTGTAAAGCCTCTGGGTC
* * *
26836 AATTATAAAGCCTCCGGGTC
1 ATTTGTAAAGCCTCTGGGTC
*
26856 ACTTGTAAAGCCTCTGGGTC
1 ATTTGTAAAGCCTCTGGGTC
* *
26876 ATTTGTAAAGCCTTTGGTTC
1 ATTTGTAAAGCCTCTGGGTC
*
26896 ATTTGTAAAG-CTTTCGGGTC
1 ATTTGTAAAGCCTCT-GGGTC
*
26916 ATTTATAAAGCCTCTGGGTC
1 ATTTGTAAAGCCTCTGGGTC
* *
26936 AATTATAAAGCCTCTGGGTC
1 ATTTGTAAAGCCTCTGGGTC
* * *
26956 ATTTTTAACGCCTCCGGGTC
1 ATTTGTAAAGCCTCTGGGTC
* *
26976 AATTGCAAAGCCTCTGGGTC
1 ATTTGTAAAGCCTCTGGGTC
26996 ATTTGTAAAGCCTCTGGGTC
1 ATTTGTAAAGCCTCTGGGTC
27016 ATTTGTAAAGCCTCTGGGTC
1 ATTTGTAAAGCCTCTGGGTC
* * *
27036 ATTTTTAACGCCTCCGGGTC
1 ATTTGTAAAGCCTCTGGGTC
*
27056 AATTGTAAAGCCTCTGGGTC
1 ATTTGTAAAGCCTCTGGGTC
***
27076 ATTTGTAAAGCCTCCAAGTC
1 ATTTGTAAAGCCTCTGGGTC
*
27096 ATTTGTAAAGCCTCCGGGTC
1 ATTTGTAAAGCCTCTGGGTC
**
27116 ATTTGTAAAGCCTC-CAGTC
1 ATTTGTAAAGCCTCTGGGTC
*
27135 ATTTGTAAAGACTCCT-GGTC
1 ATTTGTAAAGCCT-CTGGGTC
* ** *
27155 AATTAAAAAGCCTCCGGGTC
1 ATTTGTAAAGCCTCTGGGTC
27175 ATTTGTAAAGCCTCAT-GGTC
1 ATTTGTAAAGCCTC-TGGGTC
* * *
27195 ATTTGTAAAACCTCCGGGTA
1 ATTTGTAAAGCCTCTGGGTC
* *
27215 ATTTGTAAATCCTTTGGGTC
1 ATTTGTAAAGCCTCTGGGTC
27235 AT
1 AT
27237 CTATCAGTCT
Statistics
Matches: 572, Mismatches: 76, Indels: 26
0.85 0.11 0.04
Matches are distributed among these distances:
19 25 0.04
20 540 0.94
21 7 0.01
ACGTcount: A:0.23, C:0.22, G:0.23, T:0.32
Consensus pattern (20 bp):
ATTTGTAAAGCCTCTGGGTC
Found at i:27450 original size:95 final size:95
Alignment explanation
Indices: 27287--27494 Score: 317
Period size: 95 Copynumber: 2.2 Consensus size: 95
27277 TTCGTAAGAT
* * *
27287 CTCCATGAAAGAGTAGTGGAATCAAATTAACTTCGAATATGATCTTCATGGAAGAGTAGTGAAAT
1 CTCCACGAAAGAGTAGTGGAATCAAATCAACTTCGAATATGATCTTCACGGAAGAGTAGTGAAAT
* * *
27352 TAGATTCTTCTCAAGTCTATCATTTTCAGC
66 TAGATTATTCTCAAGTCAATCATTTTCAAC
* * *
27382 CTCCACGGAAGAGTTGTGGAATCAAATCAACTTCGAATCTGATCTTCACGGAAGAGTAGTGAAAT
1 CTCCACGAAAGAGTAGTGGAATCAAATCAACTTCGAATATGATCTTCACGGAAGAGTAGTGAAAT
*
27447 TAGATTATTCTCAAGTCAATTATTTTCAAC
66 TAGATTATTCTCAAGTCAATCATTTTCAAC
*
27477 CTTCACGAAAGAGTAGTG
1 CTCCACGAAAGAGTAGTG
27495 AAGTATTCCA
Statistics
Matches: 100, Mismatches: 13, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
95 100 1.00
ACGTcount: A:0.34, C:0.17, G:0.19, T:0.31
Consensus pattern (95 bp):
CTCCACGAAAGAGTAGTGGAATCAAATCAACTTCGAATATGATCTTCACGGAAGAGTAGTGAAAT
TAGATTATTCTCAAGTCAATCATTTTCAAC
Found at i:27697 original size:95 final size:95
Alignment explanation
Indices: 27567--27872 Score: 416
Period size: 95 Copynumber: 3.2 Consensus size: 95
27557 TATTATCCTC
* *
27567 AGTCTTCAAGGAAGAGTAGTGAAGA-AGAAGTAGGAGCAATATCAAAATTTGATCTCCACGGAAG
1 AGTC-TCAAGGAAGAGTAGTGAA-ACAGAAGCAGGAGCAAGATCAAAATTTGATCTCCACGGAAG
* ** * *
27631 ATTAGTGGAATGGATTTTTCAACAAAGTATGA
64 AGTAGTGGAACAGATTTTTTAGCAAAGTATGA
* * * **
27663 AGTCTCAAAGAAGAGTACTGAAACAGAAGCAGGAGCAAGATCAAAATTTGCTCTCCATAGAAGAG
1 AGTCTCAAGGAAGAGTAGTGAAACAGAAGCAGGAGCAAGATCAAAATTTGATCTCCACGGAAGAG
27728 TAGTGGAACAGATTTTTTAGCAAAGTATGA
66 TAGTGGAACAGATTTTTTAGCAAAGTATGA
* * * *
27758 AGTCTCACGGAAGAGTAGTGAAACAGACGCAGGAGCAAGATCAAAATATGATCTTCACGGAAGAG
1 AGTCTCAAGGAAGAGTAGTGAAACAGAAGCAGGAGCAAGATCAAAATTTGATCTCCACGGAAGAG
*
27823 TAGTGGAACAGATTTTTTAGTAAAGTATGA
66 TAGTGGAACAGATTTTTTAGCAAAGTATGA
* *
27853 AGTCTCACGAAAGAGTAGTG
1 AGTCTCAAGGAAGAGTAGTG
27873 GAATCAAATC
Statistics
Matches: 186, Mismatches: 23, Indels: 3
0.88 0.11 0.01
Matches are distributed among these distances:
94 1 0.01
95 181 0.97
96 4 0.02
ACGTcount: A:0.40, C:0.12, G:0.25, T:0.23
Consensus pattern (95 bp):
AGTCTCAAGGAAGAGTAGTGAAACAGAAGCAGGAGCAAGATCAAAATTTGATCTCCACGGAAGAG
TAGTGGAACAGATTTTTTAGCAAAGTATGA
Found at i:27867 original size:45 final size:45
Alignment explanation
Indices: 27722--27875 Score: 141
Period size: 45 Copynumber: 3.3 Consensus size: 45
27712 GCTCTCCATA
*
27722 GAAGAGTAGTGGAACAGATTTTTTAGCAAAGTATGAAGTCTCACG
1 GAAGAGTAGTGGAACAGATTTTTTAGTAAAGTATGAAGTCTCACG
* ****** *
27767 GAAGAGTAGTGAAACAGACGCAGGAGCAAGATCAAAATATG-A-TCTTCACG
1 GAAGAGTAGTGGAAC--A-G-ATTTTTTAG-T-AAAGTATGAAGTC-TCACG
27817 GAAGAGTAGTGGAACAGATTTTTTAGTAAAGTATGAAGTCTCACG
1 GAAGAGTAGTGGAACAGATTTTTTAGTAAAGTATGAAGTCTCACG
*
27862 AAAGAGTAGTGGAA
1 GAAGAGTAGTGGAA
27876 TCAAATCAAC
Statistics
Matches: 82, Mismatches: 18, Indels: 18
0.69 0.15 0.15
Matches are distributed among these distances:
44 7 0.09
45 34 0.41
46 5 0.06
47 2 0.02
48 2 0.02
49 5 0.06
50 20 0.24
51 7 0.09
ACGTcount: A:0.39, C:0.11, G:0.27, T:0.23
Consensus pattern (45 bp):
GAAGAGTAGTGGAACAGATTTTTTAGTAAAGTATGAAGTCTCACG
Found at i:28068 original size:15 final size:15
Alignment explanation
Indices: 28048--28094 Score: 51
Period size: 15 Copynumber: 2.9 Consensus size: 15
28038 CGAGTGACGT
28048 TTATATTATATATTA
1 TTATATTATATATTA
28063 TTATATATAATAATATTA
1 TTATAT-T-AT-ATATTA
28081 TTAATATTAT-TATT
1 TT-ATATTATATATT
28095 TACAAAGATC
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
15 10 0.36
16 1 0.04
17 4 0.14
18 9 0.32
19 4 0.14
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (15 bp):
TTATATTATATATTA
Found at i:28094 original size:12 final size:13
Alignment explanation
Indices: 28051--28093 Score: 54
Period size: 12 Copynumber: 3.5 Consensus size: 13
28041 GTGACGTTTA
*
28051 TATTATATATTAT
1 TATTATATAATAT
*
28064 TA-TATATAATAA
1 TATTATATAATAT
28076 TATTAT-TAATAT
1 TATTATATAATAT
28088 TATTAT
1 TATTAT
28094 TTACAAAGAT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
12 21 0.81
13 5 0.19
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
TATTATATAATAT
Found at i:29311 original size:28 final size:28
Alignment explanation
Indices: 29263--29317 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 28
29253 ATTATTTTAA
*
29263 TATTATTTTGAATTATGATAAATAATTT
1 TATTATTTTGAATTATAATAAATAATTT
* *
29291 TATTATTTT-ATATTTTAATAATTAATT
1 TATTATTTTGA-ATTATAATAAATAATT
29318 ATTGTTATAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
27 1 0.04
28 22 0.96
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (28 bp):
TATTATTTTGAATTATAATAAATAATTT
Found at i:31214 original size:127 final size:127
Alignment explanation
Indices: 31081--31350 Score: 425
Period size: 127 Copynumber: 2.1 Consensus size: 127
31071 AATAAATAAA
* *
31081 AAAAGTTAGTAGTTAGCAGAGTCCGAACCATAATAATGCGGATCATACCCCGGATCAGGTCACCA
1 AAAAGTTAGTAGTTAGCAGAGTCCGAACCATAATAATGCCGATCATACCCCAGATCAGGTCACCA
* ** *
31146 CAAGGTCGAATCGAATATTAGAA-ATAATAAATAAATAAACAATGGTTTGAGAGGAATAAAAT
66 CAAGGTCGAATCAAATATTAGAATA-AATAAATAAATAAACAATGGTTAAAGAGCAATAAAAT
* * *
31208 AAAAGTTAGTAATTAGCAGAGTCCGAACCATAATAATGCCGATCATACCCCATATCGGGTCACCA
1 AAAAGTTAGTAGTTAGCAGAGTCCGAACCATAATAATGCCGATCATACCCCAGATCAGGTCACCA
* *
31273 CAAGGTCGAATCAAATATTAGAATAAATAAATAAATAAATAATGGTTAAAGTGCAATAAAAT
66 CAAGGTCGAATCAAATATTAGAATAAATAAATAAATAAACAATGGTTAAAGAGCAATAAAAT
31335 AAAAGTTAGTAGTTAG
1 AAAAGTTAGTAGTTAG
31351 TTTGAAATAA
Statistics
Matches: 130, Mismatches: 12, Indels: 2
0.90 0.08 0.01
Matches are distributed among these distances:
127 129 0.99
128 1 0.01
ACGTcount: A:0.44, C:0.14, G:0.18, T:0.23
Consensus pattern (127 bp):
AAAAGTTAGTAGTTAGCAGAGTCCGAACCATAATAATGCCGATCATACCCCAGATCAGGTCACCA
CAAGGTCGAATCAAATATTAGAATAAATAAATAAATAAACAATGGTTAAAGAGCAATAAAAT
Found at i:32516 original size:15 final size:15
Alignment explanation
Indices: 32496--32546 Score: 50
Period size: 15 Copynumber: 3.4 Consensus size: 15
32486 TCTTTGTCTG
32496 AAAAATAAAGGATTT
1 AAAAATAAAGGATTT
* * *
32511 AAAAATGACAGTA-TG
1 AAAAAT-AAAGGATTT
*
32526 AAAAATAGAGGATTT
1 AAAAATAAAGGATTT
32541 AAAAAT
1 AAAAAT
32547 GAAATTGTTC
Statistics
Matches: 28, Mismatches: 6, Indels: 4
0.74 0.16 0.11
Matches are distributed among these distances:
14 4 0.14
15 20 0.71
16 4 0.14
ACGTcount: A:0.59, C:0.02, G:0.16, T:0.24
Consensus pattern (15 bp):
AAAAATAAAGGATTT
Found at i:33031 original size:139 final size:138
Alignment explanation
Indices: 32648--33113 Score: 581
Period size: 139 Copynumber: 3.3 Consensus size: 138
32638 TCAATATGGA
* * * *
32648 GATAATTTGGTGATAACAGGGTTCTTACATTATGAGGAAGTTTGATTGTCTGAGGATGACACTGC
1 GATAATTTGGAGATAACA-GGTTCCTACATGATGAGGAAGTCTGATTGTCTGAGGATGACACTGC
** * * *
32713 TTTTTACACGTTGAGGACATCTGGTCAGTGGATGACATTGTTCCTATGTGATGAGGACGTCTAGC
65 -TCCTACGCGTTGAGGAGATCTGGTCAGTGGATGACATTGTTCCTATGTGATGAGGACATCTAGC
32778 CATCTTTAGG
129 CATCTTTAGG
* * * * * * * * *
32788 GATAAATTGGAGATAACACGTTCTTACGTGATGATGAAGTCTGGTTATCAGAGGATGACACTGGT
1 GATAATTTGGAGATAACAGGTTCCTACATGATGAGGAAGTCTGATTGTCTGAGGATGACACTGCT
* * * *
32853 CCTACGCGTTGAGGTGGTCTGGTCAGTGGATGATATTGTTCCTACGTGATGAGGACATCTAGCCA
66 CCTACGCGTTGAGGAGATCTGGTCAGTGGATGACATTGTTCCTATGTGATGAGGACATCTAGCCA
32918 TCTTTAGG
131 TCTTTAGG
* * *
32926 GATAATTTGGAGACAACATGGTTCCTACATGATGAGGAAGTCTGATTGTTTGAGGATGACGCTGC
1 GATAATTTGGAGATAACA-GGTTCCTACATGATGAGGAAGTCTGATTGTCTGAGGATGACACTGC
* ** * *
32991 TCCTACGCGTTGAGGAGATTTGGTTGGTGGACGACATTGTTCTTATGTGATGAGGACATCTAGCC
65 TCCTACGCGTTGAGGAGATCTGGTCAGTGGATGACATTGTTCCTATGTGATGAGGACATCTAGCC
33056 ATCTTTAGG
130 ATCTTTAGG
* ** * *
33065 GATAATTTAGAGATAACACACTTCCTACATGATAAGAAAGTCTGATTGT
1 GATAATTTGGAGATAACA-GGTTCCTACATGATGAGGAAGTCTGATTGT
33114 AATACCCCCA
Statistics
Matches: 277, Mismatches: 48, Indels: 3
0.84 0.15 0.01
Matches are distributed among these distances:
138 81 0.29
139 180 0.65
140 16 0.06
ACGTcount: A:0.26, C:0.15, G:0.27, T:0.32
Consensus pattern (138 bp):
GATAATTTGGAGATAACAGGTTCCTACATGATGAGGAAGTCTGATTGTCTGAGGATGACACTGCT
CCTACGCGTTGAGGAGATCTGGTCAGTGGATGACATTGTTCCTATGTGATGAGGACATCTAGCCA
TCTTTAGG
Found at i:33754 original size:2 final size:2
Alignment explanation
Indices: 33711--33740 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
33701 ATAACAAGTC
33711 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
33741 CACATACAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:34037 original size:21 final size:21
Alignment explanation
Indices: 33949--34038 Score: 65
Period size: 21 Copynumber: 4.3 Consensus size: 21
33939 CCTTAAGGTT
*
33949 CACATATATATTCCAAAGGAC
1 CACATATATATCCCAAAGGAC
* * * * *
33970 CAAATATGTGTCCCGAAGAAC
1 CACATATATATCCCAAAGGAC
* * *
33991 C-CTATATATGTTCCAAAGGAT
1 CAC-ATATATATCCCAAAGGAC
* *
34012 TACATATATATCCCGAAGGAC
1 CACATATATATCCCAAAGGAC
34033 CACATA
1 CACATA
34039 GAACCCTTGA
Statistics
Matches: 49, Mismatches: 18, Indels: 4
0.69 0.25 0.06
Matches are distributed among these distances:
21 48 0.98
22 1 0.02
ACGTcount: A:0.39, C:0.23, G:0.13, T:0.24
Consensus pattern (21 bp):
CACATATATATCCCAAAGGAC
Found at i:35869 original size:30 final size:30
Alignment explanation
Indices: 35835--35944 Score: 98
Period size: 30 Copynumber: 3.5 Consensus size: 30
35825 ATACAAAATT
35835 TGTTTCAAGAGAAACAATCTCAAAGGTTTA
1 TGTTTCAAGAGAAACAATCTCAAAGGTTTA
** **
35865 TGTTTCAAGAGAAA-TGTCTCAAGCGAGACAAAATT-
1 TGTTTCAAGAGAAACAATCTCAA---AG----GTTTA
35900 TGTTTCAAGAGAAACAATCTCAAAGGTTTA
1 TGTTTCAAGAGAAACAATCTCAAAGGTTTA
*
35930 TGTTTCAAAAGAAAC
1 TGTTTCAAGAGAAAC
35945 TGTCTCAAGC
Statistics
Matches: 62, Mismatches: 9, Indels: 18
0.70 0.10 0.20
Matches are distributed among these distances:
29 8 0.13
30 28 0.45
32 2 0.03
33 2 0.03
35 14 0.23
36 8 0.13
ACGTcount: A:0.41, C:0.14, G:0.17, T:0.28
Consensus pattern (30 bp):
TGTTTCAAGAGAAACAATCTCAAAGGTTTA
Found at i:35920 original size:65 final size:66
Alignment explanation
Indices: 35816--35996 Score: 274
Period size: 65 Copynumber: 2.8 Consensus size: 66
35806 CTTAGGCTAC
* *
35816 TCTCAAGCGATACAAAATTTGTTTCAAGAGAAACAATCTCAAAGGTTTATGTTTCAAGAGAAA-T
1 TCTCAAGCGAGACAAAATTTGTTTCAAGAGAAACAATCTCAAAGGTTTATGTTTCAAAAGAAACT
35880 G
66 G
35881 TCTCAAGCGAGACAAAATTTGTTTCAAGAGAAACAATCTCAAAGGTTTATGTTTCAAAAGAAACT
1 TCTCAAGCGAGACAAAATTTGTTTCAAGAGAAACAATCTCAAAGGTTTATGTTTCAAAAGAAACT
35946 G
66 G
* **** **
35947 TCTCAAGCGAGATAAAAAAAATTTCGGGAGAAACAATCTCAAAGGTTTAT
1 TCTCAAGCGAGACAAAATTTGTTTCAAGAGAAACAATCTCAAAGGTTTAT
35997 CAATTTTGTT
Statistics
Matches: 106, Mismatches: 9, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
65 61 0.58
66 45 0.42
ACGTcount: A:0.41, C:0.14, G:0.17, T:0.27
Consensus pattern (66 bp):
TCTCAAGCGAGACAAAATTTGTTTCAAGAGAAACAATCTCAAAGGTTTATGTTTCAAAAGAAACT
G
Found at i:35985 original size:66 final size:65
Alignment explanation
Indices: 35837--35996 Score: 239
Period size: 66 Copynumber: 2.4 Consensus size: 65
35827 ACAAAATTTG
* ****
35837 TTTCAAGAGAAACAATCTCAAAGGTTTATGTTTCAAGAGAAATGTCTCAAGCGAGACAAAATTTG
1 TTTCAAGAGAAACAATCTCAAAGGTTTATGTTTCAAAAGAAATGTCTCAAGCGAGACAAAAAAAA
*
35902 TTTCAAGAGAAACAATCTCAAAGGTTTATGTTTCAAAAGAAACTGTCTCAAGCGAGATAAAAAAA
1 TTTCAAGAGAAACAATCTCAAAGGTTTATGTTTCAAAAGAAA-TGTCTCAAGCGAGACAAAAAAA
35967 A
65 A
**
35968 TTTCGGGAGAAACAATCTCAAAGGTTTAT
1 TTTCAAGAGAAACAATCTCAAAGGTTTAT
35997 CAATTTTGTT
Statistics
Matches: 86, Mismatches: 8, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
65 41 0.48
66 45 0.52
ACGTcount: A:0.42, C:0.14, G:0.17, T:0.27
Consensus pattern (65 bp):
TTTCAAGAGAAACAATCTCAAAGGTTTATGTTTCAAAAGAAATGTCTCAAGCGAGACAAAAAAAA
Found at i:36062 original size:104 final size:104
Alignment explanation
Indices: 35941--36134 Score: 237
Period size: 104 Copynumber: 1.9 Consensus size: 104
35931 GTTTCAAAAG
* * ** * *
35941 AAACTGTCTCAAGCGAGATAA-AAAAAATTTCGGGAGAAACAATCTCAAAGGTTTATCAATTTTG
1 AAACTGTCTCAAACGAGACAAGAAAAAATTTCAAGAAAAACAATATCAAAGG-TTATCAATTTTG
* *
36005 TTTCAAGTGAAATAATTTCTAAATTTTGTGTTTTGATGGA
65 TTTCAAGTGAAACAATTTCAAAATTTTGTGTTTTGATGGA
***** * *
36045 AAACTGTCTCAAACGAGACAAGATTTGTTTTTAAGAAAAACAATATCAAATGTTATCAATTTTGT
1 AAACTGTCTCAAACGAGACAAGAAAAAATTTCAAGAAAAACAATATCAAAGGTTATCAATTTTGT
36110 TTCAAGTGAAACAATTTCAAAATTT
66 TTCAAGTGAAACAATTTCAAAATTT
36135 GTATTTCTAG
Statistics
Matches: 74, Mismatches: 15, Indels: 2
0.81 0.16 0.02
Matches are distributed among these distances:
104 55 0.74
105 19 0.26
ACGTcount: A:0.40, C:0.11, G:0.14, T:0.35
Consensus pattern (104 bp):
AAACTGTCTCAAACGAGACAAGAAAAAATTTCAAGAAAAACAATATCAAAGGTTATCAATTTTGT
TTCAAGTGAAACAATTTCAAAATTTTGTGTTTTGATGGA
Found at i:36273 original size:36 final size:36
Alignment explanation
Indices: 36217--36301 Score: 109
Period size: 36 Copynumber: 2.4 Consensus size: 36
36207 GAGGAAGACT
* * * *
36217 ATCTTAAGTGAGACACAATTTGTTTTTATGAAAA-A
1 ATCTCAAGTGAGACAAAATTTGTTTTAAAGAAAACA
*
36252 TGTCTCAAGTGAGACAAAATTTGTTTTAAAGAAAACA
1 -ATCTCAAGTGAGACAAAATTTGTTTTAAAGAAAACA
36289 ATCTCAAGTGAGA
1 ATCTCAAGTGAGA
36302 TCAATTTTGT
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
36 41 0.98
37 1 0.02
ACGTcount: A:0.41, C:0.11, G:0.16, T:0.32
Consensus pattern (36 bp):
ATCTCAAGTGAGACAAAATTTGTTTTAAAGAAAACA
Found at i:36311 original size:36 final size:35
Alignment explanation
Indices: 36217--36321 Score: 97
Period size: 36 Copynumber: 2.9 Consensus size: 35
36207 GAGGAAGACT
* * * *
36217 ATCTTAAGTGAGACACAATTTGTTTTTATGAAAA-A
1 ATCTCAAGTGAGACAAAATTTG-TTTAAAGAAAACA
*
36252 TGTCTCAAGTGAGACAAAATTTGTTTTAAAGAAAACA
1 -ATCTCAAGTGAGACAAAATTTG-TTTAAAGAAAACA
* *
36289 ATCTCAAGTGAGATC-AATTTTGTTTCAAGAAAA
1 ATCTCAAGTGAGA-CAAAATTTGTTTAAAGAAAA
36322 ATTTTCTCTA
Statistics
Matches: 59, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
35 10 0.17
36 47 0.80
37 2 0.03
ACGTcount: A:0.41, C:0.10, G:0.15, T:0.33
Consensus pattern (35 bp):
ATCTCAAGTGAGACAAAATTTGTTTAAAGAAAACA
Found at i:41424 original size:21 final size:21
Alignment explanation
Indices: 41375--41432 Score: 64
Period size: 21 Copynumber: 2.8 Consensus size: 21
41365 AACATGACAG
*
41375 ATGAACTGCCATGTCAGAACC
1 ATGAACTACCATGTCAGAACC
* *
41396 AT-AGACTACCATGTCAGCATC
1 ATGA-ACTACCATGTCAGAACC
*
41417 ATGAACTACCACGTCA
1 ATGAACTACCATGTCA
41433 ACACCATAAC
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
20 1 0.03
21 29 0.94
22 1 0.03
ACGTcount: A:0.34, C:0.29, G:0.16, T:0.21
Consensus pattern (21 bp):
ATGAACTACCATGTCAGAACC
Found at i:42336 original size:30 final size:29
Alignment explanation
Indices: 42282--42360 Score: 86
Period size: 30 Copynumber: 2.7 Consensus size: 29
42272 CATCTTATCT
*
42282 TCAATTGAAGTATTCTTTCTCCCCTCCTCG
1 TCAATTGAAGTATT-TTTCCCCCCTCCTCG
* * *
42312 TCAAATGAAGTATTTTTCGCCCCCTTCTTG
1 TCAATTGAAGTATTTTTC-CCCCCTCCTCG
* *
42342 TCGATTGAAGGATTTTTCC
1 TCAATTGAAGTATTTTTCC
42361 TCCTCTTCTT
Statistics
Matches: 41, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
29 5 0.12
30 36 0.88
ACGTcount: A:0.19, C:0.27, G:0.14, T:0.41
Consensus pattern (29 bp):
TCAATTGAAGTATTTTTCCCCCCTCCTCG
Found at i:42369 original size:30 final size:30
Alignment explanation
Indices: 42317--42373 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
42307 CCTCGTCAAA
*
42317 TGAAGTATTTTTCGCCCCCTTCTTGTCGAT
1 TGAAGGATTTTTCGCCCCCTTCTTGTCGAT
*
42347 TGAAGGATTTTTC-CTCCTCTTCTTGTC
1 TGAAGGATTTTTCGC-CCCCTTCTTGTC
42374 AATTAGAGTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 1 0.04
30 23 0.96
ACGTcount: A:0.12, C:0.26, G:0.16, T:0.46
Consensus pattern (30 bp):
TGAAGGATTTTTCGCCCCCTTCTTGTCGAT
Found at i:48669 original size:138 final size:137
Alignment explanation
Indices: 48421--48843 Score: 537
Period size: 138 Copynumber: 3.1 Consensus size: 137
48411 TTAAGGTCAA
* * ** * *
48421 TTGACCTTTCTAATTGCAATAAACTATGGAAGATCCCT-GATCTATCAGGAGCCATCAACCATCA
1 TTGACCTTTCTGATTGCAAGAGTCTAAGGAAGATCCCTAG-TCTATCAGGAGCCATCAACCTTCA
* * *
48485 AAGCTTTTGCTGCAATGGGTGTGAAAATTTGGTT-AAGCTGCCTTGCCTTAACCATTTGGCATCT
65 AAGCTTTT-CTGCAATGGGTGTGAAAATTTGGTTGAA-CTACCTTGCCTCAACCAATTGGCATCT
48549 CTTGAAAAAC
128 CTTGAAAAAC
* * *
48559 TTGACCTTTCTGGTTGCAAGAGTCTAAGGAAGATCCTTAGTCTATCAAGAGCCATCAACCTTCAA
1 TTGACCTTTCTGATTGCAAGAGTCTAAGGAAGATCCCTAGTCTATCAGGAGCCATCAACCTTCAA
* *
48624 AGCATTTTCTGCAATGGGTGTGAAAATTTGATTGAACTACCTTGCCTCAACCACTTGGCATCTCT
66 AGC-TTTTCTGCAATGGGTGTGAAAATTTGGTTGAACTACCTTGCCTCAACCAATTGGCATCTCT
48689 TGAAAAAC
130 TGAAAAAC
* * * * * *
48697 TTGGCCTTTCTGACTGCAAGAGTCTAATGG-AGATCCCTAATCTATCAGGAGTCATCAAACTCCA
1 TTGACCTTTCTGATTGCAAGAGTCTAA-GGAAGATCCCTAGTCTATCAGGAGCCATCAACCTTCA
* * * *
48761 AAGCCTTTGCTGCAATGGGTGTGAAAATTTGGTTGAAATACCTTCCCTCAACCAATTGGTATCTC
65 AAG-CTTTTCTGCAATGGGTGTGAAAATTTGGTTGAACTACCTTGCCTCAACCAATTGGCATCTC
**
48826 TTGAAATCC
129 TTGAAAAAC
48835 TTGACCTTT
1 TTGACCTTT
48844 ATTGTTGCAG
Statistics
Matches: 249, Mismatches: 31, Indels: 10
0.86 0.11 0.03
Matches are distributed among these distances:
138 239 0.96
139 10 0.04
ACGTcount: A:0.28, C:0.22, G:0.18, T:0.31
Consensus pattern (137 bp):
TTGACCTTTCTGATTGCAAGAGTCTAAGGAAGATCCCTAGTCTATCAGGAGCCATCAACCTTCAA
AGCTTTTCTGCAATGGGTGTGAAAATTTGGTTGAACTACCTTGCCTCAACCAATTGGCATCTCTT
GAAAAAC
Found at i:48874 original size:138 final size:136
Alignment explanation
Indices: 48450--48964 Score: 525
Period size: 138 Copynumber: 3.7 Consensus size: 136
48440 TAAACTATGG
* *
48450 AAGATCCCTGATCTATCAGGAGCCATCAACCATCAAAGCTTTTGCTGCAATGGGTGTGAAAATTT
1 AAGATCCCTAATCTATCAGGAGCCATCAACC-TCAAAGCATTTGCTGCAATGGGTGTGAAAATTT
* * * *
48515 GGTT-AAGCTGCCTTGCCTTAACCATTTGGCATCTCTTGAAAAACTTGACCTTTCTGGTTGCAAG
65 GGTTGAA-CTACCTTGCCTCAACCAATTGGCATCTCTTGAAAAACTTGACCTTT-TTGTTGCAAG
*
48579 AGTCTAAGG
128 AGTCTAAGT
* * * *
48588 AAGATCCTTAGTCTATCAAGAGCCATCAACCTTCAAAGCATTTTCTGCAATGGGTGTGAAAATTT
1 AAGATCCCTAATCTATCAGGAGCCATCAACC-TCAAAGCATTTGCTGCAATGGGTGTGAAAATTT
* * * * *
48653 GATTGAACTACCTTGCCTCAACCACTTGGCATCTCTTGAAAAACTTGGCCTTTCTGACTGCAAGA
65 GGTTGAACTACCTTGCCTCAACCAATTGGCATCTCTTGAAAAACTTGACCTTTTTG-TTGCAAGA
48718 GTCTAA-T
129 GTCTAAGT
* * * *
48725 GGAGATCCCTAATCTATCAGGAGTCATCAAACTCCAAAGCCTTTGCTGCAATGGGTGTGAAAATT
1 -AAGATCCCTAATCTATCAGGAGCCATCAACCT-CAAAGCATTTGCTGCAATGGGTGTGAAAATT
* * * ** *
48790 TGGTTGAAATACCTTCCCTCAACCAATTGGTATCTCTTGAAATCCTTGACCTTTATTGTTGCAGG
64 TGGTTGAACTACCTTGCCTCAACCAATTGGCATCTCTTGAAAAACTTGACCTTT-TTGTTGCAAG
* *
48855 AATTTAAGT
128 AGTCTAAGT
* * ** * * * * *** *
48864 AAGATTCCTAATCCATTTGTAGCCATCAACCTTAAATCACTTAAG-TGCAATTACTGT-ACAAGT
1 AAGATCCCTAATCTATCAGGAGCCATCAACCTCAAAGCA-TT-TGCTGCAATGGGTGTGA-AAAT
* *
48927 TTGGTTGAACTACCTAGCCTCAATCAATTGGCATCTCT
63 TTGGTTGAACTACCTTGCCTCAACCAATTGGCATCTCT
48965 CAAAGAGCTT
Statistics
Matches: 310, Mismatches: 58, Indels: 18
0.80 0.15 0.05
Matches are distributed among these distances:
137 7 0.02
138 297 0.96
139 6 0.02
ACGTcount: A:0.29, C:0.22, G:0.18, T:0.31
Consensus pattern (136 bp):
AAGATCCCTAATCTATCAGGAGCCATCAACCTCAAAGCATTTGCTGCAATGGGTGTGAAAATTTG
GTTGAACTACCTTGCCTCAACCAATTGGCATCTCTTGAAAAACTTGACCTTTTTGTTGCAAGAGT
CTAAGT
Found at i:48937 original size:276 final size:277
Alignment explanation
Indices: 48446--48964 Score: 629
Period size: 276 Copynumber: 1.9 Consensus size: 277
48436 GCAATAAACT
* * *
48446 ATGGAAGATCCCTGATCTATCAGGAGCCATCAACCATCAAAGCTTTTGCTGCAATGGGTGTGAAA
1 ATGGAAGATCCCTAATCTATCAGGAGCCATCAAACATCAAAGCCTTTGCTGCAATGGGTGTGAAA
* * * * * *
48511 ATTTGGTTAAGCTGCCTTGCCTTAACCATTTGGCATCTCTTGAAAAACTTGACCTTTCTGGTTGC
66 ATTTGGTTAAGATACCTTCCCTCAACCAATTGGCATCTCTTGAAAAACTTGACCTTTATGGTTGC
* * * ** *
48576 AAGAGTCTAAGGAAGATCCTTAGTCTATCAAGAGCCATCAACCTTCAAAGCATTTTCTGCAATGG
131 AAGAATCTAAGGAAGATCCTTAATCCATCAAGAGCCATCAACCTTCAAAGCATTAACTGCAATGA
* * *
48641 GTGTGAAAATTTGATTGAACTACCTTGCCTCAACCACTTGGCATCTCTTGAAAAACTTGGCCTTT
196 CTGTGAAAATTTGATTGAACTACCTAGCCTCAACCAATTGGCATCTCTTGAAAAACTTGGCCTTT
48706 CTGACTGCAAGAGTCTA
261 CTGACTGCAAGAGTCTA
*
48723 ATGG-AGATCCCTAATCTATCAGGAGTCATCAAAC-TCCAAAGCCTTTGCTGCAATGGGTGTGAA
1 ATGGAAGATCCCTAATCTATCAGGAGCCATCAAACAT-CAAAGCCTTTGCTGCAATGGGTGTGAA
* ** *
48786 AATTTGGTTGAA-ATACCTTCCCTCAACCAATTGGTATCTCTTGAAATCCTTGACCTTTATTGTT
65 AATTTGGTT-AAGATACCTTCCCTCAACCAATTGGCATCTCTTGAAAAACTTGACCTTTATGGTT
* * * ** * *
48850 GCAGGAATTTAAGTAAGATTCC-TAATCCAT-TTGTAGCCATCAACCTT-AAATCACTTAAGTGC
129 GCAAGAATCTAAGGAAGA-TCCTTAATCCATCAAG-AGCCATCAACCTTCAAAGCA-TTAACTGC
* * * *
48912 AATTACTGT-ACAAGTTTGGTTGAACTACCTAGCCTCAATCAATTGGCATCTCT
191 AATGACTGTGA-AAATTTGATTGAACTACCTAGCCTCAACCAATTGGCATCTCT
48965 CAAAGAGCTT
Statistics
Matches: 202, Mismatches: 34, Indels: 13
0.81 0.14 0.05
Matches are distributed among these distances:
275 8 0.04
276 185 0.92
277 9 0.04
ACGTcount: A:0.29, C:0.22, G:0.18, T:0.31
Consensus pattern (277 bp):
ATGGAAGATCCCTAATCTATCAGGAGCCATCAAACATCAAAGCCTTTGCTGCAATGGGTGTGAAA
ATTTGGTTAAGATACCTTCCCTCAACCAATTGGCATCTCTTGAAAAACTTGACCTTTATGGTTGC
AAGAATCTAAGGAAGATCCTTAATCCATCAAGAGCCATCAACCTTCAAAGCATTAACTGCAATGA
CTGTGAAAATTTGATTGAACTACCTAGCCTCAACCAATTGGCATCTCTTGAAAAACTTGGCCTTT
CTGACTGCAAGAGTCTA
Found at i:52233 original size:29 final size:29
Alignment explanation
Indices: 52200--52281 Score: 112
Period size: 29 Copynumber: 2.9 Consensus size: 29
52190 TCTCATACAT
* *
52200 AATCAGAACGGGGAATATATCCCATGAAG
1 AATCAGGACGGGGAATAAATCCCATGAAG
* * *
52229 AATCAGGACGAGGAATAAATCCCCTGCAG
1 AATCAGGACGGGGAATAAATCCCATGAAG
52258 AATCAGGACGGGG-ATAAATCCCAT
1 AATCAGGACGGGGAATAAATCCCAT
52282 TCAGATATCA
Statistics
Matches: 46, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
28 10 0.22
29 36 0.78
ACGTcount: A:0.39, C:0.21, G:0.24, T:0.16
Consensus pattern (29 bp):
AATCAGGACGGGGAATAAATCCCATGAAG
Found at i:52291 original size:29 final size:28
Alignment explanation
Indices: 52200--52292 Score: 105
Period size: 29 Copynumber: 3.2 Consensus size: 28
52190 TCTCATACAT
* * *
52200 AATCAGAACGGGGAATATATCCCATGAAG
1 AATCAGGACGGGG-ATAAATCCCATGCAG
* *
52229 AATCAGGACGAGGAATAAATCCCCTGCAG
1 AATCAGGACG-GGGATAAATCCCATGCAG
*
52258 AATCAGGACGGGGATAAATCCCATTCAG
1 AATCAGGACGGGGATAAATCCCATGCAG
52286 ATATCAG
1 A-ATCAG
52293 AAATGCATCA
Statistics
Matches: 54, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
28 16 0.30
29 36 0.67
30 2 0.04
ACGTcount: A:0.39, C:0.20, G:0.24, T:0.17
Consensus pattern (28 bp):
AATCAGGACGGGGATAAATCCCATGCAG
Found at i:52364 original size:2 final size:2
Alignment explanation
Indices: 52357--52396 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
52347 TGTCACGTAA
52357 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
52397 CAATTCACGA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:52944 original size:13 final size:14
Alignment explanation
Indices: 52894--52951 Score: 57
Period size: 13 Copynumber: 4.3 Consensus size: 14
52884 TTAGAAAATT
*
52894 TCAACGATCAACGG
1 TCAACAATCAACGG
*
52908 TCAACAGTCAA-GG
1 TCAACAATCAACGG
**
52921 TCAACTTTCAACGG
1 TCAACAATCAACGG
*
52935 TCAA-AATCAATGG
1 TCAACAATCAACGG
52948 TCAA
1 TCAA
52952 TGGGTCGGGT
Statistics
Matches: 36, Mismatches: 7, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
13 21 0.58
14 15 0.42
ACGTcount: A:0.38, C:0.24, G:0.17, T:0.21
Consensus pattern (14 bp):
TCAACAATCAACGG
Found at i:52973 original size:17 final size:17
Alignment explanation
Indices: 52948--52991 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 17
52938 AAATCAATGG
*
52948 TCAATGGGTCGGGTCGA
1 TCAACGGGTCGGGTCGA
* *
52965 TCAACGGGTCGGTTCGG
1 TCAACGGGTCGGGTCGA
*
52982 TTAACGGGTC
1 TCAACGGGTC
52992 AATTGGTTTA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.16, C:0.20, G:0.39, T:0.25
Consensus pattern (17 bp):
TCAACGGGTCGGGTCGA
Found at i:54153 original size:21 final size:21
Alignment explanation
Indices: 54128--54189 Score: 106
Period size: 21 Copynumber: 3.0 Consensus size: 21
54118 CTATAACAGG
54128 GGGTATTGGTACCCCTTCATA
1 GGGTATTGGTACCCCTTCATA
54149 GGGTATTGGTACCCCTTCATA
1 GGGTATTGGTACCCCTTCATA
* *
54170 GGGTATTAGTACACCTTCAT
1 GGGTATTGGTACCCCTTCAT
54190 TAAATTCAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 39 1.00
ACGTcount: A:0.21, C:0.23, G:0.23, T:0.34
Consensus pattern (21 bp):
GGGTATTGGTACCCCTTCATA
Found at i:55137 original size:32 final size:31
Alignment explanation
Indices: 55101--55176 Score: 89
Period size: 31 Copynumber: 2.4 Consensus size: 31
55091 GGGGCCGTGA
*
55101 GGCCTACCTAAGAACACATCTTAGGGCCGCAG
1 GGCCTACCTAAGAA-ACATCTCAGGGCCGCAG
** **
55133 GGCCTACCCGAGAATGATCTCAGGGCCGCAG
1 GGCCTACCTAAGAAACATCTCAGGGCCGCAG
*
55164 AGCCTACCTAAGA
1 GGCCTACCTAAGA
55177 GTCACATTAG
Statistics
Matches: 36, Mismatches: 8, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
31 24 0.67
32 12 0.33
ACGTcount: A:0.28, C:0.32, G:0.26, T:0.14
Consensus pattern (31 bp):
GGCCTACCTAAGAAACATCTCAGGGCCGCAG
Found at i:55159 original size:63 final size:63
Alignment explanation
Indices: 55053--55176 Score: 155
Period size: 63 Copynumber: 2.0 Consensus size: 63
55043 CCCTAAGGGA
* * *
55053 ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATTTCGGGGCCG-TGAGGCCTACCTAAGAAC
1 ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATCTCAGGGCCGCAGA-GCCTACCTAAGAAC
* *
55116 ACATCTTAGGGCC-GCAGGGCCTACCCGAGA-ATGATCTCAGGGCCGCAGAGCCTACCTAAGA
1 ACATCTTAGGGCCTG-AGAGCCTACCCAAGATA-GATCTCAGGGCCGCAGAGCCTACCTAAGA
55177 GTCACATTAG
Statistics
Matches: 53, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
62 2 0.04
63 49 0.92
64 2 0.04
ACGTcount: A:0.27, C:0.29, G:0.27, T:0.17
Consensus pattern (63 bp):
ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATCTCAGGGCCGCAGAGCCTACCTAAGAAC
Found at i:55992 original size:13 final size:14
Alignment explanation
Indices: 55970--56006 Score: 67
Period size: 13 Copynumber: 2.7 Consensus size: 14
55960 GTCAAAGAAA
55970 GTCAACGGTCAACG
1 GTCAACGGTCAACG
55984 GTC-ACGGTCAACG
1 GTCAACGGTCAACG
55997 GTCAACGGTC
1 GTCAACGGTC
56007 GGGTCGGGTC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
13 13 0.59
14 9 0.41
ACGTcount: A:0.24, C:0.30, G:0.30, T:0.16
Consensus pattern (14 bp):
GTCAACGGTCAACG
Found at i:56018 original size:17 final size:17
Alignment explanation
Indices: 55996--56053 Score: 89
Period size: 17 Copynumber: 3.4 Consensus size: 17
55986 CACGGTCAAC
55996 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
56013 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
* * *
56030 GGTCAACAGTCGAGTCA
1 GGTCAACGGTCGGGTCG
56047 GGTCAAC
1 GGTCAAC
56054 CCGGTTCAGA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
17 38 1.00
ACGTcount: A:0.19, C:0.24, G:0.40, T:0.17
Consensus pattern (17 bp):
GGTCAACGGTCGGGTCG
Found at i:56023 original size:7 final size:7
Alignment explanation
Indices: 55970--56006 Score: 67
Period size: 7 Copynumber: 5.4 Consensus size: 7
55960 GTCAAAGAAA
55970 GTCAACG
1 GTCAACG
55977 GTCAACG
1 GTCAACG
55984 GTC-ACG
1 GTCAACG
55990 GTCAACG
1 GTCAACG
55997 GTCAACG
1 GTCAACG
56004 GTC
1 GTC
56007 GGGTCGGGTC
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
6 6 0.21
7 23 0.79
ACGTcount: A:0.24, C:0.30, G:0.30, T:0.16
Consensus pattern (7 bp):
GTCAACG
Found at i:56071 original size:19 final size:19
Alignment explanation
Indices: 56047--56116 Score: 115
Period size: 19 Copynumber: 3.7 Consensus size: 19
56037 AGTCGAGTCA
*
56047 GGTCAACCCGGTTCAGACC
1 GGTCAAACCGGTTCAGACC
56066 GGTCAAACCGGTTCAGACC
1 GGTCAAACCGGTTCAGACC
56085 GGTCAAACCGGTTC-GAACC
1 GGTCAAACCGGTTCAG-ACC
56104 GGTCAAACCGGTT
1 GGTCAAACCGGTT
56117 TTCCAGCAGC
Statistics
Matches: 49, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
18 1 0.02
19 48 0.98
ACGTcount: A:0.24, C:0.31, G:0.27, T:0.17
Consensus pattern (19 bp):
GGTCAAACCGGTTCAGACC
Found at i:56077 original size:9 final size:9
Alignment explanation
Indices: 56047--56115 Score: 75
Period size: 9 Copynumber: 7.3 Consensus size: 9
56037 AGTCGAGTCA
*
56047 GGTCAACCC
1 GGTCAAACC
*
56056 GGTTCAGACC
1 GG-TCAAACC
56066 GGTCAAACC
1 GGTCAAACC
*
56075 GGTTCAGACC
1 GG-TCAAACC
56085 GGTCAAACC
1 GGTCAAACC
*
56094 GGTTCGAACC
1 GG-TCAAACC
56104 GGTCAAACC
1 GGTCAAACC
56113 GGT
1 GGT
56116 TTTCCAGCAG
Statistics
Matches: 50, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
9 27 0.54
10 23 0.46
ACGTcount: A:0.25, C:0.32, G:0.28, T:0.16
Consensus pattern (9 bp):
GGTCAAACC
Found at i:62433 original size:60 final size:61
Alignment explanation
Indices: 62318--62437 Score: 149
Period size: 62 Copynumber: 2.0 Consensus size: 61
62308 CCCTAAGGGA
* *
62318 ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATTTCGGGCCGTGAGGCCTACCTAAGAAC
1 ACATCTTAGGGCCTGAGAGCCTACCC-AGATAGATCTCGGGCCGAGAGGCCTACCTAAGAAC
*
62380 ACATCTTAGGGCC-GCAGGGCCTACCC-GAT-GATCTCAGGGCCGCAGA-GCCTACCTAAGA
1 ACATCTTAGGGCCTG-AGAGCCTACCCAGATAGATCTC-GGGCCG-AGAGGCCTACCTAAGA
62438 GTCACATTAG
Statistics
Matches: 52, Mismatches: 3, Indels: 8
0.83 0.05 0.13
Matches are distributed among these distances:
59 5 0.10
60 21 0.40
61 3 0.06
62 23 0.44
ACGTcount: A:0.26, C:0.30, G:0.27, T:0.17
Consensus pattern (61 bp):
ACATCTTAGGGCCTGAGAGCCTACCCAGATAGATCTCGGGCCGAGAGGCCTACCTAAGAAC
Found at i:63271 original size:17 final size:17
Alignment explanation
Indices: 63249--63295 Score: 85
Period size: 17 Copynumber: 2.8 Consensus size: 17
63239 CACGGTCAAC
63249 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
63266 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
*
63283 GGTCAACAGTCGG
1 GGTCAACGGTCGG
63296 TCAACCCAGT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
17 29 1.00
ACGTcount: A:0.15, C:0.23, G:0.45, T:0.17
Consensus pattern (17 bp):
GGTCAACGGTCGGGTCG
Found at i:63274 original size:24 final size:26
Alignment explanation
Indices: 63224--63276 Score: 74
Period size: 24 Copynumber: 2.1 Consensus size: 26
63214 GTCAAAGAAA
63224 GTCAACGGTCACGGTCACGGTCAACG
1 GTCAACGGTCACGGTCACGGTCAACG
* *
63250 GTCAACGGTC-GGGTC-GGGTCAACG
1 GTCAACGGTCACGGTCACGGTCAACG
63274 GTC
1 GTC
63277 GGGTCGGGTC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 11 0.44
25 4 0.16
26 10 0.40
ACGTcount: A:0.19, C:0.28, G:0.36, T:0.17
Consensus pattern (26 bp):
GTCAACGGTCACGGTCACGGTCAACG
Found at i:63276 original size:7 final size:7
Alignment explanation
Indices: 63224--63259 Score: 58
Period size: 7 Copynumber: 5.4 Consensus size: 7
63214 GTCAAAGAAA
63224 GTCAACG
1 GTCAACG
63231 GTC-ACG
1 GTCAACG
63237 GTC-ACG
1 GTCAACG
63243 GTCAACG
1 GTCAACG
63250 GTCAACG
1 GTCAACG
63257 GTC
1 GTC
63260 GGGTCGGGTC
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
6 12 0.43
7 16 0.57
ACGTcount: A:0.22, C:0.31, G:0.31, T:0.17
Consensus pattern (7 bp):
GTCAACG
Done.