Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr3
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: 36364294
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 2168405 characters in sequence are not A, C, G, or T
File 18 of 91
Found at i:5835785 original size:15 final size:15
Alignment explanation
Indices: 5835765--5835795 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
5835755 TTAAATCGCA
5835765 ACTCAAATTGAGAGT
1 ACTCAAATTGAGAGT
*
5835780 ACTCAAATTGTGAGT
1 ACTCAAATTGAGAGT
5835795 A
1 A
5835796 AAGGTTAGGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.39, C:0.13, G:0.19, T:0.29
Consensus pattern (15 bp):
ACTCAAATTGAGAGT
Found at i:5835952 original size:45 final size:45
Alignment explanation
Indices: 5835858--5835954 Score: 106
Period size: 45 Copynumber: 2.2 Consensus size: 45
5835848 GTTGCTATGG
* * * * *
5835858 TGAGGGTTAAGGTTAAGGTTTCGATTAGGAATTGGGGACTTAGGG
1 TGAGGGTCAAGATTAAGGTTTCGATTAGGAATTAGGGACTTAAGA
* * *
5835903 TGAGGGTCAAGATTAGGGTTTCGCTTA-GAATTTAGGGATTTAAGA
1 TGAGGGTCAAGATTAAGGTTTCGATTAGGAA-TTAGGGACTTAAGA
5835948 TGAGGGT
1 TGAGGGT
5835955 AGGGTTTTAT
Statistics
Matches: 43, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
44 3 0.07
45 40 0.93
ACGTcount: A:0.26, C:0.05, G:0.37, T:0.32
Consensus pattern (45 bp):
TGAGGGTCAAGATTAAGGTTTCGATTAGGAATTAGGGACTTAAGA
Found at i:5838311 original size:6 final size:6
Alignment explanation
Indices: 5838300--5838345 Score: 56
Period size: 6 Copynumber: 7.7 Consensus size: 6
5838290 TTCAAGTATT
* * * *
5838300 GGTAGA GGTAGA GTTAAA GGTAAA GGTAGA GGTAGA GGTAAA GGTA
1 GGTAGA GGTAGA GGTAGA GGTAGA GGTAGA GGTAGA GGTAGA GGTA
5838346 AAAGACCTTC
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 35 1.00
ACGTcount: A:0.39, C:0.00, G:0.41, T:0.20
Consensus pattern (6 bp):
GGTAGA
Found at i:5838326 original size:18 final size:18
Alignment explanation
Indices: 5838300--5838345 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 18
5838290 TTCAAGTATT
* *
5838300 GGTAGAGGTAGAGTTAAA
1 GGTAAAGGTAGAGGTAAA
*
5838318 GGTAAAGGTAGAGGTAGA
1 GGTAAAGGTAGAGGTAAA
5838336 GGTAAAGGTA
1 GGTAAAGGTA
5838346 AAAGACCTTC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.39, C:0.00, G:0.41, T:0.20
Consensus pattern (18 bp):
GGTAAAGGTAGAGGTAAA
Found at i:5838332 original size:24 final size:24
Alignment explanation
Indices: 5838300--5838347 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
5838290 TTCAAGTATT
*
5838300 GGTAGAGGTAGAGTTAAAGGTAAA
1 GGTAGAGGTAGAGGTAAAGGTAAA
5838324 GGTAGAGGTAGAGGTAAAGGTAAA
1 GGTAGAGGTAGAGGTAAAGGTAAA
5838348 AGACCTTCTG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.42, C:0.00, G:0.40, T:0.19
Consensus pattern (24 bp):
GGTAGAGGTAGAGGTAAAGGTAAA
Found at i:5842061 original size:28 final size:27
Alignment explanation
Indices: 5842027--5842079 Score: 81
Period size: 28 Copynumber: 1.9 Consensus size: 27
5842017 TTTGGAATAA
5842027 AAGGGTAAAA-TGATAATTTTGCCACCTC
1 AAGGGTAAAATTG-TAATTTT-CCACCTC
5842055 AAGGGTAAAATTGTAATTTTCCACC
1 AAGGGTAAAATTGTAATTTTCCACC
5842080 ATCAGGACAT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
27 5 0.21
28 17 0.71
29 2 0.08
ACGTcount: A:0.36, C:0.17, G:0.17, T:0.30
Consensus pattern (27 bp):
AAGGGTAAAATTGTAATTTTCCACCTC
Found at i:5849939 original size:20 final size:20
Alignment explanation
Indices: 5849914--5849959 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
5849904 TTTTGACCCC
*
5849914 ATTTGACTTATTGGAGTATA
1 ATTTGACTTATTGAAGTATA
*
5849934 ATTTGACTTATTGAAGTATG
1 ATTTGACTTATTGAAGTATA
5849954 ATTTGA
1 ATTTGA
5849960 GGTTTAGAAG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.30, C:0.04, G:0.20, T:0.46
Consensus pattern (20 bp):
ATTTGACTTATTGAAGTATA
Found at i:5850035 original size:28 final size:27
Alignment explanation
Indices: 5850004--5850056 Score: 79
Period size: 28 Copynumber: 1.9 Consensus size: 27
5849994 TTTGGAGTAT
*
5850004 AGGGGTAAAATGGTAATTTTGCCACCTC
1 AGGGGCAAAATGGTAATTTT-CCACCTC
*
5850032 AGGGGCAAAATTGTAATTTTCCACC
1 AGGGGCAAAATGGTAATTTTCCACC
5850057 ACCAGGATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
27 5 0.22
28 18 0.78
ACGTcount: A:0.30, C:0.19, G:0.23, T:0.28
Consensus pattern (27 bp):
AGGGGCAAAATGGTAATTTTCCACCTC
Found at i:5850062 original size:28 final size:28
Alignment explanation
Indices: 5850004--5850062 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 28
5849994 TTTGGAGTAT
* *
5850004 AGGGGTAAAATGGTAATTTTGCCACCTC
1 AGGGGCAAAATGGTAATTTTGCCACCCC
*
5850032 AGGGGCAAAATTGTAATTTT-CCACCACC
1 AGGGGCAAAATGGTAATTTTGCCACC-CC
5850060 AGG
1 AGG
5850063 ATATTTTTTC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
27 5 0.19
28 22 0.81
ACGTcount: A:0.31, C:0.20, G:0.24, T:0.25
Consensus pattern (28 bp):
AGGGGCAAAATGGTAATTTTGCCACCCC
Found at i:5878176 original size:20 final size:20
Alignment explanation
Indices: 5878133--5878178 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
5878123 TTTTGGCCCC
*
5878133 ATTTGACTCATTGGAGTGTA
1 ATTTGACTCATTGGAGTATA
* *
5878153 ATTTGACTTATTGGAGTATG
1 ATTTGACTCATTGGAGTATA
5878173 ATTTGA
1 ATTTGA
5878179 GGTTTATAAG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.26, C:0.07, G:0.24, T:0.43
Consensus pattern (20 bp):
ATTTGACTCATTGGAGTATA
Found at i:5881737 original size:8 final size:8
Alignment explanation
Indices: 5881720--5881752 Score: 57
Period size: 8 Copynumber: 4.1 Consensus size: 8
5881710 GTGTGGGATT
*
5881720 TCAAGGAA
1 TCAAGCAA
5881728 TCAAGCAA
1 TCAAGCAA
5881736 TCAAGCAA
1 TCAAGCAA
5881744 TCAAGCAA
1 TCAAGCAA
5881752 T
1 T
5881753 TAAAGGTAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 24 1.00
ACGTcount: A:0.48, C:0.21, G:0.15, T:0.15
Consensus pattern (8 bp):
TCAAGCAA
Found at i:5882055 original size:10 final size:10
Alignment explanation
Indices: 5882020--5882058 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
5882010 TTGTGGCTGA
5882020 ATTTGATGAT
1 ATTTGATGAT
*
5882030 ATTTCATGAT
1 ATTTGATGAT
*
5882040 ATTTTGGTGAT
1 A-TTTGATGAT
5882051 ATTTGATG
1 ATTTGATG
5882059 TTTGGTGAGG
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
10 16 0.67
11 8 0.33
ACGTcount: A:0.26, C:0.03, G:0.21, T:0.51
Consensus pattern (10 bp):
ATTTGATGAT
Found at i:5884258 original size:59 final size:58
Alignment explanation
Indices: 5884148--5884302 Score: 186
Period size: 59 Copynumber: 2.7 Consensus size: 58
5884138 TGATAGCTTT
* * * * *
5884148 AACATGTTTGTCTTAATTTGGATAA-AAAAACATGTTTGGTCTTAATTTAGACAAGAA
1 AACATGTTTGTCTTAATTTAGACAAGAAAAATATTTTTGGTCTTAATCTAGACAAGAA
* * *
5884205 AATATGTTTGTCTTAATTAAAGACAAGAAAAATATTTTTTGTCTTAATCTAGACAAGAA
1 AACATGTTTGTCTTAATT-TAGACAAGAAAAATATTTTTGGTCTTAATCTAGACAAGAA
* * *
5884264 AACATATTTATCTCAATTTAGACAAGATAAAATATTTTT
1 AACATGTTTGTCTTAATTTAGACAAGA-AAAATATTTTT
5884303 ATTTTAATTA
Statistics
Matches: 82, Mismatches: 13, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
57 17 0.21
58 12 0.15
59 53 0.65
ACGTcount: A:0.41, C:0.09, G:0.12, T:0.38
Consensus pattern (58 bp):
AACATGTTTGTCTTAATTTAGACAAGAAAAATATTTTTGGTCTTAATCTAGACAAGAA
Found at i:5884298 original size:28 final size:28
Alignment explanation
Indices: 5884148--5884300 Score: 139
Period size: 28 Copynumber: 5.3 Consensus size: 28
5884138 TGATAGCTTT
* * * *
5884148 AACATGTTTGTCTTAATTTGGATAAAAA
1 AACATATTTGTCTTAATTTAGACAAGAA
*
5884176 AACATGTTTGGTCTTAATTTAGACAAGAA
1 AACATATTT-GTCTTAATTTAGACAAGAA
* * *
5884205 AATATGTTTGTCTTAATTAAAGACAAGAA
1 AACATATTTGTCTTAATT-TAGACAAGAA
*
5884234 AA-ATATTTTTTGTCTTAATCTAGACAAGAA
1 AACATA---TTTGTCTTAATTTAGACAAGAA
* *
5884264 AACATATTTATCTCAATTTAGACAAGATA
1 AACATATTTGTCTTAATTTAGACAAGA-A
5884293 AA-ATATTT
1 AACATATTT
5884301 TTATTTTAAT
Statistics
Matches: 107, Mismatches: 11, Indels: 14
0.81 0.08 0.11
Matches are distributed among these distances:
28 44 0.41
29 38 0.36
30 11 0.10
31 14 0.13
ACGTcount: A:0.42, C:0.09, G:0.12, T:0.37
Consensus pattern (28 bp):
AACATATTTGTCTTAATTTAGACAAGAA
Found at i:5884691 original size:14 final size:15
Alignment explanation
Indices: 5884667--5884695 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
5884657 ATAAAAAAAG
5884667 AAGAGAATGGAAGTA
1 AAGAGAATGGAAGTA
5884682 AAGA-AATGGAAGTA
1 AAGAGAATGGAAGTA
5884696 CTTTTTTTGG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.55, C:0.00, G:0.31, T:0.14
Consensus pattern (15 bp):
AAGAGAATGGAAGTA
Found at i:5885640 original size:6 final size:6
Alignment explanation
Indices: 5885614--5885643 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
5885604 TAGATGTTGA
*
5885614 TGGTGT TGATGT TGGTGT TGGTGT TGGTGT
1 TGGTGT TGGTGT TGGTGT TGGTGT TGGTGT
5885644 CTCACTAGTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.03, C:0.00, G:0.47, T:0.50
Consensus pattern (6 bp):
TGGTGT
Found at i:5885851 original size:85 final size:85
Alignment explanation
Indices: 5885716--5886118 Score: 553
Period size: 85 Copynumber: 4.8 Consensus size: 85
5885706 ATTAATTCAA
* * *
5885716 AATGTTTAATTCTAGCATATTGCCAATCATTTTAATTAAAAATCTAAACAATAATTCTTAACATT
1 AATGTTTAATTCTAGCATATTACCAATCATTTTAATTAAAAATCCAAACAATAATTCTAAACATT
5885781 AATTCCCAAACATAATTCTT
66 AATTCCCAAACATAATTCTT
* ** * * *
5885801 AATTTTTAATTCTAGCATATTGTCAATCATTTTAATTGAAAATCCAAACAATAACTCTAAATATT
1 AATGTTTAATTCTAGCATATTACCAATCATTTTAATTAAAAATCCAAACAATAATTCTAAACATT
*
5885866 AATTCCCAAACATAATTTTT
66 AATTCCCAAACATAATTCTT
* * *** *
5885886 AATGTTTAGTTCTAACATATTACCAATCATTTTAATTAATTGTCCAAACAATAATTCTAAGCATT
1 AATGTTTAATTCTAGCATATTACCAATCATTTTAATTAAAAATCCAAACAATAATTCTAAACATT
* *
5885951 AATTTCCAAACATAATTTTT
66 AATTCCCAAACATAATTCTT
*
5885971 AATGTTTAGTTCTAGCATATTACCAATCATTTTAATTAAAAATCCAAACAATAATTCTAAACATT
1 AATGTTTAATTCTAGCATATTACCAATCATTTTAATTAAAAATCCAAACAATAATTCTAAACATT
5886036 AATTCCCAAACATAATTCTT
66 AATTCCCAAACATAATTCTT
* * * ** *
5886056 AATGTTTAATTCTA--ACA-T-CAAATCACTTTAATTAATTATCCAAACAATAATTCTAAACGTT
1 AATGTTTAATTCTAGCATATTACCAATCATTTTAATTAAAAATCCAAACAATAATTCTAAACATT
5886117 AA
66 AA
5886119 GCTCTTTGAA
Statistics
Matches: 283, Mismatches: 35, Indels: 4
0.88 0.11 0.01
Matches are distributed among these distances:
81 40 0.14
82 1 0.00
83 2 0.01
85 240 0.85
ACGTcount: A:0.41, C:0.16, G:0.04, T:0.39
Consensus pattern (85 bp):
AATGTTTAATTCTAGCATATTACCAATCATTTTAATTAAAAATCCAAACAATAATTCTAAACATT
AATTCCCAAACATAATTCTT
Found at i:5890382 original size:10 final size:10
Alignment explanation
Indices: 5890367--5890418 Score: 50
Period size: 10 Copynumber: 4.9 Consensus size: 10
5890357 TTCAATATTT
5890367 CAACAACTTA
1 CAACAACTTA
5890377 CAACAACCTTTA
1 CAACAA-C-TTA
* * *
5890389 CATTCAAATTT
1 CA-ACAACTTA
5890400 CAACAACTTA
1 CAACAACTTA
5890410 CAACAACTT
1 CAACAACTT
5890419 TTGCATTCAA
Statistics
Matches: 33, Mismatches: 6, Indels: 6
0.73 0.13 0.13
Matches are distributed among these distances:
10 20 0.61
11 5 0.15
12 5 0.15
13 3 0.09
ACGTcount: A:0.44, C:0.29, G:0.00, T:0.27
Consensus pattern (10 bp):
CAACAACTTA
Found at i:5890439 original size:34 final size:34
Alignment explanation
Indices: 5890323--5890454 Score: 173
Period size: 33 Copynumber: 4.0 Consensus size: 34
5890313 TAATTATGCC
* *
5890323 CATTCAATATATTCAA-TA-TTCCAACAA-TTTTG
1 CATTCAATAT-TTCAACAACTTACAACAACTTTTG
* *
5890355 CATTCAATATTTCAACAACTTACAACAACCTTTA
1 CATTCAATATTTCAACAACTTACAACAACTTTTG
5890389 CATTCAA-ATTTCAACAACTTACAACAACTTTTG
1 CATTCAATATTTCAACAACTTACAACAACTTTTG
**
5890422 CATTCAATATTTCAACAACACACAACAACTTTT
1 CATTCAATATTTCAACAACTTACAACAACTTTT
5890455 ATCAAACAAA
Statistics
Matches: 88, Mismatches: 8, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
31 5 0.06
32 11 0.12
33 39 0.44
34 33 0.38
ACGTcount: A:0.40, C:0.24, G:0.02, T:0.34
Consensus pattern (34 bp):
CATTCAATATTTCAACAACTTACAACAACTTTTG
Found at i:5890617 original size:36 final size:36
Alignment explanation
Indices: 5890570--5890646 Score: 136
Period size: 36 Copynumber: 2.1 Consensus size: 36
5890560 TTCATTTTTT
*
5890570 CTTCCTCTCTTCCCATGTTTTGCACCTACTGGAGAA
1 CTTCCTCTCTTCCCATGTTTTGCACCTACTAGAGAA
*
5890606 CTTCCTCTCTTCTCATGTTTTGCACCTACTAGAGAA
1 CTTCCTCTCTTCCCATGTTTTGCACCTACTAGAGAA
5890642 CTTCC
1 CTTCC
5890647 ATTTCAAGAA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.17, C:0.34, G:0.12, T:0.38
Consensus pattern (36 bp):
CTTCCTCTCTTCCCATGTTTTGCACCTACTAGAGAA
Found at i:5895225 original size:27 final size:27
Alignment explanation
Indices: 5895066--5895228 Score: 182
Period size: 27 Copynumber: 6.0 Consensus size: 27
5895056 ATATGTCATA
* * * *
5895066 TTAAAAATTTAGTTGTTACACACGATA
1 TTAAAAATTTAATTGTTACACGCCATG
** *
5895093 TTAAAAAAATAATTGTTACACGTCATG
1 TTAAAAATTTAATTGTTACACGCCATG
* * *
5895120 TTAAAAATTTAGTTGTTGCACGTCATG
1 TTAAAAATTTAATTGTTACACGCCATG
* *
5895147 TTGAAAAATGTAATTGTTACACGCTATG
1 TT-AAAAATTTAATTGTTACACGCCATG
* * *
5895175 TTGAAGATTTAGTTGTTACACGCCATG
1 TTAAAAATTTAATTGTTACACGCCATG
5895202 TTAAAAATTTAATTGTTACACGCCATG
1 TTAAAAATTTAATTGTTACACGCCATG
5895229 CCATAATTTG
Statistics
Matches: 111, Mismatches: 24, Indels: 2
0.81 0.18 0.01
Matches are distributed among these distances:
27 89 0.80
28 22 0.20
ACGTcount: A:0.36, C:0.12, G:0.15, T:0.37
Consensus pattern (27 bp):
TTAAAAATTTAATTGTTACACGCCATG
Found at i:5899830 original size:25 final size:26
Alignment explanation
Indices: 5899794--5899844 Score: 77
Period size: 25 Copynumber: 2.0 Consensus size: 26
5899784 TTGCTCCTTT
5899794 ATTTTGTCCAATTAAATAA-AAATCA
1 ATTTTGTCCAATTAAATAACAAATCA
* *
5899819 ATTTTGTTCAATTTAATAACAAATCA
1 ATTTTGTCCAATTAAATAACAAATCA
5899845 CCAAACTCTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 17 0.74
26 6 0.26
ACGTcount: A:0.45, C:0.12, G:0.04, T:0.39
Consensus pattern (26 bp):
ATTTTGTCCAATTAAATAACAAATCA
Found at i:5901439 original size:22 final size:23
Alignment explanation
Indices: 5901398--5901441 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
5901388 TGGCTAGAAA
*
5901398 AAAAAATGAATTAATAAATATTT
1 AAAAAATGAATAAATAAATATTT
*
5901421 AAAATATGAATAAAT-AATATT
1 AAAAAATGAATAAATAAATATT
5901442 ATTTCATTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 6 0.32
23 13 0.68
ACGTcount: A:0.61, C:0.00, G:0.05, T:0.34
Consensus pattern (23 bp):
AAAAAATGAATAAATAAATATTT
Found at i:5905862 original size:31 final size:32
Alignment explanation
Indices: 5905827--5905888 Score: 83
Period size: 31 Copynumber: 2.0 Consensus size: 32
5905817 TATTAATAAT
*
5905827 TTAATATAGTAACTTA-TTAATA-TACTATATA
1 TTAATATAGTAA-TGACTTAATATTACTATATA
*
5905858 TTAATATATTAATGACTTAATATTACTATAT
1 TTAATATAGTAATGACTTAATATTACTATAT
5905889 TATAATAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
30 2 0.07
31 17 0.63
32 8 0.30
ACGTcount: A:0.44, C:0.06, G:0.03, T:0.47
Consensus pattern (32 bp):
TTAATATAGTAATGACTTAATATTACTATATA
Found at i:5905866 original size:8 final size:8
Alignment explanation
Indices: 5905816--5905870 Score: 53
Period size: 8 Copynumber: 7.0 Consensus size: 8
5905806 AATATAACTC
5905816 ATATTAAT
1 ATATTAAT
5905824 A-ATTTAAT
1 ATA-TTAAT
*
5905832 ATAGTAACT
1 ATATTAA-T
5905841 -TATTAAT
1 ATATTAAT
*
5905848 ATACT-AT
1 ATATTAAT
5905855 ATATTAAT
1 ATATTAAT
5905863 ATATTAAT
1 ATATTAAT
5905871 GACTTAATAT
Statistics
Matches: 38, Mismatches: 4, Indels: 10
0.73 0.08 0.19
Matches are distributed among these distances:
7 8 0.21
8 28 0.74
9 2 0.05
ACGTcount: A:0.47, C:0.04, G:0.02, T:0.47
Consensus pattern (8 bp):
ATATTAAT
Found at i:5911403 original size:23 final size:23
Alignment explanation
Indices: 5911357--5911404 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
5911347 TTTCTAAATA
* *
5911357 ATTTCCACCCAAATCCATCTTAT
1 ATTTCCACACAAATCCATCATAT
5911380 ATTTCCACACATAATCCA-CATAT
1 ATTTCCACACA-AATCCATCATAT
5911403 AT
1 AT
5911405 GGTAGCAACA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 16 0.73
24 6 0.27
ACGTcount: A:0.35, C:0.31, G:0.00, T:0.33
Consensus pattern (23 bp):
ATTTCCACACAAATCCATCATAT
Found at i:5920763 original size:80 final size:78
Alignment explanation
Indices: 5920522--5920769 Score: 289
Period size: 80 Copynumber: 3.1 Consensus size: 78
5920512 CATGAGTTCC
*
5920522 ATTTATGAGATTATGACATGTATGCCATGAGATGTATGTGTTGAGAATATCATGTACACTATAGG
1 ATTTATGAGATTATGACATGTATGCCATGAGATGTATGTGTTGAG-ATATCATGTACACTATGGG
*
5920587 TTAAGCATGTGGATG
65 CTAAGCATGT-GATG
* * * * * * * *
5920602 AATTATGAGATTATGACATGTATGTCATGAGTTGTATATGTTAAACATATCATGTGCACTAAGGG
1 ATTTATGAGATTATGACATGTATGCCATGAGATGTATGTGTT-GAGATATCATGTACACTATGGG
*
5920667 CTAATCATGTGAATG
65 CTAAGCATGTG-ATG
* * * *
5920682 ATTTACGAGATTATGAAATGTATGCCATTAGATGTATGTGTTGAGATAGTCATATACACTATGGG
1 ATTTATGAGATTATGACATGTATGCCATGAGATGTATGTGTTGAGATA-TCATGTACACTATGGG
*
5920747 CTGAGCATGATGATG
65 CTAAGCATG-TGATG
*
5920762 ATATATGA
1 ATTTATGA
5920770 AAATGTTACA
Statistics
Matches: 137, Mismatches: 27, Indels: 8
0.80 0.16 0.05
Matches are distributed among these distances:
79 5 0.04
80 129 0.94
81 3 0.02
ACGTcount: A:0.33, C:0.09, G:0.23, T:0.35
Consensus pattern (78 bp):
ATTTATGAGATTATGACATGTATGCCATGAGATGTATGTGTTGAGATATCATGTACACTATGGGC
TAAGCATGTGATG
Found at i:5934983 original size:33 final size:33
Alignment explanation
Indices: 5934945--5935009 Score: 130
Period size: 33 Copynumber: 2.0 Consensus size: 33
5934935 AGCACTCTAC
5934945 TGATCCAAATCAAAAAAAGAAAAAGGCCATTAG
1 TGATCCAAATCAAAAAAAGAAAAAGGCCATTAG
5934978 TGATCCAAATCAAAAAAAGAAAAAGGCCATTA
1 TGATCCAAATCAAAAAAAGAAAAAGGCCATTA
5935010 ACTCATATTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.55, C:0.15, G:0.14, T:0.15
Consensus pattern (33 bp):
TGATCCAAATCAAAAAAAGAAAAAGGCCATTAG
Found at i:5940707 original size:669 final size:662
Alignment explanation
Indices: 5939435--5940722 Score: 1770
Period size: 669 Copynumber: 1.9 Consensus size: 662
5939425 CAGTGGGCGG
* **
5939435 GTTTTCGTGGACCAACCTATTAGAGGGGCACGGTAAACCCCGTTATATTTTACCTTAGGACGAGA
1 GTTTTCGTGGACCAACCTATGAGAGGGGCACAATAAACCCCGTTATATTTTACCTTAGGACGAGA
** ** *
5939500 GGCACGGAGGGTATCTCCTAAGGTAAGTTTAGAGTTCACTTCACGTCGAACTACCACGTGAGGAT
66 GGCACGGAGGGTATCTCCTAAGGTAACATTAGAGTTCACTTCACACCGAACCACCACGTGAGGAT
* * **
5939565 GAAACTCAGCCAACGCCAAGGAATGACTATATTTTAAAAGTAAAAATATGTTTTATGGGTATATG
131 GAAACTCAGCCAACGCCAAGGAAGGACTATATTTTAAAAGTAAAAAAATGTTTTATGACTATATG
* * * * * *
5939630 TCGTTTTAACATCCTTGGCGGATTCGGTTGGATGCTCGGGCCAAGGTGTCACCGAGTATGAGTTT
196 TCATTTTAACAGCCTTGGCAGACTCGGTTGGATGCCCGGGCCAAGGTGTCACCGAGTATAAGTTT
*
5939695 TGGCACAAGCCAAATTTTTAAGAGAATCACAAGCCTTGTTGATTATTTCGATAAAATGTAATTAT
261 TGGCACAAGCCAAAGTTTTAAGAGAATCACAAGCCTTGTTGATTATTTCGATAAAATGTAATTAT
* *
5939760 TTTATATGAATTGAAATGAGTTTTAAATGTTATGAATCATATTATAATGGGATGATTTAACTGTC
326 TTTATAAGAATTGAAATGAGTTTTAAATGTTATGAATCATATTATAATGAGATGATTTAACTGTC
* *
5939825 TCAATTTACTCAGCTTTAGATGTTGTAGATGAACTTTGGTTACTCATTGGGTTTATAAAAACTCA
391 TCAATTTACTCAGCTTTAGATGTTGTAGATGAACTTTGCTTACTCACTGGGTTTATAAAAACTCA
* ** * *
5939890 CCCCTTTTTTTTACCTATTTTAGGCTCAGGACAGTCTGTAAACAGTCGATTTTGTCGAGGGTTGC
456 CCCCTTCTTTCAACCTATTTCAAGCTCAGGACAGTCTGTAAACAGTCGATTTTGTCGAGGGTTGC
* * * * *
5939955 TTTTGGATTTACATCCTTAGAAATCGAAGGTCTACAGTCTTGTATATTTTCGGTTATTTTGGAGC
521 TGTTGGATTCACACCCTTAGAAATCGAAGGTCTACAATCGTGTATATTTTCGGTTATTTTGGAGC
*
5940020 CCACATGTCATTGTAGAATATTTTTGTATACCTGGTTTAGTGTGCTATTATATATATGAATTTAT
586 CCACATGTCATTGTAGAATA-TTTTATATACCTGGTTTAGTGTGCTATTATATATATGAATTTAT
5940085 TTTACTCTTANTGA
650 TTTACTCTTA-TGA
* *
5940099 GTTTTCGTGGACCAGCCTATGAGAGGGGCCCAATAAACCCCGTTATATTTTACCTT-GGTACGAG
1 GTTTTCGTGGACCAACCTATGAGAGGGGCACAATAAACCCCGTTATATTTTACCTTAGG-ACGAG
*
5940163 AGGCGCGGAGGGTATCTCCTAAGGTAACATTAGAGTTCACTTCACACCGAACCACCACGTGAAGG
65 AGGCACGGAGGGTATCTCCTAAGGTAACATTAGAGTTCACTTCACACCGAACCACCACGTG-AGG
* * * *
5940228 -TGAAACTCAGCCAACGCCAAGGAAGGGCTGTGCTTTTAAATGTAAAAAAAAAATGAGTTTTAT-
129 ATGAAACTCAGCCAACGCCAAGGAAGGACTAT-ATTTTAAAAGT---AAAAAAAT--GTTTTATG
* *
5940291 ACTCATATGTTATTTTAACAGCCTTGGCAGACTCGGTTGGATGCCCCGGGCCAAGGTGTCATCGA
188 ACT-ATATGTCATTTTAACAGCCTTGGCAGACTCGGTTGGATG-CCCGGGCCAAGGTGTCACCGA
* * * * * *
5940356 GTATAAG-TTTGGTACGAGCC-AAGTTTTAAGAGAGTCATAAGCCTTGTTGATTATTTTTGATGA
251 GTATAAGTTTTGGCACAAGCCAAAGTTTTAAGAGAATCACAAGCCTTGTTGATTA-TTTCGATAA
* *
5940419 AATGTAAATTGTTTTATAAG-GTTGAAATGAGTTTT-AATGTTATGAATCATATTATGAA-GAGA
315 AATGT-AATTATTTTATAAGAATTGAAATGAGTTTTAAATGTTATGAATCATATTAT-AATGAGA
* * * *
5940481 TGTTTTAATTGTCTCTATTTACTCGGCTTTAGATGTTGTAGATGAACTTTGCTTACTCACTGGGT
378 TGATTTAACTGTCTCAATTTACTCAGCTTTAGATGTTGTAGATGAACTTTGCTTACTCACTGGGT
* * *
5940546 TTATAAAAACTCACCCCTTCTTTCAACC-ATTTCAAGCTTAGGGCAGTCTGTAGACCA-TCGATT
443 TTATAAAAACTCACCCCTTCTTTCAACCTATTTCAAGCTCAGGACAGTCTGTA-AACAGTCGATT
* * *
5940609 TTGTCGAGGGTTTGCTGTTGGATTCACACCCTTAGAAATCGCAGGTTTACAATCGTGTTTATTTT
507 TTGTCGAGGG-TTGCTGTTGGATTCACACCCTTAGAAATCGAAGGTCTACAATCGTGTATATTTT
* *
5940674 -GGTTATTTTGGGGGCCTACATGTCATTGTAGAATATTTTATATACCTGG
571 CGGTTATTTT-GGAGCCCACATGTCATTGTAGAATATTTTATATACCTGG
5940723 CTGCGTGTAC
Statistics
Matches: 545, Mismatches: 63, Indels: 28
0.86 0.10 0.04
Matches are distributed among these distances:
663 2 0.00
664 139 0.26
665 12 0.02
668 65 0.12
669 210 0.39
670 80 0.15
671 37 0.07
ACGTcount: A:0.27, C:0.16, G:0.21, T:0.35
Consensus pattern (662 bp):
GTTTTCGTGGACCAACCTATGAGAGGGGCACAATAAACCCCGTTATATTTTACCTTAGGACGAGA
GGCACGGAGGGTATCTCCTAAGGTAACATTAGAGTTCACTTCACACCGAACCACCACGTGAGGAT
GAAACTCAGCCAACGCCAAGGAAGGACTATATTTTAAAAGTAAAAAAATGTTTTATGACTATATG
TCATTTTAACAGCCTTGGCAGACTCGGTTGGATGCCCGGGCCAAGGTGTCACCGAGTATAAGTTT
TGGCACAAGCCAAAGTTTTAAGAGAATCACAAGCCTTGTTGATTATTTCGATAAAATGTAATTAT
TTTATAAGAATTGAAATGAGTTTTAAATGTTATGAATCATATTATAATGAGATGATTTAACTGTC
TCAATTTACTCAGCTTTAGATGTTGTAGATGAACTTTGCTTACTCACTGGGTTTATAAAAACTCA
CCCCTTCTTTCAACCTATTTCAAGCTCAGGACAGTCTGTAAACAGTCGATTTTGTCGAGGGTTGC
TGTTGGATTCACACCCTTAGAAATCGAAGGTCTACAATCGTGTATATTTTCGGTTATTTTGGAGC
CCACATGTCATTGTAGAATATTTTATATACCTGGTTTAGTGTGCTATTATATATATGAATTTATT
TTACTCTTATGA
Found at i:5950222 original size:21 final size:21
Alignment explanation
Indices: 5950180--5950222 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
5950170 CTTGTACCGG
*
5950180 TGGTGGAACTAAAGGAGTAAC
1 TGGTGGAACTAAAGGAGGAAC
* * *
5950201 TGGTGGTACTATAGGTGGAAC
1 TGGTGGAACTAAAGGAGGAAC
5950222 T
1 T
5950223 TGACCAGTCG
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.09, G:0.35, T:0.26
Consensus pattern (21 bp):
TGGTGGAACTAAAGGAGGAAC
Found at i:5961788 original size:15 final size:15
Alignment explanation
Indices: 5961768--5961814 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
5961758 TAAAACAACC
5961768 TTAAAATCAAAAACT
1 TTAAAATCAAAAACT
* *
5961783 TTAAAATCCAAAGCT
1 TTAAAATCAAAAACT
* *
5961798 TTAAAACCAAAATCT
1 TTAAAATCAAAAACT
5961813 TT
1 TT
5961815 GATCTTTAAA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.51, C:0.17, G:0.02, T:0.30
Consensus pattern (15 bp):
TTAAAATCAAAAACT
Found at i:5963226 original size:13 final size:13
Alignment explanation
Indices: 5963208--5963232 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5963198 TTCCAGAAAA
5963208 TTTATAAAATCAT
1 TTTATAAAATCAT
5963221 TTTATAAAATCA
1 TTTATAAAATCA
5963233 CAATTTCTCT
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:0.48, C:0.08, G:0.00, T:0.44
Consensus pattern (13 bp):
TTTATAAAATCAT
Found at i:5964403 original size:27 final size:27
Alignment explanation
Indices: 5964352--5964403 Score: 70
Period size: 28 Copynumber: 1.9 Consensus size: 27
5964342 ATGTCCTGGT
*
5964352 GGTGGAAAATTACAATTTTGCCCCTAG
1 GGTGGAAAATTACAATTTTGACCCTAG
*
5964379 GGTGGCAAAATTACCATTTT-ACCCT
1 GGTGG-AAAATTACAATTTTGACCCT
5964404 TTTACTTCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
27 9 0.41
28 13 0.59
ACGTcount: A:0.29, C:0.21, G:0.19, T:0.31
Consensus pattern (27 bp):
GGTGGAAAATTACAATTTTGACCCTAG
Found at i:5964474 original size:20 final size:20
Alignment explanation
Indices: 5964457--5964494 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
5964447 CCTCAAATCT
5964457 TACTCCAATAAGTCAAATTA
1 TACTCCAATAAGTCAAATTA
5964477 TACTCCAATAAGTCAAAT
1 TACTCCAATAAGTCAAAT
5964495 GGGGCCAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.45, C:0.21, G:0.05, T:0.29
Consensus pattern (20 bp):
TACTCCAATAAGTCAAATTA
Found at i:5973883 original size:13 final size:13
Alignment explanation
Indices: 5973865--5973896 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
5973855 AATATTTTTG
5973865 TAGAATTCTATTT
1 TAGAATTCTATTT
5973878 TAGAATTCTATTT
1 TAGAATTCTATTT
5973891 TAGAAT
1 TAGAAT
5973897 AATGTATTCG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.34, C:0.06, G:0.09, T:0.50
Consensus pattern (13 bp):
TAGAATTCTATTT
Found at i:5975475 original size:13 final size:13
Alignment explanation
Indices: 5975457--5975482 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
5975447 AAAATGGGAG
5975457 AAAATAAAAAAAT
1 AAAATAAAAAAAT
5975470 AAAATAAAAAAAT
1 AAAATAAAAAAAT
5975483 TATTTATTTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (13 bp):
AAAATAAAAAAAT
Found at i:5987103 original size:8 final size:8
Alignment explanation
Indices: 5987059--5987122 Score: 66
Period size: 8 Copynumber: 8.5 Consensus size: 8
5987049 TAGGCTCAAC
5987059 CTTCCTTGT
1 CTTCCTT-T
5987068 CTT--TTT
1 CTTCCTTT
5987074 CTT-CTTT
1 CTTCCTTT
*
5987081 C-TCCATT
1 CTTCCTTT
*
5987088 CTTTCTTT
1 CTTCCTTT
5987096 CTTCCTTT
1 CTTCCTTT
5987104 CTTCCTTT
1 CTTCCTTT
5987112 C-TCCTTT
1 CTTCCTTT
5987119 CTTC
1 CTTC
5987123 AAAGCTGATT
Statistics
Matches: 47, Mismatches: 4, Indels: 9
0.78 0.07 0.15
Matches are distributed among these distances:
6 5 0.11
7 17 0.36
8 22 0.47
9 3 0.06
ACGTcount: A:0.02, C:0.34, G:0.02, T:0.62
Consensus pattern (8 bp):
CTTCCTTT
Found at i:5987122 original size:15 final size:15
Alignment explanation
Indices: 5987071--5987122 Score: 70
Period size: 15 Copynumber: 3.5 Consensus size: 15
5987061 TCCTTGTCTT
5987071 TTTCTT-CTTTCTCC
1 TTTCTTCCTTTCTCC
* *
5987085 ATTCTTTCTTTCTTCC
1 TTTCTTCCTTTC-TCC
5987101 TTTCTTCCTTTCTCC
1 TTTCTTCCTTTCTCC
5987116 TTTCTTC
1 TTTCTTC
5987123 AAAGCTGATT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
14 5 0.15
15 15 0.45
16 13 0.39
ACGTcount: A:0.02, C:0.35, G:0.00, T:0.63
Consensus pattern (15 bp):
TTTCTTCCTTTCTCC
Found at i:5990137 original size:168 final size:168
Alignment explanation
Indices: 5989849--5990160 Score: 455
Period size: 168 Copynumber: 1.9 Consensus size: 168
5989839 AGTTTCGTTT
* * ** * *
5989849 TCCTCAACATGTATATTTTGGGTTACAAGTACCAACTTTGAACCGTTTTTCTAGGCTTCATTCTT
1 TCCTCAACATGTATATCTTGAGTTACAACAACCAAATTTGAACCATTTTTCTAGGCTTCATTCTT
* * * * * *
5989914 TTAAGCAACATTGTTTTTAAGTGTTTTCTCTTCTACTTGTTTTTTCCTTTTCCTCTTTAGCATTG
66 TTAAGCAACATTATCTCTAAGTGTTTTCTCTTCTACCTGTTCTTTCCTCTTCCTCTTTAGCATTG
5989979 CTCCATCTTCAAGAGCCACTTGAGTGGAAGCTTCCTTA
131 CTCCATCTTCAAGAGCCACTTGAGTGGAAGCTTCCTTA
*
5990017 TCCTCAACATGTATATCTTGAGTTACAACAACCAAATTTGAACTATTTTTCTAGGCTTCATTCTC
1 TCCTCAACATGTATATCTTGAGTTACAACAACCAAATTTGAACCATTTTTCTAGGCTTCATTCT-
* * * *
5990082 TTT-TGCAACATTATCTCTGAGTGTTTTCTCTTTTACCTGTTCTTTCCTCTTCCTCTTTAGCTTT
65 TTTAAGCAACATTATCTCTAAGTGTTTTCTCTTCTACCTGTTCTTTCCTCTTCCTCTTTAGCATT
5990146 GCTCCATCTTCAAGA
130 GCTCCATCTTCAAGA
5990161 ACCTCCTAAC
Statistics
Matches: 126, Mismatches: 17, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
168 123 0.98
169 3 0.02
ACGTcount: A:0.21, C:0.23, G:0.12, T:0.44
Consensus pattern (168 bp):
TCCTCAACATGTATATCTTGAGTTACAACAACCAAATTTGAACCATTTTTCTAGGCTTCATTCTT
TTAAGCAACATTATCTCTAAGTGTTTTCTCTTCTACCTGTTCTTTCCTCTTCCTCTTTAGCATTG
CTCCATCTTCAAGAGCCACTTGAGTGGAAGCTTCCTTA
Found at i:5991112 original size:21 final size:21
Alignment explanation
Indices: 5991082--5991134 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
5991072 GTTTTTAGGC
*
5991082 ATTGCATGACTGACTTTGGAT
1 ATTGCGTGACTGACTTTGGAT
* *
5991103 GTTGCGTGACTGACTTTGGGT
1 ATTGCGTGACTGACTTTGGAT
5991124 ATTGCGTGACT
1 ATTGCGTGACT
5991135 AATTTTTGAT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.17, C:0.15, G:0.30, T:0.38
Consensus pattern (21 bp):
ATTGCGTGACTGACTTTGGAT
Found at i:5991198 original size:23 final size:23
Alignment explanation
Indices: 5991144--5991226 Score: 89
Period size: 23 Copynumber: 3.7 Consensus size: 23
5991134 TAATTTTTGA
* *
5991144 TAAGGCATCGTGTGACTAGTT-G
1 TAAGGCATTGCGTGACTAGTTAG
* * *
5991166 -ATACGCATTGCGTGACTTGTTAT
1 TA-AGGCATTGCGTGACTAGTTAG
5991189 TAAGGCATTGCGTGACTAGTTAG
1 TAAGGCATTGCGTGACTAGTTAG
*
5991212 TAAGGCATTGTGTGA
1 TAAGGCATTGCGTGA
5991227 TTTAGACACT
Statistics
Matches: 49, Mismatches: 9, Indels: 5
0.78 0.14 0.08
Matches are distributed among these distances:
21 1 0.02
22 15 0.31
23 32 0.65
24 1 0.02
ACGTcount: A:0.24, C:0.13, G:0.29, T:0.34
Consensus pattern (23 bp):
TAAGGCATTGCGTGACTAGTTAG
Found at i:5991272 original size:22 final size:22
Alignment explanation
Indices: 5991240--5991324 Score: 109
Period size: 22 Copynumber: 3.9 Consensus size: 22
5991230 AGACACTACT
* *
5991240 TAAAAATCAGTCACGCAATGCC
1 TAAAAACCAATCACGCAATGCC
*
5991262 TAAAAACCAGTCACGCAATGCC
1 TAAAAACCAATCACGCAATGCC
*
5991284 T-AAAACCAATCACGTAATGCC
1 TAAAAACCAATCACGCAATGCC
* *
5991305 TAAAAGCCAATCATGCAATG
1 TAAAAACCAATCACGCAATG
5991325 ATTAAGTCAC
Statistics
Matches: 56, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
21 19 0.34
22 37 0.66
ACGTcount: A:0.42, C:0.27, G:0.13, T:0.18
Consensus pattern (22 bp):
TAAAAACCAATCACGCAATGCC
Found at i:5991377 original size:22 final size:22
Alignment explanation
Indices: 5991329--5991377 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
5991319 GCAATGATTA
* * *
5991329 AGTCACGTAATGCCTAAAAATC
1 AGTCTCGTAATACCTAAAAACC
*
5991351 AGTCTCGTAATACTTAAAAACC
1 AGTCTCGTAATACCTAAAAACC
5991373 AGTCT
1 AGTCT
5991378 AATCAATTTC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.39, C:0.22, G:0.12, T:0.27
Consensus pattern (22 bp):
AGTCTCGTAATACCTAAAAACC
Found at i:5995666 original size:17 final size:18
Alignment explanation
Indices: 5995646--5995681 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
5995636 TATTTTTTCA
5995646 TTGTTC-TTGTTTTTGTT
1 TTGTTCATTGTTTTTGTT
*
5995663 TTGTTCATTTTTTTTGTT
1 TTGTTCATTGTTTTTGTT
5995681 T
1 T
5995682 AGATTTTGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 6 0.35
18 11 0.65
ACGTcount: A:0.03, C:0.06, G:0.14, T:0.78
Consensus pattern (18 bp):
TTGTTCATTGTTTTTGTT
Found at i:6002286 original size:19 final size:19
Alignment explanation
Indices: 6002262--6002303 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
6002252 AAGTTTTCTC
* *
6002262 AATTAGTGTCTAGCTTTAA
1 AATTAGTATCAAGCTTTAA
*
6002281 AATTAGTATCAAGCTTTAT
1 AATTAGTATCAAGCTTTAA
6002300 AATT
1 AATT
6002304 GTCTCTTCTC
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:0.36, C:0.10, G:0.12, T:0.43
Consensus pattern (19 bp):
AATTAGTATCAAGCTTTAA
Found at i:6007370 original size:35 final size:36
Alignment explanation
Indices: 6007325--6007393 Score: 95
Period size: 35 Copynumber: 1.9 Consensus size: 36
6007315 TGAAAAGTTA
* *
6007325 GTTGTTAGGTTTTGGTTGATCCCATGAAAAACCATT
1 GTTGTTAGGTTGTGGTTGAGCCCATGAAAAACCATT
**
6007361 GTTG-TAGGTTGTGGTTGAGCCTTTGAAAAACCA
1 GTTGTTAGGTTGTGGTTGAGCCCATGAAAAACCA
6007394 CTTTGGGTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
35 25 0.86
36 4 0.14
ACGTcount: A:0.25, C:0.13, G:0.26, T:0.36
Consensus pattern (36 bp):
GTTGTTAGGTTGTGGTTGAGCCCATGAAAAACCATT
Found at i:6011824 original size:16 final size:17
Alignment explanation
Indices: 6011788--6011824 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
6011778 TAGTTCTTGT
*
6011788 TTTTAGTTTTACTTTAA
1 TTTTAGTTTTACTTCAA
6011805 TTTTAGTTTT-CTTCAA
1 TTTTAGTTTTACTTCAA
6011821 TTTT
1 TTTT
6011825 CACTGTCTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 9 0.47
17 10 0.53
ACGTcount: A:0.19, C:0.08, G:0.05, T:0.68
Consensus pattern (17 bp):
TTTTAGTTTTACTTCAA
Found at i:6018965 original size:17 final size:18
Alignment explanation
Indices: 6018933--6018966 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
6018923 AAGATGGCAA
*
6018933 TTTTGATTTCAAAAGAAC
1 TTTTCATTTCAAAAGAAC
6018951 TTTTCATTT-AAAAGAA
1 TTTTCATTTCAAAAGAA
6018967 AGGTCATCTT
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:0.41, C:0.09, G:0.09, T:0.41
Consensus pattern (18 bp):
TTTTCATTTCAAAAGAAC
Found at i:6020089 original size:27 final size:27
Alignment explanation
Indices: 6019989--6020472 Score: 322
Period size: 27 Copynumber: 17.9 Consensus size: 27
6019979 TGTAATAACT
* * * *
6019989 TTTTCATCATGGCATGTAATAACTAAA
1 TTTTCAACATGACGTGTAACAACTAAA
* * * *
6020016 TATTTTAACATAACATGTAACAACTACAT
1 T-TTTCAACATGACGTGTAACAACTA-AA
* *
6020045 TTTTTATCAT-AGCGTGTAACAACTAAA
1 TTTTCAACATGA-CGTGTAACAACTAAA
* * *
6020072 TTTTCAACATGACATGTAATAACTACAT
1 TTTTCAACATGACGTGTAACAACTA-AA
* * * *
6020100 TTTTCAATAT-AGCATATAATAACTAAA
1 TTTTCAACATGA-CGTGTAACAACTAAA
* * *
6020127 TTTTCAACATAATGTGTAACAACTACAT
1 TTTTCAACATGACGTGTAACAACTA-AA
* ** *
6020155 TTTTCAATATGGTGTGTGACAACTAAA
1 TTTTCAACATGACGTGTAACAACTAAA
** **
6020182 TTTTCAACATGGTGTGTAACAGTTAAA
1 TTTTCAACATGACGTGTAACAACTAAA
* * *
6020209 TATTCAACATGGCGTGTAACAACTATAT
1 TTTTCAACATGACGTGTAACAACTA-AA
* * * *
6020237 TTTTTAACATAACATGTAACAACTATA
1 TTTTCAACATGACGTGTAACAACTAAA
* *
6020264 TTTTCAACATGATGTGTAACAACTATAT
1 TTTTCAACATGACGTGTAACAACTA-AA
*
6020292 TTTTCAACAT-AGCATGTAACAACTAAA
1 TTTTCAACATGA-CGTGTAACAACTAAA
* **
6020319 TTTTCAACATGACGTGTAACAATTGCA
1 TTTTCAACATGACGTGTAACAACTAAA
* * *
6020346 TTTTCAACATGGCGTGTAATAA-T-TA
1 TTTTCAACATGACGTGTAACAACTAAA
* * *
6020371 TTTTCAACATAACATGTAACAA-T-TA
1 TTTTCAACATGACGTGTAACAACTAAA
*
6020396 TTTTCAACAT-AGCGTGTAACAATTAAA
1 TTTTCAACATGA-CGTGTAACAACTAAA
* * *
6020423 TTTTAGAACATGACGTGTAA-TACTATAT
1 TTTT-CAACATGACGTGTAACAACTA-AA
*
6020451 TTTTCAACATGGCGT-TAACAAC
1 TTTTCAACATGACGTGTAACAAC
6020473 ATTTTTTCCA
Statistics
Matches: 365, Mismatches: 73, Indels: 38
0.77 0.15 0.08
Matches are distributed among these distances:
24 1 0.00
25 41 0.11
26 5 0.01
27 170 0.47
28 145 0.40
29 3 0.01
ACGTcount: A:0.38, C:0.15, G:0.11, T:0.36
Consensus pattern (27 bp):
TTTTCAACATGACGTGTAACAACTAAA
Found at i:6020101 original size:55 final size:55
Alignment explanation
Indices: 6019988--6020355 Score: 314
Period size: 55 Copynumber: 6.7 Consensus size: 55
6019978 ATGTAATAAC
* * *
6019988 TTTTTCATCATGGCATGTAATAACTAAATATTTTAACATAACATGTAACAACTACA
1 TTTTTCATCATGGCGTGTAACAACTAAAT-TTTCAACATAACATGTAACAACTACA
* * * *
6020044 TTTTTTATCATAGCGTGTAACAACTAAATTTTCAACATGACATGTAATAACTACA
1 TTTTTCATCATGGCGTGTAACAACTAAATTTTCAACATAACATGTAACAACTACA
* * * * **
6020099 TTTTTCAAT-ATAGCATATAATAACTAAATTTTCAACATAATGTGTAACAACTACA
1 TTTTTC-ATCATGGCGTGTAACAACTAAATTTTCAACATAACATGTAACAACTACA
* * **** **
6020154 TTTTTCAAT-ATGGTGTGTGACAACTAAATTTTCAACATGGTGTGTAACAGTTA-A
1 TTTTTC-ATCATGGCGTGTAACAACTAAATTTTCAACATAACATGTAACAACTACA
* * * * * *
6020208 ATATTCAACATGGCGTGTAACAACTATATTTTTTAACATAACATGTAACAACTATA
1 TTTTTCATCATGGCGTGTAACAACTA-AATTTTCAACATAACATGTAACAACTACA
* ** * *
6020264 -TTTTCAACATGATGTGTAACAACTATATTTTTCAACATAGCATGTAACAACTA-A
1 TTTTTCATCATGGCGTGTAACAACTA-AATTTTCAACATAACATGTAACAACTACA
* * * * **
6020318 ATTTTCAACATGACGTGTAACAATTGCATTTTCAACAT
1 TTTTTCATCATGGCGTGTAACAACTAAATTTTCAACAT
6020356 GGCGTGTAAT
Statistics
Matches: 259, Mismatches: 48, Indels: 12
0.81 0.15 0.04
Matches are distributed among these distances:
53 1 0.00
54 31 0.12
55 199 0.77
56 28 0.11
ACGTcount: A:0.39, C:0.15, G:0.10, T:0.36
Consensus pattern (55 bp):
TTTTTCATCATGGCGTGTAACAACTAAATTTTCAACATAACATGTAACAACTACA
Found at i:6020209 original size:82 final size:81
Alignment explanation
Indices: 6020059--6020426 Score: 314
Period size: 82 Copynumber: 4.5 Consensus size: 81
6020049 TATCATAGCG
* * * * * * ** * * *
6020059 TGTAACAACTAAATTTTCAACATGACATGTAATAACTACATTTTTCAATATAGCATATAATAACT
1 TGTAACAACTAATTTTTCAACATGACGTGTAACAACTA-AATTTTCAACATGGTGTGTAACAATT
**
6020124 AAATTTTCAACATAATG
65 AAATTTTCAACATAACA
* ** * *
6020141 TGTAACAACTACATTTTTCAATATGGTGTGTGACAACTAAATTTTCAACATGGTGTGTAACAGTT
1 TGTAACAACTA-ATTTTTCAACATGACGTGTAACAACTAAATTTTCAACATGGTGTGTAACAATT
* ** *
6020206 AAATATTCAACATGGCG
65 AAATTTTCAACATAACA
* * * * * *
6020223 TGTAACAACTATATTTTTTAACATAACATGTAACAACTATATTTTCAACATGATGTGTAACAACT
1 TGTAACAACTA-ATTTTTCAACATGACGTGTAACAACTAAATTTTCAACATGGTGTGTAACAATT
* *
6020288 ATATTTTTCAACATAGCA
65 A-AATTTTCAACATAACA
* * ** * *
6020306 TGTAACAACTAAATTTTCAACATGACGTGTAACAATTGCATTTTCAACATGGCGTGTAATAATT-
1 TGTAACAACTAATTTTTCAACATGACGTGTAACAACTAAATTTTCAACATGGTGTGTAACAATTA
6020370 -ATTTTCAACATAACA
66 AATTTTCAACATAACA
* *
6020385 TGTAACAA-TTA-TTTTCAACAT-AGCGTGTAACAATTAAATTTT
1 TGTAACAACTAATTTTTCAACATGA-CGTGTAACAACTAAATTTT
6020427 AGAACATGAC
Statistics
Matches: 231, Mismatches: 52, Indels: 11
0.79 0.18 0.04
Matches are distributed among these distances:
76 1 0.00
77 27 0.12
78 2 0.01
79 21 0.09
82 137 0.59
83 43 0.19
ACGTcount: A:0.39, C:0.15, G:0.10, T:0.36
Consensus pattern (81 bp):
TGTAACAACTAATTTTTCAACATGACGTGTAACAACTAAATTTTCAACATGGTGTGTAACAATTA
AATTTTCAACATAACA
Found at i:6020239 original size:137 final size:137
Alignment explanation
Indices: 6020003--6020426 Score: 430
Period size: 137 Copynumber: 3.1 Consensus size: 137
6019993 CATCATGGCA
* * * * * *
6020003 TGTAATAACTAAATATTTT-AACATAACATGTAACAACTACATTTTTTATCAT-AGCGTGTAACA
1 TGTAACAACTACAT-TTTTCAACATAGCATGTAACAACTA-AATTTTCAACATGA-CGTGTAACA
* * * * * * *
6020066 ACTAAATTTTCAACATGACATGTAATAACTACATTTTTCAATATAGCATATAATAACTAAATTTT
63 ATTAAATTTTCAACATGGCGTGTAACAACTACATTTTTCAACATAACATATAACAACTAAATTTT
6020131 CAACATAATG
128 CAACATAATG
* * ** * ** *
6020141 TGTAACAACTACATTTTTCAATATGGTGTGTGACAACTAAATTTTCAACATGGTGTGTAACAGTT
1 TGTAACAACTACATTTTTCAACATAGCATGTAACAACTAAATTTTCAACATGACGTGTAACAATT
* * * * *
6020206 AAATATTCAACATGGCGTGTAACAACTATATTTTTTAACATAACATGTAACAACTATATTTTCAA
66 AAATTTTCAACATGGCGTGTAACAACTACATTTTTCAACATAACATATAACAACTAAATTTTCAA
*
6020271 CATGATG
131 CATAATG
*
6020278 TGTAACAACTATATTTTTCAACATAGCATGTAACAACTAAATTTTCAACATGACGTGTAACAATT
1 TGTAACAACTACATTTTTCAACATAGCATGTAACAACTAAATTTTCAACATGACGTGTAACAATT
** * * * *
6020343 GCATTTTCAACATGGCGTGTAATAA-T-TA-TTTTCAACATAACATGTAACAA-T-TATTTTCAA
66 AAATTTTCAACATGGCGTGTAACAACTACATTTTTCAACATAACATATAACAACTAAATTTTCAA
**
6020403 CATAGCG
131 CATAATG
* *
6020410 TGTAACAATTAAATTTT
1 TGTAACAACTACATTTT
6020427 AGAACATGAC
Statistics
Matches: 238, Mismatches: 46, Indels: 10
0.81 0.16 0.03
Matches are distributed among these distances:
132 28 0.12
133 1 0.00
134 21 0.09
135 2 0.01
136 1 0.00
137 159 0.67
138 26 0.11
ACGTcount: A:0.39, C:0.15, G:0.10, T:0.36
Consensus pattern (137 bp):
TGTAACAACTACATTTTTCAACATAGCATGTAACAACTAAATTTTCAACATGACGTGTAACAATT
AAATTTTCAACATGGCGTGTAACAACTACATTTTTCAACATAACATATAACAACTAAATTTTCAA
CATAATG
Found at i:6020389 original size:52 final size:50
Alignment explanation
Indices: 6020181--6020420 Score: 183
Period size: 55 Copynumber: 4.5 Consensus size: 50
6020171 TGACAACTAA
* * * * ** *
6020181 ATTTTCAACATGGTGTGTAACAGTTAAATATTCAACATGGCGTGTAACAACTAT
1 ATTTTCAACATAGCGTGTAACAATT--ATTTTCAACATAACATGTAACAA-T-T
* * * * **
6020235 ATTTTTTAACATAACATGTAACAACTATATTTTCAACATGATGTGTAACAACTAT
1 A-TTTTCAACATAGCGTGTAACAA-T-TATTTTCAACATAACATGTAACAA-T-T
* * * *
6020290 ATTTTTCAACATAGCATGTAACAACTAAATTTTCAACATGACGTGTAACAATT
1 A-TTTTCAACATAGCGTGTAACAA-T-TATTTTCAACATAACATGTAACAATT
* *
6020343 GCATTTTCAACATGGCGTGTAATAATTATTTTCAACATAACATGTAACAATT
1 --ATTTTCAACATAGCGTGTAACAATTATTTTCAACATAACATGTAACAATT
6020395 ATTTTCAACATAGCGTGTAACAATTA
1 ATTTTCAACATAGCGTGTAACAATTA
6020421 AATTTTAGAA
Statistics
Matches: 160, Mismatches: 21, Indels: 14
0.82 0.11 0.07
Matches are distributed among these distances:
50 24 0.15
52 23 0.14
53 2 0.01
54 21 0.13
55 88 0.55
56 1 0.01
57 1 0.01
ACGTcount: A:0.38, C:0.15, G:0.11, T:0.35
Consensus pattern (50 bp):
ATTTTCAACATAGCGTGTAACAATTATTTTCAACATAACATGTAACAATT
Found at i:6030545 original size:21 final size:21
Alignment explanation
Indices: 6030519--6030586 Score: 68
Period size: 21 Copynumber: 3.3 Consensus size: 21
6030509 CATCCCCTCA
6030519 CATCGTGCACATAACCGGAGT
1 CATCGTGCACATAACCGGAGT
** ** **
6030540 CATCGTGTGCATCCCCCCA--
1 CATCGTGCACATAACCGGAGT
6030559 CATCGTGCACATAACCGGAGT
1 CATCGTGCACATAACCGGAGT
6030580 CATCGTG
1 CATCGTG
6030587 TGCATCCCCC
Statistics
Matches: 33, Mismatches: 12, Indels: 4
0.67 0.24 0.08
Matches are distributed among these distances:
19 13 0.39
21 20 0.61
ACGTcount: A:0.24, C:0.34, G:0.22, T:0.21
Consensus pattern (21 bp):
CATCGTGCACATAACCGGAGT
Found at i:6030609 original size:41 final size:40
Alignment explanation
Indices: 6030505--6030610 Score: 194
Period size: 40 Copynumber: 2.6 Consensus size: 40
6030495 ACCTAGCTCA
*
6030505 TGTGCATCCCCTCACATCGTGCACATAACCGGAGTCATCG
1 TGTGCATCCCCCCACATCGTGCACATAACCGGAGTCATCG
6030545 TGTGCATCCCCCCACATCGTGCACATAACCGGAGTCATCG
1 TGTGCATCCCCCCACATCGTGCACATAACCGGAGTCATCG
6030585 TGTGCATCCCCCCCACATCGTGCACA
1 TGTGCAT-CCCCCCACATCGTGCACA
6030611 GTCAGTGCCA
Statistics
Matches: 64, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
40 46 0.72
41 18 0.28
ACGTcount: A:0.22, C:0.39, G:0.19, T:0.21
Consensus pattern (40 bp):
TGTGCATCCCCCCACATCGTGCACATAACCGGAGTCATCG
Found at i:6038029 original size:2 final size:2
Alignment explanation
Indices: 6038022--6038075 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
6038012 TCAATGCACA
6038022 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
6038064 AT AT AT AT AT AT
1 AT AT AT AT AT AT
6038076 CAACATAATG
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6038533 original size:117 final size:116
Alignment explanation
Indices: 6038338--6038569 Score: 383
Period size: 117 Copynumber: 2.0 Consensus size: 116
6038328 TATACACACC
* * *
6038338 CAACATCACAACCAACCCAAATTGGCATTAATAAAATTCTAAAAGCTATTTCTTAACTTAAGTTC
1 CAACATCACAAACAACCCAAATTGGAATTAATAAAATTCTAAAAGCTATTTCTTAACTCAAGTTC
*
6038403 AACTAGTTATTCCTAACTAGTTTTCAATCACCATTAGGTGGCTATATATTNA
66 AACTAGTTATTCCTAACTAGCTTTCAATCACCATTAGGTGGCTATATATT-A
*
6038455 CAACATCACAAATAACCCAAATTGGAATTAATAAAATTCTAAAAGCTATTTCTTAACTCAAGTTC
1 CAACATCACAAACAACCCAAATTGGAATTAATAAAATTCTAAAAGCTATTTCTTAACTCAAGTTC
* * *
6038520 AGCTAGTTATTCCTAACTAGCTTTCAATCACCATTAGGTGGTTATTTATT
66 AACTAGTTATTCCTAACTAGCTTTCAATCACCATTAGGTGGCTATATATT
6038570 TCATTACTCT
Statistics
Matches: 107, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
117 107 1.00
ACGTcount: A:0.37, C:0.20, G:0.09, T:0.34
Consensus pattern (116 bp):
CAACATCACAAACAACCCAAATTGGAATTAATAAAATTCTAAAAGCTATTTCTTAACTCAAGTTC
AACTAGTTATTCCTAACTAGCTTTCAATCACCATTAGGTGGCTATATATTA
Found at i:6047633 original size:26 final size:26
Alignment explanation
Indices: 6047563--6047625 Score: 108
Period size: 26 Copynumber: 2.4 Consensus size: 26
6047553 CTAGTATAGT
**
6047563 TGATTTTTCTTAATTTTCATTTTGAG
1 TGATTTTTCTTAATTTTTGTTTTGAG
6047589 TGATTTTTCTTAATTTTTGTTTTGAG
1 TGATTTTTCTTAATTTTTGTTTTGAG
6047615 TGATTTTTCTT
1 TGATTTTTCTT
6047626 GTTATTTGAC
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 35 1.00
ACGTcount: A:0.16, C:0.06, G:0.13, T:0.65
Consensus pattern (26 bp):
TGATTTTTCTTAATTTTTGTTTTGAG
Found at i:6051830 original size:19 final size:20
Alignment explanation
Indices: 6051792--6051831 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
6051782 AGAAGAAAAC
*
6051792 AAGCTGCTGGAAATTTCAAG
1 AAGCTACTGGAAATTTCAAG
6051812 AAGCTACTGGAAA-TTCAAG
1 AAGCTACTGGAAATTTCAAG
6051831 A
1 A
6051832 TATTTATAGG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 7 0.37
20 12 0.63
ACGTcount: A:0.40, C:0.15, G:0.23, T:0.23
Consensus pattern (20 bp):
AAGCTACTGGAAATTTCAAG
Found at i:6053238 original size:82 final size:82
Alignment explanation
Indices: 6053101--6053251 Score: 214
Period size: 82 Copynumber: 1.8 Consensus size: 82
6053091 CCTAAAAATA
*
6053101 CTAATGAAAATCATTTGATACAATTAGAATTCTTATTTACAAATCAAAACAATCTTGTTAATATT
1 CTAATGAAAATCATTTGATACAATTAGAATTCTTATTTACAAATCAAAACAATCTTATTAATATT
6053166 TATAGGAAAAAGTATTT
66 TATAGGAAAAAGTATTT
* * * * * * *
6053183 CTAATGGAAGTCATTTGATGCAATTAGTATTCTTATTTGCAAATTAGATA-AATCTTATTAATAT
1 CTAATGAAAATCATTTGATACAATTAGAATTCTTATTTACAAATCA-AAACAATCTTATTAATAT
6053247 TTATA
65 TTATA
6053252 ATAAAAATAT
Statistics
Matches: 60, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
82 58 0.97
83 2 0.03
ACGTcount: A:0.40, C:0.09, G:0.10, T:0.40
Consensus pattern (82 bp):
CTAATGAAAATCATTTGATACAATTAGAATTCTTATTTACAAATCAAAACAATCTTATTAATATT
TATAGGAAAAAGTATTT
Found at i:6054652 original size:56 final size:56
Alignment explanation
Indices: 6054580--6054745 Score: 206
Period size: 56 Copynumber: 3.0 Consensus size: 56
6054570 TTTTGTAAAT
* * * *
6054580 TTATCATGTAACCAAGTGTATTTAGATTAAGCTAGTTTAACTTATCTTATCTTACC
1 TTATCATGTAATCAAGTGTATCTAGATTAAGCTAGTTTATCTTATCTTATCCTACC
* * * * * *
6054636 TTATCATGTAATCAAGTGCATCCAGATTATGCTATTTTATCTTATTTTATCCTAGC
1 TTATCATGTAATCAAGTGTATCTAGATTAAGCTAGTTTATCTTATCTTATCCTACC
* * * *
6054692 TTATCATATAATCAAGTGTATCTAGATTAAGTTAGTATATCTTATCTTACCCTA
1 TTATCATGTAATCAAGTGTATCTAGATTAAGCTAGTTTATCTTATCTTATCCTA
6054746 AGGTGTATTA
Statistics
Matches: 91, Mismatches: 19, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
56 91 1.00
ACGTcount: A:0.30, C:0.16, G:0.10, T:0.43
Consensus pattern (56 bp):
TTATCATGTAATCAAGTGTATCTAGATTAAGCTAGTTTATCTTATCTTATCCTACC
Found at i:6059948 original size:21 final size:22
Alignment explanation
Indices: 6059919--6059961 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
6059909 AAATCTTACC
*
6059919 TTTTTCACATGTTTTC-CTTGA
1 TTTTCCACATGTTTTCTCTTGA
*
6059940 TTTTCCACATTTTTTCTCTTGA
1 TTTTCCACATGTTTTCTCTTGA
6059962 AATTCTCCAC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 14 0.74
22 5 0.26
ACGTcount: A:0.14, C:0.21, G:0.07, T:0.58
Consensus pattern (22 bp):
TTTTCCACATGTTTTCTCTTGA
Found at i:6063982 original size:28 final size:29
Alignment explanation
Indices: 6063941--6064000 Score: 68
Period size: 30 Copynumber: 2.1 Consensus size: 29
6063931 GTCTATGGGC
*
6063941 AATTTTTCAATTTT-TGGGGCAAAAATGT
1 AATTTTTCAATTTTCGGGGGCAAAAATGT
* * *
6063969 AATTTTTTACTTTTGCGGGGGCAAAAGTGT
1 AATTTTTCAATTTT-CGGGGGCAAAAATGT
6063999 AA
1 AA
6064001 ATTTCAAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
28 12 0.46
30 14 0.54
ACGTcount: A:0.30, C:0.08, G:0.22, T:0.40
Consensus pattern (29 bp):
AATTTTTCAATTTTCGGGGGCAAAAATGT
Found at i:6067623 original size:10 final size:10
Alignment explanation
Indices: 6067595--6067633 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
6067585 CCTCACCAAA
6067595 CATCAAATAT
1 CATCAAATAT
*
6067605 CACCAAAATAT
1 CATC-AAATAT
*
6067616 CATGAAATAT
1 CATCAAATAT
6067626 CATCAAAT
1 CATCAAAT
6067634 TCAGCCACAA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
10 16 0.67
11 8 0.33
ACGTcount: A:0.51, C:0.21, G:0.03, T:0.26
Consensus pattern (10 bp):
CATCAAATAT
Found at i:6070117 original size:6 final size:6
Alignment explanation
Indices: 6070106--6070176 Score: 56
Period size: 6 Copynumber: 11.8 Consensus size: 6
6070096 TAATAGATAT
* * *
6070106 ATATAC ATATAC ATATAA ATAAATAT ATATAC ATATAC ATAT-- ATATAA
1 ATATAC ATATAC ATATAC AT--ATAC ATATAC ATATAC ATATAC ATATAC
* * *
6070154 ATATAT ATATAT GTATAC ATATA
1 ATATAC ATATAC ATATAC ATATA
6070177 TATACTTATA
Statistics
Matches: 54, Mismatches: 7, Indels: 8
0.78 0.10 0.12
Matches are distributed among these distances:
4 4 0.07
6 45 0.83
8 5 0.09
ACGTcount: A:0.54, C:0.07, G:0.01, T:0.38
Consensus pattern (6 bp):
ATATAC
Found at i:6070131 original size:10 final size:10
Alignment explanation
Indices: 6070102--6070190 Score: 65
Period size: 10 Copynumber: 8.9 Consensus size: 10
6070092 ATTATAATAG
6070102 ATATATATACA
1 ATATATATA-A
*
6070113 TATACATATAA
1 -ATATATATAA
* *
6070124 ATAAATATAT
1 ATATATATAA
* *
6070134 ATACATATAC
1 ATATATATAA
6070144 ATATATATAA
1 ATATATATAA
6070154 ATATATAT--
1 ATATATATAA
* *
6070162 ATATGTATAC
1 ATATATATAA
*
6070172 ATATATATAC
1 ATATATATAA
*
6070182 TTATATATA
1 ATATATATA
6070191 TGTATGTATA
Statistics
Matches: 65, Mismatches: 10, Indels: 6
0.80 0.12 0.07
Matches are distributed among these distances:
8 7 0.11
10 49 0.75
11 1 0.02
12 8 0.12
ACGTcount: A:0.52, C:0.07, G:0.01, T:0.40
Consensus pattern (10 bp):
ATATATATAA
Found at i:6070195 original size:26 final size:26
Alignment explanation
Indices: 6070103--6070190 Score: 113
Period size: 26 Copynumber: 3.3 Consensus size: 26
6070093 TTATAATAGA
* *
6070103 TATATATACATATACATATAAATAAA
1 TATATATACATATACATATATATAAT
6070129 TATATATACATATACATATATATAAAT
1 TATATATACATATACATATATAT-AAT
** *
6070156 ATATATATATGTATACATATATATACT
1 -TATATATACATATACATATATATAAT
6070183 TATATATA
1 TATATATA
6070191 TGTATGTATA
Statistics
Matches: 55, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
26 30 0.55
27 4 0.07
28 21 0.38
ACGTcount: A:0.51, C:0.07, G:0.01, T:0.41
Consensus pattern (26 bp):
TATATATACATATACATATATATAAT
Found at i:6077012 original size:79 final size:80
Alignment explanation
Indices: 6076855--6077030 Score: 203
Period size: 79 Copynumber: 2.2 Consensus size: 80
6076845 TTATGTCTTG
* * *
6076855 AGATAATTTAGAGATAATATATTAATTTGACCAAATGAAAATTCACCTATCGGTCACCCAATTTA
1 AGATAATTTAAAGATAATATATTAATTTAACCAAATGAAAATTCACCTATCGCTCACCCAATTTA
6076920 TCTCTAAATAAATCA
66 TCTCTAAATAAATCA
* * * ** **
6076935 GGATAATTTAAAGATAATAT-TTAAATTTAACC-AATGAAAATTTACTTATTTCTCATTCAATTT
1 AGATAATTTAAAGATAATATATT-AATTTAACCAAATGAAAATTCACCTATCGCTCACCCAATTT
* *
6076998 ATCTTTCAATAAATCA
65 ATCTCTAAATAAATCA
**
6077014 AGATAATTGCAAGATAA
1 AGATAATTTAAAGATAA
6077031 AATCCAAATT
Statistics
Matches: 80, Mismatches: 15, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
79 54 0.68
80 26 0.32
ACGTcount: A:0.43, C:0.13, G:0.08, T:0.36
Consensus pattern (80 bp):
AGATAATTTAAAGATAATATATTAATTTAACCAAATGAAAATTCACCTATCGCTCACCCAATTTA
TCTCTAAATAAATCA
Found at i:6077097 original size:19 final size:17
Alignment explanation
Indices: 6077078--6077111 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
6077068 TTGAGATAAT
6077078 TTAGAGATAATACTCAAA
1 TTAG-GATAATACTCAAA
*
6077096 TTCGGATAATACTCAA
1 TTAGGATAATACTCAA
6077112 GTTCGGCCAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 12 0.80
18 3 0.20
ACGTcount: A:0.44, C:0.15, G:0.12, T:0.29
Consensus pattern (17 bp):
TTAGGATAATACTCAAA
Found at i:6077105 original size:17 final size:17
Alignment explanation
Indices: 6077083--6077117 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
6077073 ATAATTTAGA
6077083 GATAATACTCAAATTCG
1 GATAATACTCAAATTCG
*
6077100 GATAATACTCAAGTTCG
1 GATAATACTCAAATTCG
6077117 G
1 G
6077118 CCAATCAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.37, C:0.17, G:0.17, T:0.29
Consensus pattern (17 bp):
GATAATACTCAAATTCG
Found at i:6077333 original size:17 final size:17
Alignment explanation
Indices: 6077306--6077345 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
6077296 ACAAAGGAAG
* *
6077306 AGAACAAGGGAGAAAGA
1 AGAAGAAGGGACAAAGA
*
6077323 GGAAGAAGGGACAAAGA
1 AGAAGAAGGGACAAAGA
6077340 AGAAGA
1 AGAAGA
6077346 TTTTGAAGAT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.57, C:0.05, G:0.38, T:0.00
Consensus pattern (17 bp):
AGAAGAAGGGACAAAGA
Found at i:6077501 original size:28 final size:28
Alignment explanation
Indices: 6077456--6077516 Score: 86
Period size: 28 Copynumber: 2.2 Consensus size: 28
6077446 TCCAAATTGT
*
6077456 TCATAAGACCCTTAAGGTCAAGATCAAG
1 TCATAAGACCCTTAAGGTCAAGATCAAA
** *
6077484 TCATAAGATGCTTGAGGTCAAGATCAAA
1 TCATAAGACCCTTAAGGTCAAGATCAAA
6077512 TCATA
1 TCATA
6077517 TGATCCATAA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.39, C:0.18, G:0.18, T:0.25
Consensus pattern (28 bp):
TCATAAGACCCTTAAGGTCAAGATCAAA
Found at i:6077973 original size:17 final size:17
Alignment explanation
Indices: 6077945--6077979 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
6077935 ATTTAAACTT
6077945 TAATTGTTCAACTGTAAA
1 TAATTGTTCAACT-TAAA
6077963 TAATT-TTCAACTTAAA
1 TAATTGTTCAACTTAAA
6077979 T
1 T
6077980 TAAGTTTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 5 0.29
17 7 0.41
18 5 0.29
ACGTcount: A:0.40, C:0.11, G:0.06, T:0.43
Consensus pattern (17 bp):
TAATTGTTCAACTTAAA
Found at i:6082401 original size:28 final size:30
Alignment explanation
Indices: 6082360--6082424 Score: 80
Period size: 30 Copynumber: 2.2 Consensus size: 30
6082350 GTCTATGGGC
*
6082360 AATTTTTCAGTTTT-T-GGGGTAAAAATGT
1 AATTTTTCACTTTTATGGGGGTAAAAATGT
* *
6082388 AATTTTTGACTTTTATGGGGGTAAAAGTGT
1 AATTTTTCACTTTTATGGGGGTAAAAATGT
*
6082418 AAATTTT
1 AATTTTT
6082425 AAACAATTAC
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
28 12 0.39
29 1 0.03
30 18 0.58
ACGTcount: A:0.29, C:0.03, G:0.22, T:0.46
Consensus pattern (30 bp):
AATTTTTCACTTTTATGGGGGTAAAAATGT
Found at i:6085223 original size:38 final size:38
Alignment explanation
Indices: 6085133--6085232 Score: 137
Period size: 38 Copynumber: 2.6 Consensus size: 38
6085123 CTTAAAGCAA
* * * *
6085133 ATTCAAGATCAAGTCGTGGACTCTTGAAGAAAATACTC
1 ATTCAAGATCAAGTTGTAGACCCTTGAAAAAAATACTC
* *
6085171 ATTCAAGATCAAGTTATAGACCCTTGAAAAAAATATTC
1 ATTCAAGATCAAGTTGTAGACCCTTGAAAAAAATACTC
*
6085209 ATTCAAGATCAAGTTGCAGACCCT
1 ATTCAAGATCAAGTTGTAGACCCT
6085233 CCAAAATCAA
Statistics
Matches: 54, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
38 54 1.00
ACGTcount: A:0.39, C:0.19, G:0.15, T:0.27
Consensus pattern (38 bp):
ATTCAAGATCAAGTTGTAGACCCTTGAAAAAAATACTC
Found at i:6085365 original size:31 final size:31
Alignment explanation
Indices: 6085330--6085390 Score: 95
Period size: 31 Copynumber: 2.0 Consensus size: 31
6085320 TTATCGTGAG
*
6085330 CCTTGAAGCGAAGATTGAAGAAATTAATCAC
1 CCTTGAAACGAAGATTGAAGAAATTAATCAC
* *
6085361 CCTTGAAATGAAGATTGATGAAATTAATCA
1 CCTTGAAACGAAGATTGAAGAAATTAATCA
6085391 AAATATATTT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.43, C:0.13, G:0.18, T:0.26
Consensus pattern (31 bp):
CCTTGAAACGAAGATTGAAGAAATTAATCAC
Found at i:6088101 original size:20 final size:20
Alignment explanation
Indices: 6088073--6088125 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
6088063 AATATCCAAG
*
6088073 TTTCTAGCAACTTCTTCAAA
1 TTTCCAGCAACTTCTTCAAA
*
6088093 TTTCCAGCAGA-TTCTTCAAG
1 TTTCCAGCA-ACTTCTTCAAA
*
6088113 CTTCCAGCAACTT
1 TTTCCAGCAACTT
6088126 TTTCTTCTTC
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
19 1 0.04
20 26 0.93
21 1 0.04
ACGTcount: A:0.26, C:0.28, G:0.09, T:0.36
Consensus pattern (20 bp):
TTTCCAGCAACTTCTTCAAA
Found at i:6095728 original size:27 final size:26
Alignment explanation
Indices: 6095677--6095729 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 26
6095667 TCTTTCTTCT
* *
6095677 TCTTTTTTGTAGCAAAATTTGTAAAA
1 TCTTATTTGTAGCAAAATTTATAAAA
6095703 TCTTATTTGTAGTC-AAATTATATAAAA
1 TCTTATTTGTAG-CAAAATT-TATAAAA
6095730 AAAAAATGTT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
26 16 0.70
27 7 0.30
ACGTcount: A:0.38, C:0.08, G:0.09, T:0.45
Consensus pattern (26 bp):
TCTTATTTGTAGCAAAATTTATAAAA
Found at i:6101042 original size:2 final size:2
Alignment explanation
Indices: 6101035--6101059 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
6101025 GTTTCAAGCC
6101035 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
6101060 ATAACCTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:6103096 original size:2 final size:2
Alignment explanation
Indices: 6103089--6103120 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
6103079 TCCATGTGNG
*
6103089 TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
6103121 GTACATTGGT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:6111768 original size:15 final size:16
Alignment explanation
Indices: 6111748--6111780 Score: 59
Period size: 15 Copynumber: 2.1 Consensus size: 16
6111738 ACCATGGTGG
6111748 TGAATTTGAAA-ATTT
1 TGAATTTGAAATATTT
6111763 TGAATTTGAAATATTT
1 TGAATTTGAAATATTT
6111779 TG
1 TG
6111781 CAATAAAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.65
16 6 0.35
ACGTcount: A:0.36, C:0.00, G:0.15, T:0.48
Consensus pattern (16 bp):
TGAATTTGAAATATTT
Found at i:6115633 original size:2 final size:2
Alignment explanation
Indices: 6115626--6115653 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
6115616 NNNNNNNNNN
6115626 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
6115654 CAACATAACA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6121053 original size:7 final size:7
Alignment explanation
Indices: 6121041--6121065 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
6121031 GTGATTGCAA
6121041 TGAATGT
1 TGAATGT
6121048 TGAATGT
1 TGAATGT
6121055 TGAATGT
1 TGAATGT
6121062 TGAA
1 TGAA
6121066 ATTGTTAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.32, C:0.00, G:0.28, T:0.40
Consensus pattern (7 bp):
TGAATGT
Found at i:6122980 original size:21 final size:19
Alignment explanation
Indices: 6122954--6122994 Score: 55
Period size: 21 Copynumber: 2.1 Consensus size: 19
6122944 AATTTAAAAC
6122954 AAAATAACATAAAATTTAACT
1 AAAATAAC-TAAAA-TTAACT
*
6122975 AAAATAACTTAAATTAACT
1 AAAATAACTAAAATTAACT
6122994 A
1 A
6122995 CTTGACATGT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 7 0.37
20 4 0.21
21 8 0.42
ACGTcount: A:0.61, C:0.10, G:0.00, T:0.29
Consensus pattern (19 bp):
AAAATAACTAAAATTAACT
Found at i:6128293 original size:66 final size:66
Alignment explanation
Indices: 6128183--6128315 Score: 239
Period size: 66 Copynumber: 2.0 Consensus size: 66
6128173 TTATTTCTTG
* *
6128183 TAATCATGCTTATGCTTTAGTTGATCATAATATTCTTTTGCATGATTGCAATAAGTGCAAAATGC
1 TAATCATGCTTATGCTTTACTTGATCATAATATTCTTTTACATGATTGCAATAAGTGCAAAATGC
6128248 T
66 T
*
6128249 TAATCATGCTTATGCTTTACTTGATCATAATATTCTTTTACATGATTGCATTAAGTGCAAAATGC
1 TAATCATGCTTATGCTTTACTTGATCATAATATTCTTTTACATGATTGCAATAAGTGCAAAATGC
6128314 T
66 T
6128315 T
1 T
6128316 TGGTAATGCT
Statistics
Matches: 64, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
66 64 1.00
ACGTcount: A:0.30, C:0.14, G:0.14, T:0.42
Consensus pattern (66 bp):
TAATCATGCTTATGCTTTACTTGATCATAATATTCTTTTACATGATTGCAATAAGTGCAAAATGC
T
Found at i:6129279 original size:27 final size:26
Alignment explanation
Indices: 6129236--6129290 Score: 83
Period size: 27 Copynumber: 2.1 Consensus size: 26
6129226 GGCTGAACAA
* *
6129236 CTGAACAATGTTTATATTTTGTGATG
1 CTGAACAATGTTCATATTTTGTAATG
6129262 CTGAACAAATGTTCATATTTTGTAATG
1 CTGAAC-AATGTTCATATTTTGTAATG
6129289 CT
1 CT
6129291 AGTTTTGTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
26 6 0.23
27 20 0.77
ACGTcount: A:0.29, C:0.11, G:0.16, T:0.44
Consensus pattern (26 bp):
CTGAACAATGTTCATATTTTGTAATG
Found at i:6129339 original size:15 final size:15
Alignment explanation
Indices: 6129301--6129342 Score: 61
Period size: 13 Copynumber: 2.9 Consensus size: 15
6129291 AGTTTTGTTG
*
6129301 TTCTATGCTGAATGT
1 TTCTATGTTGAATGT
6129316 TT-T-TGTTGAATGT
1 TTCTATGTTGAATGT
6129329 TTCTATGTTGAATG
1 TTCTATGTTGAATG
6129343 GTGCTTACAT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
13 11 0.46
14 2 0.08
15 11 0.46
ACGTcount: A:0.19, C:0.07, G:0.21, T:0.52
Consensus pattern (15 bp):
TTCTATGTTGAATGT
Found at i:6130099 original size:20 final size:19
Alignment explanation
Indices: 6130065--6130111 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
6130055 GAATTCAAAT
* *
6130065 TTGAAGATTTTTTAATTAG
1 TTGAAGATATTTTAATCAG
6130084 TTGAAGTATATTTTAATCAG
1 TTGAAG-ATATTTTAATCAG
*
6130104 TTAAAGAT
1 TTGAAGAT
6130112 GAAGGGAGAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 8 0.33
20 16 0.67
ACGTcount: A:0.36, C:0.02, G:0.15, T:0.47
Consensus pattern (19 bp):
TTGAAGATATTTTAATCAG
Found at i:6134141 original size:4 final size:4
Alignment explanation
Indices: 6134124--6134194 Score: 65
Period size: 4 Copynumber: 18.0 Consensus size: 4
6134114 CTTTTCCTTA
* * * * *
6134124 ATAC ATAT ATAC ATAC ATAT ATAC AT-- ATAT ATAT ATAC ATAC ACAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
*
6134170 ATAAC ATAC ATGC ATAC ATAC ATAC
1 AT-AC ATAC ATAC ATAC ATAC ATAC
6134195 TTGGATAATA
Statistics
Matches: 55, Mismatches: 9, Indels: 6
0.79 0.13 0.09
Matches are distributed among these distances:
2 2 0.04
4 49 0.89
5 4 0.07
ACGTcount: A:0.49, C:0.20, G:0.01, T:0.30
Consensus pattern (4 bp):
ATAC
Found at i:6136793 original size:24 final size:24
Alignment explanation
Indices: 6136761--6136817 Score: 69
Period size: 24 Copynumber: 2.3 Consensus size: 24
6136751 AAATCCATAG
*
6136761 CAACCAAATCCTCAAACATTCAAA
1 CAACAAAATCCTCAAACATTCAAA
* * *
6136785 CAACAAAATCCTTAAATATTCAAT
1 CAACAAAATCCTCAAACATTCAAA
6136809 CAATCAAAA
1 CAA-CAAAA
6136818 CCATAAATTA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
24 23 0.82
25 5 0.18
ACGTcount: A:0.53, C:0.26, G:0.00, T:0.21
Consensus pattern (24 bp):
CAACAAAATCCTCAAACATTCAAA
Found at i:6136824 original size:24 final size:24
Alignment explanation
Indices: 6136761--6136825 Score: 62
Period size: 24 Copynumber: 2.7 Consensus size: 24
6136751 AAATCCATAG
* *
6136761 CAACCAAATCC-TCAAACATTCAAA
1 CAACAAAATCCAT-AAATATTCAAA
* *
6136785 CAACAAAATCCTTAAATATTCAAT
1 CAACAAAATCCATAAATATTCAAA
6136809 CAATCAAAA-CCATAAAT
1 CAA-CAAAATCCATAAAT
6136826 TAATGGAGGA
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
24 29 0.83
25 6 0.17
ACGTcount: A:0.52, C:0.26, G:0.00, T:0.22
Consensus pattern (24 bp):
CAACAAAATCCATAAATATTCAAA
Found at i:6139144 original size:21 final size:22
Alignment explanation
Indices: 6139120--6139165 Score: 60
Period size: 21 Copynumber: 2.1 Consensus size: 22
6139110 GAGTTTCTCA
*
6139120 CTGCAGC-AAGAATGCA-TTTCG
1 CTGCAGCGAA-AAGGCATTTTCG
6139141 CTGCAGCGAAAAGGCATTTTCG
1 CTGCAGCGAAAAGGCATTTTCG
6139163 CTG
1 CTG
6139166 TAGCTAAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
21 12 0.55
22 10 0.45
ACGTcount: A:0.26, C:0.24, G:0.26, T:0.24
Consensus pattern (22 bp):
CTGCAGCGAAAAGGCATTTTCG
Found at i:6139324 original size:2 final size:2
Alignment explanation
Indices: 6139312--6139352 Score: 73
Period size: 2 Copynumber: 20.0 Consensus size: 2
6139302 CAAACTTCTT
6139312 TA TA TA GTA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
6139353 AATACGTATA
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 36 0.95
3 2 0.05
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
TA
Found at i:6139527 original size:37 final size:36
Alignment explanation
Indices: 6139486--6139610 Score: 91
Period size: 37 Copynumber: 3.4 Consensus size: 36
6139476 GCATAGGCAA
6139486 TATCATCATCAGTGTGTGCACTCACACAGCACACCAC
1 TATCATCATCA-TGTGTGCACTCACACAGCACACCAC
* *
6139523 TATCA-CTGTCATGTGT--ACTTC-CACATCGCACAAGGCA-
1 TATCATC-ATCATGTGTGCAC-TCACACA--GCAC-A-CCAC
* *
6139560 TAT-GTCATTAATGTGTGCACTCACACAGCACACCAC
1 TATCATCA-TCATGTGTGCACTCACACAGCACACCAC
*
6139596 TATCACCATCATGTG
1 TATCATCATCATGTG
6139611 CACTTCCACA
Statistics
Matches: 66, Mismatches: 9, Indels: 27
0.65 0.09 0.26
Matches are distributed among these distances:
34 6 0.09
35 4 0.06
36 20 0.30
37 26 0.39
38 4 0.06
39 6 0.09
ACGTcount: A:0.29, C:0.31, G:0.14, T:0.26
Consensus pattern (36 bp):
TATCATCATCATGTGTGCACTCACACAGCACACCAC
Found at i:6139538 original size:36 final size:35
Alignment explanation
Indices: 6139498--6139610 Score: 83
Period size: 36 Copynumber: 3.1 Consensus size: 35
6139488 TCATCATCAG
6139498 TGTGTGCACTCACACAGCACACCACTATCACTGTCA
1 TGTGTGCACTCACACAGCACACCACTATCACT-TCA
* *
6139534 TGTGT--ACTTC-CACATCGCACAAGGCA-TATGTCA-TTAA
1 TGTGTGCAC-TCACACA--GCAC-A-CCACTA--TCACTTCA
*
6139571 TGTGTGCACTCACACAGCACACCACTATCACCATCA
1 TGTGTGCACTCACACAGCACACCACTATCA-CTTCA
6139607 TGTG
1 TGTG
6139611 CACTTCCACA
Statistics
Matches: 59, Mismatches: 5, Indels: 26
0.66 0.06 0.29
Matches are distributed among these distances:
34 9 0.15
35 4 0.07
36 18 0.31
37 14 0.24
38 5 0.08
39 9 0.15
ACGTcount: A:0.28, C:0.32, G:0.15, T:0.25
Consensus pattern (35 bp):
TGTGTGCACTCACACAGCACACCACTATCACTTCA
Found at i:6145484 original size:15 final size:15
Alignment explanation
Indices: 6145464--6145510 Score: 60
Period size: 14 Copynumber: 3.1 Consensus size: 15
6145454 TATATTTTTT
6145464 TTCTTTTTTTTCCTC
1 TTCTTTTTTTTCCTC
*
6145479 TTCTTTTTTTT-CTT
1 TTCTTTTTTTTCCTC
*
6145493 TTCTTTTCTTTCTCTC
1 TTCTTTTTTTTC-CTC
6145509 TT
1 TT
6145511 TCTCTTCCTC
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
14 12 0.44
15 11 0.41
16 4 0.15
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (15 bp):
TTCTTTTTTTTCCTC
Found at i:6145516 original size:6 final size:5
Alignment explanation
Indices: 6145458--6145513 Score: 55
Period size: 5 Copynumber: 11.2 Consensus size: 5
6145448 CATATATATA
*
6145458 TTTT- TTTTC TTTT- TTTTCC TCTTC TTTT- TTTTC TTTTC TTTTC TTTCTC
1 TTTTC TTTTC TTTTC TTTT-C TTTTC TTTTC TTTTC TTTTC TTTTC TTT-TC
6145507 TCTTTC T
1 T-TTTC T
6145514 CTTCCTCCTC
Statistics
Matches: 44, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
4 12 0.27
5 21 0.48
6 9 0.20
7 2 0.05
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (5 bp):
TTTTC
Found at i:6145722 original size:33 final size:33
Alignment explanation
Indices: 6145685--6145774 Score: 101
Period size: 33 Copynumber: 2.6 Consensus size: 33
6145675 CATATCCACA
6145685 TCAAAATCAGCAGCCAAGCTACTCTATT-TCTCC
1 TCAAAATCAGCAGCCAAGCTACTCTATTCTC-CC
* * *
6145718 TCAAAATCAGCAACTAAGCTGCTCTATTCTCCC
1 TCAAAATCAGCAGCCAAGCTACTCTATTCTCCC
*
6145751 TCCAAAAATCAGGAGCCAAAGCTA
1 T-C-AAAATCAGCAGCC-AAGCTA
6145775 TAAAAATTAA
Statistics
Matches: 46, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
33 28 0.61
34 3 0.07
35 10 0.22
36 5 0.11
ACGTcount: A:0.34, C:0.31, G:0.11, T:0.23
Consensus pattern (33 bp):
TCAAAATCAGCAGCCAAGCTACTCTATTCTCCC
Found at i:6145826 original size:35 final size:35
Alignment explanation
Indices: 6145787--6145855 Score: 129
Period size: 35 Copynumber: 2.0 Consensus size: 35
6145777 AAAATTAACA
*
6145787 ACCAAAACTGCACCTTTCAGCCTTGAAAATCAGCC
1 ACCAAAACTGCACCTTTCAGCCTTCAAAATCAGCC
6145822 ACCAAAACTGCACCTTTCAGCCTTCAAAATCAGC
1 ACCAAAACTGCACCTTTCAGCCTTCAAAATCAGC
6145856 ACTTAAAGCT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.35, C:0.35, G:0.10, T:0.20
Consensus pattern (35 bp):
ACCAAAACTGCACCTTTCAGCCTTCAAAATCAGCC
Found at i:6150049 original size:22 final size:22
Alignment explanation
Indices: 6150023--6150085 Score: 117
Period size: 22 Copynumber: 2.9 Consensus size: 22
6150013 TTTTTAACAA
*
6150023 CTTTAAAACCAAAAGCTCTGAT
1 CTTTAAAACCAAAAGCTCTAAT
6150045 CTTTAAAACCAAAAGCTCTAAT
1 CTTTAAAACCAAAAGCTCTAAT
6150067 CTTTAAAACCAAAAGCTCT
1 CTTTAAAACCAAAAGCTCT
6150086 TATACCAATC
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
22 40 1.00
ACGTcount: A:0.43, C:0.24, G:0.06, T:0.27
Consensus pattern (22 bp):
CTTTAAAACCAAAAGCTCTAAT
Found at i:6152120 original size:25 final size:26
Alignment explanation
Indices: 6152092--6152148 Score: 73
Period size: 25 Copynumber: 2.3 Consensus size: 26
6152082 ATGGGCTCTT
6152092 CCCATTTC-TTTCTAATTGGGCCATG
1 CCCATTTCTTTTCTAATTGGGCCATG
* *
6152117 CCCA-TTCTTTTTTTATTGGGCCATG
1 CCCATTTCTTTTCTAATTGGGCCATG
*
6152142 TCCATTT
1 CCCATTT
6152149 ATATGCATAT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
24 3 0.11
25 22 0.81
26 2 0.07
ACGTcount: A:0.14, C:0.26, G:0.14, T:0.46
Consensus pattern (26 bp):
CCCATTTCTTTTCTAATTGGGCCATG
Found at i:6152181 original size:5 final size:5
Alignment explanation
Indices: 6152168--6152244 Score: 90
Period size: 5 Copynumber: 16.0 Consensus size: 5
6152158 TATATATATA
* *
6152168 TTTTT TTTTC TTTTC TTTTC TCTTC TTTT- TTGTTC TTTTC TTTTC TTTTC
1 TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TT-TTC TTTTC TTTTC TTTTC
*
6152218 TTTTC TTTT- GTTTC -TTTC -TTTC TTTTC
1 TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC
6152245 CTCCTCTCTC
Statistics
Matches: 64, Mismatches: 4, Indels: 8
0.84 0.05 0.11
Matches are distributed among these distances:
4 13 0.20
5 49 0.77
6 2 0.03
ACGTcount: A:0.00, C:0.18, G:0.03, T:0.79
Consensus pattern (5 bp):
TTTTC
Found at i:6154754 original size:80 final size:80
Alignment explanation
Indices: 6154646--6154813 Score: 214
Period size: 80 Copynumber: 2.1 Consensus size: 80
6154636 CATAAGTTTC
* * * *
6154646 ATTTATGAGATTATGACATGTATACCATGAGATGTACATATTGAGAATA-TCATGTACACTATGG
1 ATTTATGAGATTATGAAAAGCATACCATGAGATGTACATATTGAG-ATAGTCATATACACTATGG
*
6154710 GTTAAGCATG-TGAGTG
65 GCTAAGCATGATGA-TG
* ** * *
6154726 ATTTATGAGATTATGAAAAGCATGCCATGAGATGTATGTTTTGAGATAGTCATATACATTATGGG
1 ATTTATGAGATTATGAAAAGCATACCATGAGATGTACATATTGAGATAGTCATATACACTATGGG
6154791 CTAAGCATGATGATG
66 CTAAGCATGATGATG
6154806 ATTTATGA
1 ATTTATGA
6154814 AAATGTTACT
Statistics
Matches: 76, Mismatches: 10, Indels: 4
0.84 0.11 0.04
Matches are distributed among these distances:
79 3 0.04
80 70 0.92
81 3 0.04
ACGTcount: A:0.34, C:0.09, G:0.23, T:0.35
Consensus pattern (80 bp):
ATTTATGAGATTATGAAAAGCATACCATGAGATGTACATATTGAGATAGTCATATACACTATGGG
CTAAGCATGATGATG
Found at i:6156198 original size:37 final size:37
Alignment explanation
Indices: 6156155--6156265 Score: 152
Period size: 37 Copynumber: 3.0 Consensus size: 37
6156145 TGGTGATGTT
6156155 GAGTGTGTGAGTAGGGAGTGCACACATGATGATGATG
1 GAGTGTGTGAGTAGGGAGTGCACACATGATGATGATG
* * **
6156192 GTGTGTGCGAGTAGGGAGTGCACACATGATGATGACA
1 GAGTGTGTGAGTAGGGAGTGCACACATGATGATGATG
* *
6156229 GAGTAT-TCGAGTAGGGAGTGCACACATGATGACGATG
1 GAGTGTGT-GAGTAGGGAGTGCACACATGATGATGATG
6156266 TATGTATATG
Statistics
Matches: 63, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
37 63 1.00
ACGTcount: A:0.28, C:0.12, G:0.38, T:0.23
Consensus pattern (37 bp):
GAGTGTGTGAGTAGGGAGTGCACACATGATGATGATG
Found at i:6157708 original size:20 final size:20
Alignment explanation
Indices: 6157672--6157709 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
6157662 TCATAGTTAG
*
6157672 GAAATGTTTATGGTTTATTA
1 GAAATGTTTATGATTTATTA
6157692 GAAA-GTTTATGAATTTAT
1 GAAATGTTTATG-ATTTAT
6157710 GCTAATGAGT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 7 0.44
20 9 0.56
ACGTcount: A:0.34, C:0.00, G:0.18, T:0.47
Consensus pattern (20 bp):
GAAATGTTTATGATTTATTA
Found at i:6162144 original size:59 final size:59
Alignment explanation
Indices: 6162052--6162170 Score: 211
Period size: 59 Copynumber: 2.0 Consensus size: 59
6162042 GTGAGATTTC
*
6162052 ATTTCCTGAGCAGGTGATGAAAGGTTCTTTTAGAGTAGTTGGTTGTAAAAAGATAAAAA
1 ATTTCCTGAGCAGGTGATGAAAGGTTCTTTTAGAGTAGATGGTTGTAAAAAGATAAAAA
* *
6162111 ATTTCCTGAGGAGGTGATGAAAGGTTCTTTTAGAGTGGATGGTTGTAAAAAGATAAAAA
1 ATTTCCTGAGCAGGTGATGAAAGGTTCTTTTAGAGTAGATGGTTGTAAAAAGATAAAAA
6162170 A
1 A
6162171 ATATTGCTAA
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
59 57 1.00
ACGTcount: A:0.36, C:0.06, G:0.27, T:0.31
Consensus pattern (59 bp):
ATTTCCTGAGCAGGTGATGAAAGGTTCTTTTAGAGTAGATGGTTGTAAAAAGATAAAAA
Found at i:6170882 original size:35 final size:34
Alignment explanation
Indices: 6170839--6170908 Score: 95
Period size: 35 Copynumber: 2.0 Consensus size: 34
6170829 TTTCACCAAG
* *
6170839 CTTTACAATGGCTTTTATCAGGCTCAACCAAAAC
1 CTTTACAATGGCTTTTACCAGGATCAACCAAAAC
* *
6170873 CTTTCACAATGGTTTTTACCGGGATCAACCAAAAC
1 CTTT-ACAATGGCTTTTACCAGGATCAACCAAAAC
6170908 C
1 C
6170909 CAACAACTAA
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
34 4 0.13
35 27 0.87
ACGTcount: A:0.31, C:0.27, G:0.13, T:0.29
Consensus pattern (34 bp):
CTTTACAATGGCTTTTACCAGGATCAACCAAAAC
Found at i:6200640 original size:40 final size:41
Alignment explanation
Indices: 6200564--6200643 Score: 135
Period size: 40 Copynumber: 2.0 Consensus size: 41
6200554 TTGGCTATTC
6200564 TTCACCTTAGTGGGGTTTTCTAACCTTGCCAAGATTGGTGG
1 TTCACCTTAGTGGGGTTTTCTAACCTTGCCAAGATTGGTGG
* *
6200605 TTCACCTTAGTGGGG-TTTCTAACCTTGCTATGATTGGTG
1 TTCACCTTAGTGGGGTTTTCTAACCTTGCCAAGATTGGTG
6200644 TCTTTTACAA
Statistics
Matches: 37, Mismatches: 2, Indels: 1
0.93 0.05 0.03
Matches are distributed among these distances:
40 22 0.59
41 15 0.41
ACGTcount: A:0.16, C:0.19, G:0.26, T:0.39
Consensus pattern (41 bp):
TTCACCTTAGTGGGGTTTTCTAACCTTGCCAAGATTGGTGG
Found at i:6206187 original size:44 final size:44
Alignment explanation
Indices: 6206124--6206212 Score: 178
Period size: 44 Copynumber: 2.0 Consensus size: 44
6206114 AGGCTGTAAC
6206124 GTTAGGTTCTTGGTGGCTGTAGAAATGATGCTCCCACACACCTT
1 GTTAGGTTCTTGGTGGCTGTAGAAATGATGCTCCCACACACCTT
6206168 GTTAGGTTCTTGGTGGCTGTAGAAATGATGCTCCCACACACCTT
1 GTTAGGTTCTTGGTGGCTGTAGAAATGATGCTCCCACACACCTT
6206212 G
1 G
6206213 AGGCATACTT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 45 1.00
ACGTcount: A:0.20, C:0.22, G:0.26, T:0.31
Consensus pattern (44 bp):
GTTAGGTTCTTGGTGGCTGTAGAAATGATGCTCCCACACACCTT
Found at i:6213442 original size:42 final size:42
Alignment explanation
Indices: 6213396--6213591 Score: 216
Period size: 42 Copynumber: 4.7 Consensus size: 42
6213386 CAACTCATAT
* ** *
6213396 GCACTTCCCACTAGCACATGGTTGGGTCAGCA-CGGCTTATGC
1 GCAC-TCCCACTAGCACATAGCCGGGTCATCATCGGCTTATGC
* *
6213438 GCACTCCTACTCGCACATAGCCGGGTCATCATCGG-TGTATGC
1 GCACTCCCACTAGCACATAGCCGGGTCATCATCGGCT-TATGC
* * *
6213480 ACACTCCTACTAGCACATAGTCGGGTCATCATCGGCTTATGC
1 GCACTCCCACTAGCACATAGCCGGGTCATCATCGGCTTATGC
* * * *
6213522 GCACTCCCACTTGCACATAGCTGGGTCATCATTGGCGTATGC
1 GCACTCCCACTAGCACATAGCCGGGTCATCATCGGCTTATGC
* * *
6213564 ACACTCCTACTTGCACATAGCCGGGTCA
1 GCACTCCCACTAGCACATAGCCGGGTCA
6213592 GTATCATTAC
Statistics
Matches: 132, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
41 22 0.17
42 109 0.83
43 1 0.01
ACGTcount: A:0.21, C:0.32, G:0.22, T:0.24
Consensus pattern (42 bp):
GCACTCCCACTAGCACATAGCCGGGTCATCATCGGCTTATGC
Found at i:6213516 original size:84 final size:83
Alignment explanation
Indices: 6213405--6213592 Score: 277
Period size: 84 Copynumber: 2.3 Consensus size: 83
6213395 TGCACTTCCC
* * *
6213405 ACTAGCACATGGTTGGGTCAGCACGGCTTATGCGCACTCCTACTCGCACATAGCCGGGTCATCAT
1 ACTAGCACATAGTCGGGTCAGCACGGCTTATGCGCACTCCCACTCGCACATAGCCGGGTCATCAT
*
6213470 CGGTGTATGCACACTCCT
66 CGGCGTATGCACACTCCT
* * *
6213488 ACTAGCACATAGTCGGGTCATCATCGGCTTATGCGCACTCCCACTTGCACATAGCTGGGTCATCA
1 ACTAGCACATAGTCGGGTCAGCA-CGGCTTATGCGCACTCCCACTCGCACATAGCCGGGTCATCA
*
6213553 TTGGCGTATGCACACTCCT
65 TCGGCGTATGCACACTCCT
* *
6213572 ACTTGCACATAGCCGGGTCAG
1 ACTAGCACATAGTCGGGTCAG
6213593 TATCATTACA
Statistics
Matches: 93, Mismatches: 11, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
83 20 0.22
84 73 0.78
ACGTcount: A:0.21, C:0.31, G:0.23, T:0.24
Consensus pattern (83 bp):
ACTAGCACATAGTCGGGTCAGCACGGCTTATGCGCACTCCCACTCGCACATAGCCGGGTCATCAT
CGGCGTATGCACACTCCT
Found at i:6213634 original size:2 final size:2
Alignment explanation
Indices: 6213627--6213662 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
6213617 AATGCACAAC
6213627 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
6213663 CAACATAATG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6218016 original size:138 final size:137
Alignment explanation
Indices: 6217762--6218025 Score: 483
Period size: 138 Copynumber: 1.9 Consensus size: 137
6217752 AGGGTAAACT
6217762 CCCCTATGGGATATCTCCTTCCATATGATGCATGGGGATCACAAGATGTACAACTCCAAGTGTAT
1 CCCCTATGGGATATCTCCTTCCATATGATGCATGGGGATCACAAGATGTACAACTCCAAGTGTAT
*
6217827 GCCTACATATTGATAACCTCCATATATTTTATGATCATGGAAACCACAATTTGCAAAACTAGCTT
66 GCCTACATATTGACAACCTCCATATATTTTATGATCATGGAAACCACAATTTGCAAAACTAGCTT
6217892 TCTATCA
131 TCTATCA
6217899 CNCCCTATGGGATATCTCCTTCCATATGATGCATGGGGATCACAAGATGTACAACTCCAAGTGTA
1 C-CCCTATGGGATATCTCCTTCCATATGATGCATGGGGATCACAAGATGTACAACTCCAAGTGTA
* * *
6217964 TGGCTACATATTGACAACCTCCATATATTTTATGATCATGGAAACCATAATTTGTAAAACTA
65 TGCCTACATATTGACAACCTCCATATATTTTATGATCATGGAAACCACAATTTGCAAAACTA
6218026 TATTTTTATC
Statistics
Matches: 122, Mismatches: 4, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
137 1 0.01
138 121 0.99
ACGTcount: A:0.32, C:0.22, G:0.15, T:0.30
Consensus pattern (137 bp):
CCCCTATGGGATATCTCCTTCCATATGATGCATGGGGATCACAAGATGTACAACTCCAAGTGTAT
GCCTACATATTGACAACCTCCATATATTTTATGATCATGGAAACCACAATTTGCAAAACTAGCTT
TCTATCA
Found at i:6220793 original size:42 final size:42
Alignment explanation
Indices: 6220745--6220903 Score: 210
Period size: 42 Copynumber: 3.8 Consensus size: 42
6220735 GTCAGCACGG
6220745 CTTATGCGCACTCCTACTCGCACATAGCCGGGTCATCATCGA
1 CTTATGCGCACTCCTACTCGCACATAGCCGGGTCATCATCGA
* * * * *
6220787 CGTATGCACACTCGTACTCACACATAGTCGGGTCATCATCGA
1 CTTATGCGCACTCCTACTCGCACATAGCCGGGTCATCATCGA
* * * * * *
6220829 CTTATGCGCTCTCCCACTCGCACGTAGTCGGGCCATCATTGA
1 CTTATGCGCACTCCTACTCGCACATAGCCGGGTCATCATCGA
*
6220871 CTTATGCGCACTCTTACTCGCACATAGCCGGGT
1 CTTATGCGCACTCCTACTCGCACATAGCCGGGT
6220904 TAATATCATT
Statistics
Matches: 97, Mismatches: 20, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
42 97 1.00
ACGTcount: A:0.21, C:0.34, G:0.20, T:0.25
Consensus pattern (42 bp):
CTTATGCGCACTCCTACTCGCACATAGCCGGGTCATCATCGA
Found at i:6222892 original size:2 final size:2
Alignment explanation
Indices: 6222885--6222912 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
6222875 CTTTCAATTA
6222885 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
6222913 GAAATATGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6224731 original size:78 final size:78
Alignment explanation
Indices: 6224602--6224758 Score: 296
Period size: 78 Copynumber: 2.0 Consensus size: 78
6224592 TAAATCGATA
*
6224602 GGAGGTAATGTGGTTTTGAAGTTAGATATGATGAAAGCATATGGCTAGTTACATTGGGATTTGAT
1 GGAGGTAATGTGGTTTTGAAGTTAGATATGATGAAAGCATATGACTAGTTACATTGGGATTTGAT
6224667 ATATTTGATGATG
66 ATATTTGATGATG
*
6224680 GGAGGTAATGTGGTTTTGAAGTTAGATATGATGAAAGCATATGACTAGTTACATTGGGATTTTAT
1 GGAGGTAATGTGGTTTTGAAGTTAGATATGATGAAAGCATATGACTAGTTACATTGGGATTTGAT
6224745 ATATTTGATGATG
66 ATATTTGATGATG
6224758 G
1 G
6224759 CAAAATTTGG
Statistics
Matches: 77, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
78 77 1.00
ACGTcount: A:0.30, C:0.04, G:0.29, T:0.38
Consensus pattern (78 bp):
GGAGGTAATGTGGTTTTGAAGTTAGATATGATGAAAGCATATGACTAGTTACATTGGGATTTGAT
ATATTTGATGATG
Found at i:6227385 original size:23 final size:23
Alignment explanation
Indices: 6227346--6227392 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 23
6227336 AGCTTAAAAA
6227346 AAAAAACTTAATTTATTAATTTT
1 AAAAAACTTAATTTATTAATTTT
*
6227369 AAAAAA-TTCATTATATTAATTTT
1 AAAAAACTTAATT-TATTAATTTT
6227392 A
1 A
6227393 TTCCAATCCA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 5 0.23
23 17 0.77
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (23 bp):
AAAAAACTTAATTTATTAATTTT
Found at i:6231329 original size:43 final size:43
Alignment explanation
Indices: 6231260--6231377 Score: 137
Period size: 43 Copynumber: 2.7 Consensus size: 43
6231250 TGTTGACTCG
* * *
6231260 GCTATGTGCGAGTAGGGAGTGTGCATAAGCTGAGGATGCCCCG
1 GCTATGTGCGAGTAGGGAGTGCGCATAAGCTGAGGATGACCCA
* * * * *
6231303 GTTATGTGCGAGTAAGGAATGCGCATAAGCCGATGATGACCCA
1 GCTATGTGCGAGTAGGGAGTGCGCATAAGCTGAGGATGACCCA
* * *
6231346 GCCATGTGCGATTAGGGAGTGCGCATGAGCTG
1 GCTATGTGCGAGTAGGGAGTGCGCATAAGCTG
6231378 GTGATGATGA
Statistics
Matches: 60, Mismatches: 15, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
43 60 1.00
ACGTcount: A:0.24, C:0.19, G:0.36, T:0.21
Consensus pattern (43 bp):
GCTATGTGCGAGTAGGGAGTGCGCATAAGCTGAGGATGACCCA
Found at i:6231387 original size:3 final size:3
Alignment explanation
Indices: 6231379--6231437 Score: 52
Period size: 3 Copynumber: 20.7 Consensus size: 3
6231369 CATGAGCTGG
* * * * *
6231379 TGA TGA TGA TGA TGA TGA -GC TGG TGA TGA TGA TGA TG- GGT TGG TGA
1 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA
6231425 -GA TGA TGA TGA TG
1 TGA TGA TGA TGA TG
6231438 GTATATACGT
Statistics
Matches: 46, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
2 4 0.09
3 42 0.91
ACGTcount: A:0.25, C:0.02, G:0.41, T:0.32
Consensus pattern (3 bp):
TGA
Found at i:6231397 original size:23 final size:23
Alignment explanation
Indices: 6231370--6231437 Score: 99
Period size: 23 Copynumber: 3.1 Consensus size: 23
6231360 GGGAGTGCGC
6231370 ATGAGCTGGTGATGATGATGATG
1 ATGAGCTGGTGATGATGATGATG
6231393 ATGAGCTGGTGATGATGATGATG
1 ATGAGCTGGTGATGATGATGATG
*
6231416 --G-GTTGGTGA-GATGATGATG
1 ATGAGCTGGTGATGATGATGATG
6231435 ATG
1 ATG
6231438 GTATATACGT
Statistics
Matches: 42, Mismatches: 1, Indels: 6
0.86 0.02 0.12
Matches are distributed among these distances:
19 10 0.24
20 7 0.17
21 2 0.05
23 23 0.55
ACGTcount: A:0.25, C:0.03, G:0.41, T:0.31
Consensus pattern (23 bp):
ATGAGCTGGTGATGATGATGATG
Done.