Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr1
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: 106989029
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 3754247 characters in sequence are not A, C, G, or T
File 159 of 322
Found at i:52306861 original size:86 final size:86
Alignment explanation
Indices: 52306707--52306916 Score: 268
Period size: 86 Copynumber: 2.5 Consensus size: 86
52306697 GGTTACCGAG
*
52306707 ATGTGATTACATGTAAGACCA-AGTCTGGGACATTGGCATTGTTTTGTGATTACGTGTAAGACCA
1 ATGTGATTACATGTAAGACCATA-TCTGGGACATTGGCATCGTTTTGTGATTACGTGTAAGACCA
* *
52306771 TGTCTGGGGCATTGACATC-ATT
65 TGTCTGGGACAGTGACATCGA-T
* *
52306793 AT-TCGATTACGTGTAAGACCATATCTGGGACATTGGCATCGTTATT-TGATTTCGTGTAAGACC
1 ATGT-GATTACATGTAAGACCATATCTGGGACATTGGCATCGTT-TTGTGATTACGTGTAAGACC
* *
52306856 CTGTCTGGGACAGTGGCATCGAT
64 ATGTCTGGGACAGTGACATCGAT
* *
52306879 ATGTGATAACATGTAAGACCATATCTGGGATA-TGGCAT
1 ATGTGATTACATGTAAGACCATATCTGGGACATTGGCAT
52306917 TGTACGAGCT
Statistics
Matches: 109, Mismatches: 10, Indels: 11
0.84 0.08 0.08
Matches are distributed among these distances:
85 7 0.06
86 97 0.89
87 5 0.05
ACGTcount: A:0.26, C:0.16, G:0.25, T:0.32
Consensus pattern (86 bp):
ATGTGATTACATGTAAGACCATATCTGGGACATTGGCATCGTTTTGTGATTACGTGTAAGACCAT
GTCTGGGACAGTGACATCGAT
Found at i:52309516 original size:19 final size:19
Alignment explanation
Indices: 52309487--52309523 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
52309477 AAACCTTCAA
52309487 TTTTCCCTTTC-TTCTTTT
1 TTTTCCCTTTCTTTCTTTT
52309505 TTTTCTCCTTTCTTTCTTT
1 TTTTC-CCTTTCTTTCTTT
52309524 CTTTCCCTGC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 5 0.29
19 6 0.35
20 6 0.35
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (19 bp):
TTTTCCCTTTCTTTCTTTT
Found at i:52309528 original size:19 final size:18
Alignment explanation
Indices: 52309488--52309531 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
52309478 AACCTTCAAT
*
52309488 TTTCCCTTTCTTCTTTTT
1 TTTCCCTTTCTTCTTTTC
52309506 TTTCTCCTTTCTT-TCTTTC
1 TTTC-CCTTTCTTCT-TTTC
52309525 TTTCCCT
1 TTTCCCT
52309532 GCTTTTCGTT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
18 8 0.35
19 15 0.65
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (18 bp):
TTTCCCTTTCTTCTTTTC
Found at i:52309735 original size:16 final size:15
Alignment explanation
Indices: 52309726--52309760 Score: 52
Period size: 16 Copynumber: 2.3 Consensus size: 15
52309716 TATTTATTAT
52309726 ATAATATATTATTTA
1 ATAATATATTATTTA
*
52309741 ATAATATACTTATATA
1 ATAATATA-TTATTTA
52309757 ATAA
1 ATAA
52309761 GTAAATATAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 8 0.44
16 10 0.56
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (15 bp):
ATAATATATTATTTA
Found at i:52310060 original size:54 final size:53
Alignment explanation
Indices: 52310002--52310185 Score: 140
Period size: 54 Copynumber: 3.3 Consensus size: 53
52309992 TTATTTACTT
* *
52310002 ATTTAGTCTTTTTAATTTTCTTTATTCTGTAATTAAACTTTCACACTTCATTCA
1 ATTTAATCCTTTTAATTTTCTTTATTCT-TAATTAAACTTTCACACTTCATTCA
* * * * * *
52310056 ATTTAATCCTTTT-A--TCCAATTATTCTTAATTAAATTAAATTCACTTAATTAAACTCTAACTT
1 ATTTAATCCTTTTAATTTTC-TTTATTCTTAATTAAACT---TTCAC--ACTT-CA-T-T--C-A
*
52310118 ATTTAGTCCTTTTAATTTTCTTTATTCTATAATTAAACTTTCACACTTCATTCA
1 ATTTAATCCTTTTAATTTTCTTTATTCT-TAATTAAACTTTCACACTTCATTCA
52310172 ATTTAATCCTTTTA
1 ATTTAATCCTTTTA
52310186 TCCAATTATT
Statistics
Matches: 98, Mismatches: 16, Indels: 32
0.67 0.11 0.22
Matches are distributed among these distances:
51 11 0.11
52 7 0.07
53 1 0.01
54 29 0.30
55 1 0.01
56 3 0.03
57 2 0.02
58 2 0.02
59 2 0.02
60 3 0.03
61 1 0.01
62 17 0.17
63 1 0.01
64 7 0.07
65 11 0.11
ACGTcount: A:0.30, C:0.17, G:0.02, T:0.51
Consensus pattern (53 bp):
ATTTAATCCTTTTAATTTTCTTTATTCTTAATTAAACTTTCACACTTCATTCA
Found at i:52310144 original size:116 final size:116
Alignment explanation
Indices: 52309998--52310230 Score: 448
Period size: 116 Copynumber: 2.0 Consensus size: 116
52309988 TGGCTTATTT
* *
52309998 ACTTATTTAGTCTTTTTAATTTTCTTTATTCTGTAATTAAACTTTCACACTTCATTCAATTTAAT
1 ACTTATTTAGTCCTTTTAATTTTCTTTATTCTATAATTAAACTTTCACACTTCATTCAATTTAAT
52310063 CCTTTTATCCAATTATTCTTAATTAAATTAAATTCACTTAATTAAACTCTA
66 CCTTTTATCCAATTATTCTTAATTAAATTAAATTCACTTAATTAAACTCTA
52310114 ACTTATTTAGTCCTTTTAATTTTCTTTATTCTATAATTAAACTTTCACACTTCATTCAATTTAAT
1 ACTTATTTAGTCCTTTTAATTTTCTTTATTCTATAATTAAACTTTCACACTTCATTCAATTTAAT
52310179 CCTTTTATCCAATTATTCTTAATTAAATTAAATTCACTTAATTAAACTCTA
66 CCTTTTATCCAATTATTCTTAATTAAATTAAATTCACTTAATTAAACTCTA
52310230 A
1 A
52310231 TTAACCACTC
Statistics
Matches: 115, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
116 115 1.00
ACGTcount: A:0.33, C:0.17, G:0.01, T:0.49
Consensus pattern (116 bp):
ACTTATTTAGTCCTTTTAATTTTCTTTATTCTATAATTAAACTTTCACACTTCATTCAATTTAAT
CCTTTTATCCAATTATTCTTAATTAAATTAAATTCACTTAATTAAACTCTA
Found at i:52314733 original size:18 final size:18
Alignment explanation
Indices: 52314712--52314747 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
52314702 ATTTATTTCT
52314712 AAAAAT-ATGTTAAAAATA
1 AAAAATAAT-TTAAAAATA
52314730 AAAAATAATTTAAAAATA
1 AAAAATAATTTAAAAATA
52314748 GCTCGTTCTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 15 0.88
19 2 0.12
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.28
Consensus pattern (18 bp):
AAAAATAATTTAAAAATA
Found at i:52318023 original size:23 final size:22
Alignment explanation
Indices: 52317984--52318048 Score: 78
Period size: 23 Copynumber: 2.9 Consensus size: 22
52317974 ATTTGAATTT
*
52317984 TTAAA-TTTAAAAAATAAATAGA
1 TTAAATTTTAAAAAATAAA-AAA
*
52318006 TTAAATTTTTAAAAATAAAAAA
1 TTAAATTTTAAAAAATAAAAAA
*
52318028 TTAAATTTTAAATATATAAAA
1 TTAAATTTTAAA-AAATAAAA
52318049 GGGTATTATG
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
22 18 0.49
23 19 0.51
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.37
Consensus pattern (22 bp):
TTAAATTTTAAAAAATAAAAAA
Found at i:52318036 original size:22 final size:23
Alignment explanation
Indices: 52317984--52318039 Score: 80
Period size: 22 Copynumber: 2.5 Consensus size: 23
52317974 ATTTGAATTT
*
52317984 TTAAA-TTTAAAAAATAAATAGA
1 TTAAATTTTAAAAAATAAATAAA
*
52318006 TTAAATTTTTAAAAATAAA-AAA
1 TTAAATTTTAAAAAATAAATAAA
52318028 TTAAATTTTAAA
1 TTAAATTTTAAA
52318040 TATATAAAAG
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
22 18 0.60
23 12 0.40
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.38
Consensus pattern (23 bp):
TTAAATTTTAAAAAATAAATAAA
Found at i:52318048 original size:22 final size:22
Alignment explanation
Indices: 52317984--52318049 Score: 73
Period size: 22 Copynumber: 3.0 Consensus size: 22
52317974 ATTTGAATTT
*
52317984 TTAAA-TTTAAAAAATAAATAGA
1 TTAAATTTTAAAATATAAA-AGA
*
52318006 TTAAATTTTTAAAA-ATAAAAAA
1 TTAAA-TTTTAAAATATAAAAGA
52318028 TTAAATTTTAAATATATAAAAG
1 TTAAATTTTAAA-ATATAAAAG
52318050 GGTATTATGA
Statistics
Matches: 38, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
21 7 0.18
22 13 0.34
23 11 0.29
24 7 0.18
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (22 bp):
TTAAATTTTAAAATATAAAAGA
Found at i:52322963 original size:21 final size:21
Alignment explanation
Indices: 52322934--52322981 Score: 78
Period size: 21 Copynumber: 2.3 Consensus size: 21
52322924 TTCATCGATT
*
52322934 ACATTAGATATTACGTGATAA
1 ACATCAGATATTACGTGATAA
*
52322955 ACATCAGATATTATGTGATAA
1 ACATCAGATATTACGTGATAA
52322976 ACATCA
1 ACATCA
52322982 ATTTCCATTA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.44, C:0.12, G:0.12, T:0.31
Consensus pattern (21 bp):
ACATCAGATATTACGTGATAA
Found at i:52323597 original size:30 final size:32
Alignment explanation
Indices: 52323561--52323619 Score: 79
Period size: 30 Copynumber: 1.9 Consensus size: 32
52323551 AATTCAATTA
52323561 GAAATTA-TCAATAATTT-AT-TATTTTTTAAT
1 GAAATTAGTC-ATAATTTAATATATTTTTTAAT
*
52323591 GAAATTAGTCATATTTTAATATATTTTTT
1 GAAATTAGTCATAATTTAATATATTTTTT
52323620 TAACATCATT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
30 13 0.52
31 4 0.16
32 8 0.32
ACGTcount: A:0.37, C:0.03, G:0.05, T:0.54
Consensus pattern (32 bp):
GAAATTAGTCATAATTTAATATATTTTTTAAT
Found at i:52325836 original size:21 final size:21
Alignment explanation
Indices: 52325810--52325852 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
52325800 GAGTATTTTA
* *
52325810 TTTTATAATTTTTTTAACTTT
1 TTTTATAATTTTTATAAATTT
*
52325831 TTTTATTATTTTTATAAATTT
1 TTTTATAATTTTTATAAATTT
52325852 T
1 T
52325853 AAATTTTTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.72
Consensus pattern (21 bp):
TTTTATAATTTTTATAAATTT
Found at i:52328487 original size:19 final size:18
Alignment explanation
Indices: 52328454--52328499 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
52328444 AAGTTAAGTG
*
52328454 AAATAATA-AGTTAAGAA
1 AAATAATATTGTTAAGAA
52328471 AAGATAATATTGTTAAGAA
1 AA-ATAATATTGTTAAGAA
*
52328490 GAATAATATT
1 AAATAATATT
52328500 TAAATTTAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 2 0.08
18 14 0.56
19 9 0.36
ACGTcount: A:0.57, C:0.00, G:0.13, T:0.30
Consensus pattern (18 bp):
AAATAATATTGTTAAGAA
Found at i:52328495 original size:18 final size:19
Alignment explanation
Indices: 52328463--52328499 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
52328453 GAAATAATAA
52328463 GTTAAGAAAAGATAATATT
1 GTTAAGAAAAGATAATATT
*
52328482 GTTAAGAAGA-ATAATATT
1 GTTAAGAAAAGATAATATT
52328500 TAAATTTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.51, C:0.00, G:0.16, T:0.32
Consensus pattern (19 bp):
GTTAAGAAAAGATAATATT
Found at i:52333569 original size:13 final size:13
Alignment explanation
Indices: 52333551--52333579 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
52333541 ATTTTAATGT
52333551 TTACATTATAGTA
1 TTACATTATAGTA
52333564 TTACATTATAGTA
1 TTACATTATAGTA
52333577 TTA
1 TTA
52333580 TATAAAATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.38, C:0.07, G:0.07, T:0.48
Consensus pattern (13 bp):
TTACATTATAGTA
Found at i:52336754 original size:257 final size:257
Alignment explanation
Indices: 52336291--52336813 Score: 1010
Period size: 257 Copynumber: 2.0 Consensus size: 257
52336281 AAATTAGCTA
* *
52336291 AATAAAAATGGGACTAAATTGGAATATCTAGAATTCTCTTCATTTTTCTTTATTTTCATCAGCTG
1 AATAAACATGGGACTAAATTGGAATATCCAGAATTCTCTTCATTTTTCTTTATTTTCATCAGCTG
52336356 AAAAACAGCCATGGAAGAGGGTTCAAGCTGGTTTTCATTCTCTAGCTACATGTAAGTTTAATTCT
66 AAAAACAGCCATGGAAGAGGGTTCAAGCTGGTTTTCATTCTCTAGCTACATGTAAGTTTAATTCT
52336421 TGCTTTCTCCTAGAAATTTCTATGTTTTTGGACTTTTACAATTAGGTCCAACTTACTATTTCATT
131 TGCTTTCTCCTAGAAATTTCTATGTTTTTGGACTTTTACAATTAGGTCCAACTTACTATTTCATT
52336486 AGTTTTTGATTTCATGGTTAATTTTTAAAGTTTTTATGGATTAGTGATGGAAGAATATGATG
196 AGTTTTTGATTTCATGGTTAATTTTTAAAGTTTTTATGGATTAGTGATGGAAGAATATGATG
52336548 AATAAACATGGGACTAAATTGGAATATCCAGAATTCTCTTCATTTTTCTTTATTTTCATCAGCTG
1 AATAAACATGGGACTAAATTGGAATATCCAGAATTCTCTTCATTTTTCTTTATTTTCATCAGCTG
52336613 AAAAACAGCCATGGAAGAGGGTTCAAGCTGGTTTTCATTCTCTAGCTACATGTAAGTTTAATTCT
66 AAAAACAGCCATGGAAGAGGGTTCAAGCTGGTTTTCATTCTCTAGCTACATGTAAGTTTAATTCT
*
52336678 TGCTTTCTCCTAGAAATTTCTATGTTTTTGGACTTTTACAATTAGGTCCAACTTACTATTTCGTT
131 TGCTTTCTCCTAGAAATTTCTATGTTTTTGGACTTTTACAATTAGGTCCAACTTACTATTTCATT
*
52336743 AGTTTTTGATTTCATGGTTAATTTTTAAAGTTTTTATGGATTAGTGATGGAAGTATATGATG
196 AGTTTTTGATTTCATGGTTAATTTTTAAAGTTTTTATGGATTAGTGATGGAAGAATATGATG
52336805 AATAAACAT
1 AATAAACAT
52336814 ATAATTGAAG
Statistics
Matches: 262, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
257 262 1.00
ACGTcount: A:0.29, C:0.13, G:0.16, T:0.42
Consensus pattern (257 bp):
AATAAACATGGGACTAAATTGGAATATCCAGAATTCTCTTCATTTTTCTTTATTTTCATCAGCTG
AAAAACAGCCATGGAAGAGGGTTCAAGCTGGTTTTCATTCTCTAGCTACATGTAAGTTTAATTCT
TGCTTTCTCCTAGAAATTTCTATGTTTTTGGACTTTTACAATTAGGTCCAACTTACTATTTCATT
AGTTTTTGATTTCATGGTTAATTTTTAAAGTTTTTATGGATTAGTGATGGAAGAATATGATG
Found at i:52338116 original size:35 final size:35
Alignment explanation
Indices: 52338077--52338410 Score: 431
Period size: 35 Copynumber: 9.6 Consensus size: 35
52338067 CATGGAAAAG
52338077 TGTGAAACGTAGGTATGGTATCATCCATACCGAGT
1 TGTGAAACGTAGGTATGGTATCATCCATACCGAGT
* * * *
52338112 TGTGAAATGTAGGTATGGTATTAACCATACCTAGT
1 TGTGAAACGTAGGTATGGTATCATCCATACCGAGT
* *
52338147 TGTGAAACGTAGGTGTGATATCATCCATACCGAGT
1 TGTGAAACGTAGGTATGGTATCATCCATACCGAGT
* * *
52338182 TGTGAAACGTAGGTATGGTGTTAACCATACCGAGT
1 TGTGAAACGTAGGTATGGTATCATCCATACCGAGT
*
52338217 TGTGAAATGTAGGTATGGTATCATCCATACCGAGT
1 TGTGAAACGTAGGTATGGTATCATCCATACCGAGT
* * *
52338252 TGTGAAA-GTAGGTATGGTATTAACCATACTGAGT
1 TGTGAAACGTAGGTATGGTATCATCCATACCGAGT
* *
52338286 TGTGAAACATAGGTATGATATCATCCATACCGAGT
1 TGTGAAACGTAGGTATGGTATCATCCATACCGAGT
* * *
52338321 TGTGAAACATAGGTATGGTATTATCCATACTGAGT
1 TGTGAAACGTAGGTATGGTATCATCCATACCGAGT
** * *
52338356 TAAG-AACGTAGGTATGGCAT-TTCCCATACCGAGT
1 TGTGAAACGTAGGTATGGTATCAT-CCATACCGAGT
*
52338390 TGTGAAATGTAGGTATGGTAT
1 TGTGAAACGTAGGTATGGTAT
52338411 TTCAATAAGG
Statistics
Matches: 256, Mismatches: 40, Indels: 6
0.85 0.13 0.02
Matches are distributed among these distances:
33 1 0.00
34 57 0.22
35 198 0.77
ACGTcount: A:0.30, C:0.14, G:0.25, T:0.31
Consensus pattern (35 bp):
TGTGAAACGTAGGTATGGTATCATCCATACCGAGT
Found at i:52338194 original size:70 final size:70
Alignment explanation
Indices: 52338077--52338411 Score: 482
Period size: 70 Copynumber: 4.8 Consensus size: 70
52338067 CATGGAAAAG
* *
52338077 TGTGAAACGTAGGTATGGTATCATCCATACCGAGTTGTGAAATGTAGGTATGGTATTAACCATAC
1 TGTGAAACGTAGGTATGATATCATCCATACCGAGTTGTGAAACGTAGGTATGGTATTAACCATA-
52338142 CT-AGT
65 CTGAGT
* *
52338147 TGTGAAACGTAGGTGTGATATCATCCATACCGAGTTGTGAAACGTAGGTATGGTGTTAACCATAC
1 TGTGAAACGTAGGTATGATATCATCCATACCGAGTTGTGAAACGTAGGTATGGTATTAACCATAC
*
52338212 CGAGT
66 TGAGT
* *
52338217 TGTGAAATGTAGGTATGGTATCATCCATACCGAGTTGTGAAA-GTAGGTATGGTATTAACCATAC
1 TGTGAAACGTAGGTATGATATCATCCATACCGAGTTGTGAAACGTAGGTATGGTATTAACCATAC
52338281 TGAGT
66 TGAGT
* * *
52338286 TGTGAAACATAGGTATGATATCATCCATACCGAGTTGTGAAACATAGGTATGGTATTATCCATAC
1 TGTGAAACGTAGGTATGATATCATCCATACCGAGTTGTGAAACGTAGGTATGGTATTAACCATAC
52338351 TGAGT
66 TGAGT
** * *
52338356 TAAG-AACGTAGGTATGGCATTTC--CCATACCGAGTTGTGAAATGTAGGTATGGTATT
1 TGTGAAACGTAGGTAT-G-ATATCATCCATACCGAGTTGTGAAACGTAGGTATGGTATT
52338412 TCAATAAGGA
Statistics
Matches: 240, Mismatches: 21, Indels: 9
0.89 0.08 0.03
Matches are distributed among these distances:
69 106 0.44
70 130 0.54
71 4 0.02
ACGTcount: A:0.30, C:0.14, G:0.25, T:0.31
Consensus pattern (70 bp):
TGTGAAACGTAGGTATGATATCATCCATACCGAGTTGTGAAACGTAGGTATGGTATTAACCATAC
TGAGT
Found at i:52338326 original size:104 final size:104
Alignment explanation
Indices: 52338077--52338410 Score: 452
Period size: 104 Copynumber: 3.2 Consensus size: 104
52338067 CATGGAAAAG
*
52338077 TGTGAAACGTAGGTATGGTATCATCCATACCGAGTTGTGAAATGTAGGTATGGTATTAACCATAC
1 TGTGAAACGTAGGTATGGTATCATCCATACCGAGTTGTGAAATGTAGGTATGGTATTATCCATAC
* * * * *
52338142 CTAGTTGTGAAACGTAGGTGTGATATCATCCATACCGAGT
66 CGAGTTGTGAAA-GTAGGTATGGTATTAACCATACCGAGT
* * * *
52338182 TGTGAAACGTAGGTATGGTGTTAACCATACCGAGTTGTGAAATGTAGGTATGGTATCATCCATAC
1 TGTGAAACGTAGGTATGGTATCATCCATACCGAGTTGTGAAATGTAGGTATGGTATTATCCATAC
*
52338247 CGAGTTGTGAAAGTAGGTATGGTATTAACCATACTGAGT
66 CGAGTTGTGAAAGTAGGTATGGTATTAACCATACCGAGT
* * **
52338286 TGTGAAACATAGGTATGATATCATCCATACCGAGTTGTGAAACATAGGTATGGTATTATCCATAC
1 TGTGAAACGTAGGTATGGTATCATCCATACCGAGTTGTGAAATGTAGGTATGGTATTATCCATAC
* ** * * **
52338351 TGAGTTAAGAACGTAGGTATGGCATTTCCCATACCGAGT
66 CGAGTTGTGAAAGTAGGTATGGTATTAACCATACCGAGT
*
52338390 TGTGAAATGTAGGTATGGTAT
1 TGTGAAACGTAGGTATGGTAT
52338411 TTCAATAAGG
Statistics
Matches: 199, Mismatches: 30, Indels: 1
0.87 0.13 0.00
Matches are distributed among these distances:
104 128 0.64
105 71 0.36
ACGTcount: A:0.30, C:0.14, G:0.25, T:0.31
Consensus pattern (104 bp):
TGTGAAACGTAGGTATGGTATCATCCATACCGAGTTGTGAAATGTAGGTATGGTATTATCCATAC
CGAGTTGTGAAAGTAGGTATGGTATTAACCATACCGAGT
Found at i:52338871 original size:24 final size:24
Alignment explanation
Indices: 52338812--52338882 Score: 70
Period size: 24 Copynumber: 2.9 Consensus size: 24
52338802 AAGACATGGC
* * *
52338812 CAGTAAGCTCTTTATGAGCTGATAA
1 CAGTAAACTCTAT-TGAGCTGAAAA
52338837 CAGTAAACTCTATTGAGCTGAAAA
1 CAGTAAACTCTATTGAGCTGAAAA
* ** *
52338861 CGGTATGCTCTATTGAGTTGAA
1 CAGTAAACTCTATTGAGCTGAA
52338883 CAATAAGCTC
Statistics
Matches: 39, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
24 28 0.72
25 11 0.28
ACGTcount: A:0.32, C:0.15, G:0.21, T:0.31
Consensus pattern (24 bp):
CAGTAAACTCTATTGAGCTGAAAA
Found at i:52340010 original size:42 final size:42
Alignment explanation
Indices: 52339939--52340065 Score: 143
Period size: 42 Copynumber: 3.0 Consensus size: 42
52339929 CTTCGTTTTC
** * * *
52339939 TCGATGCCATAGTTCAACTATGGTATTACACATCTTCACATAA
1 TCGATGCCATAGCCCAGCTATGGTCTTACACATATTCACAT-A
* * *
52339982 T-GATGTCATAGCCCAGCTATGGTCTTACACATATTTATATA
1 TCGATGCCATAGCCCAGCTATGGTCTTACACATATTCACATA
52340023 TCGATGCCATAGCCCAGCTATGGTCTTACACGA-A-TCACATA
1 TCGATGCCATAGCCCAGCTATGGTCTTACAC-ATATTCACATA
52340064 TC
1 TC
52340066 TTACTGATGC
Statistics
Matches: 71, Mismatches: 11, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
41 9 0.13
42 60 0.85
43 2 0.03
ACGTcount: A:0.30, C:0.24, G:0.14, T:0.31
Consensus pattern (42 bp):
TCGATGCCATAGCCCAGCTATGGTCTTACACATATTCACATA
Found at i:52340164 original size:31 final size:31
Alignment explanation
Indices: 52340124--52340232 Score: 137
Period size: 31 Copynumber: 3.5 Consensus size: 31
52340114 ACTTGTAGAT
* * *
52340124 GAAGCTACCACTATTCACTGAACAGGTAGCC
1 GAAGCTACCACTTTTCACTGATCAGGTAGCA
* *
52340155 GGAGCTACCATTTTTCACTGATCAGGTAGCA
1 GAAGCTACCACTTTTCACTGATCAGGTAGCA
* *
52340186 GAAGCTACCACTTTTCACTGATCAGGGAGCT
1 GAAGCTACCACTTTTCACTGATCAGGTAGCA
* *
52340217 GAGGCTACCACGTTTC
1 GAAGCTACCACTTTTC
52340233 TCTTGTCATT
Statistics
Matches: 67, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 67 1.00
ACGTcount: A:0.27, C:0.27, G:0.22, T:0.25
Consensus pattern (31 bp):
GAAGCTACCACTTTTCACTGATCAGGTAGCA
Found at i:52340299 original size:50 final size:50
Alignment explanation
Indices: 52340242--52340385 Score: 220
Period size: 50 Copynumber: 2.9 Consensus size: 50
52340232 CTCTTGTCAT
* *
52340242 TTGTCATTGATCAGATAAGTGTAGCCGAAGCTCTCACTTATCACTTTCCC
1 TTGTCATTGATCAGATAAGTGTAGCCGAAGCTATCACTTATCACTTTCAC
* * *
52340292 TTGTCATTGATCAGATAAGTGTAGCCGAAGCTATTACTTGTCACTTTCAT
1 TTGTCATTGATCAGATAAGTGTAGCCGAAGCTATCACTTATCACTTTCAC
*
52340342 TTGTC--CGATCAGATAAGTGTAGCCGAAGCTATCACTTATCACTT
1 TTGTCATTGATCAGATAAGTGTAGCCGAAGCTATCACTTATCACTT
52340386 GTTGCCATGG
Statistics
Matches: 86, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
48 36 0.42
50 50 0.58
ACGTcount: A:0.26, C:0.22, G:0.17, T:0.35
Consensus pattern (50 bp):
TTGTCATTGATCAGATAAGTGTAGCCGAAGCTATCACTTATCACTTTCAC
Found at i:52344292 original size:26 final size:26
Alignment explanation
Indices: 52344263--52344319 Score: 87
Period size: 26 Copynumber: 2.2 Consensus size: 26
52344253 GTATTCATAT
*
52344263 ATCACAATATGTATTTGTATCATTAA
1 ATCACAATATGTATTTGTATCATCAA
* *
52344289 ATCATAGTATGTATTTGTATCATCAA
1 ATCACAATATGTATTTGTATCATCAA
52344315 ATCAC
1 ATCAC
52344320 GTTATCAACT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.37, C:0.14, G:0.09, T:0.40
Consensus pattern (26 bp):
ATCACAATATGTATTTGTATCATCAA
Found at i:52350791 original size:12 final size:12
Alignment explanation
Indices: 52350774--52350798 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
52350764 TCATTTTTGC
52350774 TCATGAACATAG
1 TCATGAACATAG
52350786 TCATGAACATAG
1 TCATGAACATAG
52350798 T
1 T
52350799 GATTTCTTGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.16, G:0.16, T:0.28
Consensus pattern (12 bp):
TCATGAACATAG
Found at i:52357720 original size:52 final size:52
Alignment explanation
Indices: 52357625--52357809 Score: 214
Period size: 52 Copynumber: 3.5 Consensus size: 52
52357615 TATCCCAGGC
* ** *
52357625 ATGGTCTTATAC-GGAGGCACATTATCAC-ATCATATTGATGCCATAGCCCAACC
1 ATGGTCTTATACGGGA-GCACA-TATCACAAT-ACACCGATGCCATAGCCCAACT
*
52357678 ATGGTCTTATACGGGAGTACATATCACAATACACCGATGCCATAGCCCAACT
1 ATGGTCTTATACGGGAGCACATATCACAATACACCGATGCCATAGCCCAACT
* * ** *
52357730 ATGGTCTTATACGGGCA-CACATATCACAATGCACCAATGATATAGCCCAAAT
1 ATGGTCTTATACGGG-AGCACATATCACAATACACCGATGCCATAGCCCAACT
*
52357782 ATGGTCTTATACGGGCGCACATATCACA
1 ATGGTCTTATACGGGAGCACATATCACA
52357810 TCATTCTGTC
Statistics
Matches: 116, Mismatches: 12, Indels: 9
0.85 0.09 0.07
Matches are distributed among these distances:
52 94 0.81
53 19 0.16
54 3 0.03
ACGTcount: A:0.32, C:0.26, G:0.17, T:0.24
Consensus pattern (52 bp):
ATGGTCTTATACGGGAGCACATATCACAATACACCGATGCCATAGCCCAACT
Found at i:52360949 original size:3 final size:3
Alignment explanation
Indices: 52360941--52360980 Score: 53
Period size: 3 Copynumber: 13.3 Consensus size: 3
52360931 TTTAAAATAT
* * *
52360941 TTA TTA TTA TTA TTA TCA TCA TCA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
52360981 AATGTAATCA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.33, C:0.07, G:0.00, T:0.60
Consensus pattern (3 bp):
TTA
Found at i:52360995 original size:24 final size:25
Alignment explanation
Indices: 52360939--52360996 Score: 64
Period size: 27 Copynumber: 2.3 Consensus size: 25
52360929 ATTTTAAAAT
* *
52360939 ATTTATTATTATTATTATCATCATC
1 ATTTATTATTATTATAATCATAATC
*
52360964 ATTATTATTATTATTATAAT-GTAATC
1 A-T-TTATTATTATTATAATCATAATC
52360990 ATTTATT
1 ATTTATT
52360997 TATTTGTTAC
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
24 5 0.18
25 2 0.07
26 6 0.21
27 15 0.54
ACGTcount: A:0.34, C:0.07, G:0.02, T:0.57
Consensus pattern (25 bp):
ATTTATTATTATTATAATCATAATC
Found at i:52361083 original size:3 final size:3
Alignment explanation
Indices: 52361077--52361114 Score: 58
Period size: 3 Copynumber: 12.3 Consensus size: 3
52361067 TCGTCGTTAC
*
52361077 TAT TAT TAT TAT TAT TAT TAT TAT TAC TAT TAT ATAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT T
52361115 TTTTAAATTA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
3 29 0.91
4 3 0.09
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:52361195 original size:17 final size:17
Alignment explanation
Indices: 52361173--52361208 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
52361163 ATTACCCTTT
* *
52361173 TTATTATTATTATTGTA
1 TTATTACTATTATTATA
52361190 TTATTACTATTATTATA
1 TTATTACTATTATTATA
52361207 TT
1 TT
52361209 TACACCTATA
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:0.31, C:0.03, G:0.03, T:0.64
Consensus pattern (17 bp):
TTATTACTATTATTATA
Found at i:52361389 original size:15 final size:15
Alignment explanation
Indices: 52361366--52361395 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
52361356 ATAATTTCAT
*
52361366 ATTATTATTATTATC
1 ATTACTATTATTATC
52361381 ATTACTATTATTATC
1 ATTACTATTATTATC
52361396 CTTTTTTAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.33, C:0.10, G:0.00, T:0.57
Consensus pattern (15 bp):
ATTACTATTATTATC
Found at i:52363464 original size:3 final size:3
Alignment explanation
Indices: 52363458--52363483 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
52363448 TAAAACAATG
52363458 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
52363484 GATTACCATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:52364205 original size:18 final size:18
Alignment explanation
Indices: 52364184--52364227 Score: 79
Period size: 18 Copynumber: 2.4 Consensus size: 18
52364174 ATTTAACAGG
52364184 ATACTAATTTAATTAAAA
1 ATACTAATTTAATTAAAA
52364202 ATACTAATTTAATTAAAA
1 ATACTAATTTAATTAAAA
*
52364220 ATAATAAT
1 ATACTAAT
52364228 ATATTCTTTC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.39
Consensus pattern (18 bp):
ATACTAATTTAATTAAAA
Found at i:52380362 original size:126 final size:126
Alignment explanation
Indices: 52380203--52380570 Score: 587
Period size: 126 Copynumber: 2.9 Consensus size: 126
52380193 CTCGTTTATA
* * *
52380203 GTAGAAAAAGAGCATTCACGTGGGAGCTTTTTTCATAAATTTTGTTGACATTGCATCCTGCTTGA
1 GTAGAAAAAGAGCGTCCACGTGGGAGCTTTTTTCATAAATTTTGCTGACATTGCATCCTGCTTGA
*
52380268 AGCGTTTTTGACACTATTTGTTCAGAAACGTCTTCTCAAAATTATTTTTTCAGGAACTACT
66 AGCGTTTTTGACACTATTTGTTCAGAAACGTCTTCTCAAAATTATTTTTTCAGAAACTACT
* *
52380329 GTAGAAAAAGAGCGTCCACATGGGAGCTTTTTTCATAAATTTTGCTGACATTGTATCCTGCTTGA
1 GTAGAAAAAGAGCGTCCACGTGGGAGCTTTTTTCATAAATTTTGCTGACATTGCATCCTGCTTGA
* *
52380394 AGCGTTTTTGACACTATTTATTCAAAAACGTCTTCTCAAAATTATTTTTTCAGAAACTACT
66 AGCGTTTTTGACACTATTTGTTCAGAAACGTCTTCTCAAAATTATTTTTTCAGAAACTACT
* * * *
52380455 GTAGCAAAACAGCGTCCACGTGGGAGCTTTTTTC-TGTATTTTTGCTGACATTGCATCCTGCTTG
1 GTAGAAAAAGAGCGTCCACGTGGGAGCTTTTTTCAT-AAATTTTGCTGACATTGCATCCTGCTTG
* *
52380519 AAGCATTTTTGACACTATTTGTTCAGAAACG-CTTCTTAAAATTATTTTTTCA
65 AAGCGTTTTTGACACTATTTGTTCAGAAACGTCTTCTCAAAATTATTTTTTCA
52380571 CGGTAAAAAT
Statistics
Matches: 223, Mismatches: 18, Indels: 3
0.91 0.07 0.01
Matches are distributed among these distances:
125 21 0.09
126 202 0.91
ACGTcount: A:0.27, C:0.18, G:0.17, T:0.38
Consensus pattern (126 bp):
GTAGAAAAAGAGCGTCCACGTGGGAGCTTTTTTCATAAATTTTGCTGACATTGCATCCTGCTTGA
AGCGTTTTTGACACTATTTGTTCAGAAACGTCTTCTCAAAATTATTTTTTCAGAAACTACT
Found at i:52380672 original size:21 final size:22
Alignment explanation
Indices: 52380646--52380693 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
52380636 TAATTACTCT
52380646 ATTTAA-AAAACATAAACCCTA
1 ATTTAATAAAACATAAACCCTA
* *
52380667 ATTTAATAAACCTTAAACCCTA
1 ATTTAATAAAACATAAACCCTA
52380689 ATTTA
1 ATTTA
52380694 GTTTACTTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
21 6 0.25
22 18 0.75
ACGTcount: A:0.50, C:0.19, G:0.00, T:0.31
Consensus pattern (22 bp):
ATTTAATAAAACATAAACCCTA
Found at i:52380704 original size:22 final size:22
Alignment explanation
Indices: 52380658--52380732 Score: 71
Period size: 22 Copynumber: 3.4 Consensus size: 22
52380648 TTAAAAAACA
** *
52380658 TAAACCCTAATTTAATAAACCT
1 TAAACCCTAATTTAATTTACTT
*
52380680 TAAACCCTAATTTAGTTTACTT
1 TAAACCCTAATTTAATTTACTT
* * *
52380702 TAAATCTTAACTTAATTTA-TT
1 TAAACCCTAATTTAATTTACTT
52380723 TAAAACCCTA
1 T-AAACCCTA
52380733 GAACTCTAAT
Statistics
Matches: 42, Mismatches: 10, Indels: 2
0.78 0.19 0.04
Matches are distributed among these distances:
21 3 0.07
22 39 0.93
ACGTcount: A:0.40, C:0.19, G:0.01, T:0.40
Consensus pattern (22 bp):
TAAACCCTAATTTAATTTACTT
Found at i:52380827 original size:22 final size:22
Alignment explanation
Indices: 52380799--52380840 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
52380789 AATATTTAAT
52380799 TTAATTTATTTAAAACCCTAAC
1 TTAATTTATTTAAAACCCTAAC
52380821 TTAATTTATTTAAAACCCTA
1 TTAATTTATTTAAAACCCTA
52380841 GAACCCTAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.40, C:0.17, G:0.00, T:0.43
Consensus pattern (22 bp):
TTAATTTATTTAAAACCCTAAC
Found at i:52380884 original size:33 final size:34
Alignment explanation
Indices: 52380819--52380886 Score: 102
Period size: 34 Copynumber: 2.0 Consensus size: 34
52380809 TAAAACCCTA
* * *
52380819 ACTTAATTTATTTAAAACCCTAGAACCCTAATTT
1 ACTTAATATATTTAAAAACATAGAACCCTAATTT
52380853 ACTTAATATATTTAAAAACATA-AACCCTAATTT
1 ACTTAATATATTTAAAAACATAGAACCCTAATTT
52380886 A
1 A
52380887 ATAAACCCTA
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
33 12 0.39
34 19 0.61
ACGTcount: A:0.44, C:0.18, G:0.01, T:0.37
Consensus pattern (34 bp):
ACTTAATATATTTAAAAACATAGAACCCTAATTT
Found at i:52380911 original size:107 final size:107
Alignment explanation
Indices: 52380610--52381018 Score: 503
Period size: 108 Copynumber: 3.9 Consensus size: 107
52380600 ACACAATGTT
* * * *
52380610 ATTTTTTTAAAA-ACTA-AACCCTAATTTAATTACTCTATTTAAAAAACATAAACCCTAATTTAA
1 ATTTATTTAAAACCCTAGAACCCTAATTTACTTAATCTATTTAAAAAACATAAACCCTAATTTAA
* * * * *
52380673 TAAACCTTAAACCCTAATTTAGTTTACTTTAAATCTTAACTTA
66 TAAACCCTAAACCTTAATTTAATTTA-TTTAAACCCTAACTTA
* * ***
52380716 ATTTATTTAAAACCCTAGAACTCTAATTTACTTAATCTATTTAAAAAACATAAGCCCTAATTCCC
1 ATTTATTTAAAACCCTAGAACCCTAATTTACTTAATCTATTTAAAAAACATAAACCCTAATTTAA
**
52380781 TAAACCC-AAATATTTAATTTAATTTATTTAAAACCCTAACTTA
66 TAAACCCTAAA-CCTTAATTTAATTTATTT-AAACCCTAACTTA
*
52380824 ATTTATTTAAAACCCTAGAACCCTAATTTACTTAATATATTT-AAAAACATAAACCCTAATTTAA
1 ATTTATTTAAAACCCTAGAACCCTAATTTACTTAATCTATTTAAAAAACATAAACCCTAATTTAA
*
52380888 TAAACCCTAAACCTTAATTTAATTTATTTTAAACACTAACTTA
66 TAAACCCTAAACCTTAATTTAATTTA-TTTAAACCCTAACTTA
* * *
52380931 ATTTATTTAAAATCCTAGAACCCTAATTTACTTAATCTATTT--AAAACCTAAGCCCTAATTTAT
1 ATTTATTTAAAACCCTAGAACCCTAATTTACTTAATCTATTTAAAAAACATAAACCCTAATTTA-
*
52380994 TTAAAACCCT-AA-CTTAATTT-ATTTA
65 AT-AAACCCTAAACCTTAATTTAATTTA
52381019 AAAATAATTA
Statistics
Matches: 265, Mismatches: 30, Indels: 17
0.85 0.10 0.05
Matches are distributed among these distances:
105 5 0.02
106 37 0.14
107 102 0.38
108 121 0.46
ACGTcount: A:0.42, C:0.18, G:0.01, T:0.39
Consensus pattern (107 bp):
ATTTATTTAAAACCCTAGAACCCTAATTTACTTAATCTATTTAAAAAACATAAACCCTAATTTAA
TAAACCCTAAACCTTAATTTAATTTATTTAAACCCTAACTTA
Found at i:52380965 original size:34 final size:32
Alignment explanation
Indices: 52380926--52380997 Score: 99
Period size: 34 Copynumber: 2.2 Consensus size: 32
52380916 TTAAACACTA
*
52380926 ACTTAATTTATTTAAAATCCTAGAACCCTAATTT
1 ACTTAATCTATTTAAAA-CCTA-AACCCTAATTT
*
52380960 ACTTAATCTATTTAAAACCTAAGCCCTAATTT
1 ACTTAATCTATTTAAAACCTAAACCCTAATTT
*
52380992 ATTTAA
1 ACTTAA
52380998 AACCCTAACT
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
32 15 0.43
33 4 0.11
34 16 0.46
ACGTcount: A:0.39, C:0.18, G:0.03, T:0.40
Consensus pattern (32 bp):
ACTTAATCTATTTAAAACCTAAACCCTAATTT
Found at i:52380972 original size:56 final size:57
Alignment explanation
Indices: 52380799--52381004 Score: 227
Period size: 56 Copynumber: 3.8 Consensus size: 57
52380789 AATATTTAAT
* *
52380799 TTAATTTATTTAAAACCCTAA-CTTAATTTATTTAAAACCCTAGAACCCTAATTTAC
1 TTAATTTATTTAAAACACTAACCCTAATTTATTTAAAACCCTAGAACCCTAATTTAC
* * *
52380855 TTAATATATTTAAAA-ACATAAACCCTAATTTA-AT-AAACCCTA-AACCTTAA--T--
1 TTAATTTATTTAAAACAC-T-AACCCTAATTTATTTAAAACCCTAGAACCCTAATTTAC
* * *
52380906 TTAATTTATTTTAAACACTAA-CTTAATTTATTTAAAATCCTAGAACCCTAATTTAC
1 TTAATTTATTTAAAACACTAACCCTAATTTATTTAAAACCCTAGAACCCTAATTTAC
*
52380962 TTAATCTATTTAAAAC-CTAAGCCCTAATTTATTTAAAACCCTA
1 TTAATTTATTTAAAACACTAA-CCCTAATTTATTTAAAACCCTA
52381005 ACTTAATTTA
Statistics
Matches: 122, Mismatches: 15, Indels: 25
0.75 0.09 0.15
Matches are distributed among these distances:
49 8 0.07
50 3 0.02
51 21 0.17
52 9 0.07
53 1 0.01
54 1 0.01
55 12 0.10
56 37 0.30
57 22 0.18
58 8 0.07
ACGTcount: A:0.42, C:0.18, G:0.01, T:0.38
Consensus pattern (57 bp):
TTAATTTATTTAAAACACTAACCCTAATTTATTTAAAACCCTAGAACCCTAATTTAC
Found at i:52381022 original size:23 final size:21
Alignment explanation
Indices: 52380960--52381021 Score: 79
Period size: 22 Copynumber: 2.8 Consensus size: 21
52380950 ACCCTAATTT
*
52380960 ACTTAATCTATTTAAAACCTA
1 ACTTAATTTATTTAAAACCTA
*
52380981 AGCCCTAATTTATTTAAAACCCTA
1 A--CTTAATTTATTTAAAA-CCTA
52381005 ACTTAATTTATTTAAAA
1 ACTTAATTTATTTAAAA
52381022 ATAATTAACC
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
21 1 0.03
22 15 0.43
23 14 0.40
24 5 0.14
ACGTcount: A:0.42, C:0.18, G:0.02, T:0.39
Consensus pattern (21 bp):
ACTTAATTTATTTAAAACCTA
Found at i:52382426 original size:18 final size:17
Alignment explanation
Indices: 52382376--52382426 Score: 52
Period size: 16 Copynumber: 3.0 Consensus size: 17
52382366 TTCATAACAC
52382376 TTTTTATAAATAATT-T
1 TTTTTATAAATAATTAT
* *
52382392 TTTTTTTCAAA-ATTTAT
1 TTTTTAT-AAATAATTAT
52382409 TTTTTATAAATAAGTTAT
1 TTTTTATAAATAA-TTAT
52382427 AATAAAAAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 6
0.73 0.11 0.16
Matches are distributed among these distances:
16 12 0.44
17 11 0.41
18 4 0.15
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.61
Consensus pattern (17 bp):
TTTTTATAAATAATTAT
Found at i:52382661 original size:24 final size:24
Alignment explanation
Indices: 52382607--52382659 Score: 74
Period size: 22 Copynumber: 2.3 Consensus size: 24
52382597 ATTTTAGAAC
52382607 TTTTTTTAAGATTTAAATAATATA
1 TTTTTTTAAGATTTAAATAATATA
* *
52382631 ATTTTTTAATATTT--ATAATATA
1 TTTTTTTAAGATTTAAATAATATA
52382653 TTTTTTT
1 TTTTTTT
52382660 TTGTTGTAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
22 14 0.54
24 12 0.46
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (24 bp):
TTTTTTTAAGATTTAAATAATATA
Found at i:52383911 original size:22 final size:22
Alignment explanation
Indices: 52383862--52383905 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 22
52383852 TCACGTTAAT
52383862 AAATAATTTAAAAATTATAAAA
1 AAATAATTTAAAAATTATAAAA
*
52383884 AAATAA-TTATAAATTA-AAAA
1 AAATAATTTAAAAATTATAAAA
52383904 AA
1 AA
52383906 TCATAAACGT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 6 0.29
21 9 0.43
22 6 0.29
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (22 bp):
AAATAATTTAAAAATTATAAAA
Found at i:52392676 original size:5 final size:5
Alignment explanation
Indices: 52392650--52392707 Score: 53
Period size: 5 Copynumber: 10.8 Consensus size: 5
52392640 ATGTGTTAAA
* **
52392650 ATATAT ATATT AAATT ATTATT ATATT ATAGA ATATT ATATTAT ATATT
1 ATAT-T ATATT ATATT A-TATT ATATT ATATT ATATT ATA-T-T ATATT
52392699 ATATT ATAT
1 ATATT ATAT
52392708 AAATAAGTAA
Statistics
Matches: 43, Mismatches: 6, Indels: 7
0.77 0.11 0.12
Matches are distributed among these distances:
5 29 0.67
6 10 0.23
7 4 0.09
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (5 bp):
ATATT
Found at i:52392699 original size:12 final size:12
Alignment explanation
Indices: 52392653--52392708 Score: 69
Period size: 12 Copynumber: 4.5 Consensus size: 12
52392643 TGTTAAAATA
*
52392653 TATATATTAAAT
1 TATATATTATAT
52392665 TAT-TATTATAT
1 TATATATTATAT
52392676 TATAGAATATTATAT
1 TAT---ATATTATAT
52392691 TATATATTATAT
1 TATATATTATAT
52392703 TATATA
1 TATATA
52392709 AATAAGTAAA
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
11 10 0.26
12 18 0.46
15 11 0.28
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.54
Consensus pattern (12 bp):
TATATATTATAT
Found at i:52393627 original size:18 final size:19
Alignment explanation
Indices: 52393604--52393642 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
52393594 ATATATAGAT
52393604 ATATATATTGAATA-TTGA
1 ATATATATTGAATATTTGA
*
52393622 ATATATATTGATTATTTGA
1 ATATATATTGAATATTTGA
52393641 AT
1 AT
52393643 TGAATTGAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 13 0.68
19 6 0.32
ACGTcount: A:0.41, C:0.00, G:0.10, T:0.49
Consensus pattern (19 bp):
ATATATATTGAATATTTGA
Found at i:52393992 original size:39 final size:39
Alignment explanation
Indices: 52393882--52394016 Score: 112
Period size: 39 Copynumber: 3.4 Consensus size: 39
52393872 GACCTCGAGT
* * * *
52393882 CGATGAGACACTGGGTGTCACTATATTTCTTCGGATAGATT
1 CGATGAGACACTGGGTGTCA-AATATTACTTCGGCTAG-TC
** ** * *
52393923 CGATGAGGTACTGGGTACCAACT-TTACTTCGGCTAGGC
1 CGATGAGACACTGGGTGTCAAATATTACTTCGGCTAGTC
* *
52393961 CGATGAGACACTGGGTGTCAAATATTGCTTCGAACTA-TC
1 CGATGAGACACTGGGTGTCAAATATTACTTCG-GCTAGTC
*
52394000 CGATGAGGCACTGGGTG
1 CGATGAGACACTGGGTG
52394017 CCATATTGGT
Statistics
Matches: 73, Mismatches: 19, Indels: 6
0.74 0.19 0.06
Matches are distributed among these distances:
38 18 0.25
39 35 0.48
40 4 0.05
41 16 0.22
ACGTcount: A:0.24, C:0.20, G:0.28, T:0.28
Consensus pattern (39 bp):
CGATGAGACACTGGGTGTCAAATATTACTTCGGCTAGTC
Found at i:52394160 original size:18 final size:19
Alignment explanation
Indices: 52394139--52394179 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
52394129 AATGAAATGA
52394139 GAAATTGA-AT-TGAGAATT
1 GAAATTGAGATATGAG-ATT
52394157 GAAATTGAGATATGAGATT
1 GAAATTGAGATATGAGATT
52394176 GAAA
1 GAAA
52394180 ACATGAACCA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.38
19 9 0.43
20 4 0.19
ACGTcount: A:0.46, C:0.00, G:0.24, T:0.29
Consensus pattern (19 bp):
GAAATTGAGATATGAGATT
Found at i:52394911 original size:65 final size:65
Alignment explanation
Indices: 52394807--52394937 Score: 235
Period size: 65 Copynumber: 2.0 Consensus size: 65
52394797 GCCCATTAAA
* *
52394807 GGGACGACATCTTAAAACTAGGATGTGTGTAAATATTTATTTTAATTAATGACCGAAATTGGACT
1 GGGACGACATCTTAAAACTAGGATGTGTGTAAATATTTATTTTAATTAACGACAGAAATTGGACT
*
52394872 GGGACGATATCTTAAAACTAGGATGTGTGTAAATATTTATTTTAATTAACGACAGAAATTGGACT
1 GGGACGACATCTTAAAACTAGGATGTGTGTAAATATTTATTTTAATTAACGACAGAAATTGGACT
52394937 G
1 G
52394938 TACTGACTGG
Statistics
Matches: 63, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
65 63 1.00
ACGTcount: A:0.36, C:0.10, G:0.21, T:0.34
Consensus pattern (65 bp):
GGGACGACATCTTAAAACTAGGATGTGTGTAAATATTTATTTTAATTAACGACAGAAATTGGACT
Found at i:52396486 original size:30 final size:30
Alignment explanation
Indices: 52396450--52396511 Score: 124
Period size: 30 Copynumber: 2.1 Consensus size: 30
52396440 TCTATTAACG
52396450 CACTATAGGTAACAACATCAGGCTCAATGC
1 CACTATAGGTAACAACATCAGGCTCAATGC
52396480 CACTATAGGTAACAACATCAGGCTCAATGC
1 CACTATAGGTAACAACATCAGGCTCAATGC
52396510 CA
1 CA
52396512 TGCTTTCTCA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.37, C:0.27, G:0.16, T:0.19
Consensus pattern (30 bp):
CACTATAGGTAACAACATCAGGCTCAATGC
Found at i:52402629 original size:24 final size:24
Alignment explanation
Indices: 52402602--52402653 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
52402592 TTAGTAAGTC
*
52402602 AAATAAACTATACTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
52402626 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
52402650 AAAT
1 AAAT
52402654 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:52404591 original size:24 final size:24
Alignment explanation
Indices: 52404564--52404615 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
52404554 TTAGTAAGTC
*
52404564 AAATAGACTATACTAATAAATGCT
1 AAATAGACTATACTAATAAATACT
* *
52404588 AAATATATTATACTAATAAATACT
1 AAATAGACTATACTAATAAATACT
52404612 AAAT
1 AAAT
52404616 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.54, C:0.10, G:0.04, T:0.33
Consensus pattern (24 bp):
AAATAGACTATACTAATAAATACT
Found at i:52409480 original size:28 final size:31
Alignment explanation
Indices: 52409449--52409515 Score: 77
Period size: 32 Copynumber: 2.2 Consensus size: 31
52409439 CCACTATTCT
*
52409449 TTTTTA-ATTATT-TA-ATATTTTTAATAAA
1 TTTTTATATTATTATACATAATTTTAATAAA
*
52409477 TTTTTATGTTATTGATACATAATTTTAATAAA
1 TTTTTATATTATT-ATACATAATTTTAATAAA
52409509 TATTTTA
1 T-TTTTA
52409516 CTCTGAATCC
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
28 6 0.19
29 5 0.16
31 2 0.06
32 14 0.44
33 5 0.16
ACGTcount: A:0.37, C:0.01, G:0.03, T:0.58
Consensus pattern (31 bp):
TTTTTATATTATTATACATAATTTTAATAAA
Found at i:52410465 original size:14 final size:14
Alignment explanation
Indices: 52410446--52410476 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
52410436 ATTGTGTGTT
52410446 GGTATGATAATTAA
1 GGTATGATAATTAA
52410460 GGTATGATAATTAA
1 GGTATGATAATTAA
52410474 GGT
1 GGT
52410477 GTTCACTGTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.39, C:0.00, G:0.26, T:0.35
Consensus pattern (14 bp):
GGTATGATAATTAA
Found at i:52411303 original size:15 final size:14
Alignment explanation
Indices: 52411283--52411330 Score: 62
Period size: 15 Copynumber: 3.3 Consensus size: 14
52411273 TTTTAAATTC
52411283 TAAAAATATAATAAT
1 TAAAAATATAA-AAT
52411298 TAAAAATAATAAAAT
1 TAAAAAT-ATAAAAT
52411313 T-AAAATATAAATAT
1 TAAAAATATAAA-AT
52411327 TAAA
1 TAAA
52411331 TCTATAACTT
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
13 5 0.17
14 8 0.27
15 13 0.43
16 4 0.13
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (14 bp):
TAAAAATATAAAAT
Found at i:52411322 original size:13 final size:13
Alignment explanation
Indices: 52411285--52411330 Score: 56
Period size: 14 Copynumber: 3.2 Consensus size: 13
52411275 TTAAATTCTA
52411285 AAAATATAATAATT
1 AAAATATAA-AATT
52411299 AAAAATAATAAAATT
1 -AAAAT-ATAAAATT
52411314 AAAATATAAATATT
1 AAAATATAAA-ATT
52411328 AAA
1 AAA
52411331 TCTATAACTT
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
13 5 0.17
14 11 0.38
15 9 0.31
16 4 0.14
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (13 bp):
AAAATATAAAATT
Found at i:52421852 original size:105 final size:105
Alignment explanation
Indices: 52421743--52421943 Score: 262
Period size: 105 Copynumber: 1.9 Consensus size: 105
52421733 TATAGGTAAC
* **
52421743 AACATCAGGCTCAATGCCTTGCTTTATCATTGTGTCAACAATATCTTTAGCTT-TAGAAAGCATC
1 AACATCAGGCTCAATGCCATGCTTTATCATTGTGTCAACAATATCTACAGCTTCT-GAAAGCATC
* *
52421807 CCTTCTTTGCAACATGCATCGATGC-ATATATTGTACGTGAT
65 CCCTCCTTGCAACATGCATCGAT-CAATATATTGTACGTGAT
* * * * *
52421848 AACATTAGGCTCAATGCCATGCTTTCTCATTGTGTCAACGATTTCTACAGCTTCTGAAATCATCC
1 AACATCAGGCTCAATGCCATGCTTTATCATTGTGTCAACAATATCTACAGCTTCTGAAAGCATCC
* *
52421913 CCTCCTTGCAACGTGCGTCGATCAATATATT
66 CCTCCTTGCAACATGCATCGATCAATATATT
52421944 ATATGTGTAG
Statistics
Matches: 82, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
104 1 0.01
105 80 0.98
106 1 0.01
ACGTcount: A:0.26, C:0.24, G:0.15, T:0.34
Consensus pattern (105 bp):
AACATCAGGCTCAATGCCATGCTTTATCATTGTGTCAACAATATCTACAGCTTCTGAAAGCATCC
CCTCCTTGCAACATGCATCGATCAATATATTGTACGTGAT
Found at i:52425779 original size:15 final size:17
Alignment explanation
Indices: 52425753--52425784 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
52425743 TTCTATATTT
52425753 TTTTATATAATT-AATA
1 TTTTATATAATTCAATA
52425769 TTTTA-ATAATTCAATA
1 TTTTATATAATTCAATA
52425785 ATTATATTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 6 0.40
16 9 0.60
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (17 bp):
TTTTATATAATTCAATA
Found at i:52430706 original size:20 final size:21
Alignment explanation
Indices: 52430669--52430707 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
52430659 CCGATAGTTG
* *
52430669 AATTATTTTTCTCTATTTTTT
1 AATTATTTTTATCAATTTTTT
52430690 AATT-TTTTTATCAATTTT
1 AATTATTTTTATCAATTTT
52430708 AATAATTTAT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 12 0.75
21 4 0.25
ACGTcount: A:0.23, C:0.08, G:0.00, T:0.69
Consensus pattern (21 bp):
AATTATTTTTATCAATTTTTT
Found at i:52444923 original size:25 final size:26
Alignment explanation
Indices: 52444863--52444911 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
52444853 ATTTGTTTTA
*
52444863 ATATTTG-TTT-TTATGTTTTTAAAT
1 ATATTTGATTTATTATATTTTTAAAT
52444887 ATATTTGATTTATTATATTTTTAAA
1 ATATTTGATTTATTATATTTTTAAA
52444912 ATTTTTTATT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 7 0.32
25 3 0.14
26 12 0.55
ACGTcount: A:0.31, C:0.00, G:0.06, T:0.63
Consensus pattern (26 bp):
ATATTTGATTTATTATATTTTTAAAT
Found at i:52445883 original size:21 final size:20
Alignment explanation
Indices: 52445845--52445884 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
52445835 AATATAAGAT
**
52445845 TAACTCATATATCCTTATAG
1 TAACTCATATATAATTATAG
52445865 TAACTCTATATATAATTATA
1 TAACTC-ATATATAATTATA
52445885 ATAGTAAATT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.40, C:0.15, G:0.03, T:0.42
Consensus pattern (20 bp):
TAACTCATATATAATTATAG
Found at i:52446995 original size:6 final size:6
Alignment explanation
Indices: 52446986--52447018 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
52446976 AAAAGAAAAA
52446986 GTGTGG GTGTGG GTGTGG GTGTGG GTGTGG GTG
1 GTGTGG GTGTGG GTGTGG GTGTGG GTGTGG GTG
52447019 GCATCGACTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.00, C:0.00, G:0.67, T:0.33
Consensus pattern (6 bp):
GTGTGG
Found at i:52458636 original size:16 final size:16
Alignment explanation
Indices: 52458617--52458661 Score: 58
Period size: 15 Copynumber: 2.9 Consensus size: 16
52458607 TTTTTTTTCA
52458617 ATTTTAATATTTTATT
1 ATTTTAATATTTTATT
*
52458633 A-TTTAATGTTTT-TT
1 ATTTTAATATTTTATT
52458647 ATTCTTAATATTTTA
1 ATT-TTAATATTTTA
52458662 ATAATTCAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
14 3 0.12
15 11 0.46
16 10 0.42
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.67
Consensus pattern (16 bp):
ATTTTAATATTTTATT
Found at i:52468256 original size:25 final size:22
Alignment explanation
Indices: 52468202--52468256 Score: 56
Period size: 22 Copynumber: 2.4 Consensus size: 22
52468192 TATTATTTTA
* *
52468202 TGTAAATATTTTCTAAATTTAT
1 TGTATATATTTTCTAAAATTAT
*
52468224 TGTGTATATTTTCTTTAAAATTAT
1 TGTATATATTTTC--TAAAATTAT
52468248 TCGTATATA
1 T-GTATATA
52468257 GCTTGGCTTT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
22 11 0.42
24 9 0.35
25 6 0.23
ACGTcount: A:0.33, C:0.05, G:0.07, T:0.55
Consensus pattern (22 bp):
TGTATATATTTTCTAAAATTAT
Found at i:52473725 original size:16 final size:16
Alignment explanation
Indices: 52473694--52473769 Score: 107
Period size: 16 Copynumber: 4.8 Consensus size: 16
52473684 AAACACAAGA
*
52473694 ATTCTATTACAGCTCT
1 ATTCCATTACAGCTCT
* *
52473710 ATTCCATCACAACTCT
1 ATTCCATTACAGCTCT
*
52473726 ATTCCATTACAGTTCT
1 ATTCCATTACAGCTCT
*
52473742 ATTCAATTACAGCTCT
1 ATTCCATTACAGCTCT
52473758 ATTCCATTACAG
1 ATTCCATTACAG
52473770 TGAACCAAAC
Statistics
Matches: 51, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
16 51 1.00
ACGTcount: A:0.29, C:0.28, G:0.05, T:0.38
Consensus pattern (16 bp):
ATTCCATTACAGCTCT
Found at i:52474933 original size:25 final size:25
Alignment explanation
Indices: 52474905--52474968 Score: 62
Period size: 23 Copynumber: 2.7 Consensus size: 25
52474895 GAAAGTGATT
52474905 AAATTATATATTTTTATGATAGTAA
1 AAATTATATATTTTTATGATAGTAA
* * **
52474930 AAA-TATA-ATTTTTTTTATTTTAA
1 AAATTATATATTTTTATGATAGTAA
*
52474953 TAATT-TATATTTTTAT
1 AAATTATATATTTTTAT
52474969 AAATTTTAAA
Statistics
Matches: 31, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
23 16 0.52
24 12 0.39
25 3 0.10
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (25 bp):
AAATTATATATTTTTATGATAGTAA
Found at i:52475032 original size:7 final size:7
Alignment explanation
Indices: 52475013--52475059 Score: 51
Period size: 7 Copynumber: 6.6 Consensus size: 7
52475003 TTAGAGGAAT
*
52475013 TAAAGTA
1 TAAATTA
52475020 TAAATT-
1 TAAATTA
52475026 TATAATTA
1 TA-AATTA
*
52475034 TTAATTTA
1 -TAAATTA
52475042 TAAATTA
1 TAAATTA
52475049 TAAATTA
1 TAAATTA
52475056 TAAA
1 TAAA
52475060 AAAAACATAA
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
6 2 0.06
7 26 0.76
8 4 0.12
9 2 0.06
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (7 bp):
TAAATTA
Found at i:52475036 original size:22 final size:22
Alignment explanation
Indices: 52475011--52475056 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
52475001 TTTTAGAGGA
52475011 ATTAAAGTATAAATT-TATAATT
1 ATTAAAGTATAAATTATA-AATT
**
52475033 ATTAATTTATAAATTATAAATT
1 ATTAAAGTATAAATTATAAATT
52475055 AT
1 AT
52475057 AAAAAAAACA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 19 0.90
23 2 0.10
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (22 bp):
ATTAAAGTATAAATTATAAATT
Found at i:52477399 original size:20 final size:22
Alignment explanation
Indices: 52477368--52477421 Score: 53
Period size: 22 Copynumber: 2.5 Consensus size: 22
52477358 ATATGCTACT
52477368 TGACA-AATTTATTCA-GAA-TG
1 TGACATAA-TTATTCACGAATTG
*
52477388 TGACATAATTA-TCACTAATTTG
1 TGACATAATTATTCACGAA-TTG
52477410 TGACATAATTAT
1 TGACATAATTAT
52477422 CACTAAAAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
19 3 0.11
20 10 0.36
21 2 0.07
22 13 0.46
ACGTcount: A:0.39, C:0.11, G:0.11, T:0.39
Consensus pattern (22 bp):
TGACATAATTATTCACGAATTG
Found at i:52477412 original size:22 final size:22
Alignment explanation
Indices: 52477386--52477427 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
52477376 TTATTCAGAA
52477386 TGTGACATAATTATCACTAATT
1 TGTGACATAATTATCACTAATT
52477408 TGTGACATAATTATCACTAA
1 TGTGACATAATTATCACTAA
52477428 AAATATAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.38, C:0.14, G:0.10, T:0.38
Consensus pattern (22 bp):
TGTGACATAATTATCACTAATT
Found at i:52477695 original size:2 final size:2
Alignment explanation
Indices: 52477690--52477714 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
52477680 TTTTAAAGCA
52477690 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
52477715 AAGACAAAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:52479102 original size:20 final size:19
Alignment explanation
Indices: 52479057--52479096 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
52479047 TATAAAATCT
52479057 TTCATTAAAAATTGTAATA
1 TTCATTAAAAATTGTAATA
*
52479076 TTCATTAAAAATTTTAATA
1 TTCATTAAAAATTGTAATA
52479095 TT
1 TT
52479097 TGATTAGAGG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.45, C:0.05, G:0.03, T:0.47
Consensus pattern (19 bp):
TTCATTAAAAATTGTAATA
Found at i:52484559 original size:20 final size:20
Alignment explanation
Indices: 52484531--52484573 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
52484521 TATTTATGTT
*
52484531 AATTTATTTTTAT-TGTTAA
1 AATTTATTTTTATATATTAA
52484550 AATTTAATTTTTATATATTAA
1 AATTT-ATTTTTATATATTAA
52484571 AAT
1 AAT
52484574 AAAATGCATG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 5 0.24
20 8 0.38
21 8 0.38
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (20 bp):
AATTTATTTTTATATATTAA
Found at i:52485043 original size:25 final size:26
Alignment explanation
Indices: 52484985--52485045 Score: 69
Period size: 23 Copynumber: 2.5 Consensus size: 26
52484975 AATGAAAATG
*
52484985 ATTAATAAATAAT-TTTTTATCTATAA
1 ATTAATAAA-AATATTTTTATATATAA
52485011 A--AAT-AAAATATTTTTATATA-AA
1 ATTAATAAAAATATTTTTATATATAA
52485033 ATTAATAAAAATA
1 ATTAATAAAAATA
52485046 CATATTTAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 9
0.75 0.03 0.22
Matches are distributed among these distances:
22 6 0.20
23 11 0.37
24 6 0.20
25 6 0.20
26 1 0.03
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.43
Consensus pattern (26 bp):
ATTAATAAAAATATTTTTATATATAA
Found at i:52488306 original size:16 final size:16
Alignment explanation
Indices: 52488273--52488306 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
52488263 TCGATGTGTT
* *
52488273 AACATTAATGGGAGAC
1 AACATTAATGGCAAAC
52488289 AACATTAATGGCAAAC
1 AACATTAATGGCAAAC
52488305 AA
1 AA
52488307 TACAAAGTGG
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:0.50, C:0.15, G:0.18, T:0.18
Consensus pattern (16 bp):
AACATTAATGGCAAAC
Found at i:52491133 original size:21 final size:21
Alignment explanation
Indices: 52491107--52491147 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
52491097 AGACGAGCAA
* *
52491107 TACTCCACAGCAGGTGGAGTG
1 TACTCCAAAACAGGTGGAGTG
52491128 TACTCCAAAACAGGTGGAGT
1 TACTCCAAAACAGGTGGAGT
52491148 TTGAGCAGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.22, G:0.29, T:0.20
Consensus pattern (21 bp):
TACTCCAAAACAGGTGGAGTG
Found at i:52493086 original size:16 final size:16
Alignment explanation
Indices: 52493053--52493086 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
52493043 GGAGATTGTT
* *
52493053 AACATTAATGGGAGAC
1 AACATTAATGGCAAAC
52493069 AACATTAATGGCAAAC
1 AACATTAATGGCAAAC
52493085 AA
1 AA
52493087 TACAAAGTGG
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:0.50, C:0.15, G:0.18, T:0.18
Consensus pattern (16 bp):
AACATTAATGGCAAAC
Found at i:52494944 original size:17 final size:17
Alignment explanation
Indices: 52494924--52494958 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
52494914 ACTAAACCGA
52494924 CCACTAACTCCATCACC
1 CCACTAACTCCATCACC
52494941 CCACTAACTCCATCACC
1 CCACTAACTCCATCACC
52494958 C
1 C
52494959 TACTTGCCAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.29, C:0.54, G:0.00, T:0.17
Consensus pattern (17 bp):
CCACTAACTCCATCACC
Found at i:52494969 original size:41 final size:41
Alignment explanation
Indices: 52494924--52495007 Score: 123
Period size: 41 Copynumber: 2.0 Consensus size: 41
52494914 ACTAAACCGA
* *
52494924 CCACTAACTCCATCACCCCACTAACTCCATCACCCTACTTG
1 CCACTAACTCCATCACCCCACTAACCCCATCACCCCACTTG
* * *
52494965 CCACTAATTCTATCACCCCACTAACCCCATTACCCCACTTG
1 CCACTAACTCCATCACCCCACTAACCCCATCACCCCACTTG
52495006 CC
1 CC
52495008 TAGGAAAAGA
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
41 38 1.00
ACGTcount: A:0.26, C:0.49, G:0.02, T:0.23
Consensus pattern (41 bp):
CCACTAACTCCATCACCCCACTAACCCCATCACCCCACTTG
Found at i:52496079 original size:18 final size:18
Alignment explanation
Indices: 52496056--52496090 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
52496046 TGTAATATCG
52496056 TTGATAAATGGTGTAATA
1 TTGATAAATGGTGTAATA
52496074 TTGATAAATGGTGTAAT
1 TTGATAAATGGTGTAAT
52496091 GTATTAACTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.37, C:0.00, G:0.23, T:0.40
Consensus pattern (18 bp):
TTGATAAATGGTGTAATA
Found at i:52498357 original size:31 final size:30
Alignment explanation
Indices: 52498304--52498361 Score: 80
Period size: 31 Copynumber: 1.9 Consensus size: 30
52498294 TATAAAATGG
* *
52498304 TTAAATTTTAATTTGATATTTATATTTCAC
1 TTAAATTTAAATTTAATATTTATATTTCAC
*
52498334 TTAAATTATAAATTTAATCTTTATATTT
1 TTAAATT-TAAATTTAATATTTATATTT
52498362 TATGTAACAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
30 7 0.29
31 17 0.71
ACGTcount: A:0.36, C:0.05, G:0.02, T:0.57
Consensus pattern (30 bp):
TTAAATTTAAATTTAATATTTATATTTCAC
Found at i:52498448 original size:11 final size:11
Alignment explanation
Indices: 52498432--52498463 Score: 64
Period size: 11 Copynumber: 2.9 Consensus size: 11
52498422 ATCGAATTCG
52498432 TAAATATTTAA
1 TAAATATTTAA
52498443 TAAATATTTAA
1 TAAATATTTAA
52498454 TAAATATTTA
1 TAAATATTTA
52498464 TGAAGTTAGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (11 bp):
TAAATATTTAA
Found at i:52499817 original size:41 final size:40
Alignment explanation
Indices: 52499760--52499858 Score: 137
Period size: 41 Copynumber: 2.5 Consensus size: 40
52499750 TTCGGTTTAA
* *
52499760 CTGATGAGATATTGGGTGTCAATTTACTACTTCGAATTTAT
1 CTGATGAGACACTGGGTGTCAATTTACTACTTCGAA-TTAT
*
52499801 -TCGATGAGACACTGGGTGTCAATTTACTCCTTCGAATTAT
1 CT-GATGAGACACTGGGTGTCAATTTACTACTTCGAATTAT
*
52499841 CTGATGAGGCACTGGGTG
1 CTGATGAGACACTGGGTG
52499859 CCAAACTGGT
Statistics
Matches: 52, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
40 20 0.38
41 32 0.62
ACGTcount: A:0.24, C:0.16, G:0.24, T:0.35
Consensus pattern (40 bp):
CTGATGAGACACTGGGTGTCAATTTACTACTTCGAATTAT
Found at i:52508462 original size:25 final size:25
Alignment explanation
Indices: 52508434--52508484 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
52508424 TATAAAATTT
** *
52508434 TAAATTAAATTAATAATGATAAAAA
1 TAAATTAAACCAAAAATGATAAAAA
*
52508459 TAAATTAACCCAAAAATGATAAAAA
1 TAAATTAAACCAAAAATGATAAAAA
52508484 T
1 T
52508485 CTAAAAATGA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.63, C:0.06, G:0.04, T:0.27
Consensus pattern (25 bp):
TAAATTAAACCAAAAATGATAAAAA
Found at i:52509660 original size:316 final size:316
Alignment explanation
Indices: 52509087--52509718 Score: 1264
Period size: 316 Copynumber: 2.0 Consensus size: 316
52509077 GCGGTTTCCT
52509087 CTTCATCAAATGATGCTGGTATCAATGGAGTCCATATGGGCCCGGGTGCTACGGTATTCACACGT
1 CTTCATCAAATGATGCTGGTATCAATGGAGTCCATATGGGCCCGGGTGCTACGGTATTCACACGT
52509152 ACGCCTCGGTTCACCAGCTGTTGTGAAAGGCCTCTAGTGAAAGCCACAATTGCACCCTTGGTTGC
66 ACGCCTCGGTTCACCAGCTGTTGTGAAAGGCCTCTAGTGAAAGCCACAATTGCACCCTTGGTTGC
52509217 TGTGTAATCAAGTAGCTTGTCATTCCCTTTATATGCATTTACGGATGTAGTATTGATTATGGAGC
131 TGTGTAATCAAGTAGCTTGTCATTCCCTTTATATGCATTTACGGATGTAGTATTGATTATGGAGC
52509282 TGCCTTCTTTCATGTACTTCAGAGCATGCCTATGAATTATCAAATTATGAAATTGTTACCATCGC
196 TGCCTTCTTTCATGTACTTCAGAGCATGCCTATGAATTATCAAATTATGAAATTGTTACCATCGC
52509347 TTTTGACCGAATTTTTTCACTTGTTTTTTTGGAAAGTTCTAAAGAATTACCTGGAC
261 TTTTGACCGAATTTTTTCACTTGTTTTTTTGGAAAGTTCTAAAGAATTACCTGGAC
52509403 CTTCATCAAATGATGCTGGTATCAATGGAGTCCATATGGGCCCGGGTGCTACGGTATTCACACGT
1 CTTCATCAAATGATGCTGGTATCAATGGAGTCCATATGGGCCCGGGTGCTACGGTATTCACACGT
52509468 ACGCCTCGGTTCACCAGCTGTTGTGAAAGGCCTCTAGTGAAAGCCACAATTGCACCCTTGGTTGC
66 ACGCCTCGGTTCACCAGCTGTTGTGAAAGGCCTCTAGTGAAAGCCACAATTGCACCCTTGGTTGC
52509533 TGTGTAATCAAGTAGCTTGTCATTCCCTTTATATGCATTTACGGATGTAGTATTGATTATGGAGC
131 TGTGTAATCAAGTAGCTTGTCATTCCCTTTATATGCATTTACGGATGTAGTATTGATTATGGAGC
52509598 TGCCTTCTTTCATGTACTTCAGAGCATGCCTATGAATTATCAAATTATGAAATTGTTACCATCGC
196 TGCCTTCTTTCATGTACTTCAGAGCATGCCTATGAATTATCAAATTATGAAATTGTTACCATCGC
52509663 TTTTGACCGAATTTTTTCACTTGTTTTTTTGGAAAGTTCTAAAGAATTACCTGGAC
261 TTTTGACCGAATTTTTTCACTTGTTTTTTTGGAAAGTTCTAAAGAATTACCTGGAC
52509719 AGGAAGAATT
Statistics
Matches: 316, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
316 316 1.00
ACGTcount: A:0.24, C:0.21, G:0.21, T:0.34
Consensus pattern (316 bp):
CTTCATCAAATGATGCTGGTATCAATGGAGTCCATATGGGCCCGGGTGCTACGGTATTCACACGT
ACGCCTCGGTTCACCAGCTGTTGTGAAAGGCCTCTAGTGAAAGCCACAATTGCACCCTTGGTTGC
TGTGTAATCAAGTAGCTTGTCATTCCCTTTATATGCATTTACGGATGTAGTATTGATTATGGAGC
TGCCTTCTTTCATGTACTTCAGAGCATGCCTATGAATTATCAAATTATGAAATTGTTACCATCGC
TTTTGACCGAATTTTTTCACTTGTTTTTTTGGAAAGTTCTAAAGAATTACCTGGAC
Found at i:52511955 original size:41 final size:41
Alignment explanation
Indices: 52511891--52511973 Score: 105
Period size: 41 Copynumber: 2.0 Consensus size: 41
52511881 CATATTGGTT
* *
52511891 AATTTACAAACAATTTATGAATAAACAACAAATATATTAAA
1 AATTTACAAACAATTTATAAATAAACAACAAACATATTAAA
* **
52511932 AATTTACAAATAATTCT-TAAATAAATGACAAACATATTAAA
1 AATTTACAAACAATT-TATAAATAAACAACAAACATATTAAA
52511973 A
1 A
52511974 TATAACCATA
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
41 35 0.97
42 1 0.03
ACGTcount: A:0.58, C:0.10, G:0.02, T:0.30
Consensus pattern (41 bp):
AATTTACAAACAATTTATAAATAAACAACAAACATATTAAA
Found at i:52513839 original size:102 final size:102
Alignment explanation
Indices: 52513658--52513863 Score: 385
Period size: 102 Copynumber: 2.0 Consensus size: 102
52513648 TTCCAAATTC
52513658 AGAAAAGGGGAACCCGAAATCATTCTGACCTTATCTCACAAAATTCATTATATCTCATGATTTAC
1 AGAAAAGGGGAACCCGAAATCATTCTGACCTTATCTCACAAAATTCATTATATCTCATGATTTAC
52513723 AAATCCTTTGCTTACACTGTTTCTTCTATGAGAAACT
66 AAATCCTTTGCTTACACTGTTTCTTCTATGAGAAACT
* * *
52513760 AGAACAGGGGAACTCGAATTCATTCTGACCTTATCTCACAAAATTCATTATATCTCATGATTTAC
1 AGAAAAGGGGAACCCGAAATCATTCTGACCTTATCTCACAAAATTCATTATATCTCATGATTTAC
52513825 AAATCCTTTGCTTACACTGTTTCTTCTATGAGAAACT
66 AAATCCTTTGCTTACACTGTTTCTTCTATGAGAAACT
52513862 AG
1 AG
52513864 GCTCAATAAG
Statistics
Matches: 101, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
102 101 1.00
ACGTcount: A:0.33, C:0.21, G:0.12, T:0.34
Consensus pattern (102 bp):
AGAAAAGGGGAACCCGAAATCATTCTGACCTTATCTCACAAAATTCATTATATCTCATGATTTAC
AAATCCTTTGCTTACACTGTTTCTTCTATGAGAAACT
Found at i:52514216 original size:21 final size:21
Alignment explanation
Indices: 52514190--52514232 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
52514180 TATTGAAATT
*
52514190 ACCTAATAGAATCATATCATA
1 ACCTAATAAAATCATATCATA
*
52514211 ACCTAATAAAATCATCTCATA
1 ACCTAATAAAATCATATCATA
52514232 A
1 A
52514233 ACAAATTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.49, C:0.21, G:0.02, T:0.28
Consensus pattern (21 bp):
ACCTAATAAAATCATATCATA
Found at i:52516840 original size:11 final size:11
Alignment explanation
Indices: 52516802--52516839 Score: 67
Period size: 11 Copynumber: 3.5 Consensus size: 11
52516792 TTCTAACATA
52516802 ATTTAGTAAAT
1 ATTTAGTAAAT
52516813 ATTTAGTAAAT
1 ATTTAGTAAAT
*
52516824 ATTTATTAAAT
1 ATTTAGTAAAT
52516835 ATTTA
1 ATTTA
52516840 TGAGTCTGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
11 26 1.00
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (11 bp):
ATTTAGTAAAT
Found at i:52517460 original size:5 final size:5
Alignment explanation
Indices: 52517446--52517482 Score: 65
Period size: 5 Copynumber: 7.2 Consensus size: 5
52517436 ATTATTAGAT
52517446 TATTA TTATTA TATTA TATTA TATTA TATTA TATTA T
1 TATTA -TATTA TATTA TATTA TATTA TATTA TATTA T
52517483 TAAATAAATA
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 26 0.84
6 5 0.16
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (5 bp):
TATTA
Found at i:52518435 original size:18 final size:19
Alignment explanation
Indices: 52518400--52518438 Score: 62
Period size: 20 Copynumber: 2.1 Consensus size: 19
52518390 TGAGTATTGA
52518400 TATTGAATTGAATGAAAATG
1 TATTGAATTG-ATGAAAATG
52518420 TATTGAATTG-TGAAAATG
1 TATTGAATTGATGAAAATG
52518438 T
1 T
52518439 GTGAATATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 9 0.47
20 10 0.53
ACGTcount: A:0.41, C:0.00, G:0.21, T:0.38
Consensus pattern (19 bp):
TATTGAATTGATGAAAATG
Found at i:52521622 original size:21 final size:22
Alignment explanation
Indices: 52521593--52521639 Score: 78
Period size: 21 Copynumber: 2.2 Consensus size: 22
52521583 CAGAAGGAGT
*
52521593 GAGTAGTACTTCGCAGCAGGTG
1 GAGTAGTACTCCGCAGCAGGTG
52521615 GAGT-GTACTCCGCAGCAGGTG
1 GAGTAGTACTCCGCAGCAGGTG
52521636 GAGT
1 GAGT
52521640 TTGAGCAGAG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.21, C:0.19, G:0.38, T:0.21
Consensus pattern (22 bp):
GAGTAGTACTCCGCAGCAGGTG
Found at i:52525599 original size:15 final size:15
Alignment explanation
Indices: 52525579--52525635 Score: 89
Period size: 15 Copynumber: 3.9 Consensus size: 15
52525569 CGATGAATTT
52525579 ATTGAATTTATATTG
1 ATTGAATTTATATTG
* *
52525594 ATTGAAATTATTTTG
1 ATTGAATTTATATTG
52525609 ATTGAATTTATATTG
1 ATTGAATTTATATTG
52525624 ATTGAA-TTATAT
1 ATTGAATTTATAT
52525636 AATATATATG
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
14 6 0.16
15 32 0.84
ACGTcount: A:0.35, C:0.00, G:0.12, T:0.53
Consensus pattern (15 bp):
ATTGAATTTATATTG
Found at i:52526037 original size:23 final size:21
Alignment explanation
Indices: 52526006--52526113 Score: 126
Period size: 21 Copynumber: 5.0 Consensus size: 21
52525996 GGCTTTACCA
*
52526006 ATTAGGCACTTTATGTGTCGT
1 ATTAGGCACCTTATGTGTCGT
52526027 ATTTTAGGCACCTTATGTGTCGT
1 A--TTAGGCACCTTATGTGTCGT
* *
52526050 ATCAGGCACCTTGTGTGTCGT
1 ATTAGGCACCTTATGTGTCGT
* **
52526071 ATCAGGCACCTCGTGTGTCGT
1 ATTAGGCACCTTATGTGTCGT
* *
52526092 TTTAGGCACTTTATGTGTCGT
1 ATTAGGCACCTTATGTGTCGT
52526113 A
1 A
52526114 CTCTGATCAG
Statistics
Matches: 75, Mismatches: 10, Indels: 4
0.84 0.11 0.04
Matches are distributed among these distances:
21 55 0.73
23 20 0.27
ACGTcount: A:0.17, C:0.19, G:0.25, T:0.39
Consensus pattern (21 bp):
ATTAGGCACCTTATGTGTCGT
Found at i:52528516 original size:3 final size:3
Alignment explanation
Indices: 52528508--52528538 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
52528498 TTTTAGTCCT
*
52528508 TTC TTC TTC TTC TTC TTC TTC TTC CTC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T
52528539 CTGTATAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (3 bp):
TTC
Found at i:52535799 original size:20 final size:20
Alignment explanation
Indices: 52535774--52535812 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
52535764 CCACATATAA
52535774 ATATCTTAAAAATAAAATAT
1 ATATCTTAAAAATAAAATAT
*
52535794 ATATCTTAAAATTAAAATA
1 ATATCTTAAAAATAAAATA
52535813 CAACTATTAG
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:0.59, C:0.05, G:0.00, T:0.36
Consensus pattern (20 bp):
ATATCTTAAAAATAAAATAT
Found at i:52547733 original size:21 final size:21
Alignment explanation
Indices: 52547707--52547749 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
52547697 GGTGAAGAAA
52547707 GCATATCACCAGGATTAGTTG
1 GCATATCACCAGGATTAGTTG
*
52547728 GCATATCACCTGGATTAGTTG
1 GCATATCACCAGGATTAGTTG
52547749 G
1 G
52547750 ACCCATGTGA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.26, C:0.19, G:0.26, T:0.30
Consensus pattern (21 bp):
GCATATCACCAGGATTAGTTG
Found at i:52551301 original size:11 final size:11
Alignment explanation
Indices: 52551267--52551307 Score: 57
Period size: 11 Copynumber: 3.6 Consensus size: 11
52551257 TTATAATTAC
52551267 TTATTTTAAAA
1 TTATTTTAAAA
52551278 TT-TTATATAAAA
1 TTATT-T-TAAAA
52551290 TTATTTTAAAA
1 TTATTTTAAAA
52551301 TTATTTT
1 TTATTTT
52551308 TTTACATTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
10 2 0.07
11 15 0.56
12 8 0.30
13 2 0.07
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (11 bp):
TTATTTTAAAA
Found at i:52560561 original size:29 final size:29
Alignment explanation
Indices: 52560526--52560581 Score: 112
Period size: 29 Copynumber: 1.9 Consensus size: 29
52560516 TCAAAACCTA
52560526 CTTTTAGCATATTTGTGATACCCAAAACG
1 CTTTTAGCATATTTGTGATACCCAAAACG
52560555 CTTTTAGCATATTTGTGATACCCAAAA
1 CTTTTAGCATATTTGTGATACCCAAAA
52560582 AGAATGAAGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.32, C:0.20, G:0.12, T:0.36
Consensus pattern (29 bp):
CTTTTAGCATATTTGTGATACCCAAAACG
Found at i:52570615 original size:33 final size:32
Alignment explanation
Indices: 52570578--52570657 Score: 88
Period size: 33 Copynumber: 2.4 Consensus size: 32
52570568 CCCCATTTGG
52570578 CCCATTTGACCCATATTGTAACCCATCTGACCA
1 CCCATTTGACCCATATT-TAACCCATCTGACCA
* ** * *
52570611 CCCATCTGACCACCCATTTGACCCATCTGACGA
1 CCCATTTGACC-CATATTTAACCCATCTGACCA
*
52570644 CCCATTTGGCCCAT
1 CCCATTTGACCCAT
52570658 CTGCCCCATA
Statistics
Matches: 37, Mismatches: 9, Indels: 3
0.76 0.18 0.06
Matches are distributed among these distances:
32 1 0.03
33 32 0.86
34 4 0.11
ACGTcount: A:0.24, C:0.40, G:0.11, T:0.25
Consensus pattern (32 bp):
CCCATTTGACCCATATTTAACCCATCTGACCA
Found at i:52570636 original size:21 final size:21
Alignment explanation
Indices: 52570610--52570660 Score: 84
Period size: 21 Copynumber: 2.4 Consensus size: 21
52570600 CCATCTGACC
52570610 ACCCATCTGACCACCCATTTG
1 ACCCATCTGACCACCCATTTG
*
52570631 ACCCATCTGACGACCCATTTG
1 ACCCATCTGACCACCCATTTG
*
52570652 GCCCATCTG
1 ACCCATCTG
52570661 CCCCATATTC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.22, C:0.41, G:0.14, T:0.24
Consensus pattern (21 bp):
ACCCATCTGACCACCCATTTG
Found at i:52570648 original size:12 final size:12
Alignment explanation
Indices: 52570598--52570633 Score: 63
Period size: 12 Copynumber: 3.0 Consensus size: 12
52570588 CCATATTGTA
52570598 ACCCATCTGACC
1 ACCCATCTGACC
52570610 ACCCATCTGACC
1 ACCCATCTGACC
*
52570622 ACCCATTTGACC
1 ACCCATCTGACC
52570634 CATCTGACGA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.25, C:0.47, G:0.08, T:0.19
Consensus pattern (12 bp):
ACCCATCTGACC
Found at i:52571301 original size:12 final size:12
Alignment explanation
Indices: 52571286--52571339 Score: 72
Period size: 12 Copynumber: 4.5 Consensus size: 12
52571276 TTCATCATCA
*
52571286 TCATCATCGAAC
1 TCATCATCAAAC
*
52571298 TCATCATCAAAT
1 TCATCATCAAAC
*
52571310 TCATCATCGAAC
1 TCATCATCAAAC
*
52571322 TCATCACCAAAC
1 TCATCATCAAAC
52571334 TCATCA
1 TCATCA
52571340 AAATCACAAT
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 36 1.00
ACGTcount: A:0.37, C:0.33, G:0.04, T:0.26
Consensus pattern (12 bp):
TCATCATCAAAC
Found at i:52571313 original size:24 final size:24
Alignment explanation
Indices: 52571286--52571339 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
52571276 TTCATCATCA
* *
52571286 TCATCATCGAACTCATCATCAAAT
1 TCATCATCGAACTCATCACCAAAC
52571310 TCATCATCGAACTCATCACCAAAC
1 TCATCATCGAACTCATCACCAAAC
52571334 TCATCA
1 TCATCA
52571340 AAATCACAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.37, C:0.33, G:0.04, T:0.26
Consensus pattern (24 bp):
TCATCATCGAACTCATCACCAAAC
Found at i:52572123 original size:12 final size:12
Alignment explanation
Indices: 52572106--52572136 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
52572096 AGAAAGAAAA
52572106 AGACAGACAAAG
1 AGACAGACAAAG
*
52572118 AGACAGACAGAG
1 AGACAGACAAAG
52572130 AGACAGA
1 AGACAGA
52572137 AGATGAAAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.55, C:0.16, G:0.29, T:0.00
Consensus pattern (12 bp):
AGACAGACAAAG
Found at i:52573520 original size:46 final size:46
Alignment explanation
Indices: 52573468--52573565 Score: 160
Period size: 46 Copynumber: 2.1 Consensus size: 46
52573458 AAATGATGAT
*
52573468 ACTTTGTCAAGAATGCAACAACATTGGAGAATTCTTTTGTGGCTTA
1 ACTTTGTCAAGAATACAACAACATTGGAGAATTCTTTTGTGGCTTA
* * *
52573514 ACTTTGTCAGGAATACAATAACATTGGAGTATTCTTTTGTGGCTTA
1 ACTTTGTCAAGAATACAACAACATTGGAGAATTCTTTTGTGGCTTA
52573560 ACTTTG
1 ACTTTG
52573566 CGGCAACATA
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
46 48 1.00
ACGTcount: A:0.29, C:0.14, G:0.19, T:0.38
Consensus pattern (46 bp):
ACTTTGTCAAGAATACAACAACATTGGAGAATTCTTTTGTGGCTTA
Found at i:52574529 original size:16 final size:17
Alignment explanation
Indices: 52574505--52574553 Score: 57
Period size: 16 Copynumber: 2.9 Consensus size: 17
52574495 TTTTAATTTA
52574505 TTAAATAAAA-ATTATC
1 TTAAATAAAATATTATC
*
52574521 TTAATTAAAATATTAT-
1 TTAAATAAAATATTATC
*
52574537 TTCAATAAAATAATTAT
1 TTAAATAAAAT-ATTAT
52574554 ATTTCACATT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
16 18 0.64
17 10 0.36
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.43
Consensus pattern (17 bp):
TTAAATAAAATATTATC
Found at i:52574572 original size:21 final size:18
Alignment explanation
Indices: 52574527--52574576 Score: 55
Period size: 19 Copynumber: 2.6 Consensus size: 18
52574517 TATCTTAATT
52574527 AAAATATTATTTCAATAAA
1 AAAAT-TTATTTCAATAAA
*
52574546 ATAATTATATTTCACATTAAA
1 AAAATT-TATTTCA-A-TAAA
52574567 AAAATTTATT
1 AAAATTTATT
52574577 AATCGTATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
18 1 0.04
19 11 0.42
20 5 0.19
21 9 0.35
ACGTcount: A:0.52, C:0.06, G:0.00, T:0.42
Consensus pattern (18 bp):
AAAATTTATTTCAATAAA
Found at i:52585036 original size:23 final size:24
Alignment explanation
Indices: 52585005--52585052 Score: 64
Period size: 22 Copynumber: 2.0 Consensus size: 24
52584995 TAGAGGTTTG
*
52585005 AATTCTATTTTTCCAAAATAA-TAT
1 AATTCTA-TTTTACAAAATAACTAT
52585029 AATT-TATTTTACAAAATAACTAT
1 AATTCTATTTTACAAAATAACTAT
52585052 A
1 A
52585053 TTTTCATAGT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 12 0.55
23 6 0.27
24 4 0.18
ACGTcount: A:0.46, C:0.10, G:0.00, T:0.44
Consensus pattern (24 bp):
AATTCTATTTTACAAAATAACTAT
Found at i:52588493 original size:9 final size:9
Alignment explanation
Indices: 52588479--52588508 Score: 60
Period size: 9 Copynumber: 3.3 Consensus size: 9
52588469 CAATGTTCAT
52588479 TTAACTGAA
1 TTAACTGAA
52588488 TTAACTGAA
1 TTAACTGAA
52588497 TTAACTGAA
1 TTAACTGAA
52588506 TTA
1 TTA
52588509 GTAATAGTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.43, C:0.10, G:0.10, T:0.37
Consensus pattern (9 bp):
TTAACTGAA
Found at i:52596977 original size:12 final size:12
Alignment explanation
Indices: 52596960--52596985 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
52596950 TAATTTTTTT
52596960 AAAAAATTATAA
1 AAAAAATTATAA
52596972 AAAAAATTATAA
1 AAAAAATTATAA
52596984 AA
1 AA
52596986 TTTAATTAAA
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:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (12 bp):
AAAAAATTATAA
Found at i:52598123 original size:99 final size:99
Alignment explanation
Indices: 52597938--52598133 Score: 320
Period size: 99 Copynumber: 2.0 Consensus size: 99
52597928 CCCCCCTTTC
* * * *
52597938 TTCTCTTATTTCTAAATTATTGTCGTTATTTTGAGCCTCGAGGTCTAACTCGATGACTGTATTAT
1 TTCTCTTATTTCTAAATCATTGTCGTTATTTTGAGCCTCGAAGTCTAACTCAATAACTGTATTAT
* *
52598003 CTAACTCAATGGGTTGGCTCACAGGATCACCAAG
66 CTAACTCAATGAGTTGACTCACAGGATCACCAAG
* *
52598037 TTCTGTTATTTCTAAATCATTGTCGTTATTTTGAGCCTCGAAGTTTAACTCAATAACTGTATTAT
1 TTCTCTTATTTCTAAATCATTGTCGTTATTTTGAGCCTCGAAGTCTAACTCAATAACTGTATTAT
52598102 CTAACTCAATGAGTTGACTCACAGGATCACCA
66 CTAACTCAATGAGTTGACTCACAGGATCACCA
52598134 GGTTGAGTAG
Statistics
Matches: 89, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
99 89 1.00
ACGTcount: A:0.27, C:0.20, G:0.16, T:0.38
Consensus pattern (99 bp):
TTCTCTTATTTCTAAATCATTGTCGTTATTTTGAGCCTCGAAGTCTAACTCAATAACTGTATTAT
CTAACTCAATGAGTTGACTCACAGGATCACCAAG
Found at i:52602614 original size:14 final size:16
Alignment explanation
Indices: 52602595--52602627 Score: 52
Period size: 14 Copynumber: 2.2 Consensus size: 16
52602585 AATTTTTTTA
52602595 TTTTTA-ATTAA-TTT
1 TTTTTATATTAACTTT
52602609 TTTTTATATTAACTTT
1 TTTTTATATTAACTTT
52602625 TTT
1 TTT
52602628 GCTTAAATGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 6 0.35
15 5 0.29
16 6 0.35
ACGTcount: A:0.24, C:0.03, G:0.00, T:0.73
Consensus pattern (16 bp):
TTTTTATATTAACTTT
Found at i:52611310 original size:29 final size:29
Alignment explanation
Indices: 52611268--52611326 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
52611258 TTAACGAAAG
52611268 TTAATAGTTAAATGATAAAAATATAACAA
1 TTAATAGTTAAATGATAAAAATATAACAA
52611297 TTAATAGTTAAATGATAAAAATATAACAA
1 TTAATAGTTAAATGATAAAAATATAACAA
52611326 T
1 T
52611327 CTGATAATTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.58, C:0.03, G:0.07, T:0.32
Consensus pattern (29 bp):
TTAATAGTTAAATGATAAAAATATAACAA
Found at i:52612400 original size:48 final size:48
Alignment explanation
Indices: 52612329--52612427 Score: 189
Period size: 48 Copynumber: 2.1 Consensus size: 48
52612319 GAGAAAACAA
52612329 CATTTTATAAGCCACCATCACATGTAAACAAAGAGAAAAGGAATCTAC
1 CATTTTATAAGCCACCATCACATGTAAACAAAGAGAAAAGGAATCTAC
*
52612377 CATTTTATAAGCCATCATCACATGTAAACAAAGAGAAAAGGAATCTAC
1 CATTTTATAAGCCACCATCACATGTAAACAAAGAGAAAAGGAATCTAC
52612425 CAT
1 CAT
52612428 ATGAAAAGAC
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
48 50 1.00
ACGTcount: A:0.45, C:0.20, G:0.12, T:0.22
Consensus pattern (48 bp):
CATTTTATAAGCCACCATCACATGTAAACAAAGAGAAAAGGAATCTAC
Found at i:52617193 original size:6 final size:6
Alignment explanation
Indices: 52617182--52617209 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
52617172 TAAAGTGAGA
52617182 TGGTGT TGGTGT TGGTGT TGGTGT TGGT
1 TGGTGT TGGTGT TGGTGT TGGTGT TGGT
52617210 CACTACTAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (6 bp):
TGGTGT
Found at i:52620520 original size:75 final size:75
Alignment explanation
Indices: 52620397--52620541 Score: 290
Period size: 75 Copynumber: 1.9 Consensus size: 75
52620387 ATTTTTCCCC
52620397 CCTTTCCATCGTTATGTTCGTAATCGCGATAAACACCAAATCTCAAAGTAATAATGTATTTTCTT
1 CCTTTCCATCGTTATGTTCGTAATCGCGATAAACACCAAATCTCAAAGTAATAATGTATTTTCTT
52620462 TGATTTTCAA
66 TGATTTTCAA
52620472 CCTTTCCATCGTTATGTTCGTAATCGCGATAAACACCAAATCTCAAAGTAATAATGTATTTTCTT
1 CCTTTCCATCGTTATGTTCGTAATCGCGATAAACACCAAATCTCAAAGTAATAATGTATTTTCTT
52620537 TGATT
66 TGATT
52620542 AGGGTGATCA
Statistics
Matches: 70, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
75 70 1.00
ACGTcount: A:0.30, C:0.20, G:0.11, T:0.39
Consensus pattern (75 bp):
CCTTTCCATCGTTATGTTCGTAATCGCGATAAACACCAAATCTCAAAGTAATAATGTATTTTCTT
TGATTTTCAA
Done.