Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr5
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 43060996
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2186021 characters in sequence are not A, C, G, or T
File 58 of 128
Found at i:18267875 original size:27 final size:27
Alignment explanation
Indices: 18267674--18267898 Score: 166
Period size: 27 Copynumber: 8.4 Consensus size: 27
18267664 GGGAAAAATA
* * * *
18267674 GTCA-TTTACCCTCTAGGGGCATTACA
1 GTCATTTTACCCTATGGGGGTATTACG
** * **
18267700 GTCATTTTACCCTA-CAGGGCATTATA
1 GTCATTTTACCCTATGGGGGTATTACG
* * ** *
18267726 GTTATTGTACCCTATAAGGGAATTACG
1 GTCATTTTACCCTATGGGGGTATTACG
* * ** * *
18267753 ATCATTTTACCTTACAGGGGCATTACA
1 GTCATTTTACCCTATGGGGGTATTACG
** * * *
18267780 ACCATTTTACCCAATAGGGGCATTACG
1 GTCATTTTACCCTATGGGGGTATTACG
* *
18267807 ATCATTTTACCCTATGAGGGTATTACG
1 GTCATTTTACCCTATGGGGGTATTACG
18267834 GTCATTTTACCCTATGGGGGTATTACG
1 GTCATTTTACCCTATGGGGGTATTACG
*
18267861 GTTATTTTACCCTATGGGGGTATTACG
1 GTCATTTTACCCTATGGGGGTATTACG
* *
18267888 ATCATTATACC
1 GTCATTTTACC
18267899 TATTTTATGG
Statistics
Matches: 163, Mismatches: 34, Indels: 3
0.81 0.17 0.01
Matches are distributed among these distances:
26 25 0.15
27 138 0.85
ACGTcount: A:0.26, C:0.21, G:0.19, T:0.34
Consensus pattern (27 bp):
GTCATTTTACCCTATGGGGGTATTACG
Found at i:18274800 original size:100 final size:101
Alignment explanation
Indices: 18274627--18274828 Score: 397
Period size: 100 Copynumber: 2.0 Consensus size: 101
18274617 TTGCATTAAG
18274627 TGAACCAATGGTAAGGTTAAATATCTTTCTGGCCAAGGTCGGTCCAAATATTCATCATTTTATAT
1 TGAACCAATGGTAAGGTTAAATATCTTTCTGGCCAAGGTCGGTCCAAATATTCATCATTTTATAT
18274692 AATTTATATTTAATTTTTATACAAG-TAAATTGGGT
66 AATTTATATTTAATTTTTATACAAGTTAAATTGGGT
18274727 TGAACCAATGGTAAGGTTAAATATCTTTCTGGCCAAGGTCGGTCCAAATATTCATCATTTTATAT
1 TGAACCAATGGTAAGGTTAAATATCTTTCTGGCCAAGGTCGGTCCAAATATTCATCATTTTATAT
18274792 AATTTATATTTAATTTTTATACAAGTTAAATTGGGT
66 AATTTATATTTAATTTTTATACAAGTTAAATTGGGT
18274828 T
1 T
18274829 AAAAATTAAT
Statistics
Matches: 101, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
100 90 0.89
101 11 0.11
ACGTcount: A:0.33, C:0.12, G:0.15, T:0.41
Consensus pattern (101 bp):
TGAACCAATGGTAAGGTTAAATATCTTTCTGGCCAAGGTCGGTCCAAATATTCATCATTTTATAT
AATTTATATTTAATTTTTATACAAGTTAAATTGGGT
Found at i:18276328 original size:10 final size:10
Alignment explanation
Indices: 18276307--18276335 Score: 51
Period size: 9 Copynumber: 3.0 Consensus size: 10
18276297 TGTATTTTGG
18276307 TTTTTCTATT
1 TTTTTCTATT
18276317 TTTTT-TATT
1 TTTTTCTATT
18276326 TTTTTCTATT
1 TTTTTCTATT
18276336 CAATTTTAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
9 9 0.50
10 9 0.50
ACGTcount: A:0.10, C:0.07, G:0.00, T:0.83
Consensus pattern (10 bp):
TTTTTCTATT
Found at i:18278479 original size:27 final size:28
Alignment explanation
Indices: 18278449--18278507 Score: 66
Period size: 27 Copynumber: 2.1 Consensus size: 28
18278439 TTTTTGTCAA
* *
18278449 AATTCATACTTTAATTA-TAAAATAATT
1 AATTCACACTTGAATTATTAAAATAATT
* * *
18278476 AATTTACACTTGAATTATTAACATATTT
1 AATTCACACTTGAATTATTAAAATAATT
18278504 AATT
1 AATT
18278508 TTAATTATTT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
27 14 0.54
28 12 0.46
ACGTcount: A:0.44, C:0.08, G:0.02, T:0.46
Consensus pattern (28 bp):
AATTCACACTTGAATTATTAAAATAATT
Found at i:18281148 original size:31 final size:31
Alignment explanation
Indices: 18281113--18281175 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
18281103 AAACAATTAC
18281113 TTAGTTTTAACAACGGATTTAAGTAAAAAGG
1 TTAGTTTTAACAACGGATTTAAGTAAAAAGG
18281144 TTAGTTTTAACAACGGATTTAAGTAAAAAGG
1 TTAGTTTTAACAACGGATTTAAGTAAAAAGG
18281175 T
1 T
18281176 GATAAATCAC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.41, C:0.06, G:0.19, T:0.33
Consensus pattern (31 bp):
TTAGTTTTAACAACGGATTTAAGTAAAAAGG
Found at i:18289969 original size:20 final size:20
Alignment explanation
Indices: 18289946--18289989 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
18289936 GTAATGTTAG
*
18289946 AAATAA-ATCACATTAAAAAT
1 AAATAATATCACA-AAAAAAT
*
18289966 AAATAATTTCACAAAAAAAT
1 AAATAATATCACAAAAAAAT
18289986 AAAT
1 AAAT
18289990 CACTATGGCA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 16 0.76
21 5 0.24
ACGTcount: A:0.66, C:0.09, G:0.00, T:0.25
Consensus pattern (20 bp):
AAATAATATCACAAAAAAAT
Found at i:18293257 original size:21 final size:21
Alignment explanation
Indices: 18293215--18293258 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
18293205 TGGTTCGATC
* *
18293215 TCTTTGGGATCTTCTTCTTCT
1 TCTTTGGGATCATCCTCTTCT
18293236 TCTTTGGGATCATCACTC-TCT
1 TCTTTGGGATCATC-CTCTTCT
18293257 TC
1 TC
18293259 AACTCATTGC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 18 0.90
22 2 0.10
ACGTcount: A:0.09, C:0.27, G:0.14, T:0.50
Consensus pattern (21 bp):
TCTTTGGGATCATCCTCTTCT
Found at i:18295974 original size:27 final size:27
Alignment explanation
Indices: 18295944--18296137 Score: 225
Period size: 27 Copynumber: 7.2 Consensus size: 27
18295934 TATAACAGTC
* * *
18295944 ATTTTACCCTACGGGGGTATTTTGATA
1 ATTTTACCCTTCGAGGGTATTTCGATA
18295971 ATTTTACCCTTCGAGGGTATTTCGATA
1 ATTTTACCCTTCGAGGGTATTTCGATA
* *
18295998 ATTTTACCCTTTGGGGGTATTTCGATA
1 ATTTTACCCTTCGAGGGTATTTCGATA
* *
18296025 ATTTTACCCTTTGAGGGCATTTCGATA
1 ATTTTACCCTTCGAGGGTATTTCGATA
* * *
18296052 ATTTTACCATTCGAGGGTATTCCGGTA
1 ATTTTACCCTTCGAGGGTATTTCGATA
18296079 ATTTTACCCTAT-G-GGAGTATTTCTG-TA
1 ATTTTACCCT-TCGAGG-GTATTTC-GATA
*
18296106 ATTTTACCCTTTGAGGGTATTTCAGA-A
1 ATTTTACCCTTCGAGGGTATTTC-GATA
18296133 ATTTT
1 ATTTT
18296138 CAGGCCCAAG
Statistics
Matches: 146, Mismatches: 15, Indels: 12
0.84 0.09 0.07
Matches are distributed among these distances:
26 3 0.02
27 139 0.95
28 4 0.03
ACGTcount: A:0.22, C:0.16, G:0.20, T:0.42
Consensus pattern (27 bp):
ATTTTACCCTTCGAGGGTATTTCGATA
Found at i:18296065 original size:81 final size:81
Alignment explanation
Indices: 18295944--18296137 Score: 266
Period size: 81 Copynumber: 2.4 Consensus size: 81
18295934 TATAACAGTC
** * * * * *
18295944 ATTTTACCCTACGGGGGTATTTTGATAATTTTACCCTTCGAGGGTATTTCGATAATTTTACCCTT
1 ATTTTACCCTTTGAGGGTATTTCGATAATTTTACCATTCGAGGGTATTCCGATAATTTTACCCTA
*
18296009 TGGGGGTATTTC-GATA
66 TGGGAGTATTTCTG-TA
* *
18296025 ATTTTACCCTTTGAGGGCATTTCGATAATTTTACCATTCGAGGGTATTCCGGTAATTTTACCCTA
1 ATTTTACCCTTTGAGGGTATTTCGATAATTTTACCATTCGAGGGTATTCCGATAATTTTACCCTA
18296090 TGGGAGTATTTCTGTA
66 TGGGAGTATTTCTGTA
18296106 ATTTTACCCTTTGAGGGTATTTCAGA-AATTTT
1 ATTTTACCCTTTGAGGGTATTTC-GATAATTTT
18296138 CAGGCCCAAG
Statistics
Matches: 100, Mismatches: 11, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
81 97 0.97
82 3 0.03
ACGTcount: A:0.22, C:0.16, G:0.20, T:0.42
Consensus pattern (81 bp):
ATTTTACCCTTTGAGGGTATTTCGATAATTTTACCATTCGAGGGTATTCCGATAATTTTACCCTA
TGGGAGTATTTCTGTA
Found at i:18308595 original size:20 final size:21
Alignment explanation
Indices: 18308570--18308709 Score: 89
Period size: 20 Copynumber: 7.0 Consensus size: 21
18308560 ATTTCTACTT
18308570 CGGTACCCCTGATTGCACATA
1 CGGTACCCCTGATTGCACATA
* * *
18308591 C-GTACCCCTGTTTGTAC-TT
1 CGGTACCCCTGATTGCACATA
* * *
18308610 CGGTACCCTTGGTTGTACATA
1 CGGTACCCCTGATTGCACATA
* * *
18308631 C-GTGCCCCT-ATTTGTAC-TT
1 CGGTACCCCTGA-TTGCACATA
*
18308650 CGGTACCCCTGATTGCAGATA
1 CGGTACCCCTGATTGCACATA
* *
18308671 C-GTGCCCCT-ATTTGCAC-TT
1 CGGTACCCCTGA-TTGCACATA
*
18308690 CGGTACCCCTTATTGCACAT
1 CGGTACCCCTGATTGCACAT
18308710 GTGTGCCCCT
Statistics
Matches: 91, Mismatches: 18, Indels: 20
0.71 0.14 0.16
Matches are distributed among these distances:
19 7 0.08
20 76 0.84
21 8 0.09
ACGTcount: A:0.17, C:0.31, G:0.19, T:0.33
Consensus pattern (21 bp):
CGGTACCCCTGATTGCACATA
Found at i:18308599 original size:40 final size:40
Alignment explanation
Indices: 18308539--18308779 Score: 277
Period size: 40 Copynumber: 6.0 Consensus size: 40
18308529 TAATTATTGA
*
18308539 TGATTGCACATATGTGCCCCTATTTCTACTTCGGTACCCC
1 TGATTGCACATACGTGCCCCTATTTCTACTTCGGTACCCC
* * * *
18308579 TGATTGCACATACGTACCCCTGTTTGTACTTCGGTACCCT
1 TGATTGCACATACGTGCCCCTATTTCTACTTCGGTACCCC
* * *
18308619 TGGTTGTACATACGTGCCCCTATTTGTACTTCGGTACCCC
1 TGATTGCACATACGTGCCCCTATTTCTACTTCGGTACCCC
*
18308659 TGATTGCAGATACGTGCCCCTATTTGC-ACTTCGGTACCCC
1 TGATTGCACATACGTGCCCCTATTT-CTACTTCGGTACCCC
* ** * * * *
18308699 TTATTGCACATGTGTGCCCCTGTTTTTACTTCAGTACCCT
1 TGATTGCACATACGTGCCCCTATTTCTACTTCGGTACCCC
* * * * *
18308739 TGATTGTAAATGCGTGCCCCTATTTATACTTAGGTACCCC
1 TGATTGCACATACGTGCCCCTATTTCTACTTCGGTACCCC
18308779 T
1 T
18308780 AAATGCACTT
Statistics
Matches: 168, Mismatches: 31, Indels: 4
0.83 0.15 0.02
Matches are distributed among these distances:
40 168 1.00
ACGTcount: A:0.17, C:0.29, G:0.17, T:0.36
Consensus pattern (40 bp):
TGATTGCACATACGTGCCCCTATTTCTACTTCGGTACCCC
Found at i:18308755 original size:120 final size:120
Alignment explanation
Indices: 18308539--18308779 Score: 349
Period size: 120 Copynumber: 2.0 Consensus size: 120
18308529 TAATTATTGA
*
18308539 TGATTGCACATATGTGCCCCTATTTCTACTTCGGTACCCCTGATTGCACATACGTACCCCTGTTT
1 TGATTGCACATACGTGCCCCTATTTCTACTTCGGTACCCCTGATTGCACATACGTACCCCTGTTT
* * * * *
18308604 GTACTTCGGTACCCTTGGTTGTACATACGTGCCCCTATTTGTACTTCGGTACCCC
66 GTACTTCAGTACCCTTGATTGTAAATACGTGCCCCTATTTATACTTAGGTACCCC
* * ** *
18308659 TGATTGCAGATACGTGCCCCTATTTGC-ACTTCGGTACCCCTTATTGCACATGTGTGCCCCTGTT
1 TGATTGCACATACGTGCCCCTATTT-CTACTTCGGTACCCCTGATTGCACATACGTACCCCTGTT
* *
18308723 TTTACTTCAGTACCCTTGATTGTAAATGCGTGCCCCTATTTATACTTAGGTACCCC
65 TGTACTTCAGTACCCTTGATTGTAAATACGTGCCCCTATTTATACTTAGGTACCCC
18308779 T
1 T
18308780 AAATGCACTT
Statistics
Matches: 107, Mismatches: 13, Indels: 2
0.88 0.11 0.02
Matches are distributed among these distances:
120 106 0.99
121 1 0.01
ACGTcount: A:0.17, C:0.29, G:0.17, T:0.36
Consensus pattern (120 bp):
TGATTGCACATACGTGCCCCTATTTCTACTTCGGTACCCCTGATTGCACATACGTACCCCTGTTT
GTACTTCAGTACCCTTGATTGTAAATACGTGCCCCTATTTATACTTAGGTACCCC
Found at i:18310377 original size:25 final size:25
Alignment explanation
Indices: 18310349--18310414 Score: 78
Period size: 25 Copynumber: 2.6 Consensus size: 25
18310339 GCTTGCTGAC
*
18310349 TTACAGCTCGTGAGAGCATACCAAT
1 TTACAGCTCGTGAGAGAATACCAAT
* * *
18310374 TTACAGCTCATGAAAGAATACCGAT
1 TTACAGCTCGTGAGAGAATACCAAT
* *
18310399 TTACAGGTCGAGAGAG
1 TTACAGCTCGTGAGAG
18310415 TATAACGATT
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
25 33 1.00
ACGTcount: A:0.35, C:0.20, G:0.23, T:0.23
Consensus pattern (25 bp):
TTACAGCTCGTGAGAGAATACCAAT
Found at i:18317637 original size:25 final size:25
Alignment explanation
Indices: 18317572--18317641 Score: 79
Period size: 25 Copynumber: 2.8 Consensus size: 25
18317562 GCGGACACAC
*
18317572 CACAGCTCGTATGAGCTTACCAATT
1 CACAGCTCGTATGAGCATACCAATT
* * * *
18317597 TACAACTCG-AGAGAGCATACCGATT
1 CACAGCTCGTA-TGAGCATACCAATT
18317622 CACAGCTCGTATGAGCATAC
1 CACAGCTCGTATGAGCATAC
18317642 ATGTACAAGA
Statistics
Matches: 35, Mismatches: 8, Indels: 4
0.74 0.17 0.09
Matches are distributed among these distances:
24 1 0.03
25 33 0.94
26 1 0.03
ACGTcount: A:0.31, C:0.27, G:0.19, T:0.23
Consensus pattern (25 bp):
CACAGCTCGTATGAGCATACCAATT
Found at i:18321934 original size:27 final size:27
Alignment explanation
Indices: 18321894--18321964 Score: 90
Period size: 27 Copynumber: 2.6 Consensus size: 27
18321884 CATTTCGACC
* *
18321894 CACAGCTCGAGTGAGCAAGCTTC-TATT
1 CACAGCTCGTGTGAGCAAGC-CCATATT
*
18321921 CACAGATCGTGTGAGCAAGCCCATATT
1 CACAGCTCGTGTGAGCAAGCCCATATT
*
18321948 CACAGCTCATGTGAGCA
1 CACAGCTCGTGTGAGCA
18321965 TTTTGATCCA
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
26 1 0.03
27 37 0.97
ACGTcount: A:0.28, C:0.27, G:0.23, T:0.23
Consensus pattern (27 bp):
CACAGCTCGTGTGAGCAAGCCCATATT
Found at i:18330655 original size:16 final size:16
Alignment explanation
Indices: 18330631--18330661 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
18330621 CACTATAGTA
*
18330631 TCAGTATCTAGAGTTC
1 TCAGAATCTAGAGTTC
18330647 TCAGAATCTAGAGTT
1 TCAGAATCTAGAGTT
18330662 TCATAGTATA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.29, C:0.16, G:0.19, T:0.35
Consensus pattern (16 bp):
TCAGAATCTAGAGTTC
Found at i:18342243 original size:2 final size:2
Alignment explanation
Indices: 18342236--18342264 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
18342226 TTTAACTCTT
18342236 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
18342265 TTACTCTATG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:18343899 original size:15 final size:15
Alignment explanation
Indices: 18343877--18343957 Score: 81
Period size: 15 Copynumber: 5.4 Consensus size: 15
18343867 GTTCGTATAT
18343877 AGGGTTTGCACATAC
1 AGGGTTTGCACATAC
* *
18343892 AAGGTTTGCATATAC
1 AGGGTTTGCACATAC
**
18343907 AGGGTTCACACATAC
1 AGGGTTTGCACATAC
* * *
18343922 AGGGTTCGCATATTC
1 AGGGTTTGCACATAC
* *
18343937 AGGATTCGCACATAC
1 AGGGTTTGCACATAC
18343952 AGGGTT
1 AGGGTT
18343958 CACATGTAGG
Statistics
Matches: 53, Mismatches: 13, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
15 53 1.00
ACGTcount: A:0.28, C:0.20, G:0.25, T:0.27
Consensus pattern (15 bp):
AGGGTTTGCACATAC
Found at i:18343919 original size:30 final size:30
Alignment explanation
Indices: 18343885--18343958 Score: 103
Period size: 30 Copynumber: 2.5 Consensus size: 30
18343875 ATAGGGTTTG
* * *
18343885 CACATACAAGGTTTGCATATACAGGGTTCA
1 CACATACAGGGTTCGCATATACAGGATTCA
* *
18343915 CACATACAGGGTTCGCATATTCAGGATTCG
1 CACATACAGGGTTCGCATATACAGGATTCA
18343945 CACATACAGGGTTC
1 CACATACAGGGTTC
18343959 ACATGTAGGG
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 39 1.00
ACGTcount: A:0.30, C:0.23, G:0.22, T:0.26
Consensus pattern (30 bp):
CACATACAGGGTTCGCATATACAGGATTCA
Found at i:18343994 original size:24 final size:24
Alignment explanation
Indices: 18343965--18344188 Score: 138
Period size: 24 Copynumber: 9.5 Consensus size: 24
18343955 GTTCACATGT
*
18343965 AGGGTTCGAATAATAAATCACATA
1 AGGGTTCGCATAATAAATCACATA
*
18343989 AGGGTTCGCATATTAAA--ACATA
1 AGGGTTCGCATAATAAATCACATA
* **
18344011 TGGGGTTCGCATGCTAAATC-CATA
1 -AGGGTTCGCATAATAAATCACATA
* *
18344035 AGGGTTCGCATAATAAAACATATA
1 AGGGTTCGCATAATAAATCACATA
* * * *
18344059 GGGGGTTCACATACTAAAT-TCATA
1 -AGGGTTCGCATAATAAATCACATA
*
18344083 AAGGTTCGCATAATAAA--ACATA
1 AGGGTTCGCATAATAAATCACATA
* * * * *
18344105 TGGAGGTTTGCATACTAAATCATATT
1 -AG-GGTTCGCATAATAAATCACATA
* * * *
18344131 AGAGTTCGCATATTAAAACATATA
1 AGGGTTCGCATAATAAATCACATA
* **
18344155 GGGGTTCGCATACCAAATC-CATA
1 AGGGTTCGCATAATAAATCACATA
*
18344178 AGGGTTTGCAT
1 AGGGTTCGCAT
18344189 GTAGGTTCGC
Statistics
Matches: 150, Mismatches: 41, Indels: 19
0.71 0.20 0.09
Matches are distributed among these distances:
22 9 0.06
23 54 0.36
24 69 0.46
25 15 0.10
26 3 0.02
ACGTcount: A:0.38, C:0.15, G:0.19, T:0.28
Consensus pattern (24 bp):
AGGGTTCGCATAATAAATCACATA
Found at i:18344020 original size:23 final size:23
Alignment explanation
Indices: 18343990--18344167 Score: 144
Period size: 24 Copynumber: 7.5 Consensus size: 23
18343980 AATCACATAA
*
18343990 GGGTTCGCATATTAAAACATATG
1 GGGTTCGCATACTAAAACATATG
* * *
18344013 GGGTTCGCATGCTAAATCCATA-A
1 GGGTTCGCATACTAAA-ACATATG
*
18344036 GGGTTCGCATAATAAAACATATAGG
1 GGGTTCGCATACTAAAACATAT--G
* * *
18344061 GGGTTCACATACTAAATTCATA-A
1 GGGTTCGCATACTAAA-ACATATG
* *
18344084 AGGTTCGCATAATAAAACATATG
1 GGGTTCGCATACTAAAACATATG
* * *
18344107 GAGGTTTGCATACTAAATCATATTA
1 G-GGTTCGCATACTAAAACATA-TG
* *
18344132 GAGTTCGCATATTAAAACATATAG
1 GGGTTCGCATACTAAAACATAT-G
18344156 GGGTTCGCATAC
1 GGGTTCGCATAC
18344168 CAAATCCATA
Statistics
Matches: 117, Mismatches: 29, Indels: 17
0.72 0.18 0.10
Matches are distributed among these distances:
22 8 0.07
23 42 0.36
24 47 0.40
25 16 0.14
26 4 0.03
ACGTcount: A:0.37, C:0.15, G:0.20, T:0.29
Consensus pattern (23 bp):
GGGTTCGCATACTAAAACATATG
Found at i:18344083 original size:48 final size:46
Alignment explanation
Indices: 18343966--18344188 Score: 268
Period size: 48 Copynumber: 4.7 Consensus size: 46
18343956 TTCACATGTA
* * *
18343966 GGGTTCGAATAATAAATCACATAAGGGTTCGCATATTAAAACATATG
1 GGGTTCGCATACTAAATC-CATAAGGGTTCGCATAATAAAACATATG
*
18344013 GGGTTCGCATGCTAAATCCATAAGGGTTCGCATAATAAAACATATAGG
1 GGGTTCGCATACTAAATCCATAAGGGTTCGCATAATAAAACATAT--G
* * *
18344061 GGGTTCACATACTAAATTCATAAAGGTTCGCATAATAAAACATATG
1 GGGTTCGCATACTAAATCCATAAGGGTTCGCATAATAAAACATATG
* * *
18344107 GAGGTTTGCATACTAAAT-CATATTAGAGTTCGCATATTAAAACATATAG
1 G-GGTTCGCATACTAAATCCATA--AGGGTTCGCATAATAAAACATAT-G
* *
18344156 GGGTTCGCATACCAAATCCATAAGGGTTTGCAT
1 GGGTTCGCATACTAAATCCATAAGGGTTCGCAT
18344189 GTAGGTTCGC
Statistics
Matches: 152, Mismatches: 17, Indels: 14
0.83 0.09 0.08
Matches are distributed among these distances:
46 32 0.21
47 38 0.25
48 76 0.50
49 6 0.04
ACGTcount: A:0.37, C:0.15, G:0.19, T:0.28
Consensus pattern (46 bp):
GGGTTCGCATACTAAATCCATAAGGGTTCGCATAATAAAACATATG
Found at i:18344630 original size:17 final size:16
Alignment explanation
Indices: 18344585--18344636 Score: 50
Period size: 17 Copynumber: 3.1 Consensus size: 16
18344575 TTGCAATAAG
18344585 ATTAGAAATTAATTTAGA
1 ATTAG-AATTAATTTA-A
**
18344603 ATTAGGGTTAATTTAA
1 ATTAGAATTAATTTAA
*
18344619 ATTAAGAATTAAATTAA
1 ATT-AGAATTAATTTAA
18344636 A
1 A
18344637 ATATAGTTTT
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
16 4 0.14
17 19 0.68
18 5 0.18
ACGTcount: A:0.50, C:0.00, G:0.12, T:0.38
Consensus pattern (16 bp):
ATTAGAATTAATTTAA
Found at i:18346534 original size:36 final size:36
Alignment explanation
Indices: 18346494--18346566 Score: 121
Period size: 36 Copynumber: 2.0 Consensus size: 36
18346484 AATAGCTTTC
18346494 TATATTATAGGAAGTAAAGGGTGAAT-AGGAGTAGTT
1 TATATTATAGGAAGTAAAGGGTG-ATCAGGAGTAGTT
*
18346530 TATATTATAGGAAGTAGAGGGTGATCAGGAGTAGTT
1 TATATTATAGGAAGTAAAGGGTGATCAGGAGTAGTT
18346566 T
1 T
18346567 TCCTATTTCA
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
35 2 0.06
36 33 0.94
ACGTcount: A:0.36, C:0.01, G:0.32, T:0.32
Consensus pattern (36 bp):
TATATTATAGGAAGTAAAGGGTGATCAGGAGTAGTT
Found at i:18353521 original size:4 final size:4
Alignment explanation
Indices: 18353514--18353551 Score: 60
Period size: 4 Copynumber: 9.8 Consensus size: 4
18353504 GGTTGGTATA
*
18353514 AAAG AAAG AAAG AAAG AAAG AAAG -AAG ATAG AAAG AAA
1 AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAA
18353552 ATGCACGGAT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
3 3 0.10
4 28 0.90
ACGTcount: A:0.74, C:0.00, G:0.24, T:0.03
Consensus pattern (4 bp):
AAAG
Found at i:18353946 original size:18 final size:17
Alignment explanation
Indices: 18353923--18353959 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 17
18353913 ATTTTTTTTA
*
18353923 TGATATATATATTTAATT
1 TGATATATAAATTT-ATT
18353941 TGATATATAAATTTATT
1 TGATATATAAATTTATT
18353958 TG
1 TG
18353960 TTTAAATCAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 5 0.28
18 13 0.72
ACGTcount: A:0.38, C:0.00, G:0.08, T:0.54
Consensus pattern (17 bp):
TGATATATAAATTTATT
Found at i:18357814 original size:9 final size:9
Alignment explanation
Indices: 18357740--18357824 Score: 86
Period size: 9 Copynumber: 9.4 Consensus size: 9
18357730 GTAGTGATTC
18357740 AATTCGGTT
1 AATTCGGTT
18357749 AATTCAGG-T
1 AATTC-GGTT
18357758 AATTCGGTT
1 AATTCGGTT
**
18357767 AATTCGGGG
1 AATTCGGTT
18357776 AA-TCAGGTT
1 AATTC-GGTT
*
18357785 AATTCAGTT
1 AATTCGGTT
*
18357794 AATACGAG-T
1 AATTCG-GTT
18357803 AATTCGGTT
1 AATTCGGTT
18357812 AATTCGGTT
1 AATTCGGTT
18357821 AATT
1 AATT
18357825 TTTAACCAAA
Statistics
Matches: 62, Mismatches: 8, Indels: 12
0.76 0.10 0.15
Matches are distributed among these distances:
8 5 0.08
9 52 0.84
10 5 0.08
ACGTcount: A:0.29, C:0.11, G:0.22, T:0.38
Consensus pattern (9 bp):
AATTCGGTT
Found at i:18372049 original size:6 final size:6
Alignment explanation
Indices: 18372040--18372069 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
18372030 AGGGAGATTT
*
18372040 AAATTA AAATTA AAATTG AAATTA AAATTA
1 AAATTA AAATTA AAATTA AAATTA AAATTA
18372070 TCAAAAGAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.33
Consensus pattern (6 bp):
AAATTA
Found at i:18382365 original size:20 final size:19
Alignment explanation
Indices: 18382318--18382365 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 19
18382308 TTTAGGGTTT
18382318 GGTTAAAAGAGAGTTTAAA
1 GGTTAAAAGAGAGTTTAAA
* * *
18382337 AGTTAAAAAGGGAGTTTTGAA
1 GGTT-AAAAGAGAG-TTTAAA
18382358 GGTTAAAA
1 GGTTAAAA
18382366 TCCAGGTACA
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
19 3 0.13
20 12 0.52
21 8 0.35
ACGTcount: A:0.46, C:0.00, G:0.27, T:0.27
Consensus pattern (19 bp):
GGTTAAAAGAGAGTTTAAA
Found at i:18382403 original size:40 final size:40
Alignment explanation
Indices: 18382359--18382520 Score: 324
Period size: 40 Copynumber: 4.0 Consensus size: 40
18382349 AGTTTTGAAG
18382359 GTTAAAATCCAGGTACAATGCAGTTAAAAGTCAACATGTT
1 GTTAAAATCCAGGTACAATGCAGTTAAAAGTCAACATGTT
18382399 GTTAAAATCCAGGTACAATGCAGTTAAAAGTCAACATGTT
1 GTTAAAATCCAGGTACAATGCAGTTAAAAGTCAACATGTT
18382439 GTTAAAATCCAGGTACAATGCAGTTAAAAGTCAACATGTT
1 GTTAAAATCCAGGTACAATGCAGTTAAAAGTCAACATGTT
18382479 GTTAAAATCCAGGTACAATGCAGTTAAAAGTCAACATGTT
1 GTTAAAATCCAGGTACAATGCAGTTAAAAGTCAACATGTT
18382519 GT
1 GT
18382521 GTAATAGGGT
Statistics
Matches: 122, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 122 1.00
ACGTcount: A:0.40, C:0.15, G:0.18, T:0.28
Consensus pattern (40 bp):
GTTAAAATCCAGGTACAATGCAGTTAAAAGTCAACATGTT
Found at i:18382404 original size:18 final size:18
Alignment explanation
Indices: 18382381--18382485 Score: 70
Period size: 18 Copynumber: 5.4 Consensus size: 18
18382371 GTACAATGCA
18382381 GTTAAAAGTCAACATGTT
1 GTTAAAAGTCAACATGTT
**
18382399 GTTAAAA-TCCAGGTACAATGCA
1 GTTAAAAGT-CA---AC-ATGTT
18382421 GTTAAAAGTCAACATGTT
1 GTTAAAAGTCAACATGTT
**
18382439 GTTAAAA-TCCAGGTACAATGCA
1 GTTAAAAGT-CA---AC-ATGTT
18382461 GTTAAAAGTCAACATGTT
1 GTTAAAAGTCAACATGTT
18382479 GTTAAAA
1 GTTAAAA
18382486 TCCAGGTACA
Statistics
Matches: 67, Mismatches: 8, Indels: 24
0.68 0.08 0.24
Matches are distributed among these distances:
17 2 0.03
18 31 0.46
19 4 0.06
21 4 0.06
22 24 0.36
23 2 0.03
ACGTcount: A:0.41, C:0.13, G:0.17, T:0.29
Consensus pattern (18 bp):
GTTAAAAGTCAACATGTT
Found at i:18396513 original size:43 final size:41
Alignment explanation
Indices: 18396435--18396555 Score: 104
Period size: 40 Copynumber: 2.9 Consensus size: 41
18396425 GAAACACATA
*
18396435 TATCACATACAATGCCATATCTCAGATATGGTCTTACATGT
1 TATCACATACAATGCCATATCCCAGATATGGTCTTACATGT
* * *
18396476 TATCACATATCAATGCCTCTGTCCCAGATA-GGATCTTACACG-
1 TATCACATA-CAATGCC-ATATCCCAGATATGG-TCTTACATGT
* * * **
18396518 -ATCAAATACGATGCCAGTGTCCCAGGCATGGTCTTACA
1 TATCACATACAATGCCA-TATCCCAGATATGGTCTTACA
18396556 CGAAAACAGA
Statistics
Matches: 66, Mismatches: 9, Indels: 11
0.77 0.10 0.13
Matches are distributed among these distances:
40 22 0.33
41 18 0.27
42 9 0.14
43 17 0.26
ACGTcount: A:0.30, C:0.26, G:0.16, T:0.29
Consensus pattern (41 bp):
TATCACATACAATGCCATATCCCAGATATGGTCTTACATGT
Found at i:18405997 original size:27 final size:27
Alignment explanation
Indices: 18405967--18406216 Score: 220
Period size: 27 Copynumber: 9.3 Consensus size: 27
18405957 TATAACAGTC
* * **
18405967 ATTTCACCCTTCAAGGGTATTTTAATA
1 ATTTTACCCTTCGAGGGTATTTCGATA
**
18405994 ATTTTACCCTTCG-GAGGTATTTCGGCA
1 ATTTTACCCTTCGAG-GGTATTTCGATA
*
18406021 ATTTTACCCTTCGAGGGTACTTC-AGTA
1 ATTTTACCCTTCGAGGGTATTTCGA-TA
* * * * *
18406048 ATTTCAACCTTCGAGGTTATTTTGGTA
1 ATTTTACCCTTCGAGGGTATTTCGATA
* *
18406075 ATTTTACCCATCGAGGGTACTTCGATA
1 ATTTTACCCTTCGAGGGTATTTCGATA
*
18406102 ATTTTACCCATCGAGGGTATTTCGATA
1 ATTTTACCCTTCGAGGGTATTTCGATA
* *
18406129 ATTTTACCAATT-GAAGGTATTTCGATA
1 ATTTTACC-CTTCGAGGGTATTTCGATA
* * * * *
18406156 ATTTTACACATCTAGGGTATTTTGGTA
1 ATTTTACCCTTCGAGGGTATTTCGATA
* *
18406183 ATTTTATCCATCGAGGGTATTTC-AGTA
1 ATTTTACCCTTCGAGGGTATTTCGA-TA
18406210 ATTTTAC
1 ATTTTAC
18406217 AACCTTCTCA
Statistics
Matches: 177, Mismatches: 39, Indels: 14
0.77 0.17 0.06
Matches are distributed among these distances:
26 2 0.01
27 173 0.98
28 2 0.01
ACGTcount: A:0.26, C:0.17, G:0.17, T:0.40
Consensus pattern (27 bp):
ATTTTACCCTTCGAGGGTATTTCGATA
Found at i:18406038 original size:54 final size:54
Alignment explanation
Indices: 18405967--18406216 Score: 243
Period size: 54 Copynumber: 4.6 Consensus size: 54
18405957 TATAACAGTC
* * * * *
18405967 ATTTCACCCTTCAAGGGTATTTTAATAATTTTACCCTTCG-GAGGTATTTCGGCA
1 ATTTTACCCTTCGAGGGTATTTCAATAATTTTACCCATCGAG-GGTATTTCGGTA
* * * * * * *
18406021 ATTTTACCCTTCGAGGGTACTTCAGTAATTTCAACCTTCGAGGTTATTTTGGTA
1 ATTTTACCCTTCGAGGGTATTTCAATAATTTTACCCATCGAGGGTATTTCGGTA
* * * *
18406075 ATTTTACCCATCGAGGGTACTTCGATAATTTTACCCATCGAGGGTATTTCGATA
1 ATTTTACCCTTCGAGGGTATTTCAATAATTTTACCCATCGAGGGTATTTCGGTA
* * * * * *
18406129 ATTTTACCAATT-GAAGGTATTTCGATAATTTTACACATCTAGGGTATTTTGGTA
1 ATTTTACC-CTTCGAGGGTATTTCAATAATTTTACCCATCGAGGGTATTTCGGTA
* * *
18406183 ATTTTATCCATCGAGGGTATTTCAGTAATTTTAC
1 ATTTTACCCTTCGAGGGTATTTCAATAATTTTAC
18406217 AACCTTCTCA
Statistics
Matches: 160, Mismatches: 33, Indels: 6
0.80 0.17 0.03
Matches are distributed among these distances:
53 1 0.01
54 157 0.98
55 2 0.01
ACGTcount: A:0.26, C:0.17, G:0.17, T:0.40
Consensus pattern (54 bp):
ATTTTACCCTTCGAGGGTATTTCAATAATTTTACCCATCGAGGGTATTTCGGTA
Found at i:18406105 original size:81 final size:80
Alignment explanation
Indices: 18405962--18406223 Score: 262
Period size: 81 Copynumber: 3.2 Consensus size: 80
18405952 AGGGGTATAA
* * * * * *
18405962 CAGTCATTTCACCCTTCAAGGGTATTTTAATAATTTTACCCTTCG-GAGGTATTTCGGCAATTTT
1 CAGTAATTTCAACCTTCGA-GGTATTTTGATAATTTTACCCATCGAG-GGTATTTCGGTAATTTT
* *
18406026 ACCCTTCGAGGGTACTT
64 ACCCATCGAGGGTATTT
* * *
18406043 CAGTAATTTCAACCTTCGAGGTTATTTTGGTAATTTTACCCATCGAGGGTACTTCGATAATTTTA
1 CAGTAATTTCAACCTTCGAGG-TATTTTGATAATTTTACCCATCGAGGGTATTTCGGTAATTTTA
18406108 CCCATCGAGGGTATTT
65 CCCATCGAGGGTATTT
* * * * *
18406124 C-GATAATTT-TACCAATT-GAAGGTATTTCGATAATTTTACACATCTAGGGTATTTTGGTAATT
1 CAG-TAATTTCAACC--TTCG-AGGTATTTTGATAATTTTACCCATCGAGGGTATTTCGGTAATT
*
18406186 TTATCCATCGAGGGTATTT
62 TTACCCATCGAGGGTATTT
18406205 CAGTAATTTTACAACCTTC
1 CAGTAA-TTT-CAACCTTC
18406224 TCAAAGGTCT
Statistics
Matches: 149, Mismatches: 21, Indels: 20
0.78 0.11 0.11
Matches are distributed among these distances:
80 6 0.04
81 128 0.86
82 12 0.08
84 3 0.02
ACGTcount: A:0.26, C:0.18, G:0.17, T:0.39
Consensus pattern (80 bp):
CAGTAATTTCAACCTTCGAGGTATTTTGATAATTTTACCCATCGAGGGTATTTCGGTAATTTTAC
CCATCGAGGGTATTT
Found at i:18409694 original size:17 final size:17
Alignment explanation
Indices: 18409672--18409707 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
18409662 TTGAAAACCT
*
18409672 TTCTTGCAATTTCAAAC
1 TTCTTGCAATTTAAAAC
*
18409689 TTCTTGCCATTTAAAAC
1 TTCTTGCAATTTAAAAC
18409706 TT
1 TT
18409708 GTACAAAACC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.28, C:0.22, G:0.06, T:0.44
Consensus pattern (17 bp):
TTCTTGCAATTTAAAAC
Found at i:18410727 original size:27 final size:27
Alignment explanation
Indices: 18410695--18410795 Score: 80
Period size: 27 Copynumber: 3.7 Consensus size: 27
18410685 TGACTTCCTA
*
18410695 GGGGTATAAT-AGTCATTTTACCCTAAG
1 GGGGTAT-ATCAGTAATTTTACCCTAAG
* **
18410722 GGGGTATTTCAGTAATTTTACCCTTCG
1 GGGGTATATCAGTAATTTTACCCTAAG
* * * **
18410749 GGGGTATTTCGGTAATTTCACCCTTCG
1 GGGGTATATCAGTAATTTTACCCTAAG
*
18410776 GGGGTATTTC-GATAATTTTA
1 GGGGTATATCAG-TAATTTTA
18410796 ACCATTGAGG
Statistics
Matches: 65, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
26 2 0.03
27 63 0.97
ACGTcount: A:0.22, C:0.16, G:0.24, T:0.39
Consensus pattern (27 bp):
GGGGTATATCAGTAATTTTACCCTAAG
Found at i:18410904 original size:27 final size:27
Alignment explanation
Indices: 18410723--18410904 Score: 210
Period size: 27 Copynumber: 6.7 Consensus size: 27
18410713 TACCCTAAGG
* *
18410723 GGGTATTTC-AGTAATTTTACCCTTCGG
1 GGGTATTTCGA-TAATTTTACCCATCGA
* * * *
18410750 GGGTATTTCGGTAATTTCACCCTTCGG
1 GGGTATTTCGATAATTTTACCCATCGA
* *
18410777 GGGTATTTCGATAATTTTAACCATTGA
1 GGGTATTTCGATAATTTTACCCATCGA
* *
18410804 GGGTACTTTAG-TAATTTTACTCATCGA
1 GGGTA-TTTCGATAATTTTACCCATCGA
18410831 GGGTATTTC-AGTAATTTTACCCATCGA
1 GGGTATTTCGA-TAATTTTACCCATCGA
18410858 GGGTATTTCTG-TAATTTTACCCATCGA
1 GGGTATTTC-GATAATTTTACCCATCGA
18410885 GGGTATTTCGATAATTTTAC
1 GGGTATTTCGATAATTTTAC
18410905 AACCTTCCCG
Statistics
Matches: 134, Mismatches: 14, Indels: 14
0.83 0.09 0.09
Matches are distributed among these distances:
26 4 0.03
27 126 0.94
28 4 0.03
ACGTcount: A:0.23, C:0.16, G:0.20, T:0.40
Consensus pattern (27 bp):
GGGTATTTCGATAATTTTACCCATCGA
Found at i:18414441 original size:43 final size:41
Alignment explanation
Indices: 18414365--18414490 Score: 128
Period size: 41 Copynumber: 3.0 Consensus size: 41
18414355 AAAACACATA
* * * * *
18414365 AATCACATACAATACC-ATATCCCAGATATGGTCTTACATG
1 AATCACATACGATGCCAATGTCCCAGACATGGTCTTACACG
* ** *
18414405 TTATCACATATCGATGCCTCTGTCCCAGACAGGGTCTTACACG
1 -AATCACATA-CGATGCCAATGTCCCAGACATGGTCTTACACG
* *
18414448 AATCATATACGATGCCAATGTCCCAAACATGGTCTTACACG
1 AATCACATACGATGCCAATGTCCCAGACATGGTCTTACACG
18414489 AA
1 AA
18414491 ATCATACCTC
Statistics
Matches: 69, Mismatches: 14, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
41 38 0.55
42 12 0.17
43 19 0.28
ACGTcount: A:0.33, C:0.27, G:0.14, T:0.26
Consensus pattern (41 bp):
AATCACATACGATGCCAATGTCCCAGACATGGTCTTACACG
Found at i:18415598 original size:15 final size:15
Alignment explanation
Indices: 18415578--18415607 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
18415568 TAAATCACGA
18415578 AATTTTCACACATAT
1 AATTTTCACACATAT
18415593 AATTTTCACACATAT
1 AATTTTCACACATAT
18415608 CAAATAACAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.40, C:0.20, G:0.00, T:0.40
Consensus pattern (15 bp):
AATTTTCACACATAT
Found at i:18418757 original size:28 final size:28
Alignment explanation
Indices: 18418725--18418803 Score: 140
Period size: 28 Copynumber: 2.8 Consensus size: 28
18418715 TTTAGGCTAG
*
18418725 TAGGGTTACTCACCCCTAAGGTAAGACC
1 TAGGGTTACTCACCCCTAAGGCAAGACC
18418753 TAGGGTTACTCACCCCTAAGGCAAGACC
1 TAGGGTTACTCACCCCTAAGGCAAGACC
*
18418781 TAGGGTTACTCATCCCTAAGGCA
1 TAGGGTTACTCACCCCTAAGGCA
18418804 CTATATGTCT
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 49 1.00
ACGTcount: A:0.28, C:0.29, G:0.22, T:0.22
Consensus pattern (28 bp):
TAGGGTTACTCACCCCTAAGGCAAGACC
Found at i:18425679 original size:16 final size:16
Alignment explanation
Indices: 18425646--18425675 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
18425636 CAATCAAAAA
18425646 CATTCATATATTATAT
1 CATTCATATATTATAT
18425662 CATTCA-ATATTATA
1 CATTCATATATTATA
18425676 ATCACATCGT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.40, C:0.13, G:0.00, T:0.47
Consensus pattern (16 bp):
CATTCATATATTATAT
Found at i:18427920 original size:23 final size:24
Alignment explanation
Indices: 18427871--18427922 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
18427861 GCGTACTAAA
* *
18427871 ACAACAAATCTTACCAAAGTAAGT
1 ACAACAAATCGTACCAAAATAAGT
18427895 ACAACAAATCGT-CCAATAATAA-T
1 ACAACAAATCGTACCAA-AATAAGT
18427918 ACAAC
1 ACAAC
18427923 CATATGTGTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 10 0.40
24 15 0.60
ACGTcount: A:0.52, C:0.23, G:0.06, T:0.19
Consensus pattern (24 bp):
ACAACAAATCGTACCAAAATAAGT
Found at i:18442803 original size:24 final size:25
Alignment explanation
Indices: 18442751--18442824 Score: 80
Period size: 24 Copynumber: 3.0 Consensus size: 25
18442741 TCATTAGGGA
*
18442751 TTACCGATTCTCAGCTCGTATGAGC
1 TTACCGATTCGCAGCTCGTATGAGC
*
18442776 TTACCGATT-GCAGCTCGTGA-GAGT
1 TTACCGATTCGCAGCTCGT-ATGAGC
* * *
18442800 TTACCGATTCTCAGCTTGTTTGAGC
1 TTACCGATTCGCAGCTCGTATGAGC
18442825 CTACTAATTT
Statistics
Matches: 40, Mismatches: 6, Indels: 6
0.77 0.12 0.12
Matches are distributed among these distances:
24 20 0.50
25 20 0.50
ACGTcount: A:0.19, C:0.24, G:0.23, T:0.34
Consensus pattern (25 bp):
TTACCGATTCGCAGCTCGTATGAGC
Found at i:18442824 original size:49 final size:50
Alignment explanation
Indices: 18442751--18442874 Score: 144
Period size: 50 Copynumber: 2.5 Consensus size: 50
18442741 TCATTAGGGA
* * * * *
18442751 TTACCGATTCTCAGCTCGTATGAGCTTACCGA-TTGCAGCTCGTGAGAGT
1 TTACCGATTCTCAGCTTGTATGAGCCTACCAATTTACAGCTCGTGAGAGG
* * *
18442800 TTACCGATTCTCAGCTTGTTTGAGCCTACTAATTTATAGCTCGTGAGAGG
1 TTACCGATTCTCAGCTTGTATGAGCCTACCAATTTACAGCTCGTGAGAGG
*
18442850 ATACCGATTCAT-AGCTTGTATGAGC
1 TTACCGATTC-TCAGCTTGTATGAGC
18442875 ATACATGTAC
Statistics
Matches: 63, Mismatches: 10, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
49 27 0.43
50 35 0.56
51 1 0.02
ACGTcount: A:0.23, C:0.22, G:0.23, T:0.33
Consensus pattern (50 bp):
TTACCGATTCTCAGCTTGTATGAGCCTACCAATTTACAGCTCGTGAGAGG
Found at i:18442878 original size:25 final size:25
Alignment explanation
Indices: 18442801--18442878 Score: 61
Period size: 25 Copynumber: 3.1 Consensus size: 25
18442791 CGTGAGAGTT
* *
18442801 TACCGATTC-TCAGCTTGTTTGAGCC
1 TACCGATTCAT-AGCTTGTATGAGCA
** * * *
18442826 TACTAATTTATAGCTCGTGA-GAGGA
1 TACCGATTCATAGCTTGT-ATGAGCA
18442851 TACCGATTCATAGCTTGTATGAGCA
1 TACCGATTCATAGCTTGTATGAGCA
18442876 TAC
1 TAC
18442879 ATGTACAGGA
Statistics
Matches: 38, Mismatches: 12, Indels: 6
0.68 0.21 0.11
Matches are distributed among these distances:
24 1 0.03
25 36 0.95
26 1 0.03
ACGTcount: A:0.26, C:0.21, G:0.21, T:0.33
Consensus pattern (25 bp):
TACCGATTCATAGCTTGTATGAGCA
Found at i:18443066 original size:30 final size:30
Alignment explanation
Indices: 18443027--18443088 Score: 76
Period size: 31 Copynumber: 2.1 Consensus size: 30
18443017 TACATGAAAT
18443027 ACATGGAAAT-GAT-ATTACATGATATATTGAA
1 ACATGGAAATGGATGA-TACATG-TATA-TGAA
18443058 ACAT-GAAATGGATGATACATGTATATGAA
1 ACATGGAAATGGATGATACATGTATATGAA
18443087 AC
1 AC
18443089 TTTTTTAGTG
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
29 6 0.21
30 9 0.31
31 13 0.45
32 1 0.03
ACGTcount: A:0.45, C:0.08, G:0.18, T:0.29
Consensus pattern (30 bp):
ACATGGAAATGGATGATACATGTATATGAA
Found at i:18445243 original size:51 final size:50
Alignment explanation
Indices: 18445121--18445304 Score: 162
Period size: 51 Copynumber: 3.7 Consensus size: 50
18445111 AAAGTGATGG
* * *
18445121 TCACGTGTGTAGTACTAT-TGCAGGCTACTACGTC-TACCAGAAT-G-ATAGG
1 TCACATGTGTAGTACTATGTGCAGGCTACTATG-CGTACCA-AATAGTAT-GA
*
18445170 TCGCATGTGTAGTACTATGTGCAGGCTACTATGCGTACCAAATAGCT-TCGA
1 TCACATGTGTAGTACTATGTGCAGGCTACTATGCGTACCAAATAG-TAT-GA
* * * * * * * *
18445221 TCACGTGTGTAATACTATGTGCAAGCTACTAAGTGTATCAGATAGTGATGG
1 TCACATGTGTAGTACTATGTGCAGGCTACTATGCGTACCAAATAGT-ATGA
*
18445272 TCACATGTGCAGTACTATGTGCAGGCTACTATG
1 TCACATGTGTAGTACTATGTGCAGGCTACTATG
18445305 TGAACCGGTA
Statistics
Matches: 109, Mismatches: 19, Indels: 12
0.78 0.14 0.09
Matches are distributed among these distances:
49 20 0.18
50 20 0.18
51 68 0.62
52 1 0.01
ACGTcount: A:0.27, C:0.19, G:0.24, T:0.30
Consensus pattern (50 bp):
TCACATGTGTAGTACTATGTGCAGGCTACTATGCGTACCAAATAGTATGA
Found at i:18445298 original size:102 final size:100
Alignment explanation
Indices: 18445121--18445304 Score: 271
Period size: 102 Copynumber: 1.8 Consensus size: 100
18445111 AAAGTGATGG
* * * * *
18445121 TCACGTGTGTAGTACTATTGCAGGCTACTACGTCTACCAGAATGATAGGTCGCATGTGTAGTACT
1 TCACGTGTGTAATACTATTGCAAGCTACTAAGTCTACCAGAATGATAGGTCACATGTGCAGTACT
18445186 ATGTGCAGGCTACTATGCGTACCAAATAGCTTCGA
66 ATGTGCAGGCTACTATGCGTACCAAATAGCTTCGA
* *
18445221 TCACGTGTGTAATACTATGTGCAAGCTACTAAGTGTATCAGATAGTGAT-GGTCACATGTGCAGT
1 TCACGTGTGTAATACTAT-TGCAAGCTACTAAGTCTACCAGA-A-TGATAGGTCACATGTGCAGT
18445285 ACTATGTGCAGGCTACTATG
63 ACTATGTGCAGGCTACTATG
18445305 TGAACCGGTA
Statistics
Matches: 74, Mismatches: 7, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
100 17 0.23
101 19 0.26
102 34 0.46
103 4 0.05
ACGTcount: A:0.27, C:0.19, G:0.24, T:0.30
Consensus pattern (100 bp):
TCACGTGTGTAATACTATTGCAAGCTACTAAGTCTACCAGAATGATAGGTCACATGTGCAGTACT
ATGTGCAGGCTACTATGCGTACCAAATAGCTTCGA
Found at i:18453460 original size:40 final size:40
Alignment explanation
Indices: 18453349--18453490 Score: 155
Period size: 40 Copynumber: 3.5 Consensus size: 40
18453339 TATGTGAATT
* * *
18453349 TACTTTGGTA-CCCTGAATGCACATACGTGCCCTTATTTG
1 TACTTCGGTACCCCTGAATGCACATACGTGCCCCTGTTTG
* * * *
18453388 TACTTTGGTACCCCCT-AATTACACATATGTGCCCCTGTTGG
1 TACTTCGGTA-CCCCTGAA-TGCACATACGTGCCCCTGTTTG
18453429 TACTTCGGTACCCCTGAATGC-CTATACGTGCCCCTGTTTG
1 TACTTCGGTACCCCTGAATGCAC-ATACGTGCCCCTGTTTG
* *
18453469 TACTTCAGTATCCCTGAATGCA
1 TACTTCGGTACCCCTGAATGCA
18453491 TTTTAATGTC
Statistics
Matches: 86, Mismatches: 11, Indels: 10
0.80 0.10 0.09
Matches are distributed among these distances:
39 11 0.13
40 43 0.50
41 32 0.37
ACGTcount: A:0.20, C:0.29, G:0.18, T:0.34
Consensus pattern (40 bp):
TACTTCGGTACCCCTGAATGCACATACGTGCCCCTGTTTG
Found at i:18468874 original size:16 final size:16
Alignment explanation
Indices: 18468850--18468883 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
18468840 ATTAAATCCT
18468850 AATTACTAAAGAAATA
1 AATTACTAAAGAAATA
* *
18468866 AATTCCTAAAGACATA
1 AATTACTAAAGAAATA
18468882 AA
1 AA
18468884 AAAAACAATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.59, C:0.12, G:0.06, T:0.24
Consensus pattern (16 bp):
AATTACTAAAGAAATA
Found at i:18489728 original size:16 final size:18
Alignment explanation
Indices: 18489709--18489743 Score: 56
Period size: 16 Copynumber: 2.1 Consensus size: 18
18489699 TTGAGAAATA
18489709 TGAATG-ATATG-ATTAT
1 TGAATGAATATGAATTAT
18489725 TGAATGAATATGAATTAT
1 TGAATGAATATGAATTAT
18489743 T
1 T
18489744 ACAGTTTACG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.35
17 5 0.29
18 6 0.35
ACGTcount: A:0.40, C:0.00, G:0.17, T:0.43
Consensus pattern (18 bp):
TGAATGAATATGAATTAT
Found at i:18491087 original size:27 final size:27
Alignment explanation
Indices: 18491017--18491415 Score: 394
Period size: 27 Copynumber: 14.9 Consensus size: 27
18491007 CGAGACCCCA
* * *
18491017 AAATACACTCATAGGGTAAAATGATCG
1 AAATACCCCCATAGGGTAAAATGACCG
*
18491044 AAATA-CCCCATAGGGTAAAATGATCG
1 AAATACCCCCATAGGGTAAAATGACCG
* *
18491070 AAATACCCCCATAGGGTAAATTGACTG
1 AAATACCCCCATAGGGTAAAATGACCG
** * *
18491097 AAATA-CCGTATAGGGTAAAATAATCG
1 AAATACCCCCATAGGGTAAAATGACCG
* * *
18491123 AAATACTCCCATAGGGTAAAAT-AACT
1 AAATACCCCCATAGGGTAAAATGACCG
* *
18491149 AATATACCCTCATAGGGAAAAATGACCG
1 AA-ATACCCCCATAGGGTAAAATGACCG
* *
18491177 AAATA-CCCCATAAGGTAGAATGACCG
1 AAATACCCCCATAGGGTAAAATGACCG
** * *
18491203 AAATATGCCCATAGAGTAAAATGAAC-
1 AAATACCCCCATAGGGTAAAATGACCG
*
18491229 AAATACCCCCATAGGGTAAAATAACCG
1 AAATACCCCCATAGGGTAAAATGACCG
** *
18491256 AAATACCCCTGTAGGGTAAAATGATCG
1 AAATACCCCCATAGGGTAAAATGACCG
* * * * *
18491283 AAATACCCCCGTAAGGTAGAATGATCA
1 AAATACCCCCATAGGGTAAAATGACCG
* * *
18491310 AAATACCCCTATAGGATAAAATGACAG
1 AAATACCCCCATAGGGTAAAATGACCG
** * *
18491337 TTATACCCGCGTAGGGTAAAATGACCG
1 AAATACCCCCATAGGGTAAAATGACCG
* * *
18491364 AAATACCCCCGTAAGGTAGAATGACCG
1 AAATACCCCCATAGGGTAAAATGACCG
18491391 AAATACCCCCATAGGGTAAAATGAC
1 AAATACCCCCATAGGGTAAAATGAC
18491416 AGTTATACCC
Statistics
Matches: 300, Mismatches: 66, Indels: 12
0.79 0.17 0.03
Matches are distributed among these distances:
26 91 0.30
27 205 0.68
28 4 0.01
ACGTcount: A:0.42, C:0.20, G:0.18, T:0.19
Consensus pattern (27 bp):
AAATACCCCCATAGGGTAAAATGACCG
Found at i:18491100 original size:53 final size:53
Alignment explanation
Indices: 18491017--18491415 Score: 378
Period size: 53 Copynumber: 7.5 Consensus size: 53
18491007 CGAGACCCCA
* *
18491017 AAATACACTCATAGGGTAAAATGA-TCGAAATACCCCATAGGGTAAAATGATCG
1 AAATACCCCCATAGGGTAAAATGACT-GAAATACCCCATAGGGTAAAATGATCG
* ** *
18491070 AAATACCCCCATAGGGTAAATTGACTGAAATACCGTATAGGGTAAAATAATCG
1 AAATACCCCCATAGGGTAAAATGACTGAAATACCCCATAGGGTAAAATGATCG
* * * *
18491123 AAATACTCCCATAGGGTAAAATAACT-AATATACCCTCATAGGGAAAAATGACCG
1 AAATACCCCCATAGGGTAAAATGACTGAA-ATACCC-CATAGGGTAAAATGATCG
* * * * * *
18491177 AAATA-CCCCATAAGGTAGAATGACCGAAATATGCCCATAGAGTAAAATGAAC-
1 AAATACCCCCATAGGGTAAAATGACTGAAATA-CCCCATAGGGTAAAATGATCG
* * *
18491229 AAATACCCCCATAGGGTAAAATAACCGAAATACCCCTGTAGGGTAAAATGATCG
1 AAATACCCCCATAGGGTAAAATGACTGAAATACCCC-ATAGGGTAAAATGATCG
* * * * *
18491283 AAATACCCCCGTAAGGTAGAATGA-TCAAAATACCCCTATAGGATAAAATGA-CAG
1 AAATACCCCCATAGGGTAAAATGACT-GAAATACCCC-ATAGGGTAAAATGATC-G
** * * * * * * *
18491337 TTATACCCGCGTAGGGTAAAATGACCGAAATACCCCCGTAAGGTAGAATGACCG
1 AAATACCCCCATAGGGTAAAATGACTGAAATA-CCCCATAGGGTAAAATGATCG
18491391 AAATACCCCCATAGGGTAAAATGAC
1 AAATACCCCCATAGGGTAAAATGAC
18491416 AGTTATACCC
Statistics
Matches: 280, Mismatches: 53, Indels: 25
0.78 0.15 0.07
Matches are distributed among these distances:
52 10 0.04
53 142 0.51
54 123 0.44
55 5 0.02
ACGTcount: A:0.42, C:0.20, G:0.18, T:0.19
Consensus pattern (53 bp):
AAATACCCCCATAGGGTAAAATGACTGAAATACCCCATAGGGTAAAATGATCG
Found at i:18493100 original size:53 final size:54
Alignment explanation
Indices: 18493031--18493182 Score: 166
Period size: 53 Copynumber: 2.8 Consensus size: 54
18493021 CTTAAAGAGC
* * *
18493031 AAAATGACTGAAATACCCCTGATAGGTAAAATAACGAAAATACCCTCGATTGGT
1 AAAATGATTGAAATACCCCCGATAGGTAAAATAACGAAAATACCCTCGATGGGT
* * * * *
18493085 GAAA-GATTGAAATACCCCCGA-AGGGTAAAATGACTAAAATATCCTGGATGGGT
1 AAAATGATTGAAATACCCCCGATA-GGTAAAATAACGAAAATACCCTCGATGGGT
* * *
18493138 AAAATGATCGAAATACCCCCGATGGGTAAAATGATCG-AAATACCC
1 AAAATGATTGAAATACCCCCGATAGGTAAAAT-AACGAAAATACCC
18493183 CTAGGAGTTG
Statistics
Matches: 79, Mismatches: 15, Indels: 8
0.77 0.15 0.08
Matches are distributed among these distances:
52 1 0.01
53 43 0.54
54 34 0.43
55 1 0.01
ACGTcount: A:0.41, C:0.18, G:0.20, T:0.20
Consensus pattern (54 bp):
AAAATGATTGAAATACCCCCGATAGGTAAAATAACGAAAATACCCTCGATGGGT
Found at i:18493152 original size:80 final size:81
Alignment explanation
Indices: 18493000--18493183 Score: 196
Period size: 80 Copynumber: 2.3 Consensus size: 81
18492990 TTGCGATTCG
* *** * * *
18493000 TGGG-AAAATTATCGAAATACCCTTAAAGAGCAAAATGACTGAAATACCCCTGATAGGTAAAATA
1 TGGGTAAAATGATCGAAATACCCCCGAAGGGTAAAATGACTAAAATACCCCTGATAGGTAAAATA
*
18493064 ACGAAAATACCCTCGA
66 ACGAAAATACCCCCGA
* * * * *
18493080 TTGGTGAAA-GATTGAAATACCCCCGAAGGGTAAAATGACTAAAATA-TCCTGGATGGGTAAAAT
1 TGGGTAAAATGATCGAAATACCCCCGAAGGGTAAAATGACTAAAATACCCCT-GATAGGTAAAAT
*
18493143 GATCG-AAATACCCCCGA
65 -AACGAAAATACCCCCGA
18493160 TGGGTAAAATGATCGAAATACCCC
1 TGGGTAAAATGATCGAAATACCCC
18493184 TAGGAGTTGA
Statistics
Matches: 83, Mismatches: 17, Indels: 7
0.78 0.16 0.07
Matches are distributed among these distances:
79 3 0.04
80 61 0.73
81 19 0.23
ACGTcount: A:0.41, C:0.18, G:0.20, T:0.21
Consensus pattern (81 bp):
TGGGTAAAATGATCGAAATACCCCCGAAGGGTAAAATGACTAAAATACCCCTGATAGGTAAAATA
ACGAAAATACCCCCGA
Found at i:18493196 original size:27 final size:27
Alignment explanation
Indices: 18493031--18493183 Score: 143
Period size: 27 Copynumber: 5.7 Consensus size: 27
18493021 CTTAAAGAGC
* *
18493031 AAAATGA-CTGAAATACCCCTGATAGGT
1 AAAATGATC-GAAATACCCCCGATGGGT
* * *
18493058 AAAAT-AACGAAAATACCCTCGATTGGT
1 AAAATGATCG-AAATACCCCCGATGGGT
* * *
18493085 GAAA-GATTGAAATACCCCCGAAGGGT
1 AAAATGATCGAAATACCCCCGATGGGT
* * **
18493111 AAAATGA-CTAAAATATCCTGGATGGGT
1 AAAATGATC-GAAATACCCCCGATGGGT
18493138 AAAATGATCGAAATACCCCCGATGGGT
1 AAAATGATCGAAATACCCCCGATGGGT
18493165 AAAATGATCGAAATACCCC
1 AAAATGATCGAAATACCCC
18493184 TAGGAGTTGA
Statistics
Matches: 100, Mismatches: 20, Indels: 12
0.76 0.15 0.09
Matches are distributed among these distances:
26 19 0.19
27 80 0.80
28 1 0.01
ACGTcount: A:0.41, C:0.19, G:0.20, T:0.20
Consensus pattern (27 bp):
AAAATGATCGAAATACCCCCGATGGGT
Found at i:18496671 original size:50 final size:50
Alignment explanation
Indices: 18496598--18496793 Score: 185
Period size: 50 Copynumber: 3.8 Consensus size: 50
18496588 TCTTGTACTA
* * **
18496598 CCAATGCCATATCCCAGATATGGTCTTACATGGGAGTTCTCATATCGGTG
1 CCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGGTG
* *** * *
18496648 CCCATGCCATGTCCCAGACATGGTCTTATGGGGGACCTCTCATCTTGGTG
1 CCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGGTG
* * * * *
18496698 CCAACGCCATGTCCTAGACATGGTTTTACATAGGACCTCTCATAATCTCAATGATG
1 CCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCAT-A--TC---GGTG
* *
18496754 CCAATGCCATGTCCCAGACATGGTCTTCCATGGGATCTCT
1 CCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
18496794 TTACCCAAAT
Statistics
Matches: 113, Mismatches: 27, Indels: 6
0.77 0.18 0.04
Matches are distributed among these distances:
50 75 0.66
53 1 0.01
56 37 0.33
ACGTcount: A:0.22, C:0.28, G:0.21, T:0.29
Consensus pattern (50 bp):
CCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGGTG
Found at i:18497909 original size:11 final size:11
Alignment explanation
Indices: 18497893--18497925 Score: 57
Period size: 11 Copynumber: 3.0 Consensus size: 11
18497883 TTGTAGGCCA
*
18497893 TAAAAATATAG
1 TAAAAACATAG
18497904 TAAAAACATAG
1 TAAAAACATAG
18497915 TAAAAACATAG
1 TAAAAACATAG
18497926 ACACATGGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.64, C:0.06, G:0.09, T:0.21
Consensus pattern (11 bp):
TAAAAACATAG
Found at i:18513053 original size:27 final size:27
Alignment explanation
Indices: 18512801--18513042 Score: 313
Period size: 27 Copynumber: 9.0 Consensus size: 27
18512791 GCAATTGTCT
18512801 GAAATACCCCCGAAGGGTAAAATGACC
1 GAAATACCCCCGAAGGGTAAAATGACC
18512828 GAAATACCCCCGAAGGGTAAAATGACC
1 GAAATACCCCCGAAGGGTAAAATGACC
*
18512855 GAAATACCCCCGATGGGTAAAATGACC
1 GAAATACCCCCGAAGGGTAAAATGACC
* * * *
18512882 GAAATACTCCAGATGGGTAAAATGATC
1 GAAATACCCCCGAAGGGTAAAATGACC
* *
18512909 AAAATACCCCTGAAGGGTAAAATGACC
1 GAAATACCCCCGAAGGGTAAAATGACC
*
18512936 GAAATACCACCGAAGGGTAAAATGACC
1 GAAATACCCCCGAAGGGTAAAATGACC
*** * * *
18512963 GAAATACCCTTAAAAGGTAAAATGTCT
1 GAAATACCCCCGAAGGGTAAAATGACC
* * * *
18512990 GAAATAACCCCAAAGGATAAAATGATC
1 GAAATACCCCCGAAGGGTAAAATGACC
*
18513017 GAAATACCCCCGATGGGTAAAATGAC
1 GAAATACCCCCGAAGGGTAAAATGAC
18513043 TGTTATACCC
Statistics
Matches: 183, Mismatches: 32, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 183 1.00
ACGTcount: A:0.43, C:0.21, G:0.20, T:0.16
Consensus pattern (27 bp):
GAAATACCCCCGAAGGGTAAAATGACC
Found at i:18513192 original size:27 final size:27
Alignment explanation
Indices: 18513147--18513219 Score: 87
Period size: 26 Copynumber: 2.8 Consensus size: 27
18513137 ATAGAGGAAG
**
18513147 TATACTG-TACTGGTGGCTTTGCCACA
1 TATACTGTTACTGGCAGCTTTGCCACA
** *
18513173 TATACTGTTACTGGCAGCTTTGCTGCG
1 TATACTGTTACTGGCAGCTTTGCCACA
18513200 T-TACTGTTACTGGCAGCTTT
1 TATACTGTTACTGGCAGCTTT
18513220 ATTGCGATAT
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
26 26 0.63
27 15 0.37
ACGTcount: A:0.16, C:0.22, G:0.23, T:0.38
Consensus pattern (27 bp):
TATACTGTTACTGGCAGCTTTGCCACA
Found at i:18513225 original size:26 final size:26
Alignment explanation
Indices: 18513175--18513225 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 26
18513165 TTGCCACATA
*
18513175 TACTGTTACTGGCAGCTTTGCTGCGT
1 TACTGTTACTGGCAGCTTTACTGCGT
*
18513201 TACTGTTACTGGCAGCTTTATTGCG
1 TACTGTTACTGGCAGCTTTACTGCG
18513226 ATATTGGTGT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.14, C:0.22, G:0.25, T:0.39
Consensus pattern (26 bp):
TACTGTTACTGGCAGCTTTACTGCGT
Found at i:18514039 original size:28 final size:28
Alignment explanation
Indices: 18513999--18514104 Score: 149
Period size: 28 Copynumber: 3.8 Consensus size: 28
18513989 TGTTGGCTGG
18513999 ATTGGGCTAAGGCCCACACTATTTCTGT
1 ATTGGGCTAAGGCCCACACTATTTCTGT
*
18514027 ATTGGGCTAAGGCCCATACTATTTCTGT
1 ATTGGGCTAAGGCCCACACTATTTCTGT
* * * * *
18514055 ACTGGGCTAAGGCCTACACTGTTACTAT
1 ATTGGGCTAAGGCCCACACTATTTCTGT
*
18514083 ATCGGGCTAAGGCCCACACTAT
1 ATTGGGCTAAGGCCCACACTAT
18514105 ACTGTTACTG
Statistics
Matches: 67, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 67 1.00
ACGTcount: A:0.24, C:0.25, G:0.22, T:0.29
Consensus pattern (28 bp):
ATTGGGCTAAGGCCCACACTATTTCTGT
Found at i:18514110 original size:33 final size:34
Alignment explanation
Indices: 18514072--18514142 Score: 92
Period size: 33 Copynumber: 2.1 Consensus size: 34
18514062 TAAGGCCTAC
*
18514072 ACTGTTACT-ATATCGGGCTAAGGCCCACACTA-T
1 ACTGTTACTGA-ATAGGGCTAAGGCCCACACTATT
* *
18514105 ACTGTTACTGAATAGGGCTCAGGCCCAGACTATT
1 ACTGTTACTGAATAGGGCTAAGGCCCACACTATT
18514139 ACTG
1 ACTG
18514143 CATTTGTAGG
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
33 27 0.82
34 6 0.18
ACGTcount: A:0.27, C:0.25, G:0.21, T:0.27
Consensus pattern (34 bp):
ACTGTTACTGAATAGGGCTAAGGCCCACACTATT
Found at i:18519986 original size:23 final size:23
Alignment explanation
Indices: 18519960--18520036 Score: 64
Period size: 23 Copynumber: 3.7 Consensus size: 23
18519950 GGCCTTACAA
18519960 GTATTGTGA-TATATGCTTAAAT
1 GTATTGTGATTATATGCTTAAAT
*
18519982 GGTA-TGTAATTATATG-----A-
1 -GTATTGTGATTATATGCTTAAAT
18519999 GTATTGTGA-TATATGCTTAAAT
1 GTATTGTGATTATATGCTTAAAT
*
18520021 GTTTTGTGATTATATG
1 GTATTGTGATTATATG
18520037 AGTATTGTAA
Statistics
Matches: 42, Mismatches: 3, Indels: 18
0.67 0.05 0.29
Matches are distributed among these distances:
16 9 0.21
17 4 0.10
18 1 0.02
21 1 0.02
22 12 0.29
23 15 0.36
ACGTcount: A:0.30, C:0.03, G:0.21, T:0.47
Consensus pattern (23 bp):
GTATTGTGATTATATGCTTAAAT
Found at i:18520013 original size:39 final size:39
Alignment explanation
Indices: 18519959--18520097 Score: 206
Period size: 39 Copynumber: 3.6 Consensus size: 39
18519949 GGGCCTTACA
*
18519959 AGTATTGTGATATATGCTTAAATGGTATGTAATTATATG
1 AGTATTGTGATATATGCTTAAATGTTATGTAATTATATG
* *
18519998 AGTATTGTGATATATGCTTAAATGTTTTGTGATTATATG
1 AGTATTGTGATATATGCTTAAATGTTATGTAATTATATG
* *
18520037 AGTATTGTAATATATGCTTAAATTTTATGTAATTATATG
1 AGTATTGTGATATATGCTTAAATGTTATGTAATTATATG
* * *
18520076 TGTAATGTGATATATGCCTAAA
1 AGTATTGTGATATATGCTTAAA
18520098 AGTGAATATG
Statistics
Matches: 89, Mismatches: 11, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
39 89 1.00
ACGTcount: A:0.33, C:0.04, G:0.18, T:0.45
Consensus pattern (39 bp):
AGTATTGTGATATATGCTTAAATGTTATGTAATTATATG
Found at i:18539747 original size:16 final size:17
Alignment explanation
Indices: 18539722--18539756 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
18539712 TTTTTTTCAA
18539722 TCATCCCTCATCC-CTC
1 TCATCCCTCATCCTCTC
*
18539738 TCATCTCTCATCCTCTC
1 TCATCCCTCATCCTCTC
18539755 TC
1 TC
18539757 TCAACTCTCT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 12 0.71
17 5 0.29
ACGTcount: A:0.11, C:0.51, G:0.00, T:0.37
Consensus pattern (17 bp):
TCATCCCTCATCCTCTC
Found at i:18542392 original size:29 final size:29
Alignment explanation
Indices: 18542346--18542406 Score: 79
Period size: 29 Copynumber: 2.1 Consensus size: 29
18542336 GCTTAGCGCA
* *
18542346 TTTTAAGGAAAGCAGCCC-TTTCCAGTAAT
1 TTTTAAAGAAAACAGCCCATTTCCA-TAAT
*
18542375 TTTTAAAGAAAACGGCCCATTTCCATAAT
1 TTTTAAAGAAAACAGCCCATTTCCATAAT
18542404 TTT
1 TTT
18542407 CTTTTGGAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
29 22 0.79
30 6 0.21
ACGTcount: A:0.33, C:0.20, G:0.13, T:0.34
Consensus pattern (29 bp):
TTTTAAAGAAAACAGCCCATTTCCATAAT
Found at i:18544171 original size:156 final size:156
Alignment explanation
Indices: 18543887--18544199 Score: 617
Period size: 156 Copynumber: 2.0 Consensus size: 156
18543877 AAGTTAAACT
18543887 ATCACAACTATTCAACATAAATTTCAGGTTTATTCAAGCTTTTTATACATTTTGAATGTGCAACT
1 ATCACAACTATTCAACATAAATTTCAGGTTTATTCAAGCTTTTTATACATTTTGAATGTGCAACT
18543952 CTCTGGTGTTCACTTTAGGTCCGTTTTTTTATATTTTTGAGGTCCTAATTAAAATAATAAATTGG
66 CTCTGGTGTTCACTTTAGGTCCGTTTTTTTATATTTTTGAGGTCCTAATTAAAATAATAAATTGG
*
18544017 GTCCTTTTAAAAATTATATAAAATAA
131 GTCCTTTTAAAAAATATATAAAATAA
18544043 ATCACAACTATTCAACATAAATTTCAGGTTTATTCAAGCTTTTTATACATTTTGAATGTGCAACT
1 ATCACAACTATTCAACATAAATTTCAGGTTTATTCAAGCTTTTTATACATTTTGAATGTGCAACT
18544108 CTCTGGTGTTCACTTTAGGTCCGTTTTTTTATATTTTTGAGGTCCTAATTAAAATAATAAATTGG
66 CTCTGGTGTTCACTTTAGGTCCGTTTTTTTATATTTTTGAGGTCCTAATTAAAATAATAAATTGG
18544173 GTCCTTTTAAAAAATATATAAAATAA
131 GTCCTTTTAAAAAATATATAAAATAA
18544199 A
1 A
18544200 ATAAAAAAAA
Statistics
Matches: 156, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
156 156 1.00
ACGTcount: A:0.33, C:0.13, G:0.12, T:0.42
Consensus pattern (156 bp):
ATCACAACTATTCAACATAAATTTCAGGTTTATTCAAGCTTTTTATACATTTTGAATGTGCAACT
CTCTGGTGTTCACTTTAGGTCCGTTTTTTTATATTTTTGAGGTCCTAATTAAAATAATAAATTGG
GTCCTTTTAAAAAATATATAAAATAA
Found at i:18546417 original size:13 final size:13
Alignment explanation
Indices: 18546399--18546428 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
18546389 TATAATCGTT
*
18546399 TTTAAAAAATTGA
1 TTTAAAAAATTAA
18546412 TTTAAAAAATTAA
1 TTTAAAAAATTAA
18546425 TTTA
1 TTTA
18546429 TATTTAATCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.43
Consensus pattern (13 bp):
TTTAAAAAATTAA
Found at i:18549746 original size:23 final size:22
Alignment explanation
Indices: 18549703--18549746 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 22
18549693 TTCTAAGTCG
18549703 ATATTCAATTCAATTCCACACCT
1 ATATTCAATTCAATT-CACACCT
18549726 ATATTCATTATTCAATT-ACAC
1 ATATTCA--ATTCAATTCACAC
18549747 TTAGTCAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
23 11 0.58
25 8 0.42
ACGTcount: A:0.36, C:0.25, G:0.00, T:0.39
Consensus pattern (22 bp):
ATATTCAATTCAATTCACACCT
Found at i:18549859 original size:45 final size:45
Alignment explanation
Indices: 18549799--18549884 Score: 145
Period size: 45 Copynumber: 1.9 Consensus size: 45
18549789 CTCGGTGGAT
*
18549799 TTAGCACATACCAACCACCTTATTAATCAATGATGTCCGGTGAAA
1 TTAGCACATACCAACCACCTTACTAATCAATGATGTCCGGTGAAA
* *
18549844 TTAGCACATAGCAACCACCTTACTAATCAATGATGTTCGGT
1 TTAGCACATACCAACCACCTTACTAATCAATGATGTCCGGT
18549885 TCACATAGTA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 38 1.00
ACGTcount: A:0.34, C:0.24, G:0.14, T:0.28
Consensus pattern (45 bp):
TTAGCACATACCAACCACCTTACTAATCAATGATGTCCGGTGAAA
Found at i:18549948 original size:51 final size:51
Alignment explanation
Indices: 18549886--18550026 Score: 194
Period size: 51 Copynumber: 2.8 Consensus size: 51
18549876 ATGTTCGGTT
* *
18549886 CACATAGTAGCCTACACATAGTACTACACATGTGACCATTACCATCCGATA
1 CACATAGTAGCCTGCACATAGTACTACACATGTGACCATAACCATCCGATA
* * * * *
18549937 CACGTAGTAGCCTGCACATAGTACTACACATGTGATCGA-AACTATCTGGTA
1 CACATAGTAGCCTGCACATAGTACTACACATGTGA-CCATAACCATCCGATA
*
18549988 CACATAGTAGCCTGCACATAGTACTACACACGTGACCAT
1 CACATAGTAGCCTGCACATAGTACTACACATGTGACCAT
18550027 CACTTTCACT
Statistics
Matches: 78, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
50 2 0.03
51 74 0.95
52 2 0.03
ACGTcount: A:0.33, C:0.28, G:0.16, T:0.23
Consensus pattern (51 bp):
CACATAGTAGCCTGCACATAGTACTACACATGTGACCATAACCATCCGATA
Found at i:18550044 original size:51 final size:49
Alignment explanation
Indices: 18549887--18550058 Score: 157
Period size: 51 Copynumber: 3.4 Consensus size: 49
18549877 TGTTCGGTTC
* * *
18549887 ACATAGTAGCCTACACATAGTACTACACATGTGACCATTACCATCCGAT
1 ACATAGTAGCCTACACATAGTACTACACATGTGACCATAACTATCCTAT
* * * *
18549936 ACACGTAGTAGCCTGCACATAGTACTACACATGTGATCGA-AACTATCTGGTAC
1 ACA--TAGTAGCCTACACATAGTACTACACATGTGA-CCATAACTATC--CTAT
* * * * *
18549989 ACATAGTAGCCTGCACATAGTACTACACACGTGACCATCACTTTCACTTTT
1 ACATAGTAGCCTACACATAGTACTACACATGTGACCATAACTATC-C-TAT
*
18550040 ACATAGTGGCCTACACATA
1 ACATAGTAGCCTACACATA
18550059 ATTCGTGCCA
Statistics
Matches: 99, Mismatches: 17, Indels: 12
0.77 0.13 0.09
Matches are distributed among these distances:
49 3 0.03
50 2 0.02
51 88 0.89
52 2 0.02
53 4 0.04
ACGTcount: A:0.33, C:0.27, G:0.15, T:0.26
Consensus pattern (49 bp):
ACATAGTAGCCTACACATAGTACTACACATGTGACCATAACTATCCTAT
Found at i:18553995 original size:50 final size:50
Alignment explanation
Indices: 18553925--18554169 Score: 251
Period size: 50 Copynumber: 4.8 Consensus size: 50
18553915 TGTATTACCA
* * * ** *
18553925 ATGCCATATCCCAGATATGGTCTTACATGTGAGTTCTCATATAGGTGCCC
1 ATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTAGGTGCCC
* ** * *
18553975 ATGCCATGTCCTAGACATGGTCTTACGGGGGACCTCTCATCTTGGTTCCC
1 ATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTAGGTGCCC
* * *
18554025 ATGCCATGTCCTAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCA
1 ATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTAGGTGCCC
* * * *
18554075 ATGCCATGTCCCAGACATGATCTTACATGGGACCTCCCATAATCTCGATGATGCCA
1 ATGCCATGTCCCAGACATGGTCTTACATGGGACCT--C-TCATCT--A-GGTGCCC
*
18554131 ATGCCATTTCCCAGACATGGTCTTACATGGGA--TCTCATC
1 ATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATC
18554170 CTCTTAATGT
Statistics
Matches: 165, Mismatches: 24, Indels: 11
0.82 0.12 0.05
Matches are distributed among these distances:
50 117 0.71
51 4 0.02
52 2 0.01
53 5 0.03
54 1 0.01
56 36 0.22
ACGTcount: A:0.22, C:0.29, G:0.20, T:0.29
Consensus pattern (50 bp):
ATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTAGGTGCCC
Found at i:18559135 original size:20 final size:21
Alignment explanation
Indices: 18559110--18559148 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 21
18559100 TGGTGTCGCG
18559110 AGGAATAATTTAAG-CTTGCA
1 AGGAATAATTTAAGTCTTGCA
18559130 AGGAATAATTTAAGTCTTG
1 AGGAATAATTTAAGTCTTG
18559149 AGTTGAATAG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.38, C:0.08, G:0.21, T:0.33
Consensus pattern (21 bp):
AGGAATAATTTAAGTCTTGCA
Found at i:18571102 original size:29 final size:29
Alignment explanation
Indices: 18571060--18571118 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
18571050 ATCTATGATC
*
18571060 AGGTGTGGGTTTTAACACTAAACCAGATT
1 AGGTGTGGGTTTTAACACTAAACCAAATT
18571089 AGGTGTGGGTTTTAACACTAAACCAAATT
1 AGGTGTGGGTTTTAACACTAAACCAAATT
18571118 A
1 A
18571119 AGTCTATGTT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.34, C:0.14, G:0.22, T:0.31
Consensus pattern (29 bp):
AGGTGTGGGTTTTAACACTAAACCAAATT
Found at i:18571129 original size:29 final size:29
Alignment explanation
Indices: 18571067--18571131 Score: 85
Period size: 29 Copynumber: 2.2 Consensus size: 29
18571057 ATCAGGTGTG
* * * *
18571067 GGTTTTAACACTAAACCAGATTAGGTGTG
1 GGTTTTAACACTAAACCAAATTAAGTCTA
18571096 GGTTTTAACACTAAACCAAATTAAGTCTA
1 GGTTTTAACACTAAACCAAATTAAGTCTA
*
18571125 TGTTTTA
1 GGTTTTA
18571132 TATTGATAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.34, C:0.14, G:0.17, T:0.35
Consensus pattern (29 bp):
GGTTTTAACACTAAACCAAATTAAGTCTA
Found at i:18571555 original size:47 final size:47
Alignment explanation
Indices: 18571484--18571598 Score: 149
Period size: 47 Copynumber: 2.4 Consensus size: 47
18571474 AAGGTGGAAG
* * * ** *
18571484 TTATTGTCAGTTTATATACGATTTTGGTGGCTTGTCCATTATTTTGA
1 TTATTGACAGTTTATCTACAATTTTGGTGGCTTGTCCACAATATTGA
*
18571531 TTATTGACAGTATATCTACAATTTTGGTGGCTTGTCCACAATATTGA
1 TTATTGACAGTTTATCTACAATTTTGGTGGCTTGTCCACAATATTGA
*
18571578 TTATGTGGCAGTTTATCTACA
1 TTAT-TGACAGTTTATCTACA
18571599 TTATTGTGAC
Statistics
Matches: 58, Mismatches: 9, Indels: 1
0.85 0.13 0.01
Matches are distributed among these distances:
47 44 0.76
48 14 0.24
ACGTcount: A:0.23, C:0.13, G:0.18, T:0.45
Consensus pattern (47 bp):
TTATTGACAGTTTATCTACAATTTTGGTGGCTTGTCCACAATATTGA
Found at i:18591520 original size:21 final size:21
Alignment explanation
Indices: 18591491--18591530 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
18591481 TTGTATTTAG
18591491 TTGTCAAATGAATTAAATTAA
1 TTGTCAAATGAATTAAATTAA
* * *
18591512 TTGTTAAATTAATTTAATT
1 TTGTCAAATGAATTAAATT
18591531 TGATAGTTAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.42, C:0.03, G:0.07, T:0.47
Consensus pattern (21 bp):
TTGTCAAATGAATTAAATTAA
Found at i:18593816 original size:21 final size:21
Alignment explanation
Indices: 18593791--18593839 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
18593781 GTGGGGGTCT
*
18593791 ACACGCCCATGTGGAGGCCAC
1 ACACGCCCATGTGAAGGCCAC
**
18593812 ACACGCCTGTGTGAAGGCCAC
1 ACACGCCCATGTGAAGGCCAC
*
18593833 AAACGCC
1 ACACGCC
18593840 AGTGTGACCA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.27, C:0.37, G:0.27, T:0.10
Consensus pattern (21 bp):
ACACGCCCATGTGAAGGCCAC
Found at i:18593844 original size:21 final size:21
Alignment explanation
Indices: 18593800--18593846 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
18593790 TACACGCCCA
* * *
18593800 TGTGGAGGCCACACACGCCTG
1 TGTGAAGGCCACAAACGCCAG
18593821 TGTGAAGGCCACAAACGCCAG
1 TGTGAAGGCCACAAACGCCAG
18593842 TGTGA
1 TGTGA
18593847 CCAGCCCGTG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.26, C:0.28, G:0.32, T:0.15
Consensus pattern (21 bp):
TGTGAAGGCCACAAACGCCAG
Found at i:18594521 original size:20 final size:20
Alignment explanation
Indices: 18594476--18594522 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
18594466 TGAGAAGAAG
18594476 AAAAGAAGAAAACATATGGA
1 AAAAGAAGAAAACATATGGA
* *
18594496 ATAAGAAGAAAAGA-ATGTGA
1 AAAAGAAGAAAACATATG-GA
18594516 AAAAGAA
1 AAAAGAA
18594523 CTTGACTTCT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
19 3 0.13
20 20 0.87
ACGTcount: A:0.66, C:0.02, G:0.21, T:0.11
Consensus pattern (20 bp):
AAAAGAAGAAAACATATGGA
Found at i:18599887 original size:26 final size:27
Alignment explanation
Indices: 18599832--18599889 Score: 73
Period size: 26 Copynumber: 2.2 Consensus size: 27
18599822 AACTGATATG
* *
18599832 AAATGATTGTTATGCCCCCATGTGGTA
1 AAATGACTGTTATGCCCCCATGTGATA
* *
18599859 AAATGACTGTTATG-CCCTATGTTATA
1 AAATGACTGTTATGCCCCCATGTGATA
18599885 AAATG
1 AAATG
18599890 GTTGTATGTT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
26 14 0.52
27 13 0.48
ACGTcount: A:0.31, C:0.16, G:0.19, T:0.34
Consensus pattern (27 bp):
AAATGACTGTTATGCCCCCATGTGATA
Found at i:18600225 original size:27 final size:26
Alignment explanation
Indices: 18600177--18600230 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 26
18600167 TACTGTCATC
*
18600177 GTAATGGGCTAAGGCCACACTAATACT
1 GTAATAGGCTAAGGCCACACTAA-ACT
18600204 GTAATAGGCTAAGGCC-CAACTAAACT
1 GTAATAGGCTAAGGCCAC-ACTAAACT
18600230 G
1 G
18600231 AACTGTTATT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
26 5 0.20
27 20 0.80
ACGTcount: A:0.35, C:0.22, G:0.22, T:0.20
Consensus pattern (26 bp):
GTAATAGGCTAAGGCCACACTAAACT
Found at i:18607854 original size:50 final size:50
Alignment explanation
Indices: 18607681--18607918 Score: 160
Period size: 50 Copynumber: 4.7 Consensus size: 50
18607671 ATTTGGGTAA
* * **
18607681 AGAGATCTCATGTAAGACCATGTCTAGGACATGACATTGGTATCATTGAGATTATG
1 AGAGATCCCATGTAAGACCATGTCTAGGACATGACA-TGG--GCACCGA-A--ATG
* * * * * *
18607737 AGAGGTCTCATGTAAGAACATGTCTAGGACATGGCGTTGGCACCGAAATG
1 AGAGATCCCATGTAAGACCATGTCTAGGACATGACATGGGCACCGAAATG
** * *
18607787 AGAGATCCCCCGTAAGACCATGTCTAGGACCTGACATGGGCACCGATATG
1 AGAGATCCCATGTAAGACCATGTCTAGGACATGACATGGGCACCGAAATG
* ** * * *
18607837 AGA-ACTCCCATGTAAGACCATATCCGGGATATGACAAT-GGCA--GTACAGG
1 AGAGA-TCCCATGTAAGACCATGTCTAGGACATGAC-ATGGGCACCG-AAATG
* * *
18607886 AAACATCCCATGTAAGACCATGTCTGGGACATG
1 AGAGATCCCATGTAAGACCATGTCTAGGACATG
18607919 GCTTTGTCAT
Statistics
Matches: 147, Mismatches: 31, Indels: 15
0.76 0.16 0.08
Matches are distributed among these distances:
48 1 0.01
49 31 0.21
50 74 0.50
51 2 0.01
52 1 0.01
53 4 0.03
55 2 0.01
56 32 0.22
ACGTcount: A:0.32, C:0.21, G:0.25, T:0.22
Consensus pattern (50 bp):
AGAGATCCCATGTAAGACCATGTCTAGGACATGACATGGGCACCGAAATG
Found at i:18609396 original size:14 final size:14
Alignment explanation
Indices: 18609374--18609462 Score: 51
Period size: 14 Copynumber: 6.3 Consensus size: 14
18609364 CCCTTAGTCT
*
18609374 TTTTCTTTTTATTA
1 TTTTATTTTTATTA
18609388 TTTTA-TTTTATTTA
1 TTTTATTTTTA-TTA
*
18609402 TTTTATTTAGTAATT-
1 TTTTATTT--TTATTA
* *
18609417 TTTTATTATTCTTA
1 TTTTATTTTTATTA
* *
18609431 TTATCTTTCTTATTA
1 TTTTATTT-TTATTA
18609446 TTTT-TCTTTTATT-
1 TTTTAT-TTTTATTA
18609459 TTTT
1 TTTT
18609463 TCTAGTCTTA
Statistics
Matches: 58, Mismatches: 10, Indels: 15
0.70 0.12 0.18
Matches are distributed among these distances:
13 12 0.21
14 23 0.40
15 19 0.33
16 2 0.03
17 2 0.03
ACGTcount: A:0.18, C:0.06, G:0.01, T:0.75
Consensus pattern (14 bp):
TTTTATTTTTATTA
Found at i:18609462 original size:12 final size:12
Alignment explanation
Indices: 18609419--18609461 Score: 61
Period size: 12 Copynumber: 3.7 Consensus size: 12
18609409 TAGTAATTTT
*
18609419 TTATTATTCTTA
1 TTATTTTTCTTA
*
18609431 TTATCTTTCTTA
1 TTATTTTTCTTA
18609443 TTATTTTTCTT-
1 TTATTTTTCTTA
18609454 TTATTTTT
1 TTATTTTT
18609462 TTCTAGTCTT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
11 8 0.29
12 20 0.71
ACGTcount: A:0.16, C:0.09, G:0.00, T:0.74
Consensus pattern (12 bp):
TTATTTTTCTTA
Found at i:18609473 original size:16 final size:15
Alignment explanation
Indices: 18609437--18609479 Score: 54
Period size: 13 Copynumber: 2.9 Consensus size: 15
18609427 CTTATTATCT
18609437 TTCTTATTATTTTTC
1 TTCTTATTATTTTTC
18609452 TT-TTATT-TTTTTC
1 TTCTTATTATTTTTC
18609465 TAGTCTTATTATTTT
1 T--TCTTATTATTTT
18609480 GATGTACTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
13 7 0.29
14 5 0.21
15 3 0.12
16 5 0.21
17 4 0.17
ACGTcount: A:0.14, C:0.09, G:0.02, T:0.74
Consensus pattern (15 bp):
TTCTTATTATTTTTC
Found at i:18611068 original size:18 final size:18
Alignment explanation
Indices: 18611042--18611080 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
18611032 GCTTTCTTTA
*
18611042 TTTTCTTTTCAGTTTTGT
1 TTTTATTTTCAGTTTTGT
* *
18611060 TTTTATTTTTATTTTTGT
1 TTTTATTTTCAGTTTTGT
18611078 TTT
1 TTT
18611081 GGTTGTTTTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.08, C:0.05, G:0.08, T:0.79
Consensus pattern (18 bp):
TTTTATTTTCAGTTTTGT
Found at i:18621981 original size:27 final size:26
Alignment explanation
Indices: 18621960--18622234 Score: 343
Period size: 27 Copynumber: 10.2 Consensus size: 26
18621950 CGGTATAACA
18621960 GTCATTTTACCCTATGGAGGTATTTCG
1 GTCATTTTACCCTATGG-GGTATTTCG
*
18621987 GTCATTTTACCCTATAGGGGTATTTAG
1 GTCATTTTACCCTAT-GGGGTATTTCG
*
18622014 GTCATTCTACCCTATAGGGGTATTTCG
1 GTCATTTTACCCTAT-GGGGTATTTCG
18622041 GTCATTTTACCCTATGGGGGTATTTCG
1 GTCATTTTACCCTAT-GGGGTATTTCG
* * *
18622068 ATCATTCTATCCTATAGGGGTATTTCG
1 GTCATTTTACCCTAT-GGGGTATTTCG
*
18622095 ATCATTTTACCCTATGAGGGTATTTCG
1 GTCATTTTACCCTATG-GGGTATTTCG
* * * *
18622122 GTTATTCTACCCCATAAGGGTATTTCG
1 GTCATTTTACCCTAT-GGGGTATTTCG
*
18622149 ATCATTTTACCCTATGTGGGTATTTCG
1 GTCATTTTACCCTATG-GGGTATTTCG
18622176 GTCATTTTACCCTATGGGGGTATTTCG
1 GTCATTTTACCCTAT-GGGGTATTTCG
* *
18622203 GTCATTTTACCCTATAGAGGTATTTTG
1 GTCATTTTACCCTAT-GGGGTATTTCG
18622230 GTCAT
1 GTCAT
18622235 AACAGTGTAA
Statistics
Matches: 218, Mismatches: 25, Indels: 10
0.86 0.10 0.04
Matches are distributed among these distances:
26 1 0.00
27 214 0.98
28 3 0.01
ACGTcount: A:0.20, C:0.19, G:0.21, T:0.41
Consensus pattern (26 bp):
GTCATTTTACCCTATGGGGTATTTCG
Found at i:18630006 original size:16 final size:17
Alignment explanation
Indices: 18629979--18630013 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
18629969 AGAGATTTGA
18629979 GAGAGAGGATGAGAGAT
1 GAGAGAGGATGAGAGAT
*
18629996 GAGAG-GGATGAGGGAT
1 GAGAGAGGATGAGAGAT
18630012 GA
1 GA
18630014 AGGATGATGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 12 0.71
17 5 0.29
ACGTcount: A:0.37, C:0.00, G:0.51, T:0.11
Consensus pattern (17 bp):
GAGAGAGGATGAGAGAT
Found at i:18630526 original size:91 final size:91
Alignment explanation
Indices: 18630423--18630591 Score: 311
Period size: 91 Copynumber: 1.9 Consensus size: 91
18630413 TTAATTAATT
18630423 AATTTACTTAATTAATTAAACCCAATTTTATTAATGAAATATTTAAAATGAATTATTAAAATACA
1 AATTTACTTAATTAATTAAACCCAATTTTATTAATGAAATATTTAAAATGAATTATTAAAATACA
*
18630488 AAATTATGTTTTATTATTTAATTTAA
66 AAATTATATTTTATTATTTAATTTAA
*
18630514 AATTTACTTAATTAATTAAACCCAATTTTATTAATGAAATATTTAAAATGAATTATTAAAATATA
1 AATTTACTTAATTAATTAAACCCAATTTTATTAATGAAATATTTAAAATGAATTATTAAAATACA
*
18630579 ACATTATATTTTA
66 AAATTATATTTTA
18630592 CCATTTAGTT
Statistics
Matches: 75, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
91 75 1.00
ACGTcount: A:0.47, C:0.06, G:0.03, T:0.44
Consensus pattern (91 bp):
AATTTACTTAATTAATTAAACCCAATTTTATTAATGAAATATTTAAAATGAATTATTAAAATACA
AAATTATATTTTATTATTTAATTTAA
Found at i:18642574 original size:78 final size:77
Alignment explanation
Indices: 18642445--18642677 Score: 295
Period size: 79 Copynumber: 3.0 Consensus size: 77
18642435 AGGCGCGTAT
* * * *
18642445 GTACCGCAGTACAACAGGGGCACGTATGTGCATACAGAGGTACTCAAGTACAATAGGGGAACGTA
1 GTACCGAAGTACAACAGGGGCACGTATGTGCATTCAGGGGTAC-CAAGTACAATAGGGGCACGTA
*
18642510 TGTGCATTTAGGG
65 TGTGCATTCAGGG
* * *
18642523 GTACCGAAGTACAACAGGGGCATGTATGTGCATTCAGGGGTACCAAAGTACAAATAAGGGCATGT
1 GTACCGAAGTACAACAGGGGCACGTATGTGCATTCAGGGGTACC-AAGTAC-AATAGGGGCACGT
18642588 ATGTGCATTCAGGG
64 ATGTGCATTCAGGG
** * * *
18642602 GTACCGAAGTACAAGCAATGGCACGTATGTGCATTCGGGGGTAACGAAGTACAACAGGGGCACGT
1 GTACCGAAGTACAA-CAGGGGCACGTATGTGCATTCAGGGGT-ACCAAGTACAATAGGGGCACGT
*
18642667 ATGTGTATTCA
64 ATGTGCATTCA
18642678 TACAATAATT
Statistics
Matches: 134, Mismatches: 17, Indels: 7
0.85 0.11 0.04
Matches are distributed among these distances:
77 1 0.01
78 45 0.34
79 57 0.43
80 29 0.22
81 2 0.01
ACGTcount: A:0.31, C:0.18, G:0.30, T:0.21
Consensus pattern (77 bp):
GTACCGAAGTACAACAGGGGCACGTATGTGCATTCAGGGGTACCAAGTACAATAGGGGCACGTAT
GTGCATTCAGGG
Found at i:18642595 original size:40 final size:39
Alignment explanation
Indices: 18642445--18642677 Score: 288
Period size: 39 Copynumber: 5.9 Consensus size: 39
18642435 AGGCGCGTAT
* * *
18642445 GTACCGCAGTACAACAGGGGCACGTATGTGCATACAGAG
1 GTACCGAAGTACAACAGGGGCACGTATGTGCATTCAGGG
* * *
18642484 GTACTC-AAGTACAATAGGGGAACGTATGTGCATTTAGGG
1 GTAC-CGAAGTACAACAGGGGCACGTATGTGCATTCAGGG
*
18642523 GTACCGAAGTACAACAGGGGCATGTATGTGCATTCAGGG
1 GTACCGAAGTACAACAGGGGCACGTATGTGCATTCAGGG
* * * *
18642562 GTACCAAAGTACAAATAAGGGCATGTATGTGCATTCAGGG
1 GTACCGAAGTAC-AACAGGGGCACGTATGTGCATTCAGGG
** *
18642602 GTACCGAAGTACAAGCAATGGCACGTATGTGCATTCGGGG
1 GTACCGAAGTACAA-CAGGGGCACGTATGTGCATTCAGGG
* *
18642642 GTAACGAAGTACAACAGGGGCACGTATGTGTATTCA
1 GTACCGAAGTACAACAGGGGCACGTATGTGCATTCA
18642678 TACAATAATT
Statistics
Matches: 167, Mismatches: 23, Indels: 8
0.84 0.12 0.04
Matches are distributed among these distances:
38 1 0.01
39 95 0.57
40 71 0.43
ACGTcount: A:0.31, C:0.18, G:0.30, T:0.21
Consensus pattern (39 bp):
GTACCGAAGTACAACAGGGGCACGTATGTGCATTCAGGG
Found at i:18647002 original size:25 final size:25
Alignment explanation
Indices: 18646974--18647043 Score: 79
Period size: 25 Copynumber: 2.8 Consensus size: 25
18646964 GACCCATTTC
18646974 ACAGCTTGTGTGAGCATTTATAATT
1 ACAGCTTGTGTGAGCATTTATAATT
** * *
18646999 ACAGCTCATGTGAGCAATTATAGTT
1 ACAGCTTGTGTGAGCATTTATAATT
* *
18647024 ACAGCATGAGTGAGC-TTTAT
1 ACAGCTTGTGTGAGCATTTAT
18647044 TCTCGTGTAT
Statistics
Matches: 36, Mismatches: 9, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
24 4 0.11
25 32 0.89
ACGTcount: A:0.30, C:0.14, G:0.21, T:0.34
Consensus pattern (25 bp):
ACAGCTTGTGTGAGCATTTATAATT
Found at i:18647129 original size:40 final size:41
Alignment explanation
Indices: 18647086--18647210 Score: 171
Period size: 40 Copynumber: 3.0 Consensus size: 41
18647076 CATCATGAGG
*
18647086 AAAATGAATATATAAAATGATTATATGAATCGGTGATATGA
1 AAAATGAATATATAAAATGATTATATGAATCGATGATATGA
**
18647127 AAAATGAATATAT-AAATGATTATATGAATCGATTCTATGA
1 AAAATGAATATATAAAATGATTATATGAATCGATGATATGA
* * * *
18647167 AAAATGAATATATAAAATTATTACATGAATAGATTATATAGA
1 AAAATGAATATATAAAATGATTATATGAATCGATGATAT-GA
18647209 AA
1 AA
18647211 TAGATATACG
Statistics
Matches: 75, Mismatches: 7, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
40 37 0.49
41 34 0.45
42 4 0.05
ACGTcount: A:0.51, C:0.03, G:0.13, T:0.33
Consensus pattern (41 bp):
AAAATGAATATATAAAATGATTATATGAATCGATGATATGA
Found at i:18647252 original size:14 final size:13
Alignment explanation
Indices: 18647194--18647286 Score: 66
Period size: 13 Copynumber: 6.9 Consensus size: 13
18647184 TTATTACATG
18647194 AATAGATTATATAGA
1 AATAG-TTATAT-GA
* *
18647209 AATAGATATACGA
1 AATAGTTATATGA
* *
18647222 AA-CGATTATACGA
1 AATAG-TTATATGA
18647235 AATAGTTATATGGA
1 AATAGTTATAT-GA
18647249 AATAGTTATATG-
1 AATAGTTATATGA
*
18647261 AATTGTGTATATGA
1 AATAGT-TATATGA
18647275 AAT-GTTTATATG
1 AATAG-TTATATG
18647287 GATAGATATG
Statistics
Matches: 65, Mismatches: 7, Indels: 14
0.76 0.08 0.16
Matches are distributed among these distances:
12 6 0.09
13 32 0.49
14 22 0.34
15 5 0.08
ACGTcount: A:0.44, C:0.03, G:0.17, T:0.35
Consensus pattern (13 bp):
AATAGTTATATGA
Found at i:18649064 original size:73 final size:73
Alignment explanation
Indices: 18648945--18649090 Score: 265
Period size: 73 Copynumber: 2.0 Consensus size: 73
18648935 GAATCCAATC
*
18648945 GAGTAGGTTCCGATGAACTACAGAGTAATCTTCTAGCCACCGATCTAAGGGCTATTCATAATGTG
1 GAGTAGGTTCCAATGAACTACAGAGTAATCTTCTAGCCACCGATCTAAGGGCTATTCATAATGTG
18649010 CCCAAATT
66 CCCAAATT
* *
18649018 GAGTAGGTTCCAATGAACTACAGAGTAATGTTCTAGCCACCGATCTAAGGGCTATTCATCATGTG
1 GAGTAGGTTCCAATGAACTACAGAGTAATCTTCTAGCCACCGATCTAAGGGCTATTCATAATGTG
18649083 CCCAAATT
66 CCCAAATT
18649091 TTAAGAGCAT
Statistics
Matches: 70, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
73 70 1.00
ACGTcount: A:0.30, C:0.22, G:0.21, T:0.27
Consensus pattern (73 bp):
GAGTAGGTTCCAATGAACTACAGAGTAATCTTCTAGCCACCGATCTAAGGGCTATTCATAATGTG
CCCAAATT
Found at i:18650858 original size:56 final size:50
Alignment explanation
Indices: 18650793--18651035 Score: 229
Period size: 50 Copynumber: 4.8 Consensus size: 50
18650783 GGGAATGAGA
* *
18650793 TCCCATGTAAGACCATGTTTGGGACATGGCATTGGCATTATTGAGGTTATGAGAGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACTA---A-G--ATGAGAGG
*
18650849 TCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACTAAGATGAGAGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACTAAGATGAGAGG
** * * * * **
18650899 TCCCCCGTAAGACCATGTCTAGGACATGGCATGGGCACCAATATGAGAAC
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACTAAGATGAGAGG
* * * * * * **
18650949 TCCAATGTAAGACCATATCTGGGATATGACATTGGCAGTACAG--GAAACA
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACTA-AGATGAGAGG
*
18650998 TCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCAC
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCAC
18651036 GTTATTATCA
Statistics
Matches: 154, Mismatches: 32, Indels: 9
0.79 0.16 0.05
Matches are distributed among these distances:
49 35 0.23
50 79 0.51
51 1 0.01
52 1 0.01
53 1 0.01
56 37 0.24
ACGTcount: A:0.28, C:0.21, G:0.27, T:0.24
Consensus pattern (50 bp):
TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACTAAGATGAGAGG
Found at i:18651252 original size:20 final size:21
Alignment explanation
Indices: 18651227--18651274 Score: 57
Period size: 20 Copynumber: 2.4 Consensus size: 21
18651217 TGAGTTATTT
18651227 AAGTAAGCAG-GTAAGTAAAC
1 AAGTAAGCAGAGTAAGTAAAC
* *
18651247 AAGTAA-AAGAGTAAGTAAAG
1 AAGTAAGCAGAGTAAGTAAAC
18651267 AAG-AAGCA
1 AAGTAAGCA
18651275 AAGACCATGA
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
19 4 0.17
20 19 0.83
ACGTcount: A:0.56, C:0.06, G:0.25, T:0.12
Consensus pattern (21 bp):
AAGTAAGCAGAGTAAGTAAAC
Found at i:18652460 original size:41 final size:40
Alignment explanation
Indices: 18652403--18652557 Score: 170
Period size: 41 Copynumber: 3.8 Consensus size: 40
18652393 TCATCGGGTG
*
18652403 GAAAATGAATTTATAAAATGATTATATGAATC-AGTTATAT
1 GAAAATGAATATATAAAATGATTATATGAATCGA-TTATAT
*
18652443 AGAAAATGAATATATAAAATGAGTATATGAATCGATTATAT
1 -GAAAATGAATATATAAAATGATTATATGAATCGATTATAT
* * * *
18652484 GAAAAATGAATATATAAATTGTTTATATGATTTGATTATAT
1 G-AAAATGAATATATAAAATGATTATATGAATCGATTATAT
* * * *
18652525 GGAAAT-AGATATACAAAATGATTTTAAGAATCG
1 GAAAATGA-ATATATAAAATGATTATATGAATCG
18652558 GGCATATGGA
Statistics
Matches: 96, Mismatches: 15, Indels: 7
0.81 0.13 0.06
Matches are distributed among these distances:
39 1 0.01
40 23 0.24
41 71 0.74
42 1 0.01
ACGTcount: A:0.48, C:0.03, G:0.14, T:0.35
Consensus pattern (40 bp):
GAAAATGAATATATAAAATGATTATATGAATCGATTATAT
Found at i:18652470 original size:13 final size:13
Alignment explanation
Indices: 18652439--18652501 Score: 56
Period size: 13 Copynumber: 4.7 Consensus size: 13
18652429 TGAATCAGTT
*
18652439 ATATAGAAAATGA
1 ATATATAAAATGA
18652452 ATATATAAAATGA
1 ATATATAAAATGA
* *
18652465 GTATAT-GAATCGA
1 ATATATAAAAT-GA
*
18652478 TTATATGAAAAATGA
1 ATATAT--AAAATGA
18652493 ATATATAAA
1 ATATATAAA
18652502 TTGTTTATAT
Statistics
Matches: 40, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
12 3 0.08
13 27 0.68
15 7 0.17
16 3 0.08
ACGTcount: A:0.56, C:0.02, G:0.13, T:0.30
Consensus pattern (13 bp):
ATATATAAAATGA
Found at i:18652509 original size:28 final size:28
Alignment explanation
Indices: 18652458--18652513 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
18652448 ATGAATATAT
* *
18652458 AAAATGAGTATATGAATCGATTATATGA
1 AAAATGAATATATAAATCGATTATATGA
* *
18652486 AAAATGAATATATAAATTGTTTATATGA
1 AAAATGAATATATAAATCGATTATATGA
18652514 TTTGATTATA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.48, C:0.02, G:0.14, T:0.36
Consensus pattern (28 bp):
AAAATGAATATATAAATCGATTATATGA
Found at i:18653849 original size:21 final size:21
Alignment explanation
Indices: 18653821--18653874 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 21
18653811 TATTACAGGT
*
18653821 TTTG-GCCACACGATAATGTG
1 TTTGAGCCACACGACAATGTG
* * *
18653841 TTTGAGCCATACGGCCATGTG
1 TTTGAGCCACACGACAATGTG
*
18653862 TTTGAACCACACG
1 TTTGAGCCACACG
18653875 GTCTGAGCTC
Statistics
Matches: 27, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
20 4 0.15
21 23 0.85
ACGTcount: A:0.24, C:0.24, G:0.24, T:0.28
Consensus pattern (21 bp):
TTTGAGCCACACGACAATGTG
Found at i:18653875 original size:21 final size:21
Alignment explanation
Indices: 18653836--18653875 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
18653826 CCACACGATA
* *
18653836 ATGTGTTTGAGCCATACGGCC
1 ATGTGTTTGAACCACACGGCC
18653857 ATGTGTTTGAACCACACGG
1 ATGTGTTTGAACCACACGG
18653876 TCTGAGCTCT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.23, C:0.23, G:0.28, T:0.28
Consensus pattern (21 bp):
ATGTGTTTGAACCACACGGCC
Found at i:18655007 original size:12 final size:13
Alignment explanation
Indices: 18654990--18655020 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
18654980 GCAATAAGGG
18654990 AAAAAAGA-GAAA
1 AAAAAAGATGAAA
18655002 AAAAAAGATGAAA
1 AAAAAAGATGAAA
18655015 AAAAAA
1 AAAAAA
18655021 CCTCTACATA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 8 0.44
13 10 0.56
ACGTcount: A:0.84, C:0.00, G:0.13, T:0.03
Consensus pattern (13 bp):
AAAAAAGATGAAA
Found at i:18667148 original size:20 final size:20
Alignment explanation
Indices: 18667131--18667169 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
18667121 TATTGATACT
*
18667131 TTTCTTAAGGTATCGATATA
1 TTTCCTAAGGTATCGATATA
18667151 TTTCCTAAGGTATCGATAT
1 TTTCCTAAGGTATCGATAT
18667170 TCCTACTCCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.28, C:0.13, G:0.15, T:0.44
Consensus pattern (20 bp):
TTTCCTAAGGTATCGATATA
Found at i:18667174 original size:17 final size:19
Alignment explanation
Indices: 18667131--18667174 Score: 56
Period size: 20 Copynumber: 2.4 Consensus size: 19
18667121 TATTGATACT
*
18667131 TTTCTTAAGGTATCGATATA
1 TTTCCTAAGGTATCGA-ATA
18667151 TTTCCTAAGGTATCG-ATA
1 TTTCCTAAGGTATCGAATA
18667169 -TTCCTA
1 TTTCCTA
18667175 CTCCAACGGT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
17 6 0.26
18 3 0.13
20 14 0.61
ACGTcount: A:0.27, C:0.16, G:0.14, T:0.43
Consensus pattern (19 bp):
TTTCCTAAGGTATCGAATA
Found at i:18682005 original size:16 final size:16
Alignment explanation
Indices: 18681984--18682014 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
18681974 CATGTTAGAG
18681984 CATATAAATTTGAAAC
1 CATATAAATTTGAAAC
*
18682000 CATATATATTTGAAA
1 CATATAAATTTGAAA
18682015 AAAAATTCAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.48, C:0.10, G:0.06, T:0.35
Consensus pattern (16 bp):
CATATAAATTTGAAAC
Found at i:18682132 original size:19 final size:20
Alignment explanation
Indices: 18682104--18682174 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
18682094 AAAAATATAA
* *
18682104 ATTTTAAATTTTTATAAA-T
1 ATTTTGAATTTTTAAAAATT
18682123 ATTTTGAA-TTTTAAAAATT
1 ATTTTGAATTTTTAAAAATT
*
18682142 ATTTTGAGTTTTTAAAAATT
1 ATTTTGAATTTTTAAAAATT
18682162 ATTTTGAATTTTT
1 ATTTTGAATTTTT
18682175 TTTATAATTT
Statistics
Matches: 46, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
18 8 0.17
19 15 0.33
20 23 0.50
ACGTcount: A:0.37, C:0.00, G:0.06, T:0.58
Consensus pattern (20 bp):
ATTTTGAATTTTTAAAAATT
Found at i:18686563 original size:23 final size:23
Alignment explanation
Indices: 18686497--18686779 Score: 295
Period size: 23 Copynumber: 12.3 Consensus size: 23
18686487 ACAGAACTTA
*
18686497 CCAC-AAGGACATTACAAAATATG
1 CCACAAAGG-CATTACAGAATATG
* ** *
18686520 TCGTAAAGTCATTACAGAATATG
1 CCACAAAGGCATTACAGAATATG
* *
18686543 CCACATAGGCACTACTA-AATATG
1 CCACAAAGGCATTAC-AGAATATG
18686566 CCACAAAGGCATTACAGAATATG
1 CCACAAAGGCATTACAGAATATG
* *
18686589 TCACAAAGGTATTACAGAATATG
1 CCACAAAGGCATTACAGAATATG
* *
18686612 TCACAAAGACATTACAGAATATG
1 CCACAAAGGCATTACAGAATATG
*
18686635 CCACAAGGGCATTACAGAATATG
1 CCACAAAGGCATTACAGAATATG
* * *
18686658 CCACAAAGGCATTATAAAATACG
1 CCACAAAGGCATTACAGAATATG
* * *
18686681 CCATAAAGACATTATAGAATACT-
1 CCACAAAGGCATTACAGAATA-TG
* *
18686704 CCACAAAGACATTAAAGAATATG
1 CCACAAAGGCATTACAGAATATG
*
18686727 TCACAAAGGCATTACAGAATATG
1 CCACAAAGGCATTACAGAATATG
* *
18686750 CCATAAAGGCATTA-TGAAATATG
1 CCACAAAGGCATTACAG-AATATG
18686773 CCACAAA
1 CCACAAA
18686780 AGCTCTGTTT
Statistics
Matches: 217, Mismatches: 37, Indels: 12
0.82 0.14 0.05
Matches are distributed among these distances:
22 3 0.01
23 210 0.97
24 4 0.02
ACGTcount: A:0.45, C:0.19, G:0.15, T:0.21
Consensus pattern (23 bp):
CCACAAAGGCATTACAGAATATG
Found at i:18687160 original size:20 final size:20
Alignment explanation
Indices: 18687135--18687174 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
18687125 GGCTTTACTC
18687135 ATACTCATAATCGAATCATA
1 ATACTCATAATCGAATCATA
18687155 ATACTCATAATCGAATCATA
1 ATACTCATAATCGAATCATA
18687175 CTTCTGTACA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.45, C:0.20, G:0.05, T:0.30
Consensus pattern (20 bp):
ATACTCATAATCGAATCATA
Found at i:18699675 original size:15 final size:15
Alignment explanation
Indices: 18699664--18699700 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
18699654 GAATTATTGT
18699664 AAAATGAGTTATTTG
1 AAAATGAGTTATTTG
*
18699679 AATATGAGTTATTTG
1 AAAATGAGTTATTTG
*
18699694 AATATGA
1 AAAATGA
18699701 CTTGAGTATA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.41, C:0.00, G:0.19, T:0.41
Consensus pattern (15 bp):
AAAATGAGTTATTTG
Found at i:18701159 original size:62 final size:59
Alignment explanation
Indices: 18701087--18701202 Score: 151
Period size: 62 Copynumber: 1.9 Consensus size: 59
18701077 GTAATTATCG
* * * *
18701087 TAATAGTAAATTTAATTTAATGTTTATTTTGTAGATAAATATTCTATTAATTTAATAAGATT
1 TAATAGTAAATTTAATATAATATTTATCTTGT---TAAATATTATATTAATTTAATAAGATT
* *
18701149 TAATATTAAATTTAATATAATATTTATCTTGTTGAATATTATATTAATTTAATA
1 TAATAGTAAATTTAATATAATATTTATCTTGTTAAATATTATATTAATTTAATA
18701203 TTAAAGTGAT
Statistics
Matches: 48, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
59 20 0.42
62 28 0.58
ACGTcount: A:0.41, C:0.02, G:0.06, T:0.51
Consensus pattern (59 bp):
TAATAGTAAATTTAATATAATATTTATCTTGTTAAATATTATATTAATTTAATAAGATT
Found at i:18710371 original size:29 final size:29
Alignment explanation
Indices: 18710333--18710516 Score: 226
Period size: 29 Copynumber: 6.3 Consensus size: 29
18710323 TCGTCACCAC
*
18710333 CCCTTTTCATAATCGATAGCCAAAGCTAT
1 CCCTTTTCATAATCGATAGCCGAAGCTAT
*
18710362 CCCTTTTCATAATCAATAGCCGAAGCTAT
1 CCCTTTTCATAATCGATAGCCGAAGCTAT
* * * * * *
18710391 CCCTTTTCATATTTGATGGTCGTCA-CCAT
1 CCCTTTTCATAATCGATAGCCG-AAGCTAT
* *
18710420 CCTTTTTCATAATCGATAGCCAAAGCTAT
1 CCCTTTTCATAATCGATAGCCGAAGCTAT
*
18710449 CCCTTTTCATATTCGATAGCCGAAGCTAT
1 CCCTTTTCATAATCGATAGCCGAAGCTAT
* *
18710478 CCCTTTTCATATTCAATAGCCGAAGCTAT
1 CCCTTTTCATAATCGATAGCCGAAGCTAT
*
18710507 CCTTTTTCAT
1 CCCTTTTCAT
18710517 TGGTTGATGA
Statistics
Matches: 131, Mismatches: 22, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
28 1 0.01
29 129 0.98
30 1 0.01
ACGTcount: A:0.26, C:0.27, G:0.11, T:0.36
Consensus pattern (29 bp):
CCCTTTTCATAATCGATAGCCGAAGCTAT
Found at i:18710434 original size:87 final size:87
Alignment explanation
Indices: 18710319--18710490 Score: 308
Period size: 87 Copynumber: 2.0 Consensus size: 87
18710309 TCATTAACCA
18710319 ATGGTCGTCACCACCCCTTTTCATAATCGATAGCCAAAGCTATCCCTTTTCATAATCAATAGCCG
1 ATGGTCGTCACCACCCCTTTTCATAATCGATAGCCAAAGCTATCCCTTTTCATAATCAATAGCCG
18710384 AAGCTATCCCTTTTCATATTTG
66 AAGCTATCCCTTTTCATATTTG
* * * *
18710406 ATGGTCGTCACCATCCTTTTTCATAATCGATAGCCAAAGCTATCCCTTTTCATATTCGATAGCCG
1 ATGGTCGTCACCACCCCTTTTCATAATCGATAGCCAAAGCTATCCCTTTTCATAATCAATAGCCG
18710471 AAGCTATCCCTTTTCATATT
66 AAGCTATCCCTTTTCATATT
18710491 CAATAGCCGA
Statistics
Matches: 81, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
87 81 1.00
ACGTcount: A:0.26, C:0.28, G:0.12, T:0.35
Consensus pattern (87 bp):
ATGGTCGTCACCACCCCTTTTCATAATCGATAGCCAAAGCTATCCCTTTTCATAATCAATAGCCG
AAGCTATCCCTTTTCATATTTG
Found at i:18710509 original size:87 final size:87
Alignment explanation
Indices: 18710336--18710516 Score: 274
Period size: 87 Copynumber: 2.1 Consensus size: 87
18710326 TCACCACCCC
18710336 TTTTCATAATCGATAGCCAAAGCTATCCCTTTTCATAATCAATAGCCGAAGCTATCCCTTTTCAT
1 TTTTCATAATCGATAGCCAAAGCTATCCCTTTTCATAATCAATAGCCGAAGCTATCCCTTTTCAT
** * * *
18710401 ATTTGATGGTCGTCACCATCCT
66 ATTCAATAGCCGTAACCATCCT
* *
18710423 TTTTCATAATCGATAGCCAAAGCTATCCCTTTTCATATTCGATAGCCGAAGCTATCCCTTTTCAT
1 TTTTCATAATCGATAGCCAAAGCTATCCCTTTTCATAATCAATAGCCGAAGCTATCCCTTTTCAT
*
18710488 ATTCAATAGCCG-AAGCTATCCT
66 ATTCAATAGCCGTAA-CCATCCT
18710510 TTTTCAT
1 TTTTCAT
18710517 TGGTTGATGA
Statistics
Matches: 85, Mismatches: 8, Indels: 2
0.89 0.08 0.02
Matches are distributed among these distances:
86 1 0.01
87 84 0.99
ACGTcount: A:0.27, C:0.26, G:0.11, T:0.36
Consensus pattern (87 bp):
TTTTCATAATCGATAGCCAAAGCTATCCCTTTTCATAATCAATAGCCGAAGCTATCCCTTTTCAT
ATTCAATAGCCGTAACCATCCT
Found at i:18729181 original size:16 final size:16
Alignment explanation
Indices: 18729160--18729192 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
18729150 TAACGAAATG
18729160 GTAAGTTATGTTTTAT
1 GTAAGTTATGTTTTAT
18729176 GTAAGTTATGTTTTAT
1 GTAAGTTATGTTTTAT
18729192 G
1 G
18729193 ATATACGAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.24, C:0.00, G:0.21, T:0.55
Consensus pattern (16 bp):
GTAAGTTATGTTTTAT
Found at i:18744164 original size:28 final size:28
Alignment explanation
Indices: 18744132--18744236 Score: 113
Period size: 28 Copynumber: 3.8 Consensus size: 28
18744122 AAACATGCCA
* *
18744132 GAAAAAGAAAGTCTTTGTGGTGATCTAT
1 GAAAAAGAAAGCCTTTGTGGTGATCTAC
* * *
18744160 GAAAAATAAAGGCTTTGTGGCGATCTAC
1 GAAAAAGAAAGCCTTTGTGGTGATCTAC
* * *
18744188 GAAAAAGGAAGCCTTTATGGTTATCTAC
1 GAAAAAGAAAGCCTTTGTGGTGATCTAC
* *
18744216 GAAAAA-AAAACCTTTATGGTG
1 GAAAAAGAAAGCCTTTGTGGTG
18744237 TACTCTAAAT
Statistics
Matches: 64, Mismatches: 13, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
27 12 0.19
28 52 0.81
ACGTcount: A:0.38, C:0.11, G:0.23, T:0.28
Consensus pattern (28 bp):
GAAAAAGAAAGCCTTTGTGGTGATCTAC
Done.