Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold92
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: 2337674
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 499 characters in sequence are not A, C, G, or T
File 1 of 19
Found at i:5287 original size:156 final size:157
Alignment explanation
Indices: 5046--5370 Score: 361
Period size: 156 Copynumber: 2.1 Consensus size: 157
5036 AAAAACGGGA
* * * * **
5046 TTGGA-TATCCCCTCAAAAATAATAGGGTTGGAGTATCCTCGATTATGAAAATTGGTGTTTTGAA
1 TTGGAGTATCCCCTCAAAAATAACAGGGTTAGAGTATCCCCGATGATGAAAATCAGTGTTTTGAA
** * *
5110 AATAAAACTAGAGTTGGAGTATCCCTTCGAAAATAACGAGCTTGGAGTATCCCCGATTGTGAAAA
66 AATAAAACTAGAGTTAAAGTATCCCTTCGAAAATAACGAGCTTGGAGTATCCCCAATGGTGAAAA
*** * *
5175 ATTGGTGTTTT-AGAATAAAATTGAGG
131 ATCAATGTTTTGAAAATAAAATCGAGG
* * *
5201 TTGGAGTACCCCCTCGAAAATAACGGGGTTAGAGTATCCCCGATGATGAAAAATCAGTGTTTT-A
1 TTGGAGTATCCCCTCAAAAATAACAGGGTTAGAGTATCCCCGATGATG-AAAATCAGTGTTTTGA
* * * * * * * *
5265 GAATAAAACCT-GGGTTAAAGTATCCCTTTGGAAATAACGGGGTTTGAGTATCCCCAATGGTGGA
65 AAATAAAA-CTAGAGTTAAAGTATCCCTTCGAAAATAACGAGCTTGGAGTATCCCCAATGGTGAA
*
5329 AAATCAATGTTTTGAAAATAAAATCGGGG
129 AAATCAATGTTTTGAAAATAAAATCGAGG
5358 TTGGAGTATCCCC
1 TTGGAGTATCCCC
5371 GATGGTGAAA
Statistics
Matches: 138, Mismatches: 28, Indels: 6
0.80 0.16 0.03
Matches are distributed among these distances:
155 5 0.04
156 95 0.69
157 38 0.28
ACGTcount: A:0.33, C:0.14, G:0.23, T:0.29
Consensus pattern (157 bp):
TTGGAGTATCCCCTCAAAAATAACAGGGTTAGAGTATCCCCGATGATGAAAATCAGTGTTTTGAA
AATAAAACTAGAGTTAAAGTATCCCTTCGAAAATAACGAGCTTGGAGTATCCCCAATGGTGAAAA
ATCAATGTTTTGAAAATAAAATCGAGG
Found at i:5300 original size:78 final size:78
Alignment explanation
Indices: 5037--5369 Score: 309
Period size: 78 Copynumber: 4.3 Consensus size: 78
5027 TTTGGAGATA
* * ** * * *
5037 AAAAC-GGGATTGGA-TATCCCCTCAAAAATAATAGGGTTGGAGTATCCTCGATTATG-AAAATT
1 AAAACTGGG-TTGGAGTATCCCTTCGAAAATAACGGGGTTGGAGTATCCCCGATGATGAAAAATC
*
5099 GGTGTTTTGAAAAT
65 AGTGTTTTGAAAAT
* * *
5113 AAAACTAGAGTTGGAGTATCCCTTCGAAAATAACGAGCTTGGAGTATCCCCGATTG-TGAAAAAT
1 AAAACT-GGGTTGGAGTATCCCTTCGAAAATAACGGGGTTGGAGTATCCCCGA-TGATGAAAAAT
** *
5177 TGGTGTTTT-AGAAT
64 CAGTGTTTTGAAAAT
* * * *
5191 AAAATTGAGGTTGGAGTACCCCCTCGAAAATAACGGGGTTAGAGTATCCCCGATGATGAAAAATC
1 AAAACTG-GGTTGGAGTATCCCTTCGAAAATAACGGGGTTGGAGTATCCCCGATGATGAAAAATC
*
5256 AGTGTTTT-AGAAT
65 AGTGTTTTGAAAAT
** * * * * * *
5269 AAAACCTGGGTTAAAGTATCCCTTTGGAAATAACGGGGTTTGAGTATCCCCAATGGTGGAAAATC
1 AAAA-CTGGGTTGGAGTATCCCTTCGAAAATAACGGGGTTGGAGTATCCCCGATGATGAAAAATC
*
5334 AATGTTTTGAAAAT
65 AGTGTTTTGAAAAT
*
5348 AAAATCGGGGTTGGAGTATCCC
1 AAAA-CTGGGTTGGAGTATCCC
5370 CGATGGTGAA
Statistics
Matches: 212, Mismatches: 36, Indels: 15
0.81 0.14 0.06
Matches are distributed among these distances:
76 5 0.02
77 8 0.04
78 160 0.75
79 39 0.18
ACGTcount: A:0.34, C:0.14, G:0.24, T:0.28
Consensus pattern (78 bp):
AAAACTGGGTTGGAGTATCCCTTCGAAAATAACGGGGTTGGAGTATCCCCGATGATGAAAAATCA
GTGTTTTGAAAAT
Found at i:5369 original size:51 final size:51
Alignment explanation
Indices: 5302--5416 Score: 151
Period size: 51 Copynumber: 2.3 Consensus size: 51
5292 TTGGAAATAA
* * *
5302 CGGGGTTTGAGTATCCCCAATGGTGGAAAATCAATGTTTT-GAAAATAAAAT
1 CGGGGTTGGAGTATCCCCAATGGTGAAAAATCAATATTTTAG-AAATAAAAT
* **
5353 CGGGGTTGGAGTATCCCCGATGGTGAAAAATCGGTATTTTAGAAATAAAAT
1 CGGGGTTGGAGTATCCCCAATGGTGAAAAATCAATATTTTAGAAATAAAAT
*
5404 CGAGGTTGGAGTA
1 CGGGGTTGGAGTA
5417 ACCTCGAGAT
Statistics
Matches: 56, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
51 55 0.98
52 1 0.02
ACGTcount: A:0.33, C:0.11, G:0.28, T:0.28
Consensus pattern (51 bp):
CGGGGTTGGAGTATCCCCAATGGTGAAAAATCAATATTTTAGAAATAAAAT
Found at i:7746 original size:50 final size:50
Alignment explanation
Indices: 7692--7816 Score: 187
Period size: 50 Copynumber: 2.5 Consensus size: 50
7682 ATACATTGAG
* *
7692 AAATGTATCGATACATCTGGGTAAAACCCATAATGAATCGATACAATAAA
1 AAATGTATCGATACATTTGGGTAAAACCCAGAATGAATCGATACAATAAA
* * *
7742 AAATGTATCGATACATTTAGGTAAAACCCAGAATGTATCGATACAATGAA
1 AAATGTATCGATACATTTGGGTAAAACCCAGAATGAATCGATACAATAAA
* *
7792 GAATATATCGATACATTTGGGTAAA
1 AAATGTATCGATACATTTGGGTAAA
7817 TTTTGAATTT
Statistics
Matches: 67, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
50 67 1.00
ACGTcount: A:0.44, C:0.14, G:0.16, T:0.26
Consensus pattern (50 bp):
AAATGTATCGATACATTTGGGTAAAACCCAGAATGAATCGATACAATAAA
Found at i:8461 original size:40 final size:40
Alignment explanation
Indices: 8417--8515 Score: 110
Period size: 43 Copynumber: 2.4 Consensus size: 40
8407 CTTGCTCTTC
* *
8417 GAGGACAAAGGAAAAG-AGAATGAAATGGGTCCTACTCCTT
1 GAGGACAAAGGAAAAGAAAAAGGAAA-GGGTCCTACTCCTT
* *
8457 GAGGACAAAGGAAAAAAAGAAAAAGGAAAGTGTCCTGCTCCTT
1 GAGGACAAAGG---AAAAGAAAAAGGAAAGGGTCCTACTCCTT
8500 GAGGACAAAGGGAAAA
1 GAGGACAAA-GGAAAA
8516 ATAGTACGTC
Statistics
Matches: 50, Mismatches: 4, Indels: 9
0.79 0.06 0.14
Matches are distributed among these distances:
40 11 0.22
41 4 0.08
43 26 0.52
44 9 0.18
ACGTcount: A:0.45, C:0.13, G:0.28, T:0.13
Consensus pattern (40 bp):
GAGGACAAAGGAAAAGAAAAAGGAAAGGGTCCTACTCCTT
Found at i:8575 original size:42 final size:42
Alignment explanation
Indices: 8523--8764 Score: 220
Period size: 42 Copynumber: 5.7 Consensus size: 42
8513 AAAATAGTAC
* * * *
8523 GTCCTACTCTTCGAGGATAAAGGAAAAAAGGAAATGAAGTGT
1 GTCCTGCTCTTTGAGGACAAAGGAAAAAAGGAAATGAAATGT
* * ** *
8565 G-CCATGCTCTTTAAAGACAAAGGGGAAAAGGAAAT-AAAGTGC
1 GTCC-TGCTCTTTGAGGACAAAGGAAAAAAGGAAATGAAA-TGT
*
8607 GTCCTGCTCTTTGGGGACAAAGGGAAAAGAAGGAAATGAAATGT
1 GTCCTGCTCTTTGAGGACAAA-GGAAAA-AAGGAAATGAAATGT
* * * *
8651 GTCCTACTCTTTGAAGATAAAGGAAAAAA-GAGAACGAAATGT
1 GTCCTGCTCTTTGAGGACAAAGGAAAAAAGGA-AATGAAATGT
* * *
8693 GTCCTGCTCTTTGAGGAAAAAGAAAAAAAAGGAAATGAAATGC
1 GTCCTGCTCTTTGAGGACAAAG-GAAAAAAGGAAATGAAATGT
* * * *
8736 ATCTTGCTTTTTGAGGACAAAAGAAAAAA
1 GTCCTGCTCTTTGAGGACAAAGGAAAAAA
8765 AAGAAAAAGC
Statistics
Matches: 159, Mismatches: 32, Indels: 18
0.76 0.15 0.09
Matches are distributed among these distances:
41 6 0.04
42 78 0.49
43 43 0.27
44 29 0.18
45 3 0.02
ACGTcount: A:0.43, C:0.12, G:0.25, T:0.21
Consensus pattern (42 bp):
GTCCTGCTCTTTGAGGACAAAGGAAAAAAGGAAATGAAATGT
Found at i:8591 original size:78 final size:78
Alignment explanation
Indices: 8445--8593 Score: 180
Period size: 77 Copynumber: 1.9 Consensus size: 78
8435 AATGAAATGG
* *
8445 GTCCTACTCCTTGAGGACAAAGGAAAAAAAGAAAAAGGAAAGTGTCCTGCTCCTTGAGGACAAAG
1 GTCCTACTCCTTGAGGACAAAGGAAAAAAAGAAAAAGGAAAGTGTCCTGCTCCTTAAAGACAAAG
8510 GGAAAAATAGTAC
66 GGAAAAATAGTAC
* * * *
8523 GTCCTACT-CTTCGAGGATAAAGG-AAAAAAG-GAAATG-AAGTGTGCCATGCTCTTTAAAGACA
1 GTCCTACTCCTT-GAGGACAAAGGAAAAAAAGAAAAAGGAAAGTGT-CC-TGCTCCTTAAAGACA
*
8584 AAGGGGAAAA
63 AAGGGAAAAA
8594 GGAAATAAAG
Statistics
Matches: 61, Mismatches: 7, Indels: 7
0.81 0.09 0.09
Matches are distributed among these distances:
75 6 0.10
76 6 0.10
77 31 0.51
78 18 0.30
ACGTcount: A:0.42, C:0.15, G:0.25, T:0.18
Consensus pattern (78 bp):
GTCCTACTCCTTGAGGACAAAGGAAAAAAAGAAAAAGGAAAGTGTCCTGCTCCTTAAAGACAAAG
GGAAAAATAGTAC
Found at i:8673 original size:86 final size:83
Alignment explanation
Indices: 8522--8734 Score: 223
Period size: 86 Copynumber: 2.5 Consensus size: 83
8512 AAAAATAGTA
* * * *
8522 CGTCCTACTCTTCGAGGATAAAGGAAAAAAGGAAATGAAGTGTGCCATGCTCTTTAAAGACAAAG
1 CGTCCTGCTCTTTGAGGA-AAAGGAAAAAAGGAAATGAAATGTGCCATACTCTTTAAAGACAAAG
** *
8587 GGGAAAAG-GAAATAAAGTG
65 GAAAAAAGAGAAAGAAA-TG
* * *
8606 CGTCCTGCTCTTTGGGGACAAAGGGAAAAGAAGGAAATGAAATGTGTCC-TACTCTTTGAAGATA
1 CGTCCTGCTCTTTGAGGA-AAA-GGAAAA-AAGGAAATGAAATGTG-CCATACTCTTTAAAGACA
*
8670 AAGGAAAAAAGAGAACGAAATG
62 AAGGAAAAAAGAGAAAGAAATG
* *
8692 TGTCCTGCTCTTTGAGGAAAAAGAAAAAAAAGGAAATGAAATG
1 CGTCCTGCTCTTTGAGG-AAAAG-GAAAAAAGGAAATGAAATG
8735 CATCTTGCTT
Statistics
Matches: 108, Mismatches: 15, Indels: 11
0.81 0.11 0.08
Matches are distributed among these distances:
84 18 0.17
85 21 0.19
86 60 0.56
87 9 0.08
ACGTcount: A:0.42, C:0.12, G:0.26, T:0.20
Consensus pattern (83 bp):
CGTCCTGCTCTTTGAGGAAAAGGAAAAAAGGAAATGAAATGTGCCATACTCTTTAAAGACAAAGG
AAAAAAGAGAAAGAAATG
Found at i:8762 original size:85 final size:86
Alignment explanation
Indices: 8607--8769 Score: 202
Period size: 85 Copynumber: 1.9 Consensus size: 86
8597 AATAAAGTGC
* * * * ** *
8607 GTCCTGCTCTTTGGGGACAAAGGGAAAAGAAGGAAATGAAATGTGTCCTACTCTTTGAAGATAAA
1 GTCCTGCTCTTTGAGGACAAAAGAAAAAAAAGGAAATGAAATGCATCCTACTCTTTGAAGACAAA
* *
8672 GGAAAAAAGAGAACGAAATGT
66 AGAAAAAAAAGAACGAAATGT
* * * *
8693 GTCCTGCTCTTTGAGGA-AAAAGAAAAAAAAGGAAATGAAATGCATCTTGCTTTTTGAGGACAAA
1 GTCCTGCTCTTTGAGGACAAAAGAAAAAAAAGGAAATGAAATGCATCCTACTCTTTGAAGACAAA
8757 AGAAAAAAAAGAA
66 AGAAAAAAAAGAA
8770 AAAGCGTCCT
Statistics
Matches: 64, Mismatches: 13, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
85 48 0.75
86 16 0.25
ACGTcount: A:0.44, C:0.11, G:0.24, T:0.21
Consensus pattern (86 bp):
GTCCTGCTCTTTGAGGACAAAAGAAAAAAAAGGAAATGAAATGCATCCTACTCTTTGAAGACAAA
AGAAAAAAAAGAACGAAATGT
Found at i:8762 original size:128 final size:128
Alignment explanation
Indices: 8523--8762 Score: 281
Period size: 128 Copynumber: 1.9 Consensus size: 128
8513 AAAATAGTAC
* * * * *
8523 GTCCTACTCTTCGAGGATAAAGGAAAAAAGGAAATGAAGTGTGCCATGCTCTTTAAAGACAAAGG
1 GTCCTACTCTTCGAAGATAAAGGAAAAAAGGAAACGAAATGTGCCATGCTCTTTAAAGAAAAAGA
** * * *
8588 GGAAAAGGAAATAAAGTGCGTCCTGCTCTTTGGGGACAAAGGGAAAAGAAGGAAATGAAATGT
66 AAAAAAGGAAATAAAGTGCATCCTGCTCTTTGAGGACAAAGAGAAAAGAAGGAAATGAAATGT
* * *
8651 GTCCTACTCTTTGAAGATAAAGGAAAAAA-GAGAACGAAATGTGTCC-TGCTCTTTGAGGAAAAA
1 GTCCTACTCTTCGAAGATAAAGGAAAAAAGGA-AACGAAATGTG-CCATGCTCTTTAAAGAAAAA
* *
8714 GAAAAAAAAGGAAATGAAA-TGCATCTTGCTTTTTGAGGACAAA-AGAAAA
64 G-AAAAAAAGGAAAT-AAAGTGCATCCTGCTCTTTGAGGACAAAGAGAAAA
8763 AAAAGAAAAA
Statistics
Matches: 93, Mismatches: 15, Indels: 8
0.80 0.13 0.07
Matches are distributed among these distances:
127 2 0.02
128 56 0.60
129 32 0.34
130 3 0.03
ACGTcount: A:0.42, C:0.12, G:0.25, T:0.21
Consensus pattern (128 bp):
GTCCTACTCTTCGAAGATAAAGGAAAAAAGGAAACGAAATGTGCCATGCTCTTTAAAGAAAAAGA
AAAAAAGGAAATAAAGTGCATCCTGCTCTTTGAGGACAAAGAGAAAAGAAGGAAATGAAATGT
Found at i:8925 original size:61 final size:61
Alignment explanation
Indices: 8763--8987 Score: 217
Period size: 61 Copynumber: 3.7 Consensus size: 61
8753 CAAAAGAAAA
* * * * *
8763 AAAAGAAAAA-GCGTCCTGCTTTTTTAGGACT-AAAGGATGCCACCAACTCGTGTGGCCTTT
1 AAAAGAAAAAGGCGTCCTACTCTTTGAGGACTAAAAGG-TGCCACCAACTCGTGTGGGCTTC
** * * * *
8823 AAAAG-AAAAGTTGTCTTACTTTTTGAGGACAAAAAGGTGCCACCAGCTCGTGTGGGCTTC
1 AAAAGAAAAAGGCGTCCTACTCTTTGAGGACTAAAAGGTGCCACCAACTCGTGTGGGCTTC
* * * *
8883 AAAAGAAAAAGGCGTCCAACTCTTTGAGGACTAAAATGTGCCACCAACTTGTGTCGGCTTTC
1 AAAAGAAAAAGGCGTCCTACTCTTTGAGGACTAAAAGGTGCCACCAACTCGTGTGGGC-TTC
* * * *
8945 -AAACAAAAGGGCGTCTTGCTCTTTGAGGACT-AAAGTGTGCCAC
1 AAAAGAAAAAGGCGTCCTACTCTTTGAGGACTAAAAG-GTGCCAC
8988 TGTCGCGACG
Statistics
Matches: 135, Mismatches: 25, Indels: 9
0.80 0.15 0.05
Matches are distributed among these distances:
59 4 0.03
60 48 0.36
61 80 0.59
62 3 0.02
ACGTcount: A:0.31, C:0.21, G:0.23, T:0.25
Consensus pattern (61 bp):
AAAAGAAAAAGGCGTCCTACTCTTTGAGGACTAAAAGGTGCCACCAACTCGTGTGGGCTTC
Found at i:10174 original size:107 final size:108
Alignment explanation
Indices: 10047--10246 Score: 262
Period size: 107 Copynumber: 1.9 Consensus size: 108
10037 AAAATCAGGA
*
10047 TTGGAGTATCCCCTAAAAAATAACG-GCGTTGGAGTATCCCCAATTATGAGAAAA-CAATA-TTT
1 TTGGAGTATCCCCGAAAAAATAACGAG-GTTGGAGTATCCCCAATTATGA-AAAATCAATATTTT
* * *
10109 TGGGAATAAAGCCGGGGTTGGAGTATCCCCTCGGAAGTAACGGGG
64 TGGAAATAAAACCGGAGTTGGAGTATCCCCTCGGAAGTAACGGGG
* * * * * *
10154 TTGGAGTATCCCCGATAAAATAACGAGGTTGGAGTATCCTCGATTGTGAAAAATTAGTATTTTTG
1 TTGGAGTATCCCCGAAAAAATAACGAGGTTGGAGTATCCCCAATTATGAAAAATCAATATTTTTG
*
10219 GAAATAAAATCGGAGTTGGAGTATCCCC
66 GAAATAAAACCGGAGTTGGAGTATCCCC
10247 GATTAAAGGT
Statistics
Matches: 79, Mismatches: 11, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
106 4 0.05
107 45 0.57
108 30 0.38
ACGTcount: A:0.32, C:0.16, G:0.26, T:0.27
Consensus pattern (108 bp):
TTGGAGTATCCCCGAAAAAATAACGAGGTTGGAGTATCCCCAATTATGAAAAATCAATATTTTTG
GAAATAAAACCGGAGTTGGAGTATCCCCTCGGAAGTAACGGGG
Found at i:10177 original size:28 final size:28
Alignment explanation
Indices: 10121--10197 Score: 91
Period size: 28 Copynumber: 2.8 Consensus size: 28
10111 GGAATAAAGC
**** *
10121 CGGGGTTGGAGTATCCCCTCGGAAGTAA
1 CGGGGTTGGAGTATCCCCGATAAAATAA
10149 CGGGGTTGGAGTATCCCCGATAAAATAA
1 CGGGGTTGGAGTATCCCCGATAAAATAA
* *
10177 CGAGGTTGGAGTATCCTCGAT
1 CGGGGTTGGAGTATCCCCGAT
10198 TGTGAAAAAT
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 42 1.00
ACGTcount: A:0.25, C:0.19, G:0.32, T:0.23
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCGATAAAATAA
Found at i:10250 original size:52 final size:51
Alignment explanation
Indices: 10180--10569 Score: 303
Period size: 51 Copynumber: 7.4 Consensus size: 51
10170 AAAATAACGA
* *
10180 GGTTGGAGTATCCTCGATTGTGAAAAATTAGTATTTTTGGAAATAAAATCGG
1 GGTTGGAGTATCCCCGATTGTGAAAAATTAGT-GTTTTGGAAATAAAATCGG
* * * * *
10232 AGTTGGAGTATCCCCGATTAAAG-GTAAAATTGGTGTTTTGAAAATAAAACCGG
1 GGTTGGAGTATCCCCGATT---GTGAAAAATTAGTGTTTTGGAAATAAAATCGG
* * * *
10285 GGTTGGAGTATCTCCGATTGTGGAAAAATTAGTGTTTTAGCAATAAAACCGG
1 GGTTGGAGTATCCCCGATTGT-GAAAAATTAGTGTTTTGGAAATAAAATCGG
* * * * *
10337 GGTTGGAGTATCCCCGATTATGAAAAATCAATATTTTGGAAATAAAGTCGG
1 GGTTGGAGTATCCCCGATTGTGAAAAATTAGTGTTTTGGAAATAAAATCGG
* ** *
10388 GGTTGGAGTATCCCC--TCG-GAAATAA-T-G-GGGTTGGAGTATCCCCGATGATTAA-CGG
1 GGTTGGAGTATCCCCGATTGTGAAA-AATTAGTGTTTTGGA--A------AT-A-AAATCGG
*
10443 GGTTGGAGTATCCCCGATTGTGAAGAAATTGGTGTTTTTTGGAAATAAAATCGG
1 GGTTGGAGTATCCCCGATTGTGAA-AAATTAGTG--TTTTGGAAATAAAATCGG
* * *
10497 AGTTGGAGTATCCCCGATTAT-AGAAAATTAGTGTTTTGAAAATAAAATCGG
1 GGTTGGAGTATCCCCGATTGTGA-AAAATTAGTGTTTTGGAAATAAAATCGG
* *
10548 AGTTGGAATATCCCCGATTGTG
1 GGTTGGAGTATCCCCGATTGTG
10570 GAGAATTGAG
Statistics
Matches: 268, Mismatches: 42, Indels: 56
0.73 0.11 0.15
Matches are distributed among these distances:
46 5 0.02
48 5 0.02
49 3 0.01
50 1 0.00
51 74 0.28
52 61 0.23
53 44 0.16
54 35 0.13
55 22 0.08
56 1 0.00
57 2 0.01
58 5 0.02
59 2 0.01
60 1 0.00
61 2 0.01
63 5 0.02
ACGTcount: A:0.31, C:0.12, G:0.26, T:0.31
Consensus pattern (51 bp):
GGTTGGAGTATCCCCGATTGTGAAAAATTAGTGTTTTGGAAATAAAATCGG
Found at i:10290 original size:53 final size:53
Alignment explanation
Indices: 10180--10402 Score: 208
Period size: 52 Copynumber: 4.3 Consensus size: 53
10170 AAAATAACGA
* * * *
10180 GGTTGGAGTATCCTCGATT---GTGAAAAATTAGTATTTTTGGAAATAAAATCGG
1 GGTTGGAGTATCCCCGATTAAAG-GAAAAATTAGT-GTTTTGAAAATAAAACCGG
* * *
10232 AGTTGGAGTATCCCCGATTAAAGGTAAAATTGGTGTTTTGAAAATAAAACCGG
1 GGTTGGAGTATCCCCGATTAAAGGAAAAATTAGTGTTTTGAAAATAAAACCGG
* ** *
10285 GGTTGGAGTATCTCCGATT-GTGGAAAAATTAGTGTTTT-AGCAATAAAACCGG
1 GGTTGGAGTATCCCCGATTAAAGGAAAAATTAGTGTTTTGA-AAATAAAACCGG
* * * * * **
10337 GGTTGGAGTATCCCCGATT--ATGAAAAATCAATATTTTGGAAATAAAGTCGG
1 GGTTGGAGTATCCCCGATTAAAGGAAAAATTAGTGTTTTGAAAATAAAACCGG
10388 GGTTGGAGTATCCCC
1 GGTTGGAGTATCCCC
10403 TCGGAAATAA
Statistics
Matches: 142, Mismatches: 24, Indels: 11
0.80 0.14 0.06
Matches are distributed among these distances:
51 38 0.27
52 61 0.43
53 33 0.23
54 9 0.06
55 1 0.01
ACGTcount: A:0.32, C:0.12, G:0.26, T:0.30
Consensus pattern (53 bp):
GGTTGGAGTATCCCCGATTAAAGGAAAAATTAGTGTTTTGAAAATAAAACCGG
Found at i:10405 original size:264 final size:263
Alignment explanation
Indices: 10074--10571 Score: 786
Period size: 264 Copynumber: 1.9 Consensus size: 263
10064 AAATAACGGC
*
10074 GTTGGAGTATCCCCAATTATGAGAAAACAATATTTTGGGAATAAAGCCGGGGTTGGAGTATCCCC
1 GTTGGAGTATCCCCAATTATGAGAAAACAATATTTTGGAAATAAAGCCGGGGTTGGAGTATCCCC
* *
10139 TCGGAAGTAACGGGGTTGGAGTATCCCCGATAAAATAACGAGGTTGGAGTATCCTCGATTGTGAA
66 TCGGAAATAACGGGGTTGGAGTATCCCCGAT-AAATAACGAGGTTGGAGTATCCCCGATTGTGAA
*
10204 -AAATTAGT-ATTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCGATTAAAGGTAAAATTGGTG
130 GAAATTAGTGATTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCGATTAAA-G-AAAATTAGTG
* * *
10267 TTTTGAAAATAAAACCGGGGTTGGAGTATCTCCGATTGTGGAAAAATTAGTGTTTTAGCAATAAA
193 TTTTGAAAATAAAACCGGAGTTGGAATATCCCCGATTGTGGAAAAATTAGTGTTTTAGCAATAAA
10332 ACCGGG
258 ACCGGG
* *
10338 GTTGGAGTATCCCCGATTATGA-AAAATCAATATTTTGGAAATAAAGTCGGGGTTGGAGTATCCC
1 GTTGGAGTATCCCCAATTATGAGAAAA-CAATATTTTGGAAATAAAGCCGGGGTTGGAGTATCCC
* * * *
10402 CTCGGAAATAATGGGGTTGGAGTATCCCCGATGATTAACGGGGTTGGAGTATCCCCGATTGTGAA
65 CTCGGAAATAACGGGGTTGGAGTATCCCCGATAAATAACGAGGTTGGAGTATCCCCGATTGTGAA
* * *
10467 GAAATTGGTGTTTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCGATTATAGAAAATTAGTGTT
130 GAAATTAGTGATTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCGATTAAAGAAAATTAGTGTT
*
10532 TTGAAAATAAAATCGGAGTTGGAATATCCCCGATTGTGGA
195 TTGAAAATAAAACCGGAGTTGGAATATCCCCGATTGTGGA
10572 GAATTGAGAA
Statistics
Matches: 214, Mismatches: 17, Indels: 7
0.90 0.07 0.03
Matches are distributed among these distances:
263 80 0.37
264 94 0.44
265 40 0.19
ACGTcount: A:0.32, C:0.13, G:0.27, T:0.29
Consensus pattern (263 bp):
GTTGGAGTATCCCCAATTATGAGAAAACAATATTTTGGAAATAAAGCCGGGGTTGGAGTATCCCC
TCGGAAATAACGGGGTTGGAGTATCCCCGATAAATAACGAGGTTGGAGTATCCCCGATTGTGAAG
AAATTAGTGATTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCGATTAAAGAAAATTAGTGTTT
TGAAAATAAAACCGGAGTTGGAATATCCCCGATTGTGGAAAAATTAGTGTTTTAGCAATAAAACC
GGG
Found at i:10452 original size:27 final size:28
Alignment explanation
Indices: 10385--10460 Score: 100
Period size: 27 Copynumber: 2.8 Consensus size: 28
10375 GAAATAAAGT
***
10385 CGGGGTTGGAGTATCCCCTCGGAAATAA
1 CGGGGTTGGAGTATCCCCGATGAAATAA
* *
10413 TGGGGTTGGAGTATCCCCGATG-ATTAA
1 CGGGGTTGGAGTATCCCCGATGAAATAA
10440 CGGGGTTGGAGTATCCCCGAT
1 CGGGGTTGGAGTATCCCCGAT
10461 TGTGAAGAAA
Statistics
Matches: 42, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
27 24 0.57
28 18 0.43
ACGTcount: A:0.21, C:0.20, G:0.34, T:0.25
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCGATGAAATAA
Found at i:12934 original size:13 final size:13
Alignment explanation
Indices: 12916--12942 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
12906 AAAATTTCCA
12916 AATGTATCGATAC
1 AATGTATCGATAC
12929 AATGTATCGATAC
1 AATGTATCGATAC
12942 A
1 A
12943 TAGAAAAATG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
AATGTATCGATAC
Found at i:13011 original size:19 final size:17
Alignment explanation
Indices: 12987--13051 Score: 66
Period size: 19 Copynumber: 3.8 Consensus size: 17
12977 GCTAAATATA
12987 TATCGATACAATAGTTATG
1 TATCGATACAA-A-TTATG
13006 TATCGATAC--A-T-TG
1 TATCGATACAAATTATG
13019 TATCGATACAAAACTTATG
1 TATCGATAC-AAA-TTATG
13038 TATCGATACAAATT
1 TATCGATACAAATT
13052 GTTGAATTTC
Statistics
Matches: 40, Mismatches: 0, Indels: 14
0.74 0.00 0.26
Matches are distributed among these distances:
13 11 0.28
14 1 0.03
16 2 0.05
17 2 0.05
18 4 0.10
19 20 0.50
ACGTcount: A:0.38, C:0.14, G:0.12, T:0.35
Consensus pattern (17 bp):
TATCGATACAAATTATG
Found at i:13022 original size:13 final size:13
Alignment explanation
Indices: 13004--13028 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
12994 ACAATAGTTA
13004 TGTATCGATACAT
1 TGTATCGATACAT
13017 TGTATCGATACA
1 TGTATCGATACA
13029 AAACTTATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:13028 original size:32 final size:32
Alignment explanation
Indices: 12987--13047 Score: 104
Period size: 32 Copynumber: 1.9 Consensus size: 32
12977 GCTAAATATA
* *
12987 TATCGATACAATAGTTATGTATCGATACATTG
1 TATCGATACAAAACTTATGTATCGATACATTG
13019 TATCGATACAAAACTTATGTATCGATACA
1 TATCGATACAAAACTTATGTATCGATACA
13048 AATTGTTGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.38, C:0.15, G:0.13, T:0.34
Consensus pattern (32 bp):
TATCGATACAAAACTTATGTATCGATACATTG
Found at i:13425 original size:61 final size:59
Alignment explanation
Indices: 13311--13857 Score: 596
Period size: 61 Copynumber: 8.9 Consensus size: 59
13301 GGTGTTTACA
* ** * **
13311 GCCACCAACTCATGTAAGCTTTTAAAAGAAAAAGATGTCTTGCTCTTTGAGGACTAAAAAAT
1 GCCACCAACTCGTGTGGGC-TTTAAAAGAAAAAG-TG-CCTGCTCTTTGAGGACTAAAAGGT
* * *
13373 GCTACCAACTTGTGTGGGCTTTAAAAAGAAAAAGTGCCTTGCTCTTTGAGGACTAAGAGGT
1 GCCACCAACTCGTGTGGGCTTT-AAAAGAAAAAGTGCC-TGCTCTTTGAGGACTAAAAGGT
* * *
13434 GACACCAACTCGTGTGGGCTTTAAAAG-AAAAGGGCATTCTACTCTTTGAGGACTAAAAGGT
1 GCCACCAACTCGTGTGGGCTTTAAAAGAAAAAGTGC---CTGCTCTTTGAGGACTAAAAGGT
* *
13495 GCCACCAACTCGTGTGGGCTTTAAAAGAAAAGGTGTCATGCTCTTTGAGGACTAAAAGGT
1 GCCACCAACTCGTGTGGGCTTTAAAAGAAAAAGTG-CCTGCTCTTTGAGGACTAAAAGGT
* * * *
13555 GCCACCAACTTGTGTGGGCTTTAAAAAGGAAAAGCGCCCTGCTCTTTAAGGACTAAAAGGT
1 GCCACCAACTCGTGTGGGCTTT-AAAAGAAAAAGTG-CCTGCTCTTTGAGGACTAAAAGGT
*
13616 GCCACCAACTCGTGTGGGCTTTAAAAGAAAAAG-GCATCCTGCTCTTTGAGGACTAAAAAGT
1 GCCACCAACTCGTGTGGGCTTTAAAAGAAAAAGTG---CCTGCTCTTTGAGGACTAAAAGGT
* * * * *
13677 GCCACCAACTTGTGTAGGCTTTAAACAG-AAAGGTGTCCTACTCTTTGAGGACTAGAAGGGT
1 GCCACCAACTCGTGTGGGCTTTAAA-AGAAAAAGTG-CCTGCTCTTTGAGGACTA-AAAGGT
* * * *
13738 GCCACCAGCTTGTGTGGGCTTTGAAAAGAAAAAGGTATCCTACTCTTTGAGGACTAAAAGGT
1 GCCACCAACTCGTGTGGGCTTT-AAAAGAAAAA-GT-GCCTGCTCTTTGAGGACTAAAAGGT
* *
13800 GCCACCAACTCGTGTGGGCTTTGAAAAGAAAAAGGTATCCTACTCTTTGAGGACTAAA
1 GCCACCAACTCGTGTGGGCTTT-AAAAGAAAAA-GT-GCCTGCTCTTTGAGGACTAAA
13858 GGGAAAAAAA
Statistics
Matches: 423, Mismatches: 45, Indels: 34
0.84 0.09 0.07
Matches are distributed among these distances:
59 8 0.02
60 76 0.18
61 217 0.51
62 101 0.24
63 21 0.05
ACGTcount: A:0.32, C:0.19, G:0.24, T:0.25
Consensus pattern (59 bp):
GCCACCAACTCGTGTGGGCTTTAAAAGAAAAAGTGCCTGCTCTTTGAGGACTAAAAGGT
Found at i:13502 original size:122 final size:120
Alignment explanation
Indices: 13353--13857 Score: 624
Period size: 121 Copynumber: 4.1 Consensus size: 120
13343 AGATGTCTTG
** * *
13353 CTCTTTGAGGACTAAAAAATGCTACCAACTTGTGTGGGCTTTAAAAAGAAAAAGTGCCTTGCTCT
1 CTCTTTGAGGACTAAAAGGTGCCACCAACTCGTGTGGGCTTT-AAAAGAAAAAGTGCC-TGCTCT
* * *
13418 TTGAGGACTAAGAGGTGACACCAACTCGTGTGGGCTTT-AAAAGAAAAGGGCATTCTA
64 TTGAGGACTAAAAGGTGCCACCAACTCGTGTGGGCTTTAAAAAGAAAAGGGC-TCCTA
* *
13475 CTCTTTGAGGACTAAAAGGTGCCACCAACTCGTGTGGGCTTTAAAAGAAAAGGTGTCATGCTCTT
1 CTCTTTGAGGACTAAAAGGTGCCACCAACTCGTGTGGGCTTTAAAAGAAAAAGTG-CCTGCTCTT
* * *
13540 TGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAAGGAAAAGCGC-CCTG
65 TGAGGACTAAAAGGTGCCACCAACTCGTGTGGGCTTTAAAAA-GAAAAGGGCTCCTA
*
13596 CTCTTTAAGGACTAAAAGGTGCCACCAACTCGTGTGGGCTTTAAAAGAAAAAG-GCATCCTGCTC
1 CTCTTTGAGGACTAAAAGGTGCCACCAACTCGTGTGGGCTTTAAAAGAAAAAGTG---CCTGCTC
* * * *
13660 TTTGAGGACTAAAAAGTGCCACCAACTTGTGTAGGCTTTAAACAG-AAAGGTG-TCCTA
63 TTTGAGGACTAAAAGGTGCCACCAACTCGTGTGGGCTTTAAAAAGAAAAGG-GCTCCTA
* * * * *
13717 CTCTTTGAGGACTAGAAGGGTGCCACCAGCTTGTGTGGGCTTTGAAAAGAAAAAGGTATCCTACT
1 CTCTTTGAGGACTA-AAAGGTGCCACCAACTCGTGTGGGCTTT-AAAAGAAAAA-GT-GCCTGCT
* **
13782 CTTTGAGGACTAAAAGGTGCCACCAACTCGTGTGGGCTTTGAAAAGAAAAAGGTATCCTA
62 CTTTGAGGACTAAAAGGTGCCACCAACTCGTGTGGGCTTTAAAAAG-AAAAGGGCTCCTA
13842 CTCTTTGAGGACTAAA
1 CTCTTTGAGGACTAAA
13858 GGGAAAAAAA
Statistics
Matches: 336, Mismatches: 32, Indels: 28
0.85 0.08 0.07
Matches are distributed among these distances:
120 5 0.01
121 124 0.37
122 116 0.35
123 64 0.19
124 3 0.01
125 24 0.07
ACGTcount: A:0.31, C:0.19, G:0.25, T:0.25
Consensus pattern (120 bp):
CTCTTTGAGGACTAAAAGGTGCCACCAACTCGTGTGGGCTTTAAAAGAAAAAGTGCCTGCTCTTT
GAGGACTAAAAGGTGCCACCAACTCGTGTGGGCTTTAAAAAGAAAAGGGCTCCTA
Found at i:13663 original size:182 final size:181
Alignment explanation
Indices: 13311--13857 Score: 772
Period size: 182 Copynumber: 3.0 Consensus size: 181
13301 GGTGTTTACA
* * * * ** *
13311 GCCACCAACTCATGTAAGCTTTTAAAAGAAAAAGATGTCTTGCTCTTTGAGGACTAAAAAATGCT
1 GCCACCAACTCGTGTAGGC-TTTAAAAG-AAAAGGTGTCATGCTCTTTGAGGACTAAAAGGTGCC
* * *
13376 ACCAACTTGTGTGGGCTTTAAAAAGAAAAAGTGCCTTGCTCTTTGAGGACTAAGAGGTGACACCA
64 ACCAACTTGTGTGGGCTTTAAAAAGAAAAAG-GCCCTGCTCTTTGAGGACTAAAAGGTGCCACCA
* * *
13441 ACTCGTGTGGGCTTTAAAAGAAAAGGGCATTCTACTCTTTGAGGACTAAAAGGT
128 ACTCGTGTGGGCTTTAAAAGAAAAAGGCATCCTACTCTTTGAGGACTAAAAAGT
*
13495 GCCACCAACTCGTGTGGGCTTTAAAAGAAAAGGTGTCATGCTCTTTGAGGACTAAAAGGTGCCAC
1 GCCACCAACTCGTGTAGGCTTTAAAAGAAAAGGTGTCATGCTCTTTGAGGACTAAAAGGTGCCAC
* *
13560 CAACTTGTGTGGGCTTTAAAAAGGAAAAGCGCCCTGCTCTTTAAGGACTAAAAGGTGCCACCAAC
66 CAACTTGTGTGGGCTTTAAAAAGAAAAAG-GCCCTGCTCTTTGAGGACTAAAAGGTGCCACCAAC
*
13625 TCGTGTGGGCTTTAAAAGAAAAAGGCATCCTGCTCTTTGAGGACTAAAAAGT
130 TCGTGTGGGCTTTAAAAGAAAAAGGCATCCTACTCTTTGAGGACTAAAAAGT
* * * *
13677 GCCACCAACTTGTGTAGGCTTTAAACAG-AAAGGTGTCCTACTCTTTGAGGACTAGAAGGGTGCC
1 GCCACCAACTCGTGTAGGCTTTAAA-AGAAAAGGTGTCATGCTCTTTGAGGACTA-AAAGGTGCC
* * * *
13741 ACCAGCTTGTGTGGGCTTTGAAAAGAAAAAGGTATCCTACTCTTTGAGGACTAAAAGGTGCCACC
64 ACCAACTTGTGTGGGCTTTAAAAAGAAAAAGG--CCCTGCTCTTTGAGGACTAAAAGGTGCCACC
*
13806 AACTCGTGTGGGCTTTGAAAAGAAAAAGGTATCCTACTCTTTGAGGACTAAA
127 AACTCGTGTGGGCTTT-AAAAGAAAAAGGCATCCTACTCTTTGAGGACTAAA
13858 GGGAAAAAAA
Statistics
Matches: 327, Mismatches: 31, Indels: 9
0.89 0.08 0.02
Matches are distributed among these distances:
182 188 0.57
183 46 0.14
184 60 0.18
185 33 0.10
ACGTcount: A:0.32, C:0.19, G:0.24, T:0.25
Consensus pattern (181 bp):
GCCACCAACTCGTGTAGGCTTTAAAAGAAAAGGTGTCATGCTCTTTGAGGACTAAAAGGTGCCAC
CAACTTGTGTGGGCTTTAAAAAGAAAAAGGCCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACT
CGTGTGGGCTTTAAAAGAAAAAGGCATCCTACTCTTTGAGGACTAAAAAGT
Found at i:15122 original size:23 final size:24
Alignment explanation
Indices: 15080--15124 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
15070 CCTTTGCTCT
*
15080 TTTCTCATTTTTGTTTCTTTTGTG
1 TTTCTCATTTTTGTTGCTTTTGTG
15104 TTTCTCATTTTTG-TGCTTTTG
1 TTTCTCATTTTTGTTGCTTTTG
15125 CCCTTCTTCT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 7 0.35
24 13 0.65
ACGTcount: A:0.04, C:0.13, G:0.13, T:0.69
Consensus pattern (24 bp):
TTTCTCATTTTTGTTGCTTTTGTG
Found at i:15131 original size:23 final size:24
Alignment explanation
Indices: 15081--15131 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
15071 CTTTGCTCTT
* ***
15081 TTCTCATTTTTGTTTCTTTTGTGT
1 TTCTCATTTTTGTTGCTTTTGCCC
15105 TTCTCATTTTTG-TGCTTTTGCCC
1 TTCTCATTTTTGTTGCTTTTGCCC
15128 TTCT
1 TTCT
15132 TCTTTTTTTT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
23 11 0.48
24 12 0.52
ACGTcount: A:0.04, C:0.20, G:0.12, T:0.65
Consensus pattern (24 bp):
TTCTCATTTTTGTTGCTTTTGCCC
Found at i:20155 original size:78 final size:78
Alignment explanation
Indices: 20031--20312 Score: 276
Period size: 78 Copynumber: 3.7 Consensus size: 78
20021 TATTTTGGAG
* * * * *
20031 ATAAAAACGGGGTTGGA-TATCCCCTCAAAAATAATGGGGTTCGAGTATCCTCGATTGT-GACAA
1 ATAAAACCAGGGTTGGAGTATCCCCTCAAAAATAACGAGGTTGGAGTATCCTCGATTGTGGA-AA
*
20094 TAT-GTGTTTTGGAA
65 TATCGTGTTTTAG-A
* * *
20108 ATAAAACCAAGGTTGGAGTATCCCCTCGAAAATAACGAGGTTGGAGTATCCCCGATTGTGGAAA-
1 ATAAAACCAGGGTTGGAGTATCCCCTCAAAAATAACGAGGTTGGAGTATCCTCGATTGTGGAAAT
* *
20172 ATTGGTATTTTAGA
66 A-TCGTGTTTTAGA
* * * *
20186 ATAAAACTAGGGTTGGAGCA-CCCTCTCAAAAATAACGAGGATGGAGTATCCTC-AATGATGGAA
1 ATAAAACCAGGGTTGGAGTATCCC-CTCAAAAATAACGAGGTTGGAGTATCCTCGATTG-TGGAA
20249 A-ATCGATGTTTTAGA
64 ATATCG-TGTTTTAGA
* * * *
20264 ATAAAA-TAGGGCTGGAGTATCCCCTC-AAAATAACGGGGTTAGAGTATCC
1 ATAAAACCAGGGTTGGAGTATCCCCTCAAAAATAACGAGGTTGGAGTATCC
20313 CCTCGAAATA
Statistics
Matches: 173, Mismatches: 24, Indels: 17
0.81 0.11 0.08
Matches are distributed among these distances:
76 20 0.12
77 37 0.21
78 107 0.62
79 9 0.05
ACGTcount: A:0.34, C:0.16, G:0.24, T:0.26
Consensus pattern (78 bp):
ATAAAACCAGGGTTGGAGTATCCCCTCAAAAATAACGAGGTTGGAGTATCCTCGATTGTGGAAAT
ATCGTGTTTTAGA
Found at i:20368 original size:28 final size:28
Alignment explanation
Indices: 20276--20372 Score: 126
Period size: 28 Copynumber: 3.4 Consensus size: 28
20266 AAAATAGGGC
*
20276 TGGAGTATCCCCTC-AAAATAACGGGGT
1 TGGAGTATCCCCTCAAAAATAACGAGGT
* *
20303 TAGAGTATCCCCTCGAAATAA-AACCAAGGT
1 TGGAGTATCCCCTC-AAA-AATAA-CGAGGT
20333 TGGAGTATCCCCTCAAAAATAACGAGGT
1 TGGAGTATCCCCTCAAAAATAACGAGGT
20361 TGGAGTATCCCC
1 TGGAGTATCCCC
20373 GATTGTGGAA
Statistics
Matches: 60, Mismatches: 5, Indels: 9
0.81 0.07 0.12
Matches are distributed among these distances:
27 13 0.22
28 19 0.32
29 9 0.15
30 19 0.32
ACGTcount: A:0.33, C:0.24, G:0.22, T:0.22
Consensus pattern (28 bp):
TGGAGTATCCCCTCAAAAATAACGAGGT
Found at i:20472 original size:212 final size:213
Alignment explanation
Indices: 20105--20527 Score: 794
Period size: 212 Copynumber: 2.0 Consensus size: 213
20095 ATGTGTTTTG
*
20105 GAAATAAAACCAAGGTTGGAGTATCCCCTCGAAAATAACGAGGTTGGAGTATCCCCGATTGTGGA
1 GAAATAAAACCAAGGTTGGAGTATCCCCTCAAAAATAACGAGGTTGGAGTATCCCCGATTGTGGA
*
20170 AAATTGGTATTTTAGAATAAAACTAGGGTTGGAGCACCCTCTCAAAAATAACGAGGATGGAGTAT
66 AAATTGGTATTTTAGAATAAAACCAGGGTTGGAGCACCCTCTCAAAAATAACGAGGATGGAGTAT
*
20235 CCTCAATGATGGAAAATCGATGTTTTAGAATAAAATAGGGCTGGAGTATCCCCTC-AAAATAACG
131 CCTCAATGATGGAAAATCGATGTTTTAGAATAAAATAGGGCTAGAGTATCCCCTCGAAAATAACG
20299 GGGTTAGAGTATCCCCTC
196 GGGTTAGAGTATCCCCTC
20317 GAAATAAAACCAAGGTTGGAGTATCCCCTCAAAAATAACGAGGTTGGAGTATCCCCGATTGTGGA
1 GAAATAAAACCAAGGTTGGAGTATCCCCTCAAAAATAACGAGGTTGGAGTATCCCCGATTGTGGA
* *
20382 AAATTGGTATTTTAGAATAAAACCAGGGTTGGAGCACCTTCTCGAAAATAACGAGGATGGAGTAT
66 AAATTGGTATTTTAGAATAAAACCAGGGTTGGAGCACCCTCTCAAAAATAACGAGGATGGAGTAT
20447 CCTCAATGATGGAAAATCGATGTTTTAGAATAAAATAGGGCTAGAGTATCCCCTCGAAAATAACG
131 CCTCAATGATGGAAAATCGATGTTTTAGAATAAAATAGGGCTAGAGTATCCCCTCGAAAATAACG
20512 GGGTTAGAGTATCCCC
196 GGGTTAGAGTATCCCC
20528 AATGGAGGAA
Statistics
Matches: 205, Mismatches: 5, Indels: 1
0.97 0.02 0.00
Matches are distributed among these distances:
212 180 0.88
213 25 0.12
ACGTcount: A:0.35, C:0.17, G:0.24, T:0.24
Consensus pattern (213 bp):
GAAATAAAACCAAGGTTGGAGTATCCCCTCAAAAATAACGAGGTTGGAGTATCCCCGATTGTGGA
AAATTGGTATTTTAGAATAAAACCAGGGTTGGAGCACCCTCTCAAAAATAACGAGGATGGAGTAT
CCTCAATGATGGAAAATCGATGTTTTAGAATAAAATAGGGCTAGAGTATCCCCTCGAAAATAACG
GGGTTAGAGTATCCCCTC
Found at i:20560 original size:290 final size:291
Alignment explanation
Indices: 20041--20589 Score: 711
Period size: 290 Copynumber: 1.9 Consensus size: 291
20031 ATAAAAACGG
* * * * * *
20041 GGTTGGATATCCCCTCAAAAATAATGGGGTTCGAGTATCCTCGATTGTGACAATATGTGTTTTGG
1 GGTTGGATATCCCCTCAAAAATAACGAGGTTCGAGTATCCCCGATTGTGAAAATATGTATTTTAG
* * *
20106 AAATAAAACCAAGGTTGGAGTATCCCCTCGAAAATAACGAGGTTGGAGTATCCCCGATTGTGGAA
66 AAATAAAACCAAGGTTGGAGCATCCCCTCGAAAATAACGAGGATGGAGTATCCCCGAATGTGGAA
* * * * *
20171 AATTGGTATTTTAGAATAAAACTAGGGTTGGAGCACCCTCTCAAAAATAACGAGGATGGAGTATC
131 AATCGATATTTTAGAATAAAACTAGGGCTAGAGCACCCTCTCAAAAATAACGAGGATAGAGTATC
* *
20236 CTCAATGATGGAAAATCGATGTTTTAGAATAAAA-TAGGGCTGGAGTATCCCCTCA-AAATAACG
196 CCCAATGATGGAAAATCGATGTTTTAAAATAAAATTAGGGCTGGAGTATCCCCTCAGAAATAACG
20299 GGGTTAGAGTATCCCCTCGAAATAAAACCAA
261 GGGTTAGAGTATCCCCTCGAAATAAAACCAA
*
20330 GGTTGGAGTATCCCCTCAAAAATAACGAGGTTGGAGTATCCCCGATTGTGGAAAAT-TGGTATTT
1 GGTTGGA-TATCCCCTCAAAAATAACGAGGTTCGAGTATCCCCGATTGT-GAAAATAT-GTATTT
* * *
20394 TAG-AATAAAACCAGGGTTGGAGCA-CCTTCTCGAAAATAACGAGGATGGAGTATCCTC-AATGA
63 TAGAAATAAAACCAAGGTTGGAGCATCC-CCTCGAAAATAACGAGGATGGAGTATCCCCGAATG-
* * * * *
20456 TGGAAAATCGATGTTTTAGAATAAAA-TAGGGCTAGAGTATCCC-CTCGAAAATAACGGGGTTAG
126 TGGAAAATCGATATTTTAGAATAAAACTAGGGCTAGAGCA-CCCTCTCAAAAATAACGAGGATAG
* * *
20519 AGTATCCCCAATGGA-GGAAAATCGGTGTTTTGAAAATAAAATTGGGGTTGGAGTATCCCCTCAG
190 AGTATCCCCAAT-GATGGAAAATCGATGTTTT-AAAATAAAATTAGGGCTGGAGTATCCCCTCAG
20583 AAATAAC
253 AAATAAC
20590 CAAGTTGGAG
Statistics
Matches: 222, Mismatches: 28, Indels: 17
0.83 0.10 0.06
Matches are distributed among these distances:
289 64 0.29
290 120 0.54
291 31 0.14
292 7 0.03
ACGTcount: A:0.34, C:0.16, G:0.24, T:0.26
Consensus pattern (291 bp):
GGTTGGATATCCCCTCAAAAATAACGAGGTTCGAGTATCCCCGATTGTGAAAATATGTATTTTAG
AAATAAAACCAAGGTTGGAGCATCCCCTCGAAAATAACGAGGATGGAGTATCCCCGAATGTGGAA
AATCGATATTTTAGAATAAAACTAGGGCTAGAGCACCCTCTCAAAAATAACGAGGATAGAGTATC
CCCAATGATGGAAAATCGATGTTTTAAAATAAAATTAGGGCTGGAGTATCCCCTCAGAAATAACG
GGGTTAGAGTATCCCCTCGAAATAAAACCAA
Found at i:20602 original size:79 final size:78
Alignment explanation
Indices: 20318--20655 Score: 342
Period size: 78 Copynumber: 4.3 Consensus size: 78
20308 TATCCCCTCG
* * * * * *
20318 AAATAAAACCAAGGTTGGAGTATCCCCTCAAAAATAACGAGGTTGGAGTATCCCCGATTGTGGAA
1 AAATAAAATCAGGGTTGGAGTATCCCCTCGAAAATAACGAGGTTGGAGTATCCCCAATGGAGGAA
* *
20383 AATTGGTATTTTA
66 AATCGGTGTTTTA
* * * * * *
20396 GAATAAAACCAGGGTTGGAGCA-CCTTCTCGAAAATAACGAGGATGGAGTATCCTCAAT-GATGG
1 AAATAAAATCAGGGTTGGAGTATCC-CCTCGAAAATAACGAGGTTGGAGTATCCCCAATGGA-GG
*
20459 AAAATCGATGTTTTA
64 AAAATCGGTGTTTTA
* * * * *
20474 GAATAAAAT-AGGGCTAGAGTATCCCCTCGAAAATAACGGGGTTAGAGTATCCCCAATGGAGGAA
1 AAATAAAATCAGGGTTGGAGTATCCCCTCGAAAATAACGAGGTTGGAGTATCCCCAATGGAGGAA
20538 AATCGGTGTTTTGA
66 AATCGGTGTTTT-A
** * * * * *
20552 AAATAAAATTGGGGTTGGAGTATCCCCTC-AGAAATAACCAAGTTGGAGTATCTCCTATGGTGGA
1 AAATAAAATCAGGGTTGGAGTATCCCCTCGA-AAATAACGAGGTTGGAGTATCCCCAATGGAGGA
*
20616 AAATCAGTGTTTTA
65 AAATCGGTGTTTTA
*
20630 GAAATAAAATCGGGGTTGGAGTATCC
1 -AAATAAAATCAGGGTTGGAGTATCC
20656 TTGAGATGAC
Statistics
Matches: 217, Mismatches: 35, Indels: 15
0.81 0.13 0.06
Matches are distributed among these distances:
77 55 0.25
78 84 0.39
79 78 0.36
ACGTcount: A:0.35, C:0.15, G:0.25, T:0.26
Consensus pattern (78 bp):
AAATAAAATCAGGGTTGGAGTATCCCCTCGAAAATAACGAGGTTGGAGTATCCCCAATGGAGGAA
AATCGGTGTTTTA
Found at i:22817 original size:36 final size:36
Alignment explanation
Indices: 22770--22841 Score: 144
Period size: 36 Copynumber: 2.0 Consensus size: 36
22760 ATTAAGGGCA
22770 TGTATCGATACATTTTGGCAAAAATGTGGTTTTCTC
1 TGTATCGATACATTTTGGCAAAAATGTGGTTTTCTC
22806 TGTATCGATACATTTTGGCAAAAATGTGGTTTTCTC
1 TGTATCGATACATTTTGGCAAAAATGTGGTTTTCTC
22842 ATACTTTTTG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.25, C:0.14, G:0.19, T:0.42
Consensus pattern (36 bp):
TGTATCGATACATTTTGGCAAAAATGTGGTTTTCTC
Found at i:28309 original size:27 final size:26
Alignment explanation
Indices: 28267--28319 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 26
28257 TTCGAAATAT
28267 CCTAAACCTAACAACCAAAAACAAAA
1 CCTAAACCTAACAACCAAAAACAAAA
*
28293 CCTACAACC-AACTAACCAAGAACAAAA
1 CCTA-AACCTAAC-AACCAAAAACAAAA
28320 TAACACAATA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
26 7 0.29
27 17 0.71
ACGTcount: A:0.58, C:0.32, G:0.02, T:0.08
Consensus pattern (26 bp):
CCTAAACCTAACAACCAAAAACAAAA
Found at i:33357 original size:2 final size:2
Alignment explanation
Indices: 33350--33383 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
33340 TAAAATTTGG
33350 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
33384 GTACCAGAGC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:33772 original size:2 final size:2
Alignment explanation
Indices: 33765--33797 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
33755 AAGAAGAAAA
*
33765 AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
33798 AGTAAAAGTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:39234 original size:13 final size:13
Alignment explanation
Indices: 39216--39241 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
39206 ACATAAGTGT
39216 TGTATCGATACAA
1 TGTATCGATACAA
39229 TGTATCGATACAA
1 TGTATCGATACAA
39242 AAACTATCTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:54740 original size:28 final size:28
Alignment explanation
Indices: 54702--54866 Score: 195
Period size: 28 Copynumber: 5.7 Consensus size: 28
54692 CATTCCTCAC
54702 CCTTTTCAAAGCCCACAAGTCAGTGGCA
1 CCTTTTCAAAGCCCACAAGTCAGTGGCA
* *
54730 CCTTTTCAAAGCCTACTAGTCAGTGGCA
1 CCTTTTCAAAGCCCACAAGTCAGTGGCA
*
54758 TCTTTTCAAAGCCCACAAGTCAGTGGCACCA
1 CCTTTTCAAAGCCCACAAGTCAGTGG---CA
* * *
54789 CCCCTTTCAAAAGCCCATAAGTCGGTGGCA
1 -CCTTTTC-AAAGCCCACAAGTCAGTGGCA
* *
54819 CCCCTTTCAAAGCCCACAAGTTAGTGGCA
1 -CCTTTTCAAAGCCCACAAGTCAGTGGCA
*
54848 CATTTTCAAAGCCCACAAG
1 CCTTTTCAAAGCCCACAAG
54867 ATAATGGCAA
Statistics
Matches: 118, Mismatches: 14, Indels: 10
0.83 0.10 0.07
Matches are distributed among these distances:
28 66 0.56
29 18 0.15
30 10 0.08
31 2 0.02
32 5 0.04
33 17 0.14
ACGTcount: A:0.28, C:0.32, G:0.17, T:0.22
Consensus pattern (28 bp):
CCTTTTCAAAGCCCACAAGTCAGTGGCA
Found at i:54859 original size:90 final size:88
Alignment explanation
Indices: 54699--54866 Score: 239
Period size: 90 Copynumber: 1.9 Consensus size: 88
54689 AAACATTCCT
* * * *
54699 CACCCTTTTCAAAGCCCACAAGTCAGTGGCACCTTTTCAAAGCCTACTAGTCAGTGGCATCTTTT
1 CACCCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCATCTTTT
54764 CAAAGCCCACAAGTCAGTGGCAC
66 CAAAGCCCACAAGTCAGTGGCAC
* * *
54787 CACCCCTTTCAAAAGCCCATAAGTCGGTGGCACCCCTTTCAAAGCCCACAAGTTAGTGGCA-CAT
1 CACCCCTTTC-AAAGCCCACAAGTCAGTGGCA-CCCTTTCAAAGCCCACAAGTCAGTGGCATC-T
54851 TTTCAAAGCCCACAAG
63 TTTCAAAGCCCACAAG
54867 ATAATGGCAA
Statistics
Matches: 70, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
88 9 0.13
89 20 0.29
90 41 0.59
ACGTcount: A:0.29, C:0.33, G:0.17, T:0.22
Consensus pattern (88 bp):
CACCCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCATCTTTT
CAAAGCCCACAAGTCAGTGGCAC
Found at i:54874 original size:28 final size:27
Alignment explanation
Indices: 54822--54892 Score: 88
Period size: 28 Copynumber: 2.6 Consensus size: 27
54812 GGTGGCACCC
* *
54822 CTTTCAAAGCCCACAAGTTAGTGGCACA
1 CTTTCAAAGCCCACAAGATAATGGCA-A
*
54850 TTTTCAAAGCCCACAAGATAATGGCAA
1 CTTTCAAAGCCCACAAGATAATGGCAA
*
54877 CCTTCAAAAGCCCACA
1 CTTTC-AAAGCCCACA
54893 CAAGTTGGTG
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
27 4 0.11
28 33 0.89
ACGTcount: A:0.37, C:0.30, G:0.14, T:0.20
Consensus pattern (27 bp):
CTTTCAAAGCCCACAAGATAATGGCAA
Found at i:54985 original size:49 final size:49
Alignment explanation
Indices: 54924--55333 Score: 326
Period size: 49 Copynumber: 8.5 Consensus size: 49
54914 AAGTCCGATA
54924 TCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGACCAATG
1 TCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGACCAATG
* * * * *
54973 TCGCCGGCCTTGAATCAACACATTGGCACCTTCATTTTTAAGTCCAATA
1 TCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGACCAATG
* * * *
55022 TCGATGGCCTTGAATCAGCATATTGGCGCCTTCGTCATCTTTAAGACCAAGG
1 TCGCTGGCCTTGAATCAGCACATTGGCACC-T--TCATCTTTAAGACCAATG
* * * *
55074 TCGCCGGCCTTGAATCAGTACATTGG------CA----TAAGCCCAATA
1 TCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGACCAATG
* * * *
55113 TCGCTGGCCTTGAATCAACATATTGACACCTT-GTCTTTAAGACCAATG
1 TCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGACCAATG
* * * ** *
55161 TCGCTGGCCTTGAATCAGCATATTGGCACTTTCATCTTTAAGTCTGATA
1 TCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGACCAATG
* * * * *
55210 TCGTTGGGCTTGAATCAGCATATTGGCATCTTTAACAT-TCTTAAGCCCAATG
1 TCGCTGGCCTTGAATCAGCACATTGGCA-CCTT--CATCT-TTAAGACCAATG
* ** * * * * *
55262 TCGTTGGCCTTGTCTCAGCAAATTGGCA--TTCTTCTTCAAGTCTAATG
1 TCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGACCAATG
*
55309 TCGCTGGCCATGAATCAGCACATTG
1 TCGCTGGCCTTGAATCAGCACATTG
55334 TCATTCTTCG
Statistics
Matches: 286, Mismatches: 56, Indels: 40
0.75 0.15 0.10
Matches are distributed among these distances:
39 29 0.10
43 2 0.01
47 31 0.11
48 39 0.14
49 108 0.38
50 5 0.02
51 1 0.00
52 71 0.25
ACGTcount: A:0.24, C:0.25, G:0.19, T:0.31
Consensus pattern (49 bp):
TCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGACCAATG
Found at i:55176 original size:87 final size:89
Alignment explanation
Indices: 55011--55188 Score: 243
Period size: 87 Copynumber: 2.0 Consensus size: 89
55001 CCTTCATTTT
* * * *
55011 TAAGTCCAATATCGATGGCCTTGAATCAGCATATTGGCGCCTTCGTCATCTTTAAGACCAAGGTC
1 TAAGCCCAATATCGATGGCCTTGAATCAACATATTGACACCTTCG--ATCTTTAAGACCAAGGTC
*
55076 GCCGGCCTTGAATCAGTACATTGGCA
64 GCCGGCCTTGAATCAGCACATTGGCA
* *
55102 TAAGCCCAATATCGCTGGCCTTGAATCAACATATTGACACCTT-G-TCTTTAAGACCAATGTCGC
1 TAAGCCCAATATCGATGGCCTTGAATCAACATATTGACACCTTCGATCTTTAAGACCAAGGTCGC
* *
55165 TGGCCTTGAATCAGCATATTGGCA
66 CGGCCTTGAATCAGCACATTGGCA
55189 CTTTCATCTT
Statistics
Matches: 78, Mismatches: 9, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
87 39 0.50
90 1 0.01
91 38 0.49
ACGTcount: A:0.26, C:0.25, G:0.20, T:0.28
Consensus pattern (89 bp):
TAAGCCCAATATCGATGGCCTTGAATCAACATATTGACACCTTCGATCTTTAAGACCAAGGTCGC
CGGCCTTGAATCAGCACATTGGCA
Found at i:55183 original size:48 final size:49
Alignment explanation
Indices: 55102--55234 Score: 160
Period size: 48 Copynumber: 2.7 Consensus size: 49
55092 TACATTGGCA
* * *
55102 TAAGCCCAATATCGCTGGCCTTGAATCAACATATTGACACCTT-GTCTT
1 TAAGACCAATATCGCTGGCCTTGAATCAGCATATTGACACCTTCATCTT
* * *
55150 TAAGACCAATGTCGCTGGCCTTGAATCAGCATATTGGCACTTTCATCTT
1 TAAGACCAATATCGCTGGCCTTGAATCAGCATATTGACACCTTCATCTT
* ** * *
55199 TAAGTCTGATATCGTTGGGCTTGAATCAGCATATTG
1 TAAGACCAATATCGCTGGCCTTGAATCAGCATATTG
55235 GCATCTTTAA
Statistics
Matches: 72, Mismatches: 12, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
48 38 0.53
49 34 0.47
ACGTcount: A:0.26, C:0.23, G:0.19, T:0.33
Consensus pattern (49 bp):
TAAGACCAATATCGCTGGCCTTGAATCAGCATATTGACACCTTCATCTT
Found at i:55273 original size:188 final size:189
Alignment explanation
Indices: 54921--55273 Score: 485
Period size: 188 Copynumber: 1.9 Consensus size: 189
54911 TTCAAGTCCG
* *
54921 ATATCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGACCAATGTCGCCGGCCTTGA
1 ATATCGCTGGCCTTGAATCAACACATTGACACCTTCATCTTTAAGACCAATGTCGCCGGCCTTGA
* *
54986 ATCAACACATTGGCACCTTCATTTTTAAGTCCAATATCGATGGCCTTGAATCAGCATATTGGCGC
66 ATCAACACATTGGCACCTTCATCTTTAAGTCCAATATCGATGGCCTTGAATCAGCATATTGGCAC
**
55051 CTTCGTCATCTTTAAGACCAAGGTCGCCGGCCTTGAATCAGTACATTGGCATAAGCCCA
131 CTTCAACATCTTTAAGACCAAGGTCGCCGGCCTTGAATCAGTACATTGGCATAAGCCCA
* * *
55110 ATATCGCTGGCCTTGAATCAACATATTGACACCTT-GTCTTTAAGACCAATGTCGCTGGCCTTGA
1 ATATCGCTGGCCTTGAATCAACACATTGACACCTTCATCTTTAAGACCAATGTCGCCGGCCTTGA
* * * ** * * *
55174 ATCAGCATATTGGCACTTTCATCTTTAAGTCTGATATCGTTGGGCTTGAATCAGCATATTGGCAT
66 ATCAACACATTGGCACCTTCATCTTTAAGTCCAATATCGATGGCCTTGAATCAGCATATTGGCAC
* * * **
55239 CTTTAACAT-TCTTAAGCCCAATGTCGTTGGCCTTG
131 CTTCAACATCT-TTAAGACCAAGGTCGCCGGCCTTG
55274 TCTCAGCAAA
Statistics
Matches: 141, Mismatches: 22, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
187 1 0.01
188 108 0.77
189 32 0.23
ACGTcount: A:0.25, C:0.25, G:0.19, T:0.31
Consensus pattern (189 bp):
ATATCGCTGGCCTTGAATCAACACATTGACACCTTCATCTTTAAGACCAATGTCGCCGGCCTTGA
ATCAACACATTGGCACCTTCATCTTTAAGTCCAATATCGATGGCCTTGAATCAGCATATTGGCAC
CTTCAACATCTTTAAGACCAAGGTCGCCGGCCTTGAATCAGTACATTGGCATAAGCCCA
Found at i:55281 original size:101 final size:99
Alignment explanation
Indices: 55149--55333 Score: 235
Period size: 99 Copynumber: 1.8 Consensus size: 99
55139 CACCTTGTCT
* * * *
55149 TTAAGACCAATGTCGCTGGCCTTGAATCAGCATATTGGCACTTTCATCTTTAAGTCTGATATCGT
1 TTAAGACCAATGTCGCTGGCCTTGAATCAGCAAATTGGCA--TTCATCTTCAAGTCTAATATCGC
* * *
55214 TGGGCTTGAATCAGCATATTGGCATCTTTAACATTC
64 TGGCCATGAATCAGCACATTGGCATCTTTAACATTC
* * ** * *
55250 TTAAGCCCAATGTCGTTGGCCTTGTCTCAGCAAATTGGCATTCTTCTTCAAGTCTAATGTCGCTG
1 TTAAGACCAATGTCGCTGGCCTTGAATCAGCAAATTGGCATTCATCTTCAAGTCTAATATCGCTG
55315 GCCATGAATCAGCACATTG
66 GCCATGAATCAGCACATTG
55334 TCATTCTTCG
Statistics
Matches: 71, Mismatches: 13, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
99 36 0.51
101 35 0.49
ACGTcount: A:0.24, C:0.23, G:0.19, T:0.34
Consensus pattern (99 bp):
TTAAGACCAATGTCGCTGGCCTTGAATCAGCAAATTGGCATTCATCTTCAAGTCTAATATCGCTG
GCCATGAATCAGCACATTGGCATCTTTAACATTC
Found at i:56096 original size:13 final size:13
Alignment explanation
Indices: 56078--56103 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
56068 CATAAGTGTT
56078 GTATCGATACAAA
1 GTATCGATACAAA
56091 GTATCGATACAAA
1 GTATCGATACAAA
56104 AGCTATCTTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.15, G:0.15, T:0.23
Consensus pattern (13 bp):
GTATCGATACAAA
Found at i:60798 original size:27 final size:27
Alignment explanation
Indices: 60762--60818 Score: 78
Period size: 27 Copynumber: 2.1 Consensus size: 27
60752 TCATTCAAAT
60762 ATATTTTTTATAAAAAATAATATATAA
1 ATATTTTTTATAAAAAATAATATATAA
** * *
60789 ATATTTTTTATCTAAAATAATTTTTAA
1 ATATTTTTTATAAAAAATAATATATAA
60816 ATA
1 ATA
60819 ATTATAAATA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (27 bp):
ATATTTTTTATAAAAAATAATATATAA
Found at i:65361 original size:2 final size:2
Alignment explanation
Indices: 65354--65378 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
65344 CCTAATCTGC
65354 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 A
65379 GAACCTGAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:70681 original size:14 final size:14
Alignment explanation
Indices: 70662--70688 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
70652 TGGGCATGAC
70662 GGATCGATAGGGAT
1 GGATCGATAGGGAT
70676 GGATCGATAGGGA
1 GGATCGATAGGGA
70689 GCTTACTCAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.30, C:0.07, G:0.44, T:0.19
Consensus pattern (14 bp):
GGATCGATAGGGAT
Found at i:79750 original size:13 final size:13
Alignment explanation
Indices: 79732--79759 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
79722 ATACAATGAT
79732 CAATGTATCGATA
1 CAATGTATCGATA
79745 CAATGTATCGATA
1 CAATGTATCGATA
79758 CA
1 CA
79760 TTTACTAATG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.39, C:0.18, G:0.14, T:0.29
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:79756 original size:33 final size:33
Alignment explanation
Indices: 79714--79777 Score: 94
Period size: 33 Copynumber: 1.9 Consensus size: 33
79704 AAATTCTCAT
79714 ATGTATCGATACAATGA-TCAATGTATCGATACA
1 ATGTATCGATACAATGACT-AATGTATCGATACA
* *
79747 ATGTATCGATACATTTACTAATGTATCGATA
1 ATGTATCGATACAATGACTAATGTATCGATA
79778 GATTTTCTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 27 0.96
34 1 0.04
ACGTcount: A:0.38, C:0.14, G:0.14, T:0.34
Consensus pattern (33 bp):
ATGTATCGATACAATGACTAATGTATCGATACA
Found at i:83381 original size:16 final size:16
Alignment explanation
Indices: 83356--83387 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
83346 GATGAAAAGA
*
83356 ATTTTTTTATTATTTT
1 ATTTTGTTATTATTTT
83372 ATTTTGTTATTATTTT
1 ATTTTGTTATTATTTT
83388 TTATTATATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.19, C:0.00, G:0.03, T:0.78
Consensus pattern (16 bp):
ATTTTGTTATTATTTT
Found at i:84386 original size:31 final size:31
Alignment explanation
Indices: 84348--84437 Score: 117
Period size: 31 Copynumber: 2.9 Consensus size: 31
84338 TGCTGTGTTT
* * *
84348 GTGGAAGCTAGAAGAAGCACGAGCTGCTGTC
1 GTGGAAGCTGGAAGAAGCTCGAGCTGCTGGC
* *
84379 GTGGAAGCTGGAAGAGGCTCGAGCTACTGGC
1 GTGGAAGCTGGAAGAAGCTCGAGCTGCTGGC
* *
84410 GTGGAAGATGGAAGAAGCTCGAACTGCT
1 GTGGAAGCTGGAAGAAGCTCGAGCTGCT
84438 AGTTTCGAGT
Statistics
Matches: 50, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 50 1.00
ACGTcount: A:0.28, C:0.18, G:0.38, T:0.17
Consensus pattern (31 bp):
GTGGAAGCTGGAAGAAGCTCGAGCTGCTGGC
Found at i:85006 original size:31 final size:31
Alignment explanation
Indices: 84964--85024 Score: 104
Period size: 31 Copynumber: 2.0 Consensus size: 31
84954 TTCATTTTCT
84964 TGTGTCCCCCATGATTGCATGCTACATTGCA
1 TGTGTCCCCCATGATTGCATGCTACATTGCA
* *
84995 TGTGTCTCCCATGTTTGCATGCTACATTGC
1 TGTGTCCCCCATGATTGCATGCTACATTGC
85025 CTTGCATGCA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.16, C:0.28, G:0.20, T:0.36
Consensus pattern (31 bp):
TGTGTCCCCCATGATTGCATGCTACATTGCA
Found at i:85095 original size:19 final size:17
Alignment explanation
Indices: 85063--85101 Score: 51
Period size: 19 Copynumber: 2.2 Consensus size: 17
85053 CCTTGCATGC
*
85063 ATTTCATTATTTTTTTT
1 ATTTCATTATTTTTATT
85080 ATTTCTATTAATTTTTATT
1 ATTTC-ATT-ATTTTTATT
85099 ATT
1 ATT
85102 ATTTTTTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 5 0.26
18 3 0.16
19 11 0.58
ACGTcount: A:0.23, C:0.05, G:0.00, T:0.72
Consensus pattern (17 bp):
ATTTCATTATTTTTATT
Found at i:85733 original size:79 final size:80
Alignment explanation
Indices: 85645--85857 Score: 240
Period size: 79 Copynumber: 2.7 Consensus size: 80
85635 CAGGGTACGT
** * * *
85645 GGTTGGAGTACATCCCCCGA-TA-AAAAGTTTAATATTTTGGAGAT-AAATCGGGGTTGGAGTAT
1 GGTTGGAGTA-AT-CCCCGATTATAAAAAATCAATATTTTGGAAATAAAATCGGGGTTAGAGTAT
85707 CCCCTC-GAAAATAACGG
64 CCCCTCAG-AAATAACGG
*
85724 GGTTGGAGT-ATCCCCGATTATAAAAAATCGATATTTTGGAAATAAAATCGGGGTTAGAGTATCC
1 GGTTGGAGTAATCCCCGATTATAAAAAATCAATATTTTGGAAATAAAATCGGGGTTAGAGTATCC
85788 CCTCAGAAATAACGG
66 CCTCAGAAATAACGG
* * ** * * *
85803 GGTTAGAGT-ATCCCCGATTTTGGAAAATCGATGTTTTAGAAATAAAATCGGGGTT
1 GGTTGGAGTAATCCCCGATTATAAAAAATCAATATTTTGGAAATAAAATCGGGGTT
85858 GGACTATCTT
Statistics
Matches: 118, Mismatches: 12, Indels: 8
0.86 0.09 0.06
Matches are distributed among these distances:
76 6 0.05
77 4 0.03
78 17 0.14
79 90 0.76
80 1 0.01
ACGTcount: A:0.33, C:0.15, G:0.24, T:0.28
Consensus pattern (80 bp):
GGTTGGAGTAATCCCCGATTATAAAAAATCAATATTTTGGAAATAAAATCGGGGTTAGAGTATCC
CCTCAGAAATAACGG
Found at i:85872 original size:130 final size:130
Alignment explanation
Indices: 85721--85996 Score: 347
Period size: 130 Copynumber: 2.1 Consensus size: 130
85711 TCGAAAATAA
* *
85721 CGGGGTTGGAGTATCCCCGATTATAAAAAATCGATATTTT-GGAAATAAAATCGGGGTTAGAGTA
1 CGGGGTTGGAGTATCCCCGATTATAAAAAATCGATATTTTAGG-AATAAAACCGAGGTTAGAGTA
* * * * * * *
85785 TCCCCTCAGAAATAACGGGGTTAGAGTATCCCCGATTTTGGAAAATCGATGTTTTAGAAATAAAA
65 TCCCCTCAAAAATAACGAGGTTAGAGTATCCCCGATTGTGGAAAATCAATATTCTAAAAATAAAA
85850 T
130 T
* ** * * * * * * *
85851 CGGGGTTGGACTATCTTCGATTGTGAAAATTTGGTGTTTTAGGAATAAAACCGAGGTTGGAGTAT
1 CGGGGTTGGAGTATCCCCGATTATAAAAAATCGATATTTTAGGAATAAAACCGAGGTTAGAGTAT
*
85916 CCCCTCAAAAATAACGAGGTTGGAGTATCCCCGATTGTGGAAAATCAATATTCTAAAAATAAAAT
66 CCCCTCAAAAATAACGAGGTTAGAGTATCCCCGATTGTGGAAAATCAATATTCTAAAAATAAAAT
*
85981 CGGAGTTGGAGTATCC
1 CGGGGTTGGAGTATCC
85997 TCCTAGAAAT
Statistics
Matches: 122, Mismatches: 23, Indels: 2
0.83 0.16 0.01
Matches are distributed among these distances:
130 120 0.98
131 2 0.02
ACGTcount: A:0.33, C:0.14, G:0.24, T:0.29
Consensus pattern (130 bp):
CGGGGTTGGAGTATCCCCGATTATAAAAAATCGATATTTTAGGAATAAAACCGAGGTTAGAGTAT
CCCCTCAAAAATAACGAGGTTAGAGTATCCCCGATTGTGGAAAATCAATATTCTAAAAATAAAAT
Found at i:85989 original size:79 final size:78
Alignment explanation
Indices: 85851--86166 Score: 346
Period size: 79 Copynumber: 4.0 Consensus size: 78
85841 GAAATAAAAT
* ** * * * * * *
85851 CGGGGTTGGACTATCTTCGATTGTGAAAATTTGGTGTTTTAGGAATAAAACCGAGGTTGGAGTAT
1 CGGGGTTGGAGTATCCCCGATTGTGAAAAATCGATGTTCTAGAAATAAAATCG-GGTTGGAGTAT
85916 CCCCTCAAAAATAA
65 CCCCTCAAAAATAA
* * * * *
85930 CGAGGTTGGAGTATCCCCGATTGTGGAAAATCAATATTCTAAAAATAAAATCGGAGTTGGAGTAT
1 CGGGGTTGGAGTATCCCCGATTGTGAAAAATCGATGTTCTAGAAATAAAATCGG-GTTGGAGTAT
*
85995 CCTCCT-AGAAATAA
65 CC-CCTCAAAAATAA
* * * * *
86009 CGGGGTTGGAGTATCACCAATTGTGAAAAATTGGTGTTTTAGAAATAAAATCGGGATTGGAGTAT
1 CGGGGTTGGAGTATCCCCGATTGTGAAAAATCGATGTTCTAGAAATAAAATCGGG-TTGGAGTAT
*
86074 CCCCTCGAAAATAA
65 CCCCTCAAAAATAA
* * *
86088 CGGGGTTAGAGTATCCCCGATTGTGAAAAATCGATGTTCTGGACATAAAATCGGGGTTGGAGTAT
1 CGGGGTTGGAGTATCCCCGATTGTGAAAAATCGATGTTCTAGAAATAAAATC-GGGTTGGAGTAT
* *
86153 CCCTTCGAAAATAA
65 CCCCTCAAAAATAA
86167 AAACATGAAA
Statistics
Matches: 196, Mismatches: 36, Indels: 10
0.81 0.15 0.04
Matches are distributed among these distances:
78 5 0.03
79 185 0.94
80 6 0.03
ACGTcount: A:0.33, C:0.15, G:0.25, T:0.28
Consensus pattern (78 bp):
CGGGGTTGGAGTATCCCCGATTGTGAAAAATCGATGTTCTAGAAATAAAATCGGGTTGGAGTATC
CCCTCAAAAATAA
Found at i:86007 original size:209 final size:209
Alignment explanation
Indices: 85696--86074 Score: 562
Period size: 209 Copynumber: 1.8 Consensus size: 209
85686 GATAAATCGG
* * * *
85696 GGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTATAAAAAATCGATATTTT
1 GGTTGGAGTATCCCCTCAAAAATAACGAGGTTGGAGTATCCCCGATTATAAAAAATCAATATTCT
** * * * * *
85761 GGAAATAAAATCGGGGTTAGAGTATCCCCTCAGAAATAACGGGGTTAGAGTATCCCCGATTTTGG
66 AAAAATAAAATCGGAGTTAGAGTATCCCCTCAGAAATAACGGGGTTAGAGTATCACCAATTGTGA
*
85826 AAAATCGATGTTTTAGAAATAAAATCGGGGTTGGACTATCTTCGATTGTGAAAATTTGGTGTTTT
131 AAAATCGATGTTTTAGAAATAAAATCGGGATTGGACTATCTTCGATTGTGAAAATTTGGTGTTTT
85891 AGGAATAAAACCGA
196 AGGAATAAAACCGA
* **
85905 GGTTGGAGTATCCCCTCAAAAATAACGAGGTTGGAGTATCCCCGATTGTGGAAAATCAATATTCT
1 GGTTGGAGTATCCCCTCAAAAATAACGAGGTTGGAGTATCCCCGATTATAAAAAATCAATATTCT
* *
85970 AAAAATAAAATCGGAGTTGGAGTATCCTCCT-AGAAATAACGGGGTTGGAGTATCACCAATTGTG
66 AAAAATAAAATCGGAGTTAGAGTATCC-CCTCAGAAATAACGGGGTTAGAGTATCACCAATTGTG
* * *
86034 AAAAATTGGTGTTTTAGAAATAAAATCGGGATTGGAGTATC
130 AAAAATCGATGTTTTAGAAATAAAATCGGGATTGGACTATC
86075 CCCTCGAAAA
Statistics
Matches: 149, Mismatches: 20, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
209 146 0.98
210 3 0.02
ACGTcount: A:0.34, C:0.14, G:0.24, T:0.28
Consensus pattern (209 bp):
GGTTGGAGTATCCCCTCAAAAATAACGAGGTTGGAGTATCCCCGATTATAAAAAATCAATATTCT
AAAAATAAAATCGGAGTTAGAGTATCCCCTCAGAAATAACGGGGTTAGAGTATCACCAATTGTGA
AAAATCGATGTTTTAGAAATAAAATCGGGATTGGACTATCTTCGATTGTGAAAATTTGGTGTTTT
AGGAATAAAACCGA
Found at i:86069 original size:158 final size:158
Alignment explanation
Indices: 85851--86154 Score: 439
Period size: 158 Copynumber: 1.9 Consensus size: 158
85841 GAAATAAAAT
** * * *
85851 CGGGGTTGGACTATCTTCGATTGTGAAAATTTGGTGTTTTAGGAATAAAACCGAGGTTGGAGTAT
1 CGGGGTTGGACTATCACCAATTGTGAAAAATTGGTGTTTTAGAAATAAAACCGAGGTTGGAGTAT
* *
85916 CCCCTCAAAAATAACGAGGTTGGAGTATCCCCGATTGTGGAAAATCAATATTCTAAAAATAAAAT
66 CCCCTCAAAAATAACGAGGTTAGAGTATCCCCGATTGTGAAAAATCAATATTCTAAAAATAAAAT
85981 CGGAGTTGGAGTATCCTCCTAGAAATAA
131 CGGAGTTGGAGTATCCTCCTAGAAATAA
* *
86009 CGGGGTTGGAGTATCACCAATTGTGAAAAATTGGTGTTTTAGAAATAAAATCG-GGATTGGAGTA
1 CGGGGTTGGACTATCACCAATTGTGAAAAATTGGTGTTTTAGAAATAAAACCGAGG-TTGGAGTA
* * * * ** *
86073 TCCCCTCGAAAATAACGGGGTTAGAGTATCCCCGATTGTGAAAAATCGATGTTCTGGACATAAAA
65 TCCCCTCAAAAATAACGAGGTTAGAGTATCCCCGATTGTGAAAAATCAATATTCTAAAAATAAAA
*
86138 TCGGGGTTGGAGTATCC
130 TCGGAGTTGGAGTATCC
86155 CTTCGAAAAT
Statistics
Matches: 128, Mismatches: 17, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
157 2 0.02
158 126 0.98
ACGTcount: A:0.32, C:0.14, G:0.25, T:0.28
Consensus pattern (158 bp):
CGGGGTTGGACTATCACCAATTGTGAAAAATTGGTGTTTTAGAAATAAAACCGAGGTTGGAGTAT
CCCCTCAAAAATAACGAGGTTAGAGTATCCCCGATTGTGAAAAATCAATATTCTAAAAATAAAAT
CGGAGTTGGAGTATCCTCCTAGAAATAA
Found at i:86197 original size:158 final size:159
Alignment explanation
Indices: 85875--86199 Score: 338
Period size: 158 Copynumber: 2.1 Consensus size: 159
85865 CTTCGATTGT
* *
85875 GAAAATTTGGTGTTTTAGGAATAAAACCGAGGTTGGAGTATCCCCTCAAAAATAACGAGGTTGGA
1 GAAAA-TTGGTGTTTTAGAAATAAAACCGAGGTTGGAGTATCCCCTCAAAAATAACGAGGTTAGA
* *
85940 GTATCCCCGATTGTGGAAAATCAATATTCTAAAAATAAAATCGGAGTTGGAGTATCCTCCTAGAA
65 GTATCCCCGATTGTGAAAAATCAATATTCTAAAAATAAAATCGGAGTTGGAGTATCCTCCGAGAA
***** * ** ** *
86005 ATAACGGGGTTGGAGTATCACCAATTGTGA
130 ATAACAAACATGGAGAAAAAAAAATTATGA
* * *
86035 -AAAATTGGTGTTTTAGAAATAAAATCG-GGATTGGAGTATCCCCTCGAAAATAACGGGGTTAGA
1 GAAAATTGGTGTTTTAGAAATAAAACCGAGG-TTGGAGTATCCCCTCAAAAATAACGAGGTTAGA
* * ** * * *
86098 GTATCCCCGATTGTGAAAAATCGATGTTCTGGACATAAAATCGGGGTTGGAGTATCCCTTCGA-A
65 GTATCCCCGATTGTGAAAAATCAATATTCTAAAAATAAAATCGGAGTTGGAGTAT-CCTCCGAGA
86162 AATAA-AAACAT-GA-AAAAAAAAATTTATGAA
129 AATAACAAACATGGAGAAAAAAAAA-TTATG-A
86192 GAAAATTG
1 GAAAATTG
86200 ACGTAAGCGA
Statistics
Matches: 135, Mismatches: 25, Indels: 12
0.78 0.15 0.07
Matches are distributed among these distances:
155 4 0.03
156 6 0.04
157 4 0.03
158 112 0.83
159 9 0.07
ACGTcount: A:0.38, C:0.13, G:0.23, T:0.26
Consensus pattern (159 bp):
GAAAATTGGTGTTTTAGAAATAAAACCGAGGTTGGAGTATCCCCTCAAAAATAACGAGGTTAGAG
TATCCCCGATTGTGAAAAATCAATATTCTAAAAATAAAATCGGAGTTGGAGTATCCTCCGAGAAA
TAACAAACATGGAGAAAAAAAAATTATGA
Found at i:96303 original size:26 final size:26
Alignment explanation
Indices: 96247--96297 Score: 93
Period size: 26 Copynumber: 2.0 Consensus size: 26
96237 TGTAGAGATA
96247 AGATTGATAAAGTTTAACTTCATCTG
1 AGATTGATAAAGTTTAACTTCATCTG
*
96273 AGATTGATAAAGTTTAACTTTATCT
1 AGATTGATAAAGTTTAACTTCATCT
96298 AGGATTTTAG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.35, C:0.10, G:0.14, T:0.41
Consensus pattern (26 bp):
AGATTGATAAAGTTTAACTTCATCTG
Found at i:98049 original size:2 final size:2
Alignment explanation
Indices: 98042--98070 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
98032 AGGAATTGAC
98042 AT AT AT AT AT AT AT AT A- AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
98071 TAATGAATAA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:98064 original size:15 final size:14
Alignment explanation
Indices: 98044--98074 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
98034 GAATTGACAT
98044 ATATATATATATATA
1 ATATATATATAT-TA
98059 ATATATATATATTA
1 ATATATATATATTA
98073 AT
1 AT
98075 GAATAAAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.25
15 12 0.75
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (14 bp):
ATATATATATATTA
Found at i:99101 original size:2 final size:2
Alignment explanation
Indices: 99094--99118 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
99084 TTCAACCAAA
99094 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
99119 AAACGATTAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:101065 original size:2 final size:2
Alignment explanation
Indices: 101058--101083 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
101048 TAAAAATGAC
101058 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
101084 TTGATTTGCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:102718 original size:3 final size:3
Alignment explanation
Indices: 102710--102752 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
102700 AAGCAGATTC
102710 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
102753 TCCTTTGAAT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TCT
Found at i:103096 original size:2 final size:2
Alignment explanation
Indices: 103091--103136 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
103081 TTTTTAAACG
103091 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
103133 CT CT
1 CT CT
103137 ATATATATAT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:103190 original size:2 final size:2
Alignment explanation
Indices: 103136--103174 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
103126 TCTCTCTCTC
103136 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
103175 GCTCCATCAG
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:103446 original size:3 final size:3
Alignment explanation
Indices: 103440--103471 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
103430 AAAAGCACGG
103440 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
103472 CCAACTATAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:103637 original size:6 final size:6
Alignment explanation
Indices: 103626--103653 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
103616 TTCCACAACT
103626 ATAGCC ATAGCC ATAGCC ATAGCC ATAG
1 ATAGCC ATAGCC ATAGCC ATAGCC ATAG
103654 GGACAACAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.36, C:0.29, G:0.18, T:0.18
Consensus pattern (6 bp):
ATAGCC
Found at i:104700 original size:16 final size:17
Alignment explanation
Indices: 104679--104711 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
104669 TCCTCAAACA
*
104679 CAGAAATGACCC-CAAG
1 CAGAAAAGACCCACAAG
104695 CAGAAAAGACCCACAAG
1 CAGAAAAGACCCACAAG
104712 AGAGTACAAG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.48, C:0.30, G:0.18, T:0.03
Consensus pattern (17 bp):
CAGAAAAGACCCACAAG
Found at i:112038 original size:2 final size:2
Alignment explanation
Indices: 112031--112056 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
112021 ATTTTTATTA
112031 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
112057 TACTTAAATG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:116876 original size:2 final size:2
Alignment explanation
Indices: 116869--116905 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
116859 CTTGGACCAT
*
116869 AC AC AC AC AT AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
116906 TATATAGCTG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.46, G:0.00, T:0.03
Consensus pattern (2 bp):
AC
Found at i:118555 original size:3 final size:3
Alignment explanation
Indices: 118547--118597 Score: 102
Period size: 3 Copynumber: 17.0 Consensus size: 3
118537 TATTGGTTTC
118547 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
118595 ATT
1 ATT
118598 TTCTTTTCTT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:126775 original size:2 final size:2
Alignment explanation
Indices: 126768--126796 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
126758 AGCAGTATTT
126768 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
126797 TTTCTTGGTT
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:135060 original size:2 final size:2
Alignment explanation
Indices: 135053--135081 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
135043 ATGTTGCATA
135053 TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
135082 ATTGAGTCTT
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:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:137694 original size:3 final size:3
Alignment explanation
Indices: 137686--137727 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
137676 TCTTTTTATG
137686 TAA TAA TAA 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
137728 AGATCATAAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:141470 original size:2 final size:2
Alignment explanation
Indices: 141463--141492 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
141453 CAGTGTTGCG
141463 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
141493 TTTGTTGGGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:149819 original size:13 final size:12
Alignment explanation
Indices: 149770--149819 Score: 50
Period size: 12 Copynumber: 4.2 Consensus size: 12
149760 ATTTTTAAAA
*
149770 TAAAATTAATTT
1 TAAAAATAATTT
*
149782 TAAAAATTA-TT
1 TAAAAATAATTT
149793 TATAAAA-AATTT
1 TA-AAAATAATTT
149805 TAAAAATAATATT
1 TAAAAATAAT-TT
149818 TA
1 TA
149820 TTTTTAACAC
Statistics
Matches: 31, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
11 9 0.29
12 18 0.58
13 4 0.13
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (12 bp):
TAAAAATAATTT
Found at i:150160 original size:6 final size:6
Alignment explanation
Indices: 150149--150288 Score: 62
Period size: 6 Copynumber: 23.5 Consensus size: 6
150139 CATCATAATT
* * *
150149 TTTATA TTTATA TTTAAAA TGTTAT- TTATATT TTTATAA TTT-TA -ATATA
1 TTTATA TTTATA TTT-ATA T-TTATA TT-TATA TTTAT-A TTTATA TTTATA
* * * *
150198 TTTATA TTTCATA -TTATA TATATA TTT-TA -ATATG TTTATA TATATA
1 TTTATA TTT-ATA TTTATA TTTATA TTTATA TTTATA TTTATA TTTATA
* * * *
150244 TATATA TATTATA TTTTTA TTAAT- TTTTTA TATTATA -TTATA TTT
1 TTTATA T-TTATA TTTATA TTTATA TTTATA T-TTATA TTTATA TTT
150289 TAATTATTTT
Statistics
Matches: 100, Mismatches: 19, Indels: 30
0.67 0.13 0.20
Matches are distributed among these distances:
4 2 0.02
5 18 0.18
6 57 0.57
7 21 0.21
8 2 0.02
ACGTcount: A:0.36, C:0.01, G:0.01, T:0.62
Consensus pattern (6 bp):
TTTATA
Found at i:150222 original size:43 final size:41
Alignment explanation
Indices: 150143--150287 Score: 121
Period size: 43 Copynumber: 3.7 Consensus size: 41
150133 TTTAAACATC
* * *
150143 ATAATTTT-TATATTTATATTTAAAATGT-TATTTATATTTTT
1 ATAATTTTATATATTTATATTT-ATAT-TATATATATATTTTA
150184 ATAATTTTAATATATTTATATTTCATATTATATATATATTTTA
1 ATAATTTT-ATATATTTATATTT-ATATTATATATATATTTTA
*
150227 AT-ATGTTTATATA--TATATATATA-TAT-TATAT-TTTTA
1 ATAAT-TTTATATATTTATATTTATATTATATATATATTTTA
* *
150263 TTAATTTTTTATA-TTATA-TTATATT
1 ATAATTTTATATATTTATATTTATATT
150288 TTAATTATTT
Statistics
Matches: 89, Mismatches: 8, Indels: 18
0.77 0.07 0.16
Matches are distributed among these distances:
36 17 0.19
37 12 0.13
38 3 0.03
39 3 0.03
40 6 0.07
41 8 0.09
42 8 0.09
43 32 0.36
ACGTcount: A:0.37, C:0.01, G:0.01, T:0.61
Consensus pattern (41 bp):
ATAATTTTATATATTTATATTTATATTATATATATATTTTA
Found at i:150240 original size:10 final size:9
Alignment explanation
Indices: 150173--150290 Score: 72
Period size: 8 Copynumber: 13.4 Consensus size: 9
150163 TAAAATGTTA
150173 TTTATAT-T
1 TTTATATAT
150181 TTTATA-AT
1 TTTATATAT
150189 TTTA-ATAT
1 TTTATATAT
*
150197 ATT-TATAT
1 TTTATATAT
*
150205 TTCATAT-T
1 TTTATATAT
*
150213 ATATATATAT
1 -TTTATATAT
150223 TTTA-ATAT
1 TTTATATAT
150231 GTTTATATAT
1 -TTTATATAT
*
150241 ATATATATAT
1 -TTTATATAT
*
150251 ATTATAT-T
1 TTTATATAT
150259 TTTAT-TAAT
1 TTTATAT-AT
*
150268 TTTTTATAT
1 TTTATATAT
*
150277 TATATTATAT
1 TTTA-TATAT
150287 TTTA
1 TTTA
150291 ATTATTTTTT
Statistics
Matches: 83, Mismatches: 15, Indels: 22
0.69 0.12 0.18
Matches are distributed among these distances:
7 2 0.02
8 30 0.36
9 29 0.35
10 22 0.27
ACGTcount: A:0.36, C:0.01, G:0.01, T:0.63
Consensus pattern (9 bp):
TTTATATAT
Found at i:150264 original size:11 final size:11
Alignment explanation
Indices: 150250--150304 Score: 50
Period size: 9 Copynumber: 5.5 Consensus size: 11
150240 TATATATATA
150250 TATTATATTTT
1 TATTATATTTT
150261 TATTA-A-TTT
1 TATTATATTTT
*
150270 T-TTATA-TTA
1 TATTATATTTT
150279 TATTATATTTT
1 TATTATATTTT
*
150290 AATTAT-TTTT
1 TATTATATTTT
150300 T-TTAT
1 TATTAT
150305 CATATATACA
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
8 3 0.08
9 12 0.32
10 10 0.27
11 12 0.32
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (11 bp):
TATTATATTTT
Found at i:150275 original size:28 final size:29
Alignment explanation
Indices: 150244--150311 Score: 93
Period size: 29 Copynumber: 2.3 Consensus size: 29
150234 TATATATATA
*
150244 TATATATATTATATTTTTATTA-ATTTTT
1 TATATATATTATATTTTAATTATATTTTT
*
150272 TATATTATATTATATTTTAATTATTTTTTT
1 TATA-TATATTATATTTTAATTATATTTTT
150302 TATCATATAT
1 TAT-ATATAT
150312 ACATCATATA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
28 4 0.11
29 17 0.49
30 13 0.37
31 1 0.03
ACGTcount: A:0.32, C:0.01, G:0.00, T:0.66
Consensus pattern (29 bp):
TATATATATTATATTTTAATTATATTTTT
Found at i:150288 original size:19 final size:19
Alignment explanation
Indices: 150232--150289 Score: 57
Period size: 19 Copynumber: 3.1 Consensus size: 19
150222 TTTTAATATG
*
150232 TTTATA-TATATATATATAT
1 TTTATATTATAT-TATATTT
* *
150251 ATTATATTTTTATTA-ATTT
1 TTTATA-TTATATTATATTT
150270 TTTATATTATATTATATTT
1 TTTATATTATATTATATTT
150289 T
1 T
150290 AATTATTTTT
Statistics
Matches: 31, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
18 7 0.23
19 18 0.58
20 2 0.06
21 4 0.13
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (19 bp):
TTTATATTATATTATATTT
Found at i:155518 original size:22 final size:23
Alignment explanation
Indices: 155470--155520 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 23
155460 ATATTAAAAC
*
155470 TATTAATAATAATATTTAGAAATA
1 TATTAAAAATAATATTTA-AAATA
*
155494 TATTAAAAATAATATTT-TAATA
1 TATTAAAAATAATATTTAAAATA
155516 TATTA
1 TATTA
155521 TTATATTAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 9 0.36
24 16 0.64
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (23 bp):
TATTAAAAATAATATTTAAAATA
Found at i:155615 original size:25 final size:26
Alignment explanation
Indices: 155581--155634 Score: 83
Period size: 25 Copynumber: 2.1 Consensus size: 26
155571 TATTTTCTTA
*
155581 AAAAATAATATTTAAATAT-ATATTT
1 AAAAATAATATTTAAAAATAATATTT
*
155606 AAAATTAATATTTAAAAATAATATTT
1 AAAAATAATATTTAAAAATAATATTT
155632 AAA
1 AAA
155635 TATATGAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
25 17 0.65
26 9 0.35
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (26 bp):
AAAAATAATATTTAAAAATAATATTT
Found at i:155616 original size:13 final size:13
Alignment explanation
Indices: 155581--155634 Score: 83
Period size: 13 Copynumber: 4.2 Consensus size: 13
155571 TATTTTCTTA
155581 AAAAATAATATTT
1 AAAAATAATATTT
*
155594 AAATAT-ATATTT
1 AAAAATAATATTT
*
155606 AAAATTAATATTT
1 AAAAATAATATTT
155619 AAAAATAATATTT
1 AAAAATAATATTT
155632 AAA
1 AAA
155635 TATATGAAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
12 10 0.28
13 26 0.72
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (13 bp):
AAAAATAATATTT
Found at i:160601 original size:3 final size:3
Alignment explanation
Indices: 160593--160619 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
160583 ATTATGATCT
160593 TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA
160620 ATAGAAATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:163024 original size:19 final size:19
Alignment explanation
Indices: 162970--163025 Score: 76
Period size: 20 Copynumber: 2.9 Consensus size: 19
162960 TTATAATCTC
*
162970 AATAAATTTATTCATATAA
1 AATAAATTTATTAATATAA
*
162989 AATATATTTAATTAATATAA
1 AATAAATTT-ATTAATATAA
*
163009 AATAAATTTTTTAATAT
1 AATAAATTTATTAATAT
163026 TATTTTAAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
19 15 0.47
20 17 0.53
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (19 bp):
AATAAATTTATTAATATAA
Found at i:163050 original size:18 final size:18
Alignment explanation
Indices: 163029--163081 Score: 54
Period size: 18 Copynumber: 3.0 Consensus size: 18
163019 TTAATATTAT
163029 TTTAAATAAAAATATAAA
1 TTTAAATAAAAATATAAA
* *
163047 TTTAAATTAAATTA-AAA
1 TTTAAATAAAAATATAAA
* * *
163064 TTAAAAAAAAAATTTAAA
1 TTTAAATAAAAATATAAA
163082 CCTCATTCGA
Statistics
Matches: 27, Mismatches: 7, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
17 12 0.44
18 15 0.56
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (18 bp):
TTTAAATAAAAATATAAA
Found at i:163059 original size:11 final size:11
Alignment explanation
Indices: 163030--163068 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
163020 TAATATTATT
*
163030 TTAAATAAAAA
1 TTAAATTAAAA
*
163041 TATAAATTTAAA
1 T-TAAATTAAAA
163053 TTAAATTAAAA
1 TTAAATTAAAA
163064 TTAAA
1 TTAAA
163069 AAAAAAATTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
11 15 0.62
12 9 0.38
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (11 bp):
TTAAATTAAAA
Found at i:167322 original size:2 final size:2
Alignment explanation
Indices: 167315--167354 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
167305 TAATTGTTTG
*
167315 TA TA TA TA TG 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
167355 GTTCATGCAT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:168937 original size:29 final size:28
Alignment explanation
Indices: 168905--168963 Score: 73
Period size: 29 Copynumber: 2.1 Consensus size: 28
168895 TTTCATTTAA
* * *
168905 TTAATTTTAAAATTTATTTTTTTATAATT
1 TTAAATTTAAAATTTAATATTTTA-AATT
*
168934 TTAAATTTAAATTTTAATATTTTAAATT
1 TTAAATTTAAAATTTAATATTTTAAATT
168962 TT
1 TT
168964 GTATGGTAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
28 6 0.23
29 20 0.77
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (28 bp):
TTAAATTTAAAATTTAATATTTTAAATT
Found at i:168949 original size:7 final size:7
Alignment explanation
Indices: 168924--168963 Score: 55
Period size: 7 Copynumber: 5.6 Consensus size: 7
168914 AAATTTATTT
168924 TTTTATAA
1 TTTTA-AA
168932 TTTTAAA
1 TTTTAAA
168939 -TTTAAA
1 TTTTAAA
168945 TTTTAATA
1 TTTTAA-A
168953 TTTTAAA
1 TTTTAAA
168960 TTTT
1 TTTT
168964 GTATGGTAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
6 6 0.20
7 12 0.40
8 12 0.40
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (7 bp):
TTTTAAA
Found at i:168959 original size:15 final size:15
Alignment explanation
Indices: 168908--168963 Score: 62
Period size: 15 Copynumber: 3.8 Consensus size: 15
168898 CATTTAATTA
* *
168908 ATTTTAAAATTTATT
1 ATTTTAAATTTTAAT
*
168923 TTTTTATAATTTTAA-
1 ATTTTA-AATTTTAAT
168938 A-TTTAAATTTTAAT
1 ATTTTAAATTTTAAT
168952 ATTTTAAATTTT
1 ATTTTAAATTTT
168964 GTATGGTAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
13 8 0.24
14 5 0.15
15 15 0.44
16 6 0.18
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (15 bp):
ATTTTAAATTTTAAT
Found at i:171120 original size:2 final size:2
Alignment explanation
Indices: 171113--171139 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
171103 TCATGACTTG
171113 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
171140 ATTAAAACTT
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:176177 original size:2 final size:2
Alignment explanation
Indices: 176170--176195 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
176160 AAAACAAAAT
176170 TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG
176196 AGAGAGAGAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:180973 original size:19 final size:20
Alignment explanation
Indices: 180954--181019 Score: 64
Period size: 23 Copynumber: 3.2 Consensus size: 20
180944 TGTAAACATA
180954 ATATAGATTATTAAATATA-
1 ATATAGATTATTAAATATAT
* *
180973 ATACA-ATTTTTAAATATAT
1 ATATAGATTATTAAATATAT
*
180992 ATATATGATATATATATATATAT
1 ATATA-GAT-TAT-TAAATATAT
181015 ATATA
1 ATATA
181020 TATATAAACC
Statistics
Matches: 37, Mismatches: 5, Indels: 6
0.77 0.10 0.12
Matches are distributed among these distances:
18 12 0.32
19 8 0.22
21 2 0.05
22 2 0.05
23 13 0.35
ACGTcount: A:0.50, C:0.02, G:0.03, T:0.45
Consensus pattern (20 bp):
ATATAGATTATTAAATATAT
Found at i:180993 original size:2 final size:2
Alignment explanation
Indices: 180986--181025 Score: 71
Period size: 2 Copynumber: 19.5 Consensus size: 2
180976 CAATTTTTAA
180986 AT AT AT AT AT AT GAT 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 AT AT AT AT AT A
181026 AACCAAAGAT
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 35 0.95
3 2 0.05
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:182582 original size:14 final size:16
Alignment explanation
Indices: 182563--182599 Score: 51
Period size: 14 Copynumber: 2.4 Consensus size: 16
182553 ATAAATAAAA
182563 TATAAAATATA-ATTG
1 TATAAAATATAGATTG
*
182578 T-TAAATTATAGATTG
1 TATAAAATATAGATTG
182593 TATAAAA
1 TATAAAA
182600 ATTATAAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 3
0.78 0.09 0.13
Matches are distributed among these distances:
14 8 0.44
15 6 0.33
16 4 0.22
ACGTcount: A:0.51, C:0.00, G:0.08, T:0.41
Consensus pattern (16 bp):
TATAAAATATAGATTG
Found at i:187465 original size:3 final size:3
Alignment explanation
Indices: 187447--187493 Score: 67
Period size: 3 Copynumber: 15.3 Consensus size: 3
187437 GGGCCCCTTG
* *
187447 TAT TCT TAT ATAT TAT TAT TAT TAT TAT TGT TAT TAT TAT TAT TAT
1 TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
187493 T
1 T
187494 TTTGTTTACT
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
3 36 0.92
4 3 0.08
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:190561 original size:2 final size:2
Alignment explanation
Indices: 190554--190579 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
190544 TTTCGTCAAG
190554 TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC
190580 CCCGTTTCGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:195434 original size:2 final size:2
Alignment explanation
Indices: 195427--195458 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
195417 TACCATCAAA
*
195427 TC TC TC TC TC TC TC TC GC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
195459 GTGCTTGTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.50, G:0.03, T:0.47
Consensus pattern (2 bp):
TC
Found at i:196168 original size:3 final size:3
Alignment explanation
Indices: 196160--196194 Score: 61
Period size: 3 Copynumber: 11.3 Consensus size: 3
196150 GAACAAAGAT
196160 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA CATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA -ATA A
196195 AACTTATCCA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 28 0.90
4 3 0.10
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:201101 original size:16 final size:17
Alignment explanation
Indices: 201068--201103 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
201058 TATGAATGCA
201068 ATATAATTTATATAAAT
1 ATATAATTTATATAAAT
201085 ATATAATTTAT-TAAAT
1 ATATAATTTATATAAAT
201101 ATA
1 ATA
201104 ATTATAATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 8 0.42
17 11 0.58
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
ATATAATTTATATAAAT
Found at i:201135 original size:12 final size:12
Alignment explanation
Indices: 201111--201144 Score: 52
Period size: 12 Copynumber: 2.8 Consensus size: 12
201101 ATAATTATAA
201111 TATAAAA-ATTT
1 TATAAAATATTT
201122 TATAAAATATTT
1 TATAAAATATTT
201134 TATAAATATAT
1 TATAAA-ATAT
201145 GAATTATTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 7 0.33
12 10 0.48
13 4 0.19
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (12 bp):
TATAAAATATTT
Found at i:201149 original size:29 final size:28
Alignment explanation
Indices: 201073--201149 Score: 77
Period size: 29 Copynumber: 2.7 Consensus size: 28
201063 ATGCAATATA
*
201073 ATTTATATAAATATATAA-TTTATTAAAT
1 ATTT-TATAAATATATAATTTTATAAAAT
* *
201101 ATAATTAT-AATATAAAAATTTTATAAAAT
1 AT-TTTATAAATAT-ATAATTTTATAAAAT
201130 ATTTTATAAATATATGAATT
1 ATTTTATAAATATAT-AATT
201150 ATTTTTTATT
Statistics
Matches: 39, Mismatches: 5, Indels: 9
0.74 0.09 0.17
Matches are distributed among these distances:
27 5 0.13
28 13 0.33
29 21 0.54
ACGTcount: A:0.52, C:0.00, G:0.01, T:0.47
Consensus pattern (28 bp):
ATTTTATAAATATATAATTTTATAAAAT
Found at i:201170 original size:3 final size:3
Alignment explanation
Indices: 201162--201208 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
201152 TTTTTATTTA
201162 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
201209 ATAGCTTTGT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:201377 original size:2 final size:2
Alignment explanation
Indices: 201370--201394 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
201360 ATAATTTGAC
201370 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 A
201395 GACACACACA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:202854 original size:9 final size:9
Alignment explanation
Indices: 202841--202882 Score: 57
Period size: 9 Copynumber: 4.7 Consensus size: 9
202831 TCACATGCGG
*
202841 AAGAAGAAG
1 AAGAAGAAA
202850 AAGAAGAAA
1 AAGAAGAAA
*
202859 AAGACGAAA
1 AAGAAGAAA
202868 AAGAAGAAA
1 AAGAAGAAA
*
202877 CAGAAG
1 AAGAAG
202883 CCAAATTCTG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 29 1.00
ACGTcount: A:0.69, C:0.05, G:0.26, T:0.00
Consensus pattern (9 bp):
AAGAAGAAA
Found at i:207482 original size:18 final size:18
Alignment explanation
Indices: 207401--207473 Score: 89
Period size: 18 Copynumber: 4.2 Consensus size: 18
207391 ATATCAATAT
207401 AAATCACAGA--TTTTAA
1 AAATCACAGATTTTTTAA
** *
207417 CGAT-ACAGATTTCTTAA
1 AAATCACAGATTTTTTAA
*
207434 AAATCACATATTTTTTAA
1 AAATCACAGATTTTTTAA
207452 AAATCACAGATTTTTTAA
1 AAATCACAGATTTTTTAA
207470 AAAT
1 AAAT
207474 TATAGATTTC
Statistics
Matches: 46, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
15 5 0.11
16 2 0.04
17 7 0.15
18 32 0.70
ACGTcount: A:0.45, C:0.12, G:0.05, T:0.37
Consensus pattern (18 bp):
AAATCACAGATTTTTTAA
Found at i:216538 original size:15 final size:15
Alignment explanation
Indices: 216511--216548 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
216501 AAAGTTTTGT
*
216511 TTTTTAC-ATAATAA
1 TTTTTACAAAAATAA
216525 TTTTTACAAAAATAA
1 TTTTTACAAAAATAA
*
216540 CTTTTACAA
1 TTTTTACAA
216549 TTCAAGAGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 7 0.33
15 14 0.67
ACGTcount: A:0.45, C:0.11, G:0.00, T:0.45
Consensus pattern (15 bp):
TTTTTACAAAAATAA
Found at i:227395 original size:6 final size:6
Alignment explanation
Indices: 227384--227414 Score: 53
Period size: 6 Copynumber: 5.0 Consensus size: 6
227374 TGTATGACCG
227384 CACCCA CACCCA CACCCA CACCCA CAACCCA
1 CACCCA CACCCA CACCCA CACCCA C-ACCCA
227415 GTGTCTCTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 19 0.79
7 5 0.21
ACGTcount: A:0.35, C:0.65, G:0.00, T:0.00
Consensus pattern (6 bp):
CACCCA
Found at i:227807 original size:2 final size:2
Alignment explanation
Indices: 227798--227826 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
227788 AAATGTTTAT
227798 TA TA -A 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
227827 AACCTGACCT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:229677 original size:13 final size:13
Alignment explanation
Indices: 229659--229684 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
229649 GTTTTAGTGG
229659 CACTAGCCTTCAC
1 CACTAGCCTTCAC
229672 CACTAGCCTTCAC
1 CACTAGCCTTCAC
229685 TCATTCTCTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.46, G:0.08, T:0.23
Consensus pattern (13 bp):
CACTAGCCTTCAC
Found at i:247769 original size:1 final size:1
Alignment explanation
Indices: 247763--247788 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
247753 CCCTACCTTA
247763 CCCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCC
247789 GGCCCGTATC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:0.00, C:1.00, G:0.00, T:0.00
Consensus pattern (1 bp):
C
Found at i:250891 original size:2 final size:2
Alignment explanation
Indices: 250884--250911 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
250874 TACTTCTAGG
250884 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
250912 GATTCTGAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:256583 original size:17 final size:16
Alignment explanation
Indices: 256557--256590 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
256547 CTAATTTCAT
256557 ATTAAATTAAATGTTTA
1 ATTAAATTAAAT-TTTA
*
256574 ATTAACTTAAATTTTA
1 ATTAAATTAAATTTTA
256590 A
1 A
256591 GTTTATAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (16 bp):
ATTAAATTAAATTTTA
Found at i:260799 original size:16 final size:17
Alignment explanation
Indices: 260765--260810 Score: 51
Period size: 15 Copynumber: 2.8 Consensus size: 17
260755 AATAATTTTA
*
260765 TTATATTAAAATATTATT
1 TTATA-TAAAATATAATT
260783 TTATATAAAATA-AATT
1 TTATATAAAATATAATT
*
260799 TT-TACAAAATAT
1 TTATATAAAATAT
260811 CTTAAAATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
15 8 0.32
16 5 0.20
17 7 0.28
18 5 0.20
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (17 bp):
TTATATAAAATATAATT
Done.