Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A10
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: 110302803
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1825971 characters in sequence are not A, C, G, or T
File 177 of 343
Found at i:58637047 original size:3 final size:3
Alignment explanation
Indices: 58637035--58637085 Score: 52
Period size: 3 Copynumber: 17.3 Consensus size: 3
58637025 GTTTGAAAAA
* *
58637035 AAG AAA AAG AAG AAG AAG -AG AAG CAGG AAG -AG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG -AAG AAG AAG AAG AAG AAG AAG
*
58637079 GAG AAG A
1 AAG AAG A
58637086 GGAAAAATGG
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
2 4 0.10
3 33 0.85
4 2 0.05
ACGTcount: A:0.63, C:0.02, G:0.35, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:58637733 original size:59 final size:59
Alignment explanation
Indices: 58637634--58637776 Score: 216
Period size: 59 Copynumber: 2.4 Consensus size: 59
58637624 TGTTGTTGTT
* * *
58637634 TACAAATTGCTTAACACTTGGTATACATGGCTGCTGGTTAGAAAAGATAACAATTGATA
1 TACAAATTGCTTAACAGTTGGTATAAATGGCTGCTAGTTAGAAAAGATAACAATTGATA
* * * *
58637693 TAGAAATTGTTTAACAGTTGGTATAAATGGCTGCTAGTTAGAAAAGATAACAGTTGGTA
1 TACAAATTGCTTAACAGTTGGTATAAATGGCTGCTAGTTAGAAAAGATAACAATTGATA
58637752 TACAAATTGCTTAACAGTTGG-ATAA
1 TACAAATTGCTTAACAGTTGGTATAA
58637777 CAAATAGCAT
Statistics
Matches: 75, Mismatches: 9, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
58 4 0.05
59 71 0.95
ACGTcount: A:0.38, C:0.10, G:0.20, T:0.31
Consensus pattern (59 bp):
TACAAATTGCTTAACAGTTGGTATAAATGGCTGCTAGTTAGAAAAGATAACAATTGATA
Found at i:58638192 original size:21 final size:20
Alignment explanation
Indices: 58638168--58638222 Score: 83
Period size: 21 Copynumber: 2.6 Consensus size: 20
58638158 CAGCTTCTTG
*
58638168 ATGAGTTAGGGCAGTAGGTA
1 ATGAGTTGGGGCAGTAGGTA
58638188 TATGAGTTGGGGCAGTAGGTA
1 -ATGAGTTGGGGCAGTAGGTA
58638209 ACTGAGTTGGGGCA
1 A-TGAGTTGGGGCA
58638223 CCTTATTGAG
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
20 1 0.03
21 31 0.97
ACGTcount: A:0.25, C:0.07, G:0.42, T:0.25
Consensus pattern (20 bp):
ATGAGTTGGGGCAGTAGGTA
Found at i:58638259 original size:21 final size:21
Alignment explanation
Indices: 58638233--58638272 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
58638223 CCTTATTGAG
58638233 TTGGGGTACCCTCTTGCTGAC
1 TTGGGGTACCCTCTTGCTGAC
* *
58638254 TTGGGGTAGCCTGTTGCTG
1 TTGGGGTACCCTCTTGCTG
58638273 GGTTCGGTCA
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:0.07, C:0.23, G:0.35, T:0.35
Consensus pattern (21 bp):
TTGGGGTACCCTCTTGCTGAC
Found at i:58639029 original size:43 final size:43
Alignment explanation
Indices: 58638940--58639117 Score: 229
Period size: 43 Copynumber: 4.2 Consensus size: 43
58638930 AAAAAAAAAC
* * *
58638940 TCATTGCATGTATATTAAAAAATAGGCAACAG---ACCAACAA
1 TCATTGCATGCATATTAAAAAATAGTCAACAGCTTTCCAACAA
*
58638980 TCATTGCATGCATATTAAAAAATAGTCAATAGCTTTCCAACAA
1 TCATTGCATGCATATTAAAAAATAGTCAACAGCTTTCCAACAA
* *
58639023 TCATTGCATGCATATTAAAAAATAGTCAACAACTTTCCAATAA
1 TCATTGCATGCATATTAAAAAATAGTCAACAGCTTTCCAACAA
* ** *
58639066 TCATTACATATATATTAAAAAA-AGTCAATAGCTTTCCAACAA
1 TCATTGCATGCATATTAAAAAATAGTCAACAGCTTTCCAACAA
*
58639108 TCACTGCATG
1 TCATTGCATG
58639118 TGATCAGCAA
Statistics
Matches: 119, Mismatches: 16, Indels: 4
0.86 0.12 0.03
Matches are distributed among these distances:
40 29 0.24
42 24 0.20
43 66 0.55
ACGTcount: A:0.44, C:0.19, G:0.09, T:0.29
Consensus pattern (43 bp):
TCATTGCATGCATATTAAAAAATAGTCAACAGCTTTCCAACAA
Found at i:58639116 original size:85 final size:83
Alignment explanation
Indices: 58638944--58639117 Score: 235
Period size: 85 Copynumber: 2.1 Consensus size: 83
58638934 AAAAACTCAT
* * *
58638944 TGCATGTATATTAAAAAATAGGCAACAGACCAACAATCATTGCATGCATATTAAAAAATAGTCAA
1 TGCATGCATATTAAAAAATAGGCAACAGACCAACAATCATTACATACATATTAAAAAATAGTCAA
*
58639009 TAGCTTTCCAACAATCAT
66 TAGCTTTCCAACAATCAC
* * *
58639027 TGCATGCATATTAAAAAATAGTCAACA-ACTTTCCAATAATCATTACATATATATTAAAAAA-AG
1 TGCATGCATATTAAAAAATAGGCAACAGA----CCAACAATCATTACATACATATTAAAAAATAG
58639090 TCAATAGCTTTCCAACAATCAC
62 TCAATAGCTTTCCAACAATCAC
58639112 TGCATG
1 TGCATG
58639118 TGATCAGCAA
Statistics
Matches: 80, Mismatches: 7, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
82 1 0.01
83 25 0.31
85 29 0.36
86 25 0.31
ACGTcount: A:0.44, C:0.18, G:0.09, T:0.28
Consensus pattern (83 bp):
TGCATGCATATTAAAAAATAGGCAACAGACCAACAATCATTACATACATATTAAAAAATAGTCAA
TAGCTTTCCAACAATCAC
Found at i:58640779 original size:15 final size:16
Alignment explanation
Indices: 58640754--58640787 Score: 61
Period size: 15 Copynumber: 2.2 Consensus size: 16
58640744 TCAGATGCAT
58640754 CACTATCACTACCAGA
1 CACTATCACTACCAGA
58640770 CACT-TCACTACCAGA
1 CACTATCACTACCAGA
58640785 CAC
1 CAC
58640788 GTTTTCTTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 14 0.78
16 4 0.22
ACGTcount: A:0.35, C:0.41, G:0.06, T:0.18
Consensus pattern (16 bp):
CACTATCACTACCAGA
Found at i:58641136 original size:46 final size:46
Alignment explanation
Indices: 58641081--58641183 Score: 179
Period size: 46 Copynumber: 2.2 Consensus size: 46
58641071 GGATACAAAC
*
58641081 AATGACAGATATACACAATAAACATCAGTTTAATAATGTATAATTT
1 AATGGCAGATATACACAATAAACATCAGTTTAATAATGTATAATTT
*
58641127 AATGGCAGATATACACAATAAACATCAGTTTGATAATGTATAATTT
1 AATGGCAGATATACACAATAAACATCAGTTTAATAATGTATAATTT
*
58641173 AATAGCAGATA
1 AATGGCAGATA
58641184 CAAACAATGA
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
46 54 1.00
ACGTcount: A:0.47, C:0.11, G:0.12, T:0.31
Consensus pattern (46 bp):
AATGGCAGATATACACAATAAACATCAGTTTAATAATGTATAATTT
Found at i:58641240 original size:48 final size:48
Alignment explanation
Indices: 58641187--58641341 Score: 229
Period size: 48 Copynumber: 3.2 Consensus size: 48
58641177 GCAGATACAA
* * *
58641187 ACAATGATAGATATACACAATAAACATCAATTTGAAAATGACATTCAT
1 ACAATGACAGATATACACAATAAAGATCAATTTGATAATGACATTCAT
* * *
58641235 ACAATGGCAGATATACACAATAAAGATCAATTTGCTAATGACATTCAC
1 ACAATGACAGATATACACAATAAAGATCAATTTGATAATGACATTCAT
* * *
58641283 ACAATGGCAGATATACACAATAAAGATCAGTTTGATAATGGCATTCAT
1 ACAATGACAGATATACACAATAAAGATCAATTTGATAATGACATTCAT
58641331 ACAATGACAGA
1 ACAATGACAGA
58641342 GACAAGCAAT
Statistics
Matches: 96, Mismatches: 11, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
48 96 1.00
ACGTcount: A:0.46, C:0.16, G:0.13, T:0.25
Consensus pattern (48 bp):
ACAATGACAGATATACACAATAAAGATCAATTTGATAATGACATTCAT
Found at i:58641333 original size:34 final size:34
Alignment explanation
Indices: 58641295--58641397 Score: 78
Period size: 34 Copynumber: 3.1 Consensus size: 34
58641285 AATGGCAGAT
58641295 ATACACAATAAAGATCAGTTTGATAATGGCATTC
1 ATACACAATAAAGATCAGTTTGATAATGGCATTC
* * *
58641329 AT--ACAATGACAGAGA-CA---AG-CAATGGCAGAT-
1 ATACACAAT-A-A-AGATCAGTTTGATAATGGCA-TTC
*
58641359 ATACACAATAAAGATCAGTTTGATAATGGCGTTC
1 ATACACAATAAAGATCAGTTTGATAATGGCATTC
58641393 ATACA
1 ATACA
58641398 ATGGCAGATA
Statistics
Matches: 50, Mismatches: 7, Indels: 24
0.62 0.09 0.30
Matches are distributed among these distances:
29 3 0.06
30 12 0.24
31 3 0.06
32 10 0.20
33 3 0.06
34 16 0.32
35 3 0.06
ACGTcount: A:0.43, C:0.16, G:0.17, T:0.24
Consensus pattern (34 bp):
ATACACAATAAAGATCAGTTTGATAATGGCATTC
Found at i:58641354 original size:64 final size:64
Alignment explanation
Indices: 58641283--58641415 Score: 230
Period size: 64 Copynumber: 2.1 Consensus size: 64
58641273 TGACATTCAC
58641283 ACAATGGCAGATATACACAATAAAGATCAGTTTGATAATGGCATTCATACAATGACAGAGACAA
1 ACAATGGCAGATATACACAATAAAGATCAGTTTGATAATGGCATTCATACAATGACAGAGACAA
* * * *
58641347 GCAATGGCAGATATACACAATAAAGATCAGTTTGATAATGGCGTTCATACAATGGCAGATACAA
1 ACAATGGCAGATATACACAATAAAGATCAGTTTGATAATGGCATTCATACAATGACAGAGACAA
58641411 ACAAT
1 ACAAT
58641416 AAACATCAAA
Statistics
Matches: 64, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
64 64 1.00
ACGTcount: A:0.44, C:0.16, G:0.18, T:0.23
Consensus pattern (64 bp):
ACAATGGCAGATATACACAATAAAGATCAGTTTGATAATGGCATTCATACAATGACAGAGACAA
Found at i:58641572 original size:12 final size:12
Alignment explanation
Indices: 58641555--58641594 Score: 55
Period size: 12 Copynumber: 3.3 Consensus size: 12
58641545 CGAAATAACC
*
58641555 CTAAATTGAAAT
1 CTAAATCGAAAT
58641567 CTAAATCGAAAT
1 CTAAATCGAAAT
58641579 CTAAATC-AAATT
1 CTAAATCGAAA-T
58641591 CTAA
1 CTAA
58641595 TCCTAAATTG
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
11 3 0.12
12 23 0.88
ACGTcount: A:0.50, C:0.15, G:0.05, T:0.30
Consensus pattern (12 bp):
CTAAATCGAAAT
Found at i:58641620 original size:18 final size:18
Alignment explanation
Indices: 58641599--58641638 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
58641589 TTCTAATCCT
* *
58641599 AAATTGAGATTGAAATCG
1 AAATTGAAATTAAAATCG
*
58641617 AAATTGAAATTAAAATCT
1 AAATTGAAATTAAAATCG
58641635 AAAT
1 AAAT
58641639 CAGAATTAGT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.53, C:0.05, G:0.12, T:0.30
Consensus pattern (18 bp):
AAATTGAAATTAAAATCG
Found at i:58641636 original size:42 final size:42
Alignment explanation
Indices: 58641554--58641636 Score: 107
Period size: 42 Copynumber: 2.0 Consensus size: 42
58641544 TCGAAATAAC
*
58641554 CCTAAATTGAAATCTAAATCGAAATCTAAATCAAATTCTAAT
1 CCTAAATTGAAATCTAAATCGAAATCTAAATCAAAATCTAAT
* *
58641596 CCTAAATTGAGAT-TGAAATCGAAAT-TGAAATTAAAATCTAA
1 CCTAAATTGAAATCT-AAATCGAAATCT-AAATCAAAATCTAA
58641637 ATCAGAATTA
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
41 2 0.06
42 34 0.94
ACGTcount: A:0.48, C:0.13, G:0.08, T:0.30
Consensus pattern (42 bp):
CCTAAATTGAAATCTAAATCGAAATCTAAATCAAAATCTAAT
Found at i:58641680 original size:18 final size:18
Alignment explanation
Indices: 58641659--58641721 Score: 74
Period size: 18 Copynumber: 3.6 Consensus size: 18
58641649 GAGTGTTTCT
*
58641659 AAATTGTAATCAAAATCA
1 AAATTGAAATCAAAATCA
* *
58641677 AAATAGAAATCGAAATCA
1 AAATTGAAATCAAAATCA
**
58641695 AAATCAAAATCAAAATCA
1 AAATTGAAATCAAAATCA
58641713 AAATT-AAAT
1 AAATTGAAAT
58641722 TTGAAATCGA
Statistics
Matches: 38, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
17 4 0.11
18 34 0.89
ACGTcount: A:0.62, C:0.11, G:0.05, T:0.22
Consensus pattern (18 bp):
AAATTGAAATCAAAATCA
Found at i:58641734 original size:6 final size:6
Alignment explanation
Indices: 58641666--58641716 Score: 77
Period size: 6 Copynumber: 8.5 Consensus size: 6
58641656 TCTAAATTGT
*
58641666 AATCAA AATCAA AAT-AGA AATCGA AATCAA AATCAA AATCAA AATCAA
1 AATCAA AATCAA AATCA-A AATCAA AATCAA AATCAA AATCAA AATCAA
58641714 AAT
1 AAT
58641717 TAAATTTGAA
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
5 1 0.02
6 40 0.98
ACGTcount: A:0.65, C:0.14, G:0.04, T:0.18
Consensus pattern (6 bp):
AATCAA
Found at i:58642281 original size:31 final size:29
Alignment explanation
Indices: 58642243--58642315 Score: 83
Period size: 31 Copynumber: 2.4 Consensus size: 29
58642233 GGTAACTGTT
*
58642243 AGTTAGTGACTGTTTTGTCACTTTTTTATA
1 AGTTAGTGACTGTTTTGTCACTTTTTGA-A
** *
58642273 ATGTTAGTGACCATTTTGTTACTTTTTGAA
1 A-GTTAGTGACTGTTTTGTCACTTTTTGAA
58642303 AGTTAAGTGACTG
1 AGTT-AGTGACTG
58642316 AAATGAAACC
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
29 3 0.09
30 9 0.26
31 23 0.66
ACGTcount: A:0.23, C:0.10, G:0.19, T:0.48
Consensus pattern (29 bp):
AGTTAGTGACTGTTTTGTCACTTTTTGAA
Found at i:58651608 original size:46 final size:46
Alignment explanation
Indices: 58651556--58651860 Score: 394
Period size: 46 Copynumber: 6.6 Consensus size: 46
58651546 GCTTTCTGAA
** * * *
58651556 ATGAAATGTGTAAGACCATGGTTGAAAGATATCATGGAAACATGAT
1 ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGAC
* *
58651602 ATGAAATGTATAAGACCATGGTTGAAAGATACCATGGCAACGTGAC
1 ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGAC
* * * *
58651648 ATGAAATGAACAAGACCATGGTTGAAAGATATCATGGAAACGTGAC
1 ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGAC
* *
58651694 ATGAAATGAACAAGACCATGGTTGAAAGATACCATGGCAACATGAT
1 ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGAC
** * **
58651740 GGGAAATGAATAAGACCACGGTTGAAAGATACCATGGCAATGTGAC
1 ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGAC
* *
58651786 ATGAAATGAACAAGACCATGGTTGAAAGATACCATGGCAAGATGAC
1 ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGAC
* * * *
58651832 AGGAAATGAGTAAGACCGTAGTTGAAAGA
1 ATGAAATGAATAAGACCATGGTTGAAAGA
58651861 CACTATGACA
Statistics
Matches: 228, Mismatches: 31, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
46 228 1.00
ACGTcount: A:0.42, C:0.13, G:0.25, T:0.20
Consensus pattern (46 bp):
ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGAC
Found at i:58651627 original size:21 final size:21
Alignment explanation
Indices: 58651557--58651628 Score: 56
Period size: 21 Copynumber: 3.2 Consensus size: 21
58651547 CTTTCTGAAA
*
58651557 TGAAATGTGTAAGACCATGGT
1 TGAAATGTATAAGACCATGGT
* * *
58651578 TGAAA-GATATCATGGAAACATGAT
1 TGAAATG-TAT-A-AG-ACCATGGT
58651602 ATGAAATGTATAAGACCATGGT
1 -TGAAATGTATAAGACCATGGT
58651624 TGAAA
1 TGAAA
58651629 GATACCATGG
Statistics
Matches: 38, Mismatches: 7, Indels: 12
0.67 0.12 0.21
Matches are distributed among these distances:
20 1 0.03
21 12 0.32
22 7 0.18
23 2 0.05
24 7 0.18
25 8 0.21
26 1 0.03
ACGTcount: A:0.42, C:0.08, G:0.24, T:0.26
Consensus pattern (21 bp):
TGAAATGTATAAGACCATGGT
Found at i:58651804 original size:138 final size:138
Alignment explanation
Indices: 58651567--58651860 Score: 446
Period size: 138 Copynumber: 2.1 Consensus size: 138
58651557 TGAAATGTGT
* * * *
58651567 AAGACCATGGTTGAAAGATATCATGGAAACATGATATGAAATGTATAAGACCATGGTTGAAAGAT
1 AAGACCATGGTTGAAAGATACCATGGAAACATGATAGGAAATGAATAAGACCACGGTTGAAAGAT
* *
58651632 ACCATGGCAACGTGACATGAAATGAACAAGACCATGGTTGAAAGATATCATGGAAACG-TGACAT
66 ACCATGGCAACGTGACATGAAATGAACAAGACCATGGTTGAAAGATACCATGGAAA-GATGACAG
58651696 GAAATGAAC
130 GAAATGAAC
* *
58651705 AAGACCATGGTTGAAAGATACCATGGCAACATGATGGGAAATGAATAAGACCACGGTTGAAAGAT
1 AAGACCATGGTTGAAAGATACCATGGAAACATGATAGGAAATGAATAAGACCACGGTTGAAAGAT
* *
58651770 ACCATGGCAATGTGACATGAAATGAACAAGACCATGGTTGAAAGATACCATGGCAAGATGACAGG
66 ACCATGGCAACGTGACATGAAATGAACAAGACCATGGTTGAAAGATACCATGGAAAGATGACAGG
**
58651835 AAATGAGT
131 AAATGAAC
* *
58651843 AAGACCGTAGTTGAAAGA
1 AAGACCATGGTTGAAAGA
58651861 CACTATGACA
Statistics
Matches: 141, Mismatches: 14, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
137 1 0.01
138 140 0.99
ACGTcount: A:0.42, C:0.14, G:0.25, T:0.19
Consensus pattern (138 bp):
AAGACCATGGTTGAAAGATACCATGGAAACATGATAGGAAATGAATAAGACCACGGTTGAAAGAT
ACCATGGCAACGTGACATGAAATGAACAAGACCATGGTTGAAAGATACCATGGAAAGATGACAGG
AAATGAAC
Found at i:58659472 original size:50 final size:50
Alignment explanation
Indices: 58659348--58659596 Score: 284
Period size: 50 Copynumber: 4.8 Consensus size: 50
58659338 GATAATAACA
* * ** * *
58659348 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCGTGAT-GG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGA-CCTCTCAT-CTCGG
* *
58659399 TGCCCATGCCATGTCCCAGACATGGTCTTATAGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* * *
58659449 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* *
58659499 TGCCCATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATGATCTTAAGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTC---ATC-T-CGG
* *
58659554 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 -TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCT
58659597 TTACCCAAAT
Statistics
Matches: 170, Mismatches: 21, Indels: 9
0.85 0.10 0.05
Matches are distributed among these distances:
49 1 0.01
50 92 0.54
51 33 0.19
53 2 0.01
54 1 0.01
55 2 0.01
56 39 0.23
ACGTcount: A:0.20, C:0.29, G:0.24, T:0.26
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
Found at i:58659526 original size:100 final size:104
Alignment explanation
Indices: 58659347--58659596 Score: 357
Period size: 100 Copynumber: 2.4 Consensus size: 104
58659337 TGATAATAAC
**
58659347 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCGTGATGGTGCCCATGCCATG
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCGTGATGGTGCCCATGCCATG
* *
58659412 TCCCAGACATGGTCTTATAGGGGACCTCTC-ATC-T-CGG
65 TCCCAGACATGGTCTTACAGGGGACCTCTCAATCTTAAGG
* *
58659449 -TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGT-CTCGGTGCCCATGCCATG
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTGAT-GGTGCCCATGCCATG
58659512 TCCCAGACATGGTCTTACAGGGGACCTCTCATGATCTTAAGG
65 TCCCAGACATGGTCTTACAGGGGACCTCTCA--ATCTTAAGG
* *
58659554 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
58659597 TTACCCAAAT
Statistics
Matches: 133, Mismatches: 8, Indels: 10
0.88 0.05 0.07
Matches are distributed among these distances:
99 1 0.01
100 50 0.38
101 36 0.27
103 3 0.02
104 1 0.01
105 2 0.02
106 40 0.30
ACGTcount: A:0.21, C:0.29, G:0.24, T:0.26
Consensus pattern (104 bp):
ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTGATGGTGCCCATGCCATGT
CCCAGACATGGTCTTACAGGGGACCTCTCAATCTTAAGG
Found at i:58659712 original size:13 final size:13
Alignment explanation
Indices: 58659691--58659722 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
58659681 GCTTGGATCA
*
58659691 TCATCAAATAAAT
1 TCATAAAATAAAT
58659704 TCATAAAATAAAT
1 TCATAAAATAAAT
58659717 TCATAA
1 TCATAA
58659723 TTGCTGGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.31
Consensus pattern (13 bp):
TCATAAAATAAAT
Found at i:58659969 original size:30 final size:30
Alignment explanation
Indices: 58659934--58659991 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
58659924 CCTCGACTCT
*
58659934 AACTTTTTCAAAATTACAATTTTGCCCCTA
1 AACTTTTACAAAATTACAATTTTGCCCCTA
* *
58659964 AACTTTTACATAATTACATTTTTGCCCC
1 AACTTTTACAAAATTACAATTTTGCCCC
58659992 AAGGCTCGGA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.31, C:0.24, G:0.03, T:0.41
Consensus pattern (30 bp):
AACTTTTACAAAATTACAATTTTGCCCCTA
Found at i:58664351 original size:14 final size:14
Alignment explanation
Indices: 58664332--58664359 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
58664322 CCTGATCTAA
58664332 GATTACGAAACCAT
1 GATTACGAAACCAT
58664346 GATTACGAAACCAT
1 GATTACGAAACCAT
58664360 TGTTCCGATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.21, G:0.14, T:0.21
Consensus pattern (14 bp):
GATTACGAAACCAT
Found at i:58668688 original size:40 final size:40
Alignment explanation
Indices: 58668598--58668822 Score: 278
Period size: 40 Copynumber: 5.7 Consensus size: 40
58668588 TCGAATGATG
* * * *
58668598 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
* * *
58668638 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
* * *
58668678 TCTGGGCTAAG-CTCGAAGGCATTGGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
58668717 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
58668757 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
*
58668798 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
58668823 AACGAGTAGC
Statistics
Matches: 161, Mismatches: 19, Indels: 10
0.85 0.10 0.05
Matches are distributed among these distances:
39 32 0.20
40 119 0.74
41 10 0.06
ACGTcount: A:0.24, C:0.21, G:0.28, T:0.26
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:58668844 original size:119 final size:119
Alignment explanation
Indices: 58668598--58668845 Score: 272
Period size: 119 Copynumber: 2.1 Consensus size: 119
58668588 TCGAATGATG
* *
58668598 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATTT
1 TCCGGGTTAAGTCCCGAAGGCTTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATTT
* * * **
58668663 GTGCGAGATACTAATTCTGGGCTAAGCTCGAAGGCATTGGTGCGAGTTACTAAA
66 GTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTGGAACGAGTTACTAAA
* * * **
58668717 TCCGGGTTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCAT
1 TCCGGGTTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCAT
* * * *
58668780 TTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGCTATA
64 TTGTGCGAGATACTAAT-ACCGGGCTAAG-CCCGAAGGCATTGGAACGAGTTA-CTAAA
58668837 TCC-GGTTAA
1 TCCGGGTTAA
58668846 ATTCCAAAGG
Statistics
Matches: 108, Mismatches: 16, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
118 3 0.03
119 75 0.69
120 30 0.28
ACGTcount: A:0.25, C:0.21, G:0.27, T:0.26
Consensus pattern (119 bp):
TCCGGGTTAAGTCCCGAAGGCTTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATTT
GTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTGGAACGAGTTACTAAA
Found at i:58674602 original size:41 final size:41
Alignment explanation
Indices: 58674540--58674689 Score: 142
Period size: 41 Copynumber: 3.7 Consensus size: 41
58674530 TTGGGGTTTA
*
58674540 AATCCGAGCTTGGTCTCGAAGGGATTTTGAGCCAGTGTAAT
1 AATCCAAGCTTGGTCTCGAAGGGATTTTGAGCCAGTGTAAT
* * *
58674581 AATCCAAGCTTGGTCTTGAAGGGCTTTTGAGCCAGTGTTAT
1 AATCCAAGCTTGGTCTCGAAGGGATTTTGAGCCAGTGTAAT
* * * ** * * * *
58674622 AA-CCGAA-CCTAGTTTCGAAGGGCCTTCGGGCCAATGTCAT
1 AATCC-AAGCTTGGTCTCGAAGGGATTTTGAGCCAGTGTAAT
* *
58674662 AATCCGAGCTTGGTCTCGAAGGGCTTTT
1 AATCCAAGCTTGGTCTCGAAGGGATTTT
58674690 TGAGTCAGCG
Statistics
Matches: 87, Mismatches: 19, Indels: 6
0.78 0.17 0.05
Matches are distributed among these distances:
40 29 0.33
41 58 0.67
ACGTcount: A:0.23, C:0.21, G:0.27, T:0.29
Consensus pattern (41 bp):
AATCCAAGCTTGGTCTCGAAGGGATTTTGAGCCAGTGTAAT
Found at i:58691167 original size:40 final size:40
Alignment explanation
Indices: 58691099--58691267 Score: 214
Period size: 40 Copynumber: 4.2 Consensus size: 40
58691089 CCTTCGGAGT
* * * * * *
58691099 TTAG-CCGGATATAGCAACTAGCTCAAATGCCTTTGGGAC
1 TTAGCCCGGATATAGTAGCTCGCACAAACGCCTTCGGGAC
* * * * *
58691138 TTAGCCCGGTTAGAGTAACTTGCACAAATGCCTTCGGGAC
1 TTAGCCCGGATATAGTAGCTCGCACAAACGCCTTCGGGAC
*
58691178 TTAGCCCGGATATAATAGCTCGCACAAACGCCTTCGGGAC
1 TTAGCCCGGATATAGTAGCTCGCACAAACGCCTTCGGGAC
*
58691218 TTAGCCCGGATATAGTAGCTCGCACGAACGCCTTCGGGAC
1 TTAGCCCGGATATAGTAGCTCGCACAAACGCCTTCGGGAC
58691258 TTAGCCCGGA
1 TTAGCCCGGA
58691268 ATTAGCCACT
Statistics
Matches: 115, Mismatches: 14, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
39 4 0.03
40 111 0.97
ACGTcount: A:0.25, C:0.27, G:0.25, T:0.22
Consensus pattern (40 bp):
TTAGCCCGGATATAGTAGCTCGCACAAACGCCTTCGGGAC
Found at i:58691295 original size:80 final size:81
Alignment explanation
Indices: 58691107--58691306 Score: 239
Period size: 80 Copynumber: 2.5 Consensus size: 81
58691097 GTTTAGCCGG
* * * *
58691107 ATATAGCAACTAGCTCAAATGCCTTTGGGACTTAGCCCGGTTAGAGTAACTTGCACAAATGCCTT
1 ATATAGC-ACTAGCTCAAATGCCTTCGGGACTTAGCCCGGATAGAGTAACTCGCACAAACGCCTT
58691172 CGGGACTTAGCCCGGAT
65 CGGGACTTAGCCCGGAT
* * * * * *
58691189 ATAATAG--CTCGCACAAACGCCTTCGGGACTTAGCCCGGATATAGTAGCTCGCACGAACGCCTT
1 AT-ATAGCACTAGCTCAAATGCCTTCGGGACTTAGCCCGGATAGAGTAACTCGCACAAACGCCTT
58691252 CGGGACTTAGCCCGGA-
65 CGGGACTTAGCCCGGAT
58691268 AT-TAGCCACTAGCTCAAATG-CTCTCGGGACTTAGCCCGG
1 ATATAG-CACTAGCTCAAATGCCT-TCGGGACTTAGCCCGG
58691307 TTATCATCCG
Statistics
Matches: 100, Mismatches: 13, Indels: 12
0.80 0.10 0.10
Matches are distributed among these distances:
77 3 0.03
79 4 0.04
80 87 0.87
82 2 0.02
83 4 0.04
ACGTcount: A:0.26, C:0.28, G:0.24, T:0.23
Consensus pattern (81 bp):
ATATAGCACTAGCTCAAATGCCTTCGGGACTTAGCCCGGATAGAGTAACTCGCACAAACGCCTTC
GGGACTTAGCCCGGAT
Found at i:58699166 original size:40 final size:40
Alignment explanation
Indices: 58699122--58699264 Score: 214
Period size: 40 Copynumber: 3.6 Consensus size: 40
58699112 GCCACTAGCT
* * * *
58699122 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTTGCA
1 CAAACGCCTTCGGGACTTAGCCCGGATATAGTAGCTCGCA
* *
58699162 CAAATGCCTTCGGGACTTAGCCCGGATATAATAGCTCGCA
1 CAAACGCCTTCGGGACTTAGCCCGGATATAGTAGCTCGCA
*
58699202 CAAACGCCTTTGGGACTTAGCCCGGATATAGTAGCTCGCA
1 CAAACGCCTTCGGGACTTAGCCCGGATATAGTAGCTCGCA
*
58699242 CGAACGCCTTCGGGACTTAGCCC
1 CAAACGCCTTCGGGACTTAGCCC
58699265 AAAATTAGCC
Statistics
Matches: 94, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
40 94 1.00
ACGTcount: A:0.24, C:0.29, G:0.24, T:0.23
Consensus pattern (40 bp):
CAAACGCCTTCGGGACTTAGCCCGGATATAGTAGCTCGCA
Found at i:58699297 original size:80 final size:82
Alignment explanation
Indices: 58699109--58699303 Score: 233
Period size: 80 Copynumber: 2.4 Consensus size: 82
58699099 TTAGCCGGAT
* * *
58699109 ATAGCCACTAGCTCAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTTGCACAAATGCCTTCG
1 ATAGCCACTAGCTCAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAACGCCTTCG
58699174 GGACTTAGCCCGGATATA
66 GGACTTAGCCC-GATATA
* * * * * *
58699192 ATAG---CTCGCACAAACGCCTTTGGGACTTAGCCCGGATATAGTAGCTCGCACGAACGCCTTCG
1 ATAGCCACTAGCTCAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAACGCCTTCG
58699254 GGACTTAGCCC-A-A-A
66 GGACTTAGCCCGATATA
58699268 ATTAGCCACTAGCTCAAATG-CTCTCGGGACTTAGCC
1 A-TAGCCACTAGCTCAAATGCCT-TCGGGACTTAGCC
58699304 TGGTTATCAT
Statistics
Matches: 94, Mismatches: 13, Indels: 13
0.78 0.11 0.11
Matches are distributed among these distances:
76 2 0.02
77 4 0.04
78 1 0.01
79 2 0.02
80 81 0.86
83 4 0.04
ACGTcount: A:0.26, C:0.29, G:0.22, T:0.23
Consensus pattern (82 bp):
ATAGCCACTAGCTCAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAACGCCTTCG
GGACTTAGCCCGATATA
Found at i:58703041 original size:43 final size:43
Alignment explanation
Indices: 58702946--58703047 Score: 134
Period size: 43 Copynumber: 2.4 Consensus size: 43
58702936 ATCGAGATGT
* * *
58702946 GATTACATGTAAGACCATGTCTGGGACATTGATATTGTATTGA
1 GATTACGTGTAAGACCATGTCTGGGACATTGACATTGTAATGA
* *
58702989 GATTACGTGTAAGACCATGTCTGGGACATTGGCATTGTTAAT-C
1 GATTACGTGTAAGACCATGTCTGGGACATTGACATTG-TAATGA
*
58703032 GATTTCGTGTAAGACC
1 GATTACGTGTAAGACC
58703048 CTGTTTGGTA
Statistics
Matches: 52, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
43 49 0.94
44 3 0.06
ACGTcount: A:0.27, C:0.15, G:0.25, T:0.33
Consensus pattern (43 bp):
GATTACGTGTAAGACCATGTCTGGGACATTGACATTGTAATGA
Found at i:58705348 original size:24 final size:23
Alignment explanation
Indices: 58705316--58705361 Score: 65
Period size: 24 Copynumber: 2.0 Consensus size: 23
58705306 TACATAAGTC
* *
58705316 AAAGATTTCTTGATTTGAAACAT
1 AAAGATTTCTAGAATTGAAACAT
58705339 AAAGAATTTCTAGAATTGAAACA
1 AAAG-ATTTCTAGAATTGAAACA
58705362 AGGCGGAATG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 4 0.20
24 16 0.80
ACGTcount: A:0.46, C:0.09, G:0.13, T:0.33
Consensus pattern (23 bp):
AAAGATTTCTAGAATTGAAACAT
Found at i:58707550 original size:48 final size:48
Alignment explanation
Indices: 58707343--58707620 Score: 245
Period size: 48 Copynumber: 5.7 Consensus size: 48
58707333 GAAGGTAAAT
* * * *
58707343 TGCCGATGCCATGTCTCAAACATGGTCTTACATTGGCTCACATGTCGA
1 TGCCGATGCCATGTCCCAAACATGGTCTTACACTGGCTCACATATCAA
* ** * * * * * * *
58707391 -GACTGATGCTGTGTCCTAGACATGGACTTACACTAGCTCTCGTCTCAA
1 TG-CCGATGCCATGTCCCAAACATGGTCTTACACTGGCTCACATATCAA
* * *
58707439 TGCCGATGCCATGTCCCAGACATGGTCTTACACTTGCACACACATATCAA
1 TGCCGATGCCATGTCCCAAACATGGTCTTACAC-TG-GCTCACATATCAA
* * *
58707489 CGCCGATGCCATGTTCCAAACATGGTCTTACACTGGCTCACATAACAA
1 TGCCGATGCCATGTCCCAAACATGGTCTTACACTGGCTCACATATCAA
* * *
58707537 TGCCGATGCCATGTCCCAAACATGGTCTTACATTGGCTCTCACA-CAA
1 TGCCGATGCCATGTCCCAAACATGGTCTTACACTGGCTCACATATCAA
* * * *
58707584 CGGTGTCGCTACCATGTCCCGAACATGGTCTTACACT
1 ---TGCCGATGCCATGTCCCAAACATGGTCTTACACT
58707621 ACCTCACGTA
Statistics
Matches: 183, Mismatches: 40, Indels: 12
0.78 0.17 0.05
Matches are distributed among these distances:
47 4 0.02
48 108 0.59
49 4 0.02
50 67 0.37
ACGTcount: A:0.25, C:0.30, G:0.19, T:0.26
Consensus pattern (48 bp):
TGCCGATGCCATGTCCCAAACATGGTCTTACACTGGCTCACATATCAA
Found at i:58707599 original size:98 final size:98
Alignment explanation
Indices: 58707436--58707620 Score: 237
Period size: 98 Copynumber: 1.9 Consensus size: 98
58707426 GCTCTCGTCT
* * * *
58707436 CAATGCCGATGCCATGTCCCAGACATGGTCTTACACTTGCACACACATATCAACGCCGATGCCAT
1 CAATGCCGATGCCATGTCCCAAACATGGTCTTACACTTGCACACACACAACAACGCCGATACCAT
*
58707501 GTTCCAAACATGGTCTTACACTGGCTCACATAA
66 GTCCCAAACATGGTCTTACACTGGCTCACATAA
* * *** * *
58707534 CAATGCCGATGCCATGTCCCAAACATGGTCTTACA-TTGGCTCTCACACAACGGTGTCGCTACCA
1 CAATGCCGATGCCATGTCCCAAACATGGTCTTACACTT-GCACACACACAACAACGCCGATACCA
*
58707598 TGTCCCGAACATGGTCTTACACT
65 TGTCCCAAACATGGTCTTACACT
58707621 ACCTCACGTA
Statistics
Matches: 73, Mismatches: 13, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
97 2 0.03
98 71 0.97
ACGTcount: A:0.26, C:0.32, G:0.17, T:0.24
Consensus pattern (98 bp):
CAATGCCGATGCCATGTCCCAAACATGGTCTTACACTTGCACACACACAACAACGCCGATACCAT
GTCCCAAACATGGTCTTACACTGGCTCACATAA
Found at i:58707603 original size:50 final size:48
Alignment explanation
Indices: 58707436--58707620 Score: 199
Period size: 50 Copynumber: 3.8 Consensus size: 48
58707426 GCTCTCGTCT
* * * *
58707436 CAATGCCGATGCCATGTCCCAGACATGGTCTTACACTTGCACACACATA
1 CAATGCCGATACCATGTCCCAAACATGGTCTTACACTGGCTCACACA-A
* * * *
58707485 TCAACGCCGATGCCATGTTCCAAACATGGTCTTACACTGGCTCACATAA
1 -CAATGCCGATACCATGTCCCAAACATGGTCTTACACTGGCTCACACAA
* *
58707534 CAATGCCGATGCCATGTCCCAAACATGGTCTTACATTGGCTCTCACACAA
1 CAATGCCGATACCATGTCCCAAACATGGTCTTACACTGG--CTCACACAA
** * * *
58707584 CGGTGTCGCTACCATGTCCCGAACATGGTCTTACACT
1 CAATGCCGATACCATGTCCCAAACATGGTCTTACACT
58707621 ACCTCACGTA
Statistics
Matches: 116, Mismatches: 17, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
48 36 0.31
49 1 0.01
50 79 0.68
ACGTcount: A:0.26, C:0.32, G:0.17, T:0.24
Consensus pattern (48 bp):
CAATGCCGATACCATGTCCCAAACATGGTCTTACACTGGCTCACACAA
Found at i:58713352 original size:43 final size:43
Alignment explanation
Indices: 58713300--58713409 Score: 141
Period size: 43 Copynumber: 2.6 Consensus size: 43
58713290 CGAGATGTGC
* *
58713300 TTACATGTAAGACCATGTCTGGGACATGGGCATTG-TATTGAGA
1 TTACGTGTAAGACCATGTCTGGGACATGGGCATTGTTAAT-AGA
* *
58713343 TTACGTGTAAGACCATGTCTGGGACATTGGCATTGTTAATCGA
1 TTACGTGTAAGACCATGTCTGGGACATGGGCATTGTTAATAGA
* * *
58713386 TTTCGTGTAAGACCTTGTTTGGGA
1 TTACGTGTAAGACCATGTCTGGGA
58713410 AAGTGGCATC
Statistics
Matches: 59, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
43 56 0.95
44 3 0.05
ACGTcount: A:0.25, C:0.15, G:0.27, T:0.34
Consensus pattern (43 bp):
TTACGTGTAAGACCATGTCTGGGACATGGGCATTGTTAATAGA
Found at i:58723983 original size:50 final size:50
Alignment explanation
Indices: 58723738--58724031 Score: 270
Period size: 50 Copynumber: 5.8 Consensus size: 50
58723728 ACTGAAGCTC
* * * *
58723738 TCTGGTACGCATAGTAGCCTGCATTTAGTACTACACATGCGACCTAACAA
1 TCTGGTACACGTAGTAGCCTGCACTTAGTACTACACATGTGACCTAACAA
* * * * *
58723788 TTTGGTACATGGAGTGGCCTGCACTTAGTACTACACACT-TGACCTAACCA
1 TCTGGTACACGTAGTAGCCTGCACTTAGTACTACACA-TGTGACCTAACAA
* * * *
58723838 TCTGATACACGTAGTAGCTTGCACTTAGTACTACACATGTGA-TTGAAGCTA
1 TCTGGTACACGTAGTAGCCTGCACTTAGTACTACACATGTGACCT-AA-CAA
* * * *
58723889 TCGGGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCTAACAA
1 TCTGGTACACGTAGTAGCCTGCACTTAGTACTACACATGTGACCTAACAA
* * **
58723939 TCTGGTACATGTGGTAGCCTGCACTTAGTACTACACACATGACCTAA-AA
1 TCTGGTACACGTAGTAGCCTGCACTTAGTACTACACATGTGACCTAACAA
*** * * *
58723988 CCGTCTTAAACACATAGTAGCCTACACATAGTACTACACATGTG
1 ---TCTGGTACACGTAGTAGCCTGCACTTAGTACTACACATGTG
58724032 TTCTCACAAC
Statistics
Matches: 193, Mismatches: 43, Indels: 14
0.77 0.17 0.06
Matches are distributed among these distances:
49 4 0.02
50 116 0.60
51 41 0.21
52 32 0.17
ACGTcount: A:0.30, C:0.25, G:0.18, T:0.27
Consensus pattern (50 bp):
TCTGGTACACGTAGTAGCCTGCACTTAGTACTACACATGTGACCTAACAA
Found at i:58727334 original size:18 final size:18
Alignment explanation
Indices: 58727297--58727336 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
58727287 TAGTTATAAT
58727297 CAAAACAAATAAAAATCC
1 CAAAACAAATAAAAATCC
*
58727315 CAAAATCAAATGAAAA-CC
1 CAAAA-CAAATAAAAATCC
58727333 CAAA
1 CAAA
58727337 GAGGCCATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 11 0.55
19 9 0.45
ACGTcount: A:0.65, C:0.23, G:0.03, T:0.10
Consensus pattern (18 bp):
CAAAACAAATAAAAATCC
Found at i:58730369 original size:25 final size:27
Alignment explanation
Indices: 58730332--58730384 Score: 74
Period size: 26 Copynumber: 2.0 Consensus size: 27
58730322 TCAAACATGC
58730332 ATTTAGGTCAATTTAAC-CCTAGGGGT
1 ATTTAGGTCAATTTAACTCCTAGGGGT
* *
58730358 ATTTCGGT-AATTTATCTCCTAGGGGT
1 ATTTAGGTCAATTTAACTCCTAGGGGT
58730384 A
1 A
58730385 AAACTGTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 7 0.29
26 17 0.71
ACGTcount: A:0.25, C:0.15, G:0.23, T:0.38
Consensus pattern (27 bp):
ATTTAGGTCAATTTAACTCCTAGGGGT
Found at i:58733158 original size:18 final size:18
Alignment explanation
Indices: 58733135--58733174 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
58733125 CAATTCTGCT
*
58733135 AACAGACTTCAATCGT-CA
1 AACAGAC-TCAAACGTGCA
58733153 AACAGACTCAAACGTGCA
1 AACAGACTCAAACGTGCA
58733171 AACA
1 AACA
58733175 AGGGTCTCAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.45, C:0.28, G:0.12, T:0.15
Consensus pattern (18 bp):
AACAGACTCAAACGTGCA
Found at i:58737446 original size:32 final size:30
Alignment explanation
Indices: 58737402--58737481 Score: 70
Period size: 32 Copynumber: 2.5 Consensus size: 30
58737392 TCAAGCCCAT
*
58737402 TGGGCCTAAGCCCATTCAGATAACAGTGATAC
1 TGGGCC-AAGCCCATTCAGATAACA-TGAAAC
* * *
58737434 TGGGCCAGAGCCCTGTTCAGATTACATTAAAC
1 TGGGCCA-AGCCC-ATTCAGATAACATGAAAC
*
58737466 TGGGCCTTAGCCCATT
1 TGGGCC-AAGCCCATT
58737482 ATTTAGATAA
Statistics
Matches: 39, Mismatches: 6, Indels: 7
0.75 0.12 0.13
Matches are distributed among these distances:
31 3 0.08
32 26 0.67
33 10 0.26
ACGTcount: A:0.26, C:0.26, G:0.23, T:0.25
Consensus pattern (30 bp):
TGGGCCAAGCCCATTCAGATAACATGAAAC
Found at i:58738357 original size:23 final size:23
Alignment explanation
Indices: 58738324--58738372 Score: 89
Period size: 23 Copynumber: 2.1 Consensus size: 23
58738314 CACCGGTTCC
*
58738324 TTCGGCTAATGATCCCAATTAAT
1 TTCGGCCAATGATCCCAATTAAT
58738347 TTCGGCCAATGATCCCAATTAAT
1 TTCGGCCAATGATCCCAATTAAT
58738370 TTC
1 TTC
58738373 TACTCAATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.29, C:0.24, G:0.12, T:0.35
Consensus pattern (23 bp):
TTCGGCCAATGATCCCAATTAAT
Found at i:58742050 original size:40 final size:40
Alignment explanation
Indices: 58741952--58742246 Score: 382
Period size: 40 Copynumber: 7.4 Consensus size: 40
58741942 TCCTCGTTCA
* * * * *
58741952 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* *
58741991 AATGCCTTCGGGACATAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
*
58742031 ACTGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
58742071 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
58742111 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * *
58742151 AATGCCTTC-GGACTTAACCCGGATTTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * * * * *
58742190 AAGGCCTTC-GGATCTTAATCCGGATATATTCACTTAGCAC-
1 AATGCCTTCGGGA-CTTAACCCGGATTTAATAAC-TCGCACG
*
58742230 AAAGCCTTCGGGACTTA
1 AATGCCTTCGGGACTTA
58742247 GCCGGACAGC
Statistics
Matches: 232, Mismatches: 20, Indels: 7
0.90 0.08 0.03
Matches are distributed among these distances:
39 72 0.31
40 152 0.66
41 8 0.03
ACGTcount: A:0.27, C:0.28, G:0.20, T:0.25
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
Found at i:58742186 original size:119 final size:119
Alignment explanation
Indices: 58741950--58742246 Score: 391
Period size: 119 Copynumber: 2.5 Consensus size: 119
58741940 GCTCCTCGTT
* * * * * *
58741950 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACACAATGCCTTCGGGACATAACCCGGA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACAATGCCTTCGGGACTTAACCCGGA
*
58742015 TTTAACAACTCGCACGACTGCCTTCGGGACTTAACCCGGATTTAATAACTCGCA
66 TTTAACAACTCGCACGAATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCA
*
58742069 CGAATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACGAATGCCTTCGGGACTTAACCCGG
1 CAAATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCAC-AATGCCTTCGGGACTTAACCCGG
* * *
58742134 ATTTAATAACTCGCACGAATGCCTTC-GGACTTAACCCGGATTTAGTATCTCGCA
65 ATTTAACAACTCGCACGAATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCA
* * * * * * *
58742188 CAAAGGCCTTC-GGATCTTAATCCGGATATATTCACTTAGCACAAAGCCTTCGGGACTTA
1 CAAATGCCTTCGGGA-CTTAACCCGGATTTAATAAC-TCGCACAATGCCTTCGGGACTTA
58742247 GCCGGACAGC
Statistics
Matches: 156, Mismatches: 19, Indels: 6
0.86 0.10 0.03
Matches are distributed among these distances:
118 3 0.02
119 102 0.65
120 51 0.33
ACGTcount: A:0.27, C:0.28, G:0.20, T:0.25
Consensus pattern (119 bp):
CAAATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACAATGCCTTCGGGACTTAACCCGGA
TTTAACAACTCGCACGAATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCA
Found at i:58749652 original size:13 final size:13
Alignment explanation
Indices: 58749634--58749658 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
58749624 ACGAGGCTCC
58749634 TTTGCTTCCTTTA
1 TTTGCTTCCTTTA
58749647 TTTGCTTCCTTT
1 TTTGCTTCCTTT
58749659 GCTGATGGCT
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:0.04, C:0.24, G:0.08, T:0.64
Consensus pattern (13 bp):
TTTGCTTCCTTTA
Found at i:58753348 original size:118 final size:117
Alignment explanation
Indices: 58753156--58753404 Score: 324
Period size: 118 Copynumber: 2.1 Consensus size: 117
58753146 GCTCCTCGTT
* * *
58753156 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACACAATGCCTTCGGGACATAACCCGGA
1 CAAATGCCTTCGGGACATAACCCGGATTTAATAACTCACACAATGCCTTCGGGACATAACCCGGA
*
58753221 TTAACAACTCGCACGACTGCCTTCGGGACTTAACCCGGATTTAATAACTCGCA
66 TT-ACAACTCGCACGAATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCA
* * * *
58753274 CGAATGCCTTCGGGACTTAACCC-GATTTAATAACTCGCACGAATGCCTTC-GGACTTAACCGCG
1 CAAATGCCTTCGGGACATAACCCGGATTTAATAACTCACAC-AATGCCTTCGGGACATAACC-CG
* * *
58753337 AGTATT-TAACTCGCACGAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCA
64 -G-ATTACAACTCGCACGAATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCA
*
58753392 CAAAGGCCTTCGG
1 CAAATGCCTTCGG
58753405 ATCTTAATCC
Statistics
Matches: 114, Mismatches: 13, Indels: 8
0.84 0.10 0.06
Matches are distributed among these distances:
117 23 0.20
118 87 0.76
119 1 0.01
120 3 0.03
ACGTcount: A:0.27, C:0.29, G:0.20, T:0.24
Consensus pattern (117 bp):
CAAATGCCTTCGGGACATAACCCGGATTTAATAACTCACACAATGCCTTCGGGACATAACCCGGA
TTACAACTCGCACGAATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCA
Found at i:58753411 original size:40 final size:40
Alignment explanation
Indices: 58753158--58753404 Score: 310
Period size: 39 Copynumber: 6.3 Consensus size: 40
58753148 TCCTCGTTCA
* * * * *
58753158 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* *
58753197 AATGCCTTCGGGACATAACCCGGA-TTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
*
58753236 ACTGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
58753276 AATGCCTTCGGGACTTAACCC-GATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
58753315 AATGCCTTC-GGACTTAA-CCGCGAGTATT--TAACTCGCACG
1 AATGCCTTCGGGACTTAACCCG-GA-T-TTAATAACTCGCACG
* * *
58753354 AATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
*
58753394 AAGGCCTTCGG
1 AATGCCTTCGG
58753405 ATCTTAATCC
Statistics
Matches: 186, Mismatches: 12, Indels: 19
0.86 0.06 0.09
Matches are distributed among these distances:
37 2 0.01
38 21 0.11
39 94 0.51
40 64 0.34
41 5 0.03
ACGTcount: A:0.26, C:0.29, G:0.21, T:0.24
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
Found at i:58757079 original size:24 final size:24
Alignment explanation
Indices: 58757047--58757117 Score: 115
Period size: 24 Copynumber: 3.0 Consensus size: 24
58757037 CTGTCAGGAG
58757047 AGGATTTAGGAGTTGATAAGGGAT
1 AGGATTTAGGAGTTGATAAGGGAT
*
58757071 AGGATTTAGGAGTTGATGAGGGAT
1 AGGATTTAGGAGTTGATAAGGGAT
**
58757095 AGGATTTAGGAGCAGATAAGGGA
1 AGGATTTAGGAGTTGATAAGGGA
58757118 GGAAATCTAG
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 43 1.00
ACGTcount: A:0.34, C:0.01, G:0.39, T:0.25
Consensus pattern (24 bp):
AGGATTTAGGAGTTGATAAGGGAT
Found at i:58758554 original size:27 final size:27
Alignment explanation
Indices: 58758514--58758625 Score: 138
Period size: 27 Copynumber: 4.1 Consensus size: 27
58758504 AGGAAGCGTC
*
58758514 CTGGTGGCTATGCCACAATTATCTGAT
1 CTGGTGGCTCTGCCACAATTATCTGAT
*
58758541 CTGGTGGCTCTGCCACATATT-TCTGTT
1 CTGGTGGCTCTGCCACA-ATTATCTGAT
*
58758568 CTGGTGGCTCTGCCACGATTATCTGTAT
1 CTGGTGGCTCTGCCACAATTATCTG-AT
* * *
58758596 CTGGTGACTCTGTCAC-ATTATCTGTT
1 CTGGTGGCTCTGCCACAATTATCTGAT
58758622 CTGG
1 CTGG
58758626 CAGCCATGCT
Statistics
Matches: 75, Mismatches: 7, Indels: 7
0.84 0.08 0.08
Matches are distributed among these distances:
26 8 0.11
27 49 0.65
28 18 0.24
ACGTcount: A:0.15, C:0.24, G:0.23, T:0.38
Consensus pattern (27 bp):
CTGGTGGCTCTGCCACAATTATCTGAT
Found at i:58758620 original size:54 final size:54
Alignment explanation
Indices: 58758514--58758625 Score: 163
Period size: 54 Copynumber: 2.1 Consensus size: 54
58758504 AGGAAGCGTC
* *
58758514 CTGGTGGCTATGCCACAATTATCTGATCTGGTGGCTCTGCCACATATTTCTGTT
1 CTGGTGGCTATGCCACAATTATCTGATCTGGTGACTCTGCCACATATATCTGTT
* * *
58758568 CTGGTGGCTCTGCCACGATTATCTGTATCTGGTGACTCTGTCACAT-TATCTGTT
1 CTGGTGGCTATGCCACAATTATCTG-ATCTGGTGACTCTGCCACATATATCTGTT
58758622 CTGG
1 CTGG
58758626 CAGCCATGCT
Statistics
Matches: 52, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
54 34 0.65
55 18 0.35
ACGTcount: A:0.15, C:0.24, G:0.23, T:0.38
Consensus pattern (54 bp):
CTGGTGGCTATGCCACAATTATCTGATCTGGTGACTCTGCCACATATATCTGTT
Found at i:58759697 original size:11 final size:10
Alignment explanation
Indices: 58759669--58759702 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
58759659 AGCCTGTAAG
58759669 TATTCTGAAT
1 TATTCTGAAT
*
58759679 TTTTCTGAAT
1 TATTCTGAAT
58759689 ATATTCTGAAT
1 -TATTCTGAAT
58759700 TAT
1 TAT
58759703 CTGTCTGTAC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
10 12 0.57
11 9 0.43
ACGTcount: A:0.29, C:0.09, G:0.09, T:0.53
Consensus pattern (10 bp):
TATTCTGAAT
Found at i:58764877 original size:24 final size:24
Alignment explanation
Indices: 58764850--58764920 Score: 106
Period size: 24 Copynumber: 3.0 Consensus size: 24
58764840 CTGTCAGGAG
*
58764850 AGGATTTAGAAGTTGATAAGGGAT
1 AGGATTTAGGAGTTGATAAGGGAT
*
58764874 AGGATTTAGGAGTTGATGAGGGAT
1 AGGATTTAGGAGTTGATAAGGGAT
**
58764898 AGGATTTAGGAGCAGATAAGGGA
1 AGGATTTAGGAGTTGATAAGGGA
58764921 GGAAATCTAG
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 42 1.00
ACGTcount: A:0.35, C:0.01, G:0.38, T:0.25
Consensus pattern (24 bp):
AGGATTTAGGAGTTGATAAGGGAT
Found at i:58766376 original size:27 final size:27
Alignment explanation
Indices: 58766336--58766447 Score: 97
Period size: 27 Copynumber: 4.1 Consensus size: 27
58766326 AGGAAGCGTC
*
58766336 CTGGTGGCTATGCCACAATTATCTGAT
1 CTGGTGGCTCTGCCACAATTATCTGAT
58766363 CTGGTGGCTCTGCCACATATT-TCT-ATT
1 CTGGTGGCTCTGCCACA-ATTATCTGA-T
* * *
58766390 CTGGTGGTTCTACAACGAA-TATCTGTAT
1 CTGGTGGCTCTGCCAC-AATTATCTG-AT
* * *
58766418 CTGGTGACTCTGTCAC-ATTATCTGTT
1 CTGGTGGCTCTGCCACAATTATCTGAT
58766444 CTGG
1 CTGG
58766448 CAGTCATGCT
Statistics
Matches: 68, Mismatches: 10, Indels: 15
0.73 0.11 0.16
Matches are distributed among these distances:
26 8 0.12
27 43 0.63
28 16 0.24
29 1 0.01
ACGTcount: A:0.19, C:0.22, G:0.21, T:0.38
Consensus pattern (27 bp):
CTGGTGGCTCTGCCACAATTATCTGAT
Found at i:58768362 original size:29 final size:29
Alignment explanation
Indices: 58768318--58768375 Score: 107
Period size: 29 Copynumber: 2.0 Consensus size: 29
58768308 GATTGTATAC
58768318 TCTTTTTCCTTCATTAGGTTTTTATCGTA
1 TCTTTTTCCTTCATTAGGTTTTTATCGTA
*
58768347 TCTTTTTCCTTTATTAGGTTTTTATCGTA
1 TCTTTTTCCTTCATTAGGTTTTTATCGTA
58768376 CAAGGTTTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.14, C:0.16, G:0.10, T:0.60
Consensus pattern (29 bp):
TCTTTTTCCTTCATTAGGTTTTTATCGTA
Found at i:58769493 original size:33 final size:33
Alignment explanation
Indices: 58769456--58769538 Score: 96
Period size: 33 Copynumber: 2.5 Consensus size: 33
58769446 CTTGTACTAT
* * *
58769456 GTTTAACTTTTATCTTTAGTATTTAGGAATCAA
1 GTTTAACTTTTGTCTTTAGCATTTAGGAACCAA
* * * *
58769489 GTTTAACCTTTGTCTATAGCCTTTAGTAACCAA
1 GTTTAACTTTTGTCTTTAGCATTTAGGAACCAA
58769522 GTTTAA-TTTTGTCTTTA
1 GTTTAACTTTTGTCTTTA
58769539 CTTAGTGAAA
Statistics
Matches: 41, Mismatches: 9, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
32 9 0.22
33 32 0.78
ACGTcount: A:0.27, C:0.13, G:0.12, T:0.48
Consensus pattern (33 bp):
GTTTAACTTTTGTCTTTAGCATTTAGGAACCAA
Found at i:58769915 original size:13 final size:13
Alignment explanation
Indices: 58769866--58769918 Score: 52
Period size: 13 Copynumber: 4.1 Consensus size: 13
58769856 AATTTAGCAT
*
58769866 TGCTTTTAAAAAG
1 TGCTTTTGAAAAG
* * *
58769879 TGTTTTTTAAAAA
1 TGCTTTTGAAAAG
* *
58769892 TGCTATAGAAAAG
1 TGCTTTTGAAAAG
58769905 TGCTTTTGAAAAG
1 TGCTTTTGAAAAG
58769918 T
1 T
58769919 TTAGTTTAAG
Statistics
Matches: 30, Mismatches: 10, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
13 30 1.00
ACGTcount: A:0.38, C:0.06, G:0.17, T:0.40
Consensus pattern (13 bp):
TGCTTTTGAAAAG
Found at i:58771986 original size:28 final size:27
Alignment explanation
Indices: 58771934--58771988 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 27
58771924 CTCCCTTTCA
* *
58771934 CTCCCCTTGTTCCCTCTCTTTCCTTTT
1 CTCCCCTTGTTCACTCTCTTACCTTTT
58771961 CTCCCTCTTGTTTCACTC-CTTACCTTTT
1 CTCCC-CTTG-TTCACTCTCTTACCTTTT
58771989 TCTATCCTCT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
27 5 0.21
28 13 0.54
29 6 0.25
ACGTcount: A:0.04, C:0.42, G:0.04, T:0.51
Consensus pattern (27 bp):
CTCCCCTTGTTCACTCTCTTACCTTTT
Found at i:58772078 original size:20 final size:20
Alignment explanation
Indices: 58772045--58772084 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
58772035 AAACATTTTG
*
58772045 TTTCTCTCCCCTTTTATTCT
1 TTTCTCTCACCTTTTATTCT
* *
58772065 TTTCTCTCATCTTTTTTTCT
1 TTTCTCTCACCTTTTATTCT
58772085 CATCTTCCAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.05, C:0.30, G:0.00, T:0.65
Consensus pattern (20 bp):
TTTCTCTCACCTTTTATTCT
Found at i:58775036 original size:25 final size:25
Alignment explanation
Indices: 58775002--58775054 Score: 106
Period size: 25 Copynumber: 2.1 Consensus size: 25
58774992 AGGAAAGAGA
58775002 AGAAAAGAGGAAGAAAACTCACGTC
1 AGAAAAGAGGAAGAAAACTCACGTC
58775027 AGAAAAGAGGAAGAAAACTCACGTC
1 AGAAAAGAGGAAGAAAACTCACGTC
58775052 AGA
1 AGA
58775055 TTCTTTTTGG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.53, C:0.15, G:0.25, T:0.08
Consensus pattern (25 bp):
AGAAAAGAGGAAGAAAACTCACGTC
Found at i:58789816 original size:16 final size:16
Alignment explanation
Indices: 58789795--58789836 Score: 75
Period size: 16 Copynumber: 2.6 Consensus size: 16
58789785 ATCGGTAAAA
*
58789795 GCCAAAATGCTGAAAT
1 GCCAAAAAGCTGAAAT
58789811 GCCAAAAAGCTGAAAT
1 GCCAAAAAGCTGAAAT
58789827 GCCAAAAAGC
1 GCCAAAAAGC
58789837 CAAAAGTTTG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.48, C:0.21, G:0.19, T:0.12
Consensus pattern (16 bp):
GCCAAAAAGCTGAAAT
Found at i:58790097 original size:29 final size:29
Alignment explanation
Indices: 58790064--58790139 Score: 107
Period size: 29 Copynumber: 2.6 Consensus size: 29
58790054 TGAATATGAC
** *
58790064 TGGGCCTAATGGGCCATATAAATTTTATT
1 TGGGCCTAATGGGCCATATAAAGGTGATT
* *
58790093 TGGGCCTAATGGGCTATATACAGGTGATT
1 TGGGCCTAATGGGCCATATAAAGGTGATT
58790122 TGGGCCTAATGGGCCATA
1 TGGGCCTAATGGGCCATA
58790140 CGAATATGAT
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 41 1.00
ACGTcount: A:0.25, C:0.16, G:0.28, T:0.32
Consensus pattern (29 bp):
TGGGCCTAATGGGCCATATAAAGGTGATT
Found at i:58790149 original size:29 final size:27
Alignment explanation
Indices: 58790055--58790163 Score: 92
Period size: 29 Copynumber: 3.9 Consensus size: 27
58790045 GCATGAATAT
*
58790055 GAATATGACTGGGCCTAATGGGCCATA
1 GAATATGATTGGGCCTAATGGGCCATA
* * * *
58790082 TAAATTTTATTTGGGCCTAATGGGCTATA
1 -GAATATGA-TTGGGCCTAATGGGCCATA
* **
58790111 TACAGGTGATTTGGGCCTAATGGGCCATA
1 GA-ATATGA-TTGGGCCTAATGGGCCATA
*
58790140 CGAATATGATTGGGCTTAATGGGC
1 -GAATATGATTGGGCCTAATGGGC
58790164 TAGATACAGG
Statistics
Matches: 64, Mismatches: 14, Indels: 6
0.76 0.17 0.07
Matches are distributed among these distances:
28 20 0.31
29 43 0.67
30 1 0.02
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
GAATATGATTGGGCCTAATGGGCCATA
Found at i:58790171 original size:57 final size:58
Alignment explanation
Indices: 58790064--58790174 Score: 161
Period size: 57 Copynumber: 1.9 Consensus size: 58
58790054 TGAATATGAC
* * * *
58790064 TGGGCCTAATGGGCCATATAAATTTTATTTGGGCCTAATGGGCTATATACAGGTGATT
1 TGGGCCTAATGGGCCATACAAATATGATTTGGGCCTAATGGGCTAGATACAGGTGATT
* *
58790122 TGGGCCTAATGGGCCATACGAATATGA-TTGGGCTTAATGGGCTAGATACAGGT
1 TGGGCCTAATGGGCCATACAAATATGATTTGGGCCTAATGGGCTAGATACAGGT
58790175 ATGTGAATTT
Statistics
Matches: 47, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
57 24 0.51
58 23 0.49
ACGTcount: A:0.26, C:0.14, G:0.29, T:0.31
Consensus pattern (58 bp):
TGGGCCTAATGGGCCATACAAATATGATTTGGGCCTAATGGGCTAGATACAGGTGATT
Found at i:58792833 original size:8 final size:8
Alignment explanation
Indices: 58792816--58792858 Score: 59
Period size: 8 Copynumber: 5.4 Consensus size: 8
58792806 GCAAAAGTCA
58792816 AAATGCCG
1 AAATGCCG
*
58792824 AAATGTCG
1 AAATGCCG
*
58792832 AAATACCG
1 AAATGCCG
58792840 AAATGCCG
1 AAATGCCG
*
58792848 AAATGTCG
1 AAATGCCG
58792856 AAA
1 AAA
58792859 AGTCAAAAGT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
8 30 1.00
ACGTcount: A:0.44, C:0.19, G:0.21, T:0.16
Consensus pattern (8 bp):
AAATGCCG
Found at i:58793133 original size:29 final size:29
Alignment explanation
Indices: 58793077--58793172 Score: 113
Period size: 29 Copynumber: 3.3 Consensus size: 29
58793067 GTGGGCATGA
* * *
58793077 ATATGAATGTGA-CTGGGCCTAACAGGCC
1 ATATAAATGTGATTTGGGCCTAATAGGCC
*
58793105 ATATAAATGTGATTTGGGCCTAATGGGCC
1 ATATAAATGTGATTTGGGCCTAATAGGCC
* * *
58793134 ATATACAGGTGATTTGGGCCTAATTGGCC
1 ATATAAATGTGATTTGGGCCTAATAGGCC
*
58793163 ATATACATGT
1 ATATAAATGT
58793173 AAGTGAATTT
Statistics
Matches: 59, Mismatches: 8, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
28 11 0.19
29 48 0.81
ACGTcount: A:0.28, C:0.17, G:0.26, T:0.29
Consensus pattern (29 bp):
ATATAAATGTGATTTGGGCCTAATAGGCC
Found at i:58794484 original size:28 final size:28
Alignment explanation
Indices: 58794438--58794502 Score: 87
Period size: 28 Copynumber: 2.3 Consensus size: 28
58794428 TCAGTGTATG
*
58794438 AAATATTGAGAATTGCACTTAATGTGCG
1 AAATATTGAGAATTGCACTTAATGTGCA
* *
58794466 AGATATTGAGAA-TGACACTTAGTGTGCA
1 AAATATTGAGAATTG-CACTTAATGTGCA
58794494 AAATATTGA
1 AAATATTGA
58794503 ATGATTAAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
27 2 0.06
28 30 0.94
ACGTcount: A:0.38, C:0.09, G:0.22, T:0.31
Consensus pattern (28 bp):
AAATATTGAGAATTGCACTTAATGTGCA
Found at i:58794621 original size:39 final size:39
Alignment explanation
Indices: 58794575--58794797 Score: 340
Period size: 39 Copynumber: 5.7 Consensus size: 39
58794565 GACTTTATAA
*
58794575 TGGTGTTATATCCGGGCTAAGTCCCGAAGGCATTCGTGT
1 TGGTGTTATATCCGGGCTAAGTCCCGAAGGCATTCGTGC
*
58794614 TGGTGTTATATCCGGGCTAAGTCCTGAAGGCATTCGTGC
1 TGGTGTTATATCCGGGCTAAGTCCCGAAGGCATTCGTGC
* *
58794653 TGGTGTTATATCCGGGCTAAGTCTCGAAGGCATTTGTGC
1 TGGTGTTATATCCGGGCTAAGTCCCGAAGGCATTCGTGC
*
58794692 TGGTGTTATATCCGGGCTAAGCCCCGAAGGCATTCGTGC
1 TGGTGTTATATCCGGGCTAAGTCCCGAAGGCATTCGTGC
* *
58794731 TGGTGTTATATCCGGGCTAAAGTCCCGCAGGC-TTTGTGC
1 TGGTGTTATATCCGGGCT-AAGTCCCGAAGGCATTCGTGC
*
58794770 TGGTATTATATCCGGGCTTAAAGTCCCG
1 TGGTGTTATATCCGGGC-T-AAGTCCCG
58794798 CATGCTTTGT
Statistics
Matches: 170, Mismatches: 12, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
39 149 0.88
40 21 0.12
ACGTcount: A:0.18, C:0.22, G:0.30, T:0.30
Consensus pattern (39 bp):
TGGTGTTATATCCGGGCTAAGTCCCGAAGGCATTCGTGC
Found at i:58797629 original size:36 final size:36
Alignment explanation
Indices: 58797582--58797656 Score: 150
Period size: 36 Copynumber: 2.1 Consensus size: 36
58797572 CAATCTTGAA
58797582 CTAATCTTAGAACTTAAGAGAACTCTAAGAAAATTT
1 CTAATCTTAGAACTTAAGAGAACTCTAAGAAAATTT
58797618 CTAATCTTAGAACTTAAGAGAACTCTAAGAAAATTT
1 CTAATCTTAGAACTTAAGAGAACTCTAAGAAAATTT
58797654 CTA
1 CTA
58797657 GGGTTGAGCC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.44, C:0.15, G:0.11, T:0.31
Consensus pattern (36 bp):
CTAATCTTAGAACTTAAGAGAACTCTAAGAAAATTT
Found at i:58799282 original size:43 final size:43
Alignment explanation
Indices: 58799198--58799284 Score: 111
Period size: 43 Copynumber: 2.0 Consensus size: 43
58799188 GTTACATGAA
* * * *
58799198 TCGCATCCATCATGAACTCAAACCACTCAACTAGCTTGGATGC
1 TCGCATCCATAATAAACTCAAACCACTCAACGAGCTCGGATGC
* * *
58799241 TCGCATCCATAATAAACTCAGACCTCTCAACGATCTCGGATGC
1 TCGCATCCATAATAAACTCAAACCACTCAACGAGCTCGGATGC
58799284 T
1 T
58799285 ACATACCTCA
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
43 37 1.00
ACGTcount: A:0.30, C:0.32, G:0.14, T:0.24
Consensus pattern (43 bp):
TCGCATCCATAATAAACTCAAACCACTCAACGAGCTCGGATGC
Found at i:58802996 original size:79 final size:81
Alignment explanation
Indices: 58802860--58803044 Score: 236
Period size: 79 Copynumber: 2.3 Consensus size: 81
58802850 TTGAATGATG
*
58802860 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
58802924 TGTGCGAGATACTA-A
66 TGTGCGAGATACTATA
* * * **
58802939 TTCCGGGCTAAG-CCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCA
1 -TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCA
*
58803001 TTTGTGCGAGTTACTATA
64 TTTGTGCGAGATACTATA
* *
58803019 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
58803045 AACGAGTAGC
Statistics
Matches: 92, Mismatches: 9, Indels: 8
0.84 0.08 0.07
Matches are distributed among these distances:
78 1 0.01
79 58 0.63
80 33 0.36
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
TGTGCGAGATACTATA
Found at i:58803058 original size:40 final size:40
Alignment explanation
Indices: 58802861--58803044 Score: 216
Period size: 40 Copynumber: 4.6 Consensus size: 40
58802851 TGAATGATGT
* * * *
58802861 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTATAA
* * *
58802901 CCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTA-ATT
1 CCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTATA-A
58802941 CCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTA-AA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
58802979 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 -CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
58803020 CCGGGCTATGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTG
58803045 AACGAGTAGC
Statistics
Matches: 126, Mismatches: 11, Indels: 14
0.83 0.07 0.09
Matches are distributed among these distances:
39 35 0.28
40 81 0.64
41 10 0.08
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
Found at i:58803066 original size:79 final size:79
Alignment explanation
Indices: 58802913--58803077 Score: 210
Period size: 79 Copynumber: 2.1 Consensus size: 79
58802903 GGACTAAGAT
* **
58802913 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAA
1 CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
*
58802978 ATCCGGGTTAAGTC
66 ATCCGGGTTAAATC
* *
58802992 CCGAAGGCATTTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGC
1 CCGAAGGCATTTGTGCGAGATACTAAT-ACCGGGCTAAG-CCCGAAGGCATTTGAACGAGTTA-C
* *
58803055 TATATCC-GGTTAAATT
63 TAAATCCGGGTTAAATC
58803071 CCGAAGG
1 CCGAAGG
58803078 TACGTGATTT
Statistics
Matches: 75, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
78 2 0.03
79 48 0.64
80 25 0.33
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.25
Consensus pattern (79 bp):
CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
ATCCGGGTTAAATC
Found at i:58810050 original size:79 final size:82
Alignment explanation
Indices: 58809910--58810094 Score: 229
Period size: 79 Copynumber: 2.3 Consensus size: 82
58809900 TTGAATGATG
*
58809910 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
*
58809974 TGTGCGAGATACTA-AT
66 TGTGCGAGATACTATAA
* * * * **
58809990 TCCGGGCTAAG-CCCGAAGGCATTTGTGC-GAGTTACTAAATTCGGGTTAAG-TCCCGAAGGCAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCAT
*
58810052 TTGTGCGAGTTACTATAA
65 TTGTGCGAGATACTATAA
*
58810070 T-CGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
58810095 AATGAGTAGC
Statistics
Matches: 91, Mismatches: 10, Indels: 8
0.83 0.09 0.07
Matches are distributed among these distances:
78 1 0.01
79 56 0.62
80 34 0.37
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (82 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
TGTGCGAGATACTATAA
Found at i:58810108 original size:40 final size:41
Alignment explanation
Indices: 58809912--58810094 Score: 211
Period size: 40 Copynumber: 4.6 Consensus size: 41
58809902 GAATGATGTC
* * * *
58809912 CGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCAT-ATC
1 CGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTATAATT
* *
58809952 CGGACTAAGAT-CCGAAGGCATTTGTGCGAGATAC--TAATT
1 CGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTATAATT
58809991 CCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTA-AATT
1 -CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAATT
*
58810031 CGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA-T
1 CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAATT
*
58810071 CGGGCTATGTCCCGAAGGCATTTG
1 CGGGCTAAGTCCCGAAGGCATTTG
58810095 AATGAGTAGC
Statistics
Matches: 124, Mismatches: 10, Indels: 18
0.82 0.07 0.12
Matches are distributed among these distances:
38 1 0.01
39 32 0.26
40 81 0.65
41 10 0.08
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (41 bp):
CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAATT
Found at i:58810116 original size:79 final size:79
Alignment explanation
Indices: 58809963--58810117 Score: 190
Period size: 79 Copynumber: 2.0 Consensus size: 79
58809953 GGACTAAGAT
* **
58809963 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAA
1 CCGAAGGCATTTGTGCGAGATACTAAATCCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
*
58810028 ATTCGGGTTAAGTC
66 ATTCCGGTTAAGTC
* * *
58810042 CCGAAGGCATTTGTGCGAGTTACTATAAT-CGGGCTATGTCCCGAAGGCATTTGAATGAG-TAGC
1 CCGAAGGCATTTGTGCGAGATACTA-AATCCGGGCTAAG-CCCGAAGGCATTTGAACGAGTTA-C
*
58810105 TATA-TCCGGTTAA
63 TAAATTCCGGTTAA
58810118 ATTTCGAAGG
Statistics
Matches: 65, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
79 42 0.65
80 23 0.35
ACGTcount: A:0.26, C:0.19, G:0.27, T:0.28
Consensus pattern (79 bp):
CCGAAGGCATTTGTGCGAGATACTAAATCCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
ATTCCGGTTAAGTC
Found at i:58812211 original size:18 final size:19
Alignment explanation
Indices: 58812180--58812215 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
58812170 AAATTTAGTG
*
58812180 AATTAATTGAATTATGGTA
1 AATTAAATGAATTATGGTA
58812199 AATTAAATG-ATTATGGT
1 AATTAAATGAATTATGGT
58812216 GCCAAGTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.42, C:0.00, G:0.17, T:0.42
Consensus pattern (19 bp):
AATTAAATGAATTATGGTA
Found at i:58812775 original size:66 final size:66
Alignment explanation
Indices: 58812647--58812775 Score: 172
Period size: 67 Copynumber: 1.9 Consensus size: 66
58812637 TACTATGTGT
* *
58812647 ACACCATGTAGACAAGAGAGATACTGGATATATGTAGCTAGGTCACATGCGTGGTTCCAAGTGAA
1 ACACCATGTAGACAAGAGAGATACTGGATAAATG-AGCTAGGTCACATGCGTGGTACCAAGTGAA
58812712 GG
65 GG
* * *
58812714 ACACCATGTAGACAAGAGAGCTAC-GAGATAAACTG-GCTAGGTCACATGGGTGGTACTAAGTG
1 ACACCATGTAGACAAGAGAGATACTG-GATAAA-TGAGCTAGGTCACATGCGTGGTACCAAGTG
58812776 TTCACCATGT
Statistics
Matches: 55, Mismatches: 5, Indels: 5
0.85 0.08 0.08
Matches are distributed among these distances:
66 25 0.45
67 28 0.51
68 2 0.04
ACGTcount: A:0.33, C:0.17, G:0.29, T:0.21
Consensus pattern (66 bp):
ACACCATGTAGACAAGAGAGATACTGGATAAATGAGCTAGGTCACATGCGTGGTACCAAGTGAAG
G
Found at i:58815037 original size:18 final size:18
Alignment explanation
Indices: 58814997--58815038 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
58814987 GCGGGTCCAT
* *
58814997 ACGCCCATGT-AGCTCAC
1 ACGCCCATGTGGGCCCAC
58815014 ACGCCCATGTGGGCCCAC
1 ACGCCCATGTGGGCCCAC
*
58815032 ATGCCCA
1 ACGCCCA
58815039 ACCTGGCCTG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
17 10 0.48
18 11 0.52
ACGTcount: A:0.21, C:0.43, G:0.21, T:0.14
Consensus pattern (18 bp):
ACGCCCATGTGGGCCCAC
Found at i:58816709 original size:18 final size:17
Alignment explanation
Indices: 58816676--58816709 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
58816666 TTAATTATTG
*
58816676 TGTATGAAAAATTGATT
1 TGTATCAAAAATTGATT
58816693 TGTATCAAAAATATGAT
1 TGTATCAAAAAT-TGAT
58816710 CAGTACTAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.44, C:0.03, G:0.15, T:0.38
Consensus pattern (17 bp):
TGTATCAAAAATTGATT
Found at i:58834361 original size:29 final size:29
Alignment explanation
Indices: 58834287--58834418 Score: 171
Period size: 29 Copynumber: 4.7 Consensus size: 29
58834277 CCCTTACAAA
* *
58834287 GCCC-AAT-ACATGCATATGGCCCACTAG
1 GCCCAAATCACATTCATATGGCCCATTAG
*
58834314 GCCC-AATCTCATTCATATGGCCCATTAG
1 GCCCAAATCACATTCATATGGCCCATTAG
** * *
58834342 GCTTAAATCACATTCGTATGACCCATTAG
1 GCCCAAATCACATTCATATGGCCCATTAG
*
58834371 GCCCAAATCACATTCATATGGACCATTAG
1 GCCCAAATCACATTCATATGGCCCATTAG
58834400 GCCCAAATCACATTCATAT
1 GCCCAAATCACATTCATAT
58834419 TCATGCTTTC
Statistics
Matches: 90, Mismatches: 13, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
27 7 0.08
28 19 0.21
29 64 0.71
ACGTcount: A:0.31, C:0.30, G:0.14, T:0.26
Consensus pattern (29 bp):
GCCCAAATCACATTCATATGGCCCATTAG
Found at i:58834498 original size:17 final size:18
Alignment explanation
Indices: 58834476--58834509 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
58834466 TGCCTATTAT
58834476 GGGCCCA-ATAGCCCATC
1 GGGCCCATATAGCCCATC
*
58834493 GGGCCCATTTAGCCCAT
1 GGGCCCATATAGCCCAT
58834510 TCTAGCCCGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.21, C:0.38, G:0.24, T:0.18
Consensus pattern (18 bp):
GGGCCCATATAGCCCATC
Found at i:58839270 original size:28 final size:28
Alignment explanation
Indices: 58839174--58839274 Score: 123
Period size: 27 Copynumber: 3.6 Consensus size: 28
58839164 ATACAGAAAA
* * *
58839174 TGTGACAGAGTCACCAGATACAGATATTT
1 TGTGGCAGAGCCACCAGA-ACAGATAATT
* *
58839203 TGTGGCAGTGCCACCAGAACAGAT-ATA
1 TGTGGCAGAGCCACCAGAACAGATAATT
*
58839230 TGTGGCAGGGCCACCAGAACAGATAATT
1 TGTGGCAGAGCCACCAGAACAGATAATT
*
58839258 TGTGGCACAGCCACCAG
1 TGTGGCAGAGCCACCAG
58839275 GACTCTTCCT
Statistics
Matches: 62, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
27 24 0.39
28 23 0.37
29 15 0.24
ACGTcount: A:0.32, C:0.23, G:0.26, T:0.20
Consensus pattern (28 bp):
TGTGGCAGAGCCACCAGAACAGATAATT
Found at i:58847045 original size:27 final size:27
Alignment explanation
Indices: 58846977--58847077 Score: 103
Period size: 28 Copynumber: 3.6 Consensus size: 27
58846967 ATACAGAAAA
* *
58846977 TGTGACAGAGTCACCAGATACAGATATTT
1 TGTGGCAGAGCCACCAGA-ACAGATA-TT
* * * *
58847006 TGTGGTAGTGCCACCAGAATAGATATA
1 TGTGGCAGAGCCACCAGAACAGATATT
*
58847033 TGTGGCAGGGCCACCAGAACAGATAATT
1 TGTGGCAGAGCCACCAGAACAGAT-ATT
*
58847061 TGTGGCATAGCCACCAG
1 TGTGGCAGAGCCACCAG
58847078 GACGCTTCCT
Statistics
Matches: 59, Mismatches: 12, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
27 22 0.37
28 23 0.39
29 14 0.24
ACGTcount: A:0.32, C:0.20, G:0.26, T:0.23
Consensus pattern (27 bp):
TGTGGCAGAGCCACCAGAACAGATATT
Found at i:58847073 original size:28 final size:27
Alignment explanation
Indices: 58846988--58847077 Score: 92
Period size: 27 Copynumber: 3.2 Consensus size: 27
58846978 GTGACAGAGT
* *
58846988 CACCAGATACAGATATTTTGTGGTAGTGC
1 CACCAGA-ACAGATAATTTGTGGCA-TGC
* * *
58847017 CACCAGAATAGAT-ATATGTGGCAGGGC
1 CACCAGAACAGATAATTTGTGGCA-TGC
58847044 CACCAGAACAGATAATTTGTGGCATAGC
1 CACCAGAACAGATAATTTGTGGCAT-GC
58847072 CACCAG
1 CACCAG
58847078 GACGCTTCCT
Statistics
Matches: 51, Mismatches: 8, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
27 22 0.43
28 22 0.43
29 7 0.14
ACGTcount: A:0.32, C:0.21, G:0.24, T:0.22
Consensus pattern (27 bp):
CACCAGAACAGATAATTTGTGGCATGC
Found at i:58848535 original size:8 final size:8
Alignment explanation
Indices: 58848508--58848538 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
58848498 CCAAAATACT
58848508 GGCTTTTC
1 GGCTTTTC
*
58848516 GGCATTTC
1 GGCTTTTC
58848524 GGCTTTTC
1 GGCTTTTC
58848532 GGCTTTT
1 GGCTTTT
58848539 GCCGATCTAG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.03, C:0.23, G:0.26, T:0.48
Consensus pattern (8 bp):
GGCTTTTC
Found at i:58851612 original size:40 final size:40
Alignment explanation
Indices: 58851551--58851797 Score: 327
Period size: 40 Copynumber: 6.2 Consensus size: 40
58851541 CGGAAATTAG
* * * *
58851551 CCGGATATAACCACAAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATAAAATCACTAGCACAAATGCCTTCGGGTCTTAAC
* * * * *
58851591 CCGGGT-ATAGCAACTCGCACAAATGCCTTCGGGTCTTAGC
1 CCGGATAAAATC-ACTAGCACAAATGCCTTCGGGTCTTAAC
* * *
58851631 CCGGAT-ATATCAACTCGCACAAATGCCTTCGGGTCTTAGC
1 CCGGATAAAATC-ACTAGCACAAATGCCTTCGGGTCTTAAC
58851671 CCGGATAAAATCACTAGCACAAATGCCTTCGGGTCTTAAC
1 CCGGATAAAATCACTAGCACAAATGCCTTCGGGTCTTAAC
*
58851711 CCGGATAAAATCACTAGCATAAATGCCTTCGGGTCTTAAC
1 CCGGATAAAATCACTAGCACAAATGCCTTCGGGTCTTAAC
* *
58851751 CCGGATAAAATCACTAGCACAAATGCCTTCGGGACTTAGC
1 CCGGATAAAATCACTAGCACAAATGCCTTCGGGTCTTAAC
58851791 CCGGATA
1 CCGGATA
58851798 TCATTCAAAT
Statistics
Matches: 188, Mismatches: 17, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
39 2 0.01
40 182 0.97
41 4 0.02
ACGTcount: A:0.29, C:0.28, G:0.20, T:0.23
Consensus pattern (40 bp):
CCGGATAAAATCACTAGCACAAATGCCTTCGGGTCTTAAC
Found at i:58858944 original size:79 final size:80
Alignment explanation
Indices: 58858813--58858960 Score: 237
Period size: 79 Copynumber: 1.9 Consensus size: 80
58858803 TATTCGGATG
* *
58858813 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTAATTCCGGGCTAAG-CCCGAAGGCA
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACTAATACCGGGCTAAGTCCCGAAGGCA
58858877 TTTGTGCGAGTTACT
66 TTTGTGCGAGTTACT
* *
58858892 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT-ATAACCGGGCTAAGTCCCGATGGC
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACTAAT-ACCGGGCTAAGTCCCGAAGGC
58858956 ATTTG
65 ATTTG
58858961 AGCAAGTAGC
Statistics
Matches: 63, Mismatches: 4, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
78 2 0.03
79 48 0.76
80 13 0.21
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (80 bp):
ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACTAATACCGGGCTAAGTCCCGAAGGCA
TTTGTGCGAGTTACT
Found at i:58858974 original size:40 final size:40
Alignment explanation
Indices: 58858813--58858960 Score: 237
Period size: 40 Copynumber: 3.7 Consensus size: 40
58858803 TATTCGGATG
* *
58858813 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
*
58858853 A-ATTCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACT
1 ATA-ACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
58858892 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
*
58858932 ATAACCGGGCTAAGTCCCGATGGCATTTG
1 ATAACCGGGCTAAGTCCCGAAGGCATTTG
58858961 AGCAAGTAGC
Statistics
Matches: 100, Mismatches: 5, Indels: 6
0.90 0.05 0.05
Matches are distributed among these distances:
39 35 0.35
40 65 0.65
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (40 bp):
ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
Found at i:58858982 original size:79 final size:79
Alignment explanation
Indices: 58858813--58858983 Score: 231
Period size: 79 Copynumber: 2.2 Consensus size: 79
58858803 TATTCGGATG
* *
58858813 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTAATTCCGGGCTAAGCCCGAAGGCAT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACTAATACCGGGCTAAGCCCGAAGGCAT
* *
58858878 TTGTGCGAGTTACT
66 TTGAGCAAGTTACT
* *
58858892 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT-ATAACCGGGCTAAGTCCCGATGGC
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACTAAT-ACCGGGCTAAG-CCCGAAGGC
58858956 ATTTGAGCAAG-TAGCT
64 ATTTGAGCAAGTTA-CT
*
58858972 ATATCC-GGCTAA
1 ATAACCGGGCTAA
58858984 AATTCGAAGG
Statistics
Matches: 82, Mismatches: 7, Indels: 6
0.86 0.07 0.06
Matches are distributed among these distances:
78 2 0.02
79 56 0.68
80 24 0.29
ACGTcount: A:0.26, C:0.23, G:0.27, T:0.25
Consensus pattern (79 bp):
ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACTAATACCGGGCTAAGCCCGAAGGCAT
TTGAGCAAGTTACT
Found at i:58863181 original size:46 final size:45
Alignment explanation
Indices: 58862999--58863196 Score: 197
Period size: 46 Copynumber: 4.3 Consensus size: 45
58862989 CACTTATGTG
* * *
58862999 AGCTAGTGTAAGACATGTCTGGGACATGCATCGGCCAC-ATTATGA
1 AGCTAGTGTAAGACATGTCTAGGACATGCATCGGCTACGA-GATGA
* * * * *
58863044 GAGCCAGTGTAAGACCATGTTTGGGACATGGCATCGGC-ATTGAGACGA
1 -AGCTAGTGTAAGA-CATGTCTAGGACAT-GCATCGGCTA-CGAGATGA
* *
58863092 GAGCTAATGTAAGACATGTCTAGGACATGTATCGGCCTA-GAGATGTA
1 -AGCTAGTGTAAGACATGTCTAGGACATGCATCGG-CTACGAGATG-A
58863139 AGCTAGTGTAAGACATGTCTAGGACATGCATCGGCTACGAGATG-
1 AGCTAGTGTAAGACATGTCTAGGACATGCATCGGCTACGAGATGA
*
58863183 AGCCAGTGTAAGAC
1 AGCTAGTGTAAGAC
58863197 TGTAACACCC
Statistics
Matches: 130, Mismatches: 14, Indels: 18
0.80 0.09 0.11
Matches are distributed among these distances:
44 13 0.10
45 3 0.02
46 61 0.47
47 28 0.22
48 24 0.18
49 1 0.01
ACGTcount: A:0.30, C:0.18, G:0.29, T:0.23
Consensus pattern (45 bp):
AGCTAGTGTAAGACATGTCTAGGACATGCATCGGCTACGAGATGA
Found at i:58865110 original size:29 final size:30
Alignment explanation
Indices: 58865053--58865120 Score: 75
Period size: 30 Copynumber: 2.3 Consensus size: 30
58865043 CACCCTTAAA
* * * *
58865053 ATATTTGCACTATTAGTCCTTCAACTTTTC
1 ATATTTACACTATTAATCCCTCAAATTTTC
*
58865083 ATATTTACACT-TTAATCCCTCAAATTTTG
1 ATATTTACACTATTAATCCCTCAAATTTTC
58865112 AGTATTTAC
1 A-TATTTAC
58865121 TCTTGGGCCA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
29 15 0.47
30 17 0.53
ACGTcount: A:0.28, C:0.21, G:0.06, T:0.46
Consensus pattern (30 bp):
ATATTTACACTATTAATCCCTCAAATTTTC
Found at i:58869479 original size:30 final size:29
Alignment explanation
Indices: 58869445--58869512 Score: 75
Period size: 30 Copynumber: 2.3 Consensus size: 29
58869435 CACCCTTAAA
* *
58869445 ATATTTTCACTATTAGT-CCTTAAAATTTTC
1 ATATTTACACT-TTAATCCCTT-AAATTTTC
*
58869475 ATATTTACACTTTAATCCCTTAAATTTTG
1 ATATTTACACTTTAATCCCTTAAATTTTC
58869504 AGTATTTAC
1 A-TATTTAC
58869513 TCTTGGGCCA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
29 12 0.36
30 21 0.64
ACGTcount: A:0.31, C:0.16, G:0.04, T:0.49
Consensus pattern (29 bp):
ATATTTACACTTTAATCCCTTAAATTTTC
Found at i:58872957 original size:40 final size:40
Alignment explanation
Indices: 58872899--58873043 Score: 263
Period size: 40 Copynumber: 3.6 Consensus size: 40
58872889 CAGATGATAA
*
58872899 CCGGGCTAAGTCCTGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
*
58872939 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTACAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
*
58872979 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
58873019 CCGGGCTAAGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTG
58873044 AGCAAGTAGT
Statistics
Matches: 101, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
40 101 1.00
ACGTcount: A:0.23, C:0.23, G:0.28, T:0.26
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
Found at i:58873343 original size:22 final size:21
Alignment explanation
Indices: 58873302--58873346 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 21
58873292 GAATGTGCAT
58873302 ATATGAAGTTATCCATTTAGCC
1 ATATGAAGTTATCCA-TTAGCC
58873324 ATATGAATGTTATACC-TTAGCC
1 ATATGAA-GTTAT-CCATTAGCC
58873346 A
1 A
58873347 AAACTAATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
22 14 0.67
23 5 0.24
24 2 0.10
ACGTcount: A:0.33, C:0.18, G:0.13, T:0.36
Consensus pattern (21 bp):
ATATGAAGTTATCCATTAGCC
Found at i:58897241 original size:20 final size:20
Alignment explanation
Indices: 58897216--58897268 Score: 97
Period size: 20 Copynumber: 2.6 Consensus size: 20
58897206 GAGACAATGC
58897216 ACACGCCCGTGTGCTTTTGG
1 ACACGCCCGTGTGCTTTTGG
58897236 ACACGCCCGTGTGCTTTTGG
1 ACACGCCCGTGTGCTTTTGG
*
58897256 ACACGCCTGTGTG
1 ACACGCCCGTGTG
58897269 ATCGCCCATG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.11, C:0.30, G:0.30, T:0.28
Consensus pattern (20 bp):
ACACGCCCGTGTGCTTTTGG
Found at i:58898303 original size:99 final size:99
Alignment explanation
Indices: 58898132--58898328 Score: 340
Period size: 99 Copynumber: 2.0 Consensus size: 99
58898122 GAGGGGTAAG
*
58898132 CATTTACATGCTTAGTAAGCCTGAATAACTGGAAAGTAAACTTACCGATTAATTAGCATGCATCC
1 CATTTACATGCTTAGTAAGCCTGAATAACTAGAAAGTAAACTTACCGATTAATTAGCATGCATCC
* *
58898197 ATATTAGGTAATAAAACCAAAAAGCATGAAATAT
66 ATATTAGGCAACAAAACCAAAAAGCATGAAATAT
*
58898231 CATTTACATGCTTAGTAAGCCTGAATAACTAGAAAGTAAACTTACCGATTAATTAGCATGCGTCC
1 CATTTACATGCTTAGTAAGCCTGAATAACTAGAAAGTAAACTTACCGATTAATTAGCATGCATCC
* *
58898296 ATTTTAGGCAACAAAACCAACAAGCATGAAATA
66 ATATTAGGCAACAAAACCAAAAAGCATGAAATA
58898329 GTTTCCCTAT
Statistics
Matches: 92, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
99 92 1.00
ACGTcount: A:0.42, C:0.18, G:0.14, T:0.26
Consensus pattern (99 bp):
CATTTACATGCTTAGTAAGCCTGAATAACTAGAAAGTAAACTTACCGATTAATTAGCATGCATCC
ATATTAGGCAACAAAACCAAAAAGCATGAAATAT
Found at i:58903376 original size:26 final size:26
Alignment explanation
Indices: 58903319--58903387 Score: 93
Period size: 26 Copynumber: 2.6 Consensus size: 26
58903309 AAATTGTACA
** * *
58903319 GCACTAAGTGTGCGATTCGATTATGTT
1 GCACTAAGTGTGCGA-AAGAATATGAT
58903346 GCACTAAGTGTGCGAAAGAATATGAT
1 GCACTAAGTGTGCGAAAGAATATGAT
58903372 GCACTAAGTGTGCGAA
1 GCACTAAGTGTGCGAA
58903388 TTGACCATGC
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
26 23 0.61
27 15 0.39
ACGTcount: A:0.30, C:0.14, G:0.28, T:0.28
Consensus pattern (26 bp):
GCACTAAGTGTGCGAAAGAATATGAT
Found at i:58903378 original size:53 final size:54
Alignment explanation
Indices: 58903318--58903469 Score: 166
Period size: 56 Copynumber: 2.8 Consensus size: 54
58903308 TAAATTGTAC
*
58903318 AGCACTAAGTGTGCGATTCGATTATGTTGCACTAAGTGTGCGAA-AGAA-TATG-
1 AGCACTAAGTGTGCGATT-GATTATGTGGCACTAAGTGTGCGAATAGAACTATGT
** * **
58903370 ATGCACTAAGTGTGCGAATTGACCATGCGGCACTAAGTGGTGCGAATCTAACTATGT
1 A-GCACTAAGTGTGCG-ATTGATTATGTGGCACTAAGT-GTGCGAATAGAACTATGT
* *
58903427 AGCACTAAGGGTGCGATTTGATTACGTGGCACTAAGTGTGCGA
1 AGCACTAAGTGTGCGA-TTGATTATGTGGCACTAAGTGTGCGA
58903470 GTTGAGTGAA
Statistics
Matches: 82, Mismatches: 11, Indels: 11
0.79 0.11 0.11
Matches are distributed among these distances:
52 1 0.01
53 28 0.34
54 10 0.12
55 9 0.11
56 33 0.40
57 1 0.01
ACGTcount: A:0.28, C:0.16, G:0.28, T:0.27
Consensus pattern (54 bp):
AGCACTAAGTGTGCGATTGATTATGTGGCACTAAGTGTGCGAATAGAACTATGT
Found at i:58903439 original size:28 final size:27
Alignment explanation
Indices: 58903372--58903442 Score: 79
Period size: 28 Copynumber: 2.6 Consensus size: 27
58903362 AGAATATGAT
* * *
58903372 GCACTAAGTGTGCGAATTGACCATGCG
1 GCACTAAGGGTGCGAATTAACCATGCA
* *
58903399 GCACTAAGTGGTGCGAATCTAACTATGTA
1 GCACTAAG-GGTGCGAAT-TAACCATGCA
58903428 GCACTAAGGGTGCGA
1 GCACTAAGGGTGCGA
58903443 TTTGATTACG
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
27 8 0.22
28 15 0.41
29 14 0.38
ACGTcount: A:0.28, C:0.20, G:0.30, T:0.23
Consensus pattern (27 bp):
GCACTAAGGGTGCGAATTAACCATGCA
Found at i:58903474 original size:27 final size:26
Alignment explanation
Indices: 58903319--58903474 Score: 125
Period size: 27 Copynumber: 5.7 Consensus size: 26
58903309 AAATTGTACA
* *
58903319 GCACTAAGTGTGCGATTCGATTATGTT
1 GCACTAAGTGTGCGATT-GACTATGTG
** *
58903346 GCACTAAGTGTGCGAAAGAATATGAT-
1 GCACTAAGTGTGCGATTGACTATG-TG
* *
58903372 GCACTAAGTGTGCGAATTGACCATGCG
1 GCACTAAGTGTGCG-ATTGACTATGTG
* *
58903399 GCACTAAGTGGTGCGAATCTAACTATGTA
1 GCACTAAGT-GTGCG-AT-TGACTATGTG
* * *
58903428 GCACTAAGGGTGCGATTTGATTACGTG
1 GCACTAAGTGTGCGA-TTGACTATGTG
58903455 GCACTAAGTGTGCGAGTTGA
1 GCACTAAGTGTGCGA-TTGA
58903475 GTGAATAGCA
Statistics
Matches: 104, Mismatches: 19, Indels: 12
0.77 0.14 0.09
Matches are distributed among these distances:
26 20 0.19
27 56 0.54
28 14 0.13
29 14 0.13
ACGTcount: A:0.28, C:0.16, G:0.29, T:0.28
Consensus pattern (26 bp):
GCACTAAGTGTGCGATTGACTATGTG
Found at i:58908349 original size:28 final size:27
Alignment explanation
Indices: 58908282--58908351 Score: 86
Period size: 28 Copynumber: 2.6 Consensus size: 27
58908272 AGAATATGAT
* *
58908282 GCACTAAGTGTGCGAATTGACCATGCG
1 GCACTAAGTGTGCGAATTAACCATGCA
* *
58908309 GCACTAAGTGTGCGAATCTAACTATGTA
1 GCACTAAGTGTGCGAAT-TAACCATGCA
*
58908337 GCACTAAGGGTGCGA
1 GCACTAAGTGTGCGA
58908352 TTTGATTACG
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
27 17 0.46
28 20 0.54
ACGTcount: A:0.29, C:0.20, G:0.29, T:0.23
Consensus pattern (27 bp):
GCACTAAGTGTGCGAATTAACCATGCA
Found at i:58908367 original size:55 final size:53
Alignment explanation
Indices: 58908227--58908378 Score: 178
Period size: 55 Copynumber: 2.8 Consensus size: 53
58908217 TAAATTGTAC
* *
58908227 AGCACTAAGTGTGCGATTCGATTATGTTGCACTAAGTGTGCGAAAAGAATATG
1 AGCACTAAGTGTGCGATTTGATTATGTGGCACTAAGTGTGCGAAAAGAATATG
* ** * ***
58908280 ATGCACTAAGTGTGCGAATTGACCATGCGGCACTAAGTGTGCGAATCTAACTATG
1 A-GCACTAAGTGTGCGATTTGATTATGTGGCACTAAGTGTGCGAAAAGAA-TATG
* *
58908335 TAGCACTAAGGGTGCGATTTGATTACGTGGCACTAAGTGTGCGA
1 -AGCACTAAGTGTGCGATTTGATTATGTGGCACTAAGTGTGCGA
58908379 GTTGAGTGAA
Statistics
Matches: 81, Mismatches: 15, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
53 1 0.01
54 39 0.48
55 40 0.49
56 1 0.01
ACGTcount: A:0.29, C:0.16, G:0.28, T:0.27
Consensus pattern (53 bp):
AGCACTAAGTGTGCGATTTGATTATGTGGCACTAAGTGTGCGAAAAGAATATG
Found at i:58908383 original size:27 final size:27
Alignment explanation
Indices: 58908228--58908383 Score: 145
Period size: 27 Copynumber: 5.7 Consensus size: 27
58908218 AAATTGTACA
* *
58908228 GCACTAAGTGTGCG-ATTCGATTATGTT
1 GCACTAAGTGTGCGAATT-GACTATGTG
** *
58908255 GCACTAAGTGTGCGAAAAGAATATGAT-
1 GCACTAAGTGTGCGAATTGACTATG-TG
* *
58908282 GCACTAAGTGTGCGAATTGACCATGCG
1 GCACTAAGTGTGCGAATTGACTATGTG
* *
58908309 GCACTAAGTGTGCGAATCTAACTATGTA
1 GCACTAAGTGTGCGAAT-TGACTATGTG
* * * *
58908337 GCACTAAGGGTGCGATTTGATTACGTG
1 GCACTAAGTGTGCGAATTGACTATGTG
*
58908364 GCACTAAGTGTGCGAGTTGA
1 GCACTAAGTGTGCGAATTGA
58908384 GTGAATAGCA
Statistics
Matches: 105, Mismatches: 20, Indels: 8
0.79 0.15 0.06
Matches are distributed among these distances:
27 82 0.78
28 23 0.22
ACGTcount: A:0.28, C:0.16, G:0.28, T:0.28
Consensus pattern (27 bp):
GCACTAAGTGTGCGAATTGACTATGTG
Found at i:58916284 original size:9 final size:9
Alignment explanation
Indices: 58916270--58916294 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
58916260 TAGTTGTGGT
58916270 TTTGGTTGA
1 TTTGGTTGA
58916279 TTTGGTTGA
1 TTTGGTTGA
58916288 TTTGGTT
1 TTTGGTT
58916295 TTGATATATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.08, C:0.00, G:0.32, T:0.60
Consensus pattern (9 bp):
TTTGGTTGA
Found at i:58917776 original size:14 final size:15
Alignment explanation
Indices: 58917747--58917790 Score: 54
Period size: 14 Copynumber: 2.9 Consensus size: 15
58917737 GTTATAATTA
58917747 TATGAGCATATGAGT
1 TATGAGCATATGAGT
*
58917762 TATGA-CATTTGAGT
1 TATGAGCATATGAGT
58917776 TATGATGCTATATGA
1 TATGA-GC-ATATGA
58917791 AAATTTCAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
14 13 0.54
15 5 0.21
16 1 0.04
17 5 0.21
ACGTcount: A:0.32, C:0.07, G:0.23, T:0.39
Consensus pattern (15 bp):
TATGAGCATATGAGT
Found at i:58922014 original size:43 final size:41
Alignment explanation
Indices: 58921883--58922037 Score: 125
Period size: 43 Copynumber: 3.6 Consensus size: 41
58921873 TGTTCTTGTA
* * * *
58921883 TAAGACCATGTCTGAGACATTGGCACCGATATGTGATT-TTGAG
1 TAAGACCATGTCTGGGACAGTGGCATCGA-ATGTGATTCAT--G
* * * * *
58921926 TAAGACCATGTCTGGGACATTGACGTTGTAATTGTGATTCGTG
1 TAAGACCATGTCTGGGACAGTGGCATCG-AA-TGTGATTCATG
*
58921969 TAAGACCCTGTCTGGGACAGTGGCATCGACATGTGATTACATG
1 TAAGACCATGTCTGGGACAGTGGCATCGA-ATGTGATT-CATG
*
58922012 TAAGACCACGTCTGGGAC-GTTGGCAT
1 TAAGACCATGTCTGGGACAG-TGGCAT
58922038 TGTACGATAT
Statistics
Matches: 92, Mismatches: 14, Indels: 12
0.78 0.12 0.10
Matches are distributed among these distances:
42 9 0.10
43 74 0.80
44 8 0.09
45 1 0.01
ACGTcount: A:0.25, C:0.18, G:0.28, T:0.29
Consensus pattern (41 bp):
TAAGACCATGTCTGGGACAGTGGCATCGAATGTGATTCATG
Found at i:58922041 original size:86 final size:86
Alignment explanation
Indices: 58921883--58922041 Score: 203
Period size: 86 Copynumber: 1.8 Consensus size: 86
58921873 TGTTCTTGTA
* * ** *
58921883 TAAGACCATGTCTGAGACATTGGCACCGATATGTGATTTTGAGTAAGACCATGTCTGGGACATTG
1 TAAGACCATGTCTGAGACAGTGGCACCGACATGTGATTTACAGTAAGACCACGTCTGGGACATTG
*
58921948 ACGTTGTAATTGTGATTCGTG
66 ACATTGTAATTGTGATTCGTG
* * * *
58921969 TAAGACCCTGTCTGGGACAGTGGCATCGACATGTGA-TTACATGTAAGACCACGTCTGGGACGTT
1 TAAGACCATGTCTGAGACAGTGGCACCGACATGTGATTTACA-GTAAGACCACGTCTGGGACATT
*
58922033 GGCATTGTA
65 GACATTGTA
58922042 CGATATGTGT
Statistics
Matches: 61, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
85 3 0.05
86 58 0.95
ACGTcount: A:0.25, C:0.18, G:0.28, T:0.30
Consensus pattern (86 bp):
TAAGACCATGTCTGAGACAGTGGCACCGACATGTGATTTACAGTAAGACCACGTCTGGGACATTG
ACATTGTAATTGTGATTCGTG
Found at i:58928467 original size:9 final size:9
Alignment explanation
Indices: 58928453--58928502 Score: 50
Period size: 9 Copynumber: 5.6 Consensus size: 9
58928443 TTAAAAATAT
58928453 ATTTTTATA
1 ATTTTTATA
58928462 ATTTTTA-A
1 ATTTTTATA
*
58928470 ATTTTTTTAA
1 ATTTTTAT-A
58928480 ATTTTT-TGA
1 ATTTTTAT-A
*
58928489 ATTTTTAAA
1 ATTTTTATA
58928498 ATTTT
1 ATTTT
58928503 AAAAAATTAA
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
8 7 0.20
9 21 0.60
10 7 0.20
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (9 bp):
ATTTTTATA
Found at i:58928472 original size:8 final size:8
Alignment explanation
Indices: 58928453--58928505 Score: 52
Period size: 8 Copynumber: 6.1 Consensus size: 8
58928443 TTAAAAATAT
58928453 ATTTTTATA
1 ATTTTTA-A
58928462 ATTTTTAA
1 ATTTTTAA
58928470 ATTTTTTTAA
1 A--TTTTTAA
*
58928480 ATTTTTTGA
1 A-TTTTTAA
58928489 ATTTTTAA
1 ATTTTTAA
*
58928497 AATTTTAA
1 ATTTTTAA
58928505 A
1 A
58928506 AAATTAATTA
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
8 16 0.41
9 15 0.38
10 8 0.21
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (8 bp):
ATTTTTAA
Found at i:58928493 original size:18 final size:19
Alignment explanation
Indices: 58928454--58928494 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
58928444 TAAAAATATA
58928454 TTTTTATAA-TTTTTAAATT
1 TTTTTA-AATTTTTTAAATT
*
58928473 TTTTTAAATTTTTTGAATT
1 TTTTTAAATTTTTTAAATT
58928492 TTT
1 TTT
58928495 AAAATTTTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 2 0.10
19 18 0.90
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.71
Consensus pattern (19 bp):
TTTTTAAATTTTTTAAATT
Found at i:58928499 original size:18 final size:18
Alignment explanation
Indices: 58928453--58928502 Score: 57
Period size: 18 Copynumber: 2.8 Consensus size: 18
58928443 TTAAAAATAT
*
58928453 ATTTTTATAA-TTTTTAA
1 ATTTTTAAAATTTTTTAA
* *
58928470 ATTTTTTTAAATTTTTTGA
1 A-TTTTTAAAATTTTTTAA
58928489 ATTTTTAAAATTTT
1 ATTTTTAAAATTTT
58928503 AAAAAATTAA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
17 1 0.04
18 19 0.70
19 7 0.26
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (18 bp):
ATTTTTAAAATTTTTTAA
Found at i:58942956 original size:37 final size:37
Alignment explanation
Indices: 58942906--58943021 Score: 196
Period size: 37 Copynumber: 3.1 Consensus size: 37
58942896 TTATTACGAA
58942906 GTCTTACCCGGACATAATCTCCACACGAAGTTATCGG
1 GTCTTACCCGGACATAATCTCCACACGAAGTTATCGG
58942943 GTCTTACCCGGACATAATCTCCACACGAAGTTATCGG
1 GTCTTACCCGGACATAATCTCCACACGAAGTTATCGG
* * * *
58942980 GTCTTACCCGGACAAAATCCCCACACGTAGTCATCGG
1 GTCTTACCCGGACATAATCTCCACACGAAGTTATCGG
58943017 GTCTT
1 GTCTT
58943022 TAGAGCTCGG
Statistics
Matches: 75, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 75 1.00
ACGTcount: A:0.26, C:0.31, G:0.19, T:0.24
Consensus pattern (37 bp):
GTCTTACCCGGACATAATCTCCACACGAAGTTATCGG
Found at i:58943214 original size:49 final size:49
Alignment explanation
Indices: 58943140--58943574 Score: 701
Period size: 47 Copynumber: 9.1 Consensus size: 49
58943130 CCCTTCGGGA
* * * * *
58943140 CTTATCACAT-T-TATACACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * *
58943187 CCTGTCACATATATATACACTTCCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
58943236 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
58943283 CCTATCACATATATATACACTTTCACATTCATCGCATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
58943332 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
58943379 CCTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
58943428 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
58943475 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
58943524 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
58943571 CTTA
1 CTTA
58943575 CTATCATTTC
Statistics
Matches: 363, Mismatches: 17, Indels: 16
0.92 0.04 0.04
Matches are distributed among these distances:
47 188 0.52
48 1 0.00
49 174 0.48
ACGTcount: A:0.29, C:0.31, G:0.09, T:0.31
Consensus pattern (49 bp):
CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:58943574 original size:96 final size:96
Alignment explanation
Indices: 58943140--58943571 Score: 774
Period size: 96 Copynumber: 4.5 Consensus size: 96
58943130 CCCTTCGGGA
* * * * * * *
58943140 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGCCCTGTCACATATATATAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCCTATCACATATATATAC
*
58943205 ACTTCCACATTCATCACATCGGCCATTAGGC
66 ACTTTCACATTCATCACATCGGCCATTAGGC
58943236 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCCTATCACATATATATAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCCTATCACATATATATAC
*
58943301 ACTTTCACATTCATCGCATCGGCCATTAGGC
66 ACTTTCACATTCATCACATCGGCCATTAGGC
58943332 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCCTATCACATATATATAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCCTATCACATATATATAC
58943397 ACTTTCACATTCATCACATCGGCCATTAGGC
66 ACTTTCACATTCATCACATCGGCCATTAGGC
*
58943428 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCCTATCACATATATATAC
58943493 ACTTTCACATTCATCACATCGGCCATTAGGC
66 ACTTTCACATTCATCACATCGGCCATTAGGC
58943524 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCC
58943572 TTACTATCAT
Statistics
Matches: 325, Mismatches: 11, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
96 325 1.00
ACGTcount: A:0.29, C:0.31, G:0.09, T:0.31
Consensus pattern (96 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCCTATCACATATATATAC
ACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:58946517 original size:45 final size:45
Alignment explanation
Indices: 58946452--58946618 Score: 189
Period size: 45 Copynumber: 3.6 Consensus size: 45
58946442 CATATTTTTA
*
58946452 CCGATGCCATGTCCCAGACATGGTCTTACACTGACACATCTCGTA-G
1 CCGATGCCATGTCCCAGACAT-GTCTTACACTGACACGTCTCG-AGG
*
58946498 CCGATG-CATGTCCCAGACATGT-TTACACTAACTTACGTCTCGAGG
1 CCGATGCCATGTCCCAGACATGTCTTACACTGAC--ACGTCTCGAGG
* * *
58946543 CCGATG-CATGTCCCAGACATGTCTTACACTAGCACTCGTCTCAATG
1 CCGATGCCATGTCCCAGACATGTCTTACACT-G-ACACGTCTCGAGG
*
58946589 CCGATGCCATTTCCCAGACATGGTCTTACA
1 CCGATGCCATGTCCCAGACAT-GTCTTACA
58946619 TTGGCTCTCA
Statistics
Matches: 106, Mismatches: 7, Indels: 14
0.83 0.06 0.11
Matches are distributed among these distances:
43 9 0.08
44 3 0.03
45 44 0.42
46 27 0.25
47 13 0.12
48 10 0.09
ACGTcount: A:0.24, C:0.32, G:0.19, T:0.26
Consensus pattern (45 bp):
CCGATGCCATGTCCCAGACATGTCTTACACTGACACGTCTCGAGG
Found at i:58971704 original size:22 final size:22
Alignment explanation
Indices: 58971671--58971712 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
58971661 AATATTGGTC
*
58971671 TTTGTGTGGCAACAT-GGGAAG
1 TTTGTGTCGCAACATAGGGAAG
58971692 TTTGATGTCGCAACATAGGGA
1 TTTG-TGTCGCAACATAGGGA
58971713 GCATAATGCA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 4 0.22
22 10 0.56
23 4 0.22
ACGTcount: A:0.26, C:0.12, G:0.33, T:0.29
Consensus pattern (22 bp):
TTTGTGTCGCAACATAGGGAAG
Found at i:58980540 original size:46 final size:44
Alignment explanation
Indices: 58980490--58980606 Score: 164
Period size: 46 Copynumber: 2.6 Consensus size: 44
58980480 GAGCGCTAGA
*
58980490 GTAAGACATGTCTGGGACATGCATTAGCCT-CGAGAAGTAAGTCAGT
1 GTAAGACATGTCTGGGACATGCATCAG-CTACGAGAAGT--GTCAGT
*
58980536 GTAAGACATGTCTGGGACATGCATCAGCTACGAGATGTGTCAGT
1 GTAAGACATGTCTGGGACATGCATCAGCTACGAGAAGTGTCAGT
58980580 GTAAGACCATGTCTGGGACATGGCATC
1 GTAAGA-CATGTCTGGGACAT-GCATC
58980607 GGCACAGATA
Statistics
Matches: 66, Mismatches: 2, Indels: 6
0.89 0.03 0.08
Matches are distributed among these distances:
44 12 0.18
45 16 0.24
46 38 0.58
ACGTcount: A:0.28, C:0.19, G:0.29, T:0.24
Consensus pattern (44 bp):
GTAAGACATGTCTGGGACATGCATCAGCTACGAGAAGTGTCAGT
Found at i:58988084 original size:46 final size:46
Alignment explanation
Indices: 58988025--58988191 Score: 180
Period size: 46 Copynumber: 3.6 Consensus size: 46
58988015 GCCCATAAGC
*
58988025 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCACATCCATAAAT
1 GAACTCGGACTCAACTCAACGAGTTCGGGCGTTCACATCCATAAAT
** *
58988071 GAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT---TTCAC
1 GAACTCGGACTCAACTCAACGAGTTCGG--G-C--GTTCACATCCATAAAT
* * * * *
58988118 GAACTCGGACTCAACTCAACGAGTTTGGACATTCGCATCCATAAGT
1 GAACTCGGACTCAACTCAACGAGTTCGGGCGTTCACATCCATAAAT
58988164 GAACTCGGACTCAACTCAACGAGTTCGG
1 GAACTCGGACTCAACTCAACGAGTTCGG
58988192 ATGCCCAAAT
Statistics
Matches: 99, Mismatches: 13, Indels: 18
0.76 0.10 0.14
Matches are distributed among these distances:
42 2 0.02
43 3 0.03
44 1 0.01
46 55 0.56
47 29 0.29
48 1 0.01
49 1 0.01
50 4 0.04
51 3 0.03
ACGTcount: A:0.29, C:0.28, G:0.20, T:0.22
Consensus pattern (46 bp):
GAACTCGGACTCAACTCAACGAGTTCGGGCGTTCACATCCATAAAT
Done.