Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr5
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: 55438857
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1812582 characters in sequence are not A, C, G, or T
File 166 of 167
Found at i:54876195 original size:27 final size:26
Alignment explanation
Indices: 54876153--54876254 Score: 132
Period size: 27 Copynumber: 3.8 Consensus size: 26
54876143 GCTCAGTTAT
* *
54876153 CAGATATTGTGACAGAGTCACCAGATA
1 CAGATATTGTGGCAGAGCCACCAGA-A
54876180 CAGATATTGTGGCAGAGCCACCAGAA
1 CAGATATTGTGGCAGAGCCACCAGAA
*
54876206 CAGATATTTGTGGCATAGCCACCAGAAA
1 CAGATA-TTGTGGCAGAGCCACCAG-AA
* *
54876234 CAGATAATGTGGCAAAGCCAC
1 CAGATATTGTGGCAGAGCCAC
54876255 TTAACAGAAT
Statistics
Matches: 68, Mismatches: 5, Indels: 4
0.88 0.06 0.05
Matches are distributed among these distances:
26 7 0.10
27 53 0.78
28 8 0.12
ACGTcount: A:0.36, C:0.22, G:0.24, T:0.19
Consensus pattern (26 bp):
CAGATATTGTGGCAGAGCCACCAGAA
Found at i:54876441 original size:22 final size:22
Alignment explanation
Indices: 54876413--54876477 Score: 69
Period size: 22 Copynumber: 3.0 Consensus size: 22
54876403 GCAAATACGT
*
54876413 TTGGCACACAACCATAATCAGG
1 TTGGCACAAAACCATAATCAGG
* * *
54876435 TTGGCACAGAGCCAT-ATGTAGG
1 TTGGCACAAAACCATAAT-CAGG
*
54876457 TTGACACAAAACCATAATCAG
1 TTGGCACAAAACCATAATCAG
54876478 AAGGCTTTAA
Statistics
Matches: 34, Mismatches: 7, Indels: 4
0.76 0.16 0.09
Matches are distributed among these distances:
21 2 0.06
22 30 0.88
23 2 0.06
ACGTcount: A:0.37, C:0.23, G:0.20, T:0.20
Consensus pattern (22 bp):
TTGGCACAAAACCATAATCAGG
Found at i:54876953 original size:27 final size:27
Alignment explanation
Indices: 54876905--54877145 Score: 272
Period size: 27 Copynumber: 9.0 Consensus size: 27
54876895 GGGCAAAATG
* * * *
54876905 GTAATTTTACCCCACA-AGGTATCTCA
1 GTAATTCTACCCTACAGGGGTATTTCA
* * * *
54876931 ATAATTCCACCTTACAGGGGTATTTTA
1 GTAATTCTACCCTACAGGGGTATTTCA
54876958 GTAATTCTACCCTACAGGGGTATTTC-
1 GTAATTCTACCCTACAGGGGTATTTCA
* *
54876984 GATAATTCTACCTTACAGGGGTATTAC-
1 G-TAATTCTACCCTACAGGGGTATTTCA
*
54877011 GATAATTCTACCCTACAGGGGTATTTCG
1 G-TAATTCTACCCTACAGGGGTATTTCA
* * * * *
54877039 GCAATTTTACCTTATAGGGGTATTTTA
1 GTAATTCTACCCTACAGGGGTATTTCA
*
54877066 GTAATTCTACCCTATAGGGGTATTTCA
1 GTAATTCTACCCTACAGGGGTATTTCA
* *
54877093 GTAATTCTACCCTACAGGGGTATTCCG
1 GTAATTCTACCCTACAGGGGTATTTCA
54877120 GTAATTCTACCCTACAGGGGTATTTC
1 GTAATTCTACCCTACAGGGGTATTTC
54877146 GATATTTTAC
Statistics
Matches: 182, Mismatches: 30, Indels: 5
0.84 0.14 0.02
Matches are distributed among these distances:
26 12 0.07
27 169 0.93
28 1 0.01
ACGTcount: A:0.26, C:0.21, G:0.18, T:0.35
Consensus pattern (27 bp):
GTAATTCTACCCTACAGGGGTATTTCA
Found at i:54876990 original size:54 final size:54
Alignment explanation
Indices: 54876905--54877149 Score: 300
Period size: 54 Copynumber: 4.6 Consensus size: 54
54876895 GGGCAAAATG
* * * * * *
54876905 GTAATTTTACCCCACA-AGGTATCTCAATAATTCCACCTTACAGGGGTATTTTA
1 GTAATTCTACCCTACAGGGGTATTTCGATAATTCTACCTTACAGGGGTATTTTA
54876958 GTAATTCTACCCTACAGGGGTATTTCGATAATTCTACCTTACAGGGGTA--TTA
1 GTAATTCTACCCTACAGGGGTATTTCGATAATTCTACCTTACAGGGGTATTTTA
** * *
54877010 CGATAATTCTACCCTACAGGGGTATTTCGGCAATTTTACCTTATAGGGGTATTTTA
1 -G-TAATTCTACCCTACAGGGGTATTTCGATAATTCTACCTTACAGGGGTATTTTA
* * ***
54877066 GTAATTCTACCCTATAGGGGTATTTC-AGTAATTCTACCCTACAGGGGTATTCCG
1 GTAATTCTACCCTACAGGGGTATTTCGA-TAATTCTACCTTACAGGGGTATTTTA
54877120 GTAATTCTACCCTACAGGGGTATTTCGATA
1 GTAATTCTACCCTACAGGGGTATTTCGATA
54877150 TTTTACAAAT
Statistics
Matches: 165, Mismatches: 20, Indels: 13
0.83 0.10 0.07
Matches are distributed among these distances:
52 3 0.02
53 15 0.09
54 142 0.86
55 2 0.01
56 3 0.02
ACGTcount: A:0.27, C:0.20, G:0.18, T:0.35
Consensus pattern (54 bp):
GTAATTCTACCCTACAGGGGTATTTCGATAATTCTACCTTACAGGGGTATTTTA
Found at i:54877111 original size:108 final size:108
Alignment explanation
Indices: 54876939--54877146 Score: 355
Period size: 108 Copynumber: 1.9 Consensus size: 108
54876929 CAATAATTCC
*
54876939 ACCTTACAGGGGTATTTTAGTAATTCTACCCTACAGGGGTATTTCGATAATTCTACCTTACAGGG
1 ACCTTACAGGGGTATTTTAGTAATTCTACCCTACAGGGGTATTTCGATAATTCTACCCTACAGGG
54877004 GTATTACGATAATTCTACCCTACAGGGGTATTTCGGCAATTTT
66 GTATTACGATAATTCTACCCTACAGGGGTATTTCGGCAATTTT
* *
54877047 ACCTTATAGGGGTATTTTAGTAATTCTACCCTATAGGGGTATTTC-AGTAATTCTACCCTACAGG
1 ACCTTACAGGGGTATTTTAGTAATTCTACCCTACAGGGGTATTTCGA-TAATTCTACCCTACAGG
* *
54877111 GGTATTCCGGTAATTCTACCCTACAGGGGTATTTCG
65 GGTATTACGATAATTCTACCCTACAGGGGTATTTCG
54877147 ATATTTTACA
Statistics
Matches: 94, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
107 1 0.01
108 93 0.99
ACGTcount: A:0.25, C:0.20, G:0.20, T:0.35
Consensus pattern (108 bp):
ACCTTACAGGGGTATTTTAGTAATTCTACCCTACAGGGGTATTTCGATAATTCTACCCTACAGGG
GTATTACGATAATTCTACCCTACAGGGGTATTTCGGCAATTTT
Found at i:54877196 original size:27 final size:27
Alignment explanation
Indices: 54877134--54877287 Score: 154
Period size: 27 Copynumber: 5.8 Consensus size: 27
54877124 TTCTACCCTA
* *
54877134 CAGGGGTATTTCGAT-ATTTTACAAAT
1 CAGGGGTATTTTGGTAATTTTACAAAT
** * *
54877160 C-GAGAATATTTTGATAATTTCACAAAT
1 CAG-GGGTATTTTGGTAATTTTACAAAT
*
54877187 CAGGGGTATTTTGGTAATTTTACAAGT
1 CAGGGGTATTTTGGTAATTTTACAAAT
*
54877214 TAGGGGTATTTTGGTAATTTTACAAA-
1 CAGGGGTATTTTGGTAATTTTACAAAT
**
54877240 CTAGGGGTATTTTGGTAATTTTACTGAT
1 C-AGGGGTATTTTGGTAATTTTACAAAT
* *
54877268 -TGAGGTATTTTGGTAATTTT
1 CAGGGGTATTTTGGTAATTTT
54877288 GTAAACTAAG
Statistics
Matches: 107, Mismatches: 16, Indels: 10
0.80 0.12 0.08
Matches are distributed among these distances:
25 1 0.01
26 28 0.26
27 77 0.72
28 1 0.01
ACGTcount: A:0.29, C:0.07, G:0.21, T:0.43
Consensus pattern (27 bp):
CAGGGGTATTTTGGTAATTTTACAAAT
Found at i:54877294 original size:53 final size:54
Alignment explanation
Indices: 54877166--54877304 Score: 176
Period size: 54 Copynumber: 2.6 Consensus size: 54
54877156 AAATCGAGAA
* * *
54877166 TATTTTGATAATTTCACAAA-TCAGGGGTATTTTGGTAATTTTACAAGTTAGGGG
1 TATTTTGGTAATTTTACAAACT-AGGGGTATTTTGGTAATTTTACAAGTTAGAGG
*
54877220 TATTTTGGTAATTTTACAAACTAGGGGTATTTTGGTAATTTTAC-TGATT-GAGG
1 TATTTTGGTAATTTTACAAACTAGGGGTATTTTGGTAATTTTACAAG-TTAGAGG
** *
54877273 TATTTTGGTAATTTTGTAAACTAAGGGTATTT
1 TATTTTGGTAATTTTACAAACTAGGGGTATTT
54877305 CAATAAGTTT
Statistics
Matches: 76, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
53 33 0.43
54 42 0.55
55 1 0.01
ACGTcount: A:0.28, C:0.06, G:0.22, T:0.45
Consensus pattern (54 bp):
TATTTTGGTAATTTTACAAACTAGGGGTATTTTGGTAATTTTACAAGTTAGAGG
Found at i:54877581 original size:27 final size:27
Alignment explanation
Indices: 54877316--54877574 Score: 401
Period size: 27 Copynumber: 9.6 Consensus size: 27
54877306 AATAAGTTTG
* * *
54877316 TAAATCGAGGATAAAACGGTAATTCTG
1 TAAATCGAGGGTAAAACAGTAATTCTA
*
54877343 TAAATCGAGGGTAAAACGGTAATTCTA
1 TAAATCGAGGGTAAAACAGTAATTCTA
*
54877370 TAAATCGAGGGTAAAATAGTAATTCTA
1 TAAATCGAGGGTAAAACAGTAATTCTA
*
54877397 TAAATCGAGGGTAAAACAATAATTCTA
1 TAAATCGAGGGTAAAACAGTAATTCTA
* *
54877424 TAAATCGAGGGTAAAATAGTAATTCTG
1 TAAATCGAGGGTAAAACAGTAATTCTA
54877451 TAAATCGAGGGTAAAACAGTAATTCTA
1 TAAATCGAGGGTAAAACAGTAATTCTA
* *
54877478 TAAATCGAGGGTAAAATAGTAATTCTG
1 TAAATCGAGGGTAAAACAGTAATTCTA
*
54877505 TAAATCGAGGGTAAAATAGTAATTCTA
1 TAAATCGAGGGTAAAACAGTAATTCTA
*
54877532 TAAATCGAGGGTAAAACAGTAATTCTG
1 TAAATCGAGGGTAAAACAGTAATTCTA
*
54877559 TAAATCGATGGTAAAA
1 TAAATCGAGGGTAAAA
54877575 TGGTAATCCT
Statistics
Matches: 215, Mismatches: 17, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 215 1.00
ACGTcount: A:0.43, C:0.09, G:0.20, T:0.27
Consensus pattern (27 bp):
TAAATCGAGGGTAAAACAGTAATTCTA
Found at i:54877619 original size:27 final size:27
Alignment explanation
Indices: 54877589--54877680 Score: 96
Period size: 27 Copynumber: 3.4 Consensus size: 27
54877579 AATCCTATCT
*
54877589 TATTTCAGTAATTTTACAAATCGAGGA
1 TATTTCAGTAATTTTACAAATCGAGGG
** * *
54877616 TATTTGGGTAATTTTATAAATCGGGGG
1 TATTTCAGTAATTTTACAAATCGAGGG
* * *
54877643 TACTTT-GGTAATTTTACAAGTCCAGGG
1 TA-TTTCAGTAATTTTACAAATCGAGGG
54877670 TATTTCAGTAA
1 TATTTCAGTAA
54877681 CTTGGTAAAC
Statistics
Matches: 53, Mismatches: 10, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
26 3 0.06
27 47 0.89
28 3 0.06
ACGTcount: A:0.30, C:0.10, G:0.21, T:0.39
Consensus pattern (27 bp):
TATTTCAGTAATTTTACAAATCGAGGG
Found at i:54887457 original size:49 final size:49
Alignment explanation
Indices: 54887384--54887481 Score: 178
Period size: 49 Copynumber: 2.0 Consensus size: 49
54887374 TTATGTATGA
*
54887384 AAAGTCATTGGTTATATACCTGTTATACACATGAAAAATAAGATTCACT
1 AAAGTCATTGGTTATATACATGTTATACACATGAAAAATAAGATTCACT
*
54887433 AAAGTCATTGGTTATATACATGTTATATACATGAAAAATAAGATTCACT
1 AAAGTCATTGGTTATATACATGTTATACACATGAAAAATAAGATTCACT
54887482 CTCAAAGTTT
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
49 47 1.00
ACGTcount: A:0.42, C:0.12, G:0.12, T:0.34
Consensus pattern (49 bp):
AAAGTCATTGGTTATATACATGTTATACACATGAAAAATAAGATTCACT
Found at i:54895527 original size:30 final size:30
Alignment explanation
Indices: 54895491--54895572 Score: 110
Period size: 30 Copynumber: 2.7 Consensus size: 30
54895481 CATGACACAT
* *
54895491 GGGCGTGTGGCCTACCCGTGTGTTTAACAC
1 GGGCGTGTGGCCTACCCGTGTGTCTAACAA
*
54895521 GGGCGTGTGACCTACCCGTGTGTCTAACAA
1 GGGCGTGTGGCCTACCCGTGTGTCTAACAA
* **
54895551 GGGTGTGTGGATTACCCGTGTG
1 GGGCGTGTGGCCTACCCGTGTG
54895573 GAAGTGCCTA
Statistics
Matches: 45, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 45 1.00
ACGTcount: A:0.15, C:0.23, G:0.35, T:0.27
Consensus pattern (30 bp):
GGGCGTGTGGCCTACCCGTGTGTCTAACAA
Found at i:54908940 original size:27 final size:28
Alignment explanation
Indices: 54908910--54908966 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 28
54908900 TTTGTGTATT
*
54908910 TGTGAAA-GAGGGACTAAATTGTAAAAA
1 TGTGAAACGAGGGACTAAAGTGTAAAAA
* *
54908937 TGTGAAACTTAGGGGCTAAAGTGTAAAAA
1 TGTGAAAC-GAGGGACTAAAGTGTAAAAA
54908966 T
1 T
54908967 TCCCAAATAG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 7 0.28
29 18 0.72
ACGTcount: A:0.44, C:0.05, G:0.26, T:0.25
Consensus pattern (28 bp):
TGTGAAACGAGGGACTAAAGTGTAAAAA
Found at i:54909400 original size:43 final size:42
Alignment explanation
Indices: 54909318--54909473 Score: 154
Period size: 43 Copynumber: 3.7 Consensus size: 42
54909308 TGTGACTACA
* * *
54909318 TGTAAGACCATGTCTGGGACATTGGCATTGTATTTTGATTACG
1 TGTAAGACCATGTCTGGGATATTGGCATCGTA-TATGATTACG
* *
54909361 TGTAAGACCATGTCTGGGATATTGGCACCGTTATATGATTTCG
1 TGTAAGACCATGTCTGGGATATTGGCATCG-TATATGATTACG
* * * * * *
54909404 TGTAAGA-CACTGTTTAGGATAGTGGCATCGATATGTGATAACA
1 TGTAAGACCA-TGTCTGGGATATTGGCATCG-TATATGATTACG
*
54909447 TGTAAGACCATATCTGGGATA-TGGCAT
1 TGTAAGACCATGTCTGGGATATTGGCAT
54909474 TGTACGAGCT
Statistics
Matches: 93, Mismatches: 17, Indels: 7
0.79 0.15 0.06
Matches are distributed among these distances:
42 8 0.09
43 81 0.87
44 4 0.04
ACGTcount: A:0.27, C:0.14, G:0.26, T:0.33
Consensus pattern (42 bp):
TGTAAGACCATGTCTGGGATATTGGCATCGTATATGATTACG
Found at i:54909633 original size:22 final size:22
Alignment explanation
Indices: 54909608--54909652 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
54909598 AGTATTTGAA
54909608 AAGGGAAGTATTTGATGAACTC
1 AAGGGAAGTATTTGATGAACTC
54909630 AAGGGAAGTATTTGATGAACTC
1 AAGGGAAGTATTTGATGAACTC
54909652 A
1 A
54909653 CTTACGAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.38, C:0.09, G:0.27, T:0.27
Consensus pattern (22 bp):
AAGGGAAGTATTTGATGAACTC
Found at i:54911699 original size:18 final size:18
Alignment explanation
Indices: 54911654--54911699 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 18
54911644 ATGCTAGAAC
54911654 TTATATG-TTTAATATTA
1 TTATATGATTTAATATTA
* *
54911671 -TAAATGTATTTAATTTTA
1 TTATATG-ATTTAATATTA
54911689 TTATATGATTT
1 TTATATGATTT
54911700 TTTTTCTTAC
Statistics
Matches: 23, Mismatches: 3, Indels: 5
0.74 0.10 0.16
Matches are distributed among these distances:
16 5 0.22
18 13 0.57
19 5 0.22
ACGTcount: A:0.35, C:0.00, G:0.07, T:0.59
Consensus pattern (18 bp):
TTATATGATTTAATATTA
Found at i:54913138 original size:13 final size:13
Alignment explanation
Indices: 54913115--54913143 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
54913105 TTTGCTTATA
54913115 TTTGTTGCTTGTG
1 TTTGTTGCTTGTG
54913128 TTTGTTGCTTGTG
1 TTTGTTGCTTGTG
54913141 TTT
1 TTT
54913144 TAGATCCTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.00, C:0.07, G:0.28, T:0.66
Consensus pattern (13 bp):
TTTGTTGCTTGTG
Found at i:54915140 original size:40 final size:40
Alignment explanation
Indices: 54915076--54915176 Score: 134
Period size: 40 Copynumber: 2.6 Consensus size: 40
54915066 ATACGGTACC
* *
54915076 ACTTGGTGTGTAGGGTTGGATGGGTCGATTTTATCCCCAT
1 ACTTGGTGTGTAGGGCTGGATGGGTCGATTTCATCCCCAT
*
54915116 ACTTGGTGTGTAGGGCTGGGTGGGTCGATTTCATCCCC--
1 ACTTGGTGTGTAGGGCTGGATGGGTCGATTTCATCCCCAT
* * *
54915154 ACATGGTGTGTTGGGTTGGATGG
1 ACTTGGTGTGTAGGGCTGGATGG
54915177 AGATGGTGTC
Statistics
Matches: 54, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
38 19 0.35
40 35 0.65
ACGTcount: A:0.13, C:0.15, G:0.38, T:0.35
Consensus pattern (40 bp):
ACTTGGTGTGTAGGGCTGGATGGGTCGATTTCATCCCCAT
Found at i:54928635 original size:13 final size:13
Alignment explanation
Indices: 54928617--54928642 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
54928607 AGAGGACGAC
54928617 GCACACGGGCGTG
1 GCACACGGGCGTG
54928630 GCACACGGGCGTG
1 GCACACGGGCGTG
54928643 TCCCTGCCGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.31, G:0.46, T:0.08
Consensus pattern (13 bp):
GCACACGGGCGTG
Found at i:54933542 original size:7 final size:6
Alignment explanation
Indices: 54933511--54933540 Score: 51
Period size: 6 Copynumber: 4.8 Consensus size: 6
54933501 TTCAAACTAC
54933511 TTTTTA TTTTTTA TTTTTA TTTTTA TTTTT
1 TTTTTA -TTTTTA TTTTTA TTTTTA TTTTT
54933541 TAGCATATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 17 0.74
7 6 0.26
ACGTcount: A:0.13, C:0.00, G:0.00, T:0.87
Consensus pattern (6 bp):
TTTTTA
Found at i:54941498 original size:13 final size:13
Alignment explanation
Indices: 54941480--54941508 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
54941470 CTAGCTATGT
54941480 TTTGTTCTTGATA
1 TTTGTTCTTGATA
54941493 TTTGTTCTTGATA
1 TTTGTTCTTGATA
54941506 TTT
1 TTT
54941509 AGTCTATATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.14, C:0.07, G:0.14, T:0.66
Consensus pattern (13 bp):
TTTGTTCTTGATA
Found at i:54951914 original size:16 final size:16
Alignment explanation
Indices: 54951893--54951929 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
54951883 GTAGATTGGT
54951893 AAAAGTCGAAATGCCG
1 AAAAGTCGAAATGCCG
*
54951909 AAAAGTCGAAATGTCG
1 AAAAGTCGAAATGCCG
54951925 AAAAG
1 AAAAG
54951930 CCAAAAGTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.49, C:0.14, G:0.24, T:0.14
Consensus pattern (16 bp):
AAAAGTCGAAATGCCG
Found at i:54952062 original size:19 final size:18
Alignment explanation
Indices: 54952040--54952076 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
54952030 TGAATAGGCC
54952040 AAATGGGCCAGAATGGGCT
1 AAATGGGCCAGAA-GGGCT
*
54952059 AAATGGGCCCGAAGGGCT
1 AAATGGGCCAGAAGGGCT
54952077 GTTGGGCCCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.30, C:0.19, G:0.38, T:0.14
Consensus pattern (18 bp):
AAATGGGCCAGAAGGGCT
Found at i:54952226 original size:29 final size:29
Alignment explanation
Indices: 54952145--54952291 Score: 149
Period size: 29 Copynumber: 5.2 Consensus size: 29
54952135 GTGAGCATGA
* **
54952145 ATAT-AATGTGATTTGGGCAGGATGGGCC
1 ATATGAATGTGAATTGGGCCTGATGGGCC
* * *
54952173 ATATAAATGAG-ATTGGGCCTAATGGGCC
1 ATATGAATGTGAATTGGGCCTGATGGGCC
*
54952201 ATATGAATGTGAATTGGGCCTGATGGGTC
1 ATATGAATGTGAATTGGGCCTGATGGGCC
* *
54952230 ATATGAACGTGAATTGGGCCCGATGGGCC
1 ATATGAATGTGAATTGGGCCTGATGGGCC
* * *
54952259 ATATAAATGAG-ATTGGGCCT-AGTTGGCC
1 ATATGAATGTGAATTGGGCCTGA-TGGGCC
54952287 ATATG
1 ATATG
54952292 CAAGTATGTA
Statistics
Matches: 98, Mismatches: 18, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
27 1 0.01
28 43 0.44
29 54 0.55
ACGTcount: A:0.27, C:0.14, G:0.32, T:0.27
Consensus pattern (29 bp):
ATATGAATGTGAATTGGGCCTGATGGGCC
Found at i:54954428 original size:40 final size:40
Alignment explanation
Indices: 54954352--54954495 Score: 213
Period size: 40 Copynumber: 3.6 Consensus size: 40
54954342 CAAACCCAAG
*
54954352 TACCTTCGGGATTTAG-CCGGATATAG-CAACTCGCACAAA
1 TACCTTCGGGATTTAGCCCGGATATAGTC-ACTAGCACAAA
54954391 TACCTTCGGG-TCTTAGCCCGGATATAGTCACTAGCACAAA
1 TACCTTCGGGAT-TTAGCCCGGATATAGTCACTAGCACAAA
*
54954431 TGCCTTCGGGATTTAGCCCGGATATAGTCACTAGCACAAA
1 TACCTTCGGGATTTAGCCCGGATATAGTCACTAGCACAAA
* *
54954471 TGCCTTCGGGACTTAGCCCGGATAT
1 TACCTTCGGGATTTAGCCCGGATAT
54954496 CATTCGAATA
Statistics
Matches: 98, Mismatches: 3, Indels: 7
0.91 0.03 0.06
Matches are distributed among these distances:
38 1 0.01
39 14 0.14
40 81 0.83
41 2 0.02
ACGTcount: A:0.26, C:0.26, G:0.22, T:0.25
Consensus pattern (40 bp):
TACCTTCGGGATTTAGCCCGGATATAGTCACTAGCACAAA
Found at i:54963338 original size:31 final size:31
Alignment explanation
Indices: 54963298--54963371 Score: 121
Period size: 31 Copynumber: 2.4 Consensus size: 31
54963288 GTGCCCCAAG
*
54963298 CCACCCGGGCGTGTGAGTCTACACAGCCCAT
1 CCACACGGGCGTGTGAGTCTACACAGCCCAT
54963329 CCACACGGGCGTGTGAGTCTACACAGCCCAT
1 CCACACGGGCGTGTGAGTCTACACAGCCCAT
* *
54963360 CTACACGAGCGT
1 CCACACGGGCGT
54963372 TGACACTTTA
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 40 1.00
ACGTcount: A:0.22, C:0.36, G:0.26, T:0.16
Consensus pattern (31 bp):
CCACACGGGCGTGTGAGTCTACACAGCCCAT
Found at i:54973764 original size:29 final size:29
Alignment explanation
Indices: 54973680--54973822 Score: 139
Period size: 29 Copynumber: 5.0 Consensus size: 29
54973670 GTGAGCATGA
* **
54973680 ATAT-AATGTGATTTGGGCCGGATGGGCC
1 ATATAAATGTGAATTGGGCCTAATGGGCC
* *
54973708 ATATAAATGAG-ATTGGGCCTAATAGGCC
1 ATATAAATGTGAATTGGGCCTAATGGGCC
* *
54973736 ATATGAATGTGAATTGGGCCTGATGGGCC
1 ATATAAATGTGAATTGGGCCTAATGGGCC
* * * *
54973765 ATATGAACGTGAATTGGGTCAAATGGGCC
1 ATATAAATGTGAATTGGGCCTAATGGGCC
* * *
54973794 ATATAAATGAG-ATTCGGCCTAGTGGGCC
1 ATATAAATGTGAATTGGGCCTAATGGGCC
54973822 A
1 A
54973823 CATGCAGGTA
Statistics
Matches: 93, Mismatches: 20, Indels: 4
0.79 0.17 0.03
Matches are distributed among these distances:
28 40 0.43
29 53 0.57
ACGTcount: A:0.29, C:0.15, G:0.31, T:0.26
Consensus pattern (29 bp):
ATATAAATGTGAATTGGGCCTAATGGGCC
Found at i:54973813 original size:57 final size:57
Alignment explanation
Indices: 54973695--54973822 Score: 136
Period size: 57 Copynumber: 2.2 Consensus size: 57
54973685 ATGTGATTTG
* * * * *
54973695 GGCCGGATGGGCCATATAAATGAGATTGGGCCTAATAGGCCATATGAATGTGAATTG
1 GGCCTGATGGGCCATATAAATGAGATTGGGCCAAATAGGCCATATAAATGAGAATTC
* * *
54973752 GGCCTGATGGGCCATATGAACGTGA-ATTGGGTCAAATGGGCCATATAAATGAG-ATTC
1 GGCCTGATGGGCCATAT-AA-ATGAGATTGGGCCAAATAGGCCATATAAATGAGAATTC
54973809 GGCCT-AGTGGGCCA
1 GGCCTGA-TGGGCCA
54973823 CATGCAGGTA
Statistics
Matches: 60, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
56 1 0.02
57 31 0.52
58 25 0.42
59 3 0.05
ACGTcount: A:0.28, C:0.16, G:0.32, T:0.23
Consensus pattern (57 bp):
GGCCTGATGGGCCATATAAATGAGATTGGGCCAAATAGGCCATATAAATGAGAATTC
Found at i:54975372 original size:14 final size:14
Alignment explanation
Indices: 54975349--54975378 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
54975339 TGTATTCATG
*
54975349 ATGTTTATAAGTTT
1 ATGTTAATAAGTTT
54975363 ATGTTAATAAGTTT
1 ATGTTAATAAGTTT
54975377 AT
1 AT
54975379 TTGTATATGG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.33, C:0.00, G:0.13, T:0.53
Consensus pattern (14 bp):
ATGTTAATAAGTTT
Found at i:54975690 original size:232 final size:232
Alignment explanation
Indices: 54975284--54975733 Score: 801
Period size: 232 Copynumber: 1.9 Consensus size: 232
54975274 TTTGAGAACA
*
54975284 TATGAATTATAGGTAAATCATGTGATATAAGTTAGTATCTTGGTCATAAAGTACATGTATTCATG
1 TATGAATTATAGGTAAACCATGTGATATAAGTTAGTATCTTGGTCATAAAGTACATGTATTCATG
*
54975349 ATGTTTATAAGTTTATGTTAATAAGTTTATTTGTATATGGCTTACTAAGCTTTTGAAAGCTTACT
66 ATGTTTATAAGTATATGTTAATAAGTTTATTTGTATATGGCTTACTAAGCTTTTGAAAGCTTACT
*
54975414 CTATGTATATTTGCATTGTTTTATAGATATCGAAGTTACTGTGAGCTCAGGGATCATCGAGGATC
131 CTATGTATATTTGCATTGTTTTATAGATATCGAAGCTACTGTGAGCTCAGGGATCATCGAGGATC
54975479 ATCACCACACTATCGAACCTTATAATTCATATGTTAG
196 ATCACCACACTATCGAACCTTATAATTCATATGTTAG
*
54975516 TATGAATTATAGGTAAACCATGTGATATATGTTAGTATCTTGGTCATAAAGTACATGTATTCATG
1 TATGAATTATAGGTAAACCATGTGATATAAGTTAGTATCTTGGTCATAAAGTACATGTATTCATG
*
54975581 ATGTTTATAAGTATATGTTGATAAGTTTATTTGTATATGGCTTACTAAGCTTTTGAAAGCTTACT
66 ATGTTTATAAGTATATGTTAATAAGTTTATTTGTATATGGCTTACTAAGCTTTTGAAAGCTTACT
* * * *
54975646 CTATGTATGTTTGCATTGTTTTATTGATATCGAAGCTACTGTGAGCTCGGGGATCGTCGAGGATC
131 CTATGTATATTTGCATTGTTTTATAGATATCGAAGCTACTGTGAGCTCAGGGATCATCGAGGATC
* *
54975711 ATCACCACACTATTGAGCCTTAT
196 ATCACCACACTATCGAACCTTAT
54975734 TTTGGTACTT
Statistics
Matches: 207, Mismatches: 11, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
232 207 1.00
ACGTcount: A:0.30, C:0.12, G:0.18, T:0.40
Consensus pattern (232 bp):
TATGAATTATAGGTAAACCATGTGATATAAGTTAGTATCTTGGTCATAAAGTACATGTATTCATG
ATGTTTATAAGTATATGTTAATAAGTTTATTTGTATATGGCTTACTAAGCTTTTGAAAGCTTACT
CTATGTATATTTGCATTGTTTTATAGATATCGAAGCTACTGTGAGCTCAGGGATCATCGAGGATC
ATCACCACACTATCGAACCTTATAATTCATATGTTAG
Found at i:54976243 original size:21 final size:22
Alignment explanation
Indices: 54976217--54976257 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
54976207 GACACGGGCG
*
54976217 TGTGTCTC-AGCCGTGTGTGCC
1 TGTGTCTCTACCCGTGTGTGCC
54976238 TGTGTCTCTACCCGTGTGTG
1 TGTGTCTCTACCCGTGTGTG
54976258 ACACACGGCT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.05, C:0.27, G:0.32, T:0.37
Consensus pattern (22 bp):
TGTGTCTCTACCCGTGTGTGCC
Found at i:54978584 original size:26 final size:26
Alignment explanation
Indices: 54978555--54978628 Score: 107
Period size: 26 Copynumber: 2.9 Consensus size: 26
54978545 AGCTATGACT
*
54978555 AGTAAGCTCCTCCTTAGCTGATAGAC
1 AGTAAGCTCCTCCTGAGCTGATAGAC
*
54978581 AGTAAGCTCCTCCTGAGCTGATGGAC
1 AGTAAGCTCCTCCTGAGCTGATAGAC
54978607 AGTAAGCTCCAT--TGAGCTGATA
1 AGTAAGCTCC-TCCTGAGCTGATA
54978629 TATTAGTAAG
Statistics
Matches: 44, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
25 9 0.20
26 34 0.77
27 1 0.02
ACGTcount: A:0.27, C:0.24, G:0.23, T:0.26
Consensus pattern (26 bp):
AGTAAGCTCCTCCTGAGCTGATAGAC
Found at i:54984057 original size:16 final size:16
Alignment explanation
Indices: 54984036--54984070 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
54984026 GACAAAAGAA
*
54984036 AAATGCTGAAAAGCCG
1 AAATGCCGAAAAGCCG
54984052 AAATGCCGAAAAGCCG
1 AAATGCCGAAAAGCCG
54984068 AAA
1 AAA
54984071 GTTTGGCTGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.49, C:0.20, G:0.23, T:0.09
Consensus pattern (16 bp):
AAATGCCGAAAAGCCG
Found at i:54984323 original size:29 final size:28
Alignment explanation
Indices: 54984282--54984342 Score: 104
Period size: 29 Copynumber: 2.1 Consensus size: 28
54984272 ATGAGCATGA
54984282 ATATAAGGTGATTTGGGCCTAACGGGCC
1 ATATAAGGTGATTTGGGCCTAACGGGCC
*
54984310 ATATCAAGGTGATTTGGGCCTAATGGGCC
1 ATAT-AAGGTGATTTGGGCCTAACGGGCC
54984339 ATAT
1 ATAT
54984343 GAATATGAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
28 4 0.13
29 27 0.87
ACGTcount: A:0.26, C:0.16, G:0.30, T:0.28
Consensus pattern (28 bp):
ATATAAGGTGATTTGGGCCTAACGGGCC
Found at i:54984355 original size:29 final size:29
Alignment explanation
Indices: 54984294--54984375 Score: 101
Period size: 29 Copynumber: 2.8 Consensus size: 29
54984284 ATAAGGTGAT
* * ** *
54984294 TTGGGCCTAACGGGCCATATCAAGGTGAT
1 TTGGGCCTAATGGGCCATATGAATATGAA
54984323 TTGGGCCTAATGGGCCATATGAATATGAA
1 TTGGGCCTAATGGGCCATATGAATATGAA
* *
54984352 TTGGGCCTGATAGGCCATATGAAT
1 TTGGGCCTAATGGGCCATATGAAT
54984376 GAGATGGGCC
Statistics
Matches: 46, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 46 1.00
ACGTcount: A:0.27, C:0.17, G:0.29, T:0.27
Consensus pattern (29 bp):
TTGGGCCTAATGGGCCATATGAATATGAA
Found at i:54989154 original size:40 final size:40
Alignment explanation
Indices: 54989080--54989264 Score: 232
Period size: 40 Copynumber: 4.6 Consensus size: 40
54989070 AACCCAAGTA
* * *
54989080 CCTTCGGGATTTAG-CCGGATATAGCAACTCGCACACATG
1 CCTTCGGGACTTAGCCCGGATATAGCAACTAGCACAAATG
*
54989119 CCTTCGGGTCTTAGCCCGGATATAGTC-ACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAG-CAACTAGCACAAATG
* *
54989159 CCTTCGGGACTTAGCTCGGGTATAGCAACTACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGCAACTA---GCACAAATG
*
54989202 CCTTCGGGACTTCGCCCGGATATAGTC-ACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAG-CAACTAGCACAAATG
*
54989242 CCTACGGGACTTAGCCCGGATAT
1 CCTTCGGGACTTAGCCCGGATAT
54989265 CATCCGAATA
Statistics
Matches: 127, Mismatches: 12, Indels: 13
0.84 0.08 0.09
Matches are distributed among these distances:
39 13 0.10
40 77 0.61
41 1 0.01
43 35 0.28
44 1 0.01
ACGTcount: A:0.25, C:0.29, G:0.23, T:0.23
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGCAACTAGCACAAATG
Found at i:54989203 original size:83 final size:79
Alignment explanation
Indices: 54989080--54989264 Score: 271
Period size: 83 Copynumber: 2.3 Consensus size: 79
54989070 AACCCAAGTA
* * *
54989080 CCTTCGGGATTTAGCCGGATATAGCAACTCGCACACATGCCTTCGGGTCTTAGCCCGGATATAGT
1 CCTTCGGGACTTAGCCGGATATAGCAACTCGCACAAATGCCTTCGGGACTTAGCCCGGATATAGT
54989145 CACTAGCACAAATG
66 CACTAGCACAAATG
* *
54989159 CCTTCGGGACTTAGCTCGGGTATAGCAACTACTCGCACAAATGCCTTCGGGACTTCGCCCGGATA
1 CCTTCGGGACTTAGC-CGGATATAGC-A--ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATA
54989224 TAGTCACTAGCACAAATG
62 TAGTCACTAGCACAAATG
*
54989242 CCTACGGGACTTAGCCCGGATAT
1 CCTTCGGGACTTAG-CCGGATAT
54989265 CATCCGAATA
Statistics
Matches: 94, Mismatches: 7, Indels: 6
0.88 0.07 0.06
Matches are distributed among these distances:
79 14 0.15
80 9 0.10
81 1 0.01
83 69 0.73
84 1 0.01
ACGTcount: A:0.25, C:0.29, G:0.23, T:0.23
Consensus pattern (79 bp):
CCTTCGGGACTTAGCCGGATATAGCAACTCGCACAAATGCCTTCGGGACTTAGCCCGGATATAGT
CACTAGCACAAATG
Found at i:54995006 original size:33 final size:33
Alignment explanation
Indices: 54994969--54995042 Score: 130
Period size: 33 Copynumber: 2.2 Consensus size: 33
54994959 CTTGCTACCG
54994969 AAAACCCTATTCTCTTCAAGATCCAAAAAGCCA
1 AAAACCCTATTCTCTTCAAGATCCAAAAAGCCA
* *
54995002 AAAACCTTATTCTCTTCAAGATCCAAAAAGCCG
1 AAAACCCTATTCTCTTCAAGATCCAAAAAGCCA
54995035 AAAACCCT
1 AAAACCCT
54995043 TGCTTCTTTC
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 38 1.00
ACGTcount: A:0.42, C:0.30, G:0.07, T:0.22
Consensus pattern (33 bp):
AAAACCCTATTCTCTTCAAGATCCAAAAAGCCA
Found at i:54996043 original size:28 final size:29
Alignment explanation
Indices: 54995933--54996047 Score: 146
Period size: 29 Copynumber: 4.0 Consensus size: 29
54995923 GTAAGCACGA
* *
54995933 ATATGAATGTGA-CTGGGCCTAACGGGCC
1 ATATGAATGTGATTTGGGCCTAATGGGCC
*
54995961 ATATAAATGTGATTTGGGCCTAATGGGCC
1 ATATGAATGTGATTTGGGCCTAATGGGCC
*
54995990 ATAT-ACAGGTGATTTGGGCCTAATGGGCC
1 ATATGA-ATGTGATTTGGGCCTAATGGGCC
* *
54996019 ATATGAATATGA-TTGGGCTTAATGGGCC
1 ATATGAATGTGATTTGGGCCTAATGGGCC
54996047 A
1 A
54996048 GATACAGGTA
Statistics
Matches: 77, Mismatches: 7, Indels: 6
0.86 0.08 0.07
Matches are distributed among these distances:
28 28 0.36
29 48 0.62
30 1 0.01
ACGTcount: A:0.27, C:0.16, G:0.30, T:0.28
Consensus pattern (29 bp):
ATATGAATGTGATTTGGGCCTAATGGGCC
Found at i:54996055 original size:57 final size:58
Alignment explanation
Indices: 54995946--54996056 Score: 170
Period size: 57 Copynumber: 1.9 Consensus size: 58
54995936 TGAATGTGAC
* *
54995946 TGGGCCTAACGGGCCATATAAATGTGATTTGGGCCTAATGGGCCATATACAGGTGATT
1 TGGGCCTAACGGGCCATATAAATATGATTTGGGCCTAATGGGCCAGATACAGGTGATT
* * *
54996004 TGGGCCTAATGGGCCATATGAATATGA-TTGGGCTTAATGGGCCAGATACAGGT
1 TGGGCCTAACGGGCCATATAAATATGATTTGGGCCTAATGGGCCAGATACAGGT
54996057 ATGTGAAATT
Statistics
Matches: 48, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
57 24 0.50
58 24 0.50
ACGTcount: A:0.26, C:0.16, G:0.31, T:0.27
Consensus pattern (58 bp):
TGGGCCTAACGGGCCATATAAATATGATTTGGGCCTAATGGGCCAGATACAGGTGATT
Found at i:54997835 original size:40 final size:40
Alignment explanation
Indices: 54997798--54997878 Score: 119
Period size: 40 Copynumber: 2.0 Consensus size: 40
54997788 GCTACTCGTT
* *
54997798 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACATAACCCGGATT-TAATAACTCGCA
*
54997838 CAAATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCA
1 CAAATGCCTTCGGGACATAACCCGGATTTAATAACTCGCA
54997878 C
1 C
54997879 NNNNNNNNNN
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
40 35 0.95
41 2 0.05
ACGTcount: A:0.28, C:0.28, G:0.20, T:0.23
Consensus pattern (40 bp):
CAAATGCCTTCGGGACATAACCCGGATTTAATAACTCGCA
Found at i:54998389 original size:200 final size:200
Alignment explanation
Indices: 54998046--54998447 Score: 777
Period size: 200 Copynumber: 2.0 Consensus size: 200
54998036 TCGTATATCT
*
54998046 TCCATCCATAAAATTTCCAGAATTTTTGGCTTGGCCAATCAATACCAGATTTTTCTTAAAGTTTC
1 TCCATCCATAAAATTTCCAGAATTTTAGGCTTGGCCAATCAATACCAGATTTTTCTTAAAGTTTC
54998111 CCCTGTTTCACTGTTTGACTAATTTGACCACTCTTCACTACGAATCAAATTTCTCATTTTACAGA
66 CCCTGTTTCACTGTTTGACTAATTTGACCACTCTTCACTACGAATCAAATTTCTCATTTTACAGA
54998176 ATTCAAAATGTGTTGTATTTGATTTCATTTGAAACTAGACTCATTAAGGAGTCTAAGCATATAAA
131 ATTCAAAATGTGTTGTATTTGATTTCATTTGAAACTAGACTCATTAAGGAGTCTAAGCATATAAA
54998241 TTTTA
196 TTTTA
* *
54998246 TCCATCCATAAAATTTCCAGAATTTTAGGTTTGGCTAATCAATACCAGATTTTTCTTAAAGTTTC
1 TCCATCCATAAAATTTCCAGAATTTTAGGCTTGGCCAATCAATACCAGATTTTTCTTAAAGTTTC
54998311 CCCTGTTTCACTGTTTGACTAATTTGACCACTCTTCACTACGAATCAAATTTCTCATTTTACAGA
66 CCCTGTTTCACTGTTTGACTAATTTGACCACTCTTCACTACGAATCAAATTTCTCATTTTACAGA
54998376 ATTCAAAATGTGTTGTATTTGATTTCATTTGAAACTAGACTCATTAAGGAGTCTAAGCATATAAA
131 ATTCAAAATGTGTTGTATTTGATTTCATTTGAAACTAGACTCATTAAGGAGTCTAAGCATATAAA
54998441 TTTTA
196 TTTTA
54998446 TC
1 TC
54998448 TTATAACCAT
Statistics
Matches: 199, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
200 199 1.00
ACGTcount: A:0.31, C:0.19, G:0.11, T:0.39
Consensus pattern (200 bp):
TCCATCCATAAAATTTCCAGAATTTTAGGCTTGGCCAATCAATACCAGATTTTTCTTAAAGTTTC
CCCTGTTTCACTGTTTGACTAATTTGACCACTCTTCACTACGAATCAAATTTCTCATTTTACAGA
ATTCAAAATGTGTTGTATTTGATTTCATTTGAAACTAGACTCATTAAGGAGTCTAAGCATATAAA
TTTTA
Found at i:54999280 original size:51 final size:52
Alignment explanation
Indices: 54999214--54999323 Score: 195
Period size: 51 Copynumber: 2.1 Consensus size: 52
54999204 TCTTTTTCCA
*
54999214 TCTTTTTCTTTCTCCTATTCGGCCAAGAACAACATGAGAGCTTTTCTCTT-T
1 TCTTTTTCTTCCTCCTATTCGGCCAAGAACAACATGAGAGCTTTTCTCTTCT
54999265 TCTTTTTCTTCCTCCTATTCGGCCAAGAACAACATGAGAGCTTTTCTCTTCT
1 TCTTTTTCTTCCTCCTATTCGGCCAAGAACAACATGAGAGCTTTTCTCTTCT
*
54999317 TTTTTTT
1 TCTTTTT
54999324 TTCTTTTTTT
Statistics
Matches: 56, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
51 49 0.88
52 7 0.12
ACGTcount: A:0.18, C:0.25, G:0.11, T:0.45
Consensus pattern (52 bp):
TCTTTTTCTTCCTCCTATTCGGCCAAGAACAACATGAGAGCTTTTCTCTTCT
Found at i:54999472 original size:56 final size:56
Alignment explanation
Indices: 54999405--55000196 Score: 1575
Period size: 56 Copynumber: 14.1 Consensus size: 56
54999395 TATTAGTTTA
*
54999405 TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
1 TTGCCCATGCTTCTTATTTTATTTTTCCATTAACACAACATGTTTCATGACATGTT
54999461 TTGCCCATGCTTCTTATTTTATTTTTCCATTAACACAACATGTTTCATGACATGTT
1 TTGCCCATGCTTCTTATTTTATTTTTCCATTAACACAACATGTTTCATGACATGTT
54999517 TTGCCCATGCTTCTTATTTTATTTTTCCATTAACACAACATGTTTCATGACATGTT
1 TTGCCCATGCTTCTTATTTTATTTTTCCATTAACACAACATGTTTCATGACATGTT
54999573 TTGCCCATGCTTCTTATTTTATTTTTCCATTAACACAACATGTTTCATGACATGTT
1 TTGCCCATGCTTCTTATTTTATTTTTCCATTAACACAACATGTTTCATGACATGTT
54999629 TTGCCCATGCTTCTTATTTTATTTTTCCATTAACACAACATGTTTCATGACATGTT
1 TTGCCCATGCTTCTTATTTTATTTTTCCATTAACACAACATGTTTCATGACATGTT
54999685 TTGCCCATGCTTCTTATTTTATTTTTCCATTAACACAACATGTTTCATGACATGTT
1 TTGCCCATGCTTCTTATTTTATTTTTCCATTAACACAACATGTTTCATGACATGTT
54999741 TTGCCCATGCTTCTTATTTTATTTTTCCATTAACACAACATGTTTCATGACATGTT
1 TTGCCCATGCTTCTTATTTTATTTTTCCATTAACACAACATGTTTCATGACATGTT
54999797 TTGCCCATGCTTCTTATTTTATTTTTCCATTAACACAACATGTTTCATGACATGTT
1 TTGCCCATGCTTCTTATTTTATTTTTCCATTAACACAACATGTTTCATGACATGTT
54999853 TTGCCCATGCTTCTTATTTTATTTTTCCATTAACACAACATGTTTCATGACATGTT
1 TTGCCCATGCTTCTTATTTTATTTTTCCATTAACACAACATGTTTCATGACATGTT
54999909 TTGCCCATGCTTCTTATTTTATTTTTCCATTAACACAACATGTTTCATGACATGTT
1 TTGCCCATGCTTCTTATTTTATTTTTCCATTAACACAACATGTTTCATGACATGTT
54999965 TTGCCCATGCTTCTTATTTTATTTTTCCATTAACACAACATGTTTCATGACATGTT
1 TTGCCCATGCTTCTTATTTTATTTTTCCATTAACACAACATGTTTCATGACATGTT
55000021 TTGCCCATGCTTCTTATTTTATTTTTCCATTAACACAACATGTTTCATGACATGTT
1 TTGCCCATGCTTCTTATTTTATTTTTCCATTAACACAACATGTTTCATGACATGTT
55000077 TTGCCCATGCTTCTTATTTTATTTTTCCATTAACACAACATGTTTCATGACATGTT
1 TTGCCCATGCTTCTTATTTTATTTTTCCATTAACACAACATGTTTCATGACATGTT
55000133 TTGCCCATGCTTCTTATTTTATTTTTCCATTAACACAACATGTTTCATGACATGTT
1 TTGCCCATGCTTCTTATTTTATTTTTCCATTAACACAACATGTTTCATGACATGTT
55000189 TTGCCCAT
1 TTGCCCAT
55000197 CATCCCTTGT
Statistics
Matches: 735, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
56 735 1.00
ACGTcount: A:0.23, C:0.22, G:0.09, T:0.46
Consensus pattern (56 bp):
TTGCCCATGCTTCTTATTTTATTTTTCCATTAACACAACATGTTTCATGACATGTT
Found at i:55001508 original size:40 final size:40
Alignment explanation
Indices: 55001463--55001777 Score: 220
Period size: 40 Copynumber: 7.9 Consensus size: 40
55001453 CGAATACACG
* * *
55001463 TCACCAGCATGATTGCTCTTCGGGACCTAGCCCGGATATA
1 TCACCAGCACGAATGCTCTTCGGGACTTAGCCCGGATATA
* ** **
55001503 ACACCAGCACGAATGCTCTTCGGGGTTTAGCATGGATATA
1 TCACCAGCACGAATGCTCTTCGGGACTTAGCCCGGATATA
* * *
55001543 TCACTAGCACGAATGCTCTTCGGAACTTAGCCCGGATACA
1 TCACCAGCACGAATGCTCTTCGGGACTTAGCCCGGATATA
* * *
55001583 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGTTATA
1 TCACCAGCACGAATGCTCTTCGGGACTTAGCCCGGATATA
* * * * *
55001623 GTAACTC-GTACAAATGC-CTTCGGGACTTAACCCGGATTTA
1 -TCAC-CAGCACGAATGCTCTTCGGGACTTAGCCCGGATATA
* *
55001663 GTAACTC-GCACCAATGC-CTTCGGG-CTTAGCCCGGA-ATTA
1 -TCAC-CAGCACGAATGCTCTTCGGGACTTAGCCCGGATA-TA
* * * *
55001702 GTAACTC-GCACAAATGC-CTTC-GGATCTTAGTCCGGATATGG
1 -TCAC-CAGCACGAATGCTCTTCGGGA-CTTAGCCCGGATAT-A
* *
55001743 TCACTTAGCAC-AAAGC-CTTCGGGACTTAGCCCGGA
1 TCAC-CAGCACGAATGCTCTTCGGGACTTAGCCCGGA
55001778 CATCATTCGA
Statistics
Matches: 227, Mismatches: 39, Indels: 18
0.80 0.14 0.06
Matches are distributed among these distances:
38 2 0.01
39 32 0.14
40 175 0.77
41 18 0.08
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25
Consensus pattern (40 bp):
TCACCAGCACGAATGCTCTTCGGGACTTAGCCCGGATATA
Found at i:55001644 original size:80 final size:78
Alignment explanation
Indices: 55001480--55001776 Score: 258
Period size: 80 Copynumber: 3.7 Consensus size: 78
55001470 CATGATTGCT
* * * * * ** **
55001480 CTTCGGGACCTAGCCCGGATATAACACCAGCACGAATGCTCTTCGGGGTTTAGCATGGATATA-T
1 CTTCGGAACTTAGCCCGGATATATCACTAGCACCAATGC-CTTCGGGACTTAGCCCGG-TATAGT
* * *
55001544 CACTAGCACGAATGC
64 AACTCGCACAAATGC
* **
55001559 TCTTCGGAACTTAGCCCGGATACATCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGTTATAG
1 -CTTCGGAACTTAGCCCGGATATATCACTAGCACCAATGC-CTTCGGGACTTAGCCCGG-TATAG
*
55001624 TAACTCGTACAAATGC
63 TAACTCGCACAAATGC
* * * * * *
55001640 CTTCGGGACTTAACCCGGATTTAGTAACTCGCACCAATGCCTTCGGG-CTTAGCCCGGAATTAGT
1 CTTCGGAACTTAGCCCGGATATA-TCACTAGCACCAATGCCTTCGGGACTTAGCCCGGTA-TAGT
55001704 AACTCGCACAAATGC
64 AACTCGCACAAATGC
* * * *
55001719 CTTCGGATCTTAGTCCGGATATGGTCACTTAGCA-CAAAGCCTTCGGGACTTAGCCCGG
1 CTTCGGAACTTAGCCCGGATAT-ATCAC-TAGCACCAATGCCTTCGGGACTTAGCCCGG
55001777 ACATCATTCG
Statistics
Matches: 177, Mismatches: 34, Indels: 12
0.79 0.15 0.05
Matches are distributed among these distances:
78 1 0.01
79 60 0.34
80 92 0.52
81 24 0.14
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25
Consensus pattern (78 bp):
CTTCGGAACTTAGCCCGGATATATCACTAGCACCAATGCCTTCGGGACTTAGCCCGGTATAGTAA
CTCGCACAAATGC
Found at i:55001715 original size:79 final size:81
Alignment explanation
Indices: 55001549--55001777 Score: 229
Period size: 79 Copynumber: 2.9 Consensus size: 81
55001539 TATATCACTA
* * * * * *
55001549 GCACGAATGCTCTTCGGAACTTAGCCCGGATACA-TCAC-TAGCATGAATGCTCTTCGGGACTTA
1 GCACAAATGC-CTTCGGATCTTAACCCGGATATAGTAACTTAGCA-CAATGC-CTTCGGGACTTA
*
55001612 GCCCGG-TTATAGTAACTC
63 GCCCGGAATATAGTAACTC
* * *
55001630 GTACAAATGCCTTCGGGA-CTTAACCCGGATTTAGTAAC-TCGCACCAATGCCTTCGGG-CTTAG
1 GCACAAATGCCTTC-GGATCTTAACCCGGATATAGTAACTTAGCA-CAATGCCTTCGGGACTTAG
55001692 CCCGGAAT-TAGTAACTC
64 CCCGGAATATAGTAACTC
** * * *
55001709 GCACAAATGCCTTCGGATCTTAGTCCGGATATGGTCACTTAGCACAAAGCCTTCGGGACTTAGCC
1 GCACAAATGCCTTCGGATCTTAACCCGGATATAGTAACTTAGCACAATGCCTTCGGGACTTAGCC
55001774 CGGA
66 CGGA
55001778 CATCATTCGA
Statistics
Matches: 124, Mismatches: 18, Indels: 13
0.80 0.12 0.08
Matches are distributed among these distances:
78 3 0.02
79 59 0.48
80 39 0.31
81 23 0.19
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.25
Consensus pattern (81 bp):
GCACAAATGCCTTCGGATCTTAACCCGGATATAGTAACTTAGCACAATGCCTTCGGGACTTAGCC
CGGAATATAGTAACTC
Found at i:55029398 original size:79 final size:81
Alignment explanation
Indices: 55029262--55029446 Score: 236
Period size: 79 Copynumber: 2.3 Consensus size: 81
55029252 TTGAATGATG
*
55029262 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
55029326 TGTGCGAGATACTA-A
66 TGTGCGAGATACTATA
* * * **
55029341 TTCCGGGCTAAG-CCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCA
1 -TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCA
*
55029403 TTTGTGCGAGTTACTATA
64 TTTGTGCGAGATACTATA
* *
55029421 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
55029447 AACGAGTAGC
Statistics
Matches: 92, Mismatches: 9, Indels: 8
0.84 0.08 0.07
Matches are distributed among these distances:
78 1 0.01
79 58 0.63
80 33 0.36
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
TGTGCGAGATACTATA
Found at i:55029460 original size:40 final size:40
Alignment explanation
Indices: 55029263--55029446 Score: 216
Period size: 40 Copynumber: 4.6 Consensus size: 40
55029253 TGAATGATGT
* * * *
55029263 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTATAA
* * *
55029303 CCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTA-ATT
1 CCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTATA-A
55029343 CCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTA-AA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
55029381 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 -CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
55029422 CCGGGCTATGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTG
55029447 AACGAGTAGC
Statistics
Matches: 126, Mismatches: 11, Indels: 14
0.83 0.07 0.09
Matches are distributed among these distances:
39 35 0.28
40 81 0.64
41 10 0.08
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
Found at i:55029468 original size:79 final size:79
Alignment explanation
Indices: 55029315--55029479 Score: 210
Period size: 79 Copynumber: 2.1 Consensus size: 79
55029305 GGACTAAGAT
* **
55029315 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAA
1 CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
*
55029380 ATCCGGGTTAAGTC
66 ATCCGGGTTAAATC
* *
55029394 CCGAAGGCATTTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGC
1 CCGAAGGCATTTGTGCGAGATACTAAT-ACCGGGCTAAG-CCCGAAGGCATTTGAACGAGTTA-C
* *
55029457 TATATCC-GGTTAAATT
63 TAAATCCGGGTTAAATC
55029473 CCGAAGG
1 CCGAAGG
55029480 TACGTGATTT
Statistics
Matches: 75, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
78 2 0.03
79 48 0.64
80 25 0.33
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.25
Consensus pattern (79 bp):
CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
ATCCGGGTTAAATC
Found at i:55033141 original size:22 final size:22
Alignment explanation
Indices: 55033092--55033144 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
55033082 TACCTAAAGT
** * *
55033092 AGTTTCAGAGTATTCTAATCAT
1 AGTTTCAGACAATTCTAAACAG
*
55033114 ATTTTCAGACAATTCTAAACAG
1 AGTTTCAGACAATTCTAAACAG
55033136 AGTTTCAGA
1 AGTTTCAGA
55033145 AAACTTACAG
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.36, C:0.15, G:0.13, T:0.36
Consensus pattern (22 bp):
AGTTTCAGACAATTCTAAACAG
Found at i:55033773 original size:16 final size:17
Alignment explanation
Indices: 55033742--55033774 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
55033732 ATCCACAGAT
55033742 ATCAAACATACAGAATA
1 ATCAAACATACAGAATA
55033759 ATCAAACAT-CAGAATA
1 ATCAAACATACAGAATA
55033775 CACTCTGGGG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.58, C:0.18, G:0.06, T:0.18
Consensus pattern (17 bp):
ATCAAACATACAGAATA
Found at i:55035509 original size:21 final size:21
Alignment explanation
Indices: 55035485--55035524 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
55035475 AGGATGAAAT
*
55035485 TGAAAAGTGA-AATAAAAAAGA
1 TGAAAAATGATAA-AAAAAAGA
55035506 TGAAAAATGATAAAAAAAA
1 TGAAAAATGATAAAAAAAA
55035525 TAAAAATATC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 15 0.88
22 2 0.12
ACGTcount: A:0.70, C:0.00, G:0.15, T:0.15
Consensus pattern (21 bp):
TGAAAAATGATAAAAAAAAGA
Found at i:55035520 original size:19 final size:18
Alignment explanation
Indices: 55035496--55035531 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
55035486 GAAAAGTGAA
*
55035496 ATAAAAAAGATGAAAAATG
1 ATAAAAAAAAT-AAAAATG
55035515 ATAAAAAAAATAAAAAT
1 ATAAAAAAAATAAAAAT
55035532 ATCATCATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 6 0.38
19 10 0.62
ACGTcount: A:0.75, C:0.00, G:0.08, T:0.17
Consensus pattern (18 bp):
ATAAAAAAAATAAAAATG
Found at i:55042032 original size:28 final size:28
Alignment explanation
Indices: 55041998--55042054 Score: 105
Period size: 28 Copynumber: 2.0 Consensus size: 28
55041988 ATATACACTT
*
55041998 TCACATTCATCACATCGGCCATTAGGCC
1 TCACATTCATCACATCGGCCACTAGGCC
55042026 TCACATTCATCACATCGGCCACTAGGCC
1 TCACATTCATCACATCGGCCACTAGGCC
55042054 T
1 T
55042055 TATCACATAT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.25, C:0.37, G:0.14, T:0.25
Consensus pattern (28 bp):
TCACATTCATCACATCGGCCACTAGGCC
Found at i:55049310 original size:47 final size:47
Alignment explanation
Indices: 55049215--55049472 Score: 435
Period size: 47 Copynumber: 5.4 Consensus size: 47
55049205 NNNNNNNNNN
*
55049215 CACATATATACACTTTCACATTCATCACATCGGCCATTAGGGGCCTTAT
1 CACATATATACACTTTCACATTCATCACATCGGCCATT--CGGCCTTAT
*
55049264 CACATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTAT
1 CACATATATACACTTTCACATTCATCACATCGGCCATTCGGCCTTAT
*
55049311 CACATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTAT
1 CACATATATACACTTTCACATTCATCACATCGGCCATTCGGCCTTAT
55049358 CACATATATACACTTTCACATTCATCACATCGGCCATTCGGCCTTAT
1 CACATATATACACTTTCACATTCATCACATCGGCCATTCGGCCTTAT
* *
55049405 CACATATATACACTTTCACGTTCATCACATCGGCCATTAGGCCTTAT
1 CACATATATACACTTTCACATTCATCACATCGGCCATTCGGCCTTAT
* *
55049452 CACATATATATACATTCACAT
1 CACATATATACACTTTCACAT
55049473 CACAATTATC
Statistics
Matches: 201, Mismatches: 8, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
47 164 0.82
49 37 0.18
ACGTcount: A:0.29, C:0.29, G:0.09, T:0.33
Consensus pattern (47 bp):
CACATATATACACTTTCACATTCATCACATCGGCCATTCGGCCTTAT
Found at i:55049315 original size:22 final size:22
Alignment explanation
Indices: 55049287--55049362 Score: 64
Period size: 22 Copynumber: 3.3 Consensus size: 22
55049277 TTTCACATTC
55049287 ATCACATTGGCCATTCGGCCTT
1 ATCACATTGGCCATTCGGCCTT
** * * *
55049309 ATCACATATATACACTTTC-ACATT
1 ATCACAT-T-GGC-CATTCGGCCTT
55049333 CATCACATTGGCCATTCGGCCTT
1 -ATCACATTGGCCATTCGGCCTT
55049356 ATCACAT
1 ATCACAT
55049363 ATATACACTT
Statistics
Matches: 39, Mismatches: 10, Indels: 10
0.66 0.17 0.17
Matches are distributed among these distances:
22 18 0.46
23 5 0.13
24 5 0.13
25 11 0.28
ACGTcount: A:0.26, C:0.30, G:0.11, T:0.33
Consensus pattern (22 bp):
ATCACATTGGCCATTCGGCCTT
Found at i:55054029 original size:43 final size:42
Alignment explanation
Indices: 55053940--55054076 Score: 143
Period size: 42 Copynumber: 3.2 Consensus size: 42
55053930 AGGCTACACA
* * * * *
55053940 GAAGCACATAAGTGCTAAATAGAAACCCACA-AGGGTTAAACG
1 GAAGCTCATAAGAGCTAAACAGAAATCCA-ATAGGGTTAAACT
* * *
55053982 GAAGCTCATAAGAGCTGAACGGAAA-CCTAATAATGGTTAAACT
1 GAAGCTCATAAGAGCTAAACAGAAATCC-AAT-AGGGTTAAACT
*
55054025 GAAGCTCAAAAGAGCTAAACAGAAATCCAATAGGGTTAAACT
1 GAAGCTCATAAGAGCTAAACAGAAATCCAATAGGGTTAAACT
*
55054067 GAAACTCATA
1 GAAGCTCATA
55054077 TGAGTTAATT
Statistics
Matches: 78, Mismatches: 13, Indels: 8
0.79 0.13 0.08
Matches are distributed among these distances:
41 3 0.04
42 39 0.50
43 34 0.44
44 2 0.03
ACGTcount: A:0.45, C:0.18, G:0.20, T:0.18
Consensus pattern (42 bp):
GAAGCTCATAAGAGCTAAACAGAAATCCAATAGGGTTAAACT
Found at i:55055692 original size:20 final size:20
Alignment explanation
Indices: 55055658--55055718 Score: 68
Period size: 20 Copynumber: 3.0 Consensus size: 20
55055648 CAGAAAGCAT
*
55055658 CGTAGTGCTATACAAAGGCAC
1 CGTAGTG-TAAACAAAGGCAC
55055679 CGTAGTGTAAACAAAGGCAC
1 CGTAGTGTAAACAAAGGCAC
** * *
55055699 CAAAGTGCAAACAGAGGCAC
1 CGTAGTGTAAACAAAGGCAC
55055719 TGATGGTAGC
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
20 28 0.80
21 7 0.20
ACGTcount: A:0.39, C:0.23, G:0.25, T:0.13
Consensus pattern (20 bp):
CGTAGTGTAAACAAAGGCAC
Found at i:55064537 original size:18 final size:18
Alignment explanation
Indices: 55064516--55064554 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
55064506 CCAAACATAT
55064516 GTTTATTTAACAACAAAA
1 GTTTATTTAACAACAAAA
* *
55064534 GTTTTTTTAACAACCAAA
1 GTTTATTTAACAACAAAA
55064552 GTT
1 GTT
55064555 ATTGACAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.41, C:0.13, G:0.08, T:0.38
Consensus pattern (18 bp):
GTTTATTTAACAACAAAA
Found at i:55068559 original size:42 final size:41
Alignment explanation
Indices: 55068430--55068592 Score: 123
Period size: 42 Copynumber: 3.8 Consensus size: 41
55068420 TAAGATGCCA
* * **
55068430 ATGCCATATCTCAGATATGGTCTTACATGGGATCACATATATCG
1 ATGCCATATC-CCGATATGGTCTTACACGAAATCA-A-ATATCG
* * * * * **
55068474 ATGTCGATAGCCCAGCTATAGTCTTACACGATATCTCGA-ATCG
1 ATG-CCATATCCC-GATATGGTCTTACACGAAATC-AAATATCG
* *
55068517 ATGCCATATCCC-ATAAATGGTTTTACATGAAATCAAATATCG
1 ATGCCATATCCCGAT--ATGGTCTTACACGAAATCAAATATCG
55068559 ATGCCATATCCCGATATGGTCTTACACGAAATCA
1 ATGCCATATCCCGATATGGTCTTACACGAAATCA
55068593 CACATAACCC
Statistics
Matches: 91, Mismatches: 21, Indels: 17
0.71 0.16 0.13
Matches are distributed among these distances:
40 1 0.01
41 18 0.20
42 37 0.41
43 9 0.10
44 5 0.05
45 21 0.23
ACGTcount: A:0.32, C:0.23, G:0.16, T:0.29
Consensus pattern (41 bp):
ATGCCATATCCCGATATGGTCTTACACGAAATCAAATATCG
Found at i:55074690 original size:40 final size:41
Alignment explanation
Indices: 55074596--55074740 Score: 190
Period size: 40 Copynumber: 3.6 Consensus size: 41
55074586 TACTCGAATG
*
55074596 ATATCCGGGCTAA-ATCCCGAAGGCTTTTGTGCTAAGCGACT
1 ATATCCGGGCTAAGATCCCGAAGGCATTTGTGCT-AGCGACT
* *
55074637 ACATCCGGACTAAGAT-CCGAAGGCATTTGTGCTAGCGACT
1 ATATCCGGGCTAAGATCCCGAAGGCATTTGTGCTAGCGACT
* * *
55074677 ATATCCGGGCTAAG-TCCCGAAGGCATTTATGCTAGTGACC
1 ATATCCGGGCTAAGATCCCGAAGGCATTTGTGCTAGCGACT
*
55074717 ATATCCGGGTTAAGA-CCCGAAGGC
1 ATATCCGGGCTAAGATCCCGAAGGC
55074741 CTTGTGCGAG
Statistics
Matches: 92, Mismatches: 9, Indels: 7
0.85 0.08 0.06
Matches are distributed among these distances:
39 1 0.01
40 62 0.67
41 27 0.29
42 2 0.02
ACGTcount: A:0.26, C:0.25, G:0.26, T:0.23
Consensus pattern (41 bp):
ATATCCGGGCTAAGATCCCGAAGGCATTTGTGCTAGCGACT
Found at i:55076681 original size:16 final size:16
Alignment explanation
Indices: 55076656--55076715 Score: 70
Period size: 16 Copynumber: 3.8 Consensus size: 16
55076646 ATGATAGTTT
*
55076656 TTAAAATTTTTATATA
1 TTAAATTTTTTATATA
55076672 TTAAA-TTTTTATA-A
1 TTAAATTTTTTATATA
55076686 TTTATAATTTTTTATATA
1 -TTA-AATTTTTTATATA
*
55076704 TTAATTTTTTTA
1 TTAAATTTTTTA
55076716 ACTTTTTTAA
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
14 1 0.03
15 11 0.28
16 15 0.38
17 11 0.28
18 1 0.03
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (16 bp):
TTAAATTTTTTATATA
Found at i:55076713 original size:15 final size:15
Alignment explanation
Indices: 55076662--55076713 Score: 68
Period size: 15 Copynumber: 3.3 Consensus size: 15
55076652 GTTTTTAAAA
*
55076662 TTTTTATATATTAAA
1 TTTTTATATATTAAT
*
55076677 TTTTTATAATTTATAAT
1 TTTTTAT-ATAT-TAAT
55076694 TTTTTATATATTAAT
1 TTTTTATATATTAAT
55076709 TTTTT
1 TTTTT
55076714 TAACTTTTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
15 16 0.50
16 6 0.19
17 10 0.31
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (15 bp):
TTTTTATATATTAAT
Found at i:55076714 original size:17 final size:16
Alignment explanation
Indices: 55076662--55076747 Score: 61
Period size: 15 Copynumber: 5.3 Consensus size: 16
55076652 GTTTTTAAAA
*
55076662 TTTTTATATATTAA-A
1 TTTTTATATATTAATT
*
55076677 TTTTTATA-ATTTATAAT
1 TTTTTATATA-TTA-ATT
55076694 TTTTTATATATTAATT
1 TTTTTATATATTAATT
* * *
55076710 TTTTTAACTTTTTTAACT
1 TTTTT-A-TATATTAATT
*
55076728 TTTATATATA-TAATT
1 TTTTTATATATTAATT
55076743 TTTTT
1 TTTTT
55076748 GAGATGTAAA
Statistics
Matches: 55, Mismatches: 10, Indels: 12
0.71 0.13 0.16
Matches are distributed among these distances:
14 1 0.02
15 19 0.35
16 10 0.18
17 13 0.24
18 12 0.22
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.66
Consensus pattern (16 bp):
TTTTTATATATTAATT
Found at i:55076731 original size:32 final size:31
Alignment explanation
Indices: 55076655--55076747 Score: 100
Period size: 32 Copynumber: 2.9 Consensus size: 31
55076645 TATGATAGTT
* *
55076655 TTTAAAAT-TTTTATATATTAAATTTTTATAA
1 TTTATAATCTTTTATATATT-AATTTTTTTAA
*
55076686 TTTATAATTTTTTATATATTAATTTTTTTAA
1 TTTATAATCTTTTATATATTAATTTTTTTAA
*
55076717 CTTTTTTAA-CTTTTATATATATAATTTTTTT
1 --TTTATAATCTTTTATATAT-TAATTTTTTT
55076748 GAGATGTAAA
Statistics
Matches: 54, Mismatches: 4, Indels: 6
0.84 0.06 0.09
Matches are distributed among these distances:
31 17 0.31
32 21 0.39
33 16 0.30
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (31 bp):
TTTATAATCTTTTATATATTAATTTTTTTAA
Found at i:55081617 original size:43 final size:43
Alignment explanation
Indices: 55081556--55082507 Score: 1607
Period size: 43 Copynumber: 22.1 Consensus size: 43
55081546 GTTAAATCCC
* *
55081556 GCAGGCTTCGTGCCGGTGATGTATATTTGGGCCTTCGTGCCTA
1 GCAGGCTTCGTGCCGGTGATGTGTATTCGGGCCTTCGTGCCTA
55081599 GCAGGCTTCGTGCCGGTGATGTGTATTCGGGCCTTCGTGCCTA
1 GCAGGCTTCGTGCCGGTGATGTGTATTCGGGCCTTCGTGCCTA
* * *
55081642 GAAGGCTTCATGCCGGTGATGTGTATTTGGGCCTTCGTGCCTA
1 GCAGGCTTCGTGCCGGTGATGTGTATTCGGGCCTTCGTGCCTA
55081685 GCAGGCTTCGTGCCGGTGATGTGTATTCGGGCCTTCGTGCCTA
1 GCAGGCTTCGTGCCGGTGATGTGTATTCGGGCCTTCGTGCCTA
* * *
55081728 GAAGGCTTCATGCCGGTGATGTGTATTTGGGCCTTCGTGCCTA
1 GCAGGCTTCGTGCCGGTGATGTGTATTCGGGCCTTCGTGCCTA
55081771 GCAGGCTTCGTGCCGGTGATGTGTATTCGGGCCTTCGTGCCTA
1 GCAGGCTTCGTGCCGGTGATGTGTATTCGGGCCTTCGTGCCTA
* * *
55081814 GAAGGCTTCATGCCGGTGATGTGTATTTGGGCCTTCGTGCCTA
1 GCAGGCTTCGTGCCGGTGATGTGTATTCGGGCCTTCGTGCCTA
55081857 GCAGGCTTCGTGCCGGTGATGTGTATTCGGGCCTTCGTGCCTA
1 GCAGGCTTCGTGCCGGTGATGTGTATTCGGGCCTTCGTGCCTA
* * *
55081900 GAAGGCTTCATGCCGGTGATGTGTATTTGGGCCTTCGTGCCTA
1 GCAGGCTTCGTGCCGGTGATGTGTATTCGGGCCTTCGTGCCTA
55081943 GCAGGCTTCGTGCCGGTGATGTGTATTCGGGCCTTCGTGCCTA
1 GCAGGCTTCGTGCCGGTGATGTGTATTCGGGCCTTCGTGCCTA
* * *
55081986 GAAGGCTTCATGCCGGTGATGTGTATTTGGGCCTTCGTGCCTA
1 GCAGGCTTCGTGCCGGTGATGTGTATTCGGGCCTTCGTGCCTA
55082029 GCAGGCTTCGTGCCGGTGATGTGTATTCGGGCCTTCGTGCCTA
1 GCAGGCTTCGTGCCGGTGATGTGTATTCGGGCCTTCGTGCCTA
* * *
55082072 GAAGGCTTCATGCCGGTGATGTGTATTTGGGCCTTCGTGCCTA
1 GCAGGCTTCGTGCCGGTGATGTGTATTCGGGCCTTCGTGCCTA
55082115 GCAGGCTTCGTGCCGGTGATGTGTATTCGGGCCTTCGTGCCTA
1 GCAGGCTTCGTGCCGGTGATGTGTATTCGGGCCTTCGTGCCTA
* * *
55082158 GAAGGCTTCATGCCGGTGATGTGTATTTGGGCCTTCGTGCCTA
1 GCAGGCTTCGTGCCGGTGATGTGTATTCGGGCCTTCGTGCCTA
55082201 GCAGGCTTCGTGCCGGTGATGTGTATTCGGGCCTTCGTGCCTA
1 GCAGGCTTCGTGCCGGTGATGTGTATTCGGGCCTTCGTGCCTA
* * *
55082244 GAAGGCTTCATGCCGGTGATGTGTATTTGGGCCTTCGTGCCTA
1 GCAGGCTTCGTGCCGGTGATGTGTATTCGGGCCTTCGTGCCTA
55082287 GCAGGCTTCGTGCCGGTGATGTGTATTCGGGCCTTCGTGCCTA
1 GCAGGCTTCGTGCCGGTGATGTGTATTCGGGCCTTCGTGCCTA
* * *
55082330 GAAGGCTTCATGCCGGTGATGTGTATTTGGGCCTTCGTGCCTA
1 GCAGGCTTCGTGCCGGTGATGTGTATTCGGGCCTTCGTGCCTA
55082373 GCAGGCTTCGTGCCGGTGATGTGTATTCGGGCCTTCGTGCCTA
1 GCAGGCTTCGTGCCGGTGATGTGTATTCGGGCCTTCGTGCCTA
* * *
55082416 GAAGGCTTCATGCCGGTGATGTGTATTTGGGCCTTCGTGCCTA
1 GCAGGCTTCGTGCCGGTGATGTGTATTCGGGCCTTCGTGCCTA
55082459 GCAGGCTTCGTGCCGGTGATGTGTATTCGGGCCTTCGTGCCTA
1 GCAGGCTTCGTGCCGGTGATGTGTATTCGGGCCTTCGTGCCTA
*
55082502 GTAGGC
1 GCAGGC
55082508 ATAATGCCGG
Statistics
Matches: 846, Mismatches: 63, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 846 1.00
ACGTcount: A:0.12, C:0.23, G:0.34, T:0.31
Consensus pattern (43 bp):
GCAGGCTTCGTGCCGGTGATGTGTATTCGGGCCTTCGTGCCTA
Found at i:55081663 original size:86 final size:86
Alignment explanation
Indices: 55081558--55082520 Score: 1881
Period size: 86 Copynumber: 11.2 Consensus size: 86
55081548 TAAATCCCGC
* *
55081558 AGGCTTCGTGCCGGTGATGTATATTTGGGCCTTCGTGCCTAGCAGGCTTCGTGCCGGTGATGTGT
1 AGGCTTCATGCCGGTGATGTGTATTTGGGCCTTCGTGCCTAGCAGGCTTCGTGCCGGTGATGTGT
55081623 ATTCGGGCCTTCGTGCCTAGA
66 ATTCGGGCCTTCGTGCCTAGA
55081644 AGGCTTCATGCCGGTGATGTGTATTTGGGCCTTCGTGCCTAGCAGGCTTCGTGCCGGTGATGTGT
1 AGGCTTCATGCCGGTGATGTGTATTTGGGCCTTCGTGCCTAGCAGGCTTCGTGCCGGTGATGTGT
55081709 ATTCGGGCCTTCGTGCCTAGA
66 ATTCGGGCCTTCGTGCCTAGA
55081730 AGGCTTCATGCCGGTGATGTGTATTTGGGCCTTCGTGCCTAGCAGGCTTCGTGCCGGTGATGTGT
1 AGGCTTCATGCCGGTGATGTGTATTTGGGCCTTCGTGCCTAGCAGGCTTCGTGCCGGTGATGTGT
55081795 ATTCGGGCCTTCGTGCCTAGA
66 ATTCGGGCCTTCGTGCCTAGA
55081816 AGGCTTCATGCCGGTGATGTGTATTTGGGCCTTCGTGCCTAGCAGGCTTCGTGCCGGTGATGTGT
1 AGGCTTCATGCCGGTGATGTGTATTTGGGCCTTCGTGCCTAGCAGGCTTCGTGCCGGTGATGTGT
55081881 ATTCGGGCCTTCGTGCCTAGA
66 ATTCGGGCCTTCGTGCCTAGA
55081902 AGGCTTCATGCCGGTGATGTGTATTTGGGCCTTCGTGCCTAGCAGGCTTCGTGCCGGTGATGTGT
1 AGGCTTCATGCCGGTGATGTGTATTTGGGCCTTCGTGCCTAGCAGGCTTCGTGCCGGTGATGTGT
55081967 ATTCGGGCCTTCGTGCCTAGA
66 ATTCGGGCCTTCGTGCCTAGA
55081988 AGGCTTCATGCCGGTGATGTGTATTTGGGCCTTCGTGCCTAGCAGGCTTCGTGCCGGTGATGTGT
1 AGGCTTCATGCCGGTGATGTGTATTTGGGCCTTCGTGCCTAGCAGGCTTCGTGCCGGTGATGTGT
55082053 ATTCGGGCCTTCGTGCCTAGA
66 ATTCGGGCCTTCGTGCCTAGA
55082074 AGGCTTCATGCCGGTGATGTGTATTTGGGCCTTCGTGCCTAGCAGGCTTCGTGCCGGTGATGTGT
1 AGGCTTCATGCCGGTGATGTGTATTTGGGCCTTCGTGCCTAGCAGGCTTCGTGCCGGTGATGTGT
55082139 ATTCGGGCCTTCGTGCCTAGA
66 ATTCGGGCCTTCGTGCCTAGA
55082160 AGGCTTCATGCCGGTGATGTGTATTTGGGCCTTCGTGCCTAGCAGGCTTCGTGCCGGTGATGTGT
1 AGGCTTCATGCCGGTGATGTGTATTTGGGCCTTCGTGCCTAGCAGGCTTCGTGCCGGTGATGTGT
55082225 ATTCGGGCCTTCGTGCCTAGA
66 ATTCGGGCCTTCGTGCCTAGA
55082246 AGGCTTCATGCCGGTGATGTGTATTTGGGCCTTCGTGCCTAGCAGGCTTCGTGCCGGTGATGTGT
1 AGGCTTCATGCCGGTGATGTGTATTTGGGCCTTCGTGCCTAGCAGGCTTCGTGCCGGTGATGTGT
55082311 ATTCGGGCCTTCGTGCCTAGA
66 ATTCGGGCCTTCGTGCCTAGA
55082332 AGGCTTCATGCCGGTGATGTGTATTTGGGCCTTCGTGCCTAGCAGGCTTCGTGCCGGTGATGTGT
1 AGGCTTCATGCCGGTGATGTGTATTTGGGCCTTCGTGCCTAGCAGGCTTCGTGCCGGTGATGTGT
55082397 ATTCGGGCCTTCGTGCCTAGA
66 ATTCGGGCCTTCGTGCCTAGA
55082418 AGGCTTCATGCCGGTGATGTGTATTTGGGCCTTCGTGCCTAGCAGGCTTCGTGCCGGTGATGTGT
1 AGGCTTCATGCCGGTGATGTGTATTTGGGCCTTCGTGCCTAGCAGGCTTCGTGCCGGTGATGTGT
*
55082483 ATTCGGGCCTTCGTGCCTAGT
66 ATTCGGGCCTTCGTGCCTAGA
* *
55082504 AGGCATAATGCCGGTGA
1 AGGCTTCATGCCGGTGA
55082521 AATGATATGT
Statistics
Matches: 872, Mismatches: 5, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
86 872 1.00
ACGTcount: A:0.12, C:0.23, G:0.34, T:0.31
Consensus pattern (86 bp):
AGGCTTCATGCCGGTGATGTGTATTTGGGCCTTCGTGCCTAGCAGGCTTCGTGCCGGTGATGTGT
ATTCGGGCCTTCGTGCCTAGA
Found at i:55086117 original size:49 final size:49
Alignment explanation
Indices: 55086058--55086246 Score: 234
Period size: 49 Copynumber: 3.8 Consensus size: 49
55086048 GTAGCCAAAG
* * *
55086058 TTATCTGGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACTAA
1 TTATCCGGTACACATAGTAGCCTGCACTTAGTACTACACATGCGACCAA
* * * * *
55086107 TTATCCGGTACACGTGGTAGCCTGCACTTAGTACTACACACGTGATCGAA
1 TTATCCGGTACACATAGTAGCCTGCACTTAGTACTACACATGCGA-CCAA
* *
55086157 GTTATCAGGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAA
1 -TTATCCGGTACACATAGTAGCCTGCACTTAGTACTACACATGCGACCAA
* * * *
55086207 TGATCCAGTACACGTAGTAGCTTGCACTTAGTACTACACA
1 TTATCCGGTACACATAGTAGCCTGCACTTAGTACTACACA
55086247 CGTGACCTCA
Statistics
Matches: 118, Mismatches: 20, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
49 73 0.62
50 6 0.05
51 39 0.33
ACGTcount: A:0.29, C:0.25, G:0.20, T:0.26
Consensus pattern (49 bp):
TTATCCGGTACACATAGTAGCCTGCACTTAGTACTACACATGCGACCAA
Found at i:55086199 original size:100 final size:100
Alignment explanation
Indices: 55086055--55086251 Score: 340
Period size: 100 Copynumber: 2.0 Consensus size: 100
55086045 CTTGTAGCCA
* * * *
55086055 AAGTTATCTGGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACTAATTATCCGGTACAC
1 AAGTTATCAGGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAATGATCCAGTACAC
*
55086120 GTGGTAGCCTGCACTTAGTACTACACACGTGATCG
66 GTAGTAGCCTGCACTTAGTACTACACACGTGATCG
55086155 AAGTTATCAGGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAATGATCCAGTACAC
1 AAGTTATCAGGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAATGATCCAGTACAC
*
55086220 GTAGTAGCTTGCACTTAGTACTACACACGTGA
66 GTAGTAGCCTGCACTTAGTACTACACACGTGA
55086252 CCTCACAATA
Statistics
Matches: 91, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
100 91 1.00
ACGTcount: A:0.29, C:0.25, G:0.20, T:0.26
Consensus pattern (100 bp):
AAGTTATCAGGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAATGATCCAGTACAC
GTAGTAGCCTGCACTTAGTACTACACACGTGATCG
Found at i:55096940 original size:24 final size:24
Alignment explanation
Indices: 55096908--55096958 Score: 102
Period size: 24 Copynumber: 2.1 Consensus size: 24
55096898 CATGCATACT
55096908 TGATTTAATAATTTGAAATGACAA
1 TGATTTAATAATTTGAAATGACAA
55096932 TGATTTAATAATTTGAAATGACAA
1 TGATTTAATAATTTGAAATGACAA
55096956 TGA
1 TGA
55096959 CAAACAGTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.45, C:0.04, G:0.14, T:0.37
Consensus pattern (24 bp):
TGATTTAATAATTTGAAATGACAA
Found at i:55098022 original size:15 final size:15
Alignment explanation
Indices: 55097981--55098029 Score: 64
Period size: 15 Copynumber: 3.1 Consensus size: 15
55097971 AAAGCGGTTC
55097981 TTAATATATAAAAAAT
1 TTAATATAT-AAAAAT
55097997 TATAA-ATTATAAAAAT
1 T-TAATA-TATAAAAAT
55098013 TTAATATATAAAAAT
1 TTAATATATAAAAAT
55098028 TT
1 TT
55098030 TAAAAACTAT
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
15 14 0.47
16 10 0.33
17 6 0.20
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (15 bp):
TTAATATATAAAAAT
Found at i:55099970 original size:39 final size:40
Alignment explanation
Indices: 55099925--55100035 Score: 98
Period size: 40 Copynumber: 2.8 Consensus size: 40
55099915 CGGGGTTTAG
* * *
55099925 CCGGATATAACCACTCGCA-CAAGGCCTTCGGGTCTTAAC
1 CCGGATATAACCACTAGCATAAAGGCCTTCGGGACTTAAC
*** * *
55099964 CCGGATATGGTCACTAGCATAAATGCCTTCGGGACTTAGC
1 CCGGATATAACCACTAGCATAAAGGCCTTCGGGACTTAAC
** * * *
55100004 CCGGATATAGTCGCTAGCACAAATGCCTTCGG
1 CCGGATATAACCACTAGCATAAAGGCCTTCGG
55100036 ATCTTAGTCC
Statistics
Matches: 60, Mismatches: 11, Indels: 1
0.83 0.15 0.01
Matches are distributed among these distances:
39 15 0.25
40 45 0.75
ACGTcount: A:0.25, C:0.29, G:0.23, T:0.23
Consensus pattern (40 bp):
CCGGATATAACCACTAGCATAAAGGCCTTCGGGACTTAAC
Found at i:55100075 original size:41 final size:41
Alignment explanation
Indices: 55099948--55100092 Score: 190
Period size: 40 Copynumber: 3.6 Consensus size: 41
55099938 CTCGCACAAG
* * * *
55099948 GCCTTCGGG-TCTTAACCCGGATATGGTCACTAGCATAAAT
1 GCCTTCGGGATCTTAGCCCGGATATAGTCGCTAGCACAAAT
55099988 GCCTTCGGGA-CTTAGCCCGGATATAGTCGCTAGCACAAAT
1 GCCTTCGGGATCTTAGCCCGGATATAGTCGCTAGCACAAAT
* * *
55100028 GCCTTC-GGATCTTAGTCCGGATGTAGTCGCTTAGCACAAAA
1 GCCTTCGGGATCTTAGCCCGGATATAGTCGC-TAGCACAAAT
55100069 GCCTTCGGGAT-TTAGCCCGGATAT
1 GCCTTCGGGATCTTAGCCCGGATAT
55100093 CATTCGAGTA
Statistics
Matches: 92, Mismatches: 9, Indels: 7
0.85 0.08 0.06
Matches are distributed among these distances:
39 3 0.03
40 59 0.64
41 26 0.28
42 4 0.04
ACGTcount: A:0.23, C:0.26, G:0.25, T:0.26
Consensus pattern (41 bp):
GCCTTCGGGATCTTAGCCCGGATATAGTCGCTAGCACAAAT
Found at i:55100084 original size:81 final size:79
Alignment explanation
Indices: 55099912--55100092 Score: 202
Period size: 81 Copynumber: 2.3 Consensus size: 79
55099902 AATCAAGCAT
* * * *
55099912 CTTCGGGGTTTAG-CCGGATATAACCACTCGCACAAGGCCTTCGGGTCTTAACCCGGATATGGTC
1 CTTCGGGATTTAGCCCGGATATAACCACTAGCACAAGGCCTTCGGATCTTAACCCGGATATAGTC
* *
55099976 ACTAGCATAAATGC
66 ACTAGCACAAAAGC
* ** * * ** *
55099990 CTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAATGCCTTCGGATCTTAGTCCGGATGTAGT
1 CTTCGGGATTTAGCCCGGATATAACCACTAGCAC-AAGGCCTTCGGATCTTAACCCGGATATAGT
*
55100055 CGCTTAGCACAAAAGC
65 CAC-TAGCACAAAAGC
55100071 CTTCGGGATTTAGCCCGGATAT
1 CTTCGGGATTTAGCCCGGATAT
55100093 CATTCGAGTA
Statistics
Matches: 84, Mismatches: 16, Indels: 3
0.82 0.16 0.03
Matches are distributed among these distances:
78 11 0.13
79 16 0.19
80 26 0.31
81 31 0.37
ACGTcount: A:0.24, C:0.26, G:0.25, T:0.25
Consensus pattern (79 bp):
CTTCGGGATTTAGCCCGGATATAACCACTAGCACAAGGCCTTCGGATCTTAACCCGGATATAGTC
ACTAGCACAAAAGC
Found at i:55106155 original size:41 final size:41
Alignment explanation
Indices: 55106096--55106175 Score: 117
Period size: 41 Copynumber: 1.9 Consensus size: 41
55106086 GGGTTATGTG
* *
55106096 TGATTTCGTGTAAGACCA-TATCGGGATATGGCATCGATATT
1 TGATTTCATGTAAAACCATTAT-GGGATATGGCATCGATATT
55106137 TGATTTCATGTAAAACCATTTATGGGATATGGCATCGAT
1 TGATTTCATGTAAAACCA-TTATGGGATATGGCATCGAT
55106176 TCGAGATATC
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
41 16 0.46
42 16 0.46
43 3 0.09
ACGTcount: A:0.29, C:0.14, G:0.23, T:0.35
Consensus pattern (41 bp):
TGATTTCATGTAAAACCATTATGGGATATGGCATCGATATT
Found at i:55106191 original size:42 final size:41
Alignment explanation
Indices: 55106101--55106191 Score: 96
Period size: 42 Copynumber: 2.2 Consensus size: 41
55106091 ATGTGTGATT
* ** *
55106101 TCGTGTAAGACCATATCGGGATATGGCATCGATATTTGATT
1 TCGTGTAAAACCATATCGGGATATGGCATCGATATGAGATA
*
55106142 TCATGTAAAACCATTTAT-GGGATATGGCATCGAT-TCGAGATA
1 TCGTGTAAAACCA--TATCGGGATATGGCATCGATAT-GAGATA
55106184 TCGTGTAA
1 TCGTGTAA
55106192 GACTATAGCT
Statistics
Matches: 41, Mismatches: 6, Indels: 5
0.79 0.12 0.10
Matches are distributed among these distances:
41 12 0.29
42 26 0.63
43 3 0.07
ACGTcount: A:0.30, C:0.14, G:0.23, T:0.33
Consensus pattern (41 bp):
TCGTGTAAAACCATATCGGGATATGGCATCGATATGAGATA
Found at i:55106253 original size:87 final size:83
Alignment explanation
Indices: 55106101--55106258 Score: 190
Period size: 87 Copynumber: 1.9 Consensus size: 83
55106091 ATGTGTGATT
* * ** * *
55106101 TCGTGTAAGACCATATCGGGATATGGCATCGATATTTGATTTCATGTAAAACCATTTATGGGATA
1 TCGTGTAAGACCATAGCGGGATATGACATCGATATTTGATCCCATGTAAAACCATATATGAGATA
55106166 TGGCATCGATTCGAGATA
66 TGGCATCGATTCGAGATA
* * * *
55106184 TCGTGTAAGACTATAGCTGGGCTATCGACATCGATATATGTGATCCCATGTAAGACCATATCTGA
1 TCGTGTAAGACCATAGC-GGGATAT-GACATCGATAT-T-TGATCCCATGTAAAACCATATATGA
55106249 GATATGGCAT
62 GATATGGCAT
55106259 TGGCATCTTA
Statistics
Matches: 61, Mismatches: 10, Indels: 4
0.81 0.13 0.05
Matches are distributed among these distances:
83 15 0.25
84 6 0.10
85 10 0.16
86 1 0.02
87 29 0.48
ACGTcount: A:0.30, C:0.16, G:0.23, T:0.31
Consensus pattern (83 bp):
TCGTGTAAGACCATAGCGGGATATGACATCGATATTTGATCCCATGTAAAACCATATATGAGATA
TGGCATCGATTCGAGATA
Found at i:55110157 original size:18 final size:18
Alignment explanation
Indices: 55110134--55110172 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
55110124 ATTTGTCAAT
55110134 AACTTTGGTTGTTAAAAA
1 AACTTTGGTTGTTAAAAA
* *
55110152 AACTTTTGTTGTTAAATA
1 AACTTTGGTTGTTAAAAA
55110170 AAC
1 AAC
55110173 ATATGTTTGG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.38, C:0.08, G:0.13, T:0.41
Consensus pattern (18 bp):
AACTTTGGTTGTTAAAAA
Found at i:55110179 original size:18 final size:18
Alignment explanation
Indices: 55110141--55110179 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
55110131 AATAACTTTG
* *
55110141 GTTGTTAAAAAAACTTTT
1 GTTGTTAAAAAAACATAT
*
55110159 GTTGTTAAATAAACATAT
1 GTTGTTAAAAAAACATAT
55110177 GTT
1 GTT
55110180 TGGTTGAACT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.38, C:0.05, G:0.13, T:0.44
Consensus pattern (18 bp):
GTTGTTAAAAAAACATAT
Found at i:55113959 original size:26 final size:27
Alignment explanation
Indices: 55113908--55113959 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 27
55113898 TAACTTTTTT
* *
55113908 TAAATTTTTAATTTTTCATAATTATTA
1 TAAATTTTTAATTTTTCAAAAATATTA
*
55113935 TAAA-TTTTAATTTTTTAAAAATATT
1 TAAATTTTTAATTTTTCAAAAATATT
55113960 TTGGATTTCT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 18 0.82
27 4 0.18
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (27 bp):
TAAATTTTTAATTTTTCAAAAATATTA
Found at i:55119012 original size:20 final size:20
Alignment explanation
Indices: 55118970--55119030 Score: 68
Period size: 20 Copynumber: 3.0 Consensus size: 20
55118960 GCTACCATCA
* * **
55118970 GTGCCTCTGTTTGCACTTTG
1 GTGCCTTTGTTTACACTACG
55118990 GTGCCTTTGTTTACACTACG
1 GTGCCTTTGTTTACACTACG
*
55119010 GTGCCTTTGTATAGCACTACG
1 GTGCCTTTGTTTA-CACTACG
55119031 ATGCTTTCTG
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
20 28 0.80
21 7 0.20
ACGTcount: A:0.13, C:0.25, G:0.23, T:0.39
Consensus pattern (20 bp):
GTGCCTTTGTTTACACTACG
Found at i:55120703 original size:43 final size:42
Alignment explanation
Indices: 55120612--55120717 Score: 133
Period size: 43 Copynumber: 2.5 Consensus size: 42
55120602 AATTAACTCA
* * *
55120612 TATGAGTTTCAGTTTAACCCTATTGGATTTCTGTTTAGCTCT
1 TATGAGCTTCAGTTTAACCCTATTGGATTTCCGTTCAGCTCT
* *
55120654 TTTGAGCTTCAGTTTAACCATTATTAGG-TTTCCGTTCAGCTCT
1 TATGAGCTTCAGTTTAACC-CTATT-GGATTTCCGTTCAGCTCT
*
55120697 TATGAGCTTCCGTTTAACCCT
1 TATGAGCTTCAGTTTAACCCT
55120718 TGTGGGTTTC
Statistics
Matches: 54, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
42 18 0.33
43 34 0.63
44 2 0.04
ACGTcount: A:0.19, C:0.21, G:0.16, T:0.44
Consensus pattern (42 bp):
TATGAGCTTCAGTTTAACCCTATTGGATTTCCGTTCAGCTCT
Found at i:55120741 original size:42 final size:41
Alignment explanation
Indices: 55120612--55120748 Score: 139
Period size: 42 Copynumber: 3.2 Consensus size: 41
55120602 AATTAACTCA
* *
55120612 TATGAGTTTCAGTTTAACCCTATTGGATTTCTGTTTAGCTCT
1 TATGAGCTTCAGTTTAACCCT-TTGGGTTTCTGTTTAGCTCT
* * * * *
55120654 TTTGAGCTTCAGTTTAACCATTATTAGGTTTCCGTTCAGCTCT
1 TATGAGCTTCAGTTTAACC-CT-TTGGGTTTCTGTTTAGCTCT
* * *
55120697 TATGAGCTTCCGTTTAACCCTTGTGGGTTTCTATTTAGCACT
1 TATGAGCTTCAGTTTAACCCTT-TGGGTTTCTGTTTAGCTCT
*
55120739 TATGTGCTTC
1 TATGAGCTTC
55120749 TGTGTAGCCT
Statistics
Matches: 77, Mismatches: 16, Indels: 4
0.79 0.16 0.04
Matches are distributed among these distances:
41 1 0.01
42 41 0.53
43 35 0.45
ACGTcount: A:0.18, C:0.20, G:0.18, T:0.45
Consensus pattern (41 bp):
TATGAGCTTCAGTTTAACCCTTTGGGTTTCTGTTTAGCTCT
Found at i:55127320 original size:42 final size:42
Alignment explanation
Indices: 55127261--55127346 Score: 172
Period size: 42 Copynumber: 2.0 Consensus size: 42
55127251 AAATGTACAC
55127261 AATTTAGTTACACGAATTTACCTCGATAATAGTTTGTATAAG
1 AATTTAGTTACACGAATTTACCTCGATAATAGTTTGTATAAG
55127303 AATTTAGTTACACGAATTTACCTCGATAATAGTTTGTATAAG
1 AATTTAGTTACACGAATTTACCTCGATAATAGTTTGTATAAG
55127345 AA
1 AA
55127347 AATCTACTAC
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 44 1.00
ACGTcount: A:0.37, C:0.12, G:0.14, T:0.37
Consensus pattern (42 bp):
AATTTAGTTACACGAATTTACCTCGATAATAGTTTGTATAAG
Found at i:55128424 original size:23 final size:23
Alignment explanation
Indices: 55128359--55128424 Score: 57
Period size: 23 Copynumber: 2.9 Consensus size: 23
55128349 CATTAATTAG
*
55128359 GAAGCTCACAAAGAG-CATAACGA
1 GAAGCTTAC-AAGAGCCATAACGA
* *
55128382 GAAGCTTAC--GGGCTATATAACGA
1 GAAGCTTACAAGAGC--CATAACGA
55128405 GAAGCTTACAAGAGCCATAA
1 GAAGCTTACAAGAGCCATAA
55128425 TCGAAAAGTT
Statistics
Matches: 33, Mismatches: 5, Indels: 10
0.69 0.10 0.21
Matches are distributed among these distances:
20 2 0.06
23 28 0.85
25 3 0.09
ACGTcount: A:0.42, C:0.20, G:0.23, T:0.15
Consensus pattern (23 bp):
GAAGCTTACAAGAGCCATAACGA
Found at i:55128463 original size:26 final size:25
Alignment explanation
Indices: 55128434--55128486 Score: 61
Period size: 26 Copynumber: 2.1 Consensus size: 25
55128424 ATCGAAAAGT
*
55128434 TCACAAAAAACTTTTAATCAGGAAGC
1 TCACAAAAAACCTTTAATCAGG-AGC
* * *
55128460 TCACGAAGAGCCTTTAATCAGGAGC
1 TCACAAAAAACCTTTAATCAGGAGC
55128485 TC
1 TC
55128487 CGGATAGCCA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
25 5 0.22
26 18 0.78
ACGTcount: A:0.38, C:0.23, G:0.17, T:0.23
Consensus pattern (25 bp):
TCACAAAAAACCTTTAATCAGGAGC
Found at i:55129617 original size:19 final size:18
Alignment explanation
Indices: 55129586--55129621 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
55129576 ATATGATGAT
*
55129586 ATTTTTATTTTTTTTATC
1 ATTTTTATCTTTTTTATC
55129604 ATTTTTCATCTTTTTTAT
1 ATTTTT-ATCTTTTTTAT
55129622 TTCACTTTTC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 6 0.38
19 10 0.62
ACGTcount: A:0.17, C:0.08, G:0.00, T:0.75
Consensus pattern (18 bp):
ATTTTTATCTTTTTTATC
Found at i:55129619 original size:21 final size:21
Alignment explanation
Indices: 55129593--55129632 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
55129583 GATATTTTTA
*
55129593 TTTTTT-TTATCATTTTTCATC
1 TTTTTTATT-TCACTTTTCATC
55129614 TTTTTTATTTCACTTTTCA
1 TTTTTTATTTCACTTTTCA
55129633 ATTTCATCCT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 15 0.88
22 2 0.12
ACGTcount: A:0.15, C:0.15, G:0.00, T:0.70
Consensus pattern (21 bp):
TTTTTTATTTCACTTTTCATC
Found at i:55131364 original size:16 final size:17
Alignment explanation
Indices: 55131343--55131375 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
55131333 CCCCAGAGTG
55131343 TATTCTG-ATGTTTGAT
1 TATTCTGTATGTTTGAT
55131359 TATTCTGTATGTTTGAT
1 TATTCTGTATGTTTGAT
55131376 ATCTGTGGAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.18, C:0.06, G:0.18, T:0.58
Consensus pattern (17 bp):
TATTCTGTATGTTTGAT
Found at i:55131998 original size:22 final size:22
Alignment explanation
Indices: 55131973--55132026 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 22
55131963 CTGTAAGTTT
* * **
55131973 TCTGAAACTCTGTTTAGAATTG
1 TCTGAAACTATGATTAGAATAC
*
55131995 TCTGAAAATATGATTAGAATAC
1 TCTGAAACTATGATTAGAATAC
55132017 TCTGAAACTA
1 TCTGAAACTA
55132027 CTTTAGGTAG
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.37, C:0.13, G:0.15, T:0.35
Consensus pattern (22 bp):
TCTGAAACTATGATTAGAATAC
Found at i:55135685 original size:40 final size:40
Alignment explanation
Indices: 55135648--55135832 Score: 216
Period size: 40 Copynumber: 4.7 Consensus size: 40
55135638 GCTACTCGTT
*
55135648 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATT-TAGTAACTCGCA
* *
55135688 CAATTGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* * *
55135728 CAAATGCCTTCGGG-CTTAGCCCAGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* * * * *
55135767 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGTAAC-TCGCA
55135808 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
55135833 CATCATTCAA
Statistics
Matches: 123, Mismatches: 17, Indels: 10
0.82 0.11 0.07
Matches are distributed among these distances:
38 2 0.02
39 32 0.26
40 76 0.62
41 13 0.11
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
Found at i:55135765 original size:79 final size:81
Alignment explanation
Indices: 55135648--55135830 Score: 214
Period size: 79 Copynumber: 2.3 Consensus size: 81
55135638 GCTACTCGTT
* ** *
55135648 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCACAATTGCCTTCGGGA-CTTAACCCG
1 CAAATGCCTTCGGGACTTAGCCCGAATATAGTAACTCGCACAAATGCCTTC-GGATCTTAACCCG
* *
55135712 GATTTAGTAAC-TCGCA
65 GATATAGTAACTTAGCA
* **
55135728 CAAATGCCTTCGGG-CTTAGCCCAGAAT-TAGTATCTCGCACAAATGCCTTCGGATCTTAGTCCG
1 CAAATGCCTTCGGGACTTAGCCC-GAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCG
* *
55135791 GATATGGTCACTTAGCA
65 GATATAGTAACTTAGCA
55135808 CAAA-GCCTTCGGGACTTAGCCCG
1 CAAATGCCTTCGGGACTTAGCCCG
55135831 GACATCATTC
Statistics
Matches: 88, Mismatches: 11, Indels: 9
0.81 0.10 0.08
Matches are distributed among these distances:
78 3 0.03
79 53 0.60
80 32 0.36
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (81 bp):
CAAATGCCTTCGGGACTTAGCCCGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGG
ATATAGTAACTTAGCA
Found at i:55178523 original size:46 final size:47
Alignment explanation
Indices: 55178417--55178538 Score: 147
Period size: 46 Copynumber: 2.6 Consensus size: 47
55178407 TGTCTTCGAC
** * *
55178417 ATGGACTTACATGAATTATTCCTGTCTCCAATGCCATATATATATCTAAT
1 ATGGACTTACATGGCTCATTCCTGTCTCCAAAGCC--A-ATATATCTAAT
* *
55178467 ATGGGCTTACATGGCTCATTCCTGTCTCCAAAGCC-ATATATCTGAT
1 ATGGACTTACATGGCTCATTCCTGTCTCCAAAGCCAATATATCTAAT
*
55178513 ATGGACTTACATGGCTCATTTCTGTC
1 ATGGACTTACATGGCTCATTCCTGTC
55178539 CTGTCCTGTC
Statistics
Matches: 64, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
46 34 0.53
50 30 0.47
ACGTcount: A:0.26, C:0.23, G:0.15, T:0.36
Consensus pattern (47 bp):
ATGGACTTACATGGCTCATTCCTGTCTCCAAAGCCAATATATCTAAT
Found at i:55179821 original size:45 final size:45
Alignment explanation
Indices: 55179756--55179842 Score: 131
Period size: 45 Copynumber: 1.9 Consensus size: 45
55179746 CAATATCATT
*
55179756 TCACCGGCATTATAGCCTGCTAGACTCGAAGG-CCTGAATAGTATC
1 TCACCGGCATTATAGCCTGCTAGACTCAAAGGTCC-GAATAGTATC
* *
55179801 TCACCGGCATTATAGTCTGCTAGGCTCAAAGGTCCGAATAGT
1 TCACCGGCATTATAGCCTGCTAGACTCAAAGGTCCGAATAGT
55179843 GCTGTACGAT
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
45 36 0.95
46 2 0.05
ACGTcount: A:0.26, C:0.25, G:0.23, T:0.25
Consensus pattern (45 bp):
TCACCGGCATTATAGCCTGCTAGACTCAAAGGTCCGAATAGTATC
Found at i:55180717 original size:50 final size:49
Alignment explanation
Indices: 55180663--55180808 Score: 168
Period size: 50 Copynumber: 2.9 Consensus size: 49
55180653 GTAACTTATT
* * *
55180663 CGGAAATAATAAGGGCAAATTTAACATAAAATATTAA-AAGCAAATTTAAC
1 CGGAATTATTAAGAGCAAATTTAACA-AAAATATTAAGAA-CAAATTTAAC
* * *
55180713 CGGAATTATTAAGAACAAATTTAACCAGAATTATTAAGAACAAATTTAAC
1 CGGAATTATTAAGAGCAAATTTAA-CAAAAATATTAAGAACAAATTTAAC
** *
55180763 CGGAATTATTAAGAGCAAATTTAACCGGAATTATTAAGAACAAATT
1 CGGAATTATTAAGAGCAAATTTAA-CAAAAATATTAAGAACAAATT
55180809 AACAAGCTTA
Statistics
Matches: 86, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
50 82 0.95
51 4 0.05
ACGTcount: A:0.50, C:0.11, G:0.12, T:0.27
Consensus pattern (49 bp):
CGGAATTATTAAGAGCAAATTTAACAAAAATATTAAGAACAAATTTAAC
Found at i:55180722 original size:25 final size:25
Alignment explanation
Indices: 55180694--55180808 Score: 196
Period size: 25 Copynumber: 4.6 Consensus size: 25
55180684 TAACATAAAA
55180694 TATTAA-AAGCAAATTTAACCGGAAT
1 TATTAAGAA-CAAATTTAACCGGAAT
*
55180719 TATTAAGAACAAATTTAACCAGAAT
1 TATTAAGAACAAATTTAACCGGAAT
55180744 TATTAAGAACAAATTTAACCGGAAT
1 TATTAAGAACAAATTTAACCGGAAT
*
55180769 TATTAAGAGCAAATTTAACCGGAAT
1 TATTAAGAACAAATTTAACCGGAAT
55180794 TATTAAGAACAAATT
1 TATTAAGAACAAATT
55180809 AACAAGCTTA
Statistics
Matches: 85, Mismatches: 4, Indels: 2
0.93 0.04 0.02
Matches are distributed among these distances:
25 83 0.98
26 2 0.02
ACGTcount: A:0.49, C:0.11, G:0.11, T:0.29
Consensus pattern (25 bp):
TATTAAGAACAAATTTAACCGGAAT
Found at i:55183943 original size:16 final size:17
Alignment explanation
Indices: 55183922--55183954 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
55183912 CCCCAGACTG
55183922 TATTCTG-ATGCTTGAT
1 TATTCTGTATGCTTGAT
*
55183938 TATTCTGTATGTTTGAT
1 TATTCTGTATGCTTGAT
55183955 ATCTGTGGGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.18, C:0.09, G:0.18, T:0.55
Consensus pattern (17 bp):
TATTCTGTATGCTTGAT
Found at i:55186980 original size:10 final size:10
Alignment explanation
Indices: 55186974--55186998 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
55186964 CAGTCGAGTT
55186974 GAGTCGAATC
1 GAGTCGAATC
55186984 GAGTCGAATC
1 GAGTCGAATC
55186994 GAGTC
1 GAGTC
55186999 AAAAGATTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.28, C:0.20, G:0.32, T:0.20
Consensus pattern (10 bp):
GAGTCGAATC
Found at i:55187499 original size:9 final size:10
Alignment explanation
Indices: 55187479--55187517 Score: 53
Period size: 10 Copynumber: 4.0 Consensus size: 10
55187469 TAAAATTTAA
55187479 AAATTTTATT
1 AAATTTTATT
55187489 AAATTTT-TT
1 AAATTTTATT
**
55187498 AAATTGAATT
1 AAATTTTATT
55187508 AAATTTTATT
1 AAATTTTATT
55187518 CACCTTACAA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
9 7 0.29
10 17 0.71
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (10 bp):
AAATTTTATT
Found at i:55188146 original size:21 final size:18
Alignment explanation
Indices: 55188120--55188160 Score: 55
Period size: 21 Copynumber: 2.1 Consensus size: 18
55188110 TTTTTTTATC
55188120 TATTGTTATAATATTCATTTT
1 TATTGTTAT--TATT-ATTTT
55188141 TATTGTTATTATTATTTT
1 TATTGTTATTATTATTTT
55188159 TA
1 TA
55188161 CATTTATTGT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
18 7 0.35
19 4 0.20
21 9 0.45
ACGTcount: A:0.27, C:0.02, G:0.05, T:0.66
Consensus pattern (18 bp):
TATTGTTATTATTATTTT
Found at i:55193823 original size:79 final size:82
Alignment explanation
Indices: 55193712--55193896 Score: 238
Period size: 79 Copynumber: 2.3 Consensus size: 82
55193702 GCTACTCGTT
* *
55193712 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCC
1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTC-GGATCTTAACCC
* *
55193775 GGATTTAGTAAC-TCGCA
65 GGATATAGTAACTTAGCA
* **
55193792 CAAATGCCTTCGGG-CTTAGCCCGGAAT-TAGTATCTCGCACAAATGCCTTCGGATCTTAGTCCG
1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCG
* *
55193855 GATATGGTCACTTAGCA
66 GATATAGTAACTTAGCA
55193872 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
55193897 CATCATTCAA
Statistics
Matches: 92, Mismatches: 9, Indels: 8
0.84 0.08 0.07
Matches are distributed among these distances:
78 3 0.03
79 55 0.60
80 34 0.37
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.24
Consensus pattern (82 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCG
GATATAGTAACTTAGCA
Found at i:55193896 original size:40 final size:40
Alignment explanation
Indices: 55193693--55193896 Score: 238
Period size: 40 Copynumber: 5.1 Consensus size: 40
55193683 CGGAATTTAA
** *
55193693 CCGGATATAGCT-ACTCGTTCAAATGCCTTCGGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
* *
55193733 CCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAAC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
*
55193773 CCGGATTTAGTAACTCGCACAAATGCCTTCGGG-CTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
55193812 CCGGA-ATTAGTATCTCGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* * *
55193852 CCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGC
1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC
55193892 CCGGA
1 CCGGA
55193897 CATCATTCAA
Statistics
Matches: 141, Mismatches: 16, Indels: 14
0.82 0.09 0.08
Matches are distributed among these distances:
38 2 0.01
39 33 0.23
40 94 0.67
41 12 0.09
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Found at i:55195889 original size:50 final size:50
Alignment explanation
Indices: 55195832--55195977 Score: 256
Period size: 50 Copynumber: 2.9 Consensus size: 50
55195822 AGCCAAAGCT
*
55195832 ATCTGGTACACATAGTAGCCTGCACTTAGTACTACACACGTGACCTAACC
1 ATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGACCTAACC
* *
55195882 ATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGACCCAATC
1 ATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGACCTAACC
*
55195932 ATCTGATACACGTAGTAGCCTGCACTTAGTACTACACACGTGACCT
1 ATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGACCT
55195978 CACAATAGAT
Statistics
Matches: 91, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
50 91 1.00
ACGTcount: A:0.29, C:0.29, G:0.17, T:0.25
Consensus pattern (50 bp):
ATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGACCTAACC
Found at i:55197476 original size:3 final size:3
Alignment explanation
Indices: 55197468--55197503 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
55197458 TTTTATAGTC
55197468 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
55197504 ACTAATGTCC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TCT
Found at i:55199353 original size:18 final size:18
Alignment explanation
Indices: 55199330--55199375 Score: 67
Period size: 18 Copynumber: 2.6 Consensus size: 18
55199320 CAAGGTCACG
55199330 ATCAATAGT-GTCACTAGC
1 ATCAATA-TCGTCACTAGC
*
55199348 ATCAATATCGTCACTATC
1 ATCAATATCGTCACTAGC
55199366 ATCAATATCG
1 ATCAATATCG
55199376 ATATCATCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
17 1 0.04
18 25 0.96
ACGTcount: A:0.35, C:0.24, G:0.11, T:0.30
Consensus pattern (18 bp):
ATCAATATCGTCACTAGC
Found at i:55199380 original size:15 final size:17
Alignment explanation
Indices: 55199341--55199385 Score: 58
Period size: 18 Copynumber: 2.7 Consensus size: 17
55199331 TCAATAGTGT
*
55199341 CACTAGCATCAATATCG
1 CACTATCATCAATATCG
55199358 TCACTATCATCAATATCG
1 -CACTATCATCAATATCG
55199376 -A-TATCATCAA
1 CACTATCATCAA
55199386 AAGAAAACCT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
15 9 0.35
16 1 0.04
18 16 0.62
ACGTcount: A:0.38, C:0.27, G:0.07, T:0.29
Consensus pattern (17 bp):
CACTATCATCAATATCG
Found at i:55202424 original size:25 final size:24
Alignment explanation
Indices: 55202367--55202424 Score: 64
Period size: 24 Copynumber: 2.4 Consensus size: 24
55202357 TTCCTGCTAC
* *
55202367 ATGGCCCTTTGTGAGCTTCCTGAT
1 ATGGCTCTTTGTGAACTTCCTGAT
*
55202391 ATGGTTCTTTGTGAACTTCCCT-ATT
1 ATGGCTCTTTGTGAACTT-CCTGA-T
55202416 ATGGCTCTT
1 ATGGCTCTT
55202425 ATGAGCTTCC
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
24 16 0.57
25 12 0.43
ACGTcount: A:0.14, C:0.22, G:0.21, T:0.43
Consensus pattern (24 bp):
ATGGCTCTTTGTGAACTTCCTGAT
Found at i:55211260 original size:13 final size:15
Alignment explanation
Indices: 55211242--55211273 Score: 50
Period size: 13 Copynumber: 2.3 Consensus size: 15
55211232 TTTATTCATC
55211242 AATCTCTT-CCTC-A
1 AATCTCTTACCTCTA
55211255 AATCTCTTACCTCTA
1 AATCTCTTACCTCTA
55211270 AATC
1 AATC
55211274 GGCTTTTCTC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 8 0.47
14 4 0.24
15 5 0.29
ACGTcount: A:0.28, C:0.34, G:0.00, T:0.38
Consensus pattern (15 bp):
AATCTCTTACCTCTA
Found at i:55217553 original size:13 final size:14
Alignment explanation
Indices: 55217535--55217563 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
55217525 CTTATGTGTT
55217535 TTTAAAGGTT-ATA
1 TTTAAAGGTTAATA
55217548 TTTAAAGGTTAATA
1 TTTAAAGGTTAATA
55217562 TT
1 TT
55217564 GGTAATTGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.67
14 5 0.33
ACGTcount: A:0.38, C:0.00, G:0.14, T:0.48
Consensus pattern (14 bp):
TTTAAAGGTTAATA
Found at i:55218515 original size:43 final size:43
Alignment explanation
Indices: 55218427--55218528 Score: 125
Period size: 43 Copynumber: 2.4 Consensus size: 43
55218417 ATAAGATGTT
**
55218427 ATTATGTGTAAGACCATGTCTGAGACATTGTTATCATTACATG
1 ATTATGTGTAAGACCATGTCTGAGACATTGGCATCATTACATG
* * * * **
55218470 ATTACGTGTAAGACCATGTTTGGGACATTGGCATCGTTATTTG
1 ATTATGTGTAAGACCATGTCTGAGACATTGGCATCATTACATG
55218513 ATT-TGTGTAAGACCAT
1 ATTATGTGTAAGACCAT
55218529 AGCTGGGCTA
Statistics
Matches: 50, Mismatches: 9, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
42 12 0.24
43 38 0.76
ACGTcount: A:0.27, C:0.14, G:0.22, T:0.37
Consensus pattern (43 bp):
ATTATGTGTAAGACCATGTCTGAGACATTGGCATCATTACATG
Found at i:55223463 original size:17 final size:17
Alignment explanation
Indices: 55223438--55223479 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
55223428 AAGTAAACAA
55223438 AGTAAGCTA-TAAAGCTT
1 AGTAAGCTATTAAA-CTT
*
55223455 AGTATGCTATTAAACTT
1 AGTAAGCTATTAAACTT
55223472 AGTAAGCT
1 AGTAAGCT
55223480 CGTATGATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 18 0.82
18 4 0.18
ACGTcount: A:0.38, C:0.12, G:0.17, T:0.33
Consensus pattern (17 bp):
AGTAAGCTATTAAACTT
Found at i:55228318 original size:17 final size:17
Alignment explanation
Indices: 55228293--55228334 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
55228283 AAGTAAACAA
55228293 AGTAAGCTA-TAAAGCTT
1 AGTAAGCTATTAAA-CTT
*
55228310 AGTATGCTATTAAACTT
1 AGTAAGCTATTAAACTT
55228327 AGTAAGCT
1 AGTAAGCT
55228335 CGTATGATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 18 0.82
18 4 0.18
ACGTcount: A:0.38, C:0.12, G:0.17, T:0.33
Consensus pattern (17 bp):
AGTAAGCTATTAAACTT
Found at i:55230190 original size:39 final size:40
Alignment explanation
Indices: 55230119--55230262 Score: 156
Period size: 39 Copynumber: 3.6 Consensus size: 40
55230109 ACTCCTCGTT
* *
55230119 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAAT-TAGTAACTCGCA
*
55230159 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCA
* * *
55230198 CAAATGCCTTC-GGATCTTAGTCCGGATATT-GTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGA-ATTAGTAAC-TCGCA
55230239 C-AA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
55230263 CATCATTCAA
Statistics
Matches: 90, Mismatches: 8, Indels: 13
0.81 0.07 0.12
Matches are distributed among these distances:
38 2 0.02
39 47 0.52
40 33 0.37
41 8 0.09
ACGTcount: A:0.24, C:0.28, G:0.23, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCA
Found at i:55250649 original size:27 final size:27
Alignment explanation
Indices: 55250563--55250650 Score: 77
Period size: 27 Copynumber: 3.3 Consensus size: 27
55250553 CCGATTTGTA
* * * * *
55250563 AAAATTACCGAAATACTCTTGTAGTGT
1 AAAATGACCGTAATACCCCTGTAGGGT
* * *
55250590 AAAACGATCGTAATGCCCCTGTAGGGT
1 AAAATGACCGTAATACCCCTGTAGGGT
* *
55250617 AAAATGACCGTAATACCTCTGTATGGT
1 AAAATGACCGTAATACCCCTGTAGGGT
*
55250644 AGAATGA
1 AAAATGA
55250651 TGATTATGCT
Statistics
Matches: 47, Mismatches: 14, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
27 47 1.00
ACGTcount: A:0.35, C:0.17, G:0.20, T:0.27
Consensus pattern (27 bp):
AAAATGACCGTAATACCCCTGTAGGGT
Found at i:55253552 original size:40 final size:40
Alignment explanation
Indices: 55253478--55253742 Score: 462
Period size: 40 Copynumber: 6.7 Consensus size: 40
55253468 AACCCAAGTA
* *
55253478 CCTTCGGGATTTAG-CCGGATATAG-CAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCAA-TAGCACAAATG
* *
55253517 CCTTCGGGTCTTAGCCCGGATATAGTCAATAGCACAAAAG
1 CCTTCGGGACTTAGCCCGGATATAGTCAATAGCACAAATG
*
55253557 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCAATAGCACAAATG
55253597 CCTTCGGGACTTAGCCCGGATATAGTCAATAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCAATAGCACAAATG
55253637 CCTTCGGGACTTAGCCCGGATATAGTCAATAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCAATAGCACAAATG
55253677 CCTTCGGGACTTAGCCCGGATATAGTCAATAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCAATAGCACAAATG
55253717 CCTTCGGGACTTAGCCCGGATATAGT
1 CCTTCGGGACTTAGCCCGGATATAGT
55253743 TCGAATAATC
Statistics
Matches: 216, Mismatches: 8, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
39 12 0.06
40 201 0.93
41 3 0.01
ACGTcount: A:0.28, C:0.26, G:0.23, T:0.23
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTCAATAGCACAAATG
Found at i:55256816 original size:26 final size:27
Alignment explanation
Indices: 55256755--55256823 Score: 86
Period size: 27 Copynumber: 2.6 Consensus size: 27
55256745 GAAATACGAT
* * *
55256755 TGTAGTGTAAAATGACTGTAATGCCCC
1 TGTAGGGTAAAATGACCGTAATGACCC
55256782 TGTAGGGTAAAATGACCGTAAT-ACCC
1 TGTAGGGTAAAATGACCGTAATGACCC
* *
55256808 TGTATGGTAGAATGAC
1 TGTAGGGTAAAATGAC
55256824 GATTATGCTG
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
26 17 0.46
27 20 0.54
ACGTcount: A:0.32, C:0.16, G:0.25, T:0.28
Consensus pattern (27 bp):
TGTAGGGTAAAATGACCGTAATGACCC
Found at i:55257289 original size:28 final size:28
Alignment explanation
Indices: 55257248--55257304 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 28
55257238 TACTAGTTTG
* * *
55257248 TATTGGGTTTAGGCCCACCTGATTCTGT
1 TATTGGGCTAAGGCCCACCTGATACTGT
*
55257276 TATTGGGCTAAGGCCTACCTGATACTGT
1 TATTGGGCTAAGGCCCACCTGATACTGT
55257304 T
1 T
55257305 TCTGTGATGG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.18, C:0.21, G:0.25, T:0.37
Consensus pattern (28 bp):
TATTGGGCTAAGGCCCACCTGATACTGT
Found at i:55258554 original size:48 final size:48
Alignment explanation
Indices: 55258231--55258543 Score: 443
Period size: 48 Copynumber: 6.5 Consensus size: 48
55258221 TAGAGTACCA
* * *
55258231 ATGCCATGTCCCCGACATGGTCTTACA-T-GAATTCACATATCATCGCCG
1 ATGCCATGTCCCAGACATGGTCTTACACTGGCA--CATATATCATCGCCG
* *
55258279 ATGCCATGTCCCAGACATGGTCTTACACTGGCACACATATCATTGCCG
1 ATGCCATGTCCCAGACATGGTCTTACACTGGCACATATATCATCGCCG
* * *
55258327 ATGCCATGTCCCAGACATGGTCTTACACTGGCACATATATCATTGACA
1 ATGCCATGTCCCAGACATGGTCTTACACTGGCACATATATCATCGCCG
* * * *
55258375 ATACCATGTCCCAAACATGGTCTTACACTGGTACACATATCATCGCCG
1 ATGCCATGTCCCAGACATGGTCTTACACTGGCACATATATCATCGCCG
*
55258423 ATGCCATGTCCCAGACATGGTTTTACACTGGCACATATATCATCGCCG
1 ATGCCATGTCCCAGACATGGTCTTACACTGGCACATATATCATCGCCG
*
55258471 ATGCCATGTCCCAAACATGGTCTTACA-TAGGCACATATATCATCGCCG
1 ATGCCATGTCCCAGACATGGTCTTACACT-GGCACATATATCATCGCCG
*
55258519 ATCCCATGTCCCAGACATGGTCTTA
1 ATGCCATGTCCCAGACATGGTCTTA
55258544 TATAGGCACA
Statistics
Matches: 240, Mismatches: 22, Indels: 6
0.90 0.08 0.02
Matches are distributed among these distances:
47 1 0.00
48 236 0.98
49 1 0.00
50 2 0.01
ACGTcount: A:0.27, C:0.30, G:0.17, T:0.26
Consensus pattern (48 bp):
ATGCCATGTCCCAGACATGGTCTTACACTGGCACATATATCATCGCCG
Found at i:55263412 original size:31 final size:32
Alignment explanation
Indices: 55263369--55263454 Score: 120
Period size: 31 Copynumber: 2.7 Consensus size: 32
55263359 TCAATATGCT
* *
55263369 AATTTTTTTTAATCAATTTTAATTTCTTCAAG
1 AATTTTTATTAATCAATTCTAATTTCTTCAAG
*
55263401 -GTTTTTATTAATCAATTCTAATTTCTTCAAG
1 AATTTTTATTAATCAATTCTAATTTCTTCAAG
*
55263432 AATTTATATTAATCAATCTCTAA
1 AATTTTTATTAATCAAT-TCTAA
55263455 AAATTATAAC
Statistics
Matches: 47, Mismatches: 5, Indels: 3
0.85 0.09 0.05
Matches are distributed among these distances:
31 28 0.60
32 14 0.30
33 5 0.11
ACGTcount: A:0.34, C:0.12, G:0.03, T:0.51
Consensus pattern (32 bp):
AATTTTTATTAATCAATTCTAATTTCTTCAAG
Found at i:55265472 original size:46 final size:45
Alignment explanation
Indices: 55265385--55265558 Score: 152
Period size: 46 Copynumber: 3.8 Consensus size: 45
55265375 ACATCTCGCA
* *
55265385 GCCGATGCATGTCCCAGACATGTTTTACACTAGCTTACGTCTCGAG
1 GCCGATGCATGTCCCAGACATGTCTTACACTAGCCT-CGTCTCGAG
* * *
55265431 GCCGATGCATGTCCCAGATATGTCTTACACTAGCACTCGTCTCAAT
1 GCCGATGCATGTCCCAGACATGTCTTACACTAGC-CTCGTCTCGAG
* * * * * * *
55265477 GTCGATACAATGTCCAAGACATGGTCTTACACTGGCTCTCATAAT-GTG
1 GCCGATGC-ATGTCCCAGACAT-GTCTTACACTAGC-CTCGT-CTCGAG
* * *
55265525 GTCGATGCATGTTCTAGACATGTCTTACACTAGC
1 GCCGATGCATGTCCCAGACATGTCTTACACTAGC
55265559 TCACAACAAG
Statistics
Matches: 104, Mismatches: 20, Indels: 8
0.79 0.15 0.06
Matches are distributed among these distances:
46 57 0.55
47 23 0.22
48 23 0.22
49 1 0.01
ACGTcount: A:0.24, C:0.26, G:0.20, T:0.29
Consensus pattern (45 bp):
GCCGATGCATGTCCCAGACATGTCTTACACTAGCCTCGTCTCGAG
Done.