Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008150.1 Hibiscus syriacus cultivar Beakdansim tig00110716_pilon, whole genome shotgun sequence
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: 3012591
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 12 of 14
Found at i:2442981 original size:79 final size:77
Alignment explanation
Indices: 2442848--2442991 Score: 198
Period size: 79 Copynumber: 1.8 Consensus size: 77
2442838 AGGTATGGGA
* * *
2442848 GAGACACATAGAGTGCAATGTGTCTTCGGGAGAAACGAGGAGACACATGGAGTGCAATGCATCTT
1 GAGACACATAGAGTGCAATGCGTATTCGGGAGAAACGAAGAGACACATGGAGTGCAATGCATCTT
2442913 CAGGGGAAGGGG
66 CAGGGGAAGGGG
* * * * *
2442925 GAGACTCATGGAGTGCAATGCGTATTCGGGGGGAAAGGGAAGAGACACATGTAGTGCAATGCATC
1 GAGACACATAGAGTGCAATGCGTATTC-GGGAGAAA-CGAAGAGACACATGGAGTGCAATGCATC
2442990 TT
64 TT
2442992 TCGTGTGTAC
Statistics
Matches: 57, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
77 23 0.40
78 7 0.12
79 27 0.47
ACGTcount: A:0.31, C:0.15, G:0.35, T:0.19
Consensus pattern (77 bp):
GAGACACATAGAGTGCAATGCGTATTCGGGAGAAACGAAGAGACACATGGAGTGCAATGCATCTT
CAGGGGAAGGGG
Found at i:2447420 original size:21 final size:21
Alignment explanation
Indices: 2447394--2447480 Score: 66
Period size: 21 Copynumber: 4.0 Consensus size: 21
2447384 AAAGTGCCAT
*
2447394 AGTACACAAAGTGCTATTACG
1 AGTACACAAAGTACTATTACG
* * *
2447415 AGTACACAAAGTACTCTTGCCAT
1 AGTACACAAAGTACTATT-AC-G
* * * *
2447438 AATACACAAAGTACTACTCCA
1 AGTACACAAAGTACTATTACG
* *
2447459 AGTACACAAAGTGCTCTTACG
1 AGTACACAAAGTACTATTACG
2447480 A
1 A
2447481 AAATGCAACA
Statistics
Matches: 50, Mismatches: 14, Indels: 4
0.74 0.21 0.06
Matches are distributed among these distances:
21 32 0.64
22 3 0.06
23 15 0.30
ACGTcount: A:0.39, C:0.24, G:0.14, T:0.23
Consensus pattern (21 bp):
AGTACACAAAGTACTATTACG
Found at i:2447437 original size:44 final size:44
Alignment explanation
Indices: 2447388--2447476 Score: 124
Period size: 44 Copynumber: 2.0 Consensus size: 44
2447378 GCGCACAAAG
* * * *
2447388 TGCCATAGTACACAAAGTGCTATTACGAGTACACAAAGTACTCT
1 TGCCATAATACACAAAGTACTACTACAAGTACACAAAGTACTCT
* *
2447432 TGCCATAATACACAAAGTACTACTCCAAGTACACAAAGTGCTCT
1 TGCCATAATACACAAAGTACTACTACAAGTACACAAAGTACTCT
2447476 T
1 T
2447477 ACGAAAATGC
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
44 39 1.00
ACGTcount: A:0.37, C:0.25, G:0.13, T:0.25
Consensus pattern (44 bp):
TGCCATAATACACAAAGTACTACTACAAGTACACAAAGTACTCT
Found at i:2447447 original size:23 final size:21
Alignment explanation
Indices: 2447417--2447476 Score: 68
Period size: 21 Copynumber: 2.8 Consensus size: 21
2447407 CTATTACGAG
2447417 TACACAAAGTACTCTTGCCATAA
1 TACACAAAGTACTCTT-CCA-AA
*
2447440 TACACAAAGTACTAC-TCCAAG
1 TACACAAAGTACT-CTTCCAAA
*
2447461 TACACAAAGTGCTCTT
1 TACACAAAGTACTCTT
2447477 ACGAAAATGC
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
20 1 0.03
21 14 0.42
22 3 0.09
23 14 0.42
24 1 0.03
ACGTcount: A:0.38, C:0.27, G:0.10, T:0.25
Consensus pattern (21 bp):
TACACAAAGTACTCTTCCAAA
Found at i:2447905 original size:13 final size:13
Alignment explanation
Indices: 2447883--2447917 Score: 61
Period size: 13 Copynumber: 2.7 Consensus size: 13
2447873 ACTCACCATG
*
2447883 TATGCTTTAATAT
1 TATGCCTTAATAT
2447896 TATGCCTTAATAT
1 TATGCCTTAATAT
2447909 TATGCCTTA
1 TATGCCTTA
2447918 CTGTAGTTCG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.29, C:0.14, G:0.09, T:0.49
Consensus pattern (13 bp):
TATGCCTTAATAT
Found at i:2464886 original size:17 final size:18
Alignment explanation
Indices: 2464864--2464897 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
2464854 TTGAAAGGTC
*
2464864 TGGAA-TAAATGATAAGT
1 TGGAATTAAATAATAAGT
2464881 TGGAATTAAATAATAAG
1 TGGAATTAAATAATAAG
2464898 ACATAATGGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.50, C:0.00, G:0.21, T:0.29
Consensus pattern (18 bp):
TGGAATTAAATAATAAGT
Found at i:2470778 original size:24 final size:25
Alignment explanation
Indices: 2470751--2470804 Score: 58
Period size: 24 Copynumber: 2.2 Consensus size: 25
2470741 ATATTTTATT
*
2470751 TGATTTC-CAACTTGAATTATGTTC
1 TGATTTCACAACCTGAATTATGTTC
* * *
2470775 TGA-TACATAACCTGAATTCTGTTC
1 TGATTTCACAACCTGAATTATGTTC
2470799 TGATTT
1 TGATTT
2470805 GGATTATGTT
Statistics
Matches: 23, Mismatches: 5, Indels: 3
0.74 0.16 0.10
Matches are distributed among these distances:
23 2 0.09
24 20 0.87
25 1 0.04
ACGTcount: A:0.26, C:0.17, G:0.13, T:0.44
Consensus pattern (25 bp):
TGATTTCACAACCTGAATTATGTTC
Found at i:2470919 original size:2 final size:2
Alignment explanation
Indices: 2470912--2470942 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2470902 GGGATGGGGG
2470912 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2470943 GTTTTAAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2472626 original size:20 final size:20
Alignment explanation
Indices: 2472603--2472646 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
2472593 ATCCTAAAAA
*
2472603 TAAAAAAAAAATATAATTCC
1 TAAAAAAAAAAGATAATTCC
* *
2472623 TAAAAACAAGAGATAATTCC
1 TAAAAAAAAAAGATAATTCC
2472643 TAAA
1 TAAA
2472647 TATAATTCTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.61, C:0.11, G:0.05, T:0.23
Consensus pattern (20 bp):
TAAAAAAAAAAGATAATTCC
Found at i:2478086 original size:15 final size:15
Alignment explanation
Indices: 2478066--2478102 Score: 65
Period size: 15 Copynumber: 2.5 Consensus size: 15
2478056 AGAGTAAAAA
2478066 GAAATAAAGATTATT
1 GAAATAAAGATTATT
2478081 GAAATAAAGATTATT
1 GAAATAAAGATTATT
*
2478096 GGAATAA
1 GAAATAA
2478103 CTGTTAGTCT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.54, C:0.00, G:0.16, T:0.30
Consensus pattern (15 bp):
GAAATAAAGATTATT
Found at i:2478475 original size:20 final size:20
Alignment explanation
Indices: 2478450--2478502 Score: 99
Period size: 20 Copynumber: 2.7 Consensus size: 20
2478440 TAACTGAGGA
2478450 TTCCGTTAGCTAATGAATTC
1 TTCCGTTAGCTAATGAATTC
2478470 TTCCGTTAGCTAATGAATTC
1 TTCCGTTAGCTAATGAATTC
2478490 TTCCGTTAG-TAAT
1 TTCCGTTAGCTAAT
2478503 TCTAAATTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
19 4 0.12
20 29 0.88
ACGTcount: A:0.25, C:0.19, G:0.15, T:0.42
Consensus pattern (20 bp):
TTCCGTTAGCTAATGAATTC
Found at i:2482733 original size:13 final size:13
Alignment explanation
Indices: 2482715--2482739 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2482705 TCAGCTTTTC
2482715 CTTTATTTTTAAG
1 CTTTATTTTTAAG
2482728 CTTTATTTTTAA
1 CTTTATTTTTAA
2482740 ATATACTAAG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.08, G:0.04, T:0.64
Consensus pattern (13 bp):
CTTTATTTTTAAG
Found at i:2486442 original size:19 final size:20
Alignment explanation
Indices: 2486410--2486453 Score: 63
Period size: 19 Copynumber: 2.2 Consensus size: 20
2486400 GTATTGATAC
*
2486410 TACTATATAGAGTAGTATTGA
1 TACTATATA-AGTAGTATCGA
2486431 TACTATAT-AGTAGTATCGA
1 TACTATATAAGTAGTATCGA
2486450 TACT
1 TACT
2486454 CCTTTGATAG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 14 0.64
21 8 0.36
ACGTcount: A:0.36, C:0.09, G:0.16, T:0.39
Consensus pattern (20 bp):
TACTATATAAGTAGTATCGA
Found at i:2489371 original size:17 final size:18
Alignment explanation
Indices: 2489315--2489381 Score: 118
Period size: 18 Copynumber: 3.8 Consensus size: 18
2489305 CTGTGCTTAT
2489315 TTTTCAAAATCAAAACAG
1 TTTTCAAAATCAAAACAG
*
2489333 TTTTCAAAATCAAAACAA
1 TTTTCAAAATCAAAACAG
2489351 TTTTCAAAATC-AAACAG
1 TTTTCAAAATCAAAACAG
2489368 TTTTCAAAATCAAA
1 TTTTCAAAATCAAA
2489382 GATTGACTTT
Statistics
Matches: 46, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
17 16 0.35
18 30 0.65
ACGTcount: A:0.51, C:0.16, G:0.03, T:0.30
Consensus pattern (18 bp):
TTTTCAAAATCAAAACAG
Found at i:2489834 original size:21 final size:22
Alignment explanation
Indices: 2489789--2489835 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 22
2489779 TAAAATCTTT
* *
2489789 TTTTATTTTTACTTTAAATCGC
1 TTTTATTATTACTTTAAATAGC
*
2489811 TTTTATTATTA-TTTAAATATC
1 TTTTATTATTACTTTAAATAGC
2489832 TTTT
1 TTTT
2489836 TACAAAAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 12 0.55
22 10 0.45
ACGTcount: A:0.26, C:0.09, G:0.02, T:0.64
Consensus pattern (22 bp):
TTTTATTATTACTTTAAATAGC
Found at i:2489836 original size:22 final size:23
Alignment explanation
Indices: 2489788--2489837 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 23
2489778 TTAAAATCTT
* *
2489788 TTTTTATTTTTACTTTAAATCGC
1 TTTTTATTATTACTTTAAATAGC
*
2489811 -TTTTATTATTA-TTTAAATATC
1 TTTTTATTATTACTTTAAATAGC
2489832 TTTTTA
1 TTTTTA
2489838 CAAAAAAACC
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
21 8 0.35
22 15 0.65
ACGTcount: A:0.26, C:0.08, G:0.02, T:0.64
Consensus pattern (23 bp):
TTTTTATTATTACTTTAAATAGC
Found at i:2492532 original size:19 final size:19
Alignment explanation
Indices: 2492491--2492534 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
2492481 TTTTCTAAAT
* *
2492491 TTTTATTATTTTCATGATT
1 TTTTAATATTTTCATGATA
2492510 TTTTAATATTTT-ATGTATA
1 TTTTAATATTTTCATG-ATA
2492529 TTTTAA
1 TTTTAA
2492535 GATCTATATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 3 0.14
19 19 0.86
ACGTcount: A:0.27, C:0.02, G:0.05, T:0.66
Consensus pattern (19 bp):
TTTTAATATTTTCATGATA
Found at i:2497343 original size:146 final size:146
Alignment explanation
Indices: 2496943--2497321 Score: 607
Period size: 146 Copynumber: 2.6 Consensus size: 146
2496933 GGATATCAGG
2496943 ATCTCCGATCAATATTCCGAACGGTCAAAAGTTGCGGAAGGCCATCACGAACAACATATTGAAAA
1 ATCTCCGATCAATATTCCGAACGGTCAAAAGTTGCGGAAGGCCATCACGAACAACATATTGAAAA
* * ** *
2497008 ATCAGGACGATCAGACGGTGGACGGTGACGGATCGGAGAAAACAAATCCGGGTGGTTTTTAGCCT
66 ATCAGGACGATCGGACGGTGGACGGTGACGGATCGGAGAAAATAAATCCGGACGATTTTTAGCCT
2497073 CTTGCCGGTGATCGGA
131 CTTGCCGGTGATCGGA
* **
2497089 ATATTTGATCAATATTCCGAACGGTCAAAAGTTGCGGAAGGCCATCACGAACAACATATTGAAAA
1 ATCTCCGATCAATATTCCGAACGGTCAAAAGTTGCGGAAGGCCATCACGAACAACATATTGAAAA
2497154 ATCAGGACGATCGGACGGTGGACGGTGACGGATCGGAGAAAATAAATCCGGACGATTTTTAGCCT
66 ATCAGGACGATCGGACGGTGGACGGTGACGGATCGGAGAAAATAAATCCGGACGATTTTTAGCCT
2497219 CTTGCCGGTGATCGGA
131 CTTGCCGGTGATCGGA
* * * * * *
2497235 ATCTGCGATCAATATTCCGAACGGTGAAAAGTTGCGCG-ATGCCAACACAAACAACCTATTGAAA
1 ATCTCCGATCAATATTCCGAACGGTCAAAAGTTGCG-GAAGGCCATCACGAACAACATATTGAAA
*
2497299 AATCAGGACAATCGGACGGTGGA
65 AATCAGGACGATCGGACGGTGGA
2497322 TGACGGCAGA
Statistics
Matches: 215, Mismatches: 17, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
146 214 1.00
147 1 0.00
ACGTcount: A:0.33, C:0.21, G:0.26, T:0.21
Consensus pattern (146 bp):
ATCTCCGATCAATATTCCGAACGGTCAAAAGTTGCGGAAGGCCATCACGAACAACATATTGAAAA
ATCAGGACGATCGGACGGTGGACGGTGACGGATCGGAGAAAATAAATCCGGACGATTTTTAGCCT
CTTGCCGGTGATCGGA
Found at i:2504168 original size:125 final size:125
Alignment explanation
Indices: 2503945--2504322 Score: 485
Period size: 125 Copynumber: 3.0 Consensus size: 125
2503935 TTAGGATATG
* * **
2503945 TTGGGGCACGACTGAACCCACATCAGGTTGAGATGACAAGATTCAGACCAATGAGGCATGAAGAA
1 TTGGGGCACGACTGAACCCACATCATGTTGAGATGACAAGATTTAGACCAAAAAGGCATGAAGAA
*
2504010 TGAGCCTTAGAATTTGAGGTGATGGGGCATTTTAAAGGCCCGTACCAGTATAAGACAATA
66 TGAGCCTTACAATTTGAGGTGATGGGGCATTTTAAAGGCCCGTACCAGTATAAGACAATA
* * *
2504070 TTGGGGCACGACTGAACCCACGTCATGTTGAGATAACAAGATTTAAACCAAAAAGGCATGAAGAA
1 TTGGGGCACGACTGAACCCACATCATGTTGAGATGACAAGATTTAGACCAAAAAGGCATGAAGAA
** * * *
2504135 TGAGCCTTACAATTTGAGGTGATGGGGTTTTTTAAAGGCCCATACCGGTATAAGACACTGA
66 TGAGCCTTACAATTTGAGGTGATGGGGCATTTTAAAGGCCCGTACCAGTATAAGACAAT-A
* * * *
2504196 -TGGGGCATGACTGCACCCACATCGTG-TGAAGATGACAAGATTTAGACCAAGAAGGCATTGAGA
1 TTGGGGCACGACTGAACCCACATCATGTTG-AGATGACAAGATTTAGACCAAAAAGGCA-TGA-A
* * * * * *
2504259 GCA--AGCCTTACAATTTGAGATGTTGGGGCATTTTGAAGGCCCGTACCAGTGTAAGATAATA
63 GAATGAGCCTTACAATTTGAGGTGATGGGGCATTTTAAAGGCCCGTACCAGTATAAGACAATA
2504320 TTG
1 TTG
2504323 TGACACTAGG
Statistics
Matches: 217, Mismatches: 31, Indels: 10
0.84 0.12 0.04
Matches are distributed among these distances:
124 3 0.01
125 207 0.95
126 4 0.02
127 3 0.01
ACGTcount: A:0.33, C:0.17, G:0.26, T:0.23
Consensus pattern (125 bp):
TTGGGGCACGACTGAACCCACATCATGTTGAGATGACAAGATTTAGACCAAAAAGGCATGAAGAA
TGAGCCTTACAATTTGAGGTGATGGGGCATTTTAAAGGCCCGTACCAGTATAAGACAATA
Found at i:2505550 original size:36 final size:36
Alignment explanation
Indices: 2505472--2505570 Score: 119
Period size: 36 Copynumber: 2.8 Consensus size: 36
2505462 TGAAGTCTTT
* * * *
2505472 ACCAAATAATAGTGAAGC-GACCATCTTAAGCCTTC
1 ACCAAAGAATAGTGAAGCAAACCATCTTAAGCATGC
* * *
2505507 ACTAAAGAGTAGTGAAGCAAACCGTCTTAAGCATGC
1 ACCAAAGAATAGTGAAGCAAACCATCTTAAGCATGC
*
2505543 ACCAAAGAATAATGAAGCAAACCATCTT
1 ACCAAAGAATAGTGAAGCAAACCATCTT
2505571 GTGTCTTCAT
Statistics
Matches: 52, Mismatches: 11, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
35 15 0.29
36 37 0.71
ACGTcount: A:0.41, C:0.22, G:0.16, T:0.20
Consensus pattern (36 bp):
ACCAAAGAATAGTGAAGCAAACCATCTTAAGCATGC
Found at i:2506076 original size:54 final size:54
Alignment explanation
Indices: 2505997--2507682 Score: 2086
Period size: 54 Copynumber: 31.7 Consensus size: 54
2505987 AGAATATTTT
* *
2505997 CGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTGAAGAAGAGGTA
1 CGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTGAAGAAGATGTC
** * * * *
2506051 CGAGTTTTATACTCCTTAAAAAAAGAGGGAGCGAACCAGTTTGAAGAAGATGTC
1 CGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTGAAGAAGATGTC
* * *
2506105 CGAGTTCAATACTCCCTAGAGAAAGAGGAAGCGAACCCGTTTGAAGAAAATGTC
1 CGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTGAAGAAGATGTC
* *
2506159 TGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTGAAGAAGATGTA
1 CGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTGAAGAAGATGTC
* *
2506213 CGAGTTCCATACTCCCTAGAGAAAGAGGGGGCGAACCCGTTTGAAGAAGATGTT
1 CGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTGAAGAAGATGTC
*
2506267 CGAGTTCTATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTGAAGAAGATGTC
1 CGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTGAAGAAGATGTC
* *
2506321 CGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTGAAGAAGGTTTC
1 CGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTGAAGAAGATGTC
* * * *
2506375 CGAGTTCCATACTTCTTAGAGAAAGAGGGAGCGAACCCG--TG-TGAAGATATC
1 CGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTGAAGAAGATGTC
* * * * *
2506426 CGAGTTCCATACTCCTTAAAGAAAGAAGGAGCGAACCCATTTGAAG-AGATGTT
1 CGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTGAAGAAGATGTC
* * *
2506479 TGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTGAAGAAGATTTT
1 CGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTGAAGAAGATGTC
* * *
2506533 CGAGTTCCATACTTCCTAGAGAAAGAGGGAGCGAACCC--TTG-TGAAGATATC
1 CGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTGAAGAAGATGTC
* * * * *
2506584 CGAGTTCCATACTCCTTAAAGAAAGAAGGAGCGAACACGTTTGAAG-AGATATC
1 CGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTGAAGAAGATGTC
* * *
2506637 CGAGTTCCATACTCCTTAAAGAAAGAAGGAGCGAACCCGTTTGAAG-AGATGTC
1 CGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTGAAGAAGATGTC
* * ** *
2506690 TGAGTTCCATACTCCCTAGAGAAAGAGGGAGTGAACCCCGTAAGAAGAAGATGTT
1 CGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAA-CCCGTTTGAAGAAGATGTC
*
2506745 CGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTT---GAAGATGTT
1 CGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTGAAGAAGATGTC
* * * *
2506796 CGAGTTCTATACTCCCTAGAGAAAGAGAGAGTGAACCCGTTT---GAAGATGTT
1 CGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTGAAGAAGATGTC
* *
2506847 CGAGTTCTATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTGAAGAAGATATC
1 CGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTGAAGAAGATGTC
* * *
2506901 TGAGTTCCATACT-CCTTGAAGAAAGAAGGAGCGAACCCGTTTGAAGAAGATGTC
1 CGAGTTCCATACTCCCTAG-AGAAAGAGGGAGCGAACCCGTTTGAAGAAGATGTC
*
2506955 CGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTGAAGAAGATTTC
1 CGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTGAAGAAGATGTC
* * * *
2507009 CGAGTTCCATACTTCCAAGAGAAAGAGGGAGCGAACCCG--TG-TGAAGATATC
1 CGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTGAAGAAGATGTC
* * ** *
2507060 CGAGTTCCATACTCCTTAAAGAAAGAATGAGCGAACCCGTTTGAAG-AGATGTT
1 CGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTGAAGAAGATGTC
* * ** * *
2507113 TGAGTTCTATACTCCCTAGAGAAAGAGGGATTGAACCCGTTTGAAGAAGATTTTT
1 CGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTGAAGAAGA-TGTC
* * * *
2507168 CGAGTTTCATACTTCCTAGAGAAAGAGGGAGCGAACCCG--TGTA-AAGATATC
1 CGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTGAAGAAGATGTC
* * * *
2507219 CGAGTTCCATACTCCTTAAAGAAAGAAGGAGCGAACCCGTTTGAAG-AGATATC
1 CGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTGAAGAAGATGTC
* * *
2507272 CGAGTTCCATACTCCTTAAAGAAAGAAGGAGCGAACCCGTTTGAAG-AGATGTC
1 CGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTGAAGAAGATGTC
* * ** *
2507325 TGAGTTCCATACTCCCTAGAGAAAGAGGGAGTGAACCCCGTAAGAAGAAGATGTT
1 CGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAA-CCCGTTTGAAGAAGATGTC
*
2507380 CGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTT---GAAGATGTT
1 CGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTGAAGAAGATGTC
* * * * *
2507431 CGAGCTCTATACTCCCTAGAGAAAGAGAGAGTGAACCCGTTTGAAG-AGATGTT
1 CGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTGAAGAAGATGTC
*
2507484 CGAGTTCTATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTGAAGAAGATGTC
1 CGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTGAAGAAGATGTC
* * *** * *
2507538 CGAGTTCCATACTCCCTAAAGAAATAGGGAGCGAACCCGAAGGCAGAAGATTGTT
1 CGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTGAAGAAGA-TGTC
* * * * * *
2507593 TGAGTTTC-TACTCCCTAAATAAAGAGGGAGCGAACCC-ATTGACAGAAGATTGTT
1 CGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTGA-AGAAGA-TGTC
* *
2507647 CGAGTTCCATACTCTCT-GAAGCAAGAGGGAGCGAAC
1 CGAGTTCCATACTCCCTAG-AGAAAGAGGGAGCGAAC
2507683 TCGTAGGCAG
Statistics
Matches: 1432, Mismatches: 168, Indels: 63
0.86 0.10 0.04
Matches are distributed among these distances:
51 303 0.21
52 11 0.01
53 335 0.23
54 634 0.44
55 149 0.10
ACGTcount: A:0.33, C:0.20, G:0.26, T:0.21
Consensus pattern (54 bp):
CGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTGAAGAAGATGTC
Found at i:2506558 original size:212 final size:213
Alignment explanation
Indices: 2505997--2507682 Score: 2147
Period size: 212 Copynumber: 7.9 Consensus size: 213
2505987 AGAATATTTT
* * * **
2505997 CGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTGAAGAAGAGGTAC-GAGTTTTAT
1 CGAGTTCCATACTCCCTAAAGAAAGAAGGAGCGAACCCGTTTGAAGAAGATGT-CTGAGTTCCAT
* * * * * *
2506061 ACTCCTTAAAAAAAGAGGGAGCGAACCAGTTTGAAGAAGATGTCCGAGTTCAATACTCCCTAGAG
65 ACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTGAAGAAGATGTTCGAGTTCCATACTCCCTAGAG
* * * *
2506126 AAAGAGGAAGCGAACCCGTTTGAAGAAAATGTCTGAGTTCCATACTCCCTAGAGAAAGAGGGAGC
130 AAAGAGGGAGCGAACCCGTTTGAAGAAGATTTCCGAGTTCCATACTCCCTAGAGAAAGAGGGAGC
* *
2506191 GAACCCGTTTGAAGAAGATGTA
195 GAACCCGTTT---GAAGATATC
* * * *
2506213 CGAGTTCCATACTCCCTAGAGAAAGAGGGGGCGAACCCGTTTGAAGAAGATGT-TCGAGTTCTAT
1 CGAGTTCCATACTCCCTAAAGAAAGAAGGAGCGAACCCGTTTGAAGAAGATGTCT-GAGTTCCAT
*
2506277 ACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTGAAGAAGATGTCCGAGTTCCATACTCCCTAGAG
65 ACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTGAAGAAGATGTTCGAGTTCCATACTCCCTAGAG
* * *
2506342 AAAGAGGGAGCGAACCCGTTTGAAGAAGGTTTCCGAGTTCCATACTTCTTAGAGAAAGAGGGAGC
130 AAAGAGGGAGCGAACCCGTTTGAAGAAGATTTCCGAGTTCCATACTCCCTAGAGAAAGAGGGAGC
*
2506407 GAACCCGTGTGAAGATATC
195 GAACCCGTTTGAAGATATC
* * *
2506426 CGAGTTCCATACTCCTTAAAGAAAGAAGGAGCGAACCCATTTGAAG-AGATGTTTGAGTTCCATA
1 CGAGTTCCATACTCCCTAAAGAAAGAAGGAGCGAACCCGTTTGAAGAAGATGTCTGAGTTCCATA
* *
2506490 CTCCCTAGAGAAAGAGGGAGCGAACCCGTTTGAAGAAGATTTTCGAGTTCCATACTTCCTAGAGA
66 CTCCCTAGAGAAAGAGGGAGCGAACCCGTTTGAAGAAGATGTTCGAGTTCCATACTCCCTAGAGA
* * * * *
2506555 AAGAGGGAGCGAACCC--TTG-TGAAGATATCCGAGTTCCATACTCCTTAAAGAAAGAAGGAGCG
131 AAGAGGGAGCGAACCCGTTTGAAGAAGATTTCCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCG
*
2506617 AACACGTTTGAAGAGATATC
196 AACCCGTTTG-A-AGATATC
*
2506637 CGAGTTCCATACTCCTTAAAGAAAGAAGGAGCGAACCCGTTTGAAG-AGATGTCTGAGTTCCATA
1 CGAGTTCCATACTCCCTAAAGAAAGAAGGAGCGAACCCGTTTGAAGAAGATGTCTGAGTTCCATA
* **
2506701 CTCCCTAGAGAAAGAGGGAGTGAACCCCGTAAGAAGAAGATGTTCGAGTTCCATACTCCCTAGAG
66 CTCCCTAGAGAAAGAGGGAGCGAA-CCCGTTTGAAGAAGATGTTCGAGTTCCATACTCCCTAGAG
* * * *
2506766 AAAGAGGGAGCGAACCCGTTTGAAGATG--TT-CGAGTTCTATACTCCCTAGAGAAAGAGAGAGT
130 AAAGAGGGAGCGAACCCGTTTGAAGAAGATTTCCGAGTTCCATACTCCCTAGAGAAAGAGGGAGC
* *
2506828 GAACCCGTTTGAAGATGTT
195 GAACCCGTTTGAAGATATC
* * * *
2506847 CGAGTTCTATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTGAAGAAGATATCTGAGTTCCATA
1 CGAGTTCCATACTCCCTAAAGAAAGAAGGAGCGAACCCGTTTGAAGAAGATGTCTGAGTTCCATA
* * *
2506912 CT-CCTTGAAGAAAGAAGGAGCGAACCCGTTTGAAGAAGATGTCCGAGTTCCATACTCCCTAGAG
66 CTCCCTAG-AGAAAGAGGGAGCGAACCCGTTTGAAGAAGATGTTCGAGTTCCATACTCCCTAGAG
* *
2506976 AAAGAGGGAGCGAACCCGTTTGAAGAAGATTTCCGAGTTCCATACTTCCAAGAGAAAGAGGGAGC
130 AAAGAGGGAGCGAACCCGTTTGAAGAAGATTTCCGAGTTCCATACTCCCTAGAGAAAGAGGGAGC
*
2507041 GAACCCGTGTGAAGATATC
195 GAACCCGTTTGAAGATATC
* * * *
2507060 CGAGTTCCATACTCCTTAAAGAAAGAATGAGCGAACCCGTTTGAAG-AGATGTTTGAGTTCTATA
1 CGAGTTCCATACTCCCTAAAGAAAGAAGGAGCGAACCCGTTTGAAGAAGATGTCTGAGTTCCATA
** * * *
2507124 CTCCCTAGAGAAAGAGGGATTGAACCCGTTTGAAGAAGATTTTTCGAGTTTCATACTTCCTAGAG
66 CTCCCTAGAGAAAGAGGGAGCGAACCCGTTTGAAGAAGA-TGTTCGAGTTCCATACTCCCTAGAG
* * * * *
2507189 AAAGAGGGAGCGAACCCG--TGTA-AAGATATCCGAGTTCCATACTCCTTAAAGAAAGAAGGAGC
130 AAAGAGGGAGCGAACCCGTTTGAAGAAGATTTCCGAGTTCCATACTCCCTAGAGAAAGAGGGAGC
2507251 GAACCCGTTTGAAGAGATATC
195 GAACCCGTTTG-A-AGATATC
*
2507272 CGAGTTCCATACTCCTTAAAGAAAGAAGGAGCGAACCCGTTTGAAG-AGATGTCTGAGTTCCATA
1 CGAGTTCCATACTCCCTAAAGAAAGAAGGAGCGAACCCGTTTGAAGAAGATGTCTGAGTTCCATA
* **
2507336 CTCCCTAGAGAAAGAGGGAGTGAACCCCGTAAGAAGAAGATGTTCGAGTTCCATACTCCCTAGAG
66 CTCCCTAGAGAAAGAGGGAGCGAA-CCCGTTTGAAGAAGATGTTCGAGTTCCATACTCCCTAGAG
* * * * *
2507401 AAAGAGGGAGCGAACCCGTTTGAAGATG--TT-CGAGCTCTATACTCCCTAGAGAAAGAGAGAGT
130 AAAGAGGGAGCGAACCCGTTTGAAGAAGATTTCCGAGTTCCATACTCCCTAGAGAAAGAGGGAGC
* *
2507463 GAACCCGTTTGAAGAGATGTT
195 GAACCCGTTTG-A-AGATATC
* * * *
2507484 CGAGTTCTATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTGAAGAAGATGTCCGAGTTCCATA
1 CGAGTTCCATACTCCCTAAAGAAAGAAGGAGCGAACCCGTTTGAAGAAGATGTCTGAGTTCCATA
* * *** * * * * *
2507549 CTCCCTAAAGAAATAGGGAGCGAACCCGAAGGCAGAAGATTGTTTGAGTTTC-TACTCCCTAAAT
66 CTCCCTAGAGAAAGAGGGAGCGAACCCGTTTGAAGAAGA-TGTTCGAGTTCCATACTCCCTAGAG
* * * *
2507613 AAAGAGGGAGCGAACCC-ATTGACAGAAGATTGTTCGAGTTCCATACTCTCT-GAAGCAAGAGGG
130 AAAGAGGGAGCGAACCCGTTTGA-AGAAGATT-TCCGAGTTCCATACTCCCTAG-AGAAAGAGGG
2507676 AGCGAAC
192 AGCGAAC
2507683 TCGTAGGCAG
Statistics
Matches: 1298, Mismatches: 142, Indels: 60
0.87 0.09 0.04
Matches are distributed among these distances:
209 45 0.03
210 163 0.13
211 134 0.10
212 489 0.38
213 239 0.18
214 7 0.01
215 7 0.01
216 214 0.16
ACGTcount: A:0.33, C:0.20, G:0.26, T:0.21
Consensus pattern (213 bp):
CGAGTTCCATACTCCCTAAAGAAAGAAGGAGCGAACCCGTTTGAAGAAGATGTCTGAGTTCCATA
CTCCCTAGAGAAAGAGGGAGCGAACCCGTTTGAAGAAGATGTTCGAGTTCCATACTCCCTAGAGA
AAGAGGGAGCGAACCCGTTTGAAGAAGATTTCCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCG
AACCCGTTTGAAGATATC
Found at i:2508608 original size:146 final size:146
Alignment explanation
Indices: 2508208--2508586 Score: 607
Period size: 146 Copynumber: 2.6 Consensus size: 146
2508198 GGATATCAGG
2508208 ATCTCCGATCAATATTCCGAACGGTCAAAAGTTGCGGAAGGCCATCACGAACAACATATTGAAAA
1 ATCTCCGATCAATATTCCGAACGGTCAAAAGTTGCGGAAGGCCATCACGAACAACATATTGAAAA
* * ** *
2508273 ATCAGGACGATCAGACGGTGGACGGTGACGGATCGGAGAAAACAAATCCGGGTGGTTTTTAGCCT
66 ATCAGGACGATCGGACGGTGGACGGTGACGGATCGGAGAAAATAAATCCGGACGATTTTTAGCCT
2508338 CTTGCCGGTGATCGGA
131 CTTGCCGGTGATCGGA
* **
2508354 ATATTTGATCAATATTCCGAACGGTCAAAAGTTGCGGAAGGCCATCACGAACAACATATTGAAAA
1 ATCTCCGATCAATATTCCGAACGGTCAAAAGTTGCGGAAGGCCATCACGAACAACATATTGAAAA
2508419 ATCAGGACGATCGGACGGTGGACGGTGACGGATCGGAGAAAATAAATCCGGACGATTTTTAGCCT
66 ATCAGGACGATCGGACGGTGGACGGTGACGGATCGGAGAAAATAAATCCGGACGATTTTTAGCCT
2508484 CTTGCCGGTGATCGGA
131 CTTGCCGGTGATCGGA
* * * * * *
2508500 ATCTGCGATCAATATTCCGAACGGTGAAAAGTTGCGCG-ATGCCAACACAAACAACCTATTGAAA
1 ATCTCCGATCAATATTCCGAACGGTCAAAAGTTGCG-GAAGGCCATCACGAACAACATATTGAAA
*
2508564 AATCAGGACAATCGGACGGTGGA
65 AATCAGGACGATCGGACGGTGGA
2508587 TGACGGCAGA
Statistics
Matches: 215, Mismatches: 17, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
146 214 1.00
147 1 0.00
ACGTcount: A:0.33, C:0.21, G:0.26, T:0.21
Consensus pattern (146 bp):
ATCTCCGATCAATATTCCGAACGGTCAAAAGTTGCGGAAGGCCATCACGAACAACATATTGAAAA
ATCAGGACGATCGGACGGTGGACGGTGACGGATCGGAGAAAATAAATCCGGACGATTTTTAGCCT
CTTGCCGGTGATCGGA
Found at i:2510429 original size:117 final size:116
Alignment explanation
Indices: 2510224--2510433 Score: 255
Period size: 117 Copynumber: 1.8 Consensus size: 116
2510214 ACCCCAAAAT
* * *
2510224 TTTGGTTAGTAACCAAAATATACATTTTGAAAGTTTGATGGCCAAAGTAGAAAATTGGGAAAAGT
1 TTTGGTTAGTAACCAAAATATAAATTTTGAAAGTTAGATGGCCAAAGTAGAAAATTGGGAAAACT
** *
2510289 TTAAGGACCTAAGTGGAGATTTTACAAAAAAAAAATTTATTCCATAAATGGA
66 TTAAGGACAAAAGAGGAGATTTTA-AAAAAAAAAATTTATTCCATAAATGGA
* * ** *
2510341 TTTGGTTAGTGACCAAAATGTAAATTTTGAAAGTTA-AGTGGCCAAAGTCTAAAATTTGGAAAAC
1 TTTGGTTAGTAACCAAAATATAAATTTTGAAAGTTAGA-TGGCCAAAGTAGAAAATTGGGAAAAC
* *
2510405 TTT-AGAGACAAAAGAGTA-ATTTTTAAAAA
65 TTTAAG-GACAAAAGAGGAGATTTTAAAAAA
2510434 TAATGTAATC
Statistics
Matches: 78, Mismatches: 13, Indels: 6
0.80 0.13 0.06
Matches are distributed among these distances:
115 5 0.06
116 8 0.10
117 65 0.83
ACGTcount: A:0.43, C:0.08, G:0.19, T:0.30
Consensus pattern (116 bp):
TTTGGTTAGTAACCAAAATATAAATTTTGAAAGTTAGATGGCCAAAGTAGAAAATTGGGAAAACT
TTAAGGACAAAAGAGGAGATTTTAAAAAAAAAAATTTATTCCATAAATGGA
Found at i:2510643 original size:19 final size:19
Alignment explanation
Indices: 2510619--2510661 Score: 86
Period size: 19 Copynumber: 2.3 Consensus size: 19
2510609 TTGCAGAAAT
2510619 ATTATTTCCACATTTTAAA
1 ATTATTTCCACATTTTAAA
2510638 ATTATTTCCACATTTTAAA
1 ATTATTTCCACATTTTAAA
2510657 ATTAT
1 ATTAT
2510662 GGAAAATAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.37, C:0.14, G:0.00, T:0.49
Consensus pattern (19 bp):
ATTATTTCCACATTTTAAA
Found at i:2519079 original size:14 final size:15
Alignment explanation
Indices: 2519062--2519095 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
2519052 TTAAAAAACA
2519062 AAAAAAT-GAAAAAG
1 AAAAAATGGAAAAAG
2519076 AAAAAATGGAAAAAG
1 AAAAAATGGAAAAAG
2519091 AAAAA
1 AAAAA
2519096 GAAAAAAAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 7 0.37
15 12 0.63
ACGTcount: A:0.79, C:0.00, G:0.15, T:0.06
Consensus pattern (15 bp):
AAAAAATGGAAAAAG
Found at i:2519079 original size:15 final size:16
Alignment explanation
Indices: 2519055--2519095 Score: 59
Period size: 15 Copynumber: 2.7 Consensus size: 16
2519045 AGGAATTTTA
*
2519055 AAAAACAAAAAAAT-G
1 AAAAAGAAAAAAATGG
2519070 AAAAAG-AAAAAATGG
1 AAAAAGAAAAAAATGG
2519085 AAAAAGAAAAA
1 AAAAAGAAAAA
2519096 GAAAAAAAGA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
14 7 0.30
15 12 0.52
16 4 0.17
ACGTcount: A:0.80, C:0.02, G:0.12, T:0.05
Consensus pattern (16 bp):
AAAAAGAAAAAAATGG
Found at i:2519079 original size:21 final size:20
Alignment explanation
Indices: 2519062--2519102 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 20
2519052 TTAAAAAACA
2519062 AAAAAATGAAAAAGAAAAAATG
1 AAAAAA-GAAAAAGAAAAAA-G
*
2519084 GAAAAAGAAAAAGAAAAAA
1 AAAAAAGAAAAAGAAAAAA
2519103 AGAGAGATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.80, C:0.00, G:0.15, T:0.05
Consensus pattern (20 bp):
AAAAAAGAAAAAGAAAAAAG
Found at i:2519103 original size:15 final size:15
Alignment explanation
Indices: 2519055--2519105 Score: 50
Period size: 15 Copynumber: 3.5 Consensus size: 15
2519045 AGGAATTTTA
* *
2519055 AAAAACAAAAAAATG
1 AAAAAGAAAAAAAAG
**
2519070 AAAAAGAAAAAATGG
1 AAAAAGAAAAAAAAG
*
2519085 AAAAAGAAAAAGAA-
1 AAAAAGAAAAAAAAG
2519099 AAAAAGA
1 AAAAAGA
2519106 GAGATAATAA
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
14 7 0.23
15 23 0.77
ACGTcount: A:0.80, C:0.02, G:0.14, T:0.04
Consensus pattern (15 bp):
AAAAAGAAAAAAAAG
Found at i:2530273 original size:18 final size:20
Alignment explanation
Indices: 2530240--2530281 Score: 70
Period size: 18 Copynumber: 2.2 Consensus size: 20
2530230 AATCTAGACC
2530240 AAAATCTATCTTTGATTTTG
1 AAAATCTATCTTTGATTTTG
2530260 AAAA-CTAT-TTTGATTTTG
1 AAAATCTATCTTTGATTTTG
2530278 AAAA
1 AAAA
2530282 ATAAGCACAG
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 14 0.64
19 4 0.18
20 4 0.18
ACGTcount: A:0.38, C:0.07, G:0.10, T:0.45
Consensus pattern (20 bp):
AAAATCTATCTTTGATTTTG
Found at i:2530282 original size:19 final size:20
Alignment explanation
Indices: 2530240--2530282 Score: 63
Period size: 19 Copynumber: 2.2 Consensus size: 20
2530230 AATCTAGACC
*
2530240 AAAATCTATCTTTGATTTTG
1 AAAAACTATCTTTGATTTTG
2530260 -AAAACTAT-TTTGATTTTG
1 AAAAACTATCTTTGATTTTG
2530278 AAAAA
1 AAAAA
2530283 TAAGCACAGA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
18 10 0.48
19 11 0.52
ACGTcount: A:0.40, C:0.07, G:0.09, T:0.44
Consensus pattern (20 bp):
AAAAACTATCTTTGATTTTG
Found at i:2538204 original size:18 final size:17
Alignment explanation
Indices: 2538182--2538225 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
2538172 GTTCTTTCTG
*
2538182 TATTTTTATTATTTTCA
1 TATTTTTATTATTTTAA
* *
2538199 TGATTTTCATTTTTTTAA
1 T-ATTTTTATTATTTTAA
2538217 TATTTTTAT
1 TATTTTTAT
2538226 GTATATTTTA
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
17 8 0.36
18 14 0.64
ACGTcount: A:0.23, C:0.05, G:0.02, T:0.70
Consensus pattern (17 bp):
TATTTTTATTATTTTAA
Found at i:2538572 original size:23 final size:22
Alignment explanation
Indices: 2538525--2538573 Score: 55
Period size: 23 Copynumber: 2.2 Consensus size: 22
2538515 TTTATTAGGT
*
2538525 ATTTTTTTCAAGTTAGTACTTA
1 ATTTTTTTCAAGTTAGTACTAA
*
2538547 ATTTCTTTTC-AGTTGGTACCTAA
1 ATTT-TTTTCAAGTTAGTA-CTAA
2538570 ATTT
1 ATTT
2538574 GGCACATTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
22 11 0.48
23 12 0.52
ACGTcount: A:0.24, C:0.12, G:0.10, T:0.53
Consensus pattern (22 bp):
ATTTTTTTCAAGTTAGTACTAA
Found at i:2547164 original size:31 final size:31
Alignment explanation
Indices: 2547090--2547164 Score: 105
Period size: 31 Copynumber: 2.4 Consensus size: 31
2547080 TTAAAACTTA
* *
2547090 CAATATAGTCCCCCAACATTTAGTCCATTTT
1 CAATATGGTCCCCCAACATTTAGTCCATTTG
* * *
2547121 CAATACGATCCCCCAACATTTAGTCTATTTG
1 CAATATGGTCCCCCAACATTTAGTCCATTTG
2547152 CAATATGGTCCCC
1 CAATATGGTCCCC
2547165 GACCGTTTGA
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 37 1.00
ACGTcount: A:0.28, C:0.31, G:0.09, T:0.32
Consensus pattern (31 bp):
CAATATGGTCCCCCAACATTTAGTCCATTTG
Found at i:2549135 original size:31 final size:31
Alignment explanation
Indices: 2549097--2549174 Score: 102
Period size: 31 Copynumber: 2.5 Consensus size: 31
2549087 TCAAACGGTC
* *
2549097 GGGGACCATATTGCAAACATATTAAATGTTA
1 GGGGACCATATTGCAAACAGACTAAATGTTA
* * *
2549128 GGGGACCATATTACAAACGGACTAAATGTTG
1 GGGGACCATATTGCAAACAGACTAAATGTTA
*
2549159 GGGGACTATATTGCAA
1 GGGGACCATATTGCAA
2549175 GTTTTAAAAG
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 40 1.00
ACGTcount: A:0.36, C:0.14, G:0.24, T:0.26
Consensus pattern (31 bp):
GGGGACCATATTGCAAACAGACTAAATGTTA
Found at i:2552712 original size:34 final size:34
Alignment explanation
Indices: 2552674--2552742 Score: 102
Period size: 34 Copynumber: 2.0 Consensus size: 34
2552664 ATTGATGTTA
* * *
2552674 TTTATAATAAGTCATGTCGCTTGGTGAATAGACT
1 TTTATAATAAGTCATATCACTTGGTAAATAGACT
*
2552708 TTTATAATAAGTCATATCACTTGGTAAATGGACT
1 TTTATAATAAGTCATATCACTTGGTAAATAGACT
2552742 T
1 T
2552743 ATTTTTTAGT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.32, C:0.12, G:0.17, T:0.39
Consensus pattern (34 bp):
TTTATAATAAGTCATATCACTTGGTAAATAGACT
Found at i:2552838 original size:20 final size:21
Alignment explanation
Indices: 2552812--2552858 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
2552802 AAAAATTAAT
* * *
2552812 CCTTTTACGAAAAGGTTAAGC
1 CCTTTAACCAAAAGGATAAGC
*
2552833 CCTTTAACCAAAAGGATAAGT
1 CCTTTAACCAAAAGGATAAGC
2552854 CCTTT
1 CCTTT
2552859 CATCGAAAGG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.34, C:0.21, G:0.15, T:0.30
Consensus pattern (21 bp):
CCTTTAACCAAAAGGATAAGC
Found at i:2554702 original size:12 final size:12
Alignment explanation
Indices: 2554682--2554719 Score: 67
Period size: 12 Copynumber: 3.2 Consensus size: 12
2554672 AATTAGACCT
*
2554682 AGAACCAAATTC
1 AGAATCAAATTC
2554694 AGAATCAAATTC
1 AGAATCAAATTC
2554706 AGAATCAAATTC
1 AGAATCAAATTC
2554718 AG
1 AG
2554720 GCAAATCTGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.50, C:0.18, G:0.11, T:0.21
Consensus pattern (12 bp):
AGAATCAAATTC
Found at i:2564190 original size:47 final size:47
Alignment explanation
Indices: 2564121--2564372 Score: 260
Period size: 47 Copynumber: 5.2 Consensus size: 47
2564111 TCCTATTATG
*
2564121 GGATGCCATAAC-AAAAATGCATGAAAGGATGCATTAAGGCATGAAA
1 GGATGCCATAACGAAAAATGCATGAAAAGATGCATTAAGGCATGAAA
* * * *
2564167 GGATGTCATAGCAAAAAATGCATGAAAGGATGCCA-TAACGAAAAATGCATGAAA
1 GGATGCCATAACGAAAAATGCATGAAAAGATG-CATTAA-G------GCATGAAA
* * *
2564221 GGATGCCATAACGAAAAATTCATGAAAATATGCATTAAGGAATGAAA
1 GGATGCCATAACGAAAAATGCATGAAAAGATGCATTAAGGCATGAAA
* *
2564268 GGATACCATAAC-AAAAATGCATGAAAAGATACATTAAGGCAAT-AAA
1 GGATGCCATAACGAAAAATGCATGAAAAGATGCATTAAGGC-ATGAAA
* * *
2564314 GGATGTCATAACGAAAAATGCATGAAATGATGCATTAAGGCATAAAAA
1 GGATGCCATAACGAAAAATGCATGAAAAGATGCATTAAGGCAT-GAAA
*
2564362 GAATGCCATAA
1 GGATGCCATAA
2564373 ATGAAATTAA
Statistics
Matches: 172, Mismatches: 20, Indels: 26
0.79 0.09 0.12
Matches are distributed among these distances:
46 49 0.28
47 68 0.40
48 15 0.09
53 3 0.02
54 37 0.22
ACGTcount: A:0.49, C:0.12, G:0.20, T:0.19
Consensus pattern (47 bp):
GGATGCCATAACGAAAAATGCATGAAAAGATGCATTAAGGCATGAAA
Found at i:2564253 original size:27 final size:27
Alignment explanation
Indices: 2564159--2564247 Score: 142
Period size: 27 Copynumber: 3.3 Consensus size: 27
2564149 ATGCATTAAG
* * *
2564159 GCATGAAAGGATGTCATAGCAAAAAAT
1 GCATGAAAGGATGCCATAACGAAAAAT
2564186 GCATGAAAGGATGCCATAACGAAAAAT
1 GCATGAAAGGATGCCATAACGAAAAAT
2564213 GCATGAAAGGATGCCATAACGAAAAAT
1 GCATGAAAGGATGCCATAACGAAAAAT
*
2564240 TCATGAAA
1 GCATGAAA
2564248 ATATGCATTA
Statistics
Matches: 58, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 58 1.00
ACGTcount: A:0.48, C:0.13, G:0.21, T:0.17
Consensus pattern (27 bp):
GCATGAAAGGATGCCATAACGAAAAAT
Found at i:2564854 original size:81 final size:81
Alignment explanation
Indices: 2564719--2564883 Score: 267
Period size: 81 Copynumber: 2.0 Consensus size: 81
2564709 CTATTTAAAA
* * * * *
2564719 TAAAAGATTAATGTCCTAGTTGTGCATTTGGCAGAAAGTTGTCAGTTATGCCAGTTAGATGAAAG
1 TAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
* *
2564784 GTTAAATATCTTTGAG
66 GTTAAATACCTTCGAG
2564800 TAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
1 TAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
2564865 GTTAAATACCTTCGAG
66 GTTAAATACCTTCGAG
2564881 TAA
1 TAA
2564884 CTGCCTTTGT
Statistics
Matches: 77, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
81 77 1.00
ACGTcount: A:0.34, C:0.12, G:0.23, T:0.32
Consensus pattern (81 bp):
TAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
GTTAAATACCTTCGAG
Found at i:2565048 original size:45 final size:44
Alignment explanation
Indices: 2564997--2565146 Score: 106
Period size: 44 Copynumber: 3.4 Consensus size: 44
2564987 TAATTGGTAA
*
2564997 GAAAAGATGTCATAAAGGAAAACATA-AACATTATATAAAAGGCAT
1 GAAAAGATGTCATAAA-GAAAACATATAACAGTATAT-AAAGGCAT
** * ** * *
2565042 GAAAAGATACCATAAATAAAATGTATAATAGTGTATAAAGGCAT
1 GAAAAGATGTCATAAAGAAAACATATAACAGTATATAAAGGCAT
* ** * * *
2565086 GAAAGGATGTCATAAATG-AAATGTATAATAGTGTACAAAAGGCAT
1 GAAAAGATGTCATAAA-GAAAACATATAACAGTATA-TAAAGGCAT
* *
2565131 GAAAGGATGCCATAAA
1 GAAAAGATGTCATAAA
2565147 TTAAATGTAT
Statistics
Matches: 88, Mismatches: 14, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
44 44 0.50
45 44 0.50
ACGTcount: A:0.51, C:0.08, G:0.19, T:0.22
Consensus pattern (44 bp):
GAAAAGATGTCATAAAGAAAACATATAACAGTATATAAAGGCAT
Found at i:2565100 original size:44 final size:44
Alignment explanation
Indices: 2565034--2565204 Score: 225
Period size: 45 Copynumber: 3.8 Consensus size: 44
2565024 ACATTATATA
* * *
2565034 AAAGGCATGAAAAGATACCATAAATAAAATGTATAATAGTGTAT
1 AAAGGCATGAAAGGATGCCATAAATGAAATGTATAATAGTGTAT
* *
2565078 AAAGGCATGAAAGGATGTCATAAATGAAATGTATAATAGTGTACA
1 AAAGGCATGAAAGGATGCCATAAATGAAATGTATAATAGTGTA-T
* **
2565123 AAAGGCATGAAAGGATGCCATAAATTAAATGTATAATAGCATAT
1 AAAGGCATGAAAGGATGCCATAAATGAAATGTATAATAGTGTAT
* *
2565167 AAAATGGCATGAAAGGATGCCAAAAATGAAATGCATAA
1 -AAA-GGCATGAAAGGATGCCATAAATGAAATGTATAA
2565205 GGGTGCATTA
Statistics
Matches: 111, Mismatches: 13, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
44 39 0.35
45 42 0.38
46 30 0.27
ACGTcount: A:0.50, C:0.08, G:0.19, T:0.23
Consensus pattern (44 bp):
AAAGGCATGAAAGGATGCCATAAATGAAATGTATAATAGTGTAT
Found at i:2565128 original size:89 final size:91
Alignment explanation
Indices: 2565033--2565204 Score: 258
Period size: 89 Copynumber: 1.9 Consensus size: 91
2565023 AACATTATAT
** *
2565033 AAAAGGCATGAAAAGATACCATAAATAAAATGTATAATAGTGTAT-AAA-GGCATGAAAGGATGT
1 AAAAGGCATGAAAAGATACCATAAATAAAATGTATAATAGCATATAAAATGGCATGAAAGGATGC
* *
2565096 CATAAATGAAATGTATAATAGTGTAC
66 CAAAAATGAAATGCATAATAGTGTAC
* * *
2565122 AAAAGGCATGAAAGGATGCCATAAATTAAATGTATAATAGCATATAAAATGGCATGAAAGGATGC
1 AAAAGGCATGAAAAGATACCATAAATAAAATGTATAATAGCATATAAAATGGCATGAAAGGATGC
2565187 CAAAAATGAAATGCATAA
66 CAAAAATGAAATGCATAA
2565205 GGGTGCATTA
Statistics
Matches: 73, Mismatches: 8, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
89 40 0.55
90 3 0.04
91 30 0.41
ACGTcount: A:0.50, C:0.08, G:0.19, T:0.23
Consensus pattern (91 bp):
AAAAGGCATGAAAAGATACCATAAATAAAATGTATAATAGCATATAAAATGGCATGAAAGGATGC
CAAAAATGAAATGCATAATAGTGTAC
Found at i:2565147 original size:45 final size:44
Alignment explanation
Indices: 2565033--2565204 Score: 227
Period size: 44 Copynumber: 3.8 Consensus size: 44
2565023 AACATTATAT
* * *
2565033 AAAAGGCATGAAAAGATACCATAAATAAAATGTATAATAGTGTA
1 AAAAGGCATGAAAGGATGCCATAAATGAAATGTATAATAGTGTA
* *
2565077 TAAAGGCATGAAAGGATGTCATAAATGAAATGTATAATAGTGTA
1 AAAAGGCATGAAAGGATGCCATAAATGAAATGTATAATAGTGTA
* *
2565121 CAAAAGGCATGAAAGGATGCCATAAATTAAATGTATAATAGCATATA
1 -AAAAGGCATGAAAGGATGCCATAAATGAAATGTATAATAG--TGTA
* * *
2565168 AAATGGCATGAAAGGATGCCAAAAATGAAATGCATAA
1 AAAAGGCATGAAAGGATGCCATAAATGAAATGTATAA
2565205 GGGTGCATTA
Statistics
Matches: 112, Mismatches: 13, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
44 39 0.35
45 37 0.33
46 33 0.29
47 3 0.03
ACGTcount: A:0.50, C:0.08, G:0.19, T:0.23
Consensus pattern (44 bp):
AAAAGGCATGAAAGGATGCCATAAATGAAATGTATAATAGTGTA
Found at i:2565237 original size:91 final size:89
Alignment explanation
Indices: 2565033--2565251 Score: 215
Period size: 91 Copynumber: 2.4 Consensus size: 89
2565023 AACATTATAT
* * ** *
2565033 AAAAGGCATGAAA-AGATACCATAAATAAAATGTATAATAGTGTATAAAGGCATGAAAGGATGTC
1 AAAAGGCATGAAAGA-ATGCAATAAATAAAATGTATAATAGCATATAAAGGCATGAAAGGATGCC
* * * *
2565097 ATAAATGAAATGTATAATAGTGTAC
65 AAAAATGAAATGCATAAGAGTGCAC
* * *
2565122 AAAAGGCATGAAAGGATGCCATAAATTAAATGTATAATAGCATATAAAATGGCATGAAAGGATGC
1 AAAAGGCATGAAAGAATGCAATAAATAAAATGTATAATAGCATAT-AAA-GGCATGAAAGGATGC
* *
2565187 CAAAAATGAAATGCATAAGGGTGCAT
64 CAAAAATGAAATGCATAAGAGTGCAC
* ** * * *
2565213 TATTGGCATGAAATAATGTAATAAATGAAAATGCATAAT
1 AAAAGGCATGAAAGAATGCAATAAAT-AAAATGTATAAT
2565252 GGTGCATTAT
Statistics
Matches: 105, Mismatches: 21, Indels: 5
0.80 0.16 0.04
Matches are distributed among these distances:
89 39 0.37
90 3 0.03
91 53 0.50
92 10 0.10
ACGTcount: A:0.48, C:0.08, G:0.20, T:0.24
Consensus pattern (89 bp):
AAAAGGCATGAAAGAATGCAATAAATAAAATGTATAATAGCATATAAAGGCATGAAAGGATGCCA
AAAATGAAATGCATAAGAGTGCAC
Found at i:2571095 original size:37 final size:38
Alignment explanation
Indices: 2571044--2571651 Score: 731
Period size: 39 Copynumber: 16.6 Consensus size: 38
2571034 AATATATAGT
* *
2571044 TTTTGAAAATATATATATATATATAGTTTTT-TAAACA
1 TTTTGAAAATATATATATATATATAGTTTTTGAAAATA
* *
2571081 TTTCGAAAACATATATATAATATATAGTTTTTGAAAATA
1 TTTTGAAAATATATATAT-ATATATAGTTTTTGAAAATA
*
2571120 TTTTG-AAATATATATATA-ATATA-----T---AGT-
1 TTTTGAAAATATATATATATATATAGTTTTTGAAAATA
*
2571147 TTTTGAAAATATATATA-ATATATAGTTTTTGAAAACA
1 TTTTGAAAATATATATATATATATAGTTTTTGAAAATA
*
2571184 TTTTG--AATATATATATATATATA-----T---AGT-
1 TTTTGAAAATATATATATATATATAGTTTTTGAAAATA
*
2571211 TTTTGAAAATACATATA-ATATATAGTTTTTGAAAATA
1 TTTTGAAAATATATATATATATATAGTTTTTGAAAATA
*
2571248 TTTTGAAAA-ATACATATAATATATAGTTTTTGAAAATA
1 TTTTGAAAATATATATAT-ATATATAGTTTTTGAAAATA
* * *
2571286 TTTTGAAAACATACATATAATATATAGTTTTTGAAAACA
1 TTTTGAAAATATATATAT-ATATATAGTTTTTGAAAATA
2571325 TTTTGAAAATATATATATAATATATAGTTTTTGAAAATA
1 TTTTGAAAATATATATAT-ATATATAGTTTTTGAAAATA
2571364 TTTTGAAAATATATATA-ATATATAGTTTTTGAAAATA
1 TTTTGAAAATATATATATATATATAGTTTTTGAAAATA
*
2571401 TTTTGAAAATATATATA-ATATATAGTTTTTGAAAACA
1 TTTTGAAAATATATATATATATATAGTTTTTGAAAATA
2571438 TTTTGAAAGCATATATATA-ATATATAGTTTTTGAAAATA
1 TTTTGAAA--ATATATATATATATATAGTTTTTGAAAATA
* *
2571477 TTTTGAAAAAATATATATAATATATACTTTTTGAAAATA
1 TTTTGAAAATATATATAT-ATATATAGTTTTTGAAAATA
*
2571516 TTTTGAAAATATATATA-ATATATAGTTTTTGAAAACA
1 TTTTGAAAATATATATATATATATAGTTTTTGAAAATA
* *
2571553 TTTTTGAATATATATATA-ATATATAGTTTTTGAAAACA
1 -TTTTGAAAATATATATATATATATAGTTTTTGAAAATA
*
2571591 TTTTGAAAATATATATAAAATATATAGTTTTTGAAAATA
1 TTTTGAAAATATATAT-ATATATATAGTTTTTGAAAATA
*
2571630 TTTTGAAAATATAT-TTTATATA
1 TTTTGAAAATATATATATATATA
2571652 AAAATATTTA
Statistics
Matches: 505, Mismatches: 31, Indels: 70
0.83 0.05 0.12
Matches are distributed among these distances:
27 11 0.02
28 26 0.05
29 9 0.02
31 2 0.00
33 2 0.00
35 10 0.02
36 20 0.04
37 141 0.28
38 91 0.18
39 193 0.38
ACGTcount: A:0.45, C:0.02, G:0.08, T:0.45
Consensus pattern (38 bp):
TTTTGAAAATATATATATATATATAGTTTTTGAAAATA
Found at i:2571197 original size:28 final size:26
Alignment explanation
Indices: 2571120--2571184 Score: 103
Period size: 26 Copynumber: 2.5 Consensus size: 26
2571110 TTTGAAAATA
*
2571120 TTTTGAAATATATATATAATATATAGT
1 TTTTGAAA-ACATATATAATATATAGT
*
2571147 TTTTGAAAATATATATAATATATAGT
1 TTTTGAAAACATATATAATATATAGT
2571173 TTTTGAAAACAT
1 TTTTGAAAACAT
2571185 TTTGAATATA
Statistics
Matches: 37, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
26 29 0.78
27 8 0.22
ACGTcount: A:0.45, C:0.02, G:0.08, T:0.46
Consensus pattern (26 bp):
TTTTGAAAACATATATAATATATAGT
Found at i:2571213 original size:26 final size:26
Alignment explanation
Indices: 2571184--2571248 Score: 103
Period size: 26 Copynumber: 2.5 Consensus size: 26
2571174 TTTGAAAACA
*
2571184 TTTTGAATATATATATATATATATAGT
1 TTTTGAAAATATATATA-ATATATAGT
*
2571211 TTTTGAAAATACATATAATATATAGT
1 TTTTGAAAATATATATAATATATAGT
2571237 TTTTGAAAATAT
1 TTTTGAAAATAT
2571249 TTTGAAAAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
26 20 0.57
27 15 0.43
ACGTcount: A:0.43, C:0.02, G:0.08, T:0.48
Consensus pattern (26 bp):
TTTTGAAAATATATATAATATATAGT
Found at i:2571367 original size:11 final size:11
Alignment explanation
Indices: 2571353--2571527 Score: 61
Period size: 11 Copynumber: 14.1 Consensus size: 11
2571343 AATATATAGT
2571353 TTTTGAAAATA
1 TTTTGAAAATA
2571364 TTTTGAAAATA
1 TTTTGAAAATA
*
2571375 TATAT-AATATATA
1 T-TTTGAA-A-ATA
2571388 GTTTTTGAAAATA
1 --TTTTGAAAATA
2571401 TTTTGAAAATA
1 TTTTGAAAATA
*
2571412 TATAT-AATATATA
1 T-TTTGAA-A-ATA
*
2571425 GTTTTTGAAAACA
1 --TTTTGAAAATA
2571438 TTTTGAAAGCATA
1 TTTTGAAA--ATA
*
2571451 TATAT-AATATATA
1 T-TTTGAA-A-ATA
2571464 GTTTTTGAAAATA
1 --TTTTGAAAATA
2571477 TTTTGAAAAAATA
1 TTTTG--AAAATA
*
2571490 TATAT-AATATATA
1 T-TTTGAA-A-ATA
2571503 CTTTTTGAAAATA
1 --TTTTGAAAATA
2571516 TTTTGAAAATA
1 TTTTGAAAATA
2571527 T
1 T
2571528 ATATAATATA
Statistics
Matches: 126, Mismatches: 11, Indels: 54
0.66 0.06 0.28
Matches are distributed among these distances:
11 55 0.44
12 7 0.06
13 35 0.28
14 17 0.13
15 12 0.10
ACGTcount: A:0.46, C:0.02, G:0.08, T:0.45
Consensus pattern (11 bp):
TTTTGAAAATA
Found at i:2571374 original size:28 final size:28
Alignment explanation
Indices: 2571325--2571378 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
2571315 TTTGAAAACA
*
2571325 TTTTGAAAATATATATATAATATATAGT
1 TTTTGAAAATATATATAAAATATATAGT
*
2571353 TTTTGAAAATAT-TTTGAAAATATATA
1 TTTTGAAAATATATAT-AAAATATATA
2571379 TAATATATAG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 2 0.09
28 21 0.91
ACGTcount: A:0.46, C:0.00, G:0.07, T:0.46
Consensus pattern (28 bp):
TTTTGAAAATATATATAAAATATATAGT
Found at i:2572986 original size:17 final size:17
Alignment explanation
Indices: 2572944--2572979 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
2572934 TTGCTATTCA
2572944 TTTATTCATTTATTTATT
1 TTTATT-ATTTATTTATT
*
2572962 TTTATTATTTTTTTATT
1 TTTATTATTTATTTATT
2572979 T
1 T
2572980 CTTTTATCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 11 0.65
18 6 0.35
ACGTcount: A:0.19, C:0.03, G:0.00, T:0.78
Consensus pattern (17 bp):
TTTATTATTTATTTATT
Found at i:2574030 original size:118 final size:118
Alignment explanation
Indices: 2573822--2574055 Score: 405
Period size: 118 Copynumber: 2.0 Consensus size: 118
2573812 AGGTGAAAGC
* * *
2573822 TACGCCTTCGTGAGAATTTATTCTCCATATAAGCCTAGCAAGTAACGTTCGGGATTCATATGCCT
1 TACGCCTTCGTGAGAATTTATTCTCCATATAAACCTAGCAAGTAACGTTCGAGATTCATATACCT
2573887 TATGTCTTCATGTGAATTTATTCTCCGTATAGACATAAGGGAATGTATCCTAG
66 TATGTCTTCATGTGAATTTATTCTCCGTATAGACATAAGGGAATGTATCCTAG
* * *
2573940 TACGCCTTCGTGATAATTTATTCTCCATATAAACCTAGCAGGTAATGTTCGAGATTCATATACCT
1 TACGCCTTCGTGAGAATTTATTCTCCATATAAACCTAGCAAGTAACGTTCGAGATTCATATACCT
*
2574005 TATGTCTTCGTGTGAATTTATTCTCCGTATAGACATAAGGGAATGTATCCT
66 TATGTCTTCATGTGAATTTATTCTCCGTATAGACATAAGGGAATGTATCCT
2574056 CTCAAGTTTA
Statistics
Matches: 109, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
118 109 1.00
ACGTcount: A:0.27, C:0.19, G:0.18, T:0.36
Consensus pattern (118 bp):
TACGCCTTCGTGAGAATTTATTCTCCATATAAACCTAGCAAGTAACGTTCGAGATTCATATACCT
TATGTCTTCATGTGAATTTATTCTCCGTATAGACATAAGGGAATGTATCCTAG
Found at i:2579998 original size:17 final size:17
Alignment explanation
Indices: 2579976--2580034 Score: 50
Period size: 17 Copynumber: 3.4 Consensus size: 17
2579966 TTTTATATCA
2579976 TTTCTTTTGAACTCAAT
1 TTTCTTTTGAACTCAAT
* * *
2579993 TTTC-TTT-CATTCAGTACC
1 TTTCTTTTGAACTCA--A-T
2580011 TTTCTTTTGAACTCAAT
1 TTTCTTTTGAACTCAAT
2580028 TTTCTTT
1 TTTCTTT
2580035 CATTCCGTAC
Statistics
Matches: 31, Mismatches: 6, Indels: 10
0.66 0.13 0.21
Matches are distributed among these distances:
15 4 0.13
16 3 0.10
17 12 0.39
18 5 0.16
19 3 0.10
20 4 0.13
ACGTcount: A:0.19, C:0.20, G:0.05, T:0.56
Consensus pattern (17 bp):
TTTCTTTTGAACTCAAT
Found at i:2580022 original size:35 final size:35
Alignment explanation
Indices: 2579976--2580044 Score: 129
Period size: 35 Copynumber: 2.0 Consensus size: 35
2579966 TTTTATATCA
2579976 TTTCTTTTGAACTCAATTTTCTTTCATTCAGTACC
1 TTTCTTTTGAACTCAATTTTCTTTCATTCAGTACC
*
2580011 TTTCTTTTGAACTCAATTTTCTTTCATTCCGTAC
1 TTTCTTTTGAACTCAATTTTCTTTCATTCAGTAC
2580045 TTCATTTCAT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.19, C:0.23, G:0.06, T:0.52
Consensus pattern (35 bp):
TTTCTTTTGAACTCAATTTTCTTTCATTCAGTACC
Found at i:2583465 original size:44 final size:44
Alignment explanation
Indices: 2583412--2583496 Score: 143
Period size: 44 Copynumber: 1.9 Consensus size: 44
2583402 AATAGTTCAC
* *
2583412 TTAGGGTGAAAACCCGAAAGGGCGCCCTAAGTTGAAAAAAACAT
1 TTAGGGTGAAAACCCGAAAGGGCGCCCTAAATTCAAAAAAACAT
*
2583456 TTAGGGTGAAAACCCGAAAGGGCGCCTTAAATTCAAAAAAA
1 TTAGGGTGAAAACCCGAAAGGGCGCCCTAAATTCAAAAAAA
2583497 AAGTAGGTCC
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
44 38 1.00
ACGTcount: A:0.42, C:0.18, G:0.24, T:0.16
Consensus pattern (44 bp):
TTAGGGTGAAAACCCGAAAGGGCGCCCTAAATTCAAAAAAACAT
Found at i:2585077 original size:39 final size:38
Alignment explanation
Indices: 2584991--2585449 Score: 292
Period size: 39 Copynumber: 13.3 Consensus size: 38
2584981 TATAATATAC
* * * * *
2584991 ATATA-TAATGTATAGTTTTT-TAAATGTTTCGAAAAC
1 ATATATTAATATATAGTTTTTGAAAATATTTTGAAAAT
2585027 ATATATATAATATATAGTTTTTGAAAATATTTTGAAAAT
1 ATATAT-TAATATATAGTTTTTGAAAATATTTTGAAAAT
2585066 ATATATCTAATATATA------G----T-TTTTGAAAAT
1 ATATAT-TAATATATAGTTTTTGAAAATATTTTGAAAAT
* *
2585094 ATATA-TAATATATAGTTTTTGAAAACATTTTGAATAT
1 ATATATTAATATATAGTTTTTGAAAATATTTTGAAAAT
*
2585131 ATATA-T-AT-TATAGTTTTTGAAAACATTTTGAAAAT
1 ATATATTAATATATAGTTTTTGAAAATATTTTGAAAAT
2585166 ATATATGTAATATATA------G----T-TTTTGAAAAT
1 ATATAT-TAATATATAGTTTTTGAAAATATTTTGAAAAT
**
2585194 ATATA-TAATATATAGTTTTCAAAAATATTTTTGAAAAT
1 ATATATTAATATATAGTTTTTGAAAATA-TTTTGAAAAT
* *
2585232 ATATATATATTATATAGTTTTTGAAAACATTTTGAAAGCAT
1 ATATAT-TAATATATAGTTTTTGAAAATATTTTGAAA--AT
2585273 ATATA-TAATATATAG-TTTTG---A-A-----AAAAT
1 ATATATTAATATATAGTTTTTGAAAATATTTTGAAAAT
2585300 ATATA-TAATATATAGTTTTTGAAAATATTTTGAAAAT
1 ATATATTAATATATAGTTTTTGAAAATATTTTGAAAAT
*
2585337 GTATA-TAATATATAGTTTTTG--AATA---T----AT
1 ATATATTAATATATAGTTTTTGAAAATATTTTGAAAAT
* * *
2585365 ATATA--AATATA-G-TTTTTAAAAACATTTTGAAAAT
1 ATATATTAATATATAGTTTTTGAAAATATTTTGAAAAT
* *
2585399 ATATATATAATATATAATTTTTGAAAATATTTTTAAAAT
1 ATATAT-TAATATATAGTTTTTGAAAATATTTTGAAAAT
2585438 ATATATT-ATATA
1 ATATATTAATATA
2585450 AAATATTTAT
Statistics
Matches: 340, Mismatches: 25, Indels: 115
0.71 0.05 0.24
Matches are distributed among these distances:
25 5 0.01
26 18 0.05
27 26 0.08
28 41 0.12
29 4 0.01
30 1 0.00
31 1 0.00
32 3 0.01
33 2 0.01
34 8 0.02
35 36 0.11
36 8 0.02
37 52 0.15
38 37 0.11
39 73 0.21
40 18 0.05
41 7 0.02
ACGTcount: A:0.45, C:0.02, G:0.08, T:0.46
Consensus pattern (38 bp):
ATATATTAATATATAGTTTTTGAAAATATTTTGAAAAT
Found at i:2585102 original size:26 final size:26
Alignment explanation
Indices: 2585056--2585327 Score: 131
Period size: 26 Copynumber: 10.5 Consensus size: 26
2585046 TTTGAAAATA
2585056 TTTTGAAAATATATATCTAATATATAGT
1 TTTTGAAAATATATA--TAATATATAGT
2585084 TTTTGAAAATATATATAATATATAGT
1 TTTTGAAAATATATATAATATATAGT
* *
2585110 TTTTGAAAACAT-TTTGAATATATA-T
1 TTTTGAAAATATATAT-AATATATAGT
* * * * *
2585135 ATATT-ATAGT-T-TTTGAA-A-ACA--
1 -TTTTGAAAATATATAT-AATATATAGT
2585156 TTTTGAAAATATATATGTAATATATAGT
1 TTTTGAAAATATATA--TAATATATAGT
2585184 TTTTGAAAATATATATAATATATAGT
1 TTTTGAAAATATATATAATATATAGT
** * * *
2585210 TTTCAAAAATATTTTTGAAAATATA-T
1 TTTTGAAAATATATAT-AATATATAGT
* * ** ** * **
2585236 ATAT-ATTATATAGT-TTTTGA-AAACA
1 TTTTGAAAATATA-TATAAT-ATATAGT
2585261 TTTTGAAAGCATATATATAATATATAG-
1 TTTTGAAA--ATATATATAATATATAGT
2585288 TTTTGAAAAAATATATATAATATATAGT
1 TTTTG--AAAATATATATAATATATAGT
2585316 TTTTGAAAATAT
1 TTTTGAAAATAT
2585328 TTTGAAAATG
Statistics
Matches: 185, Mismatches: 36, Indels: 48
0.69 0.13 0.18
Matches are distributed among these distances:
20 3 0.02
21 3 0.02
22 3 0.02
23 2 0.01
24 11 0.06
25 16 0.09
26 69 0.37
27 31 0.17
28 44 0.24
29 3 0.02
ACGTcount: A:0.44, C:0.02, G:0.08, T:0.45
Consensus pattern (26 bp):
TTTTGAAAATATATATAATATATAGT
Found at i:2585125 original size:37 final size:37
Alignment explanation
Indices: 2585084--2585449 Score: 307
Period size: 37 Copynumber: 10.6 Consensus size: 37
2585074 AATATATAGT
2585084 TTTTGAAAATATATATAATATATAGTTTTTGAAAACA
1 TTTTGAAAATATATATAATATATAGTTTTTGAAAACA
*
2585121 TTTTGAATATATATAT-AT-TATAGTTTTTGAAAACA
1 TTTTGAAAATATATATAATATATAGTTTTTGAAAACA
2585156 TTTTGAAAATATATATGTAATATATAG----T-------
1 TTTTGAAAATATATA--TAATATATAGTTTTTGAAAACA
** *
2585184 TTTTGAAAATATATATAATATATAGTTTTCAAAAATA
1 TTTTGAAAATATATATAATATATAGTTTTTGAAAACA
2585221 TTTTTGAAAATATATATATATTATATAGTTTTTGAAAACA
1 -TTTTGAAAATATATATA-A-TATATAGTTTTTGAAAACA
2585261 TTTTGAAAGCATATATATAATATATAG-TTTTG---A-A
1 TTTTGAAA--ATATATATAATATATAGTTTTTGAAAACA
*
2585295 -----AAAATATATATAATATATAGTTTTTGAAAATA
1 TTTTGAAAATATATATAATATATAGTTTTTGAAAACA
*
2585327 TTTTGAAAATGTATATAATATATAGTTTTTG---A-A
1 TTTTGAAAATATATATAATATATAGTTTTTGAAAACA
*
2585360 ---T----ATATATATAA-ATATAGTTTTTAAAAACA
1 TTTTGAAAATATATATAATATATAGTTTTTGAAAACA
* *
2585389 TTTTGAAAATATATATATAATATATAATTTTTGAAAATA
1 TTTTG-AAA-ATATATATAATATATAGTTTTTGAAAACA
* *
2585428 TTTTTAAAATATATATTATATA
1 TTTTGAAAATATATATAATATA
2585450 AAATATTTAT
Statistics
Matches: 271, Mismatches: 14, Indels: 88
0.73 0.04 0.24
Matches are distributed among these distances:
25 11 0.04
26 19 0.07
27 17 0.06
28 21 0.08
29 4 0.01
30 1 0.00
31 1 0.00
32 2 0.01
33 1 0.00
34 2 0.01
35 33 0.12
36 2 0.01
37 54 0.20
38 37 0.14
39 40 0.15
40 17 0.06
41 9 0.03
ACGTcount: A:0.45, C:0.02, G:0.07, T:0.46
Consensus pattern (37 bp):
TTTTGAAAATATATATAATATATAGTTTTTGAAAACA
Found at i:2585249 original size:66 final size:64
Alignment explanation
Indices: 2585121--2585327 Score: 208
Period size: 66 Copynumber: 3.2 Consensus size: 64
2585111 TTTGAAAACA
* * * *
2585121 TTTTGAATATATATAT-AT-TATAGTTTTTGAAAACATTTTGAAAATATATATGTAATATATAGT
1 TTTTGAAAATATATATAATATATAG-TTTTAAAAATATTTTGAAAATATATATATAATATATAGT
*
2585184 TTTTGAAAATATATATAATATATAGTTTTCAAAAATATTTTTGAAAATATATATATATTATATAG
1 TTTTGAAAATATATATAATATATAGTTTT-AAAAATA-TTTTGAAAATATATATATAATATATAG
2585249 T
64 T
* * * * * *
2585250 TTTTGAAAACAT-TTTGAA-AGCATA-TATATAATATATAGTTTTGAAAAAATATATATAATATA
1 TTTTGAAAATATATAT-AATA-TATAGT-TTTAA-AAATA-TTTTGAAAATATATATATAATATA
2585312 TAGT
61 TAGT
2585316 TTTTGAAAATAT
1 TTTTGAAAATAT
2585328 TTTGAAAATG
Statistics
Matches: 122, Mismatches: 14, Indels: 13
0.82 0.09 0.09
Matches are distributed among these distances:
63 15 0.12
64 6 0.05
65 16 0.13
66 85 0.70
ACGTcount: A:0.44, C:0.02, G:0.08, T:0.45
Consensus pattern (64 bp):
TTTTGAAAATATATATAATATATAGTTTTAAAAATATTTTGAAAATATATATATAATATATAGT
Found at i:2585330 original size:66 final size:65
Alignment explanation
Indices: 2585258--2585442 Score: 225
Period size: 64 Copynumber: 2.8 Consensus size: 65
2585248 GTTTTTGAAA
* *
2585258 ACATTTTGAAAGCATATATATAATATATAGTTTTGAAAAAATATATATAATATATAGTTTTTGAA
1 ACATTTTGAAA-TATATATATAATATATAGTTTTGAAAATATATATATAATATATAGTTTTTGAA
2585323 A
65 A
* * *
2585324 ATATTTTGAAA-ATGTATATAATATATAGTTTTTG--AATATATATATAA-ATATAGTTTTTAAA
1 ACATTTTGAAATATATATATAATATATAG-TTTTGAAAATATATATATAATATATAGTTTTTGAA
2585385 A
65 A
* * * *
2585386 ACATTTTGAAAATATATATATAATATATAATTTTTGAAAATATTTTTAAAATATATA
1 ACATTTTG-AAATATATATATAATATAT-AGTTTTGAAAATATATATATAATATATA
2585443 TTATATAAAA
Statistics
Matches: 102, Mismatches: 10, Indels: 13
0.82 0.08 0.10
Matches are distributed among these distances:
62 21 0.21
63 15 0.15
64 35 0.34
65 6 0.06
66 20 0.20
67 5 0.05
ACGTcount: A:0.47, C:0.02, G:0.07, T:0.44
Consensus pattern (65 bp):
ACATTTTGAAATATATATATAATATATAGTTTTGAAAATATATATATAATATATAGTTTTTGAAA
Found at i:2585356 original size:26 final size:25
Alignment explanation
Indices: 2585327--2585386 Score: 84
Period size: 26 Copynumber: 2.4 Consensus size: 25
2585317 TTTGAAAATA
*
2585327 TTTTGAAAATGTATATAATATATAGT
1 TTTTGAAAATATATATAA-ATATAGT
*
2585353 TTTTGAATATATATATAAATATAGT
1 TTTTGAAAATATATATAAATATAGT
*
2585378 TTTTAAAAA
1 TTTTGAAAA
2585387 CATTTTGAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
25 14 0.47
26 16 0.53
ACGTcount: A:0.45, C:0.00, G:0.08, T:0.47
Consensus pattern (25 bp):
TTTTGAAAATATATATAAATATAGT
Found at i:2585420 original size:28 final size:28
Alignment explanation
Indices: 2585389--2585442 Score: 81
Period size: 28 Copynumber: 1.9 Consensus size: 28
2585379 TTTAAAAACA
*
2585389 TTTTGAAAATATATATATAATATATAAT
1 TTTTGAAAATATATATAAAATATATAAT
* *
2585417 TTTTGAAAATATTTTTAAAATATATA
1 TTTTGAAAATATATATAAAATATATA
2585443 TTATATAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (28 bp):
TTTTGAAAATATATATAAAATATATAAT
Found at i:2585468 original size:64 final size:63
Alignment explanation
Indices: 2585220--2585457 Score: 212
Period size: 64 Copynumber: 3.7 Consensus size: 63
2585210 TTTCAAAAAT
* * * * *
2585220 ATTTTTGAAAATATATATATATTATATAGTTTTTGAAAACATTTTGAAAGCATATATATAATATA
1 ATTTTTGAAAATATATATAAAATATATA-TTTAT-AAAATATTTTGAAA--TTATATATAATATA
2585285 T-
62 TA
* * * * * *
2585286 AGTTTTGAAAAAATATATATAATATATAGTTTTTGAAAATATTTTGAAAATGTATATAATATATA
1 ATTTTTGAAAATATATATAAAATATATA-TTTAT-AAAATATTTTGAAATTATATATAATATATA
* * * *
2585351 GTTTTTGAATATATATAT-AAATATAGTTTTTA-AAAACATTTTGAAAATATATATATAATATAT
1 ATTTTTGAAAATATATATAAAATATA-TATTTATAAAATATTTTG-AAAT-TATATATAATATAT
2585414 A
63 A
* *
2585415 ATTTTTGAAAATATTTTTAAAATATATATTATATAAAATATTT
1 ATTTTTGAAAATATATATAAAATATATATT-TATAAAATATTT
2585458 ATGTATTATA
Statistics
Matches: 144, Mismatches: 21, Indels: 14
0.80 0.12 0.08
Matches are distributed among these distances:
62 10 0.07
63 3 0.02
64 54 0.38
65 24 0.17
66 53 0.37
ACGTcount: A:0.46, C:0.01, G:0.07, T:0.46
Consensus pattern (63 bp):
ATTTTTGAAAATATATATAAAATATATATTTATAAAATATTTTGAAATTATATATAATATATA
Found at i:2585486 original size:22 final size:21
Alignment explanation
Indices: 2585456--2585500 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
2585446 TATAAAATAT
2585456 TTATGTATTATATTTTATTATA
1 TTATGTATTAT-TTTTATTATA
* *
2585478 TTATTTATTATTTTTATTTTA
1 TTATGTATTATTTTTATTATA
2585499 TT
1 TT
2585501 TATTCTCTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 11 0.52
22 10 0.48
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.71
Consensus pattern (21 bp):
TTATGTATTATTTTTATTATA
Found at i:2585495 original size:26 final size:25
Alignment explanation
Indices: 2585453--2585504 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 25
2585443 TTATATAAAA
2585453 TATTTATGTATTATATTTTATTATAT
1 TATTTATGTATTATATTTTATT-TAT
*
2585479 TATTTAT-TATTTTTATTTTATTTAT
1 TATTTATGTA-TTATATTTTATTTAT
2585504 T
1 T
2585505 CTCTTTTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
25 6 0.25
26 18 0.75
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.71
Consensus pattern (25 bp):
TATTTATGTATTATATTTTATTTAT
Found at i:2585503 original size:22 final size:22
Alignment explanation
Indices: 2585453--2585519 Score: 75
Period size: 22 Copynumber: 3.0 Consensus size: 22
2585443 TTATATAAAA
* *
2585453 TATTTATGTATTATATTTTATTA
1 TATTTATTTATTAT-TTTTATTT
2585476 TA-TTATTTATTATTTTTATTT
1 TATTTATTTATTATTTTTATTT
*
2585497 TATTTATTCTCTT-TTTTTATTT
1 TATTTATT-TATTATTTTTATTT
2585519 T
1 T
2585520 GGTCCAAATA
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
21 9 0.23
22 25 0.64
23 5 0.13
ACGTcount: A:0.22, C:0.03, G:0.01, T:0.73
Consensus pattern (22 bp):
TATTTATTTATTATTTTTATTT
Found at i:2588513 original size:76 final size:76
Alignment explanation
Indices: 2588422--2588573 Score: 304
Period size: 76 Copynumber: 2.0 Consensus size: 76
2588412 GTCAATTCTT
2588422 TATTCTTTCAAGTTTTCATCTCTTTGCTTCATATTTTCATTTTCTGATAGAAAAAAAAGGAAGTT
1 TATTCTTTCAAGTTTTCATCTCTTTGCTTCATATTTTCATTTTCTGATAGAAAAAAAAGGAAGTT
2588487 GGAAAAGATGG
66 GGAAAAGATGG
2588498 TATTCTTTCAAGTTTTCATCTCTTTGCTTCATATTTTCATTTTCTGATAGAAAAAAAAGGAAGTT
1 TATTCTTTCAAGTTTTCATCTCTTTGCTTCATATTTTCATTTTCTGATAGAAAAAAAAGGAAGTT
2588563 GGAAAAGATGG
66 GGAAAAGATGG
2588574 CAAAGTATTC
Statistics
Matches: 76, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
76 76 1.00
ACGTcount: A:0.32, C:0.12, G:0.16, T:0.41
Consensus pattern (76 bp):
TATTCTTTCAAGTTTTCATCTCTTTGCTTCATATTTTCATTTTCTGATAGAAAAAAAAGGAAGTT
GGAAAAGATGG
Found at i:2600026 original size:26 final size:24
Alignment explanation
Indices: 2599964--2600026 Score: 60
Period size: 23 Copynumber: 2.6 Consensus size: 24
2599954 CATTTTAATC
2599964 AAAATAT-TAATTATTAAAATATTT
1 AAAATATAT-ATTATTAAAATATTT
*
2599988 AAAATATAT-TTATTAATAT-TTCT
1 AAAATATATATTATTAAAATATT-T
2600011 AATAATATAATATTAT
1 AA-AATAT-ATATTAT
2600027 ATTTTTAATA
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
22 2 0.06
23 12 0.36
24 12 0.36
25 3 0.09
26 4 0.12
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.48
Consensus pattern (24 bp):
AAAATATATATTATTAAAATATTT
Found at i:2600028 original size:22 final size:23
Alignment explanation
Indices: 2599998--2600044 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 23
2599988 AAAATATATT
2599998 TATTAATATTTCTAATAATATAA
1 TATTAATATTTCTAATAATATAA
* *
2600021 TATT-ATATTTTTAATATTATAA
1 TATTAATATTTCTAATAATATAA
2600043 TA
1 TA
2600045 AAATAATCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 18 0.82
23 4 0.18
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (23 bp):
TATTAATATTTCTAATAATATAA
Found at i:2600058 original size:32 final size:32
Alignment explanation
Indices: 2599992--2600068 Score: 90
Period size: 30 Copynumber: 2.5 Consensus size: 32
2599982 ATATTTAAAA
* *
2599992 TATATTTATTAATATTTCTAATAATATAATAT
1 TATATTTATTAATATTTATAATAAAATAATAT
2600024 TATATTT-TTAATA-TTATAATAAAATAATCAAT
1 TATATTTATTAATATTTATAATAAAATAAT--AT
2600056 TATA-TTA-TAATAT
1 TATATTTATTAATAT
2600069 AAGATATTAT
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
30 13 0.33
31 13 0.33
32 13 0.33
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.51
Consensus pattern (32 bp):
TATATTTATTAATATTTATAATAAAATAATAT
Found at i:2600232 original size:23 final size:23
Alignment explanation
Indices: 2600213--2600257 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
2600203 AATAATATTT
2600213 TAATAAAGATATTTAAAATATAC
1 TAATAAAGATATTTAAAATATAC
* * *
2600236 TAATTAATATTTTTAAAATATA
1 TAATAAAGATATTTAAAATATA
2600258 ATATAACACT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.42
Consensus pattern (23 bp):
TAATAAAGATATTTAAAATATAC
Found at i:2600350 original size:31 final size:30
Alignment explanation
Indices: 2600296--2600365 Score: 90
Period size: 33 Copynumber: 2.3 Consensus size: 30
2600286 TAATATAATT
2600296 ATAATATTTTTATTTCAATAAAATATATCAATA
1 ATAATATTTTTATTTCAATAAAAT-TAT-AA-A
*
2600329 TTAATATTTTTA-TT-AATAAAATTATAAA
1 ATAATATTTTTATTTCAATAAAATTATAAA
2600357 ATAATATTT
1 ATAATATTT
2600366 AATAATAAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
28 9 0.26
29 2 0.06
30 3 0.09
31 8 0.23
32 2 0.06
33 11 0.31
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (30 bp):
ATAATATTTTTATTTCAATAAAATTATAAA
Found at i:2600576 original size:14 final size:14
Alignment explanation
Indices: 2600557--2600590 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
2600547 TCATTTCCCT
*
2600557 GGAAAACGTTTTCC
1 GGAAAAAGTTTTCC
2600571 GGAAAAAGTTTTCC
1 GGAAAAAGTTTTCC
*
2600585 AGAAAA
1 GGAAAA
2600591 TGTAATTCAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.41, C:0.15, G:0.21, T:0.24
Consensus pattern (14 bp):
GGAAAAAGTTTTCC
Found at i:2600613 original size:14 final size:14
Alignment explanation
Indices: 2600594--2600623 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
2600584 CAGAAAATGT
*
2600594 AATTCATTTTTCAG
1 AATTCAATTTTCAG
2600608 AATTCAATTTTCAG
1 AATTCAATTTTCAG
2600622 AA
1 AA
2600624 AACCAATTAC
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:0.37, C:0.13, G:0.07, T:0.43
Consensus pattern (14 bp):
AATTCAATTTTCAG
Found at i:2602887 original size:30 final size:31
Alignment explanation
Indices: 2602819--2602887 Score: 79
Period size: 30 Copynumber: 2.3 Consensus size: 31
2602809 ATATATATAT
* * *
2602819 ATTATTTTTATTTTGTTTTTGTTTTTATTTC
1 ATTATTTTTATCTTATTTTTGTTTTAATTTC
**
2602850 GGT-TTTTTATCTTATTTTTG-TTTAATTTC
1 ATTATTTTTATCTTATTTTTGTTTTAATTTC
2602879 ATTATTTTT
1 ATTATTTTT
2602888 TTTCTTTTTA
Statistics
Matches: 30, Mismatches: 7, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
29 9 0.30
30 20 0.67
31 1 0.03
ACGTcount: A:0.14, C:0.04, G:0.07, T:0.74
Consensus pattern (31 bp):
ATTATTTTTATCTTATTTTTGTTTTAATTTC
Found at i:2603143 original size:2 final size:2
Alignment explanation
Indices: 2603138--2603168 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2603128 TTACATTATT
2603138 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2603169 TACTTAAAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2609978 original size:20 final size:20
Alignment explanation
Indices: 2609953--2610000 Score: 71
Period size: 20 Copynumber: 2.4 Consensus size: 20
2609943 AATAATCCAG
2609953 TAAAAATAATAT-TTAAAAAT
1 TAAAAATAATATCTT-AAAAT
2609973 TAAAAATAATATCTTAAAAT
1 TAAAAATAATATCTTAAAAT
*
2609993 TGAAAATA
1 TAAAAATA
2610001 TAAGAAATAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
20 24 0.92
21 2 0.08
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.33
Consensus pattern (20 bp):
TAAAAATAATATCTTAAAAT
Found at i:2610038 original size:31 final size:33
Alignment explanation
Indices: 2610003--2610075 Score: 89
Period size: 31 Copynumber: 2.2 Consensus size: 33
2609993 TGAAAATATA
*
2610003 AGAAATAAATAA-ACATAAAAATGA-T-ATAAAT
1 AGAAA-AAATAATAAATAAAAATGACTAATAAAT
*
2610034 AGAAAAGATAATAAATAAAAATGATCTAATAAAT
1 AGAAAAAATAATAAATAAAAATGA-CTAATAAAT
2610068 AGAAAAAA
1 AGAAAAAA
2610076 CAATTGAAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
30 5 0.14
31 16 0.46
33 1 0.03
34 13 0.37
ACGTcount: A:0.68, C:0.03, G:0.08, T:0.21
Consensus pattern (33 bp):
AGAAAAAATAATAAATAAAAATGACTAATAAAT
Found at i:2610039 original size:16 final size:17
Alignment explanation
Indices: 2610020--2610073 Score: 69
Period size: 16 Copynumber: 3.2 Consensus size: 17
2610010 AATAAACATA
2610020 AAAATGAT-ATAAATAG
1 AAAATGATAATAAATAG
2610036 AAAA-GATAATAAATA-
1 AAAATGATAATAAATAG
2610051 AAAATGATCTAATAAATAG
1 AAAATGA--TAATAAATAG
2610070 AAAA
1 AAAA
2610074 AACAATTGAA
Statistics
Matches: 33, Mismatches: 0, Indels: 7
0.82 0.00 0.17
Matches are distributed among these distances:
15 7 0.21
16 13 0.39
18 9 0.27
19 4 0.12
ACGTcount: A:0.67, C:0.02, G:0.09, T:0.22
Consensus pattern (17 bp):
AAAATGATAATAAATAG
Found at i:2610586 original size:30 final size:30
Alignment explanation
Indices: 2610550--2610610 Score: 88
Period size: 30 Copynumber: 2.0 Consensus size: 30
2610540 GCATTTGATT
2610550 ATTTAAAATAA-AAAAATTAAATATTTTAAA
1 ATTTAAAATAATAAAAATT-AATATTTTAAA
*
2610580 ATTTAAAATAATTAAAAATTAGTATTTTAAA
1 ATTTAAAATAA-TAAAAATTAATATTTTAAA
2610611 TAAATTAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
30 11 0.39
31 10 0.36
32 7 0.25
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (30 bp):
ATTTAAAATAATAAAAATTAATATTTTAAA
Found at i:2611307 original size:23 final size:25
Alignment explanation
Indices: 2611258--2611307 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
2611248 TTATGTTAGA
* *
2611258 AGATGAATTTTTAAAATTTTAAGAG
1 AGATAAATTTATAAAATTTTAAGAG
*
2611283 AGATAAATTTATAAAATTTCAAGAG
1 AGATAAATTTATAAAATTTTAAGAG
2611308 TAAAAAAATA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.48, C:0.02, G:0.14, T:0.36
Consensus pattern (25 bp):
AGATAAATTTATAAAATTTTAAGAG
Found at i:2612128 original size:16 final size:15
Alignment explanation
Indices: 2612107--2612145 Score: 60
Period size: 16 Copynumber: 2.5 Consensus size: 15
2612097 CATTTGCTTA
2612107 TATTATTTATTATTAT
1 TATTATTTA-TATTAT
2612123 TATTATGTTATATTAT
1 TATTAT-TTATATTAT
2612139 TATTATT
1 TATTATT
2612146 AAATAATAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 1 0.05
16 18 0.82
17 3 0.14
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.67
Consensus pattern (15 bp):
TATTATTTATATTAT
Found at i:2613509 original size:12 final size:11
Alignment explanation
Indices: 2613492--2613582 Score: 53
Period size: 12 Copynumber: 8.2 Consensus size: 11
2613482 TTAATTCCTT
2613492 TTATTTTAATTA
1 TTATTTT-ATTA
* *
2613504 TTATTTGCAATA
1 TTATTT-TATTA
*
2613516 TTAGTTTATTA
1 TTATTTTATTA
2613527 TTATTATTATTA
1 TTATT-TTATTA
2613539 TTA-TTTA-T-
1 TTATTTTATTA
** *
2613547 TGCTTTAATTA
1 TTATTTTATTA
* *
2613558 TTATGTCATTA
1 TTATTTTATTA
2613569 TTATTATTATTA
1 TTATT-TTATTA
2613581 TT
1 TT
2613583 TATATAAATA
Statistics
Matches: 58, Mismatches: 15, Indels: 12
0.68 0.18 0.14
Matches are distributed among these distances:
8 1 0.02
9 4 0.07
10 4 0.07
11 19 0.33
12 30 0.52
ACGTcount: A:0.30, C:0.03, G:0.04, T:0.63
Consensus pattern (11 bp):
TTATTTTATTA
Found at i:2613527 original size:3 final size:3
Alignment explanation
Indices: 2613521--2613582 Score: 63
Period size: 3 Copynumber: 19.7 Consensus size: 3
2613511 CAATATTAGT
* *
2613521 TTA TTA TTA TTA TTA TTA TTA TTTA TTGC TT- TAA TTA TTA TGTCA TTA
1 TTA TTA TTA TTA TTA TTA TTA -TTA TT-A TTA TTA TTA TTA T-T-A TTA
2613569 TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TT
2613583 TATATAAATA
Statistics
Matches: 51, Mismatches: 3, Indels: 10
0.80 0.05 0.16
Matches are distributed among these distances:
2 1 0.02
3 41 0.80
4 7 0.14
5 2 0.04
ACGTcount: A:0.29, C:0.03, G:0.03, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:2615030 original size:46 final size:49
Alignment explanation
Indices: 2614956--2615046 Score: 127
Period size: 46 Copynumber: 1.9 Consensus size: 49
2614946 TTTTATTTTC
* *
2614956 TTTTTCCTAAATAAATGCATGCGAACTAGAAATCATGCA-GTTAGGTTAA
1 TTTTTCCTAAACAAATGCATGCGAACTAGAAAGCATG-AGGTTAGGTTAA
2615005 TTTTTCC-AAACAAAT-CATG-GAACTAGAAAGCATGAGGTTAGG
1 TTTTTCCTAAACAAATGCATGCGAACTAGAAAGCATGAGGTTAGG
2615047 ATTTATGCCT
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
45 1 0.03
46 20 0.51
47 4 0.10
48 7 0.18
49 7 0.18
ACGTcount: A:0.37, C:0.14, G:0.19, T:0.30
Consensus pattern (49 bp):
TTTTTCCTAAACAAATGCATGCGAACTAGAAAGCATGAGGTTAGGTTAA
Found at i:2619441 original size:165 final size:165
Alignment explanation
Indices: 2619169--2619465 Score: 470
Period size: 165 Copynumber: 1.8 Consensus size: 165
2619159 AGGCTGAAGG
2619169 GATCCAAGCTTGATTTGATCAATTAAACCTTATTGATGAGATGAGATTGAAAGCTATTTGCCAGG
1 GATCCAAGCTTGATTTGATCAATTAAACCTTATTGATGAGATGAGATTGAAAGCTATTTGCCAGG
* *
2619234 GGCAGATATATCAAAAACGGATGATGAAAGATCATAACAAGAAAGTACATCCAAGAGAGTTCCAA
66 GGCAGATATATCAAAAACGGATGATGAAAGATCACAACAAGAAAGTACATACAAGAGAGTTCCAA
2619299 GATGTTGATCTAGTGCTAAAAAAGGAGACTGAATA
131 GATGTTGATCTAGTGCTAAAAAAGGAGACTGAATA
* * * *
2619334 GATCCAAGCTTGATTTGATCAATTAAGCTTTATTGATGAGAATG-TATTGAAAGCTATTTGCCAT
1 GATCCAAGCTTGATTTGATCAATTAAACCTTATTGATGAG-ATGAGATTGAAAGCTATTTGCCAG
* * ** **
2619398 GGGCAGATGTATCAGAAGTGGATGATGAAAGATCACAACAAGAAAGTACATATGAGAGAGTTCCA
65 GGGCAGATATATCAAAAACGGATGATGAAAGATCACAACAAGAAAGTACATACAAGAGAGTTCCA
2619463 AGA
130 AGA
2619466 GAGCGATCTA
Statistics
Matches: 119, Mismatches: 12, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
165 116 0.97
166 3 0.03
ACGTcount: A:0.39, C:0.13, G:0.23, T:0.26
Consensus pattern (165 bp):
GATCCAAGCTTGATTTGATCAATTAAACCTTATTGATGAGATGAGATTGAAAGCTATTTGCCAGG
GGCAGATATATCAAAAACGGATGATGAAAGATCACAACAAGAAAGTACATACAAGAGAGTTCCAA
GATGTTGATCTAGTGCTAAAAAAGGAGACTGAATA
Found at i:2619680 original size:7 final size:7
Alignment explanation
Indices: 2619669--2619735 Score: 73
Period size: 7 Copynumber: 8.9 Consensus size: 7
2619659 AAAAAATAGA
2619669 AAAAAAGG
1 AAAAAA-G
2619677 AAAAAAG
1 AAAAAAG
2619684 AAAAAAG
1 AAAAAAG
2619691 AAAAAAAAG
1 --AAAAAAG
2619700 AAAAAAG
1 AAAAAAG
2619707 AAAAAAGG
1 AAAAAA-G
2619715 AGAAAAA-
1 A-AAAAAG
2619722 AGAAAAAG
1 A-AAAAAG
2619730 AAAAAA
1 AAAAAA
2619736 ATTGAACCAA
Statistics
Matches: 54, Mismatches: 0, Indels: 11
0.83 0.00 0.17
Matches are distributed among these distances:
7 33 0.61
8 9 0.17
9 12 0.22
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (7 bp):
AAAAAAG
Found at i:2619685 original size:16 final size:16
Alignment explanation
Indices: 2619659--2619728 Score: 79
Period size: 17 Copynumber: 4.3 Consensus size: 16
2619649 TTATGCTTGA
*
2619659 AAAAAATAGAAAAAAAG
1 AAAAAA-AGGAAAAAAG
*
2619676 GAAAAAA-GAAAAAAG
1 AAAAAAAGGAAAAAAG
*
2619691 AAAAAAAAGAAAAAAG
1 AAAAAAAGGAAAAAAG
*
2619707 AAAAAAGGAGAAAAAAG
1 AAAAAAAG-GAAAAAAG
2619724 AAAAA
1 AAAAA
2619729 GAAAAAAATT
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
15 13 0.28
16 15 0.33
17 18 0.39
ACGTcount: A:0.83, C:0.00, G:0.16, T:0.01
Consensus pattern (16 bp):
AAAAAAAGGAAAAAAG
Found at i:2619692 original size:23 final size:22
Alignment explanation
Indices: 2619660--2619735 Score: 100
Period size: 23 Copynumber: 3.3 Consensus size: 22
2619650 TATGCTTGAA
2619660 AAAAATAGAAAAAAAGGAAAAAAG
1 AAAAA-AGAAAAAAA-GAAAAAAG
2619684 AAAAAAGAAAAAAAAGAAAAAAG
1 AAAAAAG-AAAAAAAGAAAAAAG
2619707 AAAAAAGGAGAAAAAAG-AAAAAG
1 AAAAAA-GA-AAAAAAGAAAAAAG
2619730 AAAAAA
1 AAAAAA
2619736 ATTGAACCAA
Statistics
Matches: 49, Mismatches: 0, Indels: 7
0.88 0.00 0.12
Matches are distributed among these distances:
23 29 0.59
24 20 0.41
ACGTcount: A:0.83, C:0.00, G:0.16, T:0.01
Consensus pattern (22 bp):
AAAAAAGAAAAAAAGAAAAAAG
Found at i:2619729 original size:16 final size:15
Alignment explanation
Indices: 2619669--2619736 Score: 77
Period size: 16 Copynumber: 4.4 Consensus size: 15
2619659 AAAAAATAGA
2619669 AAAAAAGGAAAAA-AG
1 AAAAAA-GAAAAAGAG
*
2619684 AAAAAAGAAAAAAAAG
1 AAAAAAG-AAAAAGAG
2619700 AAAAAAGAAAAAAGGAG
1 AAAAAAG-AAAAA-GAG
2619717 AAAAAAGAAAAAGA-
1 AAAAAAGAAAAAGAG
2619731 AAAAAA
1 AAAAAA
2619737 TTGAACCAAG
Statistics
Matches: 49, Mismatches: 1, Indels: 7
0.86 0.02 0.12
Matches are distributed among these distances:
14 7 0.14
15 13 0.27
16 20 0.41
17 9 0.18
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (15 bp):
AAAAAAGAAAAAGAG
Found at i:2624091 original size:22 final size:22
Alignment explanation
Indices: 2624065--2624122 Score: 89
Period size: 22 Copynumber: 2.6 Consensus size: 22
2624055 TACATCTATG
*
2624065 CTCTTCAAAGATGATAGATTCT
1 CTCTTCAAAGATGATAGATTCC
*
2624087 CTCTTTAAAGATGATAGATTCC
1 CTCTTCAAAGATGATAGATTCC
*
2624109 CTTTTCAAAGATGA
1 CTCTTCAAAGATGA
2624123 AGGCTCTATT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.33, C:0.17, G:0.14, T:0.36
Consensus pattern (22 bp):
CTCTTCAAAGATGATAGATTCC
Found at i:2624676 original size:112 final size:112
Alignment explanation
Indices: 2624514--2625367 Score: 1487
Period size: 112 Copynumber: 7.6 Consensus size: 112
2624504 GCTAGGTAGA
* *
2624514 GTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCA
1 GTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAGGAAGTTCATAATGAGAAGAACTTGTTCA
* *
2624579 ACCTTTTGCTCAAATCCATCACTTGATGGATCAGCATTGCCAGAAGT
66 ACCTTTTGCTCAAATCCATCACTTGATGGATCAACATTTCCAGAAGT
2624626 GTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAGGAAGTTCATAATGAGAAGAACTTGTTCA
1 GTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAGGAAGTTCATAATGAGAAGAACTTGTTCA
*
2624691 ACCTTTTGCTCAAATCCATCACTTGATGGATCAACATTGCCAGAAGT
66 ACCTTTTGCTCAAATCCATCACTTGATGGATCAACATTTCCAGAAGT
2624738 GTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAGGAAGTTCATAATGAGAAGAACTTGTTCA
1 GTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAGGAAGTTCATAATGAGAAGAACTTGTTCA
* * *
2624803 ACCTTTTTCTCAAATCCATCACTTGATGGATCAGCATTGCCAGAAGT
66 ACCTTTTGCTCAAATCCATCACTTGATGGATCAACATTTCCAGAAGT
*
2624850 GTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAGGAAGTTCATAATAAGAAGAACTTGTTCA
1 GTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAGGAAGTTCATAATGAGAAGAACTTGTTCA
*
2624915 ACCTTTTGCTCAAATCCATCACTTGATGGATCAACATTTCCAGAAAT
66 ACCTTTTGCTCAAATCCATCACTTGATGGATCAACATTTCCAGAAGT
2624962 GTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAGGAAGTTCATAATGAGAAGAACTTGTTCA
1 GTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAGGAAGTTCATAATGAGAAGAACTTGTTCA
* *
2625027 ACATTTTGCTCAAATCCATCACTTGGTGGATCAACATTTCCAGAAGT
66 ACCTTTTGCTCAAATCCATCACTTGATGGATCAACATTTCCAGAAGT
* *
2625074 GTTCATAATGAGAAGAACTCATATGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCA
1 GTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAGGAAGTTCATAATGAGAAGAACTTGTTCA
* *
2625139 ACCTTTTTCTCAAATCCATCACTTGATGGATCAACATTTCCAGAAAT
66 ACCTTTTGCTCAAATCCATCACTTGATGGATCAACATTTCCAGAAGT
*
2625186 GTTCATAATGAGAAGAACTCATCTGAATG-AGGAAGAGGAAGTTCATAATGAGAAGAACTTTTTC
1 GTTCATAATGAGAAGAACTCATCTGAA-GAAGGAAGAGGAAGTTCATAATGAGAAGAACTTGTTC
*
2625250 AACCTTTTGCTCAAATCCATCACTTGATGAATCAACATTTCCAGAAGT
65 AACCTTTTGCTCAAATCCATCACTTGATGGATCAACATTTCCAGAAGT
* * *
2625298 GTTCATAATGAGAAGAACTCATCTGAAG-AGGAAGAAGAAGTTCATAAGGAGAAGAACTTATTCA
1 GTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAGGAAGTTCATAATGAGAAGAACTTGTTCA
*
2625362 GCCTTT
66 ACCTTT
2625368 GTTTGATTCT
Statistics
Matches: 711, Mismatches: 30, Indels: 3
0.96 0.04 0.00
Matches are distributed among these distances:
111 39 0.05
112 671 0.94
113 1 0.00
ACGTcount: A:0.37, C:0.16, G:0.19, T:0.27
Consensus pattern (112 bp):
GTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAGGAAGTTCATAATGAGAAGAACTTGTTCA
ACCTTTTGCTCAAATCCATCACTTGATGGATCAACATTTCCAGAAGT
Found at i:2625702 original size:3 final size:3
Alignment explanation
Indices: 2625690--2625732 Score: 54
Period size: 3 Copynumber: 14.7 Consensus size: 3
2625680 CATTTGCTTA
*
2625690 TAT TATT TAT TAT TAT TAT TAT TA- TGT TA- TAT TAT TAT TAT TA
1 TAT TA-T TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
2625733 AATAATAAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
2 3 0.09
3 29 0.83
4 3 0.09
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:2625711 original size:16 final size:15
Alignment explanation
Indices: 2625690--2625732 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 15
2625680 CATTTGCTTA
2625690 TATTATTTATTATTAT
1 TATTATTTATTA-TAT
*
2625706 TATTATTATGTTATAT
1 TATTATT-TATTATAT
2625722 TATTA-TTATTA
1 TATTATTTATTA
2625733 AATAATAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
14 4 0.17
15 1 0.04
16 15 0.62
17 4 0.17
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (15 bp):
TATTATTTATTATAT
Found at i:2625714 original size:19 final size:19
Alignment explanation
Indices: 2625690--2625732 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
2625680 CATTTGCTTA
2625690 TATTAT-TTATTATTATTAT
1 TATTATGTTA-TATTATTAT
2625709 TATTATGTTATATTATTAT
1 TATTATGTTATATTATTAT
2625728 TATTA
1 TATTA
2625733 AATAATAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
19 20 0.87
20 3 0.13
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (19 bp):
TATTATGTTATATTATTAT
Found at i:2627201 original size:3 final size:3
Alignment explanation
Indices: 2627187--2627250 Score: 64
Period size: 3 Copynumber: 21.7 Consensus size: 3
2627177 TATTTGCAAA
2627187 ATT ATT -TT ATT ATT ATT ATT ATT ATTT ATT -TCT -TT AATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT A-TT ATT AT-T ATT -ATT ATT ATT
*
2627232 -TC ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT AT
2627251 ATAAATATAT
Statistics
Matches: 53, Mismatches: 2, Indels: 12
0.79 0.03 0.18
Matches are distributed among these distances:
2 5 0.09
3 43 0.81
4 5 0.09
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:2627260 original size:2 final size:2
Alignment explanation
Indices: 2627248--2627283 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
2627238 TTATTATTAT
*
2627248 TA TA TA AA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2627284 AAAATATTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:2628618 original size:4 final size:4
Alignment explanation
Indices: 2628595--2628658 Score: 80
Period size: 4 Copynumber: 16.8 Consensus size: 4
2628585 AATTATAAAT
* * *
2628595 ATAC ACAC ATAC ATAA ATAC ATAC AT-G ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
2628642 AT-- ATAC ATAC ATAC ATA
1 ATAC ATAC ATAC ATAC ATA
2628659 TCACACATTT
Statistics
Matches: 51, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
2 2 0.04
3 2 0.04
4 47 0.92
ACGTcount: A:0.52, C:0.22, G:0.02, T:0.25
Consensus pattern (4 bp):
ATAC
Found at i:2628629 original size:23 final size:22
Alignment explanation
Indices: 2628601--2628654 Score: 90
Period size: 23 Copynumber: 2.4 Consensus size: 22
2628591 AAATATACAC
2628601 ACATACATAAATACATACATGAT
1 ACATACATAAATACATACAT-AT
*
2628624 ACATACATACATACATACATAT
1 ACATACATAAATACATACATAT
2628646 ACATACATA
1 ACATACATA
2628655 CATATCACAC
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
22 11 0.37
23 19 0.63
ACGTcount: A:0.52, C:0.20, G:0.02, T:0.26
Consensus pattern (22 bp):
ACATACATAAATACATACATAT
Found at i:2628750 original size:32 final size:31
Alignment explanation
Indices: 2628704--2628769 Score: 105
Period size: 32 Copynumber: 2.1 Consensus size: 31
2628694 TCACATGATG
2628704 CATGCATTAATAAATTATACATACATATCATA
1 CATGCATTAATAAATTATACATACATA-CATA
* *
2628736 CATGCATTAGTAAATTATACATATATACATA
1 CATGCATTAATAAATTATACATACATACATA
2628767 CAT
1 CAT
2628770 ACATACATGA
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
31 7 0.22
32 25 0.78
ACGTcount: A:0.45, C:0.15, G:0.05, T:0.35
Consensus pattern (31 bp):
CATGCATTAATAAATTATACATACATACATA
Found at i:2628769 original size:4 final size:4
Alignment explanation
Indices: 2628752--2628837 Score: 54
Period size: 4 Copynumber: 21.8 Consensus size: 4
2628742 TTAGTAAATT
* * * * *
2628752 ATAC ATAT ATAC ATAC ATAC ATAC AT-G ATAC ATGC ATTA- ATAA AT-T
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC A-TAC ATAC ATAC
* *
2628798 ATAC ATAC ATAT ATA- GTAC ATATC ATAC ATAC ATATC ATA
1 ATAC ATAC ATAC ATAC ATAC ATA-C ATAC ATAC ATA-C ATA
2628838 ATTAAATTTA
Statistics
Matches: 64, Mismatches: 11, Indels: 13
0.73 0.12 0.15
Matches are distributed among these distances:
3 8 0.12
4 47 0.73
5 9 0.14
ACGTcount: A:0.48, C:0.16, G:0.03, T:0.33
Consensus pattern (4 bp):
ATAC
Found at i:2628784 original size:19 final size:18
Alignment explanation
Indices: 2628760--2628808 Score: 53
Period size: 19 Copynumber: 2.6 Consensus size: 18
2628750 TTATACATAT
*
2628760 ATACATACATACATACATG
1 ATACATACATA-ATAAATG
* *
2628779 ATACATGCATTAATAAATT
1 ATACATACA-TAATAAATG
2628798 ATACATACATA
1 ATACATACATA
2628809 TATAGTACAT
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
18 2 0.08
19 21 0.84
20 2 0.08
ACGTcount: A:0.49, C:0.16, G:0.04, T:0.31
Consensus pattern (18 bp):
ATACATACATAATAAATG
Found at i:2628789 original size:46 final size:47
Alignment explanation
Indices: 2628720--2628832 Score: 142
Period size: 46 Copynumber: 2.4 Consensus size: 47
2628710 TTAATAAATT
*
2628720 ATACATACAT--ATCATACATGCATTAGTAAATTATACAT-ATATAC
1 ATACATACATACATCATACATGCATTAATAAATTATACATAATATAC
* *
2628764 ATACATACATACATGATACATGCATTAATAAATTATACATACATATAT
1 ATACATACATACATCATACATGCATTAATAAATTATACATA-ATATAC
2628812 AGTACATATCATACATACATA
1 A-TACATA-CATACAT-CATA
2628833 TCATAATTAA
Statistics
Matches: 58, Mismatches: 4, Indels: 7
0.84 0.06 0.10
Matches are distributed among these distances:
44 10 0.17
46 26 0.45
48 6 0.10
49 6 0.10
50 7 0.12
51 3 0.05
ACGTcount: A:0.47, C:0.16, G:0.04, T:0.33
Consensus pattern (47 bp):
ATACATACATACATCATACATGCATTAATAAATTATACATAATATAC
Found at i:2630351 original size:194 final size:194
Alignment explanation
Indices: 2630013--2630386 Score: 502
Period size: 194 Copynumber: 1.9 Consensus size: 194
2630003 AACGTAACAC
* * *
2630013 AATAACCATATCATCATAAATTTTAAGATTATTAGATACAATATCATCGCAACACGATGAGAGAA
1 AATAACCATATCATCATAAATTTTAAGATTATTAGATACAATATCAACACAACACGACGAGAGAA
* * * ** *
2630078 TCACCTCAAAATTTTTATGATCTGAAGTCATTGTGTAATACTGCAACAAACCATATATTACGCTA
66 TCACCTCAAAAGTTTTATGATATGAACTCATTAAGTAATAATGCAACAAACCATATATTACGCTA
*
2630143 TAACACCACACAAGATTTTCAAATGGTCTTAAATGTAAAACCCCATAAATATTAATTTGAAAAT
131 CAACACCACACAAGATTTTCAAATGGTCTTAAATGTAAAACCCCATAAATATTAATTTGAAAAT
* *
2630207 AATAACCATATCATCATAAATTTTAAGATTATT-GAATGCAATATCAACACAACCCGACGAGAG-
1 AATAACCATATCATCATAAATTTTAAGATTATTAG-ATACAATATCAACACAACACGACGAGAGA
** * * * **
2630270 ATCCATGTTAAAAGTTTTATGGTATGAAACT-ATTAAGTAATAATGCAACGAGTCATATATTACG
65 AT-CACCTCAAAAGTTTTATGATATG-AACTCATTAAGTAATAATGCAACAAACCATATATTACG
* * *
2630334 CTACAATACCGCACAAGATTTTTAAATGGTCTTAAATGTAAAACCCCATAAAT
128 CTACAACACCACACAAGATTTTCAAATGGTCTTAAATGTAAAACCCCATAAAT
2630387 GAAACACTTG
Statistics
Matches: 155, Mismatches: 22, Indels: 6
0.85 0.12 0.03
Matches are distributed among these distances:
193 3 0.02
194 149 0.96
195 3 0.02
ACGTcount: A:0.42, C:0.17, G:0.11, T:0.30
Consensus pattern (194 bp):
AATAACCATATCATCATAAATTTTAAGATTATTAGATACAATATCAACACAACACGACGAGAGAA
TCACCTCAAAAGTTTTATGATATGAACTCATTAAGTAATAATGCAACAAACCATATATTACGCTA
CAACACCACACAAGATTTTCAAATGGTCTTAAATGTAAAACCCCATAAATATTAATTTGAAAAT
Found at i:2630955 original size:60 final size:61
Alignment explanation
Indices: 2630883--2631040 Score: 180
Period size: 60 Copynumber: 2.7 Consensus size: 61
2630873 TTGAGTGACT
* * ** * * *
2630883 ATTTTGTAACTTTTAATAGTTAGG-GGACTCAACAAAGTAATGCCCTATACTCGAGGGACC
1 ATTTTATAACTTTTAATAGTTAGGAGGACTCAATAAAGTAACACCCTATAATCAAAGGACC
* * *
2630943 ATTTTATAACTTTTAATAG-TAGGAGGACTCAATAAAATAGCACCCTATAATCAAATGACC
1 ATTTTATAACTTTTAATAGTTAGGAGGACTCAATAAAGTAACACCCTATAATCAAAGGACC
* *
2631003 GTTTTATAA-TTTTAATAGTT-GGATGACTCAATAAAGTA
1 ATTTTATAACTTTTAATAGTTAGGAGGACTCAATAAAGTA
2631041 TCACATTATA
Statistics
Matches: 83, Mismatches: 13, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
59 29 0.35
60 54 0.65
ACGTcount: A:0.37, C:0.15, G:0.16, T:0.33
Consensus pattern (61 bp):
ATTTTATAACTTTTAATAGTTAGGAGGACTCAATAAAGTAACACCCTATAATCAAAGGACC
Found at i:2631051 original size:59 final size:60
Alignment explanation
Indices: 2630878--2631053 Score: 162
Period size: 60 Copynumber: 3.0 Consensus size: 60
2630868 AATAGTTGAG
* * * * * * *
2630878 TGACTATTTTGTAACTTTTAATAGTTAGG-GGACTCAACAAAGTAATGC-C-CTATACTCGAG
1 TGACCATTTTATAACTTTTAATAG-TAGGAGGACTCAATAAAAT-A-GCACACTATAATCAAA
* *
2630938 GGACCATTTTATAACTTTTAATAGTAGGAGGACTCAATAAAATAGCACCCTATAATCAAA
1 TGACCATTTTATAACTTTTAATAGTAGGAGGACTCAATAAAATAGCACACTATAATCAAA
* * * * * *
2630998 TGACCGTTTTATAA-TTTTAATAGTTGGATGACTCAATAAAGTATCACATTATAATC
1 TGACCATTTTATAACTTTTAATAGTAGGAGGACTCAATAAAATAGCACACTATAATC
2631054 GGGGACCATG
Statistics
Matches: 97, Mismatches: 16, Indels: 7
0.81 0.13 0.06
Matches are distributed among these distances:
58 2 0.02
59 42 0.43
60 53 0.55
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.34
Consensus pattern (60 bp):
TGACCATTTTATAACTTTTAATAGTAGGAGGACTCAATAAAATAGCACACTATAATCAAA
Found at i:2631955 original size:17 final size:16
Alignment explanation
Indices: 2631917--2631973 Score: 53
Period size: 18 Copynumber: 3.3 Consensus size: 16
2631907 CATAATTATT
2631917 AAAAAAAATAAAAATA
1 AAAAAAAATAAAAATA
*
2631933 ACAAAAAAATACAATATA
1 A-AAAAAAATA-AAAATA
2631951 AAAAATAAA-AGGAAAATA
1 AAAAA-AAATA--AAAATA
2631969 AAAAA
1 AAAAA
2631974 TATTGATGGT
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
16 1 0.03
17 14 0.41
18 19 0.56
ACGTcount: A:0.81, C:0.04, G:0.04, T:0.12
Consensus pattern (16 bp):
AAAAAAAATAAAAATA
Found at i:2633360 original size:20 final size:20
Alignment explanation
Indices: 2633335--2633372 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
2633325 ATGATGTATA
2633335 TAAAATATATAAA-AATTACC
1 TAAAATATA-AAATAATTACC
2633355 TAAAATATAAAATAATTA
1 TAAAATATAAAATAATTA
2633373 AATTTTTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 3 0.18
20 14 0.82
ACGTcount: A:0.63, C:0.05, G:0.00, T:0.32
Consensus pattern (20 bp):
TAAAATATAAAATAATTACC
Found at i:2635166 original size:16 final size:15
Alignment explanation
Indices: 2635139--2635171 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 15
2635129 TAAGTTTATA
2635139 TATTTTTTATATTTT
1 TATTTTTTATATTTT
2635154 TATTTTCTTATATTTT
1 TATTTT-TTATATTTT
2635170 TA
1 TA
2635172 AATGTTCGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.21, C:0.03, G:0.00, T:0.76
Consensus pattern (15 bp):
TATTTTTTATATTTT
Found at i:2637629 original size:98 final size:98
Alignment explanation
Indices: 2637383--2637629 Score: 336
Period size: 98 Copynumber: 2.5 Consensus size: 98
2637373 TTGCAGCCAG
* * * * *
2637383 GGGGTATGGATACCCCTGCATGGGTATCGGTACACCCGGGTATGGATAACCATATGGGTATCGAT
1 GGGGTATGGATACCCCTACAGGGGTATTGGTACACCCGGGTATGGATACCCATAGGGGTATCGAT
* * *
2637448 ACCCTTTTTGTATTCGGTGTTTGAGCAGTCATA
66 ACCCTTTTTGCATTCGGTGTTTGAACAATCATA
* *
2637481 GGGGTAT-GATACCCCCTACAGGGGGTA-TAGTACACCCGGGTATGGATACCCATAGGGGTATTG
1 GGGGTATGGATA-CCCCTACA-GGGGTATTGGTACACCCGGGTATGGATACCCATAGGGGTATCG
* *
2637544 GTACCCTTTTTGCATTCGGTGTTTGAATAATCATA
64 ATACCCTTTTTGCATTCGGTGTTTGAACAATCATA
* *
2637579 GGGGTATGGATACCCCTACAGGAGTATTGGTACACCCGGGTATGGTTACCC
1 GGGGTATGGATACCCCTACAGGGGTATTGGTACACCCGGGTATGGATACCC
2637630 TTTGAAGGGG
Statistics
Matches: 130, Mismatches: 15, Indels: 8
0.85 0.10 0.05
Matches are distributed among these distances:
97 9 0.07
98 112 0.86
99 9 0.07
ACGTcount: A:0.22, C:0.20, G:0.29, T:0.29
Consensus pattern (98 bp):
GGGGTATGGATACCCCTACAGGGGTATTGGTACACCCGGGTATGGATACCCATAGGGGTATCGAT
ACCCTTTTTGCATTCGGTGTTTGAACAATCATA
Found at i:2639509 original size:12 final size:12
Alignment explanation
Indices: 2639488--2639540 Score: 70
Period size: 12 Copynumber: 4.4 Consensus size: 12
2639478 CTTGACCATC
* *
2639488 TCATCTTCTTGT
1 TCATCGTCTTCT
*
2639500 TCATTGTCTTCT
1 TCATCGTCTTCT
2639512 TCATCGTCTTCT
1 TCATCGTCTTCT
*
2639524 TTATCGTCTTCT
1 TCATCGTCTTCT
2639536 TCATC
1 TCATC
2639541 CATCTCATCA
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 35 1.00
ACGTcount: A:0.09, C:0.28, G:0.08, T:0.55
Consensus pattern (12 bp):
TCATCGTCTTCT
Found at i:2641283 original size:17 final size:16
Alignment explanation
Indices: 2641261--2641294 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
2641251 TAAAAACAGT
2641261 AAATAAAAAGATAAATA
1 AAATAAAAAGA-AAATA
*
2641278 AAATAAGAAGAAAATA
1 AAATAAAAAGAAAATA
2641294 A
1 A
2641295 TCCTCACGTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.76, C:0.00, G:0.09, T:0.15
Consensus pattern (16 bp):
AAATAAAAAGAAAATA
Found at i:2651102 original size:18 final size:18
Alignment explanation
Indices: 2651087--2651121 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
2651077 CAAGTAAACT
2651087 ATACAAAA-AAAATAAAA
1 ATACAAAACAAAATAAAA
*
2651104 ATGCAAAACAAAATAAAA
1 ATACAAAACAAAATAAAA
2651122 TGCTCTGGCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.77, C:0.09, G:0.03, T:0.11
Consensus pattern (18 bp):
ATACAAAACAAAATAAAA
Found at i:2651523 original size:17 final size:16
Alignment explanation
Indices: 2651501--2651534 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
2651491 TAAAAACAGT
2651501 AAATAAAAAGATAAATA
1 AAATAAAAAGA-AAATA
*
2651518 AAATAAGAAGAAAATA
1 AAATAAAAAGAAAATA
2651534 A
1 A
2651535 TCCTCACGTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.76, C:0.00, G:0.09, T:0.15
Consensus pattern (16 bp):
AAATAAAAAGAAAATA
Found at i:2653963 original size:144 final size:140
Alignment explanation
Indices: 2653610--2654048 Score: 409
Period size: 144 Copynumber: 3.1 Consensus size: 140
2653600 GAAAGAGAAT
* * * * **
2653610 GACGTGAATAATTAAGATTGTCTGTCCATTGAAATTATTATTGTTTCATATTTGAATTTTTTTTG
1 GACGTGAATAGTTAAGATTCTCTGTCCATTGAAATTATTATTGTCTCAGATTTGAATTTTTTCAG
* * * * * * *
2653675 AGCACTTATAATTATATG-TTTTTATGTT-AATATAAATCTAATTTTAATATAAGATAATGTTTC
66 AG-AC-TATAATTATATGATTTTTATGTTCAATATAAAACTACTTCTGATATGAGGTGATGTTTC
*
2653738 ATTTAAACCATAAG
129 A-TT-GACCATAAG
* * * * * * *
2653752 CACGTGAATACTTAAGATTCTCTGTCCAATAAAATTGTTGTTGTCCCAGATTTGTAATTTTTTCA
1 GACGTGAATAGTTAAGATTCTCTGTCCATTGAAATTATTATTGTCTCAGATTTG-AATTTTTTCA
* *
2653817 GAGTACCTATAATTACATGATTGTTATGTGTCAATATAAAACTACTTCTGATATGAGGTGATGTT
65 GAG-A-CTATAATTATATGATTTTTATGT-TCAATATAAAACTACTTCTGATATGAGGTGATGTT
* *
2653882 TTACTGACCATAAG
127 TCATTGACCATAAG
* ***
2653896 GACGTGAATAGTTAAGATTCTCTGTCCATTGAAATTATTATTGTCTCAGGTTTGAAATTTCAACA
1 GACGTGAATAGTTAAGATTCTCTGTCCATTGAAATTATTATTGTCTCAGATTTG-AATTTTTTCA
* * * * * * *
2653961 GAGA--AAAATGATTTGATTTTTTTCTATCAATATAAACCTACTTCTGATATGAGGTGATGTGTC
65 GAGACTATAATTATATGATTTTTATGT-TCAATATAAAACTACTTCTGATATGAGGTGATGTTTC
* *
2654024 ATTGAAACAAAAG
129 ATTG-ACCATAAG
2654037 GACGTGAATAGT
1 GACGTGAATAGT
2654049 ATTGATAGAT
Statistics
Matches: 240, Mismatches: 51, Indels: 13
0.79 0.17 0.04
Matches are distributed among these distances:
140 51 0.21
141 18 0.08
142 44 0.18
143 24 0.10
144 73 0.30
145 2 0.01
146 28 0.12
ACGTcount: A:0.33, C:0.11, G:0.15, T:0.40
Consensus pattern (140 bp):
GACGTGAATAGTTAAGATTCTCTGTCCATTGAAATTATTATTGTCTCAGATTTGAATTTTTTCAG
AGACTATAATTATATGATTTTTATGTTCAATATAAAACTACTTCTGATATGAGGTGATGTTTCAT
TGACCATAAG
Found at i:2654250 original size:14 final size:14
Alignment explanation
Indices: 2654211--2654303 Score: 73
Period size: 14 Copynumber: 6.6 Consensus size: 14
2654201 CAAAAAAGAT
*
2654211 TAACTAGAAAACCC
1 TAACTACAAAACCC
** *
2654225 -AATCTAGTAAACTC
1 TAA-CTACAAAACCC
2654239 TAACTACAAAACCC
1 TAACTACAAAACCC
* *
2654253 TAAATAAAAAACCC
1 TAACTACAAAACCC
* * *
2654267 TAATTATAAAATCC
1 TAACTACAAAACCC
2654281 TAACTA-AGAAACCC
1 TAACTACA-AAACCC
2654295 TAACTACAA
1 TAACTACAA
2654304 TGTATTATTA
Statistics
Matches: 63, Mismatches: 12, Indels: 8
0.76 0.14 0.10
Matches are distributed among these distances:
13 3 0.05
14 57 0.90
15 3 0.05
ACGTcount: A:0.52, C:0.25, G:0.03, T:0.20
Consensus pattern (14 bp):
TAACTACAAAACCC
Found at i:2654264 original size:28 final size:28
Alignment explanation
Indices: 2654233--2654303 Score: 88
Period size: 28 Copynumber: 2.5 Consensus size: 28
2654223 CCAATCTAGT
*
2654233 AAACTCTAACTACAAAACCCTAAATAAA
1 AAACCCTAACTACAAAACCCTAAATAAA
* * * * *
2654261 AAACCCTAATTATAAAATCCTAACTAAG
1 AAACCCTAACTACAAAACCCTAAATAAA
2654289 AAACCCTAACTACAA
1 AAACCCTAACTACAA
2654304 TGTATTATTA
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
28 35 1.00
ACGTcount: A:0.54, C:0.25, G:0.01, T:0.20
Consensus pattern (28 bp):
AAACCCTAACTACAAAACCCTAAATAAA
Found at i:2654534 original size:14 final size:14
Alignment explanation
Indices: 2654361--2654528 Score: 183
Period size: 14 Copynumber: 12.0 Consensus size: 14
2654351 ATCTACTAAT
2654361 CCCTAACTACAAAA
1 CCCTAACTACAAAA
* *
2654375 CCCTAAATATAAAA
1 CCCTAACTACAAAA
* * *
2654389 CTCTAATTAGAAAA
1 CCCTAACTACAAAA
* *
2654403 CCTTAACTATAAAA
1 CCCTAACTACAAAA
2654417 CCCTAACTACAAAA
1 CCCTAACTACAAAA
** * *
2654431 CTATAACCAGAAAA
1 CCCTAACTACAAAA
* *
2654445 CCCTAAATAAAAAA
1 CCCTAACTACAAAA
*
2654459 CCCTAAGTACAAAA
1 CCCTAACTACAAAA
*
2654473 CCCTAACTATAAAA
1 CCCTAACTACAAAA
*
2654487 CCCTAAATACAAAA
1 CCCTAACTACAAAA
*
2654501 CCCTAAATACAAAA
1 CCCTAACTACAAAA
2654515 CCCTAACTACAAAA
1 CCCTAACTACAAAA
2654529 TGCTAAACAC
Statistics
Matches: 127, Mismatches: 27, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
14 127 1.00
ACGTcount: A:0.54, C:0.27, G:0.02, T:0.18
Consensus pattern (14 bp):
CCCTAACTACAAAA
Found at i:2654534 original size:28 final size:28
Alignment explanation
Indices: 2654361--2654552 Score: 177
Period size: 28 Copynumber: 6.8 Consensus size: 28
2654351 ATCTACTAAT
* * *
2654361 CCCTAACTACAAAACCCTAAATATAAAA
1 CCCTAAATACAAAACCCTAACTACAAAA
* * * * *
2654389 CTCTAATTAGAAAACCTTAACTATAAAA
1 CCCTAAATACAAAACCCTAACTACAAAA
* ** * *
2654417 CCCTAACTACAAAACTATAACCAGAAAA
1 CCCTAAATACAAAACCCTAACTACAAAA
* *
2654445 CCCTAAATAAAAAACCCTAAGTACAAAA
1 CCCTAAATACAAAACCCTAACTACAAAA
* * *
2654473 CCCTAACTATAAAACCCTAAATACAAAA
1 CCCTAAATACAAAACCCTAACTACAAAA
2654501 CCCTAAATACAAAACCCTAACTACAAAA
1 CCCTAAATACAAAACCCTAACTACAAAA
** * *
2654529 TGCTAAACACTAAAATCCTAACTA
1 CCCTAAATAC-AAAACCCTAACTA
2654553 ACTAAAAATA
Statistics
Matches: 134, Mismatches: 29, Indels: 1
0.82 0.18 0.01
Matches are distributed among these distances:
28 122 0.91
29 12 0.09
ACGTcount: A:0.53, C:0.27, G:0.02, T:0.19
Consensus pattern (28 bp):
CCCTAAATACAAAACCCTAACTACAAAA
Done.