Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr2
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: 43198478
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2088848 characters in sequence are not A, C, G, or T
File 62 of 131
Found at i:20276187 original size:20 final size:20
Alignment explanation
Indices: 20276162--20276227 Score: 60
Period size: 20 Copynumber: 3.3 Consensus size: 20
20276152 ATCAGGAAGC
*
20276162 TTTGGTAACTTGTCTGCAAT
1 TTTGGTAACTTGTCTACAAT
**
20276182 TTTGGTGGCTTGTCTACAAT
1 TTTGGTAACTTGTCTACAAT
** * *
20276202 ACTGGCAATTTGTCTACAAT
1 TTTGGTAACTTGTCTACAAT
*
20276222 TCTGGT
1 TTTGGT
20276228 GGCTTGTTAA
Statistics
Matches: 35, Mismatches: 11, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.20, C:0.17, G:0.21, T:0.42
Consensus pattern (20 bp):
TTTGGTAACTTGTCTACAAT
Found at i:20276234 original size:20 final size:20
Alignment explanation
Indices: 20276170--20276234 Score: 67
Period size: 20 Copynumber: 3.2 Consensus size: 20
20276160 GCTTTGGTAA
* *
20276170 CTTGTCTGCAATTTTGGTGG
1 CTTGTCTACAATTCTGGTGG
* ***
20276190 CTTGTCTACAATACTGGCAA
1 CTTGTCTACAATTCTGGTGG
*
20276210 TTTGTCTACAATTCTGGTGG
1 CTTGTCTACAATTCTGGTGG
20276230 CTTGT
1 CTTGT
20276235 TAATCTACCA
Statistics
Matches: 33, Mismatches: 12, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.17, C:0.18, G:0.23, T:0.42
Consensus pattern (20 bp):
CTTGTCTACAATTCTGGTGG
Found at i:20280418 original size:27 final size:26
Alignment explanation
Indices: 20280386--20280522 Score: 130
Period size: 27 Copynumber: 5.1 Consensus size: 26
20280376 AACACGTTAG
* *
20280386 GAAAGAAAATCCTTTGTGATAAACTTT
1 GAAAGAAAA-CCTTTGTGGTGAACTTT
*
20280413 GAAAGAAAACCTTCTGTGGCGAACTTT
1 GAAAGAAAACCTT-TGTGGTGAACTTT
* *
20280440 GAAAGAAAGCCTTTGTGGTGAACTCT
1 GAAAGAAAACCTTTGTGGTGAACTTT
* * *
20280466 AAAAGAAAACCCTTGGCGGTGAACTTT
1 GAAAGAAAA-CCTTTGTGGTGAACTTT
* * * *
20280493 CAAAAAAAACCCTTTGTGGCGAACTCT
1 GAAAGAAAA-CCTTTGTGGTGAACTTT
20280520 GAA
1 GAA
20280523 TGGACTGTCC
Statistics
Matches: 90, Mismatches: 18, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
26 22 0.24
27 68 0.76
ACGTcount: A:0.36, C:0.18, G:0.20, T:0.26
Consensus pattern (26 bp):
GAAAGAAAACCTTTGTGGTGAACTTT
Found at i:20290150 original size:16 final size:16
Alignment explanation
Indices: 20290096--20290150 Score: 53
Period size: 16 Copynumber: 3.6 Consensus size: 16
20290086 GTAAATTTCG
* **
20290096 CAAGTTAAGTATCCAC
1 CAAGTAAAGTATCTGC
20290112 CAAGTAAAGT-T-TG-
1 CAAGTAAAGTATCTGC
*
20290125 CAAGTCAAGTATCTGC
1 CAAGTAAAGTATCTGC
20290141 CAAGTAAAGT
1 CAAGTAAAGT
20290151 TCCCAAATCA
Statistics
Matches: 31, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
13 9 0.29
14 1 0.03
15 3 0.10
16 18 0.58
ACGTcount: A:0.38, C:0.18, G:0.18, T:0.25
Consensus pattern (16 bp):
CAAGTAAAGTATCTGC
Found at i:20290161 original size:29 final size:29
Alignment explanation
Indices: 20290070--20290172 Score: 116
Period size: 29 Copynumber: 3.6 Consensus size: 29
20290060 AAGGGAGGAG
** *
20290070 GTCAAGTATCCAACAAGTAAATTTCGCAA
1 GTCAAGTATCCGCCAAGTAAAGTTCGCAA
* * *
20290099 GTTAAGTATCCACCAAGTAAAGTTTGCAA
1 GTCAAGTATCCGCCAAGTAAAGTTCGCAA
* *
20290128 GTCAAGTATCTGCCAAGTAAAGTTCCCAA
1 GTCAAGTATCCGCCAAGTAAAGTTCGCAA
* *
20290157 ATCAAGTGTCCGCCAA
1 GTCAAGTATCCGCCAA
20290173 ATGCACTTGC
Statistics
Matches: 62, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 62 1.00
ACGTcount: A:0.37, C:0.22, G:0.17, T:0.24
Consensus pattern (29 bp):
GTCAAGTATCCGCCAAGTAAAGTTCGCAA
Found at i:20302396 original size:27 final size:27
Alignment explanation
Indices: 20302358--20302412 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 27
20302348 GAGTTAGTGC
20302358 GTGAATTCTATGCGAATTTAACCTCAA
1 GTGAATTCTATGCGAATTTAACCTCAA
*
20302385 GTGACTTCTATGCGAATTTAACCTCAA
1 GTGAATTCTATGCGAATTTAACCTCAA
20302412 G
1 G
20302413 CGAGTTGACG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.31, C:0.20, G:0.16, T:0.33
Consensus pattern (27 bp):
GTGAATTCTATGCGAATTTAACCTCAA
Found at i:20315627 original size:26 final size:26
Alignment explanation
Indices: 20315589--20315678 Score: 128
Period size: 26 Copynumber: 3.4 Consensus size: 26
20315579 TGAACTCCTC
*
20315589 AGTTCACCAAAGTACTGGAAACCCTT
1 AGTTCACCGAAGTACTGGAAACCCTT
20315615 AGTTCACCGAAGTACTGGAAACCCTT
1 AGTTCACCGAAGTACTGGAAACCCTT
* *
20315641 AGTTCACCGAAGTA-TGGGTGAACCCCT
1 AGTTCACCGAAGTACT-GG-AAACCCTT
20315668 AGTTCACCGAA
1 AGTTCACCGAA
20315679 ACACTGGTGT
Statistics
Matches: 59, Mismatches: 3, Indels: 3
0.91 0.05 0.05
Matches are distributed among these distances:
25 1 0.02
26 41 0.69
27 17 0.29
ACGTcount: A:0.31, C:0.27, G:0.20, T:0.22
Consensus pattern (26 bp):
AGTTCACCGAAGTACTGGAAACCCTT
Found at i:20315687 original size:27 final size:27
Alignment explanation
Indices: 20315576--20315687 Score: 97
Period size: 26 Copynumber: 4.2 Consensus size: 27
20315566 AATACTCTTT
*
20315576 TGGTGAACTCCTCAGTTCACC-AAAGTAC
1 TGGTGAACCCCT-AGTTCACCGAAA-TAC
* * *
20315604 TGG-AAACCCTTAGTTCACCGAAGTAC
1 TGGTGAACCCCTAGTTCACCGAAATAC
* * *
20315630 TGG-AAACCCTTAGTTCACCGAAGTA-
1 TGGTGAACCCCTAGTTCACCGAAATAC
*
20315655 TGGGTGAACCCCTAGTTCACCGAAACAC
1 T-GGTGAACCCCTAGTTCACCGAAATAC
20315683 TGGTG
1 TGGTG
20315688 TAGTGAAAAA
Statistics
Matches: 72, Mismatches: 8, Indels: 9
0.81 0.09 0.10
Matches are distributed among these distances:
25 1 0.01
26 38 0.53
27 29 0.40
28 4 0.06
ACGTcount: A:0.29, C:0.27, G:0.21, T:0.23
Consensus pattern (27 bp):
TGGTGAACCCCTAGTTCACCGAAATAC
Found at i:20329853 original size:12 final size:14
Alignment explanation
Indices: 20329821--20329854 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
20329811 AAGCCTTCCG
20329821 GTACACATAGTAGC
1 GTACACATAGTAGC
20329835 GTACACATAGTA-C
1 GTACACATAGTAGC
20329848 -TACACAT
1 GTACACAT
20329855 GTGACCATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 7 0.35
13 1 0.05
14 12 0.60
ACGTcount: A:0.38, C:0.24, G:0.15, T:0.24
Consensus pattern (14 bp):
GTACACATAGTAGC
Found at i:20329877 original size:51 final size:51
Alignment explanation
Indices: 20329777--20329908 Score: 151
Period size: 51 Copynumber: 2.6 Consensus size: 51
20329767 TCGGTTCACG
*
20329777 TAGTAGCCTGCACATAGTACTACACACGTGACCAAAGCCTTCCGGTACACA
1 TAGTAGCCTGCACATAGTACTACACACGTGACCAAAGCCTTCCGATACACA
* * * * * *
20329828 TAGTAGCGTACACATAGTACTACACATGTGACCATTA-TCTAT-CGATACACG
1 TAGTAGCCTGCACATAGTACTACACACGTGACCA-AAGCCT-TCCGATACACA
* *
20329879 TAGTAGCCTGCACTTTGTACTACACACGTG
1 TAGTAGCCTGCACATAGTACTACACACGTG
20329909 TTTATAGGCA
Statistics
Matches: 67, Mismatches: 12, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
51 65 0.97
52 2 0.03
ACGTcount: A:0.30, C:0.27, G:0.17, T:0.25
Consensus pattern (51 bp):
TAGTAGCCTGCACATAGTACTACACACGTGACCAAAGCCTTCCGATACACA
Found at i:20335655 original size:17 final size:17
Alignment explanation
Indices: 20335619--20335665 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 17
20335609 CATTGTCCCC
* *
20335619 AATGCACTAAC-ATGAA
1 AATGCAATAACAATAAA
* *
20335635 AATGTAATGACAATAAA
1 AATGCAATAACAATAAA
20335652 AATGCAATAACAAT
1 AATGCAATAACAAT
20335666 GTGTAGTTAT
Statistics
Matches: 24, Mismatches: 6, Indels: 1
0.77 0.19 0.03
Matches are distributed among these distances:
16 8 0.33
17 16 0.67
ACGTcount: A:0.55, C:0.13, G:0.11, T:0.21
Consensus pattern (17 bp):
AATGCAATAACAATAAA
Found at i:20336037 original size:7 final size:8
Alignment explanation
Indices: 20336020--20336045 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
20336010 AAACTTGACC
20336020 AAAAATAA
1 AAAAATAA
20336028 AAAAATAA
1 AAAAATAA
20336036 AAAAATAA
1 AAAAATAA
20336044 AA
1 AA
20336046 TCACATAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (8 bp):
AAAAATAA
Found at i:20336076 original size:16 final size:16
Alignment explanation
Indices: 20336036--20336078 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 16
20336026 AAAAAAATAA
*
20336036 AAAAATAAAATCACAT
1 AAAAATAAATTCACAT
*
20336052 AATAATAAATTCA-AT
1 AAAAATAAATTCACAT
20336067 AAAAATTAAATT
1 AAAAA-TAAATT
20336079 TTTTCGACCA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
15 6 0.26
16 17 0.74
ACGTcount: A:0.65, C:0.07, G:0.00, T:0.28
Consensus pattern (16 bp):
AAAAATAAATTCACAT
Found at i:20341034 original size:13 final size:13
Alignment explanation
Indices: 20341016--20341051 Score: 63
Period size: 13 Copynumber: 2.8 Consensus size: 13
20341006 AGGGGTCACA
20341016 CGGCCGTGTGGCC
1 CGGCCGTGTGGCC
20341029 CGGCCGTGTGGCC
1 CGGCCGTGTGGCC
*
20341042 AGGCCGTGTG
1 CGGCCGTGTG
20341052 ACTCACATAG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.03, C:0.33, G:0.47, T:0.17
Consensus pattern (13 bp):
CGGCCGTGTGGCC
Found at i:20342548 original size:25 final size:25
Alignment explanation
Indices: 20342520--20342593 Score: 121
Period size: 25 Copynumber: 3.0 Consensus size: 25
20342510 CCGAGTTGAA
20342520 TAATGGTAAGCTCATATGAGCTGAG
1 TAATGGTAAGCTCATATGAGCTGAG
*
20342545 TAATGGTAAGCTTATATGAGCTGAG
1 TAATGGTAAGCTCATATGAGCTGAG
* *
20342570 CAATGGTAAGCTCATAAGAGCTGA
1 TAATGGTAAGCTCATATGAGCTGA
20342594 AACTGATAAT
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 45 1.00
ACGTcount: A:0.34, C:0.12, G:0.27, T:0.27
Consensus pattern (25 bp):
TAATGGTAAGCTCATATGAGCTGAG
Found at i:20347387 original size:44 final size:44
Alignment explanation
Indices: 20347337--20347474 Score: 199
Period size: 44 Copynumber: 3.1 Consensus size: 44
20347327 AAAGTAGGAG
20347337 TCAGTTTAGAGACTCACCTGTTAGGTTCCAAGTCAGCATAAACA
1 TCAGTTTAGAGACTCACCTGTTAGGTTCCAAGTCAGCATAAACA
* * *
20347381 TCAGTTTAGAGACTCACCTGTTAGGTTCCAAGT-A-TAAAAGTAGGA
1 TCAGTTTAGAGACTCACCTGTTAGGTTCCAAGTCAGCATAA--A-CA
20347426 GTCAGTTTAGAGACTCACCTGTTAGGTTCCAAGTCAGCATAAACA
1 -TCAGTTTAGAGACTCACCTGTTAGGTTCCAAGTCAGCATAAACA
20347471 TCAG
1 TCAG
20347475 ATCCTTTTGC
Statistics
Matches: 82, Mismatches: 6, Indels: 12
0.82 0.06 0.12
Matches are distributed among these distances:
42 3 0.04
43 1 0.01
44 38 0.46
45 2 0.02
46 34 0.41
47 1 0.01
48 3 0.04
ACGTcount: A:0.32, C:0.20, G:0.20, T:0.28
Consensus pattern (44 bp):
TCAGTTTAGAGACTCACCTGTTAGGTTCCAAGTCAGCATAAACA
Found at i:20347448 original size:46 final size:46
Alignment explanation
Indices: 20347319--20347459 Score: 209
Period size: 46 Copynumber: 3.1 Consensus size: 46
20347309 GATTAACATG
20347319 CAAGTATAAAAGTAGGAGTCAGTTTAGAGACTCACCTGTTAGGTTC
1 CAAGTATAAAAGTAGGAGTCAGTTTAGAGACTCACCTGTTAGGTTC
* * *
20347365 CAAGTCAGCATAA--A-CA-TCAGTTTAGAGACTCACCTGTTAGGTTC
1 CAAGT-A-TAAAAGTAGGAGTCAGTTTAGAGACTCACCTGTTAGGTTC
20347409 CAAGTATAAAAGTAGGAGTCAGTTTAGAGACTCACCTGTTAGGTTC
1 CAAGTATAAAAGTAGGAGTCAGTTTAGAGACTCACCTGTTAGGTTC
20347455 CAAGT
1 CAAGT
20347460 CAGCATAAAC
Statistics
Matches: 83, Mismatches: 6, Indels: 12
0.82 0.06 0.12
Matches are distributed among these distances:
42 3 0.04
43 1 0.01
44 34 0.41
45 2 0.02
46 39 0.47
47 1 0.01
48 3 0.04
ACGTcount: A:0.33, C:0.18, G:0.22, T:0.28
Consensus pattern (46 bp):
CAAGTATAAAAGTAGGAGTCAGTTTAGAGACTCACCTGTTAGGTTC
Found at i:20350671 original size:13 final size:14
Alignment explanation
Indices: 20350653--20350682 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
20350643 TGAATGATCA
20350653 ATATATGCATG-AC
1 ATATATGCATGAAC
20350666 ATATATGCATGAAC
1 ATATATGCATGAAC
20350680 ATA
1 ATA
20350683 CATTTGTAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.69
14 5 0.31
ACGTcount: A:0.43, C:0.13, G:0.13, T:0.30
Consensus pattern (14 bp):
ATATATGCATGAAC
Found at i:20350804 original size:8 final size:8
Alignment explanation
Indices: 20350784--20350814 Score: 53
Period size: 8 Copynumber: 3.8 Consensus size: 8
20350774 TTTATCCTAG
20350784 AAAATTAAT
1 AAAATT-AT
20350793 AAAATTAT
1 AAAATTAT
20350801 AAAATTAT
1 AAAATTAT
20350809 AAAATT
1 AAAATT
20350815 CACCCCAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 16 0.73
9 6 0.27
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (8 bp):
AAAATTAT
Found at i:20350917 original size:17 final size:17
Alignment explanation
Indices: 20350877--20350911 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
20350867 CGGTACTAAT
* *
20350877 TCACATTTCCATCGTCA
1 TCACCTTTCCATCATCA
20350894 TCACCTTTCCATCATCA
1 TCACCTTTCCATCATCA
20350911 T
1 T
20350912 TTCCTTGTCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.23, C:0.37, G:0.03, T:0.37
Consensus pattern (17 bp):
TCACCTTTCCATCATCA
Found at i:20352432 original size:31 final size:31
Alignment explanation
Indices: 20352396--20352478 Score: 139
Period size: 31 Copynumber: 2.7 Consensus size: 31
20352386 GTAGTCTTGT
* * *
20352396 GTGTGAACAATCGGCAATGAGGAGTCTTTAG
1 GTGTGAACAATCAGCAATGAAGAGCCTTTAG
20352427 GTGTGAACAATCAGCAATGAAGAGCCTTTAG
1 GTGTGAACAATCAGCAATGAAGAGCCTTTAG
20352458 GTGTGAACAATCAGCAATGAA
1 GTGTGAACAATCAGCAATGAA
20352479 AAGTAAAATA
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 49 1.00
ACGTcount: A:0.35, C:0.14, G:0.28, T:0.23
Consensus pattern (31 bp):
GTGTGAACAATCAGCAATGAAGAGCCTTTAG
Found at i:20353800 original size:6 final size:6
Alignment explanation
Indices: 20353782--20353811 Score: 51
Period size: 6 Copynumber: 4.8 Consensus size: 6
20353772 GCAAATGGAT
20353782 CATTTC TCATTTC CATTTC CATTTC CATTT
1 CATTTC -CATTTC CATTTC CATTTC CATTT
20353812 TTATTTTTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 17 0.74
7 6 0.26
ACGTcount: A:0.17, C:0.30, G:0.00, T:0.53
Consensus pattern (6 bp):
CATTTC
Found at i:20354057 original size:23 final size:24
Alignment explanation
Indices: 20354021--20354066 Score: 58
Period size: 23 Copynumber: 1.9 Consensus size: 24
20354011 ATGATTTATA
*
20354021 ATTAAGTTTCAACT-TTTTTTCCT
1 ATTAAGTTTAAACTATTTTTTCCT
*
20354044 ATTAATTTTAAACTCATTTTTTC
1 ATTAAGTTTAAACT-ATTTTTTC
20354067 ACAAATTCAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 12 0.63
25 7 0.37
ACGTcount: A:0.26, C:0.15, G:0.02, T:0.57
Consensus pattern (24 bp):
ATTAAGTTTAAACTATTTTTTCCT
Found at i:20358378 original size:40 final size:40
Alignment explanation
Indices: 20358333--20358434 Score: 123
Period size: 40 Copynumber: 2.5 Consensus size: 40
20358323 TTCATAGCAA
* ** * *
20358333 ACTGAAGTGCAAATAAAGGCATGAATGTGCTATCAGAGCC
1 ACTGAAGTGCAAATAGAGGCACAAATGTGCGATCAAAGCC
* *
20358373 ACTGAAGTGCAAACAGAGGCACAAATGTGCGATCAAAGGC
1 ACTGAAGTGCAAATAGAGGCACAAATGTGCGATCAAAGCC
* *
20358413 ACCGAAGTACAAATAGAGGCAC
1 ACTGAAGTGCAAATAGAGGCAC
20358435 CGAAGTGAAA
Statistics
Matches: 52, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
40 52 1.00
ACGTcount: A:0.40, C:0.20, G:0.25, T:0.15
Consensus pattern (40 bp):
ACTGAAGTGCAAATAGAGGCACAAATGTGCGATCAAAGCC
Found at i:20358389 original size:20 final size:20
Alignment explanation
Indices: 20358333--20358390 Score: 55
Period size: 20 Copynumber: 2.9 Consensus size: 20
20358323 TTCATAGCAA
* * *
20358333 ACTGAAGTGCAAATAAAGGC
1 ACTGAAGTGCAAACAGAGCC
* *
20358353 A-TGAATGTGCTATCAGAGCC
1 ACTGAA-GTGCAAACAGAGCC
20358373 ACTGAAGTGCAAACAGAG
1 ACTGAAGTGCAAACAGAG
20358391 GCACAAATGT
Statistics
Matches: 29, Mismatches: 7, Indels: 4
0.73 0.17 0.10
Matches are distributed among these distances:
19 4 0.14
20 21 0.72
21 4 0.14
ACGTcount: A:0.40, C:0.17, G:0.26, T:0.17
Consensus pattern (20 bp):
ACTGAAGTGCAAACAGAGCC
Found at i:20359407 original size:16 final size:17
Alignment explanation
Indices: 20359382--20359414 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
20359372 AGATGATGGC
*
20359382 ATTATTGTTTT-ATTTA
1 ATTATAGTTTTAATTTA
20359398 ATTATAGTTTTAATTTA
1 ATTATAGTTTTAATTTA
20359415 TAAATTATAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.30, C:0.00, G:0.06, T:0.64
Consensus pattern (17 bp):
ATTATAGTTTTAATTTA
Found at i:20368953 original size:26 final size:26
Alignment explanation
Indices: 20368923--20368975 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
20368913 TTCACAAAAG
20368923 GCCTAAAGGTTTATGCATGATTTGGT
1 GCCTAAAGGTTTATGCATGATTTGGT
20368949 GCCTAAAGGTTTATGCATGATTTGGT
1 GCCTAAAGGTTTATGCATGATTTGGT
20368975 G
1 G
20368976 TTGGAAATGG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.23, C:0.11, G:0.28, T:0.38
Consensus pattern (26 bp):
GCCTAAAGGTTTATGCATGATTTGGT
Found at i:20370650 original size:26 final size:26
Alignment explanation
Indices: 20370591--20370682 Score: 103
Period size: 26 Copynumber: 3.5 Consensus size: 26
20370581 GCTCGCCATG
* ***
20370591 AAGGCTTCCATTTCATATATTGTCACA
1 AAGGCTTCCATTTCAGATA-CACCACA
* *
20370618 AAGGCTTTCTTTTCAGATACACCACA
1 AAGGCTTCCATTTCAGATACACCACA
*
20370644 AAGGCTTCCATTTCAGATACTCCACA
1 AAGGCTTCCATTTCAGATACACCACA
*
20370670 AAGACTTCCATTT
1 AAGGCTTCCATTT
20370683 TCTGACGTGT
Statistics
Matches: 55, Mismatches: 10, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
26 39 0.71
27 16 0.29
ACGTcount: A:0.30, C:0.26, G:0.11, T:0.33
Consensus pattern (26 bp):
AAGGCTTCCATTTCAGATACACCACA
Found at i:20373675 original size:29 final size:29
Alignment explanation
Indices: 20373633--20373696 Score: 101
Period size: 29 Copynumber: 2.2 Consensus size: 29
20373623 ATTTTTTTTT
*
20373633 TTTGTTTAAATTAGGCCCTGAACTTGGCA
1 TTTGTTCAAATTAGGCCCTGAACTTGGCA
*
20373662 TTTGTTCAAATTAGGTCCTGAACTTGGCA
1 TTTGTTCAAATTAGGCCCTGAACTTGGCA
*
20373691 ATTGTT
1 TTTGTT
20373697 TTCACATTGG
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.23, C:0.16, G:0.20, T:0.41
Consensus pattern (29 bp):
TTTGTTCAAATTAGGCCCTGAACTTGGCA
Found at i:20373743 original size:57 final size:58
Alignment explanation
Indices: 20373672--20373785 Score: 133
Period size: 57 Copynumber: 2.0 Consensus size: 58
20373662 TTTGTTCAAA
* * * * ** *
20373672 TTAGGTCCTGAACTTGGCAATTGTTTTCACATTGGGGCTT-AAACTTTTTTT-TCCAAG
1 TTAGGCCCTAAACTTGGCAAATATTCCCACATTGGGACTTCAAA-TTTTTTTATCCAAG
*
20373729 TTAGGCCCTAAACTTGGTAAATATTCCCACATTGGGACTTCAAATTTTTTTATCCAA
1 TTAGGCCCTAAACTTGGCAAATATTCCCACATTGGGACTTCAAATTTTTTTATCCAA
20373786 ATTGGTCCTT
Statistics
Matches: 47, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
57 39 0.83
58 8 0.17
ACGTcount: A:0.25, C:0.19, G:0.16, T:0.39
Consensus pattern (58 bp):
TTAGGCCCTAAACTTGGCAAATATTCCCACATTGGGACTTCAAATTTTTTTATCCAAG
Found at i:20374377 original size:15 final size:16
Alignment explanation
Indices: 20374357--20374386 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
20374347 TAAATAAAAT
20374357 AAAATTT-TAATTTTA
1 AAAATTTCTAATTTTA
20374372 AAAATTTCTAATTTT
1 AAAATTTCTAATTTT
20374387 TTCATTAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.53
Consensus pattern (16 bp):
AAAATTTCTAATTTTA
Found at i:20377617 original size:92 final size:93
Alignment explanation
Indices: 20377449--20377635 Score: 367
Period size: 92 Copynumber: 2.0 Consensus size: 93
20377439 TTTAATTTTG
20377449 ATTTAATCAAGCACATTTAAAGAAATAAATACATCAATTTATTTTTATATTTGATAAATATAATT
1 ATTTAATCAAGCACATTTAAAGAAATAAATACATCAATTTATTTTTATATTTGATAAATATAATT
20377514 ATTTATGTATGAAATATATAAATACAAA
66 ATTTATGTATGAAATATATAAATACAAA
20377542 ATTTAATCAA-CACATTTAAAGAAATAAATACATCAATTTATTTTTATATTTGATAAATATAATT
1 ATTTAATCAAGCACATTTAAAGAAATAAATACATCAATTTATTTTTATATTTGATAAATATAATT
20377606 ATTTATGTATGAAATATATAAATACAAA
66 ATTTATGTATGAAATATATAAATACAAA
20377634 AT
1 AT
20377636 GATATTATAT
Statistics
Matches: 94, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
92 84 0.89
93 10 0.11
ACGTcount: A:0.49, C:0.06, G:0.05, T:0.40
Consensus pattern (93 bp):
ATTTAATCAAGCACATTTAAAGAAATAAATACATCAATTTATTTTTATATTTGATAAATATAATT
ATTTATGTATGAAATATATAAATACAAA
Found at i:20377724 original size:29 final size:30
Alignment explanation
Indices: 20377681--20377739 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 30
20377671 AAATTAGATC
* *
20377681 AAATCAAATTTTCATGTATAAAATTACACA
1 AAATCAAATATTCATATATAAAATTACACA
* *
20377711 AAATCAAA-ATTCATATATATAATTGCACA
1 AAATCAAATATTCATATATAAAATTACACA
20377740 TTAAACTACA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
29 17 0.68
30 8 0.32
ACGTcount: A:0.51, C:0.14, G:0.03, T:0.32
Consensus pattern (30 bp):
AAATCAAATATTCATATATAAAATTACACA
Found at i:20380093 original size:140 final size:142
Alignment explanation
Indices: 20379767--20380117 Score: 501
Period size: 142 Copynumber: 2.5 Consensus size: 142
20379757 ATATTGTTTC
* * *
20379767 AAGCTTGAAGCAACATAAAATAAAAAAATACAAATGTGAGTAGTAGAGGAATTGAACTCGAGACT
1 AAGCTTGAAGCAACATGAAATAAAAAAATACAAATGTGAGTAGGAGAGAAATTGAACTCGAGACT
* * *
20379832 -AAGGATGTAATTGCAACTATATAATCATCCAACAAAAGAACTAATATGTTAAAAAAAATTAATT
66 CAAGGATGTAATTGCAACTATATAACCATCCAACAAAAGAACTAACATATTAAAAAAAATTAATT
20379896 AAAATTAAAAAAA
131 AAAATT-AAAAAA
* * * *
20379909 AAACTTGAAGCAACATGAAATAAAAAAATACAAATGTGAATAGGAAAGAAATTGAACTTGAGACT
1 AAGCTTGAAGCAACATGAAATAAAAAAATACAAATGTGAGTAGGAGAGAAATTGAACTCGAGACT
* * * * *
20379974 CAATGATGTATTTGCAACTATCTAACCATCTAACTAAAGAACTAACATATT-AAAAAAATTAATT
66 CAAGGATGTAATTGCAACTATATAACCATCCAACAAAAGAACTAACATATTAAAAAAAATTAATT
*
20380038 AAAATT-TAAAA
131 AAAATTAAAAAA
* * *
20380049 AAGCCTGAAGCAACATGAAATAAAAAAATACAAATGTGAGTAGGAGAGAAATCGAACCCGAGACT
1 AAGCTTGAAGCAACATGAAATAAAAAAATACAAATGTGAGTAGGAGAGAAATTGAACTCGAGACT
20380114 CAAG
66 CAAG
20380118 AATAAAAGAA
Statistics
Matches: 184, Mismatches: 24, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
140 65 0.35
142 77 0.42
143 42 0.23
ACGTcount: A:0.52, C:0.12, G:0.14, T:0.22
Consensus pattern (142 bp):
AAGCTTGAAGCAACATGAAATAAAAAAATACAAATGTGAGTAGGAGAGAAATTGAACTCGAGACT
CAAGGATGTAATTGCAACTATATAACCATCCAACAAAAGAACTAACATATTAAAAAAAATTAATT
AAAATTAAAAAA
Found at i:20381917 original size:19 final size:17
Alignment explanation
Indices: 20381893--20381932 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 17
20381883 TAATAATTAA
20381893 AATAAAACCAAATTATCCT
1 AATAAAA-CAAATT-TCCT
*
20381912 AATAAAATAAATTTCCT
1 AATAAAACAAATTTCCT
20381929 AATA
1 AATA
20381933 TAATTAAACT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 8 0.40
18 5 0.25
19 7 0.35
ACGTcount: A:0.55, C:0.15, G:0.00, T:0.30
Consensus pattern (17 bp):
AATAAAACAAATTTCCT
Found at i:20381952 original size:3 final size:3
Alignment explanation
Indices: 20381944--20381979 Score: 65
Period size: 3 Copynumber: 12.3 Consensus size: 3
20381934 AATTAAACTA
20381944 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
20381980 CACAACACAC
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 30 0.94
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:20384180 original size:20 final size:21
Alignment explanation
Indices: 20384137--20384216 Score: 71
Period size: 20 Copynumber: 3.9 Consensus size: 21
20384127 ATAAACATTA
*
20384137 AATTAAACTTAATATTAAGAT
1 AATTAAATTTAATATTAAGAT
20384158 AA-TAAATTTAATATTAA-ATT
1 AATTAAATTTAATATTAAGA-T
*
20384178 AATTAAA--TACTATTAAGAT
1 AATTAAATTTAATATTAAGAT
20384197 AAGTATTAAATTTAAT-TTAA
1 -A--ATTAAATTTAATATTAA
20384217 TATTAAACTA
Statistics
Matches: 48, Mismatches: 3, Indels: 14
0.74 0.05 0.22
Matches are distributed among these distances:
19 10 0.21
20 19 0.40
21 6 0.12
22 6 0.12
23 4 0.08
24 3 0.06
ACGTcount: A:0.53, C:0.03, G:0.04, T:0.41
Consensus pattern (21 bp):
AATTAAATTTAATATTAAGAT
Found at i:20390727 original size:18 final size:19
Alignment explanation
Indices: 20390704--20390749 Score: 67
Period size: 19 Copynumber: 2.5 Consensus size: 19
20390694 CTGTGCTGCG
20390704 GCCGTGTGG-AAGGCCTAA
1 GCCGTGTGGAAAGGCCTAA
*
20390722 GCCGTGTGGAAAGGCCTAG
1 GCCGTGTGGAAAGGCCTAA
*
20390741 GTCGTGTGG
1 GCCGTGTGG
20390750 GGGTCAACAT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
18 9 0.36
19 16 0.64
ACGTcount: A:0.17, C:0.20, G:0.43, T:0.20
Consensus pattern (19 bp):
GCCGTGTGGAAAGGCCTAA
Found at i:20401896 original size:89 final size:88
Alignment explanation
Indices: 20401744--20402055 Score: 335
Period size: 89 Copynumber: 3.5 Consensus size: 88
20401734 TTGCCACCCT
* * * * * * *
20401744 TTTTCATAGTTCGATAGCCGAAGCTATTCCTTTTGATATTTTGATGGCC-ATCACCATCTCTTTT
1 TTTTCATAGTTCGATAGCCGAAGCTATCCCTTTTCATAATTCGATAGCCGA--ACTATCCCTTTT
* *
20401808 CATATTTGATGGTTGTCACTATCCC
64 CATATTTAATGGTCGTCACTATCCC
*
20401833 TTTTCATAGTTTGATAGCCGAAGCTATCCCTTTTCATAATTCGATAGCCGAAGCTATCCCTTTTC
1 TTTTCATAGTTCGATAGCCGAAGCTATCCCTTTTCATAATTCGATAGCCGAA-CTATCCCTTTTC
* *
20401898 ATAGTTCAATGGTCGTCACCATCCC
65 ATA-TTTAATGGTCGTCACTATCCC
* * * * * *
20401923 TTTTCATAGTT-GATGGCCGTCA-CCATCCTTTTTCATAATTTGATAGTCGAAACTATCCCTTTT
1 TTTTCATAGTTCGATAGCCG-AAGCTATCCCTTTTCATAATTCGATAGCCG-AACTATCCCTTTT
* *
20401986 CATATTTCAATAGTCG-AAGCTATCCC
64 CATATTT-AATGGTCGTCA-CTATCCC
*
20402012 TTTTGATAGTTCGATAGCCGAAGCTATCCCTTTTCATAATTCGA
1 TTTTCATAGTTCGATAGCCGAAGCTATCCCTTTTCATAATTCGA
20402056 CATTCGAAGC
Statistics
Matches: 186, Mismatches: 28, Indels: 17
0.81 0.12 0.07
Matches are distributed among these distances:
88 4 0.02
89 125 0.67
90 57 0.31
ACGTcount: A:0.23, C:0.24, G:0.14, T:0.39
Consensus pattern (88 bp):
TTTTCATAGTTCGATAGCCGAAGCTATCCCTTTTCATAATTCGATAGCCGAACTATCCCTTTTCA
TATTTAATGGTCGTCACTATCCC
Found at i:20401956 original size:119 final size:119
Alignment explanation
Indices: 20401744--20402023 Score: 380
Period size: 119 Copynumber: 2.4 Consensus size: 119
20401734 TTGCCACCCT
* * * ** *
20401744 TTTTCATAGTTCGATAGCCGAAGCTATTCCTTTTGATATTTTGATGGCCATCACCATCTCTTTTC
1 TTTTCATAATTCGATAGCCGAAGCTATCCCTTTTGATAGTTCAATGGCCATCACCATCCCTTTTC
* ** * * *
20401809 ATATTTGATGGTTGTCACTATCCCTTTTCATAGTTTGATAGCCGAAGCTATCCC
66 ATAGTTGATGGCCGTCACCATCCCTTTTCATAATTTGATAGCCGAAACTATCCC
* * *
20401863 TTTTCATAATTCGATAGCCGAAGCTATCCCTTTTCATAGTTCAATGGTCGTCACCATCCCTTTTC
1 TTTTCATAATTCGATAGCCGAAGCTATCCCTTTTGATAGTTCAATGGCCATCACCATCCCTTTTC
* *
20401928 ATAGTTGATGGCCGTCACCATCCTTTTTCATAATTTGATAGTCGAAACTATCCC
66 ATAGTTGATGGCCGTCACCATCCCTTTTCATAATTTGATAGCCGAAACTATCCC
* * *
20401982 TTTTCATATTTCAATAGTCGAAGCTATCCCTTTTGATAGTTC
1 TTTTCATAATTCGATAGCCGAAGCTATCCCTTTTGATAGTTC
20402024 GATAGCCGAA
Statistics
Matches: 140, Mismatches: 21, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
119 140 1.00
ACGTcount: A:0.23, C:0.24, G:0.14, T:0.40
Consensus pattern (119 bp):
TTTTCATAATTCGATAGCCGAAGCTATCCCTTTTGATAGTTCAATGGCCATCACCATCCCTTTTC
ATAGTTGATGGCCGTCACCATCCCTTTTCATAATTTGATAGCCGAAACTATCCC
Found at i:20402065 original size:30 final size:30
Alignment explanation
Indices: 20401744--20402055 Score: 242
Period size: 30 Copynumber: 10.5 Consensus size: 30
20401734 TTGCCACCCT
*
20401744 TTTTCATAGTTCGATAGCCGAAGCTATTCC
1 TTTTCATAGTTCGATAGCCGAAGCTATCCC
* * * * * *
20401774 TTTTGATATTTTGATGGCC-ATCA-CCATCTC
1 TTTTCATAGTTCGATAGCCGA--AGCTATCCC
* * ** *
20401804 TTTTCATA-TTTGATGGTTGTCA-CTATCCC
1 TTTTCATAGTTCGATAGCCG-AAGCTATCCC
*
20401833 TTTTCATAGTTTGATAGCCGAAGCTATCCC
1 TTTTCATAGTTCGATAGCCGAAGCTATCCC
*
20401863 TTTTCATAATTCGATAGCCGAAGCTATCCC
1 TTTTCATAGTTCGATAGCCGAAGCTATCCC
* * * * *
20401893 TTTTCATAGTTCAATGGTCGTCA-CCATCCC
1 TTTTCATAGTTCGATAGCCG-AAGCTATCCC
* * * *
20401923 TTTTCATAGTT-GATGGCCGTCA-CCATCCT
1 TTTTCATAGTTCGATAGCCG-AAGCTATCCC
* * * *
20401952 TTTTCATAATTTGATAGTCGAAACTATCCC
1 TTTTCATAGTTCGATAGCCGAAGCTATCCC
* * *
20401982 TTTTCATATTTCAATAGTCGAAGCTATCCC
1 TTTTCATAGTTCGATAGCCGAAGCTATCCC
*
20402012 TTTTGATAGTTCGATAGCCGAAGCTATCCC
1 TTTTCATAGTTCGATAGCCGAAGCTATCCC
*
20402042 TTTTCATAATTCGA
1 TTTTCATAGTTCGA
20402056 CATTCGAAGC
Statistics
Matches: 229, Mismatches: 44, Indels: 18
0.79 0.15 0.06
Matches are distributed among these distances:
29 50 0.22
30 177 0.77
31 2 0.01
ACGTcount: A:0.23, C:0.24, G:0.14, T:0.39
Consensus pattern (30 bp):
TTTTCATAGTTCGATAGCCGAAGCTATCCC
Found at i:20402076 original size:149 final size:147
Alignment explanation
Indices: 20401784--20402078 Score: 382
Period size: 149 Copynumber: 2.0 Consensus size: 147
20401774 TTTTGATATT
* * ** *
20401784 TTGATGGCCATCACCATCTCTTTTCATATTTGATGGTTGTCACTATCCCTTTTCATAGTTTGATA
1 TTGATGGCCATCACCATCTCTTTTCATATTTGATAGTCGAAACTATCCCTTTTCATAGTTTAATA
*
20401849 GCCGAAGCTATCCCTTTTCATAATTCGATAGCCGAAGCTATCCCTTTTCATAGTTCAATGGTCGT
66 GCCGAAGCTATCCCTTTTCATAATTCGATAGCCGAAGCTATCCCTTTTCATAATTCAAT-GTCGT
* *
20401914 CACCATCCCTTTTCATAG
130 AACCATACCTTTTCATAG
*
20401932 TTGATGGCCGTCACCATC-CTTTTTCATAATTTGATAGTCGAAACTATCCCTTTTCATA-TTTCA
1 TTGATGGCCATCACCATCTC-TTTTCAT-ATTTGATAGTCGAAACTATCCCTTTTCATAGTTT-A
* * *
20401995 ATAGTCGAAGCTATCCCTTTTGATAGTTCGATAGCCGAAGCTATCCCTTTTCATAATTCGACAT-
63 ATAGCCGAAGCTATCCCTTTTCATAATTCGATAGCCGAAGCTATCCCTTTTCATAATTC-A-ATG
*
20402059 TCG-AAGCCATACTTTTTCAT
126 TCGTAA-CCATACCTTTTCAT
20402079 TGGTCGATGA
Statistics
Matches: 128, Mismatches: 13, Indels: 11
0.84 0.09 0.07
Matches are distributed among these distances:
147 1 0.01
148 28 0.22
149 96 0.75
150 1 0.01
151 2 0.02
ACGTcount: A:0.23, C:0.25, G:0.14, T:0.38
Consensus pattern (147 bp):
TTGATGGCCATCACCATCTCTTTTCATATTTGATAGTCGAAACTATCCCTTTTCATAGTTTAATA
GCCGAAGCTATCCCTTTTCATAATTCGATAGCCGAAGCTATCCCTTTTCATAATTCAATGTCGTA
ACCATACCTTTTCATAG
Found at i:20402086 original size:60 final size:60
Alignment explanation
Indices: 20401831--20402086 Score: 151
Period size: 60 Copynumber: 4.3 Consensus size: 60
20401821 TGTCACTATC
* * * * * * * *
20401831 CCTTTTCATAGTTTGATAGCCGAAGCTATCCCTTTTCATAATTCGATAGCCGAAGCTATC
1 CCTTTTCATAGGTCGATAGCCGAAACTATCCCTTTTCATAATTCAACAGTCGAAGCCATA
* * * * ** * * * * *
20401891 CCTTTTCATAGTTCAATGGTCGTCACCATCCCTTTTCATAGTTGATGGCCGTC--A-CCAT-
1 CCTTTTCATAGGTCGATAGCCGAAACTATCCCTTTTCATAATTCA--ACAGTCGAAGCCATA
** * * * * * *
20401949 CCTTTTTCATAATTTGATAGTCGAAACTATCCCTTTTCATATTTCAATAGTCGAAGCTATC
1 CC-TTTTCATAGGTCGATAGCCGAAACTATCCCTTTTCATAATTCAACAGTCGAAGCCATA
* * * * *
20402010 CCTTTTGATAGTTCGATAGCCGAAGCTATCCCTTTTCATAATTCGACATTCGAAGCCATA
1 CCTTTTCATAGGTCGATAGCCGAAACTATCCCTTTTCATAATTCAACAGTCGAAGCCATA
* *
20402070 CTTTTTCATTGGTCGAT
1 CCTTTTCATAGGTCGAT
20402087 GACCGTCGAT
Statistics
Matches: 145, Mismatches: 44, Indels: 14
0.71 0.22 0.07
Matches are distributed among these distances:
57 3 0.02
58 2 0.01
59 38 0.26
60 98 0.68
61 2 0.01
62 2 0.01
ACGTcount: A:0.24, C:0.25, G:0.14, T:0.38
Consensus pattern (60 bp):
CCTTTTCATAGGTCGATAGCCGAAACTATCCCTTTTCATAATTCAACAGTCGAAGCCATA
Found at i:20404022 original size:109 final size:109
Alignment explanation
Indices: 20403831--20404048 Score: 427
Period size: 109 Copynumber: 2.0 Consensus size: 109
20403821 ATCACGGGAA
*
20403831 TAAATCAAAATGTCATCTATGAATACTACCACAAACTGATCCAGCTATCATCTGAAGATCCGATT
1 TAAATCAAAATGTCATCTATGAATACTACCACAAACTGATCCAGCTACCATCTGAAGATCCGATT
20403896 CATCAAATCCATAAAAATAGCAGGTGCATTAGTAAGTCCGAAAG
66 CATCAAATCCATAAAAATAGCAGGTGCATTAGTAAGTCCGAAAG
20403940 TAAATCAAAATGTCATCTATGAATACTACCACAAACTGATCCAGCTACCATCTGAAGATCCGATT
1 TAAATCAAAATGTCATCTATGAATACTACCACAAACTGATCCAGCTACCATCTGAAGATCCGATT
20404005 CATCAAATCCATAAAAATAGCAGGTGCATTAGTAAGTCCGAAAG
66 CATCAAATCCATAAAAATAGCAGGTGCATTAGTAAGTCCGAAAG
20404049 CCATAACCAG
Statistics
Matches: 108, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
109 108 1.00
ACGTcount: A:0.40, C:0.22, G:0.14, T:0.24
Consensus pattern (109 bp):
TAAATCAAAATGTCATCTATGAATACTACCACAAACTGATCCAGCTACCATCTGAAGATCCGATT
CATCAAATCCATAAAAATAGCAGGTGCATTAGTAAGTCCGAAAG
Found at i:20406380 original size:23 final size:23
Alignment explanation
Indices: 20406342--20406422 Score: 74
Period size: 23 Copynumber: 3.4 Consensus size: 23
20406332 ATCTACCTTG
*
20406342 TTTGGACAGC-TATTATACATCAA
1 TTTGGACAGCAT-TTATACACCAA
*
20406365 TTTGGACAGCATTTATATACCAA
1 TTTGGACAGCATTTATACACCAA
* ** *
20406388 ATTAAACATCATTTATACACCAAAA
1 TTTGGACAGCATTTATACACC--AA
20406413 TTTGGACAGC
1 TTTGGACAGC
20406423 TGATATACAA
Statistics
Matches: 44, Mismatches: 11, Indels: 4
0.75 0.19 0.07
Matches are distributed among these distances:
23 35 0.80
24 1 0.02
25 8 0.18
ACGTcount: A:0.38, C:0.19, G:0.11, T:0.32
Consensus pattern (23 bp):
TTTGGACAGCATTTATACACCAA
Found at i:20406516 original size:69 final size:69
Alignment explanation
Indices: 20406371--20406591 Score: 327
Period size: 69 Copynumber: 3.2 Consensus size: 69
20406361 TCAATTTGGA
* * * * * * *
20406371 CAGCATTTATATACCAAATTAAACATCATTTATACACCAAAATTTGGACAGC-TGATATACAACA
1 CAGCATATACATACCAAATTGAGCAACATTTTTACACCAAAATTT-AACAGCAT-ATATACAACA
20406435 AATGGG
64 AATGGG
* *
20406441 CAGCATATACATACCAAATTGAGTAGCATTTTTACACCAAAATTTAACAGCATATATACAACAAA
1 CAGCATATACATACCAAATTGAGCAACATTTTTACACCAAAATTTAACAGCATATATACAACAAA
20406506 TGGG
66 TGGG
*
20406510 CAGCATATACGTACCAAATTGAGCAACATTTTTACACCAAAATTTAACAGCATATATACAACAAA
1 CAGCATATACATACCAAATTGAGCAACATTTTTACACCAAAATTTAACAGCATATATACAACAAA
20406575 TGGG
66 TGGG
20406579 CAGCATATACATA
1 CAGCATATACATA
20406592 ATACATCATA
Statistics
Matches: 138, Mismatches: 12, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
69 99 0.72
70 39 0.28
ACGTcount: A:0.43, C:0.19, G:0.11, T:0.26
Consensus pattern (69 bp):
CAGCATATACATACCAAATTGAGCAACATTTTTACACCAAAATTTAACAGCATATATACAACAAA
TGGG
Found at i:20407446 original size:41 final size:41
Alignment explanation
Indices: 20407401--20407557 Score: 217
Period size: 41 Copynumber: 3.8 Consensus size: 41
20407391 TTGTATAAAA
* * * * *
20407401 CACCGGCATAAAGCCTGCTAGGCACAAAGCCCGATACATTT
1 CACCGGCACAAAGCCTGCTAGGCATAAAGCCTGATATAATT
* *
20407442 CACCGGCACAAAGCCTGCTAGACATAAAGTCTGATATAATT
1 CACCGGCACAAAGCCTGCTAGGCATAAAGCCTGATATAATT
*
20407483 CACCGGCACAGAA-CCTGCTAGGCATAACGCCTGATATAATT
1 CACCGGCACA-AAGCCTGCTAGGCATAAAGCCTGATATAATT
*
20407524 CACCGGCATAAAGCCTGCTAGGCATAAAGCCTGA
1 CACCGGCACAAAGCCTGCTAGGCATAAAGCCTGA
20407558 ACTTACAAAA
Statistics
Matches: 102, Mismatches: 12, Indels: 4
0.86 0.10 0.03
Matches are distributed among these distances:
40 2 0.02
41 98 0.96
42 2 0.02
ACGTcount: A:0.33, C:0.29, G:0.20, T:0.18
Consensus pattern (41 bp):
CACCGGCACAAAGCCTGCTAGGCATAAAGCCTGATATAATT
Found at i:20410013 original size:13 final size:13
Alignment explanation
Indices: 20409997--20410021 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
20409987 TTTAAAAAAA
20409997 TTTTTTAAAATTT
1 TTTTTTAAAATTT
20410010 TTTTTTAAAATT
1 TTTTTTAAAATT
20410022 GGTGTTTATT
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:0.00, G:0.00, T:0.68
Consensus pattern (13 bp):
TTTTTTAAAATTT
Found at i:20416377 original size:15 final size:15
Alignment explanation
Indices: 20416353--20416384 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
20416343 TATGCTTGCA
*
20416353 AAATATAAAAGACAT
1 AAATACAAAAGACAT
20416368 AAATACAAAAGACAT
1 AAATACAAAAGACAT
20416383 AA
1 AA
20416385 TAGTGAAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.69, C:0.09, G:0.06, T:0.16
Consensus pattern (15 bp):
AAATACAAAAGACAT
Found at i:20423808 original size:71 final size:71
Alignment explanation
Indices: 20423715--20423852 Score: 174
Period size: 71 Copynumber: 1.9 Consensus size: 71
20423705 CTTTCCCCCC
* * ** *
20423715 AAAAATTTTACTTTCCCTCAAACCC-CACAACTTTTTTTCCTTTTATTTTTCCCCAAAAATTTTA
1 AAAAATTTTACTTTCCCCCAAACCCTCAAAAC-TTTTTTCCTTTT-GCTTCCCCCAAAAATTTTA
20423779 CTTCTCTT
64 CTTCTCTT
*
20423787 AAAAA-TTTAC-TTCCTCCCAAACCCTCAAAACTTTTTTCCTTTTGCTTCCCCCAAAACTTTTAC
1 AAAAATTTTACTTTCC-CCCAAACCCTCAAAACTTTTTTCCTTTTGCTTCCCCCAAAAATTTTAC
20423850 TTC
65 TTC
20423853 CTCCTAAACC
Statistics
Matches: 58, Mismatches: 6, Indels: 6
0.83 0.09 0.09
Matches are distributed among these distances:
70 23 0.40
71 25 0.43
72 10 0.17
ACGTcount: A:0.27, C:0.30, G:0.01, T:0.42
Consensus pattern (71 bp):
AAAAATTTTACTTTCCCCCAAACCCTCAAAACTTTTTTCCTTTTGCTTCCCCCAAAAATTTTACT
TCTCTT
Found at i:20425552 original size:37 final size:38
Alignment explanation
Indices: 20425506--20425596 Score: 116
Period size: 37 Copynumber: 2.4 Consensus size: 38
20425496 TAGTTCCACA
*
20425506 AATT-TGGTGTGTAGGGTGGATGGGCTTAT-TATGGTCC
1 AATTGTGGTGTGTAGGGTGGATGGGCTT-TCTATAGTCC
* * *
20425543 TA-TGTGGTGTGCAGGGTGGATGGGCTTTCTTTAGTCC
1 AATTGTGGTGTGTAGGGTGGATGGGCTTTCTATAGTCC
20425580 AATTGTGGTGTGTAGGG
1 AATTGTGGTGTGTAGGG
20425597 GGCCAGAGTG
Statistics
Matches: 45, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
36 2 0.04
37 30 0.67
38 13 0.29
ACGTcount: A:0.14, C:0.09, G:0.40, T:0.37
Consensus pattern (38 bp):
AATTGTGGTGTGTAGGGTGGATGGGCTTTCTATAGTCC
Found at i:20435447 original size:266 final size:265
Alignment explanation
Indices: 20434949--20435478 Score: 1015
Period size: 266 Copynumber: 2.0 Consensus size: 265
20434939 CGCAGTGCTC
*
20434949 TTTGCTCCCTTCCGGTCATTCTCCTCTAGTTGATGGTGTATTTCAGCTAAGTTTTTTTTTGTGTG
1 TTTGCTCCCTTCCGGTCATTCTCCTCTAATTGATGGTGTATTTCAGCTAAGTTTTTTTTTGTGTG
20435014 GGATCTCTTTTGTGTTTTTATGAGTGGTTTTTGTTATAATTTTTCCAAGCAGATTTTTTTTTGGG
66 GGATCTCTTTTGTGTTTTTATGAGTGGTTTTTGTTATAATTTTTCCAAGCAGATTTTTTTTTGGG
*
20435079 TATTAGTTAATTTTTTCAGCATTATGTTGAAAGACAAGAAGCTTGTGATTCCAACCAATAATCAC
131 TATTAGTTAATTTTCTCAGCATTATGTTGAAAGACAAGAAGCTTGTGATTCCAACCAATAATCAC
20435144 TCATTGCAAATTAGTCCTGTTAAGCTTGATGGACATAATTACCTTGCTTGGTCAAGGTCCTACTT
196 TCATTGCAAATTAGTCCTGTTAAGCTTGATGGACATAATTACCTTGCTTGGTCAAGGTCCTACTT
20435209 GTTTT
261 GTTTT
*
20435214 TTTGCTCCCTTCCGGTCATTCTCCTCTAATTGGTGGTGTATTTCAGCTAAGTTTTTTTTTGTGTG
1 TTTGCTCCCTTCCGGTCATTCTCCTCTAATTGATGGTGTATTTCAGCTAAGTTTTTTTTTGTGTG
20435279 GGATCTCTTTTGTGTTTTTATGAGTGGTTTTTGTTATAATTTTTCCAAGCAGATTTTCTTTTTGG
66 GGATCTCTTTTGTGTTTTTATGAGTGGTTTTTGTTATAATTTTTCCAAGCAGATTTT-TTTTTGG
*
20435344 GTATTAGTTAATTTTCTCAGCATTATGTTGAAAGACAAGAAGCTTGTGATTCCAACCAATAATCC
130 GTATTAGTTAATTTTCTCAGCATTATGTTGAAAGACAAGAAGCTTGTGATTCCAACCAATAATCA
20435409 CTCATTGCAAATTAGTCCTGTTAAGCTTGATGGACATAATTACCTTGCTTGGTCAAGGTCCTACT
195 CTCATTGCAAATTAGTCCTGTTAAGCTTGATGGACATAATTACCTTGCTTGGTCAAGGTCCTACT
20435474 TGTTT
260 TGTTT
20435479 ATCAAGGCTC
Statistics
Matches: 260, Mismatches: 4, Indels: 1
0.98 0.02 0.00
Matches are distributed among these distances:
265 120 0.46
266 140 0.54
ACGTcount: A:0.21, C:0.16, G:0.18, T:0.45
Consensus pattern (265 bp):
TTTGCTCCCTTCCGGTCATTCTCCTCTAATTGATGGTGTATTTCAGCTAAGTTTTTTTTTGTGTG
GGATCTCTTTTGTGTTTTTATGAGTGGTTTTTGTTATAATTTTTCCAAGCAGATTTTTTTTTGGG
TATTAGTTAATTTTCTCAGCATTATGTTGAAAGACAAGAAGCTTGTGATTCCAACCAATAATCAC
TCATTGCAAATTAGTCCTGTTAAGCTTGATGGACATAATTACCTTGCTTGGTCAAGGTCCTACTT
GTTTT
Found at i:20442704 original size:30 final size:30
Alignment explanation
Indices: 20442644--20442712 Score: 77
Period size: 30 Copynumber: 2.3 Consensus size: 30
20442634 TCTACTTATA
*
20442644 TTTATTTTATTTTGTTTCATATTTATATTT
1 TTTATTTTATTTTGTTTCATATTTAAATTT
* **
20442674 TTTATTTTGTTTTGTTTTGT-TTTAAAATTT
1 TTTATTTTATTTTGTTTCATATTT-AAATTT
20442704 TTATATTTT
1 TT-TATTTT
20442713 TAATTAATAT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
29 3 0.09
30 24 0.73
31 6 0.18
ACGTcount: A:0.19, C:0.01, G:0.06, T:0.74
Consensus pattern (30 bp):
TTTATTTTATTTTGTTTCATATTTAAATTT
Found at i:20444096 original size:46 final size:44
Alignment explanation
Indices: 20444014--20444101 Score: 113
Period size: 46 Copynumber: 2.0 Consensus size: 44
20444004 TTTTTATTTC
*
20444014 ATATTGTTTCAAGTTTTTTTAACTAATGTTTATAATTAATAAAT
1 ATATTGTTTCAAGTTTTTTTAACTAATCTTTATAATTAATAAAT
* * * *
20444058 ATATTGTTTTCAATTGTTTTTTAATTCATCTTTTTAATTAATAA
1 ATATTG-TTTCAAGT-TTTTTTAACTAATCTTTATAATTAATAA
20444102 CTCTTTTAAT
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
44 6 0.16
45 7 0.19
46 24 0.65
ACGTcount: A:0.33, C:0.06, G:0.06, T:0.56
Consensus pattern (44 bp):
ATATTGTTTCAAGTTTTTTTAACTAATCTTTATAATTAATAAAT
Found at i:20444712 original size:28 final size:27
Alignment explanation
Indices: 20444666--20444723 Score: 89
Period size: 28 Copynumber: 2.1 Consensus size: 27
20444656 TGTATCTCGG
20444666 TAAATATAAAAAAACAACATACTTATT
1 TAAATATAAAAAAACAACATACTTATT
* *
20444693 TAAATATTAAAAAAACAACATATTTCTT
1 TAAATA-TAAAAAAACAACATACTTATT
20444721 TAA
1 TAA
20444724 TTCCACTAGG
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
27 6 0.21
28 22 0.79
ACGTcount: A:0.57, C:0.10, G:0.00, T:0.33
Consensus pattern (27 bp):
TAAATATAAAAAAACAACATACTTATT
Found at i:20447602 original size:23 final size:23
Alignment explanation
Indices: 20447537--20447602 Score: 55
Period size: 23 Copynumber: 2.8 Consensus size: 23
20447527 TCACATGTAT
*
20447537 TATTTATTTAAAATTTATATATG
1 TATTTATTTAAAATTTATATATA
**
20447560 TAATTTAATTT-ACTTCTTATATA-A
1 T-ATTT-ATTTAAAAT-TTATATATA
20447584 TATTTACTTTAAAATTTAT
1 TATTTA-TTTAAAATTTAT
20447603 TTAGATACTA
Statistics
Matches: 33, Mismatches: 5, Indels: 10
0.69 0.10 0.21
Matches are distributed among these distances:
22 1 0.03
23 12 0.36
24 9 0.27
25 11 0.33
ACGTcount: A:0.38, C:0.05, G:0.02, T:0.56
Consensus pattern (23 bp):
TATTTATTTAAAATTTATATATA
Found at i:20454542 original size:87 final size:87
Alignment explanation
Indices: 20454390--20454832 Score: 670
Period size: 87 Copynumber: 5.1 Consensus size: 87
20454380 AGATCAGTGA
* * *
20454390 AGATTGAAAACAAAGCCTTGCCTCCACCGGTTGCAGTGGAGCTGGTTAAAGATAGCAGATATTGC
1 AGATCGAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAGCAGATCTTGC
* *
20454455 CTTCTTGCGTTAACAACGAAGC
66 CTTCCTGCGTTAACAGCGAAGC
* *
20454477 AGATCGAAAACAAAGCCTTGCCTCCATCGATTGCAGTGGAGCTGGTTAAAGATAGCAAATCTTGC
1 AGATCGAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAGCAGATCTTGC
* *
20454542 CTTCCTGCATTGACAGCGAAGC
66 CTTCCTGCGTTAACAGCGAAGC
* * *
20454564 AGATCGAAAACAAAGCCTTGCCTCTATCGGTTGCAGTGGAGTTGGTTAAAGATAGCAGATTTTGC
1 AGATCGAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAGCAGATCTTGC
* *
20454629 CTTCCTACATTAACAGCGAAGC
66 CTTCCTGCGTTAACAGCGAAGC
** *
20454651 AGATAAAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTGAAGATAGCAGATCTTGC
1 AGATCGAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAGCAGATCTTGC
*
20454716 CTTCCTGTGTTAACAGCGAAGC
66 CTTCCTGCGTTAACAGCGAAGC
* *
20454738 AAATCGAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAGCAAATCTTGC
1 AGATCGAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAGCAGATCTTGC
* ** *
20454803 CCTCCTGCGTCGACAGTGAAGC
66 CTTCCTGCGTTAACAGCGAAGC
20454825 AGATCGAA
1 AGATCGAA
20454833 GATTACAAGT
Statistics
Matches: 320, Mismatches: 36, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
87 320 1.00
ACGTcount: A:0.30, C:0.23, G:0.24, T:0.24
Consensus pattern (87 bp):
AGATCGAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAGCAGATCTTGC
CTTCCTGCGTTAACAGCGAAGC
Found at i:20454586 original size:43 final size:43
Alignment explanation
Indices: 20454451--20454586 Score: 100
Period size: 45 Copynumber: 3.1 Consensus size: 43
20454441 ATAGCAGATA
* * * *
20454451 TTGCCTTCTTGCGTTAACAACGAAGCAGATCGAAAACAAAGCC
1 TTGCCTTCCTGCATTGACAGCGAAGCAGATCGAAAACAAAGCC
* * * * ** *
20454494 TTGCC-TCCAT-CGATTG-CAGTGGAGCTGGTTAAAGATAGCAAA-TC
1 TTGCCTTCC-TGC-ATTGACAGCGAAGCAGATCGAA-A-A-CAAAGCC
20454538 TTGCCTTCCTGCATTGACAGCGAAGCAGATCGAAAACAAAGCC
1 TTGCCTTCCTGCATTGACAGCGAAGCAGATCGAAAACAAAGCC
20454581 TTGCCT
1 TTGCCT
20454587 CTATCGGTTG
Statistics
Matches: 66, Mismatches: 18, Indels: 18
0.65 0.18 0.18
Matches are distributed among these distances:
42 17 0.26
43 17 0.26
44 13 0.20
45 19 0.29
ACGTcount: A:0.30, C:0.25, G:0.21, T:0.24
Consensus pattern (43 bp):
TTGCCTTCCTGCATTGACAGCGAAGCAGATCGAAAACAAAGCC
Found at i:20454980 original size:44 final size:45
Alignment explanation
Indices: 20454927--20455112 Score: 135
Period size: 44 Copynumber: 4.0 Consensus size: 45
20454917 TGAAGCTAGT
*
20454927 AATCCTATCTCCCTGAGATTACAGTGGAGCGGATTAAAATAAAG-
1 AATCTTATCTCCCTGAGATTACAGTGGAGCGGATTAAAATAAAGA
* * * * * *
20454971 GATCTTATCTCTCTGAGGTTACAGTAGAGTAGATCGCATTAGATTGAAACCAGA
1 AATCTTATCTCCCTGAGATTACAGT-G-G-AG--CGGATTAAAAT--AA--AGA
* * * ** *
20455025 AATCTTATCTCCTTGAGATTACAGCGGAGCAGATTGAAGCT--AGT
1 AATCTTATCTCCCTGAGATTACAGTGGAGCGGATT-AAAATAAAGA
*
20455069 AATCCTATCTCCCTGAGATTACAGTGGAGCGGATTAAAATAAAG
1 AATCTTATCTCCCTGAGATTACAGTGGAGCGGATTAAAATAAAG
20455113 GATCAGTTAC
Statistics
Matches: 105, Mismatches: 24, Indels: 25
0.68 0.16 0.16
Matches are distributed among these distances:
43 3 0.03
44 54 0.51
45 3 0.03
46 1 0.01
47 2 0.02
49 12 0.11
50 2 0.02
51 4 0.04
52 1 0.01
53 3 0.03
54 20 0.19
ACGTcount: A:0.33, C:0.18, G:0.22, T:0.27
Consensus pattern (45 bp):
AATCTTATCTCCCTGAGATTACAGTGGAGCGGATTAAAATAAAGA
Found at i:20455372 original size:50 final size:50
Alignment explanation
Indices: 20455220--20455382 Score: 164
Period size: 50 Copynumber: 3.3 Consensus size: 50
20455210 AGTGGAACAA
* * * *
20455220 ATTAAAGCCACATCGGTGAATCTTGCTTCCCCGACATTGCGGTTAAAAAG
1 ATTAAAGCCACAACGGTGAATCTTGCCTCCCAGACATTGCAGTTAAAAAG
* *** * * * * ** *
20455270 ATTAAAGCTACAGTAGTGAATCTTACCTCCCAGGCAGTACAGTGGAACAG
1 ATTAAAGCCACAACGGTGAATCTTGCCTCCCAGACATTGCAGTTAAAAAG
* * *
20455320 ATTAAAGCCACAACGGTAAATCTTGCCTCCCTGACATTGTAGTTAAAAAG
1 ATTAAAGCCACAACGGTGAATCTTGCCTCCCAGACATTGCAGTTAAAAAG
20455370 ATTAAAGCCACAA
1 ATTAAAGCCACAA
20455383 TGGCGAACTT
Statistics
Matches: 85, Mismatches: 28, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
50 85 1.00
ACGTcount: A:0.35, C:0.23, G:0.18, T:0.24
Consensus pattern (50 bp):
ATTAAAGCCACAACGGTGAATCTTGCCTCCCAGACATTGCAGTTAAAAAG
Found at i:20455965 original size:14 final size:14
Alignment explanation
Indices: 20455942--20455976 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
20455932 CAACACACAA
*
20455942 AAGAACAAAAAAGG
1 AAGAAAAAAAAAGG
20455956 AAGAAAAAAAAAGG
1 AAGAAAAAAAAAGG
20455970 -AGAAAAA
1 AAGAAAAA
20455977 TAGCAAACAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 7 0.35
14 13 0.65
ACGTcount: A:0.77, C:0.03, G:0.20, T:0.00
Consensus pattern (14 bp):
AAGAAAAAAAAAGG
Found at i:20457079 original size:23 final size:23
Alignment explanation
Indices: 20457014--20457079 Score: 55
Period size: 23 Copynumber: 2.8 Consensus size: 23
20457004 TCACATGTAT
*
20457014 TATTTATTTAAAATTTATATATG
1 TATTTATTTAAAATTTATATATA
**
20457037 TATTTTAATTT-ACTTCTTATATA-A
1 TA-TTT-ATTTAAAAT-TTATATATA
20457061 TATTTACTTTAAAATTTAT
1 TATTTA-TTTAAAATTTAT
20457080 TTAGATACTA
Statistics
Matches: 33, Mismatches: 5, Indels: 10
0.69 0.10 0.21
Matches are distributed among these distances:
22 1 0.03
23 12 0.36
24 9 0.27
25 11 0.33
ACGTcount: A:0.36, C:0.05, G:0.02, T:0.58
Consensus pattern (23 bp):
TATTTATTTAAAATTTATATATA
Found at i:20463643 original size:50 final size:50
Alignment explanation
Indices: 20463545--20463685 Score: 149
Period size: 50 Copynumber: 2.8 Consensus size: 50
20463535 TATTGAGGTT
* * * *
20463545 ATGAGAGGTCCCACGTATGACCATGTCTGAGACATGGCGTTGGTACCGAG
1 ATGAGAGGTCCCACATAAGACCATGTCTGAGACATGGCATTGGCACCGAG
* *
20463595 ATGAGAGGTCCCCCATAAGACCATGTCTGAGACATGGCATAT-GCACCGAT
1 ATGAGAGGTCCCACATAAGACCATGTCTGAGACATGGCAT-TGGCACCGAG
** ** * * *
20463645 ATGAGAACTCCCATGTAAGACCATATCTGGGATATGGCATT
1 ATGAGAGGTCCCACATAAGACCATGTCTGAGACATGGCATT
20463686 TGCAGTACAG
Statistics
Matches: 76, Mismatches: 14, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
49 1 0.01
50 74 0.97
51 1 0.01
ACGTcount: A:0.28, C:0.23, G:0.26, T:0.23
Consensus pattern (50 bp):
ATGAGAGGTCCCACATAAGACCATGTCTGAGACATGGCATTGGCACCGAG
Found at i:20467802 original size:26 final size:26
Alignment explanation
Indices: 20467773--20467830 Score: 80
Period size: 26 Copynumber: 2.2 Consensus size: 26
20467763 TTAACGTGGT
*
20467773 TAAAATCATCAAAATTTTACCGAGGG
1 TAAAATCATCAAAATATTACCGAGGG
* * *
20467799 TAAAATCGTCAAAATATTACCTAGTG
1 TAAAATCATCAAAATATTACCGAGGG
20467825 TAAAAT
1 TAAAAT
20467831 TGGAGTGAGA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.45, C:0.14, G:0.12, T:0.29
Consensus pattern (26 bp):
TAAAATCATCAAAATATTACCGAGGG
Found at i:20471577 original size:14 final size:14
Alignment explanation
Indices: 20471558--20471586 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
20471548 TACATTTTGA
20471558 TGGAGTCATATGTT
1 TGGAGTCATATGTT
20471572 TGGAGTCATATGTT
1 TGGAGTCATATGTT
20471586 T
1 T
20471587 AACTTTCTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.21, C:0.07, G:0.28, T:0.45
Consensus pattern (14 bp):
TGGAGTCATATGTT
Found at i:20473453 original size:40 final size:40
Alignment explanation
Indices: 20473399--20473483 Score: 154
Period size: 40 Copynumber: 2.1 Consensus size: 40
20473389 CCTTTGACTT
*
20473399 TAAAA-CTTTTATCAACCTCTTTAGCTTCAATTTCAATAC
1 TAAAACCTTTTATCAACCTCCTTAGCTTCAATTTCAATAC
20473438 TAAAACCTTTTATCAACCTCCTTAGCTTCAATTTCAATAC
1 TAAAACCTTTTATCAACCTCCTTAGCTTCAATTTCAATAC
20473478 TAAAAC
1 TAAAAC
20473484 AAAAAATTAA
Statistics
Matches: 44, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
39 5 0.11
40 39 0.89
ACGTcount: A:0.35, C:0.25, G:0.02, T:0.38
Consensus pattern (40 bp):
TAAAACCTTTTATCAACCTCCTTAGCTTCAATTTCAATAC
Found at i:20476461 original size:37 final size:37
Alignment explanation
Indices: 20476397--20476505 Score: 114
Period size: 37 Copynumber: 3.0 Consensus size: 37
20476387 TGTACACAAG
* *
20476397 TAATCCAACC-AAAACATGCCAAGTGCTCCAAAGAGA
1 TAATCCAACCGATAACATGCCAAATGCTCCAAAGAGA
** * *
20476433 TAATCCAATTGATAACATGTCAAATGCT-CAGAAGAGT
1 TAATCCAACCGATAACATGCCAAATGCTCCA-AAGAGA
* * *
20476470 TAATCCAACCGATAACACGCCAAATGTTCCGAAGAG
1 TAATCCAACCGATAACATGCCAAATGCTCCAAAGAG
20476506 CTATACATCT
Statistics
Matches: 58, Mismatches: 12, Indels: 5
0.77 0.16 0.07
Matches are distributed among these distances:
36 10 0.17
37 47 0.81
38 1 0.02
ACGTcount: A:0.41, C:0.24, G:0.16, T:0.19
Consensus pattern (37 bp):
TAATCCAACCGATAACATGCCAAATGCTCCAAAGAGA
Found at i:20485795 original size:20 final size:19
Alignment explanation
Indices: 20485734--20485793 Score: 70
Period size: 19 Copynumber: 3.2 Consensus size: 19
20485724 GTCTCTCTCA
20485734 ATAAAAATTACAAAATAATTT
1 ATAAAAATT-CAAAAT-ATTT
*
20485755 -TTAAAATTCAAAATATTT
1 ATAAAAATTCAAAATATTT
*
20485773 ATAAAAATTCTAAA-ATTT
1 ATAAAAATTCAAAATATTT
20485791 ATA
1 ATA
20485794 TATTTTTAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
18 11 0.31
19 17 0.49
20 7 0.20
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.38
Consensus pattern (19 bp):
ATAAAAATTCAAAATATTT
Found at i:20485815 original size:17 final size:18
Alignment explanation
Indices: 20485784--20485817 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
20485774 TAAAAATTCT
*
20485784 AAAATTTATATATTTTTA
1 AAAATTTATAAATTTTTA
20485802 AAAATTT-TAAATTTTT
1 AAAATTTATAAATTTTT
20485818 TTTGCAAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
AAAATTTATAAATTTTTA
Found at i:20487333 original size:18 final size:18
Alignment explanation
Indices: 20487312--20487354 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
20487302 TTTTTCTAAA
*
20487312 CTCTTAACTCTCTCAAGT
1 CTCTCAACTCTCTCAAGT
*
20487330 CTCTCAACTCTCTCAATT
1 CTCTCAACTCTCTCAAGT
20487348 CTCTCAA
1 CTCTCAA
20487355 GTTTTGTTCA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.23, C:0.37, G:0.02, T:0.37
Consensus pattern (18 bp):
CTCTCAACTCTCTCAAGT
Found at i:20487351 original size:11 final size:9
Alignment explanation
Indices: 20487312--20487354 Score: 59
Period size: 9 Copynumber: 4.8 Consensus size: 9
20487302 TTTTTCTAAA
*
20487312 CTCTTAACT
1 CTCTCAACT
*
20487321 CTCTCAAGT
1 CTCTCAACT
20487330 CTCTCAACT
1 CTCTCAACT
*
20487339 CTCTCAATT
1 CTCTCAACT
20487348 CTCTCAA
1 CTCTCAA
20487355 GTTTTGTTCA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 30 1.00
ACGTcount: A:0.23, C:0.37, G:0.02, T:0.37
Consensus pattern (9 bp):
CTCTCAACT
Found at i:20490575 original size:96 final size:96
Alignment explanation
Indices: 20490450--20490653 Score: 354
Period size: 96 Copynumber: 2.1 Consensus size: 96
20490440 TTTCTAGTTA
*
20490450 GATATTTAACTGGACACTAGAAACCCTTATGATCTTTTGAACTACACCAATAACATTGCACAAAA
1 GATATTTAATTGGACACTAGAAACCCTTATGATCTTTTGAACTACACCAATAACATTGCACAAAA
20490515 AGTGATATCTCAATTGTATTCTCACTATTTG
66 AGTGATATCTCAATTGTATTCTCACTATTTG
* * *
20490546 GATATTTAATTTGACATTGGAAACCCTTATGATCTTTTGAACTACACCAATAACATTGCACAAAA
1 GATATTTAATTGGACACTAGAAACCCTTATGATCTTTTGAACTACACCAATAACATTGCACAAAA
* *
20490611 GGTGATATCTCAATTGTATTCTCTCTATTTG
66 AGTGATATCTCAATTGTATTCTCACTATTTG
20490642 GATATTTAATTG
1 GATATTTAATTG
20490654 AAAAAAATGT
Statistics
Matches: 101, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
96 101 1.00
ACGTcount: A:0.34, C:0.18, G:0.12, T:0.36
Consensus pattern (96 bp):
GATATTTAATTGGACACTAGAAACCCTTATGATCTTTTGAACTACACCAATAACATTGCACAAAA
AGTGATATCTCAATTGTATTCTCACTATTTG
Found at i:20504001 original size:581 final size:581
Alignment explanation
Indices: 20502898--20504060 Score: 2308
Period size: 581 Copynumber: 2.0 Consensus size: 581
20502888 AAGACCTAGT
20502898 ACAGATGAAGAGTTAGTTCATGAATTTTATGCCAATTTAACCTCAATCGAATTAACAGAAGTTTC
1 ACAGATGAAGAGTTAGTTCATGAATTTTATGCCAATTTAACCTCAATCGAATTAACAGAAGTTTC
20502963 TGTCCGAGGAATTAAGGTACCAATAACCTCAAACGCTATTAATGAATTCTTTAAATTACCTGATT
66 TGTCCGAGGAATTAAGGTACCAATAACCTCAAACGCTATTAATGAATTCTTTAAATTACCTGATT
20503028 TTGAAGACGATTAATATTCTTCCTTGATGAGAATATTACAGTTCCATGTTCTAAGTGGACTGTTT
131 TTGAAGACGATTAATATTCTTCCTTGATGAGAATATTACAGTTCCATGTTCTAAGTGGACTGTTT
20503093 CAAAGCATGGAACTCACACTTGTCGTAGGGAATATTTGACACCAATAGCGAATGTATGGTTCTAT
196 CAAAGCATGGAACTCACACTTGTCGTAGGGAATATTTGACACCAATAGCGAATGTATGGTTCTAT
* *
20503158 TTCATTTGATTCAGCTTTATGCCTATTTCACATGGGACTATAATTTCATTAGAGCGAATGGTCTT
261 TTCATTTGATTCAGCTTTATGCCTATTTCACACGGGACTACAATTTCATTAGAGCGAATGGTCTT
20503223 GTTATACTCGATTTTTATTACAAAGACCATTGATGTGGGAAAAATCATTCTAAGAGAAATGTGAA
326 GTTATACTCGATTTTTATTACAAAGACCATTGATGTGGGAAAAATCATTCTAAGAGAAATGTGAA
20503288 ATTGTGCCGTTAGACATTTTAGCCTAACTTACTTTCCCTTTACGATAACAATTTTGTGCTTGAAA
391 ATTGTGCCGTTAGACATTTTAGCCTAACTTACTTTCCCTTTACGATAACAATTTTGTGCTTGAAA
20503353 GCTAAAATTCTTGCAAACATAAAGAAGACAGGTTATAGCCAAGCACAATCATAGATTAGGACCTC
456 GCTAAAATTCTTGCAAACATAAAGAAGACAGGTTATAGCCAAGCACAATCATAGATTAGGACCTC
20503418 TACTGAATAGTTTGAGATTCTTATCTACAGCAACGAGTTAAAGAGACTGAGGATCTCGAAG
521 TACTGAATAGTTTGAGATTCTTATCTACAGCAACGAGTTAAAGAGACTGAGGATCTCGAAG
20503479 ACAGATGAAGAGTTAGTTCATGAATTTTATGCCAATTTAACCTCAATCGAATTAACAGAAGTTTC
1 ACAGATGAAGAGTTAGTTCATGAATTTTATGCCAATTTAACCTCAATCGAATTAACAGAAGTTTC
20503544 TGTCCGAGGAATTAAGGTACCAATAACCTCAAACGCTATTAATGAATTCTTTAAATTACCTGATT
66 TGTCCGAGGAATTAAGGTACCAATAACCTCAAACGCTATTAATGAATTCTTTAAATTACCTGATT
20503609 TTGAAGACGATTAATATTCTTCCTTGATGAGAATATTACAGTTCCATGTTCTAAGTGGACTGTTT
131 TTGAAGACGATTAATATTCTTCCTTGATGAGAATATTACAGTTCCATGTTCTAAGTGGACTGTTT
20503674 CAAAGCATGGAACTCACACTTGTCGTAGGGAATATTTGACACCAATAGCGAATGTATGGTTCTAT
196 CAAAGCATGGAACTCACACTTGTCGTAGGGAATATTTGACACCAATAGCGAATGTATGGTTCTAT
20503739 TTCATTTGATTCAGCTTTATGCCTATTTCACACGGGACTACAATTTCATTAGAGCGAATGGTCTT
261 TTCATTTGATTCAGCTTTATGCCTATTTCACACGGGACTACAATTTCATTAGAGCGAATGGTCTT
20503804 GTTATACTCGATTTTTATTACAAAGACCATTGATGTGGGAAAAATCATTCTAAGAGAAATGTGAA
326 GTTATACTCGATTTTTATTACAAAGACCATTGATGTGGGAAAAATCATTCTAAGAGAAATGTGAA
20503869 ATTGTGCCGTTAGACATTTTAGCCTAACTTACTTTCCCTTTACGATAACAATTTTGTGCTTGAAA
391 ATTGTGCCGTTAGACATTTTAGCCTAACTTACTTTCCCTTTACGATAACAATTTTGTGCTTGAAA
20503934 GCTAAAATTCTTGCAAACATAAAGAAGACAGGTTATAGCCAAGCACAATCATAGATTAGGACCTC
456 GCTAAAATTCTTGCAAACATAAAGAAGACAGGTTATAGCCAAGCACAATCATAGATTAGGACCTC
20503999 TACTGAATAGTTTGAGATTCTTATCTACAGCAACGAGTTAAAGAGACTGAGGATCTCGAAG
521 TACTGAATAGTTTGAGATTCTTATCTACAGCAACGAGTTAAAGAGACTGAGGATCTCGAAG
20504060 A
1 A
20504061 AGAAGAATGA
Statistics
Matches: 580, Mismatches: 2, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
581 580 1.00
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
Consensus pattern (581 bp):
ACAGATGAAGAGTTAGTTCATGAATTTTATGCCAATTTAACCTCAATCGAATTAACAGAAGTTTC
TGTCCGAGGAATTAAGGTACCAATAACCTCAAACGCTATTAATGAATTCTTTAAATTACCTGATT
TTGAAGACGATTAATATTCTTCCTTGATGAGAATATTACAGTTCCATGTTCTAAGTGGACTGTTT
CAAAGCATGGAACTCACACTTGTCGTAGGGAATATTTGACACCAATAGCGAATGTATGGTTCTAT
TTCATTTGATTCAGCTTTATGCCTATTTCACACGGGACTACAATTTCATTAGAGCGAATGGTCTT
GTTATACTCGATTTTTATTACAAAGACCATTGATGTGGGAAAAATCATTCTAAGAGAAATGTGAA
ATTGTGCCGTTAGACATTTTAGCCTAACTTACTTTCCCTTTACGATAACAATTTTGTGCTTGAAA
GCTAAAATTCTTGCAAACATAAAGAAGACAGGTTATAGCCAAGCACAATCATAGATTAGGACCTC
TACTGAATAGTTTGAGATTCTTATCTACAGCAACGAGTTAAAGAGACTGAGGATCTCGAAG
Found at i:20512726 original size:7 final size:6
Alignment explanation
Indices: 20512705--20512736 Score: 55
Period size: 6 Copynumber: 5.2 Consensus size: 6
20512695 ATTTTTCAGG
20512705 TCATTT TCATTT TCATTTT TCATTT TCATTT T
1 TCATTT TCATTT TCA-TTT TCATTT TCATTT T
20512737 GGAGAAAACC
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
6 19 0.76
7 6 0.24
ACGTcount: A:0.16, C:0.16, G:0.00, T:0.69
Consensus pattern (6 bp):
TCATTT
Found at i:20512726 original size:13 final size:13
Alignment explanation
Indices: 20512708--20512736 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
20512698 TTTCAGGTCA
20512708 TTTTCATTTTCAT
1 TTTTCATTTTCAT
20512721 TTTTCATTTTCAT
1 TTTTCATTTTCAT
20512734 TTT
1 TTT
20512737 GGAGAAAACC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.14, C:0.14, G:0.00, T:0.72
Consensus pattern (13 bp):
TTTTCATTTTCAT
Found at i:20512840 original size:57 final size:57
Alignment explanation
Indices: 20512721--20512838 Score: 155
Period size: 57 Copynumber: 2.1 Consensus size: 57
20512711 TCATTTTCAT
** * ** *
20512721 TTTTCATTTTCATTTTGGAGAAAACCACATTCATTTCCAAATTATTTTATTTTTCTA
1 TTTTCATTTTCATTTTCAAGAAAACCACAATCATTTCCAAAAGATTTTATTTTTCCA
**
20512778 TTTTCATTTTCATTTTCAAGAAAACCTTAATCATTTCCAAAAGATTCTTATTTTTCCA
1 TTTTCATTTTCATTTTCAAGAAAACCACAATCATTTCCAAAAGATT-TTATTTTTCCA
20512836 TTT
1 TTT
20512839 CACCATTTCT
Statistics
Matches: 52, Mismatches: 8, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
57 39 0.75
58 13 0.25
ACGTcount: A:0.29, C:0.17, G:0.04, T:0.50
Consensus pattern (57 bp):
TTTTCATTTTCATTTTCAAGAAAACCACAATCATTTCCAAAAGATTTTATTTTTCCA
Found at i:20518879 original size:23 final size:23
Alignment explanation
Indices: 20518853--20518899 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 23
20518843 CAGGATGGCG
20518853 CCAAAGTGCCAAG-AACAGGAGCA
1 CCAAAGTG-CAAGTAACAGGAGCA
*
20518876 CCAAAGTGCAAGTAACAGGGGCA
1 CCAAAGTGCAAGTAACAGGAGCA
20518899 C
1 C
20518900 TGATAAGCTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 4 0.18
23 18 0.82
ACGTcount: A:0.40, C:0.26, G:0.28, T:0.06
Consensus pattern (23 bp):
CCAAAGTGCAAGTAACAGGAGCA
Found at i:20519119 original size:30 final size:30
Alignment explanation
Indices: 20519085--20519144 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
20519075 TATTTTTAGA
*
20519085 AGCCACACGGGCTAGG-CACACGCCCGTGTG
1 AGCCACACGGGCT-GGACACACGCCCATGTG
*
20519115 AGCCACATGGGCTGGACACACGCCCATGTG
1 AGCCACACGGGCTGGACACACGCCCATGTG
20519145 CCAGCCCGTG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
29 2 0.07
30 25 0.93
ACGTcount: A:0.22, C:0.35, G:0.32, T:0.12
Consensus pattern (30 bp):
AGCCACACGGGCTGGACACACGCCCATGTG
Found at i:20525996 original size:15 final size:16
Alignment explanation
Indices: 20525976--20526010 Score: 54
Period size: 17 Copynumber: 2.2 Consensus size: 16
20525966 AAGCAATTAC
20525976 GACATG-AAAATATAT
1 GACATGAAAAATATAT
20525991 GACATGAAAAAATATAT
1 GACATG-AAAAATATAT
20526008 GAC
1 GAC
20526011 CATGTTGAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 6 0.33
17 12 0.67
ACGTcount: A:0.54, C:0.09, G:0.14, T:0.23
Consensus pattern (16 bp):
GACATGAAAAATATAT
Found at i:20536298 original size:6 final size:6
Alignment explanation
Indices: 20536287--20536317 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
20536277 GAATGTCGTG
20536287 ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT A
1 ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT A
20536318 CAAATACATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (6 bp):
ATTTTT
Found at i:20537263 original size:14 final size:14
Alignment explanation
Indices: 20537246--20537275 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
20537236 TTTTAAAGAA
*
20537246 TTCTTTTTCATATT
1 TTCTTTTACATATT
20537260 TTCTTTTACATATT
1 TTCTTTTACATATT
20537274 TT
1 TT
20537276 TAAAGGGTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.17, C:0.13, G:0.00, T:0.70
Consensus pattern (14 bp):
TTCTTTTACATATT
Found at i:20537450 original size:6 final size:6
Alignment explanation
Indices: 20537439--20537469 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
20537429 ATTTTTAATA
20537439 TATTTT TATTTT TATTTT TATTTT TATTTT T
1 TATTTT TATTTT TATTTT TATTTT TATTTT T
20537470 TAATAATTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (6 bp):
TATTTT
Found at i:20538280 original size:21 final size:21
Alignment explanation
Indices: 20538256--20538296 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
20538246 ATTATTTTTT
*
20538256 TAAAAAA-ATTTAATGAATTTC
1 TAAAAAATAATTAAT-AATTTC
20538277 TAAAAAATAATTAATAATTT
1 TAAAAAATAATTAATAATTT
20538297 GAAAACTAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.39
Consensus pattern (21 bp):
TAAAAAATAATTAATAATTTC
Found at i:20538339 original size:70 final size:70
Alignment explanation
Indices: 20538252--20538425 Score: 203
Period size: 75 Copynumber: 2.4 Consensus size: 70
20538242 TAATATTATT
* *
20538252 TTTTTAAAAAAATTTAATGAATTTCTAAAAAATAATTAATAA-T-TTGAAAACTAATGTAATTAT
1 TTTTTAAAAATATTTAAT-AATTTATAAAAAATAATTAATAATTATTGAAAACTAATGTAATTAT
20538315 AAAATA
65 AAAATA
*
20538321 TTTTTAAAAATATTT--TAATTTGTAAAATAAAAATAATTAATAATTTGAATTGAAAACTAATGT
1 TTTTTAAAAATATTTAATAA-TT-T-ATA-AAAAATAATTAATAA-TT--ATTGAAAACTAATGT
20538384 AATTATAAAATA
59 AATTATAAAATA
*
20538396 TTTTTAAAAATATTTAATTAATTTGTAAAA
1 TTTTTAAAAATATTTAA-TAATTTATAAAA
20538426 GTATTTTTCA
Statistics
Matches: 88, Mismatches: 5, Indels: 19
0.79 0.04 0.17
Matches are distributed among these distances:
66 2 0.02
67 3 0.03
68 1 0.01
69 15 0.17
70 15 0.17
72 1 0.01
74 3 0.03
75 42 0.48
76 1 0.01
77 2 0.02
78 3 0.03
ACGTcount: A:0.52, C:0.02, G:0.05, T:0.42
Consensus pattern (70 bp):
TTTTTAAAAATATTTAATAATTTATAAAAAATAATTAATAATTATTGAAAACTAATGTAATTATA
AAATA
Found at i:20544876 original size:31 final size:31
Alignment explanation
Indices: 20544805--20544879 Score: 78
Period size: 31 Copynumber: 2.4 Consensus size: 31
20544795 TGAGTTGGTA
* * * *
20544805 CAATTATACACATGACACTTTGATTGTGGTT
1 CAATTATATACATGAAACTTTAATTGTGATT
* ** *
20544836 TAAAAATATACATGAAACTTTAATTTTGATT
1 CAATTATATACATGAAACTTTAATTGTGATT
20544867 CAATTATATACAT
1 CAATTATATACAT
20544880 TTAAAGAAAT
Statistics
Matches: 33, Mismatches: 11, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.39, C:0.12, G:0.09, T:0.40
Consensus pattern (31 bp):
CAATTATATACATGAAACTTTAATTGTGATT
Found at i:20549471 original size:154 final size:156
Alignment explanation
Indices: 20549271--20549570 Score: 516
Period size: 156 Copynumber: 1.9 Consensus size: 156
20549261 GTGTTTTTTC
20549271 ATATACTATTTTTAAAAAATGTATTCATTAAAATTTTTTATTGATGATATGTACAGGATATATTA
1 ATATACTATTTTTAAAAAATGTATTCATTAAAATTTTTTATTGATGATATGTACAGGATATATTA
* **
20549336 TTTATA-GGAGAGAGTGATCCTATGAGA-TTTTTTATTTAATAATTTTATTATTTTTCATTTCCT
66 TTTATAGGGAGAGAGTGATCATATGAGATTTTTTTATTTAATAATTTTATTATTTTTCATTGACT
20549399 TCTATATTAAATTCTTAATAAAGCAA
131 TCTATATTAAATTCTTAATAAAGCAA
* * *
20549425 ATATACTATTTTTTTAAAAATGTATTCATT-AATTTTTTTATTGATGATATGTGCAGGATATATT
1 ATATACTA-TTTTTAAAAAATGTATTCATTAAAATTTTTTATTGATGATATGTACAGGATATATT
20549489 ATTTATAGGGAGAGAGTGATCATATGAGATTTTTTTATTTAATAATTTTATTATTTTTCATTGAC
65 ATTTATAGGGAGAGAGTGATCATATGAGATTTTTTTATTTAATAATTTTATTATTTTTCATTGAC
20549554 TTCTATATTAAATTCTT
130 TTCTATATTAAATTCTT
20549571 TATGGAAAAT
Statistics
Matches: 137, Mismatches: 6, Indels: 4
0.93 0.04 0.03
Matches are distributed among these distances:
154 47 0.34
155 40 0.29
156 50 0.36
ACGTcount: A:0.34, C:0.06, G:0.11, T:0.49
Consensus pattern (156 bp):
ATATACTATTTTTAAAAAATGTATTCATTAAAATTTTTTATTGATGATATGTACAGGATATATTA
TTTATAGGGAGAGAGTGATCATATGAGATTTTTTTATTTAATAATTTTATTATTTTTCATTGACT
TCTATATTAAATTCTTAATAAAGCAA
Found at i:20553443 original size:15 final size:15
Alignment explanation
Indices: 20553423--20553452 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
20553413 CCCAGTAAGT
20553423 GTAACTTTTTGTAAC
1 GTAACTTTTTGTAAC
20553438 GTAACTTTTTGTAAC
1 GTAACTTTTTGTAAC
20553453 ACTCCTAACC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.27, C:0.13, G:0.13, T:0.47
Consensus pattern (15 bp):
GTAACTTTTTGTAAC
Found at i:20556588 original size:42 final size:42
Alignment explanation
Indices: 20556492--20556689 Score: 240
Period size: 42 Copynumber: 4.7 Consensus size: 42
20556482 CAATGTCATA
* * * *
20556492 TCCCAGATATGGTCTTACATGCTATCACATATCGATGCCAATAG
1 TCCCAGACATGGTCTTACACG-AATCACATAACGATGCCAAT-G
*
20556536 --CCAG-CTATGGTCTTACACGAATCTCATAACGATGCCAATG
1 TCCCAGAC-ATGGTCTTACACGAATCACATAACGATGCCAATG
* *
20556576 TCCCAGACATGGTCTTACACGAATCTCATATCGATGCCAATG
1 TCCCAGACATGGTCTTACACGAATCACATAACGATGCCAATG
* *
20556618 TCCCAGACATGGTCTTACACGAATCACATAATGATGTCAATG
1 TCCCAGACATGGTCTTACACGAATCACATAACGATGCCAATG
* *
20556660 TCCCAAACATGATCTTACACGTAATCACAT
1 TCCCAGACATGGTCTTACACG-AATCACAT
20556690 CAAAGTATCC
Statistics
Matches: 137, Mismatches: 12, Indels: 11
0.86 0.08 0.07
Matches are distributed among these distances:
40 1 0.01
41 17 0.12
42 110 0.80
43 9 0.07
ACGTcount: A:0.31, C:0.27, G:0.15, T:0.27
Consensus pattern (42 bp):
TCCCAGACATGGTCTTACACGAATCACATAACGATGCCAATG
Found at i:20560000 original size:45 final size:45
Alignment explanation
Indices: 20559927--20560028 Score: 172
Period size: 45 Copynumber: 2.3 Consensus size: 45
20559917 TACATATGAT
20559927 CACTTATCAC-TTGTCCCTGATCAGATAAGTGTAGCT-AGGCTAC
1 CACTTATCACTTTGTCCCTGATCAGATAAGTGTAGCTAAGGCTAC
*
20559970 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGGCTAC
1 CACTTATCACTTTGTC-CCTGATCAGATAAGTGTAGCTAAGGCTAC
20560016 CACTTATCACTTT
1 CACTTATCACTTT
20560029 NNNNNNNNNN
Statistics
Matches: 55, Mismatches: 1, Indels: 3
0.93 0.02 0.05
Matches are distributed among these distances:
43 10 0.18
44 5 0.09
45 20 0.36
46 20 0.36
ACGTcount: A:0.26, C:0.25, G:0.16, T:0.33
Consensus pattern (45 bp):
CACTTATCACTTTGTCCCTGATCAGATAAGTGTAGCTAAGGCTAC
Found at i:20563620 original size:64 final size:63
Alignment explanation
Indices: 20563510--20563628 Score: 152
Period size: 64 Copynumber: 1.9 Consensus size: 63
20563500 TTTAAACTTA
* * * *
20563510 ATTATTTAAAATTATAAAAAAATATTTTTTAAATTTTAATTAAAAAAGTATAAATTTGTAAAAT
1 ATTATTCAAAATTATAAAAAAATATTTATTAAATTTAAATTAAAAAAATA-AAATTTGTAAAAT
*
20563574 ATTATTCAAATTTAT-AAAAAATATTATATTAAA-TTAAATTAAAAAAAATAAAATT
1 ATTATTCAAAATTATAAAAAAATATT-TATTAAATTTAAATT-AAAAAAATAAAATT
20563629 AATAAAACTA
Statistics
Matches: 48, Mismatches: 5, Indels: 5
0.83 0.09 0.09
Matches are distributed among these distances:
63 21 0.44
64 27 0.56
ACGTcount: A:0.56, C:0.01, G:0.02, T:0.41
Consensus pattern (63 bp):
ATTATTCAAAATTATAAAAAAATATTTATTAAATTTAAATTAAAAAAATAAAATTTGTAAAAT
Found at i:20563635 original size:63 final size:65
Alignment explanation
Indices: 20563510--20563640 Score: 153
Period size: 63 Copynumber: 2.0 Consensus size: 65
20563500 TTTAAACTTA
* * * * **
20563510 ATTATTTAAAATTATAAAAAAATATTTTTTAAATTTTAATTAAAAAAGTATAAATTTGTAAAA-T
1 ATTATTCAAAATTATAAAAAAATATTTATTAAATTTAAATTAAAAAAATATAAATTAATAAAACT
*
20563574 ATTATTCAAATTTAT-AAAAAATATTATATTAAA-TTAAATTAAAAAAA-ATAAAATTAATAAAA
1 ATTATTCAAAATTATAAAAAAATATT-TATTAAATTTAAATTAAAAAAATAT-AAATTAATAAAA
20563636 CT
64 CT
20563638 ATT
1 ATT
20563641 TAAAAATTAA
Statistics
Matches: 57, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
62 2 0.04
63 32 0.56
64 23 0.40
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (65 bp):
ATTATTCAAAATTATAAAAAAATATTTATTAAATTTAAATTAAAAAAATATAAATTAATAAAACT
Found at i:20570329 original size:22 final size:22
Alignment explanation
Indices: 20570287--20570329 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
20570277 AATAGGGGAC
*
20570287 TTCTGTTACTAGTGCTATGATG
1 TTCTGTTACTAGTACTATGATG
* *
20570309 TTCTGTTATTAGTACTTTGAT
1 TTCTGTTACTAGTACTATGAT
20570330 ACTTCGATTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.19, C:0.12, G:0.19, T:0.51
Consensus pattern (22 bp):
TTCTGTTACTAGTACTATGATG
Found at i:20572143 original size:3 final size:3
Alignment explanation
Indices: 20572135--20572169 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
20572125 GTTCCTAGAT
20572135 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
20572170 TATTTATTTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:20575589 original size:59 final size:58
Alignment explanation
Indices: 20575518--20575649 Score: 169
Period size: 61 Copynumber: 2.2 Consensus size: 58
20575508 ATCATTTTAA
* *
20575518 TATTAAATTAATATAATAGTTA-T-CAAGATAAAAATTAGATTAAATTTAATATTAAATC
1 TATTAAAATAATATAATA-TTACTACAAGATAAAAATTAAATTAAATTTAATATTAAA-C
* *
20575576 TTATTAAAATAATAGAATATTATCTACAAGATAAACATTAAATTAAATTTAATATTAAAC
1 -TATTAAAATAATATAATATTA-CTACAAGATAAAAATTAAATTAAATTTAATATTAAAC
*
20575636 CATTAAAATAATAT
1 TATTAAAATAATAT
20575650 CATTTTTGAA
Statistics
Matches: 64, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
58 3 0.05
59 28 0.44
60 2 0.03
61 31 0.48
ACGTcount: A:0.53, C:0.05, G:0.04, T:0.38
Consensus pattern (58 bp):
TATTAAAATAATATAATATTACTACAAGATAAAAATTAAATTAAATTTAATATTAAAC
Found at i:20586663 original size:31 final size:31
Alignment explanation
Indices: 20586625--20587022 Score: 327
Period size: 31 Copynumber: 13.0 Consensus size: 31
20586615 ATATACATAT
*
20586625 TCATATACGAATCAGA-TTCAAG-AATGTATAA
1 TCATATACAAATCA-ATTTC-AGCAATGTATAA
* *
20586656 TCATATACAAATCAATTT-GGCAATGGATAA
1 TCATATACAAATCAATTTCAGCAATGTATAA
* ** * * *
20586686 CCATATATGAATCAAGTTCGGGAATGTATAA
1 TCATATACAAATCAATTTCAGCAATGTATAA
*
20586717 TCATATACAAATTAA-TTCAGCAACT-TAT-A
1 TCATATACAAATCAATTTCAGCAA-TGTATAA
* *
20586746 TCCATATACAATTCAATTTCAACAATGTATAA
1 T-CATATACAAATCAATTTCAGCAATGTATAA
* * *
20586778 CCATATACAAATTAATTTCAGCAAAGTATAA
1 TCATATACAAATCAATTTCAGCAATGTATAA
* **
20586809 TCATATACGAATCAA-TTCAGCAACT-TATCT
1 TCATATACAAATCAATTTCAGCAA-TGTATAA
20586839 TCATATACAAATCAATTTC-GACAATGTATAA
1 TCATATACAAATCAATTTCAG-CAATGTATAA
* *
20586870 CCATATACAAATAAATTTCAGCAATGTATAA
1 TCATATACAAATCAATTTCAGCAATGTATAA
* * * **
20586901 TTATATACGAATCAA-TTCGGCAACT-TATCT
1 TCATATACAAATCAATTTCAGCAA-TGTATAA
* *
20586931 TCATATATAAATCAATTTC-GATAATGTATAA
1 TCATATACAAATCAATTTCAG-CAATGTATAA
* * *
20586962 CCATATACAAATAAATTTCAACAATGTATAA
1 TCATATACAAATCAATTTCAGCAATGTATAA
* * * *
20586993 TTATATACGAATTAA-TTCGGCAATGTATAA
1 TCATATACAAATCAATTTCAGCAATGTATAA
20587023 AACAATCAAA
Statistics
Matches: 291, Mismatches: 58, Indels: 37
0.75 0.15 0.10
Matches are distributed among these distances:
29 3 0.01
30 109 0.37
31 177 0.61
32 2 0.01
ACGTcount: A:0.43, C:0.16, G:0.09, T:0.32
Consensus pattern (31 bp):
TCATATACAAATCAATTTCAGCAATGTATAA
Found at i:20586711 original size:61 final size:61
Alignment explanation
Indices: 20586626--20587022 Score: 297
Period size: 61 Copynumber: 6.5 Consensus size: 61
20586616 TATACATATT
* *
20586626 CATATACGAATCAGA-TTCAAG-AATGTATAATCATATACAAATCAATTTGGCAATGGATAAC
1 CATATACAAATCA-ATTTC-AGCAATGTATAATCATATACAAATCAATTTGGCAATGTATAAC
** * * * * ** *
20586687 CATATATGAATCAAGTTCGGGAATGTATAATCATATACAAATTAATTCAGCAACT-TATATC
1 CATATACAAATCAATTTCAGCAATGTATAATCATATACAAATCAATTTGGCAA-TGTATAAC
* * * * * * *
20586748 CATATACAATTCAATTTCAACAATGTATAACCATATACAAATTAATTTCAGCAAAGTATAAT
1 CATATACAAATCAATTTCAGCAATGTATAATCATATACAAATCAATTT-GGCAATGTATAAC
* ** *
20586810 CATATACGAATCAA-TTCAGCAACT-TATCTTCATATACAAATCAATTTCGACAATGTATAAC
1 CATATACAAATCAATTTCAGCAA-TGTATAATCATATACAAATCAATTT-GGCAATGTATAAC
* * * * ***
20586871 CATATACAAATAAATTTCAGCAATGTATAATTATATACGAATCAATTCGGCAACT-TATCTT
1 CATATACAAATCAATTTCAGCAATGTATAATCATATACAAATCAATTTGGCAA-TGTATAAC
* * * * ** *
20586932 CATATATAAATCAATTTC-GATAATGTATAACCATATACAAATAAATTTCAACAATGTATAAT
1 CATATACAAATCAATTTCAG-CAATGTATAATCATATACAAATCAATTT-GGCAATGTATAAC
* * * *
20586994 TATATACGAATTAA-TTCGGCAATGTATAA
1 CATATACAAATCAATTTCAGCAATGTATAA
20587023 AACAATCAAA
Statistics
Matches: 265, Mismatches: 58, Indels: 26
0.76 0.17 0.07
Matches are distributed among these distances:
60 3 0.01
61 194 0.73
62 68 0.26
ACGTcount: A:0.44, C:0.16, G:0.09, T:0.32
Consensus pattern (61 bp):
CATATACAAATCAATTTCAGCAATGTATAATCATATACAAATCAATTTGGCAATGTATAAC
Found at i:20586782 original size:92 final size:92
Alignment explanation
Indices: 20586625--20587015 Score: 500
Period size: 92 Copynumber: 4.2 Consensus size: 92
20586615 ATATACATAT
** * *
20586625 TCATATACGAATCAGATTCAAG-AA-TGTATAATCATATACAAATCAATTT-GGCAATGGATAAC
1 TCATATACGAATCA-ATTC-AGCAACT-TATCTTCATATACAAATCAATTTCGACAATGTATAAC
** * * * *
20586687 CATATATGAATCAAGTTCGGGAATGTATAA
63 CATATACAAATAAATTTCAGCAATGTATAA
* * * * * *
20586717 TCATATACAAATTAATTCAGCAACTTATATCCATATACAATTCAATTTCAACAATGTATAACCAT
1 TCATATACGAATCAATTCAGCAACTTATCTTCATATACAAATCAATTTCGACAATGTATAACCAT
* *
20586782 ATACAAATTAATTTCAGCAAAGTATAA
66 ATACAAATAAATTTCAGCAATGTATAA
20586809 TCATATACGAATCAATTCAGCAACTTATCTTCATATACAAATCAATTTCGACAATGTATAACCAT
1 TCATATACGAATCAATTCAGCAACTTATCTTCATATACAAATCAATTTCGACAATGTATAACCAT
20586874 ATACAAATAAATTTCAGCAATGTATAA
66 ATACAAATAAATTTCAGCAATGTATAA
* * * *
20586901 TTATATACGAATCAATTCGGCAACTTATCTTCATATATAAATCAATTTCGATAATGTATAACCAT
1 TCATATACGAATCAATTCAGCAACTTATCTTCATATACAAATCAATTTCGACAATGTATAACCAT
*
20586966 ATACAAATAAATTTCAACAATGTATAA
66 ATACAAATAAATTTCAGCAATGTATAA
* * *
20586993 TTATATACGAATTAATTCGGCAA
1 TCATATACGAATCAATTCAGCAA
20587016 TGTATAAAAC
Statistics
Matches: 267, Mismatches: 29, Indels: 6
0.88 0.10 0.02
Matches are distributed among these distances:
90 2 0.01
91 26 0.10
92 239 0.90
ACGTcount: A:0.43, C:0.16, G:0.08, T:0.32
Consensus pattern (92 bp):
TCATATACGAATCAATTCAGCAACTTATCTTCATATACAAATCAATTTCGACAATGTATAACCAT
ATACAAATAAATTTCAGCAATGTATAA
Found at i:20600582 original size:21 final size:21
Alignment explanation
Indices: 20600558--20600601 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
20600548 GTCGTGTTGA
20600558 TATATAAAATCGGTTCTTTTC
1 TATATAAAATCGGTTCTTTTC
*
20600579 TATATAACATCGGTTCTTTTC
1 TATATAAAATCGGTTCTTTTC
20600600 TA
1 TA
20600602 GTTCATTTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.27, C:0.16, G:0.09, T:0.48
Consensus pattern (21 bp):
TATATAAAATCGGTTCTTTTC
Found at i:20620965 original size:38 final size:38
Alignment explanation
Indices: 20620896--20620968 Score: 92
Period size: 38 Copynumber: 1.9 Consensus size: 38
20620886 TGAATATACT
* * *
20620896 AAACGTGCTTAAAAGAGCAATGTCTATTGATTATATTG
1 AAACGTGCTTAAAAGAGCAATATCCACTGATTATATTG
* * *
20620934 AAACTTGCTTAAACGAGCGATATCCACTGATTATA
1 AAACGTGCTTAAAAGAGCAATATCCACTGATTATA
20620969 CAGAATGGGC
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
38 29 1.00
ACGTcount: A:0.37, C:0.15, G:0.16, T:0.32
Consensus pattern (38 bp):
AAACGTGCTTAAAAGAGCAATATCCACTGATTATATTG
Found at i:20621132 original size:135 final size:135
Alignment explanation
Indices: 20620886--20621133 Score: 372
Period size: 135 Copynumber: 1.8 Consensus size: 135
20620876 AGTTGAATAT
* * * *
20620886 TGAATATACTAAACGTGCTTAAAAGAGCAATGTCTATTGATTATATTGAAACTTGCTTAAACGAG
1 TGAATATACTAAACGTGCTCAAAAGAGCAATGTCTATTGATTATACTGAAACTCGCTCAAACGAG
* *
20620951 CGATATCCACTGATTATACAGAATGGGCTCAAATGAGCAATGTCTACTTGTACAAACGAGCAATA
66 CGATATCCACTGATTATACAGAATGGGCTCAAATGAGAAATATCTACTTGTACAAACGAGCAATA
20621016 TCTAC
131 TCTAC
* * * *
20621021 TGAATCTACTAAACGTGCTCAAAAGAGCAATGTTTATTGATTATACTGAAAGTCGGTCAAACGAG
1 TGAATATACTAAACGTGCTCAAAAGAGCAATGTCTATTGATTATACTGAAACTCGCTCAAACGAG
* *
20621086 TGATATTCACTGATTATACTA-AATGGGCTCAAATGAGAAATATCTACT
66 CGATATCCACTGATTATAC-AGAATGGGCTCAAATGAGAAATATCTACT
20621134 GAATATACTG
Statistics
Matches: 100, Mismatches: 12, Indels: 2
0.88 0.11 0.02
Matches are distributed among these distances:
135 99 0.99
136 1 0.01
ACGTcount: A:0.37, C:0.16, G:0.17, T:0.29
Consensus pattern (135 bp):
TGAATATACTAAACGTGCTCAAAAGAGCAATGTCTATTGATTATACTGAAACTCGCTCAAACGAG
CGATATCCACTGATTATACAGAATGGGCTCAAATGAGAAATATCTACTTGTACAAACGAGCAATA
TCTAC
Found at i:20621135 original size:37 final size:37
Alignment explanation
Indices: 20621003--20621252 Score: 182
Period size: 37 Copynumber: 6.7 Consensus size: 37
20620993 TCTACTTGTA
* * * *
20621003 CAAACGAGCAATATCTACTGAATCTACTAAACGTGCT
1 CAAACGAGCAATATCTACTGATTATACTAAATGGGCT
* * * * *
20621040 CAAAAGAGCAATGTTTATTGATTATACTGAAAGTCGG-T
1 CAAACGAGCAATATCTACTGATTATACT-AAA-TGGGCT
**
20621078 CAAACGAGTGATAT-TCACTGATTATACTAAATGGGCT
1 CAAACGAGCAATATCT-ACTGATTATACTAAATGGGCT
* * * * * **
20621115 CAAATGAGAAATATCTACTGAATATACTGAACGTTCT
1 CAAACGAGCAATATCTACTGATTATACTAAATGGGCT
* * * * *
20621152 CAAAAGAGAAATGTATACTGATTATACTAAAAT-TGCT
1 CAAACGAGCAATATCTACTGATTATACT-AAATGGGCT
* * *
20621189 CAAACAAGCAATATCCATTGATTATACTAAATGGGCT
1 CAAACGAGCAATATCTACTGATTATACTAAATGGGCT
** *
20621226 CAAACGAGTGATATCTACTAATTATAC
1 CAAACGAGCAATATCTACTGATTATAC
20621253 GGAATGCATG
Statistics
Matches: 162, Mismatches: 44, Indels: 14
0.74 0.20 0.06
Matches are distributed among these distances:
36 7 0.04
37 126 0.78
38 28 0.17
39 1 0.01
ACGTcount: A:0.40, C:0.16, G:0.15, T:0.29
Consensus pattern (37 bp):
CAAACGAGCAATATCTACTGATTATACTAAATGGGCT
Found at i:20626206 original size:19 final size:21
Alignment explanation
Indices: 20626163--20626214 Score: 63
Period size: 20 Copynumber: 2.5 Consensus size: 21
20626153 ATATTTTTCT
* *
20626163 TTTATATTTTTAATCACTATT
1 TTTATATTTTTAATCAATATA
20626184 TTTA-ATTTTTAAT-AATATA
1 TTTATATTTTTAATCAATATA
20626203 TTTATATCTTTT
1 TTTATAT-TTTT
20626215 GCATAGGAGT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
19 8 0.30
20 11 0.41
21 8 0.30
ACGTcount: A:0.31, C:0.06, G:0.00, T:0.63
Consensus pattern (21 bp):
TTTATATTTTTAATCAATATA
Found at i:20626638 original size:11 final size:11
Alignment explanation
Indices: 20626574--20626639 Score: 52
Period size: 10 Copynumber: 6.2 Consensus size: 11
20626564 AAAAATAAAT
20626574 AAATTATA-AA
1 AAATTATATAA
20626584 AAATTGA-A-AA
1 AAATT-ATATAA
*
20626594 AAACTTATTTAA
1 AAA-TTATATAA
*
20626606 AAACTA-ATAGA
1 AAATTATATA-A
20626617 AAATTAT-TAA
1 AAATTATATAA
20626627 AAATTATATAA
1 AAATTATATAA
20626638 AA
1 AA
20626640 TTTAAAAATA
Statistics
Matches: 45, Mismatches: 4, Indels: 13
0.73 0.06 0.21
Matches are distributed among these distances:
10 22 0.49
11 18 0.40
12 5 0.11
ACGTcount: A:0.64, C:0.03, G:0.03, T:0.30
Consensus pattern (11 bp):
AAATTATATAA
Found at i:20626694 original size:19 final size:19
Alignment explanation
Indices: 20626670--20626711 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
20626660 GAAGAAATAT
* * *
20626670 AAAAATTTTAAAATTTTAA
1 AAAAATTATAAAAGTGTAA
20626689 AAAAATTATAAAAGTGTAA
1 AAAAATTATAAAAGTGTAA
20626708 AAAA
1 AAAA
20626712 GTATAAAAAC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.64, C:0.00, G:0.05, T:0.31
Consensus pattern (19 bp):
AAAAATTATAAAAGTGTAA
Found at i:20634872 original size:30 final size:30
Alignment explanation
Indices: 20634838--20634894 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 30
20634828 CTTGATTTGG
20634838 ACTTTGGCAAAATTATGA-TTTTGTCCCTAA
1 ACTTTGGCAAAATTAT-ACTTTTGTCCCTAA
* * *
20634868 ACTTTTGCATATTTATACTTTTGTCCC
1 ACTTTGGCAAAATTATACTTTTGTCCC
20634895 AAAGCTTGGA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
29 1 0.04
30 22 0.96
ACGTcount: A:0.25, C:0.19, G:0.11, T:0.46
Consensus pattern (30 bp):
ACTTTGGCAAAATTATACTTTTGTCCCTAA
Found at i:20641875 original size:50 final size:49
Alignment explanation
Indices: 20641791--20641952 Score: 159
Period size: 50 Copynumber: 3.3 Consensus size: 49
20641781 ATGCAAGGCT
* * * *
20641791 TAATT-AGATGCAAACTAAATAAACAAATGAGTTACATAATGCATGACA
1 TAATTAAGATGCAAACTTAATTAACATAGGAGTTACATAATGCATGACA
*
20641839 TAATTTAAGATGCAAACTTAATTAACATAGGTGTTACATAATGCATGACA
1 TAA-TTAAGATGCAAACTTAATTAACATAGGAGTTACATAATGCATGACA
* ** * * * * *
20641889 TAATTAAAACACAAACTTTATTAACAT-GTGAGATGCTTTAATGCATGACT
1 TAATTAAGATGCAAACTTAATTAACATAG-GAGTTAC-ATAATGCATGACA
20641939 TAATTAA-ATGCAAA
1 TAATTAAGATGCAAA
20641953 ACACATAATG
Statistics
Matches: 94, Mismatches: 16, Indels: 7
0.80 0.14 0.06
Matches are distributed among these distances:
48 4 0.04
49 31 0.33
50 59 0.63
ACGTcount: A:0.45, C:0.12, G:0.12, T:0.30
Consensus pattern (49 bp):
TAATTAAGATGCAAACTTAATTAACATAGGAGTTACATAATGCATGACA
Found at i:20651065 original size:25 final size:24
Alignment explanation
Indices: 20651005--20651070 Score: 69
Period size: 25 Copynumber: 2.7 Consensus size: 24
20650995 CTCCTAAATT
* *
20651005 TTAATTTAATTATCTAATTTTTTAA
1 TTAATTAAATTAT-TAATATTTTAA
* *
20651030 TTTATTGAATTATTAATATTTTATA
1 TTAATTAAATTATTAATATTTTA-A
*
20651055 TTAATTAAATTTTTAA
1 TTAATTAAATTATTAA
20651071 GAAAATAATT
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
24 9 0.26
25 25 0.74
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.59
Consensus pattern (24 bp):
TTAATTAAATTATTAATATTTTAA
Found at i:20655259 original size:18 final size:18
Alignment explanation
Indices: 20655236--20655271 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
20655226 TGAAAATACG
20655236 TGTTTGTCT-TGAAAACAT
1 TGTTTGT-TGTGAAAACAT
20655254 TGTTTGTTGTGAAAACAT
1 TGTTTGTTGTGAAAACAT
20655272 ATTTGTTTCC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 1 0.06
18 16 0.94
ACGTcount: A:0.28, C:0.08, G:0.19, T:0.44
Consensus pattern (18 bp):
TGTTTGTTGTGAAAACAT
Found at i:20655278 original size:17 final size:18
Alignment explanation
Indices: 20655245--20655278 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
20655235 GTGTTTGTCT
*
20655245 TGAAAACATTGTTTGTTG
1 TGAAAACATTATTTGTTG
20655263 TGAAAACA-TATTTGTT
1 TGAAAACATTATTTGTT
20655279 TCCGTTAAGC
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:0.32, C:0.06, G:0.18, T:0.44
Consensus pattern (18 bp):
TGAAAACATTATTTGTTG
Found at i:20655837 original size:27 final size:27
Alignment explanation
Indices: 20655802--20655866 Score: 89
Period size: 27 Copynumber: 2.4 Consensus size: 27
20655792 AGCAGAGCTG
20655802 CCAGT-ACAGT-ATATGTGGCAAAGCCA
1 CCAGTAACAGTAAT-TGTGGCAAAGCCA
*
20655828 CCAGTAACAGTAATTGTGGCAGAGCCA
1 CCAGTAACAGTAATTGTGGCAAAGCCA
*
20655855 CCAATAACAGTA
1 CCAGTAACAGTA
20655867 CTTCTTCCAT
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
26 5 0.14
27 28 0.80
28 2 0.06
ACGTcount: A:0.37, C:0.23, G:0.22, T:0.18
Consensus pattern (27 bp):
CCAGTAACAGTAATTGTGGCAAAGCCA
Found at i:20670156 original size:11 final size:11
Alignment explanation
Indices: 20670140--20670164 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
20670130 CATCAAAAAA
20670140 ATTATTTTAAT
1 ATTATTTTAAT
20670151 ATTATTTTAAT
1 ATTATTTTAAT
20670162 ATT
1 ATT
20670165 TACAACATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (11 bp):
ATTATTTTAAT
Found at i:20679066 original size:15 final size:14
Alignment explanation
Indices: 20679032--20679067 Score: 54
Period size: 14 Copynumber: 2.5 Consensus size: 14
20679022 GTAGATTTTG
*
20679032 ATGATTTTTGAGTC
1 ATGATTTTTGAGTA
20679046 ATGATTTTTGAGTA
1 ATGATTTTTGAGTA
20679060 ATGGATTT
1 AT-GATTT
20679068 AGCCATTATG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
14 15 0.75
15 5 0.25
ACGTcount: A:0.25, C:0.03, G:0.22, T:0.50
Consensus pattern (14 bp):
ATGATTTTTGAGTA
Found at i:20679712 original size:12 final size:12
Alignment explanation
Indices: 20679695--20679720 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
20679685 GCTATTACAA
20679695 GGCCTAGCACAC
1 GGCCTAGCACAC
20679707 GGCCTAGCACAC
1 GGCCTAGCACAC
20679719 GG
1 GG
20679721 GCGTGTGAGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.23, C:0.38, G:0.31, T:0.08
Consensus pattern (12 bp):
GGCCTAGCACAC
Found at i:20693138 original size:28 final size:28
Alignment explanation
Indices: 20693098--20693154 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
20693088 GACCAGTTGA
20693098 AAGCACTATTGATCGAAGTACCCGTTCT
1 AAGCACTATTGATCGAAGTACCCGTTCT
20693126 AAGCACTATTGATCGAAGTACCCGTTCT
1 AAGCACTATTGATCGAAGTACCCGTTCT
20693154 A
1 A
20693155 GTTTAACCTG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.30, C:0.25, G:0.18, T:0.28
Consensus pattern (28 bp):
AAGCACTATTGATCGAAGTACCCGTTCT
Found at i:20696179 original size:39 final size:39
Alignment explanation
Indices: 20696125--20696357 Score: 333
Period size: 39 Copynumber: 6.0 Consensus size: 39
20696115 TAGTAGAAAA
20696125 CTGTTGTACTTCGGTACCCCTGAAT-GCACTTACGTGCCC
1 CTGTTGTACTTCGGTACCCCTG-ATCGCACTTACGTGCCC
*
20696164 CTGTTGTACTTCGGTACCCCTGATCGCACTTACATGCCC
1 CTGTTGTACTTCGGTACCCCTGATCGCACTTACGTGCCC
* * * *
20696203 CGGTTGTACTTCGATACCCCTGATCGCTCTTAAGTGCCC
1 CTGTTGTACTTCGGTACCCCTGATCGCACTTACGTGCCC
* * *
20696242 TTGTTGTACTTCGGTACCCTTGATCACACTTACGTGCCC
1 CTGTTGTACTTCGGTACCCCTGATCGCACTTACGTGCCC
* *
20696281 CTATTGTACTTCAGTACCCCTGATCGCACTTACGTGCCC
1 CTGTTGTACTTCGGTACCCCTGATCGCACTTACGTGCCC
* * *
20696320 CTGTTGTACTTCGCTACCCTTGATCGCACTTTCGTGCC
1 CTGTTGTACTTCGGTACCCCTGATCGCACTTACGTGCC
20696358 GTGGTTACGT
Statistics
Matches: 170, Mismatches: 23, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
38 2 0.01
39 168 0.99
ACGTcount: A:0.15, C:0.34, G:0.18, T:0.33
Consensus pattern (39 bp):
CTGTTGTACTTCGGTACCCCTGATCGCACTTACGTGCCC
Found at i:20700703 original size:70 final size:70
Alignment explanation
Indices: 20700612--20700815 Score: 223
Period size: 70 Copynumber: 2.9 Consensus size: 70
20700602 GTATGCCTAG
* * *
20700612 CACTATTCGAACGA-TTCGACAAATTATTACGCCCAGCGCTAGTAGGATAACCGACGATACTTGT
1 CACTAGTCGAACGAGTT-GACAAATTATTACGCCCAGCGCTAGTAGGATAACTGACGATAGTTGT
20700676 GCCCAT
65 GCCCAT
* * * * * * *
20700682 CACTAGTCGAATGAGTTGACAAATTAGTACGCCCAGTGCTACTCA-GATAACTGGCAATAGTTAT
1 CACTAGTCGAACGAGTTGACAAATTATTACGCCCAGCGCTAGT-AGGATAACTGACGATAGTTGT
*
20700746 GTCCAT
65 GCCCAT
* * * * * *
20700752 CACTAGTCAAACAAGTTAACAAATTATTGCGCCCAGCACTAGTCGGATAACTGACGATAGTTGT
1 CACTAGTCGAACGAGTTGACAAATTATTACGCCCAGCGCTAGTAGGATAACTGACGATAGTTGT
20700816 CATCCGCAAT
Statistics
Matches: 107, Mismatches: 24, Indels: 6
0.78 0.18 0.04
Matches are distributed among these distances:
70 104 0.97
71 3 0.03
ACGTcount: A:0.32, C:0.24, G:0.19, T:0.25
Consensus pattern (70 bp):
CACTAGTCGAACGAGTTGACAAATTATTACGCCCAGCGCTAGTAGGATAACTGACGATAGTTGTG
CCCAT
Found at i:20708117 original size:42 final size:43
Alignment explanation
Indices: 20708069--20708160 Score: 141
Period size: 42 Copynumber: 2.2 Consensus size: 43
20708059 AATATTATTA
* *
20708069 TTTAATATTTACGATTCAATTATAATATTATATTGACTTTTAG
1 TTTAATATTTACGAGTCAATTATAATATTATATTGAATTTTAG
* *
20708112 -TTAATATTTATGAGTCAATTATAATATTATATTGAATTTTTG
1 TTTAATATTTACGAGTCAATTATAATATTATATTGAATTTTAG
20708154 TTTAATA
1 TTTAATA
20708161 ATTTTTGCAA
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
42 38 0.86
43 6 0.14
ACGTcount: A:0.36, C:0.04, G:0.08, T:0.52
Consensus pattern (43 bp):
TTTAATATTTACGAGTCAATTATAATATTATATTGAATTTTAG
Found at i:20709054 original size:19 final size:19
Alignment explanation
Indices: 20709030--20709072 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
20709020 ACTAAATTGA
*
20709030 ATAAAA-GGTAAAATTTTAG
1 ATAAAATGGTAAAATGTT-G
*
20709049 ATAAAATTGTAAAATGTTG
1 ATAAAATGGTAAAATGTTG
20709068 ATAAA
1 ATAAA
20709073 GAGTCAAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 12 0.57
20 9 0.43
ACGTcount: A:0.53, C:0.00, G:0.14, T:0.33
Consensus pattern (19 bp):
ATAAAATGGTAAAATGTTG
Found at i:20724138 original size:19 final size:19
Alignment explanation
Indices: 20724114--20724152 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
20724104 TTTTATTTGA
20724114 ACCTTTGCAATATTTAGTC
1 ACCTTTGCAATATTTAGTC
20724133 ACCTTTGCAATATTTAGTC
1 ACCTTTGCAATATTTAGTC
20724152 A
1 A
20724153 TCACTTCTCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.28, C:0.21, G:0.10, T:0.41
Consensus pattern (19 bp):
ACCTTTGCAATATTTAGTC
Found at i:20727079 original size:22 final size:22
Alignment explanation
Indices: 20727051--20727098 Score: 69
Period size: 22 Copynumber: 2.2 Consensus size: 22
20727041 CCACTACCAA
*
20727051 ACCATCATACCACTACCTTAGC
1 ACCATCATACCACAACCTTAGC
* *
20727073 ACCATCATACTACAACCTTTGC
1 ACCATCATACCACAACCTTAGC
20727095 ACCA
1 ACCA
20727099 CCTTGAAACA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.33, C:0.40, G:0.04, T:0.23
Consensus pattern (22 bp):
ACCATCATACCACAACCTTAGC
Done.