Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D07
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 58101237
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1550000 characters in sequence are not A, C, G, or T
File 41 of 199
Found at i:12410527 original size:13 final size:13
Alignment explanation
Indices: 12410509--12410533 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
12410499 TAATATATTT
12410509 ATTAATTAAAAAC
1 ATTAATTAAAAAC
12410522 ATTAATTAAAAA
1 ATTAATTAAAAA
12410534 AAAAGCTTTA
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:0.64, C:0.04, G:0.00, T:0.32
Consensus pattern (13 bp):
ATTAATTAAAAAC
Found at i:12411942 original size:10 final size:10
Alignment explanation
Indices: 12411908--12411943 Score: 54
Period size: 10 Copynumber: 3.5 Consensus size: 10
12411898 AATTAGTGTT
12411908 ACTTGCACCAA
1 ACTT-CACCAA
*
12411919 ACTCCACCAA
1 ACTTCACCAA
12411929 ACTTCACCAA
1 ACTTCACCAA
12411939 ACTTC
1 ACTTC
12411944 GACCTATATT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
10 20 0.87
11 3 0.13
ACGTcount: A:0.36, C:0.42, G:0.03, T:0.19
Consensus pattern (10 bp):
ACTTCACCAA
Found at i:12416691 original size:3 final size:3
Alignment explanation
Indices: 12416683--12416723 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
12416673 TACTATGACT
12416683 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
12416724 CCTACTATAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:12428005 original size:45 final size:45
Alignment explanation
Indices: 12427883--12428264 Score: 209
Period size: 45 Copynumber: 8.6 Consensus size: 45
12427873 GAGCAGGTTG
* * * * * *
12427883 AAAGATAA-CAGATCTTGTCTTCATGTACTAG-CGTGAAGTAGATC
1 AAAGA-AAGCAGATCTTGTCTTCCTATACTGGTGGCGAAGCAGATC
* * * * ** * * * *
12427927 ATAGATACCAGATCTTGTCTCCCCGTACAGGTGGTGGAGTAGATC
1 AAAGAAAGCAGATCTTGTCTTCCTATACTGGTGGCGAAGCAGATC
* * * *
12427972 GAAGAAAGCAGATCTTGCCTTCCTATACTGGTGGCGAAACAGACC
1 AAAGAAAGCAGATCTTGTCTTCCTATACTGGTGGCGAAGCAGATC
* * * * * * * *
12428017 AAAGAAAACAGATATTGTCTTCATGTATTGG-CGTGAAGTAGATC
1 AAAGAAAGCAGATCTTGTCTTCCTATACTGGTGGCGAAGCAGATC
* * *
12428061 AGAG-AAGCAGATCTTGTCTTCCCATACTGGTGGCGAAGCAGACC
1 AAAGAAAGCAGATCTTGTCTTCCTATACTGGTGGCGAAGCAGATC
* * * * * * * *
12428105 AAAGAAAGTAGATCTTGTCTTCATGTATTGG-CGTGAAGTAAATC
1 AAAGAAAGCAGATCTTGTCTTCCTATACTGGTGGCGAAGCAGATC
* * * * * *
12428149 AGAGATACCAGATCTTGCCTTCCCATACTGGTGGCGAAGCAAATC
1 AAAGAAAGCAGATCTTGTCTTCCTATACTGGTGGCGAAGCAGATC
* * * * * * *
12428194 AAAGAAAGCAGATCTTGTTTTCATGTACCGG-CGTGAAACAGATC
1 AAAGAAAGCAGATCTTGTCTTCCTATACTGGTGGCGAAGCAGATC
* * * *
12428238 AAAGATAGTAGGTCCTGTCTTCCTATA
1 AAAGAAAGCAGATCTTGTCTTCCTATA
12428265 TCGGTAGCGA
Statistics
Matches: 244, Mismatches: 89, Indels: 10
0.71 0.26 0.03
Matches are distributed among these distances:
43 21 0.09
44 104 0.43
45 119 0.49
ACGTcount: A:0.31, C:0.19, G:0.23, T:0.26
Consensus pattern (45 bp):
AAAGAAAGCAGATCTTGTCTTCCTATACTGGTGGCGAAGCAGATC
Found at i:12428088 original size:88 final size:88
Alignment explanation
Indices: 12427964--12428230 Score: 383
Period size: 88 Copynumber: 3.0 Consensus size: 88
12427954 CAGGTGGTGG
* * *
12427964 AGTAGATC-GAAGAAAGCAGATCTTGCCTTCCTATACTGGTGGCGAAACAGACCAAAGAAAACAG
1 AGTAGATCAG-AG-AAGCAGATCTTGCCTTCCCATACTGGTGGCGAAGCAGACCAAAGAAAGCAG
*
12428028 ATATTGTCTTCATGTATTGGCGTGA
64 ATCTTGTCTTCATGTATTGGCGTGA
* *
12428053 AGTAGATCAGAGAAGCAGATCTTGTCTTCCCATACTGGTGGCGAAGCAGACCAAAGAAAGTAGAT
1 AGTAGATCAGAGAAGCAGATCTTGCCTTCCCATACTGGTGGCGAAGCAGACCAAAGAAAGCAGAT
12428118 CTTGTCTTCATGTATTGGCGTGA
66 CTTGTCTTCATGTATTGGCGTGA
* * * *
12428141 AGTAAATCAGAGATACCAGATCTTGCCTTCCCATACTGGTGGCGAAGCAAATCAAAGAAAGCAGA
1 AGTAGATCAGAGA-AGCAGATCTTGCCTTCCCATACTGGTGGCGAAGCAGACCAAAGAAAGCAGA
* **
12428206 TCTTGTTTTCATGTACCGGCGTGA
65 TCTTGTCTTCATGTATTGGCGTGA
12428230 A
1 A
12428231 ACAGATCAAA
Statistics
Matches: 161, Mismatches: 15, Indels: 4
0.89 0.08 0.02
Matches are distributed among these distances:
88 82 0.51
89 78 0.48
90 1 0.01
ACGTcount: A:0.32, C:0.19, G:0.24, T:0.25
Consensus pattern (88 bp):
AGTAGATCAGAGAAGCAGATCTTGCCTTCCCATACTGGTGGCGAAGCAGACCAAAGAAAGCAGAT
CTTGTCTTCATGTATTGGCGTGA
Found at i:12428275 original size:89 final size:89
Alignment explanation
Indices: 12427964--12428260 Score: 382
Period size: 89 Copynumber: 3.3 Consensus size: 89
12427954 CAGGTGGTGG
* * * * *
12427964 AGTAGATC-GAAGAAAGCAGATCTTGCCTTCCTATACTGGTGGCGAAACAGACCAAAGAAAACAG
1 AGTAGATCAG-AGATAGCAGATCTTGTCTTCCCATACTGGTGGCGAAGCAGACCAAAGAAAGCAG
*
12428028 ATATTGTCTTCATGTATTGGCGTGA
65 ATCTTGTCTTCATGTATTGGCGTGA
*
12428053 AGTAGATCAGAGA-AGCAGATCTTGTCTTCCCATACTGGTGGCGAAGCAGACCAAAGAAAGTAGA
1 AGTAGATCAGAGATAGCAGATCTTGTCTTCCCATACTGGTGGCGAAGCAGACCAAAGAAAGCAGA
12428117 TCTTGTCTTCATGTATTGGCGTGA
66 TCTTGTCTTCATGTATTGGCGTGA
* * * * *
12428141 AGTAAATCAGAGATACCAGATCTTGCCTTCCCATACTGGTGGCGAAGCAAATCAAAGAAAGCAGA
1 AGTAGATCAGAGATAGCAGATCTTGTCTTCCCATACTGGTGGCGAAGCAGACCAAAGAAAGCAGA
* **
12428206 TCTTGTTTTCATGTACCGGCGTGA
66 TCTTGTCTTCATGTATTGGCGTGA
** * * * *
12428230 AACAGATCAAAGATAGTAGGTCCTGTCTTCC
1 AGTAGATCAGAGATAGCAGATCTTGTCTTCC
12428261 TATATCGGTA
Statistics
Matches: 182, Mismatches: 24, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
88 81 0.45
89 100 0.55
90 1 0.01
ACGTcount: A:0.32, C:0.20, G:0.24, T:0.25
Consensus pattern (89 bp):
AGTAGATCAGAGATAGCAGATCTTGTCTTCCCATACTGGTGGCGAAGCAGACCAAAGAAAGCAGA
TCTTGTCTTCATGTATTGGCGTGA
Found at i:12428760 original size:44 final size:44
Alignment explanation
Indices: 12428712--12428851 Score: 124
Period size: 44 Copynumber: 3.2 Consensus size: 44
12428702 CAGAGCAAAT
* *
12428712 TGAAGATACAAGTCTTATCTCCCTGAAGTTGCAGTGAAGCAGAC
1 TGAAGATACAAGTCTTATCTCCTTGAAGTTGCAGTGGAGCAGAC
** * *
12428756 TGAAG-TAACCAA-TCCAATCTCCTTGAAGTTGCAATGGAGCGGA-
1 TGAAGAT-A-CAAGTCTTATCTCCTTGAAGTTGCAGTGGAGCAGAC
* * ** *
12428799 TTAAAACCGCAGGTCTTATCTCCTTGAAGTTGCAGTGGAGCAGAC
1 TGAAGA-TACAAGTCTTATCTCCTTGAAGTTGCAGTGGAGCAGAC
*
12428844 TAAAGATA
1 TGAAGATA
12428852 GTAAATTTTG
Statistics
Matches: 71, Mismatches: 19, Indels: 12
0.70 0.19 0.12
Matches are distributed among these distances:
43 6 0.08
44 58 0.82
45 7 0.10
ACGTcount: A:0.32, C:0.20, G:0.23, T:0.25
Consensus pattern (44 bp):
TGAAGATACAAGTCTTATCTCCTTGAAGTTGCAGTGGAGCAGAC
Found at i:12429187 original size:7 final size:7
Alignment explanation
Indices: 12429175--12429199 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
12429165 GGCCCAAAGC
12429175 AAAACAA
1 AAAACAA
12429182 AAAACAA
1 AAAACAA
12429189 AAAACAA
1 AAAACAA
12429196 AAAA
1 AAAA
12429200 GAACCCTAGC
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:0.88, C:0.12, G:0.00, T:0.00
Consensus pattern (7 bp):
AAAACAA
Found at i:12429917 original size:25 final size:25
Alignment explanation
Indices: 12429888--12429945 Score: 116
Period size: 25 Copynumber: 2.3 Consensus size: 25
12429878 TGGGAAATTT
12429888 GCGCGTTTAGTCCCTCCCTTCTGCA
1 GCGCGTTTAGTCCCTCCCTTCTGCA
12429913 GCGCGTTTAGTCCCTCCCTTCTGCA
1 GCGCGTTTAGTCCCTCCCTTCTGCA
12429938 GCGCGTTT
1 GCGCGTTT
12429946 CGATTAACCC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 33 1.00
ACGTcount: A:0.07, C:0.38, G:0.22, T:0.33
Consensus pattern (25 bp):
GCGCGTTTAGTCCCTCCCTTCTGCA
Found at i:12431939 original size:20 final size:20
Alignment explanation
Indices: 12431911--12431975 Score: 57
Period size: 20 Copynumber: 3.5 Consensus size: 20
12431901 AATTATAATT
*
12431911 TATATTTTTCATTAATTTTA
1 TATAATTTTCATTAATTTTA
*
12431931 TATAATTTTAATT-A--TTA
1 TATAATTTTCATTAATTTTA
* * *
12431948 CAT-TTTTTCATTAATTGTA
1 TATAATTTTCATTAATTTTA
12431967 TATAATTTT
1 TATAATTTT
12431976 AATTGATATA
Statistics
Matches: 33, Mismatches: 8, Indels: 8
0.67 0.16 0.16
Matches are distributed among these distances:
16 7 0.21
17 6 0.18
19 5 0.15
20 15 0.45
ACGTcount: A:0.32, C:0.05, G:0.02, T:0.62
Consensus pattern (20 bp):
TATAATTTTCATTAATTTTA
Found at i:12431986 original size:15 final size:16
Alignment explanation
Indices: 12431958--12431987 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
12431948 CATTTTTTCA
12431958 TTAATTGTATATAATT
1 TTAATTGTATATAATT
12431974 TTAATTG-ATATAAT
1 TTAATTGTATATAAT
12431988 AACGAATTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.40, C:0.00, G:0.07, T:0.53
Consensus pattern (16 bp):
TTAATTGTATATAATT
Found at i:12432832 original size:21 final size:20
Alignment explanation
Indices: 12432790--12432849 Score: 59
Period size: 21 Copynumber: 3.0 Consensus size: 20
12432780 AACTTATTTA
* **
12432790 TATTTTAATTAATCATGTTT
1 TATTTTAATTAATCTTAATT
12432810 TAGTTTTAATTAATCTTAATT
1 TA-TTTTAATTAATCTTAATT
* *
12432831 TA-CTTAATTAAGCTTAATT
1 TATTTTAATTAATCTTAATT
12432850 ATTAATTTCG
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
19 15 0.44
20 2 0.06
21 17 0.50
ACGTcount: A:0.33, C:0.07, G:0.05, T:0.55
Consensus pattern (20 bp):
TATTTTAATTAATCTTAATT
Found at i:12435241 original size:15 final size:15
Alignment explanation
Indices: 12435221--12435257 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
12435211 ATTCAACTTG
12435221 CCTCATATTTCTCTC
1 CCTCATATTTCTCTC
* *
12435236 CCTCATTTTTCTTTC
1 CCTCATATTTCTCTC
12435251 CCTCATA
1 CCTCATA
12435258 GACAAGGTAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.14, C:0.38, G:0.00, T:0.49
Consensus pattern (15 bp):
CCTCATATTTCTCTC
Found at i:12436653 original size:72 final size:72
Alignment explanation
Indices: 12436530--12436876 Score: 284
Period size: 72 Copynumber: 4.7 Consensus size: 72
12436520 AGATGGGCGT
* * * * * *
12436530 TGAATTGCTACCAAAGCTTTTAGATGGTTCTATAATTGCCAACAG-GATGGGTACGAATATGGAG
1 TGAATTGCTACCAAAGCTTATAGAAGATTCTACAAGTGCTAA-AGAGATGGGTACGAATATGGAG
12436594 GTGAACAC
65 GTGAACAC
* * * * *
12436602 TGAATTGCTACCATATCTTATAGAAGATTCTACAAGTGCTAAAGAGATGGGTAAGACTATGGAGA
1 TGAATTGCTACCAAAGCTTATAGAAGATTCTACAAGTGCTAAAGAGATGGGTACGAATATGGAGG
*
12436667 TGAACAT
66 TGAACAC
* *
12436674 TGAATTGTTACCAAAGCTTATAGAAGATTCTACAAGTCCTAAAGAGATGGGT-CGTAATATGGAG
1 TGAATTGCTACCAAAGCTTATAGAAGATTCTACAAGTGCTAAAGAGATGGGTACG-AATATGGA-
* * *
12436738 GAGTGGAGAA
64 G-GTGAACAC
* * * * * * * * * *
12436748 TCGAATTGATATCAAAGCGTATAGAAGATTTTCCGAGTGCTAAAGAGATAGATATGAATAAGGAG
1 T-GAATTGCTACCAAAGCTTATAGAAGATTCTACAAGTGCTAAAGAGATGGGTACGAAT-ATG-G
* **
12436813 AAGGAGAACGT
63 -AGGTGAACAC
* ** * * *
12436824 TGAATTGATGTCAAAGCTTACAGAAGATTCTTCAAATGCTAAAGAGATGGGTA
1 TGAATTGCTACCAAAGCTTATAGAAGATTCTACAAGTGCTAAAGAGATGGGTA
12436877 AGGATGTGGC
Statistics
Matches: 219, Mismatches: 47, Indels: 15
0.78 0.17 0.05
Matches are distributed among these distances:
71 3 0.01
72 112 0.51
73 1 0.00
74 5 0.02
75 88 0.40
76 7 0.03
77 2 0.01
78 1 0.00
ACGTcount: A:0.37, C:0.12, G:0.25, T:0.27
Consensus pattern (72 bp):
TGAATTGCTACCAAAGCTTATAGAAGATTCTACAAGTGCTAAAGAGATGGGTACGAATATGGAGG
TGAACAC
Found at i:12438633 original size:27 final size:27
Alignment explanation
Indices: 12438602--12438670 Score: 86
Period size: 27 Copynumber: 2.6 Consensus size: 27
12438592 CGTCTATCTC
12438602 AGAGGCGCCAATGGTGGTGCC-TATCTG
1 AGAGGCGCCAATGGTGGTGCCATA-CTG
* * **
12438629 GGAGGCGCCATTATTGGTGCCATACTG
1 AGAGGCGCCAATGGTGGTGCCATACTG
12438656 AGAGGCGCCAATGGT
1 AGAGGCGCCAATGGT
12438671 CTGATTTTTC
Statistics
Matches: 33, Mismatches: 8, Indels: 2
0.77 0.19 0.05
Matches are distributed among these distances:
27 31 0.94
28 2 0.06
ACGTcount: A:0.20, C:0.22, G:0.36, T:0.22
Consensus pattern (27 bp):
AGAGGCGCCAATGGTGGTGCCATACTG
Found at i:12438760 original size:18 final size:18
Alignment explanation
Indices: 12438727--12438775 Score: 62
Period size: 18 Copynumber: 2.6 Consensus size: 18
12438717 AGAGAAACGG
12438727 AAGAAATAAGAAGGAAGCAA
1 AAGAAA-AA-AAGGAAGCAA
*
12438747 AAGAAAAAAAGGAAGGAA
1 AAGAAAAAAAGGAAGCAA
12438765 AAGAAGAAAAA
1 AAGAA-AAAAA
12438776 AATAAGGTAT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
18 14 0.52
19 7 0.26
20 6 0.22
ACGTcount: A:0.71, C:0.02, G:0.24, T:0.02
Consensus pattern (18 bp):
AAGAAAAAAAGGAAGCAA
Found at i:12441760 original size:27 final size:27
Alignment explanation
Indices: 12441730--12441796 Score: 116
Period size: 27 Copynumber: 2.4 Consensus size: 27
12441720 GCAAAATAAA
12441730 AAAAAAACATTATAATTTTATTTACAT
1 AAAAAAACATTATAATTTTATTTACAT
*
12441757 AAAAAACCATTATAATTTTATTTACAT
1 AAAAAAACATTATAATTTTATTTACAT
12441784 AAAAAAATCATTA
1 AAAAAAA-CATTA
12441797 CATAAATATG
Statistics
Matches: 37, Mismatches: 2, Indels: 1
0.93 0.05 0.03
Matches are distributed among these distances:
27 32 0.86
28 5 0.14
ACGTcount: A:0.54, C:0.09, G:0.00, T:0.37
Consensus pattern (27 bp):
AAAAAAACATTATAATTTTATTTACAT
Found at i:12443902 original size:36 final size:37
Alignment explanation
Indices: 12443861--12443939 Score: 151
Period size: 36 Copynumber: 2.2 Consensus size: 37
12443851 AAAAAGTCGG
12443861 TTATAATTAAACTTTTAATAAAATGATTTTTAA-TTT
1 TTATAATTAAACTTTTAATAAAATGATTTTTAATTTT
12443897 TTATAATTAAACTTTTAATAAAATGATTTTTAATTTT
1 TTATAATTAAACTTTTAATAAAATGATTTTTAATTTT
12443934 TTATAA
1 TTATAA
12443940 ACTTTATATG
Statistics
Matches: 42, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
36 33 0.79
37 9 0.21
ACGTcount: A:0.42, C:0.03, G:0.03, T:0.53
Consensus pattern (37 bp):
TTATAATTAAACTTTTAATAAAATGATTTTTAATTTT
Found at i:12444049 original size:60 final size:60
Alignment explanation
Indices: 12443973--12444094 Score: 167
Period size: 60 Copynumber: 2.0 Consensus size: 60
12443963 ATACTAAACT
* * * *
12443973 AAACACAACAACTTATAGCT-TAATCCTAAATTACTAATAAATTAAATT-TTAAATAATTAC
1 AAACACAAAAACTTATA-ATATAATCCTAAATTACTAACAAATT-AATTATAAAATAATTAC
*
12444033 AAACACAAAAATTTATAATATAATCCTAAATTACTAACAAATTAATTATAAAATAATTAC
1 AAACACAAAAACTTATAATATAATCCTAAATTACTAACAAATTAATTATAAAATAATTAC
12444093 AA
1 AA
12444095 TATTCATACA
Statistics
Matches: 55, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
59 5 0.09
60 50 0.91
ACGTcount: A:0.54, C:0.13, G:0.01, T:0.32
Consensus pattern (60 bp):
AAACACAAAAACTTATAATATAATCCTAAATTACTAACAAATTAATTATAAAATAATTAC
Found at i:12444149 original size:21 final size:21
Alignment explanation
Indices: 12444117--12444205 Score: 56
Period size: 21 Copynumber: 4.0 Consensus size: 21
12444107 AAATTACAAT
12444117 ATTACAATATTCATACAAAAA
1 ATTACAATATTCATACAAAAA
* * *
12444138 ATTGCATTATTCAT--ATAAA
1 ATTACAATATTCATACAAAAA
*
12444157 ATTATAATATTACAATATTCATACAAAA
1 ATTACAATATT-C-ATA--C--A-AAAA
12444185 AATTACAATATTCATACAAAA
1 -ATTACAATATTCATACAAAA
12444206 TACTAATCCA
Statistics
Matches: 50, Mismatches: 8, Indels: 19
0.65 0.10 0.25
Matches are distributed among these distances:
19 12 0.24
20 1 0.02
21 14 0.28
22 3 0.06
23 1 0.02
25 1 0.02
27 4 0.08
28 4 0.08
29 10 0.20
ACGTcount: A:0.53, C:0.12, G:0.01, T:0.34
Consensus pattern (21 bp):
ATTACAATATTCATACAAAAA
Found at i:12444166 original size:48 final size:48
Alignment explanation
Indices: 12444082--12444206 Score: 187
Period size: 48 Copynumber: 2.5 Consensus size: 48
12444072 AATTAATTAT
12444082 AAAATAATTACAATATTCATACAAAAAATTACAATATTACAATATTCATAC
1 AAAA-AATTACAATATTCATAC--AAAATTACAATATTACAATATTCATAC
* * * *
12444133 AAAAAATTGCATTATTCATATAAAATTATAATATTACAATATTCATAC
1 AAAAAATTACAATATTCATACAAAATTACAATATTACAATATTCATAC
12444181 AAAAAATTACAATATTCATACAAAAT
1 AAAAAATTACAATATTCATACAAAAT
12444207 ACTAATCCAA
Statistics
Matches: 67, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
48 49 0.73
50 14 0.21
51 4 0.06
ACGTcount: A:0.54, C:0.12, G:0.01, T:0.33
Consensus pattern (48 bp):
AAAAAATTACAATATTCATACAAAATTACAATATTACAATATTCATAC
Found at i:12444270 original size:19 final size:19
Alignment explanation
Indices: 12444246--12444309 Score: 92
Period size: 19 Copynumber: 3.2 Consensus size: 19
12444236 ATTATAAAAT
12444246 AATTACAATATTCATACAA
1 AATTACAATATTCATACAA
12444265 AATTACAATATTCATACAAAAA
1 AATTACAATATTCATAC---AA
*
12444287 AATTAAAATATTCATACAA
1 AATTACAATATTCATACAA
12444306 AATT
1 AATT
12444310 CTAATCCAAA
Statistics
Matches: 41, Mismatches: 1, Indels: 6
0.85 0.02 0.12
Matches are distributed among these distances:
19 23 0.56
22 18 0.44
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.31
Consensus pattern (19 bp):
AATTACAATATTCATACAA
Found at i:12444288 original size:22 final size:22
Alignment explanation
Indices: 12444241--12444307 Score: 95
Period size: 22 Copynumber: 3.2 Consensus size: 22
12444231 ATTTAATTAT
*
12444241 AAAATAATTACAATATTCATAC
1 AAAAAAATTACAATATTCATAC
12444263 ---AAAATTACAATATTCATAC
1 AAAAAAATTACAATATTCATAC
*
12444282 AAAAAAATTAAAATATTCATAC
1 AAAAAAATTACAATATTCATAC
12444304 AAAA
1 AAAA
12444308 TTCTAATCCA
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
19 18 0.45
22 22 0.55
ACGTcount: A:0.60, C:0.12, G:0.00, T:0.28
Consensus pattern (22 bp):
AAAAAAATTACAATATTCATAC
Found at i:12444393 original size:12 final size:12
Alignment explanation
Indices: 12444376--12444401 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
12444366 AAAAATTCAC
12444376 AATATCTTCTAA
1 AATATCTTCTAA
12444388 AATATCTTCTAA
1 AATATCTTCTAA
12444400 AA
1 AA
12444402 AATTCACAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.46, C:0.15, G:0.00, T:0.38
Consensus pattern (12 bp):
AATATCTTCTAA
Found at i:12444481 original size:3 final size:3
Alignment explanation
Indices: 12444475--12444507 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
12444465 TTTTTTTTCT
*
12444475 TTC TTC TTC TTC TTC TTC -TC TTC TTC TCC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T
12444508 CTCCTTCTGC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
2 2 0.07
3 25 0.93
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (3 bp):
TTC
Found at i:12444498 original size:14 final size:14
Alignment explanation
Indices: 12444479--12444515 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
12444469 TTTTCTTTCT
*
12444479 TCTTCTTCTTCTTC
1 TCTTCTTCTCCTTC
12444493 TCTTCTTCTCCTTC
1 TCTTCTTCTCCTTC
*
12444507 TCTCCTTCT
1 TCTTCTTCT
12444516 GCTTTCTCTC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.00, C:0.41, G:0.00, T:0.59
Consensus pattern (14 bp):
TCTTCTTCTCCTTC
Found at i:12444498 original size:17 final size:16
Alignment explanation
Indices: 12444471--12444507 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 16
12444461 TACTTTTTTT
*
12444471 TTCTTTCTTCTTCTTC
1 TTCTTTCTTCTTCTCC
12444487 TTCTTCTCTTCTTCTCC
1 TTCTT-TCTTCTTCTCC
12444504 TTCT
1 TTCT
12444508 CTCCTTCTGC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 5 0.26
17 14 0.74
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (16 bp):
TTCTTTCTTCTTCTCC
Found at i:12446100 original size:3 final size:3
Alignment explanation
Indices: 12446092--12446121 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
12446082 TACCGTCCGA
*
12446092 GTC GTC GTC GTA GTC GTC GTC GTC GTC GTC
1 GTC GTC GTC GTC GTC GTC GTC GTC GTC GTC
12446122 TTCCTCGTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.03, C:0.30, G:0.33, T:0.33
Consensus pattern (3 bp):
GTC
Found at i:12450588 original size:17 final size:17
Alignment explanation
Indices: 12450553--12450614 Score: 56
Period size: 16 Copynumber: 3.8 Consensus size: 17
12450543 TTTCAATAAT
* *
12450553 TTCAAATAAATTTGA-A
1 TTCAAATTAATTTTAGA
12450569 TTCAAATTAATTTTAGA
1 TTCAAATTAATTTTAGA
* **
12450586 TTCAAGTTTTTTTTAG-
1 TTCAAATTAATTTTAGA
*
12450602 TTCAAATCAATTT
1 TTCAAATTAATTT
12450615 GAATCTACTT
Statistics
Matches: 36, Mismatches: 9, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
16 22 0.61
17 14 0.39
ACGTcount: A:0.37, C:0.08, G:0.06, T:0.48
Consensus pattern (17 bp):
TTCAAATTAATTTTAGA
Found at i:12450852 original size:13 final size:13
Alignment explanation
Indices: 12450834--12450895 Score: 63
Period size: 13 Copynumber: 4.8 Consensus size: 13
12450824 TTAACAATTT
*
12450834 TTTTAAAAAGTGC
1 TTTTAAAAAGTAC
12450847 TTTT-AAAAGTAC
1 TTTTAAAAAGTAC
** * *
12450859 CGTAAAAAAGTTC
1 TTTTAAAAAGTAC
12450872 TTTTAAAAAGTAC
1 TTTTAAAAAGTAC
*
12450885 TTTTGAAAAGT
1 TTTTAAAAAGT
12450896 TTGATTTAAG
Statistics
Matches: 38, Mismatches: 10, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
12 8 0.21
13 30 0.79
ACGTcount: A:0.42, C:0.08, G:0.13, T:0.37
Consensus pattern (13 bp):
TTTTAAAAAGTAC
Found at i:12452784 original size:24 final size:24
Alignment explanation
Indices: 12452752--12452800 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 24
12452742 GATGCATAAG
* *
12452752 AAAACCACCACATAGTCGTCATTT
1 AAAACCACCACATAATCATCATTT
12452776 AAAACCACCACATAATCATCATTT
1 AAAACCACCACATAATCATCATTT
12452800 A
1 A
12452801 TATCATATAG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.43, C:0.29, G:0.04, T:0.24
Consensus pattern (24 bp):
AAAACCACCACATAATCATCATTT
Found at i:12460303 original size:14 final size:15
Alignment explanation
Indices: 12460279--12460308 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
12460269 ATAAATAGAT
12460279 AAATAGATAATAATA
1 AAATAGATAATAATA
12460294 AAATAG-TAATAATA
1 AAATAGATAATAATA
12460308 A
1 A
12460309 TGAAGGAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.60
15 6 0.40
ACGTcount: A:0.67, C:0.00, G:0.07, T:0.27
Consensus pattern (15 bp):
AAATAGATAATAATA
Found at i:12460345 original size:28 final size:29
Alignment explanation
Indices: 12460287--12460354 Score: 79
Period size: 28 Copynumber: 2.4 Consensus size: 29
12460277 ATAAATAGAT
*
12460287 AATAATAAAATAGTAATAATAATGAAGGAA
1 AATAATAAAATAG-AATAATAATGAACGAA
*
12460317 AA-AATAAAATA-AATAATCGATGAACGAA
1 AATAATAAAATAGAATAAT-AATGAACGAA
12460345 AATAA-AAAAT
1 AATAATAAAAT
12460355 TAAAATATAA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
27 6 0.18
28 15 0.44
29 11 0.32
30 2 0.06
ACGTcount: A:0.66, C:0.03, G:0.10, T:0.21
Consensus pattern (29 bp):
AATAATAAAATAGAATAATAATGAACGAA
Found at i:12460422 original size:18 final size:20
Alignment explanation
Indices: 12460401--12460447 Score: 64
Period size: 18 Copynumber: 2.5 Consensus size: 20
12460391 ATGCAAGGAT
12460401 TAAAATAAAAT-A-AATGAA
1 TAAAATAAAATAATAATGAA
12460419 TAAAATAAAATGAATAATGAA
1 TAAAATAAAAT-AATAATGAA
12460440 T-AAATAAA
1 TAAAATAAA
12460448 CAAGTAAATA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
18 11 0.42
20 8 0.31
21 7 0.27
ACGTcount: A:0.70, C:0.00, G:0.06, T:0.23
Consensus pattern (20 bp):
TAAAATAAAATAATAATGAA
Found at i:12460431 original size:14 final size:13
Alignment explanation
Indices: 12460404--12460479 Score: 59
Period size: 14 Copynumber: 5.7 Consensus size: 13
12460394 CAAGGATTAA
12460404 AATAAAATAAATG
1 AATAAAATAAATG
12460417 AATAAAATAAAATG
1 AATAAAAT-AAATG
12460431 AATAATGAATAAAT-
1 AATAA--AATAAATG
* *
12460445 AA-ACAAGTAAATA
1 AATA-AAATAAATG
*
12460458 AAT-AAATAAAGG
1 AATAAAATAAATG
12460470 AAATAAAATA
1 -AATAAAATA
12460480 TAAAAAAAAA
Statistics
Matches: 51, Mismatches: 4, Indels: 15
0.73 0.06 0.21
Matches are distributed among these distances:
12 12 0.24
13 14 0.27
14 18 0.35
15 4 0.08
16 3 0.06
ACGTcount: A:0.70, C:0.01, G:0.08, T:0.21
Consensus pattern (13 bp):
AATAAAATAAATG
Found at i:12460447 original size:4 final size:4
Alignment explanation
Indices: 12460403--12460467 Score: 51
Period size: 4 Copynumber: 15.8 Consensus size: 4
12460393 GCAAGGATTA
* * * * *
12460403 AAAT AAAAT AAAT GAAT AAAAT AAAAT GAAT -AAT GAAT AAAT AAAC AAGT
1 AAAT -AAAT AAAT AAAT -AAAT -AAAT AAAT AAAT AAAT AAAT AAAT AAAT
12460453 AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAA
12460468 GGAAATAAAA
Statistics
Matches: 50, Mismatches: 8, Indels: 5
0.79 0.13 0.08
Matches are distributed among these distances:
3 3 0.06
4 35 0.70
5 12 0.24
ACGTcount: A:0.71, C:0.02, G:0.06, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:12462406 original size:44 final size:44
Alignment explanation
Indices: 12462358--12462853 Score: 275
Period size: 44 Copynumber: 10.9 Consensus size: 44
12462348 AGGCTTTGTC
12462358 GCTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTAGTT
1 GCTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTAGTT
* * * * * * * *
12462402 GCTTCAAACGGTTCCATTACAACTTCAGAGAGATTAGATTCACTAT
1 GCTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATT-AGT-T
* * * *
12462448 -CTTCAATATTCTCCATTGCAACTTCAGGGAGATAAGATTCACTAT
1 GCTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATT-AGT-T
* * *
12462493 -CTTCAATCTGCTCCACTACAACTTCAGGGAGATGAGACTCGCTATGGTA
1 GCTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGA-T---TA--GTT
* * * * * * * *
12462542 GATTTAATCCGAC-CTACTGCAACTTCAGAGG-TATAGGATTTGTC
1 GCTTCAATCTG-CTCCACTGCAACTTCAG-GGAGATAAGATTAGTT
* * * * *
12462586 ACTTCAATCTACTCCACTGCTACTTAAGGGAGATAAGACTT-GTA
1 GCTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGA-TTAGTT
* * * * *
12462630 ACTTCTATCTGCTCCACTGTAACTCCAGGGAGATAAGATTTGTAACTTGTA
1 GCTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGA--T-T-A---GTT
* ** * * * *
12462681 GCTTTAATCTATTCTACTACAACTTCAGGGAAATAAGATTTGCTAT
1 GCTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTAG-T-T
* * *
12462727 -CTTCAATCTGCTCTACTGCAACTTCAGGAAGATAAGATTTGTT
1 GCTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTAGTT
* * * * * *
12462770 GTTTTAATCTGCTCCTCTACAACTTCAGGGAGATAAGATTTGTG
1 GCTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTAGTT
* * * *
12462814 GCTTTAATCTGCTCCACTGCATCTTTAGTGAGATAAGATT
1 GCTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATT
12462854 CGCCATGATG
Statistics
Matches: 346, Mismatches: 82, Indels: 48
0.73 0.17 0.10
Matches are distributed among these distances:
43 4 0.01
44 164 0.47
45 110 0.32
46 4 0.01
48 2 0.01
49 3 0.01
50 25 0.07
51 34 0.10
ACGTcount: A:0.29, C:0.21, G:0.17, T:0.33
Consensus pattern (44 bp):
GCTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTAGTT
Found at i:12462470 original size:45 final size:45
Alignment explanation
Indices: 12462359--12462525 Score: 187
Period size: 45 Copynumber: 3.7 Consensus size: 45
12462349 GGCTTTGTCG
* * * *
12462359 CTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATT-AGT-T
1 CTTCAATATGCTCCATTACAACTTCAGGGAGATAAGATTCACTAT
* * * *
12462402 GCTTCAA-ACGGTTCCATTACAACTTCAGAGAGATTAGATTCACTAT
1 -CTTCAATA-TGCTCCATTACAACTTCAGGGAGATAAGATTCACTAT
* *
12462448 CTTCAATATTCTCCATTGCAACTTCAGGGAGATAAGATTCACTAT
1 CTTCAATATGCTCCATTACAACTTCAGGGAGATAAGATTCACTAT
* *
12462493 CTTCAATCTGCTCCACTACAACTTCAGGGAGAT
1 CTTCAATATGCTCCATTACAACTTCAGGGAGAT
12462526 GAGACTCGCT
Statistics
Matches: 101, Mismatches: 18, Indels: 7
0.80 0.14 0.06
Matches are distributed among these distances:
44 31 0.31
45 68 0.67
46 2 0.02
ACGTcount: A:0.30, C:0.24, G:0.16, T:0.31
Consensus pattern (45 bp):
CTTCAATATGCTCCATTACAACTTCAGGGAGATAAGATTCACTAT
Found at i:12462777 original size:89 final size:88
Alignment explanation
Indices: 12462352--12462853 Score: 251
Period size: 89 Copynumber: 5.5 Consensus size: 88
12462342 AGGTATAGGC
* * * * * * * *
12462352 TTTGTCGCTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTAGTTGCTTCAAACGGTTCC
1 TTTGTAGCTTCAATCTGCTCCACTGCAACTTCAGTGAGATAAGATTTGTTGTTTTAATCTGATCC
* * *
12462417 AT-TACAACTTCAGAGAGATTAGA
66 -TCTACAACTTCAGGGAAATAAGA
** * * * * * *** * * *
12462440 TTCACTATCTTCAATATTCTCCATTGCAACTTCAGGGAGATAAGATTCACTATCTTCAATCTGCT
1 TT-TGTAGCTTCAATCTGCTCCACTGCAACTTCAGTGAGATAAGATTTGTTGT-TTTAATCTGAT
* * *
12462505 CCACTACAACTTCAGGGAGATGAGA
64 CCTCTACAACTTCAGGGAAATAAGA
* * * * * * *** *
12462530 CTCGCTATGGTAGATTTAATCCGAC-CTACTGCAACTTCAGAG-GTATAGGATTTGTCACTTCAA
1 -T---T-T-GTAGCTTCAATCTG-CTCCACTGCAACTTCAGTGAG-ATAAGATTTGTTGTTTTAA
* * * * *
12462593 TCT-ACTCCACTGCTACTTAAGGGAGATAAGA
58 TCTGA-TCCTCTACAACTTCAGGGAAATAAGA
* * * * * *
12462624 CTTGTAACTTCTATCTGCTCCACTGTAACTCCAGGGAGATAAGATTTGTAACTTGTAGCTTTAAT
1 TTTGTAGCTTCAATCTGCTCCACTGCAACTTCAGTGAGATAAGATTTG----TTGT---TTTAAT
*
12462689 CT-ATTCTACTACAACTTCAGGGAAATAAGA
59 CTGATCCT-CTACAACTTCAGGGAAATAAGA
* * *
12462719 TTTGCTATCTTCAATCTGCTCTACTGCAACTTCAG-GAAGATAAGATTTGTTGTTTTAATCTGCT
1 TTTG-TAGCTTCAATCTGCTCCACTGCAACTTCAGTG-AGATAAGATTTGTTGTTTTAATCTGAT
*
12462783 CCTCTACAACTTCAGGGAGATAAGA
64 CCTCTACAACTTCAGGGAAATAAGA
* * * *
12462808 TTTGTGGCTTTAATCTGCTCCACTGCATCTTTAGTGAGATAAGATT
1 TTTGTAGCTTCAATCTGCTCCACTGCAACTTCAGTGAGATAAGATT
12462854 CGCCATGATG
Statistics
Matches: 312, Mismatches: 77, Indels: 50
0.71 0.18 0.11
Matches are distributed among these distances:
87 1 0.00
88 67 0.21
89 74 0.24
90 33 0.11
91 1 0.00
92 5 0.02
94 34 0.11
95 59 0.19
96 38 0.12
ACGTcount: A:0.28, C:0.21, G:0.17, T:0.33
Consensus pattern (88 bp):
TTTGTAGCTTCAATCTGCTCCACTGCAACTTCAGTGAGATAAGATTTGTTGTTTTAATCTGATCC
TCTACAACTTCAGGGAAATAAGA
Found at i:12465674 original size:84 final size:84
Alignment explanation
Indices: 12465533--12465701 Score: 311
Period size: 84 Copynumber: 2.0 Consensus size: 84
12465523 CTTCTTGATA
*
12465533 ATGTAGTATATCACTCTTTTTTCCTTCCTGACTCATCGTGTTGGCCGAGCACGCATCCCATCGAA
1 ATGTAGTATATCACTCTTTTTTCCTTCCTAACTCATCGTGTTGGCCGAGCACGCATCCCATCGAA
*
12465598 TTCCCAAATACTGCCAAGT
66 TTCCCAAATACTACCAAGT
*
12465617 ATGTAGTATATCATTCTTTTTTCCTTCCTAACTCATCGTGTTGGCCGAGCACGCATCCCATCGAA
1 ATGTAGTATATCACTCTTTTTTCCTTCCTAACTCATCGTGTTGGCCGAGCACGCATCCCATCGAA
12465682 TTCCCAAATACTACCAAGT
66 TTCCCAAATACTACCAAGT
12465701 A
1 A
12465702 CAGTACTACC
Statistics
Matches: 82, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
84 82 1.00
ACGTcount: A:0.24, C:0.29, G:0.14, T:0.33
Consensus pattern (84 bp):
ATGTAGTATATCACTCTTTTTTCCTTCCTAACTCATCGTGTTGGCCGAGCACGCATCCCATCGAA
TTCCCAAATACTACCAAGT
Found at i:12467410 original size:15 final size:15
Alignment explanation
Indices: 12467390--12467427 Score: 67
Period size: 15 Copynumber: 2.5 Consensus size: 15
12467380 TCCTTTCTTG
*
12467390 TTTCTTTTCCAGCTC
1 TTTCTTCTCCAGCTC
12467405 TTTCTTCTCCAGCTC
1 TTTCTTCTCCAGCTC
12467420 TTTCTTCT
1 TTTCTTCT
12467428 TTTGAATTGT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.05, C:0.34, G:0.05, T:0.55
Consensus pattern (15 bp):
TTTCTTCTCCAGCTC
Found at i:12468663 original size:31 final size:31
Alignment explanation
Indices: 12468570--12468665 Score: 174
Period size: 31 Copynumber: 3.1 Consensus size: 31
12468560 GGCAAATTAC
*
12468570 AAGAGTAATTGAATCCTAATAAAACTCTTTC
1 AAGAGTAATTGAATCCTAATAAAACTCTTTA
12468601 AAGAGTAATTGAATCCTAATAAAAACTCTTTA
1 AAGAGTAATTGAATCCTAAT-AAAACTCTTTA
12468633 AAGAGTAATTGAATCCTAATAAAACTCTTTA
1 AAGAGTAATTGAATCCTAATAAAACTCTTTA
12468664 AA
1 AA
12468666 ATTATCTAAG
Statistics
Matches: 63, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
31 33 0.52
32 30 0.48
ACGTcount: A:0.46, C:0.14, G:0.09, T:0.31
Consensus pattern (31 bp):
AAGAGTAATTGAATCCTAATAAAACTCTTTA
Found at i:12473208 original size:13 final size:13
Alignment explanation
Indices: 12473190--12473236 Score: 58
Period size: 13 Copynumber: 3.5 Consensus size: 13
12473180 AGGTAGGCAA
12473190 CTTTTTTTTTGCG
1 CTTTTTTTTTGCG
**
12473203 CTTTTTTGCTTTTTG
1 CTTTTTT--TTTGCG
12473218 CTTTTTTTTTGCG
1 CTTTTTTTTTGCG
12473231 CTTTTT
1 CTTTTT
12473237 ACTCTCTCTT
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
13 17 0.61
15 11 0.39
ACGTcount: A:0.00, C:0.15, G:0.13, T:0.72
Consensus pattern (13 bp):
CTTTTTTTTTGCG
Found at i:12473209 original size:10 final size:10
Alignment explanation
Indices: 12473194--12473277 Score: 52
Period size: 10 Copynumber: 8.5 Consensus size: 10
12473184 AGGCAACTTT
12473194 TTTTTTGCGC
1 TTTTTTGCGC
12473204 TTTTTT--GC
1 TTTTTTGCGC
**
12473212 -TTTTTGCTTT
1 TTTTTTGC-GC
12473222 TTTTTTGCGC
1 TTTTTTGCGC
*
12473232 TTTTTACT-CTC
1 TTTTT--TGCGC
12473243 TCTTTTTGCGC
1 T-TTTTTGCGC
*
12473254 TTTTTT-TGC
1 TTTTTTGCGC
*
12473263 TTTTTTGTGC
1 TTTTTTGCGC
12473273 TTTTT
1 TTTTT
12473278 ACTCTCTTTT
Statistics
Matches: 58, Mismatches: 7, Indels: 18
0.70 0.08 0.22
Matches are distributed among these distances:
7 5 0.09
8 2 0.03
9 8 0.14
10 25 0.43
11 13 0.22
12 5 0.09
ACGTcount: A:0.01, C:0.17, G:0.13, T:0.69
Consensus pattern (10 bp):
TTTTTTGCGC
Found at i:12473248 original size:41 final size:41
Alignment explanation
Indices: 12473203--12473308 Score: 119
Period size: 41 Copynumber: 2.5 Consensus size: 41
12473193 TTTTTTTGCG
12473203 CTTTTTTGCTTTTTGCTTTTTTTTTGCGCTTTTTACTCTCT
1 CTTTTTTGCTTTTTGCTTTTTTTTTGCGCTTTTTACTCTCT
* * *
12473244 CTTTTTGCGCTTTTT--TTGCTTTTTTGTGCTTTTTACTCTCT
1 CTTTTT-TGCTTTTTGCTT-TTTTTTTGCGCTTTTTACTCTCT
12473285 -TTTTTTACGCTTTTTTGCTTTTTT
1 CTTTTTT--GC-TTTTTGCTTTTTT
12473309 GTTTTTTTGC
Statistics
Matches: 53, Mismatches: 5, Indels: 12
0.76 0.07 0.17
Matches are distributed among these distances:
40 7 0.13
41 29 0.55
42 12 0.23
43 3 0.06
44 2 0.04
ACGTcount: A:0.03, C:0.18, G:0.10, T:0.69
Consensus pattern (41 bp):
CTTTTTTGCTTTTTGCTTTTTTTTTGCGCTTTTTACTCTCT
Found at i:12473251 original size:22 final size:21
Alignment explanation
Indices: 12473222--12473299 Score: 90
Period size: 22 Copynumber: 3.7 Consensus size: 21
12473212 TTTTTGCTTT
12473222 TTTTTTGCGCTTTTTACTCTC
1 TTTTTTGCGCTTTTTACTCTC
12473243 TCTTTTTGCGCTTTTT--T-TGC
1 T-TTTTTGCGCTTTTTACTCT-C
*
12473263 TTTTTTGTGCTTTTTACTCTC
1 TTTTTTGCGCTTTTTACTCTC
*
12473284 TTTTTTTACGCTTTTT
1 -TTTTTTGCGCTTTTT
12473300 TGCTTTTTTG
Statistics
Matches: 48, Mismatches: 3, Indels: 11
0.77 0.05 0.18
Matches are distributed among these distances:
19 14 0.29
20 3 0.06
21 3 0.06
22 28 0.58
ACGTcount: A:0.04, C:0.19, G:0.10, T:0.67
Consensus pattern (21 bp):
TTTTTTGCGCTTTTTACTCTC
Found at i:12473307 original size:9 final size:9
Alignment explanation
Indices: 12473252--12473343 Score: 66
Period size: 9 Copynumber: 9.7 Consensus size: 9
12473242 CTCTTTTTGC
12473252 GCTTTTTTT
1 GCTTTTTTT
12473261 GCTTTTTTGT
1 GCTTTTTT-T
12473271 GCTTTTTACTCT
1 GCTTTTT--T-T
12473283 -CTTTTTTT
1 GCTTTTTTT
12473291 ACGC-TTTTTT
1 --GCTTTTTTT
12473301 GC-TTTTTT
1 GCTTTTTTT
12473309 G-TTTTTTT
1 GCTTTTTTT
*
12473317 GCTGTTTTT
1 GCTTTTTTT
12473326 GCTGTTCTTTTT
1 GC--TT-TTTTT
12473338 GCTTTT
1 GCTTTT
12473344 ATTTAAAAAA
Statistics
Matches: 69, Mismatches: 3, Indels: 22
0.73 0.03 0.23
Matches are distributed among these distances:
8 17 0.25
9 19 0.28
10 16 0.23
11 8 0.12
12 9 0.13
ACGTcount: A:0.02, C:0.14, G:0.13, T:0.71
Consensus pattern (9 bp):
GCTTTTTTT
Found at i:12473309 original size:40 final size:41
Alignment explanation
Indices: 12473222--12473310 Score: 144
Period size: 41 Copynumber: 2.2 Consensus size: 41
12473212 TTTTTGCTTT
* *
12473222 TTTTTTGCGCTTTTTACTCTCTCTTTTTGCGCTTTTTTTGC
1 TTTTTTGTGCTTTTTACTCTCTCTTTTTACGCTTTTTTTGC
*
12473263 TTTTTTGTGCTTTTTACTCTCTTTTTTTACGC-TTTTTTGC
1 TTTTTTGTGCTTTTTACTCTCTCTTTTTACGCTTTTTTTGC
12473303 TTTTTTGT
1 TTTTTTGT
12473311 TTTTTTGCTG
Statistics
Matches: 45, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
40 16 0.36
41 29 0.64
ACGTcount: A:0.03, C:0.18, G:0.11, T:0.67
Consensus pattern (41 bp):
TTTTTTGTGCTTTTTACTCTCTCTTTTTACGCTTTTTTTGC
Found at i:12473313 original size:7 final size:8
Alignment explanation
Indices: 12473293--12473328 Score: 54
Period size: 8 Copynumber: 4.4 Consensus size: 8
12473283 CTTTTTTTAC
12473293 GCTTTTTT
1 GCTTTTTT
12473301 GCTTTTTT
1 GCTTTTTT
*
12473309 GTTTTTTT
1 GCTTTTTT
12473317 GCTGTTTTT
1 GCT-TTTTT
12473326 GCT
1 GCT
12473329 GTTCTTTTTG
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
8 17 0.68
9 8 0.32
ACGTcount: A:0.00, C:0.11, G:0.17, T:0.72
Consensus pattern (8 bp):
GCTTTTTT
Found at i:12473573 original size:4 final size:4
Alignment explanation
Indices: 12473559--12473589 Score: 55
Period size: 4 Copynumber: 8.0 Consensus size: 4
12473549 TAAAATTAGT
12473559 TAAA T-AA TAAA TAAA TAAA TAAA TAAA TAAA
1 TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA
12473590 AAGGATAGAT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 3 0.12
4 23 0.88
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (4 bp):
TAAA
Found at i:12473982 original size:31 final size:31
Alignment explanation
Indices: 12473889--12473984 Score: 174
Period size: 31 Copynumber: 3.1 Consensus size: 31
12473879 GGCAAATTAC
*
12473889 AAGAGTAATTGAATCCTAATAAAACTCTTTC
1 AAGAGTAATTGAATCCTAATAAAACTCTTTA
12473920 AAGAGTAATTGAATCCTAATAAAAACTCTTTA
1 AAGAGTAATTGAATCCTAAT-AAAACTCTTTA
12473952 AAGAGTAATTGAATCCTAATAAAACTCTTTA
1 AAGAGTAATTGAATCCTAATAAAACTCTTTA
12473983 AA
1 AA
12473985 ATTATCTAAG
Statistics
Matches: 63, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
31 33 0.52
32 30 0.48
ACGTcount: A:0.46, C:0.14, G:0.09, T:0.31
Consensus pattern (31 bp):
AAGAGTAATTGAATCCTAATAAAACTCTTTA
Found at i:12475021 original size:3 final size:3
Alignment explanation
Indices: 12475013--12475047 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
12475003 GGTAAGTAAT
12475013 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
12475048 CAATAAATGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:12475133 original size:23 final size:21
Alignment explanation
Indices: 12475107--12475155 Score: 57
Period size: 23 Copynumber: 2.3 Consensus size: 21
12475097 ATAAAAAGGG
12475107 TAATAAAT-AAATAGATAAATAGA
1 TAATAAATAAAATAG-T-AATA-A
12475130 TAAT-AATAAAATAGTAATAA
1 TAATAAATAAAATAGTAATAA
12475150 TAATAA
1 TAATAA
12475156 TAATGAAGGC
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
20 5 0.21
21 5 0.21
22 4 0.17
23 10 0.42
ACGTcount: A:0.65, C:0.00, G:0.06, T:0.29
Consensus pattern (21 bp):
TAATAAATAAAATAGTAATAA
Found at i:12475147 original size:14 final size:15
Alignment explanation
Indices: 12475123--12475157 Score: 54
Period size: 15 Copynumber: 2.3 Consensus size: 15
12475113 ATAAATAGAT
12475123 AAATAGATAATAATA
1 AAATAGATAATAATA
12475138 AAATAG-TAATAATA
1 AAATAGATAATAATA
12475152 ATAATA
1 A-AATA
12475158 ATGAAGGCAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 9 0.47
15 10 0.53
ACGTcount: A:0.66, C:0.00, G:0.06, T:0.29
Consensus pattern (15 bp):
AAATAGATAATAATA
Found at i:12475229 original size:25 final size:25
Alignment explanation
Indices: 12475123--12475226 Score: 90
Period size: 26 Copynumber: 4.1 Consensus size: 25
12475113 ATAAATAGAT
*
12475123 AAATAGATAATAAT-AA--AATAGTA
1 AAATA-ATAATAATGAAGGAATAATA
*
12475146 ATAATAATAATAATGAAGGCATAAATA
1 A-AATAATAATAATGAAGGAAT-AATA
* *
12475173 AAATAAATAATCGATGAAAGAA-AATA
1 AAAT-AATAAT-AATGAAGGAATAATA
12475199 AAATAATAATAAATGAAGGAATAATA
1 AAATAATAAT-AATGAAGGAATAATA
12475225 AA
1 AA
12475227 TAAATGAATA
Statistics
Matches: 65, Mismatches: 8, Indels: 13
0.76 0.09 0.15
Matches are distributed among these distances:
23 9 0.14
24 6 0.09
25 14 0.22
26 19 0.29
27 10 0.15
28 7 0.11
ACGTcount: A:0.64, C:0.02, G:0.11, T:0.23
Consensus pattern (25 bp):
AAATAATAATAATGAAGGAATAATA
Found at i:12475230 original size:4 final size:4
Alignment explanation
Indices: 12475221--12475368 Score: 84
Period size: 4 Copynumber: 36.5 Consensus size: 4
12475211 ATGAAGGAAT
* ** * * *
12475221 AATA AATA AATG AATA CAAGG ATTA AAATA AAAA AATA AATA AATA AATC
1 AATA AATA AATA AATA -AATA AATA AA-TA AATA AATA AATA AATA AATA
* * * * * *
12475271 AAT- AATA TATG AATA AATA AGTA AATG AACA AATA AATT AATAA AATCA
1 AATA AATA AATA AATA AATA AATA AATA AATA AATA AATA AAT-A AAT-A
** * * * *
12475320 AAGG AAT- AATG AATA AATA AACA AGTA AATA AGTA AATA AATA AATA
1 AATA AATA AATA AATA AATA AATA AATA AATA AATA AATA AATA AATA
12475367 AA
1 AA
12475369 AGAATTAAAA
Statistics
Matches: 105, Mismatches: 34, Indels: 10
0.70 0.23 0.07
Matches are distributed among these distances:
3 6 0.06
4 87 0.83
5 12 0.11
ACGTcount: A:0.66, C:0.03, G:0.07, T:0.23
Consensus pattern (4 bp):
AATA
Found at i:12475962 original size:24 final size:24
Alignment explanation
Indices: 12475915--12475974 Score: 102
Period size: 24 Copynumber: 2.5 Consensus size: 24
12475905 GGTATATATT
12475915 AAATATATATATTTCATTTTTAATC
1 AAATATATAT-TTTCATTTTTAATC
*
12475940 AAATATATATTTTTATTTTTAATC
1 AAATATATATTTTCATTTTTAATC
12475964 AAATATATATT
1 AAATATATATT
12475975 ATATATATTT
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
24 24 0.71
25 10 0.29
ACGTcount: A:0.42, C:0.05, G:0.00, T:0.53
Consensus pattern (24 bp):
AAATATATATTTTCATTTTTAATC
Found at i:12484379 original size:22 final size:22
Alignment explanation
Indices: 12484339--12484380 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
12484329 AATAACATAG
* * *
12484339 TTTTGATAAATGCAGAAAAATC
1 TTTTAATAAATGAAAAAAAATC
12484361 TTTTAATAAATGAAAAAAAA
1 TTTTAATAAATGAAAAAAAA
12484381 ATTGAACTGT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.55, C:0.05, G:0.10, T:0.31
Consensus pattern (22 bp):
TTTTAATAAATGAAAAAAAATC
Found at i:12486477 original size:19 final size:19
Alignment explanation
Indices: 12486455--12486501 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
12486445 AGTTAGATCT
12486455 AAATATATTTTTTA-TTAA
1 AAATATATTTTTTATTTAA
12486473 GAAATAT-TTTTTTATTTAA
1 -AAATATATTTTTTATTTAA
12486492 ATAATATATT
1 A-AATATATT
12486502 CTATGTGATA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
18 8 0.32
19 15 0.60
20 2 0.08
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (19 bp):
AAATATATTTTTTATTTAA
Found at i:12486493 original size:16 final size:18
Alignment explanation
Indices: 12486454--12486494 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
12486444 TAGTTAGATC
12486454 TAAATATATTTTTTATTAA
1 TAAATATATTTTTTATT-A
*
12486473 GAAATAT-TTTTTTATT-
1 TAAATATATTTTTTATTA
12486489 TAAATA
1 TAAATA
12486495 ATATATTCTA
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
16 5 0.25
18 9 0.45
19 6 0.30
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.56
Consensus pattern (18 bp):
TAAATATATTTTTTATTA
Found at i:12491872 original size:13 final size:13
Alignment explanation
Indices: 12491844--12491886 Score: 54
Period size: 13 Copynumber: 3.4 Consensus size: 13
12491834 TAGTTCATTC
*
12491844 AAAAAAATTATAT
1 AAAAAATTTATAT
12491857 AAAAACATTTAT-T
1 AAAAA-ATTTATAT
12491870 -AAAAATTTATAT
1 AAAAAATTTATAT
12491882 AAAAA
1 AAAAA
12491887 TTAAATGAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
11 6 0.23
12 5 0.19
13 10 0.38
14 5 0.19
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (13 bp):
AAAAAATTTATAT
Found at i:12491873 original size:12 final size:12
Alignment explanation
Indices: 12491845--12491888 Score: 54
Period size: 12 Copynumber: 3.6 Consensus size: 12
12491835 AGTTCATTCA
*
12491845 AAAAAATTATAT
1 AAAAATTTATAT
12491857 AAAAACATTTAT-T
1 -AAAA-ATTTATAT
12491870 AAAAATTTATAT
1 AAAAATTTATAT
12491882 AAAAATT
1 AAAAATT
12491889 AAATGAAATT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
11 6 0.21
12 12 0.43
13 5 0.18
14 5 0.18
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.36
Consensus pattern (12 bp):
AAAAATTTATAT
Found at i:12513641 original size:29 final size:30
Alignment explanation
Indices: 12513579--12513642 Score: 78
Period size: 29 Copynumber: 2.2 Consensus size: 30
12513569 AACCCTGTCC
* *
12513579 AAAAAATAAATAGACTAAATTCTTAAATTT
1 AAAAAATAAATAGACCAAATTCTCAAATTT
* *
12513609 -AAAAGTACATAGACCAAATT-TCAAATTT
1 AAAAAATAAATAGACCAAATTCTCAAATTT
12513637 AAAAAA
1 AAAAAA
12513643 GTATAAATGG
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
28 7 0.25
29 21 0.75
ACGTcount: A:0.58, C:0.09, G:0.05, T:0.28
Consensus pattern (30 bp):
AAAAAATAAATAGACCAAATTCTCAAATTT
Found at i:12514839 original size:21 final size:22
Alignment explanation
Indices: 12514813--12514855 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
12514803 TATTAAATAC
12514813 TTTTATT-TACATTTTC-CAAAA
1 TTTTATTATAC-TTTTCTCAAAA
12514834 TTTTATTATACTTTTCTCAAAA
1 TTTTATTATACTTTTCTCAAAA
12514856 ATCCAATATG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
21 12 0.60
22 8 0.40
ACGTcount: A:0.33, C:0.14, G:0.00, T:0.53
Consensus pattern (22 bp):
TTTTATTATACTTTTCTCAAAA
Found at i:12515837 original size:17 final size:16
Alignment explanation
Indices: 12515804--12515833 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
12515794 ATTTGTTTTT
12515804 ACTTTATTTTATAATC
1 ACTTTATTTTATAATC
12515820 ACTTTATTTT-TAAT
1 ACTTTATTTTATAAT
12515834 ATCATTTTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.30, C:0.10, G:0.00, T:0.60
Consensus pattern (16 bp):
ACTTTATTTTATAATC
Found at i:12527423 original size:26 final size:26
Alignment explanation
Indices: 12527391--12527443 Score: 88
Period size: 26 Copynumber: 2.0 Consensus size: 26
12527381 TTAATCAAAT
*
12527391 TAATCGATTTAATTGAATTATTTCAG
1 TAATCGATCTAATTGAATTATTTCAG
*
12527417 TAATCGATCTAATTGAGTTATTTCAG
1 TAATCGATCTAATTGAATTATTTCAG
12527443 T
1 T
12527444 CAGCCATCAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.32, C:0.09, G:0.13, T:0.45
Consensus pattern (26 bp):
TAATCGATCTAATTGAATTATTTCAG
Found at i:12527555 original size:62 final size:62
Alignment explanation
Indices: 12527489--12527613 Score: 223
Period size: 62 Copynumber: 2.0 Consensus size: 62
12527479 AGTTTTTTGA
* * *
12527489 ATTTTTAGTTAATGATTAATTCGGTTCAAAATTAAATAATTAACCGATTACTTAAAATTATT
1 ATTTTTAGTTAACGATTAATTCAGTTCAAAATCAAATAATTAACCGATTACTTAAAATTATT
12527551 ATTTTTAGTTAACGATTAATTCAGTTCAAAATCAAATAATTAACCGATTACTTAAAATTATT
1 ATTTTTAGTTAACGATTAATTCAGTTCAAAATCAAATAATTAACCGATTACTTAAAATTATT
12527613 A
1 A
12527614 ATAATAAAAT
Statistics
Matches: 60, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
62 60 1.00
ACGTcount: A:0.42, C:0.10, G:0.07, T:0.42
Consensus pattern (62 bp):
ATTTTTAGTTAACGATTAATTCAGTTCAAAATCAAATAATTAACCGATTACTTAAAATTATT
Found at i:12527932 original size:93 final size:93
Alignment explanation
Indices: 12527827--12528002 Score: 246
Period size: 93 Copynumber: 1.9 Consensus size: 93
12527817 TCTCAAACTC
** * *
12527827 AAAACAAAGTCTAGGTAGAGATGGTAATTTTTCGGATAATAAAAATACTATCCGTTACGGATGC-
1 AAAACAAAGTCTAGGTAGAGATGACAATTTTTCGAATAATAAAAATACTATCCGATACGGATGCA
12527891 GTATTTAACCCCATGAATAATGGATAGTA
66 G-ATTTAACCCCATGAATAATGGATAGTA
* * ** *
12527920 AAAACAAAGTCTAGGTAGAGATGACAATTTTTCGAATAGTAAAAATATTATTTGATGCGGATGCA
1 AAAACAAAGTCTAGGTAGAGATGACAATTTTTCGAATAATAAAAATACTATCCGATACGGATGCA
*
12527985 GATTTAACCCCTTGAATA
66 GATTTAACCCCATGAATA
12528003 TCTCAATTAT
Statistics
Matches: 72, Mismatches: 10, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
93 71 0.99
94 1 0.01
ACGTcount: A:0.39, C:0.12, G:0.19, T:0.30
Consensus pattern (93 bp):
AAAACAAAGTCTAGGTAGAGATGACAATTTTTCGAATAATAAAAATACTATCCGATACGGATGCA
GATTTAACCCCATGAATAATGGATAGTA
Found at i:12529586 original size:31 final size:32
Alignment explanation
Indices: 12529538--12529597 Score: 81
Period size: 31 Copynumber: 1.9 Consensus size: 32
12529528 TTTTAAAAAA
12529538 AATATATTTATATTATTTTTAATTT-TTAATTT
1 AATATATTTATATTATTTTT-ATTTATTAATTT
12529570 AATA-ATTTA-ATATATTTTTATTTATTAA
1 AATATATTTATAT-TATTTTTATTTATTAA
12529598 AATTTTATAT
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
30 6 0.23
31 16 0.62
32 4 0.15
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (32 bp):
AATATATTTATATTATTTTTATTTATTAATTT
Found at i:12533447 original size:21 final size:22
Alignment explanation
Indices: 12533405--12533447 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
12533395 CCAATTAATC
12533405 TAGCCCAAACACTAAACCCAAT
1 TAGCCCAAACACTAAACCCAAT
* *
12533427 TAGCCTAAAC-CTAAGCCCAAT
1 TAGCCCAAACACTAAACCCAAT
12533448 ACCCTGGCCC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 10 0.53
22 9 0.47
ACGTcount: A:0.42, C:0.35, G:0.07, T:0.16
Consensus pattern (22 bp):
TAGCCCAAACACTAAACCCAAT
Found at i:12536823 original size:28 final size:28
Alignment explanation
Indices: 12536758--12536834 Score: 70
Period size: 28 Copynumber: 2.7 Consensus size: 28
12536748 ACATTAAAAA
12536758 AAAAGAAGAAAGAAAAAAAAGAGAACGAC
1 AAAA-AAGAAAGAAAAAAAAGAGAACGAC
*
12536787 AAAATAGAAA-AAAAATAAAGAGAGA-GA-
1 AAAAAAGAAAGAAAAA-AAAGAGA-ACGAC
**
12536814 AATAAAAGAATTAAAAAAAAG
1 AA-AAAAGAAAGAAAAAAAAG
12536835 TATATTTTAA
Statistics
Matches: 41, Mismatches: 3, Indels: 9
0.77 0.06 0.17
Matches are distributed among these distances:
27 7 0.17
28 24 0.59
29 10 0.24
ACGTcount: A:0.74, C:0.03, G:0.17, T:0.06
Consensus pattern (28 bp):
AAAAAAGAAAGAAAAAAAAGAGAACGAC
Found at i:12541686 original size:16 final size:16
Alignment explanation
Indices: 12541665--12541695 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
12541655 TAAATTTTAT
*
12541665 ATAATATTTTAAAAAA
1 ATAATATTGTAAAAAA
12541681 ATAATATTGTAAAAA
1 ATAATATTGTAAAAA
12541696 TTATTTTACT
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:0.61, C:0.00, G:0.03, T:0.35
Consensus pattern (16 bp):
ATAATATTGTAAAAAA
Found at i:12558943 original size:30 final size:31
Alignment explanation
Indices: 12558907--12558975 Score: 88
Period size: 31 Copynumber: 2.3 Consensus size: 31
12558897 TGGTTTGAAT
12558907 TTAGTCACTCAAC-TT-TCAAAAAATAACAAA
1 TTAGTCACT-AACGTTATCAAAAAATAACAAA
* *
12558937 TTAGTCACTAACGTTATCAAAAAGTGACAAA
1 TTAGTCACTAACGTTATCAAAAAATAACAAA
*
12558968 TCAGTCAC
1 TTAGTCAC
12558976 CTATTAACAT
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
29 3 0.09
30 11 0.32
31 20 0.59
ACGTcount: A:0.45, C:0.20, G:0.09, T:0.26
Consensus pattern (31 bp):
TTAGTCACTAACGTTATCAAAAAATAACAAA
Found at i:12559517 original size:6 final size:7
Alignment explanation
Indices: 12559491--12559516 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
12559481 TGGACGGGCA
12559491 AAAAAAG
1 AAAAAAG
12559498 AAAAAAG
1 AAAAAAG
12559505 AAAAAAG
1 AAAAAAG
12559512 AAAAA
1 AAAAA
12559517 GGGGAGATTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (7 bp):
AAAAAAG
Found at i:12561455 original size:13 final size:12
Alignment explanation
Indices: 12561438--12561494 Score: 53
Period size: 13 Copynumber: 4.4 Consensus size: 12
12561428 TTTTAATTTT
12561438 AAATTTTTTAAA
1 AAATTTTTTAAA
12561450 AGAATTTAATTTAAA
1 A-AATTT--TTTAAA
*
12561465 AAATGGTTTT-AA
1 AAAT-TTTTTAAA
12561477 AAATATTTTTAAA
1 AAAT-TTTTTAAA
12561490 AAATT
1 AAATT
12561495 ATTAAAACAA
Statistics
Matches: 37, Mismatches: 3, Indels: 10
0.74 0.06 0.20
Matches are distributed among these distances:
12 12 0.32
13 14 0.38
14 3 0.08
15 8 0.22
ACGTcount: A:0.51, C:0.00, G:0.05, T:0.44
Consensus pattern (12 bp):
AAATTTTTTAAA
Found at i:12561485 original size:11 final size:11
Alignment explanation
Indices: 12561459--12561511 Score: 52
Period size: 12 Copynumber: 4.5 Consensus size: 11
12561449 AAGAATTTAA
12561459 TTTAAAAAATGGT
1 TTTAAAAAAT--T
12561472 TTTAAAAATATT
1 TTTAAAAA-ATT
12561484 TTTAAAAAATT
1 TTTAAAAAATT
* *
12561495 ATTAAAACAATA
1 TTTAAAA-AATT
12561507 TTTAA
1 TTTAA
12561512 TGTATTATTA
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
11 9 0.26
12 16 0.46
13 8 0.23
14 2 0.06
ACGTcount: A:0.53, C:0.02, G:0.04, T:0.42
Consensus pattern (11 bp):
TTTAAAAAATT
Found at i:12574652 original size:34 final size:35
Alignment explanation
Indices: 12574596--12574662 Score: 91
Period size: 34 Copynumber: 1.9 Consensus size: 35
12574586 CAAACACCAG
* *
12574596 AAAATATTTTACAGTAAGTCATTTTACAGAAAAGT
1 AAAACATTTTACAGTAAATCATTTTACAGAAAAGT
* *
12574631 AAAACATTTTCCAG-AAATCATTTTACGGAAAA
1 AAAACATTTTACAGTAAATCATTTTACAGAAAA
12574663 CATTTTACTG
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
34 16 0.57
35 12 0.43
ACGTcount: A:0.46, C:0.12, G:0.10, T:0.31
Consensus pattern (35 bp):
AAAACATTTTACAGTAAATCATTTTACAGAAAAGT
Found at i:12574654 original size:14 final size:14
Alignment explanation
Indices: 12574631--12574670 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
12574621 ACAGAAAAGT
*
12574631 AAAACATTTTCCAG
1 AAAACATTTTACAG
* *
12574645 AAATCATTTTACGG
1 AAAACATTTTACAG
12574659 AAAACATTTTAC
1 AAAACATTTTAC
12574671 TGCCAATCAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.42, C:0.17, G:0.07, T:0.33
Consensus pattern (14 bp):
AAAACATTTTACAG
Found at i:12575457 original size:92 final size:92
Alignment explanation
Indices: 12575358--12575572 Score: 376
Period size: 92 Copynumber: 2.3 Consensus size: 92
12575348 ATGCTGCAAT
* *
12575358 TTTTAACCTATTTGTATATTTAATAAAATATGAACCTATTTGTATCAAAGTTTGCATATAAGCTA
1 TTTTAACCTATTTGTATATTTAATAAAATATAAACCTATTTGTATCAAAGTATGCATATAAGCTA
* *
12575423 CAATTTAGACAGCAAGTATGCATTTTG
66 CAAGTTAAACAGCAAGTATGCATTTTG
*
12575450 TTTTAACCTATTTGTATATTTAATAAAATATAAAGCTATTTGTATCAAAGTATGCATATAAGCTA
1 TTTTAACCTATTTGTATATTTAATAAAATATAAACCTATTTGTATCAAAGTATGCATATAAGCTA
*
12575515 TAAGTTAAACAGCAAGTATGCATTTTG
66 CAAGTTAAACAGCAAGTATGCATTTTG
12575542 TTTTAACCTATTTGTATATTTAATAAAATAT
1 TTTTAACCTATTTGTATATTTAATAAAATAT
12575573 TTGTATATAT
Statistics
Matches: 117, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
92 117 1.00
ACGTcount: A:0.38, C:0.10, G:0.11, T:0.41
Consensus pattern (92 bp):
TTTTAACCTATTTGTATATTTAATAAAATATAAACCTATTTGTATCAAAGTATGCATATAAGCTA
CAAGTTAAACAGCAAGTATGCATTTTG
Found at i:12576809 original size:60 final size:62
Alignment explanation
Indices: 12576698--12576816 Score: 179
Period size: 60 Copynumber: 1.9 Consensus size: 62
12576688 GATTTTAAGA
* *
12576698 TTGGTAAATCCTGCACATGTAATATTGGTAAATGATAGCAATTGAAAGTGATAACATTGTTAT
1 TTGGTAAATCCTGCACATGGAATATTGG-AAAGGATAGCAATTGAAAGTGATAACATTGTTAT
* *
12576761 TTGGTAAATCCTGCACATGGCA-ATTGG-CAGGATAGCAATTGAAAGTGATAACATTG
1 TTGGTAAATCCTGCACATGGAATATTGGAAAGGATAGCAATTGAAAGTGATAACATTG
12576817 GTGATTGGTG
Statistics
Matches: 52, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
60 27 0.52
62 5 0.10
63 20 0.38
ACGTcount: A:0.35, C:0.12, G:0.22, T:0.31
Consensus pattern (62 bp):
TTGGTAAATCCTGCACATGGAATATTGGAAAGGATAGCAATTGAAAGTGATAACATTGTTAT
Found at i:12576944 original size:9 final size:9
Alignment explanation
Indices: 12576930--12576973 Score: 74
Period size: 9 Copynumber: 5.1 Consensus size: 9
12576920 TTTTGTTACA
12576930 ACAATTAAT
1 ACAATTAAT
12576939 ACAATTAAT
1 ACAATTAAT
12576948 ACAATT-A-
1 ACAATTAAT
12576955 ACAATTAAT
1 ACAATTAAT
12576964 ACAATTAAT
1 ACAATTAAT
12576973 A
1 A
12576974 ATTTGATAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
7 6 0.18
8 2 0.06
9 25 0.76
ACGTcount: A:0.57, C:0.11, G:0.00, T:0.32
Consensus pattern (9 bp):
ACAATTAAT
Found at i:12576960 original size:16 final size:16
Alignment explanation
Indices: 12576939--12576976 Score: 67
Period size: 16 Copynumber: 2.4 Consensus size: 16
12576929 AACAATTAAT
12576939 ACAATTAATACAATTA
1 ACAATTAATACAATTA
12576955 ACAATTAATACAATTA
1 ACAATTAATACAATTA
*
12576971 ATAATT
1 ACAATT
12576977 TGATAATTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.55, C:0.11, G:0.00, T:0.34
Consensus pattern (16 bp):
ACAATTAATACAATTA
Found at i:12577071 original size:22 final size:23
Alignment explanation
Indices: 12577046--12577095 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
12577036 AAAAATTTGA
* * *
12577046 TAATTTTA-CTAACAATTAGTTT
1 TAATTTTATCAAAAAATTAATTT
12577068 TAATTTTATCAAAAAATTAATTT
1 TAATTTTATCAAAAAATTAATTT
12577091 TAATT
1 TAATT
12577096 AAAAACGGGC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
22 8 0.33
23 16 0.67
ACGTcount: A:0.42, C:0.06, G:0.02, T:0.50
Consensus pattern (23 bp):
TAATTTTATCAAAAAATTAATTT
Found at i:12577086 original size:66 final size:68
Alignment explanation
Indices: 12576955--12577088 Score: 161
Period size: 66 Copynumber: 2.0 Consensus size: 68
12576945 AATACAATTA
* * * *
12576955 ACAATTAATACAATTAATAATTTGATAATTTTACTAATCAAATGTTAGATTTTGTTACAACAATT
1 ACAATTAATACAATTAAAAATTTGATAATTTTACTAATCAAATGTTAGATTTTATCACAAAAATT
12577020 AAT
66 AAT
*
12577023 ACAATTAA-A-AATTAAAAATTTGATAATTTTACTAA-CAATTAGTTTTA-ATTTTATCA-AAAA
1 ACAATTAATACAATTAAAAATTTGATAATTTTACTAATCAA--A-TGTTAGATTTTATCACAAAA
12577083 ATTAAT
63 ATTAAT
12577089 TTTAATTAAA
Statistics
Matches: 58, Mismatches: 5, Indels: 8
0.82 0.07 0.11
Matches are distributed among these distances:
65 3 0.05
66 34 0.59
67 9 0.16
68 12 0.21
ACGTcount: A:0.47, C:0.07, G:0.04, T:0.41
Consensus pattern (68 bp):
ACAATTAATACAATTAAAAATTTGATAATTTTACTAATCAAATGTTAGATTTTATCACAAAAATT
AAT
Found at i:12578454 original size:31 final size:31
Alignment explanation
Indices: 12578403--12578483 Score: 103
Period size: 31 Copynumber: 2.6 Consensus size: 31
12578393 TCACTTAGTT
*
12578403 AAAAAATTTATAATTT-AGTCATTAAACTATTC
1 AAAAAATTT-T-ATTTAAGTCACTAAACTATTC
*
12578435 -AAAAGTTTTCATTTAAGTCACTAAACTATTC
1 AAAAAATTTT-ATTTAAGTCACTAAACTATTC
12578466 AAAAAATTTTATTTAAGT
1 AAAAAATTTTATTTAAGT
12578484 TACTGGGTTA
Statistics
Matches: 43, Mismatches: 4, Indels: 5
0.83 0.08 0.10
Matches are distributed among these distances:
30 5 0.12
31 30 0.70
32 8 0.19
ACGTcount: A:0.44, C:0.10, G:0.05, T:0.41
Consensus pattern (31 bp):
AAAAAATTTTATTTAAGTCACTAAACTATTC
Found at i:12585523 original size:15 final size:15
Alignment explanation
Indices: 12585481--12585530 Score: 57
Period size: 15 Copynumber: 3.3 Consensus size: 15
12585471 TTGTTAGGTA
12585481 TGTTACTTATATTAT
1 TGTTACTTATATTAT
*
12585496 TATTA-TTATTATTAT
1 TGTTACTTA-TATTAT
*
12585511 TGTTACTTGTATTAT
1 TGTTACTTATATTAT
*
12585526 CGTTA
1 TGTTA
12585531 GCATCATTCT
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
14 3 0.10
15 24 0.83
16 2 0.07
ACGTcount: A:0.26, C:0.06, G:0.08, T:0.60
Consensus pattern (15 bp):
TGTTACTTATATTAT
Found at i:12587159 original size:11 final size:11
Alignment explanation
Indices: 12587143--12587194 Score: 95
Period size: 11 Copynumber: 4.7 Consensus size: 11
12587133 ATGCCCTAAT
*
12587143 TTTCATTAGAA
1 TTTCATTAAAA
12587154 TTTCATTAAAA
1 TTTCATTAAAA
12587165 TTTCATTAAAA
1 TTTCATTAAAA
12587176 TTTCATTAAAA
1 TTTCATTAAAA
12587187 TTTCATTA
1 TTTCATTA
12587195 GATGCCCTAA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
11 40 1.00
ACGTcount: A:0.40, C:0.10, G:0.02, T:0.48
Consensus pattern (11 bp):
TTTCATTAAAA
Found at i:12590250 original size:27 final size:27
Alignment explanation
Indices: 12590220--12590288 Score: 95
Period size: 27 Copynumber: 2.6 Consensus size: 27
12590210 TGCTTATCTC
*
12590220 AGAGGCGCCAATGGTGGTGCCTAT-TTG
1 AGAGGCGCCAATGGTGCTGCCT-TGTTG
* *
12590247 AGAGGCGCCACTAGTGCTGCCTTGTTG
1 AGAGGCGCCAATGGTGCTGCCTTGTTG
12590274 AGAGGCGCCAATGGT
1 AGAGGCGCCAATGGT
12590289 CTGATTTTTC
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
26 1 0.03
27 35 0.97
ACGTcount: A:0.19, C:0.22, G:0.36, T:0.23
Consensus pattern (27 bp):
AGAGGCGCCAATGGTGCTGCCTTGTTG
Found at i:12590391 original size:19 final size:19
Alignment explanation
Indices: 12590351--12590402 Score: 52
Period size: 19 Copynumber: 2.7 Consensus size: 19
12590341 CGAAAGAAAC
*
12590351 AAAAAGGAAGGCAGAAGAA
1 AAAAAGAAAGGCAGAAGAA
*
12590370 AAAAAGAAAGGGA-AAGAGA
1 AAAAAGAAAGGCAGAAGA-A
*
12590389 AAAATGATAAGGCA
1 AAAAAGA-AAGGCA
12590403 TTTTGGTTTA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
18 4 0.15
19 18 0.67
20 5 0.19
ACGTcount: A:0.63, C:0.04, G:0.29, T:0.04
Consensus pattern (19 bp):
AAAAAGAAAGGCAGAAGAA
Found at i:12593353 original size:16 final size:15
Alignment explanation
Indices: 12593322--12593365 Score: 61
Period size: 16 Copynumber: 2.8 Consensus size: 15
12593312 ACAAAATCAA
12593322 ATAAAATTAAATTAT
1 ATAAAATTAAATTAT
*
12593337 ATAAAAGTTACATTAT
1 ATAAAA-TTAAATTAT
12593353 ATAAAAATTAAAT
1 AT-AAAATTAAAT
12593366 GAGTTAACAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 6 0.24
16 15 0.60
17 4 0.16
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.36
Consensus pattern (15 bp):
ATAAAATTAAATTAT
Found at i:12593772 original size:19 final size:19
Alignment explanation
Indices: 12593747--12593807 Score: 86
Period size: 19 Copynumber: 3.2 Consensus size: 19
12593737 ATTATAAAAT
12593747 AATTACAATATTCATACAA
1 AATTACAATATTCATACAA
* *
12593766 CATTACAATATTCATAAAAA
1 AATTACAATATTCAT-ACAA
*
12593786 AATTAGAATATTCATACAA
1 AATTACAATATTCATACAA
12593805 AAT
1 AAT
12593808 ACTAATCCAA
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
19 20 0.56
20 16 0.44
ACGTcount: A:0.54, C:0.13, G:0.02, T:0.31
Consensus pattern (19 bp):
AATTACAATATTCATACAA
Found at i:12593795 original size:20 final size:20
Alignment explanation
Indices: 12593740--12593806 Score: 82
Period size: 20 Copynumber: 3.4 Consensus size: 20
12593730 AAATTTAATT
*
12593740 ATAAAATAATTACAATATTC
1 ATAAAAAAATTACAATATTC
* *
12593760 AT-ACAACATTACAATATTC
1 ATAAAAAAATTACAATATTC
*
12593779 ATAAAAAAATTAGAATATTC
1 ATAAAAAAATTACAATATTC
12593799 ATACAAAA
1 ATA-AAAA
12593807 TACTAATCCA
Statistics
Matches: 39, Mismatches: 6, Indels: 3
0.81 0.12 0.06
Matches are distributed among these distances:
19 16 0.41
20 19 0.49
21 4 0.10
ACGTcount: A:0.57, C:0.12, G:0.01, T:0.30
Consensus pattern (20 bp):
ATAAAAAAATTACAATATTC
Found at i:12593997 original size:14 final size:15
Alignment explanation
Indices: 12593980--12594011 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
12593970 ACCTTTTTCT
12593980 TTCTTTCTT-TCTTC
1 TTCTTTCTTCTCTTC
12593994 TTC-TTCTTCTCTTC
1 TTCTTTCTTCTCTTC
12594008 TTCT
1 TTCT
12594012 CCTTTCTCTC
Statistics
Matches: 16, Mismatches: 0, Indels: 3
0.84 0.00 0.16
Matches are distributed among these distances:
13 5 0.31
14 11 0.69
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (15 bp):
TTCTTTCTTCTCTTC
Found at i:12594176 original size:27 final size:27
Alignment explanation
Indices: 12594146--12594209 Score: 76
Period size: 27 Copynumber: 2.4 Consensus size: 27
12594136 AGAAGGCCAC
*
12594146 CATTGATGCCTC-CTTATGAGGCACATT
1 CATTGACGCCTCTC-TATGAGGCACATT
* *
12594173 CATTGGCGCCTCTCTATGAGGCATATT
1 CATTGACGCCTCTCTATGAGGCACATT
*
12594200 CATTGGCGCC
1 CATTGACGCC
12594210 AACTTGATAG
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
27 32 0.97
28 1 0.03
ACGTcount: A:0.19, C:0.28, G:0.22, T:0.31
Consensus pattern (27 bp):
CATTGACGCCTCTCTATGAGGCACATT
Found at i:12595891 original size:25 final size:25
Alignment explanation
Indices: 12595863--12596030 Score: 87
Period size: 25 Copynumber: 6.8 Consensus size: 25
12595853 TGTTATATGA
12595863 CTCTCATGAGCTTCCCGATATTTGG
1 CTCTCATGAGCTTCCCGATATTTGG
*
12595888 CTCTCATGACCTTCCC-A-ATTAATGG
1 CTCTCATGAGCTTCCCGATATT--TGG
* * * *
12595913 CTTTCTTGAGATTCCTG-T-TTATGG
1 CTCTCATGAGCTTCCCGATATT-TGG
* *
12595937 CTCGT-ATGAGCTTCCCAATAATTGG
1 CTC-TCATGAGCTTCCCGATATTTGG
* * * *
12595962 CT-TGCAAGAGCTTCCTGTTATATGG
1 CTCT-CATGAGCTTCCCGATATTTGG
* * **
12595987 CTCACATGAGCTTCCCGTTACATGG
1 CTCTCATGAGCTTCCCGATATTTGG
** *
12596012 CTCAAAAGAGCTTCCCGAT
1 CTCTCATGAGCTTCCCGAT
12596031 TACATACTCG
Statistics
Matches: 108, Mismatches: 25, Indels: 20
0.71 0.16 0.13
Matches are distributed among these distances:
23 4 0.04
24 15 0.14
25 88 0.81
26 1 0.01
ACGTcount: A:0.21, C:0.26, G:0.19, T:0.34
Consensus pattern (25 bp):
CTCTCATGAGCTTCCCGATATTTGG
Found at i:12595963 original size:49 final size:49
Alignment explanation
Indices: 12595885--12596002 Score: 132
Period size: 49 Copynumber: 2.4 Consensus size: 49
12595875 TCCCGATATT
* * **
12595885 TGGCTCTCATGACCTTCCCAATTAATGGCTTTCTTGAGATTCCTGTT-TA
1 TGGCTCT-ATGAGCTTCCCAATTAATGGCTTGCAAGAGATTCCTGTTATA
*
12595934 TGGCTCGTATGAGCTTCCCAA-TAATTGGCTTGCAAGAGCTTCCTGTTATA
1 TGGCTC-TATGAGCTTCCCAATTAA-TGGCTTGCAAGAGATTCCTGTTATA
*
12595984 TGGCTCACATGAGCTTCCC
1 TGGCTC-TATGAGCTTCCC
12596003 GTTACATGGC
Statistics
Matches: 59, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
48 3 0.05
49 36 0.61
50 20 0.34
ACGTcount: A:0.19, C:0.25, G:0.19, T:0.36
Consensus pattern (49 bp):
TGGCTCTATGAGCTTCCCAATTAATGGCTTGCAAGAGATTCCTGTTATA
Found at i:12596021 original size:50 final size:49
Alignment explanation
Indices: 12595924--12596026 Score: 118
Period size: 50 Copynumber: 2.1 Consensus size: 49
12595914 TTTCTTGAGA
** ***
12595924 TTCCTGTTTATGGCTCGTATGAGCTTCCCAATAATTGGCTTGCAAGAGC
1 TTCCTGTTTATGGCTCACATGAGCTTCCCAATAATTGGCTCAAAAGAGC
**
12595973 TTCCTGTTATATGGCTCACATGAGCTTCCCGTTACA-TGGCTCAAAAGAGC
1 TTCCTGTT-TATGGCTCACATGAGCTTCCCAATA-ATTGGCTCAAAAGAGC
12596023 TTCC
1 TTCC
12596027 CGATTACATA
Statistics
Matches: 45, Mismatches: 7, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
49 8 0.18
50 36 0.80
51 1 0.02
ACGTcount: A:0.21, C:0.25, G:0.20, T:0.33
Consensus pattern (49 bp):
TTCCTGTTTATGGCTCACATGAGCTTCCCAATAATTGGCTCAAAAGAGC
Found at i:12606201 original size:35 final size:35
Alignment explanation
Indices: 12606155--12606226 Score: 126
Period size: 35 Copynumber: 2.1 Consensus size: 35
12606145 GTTGTATTTG
12606155 GTTGCAAGATGGCTTGTGTAACGACCTGGTTTTCA
1 GTTGCAAGATGGCTTGTGTAACGACCTGGTTTTCA
**
12606190 GTTGCAAGATGGCTTGTGTAACGGTCTGGTTTTCA
1 GTTGCAAGATGGCTTGTGTAACGACCTGGTTTTCA
12606225 GT
1 GT
12606227 GGTGTCAAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.18, C:0.15, G:0.31, T:0.36
Consensus pattern (35 bp):
GTTGCAAGATGGCTTGTGTAACGACCTGGTTTTCA
Found at i:12606682 original size:17 final size:17
Alignment explanation
Indices: 12606662--12606696 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
12606652 AATTTTAATT
**
12606662 ATAATAAAGTAAATAAA
1 ATAATAAAACAAATAAA
12606679 ATAATAAAACAAATAAA
1 ATAATAAAACAAATAAA
12606696 A
1 A
12606697 GGAAAAAAAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.74, C:0.03, G:0.03, T:0.20
Consensus pattern (17 bp):
ATAATAAAACAAATAAA
Found at i:12613301 original size:19 final size:18
Alignment explanation
Indices: 12613277--12613349 Score: 56
Period size: 19 Copynumber: 3.9 Consensus size: 18
12613267 TTTTTCTTCT
12613277 CTTCAACAGAAAGCAAAAA
1 CTTCAACAGAAA-CAAAAA
**
12613296 CTTCAACTCAAACAAAAGA
1 CTTCAACAGAAACAAAA-A
* *
12613315 CTTAAATAGAAACACAAAA
1 CTTCAACAGAAACA-AAAA
* * *
12613334 CATCAATAGAAGCAAA
1 CTTCAACAGAAACAAA
12613350 TTTTTGGTTG
Statistics
Matches: 43, Mismatches: 9, Indels: 5
0.75 0.16 0.09
Matches are distributed among these distances:
18 7 0.16
19 33 0.77
20 3 0.07
ACGTcount: A:0.58, C:0.21, G:0.08, T:0.14
Consensus pattern (18 bp):
CTTCAACAGAAACAAAAA
Found at i:12623548 original size:33 final size:33
Alignment explanation
Indices: 12623506--12623571 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
12623496 AGAATTGTTT
12623506 TATAAAATTGTTTATTTTACACGTACGTGCAAA
1 TATAAAATTGTTTATTTTACACGTACGTGCAAA
12623539 TATAAAATTGTTTATTTTACACGTACGTGCAAA
1 TATAAAATTGTTTATTTTACACGTACGTGCAAA
12623572 CTCACCGATC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.36, C:0.12, G:0.12, T:0.39
Consensus pattern (33 bp):
TATAAAATTGTTTATTTTACACGTACGTGCAAA
Found at i:12625510 original size:3 final size:3
Alignment explanation
Indices: 12625498--12625577 Score: 69
Period size: 3 Copynumber: 27.3 Consensus size: 3
12625488 ATTTTTTAGC
* * * *
12625498 TAT T-T TAT TAT TAT TAT TAT TA- TGT TAT TAT CAT TA- TAC CAT TATT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T
*
12625544 TAT TAT TA- TAT TATT TAT TAT CAT TAT TAT TAT T
1 TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT T
12625578 TCTATATTCA
Statistics
Matches: 62, Mismatches: 9, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
2 7 0.11
3 49 0.79
4 6 0.10
ACGTcount: A:0.31, C:0.05, G:0.01, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:12625588 original size:21 final size:19
Alignment explanation
Indices: 12625501--12625588 Score: 69
Period size: 19 Copynumber: 4.6 Consensus size: 19
12625491 TTTTAGCTAT
12625501 TTTATTATT-ATTATTATTA
1 TTTATTATTCATTA-TATTA
**
12625520 TGTTATTA-TCATTATACCA
1 T-TTATTATTCATTATATTA
12625539 -TTATTTATT-ATTATATTA
1 TTTA-TTATTCATTATATTA
12625557 TTTATTA-TCATTATTATTA
1 TTTATTATTCATTA-TATTA
*
12625576 TTTCTATATTCAT
1 TTTAT-TATTCAT
12625589 ACACACGCAT
Statistics
Matches: 55, Mismatches: 5, Indels: 16
0.72 0.07 0.21
Matches are distributed among these distances:
17 4 0.07
18 17 0.31
19 18 0.33
20 12 0.22
21 4 0.07
ACGTcount: A:0.31, C:0.07, G:0.01, T:0.61
Consensus pattern (19 bp):
TTTATTATTCATTATATTA
Found at i:12625631 original size:22 final size:22
Alignment explanation
Indices: 12625595--12625686 Score: 85
Period size: 22 Copynumber: 3.9 Consensus size: 22
12625585 TCATACACAC
*
12625595 GCATTGTTTTTTATAATATATAT
1 GCATT-TTTTATATAATATATAT
* *
12625618 GCATTTTTTATATAGTATACAT
1 GCATTTTTTATATAATATATAT
12625640 GCATTGTTTTTATAATATATATATATAT
1 GCA---TTTTT-T-ATATA-ATATATAT
*
12625668 GCATTTTTTATATAGTATA
1 GCATTTTTTATATAATATA
12625687 CATATACCAA
Statistics
Matches: 57, Mismatches: 6, Indels: 13
0.75 0.08 0.17
Matches are distributed among these distances:
22 21 0.37
23 10 0.18
24 1 0.02
25 10 0.18
26 1 0.02
27 5 0.09
28 9 0.16
ACGTcount: A:0.33, C:0.05, G:0.09, T:0.53
Consensus pattern (22 bp):
GCATTTTTTATATAATATATAT
Found at i:12625669 original size:28 final size:28
Alignment explanation
Indices: 12625626--12625693 Score: 84
Period size: 28 Copynumber: 2.4 Consensus size: 28
12625616 ATGCATTTTT
12625626 TATATAGTATACATGCATTGTTTT-TATAA
1 TATATA-TATACATGCATT-TTTTATATAA
* *
12625655 TATATATATATATGCATTTTTTATATAG
1 TATATATATACATGCATTTTTTATATAA
*
12625683 TATACATATAC
1 TATATATATAC
12625694 CAATATATAT
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
27 4 0.12
28 24 0.71
29 6 0.18
ACGTcount: A:0.37, C:0.07, G:0.07, T:0.49
Consensus pattern (28 bp):
TATATATATACATGCATTTTTTATATAA
Found at i:12626457 original size:3 final size:3
Alignment explanation
Indices: 12626445--12626524 Score: 69
Period size: 3 Copynumber: 27.3 Consensus size: 3
12626435 ATTTTTTAGC
* * * *
12626445 TAT T-T TAT TAT TAT TAT TAT TA- TGT TAT TAT CAT TA- TAC CAT TATT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T
*
12626491 TAT TAT TA- TAT TATT TAT TAT CAT TAT TAT TAT T
1 TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT T
12626525 TCTATATTCA
Statistics
Matches: 62, Mismatches: 9, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
2 7 0.11
3 49 0.79
4 6 0.10
ACGTcount: A:0.31, C:0.05, G:0.01, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:12626535 original size:21 final size:19
Alignment explanation
Indices: 12626448--12626535 Score: 69
Period size: 19 Copynumber: 4.6 Consensus size: 19
12626438 TTTTAGCTAT
12626448 TTTATTATT-ATTATTATTA
1 TTTATTATTCATTA-TATTA
**
12626467 TGTTATTA-TCATTATACCA
1 T-TTATTATTCATTATATTA
12626486 -TTATTTATT-ATTATATTA
1 TTTA-TTATTCATTATATTA
12626504 TTTATTA-TCATTATTATTA
1 TTTATTATTCATTA-TATTA
*
12626523 TTTCTATATTCAT
1 TTTAT-TATTCAT
12626536 ACACACGCAT
Statistics
Matches: 55, Mismatches: 5, Indels: 16
0.72 0.07 0.21
Matches are distributed among these distances:
17 4 0.07
18 17 0.31
19 18 0.33
20 12 0.22
21 4 0.07
ACGTcount: A:0.31, C:0.07, G:0.01, T:0.61
Consensus pattern (19 bp):
TTTATTATTCATTATATTA
Found at i:12626580 original size:24 final size:25
Alignment explanation
Indices: 12626542--12626636 Score: 110
Period size: 24 Copynumber: 4.0 Consensus size: 25
12626532 TCATACACAC
*
12626542 GCATTGTTTTTTATAATATATATAT
1 GCATTGTTTTATATAATATATATAT
* *
12626567 GCATT-TTTTATAT-A-GTATACAT
1 GCATTGTTTTATATAATATATATAT
12626589 GCATTGTTTT-TATAATATATATAT
1 GCATTGTTTTATATAATATATATAT
* *
12626613 GCATT-TTTTATATAGTATACATAT
1 GCATTGTTTTATATAATATATATAT
12626637 ACCAATATAT
Statistics
Matches: 59, Mismatches: 7, Indels: 9
0.79 0.09 0.12
Matches are distributed among these distances:
22 14 0.24
23 10 0.17
24 30 0.51
25 5 0.08
ACGTcount: A:0.33, C:0.06, G:0.08, T:0.53
Consensus pattern (25 bp):
GCATTGTTTTATATAATATATATAT
Found at i:12626605 original size:46 final size:47
Alignment explanation
Indices: 12626542--12626634 Score: 179
Period size: 46 Copynumber: 2.0 Consensus size: 47
12626532 TCATACACAC
12626542 GCATTGTTTTTTATAATATATATATGCATTTTTTATATAGTATACAT
1 GCATTGTTTTTTATAATATATATATGCATTTTTTATATAGTATACAT
12626589 GCATTG-TTTTTATAATATATATATGCATTTTTTATATAGTATACAT
1 GCATTGTTTTTTATAATATATATATGCATTTTTTATATAGTATACAT
12626635 ATACCAATAT
Statistics
Matches: 46, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
46 40 0.87
47 6 0.13
ACGTcount: A:0.32, C:0.06, G:0.09, T:0.53
Consensus pattern (47 bp):
GCATTGTTTTTTATAATATATATATGCATTTTTTATATAGTATACAT
Found at i:12626631 original size:22 final size:22
Alignment explanation
Indices: 12626548--12626624 Score: 111
Period size: 22 Copynumber: 3.4 Consensus size: 22
12626538 ACACGCATTG
12626548 TTTTTTATAATATATATATGCA
1 TTTTTTATAATATATATATGCA
*
12626570 TTTTTTAT-ATAGTATACATGCA
1 TTTTTTATAATA-TATATATGCA
12626592 TTGTTTTTATAATATATATATGCA
1 -T-TTTTTATAATATATATATGCA
12626616 TTTTTTATA
1 TTTTTTATA
12626625 TAGTATACAT
Statistics
Matches: 49, Mismatches: 2, Indels: 8
0.83 0.03 0.14
Matches are distributed among these distances:
21 3 0.06
22 25 0.51
23 2 0.04
24 16 0.33
25 3 0.06
ACGTcount: A:0.32, C:0.05, G:0.06, T:0.56
Consensus pattern (22 bp):
TTTTTTATAATATATATATGCA
Found at i:12626733 original size:948 final size:948
Alignment explanation
Indices: 12624874--12626770 Score: 3687
Period size: 948 Copynumber: 2.0 Consensus size: 948
12624864 GGGTAATAAA
12624874 ATTAAAGGTGATTGCGATTCCATTTTTTTCTTTTTATGTTCATTTTATTTTTTAACAAAAATAGC
1 ATTAAAGGTGATTGCGATTCCATTTTTTTCTTTTTATGTTCATTTTATTTTTTAACAAAAATAGC
12624939 AATAGAGAAAGAGGGGATTCTTACCTACGTGGTCTCGCCGTCGAAAACCCAGGCCTGCTTCACTT
66 AATAGAGAAAGAGGGGATTCTTACCTACGTGGTCTCGCCGTCGAAAACCCAGGCCTGCTTCACTT
*
12625004 GGATCGGAGCTGGAATAGTGGGATTTGAACCGGCCGATTGGCTGAGAACGGCGACGACCTTAGAA
131 GGATCGGAGCTGGAATAGTGGGATTTGAACCGGCCGATTGGCCGAGAACGGCGACGACCTTAGAA
12625069 GCTAGGGACGAAACCCTAGCAGAGGGTGTTTAGTTTTTTTTCTTTTCTGCTGCAAATATGTTTTT
196 GCTAGGGACGAAACCCTAGCAGAGGGTGTTTAGTTTTTTTTCTTTTCTGCTGCAAATATGTTTTT
12625134 TAGAAAGAAAACTGTTTTAAATAACAGAGGTAAACGACGCCATTTTAGTGGCCAGATTCGCGCGT
261 TAGAAAGAAAACTGTTTTAAATAACAGAGGTAAACGACGCCATTTTAGTGGCCAGATTCGCGCGT
*
12625199 CGACCCGACTCGACCCGTAAGCAGGGTCCGTGCGTTCTGGCCTAAATGGTAAATTTGTGCAGTTA
326 CGACCCGACTCGACCCGCAAGCAGGGTCCGTGCGTTCTGGCCTAAATGGTAAATTTGTGCAGTTA
12625264 GGCCCTCCCTTTTGCGAAGCGTTTTAATCAAGTCCGTAGCTTTTTTTTAAATTTGGCCCAAATAT
391 GGCCCTCCCTTTTGCGAAGCGTTTTAATCAAGTCCGTAGCTTTTTTTTAAATTTGGCCCAAATAT
*
12625329 TTTACCCGTGTGACGTTTAATTCTAGGGCTACCCAGCGTTTAGGAGGGCAGGGTATTTCCCTTTT
456 TTTACCCGTGTGACGTTTAATTCTAGGGCTACCCAGCGTTTAGGAGGGCAAGGTATTTCCCTTTT
12625394 GGTCCTCCATTGTAGTTCGCGCATTCAAATTAGTCCTGTCTTTTAAGTTATTTCAAATCTGCCCC
521 GGTCCTCCATTGTAGTTCGCGCATTCAAATTAGTCCTGTCTTTTAAGTTATTTCAAATCTGCCCC
12625459 ATTTTTTTGTTTTTAGTTCAATTTAGTCCATTTTTTAGCTATTTTATTATTATTATTATTATGTT
586 ATTTTTTTGTTTTTAGTTCAATTTAGTCCATTTTTTAGCTATTTTATTATTATTATTATTATGTT
12625524 ATTATCATTATACCATTATTTATTATTATATTATTTATTATCATTATTATTATTTCTATATTCAT
651 ATTATCATTATACCATTATTTATTATTATATTATTTATTATCATTATTATTATTTCTATATTCAT
12625589 ACACACGCATTGTTTTTTATAATATATATGCATTTTTTATATAGTATACATGCATTGTTTTTATA
716 ACACACGCATTGTTTTTTATAATATATATGCATTTTTTATATAGTATACATGCATTGTTTTTATA
12625654 ATATATATATATATGCATTTTTTATATAGTATACATATACCAATATATATTTTATACATATTATT
781 ATATATATATATATGCATTTTTTATATAGTATACATATACCAATATATATTTTATACATATTATT
12625719 ATTATTATTTTATTTCCTAACTTTAATATACATATATATACTTTTATATTTTAGTTTCAATTTTT
846 ATTATTATTTTATTTCCTAACTTTAATATACATATATATACTTTTATATTTTAGTTTCAATTTTT
12625784 TTTTACTTTTGTAAATATGTATATACGTATGTTTTTAT
911 TTTTACTTTTGTAAATATGTATATACGTATGTTTTTAT
12625822 ATTAAAGGTGATTGCGATTCCATTTTTTTCTTTTTATGTTCATTTTATTTTTTAACAAAAATAGC
1 ATTAAAGGTGATTGCGATTCCATTTTTTTCTTTTTATGTTCATTTTATTTTTTAACAAAAATAGC
12625887 AATAGAGAAAGAGGGGATTCTTACCTACGTGGTCTCGCCGTCGAAAACCCAGGCCTGCTTCACTT
66 AATAGAGAAAGAGGGGATTCTTACCTACGTGGTCTCGCCGTCGAAAACCCAGGCCTGCTTCACTT
12625952 GGATCGGAGCTGGAATAGTGGGATTTGAACCGGCCGATTGGCCGAGAACGGCGACGACCTTAGAA
131 GGATCGGAGCTGGAATAGTGGGATTTGAACCGGCCGATTGGCCGAGAACGGCGACGACCTTAGAA
12626017 GCTAGGGACGAAACCCTAGCAGAGGGTGTTTAGTTTTTTTTCTTTTCTGCTGCAAATATGTTTTT
196 GCTAGGGACGAAACCCTAGCAGAGGGTGTTTAGTTTTTTTTCTTTTCTGCTGCAAATATGTTTTT
12626082 TAGAAAGAAAACTGTTTTAAATAACAGAGGTAAACGACGCCATTTTAGTGGCCAGATTCGCGCGT
261 TAGAAAGAAAACTGTTTTAAATAACAGAGGTAAACGACGCCATTTTAGTGGCCAGATTCGCGCGT
12626147 CGACCCGACTCGACCCGCAAGCAGGGTCCGTGCGTTCTGGCCTAAATGGTAAATTTGTGCAGTTA
326 CGACCCGACTCGACCCGCAAGCAGGGTCCGTGCGTTCTGGCCTAAATGGTAAATTTGTGCAGTTA
12626212 GGCCCTCCCTTTTGCGAAGCGTTTTAATCAAGTCCGTAGC-TTTTTTTAAATTTGGCCCAAATAT
391 GGCCCTCCCTTTTGCGAAGCGTTTTAATCAAGTCCGTAGCTTTTTTTTAAATTTGGCCCAAATAT
12626276 TTTACCCGTGTGACGTTTAATTCTAGGGCTACCCAGCGTTTAGGAGGGCAAGGTATTTCCCTTTT
456 TTTACCCGTGTGACGTTTAATTCTAGGGCTACCCAGCGTTTAGGAGGGCAAGGTATTTCCCTTTT
*
12626341 GGTCCTCCATTGTAGTTCGCGCATTCAAATTAGTCCTGTCTTTTAAGTTATTTTAAATCTGCCCC
521 GGTCCTCCATTGTAGTTCGCGCATTCAAATTAGTCCTGTCTTTTAAGTTATTTCAAATCTGCCCC
12626406 ATTTTTTTGTTTTTAGTTCAATTTAGTCCATTTTTTAGCTATTTTATTATTATTATTATTATGTT
586 ATTTTTTTGTTTTTAGTTCAATTTAGTCCATTTTTTAGCTATTTTATTATTATTATTATTATGTT
12626471 ATTATCATTATACCATTATTTATTATTATATTATTTATTATCATTATTATTATTTCTATATTCAT
651 ATTATCATTATACCATTATTTATTATTATATTATTTATTATCATTATTATTATTTCTATATTCAT
12626536 ACACACGCATTGTTTTTTATAATATATATATGCATTTTTTATATAGTATACATGCATTG-TTTT-
716 ACACACGCATTGTTTTTTAT-A-ATATATATGCATTTTTTATATAGTATACATGCATTGTTTTTA
*
12626599 T-ATA-ATATATATATGCATTTTTTATATAGTATACATATACCAATATATATTTTATACATATTT
779 TAATATATATATATATGCATTTTTTATATAGTATACATATACCAATATATATTTTATACATATTA
12626662 TTATTATTATTTTATTTCCTAACTTTAATATACATATATATACTTTTATATTTTAGTTTCAATTT
844 TTATTATTATTTTATTTCCTAACTTTAATATACATATATATACTTTTATATTTTAGTTTCAA-TT
12626727 TTTTTTTACTTTTGTAAATATGTATATACGTATGTTTTTAT
908 TTTTTTTACTTTTGTAAATATGTATATACGTATGTTTTTAT
12626768 ATT
1 ATT
12626771 TTTTTATATT
Statistics
Matches: 941, Mismatches: 5, Indels: 8
0.99 0.01 0.01
Matches are distributed among these distances:
945 120 0.13
946 49 0.05
947 303 0.32
948 433 0.46
949 36 0.04
ACGTcount: A:0.26, C:0.16, G:0.16, T:0.42
Consensus pattern (948 bp):
ATTAAAGGTGATTGCGATTCCATTTTTTTCTTTTTATGTTCATTTTATTTTTTAACAAAAATAGC
AATAGAGAAAGAGGGGATTCTTACCTACGTGGTCTCGCCGTCGAAAACCCAGGCCTGCTTCACTT
GGATCGGAGCTGGAATAGTGGGATTTGAACCGGCCGATTGGCCGAGAACGGCGACGACCTTAGAA
GCTAGGGACGAAACCCTAGCAGAGGGTGTTTAGTTTTTTTTCTTTTCTGCTGCAAATATGTTTTT
TAGAAAGAAAACTGTTTTAAATAACAGAGGTAAACGACGCCATTTTAGTGGCCAGATTCGCGCGT
CGACCCGACTCGACCCGCAAGCAGGGTCCGTGCGTTCTGGCCTAAATGGTAAATTTGTGCAGTTA
GGCCCTCCCTTTTGCGAAGCGTTTTAATCAAGTCCGTAGCTTTTTTTTAAATTTGGCCCAAATAT
TTTACCCGTGTGACGTTTAATTCTAGGGCTACCCAGCGTTTAGGAGGGCAAGGTATTTCCCTTTT
GGTCCTCCATTGTAGTTCGCGCATTCAAATTAGTCCTGTCTTTTAAGTTATTTCAAATCTGCCCC
ATTTTTTTGTTTTTAGTTCAATTTAGTCCATTTTTTAGCTATTTTATTATTATTATTATTATGTT
ATTATCATTATACCATTATTTATTATTATATTATTTATTATCATTATTATTATTTCTATATTCAT
ACACACGCATTGTTTTTTATAATATATATGCATTTTTTATATAGTATACATGCATTGTTTTTATA
ATATATATATATATGCATTTTTTATATAGTATACATATACCAATATATATTTTATACATATTATT
ATTATTATTTTATTTCCTAACTTTAATATACATATATATACTTTTATATTTTAGTTTCAATTTTT
TTTTACTTTTGTAAATATGTATATACGTATGTTTTTAT
Found at i:12627061 original size:33 final size:33
Alignment explanation
Indices: 12627024--12627086 Score: 90
Period size: 33 Copynumber: 1.9 Consensus size: 33
12627014 ATGACTTACC
* * **
12627024 AATATATATACTTATACACTTTTTTATTTTGTA
1 AATATATACACATATACACACTTTTATTTTGTA
12627057 AATATATACACATATACACACTTTTATTTT
1 AATATATACACATATACACACTTTTATTTT
12627087 TTTTTTGTAT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 26 1.00
ACGTcount: A:0.37, C:0.13, G:0.02, T:0.49
Consensus pattern (33 bp):
AATATATACACATATACACACTTTTATTTTGTA
Found at i:12627292 original size:15 final size:15
Alignment explanation
Indices: 12627272--12627308 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
12627262 CAAATTTTCT
**
12627272 TATATATTGTACTTA
1 TATATATTGTAAATA
12627287 TATATATTGTAAATA
1 TATATATTGTAAATA
12627302 TATATAT
1 TATATAT
12627309 AATTCATATT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.41, C:0.03, G:0.05, T:0.51
Consensus pattern (15 bp):
TATATATTGTAAATA
Found at i:12629717 original size:11 final size:10
Alignment explanation
Indices: 12629700--12629728 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
12629690 TCAAAGAATA
12629700 TAAAAAAATT
1 TAAAAAAATT
12629710 TAAAAAAATT
1 TAAAAAAATT
12629720 TAAAAAAAT
1 TAAAAAAAT
12629729 CTATAATATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (10 bp):
TAAAAAAATT
Found at i:12630875 original size:22 final size:19
Alignment explanation
Indices: 12630828--12630866 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 19
12630818 TGGAAGGCTG
12630828 AAAGAAAGGAAACAAAATC
1 AAAGAAAGGAAACAAAATC
12630847 AAAGAAAGAAGAAACAAAAT
1 AAAGAAAG--GAAACAAAAT
12630867 ATAAAGAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 8 0.44
21 10 0.56
ACGTcount: A:0.72, C:0.08, G:0.15, T:0.05
Consensus pattern (19 bp):
AAAGAAAGGAAACAAAATC
Found at i:12631481 original size:29 final size:30
Alignment explanation
Indices: 12631424--12631481 Score: 73
Period size: 30 Copynumber: 2.0 Consensus size: 30
12631414 GGCTCGGGTG
* * *
12631424 ACTGATTTGTCACTTTCATAAAGTTTAGTA
1 ACTGAGTTGTAACTTTCATAAAGTGTAGTA
*
12631454 ACTGAGTTGTAACTTT-TTAAAGTGTAGT
1 ACTGAGTTGTAACTTTCATAAAGTGTAGT
12631482 GACTATTTTG
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
29 10 0.42
30 14 0.58
ACGTcount: A:0.29, C:0.10, G:0.17, T:0.43
Consensus pattern (30 bp):
ACTGAGTTGTAACTTTCATAAAGTGTAGTA
Found at i:12631664 original size:20 final size:18
Alignment explanation
Indices: 12631622--12631672 Score: 59
Period size: 18 Copynumber: 2.8 Consensus size: 18
12631612 ATAAAATATA
*
12631622 AAAATTCAAAAAAATTAT
1 AAAATTCAAAAAAACTAT
12631640 AAAATTCATAAAAGAACTAT
1 AAAATTCA-AAAA-AACTAT
*
12631660 TAAATT-AAAAAAA
1 AAAATTCAAAAAAA
12631673 AAAAATCAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
17 2 0.07
18 12 0.41
19 5 0.17
20 10 0.34
ACGTcount: A:0.67, C:0.06, G:0.02, T:0.25
Consensus pattern (18 bp):
AAAATTCAAAAAAACTAT
Found at i:12631761 original size:19 final size:19
Alignment explanation
Indices: 12631739--12631787 Score: 55
Period size: 19 Copynumber: 2.6 Consensus size: 19
12631729 AACACTATAT
12631739 AAAATATAAATAATTCAAA
1 AAAATATAAATAATTCAAA
* * *
12631758 AAAATCTAAA-ATTTTAAA
1 AAAATATAAATAATTCAAA
12631776 AAATATATAAAT
1 AAA-ATATAAAT
12631788 TAAAATGATC
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
18 9 0.38
19 15 0.62
ACGTcount: A:0.65, C:0.04, G:0.00, T:0.31
Consensus pattern (19 bp):
AAAATATAAATAATTCAAA
Found at i:12632159 original size:3 final size:3
Alignment explanation
Indices: 12632146--12632224 Score: 151
Period size: 3 Copynumber: 26.7 Consensus size: 3
12632136 CAATAATGTA
12632146 AAG AA- AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
12632193 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
12632225 ATTGTTTATG
Statistics
Matches: 75, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
2 2 0.03
3 73 0.97
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:12645329 original size:91 final size:89
Alignment explanation
Indices: 12645234--12645419 Score: 228
Period size: 89 Copynumber: 2.1 Consensus size: 89
12645224 TTAGTGTTTT
** * *
12645234 GTGTTTTGTGATTTTTTAGTAATGTAAAATATTAAAAAAATATTTTTATAGTTATTTCGTTAGTA
1 GTGTTTTGTGATTTAATAGTAATGTAAAATATT--AAAAATAATGTTATAGTTATTTCGTTAGTA
12645299 ATTTATAATTAGTTTACAAATTGTTA
64 ATTTATAATTAGTTTACAAATTGTTA
* * ***** *
12645325 GTGTTTTGTGATTTAATAGTAATGTAAATTCTTTTTTTTAATGTTATAGTTATTTTGTTAGTAAT
1 GTGTTTTGTGATTTAATAGTAATGTAAAATATTAAAAATAATGTTATAGTTATTTCGTTAGTAAT
* *
12645390 TTATGATTAGTTTATAAATTGTTA
66 TTATAATTAGTTTACAAATTGTTA
12645414 GTGTTT
1 GTGTTT
12645420 AGTTTATGGT
Statistics
Matches: 81, Mismatches: 14, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
89 52 0.64
91 29 0.36
ACGTcount: A:0.31, C:0.02, G:0.14, T:0.54
Consensus pattern (89 bp):
GTGTTTTGTGATTTAATAGTAATGTAAAATATTAAAAATAATGTTATAGTTATTTCGTTAGTAAT
TTATAATTAGTTTACAAATTGTTA
Done.