Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001355.1 Hibiscus syriacus cultivar Beakdansim tig00002638_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: 110253
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
Found at i:1029 original size:64 final size:63
Alignment explanation
Indices: 916--1046 Score: 237
Period size: 63 Copynumber: 2.1 Consensus size: 63
906 ACCTACGCAT
*
916 GAAAAACACACACGCTAAGTCGATGACTTAGTGAGCAATACTAATAGTGCTAACTTATTAACA
1 GAAAAAAACACACGCTAAGTCGATGACTTAGTGAGCAATACTAATAGTGCTAACTTATTAACA
979 GAAAAAAACACACGCTAAGTCGATGACTTAGTGAGGCAATACTAATAGTGCTAACTTATTAACA
1 GAAAAAAACACACGCTAAGTCGATGACTTAGTGA-GCAATACTAATAGTGCTAACTTATTAACA
1043 -AAAA
1 GAAAA
1047 TCTTATTTAG
Statistics
Matches: 66, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
63 37 0.56
64 29 0.44
ACGTcount: A:0.44, C:0.18, G:0.16, T:0.23
Consensus pattern (63 bp):
GAAAAAAACACACGCTAAGTCGATGACTTAGTGAGCAATACTAATAGTGCTAACTTATTAACA
Found at i:1254 original size:21 final size:21
Alignment explanation
Indices: 1229--1296 Score: 68
Period size: 21 Copynumber: 3.1 Consensus size: 21
1219 GTAATTTGCA
1229 CCGAAGTGCCACATAATTATC
1 CCGAAGTGCCACATAATTATC
*
1250 CCGAA-TGACCATATAGATT-TGC
1 CCGAAGTG-CCACATA-ATTAT-C
*
1272 ACCGAAGTGCCACATATTTATC
1 -CCGAAGTGCCACATAATTATC
1294 CCG
1 CCG
1297 GAGGACCACA
Statistics
Matches: 38, Mismatches: 3, Indels: 12
0.72 0.06 0.23
Matches are distributed among these distances:
20 2 0.05
21 15 0.39
22 7 0.18
23 12 0.32
24 2 0.05
ACGTcount: A:0.31, C:0.28, G:0.16, T:0.25
Consensus pattern (21 bp):
CCGAAGTGCCACATAATTATC
Found at i:3239 original size:2 final size:2
Alignment explanation
Indices: 3177--3230 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
3167 GTAATATGTA
3177 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3219 AT AT AT AT AT AT
1 AT AT AT AT AT AT
3231 TTCTATATAC
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4382 original size:21 final size:21
Alignment explanation
Indices: 4356--4406 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
4346 CATAGAGTTT
4356 GTTCACATTCAATGATTCAAA
1 GTTCACATTCAATGATTCAAA
* * *
4377 GTTCACATTCACTTATTCATA
1 GTTCACATTCAATGATTCAAA
4398 GTTCACATT
1 GTTCACATT
4407 TCCATAATAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.31, C:0.22, G:0.08, T:0.39
Consensus pattern (21 bp):
GTTCACATTCAATGATTCAAA
Found at i:4874 original size:54 final size:54
Alignment explanation
Indices: 4791--4915 Score: 162
Period size: 54 Copynumber: 2.3 Consensus size: 54
4781 GATACTACCA
* * *
4791 TTCAAGGGCATCGATACCTCCTCATGGTACCGATACCGAA-ATAGCATTCGATGT
1 TTCAAGGGTATCGATACCTCCTCAAGGTACCGATACC-AATATAGCAATCGATGT
* * * *
4845 TTCAAGGGTATCTATACCTCCTCAAGGTACCGATATCAATCTGGCAATCGATGT
1 TTCAAGGGTATCGATACCTCCTCAAGGTACCGATACCAATATAGCAATCGATGT
*
4899 TTTAAGGGTATCGATAC
1 TTCAAGGGTATCGATAC
4916 TATCTTTCAA
Statistics
Matches: 61, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
53 2 0.03
54 59 0.97
ACGTcount: A:0.28, C:0.23, G:0.20, T:0.29
Consensus pattern (54 bp):
TTCAAGGGTATCGATACCTCCTCAAGGTACCGATACCAATATAGCAATCGATGT
Found at i:6155 original size:31 final size:31
Alignment explanation
Indices: 6113--6172 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
6103 AATTAGAGAA
*
6113 TGAACTATTTCAAAAAGTTTAAAAAATAATT
1 TGAACTATTTCAAAAAGTTCAAAAAATAATT
*
6144 TGAATTATTTCAAAAAGTTCAAAAAATAA
1 TGAACTATTTCAAAAAGTTCAAAAAATAA
6173 CTATATATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.53, C:0.07, G:0.07, T:0.33
Consensus pattern (31 bp):
TGAACTATTTCAAAAAGTTCAAAAAATAATT
Found at i:7342 original size:28 final size:28
Alignment explanation
Indices: 7288--7342 Score: 65
Period size: 28 Copynumber: 2.0 Consensus size: 28
7278 ACAAAAATAA
* ** * *
7288 TTTAAAGTTTAATGATGAAATTGAAAAG
1 TTTAAACTTTAATGACCAAAATAAAAAG
7316 TTTAAACTTTAATGACCAAAATAAAAA
1 TTTAAACTTTAATGACCAAAATAAAAA
7343 TGAAAAAATA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
28 22 1.00
ACGTcount: A:0.51, C:0.05, G:0.11, T:0.33
Consensus pattern (28 bp):
TTTAAACTTTAATGACCAAAATAAAAAG
Found at i:7685 original size:17 final size:17
Alignment explanation
Indices: 7665--7698 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
7655 AAGAAACTAT
*
7665 TTTTTTATTGTTTTAAA
1 TTTTTAATTGTTTTAAA
*
7682 TTTTTAATTTTTTTAAA
1 TTTTTAATTGTTTTAAA
7699 ATTAAATTAT
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:0.26, C:0.00, G:0.03, T:0.71
Consensus pattern (17 bp):
TTTTTAATTGTTTTAAA
Found at i:8497 original size:3 final size:3
Alignment explanation
Indices: 8491--8542 Score: 86
Period size: 3 Copynumber: 17.0 Consensus size: 3
8481 ATTTGTTACT
*
8491 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TAA TTA TTA TTGA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT-A
8540 TTA
1 TTA
8543 ATATGGGGTC
Statistics
Matches: 46, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
3 43 0.93
4 3 0.07
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:10981 original size:60 final size:58
Alignment explanation
Indices: 10885--11020 Score: 179
Period size: 60 Copynumber: 2.3 Consensus size: 58
10875 GTAATTTGAG
10885 ATTCTAATTTCAT-CCC-AACTATGACTCATTCTAAATT-AGTCCTTAAACTTTTGAAT
1 ATTCTAATTTCATCCCCAAACTATGACTCATTCTAAATTGA-TCCTTAAACTTTTGAAT
* * *
10941 ATTTTAATTTCATCCCCAAACTATGAGTGTCATTCTAAATTGATCCTTGAACTTTTGAAT
1 ATTCTAATTTCATCCCCAAACTATGA--CTCATTCTAAATTGATCCTTAAACTTTTGAAT
* *
11001 ATTCCAACTTCATCCCCAAA
1 ATTCTAATTTCATCCCCAAA
11021 TTCATGGAAA
Statistics
Matches: 69, Mismatches: 6, Indels: 6
0.85 0.07 0.07
Matches are distributed among these distances:
56 12 0.17
57 3 0.04
58 8 0.12
60 45 0.65
61 1 0.01
ACGTcount: A:0.32, C:0.23, G:0.07, T:0.39
Consensus pattern (58 bp):
ATTCTAATTTCATCCCCAAACTATGACTCATTCTAAATTGATCCTTAAACTTTTGAAT
Found at i:11521 original size:48 final size:48
Alignment explanation
Indices: 11450--11543 Score: 188
Period size: 48 Copynumber: 2.0 Consensus size: 48
11440 CTTTAATTAC
11450 TTTGGGTTAGCTTTCTTCGTATTGGTCAACTCTGGTATGTGCAATGAT
1 TTTGGGTTAGCTTTCTTCGTATTGGTCAACTCTGGTATGTGCAATGAT
11498 TTTGGGTTAGCTTTCTTCGTATTGGTCAACTCTGGTATGTGCAATG
1 TTTGGGTTAGCTTTCTTCGTATTGGTCAACTCTGGTATGTGCAATG
11544 GTTGGTGAAT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 46 1.00
ACGTcount: A:0.16, C:0.15, G:0.26, T:0.44
Consensus pattern (48 bp):
TTTGGGTTAGCTTTCTTCGTATTGGTCAACTCTGGTATGTGCAATGAT
Found at i:13164 original size:22 final size:22
Alignment explanation
Indices: 13117--13164 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
13107 ATATTTTATT
**
13117 TTAAATAATTTATAATAAGATT
1 TTAAATAATTTATAATAAGACG
* *
13139 TTAAATAATTTATAATTATACG
1 TTAAATAATTTATAATAAGACG
13161 TTAA
1 TTAA
13165 TTTATTTAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.48, C:0.02, G:0.04, T:0.46
Consensus pattern (22 bp):
TTAAATAATTTATAATAAGACG
Found at i:21916 original size:20 final size:20
Alignment explanation
Indices: 21893--21963 Score: 99
Period size: 20 Copynumber: 3.5 Consensus size: 20
21883 GATTTTGGAC
21893 TATCGCAACGAATTTGGGAA
1 TATCGCAACGAATTTGGGAA
21913 TATCGCAACGAATTTGGGAA
1 TATCGCAACGAATTTGGGAA
* *
21933 TATCACAACGAACTT-GGAA
1 TATCGCAACGAATTTGGGAA
21952 TAAATCGCAACG
1 T--ATCGCAACG
21964 CGAACTTCGA
Statistics
Matches: 46, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
19 5 0.11
20 33 0.72
21 8 0.17
ACGTcount: A:0.38, C:0.18, G:0.21, T:0.23
Consensus pattern (20 bp):
TATCGCAACGAATTTGGGAA
Found at i:21983 original size:42 final size:42
Alignment explanation
Indices: 21890--22150 Score: 359
Period size: 42 Copynumber: 6.3 Consensus size: 42
21880 TGCGATTTTG
* * *
21890 GACTATCGCAACGAATTTGGGAAT--ATCGCAA--CGAATTTGG
1 GACTATCGCAACGAACTT-GGAATAAATCGCAACGCGAACTT-C
* *
21930 GAATATCACAACGAACTTGGAATAAATCGCAACGCGAACTTC
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
* * * *
21972 GACTATCACAACGAATTTGGAATAAATTGCAATGCGAACTTC
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
* *
22014 AACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTG
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
*
22056 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
*
22098 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTG
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
22140 GACTATCGCAA
1 GACTATCGCAA
22151 TTCGAATATG
Statistics
Matches: 197, Mismatches: 20, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
39 5 0.03
40 15 0.08
41 7 0.04
42 164 0.83
43 6 0.03
ACGTcount: A:0.37, C:0.22, G:0.20, T:0.21
Consensus pattern (42 bp):
GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
Found at i:22147 original size:84 final size:83
Alignment explanation
Indices: 21887--22150 Score: 399
Period size: 84 Copynumber: 3.2 Consensus size: 83
21877 CGTTGCGATT
* * * *
21887 TTGGACTATCGCAACGAATTTGGGAAT--ATCGCAA-CGAATTTGGGAATATCACAACGAACTTG
1 TTGGACTATCGCAACGAATTT-GGAATAAATCGCAAGCGAACTT-CGACTATCGCAACGAACTTG
21949 GAATAAATCGCAACGCGAAC
64 GAATAAATCGCAACGCGAAC
* * * *
21969 TTCGACTATCACAACGAATTTGGAATAAATTGCAATGCGAACTTCAACTATCGCAACGAACTTGG
1 TTGGACTATCGCAACGAATTTGGAATAAATCGCAA-GCGAACTTCGACTATCGCAACGAACTTGG
22034 AATAAATCGCAACGCGAAC
65 AATAAATCGCAACGCGAAC
22053 TTGGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACGAACTTGG
1 TTGGACTATCGCAACGAATTTGGAATAAATCGCAA-GCGAACTTCGACTATCGCAACGAACTTGG
22118 AATAAATCGCAACGCGAAC
65 AATAAATCGCAACGCGAAC
22137 TTGGACTATCGCAA
1 TTGGACTATCGCAA
22151 TTCGAATATG
Statistics
Matches: 165, Mismatches: 13, Indels: 6
0.90 0.07 0.03
Matches are distributed among these distances:
81 5 0.03
82 19 0.12
83 6 0.04
84 129 0.78
85 6 0.04
ACGTcount: A:0.36, C:0.22, G:0.20, T:0.22
Consensus pattern (83 bp):
TTGGACTATCGCAACGAATTTGGAATAAATCGCAAGCGAACTTCGACTATCGCAACGAACTTGGA
ATAAATCGCAACGCGAAC
Found at i:22156 original size:21 final size:20
Alignment explanation
Indices: 21887--22150 Score: 164
Period size: 21 Copynumber: 12.7 Consensus size: 20
21877 CGTTGCGATT
*
21887 TTGGACTATCGCAA-CGAAT
1 TTGGACTATCGCAAGCGAAC
* *
21906 TTGGGAATATCGCAA-CGAAT
1 TT-GGACTATCGCAAGCGAAC
* *
21926 TTGGGAATATCACAA-CGAAC
1 TT-GGACTATCGCAAGCGAAC
*
21946 TTGGAATAAATCGCAACGCGAAC
1 TTGGACT--ATCGCAA-GCGAAC
* * *
21969 TTCGACTATCACAA-CGAAT
1 TTGGACTATCGCAAGCGAAC
* *
21988 TTGGAATAAATTGCAATGCGAAC
1 TTGGACT--ATCGCAA-GCGAAC
**
22011 TTCAACTATCGCAA-CGAAC
1 TTGGACTATCGCAAGCGAAC
*
22030 TTGGAATAAATCGCAACGCGAAC
1 TTGGACT--ATCGCAA-GCGAAC
*
22053 TTGGACTATCGCAA-CGAAT
1 TTGGACTATCGCAAGCGAAC
*
22072 TTGGAATAAATCGCAACGCGAAC
1 TTGGACT--ATCGCAA-GCGAAC
*
22095 TTCGACTATCGCAA-CGAAC
1 TTGGACTATCGCAAGCGAAC
*
22114 TTGGAATAAATCGCAACGCGAAC
1 TTGGACT--ATCGCAA-GCGAAC
22137 TTGGACTATCGCAA
1 TTGGACTATCGCAA
22151 TTCGAATATG
Statistics
Matches: 195, Mismatches: 29, Indels: 40
0.74 0.11 0.15
Matches are distributed among these distances:
19 45 0.23
20 36 0.18
21 65 0.33
23 49 0.25
ACGTcount: A:0.36, C:0.22, G:0.20, T:0.22
Consensus pattern (20 bp):
TTGGACTATCGCAAGCGAAC
Found at i:23769 original size:3 final size:3
Alignment explanation
Indices: 23763--23816 Score: 99
Period size: 3 Copynumber: 18.0 Consensus size: 3
23753 ATATATTTTT
*
23763 TAA TAA TAA TAA TGA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
23811 TAA TAA
1 TAA TAA
23817 ATAACAAATG
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 49 1.00
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:24447 original size:121 final size:122
Alignment explanation
Indices: 24186--24630 Score: 506
Period size: 122 Copynumber: 3.7 Consensus size: 122
24176 GAATTAAGGC
* *
24186 AAGGTTGAACAAGTTTTTCTCATTATGAACTTCTT-TTCCTTCTTCAGATGAGTTCTTCTCATTA
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATAAGTTCTTCTCATTA
* * *
24250 TGAACACTTCTGGAAATGTTGATGTTGATATATCTCTTTCTCTGATAGAATCATGCAA
66 TGAAC-TTTCTGGAAATGTTGATGATGATATATCTCCTTCTCTGATAGAATCATGCAA
24308 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTT-CTTCTTCAGATAAGTTCTTCTCATTA
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATAAGTTCTTCTCATTA
* * * *
24372 TGAACTTTCTGGAAGTGTTGATGATGATCTATCTCCTTCTGTGATAGAGTCATGCAA
66 TGAACTTTCTGGAAATGTTGATGATGATATATCTCCTTCTCTGATAGAATCATGCAA
* * *
24429 AAGGTTAAACAAGCTCTTCTCATTATGAACTTCTTCTTCCCTCTTCAGATAAGTTCTTCTCATTA
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATAAGTTCTTCTCATTA
* * ** **
24494 TGAACTTTCTCTGGAAA-----AT--T--T-GA--TCCATCGAGTGAT-GAATTCAAACAAA
66 TGAAC-TT-TCTGGAAATGTTGATGATGATATATCTCCTTC-TCTGATAGAA-TCATGC-AA
* * * * * *
24543 AAGTTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAAATGAGTTATTCTCATTA
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATAAGTTCTTCTCATTA
24608 TGAACTTCTCTGGAAATGTTGAT
66 TGAACTT-TCTGGAAATGTTGAT
24631 CCATCGAATG
Statistics
Matches: 283, Mismatches: 28, Indels: 28
0.83 0.08 0.08
Matches are distributed among these distances:
112 7 0.02
113 20 0.07
114 64 0.23
115 1 0.00
117 1 0.00
118 2 0.01
119 2 0.01
121 81 0.29
122 94 0.33
123 4 0.01
124 7 0.02
ACGTcount: A:0.27, C:0.18, G:0.14, T:0.40
Consensus pattern (122 bp):
AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATAAGTTCTTCTCATTA
TGAACTTTCTGGAAATGTTGATGATGATATATCTCCTTCTCTGATAGAATCATGCAA
Found at i:24571 original size:114 final size:113
Alignment explanation
Indices: 24443--24651 Score: 330
Period size: 114 Copynumber: 1.8 Consensus size: 113
24433 TTAAACAAGC
* *
24443 TCTTCTCATTATGAACTTCTTCTTCCCTCTTCAGATAAGTTCTTCTCATTATGAACTTTCTCTGG
1 TCTTCTCATTATGAACTTCTTCTTCCCTCTTCAAATAAGTTATTCTCATTATGAAC-TTCTCTGG
*
24508 AAAAT-TTGATCCATCGAGTGATGAATTCAAACAAAAAGTTTGAACAAAT
65 -AAATGTTGATCCATCGAATGATGAATTCAAACAAAAAGTTTGAACAAAT
* * *
24557 TCTTCTCATTATGAATTTCTTCTTCCTTCTTCAAATGAGTTATTCTCATTATGAACTTCTCTGGA
1 TCTTCTCATTATGAACTTCTTCTTCCCTCTTCAAATAAGTTATTCTCATTATGAACTTCTCTGGA
*
24622 AATGTTGATCCATCGAATGATGGATTCAAA
66 AATGTTGATCCATCGAATGATGAATTCAAA
24652 TCTTTTCTAA
Statistics
Matches: 87, Mismatches: 7, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
112 4 0.05
113 32 0.37
114 51 0.59
ACGTcount: A:0.29, C:0.20, G:0.12, T:0.40
Consensus pattern (113 bp):
TCTTCTCATTATGAACTTCTTCTTCCCTCTTCAAATAAGTTATTCTCATTATGAACTTCTCTGGA
AATGTTGATCCATCGAATGATGAATTCAAACAAAAAGTTTGAACAAAT
Found at i:25820 original size:18 final size:19
Alignment explanation
Indices: 25792--25847 Score: 78
Period size: 20 Copynumber: 2.9 Consensus size: 19
25782 TTTACAAAAT
25792 AAAAGAATAAATTGAATTTC
1 AAAA-AATAAATTGAATTTC
*
25812 -AAAAATAAATTGAATCTC
1 AAAAAATAAATTGAATTTC
25830 AAAAAAATAAATTGAATT
1 -AAAAAATAAATTGAATT
25848 CAGAGAAACT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
18 14 0.44
19 3 0.09
20 15 0.47
ACGTcount: A:0.59, C:0.05, G:0.07, T:0.29
Consensus pattern (19 bp):
AAAAAATAAATTGAATTTC
Found at i:25837 original size:20 final size:20
Alignment explanation
Indices: 25792--25846 Score: 78
Period size: 18 Copynumber: 2.9 Consensus size: 20
25782 TTTACAAAAT
* *
25792 AAAAGAATAAATTGAATTTC
1 AAAAAAATAAATTGAATCTC
25812 --AAAAATAAATTGAATCTC
1 AAAAAAATAAATTGAATCTC
25830 AAAAAAATAAATTGAAT
1 AAAAAAATAAATTGAAT
25847 TCAGAGAAAC
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
18 16 0.52
20 15 0.48
ACGTcount: A:0.60, C:0.05, G:0.07, T:0.27
Consensus pattern (20 bp):
AAAAAAATAAATTGAATCTC
Found at i:26238 original size:10 final size:10
Alignment explanation
Indices: 26225--26261 Score: 58
Period size: 10 Copynumber: 3.7 Consensus size: 10
26215 TTTTTCAACA
26225 TTTTTTTTTC
1 TTTTTTTTTC
26235 TTTTTTTTTC
1 TTTTTTTTTC
26245 TTTTTTCTTT-
1 TTTTTT-TTTC
26255 TTTTTTT
1 TTTTTTT
26262 CAAGCATAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
9 1 0.04
10 22 0.85
11 3 0.12
ACGTcount: A:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (10 bp):
TTTTTTTTTC
Found at i:26248 original size:17 final size:17
Alignment explanation
Indices: 26228--26260 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
26218 TTCAACATTT
26228 TTTTTTCTTTTTTTTTC
1 TTTTTTCTTTTTTTTTC
26245 TTTTTTCTTTTTTTTT
1 TTTTTTCTTTTTTTTT
26261 TCAAGCATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.00, C:0.09, G:0.00, T:0.91
Consensus pattern (17 bp):
TTTTTTCTTTTTTTTTC
Found at i:29814 original size:9 final size:9
Alignment explanation
Indices: 29791--29821 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
29781 GAAAAATAAT
29791 GAATGTAAA
1 GAATGTAAA
29800 -AATGTAAA
1 GAATGTAAA
29808 GAATGTAAA
1 GAATGTAAA
29817 GAATG
1 GAATG
29822 ATTTCCATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
8 8 0.38
9 13 0.62
ACGTcount: A:0.55, C:0.00, G:0.23, T:0.23
Consensus pattern (9 bp):
GAATGTAAA
Found at i:35716 original size:2 final size:2
Alignment explanation
Indices: 35709--35737 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
35699 ATTTTCCTAT
35709 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
35738 TATTATTATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:35790 original size:14 final size:14
Alignment explanation
Indices: 35752--35799 Score: 51
Period size: 14 Copynumber: 3.1 Consensus size: 14
35742 ATTATTATTA
35752 TTTTTTATCTATGTT
1 TTTTTTA-CTATGTT
35767 TACTTATTTACTATGTT
1 T--TT-TTTACTATGTT
*
35784 TTTTTTACTATATT
1 TTTTTTACTATGTT
35798 TT
1 TT
35800 CCTAACGTTA
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
14 12 0.41
15 3 0.10
17 10 0.34
18 4 0.14
ACGTcount: A:0.19, C:0.08, G:0.04, T:0.69
Consensus pattern (14 bp):
TTTTTTACTATGTT
Found at i:35951 original size:22 final size:22
Alignment explanation
Indices: 35924--35985 Score: 63
Period size: 22 Copynumber: 2.7 Consensus size: 22
35914 CTATTTAGTA
35924 TTTTATTTTATTATACATACAT
1 TTTTATTTTATTATACATACAT
* **
35946 TTTTATATTT-TTATATATATTT
1 TTTTAT-TTTATTATACATACAT
35968 TTATTATTTTATTTATAC
1 TT-TTATTTTA-TTATAC
35986 TATTTATTTA
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
22 20 0.62
23 7 0.22
24 5 0.16
ACGTcount: A:0.29, C:0.05, G:0.00, T:0.66
Consensus pattern (22 bp):
TTTTATTTTATTATACATACAT
Found at i:35969 original size:20 final size:20
Alignment explanation
Indices: 35944--36012 Score: 61
Period size: 22 Copynumber: 3.4 Consensus size: 20
35934 TTATACATAC
35944 ATTTTTATATTTTTATATAT
1 ATTTTTATATTTTTATATAT
*
35964 ATTTTTATTATTTTATTTATACT
1 ATTTTTA-TATTTT-TATATA-T
*
35987 ATTTATT-TATTTTCAT-TAT
1 ATTT-TTATATTTTTATATAT
*
36006 GTTTTTA
1 ATTTTTA
36013 GTTTCTTTGC
Statistics
Matches: 40, Mismatches: 4, Indels: 11
0.73 0.07 0.20
Matches are distributed among these distances:
18 2 0.05
19 4 0.10
20 9 0.22
21 7 0.17
22 11 0.28
23 5 0.12
24 2 0.05
ACGTcount: A:0.26, C:0.03, G:0.01, T:0.70
Consensus pattern (20 bp):
ATTTTTATATTTTTATATAT
Found at i:35996 original size:22 final size:22
Alignment explanation
Indices: 35893--35999 Score: 62
Period size: 22 Copynumber: 4.6 Consensus size: 22
35883 TTTATTTTTC
35893 ATTTATTTATTATTATTGT-TACT
1 ATTTATTTATT-TTATT-TATACT
35916 ATTTAGTATTTTATTTTA-TTATACAT
1 A-TT--TA-TTTATTTTATTTATAC-T
*
35942 ACATTT-TTATATTTT-TATATA-T
1 --ATTTATT-TATTTTATTTATACT
*
35964 ATTTTTATTATTTTATTTATACT
1 ATTTAT-TTATTTTATTTATACT
35987 ATTTATTTATTTT
1 ATTTATTTATTTT
36000 CATTATGTTT
Statistics
Matches: 67, Mismatches: 3, Indels: 29
0.68 0.03 0.29
Matches are distributed among these distances:
20 4 0.06
21 7 0.10
22 14 0.21
23 9 0.13
24 13 0.19
25 5 0.07
26 6 0.09
27 8 0.12
28 1 0.01
ACGTcount: A:0.28, C:0.04, G:0.02, T:0.66
Consensus pattern (22 bp):
ATTTATTTATTTTATTTATACT
Found at i:41649 original size:22 final size:22
Alignment explanation
Indices: 41616--41688 Score: 112
Period size: 22 Copynumber: 3.3 Consensus size: 22
41606 GCTACCCCAT
41616 CAAACCGT-TGAGCATCAAATGC
1 CAAACC-TATGAGCATCAAATGC
*
41638 CAAACCTATGAGCATCAAATAC
1 CAAACCTATGAGCATCAAATGC
*
41660 CAAACCTATGAGCATCAAATGT
1 CAAACCTATGAGCATCAAATGC
41682 CAAACCT
1 CAAACCT
41689 TTGACCAAAC
Statistics
Matches: 47, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
21 1 0.02
22 46 0.98
ACGTcount: A:0.41, C:0.27, G:0.12, T:0.19
Consensus pattern (22 bp):
CAAACCTATGAGCATCAAATGC
Found at i:42654 original size:106 final size:106
Alignment explanation
Indices: 42497--43772 Score: 1913
Period size: 106 Copynumber: 12.0 Consensus size: 106
42487 ATATCGTGCC
* * * *
42497 ACTCAAGACAACACAAGTTCAACTTCACAACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
*
42562 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTAG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* ** * * *
42603 ACTCTAGACAACGCAAGTTCAACTTCAATACGAAAGGACCGCTGGTTGTCAATAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* *
42668 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTAG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* ** * * *
42709 ACTCCAGACAACGCAAGTTAAACTTCATAACGAAGGGACCGCTGGTTATCAACAAACGACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
*
42774 AATTTTAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * * *
42815 ACTCCAGACAACGCAAGTTCAACTTCACGATGAAGGGATCGCTGGTTGTCAATAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* * *
42880 AATTTCAGAGCCAATTTCAACTTCACATCGTATGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * *
42921 ACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCA
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
*
42986 AATTTCAGAGCCAATTTCAACTTCACAACGAAGAATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * *
43027 ACTCCAAACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAATAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* *
43092 AATTTTAGAGCCAATTTCAACTTCACAACGAATGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * *
43133 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACTGCTGGTTGTCAACAAATAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
**
43198 AATTTCAGAGCCAATTTCAACTTCACAGTGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* *
43239 ACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* *
43304 AATTTCAGAGCCAATTTTAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* *
43345 ACTCCAGACAACGCAAGTTCAACTTCACGATGAAGGGACCGCTGGTTGTCAACAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* * * *
43410 AATTTCGGAGCCAATTTCAACTTAATAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * *
43451 ACTACAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
43516 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * * *
43557 ACTCCAGATAACGCAAGTTCAACTTGAAGATGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
*
43622 AATTTCAGAGCCAATTTCAACTTCACAACAAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * * ** * *
43663 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGATGGCTGGTTGTCAACAAACAATTTTCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* * * * *
43728 GATTCCAGAGCCAATTTCAAATTCACGACGGAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
43769 ACTC
1 ACTC
43773 GGAACAATGC
Statistics
Matches: 1059, Mismatches: 111, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
106 1059 1.00
ACGTcount: A:0.35, C:0.24, G:0.18, T:0.23
Consensus pattern (106 bp):
ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
Found at i:44612 original size:37 final size:37
Alignment explanation
Indices: 44522--44618 Score: 131
Period size: 37 Copynumber: 2.6 Consensus size: 37
44512 CCTTTTCGTC
44522 CTACTAGGATTCAAACTCCTAAAAATATAATAGAATT
1 CTACTAGGATTCAAACTCCTAAAAATATAATAGAATT
* * * *
44559 TTGCTAGGATTCAAACTCCTAAAAATATGATAGAGTT
1 CTACTAGGATTCAAACTCCTAAAAATATAATAGAATT
** *
44596 CTACTATTATTTAAACTCCTAAA
1 CTACTAGGATTCAAACTCCTAAA
44619 GATAGGATCC
Statistics
Matches: 51, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
37 51 1.00
ACGTcount: A:0.41, C:0.16, G:0.09, T:0.33
Consensus pattern (37 bp):
CTACTAGGATTCAAACTCCTAAAAATATAATAGAATT
Found at i:45101 original size:2 final size:2
Alignment explanation
Indices: 45096--45136 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
45086 ATTTTCCTAT
45096 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
45137 TTTTTATCTA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:45338 original size:9 final size:8
Alignment explanation
Indices: 45319--45362 Score: 52
Period size: 8 Copynumber: 5.1 Consensus size: 8
45309 ATATACATAC
45319 ATTTTTAT
1 ATTTTTAT
45327 ATTTTATAT
1 ATTTT-TAT
45336 ATTTTTTAT
1 A-TTTTTAT
45345 ATTTTTAT
1 ATTTTTAT
*
45353 TTTATTTAT
1 ATT-TTTAT
45362 A
1 A
45363 CTATTTATTT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
8 14 0.45
9 13 0.42
10 4 0.13
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (8 bp):
ATTTTTAT
Found at i:45341 original size:17 final size:17
Alignment explanation
Indices: 45319--45386 Score: 57
Period size: 18 Copynumber: 3.8 Consensus size: 17
45309 ATATACATAC
45319 ATTTTTATATTTTATAT
1 ATTTTTATATTTTATAT
45336 ATTTTTTATATTTT-TAT
1 A-TTTTTATATTTTATAT
* *
45353 TTTATTTATACTATTTATTT
1 ATT-TTTATA-T-TTTATAT
*
45373 ATTTATTATGTTTT
1 ATTT-TTATATTTT
45387 TAGTTTTTTT
Statistics
Matches: 41, Mismatches: 4, Indels: 11
0.73 0.07 0.20
Matches are distributed among these distances:
16 2 0.05
17 10 0.24
18 16 0.39
19 5 0.12
20 8 0.20
ACGTcount: A:0.25, C:0.01, G:0.01, T:0.72
Consensus pattern (17 bp):
ATTTTTATATTTTATAT
Found at i:45362 original size:26 final size:25
Alignment explanation
Indices: 45319--45379 Score: 61
Period size: 26 Copynumber: 2.4 Consensus size: 25
45309 ATATACATAC
* *
45319 ATTTTTATATTTTATATATTTTTTAT
1 ATTTTTAT-TTTTATATACTATTTAT
*
45345 ATTTTTATTTTATTTATACTATTTAT
1 ATTTTTATTTT-TATATACTATTTAT
45371 -TTATTTATT
1 ATT-TTTATT
45380 ATGTTTTTAG
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
25 5 0.17
26 25 0.83
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.72
Consensus pattern (25 bp):
ATTTTTATTTTTATATACTATTTAT
Found at i:45370 original size:37 final size:36
Alignment explanation
Indices: 45322--45393 Score: 92
Period size: 37 Copynumber: 2.0 Consensus size: 36
45312 TACATACATT
*
45322 TTTATATTTTATATATTTTTTATATTTTTA-TTTTA
1 TTTATATTTTATATATTTATTATATTTTTAGTTTTA
* *
45357 TTTATACTATTTATTTATTTATTATGTTTTTAGTTTT
1 TTTATA-T-TTTATATATTTATTATATTTTTAGTTTT
45394 TTTGCTCTTA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
35 6 0.19
36 1 0.03
37 20 0.65
38 4 0.13
ACGTcount: A:0.24, C:0.01, G:0.03, T:0.72
Consensus pattern (36 bp):
TTTATATTTTATATATTTATTATATTTTTAGTTTTA
Found at i:45395 original size:45 final size:45
Alignment explanation
Indices: 45295--45395 Score: 102
Period size: 45 Copynumber: 2.2 Consensus size: 45
45285 ATTGTTACTA
*
45295 TTTAGTATTTTATTATATACATACATTTTTATATTTTATATATTT
1 TTTAGTTTTTTATTATATACATACATTTTTATATTTTATATATTT
* **
45340 TTTA-TATTTTTATTTTATTTATACTATTTATT-TA-TTTAT-TATGTT
1 TTTAGT-TTTTTATTATATACATAC-ATTT-TTATATTTTATATAT-TT
45385 TTTAGTTTTTT
1 TTTAGTTTTTT
45396 TGCTCTTATT
Statistics
Matches: 47, Mismatches: 4, Indels: 10
0.77 0.07 0.16
Matches are distributed among these distances:
44 4 0.09
45 34 0.72
46 7 0.15
47 2 0.04
ACGTcount: A:0.26, C:0.03, G:0.03, T:0.68
Consensus pattern (45 bp):
TTTAGTTTTTTATTATATACATACATTTTTATATTTTATATATTT
Found at i:50081 original size:3 final size:3
Alignment explanation
Indices: 50073--50116 Score: 52
Period size: 3 Copynumber: 14.3 Consensus size: 3
50063 GGTCTGAAAT
* * *
50073 ATA ATA ATA ATA TATA TTT TTA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA -ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
50117 ATAACAAATG
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
3 33 0.92
4 3 0.08
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (3 bp):
ATA
Found at i:53431 original size:19 final size:20
Alignment explanation
Indices: 53393--53431 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
53383 GTATAGTTGG
*
53393 AGATTGGTTCCAATTGGGGC
1 AGATTGATTCCAATTGGGGC
*
53413 AGATTGATTCGAA-TGGGGC
1 AGATTGATTCCAATTGGGGC
53432 CTTGGGGCGA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.23, C:0.13, G:0.36, T:0.28
Consensus pattern (20 bp):
AGATTGATTCCAATTGGGGC
Found at i:54707 original size:21 final size:21
Alignment explanation
Indices: 54683--54726 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
54673 AATATGTAAA
*
54683 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGAGATTTTCCAAAT
*
54704 TCGCGTTGAGATTTTCCAAAT
1 TCGCATTGAGATTTTCCAAAT
54725 TC
1 TC
54727 ACAACGCGAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.23, C:0.23, G:0.16, T:0.39
Consensus pattern (21 bp):
TCGCATTGAGATTTTCCAAAT
Found at i:54756 original size:20 final size:20
Alignment explanation
Indices: 54728--54851 Score: 121
Period size: 20 Copynumber: 6.2 Consensus size: 20
54718 TCCAAATTCA
54728 CAACGCGAATATGTAAATCG
1 CAACGCGAATATGTAAATCG
* *
54748 CAACTCGAATTTGTAAATCG
1 CAACGCGAATATGTAAATCG
* *
54768 CAACAC--ATAAGTCAAATTCG
1 CAACGCGAATATGT-AAA-TCG
54788 CAACGCG-ATA-GTCAAATTCG
1 CAACGCGAATATGT-AAA-TCG
* *
54808 TAACGCGAATCTGTAAATCG
1 CAACGCGAATATGTAAATCG
*
54828 CAACGCGAATCTGTAAATCG
1 CAACGCGAATATGTAAATCG
54848 CAAC
1 CAAC
54852 ACAGAAGTCA
Statistics
Matches: 90, Mismatches: 9, Indels: 10
0.83 0.08 0.09
Matches are distributed among these distances:
18 4 0.04
19 3 0.03
20 73 0.81
21 8 0.09
22 2 0.02
ACGTcount: A:0.38, C:0.23, G:0.17, T:0.22
Consensus pattern (20 bp):
CAACGCGAATATGTAAATCG
Found at i:54813 original size:80 final size:80
Alignment explanation
Indices: 54720--54918 Score: 280
Period size: 80 Copynumber: 2.5 Consensus size: 80
54710 TGAGATTTTC
* *
54720 CAAATTCACAACGCGAATATGTAAATCGCAACTCGAATTTGTAAATCGCAACACATAAGTCAAAT
1 CAAATTCGCAACGCGAATATGTAAATCGCAACTCGAATTTGTAAATCGCAACACAGAAGTCAAAT
*
54785 TCGCAACGC-GATAGT
66 TCGCAACACAGA-AGT
* * * *
54800 CAAATTCGTAACGCGAATCTGTAAATCGCAACGCGAATCTGTAAATCGCAACACAGAAGTCAAAT
1 CAAATTCGCAACGCGAATATGTAAATCGCAACTCGAATTTGTAAATCGCAACACAGAAGTCAAAT
54865 TCGCAACACAGAAGT
66 TCGCAACACAGAAGT
54880 CAAATTCGCAACGCG-ATA-GTCAAATTCGCAACT-GAATTT
1 CAAATTCGCAACGCGAATATGT-AAA-TCGCAACTCGAATTT
54919 CAAATTCGCA
Statistics
Matches: 105, Mismatches: 11, Indels: 7
0.85 0.09 0.06
Matches are distributed among these distances:
78 2 0.02
79 10 0.10
80 91 0.87
81 2 0.02
ACGTcount: A:0.39, C:0.23, G:0.16, T:0.22
Consensus pattern (80 bp):
CAAATTCGCAACGCGAATATGTAAATCGCAACTCGAATTTGTAAATCGCAACACAGAAGTCAAAT
TCGCAACACAGAAGT
Found at i:54845 original size:100 final size:100
Alignment explanation
Indices: 54728--54907 Score: 285
Period size: 100 Copynumber: 1.8 Consensus size: 100
54718 TCCAAATTCA
* *
54728 CAACGCGAATATGTAAATCGCAACTC-GAATTTGT-AAA-TCGCAACACATAAGTCAAATTCGCA
1 CAACGCGAATATGTAAATCGCAACACAGAA---GTCAAATTCGCAACACAGAAGTCAAATTCGCA
54790 ACGCGATAGTCAAATTCGTAACGCGAATCTGTAAATCG
63 ACGCGATAGTCAAATTCGTAACGCGAATCTGTAAATCG
*
54828 CAACGCGAATCTGTAAATCGCAACACAGAAGTCAAATTCGCAACACAGAAGTCAAATTCGCAACG
1 CAACGCGAATATGTAAATCGCAACACAGAAGTCAAATTCGCAACACAGAAGTCAAATTCGCAACG
54893 CGATAGTCAAATTCG
66 CGATAGTCAAATTCG
54908 CAACTGAATT
Statistics
Matches: 74, Mismatches: 3, Indels: 6
0.89 0.04 0.07
Matches are distributed among these distances:
98 2 0.03
99 3 0.04
100 66 0.89
101 3 0.04
ACGTcount: A:0.39, C:0.23, G:0.17, T:0.21
Consensus pattern (100 bp):
CAACGCGAATATGTAAATCGCAACACAGAAGTCAAATTCGCAACACAGAAGTCAAATTCGCAACG
CGATAGTCAAATTCGTAACGCGAATCTGTAAATCG
Found at i:54868 original size:20 final size:20
Alignment explanation
Indices: 54845--54911 Score: 109
Period size: 20 Copynumber: 3.4 Consensus size: 20
54835 AATCTGTAAA
54845 TCGCAACACAGAAGTCAAAT
1 TCGCAACACAGAAGTCAAAT
54865 TCGCAACACAGAAGTCAAAT
1 TCGCAACACAGAAGTCAAAT
*
54885 TCGCAACGC-GATAGTCAAAT
1 TCGCAACACAGA-AGTCAAAT
54905 TCGCAAC
1 TCGCAAC
54912 TGAATTTCAA
Statistics
Matches: 45, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
19 2 0.04
20 43 0.96
ACGTcount: A:0.40, C:0.27, G:0.16, T:0.16
Consensus pattern (20 bp):
TCGCAACACAGAAGTCAAAT
Found at i:54944 original size:20 final size:20
Alignment explanation
Indices: 54779--54968 Score: 105
Period size: 20 Copynumber: 9.7 Consensus size: 20
54769 AACACATAAG
* *
54779 TCAAATTCGCAACGCG-ATAG
1 TCAAATTCGCAACTCGAAT-T
* *
54799 TCAAATTCGTAACGCGAATCT
1 TCAAATTCGCAACTCGAAT-T
*
54820 GT-AAA-TCGCAACGCGAATCT
1 -TCAAATTCGCAACTCGAAT-T
* *
54840 GT-AAA-TCGCAACACAGAA-G
1 -TCAAATTCGCAACTC-GAATT
* *
54859 TCAAATTCGCAACACAGAA-G
1 TCAAATTCGCAACTC-GAATT
* *
54879 TCAAATTCGCAACGCG-ATAG
1 TCAAATTCGCAACTCGAAT-T
54899 TCAAATTCGCAACT-GAATT
1 TCAAATTCGCAACTCGAATT
*
54918 TCAAATTCGCAACTCGATTT
1 TCAAATTCGCAACTCGAATT
* *
54938 TCGAATTCGCAACACGAATT
1 TCAAATTCGCAACTCGAATT
54958 T--AATTCGCAAC
1 TCAAATTCGCAAC
54969 AGGTTTAGTT
Statistics
Matches: 148, Mismatches: 13, Indels: 20
0.82 0.07 0.11
Matches are distributed among these distances:
18 12 0.08
19 19 0.13
20 108 0.73
21 8 0.05
22 1 0.01
ACGTcount: A:0.37, C:0.24, G:0.16, T:0.23
Consensus pattern (20 bp):
TCAAATTCGCAACTCGAATT
Found at i:54945 original size:39 final size:40
Alignment explanation
Indices: 54720--54968 Score: 157
Period size: 40 Copynumber: 6.3 Consensus size: 40
54710 TGAGATTTTC
* *
54720 CAAATTCACAACGCGAATATGT-AAA-TCGCAACTCGAATTT
1 CAAATTCGCAACGCG-ATA-GTCAAATTCGCAACACGAATTT
* * * *
54760 GTAAA-TCGCAACAC-ATAAGTCAAATTCGCAACGCG-ATAGT
1 -CAAATTCGCAACGCGAT-AGTCAAATTCGCAACACGAAT-TT
* * *
54800 CAAATTCGTAACGCGAATCTGT-AAA-TCGCAACGCGAATCTGT
1 CAAATTCGCAACGCG-AT-AGTCAAATTCGCAACACGAAT-T-T
* *
54842 -AAA-TCGCAACACAGA-AGTCAAATTCGCAACACAGAA-GT
1 CAAATTCGCAACGC-GATAGTCAAATTCGCAACAC-GAATTT
*
54880 CAAATTCGCAACGCGATAGTCAAATTCGCAAC-TGAATTT
1 CAAATTCGCAACGCGATAGTCAAATTCGCAACACGAATTT
* ** *
54919 CAAATTCGCAACTCGATTTTCGAATTCGCAACACGAATTT
1 CAAATTCGCAACGCGATAGTCAAATTCGCAACACGAATTT
54959 --AATTCGCAAC
1 CAAATTCGCAAC
54969 AGGTTTAGTT
Statistics
Matches: 165, Mismatches: 25, Indels: 39
0.72 0.11 0.17
Matches are distributed among these distances:
38 20 0.12
39 46 0.28
40 79 0.48
41 15 0.09
42 5 0.03
ACGTcount: A:0.38, C:0.24, G:0.15, T:0.23
Consensus pattern (40 bp):
CAAATTCGCAACGCGATAGTCAAATTCGCAACACGAATTT
Found at i:56248 original size:17 final size:18
Alignment explanation
Indices: 56220--56253 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
56210 TCATTTGTTT
56220 TATTTAATATATATTTGA
1 TATTTAATATATATTTGA
*
56238 TATTT-ATATATTTTTG
1 TATTTAATATATATTTG
56254 TGTTTTTAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.32, C:0.00, G:0.06, T:0.62
Consensus pattern (18 bp):
TATTTAATATATATTTGA
Found at i:56406 original size:27 final size:26
Alignment explanation
Indices: 56376--56458 Score: 73
Period size: 24 Copynumber: 3.3 Consensus size: 26
56366 GTTTTAGTTT
*
56376 TTTTTATTTATTACTATTATATATATC
1 TTTTTATTT-TTACCATTATATATATC
* * *
56403 TTTTTATTTTTCCCATTGTTTATATC
1 TTTTTATTTTTACCATTATATATATC
* * *
56429 --TTTATTATTACCATCATATAT-TA
1 TTTTTATTTTTACCATTATATATATC
56452 TTTTTAT
1 TTTTTAT
56459 ATCTATATTT
Statistics
Matches: 44, Mismatches: 10, Indels: 6
0.73 0.17 0.10
Matches are distributed among these distances:
23 1 0.02
24 16 0.36
25 5 0.11
26 13 0.30
27 9 0.20
ACGTcount: A:0.25, C:0.11, G:0.01, T:0.63
Consensus pattern (26 bp):
TTTTTATTTTTACCATTATATATATC
Found at i:59994 original size:206 final size:206
Alignment explanation
Indices: 59640--60051 Score: 824
Period size: 206 Copynumber: 2.0 Consensus size: 206
59630 CAGAAGAGAC
59640 TATCTTCAGATTTCATCCCGCCCATCAGGATTAATCTTTGTTTGCAAAAAAACAATGTAATTAAT
1 TATCTTCAGATTTCATCCCGCCCATCAGGATTAATCTTTGTTTGCAAAAAAACAATGTAATTAAT
59705 GTATGGTAGAGAAAAATAACAAAGGGGGGTTCAAGACGTAAATCCTGAATAACGTCTTGAAACCA
66 GTATGGTAGAGAAAAATAACAAAGGGGGGTTCAAGACGTAAATCCTGAATAACGTCTTGAAACCA
59770 AAGGAGGATTCGAGTTGAAAACCTGAAAAGGTGGCTCGAATATAAAAATTGTGCAACTGAGGCGA
131 AAGGAGGATTCGAGTTGAAAACCTGAAAAGGTGGCTCGAATATAAAAATTGTGCAACTGAGGCGA
59835 TCACACAAATT
196 TCACACAAATT
59846 TATCTTCAGATTTCATCCCGCCCATCAGGATTAATCTTTGTTTGCAAAAAAACAATGTAATTAAT
1 TATCTTCAGATTTCATCCCGCCCATCAGGATTAATCTTTGTTTGCAAAAAAACAATGTAATTAAT
59911 GTATGGTAGAGAAAAATAACAAAGGGGGGTTCAAGACGTAAATCCTGAATAACGTCTTGAAACCA
66 GTATGGTAGAGAAAAATAACAAAGGGGGGTTCAAGACGTAAATCCTGAATAACGTCTTGAAACCA
59976 AAGGAGGATTCGAGTTGAAAACCTGAAAAGGTGGCTCGAATATAAAAATTGTGCAACTGAGGCGA
131 AAGGAGGATTCGAGTTGAAAACCTGAAAAGGTGGCTCGAATATAAAAATTGTGCAACTGAGGCGA
60041 TCACACAAATT
196 TCACACAAATT
60052 CCTTGATAAG
Statistics
Matches: 206, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
206 206 1.00
ACGTcount: A:0.38, C:0.16, G:0.20, T:0.25
Consensus pattern (206 bp):
TATCTTCAGATTTCATCCCGCCCATCAGGATTAATCTTTGTTTGCAAAAAAACAATGTAATTAAT
GTATGGTAGAGAAAAATAACAAAGGGGGGTTCAAGACGTAAATCCTGAATAACGTCTTGAAACCA
AAGGAGGATTCGAGTTGAAAACCTGAAAAGGTGGCTCGAATATAAAAATTGTGCAACTGAGGCGA
TCACACAAATT
Found at i:61081 original size:36 final size:36
Alignment explanation
Indices: 61034--61136 Score: 138
Period size: 36 Copynumber: 2.9 Consensus size: 36
61024 GTGCTTACCA
61034 TTGTCTCTCTTGAGACAGTTTCCCTTGAAA-AAAACT
1 TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAA-T
*
61070 TTGTCTCTCTTGAGACAGTTTCCCTTTAAACAAAAT
1 TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAAT
* * * *
61106 TTTTTTCCCTTGAGACAG-TTCTCTTGAAACA
1 TTGTCTCTCTTGAGACAGTTTCCCTTGAAACA
61137 TAAACATTGA
Statistics
Matches: 60, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
35 11 0.18
36 45 0.75
37 4 0.07
ACGTcount: A:0.26, C:0.22, G:0.13, T:0.39
Consensus pattern (36 bp):
TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAAT
Found at i:61227 original size:37 final size:37
Alignment explanation
Indices: 61168--61442 Score: 159
Period size: 37 Copynumber: 7.9 Consensus size: 37
61158 TTGAAATGAG
*
61168 TTTTGTCTCTC-TTGAGATAGTTTCCCTTGAAACAAAA
1 TTTTGTCTC-CATTGAGACAGTTTCCCTTGAAACAAAA
* *
61205 TTTCGTCTCCATTGAGACAGTTTCTCTTGAAACATAAA
1 TTTTGTCTCCATTGAGACAGTTTCCCTTGAAACA-AAA
* **
61243 ---------CATTGGAAACA-TTTCCCTTGAAA-TGAA
1 TTTTGTCTCCATT-GAGACAGTTTCCCTTGAAACAAAA
* *
61270 TTTTGTCTCTC-TTGAGATAGTTTTCCTTGAAACAAAA
1 TTTTGTCTC-CATTGAGACAGTTTCCCTTGAAACAAAA
* *
61307 TTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAA
1 TTTTGTCTCCATTGAGACAGTTTCCCTTGAAACA-AAA
* **
61345 ---------CATTGAAAACA-TTTCCCTTGAAA-TGAA
1 TTTTGTCTCCATTG-AGACAGTTTCCCTTGAAACAAAA
* *
61372 TTTTGTCTCTC-TTGAGATAGTTTCCCTCGAAACAAAA
1 TTTTGTCTC-CATTGAGACAGTTTCCCTTGAAACAAAA
* *
61409 TTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACA
1 TTTTGTCTCCATTGAGACAGTTTCCCTTGAAACA
61443 TAAACATTGA
Statistics
Matches: 179, Mismatches: 28, Indels: 62
0.67 0.10 0.23
Matches are distributed among these distances:
27 4 0.02
29 30 0.17
30 9 0.05
35 7 0.04
36 30 0.17
37 93 0.52
38 6 0.03
ACGTcount: A:0.29, C:0.20, G:0.13, T:0.38
Consensus pattern (37 bp):
TTTTGTCTCCATTGAGACAGTTTCCCTTGAAACAAAA
Found at i:61261 original size:102 final size:102
Alignment explanation
Indices: 61052--61507 Score: 772
Period size: 102 Copynumber: 4.5 Consensus size: 102
61042 CTTGAGACAG
** * * * *
61052 TTTCCCTTGAAAAAAACTTTGTCTCTCTTGAGACAGTTTCCCTTTAAACAAAATTTT-TTTCCCT
1 TTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCT
61116 TGAGACAG-TTCTCTTGAAACATAAACATTGAAAACA
66 TGAGACAGTTTCTCTTGAAACATAAACATTGAAAACA
* * *
61152 TTTCCCTTGAAATGAGTTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTCGTCTCCAT
1 TTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCT
*
61217 TGAGACAGTTTCTCTTGAAACATAAACATTGGAAACA
66 TGAGACAGTTTCTCTTGAAACATAAACATTGAAAACA
*
61254 TTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTTCCTTGAAACAAAATTTTGTCTCCCT
1 TTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCT
61319 TGAGACAGTTTCTCTTGAAACATAAACATTGAAAACA
66 TGAGACAGTTTCTCTTGAAACATAAACATTGAAAACA
*
61356 TTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTCGAAACAAAATTTTGTCTCCCT
1 TTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCT
61421 TGAGACAGTTTCTCTTGAAACATAAACATTGAAAACA
66 TGAGACAGTTTCTCTTGAAACATAAACATTGAAAACA
* *
61458 TTTCCCTTGAAATGAATTTCGTCTCTCTTGAGATAGTTTCTCTTGAAACA
1 TTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACA
61508 TAAAACATTG
Statistics
Matches: 334, Mismatches: 20, Indels: 2
0.94 0.06 0.01
Matches are distributed among these distances:
100 50 0.15
101 13 0.04
102 271 0.81
ACGTcount: A:0.30, C:0.20, G:0.13, T:0.37
Consensus pattern (102 bp):
TTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCT
TGAGACAGTTTCTCTTGAAACATAAACATTGAAAACA
Found at i:61568 original size:22 final size:23
Alignment explanation
Indices: 61543--61588 Score: 85
Period size: 22 Copynumber: 2.0 Consensus size: 23
61533 TCTTGAAGCT
61543 TTGAATATGTTTT-CCTTGGAAC
1 TTGAATATGTTTTCCCTTGGAAC
61565 TTGAATATGTTTTCCCTTGGAAC
1 TTGAATATGTTTTCCCTTGGAAC
61588 T
1 T
61589 ATTTCATCTC
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
22 13 0.57
23 10 0.43
ACGTcount: A:0.22, C:0.15, G:0.17, T:0.46
Consensus pattern (23 bp):
TTGAATATGTTTTCCCTTGGAAC
Found at i:61669 original size:37 final size:37
Alignment explanation
Indices: 61628--61701 Score: 94
Period size: 37 Copynumber: 2.0 Consensus size: 37
61618 TGGAACTAAG
* * **
61628 TTTTGTCTCTCTTGAGACAGTTTTTCTTAAAACAAAA
1 TTTTGTCTCCCTTAAGACAGTTTCCCTTAAAACAAAA
* *
61665 TTTTGTCTCCCTTAAGACCGTTTCCCTTGAAACAAAA
1 TTTTGTCTCCCTTAAGACAGTTTCCCTTAAAACAAAA
61702 AATATCTTTG
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
37 31 1.00
ACGTcount: A:0.28, C:0.22, G:0.11, T:0.39
Consensus pattern (37 bp):
TTTTGTCTCCCTTAAGACAGTTTCCCTTAAAACAAAA
Found at i:62458 original size:106 final size:98
Alignment explanation
Indices: 62297--62587 Score: 339
Period size: 98 Copynumber: 2.9 Consensus size: 98
62287 GCCATCCGCG
* * *
62297 ATTTCAACTCCACAACGGAGGATATCGTGGCACTCGAGACAACACAAGTTCAACTTCACAACGAA
1 ATTTCAACTTCACAGCGAAGGATAT--TGG-ACTCGAGACAACACAAGTTCAACTTCACAACGAA
** *
62362 GGGATGGCTGGTTGTCAACAAACAACTTCTCAGTTTTAGGGCCA
63 GGGGCGGCTGGTTGTCAACAAACAA-TT-TC-G-----GAGCCA
* * * *
62406 ATTTCAACTTCACAGCGAAGGATATTGGACCCAAGACAGCACAAGCTCAACTTCACAACGAAGGG
1 ATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAACGAAGGG
** * *
62471 GCGGCTGACTGTCGACAAGCAATTTCGGAGCCA
66 GCGGCTGGTTGTCAACAAACAATTTCGGAGCCA
*
62504 ATCTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAACGAAGGG
1 ATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAACGAAGGG
*
62569 GCCGCTGGTTGTCAACAAA
66 GCGGCTGGTTGTCAACAAA
62588 ATTTCCCAGT
Statistics
Matches: 158, Mismatches: 24, Indels: 11
0.82 0.12 0.06
Matches are distributed among these distances:
98 79 0.50
103 1 0.01
104 2 0.01
105 2 0.01
106 49 0.31
107 3 0.02
109 22 0.14
ACGTcount: A:0.33, C:0.25, G:0.22, T:0.20
Consensus pattern (98 bp):
ATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAACGAAGGG
GCGGCTGGTTGTCAACAAACAATTTCGGAGCCA
Found at i:62696 original size:65 final size:65
Alignment explanation
Indices: 62537--62890 Score: 545
Period size: 65 Copynumber: 5.5 Consensus size: 65
62527 ATTGGACTCG
62537 AGACAACACAAGTTCAACTTCACAACGAAGGGGCCGCTGGTTGTCAAC-AAAATTTCCCAGTTTC
1 AGACAACACAAGTTCAACTTCACAACGAAGGGGCCGCTGGTTGTCAACAAAAATTTCCCAGTTTC
* *
62601 AGACAACACAAGTTCAACTTCACAATGAAGGGGCCGCTGGTTGTCAACAAAAATTTCCCAGTGTC
1 AGACAACACAAGTTCAACTTCACAACGAAGGGGCCGCTGGTTGTCAACAAAAATTTCCCAGTTTC
* * *
62666 AGACAACACAAGTTCAACTTCACGACGAAGGGGCCGCTGGTTGTCGACAAAAATTTCCCAGTATC
1 AGACAACACAAGTTCAACTTCACAACGAAGGGGCCGCTGGTTGTCAACAAAAATTTCCCAGTTTC
* *
62731 AGACAACACAAGTTCAACTTCAAAACGAAGGGGCCGCTGGTTGTCAACAAAAATTTCCCAGTTTA
1 AGACAACACAAGTTCAACTTCACAACGAAGGGGCCGCTGGTTGTCAACAAAAATTTCCCAGTTTC
* * * *
62796 AGACAGCACAAGTTCAACTTCACAACGAAGGGGCCGCTGGCTGTCAACAAAAAACTTCCCCAATT
1 AGACAACACAAGTTCAACTTCACAACGAAGGGGCCGCTGGTTGTCAAC-AAAAA-TTTCCCAGTT
62861 TC
64 TC
* *
62863 AG--AAC-CAATTTCAACTTCACAGCGAAGG
1 AGACAACACAAGTTCAACTTCACAACGAAGG
62891 ATATTGGACT
Statistics
Matches: 267, Mismatches: 20, Indels: 6
0.91 0.07 0.02
Matches are distributed among these distances:
64 68 0.25
65 183 0.69
66 5 0.02
67 11 0.04
ACGTcount: A:0.34, C:0.26, G:0.19, T:0.20
Consensus pattern (65 bp):
AGACAACACAAGTTCAACTTCACAACGAAGGGGCCGCTGGTTGTCAACAAAAATTTCCCAGTTTC
Found at i:63008 original size:105 final size:107
Alignment explanation
Indices: 62804--63018 Score: 317
Period size: 105 Copynumber: 2.0 Consensus size: 107
62794 TAAGACAGCA
*
62804 CAAGTTCAACTTCACAACGAAGGGGCCGCTGGCTGTCAACAAAAAACTTCCCCAATTTCAGAACC
1 CAAGTTCAACTTCACAACGAAGGGGCCGATGGCTGTCAACAAAAAACTTCCCCAATTTCAGAACC
*
62869 AATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACG
66 AATTTCAACTTCACAGCGAAGGATATTGGACTCGAAACAACG
* * ** * * **
62911 CAAGTTCAACTTCACAACGAAGGGGCCGATGGTTGTCAA-TAAACGCTT-TCCAGTTTCAGAGTC
1 CAAGTTCAACTTCACAACGAAGGGGCCGATGGCTGTCAACAAAAAACTTCCCCAATTTCAGAACC
*
62974 AATTTCAACTTCACAGCGAAGGATATTGGCCTCGAAACAACG
66 AATTTCAACTTCACAGCGAAGGATATTGGACTCGAAACAACG
63016 CAA
1 CAA
63019 CTTGCATTGG
Statistics
Matches: 97, Mismatches: 11, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
105 54 0.56
106 6 0.06
107 37 0.38
ACGTcount: A:0.33, C:0.26, G:0.20, T:0.21
Consensus pattern (107 bp):
CAAGTTCAACTTCACAACGAAGGGGCCGATGGCTGTCAACAAAAAACTTCCCCAATTTCAGAACC
AATTTCAACTTCACAGCGAAGGATATTGGACTCGAAACAACG
Found at i:68202 original size:18 final size:18
Alignment explanation
Indices: 68176--68211 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
68166 AAGCAAAAGG
*
68176 AAATTAAAATCACAATCA
1 AAATCAAAATCACAATCA
*
68194 AAATCAAAATCCCAATCA
1 AAATCAAAATCACAATCA
68212 CAACCGGCTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.58, C:0.22, G:0.00, T:0.19
Consensus pattern (18 bp):
AAATCAAAATCACAATCA
Found at i:68656 original size:14 final size:14
Alignment explanation
Indices: 68637--68677 Score: 57
Period size: 14 Copynumber: 3.0 Consensus size: 14
68627 TTATTTACAC
68637 ATCAAATTAAACAA
1 ATCAAATTAAACAA
**
68651 ATCAAATTTTACAA
1 ATCAAATTAAACAA
68665 ATC-AATTAAACAA
1 ATCAAATTAAACAA
68678 GCAAAAAATA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
13 8 0.35
14 15 0.65
ACGTcount: A:0.59, C:0.15, G:0.00, T:0.27
Consensus pattern (14 bp):
ATCAAATTAAACAA
Found at i:68663 original size:66 final size:64
Alignment explanation
Indices: 68580--68719 Score: 235
Period size: 66 Copynumber: 2.2 Consensus size: 64
68570 AATTTAAAAC
*
68580 AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAAATAATTCTTATTTACACATCAAATT
1 AACAAATCAAATTTTACAAATCAATTAAACAAGC-AAAAAATAATTCTTATTTACACATC-AATT
68645 A
64 A
* *
68646 AACAAATCAAATTTTACAAATCAATTAAACAAGCAAAAAATAATTCTTATTTCCTCATCAATTA
1 AACAAATCAAATTTTACAAATCAATTAAACAAGCAAAAAATAATTCTTATTTACACATCAATTA
68710 AACAAATCAA
1 AACAAATCAA
68720 CTTTCAATGT
Statistics
Matches: 71, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
64 15 0.21
65 23 0.32
66 33 0.46
ACGTcount: A:0.53, C:0.17, G:0.01, T:0.29
Consensus pattern (64 bp):
AACAAATCAAATTTTACAAATCAATTAAACAAGCAAAAAATAATTCTTATTTACACATCAATTA
Found at i:70121 original size:21 final size:21
Alignment explanation
Indices: 70097--70179 Score: 66
Period size: 21 Copynumber: 4.0 Consensus size: 21
70087 GAATGGTGGG
70097 AGGGACC-CATTGAACGATGAC
1 AGGGACCTC-TTGAACGATGAC
* *
70118 AGGGGCCTCTTGAACGATGAG
1 AGGGACCTCTTGAACGATGAC
* *
70139 A-AGAGCCTCTTGAACGAT-AGG
1 AGGGA-CCTCTTGAACGATGA-C
70160 AGGTG-CCTCTTGAACGATGA
1 AGG-GACCTCTTGAACGATGA
70180 AGGTGAATCA
Statistics
Matches: 51, Mismatches: 5, Indels: 11
0.76 0.07 0.16
Matches are distributed among these distances:
20 2 0.04
21 46 0.90
22 2 0.04
23 1 0.02
ACGTcount: A:0.29, C:0.20, G:0.31, T:0.19
Consensus pattern (21 bp):
AGGGACCTCTTGAACGATGAC
Found at i:70597 original size:63 final size:62
Alignment explanation
Indices: 70467--70585 Score: 150
Period size: 63 Copynumber: 1.9 Consensus size: 62
70457 TAGAGCGGCT
* * *
70467 ACCTCATCACGTAAAGTAGTACCTCATCACATAGTGCACCATTGTCATCGCGTAAAACATCC
1 ACCTCACCACGTAAAGTAGTACCTCATCACACAGTGCACCATTGTCATCACGTAAAACATCC
* * * *
70529 ACCTCACCACGTGAAGATTGTACCTCATCACGCCA-TGCACCATTGTCTTCACGTAAA
1 ACCTCACCACGTAAAG-TAGTACCTCATCAC-ACAGTGCACCATTGTCATCACGTAAA
70586 GTACCGACCT
Statistics
Matches: 48, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
62 14 0.29
63 33 0.69
64 1 0.02
ACGTcount: A:0.30, C:0.32, G:0.13, T:0.24
Consensus pattern (62 bp):
ACCTCACCACGTAAAGTAGTACCTCATCACACAGTGCACCATTGTCATCACGTAAAACATCC
Found at i:70605 original size:21 final size:21
Alignment explanation
Indices: 70577--70626 Score: 82
Period size: 21 Copynumber: 2.4 Consensus size: 21
70567 ACCATTGTCT
*
70577 TCACGTAAAGTACCGACCTCA
1 TCACGTAAAGCACCGACCTCA
*
70598 TGACGTAAAGCACCGACCTCA
1 TCACGTAAAGCACCGACCTCA
70619 TCACGTAA
1 TCACGTAA
70627 CTCCCCTAAC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.34, C:0.32, G:0.16, T:0.18
Consensus pattern (21 bp):
TCACGTAAAGCACCGACCTCA
Found at i:72418 original size:20 final size:20
Alignment explanation
Indices: 72379--72418 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
72369 TGCGATTTTG
* * *
72379 GTGTTGCGATTTTCATTTTC
1 GTGTTGCGAATTTAAGTTTC
72399 GTGTTGCGAATTTAAGTTTC
1 GTGTTGCGAATTTAAGTTTC
72419 AAAAACTATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.15, C:0.12, G:0.23, T:0.50
Consensus pattern (20 bp):
GTGTTGCGAATTTAAGTTTC
Found at i:73660 original size:35 final size:35
Alignment explanation
Indices: 73567--73663 Score: 115
Period size: 35 Copynumber: 2.8 Consensus size: 35
73557 AACACATTCA
* * *
73567 TCAATTACATTCTAAACCCCAAAATAAAAAATGCT
1 TCAATTACATTCTAAACCCCAAATTCAAAAATACT
** * *
73602 TCAATTACATTCTAAACATCAAATTCCAACATACT
1 TCAATTACATTCTAAACCCCAAATTCAAAAATACT
73637 TCAATTACATATCT-AACCCCAAATTCA
1 TCAATTACAT-TCTAAACCCCAAATTCA
73664 CAATCCATTC
Statistics
Matches: 51, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
35 48 0.94
36 3 0.06
ACGTcount: A:0.44, C:0.26, G:0.01, T:0.29
Consensus pattern (35 bp):
TCAATTACATTCTAAACCCCAAATTCAAAAATACT
Found at i:74018 original size:148 final size:148
Alignment explanation
Indices: 73824--74116 Score: 489
Period size: 148 Copynumber: 2.0 Consensus size: 148
73814 AAATACTCAA
73824 TTCAATTTATAAAATAGCTGACTCAAAATTTTTTCGATTTGAGTTTATAAAATTTAAATCAAGTC
1 TTCAATTTATAAAATAGCTGACTCAAAATTTTTTCGATTTGAGTTTATAAAATTTAAATCAAGTC
* * *
73889 GAATTGAATTGAATTTTCT-AGTTTCTGTTTAAATTTAATTATAAATATTTATCATATTATAATA
66 GAATTGAATTGAATTTT-TGAGTTTCTGTATAAATTTAATTATAAATATTTATAATACTATAATA
*
73953 TCATTTGATTCTAATTCAG
130 TCATTTGATTCAAATTCAG
* * * *
73972 TTCAGTTTATAAAATAGTTGACTCGAACTTTTTTCGATTTGAGTTTATAAAATTTAAATCAAGTC
1 TTCAATTTATAAAATAGCTGACTCAAAATTTTTTCGATTTGAGTTTATAAAATTTAAATCAAGTC
74037 GAATTGAATTGAATTTTTGAGTTTCTGTATAAATTTAATTATAAATATTTATAATACTATAATAT
66 GAATTGAATTGAATTTTTGAGTTTCTGTATAAATTTAATTATAAATATTTATAATACTATAATAT
*
74102 TATTTGATTCAAATT
131 CATTTGATTCAAATT
74117 TAAATAGTTT
Statistics
Matches: 135, Mismatches: 9, Indels: 2
0.92 0.06 0.01
Matches are distributed among these distances:
147 1 0.01
148 134 0.99
ACGTcount: A:0.37, C:0.08, G:0.10, T:0.46
Consensus pattern (148 bp):
TTCAATTTATAAAATAGCTGACTCAAAATTTTTTCGATTTGAGTTTATAAAATTTAAATCAAGTC
GAATTGAATTGAATTTTTGAGTTTCTGTATAAATTTAATTATAAATATTTATAATACTATAATAT
CATTTGATTCAAATTCAG
Found at i:74660 original size:36 final size:36
Alignment explanation
Indices: 74617--74698 Score: 119
Period size: 36 Copynumber: 2.3 Consensus size: 36
74607 GGGGTTGGTC
*
74617 ATATAATTAAAGTATTTTGGGAATTTGAGGTTTAGA
1 ATATAATTAAAGCATTTTGGGAATTTGAGGTTTAGA
* ** *
74653 ATGTAATTAAAGCATTTTTTGAATTTGGGGTTTAGA
1 ATATAATTAAAGCATTTTGGGAATTTGAGGTTTAGA
74689 ATATAATTAA
1 ATATAATTAA
74699 TGATTGTGTT
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
36 40 1.00
ACGTcount: A:0.37, C:0.01, G:0.20, T:0.43
Consensus pattern (36 bp):
ATATAATTAAAGCATTTTGGGAATTTGAGGTTTAGA
Found at i:75058 original size:20 final size:20
Alignment explanation
Indices: 75014--75059 Score: 58
Period size: 19 Copynumber: 2.3 Consensus size: 20
75004 ATAATTTATT
*
75014 TTTTATTTTTTATATTTATAA
1 TTTTA-TTTTCATATTTATAA
*
75035 -TTTATTTTCATCTTTATAA
1 TTTTATTTTCATATTTATAA
75054 TTTTAT
1 TTTTAT
75060 AAACATGGTT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
19 13 0.59
20 9 0.41
ACGTcount: A:0.26, C:0.04, G:0.00, T:0.70
Consensus pattern (20 bp):
TTTTATTTTCATATTTATAA
Found at i:75058 original size:27 final size:27
Alignment explanation
Indices: 75003--75061 Score: 68
Period size: 27 Copynumber: 2.2 Consensus size: 27
74993 TAATCTTTTA
* *
75003 TATAATTTATTTTTTATTTTTTATATT
1 TATAATTTATTTTTCATTTTTAATATT
75030 TATAATTTA-TTTTCATCTTTATAAT-TT
1 TATAATTTATTTTTCAT-TTT-TAATATT
75057 TATAA
1 TATAA
75062 ACATGGTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
26 6 0.21
27 19 0.68
28 3 0.11
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.66
Consensus pattern (27 bp):
TATAATTTATTTTTCATTTTTAATATT
Found at i:77914 original size:15 final size:15
Alignment explanation
Indices: 77894--77927 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
77884 AATTCATTTT
77894 CAAACATATAGATTA
1 CAAACATATAGATTA
*
77909 CAAACATATGGATTA
1 CAAACATATAGATTA
77924 CAAA
1 CAAA
77928 AGCAATCCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.53, C:0.15, G:0.09, T:0.24
Consensus pattern (15 bp):
CAAACATATAGATTA
Found at i:78094 original size:40 final size:40
Alignment explanation
Indices: 78039--78118 Score: 160
Period size: 40 Copynumber: 2.0 Consensus size: 40
78029 ATTCCAATCG
78039 ATGGAAGTGGAACCATTGGAACATATTTAATATTATCCTC
1 ATGGAAGTGGAACCATTGGAACATATTTAATATTATCCTC
78079 ATGGAAGTGGAACCATTGGAACATATTTAATATTATCCTC
1 ATGGAAGTGGAACCATTGGAACATATTTAATATTATCCTC
78119 CTATACATCA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.35, C:0.15, G:0.17, T:0.33
Consensus pattern (40 bp):
ATGGAAGTGGAACCATTGGAACATATTTAATATTATCCTC
Found at i:79959 original size:3 final size:3
Alignment explanation
Indices: 79951--79984 Score: 59
Period size: 3 Copynumber: 11.0 Consensus size: 3
79941 CAGTTTGTTT
79951 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA
79985 AATAAATATT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 27 0.90
4 3 0.10
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:81494 original size:26 final size:26
Alignment explanation
Indices: 81429--81505 Score: 68
Period size: 26 Copynumber: 2.9 Consensus size: 26
81419 CTTTGATTAT
* *
81429 TATTTTTTTATTATTTT-AA-TATATAT
1 TATTTATTTATT-TTTTAAATTA-ATAA
*
81455 TATTTAATTAATTTTTTAAATTAATAA
1 TATTT-ATTTATTTTTTAAATTAATAA
*
81482 TATTTATTTATTTTTCAATATTAA
1 TATTTATTTATTTTTTAA-ATTAA
81506 GAAAGGGCAG
Statistics
Matches: 42, Mismatches: 5, Indels: 7
0.78 0.09 0.13
Matches are distributed among these distances:
26 20 0.48
27 20 0.48
28 2 0.05
ACGTcount: A:0.36, C:0.01, G:0.00, T:0.62
Consensus pattern (26 bp):
TATTTATTTATTTTTTAAATTAATAA
Found at i:81645 original size:140 final size:140
Alignment explanation
Indices: 81479--81730 Score: 350
Period size: 140 Copynumber: 1.8 Consensus size: 140
81469 TTTAAATTAA
* * *
81479 TAATATTTATTTATTTTTCAATATTAAG-AAAGGGCAGTCTTAAAGCAAATGGATGTCCATTTTC
1 TAATATTTATTTATTTTTCAATATTAAGAAAAGAGCAGTCTTAAAGCAAATAGAAGT-CATTTTC
* *
81543 TGATATTTTTAAATAAATAAATATCTTATTTTTTAAA-AT-TATATATAATAATCTATTTTTATA
65 TGATATTTCTAAATAAATAAATATCTTA-TTTATAAATATATATATATAATAATCTATTTTTATA
81606 TAAATGTTTTAT
129 TAAATGTTTTAT
** **
81618 TAATATTTATTTACTTTTT-ATATATTAAGAAAAGAGTTGTCTTAAAGCACCTAGAAGTCATTTT
1 TAATATTTATTTA-TTTTTCA-ATATTAAGAAAAGAGCAGTCTTAAAGCAAATAGAAGTCATTTT
*
81682 CTGATATTTCTAAGTAAATAAATATCTTATTTATAAATATATATATATA
64 CTGATATTTCTAAATAAATAAATATCTTATTTATAAATATATATATATA
81731 TATATATATA
Statistics
Matches: 98, Mismatches: 10, Indels: 8
0.84 0.09 0.07
Matches are distributed among these distances:
139 21 0.21
140 48 0.49
141 29 0.30
ACGTcount: A:0.39, C:0.07, G:0.08, T:0.46
Consensus pattern (140 bp):
TAATATTTATTTATTTTTCAATATTAAGAAAAGAGCAGTCTTAAAGCAAATAGAAGTCATTTTCT
GATATTTCTAAATAAATAAATATCTTATTTATAAATATATATATATAATAATCTATTTTTATATA
AATGTTTTAT
Found at i:81725 original size:2 final size:2
Alignment explanation
Indices: 81713--81789 Score: 104
Period size: 2 Copynumber: 39.5 Consensus size: 2
81703 ATATCTTATT
*
81713 TA TA AA 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
* * *
81755 TA T- TA TA TG TT TT TA TA -A TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
81790 TAATATGGTT
Statistics
Matches: 68, Mismatches: 5, Indels: 4
0.88 0.06 0.05
Matches are distributed among these distances:
1 2 0.03
2 66 0.97
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.52
Consensus pattern (2 bp):
TA
Found at i:81759 original size:140 final size:139
Alignment explanation
Indices: 81479--81759 Score: 329
Period size: 140 Copynumber: 2.0 Consensus size: 139
81469 TTTAAATTAA
* * *
81479 TAATATTTATTTATTTTTCAATATTAAGAAAGGGCAGTCTTAAAGCAAATGGATGTCCATTTTCT
1 TAATATTTATTTATTTTTCAATATTAAGAAAGAGCAGTCTTAAAGCAAATAGAAGTCCATTTTCT
* * * * *
81544 GATATTTTTAAATAAATAAATATCTTATTTTTTAAAATTATATATAATAATCTATTTTTATATAA
66 GATATTTCTAAATAAATAAATATCTTATTTTATAAAATTATATATAATAATATATATATATATAA
* *
81609 ATGTTTTAT
131 ATGATATAT
** **
81618 TAATATTTATTTACTTTTT-ATATATTAAGAAAAGAGTTGTCTTAAAGCACCTAGAAGT-CATTT
1 TAATATTTATTTA-TTTTTCA-ATATTAAG-AAAGAGCAGTCTTAAAGCAAATAGAAGTCCATTT
*
81681 TCTGATATTTCTAAGTAAATAAATATCTTA-TTTAT-AAATATATATATATATATATATATATAT
63 TCTGATATTTCTAAATAAATAAATATCTTATTTTATAAAAT-TATATATA-ATA-ATATATATAT
*
81744 ATATATAT-ATATAT
125 ATATAAATGATATAT
81758 TA
1 TA
81760 TATGTTTTTA
Statistics
Matches: 120, Mismatches: 16, Indels: 11
0.82 0.11 0.07
Matches are distributed among these distances:
138 4 0.03
139 26 0.22
140 55 0.46
141 35 0.29
ACGTcount: A:0.40, C:0.06, G:0.07, T:0.47
Consensus pattern (139 bp):
TAATATTTATTTATTTTTCAATATTAAGAAAGAGCAGTCTTAAAGCAAATAGAAGTCCATTTTCT
GATATTTCTAAATAAATAAATATCTTATTTTATAAAATTATATATAATAATATATATATATATAA
ATGATATAT
Found at i:81813 original size:34 final size:32
Alignment explanation
Indices: 81740--81813 Score: 105
Period size: 32 Copynumber: 2.2 Consensus size: 32
81730 ATATATATAT
*
81740 ATATATATATATATATATTATATGTTTTTATA
1 ATATATATATATATATATTATATGTTTTTAAA
81772 ATATATATATATATATATTAATATGGTTTCTTAAA
1 ATATATATATATATATATT-ATAT-GTTT-TTAAA
81807 AT-TATAT
1 ATATATAT
81814 TAATAAATTT
Statistics
Matches: 38, Mismatches: 1, Indels: 4
0.88 0.02 0.09
Matches are distributed among these distances:
32 19 0.50
33 4 0.11
34 9 0.24
35 6 0.16
ACGTcount: A:0.42, C:0.01, G:0.04, T:0.53
Consensus pattern (32 bp):
ATATATATATATATATATTATATGTTTTTAAA
Found at i:84047 original size:7 final size:7
Alignment explanation
Indices: 84005--84037 Score: 59
Period size: 7 Copynumber: 4.9 Consensus size: 7
83995 CATATATTTA
84005 CATTTT-
1 CATTTTG
84011 CATTTTG
1 CATTTTG
84018 CATTTTG
1 CATTTTG
84025 CATTTTG
1 CATTTTG
84032 CATTTT
1 CATTTT
84038 TTTCATTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 6 0.23
7 20 0.77
ACGTcount: A:0.15, C:0.15, G:0.09, T:0.61
Consensus pattern (7 bp):
CATTTTG
Found at i:91517 original size:22 final size:22
Alignment explanation
Indices: 91491--91602 Score: 172
Period size: 22 Copynumber: 5.1 Consensus size: 22
91481 TACATCTACA
91491 CTCTTCAAAGATGATAGATTCT
1 CTCTTCAAAGATGATAGATTCT
*
91513 CTCTTCAAGGATGATAGATTCT
1 CTCTTCAAAGATGATAGATTCT
*
91535 CTCTCCAAAGATGATAGATTCT
1 CTCTTCAAAGATGATAGATTCT
91557 CTC-TCAAAAGATGATAGATTCT
1 CTCTTC-AAAGATGATAGATTCT
* *
91579 CTCTTTAAAGATGATAAATTCT
1 CTCTTCAAAGATGATAGATTCT
91601 CT
1 CT
91603 TTTTCAAATA
Statistics
Matches: 82, Mismatches: 6, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
21 1 0.01
22 80 0.98
23 1 0.01
ACGTcount: A:0.32, C:0.19, G:0.13, T:0.36
Consensus pattern (22 bp):
CTCTTCAAAGATGATAGATTCT
Found at i:92344 original size:46 final size:46
Alignment explanation
Indices: 92277--92867 Score: 937
Period size: 46 Copynumber: 12.9 Consensus size: 46
92267 CTATTTCCCA
*
92277 CATCTGTAAGCCCTTCAGTGCATGATGTTTTTC-AAAACCATCGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATG-TTTTCAAAAACCTTCGGGT
92323 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAAACCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAAACCTTCGGGT
* *
92369 CATCTGTAAGTCCTTCAGTGCATGATGTTATCAAAAACCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAAACCTTCGGGT
**
92415 CATCTGTAAGTTCTTCAGTGCATGATGTTTTCAAAAACCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAAACCTTCGGGT
*
92461 CATCTGTAAGCCCTTCAGTGCATGATGTTTTTC-AAAACCTTTGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATG-TTTTCAAAAACCTTCGGGT
*
92507 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAAACCTTCAGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAAACCTTCGGGT
* * * *
92553 CATCTGTAAGTCCTTTAGTGCATGATGTTATCAAAAACCTCCGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAAACCTTCGGGT
92599 CATCTGTAAGCCCTTCAGTGCATGATGTTTTTC-AAAACCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATG-TTTTCAAAAACCTTCGGGT
* *
92645 CATCTGTAAGTCCTTCAGTGCATGATGTTATCAAAAACCTTC-GGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAAACCTTCGGGT
* *
92690 CATCTGTAAGTCCTTCAGTGCATGATGTTATCAAAAAACCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTC-AAAAACCTTCGGGT
92737 CATCTGTAAGCCCTTCAGTGCATGATGTTTTC-AAAACCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAAACCTTCGGGT
92782 CATCTGTAAGCCCTTCAGTGCATGATGTTTTC-AAAACCTTC-GGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAAACCTTCGGGT
* *
92826 CATTTGTAAGCCCTTCAGTGCATGATGTTTT-TAAAACCTTCG
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAAACCTTCG
92868 AGAGCTTTTT
Statistics
Matches: 512, Mismatches: 24, Indels: 19
0.92 0.04 0.03
Matches are distributed among these distances:
44 42 0.08
45 103 0.20
46 325 0.63
47 42 0.08
ACGTcount: A:0.24, C:0.23, G:0.19, T:0.34
Consensus pattern (46 bp):
CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAAACCTTCGGGT
Found at i:92865 original size:25 final size:25
Alignment explanation
Indices: 92793--92866 Score: 61
Period size: 25 Copynumber: 3.2 Consensus size: 25
92783 ATCTGTAAGC
*
92793 CCTTCAGTGCATGATGTTTTCAAAA
1 CCTTCAGTGCATGATGTTTTTAAAA
* * **
92818 CCTTC-G-G--TCA--TTTGTAAGC
1 CCTTCAGTGCATGATGTTTTTAAAA
92837 CCTTCAGTGCATGATGTTTTTAAAA
1 CCTTCAGTGCATGATGTTTTTAAAA
92862 CCTTC
1 CCTTC
92867 GAGAGCTTTT
Statistics
Matches: 34, Mismatches: 9, Indels: 12
0.62 0.16 0.22
Matches are distributed among these distances:
19 10 0.29
20 1 0.03
21 3 0.09
23 3 0.09
24 1 0.03
25 16 0.47
ACGTcount: A:0.23, C:0.23, G:0.16, T:0.38
Consensus pattern (25 bp):
CCTTCAGTGCATGATGTTTTTAAAA
Found at i:93109 original size:3 final size:3
Alignment explanation
Indices: 93101--93170 Score: 122
Period size: 3 Copynumber: 23.0 Consensus size: 3
93091 CAGTTTGTTT
*
93101 TTA TTA TTA TTA TTA TTA TTA TTA TTA TACA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA
93147 TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA
93171 AATAAATATT
Statistics
Matches: 64, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
3 62 0.97
4 2 0.03
ACGTcount: A:0.34, C:0.01, G:0.00, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:94788 original size:26 final size:25
Alignment explanation
Indices: 94728--94790 Score: 65
Period size: 26 Copynumber: 2.4 Consensus size: 25
94718 TTTTCTAATA
*
94728 TTTTTAAATAAATAAATATCTTATT
1 TTTTTAATTAAATAAATATCTTATT
* *
94753 TTTTAAAATTATATATAATAATC-TATT
1 TTTT-TAATTAAATA-AAT-ATCTTATT
94780 TTTTTAATTAA
1 TTTTTAATTAA
94791 TTATTTTTAT
Statistics
Matches: 30, Mismatches: 5, Indels: 5
0.75 0.12 0.12
Matches are distributed among these distances:
25 4 0.13
26 12 0.40
27 11 0.37
28 3 0.10
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.54
Consensus pattern (25 bp):
TTTTTAATTAAATAAATATCTTATT
Found at i:97169 original size:21 final size:21
Alignment explanation
Indices: 97143--97185 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
97133 TCCGAAGTTA
*
97143 CTGTAGCAGGGTATCGGTACC
1 CTGTAGCAGGGTATCGATACC
97164 CTGTAGCAGGGTATCGATACC
1 CTGTAGCAGGGTATCGATACC
97185 C
1 C
97186 CTGAAGCAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.21, C:0.26, G:0.30, T:0.23
Consensus pattern (21 bp):
CTGTAGCAGGGTATCGATACC
Found at i:97193 original size:22 final size:21
Alignment explanation
Indices: 97147--97193 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
97137 AAGTTACTGT
* *
97147 AGCAGGGTATCGGTACCCTGT
1 AGCAGGGTATCGATACCCTGA
97168 AGCAGGGTATCGATACCCCTGA
1 AGCAGGGTATCGATA-CCCTGA
97190 AGCA
1 AGCA
97194 ATCTGGAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 14 0.61
22 9 0.39
ACGTcount: A:0.26, C:0.26, G:0.30, T:0.19
Consensus pattern (21 bp):
AGCAGGGTATCGATACCCTGA
Found at i:104441 original size:21 final size:22
Alignment explanation
Indices: 104399--104443 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 22
104389 TGTTAAGTAT
* * *
104399 TTTTTACTTTAACATTAGAATA
1 TTTTTACTCTAACAATAAAATA
104421 TTTTTACTCTAA-AATAAAATA
1 TTTTTACTCTAACAATAAAATA
104442 TT
1 TT
104444 GAGAGTTAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 9 0.45
22 11 0.55
ACGTcount: A:0.40, C:0.09, G:0.02, T:0.49
Consensus pattern (22 bp):
TTTTTACTCTAACAATAAAATA
Found at i:104544 original size:60 final size:60
Alignment explanation
Indices: 104472--104606 Score: 155
Period size: 60 Copynumber: 2.2 Consensus size: 60
104462 AAAGTTTTAG
* * * * * *
104472 AGTTACAAAATAGTCCCCTAATTATATGATAA-TATTTTATTGAGTCTCTTGATTATTAAA
1 AGTTACAAAATAGTCCCCTAACTATA-GAGAATTACTTTATTCAGTCCCTTGACTATTAAA
* ** *
104532 AGTTACAAAATAGTCCTCTGGCTATAGAGAATTACTTTGTTCAGTCCCTTGACTATTAAA
1 AGTTACAAAATAGTCCCCTAACTATAGAGAATTACTTTATTCAGTCCCTTGACTATTAAA
*
104592 AGTTATAAAATAGTC
1 AGTTACAAAATAGTC
104607 ACTCGACTAT
Statistics
Matches: 63, Mismatches: 11, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
59 4 0.06
60 59 0.94
ACGTcount: A:0.36, C:0.14, G:0.13, T:0.38
Consensus pattern (60 bp):
AGTTACAAAATAGTCCCCTAACTATAGAGAATTACTTTATTCAGTCCCTTGACTATTAAA
Found at i:105518 original size:12 final size:12
Alignment explanation
Indices: 105470--105543 Score: 50
Period size: 12 Copynumber: 6.4 Consensus size: 12
105460 GAAATATTTT
105470 TTATAATAATTAA
1 TTATAATAA-TAA
* *
105483 TTAT-ATGAT-T
1 TTATAATAATAA
105493 TTAT-AT-ATAA
1 TTATAATAATAA
105503 -TATAATAATAA
1 TTATAATAATAA
*
105514 TTATAATCATAA
1 TTATAATAATAA
* *
105526 TCATAATCAATCA
1 TTATAAT-AATAA
105539 TTATA
1 TTATA
105544 TATATTAAAC
Statistics
Matches: 48, Mismatches: 8, Indels: 10
0.73 0.12 0.15
Matches are distributed among these distances:
9 5 0.10
10 8 0.17
11 5 0.10
12 19 0.40
13 11 0.23
ACGTcount: A:0.49, C:0.05, G:0.01, T:0.45
Consensus pattern (12 bp):
TTATAATAATAA
Found at i:106091 original size:20 final size:20
Alignment explanation
Indices: 106066--106103 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
106056 TGTAAATCGC
* *
106066 AACACATAAGTTAAATTCGT
1 AACACAGAAGTCAAATTCGT
106086 AACACAGAAGTCAAATTC
1 AACACAGAAGTCAAATTC
106104 ACAAAGCGCG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.47, C:0.18, G:0.11, T:0.24
Consensus pattern (20 bp):
AACACAGAAGTCAAATTCGT
Found at i:106287 original size:22 final size:22
Alignment explanation
Indices: 106262--106312 Score: 84
Period size: 22 Copynumber: 2.3 Consensus size: 22
106252 TCACTCTCTA
*
106262 CGGCGACATCCGTCCCCATCTC
1 CGGCGACATCCGTCCCCATATC
106284 CGGCGACATCCGTCCCCATATC
1 CGGCGACATCCGTCCCCATATC
*
106306 CGACGAC
1 CGGCGAC
106313 CCTCCTCTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.18, C:0.47, G:0.20, T:0.16
Consensus pattern (22 bp):
CGGCGACATCCGTCCCCATATC
Found at i:106718 original size:20 final size:20
Alignment explanation
Indices: 106695--106750 Score: 78
Period size: 20 Copynumber: 2.8 Consensus size: 20
106685 CGATTTTAGC
106695 TTCGCGTTGCGAATTTCATT
1 TTCGCGTTGCGAATTTCATT
* *
106715 TTCGCATTGTGAATTTCATT
1 TTCGCGTTGCGAATTTCATT
106735 TTC-CTGTTGCGAATTT
1 TTCGC-GTTGCGAATTT
106751 AAGTTTCAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
19 1 0.03
20 30 0.97
ACGTcount: A:0.16, C:0.18, G:0.18, T:0.48
Consensus pattern (20 bp):
TTCGCGTTGCGAATTTCATT
Found at i:108418 original size:20 final size:21
Alignment explanation
Indices: 108373--108421 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
108363 GTTAGGGGAG
*
108373 TTACGTGATGAGGTCAGAGTT
1 TTACGTGATGAGGTCAGAGCT
108394 TTACGTGATGAGGTC-GTA-CT
1 TTACGTGATGAGGTCAG-AGCT
108414 TTACGTGA
1 TTACGTGA
108422 CGAAAATGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
20 10 0.38
21 16 0.62
ACGTcount: A:0.22, C:0.12, G:0.31, T:0.35
Consensus pattern (21 bp):
TTACGTGATGAGGTCAGAGCT
Found at i:108480 original size:20 final size:20
Alignment explanation
Indices: 108455--108507 Score: 61
Period size: 21 Copynumber: 2.6 Consensus size: 20
108445 AAGTATGGTC
*
108455 TTTACGTGGTGATATGATGT
1 TTTACGTGGTGAAATGATGT
* * *
108475 TTTACGCGATGAAAATTATGT
1 TTTACGTGGTG-AAATGATGT
108496 TTTACGTGGTGA
1 TTTACGTGGTGA
108508 GGTATCTACT
Statistics
Matches: 26, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
20 10 0.38
21 16 0.62
ACGTcount: A:0.25, C:0.08, G:0.26, T:0.42
Consensus pattern (20 bp):
TTTACGTGGTGAAATGATGT
Done.