Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D07
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: 58101237
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1550000 characters in sequence are not A, C, G, or T
File 139 of 199
Found at i:40525871 original size:50 final size:50
Alignment explanation
Indices: 40525751--40525877 Score: 159
Period size: 51 Copynumber: 2.5 Consensus size: 50
40525741 GTACTCAATT
* * * *
40525751 CACATAGCAGCCTGCACATTGTACTACACATGTGACCATTTCCATCTGATA
1 CACATAGTAGCCTGCACATAGTACTACACATGCGACCA-TTCCATCCGATA
40525802 CACATAGTAGCCTGCACATAGTACTACACATGCGACCCA-T-CATTCCGATA
1 CACATAGTAGCCTGCACATAGTACTACACATGCGA-CCATTCCA-TCCGATA
* *
40525852 CACGTTGTAGCCTGCACATAGTACTA
1 CACATAGTAGCCTGCACATAGTACTA
40525878 GATACGTGAC
Statistics
Matches: 68, Mismatches: 6, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
49 2 0.03
50 31 0.46
51 32 0.47
52 3 0.04
ACGTcount: A:0.30, C:0.30, G:0.15, T:0.25
Consensus pattern (50 bp):
CACATAGTAGCCTGCACATAGTACTACACATGCGACCATTCCATCCGATA
Found at i:40529335 original size:28 final size:28
Alignment explanation
Indices: 40529303--40529389 Score: 122
Period size: 28 Copynumber: 3.1 Consensus size: 28
40529293 GAGAAAAACG
*
40529303 TATGAAAATTGAAGCCTTTGTGGAAATC
1 TATGAAAATTGAAGCCTTTGTGGCAATC
*
40529331 TATGAAAATGGAAGCCTTT-TGGCAATC
1 TATGAAAATTGAAGCCTTTGTGGCAATC
* * *
40529358 TATGAAAATTGAAGTCTTCGTGGCGATC
1 TATGAAAATTGAAGCCTTTGTGGCAATC
40529386 TATG
1 TATG
40529390 GAATGGGACG
Statistics
Matches: 52, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
27 23 0.44
28 29 0.56
ACGTcount: A:0.32, C:0.13, G:0.23, T:0.32
Consensus pattern (28 bp):
TATGAAAATTGAAGCCTTTGTGGCAATC
Found at i:40535726 original size:28 final size:28
Alignment explanation
Indices: 40535647--40535754 Score: 130
Period size: 28 Copynumber: 3.9 Consensus size: 28
40535637 CGTGAAAAAG
* * *
40535647 TATGAAAATGGAAGTCTTTGGGGCAATA
1 TATGAAAATGGAAGCCTTTGTGGCAATC
*
40535675 TATGAAAACGGAAGCCTTTGTGGCAATC
1 TATGAAAATGGAAGCCTTTGTGGCAATC
40535703 TATGAAAATGGAAGCCTTCT-TGGCAATC
1 TATGAAAATGGAAGCCTT-TGTGGCAATC
* *
40535731 TATGGAAAT-GAATGCCTTCGTGGC
1 TATGAAAATGGAA-GCCTTTGTGGC
40535755 GCACTCCAAT
Statistics
Matches: 70, Mismatches: 7, Indels: 6
0.84 0.08 0.07
Matches are distributed among these distances:
27 3 0.04
28 66 0.94
29 1 0.01
ACGTcount: A:0.31, C:0.15, G:0.26, T:0.28
Consensus pattern (28 bp):
TATGAAAATGGAAGCCTTTGTGGCAATC
Found at i:40537503 original size:22 final size:21
Alignment explanation
Indices: 40537460--40537504 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 21
40537450 CAATAGAATT
40537460 TTAAATACATATTAACATATAA
1 TTAAATACATA-TAACATATAA
40537482 TTAAATAACATA-AACATAATAA
1 TTAAAT-ACATATAACAT-ATAA
40537504 T
1 T
40537505 CCGTACATAC
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
21 5 0.24
22 11 0.52
23 5 0.24
ACGTcount: A:0.58, C:0.09, G:0.00, T:0.33
Consensus pattern (21 bp):
TTAAATACATATAACATATAA
Found at i:40537630 original size:19 final size:19
Alignment explanation
Indices: 40537606--40537646 Score: 82
Period size: 19 Copynumber: 2.2 Consensus size: 19
40537596 GTCTATCTTG
40537606 ATCTAAATAGAAAAATTCA
1 ATCTAAATAGAAAAATTCA
40537625 ATCTAAATAGAAAAATTCA
1 ATCTAAATAGAAAAATTCA
40537644 ATC
1 ATC
40537647 CATTTAATAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.56, C:0.12, G:0.05, T:0.27
Consensus pattern (19 bp):
ATCTAAATAGAAAAATTCA
Found at i:40539583 original size:27 final size:27
Alignment explanation
Indices: 40539553--40539730 Score: 214
Period size: 27 Copynumber: 6.6 Consensus size: 27
40539543 ATATCGAGTC
* * * *
40539553 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
*
40539580 CGCACACTTAGTGCTACATAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
40539607 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
40539635 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
40539662 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
40539689 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
40539716 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
40539731 GTACAATTTA
Statistics
Matches: 132, Mismatches: 16, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
27 108 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:40539692 original size:82 final size:81
Alignment explanation
Indices: 40539574--40539729 Score: 242
Period size: 82 Copynumber: 1.9 Consensus size: 81
40539564 TGCTATATAA
*
40539574 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
40539639 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
40539656 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
40539720 CACTTAGTGC
65 CACTTAGTGC
40539730 TGTACAATTT
Statistics
Matches: 68, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
81 16 0.24
82 52 0.76
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:40547606 original size:27 final size:27
Alignment explanation
Indices: 40547576--40547753 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
40547566 ATATCGAGTC
* * * *
40547576 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
*
40547603 CGCACACTTAGTGCTACATAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
40547630 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
*** * *
40547658 CGCACACTTAGTGCCGTATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
40547685 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
40547712 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
40547739 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
40547754 GTACAATTTA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 107 0.82
28 23 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.28
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:40547715 original size:82 final size:81
Alignment explanation
Indices: 40547597--40547752 Score: 242
Period size: 82 Copynumber: 1.9 Consensus size: 81
40547587 TGCTATATAA
*
40547597 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
40547662 CACTTAGTGCCGTATGG
65 CACTTAGTGCCGTATGG
* * **
40547679 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
40547743 CACTTAGTGC
65 CACTTAGTGC
40547753 TGTACAATTT
Statistics
Matches: 68, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
81 16 0.24
82 52 0.76
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.28
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGTATGG
Found at i:40559053 original size:27 final size:27
Alignment explanation
Indices: 40559023--40559200 Score: 178
Period size: 27 Copynumber: 6.6 Consensus size: 27
40559013 ATATTGAGTC
* *
40559023 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAATCAACT
* *
40559050 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
*
40559077 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAATC-AACT
** ** **
40559105 CGCACACTTAGTGCCGCATGGTCAGTT
1 CGCACACTTAGTGCTACATAATCAACT
* **
40559132 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAATCAACT
* * *
40559159 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
40559186 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
40559201 GTACAATTTA
Statistics
Matches: 128, Mismatches: 20, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
27 104 0.81
28 24 0.19
ACGTcount: A:0.29, C:0.28, G:0.16, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAACT
Found at i:40559162 original size:82 final size:81
Alignment explanation
Indices: 40559049--40559199 Score: 232
Period size: 82 Copynumber: 1.9 Consensus size: 81
40559039 TATAATCAAC
* *
40559049 TCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCACACTT
1 TCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCACACTT
40559114 AGTGCCGCATGGTCAGT
65 AGTGCCGCATGGTCAGT
* **
40559131 TCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCACACTT
1 TCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCACACTT
40559195 AGTGC
65 AGTGC
40559200 TGTACAATTT
Statistics
Matches: 63, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
81 16 0.25
82 47 0.75
ACGTcount: A:0.28, C:0.28, G:0.17, T:0.27
Consensus pattern (81 bp):
TCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCACACTTA
GTGCCGCATGGTCAGT
Found at i:40567105 original size:27 final size:27
Alignment explanation
Indices: 40567074--40567251 Score: 178
Period size: 27 Copynumber: 6.6 Consensus size: 27
40567064 TATATGAGTC
* *
40567074 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAATCAACT
* *
40567101 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
*
40567128 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAATC-AACT
** ** **
40567156 CGCACACTTAGTGCCGCATGGTCAGTT
1 CGCACACTTAGTGCTACATAATCAACT
* **
40567183 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAATCAACT
* * *
40567210 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
40567237 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
40567252 GTACAATTTA
Statistics
Matches: 128, Mismatches: 20, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
27 104 0.81
28 24 0.19
ACGTcount: A:0.29, C:0.28, G:0.16, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAACT
Found at i:40567213 original size:82 final size:81
Alignment explanation
Indices: 40567100--40567250 Score: 232
Period size: 82 Copynumber: 1.9 Consensus size: 81
40567090 TATAATCAAC
* *
40567100 TCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCACACTT
1 TCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCACACTT
40567165 AGTGCCGCATGGTCAGT
65 AGTGCCGCATGGTCAGT
* **
40567182 TCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCACACTT
1 TCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCACACTT
40567246 AGTGC
65 AGTGC
40567251 TGTACAATTT
Statistics
Matches: 63, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
81 16 0.25
82 47 0.75
ACGTcount: A:0.28, C:0.28, G:0.17, T:0.27
Consensus pattern (81 bp):
TCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCACACTTA
GTGCCGCATGGTCAGT
Found at i:40574379 original size:29 final size:29
Alignment explanation
Indices: 40574347--40574406 Score: 111
Period size: 29 Copynumber: 2.1 Consensus size: 29
40574337 AAACAAAAGT
40574347 TTGCCTCAGACATTTTCAAAATTCCATGC
1 TTGCCTCAGACATTTTCAAAATTCCATGC
*
40574376 TTGCCTCAGACATTTTCAAAATTTCATGC
1 TTGCCTCAGACATTTTCAAAATTCCATGC
40574405 TT
1 TT
40574407 CCTAGGATTT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.27, C:0.25, G:0.10, T:0.38
Consensus pattern (29 bp):
TTGCCTCAGACATTTTCAAAATTCCATGC
Found at i:40577091 original size:16 final size:15
Alignment explanation
Indices: 40577066--40577099 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
40577056 AAAGTTGATA
*
40577066 ATAATTAATATACATT
1 ATAATAAATATA-ATT
40577082 ATAATAAATATAATT
1 ATAATAAATATAATT
40577097 ATA
1 ATA
40577100 TATTAGTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (15 bp):
ATAATAAATATAATT
Found at i:40580846 original size:25 final size:25
Alignment explanation
Indices: 40580777--40580846 Score: 79
Period size: 25 Copynumber: 2.8 Consensus size: 25
40580767 CTGTACATGT
* *
40580777 ATGCTCTCACGAGCTGTAAATCAGA
1 ATGCTCACACGAGCTGTGAATCAGA
* *
40580802 ATGCTCACATGAGCTATGAATCA-A
1 ATGCTCACACGAGCTGTGAATCAGA
*
40580826 ATTGCTCACACAAGCTGTGAA
1 A-TGCTCACACGAGCTGTGAA
40580847 AATGGGCCTG
Statistics
Matches: 37, Mismatches: 7, Indels: 2
0.80 0.15 0.04
Matches are distributed among these distances:
24 2 0.05
25 35 0.95
ACGTcount: A:0.34, C:0.23, G:0.19, T:0.24
Consensus pattern (25 bp):
ATGCTCACACGAGCTGTGAATCAGA
Found at i:40581975 original size:12 final size:12
Alignment explanation
Indices: 40581958--40581987 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
40581948 ACCTACACGT
40581958 CCATGTGCCAGG
1 CCATGTGCCAGG
*
40581970 CCATGTGCTAGG
1 CCATGTGCCAGG
40581982 CCATGT
1 CCATGT
40581988 AACAGCCTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.17, C:0.30, G:0.30, T:0.23
Consensus pattern (12 bp):
CCATGTGCCAGG
Found at i:40587347 original size:21 final size:20
Alignment explanation
Indices: 40587321--40587360 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 20
40587311 GGACTAAATC
40587321 GAAAACATATAGAAT-TTTTCA
1 GAAAACA-AT-GAATATTTTCA
40587342 GAAAACAATGAATATTTTC
1 GAAAACAATGAATATTTTC
40587361 GAACTACAGG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 4 0.22
20 7 0.39
21 7 0.39
ACGTcount: A:0.47, C:0.10, G:0.10, T:0.33
Consensus pattern (20 bp):
GAAAACAATGAATATTTTCA
Found at i:40588780 original size:21 final size:20
Alignment explanation
Indices: 40588744--40588785 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 20
40588734 CTAAATATGC
40588744 GTCTGTTTGTTAGAACATTTT
1 GTCTGTTTGTTAGAAC-TTTT
40588765 GTCTGTTTGTGT-GAACTTTT
1 GTCTGTTTGT-TAGAACTTTT
40588785 G
1 G
40588786 GTTATTGACA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 5 0.25
21 14 0.70
22 1 0.05
ACGTcount: A:0.14, C:0.10, G:0.24, T:0.52
Consensus pattern (20 bp):
GTCTGTTTGTTAGAACTTTT
Found at i:40589172 original size:32 final size:32
Alignment explanation
Indices: 40589136--40589201 Score: 105
Period size: 32 Copynumber: 2.1 Consensus size: 32
40589126 TTAAGTCGGT
*
40589136 TTGTAAAATGATTATATAAATTGCGGTACAAG
1 TTGTAAAATGATTATATAAACTGCGGTACAAG
* *
40589168 TTGTACAATGATTATATAAACTGTGGTACAAG
1 TTGTAAAATGATTATATAAACTGCGGTACAAG
40589200 TT
1 TT
40589202 TTTATGGTGG
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.38, C:0.08, G:0.18, T:0.36
Consensus pattern (32 bp):
TTGTAAAATGATTATATAAACTGCGGTACAAG
Found at i:40592058 original size:21 final size:22
Alignment explanation
Indices: 40592029--40592080 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 22
40592019 TCTCTCTCGC
*
40592029 TTTCCTTTTCACCTTTTTCA-T
1 TTTCATTTTCACCTTTTTCACT
**
40592050 TTTCATTTTCTTCTTTTTCACT
1 TTTCATTTTCACCTTTTTCACT
40592072 TTT-ATTTTC
1 TTTCATTTTC
40592081 TCTTCTCCTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
21 23 0.85
22 4 0.15
ACGTcount: A:0.10, C:0.23, G:0.00, T:0.67
Consensus pattern (22 bp):
TTTCATTTTCACCTTTTTCACT
Found at i:40592081 original size:21 final size:21
Alignment explanation
Indices: 40592041--40592081 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
40592031 TCCTTTTCAC
40592041 CTTTTTCATTTTCATTTTCTT
1 CTTTTTCATTTTCATTTTCTT
40592062 CTTTTTCACTTTT-ATTTTCT
1 CTTTTTCA-TTTTCATTTTCT
40592082 CTTCTCCTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 15 0.79
22 4 0.21
ACGTcount: A:0.10, C:0.20, G:0.00, T:0.71
Consensus pattern (21 bp):
CTTTTTCATTTTCATTTTCTT
Found at i:40595636 original size:40 final size:41
Alignment explanation
Indices: 40595581--40595660 Score: 101
Period size: 40 Copynumber: 2.0 Consensus size: 41
40595571 AAGCGCTTTG
*
40595581 TCCACGTGGACACAAAGTAC-GCCTTCAAGGAAGCGTTTTCTA
1 TCCACGTGGA-ACAAAGTACTGCCTT-AAGGAAGCATTTTCTA
* *
40595623 TCCACGTGG-ACAAAGTGCTTCCTTAAGGAAGCATTTTC
1 TCCACGTGGAACAAAGTACTGCCTTAAGGAAGCATTTTC
40595661 CTGCTTTATC
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
40 21 0.62
41 4 0.12
42 9 0.26
ACGTcount: A:0.28, C:0.25, G:0.21, T:0.26
Consensus pattern (41 bp):
TCCACGTGGAACAAAGTACTGCCTTAAGGAAGCATTTTCTA
Found at i:40602989 original size:26 final size:26
Alignment explanation
Indices: 40602915--40603021 Score: 97
Period size: 26 Copynumber: 4.1 Consensus size: 26
40602905 TGAAGGAATT
* * *
40602915 ATACTGTTACTAGCAGCTTTGCGGCG
1 ATACTATTACTAGCAGCTTTACTGCG
** * *
40602941 ATACTGGTACTGGTAGCTTTACTGCG
1 ATACTATTACTAGCAGCTTTACTGCG
* **
40602967 ATACTATTACTAGCAGTTTTACTATG
1 ATACTATTACTAGCAGCTTTACTGCG
* * *
40602993 ATACTATTATTGGCAGCTTTGCTGCG
1 ATACTATTACTAGCAGCTTTACTGCG
40603019 ATA
1 ATA
40603022 TTGGTGTGTT
Statistics
Matches: 63, Mismatches: 18, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
26 63 1.00
ACGTcount: A:0.23, C:0.19, G:0.21, T:0.36
Consensus pattern (26 bp):
ATACTATTACTAGCAGCTTTACTGCG
Found at i:40604233 original size:50 final size:50
Alignment explanation
Indices: 40604144--40604329 Score: 223
Period size: 50 Copynumber: 3.7 Consensus size: 50
40604134 GTGAAGTTGC
* * *
40604144 TAGATCACGTGTGTAGTACTATGTGCAGGCTACTGCGTGTACCGGAATGA
1 TAGATCTCATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGAATGA
* *
40604194 TAGGT-TGCATGTGTAGTATTATGTGCAGGCTACTACGTGTACCGGAATGA
1 TAGATCT-CATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGAATGA
* * * *
40604244 TAGATCTCATGTGTAGTACTATGTGTAGGCTACTATGCGTACCGG-ATAGCT
1 TAGATCTCATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGAAT-G-A
* * *
40604295 TCGATCACATGTGTAGTACTATGTGTAGGCTACTA
1 TAGATCTCATGTGTAGTACTATGTGCAGGCTACTA
40604330 TGTGAATCGG
Statistics
Matches: 119, Mismatches: 13, Indels: 7
0.86 0.09 0.05
Matches are distributed among these distances:
49 2 0.02
50 83 0.70
51 34 0.29
ACGTcount: A:0.24, C:0.17, G:0.27, T:0.32
Consensus pattern (50 bp):
TAGATCTCATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGAATGA
Found at i:40606904 original size:26 final size:26
Alignment explanation
Indices: 40606868--40606920 Score: 88
Period size: 26 Copynumber: 2.0 Consensus size: 26
40606858 ATGTGATAAT
*
40606868 GTGATTCCGTGTAAGACCATAGCTGG
1 GTGATTACGTGTAAGACCATAGCTGG
*
40606894 GTGATTACGTGTATGACCATAGCTGG
1 GTGATTACGTGTAAGACCATAGCTGG
40606920 G
1 G
40606921 CTATGACATC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.23, C:0.17, G:0.32, T:0.28
Consensus pattern (26 bp):
GTGATTACGTGTAAGACCATAGCTGG
Found at i:40610182 original size:50 final size:51
Alignment explanation
Indices: 40610102--40610237 Score: 168
Period size: 50 Copynumber: 2.7 Consensus size: 51
40610092 GTGAAGTCGC
* * * *
40610102 TAGGTCACGTGTGTAGTACTATGTGGAGGCTACTACGTGTACCGGA-ATG-A
1 TAGGTCACATGTGTAGTACTATGTGCAGGCTACTACGCGTACCAGATA-GCA
* * *
40610152 TAGGTCGCATGTGTAGTACTATGTGCAGGCTACTATGCGTACCAGATAGCT
1 TAGGTCACATGTGTAGTACTATGTGCAGGCTACTACGCGTACCAGATAGCA
* *
40610203 TCGATCACATGTGTAGTACTATGTGCAGGCTACTA
1 TAGGTCACATGTGTAGTACTATGTGCAGGCTACTA
40610238 TGTCAACCGG
Statistics
Matches: 74, Mismatches: 10, Indels: 3
0.85 0.11 0.03
Matches are distributed among these distances:
50 41 0.55
51 33 0.45
ACGTcount: A:0.24, C:0.18, G:0.28, T:0.29
Consensus pattern (51 bp):
TAGGTCACATGTGTAGTACTATGTGCAGGCTACTACGCGTACCAGATAGCA
Found at i:40613552 original size:40 final size:40
Alignment explanation
Indices: 40613371--40613592 Score: 227
Period size: 40 Copynumber: 5.6 Consensus size: 40
40613361 TCCTCGTTCA
* * * * *
40613371 AATGCCTTCGGG-CATAGCCCGGTTTTAGTAACTCACAC-
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* *
40613409 AATGCCTTCGGGACATAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
40613449 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * *
40613489 AATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* ** * * * *
40613529 AAGGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCAC-
1 AATGCCTTCGGGA-CTTAACCCGGATTTAATAAC-TCGCACG
* *
40613569 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
40613593 CAGCATTTAA
Statistics
Matches: 159, Mismatches: 20, Indels: 8
0.85 0.11 0.04
Matches are distributed among these distances:
38 12 0.08
39 24 0.15
40 115 0.72
41 8 0.05
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
Found at i:40622837 original size:23 final size:22
Alignment explanation
Indices: 40622785--40622837 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
40622775 TTCACGTCTT
*
40622785 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
40622807 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
40622830 TTTCTTTT
1 TTTCTTTT
40622838 TCACTCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:40626281 original size:40 final size:40
Alignment explanation
Indices: 40626099--40626321 Score: 236
Period size: 40 Copynumber: 5.6 Consensus size: 40
40626089 TCCTCGATCA
* * * * *
40626099 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* *
40626138 AATGCCTTCGGGACATAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
40626178 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * *
40626218 AATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* ** * * * *
40626258 AAGGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCAC-
1 AATGCCTTCGGGA-CTTAACCCGGATTTAATAAC-TCGCACG
* *
40626298 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
40626322 CAGCATTCAA
Statistics
Matches: 160, Mismatches: 20, Indels: 7
0.86 0.11 0.04
Matches are distributed among these distances:
39 37 0.23
40 115 0.72
41 8 0.05
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
Found at i:40626330 original size:41 final size:41
Alignment explanation
Indices: 40626253--40626330 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
40626243 TTAGTATCTC
* * *
40626253 GCACAAAGGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAAGGCCTTCGGATCTTAGCCCGGACACATTCACTTA
40626294 GCACAAA-GCCTTCGGGA-CTTAGCCCGGACAGCATTCA
1 GCACAAAGGCCTTC-GGATCTTAGCCCGGACA-CATTCA
40626331 ATTAATCATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 17 0.53
41 15 0.47
ACGTcount: A:0.27, C:0.28, G:0.22, T:0.23
Consensus pattern (41 bp):
GCACAAAGGCCTTCGGATCTTAGCCCGGACACATTCACTTA
Found at i:40644528 original size:29 final size:31
Alignment explanation
Indices: 40644462--40644521 Score: 79
Period size: 29 Copynumber: 2.0 Consensus size: 31
40644452 GATATCAGTC
*
40644462 ATGCAGTGAACAGTATGTAATATCATTAATCG
1 ATGCAGTGAACAGTA-GTAAAATCATTAATCG
*
40644494 ATGCAGT-AACAGTA-TAAAATCCTTAATC
1 ATGCAGTGAACAGTAGTAAAATCATTAATC
40644522 AGTGCAGATA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
29 12 0.46
31 7 0.27
32 7 0.27
ACGTcount: A:0.40, C:0.15, G:0.15, T:0.30
Consensus pattern (31 bp):
ATGCAGTGAACAGTAGTAAAATCATTAATCG
Found at i:40644955 original size:27 final size:27
Alignment explanation
Indices: 40644925--40645007 Score: 112
Period size: 27 Copynumber: 3.1 Consensus size: 27
40644915 TATAACAATT
* *
40644925 ATTTTACCCTATGGGGGTACTTCAGTC
1 ATTTTACCCTATGGGGGTATTTCGGTC
* * *
40644952 ATTTTACCCTATAGAGGTATTTTGGTC
1 ATTTTACCCTATGGGGGTATTTCGGTC
*
40644979 ATTTTACCCTATGAGGGTATTTCGGTC
1 ATTTTACCCTATGGGGGTATTTCGGTC
40645006 AT
1 AT
40645008 AATAATGTAA
Statistics
Matches: 47, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 47 1.00
ACGTcount: A:0.20, C:0.18, G:0.20, T:0.41
Consensus pattern (27 bp):
ATTTTACCCTATGGGGGTATTTCGGTC
Found at i:40645639 original size:12 final size:12
Alignment explanation
Indices: 40645622--40645663 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
40645612 ATCTCAATAT
40645622 TCTCTCCTCAAA
1 TCTCTCCTCAAA
*
40645634 TCTCTCC-AAATA
1 TCTCTCCTCAA-A
*
40645646 TCCCTCCTCAAA
1 TCTCTCCTCAAA
40645658 TCTCTC
1 TCTCTC
40645664 TATGATCAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
11 2 0.08
12 20 0.83
13 2 0.08
ACGTcount: A:0.24, C:0.43, G:0.00, T:0.33
Consensus pattern (12 bp):
TCTCTCCTCAAA
Found at i:40656081 original size:24 final size:24
Alignment explanation
Indices: 40656021--40656081 Score: 61
Period size: 24 Copynumber: 2.5 Consensus size: 24
40656011 GGAAAAGAAT
*
40656021 AAAGAGAGTGAAATAAAAATGAGA
1 AAAGAGAATGAAATAAAAATGAGA
* * *
40656045 GAAGAAAAAGAAATAAAAGATGA-A
1 AAAGAGAATGAAATAAAA-ATGAGA
*
40656069 AAAGAGATTGAAA
1 AAAGAGAATGAAA
40656082 AATTAAGTGT
Statistics
Matches: 28, Mismatches: 8, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
24 24 0.86
25 4 0.14
ACGTcount: A:0.66, C:0.00, G:0.23, T:0.11
Consensus pattern (24 bp):
AAAGAGAATGAAATAAAAATGAGA
Found at i:40661018 original size:9 final size:9
Alignment explanation
Indices: 40660992--40661024 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
40660982 AGAAGTTATC
40660992 GATCAGAAT
1 GATCAGAAT
40661001 GATTCAGAAT
1 GA-TCAGAAT
40661011 GATCAGAAT
1 GATCAGAAT
40661020 G-TCAG
1 GATCAG
40661025 CTTTAGAGGA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
8 4 0.17
9 10 0.43
10 9 0.39
ACGTcount: A:0.39, C:0.12, G:0.24, T:0.24
Consensus pattern (9 bp):
GATCAGAAT
Found at i:40666620 original size:16 final size:18
Alignment explanation
Indices: 40666594--40666626 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
40666584 TTCAATTAAC
40666594 TAAATTAA-TTTCTCAAT
1 TAAATTAATTTTCTCAAT
40666611 TAAA-TAATTTTCTCAA
1 TAAATTAATTTTCTCAA
40666627 GTCAGTTCTG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 3 0.20
17 12 0.80
ACGTcount: A:0.42, C:0.12, G:0.00, T:0.45
Consensus pattern (18 bp):
TAAATTAATTTTCTCAAT
Found at i:40666766 original size:14 final size:13
Alignment explanation
Indices: 40666723--40666775 Score: 52
Period size: 14 Copynumber: 3.8 Consensus size: 13
40666713 TCATAAGGTC
40666723 TAATTAATTTAATT
1 TAATT-ATTTAATT
* *
40666737 TCATTTTTTAACTT
1 TAATTATTTAA-TT
40666751 TAATTATTTAATTT
1 TAATTATTTAA-TT
*
40666765 TAATTAATTAA
1 TAATTATTTAA
40666776 ATAATAATTT
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
13 5 0.16
14 27 0.84
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.58
Consensus pattern (13 bp):
TAATTATTTAATT
Found at i:40668691 original size:30 final size:31
Alignment explanation
Indices: 40668655--40668723 Score: 88
Period size: 31 Copynumber: 2.3 Consensus size: 31
40668645 TGCTTTTAAT
*
40668655 TCAGTCACTCAAC-TT-TTGAAAAATAACAAA
1 TCAGTCACT-AACGTTATCGAAAAATAACAAA
* *
40668685 TCAGTCACTAACGTTATCGAAAAGTGACAAA
1 TCAGTCACTAACGTTATCGAAAAATAACAAA
40668716 TCAGTCAC
1 TCAGTCAC
40668724 CCATTAACAT
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
29 3 0.09
30 11 0.32
31 20 0.59
ACGTcount: A:0.42, C:0.22, G:0.12, T:0.25
Consensus pattern (31 bp):
TCAGTCACTAACGTTATCGAAAAATAACAAA
Found at i:40669607 original size:3 final size:3
Alignment explanation
Indices: 40669599--40669682 Score: 145
Period size: 3 Copynumber: 28.3 Consensus size: 3
40669589 ACATCTCAAT
40669599 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
40669647 TTC TTC TTC TTC TTC TTC -TC TT- TCTC TTC TTC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC T-TC TTC TTC TTC T
40669683 ACAGCCTAGT
Statistics
Matches: 78, Mismatches: 0, Indels: 6
0.93 0.00 0.07
Matches are distributed among these distances:
2 3 0.04
3 74 0.95
4 1 0.01
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:40674629 original size:39 final size:39
Alignment explanation
Indices: 40674575--40674654 Score: 151
Period size: 39 Copynumber: 2.1 Consensus size: 39
40674565 GGTACTAGTT
*
40674575 ATATTTCTGTGTTGCACTAGACAACCTTCCTTGCTGTTA
1 ATATTTATGTGTTGCACTAGACAACCTTCCTTGCTGTTA
40674614 ATATTTATGTGTTGCACTAGACAACCTTCCTTGCTGTTA
1 ATATTTATGTGTTGCACTAGACAACCTTCCTTGCTGTTA
40674653 AT
1 AT
40674655 GTGTCTGAAC
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.23, C:0.21, G:0.15, T:0.41
Consensus pattern (39 bp):
ATATTTATGTGTTGCACTAGACAACCTTCCTTGCTGTTA
Found at i:40690372 original size:120 final size:122
Alignment explanation
Indices: 40690152--40690392 Score: 389
Period size: 120 Copynumber: 2.0 Consensus size: 122
40690142 TTCGTACTAC
* * *
40690152 ATGTATTAACTATACCATTTTTCTGATCTTGGTACTTAATTGTTTTTTTTGTCACAAGTGATACC
1 ATGTATTAACTATACCATTTTTCTCATCTAGGTACTTAATTGTATTTTTTGTCACAAGTGATACC
* *
40690217 CTTTTTGCTCTAGTTAGTACCTCCGTTAGTTAAACAATTAAATCTATTTTAAAAAAT
66 CTTTTTGCTCTAGTTAGCACCTCCGTTAGTCAAACAATTAAATCTATTTTAAAAAAT
40690274 ATGTATTAACTATACCATTTTTCTCATCTAGGTACTTAA-T-TATTTTTTGTCACAAGTGATACC
1 ATGTATTAACTATACCATTTTTCTCATCTAGGTACTTAATTGTATTTTTTGTCACAAGTGATACC
* *
40690337 CTTTTTGC-CGTAGTTGGCACCTCCGTTAGTCAAACAGTTAAATCTATTTTAAAAAA
66 CTTTTTGCTC-TAGTTAGCACCTCCGTTAGTCAAACAATTAAATCTATTTTAAAAAA
40690393 GTGTAAATTA
Statistics
Matches: 111, Mismatches: 7, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
119 1 0.01
120 72 0.65
121 1 0.01
122 37 0.33
ACGTcount: A:0.29, C:0.17, G:0.11, T:0.43
Consensus pattern (122 bp):
ATGTATTAACTATACCATTTTTCTCATCTAGGTACTTAATTGTATTTTTTGTCACAAGTGATACC
CTTTTTGCTCTAGTTAGCACCTCCGTTAGTCAAACAATTAAATCTATTTTAAAAAAT
Found at i:40690695 original size:17 final size:17
Alignment explanation
Indices: 40690673--40690708 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
40690663 CTTAAAAATT
*
40690673 AAAAATTAAAAATTAAA
1 AAAAATTAAAAACTAAA
*
40690690 AAAAATTTAAAACTAAA
1 AAAAATTAAAAACTAAA
40690707 AA
1 AA
40690709 TTATTTAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.75, C:0.03, G:0.00, T:0.22
Consensus pattern (17 bp):
AAAAATTAAAAACTAAA
Found at i:40690708 original size:7 final size:7
Alignment explanation
Indices: 40690664--40690691 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
40690654 GTTTTACTTC
40690664 TTAAAAA
1 TTAAAAA
40690671 TTAAAAA
1 TTAAAAA
40690678 TTAAAAA
1 TTAAAAA
40690685 TTAAAAA
1 TTAAAAA
40690692 AAATTTAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (7 bp):
TTAAAAA
Found at i:40690718 original size:24 final size:24
Alignment explanation
Indices: 40690666--40690711 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
40690656 TTTACTTCTT
*
40690666 AAAAATTAAAAATTAAAAATTAAA
1 AAAAATTAAAAACTAAAAATTAAA
*
40690690 AAAAATTTAAAACTAAAAATTA
1 AAAAATTAAAAACTAAAAATTA
40690712 TTTAAAAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.72, C:0.02, G:0.00, T:0.26
Consensus pattern (24 bp):
AAAAATTAAAAACTAAAAATTAAA
Found at i:40690834 original size:19 final size:20
Alignment explanation
Indices: 40690801--40690845 Score: 58
Period size: 19 Copynumber: 2.3 Consensus size: 20
40690791 ATTTATTTAT
40690801 TAAAATAATAC-TTTTATAAA
1 TAAAATAATACTTTTTA-AAA
*
40690821 TAAAA-AATATTTTTTAAAA
1 TAAAATAATACTTTTTAAAA
40690840 TAAAAT
1 TAAAAT
40690846 CGCACAAACA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
19 12 0.55
20 10 0.45
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (20 bp):
TAAAATAATACTTTTTAAAA
Found at i:40691974 original size:20 final size:20
Alignment explanation
Indices: 40691949--40691986 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
40691939 CTTAAATTGT
*
40691949 TTTTATTTATAATATTATTA
1 TTTTATTTATAAAATTATTA
*
40691969 TTTTATTTTTAAAATTAT
1 TTTTATTTATAAAATTAT
40691987 AAATTTAATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (20 bp):
TTTTATTTATAAAATTATTA
Found at i:40691993 original size:20 final size:20
Alignment explanation
Indices: 40691950--40691993 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
40691940 TTAAATTGTT
* * *
40691950 TTTATTTATAATATTATTAT
1 TTTATTTATAAAATTATAAA
*
40691970 TTTATTTTTAAAATTATAAA
1 TTTATTTATAAAATTATAAA
40691990 TTTA
1 TTTA
40691994 ATTAATAAAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (20 bp):
TTTATTTATAAAATTATAAA
Found at i:40692075 original size:20 final size:20
Alignment explanation
Indices: 40692052--40692097 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
40692042 TATTTATAAA
*
40692052 TATTTTCAT-AATTTTGTATG
1 TATTTTCATAAACTTT-TATG
*
40692072 TATTTTTATAAACTTTTATG
1 TATTTTCATAAACTTTTATG
40692092 TATTTT
1 TATTTT
40692098 TATCGAAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 18 0.78
21 5 0.22
ACGTcount: A:0.26, C:0.04, G:0.07, T:0.63
Consensus pattern (20 bp):
TATTTTCATAAACTTTTATG
Found at i:40695181 original size:9 final size:9
Alignment explanation
Indices: 40695169--40695255 Score: 68
Period size: 9 Copynumber: 9.7 Consensus size: 9
40695159 TGCAGCACAT
40695169 TGCATGGAA
1 TGCATGGAA
*
40695178 TGCATGG-T
1 TGCATGGAA
*
40695186 TCGCATGAAA
1 T-GCATGGAA
*
40695196 TGCATGGAT
1 TGCATGGAA
*
40695205 TGCATGGGA
1 TGCATGGAA
*
40695214 TGCATGAAA
1 TGCATGGAA
***
40695223 TGCATGTTT
1 TGCATGGAA
40695232 TGCATGGAA
1 TGCATGGAA
* *
40695241 CGCATGGAG
1 TGCATGGAA
40695250 TGCATG
1 TGCATG
40695256 CCCAAAATCG
Statistics
Matches: 58, Mismatches: 18, Indels: 4
0.73 0.22 0.05
Matches are distributed among these distances:
8 1 0.02
9 56 0.97
10 1 0.02
ACGTcount: A:0.26, C:0.14, G:0.32, T:0.28
Consensus pattern (9 bp):
TGCATGGAA
Found at i:40695245 original size:27 final size:27
Alignment explanation
Indices: 40695169--40695255 Score: 93
Period size: 27 Copynumber: 3.2 Consensus size: 27
40695159 TGCAGCACAT
* **
40695169 TGCATGGAATGCATGGTTCGCATGAAA
1 TGCATGGATTGCATGGAACGCATGAAA
* *
40695196 TGCATGGATTGCATGGGATGCATGAAA
1 TGCATGGATTGCATGGAACGCATGAAA
** * *
40695223 TGCATGTTTTGCATGGAACGCATGGAG
1 TGCATGGATTGCATGGAACGCATGAAA
40695250 TGCATG
1 TGCATG
40695256 CCCAAAATCG
Statistics
Matches: 50, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 50 1.00
ACGTcount: A:0.26, C:0.14, G:0.32, T:0.28
Consensus pattern (27 bp):
TGCATGGATTGCATGGAACGCATGAAA
Found at i:40700018 original size:39 final size:36
Alignment explanation
Indices: 40699937--40700022 Score: 118
Period size: 36 Copynumber: 2.4 Consensus size: 36
40699927 AGATCAAGCA
* *
40699937 CACACCACCACCACCAATAACATTCCTTTCGGGACG
1 CACACCACCACCACCAACAACATTCCTTTCGAGACG
* * * *
40699973 CACACCATCTCTACCAACAATATTCCTTTCGAGACG
1 CACACCACCACCACCAACAACATTCCTTTCGAGACG
40700009 CACACCACCACCAC
1 CACACCACCACCAC
40700023 TAGCGGTACT
Statistics
Matches: 41, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
36 41 1.00
ACGTcount: A:0.31, C:0.43, G:0.08, T:0.17
Consensus pattern (36 bp):
CACACCACCACCACCAACAACATTCCTTTCGAGACG
Found at i:40702126 original size:27 final size:27
Alignment explanation
Indices: 40702096--40702273 Score: 178
Period size: 27 Copynumber: 6.6 Consensus size: 27
40702086 ATATTGAGTC
* *
40702096 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAATCAACT
* *
40702123 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
*
40702150 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAATC-AACT
** ** **
40702178 CGCACACTTAGTGCCGCATGGTCAGTT
1 CGCACACTTAGTGCTACATAATCAACT
* **
40702205 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAATCAACT
* * *
40702232 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
40702259 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
40702274 GTACAATTTA
Statistics
Matches: 128, Mismatches: 20, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
27 104 0.81
28 24 0.19
ACGTcount: A:0.29, C:0.28, G:0.16, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAACT
Found at i:40702235 original size:82 final size:81
Alignment explanation
Indices: 40702122--40702272 Score: 232
Period size: 82 Copynumber: 1.9 Consensus size: 81
40702112 TATAATCAAC
* *
40702122 TCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCACACTT
1 TCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCACACTT
40702187 AGTGCCGCATGGTCAGT
65 AGTGCCGCATGGTCAGT
* **
40702204 TCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCACACTT
1 TCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCACACTT
40702268 AGTGC
65 AGTGC
40702273 TGTACAATTT
Statistics
Matches: 63, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
81 16 0.25
82 47 0.75
ACGTcount: A:0.28, C:0.28, G:0.17, T:0.27
Consensus pattern (81 bp):
TCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCACACTTA
GTGCCGCATGGTCAGT
Found at i:40717880 original size:95 final size:95
Alignment explanation
Indices: 40717717--40717888 Score: 317
Period size: 95 Copynumber: 1.8 Consensus size: 95
40717707 TTCAAATCAA
40717717 ATTATTCTTAAAAAGGGTTTAGTTCAACAAATATAAAATTATATTTCGAAATAGGATTACAATAA
1 ATTATTCTTAAAAAGGGTTTAGTTCAACAAATATAAAATTATATTTCGAAATAGGATTACAATAA
40717782 TATAATATTACATGCGATATCTTATCTTAT
66 TATAATATTACATGCGATATCTTATCTTAT
* * *
40717812 ATTATTCTTAAAAGGGGTTTAGTTCAACAAGTATAAGATTATATTTCGAAATAGGATTACAATAA
1 ATTATTCTTAAAAAGGGTTTAGTTCAACAAATATAAAATTATATTTCGAAATAGGATTACAATAA
40717877 TATAATATTACA
66 TATAATATTACA
40717889 ATAATATAAT
Statistics
Matches: 74, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
95 74 1.00
ACGTcount: A:0.42, C:0.09, G:0.11, T:0.38
Consensus pattern (95 bp):
ATTATTCTTAAAAAGGGTTTAGTTCAACAAATATAAAATTATATTTCGAAATAGGATTACAATAA
TATAATATTACATGCGATATCTTATCTTAT
Found at i:40717888 original size:16 final size:16
Alignment explanation
Indices: 40717867--40717901 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
40717857 TCGAAATAGG
40717867 ATTACAATAATATAAT
1 ATTACAATAATATAAT
40717883 ATTACAATAATATAAT
1 ATTACAATAATATAAT
40717899 ATT
1 ATT
40717902 TCGAAATAGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.54, C:0.06, G:0.00, T:0.40
Consensus pattern (16 bp):
ATTACAATAATATAAT
Found at i:40724718 original size:47 final size:47
Alignment explanation
Indices: 40724654--40725443 Score: 1292
Period size: 47 Copynumber: 16.6 Consensus size: 47
40724644 AGTATATGTG
*
40724654 GAATGTGAAAGTATATATATGTGATAAGGCCTAATGGCCGATGTGAT
1 GAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGAT
*
40724701 GAATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGAT
1 GAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGAT
40724748 GAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGAT
1 GAATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGAT
*
40724797 GAATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGAT
1 GAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGAT
*
40724844 GAATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGAT
1 GAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGAT
40724891 GAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGAT
1 GAATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGAT
*
40724940 GAATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGAT
1 GAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGAT
40724987 GAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGAT
1 GAATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGAT
*
40725036 GAATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCGATGTGAT
1 GAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGAT
*
40725083 GAATGTGAAAGTATATATATGTGATAAGGCCTAATGGCCGATGTGAT
1 GAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGAT
*
40725130 GAATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGAT
1 GAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGAT
40725177 GAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGAT
1 GAATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGAT
* *
40725226 GAATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGAT
1 GAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGAT
*
40725273 GAATGTGAAAGTGTATATACATGTGATAAGGCCTAATGGCCAATGTGAT
1 GAATGTGAAAGTGTATAT--ATGTGATAAGGCCTAATGGCCGATGTGAT
* *
40725322 GAATGTGAAGGTGTATATATGTGATAAGGCCTAATAGCCGATGTGAT
1 GAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGAT
* * * * * *
40725369 GAATGTGAAAGTGTATATATGTGACAGGGCCGAGTGGCCAACGTGAT
1 GAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGAT
* * *
40725416 GGACGTGAAAGTGTATAAATGTGATAAG
1 GAATGTGAAAGTGTATATATGTGATAAG
40725444 TCCCGAAGGG
Statistics
Matches: 701, Mismatches: 32, Indels: 20
0.93 0.04 0.03
Matches are distributed among these distances:
47 472 0.67
49 229 0.33
ACGTcount: A:0.33, C:0.09, G:0.29, T:0.29
Consensus pattern (47 bp):
GAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGAT
Found at i:40724816 original size:96 final size:94
Alignment explanation
Indices: 40724654--40725443 Score: 1292
Period size: 96 Copynumber: 8.3 Consensus size: 94
40724644 AGTATATGTG
* *
40724654 GAATGTGAAAGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATAT
1 GAATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATAT
*
40724719 ATGTGATAAGGCCTAATAGCCGATGTGAT
66 ATGTGATAAGGCCTAATGGCCGATGTGAT
*
40724748 GAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTAT
1 GAATGTGAAAGTG--TATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTAT
*
40724813 ATATGTGATAAGGCCTAATAGCCGATGTGAT
64 ATATGTGATAAGGCCTAATGGCCGATGTGAT
40724844 GAATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATAT
1 GAATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTG--TAT
40724909 ATATGTGATAAGGCCTAATGGCCGATGTGAT
64 ATATGTGATAAGGCCTAATGGCCGATGTGAT
40724940 GAATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATAT
1 GAATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTG--TAT
40725005 ATATGTGATAAGGCCTAATGGCCGATGTGAT
64 ATATGTGATAAGGCCTAATGGCCGATGTGAT
* * *
40725036 GAATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCGATGTGATGAATGTGAAAGTATATAT
1 GAATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATAT
40725101 ATGTGATAAGGCCTAATGGCCGATGTGAT
66 ATGTGATAAGGCCTAATGGCCGATGTGAT
40725130 GAATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATAT
1 GAATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTG--TAT
40725195 ATATGTGATAAGGCCTAATGGCCGATGTGAT
64 ATATGTGATAAGGCCTAATGGCCGATGTGAT
* * *
40725226 GAATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATAT
1 GAATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATAT
*
40725291 ACATGTGATAAGGCCTAATGGCCAATGTGAT
66 --ATGTGATAAGGCCTAATGGCCGATGTGAT
*
40725322 GAATGTGAAGGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATAT
1 GAATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATAT
* * * * * *
40725387 ATGTGACAGGGCCGAGTGGCCAACGTGAT
66 ATGTGATAAGGCCTAATGGCCGATGTGAT
* * *
40725416 GGACGTGAAAGTGTATAAATGTGATAAG
1 GAATGTGAAAGTGTATATATGTGATAAG
40725444 TCCCGAAGGG
Statistics
Matches: 662, Mismatches: 26, Indels: 16
0.94 0.04 0.02
Matches are distributed among these distances:
94 202 0.31
96 460 0.69
ACGTcount: A:0.33, C:0.09, G:0.29, T:0.29
Consensus pattern (94 bp):
GAATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATAT
ATGTGATAAGGCCTAATGGCCGATGTGAT
Found at i:40724909 original size:143 final size:143
Alignment explanation
Indices: 40724654--40725443 Score: 1327
Period size: 143 Copynumber: 5.5 Consensus size: 143
40724644 AGTATATGTG
*
40724654 GAATGTGAAAGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATAT
1 GAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATAT
40724719 ATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAA
66 ATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAA
40724784 TGGCCGATGTGAT
131 TGGCCGATGTGAT
*
40724797 GAATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATAT
1 GAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATAT
40724862 ATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAA
66 ATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAA
40724927 TGGCCGATGTGAT
131 TGGCCGATGTGAT
*
40724940 GAATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATAT
1 GAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TAT
* *
40725005 ATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TATATATGTGATAAGGCCG
64 ATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCT
40725068 AATGGCCGATGTGAT
129 AATGGCCGATGTGAT
*
40725083 GAATGTGAAAGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATAT
1 GAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATAT
40725148 ATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAA
66 ATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAA
40725213 TGGCCGATGTGAT
131 TGGCCGATGTGAT
* *
40725226 GAATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATAT
1 GAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATAT
* * *
40725291 ACATGTGATAAGGCCTAATGGCCAATGTGATGAATGTG-AAG-GTGTATATATGTGATAAGGCCT
66 --ATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCT
*
40725354 AATAGCCGATGTGAT
129 AATGGCCGATGTGAT
* * * * * * * * *
40725369 GAATGTGAAAGTGTATATATGTGACAGGGCCGAGTGGCCAACGTGATGGACGTGAAAGTGTATAA
1 GAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATAT
40725434 ATGTGATAAG
66 ATGTGATAAG
40725444 TCCCGAAGGG
Statistics
Matches: 619, Mismatches: 22, Indels: 14
0.95 0.03 0.02
Matches are distributed among these distances:
141 56 0.09
143 480 0.78
144 3 0.00
145 80 0.13
ACGTcount: A:0.33, C:0.09, G:0.29, T:0.29
Consensus pattern (143 bp):
GAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATAT
ATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAA
TGGCCGATGTGAT
Found at i:40728912 original size:20 final size:20
Alignment explanation
Indices: 40728887--40728991 Score: 68
Period size: 20 Copynumber: 5.2 Consensus size: 20
40728877 TACTTCGGTA
40728887 CCCCTGAATGCACATACGTG
1 CCCCTGAATGCACATACGTG
* * * *
40728907 CCCCTGATTGTAC-TTCAGTA
1 CCCCTGAATGCACATAC-GTG
*
40728927 CCCCTGAATGCACATATGTG
1 CCCCTGAATGCACATACGTG
* * * ** *
40728947 CCCTTGATTGCACTTTGGTA
1 CCCCTGAATGCACATACGTG
* * *
40728967 TCCCTGAATGCACATGCATG
1 CCCCTGAATGCACATACGTG
40728987 CCCCT
1 CCCCT
40728992 ATTTATACTT
Statistics
Matches: 59, Mismatches: 24, Indels: 4
0.68 0.28 0.05
Matches are distributed among these distances:
19 2 0.03
20 56 0.95
21 1 0.02
ACGTcount: A:0.21, C:0.32, G:0.18, T:0.29
Consensus pattern (20 bp):
CCCCTGAATGCACATACGTG
Found at i:40729006 original size:40 final size:40
Alignment explanation
Indices: 40728851--40728991 Score: 169
Period size: 40 Copynumber: 3.5 Consensus size: 40
40728841 TAATTATTAT
*
40728851 CTGAATGCACATACATACCCC--ATTTGTACTTCGGTACCC
1 CTGAATGCACATACATGCCCCTGA-TTGTACTTCGGTACCC
* *
40728890 CTGAATGCACATACGTGCCCCTGATTGTACTTCAGTACCC
1 CTGAATGCACATACATGCCCCTGATTGTACTTCGGTACCC
** * * * *
40728930 CTGAATGCACATATGTGCCCTTGATTGCACTTTGGTATCC
1 CTGAATGCACATACATGCCCCTGATTGTACTTCGGTACCC
*
40728970 CTGAATGCACATGCATGCCCCT
1 CTGAATGCACATACATGCCCCT
40728992 ATTTATACTT
Statistics
Matches: 87, Mismatches: 13, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
39 19 0.22
40 67 0.77
41 1 0.01
ACGTcount: A:0.23, C:0.31, G:0.17, T:0.29
Consensus pattern (40 bp):
CTGAATGCACATACATGCCCCTGATTGTACTTCGGTACCC
Found at i:40729701 original size:30 final size:30
Alignment explanation
Indices: 40729648--40729711 Score: 74
Period size: 30 Copynumber: 2.1 Consensus size: 30
40729638 CATACGGCCT
* *
40729648 TGTGACACACGTGACTTGACGACACAACCA
1 TGTGACACACATGACCTGACGACACAACCA
* * **
40729678 TGTGACACACATGGCCTGGCGACATGACCA
1 TGTGACACACATGACCTGACGACACAACCA
40729708 TGTG
1 TGTG
40729712 TCATTTGTAA
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.28, C:0.28, G:0.25, T:0.19
Consensus pattern (30 bp):
TGTGACACACATGACCTGACGACACAACCA
Found at i:40731738 original size:27 final size:27
Alignment explanation
Indices: 40731708--40731953 Score: 118
Period size: 27 Copynumber: 9.1 Consensus size: 27
40731698 AATCACAATC
*
40731708 ATTTTATCCTACAGGGGTATTTCGATA
1 ATTTTACCCTACAGGGGTATTTCGATA
*
40731735 ATTTTACCCTATAGGGGTATTTCGATA
1 ATTTTACCCTACAGGGGTATTTCGATA
** * *
40731762 ATTTTACCC-ATTGGGGGTATTTTGGTA
1 ATTTTACCCTA-CAGGGGTATTTCGATA
** * * * *
40731789 AAATTACCATTC-GAGGTATTT-TAGTA
1 ATTTTACCCTACAGGGGTATTTCGA-TA
* *
40731815 ATTTTACCC-ATCGGGGGTATTTTGATA
1 ATTTTACCCTA-CAGGGGTATTTCGATA
*
40731842 ATTTTACCC-ATC-GAGGATATTTC-AGTA
1 ATTTTACCCTA-CAG-GGGTATTTCGA-TA
** *
40731869 ATTTTACCCT-TTGAGGGTATTTCAATA
1 ATTTTACCCTACAG-GGGTATTTCGATA
* * * *
40731896 ATTTTATCC-ATCAAGGGTATTTTGGTA
1 ATTTTACCCTA-CAGGGGTATTTCGATA
*
40731923 ATTTTACCCTTC-GAGGGTATTTC-AGTA
1 ATTTTACCCTACAG-GGGTATTTCGA-TA
40731950 ATTT
1 ATTT
40731954 GCTCACGAAT
Statistics
Matches: 168, Mismatches: 35, Indels: 32
0.71 0.15 0.14
Matches are distributed among these distances:
26 20 0.12
27 146 0.87
28 2 0.01
ACGTcount: A:0.26, C:0.14, G:0.18, T:0.42
Consensus pattern (27 bp):
ATTTTACCCTACAGGGGTATTTCGATA
Found at i:40731779 original size:54 final size:54
Alignment explanation
Indices: 40731721--40731953 Score: 201
Period size: 54 Copynumber: 4.3 Consensus size: 54
40731711 TTATCCTACA
40731721 GGGGTATTTCGATAATTTTACCCTATAGGGGTATTTCGA-TAATTTTACCCATTG
1 GGGGTATTTCGATAATTTTACCC-ATAGGGGTATTTCGAGTAATTTTACCCATTG
* * ** * * * *
40731775 GGGGTATTTTGGTAAAATTA-CCATTCGAGGTATTT-TAGTAATTTTACCCATCG
1 GGGGTATTTCGATAATTTTACCCA-TAGGGGTATTTCGAGTAATTTTACCCATTG
* * * *
40731828 GGGGTATTTTGATAATTTTACCCATCGAGGATATTTC-AGTAATTTTACCCTTTG
1 GGGGTATTTCGATAATTTTACCCATAG-GGGTATTTCGAGTAATTTTACCCATTG
* * * * *
40731882 AGGGTATTTCAATAATTTTATCCATCAAGGGTATTTTG-GTAATTTTACCC-TTCG
1 GGGGTATTTCGATAATTTTACCCAT-AGGGGTATTTCGAGTAATTTTACCCATT-G
*
40731936 AGGGTATTTC-AGTAATTT
1 GGGGTATTTCGA-TAATTT
40731954 GCTCACGAAT
Statistics
Matches: 147, Mismatches: 23, Indels: 18
0.78 0.12 0.10
Matches are distributed among these distances:
52 2 0.01
53 48 0.33
54 97 0.66
ACGTcount: A:0.25, C:0.14, G:0.19, T:0.42
Consensus pattern (54 bp):
GGGGTATTTCGATAATTTTACCCATAGGGGTATTTCGAGTAATTTTACCCATTG
Found at i:40731916 original size:81 final size:81
Alignment explanation
Indices: 40731722--40731953 Score: 279
Period size: 80 Copynumber: 2.9 Consensus size: 81
40731712 TATCCTACAG
* * * * **
40731722 GGGTATTTCGATAATTTTACCCTAT-AGGGGTATTTCGATAATTTTACCCATTGGGGGTATTTTG
1 GGGTATTTCAATAATTTTACCC-ATCAGGGGTATTTTGATAATTTTACCCATCGAGGGTATTTCA
**
40731786 GTAAAATTACCATTCGA
65 GTAATTTTACCATTCGA
* * * *
40731803 -GGTATTTTAGTAATTTTACCCATCGGGGGTATTTTGATAATTTTACCCATCGAGGATATTTCAG
1 GGGTATTTCAATAATTTTACCCATCAGGGGTATTTTGATAATTTTACCCATCGAGGGTATTTCAG
* *
40731867 TAATTTTACCCTTTGA
66 TAATTTTACCATTCGA
* * * *
40731883 GGGTATTTCAATAATTTTATCCATCAAGGGTATTTTGGTAATTTTACCCTTCGAGGGTATTTCAG
1 GGGTATTTCAATAATTTTACCCATCAGGGGTATTTTGATAATTTTACCCATCGAGGGTATTTCAG
40731948 TAATTT
66 TAATTT
40731954 GCTCACGAAT
Statistics
Matches: 127, Mismatches: 22, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
79 2 0.02
80 63 0.50
81 62 0.49
ACGTcount: A:0.25, C:0.14, G:0.19, T:0.42
Consensus pattern (81 bp):
GGGTATTTCAATAATTTTACCCATCAGGGGTATTTTGATAATTTTACCCATCGAGGGTATTTCAG
TAATTTTACCATTCGA
Found at i:40732546 original size:49 final size:49
Alignment explanation
Indices: 40732490--40732588 Score: 198
Period size: 49 Copynumber: 2.0 Consensus size: 49
40732480 AGAAACCGAC
40732490 AAGATGAGGAGGAAACATAAAAGAAGAGGTGGGAAAAGAGTGATGTAGA
1 AAGATGAGGAGGAAACATAAAAGAAGAGGTGGGAAAAGAGTGATGTAGA
40732539 AAGATGAGGAGGAAACATAAAAGAAGAGGTGGGAAAAGAGTGATGTAGA
1 AAGATGAGGAGGAAACATAAAAGAAGAGGTGGGAAAAGAGTGATGTAGA
40732588 A
1 A
40732589 TTCGGCTACA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 50 1.00
ACGTcount: A:0.49, C:0.02, G:0.36, T:0.12
Consensus pattern (49 bp):
AAGATGAGGAGGAAACATAAAAGAAGAGGTGGGAAAAGAGTGATGTAGA
Found at i:40734894 original size:37 final size:37
Alignment explanation
Indices: 40734844--40734922 Score: 113
Period size: 37 Copynumber: 2.1 Consensus size: 37
40734834 TTATTACGAA
* * * *
40734844 GTCTTACCCGGACATAATCTCCACACGAAGTTATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCAG
*
40734881 GTCTTACCCGGACAAAATCCCCACACGTAGTCATCAG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCAG
40734918 GTCTT
1 GTCTT
40734923 TAGAGCTCGG
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.27, C:0.32, G:0.18, T:0.24
Consensus pattern (37 bp):
GTCTTACCCGGACAAAATCCCCACACGAAGTCATCAG
Found at i:40735167 original size:47 final size:47
Alignment explanation
Indices: 40735041--40735474 Score: 715
Period size: 47 Copynumber: 9.1 Consensus size: 47
40735031 CCCTTCGGGA
* * * * * *
40735041 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * *
40735088 CCTGTCACATATATATACACTTCCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
40735137 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
40735184 CTTATCACATATAAACACTTTCACATTCATCACATTGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
40735231 CCTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
40735278 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
40735325 CCTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
40735372 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
40735421 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
40735468 CTTATCA
1 CTTATCA
40735475 TCATTTCATA
Statistics
Matches: 363, Mismatches: 20, Indels: 8
0.93 0.05 0.02
Matches are distributed among these distances:
47 278 0.77
49 85 0.23
ACGTcount: A:0.29, C:0.31, G:0.09, T:0.31
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:40738093 original size:40 final size:41
Alignment explanation
Indices: 40737871--40738186 Score: 258
Period size: 40 Copynumber: 7.9 Consensus size: 41
40737861 CCGAATACAC
* * * * * *
40737871 GTCACCAGCATGATTGCTCTTCGGGACCTAGCCTGGATATA
1 GTCACTAGCACGAATGCTCTTCGGAACTTAGCCCGGATATA
* * *** *
40737912 -ACACCAGCACGAATGCTCTTCGGGGTTTAGCACGGATATA
1 GTCACTAGCACGAATGCTCTTCGGAACTTAGCCCGGATATA
*
40737952 -TCACTAGCACGAATGCTCTTCGGAACTTAGCCCGGATACA
1 GTCACTAGCACGAATGCTCTTCGGAACTTAGCCCGGATATA
* * *
40737992 -TCACTAGCATGAATGCTCTTCAGAACTTAGCCCGGATACA
1 GTCACTAGCACGAATGCTCTTCGGAACTTAGCCCGGATATA
* *
40738032 -TCACTAGCATGAATGCTCTTCGGAACTTAGCCCGGATTTA
1 GTCACTAGCACGAATGCTCTTCGGAACTTAGCCCGGATATA
* * * * *
40738072 GTAACTCGCACCAATGC-CTTCGG-GCTTAGCCC-GAAATTA
1 GTCACTAGCACGAATGCTCTTCGGAACTTAGCCCGGATA-TA
* * * * *
40738111 GT-ATCTCGCACAAATGC-CTTCGGATCTTAGTCCGGATATG
1 GTCA-CTAGCACGAATGCTCTTCGGAACTTAGCCCGGATATA
* *
40738151 GTCACTTAGCAC-AAAGC-CTTCGGGACTTAGCCCGGA
1 GTCAC-TAGCACGAATGCTCTTCGGAACTTAGCCCGGA
40738187 CATCATTCGA
Statistics
Matches: 231, Mismatches: 37, Indels: 15
0.82 0.13 0.05
Matches are distributed among these distances:
38 3 0.01
39 30 0.13
40 177 0.77
41 21 0.09
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.25
Consensus pattern (41 bp):
GTCACTAGCACGAATGCTCTTCGGAACTTAGCCCGGATATA
Found at i:40738112 original size:39 final size:40
Alignment explanation
Indices: 40738043--40738184 Score: 128
Period size: 39 Copynumber: 3.5 Consensus size: 40
40738033 CACTAGCATG
* * *
40738043 AATGCTCTTCGGAACTTAGCCCGGATTTAGTAACTCGCACC
1 AATGC-CTTCGGAACTTAGCCCGAAATTAGTAACTCGCACA
* *
40738084 AATGCCTTCGG-GCTTAGCCCGAAATTAGTATCTCGCACA
1 AATGCCTTCGGAACTTAGCCCGAAATTAGTAACTCGCACA
* * * * * *
40738123 AATGCCTTCGGATCTTAGTCCG-GATATGGTCACTTAGCACA
1 AATGCCTTCGGAACTTAGCCCGAAAT-TAGTAAC-TCGCACA
*
40738164 AA-GCCTTCGGGACTTAGCCCG
1 AATGCCTTCGGAACTTAGCCCG
40738185 GACATCATTC
Statistics
Matches: 83, Mismatches: 15, Indels: 7
0.79 0.14 0.07
Matches are distributed among these distances:
39 36 0.43
40 34 0.41
41 13 0.16
ACGTcount: A:0.24, C:0.28, G:0.22, T:0.26
Consensus pattern (40 bp):
AATGCCTTCGGAACTTAGCCCGAAATTAGTAACTCGCACA
Found at i:40738533 original size:29 final size:29
Alignment explanation
Indices: 40738494--40738572 Score: 97
Period size: 29 Copynumber: 2.7 Consensus size: 29
40738484 CTTAATAATC
*
40738494 AACTACGCACACTTAGTGCCATGTACTTT-A
1 AACT-CGCACACTTAGTGCCATGCA-TTTCA
*
40738524 AACTCGCACACTTAGTGCTATGCATTTCA
1 AACTCGCACACTTAGTGCCATGCATTTCA
* *
40738553 AGCCCGCACACTTAGTGCCA
1 AACTCGCACACTTAGTGCCA
40738573 ATCTCACAAC
Statistics
Matches: 43, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
28 3 0.07
29 36 0.84
30 4 0.09
ACGTcount: A:0.28, C:0.30, G:0.15, T:0.27
Consensus pattern (29 bp):
AACTCGCACACTTAGTGCCATGCATTTCA
Found at i:40738615 original size:43 final size:43
Alignment explanation
Indices: 40738554--40738680 Score: 254
Period size: 43 Copynumber: 3.0 Consensus size: 43
40738544 TGCATTTCAA
40738554 GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTATT
1 GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTATT
40738597 GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTATT
1 GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTATT
40738640 GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTA
1 GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTA
40738681 GTGCTGAAAA
Statistics
Matches: 84, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 84 1.00
ACGTcount: A:0.28, C:0.35, G:0.14, T:0.22
Consensus pattern (43 bp):
GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTATT
Found at i:40740849 original size:47 final size:47
Alignment explanation
Indices: 40740726--40741210 Score: 790
Period size: 47 Copynumber: 10.1 Consensus size: 47
40740716 CCCTTCGGGA
* * * * * *
40740726 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * *
40740773 CCTGTCACATTTATATACACTTCCACATTCATCACATCGGCCATTAGGC
1 CTTATCACA--TATATACACTTTCACATTCATCACATCGGCCATTAGGC
40740822 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
40740869 CCTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
40740916 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
40740963 CCTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
40741012 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
40741061 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGT
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
40741108 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
40741157 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
40741204 CTTATCA
1 CTTATCA
40741211 TCATTTCATA
Statistics
Matches: 414, Mismatches: 18, Indels: 12
0.93 0.04 0.03
Matches are distributed among these distances:
47 235 0.57
49 179 0.43
ACGTcount: A:0.29, C:0.30, G:0.09, T:0.32
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:40740930 original size:96 final size:96
Alignment explanation
Indices: 40740726--40741210 Score: 802
Period size: 96 Copynumber: 5.1 Consensus size: 96
40740716 CCCTTCGGGA
* * * * * *
40740726 CTTATCACAT-T-TATACACTTTCACATCCATCACGTTGGCCACTCGGCCCTGTCACATTTATAT
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCCTATCACA--TATAT
*
40740789 ACACTTCCACATTCATCACATCGGCCATTAGGC
64 ACACTTTCACATTCATCACATCGGCCATTAGGC
40740822 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGCCCTATCACATATATAC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCCTATCACATATATAC
40740885 ACTTTCACATTCATCACATCGGCCATTAGGC
66 ACTTTCACATTCATCACATCGGCCATTAGGC
40740916 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGCCCTATCACATATATAT
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCCTATCAC--ATATAT
40740979 ACACTTTCACATTCATCACATCGGCCATTAGGC
64 ACACTTTCACATTCATCACATCGGCCATTAGGC
*
40741012 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCCTATCACATATATAC
*
40741077 ACTTTCACATTCATCACATCGGCCATTAGGT
66 ACTTTCACATTCATCACATCGGCCATTAGGC
*
40741108 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCCTATCACATATATAC
40741173 ACTTTCACATTCATCACATCGGCCATTAGGC
66 ACTTTCACATTCATCACATCGGCCATTAGGC
40741204 CTTATCA
1 CTTATCA
40741211 TCATTTCATA
Statistics
Matches: 373, Mismatches: 10, Indels: 12
0.94 0.03 0.03
Matches are distributed among these distances:
94 92 0.25
95 1 0.00
96 234 0.63
98 46 0.12
ACGTcount: A:0.29, C:0.30, G:0.09, T:0.32
Consensus pattern (96 bp):
CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCCTATCACATATATAC
ACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:40747603 original size:51 final size:51
Alignment explanation
Indices: 40747543--40747644 Score: 152
Period size: 51 Copynumber: 2.0 Consensus size: 51
40747533 TTTTGTGGTG
40747543 AATGTTGGTTAAACACTCTTCTACACCCTA-GAGTTTTATTTTATGATTCCT
1 AATGTTGGTTAAACACTCTTCTACACCCTAGGA-TTTTATTTTATGATTCCT
* * **
40747594 AATGTTGGTTAAACACTGTTCTGCATGCTAGGATTTTATTTTATGATTCCT
1 AATGTTGGTTAAACACTCTTCTACACCCTAGGATTTTATTTTATGATTCCT
40747645 TTCTTTTTAT
Statistics
Matches: 46, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
51 44 0.96
52 2 0.04
ACGTcount: A:0.25, C:0.17, G:0.15, T:0.44
Consensus pattern (51 bp):
AATGTTGGTTAAACACTCTTCTACACCCTAGGATTTTATTTTATGATTCCT
Found at i:40755617 original size:56 final size:51
Alignment explanation
Indices: 40755520--40755760 Score: 202
Period size: 50 Copynumber: 4.7 Consensus size: 51
40755510 ATTTGGGTAA
**
40755520 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCACTGGCATCCTTGAGATCATG
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCATCC--GAGA-C--G
* * *
40755576 AGAGGTCCCATGTAAGACCATGTCTGGAACATGGTGTTGGCAT-CGAGACG
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCATCCGAGACG
* * * *
40755626 AGAGCTCCCATCTGAGACCATGTCTGGGACATGGCGTTGGCAT-CGAGATG
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCATCCGAGACG
* * ** * * * * *
40755676 TGAGGTCCCCCGTAAGACCATGTCTAGGACATGGCATGGGCAT-CGATATG
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCATCCGAGACG
* * * *
40755726 AGA-ACTCCCATGTAATACCATATCTGCGAGATGGC
1 AGAGA-TCCCATGTAAGACCATGTCTGGGACATGGC
40755761 ATCGGCAGTA
Statistics
Matches: 154, Mismatches: 30, Indels: 8
0.80 0.16 0.04
Matches are distributed among these distances:
50 110 0.71
52 1 0.01
53 4 0.03
55 1 0.01
56 38 0.25
ACGTcount: A:0.26, C:0.23, G:0.29, T:0.22
Consensus pattern (51 bp):
AGAGATCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCATCCGAGACG
Found at i:40755719 original size:100 final size:103
Alignment explanation
Indices: 40755520--40755761 Score: 249
Period size: 100 Copynumber: 2.3 Consensus size: 103
40755510 ATTTGGGTAA
* *
40755520 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCACTGGCATCCTTGAGATCATGAGAGGTCCC
1 AGAGCTCCCATCTAAGACCATGTCTGGGACATGGCACTGGCATCC-TGAGA--ATGAGAGGTCCC
* ** *
40755585 ATGTAAGACCATGTCTGGAACATGGTGTTGGCATCGAGACG
63 ACGTAAGACCATGTCTGGAACATGGCATGGGCATCGAGACG
* ** * *
40755626 AGAGCTCCCATCTGAGACCATGTCTGGGACATGGCGTTGGCAT-C-GAG-ATGTGAGGTCCCCCG
1 AGAGCTCCCATCTAAGACCATGTCTGGGACATGGCACTGGCATCCTGAGAATGAGAGGTCCCACG
* *
40755688 TAAGACCATGTCTAGG-ACATGGCATGGGCATCGATATG
66 TAAGACCATGTCT-GGAACATGGCATGGGCATCGAGACG
* * * * * *
40755726 AGAACTCCCATGTAATACCATATCTGCGAGATGGCA
1 AGAGCTCCCATCTAAGACCATGTCTGGGACATGGCA
40755762 TCGGCAGTAC
Statistics
Matches: 114, Mismatches: 21, Indels: 8
0.80 0.15 0.06
Matches are distributed among these distances:
100 70 0.61
101 2 0.02
103 3 0.03
105 1 0.01
106 38 0.33
ACGTcount: A:0.26, C:0.23, G:0.29, T:0.22
Consensus pattern (103 bp):
AGAGCTCCCATCTAAGACCATGTCTGGGACATGGCACTGGCATCCTGAGAATGAGAGGTCCCACG
TAAGACCATGTCTGGAACATGGCATGGGCATCGAGACG
Found at i:40763197 original size:50 final size:50
Alignment explanation
Indices: 40763076--40763373 Score: 303
Period size: 50 Copynumber: 5.9 Consensus size: 50
40763066 ATTTGGGTAA
* * *
40763076 AGAGATCCCATGTAAGACCATGTCTTGGACATGACATTGGCATCCTTGAGATCATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCAT-C--GAG---ATG
* * * *
40763132 AGAGGTGCCAGGTAAGACCATGTCTGGGACATGGCGTTGGCATCGAGACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCGAGATG
* * * *
40763182 AGAGGTCCCATGTAAGACCATGCCTGGGACATGGCGTTGGCACCGGGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCGAGATG
** * *
40763232 AGAGGTCCCCCGTAAGACCATGTCTGGGACATGGCATGGGCATCGATATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCGAGATG
** * *
40763282 AGAACTCCCATGTAAGACCATGTTTGGGACATGGCATTGGCA--GTACATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCG-AGATG
* ** * *
40763331 AAACATCCCATGTAAGACCATGTTTGGGACATGGCTTTGGCAT
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCAT
40763374 GTTATTATAA
Statistics
Matches: 208, Mismatches: 32, Indels: 10
0.83 0.13 0.04
Matches are distributed among these distances:
48 1 0.00
49 42 0.20
50 124 0.60
53 3 0.01
55 1 0.00
56 37 0.18
ACGTcount: A:0.26, C:0.22, G:0.30, T:0.22
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCGAGATG
Found at i:40767382 original size:26 final size:27
Alignment explanation
Indices: 40767353--40767403 Score: 68
Period size: 26 Copynumber: 1.9 Consensus size: 27
40767343 TATTGTAATG
*
40767353 CCCCTAAAGGGTAAATGACT-ATTTTA
1 CCCCTAAAGGGTAAATAACTGATTTTA
**
40767379 CCCCTCGAGGGTAAATAACTGATTT
1 CCCCTAAAGGGTAAATAACTGATTT
40767404 GTGCTATGGT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 17 0.81
27 4 0.19
ACGTcount: A:0.31, C:0.22, G:0.18, T:0.29
Consensus pattern (27 bp):
CCCCTAAAGGGTAAATAACTGATTTTA
Found at i:40776369 original size:27 final size:27
Alignment explanation
Indices: 40776331--40776429 Score: 137
Period size: 27 Copynumber: 3.7 Consensus size: 27
40776321 TTCGTGGGCT
*
40776331 AATGATCGAAATACCCTCGAAGGGTAA
1 AATGACCGAAATACCCTCGAAGGGTAA
*
40776358 AATGACCGAAATACCCCCGAAGGGTAA
1 AATGACCGAAATACCCTCGAAGGGTAA
* *
40776385 AATGACCGAAATACCC-CCACAGGATAA
1 AATGACCGAAATACCCTCGA-AGGGTAA
*
40776412 AATGACTGAAATACCCTC
1 AATGACCGAAATACCCTC
40776430 AAATGATAAT
Statistics
Matches: 65, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
26 2 0.03
27 62 0.95
28 1 0.02
ACGTcount: A:0.41, C:0.25, G:0.18, T:0.15
Consensus pattern (27 bp):
AATGACCGAAATACCCTCGAAGGGTAA
Found at i:40776437 original size:27 final size:27
Alignment explanation
Indices: 40776331--40776445 Score: 131
Period size: 27 Copynumber: 4.3 Consensus size: 27
40776321 TTCGTGGGCT
* * * *
40776331 AATGATCGAAATACCCTCGAAGGGTAA
1 AATGACCGAAATACCCCCAAAGGATAA
* *
40776358 AATGACCGAAATACCCCCGAAGGGTAA
1 AATGACCGAAATACCCCCAAAGGATAA
*
40776385 AATGACCGAAATACCCCCACAGGATAA
1 AATGACCGAAATACCCCCAAAGGATAA
* * *
40776412 AATGACTGAAATACCCTCAAATGATAA
1 AATGACCGAAATACCCCCAAAGGATAA
*
40776439 TATGACC
1 AATGACC
40776446 ATTACACCCC
Statistics
Matches: 77, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 77 1.00
ACGTcount: A:0.43, C:0.23, G:0.17, T:0.17
Consensus pattern (27 bp):
AATGACCGAAATACCCCCAAAGGATAA
Found at i:40778092 original size:27 final size:26
Alignment explanation
Indices: 40778061--40778238 Score: 169
Period size: 27 Copynumber: 6.6 Consensus size: 26
40778051 TAAATTGTAC
40778061 AGCACTAAGTGTGCGATTCGACTATGT
1 AGCACTAAGTGTGCGATT-GACTATGT
* * *
40778088 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCG-ATTGACTATGT
* * *
40778114 ATGCACTAAGTGTGCAAATTGACCATGC
1 A-GCACTAAGTGTGC-GATTGACTATGT
*
40778142 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA--TTGACTATGT
* *
40778170 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGA-TTGACTATGT
* *
40778197 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGA-TTGACTATGT
*
40778224 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
40778239 GGCTCAATAT
Statistics
Matches: 126, Mismatches: 19, Indels: 12
0.80 0.12 0.08
Matches are distributed among these distances:
26 1 0.01
27 100 0.79
28 25 0.20
ACGTcount: A:0.28, C:0.16, G:0.28, T:0.29
Consensus pattern (26 bp):
AGCACTAAGTGTGCGATTGACTATGT
Found at i:40778229 original size:82 final size:81
Alignment explanation
Indices: 40778058--40778238 Score: 211
Period size: 82 Copynumber: 2.2 Consensus size: 81
40778048 GATTAAATTG
* *
40778058 TACAGCACTAAGTGTGCGATTCGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTCGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
40778123 GTGTGCAAATTGACCA
66 GTGTGCAAATTGACCA
* * * ** *
40778139 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTCGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* * **
40778203 AAGTGTGCGAGTTGATTA
64 AAGTGTGCAAATTGACCA
* *
40778221 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
40778239 GGCTCAATAT
Statistics
Matches: 82, Mismatches: 16, Indels: 3
0.81 0.16 0.03
Matches are distributed among these distances:
81 18 0.22
82 64 0.78
ACGTcount: A:0.28, C:0.16, G:0.27, T:0.29
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTCGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCAAATTGACCA
Found at i:40778249 original size:27 final size:27
Alignment explanation
Indices: 40778143--40778249 Score: 70
Period size: 27 Copynumber: 3.9 Consensus size: 27
40778133 TGACCATGCG
* * * *
40778143 GCACTAAGTGTGCGAGTTTGACTATGTA
1 GCACTAAGTGTGCGAG-CTCAATATATA
** * * **
40778171 GCACTAAGTGTGCGATTTGATTACGTA
1 GCACTAAGTGTGCGAGCTCAATATATA
* * *
40778198 GCACTAAGTGTGCGAGTTGATTATATA
1 GCACTAAGTGTGCGAGCTCAATATATA
* *
40778225 GCACTGAGTGTGCGGGCTCAATATA
1 GCACTAAGTGTGCGAGCTCAATATA
40778250 CATTCGTGAA
Statistics
Matches: 68, Mismatches: 11, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
27 53 0.78
28 15 0.22
ACGTcount: A:0.26, C:0.15, G:0.28, T:0.31
Consensus pattern (27 bp):
GCACTAAGTGTGCGAGCTCAATATATA
Found at i:40779778 original size:28 final size:28
Alignment explanation
Indices: 40779737--40779940 Score: 255
Period size: 28 Copynumber: 7.3 Consensus size: 28
40779727 GTTGCATTAT
* *
40779737 CACACTGTTTCTGTTTTAGGCTAAGGCC
1 CACACTGTTTCTGTATTGGGCTAAGGCC
* *
40779765 CACACTGTTACTGTAATGGGCTAAGGCC
1 CACACTGTTTCTGTATTGGGCTAAGGCC
*
40779793 CACACTATTTCTGTATTGGGCTAAGGCC
1 CACACTGTTTCTGTATTGGGCTAAGGCC
* *
40779821 CACATTGTTTCTGTTTTGGGCTAAGGCC
1 CACACTGTTTCTGTATTGGGCTAAGGCC
* * * *
40779849 CACACTGTTACTATAATGGGATAAGGCC
1 CACACTGTTTCTGTATTGGGCTAAGGCC
* *
40779877 CATATTGTTTCTGTATTGGGCTAAGGCC
1 CACACTGTTTCTGTATTGGGCTAAGGCC
* * * *
40779905 CACATTGTTACCGTATCGGGCTAAGGCC
1 CACACTGTTTCTGTATTGGGCTAAGGCC
40779933 CACACTGT
1 CACACTGT
40779941 ACTATTACCG
Statistics
Matches: 149, Mismatches: 27, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 149 1.00
ACGTcount: A:0.22, C:0.24, G:0.23, T:0.31
Consensus pattern (28 bp):
CACACTGTTTCTGTATTGGGCTAAGGCC
Found at i:40779845 original size:84 final size:84
Alignment explanation
Indices: 40779737--40779945 Score: 312
Period size: 84 Copynumber: 2.5 Consensus size: 84
40779727 GTTGCATTAT
* * * *
40779737 CACACTGTTTCTGTTTTAGGCTAAGGCCCACACTGTTACTGTAATGGGCTAAGGCCCACACTATT
1 CACATTGTTTCTGTTTTGGGCTAAGGCCCACACTGTTACTATAATGGGATAAGGCCCACACTATT
40779802 TCTGTATTGGGCTAAGGCC
66 TCTGTATTGGGCTAAGGCC
* * *
40779821 CACATTGTTTCTGTTTTGGGCTAAGGCCCACACTGTTACTATAATGGGATAAGGCCCATATTGTT
1 CACATTGTTTCTGTTTTGGGCTAAGGCCCACACTGTTACTATAATGGGATAAGGCCCACACTATT
40779886 TCTGTATTGGGCTAAGGCC
66 TCTGTATTGGGCTAAGGCC
* * * *
40779905 CACATTGTTACCGTATCGGGCTAAGGCCCACACTG-TACTAT
1 CACATTGTTTCTGTTTTGGGCTAAGGCCCACACTGTTACTAT
40779946 TACCGCGTTG
Statistics
Matches: 114, Mismatches: 11, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
83 6 0.05
84 108 0.95
ACGTcount: A:0.22, C:0.24, G:0.22, T:0.32
Consensus pattern (84 bp):
CACATTGTTTCTGTTTTGGGCTAAGGCCCACACTGTTACTATAATGGGATAAGGCCCACACTATT
TCTGTATTGGGCTAAGGCC
Found at i:40782733 original size:40 final size:40
Alignment explanation
Indices: 40782649--40782832 Score: 205
Period size: 40 Copynumber: 4.6 Consensus size: 40
40782639 TTGAATGCTG
* * * *
40782649 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACT-AT
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGC-GAGTTATTAAT
**
40782688 ATCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGTTATTAAT
1 -TCCGGGTTAAG-TCCCGAAGGCATTTGTGCGAGTTATTAAT
* * *
40782729 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAGATACTAAT
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATTAAT
* *
40782769 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTT-TTAAAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATT-AAT
40782809 TCCGGGTTAAGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
40782833 GTATGAGTTA
Statistics
Matches: 125, Mismatches: 14, Indels: 10
0.84 0.09 0.07
Matches are distributed among these distances:
39 2 0.02
40 113 0.90
41 10 0.08
ACGTcount: A:0.24, C:0.21, G:0.27, T:0.28
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATTAAT
Found at i:40782786 original size:80 final size:81
Alignment explanation
Indices: 40782649--40782829 Score: 230
Period size: 80 Copynumber: 2.3 Consensus size: 81
40782639 TTGAATGCTG
* *
40782649 TCCGGGCTAAGTCCCGAAGG-CTTTGTGCTAAGTGACTATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAAGTGACTATATCCGGACTAAGATCCGAAGGCATT
* *
40782713 TGTGCGAGTTATT-AAT
66 CGTGCGAGTT-TTAAAA
**
40782729 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCG-AGAT-ACTA-ATTCCGGGTTAAG-TCCCGAAGGC
1 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAAG-TGACTATA-TCCGGACTAAGAT-CCGAAGGC
40782790 ATTCGTGCGAGTTTTAAAA
63 ATTCGTGCGAGTTTTAAAA
40782809 TCCGGGTTAAGTCCCGAAGGC
1 TCCGGGTTAAGTCCCGAAGGC
40782830 ATTGTATGAG
Statistics
Matches: 90, Mismatches: 6, Indels: 10
0.85 0.06 0.09
Matches are distributed among these distances:
79 4 0.04
80 77 0.86
81 9 0.10
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.27
Consensus pattern (81 bp):
TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAAGTGACTATATCCGGACTAAGATCCGAAGGCATT
CGTGCGAGTTTTAAAA
Found at i:40784823 original size:28 final size:28
Alignment explanation
Indices: 40784765--40784823 Score: 66
Period size: 28 Copynumber: 2.1 Consensus size: 28
40784755 GTATCAGTAT
* * *
40784765 AGTGTGGGCCTTAGACCATTACAGTAAC
1 AGTGTGGGCCCTAGACCAATACAGAAAC
*
40784793 AGTGTGGGCCCTA-CCCAATACAGAAATC
1 AGTGTGGGCCCTAGACCAATACAGAAA-C
40784821 AGT
1 AGT
40784824 ATAATGTTGT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
27 10 0.38
28 16 0.62
ACGTcount: A:0.31, C:0.24, G:0.24, T:0.22
Consensus pattern (28 bp):
AGTGTGGGCCCTAGACCAATACAGAAAC
Found at i:40784960 original size:26 final size:26
Alignment explanation
Indices: 40784926--40784976 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
40784916 AACACACCAA
* *
40784926 TAACGCAGCCAAGCTGCCAATAACAG
1 TAACACAGCAAAGCTGCCAATAACAG
*
40784952 TAACACAGCAAAGCTGCCAGTAACA
1 TAACACAGCAAAGCTGCCAATAACA
40784977 TTATATGTGG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.41, C:0.29, G:0.18, T:0.12
Consensus pattern (26 bp):
TAACACAGCAAAGCTGCCAATAACAG
Found at i:40785187 original size:27 final size:26
Alignment explanation
Indices: 40785157--40785264 Score: 108
Period size: 27 Copynumber: 4.0 Consensus size: 26
40785147 GGGGTATAAT
*
40785157 AGTCATTTTACCTTATGGAGATATTTC
1 AGTCATTTTACCTT-TGGAGGTATTTC
* *
40785184 AGTCATTTTACCCTTTGGGGGTAATTC
1 AGTCATTTTA-CCTTTGGAGGTATTTC
* *
40785211 AATTATTTTACCTTTCGGAGGTATTTC
1 AGTCATTTTACCTTT-GGAGGTATTTC
* * *
40785238 GGTAATTTTACCCTTTGAAGGTATTTC
1 AGTCATTTTA-CCTTTGGAGGTATTTC
40785265 GGTAATTTGT
Statistics
Matches: 67, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
26 5 0.07
27 53 0.79
28 9 0.13
ACGTcount: A:0.22, C:0.16, G:0.18, T:0.44
Consensus pattern (26 bp):
AGTCATTTTACCTTTGGAGGTATTTC
Found at i:40788901 original size:19 final size:19
Alignment explanation
Indices: 40788877--40788918 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
40788867 AGGATTAGAA
40788877 AATATTTATCA-ATCATAAT
1 AATATTTATCACATCAT-AT
*
40788896 AATATTTGTCACATCATAT
1 AATATTTATCACATCATAT
40788915 AATA
1 AATA
40788919 AAAATCAAGT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 16 0.76
20 5 0.24
ACGTcount: A:0.45, C:0.12, G:0.02, T:0.40
Consensus pattern (19 bp):
AATATTTATCACATCATAT
Found at i:40789580 original size:11 final size:11
Alignment explanation
Indices: 40789559--40789622 Score: 67
Period size: 11 Copynumber: 5.8 Consensus size: 11
40789549 GGTACGGTTT
*
40789559 TGATGTGGTGG
1 TGATTTGGTGG
*
40789570 TGGTTTGGTGG
1 TGATTTGGTGG
**
40789581 TGATAGGGTGG
1 TGATTTGGTGG
40789592 TGATTTGGTGG
1 TGATTTGGTGG
*
40789603 TTG-TTGGGTGG
1 -TGATTTGGTGG
40789614 TGATTTGGT
1 TGATTTGGT
40789623 TTGCGATACA
Statistics
Matches: 42, Mismatches: 9, Indels: 4
0.76 0.16 0.07
Matches are distributed among these distances:
10 2 0.05
11 38 0.90
12 2 0.05
ACGTcount: A:0.08, C:0.00, G:0.50, T:0.42
Consensus pattern (11 bp):
TGATTTGGTGG
Found at i:40789584 original size:22 final size:22
Alignment explanation
Indices: 40789558--40789622 Score: 87
Period size: 22 Copynumber: 2.9 Consensus size: 22
40789548 TGGTACGGTT
*
40789558 TTGATGTGGTGGTGGTTTGGTGG
1 TTGATG-GGTGGTGATTTGGTGG
40789581 -TGATAGGGTGGTGATTTGGTGG
1 TTGAT-GGGTGGTGATTTGGTGG
*
40789603 TTGTTGGGTGGTGATTTGGT
1 TTGATGGGTGGTGATTTGGT
40789623 TTGCGATACA
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
22 34 0.89
23 4 0.11
ACGTcount: A:0.08, C:0.00, G:0.49, T:0.43
Consensus pattern (22 bp):
TTGATGGGTGGTGATTTGGTGG
Found at i:40793709 original size:26 final size:26
Alignment explanation
Indices: 40793672--40793742 Score: 79
Period size: 26 Copynumber: 2.7 Consensus size: 26
40793662 CGTTTCGACC
* *
40793672 CACAACTCGTGTGAGCATGCCCATTT
1 CACAGCTCGTGTGAGCATACCCATTT
* * * *
40793698 CACAGCTTGTGTAAGAATACTCATTT
1 CACAGCTCGTGTGAGCATACCCATTT
*
40793724 CATAGCTCGTGTGAGCATA
1 CACAGCTCGTGTGAGCATA
40793743 TATGTACCGA
Statistics
Matches: 35, Mismatches: 10, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
26 35 1.00
ACGTcount: A:0.27, C:0.24, G:0.20, T:0.30
Consensus pattern (26 bp):
CACAGCTCGTGTGAGCATACCCATTT
Found at i:40794492 original size:54 final size:52
Alignment explanation
Indices: 40794429--40794588 Score: 130
Period size: 52 Copynumber: 3.0 Consensus size: 52
40794419 TAATATTATG
40794429 CTTATGGTTTATACTAGCTTACTAAGAATTTATTGTTTATGTGGTTATCTTT
1 CTTATGGTTTATACTAGCTTACTAAGAATTTATTGTTTATGTGGTTATCTTT
* * * * * ** * *
40794481 CTATATAGGTTTATATTTAACCTA-T-A-AATTTCATTATTGAAAT-GTAATATTAT
1 CT-TAT-GGTTTATA-CTAGCTTACTAAGAATTT-ATTGTTTATGTGGTTATCTT-T
* * *
40794534 GCTTATGGTTTATACGAGCTTACTAAGCATTTATTGCTTATGTGGTTATCTTT
1 -CTTATGGTTTATACTAGCTTACTAAGAATTTATTGTTTATGTGGTTATCTTT
40794587 CT
1 CT
40794589 CTTACTTTAC
Statistics
Matches: 77, Mismatches: 21, Indels: 20
0.65 0.18 0.17
Matches are distributed among these distances:
51 4 0.05
52 24 0.31
53 23 0.30
54 21 0.27
55 5 0.06
ACGTcount: A:0.27, C:0.11, G:0.14, T:0.49
Consensus pattern (52 bp):
CTTATGGTTTATACTAGCTTACTAAGAATTTATTGTTTATGTGGTTATCTTT
Found at i:40794544 original size:52 final size:51
Alignment explanation
Indices: 40794382--40794547 Score: 149
Period size: 52 Copynumber: 3.2 Consensus size: 51
40794372 CATTGGTGTA
*
40794382 GGTTTATATTTAACCTTTAAATTTAATTATTGAAATGTAATATTATGCTTAT
1 GGTTTATATTTAACCTATAAATTT-ATTATTGAAATGTAATATTATGCTTAT
* * * * * ** * *
40794434 GGTTTATA-CTAGCTTACTAAGAATTTATTGTTTATGTGGTTATCTT-T-CTATAT
1 GGTTTATATTTAACCTA-T-A-AATTTATTATTGAAAT-GTAATATTATGCT-TAT
40794487 AGGTTTATATTTAACCTATAAATTTCATTATTGAAATGTAATATTATGCTTAT
1 -GGTTTATATTTAACCTATAAATTT-ATTATTGAAATGTAATATTATGCTTAT
40794540 GGTTTATA
1 GGTTTATA
40794548 CGAGCTTACT
Statistics
Matches: 85, Mismatches: 19, Indels: 20
0.69 0.15 0.16
Matches are distributed among these distances:
51 4 0.05
52 30 0.35
53 24 0.28
54 22 0.26
55 5 0.06
ACGTcount: A:0.31, C:0.07, G:0.12, T:0.49
Consensus pattern (51 bp):
GGTTTATATTTAACCTATAAATTTATTATTGAAATGTAATATTATGCTTAT
Found at i:40794566 original size:106 final size:106
Alignment explanation
Indices: 40794380--40794588 Score: 373
Period size: 106 Copynumber: 2.0 Consensus size: 106
40794370 GGCATTGGTG
* *
40794380 TAGGTTTATATTTAACCTTTAAATTTAATTATTGAAATGTAATATTATGCTTATGGTTTATACTA
1 TAGGTTTATATTTAACCTATAAATTTAATTATTGAAATGTAATATTATGCTTATGGTTTATACGA
*
40794445 GCTTACTAAGAATTTATTGTTTATGTGGTTATCTTTCTATA
66 GCTTACTAAGAATTTATTGCTTATGTGGTTATCTTTCTATA
*
40794486 TAGGTTTATATTTAACCTATAAATTTCATTATTGAAATGTAATATTATGCTTATGGTTTATACGA
1 TAGGTTTATATTTAACCTATAAATTTAATTATTGAAATGTAATATTATGCTTATGGTTTATACGA
*
40794551 GCTTACTAAGCATTTATTGCTTATGTGGTTATCTTTCT
66 GCTTACTAAGAATTTATTGCTTATGTGGTTATCTTTCT
40794589 CTTACTTTAC
Statistics
Matches: 98, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
106 98 1.00
ACGTcount: A:0.29, C:0.09, G:0.13, T:0.49
Consensus pattern (106 bp):
TAGGTTTATATTTAACCTATAAATTTAATTATTGAAATGTAATATTATGCTTATGGTTTATACGA
GCTTACTAAGAATTTATTGCTTATGTGGTTATCTTTCTATA
Found at i:40803874 original size:34 final size:34
Alignment explanation
Indices: 40803827--40803894 Score: 84
Period size: 34 Copynumber: 2.0 Consensus size: 34
40803817 GCACAGTTGA
* *
40803827 ACAGTCTTAGGCCTAAGCCCTTTTCAGTATCAGTG
1 ACAGTCTTAGGCCTAAGCCCATCTCAGTA-CAGTG
* *
40803862 ACAGT-TTGGGCCTTAGCCCATCTCAGTACAGTG
1 ACAGTCTTAGGCCTAAGCCCATCTCAGTACAGTG
40803895 TAAAAAATGC
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
33 5 0.17
34 19 0.66
35 5 0.17
ACGTcount: A:0.22, C:0.26, G:0.22, T:0.29
Consensus pattern (34 bp):
ACAGTCTTAGGCCTAAGCCCATCTCAGTACAGTG
Found at i:40806202 original size:20 final size:20
Alignment explanation
Indices: 40806156--40806202 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
40806146 AGCTCGTTTC
*
40806156 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* *
40806176 CAACTCACTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
40806196 CAGCTCA
1 CAGCTCA
40806203 ATCTTAACCC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.30, C:0.36, G:0.13, T:0.21
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:40808513 original size:31 final size:32
Alignment explanation
Indices: 40808453--40808513 Score: 88
Period size: 31 Copynumber: 1.9 Consensus size: 32
40808443 TATCCTTGGT
40808453 TAAACAAGTATCTTATTTAATAAAATTTTTTA
1 TAAACAAGTATCTTATTTAATAAAATTTTTTA
* * *
40808485 TAAACAATTATCTT-TTTGATAAACTTTTT
1 TAAACAAGTATCTTATTTAATAAAATTTTT
40808514 CATACACATT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
31 13 0.50
32 13 0.50
ACGTcount: A:0.39, C:0.08, G:0.03, T:0.49
Consensus pattern (32 bp):
TAAACAAGTATCTTATTTAATAAAATTTTTTA
Found at i:40811495 original size:26 final size:26
Alignment explanation
Indices: 40811463--40811513 Score: 93
Period size: 26 Copynumber: 2.0 Consensus size: 26
40811453 TCTAGCAGAA
40811463 TAATTAACATATATAAGACCAATAAG
1 TAATTAACATATATAAGACCAATAAG
*
40811489 TAATTAACATATATAAGACTAATAA
1 TAATTAACATATATAAGACCAATAA
40811514 CAAAAAAATC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.55, C:0.10, G:0.06, T:0.29
Consensus pattern (26 bp):
TAATTAACATATATAAGACCAATAAG
Found at i:40811816 original size:23 final size:24
Alignment explanation
Indices: 40811786--40811833 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 24
40811776 CTAACAAATT
*
40811786 AATAGATGG-TTTTTAATGATTTC
1 AATAGATGGCCTTTTAATGATTTC
40811809 AATAGATGGCCTTTTAATGATTTC
1 AATAGATGGCCTTTTAATGATTTC
40811833 A
1 A
40811834 GTACCCGCCA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 9 0.39
24 14 0.61
ACGTcount: A:0.31, C:0.08, G:0.17, T:0.44
Consensus pattern (24 bp):
AATAGATGGCCTTTTAATGATTTC
Found at i:40821610 original size:28 final size:29
Alignment explanation
Indices: 40821553--40821610 Score: 66
Period size: 28 Copynumber: 2.0 Consensus size: 29
40821543 TTTAAATAAA
* *
40821553 TATGGACTTTTATTTATGATTTGGATTTT
1 TATGGACTTTTATTGATGATTTGGAATTT
*
40821582 TATGGAC-TTTATTGCT-ATTTGGGAATTT
1 TATGGACTTTTATTGATGATTT-GGAATTT
40821610 T
1 T
40821611 TATGTTAAAC
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
27 4 0.16
28 14 0.56
29 7 0.28
ACGTcount: A:0.21, C:0.05, G:0.19, T:0.55
Consensus pattern (29 bp):
TATGGACTTTTATTGATGATTTGGAATTT
Found at i:40839712 original size:85 final size:85
Alignment explanation
Indices: 40839569--40839747 Score: 349
Period size: 85 Copynumber: 2.1 Consensus size: 85
40839559 GGCCGGCCAT
40839569 GAGCATGGGTGGACAAGATGTTATGGCTAAAAACATGTCATAAACATGTTGGGGTAGTGCATTAT
1 GAGCATGGGTGGACAAGATGTTATGGCTAAAAACATGTCATAAACATGTTGGGGTAGTGCATTAT
40839634 GTAAGGATTAATAAAATAAA
66 GTAAGGATTAATAAAATAAA
40839654 GAGCATGGGTGGACAAGATGTTATGGCTAAAAACATGTCATAAACATGTTGGGGTAGTGCATTAT
1 GAGCATGGGTGGACAAGATGTTATGGCTAAAAACATGTCATAAACATGTTGGGGTAGTGCATTAT
40839719 GTAAGGATTAATAAAATAAA
66 GTAAGGATTAATAAAATAAA
*
40839739 GGGCATGGG
1 GAGCATGGG
40839748 CAATAAAATA
Statistics
Matches: 93, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
85 93 1.00
ACGTcount: A:0.37, C:0.08, G:0.28, T:0.26
Consensus pattern (85 bp):
GAGCATGGGTGGACAAGATGTTATGGCTAAAAACATGTCATAAACATGTTGGGGTAGTGCATTAT
GTAAGGATTAATAAAATAAA
Found at i:40841060 original size:47 final size:47
Alignment explanation
Indices: 40841006--40841505 Score: 715
Period size: 47 Copynumber: 10.6 Consensus size: 47
40840996 TATTTGAATA
* *
40841006 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
* *
40841053 AATGTGAAAGTGTATATATATGTGATAAGGCCTAAT-GCCGATGTGATG
1 AATGTGAAAGTG--TATATATGTGATAAGGCCGAATGGCCAATGTGATG
40841101 AATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
40841148 AATGTGAAAGTGTATATATATGTGATAAGGCCGAATGGCCAATGTGATG
1 AATGTGAAAGTG--TATATATGTGATAAGGCCGAATGGCCAATGTGATG
* *
40841197 AATGTGAACA-TGTGTATGTGTGATAAGGCCGAATGGCCAATGTGATG
1 AATGTGAA-AGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
* *
40841244 AATGTGAACA-TGCATATATGAGATAAGGCCGAATGGCCAATGTGATG
1 AATGTGAA-AGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
* *
40841291 AATGTGAACA-TGTGTATGTGTGATAAGGCCGAATGGCCAATGTGATG
1 AATGTGAA-AGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
* *
40841338 AATGTGAACA-TGTGTATGTGTGATAAGGCCGAATGGCCAATGTGATG
1 AATGTGAA-AGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
* *
40841385 AATGTGAACA-TGCATATATGAGATAAGGCCGAATGGCCAATGTGATG
1 AATGTGAA-AGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
40841432 AATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
* * * *
40841479 GATGTGGAAGCGTATAAATGTGATAAG
1 AATGTGAAAGTGTATATATGTGATAAG
40841506 TCCCGAAGGG
Statistics
Matches: 424, Mismatches: 22, Indels: 14
0.92 0.05 0.03
Matches are distributed among these distances:
46 22 0.05
47 310 0.73
48 24 0.06
49 67 0.16
50 1 0.00
ACGTcount: A:0.33, C:0.10, G:0.30, T:0.27
Consensus pattern (47 bp):
AATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
Found at i:40841383 original size:22 final size:22
Alignment explanation
Indices: 40841356--40841477 Score: 61
Period size: 22 Copynumber: 5.3 Consensus size: 22
40841346 CATGTGTATG
40841356 TGTGATAAGGCCGAATGGCCAA
1 TGTGATAAGGCCGAATGGCCAA
* * *
40841378 TGTGATGAATG-TGAACAT-GCATATA
1 TGTGAT-AAGGCCG-A-ATGGC-CA-A
*
40841403 TGAGATAAGGCCGAATGGCCAA
1 TGTGATAAGGCCGAATGGCCAA
* * ***
40841425 TGTGATGAATG-TGAAAGTGTATATA
1 TGTGAT-AAGGCCG-AA-TGGCCA-A
40841450 TGTGATAAGGCCGAATGGCCAA
1 TGTGATAAGGCCGAATGGCCAA
40841472 TGTGAT
1 TGTGAT
40841478 GGATGTGGAA
Statistics
Matches: 70, Mismatches: 18, Indels: 24
0.62 0.16 0.21
Matches are distributed among these distances:
22 21 0.30
23 17 0.24
24 17 0.24
25 15 0.21
ACGTcount: A:0.34, C:0.11, G:0.30, T:0.25
Consensus pattern (22 bp):
TGTGATAAGGCCGAATGGCCAA
Found at i:40844000 original size:38 final size:38
Alignment explanation
Indices: 40843936--40844008 Score: 103
Period size: 38 Copynumber: 1.9 Consensus size: 38
40843926 AATCTGAGTT
*
40843936 TAAAGACCCGCTGACTATATGAAGAGATTATGTCCAGG
1 TAAAGACCCGATGACTATATGAAGAGATTATGTCCAGG
* *
40843974 TAAAGACCCGATGGCTATGT-ACAGAGATTATGTCC
1 TAAAGACCCGATGACTATATGA-AGAGATTATGTCC
40844009 GGATTAAAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
37 1 0.03
38 30 0.97
ACGTcount: A:0.33, C:0.19, G:0.23, T:0.25
Consensus pattern (38 bp):
TAAAGACCCGATGACTATATGAAGAGATTATGTCCAGG
Found at i:40844123 original size:40 final size:40
Alignment explanation
Indices: 40844064--40844344 Score: 411
Period size: 40 Copynumber: 7.0 Consensus size: 40
40844054 AGGTCTCGAC
*
40844064 GATG-ATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGT
1 GATGTATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGT
*
40844103 GATGTATCCGGGCTAAGTCCCAAAGAGCATTCATGCTAGT
1 GATGTATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGT
*
40844143 GATGTATCCGGGCTAAGTTCCGAAGAGCATTCATGCTAGT
1 GATGTATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGT
40844183 GATGTATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGT
1 GATGTATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGT
* *
40844223 GATGTATCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGT
1 GATGTATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGT
* * ** * *
40844263 GATATATCCGTGCTAAACCCCGAAGAGCATTCGTGCTGGT
1 GATGTATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGT
* * * * *
40844303 GTTATATCCGGGCTAGGTCCCGAAGAGCAATCATGCTGGT
1 GATGTATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGT
40844343 GA
1 GA
40844345 CGTGTATTCG
Statistics
Matches: 220, Mismatches: 21, Indels: 1
0.91 0.09 0.00
Matches are distributed among these distances:
39 4 0.02
40 216 0.98
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (40 bp):
GATGTATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGT
Found at i:40845744 original size:85 final size:85
Alignment explanation
Indices: 40845601--40845779 Score: 349
Period size: 85 Copynumber: 2.1 Consensus size: 85
40845591 GGCCGGCCAT
40845601 GAGCATGGGTGGACAAGATGTTATGGCTAAAAACATGTCATAAACATGTTGGGGTAGTGCATTAT
1 GAGCATGGGTGGACAAGATGTTATGGCTAAAAACATGTCATAAACATGTTGGGGTAGTGCATTAT
40845666 GTAAGGATTAATAAAATAAA
66 GTAAGGATTAATAAAATAAA
40845686 GAGCATGGGTGGACAAGATGTTATGGCTAAAAACATGTCATAAACATGTTGGGGTAGTGCATTAT
1 GAGCATGGGTGGACAAGATGTTATGGCTAAAAACATGTCATAAACATGTTGGGGTAGTGCATTAT
40845751 GTAAGGATTAATAAAATAAA
66 GTAAGGATTAATAAAATAAA
*
40845771 GGGCATGGG
1 GAGCATGGG
40845780 CAATAAAATA
Statistics
Matches: 93, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
85 93 1.00
ACGTcount: A:0.37, C:0.08, G:0.28, T:0.26
Consensus pattern (85 bp):
GAGCATGGGTGGACAAGATGTTATGGCTAAAAACATGTCATAAACATGTTGGGGTAGTGCATTAT
GTAAGGATTAATAAAATAAA
Found at i:40847098 original size:47 final size:47
Alignment explanation
Indices: 40847044--40847544 Score: 708
Period size: 47 Copynumber: 10.6 Consensus size: 47
40847034 TATTTGAATA
* **
40847044 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCTGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
* *
40847091 AATGTGAAAGTGTATATCTATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATA--TATGTGATAAGGCCGAATGGCCAATGTGATG
40847140 AATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
40847187 AATGTGAAAGTGTATATATATGTGATAAGGCCGAATGGCCAATGTGATG
1 AATGTGAAAGTG--TATATATGTGATAAGGCCGAATGGCCAATGTGATG
* *
40847236 AATGTGAACA-TGTGTATGTGTGATAAGGCCGAATGGCCAATGTGATG
1 AATGTGAA-AGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
* *
40847283 AATGTGAACA-TGCATATATGAGATAAGGCCGAATGGCCAATGTGATG
1 AATGTGAA-AGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
* *
40847330 AATGTGAACA-TGTGTATGTGTGATAAGGCCGAATGGCCAATGTGATG
1 AATGTGAA-AGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
* *
40847377 AATGTGAACA-TGTGTATGTGTGATAAGGCCGAATGGCCAATGTGATG
1 AATGTGAA-AGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
* *
40847424 AATGTGAACA-TGCATATATGAGATAAGGCCGAATGGCCAATGTGATG
1 AATGTGAA-AGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
40847471 AATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGAT-
1 AATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
* * *
40847517 AGATGTGGAAGCGTATAAATGTGATAAG
1 A-ATGTGAAAGTGTATATATGTGATAAG
40847545 TCCCGAAGGG
Statistics
Matches: 425, Mismatches: 22, Indels: 14
0.92 0.05 0.03
Matches are distributed among these distances:
46 2 0.00
47 331 0.78
49 91 0.21
50 1 0.00
ACGTcount: A:0.33, C:0.10, G:0.30, T:0.28
Consensus pattern (47 bp):
AATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
Found at i:40847422 original size:22 final size:22
Alignment explanation
Indices: 40847395--40847517 Score: 63
Period size: 22 Copynumber: 5.3 Consensus size: 22
40847385 CATGTGTATG
40847395 TGTGATAAGGCCGAATGGCCAA
1 TGTGATAAGGCCGAATGGCCAA
* * *
40847417 TGTGATGAATG-TGAACAT-GCATATA
1 TGTGAT-AAGGCCG-A-ATGGC-CA-A
*
40847442 TGAGATAAGGCCGAATGGCCAA
1 TGTGATAAGGCCGAATGGCCAA
* * ***
40847464 TGTGATGAATG-TGAAAGTGTATATA
1 TGTGAT-AAGGCCG-AA-TGGCCA-A
40847489 TGTGATAAGGCCGAATGGCCAA
1 TGTGATAAGGCCGAATGGCCAA
40847511 TGTGATA
1 TGTGATA
40847518 GATGTGGAAG
Statistics
Matches: 71, Mismatches: 18, Indels: 24
0.63 0.16 0.21
Matches are distributed among these distances:
22 22 0.31
23 17 0.24
24 17 0.24
25 15 0.21
ACGTcount: A:0.34, C:0.11, G:0.29, T:0.25
Consensus pattern (22 bp):
TGTGATAAGGCCGAATGGCCAA
Found at i:40849785 original size:16 final size:16
Alignment explanation
Indices: 40849755--40849785 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
40849745 GAGCATTGAA
*
40849755 AAAGAAAATGAAAAAG
1 AAAGAAAATAAAAAAG
40849771 AAAGAAAATAAAAAA
1 AAAGAAAATAAAAAA
40849786 CTAAAAGAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.81, C:0.00, G:0.13, T:0.06
Consensus pattern (16 bp):
AAAGAAAATAAAAAAG
Found at i:40861143 original size:40 final size:40
Alignment explanation
Indices: 40861045--40861211 Score: 228
Period size: 40 Copynumber: 4.2 Consensus size: 40
40861035 TCCTCGTTCA
* * * *
40861045 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-
1 AATGCCTTCGGGACATAACCCGGATTTAATAACTCGCACG
*
40861084 AATGCCTTCGGGACATAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACATAACCCGGATTTAATAACTCGCACG
*
40861124 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACATAACCCGGATTTAATAACTCGCACG
* * * *
40861164 AATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACA
1 AATGCCTTCGGGACATAACCCGGATTTAATAACTCGCACG
*
40861204 AAGGCCTT
1 AATGCCTT
40861212 TGGATCTTAG
Statistics
Matches: 116, Mismatches: 11, Indels: 1
0.91 0.09 0.01
Matches are distributed among these distances:
39 34 0.29
40 82 0.71
ACGTcount: A:0.27, C:0.28, G:0.20, T:0.25
Consensus pattern (40 bp):
AATGCCTTCGGGACATAACCCGGATTTAATAACTCGCACG
Found at i:40861146 original size:79 final size:80
Alignment explanation
Indices: 40861045--40861191 Score: 233
Period size: 79 Copynumber: 1.9 Consensus size: 80
40861035 TCCTCGTTCA
* * *
40861045 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-AATGCCTTCGGGACATAACCCGGAT
1 AATGCCTTCGGGACATAACCCGGATTTAATAACTCACACGAATGCCTTCGGGACATAACCCGGAT
40861109 TTAACAACTCGCACG
66 TTAACAACTCGCACG
* * *
40861124 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACGAATGCCTTCGGGACTTAACCCGGAT
1 AATGCCTTCGGGACATAACCCGGATTTAATAACTCACACGAATGCCTTCGGGACATAACCCGGAT
40861189 TTA
66 TTA
40861192 GTATCTCGCA
Statistics
Matches: 61, Mismatches: 6, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
79 34 0.56
80 27 0.44
ACGTcount: A:0.27, C:0.28, G:0.20, T:0.24
Consensus pattern (80 bp):
AATGCCTTCGGGACATAACCCGGATTTAATAACTCACACGAATGCCTTCGGGACATAACCCGGAT
TTAACAACTCGCACG
Found at i:40861227 original size:40 final size:40
Alignment explanation
Indices: 40861043--40861267 Score: 204
Period size: 40 Copynumber: 5.7 Consensus size: 40
40861033 GCTCCTCGTT
* * * * * *
40861043 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACA
1 CAAAGGCCTTCGGGACTTAACCCGGATTTAATAACTCGCA
* * *
40861083 C-AATGCCTTCGGGACATAACCCGGATTTAACAACTCGCA
1 CAAAGGCCTTCGGGACTTAACCCGGATTTAATAACTCGCA
* *
40861122 CGAATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCA
1 CAAAGGCCTTCGGGACTTAACCCGGATTTAATAACTCGCA
* * * *
40861162 CGAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCA
1 CAAAGGCCTTCGGGACTTAACCCGGATTTAATAACTCGCA
* ** * * * *
40861202 CAAAGGCCTT-TGGATCTTAGTCCGGATATATTCACTTAGCA
1 CAAAGGCCTTCGGGA-CTTAACCCGGATTTAATAAC-TCGCA
*
40861243 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAAGGCCTTCGGGACTTAACCCGGA
40861268 CAGCATTCAA
Statistics
Matches: 160, Mismatches: 21, Indels: 8
0.85 0.11 0.04
Matches are distributed among these distances:
39 37 0.23
40 112 0.70
41 11 0.07
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.25
Consensus pattern (40 bp):
CAAAGGCCTTCGGGACTTAACCCGGATTTAATAACTCGCA
Found at i:40861227 original size:80 final size:79
Alignment explanation
Indices: 40861043--40861267 Score: 227
Period size: 80 Copynumber: 2.8 Consensus size: 79
40861033 GCTCCTCGTT
* * * * * * *
40861043 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACACAATGCCTTCGGGACATAACCCGGA
1 CAAAGGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACAATGCCTTCGGGACTTAACCCGGA
40861108 TTTAACAACTCGCA
66 TTTAACAACTCGCA
* *
40861122 CGAATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACGAATGCCTTCGGGACTTAACCCGG
1 CAAAGGCCTTCGGGACTTAACCCGGATTTAATAACTCGCAC-AATGCCTTCGGGACTTAACCCGG
** *
40861187 ATTTAGTATCTCGCA
65 ATTTAACAACTCGCA
* ** * * * * * *
40861202 CAAAGGCCTT-TGGATCTTAGTCCGGATATATTCACTTAGCACAAAGCCTTCGGGACTTAGCCCG
1 CAAAGGCCTTCGGGA-CTTAACCCGGATTTAATAAC-TCGCACAATGCCTTCGGGACTTAACCCG
40861266 GA
64 GA
40861268 CAGCATTCAA
Statistics
Matches: 122, Mismatches: 21, Indels: 5
0.82 0.14 0.03
Matches are distributed among these distances:
79 38 0.31
80 79 0.65
81 5 0.04
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.25
Consensus pattern (79 bp):
CAAAGGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACAATGCCTTCGGGACTTAACCCGGA
TTTAACAACTCGCA
Found at i:40872866 original size:13 final size:14
Alignment explanation
Indices: 40872845--40872877 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
40872835 TTTATTAATG
40872845 AAATATATTAAA-AT
1 AAAT-TATTAAATAT
40872859 AAATTATTAAATAT
1 AAATTATTAAATAT
40872873 AAATT
1 AAATT
40872878 TATATTTTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 7 0.39
14 11 0.61
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (14 bp):
AAATTATTAAATAT
Found at i:40894955 original size:40 final size:40
Alignment explanation
Indices: 40894773--40894995 Score: 236
Period size: 40 Copynumber: 5.6 Consensus size: 40
40894763 TCCTCGTTCA
* * * * *
40894773 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* *
40894812 AATGCCTTCGGGACATAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
40894852 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * *
40894892 AATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* ** * * * *
40894932 AAGGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCAC-
1 AATGCCTTCGGGA-CTTAACCCGGATTTAATAAC-TCGCACG
* *
40894972 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
40894996 CAGCATTCAA
Statistics
Matches: 160, Mismatches: 20, Indels: 7
0.86 0.11 0.04
Matches are distributed among these distances:
39 37 0.23
40 115 0.72
41 8 0.05
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
Found at i:40895004 original size:41 final size:41
Alignment explanation
Indices: 40894927--40895004 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
40894917 TTAGTATCTC
* * *
40894927 GCACAAAGGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAAGGCCTTCGGATCTTAGCCCGGACACATTCACTTA
40894968 GCACAAA-GCCTTCGGGA-CTTAGCCCGGACAGCATTCA
1 GCACAAAGGCCTTC-GGATCTTAGCCCGGACA-CATTCA
40895005 ATTAATCATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 17 0.53
41 15 0.47
ACGTcount: A:0.27, C:0.28, G:0.22, T:0.23
Consensus pattern (41 bp):
GCACAAAGGCCTTCGGATCTTAGCCCGGACACATTCACTTA
Done.