Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A09
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: 81831061
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 3560000 characters in sequence are not A, C, G, or T
File 34 of 259
Found at i:9987996 original size:24 final size:24
Alignment explanation
Indices: 9987969--9988027 Score: 75
Period size: 25 Copynumber: 2.4 Consensus size: 24
9987959 ACTGGAGCCT
9987969 AGCCTCTTTTAAT-AACTGGGGCAG
1 AGCC-CTTTTAATAAACTGGGGCAG
**
9987993 AGCCCTTTTCGGTAAACTGGGGCAG
1 AGCCCTTTT-AATAAACTGGGGCAG
9988018 AGCCCTTTTA
1 AGCCCTTTTA
9988028 GCACTTCCTC
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
23 5 0.17
24 5 0.17
25 20 0.67
ACGTcount: A:0.22, C:0.24, G:0.25, T:0.29
Consensus pattern (24 bp):
AGCCCTTTTAATAAACTGGGGCAG
Found at i:9989091 original size:30 final size:30
Alignment explanation
Indices: 9989046--9989134 Score: 92
Period size: 30 Copynumber: 3.0 Consensus size: 30
9989036 CAAAGATAAC
9989046 AAGAAAACCA-AATAAAGAAATCCAAGATA
1 AAGAAAACCAGAATAAAGAAATCCAAGATA
* *
9989075 GAGAAACCCAGAATAAAGAAATCC-AGAATA
1 AAGAAAACCAGAATAAAGAAATCCAAG-ATA
* * * * *
9989105 AAGAGATCTAGGATAAAGAAACCCAAGATA
1 AAGAAAACCAGAATAAAGAAATCCAAGATA
9989135 TGATACTATG
Statistics
Matches: 49, Mismatches: 8, Indels: 5
0.79 0.13 0.08
Matches are distributed among these distances:
29 10 0.20
30 37 0.76
31 2 0.04
ACGTcount: A:0.58, C:0.15, G:0.16, T:0.11
Consensus pattern (30 bp):
AAGAAAACCAGAATAAAGAAATCCAAGATA
Found at i:9989094 original size:15 final size:15
Alignment explanation
Indices: 9989046--9989125 Score: 83
Period size: 15 Copynumber: 5.4 Consensus size: 15
9989036 CAAAGATAAC
*
9989046 AAGAAAACCA-AATA
1 AAGAAATCCAGAATA
9989060 AAGAAATCCA-AGATA
1 AAGAAATCCAGA-ATA
* *
9989075 GAGAAACCCAGAATA
1 AAGAAATCCAGAATA
9989090 AAGAAATCCAGAATA
1 AAGAAATCCAGAATA
* * *
9989105 AAGAGATCTAGGATA
1 AAGAAATCCAGAATA
9989120 AAGAAA
1 AAGAAA
9989126 CCCAAGATAT
Statistics
Matches: 55, Mismatches: 9, Indels: 3
0.82 0.13 0.04
Matches are distributed among these distances:
14 10 0.18
15 44 0.80
16 1 0.02
ACGTcount: A:0.60, C:0.12, G:0.16, T:0.11
Consensus pattern (15 bp):
AAGAAATCCAGAATA
Found at i:9989134 original size:15 final size:15
Alignment explanation
Indices: 9989046--9989134 Score: 76
Period size: 15 Copynumber: 6.0 Consensus size: 15
9989036 CAAAGATAAC
*
9989046 AAGAAAACCAA-ATA
1 AAGAAATCCAAGATA
9989060 AAGAAATCCAAGATA
1 AAGAAATCCAAGATA
* *
9989075 GAGAAA-CCCAGAATA
1 AAGAAATCCAAG-ATA
9989090 AAGAAATCC-AGAATA
1 AAGAAATCCAAG-ATA
* * *
9989105 AAGAGATCTAGGATA
1 AAGAAATCCAAGATA
*
9989120 AAGAAACCCAAGATA
1 AAGAAATCCAAGATA
9989135 TGATACTATG
Statistics
Matches: 60, Mismatches: 11, Indels: 7
0.77 0.14 0.09
Matches are distributed among these distances:
14 14 0.23
15 43 0.72
16 3 0.05
ACGTcount: A:0.58, C:0.15, G:0.16, T:0.11
Consensus pattern (15 bp):
AAGAAATCCAAGATA
Found at i:9992162 original size:46 final size:46
Alignment explanation
Indices: 9992095--9992269 Score: 201
Period size: 46 Copynumber: 3.8 Consensus size: 46
9992085 TGTAACCCGC
9992095 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCATTCGTAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCATTCGTAT
* *
9992141 CCATAAGTGAACTCGGACTCAACTCAACGAGCTC-GG-ATGCCTAGTT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCATTCGTA--T
* *** * * * *
9992187 ACATCTCTCGAACTCGGACTCAACTCAACGAGTTCAGACATTCGCAT
1 CCATAAGT-GAACTCGGACTCAACTCAACGAGCTCGGGCATTCGTAT
* *
9992234 CCATAAGTGAACTCGAACTCAACTCAACGAGTTCGG
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGG
9992270 ATGCCCAAAT
Statistics
Matches: 107, Mismatches: 17, Indels: 10
0.80 0.13 0.07
Matches are distributed among these distances:
44 5 0.05
45 2 0.02
46 65 0.61
47 30 0.28
48 1 0.01
49 4 0.04
ACGTcount: A:0.30, C:0.29, G:0.19, T:0.22
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCATTCGTAT
Found at i:9992215 original size:93 final size:93
Alignment explanation
Indices: 9992103--9992274 Score: 290
Period size: 93 Copynumber: 1.8 Consensus size: 93
9992093 GCCCATAAGT
* * * *
9992103 GAACTCGGACTCAACTCAACGAGCTCGGGCATTCGTATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCAGACATTCGCATCCATAAGTGAACTCGAACTCAACTCAA
9992168 CGAGCTCGGATGCCTAGTTACATCTCTC
66 CGAGCTCGGATGCCTAGTTACATCTCTC
*
9992196 GAACTCGGACTCAACTCAACGAGTTCAGACATTCGCATCCATAAGTGAACTCGAACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCAGACATTCGCATCCATAAGTGAACTCGAACTCAACTCAA
*
9992261 CGAGTTCGGATGCC
66 CGAGCTCGGATGCC
9992275 CAAATATCCT
Statistics
Matches: 73, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
93 73 1.00
ACGTcount: A:0.29, C:0.30, G:0.20, T:0.22
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCAGACATTCGCATCCATAAGTGAACTCGAACTCAACTCAA
CGAGCTCGGATGCCTAGTTACATCTCTC
Found at i:9994304 original size:27 final size:27
Alignment explanation
Indices: 9994243--9994306 Score: 76
Period size: 27 Copynumber: 2.4 Consensus size: 27
9994233 GGCATATTCA
9994243 TCATTTTACCATACAAGGGTATTACGG
1 TCATTTTACCATACAAGGGTATTACGG
* * *
9994270 TCACTTTACCCTACATGGGCT-TTACGG
1 TCATTTTACCATACAAGGG-TATTACGG
*
9994297 TCTTTTTACC
1 TCATTTTACC
9994307 TATTAGGGGT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
27 30 0.97
28 1 0.03
ACGTcount: A:0.22, C:0.25, G:0.16, T:0.38
Consensus pattern (27 bp):
TCATTTTACCATACAAGGGTATTACGG
Found at i:9994389 original size:27 final size:27
Alignment explanation
Indices: 9994359--9994411 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
9994349 GGTAAATCTA
*
9994359 CAAACCAAGGGTATTTCAATAATTTTG
1 CAAACCAAGGGTATTCCAATAATTTTG
* *
9994386 CAAACCAATGGTATTCCTATAATTTT
1 CAAACCAAGGGTATTCCAATAATTTT
9994412 TAAAAAAGTC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.36, C:0.17, G:0.11, T:0.36
Consensus pattern (27 bp):
CAAACCAAGGGTATTCCAATAATTTTG
Found at i:9994464 original size:27 final size:27
Alignment explanation
Indices: 9994423--9994494 Score: 85
Period size: 27 Copynumber: 2.7 Consensus size: 27
9994413 AAAAAAGTCA
**
9994423 AGGGTATTTCTGTAATTTTGTAAATT-
1 AGGGTATTTCTGTAATTTTACAAATTG
9994449 AGGGGTATTT-TGGTAATTTTACAAATTG
1 A-GGGTATTTCT-GTAATTTTACAAATTG
*
9994477 AGGGTATTTCTATAATTT
1 AGGGTATTTCTGTAATTT
9994495 CTCAAACCAG
Statistics
Matches: 39, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
26 2 0.05
27 35 0.90
28 2 0.05
ACGTcount: A:0.28, C:0.04, G:0.21, T:0.47
Consensus pattern (27 bp):
AGGGTATTTCTGTAATTTTACAAATTG
Found at i:9994590 original size:27 final size:27
Alignment explanation
Indices: 9994550--9994641 Score: 123
Period size: 27 Copynumber: 3.4 Consensus size: 27
9994540 GTAATTTCAC
*
9994550 AATCGATGGTAAAACGGTAATTTTGTA
1 AATCGAGGGTAAAACGGTAATTTTGTA
*
9994577 AA-CTGAGGGTAAAATGGTAATTTTGTA
1 AATC-GAGGGTAAAACGGTAATTTTGTA
* * *
9994604 AATCGAGGGTAAAACGATAATTCTATA
1 AATCGAGGGTAAAACGGTAATTTTGTA
9994631 AATCGAGGGTA
1 AATCGAGGGTA
9994642 CTTTGGTAAT
Statistics
Matches: 57, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
26 1 0.02
27 55 0.96
28 1 0.02
ACGTcount: A:0.39, C:0.08, G:0.24, T:0.29
Consensus pattern (27 bp):
AATCGAGGGTAAAACGGTAATTTTGTA
Found at i:9994639 original size:54 final size:54
Alignment explanation
Indices: 9994540--9994668 Score: 136
Period size: 54 Copynumber: 2.4 Consensus size: 54
9994530 GGGTATTTCA
* * * * *
9994540 GTAATTTCAC-AATCGATGGTAAAACGGTAATTTTGTAAACTGAGGGTAAAATG
1 GTAATTTTACAAATCGAGGGTAAAACGATAATTCTATAAACTGAGGGTAAAATG
** ***
9994593 GTAATTTTGTAAATCGAGGGTAAAACGATAATTCTATAAA-TCGAGGGTACTTTG
1 GTAATTTTACAAATCGAGGGTAAAACGATAATTCTATAAACT-GAGGGTAAAATG
*
9994647 GTAATTTTACAAGTCGAGGGTA
1 GTAATTTTACAAATCGAGGGTA
9994669 TTTCAGTAAT
Statistics
Matches: 61, Mismatches: 13, Indels: 3
0.79 0.17 0.04
Matches are distributed among these distances:
53 8 0.13
54 53 0.87
ACGTcount: A:0.36, C:0.09, G:0.23, T:0.32
Consensus pattern (54 bp):
GTAATTTTACAAATCGAGGGTAAAACGATAATTCTATAAACTGAGGGTAAAATG
Found at i:9995864 original size:12 final size:12
Alignment explanation
Indices: 9995847--9995871 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
9995837 GCCGACTACT
9995847 GTTACTGTTACC
1 GTTACTGTTACC
9995859 GTTACTGTTACC
1 GTTACTGTTACC
9995871 G
1 G
9995872 ATTTAACACT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.24, G:0.20, T:0.40
Consensus pattern (12 bp):
GTTACTGTTACC
Found at i:9995899 original size:45 final size:45
Alignment explanation
Indices: 9995849--9995955 Score: 151
Period size: 45 Copynumber: 2.4 Consensus size: 45
9995839 CGACTACTGT
* *
9995849 TACTGTTACCGTTACTGTTACCGATTTAACACTTTGTGTGTCAAA
1 TACTGTTACCGTTACTGTTACAGATTCAACACTTTGTGTGTCAAA
* **
9995894 TACTGTTACCGTTACTGTTACAGATTCAGCACTTTGTGTGTTGAA
1 TACTGTTACCGTTACTGTTACAGATTCAACACTTTGTGTGTCAAA
* *
9995939 TACTGTAACTGTTACTG
1 TACTGTTACCGTTACTG
9995956 ATACTGCTAC
Statistics
Matches: 55, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
45 55 1.00
ACGTcount: A:0.23, C:0.19, G:0.18, T:0.40
Consensus pattern (45 bp):
TACTGTTACCGTTACTGTTACAGATTCAACACTTTGTGTGTCAAA
Found at i:10005588 original size:43 final size:43
Alignment explanation
Indices: 10005540--10005651 Score: 206
Period size: 43 Copynumber: 2.6 Consensus size: 43
10005530 CCAGCATTAC
10005540 GCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGCACGAA
1 GCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGCACGAA
* *
10005583 GCCTGCTAGGTACGAAGGCCCGAATACACATCACTGGCACGAA
1 GCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGCACGAA
10005626 GCCTGCTAGGCACGAAGGCCCGAATA
1 GCCTGCTAGGCACGAAGGCCCGAATA
10005652 TAATACCAGC
Statistics
Matches: 66, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
43 66 1.00
ACGTcount: A:0.29, C:0.32, G:0.27, T:0.12
Consensus pattern (43 bp):
GCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGCACGAA
Found at i:10005694 original size:38 final size:38
Alignment explanation
Indices: 10005644--10005845 Score: 305
Period size: 38 Copynumber: 5.3 Consensus size: 38
10005634 GGCACGAAGG
* * * *
10005644 CCCGAATATAATACCAGCACTAGGCCTGCGGGATTTAT
1 CCCGGATATAATACCAGCACGAAGCCTGCGGGATTTAA
*
10005682 CCCGGACATAATACCAGCACGAAGCCTGCGGGATTTAA
1 CCCGGATATAATACCAGCACGAAGCCTGCGGGATTTAA
** *
10005720 CCCGGATATTTTACCAGCACGAAGCCTGCGGGTCTTTAA
1 CCCGGATATAATACCAGCACGAAGCCTGCGGG-ATTTAA
*
10005759 GCCCGGATATAATACCAGCACGAAGCCTGCGAGATTTAA
1 -CCCGGATATAATACCAGCACGAAGCCTGCGGGATTTAA
10005798 CCCGGATATAATACCAGCACGAAGCCTGCGGGATTTAA
1 CCCGGATATAATACCAGCACGAAGCCTGCGGGATTTAA
10005836 CCCGGATATA
1 CCCGGATATA
10005846 CATCGAATAT
Statistics
Matches: 148, Mismatches: 14, Indels: 4
0.89 0.08 0.02
Matches are distributed among these distances:
38 109 0.74
39 10 0.07
40 29 0.20
ACGTcount: A:0.30, C:0.27, G:0.23, T:0.20
Consensus pattern (38 bp):
CCCGGATATAATACCAGCACGAAGCCTGCGGGATTTAA
Found at i:10005778 original size:78 final size:76
Alignment explanation
Indices: 10005644--10005845 Score: 305
Period size: 78 Copynumber: 2.6 Consensus size: 76
10005634 GGCACGAAGG
* * * * *
10005644 CCCGAATATAATACCAGCACTAGGCCTGCGGGATTTATCCCGGACATAATACCAGCACGAAGCCT
1 CCCGGATATAATACCAGCACGAAGCCTGCGGGATTTAACCCGGATATAATACCAGCACGAAGCCT
*
10005709 GCGGGATTTAA
66 GCGAGATTTAA
** *
10005720 CCCGGATATTTTACCAGCACGAAGCCTGCGGGTCTTTAAGCCCGGATATAATACCAGCACGAAGC
1 CCCGGATATAATACCAGCACGAAGCCTGCGGG-ATTTAA-CCCGGATATAATACCAGCACGAAGC
10005785 CTGCGAGATTTAA
64 CTGCGAGATTTAA
10005798 CCCGGATATAATACCAGCACGAAGCCTGCGGGATTTAACCCGGATATA
1 CCCGGATATAATACCAGCACGAAGCCTGCGGGATTTAACCCGGATATA
10005846 CATCGAATAT
Statistics
Matches: 112, Mismatches: 12, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
76 37 0.33
77 9 0.08
78 66 0.59
ACGTcount: A:0.30, C:0.27, G:0.23, T:0.20
Consensus pattern (76 bp):
CCCGGATATAATACCAGCACGAAGCCTGCGGGATTTAACCCGGATATAATACCAGCACGAAGCCT
GCGAGATTTAA
Found at i:10013982 original size:181 final size:181
Alignment explanation
Indices: 10013650--10014026 Score: 494
Period size: 181 Copynumber: 2.1 Consensus size: 181
10013640 AAATTTTTTA
*
10013650 TTTTATACCCATAAAAAGATAGATAAATGTTTATAATGTATAATTTAAACATTCTGGCAGTATTT
1 TTTTATACCCATAAAAAGATAGATAAATGTTTATAATGTATAATTTAAACATTCTGGCACTATTT
* * * *
10013715 TAATATAATATTAGAATCCCTACTTTTGCAAGTTTTTTTTTCTTTATTCCAATGAAGTGCATTAT
66 TAATATAATATTAGAAACCCTACTTCT-CAAGGTTTTTTTCCTTTATTCCAATGAAGTGCATTAT
*
10013780 TTTTATTTTACACTCAAACATGTTTTTTTTCTAAATTGTGCCTAAATAATTT
130 TTTTATTTTACACTCAAACATGTTTTTTTTATAAATTGTGCCTAAATAATTT
* *
10013832 TTTTATACCCA-AAAAAGTATAGATAAATTTTTATAATGTACT-GTTTAAACATT-TGGCACTAT
1 TTTTATACCCATAAAAAG-ATAGATAAATGTTTATAATGTA-TAATTTAAACATTCTGGCACTAT
* **
10013894 TTTAATATAATATTAGAAACCAC-GCTTCT-ATAGGTTTTTTTCCTTTATTTTAATGAAGTGCAT
64 TTTAATATAATATTAGAAACC-CTACTTCTCA-AGGTTTTTTTCCTTTATTCCAATGAAGTGCAT
* * *** *
10013957 TAGTTTTTGTTTTACACTTAAACATGTTTTTTTTATAAATTGTATTTAAAAAATTT
127 TA-TTTTTATTTTACACTCAAACATGTTTTTTTTATAAATTGTGCCTAAATAATTT
10014013 CATTTTATACCCAT
1 --TTTTATACCCAT
10014027 TAAGCATTTT
Statistics
Matches: 170, Mismatches: 17, Indels: 14
0.85 0.08 0.07
Matches are distributed among these distances:
179 1 0.01
180 30 0.18
181 84 0.49
182 43 0.25
183 12 0.07
ACGTcount: A:0.33, C:0.12, G:0.09, T:0.46
Consensus pattern (181 bp):
TTTTATACCCATAAAAAGATAGATAAATGTTTATAATGTATAATTTAAACATTCTGGCACTATTT
TAATATAATATTAGAAACCCTACTTCTCAAGGTTTTTTTCCTTTATTCCAATGAAGTGCATTATT
TTTATTTTACACTCAAACATGTTTTTTTTATAAATTGTGCCTAAATAATTT
Found at i:10015391 original size:59 final size:61
Alignment explanation
Indices: 10015324--10015440 Score: 166
Period size: 62 Copynumber: 1.9 Consensus size: 61
10015314 ATCAATTTAG
* * *
10015324 TATTAAATTAATATAATATTTA-T-CAAGATAAATATTAGATTAAATTTAACATTAAATCT
1 TATTAAATTAATAAAATATTTACTACAAGATAAACATTAAATTAAATTTAACATTAAATCT
* *
10015383 TATTAAATTAATAAAATATTTATCTACAAGATAAACATTAAATTTAATTTAATATTAA
1 TATTAAATTAATAAAATATTTA-CTACAAGATAAACATTAAATTAAATTTAACATTAA
10015441 GATAATCACT
Statistics
Matches: 50, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
59 21 0.42
61 1 0.02
62 28 0.56
ACGTcount: A:0.50, C:0.05, G:0.03, T:0.42
Consensus pattern (61 bp):
TATTAAATTAATAAAATATTTACTACAAGATAAACATTAAATTAAATTTAACATTAAATCT
Found at i:10021320 original size:29 final size:29
Alignment explanation
Indices: 10021242--10021320 Score: 88
Period size: 29 Copynumber: 2.8 Consensus size: 29
10021232 ACATACATGT
* *
10021242 ATATGACCCACTAGGCCC-AATCTCATTC
1 ATATGACCCATTAGGCCCAAATCACATTC
* *
10021270 ATATGACCCATTGGGCCTAAATCACATTC
1 ATATGACCCATTAGGCCCAAATCACATTC
* * *
10021299 GTATGGCCCATTAGACCCAAAT
1 ATATGACCCATTAGGCCCAAAT
10021321 AATATACATA
Statistics
Matches: 41, Mismatches: 9, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
28 15 0.37
29 26 0.63
ACGTcount: A:0.30, C:0.30, G:0.14, T:0.25
Consensus pattern (29 bp):
ATATGACCCATTAGGCCCAAATCACATTC
Found at i:10027804 original size:18 final size:18
Alignment explanation
Indices: 10027781--10027815 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
10027771 TGATTTGGAT
10027781 CGTGTGGGTCCACACGGG
1 CGTGTGGGTCCACACGGG
10027799 CGTGTGGGTCCACACGG
1 CGTGTGGGTCCACACGG
10027816 ATAGTCCACG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.11, C:0.29, G:0.43, T:0.17
Consensus pattern (18 bp):
CGTGTGGGTCCACACGGG
Found at i:10031845 original size:23 final size:23
Alignment explanation
Indices: 10031817--10031910 Score: 125
Period size: 23 Copynumber: 4.1 Consensus size: 23
10031807 ATGTGTGTAT
* *
10031817 CTTTTCATATTCAAGCCTTTTAA
1 CTTTTCATATTCAAGTCTTTTCA
* *
10031840 CTTTTCATCTTCAAGTCTCTTCA
1 CTTTTCATATTCAAGTCTTTTCA
* *
10031863 CTATTCATATTCAAGTTTTTTCA
1 CTTTTCATATTCAAGTCTTTTCA
*
10031886 CTTTTCATATTCAAGTCTCTTCA
1 CTTTTCATATTCAAGTCTTTTCA
10031909 CT
1 CT
10031911 CTTCTAACTT
Statistics
Matches: 60, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 60 1.00
ACGTcount: A:0.22, C:0.24, G:0.04, T:0.49
Consensus pattern (23 bp):
CTTTTCATATTCAAGTCTTTTCA
Found at i:10031873 original size:46 final size:46
Alignment explanation
Indices: 10031820--10031910 Score: 146
Period size: 46 Copynumber: 2.0 Consensus size: 46
10031810 TGTGTATCTT
*
10031820 TTCATATTCAAGCCTTTTAACTTTTCATCTTCAAGTCTCTTCACTA
1 TTCATATTCAAGCCTTTTAACTTTTCATATTCAAGTCTCTTCACTA
** *
10031866 TTCATATTCAAGTTTTTTCACTTTTCATATTCAAGTCTCTTCACT
1 TTCATATTCAAGCCTTTTAACTTTTCATATTCAAGTCTCTTCACT
10031911 CTTCTAACTT
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
46 41 1.00
ACGTcount: A:0.23, C:0.24, G:0.04, T:0.48
Consensus pattern (46 bp):
TTCATATTCAAGCCTTTTAACTTTTCATATTCAAGTCTCTTCACTA
Found at i:10036351 original size:23 final size:23
Alignment explanation
Indices: 10036323--10036416 Score: 134
Period size: 23 Copynumber: 4.1 Consensus size: 23
10036313 ATGTGTGTAT
* *
10036323 CTTTTCATATTCAAGCCTCTTAA
1 CTTTTCATATTCAAGTCTCTTCA
*
10036346 CTTTTCATCTTCAAGTCTCTTCA
1 CTTTTCATATTCAAGTCTCTTCA
* * *
10036369 CTATTCATATTCAAGTTTTTTCA
1 CTTTTCATATTCAAGTCTCTTCA
10036392 CTTTTCATATTCAAGTCTCTTCA
1 CTTTTCATATTCAAGTCTCTTCA
10036415 CT
1 CT
10036417 CTTCTAACTT
Statistics
Matches: 61, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 61 1.00
ACGTcount: A:0.22, C:0.26, G:0.04, T:0.48
Consensus pattern (23 bp):
CTTTTCATATTCAAGTCTCTTCA
Found at i:10043559 original size:22 final size:21
Alignment explanation
Indices: 10043534--10043580 Score: 51
Period size: 22 Copynumber: 2.1 Consensus size: 21
10043524 TTTTAATTTT
*
10043534 AAAT-TTAATAATAGAAAAATTA
1 AAATGTTAA-AATA-AAAAATAA
10043556 AAATGGTTAAAATAAAAAATAA
1 AAAT-GTTAAAATAAAAAATAA
10043578 AAA
1 AAA
10043581 AATAGTTTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
22 14 0.64
23 4 0.18
24 4 0.18
ACGTcount: A:0.68, C:0.00, G:0.06, T:0.26
Consensus pattern (21 bp):
AAATGTTAAAATAAAAAATAA
Found at i:10047395 original size:23 final size:23
Alignment explanation
Indices: 10047369--10047415 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
10047359 CTGTGAGAGA
10047369 TAGTCTTTGCACTCTTTCTTGCC
1 TAGTCTTTGCACTCTTTCTTGCC
10047392 TAGTCTTTGCACTCTTTCTTGCC
1 TAGTCTTTGCACTCTTTCTTGCC
10047415 T
1 T
10047416 CTTATTAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.09, C:0.30, G:0.13, T:0.49
Consensus pattern (23 bp):
TAGTCTTTGCACTCTTTCTTGCC
Found at i:10050146 original size:73 final size:73
Alignment explanation
Indices: 10050027--10050171 Score: 281
Period size: 73 Copynumber: 2.0 Consensus size: 73
10050017 ATATTATTTG
10050027 GTTCTTTTTTAATAAAGTCATTAAGTTTTTAGATCATTTTACTAAAATGACCCCAAAAAATAAAT
1 GTTCTTTTTTAATAAAGTCATTAAGTTTTTAGATCATTTTACTAAAATGACCCCAAAAAATAAAT
10050092 AATTACAT
66 AATTACAT
*
10050100 GTTCTTTTTTAATAAAGTCATTAAGTTTTTAGATCATTTTACTAAAATGATCCCAAAAAATAAAT
1 GTTCTTTTTTAATAAAGTCATTAAGTTTTTAGATCATTTTACTAAAATGACCCCAAAAAATAAAT
10050165 AATTACA
66 AATTACA
10050172 AAAATGATTA
Statistics
Matches: 71, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
73 71 1.00
ACGTcount: A:0.41, C:0.12, G:0.07, T:0.40
Consensus pattern (73 bp):
GTTCTTTTTTAATAAAGTCATTAAGTTTTTAGATCATTTTACTAAAATGACCCCAAAAAATAAAT
AATTACAT
Found at i:10050576 original size:111 final size:111
Alignment explanation
Indices: 10050445--10050646 Score: 257
Period size: 111 Copynumber: 1.8 Consensus size: 111
10050435 CACTTTTTAA
* * * * *
10050445 TATTAAAAAATAATTGTTTTTTG-GTGTTAGTAAACTGATGGTCGATAC-CTATTTTATCAGATA
1 TATTAAAAAATAA-TGTTTTTTGCGTGCTAGCAAACTAATGGTCGACACTC-ACTTTATCAGATA
* *
10050508 AAAAAATTTTGGGTTTGGGAAACTAGATAGTCAGCATCACCTTTTTCT
64 AAAAAAATTTGGGTTTAGGAAACTAGATAGTCAGCATCACCTTTTTCT
* * * *
10050556 TATTAAAAAATTAAT-TTTTTTGCTTGCTGGCACACTAATGGTTGACACTCACTTTATCAGATAA
1 TATTAAAAAA-TAATGTTTTTTGCGTGCTAGCAAACTAATGGTCGACACTCACTTTATCAGATAA
10050620 AAAAAATTTGGGTTTAGGAAACTAGAT
65 AAAAAATTTGGGTTTAGGAAACTAGAT
10050647 GGCCCGCATC
Statistics
Matches: 77, Mismatches: 11, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
110 7 0.09
111 66 0.86
112 4 0.05
ACGTcount: A:0.34, C:0.11, G:0.16, T:0.38
Consensus pattern (111 bp):
TATTAAAAAATAATGTTTTTTGCGTGCTAGCAAACTAATGGTCGACACTCACTTTATCAGATAAA
AAAAATTTGGGTTTAGGAAACTAGATAGTCAGCATCACCTTTTTCT
Found at i:10058804 original size:17 final size:17
Alignment explanation
Indices: 10058782--10058847 Score: 51
Period size: 17 Copynumber: 3.5 Consensus size: 17
10058772 TTTTCAGAAT
10058782 TGTAAATTCTCAAATAA
1 TGTAAATTCTCAAATAA
*
10058799 TGTAAATTTGTCCTAGAACTCAA
1 TGTAAA-TTCT-C-A-AA-T-AA
*
10058822 GTCTAAATTCTCAAATAA
1 -TGTAAATTCTCAAATAA
10058840 TGTAAATT
1 TGTAAATT
10058848 TGTCCTAGAA
Statistics
Matches: 38, Mismatches: 4, Indels: 14
0.68 0.07 0.25
Matches are distributed among these distances:
17 13 0.34
18 5 0.13
19 2 0.05
20 3 0.08
21 3 0.08
22 2 0.05
23 5 0.13
24 5 0.13
ACGTcount: A:0.41, C:0.14, G:0.09, T:0.36
Consensus pattern (17 bp):
TGTAAATTCTCAAATAA
Found at i:10058841 original size:41 final size:41
Alignment explanation
Indices: 10058784--10058866 Score: 166
Period size: 41 Copynumber: 2.0 Consensus size: 41
10058774 TTCAGAATTG
10058784 TAAATTCTCAAATAATGTAAATTTGTCCTAGAACTCAAGTC
1 TAAATTCTCAAATAATGTAAATTTGTCCTAGAACTCAAGTC
10058825 TAAATTCTCAAATAATGTAAATTTGTCCTAGAACTCAAGTC
1 TAAATTCTCAAATAATGTAAATTTGTCCTAGAACTCAAGTC
10058866 T
1 T
10058867 TGGAATCTTT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 42 1.00
ACGTcount: A:0.39, C:0.17, G:0.10, T:0.35
Consensus pattern (41 bp):
TAAATTCTCAAATAATGTAAATTTGTCCTAGAACTCAAGTC
Found at i:10061591 original size:24 final size:24
Alignment explanation
Indices: 10061564--10061615 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
10061554 CTAGTAGGTC
*
10061564 AAATAAACTATACTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
10061588 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
10061612 AAAT
1 AAAT
10061616 CTTCTAAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:10062431 original size:30 final size:30
Alignment explanation
Indices: 10062395--10062458 Score: 119
Period size: 30 Copynumber: 2.1 Consensus size: 30
10062385 TTAGAGTTAT
10062395 CGCTCGTTGACACTAACAAAAAATCATCAC
1 CGCTCGTTGACACTAACAAAAAATCATCAC
*
10062425 CGCTCGTTGACACTAACAAGAAATCATCAC
1 CGCTCGTTGACACTAACAAAAAATCATCAC
10062455 CGCT
1 CGCT
10062459 TTCATCGGCC
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.36, C:0.31, G:0.12, T:0.20
Consensus pattern (30 bp):
CGCTCGTTGACACTAACAAAAAATCATCAC
Found at i:10068773 original size:13 final size:13
Alignment explanation
Indices: 10068755--10068780 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
10068745 GGGGATTTTT
10068755 TTAACTAAACTAA
1 TTAACTAAACTAA
10068768 TTAACTAAACTAA
1 TTAACTAAACTAA
10068781 GAATGCACAG
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:0.54, C:0.15, G:0.00, T:0.31
Consensus pattern (13 bp):
TTAACTAAACTAA
Found at i:10075114 original size:13 final size:13
Alignment explanation
Indices: 10075096--10075121 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
10075086 GGGGATTTTT
10075096 TTAACTAAACTAA
1 TTAACTAAACTAA
10075109 TTAACTAAACTAA
1 TTAACTAAACTAA
10075122 GAATGCACAG
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:0.54, C:0.15, G:0.00, T:0.31
Consensus pattern (13 bp):
TTAACTAAACTAA
Found at i:10079095 original size:51 final size:50
Alignment explanation
Indices: 10079023--10079182 Score: 223
Period size: 51 Copynumber: 3.2 Consensus size: 50
10079013 CTGATGGCTA
* **
10079023 AATAAATTATAGGATAAATTATATTAAAAGTAATAAAATCAAAATTAAAAT
1 AATAAATTATAGGATAAATTATATTTAAAGTAAT-AAATTTAAATTAAAAT
10079074 AATAAATTATAGGATAAATTATATTTAAAGTAATAAATTTAAATTAAAAAT
1 AATAAATTATAGGATAAATTATATTTAAAGTAATAAATTTAAATT-AAAAT
* * * *
10079125 AATTAATTAAATGATAAATTATATTTAAAGTATTAAATTTAAATTAAAA-
1 AATAAATTATAGGATAAATTATATTTAAAGTAATAAATTTAAATTAAAAT
10079174 AATAGAATT
1 AATA-AATT
10079183 TAATTAAAAA
Statistics
Matches: 99, Mismatches: 8, Indels: 5
0.88 0.07 0.04
Matches are distributed among these distances:
49 3 0.03
50 17 0.17
51 79 0.80
ACGTcount: A:0.57, C:0.01, G:0.06, T:0.36
Consensus pattern (50 bp):
AATAAATTATAGGATAAATTATATTTAAAGTAATAAATTTAAATTAAAAT
Found at i:10079171 original size:19 final size:17
Alignment explanation
Indices: 10079087--10079202 Score: 76
Period size: 19 Copynumber: 6.6 Consensus size: 17
10079077 AAATTATAGG
*
10079087 ATAAATTATATTTAAAGTA
1 ATAAATTA-AATTAAA-TA
10079106 ATAAATTTAAATTAAA-A
1 ATAAA-TTAAATTAAATA
*
10079123 AT-AATT-AATTAAATG
1 ATAAATTAAATTAAATA
*
10079138 ATAAATTATATTTAAAGTA
1 ATAAATTA-AATTAAA-TA
* *
10079157 TTAAATTTAAATTAAAAA
1 ATAAA-TTAAATTAAATA
* *
10079175 ATAGAATTTAATTAAAAA
1 ATA-AATTAAATTAAATA
*
10079193 ATTAATTAAA
1 ATAAATTAAA
10079203 GGCAAAATTA
Statistics
Matches: 78, Mismatches: 11, Indels: 18
0.73 0.10 0.17
Matches are distributed among these distances:
14 7 0.09
15 4 0.05
16 6 0.08
17 9 0.12
18 22 0.28
19 24 0.31
20 6 0.08
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (17 bp):
ATAAATTAAATTAAATA
Found at i:10079228 original size:19 final size:18
Alignment explanation
Indices: 10079156--10079228 Score: 53
Period size: 18 Copynumber: 4.1 Consensus size: 18
10079146 TATTTAAAGT
*
10079156 ATTAAATTTAAATTAAAAA
1 ATTAAATTT-AAGTAAAAA
*
10079175 A-TAGAATTTAATTAAAAA
1 ATTA-AATTTAAGTAAAAA
* **
10079193 ATT-AATTAAAG-GCAAA
1 ATTAAATTTAAGTAAAAA
10079209 ATTAGAATTTAAGTAAAAA
1 ATTA-AATTTAAGTAAAAA
10079228 A
1 A
10079229 CGGTTATGGG
Statistics
Matches: 42, Mismatches: 7, Indels: 10
0.71 0.12 0.17
Matches are distributed among these distances:
16 6 0.14
17 6 0.14
18 19 0.45
19 11 0.26
ACGTcount: A:0.60, C:0.01, G:0.07, T:0.32
Consensus pattern (18 bp):
ATTAAATTTAAGTAAAAA
Found at i:10079463 original size:18 final size:19
Alignment explanation
Indices: 10079440--10079475 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
10079430 CCTTTAATTA
10079440 ATTTTTTAA-TTAAATTTT
1 ATTTTTTAATTTAAATTTT
10079458 ATTTTTTAATTTAAATTT
1 ATTTTTTAATTTAAATTT
10079476 AATACTTTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (19 bp):
ATTTTTTAATTTAAATTTT
Found at i:10079476 original size:18 final size:17
Alignment explanation
Indices: 10079435--10079476 Score: 57
Period size: 18 Copynumber: 2.4 Consensus size: 17
10079425 TTTAGCCTTT
*
10079435 AATTAATTTTTTAATTA
1 AATTTATTTTTTAATTA
10079452 AATTTTATTTTTTAATTTA
1 AA-TTTATTTTTTAA-TTA
10079471 AATTTA
1 AATTTA
10079477 ATACTTTAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
17 2 0.09
18 15 0.68
19 5 0.23
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (17 bp):
AATTTATTTTTTAATTA
Found at i:10079585 original size:51 final size:50
Alignment explanation
Indices: 10079461--10079657 Score: 261
Period size: 51 Copynumber: 3.9 Consensus size: 50
10079451 AAATTTTATT
* * * *
10079461 TTTTAATTTAAATTTAATACTTTAAATATGATTTATCCTATAATTAAATA
1 TTTTAATTTTAATTTATTACTTTAAATATAATTTATCCTATAATTAATTA
* * * * * *
10079511 TTTTAATTTTAATTTATTGCTTTAAAAATAATTTATCATTTGACTAATTA
1 TTTTAATTTTAATTTATTACTTTAAATATAATTTATCCTATAATTAATTA
10079561 TTTTTAA-TTTAGATTTATTACTTTAAATATAATTTATCCTATAATTAATTA
1 -TTTTAATTTTA-ATTTATTACTTTAAATATAATTTATCCTATAATTAATTA
*
10079612 TTTTAATTTTAATTTTATTGCTTTAAATATAATTTATCCTATAATT
1 TTTTAATTTTAA-TTTATTACTTTAAATATAATTTATCCTATAATT
10079658 TATTTAGTCA
Statistics
Matches: 126, Mismatches: 17, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
50 51 0.40
51 75 0.60
ACGTcount: A:0.37, C:0.06, G:0.03, T:0.54
Consensus pattern (50 bp):
TTTTAATTTTAATTTATTACTTTAAATATAATTTATCCTATAATTAATTA
Found at i:10079614 original size:101 final size:102
Alignment explanation
Indices: 10079460--10079649 Score: 328
Period size: 101 Copynumber: 1.9 Consensus size: 102
10079450 TAAATTTTAT
*
10079460 TTTTTAATTTAAATTTAATACTTTAAATATGATTTATCCTATAATTAAATATTTTAATTTTAA-T
1 TTTTTAATTTAAATTTAATACTTTAAATATAATTTATCCTATAATTAAATATTTTAATTTTAATT
10079524 TTATTGCTTTAAAAATAATTTATCATTTGACTAATTA
66 TTATTGCTTTAAAAATAATTTATCATTTGACTAATTA
* * *
10079561 TTTTTAATTTAGATTTATTACTTTAAATATAATTTATCCTATAATTAATTATTTTAATTTTAATT
1 TTTTTAATTTAAATTTAATACTTTAAATATAATTTATCCTATAATTAAATATTTTAATTTTAATT
*
10079626 TTATTGCTTTAAATATAATTTATC
66 TTATTGCTTTAAAAATAATTTATC
10079650 CTATAATTTA
Statistics
Matches: 83, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
101 59 0.71
102 24 0.29
ACGTcount: A:0.37, C:0.06, G:0.03, T:0.55
Consensus pattern (102 bp):
TTTTTAATTTAAATTTAATACTTTAAATATAATTTATCCTATAATTAAATATTTTAATTTTAATT
TTATTGCTTTAAAAATAATTTATCATTTGACTAATTA
Found at i:10085559 original size:21 final size:21
Alignment explanation
Indices: 10085535--10085609 Score: 82
Period size: 21 Copynumber: 3.6 Consensus size: 21
10085525 TCATATAAAA
*
10085535 ATATAGTAAAATAATTAATAC
1 ATATAGGAAAATAATTAATAC
* *
10085556 ATATTGGAAAATACA-TAGTA-
1 ATATAGGAAAATA-ATTAATAC
*
10085576 ATATAGTAAAATAATTAATAC
1 ATATAGGAAAATAATTAATAC
*
10085597 ATATTGGAAAATA
1 ATATAGGAAAATA
10085610 CATAGTATAT
Statistics
Matches: 43, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
19 1 0.02
20 15 0.35
21 26 0.60
22 1 0.02
ACGTcount: A:0.55, C:0.04, G:0.09, T:0.32
Consensus pattern (21 bp):
ATATAGGAAAATAATTAATAC
Found at i:10085591 original size:41 final size:41
Alignment explanation
Indices: 10085534--10085625 Score: 168
Period size: 41 Copynumber: 2.3 Consensus size: 41
10085524 TTCATATAAA
10085534 AATATAGTAAAATAATTAATACATATTGGAAAATACATAGT
1 AATATAGTAAAATAATTAATACATATTGGAAAATACATAGT
10085575 AATATAGTAAAATAATTAATACATATTGGAAAATACATAGT
1 AATATAGTAAAATAATTAATACATATTGGAAAATACATAGT
*
10085616 -ATATACTAAA
1 AATATAGTAAA
10085626 TTTATAAATA
Statistics
Matches: 50, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
40 9 0.18
41 41 0.82
ACGTcount: A:0.54, C:0.05, G:0.09, T:0.32
Consensus pattern (41 bp):
AATATAGTAAAATAATTAATACATATTGGAAAATACATAGT
Found at i:10085793 original size:21 final size:21
Alignment explanation
Indices: 10085755--10085811 Score: 64
Period size: 20 Copynumber: 2.7 Consensus size: 21
10085745 GTATAATAAT
* *
10085755 AATATAATAGATAAATATAGTGA
1 AATATAATA-ATATATATA-TCA
10085778 AATA-AATAATATATATATCA
1 AATATAATAATATATATATCA
10085798 AA-ATAATAATATAT
1 AATATAATAATATAT
10085812 TGGATAATAA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
19 1 0.03
20 14 0.45
21 8 0.26
22 4 0.13
23 4 0.13
ACGTcount: A:0.60, C:0.02, G:0.05, T:0.33
Consensus pattern (21 bp):
AATATAATAATATATATATCA
Found at i:10085860 original size:17 final size:16
Alignment explanation
Indices: 10085840--10085889 Score: 57
Period size: 17 Copynumber: 3.0 Consensus size: 16
10085830 TGTATTTCTT
10085840 TATAACTAATATTAAAA
1 TATAA-TAATATTAAAA
10085857 TATATATAATATTTAAAA
1 TATA-ATAATA-TTAAAA
*
10085875 TAAAATAATA-TAAAA
1 TATAATAATATTAAAA
10085890 AAAGATTAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
15 5 0.17
17 15 0.50
18 10 0.33
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (16 bp):
TATAATAATATTAAAA
Found at i:10089931 original size:30 final size:30
Alignment explanation
Indices: 10089848--10089933 Score: 127
Period size: 30 Copynumber: 2.9 Consensus size: 30
10089838 CGGCCATGAT
* * * * *
10089848 ACACGGGCATGTGGTCTGCCCGTATGCCTC
1 ACACGAGCGTGTGGTTTACCCGTGTGCCTC
10089878 ACACGAGCGTGTGGTTTACCCGTGTGCCTC
1 ACACGAGCGTGTGGTTTACCCGTGTGCCTC
10089908 ACACGAGCGTGTGGTTTACCCGTGTG
1 ACACGAGCGTGTGGTTTACCCGTGTG
10089934 GAAGTGCCTG
Statistics
Matches: 51, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 51 1.00
ACGTcount: A:0.14, C:0.29, G:0.31, T:0.26
Consensus pattern (30 bp):
ACACGAGCGTGTGGTTTACCCGTGTGCCTC
Found at i:10093018 original size:112 final size:112
Alignment explanation
Indices: 10092795--10093023 Score: 300
Period size: 112 Copynumber: 2.0 Consensus size: 112
10092785 ATACTATTCT
* * * * *
10092795 CAATCTATTTCAATAAATGACAACGGTTTTAAATGTTTATAAAATTCAAAATCAAAATGGATTGA
1 CAATTTATTACAAAAAATGACAACAGTTTCAAATGTTTATAAAATTCAAAATCAAAATGGATTGA
* * *
10092860 TTAGCGACCATGCTAAAACCTATCTTTTAGTTACTAAGCTTTTTGGC
66 TTAGAGACCATGCTAAAACCAATCTTTTAGTTACTAAGCTTATTGGC
* *
10092907 CAATTTATTACAAAAAATGACAATAGTTTCAAATGTTTATAAAATTCAAAATCAAGAT-GAGTTG
1 CAATTTATTACAAAAAATGACAACAGTTTCAAATGTTTATAAAATTCAAAATCAAAATGGA-TTG
* * **
10092971 ATTAGAGATCATGCTATAACCAATCTTTTAGTTA-TTGGACTTATTGGC
65 ATTAGAGACCATGCTAAAACCAATCTTTTAGTTACTAAG-CTTATTGGC
10093019 CAATT
1 CAATT
10093024 AAAATGATGG
Statistics
Matches: 101, Mismatches: 14, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
111 4 0.04
112 97 0.96
ACGTcount: A:0.38, C:0.14, G:0.13, T:0.36
Consensus pattern (112 bp):
CAATTTATTACAAAAAATGACAACAGTTTCAAATGTTTATAAAATTCAAAATCAAAATGGATTGA
TTAGAGACCATGCTAAAACCAATCTTTTAGTTACTAAGCTTATTGGC
Found at i:10095263 original size:14 final size:14
Alignment explanation
Indices: 10095244--10095279 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
10095234 TTAGTTGGTG
*
10095244 CATTTGCATTCATA
1 CATTTGCATACATA
*
10095258 CATTTGCATACATC
1 CATTTGCATACATA
10095272 CATTTGCA
1 CATTTGCA
10095280 AAAACCATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.28, C:0.25, G:0.08, T:0.39
Consensus pattern (14 bp):
CATTTGCATACATA
Found at i:10097992 original size:7 final size:8
Alignment explanation
Indices: 10097980--10098005 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
10097970 TAATTTTTAA
10097980 ATTTTTTT
1 ATTTTTTT
10097988 ATTTTTTT
1 ATTTTTTT
10097996 ATTTTTTT
1 ATTTTTTT
10098004 AT
1 AT
10098006 ATTGTCAATT
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:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (8 bp):
ATTTTTTT
Found at i:10097993 original size:16 final size:16
Alignment explanation
Indices: 10097972--10098005 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
10097962 TATACATATA
10097972 ATTTTTAAATTTTTTT
1 ATTTTTAAATTTTTTT
**
10097988 ATTTTTTTATTTTTTT
1 ATTTTTAAATTTTTTT
10098004 AT
1 AT
10098006 ATTGTCAATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (16 bp):
ATTTTTAAATTTTTTT
Found at i:10102219 original size:30 final size:29
Alignment explanation
Indices: 10102184--10102286 Score: 100
Period size: 30 Copynumber: 3.4 Consensus size: 29
10102174 TTAATCACAT
* *
10102184 TAATATTAAACTAATAAAATATTGTCTAGA
1 TAATATTAAATTAATAAAATA-TATCTAGA
** *
10102214 TAATATTAAATTTAATTGAATATATCATA-T
1 TAATATTAAA-TTAATAAAATATATC-TAGA
10102244 TAATATTAAATTAATAAAATACTATCTAGA
1 TAATATTAAATTAATAAAATA-TATCTAGA
*
10102274 TAGATATTTAATT
1 TA-ATATTAAATT
10102287 TAATTTAATA
Statistics
Matches: 59, Mismatches: 9, Indels: 9
0.77 0.12 0.12
Matches are distributed among these distances:
29 11 0.19
30 29 0.49
31 19 0.32
ACGTcount: A:0.49, C:0.05, G:0.05, T:0.42
Consensus pattern (29 bp):
TAATATTAAATTAATAAAATATATCTAGA
Found at i:10102275 original size:60 final size:61
Alignment explanation
Indices: 10102177--10102311 Score: 200
Period size: 60 Copynumber: 2.2 Consensus size: 61
10102167 ATTAGAATTA
* *
10102177 ATCACATTAATATTAAACTAATAAAATATTGTCTAGATA-ATATTAAATTTAATTGAATAT
1 ATCACATTAATATTAAACTAATAAAATACTATCTAGATAGATATTAAATTTAATTGAATAT
* * * *
10102237 ATCATATTAATATTAAATTAATAAAATACTATCTAGATAGATATTTAATTTAATTTAATAT
1 ATCACATTAATATTAAACTAATAAAATACTATCTAGATAGATATTAAATTTAATTGAATAT
*
10102298 CTCACATTAATATT
1 ATCACATTAATATT
10102312 TAGATTAAAT
Statistics
Matches: 66, Mismatches: 8, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
60 35 0.53
61 31 0.47
ACGTcount: A:0.47, C:0.07, G:0.04, T:0.42
Consensus pattern (61 bp):
ATCACATTAATATTAAACTAATAAAATACTATCTAGATAGATATTAAATTTAATTGAATAT
Found at i:10102311 original size:30 final size:30
Alignment explanation
Indices: 10102214--10102328 Score: 99
Period size: 31 Copynumber: 3.8 Consensus size: 30
10102204 ATTGTCTAGA
* * *
10102214 TAATATTAAATTTAATTGAATATATCATAT
1 TAATATTTAATTTAATTTAATATATCACAT
* ** *
10102244 TAATA-TTAAATTAATAAAATACTATCTAGA-
1 TAATATTTAATTTAATTTAATA-TATC-ACAT
*
10102274 TAGATATTTAATTTAATTTAATATCTCACAT
1 TA-ATATTTAATTTAATTTAATATATCACAT
*
10102305 TAATATTTAGATTAAATTTAATAT
1 TAATATTTA-ATTTAATTTAATAT
10102329 TAAATTCATT
Statistics
Matches: 68, Mismatches: 11, Indels: 11
0.76 0.12 0.12
Matches are distributed among these distances:
29 12 0.18
30 20 0.29
31 23 0.34
32 13 0.19
ACGTcount: A:0.46, C:0.05, G:0.03, T:0.45
Consensus pattern (30 bp):
TAATATTTAATTTAATTTAATATATCACAT
Found at i:10106322 original size:19 final size:19
Alignment explanation
Indices: 10106278--10106323 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
10106268 TTCATAAAAA
10106278 TAAAAAATATAAAAATTAT
1 TAAAAAATATAAAAATTAT
*
10106297 TAGAAAAATCA-AACAATTAT
1 TA-AAAAAT-ATAAAAATTAT
10106317 TAAAAAA
1 TAAAAAA
10106324 GTTTATCAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
19 7 0.29
20 16 0.67
21 1 0.04
ACGTcount: A:0.67, C:0.04, G:0.02, T:0.26
Consensus pattern (19 bp):
TAAAAAATATAAAAATTAT
Found at i:10108818 original size:27 final size:27
Alignment explanation
Indices: 10108788--10108969 Score: 188
Period size: 27 Copynumber: 6.8 Consensus size: 27
10108778 AGGCAGACCA
* ** **
10108788 TTCAGAGTTCACCACAAAAACTATTTT
1 TTCAGAGTTCGCCACAAAGGCTATCCT
** *
10108815 TTCAGAGTTTTCCAAAAAGGCTATCCT
1 TTCAGAGTTCGCCACAAAGGCTATCCT
10108842 TTCAGAGTTCGCCAC-AAGGCTATCCT
1 TTCAGAGTTCGCCACAAAGGCTATCCT
*
10108868 TTCAAAGTTCGCCACAAAGGCTATCCT
1 TTCAGAGTTCGCCACAAAGGCTATCCT
* * *
10108895 TTCAGAGTTCACCATAAAGGCTATTCT
1 TTCAGAGTTCGCCACAAAGGCTATCCT
* * * **
10108922 CTT-AAAGTTGGCCACAAAGTCTATTGT
1 -TTCAGAGTTCGCCACAAAGGCTATCCT
10108949 TTCAGAGTTCGCCACAAAGGC
1 TTCAGAGTTCGCCACAAAGGC
10108970 CATCAAAATG
Statistics
Matches: 128, Mismatches: 24, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
26 27 0.21
27 99 0.77
28 2 0.02
ACGTcount: A:0.30, C:0.25, G:0.16, T:0.30
Consensus pattern (27 bp):
TTCAGAGTTCGCCACAAAGGCTATCCT
Found at i:10115256 original size:15 final size:15
Alignment explanation
Indices: 10115236--10115267 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
10115226 TATTTCACTA
*
10115236 TTATGTCTTTTGTAT
1 TTATGTCTTTTATAT
10115251 TTATGTCTTTTATAT
1 TTATGTCTTTTATAT
10115266 TT
1 TT
10115268 TGCATGCATA
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:0.16, C:0.06, G:0.09, T:0.69
Consensus pattern (15 bp):
TTATGTCTTTTATAT
Found at i:10121951 original size:17 final size:18
Alignment explanation
Indices: 10121919--10121952 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
10121909 TATATGTGTA
10121919 CTTTTATATATAAATATT
1 CTTTTATATATAAATATT
*
10121937 CTTTTAT-TTTAAATAT
1 CTTTTATATATAAATAT
10121953 GATAATAATT
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:0.35, C:0.06, G:0.00, T:0.59
Consensus pattern (18 bp):
CTTTTATATATAAATATT
Found at i:10127660 original size:20 final size:20
Alignment explanation
Indices: 10127604--10127660 Score: 50
Period size: 20 Copynumber: 3.0 Consensus size: 20
10127594 TAATAACATT
* *
10127604 AATATATTAGTAATCTAATA
1 AATATATTGGTAATCTAATC
* *
10127624 AATA-ATAGATAA--T-ATC
1 AATATATTGGTAATCTAATC
10127640 AATATATTGGTAATCTAATC
1 AATATATTGGTAATCTAATC
10127660 A
1 A
10127661 TTAATGTATA
Statistics
Matches: 27, Mismatches: 6, Indels: 8
0.66 0.15 0.20
Matches are distributed among these distances:
16 6 0.22
17 7 0.26
19 6 0.22
20 8 0.30
ACGTcount: A:0.49, C:0.07, G:0.07, T:0.37
Consensus pattern (20 bp):
AATATATTGGTAATCTAATC
Found at i:10127726 original size:30 final size:30
Alignment explanation
Indices: 10127691--10127748 Score: 91
Period size: 30 Copynumber: 1.9 Consensus size: 30
10127681 AACAAATTAT
10127691 AATTATAATTTTATTATATAAT-TATTTTAA
1 AATTATAATTTTATTA-ATAATATATTTTAA
*
10127721 AATTATTATTTTATTAATAATATATTTT
1 AATTATAATTTTATTAATAATATATTTT
10127749 TTTGGGTGAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 5 0.19
30 21 0.81
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (30 bp):
AATTATAATTTTATTAATAATATATTTTAA
Found at i:10134929 original size:16 final size:17
Alignment explanation
Indices: 10134891--10134931 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
10134881 TTTTTTTAAA
*
10134891 AATATAATACATATATT
1 AATAAAATACATATATT
*
10134908 AA-AAAATACTTA-ATT
1 AATAAAATACATATATT
10134923 AATAAAATA
1 AATAAAATA
10134932 TAAATAATCC
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
15 5 0.24
16 14 0.67
17 2 0.10
ACGTcount: A:0.61, C:0.05, G:0.00, T:0.34
Consensus pattern (17 bp):
AATAAAATACATATATT
Found at i:10134962 original size:15 final size:13
Alignment explanation
Indices: 10134951--10134987 Score: 56
Period size: 15 Copynumber: 2.7 Consensus size: 13
10134941 CATATATCAT
10134951 ATAAAATAATATA
1 ATAAAATAATATA
10134964 ATAATATATAATATA
1 ATAA-A-ATAATATA
10134979 ATAAAATAA
1 ATAAAATAA
10134988 ATGGATTTCC
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
13 8 0.36
14 2 0.09
15 12 0.55
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (13 bp):
ATAAAATAATATA
Found at i:10134968 original size:8 final size:8
Alignment explanation
Indices: 10134955--10134987 Score: 50
Period size: 8 Copynumber: 4.2 Consensus size: 8
10134945 TATCATATAA
10134955 AATAATAT
1 AATAATAT
10134963 AATAATAT
1 AATAATAT
10134971 -ATAATAT
1 AATAATAT
*
10134978 AATAAAAT
1 AATAATAT
10134986 AA
1 AA
10134988 ATGGATTTCC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
7 7 0.30
8 16 0.70
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (8 bp):
AATAATAT
Found at i:10134972 original size:20 final size:20
Alignment explanation
Indices: 10134949--10134987 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
10134939 TCCATATATC
*
10134949 ATATAAAATAATATAATAAT
1 ATATAAAATAATAAAATAAT
*
10134969 ATATAATATAATAAAATAA
1 ATATAAAATAATAAAATAA
10134988 ATGGATTTCC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (20 bp):
ATATAAAATAATAAAATAAT
Found at i:10137152 original size:23 final size:22
Alignment explanation
Indices: 10137102--10137154 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 22
10137092 TATGATTTTA
10137102 TTTATTATTTGGGATGTTTAGT
1 TTTATTATTTGGGATGTTTAGT
*
10137124 TATTATTATTTGGTAT-TTGATAGT
1 T-TTATTATTTGGGATGTT--TAGT
10137148 TTTATTA
1 TTTATTA
10137155 ATATATGATT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
22 3 0.11
23 19 0.70
24 5 0.19
ACGTcount: A:0.23, C:0.00, G:0.17, T:0.60
Consensus pattern (22 bp):
TTTATTATTTGGGATGTTTAGT
Found at i:10137396 original size:20 final size:20
Alignment explanation
Indices: 10137351--10137397 Score: 51
Period size: 21 Copynumber: 2.3 Consensus size: 20
10137341 ATTTTTTTTA
*
10137351 TTTTCATTACTTTAAAATGT
1 TTTTTATTACTTTAAAATGT
*
10137371 TATTTTATTATTTTAAATAT-T
1 T-TTTTATTACTTTAAA-ATGT
10137392 TTTTTA
1 TTTTTA
10137398 AAATTAATAA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
20 6 0.26
21 15 0.65
22 2 0.09
ACGTcount: A:0.30, C:0.04, G:0.02, T:0.64
Consensus pattern (20 bp):
TTTTTATTACTTTAAAATGT
Found at i:10138034 original size:44 final size:41
Alignment explanation
Indices: 10137961--10138052 Score: 121
Period size: 44 Copynumber: 2.2 Consensus size: 41
10137951 ATAGTAACAT
*
10137961 ATAAAATATGTACAAAATTAAACTGTAAATATTATACTAAA
1 ATAAAATATGTACAAAATTAAAATGTAAATATTATACTAAA
* * *
10138002 ATAAAATATGTATAATGCAATTAAAATTTAAATATTATATTAAA
1 ATAAAATATGTACAA---AATTAAAATGTAAATATTATACTAAA
10138046 ATAAAAT
1 ATAAAAT
10138053 TTTAATTTAA
Statistics
Matches: 44, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
41 14 0.32
44 30 0.68
ACGTcount: A:0.57, C:0.04, G:0.04, T:0.35
Consensus pattern (41 bp):
ATAAAATATGTACAAAATTAAAATGTAAATATTATACTAAA
Found at i:10138079 original size:25 final size:25
Alignment explanation
Indices: 10138006--10138081 Score: 75
Period size: 24 Copynumber: 3.0 Consensus size: 25
10137996 ACTAAAATAA
** *
10138006 AATATGTATAATGCAATTAAAATTTA
1 AATAT-TATAATAAAATTAAAATTTT
*
10138032 AATATTATATTAAAA-TAAAATTTT
1 AATATTATAATAAAATTAAAATTTT
*
10138056 AAT-TTAATAATAAAATTAATATTTT
1 AATATT-ATAATAAAATTAAAATTTT
10138081 A
1 A
10138082 TTAATTTAAA
Statistics
Matches: 42, Mismatches: 6, Indels: 5
0.79 0.11 0.09
Matches are distributed among these distances:
23 2 0.05
24 19 0.45
25 16 0.38
26 5 0.12
ACGTcount: A:0.53, C:0.01, G:0.03, T:0.43
Consensus pattern (25 bp):
AATATTATAATAAAATTAAAATTTT
Found at i:10139185 original size:2 final size:2
Alignment explanation
Indices: 10139178--10139203 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
10139168 AAAATTAGGA
10139178 AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC
10139204 TCGAATAGAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:10151164 original size:302 final size:301
Alignment explanation
Indices: 10150619--10151200 Score: 1085
Period size: 302 Copynumber: 1.9 Consensus size: 301
10150609 ATTCTTCACC
*
10150619 ATGCTGAAACTAATTATCCCGATGTGGTCTCTGTTAACAATACCCGTGGCACCAATATGATTCAT
1 ATGCTGAAACTAATTATCCCGATGTGGTCTCTGTTAACAATACCCGTGACACCAATATGATTCAT
*
10150684 CTAAAGGTCTGTTGATCTTTGAAATTAATTGAAAATTTAGGGTGACCAATCAAGCAGTTTTCTTT
66 CTAAAGGTCTGTTGATCTTTGAAATTAATTGAAAACTTAGGGTGACCAATCAAGCAGTTTTCTTT
*
10150749 CTCTTTTTACTTCTATTGCTTTACGATTTATCATATAGACTGCACTGCATAAAAGATCTCATTCA
131 CTCTTTTTACTTCTATTGCTTTACAATTTATCATATAGACTGCACTGCATAAAAGATCTCATTCA
10150814 AGCGCACAACAAATTTACCTCAAGCTATATCATTTAATCAAATGTTCTGCTTGAAGGCAATGCGA
196 AGCGCACAACAAATTTACCTCAAGCTATATCATTTAATCAAATGTTCTGCTTGAAGGCAATGCGA
*
10150879 CATGGTAGAGCTCTTCTCCGTGTTTATGCAGTGCAGTCTAT
261 CACGGTAGAGCTCTTCTCCGTGTTTATGCAGTGCAGTCTAT
10150920 ATGCTGAAACTAATTA-CCCTGATGTGGTCTCTGTTAACAATACCCGTGACACCAATATGATTCA
1 ATGCTGAAACTAATTATCCC-GATGTGGTCTCTGTTAACAATACCCGTGACACCAATATGATTCA
10150984 TCTAAAGGTCTGTTGATCTCTTGAAATTAATTGAAAACTTAGGGTGACCAATCAAGCAGTTTTCT
65 TCTAAAGGTCTGTTGATCT-TTGAAATTAATTGAAAACTTAGGGTGACCAATCAAGCAGTTTTCT
* *
10151049 TTCTCTTTTTACTTCTATTGCTTTACAATTTATCATATAGACTGCGCTGCATACAAGATCTCATT
129 TTCTCTTTTTACTTCTATTGCTTTACAATTTATCATATAGACTGCACTGCATAAAAGATCTCATT
10151114 CAAGCGCACAACAAATTTACCTCAAGCTATATCATTTAATCAAATGTTCTGCTTGAAGGCAATGC
194 CAAGCGCACAACAAATTTACCTCAAGCTATATCATTTAATCAAATGTTCTGCTTGAAGGCAATGC
10151179 GACACGGTAGAGCTCTTCTCCG
259 GACACGGTAGAGCTCTTCTCCG
10151201 AGTATCAATT
Statistics
Matches: 273, Mismatches: 6, Indels: 3
0.97 0.02 0.01
Matches are distributed among these distances:
300 3 0.01
301 78 0.29
302 192 0.70
ACGTcount: A:0.29, C:0.21, G:0.16, T:0.34
Consensus pattern (301 bp):
ATGCTGAAACTAATTATCCCGATGTGGTCTCTGTTAACAATACCCGTGACACCAATATGATTCAT
CTAAAGGTCTGTTGATCTTTGAAATTAATTGAAAACTTAGGGTGACCAATCAAGCAGTTTTCTTT
CTCTTTTTACTTCTATTGCTTTACAATTTATCATATAGACTGCACTGCATAAAAGATCTCATTCA
AGCGCACAACAAATTTACCTCAAGCTATATCATTTAATCAAATGTTCTGCTTGAAGGCAATGCGA
CACGGTAGAGCTCTTCTCCGTGTTTATGCAGTGCAGTCTAT
Found at i:10155769 original size:22 final size:22
Alignment explanation
Indices: 10155741--10155783 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
10155731 ACTAAAACTC
10155741 AAAAAATAAAATTCCTTATTTT
1 AAAAAATAAAATTCCTTATTTT
10155763 AAAAAATAAAATTCCTTATTT
1 AAAAAATAAAATTCCTTATTT
10155784 GAATTGATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.51, C:0.09, G:0.00, T:0.40
Consensus pattern (22 bp):
AAAAAATAAAATTCCTTATTTT
Found at i:10177409 original size:30 final size:30
Alignment explanation
Indices: 10177374--10177430 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
10177364 AAGCAGTTCT
*
10177374 ACACGGGTA-ATCCACACGCCCGTGTGTGAC
1 ACACGGGTAGA-CCACACACCCGTGTGTGAC
10177404 ACACGGGTAGACCACACACCCGTGTGT
1 ACACGGGTAGACCACACACCCGTGTGT
10177431 CATGGCCATG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
30 24 0.96
31 1 0.04
ACGTcount: A:0.25, C:0.33, G:0.26, T:0.16
Consensus pattern (30 bp):
ACACGGGTAGACCACACACCCGTGTGTGAC
Found at i:10179322 original size:43 final size:42
Alignment explanation
Indices: 10179167--10179323 Score: 147
Period size: 43 Copynumber: 3.7 Consensus size: 42
10179157 ATGTGTTATC
* * *
10179167 GTGTAAGACCACGTCTAGGATGTTGGAATCGA-ATTATGATTA
1 GTGTAAGACCACGTCTGGGACGTTGGCATCGATATT-TGATTA
* *
10179209 TGTGTAAGACCACATATGGGACGTTGGCATCG-TATTTGATTTA
1 -GTGTAAGACCACGTCTGGGACGTTGGCATCGATATTTGA-TTA
** * * **
10179252 GTGTAAGACCTTGTTTGGAACAATGGCATCGATATTTGATTA
1 GTGTAAGACCACGTCTGGGACGTTGGCATCGATATTTGATTA
* *
10179294 CATGTAAGACCACGTCTGGGATGTTGGCAT
1 -GTGTAAGACCACGTCTGGGACGTTGGCAT
10179324 TGTACAAGCT
Statistics
Matches: 90, Mismatches: 20, Indels: 8
0.76 0.17 0.07
Matches are distributed among these distances:
42 30 0.33
43 60 0.67
ACGTcount: A:0.27, C:0.14, G:0.26, T:0.32
Consensus pattern (42 bp):
GTGTAAGACCACGTCTGGGACGTTGGCATCGATATTTGATTA
Found at i:10180838 original size:51 final size:50
Alignment explanation
Indices: 10180756--10180853 Score: 115
Period size: 51 Copynumber: 1.9 Consensus size: 50
10180746 ATGCCTTTAC
* * * **
10180756 AAAATAAATTTTGTTAAACGACAGGATTAAATCCTGAAACAAAATTATATT
1 AAAATAAAATCTGTTAAACGACAGGAATAAATCCCCAAA-AAAATTATATT
***
10180807 AAAATAAAATCTGTTAAACGGTGGGAATAAATCCCCAAAAAAATTAT
1 AAAATAAAATCTGTTAAACGACAGGAATAAATCCCCAAAAAAATTAT
10180854 TTGAATACGT
Statistics
Matches: 39, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
50 8 0.21
51 31 0.79
ACGTcount: A:0.50, C:0.11, G:0.11, T:0.28
Consensus pattern (50 bp):
AAAATAAAATCTGTTAAACGACAGGAATAAATCCCCAAAAAAATTATATT
Found at i:10181065 original size:84 final size:84
Alignment explanation
Indices: 10180913--10181146 Score: 297
Period size: 84 Copynumber: 2.7 Consensus size: 84
10180903 TTAGATGCTG
* * * * * *
10180913 GGAAAAAATCCCAAAACAAATTTTATTTACTTTTAATTCTAATTTGGAAACAAAATAAAATCAGA
1 GGAATAAATCCCGAAACAAATTTTATTTA-ATTTAATTTTAATTTGGAAACAAAATAAAATAAAA
*
10180978 TAAAATTTTGGTAAACGGCA
65 TAAAATCTTGGTAAACGGCA
* * *
10180998 GGAATAAATCCTGAAACAAATTTTATTTAATTTAATTTTGATTTGGAAATAAAATAAAATAAAAT
1 GGAATAAATCCCGAAACAAATTTTATTTAATTTAATTTTAATTTGGAAACAAAATAAAATAAAAT
*
10181063 AAAATCTTGTTAAACGGCA
66 AAAATCTTGGTAAACGGCA
* *
10181082 GGAATAAATCCCGAAACAGATTTTATTTAATTTTAATTTCTTATTTTCGGAAACAAAATTAAAAT
1 GGAATAAATCCCGAAACAAATTTTATTTAA-TTTAA-TT-TTAATTT-GGAAACAAAA-TAAAAT
10181147 GTAATAAATT
Statistics
Matches: 128, Mismatches: 16, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
84 75 0.59
85 31 0.24
86 2 0.02
87 5 0.04
88 9 0.07
89 6 0.05
ACGTcount: A:0.46, C:0.10, G:0.10, T:0.34
Consensus pattern (84 bp):
GGAATAAATCCCGAAACAAATTTTATTTAATTTAATTTTAATTTGGAAACAAAATAAAATAAAAT
AAAATCTTGGTAAACGGCA
Found at i:10181240 original size:79 final size:79
Alignment explanation
Indices: 10181149--10181314 Score: 230
Period size: 79 Copynumber: 2.1 Consensus size: 79
10181139 ATTAAAATGT
* *
10181149 AATAAATTCGTTGAATAG-TGGGAA-CAAATCCCGAAACGA-ATTTTATTTTACTCGTTTTTGGA
1 AATAAAATCGTTGAA-AGACGGGAATC-AATCCCGAAA-GAGATTTTATTTTACTCGTTTTTGGA
10181211 AATAAAACAAAATTTGG
63 AATAAAACAAAATTTGG
* * * *
10181228 AATAAAATCGTTGCACGACGGGAATCAATCCCGAAATAGATTTTATTTTACTCGTTTTTGTAAAT
1 AATAAAATCGTTGAAAGACGGGAATCAATCCCGAAAGAGATTTTATTTTACTCGTTTTTGGAAAT
10181293 AAAACAAAATTTGG
66 AAAACAAAATTTGG
10181307 AATAAAAT
1 AATAAAAT
10181315 TTGTAACACC
Statistics
Matches: 78, Mismatches: 6, Indels: 6
0.87 0.07 0.07
Matches are distributed among these distances:
78 2 0.03
79 75 0.96
80 1 0.01
ACGTcount: A:0.40, C:0.12, G:0.15, T:0.33
Consensus pattern (79 bp):
AATAAAATCGTTGAAAGACGGGAATCAATCCCGAAAGAGATTTTATTTTACTCGTTTTTGGAAAT
AAAACAAAATTTGG
Found at i:10189154 original size:25 final size:23
Alignment explanation
Indices: 10189121--10189183 Score: 108
Period size: 23 Copynumber: 2.7 Consensus size: 23
10189111 AAATGTCCAA
*
10189121 CCAAAACACACCAGTATAGTCCT
1 CCAAAACACACCAGTATAATCCT
*
10189144 CCAAAACACACTAGTATAATCCT
1 CCAAAACACACCAGTATAATCCT
10189167 CCAAAACACACCAGTAT
1 CCAAAACACACCAGTAT
10189184 CATATAATCC
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.43, C:0.33, G:0.06, T:0.17
Consensus pattern (23 bp):
CCAAAACACACCAGTATAATCCT
Found at i:10189213 original size:23 final size:23
Alignment explanation
Indices: 10189121--10189241 Score: 98
Period size: 23 Copynumber: 4.8 Consensus size: 23
10189111 AAATGTCCAA
* *
10189121 CCAAAACACACCAGTATAGTCCT
1 CCAAAACACACCAGAATAATCCT
* *
10189144 CCAAAACACACTAGTATAATCCT
1 CCAAAACACACCAGAATAATCCT
10189167 CCAAAACACACCAGTATCATATAATCCT
1 CCAAAACACACCAG----A-ATAATCCT
*
10189195 CCCAAACACACCAGAATAATATAACCCAT
1 CCAAAACACACCAGAAT-A-AT---CC-T
10189224 CCAAAACACACCAGAATA
1 CCAAAACACACCAGAATA
10189242 GCACAAAGTG
Statistics
Matches: 81, Mismatches: 6, Indels: 17
0.78 0.06 0.16
Matches are distributed among these distances:
23 36 0.44
24 2 0.02
25 2 0.02
28 24 0.30
29 17 0.21
ACGTcount: A:0.45, C:0.33, G:0.05, T:0.17
Consensus pattern (23 bp):
CCAAAACACACCAGAATAATCCT
Found at i:10189237 original size:29 final size:28
Alignment explanation
Indices: 10189158--10189241 Score: 123
Period size: 28 Copynumber: 3.0 Consensus size: 28
10189148 AACACACTAG
* *
10189158 TATAATCCTCCAAAACACACCAGTATCA
1 TATAATCCTCCAAAACACACCAGAATAA
*
10189186 TATAATCCTCCCAAACACACCAGAATAA
1 TATAATCCTCCAAAACACACCAGAATAA
*
10189214 TATAACCCATCCAAAACACACCAGAATA
1 TATAATCC-TCCAAAACACACCAGAATA
10189242 GCACAAAGTG
Statistics
Matches: 50, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
28 32 0.64
29 18 0.36
ACGTcount: A:0.46, C:0.32, G:0.04, T:0.18
Consensus pattern (28 bp):
TATAATCCTCCAAAACACACCAGAATAA
Found at i:10200211 original size:29 final size:29
Alignment explanation
Indices: 10200169--10200302 Score: 130
Period size: 29 Copynumber: 4.6 Consensus size: 29
10200159 CACCATCAGT
*
10200169 ACATAGTACCTGATAAATATAACACCGAC
1 ACATAGTACCTGATAAATATAACACCAAC
* *
10200198 ACATAGTGCCTGATAAATATAACACTGAATC
1 ACATAGTACCTGATAAATATAACAC-CAA-C
** * *
10200229 A-A-AGTACCTGAT-AATATGTTCATCAAT
1 ACATAGTACCTGATAAATAT-AACACCAAC
*
10200256 ACATAGTACCTGATCAATATAATCACCAAC
1 ACATAGTACCTGATAAATATAA-CACCAAC
*
10200286 ACATAGTGCCTGATAAA
1 ACATAGTACCTGATAAA
10200303 CCCTAATGAC
Statistics
Matches: 83, Mismatches: 15, Indels: 13
0.75 0.14 0.12
Matches are distributed among these distances:
27 1 0.01
28 8 0.10
29 45 0.54
30 27 0.33
31 2 0.02
ACGTcount: A:0.43, C:0.21, G:0.11, T:0.25
Consensus pattern (29 bp):
ACATAGTACCTGATAAATATAACACCAAC
Found at i:10204821 original size:21 final size:20
Alignment explanation
Indices: 10204783--10204832 Score: 64
Period size: 21 Copynumber: 2.5 Consensus size: 20
10204773 TTTAGCTCTC
*
10204783 ATGAGCTTCAATTAACTCAT
1 ATGAGTTTCAATTAACTCAT
* *
10204803 ATGAGTTTCCATTCAACTCCT
1 ATGAGTTTCAATT-AACTCAT
10204824 ATGAGTTTC
1 ATGAGTTTC
10204833 TGTTCAACCC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
20 11 0.42
21 15 0.58
ACGTcount: A:0.28, C:0.22, G:0.12, T:0.38
Consensus pattern (20 bp):
ATGAGTTTCAATTAACTCAT
Found at i:10204838 original size:21 final size:21
Alignment explanation
Indices: 10204796--10204857 Score: 63
Period size: 21 Copynumber: 3.0 Consensus size: 21
10204786 AGCTTCAATT
* **
10204796 AACTCATATGAGTTTCCATTC
1 AACTCCTATGAGTTTCTGTTC
10204817 AACTCCTATGAGTTTCTGTTC
1 AACTCCTATGAGTTTCTGTTC
* *
10204838 AAC-CCTTACGGGTTTCTGTT
1 AACTCC-TATGAGTTTCTGTT
10204858 AGCACTTATG
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
20 2 0.06
21 33 0.94
ACGTcount: A:0.21, C:0.24, G:0.15, T:0.40
Consensus pattern (21 bp):
AACTCCTATGAGTTTCTGTTC
Found at i:10212713 original size:13 final size:13
Alignment explanation
Indices: 10212659--10212728 Score: 65
Period size: 13 Copynumber: 5.5 Consensus size: 13
10212649 TTATTCAATA
*
10212659 TTAAAATTTTATA
1 TTAAAATTTTATT
10212672 TTAAAATTTTTATTT
1 TTAAAA-TTTTA-TT
*
10212687 TTCAAA-TTTATT
1 TTAAAATTTTATT
*
10212699 TTAAAATTTTCTT
1 TTAAAATTTTATT
*
10212712 TT--AATTTTAGT
1 TTAAAATTTTATT
10212723 TTAAAA
1 TTAAAA
10212729 ATATTAATAA
Statistics
Matches: 46, Mismatches: 6, Indels: 10
0.74 0.10 0.16
Matches are distributed among these distances:
11 9 0.20
12 7 0.15
13 19 0.41
14 5 0.11
15 6 0.13
ACGTcount: A:0.37, C:0.03, G:0.01, T:0.59
Consensus pattern (13 bp):
TTAAAATTTTATT
Found at i:10212941 original size:13 final size:13
Alignment explanation
Indices: 10212923--10212949 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
10212913 TACTTGTTAT
10212923 AATTAAAAAATTC
1 AATTAAAAAATTC
10212936 AATTAAAAAATTC
1 AATTAAAAAATTC
10212949 A
1 A
10212950 CTTTTTTGTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.63, C:0.07, G:0.00, T:0.30
Consensus pattern (13 bp):
AATTAAAAAATTC
Found at i:10221085 original size:16 final size:16
Alignment explanation
Indices: 10221061--10221094 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
10221051 AAATTAATAA
*
10221061 AGTTGGAATGGTTAAC
1 AGTTAGAATGGTTAAC
10221077 AGTTAGAATGGTTAAC
1 AGTTAGAATGGTTAAC
10221093 AG
1 AG
10221095 CTCCTTTCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.35, C:0.06, G:0.29, T:0.29
Consensus pattern (16 bp):
AGTTAGAATGGTTAAC
Found at i:10227057 original size:17 final size:17
Alignment explanation
Indices: 10227035--10227070 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
10227025 GTAAAATACG
*
10227035 TTAGCATCTATTTTCAT
1 TTAGCATCCATTTTCAT
10227052 TTAGCATCCATTTTCAT
1 TTAGCATCCATTTTCAT
10227069 TT
1 TT
10227071 TCTTCTTTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.22, C:0.19, G:0.06, T:0.53
Consensus pattern (17 bp):
TTAGCATCCATTTTCAT
Found at i:10234635 original size:25 final size:25
Alignment explanation
Indices: 10234566--10234661 Score: 65
Period size: 25 Copynumber: 3.8 Consensus size: 25
10234556 TATGTTAATC
*
10234566 ATTTT-AAATTCCTTTTATTATTATTT
1 ATTTTAAAATT-CTTTTA-TATTACTT
* * *
10234592 ATTTTGAACTT-TCTATATATTACTT
1 ATTTTAAAATTCT-TTTATATTACTT
*
10234617 ATTTTAAAATTCTTTTATATACTCCTT
1 ATTTTAAAATTCTTTTATAT--TACTT
*
10234644 ATCTTAAAA--CTTTTATAT
1 ATTTTAAAATTCTTTTATAT
10234662 ATGTATATGT
Statistics
Matches: 57, Mismatches: 8, Indels: 11
0.75 0.11 0.14
Matches are distributed among these distances:
25 32 0.56
26 9 0.16
27 16 0.28
ACGTcount: A:0.30, C:0.11, G:0.01, T:0.57
Consensus pattern (25 bp):
ATTTTAAAATTCTTTTATATTACTT
Found at i:10234662 original size:25 final size:25
Alignment explanation
Indices: 10234598--10234662 Score: 76
Period size: 27 Copynumber: 2.5 Consensus size: 25
10234588 ATTTATTTTG
* *
10234598 AACTTTCTATATATTACTTATTTTAA
1 AACTTT-TATATACTACTTATCTTAA
*
10234624 AATTCTTTTATATACTCCTTATCTTAA
1 AA--CTTTTATATACTACTTATCTTAA
10234651 AACTTTTATATA
1 AACTTTTATATA
10234663 TGTATATGTT
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
25 10 0.29
26 2 0.06
27 18 0.53
28 4 0.12
ACGTcount: A:0.34, C:0.14, G:0.00, T:0.52
Consensus pattern (25 bp):
AACTTTTATATACTACTTATCTTAA
Found at i:10234714 original size:26 final size:26
Alignment explanation
Indices: 10234680--10234736 Score: 78
Period size: 26 Copynumber: 2.1 Consensus size: 26
10234670 GTTACTTTGG
*
10234680 ATTATATTTATATATATTTTTATTTTAA
1 ATTAT-TTTATATATA-ATTTATTTTAA
*
10234708 ATTATTTTTTATATAATTTATTTTAA
1 ATTATTTTATATATAATTTATTTTAA
10234734 ATT
1 ATT
10234737 TCTCATTTAC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
26 13 0.48
27 9 0.33
28 5 0.19
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (26 bp):
ATTATTTTATATATAATTTATTTTAA
Found at i:10234853 original size:27 final size:26
Alignment explanation
Indices: 10234810--10234905 Score: 63
Period size: 26 Copynumber: 3.6 Consensus size: 26
10234800 TTACTTTGTG
* *
10234810 TATTATTCATTTTAATTT-ATTTAACA
1 TATTATTTATTTAAATTTGATTT-ACA
* *
10234836 TATTATTTATTTGAAATTTGCTTTATA
1 TATTATTTATTT-AAATTTGATTTACA
* *
10234863 TATTATTTTATTTCAAA-TCGA-TTATA
1 TATTA-TTTATTT-AAATTTGATTTACA
*
10234889 TTTTATTTATGTTAAAT
1 TATTATTTAT-TTAAAT
10234906 CTTTTTCACA
Statistics
Matches: 57, Mismatches: 8, Indels: 10
0.76 0.11 0.13
Matches are distributed among these distances:
25 8 0.14
26 22 0.39
27 14 0.25
28 13 0.23
ACGTcount: A:0.32, C:0.05, G:0.04, T:0.58
Consensus pattern (26 bp):
TATTATTTATTTAAATTTGATTTACA
Found at i:10251598 original size:27 final size:27
Alignment explanation
Indices: 10251568--10251745 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
10251558 ATATTGAGTC
* * * *
10251568 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
10251595 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
10251622 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
10251650 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
10251677 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
10251704 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
10251731 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
10251746 GTACAATTTA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:10251707 original size:82 final size:81
Alignment explanation
Indices: 10251589--10251744 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
10251579 TGCTATATAA
* *
10251589 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
10251654 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
10251671 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
10251735 CACTTAGTGC
65 CACTTAGTGC
10251745 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:10261697 original size:54 final size:54
Alignment explanation
Indices: 10261610--10261775 Score: 260
Period size: 54 Copynumber: 3.1 Consensus size: 54
10261600 ATTCATCCAC
* * *
10261610 ATTTATAGTTAAATCTAATTTAAGTTAGTTTAAATATTTACTTTTATTTTTATA
1 ATTTATAGTTAAATCAAATTTAAGTTAGTTTAAATATTTAATTTAATTTTTATA
* *
10261664 ATTTTTAGTTAAATCAAATTTAAGTTAGTTTAAATATTTAATTTAATTTATATA
1 ATTTATAGTTAAATCAAATTTAAGTTAGTTTAAATATTTAATTTAATTTTTATA
* * *
10261718 ATTTATAGTTAAATCGAATTTAAATTAGTTTAAACATTTAATTTAATTTTTATA
1 ATTTATAGTTAAATCAAATTTAAGTTAGTTTAAATATTTAATTTAATTTTTATA
10261772 ATTT
1 ATTT
10261776 GTATAAAAAT
Statistics
Matches: 102, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
54 102 1.00
ACGTcount: A:0.39, C:0.03, G:0.05, T:0.53
Consensus pattern (54 bp):
ATTTATAGTTAAATCAAATTTAAGTTAGTTTAAATATTTAATTTAATTTTTATA
Found at i:10261704 original size:18 final size:19
Alignment explanation
Indices: 10261680--10261729 Score: 57
Period size: 18 Copynumber: 2.6 Consensus size: 19
10261670 AGTTAAATCA
*
10261680 AATTTAAGTTAGTTTAAAT
1 AATTTAAGTTAATTTAAAT
* *
10261699 -ATTTAATTTAATTTATAT
1 AATTTAAGTTAATTTAAAT
10261717 AATTTATAGTTAA
1 AATTTA-AGTTAA
10261730 ATCGAATTTA
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
18 15 0.60
19 5 0.20
20 5 0.20
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.52
Consensus pattern (19 bp):
AATTTAAGTTAATTTAAAT
Found at i:10262862 original size:24 final size:21
Alignment explanation
Indices: 10262818--10262863 Score: 56
Period size: 21 Copynumber: 2.0 Consensus size: 21
10262808 AGTAAAACAC
*
10262818 AAATAATATTTATTTAATAGA
1 AAATAATATTTATCTAATAGA
10262839 AAATAATATTCTACTCTAAGTAGA
1 AAATAATATT-TA-TCTAA-TAGA
10262863 A
1 A
10262864 TGGGGTGGGT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 10 0.48
22 2 0.10
23 4 0.19
24 5 0.24
ACGTcount: A:0.50, C:0.07, G:0.07, T:0.37
Consensus pattern (21 bp):
AAATAATATTTATCTAATAGA
Found at i:10263184 original size:105 final size:105
Alignment explanation
Indices: 10263002--10263211 Score: 334
Period size: 105 Copynumber: 2.0 Consensus size: 105
10262992 AAGTTTTCGG
*
10263002 ATCAACTCGAATAAAAAATTAAGTTTTTCAATTTAACTCGAATATGAATTACATAATTCGAGTTA
1 ATCAACTCGAATAAAAAATTAAGTTTTTCAATTTAACTCGAATATGAATTACACAATTCGAGTTA
*
10263067 TCTGAAAATCCGAATAAGAAA-TGACAAAACTACGTCGTTT
66 TCTCAAAATCCGAATAAGAAACT-ACAAAACTACGTCGTTT
* * *
10263107 ATCAACTTGAATAAAAAATTAAGTTTTTCAATTTAATTCGAATATGAATTATACAATTCGAGTTA
1 ATCAACTCGAATAAAAAATTAAGTTTTTCAATTTAACTCGAATATGAATTACACAATTCGAGTTA
*
10263172 TC-CAAAACTCCGAATAAGAAACTACAAAACTACGTTGTTT
66 TCTCAAAA-TCCGAATAAGAAACTACAAAACTACGTCGTTT
10263212 GGATAAATAT
Statistics
Matches: 97, Mismatches: 6, Indels: 4
0.91 0.06 0.04
Matches are distributed among these distances:
104 4 0.04
105 92 0.95
106 1 0.01
ACGTcount: A:0.43, C:0.14, G:0.10, T:0.32
Consensus pattern (105 bp):
ATCAACTCGAATAAAAAATTAAGTTTTTCAATTTAACTCGAATATGAATTACACAATTCGAGTTA
TCTCAAAATCCGAATAAGAAACTACAAAACTACGTCGTTT
Found at i:10268185 original size:30 final size:30
Alignment explanation
Indices: 10268149--10268208 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
10268139 AATTAGTGAT
10268149 TAATTAAGTTATAAGGACAAAATCATAAAG
1 TAATTAAGTTATAAGGACAAAATCATAAAG
* *
10268179 TAATTAAGTTATAGGGACTAAATCATAAAG
1 TAATTAAGTTATAAGGACAAAATCATAAAG
10268209 GTGGTAAAAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.50, C:0.07, G:0.15, T:0.28
Consensus pattern (30 bp):
TAATTAAGTTATAAGGACAAAATCATAAAG
Found at i:10269659 original size:41 final size:41
Alignment explanation
Indices: 10269613--10269690 Score: 147
Period size: 41 Copynumber: 1.9 Consensus size: 41
10269603 ATGTTGTATG
10269613 GATAGTTGGTTTAATGAAAATGCATGATTAAATATTTGGTT
1 GATAGTTGGTTTAATGAAAATGCATGATTAAATATTTGGTT
*
10269654 GATAGTTGGTTTAATGAAAATGCATGATTGAATATTT
1 GATAGTTGGTTTAATGAAAATGCATGATTAAATATTT
10269691 AGTAGACATA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 36 1.00
ACGTcount: A:0.35, C:0.03, G:0.22, T:0.41
Consensus pattern (41 bp):
GATAGTTGGTTTAATGAAAATGCATGATTAAATATTTGGTT
Found at i:10276120 original size:22 final size:20
Alignment explanation
Indices: 10276095--10276147 Score: 54
Period size: 22 Copynumber: 2.5 Consensus size: 20
10276085 AAGCTCACCC
10276095 ATATTATTTTTTAAAAATATTT
1 ATATTATTTTTT--AAATATTT
*
10276117 ATATTATATTATTTTAATATTT
1 ATATTAT-TT-TTTAAATATTT
10276139 A-ATTATTTT
1 ATATTATTTT
10276148 ATTTTATTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
19 1 0.04
20 2 0.07
21 5 0.18
22 15 0.54
23 2 0.07
24 3 0.11
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (20 bp):
ATATTATTTTTTAAATATTT
Found at i:10276149 original size:21 final size:22
Alignment explanation
Indices: 10276110--10276153 Score: 72
Period size: 21 Copynumber: 2.0 Consensus size: 22
10276100 ATTTTTTAAA
10276110 AATATTTATATTATATTATTTT
1 AATATTTATATTATATTATTTT
*
10276132 AATATTTA-ATTATTTTATTTT
1 AATATTTATATTATATTATTTT
10276153 A
1 A
10276154 TTTTTTGAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 13 0.62
22 8 0.38
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (22 bp):
AATATTTATATTATATTATTTT
Found at i:10277415 original size:20 final size:20
Alignment explanation
Indices: 10277390--10277451 Score: 79
Period size: 20 Copynumber: 3.1 Consensus size: 20
10277380 TTGAAATGTT
*
10277390 AACAGAGGCACCGAAGTACA
1 AACAGAGGCACCGAAGTGCA
* *
10277410 AACAGAAGCACCGAAGTGTA
1 AACAGAGGCACCGAAGTGCA
* *
10277430 AACAAAGGCACCAAAGTGCA
1 AACAGAGGCACCGAAGTGCA
10277450 AA
1 AA
10277452 TCCCATACAA
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.48, C:0.23, G:0.23, T:0.06
Consensus pattern (20 bp):
AACAGAGGCACCGAAGTGCA
Found at i:10282074 original size:78 final size:78
Alignment explanation
Indices: 10281924--10282145 Score: 313
Period size: 78 Copynumber: 2.8 Consensus size: 78
10281914 TTGAATGATG
* * * *
10281924 TCCGGGCTAAGTCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATTT
1 TCCGGGCTAAGTCCGAAGGCATTTGTGC-GAGTTACTATATCCGGGCTAAG-TCCGAAGGCATTT
10281988 GTGCGAGTTACTAAA
64 GTGCGAGTTACTAAA
* *
10282003 TCCGGACTAAGATCCGAAGGCATTTGTGCGAGTTACTA-ATCCGGGCTAAGCCCGAAGGCATTTG
1 TCCGGGCTAAG-TCCGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCCGAAGGCATTTG
10282067 TGCGAGTTACTAAA
65 TGCGAGTTACTAAA
* * *
10282081 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAACCGGGCTATGTCCGAAGGCATTTG
1 TCCGGGCTAAGT-CCGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCCGAAGGCATTTG
10282146 AACGAGTAGC
Statistics
Matches: 128, Mismatches: 11, Indels: 8
0.87 0.07 0.05
Matches are distributed among these distances:
77 1 0.01
78 61 0.48
79 44 0.34
80 15 0.12
81 7 0.05
ACGTcount: A:0.25, C:0.22, G:0.27, T:0.26
Consensus pattern (78 bp):
TCCGGGCTAAGTCCGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCCGAAGGCATTTGT
GCGAGTTACTAAA
Found at i:10282152 original size:39 final size:39
Alignment explanation
Indices: 10281924--10282145 Score: 297
Period size: 40 Copynumber: 5.6 Consensus size: 39
10281914 TTGAATGATG
* * * *
10281924 TCCGGGCTAAGTCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCGAAGGCATTTGTGC-GAGTTACTAAA
*
10281963 TCCGGACTAAGATCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAG-TCCGAAGGCATTTGTGCGAGTTACTAAA
*
10282003 TCCGGACTAAGATCCGAAGGCATTTGTGCGAGTTACT-AA
1 TCCGGGCTAAG-TCCGAAGGCATTTGTGCGAGTTACTAAA
*
10282042 TCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCGAAGGCATTTGTGCGAGTTACTAAA
*
10282081 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGCTAAGT-CCGAAGGCATTTGTGCGAGTTACTA-AA
*
10282122 -CCGGGCTATGTCCGAAGGCATTTG
1 TCCGGGCTAAGTCCGAAGGCATTTG
10282146 AACGAGTAGC
Statistics
Matches: 167, Mismatches: 11, Indels: 10
0.89 0.06 0.05
Matches are distributed among these distances:
38 24 0.14
39 47 0.28
40 87 0.52
41 9 0.05
ACGTcount: A:0.25, C:0.22, G:0.27, T:0.26
Consensus pattern (39 bp):
TCCGGGCTAAGTCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:10282164 original size:118 final size:118
Alignment explanation
Indices: 10281924--10282152 Score: 304
Period size: 118 Copynumber: 1.9 Consensus size: 118
10281914 TTGAATGATG
* *
10281924 TCCGGGCTAAGTCCGAAGGCTTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATTTG
1 TCCGGGCTAAGCCCGAAGGCTTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATTTG
**
10281989 TGCGAGTTACTAAATCCGGACTAAGATCCGAAGGCATTTGTGCGAGTTACTAA
66 TGCGAGTTACTAAATCCGGACTAAGATCCGAAGGCATTTGAACGAGTTACTAA
* * * **
10282042 TCCGGGCTAAGCCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCATT
1 TCCGGGCTAAGCCCGAAGGC-TTTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCATT
* *
10282105 TGTGCGAGTTACTATAA-CCGGGCTATG-TCCGAAGGCATTTGAACGAGT
64 TGTGCGAGTTACTA-AATCCGGACTAAGATCCGAAGGCATTTGAACGAGT
10282153 AGCTATATCC
Statistics
Matches: 97, Mismatches: 11, Indels: 7
0.84 0.10 0.06
Matches are distributed among these distances:
117 20 0.21
118 68 0.70
119 9 0.09
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (118 bp):
TCCGGGCTAAGCCCGAAGGCTTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATTTG
TGCGAGTTACTAAATCCGGACTAAGATCCGAAGGCATTTGAACGAGTTACTAA
Found at i:10282167 original size:78 final size:77
Alignment explanation
Indices: 10281931--10282178 Score: 295
Period size: 78 Copynumber: 3.2 Consensus size: 77
10281921 ATGTCCGGGC
* * * *
10281931 TAAGTCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATTTGTGCGAG
1 TAAGTCCGAAGGCATTTGTGC-GAGTTACTATATCCGGGCTAAG-TCCGAAGGCATTTGTGCGAG
*
10281995 TTACTAAATCCGGAC
64 TTACTAAATCCGG-T
*
10282010 TAAGATCCGAAGGCATTTGTGCGAGTTACTA-ATCCGGGCTAAGCCCGAAGGCATTTGTGCGAGT
1 TAAG-TCCGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCCGAAGGCATTTGTGCGAGT
10282074 TACTAAATCCGGGT
65 TACTAAATCC-GGT
* * **
10282088 TAAGTCCCGAAGGCATTTGTGCGAGTTACTATAACCGGGCTATGTCCGAAGGCATTTGAACGAG-
1 TAAGT-CCGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCCGAAGGCATTTGTGCGAGT
*
10282152 TAGCTATATCCGGT
65 TA-CTAAATCCGGT
*
10282166 TAAATTCCGAAGG
1 T-AAGTCCGAAGG
10282179 TACGTGATTT
Statistics
Matches: 149, Mismatches: 13, Indels: 15
0.84 0.07 0.08
Matches are distributed among these distances:
77 1 0.01
78 72 0.48
79 54 0.36
80 15 0.10
81 7 0.05
ACGTcount: A:0.27, C:0.21, G:0.27, T:0.26
Consensus pattern (77 bp):
TAAGTCCGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCCGAAGGCATTTGTGCGAGTT
ACTAAATCCGGT
Found at i:10282175 original size:39 final size:40
Alignment explanation
Indices: 10281935--10282178 Score: 218
Period size: 40 Copynumber: 6.2 Consensus size: 40
10281925 CCGGGCTAAG
* * * **
10281935 TCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGA-
1 TCCGAAGGCATTTGTGC-GAGTTACTATATCCGGGTTAA-AT
* **
10281975 TCCGAAGGCATTTGTGCGAGTTACTAAATCCGGACTAAGA-
1 TCCGAAGGCATTTGTGCGAGTTACTATATCCGGGTTAA-AT
* *
10282015 TCCGAAGGCATTTGTGCGAGTTACTA-ATCCGGGCT-AAG
1 TCCGAAGGCATTTGTGCGAGTTACTATATCCGGGTTAAAT
* * *
10282053 CCCGAAGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGT
1 TCCGAAGGCATTTGTGCGAGTTACTATATCCGGGTTAAAT
* * *
10282093 CCCGAAGGCATTTGTGCGAGTTACTATAACCGGGCT--AT
1 TCCGAAGGCATTTGTGCGAGTTACTATATCCGGGTTAAAT
**
10282131 GTCCGAAGGCATTTGAACGAG-TAGCTATATCC-GGTTAAAT
1 -TCCGAAGGCATTTGTGCGAGTTA-CTATATCCGGGTTAAAT
10282171 TCCGAAGG
1 TCCGAAGG
10282179 TACGTGATTT
Statistics
Matches: 178, Mismatches: 18, Indels: 17
0.84 0.08 0.08
Matches are distributed among these distances:
37 1 0.01
38 32 0.18
39 48 0.27
40 90 0.51
41 7 0.04
ACGTcount: A:0.27, C:0.21, G:0.27, T:0.26
Consensus pattern (40 bp):
TCCGAAGGCATTTGTGCGAGTTACTATATCCGGGTTAAAT
Found at i:10290112 original size:119 final size:121
Alignment explanation
Indices: 10289896--10290160 Score: 344
Period size: 119 Copynumber: 2.2 Consensus size: 121
10289886 TTGAATGATG
* *
10289896 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAGGTGACCATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGGTGACCAAATCCGGACTAAGATCCGAAGGCATT
*
10289960 TGTACGAGTTACTAAATCTGGACTAAGATCCGAAGGCATTTGTGCGAGTTACTCA-A
66 TGTACGAGTTACTAAATCCGGACTAAGATCCGAAGGCATTTGTGCGAGTTACT-ATA
* * * **
10290016 TCCGGGTTAAGT-CCGAAGGCATTTGTGCGA-GTTACTAAATCCGGGTTAAG-TCCCGAAGGCAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGGTGACCAAATCCGGACTAAGAT-CCGAAGGCAT
* **
10290078 TTGTGCGAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCATTTGTGCGAGTTACTATA
65 TTGTACGAGTTACTAAATCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGTTACTATA
* *
10290135 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
10290161 AACGAGTAGC
Statistics
Matches: 126, Mismatches: 14, Indels: 10
0.84 0.09 0.07
Matches are distributed among these distances:
118 3 0.02
119 91 0.72
120 32 0.25
ACGTcount: A:0.25, C:0.21, G:0.27, T:0.27
Consensus pattern (121 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGGTGACCAAATCCGGACTAAGATCCGAAGGCATT
TGTACGAGTTACTAAATCCGGACTAAGATCCGAAGGCATTTGTGCGAGTTACTATA
Found at i:10290174 original size:40 final size:40
Alignment explanation
Indices: 10289896--10290160 Score: 333
Period size: 40 Copynumber: 6.7 Consensus size: 40
10289886 TTGAATGATG
* * * * *
10289896 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAGGTGACCATA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGA-GTTACTAAA
** *
10289936 TCCGGACTAAGAT-CCGAAGGCATTTGTACGAGTTACTAAA
1 TCCGGGTTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
* ** *
10289976 TCTGGACTAAGAT-CCGAAGGCATTTGTGCGAGTTACTCAA
1 TCCGGGTTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
10290016 TCCGGGTTAAGT-CCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
10290055 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
10290095 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
* *
10290136 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGTTAAGTCCCGAAGGCATTTG
10290161 AACGAGTAGC
Statistics
Matches: 206, Mismatches: 15, Indels: 8
0.90 0.07 0.03
Matches are distributed among these distances:
39 39 0.19
40 157 0.76
41 10 0.05
ACGTcount: A:0.25, C:0.21, G:0.27, T:0.27
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:10290182 original size:119 final size:119
Alignment explanation
Indices: 10289949--10290193 Score: 318
Period size: 119 Copynumber: 2.1 Consensus size: 119
10289939 GGACTAAGAT
*
10289949 CCGAAGGCATTTGTACGAGTTACTAAATCTGGACTAAGATCCGAAGGCATTTGTGCGAGTTACTC
1 CCGAAGGCATTTGTACGAGTTACTAAATCCGGACTAAGATCCGAAGGCATTTGTGCGAGTTACTC
* * ** *
10290014 AATCCGGGTTAAGTCCGAAGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGTC
66 AAACCGGGCTAAGTCCGAAGGCATTTGAACGAGTTACTAAATCCGGGTTAAATC
* **
10290068 CCGAAGGCATTTGTGCGAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCATTTGTGCGAGTTACT
1 CCGAAGGCATTTGTACGAGTTACTAAATCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGTTACT
* * *
10290132 -ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGCTATATCC-GGTTAAATT
65 CA-AACCGGGCTAAGT-CCGAAGGCATTTGAACGAGTTA-CTAAATCCGGGTTAAATC
10290187 CCGAAGG
1 CCGAAGG
10290194 TACGTGATTT
Statistics
Matches: 110, Mismatches: 12, Indels: 8
0.85 0.09 0.06
Matches are distributed among these distances:
118 2 0.02
119 84 0.76
120 24 0.22
ACGTcount: A:0.27, C:0.20, G:0.27, T:0.27
Consensus pattern (119 bp):
CCGAAGGCATTTGTACGAGTTACTAAATCCGGACTAAGATCCGAAGGCATTTGTGCGAGTTACTC
AAACCGGGCTAAGTCCGAAGGCATTTGAACGAGTTACTAAATCCGGGTTAAATC
Found at i:10306633 original size:22 final size:20
Alignment explanation
Indices: 10306608--10306660 Score: 54
Period size: 22 Copynumber: 2.5 Consensus size: 20
10306598 AAGCTCACCC
10306608 ATATTATTTTTTAAAAATATTT
1 ATATTATTTTTT--AAATATTT
*
10306630 ATATTATATTATTTTAATATTT
1 ATATTAT-TT-TTTAAATATTT
10306652 A-ATTATTTT
1 ATATTATTTT
10306661 ATTTTATTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
19 1 0.04
20 2 0.07
21 5 0.18
22 15 0.54
23 2 0.07
24 3 0.11
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (20 bp):
ATATTATTTTTTAAATATTT
Found at i:10306662 original size:21 final size:22
Alignment explanation
Indices: 10306623--10306666 Score: 72
Period size: 21 Copynumber: 2.0 Consensus size: 22
10306613 ATTTTTTAAA
10306623 AATATTTATATTATATTATTTT
1 AATATTTATATTATATTATTTT
*
10306645 AATATTTA-ATTATTTTATTTT
1 AATATTTATATTATATTATTTT
10306666 A
1 A
10306667 TTTTTGAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 13 0.62
22 8 0.38
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (22 bp):
AATATTTATATTATATTATTTT
Found at i:10307915 original size:20 final size:20
Alignment explanation
Indices: 10307890--10307951 Score: 79
Period size: 20 Copynumber: 3.1 Consensus size: 20
10307880 TTGAAATGTT
*
10307890 AACAGAGGCACCGAAGTACA
1 AACAGAGGCACCGAAGTGCA
* *
10307910 AACAGAAGCACCGAAGTGTA
1 AACAGAGGCACCGAAGTGCA
* *
10307930 AACAAAGGCACCAAAGTGCA
1 AACAGAGGCACCGAAGTGCA
10307950 AA
1 AA
10307952 TCCCATACAA
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.48, C:0.23, G:0.23, T:0.06
Consensus pattern (20 bp):
AACAGAGGCACCGAAGTGCA
Found at i:10312401 original size:40 final size:39
Alignment explanation
Indices: 10312344--10312563 Score: 147
Period size: 39 Copynumber: 5.7 Consensus size: 39
10312334 TTGAATGATG
*
10312344 TCCGGGCTAAG-TACCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGACTAAGAT-CCGAAGGCATTTGTGC-AAGTGACCA-A
* * *
10312384 TCCGGACTAAGATCCGAAGGCATTTGTGCGAGTTACTAA
1 TCCGGACTAAGATCCGAAGGCATTTGTGCAAGTGACCAA
* * *
10312423 TCCGGACTAA-AT-CGAAGGCATTTGTGCGAGTTACTAA
1 TCCGGACTAAGATCCGAAGGCATTTGTGCAAGTGACCAA
* * * * *
10312460 TTCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAA
1 -TCCGGACTAAGATCCGAAGGCATTTGTGCAAGTGACCAA
* * *
10312499 TCCGG-CT-A-ATCCCGAA-GCA-TTGTGCGAGTTACTAAA
1 TCCGGACTAAGAT-CCGAAGGCATTTGTGCAAGTGAC-CAA
**
10312535 TCCGGGTTAAG-TCCCGAAGGCATTTGTGC
1 TCCGGACTAAGAT-CCGAAGGCATTTGTGC
10312564 GAGTTACTAT
Statistics
Matches: 158, Mismatches: 9, Indels: 26
0.82 0.05 0.13
Matches are distributed among these distances:
35 13 0.08
36 11 0.07
37 33 0.21
38 24 0.15
39 39 0.25
40 30 0.19
41 8 0.05
ACGTcount: A:0.25, C:0.22, G:0.26, T:0.26
Consensus pattern (39 bp):
TCCGGACTAAGATCCGAAGGCATTTGTGCAAGTGACCAA
Found at i:10312565 original size:40 final size:40
Alignment explanation
Indices: 10312344--10312600 Score: 295
Period size: 40 Copynumber: 6.7 Consensus size: 40
10312334 TTGAATGATG
* * * * *
10312344 TCCGGGCTAAGTACCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
*
10312384 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGTTACT-AA
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
* * *
10312423 TCCGGACTAAAT--CGAAGGCATTTGTGCGAGTTACTAAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
10312461 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACT-AA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
10312499 TCC-GGCTAA-TCCCGAA-GCA-TTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
10312535 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
* *
10312576 -CCGGGCTATGTCTCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
10312601 AACGAGTAGC
Statistics
Matches: 191, Mismatches: 14, Indels: 24
0.83 0.06 0.10
Matches are distributed among these distances:
35 14 0.07
36 8 0.04
37 40 0.21
38 22 0.12
39 37 0.19
40 60 0.31
41 10 0.05
ACGTcount: A:0.25, C:0.22, G:0.26, T:0.26
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:10312567 original size:75 final size:76
Alignment explanation
Indices: 10312383--10312572 Score: 280
Period size: 76 Copynumber: 2.5 Consensus size: 76
10312373 AAGTGACCAT
* *
10312383 ATCCGGACTAAGATCCGAAGGCATTTGTGCGAGTTACTAATCCGGACTAAATCGAAGGCATTTGT
1 ATCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAATCCGGACTAAATCGAAGGCATTTGT
10312448 GCGAGTTACTAA
65 GCGAGTTACTAA
*
10312460 TTCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAATCCGG-CT-AATCCCGAA-GCA-TTG
1 ATCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAATCCGGACTAAAT--CGAAGGCATTTG
10312521 TGCGAGTTACTAA
64 TGCGAGTTACTAA
*
10312534 ATCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTA
1 ATCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTA
10312573 TAACCGGGCT
Statistics
Matches: 105, Mismatches: 5, Indels: 8
0.89 0.04 0.07
Matches are distributed among these distances:
74 29 0.28
75 31 0.30
76 35 0.33
77 10 0.10
ACGTcount: A:0.26, C:0.22, G:0.26, T:0.26
Consensus pattern (76 bp):
ATCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAATCCGGACTAAATCGAAGGCATTTGTG
CGAGTTACTAA
Found at i:10320648 original size:40 final size:39
Alignment explanation
Indices: 10320377--10320641 Score: 327
Period size: 40 Copynumber: 6.6 Consensus size: 39
10320367 TTGAATGATG
* * * *
10320377 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGT-CCGAAGGCATTTGTGC-GAGTTACTAAA
* *
10320417 TCCGGACTAAGATCCGAAGACATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAG-TCCGAAGGCATTTGTGCGAGTTACTAAA
*
10320457 TCCGGACTAAGATCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAG-TCCGAAGGCATTTGTGCGAGTTACTAAA
* * *
10320497 TCCGGACTAAGATCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAG-TCCGAAGGCATTTGTGCGAGTTACTAAA
*
10320537 TCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCGAAGGCATTTGTGCGAGTTACTAAA
*
10320576 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGCTAAGT-CCGAAGGCATTTGTGCGAGTTACTA-AA
*
10320617 -CCGGGCTATGTCTCGAAGGCATTTG
1 TCCGGGCTAAGTC-CGAAGGCATTTG
10320642 AACGAGTAGC
Statistics
Matches: 203, Mismatches: 17, Indels: 10
0.88 0.07 0.04
Matches are distributed among these distances:
39 36 0.18
40 157 0.77
41 10 0.05
ACGTcount: A:0.26, C:0.22, G:0.26, T:0.26
Consensus pattern (39 bp):
TCCGGGCTAAGTCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:10320660 original size:119 final size:120
Alignment explanation
Indices: 10320414--10320660 Score: 326
Period size: 119 Copynumber: 2.1 Consensus size: 120
10320404 CTAAGTGACC
*
10320414 ATATCCGGACTAAGATCCGAAGACATTTGTGCGAGTTACTAAATCCGGACTAAGATCCGAAGGCA
1 ATATCCGGACTAAGACCCGAAGACATTTGTGCGAGTTACTAAATCCGGACTAAGATCCGAAGGCA
**
10320479 TTTGTGCGAGTTACTAAATCCGGACTAAGATCCGAAGGCATTTGTGCGAGATACT
66 TTTGTGCGAGTTACTAAATCCGGACTAAGATCCGAAGGCATTTGAACGAGATACT
* * **
10320534 A-ATTCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAATCCGGGTTAAG-TCCCGAAGG
1 ATA-TCCGGACTAAGACCCGAAGACATTTGTGCGAGTTACTAAATCCGGACTAAGAT-CCGAAGG
* *
10320596 CATTTGTGCGAGTTACTATAA-CCGGGCTATG-TCTCGAAGGCATTTGAACGAG-TAGCT
64 CATTTGTGCGAGTTACTA-AATCCGGACTAAGATC-CGAAGGCATTTGAACGAGATA-CT
10320653 ATATCCGG
1 ATATCCGG
10320661 TTAAATTCCG
Statistics
Matches: 112, Mismatches: 9, Indels: 13
0.84 0.07 0.10
Matches are distributed among these distances:
118 5 0.04
119 93 0.83
120 14 0.12
ACGTcount: A:0.28, C:0.21, G:0.26, T:0.26
Consensus pattern (120 bp):
ATATCCGGACTAAGACCCGAAGACATTTGTGCGAGTTACTAAATCCGGACTAAGATCCGAAGGCA
TTTGTGCGAGTTACTAAATCCGGACTAAGATCCGAAGGCATTTGAACGAGATACT
Found at i:10320663 original size:79 final size:76
Alignment explanation
Indices: 10320378--10320674 Score: 301
Period size: 80 Copynumber: 3.7 Consensus size: 76
10320368 TGAATGATGT
* * * * * *
10320378 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGACATTT
1 CCGGGCTAAGT-CCGAAGGCATTTGTGC-GAGTTACTAAATCCGG-TTAAG-TCCGAAGGCATTT
10320442 GTGCGAGTTACTAAA
62 GTGCGAGTTACTAAA
* *
10320457 TCCGGACTAAGATCCGAAGGCATTTGTGCGAGTTACTAAATCCGGACTAAGATCCGAAGGCATTT
1 -CCGGGCTAAG-TCCGAAGGCATTTGTGCGAGTTACTAAATCCGG-TTAAG-TCCGAAGGCATTT
* *
10320522 GTGCGAGATACTAATT
62 GTGCGAGTTACTAA-A
*
10320538 CCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCATTTGT
1 CCGGGCTAAGTCCGAAGGCATTTGTGCGAGTTACTAAATCC-GGTTAAGT-CCGAAGGCATTTGT
10320603 GCGAGTTACTATAA
64 GCGAGTTACTA-AA
* ** * *
10320617 CCGGGCTATGTCTCGAAGGCATTTGAACGAG-TAGCTATATCCGGTTAAATTCCGAAGG
1 CCGGGCTAAGTC-CGAAGGCATTTGTGCGAGTTA-CTAAATCCGGTT-AAGTCCGAAGG
10320675 TACGTGATTT
Statistics
Matches: 189, Mismatches: 19, Indels: 19
0.83 0.08 0.08
Matches are distributed among these distances:
78 1 0.01
79 81 0.43
80 99 0.52
81 8 0.04
ACGTcount: A:0.27, C:0.21, G:0.26, T:0.25
Consensus pattern (76 bp):
CCGGGCTAAGTCCGAAGGCATTTGTGCGAGTTACTAAATCCGGTTAAGTCCGAAGGCATTTGTGC
GAGTTACTAAA
Found at i:10327955 original size:18 final size:18
Alignment explanation
Indices: 10327932--10327969 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
10327922 AAATCAAGTC
10327932 TATCATATATAAGAATTT
1 TATCATATATAAGAATTT
10327950 TATCATATATAAGAATTT
1 TATCATATATAAGAATTT
10327968 TA
1 TA
10327970 GTCTTGCTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.45, C:0.05, G:0.05, T:0.45
Consensus pattern (18 bp):
TATCATATATAAGAATTT
Found at i:10329680 original size:22 final size:22
Alignment explanation
Indices: 10329653--10329717 Score: 60
Period size: 24 Copynumber: 2.9 Consensus size: 22
10329643 TATCTGCACT
10329653 TTTGAGTGATTTATCCACATCG
1 TTTGAGTGATTTATCCACATCG
* * *
10329675 TTTGAGCAGCTTT-TCTGTACATCG
1 TTTGAG-TGATTTATC--CACATCG
*
10329699 TTTGAGTGGTTTATCCACA
1 TTTGAGTGATTTATCCACA
10329718 CCGCACTAGC
Statistics
Matches: 33, Mismatches: 6, Indels: 8
0.70 0.13 0.17
Matches are distributed among these distances:
22 11 0.33
23 8 0.24
24 14 0.42
ACGTcount: A:0.20, C:0.18, G:0.20, T:0.42
Consensus pattern (22 bp):
TTTGAGTGATTTATCCACATCG
Found at i:10333821 original size:9 final size:9
Alignment explanation
Indices: 10333809--10333871 Score: 60
Period size: 9 Copynumber: 7.1 Consensus size: 9
10333799 ATACTTTTTG
10333809 ATTTTTTAT
1 ATTTTTTAT
10333818 ATTTTTTCA-
1 ATTTTTT-AT
10333827 ATTTTTTAT
1 ATTTTTTAT
*
10333836 ATTTTATAT
1 ATTTTTTAT
*
10333845 AATGTTTTAT
1 -ATTTTTTAT
10333855 A--TTTTAT
1 ATTTTTTAT
*
10333862 ATTTTATAT
1 ATTTTTTAT
10333871 A
1 A
10333872 ATTGATATAT
Statistics
Matches: 45, Mismatches: 4, Indels: 10
0.76 0.07 0.17
Matches are distributed among these distances:
7 7 0.16
8 1 0.02
9 29 0.64
10 8 0.18
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.68
Consensus pattern (9 bp):
ATTTTTTAT
Found at i:10333824 original size:18 final size:18
Alignment explanation
Indices: 10333780--10333859 Score: 70
Period size: 19 Copynumber: 4.3 Consensus size: 18
10333770 TATATATATA
* *
10333780 ATTTTTTTAAAATTTTCAT
1 ATTTTTTT-AATTTTTTAT
* *
10333799 ATACTTTTTGATTTTTTAT
1 AT-TTTTTTAATTTTTTAT
*
10333818 ATTTTTTCAATTTTTTAT
1 ATTTTTTTAATTTTTTAT
* *
10333836 ATTTTATATAATGTTTTAT
1 ATTTT-TTTAATTTTTTAT
10333855 ATTTT
1 ATTTT
10333860 ATATTTTATA
Statistics
Matches: 49, Mismatches: 10, Indels: 4
0.78 0.16 0.06
Matches are distributed among these distances:
18 18 0.37
19 26 0.53
20 5 0.10
ACGTcount: A:0.26, C:0.04, G:0.03, T:0.68
Consensus pattern (18 bp):
ATTTTTTTAATTTTTTAT
Done.