Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003806.1 Hibiscus syriacus cultivar Beakdansim tig00008146_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: 1419252
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 7
Found at i:6749 original size:66 final size:66
Alignment explanation
Indices: 6669--6879 Score: 188
Period size: 66 Copynumber: 3.2 Consensus size: 66
6659 TTTTTGGAAC
*
6669 TTTCATTTTGGTCCTTGAACGAATCTTTTGCGTTTTCTTAATTTGGTCTTCATATTTATGAGCAC
1 TTTCATTTTAGTCCTTGAACGAATCTTTTGCGTTTTCTTAATTTGGTCTTCATATTTATGAGCAC
6734 T
66 T
* * * * * * * **
6735 TTTCATTTTAGTCC-TGAA--ATGTTTTTATGTTGTATTTATGAA-AT-GTAATTTGTAATTT-T
1 TTTCATTTTAGTCCTTGAACGA-ATCTTT-TG-CGT-TTTCTTAATTTGGT-CTTCAT-ATTTAT
*
6794 G-G--TT
60 GAGCACT
*
6798 GTTTCATTTTGGTCCTTGAACGAATCTTTTGCGTTTTCTTAATTTGGTCTTCATATTTATGAGCA
1 -TTTCATTTTAGTCCTTGAACGAATCTTTTGCGTTTTCTTAATTTGGTCTTCATATTTATGAGCA
6863 CT
65 CT
6865 TTTCATTTTAGTCCT
1 TTTCATTTTAGTCCT
6880 GAAATGTTTT
Statistics
Matches: 106, Mismatches: 23, Indels: 32
0.66 0.14 0.20
Matches are distributed among these distances:
63 12 0.11
64 25 0.24
65 18 0.17
66 39 0.37
67 12 0.11
ACGTcount: A:0.19, C:0.13, G:0.15, T:0.52
Consensus pattern (66 bp):
TTTCATTTTAGTCCTTGAACGAATCTTTTGCGTTTTCTTAATTTGGTCTTCATATTTATGAGCAC
T
Found at i:6816 original size:130 final size:130
Alignment explanation
Indices: 6654--6931 Score: 513
Period size: 130 Copynumber: 2.1 Consensus size: 130
6644 ACATTGGTTG
***
6654 TGTAATTTTTGGAACTTTCATTTTGGTCCTTGAACGAATCTTTTGCGTTTTCTTAATTTGGTCTT
1 TGTAATTTTTGGTTGTTTCATTTTGGTCCTTGAACGAATCTTTTGCGTTTTCTTAATTTGGTCTT
6719 CATATTTATGAGCACTTTTCATTTTAGTCCTGAAATGTTTTTATGTTGTATTTATGAAATGTAAT
66 CATATTTATGAGCACTTTTCATTTTAGTCCTGAAATGTTTTTATGTTGTATTTATGAAATGTAA-
6784 T
130 T
6785 TGTAA-TTTTGGTTGTTTCATTTTGGTCCTTGAACGAATCTTTTGCGTTTTCTTAATTTGGTCTT
1 TGTAATTTTTGGTTGTTTCATTTTGGTCCTTGAACGAATCTTTTGCGTTTTCTTAATTTGGTCTT
6849 CATATTTATGAGCACTTTTCATTTTAGTCCTGAAATGTTTTTATGTTGTATTTATGAAATGTAAT
66 CATATTTATGAGCACTTTTCATTTTAGTCCTGAAATGTTTTTATGTTGTATTTATGAAATGTAAT
6914 TGTAATTTTTGGTTGTTT
1 TGTAATTTTTGGTTGTTT
6932 GACAATTTAG
Statistics
Matches: 143, Mismatches: 3, Indels: 3
0.96 0.02 0.02
Matches are distributed among these distances:
129 6 0.04
130 132 0.92
131 5 0.03
ACGTcount: A:0.21, C:0.10, G:0.16, T:0.53
Consensus pattern (130 bp):
TGTAATTTTTGGTTGTTTCATTTTGGTCCTTGAACGAATCTTTTGCGTTTTCTTAATTTGGTCTT
CATATTTATGAGCACTTTTCATTTTAGTCCTGAAATGTTTTTATGTTGTATTTATGAAATGTAAT
Found at i:18337 original size:9 final size:8
Alignment explanation
Indices: 18323--18465 Score: 76
Period size: 9 Copynumber: 16.2 Consensus size: 8
18313 TCGCTTGAAG
18323 AAGAAATAA
1 AAGAAA-AA
18332 AAGAAAAA
1 AAGAAAAA
18340 AA-AACGAAA
1 AAGAA--AAA
18349 AATGAAAAAA
1 AA-G-AAAAA
*
18359 TAATAATAAA
1 -AAGAA-AAA
*
18369 AATGAGAAA
1 AA-GAAAAA
18378 AAGAAAAA
1 AAGAAAAA
18386 GAAGAAAAA
1 -AAGAAAAA
18395 AAGAAAAAA
1 AAG-AAAAA
18404 AATGAGAAAA
1 AA-GA-AAAA
*
18414 AATAAAAA
1 AAGAAAAA
18422 TAA-AAAAA
1 -AAGAAAAA
18430 AGAGAAAGAA
1 A-AGAAA-AA
*
18440 AA-ATAAA
1 AAGAAAAA
18447 AAGAGAAAA
1 AAGA-AAAA
*
18456 ATGAAAAA
1 AAGAAAAA
18464 AA
1 AA
18466 AAGAGAAATA
Statistics
Matches: 107, Mismatches: 9, Indels: 37
0.70 0.06 0.24
Matches are distributed among these distances:
7 7 0.07
8 30 0.28
9 49 0.46
10 17 0.16
11 2 0.02
12 2 0.02
ACGTcount: A:0.79, C:0.01, G:0.13, T:0.08
Consensus pattern (8 bp):
AAGAAAAA
Found at i:18350 original size:11 final size:10
Alignment explanation
Indices: 18320--18479 Score: 62
Period size: 10 Copynumber: 15.3 Consensus size: 10
18310 ATTTCGCTTG
18320 AAGAAGAAATAA
1 AAGAA-AAA-AA
18332 AAGAAAAAAA
1 AAGAAAAAAA
18342 AACG---AAAA
1 AA-GAAAAAAA
* *
18350 ATGAAAAAAT
1 AAGAAAAAAA
*
18360 AATAATAAAAA
1 AAGAA-AAAAA
*
18371 TGAGAAAAAGAAA
1 -AAG-AAAA-AAA
18384 AAGAAGAAAAA
1 AAGAA-AAAAA
18395 AAGAAAAAAA
1 AAGAAAAAAA
*
18405 ATGAGAAAAAAT
1 A--AGAAAAAAA
*
18417 AA-AAATAAA
1 AAGAAAAAAA
* *
18426 AA-AAAGAGA
1 AAGAAAAAAA
18435 AAGAAAAATAA
1 AAGAAAAA-AA
*
18446 AA-AGAGAAAA
1 AAGA-AAAAAA
*
18456 ATGAAAAAAA
1 AAGAAAAAAA
*
18466 AAGAGAAATAA
1 AAGA-AAAAAA
18477 AAG
1 AAG
18480 GAGGGTTCAA
Statistics
Matches: 112, Mismatches: 20, Indels: 33
0.68 0.12 0.20
Matches are distributed among these distances:
7 1 0.01
8 5 0.04
9 14 0.12
10 33 0.29
11 33 0.29
12 21 0.19
13 5 0.04
ACGTcount: A:0.78, C:0.01, G:0.14, T:0.07
Consensus pattern (10 bp):
AAGAAAAAAA
Found at i:18369 original size:27 final size:26
Alignment explanation
Indices: 18339--18464 Score: 75
Period size: 28 Copynumber: 4.7 Consensus size: 26
18329 TAAAAGAAAA
18339 AAAAACGAAAAATGAAAAAATAATAAT
1 AAAAA-GAAAAATGAAAAAATAATAAT
* *
18366 AAAAATGAGAAAAAGAAAAAGA-AGA-AAA
1 AAAAA-GA-AAAATGAAAAA-ATA-ATAAT
* *
18394 AAAGAAAAAAAATGAGAAAAAATAAAAAT
1 AAA-AAGAAAAAT--GAAAAAATAATAAT
*
18423 AAAAA-AAAGA-GAAAGAAA-AATAA-
1 AAAAAGAAAAATGAAA-AAATAATAAT
*
18446 AAAGAGAAAAATGAAAAAA
1 AAAAAGAAAAATGAAAAAA
18465 AAAGAGAAAT
Statistics
Matches: 78, Mismatches: 10, Indels: 25
0.69 0.09 0.22
Matches are distributed among these distances:
23 4 0.05
24 15 0.19
25 7 0.09
27 15 0.19
28 21 0.27
29 16 0.21
ACGTcount: A:0.79, C:0.01, G:0.13, T:0.08
Consensus pattern (26 bp):
AAAAAGAAAAATGAAAAAATAATAAT
Found at i:18382 original size:6 final size:6
Alignment explanation
Indices: 18373--18473 Score: 61
Period size: 6 Copynumber: 16.8 Consensus size: 6
18363 AATAAAAATG
* *
18373 AGAAAA AGAAAA AGAAGA A-AAAA AGAAAA A-AAATG AGAAAA A-ATAAA
1 AGAAAA AGAAAA AGAAAA AGAAAA AGAAAA AGAAA-A AGAAAA AGA-AAA
* * *
18420 A-ATAA A-AAAA AGAGAA AGAAAA ATAAAAA GAGAAAA ATGAAAA A-AAAA
1 AGAAAA AGAAAA AGAAAA AGAAAA A-GAAAA -AGAAAA A-GAAAA AGAAAA
18468 GAGAAA
1 -AGAAA
18474 TAAAAGGAGG
Statistics
Matches: 75, Mismatches: 10, Indels: 19
0.72 0.10 0.18
Matches are distributed among these distances:
5 19 0.25
6 35 0.47
7 20 0.27
8 1 0.01
ACGTcount: A:0.80, C:0.00, G:0.15, T:0.05
Consensus pattern (6 bp):
AGAAAA
Found at i:18405 original size:35 final size:35
Alignment explanation
Indices: 18339--18478 Score: 144
Period size: 35 Copynumber: 3.9 Consensus size: 35
18329 TAAAAGAAAA
* * *
18339 AAAAACGAAAAATGAAAAAATAATAATAAAAATGAG
1 AAAAA-GAAAAATGAAAAAAAAAGAAAAAAAATGAG
18375 AAAAAGAAAAA-GAAGAAAAAAAGAAAAAAAATGAG
1 AAAAAGAAAAATGAA-AAAAAAAGAAAAAAAATGAG
*
18410 AAAAAATAAAAAT-AAAAAAAAGAGAAAGAAAAAT-A-
1 -AAAAAGAAAAATGAAAAAAAA-AGAAA-AAAAATGAG
18445 AAAAGAGAAAAATGAAAAAAAAAGAGAAATAAAA
1 AAAA-AGAAAAATGAAAAAAAAAGA-AAA-AAAA
18479 GGAGGGTTCA
Statistics
Matches: 90, Mismatches: 5, Indels: 18
0.80 0.04 0.16
Matches are distributed among these distances:
34 7 0.08
35 40 0.44
36 37 0.41
37 6 0.07
ACGTcount: A:0.79, C:0.01, G:0.13, T:0.08
Consensus pattern (35 bp):
AAAAAGAAAAATGAAAAAAAAAGAAAAAAAATGAG
Found at i:18430 original size:51 final size:51
Alignment explanation
Indices: 18330--18466 Score: 140
Period size: 51 Copynumber: 2.7 Consensus size: 51
18320 AAGAAGAAAT
*
18330 AAAAGAAAAA-AAAACG--AAAAATGAAAAAATAATAATAAA-AATGAGAAAAAGA
1 AAAAGAAAAATAAAAAGAAAAAAATGAAAAAA-AATAA-AAATAA--A-AAAAAGA
* *
18382 AAAAGAAGAA-AAAAAGAAAAAAAATGAGAAAAAATAAAAATAAAAAAAAGA
1 AAAAGAAAAATAAAAAG-AAAAAAATGAAAAAAAATAAAAATAAAAAAAAGA
* *
18433 GAAAGAAAAATAAAAAGAGAAAAATGAAAAAAAA
1 AAAAGAAAAATAAAAAGAAAAAAATGAAAAAAAA
18467 AGAGAAATAA
Statistics
Matches: 73, Mismatches: 7, Indels: 11
0.80 0.08 0.12
Matches are distributed among these distances:
51 30 0.41
52 21 0.29
53 3 0.04
54 7 0.10
55 12 0.16
ACGTcount: A:0.80, C:0.01, G:0.12, T:0.07
Consensus pattern (51 bp):
AAAAGAAAAATAAAAAGAAAAAAATGAAAAAAAATAAAAATAAAAAAAAGA
Found at i:19831 original size:51 final size:51
Alignment explanation
Indices: 19754--20224 Score: 482
Period size: 51 Copynumber: 8.9 Consensus size: 51
19744 AAGCAAATTC
19754 GTTTGTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAA
1 GTTTGTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAA
*
19805 GTTCGTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAA
1 GTTTGTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAA
19856 GTTTGTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAA
1 GTTTGTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAA
* * **
19907 GTTCGTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGAGAGCGGACCC
1 GTTTGTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAA
* * * *
19958 GTTTTGTTGAAGATTGTTCGAGTTCTATACTCCCTGAACGG-ATAGGGAGCGAACAC
1 G-TTTGTTGAAGA---TT-GAGTCCTATACTCTCTGAA-GGAATAGGGAGCGGACAA
* * * **
20014 GTTTGTTAAAGATTGAGTCCTATACTCTCTGAAAGAATAGGGAGCGAACCT
1 GTTTGTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAA
* * * * **
20065 GTTTATTGAAGATTTTTCGAGTTCTATACTCCCTGAAGGAATAGAGAGCGGACCC
1 GTTTGTTGAAGA---TT-GAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAA
* * * * *
20120 GTTTTATTGAAGATTGTTCAAGTCTTATACTCTCTGAATGAATAGAGAGCAGACACA
1 G-TTTGTTGAAGATTG----AGTCCTATACTCTCTGAAGGAATAGGGAGCGGACA-A
*
20177 -TTT-TATGAAGATTGTTCGAGTCTTATACT-TCCTGAAGGAATAGGGAGC
1 GTTTGT-TGAAGA---TT-GAGTCCTATACTCT-CTGAAGGAATAGGGAGC
20225 ATGCTCGTCA
Statistics
Matches: 362, Mismatches: 35, Indels: 42
0.82 0.08 0.10
Matches are distributed among these distances:
50 1 0.00
51 188 0.52
52 13 0.04
53 2 0.01
54 4 0.01
55 79 0.22
56 70 0.19
57 2 0.01
58 2 0.01
59 1 0.00
ACGTcount: A:0.29, C:0.16, G:0.26, T:0.30
Consensus pattern (51 bp):
GTTTGTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAA
Found at i:20041 original size:158 final size:158
Alignment explanation
Indices: 19758--20169 Score: 532
Period size: 158 Copynumber: 2.6 Consensus size: 158
19748 AAATTCGTTT
* ** *
19758 GTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAG-TTCGTTGAAGA---TT
1 GTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTTGTTGAAGATTGTT
* * *
19819 -GAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTTGTTGAAGATTGAGTCCTATACTC
66 CGAGTTCTATACTCTCTGAAGGAATAGGGAGCGAACAAGTTTGTTAAAGATTGAGTCCTATACTC
* *
19883 TCTGAAGGAATAGGGAGCGGACAAGTTC
131 TCTGAAAGAATAGGGAGCGAACAAGTTC
19911 GTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTTGTTGAAGATTGTT
1 GTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTTGTTGAAGATTGTT
* *
19976 CGAGTTCTATACTCCCTGAACGG-ATAGGGAGCGAACACGTTTGTTAAAGATTGAGTCCTATACT
66 CGAGTTCTATACTCTCTGAA-GGAATAGGGAGCGAACAAGTTTGTTAAAGATTGAGTCCTATACT
** *
20040 CTCTGAAAGAATAGGGAGCGAACCTGTTT
130 CTCTGAAAGAATAGGGAGCGAACAAGTTC
* * * *
20069 ATTGAAGATTTTTCGAGTTCTATACTCCCTGAAGGAATAGAGAGCGGACCCGTTTTATTGAAGAT
1 GTTGAAGA---TT-GAGTCCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTTGTTGAAGAT
* * *
20134 TGTTCAAG-TCTTATACTCTCTGAATGAATAGAGAGC
62 TGTTCGAGTTC-TATACTCTCTGAAGGAATAGGGAGC
20170 AGACACATTT
Statistics
Matches: 225, Mismatches: 22, Indels: 15
0.86 0.08 0.06
Matches are distributed among these distances:
153 45 0.20
154 10 0.04
157 2 0.01
158 86 0.38
159 2 0.01
161 5 0.02
162 75 0.33
ACGTcount: A:0.29, C:0.16, G:0.26, T:0.29
Consensus pattern (158 bp):
GTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTTGTTGAAGATTGTT
CGAGTTCTATACTCTCTGAAGGAATAGGGAGCGAACAAGTTTGTTAAAGATTGAGTCCTATACTC
TCTGAAAGAATAGGGAGCGAACAAGTTC
Found at i:21526 original size:66 final size:66
Alignment explanation
Indices: 21446--21656 Score: 188
Period size: 66 Copynumber: 3.2 Consensus size: 66
21436 TTTTTGGAAC
*
21446 TTTCATTTTGGTCCTTGAACGAATCTTTTGCGTTTTCTTAATTTGGTCTTCATATTTATGAGCAC
1 TTTCATTTTAGTCCTTGAACGAATCTTTTGCGTTTTCTTAATTTGGTCTTCATATTTATGAGCAC
21511 T
66 T
* * * * * * * **
21512 TTTCATTTTAGTCC-TGAA--ATGTTTTTATGTTGTATTTATGAA-AT-GTAATTTGTAATTT-T
1 TTTCATTTTAGTCCTTGAACGA-ATCTTT-TG-CGT-TTTCTTAATTTGGT-CTTCAT-ATTTAT
*
21571 G-G--TT
60 GAGCACT
*
21575 GTTTCATTTTGGTCCTTGAACGAATCTTTTGCGTTTTCTTAATTTGGTCTTCATATTTATGAGCA
1 -TTTCATTTTAGTCCTTGAACGAATCTTTTGCGTTTTCTTAATTTGGTCTTCATATTTATGAGCA
21640 CT
65 CT
21642 TTTCATTTTAGTCCT
1 TTTCATTTTAGTCCT
21657 GAAATGTTTT
Statistics
Matches: 106, Mismatches: 23, Indels: 32
0.66 0.14 0.20
Matches are distributed among these distances:
63 12 0.11
64 25 0.24
65 18 0.17
66 39 0.37
67 12 0.11
ACGTcount: A:0.19, C:0.13, G:0.15, T:0.52
Consensus pattern (66 bp):
TTTCATTTTAGTCCTTGAACGAATCTTTTGCGTTTTCTTAATTTGGTCTTCATATTTATGAGCAC
T
Found at i:21583 original size:130 final size:130
Alignment explanation
Indices: 21446--21708 Score: 517
Period size: 130 Copynumber: 2.0 Consensus size: 130
21436 TTTTTGGAAC
21446 TTTCATTTTGGTCCTTGAACGAATCTTTTGCGTTTTCTTAATTTGGTCTTCATATTTATGAGCAC
1 TTTCATTTTGGTCCTTGAACGAATCTTTTGCGTTTTCTTAATTTGGTCTTCATATTTATGAGCAC
*
21511 TTTTCATTTTAGTCCTGAAATGTTTTTATGTTGTATTTATGAAATGTAATTTGTAATTTTGGTTG
66 TTTTCATTTTAGTCCTGAAATGTTTTTATGTTGTATTTATGAAATGTAATTTGTAACTTTGGTTG
21576 TTTCATTTTGGTCCTTGAACGAATCTTTTGCGTTTTCTTAATTTGGTCTTCATATTTATGAGCAC
1 TTTCATTTTGGTCCTTGAACGAATCTTTTGCGTTTTCTTAATTTGGTCTTCATATTTATGAGCAC
21641 TTTTCATTTTAGTCCTGAAATGTTTTTATGTTGTATTTATGAAATGTAATTTGTAACTTTGGTTG
66 TTTTCATTTTAGTCCTGAAATGTTTTTATGTTGTATTTATGAAATGTAATTTGTAACTTTGGTTG
21706 TTT
1 TTT
21709 GACAATTTAG
Statistics
Matches: 132, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
130 132 1.00
ACGTcount: A:0.21, C:0.11, G:0.16, T:0.52
Consensus pattern (130 bp):
TTTCATTTTGGTCCTTGAACGAATCTTTTGCGTTTTCTTAATTTGGTCTTCATATTTATGAGCAC
TTTTCATTTTAGTCCTGAAATGTTTTTATGTTGTATTTATGAAATGTAATTTGTAACTTTGGTTG
Found at i:26310 original size:18 final size:18
Alignment explanation
Indices: 26287--26321 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
26277 TATGTGATAT
26287 GTGGTCCTTCGGGACATA
1 GTGGTCCTTCGGGACATA
*
26305 GTGGTCCTTTGGGACAT
1 GTGGTCCTTCGGGACAT
26322 TTCTACGCAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.14, C:0.20, G:0.34, T:0.31
Consensus pattern (18 bp):
GTGGTCCTTCGGGACATA
Found at i:27034 original size:20 final size:21
Alignment explanation
Indices: 27009--27050 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
26999 TGTAGCAACA
*
27009 CTGTAGCA-GGGTATCGGTAC
1 CTGTAGCAGGGGTATCGATAC
27029 CTGTAGCAGGGGTATCGATAC
1 CTGTAGCAGGGGTATCGATAC
27050 C
1 C
27051 CCTGAAGCAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 8 0.40
21 12 0.60
ACGTcount: A:0.21, C:0.21, G:0.33, T:0.24
Consensus pattern (21 bp):
CTGTAGCAGGGGTATCGATAC
Found at i:27134 original size:22 final size:22
Alignment explanation
Indices: 27082--27134 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
27072 TTTAGAATTC
*
27082 GGTACTGTGCATTACTGTTCAA
1 GGTACTGTTCATTACTGTTCAA
* *
27104 GGTATTGTTCATTACTGTTCAC
1 GGTACTGTTCATTACTGTTCAA
*
27126 TGTACTGTT
1 GGTACTGTT
27135 TATACCGTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.19, C:0.17, G:0.21, T:0.43
Consensus pattern (22 bp):
GGTACTGTTCATTACTGTTCAA
Found at i:31116 original size:16 final size:16
Alignment explanation
Indices: 31069--31124 Score: 89
Period size: 16 Copynumber: 3.6 Consensus size: 16
31059 AAATTTAAAA
31069 TTAATCAAAAGTTTATT
1 TTAA-CAAAAGTTTATT
31086 TTAACAAAA--TTATT
1 TTAACAAAAGTTTATT
31100 TTAACAAAAGTTTATT
1 TTAACAAAAGTTTATT
31116 TTAACAAAA
1 TTAACAAAA
31125 ATCATTCGCT
Statistics
Matches: 37, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
14 14 0.38
16 19 0.51
17 4 0.11
ACGTcount: A:0.48, C:0.07, G:0.04, T:0.41
Consensus pattern (16 bp):
TTAACAAAAGTTTATT
Found at i:33140 original size:25 final size:26
Alignment explanation
Indices: 33086--33144 Score: 77
Period size: 25 Copynumber: 2.3 Consensus size: 26
33076 ACGAATTACC
33086 AATTATATTATATTTTAAAAATATAAT
1 AATTA-ATTATATTTTAAAAATATAAT
*
33113 AATTAATTAT-TTTTATAAAATAT-TT
1 AATTAATTATATTTTA-AAAATATAAT
33138 AATTAAT
1 AATTAAT
33145 AATCTCTAGA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
25 13 0.43
26 12 0.40
27 5 0.17
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (26 bp):
AATTAATTATATTTTAAAAATATAAT
Found at i:33404 original size:42 final size:42
Alignment explanation
Indices: 33345--33464 Score: 222
Period size: 42 Copynumber: 2.9 Consensus size: 42
33335 TTTTCCCGAA
*
33345 TTCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAATGTT
1 TTCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAACGTT
*
33387 TTCCCGTGTTTATTTCACGTAATTCGTTTTCCGGAAAACGTT
1 TTCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAACGTT
33429 TTCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAA
1 TTCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAA
33465 TGTAATTCAT
Statistics
Matches: 75, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
42 75 1.00
ACGTcount: A:0.17, C:0.21, G:0.18, T:0.44
Consensus pattern (42 bp):
TTCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAACGTT
Found at i:33705 original size:22 final size:24
Alignment explanation
Indices: 33659--33706 Score: 64
Period size: 22 Copynumber: 2.1 Consensus size: 24
33649 TTAAAATATT
*
33659 TAAAATATTTATTAATATTTATAA
1 TAAAATATATATTAATATTTATAA
*
33683 TAAAATA-ATATT-ATATTTTTAA
1 TAAAATATATATTAATATTTATAA
33705 TA
1 TA
33707 TTATATAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 11 0.50
23 4 0.18
24 7 0.32
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (24 bp):
TAAAATATATATTAATATTTATAA
Found at i:33708 original size:31 final size:31
Alignment explanation
Indices: 33663--33740 Score: 97
Period size: 31 Copynumber: 2.5 Consensus size: 31
33653 AATATTTAAA
33663 ATATTTATTAATATTTATAATAAAATAAT-ATT
1 ATATTTATTAATA-TTAT-ATAAAATAATAATT
33695 ATATTT-TTAATATTATATAAAATAATCAATT
1 ATATTTATTAATATTATATAAAATAAT-AATT
*
33726 ATATTATAATAATAT
1 ATATT-TATTAATAT
33741 AAGATATTAT
Statistics
Matches: 41, Mismatches: 1, Indels: 7
0.84 0.02 0.14
Matches are distributed among these distances:
29 10 0.24
30 4 0.10
31 14 0.34
32 7 0.17
33 6 0.15
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.49
Consensus pattern (31 bp):
ATATTTATTAATATTATATAAAATAATAATT
Found at i:33774 original size:54 final size:52
Alignment explanation
Indices: 33677--33779 Score: 129
Period size: 54 Copynumber: 1.9 Consensus size: 52
33667 TTATTAATAT
*
33677 TTATAATAAAATAATATTATATTTTTAATATTATATAAAATAATCAATTATA
1 TTATAATAAAATAATATTATATTTTTAATATTATATAAAATAATAAATTATA
* *
33729 TTATAATAATATAAGATATTATATTTTT-ATTTTA-ATAATATATAATAAATT
1 TTATAATAAAAT-A-ATATTATATTTTTAATATTATATAA-A-ATAATAAATT
33780 TTTTTATATA
Statistics
Matches: 44, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
52 15 0.34
53 7 0.16
54 22 0.50
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.49
Consensus pattern (52 bp):
TTATAATAAAATAATATTATATTTTTAATATTATATAAAATAATAAATTATA
Found at i:34073 original size:20 final size:20
Alignment explanation
Indices: 33995--34064 Score: 131
Period size: 20 Copynumber: 3.5 Consensus size: 20
33985 TTTCCAGATG
33995 TTTTCCAGAAATGTAATTCA
1 TTTTCCAGAAATGTAATTCA
34015 TTTTCCAGAAATGTAATTCA
1 TTTTCCAGAAATGTAATTCA
*
34035 TTTTACAGAAATGTAATTCA
1 TTTTCCAGAAATGTAATTCA
34055 TTTTCCAGAA
1 TTTTCCAGAA
34065 TTCAAATTCT
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 48 1.00
ACGTcount: A:0.36, C:0.14, G:0.10, T:0.40
Consensus pattern (20 bp):
TTTTCCAGAAATGTAATTCA
Found at i:34073 original size:40 final size:40
Alignment explanation
Indices: 33995--34073 Score: 122
Period size: 40 Copynumber: 2.0 Consensus size: 40
33985 TTTCCAGATG
* **
33995 TTTTCCAGAAATGTAATTCATTTTCCAGAAATGTAATTCA
1 TTTTACAGAAATGTAATTCATTTTCCAGAAATCAAATTCA
*
34035 TTTTACAGAAATGTAATTCATTTTCCAGAATTCAAATTC
1 TTTTACAGAAATGTAATTCATTTTCCAGAAATCAAATTC
34074 TAGTAATTCA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 35 1.00
ACGTcount: A:0.35, C:0.15, G:0.09, T:0.41
Consensus pattern (40 bp):
TTTTACAGAAATGTAATTCATTTTCCAGAAATCAAATTCA
Found at i:34083 original size:15 final size:15
Alignment explanation
Indices: 34047--34128 Score: 103
Period size: 15 Copynumber: 5.5 Consensus size: 15
34037 TTACAGAAAT
**
34047 GTAATTCATTTTCCA
1 GTAATTCAAATTCCA
*
34062 G-AATTCAAATTCTA
1 GTAATTCAAATTCCA
** *
34076 GTAATTCATTTTCTA
1 GTAATTCAAATTCCA
34091 GTAATTCAAATTCCA
1 GTAATTCAAATTCCA
34106 GTAATTCAAATTCCA
1 GTAATTCAAATTCCA
34121 GTAATTCA
1 GTAATTCA
34129 TTTTCTGGAA
Statistics
Matches: 58, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
14 11 0.19
15 47 0.81
ACGTcount: A:0.35, C:0.17, G:0.07, T:0.40
Consensus pattern (15 bp):
GTAATTCAAATTCCA
Found at i:34099 original size:30 final size:30
Alignment explanation
Indices: 34047--34128 Score: 121
Period size: 30 Copynumber: 2.8 Consensus size: 30
34037 TTACAGAAAT
*
34047 GTAATTCATTTTCCAG-AATTCAAATTCTA
1 GTAATTCATTTTCCAGTAATTCAAATTCCA
*
34076 GTAATTCATTTTCTAGTAATTCAAATTCCA
1 GTAATTCATTTTCCAGTAATTCAAATTCCA
**
34106 GTAATTCAAATTCCAGTAATTCA
1 GTAATTCATTTTCCAGTAATTCA
34129 TTTTCTGGAA
Statistics
Matches: 47, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
29 15 0.32
30 32 0.68
ACGTcount: A:0.35, C:0.17, G:0.07, T:0.40
Consensus pattern (30 bp):
GTAATTCATTTTCCAGTAATTCAAATTCCA
Found at i:34124 original size:45 final size:44
Alignment explanation
Indices: 34047--34134 Score: 140
Period size: 45 Copynumber: 2.0 Consensus size: 44
34037 TTACAGAAAT
** *
34047 GTAATTCATTTTCCAGAATTCAAATTCTAGTAATTCATTTTCTA
1 GTAATTCAAATTCCAGAATTCAAATTCCAGTAATTCATTTTCTA
34091 GTAATTCAAATTCCAGTAATTCAAATTCCAGTAATTCATTTTCT
1 GTAATTCAAATTCCAG-AATTCAAATTCCAGTAATTCATTTTCT
34135 GGAAAACCAA
Statistics
Matches: 40, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
44 14 0.35
45 26 0.65
ACGTcount: A:0.33, C:0.17, G:0.07, T:0.43
Consensus pattern (44 bp):
GTAATTCAAATTCCAGAATTCAAATTCCAGTAATTCATTTTCTA
Found at i:38010 original size:29 final size:29
Alignment explanation
Indices: 37968--38029 Score: 79
Period size: 29 Copynumber: 2.1 Consensus size: 29
37958 GAAGAAATGG
* *
37968 CGACTTAGTAGGTCACCCGGATGATATGA
1 CGACCTAGTAGGTCACCCGGATGACATGA
* **
37997 CGACCTAGTAGGTCGCCCTTATGACATGA
1 CGACCTAGTAGGTCACCCGGATGACATGA
38026 CGAC
1 CGAC
38030 TTATGTCACC
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.26, C:0.26, G:0.26, T:0.23
Consensus pattern (29 bp):
CGACCTAGTAGGTCACCCGGATGACATGA
Found at i:39259 original size:27 final size:27
Alignment explanation
Indices: 39229--39295 Score: 107
Period size: 27 Copynumber: 2.5 Consensus size: 27
39219 GTATATGTTA
* *
39229 AAAATCATTTTTAATTGTAACATTTTC
1 AAAATCACTTTTAACTGTAACATTTTC
*
39256 AAAATTACTTTTAACTGTAACATTTTC
1 AAAATCACTTTTAACTGTAACATTTTC
39283 AAAATCACTTTTA
1 AAAATCACTTTTA
39296 GTTATTAATA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.39, C:0.13, G:0.03, T:0.45
Consensus pattern (27 bp):
AAAATCACTTTTAACTGTAACATTTTC
Found at i:39802 original size:21 final size:21
Alignment explanation
Indices: 39776--39815 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
39766 TAAAGCGTCC
39776 AATAATAATATTTGAGGTAGA
1 AATAATAATATTTGAGGTAGA
* *
39797 AATAATAATCTTTTAGGTA
1 AATAATAATATTTGAGGTA
39816 ATTTTTTTAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.45, C:0.03, G:0.15, T:0.38
Consensus pattern (21 bp):
AATAATAATATTTGAGGTAGA
Found at i:40375 original size:11 final size:11
Alignment explanation
Indices: 40347--40377 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
40337 TAAACTCAAC
*
40347 TAAAAAATATT
1 TAAAAATTATT
40358 TAAAAATTATT
1 TAAAAATTATT
40369 TAAAAATTA
1 TAAAAATTA
40378 AAGAAAATGT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (11 bp):
TAAAAATTATT
Found at i:41371 original size:21 final size:21
Alignment explanation
Indices: 41342--41383 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
41332 GGAATTATTA
*
41342 TAATATTTTAAAATTAATAAT
1 TAATATTTTAAAATAAATAAT
* *
41363 TAATTTTTTATAATAAATAAT
1 TAATATTTTAAAATAAATAAT
41384 ATTAAATGTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (21 bp):
TAATATTTTAAAATAAATAAT
Found at i:41805 original size:30 final size:30
Alignment explanation
Indices: 41724--41819 Score: 74
Period size: 30 Copynumber: 3.3 Consensus size: 30
41714 AATTAGTACA
* *
41724 AAAAAATAATTAATTA-ATAA--ATTTAAAT
1 AAAAAATAA-TATTTATATAATTATTTTAAT
* * *
41752 AAATAATAAT-TATATAAATATTATTTTAAT
1 AAAAAATAATATTTATATA-ATTATTTTAAT
* *
41782 AAAAAATAATATTTATATAATTATATTACT
1 AAAAAATAATATTTATATAATTATTTTAAT
*
41812 ATAAAATA
1 AAAAAATA
41820 TAGAAACTTT
Statistics
Matches: 52, Mismatches: 11, Indels: 8
0.73 0.15 0.11
Matches are distributed among these distances:
26 2 0.04
27 3 0.06
28 9 0.17
30 32 0.62
31 6 0.12
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.41
Consensus pattern (30 bp):
AAAAAATAATATTTATATAATTATTTTAAT
Found at i:42992 original size:62 final size:63
Alignment explanation
Indices: 42874--42997 Score: 187
Period size: 62 Copynumber: 2.0 Consensus size: 63
42864 CATATATTTA
* ** *
42874 AATAAATGTTAGATCATTTTATTTAATTATATTTCATAAATTCTAAAGATTAACAAAATTTTT
1 AATAAATGTTACATCATTTTATTTAATTATAGCTCATAAATTCTAAAAATTAACAAAATTTTT
* *
42937 AATAAATGTTACATCGTTTTATTTAATTCT-GCTCATAAATTCTAAAAATTAACAAAATTTT
1 AATAAATGTTACATCATTTTATTTAATTATAGCTCATAAATTCTAAAAATTAACAAAATTTT
42998 AATCGTTAAA
Statistics
Matches: 55, Mismatches: 6, Indels: 1
0.89 0.10 0.02
Matches are distributed among these distances:
62 28 0.51
63 27 0.49
ACGTcount: A:0.42, C:0.09, G:0.05, T:0.44
Consensus pattern (63 bp):
AATAAATGTTACATCATTTTATTTAATTATAGCTCATAAATTCTAAAAATTAACAAAATTTTT
Found at i:43795 original size:23 final size:22
Alignment explanation
Indices: 43769--43813 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 22
43759 TACTCACAAA
43769 TATAGATTT-TAATTTATATTTTT
1 TATA-ATTTATAATTTA-ATTTTT
43792 TATAATTTGATAATTTAATTTT
1 TATAATTT-ATAATTTAATTTT
43814 AATTATATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
22 4 0.20
23 9 0.45
24 7 0.35
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.62
Consensus pattern (22 bp):
TATAATTTATAATTTAATTTTT
Found at i:48471 original size:15 final size:15
Alignment explanation
Indices: 48451--48558 Score: 61
Period size: 15 Copynumber: 7.6 Consensus size: 15
48441 ATTATCGATG
48451 AATTTTTATAGAAAT
1 AATTTTTATAGAAAT
**
48466 AATTTTTATTTAAAT
1 AATTTTTATAGAAAT
* *
48481 -A-TATTATCG--AT
1 AATTTTTATAGAAAT
48492 GAATTTTTATAGAAAT
1 -AATTTTTATAGAAAT
**
48508 AATTTTTATTTAAAT
1 AATTTTTATAGAAAT
* *
48523 -A-TATTATCG--AT
1 AATTTTTATAGAAAT
*
48534 GAATTTTTATATAAAT
1 -AATTTTTATAGAAAT
48550 AATTTTTAT
1 AATTTTTAT
48559 TTAAATATTT
Statistics
Matches: 68, Mismatches: 15, Indels: 20
0.66 0.15 0.19
Matches are distributed among these distances:
11 4 0.06
13 12 0.18
14 13 0.19
15 35 0.51
16 4 0.06
ACGTcount: A:0.41, C:0.02, G:0.06, T:0.52
Consensus pattern (15 bp):
AATTTTTATAGAAAT
Found at i:48484 original size:42 final size:42
Alignment explanation
Indices: 48436--48566 Score: 253
Period size: 42 Copynumber: 3.1 Consensus size: 42
48426 ATAATAAAGT
48436 AATATATTATCGATGAATTTTTATAGAAATAATTTTTATTTA
1 AATATATTATCGATGAATTTTTATAGAAATAATTTTTATTTA
48478 AATATATTATCGATGAATTTTTATAGAAATAATTTTTATTTA
1 AATATATTATCGATGAATTTTTATAGAAATAATTTTTATTTA
*
48520 AATATATTATCGATGAATTTTTATATAAATAATTTTTATTTA
1 AATATATTATCGATGAATTTTTATAGAAATAATTTTTATTTA
48562 AATAT
1 AATAT
48567 TTAGAATTCA
Statistics
Matches: 88, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
42 88 1.00
ACGTcount: A:0.41, C:0.02, G:0.06, T:0.50
Consensus pattern (42 bp):
AATATATTATCGATGAATTTTTATAGAAATAATTTTTATTTA
Found at i:58283 original size:32 final size:32
Alignment explanation
Indices: 58246--58321 Score: 91
Period size: 32 Copynumber: 2.3 Consensus size: 32
58236 ATGAACAATG
*
58246 GGGGCATATTTGA-AGATTCAACCTCAAATGTT
1 GGGGCAT-TTTGAGAGATTCAACATCAAATGTT
* * *
58278 GGGGCATTTTTAGAGATTCAACATCGAATTTT
1 GGGGCATTTTGAGAGATTCAACATCAAATGTT
58310 GGGGCATCTTTG
1 GGGGCAT-TTTG
58322 GGGATTTAAC
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
31 4 0.11
32 30 0.81
33 3 0.08
ACGTcount: A:0.26, C:0.14, G:0.25, T:0.34
Consensus pattern (32 bp):
GGGGCATTTTGAGAGATTCAACATCAAATGTT
Found at i:58819 original size:32 final size:33
Alignment explanation
Indices: 58744--58828 Score: 104
Period size: 32 Copynumber: 2.6 Consensus size: 33
58734 ACCAATTTGG
*
58744 ATTTCAACTTCACAACGAATGATATCCAATTCAA
1 ATTTCAACTTCACAACGAATGA-ATCCAATCCAA
58778 AGTTT-AACTTCACAACGAATG-ATCC-ATCCACA
1 A-TTTCAACTTCACAACGAATGAATCCAATCCA-A
*
58810 ATTTCAACTTCACGACGAA
1 ATTTCAACTTCACAACGAA
58829 GGATATCGTG
Statistics
Matches: 46, Mismatches: 2, Indels: 8
0.82 0.04 0.14
Matches are distributed among these distances:
31 7 0.15
32 19 0.41
34 17 0.37
35 3 0.07
ACGTcount: A:0.39, C:0.26, G:0.08, T:0.27
Consensus pattern (33 bp):
ATTTCAACTTCACAACGAATGAATCCAATCCAA
Found at i:59041 original size:120 final size:121
Alignment explanation
Indices: 58740--59321 Score: 586
Period size: 121 Copynumber: 4.8 Consensus size: 121
58730 CAAAACCAAT
* * * *
58740 TTGGATTTCAACTTCACAACGAATGATATCCAATTCAAAGTTTAACTTCACAACGAATGATCCAT
1 TTGGATTTCAACTTCACAACGAAGGATATCCAATTCAAAGCTCAACTTCACAACGAATGAGCCAT
* ** *
58805 CCACAATTTCAACTTCACGACGAAGGATATCGTGCCCACAAGCAGCAATGTACCCC
66 CCACGATTTCAACTTCACGACGAAGGATATCGTGCCCACAAGCAGCAATACAACCC
** * *
58861 TTGGATTTCAACTTCATGACGAAGGATATTCAATTCAAAGTTCAACTTCACAACGAATGAGCCAT
1 TTGGATTTCAACTTCACAACGAAGGATATCCAATTCAAAGCTCAACTTCACAACGAATGAGCCAT
* *
58926 CCACGATTTCAACTTCACAACGAATGATATCGTGCCCACAAGCAGC-ATACAACCC
66 CCACGATTTCAACTTCACGACGAAGGATATCGTGCCCACAAGCAGCAATACAACCC
** * *
58981 TTGGATTTCAACTTCATGATGAAGGATATCCAATTCAAAGCTCAACTTCACAATGAATGAGCCAT
1 TTGGATTTCAACTTCACAACGAAGGATATCCAATTCAAAGCTCAACTTCACAACGAATGAGCCAT
* * * * *
59046 CCATGATTTCAATTTCACGACTAAGGATATTGTGCCCACAAGCAGCAATTCAACCC
66 CCACGATTTCAACTTCACGACGAAGGATATCGTGCCCACAAGCAGCAATACAACCC
* * * * * * *
59102 TTGGATTTCAACTTCACAACGAAGGATATCAAACTCAAAGC-CAATTTGGTGA-AACTTACTCAA
1 TTGGATTTCAACTTCACAACGAAGGATATCCAATTCAAAGCTCAA-CT--TCACAAC-GAAT-GA
** * ** * * * * *
59165 G--AT--TGGATTTCAACTTCACGACGAATGATATCCAGCTCA-AAACAAATTTGGTAAAACAAT
61 GCCATCCACGATTTCAACTTCACGACGAAGGATATCGTGCCCACAAGC--A----GCAATACAAC
*
59225 TC
120 CC
* * * **
59227 TTGGATTTCAACTTCACAACGAAGAATATCCAACTCAAAGCTTAACTTCACGGCGAATGAGCCAT
1 TTGGATTTCAACTTCACAACGAAGGATATCCAATTCAAAGCTCAACTTCACAACGAATGAGCCAT
*
59292 CCACAATTTCAACTTCACGACGAAGGATAT
66 CCACGATTTCAACTTCACGACGAAGGATAT
59322 AATGTTCAAT
Statistics
Matches: 380, Mismatches: 63, Indels: 31
0.80 0.13 0.07
Matches are distributed among these distances:
119 3 0.01
120 137 0.36
121 148 0.39
122 6 0.02
123 8 0.02
124 5 0.01
125 47 0.12
126 26 0.07
ACGTcount: A:0.36, C:0.25, G:0.14, T:0.26
Consensus pattern (121 bp):
TTGGATTTCAACTTCACAACGAAGGATATCCAATTCAAAGCTCAACTTCACAACGAATGAGCCAT
CCACGATTTCAACTTCACGACGAAGGATATCGTGCCCACAAGCAGCAATACAACCC
Found at i:59256 original size:60 final size:60
Alignment explanation
Indices: 59101--59265 Score: 188
Period size: 65 Copynumber: 2.6 Consensus size: 60
59091 CAATTCAACC
* * * * *
59101 CTTGGATTTCAACTTCACAACGAAGGATATCAAACTCAAAGCCAATTTGGTGAAACTTACT
1 CTTGGATTTCAACTTCACAACGAA-GATATCCAACTCAAAACAAATTTGGTAAAACTAACT
* * *
59162 CAAGATTGGATTTCAACTTCACGACGAATGATATCCAGCTCAAAACAAATTTGGTAAAAC-AATT
1 C----TTGGATTTCAACTTCACAACGAA-GATATCCAACTCAAAACAAATTTGGTAAAACTAACT
59226 CTTGGATTTCAACTTCACAACGAAGAATATCCAACTCAAA
1 CTTGGATTTCAACTTCACAACGAAG-ATATCCAACTCAAA
59266 GCTTAACTTC
Statistics
Matches: 88, Mismatches: 11, Indels: 11
0.80 0.10 0.10
Matches are distributed among these distances:
59 1 0.01
60 35 0.40
61 1 0.01
64 3 0.03
65 48 0.55
ACGTcount: A:0.39, C:0.21, G:0.13, T:0.27
Consensus pattern (60 bp):
CTTGGATTTCAACTTCACAACGAAGATATCCAACTCAAAACAAATTTGGTAAAACTAACT
Found at i:59549 original size:85 final size:83
Alignment explanation
Indices: 59423--59664 Score: 328
Period size: 85 Copynumber: 2.9 Consensus size: 83
59413 CGAGAAGGGT
*
59423 TATCTATCAGCAAAGACCTTCGAGTTCGATTACATTCAGCTCAAAGGCACATTAAATTTACAGTA
1 TATCTATCAGC-AAGACCTTCGAGTTCGATTACATTCAGCTCAAAGGCACATCAAATTTACAGTA
*
59488 TAGCTCAAGTCGAGAAAAAC
65 TAACTCAAG-CGAGAAAAAC
* *
59508 TATCTATCTAGCAAGAACTTCGAGTTCGATTACATTCAGCTCAAAGGCACATCAAATTTACAGCA
1 TATCTATC-AGCAAGACCTTCGAGTTCGATTACATTCAGCTCAAAGGCACATCAAATTTACAGTA
* *
59573 TAACATAAAGCGAGAAAAGC
65 TAAC-TCAAGCGAGAAAAAC
* * *
59593 TATCTGTCAGCAA-ACCTTCGAGTTCGATTATATTCAGCTCATGAA--CATATCAAATTTACAGT
1 TATCTATCAGCAAGACCTTCGAGTTCGATTACATTCAGCTCA--AAGGCACATCAAATTTACAGT
59655 ATAACTCAAG
64 ATAACTCAAG
59665 GCAAGAAGGA
Statistics
Matches: 141, Mismatches: 12, Indels: 11
0.86 0.07 0.07
Matches are distributed among these distances:
82 4 0.03
83 46 0.33
84 5 0.04
85 79 0.56
86 7 0.05
ACGTcount: A:0.38, C:0.21, G:0.14, T:0.27
Consensus pattern (83 bp):
TATCTATCAGCAAGACCTTCGAGTTCGATTACATTCAGCTCAAAGGCACATCAAATTTACAGTAT
AACTCAAGCGAGAAAAAC
Found at i:59682 original size:83 final size:83
Alignment explanation
Indices: 59402--59680 Score: 323
Period size: 85 Copynumber: 3.3 Consensus size: 83
59392 CAAGTACAAC
***
59402 ATAACTCAAGGCGAGAAGGGTTATCTATCAGCAAAGACCTTCGAGTTCGATTACATTCAGCTCAA
1 ATAACTCAAGGCGAGAAGAACTATCTATCAGC-AAGACCTTCGAGTTCGATTACATTCAGCTCAA
*
59467 AGGCACATTAAATTTACAGT
65 A-GCACATCAAATTTACAGT
* * * *
59487 ATAGCTCAAGTCGAGAAAAACTATCTATCTAGCAAGAACTTCGAGTTCGATTACATTCAGCTCAA
1 ATAACTCAAGGCGAGAAGAACTATCTATC-AGCAAGACCTTCGAGTTCGATTACATTCAGCTCAA
*
59552 AGGCACATCAAATTTACAGC
65 A-GCACATCAAATTTACAGT
* * *
59572 ATAACAT-AAAGCGAGAA-AAGCTATCTGTCAGCAA-ACCTTCGAGTTCGATTATATTCAGCTCA
1 ATAAC-TCAAGGCGAGAAGAA-CTATCTATCAGCAAGACCTTCGAGTTCGATTACATTCAGCTCA
*
59634 TGAA-CATATCAAATTTACAGT
64 --AAGCACATCAAATTTACAGT
* *
59655 ATAACTCAAGGCAAGAAGGACTATCT
1 ATAACTCAAGGCGAGAAGAACTATCT
59681 GTTAACATGG
Statistics
Matches: 167, Mismatches: 20, Indels: 16
0.82 0.10 0.08
Matches are distributed among these distances:
82 1 0.01
83 60 0.36
84 8 0.05
85 94 0.56
86 4 0.02
ACGTcount: A:0.38, C:0.20, G:0.16, T:0.25
Consensus pattern (83 bp):
ATAACTCAAGGCGAGAAGAACTATCTATCAGCAAGACCTTCGAGTTCGATTACATTCAGCTCAAA
GCACATCAAATTTACAGT
Found at i:60006 original size:3 final size:3
Alignment explanation
Indices: 59998--60051 Score: 81
Period size: 3 Copynumber: 17.7 Consensus size: 3
59988 ATATATTATG
* *
59998 TTA TTA TTA TTA TTA TCA TTA TTA TTA TTTA TTA TCA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA
60044 TTA TTA TT
1 TTA TTA TT
60052 TGTTTTTACT
Statistics
Matches: 46, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
3 43 0.93
4 3 0.07
ACGTcount: A:0.31, C:0.04, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:69519 original size:73 final size:73
Alignment explanation
Indices: 69394--69534 Score: 201
Period size: 73 Copynumber: 1.9 Consensus size: 73
69384 TGATAACAAA
*
69394 AAACGCCGCAATAGGTAACGAGATATAGCGACGTTTGTCCAACAAACACCGCAATAGGTGTTGAG
1 AAACACCGCAATAGGTAACGAGATATAGCGACGTTTGTCCAACAAACACCGCAATAGGTGTTGAG
69459 ATTGAGAT
66 ATTGAGAT
** * * * * **
69467 AAACACCGCAATAGGTGTCGAGATTTAGCGGCGTTTTTCCCACAAATGCCGCAATAGGTGTTGAG
1 AAACACCGCAATAGGTAACGAGATATAGCGACGTTTGTCCAACAAACACCGCAATAGGTGTTGAG
69532 ATT
66 ATT
69535 TAGCGGCGTT
Statistics
Matches: 59, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
73 59 1.00
ACGTcount: A:0.32, C:0.20, G:0.25, T:0.23
Consensus pattern (73 bp):
AAACACCGCAATAGGTAACGAGATATAGCGACGTTTGTCCAACAAACACCGCAATAGGTGTTGAG
ATTGAGAT
Found at i:69533 original size:43 final size:43
Alignment explanation
Indices: 69467--69560 Score: 152
Period size: 43 Copynumber: 2.2 Consensus size: 43
69457 AGATTGAGAT
*
69467 AAACACCGCAATAGGTGTCGAGATTTAGCGGCGTTTTTCCCAC
1 AAACGCCGCAATAGGTGTCGAGATTTAGCGGCGTTTTTCCCAC
* * *
69510 AAATGCCGCAATAGGTGTTGAGATTTAGCGGCGTTTTTCCTAC
1 AAACGCCGCAATAGGTGTCGAGATTTAGCGGCGTTTTTCCCAC
69553 AAACGCCG
1 AAACGCCG
69561 TAAAATGCGT
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
43 46 1.00
ACGTcount: A:0.26, C:0.23, G:0.24, T:0.27
Consensus pattern (43 bp):
AAACGCCGCAATAGGTGTCGAGATTTAGCGGCGTTTTTCCCAC
Found at i:70106 original size:23 final size:21
Alignment explanation
Indices: 70053--70107 Score: 83
Period size: 21 Copynumber: 2.6 Consensus size: 21
70043 CTGCTGATAT
70053 GCTGCTTCTCTCTATGATGCA
1 GCTGCTTCTCTCTATGATGCA
* * *
70074 GTTGCTTCTCTCTATGTTGCG
1 GCTGCTTCTCTCTATGATGCA
70095 GCTGCTTCTCTCT
1 GCTGCTTCTCTCT
70108 GTGCTTCCCT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.07, C:0.29, G:0.20, T:0.44
Consensus pattern (21 bp):
GCTGCTTCTCTCTATGATGCA
Found at i:70125 original size:20 final size:20
Alignment explanation
Indices: 70096--70137 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
70086 TATGTTGCGG
* *
70096 CTGCTTCTCTCTGTGCTTCC
1 CTGCTGCTCTCTCTGCTTCC
*
70116 CTGCTGCTCTTTCTGCTTCC
1 CTGCTGCTCTCTCTGCTTCC
70136 CT
1 CT
70138 TGCTTCATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.00, C:0.40, G:0.14, T:0.45
Consensus pattern (20 bp):
CTGCTGCTCTCTCTGCTTCC
Found at i:81470 original size:12 final size:11
Alignment explanation
Indices: 81453--81499 Score: 58
Period size: 12 Copynumber: 4.1 Consensus size: 11
81443 TTCAAAGAGG
81453 TTTTATATTTAA
1 TTTTAT-TTTAA
*
81465 TTTTATATTATA
1 TTTTATTTTA-A
81477 TTTTATTTTAA
1 TTTTATTTTAA
*
81488 TTTAATTTTAA
1 TTTTATTTTAA
81499 T
1 T
81500 ATTAATTTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
11 15 0.48
12 16 0.52
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (11 bp):
TTTTATTTTAA
Found at i:81506 original size:12 final size:11
Alignment explanation
Indices: 81460--81508 Score: 53
Period size: 12 Copynumber: 4.3 Consensus size: 11
81450 AGGTTTTATA
*
81460 TTTAATTTTAT
1 TTTAATTTAAT
* *
81471 ATTATATTTTAT
1 TTTA-ATTTAAT
81483 TTTAATTTAAT
1 TTTAATTTAAT
81494 TTTAATATTAAT
1 TTTAAT-TTAAT
81506 TTT
1 TTT
81509 TTAAATAAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
11 15 0.45
12 18 0.55
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (11 bp):
TTTAATTTAAT
Found at i:81617 original size:20 final size:19
Alignment explanation
Indices: 81559--81618 Score: 54
Period size: 19 Copynumber: 3.2 Consensus size: 19
81549 GATATTTAAC
*
81559 TTTATATCA-TATAAATTAT
1 TTTATAT-ATTATTAATTAT
*
81578 TTTATATATTATTAA-AAT
1 TTTATATATTATTAATTAT
81596 TTTATAT-TTATTTTAATTAT
1 TTTATATATTA--TTAATTAT
81616 TTT
1 TTT
81619 GATTTAAGTT
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
17 3 0.09
18 10 0.29
19 16 0.47
20 5 0.15
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.62
Consensus pattern (19 bp):
TTTATATATTATTAATTAT
Found at i:81775 original size:30 final size:29
Alignment explanation
Indices: 81741--81800 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 29
81731 ATTGTTTGAT
81741 AATTAAGATTTTAAAATATAAAAAAATATA
1 AATTAAGATTTTAAAAT-TAAAAAAATATA
* * **
81771 AATTATGTTTTTAAAATTTTAAAAATATA
1 AATTAAGATTTTAAAATTAAAAAAATATA
81800 A
1 A
81801 TCACAATTAA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
29 11 0.42
30 15 0.58
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (29 bp):
AATTAAGATTTTAAAATTAAAAAAATATA
Found at i:81865 original size:25 final size:24
Alignment explanation
Indices: 81837--81896 Score: 68
Period size: 25 Copynumber: 2.5 Consensus size: 24
81827 AAATAATTTG
*
81837 ATAAATTAAAAAATATTTTCTAAAA
1 ATAAATTAAAAAATATATT-TAAAA
* *
81862 ATAAATTATGAATATATATTTAAAA
1 ATAAATTA-AAAAATATATTTAAAA
81887 A-AAATTAAAA
1 ATAAATTAAAA
81897 GTATTACATA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
23 2 0.07
24 6 0.20
25 14 0.47
26 8 0.27
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.35
Consensus pattern (24 bp):
ATAAATTAAAAAATATATTTAAAA
Found at i:82101 original size:31 final size:31
Alignment explanation
Indices: 82064--82123 Score: 86
Period size: 31 Copynumber: 1.9 Consensus size: 31
82054 TAGTTGTATG
* *
82064 AATTATTTAAATTTCAGT-ATTGTAAAACTAA
1 AATTATTTAAATCTCA-TAATTGCAAAACTAA
82095 AATTATTTAAATCTCATAATTGCAAAACT
1 AATTATTTAAATCTCATAATTGCAAAACT
82124 CTTTTAAGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
30 1 0.04
31 25 0.96
ACGTcount: A:0.45, C:0.10, G:0.05, T:0.40
Consensus pattern (31 bp):
AATTATTTAAATCTCATAATTGCAAAACTAA
Found at i:88837 original size:9 final size:8
Alignment explanation
Indices: 88809--88840 Score: 55
Period size: 8 Copynumber: 3.9 Consensus size: 8
88799 TATTATTATT
88809 ATATTTTA
1 ATATTTTA
88817 ATATTTTA
1 ATATTTTA
88825 ATATTTATA
1 ATATTT-TA
88834 ATATTTT
1 ATATTTT
88841 TTTAAGTCTG
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
8 15 0.65
9 8 0.35
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (8 bp):
ATATTTTA
Found at i:89673 original size:10 final size:10
Alignment explanation
Indices: 89650--89683 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
89640 TTATTTTTTT
*
89650 AAAATCAATA
1 AAAATGAATA
89660 AAAATGAAATA
1 AAAATG-AATA
89671 AAAATGAATA
1 AAAATGAATA
89681 AAA
1 AAA
89684 TTCAATACAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
10 12 0.55
11 10 0.45
ACGTcount: A:0.74, C:0.03, G:0.06, T:0.18
Consensus pattern (10 bp):
AAAATGAATA
Found at i:89701 original size:22 final size:23
Alignment explanation
Indices: 89670--89712 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
89660 AAAATGAAAT
*
89670 AAAAATGAATA-AAATTCAATAC
1 AAAAAAGAATATAAATTCAATAC
89692 AAAAAAGAATATAAATTCAAT
1 AAAAAAGAATATAAATTCAAT
89713 TTTTTTCAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 10 0.53
23 9 0.47
ACGTcount: A:0.65, C:0.07, G:0.05, T:0.23
Consensus pattern (23 bp):
AAAAAAGAATATAAATTCAATAC
Found at i:90569 original size:18 final size:19
Alignment explanation
Indices: 90534--90570 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
90524 TACGGAATGT
90534 AAGATTATCAGTGAGAATAA
1 AAGATTATCAG-GAGAATAA
90554 AAGATTATCA-GAGAATA
1 AAGATTATCAGGAGAATA
90571 GGATTACTGA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
20 10 0.59
ACGTcount: A:0.51, C:0.05, G:0.19, T:0.24
Consensus pattern (19 bp):
AAGATTATCAGGAGAATAA
Found at i:108810 original size:17 final size:17
Alignment explanation
Indices: 108788--108821 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
108778 GGCTTAAAAC
108788 AAATGGTTAGGGTATAG
1 AAATGGTTAGGGTATAG
*
108805 AAATGGTTATGGTATAG
1 AAATGGTTAGGGTATAG
108822 GGTAGAAAGG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.35, C:0.00, G:0.32, T:0.32
Consensus pattern (17 bp):
AAATGGTTAGGGTATAG
Found at i:126551 original size:3 final size:3
Alignment explanation
Indices: 126511--126651 Score: 79
Period size: 3 Copynumber: 45.3 Consensus size: 3
126501 TTTTTTATAT
* * * * *
126511 TAA TAA T-A TAA TTAG TAA TAA CAAA TAA TAG TAG TAA TAA TAA TAC
1 TAA TAA TAA TAA -TAA TAA TAA -TAA TAA TAA TAA TAA TAA TAA TAA
* * * * * *
126557 TAA TAT TAAA TGA TAA TAA TAGG TAA CAA TAA TAG TAA TAG TAA T-A
1 TAA TAA T-AA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA
* * *
126603 TAA TAA TATA TAA TAA TAA TATA TAA TAA TTA CAA TAGT TAA TAA TAA
1 TAA TAA TA-A TAA TAA TAA TA-A TAA TAA TAA TAA TA-A TAA TAA TAA
126651 T
1 T
126652 CATAGTAGTA
Statistics
Matches: 103, Mismatches: 26, Indels: 18
0.70 0.18 0.12
Matches are distributed among these distances:
2 4 0.04
3 83 0.81
4 16 0.16
ACGTcount: A:0.56, C:0.03, G:0.06, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:126620 original size:13 final size:13
Alignment explanation
Indices: 126602--126632 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
126592 TAATAGTAAT
126602 ATAATAATATATA
1 ATAATAATATATA
126615 ATAATAATATATA
1 ATAATAATATATA
126628 ATAAT
1 ATAAT
126633 TACAATAGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (13 bp):
ATAATAATATATA
Found at i:126656 original size:16 final size:16
Alignment explanation
Indices: 126534--126657 Score: 64
Period size: 16 Copynumber: 7.8 Consensus size: 16
126524 AGTAATAACA
*
126534 AATAATAGTAGTAATAAT
1 AATAATAATAGT--TAAT
*
126552 AATACTAATA-TTAAAT
1 AATAATAATAGTT-AAT
* *
126568 GATAATAATAGGTAACAAT
1 AATAATAATA-GT--TAAT
*
126587 AATAGTAATAG-TAAT
1 AATAATAATAGTTAAT
126602 -ATAATAATA--T-AT
1 AATAATAATAGTTAAT
126614 AATAATAATA-TATAAT
1 AATAATAATAGT-TAAT
* *
126630 AATTACAATAGTTAAT
1 AATAATAATAGTTAAT
*
126646 AATAATCATAGT
1 AATAATAATAGT
126658 AGTACGTAAG
Statistics
Matches: 82, Mismatches: 14, Indels: 22
0.69 0.12 0.19
Matches are distributed among these distances:
12 2 0.02
13 10 0.12
14 8 0.10
15 5 0.06
16 34 0.41
17 2 0.02
18 10 0.12
19 11 0.13
ACGTcount: A:0.55, C:0.03, G:0.07, T:0.35
Consensus pattern (16 bp):
AATAATAATAGTTAAT
Found at i:126819 original size:3 final size:3
Alignment explanation
Indices: 126813--127022 Score: 68
Period size: 3 Copynumber: 72.3 Consensus size: 3
126803 TAACAACAAC
* * *
126813 AAT AAT AAT -AT AAT -AT AAT -AT AAT -AT AAT AAC AGT AGT -AT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * * * *
126856 -AT AAT AAT -AT AAC ACT AAT AAT ACT AAT AGT -AT ATT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * * * * *
126901 -AT AAT AGT GGGAT AAT AAC AAT AGT ACTT AAT AAT AAT AAT ACTT AAT
1 AAT AAT AAT --AAT AAT AAT AAT AAT A-AT AAT AAT AAT AAT A-AT AAT
** * * * *
126949 -AT GGT AAT AAC AAT AAT AGT -AT AAC AAT AAT ACT AAT -AT AAT AGA-
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT
* * *
126994 AAT AAT AGT ACT AAT ATT AAGT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AA-T AAT AAT A
127023 TTATTTAAAC
Statistics
Matches: 147, Mismatches: 41, Indels: 38
0.65 0.18 0.17
Matches are distributed among these distances:
2 22 0.15
3 116 0.79
4 8 0.05
5 1 0.01
ACGTcount: A:0.55, C:0.05, G:0.07, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:126874 original size:19 final size:18
Alignment explanation
Indices: 126822--126906 Score: 75
Period size: 19 Copynumber: 4.6 Consensus size: 18
126812 CAATAATAAT
126822 ATAATATAATATAATATA
1 ATAATATAATATAATATA
* *
126840 ATAACAGTAGTATAATATA
1 ATAATA-TAATATAATATA
*
126859 ATAATATAACACTAATAATA
1 ATAATATAATA-TAAT-ATA
* *
126879 CTAATAGT-ATATTA-ATA
1 ATAATA-TAATATAATATA
126896 ATAATATAATA
1 ATAATATAATA
126907 GTGGGATAAT
Statistics
Matches: 53, Mismatches: 9, Indels: 11
0.73 0.12 0.15
Matches are distributed among these distances:
16 1 0.02
17 11 0.21
18 8 0.15
19 22 0.42
20 10 0.19
21 1 0.02
ACGTcount: A:0.56, C:0.05, G:0.04, T:0.35
Consensus pattern (18 bp):
ATAATATAATATAATATA
Found at i:126906 original size:5 final size:5
Alignment explanation
Indices: 126817--126842 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
126807 AACAACAATA
126817 ATAAT ATAAT ATAAT ATAAT ATAAT A
1 ATAAT ATAAT ATAAT ATAAT ATAAT A
126843 ACAGTAGTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (5 bp):
ATAAT
Found at i:126932 original size:16 final size:16
Alignment explanation
Indices: 126913--126949 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
126903 AATAGTGGGA
*
126913 TAATAACAATAGTACT
1 TAATAACAATAATACT
*
126929 TAATAATAATAATACT
1 TAATAACAATAATACT
126945 TAATA
1 TAATA
126950 TGGTAATAAC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.54, C:0.08, G:0.03, T:0.35
Consensus pattern (16 bp):
TAATAACAATAATACT
Found at i:127531 original size:105 final size:105
Alignment explanation
Indices: 127269--127849 Score: 668
Period size: 105 Copynumber: 5.5 Consensus size: 105
127259 GGAAACAAAC
** * *
127269 AAGTTCTTCTCATTATGAACTTT-TTCTCATCAGGGCAAGTTCTTCTCATTATGAACTATTCCAG
1 AAGTTCTTCTCATTATGAACTTTCTTCT--TTGGGGCGAGTTCTTCTCATTATGAACTATTCTAG
* * * * *
127333 AAATGTTGATTCACCTCTTTCTACGAT-GAGTTTGAATGGAAT
64 AAATGTCGGTCCACCTCATTCTACGATGGA-TTTGAAAGGAAT
* * * * *
127375 AAGTT-TTCTCATTATGAACCTTCTTCTTTGGGACTAGTTCTTCTCATTATGAATTATTCTAAAA
1 AAGTTCTTCTCATTATGAACTTTCTTCTTTGGGGCGAGTTCTTCTCATTATGAACTATTCTAGAA
* * * *
127439 ATATTGGTCCACCTCATTCTTCGATGGATTCGAAAGGAAT
66 ATGTCGGTCCACCTCATTCTACGATGGATTTGAAAGGAAT
** * *
127479 AAGTTCTTCTCATTATGAACTTTCTGATTTGGGGCGAGTTCTTCTCATTATGAACTATTTTGGAA
1 AAGTTCTTCTCATTATGAACTTTCTTCTTTGGGGCGAGTTCTTCTCATTATGAACTATTCTAGAA
* * *
127544 ATGTCGGTCCACCTCCTTCTGCAATGGATTTGAAAGGAAT
66 ATGTCGGTCCACCTCATTCTACGATGGATTTGAAAGGAAT
* * *
127584 AAGTTCTTCTCATTATGAACTTT-TTCCTTAGGGGCGATTTCTTCTCATTATGAACTCTT-TAGG
1 AAGTTCTTCTCATTATGAACTTTCTT-CTTTGGGGCGAGTTCTTCTCATTATGAACTATTCTA-G
* * * * * * *
127647 AAATGTCAGTCTACCTCCTTGTGCGATGAATTTAAAAGGAAT
64 AAATGTCGGTCCACCTCATTCTACGATGGATTTGAAAGGAAT
* * * * *
127689 AAGTTCTTCTTATTATGAACTTTCTTCTTTGGGGTGAGTTCTTCTCATTATGAAATCTTCTGGAA
1 AAGTTCTTCTCATTATGAACTTTCTTCTTTGGGGCGAGTTCTTCTCATTATGAACTATTCTAGAA
* *
127754 ATGTCGATCCACCTCATTCGACGATGGATTTGAAAGGAAT
66 ATGTCGGTCCACCTCATTCTACGATGGATTTGAAAGGAAT
* * * *
127794 AAGTTCTTCTCATTATGAACTTTTTTCTTTGGGGTGAGTTTTTATCATTATGAACT
1 AAGTTCTTCTCATTATGAACTTTCTTCTTTGGGGCGAGTTCTTCTCATTATGAACT
127850 CGGTCCACCT
Statistics
Matches: 406, Mismatches: 62, Indels: 15
0.84 0.13 0.03
Matches are distributed among these distances:
104 67 0.17
105 327 0.81
106 12 0.03
ACGTcount: A:0.25, C:0.18, G:0.17, T:0.40
Consensus pattern (105 bp):
AAGTTCTTCTCATTATGAACTTTCTTCTTTGGGGCGAGTTCTTCTCATTATGAACTATTCTAGAA
ATGTCGGTCCACCTCATTCTACGATGGATTTGAAAGGAAT
Found at i:127844 original size:315 final size:315
Alignment explanation
Indices: 127269--127849 Score: 794
Period size: 315 Copynumber: 1.8 Consensus size: 315
127259 GGAAACAAAC
127269 AAGTTCTTCTCATTATGAACTTTTTCTCATCAGGGCAAGTTCTTCTCATTATGAACTATTCCAGA
1 AAGTTCTTCTCATTATGAACTTTTTCTCATCAGGGCAAGTTCTTCTCATTATGAACTATTCCAGA
* * * * * *
127334 AATGTTGATTCACCTCTTTCTACGATGAGTTTGAATGGAATAAGTTTTCTCATTATGAACCTTCT
66 AATGTTCAGTCACCTCCTTCTACGATGAATTTAAAAGGAATAAGTTTTCTCATTATGAACCTTCT
* * * **
127399 TCTTTGGGACTAGTTCTTCTCATTATGAATTATTCTAAAAATATTGGTCCACCTCATTCTTCGAT
131 TCTTTGGGACTAGTTCTTCTCATTATGAAATATTCTAAAAATATCGATCCACCTCATTCGACGAT
*
127464 GGATTCGAAAGGAATAAGTTCTTCTCATTATGAACTTTCTGATTTGGGGCGAGTTCTTCTCATTA
196 GGATTCGAAAGGAATAAGTTCTTCTCATTATGAACTTTCTGATTTGGGGCGAGTTCTTATCATTA
127529 TGAACTATTTTGGAAATGTCGGTCCACCTCCTTCTGCAATGGATTTGAAAGGAAT
261 TGAACTATTTTGGAAATGTCGGTCCACCTCCTTCTGCAATGGATTTGAAAGGAAT
* * * * *
127584 AAGTTCTTCTCATTATGAACTTTTTC-C-TTAGGGGCGATTTCTTCTCATTATGAACTCTT-TAG
1 AAGTTCTTCTCATTATGAACTTTTTCTCATCA-GGGCAAGTTCTTCTCATTATGAACTATTCCA-
* * * *
127646 GAAATG-TCAGTCTACCTCCTTGTGCGATGAATTTAAAAGGAATAAGTTCTTCTTATTATGAACT
64 GAAATGTTCAGTC-ACCTCCTTCTACGATGAATTTAAAAGGAATAAGTT-TTCTCATTATGAACC
* * ** *
127710 TTCTTCTTTGGG-GTGAGTTCTTCTCATTATGAAATCTTCTGGAAATGTCGATCCACCTCATTCG
127 TTCTTCTTTGGGACT-AGTTCTTCTCATTATGAAATATTCTAAAAATATCGATCCACCTCATTCG
* * ** * *
127774 ACGATGGATTTGAAAGGAATAAGTTCTTCTCATTATGAACTTTTTTCTTTGGGGTGAGTTTTTAT
191 ACGATGGATTCGAAAGGAATAAGTTCTTCTCATTATGAACTTTCTGATTTGGGGCGAGTTCTTAT
127839 CATTATGAACT
256 CATTATGAACT
127850 CGGTCCACCT
Statistics
Matches: 229, Mismatches: 32, Indels: 10
0.85 0.12 0.04
Matches are distributed among these distances:
313 7 0.03
314 62 0.27
315 160 0.70
ACGTcount: A:0.25, C:0.18, G:0.17, T:0.40
Consensus pattern (315 bp):
AAGTTCTTCTCATTATGAACTTTTTCTCATCAGGGCAAGTTCTTCTCATTATGAACTATTCCAGA
AATGTTCAGTCACCTCCTTCTACGATGAATTTAAAAGGAATAAGTTTTCTCATTATGAACCTTCT
TCTTTGGGACTAGTTCTTCTCATTATGAAATATTCTAAAAATATCGATCCACCTCATTCGACGAT
GGATTCGAAAGGAATAAGTTCTTCTCATTATGAACTTTCTGATTTGGGGCGAGTTCTTATCATTA
TGAACTATTTTGGAAATGTCGGTCCACCTCCTTCTGCAATGGATTTGAAAGGAAT
Found at i:128411 original size:2 final size:2
Alignment explanation
Indices: 128404--128437 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
128394 ATAAGATGCT
128404 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
128438 AAATGAATAT
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:134253 original size:65 final size:64
Alignment explanation
Indices: 134099--134308 Score: 169
Period size: 65 Copynumber: 3.2 Consensus size: 64
134089 TTTTTCAGAG
* * * * *
134099 TGATGCACCGATGCACCAATTCATGCATCGATGCAC-CATGA-ATTAAATTG-AACATTGAATGC
1 TGATGCATCGATGCACC-ATACATGCACCGATGCACTCAGGATATT--A-TGAAACATCGAATGC
134161 ATT
62 ATT
* * * *
134164 TCATGCATCGATGCA-CATACCATGCACCGATGCACTGAGGATGTTATGAAAACATCGAATGGAT
1 TGATGCATCGATGCACCATA-CATGCACCGATGCACTCAGGATATTATG-AAACATCGAATGCAT
134228 T
64 T
*** * * * *
134229 TGATGCATCGATGCACCAGT-CATGCTTTGATGCACTCTGGCTATTTTGAAACATCGAATGCACT
1 TGATGCATCGATGCACCA-TACATGCACCGATGCACTCAGGATATTATGAAACATCGAATGCATT
*
134293 TGATGCATCGTTGCAC
1 TGATGCATCGATGCAC
134309 TCTTAGTGCA
Statistics
Matches: 117, Mismatches: 21, Indels: 15
0.76 0.14 0.10
Matches are distributed among these distances:
63 4 0.03
64 45 0.38
65 63 0.54
66 4 0.03
67 1 0.01
ACGTcount: A:0.30, C:0.22, G:0.20, T:0.28
Consensus pattern (64 bp):
TGATGCATCGATGCACCATACATGCACCGATGCACTCAGGATATTATGAAACATCGAATGCATT
Found at i:135440 original size:21 final size:21
Alignment explanation
Indices: 135414--135453 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
135404 AAGAATATAT
135414 TTTCAAAATACAAAAATGATA
1 TTTCAAAATACAAAAATGATA
**
135435 TTTCAAAATTGAAAAATGA
1 TTTCAAAATACAAAAATGA
135454 AAATAGTCTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.55, C:0.07, G:0.07, T:0.30
Consensus pattern (21 bp):
TTTCAAAATACAAAAATGATA
Found at i:141678 original size:22 final size:22
Alignment explanation
Indices: 141652--141696 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
141642 TAGTAAGGGG
141652 AGTAATTTGGAGTAATTTTCAA
1 AGTAATTTGGAGTAATTTTCAA
141674 AGTAATTTGGAGTAATTTTCAA
1 AGTAATTTGGAGTAATTTTCAA
141696 A
1 A
141697 ATTGATTTCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.38, C:0.04, G:0.18, T:0.40
Consensus pattern (22 bp):
AGTAATTTGGAGTAATTTTCAA
Found at i:142181 original size:65 final size:63
Alignment explanation
Indices: 142069--142225 Score: 176
Period size: 65 Copynumber: 2.4 Consensus size: 63
142059 AATTAAATCG
* * *
142069 AACATCAAATGCATTTCATGCATCGATGCATATACCATGCACTGATGCACTGA-GGATGTTATGA
1 AACATCGAATGCATTTGATGCATCGATGCATATA-CATGCACTGATGCACT-ATGGATATTATG-
142133 A
63 A
* * *
142134 AACATCGAATGCATTTGATGCATCGATGCACTAGT-CATGTA-TCGATGCACTATGGCTATTTTG
1 AACATCGAATGCATTTGATGCATCGATGCA-TA-TACATGCACT-GATGCACTATGGATATTATG
142197 A
63 A
*
142198 AACATCGAATGCACTTGATGCATCGATG
1 AACATCGAATGCATTTGATGCATCGATG
142226 TACTCTTAGT
Statistics
Matches: 81, Mismatches: 7, Indels: 9
0.84 0.07 0.09
Matches are distributed among these distances:
64 30 0.37
65 48 0.59
66 2 0.02
67 1 0.01
ACGTcount: A:0.31, C:0.20, G:0.20, T:0.29
Consensus pattern (63 bp):
AACATCGAATGCATTTGATGCATCGATGCATATACATGCACTGATGCACTATGGATATTATGA
Found at i:146123 original size:5 final size:5
Alignment explanation
Indices: 146113--146140 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
146103 TGTCTTTACC
146113 TTTCA TTTCA TTTCA TTTCA TTTCA TTT
1 TTTCA TTTCA TTTCA TTTCA TTTCA TTT
146141 TGGCTTCTCC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.18, C:0.18, G:0.00, T:0.64
Consensus pattern (5 bp):
TTTCA
Found at i:152536 original size:13 final size:13
Alignment explanation
Indices: 152515--152553 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
152505 GGTGCTGCAA
*
152515 AATATGTAATAAT
1 AATAAGTAATAAT
152528 AATAAGTAATAAT
1 AATAAGTAATAAT
*
152541 AAT-ATTAATAAT
1 AATAAGTAATAAT
152553 A
1 A
152554 TTTATATTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
12 9 0.38
13 15 0.62
ACGTcount: A:0.59, C:0.00, G:0.05, T:0.36
Consensus pattern (13 bp):
AATAAGTAATAAT
Found at i:152895 original size:46 final size:48
Alignment explanation
Indices: 152796--152912 Score: 159
Period size: 48 Copynumber: 2.5 Consensus size: 48
152786 TGTTCCGTTG
*
152796 TCTCTGAAGGGAATATCAAATC-TTGAAGAAGAGAGATTTGTTCCGCTT
1 TCTCTGAAGGGAATATCAAATCTTTGAAGAAGAGAGA-TTGTTCCACTT
* *
152844 ACTCTGAAGGGAATATCAAATCTTTG-AGAAGAGAGA-TGTTCTACTT
1 TCTCTGAAGGGAATATCAAATCTTTGAAGAAGAGAGATTGTTCCACTT
* *
152890 TCTCTGAAGGGACTATCAGATCT
1 TCTCTGAAGGGAATATCAAATCT
152913 GGGGAAGTTG
Statistics
Matches: 62, Mismatches: 6, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
46 28 0.45
48 31 0.50
49 3 0.05
ACGTcount: A:0.32, C:0.15, G:0.22, T:0.31
Consensus pattern (48 bp):
TCTCTGAAGGGAATATCAAATCTTTGAAGAAGAGAGATTGTTCCACTT
Found at i:153042 original size:113 final size:112
Alignment explanation
Indices: 152833--153272 Score: 625
Period size: 113 Copynumber: 3.9 Consensus size: 112
152823 GAAGAGAGAT
* * * ** *
152833 TTGTTCCGCTTACTCTGAAGGGAATATCAAATCTTTGAGAAGAGAG--ATGTTCTACTTTCTCTG
1 TTGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGAAAAGAGAGACATGTTCCGCTTACTCTG
*
152896 AAGGGACTATCAGATCTGGGGAAGTTGATCCATTGAATCGAAGCAGAC
66 AAGGGAATATCAGATCTGGGG-AGTTGATCCATTGAATCGAAGCAGAC
*
152944 TTGTTCCACTTACTCTGAAGGGAATATCAAATATTGGAAAAGAGAGACATGTTCCGCTTACTCTG
1 TTGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGAAAAGAGAGACATGTTCCGCTTACTCTG
* * * *
153009 AAGGGAATATCATATATGGGGTAGTTAATCCATTGAATAGAAGCAGAC
66 AAGGGAATATCAGATCTGGGG-AGTTGATCCATTGAATCGAAGCAGAC
* *
153057 TTGTTCCACTTACTCTGAAGGGAATATCAAATCTTAGAAAAAAGAGACATGTTCCGCTTACTCTG
1 TTGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGAAAAGAGAGACATGTTCCGCTTACTCTG
* * *
153122 AAGGGAATATCATATCTGGGGGAGTTGATCCATTGAATC-AGGATAGAC
66 AAGGGAATATCAGATCT-GGGGAGTTGATCCATTGAATCGAAG-CAGAC
* * *
153170 TTGTTCCACATACTCTGAAGGGAATATCAAATCTTGGATAAGAGAGACCTGTTCCGCTTACTCTG
1 TTGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGAAAAGAGAGACATGTTCCGCTTACTCTG
*
153235 AAGGGAATATCAGATCTGGAGGAATTGATCCATTGAAT
66 AAGGGAATATCAGATCTGG-GGAGTTGATCCATTGAAT
153273 ATGGATCGAA
Statistics
Matches: 296, Mismatches: 28, Indels: 8
0.89 0.08 0.02
Matches are distributed among these distances:
111 42 0.14
112 4 0.01
113 246 0.83
114 4 0.01
ACGTcount: A:0.32, C:0.17, G:0.23, T:0.29
Consensus pattern (112 bp):
TTGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGAAAAGAGAGACATGTTCCGCTTACTCTG
AAGGGAATATCAGATCTGGGGAGTTGATCCATTGAATCGAAGCAGAC
Found at i:158443 original size:17 final size:17
Alignment explanation
Indices: 158421--158461 Score: 82
Period size: 17 Copynumber: 2.4 Consensus size: 17
158411 TCCTGACTAA
158421 CCTGGCTTTCCTCCTTT
1 CCTGGCTTTCCTCCTTT
158438 CCTGGCTTTCCTCCTTT
1 CCTGGCTTTCCTCCTTT
158455 CCTGGCT
1 CCTGGCT
158462 CTTTTGAACA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.00, C:0.41, G:0.15, T:0.44
Consensus pattern (17 bp):
CCTGGCTTTCCTCCTTT
Found at i:158448 original size:9 final size:9
Alignment explanation
Indices: 158421--158461 Score: 50
Period size: 8 Copynumber: 4.8 Consensus size: 9
158411 TCCTGACTAA
158421 CCTGGCTTT
1 CCTGGCTTT
*
158430 CCT-CCTTT
1 CCTGGCTTT
158438 CCTGGCTTT
1 CCTGGCTTT
*
158447 CCT-CCTTT
1 CCTGGCTTT
158455 CCTGGCT
1 CCTGGCT
158462 CTTTTGAACA
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
8 14 0.54
9 12 0.46
ACGTcount: A:0.00, C:0.41, G:0.15, T:0.44
Consensus pattern (9 bp):
CCTGGCTTT
Found at i:161644 original size:11 final size:11
Alignment explanation
Indices: 161630--161659 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
161620 TGCAATGTAG
161630 ATGCAATATGA
1 ATGCAATATGA
*
161641 ATGCAAGATGA
1 ATGCAATATGA
161652 ATGCAATA
1 ATGCAATA
161660 CAAGGTGTTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.47, C:0.10, G:0.20, T:0.23
Consensus pattern (11 bp):
ATGCAATATGA
Found at i:164722 original size:40 final size:40
Alignment explanation
Indices: 164678--164758 Score: 144
Period size: 40 Copynumber: 2.0 Consensus size: 40
164668 TGCAAACAAA
* *
164678 ACTTATTTAAAACAATACAAGGGTTCAAAAACCAAATTAG
1 ACTTATTTAAAACAAAACAAGGGATCAAAAACCAAATTAG
164718 ACTTATTTAAAACAAAACAAGGGATCAAAAACCAAATTAG
1 ACTTATTTAAAACAAAACAAGGGATCAAAAACCAAATTAG
164758 A
1 A
164759 ACGAACTTGT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 39 1.00
ACGTcount: A:0.53, C:0.15, G:0.10, T:0.22
Consensus pattern (40 bp):
ACTTATTTAAAACAAAACAAGGGATCAAAAACCAAATTAG
Found at i:168904 original size:22 final size:21
Alignment explanation
Indices: 168872--168954 Score: 87
Period size: 23 Copynumber: 3.8 Consensus size: 21
168862 TTTAGTGCAG
*
168872 AGGGAATCGATACCCCCTTGA
1 AGGGAACCGATACCCCCTTGA
*
168893 AGAGGAACCGATCCCCCCTTTGA
1 AG-GGAACCGATACCCCC-TTGA
*
168916 ATGGGAACCGATTCCCTCCTTG-
1 A-GGGAACCGATACCC-CCTTGA
*
168938 AGGGAATCGATACCCCC
1 AGGGAACCGATACCCCC
168955 CACGGGTTCT
Statistics
Matches: 53, Mismatches: 5, Indels: 9
0.79 0.07 0.13
Matches are distributed among these distances:
20 2 0.04
21 14 0.26
22 14 0.26
23 20 0.38
24 3 0.06
ACGTcount: A:0.25, C:0.33, G:0.23, T:0.19
Consensus pattern (21 bp):
AGGGAACCGATACCCCCTTGA
Found at i:178367 original size:3 final size:3
Alignment explanation
Indices: 178361--178802 Score: 109
Period size: 3 Copynumber: 144.7 Consensus size: 3
178351 GTATTTTGTT
* * * * *
178361 TAA TAA TAA TAA -CA TAA TTAA TAA TAA CAAA TAG TAG TAG TAA TAA
1 TAA TAA TAA TAA TAA TAA -TAA TAA TAA -TAA TAA TAA TAA TAA TAA
* * * * *
178407 TAA TAT TAA TAT TAAA TAA TAA TAGG TAA TAA TAA TAT TAA TAT TAAA
1 TAA TAA TAA TAA T-AA TAA TAA TA-A TAA TAA TAA TAA TAA TAA T-AA
* * *
178455 TAA TAA TAGGA -AA TAA TAA TAG TAA TAG TAG T-A TAA TAA TTAA TAA
1 TAA TAA TA--A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA -TAA TAA
* * * * * **
178501 TTA CAA TAGC TAA TAA TAA TAA TAG TAG TGTG TAA GTAA TAA TAA -ATA
1 TAA TAA TA-A TAA TAA TAA TAA TAA TAA T-AA TAA -TAA TAA TAA TA-A
* * * * * * * * *
178549 TAA TCA TAA TAA CACT TAA T-A TAA CAT TAA TAA TAG TAG TAG TAG
1 TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * *** * * *
178594 T-A TAG TAA TAC TAA TACA CGT TAA TAG TGAG TAA TAA TAA TAG T-A
1 TAA TAA TAA TAA TAA TA-A TAA TAA TAA T-AA TAA TAA TAA TAA TAA
** * * *
178639 TGG TAA TAA TATT TAA -CA TAA -ACT TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TA-A TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA
* * * *
178684 TAA TAA TAA T-A TAA TAG TGGGA TAA TAA TAA TAG TACT TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA T--AA TAA TAA TAA TAA TA-A TAA TAA TAA
* ** * * * *
178731 TAA TACT TAA T-A TGG TAA TAA CAA TAA T-A GAA TAA TAG TAA TAC
1 TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* *
178775 TAA T-G TAA TAG TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
178803 TCATTTAAAC
Statistics
Matches: 316, Mismatches: 89, Indels: 68
0.67 0.19 0.14
Matches are distributed among these distances:
2 16 0.05
3 263 0.83
4 35 0.11
5 2 0.01
ACGTcount: A:0.53, C:0.04, G:0.09, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:178436 original size:32 final size:32
Alignment explanation
Indices: 178400--178481 Score: 146
Period size: 32 Copynumber: 2.6 Consensus size: 32
178390 AATAGTAGTA
178400 GTAATAATAATATTAATATTAAATAATAATAG
1 GTAATAATAATATTAATATTAAATAATAATAG
178432 GTAATAATAATATTAATATTAAATAATAATAG
1 GTAATAATAATATTAATATTAAATAATAATAG
* *
178464 GAAATAATAATAGTAATA
1 GTAATAATAATATTAATA
178482 GTAGTATAAT
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
32 48 1.00
ACGTcount: A:0.57, C:0.00, G:0.07, T:0.35
Consensus pattern (32 bp):
GTAATAATAATATTAATATTAAATAATAATAG
Found at i:178468 original size:13 final size:13
Alignment explanation
Indices: 178452--178476 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
178442 TATTAATATT
178452 AAATAATAATAGG
1 AAATAATAATAGG
178465 AAATAATAATAG
1 AAATAATAATAG
178477 TAATAGTAGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.64, C:0.00, G:0.12, T:0.24
Consensus pattern (13 bp):
AAATAATAATAGG
Found at i:178688 original size:108 final size:106
Alignment explanation
Indices: 178444--178691 Score: 229
Period size: 108 Copynumber: 2.3 Consensus size: 106
178434 AATAATAATA
*
178444 TTAATATTAAATAATAATAGGAAATAATAATAGTAATAGTAGTATAATAATTAATAATTACAATA
1 TTAATAAT-AATAATAATA--AAATAATAATAGTAATAGTAGTATAATAATTAATAATTA-AATA
* *
178509 GCTAATAATAATAATAGTAGTGTGTAAGTAATAATAAATATAATC
62 GCTAATAATAATAATAGTAGTGTGTAAGTAATAATAAACATAAAC
* * * * * *
178554 ATAATAACACTTAAT-ATAACATTAATAATAGTAGTAGTAGTATAGTAATACTAATACACGTT-A
1 TTAATAATA-ATAATAATAA-AATAATAATAGTAATAGTAGTATAATAAT--TAATA-A--TTAA
* * *
178617 ATAG-TGAGTAATAATAATAGTA-TG-GTAA-TAATATTTAACATAAAC
59 ATAGCT-AATAATAATAATAGTAGTGTGTAAGTAATAATAAACATAAAC
178662 TTAATAATAATAATAATAATAATAATAATA
1 TTAATAATAATAATAATAA-AATAATAATA
178692 ATATAATAGT
Statistics
Matches: 112, Mismatches: 17, Indels: 20
0.75 0.11 0.13
Matches are distributed among these distances:
107 5 0.04
108 59 0.53
109 8 0.07
110 17 0.15
111 21 0.19
113 2 0.02
ACGTcount: A:0.52, C:0.04, G:0.09, T:0.34
Consensus pattern (106 bp):
TTAATAATAATAATAATAAAATAATAATAGTAATAGTAGTATAATAATTAATAATTAAATAGCTA
ATAATAATAATAGTAGTGTGTAAGTAATAATAAACATAAAC
Found at i:178725 original size:16 final size:16
Alignment explanation
Indices: 178706--178742 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
178696 AATAGTGGGA
*
178706 TAATAATAATAGTACT
1 TAATAATAATAATACT
178722 TAATAATAATAATACT
1 TAATAATAATAATACT
178738 TAATA
1 TAATA
178743 TGGTAATAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.54, C:0.05, G:0.03, T:0.38
Consensus pattern (16 bp):
TAATAATAATAATACT
Found at i:181024 original size:18 final size:18
Alignment explanation
Indices: 180986--181025 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
180976 GTCATATATG
* * *
180986 TCCCGTAGGGCCCCTATA
1 TCCCGTAGGACCACTACA
181004 TCCCGTAGGACCACTACA
1 TCCCGTAGGACCACTACA
181022 TCCC
1 TCCC
181026 AAAGGACTAC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.20, C:0.42, G:0.17, T:0.20
Consensus pattern (18 bp):
TCCCGTAGGACCACTACA
Found at i:181040 original size:15 final size:15
Alignment explanation
Indices: 181016--181049 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
181006 CCGTAGGACC
181016 ACTACATCCCAAAGG
1 ACTACATCCCAAAGG
* *
181031 ACTACGTCCCGAAGG
1 ACTACATCCCAAAGG
181046 ACTA
1 ACTA
181050 TTATACCCTC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.35, C:0.32, G:0.18, T:0.15
Consensus pattern (15 bp):
ACTACATCCCAAAGG
Found at i:181176 original size:29 final size:29
Alignment explanation
Indices: 181134--181214 Score: 128
Period size: 29 Copynumber: 2.8 Consensus size: 29
181124 TTTCATATGT
181134 TCATGTA-CTCATGTCATTTCTCTTGTGA
1 TCATGTAGCTCATGTCATTTCTCTTGTGA
* *
181162 TCATGTAGCTCATGTCATCTCTTTTGTGA
1 TCATGTAGCTCATGTCATTTCTCTTGTGA
181191 TCATGTAGCTCATGTCATGTTCTC
1 TCATGTAGCTCATGTCAT-TTCTC
181215 ATATCACATA
Statistics
Matches: 47, Mismatches: 4, Indels: 2
0.89 0.08 0.04
Matches are distributed among these distances:
28 7 0.15
29 37 0.79
30 3 0.06
ACGTcount: A:0.17, C:0.22, G:0.16, T:0.44
Consensus pattern (29 bp):
TCATGTAGCTCATGTCATTTCTCTTGTGA
Found at i:181667 original size:64 final size:63
Alignment explanation
Indices: 181598--181754 Score: 167
Period size: 64 Copynumber: 2.5 Consensus size: 63
181588 TAATGAAGGT
* * **
181598 ATGCATCAATGCACTACTTGTGCATCGGTGCA-TAAAATGCATTCGAT-GTTTTATTATTAATGG
1 ATGCATCGATGCACTACTTGTGCATCGATGCAGT-AAATGCATTCGATCGTTTTATT-TTAA-AA
181661 G
63 G
* * * *
181662 ATGCATCGATGCA-TGCCTTATGCATCGATGCAGTAATTGCATTCGATCTTTTTATTTTAAAAG
1 ATGCATCGATGCACT-ACTTGTGCATCGATGCAGTAAATGCATTCGATCGTTTTATTTTAAAAG
*
181725 AGTGCATCGATGCACTACCTGTGCATCGAT
1 A-TGCATCGATGCACTACTTGTGCATCGAT
181755 ACACCTTCAA
Statistics
Matches: 77, Mismatches: 11, Indels: 10
0.79 0.11 0.10
Matches are distributed among these distances:
63 3 0.04
64 65 0.84
65 9 0.12
ACGTcount: A:0.27, C:0.18, G:0.20, T:0.35
Consensus pattern (63 bp):
ATGCATCGATGCACTACTTGTGCATCGATGCAGTAAATGCATTCGATCGTTTTATTTTAAAAG
Found at i:181814 original size:21 final size:21
Alignment explanation
Indices: 181788--181844 Score: 105
Period size: 21 Copynumber: 2.7 Consensus size: 21
181778 TTTAACCTTG
181788 ATGCATCGATGCACTATGAAT
1 ATGCATCGATGCACTATGAAT
*
181809 ATGCATCAATGCACTATGAAT
1 ATGCATCGATGCACTATGAAT
181830 ATGCATCGATGCACT
1 ATGCATCGATGCACT
181845 CTGCCCATAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.33, C:0.21, G:0.18, T:0.28
Consensus pattern (21 bp):
ATGCATCGATGCACTATGAAT
Found at i:187909 original size:18 final size:18
Alignment explanation
Indices: 187886--187932 Score: 67
Period size: 18 Copynumber: 2.6 Consensus size: 18
187876 GTCATATATG
* *
187886 TCCCGTAGGACCCCTATA
1 TCCCGTAGGACCACTACA
187904 TCCCGTAGGACCACTACA
1 TCCCGTAGGACCACTACA
*
187922 TCCCGAAGGAC
1 TCCCGTAGGAC
187933 TACATCCCGA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.26, C:0.38, G:0.19, T:0.17
Consensus pattern (18 bp):
TCCCGTAGGACCACTACA
Found at i:187936 original size:15 final size:15
Alignment explanation
Indices: 187916--187949 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
187906 CCGTAGGACC
187916 ACTACATCCCGAAGG
1 ACTACATCCCGAAGG
187931 ACTACATCCCGAAGG
1 ACTACATCCCGAAGG
187946 ACTA
1 ACTA
187950 TTATACCCTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.35, C:0.32, G:0.18, T:0.15
Consensus pattern (15 bp):
ACTACATCCCGAAGG
Found at i:188076 original size:29 final size:29
Alignment explanation
Indices: 188034--188114 Score: 128
Period size: 29 Copynumber: 2.8 Consensus size: 29
188024 TTTTATATAT
188034 TCATGTA-CTCATGTCATTTCTCTTGTGA
1 TCATGTAGCTCATGTCATTTCTCTTGTGA
* *
188062 TCATGTAGCTCATGTCATCTCTTTTGTGA
1 TCATGTAGCTCATGTCATTTCTCTTGTGA
188091 TCATGTAGCTCATGTCATGTTCTC
1 TCATGTAGCTCATGTCAT-TTCTC
188115 ATATCACATA
Statistics
Matches: 47, Mismatches: 4, Indels: 2
0.89 0.08 0.04
Matches are distributed among these distances:
28 7 0.15
29 37 0.79
30 3 0.06
ACGTcount: A:0.17, C:0.22, G:0.16, T:0.44
Consensus pattern (29 bp):
TCATGTAGCTCATGTCATTTCTCTTGTGA
Found at i:193649 original size:2 final size:2
Alignment explanation
Indices: 193642--193700 Score: 111
Period size: 2 Copynumber: 30.0 Consensus size: 2
193632 TCTATTTATC
193642 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
193684 T- TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA
193701 GACTTAAGAA
Statistics
Matches: 56, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.02
2 55 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:195707 original size:5 final size:5
Alignment explanation
Indices: 195697--195790 Score: 75
Period size: 5 Copynumber: 18.8 Consensus size: 5
195687 TTCGTTCTAT
* **** *
195697 TTTTA TTTTA TTTTG TTTT- TTTTA TTTTA TTTTTA GCAAA CTTTA TTTTCA
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA -TTTTA TTTTA TTTTA TTTT-A
* * *
195748 TTCTA -TTTA TTTTA TTTTA TTTTA ATTAA TTTTA TTTTA TTTT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTT
195791 TATCTGAACA
Statistics
Matches: 69, Mismatches: 16, Indels: 8
0.74 0.17 0.09
Matches are distributed among these distances:
4 7 0.10
5 53 0.77
6 9 0.13
ACGTcount: A:0.21, C:0.04, G:0.02, T:0.72
Consensus pattern (5 bp):
TTTTA
Found at i:195721 original size:14 final size:14
Alignment explanation
Indices: 195697--195730 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
195687 TTCGTTCTAT
*
195697 TTTTATTTTATTTTG
1 TTTT-TTTTATTTTA
195712 TTTTTTTTATTTTA
1 TTTTTTTTATTTTA
195726 TTTTT
1 TTTTT
195731 AGCAAACTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 14 0.78
15 4 0.22
ACGTcount: A:0.12, C:0.00, G:0.03, T:0.85
Consensus pattern (14 bp):
TTTTTTTTATTTTA
Found at i:198612 original size:25 final size:25
Alignment explanation
Indices: 198557--198629 Score: 85
Period size: 25 Copynumber: 2.8 Consensus size: 25
198547 ATATTGTTCG
* *
198557 TTGTTTCGAACAGCAAAAAACA-TTCA
1 TTGTTTCGAACA-TAAAAAA-AGTCCA
*
198583 CTGTTTCGAACATAAAAAAAGTCCA
1 TTGTTTCGAACATAAAAAAAGTCCA
198608 TTGTTTCGAACATAGAAAAAAG
1 TTGTTTCGAACATA-AAAAAAG
198630 AAGAAGAAGG
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
24 1 0.02
25 22 0.54
26 18 0.44
ACGTcount: A:0.44, C:0.16, G:0.14, T:0.26
Consensus pattern (25 bp):
TTGTTTCGAACATAAAAAAAGTCCA
Found at i:200292 original size:4 final size:4
Alignment explanation
Indices: 200283--200321 Score: 57
Period size: 4 Copynumber: 10.5 Consensus size: 4
200273 CTTTATCTCA
200283 ATTT ATTT A-TT -TTT ATTT ATTT ATTT ATTT ATTT -TTT AT
1 ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT AT
200322 CTCATTATAC
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
3 7 0.22
4 25 0.78
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
ATTT
Found at i:200753 original size:18 final size:18
Alignment explanation
Indices: 200730--200786 Score: 64
Period size: 18 Copynumber: 3.2 Consensus size: 18
200720 GAATCATCTC
200730 TCATAATAATACATTTCA
1 TCATAATAATACATTTCA
* *
200748 TCATAA-AAT-CCTTATCTC
1 TCATAATAATACATT-TC-A
200766 TCATAATAATACATTTCA
1 TCATAATAATACATTTCA
200784 TCA
1 TCA
200787 CAAAATTCCC
Statistics
Matches: 31, Mismatches: 4, Indels: 8
0.72 0.09 0.19
Matches are distributed among these distances:
16 3 0.10
17 5 0.16
18 15 0.48
19 5 0.16
20 3 0.10
ACGTcount: A:0.40, C:0.21, G:0.00, T:0.39
Consensus pattern (18 bp):
TCATAATAATACATTTCA
Found at i:203945 original size:13 final size:12
Alignment explanation
Indices: 203923--203968 Score: 51
Period size: 13 Copynumber: 3.9 Consensus size: 12
203913 TATTAACATT
*
203923 TATTATTATTAC
1 TATTAATATTAC
203935 TACTTAATATTAC
1 TA-TTAATATTAC
*
203948 TATTATTATTA-
1 TATTAATATTAC
203959 T-TTAATATTA
1 TATTAATATTA
203969 TTTACTTATT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
10 8 0.27
11 1 0.03
12 10 0.33
13 11 0.37
ACGTcount: A:0.37, C:0.07, G:0.00, T:0.57
Consensus pattern (12 bp):
TATTAATATTAC
Found at i:203984 original size:21 final size:22
Alignment explanation
Indices: 203909--203990 Score: 73
Period size: 22 Copynumber: 3.8 Consensus size: 22
203899 TTTGTCCGGG
* *
203909 TTATTA-TTAACATTTATTATTA
1 TTATTATTTAATA-TTACTATTA
* *
203931 TTACTACTTAATATTACTATTA
1 TTATTATTTAATATTACTATTA
203953 TTATTATTTAATATTA-T-TTA
1 TTATTATTTAATATTACTATTA
203973 CTTATT-TATTAATATTAC
1 -TTATTAT-TTAATATTAC
203991 AGATTTTGTT
Statistics
Matches: 51, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
20 4 0.08
21 15 0.29
22 27 0.53
23 5 0.10
ACGTcount: A:0.35, C:0.07, G:0.00, T:0.57
Consensus pattern (22 bp):
TTATTATTTAATATTACTATTA
Found at i:204407 original size:19 final size:20
Alignment explanation
Indices: 204379--204418 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
204369 TCTCACCGAA
*
204379 AAAAGTAACAAAAAA-AATC
1 AAAAGAAACAAAAAAGAATC
204398 AAAAGAAACAAAAAAGAATC
1 AAAAGAAACAAAAAAGAATC
204418 A
1 A
204419 GTCCCATAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.75, C:0.10, G:0.07, T:0.07
Consensus pattern (20 bp):
AAAAGAAACAAAAAAGAATC
Found at i:208110 original size:44 final size:44
Alignment explanation
Indices: 208028--208159 Score: 194
Period size: 44 Copynumber: 3.0 Consensus size: 44
208018 TACCATGAGC
* *
208028 GGCACATTTTATGCCAATAATGCACCGTTAT-CATTTTCATTTAT
1 GGCACA-TTTCTGCTAATAATGCACCGTTATGCATTTTCATTTAT
* * *
208072 GGCACCTTTCTGTTAATAATGCACCGTTATGTATTTTCATTTAT
1 GGCACATTTCTGCTAATAATGCACCGTTATGCATTTTCATTTAT
*
208116 GGCACATTTCTGCTAATAATCCACCGTTATGCATTTTCATTTAT
1 GGCACATTTCTGCTAATAATGCACCGTTATGCATTTTCATTTAT
208160 TTCAGTAACA
Statistics
Matches: 78, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
43 21 0.27
44 57 0.73
ACGTcount: A:0.25, C:0.20, G:0.12, T:0.42
Consensus pattern (44 bp):
GGCACATTTCTGCTAATAATGCACCGTTATGCATTTTCATTTAT
Found at i:217467 original size:23 final size:21
Alignment explanation
Indices: 217413--217474 Score: 81
Period size: 23 Copynumber: 2.9 Consensus size: 21
217403 TTTTGGTGCA
217413 GAGGGAATCGA-TCCCCCCTT
1 GAGGGAATCGATTCCCCCCTT
* *
217433 GAGGGAACCGATTCCCCCTTT
1 GAGGGAATCGATTCCCCCCTT
217454 GAAGGGGAATCGATTCCCCCC
1 G-A-GGGAATCGATTCCCCCC
217475 ACAGGGAAAT
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
20 10 0.29
21 9 0.26
22 1 0.03
23 15 0.43
ACGTcount: A:0.21, C:0.34, G:0.26, T:0.19
Consensus pattern (21 bp):
GAGGGAATCGATTCCCCCCTT
Found at i:217493 original size:20 final size:21
Alignment explanation
Indices: 217456--217494 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
217446 CCCCCTTTGA
* *
217456 AGGGGAATCGATTCCCCCCAC
1 AGGGAAATCGATTACCCCCAC
217477 AGGGAAATCGA-TACCCCC
1 AGGGAAATCGATTACCCCC
217495 TGGGGTTCTG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 6 0.38
21 10 0.62
ACGTcount: A:0.28, C:0.36, G:0.23, T:0.13
Consensus pattern (21 bp):
AGGGAAATCGATTACCCCCAC
Found at i:223452 original size:19 final size:19
Alignment explanation
Indices: 223430--223473 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
223420 TAAAATATAC
223430 TAATATTATAGTAAT-ATTA
1 TAATATTA-AGTAATGATTA
*
223449 TAATAATAAGTAATGATTA
1 TAATATTAAGTAATGATTA
*
223468 AAATAT
1 TAATAT
223474 AAAATAGTAA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
18 6 0.29
19 15 0.71
ACGTcount: A:0.52, C:0.00, G:0.07, T:0.41
Consensus pattern (19 bp):
TAATATTAAGTAATGATTA
Found at i:224749 original size:17 final size:17
Alignment explanation
Indices: 224727--224759 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
224717 CTCGGGTTGG
224727 GTTGT-AATCGGGCCTTT
1 GTTGTAAAT-GGGCCTTT
224744 GTTGTAAATGGGCCTT
1 GTTGTAAATGGGCCTT
224760 CAGGTTAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 12 0.80
18 3 0.20
ACGTcount: A:0.15, C:0.15, G:0.30, T:0.39
Consensus pattern (17 bp):
GTTGTAAATGGGCCTTT
Found at i:232100 original size:20 final size:21
Alignment explanation
Indices: 232076--232155 Score: 65
Period size: 21 Copynumber: 3.8 Consensus size: 21
232066 AGAACCCCAT
*
232076 GGGGGTATCGATTCCCCTGTG
1 GGGGGAATCGATTCCCCTGTG
* *
232097 GGGGGAATCGGTTCCCCT-TCAAA
1 GGGGGAATCGATTCCCCTGT---G
* * *
232120 GGGGGAATCGGTTCCCTTATG
1 GGGGGAATCGATTCCCCTGTG
232141 GGGGG-ATCGATTCCC
1 GGGGGAATCGATTCCC
232156 TCTGCACCAA
Statistics
Matches: 49, Mismatches: 6, Indels: 9
0.77 0.09 0.14
Matches are distributed among these distances:
20 10 0.20
21 21 0.43
23 17 0.35
24 1 0.02
ACGTcount: A:0.15, C:0.24, G:0.36, T:0.25
Consensus pattern (21 bp):
GGGGGAATCGATTCCCCTGTG
Found at i:232145 original size:22 final size:23
Alignment explanation
Indices: 232096--232155 Score: 72
Period size: 23 Copynumber: 2.7 Consensus size: 23
232086 ATTCCCCTGT
232096 GGGGGGAATCGGTTCCCCTTCAA
1 GGGGGGAATCGGTTCCCCTTCAA
* *
232119 AGGGGGAATCGGTT-CCCTT-AT
1 GGGGGGAATCGGTTCCCCTTCAA
*
232140 GGGGGG-ATCGATTCCC
1 GGGGGGAATCGGTTCCC
232156 TCTGCACCAA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
20 6 0.19
21 8 0.25
22 5 0.16
23 13 0.41
ACGTcount: A:0.17, C:0.23, G:0.37, T:0.23
Consensus pattern (23 bp):
GGGGGGAATCGGTTCCCCTTCAA
Found at i:242317 original size:18 final size:18
Alignment explanation
Indices: 242294--242334 Score: 82
Period size: 18 Copynumber: 2.3 Consensus size: 18
242284 TGTTTACTTT
242294 TCCTGGCTGAGTAAATAC
1 TCCTGGCTGAGTAAATAC
242312 TCCTGGCTGAGTAAATAC
1 TCCTGGCTGAGTAAATAC
242330 TCCTG
1 TCCTG
242335 ACTGGGCTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.24, C:0.24, G:0.22, T:0.29
Consensus pattern (18 bp):
TCCTGGCTGAGTAAATAC
Found at i:247261 original size:17 final size:17
Alignment explanation
Indices: 247228--247261 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
247218 GCTCGGGTTG
*
247228 GGTTGTAATCGGGCCTT
1 GGTTGTAATCGGACCTT
*
247245 GGTTGTAATTGGACCTT
1 GGTTGTAATCGGACCTT
247262 CGGGTTTAAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.15, C:0.15, G:0.32, T:0.38
Consensus pattern (17 bp):
GGTTGTAATCGGACCTT
Found at i:252904 original size:22 final size:21
Alignment explanation
Indices: 252865--252909 Score: 63
Period size: 22 Copynumber: 2.1 Consensus size: 21
252855 GAGTCATACC
252865 TAACATAATATAACATAAAAA
1 TAACATAATATAACATAAAAA
* *
252886 TAACATAATTATAATATAATAA
1 TAACATAA-TATAACATAAAAA
252908 TA
1 TA
252910 TAATTATATT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 8 0.38
22 13 0.62
ACGTcount: A:0.62, C:0.07, G:0.00, T:0.31
Consensus pattern (21 bp):
TAACATAATATAACATAAAAA
Found at i:252997 original size:17 final size:17
Alignment explanation
Indices: 252970--253010 Score: 64
Period size: 17 Copynumber: 2.4 Consensus size: 17
252960 TTTAGCAGCA
*
252970 TCACCCGTCTAAACTGC
1 TCACCCATCTAAACTGC
*
252987 TGACCCATCTAAACTGC
1 TCACCCATCTAAACTGC
253004 TCACCCA
1 TCACCCA
253011 CATACTTGTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.27, C:0.41, G:0.10, T:0.22
Consensus pattern (17 bp):
TCACCCATCTAAACTGC
Found at i:254420 original size:44 final size:44
Alignment explanation
Indices: 254351--254553 Score: 343
Period size: 44 Copynumber: 4.6 Consensus size: 44
254341 TTATGCGAAC
* *
254351 AATGCACCATTATACATTTTCATTTATGGCACCTTTCTGCCAAT
1 AATGCACCGTTATGCATTTTCATTTATGGCACCTTTCTGCCAAT
* *
254395 AATACACCGTTATGCATTTTTATTTATGGCACCTTTCTGCCAAT
1 AATGCACCGTTATGCATTTTCATTTATGGCACCTTTCTGCCAAT
**
254439 AATGCACCGTTATGCATTTTCATTTATGGCATATTTCTGCCAAT
1 AATGCACCGTTATGCATTTTCATTTATGGCACCTTTCTGCCAAT
*
254483 AATGCACCGTTATGCATTTTCATTTATGACACCTTTCTGCCAAT
1 AATGCACCGTTATGCATTTTCATTTATGGCACCTTTCTGCCAAT
254527 AATGCACCGTTATGCATTTTCATTTAT
1 AATGCACCGTTATGCATTTTCATTTAT
254554 TTCAGTAACA
Statistics
Matches: 148, Mismatches: 11, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
44 148 1.00
ACGTcount: A:0.26, C:0.23, G:0.11, T:0.40
Consensus pattern (44 bp):
AATGCACCGTTATGCATTTTCATTTATGGCACCTTTCTGCCAAT
Found at i:255157 original size:21 final size:21
Alignment explanation
Indices: 255127--255184 Score: 71
Period size: 21 Copynumber: 2.8 Consensus size: 21
255117 TCGATACCCA
* *
255127 CAACAATATCGATATTAATTG
1 CAACAGTATCAATATTAATTG
*
255148 CAACAGTATCAATACTAATTG
1 CAACAGTATCAATATTAATTG
* *
255169 CATCAGTATCTATATT
1 CAACAGTATCAATATT
255185 GATCATCGTA
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.40, C:0.17, G:0.09, T:0.34
Consensus pattern (21 bp):
CAACAGTATCAATATTAATTG
Found at i:262671 original size:258 final size:258
Alignment explanation
Indices: 262192--262737 Score: 735
Period size: 258 Copynumber: 2.1 Consensus size: 258
262182 AGTTATTTTG
* * *
262192 AAAAATAAGAAAGCGATTTCCAAAGTTTCTCGTTTAAATCTTTTCTGAAAACGAATTTTTTGAAA
1 AAAAATGAGAAAGCGATTTCCAAAGTTTCTCATTTAAATATTTTCTGAAAACGAATTTTTTGAAA
* * ***
262257 AGTAAGAAAGTATTTTCCAAAGTTTTTACATTTTAAACTATTTCCCAAATTGGTAAGTCCTTCAA
66 AGTAAGAAAGGATTCTCCAAAGTTTTTACACAATAAACTATTTCCCAAATTGGTAAGTCCTTCAA
* * * *
262322 GCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTTGGTTCATCTGTAATTCTTTCGAGCA
131 GCCATCAGTAAATCTTTCGAGCATGATGATTAAATCCTTAGGTTCATCTGTAAGTCTTTCGAACA
* * * * *
262387 AGATGATAAGTTCTTCGGGACATCCATAAGACCTTCGAGTAGGATGTTTTCACATGAATTT-A
196 AGATGATAAATTATTCGAGACATCCATAAGACCTTCGAGAAGGATGTTTCCACATGAATTTCA
* * *
262449 AAAAATGAGAAAGCGATTTCCAAAGTTTCTCATTT-AGTATTTTCAT-AAAATGAAATTTTTTTA
1 AAAAATGAGAAAGCGATTTCCAAAGTTTCTCATTTAAATATTTTC-TGAAAACG-AATTTTTTGA
* *
262512 AAAGTAAGAAAGCGATTCT-CAAGGTTTCTTACCCAATAAACTATTTCCCAAATTGGTAAGTCCT
64 AAAGTAAGAAAG-GATTCTCCAAAGTTT-TTACACAATAAACTATTTCCCAAATTGGTAAGTCCT
** * *
262576 TCGGGCCATTAGTAAATCTTTCGAGCATGATGTTTAAATCCTTCAGG-TCATCTGTAAGTCTTTC
127 TCAAGCCATCAGTAAATCTTTCGAGCATGATGATTAAATCCTT-AGGTTCATCTGTAAGTCTTTC
* * *
262640 GAACAAGATGATAAATTATTC-AGACCATCCATAAGACCTTCGGGAAGTATGTTTCCACATGATT
191 GAACAAGATGATAAATTATTCGAGA-CATCCATAAGACCTTCGAGAAGGATGTTTCCACATGAAT
262704 TTCA
255 TTCA
262708 AAAAATGAGAAAGCGATTTCCAAAGTTTCT
1 AAAAATGAGAAAGCGATTTCCAAAGTTTCT
262738 TACCTAGTAA
Statistics
Matches: 253, Mismatches: 29, Indels: 12
0.86 0.10 0.04
Matches are distributed among these distances:
256 12 0.05
257 64 0.25
258 144 0.57
259 33 0.13
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.34
Consensus pattern (258 bp):
AAAAATGAGAAAGCGATTTCCAAAGTTTCTCATTTAAATATTTTCTGAAAACGAATTTTTTGAAA
AGTAAGAAAGGATTCTCCAAAGTTTTTACACAATAAACTATTTCCCAAATTGGTAAGTCCTTCAA
GCCATCAGTAAATCTTTCGAGCATGATGATTAAATCCTTAGGTTCATCTGTAAGTCTTTCGAACA
AGATGATAAATTATTCGAGACATCCATAAGACCTTCGAGAAGGATGTTTCCACATGAATTTCA
Found at i:262831 original size:42 final size:41
Alignment explanation
Indices: 262769--262871 Score: 127
Period size: 42 Copynumber: 2.5 Consensus size: 41
262759 AATTTGTAAG
* * * *
262769 TCCTTCGAGCCATCAGTAAGTCTTTCGAGCATGATGAATAAAT
1 TCCTTCGGGCCATCTGTAAGTCTTTCGAACAAGATG-AT-AAT
*
262812 T-CTTCGGGTCATCTGTAAGTCTTTCGAACAAGATGATAAT
1 TCCTTCGGGCCATCTGTAAGTCTTTCGAACAAGATGATAAT
*
262852 TCCTTCGGGCCATCTATAAG
1 TCCTTCGGGCCATCTGTAAG
262872 ACCTTTGGGC
Statistics
Matches: 52, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
40 4 0.08
41 18 0.35
42 29 0.56
43 1 0.02
ACGTcount: A:0.27, C:0.21, G:0.19, T:0.32
Consensus pattern (41 bp):
TCCTTCGGGCCATCTGTAAGTCTTTCGAACAAGATGATAAT
Found at i:262873 original size:197 final size:196
Alignment explanation
Indices: 262518--262933 Score: 577
Period size: 197 Copynumber: 2.1 Consensus size: 196
262508 TTTAAAAGTA
* * *
262518 AGAAAGCGA-TTCTCAAGGTTTCTTACCCAATAAACTATTTCCCAAATTGGTAAGTCCTTCGGGC
1 AGAAAGCGATTTC-CAAAGTTTCTTACCCAATAAACTATTTCCAAAATTGGTAAGTCCTTCGAGC
* **
262582 CATTAGTAAATCTTTCGAGCATGATGTTTAAATCCTTCAGGTCATCTGTAAGTCTTTCGAACAAG
65 CATCAGTAAATCTTTCGAGCATGATGAATAAATCCTTCAGGTCATCTGTAAGTCTTTCGAACAAG
**
262647 ATGATAAATTATTCAGACCATCCATAAGACCTTCGGGAA-GTATGTTTCCACATGATTTTCAAAA
130 ATGATAAATTATTCAGACCATCCATAAGACCTTCGGGAATG-ATGTTTCCACATGAAATT-AAAA
262711 AATG
193 AATG
* * *
262715 AGAAAGCGATTTCCAAAGTTTCTTACCTAGTAAACTATTTCCAAAATTTGTAAGTCCTTCGAGCC
1 AGAAAGCGATTTCCAAAGTTTCTTACCCAATAAACTATTTCCAAAATTGGTAAGTCCTTCGAGCC
* * *
262780 ATCAGTAAGTCTTTCGAGCATGATGAATAAATTCTTCGGGTCATCTGTAAGTCTTTCGAACAAGA
66 ATCAGTAAATCTTTCGAGCATGATGAATAAATCCTTCAGGTCATCTGTAAGTCTTTCGAACAAGA
* * * * * * * *
262845 TGAT-AATTCCTTCGGGCCATCTATAAGACCTTTGGGCATGATGTTTTCACATGAAATTGAAAAA
131 TGATAAATT-ATTCAGACCATCCATAAGACCTTCGGGAATGATGTTTCCACATGAAATTAAAAAA
262909 TG
195 TG
262911 AGAAAGCGATTTCCAAAGTTTCT
1 AGAAAGCGATTTCCAAAGTTTCT
262934 CATTTAATAT
Statistics
Matches: 194, Mismatches: 22, Indels: 7
0.87 0.10 0.03
Matches are distributed among these distances:
196 34 0.18
197 156 0.80
198 4 0.02
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Consensus pattern (196 bp):
AGAAAGCGATTTCCAAAGTTTCTTACCCAATAAACTATTTCCAAAATTGGTAAGTCCTTCGAGCC
ATCAGTAAATCTTTCGAGCATGATGAATAAATCCTTCAGGTCATCTGTAAGTCTTTCGAACAAGA
TGATAAATTATTCAGACCATCCATAAGACCTTCGGGAATGATGTTTCCACATGAAATTAAAAAAT
G
Found at i:263220 original size:3 final size:3
Alignment explanation
Indices: 263212--263272 Score: 59
Period size: 3 Copynumber: 19.0 Consensus size: 3
263202 TTTATTCGTG
**
263212 TTA TTA TTA ACA TTTA TTA TTA TTA TTA TTA TTA TTA TTA TTTA CTTA
1 TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA TTA TTA -TTA -TTA
*
263260 TTTA TTA ATA TTA
1 -TTA TTA TTA TTA
263273 CAGATTTTTT
Statistics
Matches: 48, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
3 37 0.77
4 11 0.23
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.62
Consensus pattern (3 bp):
TTA
Done.