Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007819.1 Hibiscus syriacus cultivar Beakdansim tig00110156_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: 3855360
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2745 characters in sequence are not A, C, G, or T
File 1 of 17
Found at i:3065 original size:15 final size:16
Alignment explanation
Indices: 3037--3068 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
3027 AAAATCTTTC
3037 TTTCCCGTTCTGGATT
1 TTTCCCGTTCTGGATT
3053 TTTCCCG-TCTGGATT
1 TTTCCCGTTCTGGATT
3068 T
1 T
3069 GGATCTGCCA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.06, C:0.25, G:0.19, T:0.50
Consensus pattern (16 bp):
TTTCCCGTTCTGGATT
Found at i:3836 original size:16 final size:16
Alignment explanation
Indices: 3812--3845 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
3802 TATCGCCGAC
*
3812 CGAATTTCACTATTCA
1 CGAAATTCACTATTCA
3828 CGAAATTCACTATTCA
1 CGAAATTCACTATTCA
3844 CG
1 CG
3846 TGAATAGTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.32, C:0.26, G:0.09, T:0.32
Consensus pattern (16 bp):
CGAAATTCACTATTCA
Found at i:6387 original size:81 final size:79
Alignment explanation
Indices: 6209--6496 Score: 238
Period size: 81 Copynumber: 3.6 Consensus size: 79
6199 ACAAACACTG
* * * *
6209 CAATAGAGTAGTACTTTAGTAGCATTTTTATATAAACGCCGCAATAGGTACATGTAGTGGCGTTT
1 CAATAGAGTAGTACTTTAGTGGCATTTTTATACAAACGCCGCAATAGGTACATATAGTGGCATTT
*
6274 TTCCATAAACGCCA
66 TTCCACAAACGCCA
* * * * *
6288 CAACAGAGTAGTACTTTAGCGGCATCTTTATACAAACTCCGCAATAGGTCCATCTATAGTGGCAT
1 CAATAGAGTAGTACTTTAGTGGCATTTTTATACAAACGCCGCAATAGGTACA--TATAGTGGCAT
**
6353 TTTTTGACAAACGCCA
64 TTTTCCACAAACGCCA
* * * * * * ** * *
6369 TAATAGATTAGTATTTTAGTGGCATTTTTATAAAAATGTCATAATAGGGTTCACCTATAGTGGCT
1 CAATAGAGTAGTACTTTAGTGGCATTTTTATACAAACGCCGCAATA-GG-T-ACATATAGTGGCA
* * *
6434 TTTTTCAATC-AATGTCA
63 TTTTTCCA-CAAACGCCA
* * * *
6451 CAACAGATTA-TAACTTTAGCGGCATTTTTACACAAACGCCGCAATA
1 CAATAGAGTAGT-ACTTTAGTGGCATTTTTATACAAACGCCGCAATA
6497 TTTGATAATT
Statistics
Matches: 161, Mismatches: 41, Indels: 11
0.76 0.19 0.05
Matches are distributed among these distances:
79 45 0.28
81 57 0.35
82 56 0.35
83 2 0.01
84 1 0.01
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Consensus pattern (79 bp):
CAATAGAGTAGTACTTTAGTGGCATTTTTATACAAACGCCGCAATAGGTACATATAGTGGCATTT
TTCCACAAACGCCA
Found at i:9812 original size:42 final size:42
Alignment explanation
Indices: 9745--10041 Score: 258
Period size: 42 Copynumber: 7.0 Consensus size: 42
9735 TAATTAGCGG
*
9745 CGTTTGTATCCAAAAACGCCGCTATAGATCTGACCTTTTGTGA
1 CGTTTGT-TCCAAAAACGCCGCTATAGATCTGACCTTTTGCGA
* * * * * *
9788 CATTTTTTCCAAAAACGTCGCTATATATCTTGACATTTTTC-A
1 CGTTTGTTCCAAAAACGCCGCTATAGATC-TGACCTTTTGCGA
* * * * *
9830 GCGTTTGTTTCAAAAATGCCGCTATAGATATCGA-TTTTTGCGG
1 -CGTTTGTTCCAAAAACGCCGCTATAGATCT-GACCTTTTGCGA
* * * *
9873 CGTTTGTTCCAAAAACGCCGCTATAGATATCGATCTTTTACGG
1 CGTTTGTTCCAAAAACGCCGCTATAGATCT-GACCTTTTGCGA
* * * * *
9916 TGTTTGTTCTAAAAAATGTCGTTATAGATCTGACCTTTTGCGA
1 CGTTTGTTC-CAAAAACGCCGCTATAGATCTGACCTTTTGCGA
* * *
9959 CGTTTGTTCAAAAAACGCCGCTATAGATCTCAACCTTTTGCGG
1 CGTTTGTTCCAAAAACGCCGCTATAGATCT-GACCTTTTGCGA
* * * *
10002 CGTTTGTT-CAAAAAAGTCGCTATATATCTAACCTTTTGCG
1 CGTTTGTTCCAAAAACGCCGCTATAGATCTGACCTTTTGCG
10042 GCATTATATA
Statistics
Matches: 207, Mismatches: 40, Indels: 16
0.79 0.15 0.06
Matches are distributed among these distances:
41 11 0.05
42 93 0.45
43 87 0.42
44 16 0.08
ACGTcount: A:0.26, C:0.21, G:0.17, T:0.36
Consensus pattern (42 bp):
CGTTTGTTCCAAAAACGCCGCTATAGATCTGACCTTTTGCGA
Found at i:9967 original size:86 final size:85
Alignment explanation
Indices: 9742--10041 Score: 304
Period size: 86 Copynumber: 3.5 Consensus size: 85
9732 AGGTAATTAG
* * * * * * *
9742 CGGCGTTTGTATC-CAAAAACGCCGCTATAGATCTGACCTTTTGTGACATTTTTTCCAAAAACGT
1 CGGCGTTTGT-TCTAAAAAATGTCGCTATAGATCTGACCTTTTGCGACGTTTGTTCCAAAAACGC
* * *
9806 CGCTATATATCTTGACATTTTT
65 CGCTATAGATCTCGAC-TTTTA
* * * * * *
9828 CAGCGTTTGTT-TCAAAAATGCCGCTATAGATATCGA-TTTTTGCGGCGTTTGTTCCAAAAACGC
1 CGGCGTTTGTTCTAAAAAATGTCGCTATAGATCT-GACCTTTTGCGACGTTTGTTCCAAAAACGC
*
9891 CGCTATAGATATCGATCTTTTA
65 CGCTATAGATCTCGA-CTTTTA
* * *
9913 CGGTGTTTGTTCTAAAAAATGTCGTTATAGATCTGACCTTTTGCGACGTTTGTTCAAAAAACGCC
1 CGGCGTTTGTTCTAAAAAATGTCGCTATAGATCTGACCTTTTGCGACGTTTGTTCCAAAAACGCC
* *
9978 GCTATAGATCTCAACCTTTTG
66 GCTATAGATCTCGA-CTTTTA
* *
9999 CGGCGTTTGTTC-AAAAAA-GTCGCTATATATCTAACCTTTTGCG
1 CGGCGTTTGTTCTAAAAAATGTCGCTATAGATCTGACCTTTTGCG
10042 GCATTATATA
Statistics
Matches: 179, Mismatches: 30, Indels: 12
0.81 0.14 0.05
Matches are distributed among these distances:
84 22 0.12
85 74 0.41
86 83 0.46
ACGTcount: A:0.26, C:0.21, G:0.18, T:0.36
Consensus pattern (85 bp):
CGGCGTTTGTTCTAAAAAATGTCGCTATAGATCTGACCTTTTGCGACGTTTGTTCCAAAAACGCC
GCTATAGATCTCGACTTTTA
Found at i:10138 original size:43 final size:43
Alignment explanation
Indices: 10070--10183 Score: 138
Period size: 43 Copynumber: 2.6 Consensus size: 43
10060 TTTTGCGGCG
* * * **
10070 TTTGTTCCAAAAAAACGCTGCTATAGATATCGATTTTTTACGGGT
1 TTTGTTCCAAAAACAC-C-GCTATAGATATCGATCTTTTACAGCA
* *
10115 TTTGTTCCAAAAACCCCGCTATAGATATCGATCTTTTGCAGCA
1 TTTGTTCCAAAAACACCGCTATAGATATCGATCTTTTACAGCA
*
10158 TTTGTTCCAAAAACATCGCTATAGAT
1 TTTGTTCCAAAAACACCGCTATAGAT
10184 CTTAACATAT
Statistics
Matches: 60, Mismatches: 9, Indels: 2
0.85 0.13 0.03
Matches are distributed among these distances:
43 45 0.75
44 1 0.02
45 14 0.23
ACGTcount: A:0.30, C:0.20, G:0.15, T:0.35
Consensus pattern (43 bp):
TTTGTTCCAAAAACACCGCTATAGATATCGATCTTTTACAGCA
Found at i:13938 original size:2 final size:2
Alignment explanation
Indices: 13931--13988 Score: 116
Period size: 2 Copynumber: 29.0 Consensus size: 2
13921 TACTTTCATA
13931 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
13973 AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT
13989 CTACTTTTAT
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 56 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:21721 original size:111 final size:111
Alignment explanation
Indices: 21588--21807 Score: 413
Period size: 111 Copynumber: 2.0 Consensus size: 111
21578 AATAATTACA
21588 AATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTAAA
1 AATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTAAA
* *
21653 TTAAAACGTTAAACTGTTACCGTATCAGCAAAGTGTCGAGATATTT
66 TTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTAGAGATATTT
21699 AATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTAAA
1 AATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTAAA
*
21764 TTAAAACGTTAAAATGTTATCGTATCAGCAAAGTGTAGAGATAT
66 TTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTAGAGATAT
21808 ATGATTTTCA
Statistics
Matches: 106, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
111 106 1.00
ACGTcount: A:0.45, C:0.11, G:0.08, T:0.36
Consensus pattern (111 bp):
AATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTAAA
TTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTAGAGATATTT
Found at i:21912 original size:17 final size:18
Alignment explanation
Indices: 21869--21909 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
21859 GAATTATATT
21869 AGTAAAATA-TTAAATAA
1 AGTAAAATACTTAAATAA
21886 AGTAAAATACTTAAATAA
1 AGTAAAATACTTAAATAA
*
21904 ATTAAA
1 AGTAAA
21910 TACATAATAG
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 9 0.41
18 13 0.59
ACGTcount: A:0.63, C:0.02, G:0.05, T:0.29
Consensus pattern (18 bp):
AGTAAAATACTTAAATAA
Found at i:22168 original size:50 final size:49
Alignment explanation
Indices: 22114--22222 Score: 119
Period size: 49 Copynumber: 2.2 Consensus size: 49
22104 AGATACCCAG
* * * * **
22114 GTATAGCGCGAATCAGGGGGCGCGCTATACTCACATGGCGCCAAATCATT
1 GTATAGCGCGAAGCA-GGGGAGCGCTATACCCACATGACGCCAAATCAGC
* * * *
22164 GTATATCACGAGGCAGGGGAGCGCTATACCCACGTGACGCCAAATCAGC
1 GTATAGCGCGAAGCAGGGGAGCGCTATACCCACATGACGCCAAATCAGC
22213 GTATAGCGCG
1 GTATAGCGCG
22223 GTTCAGGACG
Statistics
Matches: 47, Mismatches: 12, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
49 36 0.77
50 11 0.23
ACGTcount: A:0.27, C:0.27, G:0.29, T:0.17
Consensus pattern (49 bp):
GTATAGCGCGAAGCAGGGGAGCGCTATACCCACATGACGCCAAATCAGC
Found at i:22294 original size:29 final size:29
Alignment explanation
Indices: 22252--22328 Score: 129
Period size: 29 Copynumber: 2.7 Consensus size: 29
22242 CTGCTACGGG
*
22252 TGTTAGATCGGAGAATATAATCTTACTGA
1 TGTTAGATCGGAGAATATAATCTGACTGA
22281 TGTTAGATCGGAGAATATAATCTGACTGA
1 TGTTAGATCGGAGAATATAATCTGACTGA
22310 TGTTAGATCGGTA-AATATA
1 TGTTAGATCGG-AGAATATA
22329 CCGATCACTG
Statistics
Matches: 46, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
29 45 0.98
30 1 0.02
ACGTcount: A:0.35, C:0.09, G:0.22, T:0.34
Consensus pattern (29 bp):
TGTTAGATCGGAGAATATAATCTGACTGA
Found at i:23337 original size:15 final size:16
Alignment explanation
Indices: 23317--23358 Score: 59
Period size: 15 Copynumber: 2.7 Consensus size: 16
23307 ACTATTTTAA
23317 ATATTTTAAAAAAT-T
1 ATATTTTAAAAAATAT
*
23332 ATATTTTATAAAATAT
1 ATATTTTAAAAAATAT
*
23348 ATACTTTAAAA
1 ATATTTTAAAA
23359 TCACTTGATT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
15 13 0.57
16 10 0.43
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (16 bp):
ATATTTTAAAAAATAT
Found at i:23603 original size:15 final size:15
Alignment explanation
Indices: 23583--23611 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
23573 AAGTAGTTTA
23583 TCTAATTTTATAATG
1 TCTAATTTTATAATG
23598 TCTAATTTTATAAT
1 TCTAATTTTATAAT
23612 TTTTTTTTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.34, C:0.07, G:0.03, T:0.55
Consensus pattern (15 bp):
TCTAATTTTATAATG
Found at i:23812 original size:22 final size:23
Alignment explanation
Indices: 23770--23814 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
23760 ATAATATTTT
*
23770 TTAATATTTCTAATCAGTTGATG
1 TTAATATTTCTAATCAATTGATG
*
23793 TTAATCTTTC-AATCAATTGATG
1 TTAATATTTCTAATCAATTGATG
23815 ATGTTCAGAC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 11 0.55
23 9 0.45
ACGTcount: A:0.31, C:0.11, G:0.11, T:0.47
Consensus pattern (23 bp):
TTAATATTTCTAATCAATTGATG
Found at i:25405 original size:17 final size:17
Alignment explanation
Indices: 25383--25435 Score: 79
Period size: 17 Copynumber: 3.1 Consensus size: 17
25373 AATTAAAATT
25383 TAGTTTAATAAATGAAC
1 TAGTTTAATAAATGAAC
* *
25400 TAGTTTGATGAATGAAC
1 TAGTTTAATAAATGAAC
*
25417 TAGTTTAATTAATGAAC
1 TAGTTTAATAAATGAAC
25434 TA
1 TA
25436 ACTTTGTTAA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 32 1.00
ACGTcount: A:0.42, C:0.06, G:0.15, T:0.38
Consensus pattern (17 bp):
TAGTTTAATAAATGAAC
Found at i:25482 original size:17 final size:17
Alignment explanation
Indices: 25441--25487 Score: 58
Period size: 17 Copynumber: 2.8 Consensus size: 17
25431 AACTAACTTT
25441 GTTAAATGAAATGCATA
1 GTTAAATGAAATGCATA
* *
25458 GCTGAATGAAATGCATA
1 GTTAAATGAAATGCATA
* *
25475 TTTAAATGCAATG
1 GTTAAATGAAATG
25488 AATGCTTTAA
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.43, C:0.09, G:0.19, T:0.30
Consensus pattern (17 bp):
GTTAAATGAAATGCATA
Found at i:30043 original size:11 final size:12
Alignment explanation
Indices: 30027--30055 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
30017 GACACTTTAA
30027 TATTAT-GATTT
1 TATTATGGATTT
30038 TATTATGGATTT
1 TATTATGGATTT
30050 TATTAT
1 TATTAT
30056 TATGAGTTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 6 0.35
12 11 0.65
ACGTcount: A:0.28, C:0.00, G:0.10, T:0.62
Consensus pattern (12 bp):
TATTATGGATTT
Found at i:30089 original size:74 final size:74
Alignment explanation
Indices: 29988--30125 Score: 224
Period size: 74 Copynumber: 1.9 Consensus size: 74
29978 TTTTCTAGAC
*
29988 TTAATATTATGGTTTGAGTCTTAAAATTTGACACTTTAATATTATGATTT-TATTATGGATTTTA
1 TTAATATTATGGTTTGAATCTTAAAATTTGACACTTTAATATTATGATTTGT-TTATGGATTTTA
30052 TTATTATGAG
65 TTATTATGAG
* * *
30062 TTAATATTATGGTTTGAATCTTGAAATTTGACATTTTAATATTATGGTTTGTTTATGGATTTTA
1 TTAATATTATGGTTTGAATCTTAAAATTTGACACTTTAATATTATGATTTGTTTATGGATTTTA
30126 CTGTTCTAAA
Statistics
Matches: 59, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
74 58 0.98
75 1 0.02
ACGTcount: A:0.30, C:0.04, G:0.14, T:0.52
Consensus pattern (74 bp):
TTAATATTATGGTTTGAATCTTAAAATTTGACACTTTAATATTATGATTTGTTTATGGATTTTAT
TATTATGAG
Found at i:42461 original size:18 final size:18
Alignment explanation
Indices: 42440--42487 Score: 62
Period size: 18 Copynumber: 2.6 Consensus size: 18
42430 GTTGTTTTTA
42440 AAATAAAAAATAACAATT
1 AAATAAAAAATAACAATT
*
42458 AAATAAAAGAA-GACAATT
1 AAATAAAA-AATAACAATT
42476 AAATAAATAAAT
1 AAATAAA-AAAT
42488 TAAAGAGTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
18 23 0.88
19 3 0.12
ACGTcount: A:0.71, C:0.04, G:0.04, T:0.21
Consensus pattern (18 bp):
AAATAAAAAATAACAATT
Found at i:43047 original size:12 final size:12
Alignment explanation
Indices: 43032--43058 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
43022 AAATAATAAT
43032 AATAATATTTTA
1 AATAATATTTTA
43044 AATAATATTTTA
1 AATAATATTTTA
43056 AAT
1 AAT
43059 CCTAATTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (12 bp):
AATAATATTTTA
Found at i:43116 original size:77 final size:77
Alignment explanation
Indices: 42973--43192 Score: 279
Period size: 76 Copynumber: 2.9 Consensus size: 77
42963 AAGCTAAAAC
* * *
42973 ATCTTAAATCCTAATTTAAACACTTAAAA-CTATTTAAACTAAAATACCTAAATA-ATA-ATAAT
1 ATCTTAAATCCTAATTAAAATAC-TAAAACCTATTTAAACTAAAATACCTAAA-ACAAAGATAA-
**
43035 AATATTTTAAATAAT
63 AATATTAAAAATAAT
*
43050 ATTTTAAATCCTAATTAAAATA-TGAAAACCTATTTAAACTAAAATACCTAAAACAAAGATAAAA
1 ATCTTAAATCCTAATTAAAATACT-AAAACCTATTTAAACTAAAATACCTAAAACAAAGATAAAA
43114 TA-TAAAAATAAT
65 TATTAAAAATAAT
* * * *
43126 ATCCTAAAACTTAATTAAAATACTAAAACTTATTTAAACTAAAATACCTAAAACAAAGATAAAAT
1 ATCTTAAATCCTAATTAAAATACTAAAACCTATTTAAACTAAAATACCTAAAACAAAGATAAAAT
43191 AT
66 AT
43193 AATGTATAAA
Statistics
Matches: 126, Mismatches: 11, Indels: 12
0.85 0.07 0.08
Matches are distributed among these distances:
75 1 0.01
76 72 0.57
77 49 0.39
78 4 0.03
ACGTcount: A:0.55, C:0.12, G:0.01, T:0.31
Consensus pattern (77 bp):
ATCTTAAATCCTAATTAAAATACTAAAACCTATTTAAACTAAAATACCTAAAACAAAGATAAAAT
ATTAAAAATAAT
Found at i:44201 original size:2 final size:2
Alignment explanation
Indices: 44174--44226 Score: 62
Period size: 2 Copynumber: 29.0 Consensus size: 2
44164 AATAATTCAT
*
44174 TA TA T- TA TA T- TA TA T- TA TA T- TA TA TA TA TA CA 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
44212 TA TA TA TA TA -A TA TA
1 TA TA TA TA TA TA TA TA
44227 AAAAAATAAA
Statistics
Matches: 44, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
1 5 0.11
2 39 0.89
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:44208 original size:6 final size:6
Alignment explanation
Indices: 44174--44226 Score: 62
Period size: 5 Copynumber: 9.7 Consensus size: 6
44164 AATAATTCAT
*
44174 TATAT- TATAT- TATAT- TATAT- TATATA TATACA TATATA TATATA
1 TATATA TATATA TATATA TATATA TATATA TATATA TATATA TATATA
44218 TATA-A TATA
1 TATATA TATA
44227 AAAAAATAAA
Statistics
Matches: 45, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
5 25 0.56
6 20 0.44
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (6 bp):
TATATA
Found at i:50308 original size:31 final size:30
Alignment explanation
Indices: 50273--50339 Score: 82
Period size: 31 Copynumber: 2.2 Consensus size: 30
50263 ATTCATTTTT
50273 TTAAAA-TCAATAAAAATGCAATAAAAAAGAA
1 TTAAAAGTCAAT-AAAATGCAAT-AAAAAGAA
* *
50304 TTAAAAGTGAATAAAATTCAATAAAAAGAA
1 TTAAAAGTCAATAAAATGCAATAAAAAGAA
50334 TGTAAA
1 T-TAAA
50340 GCTAAAAAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
30 9 0.28
31 19 0.59
32 4 0.12
ACGTcount: A:0.64, C:0.04, G:0.09, T:0.22
Consensus pattern (30 bp):
TTAAAAGTCAATAAAATGCAATAAAAAGAA
Found at i:50330 original size:21 final size:21
Alignment explanation
Indices: 50274--50331 Score: 57
Period size: 21 Copynumber: 2.8 Consensus size: 21
50264 TTCATTTTTT
50274 TAAAATCAATAAAAA-TGCAA
1 TAAAATCAATAAAAAGTGCAA
** *
50294 TAAAAAAGAATTAAAAGTG-AA
1 T-AAAATCAATAAAAAGTGCAA
50315 TAAAATTCAATAAAAAG
1 TAAAA-TCAATAAAAAG
50332 AATGTAAAGC
Statistics
Matches: 29, Mismatches: 6, Indels: 5
0.73 0.15 0.12
Matches are distributed among these distances:
20 5 0.17
21 22 0.76
22 2 0.07
ACGTcount: A:0.66, C:0.05, G:0.09, T:0.21
Consensus pattern (21 bp):
TAAAATCAATAAAAAGTGCAA
Found at i:50939 original size:338 final size:341
Alignment explanation
Indices: 50403--51084 Score: 1119
Period size: 342 Copynumber: 2.0 Consensus size: 341
50393 TATTAAATTC
* * * * * *
50403 TAATTTTATTAAAAATGAATAAACATTATTAATTGTTTTTAAAAAATAATAATTAATGAATAATA
1 TAATTTTATTAAAAATGAAAAAAAATTATTAACTATTGTTAAAAAATAATAATTAATAAATAATA
*
50468 ATTTATTTGATCCTAAATTGTAATTAAAAGTTTATTTTAATATTTTTTTTATATTTTTAAACAAT
66 ATTCATTTGATCCTAAATTGTAATTAAAAGTTTATTTTAATA-TTTTTTTATATTTTTAAACAAT
50533 TAATTTTAAAAGTCAATAAATTTTTAAAAATATATGAAATTTATATATTTTTTAAATTATAAAAT
130 TAATTTTAAAAGTCAATAAATTTTTAAAAATATATGAAATTTATATATTTTTTAAATTATAAAAT
*
50598 ATTTATTAT-T-ATCATCATCATCATTTTGTAAAA-AAATACTTGTTATAAAACTTTTATAAAAT
195 ATTTATTATATCATCATCATCATCATTTTGTAAAAGAAATACTAGTTATAAAACTTTTATAAAAT
50660 TATTCATATTTTAAAATACTTACCCTCAAAGTTTTCCTATACTAGATTAAACGTATTGTGTAATT
260 TATTCATATTTTAAAATACTTACCCTCAAAGTTTTCCTATACTAGATTAAACGTATTGTGTAATT
50725 T-TATGCAAAAATCAAAA
325 TCT-TGCAAAAATCAAAA
50742 TAATTTTATT-AAAATGAAAAAAAAAATTATTAACTATTGTT-AAAAATAATAATTAATAAATAA
1 TAATTTTATTAAAAATG--AAAAAAAATTATTAACTATTGTTAAAAAATAATAATTAATAAATAA
*
50805 TAATTCATTTGATCCCTTAATTGTAATTAAAAGTTTATTTTAATA-TTTTTTATATTTTTAAACA
64 TAATTCATTTGAT-CCTAAATTGTAATTAAAAGTTTATTTTAATATTTTTTTATATTTTTAAACA
50869 ATTAATTTTAAAAGTCAATAAATTTTTCAAAAATATATGAAATTTATA-ATTTTTTAAATTATAA
128 ATTAATTTTAAAAGTCAATAAATTTTT-AAAAATATATGAAATTTATATATTTTTTAAATTATAA
*
50933 AATATTTATTATCATCATCATCGTCATCATTTTGTAAAAGAAATACTAGTTATAAAACTTTTATA
192 AATATTTATTAT-ATCATCATCATCATCATTTTGTAAAAGAAATACTAGTTATAAAACTTTTATA
* * *
50998 AAATTATTCATATTTTAAAATACTTACTCTCAAAGTTTTCCTATACTAGATTATAGGTATTGTGT
256 AAATTATTCATATTTTAAAATACTTACCCTCAAAGTTTTCCTATACTAGATTAAACGTATTGTGT
*
51063 AATTTCTTTCAAAAATCAAAA
321 AATTTCTTGCAAAAATCAAAA
51084 T
1 T
51085 TTATCGAGTT
Statistics
Matches: 320, Mismatches: 14, Indels: 15
0.92 0.04 0.04
Matches are distributed among these distances:
338 80 0.25
339 63 0.20
340 49 0.15
341 22 0.07
342 105 0.33
343 1 0.00
ACGTcount: A:0.43, C:0.07, G:0.05, T:0.44
Consensus pattern (341 bp):
TAATTTTATTAAAAATGAAAAAAAATTATTAACTATTGTTAAAAAATAATAATTAATAAATAATA
ATTCATTTGATCCTAAATTGTAATTAAAAGTTTATTTTAATATTTTTTTATATTTTTAAACAATT
AATTTTAAAAGTCAATAAATTTTTAAAAATATATGAAATTTATATATTTTTTAAATTATAAAATA
TTTATTATATCATCATCATCATCATTTTGTAAAAGAAATACTAGTTATAAAACTTTTATAAAATT
ATTCATATTTTAAAATACTTACCCTCAAAGTTTTCCTATACTAGATTAAACGTATTGTGTAATTT
CTTGCAAAAATCAAAA
Found at i:62315 original size:20 final size:21
Alignment explanation
Indices: 62271--62310 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
62261 TCCCCTTTGA
*
62271 AGGGGAACCGATTCCCCCCAC
1 AGGGGAACCGATACCCCCCAC
*
62292 AGGGGAATCGATACCCCCC
1 AGGGGAACCGATACCCCCC
62311 TAGGGTTCTG
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:0.25, C:0.40, G:0.25, T:0.10
Consensus pattern (21 bp):
AGGGGAACCGATACCCCCCAC
Found at i:68507 original size:20 final size:21
Alignment explanation
Indices: 68479--68517 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
68469 TATATTTTCA
68479 AACAATTTG-TAACAATTGAT
1 AACAATTTGTTAACAATTGAT
*
68499 AACATTTTGTTAACAATTG
1 AACAATTTGTTAACAATTG
68518 GTATTTTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.41, C:0.10, G:0.10, T:0.38
Consensus pattern (21 bp):
AACAATTTGTTAACAATTGAT
Found at i:68776 original size:21 final size:22
Alignment explanation
Indices: 68750--68808 Score: 77
Period size: 23 Copynumber: 2.7 Consensus size: 22
68740 AGGTTGTCAA
*
68750 AGTGCATCCATGCACC-CCTGC-
1 AGTGCATCCATGCACCGCC-ACT
68771 AGTGCATCCATGCACCTGCCACT
1 AGTGCATCCATGCACC-GCCACT
68794 AGTGCATCCATGCAC
1 AGTGCATCCATGCAC
68809 TCCATTTCGA
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
21 16 0.47
22 1 0.03
23 17 0.50
ACGTcount: A:0.22, C:0.39, G:0.19, T:0.20
Consensus pattern (22 bp):
AGTGCATCCATGCACCGCCACT
Found at i:71986 original size:21 final size:21
Alignment explanation
Indices: 71960--71999 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
71950 AAACAATTGG
71960 TAACAATTGATATCATTTTGT
1 TAACAATTGATATCATTTTGT
* *
71981 TAACAATTGGTATCTTTTT
1 TAACAATTGATATCATTTT
72000 CATTAAACAT
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:0.30, C:0.10, G:0.10, T:0.50
Consensus pattern (21 bp):
TAACAATTGATATCATTTTGT
Found at i:74148 original size:22 final size:21
Alignment explanation
Indices: 74108--74156 Score: 55
Period size: 22 Copynumber: 2.3 Consensus size: 21
74098 CGAAATAATG
74108 ATAAAAATATATTTATAATATT
1 ATAAAAATATATTTATAAT-TT
*
74130 ATAAAAATAT-TTATTTAATTT
1 ATAAAAATATATT-TATAATTT
*
74151 TTAAAA
1 ATAAAA
74157 TCAAATTATT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 9 0.38
22 15 0.62
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (21 bp):
ATAAAAATATATTTATAATTT
Found at i:74341 original size:23 final size:23
Alignment explanation
Indices: 74303--74391 Score: 78
Period size: 23 Copynumber: 4.0 Consensus size: 23
74293 ATATATAATG
74303 TAAA-AAATAA-ATTATTTAAAA
1 TAAATAAATAATATTATTTAAAA
* **
74324 TAAATAATTAATATTATTTCGAA
1 TAAATAAATAATATTATTTAAAA
* * *
74347 TAAATAAATAATGTGATTTTAAA
1 TAAATAAATAATATTATTTAAAA
* *
74370 -AATTAAATAA-ATAATTTAAAA
1 TAAATAAATAATATTATTTAAAA
74391 T
1 T
74392 TATTTTATAA
Statistics
Matches: 53, Mismatches: 12, Indels: 5
0.76 0.17 0.07
Matches are distributed among these distances:
21 12 0.23
22 14 0.26
23 27 0.51
ACGTcount: A:0.57, C:0.01, G:0.03, T:0.38
Consensus pattern (23 bp):
TAAATAAATAATATTATTTAAAA
Found at i:75762 original size:2 final size:2
Alignment explanation
Indices: 75755--75783 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
75745 ATTAAATAGT
75755 TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
75784 AATCATATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:75868 original size:21 final size:21
Alignment explanation
Indices: 75833--75891 Score: 61
Period size: 21 Copynumber: 2.9 Consensus size: 21
75823 GTCTTTTTAC
*
75833 ATTTTA-AACTAATTTTAAT-
1 ATTTTATAATTAATTTTAATA
75852 ATTTTCATAATTAATTTT-ATA
1 ATTTT-ATAATTAATTTTAATA
* *
75873 ATTTTATATTTATTTTTAA
1 ATTTTATAATTAATTTTAA
75892 AAATATAAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
19 5 0.15
20 13 0.39
21 15 0.45
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.59
Consensus pattern (21 bp):
ATTTTATAATTAATTTTAATA
Found at i:85691 original size:14 final size:14
Alignment explanation
Indices: 85658--85696 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
85648 ACTTGAAAAA
*
85658 ATAAATATATATTAT
1 ATAAATTTA-ATTAT
85673 ATAAATTTAATTAT
1 ATAAATTTAATTAT
*
85687 TTAAATTTAA
1 ATAAATTTAA
85697 AATCCTTAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 14 0.64
15 8 0.36
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (14 bp):
ATAAATTTAATTAT
Found at i:86606 original size:7 final size:7
Alignment explanation
Indices: 86594--86622 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
86584 TTTCAATTTT
86594 TTTTTAA
1 TTTTTAA
86601 TTTTTAA
1 TTTTTAA
86608 TTTTTAA
1 TTTTTAA
86615 TTTTTAA
1 TTTTTAA
86622 T
1 T
86623 ATTATATATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (7 bp):
TTTTTAA
Found at i:87278 original size:2 final size:2
Alignment explanation
Indices: 87271--87297 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
87261 AGCAAAGCAA
87271 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
87298 ACCTAACTCC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:87816 original size:19 final size:19
Alignment explanation
Indices: 87792--87828 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
87782 AATCCTAACC
*
87792 ATTAGGCTATAATTTAGGA
1 ATTAGGCTATAACTTAGGA
87811 ATTAGGCTATAACTTAGG
1 ATTAGGCTATAACTTAGG
87829 CAACTAAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.35, C:0.08, G:0.22, T:0.35
Consensus pattern (19 bp):
ATTAGGCTATAACTTAGGA
Found at i:87889 original size:74 final size:74
Alignment explanation
Indices: 87805--87953 Score: 298
Period size: 74 Copynumber: 2.0 Consensus size: 74
87795 AGGCTATAAT
87805 TTAGGAATTAGGCTATAACTTAGGCAACTAAATATACAATAGTAAATACAAAATATTTGGAGAAT
1 TTAGGAATTAGGCTATAACTTAGGCAACTAAATATACAATAGTAAATACAAAATATTTGGAGAAT
87870 ATTTTGTAA
66 ATTTTGTAA
87879 TTAGGAATTAGGCTATAACTTAGGCAACTAAATATACAATAGTAAATACAAAATATTTGGAGAAT
1 TTAGGAATTAGGCTATAACTTAGGCAACTAAATATACAATAGTAAATACAAAATATTTGGAGAAT
87944 ATTTTGTAA
66 ATTTTGTAA
87953 T
1 T
87954 CTATCACTCC
Statistics
Matches: 75, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
74 75 1.00
ACGTcount: A:0.44, C:0.08, G:0.15, T:0.33
Consensus pattern (74 bp):
TTAGGAATTAGGCTATAACTTAGGCAACTAAATATACAATAGTAAATACAAAATATTTGGAGAAT
ATTTTGTAA
Found at i:92317 original size:19 final size:19
Alignment explanation
Indices: 92293--92329 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
92283 AATCCTAACC
*
92293 ATTAGGCTATAATTTAGGA
1 ATTAGGCTATAACTTAGGA
92312 ATTAGGCTATAACTTAGG
1 ATTAGGCTATAACTTAGG
92330 CAACTAAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.35, C:0.08, G:0.22, T:0.35
Consensus pattern (19 bp):
ATTAGGCTATAACTTAGGA
Found at i:92390 original size:74 final size:74
Alignment explanation
Indices: 92306--92454 Score: 298
Period size: 74 Copynumber: 2.0 Consensus size: 74
92296 AGGCTATAAT
92306 TTAGGAATTAGGCTATAACTTAGGCAACTAAATATACAATAGTAAATACAAAATATTTGGAGAAT
1 TTAGGAATTAGGCTATAACTTAGGCAACTAAATATACAATAGTAAATACAAAATATTTGGAGAAT
92371 ATTTTGTAA
66 ATTTTGTAA
92380 TTAGGAATTAGGCTATAACTTAGGCAACTAAATATACAATAGTAAATACAAAATATTTGGAGAAT
1 TTAGGAATTAGGCTATAACTTAGGCAACTAAATATACAATAGTAAATACAAAATATTTGGAGAAT
92445 ATTTTGTAA
66 ATTTTGTAA
92454 T
1 T
92455 CTATCATAAC
Statistics
Matches: 75, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
74 75 1.00
ACGTcount: A:0.44, C:0.08, G:0.15, T:0.33
Consensus pattern (74 bp):
TTAGGAATTAGGCTATAACTTAGGCAACTAAATATACAATAGTAAATACAAAATATTTGGAGAAT
ATTTTGTAA
Found at i:97822 original size:11 final size:11
Alignment explanation
Indices: 97806--97833 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
97796 TGTGGTGCAT
97806 ATATCACAATA
1 ATATCACAATA
97817 ATATCACAATA
1 ATATCACAATA
97828 ATATCA
1 ATATCA
97834 TATCTACCAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.54, C:0.18, G:0.00, T:0.29
Consensus pattern (11 bp):
ATATCACAATA
Found at i:102553 original size:14 final size:14
Alignment explanation
Indices: 102534--102569 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
102524 AGAAAATAGT
*
102534 AAATTAAAGTAATG
1 AAATTAAAGGAATG
*
102548 AAATTAAAGGACTG
1 AAATTAAAGGAATG
102562 AAATTAAA
1 AAATTAAA
102570 TAAATAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.58, C:0.03, G:0.14, T:0.25
Consensus pattern (14 bp):
AAATTAAAGGAATG
Found at i:102593 original size:29 final size:31
Alignment explanation
Indices: 102548--102615 Score: 79
Period size: 29 Copynumber: 2.3 Consensus size: 31
102538 TAAAGTAATG
102548 AAATTAAAGGACTGAAA-TTAAATAAATA-A
1 AAATTAAAGGACTGAAATTTAAATAAATATA
* *
102577 AAATTAAAGG-GTAGAAATTTAAATATATATA
1 AAATTAAAGGACT-GAAATTTAAATAAATATA
*
102608 TAATTAAA
1 AAATTAAA
102616 TAACAAAAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
28 1 0.03
29 14 0.42
30 10 0.30
31 8 0.24
ACGTcount: A:0.59, C:0.01, G:0.10, T:0.29
Consensus pattern (31 bp):
AAATTAAAGGACTGAAATTTAAATAAATATA
Found at i:103176 original size:21 final size:20
Alignment explanation
Indices: 103138--103176 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
103128 TTAATAAATA
* *
103138 AAATAAAATAACACATAACC
1 AAATAAAATAAAAAATAACC
103158 AAATAAACATAAAAAATAA
1 AAATAAA-ATAAAAAATAA
103177 AAATAGCGCA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 7 0.44
21 9 0.56
ACGTcount: A:0.72, C:0.13, G:0.00, T:0.15
Consensus pattern (20 bp):
AAATAAAATAAAAAATAACC
Found at i:104804 original size:100 final size:99
Alignment explanation
Indices: 104632--104848 Score: 348
Period size: 100 Copynumber: 2.2 Consensus size: 99
104622 TCGTCGGATG
* *
104632 AGTTCTTCTTATTATGAACTCTATACTGAAATGTTGATCCCTCGAGTGAGATGTTGCTAATTCAA
1 AGTTCTTCTCATTATGAACTCTATACTGAAATGTTGATCCCTCGAGTGAGATGTTACTAATTCAA
*
104697 CTCCATATGTGATGAATCGAGTTAAAGTTGAACA
66 CTCCATATGTGATGAATCGAGATAAAGTTGAACA
* * *
104731 AGTTCTTCTCATTATGAACTCTCTACTGGAAATGTTGATCCCTCGAGTGAGGTGTTACTGATTCA
1 AGTTCTTCTCATTATGAACTCTATACT-GAAATGTTGATCCCTCGAGTGAGATGTTACTAATTCA
*
104796 ACTCCATATGTGATGAATCGAGATAAGGTTGAACA
65 ACTCCATATGTGATGAATCGAGATAAAGTTGAACA
104831 A--TCTTCTCATTATGAACT
1 AGTTCTTCTCATTATGAACT
104849 TTTTCTCCCT
Statistics
Matches: 110, Mismatches: 7, Indels: 3
0.92 0.06 0.03
Matches are distributed among these distances:
98 17 0.15
99 25 0.23
100 68 0.62
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.35
Consensus pattern (99 bp):
AGTTCTTCTCATTATGAACTCTATACTGAAATGTTGATCCCTCGAGTGAGATGTTACTAATTCAA
CTCCATATGTGATGAATCGAGATAAAGTTGAACA
Found at i:105420 original size:99 final size:99
Alignment explanation
Indices: 105288--105576 Score: 409
Period size: 98 Copynumber: 2.9 Consensus size: 99
105278 AAATTTTTTG
* * * *
105288 TTTCAAGGGAAACAATTTCAAAATTTATGTTTCAAGGGAAACTGCCTCAAAAAGAAGAAATTAAT
1 TTTCAAGTGAAACAATTTCAAAATTTGTGTTTCAAGGGAAATTGCCTAAAAAAGAAGAAATTAAT
105353 TTTAAGAGAAATCATCTCAAGTGAGATAATAATT
66 TTTAAGAGAAATCATCTCAAGTGAGATAATAATT
* * **
105387 TTTCAAGTGAAACAATTTCAAAAATTGTGTTTCAA-GAAAATTGCCTAAAAAAGGCGAAATTAAT
1 TTTCAAGTGAAACAATTTCAAAATTTGTGTTTCAAGGGAAATTGCCTAAAAAAGAAGAAATTAAT
*
105451 TTTAAGAGAAACCATCTCAAGTGAGATAATAATT
66 TTTAAGAGAAATCATCTCAAGTGAGATAATAATT
** * * * *
105485 TTTTGAGTGAAACAATTTCAAAATTTGTGTTTCGAGGGAAATTGCCTAAAAAAAGATGTAATTTA
1 TTTCAAGTGAAACAATTTCAAAATTTGTGTTTCAAGGGAAATTGCCT-AAAAAAGAAGAAATTAA
* *
105550 TTTTAAGAAAAATAATCTCAAGTGAGA
65 TTTTAAGAGAAATCATCTCAAGTGAGA
105577 AAAAATTCAT
Statistics
Matches: 167, Mismatches: 21, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
98 88 0.53
99 42 0.25
100 37 0.22
ACGTcount: A:0.44, C:0.10, G:0.16, T:0.31
Consensus pattern (99 bp):
TTTCAAGTGAAACAATTTCAAAATTTGTGTTTCAAGGGAAATTGCCTAAAAAAGAAGAAATTAAT
TTTAAGAGAAATCATCTCAAGTGAGATAATAATT
Found at i:106778 original size:30 final size:30
Alignment explanation
Indices: 106742--106805 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 30
106732 GAAGGACCTG
* *
106742 TCCAGAGGTTACAAAGAACCCCGGTAACTA
1 TCCAGAGGTCACAAAGAACCCCGGCAACTA
* * *
106772 TCCAGAGGTCATAAAGATCCTCGGCAACTA
1 TCCAGAGGTCACAAAGAACCCCGGCAACTA
106802 TCCA
1 TCCA
106806 TATGTTCCTT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.34, C:0.28, G:0.19, T:0.19
Consensus pattern (30 bp):
TCCAGAGGTCACAAAGAACCCCGGCAACTA
Found at i:107615 original size:64 final size:63
Alignment explanation
Indices: 107479--107690 Score: 221
Period size: 64 Copynumber: 3.3 Consensus size: 63
107469 TCTTTCAATG
* * * *
107479 AAGGTATGCATCGATGCACTACTTGTGCATCGGTGCATAAAATGCATTCGATGTTTCCTTATT-
1 AAGGAATGCATCGATGCACTACTTATGCATCGATGCATAAAATGCATTCGATGTTTTCTT-TTA
* * * ** * *
107542 AATGAGATGCATTGATGCACTCCTTATGCATCGATGCATTGATTGCATTCGATGTTATTATTTTA
1 AAGGA-ATGCATCGATGCACTACTTATGCATCGATGCATAAAATGCATTCGATGTT-TTCTTTT-
107607 A
63 A
* ** * *
107608 AAGG-ATGCATCGATGCATTAGATATGCATCGATGCATCAAAGGCATTCGATGTTCTTCTTTTA
1 AAGGAATGCATCGATGCACTACTTATGCATCGATGCATAAAATGCATTCGATGTT-TTCTTTTA
107671 AAGGAATGCATCGATGCACT
1 AAGGAATGCATCGATGCACT
107691 TATGAATGTG
Statistics
Matches: 120, Mismatches: 24, Indels: 9
0.78 0.16 0.06
Matches are distributed among these distances:
63 8 0.07
64 106 0.88
65 3 0.03
66 3 0.03
ACGTcount: A:0.28, C:0.17, G:0.20, T:0.34
Consensus pattern (63 bp):
AAGGAATGCATCGATGCACTACTTATGCATCGATGCATAAAATGCATTCGATGTTTTCTTTTA
Found at i:109333 original size:3 final size:3
Alignment explanation
Indices: 109325--109380 Score: 112
Period size: 3 Copynumber: 18.7 Consensus size: 3
109315 ACTTTATTGT
109325 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
109373 ATA ATA AT
1 ATA ATA AT
109381 TTTTTAACCT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 53 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:110592 original size:22 final size:23
Alignment explanation
Indices: 110567--110618 Score: 61
Period size: 26 Copynumber: 2.2 Consensus size: 23
110557 GAGAATTGGG
*
110567 TAAAT-GAGTTTGTTCATGAATA
1 TAAATAGAGTTTGTTCATGAACA
110589 TAAATGAACGAGTTTGTTCATGAACA
1 TAAAT--A-GAGTTTGTTCATGAACA
110615 TAAA
1 TAAA
110619 CGGACTGAAC
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
22 5 0.20
26 20 0.80
ACGTcount: A:0.40, C:0.08, G:0.17, T:0.35
Consensus pattern (23 bp):
TAAATAGAGTTTGTTCATGAACA
Found at i:112929 original size:25 final size:24
Alignment explanation
Indices: 112901--112947 Score: 58
Period size: 25 Copynumber: 1.9 Consensus size: 24
112891 TTATATTTTT
*
112901 ATGAACATATAATTGTTTTTTAATA
1 ATGAAAATATAATT-TTTTTTAATA
* *
112926 ATGAAAATGTTATTTTTTTTAA
1 ATGAAAATATAATTTTTTTTAA
112948 ATAAGAATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 8 0.42
25 11 0.58
ACGTcount: A:0.38, C:0.02, G:0.09, T:0.51
Consensus pattern (24 bp):
ATGAAAATATAATTTTTTTTAATA
Found at i:119618 original size:21 final size:22
Alignment explanation
Indices: 119594--119636 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
119584 CAGTTAAATA
119594 AATTTGTATAATTT-TATATTT
1 AATTTGTATAATTTATATATTT
* *
119615 AATTTTTATTATTTATATATTT
1 AATTTGTATAATTTATATATTT
119637 TATTAATTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 12 0.63
22 7 0.37
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (22 bp):
AATTTGTATAATTTATATATTT
Found at i:119629 original size:14 final size:14
Alignment explanation
Indices: 119605--119663 Score: 57
Period size: 14 Copynumber: 4.1 Consensus size: 14
119595 ATTTGTATAA
119605 TTTTA-TATTTAAT
1 TTTTATTATTTAAT
119618 TTTTATTATTTATAT
1 TTTTATTATTTA-AT
*
119633 ATTTTATTAATTTTAT
1 -TTTTATT-ATTTAAT
* *
119649 TTTAATCATTTAAT
1 TTTTATTATTTAAT
119663 T
1 T
119664 ATAAAAAATT
Statistics
Matches: 38, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
13 5 0.13
14 13 0.34
15 7 0.18
16 9 0.24
17 4 0.11
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.68
Consensus pattern (14 bp):
TTTTATTATTTAAT
Found at i:127753 original size:17 final size:18
Alignment explanation
Indices: 127731--127764 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
127721 AACCAAACAA
127731 AAAAGAAAAGA-AAAACG
1 AAAAGAAAAGAGAAAACG
*
127748 AAAAGAAGAGAGAAAAC
1 AAAAGAAAAGAGAAAAC
127765 AAGAGTTGAT
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:0.74, C:0.06, G:0.21, T:0.00
Consensus pattern (18 bp):
AAAAGAAAAGAGAAAACG
Found at i:127977 original size:20 final size:20
Alignment explanation
Indices: 127952--127989 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
127942 TTTGGTTCAC
127952 GGAATGGAAGATTATCAGTA
1 GGAATGGAAGATTATCAGTA
* *
127972 GGAATGTAAGATTGTCAG
1 GGAATGGAAGATTATCAG
127990 GGAATAGGAT
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:0.37, C:0.05, G:0.32, T:0.26
Consensus pattern (20 bp):
GGAATGGAAGATTATCAGTA
Found at i:128216 original size:37 final size:37
Alignment explanation
Indices: 128143--128217 Score: 98
Period size: 38 Copynumber: 2.0 Consensus size: 37
128133 GTTGGAAAAT
* *
128143 ATTTATATATTTTCTTTAAAAAATTTAAATTCATAAA
1 ATTTATATATTTTCTTTAAAAAATTAAAAATCATAAA
* *
128180 ATTTATATAATTTTTTTTACAAAATTAAAAAT-ATAAA
1 ATTTATAT-ATTTTCTTTAAAAAATTAAAAATCATAAA
128217 A
1 A
128218 AAGTTTAATG
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
37 14 0.42
38 19 0.58
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (37 bp):
ATTTATATATTTTCTTTAAAAAATTAAAAATCATAAA
Found at i:129049 original size:16 final size:17
Alignment explanation
Indices: 129014--129050 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
129004 TATGGGATGA
129014 AAAAATAGTATTATTGT
1 AAAAATAGTATTATTGT
129031 AAAAAT-GTAATTATT-T
1 AAAAATAGT-ATTATTGT
129047 AAAA
1 AAAA
129051 TAATATTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 7 0.37
17 12 0.63
ACGTcount: A:0.54, C:0.00, G:0.08, T:0.38
Consensus pattern (17 bp):
AAAAATAGTATTATTGT
Found at i:130299 original size:17 final size:17
Alignment explanation
Indices: 130259--130299 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
130249 TTGACATGTC
130259 TCATTT-TTTTTATTAT
1 TCATTTATTTTTATTAT
*
130275 TCAATTATTTTT-TTAT
1 TCATTTATTTTTATTAT
130291 TGCATTTAT
1 T-CATTTAT
130300 GTTCGATTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
16 10 0.48
17 11 0.52
ACGTcount: A:0.22, C:0.07, G:0.02, T:0.68
Consensus pattern (17 bp):
TCATTTATTTTTATTAT
Found at i:135308 original size:20 final size:21
Alignment explanation
Indices: 135278--135317 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
135268 AGCTGTTAGG
135278 GCCTGATGGTATCGATACTAA
1 GCCTGATGGTATCGATACTAA
*
135299 GCCT-ATGGTATTGATACTA
1 GCCTGATGGTATCGATACTA
135318 CTATGTAAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.28, C:0.17, G:0.23, T:0.33
Consensus pattern (21 bp):
GCCTGATGGTATCGATACTAA
Found at i:137679 original size:20 final size:20
Alignment explanation
Indices: 137654--137695 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
137644 ATACTTAGAT
**
137654 ATGAAATTGATTGAAAATGA
1 ATGAAATTGAAAGAAAATGA
137674 ATGAAATTGAAAGAAAATGA
1 ATGAAATTGAAAGAAAATGA
137694 AT
1 AT
137696 TTTGGGTGAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.55, C:0.00, G:0.19, T:0.26
Consensus pattern (20 bp):
ATGAAATTGAAAGAAAATGA
Found at i:139518 original size:2 final size:2
Alignment explanation
Indices: 139465--139503 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
139455 TTTAAATGTT
139465 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 T
139504 TGATACTTTA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:144867 original size:22 final size:22
Alignment explanation
Indices: 144824--144867 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
144814 GTTGTATTTA
* **
144824 AAATTAACAAAATTAACAAAAT
1 AAATTAAAAAAACCAACAAAAT
*
144846 AAATTAAAAAAACCAACCAAAT
1 AAATTAAAAAAACCAACAAAAT
144868 TAACAAAATA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.68, C:0.14, G:0.00, T:0.18
Consensus pattern (22 bp):
AAATTAAAAAAACCAACAAAAT
Found at i:145068 original size:3 final size:3
Alignment explanation
Indices: 145060--145100 Score: 55
Period size: 3 Copynumber: 13.7 Consensus size: 3
145050 CTCCTCGCTG
* * *
145060 TCA TCA TCA TCA CCA TCA TCA TCA TCA TCG TCA TCG TCA TC
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TC
145101 GTCAAGAGCA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.27, C:0.37, G:0.05, T:0.32
Consensus pattern (3 bp):
TCA
Found at i:147108 original size:5 final size:5
Alignment explanation
Indices: 147098--147172 Score: 59
Period size: 5 Copynumber: 15.0 Consensus size: 5
147088 AAAAAATATT
* * *
147098 AAATA AAAT- -AATT AAAT- AATTA AA-TA AAATA CTAATA AAATA AAATA
1 AAATA AAATA AAATA AAATA AAATA AAATA AAATA -AAATA AAATA AAATA
147145 ATAATAA AATATA AAATA AAATA AAATA
1 A-AAT-A AA-ATA AAATA AAATA AAATA
147173 TACCTTAAAT
Statistics
Matches: 59, Mismatches: 3, Indels: 16
0.76 0.04 0.21
Matches are distributed among these distances:
3 3 0.05
4 7 0.12
5 34 0.58
6 11 0.19
7 4 0.07
ACGTcount: A:0.72, C:0.01, G:0.00, T:0.27
Consensus pattern (5 bp):
AAATA
Found at i:147133 original size:16 final size:16
Alignment explanation
Indices: 147086--147172 Score: 81
Period size: 16 Copynumber: 5.4 Consensus size: 16
147076 TTATAACTGC
*
147086 AAAA-AAAATATTAAAT
1 AAAATAAAATAAT-AAT
*
147102 AAAAT-AATTAAATAAT
1 AAAATAAAAT-AATAAT
* *
147118 TAAATAAAATACTAAT
1 AAAATAAAATAATAAT
147134 AAAATAAAATAATAAT
1 AAAATAAAATAATAAT
147150 AAAATATAAAATAA-AAT
1 -AAA-ATAAAATAATAAT
147167 AAAATA
1 AAAATA
147173 TACCTTAAAT
Statistics
Matches: 59, Mismatches: 7, Indels: 11
0.77 0.09 0.14
Matches are distributed among these distances:
15 3 0.05
16 36 0.61
17 11 0.19
18 9 0.15
ACGTcount: A:0.72, C:0.01, G:0.00, T:0.26
Consensus pattern (16 bp):
AAAATAAAATAATAAT
Found at i:147155 original size:8 final size:8
Alignment explanation
Indices: 147099--147163 Score: 64
Period size: 8 Copynumber: 8.2 Consensus size: 8
147089 AAAAATATTA
147099 AATAAAAT
1 AATAAAAT
*
147107 AATTAAAT
1 AATAAAAT
*
147115 AATTAAAT
1 AATAAAAT
*
147123 AA-AATACT
1 AATAA-AAT
147131 AATAAAAT
1 AATAAAAT
147139 AA-AATAAT
1 AATAA-AAT
147147 AATAAAAT
1 AATAAAAT
147155 -ATAAAAT
1 AATAAAAT
147162 AA
1 AA
147164 AATAAAATAT
Statistics
Matches: 48, Mismatches: 4, Indels: 10
0.77 0.06 0.16
Matches are distributed among these distances:
7 10 0.21
8 34 0.71
9 4 0.08
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.28
Consensus pattern (8 bp):
AATAAAAT
Found at i:147169 original size:17 final size:18
Alignment explanation
Indices: 147121--147174 Score: 78
Period size: 17 Copynumber: 3.2 Consensus size: 18
147111 AAATAATTAA
*
147121 ATAAAATACTAAT-AAA-
1 ATAAAATAATAATAAAAT
147137 ATAAAATAATAATAAAAT
1 ATAAAATAATAATAAAAT
147155 ATAAAATAA-AATAAAAT
1 ATAAAATAATAATAAAAT
147172 ATA
1 ATA
147175 CCTTAAATTG
Statistics
Matches: 35, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
16 12 0.34
17 14 0.40
18 9 0.26
ACGTcount: A:0.72, C:0.02, G:0.00, T:0.26
Consensus pattern (18 bp):
ATAAAATAATAATAAAAT
Found at i:147169 original size:28 final size:29
Alignment explanation
Indices: 147090--147172 Score: 91
Period size: 28 Copynumber: 2.8 Consensus size: 29
147080 AACTGCAAAA
147090 AAAATATTAAATAAAATAATTAAATAATTAAAT
1 AAAATA-TAAATAAAAT-A--AAATAATTAAAT
147123 AAAATACT-AATAAAATAAAATAA-T-AAT
1 AAAATA-TAAATAAAATAAAATAATTAAAT
147150 AAAATATAAAATAAAATAAAATA
1 AAAATAT-AAATAAAATAAAATA
147173 TACCTTAAAT
Statistics
Matches: 47, Mismatches: 1, Indels: 9
0.82 0.02 0.16
Matches are distributed among these distances:
26 1 0.02
27 9 0.19
28 15 0.32
29 6 0.13
31 1 0.02
32 8 0.17
33 7 0.15
ACGTcount: A:0.71, C:0.01, G:0.00, T:0.28
Consensus pattern (29 bp):
AAAATATAAATAAAATAAAATAATTAAAT
Found at i:147197 original size:10 final size:10
Alignment explanation
Indices: 147182--147244 Score: 72
Period size: 10 Copynumber: 6.3 Consensus size: 10
147172 ATACCTTAAA
147182 TTGAGAGGAT
1 TTGAGAGGAT
* *
147192 TTGAGAGAAG
1 TTGAGAGGAT
*
147202 TTGAGATGAT
1 TTGAGAGGAT
* *
147212 TTGAGAGAAG
1 TTGAGAGGAT
*
147222 TTGAGAAGAT
1 TTGAGAGGAT
147232 TTGAGAGGAT
1 TTGAGAGGAT
147242 TTG
1 TTG
147245 GTGTGATGAA
Statistics
Matches: 41, Mismatches: 12, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
10 41 1.00
ACGTcount: A:0.33, C:0.00, G:0.37, T:0.30
Consensus pattern (10 bp):
TTGAGAGGAT
Found at i:147207 original size:20 final size:20
Alignment explanation
Indices: 147182--147238 Score: 96
Period size: 20 Copynumber: 2.9 Consensus size: 20
147172 ATACCTTAAA
*
147182 TTGAGAGGATTTGAGAGAAG
1 TTGAGAAGATTTGAGAGAAG
*
147202 TTGAGATGATTTGAGAGAAG
1 TTGAGAAGATTTGAGAGAAG
147222 TTGAGAAGATTTGAGAG
1 TTGAGAAGATTTGAGAG
147239 GATTTGGTGT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.35, C:0.00, G:0.37, T:0.28
Consensus pattern (20 bp):
TTGAGAAGATTTGAGAGAAG
Found at i:147786 original size:26 final size:26
Alignment explanation
Indices: 147736--147800 Score: 82
Period size: 25 Copynumber: 2.5 Consensus size: 26
147726 TGTTAACTTA
147736 AAATATATTTT-TATATTAACTAA-TT
1 AAATATATTTTAT-TATTAACTAATTT
147761 AAATATATTTTATTATTAACTAAATTT
1 AAATATATTTTATTATTAACT-AATTT
*
147788 AAA-ATAATTTATT
1 AAATATATTTTATT
147801 TTTATTTAAA
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
25 19 0.53
26 12 0.33
27 5 0.14
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (26 bp):
AAATATATTTTATTATTAACTAATTT
Found at i:147820 original size:20 final size:20
Alignment explanation
Indices: 147784--147822 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
147774 TATTAACTAA
*
147784 ATTTAAAATAATTTATTTTT
1 ATTTAAAATAATATATTTTT
147804 ATTTAAAA-ATATATATTTT
1 ATTTAAAATA-ATATATTTT
147823 ATGTTAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 1 0.06
20 16 0.94
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (20 bp):
ATTTAAAATAATATATTTTT
Found at i:149127 original size:137 final size:137
Alignment explanation
Indices: 148881--149154 Score: 548
Period size: 137 Copynumber: 2.0 Consensus size: 137
148871 TTGTAGCAAG
148881 GATTGATTGTTTTAGTCGGATATCTGAACCTGCTATGGAAAGTGTTGTTTATTCAATATTTCGTA
1 GATTGATTGTTTTAGTCGGATATCTGAACCTGCTATGGAAAGTGTTGTTTATTCAATATTTCGTA
148946 CACCCTGTAATTTCATCTGCTGTGGTATGCACTTACACAGTGACTACAGTTGTATACCTATCAAT
66 CACCCTGTAATTTCATCTGCTGTGGTATGCACTTACACAGTGACTACAGTTGTATACCTATCAAT
149011 TCAATAA
131 TCAATAA
149018 GATTGATTGTTTTAGTCGGATATCTGAACCTGCTATGGAAAGTGTTGTTTATTCAATATTTCGTA
1 GATTGATTGTTTTAGTCGGATATCTGAACCTGCTATGGAAAGTGTTGTTTATTCAATATTTCGTA
149083 CACCCTGTAATTTCATCTGCTGTGGTATGCACTTACACAGTGACTACAGTTGTATACCTATCAAT
66 CACCCTGTAATTTCATCTGCTGTGGTATGCACTTACACAGTGACTACAGTTGTATACCTATCAAT
149148 TCAATAA
131 TCAATAA
149155 ATGATCCACC
Statistics
Matches: 137, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
137 137 1.00
ACGTcount: A:0.27, C:0.18, G:0.18, T:0.38
Consensus pattern (137 bp):
GATTGATTGTTTTAGTCGGATATCTGAACCTGCTATGGAAAGTGTTGTTTATTCAATATTTCGTA
CACCCTGTAATTTCATCTGCTGTGGTATGCACTTACACAGTGACTACAGTTGTATACCTATCAAT
TCAATAA
Found at i:151864 original size:6 final size:6
Alignment explanation
Indices: 151853--151911 Score: 55
Period size: 6 Copynumber: 9.8 Consensus size: 6
151843 AAAAGCAATG
* * ** * * *
151853 CATGTA CATGTA CATGCA CATGTA CATGTG GGTATG CATGTA CATGCA
1 CATGTA CATGTA CATGTA CATGTA CATGTA CATGTA CATGTA CATGTA
151901 CATGTA CATGT
1 CATGTA CATGT
151912 GGATATGCAT
Statistics
Matches: 41, Mismatches: 12, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
6 41 1.00
ACGTcount: A:0.29, C:0.19, G:0.22, T:0.31
Consensus pattern (6 bp):
CATGTA
Found at i:151895 original size:30 final size:30
Alignment explanation
Indices: 151859--151923 Score: 121
Period size: 30 Copynumber: 2.2 Consensus size: 30
151849 AATGCATGTA
*
151859 CATGTACATGCACATGTACATGTGGGTATG
1 CATGTACATGCACATGTACATGTGGATATG
151889 CATGTACATGCACATGTACATGTGGATATG
1 CATGTACATGCACATGTACATGTGGATATG
151919 CATGT
1 CATGT
151924 GCAAGATTAT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.28, C:0.17, G:0.25, T:0.31
Consensus pattern (30 bp):
CATGTACATGCACATGTACATGTGGATATG
Found at i:153137 original size:24 final size:24
Alignment explanation
Indices: 153109--153157 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
153099 TAACACATAC
*
153109 ATGTAACATATTTGCATATTATCA
1 ATGTAACATATATGCATATTATCA
153133 ATGTAACATATATGCATATTATCA
1 ATGTAACATATATGCATATTATCA
153157 A
1 A
153158 CATGTATACA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.41, C:0.12, G:0.08, T:0.39
Consensus pattern (24 bp):
ATGTAACATATATGCATATTATCA
Found at i:153531 original size:46 final size:47
Alignment explanation
Indices: 153480--153574 Score: 122
Period size: 47 Copynumber: 2.0 Consensus size: 47
153470 TCATTTAGTA
* * *
153480 TTTTTA-ATATGAATATTT-AATTTTTAAATTATTTTTTATTTATAAT
1 TTTTTATATATG-ATATTTAAATTTTTAAATAATTTTATATTTAAAAT
* *
153526 TTTTTATATTTGATTTTTAAATTTTTAAATAATTTTATATTTAAAAT
1 TTTTTATATATGATATTTAAATTTTTAAATAATTTTATATTTAAAAT
153573 TT
1 TT
153575 AAAATAAATT
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
46 11 0.26
47 31 0.74
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (47 bp):
TTTTTATATATGATATTTAAATTTTTAAATAATTTTATATTTAAAAT
Found at i:153541 original size:21 final size:21
Alignment explanation
Indices: 153492--153552 Score: 56
Period size: 21 Copynumber: 3.0 Consensus size: 21
153482 TTTAATATGA
* * *
153492 ATATTTAATTTTTAAATTATT
1 ATATTTGATTTATAAATTTTT
*
153513 -T-TTT-ATTTATAATTTTTT
1 ATATTTGATTTATAAATTTTT
*
153531 ATATTTGATTTTTAAATTTTT
1 ATATTTGATTTATAAATTTTT
153552 A
1 A
153553 AATAATTTTA
Statistics
Matches: 32, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
18 11 0.34
19 4 0.12
20 4 0.12
21 13 0.41
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (21 bp):
ATATTTGATTTATAAATTTTT
Found at i:155386 original size:68 final size:67
Alignment explanation
Indices: 155291--155493 Score: 218
Period size: 64 Copynumber: 3.0 Consensus size: 67
155281 TTTAGGAATT
* * *
155291 TTTAGGGTAAATTACCTATTTGGTCACTTACATCTTATCTAATTTATATTTTGATCACTCGATTA
1 TTTAGGGTAAACTACCTATTTGGTCACTTATATATTATCTAATTTATATTTTGATCACTC-ATTA
155356 TTA
65 TTA
* * * * *
155359 TTTAAGGTAAACTATCTATTTAGTCACTTATATATTATCTAATATA-ATTCAT-AT-A-T-ATTT
1 TTTAGGGTAAACTACCTATTTGGTCACTTATATATTATCTAATTTATATT-TTGATCACTCA-TT
*
155419 TTTA
64 ATTA
* * *
155423 TTTAGGGTAAACAACCTATTTGGTCACTTATATATTATCTAATTTATGTTTTGGTCACTCAATTA
1 TTTAGGGTAAACTACCTATTTGGTCACTTATATATTATCTAATTTATATTTTGATCACTC-ATTA
*
155488 TCA
65 TTA
155491 TTT
1 TTT
155494 TTTAAAAAAT
Statistics
Matches: 108, Mismatches: 19, Indels: 16
0.76 0.13 0.11
Matches are distributed among these distances:
63 1 0.01
64 47 0.44
65 4 0.04
66 2 0.02
67 6 0.06
68 47 0.44
69 1 0.01
ACGTcount: A:0.31, C:0.13, G:0.09, T:0.48
Consensus pattern (67 bp):
TTTAGGGTAAACTACCTATTTGGTCACTTATATATTATCTAATTTATATTTTGATCACTCATTAT
TA
Found at i:155711 original size:18 final size:17
Alignment explanation
Indices: 155666--155698 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
155656 TTTGAAGGAA
*
155666 AAAACCCGGGTACCCGC
1 AAAATCCGGGTACCCGC
155683 AAAATCCGGGTACCCG
1 AAAATCCGGGTACCCG
155699 GTAACATCCG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.30, C:0.36, G:0.24, T:0.09
Consensus pattern (17 bp):
AAAATCCGGGTACCCGC
Found at i:162115 original size:20 final size:20
Alignment explanation
Indices: 162065--162106 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
162055 AAATGACCAA
162065 CAAAATCGCAATGCGATCTC
1 CAAAATCGCAATGCGATCTC
162085 CAAAATCGCAATGCGATCTC
1 CAAAATCGCAATGCGATCTC
162105 CA
1 CA
162107 GTATCGCAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.36, C:0.31, G:0.14, T:0.19
Consensus pattern (20 bp):
CAAAATCGCAATGCGATCTC
Found at i:162238 original size:20 final size:20
Alignment explanation
Indices: 162215--162263 Score: 89
Period size: 20 Copynumber: 2.5 Consensus size: 20
162205 ATGTAAATCG
162215 CAACGCGATTCTGACTATCA
1 CAACGCGATTCTGACTATCA
*
162235 CAACGCGATTCTGACTATCG
1 CAACGCGATTCTGACTATCA
162255 CAACGCGAT
1 CAACGCGAT
162264 AATACAAAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.29, C:0.31, G:0.18, T:0.22
Consensus pattern (20 bp):
CAACGCGATTCTGACTATCA
Found at i:162455 original size:22 final size:22
Alignment explanation
Indices: 162430--162480 Score: 84
Period size: 22 Copynumber: 2.3 Consensus size: 22
162420 CTACAGCGAC
162430 ATCCGTCCCCATCTCCGACGAA
1 ATCCGTCCCCATCTCCGACGAA
**
162452 ATCCGTCCCCATCTCCGGTGAA
1 ATCCGTCCCCATCTCCGACGAA
162474 ATCCGTC
1 ATCCGTC
162481 TATCTCCATC
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:0.20, C:0.43, G:0.16, T:0.22
Consensus pattern (22 bp):
ATCCGTCCCCATCTCCGACGAA
Found at i:162949 original size:20 final size:20
Alignment explanation
Indices: 162856--162951 Score: 95
Period size: 20 Copynumber: 4.8 Consensus size: 20
162846 AAATCGCAAG
*
162856 TTTCGCATTGCGATTTTCA-
1 TTTCGCGTTGCGATTTTCAT
** *
162875 TTTCGCGTTGCGATAGTCAA
1 TTTCGCGTTGCGATTTTCAT
* **
162895 ATTCGCGTTGCGATAGTCAT
1 TTTCGCGTTGCGATTTTCAT
* *
162915 TTTAGTGTTGCGATTTTCAT
1 TTTCGCGTTGCGATTTTCAT
*
162935 TTTCGTGTTGCGATTTT
1 TTTCGCGTTGCGATTTT
162952 AAGTTTCATA
Statistics
Matches: 65, Mismatches: 11, Indels: 1
0.84 0.14 0.01
Matches are distributed among these distances:
19 16 0.25
20 49 0.75
ACGTcount: A:0.16, C:0.17, G:0.22, T:0.46
Consensus pattern (20 bp):
TTTCGCGTTGCGATTTTCAT
Found at i:162958 original size:20 final size:20
Alignment explanation
Indices: 162919--162958 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
162909 AGTCATTTTA
* *
162919 GTGTTGCGATTTTCATTTTC
1 GTGTTGCGATTTTAAGTTTC
162939 GTGTTGCGATTTTAAGTTTC
1 GTGTTGCGATTTTAAGTTTC
162959 ATAAACTATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.12, C:0.12, G:0.23, T:0.53
Consensus pattern (20 bp):
GTGTTGCGATTTTAAGTTTC
Found at i:164967 original size:19 final size:19
Alignment explanation
Indices: 164940--164993 Score: 63
Period size: 19 Copynumber: 2.8 Consensus size: 19
164930 CGCGAATTTA
* *
164940 GTTTTGCGTTGTGATTTTG
1 GTTTCGCGTTGCGATTTTG
*
164959 GTTTCGCGTTGCGATTTTT
1 GTTTCGCGTTGCGATTTTG
* *
164978 ATTTCGCATTGCGATT
1 GTTTCGCGTTGCGATT
164994 ATCCCGTTGC
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.09, C:0.13, G:0.26, T:0.52
Consensus pattern (19 bp):
GTTTCGCGTTGCGATTTTG
Found at i:165023 original size:20 final size:20
Alignment explanation
Indices: 164998--165066 Score: 111
Period size: 20 Copynumber: 3.5 Consensus size: 20
164988 GCGATTATCC
**
164998 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCATTTTCG
165018 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
*
165038 CATTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
165058 CGTTGCGAT
1 CGTTGCGAT
165067 TTTAAGTTTC
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 45 1.00
ACGTcount: A:0.19, C:0.20, G:0.25, T:0.36
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTTCG
Found at i:165076 original size:20 final size:20
Alignment explanation
Indices: 165053--165096 Score: 79
Period size: 20 Copynumber: 2.2 Consensus size: 20
165043 CGATAGTCAT
165053 TTTCGCGTTGCGATTTTAAG
1 TTTCGCGTTGCGATTTTAAG
*
165073 TTTCGTGTTGCGATTTTAAG
1 TTTCGCGTTGCGATTTTAAG
165093 TTTC
1 TTTC
165097 AGAAACTATT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.14, C:0.14, G:0.23, T:0.50
Consensus pattern (20 bp):
TTTCGCGTTGCGATTTTAAG
Found at i:165077 original size:40 final size:40
Alignment explanation
Indices: 165000--165086 Score: 102
Period size: 40 Copynumber: 2.2 Consensus size: 40
164990 GATTATCCCG
* *
165000 TTGCGATAGTCAAATTCGCGTTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCAAATTCGCGTTGCGATAGTAAGTTTCGCA
** ** **
165040 TTGCGATAGTCATTTTCGCGTTGCGATTTTAAGTTTCGTG
1 TTGCGATAGTCAAATTCGCGTTGCGATAGTAAGTTTCGCA
165080 TTGCGAT
1 TTGCGAT
165087 TTTAAGTTTC
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
40 39 1.00
ACGTcount: A:0.18, C:0.17, G:0.24, T:0.40
Consensus pattern (40 bp):
TTGCGATAGTCAAATTCGCGTTGCGATAGTAAGTTTCGCA
Found at i:165596 original size:21 final size:21
Alignment explanation
Indices: 165570--165698 Score: 114
Period size: 21 Copynumber: 6.1 Consensus size: 21
165560 GCCCGACTCA
165570 CCTATCATCGTTCAAGAGGCC
1 CCTATCATCGTTCAAGAGGCC
** *
165591 CCTATCATCCCTCAAGAGTCC
1 CCTATCATCGTTCAAGAGGCC
** *
165612 CCTCCCACCGTTCAAGAGGCC
1 CCTATCATCGTTCAAGAGGCC
* * *
165633 CCTGTCATCGTTGAAGAGGTC
1 CCTATCATCGTTCAAGAGGCC
** * *
165654 CCTCCCATCATTCAAGAGCCC
1 CCTATCATCGTTCAAGAGGCC
* * *
165675 CCTGTCATCGTTGAAGAGGTC
1 CCTATCATCGTTCAAGAGGCC
165696 CCT
1 CCT
165699 CCCACCATTC
Statistics
Matches: 82, Mismatches: 26, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
21 82 1.00
ACGTcount: A:0.21, C:0.37, G:0.19, T:0.23
Consensus pattern (21 bp):
CCTATCATCGTTCAAGAGGCC
Found at i:165641 original size:42 final size:42
Alignment explanation
Indices: 165580--165713 Score: 189
Period size: 42 Copynumber: 3.2 Consensus size: 42
165570 CCTATCATCG
* ** * *
165580 TTCAAGAGGCCCCTATCATCCCTCAAGA-GTCCCCTCCCACCG
1 TTCAAGAGGCCCCTGTCATCGTTGAAGAGGT-CCCTCCCACCA
*
165622 TTCAAGAGGCCCCTGTCATCGTTGAAGAGGTCCCTCCCATCA
1 TTCAAGAGGCCCCTGTCATCGTTGAAGAGGTCCCTCCCACCA
*
165664 TTCAAGAGCCCCCTGTCATCGTTGAAGAGGTCCCTCCCACCA
1 TTCAAGAGGCCCCTGTCATCGTTGAAGAGGTCCCTCCCACCA
165706 TTCAAGAG
1 TTCAAGAG
165714 CCCGATTCAC
Statistics
Matches: 83, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
42 81 0.98
43 2 0.02
ACGTcount: A:0.22, C:0.37, G:0.19, T:0.22
Consensus pattern (42 bp):
TTCAAGAGGCCCCTGTCATCGTTGAAGAGGTCCCTCCCACCA
Found at i:165712 original size:21 final size:21
Alignment explanation
Indices: 165575--165713 Score: 100
Period size: 21 Copynumber: 6.6 Consensus size: 21
165565 ACTCACCTAT
* **
165575 CATCGTTCAAGAGGCCCCTAT
1 CATCGTTCAAGAGGTCCCTCC
**
165596 CATCCCTCAAGA-GTCCCCTCC
1 CATCGTTCAAGAGGT-CCCTCC
* * **
165617 CACCGTTCAAGAGGCCCCTGT
1 CATCGTTCAAGAGGTCCCTCC
*
165638 CATCGTTGAAGAGGTCCCTCC
1 CATCGTTCAAGAGGTCCCTCC
* ** **
165659 CATCATTCAAGAGCCCCCTGT
1 CATCGTTCAAGAGGTCCCTCC
*
165680 CATCGTTGAAGAGGTCCCTCC
1 CATCGTTCAAGAGGTCCCTCC
* *
165701 CACCATTCAAGAG
1 CATCGTTCAAGAG
165714 CCCGATTCAC
Statistics
Matches: 85, Mismatches: 31, Indels: 4
0.71 0.26 0.03
Matches are distributed among these distances:
20 1 0.01
21 83 0.98
22 1 0.01
ACGTcount: A:0.22, C:0.37, G:0.19, T:0.22
Consensus pattern (21 bp):
CATCGTTCAAGAGGTCCCTCC
Found at i:167261 original size:20 final size:20
Alignment explanation
Indices: 167236--167300 Score: 87
Period size: 20 Copynumber: 3.2 Consensus size: 20
167226 AGGTACATTT
* *
167236 TCGCAACGCTAAACTCAAAA
1 TCGCAATGCGAAACTCAAAA
*
167256 TCGCAATGCGAAAGTCAAAA
1 TCGCAATGCGAAACTCAAAA
167276 TCGCAATGCGAAAGC-CAAAA
1 TCGCAATGCGAAA-CTCAAAA
167296 TCGCA
1 TCGCA
167301 TTCGAAAGTA
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
20 40 1.00
ACGTcount: A:0.43, C:0.26, G:0.17, T:0.14
Consensus pattern (20 bp):
TCGCAATGCGAAACTCAAAA
Found at i:167413 original size:20 final size:20
Alignment explanation
Indices: 167384--167500 Score: 171
Period size: 20 Copynumber: 5.8 Consensus size: 20
167374 GCGATTTTCT
* *
167384 CGTTGTGATAGTCAAATTCC
1 CGTTGCGATAGTCAAATTCG
* *
167404 CGTTGCGATAATCAAATTCA
1 CGTTGCGATAGTCAAATTCG
*
167424 TGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
*
167444 TGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
167464 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
*
167484 CGTTGCGATATTCAAAT
1 CGTTGCGATAGTCAAAT
167501 GAATGTGTAA
Statistics
Matches: 89, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 89 1.00
ACGTcount: A:0.27, C:0.18, G:0.21, T:0.33
Consensus pattern (20 bp):
CGTTGCGATAGTCAAATTCG
Found at i:169967 original size:24 final size:24
Alignment explanation
Indices: 169933--169986 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
169923 CTGAAATATC
169933 ATCAAAATCCAAGTATTGACCAAG
1 ATCAAAATCCAAGTATTGACCAAG
* * *
169957 ATCAAAGTCCAGGTATTGACCAAT
1 ATCAAAATCCAAGTATTGACCAAG
169981 ATCAAA
1 ATCAAA
169987 TTTCGAATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.44, C:0.20, G:0.13, T:0.22
Consensus pattern (24 bp):
ATCAAAATCCAAGTATTGACCAAG
Found at i:170662 original size:17 final size:17
Alignment explanation
Indices: 170640--170673 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
170630 CGGATGGTGA
170640 AGGATGTCGTTGGATAT
1 AGGATGTCGTTGGATAT
170657 AGGATGTCGTTGGATAT
1 AGGATGTCGTTGGATAT
170674 TGGAACGGAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.24, C:0.06, G:0.35, T:0.35
Consensus pattern (17 bp):
AGGATGTCGTTGGATAT
Found at i:170970 original size:20 final size:19
Alignment explanation
Indices: 170947--170992 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
170937 GAAAACTGAT
* *
170947 TTGCGATACTGGAGATCGCG
1 TTGCGAT-CTAGAGATCGCA
*
170967 TTGCGATTTAGAGATCGCA
1 TTGCGATCTAGAGATCGCA
170986 TTGCGAT
1 TTGCGAT
170993 TTTTTTGGTC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 16 0.70
20 7 0.30
ACGTcount: A:0.22, C:0.17, G:0.30, T:0.30
Consensus pattern (19 bp):
TTGCGATCTAGAGATCGCA
Found at i:170982 original size:19 final size:19
Alignment explanation
Indices: 170958--170994 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
170948 TGCGATACTG
*
170958 GAGATCGCGTTGCGATTTA
1 GAGATCGCATTGCGATTTA
170977 GAGATCGCATTGCGATTT
1 GAGATCGCATTGCGATTT
170995 TTTTGGTCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.22, C:0.16, G:0.30, T:0.32
Consensus pattern (19 bp):
GAGATCGCATTGCGATTTA
Found at i:172237 original size:2 final size:2
Alignment explanation
Indices: 172230--172258 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
172220 TCTCATATTC
172230 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
172259 ATTCACTTTC
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:175703 original size:31 final size:31
Alignment explanation
Indices: 175618--175690 Score: 137
Period size: 31 Copynumber: 2.4 Consensus size: 31
175608 GAACCTCGAC
*
175618 AACTGTCCATAGGTCCCGAAGAACCTAAGTA
1 AACTGTTCATAGGTCCCGAAGAACCTAAGTA
175649 AACTGTTCATAGGTCCCGAAGAACCTAAGTA
1 AACTGTTCATAGGTCCCGAAGAACCTAAGTA
175680 AACTGTTCATA
1 AACTGTTCATA
175691 TGTTCCTTAG
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
31 41 1.00
ACGTcount: A:0.36, C:0.23, G:0.18, T:0.23
Consensus pattern (31 bp):
AACTGTTCATAGGTCCCGAAGAACCTAAGTA
Found at i:175808 original size:32 final size:32
Alignment explanation
Indices: 175702--175788 Score: 124
Period size: 32 Copynumber: 2.8 Consensus size: 32
175692 GTTCCTTAGA
* *
175702 ACATAGGT-A-TATTGTCCATATGTCTCAAAAG
1 ACATAGGTAATTA-TGTCCATATGTCCCGAAAG
*
175733 ACATAGGTAATTCTGTCCATATGTCCCGAAAG
1 ACATAGGTAATTATGTCCATATGTCCCGAAAG
175765 ACATAGGTAATTATGTCCATATGT
1 ACATAGGTAATTATGTCCATATGT
175789 TCTGTAGAAT
Statistics
Matches: 50, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
31 8 0.16
32 41 0.82
33 1 0.02
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Consensus pattern (32 bp):
ACATAGGTAATTATGTCCATATGTCCCGAAAG
Found at i:175982 original size:2 final size:2
Alignment explanation
Indices: 175975--176012 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
175965 TCTCATATTC
175975 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
176013 GGTTCACTTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:176754 original size:21 final size:21
Alignment explanation
Indices: 176730--176784 Score: 83
Period size: 24 Copynumber: 2.5 Consensus size: 21
176720 AAAATTGTCT
176730 TAGTGCATCGGTGCCCATTCA
1 TAGTGCATCGGTGCCCATTCA
176751 TAGTGCATCATCGGTGCCCATTCA
1 TAGTG---CATCGGTGCCCATTCA
176775 TAGTGCATCG
1 TAGTGCATCG
176785 ATGCACCTAT
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
21 10 0.32
24 21 0.68
ACGTcount: A:0.20, C:0.27, G:0.24, T:0.29
Consensus pattern (21 bp):
TAGTGCATCGGTGCCCATTCA
Found at i:176767 original size:24 final size:24
Alignment explanation
Indices: 176735--176783 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
176725 TGTCTTAGTG
176735 CATCGGTGCCCATTCATAGTGCAT
1 CATCGGTGCCCATTCATAGTGCAT
176759 CATCGGTGCCCATTCATAGTGCAT
1 CATCGGTGCCCATTCATAGTGCAT
176783 C
1 C
176784 GATGCACCTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.20, C:0.31, G:0.20, T:0.29
Consensus pattern (24 bp):
CATCGGTGCCCATTCATAGTGCAT
Found at i:178913 original size:16 final size:17
Alignment explanation
Indices: 178886--178919 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
178876 ATCGTAATCA
178886 TTTTGTAAAAGTAAATG
1 TTTTGTAAAAGTAAATG
*
178903 TTTTG-AAAAGTCAATG
1 TTTTGTAAAAGTAAATG
178919 T
1 T
178920 GACACCTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.38, C:0.03, G:0.18, T:0.41
Consensus pattern (17 bp):
TTTTGTAAAAGTAAATG
Found at i:180066 original size:21 final size:21
Alignment explanation
Indices: 180040--180084 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
180030 GATTTCTGGG
* *
180040 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
180061 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
180082 CAA
1 CAA
180085 ACGAACAAGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:181845 original size:23 final size:22
Alignment explanation
Indices: 181786--181852 Score: 116
Period size: 22 Copynumber: 3.0 Consensus size: 22
181776 TATGGACATC
*
181786 ATTCTACGGGCACTACGGTGCA
1 ATTCTACGGGCACTTCGGTGCA
181808 ATTCTACGGGCACTTCGGTGCA
1 ATTCTACGGGCACTTCGGTGCA
181830 ATTCTACGGGGCACTTCGGTGCA
1 ATTCTAC-GGGCACTTCGGTGCA
181853 TTTATACGAG
Statistics
Matches: 43, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
22 28 0.65
23 15 0.35
ACGTcount: A:0.19, C:0.27, G:0.28, T:0.25
Consensus pattern (22 bp):
ATTCTACGGGCACTTCGGTGCA
Found at i:184955 original size:21 final size:21
Alignment explanation
Indices: 184929--184973 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
184919 GATTTTTGGG
* *
184929 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
184950 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
184971 CAA
1 CAA
184974 ACGAACAAGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:186725 original size:23 final size:22
Alignment explanation
Indices: 186666--186732 Score: 116
Period size: 22 Copynumber: 3.0 Consensus size: 22
186656 TATGGACATC
*
186666 ATTCTACGGGCACTACGGTGCA
1 ATTCTACGGGCACTTCGGTGCA
186688 ATTCTACGGGCACTTCGGTGCA
1 ATTCTACGGGCACTTCGGTGCA
186710 ATTCTACGGGGCACTTCGGTGCA
1 ATTCTAC-GGGCACTTCGGTGCA
186733 TTTATACGAG
Statistics
Matches: 43, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
22 28 0.65
23 15 0.35
ACGTcount: A:0.19, C:0.27, G:0.28, T:0.25
Consensus pattern (22 bp):
ATTCTACGGGCACTTCGGTGCA
Found at i:193342 original size:20 final size:20
Alignment explanation
Indices: 193313--193388 Score: 66
Period size: 20 Copynumber: 3.7 Consensus size: 20
193303 TTTGTGCTTC
*
193313 ATGCACCGATGCATTTAACA
1 ATGCATCGATGCATTTAACA
*
193333 ATGCATCGATGCATCCTTGAA-T
1 ATGCATCGATGCAT--TT-AACA
* *
193355 ATGCATCGATGCA-TAAGACC
1 ATGCATCGATGCATTTA-ACA
193375 ATGCATCGATGCAT
1 ATGCATCGATGCAT
193389 CCGTCGGGTT
Statistics
Matches: 46, Mismatches: 4, Indels: 11
0.75 0.07 0.18
Matches are distributed among these distances:
18 1 0.02
19 2 0.04
20 26 0.57
22 15 0.33
23 2 0.04
ACGTcount: A:0.32, C:0.24, G:0.18, T:0.26
Consensus pattern (20 bp):
ATGCATCGATGCATTTAACA
Found at i:195282 original size:18 final size:19
Alignment explanation
Indices: 195254--195290 Score: 67
Period size: 18 Copynumber: 2.0 Consensus size: 19
195244 TGTTAAACTT
195254 TTTGATTTGGATGTTTATG
1 TTTGATTTGGATGTTTATG
195273 TTTG-TTTGGATGTTTATG
1 TTTGATTTGGATGTTTATG
195291 ATATTTGGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.14, C:0.00, G:0.27, T:0.59
Consensus pattern (19 bp):
TTTGATTTGGATGTTTATG
Found at i:195299 original size:17 final size:18
Alignment explanation
Indices: 195258--195301 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
195248 AAACTTTTTG
*
195258 ATTTGGATGTTTATGTTT
1 ATTTGGATGTTTATGTAT
*
195276 GTTTGGATGTTTATG-AT
1 ATTTGGATGTTTATGTAT
195293 ATTTGGATG
1 ATTTGGATG
195302 CTTGACTATT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
17 9 0.39
18 14 0.61
ACGTcount: A:0.18, C:0.00, G:0.27, T:0.55
Consensus pattern (18 bp):
ATTTGGATGTTTATGTAT
Found at i:196004 original size:19 final size:19
Alignment explanation
Indices: 195980--196016 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
195970 TCGAATGCAT
195980 TCCATGCACCGATGCACTA
1 TCCATGCACCGATGCACTA
*
195999 TCCATGCATCGATGCACT
1 TCCATGCACCGATGCACT
196017 CTGAATATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.24, C:0.35, G:0.16, T:0.24
Consensus pattern (19 bp):
TCCATGCACCGATGCACTA
Found at i:196035 original size:65 final size:64
Alignment explanation
Indices: 195917--196045 Score: 158
Period size: 65 Copynumber: 2.0 Consensus size: 64
195907 TATTCAAATG
*
195917 CATGCACCGATGCATCAGTCCATGCATCGATGCATCGATGAATTAATTGAACATCGAATGCATTC
1 CATGCACCGATGCATCAGTCCATGCATCGATGCATC-ATGAATTAATTAAACATCGAATGCATTC
*
195982 CATGCACCGATGCA-CTA-TCCATGCATCGATGCACTC-TGAA-TATTTTCAAAACATCGAATGC
1 CATGCACCGATGCATC-AGTCCATGCATCGATGCA-TCATGAATTA-ATT--AAACATCGAATGC
196043 ATT
61 ATT
196046 TGATGCACAA
Statistics
Matches: 57, Mismatches: 2, Indels: 10
0.83 0.03 0.14
Matches are distributed among these distances:
62 2 0.04
63 6 0.11
64 17 0.30
65 32 0.56
ACGTcount: A:0.31, C:0.26, G:0.16, T:0.27
Consensus pattern (64 bp):
CATGCACCGATGCATCAGTCCATGCATCGATGCATCATGAATTAATTAAACATCGAATGCATTC
Found at i:196108 original size:56 final size:57
Alignment explanation
Indices: 195991--196108 Score: 159
Period size: 57 Copynumber: 2.1 Consensus size: 57
195981 CCATGCACCG
* * * *
195991 ATGCACTATCCATGCATCGATGCACTCTGAATATTTTCAAAACATCGAATGCATTTG
1 ATGCACAAGCCATGCATCGATGCACTCAGAATATTTTCAAAACATCGAATGCATTTA
**
196048 ATGCACAAGCCATGCATCGATGCAC-CAGGCTATTTTTC-AAACATCGAATGCATTTA
1 ATGCACAAGCCATGCATCGATGCACTCAGAATA-TTTTCAAAACATCGAATGCATTTA
196104 ATGCA
1 ATGCA
196109 TCGATGCACA
Statistics
Matches: 54, Mismatches: 6, Indels: 3
0.86 0.10 0.05
Matches are distributed among these distances:
56 26 0.48
57 28 0.52
ACGTcount: A:0.32, C:0.24, G:0.15, T:0.29
Consensus pattern (57 bp):
ATGCACAAGCCATGCATCGATGCACTCAGAATATTTTCAAAACATCGAATGCATTTA
Found at i:206466 original size:19 final size:19
Alignment explanation
Indices: 206442--206492 Score: 93
Period size: 19 Copynumber: 2.7 Consensus size: 19
206432 ACCAACTAAA
*
206442 TCGCAATGCGATCGATAAT
1 TCGCAACGCGATCGATAAT
206461 TCGCAACGCGATCGATAAT
1 TCGCAACGCGATCGATAAT
206480 TCGCAACGCGATC
1 TCGCAACGCGATC
206493 TCCGGTATCG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.29, C:0.27, G:0.22, T:0.22
Consensus pattern (19 bp):
TCGCAACGCGATCGATAAT
Found at i:206565 original size:21 final size:21
Alignment explanation
Indices: 206541--206761 Score: 124
Period size: 21 Copynumber: 10.6 Consensus size: 21
206531 ACTTCGACTA
206541 TCGCATTGCGATAGTCAAAGT
1 TCGCATTGCGATAGTCAAAGT
206562 TCGCATTGCGATAGTCAAAGT
1 TCGCATTGCGATAGTCAAAGT
* * * *
206583 TCGCGTTGCGA-ATTTGGAAA-C
1 TCGCATTGCGATA-GT-CAAAGT
*
206604 T-G-ATTTGCGATAGTCGAAGT
1 TCGCA-TTGCGATAGTCAAAGT
* *
206624 TCGCGTTGCGATTTATTACAAA-T
1 TCGCATTGCGA--TAGT-CAAAGT
*
206647 TCG--TTGCTATAGTCAAAGT
1 TCGCATTGCGATAGTCAAAGT
*
206666 TCGCATTGCGATTTATTCCAAA-T
1 TCGCATTGCGA--TAGT-CAAAGT
* *
206689 TCG--TTACGATAGTCGAAGT
1 TCGCATTGCGATAGTCAAAGT
* * *
206708 TCGCGTTGCGATTTATTCCAAGT
1 TCGCATTGCGA--TAGTCAAAGT
*
206731 TCG--TTGCGATAGTCGAAGT
1 TCGCATTGCGATAGTCAAAGT
206750 TCGCATTGCGAT
1 TCGCATTGCGAT
206762 TTATTCCAAA
Statistics
Matches: 153, Mismatches: 24, Indels: 46
0.69 0.11 0.21
Matches are distributed among these distances:
18 7 0.05
19 27 0.18
20 10 0.07
21 74 0.48
22 3 0.02
23 25 0.16
24 7 0.05
ACGTcount: A:0.24, C:0.18, G:0.24, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATAGTCAAAGT
Found at i:206592 original size:42 final size:41
Alignment explanation
Indices: 206541--206786 Score: 239
Period size: 42 Copynumber: 5.9 Consensus size: 41
206531 ACTTCGACTA
* *
206541 TCGCATTGCGA-TAGT-CAAAGTTCGCATTGCGATAGTCAAAGT
1 TCGCATTGCGATTATTACAAA-TTCG--TTGCGATAGTCGAAGT
* * ** *
206583 TCGCGTTGCGAAT-TTGGAAACT-GATTTGCGATAGTCGAAGT
1 TCGCATTGCGATTATTACAAATTCG-TT-GCGATAGTCGAAGT
* * *
206624 TCGCGTTGCGATTTATTACAAATTCGTTGCTATAGTCAAAGT
1 TCGCATTGCGA-TTATTACAAATTCGTTGCGATAGTCGAAGT
* *
206666 TCGCATTGCGATTTATTCCAAATTCGTTACGATAGTCGAAGT
1 TCGCATTGCGA-TTATTACAAATTCGTTGCGATAGTCGAAGT
* * *
206708 TCGCGTTGCGATTTATTCCAAGTTCGTTGCGATAGTCGAAGT
1 TCGCATTGCGA-TTATTACAAATTCGTTGCGATAGTCGAAGT
*
206750 TCGCATTGCGATTTATTCCAAATTCGTTGCGATAGTC
1 TCGCATTGCGA-TTATTACAAATTCGTTGCGATAGTC
206787 CAAAATCGCA
Statistics
Matches: 177, Mismatches: 21, Indels: 12
0.84 0.10 0.06
Matches are distributed among these distances:
40 3 0.02
41 25 0.14
42 136 0.77
43 12 0.07
44 1 0.01
ACGTcount: A:0.24, C:0.18, G:0.23, T:0.35
Consensus pattern (41 bp):
TCGCATTGCGATTATTACAAATTCGTTGCGATAGTCGAAGT
Found at i:206779 original size:21 final size:21
Alignment explanation
Indices: 206627--206782 Score: 101
Period size: 21 Copynumber: 7.4 Consensus size: 21
206617 TCGAAGTTCG
*
206627 CGTTGCGATTTATTACAAATT
1 CGTTGCGATTTATTCCAAATT
* *
206648 CGTTGC--TATAGT-CAAAGTT
1 CGTTGCGATTTATTCCAAA-TT
206667 CGCATTGCGATTTATTCCAAATT
1 CG--TTGCGATTTATTCCAAATT
* * * *
206690 CGTTACGA--TAGTCGAAGTT
1 CGTTGCGATTTATTCCAAATT
*
206709 CGCGTTGCGATTTATTCCAAGTT
1 --CGTTGCGATTTATTCCAAATT
* * *
206732 CGTTGCGA--TAGTCGAAGTT
1 CGTTGCGATTTATTCCAAATT
206751 CGCATTGCGATTTATTCCAAATT
1 CG--TTGCGATTTATTCCAAATT
206774 CGTTGCGAT
1 CGTTGCGAT
206783 AGTCCAAAAT
Statistics
Matches: 105, Mismatches: 16, Indels: 28
0.70 0.11 0.19
Matches are distributed among these distances:
18 4 0.04
19 27 0.26
21 43 0.41
23 27 0.26
24 4 0.04
ACGTcount: A:0.24, C:0.19, G:0.21, T:0.37
Consensus pattern (21 bp):
CGTTGCGATTTATTCCAAATT
Done.