Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003801.1 Hibiscus syriacus cultivar Beakdansim tig00008129_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: 67622
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.33
Found at i:7237 original size:12 final size:12
Alignment explanation
Indices: 7220--7244 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
7210 GTCAAATAAT
7220 TTAGGCACCAAA
1 TTAGGCACCAAA
7232 TTAGGCACCAAA
1 TTAGGCACCAAA
7244 T
1 T
7245 GGTGATTTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.24, G:0.16, T:0.20
Consensus pattern (12 bp):
TTAGGCACCAAA
Found at i:9796 original size:20 final size:20
Alignment explanation
Indices: 9753--9800 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
9743 CAAAGTGACC
*
9753 CAATTTC-ACATTCAAACAT
1 CAATTTCAACACTCAAACAT
*
9772 CAATTTCAACACTCTAACAT
1 CAATTTCAACACTCAAACAT
*
9792 TAATTTCAA
1 CAATTTCAA
9801 GCATAGTACA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
19 7 0.28
20 18 0.72
ACGTcount: A:0.42, C:0.25, G:0.00, T:0.33
Consensus pattern (20 bp):
CAATTTCAACACTCAAACAT
Found at i:11611 original size:370 final size:371
Alignment explanation
Indices: 10920--11668 Score: 1428
Period size: 370 Copynumber: 2.0 Consensus size: 371
10910 AATTGAAAAT
10920 TTAATTAAATACATTGAAAGAAGACCTAATAGAATAGTTTAGGACAATTATTGAGTTGAATTAAA
1 TTAATTAAATACATTGAAAGAAGACCTAATAGAATAGTTTAGGACAATTATTGAGTTGAATTAAA
10985 ACTTGGATGAATTGAATTAAACCAATTTACCTAGGAATCGATTTGAATTAAAAGTTAATTAAGAA
66 ACTTGGATGAATTGAATTAAACCAATTTACCTAGGAATCGATTTGAATTAAAAGTTAATTAAGAA
11050 ATTTAGAAAATTGATTTGATCAAATTAAAGTAACCTAATTTCAATTAAATAAAAACATTAGAATT
131 ATTTAGAAAATTGATTTGATCAAATTAAAGTAACCTAATTTCAATTAAATAAAAACATTAGAATT
11115 GAATATAATGAAGAACCTAATTGAGAGGAGTGAAAGAGTAATGACCAAATTACGGTGATCAAGTA
196 GAATATAATGAAGAACCTAATTGAGAGGAGTGAAAGAGTAATGACCAAATTACGGTGATCAAGTA
* *
11180 GGAATTATATACAAATGTTATAATTGCATGCTAAATTTCTAGATTCCTACAATTGCCCTTGAATA
261 GGAATTATATACAAATGTTATAATTGCATGCTAAATTTCTAGATTCCTAAAATTACCCTTGAATA
11245 GTTGATATCTTAAGCATTAAAGCAGGCTAATTAGGACATTT-CATC
326 GTTGATATCTTAAGCATTAAAGCAGGCTAATTAGGACATTTCCATC
11290 TTAATTAAATACATTGAAAGAAGACCTAATAGAATAGTTTAGGACAATTATTGAGTTGAATTAAA
1 TTAATTAAATACATTGAAAGAAGACCTAATAGAATAGTTTAGGACAATTATTGAGTTGAATTAAA
*
11355 ACTTGGATGAATTGAATTAAACCAATTTACCTAGGAATCTATTTGAATTAAAAGTTAATTAAGAA
66 ACTTGGATGAATTGAATTAAACCAATTTACCTAGGAATCGATTTGAATTAAAAGTTAATTAAGAA
*
11420 ATTTAGAAAATTTATTTGATCAAATTAAAGTAACCTAATTTCAATTAAATAAAAACATTAGAATT
131 ATTTAGAAAATTGATTTGATCAAATTAAAGTAACCTAATTTCAATTAAATAAAAACATTAGAATT
*
11485 TAATATAATGAAGAACCTAATTGAGAGGAGTGAAAGAGTAATGACCAAATTACGGTGATCAAGTA
196 GAATATAATGAAGAACCTAATTGAGAGGAGTGAAAGAGTAATGACCAAATTACGGTGATCAAGTA
*
11550 GGAATTATATACAAATGTTATAATTGCATGCTAAATTTCTAGATTCCTAAAATTACCCTTGAATG
261 GGAATTATATACAAATGTTATAATTGCATGCTAAATTTCTAGATTCCTAAAATTACCCTTGAATA
*
11615 GTTGATATCTTAAGCATTAAAGGAGGCTAATTAGGACATTTCCATC
326 GTTGATATCTTAAGCATTAAAGCAGGCTAATTAGGACATTTCCATC
11661 TTAATTAA
1 TTAATTAA
11669 GGATGAAGTG
Statistics
Matches: 371, Mismatches: 7, Indels: 1
0.98 0.02 0.00
Matches are distributed among these distances:
370 359 0.97
371 12 0.03
ACGTcount: A:0.43, C:0.10, G:0.15, T:0.32
Consensus pattern (371 bp):
TTAATTAAATACATTGAAAGAAGACCTAATAGAATAGTTTAGGACAATTATTGAGTTGAATTAAA
ACTTGGATGAATTGAATTAAACCAATTTACCTAGGAATCGATTTGAATTAAAAGTTAATTAAGAA
ATTTAGAAAATTGATTTGATCAAATTAAAGTAACCTAATTTCAATTAAATAAAAACATTAGAATT
GAATATAATGAAGAACCTAATTGAGAGGAGTGAAAGAGTAATGACCAAATTACGGTGATCAAGTA
GGAATTATATACAAATGTTATAATTGCATGCTAAATTTCTAGATTCCTAAAATTACCCTTGAATA
GTTGATATCTTAAGCATTAAAGCAGGCTAATTAGGACATTTCCATC
Found at i:11749 original size:15 final size:16
Alignment explanation
Indices: 11729--11765 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
11719 AGTAAAAATG
*
11729 AGAAAAATT-GGAGAA
1 AGAAAAATTAAGAGAA
11744 AGAAAAATTAAGAGAA
1 AGAAAAATTAAGAGAA
11760 AGAAAA
1 AGAAAA
11766 GAGGAGTTTG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 9 0.45
16 11 0.55
ACGTcount: A:0.68, C:0.00, G:0.22, T:0.11
Consensus pattern (16 bp):
AGAAAAATTAAGAGAA
Found at i:12529 original size:26 final size:26
Alignment explanation
Indices: 12500--12550 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 26
12490 AAATATTATA
*
12500 ATTTAGTCACTAATTTTAATACTTTC
1 ATTTAATCACTAATTTTAATACTTTC
* * *
12526 ATTTAATTACTAGTTTTATTACTTT
1 ATTTAATCACTAATTTTAATACTTT
12551 TTATATTTTA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.29, C:0.12, G:0.04, T:0.55
Consensus pattern (26 bp):
ATTTAATCACTAATTTTAATACTTTC
Found at i:12636 original size:41 final size:41
Alignment explanation
Indices: 12554--12650 Score: 99
Period size: 41 Copynumber: 2.3 Consensus size: 41
12544 TTACTTTTTA
* * *
12554 TATTTTAATATTATAGTTTTAATTTCATTTATTTTAGTTAT
1 TATTTTAATTTTATAGTTTTAATTTCATATATTTTAATTAT
* *
12595 TGTTTTAATTTTATA-TTCTTATTTTCA-ATATATTTAATTAT
1 TATTTTAATTTTATAGTT-TTAATTTCATATAT-TTTAATTAT
*
12636 TATTATTATTTTTAT
1 TATT-TTAATTTTAT
12651 TTTTAGTTAG
Statistics
Matches: 46, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
40 5 0.11
41 32 0.70
42 9 0.20
ACGTcount: A:0.29, C:0.03, G:0.03, T:0.65
Consensus pattern (41 bp):
TATTTTAATTTTATAGTTTTAATTTCATATATTTTAATTAT
Found at i:15039 original size:13 final size:13
Alignment explanation
Indices: 15021--15047 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
15011 TAATAAATAA
15021 TATTTATTTATTT
1 TATTTATTTATTT
15034 TATTTATTTATTT
1 TATTTATTTATTT
15047 T
1 T
15048 CTATTAAATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (13 bp):
TATTTATTTATTT
Found at i:17405 original size:13 final size:13
Alignment explanation
Indices: 17387--17413 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
17377 TAATAAATAA
17387 TATTTATTTATTT
1 TATTTATTTATTT
17400 TATTTATTTATTT
1 TATTTATTTATTT
17413 T
1 T
17414 CTATTAAATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (13 bp):
TATTTATTTATTT
Found at i:19107 original size:36 final size:36
Alignment explanation
Indices: 19060--19128 Score: 111
Period size: 36 Copynumber: 1.9 Consensus size: 36
19050 CTATGCACAG
* *
19060 AAAGATCCTATTATATTAATACCAAAAGTATTCCAC
1 AAAGATCCTATTAGATTAATACCAAAAGCATTCCAC
*
19096 AAAGATCCTATTAGATTGATACCAAAAGCATTC
1 AAAGATCCTATTAGATTAATACCAAAAGCATTC
19129 TATGGAAAGA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 30 1.00
ACGTcount: A:0.43, C:0.19, G:0.09, T:0.29
Consensus pattern (36 bp):
AAAGATCCTATTAGATTAATACCAAAAGCATTCCAC
Found at i:19854 original size:6 final size:6
Alignment explanation
Indices: 19843--19895 Score: 70
Period size: 6 Copynumber: 8.5 Consensus size: 6
19833 TATTCACATC
* *
19843 TTTGCA TTTGCA TTTGCA TTTTCA TTTGCA TTTTCA TTTGCA TCTTTGCA
1 TTTGCA TTTGCA TTTGCA TTTGCA TTTGCA TTTGCA TTTGCA --TTTGCA
19893 TTT
1 TTT
19896 TTATATTTGT
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
6 35 0.85
8 6 0.15
ACGTcount: A:0.15, C:0.17, G:0.11, T:0.57
Consensus pattern (6 bp):
TTTGCA
Found at i:23170 original size:7 final size:7
Alignment explanation
Indices: 23160--23192 Score: 57
Period size: 7 Copynumber: 4.6 Consensus size: 7
23150 AAAAAAGGGG
23160 AAAAGGA
1 AAAAGGA
23167 AAAAGGA
1 AAAAGGA
23174 AAAAGGAA
1 AAAAGG-A
23182 AAAAGGA
1 AAAAGGA
23189 AAAA
1 AAAA
23193 ATTAAATCAA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
7 18 0.72
8 7 0.28
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (7 bp):
AAAAGGA
Found at i:23177 original size:8 final size:8
Alignment explanation
Indices: 23150--23193 Score: 56
Period size: 8 Copynumber: 5.8 Consensus size: 8
23140 ATAAAAAATA
23150 AAAAAAGG
1 AAAAAAGG
**
23158 GGAAAAGG
1 AAAAAAGG
23166 -AAAAAGG
1 AAAAAAGG
23173 -AAAAAGG
1 AAAAAAGG
23180 AAAAAAGG
1 AAAAAAGG
23188 AAAAAA
1 AAAAAA
23194 TTAAATCAAG
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
7 13 0.41
8 19 0.59
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (8 bp):
AAAAAAGG
Found at i:23185 original size:15 final size:15
Alignment explanation
Indices: 23150--23192 Score: 61
Period size: 15 Copynumber: 2.9 Consensus size: 15
23140 ATAAAAAATA
*
23150 AAAAAAGGGGAAAAGG
1 AAAAAA-GGAAAAAGG
23166 -AAAAAGGAAAAAGG
1 AAAAAAGGAAAAAGG
23180 AAAAAAGGAAAAA
1 AAAAAAGGAAAAA
23193 ATTAAATCAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
14 8 0.32
15 17 0.68
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (15 bp):
AAAAAAGGAAAAAGG
Found at i:26530 original size:75 final size:75
Alignment explanation
Indices: 26398--26542 Score: 191
Period size: 75 Copynumber: 1.9 Consensus size: 75
26388 ACAAGAAGAA
* * * * *
26398 AATGATGGAGCATGCTGAAAGTCCATTTCAATCATAATCAGGAATAATGACATATTTTGAACGTT
1 AATGATGGAGCATGCTGAAAGCCCATTTCAATAAGAATCAGGAATAATGACACATTTTGAACGCT
26463 TGTATTAGCC
66 TGTATTAGCC
* * * ** *
26473 AATGTTGGGGCATGCTGAAAGCCCCTTTCAATAAGAATCAGGAATGTTGACGCATTTTGAACGCT
1 AATGATGGAGCATGCTGAAAGCCCATTTCAATAAGAATCAGGAATAATGACACATTTTGAACGCT
26538 TGTAT
66 TGTAT
26543 CAGCAAATCT
Statistics
Matches: 59, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
75 59 1.00
ACGTcount: A:0.32, C:0.16, G:0.21, T:0.31
Consensus pattern (75 bp):
AATGATGGAGCATGCTGAAAGCCCATTTCAATAAGAATCAGGAATAATGACACATTTTGAACGCT
TGTATTAGCC
Found at i:27694 original size:24 final size:24
Alignment explanation
Indices: 27667--27798 Score: 167
Period size: 24 Copynumber: 5.5 Consensus size: 24
27657 TATATCAAAA
* * *
27667 ATCAAATCATAATTCATGTCAAGT
1 ATCAGATCAGAATCCATGTCAAGT
* * *
27691 ATCATATCAAAATCCAGGTCAAGT
1 ATCAGATCAGAATCCATGTCAAGT
*
27715 ATCAGATCAGAATCCAAGTCAAGT
1 ATCAGATCAGAATCCATGTCAAGT
*
27739 ATCAGATAAGAATCCATGTC-AGAT
1 ATCAGATCAGAATCCATGTCAAG-T
*
27763 ATCAGATCATAATCCATGTCAAGT
1 ATCAGATCAGAATCCATGTCAAGT
27787 ATCAGATCAGAA
1 ATCAGATCAGAA
27799 ATCAAATCGA
Statistics
Matches: 94, Mismatches: 12, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
23 2 0.02
24 90 0.96
25 2 0.02
ACGTcount: A:0.42, C:0.19, G:0.14, T:0.26
Consensus pattern (24 bp):
ATCAGATCAGAATCCATGTCAAGT
Found at i:27815 original size:48 final size:48
Alignment explanation
Indices: 27664--27815 Score: 157
Period size: 48 Copynumber: 3.2 Consensus size: 48
27654 GGATATATCA
* * * *
27664 AAAATCAAATCATAATTCATGTCAAGTATCATATCA-AAATCCAGGTC
1 AAAATCAGATCATAATCCATGTCAAGTATCAGATCAGAAATCCAAGTC
* * * * *
27711 AAGTATCAGATCAGAATCCAAGTCAAGTATCAGATAAG-AATCCATGTC
1 AA-AATCAGATCATAATCCATGTCAAGTATCAGATCAGAAATCCAAGTC
* *
27759 AGATATCAGATCATAATCCATGTCAAGTATCAGATCAGAAAT-CAAATC
1 A-AAATCAGATCATAATCCATGTCAAGTATCAGATCAGAAATCCAAGTC
27807 GAAAATCAG
1 -AAAATCAG
27816 GTAAAATATT
Statistics
Matches: 86, Mismatches: 14, Indels: 9
0.79 0.13 0.08
Matches are distributed among these distances:
47 2 0.02
48 79 0.92
49 5 0.06
ACGTcount: A:0.44, C:0.18, G:0.13, T:0.24
Consensus pattern (48 bp):
AAAATCAGATCATAATCCATGTCAAGTATCAGATCAGAAATCCAAGTC
Found at i:27815 original size:72 final size:72
Alignment explanation
Indices: 27681--27815 Score: 177
Period size: 72 Copynumber: 1.9 Consensus size: 72
27671 AATCATAATT
* * *
27681 CATGTCAAGTATCATATCAAAATCCAGGTCAAGTATCAGATCAGAATCCAAGTCAAGTATCAGAT
1 CATGTCAAGTATCAGATCAAAATCCAGGTCAAGTATCAGATCAGAATCCAAATCAAGAATCAGAT
27746 AAGAATC
66 AAGAATC
* *
27753 CATGTC-AGATATCAGATCATAATCCATGTCAAGTATCAGATCAGAAAT-CAAATCGAA-AATCA
1 CATGTCAAG-TATCAGATCAAAATCCAGGTCAAGTATCAGATCAG-AATCCAAATC-AAGAATCA
27815 G
63 G
27816 GTAAAATATT
Statistics
Matches: 55, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
71 2 0.04
72 48 0.87
73 5 0.09
ACGTcount: A:0.42, C:0.19, G:0.15, T:0.24
Consensus pattern (72 bp):
CATGTCAAGTATCAGATCAAAATCCAGGTCAAGTATCAGATCAGAATCCAAATCAAGAATCAGAT
AAGAATC
Found at i:31988 original size:22 final size:22
Alignment explanation
Indices: 31958--32041 Score: 98
Period size: 22 Copynumber: 3.8 Consensus size: 22
31948 TATCAACATC
*
31958 TACATTCTTCAAAGATGATAGA
1 TACACTCTTCAAAGATGATAGA
31980 TACACTCTTCAAAGATGATAGA
1 TACACTCTTCAAAGATGATAGA
* * *
32002 TTCTCTTTTCAAAGATGATAGA
1 TACACTCTTCAAAGATGATAGA
* *
32024 TTA-TCTTTTCAAAGATGA
1 -TACACTCTTCAAAGATGA
32042 AAGCCTTATT
Statistics
Matches: 56, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
22 55 0.98
23 1 0.02
ACGTcount: A:0.37, C:0.14, G:0.13, T:0.36
Consensus pattern (22 bp):
TACACTCTTCAAAGATGATAGA
Found at i:32791 original size:36 final size:34
Alignment explanation
Indices: 32746--32867 Score: 93
Period size: 36 Copynumber: 3.4 Consensus size: 34
32736 TAGTAATTTA
32746 TCTCACTTGAGATTATTTTTCTTAAAACAAACTGTG
1 TCTCACTTGAGATTATTTTTCTTAAAACAAA-T-TG
* * ** * *
32782 TCTCGCTTGAGA-CAGTTTCACTTGAAACTACAATTTA
1 TCTCACTTGAGATTA-TTTTTCTT-AAA--ACAAATTG
*
32819 TCTCACTTGAGATTGTTTTTCTTAAAACAAGATTCG
1 TCTCACTTGAGATTATTTTTCTTAAAACAA-ATT-G
*
32855 TCTCGCTTGAGAT
1 TCTCACTTGAGAT
32868 AGTTTCATTA
Statistics
Matches: 65, Mismatches: 14, Indels: 14
0.70 0.15 0.15
Matches are distributed among these distances:
34 4 0.06
35 3 0.05
36 32 0.49
37 21 0.32
38 1 0.02
39 4 0.06
ACGTcount: A:0.28, C:0.19, G:0.14, T:0.39
Consensus pattern (34 bp):
TCTCACTTGAGATTATTTTTCTTAAAACAAATTG
Found at i:32859 original size:73 final size:73
Alignment explanation
Indices: 32740--32882 Score: 220
Period size: 73 Copynumber: 2.0 Consensus size: 73
32730 TTCAAATAGT
32740 AATTTATCTCACTTGAGATTATTTTTCTTAAAACAAACTGTGTCTCGCTTGAGACAGTTTCACTT
1 AATTTATCTCACTTGAGATTATTTTTCTTAAAACAAACTGTGTCTCGCTTGAGACAGTTTCA-TT
32805 -GAAACTAC
65 AGAAACTAC
* *
32813 AATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAGA-T-TCGTCTCGCTTGAGATAGTTTCAT
1 AATTTATCTCACTTGAGATTATTTTTCTTAAAACAA-ACTGT-GTCTCGCTTGAGACAGTTTCAT
32876 TAGAAAC
64 TAGAAAC
32883 AAAAATTTCC
Statistics
Matches: 65, Mismatches: 2, Indels: 6
0.89 0.03 0.08
Matches are distributed among these distances:
72 3 0.05
73 61 0.94
74 1 0.02
ACGTcount: A:0.30, C:0.17, G:0.13, T:0.39
Consensus pattern (73 bp):
AATTTATCTCACTTGAGATTATTTTTCTTAAAACAAACTGTGTCTCGCTTGAGACAGTTTCATTA
GAAACTAC
Found at i:32883 original size:36 final size:35
Alignment explanation
Indices: 32781--32885 Score: 90
Period size: 36 Copynumber: 2.9 Consensus size: 35
32771 AACAAACTGT
* *
32781 GTCTCGCTTGAGACAGTTTCACTT-GAAACTACAATTT
1 GTCTCGCTTGAGATAGTTTCA-TTAGAAAC-A-AATTC
* * *
32818 ATCTCACTTGAGATTGTTTTTC-TTA-AAACAAGATTC
1 GTCTCGCTTGAGATAG--TTTCATTAGAAACAA-ATTC
32854 GTCTCGCTTGAGATAGTTTCATTAGAAACAAA
1 GTCTCGCTTGAGATAGTTTCATTAGAAACAAA
32886 AATTTCCATC
Statistics
Matches: 54, Mismatches: 8, Indels: 14
0.71 0.11 0.18
Matches are distributed among these distances:
34 4 0.07
35 5 0.09
36 23 0.43
37 18 0.33
39 4 0.07
ACGTcount: A:0.30, C:0.18, G:0.15, T:0.36
Consensus pattern (35 bp):
GTCTCGCTTGAGATAGTTTCATTAGAAACAAATTC
Found at i:32898 original size:73 final size:73
Alignment explanation
Indices: 32740--32898 Score: 200
Period size: 73 Copynumber: 2.2 Consensus size: 73
32730 TTCAAATAGT
*
32740 AATTTATCTCACTTGAGATTATTTTTCTTAAAACAAACTGTGTCTCGCTTGAGACAGTTTCACTT
1 AATTTACCTCACTTGAGATTATTTTTCTTAAAACAAACTGTGTCTCGCTTGAGACAGTTTCACTT
* *
32805 GAAACTAC
66 GAAACAAA
* * *
32813 AATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAGA-T-TCGTCTCGCTTGAGATAGTTTCA-
1 AATTTACCTCACTTGAGATTATTTTTCTTAAAACAA-ACTGT-GTCTCGCTTGAGACAGTTTCAC
32875 TTAGAAACAAA
64 TT-GAAACAAA
32886 AATTT-CCATCACT
1 AATTTACC-TCACT
32899 CGATGGATCA
Statistics
Matches: 77, Mismatches: 5, Indels: 8
0.86 0.06 0.09
Matches are distributed among these distances:
72 4 0.05
73 72 0.94
74 1 0.01
ACGTcount: A:0.31, C:0.18, G:0.12, T:0.38
Consensus pattern (73 bp):
AATTTACCTCACTTGAGATTATTTTTCTTAAAACAAACTGTGTCTCGCTTGAGACAGTTTCACTT
GAAACAAA
Found at i:33314 original size:224 final size:225
Alignment explanation
Indices: 32898--33347 Score: 647
Period size: 224 Copynumber: 2.0 Consensus size: 225
32888 TTTCCATCAC
*
32898 TCGATGGATCAACATTTCTAGAGGAAGTTCATAATGAGAAGAAATCATTTGAAGAGGAAGAAGAA
1 TCGATGGATCAACATTTCTAGAGGAAGTTCATAATGAGAAGAAATCATCTGAAGAGGAAGAAGAA
* * * * * *
32963 GTTCATAATGGGAAGAACTTGTTCAACCTTTTGCTCGATTCTATCTCGGAAGGAGATAAATCAGC
66 GTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTCGACTCCATCTCAGAAAGAGATAAAGCAGC
33028 ACCAACATTTCCAGGTAGAGTTCATAATGAGAAGAACTCATCTAAAGAGGAAGAAGGAGTTCATA
131 ACCAACATTTCCAGGTAGAGTTCATAATGAGAAGAACTCATCTAAAGAGGAAGAAGGAGTTCATA
* *
33093 ATGAGAAGAACTTGTTCAACTTTAGCTTGA
196 ATGAGAAGAACTTGTTCAACCTTAACTTGA
* * *
33123 TCGATGGATCAA-ATTTTTCAGA-GAA-TTCATAATGAGGAGAACTCATCTGAAGAGGAAGAAGA
1 TCGATGGATCAACATTTCT-AGAGGAAGTTCATAATGAGAAGAAATCATCTGAAGAGGAAGAAGA
* * * *
33185 AGTTCATAATGAGAAGAACTTGTTCAACCTTTTGTTTGACTCCATTTCTATAAAGAGATAAAGCA
65 AGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTCGACTCCATCTC-AGAAAGAGATAAAGCA
* * * *
33250 GCA-GAGCCATTTCCGGGTAGAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGGAGTTC
129 GCACCA-ACATTTCCAGGTAGAGTTCATAATGAGAAGAACTCATCTAAAGAGGAAGAAGGAGTTC
* *
33314 ATAATGAGAAGAATTTGTTCGACCTTAACTTGA
193 ATAATGAGAAGAACTTGTTCAACCTTAACTTGA
33347 T
1 T
33348 TCATCACCTA
Statistics
Matches: 200, Mismatches: 22, Indels: 7
0.87 0.10 0.03
Matches are distributed among these distances:
223 77 0.38
224 108 0.54
225 15 0.08
ACGTcount: A:0.37, C:0.14, G:0.22, T:0.27
Consensus pattern (225 bp):
TCGATGGATCAACATTTCTAGAGGAAGTTCATAATGAGAAGAAATCATCTGAAGAGGAAGAAGAA
GTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTCGACTCCATCTCAGAAAGAGATAAAGCAGC
ACCAACATTTCCAGGTAGAGTTCATAATGAGAAGAACTCATCTAAAGAGGAAGAAGGAGTTCATA
ATGAGAAGAACTTGTTCAACCTTAACTTGA
Found at i:33452 original size:139 final size:138
Alignment explanation
Indices: 33269--33609 Score: 399
Period size: 139 Copynumber: 2.5 Consensus size: 138
33259 TTTCCGGGTA
* * * *
33269 GAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGGAGTTCATAATGAGAAGAATTTGTTC
1 GAGTTCATAATAAGAAGAACTCATCTGAAAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
* * * * *
33334 -GACCTTAACTTGATTCATCACCTATGGAGTTGAATGAAAGAAGAACCTCACTT-GAGGATCAAC
66 AAACCTTAACTTAATTCATCACCTATGAAGTTGAATCAAAG-A-AACCTC-CTTCAAGGATCAAC
**
33397 ATTTTTAG-AG
128 ATTTCCAGAAG
33407 GAAGTTCATAATAAGAAGAACTCATCTGAAAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
1 G-AGTTCATAATAAGAAGAACTCATCTGAAAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
** * * * *
33472 CAAACCTTGCCTTAATTCATCACTTATGAAGTTGAATCAATGACACCTCTTTCAAGGATCAACAT
65 CAAACCTTAACTTAATTCATCACCTATGAAGTTGAATCAAAGAAACCTCCTTCAAGGATCAACAT
33537 TTCCAGAAG
130 TTCCAGAAG
* * * *
33546 GAGTTCATAATGAA-AAGAAATCATATG-AAA--AAGAAGAAGTTCATAACGAGAAGAACTTATT
1 GAGTTCATAAT-AAGAAGAACTCATCTGAAAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
33607 CAA
65 CAA
33610 CTTTTTTCTA
Statistics
Matches: 177, Mismatches: 21, Indels: 13
0.84 0.10 0.06
Matches are distributed among these distances:
135 32 0.18
137 5 0.03
138 42 0.24
139 66 0.37
140 32 0.18
ACGTcount: A:0.41, C:0.14, G:0.19, T:0.26
Consensus pattern (138 bp):
GAGTTCATAATAAGAAGAACTCATCTGAAAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
AAACCTTAACTTAATTCATCACCTATGAAGTTGAATCAAAGAAACCTCCTTCAAGGATCAACATT
TCCAGAAG
Found at i:33834 original size:3 final size:3
Alignment explanation
Indices: 33826--33904 Score: 92
Period size: 3 Copynumber: 26.3 Consensus size: 3
33816 TTTTATTTAT
33826 TTA TTA TTA TTCA -TA TTA TTA TT- TTA TTTA TTA TTA TTA TTA -TA
1 TTA TTA TTA TT-A TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA
* *
33870 ATA TTA TTTA TTA TTG TTA TTA TTA TTA TTA TTA T
1 TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA T
33905 ATGCCCAAAT
Statistics
Matches: 67, Mismatches: 3, Indels: 12
0.82 0.04 0.15
Matches are distributed among these distances:
2 5 0.07
3 55 0.82
4 7 0.10
ACGTcount: A:0.32, C:0.01, G:0.01, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:33904 original size:24 final size:25
Alignment explanation
Indices: 33822--33902 Score: 103
Period size: 24 Copynumber: 3.2 Consensus size: 25
33812 TTGGTTTTAT
33822 TTATTTATTATTATTCA-TATTATTA
1 TTATTTATTATTATT-ATTATTATTA
*
33847 TTTTATTTATTATTATTATTA-TAATA
1 --TTATTTATTATTATTATTATTATTA
*
33873 TTATTTATTATTGTTATTATTATTA
1 TTATTTATTATTATTATTATTATTA
33898 TTATT
1 TTATT
33903 ATATGCCCAA
Statistics
Matches: 49, Mismatches: 3, Indels: 6
0.84 0.05 0.10
Matches are distributed among these distances:
24 18 0.37
25 9 0.18
26 5 0.10
27 17 0.35
ACGTcount: A:0.31, C:0.01, G:0.01, T:0.67
Consensus pattern (25 bp):
TTATTTATTATTATTATTATTATTA
Found at i:35666 original size:2 final size:2
Alignment explanation
Indices: 35598--35655 Score: 109
Period size: 2 Copynumber: 29.5 Consensus size: 2
35588 ATTTATAAAA
35598 AT AT A- 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
35639 AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT A
35656 AGTTAATATA
Statistics
Matches: 55, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 54 0.98
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:38260 original size:20 final size:20
Alignment explanation
Indices: 38226--38271 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
38216 AAGTGACCCG
*
38226 ATTTC-ACATTCTAACATCA
1 ATTTCAACACTCTAACATCA
*
38245 ATTTCAACACTCTAACATTA
1 ATTTCAACACTCTAACATCA
38265 ATTTCAA
1 ATTTCAA
38272 GCATAGTACA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 5 0.21
20 19 0.79
ACGTcount: A:0.39, C:0.24, G:0.00, T:0.37
Consensus pattern (20 bp):
ATTTCAACACTCTAACATCA
Found at i:39856 original size:16 final size:16
Alignment explanation
Indices: 39833--39869 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
39823 GAAAAAAATG
*
39833 AGAAAATTTG-GAGAA
1 AGAAAAATTGAGAGAA
39848 AGAAAAATTGAGAGAA
1 AGAAAAATTGAGAGAA
39864 AGAAAA
1 AGAAAA
39870 GAGGAGTTTG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 9 0.45
16 11 0.55
ACGTcount: A:0.62, C:0.00, G:0.24, T:0.14
Consensus pattern (16 bp):
AGAAAAATTGAGAGAA
Found at i:43535 original size:20 final size:20
Alignment explanation
Indices: 43499--43546 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
43489 CAAAGTGACC
*
43499 CAATTTC-ACATTCTAACAT
1 CAATTTCAACACTCTAACAT
*
43518 CAATTTCAACACTCTAACTT
1 CAATTTCAACACTCTAACAT
*
43538 TAATTTCAA
1 CAATTTCAA
43547 GCATAGTACC
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
19 7 0.28
20 18 0.72
ACGTcount: A:0.38, C:0.25, G:0.00, T:0.38
Consensus pattern (20 bp):
CAATTTCAACACTCTAACAT
Found at i:45131 original size:16 final size:16
Alignment explanation
Indices: 45108--45144 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
45098 GAAAAAAATG
*
45108 AGAAAATTTG-GAGAA
1 AGAAAAATTGAGAGAA
45123 AGAAAAATTGAGAGAA
1 AGAAAAATTGAGAGAA
45139 AGAAAA
1 AGAAAA
45145 GAGGAGTTTG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 9 0.45
16 11 0.55
ACGTcount: A:0.62, C:0.00, G:0.24, T:0.14
Consensus pattern (16 bp):
AGAAAAATTGAGAGAA
Found at i:46856 original size:20 final size:20
Alignment explanation
Indices: 46820--46867 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
46810 CAAAGTGACC
*
46820 CAATTTC-ACATTCTAACAT
1 CAATTTCAACACTCTAACAT
*
46839 CAATTTCAACACTCTAACTT
1 CAATTTCAACACTCTAACAT
*
46859 TAATTTCAA
1 CAATTTCAA
46868 GCATAGTACC
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
19 7 0.28
20 18 0.72
ACGTcount: A:0.38, C:0.25, G:0.00, T:0.38
Consensus pattern (20 bp):
CAATTTCAACACTCTAACAT
Found at i:48411 original size:16 final size:16
Alignment explanation
Indices: 48388--48424 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
48378 AGAAAAAATG
*
48388 AGAAAATTTG-GAGAA
1 AGAAAAATTGAGAGAA
48403 AGAAAAATTGAGAGAA
1 AGAAAAATTGAGAGAA
48419 AGAAAA
1 AGAAAA
48425 GAGGATTTTG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 9 0.45
16 11 0.55
ACGTcount: A:0.62, C:0.00, G:0.24, T:0.14
Consensus pattern (16 bp):
AGAAAAATTGAGAGAA
Found at i:50653 original size:21 final size:21
Alignment explanation
Indices: 50627--50682 Score: 112
Period size: 21 Copynumber: 2.7 Consensus size: 21
50617 GATACTGACT
50627 ATCGCAACGCGATAATACAAA
1 ATCGCAACGCGATAATACAAA
50648 ATCGCAACGCGATAATACAAA
1 ATCGCAACGCGATAATACAAA
50669 ATCGCAACGCGATA
1 ATCGCAACGCGATA
50683 CTGACTTTCG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.45, C:0.25, G:0.16, T:0.14
Consensus pattern (21 bp):
ATCGCAACGCGATAATACAAA
Found at i:50695 original size:20 final size:20
Alignment explanation
Indices: 50670--50762 Score: 168
Period size: 20 Copynumber: 4.7 Consensus size: 20
50660 TAATACAAAA
50670 TCGCAACGCGATACTGACTT
1 TCGCAACGCGATACTGACTT
50690 TCGCAACGCGATACTGACTT
1 TCGCAACGCGATACTGACTT
50710 TCGCAACGCGATACTGACTT
1 TCGCAACGCGATACTGACTT
*
50730 TCGCAACGCGATTCTGACTT
1 TCGCAACGCGATACTGACTT
*
50750 TCGCAACGAGATA
1 TCGCAACGCGATA
50763 ATACATAATC
Statistics
Matches: 70, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 70 1.00
ACGTcount: A:0.26, C:0.29, G:0.20, T:0.25
Consensus pattern (20 bp):
TCGCAACGCGATACTGACTT
Found at i:50935 original size:12 final size:12
Alignment explanation
Indices: 50916--50949 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
50906 CTCTCTGGCG
50916 ACATCCGTTCCT
1 ACATCCGTTCCT
*
50928 ATATCCGTTCCT
1 ACATCCGTTCCT
50940 ACATCC-TTCC
1 ACATCCGTTCC
50950 CCATCCGACA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
11 4 0.20
12 16 0.80
ACGTcount: A:0.18, C:0.41, G:0.06, T:0.35
Consensus pattern (12 bp):
ACATCCGTTCCT
Found at i:51123 original size:20 final size:20
Alignment explanation
Indices: 51098--51155 Score: 98
Period size: 20 Copynumber: 2.9 Consensus size: 20
51088 ATTCATTTGA
51098 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
51118 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
* *
51138 CTATCACAACGAGAAAAT
1 CTATCGCAACGCGAAAAT
51156 CGCAATGCGA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.40, C:0.24, G:0.21, T:0.16
Consensus pattern (20 bp):
CTATCGCAACGCGAAAATGG
Found at i:51205 original size:19 final size:19
Alignment explanation
Indices: 51183--51247 Score: 130
Period size: 19 Copynumber: 3.4 Consensus size: 19
51173 GATTTTCTCG
51183 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
51202 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
51221 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
51240 TTGCGATT
1 TTGCGATT
51248 CTCTCGTTGC
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 46 1.00
ACGTcount: A:0.15, C:0.20, G:0.17, T:0.48
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:51407 original size:14 final size:14
Alignment explanation
Indices: 51388--51424 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
51378 CATCAATTAA
51388 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
51402 ACAAATCATCTTTT
1 ACAAATCAACATTT
51416 ACAAATCAA
1 ACAAATCAA
51425 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:53453 original size:20 final size:20
Alignment explanation
Indices: 53427--53561 Score: 130
Period size: 20 Copynumber: 6.7 Consensus size: 20
53417 GATTATGTAT
53427 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
53447 AATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
53467 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
* ** *
53487 TATCTCGTTGCGATTTTTGT-AT
1 TATCGCGTTGCGA---AAGTCAG
* * *
53509 TATCGCATTGCGATAGTAAG
1 TATCGCGTTGCGAAAGTCAG
*
53529 TATCGCATTGC-AATAGTCAG
1 TATCGCGTTGCGAA-AGTCAG
*
53549 TATCGCATTGCGA
1 TATCGCGTTGCGA
53562 TTTTCCCAAT
Statistics
Matches: 97, Mismatches: 12, Indels: 11
0.81 0.10 0.09
Matches are distributed among these distances:
19 4 0.04
20 78 0.80
21 1 0.01
22 12 0.12
23 2 0.02
ACGTcount: A:0.25, C:0.19, G:0.25, T:0.31
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTCAG
Found at i:53521 original size:62 final size:62
Alignment explanation
Indices: 53448--53565 Score: 166
Period size: 62 Copynumber: 1.9 Consensus size: 62
53438 GAAAGTCAGA
* * * * *
53448 ATCGCGTTGCGAAAGTCAGTATCGCGTTGCGAA-AGTCAGTATCTCGTTGCGATTTTTGTATT
1 ATCGCATTGCGAAAGTAAGTATCGCATTGC-AATAGTCAGTATCGCATTGCGATTTTTGTATT
*
53510 ATCGCATTGCGATAGTAAGTATCGCATTGCAATAGTCAGTATCGCATTGCGATTTT
1 ATCGCATTGCGAAAGTAAGTATCGCATTGCAATAGTCAGTATCGCATTGCGATTTT
53566 CCCAATTCGC
Statistics
Matches: 49, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
61 2 0.04
62 47 0.96
ACGTcount: A:0.24, C:0.18, G:0.24, T:0.35
Consensus pattern (62 bp):
ATCGCATTGCGAAAGTAAGTATCGCATTGCAATAGTCAGTATCGCATTGCGATTTTTGTATT
Found at i:53703 original size:20 final size:20
Alignment explanation
Indices: 53680--53725 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 20
53670 CAACGCGAAT
*
53680 TTGCGATAATAGAGATCGCG
1 TTGCGATAATAGAGATCGCA
* *
53700 TTGCGA-ATTAGCGATCGCA
1 TTGCGATAATAGAGATCGCA
53719 TTGCGAT
1 TTGCGAT
53726 TTTGTTGGTC
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
19 16 0.73
20 6 0.27
ACGTcount: A:0.26, C:0.17, G:0.28, T:0.28
Consensus pattern (20 bp):
TTGCGATAATAGAGATCGCA
Found at i:55629 original size:20 final size:20
Alignment explanation
Indices: 55593--55640 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
55583 CAAAGTGACC
*
55593 CAATTTC-ACATTCTAACAT
1 CAATTTCAACACTCTAACAT
55612 CAATTTCAACACTCTAACAT
1 CAATTTCAACACTCTAACAT
*
55632 TAATTTCAA
1 CAATTTCAA
55641 GCATAGTACA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
19 7 0.27
20 19 0.73
ACGTcount: A:0.40, C:0.25, G:0.00, T:0.35
Consensus pattern (20 bp):
CAATTTCAACACTCTAACAT
Found at i:57198 original size:16 final size:16
Alignment explanation
Indices: 57175--57211 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
57165 GAAAAAAATG
*
57175 AGAAAATTTG-GAGAA
1 AGAAAAATTGAGAGAA
57190 AGAAAAATTGAGAGAA
1 AGAAAAATTGAGAGAA
57206 AGAAAA
1 AGAAAA
57212 GAGGAGTTTG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 9 0.45
16 11 0.55
ACGTcount: A:0.62, C:0.00, G:0.24, T:0.14
Consensus pattern (16 bp):
AGAAAAATTGAGAGAA
Found at i:58894 original size:49 final size:49
Alignment explanation
Indices: 58837--58948 Score: 215
Period size: 49 Copynumber: 2.3 Consensus size: 49
58827 GTTCTGTTGA
*
58837 ACAAAGAACTTGTTATCTGAGTTATTCTACCAATTCAACAACTCAGAGC
1 ACAAAGAACTTGTTATCAGAGTTATTCTACCAATTCAACAACTCAGAGC
58886 ACAAAGAACTTGTTATCAGAGTTATTCTACCAATTCAACAACTCAGAGC
1 ACAAAGAACTTGTTATCAGAGTTATTCTACCAATTCAACAACTCAGAGC
58935 ACAAAGAACTTGTT
1 ACAAAGAACTTGTT
58949 CTAACCGCTT
Statistics
Matches: 62, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 62 1.00
ACGTcount: A:0.38, C:0.21, G:0.12, T:0.28
Consensus pattern (49 bp):
ACAAAGAACTTGTTATCAGAGTTATTCTACCAATTCAACAACTCAGAGC
Found at i:61011 original size:20 final size:20
Alignment explanation
Indices: 60970--61016 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
60960 AAAGTGACCC
*
60970 AATTTC-ACATTCTAACAAT
1 AATTTCAACACTCTAACAAT
60989 AATTTCAACACTCTAA-AATT
1 AATTTCAACACTCTAACAA-T
61009 AATTTCAA
1 AATTTCAA
61017 GCATAGTACA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
19 8 0.32
20 17 0.68
ACGTcount: A:0.45, C:0.19, G:0.00, T:0.36
Consensus pattern (20 bp):
AATTTCAACACTCTAACAAT
Found at i:62603 original size:16 final size:16
Alignment explanation
Indices: 62580--62616 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
62570 GAAAAAAATG
*
62580 AGAAAATTTG-GAGAA
1 AGAAAAATTGAGAGAA
62595 AGAAAAATTGAGAGAA
1 AGAAAAATTGAGAGAA
62611 AGAAAA
1 AGAAAA
62617 GAGGATTTTG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 9 0.45
16 11 0.55
ACGTcount: A:0.62, C:0.00, G:0.24, T:0.14
Consensus pattern (16 bp):
AGAAAAATTGAGAGAA
Found at i:64311 original size:49 final size:49
Alignment explanation
Indices: 64233--64343 Score: 206
Period size: 49 Copynumber: 2.3 Consensus size: 49
64223 GTTCTGTTGA
*
64233 ACAAAGAACTTG-TATCTGAGTTATTCTACCAATTCAACAACTCAGAGC
1 ACAAAGAACTTGTTATCAGAGTTATTCTACCAATTCAACAACTCAGAGC
64281 ACAAAGAACTTGTTATCAGAGTTATTCTACCAATTCAACAACTCAGAGC
1 ACAAAGAACTTGTTATCAGAGTTATTCTACCAATTCAACAACTCAGAGC
64330 ACAAAGAACTTGTT
1 ACAAAGAACTTGTT
64344 CTAACCGCTT
Statistics
Matches: 61, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
48 12 0.20
49 49 0.80
ACGTcount: A:0.39, C:0.22, G:0.13, T:0.27
Consensus pattern (49 bp):
ACAAAGAACTTGTTATCAGAGTTATTCTACCAATTCAACAACTCAGAGC
Found at i:66404 original size:20 final size:20
Alignment explanation
Indices: 66363--66409 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
66353 AAAGTGACCC
*
66363 AATTTC-ACATTCTAACAAT
1 AATTTCAACACTCTAACAAT
66382 AATTTCAACACTCTAA-AATT
1 AATTTCAACACTCTAACAA-T
66402 AATTTCAA
1 AATTTCAA
66410 GCATAGTACA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
19 8 0.32
20 17 0.68
ACGTcount: A:0.45, C:0.19, G:0.00, T:0.36
Consensus pattern (20 bp):
AATTTCAACACTCTAACAAT
Done.