Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D03
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: 50986338
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 218898 characters in sequence are not A, C, G, or T
File 43 of 170
Found at i:12430092 original size:100 final size:100
Alignment explanation
Indices: 12429911--12430117 Score: 315
Period size: 100 Copynumber: 2.1 Consensus size: 100
12429901 CCGAAGAATT
* * * *
12429911 ACGAATCTTACCTCCCAGGCGGTGCAGTGGAACAGATTAAAGTCACATCGGTGAATCTTGCTTCC
1 ACGAATCTTACCTCCCAGGCGATCCAGCGGAACAGATTAAAGCCACATCGGTGAATCTTGCTTCC
* *
12429976 CCAACATTGCAATTCAAAAGATTAAAGCTACAACA
66 CCAACAGTGCAATTCAAAAGATTAAAGCCACAACA
*
12430011 ACGAATCTTACCTCCCAGGCGATCCAGCGGAACAGATTAAAGCCACATTGGTGAATCTTGCTTCC
1 ACGAATCTTACCTCCCAGGCGATCCAGCGGAACAGATTAAAGCCACATCGGTGAATCTTGCTTCC
* * *
12430076 CCGACAGTGTAGTTCAAAAGATTAAAGCCACAACA
66 CCAACAGTGCAATTCAAAAGATTAAAGCCACAACA
*
12430111 GCGAATC
1 ACGAATC
12430118 ATGCTTCCCC
Statistics
Matches: 96, Mismatches: 11, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
100 96 1.00
ACGTcount: A:0.33, C:0.26, G:0.19, T:0.22
Consensus pattern (100 bp):
ACGAATCTTACCTCCCAGGCGATCCAGCGGAACAGATTAAAGCCACATCGGTGAATCTTGCTTCC
CCAACAGTGCAATTCAAAAGATTAAAGCCACAACA
Found at i:12430148 original size:100 final size:100
Alignment explanation
Indices: 12429911--12430169 Score: 250
Period size: 100 Copynumber: 2.6 Consensus size: 100
12429901 CCGAAGAATT
* * * * * * * * *
12429911 ACGAATCTTACCTCCCAGGCGGTGCAGTGGAACAGATTAAAGTCACATCGGTGAATCTTGCTTCC
1 ACGAATCATACCTCCCAGACGATCCAGCGAAAAAGATTAAAGCCACATTGGTGAATCTTGCTTCC
* *
12429976 CCAACATTGCAATTCAAAAGATTAAAGCTACAACA
66 CCAACAGTGCAATTCAAAAGATTAAAGCCACAACA
* * * *
12430011 ACGAATCTTACCTCCCAGGCGATCCAGCGGAACAGATTAAAGCCACATTGGTGAATCTTGCTTCC
1 ACGAATCATACCTCCCAGACGATCCAGCGAAAAAGATTAAAGCCACATTGGTGAATCTTGCTTCC
* * *
12430076 CCGACAGTGTAGTTCAAAAGATTAAAGCCACAACA
66 CCAACAGTGCAATTCAAAAGATTAAAGCCACAACA
* * * * * ** * * *
12430111 GCGAATCATGCTTCCCCGAC-ATTGCAGTTAAAAAGATTAAAGCCATAATGGCGAATCTT
1 ACGAATCATACCTCCCAGACGA-TCCAGCGAAAAAGATTAAAGCCACATTGGTGAATCTT
12430170 ACTTTCCAAA
Statistics
Matches: 134, Mismatches: 24, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
99 1 0.01
100 133 0.99
ACGTcount: A:0.34, C:0.25, G:0.19, T:0.23
Consensus pattern (100 bp):
ACGAATCATACCTCCCAGACGATCCAGCGAAAAAGATTAAAGCCACATTGGTGAATCTTGCTTCC
CCAACAGTGCAATTCAAAAGATTAAAGCCACAACA
Found at i:12431876 original size:11 final size:11
Alignment explanation
Indices: 12431862--12431914 Score: 54
Period size: 11 Copynumber: 4.6 Consensus size: 11
12431852 ATTCAATGGT
12431862 TATTTTAATTC
1 TATTTTAATTC
* *
12431873 TATTTTGAGTC
1 TATTTTAATTC
12431884 TATTTTGAATTC
1 TATTTT-AATTC
12431896 ATATATTTAATT-
1 -TAT-TTTAATTC
12431908 TATTTTA
1 TATTTTA
12431915 GAACTTTTAT
Statistics
Matches: 35, Mismatches: 4, Indels: 7
0.76 0.09 0.15
Matches are distributed among these distances:
10 4 0.11
11 18 0.51
12 3 0.09
13 7 0.20
14 3 0.09
ACGTcount: A:0.28, C:0.06, G:0.06, T:0.60
Consensus pattern (11 bp):
TATTTTAATTC
Found at i:12434906 original size:5 final size:5
Alignment explanation
Indices: 12434887--12434919 Score: 50
Period size: 5 Copynumber: 6.6 Consensus size: 5
12434877 TAAAAACTAG
12434887 AAAA- AAAAGT AAAAT AAAAT AAAAT AAAAT AAA
1 AAAAT AAAA-T AAAAT AAAAT AAAAT AAAAT AAA
12434920 GTTCTAATGC
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
4 4 0.15
5 19 0.70
6 4 0.15
ACGTcount: A:0.82, C:0.00, G:0.03, T:0.15
Consensus pattern (5 bp):
AAAAT
Found at i:12436711 original size:31 final size:32
Alignment explanation
Indices: 12436659--12436729 Score: 83
Period size: 31 Copynumber: 2.2 Consensus size: 32
12436649 GCTCTATGGG
* *
12436659 GCGACACCGCGATGACAGTAAGGT-CTTTGAA
1 GCGACACCGCGAAGACAGTAAGGTCCTTCGAA
*
12436690 GCGACACCGCGACAG-CGGTAAGGTCCTTCGAA
1 GCGACACCGCGA-AGACAGTAAGGTCCTTCGAA
*
12436722 GTGACACC
1 GCGACACC
12436730 TCCAAGAGGT
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
31 20 0.59
32 14 0.41
ACGTcount: A:0.27, C:0.28, G:0.30, T:0.15
Consensus pattern (32 bp):
GCGACACCGCGAAGACAGTAAGGTCCTTCGAA
Found at i:12436809 original size:27 final size:27
Alignment explanation
Indices: 12436785--12436862 Score: 95
Period size: 27 Copynumber: 2.9 Consensus size: 27
12436775 AAAGAGTCCA
12436785 CCGAGACATTAAACATAGGGTAGTCTG
1 CCGAGACATTAAACATAGGGTAGTCTG
* ** *
12436812 CCGTGACATTAAACACGGGGTATTCTG
1 CCGAGACATTAAACATAGGGTAGTCTG
*
12436839 CC-AGGACATTAAACATAGAGTAGT
1 CCGA-GACATTAAACATAGGGTAGT
12436863 TCGTTGGGAC
Statistics
Matches: 41, Mismatches: 9, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
27 41 1.00
ACGTcount: A:0.33, C:0.19, G:0.24, T:0.23
Consensus pattern (27 bp):
CCGAGACATTAAACATAGGGTAGTCTG
Found at i:12436872 original size:27 final size:27
Alignment explanation
Indices: 12436841--12436908 Score: 91
Period size: 27 Copynumber: 2.5 Consensus size: 27
12436831 GTATTCTGCC
12436841 AGGACATTAAACATAGAGTAGTTCGTT
1 AGGACATTAAACATAGAGTAGTTCGTT
* * * *
12436868 GGGACATCAAACACAGGGTAGTTCGTT
1 AGGACATTAAACATAGAGTAGTTCGTT
*
12436895 AGGACGTTAAACAT
1 AGGACATTAAACAT
12436909 GAGATAAAAT
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.35, C:0.15, G:0.25, T:0.25
Consensus pattern (27 bp):
AGGACATTAAACATAGAGTAGTTCGTT
Found at i:12439542 original size:24 final size:24
Alignment explanation
Indices: 12439510--12439558 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
12439500 CGTCTCAATT
12439510 GCTTAAGGTGGTGGAAGTATCATA
1 GCTTAAGGTGGTGGAAGTATCATA
12439534 GCTTAAGGTGGTGGAAGTATCATA
1 GCTTAAGGTGGTGGAAGTATCATA
12439558 G
1 G
12439559 GAGGCATAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.29, C:0.08, G:0.35, T:0.29
Consensus pattern (24 bp):
GCTTAAGGTGGTGGAAGTATCATA
Found at i:12440287 original size:21 final size:21
Alignment explanation
Indices: 12440241--12440287 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
12440231 AGGACATGGT
* *
12440241 TGTGTGGCTACTTCACACGCC
1 TGTGTGACTACTTCACACACC
* *
12440262 CGTGTGACTACTTCACACATC
1 TGTGTGACTACTTCACACACC
12440283 TGTGT
1 TGTGT
12440288 ACACTAATCG
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.17, C:0.30, G:0.21, T:0.32
Consensus pattern (21 bp):
TGTGTGACTACTTCACACACC
Found at i:12453383 original size:8 final size:8
Alignment explanation
Indices: 12453370--12453395 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
12453360 GTTATGGAAA
12453370 ATTCATGC
1 ATTCATGC
12453378 ATTCATGC
1 ATTCATGC
12453386 ATTCATGC
1 ATTCATGC
12453394 AT
1 AT
12453396 ACTCATACAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.27, C:0.23, G:0.12, T:0.38
Consensus pattern (8 bp):
ATTCATGC
Found at i:12463035 original size:12 final size:12
Alignment explanation
Indices: 12463018--12463047 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
12463008 TAATAAATTT
12463018 AAAATTATTAAA
1 AAAATTATTAAA
12463030 AAAATTATTAAA
1 AAAATTATTAAA
12463042 AAAATT
1 AAAATT
12463048 TACTTTGACA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (12 bp):
AAAATTATTAAA
Found at i:12472219 original size:25 final size:27
Alignment explanation
Indices: 12472155--12472225 Score: 73
Period size: 25 Copynumber: 2.8 Consensus size: 27
12472145 GTTGGGAAAG
12472155 AGATGAGGAGAA-G-AAGAAAAAAAATA
1 AGATG-GGAGAAGGAAAGAAAAAAAATA
*
12472181 AGATGGGA-ACAGGAAAGAATAAAAATA
1 AGATGGGAGA-AGGAAAGAAAAAAAATA
12472208 A-A-GGGAGAAGGAAA-AAAA
1 AGATGGGAGAAGGAAAGAAAA
12472226 GTAAAATAGA
Statistics
Matches: 39, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
24 4 0.10
25 14 0.36
26 8 0.21
27 13 0.33
ACGTcount: A:0.63, C:0.01, G:0.28, T:0.07
Consensus pattern (27 bp):
AGATGGGAGAAGGAAAGAAAAAAAATA
Found at i:12475477 original size:26 final size:26
Alignment explanation
Indices: 12475441--12475494 Score: 65
Period size: 26 Copynumber: 2.1 Consensus size: 26
12475431 GATTTTAGTG
*
12475441 TTCAATTTGATAATTAA-GTTTCTTTT
1 TTCAAATTGATAATTAAGGTTT-TTTT
**
12475467 TTCAAATTGATGCTTAAGGTTTTTTT
1 TTCAAATTGATAATTAAGGTTTTTTT
12475493 TT
1 TT
12475495 GTCTCATACA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 20 0.83
27 4 0.17
ACGTcount: A:0.24, C:0.07, G:0.11, T:0.57
Consensus pattern (26 bp):
TTCAAATTGATAATTAAGGTTTTTTT
Found at i:12477034 original size:32 final size:32
Alignment explanation
Indices: 12476941--12477039 Score: 111
Period size: 27 Copynumber: 3.3 Consensus size: 32
12476931 CTAATATAAT
12476941 ATTTGGTACTTGAACTTGACAC-TTTTTCCTA
1 ATTTGGTACTTGAACTTGACACTTTTTTCCTA
* * * *
12476972 ATTTGGTACCTAAACTT-----TTTTTACCCA
1 ATTTGGTACTTGAACTTGACACTTTTTTCCTA
*
12476999 ATTTGGTACTTGAGCTTGACACTTTTTTCCTA
1 ATTTGGTACTTGAACTTGACACTTTTTTCCTA
12477031 ATTTGGTAC
1 ATTTGGTAC
12477040 CCTAATTTGG
Statistics
Matches: 53, Mismatches: 9, Indels: 11
0.73 0.12 0.15
Matches are distributed among these distances:
27 21 0.40
31 15 0.28
32 17 0.32
ACGTcount: A:0.22, C:0.19, G:0.13, T:0.45
Consensus pattern (32 bp):
ATTTGGTACTTGAACTTGACACTTTTTTCCTA
Found at i:12477045 original size:13 final size:13
Alignment explanation
Indices: 12477027--12477053 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
12477017 ACACTTTTTT
12477027 CCTAATTTGGTAC
1 CCTAATTTGGTAC
12477040 CCTAATTTGGTAC
1 CCTAATTTGGTAC
12477053 C
1 C
12477054 TAAACTTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.22, C:0.26, G:0.15, T:0.37
Consensus pattern (13 bp):
CCTAATTTGGTAC
Found at i:12477076 original size:29 final size:29
Alignment explanation
Indices: 12477032--12477117 Score: 93
Period size: 28 Copynumber: 2.9 Consensus size: 29
12477022 TTTTTCCTAA
12477032 TTTGGTACCCTAATTTGGTACCTAAACTTTT
1 TTTGG-ACCC-AATTTGGTACCTAAACTTTT
* * *
12477063 TTTGGACCCAATTTGGTACTTAAGC-ATT
1 TTTGGACCCAATTTGGTACCTAAACTTTT
* **
12477091 TTTAGATTCAATTTGGTACCTAAACTT
1 TTTGGACCCAATTTGGTACCTAAACTT
12477118 ATTAAATATT
Statistics
Matches: 45, Mismatches: 9, Indels: 4
0.78 0.16 0.07
Matches are distributed among these distances:
28 22 0.49
29 14 0.31
30 4 0.09
31 5 0.11
ACGTcount: A:0.26, C:0.17, G:0.14, T:0.43
Consensus pattern (29 bp):
TTTGGACCCAATTTGGTACCTAAACTTTT
Found at i:12477297 original size:31 final size:31
Alignment explanation
Indices: 12477259--12477392 Score: 98
Period size: 31 Copynumber: 4.4 Consensus size: 31
12477249 TTAAAAAAGA
12477259 TTAGGTACCAAATTAGGAAAAAAAGTCAAGT
1 TTAGGTACCAAATTAGGAAAAAAAGTCAAGT
* ***
12477290 TTAGGTACCAAATTGGGACCCCAAA---AAGT
1 TTAGGTACCAAATTAGGA-AAAAAAGTCAAGT
* * * *
12477319 TTAAGTACTAACTTA--AAAAAAGTGTCAAGT
1 TTAGGTACCAAATTAGGAAAAAA-AGTCAAGT
* ***
12477349 TTAGGTATCAAATTAGGAAAATGTGTCAAGT
1 TTAGGTACCAAATTAGGAAAAAAAGTCAAGT
*
12477380 TCAGGTACCAAAT
1 TTAGGTACCAAAT
12477393 GTTATATTAA
Statistics
Matches: 76, Mismatches: 20, Indels: 14
0.69 0.18 0.13
Matches are distributed among these distances:
26 2 0.03
27 1 0.01
29 15 0.20
30 15 0.20
31 36 0.47
32 7 0.09
ACGTcount: A:0.43, C:0.13, G:0.19, T:0.26
Consensus pattern (31 bp):
TTAGGTACCAAATTAGGAAAAAAAGTCAAGT
Found at i:12477677 original size:26 final size:26
Alignment explanation
Indices: 12477637--12477688 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
12477627 AACATTAAAC
*
12477637 TAGTATTATAAAATTTCAAATAAATAT
1 TAGTATTACAAAATTTCAAA-AAATAT
*
12477664 TAGTA-TACAAAATTTCATAAAATAT
1 TAGTATTACAAAATTTCAAAAAATAT
12477689 AACGTGTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
25 6 0.26
26 12 0.52
27 5 0.22
ACGTcount: A:0.52, C:0.06, G:0.04, T:0.38
Consensus pattern (26 bp):
TAGTATTACAAAATTTCAAAAAATAT
Found at i:12485684 original size:30 final size:30
Alignment explanation
Indices: 12485650--12485710 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
12485640 GACCAAGAGG
12485650 ATTTATTATGGAATAGTAAATCTAAGTCTA
1 ATTTATTATGGAATAGTAAATCTAAGTCTA
12485680 ATTTATTATGGAATAGTAAATCTAAGTCTA
1 ATTTATTATGGAATAGTAAATCTAAGTCTA
12485710 A
1 A
12485711 ATGTTTGTTG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.41, C:0.07, G:0.13, T:0.39
Consensus pattern (30 bp):
ATTTATTATGGAATAGTAAATCTAAGTCTA
Found at i:12486488 original size:20 final size:20
Alignment explanation
Indices: 12486463--12486500 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
12486453 TATTAGATCT
12486463 TAGACTCCCAAGGTATCTGG
1 TAGACTCCCAAGGTATCTGG
12486483 TAGACTCCCAAGGTATCT
1 TAGACTCCCAAGGTATCT
12486501 AGTAAATGTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.26, C:0.26, G:0.21, T:0.26
Consensus pattern (20 bp):
TAGACTCCCAAGGTATCTGG
Found at i:12495338 original size:27 final size:28
Alignment explanation
Indices: 12495308--12495367 Score: 70
Period size: 28 Copynumber: 2.2 Consensus size: 28
12495298 TTATGAGGAT
12495308 GAATGAAAA-TGAAATATAGGA-GTTTGG
1 GAATGAAAACTGAAATA-AGGAGGTTTGG
* * *
12495335 GAATCAAAACTGAATTAATGAGGTTTGG
1 GAATGAAAACTGAAATAAGGAGGTTTGG
12495363 GAATG
1 GAATG
12495368 TAAGGGACAA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
27 11 0.41
28 16 0.59
ACGTcount: A:0.42, C:0.03, G:0.28, T:0.27
Consensus pattern (28 bp):
GAATGAAAACTGAAATAAGGAGGTTTGG
Found at i:12496519 original size:26 final size:27
Alignment explanation
Indices: 12496472--12496535 Score: 87
Period size: 26 Copynumber: 2.4 Consensus size: 27
12496462 AATTTTCTCA
*
12496472 AAATTTTAC-AGGGGATAAAATCGTTG
1 AAATTTTACTAGGGGATAAAATCGTCG
* *
12496498 AAATTTTACTAGTGG-TACAATCGTCG
1 AAATTTTACTAGGGGATAAAATCGTCG
12496524 AAATTTTACTAG
1 AAATTTTACTAG
12496536 CAATAAAATT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
26 30 0.88
27 4 0.12
ACGTcount: A:0.36, C:0.11, G:0.19, T:0.34
Consensus pattern (27 bp):
AAATTTTACTAGGGGATAAAATCGTCG
Found at i:12504372 original size:17 final size:17
Alignment explanation
Indices: 12504350--12504382 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
12504340 CACTTTCTAT
*
12504350 ATGATATAATTGATATG
1 ATGATATAATTAATATG
12504367 ATGATATAATTAATAT
1 ATGATATAATTAATAT
12504383 TTTTTTAAAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.45, C:0.00, G:0.12, T:0.42
Consensus pattern (17 bp):
ATGATATAATTAATATG
Found at i:12506644 original size:126 final size:125
Alignment explanation
Indices: 12506401--12506770 Score: 562
Period size: 126 Copynumber: 3.0 Consensus size: 125
12506391 TTTAGGTCTT
*** **
12506401 GGAAGAAATAATTTTGAGTTGACGTTTCTGATAAAATAGTATAAAATCGCTTCTAGCAGGATGCT
1 GGAAGAAATAATTTTTTTTTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAGCAGGATGCT
*
12506466 ATTTGAGAGGAATTTGTGAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAGTAAGTCAC
66 ATTTGAGAAGAATTTGTGAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAGTAAGTCAC
*
12506526 GGAAGAAATAATTATTTTTTTGACGTTTCTGAGCAAATAGTTTAAAATCGCTTCTAGCAGGATGC
1 GGAAGAAATAATT-TTTTTTTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAGCAGGATGC
* * * *
12506591 TATTTGAGAAGAATTTGTGAAATCGCGGCCTCGT-CAGCGCGCTTTTGCTACAGTAGGTCAT
65 TATTTGAGAAGAATTTGTGAAATCGCGCCCTCGTGGA-CGCGCTTTTGCTACAGTAAGTCAC
* * * * *
12506652 GTAAGAAATAATTTTTTTTTGACATTTCTGAGCAAATAATATAAAATCACTTCTAGCAGGAAGCT
1 GGAAGAAATAATTTTTTTTTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAGCAGGATGCT
*
12506717 ATTTGAGAAGAATTTATGAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAGTA
66 ATTTGAGAAGAATTTGTGAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAGTA
12506771 GCATGTTTGG
Statistics
Matches: 222, Mismatches: 20, Indels: 6
0.90 0.08 0.02
Matches are distributed among these distances:
125 110 0.50
126 112 0.50
ACGTcount: A:0.30, C:0.16, G:0.22, T:0.32
Consensus pattern (125 bp):
GGAAGAAATAATTTTTTTTTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAGCAGGATGCT
ATTTGAGAAGAATTTGTGAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAGTAAGTCAC
Found at i:12506728 original size:125 final size:125
Alignment explanation
Indices: 12506393--12506771 Score: 571
Period size: 125 Copynumber: 3.0 Consensus size: 125
12506383 TAAGGGTTTT
* *** **
12506393 TAGGTCTTGGAAGAAATAATTTTGAGTTGACGTTTCTGATAAAATAGTATAAAATCGCTTCTAGC
1 TAGGTCATGGAAGAAATAATTTTTTTTTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAGC
*
12506458 AGGATGCTATTTGAGAGGAATTTGTGAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAG
66 AGGATGCTATTTGAGAAGAATTTGTGAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAG
* * *
12506518 TAAGTCACGGAAGAAATAATTATTTTTTTGACGTTTCTGAGCAAATAGTTTAAAATCGCTTCTAG
1 TAGGTCATGGAAGAAATAATT-TTTTTTTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAG
* *
12506583 CAGGATGCTATTTGAGAAGAATTTGTGAAATCGCGGCCTCGT-CAGCGCGCTTTTGCTACAG
65 CAGGATGCTATTTGAGAAGAATTTGTGAAATCGCGCCCTCGTGGA-CGCGCTTTTGCTACAG
* * * *
12506644 TAGGTCATGTAAGAAATAATTTTTTTTTGACATTTCTGAGCAAATAATATAAAATCACTTCTAGC
1 TAGGTCATGGAAGAAATAATTTTTTTTTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAGC
* *
12506709 AGGAAGCTATTTGAGAAGAATTTATGAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAG
66 AGGATGCTATTTGAGAAGAATTTGTGAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAG
12506769 TAG
1 TAG
12506772 CATGTTTGGG
Statistics
Matches: 228, Mismatches: 23, Indels: 6
0.89 0.09 0.02
Matches are distributed among these distances:
125 116 0.51
126 112 0.49
ACGTcount: A:0.30, C:0.16, G:0.22, T:0.32
Consensus pattern (125 bp):
TAGGTCATGGAAGAAATAATTTTTTTTTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAGC
AGGATGCTATTTGAGAAGAATTTGTGAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAG
Found at i:12511216 original size:27 final size:27
Alignment explanation
Indices: 12511186--12511363 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
12511176 ATATTGAGTC
* * * *
12511186 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
12511213 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
12511240 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
12511268 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
12511295 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
12511322 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
12511349 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
12511364 GTACAATTTA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:12511325 original size:82 final size:81
Alignment explanation
Indices: 12511207--12511362 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
12511197 TGCTATATAA
* *
12511207 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
12511272 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
12511289 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
12511353 CACTTAGTGC
65 CACTTAGTGC
12511363 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:12519407 original size:27 final size:27
Alignment explanation
Indices: 12519377--12519554 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
12519367 ATATTGAGTC
* * * *
12519377 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
12519404 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
12519431 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
12519459 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
12519486 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
12519513 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
12519540 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
12519555 GTACAATTTA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:12519516 original size:82 final size:81
Alignment explanation
Indices: 12519398--12519553 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
12519388 TGCTATATAA
* *
12519398 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
12519463 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
12519480 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
12519544 CACTTAGTGC
65 CACTTAGTGC
12519554 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:12521575 original size:23 final size:23
Alignment explanation
Indices: 12521546--12522062 Score: 392
Period size: 23 Copynumber: 20.9 Consensus size: 23
12521536 AAATTATGTA
12521546 AAATTAGGTTAGGGTTTTTAATT
1 AAATTAGGTTAGGGTTTTTAATT
12521569 AAATTAGGTTATGGTTAGGGTTTTTAATT
1 -AA--A--TTA-GGTTAGGGTTTTTAATT
12521598 AAATTAGGTTAGGGTTTTTAAGTT
1 AAATTAGGTTAGGGTTTTTAA-TT
*
12521622 -AA--GGGTTTAGGGTTTTTAATT
1 AAATTAGG-TTAGGGTTTTTAATT
12521643 AAATTAGGTTAGGGTTTTTAATT
1 AAATTAGGTTAGGGTTTTTAATT
*
12521666 AAATTAGGTTAGGTTTTTTAATT
1 AAATTAGGTTAGGGTTTTTAATT
12521689 AATTTAGGTTAAGGTTAGGGTTTTTAATT
1 AA---A--TT-AGGTTAGGGTTTTTAATT
*
12521718 AAATCAGGTTAGGGTTAGGGGTTTTAATT
1 -AA--A--TTA-GGTTAGGGTTTTTAATT
12521747 AAATTAGGTTAGGGTTTTTAATT
1 AAATTAGGTTAGGGTTTTTAATT
12521770 AATTTAGGTTAAGGTTAGGGTTTTTAAGTT
1 AA---A--TT-AGGTTAGGGTTTTTAA-TT
**
12521800 -AA-GGGGTTAGGGTTTTTAATT
1 AAATTAGGTTAGGGTTTTTAATT
12521821 AAATTAGGTTAGGGTTTTTAATT
1 AAATTAGGTTAGGGTTTTTAATT
12521844 AATTTAGGTTAAGGTTAGGGTTTTTAAGTT
1 AA---A--TT-AGGTTAGGGTTTTTAA-TT
** *
12521874 -AA-GGGGTTAGTGTTTTTAATT
1 AAATTAGGTTAGGGTTTTTAATT
12521895 AAATTAGGTTAGGGTTAGGGTTTTTAATT
1 -AA--A--TTA-GGTTAGGGTTTTTAATT
12521924 AAATTAGGTTAGGGTTTTTAAGTT
1 AAATTAGGTTAGGGTTTTTAA-TT
*
12521948 -AA--GGGTTTAGGGTTTTTAATT
1 AAATTAGG-TTAGGGTTTTTAATT
* *
12521969 AAATTAGGTTATGGTTTTTAACT
1 AAATTAGGTTAGGGTTTTTAATT
*
12521992 AAATTAGGTTAAGGTTAGGGTTT--TT
1 AAATTAGGTTAGGGTT----TTTAATT
*
12522017 AAGTTAAGGGTTTAGGGTTTTTAATT
1 AAATT-A-GG-TTAGGGTTTTTAATT
12522043 AAATTAGGTTAGGGTTTTTA
1 AAATTAGGTTAGGGTTTTTA
12522063 TTACATCAAA
Statistics
Matches: 411, Mismatches: 26, Indels: 113
0.75 0.05 0.21
Matches are distributed among these distances:
21 12 0.03
22 61 0.15
23 151 0.37
24 24 0.06
25 7 0.02
26 16 0.04
27 5 0.01
28 23 0.06
29 106 0.26
30 6 0.01
ACGTcount: A:0.28, C:0.00, G:0.25, T:0.46
Consensus pattern (23 bp):
AAATTAGGTTAGGGTTTTTAATT
Found at i:12521586 original size:29 final size:29
Alignment explanation
Indices: 12521552--12521613 Score: 115
Period size: 29 Copynumber: 2.1 Consensus size: 29
12521542 TGTAAAATTA
*
12521552 GGTTAGGGTTTTTAATTAAATTAGGTTAT
1 GGTTAGGGTTTTTAATTAAATTAGGTTAG
12521581 GGTTAGGGTTTTTAATTAAATTAGGTTAG
1 GGTTAGGGTTTTTAATTAAATTAGGTTAG
12521610 GGTT
1 GGTT
12521614 TTTAAGTTAA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.26, C:0.00, G:0.27, T:0.47
Consensus pattern (29 bp):
GGTTAGGGTTTTTAATTAAATTAGGTTAG
Found at i:12521706 original size:29 final size:28
Alignment explanation
Indices: 12521619--12522023 Score: 264
Period size: 29 Copynumber: 15.9 Consensus size: 28
12521609 GGGTTTTTAA
12521619 GTTAAGGGTTTAGGGTTTTTAATTAA--A-
1 GTTAA-GG-TTAGGGTTTTTAATTAATTAG
12521646 -TT-AGGTTAGGGTTTTTAATTAA--A-
1 GTTAAGGTTAGGGTTTTTAATTAATTAG
*
12521669 -TT-AGGTTAGGTTTTTTAATTAATTTAG
1 GTTAAGGTTAGGGTTTTTAATTAA-TTAG
*
12521696 GTTAAGGTTAGGGTTTTTAATTAAATCAG
1 GTTAAGGTTAGGGTTTTTAATT-AATTAG
* *
12521725 GTTAGGGTTAGGGGTTTTAATTAA--A-
1 GTTAAGGTTAGGGTTTTTAATTAATTAG
12521750 -TT-AGGTTAGGGTTTTTAATTAATTTAG
1 GTTAAGGTTAGGGTTTTTAATTAA-TTAG
12521777 GTTAAGGTTAGGGTTTTTAAGTT-A--AG
1 GTTAAGGTTAGGGTTTTTAA-TTAATTAG
12521803 G----GGTTAGGGTTTTTAATTAA--A-
1 GTTAAGGTTAGGGTTTTTAATTAATTAG
12521824 -TT-AGGTTAGGGTTTTTAATTAATTTAG
1 GTTAAGGTTAGGGTTTTTAATTAA-TTAG
12521851 GTTAAGGTTAGGGTTTTTAAGTT-A--AG
1 GTTAAGGTTAGGGTTTTTAA-TTAATTAG
*
12521877 G----GGTTAGTGTTTTTAATTAAATTAG
1 GTTAAGGTTAGGGTTTTTAATT-AATTAG
*
12521902 GTTAGGGTTAGGGTTTTTAATTAA--A-
1 GTTAAGGTTAGGGTTTTTAATTAATTAG
12521927 -TT-AGGTTAGGGTTTTTAAGTT-A--AG
1 GTTAAGGTTAGGGTTTTTAA-TTAATTAG
*
12521951 G----GTTTAGGGTTTTTAATTAA--A-
1 GTTAAGGTTAGGGTTTTTAATTAATTAG
* *
12521972 -TT-AGGTTATGGTTTTTAACTAAATTAG
1 GTTAAGGTTAGGGTTTTTAA-TTAATTAG
12521999 GTTAAGGTTAGGGTTTTTAAGTTAA
1 GTTAAGGTTAGGGTTTTTAA-TTAA
12522024 GGGTTTAGGG
Statistics
Matches: 315, Mismatches: 17, Indels: 90
0.75 0.04 0.21
Matches are distributed among these distances:
21 6 0.02
22 47 0.15
23 107 0.34
24 11 0.03
25 4 0.01
26 14 0.04
28 12 0.04
29 108 0.34
30 6 0.02
ACGTcount: A:0.28, C:0.00, G:0.25, T:0.46
Consensus pattern (28 bp):
GTTAAGGTTAGGGTTTTTAATTAATTAG
Found at i:12521817 original size:74 final size:74
Alignment explanation
Indices: 12521614--12522062 Score: 595
Period size: 74 Copynumber: 5.9 Consensus size: 74
12521604 GGTTAGGGTT
* **
12521614 TTTAAGTTAAGGGTTTAGGGTTTTTAA-TTAAATTAGGTTAGGGTTTTTAATTAAATTAGGTTAG
1 TTTAGGTTAA-GG-TTAGGGTTTTTAAGTT-AA-GGGGTTAGGGTTTTTAATTAAATTAGGTTAG
*
12521678 GTTTTTTAATTAA
62 GGTTTTTAATTAA
*
12521691 TTTAGGTTAAGGTTAGGGTTTTTAA-TTAAATCAGGTTAGGGTTAGGGGTTTTAATTAAATTAGG
1 TTTAGGTTAAGGTTAGGGTTTTTAAGTT--A--A-G---GGGTTAGGGTTTTTAATTAAATTAGG
12521755 TTAGGGTTTTTAATTAA
58 TTAGGGTTTTTAATTAA
12521772 TTTAGGTTAAGGTTAGGGTTTTTAAGTTAAGGGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTT
1 TTTAGGTTAAGGTTAGGGTTTTTAAGTTAAGGGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTT
12521837 TTTAATTAA
66 TTTAATTAA
*
12521846 TTTAGGTTAAGGTTAGGGTTTTTAAGTTAAGGGGTTAGTGTTTTTAATTAAATTAGGTTAGGGTT
1 TTTAGGTTAAGGTTAGGGTTTTTAAGTTAAGGGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTT
12521911 AGGGTTT--TTAA
66 ----TTTAATTAA
** * *
12521922 -TTAAATT-AGGTTAGGGTTTTTAAGTTAAGGGTTTAGGGTTTTTAATTAAATTAGGTTATGGTT
1 TTTAGGTTAAGGTTAGGGTTTTTAAGTTAAGGGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTT
*
12521985 TTTAACTAA
66 TTTAATTAA
* *
12521994 ATTAGGTTAAGGTTAGGGTTTTTAAGTTAAGGGTTTAGGGTTTTTAATTAAATTAGGTTAGGGTT
1 TTTAGGTTAAGGTTAGGGTTTTTAAGTTAAGGGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTT
12522059 TTTA
66 TTTA
12522063 TTACATCAAA
Statistics
Matches: 340, Mismatches: 17, Indels: 33
0.87 0.04 0.08
Matches are distributed among these distances:
70 3 0.01
72 3 0.01
73 5 0.01
74 218 0.64
75 20 0.06
76 8 0.02
77 10 0.03
78 5 0.01
80 1 0.00
81 65 0.19
82 2 0.01
ACGTcount: A:0.28, C:0.00, G:0.25, T:0.47
Consensus pattern (74 bp):
TTTAGGTTAAGGTTAGGGTTTTTAAGTTAAGGGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTT
TTTAATTAA
Found at i:12521874 original size:20 final size:21
Alignment explanation
Indices: 12521846--12521896 Score: 61
Period size: 22 Copynumber: 2.5 Consensus size: 21
12521836 TTTTAATTAA
*
12521846 TTTAGGTTAA-GGTTAGGGTT
1 TTTAAGTTAAGGGTTAGGGTT
*
12521866 TTTAAGTTAAGGGGTTAGTGTT
1 TTTAAGTTAA-GGGTTAGGGTT
12521888 TTTAA-TTAA
1 TTTAAGTTAA
12521897 ATTAGGTTAG
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
20 9 0.33
21 4 0.15
22 14 0.52
ACGTcount: A:0.25, C:0.00, G:0.27, T:0.47
Consensus pattern (21 bp):
TTTAAGTTAAGGGTTAGGGTT
Found at i:12521896 original size:21 final size:22
Alignment explanation
Indices: 12521856--12522062 Score: 89
Period size: 22 Copynumber: 8.6 Consensus size: 22
12521846 TTTAGGTTAA
12521856 GGTTAGGGTTTTTAAGTTAAGG
1 GGTTAGGGTTTTTAAGTTAAGG
*
12521878 GGTTAGTGTTTTTAA-TTAAATTAGG
1 GGTTAGGGTTTTTAAGTT--A--AGG
**
12521903 TTAGGGTTAGGGTTTTTAA-TTAAATTA
1 ---G-GTTAGGGTTTTTAAGTT-AA-GG
12521930 GGTTAGGGTTTTTAAGTTAAGG
1 GGTTAGGGTTTTTAAGTTAAGG
* **
12521952 GTTTAGGGTTTTTAA-TTAAATTA
1 GGTTAGGGTTTTTAAGTT-AA-GG
* * *
12521975 GGTTATGGTTTTTAACTAAATTAGG
1 GGTTAGGGTTTTTAAGT---TAAGG
12522000 TTAAGGTTAGGGTTTTTAAGTTAAGG
1 ----GGTTAGGGTTTTTAAGTTAAGG
* **
12522026 GTTTAGGGTTTTTAA-TTAAATTA
1 GGTTAGGGTTTTTAAGTT-AA-GG
12522049 GGTTAGGGTTTTTA
1 GGTTAGGGTTTTTA
12522063 TTACATCAAA
Statistics
Matches: 142, Mismatches: 21, Indels: 43
0.69 0.10 0.21
Matches are distributed among these distances:
21 6 0.04
22 46 0.32
23 43 0.30
24 4 0.03
25 3 0.02
26 6 0.04
27 1 0.01
28 3 0.02
29 30 0.21
ACGTcount: A:0.27, C:0.00, G:0.27, T:0.46
Consensus pattern (22 bp):
GGTTAGGGTTTTTAAGTTAAGG
Found at i:12522575 original size:18 final size:18
Alignment explanation
Indices: 12522552--12522586 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
12522542 CGAAAAAGGA
*
12522552 TACATATAAGGGTTAGGG
1 TACATATAAGGGCTAGGG
12522570 TACATATAAGGGCTAGG
1 TACATATAAGGGCTAGG
12522587 AAATGCACCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.34, C:0.09, G:0.31, T:0.26
Consensus pattern (18 bp):
TACATATAAGGGCTAGGG
Found at i:12523245 original size:7 final size:7
Alignment explanation
Indices: 12523235--12523259 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
12523225 TTATATACAT
12523235 AATACTA
1 AATACTA
12523242 AATACTA
1 AATACTA
12523249 AATACTA
1 AATACTA
12523256 AATA
1 AATA
12523260 TCAATCAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.60, C:0.12, G:0.00, T:0.28
Consensus pattern (7 bp):
AATACTA
Found at i:12524487 original size:12 final size:11
Alignment explanation
Indices: 12524449--12524487 Score: 55
Period size: 10 Copynumber: 3.6 Consensus size: 11
12524439 GAGCGAATTT
12524449 TTGA-AGGAAA
1 TTGAGAGGAAA
12524459 TTGAGAGG-AA
1 TTGAGAGGAAA
12524469 TTGAGAGGAAA
1 TTGAGAGGAAA
12524480 TATGAGAG
1 T-TGAGAG
12524488 AGGATTTGTT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
10 14 0.54
11 6 0.23
12 6 0.23
ACGTcount: A:0.44, C:0.00, G:0.36, T:0.21
Consensus pattern (11 bp):
TTGAGAGGAAA
Found at i:12525470 original size:40 final size:40
Alignment explanation
Indices: 12525415--12525492 Score: 147
Period size: 40 Copynumber: 1.9 Consensus size: 40
12525405 TGTACAGCTC
12525415 TTCTCAACCTTTTAATAGGAAGATAAGTGCACTTCAACTT
1 TTCTCAACCTTTTAATAGGAAGATAAGTGCACTTCAACTT
*
12525455 TTCTCAACCTTTTAATAGGAAGATAAGTGTACTTCAAC
1 TTCTCAACCTTTTAATAGGAAGATAAGTGCACTTCAAC
12525493 GTGCTTGAAT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
40 37 1.00
ACGTcount: A:0.33, C:0.19, G:0.13, T:0.35
Consensus pattern (40 bp):
TTCTCAACCTTTTAATAGGAAGATAAGTGCACTTCAACTT
Found at i:12532535 original size:21 final size:20
Alignment explanation
Indices: 12532490--12532537 Score: 53
Period size: 21 Copynumber: 2.4 Consensus size: 20
12532480 TCCTACTGTA
12532490 CAAATTTGTAATAAAACTAC
1 CAAATTTGTAATAAAACTAC
* *
12532510 AAAATTTGCTATTAAAA-TAC
1 CAAATTTG-TAATAAAACTAC
12532530 TCAAATTT
1 -CAAATTT
12532538 TGCATGAATT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
20 10 0.43
21 13 0.57
ACGTcount: A:0.48, C:0.12, G:0.04, T:0.35
Consensus pattern (20 bp):
CAAATTTGTAATAAAACTAC
Found at i:12535608 original size:22 final size:20
Alignment explanation
Indices: 12535583--12535622 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
12535573 CCCTTGACCA
12535583 ATGCATTAAAACATACCAAAAC
1 ATGCA-TAAAA-ATACCAAAAC
*
12535605 ATGCATAAAATTACCAAA
1 ATGCATAAAAATACCAAA
12535623 TATATATACC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 7 0.41
21 5 0.29
22 5 0.29
ACGTcount: A:0.55, C:0.20, G:0.05, T:0.20
Consensus pattern (20 bp):
ATGCATAAAAATACCAAAAC
Found at i:12537167 original size:20 final size:20
Alignment explanation
Indices: 12537144--12537329 Score: 67
Period size: 20 Copynumber: 9.3 Consensus size: 20
12537134 GTGTTATCAA
12537144 GGGCACCGAAGTGCAAATAG
1 GGGCACCGAAGTGCAAATAG
* * *
12537164 GGGCACAGATGTGC-ATTCAG
1 GGGCACCGAAGTGCAAAT-AG
* * * * *
12537184 GGGTATCGAGGTAC-AATCAA
1 GGGCACCGAAGTGCAAAT-AG
* * * *
12537204 GGGCACTGATGCGCAAACAG
1 GGGCACCGAAGTGCAAATAG
* * *
12537224 GGGTACCAAAGTAC-AATCAG
1 GGGCACCGAAGTGCAAAT-AG
*
12537244 GGGCA-CTAATGTGCAAATAG
1 GGGCACCGAA-GTGCAAATAG
* * * *
12537264 AGGTACCGAAGTACAAACAG
1 GGGCACCGAAGTGCAAATAG
* *
12537284 GGGCA-CTAATGTGCAAACAG
1 GGGCACCGAA-GTGCAAATAG
* * *
12537304 GGGTACCGAAGTACAATTAG
1 GGGCACCGAAGTGCAAATAG
12537324 GGGCAC
1 GGGCAC
12537330 TTATTCGTTT
Statistics
Matches: 115, Mismatches: 43, Indels: 16
0.66 0.25 0.09
Matches are distributed among these distances:
19 10 0.09
20 94 0.82
21 11 0.10
ACGTcount: A:0.34, C:0.19, G:0.31, T:0.15
Consensus pattern (20 bp):
GGGCACCGAAGTGCAAATAG
Found at i:12537208 original size:40 final size:40
Alignment explanation
Indices: 12537148--12537330 Score: 217
Period size: 40 Copynumber: 4.6 Consensus size: 40
12537138 TATCAAGGGC
* **
12537148 ACCGAAGTGCAAAT-AGGGGCAC-AGATGTGCATTCAGGGGT
1 ACCGAAGTAC-AATCAGGGGCACTA-ATGTGCAAACAGGGGT
* * * * *
12537188 ATCGAGGTACAATCAAGGGCACTGATGCGCAAACAGGGGT
1 ACCGAAGTACAATCAGGGGCACTAATGTGCAAACAGGGGT
* * *
12537228 ACCAAAGTACAATCAGGGGCACTAATGTGCAAATAGAGGT
1 ACCGAAGTACAATCAGGGGCACTAATGTGCAAACAGGGGT
*
12537268 ACCGAAGTACAAACAGGGGCACTAATGTGCAAACAGGGGT
1 ACCGAAGTACAATCAGGGGCACTAATGTGCAAACAGGGGT
*
12537308 ACCGAAGTACAATTAGGGGCACT
1 ACCGAAGTACAATCAGGGGCACT
12537331 TATTCGTTTC
Statistics
Matches: 119, Mismatches: 22, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
39 3 0.03
40 116 0.97
ACGTcount: A:0.35, C:0.19, G:0.30, T:0.16
Consensus pattern (40 bp):
ACCGAAGTACAATCAGGGGCACTAATGTGCAAACAGGGGT
Found at i:12539725 original size:21 final size:19
Alignment explanation
Indices: 12539679--12539734 Score: 94
Period size: 19 Copynumber: 2.8 Consensus size: 19
12539669 AATCTTCGAA
12539679 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
12539698 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
12539717 GATATATGCAATCTTAGA
1 G--ATATGCAATCTTAGA
12539735 AGATATGATT
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
19 20 0.57
21 15 0.43
ACGTcount: A:0.38, C:0.11, G:0.16, T:0.36
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:12539959 original size:19 final size:21
Alignment explanation
Indices: 12539935--12539973 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 21
12539925 TGTTTTCTTT
*
12539935 TTTTTTTCTT-TTT-CGATTA
1 TTTTTTACTTATTTACGATTA
12539954 TTTTTTACTTATTTACGATT
1 TTTTTTACTTATTTACGATT
12539974 TTAAAAAAGG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 9 0.53
20 3 0.18
21 5 0.29
ACGTcount: A:0.15, C:0.10, G:0.05, T:0.69
Consensus pattern (21 bp):
TTTTTTACTTATTTACGATTA
Found at i:12540197 original size:3 final size:3
Alignment explanation
Indices: 12540189--12540231 Score: 70
Period size: 3 Copynumber: 14.3 Consensus size: 3
12540179 ATTAATTTTG
12540189 TTA TTA TTA TTA TTA TTA TTA -TA TTA TATA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA T
12540232 ACCTACATAT
Statistics
Matches: 38, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
2 2 0.05
3 33 0.87
4 3 0.08
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:12546928 original size:132 final size:132
Alignment explanation
Indices: 12546691--12547877 Score: 1946
Period size: 132 Copynumber: 9.0 Consensus size: 132
12546681 ACCGGTGAAA
* *
12546691 CACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGAAGGTTGAAGATTGTAGATCTTTTCTCCCTAG
1 CACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGAAGGTTGAAGATTGTAGATCTTATCTCCCTAA
12546756 GCAGTAGTGGAGCAGATCGAAGACGACAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAA
66 GCAGTAGTGGAGCAGATCGAAGACGACAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAA
12546821 GC
131 GC
**
12546823 CACCAAGCCTTGTCTCCCTGAGCAGCAATGGAGAAGGTTGAAGATTGTAGATCTTATCTCCCTAA
1 CACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGAAGGTTGAAGATTGTAGATCTTATCTCCCTAA
* *
12546888 GTAGTAGTGGAGCAGATCGAAAACGACAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAA
66 GCAGTAGTGGAGCAGATCGAAGACGACAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAA
12546953 GC
131 GC
* ** *
12546955 CACCAAGCCTTGTCTCCCTGAGTAGCAGTAGAGTAGGTTGAAGATTGTAGATCTTATCTCCCTAA
1 CACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGAAGGTTGAAGATTGTAGATCTTATCTCCCTAA
* * * * *
12547020 ACAGTAGTGGGGCAGATCGAAGACGGCAAATATTATCTTTCCAAGATAGTGAGAAGCAGATTTAA
66 GCAGTAGTGGAGCAGATCGAAGACGACAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAA
12547085 GC
131 GC
* *
12547087 CACCAAGCCTTGTCTCCTTGAGCAGTAGCGGAGAAGGTTGAAGATTGTAGATCTTATCTCCCTAA
1 CACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGAAGGTTGAAGATTGTAGATCTTATCTCCCTAA
*
12547152 GCAGTAGTGGAGCAGATCGAAGATGACAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAA
66 GCAGTAGTGGAGCAGATCGAAGACGACAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAA
12547217 GC
131 GC
* * * *
12547219 CACCAAGCCTTGTCTCCCTGAGCAGCAGTGAAGTAGGTTGAAGATTGTAGATCTTATCTTCCTAA
1 CACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGAAGGTTGAAGATTGTAGATCTTATCTCCCTAA
* * *
12547284 GCAGTAGTGGAGCAGATCAAAGACAACAAATCTTATATTTCCAAGATAGTGGGAAGCAGATTTAA
66 GCAGTAGTGGAGCAGATCGAAGACGACAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAA
*
12547349 GT
131 GC
12547351 CA-CAAGCCTTGTCTCCCTGAGCAGCAGCGGAGAAGGTTGAAGATTGTAGATCTTATCTCCCTAA
1 CACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGAAGGTTGAAGATTGTAGATCTTATCTCCCTAA
* *
12547415 GCAGTAGTGGAGCAGATCAAAGACGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAA
66 GCAGTAGTGGAGCAGATCGAAGACGACAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAA
12547480 GC
131 GC
* * * *
12547482 CACCAAGCCTTGTCTCCTTGAGCAGCAGTGGAGAAGGTTGAAGATTGTAGATCTCATCTCTCTAA
1 CACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGAAGGTTGAAGATTGTAGATCTTATCTCCCTAA
* *
12547547 GTAGTAGTGGAGCAGATCGAAGACGACAAATCTTATCTTTCCAAGATAGTGGGAAGTAGATTTAA
66 GCAGTAGTGGAGCAGATCGAAGACGACAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAA
12547612 GC
131 GC
* *
12547614 TACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGTAGGTTGAAGATTGTAGATCTTATCTCCCTAA
1 CACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGAAGGTTGAAGATTGTAGATCTTATCTCCCTAA
* * *
12547679 GAAATAGTGGAGCAGATTGAAGAC-AGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTA
66 GCAGTAGTGGAGCAGATCGAAGACGA-CAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTA
*
12547743 GGC
130 AGC
* *
12547746 CACCAAGCCTTGTCTCCCTGAGTAGCAGCGGAGTAGGTTGAAGATTGTAGATCTTATCTCCCTAA
1 CACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGAAGGTTGAAGATTGTAGATCTTATCTCCCTAA
* * *
12547811 GCAGTAGTGGAGCAGATCGAAGACGGCAAATCATATCTTTCCAAGATAGTGGGAAGCAGATTAAA
66 GCAGTAGTGGAGCAGATCGAAGACGACAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAA
12547876 GC
131 GC
12547878 TGACAATCCT
Statistics
Matches: 976, Mismatches: 76, Indels: 6
0.92 0.07 0.01
Matches are distributed among these distances:
131 124 0.13
132 852 0.87
ACGTcount: A:0.31, C:0.19, G:0.25, T:0.25
Consensus pattern (132 bp):
CACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGAAGGTTGAAGATTGTAGATCTTATCTCCCTAA
GCAGTAGTGGAGCAGATCGAAGACGACAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAA
GC
Found at i:12547174 original size:44 final size:44
Alignment explanation
Indices: 12546703--12547833 Score: 212
Period size: 44 Copynumber: 25.7 Consensus size: 44
12546693 CCAAGCCTTG
* * * * * * *
12546703 TCTCCCTGAGCAGCAGCGGAGAAGGTTGAAGATTGTAGATCTTT
1 TCTCCCTAAGCAGTAGTGGAGCAGATTGAAGATTGCAGATCTTA
* * * *
12546747 TCTCCCTAGGCAGTAGTGGAGCAGATCGAAGA-CGACAAATCTTA
1 TCTCCCTAAGCAGTAGTGGAGCAGATTGAAGATTG-CAGATCTTA
* * **** * *
12546791 TCTTTCC-AAG-A-TAGTGGGAAGCAGATTTAAGCCACCA-AGCCTTG
1 TC-TCCCTAAGCAGTAGT-GG-AGCAGATTGAAGATTGCAGA-TCTTA
* * * * * *
12546835 TCTCCCTGAGCAGCAATGGAGAAGGTTGAAGATTGTAGATCTTA
1 TCTCCCTAAGCAGTAGTGGAGCAGATTGAAGATTGCAGATCTTA
* * ** *
12546879 TCTCCCTAAGTAGTAGTGGAGCAGATCGAA-AACGACAAATCTTA
1 TCTCCCTAAGCAGTAGTGGAGCAGATTGAAGATTG-CAGATCTTA
* * **** * *
12546923 TCTTTCC-AAG-A-TAGTGGGAAGCAGATTTAAGCCACCA-AGCCTTG
1 TC-TCCCTAAGCAGTAGT-GG-AGCAGATTGAAGATTGCAGA-TCTTA
* * * * * * *
12546967 TCTCCCTGAGTAGCAGTAGAGTAGGTTGAAGATTGTAGATCTTA
1 TCTCCCTAAGCAGTAGTGGAGCAGATTGAAGATTGCAGATCTTA
* * * ** * *
12547011 TCTCCCTAAACAGTAGTGGGGCAGATCGAAGACGGCAAATATTA
1 TCTCCCTAAGCAGTAGTGGAGCAGATTGAAGATTGCAGATCTTA
* * **** * *
12547055 TCTTTCC-AAG-A-TAGTGAGAAGCAGATTTAAGCCACCA-AGCCTTG
1 TC-TCCCTAAGCAGTAGTG-G-AGCAGATTGAAGATTGCAGA-TCTTA
* * * * * *
12547099 TCTCCTTGAGCAGTAGCGGAGAAGGTTGAAGATTGTAGATCTTA
1 TCTCCCTAAGCAGTAGTGGAGCAGATTGAAGATTGCAGATCTTA
* *
12547143 TCTCCCTAAGCAGTAGTGGAGCAGATCGAAGA-TGACAAATCTTA
1 TCTCCCTAAGCAGTAGTGGAGCAGATTGAAGATTG-CAGATCTTA
* * **** * *
12547187 TCTTTCC-AAG-A-TAGTGGGAAGCAGATTTAAGCCACCA-AGCCTTG
1 TC-TCCCTAAGCAGTAGT-GG-AGCAGATTGAAGATTGCAGA-TCTTA
* * * * * *
12547231 TCTCCCTGAGCAGCAGTGAAGTAGGTTGAAGATTGTAGATCTTA
1 TCTCCCTAAGCAGTAGTGGAGCAGATTGAAGATTGCAGATCTTA
* ** *** *
12547275 TCTTCCTAAGCAGTAGTGGAGCAGATCAAAGACAACAAATCTTA
1 TCTCCCTAAGCAGTAGTGGAGCAGATTGAAGATTGCAGATCTTA
* * * ** * *
12547319 TATTTCC-AAG-A-TAGTGGGAAGCAGATTTAAG-TCACA-AGCCTTG
1 T-CTCCCTAAGCAGTAGT-GG-AGCAGATTGAAGATTGCAGA-TCTTA
* * * * * *
12547362 TCTCCCTGAGCAGCAGCGGAGAAGGTTGAAGATTGTAGATCTTA
1 TCTCCCTAAGCAGTAGTGGAGCAGATTGAAGATTGCAGATCTTA
** ** *
12547406 TCTCCCTAAGCAGTAGTGGAGCAGATCAAAGACGGCAAATCTTA
1 TCTCCCTAAGCAGTAGTGGAGCAGATTGAAGATTGCAGATCTTA
* * **** * *
12547450 TCTTTCC-AAG-A-TAGTGGGAAGCAGATTTAAGCCACCA-AGCCTTG
1 TC-TCCCTAAGCAGTAGT-GG-AGCAGATTGAAGATTGCAGA-TCTTA
* * * * * * *
12547494 TCTCCTTGAGCAGCAGTGGAGAAGGTTGAAGATTGTAGATCTCA
1 TCTCCCTAAGCAGTAGTGGAGCAGATTGAAGATTGCAGATCTTA
* * * * *
12547538 TCTCTCTAAGTAGTAGTGGAGCAGATCGAAGA-CGACAAATCTTA
1 TCTCCCTAAGCAGTAGTGGAGCAGATTGAAGATTG-CAGATCTTA
* * * * ** * *
12547582 TCTTTCC-AAG-A-TAGTGGGAAGTAGATTTAAGCTACCA-AGCCTTG
1 TC-TCCCTAAGCAGTAGT-GG-AGCAGATTGAAGATTGCAGA-TCTTA
* * * * * *
12547626 TCTCCCTGAGCAGCAGCGGAGTAGGTTGAAGATTGTAGATCTTA
1 TCTCCCTAAGCAGTAGTGGAGCAGATTGAAGATTGCAGATCTTA
* * ** *
12547670 TCTCCCTAAGAAATAGTGGAGCAGATTGAAGACAGCAAATCTTA
1 TCTCCCTAAGCAGTAGTGGAGCAGATTGAAGATTGCAGATCTTA
* * * **** * *
12547714 TCTTTCC-AAG-A-TAGTGGGAAGCAGATTTAGGCCACCA-AGCCTTG
1 TC-TCCCTAAGCAGTAGT-GG-AGCAGATTGAAGATTGCAGA-TCTTA
* * * * * * *
12547758 TCTCCCTGAGTAGCAGCGGAGTAGGTTGAAGATTGTAGATCTTA
1 TCTCCCTAAGCAGTAGTGGAGCAGATTGAAGATTGCAGATCTTA
*
12547802 TCTCCCTAAGCAGTAGTGGAGCAGATCGAAGA
1 TCTCCCTAAGCAGTAGTGGAGCAGATTGAAGA
12547834 CGGCAAATCA
Statistics
Matches: 736, Mismatches: 278, Indels: 146
0.63 0.24 0.13
Matches are distributed among these distances:
42 37 0.05
43 73 0.10
44 555 0.75
45 52 0.07
46 19 0.03
ACGTcount: A:0.31, C:0.19, G:0.25, T:0.25
Consensus pattern (44 bp):
TCTCCCTAAGCAGTAGTGGAGCAGATTGAAGATTGCAGATCTTA
Found at i:12547917 original size:44 final size:44
Alignment explanation
Indices: 12547865--12548166 Score: 162
Period size: 44 Copynumber: 6.9 Consensus size: 44
12547855 GATAGTGGGA
* *
12547865 AGCAGATTAAAGCTGACAATCCTATCTCTCTGAAGTTGCAGTGG
1 AGCAGATTAAAGCTAACAATCTTATCTCTCTGAAGTTGCAGTGG
* * * *
12547909 AGCGGATTAATA--TCACAGATCTTATCTCTCTGAAGTTACAG-AG
1 AGCAGATTAA-AGCTAACA-ATCTTATCTCTCTGAAGTTGCAGTGG
* * * * * *
12547952 AGCAGA-T--CGC-ATCTAGTCTTATCTCCCTAAAGTTACAGTGG
1 AGCAGATTAAAGCTAAC-AATCTTATCTCTCTGAAGTTGCAGTGG
* * *
12547993 AACAGACT-AAG-TAAGCAAGTCTTATC-CTCCTGAAGTTGTAGT-G
1 AGCAGATTAAAGCTAA-CAA-TCTTATCTCT-CTGAAGTTGCAGTGG
* * * *
12548036 AGGCAGACTGAAGATGACAAATCTTATCTC-CATGAAGTTGCAGTGG
1 A-GCAGATTAAAGCTAAC-AATCTTATCTCTC-TGAAGTTGCAGTGG
* * * *
12548082 AGCAGATTAAAGCCAATAATCCTATCTCCCTGAAGTTGCAGTGG
1 AGCAGATTAAAGCTAACAATCTTATCTCTCTGAAGTTGCAGTGG
* * *** *
12548126 AGCGGATTAGAA-CCATGGATCTTATCTCTTTGAAGTTGCAG
1 AGCAGATTA-AAGCTAACAATCTTATCTCTCTGAAGTTGCAG
12548167 CAAAGCAGAT
Statistics
Matches: 199, Mismatches: 38, Indels: 42
0.71 0.14 0.15
Matches are distributed among these distances:
40 21 0.11
41 7 0.04
42 2 0.01
43 16 0.08
44 110 0.55
45 36 0.18
46 7 0.04
ACGTcount: A:0.30, C:0.20, G:0.22, T:0.28
Consensus pattern (44 bp):
AGCAGATTAAAGCTAACAATCTTATCTCTCTGAAGTTGCAGTGG
Found at i:12548480 original size:19 final size:19
Alignment explanation
Indices: 12548452--12548547 Score: 129
Period size: 21 Copynumber: 4.8 Consensus size: 19
12548442 AATCTTCGAG
* *
12548452 GATATCCAATCCTAGATAT
1 GATATGCAATCTTAGATAT
12548471 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
12548490 GATATATGCAATCTTAGATAT
1 G--ATATGCAATCTTAGATAT
12548511 GATATATGCAATCTTAGATAT
1 G--ATATGCAATCTTAGATAT
*
12548532 GATATGTAATCTTAGA
1 GATATGCAATCTTAGA
12548548 AGATATGATT
Statistics
Matches: 72, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
19 32 0.44
21 40 0.56
ACGTcount: A:0.38, C:0.11, G:0.15, T:0.36
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:12548498 original size:21 final size:21
Alignment explanation
Indices: 12548453--12548536 Score: 136
Period size: 21 Copynumber: 4.1 Consensus size: 21
12548443 ATCTTCGAGG
* *
12548453 ATATCCAATCCTAGATATG--
1 ATATGCAATCTTAGATATGAT
12548472 ATATGCAATCTTAGATATGAT
1 ATATGCAATCTTAGATATGAT
12548493 ATATGCAATCTTAGATATGAT
1 ATATGCAATCTTAGATATGAT
12548514 ATATGCAATCTTAGATATGAT
1 ATATGCAATCTTAGATATGAT
12548535 AT
1 AT
12548537 GTAATCTTAG
Statistics
Matches: 61, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
19 17 0.28
21 44 0.72
ACGTcount: A:0.38, C:0.12, G:0.13, T:0.37
Consensus pattern (21 bp):
ATATGCAATCTTAGATATGAT
Found at i:12548537 original size:40 final size:38
Alignment explanation
Indices: 12548452--12548554 Score: 129
Period size: 40 Copynumber: 2.7 Consensus size: 38
12548442 AATCTTCGAG
* *
12548452 GATATCCAATCCTAGATATGATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATATGATATGCAATCTTAGATAT
12548490 GATATATGCAATCTTAGATATGATATATGCAATCTTAGATAT
1 G--ATATGCAATCTTAGATATG--ATATGCAATCTTAGATAT
*
12548532 GATATGTAATCTTAGA-A-GATATG
1 GATATGCAATCTTAGATATGATATG
12548555 ATTTTGTAAT
Statistics
Matches: 58, Mismatches: 3, Indels: 10
0.82 0.04 0.14
Matches are distributed among these distances:
36 5 0.09
38 2 0.03
39 1 0.02
40 31 0.53
42 19 0.33
ACGTcount: A:0.38, C:0.11, G:0.16, T:0.36
Consensus pattern (38 bp):
GATATGCAATCTTAGATATGATATGCAATCTTAGATAT
Found at i:12548566 original size:23 final size:22
Alignment explanation
Indices: 12548465--12548570 Score: 82
Period size: 21 Copynumber: 5.0 Consensus size: 22
12548455 ATCCAATCCT
*
12548465 AGATATGATATGCAATCTTAG-
1 AGATATGATATGTAATCTTAGA
* *
12548486 ATATGAT-ATATGCAATCTTAG-
1 AGAT-ATGATATGTAATCTTAGA
* *
12548507 ATATGAT-ATATGCAATCTT---
1 AGAT-ATGATATGTAATCTTAGA
12548526 AGATATGATATGTAATCTTAGA
1 AGATATGATATGTAATCTTAGA
*
12548548 AGATATGATTTTGTAATCTTAGA
1 AGATATGA-TATGTAATCTTAGA
12548571 GATTTAATTT
Statistics
Matches: 75, Mismatches: 4, Indels: 10
0.84 0.04 0.11
Matches are distributed among these distances:
18 2 0.03
19 14 0.19
21 36 0.48
22 10 0.13
23 13 0.17
ACGTcount: A:0.38, C:0.08, G:0.16, T:0.39
Consensus pattern (22 bp):
AGATATGATATGTAATCTTAGA
Found at i:12548566 original size:42 final size:40
Alignment explanation
Indices: 12548453--12548570 Score: 132
Period size: 42 Copynumber: 2.9 Consensus size: 40
12548443 ATCTTCGAGG
* *
12548453 ATATCCAATCCTAGATATGA-TATGCAATCTTAGATATGA
1 ATATGCAATCTTAGATATGATTATGCAATCTTAGATATGA
12548492 TATATGCAATCTTAGATATGATATATGCAATCTTAGATATG-
1 -ATATGCAATCTTAGATATGAT-TATGCAATCTTAGATATGA
* * *
12548533 ATATGTAATCTTAGAAGATATGATTTTGTAATCTTAGA
1 ATATGCAATCTT---AGATATGATTATGCAATCTTAGA
12548571 GATTTAATTT
Statistics
Matches: 68, Mismatches: 5, Indels: 8
0.84 0.06 0.10
Matches are distributed among these distances:
40 29 0.43
42 30 0.44
43 9 0.13
ACGTcount: A:0.37, C:0.10, G:0.14, T:0.38
Consensus pattern (40 bp):
ATATGCAATCTTAGATATGATTATGCAATCTTAGATATGA
Found at i:12548580 original size:22 final size:23
Alignment explanation
Indices: 12548536--12548580 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
12548526 AGATATGATA
*
12548536 TGTAATCTTAGAAGATATGATTT
1 TGTAATCTTAGAAGATATAATTT
*
12548559 TGTAATCTTAG-AGATTTAATTT
1 TGTAATCTTAGAAGATATAATTT
12548581 GTAGATACCC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 9 0.45
23 11 0.55
ACGTcount: A:0.33, C:0.04, G:0.16, T:0.47
Consensus pattern (23 bp):
TGTAATCTTAGAAGATATAATTT
Found at i:12549029 original size:15 final size:14
Alignment explanation
Indices: 12549005--12549035 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
12548995 TTAATTTTGT
12549005 TATTATTATTATTA
1 TATTATTATTATTA
12549019 TATTATATATTATTA
1 TATTAT-TATTATTA
12549034 TA
1 TA
12549036 CCTACATATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.38
15 10 0.62
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (14 bp):
TATTATTATTATTA
Found at i:12549406 original size:51 final size:52
Alignment explanation
Indices: 12549296--12549407 Score: 131
Period size: 51 Copynumber: 2.2 Consensus size: 52
12549286 TTCCACGTTT
**
12549296 TATAT-TATACTTATATATTTCATTTTTTTGTAAATGCATGGATATATTTTA
1 TATATATATACTTATATATTTCATTTTTTCATAAATGCATGGATATATTTTA
* * * * *
12549347 TATGTATATATTTATAT-TTTCCTTGTTTTCATAAATGCAT-TATGTATTTTA
1 TATATATATACTTATATATTTCATT-TTTTCATAAATGCATGGATATATTTTA
12549398 TATATATATA
1 TATATATATA
12549408 AGTTTTATAA
Statistics
Matches: 51, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
51 28 0.55
52 23 0.45
ACGTcount: A:0.31, C:0.06, G:0.07, T:0.55
Consensus pattern (52 bp):
TATATATATACTTATATATTTCATTTTTTCATAAATGCATGGATATATTTTA
Found at i:12549572 original size:24 final size:24
Alignment explanation
Indices: 12549523--12549572 Score: 57
Period size: 24 Copynumber: 2.1 Consensus size: 24
12549513 GTTTATTTCC
* *
12549523 TTCATTTACTTATTGATTTATGTT
1 TTCATTTACTAATTGATTTATATT
*
12549547 TTCATTTA-TAATTTATTTGATATT
1 TTCATTTACTAATTGATTT-ATATT
12549571 TT
1 TT
12549573 ACATGTTGTT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
23 8 0.36
24 14 0.64
ACGTcount: A:0.24, C:0.06, G:0.06, T:0.64
Consensus pattern (24 bp):
TTCATTTACTAATTGATTTATATT
Found at i:12561454 original size:19 final size:19
Alignment explanation
Indices: 12561430--12561470 Score: 73
Period size: 19 Copynumber: 2.2 Consensus size: 19
12561420 ACCATTAGAA
*
12561430 GGTGTGCTAACTTGATACT
1 GGTGTGCTAACTCGATACT
12561449 GGTGTGCTAACTCGATACT
1 GGTGTGCTAACTCGATACT
12561468 GGT
1 GGT
12561471 CATTGTGTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.20, C:0.17, G:0.29, T:0.34
Consensus pattern (19 bp):
GGTGTGCTAACTCGATACT
Found at i:12562433 original size:23 final size:22
Alignment explanation
Indices: 12562407--12562458 Score: 52
Period size: 23 Copynumber: 2.3 Consensus size: 22
12562397 AATTTACTAA
12562407 ATTTTTCTATTTGAT-TTCCCATT
1 ATTTTT-TATTT-ATGTTCCCATT
* *
12562430 ATTTATTTATTTATGTTCTCTTT
1 ATTT-TTTATTTATGTTCCCATT
12562453 ATTTTT
1 ATTTTT
12562459 ATTAATAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
22 4 0.16
23 19 0.76
24 2 0.08
ACGTcount: A:0.17, C:0.12, G:0.04, T:0.67
Consensus pattern (22 bp):
ATTTTTTATTTATGTTCCCATT
Found at i:12562725 original size:21 final size:21
Alignment explanation
Indices: 12562699--12562741 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
12562689 TACATTTGGA
*
12562699 GGCGGTCAAGTTATTAGTGCC
1 GGCGGTCAAGTTATTAGCGCC
* *
12562720 GGCGGTCAGGTTGTTAGCGCC
1 GGCGGTCAAGTTATTAGCGCC
12562741 G
1 G
12562742 TTTTCGGGGA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.14, C:0.21, G:0.40, T:0.26
Consensus pattern (21 bp):
GGCGGTCAAGTTATTAGCGCC
Found at i:12567611 original size:69 final size:69
Alignment explanation
Indices: 12567523--12567673 Score: 198
Period size: 69 Copynumber: 2.2 Consensus size: 69
12567513 GTTTAAGATA
* * * *
12567523 TAAGACAATAGCTATGCTATGACAGCCAATAGCA-TCTACCAGGATAGTAAACAC-GAGGATTAT
1 TAAGACCATAGCTAGGCTATGACAACCAAT-GCAGTCTACCAGGATAGTAAACACGGA-GAATAT
12567586 AAAGTG
64 AAAGTG
* * *
12567592 TAAGACCATAGCTAGGCTATGACAACCAATGGAGTTTGCCAGGATAGTAAACACGGAGAATATAA
1 TAAGACCATAGCTAGGCTATGACAACCAATGCAGTCTACCAGGATAGTAAACACGGAGAATATAA
*
12567657 GGTG
66 AGTG
12567661 TAAGACCATAGCT
1 TAAGACCATAGCT
12567674 CAATTATGGC
Statistics
Matches: 72, Mismatches: 8, Indels: 4
0.86 0.10 0.05
Matches are distributed among these distances:
68 2 0.03
69 68 0.94
70 2 0.03
ACGTcount: A:0.39, C:0.17, G:0.23, T:0.21
Consensus pattern (69 bp):
TAAGACCATAGCTAGGCTATGACAACCAATGCAGTCTACCAGGATAGTAAACACGGAGAATATAA
AGTG
Found at i:12567687 original size:69 final size:69
Alignment explanation
Indices: 12567539--12567837 Score: 284
Period size: 69 Copynumber: 4.3 Consensus size: 69
12567529 AATAGCTATG
* * * * *
12567539 CTATGACAGCCAATAGCA-TCTACCAGGATAGTAAACACGAGGATTATAAAGTGTAAGACCATAG
1 CTATGACAACCAAT-GGAGTCTGCCAGGATAGTAAACATGAGGATTATAAGGTGTAAGACCATAG
*
12567603 CT-AGG
65 CTCA-A
* * *
12567608 CTATGACAACCAATGGAGTTTGCCAGGATAGTAAACACG-GAGAATATAAGGTGTAAGACCATAG
1 CTATGACAACCAATGGAGTCTGCCAGGATAGTAAACATGAG-GATTATAAGGTGTAAGACCATAG
12567672 CTCAA
65 CTCAA
* * * * * * * *
12567677 TTATGGCAACCAATGGAGCCCGTCGGGACAGTAAACATTAGGATTATAAGGTGTAAGACCATAGC
1 CTATGACAACCAATGGAGTCTGCCAGGATAGTAAACATGAGGATTATAAGGTGTAAGACCATAGC
*
12567742 TCGA
66 TCAA
* * ** **
12567746 CTATGGA-AACTAACGGAGTCTGTTAGGATAGTAAACATGAGGATTATAAGGCATAAGACCATAG
1 CTAT-GACAACCAATGGAGTCTGCCAGGATAGTAAACATGAGGATTATAAGGTGTAAGACCATAG
12567810 CTCGAA
65 CTC-AA
* *
12567816 -TATGACAACCAATAGATTCTGC
1 CTATGACAACCAATGGAGTCTGC
12567838 AATGACAATA
Statistics
Matches: 186, Mismatches: 37, Indels: 14
0.78 0.16 0.06
Matches are distributed among these distances:
68 5 0.03
69 177 0.95
70 4 0.02
ACGTcount: A:0.37, C:0.18, G:0.23, T:0.22
Consensus pattern (69 bp):
CTATGACAACCAATGGAGTCTGCCAGGATAGTAAACATGAGGATTATAAGGTGTAAGACCATAGC
TCAA
Found at i:12567774 original size:138 final size:138
Alignment explanation
Indices: 12567568--12567828 Score: 339
Period size: 138 Copynumber: 1.9 Consensus size: 138
12567558 CTACCAGGAT
* * *
12567568 AGTAAACACGAGGATTATAAAGTGTAAGACCATAGCTAGGCTATGACAACCAATGGAGTTTGCCA
1 AGTAAACACGAGGATTATAAAGTGTAAGACCATAGCTAGACTATGACAACCAACGGAGTCTGCCA
** *
12567633 GGATAGTAAACACGGA-GAATATAAGGTGTAAGACCATAGCTC-AATTATGGCAACCAATGGAGC
66 GGATAGTAAACA-GGAGGAATATAAGGCATAAGACCATAGCTCGAA-TATGACAACCAATGGAGC
12567696 CCGTCGGGAC
129 CCGTCGGGAC
** * * * **
12567706 AGTAAACATTAGGATTATAAGGTGTAAGACCATAGCTCGACTATGGA-AACTAACGGAGTCTGTT
1 AGTAAACACGAGGATTATAAAGTGTAAGACCATAGCTAGACTAT-GACAACCAACGGAGTCTGCC
* *
12567770 AGGATAGTAAACATGAGGATTATAAGGCATAAGACCATAGCTCGAATATGACAACCAAT
65 AGGATAGTAAACAGGAGGAATATAAGGCATAAGACCATAGCTCGAATATGACAACCAAT
12567829 AGATTCTGCA
Statistics
Matches: 105, Mismatches: 15, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
137 2 0.02
138 99 0.94
139 4 0.04
ACGTcount: A:0.38, C:0.16, G:0.24, T:0.21
Consensus pattern (138 bp):
AGTAAACACGAGGATTATAAAGTGTAAGACCATAGCTAGACTATGACAACCAACGGAGTCTGCCA
GGATAGTAAACAGGAGGAATATAAGGCATAAGACCATAGCTCGAATATGACAACCAATGGAGCCC
GTCGGGAC
Found at i:12583381 original size:100 final size:102
Alignment explanation
Indices: 12583260--12583442 Score: 246
Period size: 100 Copynumber: 1.8 Consensus size: 102
12583250 AAAGTGATGG
* * *
12583260 TCACGTGTGTAGTACGATGTGCAGGCTACTACGTGTACCAGA-A-TGATAGGTCGCAT-TGTAGT
1 TCACGTATGTAGTACGATGTGCAGGCTACTACATGTACCAGATAGTGAT-GGTCACATGTGTAGT
*
12583322 ACTATGTGTAAGCTACTATACATACCAGATAGCTTCGA
65 ACTATGTGCAAGCTACTATACATACCAGATAGCTTCGA
* * * *
12583360 TCACGTATGTCGTACTATGTGCAGGCTACTACATGTATCGGATAGTGATGGTCACATGTGTAGTA
1 TCACGTATGTAGTACGATGTGCAGGCTACTACATGTACCAGATAGTGATGGTCACATGTGTAGTA
* *
12583425 CTATTTGCAGGCTACTAT
66 CTATGTGCAAGCTACTAT
12583443 GTGAACCGGT
Statistics
Matches: 70, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
100 36 0.51
101 8 0.11
102 26 0.37
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.31
Consensus pattern (102 bp):
TCACGTATGTAGTACGATGTGCAGGCTACTACATGTACCAGATAGTGATGGTCACATGTGTAGTA
CTATGTGCAAGCTACTATACATACCAGATAGCTTCGA
Found at i:12583426 original size:51 final size:52
Alignment explanation
Indices: 12583252--12583441 Score: 169
Period size: 51 Copynumber: 3.8 Consensus size: 52
12583242 TGAAAGTGAA
* * *
12583252 AGTGAT-GGTCACGTGTGTAGTACGATGTGCAGGCTACTACGTGTACCAGA-
1 AGTGATAGGTCACATGTGTAGTACTATGTGCAGGCTACTACATGTACCAGAT
* * * * **
12583302 A-TGATAGGTCGCAT-TGTAGTACTATGTGTAAGCTACTATACATACCAGAT
1 AGTGATAGGTCACATGTGTAGTACTATGTGCAGGCTACTACATGTACCAGAT
* * * * * * *
12583352 AGCT--TCGATCACGTATGTCGTACTATGTGCAGGCTACTACATGTATCGGAT
1 AG-TGATAGGTCACATGTGTAGTACTATGTGCAGGCTACTACATGTACCAGAT
*
12583403 AGTGAT-GGTCACATGTGTAGTACTATTTGCAGGCTACTA
1 AGTGATAGGTCACATGTGTAGTACTATGTGCAGGCTACTA
12583442 TGTGAACCGG
Statistics
Matches: 107, Mismatches: 26, Indels: 13
0.73 0.18 0.09
Matches are distributed among these distances:
49 32 0.30
50 15 0.14
51 58 0.54
52 2 0.02
ACGTcount: A:0.26, C:0.18, G:0.25, T:0.31
Consensus pattern (52 bp):
AGTGATAGGTCACATGTGTAGTACTATGTGCAGGCTACTACATGTACCAGAT
Found at i:12583690 original size:16 final size:16
Alignment explanation
Indices: 12583669--12583700 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
12583659 TAATTGAAAG
*
12583669 TGAAAAAGTGAAATTA
1 TGAAAAAGTAAAATTA
12583685 TGAAAAAGTAAAATTA
1 TGAAAAAGTAAAATTA
12583701 GCAACAAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.59, C:0.00, G:0.16, T:0.25
Consensus pattern (16 bp):
TGAAAAAGTAAAATTA
Found at i:12600703 original size:25 final size:25
Alignment explanation
Indices: 12600653--12600703 Score: 59
Period size: 25 Copynumber: 2.0 Consensus size: 25
12600643 CATCTAATCC
* *
12600653 AAATAATTAATACAAATATAATTTA
1 AAATAATTAATACAAATAAAAATTA
*
12600678 AAATGAATTAATA-GAATAAAAATTA
1 AAAT-AATTAATACAAATAAAAATTA
12600703 A
1 A
12600704 GTAAATGAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
25 14 0.64
26 8 0.36
ACGTcount: A:0.63, C:0.02, G:0.04, T:0.31
Consensus pattern (25 bp):
AAATAATTAATACAAATAAAAATTA
Found at i:12600981 original size:2 final size:2
Alignment explanation
Indices: 12600974--12601001 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
12600964 AAACCAGTAA
12600974 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
12601002 GAATGCTACT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:12605467 original size:91 final size:91
Alignment explanation
Indices: 12605357--12605566 Score: 278
Period size: 91 Copynumber: 2.3 Consensus size: 91
12605347 CAAGTAATAT
* * * * **
12605357 AATAATACACAGATTGATAGTTTAAGTACCACATTGA-ATATTTTTAAATTATAAGTATTACATT
1 AATAATACACAAATTGATAGTTTAAGTACCAC-TTGAGACATTTTTAAAGTACAAGTACCACATT
* *
12605421 AGACATTTTATGAAAGTACAGGTACCG
65 AGACATTTTATGAAAGTACAAGTACCA
* * * *
12605448 AATAATACTCAAATTGATAGTTTAGGTATCACTTTAGACATTTTTAAAGTACAAGTACCACATTA
1 AATAATACACAAATTGATAGTTTAAGTACCACTTGAGACATTTTTAAAGTACAAGTACCACATTA
12605513 GACATTTTATGAAAGTACAAGTACCA
66 GACATTTTATGAAAGTACAAGTACCA
*
12605539 AATAATACACAAATTGATTAGTTCAAGT
1 AATAATACACAAATTGA-TAGTTTAAGT
12605567 TAGAGGTGTT
Statistics
Matches: 102, Mismatches: 15, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
90 3 0.03
91 91 0.89
92 8 0.08
ACGTcount: A:0.41, C:0.12, G:0.12, T:0.34
Consensus pattern (91 bp):
AATAATACACAAATTGATAGTTTAAGTACCACTTGAGACATTTTTAAAGTACAAGTACCACATTA
GACATTTTATGAAAGTACAAGTACCA
Found at i:12605531 original size:31 final size:29
Alignment explanation
Indices: 12605481--12605538 Score: 98
Period size: 31 Copynumber: 1.9 Consensus size: 29
12605471 AGGTATCACT
12605481 TTAGACATTTTTAAAGTACAAGTACCACA
1 TTAGACATTTTTAAAGTACAAGTACCACA
12605510 TTAGACATTTTATGAAAGTACAAGTACCA
1 TTAGACATTTT-T-AAAGTACAAGTACCA
12605539 AATAATACAC
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
29 11 0.41
30 1 0.04
31 15 0.56
ACGTcount: A:0.41, C:0.16, G:0.12, T:0.31
Consensus pattern (29 bp):
TTAGACATTTTTAAAGTACAAGTACCACA
Found at i:12605797 original size:12 final size:14
Alignment explanation
Indices: 12605780--12605824 Score: 53
Period size: 14 Copynumber: 3.5 Consensus size: 14
12605770 ATATATTTTT
12605780 TATTTTTAAAA-A-
1 TATTTTTAAAATAC
12605792 TA-TTTTAAAATAC
1 TATTTTTAAAATAC
*
12605805 TTTTTTTAAAATAC
1 TATTTTTAAAATAC
12605819 T-TTTTT
1 TATTTTT
12605825 TTATTTCTAA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
11 8 0.28
12 3 0.10
13 6 0.21
14 12 0.41
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.58
Consensus pattern (14 bp):
TATTTTTAAAATAC
Found at i:12605827 original size:15 final size:14
Alignment explanation
Indices: 12605794--12605825 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
12605784 TTTAAAAATA
12605794 TTTTAAAATACTTT
1 TTTTAAAATACTTT
12605808 TTTTAAAATACTTT
1 TTTTAAAATACTTT
12605822 TTTT
1 TTTT
12605826 TATTTCTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.31, C:0.06, G:0.00, T:0.62
Consensus pattern (14 bp):
TTTTAAAATACTTT
Found at i:12605856 original size:33 final size:32
Alignment explanation
Indices: 12605807--12605875 Score: 113
Period size: 32 Copynumber: 2.2 Consensus size: 32
12605797 TAAAATACTT
*
12605807 TTTTTAAAATACTTTTTTTTA-TTTCTAAAATA
1 TTTTTAAAATACTTTTTTTAATTTTCTAAAA-A
12605839 TTTTTAAAATACTTTTTTTAATTTTCTAAAAA
1 TTTTTAAAATACTTTTTTTAATTTTCTAAAAA
12605871 TTTTT
1 TTTTT
12605876 TTGGTGTTTA
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
32 26 0.74
33 9 0.26
ACGTcount: A:0.33, C:0.06, G:0.00, T:0.61
Consensus pattern (32 bp):
TTTTTAAAATACTTTTTTTAATTTTCTAAAAA
Found at i:12605862 original size:21 final size:20
Alignment explanation
Indices: 12605838--12605877 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 20
12605828 TTTCTAAAAT
12605838 ATTTT-TAAAATACTTTTTTTA
1 ATTTTCTAAAA-A-TTTTTTTA
12605859 ATTTTCTAAAAATTTTTTT
1 ATTTTCTAAAAATTTTTTT
12605878 GGTGTTTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 7 0.39
21 6 0.33
22 5 0.28
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.62
Consensus pattern (20 bp):
ATTTTCTAAAAATTTTTTTA
Found at i:12606984 original size:3 final size:3
Alignment explanation
Indices: 12606976--12607024 Score: 98
Period size: 3 Copynumber: 16.3 Consensus size: 3
12606966 AAATCGTGAT
12606976 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
12607024 T
1 T
12607025 GCTTAAGGTG
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:12607400 original size:21 final size:21
Alignment explanation
Indices: 12607374--12607429 Score: 69
Period size: 21 Copynumber: 2.6 Consensus size: 21
12607364 ATAAAAATAT
* *
12607374 TAAAAATTAG-AATTTTTTTTG
1 TAAAAATT-GTAAATTTTTTTA
12607395 TAAAAATTGTAAATTTTTTTA
1 TAAAAATTGTAAATTTTTTTA
12607416 TAAAATATTGTAAA
1 TAAAA-ATTGTAAA
12607430 ATTTAATAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
20 1 0.03
21 22 0.71
22 8 0.26
ACGTcount: A:0.45, C:0.00, G:0.07, T:0.48
Consensus pattern (21 bp):
TAAAAATTGTAAATTTTTTTA
Found at i:12607409 original size:22 final size:22
Alignment explanation
Indices: 12607387--12607429 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 22
12607377 AAATTAGAAT
*
12607387 TTTTTTTGTAAAA-ATTGTAAA
1 TTTTTTTATAAAATATTGTAAA
12607408 TTTTTTTATAAAATATTGTAAA
1 TTTTTTTATAAAATATTGTAAA
12607430 ATTTAATAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 12 0.60
22 8 0.40
ACGTcount: A:0.40, C:0.00, G:0.07, T:0.53
Consensus pattern (22 bp):
TTTTTTTATAAAATATTGTAAA
Found at i:12607720 original size:28 final size:27
Alignment explanation
Indices: 12607663--12607729 Score: 68
Period size: 27 Copynumber: 2.5 Consensus size: 27
12607653 TTTATAATTT
* **
12607663 TTTTTACA-AATTTTATATTTCTTTTCA
1 TTTTTA-ATAATTTTATATTACTTTAAA
12607690 TTTTTAATAATTTTATTATTACTTTAAA
1 TTTTTAATAATTTTA-TATTACTTTAAA
12607718 -TTTT-ATAATTTT
1 TTTTTAATAATTTT
12607730 TCCATATTTC
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
26 9 0.26
27 17 0.49
28 9 0.26
ACGTcount: A:0.30, C:0.06, G:0.00, T:0.64
Consensus pattern (27 bp):
TTTTTAATAATTTTATATTACTTTAAA
Found at i:12607808 original size:22 final size:22
Alignment explanation
Indices: 12607781--12607842 Score: 74
Period size: 22 Copynumber: 2.9 Consensus size: 22
12607771 TTAGAAAAAA
12607781 TTACAATTTTTTATAAATTTTT
1 TTACAATTTTTTATAAATTTTT
12607803 TTACAA-TTTTTAT-AATTTTT
1 TTACAATTTTTTATAAATTTTT
* * *
12607823 TTTCTAGTTTTTAATAAATT
1 TTAC-AATTTTTTATAAATT
12607843 CTAAATCTAT
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
20 10 0.29
21 8 0.24
22 12 0.35
23 4 0.12
ACGTcount: A:0.31, C:0.05, G:0.02, T:0.63
Consensus pattern (22 bp):
TTACAATTTTTTATAAATTTTT
Found at i:12607812 original size:21 final size:21
Alignment explanation
Indices: 12607781--12607842 Score: 72
Period size: 21 Copynumber: 2.9 Consensus size: 21
12607771 TTAGAAAAAA
12607781 TTACAATTTTTTATAAATTTTT
1 TTACAA-TTTTTATAAATTTTT
12607803 TTACAATTTTTAT-AATTTTT
1 TTACAATTTTTATAAATTTTT
* *
12607823 TTTCTAGTTTTTAATAAATT
1 TTAC-AATTTTT-ATAAATT
12607843 CTAAATCTAT
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
20 10 0.29
21 13 0.37
22 8 0.23
23 4 0.11
ACGTcount: A:0.31, C:0.05, G:0.02, T:0.63
Consensus pattern (21 bp):
TTACAATTTTTATAAATTTTT
Found at i:12612165 original size:31 final size:31
Alignment explanation
Indices: 12612121--12612257 Score: 111
Period size: 31 Copynumber: 4.5 Consensus size: 31
12612111 GAACATTTTC
*
12612121 AAAGTATAAGTACCACATTAGACATTTTATG
1 AAAGTACAAGTACCACATTAGACATTTTATG
* * * * **
12612152 AAAGTACATGTACCAAATAATACA-TAAATTG
1 AAAGTACAAGTACCACATTAGACATTTTA-TG
* * * *
12612183 ATAGTTCAAGTATCACATTAGACATTTT-TT
1 AAAGTACAAGTACCACATTAGACATTTTATG
* *
12612213 AAA-TACAAATACCACATCA-AGCATTTTATG
1 AAAGTACAAGTACCACATTAGA-CATTTTATG
12612243 AAAGTACAAGTACCA
1 AAAGTACAAGTACCA
12612258 AATAAAACAC
Statistics
Matches: 77, Mismatches: 24, Indels: 10
0.69 0.22 0.09
Matches are distributed among these distances:
28 1 0.01
29 18 0.23
30 9 0.12
31 48 0.62
32 1 0.01
ACGTcount: A:0.45, C:0.15, G:0.10, T:0.30
Consensus pattern (31 bp):
AAAGTACAAGTACCACATTAGACATTTTATG
Found at i:12612174 original size:91 final size:91
Alignment explanation
Indices: 12612069--12612300 Score: 254
Period size: 91 Copynumber: 2.5 Consensus size: 91
12612059 TTAACTTTAG
* * * * *
12612069 GTACCATAATAATACACAAATTGATAGTTTAGGCACCCCATT-GAACA-TTTTCAAAGTATAAGT
1 GTACCA-AATAATACACAAATTGATAGTTCAAGCACCACATTAG-ACATTTTTCAAA-TACAAAT
* *
12612132 ACCACAT-TAGACATTTTATGAAAGTACAT
63 ACCACATCAAG-CATTTTATGAAAGTACAA
* * * *
12612161 GTACCAAATAATACATAAATTGATAGTTCAAGTATCACATTAGACATTTTTTAAATACAAATACC
1 GTACCAAATAATACACAAATTGATAGTTCAAGCACCACATTAGACATTTTTCAAATACAAATACC
12612226 ACATCAAGCATTTTATGAAAGTACAA
66 ACATCAAGCATTTTATGAAAGTACAA
* ** * * *
12612252 GTACCAAATAAAACACAAATAAATAGTTCAAGTATCACATTAGATATTT
1 GTACCAAATAATACACAAATTGATAGTTCAAGCACCACATTAGACATTT
12612301 CAATATTTTA
Statistics
Matches: 121, Mismatches: 16, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
91 105 0.87
92 16 0.13
ACGTcount: A:0.44, C:0.16, G:0.10, T:0.30
Consensus pattern (91 bp):
GTACCAAATAATACACAAATTGATAGTTCAAGCACCACATTAGACATTTTTCAAATACAAATACC
ACATCAAGCATTTTATGAAAGTACAA
Found at i:12613458 original size:18 final size:17
Alignment explanation
Indices: 12613437--12613482 Score: 60
Period size: 17 Copynumber: 2.7 Consensus size: 17
12613427 AGTAGAATCA
12613437 TATTATTTGTTCCAACGT
1 TATTATTT-TTCCAACGT
12613455 TATTA-TTTTCTCAACGT
1 TATTATTTTTC-CAACGT
12613472 TA-TATTTTTCC
1 TATTATTTTTCC
12613483 TATTTTTGGC
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
16 6 0.23
17 15 0.58
18 5 0.19
ACGTcount: A:0.22, C:0.17, G:0.07, T:0.54
Consensus pattern (17 bp):
TATTATTTTTCCAACGT
Found at i:12613846 original size:358 final size:357
Alignment explanation
Indices: 12613365--12614012 Score: 818
Period size: 358 Copynumber: 1.8 Consensus size: 357
12613355 TTTTTTTTAA
*
12613365 TTTTTTACTATTTTAGTCAAACAAACTTCCTGAATTTTCTCAGGTTTCTAACGTTATTAACCAGT
1 TTTTTTACTATTTTAGTCAAACAAACTTCCTGAATTTTCTCAGGTTTCTAACGTTATTAACCAGC
* * * *
12613430 AGAATCATATTATTTGTTCCAACGTTATTATTTTCTCAACGTTATATTTTTCCTATTTTTGGCAT
66 AGAATCAAATTATTTATTCCAACGTTATTAGTTTCTCAACGTTATACTTTTCCTATTTTTGGCAT
** * * * * * * *
12613495 GCATTGTACCTGTAAATACTATGCATGACTGTACTTCAGAATCACTCAACTTGTAAATTATTCAT
131 GCACGGTACATATAAAAACCATGCATGACTGCACTTCAGAATCACTCAACCTATAAATTATTCAT
* ** * *
12613560 CTTCACTCTCAAAGCTTTCTACCTTCTCAAATCTTTC-TCCCTCAATTCCAGTTGAGTATTTTAT
196 CTTCACTCCCAAAGCTTTCTACCTTCTCAAAGATTTCTTCCC-CAATTCCAGCTGAGTATTTAAT
* *
12613624 T-GCTTTGTTCTTCCTTGTTTCTTGTTTTCCTTCAGTTAATAAATCTGCTTGTTGAATCCTTGAG
260 TAG-TTTGTTCTTCCTT-TTCCATGTTTTCCTTCAGTTAATAAATCTGCTTGTTGAATCCTTGAG
12613688 GATAAGCGGATTTGTTTTTTTTTTTCTGTATTATT
323 GATAAGCGGATTTGTTTTTTTTTTTCTGTATTATT
* ** * * * *
12613723 TTTTTTCCTATTTTAGTCAAACAAGGTTCCTTAATTTTCTTAGATTTTCTAACGTTATTAACTAG
1 TTTTTTACTATTTTAGTCAAACAAACTTCCTGAATTTTCTCAG-GTTTCTAACGTTATTAACCAG
* **
12613788 CAGAATCAAATT-TTCTATTCCAACGTTATT-GTTTCTTATTGTTATACTTTTCCTATTTTTGGC
65 CAGAATCAAATTATT-TATTCCAACGTTATTAGTTTCTCAACGTTATACTTTTCCTATTTTTGGC
* * * * * * *
12613851 ATGGACGGTATATATAAAAACCATGCATGATTGCATTTCAGAATTACTCAACCTATGAATTGTTC
129 ATGCACGGTACATATAAAAACCATGCATGACTGCACTTCAGAATCACTCAACCTATAAATTATTC
* * * * ***
12613916 ATCTTCTCTCCCAACGCTTTTTGCCTTCTCAAAGATTTCTTCCCCAATTTTGGCTGAGTATTTAA
194 ATCTTCACTCCCAAAGCTTTCTACCTTCTCAAAGATTTCTTCCCCAATTCCAGCTGAGTATTTAA
12613981 TTAGTTTGTTCTTCCTTTTCCATGTTTTCCTT
259 TTAGTTTGTTCTTCCTTTTCCATGTTTTCCTT
12614013 AAATTAACAA
Statistics
Matches: 241, Mismatches: 45, Indels: 9
0.82 0.15 0.03
Matches are distributed among these distances:
357 13 0.05
358 180 0.75
359 48 0.20
ACGTcount: A:0.24, C:0.19, G:0.11, T:0.46
Consensus pattern (357 bp):
TTTTTTACTATTTTAGTCAAACAAACTTCCTGAATTTTCTCAGGTTTCTAACGTTATTAACCAGC
AGAATCAAATTATTTATTCCAACGTTATTAGTTTCTCAACGTTATACTTTTCCTATTTTTGGCAT
GCACGGTACATATAAAAACCATGCATGACTGCACTTCAGAATCACTCAACCTATAAATTATTCAT
CTTCACTCCCAAAGCTTTCTACCTTCTCAAAGATTTCTTCCCCAATTCCAGCTGAGTATTTAATT
AGTTTGTTCTTCCTTTTCCATGTTTTCCTTCAGTTAATAAATCTGCTTGTTGAATCCTTGAGGAT
AAGCGGATTTGTTTTTTTTTTTCTGTATTATT
Found at i:12622343 original size:17 final size:16
Alignment explanation
Indices: 12622316--12622349 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
12622306 TCTGAAAAAA
*
12622316 ACAAAAGAAATATCTC
1 ACAAAAGAAATAACTC
12622332 ACAAAGAGAAATAACTC
1 ACAAA-AGAAATAACTC
12622349 A
1 A
12622350 AAGAGTTAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.59, C:0.18, G:0.09, T:0.15
Consensus pattern (16 bp):
ACAAAAGAAATAACTC
Found at i:12626915 original size:55 final size:55
Alignment explanation
Indices: 12626831--12626940 Score: 211
Period size: 55 Copynumber: 2.0 Consensus size: 55
12626821 TGTTTTTCTT
12626831 ATTTTTATAAAATAGCTTTTCTCATCACCTTAGGATTAATCGTAATATAATTTAA
1 ATTTTTATAAAATAGCTTTTCTCATCACCTTAGGATTAATCGTAATATAATTTAA
*
12626886 ATTTTTATAAAATATCTTTTCTCATCACCTTAGGATTAATCGTAATATAATTTAA
1 ATTTTTATAAAATAGCTTTTCTCATCACCTTAGGATTAATCGTAATATAATTTAA
12626941 TTAAATTATT
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
55 54 1.00
ACGTcount: A:0.36, C:0.13, G:0.06, T:0.45
Consensus pattern (55 bp):
ATTTTTATAAAATAGCTTTTCTCATCACCTTAGGATTAATCGTAATATAATTTAA
Found at i:12633251 original size:27 final size:26
Alignment explanation
Indices: 12633193--12633253 Score: 68
Period size: 27 Copynumber: 2.3 Consensus size: 26
12633183 CCTAAATATT
* *
12633193 AGATAGTCTTCACAAACTTCCACTAA
1 AGATAGTCTTCAAAAACTTCCACCAA
* * *
12633219 AAATAGTCTTGATAAAATTTCCACCAA
1 AGATAGTCTTCA-AAAACTTCCACCAA
12633246 AGATAGTC
1 AGATAGTC
12633254 CTGACGGATT
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
26 10 0.36
27 18 0.64
ACGTcount: A:0.41, C:0.21, G:0.10, T:0.28
Consensus pattern (26 bp):
AGATAGTCTTCAAAAACTTCCACCAA
Found at i:12636712 original size:50 final size:50
Alignment explanation
Indices: 12636606--12636847 Score: 182
Period size: 50 Copynumber: 4.7 Consensus size: 50
12636596 GGGAATGAGA
* * **
12636606 TCCCATGTAATACCATGTCTAGGACATGGCATTGGCATTATTGACGTTATGAGAGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGC---ACCGAC---ATGAGAGG
* *
12636662 TCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGACATGAGAGG
** ** * * * **
12636712 TCCCCCGTAAGACCATGTCTTAGACATGGCATGGGCACCGATACGAGAAC
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGACATGAGAGG
* * * * * * **
12636762 TCCCATGTAAGACCATATCTGGGATATGACATTGG--CGGTACAAGAAACA
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCG-ACATGAGAGG
* *
12636811 TCCCATGTAAGACCATGTCTAGGACATGGCTTTGGCA
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
12636848 TGTTATTATC
Statistics
Matches: 148, Mismatches: 35, Indels: 11
0.76 0.18 0.06
Matches are distributed among these distances:
48 2 0.01
49 35 0.24
50 75 0.51
53 3 0.02
56 33 0.22
ACGTcount: A:0.28, C:0.23, G:0.26, T:0.24
Consensus pattern (50 bp):
TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGACATGAGAGG
Found at i:12637099 original size:20 final size:20
Alignment explanation
Indices: 12637049--12637087 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
12637039 TGAGTTATTT
* *
12637049 AAGTAAGCAAGTAAGTAAAC
1 AAGTAAGAAAGTAAATAAAC
12637069 AAGTAAGAAAGTAAATAAA
1 AAGTAAGAAAGTAAATAAA
12637088 GAAGAAGTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.62, C:0.05, G:0.18, T:0.15
Consensus pattern (20 bp):
AAGTAAGAAAGTAAATAAAC
Found at i:12639991 original size:16 final size:17
Alignment explanation
Indices: 12639955--12639992 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
12639945 TCGCCTGACA
*
12639955 ATACTATTCACCAGGTG
1 ATACTATTCACCAGATG
*
12639972 ATACTATTCGCCA-ATG
1 ATACTATTCACCAGATG
12639988 ATACT
1 ATACT
12639993 GCCCGCCAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 7 0.37
17 12 0.63
ACGTcount: A:0.32, C:0.24, G:0.13, T:0.32
Consensus pattern (17 bp):
ATACTATTCACCAGATG
Found at i:12650875 original size:34 final size:36
Alignment explanation
Indices: 12650790--12650887 Score: 139
Period size: 34 Copynumber: 2.8 Consensus size: 36
12650780 TCACTAATTA
*
12650790 TTCGTCGGTTTATCTGACTAGCGCTGGGCGCAACTG
1 TTCGTCGGTTTATCTGACTAGCGCTGGGCACAACTG
* *
12650826 TT-GTCAGTTTATCTGACTAGTGCTGGGCAC-AC-G
1 TTCGTCGGTTTATCTGACTAGCGCTGGGCACAACTG
*
12650859 TTCGTCGGTTTATCTGACTAGCACTGGGC
1 TTCGTCGGTTTATCTGACTAGCGCTGGGC
12650888 GCAAATACTG
Statistics
Matches: 55, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
33 3 0.05
34 25 0.45
35 25 0.45
36 2 0.04
ACGTcount: A:0.15, C:0.23, G:0.29, T:0.33
Consensus pattern (36 bp):
TTCGTCGGTTTATCTGACTAGCGCTGGGCACAACTG
Found at i:12650922 original size:69 final size:69
Alignment explanation
Indices: 12650790--12650922 Score: 178
Period size: 69 Copynumber: 1.9 Consensus size: 69
12650780 TCACTAATTA
* * ** * *
12650790 TTCGTCGGTTTATCTGACTAGCGCTGGGCGCAACTGTTGTCAGTTTATCTGACTAGTGCTGGGCA
1 TTCGTCGGTTTATCTGACTAGCACTGGGCGCAAATACTGTCAGTTTATCCGACTAGTGATGGGCA
12650855 CACG
66 CACG
**
12650859 TTCGTCGGTTTATCTGACTAGCACTGGGCGCAAATACTGTTGGTTTATCCGACTAGAT-ATGGGC
1 TTCGTCGGTTTATCTGACTAGCACTGGGCGCAAATACTGTCAGTTTATCCGACTAG-TGATGGGC
12650923 TCACTAATTA
Statistics
Matches: 55, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
69 54 0.98
70 1 0.02
ACGTcount: A:0.18, C:0.22, G:0.28, T:0.32
Consensus pattern (69 bp):
TTCGTCGGTTTATCTGACTAGCACTGGGCGCAAATACTGTCAGTTTATCCGACTAGTGATGGGCA
CACG
Found at i:12655661 original size:30 final size:28
Alignment explanation
Indices: 12655606--12655664 Score: 73
Period size: 30 Copynumber: 2.0 Consensus size: 28
12655596 GATTTTTGGG
**
12655606 TTTTTTTTCTTTTCATTTGCAGATTGTT
1 TTTTTTTTCTTTTCACCTGCAGATTGTT
*
12655634 TTTTTTTTCGTTTTGCACCTGCTGATTGTT
1 TTTTTTTTC-TTTT-CACCTGCAGATTGTT
12655664 T
1 T
12655665 GTTAAGAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
28 9 0.35
29 4 0.15
30 13 0.50
ACGTcount: A:0.08, C:0.14, G:0.14, T:0.64
Consensus pattern (28 bp):
TTTTTTTTCTTTTCACCTGCAGATTGTT
Found at i:12659997 original size:28 final size:27
Alignment explanation
Indices: 12659961--12660018 Score: 73
Period size: 27 Copynumber: 2.1 Consensus size: 27
12659951 ATCCTAATAT
*
12659961 TTAAAATTTATTATAAA-TCAACAAAACA
1 TTAAAATTTA-TA-AAATTAAACAAAACA
*
12659989 TTAATATTTATAAAATTAAACAAAACA
1 TTAAAATTTATAAAATTAAACAAAACA
12660016 TTA
1 TTA
12660019 TGATTAATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
26 3 0.11
27 15 0.56
28 9 0.33
ACGTcount: A:0.57, C:0.09, G:0.00, T:0.34
Consensus pattern (27 bp):
TTAAAATTTATAAAATTAAACAAAACA
Found at i:12667117 original size:44 final size:44
Alignment explanation
Indices: 12667054--12667148 Score: 183
Period size: 44 Copynumber: 2.2 Consensus size: 44
12667044 TAAAATTCCT
12667054 CCATATCTATCGCCCCCATCTCTAGTCCCATTTATGGAAGCTAG
1 CCATATCTATCGCCCCCATCTCTAGTCCCATTTATGGAAGCTAG
12667098 CCATATCTATCGCCCCCATCTCTAGTCCCATTTATGGAAGCTAG
1 CCATATCTATCGCCCCCATCTCTAGTCCCATTTATGGAAGCTAG
12667142 CCA-ATCT
1 CCATATCT
12667149 TAATGAAAGC
Statistics
Matches: 51, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
43 4 0.08
44 47 0.92
ACGTcount: A:0.23, C:0.35, G:0.13, T:0.29
Consensus pattern (44 bp):
CCATATCTATCGCCCCCATCTCTAGTCCCATTTATGGAAGCTAG
Found at i:12676036 original size:18 final size:18
Alignment explanation
Indices: 12676009--12676051 Score: 79
Period size: 18 Copynumber: 2.4 Consensus size: 18
12675999 TAGTTGTAAA
12676009 AGTT-AGTCAAGATATTT
1 AGTTAAGTCAAGATATTT
12676026 AGTTAAGTCAAGATATTT
1 AGTTAAGTCAAGATATTT
12676044 AGTTAAGT
1 AGTTAAGT
12676052 TCAATTGTTG
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
17 4 0.16
18 21 0.84
ACGTcount: A:0.37, C:0.05, G:0.19, T:0.40
Consensus pattern (18 bp):
AGTTAAGTCAAGATATTT
Found at i:12677654 original size:18 final size:18
Alignment explanation
Indices: 12677631--12677668 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
12677621 ATCAAATCTT
12677631 AAAAGCAAAAACAATAGC
1 AAAAGCAAAAACAATAGC
12677649 AAAAGCAAAAACAATAGC
1 AAAAGCAAAAACAATAGC
12677667 AA
1 AA
12677669 CTAACTCTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.68, C:0.16, G:0.11, T:0.05
Consensus pattern (18 bp):
AAAAGCAAAAACAATAGC
Found at i:12682262 original size:19 final size:19
Alignment explanation
Indices: 12682238--12682275 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
12682228 CTAAAAATAT
*
12682238 TAAATAATTAATATTTATG
1 TAAATAACTAATATTTATG
12682257 TAAATAACTAATATTTATG
1 TAAATAACTAATATTTATG
12682276 GACCGACACA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.47, C:0.03, G:0.05, T:0.45
Consensus pattern (19 bp):
TAAATAACTAATATTTATG
Found at i:12685645 original size:9 final size:9
Alignment explanation
Indices: 12685631--12685655 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
12685621 GCTTGCTGTC
12685631 GAGAAATAA
1 GAGAAATAA
12685640 GAGAAATAA
1 GAGAAATAA
12685649 GAGAAAT
1 GAGAAAT
12685656 GATGCGAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.64, C:0.00, G:0.24, T:0.12
Consensus pattern (9 bp):
GAGAAATAA
Found at i:12693616 original size:9 final size:9
Alignment explanation
Indices: 12693602--12693634 Score: 66
Period size: 9 Copynumber: 3.7 Consensus size: 9
12693592 CAAGTATAAA
12693602 AATTAACTG
1 AATTAACTG
12693611 AATTAACTG
1 AATTAACTG
12693620 AATTAACTG
1 AATTAACTG
12693629 AATTAA
1 AATTAA
12693635 AGTATTGAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 24 1.00
ACGTcount: A:0.48, C:0.09, G:0.09, T:0.33
Consensus pattern (9 bp):
AATTAACTG
Found at i:12699767 original size:25 final size:25
Alignment explanation
Indices: 12699715--12699768 Score: 90
Period size: 25 Copynumber: 2.2 Consensus size: 25
12699705 ATGCTAATAT
*
12699715 GAGCTGTAAATCGGTATGCTCACTC
1 GAGCTGTAAATCGGTATGCTCACAC
*
12699740 GAGCTGTAAATCGGTATGCTCTCAC
1 GAGCTGTAAATCGGTATGCTCACAC
12699765 GAGC
1 GAGC
12699769 CGTGGGTTGG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.24, C:0.24, G:0.26, T:0.26
Consensus pattern (25 bp):
GAGCTGTAAATCGGTATGCTCACAC
Found at i:12704170 original size:18 final size:19
Alignment explanation
Indices: 12704144--12704180 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
12704134 TACTAAGAAG
12704144 CAATGACCTACAAACATGA
1 CAATGACCTACAAACATGA
*
12704163 CAAT-ACCTACAAGCATGA
1 CAATGACCTACAAACATGA
12704181 AAGGAAAAGC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.46, C:0.27, G:0.11, T:0.16
Consensus pattern (19 bp):
CAATGACCTACAAACATGA
Found at i:12704378 original size:15 final size:15
Alignment explanation
Indices: 12704343--12704385 Score: 52
Period size: 14 Copynumber: 2.9 Consensus size: 15
12704333 TTTCTGTCGT
12704343 GATTTTTAGTTTT-A
1 GATTTTTAGTTTTAA
*
12704357 GACTTTTAGTTTTAA
1 GATTTTTAGTTTTAA
* *
12704372 GTTTTTTATTTTTA
1 GATTTTTAGTTTTA
12704386 TTTATTAAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
14 12 0.50
15 12 0.50
ACGTcount: A:0.21, C:0.02, G:0.12, T:0.65
Consensus pattern (15 bp):
GATTTTTAGTTTTAA
Found at i:12704437 original size:13 final size:13
Alignment explanation
Indices: 12704419--12704443 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
12704409 TACGATTGGG
12704419 TTGGGTTTATATA
1 TTGGGTTTATATA
12704432 TTGGGTTTATAT
1 TTGGGTTTATAT
12704444 TGGATTGAGC
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:0.20, C:0.00, G:0.24, T:0.56
Consensus pattern (13 bp):
TTGGGTTTATATA
Found at i:12705298 original size:26 final size:26
Alignment explanation
Indices: 12705262--12705318 Score: 105
Period size: 26 Copynumber: 2.2 Consensus size: 26
12705252 GATGTAATTT
*
12705262 GTTATGCCTCCAATTATTACAAGGTA
1 GTTATGCCTCCAATTAGTACAAGGTA
12705288 GTTATGCCTCCAATTAGTACAAGGTA
1 GTTATGCCTCCAATTAGTACAAGGTA
12705314 GTTAT
1 GTTAT
12705319 TCCTGAACAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.35
Consensus pattern (26 bp):
GTTATGCCTCCAATTAGTACAAGGTA
Found at i:12706479 original size:8 final size:8
Alignment explanation
Indices: 12706466--12706498 Score: 66
Period size: 8 Copynumber: 4.1 Consensus size: 8
12706456 TTTTAAATAA
12706466 TATTTTAT
1 TATTTTAT
12706474 TATTTTAT
1 TATTTTAT
12706482 TATTTTAT
1 TATTTTAT
12706490 TATTTTAT
1 TATTTTAT
12706498 T
1 T
12706499 GTTTAGTATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 25 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (8 bp):
TATTTTAT
Found at i:12709900 original size:29 final size:30
Alignment explanation
Indices: 12709843--12709900 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
12709833 ATTTTACGAG
*
12709843 TCTAGGGGCAAAATCGTAATTTTGTCAAAC
1 TCTAGGGGCAAAATCGTAAATTTGTCAAAC
12709873 TCTAGGGGCAAAAT-GTAAAATTT-TCAAA
1 TCTAGGGGCAAAATCGT-AAATTTGTCAAA
12709901 GTGTGATTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
29 7 0.27
30 19 0.73
ACGTcount: A:0.38, C:0.14, G:0.19, T:0.29
Consensus pattern (30 bp):
TCTAGGGGCAAAATCGTAAATTTGTCAAAC
Found at i:12710432 original size:33 final size:33
Alignment explanation
Indices: 12710363--12710540 Score: 146
Period size: 27 Copynumber: 5.5 Consensus size: 33
12710353 ATGTGAAGGG
*
12710363 GGTTGCTAAGTGCTGATTCCCC----CA-AGG-
1 GGTTGCTAAGTGCTGATTCCCCGATTCATTGGT
12710390 GGTTGCTAAGTGCTGATTCCCCGATTCATTGGT
1 GGTTGCTAAGTGCTGATTCCCCGATTCATTGGT
* * *
12710423 GGTTACTAAGTGCTGATTCCACCGTATTTTAAATGTGAAGGG
1 GGTTGCTAAGTGCTGATTCC-CCG-A--TT-CAT-T---GGT
*
12710465 GGTTGCTAAGTGCTGATTCCCC----CA-AGG-
1 GGTTGCTAAGTGCTGATTCCCCGATTCATTGGT
12710492 GGTTGCTAAGTGCTGATTCCCCGATTCATTGGT
1 GGTTGCTAAGTGCTGATTCCCCGATTCATTGGT
12710525 GGTTGCTAAGTGCTGA
1 GGTTGCTAAGTGCTGA
12710541 CCGTATCATT
Statistics
Matches: 122, Mismatches: 8, Indels: 36
0.73 0.05 0.22
Matches are distributed among these distances:
27 44 0.36
28 2 0.02
31 4 0.03
32 4 0.03
33 36 0.30
34 3 0.02
35 1 0.01
37 2 0.02
38 2 0.02
39 1 0.01
41 2 0.02
42 21 0.17
ACGTcount: A:0.19, C:0.20, G:0.29, T:0.32
Consensus pattern (33 bp):
GGTTGCTAAGTGCTGATTCCCCGATTCATTGGT
Found at i:12710462 original size:102 final size:102
Alignment explanation
Indices: 12710292--12710584 Score: 428
Period size: 102 Copynumber: 3.0 Consensus size: 102
12710282 GAATATAAAG
* * *
12710292 GGGGTTGCTAAGTGCTGATTCCCC----CA-AGG-GGTTGTTAAGTGTTGATTCCACCGTATTTT
1 GGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATTTT
12710351 AAATGTGAAGGGGGTTGCTAAGTGCTGATTCCCCCAA
66 AAATGTGAAGGGGGTTGCTAAGTGCTGATTCCCCCAA
*
12710388 GGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTTACTAAGTGCTGATTCCACCGTATTTT
1 GGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATTTT
12710453 AAATGTGAAGGGGGTTGCTAAGTGCTGATTCCCCCAA
66 AAATGTGAAGGGGGTTGCTAAGTGCTGATTCCCCCAA
*
12710490 GGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTG-----ACCGTATCAT
1 GGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATTCCACCGTAT-TT
* * *
12710550 TGAATGTGAAAGGGGTTGCTAAGTGTTGATTCCCC
65 TAAATGTGAAGGGGGTTGCTAAGTGCTGATTCCCC
12710585 GAATCACTGG
Statistics
Matches: 181, Mismatches: 9, Indels: 12
0.90 0.04 0.06
Matches are distributed among these distances:
96 24 0.13
97 7 0.04
98 33 0.18
100 2 0.01
101 2 0.01
102 113 0.62
ACGTcount: A:0.20, C:0.19, G:0.29, T:0.32
Consensus pattern (102 bp):
GGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATTTT
AAATGTGAAGGGGGTTGCTAAGTGCTGATTCCCCCAA
Found at i:12712603 original size:30 final size:31
Alignment explanation
Indices: 12712569--12712639 Score: 81
Period size: 30 Copynumber: 2.3 Consensus size: 31
12712559 TGGGTCAAGA
***
12712569 GTAAATATTTAAAATTTGAAGG-GTTAAAGT
1 GTAAATATTTAAAATTTGAAGGACCAAAAGT
***
12712599 GTAAATACAAAAAATTTGAAGGACCAAAAGT
1 GTAAATATTTAAAATTTGAAGGACCAAAAGT
12712630 GTAAATATTT
1 GTAAATATTT
12712640 TAAGGTTGGA
Statistics
Matches: 31, Mismatches: 9, Indels: 1
0.76 0.22 0.02
Matches are distributed among these distances:
30 19 0.61
31 12 0.39
ACGTcount: A:0.48, C:0.04, G:0.17, T:0.31
Consensus pattern (31 bp):
GTAAATATTTAAAATTTGAAGGACCAAAAGT
Found at i:12717965 original size:12 final size:13
Alignment explanation
Indices: 12717934--12717973 Score: 55
Period size: 12 Copynumber: 3.0 Consensus size: 13
12717924 ATCTGCCAGA
12717934 GAAATTAGAAGATCT
1 GAAATT-GAA-ATCT
12717949 GAAATTGAAAT-T
1 GAAATTGAAATCT
12717961 GAAATTGAAATCT
1 GAAATTGAAATCT
12717974 TGGGATAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
12 12 0.50
13 3 0.12
14 3 0.12
15 6 0.25
ACGTcount: A:0.47, C:0.05, G:0.17, T:0.30
Consensus pattern (13 bp):
GAAATTGAAATCT
Found at i:12722719 original size:18 final size:18
Alignment explanation
Indices: 12722696--12722730 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
12722686 TCAAGAGACC
12722696 ATTAATTAAATTAAATTG
1 ATTAATTAAATTAAATTG
* *
12722714 ATTAATTTAATTTAATT
1 ATTAATTAAATTAAATT
12722731 TAATTCGATT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (18 bp):
ATTAATTAAATTAAATTG
Found at i:12726319 original size:237 final size:238
Alignment explanation
Indices: 12725893--12726362 Score: 800
Period size: 237 Copynumber: 2.0 Consensus size: 238
12725883 TTTTCACCCT
* *
12725893 GTTTTTCCCAGTCTAATTGATAAATCTATTCCAATTGATCTCTCAATGAGTCTTCTGAAACTTCT
1 GTTTTTCCCAATCTAATTGATAAATCTATTACAATTGATCTCTCAATGAGTCTTCTGAAACTTCT
* ** *
12725958 TCCTTTGTTATTTTTCCTAAATCGAAAATGTAAGAATCACCATCGCTTGAAAGTTCCTCACTCTT
66 TCCTTTGTTATTTGTCCTAAATAAAAAATGTAAGAATCACCATCGCTTGAAACTTCCTCACTCTT
*
12726023 TTTTTGAATTATCCTCATCAACCATTGATTCTTGTTTAGTAACATTCGTTAGCTCAGTCACCACT
131 TTTTTGAATTATCCTCATCAACCATTGATTCTTGTTTAGTAACATTCATTAGCTCAGTCACCACT
12726088 TTTGGTTCTCTAATCAATCCTCAAGCGTGATCGTTGTTACTTA
196 TTTGGTTCTCTAATCAATCCTCAAGCGTGATCGTTGTTACTTA
12726131 GTTTTT-CCAATCTAATTGATAAATCTATTACAATTGATCTCTCAATGAGTCTTCTGAAACTTCT
1 GTTTTTCCCAATCTAATTGATAAATCTATTACAATTGATCTCTCAATGAGTCTTCTGAAACTTCT
*
12726195 TCCTTTGTTATTTCGTCC-AAATAAAAAATGTAGGAATCACCATCGCTTGAAACTTCCTCACTCT
66 TCCTTTGTTATTT-GTCCTAAATAAAAAATGTAAGAATCACCATCGCTTGAAACTTCCTCACTCT
* * *
12726259 TTTTTTGAATTATCCTCATCATCTATTGATTCTTGTTTAGTGACATTCATTAGCTCAGTCACCAC
130 TTTTTTGAATTATCCTCATCAACCATTGATTCTTGTTTAGTAACATTCATTAGCTCAGTCACCAC
* *
12726324 TTTTGGTTCTCTAATCAGTCCTCAAGTGTGATCGTTGTT
195 TTTTGGTTCTCTAATCAATCCTCAAGCGTGATCGTTGTT
12726363 GCTTGCTTTT
Statistics
Matches: 218, Mismatches: 13, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
237 209 0.96
238 9 0.04
ACGTcount: A:0.25, C:0.22, G:0.12, T:0.41
Consensus pattern (238 bp):
GTTTTTCCCAATCTAATTGATAAATCTATTACAATTGATCTCTCAATGAGTCTTCTGAAACTTCT
TCCTTTGTTATTTGTCCTAAATAAAAAATGTAAGAATCACCATCGCTTGAAACTTCCTCACTCTT
TTTTTGAATTATCCTCATCAACCATTGATTCTTGTTTAGTAACATTCATTAGCTCAGTCACCACT
TTTGGTTCTCTAATCAATCCTCAAGCGTGATCGTTGTTACTTA
Found at i:12732753 original size:20 final size:20
Alignment explanation
Indices: 12732728--12732770 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
12732718 TTATTACATC
12732728 TTTTAAATATGACTTAAAAG
1 TTTTAAATATGACTTAAAAG
* * *
12732748 TTTTAATTGTGTCTTAAAAG
1 TTTTAAATATGACTTAAAAG
12732768 TTT
1 TTT
12732771 GCTTGAAATA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.35, C:0.05, G:0.12, T:0.49
Consensus pattern (20 bp):
TTTTAAATATGACTTAAAAG
Found at i:12734919 original size:12 final size:12
Alignment explanation
Indices: 12734904--12734961 Score: 71
Period size: 12 Copynumber: 4.8 Consensus size: 12
12734894 AAATGATATA
12734904 GAAAAAGAGTGT
1 GAAAAAGAGTGT
*
12734916 GAAAAAGAATGT
1 GAAAAAGAGTGT
**
12734928 GAAAGGGAGTGT
1 GAAAAAGAGTGT
*
12734940 GAAAAAAAGTGT
1 GAAAAAGAGTGT
12734952 GAAACAAGAG
1 GAAA-AAGAG
12734962 GAGAGAAAAG
Statistics
Matches: 37, Mismatches: 8, Indels: 1
0.80 0.17 0.02
Matches are distributed among these distances:
12 33 0.89
13 4 0.11
ACGTcount: A:0.52, C:0.02, G:0.33, T:0.14
Consensus pattern (12 bp):
GAAAAAGAGTGT
Found at i:12737280 original size:32 final size:32
Alignment explanation
Indices: 12737234--12737304 Score: 90
Period size: 32 Copynumber: 2.2 Consensus size: 32
12737224 CATCACAAGA
*
12737234 GACCATTGATGGAGGTCGT-TGGTATTATTTAGG
1 GACC-TTGATGGAGGTCGTAT-GTATTACTTAGG
* *
12737267 GACCTTGATGGAGGTTGTATGTCTTACTTAGG
1 GACCTTGATGGAGGTCGTATGTATTACTTAGG
12737299 GACCTT
1 GACCTT
12737305 CTCCCACTTA
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
32 29 0.85
33 5 0.15
ACGTcount: A:0.20, C:0.13, G:0.31, T:0.37
Consensus pattern (32 bp):
GACCTTGATGGAGGTCGTATGTATTACTTAGG
Found at i:12739120 original size:57 final size:57
Alignment explanation
Indices: 12739033--12739225 Score: 223
Period size: 57 Copynumber: 3.3 Consensus size: 57
12739023 AATTTTCAAG
12739033 TCATTT-TC-ATTTTCA-TTTCATTTTGGAGAAAACCATAATCATTTCCAAATATTT
1 TCATTTCTCTATTTTCATTTTCATTTTGGAGAAAACCATAATCATTTCCAAATATTT
* * *
12739087 TCATTTCTCTATTTTCATTTTCATTTTGGAGAAAAACATAACCATTTCCATATGA-TT
1 TCATTTCTCTATTTTCATTTTCATTTTGGAGAAAACCATAATCATTTCCAAAT-ATTT
* *
12739144 TCGTTTCTTCATTTTCATTTTCATTTTCATTTTGGAGAAAACCATAATCATTTCCAAATTATCTC
1 TCATTTC-TC----T-ATTTTCATTTTCATTTTGGAGAAAACCATAATCATTTCCAAA-TAT-TT
*
12739209 TCATTTCTCCATTTTCA
1 TCATTTCTCTATTTTCA
12739226 CCATTTCTAT
Statistics
Matches: 116, Mismatches: 10, Indels: 21
0.79 0.07 0.14
Matches are distributed among these distances:
54 6 0.05
55 2 0.02
56 7 0.06
57 40 0.34
58 3 0.03
59 7 0.06
62 1 0.01
63 40 0.34
64 3 0.03
65 7 0.06
ACGTcount: A:0.28, C:0.19, G:0.06, T:0.47
Consensus pattern (57 bp):
TCATTTCTCTATTTTCATTTTCATTTTGGAGAAAACCATAATCATTTCCAAATATTT
Found at i:12739162 original size:6 final size:6
Alignment explanation
Indices: 12739151--12739176 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
12739141 ATTTCGTTTC
12739151 TTCATT TTCATT TTCATT TTCATT TT
1 TTCATT TTCATT TTCATT TTCATT TT
12739177 GGAGAAAACC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.15, C:0.15, G:0.00, T:0.69
Consensus pattern (6 bp):
TTCATT
Found at i:12747492 original size:60 final size:54
Alignment explanation
Indices: 12747419--12747566 Score: 181
Period size: 54 Copynumber: 2.6 Consensus size: 54
12747409 CATCTTCAGA
* * *
12747419 TGAAGTGTTTTCTTCATCAGAATTATGACTAGTGACTTTTATATCTTCATCCTGATATGT
1 TGAAGTTTTTTCTTCATCAGAATTATAACTAGTAAC-TTT-TA---T-ATCCTGATATGT
*
12747479 TGAAGTTTTTTCTTCATCAG-ATTGATAACTAGTAACTTTTATATCCTGATCTGT
1 TGAAGTTTTTTCTTCATCAGAATT-ATAACTAGTAACTTTTATATCCTGATATGT
*
12747533 TGAAGTTTTTTCTTCATCAGATTTATAACTAGTA
1 TGAAGTTTTTTCTTCATCAGAATTATAACTAGTA
12747567 GCTTATAAAT
Statistics
Matches: 81, Mismatches: 5, Indels: 10
0.84 0.05 0.10
Matches are distributed among these distances:
54 41 0.51
55 3 0.04
58 2 0.02
59 6 0.07
60 29 0.36
ACGTcount: A:0.26, C:0.14, G:0.14, T:0.46
Consensus pattern (54 bp):
TGAAGTTTTTTCTTCATCAGAATTATAACTAGTAACTTTTATATCCTGATATGT
Done.