Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr02 ID=Chr02-JGI_221_v2.0
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: 62769430
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1067035 characters in sequence are not A, C, G, or T
File 143 of 206
Found at i:43798366 original size:5 final size:5
Alignment explanation
Indices: 43798356--43798381 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
43798346 CTCGAAAATT
43798356 TTCGA TTCGA TTCGA TTCGA TTCGA T
1 TTCGA TTCGA TTCGA TTCGA TTCGA T
43798382 CGAATGCTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.19, C:0.19, G:0.19, T:0.42
Consensus pattern (5 bp):
TTCGA
Found at i:43799815 original size:15 final size:15
Alignment explanation
Indices: 43799797--43799825 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
43799787 ATAAATTATC
43799797 TTATAATAAAACATT
1 TTATAATAAAACATT
43799812 TTATAATAAAACAT
1 TTATAATAAAACAT
43799826 CACACAAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.55, C:0.07, G:0.00, T:0.38
Consensus pattern (15 bp):
TTATAATAAAACATT
Found at i:43811121 original size:60 final size:61
Alignment explanation
Indices: 43811051--43811199 Score: 174
Period size: 60 Copynumber: 2.5 Consensus size: 61
43811041 AAAAAGGTGG
* * * *
43811051 GACCAAGGTGAAAGCCTACAAATGGCGCTTTGAGTAAATAAAA-AATAAAAAAAAGAGAGA
1 GACCAAGGTGAAAACCTACAAATGGCGCATTGAGTAAAAAAAAGAAAAAAAAAAAGAGAGA
* * * * *
43811111 GACCAGGGTGAAACCCTACAAAGGGAGCATTGAGTAAAAAAAAGAAAAAAAAAAAGGGAGA
1 GACCAAGGTGAAAACCTACAAATGGCGCATTGAGTAAAAAAAAGAAAAAAAAAAAGAGAGA
* * **
43811172 GGCTAAGGTGAAAACCCGCAAATGGCGC
1 GACCAAGGTGAAAACCTACAAATGGCGC
43811200 CTTAGACCAA
Statistics
Matches: 72, Mismatches: 16, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
60 37 0.51
61 35 0.49
ACGTcount: A:0.49, C:0.14, G:0.26, T:0.11
Consensus pattern (61 bp):
GACCAAGGTGAAAACCTACAAATGGCGCATTGAGTAAAAAAAAGAAAAAAAAAAAGAGAGA
Found at i:43812563 original size:50 final size:50
Alignment explanation
Indices: 43812404--43812571 Score: 183
Period size: 50 Copynumber: 3.4 Consensus size: 50
43812394 CTTAGCAGTA
*
43812404 CAGTGGAACAGATTGAAGCTACGACGGCGGATCTGGTTTCCCTGATATTG
1 CAGTGGAACAGATTGAAGCTACGACGGCGGATCTGGTTTCCCTGACATTG
* ** * * * *** * **
43812454 CAATTAAAAAGATTGAAGCCACAACGGCGGATCTTACTTCCCTAACGGTG
1 CAGTGGAACAGATTGAAGCTACGACGGCGGATCTGGTTTCCCTGACATTG
* *
43812504 CGGTGGAACAGATTGAAGCTACGACGGCGGATCTGGTTTCCCCGACATTG
1 CAGTGGAACAGATTGAAGCTACGACGGCGGATCTGGTTTCCCTGACATTG
* *
43812554 CAGTTGAACAAATTGAAG
1 CAGTGGAACAGATTGAAG
43812572 ATTACAGATC
Statistics
Matches: 88, Mismatches: 30, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
50 88 1.00
ACGTcount: A:0.29, C:0.21, G:0.27, T:0.23
Consensus pattern (50 bp):
CAGTGGAACAGATTGAAGCTACGACGGCGGATCTGGTTTCCCTGACATTG
Found at i:43812730 original size:132 final size:132
Alignment explanation
Indices: 43812565--43812808 Score: 409
Period size: 132 Copynumber: 1.8 Consensus size: 132
43812555 AGTTGAACAA
* *
43812565 ATTGAAGATTACAGATCTTATCTCCTTAAGCAGTAGTGGAGCAGATCGAAGATGGCGGATTTTAC
1 ATTGAAGATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGCAGATTTTAC
43812630 CTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAATAATTC-TATCTCACTGGGCAACAGTGGAA
66 CTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAATAA-TCATATCTCACTGGGCAACAGTGGAA
43812694 TAG
130 TAG
** * *
43812697 ATTGAAGATTACAGATCTTATCTCCCTGGGCAGTAGTGGAGTATATCGAAGATGGCAGATTTTAC
1 ATTGAAGATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGCAGATTTTAC
*
43812762 CTCCCTGAGGTTACAGTGGAGTACATTGAAGCCACTAATCATATCTC
66 CTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAATAATCATATCTC
43812809 CCTGAAGTTG
Statistics
Matches: 104, Mismatches: 7, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
131 2 0.02
132 102 0.98
ACGTcount: A:0.30, C:0.19, G:0.23, T:0.28
Consensus pattern (132 bp):
ATTGAAGATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGCAGATTTTAC
CTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAATAATCATATCTCACTGGGCAACAGTGGAAT
AG
Found at i:43812735 original size:44 final size:44
Alignment explanation
Indices: 43812671--43812768 Score: 106
Period size: 44 Copynumber: 2.2 Consensus size: 44
43812661 CCAATAATTC
* * *
43812671 TATCTCACTGGGCAACAGTGGAATAGATTGAAGATTACAGATCT
1 TATCTCCCTGGGCAACAGTGGAATAGATCGAAGATGACAGATCT
** * * * *
43812715 TATCTCCCTGGGCAGTAGTGGAGTATATCGAAGATGGCAGATTT
1 TATCTCCCTGGGCAACAGTGGAATAGATCGAAGATGACAGATCT
*
43812759 TACCTCCCTG
1 TATCTCCCTG
43812769 AGGTTACAGT
Statistics
Matches: 44, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
44 44 1.00
ACGTcount: A:0.28, C:0.19, G:0.24, T:0.29
Consensus pattern (44 bp):
TATCTCCCTGGGCAACAGTGGAATAGATCGAAGATGACAGATCT
Found at i:43812843 original size:132 final size:132
Alignment explanation
Indices: 43812575--43812852 Score: 362
Period size: 132 Copynumber: 2.1 Consensus size: 132
43812565 ATTGAAGATT
* *
43812575 ACAGATCTTATCTCCTTAAGCAGTAGTGGAGCAGATCGAAGATGGCGGATTTTACCTCCCTGAGG
1 ACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGCAGATTTTACCTCCCTGAGG
* * *
43812640 TTACAGTGGAGTACATTGAAGCCAATAATTCTATCTCACTGGGCAACAGTGGAATAGATTGAAGA
66 TTACAGTGGAGTACATTGAAGCCAATAATTCTATCTCACTGAGCAACAGTGGAACAGATTGAAAA
**
43812705 TT
131 CC
** * *
43812707 ACAGATCTTATCTCCCTGGGCAGTAGTGGAGTATATCGAAGATGGCAGATTTTACCTCCCTGAGG
1 ACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGCAGATTTTACCTCCCTGAGG
* * *** * *
43812772 TTACAGTGGAGTACATTGAAGCCACTAA-TCATATCTCCCTGAAGTTGCAGTGGAGCGGATT-AA
66 TTACAGTGGAGTACATTGAAGCCAATAATTC-TATCTCACTG-AGCAACAGTGGAACAGATTGAA
43812835 AACC
129 AACC
43812839 ACAGATCTTATCTC
1 ACAGATCTTATCTC
43812853 TCTGAAGTTG
Statistics
Matches: 126, Mismatches: 18, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
131 2 0.02
132 112 0.89
133 12 0.10
ACGTcount: A:0.29, C:0.20, G:0.23, T:0.27
Consensus pattern (132 bp):
ACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGCAGATTTTACCTCCCTGAGG
TTACAGTGGAGTACATTGAAGCCAATAATTCTATCTCACTGAGCAACAGTGGAACAGATTGAAAA
CC
Found at i:43812899 original size:41 final size:44
Alignment explanation
Indices: 43812752--43813004 Score: 185
Period size: 44 Copynumber: 5.8 Consensus size: 44
43812742 TCGAAGATGG
* * * * * * * *
43812752 CAGATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCA
1 CAGATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAACCA
* *
43812796 CTA-ATCATATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACCA
1 C-AGATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAACCA
* * *** *
43812840 CAGATCTTATCTCTCTGAAGTTGCAGTAGAGCAGA-TCGTATC-
1 CAGATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAACCA
** *
43812882 CAG-TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACAGAAGAAAC-
1 CAGATCTTATCTCCCTGAAGTTGCAGTGGAGCAGA-TTAA-AACCA
* * * ** *
43812926 CA-ATCCTATCTCCTTGAAGTTGCAATGGAGTGGATTAAAACCG
1 CAGATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAACCA
* * *
43812969 CAGATCTCATCTCTCTGAAGTTGCAGTAGAGCAGAT
1 CAGATCTTATCTCCCTGAAGTTGCAGTGGAGCAGAT
43813005 CGCATCAGAC
Statistics
Matches: 160, Mismatches: 41, Indels: 16
0.74 0.19 0.07
Matches are distributed among these distances:
41 29 0.18
42 6 0.04
43 8 0.05
44 116 0.73
45 1 0.01
ACGTcount: A:0.29, C:0.22, G:0.22, T:0.26
Consensus pattern (44 bp):
CAGATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAACCA
Found at i:43819365 original size:15 final size:14
Alignment explanation
Indices: 43819332--43819365 Score: 50
Period size: 15 Copynumber: 2.4 Consensus size: 14
43819322 AAAAGAGAAA
43819332 AAAAAGGATTAAAT
1 AAAAAGGATTAAAT
*
43819346 CAAAAGAGATTAAAT
1 AAAAAG-GATTAAAT
43819361 AAAAA
1 AAAAA
43819366 AAAACATGAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
14 5 0.29
15 12 0.71
ACGTcount: A:0.68, C:0.03, G:0.12, T:0.18
Consensus pattern (14 bp):
AAAAAGGATTAAAT
Found at i:43819459 original size:19 final size:20
Alignment explanation
Indices: 43819434--43819487 Score: 60
Period size: 19 Copynumber: 2.8 Consensus size: 20
43819424 AGTTGATGAG
43819434 AAAAAATAAATATAAATTAT
1 AAAAAATAAATATAAATTAT
* *
43819454 -AAAAAT-GATA-AGAATTTT
1 AAAAAATAAATATA-AATTAT
43819472 AAAAAATAAATATAAA
1 AAAAAATAAATATAAA
43819488 AATATTTTTA
Statistics
Matches: 27, Mismatches: 3, Indels: 8
0.71 0.08 0.21
Matches are distributed among these distances:
17 1 0.04
18 8 0.30
19 12 0.44
20 5 0.19
21 1 0.04
ACGTcount: A:0.69, C:0.00, G:0.04, T:0.28
Consensus pattern (20 bp):
AAAAAATAAATATAAATTAT
Found at i:43819524 original size:21 final size:19
Alignment explanation
Indices: 43819486--43819526 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
43819476 AATAAATATA
*
43819486 AAAATATTTTTAAGTTTTT
1 AAAATATTTTTAAATTTTT
43819505 AAAATATATTTTAGAATTTTT
1 AAAATAT-TTTTA-AATTTTT
43819526 A
1 A
43819527 GAATTATAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 7 0.37
20 5 0.26
21 7 0.37
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (19 bp):
AAAATATTTTTAAATTTTT
Found at i:43820216 original size:26 final size:25
Alignment explanation
Indices: 43820173--43820221 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 25
43820163 TTACAAACAA
*
43820173 TTTTTAAATTTTGATATATTTATTT
1 TTTTTAAATTTTGATATACTTATTT
43820198 TTTTTAATATTTT-ATTATACTTAT
1 TTTTTAA-ATTTTGA-TATACTTAT
43820222 ATAAGACACT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
25 8 0.38
26 13 0.62
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.67
Consensus pattern (25 bp):
TTTTTAAATTTTGATATACTTATTT
Found at i:43821083 original size:30 final size:30
Alignment explanation
Indices: 43821049--43821111 Score: 117
Period size: 30 Copynumber: 2.1 Consensus size: 30
43821039 ACTTATTTTA
43821049 TTGTTAATTTTGTTATTATTTTAAAGACAT
1 TTGTTAATTTTGTTATTATTTTAAAGACAT
*
43821079 TTGTTAATTTTGTTATTATTTTAGAGACAT
1 TTGTTAATTTTGTTATTATTTTAAAGACAT
43821109 TTG
1 TTG
43821112 CTTGTTAAGT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.27, C:0.03, G:0.13, T:0.57
Consensus pattern (30 bp):
TTGTTAATTTTGTTATTATTTTAAAGACAT
Found at i:43821246 original size:12 final size:12
Alignment explanation
Indices: 43821225--43821258 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
43821215 TATATATTTT
*
43821225 AAAATTATATAA
1 AAAATAATATAA
43821237 AAAATAATATAA
1 AAAATAATATAA
*
43821249 AAATTAATAT
1 AAAATAATAT
43821259 GGACTGGCCG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (12 bp):
AAAATAATATAA
Found at i:43831060 original size:12 final size:12
Alignment explanation
Indices: 43831043--43831068 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
43831033 CTCCAAACAC
43831043 TATAATTTTTTA
1 TATAATTTTTTA
43831055 TATAATTTTTTA
1 TATAATTTTTTA
43831067 TA
1 TA
43831069 CCATGAAGTT
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:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (12 bp):
TATAATTTTTTA
Found at i:43842007 original size:2 final size:2
Alignment explanation
Indices: 43842000--43842032 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
43841990 CGAATGTTTT
*
43842000 TA TA TA TA CA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
43842033 TAAAAGATCG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:43846557 original size:29 final size:29
Alignment explanation
Indices: 43846516--43846638 Score: 133
Period size: 29 Copynumber: 4.2 Consensus size: 29
43846506 ATGGATATCT
*
43846516 TTAAAAAGAAGCCTTTGTGTCGATCTCTG
1 TTAAAAGGAAGCCTTTGTGTCGATCTCTG
* *
43846545 TTAAATGGAAGCCTTTGTGTCTG-TCTCTT
1 TTAAAAGGAAGCCTTTGTGTC-GATCTCTG
* * * *
43846574 TTAAAAGGATGCATTTGTGGCTATCTCTG
1 TTAAAAGGAAGCCTTTGTGTCGATCTCTG
* *
43846603 TTAAAAGGATGCCTTTGTGGTC-ATCTATG
1 TTAAAAGGAAGCCTTTGT-GTCGATCTCTG
43846632 TTAAAAG
1 TTAAAAG
43846639 AATGCATTGT
Statistics
Matches: 79, Mismatches: 12, Indels: 6
0.81 0.12 0.06
Matches are distributed among these distances:
29 76 0.96
30 3 0.04
ACGTcount: A:0.25, C:0.15, G:0.22, T:0.38
Consensus pattern (29 bp):
TTAAAAGGAAGCCTTTGTGTCGATCTCTG
Found at i:43846636 original size:58 final size:58
Alignment explanation
Indices: 43846519--43846650 Score: 153
Period size: 58 Copynumber: 2.3 Consensus size: 58
43846509 GATATCTTTA
* * * * * *
43846519 AAAAGAA-GCCTTTGTGTCGATCTCTGTTAAATGGAAGCCTTTGTGTCTGTCTCTTTT
1 AAAAGAATGCATTTGTGGCGATCTCTGTTAAAAGGAAGCCTTTGTGTCTATCTATGTT
* * *
43846576 AAAAGGATGCATTTGTGGCTATCTCTGTTAAAAGGATGCCTTTGTGGTC-ATCTATGTT
1 AAAAGAATGCATTTGTGGCGATCTCTGTTAAAAGGAAGCCTTTGT-GTCTATCTATGTT
43846634 AAAAGAATGCA-TTGTGG
1 AAAAGAATGCATTTGTGG
43846651 AAAATTCTAT
Statistics
Matches: 63, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
57 12 0.19
58 48 0.76
59 3 0.05
ACGTcount: A:0.25, C:0.14, G:0.23, T:0.37
Consensus pattern (58 bp):
AAAAGAATGCATTTGTGGCGATCTCTGTTAAAAGGAAGCCTTTGTGTCTATCTATGTT
Found at i:43850802 original size:39 final size:39
Alignment explanation
Indices: 43850725--43850803 Score: 115
Period size: 39 Copynumber: 2.0 Consensus size: 39
43850715 TGTGCTTATC
* *
43850725 TATTGTTTTAATACTTTCGGGATATTAATTCAGGTTTAA
1 TATTGTTTTAATACTTTCGGAATATTAATTCAGATTTAA
*
43850764 TATTGTTTTAATA-TTTCTGGAATATTAATTCATATTTAA
1 TATTGTTTTAATACTTTC-GGAATATTAATTCAGATTTAA
43850803 T
1 T
43850804 GTGCTTAGTC
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
38 4 0.11
39 32 0.89
ACGTcount: A:0.30, C:0.06, G:0.11, T:0.52
Consensus pattern (39 bp):
TATTGTTTTAATACTTTCGGAATATTAATTCAGATTTAA
Found at i:43851425 original size:14 final size:14
Alignment explanation
Indices: 43851406--43851456 Score: 58
Period size: 13 Copynumber: 3.9 Consensus size: 14
43851396 TAGTCATTTC
43851406 TATTTT-ATTTTTA
1 TATTTTAATTTTTA
43851419 TATTTT--TGTTTTA
1 TATTTTAAT-TTTTA
43851432 -A-TTTAATTTTTA
1 TATTTTAATTTTTA
43851444 TATTTTAATTTTT
1 TATTTTAATTTTT
43851457 CTTTTGTTTG
Statistics
Matches: 33, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
11 3 0.09
12 7 0.21
13 13 0.39
14 10 0.30
ACGTcount: A:0.24, C:0.00, G:0.02, T:0.75
Consensus pattern (14 bp):
TATTTTAATTTTTA
Found at i:43851455 original size:25 final size:25
Alignment explanation
Indices: 43851407--43851455 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
43851397 AGTCATTTCT
* **
43851407 ATTTTATTTTTATATTTTTGTTTTA
1 ATTTAATTTTTATATTTTAATTTTA
43851432 ATTTAATTTTTATATTTTAATTTT
1 ATTTAATTTTTATATTTTAATTTT
43851456 TCTTTTGTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.02, T:0.73
Consensus pattern (25 bp):
ATTTAATTTTTATATTTTAATTTTA
Found at i:43855481 original size:26 final size:26
Alignment explanation
Indices: 43855442--43855494 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 26
43855432 CCCTTCCTCC
* *
43855442 TTTTGATTTTTTTATTTTTTATTTTA
1 TTTTGATTTTTTTATTTTGTATGTTA
43855468 TTTT-ATTTTCTTTATTTTGTATGTTA
1 TTTTGATTTT-TTTATTTTGTATGTTA
43855494 T
1 T
43855495 CTATTTTTAG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 5 0.21
26 19 0.79
ACGTcount: A:0.15, C:0.02, G:0.06, T:0.77
Consensus pattern (26 bp):
TTTTGATTTTTTTATTTTGTATGTTA
Found at i:43855502 original size:26 final size:25
Alignment explanation
Indices: 43855447--43855502 Score: 60
Period size: 26 Copynumber: 2.2 Consensus size: 25
43855437 CCTCCTTTTG
* * *
43855447 ATTTTTTTATTTTTTATTTTATTTT
1 ATTTTTTTATTTTGTATGTTATTAT
*
43855472 ATTTTCTTTATTTTGTATGTTA-TCT
1 ATTTT-TTTATTTTGTATGTTATTAT
43855497 ATTTTT
1 ATTTTT
43855503 AGTCCTTTTA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
24 1 0.04
25 12 0.44
26 14 0.52
ACGTcount: A:0.16, C:0.04, G:0.04, T:0.77
Consensus pattern (25 bp):
ATTTTTTTATTTTGTATGTTATTAT
Found at i:43857121 original size:6 final size:6
Alignment explanation
Indices: 43857112--43857154 Score: 50
Period size: 6 Copynumber: 6.5 Consensus size: 6
43857102 TTCTTTTTGG
43857112 TTTTAT TTTTATT TTTTAT TTTTAGT TGTTCTAT TTTTAT TTT
1 TTTTAT TTTTA-T TTTTAT TTTTA-T T-TT-TAT TTTTAT TTT
43857155 CTTAGACTTC
Statistics
Matches: 33, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
6 17 0.52
7 10 0.30
8 4 0.12
9 2 0.06
ACGTcount: A:0.14, C:0.02, G:0.05, T:0.79
Consensus pattern (6 bp):
TTTTAT
Found at i:43857415 original size:10 final size:10
Alignment explanation
Indices: 43857396--43857426 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
43857386 GCTTATTTTG
43857396 TGTTTATACA
1 TGTTTATACA
*
43857406 TGTTTGTACA
1 TGTTTATACA
43857416 TGTTTATACA
1 TGTTTATACA
43857426 T
1 T
43857427 TGAGGACAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.26, C:0.10, G:0.13, T:0.52
Consensus pattern (10 bp):
TGTTTATACA
Found at i:43857803 original size:60 final size:61
Alignment explanation
Indices: 43857701--43857874 Score: 233
Period size: 61 Copynumber: 2.9 Consensus size: 61
43857691 ATTATCTTGA
* *
43857701 AGTTGTTCCATAAAGGCATTCCTTAGTATCCAGTACTTGCCACAAAGGCTTT-ATGTCCAG
1 AGTTGTGCCATAAAGGCATTCCTTAGTATCCAGTACTCGCCACAAAGGCTTTCATGTCCAG
* * * * * *
43857761 AGTTGTGCCACAAAGGCATTTCTTAGTATCTATTACTCGCCACAAAGGCTTTCCTGTCTAG
1 AGTTGTGCCATAAAGGCATTCCTTAGTATCCAGTACTCGCCACAAAGGCTTTCATGTCCAG
* * * *
43857822 AGTTGTGTCATAAAGGCATTCCTTAATATCCAGTACTCACCACAAAGACTTTC
1 AGTTGTGCCATAAAGGCATTCCTTAGTATCCAGTACTCGCCACAAAGGCTTTC
43857875 TCTTTCCTAG
Statistics
Matches: 97, Mismatches: 16, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
60 46 0.47
61 51 0.53
ACGTcount: A:0.28, C:0.24, G:0.17, T:0.32
Consensus pattern (61 bp):
AGTTGTGCCATAAAGGCATTCCTTAGTATCCAGTACTCGCCACAAAGGCTTTCATGTCCAG
Found at i:43859831 original size:18 final size:19
Alignment explanation
Indices: 43859793--43859829 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
43859783 TTTAAACTCT
*
43859793 TTAAACTCAATTAAAAAAA
1 TTAAAATCAATTAAAAAAA
43859812 TTAAAATCAATTAAAAAA
1 TTAAAATCAATTAAAAAA
43859830 TTGCTACCTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.65, C:0.08, G:0.00, T:0.27
Consensus pattern (19 bp):
TTAAAATCAATTAAAAAAA
Found at i:43862245 original size:9 final size:10
Alignment explanation
Indices: 43862222--43862246 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
43862212 GCTTTATCTA
43862222 AAAAAGTTTT
1 AAAAAGTTTT
43862232 AAAAAGTTTT
1 AAAAAGTTTT
43862242 AAAAA
1 AAAAA
43862247 TTGAGAGATC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.60, C:0.00, G:0.08, T:0.32
Consensus pattern (10 bp):
AAAAAGTTTT
Found at i:43863205 original size:17 final size:17
Alignment explanation
Indices: 43863183--43863220 Score: 76
Period size: 17 Copynumber: 2.2 Consensus size: 17
43863173 TTTGTACTCG
43863183 TTTATGACTATTCTAGA
1 TTTATGACTATTCTAGA
43863200 TTTATGACTATTCTAGA
1 TTTATGACTATTCTAGA
43863217 TTTA
1 TTTA
43863221 GAACAACTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.29, C:0.11, G:0.11, T:0.50
Consensus pattern (17 bp):
TTTATGACTATTCTAGA
Found at i:43871127 original size:14 final size:17
Alignment explanation
Indices: 43871090--43871130 Score: 52
Period size: 14 Copynumber: 2.6 Consensus size: 17
43871080 CGTAGAAGAT
43871090 GATTCATAGATATGGTG
1 GATTCATAGATATGGTG
*
43871107 GACTCAT-G-TAT-GTG
1 GATTCATAGATATGGTG
43871121 GATTCATAGA
1 GATTCATAGA
43871131 AGAAATTTCA
Statistics
Matches: 20, Mismatches: 2, Indels: 5
0.74 0.07 0.19
Matches are distributed among these distances:
14 9 0.45
15 4 0.20
16 1 0.05
17 6 0.30
ACGTcount: A:0.29, C:0.10, G:0.27, T:0.34
Consensus pattern (17 bp):
GATTCATAGATATGGTG
Found at i:43875569 original size:20 final size:20
Alignment explanation
Indices: 43875506--43875611 Score: 65
Period size: 20 Copynumber: 5.3 Consensus size: 20
43875496 CCAGTTTATG
43875506 GACAAGCCACCA-ATATTGCA
1 GACAAGCCACCATA-ATTGCA
* * * **
43875526 GATAAACCAGCAGT-ATTGTG
1 GACAAGCCACCA-TAATTGCA
43875546 GACAAGCCACCATAATTGCA
1 GACAAGCCACCATAATTGCA
** **
43875566 GACAAGGTACCAGT-ATTGTG
1 GACAAGCCACCA-TAATTGCA
* *
43875586 GACAAGCCACTAGAATTGCA
1 GACAAGCCACCATAATTGCA
43875606 GACAAG
1 GACAAG
43875612 TTGTTAGTAT
Statistics
Matches: 61, Mismatches: 20, Indels: 10
0.67 0.22 0.11
Matches are distributed among these distances:
19 1 0.02
20 59 0.97
21 1 0.02
ACGTcount: A:0.38, C:0.23, G:0.22, T:0.18
Consensus pattern (20 bp):
GACAAGCCACCATAATTGCA
Found at i:43875611 original size:40 final size:40
Alignment explanation
Indices: 43875495--43875700 Score: 157
Period size: 40 Copynumber: 5.2 Consensus size: 40
43875485 CCAATAACAC
* * ***
43875495 ACCAGT-TTATGGACAAGCCACCA-ATATTGCAGATAAACC
1 ACCAGTATTGTGGACAAGCCACCAGA-ATTGCAGACAAGGT
* *
43875534 AGCAGTATTGTGGACAAGCCACCATAATTGCAGACAAGGT
1 ACCAGTATTGTGGACAAGCCACCAGAATTGCAGACAAGGT
* *
43875574 ACCAGTATTGTGGACAAGCCACTAGAATTGCAGACAAGTT
1 ACCAGTATTGTGGACAAGCCACCAGAATTGCAGACAAGGT
*** * *** * *
43875614 GTTAGTATTATGGACAAGCCACCAGTGCTGCAAACAA-GC
1 ACCAGTATTGTGGACAAGCCACCAGAATTGCAGACAAGGT
* * ** *
43875653 AGCCAATAATGTGGACAAGCCACCAGTGTTGCAGACAAGAT
1 A-CCAGTATTGTGGACAAGCCACCAGAATTGCAGACAAGGT
*
43875694 GCCAGTA
1 ACCAGTA
43875701 CTTCTTTCTT
Statistics
Matches: 130, Mismatches: 33, Indels: 7
0.76 0.19 0.04
Matches are distributed among these distances:
39 5 0.04
40 124 0.95
41 1 0.01
ACGTcount: A:0.35, C:0.22, G:0.22, T:0.20
Consensus pattern (40 bp):
ACCAGTATTGTGGACAAGCCACCAGAATTGCAGACAAGGT
Found at i:43875651 original size:80 final size:80
Alignment explanation
Indices: 43875537--43875691 Score: 188
Period size: 80 Copynumber: 1.9 Consensus size: 80
43875527 ATAAACCAGC
* * * * * * *
43875537 AGTATTGTGGACAAGCCACCATAATTGCAGACAAGGTA-CCAGTATTGTGGACAAGCCACTAGAA
1 AGTATTATGGACAAGCCACCATAACTGCAAACAA-GCAGCCAATAATGTGGACAAGCCACCAGAA
43875601 TTGCAGACAAGTTGTT
65 TTGCAGACAAGTTGTT
* **
43875617 AGTATTATGGACAAGCCACCAGT-GCTGCAAACAAGCAGCCAATAATGTGGACAAGCCACCAGTG
1 AGTATTATGGACAAGCCACCA-TAACTGCAAACAAGCAGCCAATAATGTGGACAAGCCACCAGAA
43875681 TTGCAGACAAG
65 TTGCAGACAAG
43875692 ATGCCAGTAC
Statistics
Matches: 63, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
79 2 0.03
80 60 0.95
81 1 0.02
ACGTcount: A:0.35, C:0.21, G:0.24, T:0.20
Consensus pattern (80 bp):
AGTATTATGGACAAGCCACCATAACTGCAAACAAGCAGCCAATAATGTGGACAAGCCACCAGAAT
TGCAGACAAGTTGTT
Found at i:43875689 original size:20 final size:20
Alignment explanation
Indices: 43875626--43875691 Score: 53
Period size: 20 Copynumber: 3.3 Consensus size: 20
43875616 TAGTATTATG
*
43875626 GACAAGCCACCAGTGCTGCA
1 GACAAGCCACCAGTGATGCA
* * * **
43875646 AACAAG-CAGCCAATAATGTG
1 GACAAGCCA-CCAGTGATGCA
*
43875666 GACAAGCCACCAGTGTTGCA
1 GACAAGCCACCAGTGATGCA
43875686 GACAAG
1 GACAAG
43875692 ATGCCAGTAC
Statistics
Matches: 32, Mismatches: 12, Indels: 4
0.67 0.25 0.08
Matches are distributed among these distances:
19 2 0.06
20 28 0.88
21 2 0.06
ACGTcount: A:0.36, C:0.27, G:0.24, T:0.12
Consensus pattern (20 bp):
GACAAGCCACCAGTGATGCA
Found at i:43883645 original size:96 final size:96
Alignment explanation
Indices: 43883478--43883672 Score: 381
Period size: 96 Copynumber: 2.0 Consensus size: 96
43883468 ATGTTAGGTA
43883478 TGTTAATTGACCCATTAAACAATTTTGGATGGCTTCTAAGTATAGATGACATGCTATAAGATATA
1 TGTTAATTGACCCATTAAACAATTTTGGATGGCTTCTAAGTATAGATGACATGCTATAAGATATA
43883543 TCTTAAACTCTTGTGTTATGGGTTAACCTTG
66 TCTTAAACTCTTGTGTTATGGGTTAACCTTG
43883574 TGTTAATTGACCCATTAAACAATTTTGGATGGCTTCTAAGTATAGATGACATGCTATAAGATATA
1 TGTTAATTGACCCATTAAACAATTTTGGATGGCTTCTAAGTATAGATGACATGCTATAAGATATA
*
43883639 TGTTAAACTCTTGTGTTATGGGTTAACCTTG
66 TCTTAAACTCTTGTGTTATGGGTTAACCTTG
43883670 TGT
1 TGT
43883673 ACTTGGGAGA
Statistics
Matches: 98, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
96 98 1.00
ACGTcount: A:0.30, C:0.13, G:0.18, T:0.39
Consensus pattern (96 bp):
TGTTAATTGACCCATTAAACAATTTTGGATGGCTTCTAAGTATAGATGACATGCTATAAGATATA
TCTTAAACTCTTGTGTTATGGGTTAACCTTG
Found at i:43884664 original size:21 final size:21
Alignment explanation
Indices: 43884635--43884676 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
43884625 ACCTAGATAT
* * *
43884635 TAATTTAATTTAGTTTTTTTA
1 TAATCTAATTTAATTATTTTA
43884656 TAATCTAATTTAATTATTTTA
1 TAATCTAATTTAATTATTTTA
43884677 ATTTAATTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.62
Consensus pattern (21 bp):
TAATCTAATTTAATTATTTTA
Found at i:43888190 original size:18 final size:18
Alignment explanation
Indices: 43888169--43888212 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
43888159 TTAATTCTGC
43888169 AAATA-ATGAAAAAAAGAT
1 AAATATATGAAAAAAAG-T
**
43888187 AAATATATTTAAAAAAGT
1 AAATATATGAAAAAAAGT
43888205 AAATATAT
1 AAATATAT
43888213 TAGGTGTAGT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
18 14 0.61
19 9 0.39
ACGTcount: A:0.66, C:0.00, G:0.07, T:0.27
Consensus pattern (18 bp):
AAATATATGAAAAAAAGT
Found at i:43888213 original size:18 final size:19
Alignment explanation
Indices: 43888178--43888213 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
43888168 CAAATAATGA
43888178 AAAAAAGATAAATATATTT
1 AAAAAAGATAAATATATTT
43888197 AAAAAAG-TAAATATATT
1 AAAAAAGATAAATATATT
43888214 AGGTGTAGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 10 0.59
19 7 0.41
ACGTcount: A:0.64, C:0.00, G:0.06, T:0.31
Consensus pattern (19 bp):
AAAAAAGATAAATATATTT
Found at i:43891598 original size:9 final size:9
Alignment explanation
Indices: 43891523--43891630 Score: 117
Period size: 9 Copynumber: 11.6 Consensus size: 9
43891513 TTTGGTTAAA
43891523 AATTACCCG
1 AATTACCCG
**
43891532 ACCTACCCG
1 AATTACCCG
*
43891541 ACTTACCCG
1 AATTACCCG
*
43891550 ACTTACCCG
1 AATTACCCG
*
43891559 ACTTACCCG
1 AATTACCCG
43891568 AATTACCCG
1 AATTACCCG
43891577 AAAATTACCCG
1 --AATTACCCG
43891588 AATTACCCG
1 AATTACCCG
*
43891597 AAAATTACCCA
1 --AATTACCCG
43891608 AATTACCCG
1 AATTACCCG
*
43891617 AATTACCCA
1 AATTACCCG
43891626 AATTA
1 AATTA
43891631 AATCACTACA
Statistics
Matches: 88, Mismatches: 7, Indels: 8
0.85 0.07 0.08
Matches are distributed among these distances:
9 71 0.81
11 17 0.19
ACGTcount: A:0.35, C:0.35, G:0.08, T:0.21
Consensus pattern (9 bp):
AATTACCCG
Found at i:43891659 original size:17 final size:17
Alignment explanation
Indices: 43891637--43891734 Score: 52
Period size: 17 Copynumber: 5.4 Consensus size: 17
43891627 ATTAAATCAC
43891637 TACATAATTAAAAACAT
1 TACATAATTAAAAACAT
** * *
43891654 TACATAAATATTTGAATCAC
1 TACAT--A-ATTAAAAACAT
*
43891674 TACATAATTAAAAATAT
1 TACATAATTAAAAACAT
** * *
43891691 TACATAAGTCTTTGAATCAC
1 TACATAA---TTAAAAACAT
*
43891711 TACATAATTAAAAATAT
1 TACATAATTAAAAACAT
43891728 TACATAA
1 TACATAA
43891735 GTCTTGAATT
Statistics
Matches: 56, Mismatches: 19, Indels: 12
0.64 0.22 0.14
Matches are distributed among these distances:
17 30 0.54
18 1 0.02
19 1 0.02
20 24 0.43
ACGTcount: A:0.51, C:0.12, G:0.03, T:0.34
Consensus pattern (17 bp):
TACATAATTAAAAACAT
Found at i:43891735 original size:37 final size:37
Alignment explanation
Indices: 43891631--43891743 Score: 192
Period size: 37 Copynumber: 3.1 Consensus size: 37
43891621 ACCCAAATTA
* * *
43891631 AATCACTACATAATTAAAAACATTACATAAATATTTG
1 AATCACTACATAATTAAAAATATTACATAAGTCTTTG
43891668 AATCACTACATAATTAAAAATATTACATAAGTCTTTG
1 AATCACTACATAATTAAAAATATTACATAAGTCTTTG
43891705 AATCACTACATAATTAAAAATATTACATAAGTC-TTG
1 AATCACTACATAATTAAAAATATTACATAAGTCTTTG
43891741 AAT
1 AAT
43891744 TAACACATAA
Statistics
Matches: 73, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
36 6 0.08
37 67 0.92
ACGTcount: A:0.49, C:0.13, G:0.04, T:0.34
Consensus pattern (37 bp):
AATCACTACATAATTAAAAATATTACATAAGTCTTTG
Found at i:43891811 original size:24 final size:24
Alignment explanation
Indices: 43891784--43891842 Score: 100
Period size: 24 Copynumber: 2.5 Consensus size: 24
43891774 ATTCTCCATT
*
43891784 TATATCCATTTCATCTTTCCAAAA
1 TATATCCATTTCATCTCTCCAAAA
43891808 TATATCCATTTCATCTCTCCAAAA
1 TATATCCATTTCATCTCTCCAAAA
*
43891832 TATCTCCATTT
1 TATATCCATTT
43891843 GCATTAAACC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.31, C:0.27, G:0.00, T:0.42
Consensus pattern (24 bp):
TATATCCATTTCATCTCTCCAAAA
Found at i:43895361 original size:16 final size:16
Alignment explanation
Indices: 43895340--43895373 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
43895330 TTTTTTTTCT
43895340 TACATTAATTACAATA
1 TACATTAATTACAATA
43895356 TACATTAATTACAATA
1 TACATTAATTACAATA
43895372 TA
1 TA
43895374 TTCAATAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.50, C:0.12, G:0.00, T:0.38
Consensus pattern (16 bp):
TACATTAATTACAATA
Found at i:43895382 original size:18 final size:16
Alignment explanation
Indices: 43895340--43895383 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 16
43895330 TTTTTTTTCT
*
43895340 TACATTAATTACAATA
1 TACAATAATTACAATA
*
43895356 TACATTAATTACAATA
1 TACAATAATTACAATA
43895372 TATTCAATAATT
1 TA--CAATAATT
43895384 TAAATTTTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
16 18 0.72
18 7 0.28
ACGTcount: A:0.48, C:0.11, G:0.00, T:0.41
Consensus pattern (16 bp):
TACAATAATTACAATA
Found at i:43896310 original size:16 final size:17
Alignment explanation
Indices: 43896289--43896329 Score: 66
Period size: 17 Copynumber: 2.5 Consensus size: 17
43896279 GCCTAAGACA
43896289 AAATTGGGCT-GGATTT
1 AAATTGGGCTAGGATTT
*
43896305 AAATTGGGCTAGGTTTT
1 AAATTGGGCTAGGATTT
43896322 AAATTGGG
1 AAATTGGG
43896330 AGGGAGTAGG
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
16 10 0.43
17 13 0.57
ACGTcount: A:0.27, C:0.05, G:0.32, T:0.37
Consensus pattern (17 bp):
AAATTGGGCTAGGATTT
Found at i:43922212 original size:33 final size:35
Alignment explanation
Indices: 43922174--43922254 Score: 96
Period size: 37 Copynumber: 2.3 Consensus size: 35
43922164 CAACTATAAG
*
43922174 TGCCGAATGCACATAT-TCA-CT-TATACCCACCTA
1 TGCCGAATGCACATATAT-ATATATATACCCACCTA
*
43922207 TGCCGAATGCATACATATATATATATATATCCACCTA
1 TGCCGAATGC--ACATATATATATATATACCCACCTA
43922244 TGCCGAATGCA
1 TGCCGAATGCA
43922255 TACATATACA
Statistics
Matches: 41, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
33 10 0.24
35 8 0.20
36 2 0.05
37 21 0.51
ACGTcount: A:0.33, C:0.27, G:0.11, T:0.28
Consensus pattern (35 bp):
TGCCGAATGCACATATATATATATATACCCACCTA
Found at i:43922515 original size:41 final size:41
Alignment explanation
Indices: 43922470--43922649 Score: 236
Period size: 41 Copynumber: 4.4 Consensus size: 41
43922460 CTTCACCTAA
* * *
43922470 TAGGCTTATAGTCTAATTCCGTTCACCGGCACTTAGCCTGC
1 TAGGCGTATAGTCTGATTCAGTTCACCGGCACTTAGCCTGC
* *
43922511 TAGGCCTATAGCCTGATTCAGTTCACCGGCACTTAGCCTGC
1 TAGGCGTATAGTCTGATTCAGTTCACCGGCACTTAGCCTGC
* * *
43922552 TAGGCTTGTAGCCTGATTCAGTTCACCGGCACTTAGCCTGC
1 TAGGCGTATAGTCTGATTCAGTTCACCGGCACTTAGCCTGC
* * *
43922593 T-GGACGTATAGTCCGATTCAATTCACCGACACTTAGCCTGC
1 TAGG-CGTATAGTCTGATTCAGTTCACCGGCACTTAGCCTGC
*
43922634 TAGACGTATAGTCTGA
1 TAGGCGTATAGTCTGA
43922650 ACAATTTCAC
Statistics
Matches: 123, Mismatches: 14, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
40 2 0.02
41 120 0.98
42 1 0.01
ACGTcount: A:0.21, C:0.28, G:0.22, T:0.29
Consensus pattern (41 bp):
TAGGCGTATAGTCTGATTCAGTTCACCGGCACTTAGCCTGC
Found at i:43929204 original size:41 final size:41
Alignment explanation
Indices: 43929138--43929285 Score: 197
Period size: 41 Copynumber: 3.6 Consensus size: 41
43929128 CTTAATTATT
* *
43929138 CCCTGAATTGCACATACATGCCCCTGTTTGTATTTCAGTAC
1 CCCTGAATTGCACATACGTGCCCCTGTTTGTACTTCAGTAC
* * *
43929179 CCCTGAATTACACATATGTGTCCCTGTTTGTACTTCAGTAC
1 CCCTGAATTGCACATACGTGCCCCTGTTTGTACTTCAGTAC
* ** * * *
43929220 CCTTGAATTGCAGGTACGTGTCGCTGTTTGTACTTCGGTAC
1 CCCTGAATTGCACATACGTGCCCCTGTTTGTACTTCAGTAC
43929261 CCCTGAATTGCACATACGTGCCCCT
1 CCCTGAATTGCACATACGTGCCCCT
43929286 ATTTACGCTC
Statistics
Matches: 90, Mismatches: 17, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
41 90 1.00
ACGTcount: A:0.20, C:0.28, G:0.18, T:0.34
Consensus pattern (41 bp):
CCCTGAATTGCACATACGTGCCCCTGTTTGTACTTCAGTAC
Found at i:43930000 original size:63 final size:63
Alignment explanation
Indices: 43929909--43930129 Score: 239
Period size: 63 Copynumber: 3.5 Consensus size: 63
43929899 TTACAAGAAT
** *
43929909 CACAACACGCA-AACTCATTCCCCCCATCAACACCA-TCAGCTCTGATTTATTTTACACAAGCAC
1 CACAACACGCACAA-TCATTCCCTGCATCAACA-CATTCAGCACTGATTTATTTTACACAAGCAC
* * * * *
43929972 CACAACACGCATAATCATTCCCTGCATCAACATATTAAGCACTGGTTTATTTTACACAAGTAC
1 CACAACACGCACAATCATTCCCTGCATCAACACATTCAGCACTGATTTATTTTACACAAGCAC
* * * * * * *
43930035 CACAGCACACACAATCATTGCCTACATCAATACATTCAGCACCGATTTATTTTACACAAGCGC
1 CACAACACGCACAATCATTCCCTGCATCAACACATTCAGCACTGATTTATTTTACACAAGCAC
* * * *
43930098 TACAGCACGCGCAATCATTCCTTGCATCAACA
1 CACAACACGCACAATCATTCCCTGCATCAACA
43930130 TCTTTTTTAG
Statistics
Matches: 130, Mismatches: 26, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
62 1 0.01
63 127 0.98
64 2 0.02
ACGTcount: A:0.34, C:0.33, G:0.09, T:0.24
Consensus pattern (63 bp):
CACAACACGCACAATCATTCCCTGCATCAACACATTCAGCACTGATTTATTTTACACAAGCAC
Found at i:43942560 original size:41 final size:38
Alignment explanation
Indices: 43942515--43942606 Score: 121
Period size: 40 Copynumber: 2.3 Consensus size: 38
43942505 AGCGGCATTT
43942515 TTAGTGGCGTTTGGACAAAAAACGCCGCAAAAAATCGAGCA
1 TTAGTGGCGTTT--ACAAAAAACGCCGCAAAAAAT-GAGCA
* * *
43942556 TTAGTGACGCTTTACATAAAACGCCGCTAAAAATGAGCA
1 TTAGTGGCG-TTTACAAAAAACGCCGCAAAAAATGAGCA
43942595 TTAGTGGCGTTT
1 TTAGTGGCGTTT
43942607 TTTGGAAAAA
Statistics
Matches: 46, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
38 3 0.07
39 13 0.28
40 19 0.41
41 8 0.17
42 3 0.07
ACGTcount: A:0.35, C:0.18, G:0.23, T:0.24
Consensus pattern (38 bp):
TTAGTGGCGTTTACAAAAAACGCCGCAAAAAATGAGCA
Found at i:43942710 original size:41 final size:40
Alignment explanation
Indices: 43942653--43942799 Score: 163
Period size: 41 Copynumber: 3.6 Consensus size: 40
43942643 GACATTTTGG
* *
43942653 GGCTTTAGCGACGTTTTTGAAAAAGCGCTGCTAATGCTCA
1 GGCTTTAGCGGCGTTTTTCAAAAAGCGCTGCTAATGCTCA
* * * *
43942693 GGCTTTTAACGGCGTTTTCCAAGAAGCGCCGCTAATGCTCA
1 GGC-TTTAGCGGCGTTTTTCAAAAAGCGCTGCTAATGCTCA
*
43942734 GGGCTTTAGCGGCGTTTTTGAAAAAGCG-TCGCT-ATAGCTCA
1 -GGCTTTAGCGGCGTTTTTCAAAAAGCGCT-GCTAAT-GCTCA
*
43942775 GAGCTTTAGCGGCGCTTTTCAAAAA
1 G-GCTTTAGCGGCGTTTTTCAAAAA
43942800 CATTTTATCT
Statistics
Matches: 89, Mismatches: 13, Indels: 9
0.80 0.12 0.08
Matches are distributed among these distances:
40 6 0.07
41 80 0.90
42 3 0.03
ACGTcount: A:0.24, C:0.22, G:0.26, T:0.29
Consensus pattern (40 bp):
GGCTTTAGCGGCGTTTTTCAAAAAGCGCTGCTAATGCTCA
Found at i:43943269 original size:13 final size:13
Alignment explanation
Indices: 43943251--43943275 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
43943241 TGTGATTTAT
43943251 GGGTTAGGGGTTG
1 GGGTTAGGGGTTG
43943264 GGGTTAGGGGTT
1 GGGTTAGGGGTT
43943276 AAATTAATTA
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:0.08, C:0.00, G:0.60, T:0.32
Consensus pattern (13 bp):
GGGTTAGGGGTTG
Found at i:43943342 original size:74 final size:76
Alignment explanation
Indices: 43943264--43943406 Score: 245
Period size: 76 Copynumber: 1.9 Consensus size: 76
43943254 TTAGGGGTTG
43943264 GGGTTAGGGGTTAAATTAATTAGTGTGTTTTAA-TT-TATATTAAATAAGGTTTAGGGGTTAAGG
1 GGGTTAGGGGTTAAATTAATTAGTGTGTTTTAATTTATATATTAAATAAGGTTTAGGGGTTAAGG
43943327 GTTAGGAATTT
66 GTTAGGAATTT
* * *
43943338 GGGTTAGGGTTTAGATTAATTAGTGTTTTTTAATTTATATATTAAATAAGGTTTAGGGGTTAAGG
1 GGGTTAGGGGTTAAATTAATTAGTGTGTTTTAATTTATATATTAAATAAGGTTTAGGGGTTAAGG
43943403 GTTA
66 GTTA
43943407 AGGGTTTAGG
Statistics
Matches: 64, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
74 30 0.47
75 2 0.03
76 32 0.50
ACGTcount: A:0.29, C:0.00, G:0.27, T:0.43
Consensus pattern (76 bp):
GGGTTAGGGGTTAAATTAATTAGTGTGTTTTAATTTATATATTAAATAAGGTTTAGGGGTTAAGG
GTTAGGAATTT
Found at i:43943406 original size:7 final size:7
Alignment explanation
Indices: 43943384--43943441 Score: 53
Period size: 7 Copynumber: 8.3 Consensus size: 7
43943374 ATATATTAAA
*
43943384 TAAGGTT
1 TAAGGGT
*
43943391 TAGGGGT
1 TAAGGGT
43943398 TAAGGGT
1 TAAGGGT
43943405 TAAGGGT
1 TAAGGGT
*
43943412 TTAGGGT
1 TAAGGGT
* *
43943419 TTAGGAT
1 TAAGGGT
*
43943426 TAGGGGT
1 TAAGGGT
*
43943433 TAGGGGT
1 TAAGGGT
43943440 TA
1 TA
43943442 GATGTTAGAG
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
7 43 1.00
ACGTcount: A:0.22, C:0.00, G:0.43, T:0.34
Consensus pattern (7 bp):
TAAGGGT
Found at i:43943418 original size:21 final size:20
Alignment explanation
Indices: 43943387--43943437 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
43943377 TATTAAATAA
*
43943387 GGTTTAGGGGTTAAGGGTTAAG
1 GGTTTA-GGGTTAAGGATT-AG
*
43943409 GGTTTAGGGTTTAGGATTAG
1 GGTTTAGGGTTAAGGATTAG
*
43943429 GGGTTAGGG
1 GGTTTAGGG
43943438 GTTAGATGTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
20 10 0.38
21 10 0.38
22 6 0.23
ACGTcount: A:0.20, C:0.00, G:0.47, T:0.33
Consensus pattern (20 bp):
GGTTTAGGGTTAAGGATTAG
Found at i:43943439 original size:21 final size:22
Alignment explanation
Indices: 43943390--43943441 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 22
43943380 TAAATAAGGT
* *
43943390 TTAGGGGTTAAGGGTTAAGGGT
1 TTAGGGGTTAAGGATTAAGGGG
*
43943412 TTA-GGGTTTAGGATT-AGGGG
1 TTAGGGGTTAAGGATTAAGGGG
43943432 TTAGGGGTTA
1 TTAGGGGTTA
43943442 GATGTTAGAG
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
20 7 0.28
21 15 0.60
22 3 0.12
ACGTcount: A:0.21, C:0.00, G:0.44, T:0.35
Consensus pattern (22 bp):
TTAGGGGTTAAGGATTAAGGGG
Found at i:43943442 original size:7 final size:7
Alignment explanation
Indices: 43943390--43943442 Score: 54
Period size: 7 Copynumber: 7.6 Consensus size: 7
43943380 TAAATAAGGT
43943390 TTAGGGG
1 TTAGGGG
*
43943397 TTAAGGG
1 TTAGGGG
*
43943404 TTAAGGGT
1 TT-AGGGG
*
43943412 TTAGGGT
1 TTAGGGG
*
43943419 TTA-GGA
1 TTAGGGG
43943425 TTAGGGG
1 TTAGGGG
43943432 TTAGGGG
1 TTAGGGG
43943439 TTAG
1 TTAG
43943443 ATGTTAGAGG
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
6 5 0.13
7 29 0.74
8 5 0.13
ACGTcount: A:0.21, C:0.00, G:0.45, T:0.34
Consensus pattern (7 bp):
TTAGGGG
Found at i:43943442 original size:14 final size:14
Alignment explanation
Indices: 43943390--43943442 Score: 54
Period size: 13 Copynumber: 3.8 Consensus size: 14
43943380 TAAATAAGGT
*
43943390 TTAGGGGTTAAGGG
1 TTAGGGGTTAGGGG
* *
43943404 TTAAGGGTTTAGGGT
1 TT-AGGGGTTAGGGG
*
43943419 TTA-GGATTAGGGG
1 TTAGGGGTTAGGGG
43943432 TTAGGGGTTAG
1 TTAGGGGTTAG
43943443 ATGTTAGAGG
Statistics
Matches: 31, Mismatches: 6, Indels: 4
0.76 0.15 0.10
Matches are distributed among these distances:
13 11 0.35
14 9 0.29
15 11 0.35
ACGTcount: A:0.21, C:0.00, G:0.45, T:0.34
Consensus pattern (14 bp):
TTAGGGGTTAGGGG
Found at i:43943601 original size:13 final size:14
Alignment explanation
Indices: 43943570--43943599 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
43943560 TGTGAAAGAG
43943570 GGGTTAGGGGTTAA
1 GGGTTAGGGGTTAA
*
43943584 GGGTTAGGGTTTAA
1 GGGTTAGGGGTTAA
43943598 GG
1 GG
43943600 TTTATGTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.20, C:0.00, G:0.50, T:0.30
Consensus pattern (14 bp):
GGGTTAGGGGTTAA
Found at i:43947634 original size:43 final size:43
Alignment explanation
Indices: 43947568--43947837 Score: 321
Period size: 43 Copynumber: 6.3 Consensus size: 43
43947558 TTTTTAGAAA
* * *
43947568 AAACGCCGCTAAAGACCAAGACCTCTGGCGACGCTTTTCCCAC
1 AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCCCAC
* * * *
43947611 AAACGCCGCTAAAGACCATGACCTTTGGCGGTGCTTCTCCCAC
1 AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCCCAC
*
43947654 AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTCTCCCAC
1 AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCCCAC
*
43947697 AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTCTT-CCAA
1 AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTT-TTCCCAC
* * * **
43947740 AAACGGCGCTAAAGACTCTA-ACCTTTAGCGGCACTTTTATCAC
1 AAACGCCGCTAAAGAC-CAAGACCTTTAGCGGCGCTTTTCCCAC
** * * * *
43947783 AAACGCCGCTAAAGAATAA-ACCTTTACCGGCGCTTCTCGCAA
1 AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCCCAC
43947825 AAACGCCGCTAAA
1 AAACGCCGCTAAA
43947838 AACATAACCT
Statistics
Matches: 199, Mismatches: 25, Indels: 7
0.86 0.11 0.03
Matches are distributed among these distances:
42 33 0.17
43 163 0.82
44 3 0.02
ACGTcount: A:0.30, C:0.33, G:0.18, T:0.19
Consensus pattern (43 bp):
AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCCCAC
Found at i:43954213 original size:38 final size:38
Alignment explanation
Indices: 43954170--43954242 Score: 103
Period size: 38 Copynumber: 1.9 Consensus size: 38
43954160 TCCTAACCCG
* * *
43954170 ACCCCTGAATCCCTAACTCT-TAACCCCTAACACATCTA
1 ACCCCTAAACCCCTAACCCTCTAACCCCTAA-ACATCTA
43954208 ACCCCTAAACCCCTAACCCTCTAACCCCTAAACAT
1 ACCCCTAAACCCCTAACCCTCTAACCCCTAAACAT
43954243 TAAATCCTAA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
38 21 0.68
39 10 0.32
ACGTcount: A:0.33, C:0.45, G:0.01, T:0.21
Consensus pattern (38 bp):
ACCCCTAAACCCCTAACCCTCTAACCCCTAAACATCTA
Found at i:43954220 original size:8 final size:7
Alignment explanation
Indices: 43954170--43954238 Score: 57
Period size: 7 Copynumber: 9.1 Consensus size: 7
43954160 TCCTAACCCG
43954170 ACCCCTGA
1 ACCCCT-A
*
43954178 ATCCCTA
1 ACCCCTA
* *
43954185 ACTCTTA
1 ACCCCTA
43954192 ACCCCTA
1 ACCCCTA
*
43954199 ACACATCTA
1 AC-C-CCTA
43954208 ACCCCTAA
1 ACCCCT-A
43954216 ACCCCTA
1 ACCCCTA
43954223 ACCCTCTA
1 ACCC-CTA
43954231 ACCCCTA
1 ACCCCTA
43954238 A
1 A
43954239 ACATTAAATC
Statistics
Matches: 49, Mismatches: 8, Indels: 9
0.74 0.12 0.14
Matches are distributed among these distances:
7 23 0.47
8 21 0.43
9 5 0.10
ACGTcount: A:0.32, C:0.46, G:0.01, T:0.20
Consensus pattern (7 bp):
ACCCCTA
Found at i:43954225 original size:15 final size:15
Alignment explanation
Indices: 43954190--43954277 Score: 56
Period size: 15 Copynumber: 5.9 Consensus size: 15
43954180 CCCTAACTCT
**
43954190 TAACCCCTAACACATC
1 TAACCCCTAA-ACCCC
43954206 TAACCCCTAAACCCC
1 TAACCCCTAAACCCC
43954221 TAACCCTCT-AACCCC
1 TAACCC-CTAAACCCC
* ** *
43954236 TAAACATTAAA-TCC
1 TAACCCCTAAACCCC
* *
43954250 TAACCCTTAAA-CCA
1 TAACCCCTAAACCCC
*
43954264 TAATCCCTAAACCC
1 TAACCCCTAAACCC
43954278 ATACTCCTTA
Statistics
Matches: 57, Mismatches: 12, Indels: 7
0.75 0.16 0.09
Matches are distributed among these distances:
14 22 0.39
15 23 0.40
16 12 0.21
ACGTcount: A:0.38, C:0.42, G:0.00, T:0.20
Consensus pattern (15 bp):
TAACCCCTAAACCCC
Found at i:43954230 original size:23 final size:24
Alignment explanation
Indices: 43954191--43954240 Score: 84
Period size: 23 Copynumber: 2.1 Consensus size: 24
43954181 CCTAACTCTT
43954191 AACCCCTAACACATCTAACCCCTA
1 AACCCCTAACACATCTAACCCCTA
*
43954215 AACCCCTAAC-CCTCTAACCCCTA
1 AACCCCTAACACATCTAACCCCTA
43954238 AAC
1 AAC
43954241 ATTAAATCCT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
23 15 0.60
24 10 0.40
ACGTcount: A:0.36, C:0.48, G:0.00, T:0.16
Consensus pattern (24 bp):
AACCCCTAACACATCTAACCCCTA
Found at i:43954686 original size:41 final size:41
Alignment explanation
Indices: 43954577--43954689 Score: 181
Period size: 41 Copynumber: 2.8 Consensus size: 41
43954567 TAAAATGTTT
* * * *
43954577 TTAGCGGCGCTTTTTAAAAAACGCCGCGAAAGTCCTGAGCA
1 TTAGCGGCGCTTCTTAAAAAACGCCGCTAAAGACCAGAGCA
*
43954618 TTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGACCAGAGCA
1 TTAGCGGCGCTTCTTAAAAAACGCCGCTAAAGACCAGAGCA
43954659 TTAGCGGCGCTTCTTAAAAAACGCCGCTAAA
1 TTAGCGGCGCTTCTTAAAAAACGCCGCTAAA
43954690 TCCCAAAAAA
Statistics
Matches: 66, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 66 1.00
ACGTcount: A:0.31, C:0.27, G:0.22, T:0.20
Consensus pattern (41 bp):
TTAGCGGCGCTTCTTAAAAAACGCCGCTAAAGACCAGAGCA
Found at i:43954771 original size:38 final size:39
Alignment explanation
Indices: 43954747--43954862 Score: 110
Period size: 40 Copynumber: 2.9 Consensus size: 39
43954737 GCGCTTTTTG
*
43954747 GAAAAG-GCCGCTAATGCTCATTTTTAGCGGCGTTTTCA
1 GAAAAGCGCCGCTAATACTCATTTTTAGCGGCGTTTTCA
* * *
43954785 GAAAAGCGCCGCTAATACTCAATCTTTAGCGGTGTTTTTTA
1 GAAAAGCGCCGCTAATACTC-ATTTTTAGCGGCG-TTTTCA
** * * *
43954826 G-ATTGCGCCGCTAATGATTGATTTTTAGCGGTGTTTT
1 GAAAAGCGCCGCTAAT-ACTCATTTTTAGCGGCGTTTT
43954863 TTATCCAAAC
Statistics
Matches: 65, Mismatches: 9, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
38 6 0.09
39 16 0.25
40 35 0.54
41 8 0.12
ACGTcount: A:0.22, C:0.18, G:0.23, T:0.36
Consensus pattern (39 bp):
GAAAAGCGCCGCTAATACTCATTTTTAGCGGCGTTTTCA
Found at i:43956535 original size:42 final size:42
Alignment explanation
Indices: 43956476--43956587 Score: 131
Period size: 41 Copynumber: 2.7 Consensus size: 42
43956466 TAATTTTTTT
*
43956476 TAAAGGTTATGTT-TTTAGCGGCGTTTTTGTGAGAAGCGCCGC
1 TAAAGGTT-TGTTCTTTAGCGGCGTTTTTGTGACAAGCGCCGC
*
43956518 TAAAGGTTTGTTCTTTAGCGGGCG--TTTGTGACAAGCGTCGC
1 TAAAGGTTTGTTCTTTAGC-GGCGTTTTTGTGACAAGCGCCGC
* **
43956559 TAAAGGTCATGACCTTTAGCGGCGTTTTT
1 TAAAGGT-TTGTTCTTTAGCGGCGTTTTT
43956588 TCATATAAAC
Statistics
Matches: 60, Mismatches: 5, Indels: 9
0.81 0.07 0.12
Matches are distributed among these distances:
41 30 0.50
42 23 0.38
43 7 0.12
ACGTcount: A:0.19, C:0.16, G:0.29, T:0.36
Consensus pattern (42 bp):
TAAAGGTTTGTTCTTTAGCGGCGTTTTTGTGACAAGCGCCGC
Found at i:43957233 original size:13 final size:13
Alignment explanation
Indices: 43957212--43957242 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
43957202 TTAGTCTGTT
*
43957212 ACACAGCTTGGCG
1 ACACGGCTTGGCG
43957225 ACACGGCTTGGCG
1 ACACGGCTTGGCG
43957238 ACACG
1 ACACG
43957243 ACCATGTAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.23, C:0.32, G:0.32, T:0.13
Consensus pattern (13 bp):
ACACGGCTTGGCG
Found at i:43961600 original size:20 final size:21
Alignment explanation
Indices: 43961577--43961628 Score: 72
Period size: 20 Copynumber: 2.5 Consensus size: 21
43961567 GTGAACAGGG
43961577 GCACCAAAGTGCAAA-TAGT-A
1 GCACCAAAGTGCAAAGTA-TAA
*
43961597 GCACCGAAGTGCAAAGTATAA
1 GCACCAAAGTGCAAAGTATAA
43961618 GCACCAAAGTG
1 GCACCAAAGTG
43961629 TAAACCCGTA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
20 15 0.54
21 13 0.46
ACGTcount: A:0.42, C:0.21, G:0.23, T:0.13
Consensus pattern (21 bp):
GCACCAAAGTGCAAAGTATAA
Found at i:43973996 original size:3 final size:3
Alignment explanation
Indices: 43973988--43974041 Score: 90
Period size: 3 Copynumber: 18.0 Consensus size: 3
43973978 CTTTACCATT
* *
43973988 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA GGA TGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
43974036 AGA AGA
1 AGA AGA
43974042 GGGTGGTGCC
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.63, C:0.00, G:0.35, T:0.02
Consensus pattern (3 bp):
AGA
Found at i:43974120 original size:24 final size:23
Alignment explanation
Indices: 43974057--43974121 Score: 58
Period size: 24 Copynumber: 2.7 Consensus size: 23
43974047 GTGCCGGAAA
*
43974057 AAGAAAAGAAAAAGAGAGAAAGAG
1 AAGAAAA-AAAAAGAAAGAAAGAG
* * **
43974081 AATAGAGAAAGGAGAAAGAAAGAG
1 AAGA-AAAAAAAAGAAAGAAAGAG
43974105 AAGAAAAAAAATAGAAA
1 AAGAAAAAAAA-AGAAA
43974122 AAATAAGGTA
Statistics
Matches: 30, Mismatches: 9, Indels: 4
0.70 0.21 0.09
Matches are distributed among these distances:
23 4 0.13
24 24 0.80
25 2 0.07
ACGTcount: A:0.71, C:0.00, G:0.26, T:0.03
Consensus pattern (23 bp):
AAGAAAAAAAAAGAAAGAAAGAG
Found at i:43974203 original size:21 final size:20
Alignment explanation
Indices: 43974158--43974204 Score: 51
Period size: 20 Copynumber: 2.2 Consensus size: 20
43974148 TATCTTGTTA
*
43974158 TTATGTTTTTTTGTATATTTT
1 TTAT-TTTTTTTGTATATTTG
43974179 TTATTTTTTTTGT-TAGTTTAG
1 TTATTTTTTTTGTATA-TTT-G
43974200 TTATT
1 TTATT
43974205 ATTGTTAGTT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
19 2 0.09
20 12 0.52
21 9 0.39
ACGTcount: A:0.15, C:0.00, G:0.11, T:0.74
Consensus pattern (20 bp):
TTATTTTTTTTGTATATTTG
Found at i:43974428 original size:76 final size:77
Alignment explanation
Indices: 43974329--43974477 Score: 212
Period size: 76 Copynumber: 1.9 Consensus size: 77
43974319 TAAAAAAATA
43974329 ATATTATTATTATGGTTAGTTATTAGGATTAGTAAAAACCATAATTATTATT-TTAGTTAGTATG
1 ATATTATTATTATGGTTAGTTATTAGGATTAGT-AAAACCATAATTATTATTGTTAGTTAGTATG
43974393 ATTTTTAGTTTTT
65 ATTTTTAGTTTTT
* **** * *
43974406 ATATTA-TATTATTGTTAGTTATTTTTTTTAGTAAAACCCTAATTATTATTGTTAGTTAGTATTA
1 ATATTATTATTATGGTTAGTTATTAGGATTAGTAAAACCATAATTATTATTGTTAGTTAGTATGA
43974470 TTTTTAGT
66 TTTTTAGT
43974478 AAAAAACTAT
Statistics
Matches: 64, Mismatches: 7, Indels: 3
0.86 0.09 0.04
Matches are distributed among these distances:
75 17 0.27
76 41 0.64
77 6 0.09
ACGTcount: A:0.31, C:0.03, G:0.11, T:0.54
Consensus pattern (77 bp):
ATATTATTATTATGGTTAGTTATTAGGATTAGTAAAACCATAATTATTATTGTTAGTTAGTATGA
TTTTTAGTTTTT
Found at i:43974474 original size:42 final size:40
Alignment explanation
Indices: 43974407--43974509 Score: 99
Period size: 40 Copynumber: 2.6 Consensus size: 40
43974397 TTAGTTTTTA
* **
43974407 TATTA-TATTATTGTTAG--TTATTTTTTTTAGTAAAACCC
1 TATTATTATTATTATTAGTATTA-TTTTTTTAGTAAAAAAC
*
43974445 TAATTATTATTGTTAGTTAGTATTA--TTTTTAGTAAAAAAC
1 T-ATTATTATTATTA-TTAGTATTATTTTTTTAGTAAAAAAC
*
43974485 TATTATTATTATTATTATTATTATT
1 TATTATTATTATTATTAGTATTATT
43974510 ATTATTATTA
Statistics
Matches: 52, Mismatches: 6, Indels: 12
0.74 0.09 0.17
Matches are distributed among these distances:
38 9 0.17
39 16 0.31
40 20 0.38
41 4 0.08
43 3 0.06
ACGTcount: A:0.33, C:0.04, G:0.07, T:0.56
Consensus pattern (40 bp):
TATTATTATTATTATTAGTATTATTTTTTTAGTAAAAAAC
Found at i:43974492 original size:76 final size:77
Alignment explanation
Indices: 43974287--43974504 Score: 192
Period size: 76 Copynumber: 2.8 Consensus size: 77
43974277 GTTTAGTTAT
* * **
43974287 TAATAATTATTGTTACTTAGTATTATTGCTAGTAAAAAAATAATATTATTATTATGGTTAGTTAT
1 TAATTATTATTGTTAGTTAGTATTATTTTTAGT--AAAAA-AATATTATTA-T-T-GTTAGTTAT
43974352 TAGGATTAGTAAAAACCA
60 TAGGATTAGTAAAAACCA
* **** * ****
43974370 TAATTATTATT-TTAGTTAGTATGATTTTTAGTTTTTATAT-TATATTATTGTTAGTTATTTTTT
1 TAATTATTATTGTTAGTTAGTATTATTTTTAGTAAAAAAATAT-TATTATTGTTAGTTATTAGGA
*
43974433 TTAGT-AAAACCC
65 TTAGTAAAAACCA
* *
43974445 TAATTATTATTGTTAGTTAGTATTATTTTTAGTAAAAAACTATTATTATTATTA-TTATTA
1 TAATTATTATTGTTAGTTAGTATTATTTTTAGTAAAAAAATATTATTATTGTTAGTTATTA
43974505 TTATTATTAT
Statistics
Matches: 108, Mismatches: 24, Indels: 14
0.74 0.16 0.10
Matches are distributed among these distances:
75 22 0.20
76 47 0.44
77 2 0.02
78 2 0.02
79 7 0.06
80 1 0.01
82 17 0.16
83 10 0.09
ACGTcount: A:0.35, C:0.04, G:0.10, T:0.51
Consensus pattern (77 bp):
TAATTATTATTGTTAGTTAGTATTATTTTTAGTAAAAAAATATTATTATTGTTAGTTATTAGGAT
TAGTAAAAACCA
Found at i:43974493 original size:3 final size:3
Alignment explanation
Indices: 43974485--43974521 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
43974475 AGTAAAAAAC
43974485 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
43974522 GTGTTAGTTA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:43977113 original size:29 final size:29
Alignment explanation
Indices: 43977067--43977126 Score: 102
Period size: 29 Copynumber: 2.1 Consensus size: 29
43977057 GCTAACATGA
*
43977067 TTTATTTCTATATGTTACGTATACCCTTT
1 TTTATTTCTATATATTACGTATACCCTTT
*
43977096 TTTATTTCTATATATTACGTATATCCTTT
1 TTTATTTCTATATATTACGTATACCCTTT
43977125 TT
1 TT
43977127 CAATAGAACT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.22, C:0.15, G:0.05, T:0.58
Consensus pattern (29 bp):
TTTATTTCTATATATTACGTATACCCTTT
Found at i:43977785 original size:159 final size:158
Alignment explanation
Indices: 43977236--43977814 Score: 849
Period size: 152 Copynumber: 3.6 Consensus size: 158
43977226 CTATAACTTC
*
43977236 AAAACAAATTTAGTAAAAAACCCTTATTTTGGCCCTTTGTTCGTATTTCGTATTTTTCTTTTTTC
1 AAAATAAATTTAGTAAAAAACCCTTATTTTGGCCC--T-TT-G---TTCGTATTTTTCTTTTTT-
43977301 CCAGATTTTATTACTTTCAAAAAATATACTATTTTCGTATTTTATTATTTTATATTATTTTAGTA
58 CCAGATTTTATTACTTTCAAAAAATATACTATTTTCGT-TTTTATTATTTTATATTATTTTAGTA
43977366 CATTATGTTTGAAATGTATTAATTTA--GTGTTTTTT
122 CATTATGTTTGAAATGTATTAATTTAGTGTGTTTTTT
* *
43977401 AATATAAATTTAGTAAAAAACCCTTCTTTTGGCCCTTTGTTCGTATTTTTCTTTTTTCCCA-AGT
1 AAAATAAATTTAGTAAAAAACCCTTATTTTGGCCCTTTGTTCGTATTTTTCTTTTTT-CCAGA-T
*
43977465 TTTATTACTTTCAAAAAATATACTATTTTC-------TTATTTTATATTAATTTTAGTACATAAT
64 TTTATTACTTTCAAAAAATATACTATTTTCGTTTTTATTATTTTATATT-ATTTTAGTACATTAT
43977523 GTTTGAAATGTATTAATTTAGTGTGTTTTTT
128 GTTTGAAATGTATTAATTTAGTGTGTTTTTT
* * *
43977554 -ATATAAATTTAGTAAAAAACCCTTATTTTGGCCCTTTGTTCTTATTTTTCTTTTTTCTCAAATT
1 AAAATAAATTTAGTAAAAAACCCTTATTTTGGCCCTTTGTTCGTATTTTTCTTTTTTC-CAGATT
43977618 TTATTACTTTCAAAAAATATACTATTTTCGTGTTTTATTATTTTATATTATTTTAGTACATTATG
65 TTATTACTTTCAAAAAATATACTATTTTCGT-TTTTATTATTTTATATTATTTTAGTACATTATG
*
43977683 TTTGAAATGTATTATTTTAGTGTGTTTTTT
129 TTTGAAATGTATTAATTTAGTGTGTTTTTT
43977713 AAAATAAATTTAGTAAAAAACCCTTATTTTGGCCCTTTGTTCGTATTTTTCTTATTTT-CAGATT
1 AAAATAAATTTAGTAAAAAACCCTTATTTTGGCCCTTTGTTCGTATTTTTCTT-TTTTCCAGATT
**
43977777 TTATTACTTTCAGTAAATATACTATTTTCGTTTTTATT
65 TTATTACTTTCAAAAAATATACTATTTTCGTTTTTATT
43977815 TCTTTTCGTA
Statistics
Matches: 385, Mismatches: 13, Indels: 39
0.88 0.03 0.09
Matches are distributed among these distances:
150 12 0.03
151 35 0.09
152 87 0.23
153 10 0.03
157 1 0.00
158 60 0.16
159 78 0.20
160 62 0.16
161 5 0.01
162 2 0.01
163 1 0.00
165 32 0.08
ACGTcount: A:0.28, C:0.11, G:0.08, T:0.53
Consensus pattern (158 bp):
AAAATAAATTTAGTAAAAAACCCTTATTTTGGCCCTTTGTTCGTATTTTTCTTTTTTCCAGATTT
TATTACTTTCAAAAAATATACTATTTTCGTTTTTATTATTTTATATTATTTTAGTACATTATGTT
TGAAATGTATTAATTTAGTGTGTTTTTT
Found at i:43977822 original size:16 final size:17
Alignment explanation
Indices: 43977801--43977832 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
43977791 AAATATACTA
43977801 TTTTCGT-TTTTATTTC
1 TTTTCGTATTTTATTTC
43977817 TTTTCGTATTTTATTT
1 TTTTCGTATTTTATTT
43977833 TTTCATAAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.09, C:0.09, G:0.06, T:0.75
Consensus pattern (17 bp):
TTTTCGTATTTTATTTC
Found at i:43977991 original size:19 final size:20
Alignment explanation
Indices: 43977967--43978005 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
43977957 TTTTTTACAC
43977967 AAATAATA-CAAAAAAATTA
1 AAATAATACCAAAAAAATTA
43977986 AAATAATACCAAAAAAATTA
1 AAATAATACCAAAAAAATTA
43978006 CCTTTCCTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 8 0.42
20 11 0.58
ACGTcount: A:0.72, C:0.08, G:0.00, T:0.21
Consensus pattern (20 bp):
AAATAATACCAAAAAAATTA
Found at i:43978062 original size:6 final size:6
Alignment explanation
Indices: 43978045--43978136 Score: 51
Period size: 6 Copynumber: 14.5 Consensus size: 6
43978035 TTTCCTCCCT
* * * * *
43978045 CTTCTT CTTCTC CTTCTC TTTCTC TTTTTC CTGTGCCTC CTTCTC CTTCTT
1 CTTCTC CTTCTC CTTCTC CTTCTC CTTCTC CT-T--CTC CTTCTC CTTCTC
* * *
43978096 CTTCTT CTTCTT CTTCTT CTTCCTC TTCTTCTC CTT-TC CTT
1 CTTCTC CTTCTC CTTCTC CTT-CTC --CTTCTC CTTCTC CTT
43978137 TTCTTTCTTT
Statistics
Matches: 73, Mismatches: 7, Indels: 13
0.78 0.08 0.14
Matches are distributed among these distances:
5 5 0.07
6 54 0.74
7 3 0.04
8 4 0.05
9 7 0.10
ACGTcount: A:0.00, C:0.39, G:0.02, T:0.59
Consensus pattern (6 bp):
CTTCTC
Found at i:43978096 original size:9 final size:9
Alignment explanation
Indices: 43978084--43978131 Score: 51
Period size: 9 Copynumber: 5.0 Consensus size: 9
43978074 CCTGTGCCTC
43978084 CTTCTCCTT
1 CTTCTCCTT
*
43978093 CTTCTTCTT
1 CTTCTCCTT
*
43978102 CTTCTTCTT
1 CTTCTCCTT
43978111 CTTCTTCCTCTT
1 CTTC-T-C-CTT
43978123 CTTCTCCTT
1 CTTCTCCTT
43978132 TCCTTTTCTT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
9 24 0.71
10 2 0.06
11 1 0.03
12 7 0.21
ACGTcount: A:0.00, C:0.40, G:0.00, T:0.60
Consensus pattern (9 bp):
CTTCTCCTT
Found at i:43978148 original size:10 final size:10
Alignment explanation
Indices: 43978129--43978205 Score: 82
Period size: 10 Copynumber: 7.7 Consensus size: 10
43978119 TCTTCTTCTC
*
43978129 CTTTCCTTTT
1 CTTTCTTTTT
43978139 CTTTCTTTTT
1 CTTTCTTTTT
* *
43978149 CTTTCTTCTC
1 CTTTCTTTTT
*
43978159 CTTTCCTTTT
1 CTTTCTTTTT
43978169 CTTTCTTTTT
1 CTTTCTTTTT
* *
43978179 CTTTCTTCTC
1 CTTTCTTTTT
*
43978189 CTTTCCTTTT
1 CTTTCTTTTT
*
43978199 CTATCTT
1 CTTTCTT
43978206 CTCCTTCAGC
Statistics
Matches: 53, Mismatches: 14, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
10 53 1.00
ACGTcount: A:0.01, C:0.30, G:0.00, T:0.69
Consensus pattern (10 bp):
CTTTCTTTTT
Found at i:43978155 original size:30 final size:30
Alignment explanation
Indices: 43978121--43978205 Score: 161
Period size: 30 Copynumber: 2.8 Consensus size: 30
43978111 CTTCTTCCTC
43978121 TTCTTCTCCTTTCCTTTTCTTTCTTTTTCT
1 TTCTTCTCCTTTCCTTTTCTTTCTTTTTCT
43978151 TTCTTCTCCTTTCCTTTTCTTTCTTTTTCT
1 TTCTTCTCCTTTCCTTTTCTTTCTTTTTCT
*
43978181 TTCTTCTCCTTTCCTTTTCTATCTT
1 TTCTTCTCCTTTCCTTTTCTTTCTT
43978206 CTCCTTCAGC
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
30 54 1.00
ACGTcount: A:0.01, C:0.31, G:0.00, T:0.68
Consensus pattern (30 bp):
TTCTTCTCCTTTCCTTTTCTTTCTTTTTCT
Found at i:43978206 original size:20 final size:20
Alignment explanation
Indices: 43978081--43978211 Score: 97
Period size: 20 Copynumber: 6.3 Consensus size: 20
43978071 TTTCCTGTGC
43978081 CTCCTTCTCCTTCTTC-TTCTT
1 CTCCTT-TCCTT-TTCTTTCTT
* *
43978102 CTTCTTCTTCTTCTTCCTCTTCTT
1 CTCCTT-TCCTT-TT-CT-TTCTT
43978126 CTCCTTTCCTTTTCTTTCTT
1 CTCCTTTCCTTTTCTTTCTT
* * *
43978146 TTTCTTT-CTTCTCCTTTCCTT
1 CTCCTTTCCTT-TTCTTT-CTT
* *
43978167 -TTCTTTCTTTTTCTTTCTT
1 CTCCTTTCCTTTTCTTTCTT
*
43978186 CTCCTTTCCTTTTCTATCTT
1 CTCCTTTCCTTTTCTTTCTT
43978206 CTCCTT
1 CTCCTT
43978212 CAGCCGAATC
Statistics
Matches: 91, Mismatches: 12, Indels: 15
0.77 0.10 0.13
Matches are distributed among these distances:
19 6 0.07
20 48 0.53
21 20 0.22
22 3 0.03
23 4 0.04
24 10 0.11
ACGTcount: A:0.01, C:0.35, G:0.00, T:0.64
Consensus pattern (20 bp):
CTCCTTTCCTTTTCTTTCTT
Found at i:43981465 original size:33 final size:33
Alignment explanation
Indices: 43981428--43981530 Score: 81
Period size: 33 Copynumber: 3.2 Consensus size: 33
43981418 TCCTCTTCTG
43981428 TTAAGATATTGAAATAGAACTTAAAAAATATAT
1 TTAAGATATTGAAATAGAACTTAAAAAATATAT
* * * * *
43981461 TTAAGTTAATT-AAGA-AGTCAC-GACAAATTAT-T
1 TTAAGAT-ATTGAA-ATAG-AACTTAAAAAATATAT
*
43981493 TCTCA-ATATTGAAATAGAACTTAAAAAATATAT
1 T-TAAGATATTGAAATAGAACTTAAAAAATATAT
43981526 TTAAG
1 TTAAG
43981531 TTAATAATAA
Statistics
Matches: 49, Mismatches: 12, Indels: 18
0.62 0.15 0.23
Matches are distributed among these distances:
31 6 0.12
32 16 0.33
33 21 0.43
34 6 0.12
ACGTcount: A:0.50, C:0.07, G:0.10, T:0.34
Consensus pattern (33 bp):
TTAAGATATTGAAATAGAACTTAAAAAATATAT
Found at i:43981786 original size:45 final size:44
Alignment explanation
Indices: 43981695--43981786 Score: 112
Period size: 45 Copynumber: 2.1 Consensus size: 44
43981685 ACCTTTATTC
* * *
43981695 CATTCAACCAAACACAAGATTACTATTACGCCTCTATTCCATTA
1 CATTCAACCAAACACAAGATTACTATTACACCTCTAATCCAATA
*** *
43981739 CATTCAACCAAACAGTTGATTTGCTATTACACCTCTAATCCAATA
1 CATTCAACCAAACACAAGA-TTACTATTACACCTCTAATCCAATA
43981784 CAT
1 CAT
43981787 CTCTAATCCA
Statistics
Matches: 40, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
44 16 0.40
45 24 0.60
ACGTcount: A:0.36, C:0.28, G:0.05, T:0.30
Consensus pattern (44 bp):
CATTCAACCAAACACAAGATTACTATTACACCTCTAATCCAATA
Found at i:43981790 original size:16 final size:16
Alignment explanation
Indices: 43981766--43981801 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
43981756 GATTTGCTAT
43981766 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
*
43981782 TACATCTCTAATCCAA
1 TACACCTCTAATCCAA
43981798 TACA
1 TACA
43981802 GCGAACCAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.39, C:0.33, G:0.00, T:0.28
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:43987639 original size:16 final size:16
Alignment explanation
Indices: 43987618--43987648 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
43987608 GAAGAACTTC
43987618 TATTTTTATAAGATTA
1 TATTTTTATAAGATTA
*
43987634 TATTTTTATGAGATT
1 TATTTTTATAAGATT
43987649 TCTATGAAGT
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:0.32, C:0.00, G:0.10, T:0.58
Consensus pattern (16 bp):
TATTTTTATAAGATTA
Found at i:43997336 original size:29 final size:29
Alignment explanation
Indices: 43997294--43997489 Score: 209
Period size: 29 Copynumber: 6.8 Consensus size: 29
43997284 GTGCTAAACA
* * *
43997294 ATGGTTGTAACCATCCCTTTCCAAATTCG
1 ATGGTCGTCACCATCCCTTTTCAAATTCG
*
43997323 ATGGTCGTCACCAT-CCTTTTCATATTCG
1 ATGGTCGTCACCATCCCTTTTCAAATTCG
* *
43997351 ATGGTCGTCACCATCCATTTTCATATTCG
1 ATGGTCGTCACCATCCCTTTTCAAATTCG
* *
43997380 ATGGTCGTAACCATCCCTTTTCATCAA-TCA
1 ATGGTCGTCACCATCCCTTTTCA--AATTCG
*
43997410 ATGGTCGTCACCATCCCTTTTCATAGTT-G
1 ATGGTCGTCACCATCCCTTTTCA-AATTCG
* *
43997439 ATGGTCGTCACCATCCCTTTTCATAGTCG
1 ATGGTCGTCACCATCCCTTTTCAAATTCG
* ** *
43997468 ATAGTCGAAACTATCCCTTTTC
1 ATGGTCGTCACCATCCCTTTTC
43997490 TTTAATCGAT
Statistics
Matches: 142, Mismatches: 20, Indels: 10
0.83 0.12 0.06
Matches are distributed among these distances:
28 27 0.19
29 89 0.63
30 25 0.18
31 1 0.01
ACGTcount: A:0.21, C:0.29, G:0.14, T:0.36
Consensus pattern (29 bp):
ATGGTCGTCACCATCCCTTTTCAAATTCG
Found at i:43997431 original size:59 final size:58
Alignment explanation
Indices: 43997292--43997463 Score: 240
Period size: 59 Copynumber: 3.0 Consensus size: 58
43997282 GTGTGCTAAA
* * * * *
43997292 CAATGGTTGTAACCATCCCTTTCCAAATTCGATGGTCGTCACCAT-CCTTTTCATATT
1 CAATGGTCGTCACCATCCCTTTTCATATTCGATGGTCGTCACCATCCCTTTTCATAAT
* * *
43997349 CGATGGTCGTCACCATCCATTTTCATATTCGATGGTCGTAACCATCCCTTTTCATCAAT
1 CAATGGTCGTCACCATCCCTTTTCATATTCGATGGTCGTCACCATCCCTTTTCAT-AAT
43997408 CAATGGTCGTCACCATCCCTTTTCATAGTT-GATGGTCGTCACCATCCCTTTTCATA
1 CAATGGTCGTCACCATCCCTTTTCATA-TTCGATGGTCGTCACCATCCCTTTTCATA
43997464 GTCGATAGTC
Statistics
Matches: 101, Mismatches: 11, Indels: 5
0.86 0.09 0.04
Matches are distributed among these distances:
57 38 0.38
58 10 0.10
59 51 0.50
60 2 0.02
ACGTcount: A:0.22, C:0.29, G:0.13, T:0.36
Consensus pattern (58 bp):
CAATGGTCGTCACCATCCCTTTTCATATTCGATGGTCGTCACCATCCCTTTTCATAAT
Found at i:43997446 original size:88 final size:86
Alignment explanation
Indices: 43997294--43997489 Score: 270
Period size: 88 Copynumber: 2.3 Consensus size: 86
43997284 GTGCTAAACA
* * *
43997294 ATGGTTGTAACCATCCCTTTCCAAATTCGATGGTCGTCACCATCCTTTTCATATTCGATGGTCGT
1 ATGGTCGTAACCATCCCTTTTCAAATTCAATGGTCGTCACCATCCTTTTCATATTCGATGGTCGT
*
43997359 CACCATCCATTTTCATATTCG
66 CACCATCCATTTTCATAGTCG
43997380 ATGGTCGTAACCATCCCTTTTCATCAA-TCAATGGTCGTCACCATCCCTTTTCATAGTT-GATGG
1 ATGGTCGTAACCATCCCTTTTCA--AATTCAATGGTCGTCACCAT-CCTTTTCATA-TTCGATGG
*
43997443 TCGTCACCATCCCTTTTCATAGTCG
62 TCGTCACCATCCATTTTCATAGTCG
* * *
43997468 ATAGTCGAAACTATCCCTTTTC
1 ATGGTCGTAACCATCCCTTTTC
43997490 TTTAATCGAT
Statistics
Matches: 98, Mismatches: 8, Indels: 6
0.88 0.07 0.05
Matches are distributed among these distances:
86 21 0.21
87 16 0.16
88 59 0.60
89 2 0.02
ACGTcount: A:0.21, C:0.29, G:0.14, T:0.36
Consensus pattern (86 bp):
ATGGTCGTAACCATCCCTTTTCAAATTCAATGGTCGTCACCATCCTTTTCATATTCGATGGTCGT
CACCATCCATTTTCATAGTCG
Found at i:44000716 original size:27 final size:26
Alignment explanation
Indices: 44000697--44000775 Score: 104
Period size: 27 Copynumber: 3.0 Consensus size: 26
44000687 GGGTATAACA
*
44000697 GTCACTTTACCCTATGGGGGTATTTC
1 GTCATTTTACCCTATGGGGGTATTTC
* *
44000723 GATCATTTTAACCTATGGGGGTATTTTG
1 G-TCATTTTACCCTATGGGGGTA-TTTC
*
44000751 GTCATTTTACCCTATGGGGGCATTT
1 GTCATTTTACCCTATGGGGGTATTT
44000776 ATATCATATA
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
26 4 0.09
27 38 0.83
28 4 0.09
ACGTcount: A:0.18, C:0.18, G:0.24, T:0.41
Consensus pattern (26 bp):
GTCATTTTACCCTATGGGGGTATTTC
Found at i:44005267 original size:29 final size:29
Alignment explanation
Indices: 44005232--44005451 Score: 201
Period size: 29 Copynumber: 7.6 Consensus size: 29
44005222 GAAGGTCGTA
44005232 ACCATCCCTTTTCATATTTGATGGTCATC
1 ACCATCCCTTTTCATATTTGATGGTCATC
* * *
44005261 ACCATCCATTTTCATATTCGATGGTCGTC
1 ACCATCCCTTTTCATATTTGATGGTCATC
* * *
44005290 ACCATCCTTTTTCATATTTGATAGTCTTC
1 ACCATCCCTTTTCATATTTGATGGTCATC
* * * * **
44005319 ACCATCCCTTTTCATCAATCGGTAGTTGTC
1 ACCATCCCTTTTCAT-ATTTGATGGTCATC
* * * * *
44005349 ACCATCGCTTTTCATAGTTGATAGACGA-A
1 ACCATCCCTTTTCATATTTGATGGTC-ATC
* * *
44005378 ACTATCTCTTTTCATATATGATGGT-AGTC
1 ACCATCCCTTTTCATATTTGATGGTCA-TC
*
44005407 ACCATCCCTTTTCATAGTTGATGGTCATC
1 ACCATCCCTTTTCATATTTGATGGTCATC
*
44005436 ACCATCCCCTTTCATA
1 ACCATCCCTTTTCATA
44005452 GTCGATAGTC
Statistics
Matches: 153, Mismatches: 33, Indels: 10
0.78 0.17 0.05
Matches are distributed among these distances:
27 1 0.01
29 128 0.84
30 24 0.16
ACGTcount: A:0.23, C:0.26, G:0.12, T:0.39
Consensus pattern (29 bp):
ACCATCCCTTTTCATATTTGATGGTCATC
Found at i:44005321 original size:58 final size:58
Alignment explanation
Indices: 44005225--44005477 Score: 249
Period size: 58 Copynumber: 4.3 Consensus size: 58
44005215 GTTAAACGAA
* * * *
44005225 GGTCGTAACCATCCCTTTTCATATTTGATGGTCATCACCATCCATTTTCATATTCGAT
1 GGTCGTCACCATCCCTTTTCATAGTTGATAGTCATCACCATCCCTTTTCATATTCGAT
* * * * *
44005283 GGTCGTCACCATCCTTTTTCATATTTGATAGTCTTCACCATCCCTTTTCATCAATCGGT
1 GGTCGTCACCATCCCTTTTCATAGTTGATAGTCATCACCATCCCTTTTCAT-ATTCGAT
* * * * * * *
44005342 AGTTGTCACCATCGCTTTTCATAGTTGATAGACGA-AACTATCTCTTTTCATATAT-GAT
1 GGTCGTCACCATCCCTTTTCATAGTTGATAGTC-ATCACCATCCCTTTTCATAT-TCGAT
* * * *
44005400 GGTAGTCACCATCCCTTTTCATAGTTGATGGTCATCACCATCCCCTTTCATAGTCGAT
1 GGTCGTCACCATCCCTTTTCATAGTTGATAGTCATCACCATCCCTTTTCATATTCGAT
* ** *
44005458 AGTCGAAACTATCCCTTTTC
1 GGTCGTCACCATCCCTTTTC
44005478 TTTAATCGAT
Statistics
Matches: 156, Mismatches: 34, Indels: 10
0.78 0.17 0.05
Matches are distributed among these distances:
57 2 0.01
58 108 0.69
59 46 0.29
ACGTcount: A:0.23, C:0.26, G:0.13, T:0.38
Consensus pattern (58 bp):
GGTCGTCACCATCCCTTTTCATAGTTGATAGTCATCACCATCCCTTTTCATATTCGAT
Found at i:44005718 original size:23 final size:23
Alignment explanation
Indices: 44005690--44005733 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
44005680 AATTAATAAG
44005690 TTTATTCAATATATTAATTTAAC
1 TTTATTCAATATATTAATTTAAC
*
44005713 TTTATTCAATCTATTAATTTA
1 TTTATTCAATATATTAATTTA
44005734 GATATTAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.36, C:0.09, G:0.00, T:0.55
Consensus pattern (23 bp):
TTTATTCAATATATTAATTTAAC
Found at i:44008954 original size:51 final size:51
Alignment explanation
Indices: 44008892--44009032 Score: 178
Period size: 50 Copynumber: 2.8 Consensus size: 51
44008882 AAATGATACT
* * * *
44008892 CGGTTCACATAGTAGCCTGCACATAGTACTACACACGTGATCGAAGCTATT-
1 CGGTACACATAGTAGCCTGCACATAGTACTACACATGTGAGCCAAGC-ATTC
* * * *
44008943 CGGTACGCATAGTAGCCTGCACATAGTACTACACATGCG-GCCTATCATTC
1 CGGTACACATAGTAGCCTGCACATAGTACTACACATGTGAGCCAAGCATTC
*
44008993 CGGTACACGTAGTAGCCTGCACATAGTACTACACATGTGA
1 CGGTACACATAGTAGCCTGCACATAGTACTACACATGTGA
44009033 CCTAGCAACT
Statistics
Matches: 77, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
49 3 0.04
50 39 0.51
51 35 0.45
ACGTcount: A:0.28, C:0.27, G:0.21, T:0.24
Consensus pattern (51 bp):
CGGTACACATAGTAGCCTGCACATAGTACTACACATGTGAGCCAAGCATTC
Found at i:44011825 original size:42 final size:42
Alignment explanation
Indices: 44011745--44011826 Score: 112
Period size: 42 Copynumber: 2.0 Consensus size: 42
44011735 CGTTTTCTCT
* **
44011745 ATGCCATAGTCCAACTATGGTCTTACACATATTTACATATTG
1 ATGCCATAGCCCAACTATGGTCTTACACATATGCACATATTG
*
44011787 ATGCCATAGCCCAGCTATGGTCTTACACAGTA-GCACATAT
1 ATGCCATAGCCCAACTATGGTCTTACACA-TATGCACATAT
44011827 CACACCGATG
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
42 33 0.94
43 2 0.06
ACGTcount: A:0.30, C:0.24, G:0.15, T:0.30
Consensus pattern (42 bp):
ATGCCATAGCCCAACTATGGTCTTACACATATGCACATATTG
Found at i:44013214 original size:43 final size:43
Alignment explanation
Indices: 44013158--44013513 Score: 383
Period size: 43 Copynumber: 8.3 Consensus size: 43
44013148 TTTAGAAAAG
* *
44013158 AACGCCACTAAAGACCAAGACCTTTAGCAGCGCTTTTCCCACA
1 AACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCCCACA
* * *** *
44013201 AACGTCGCTAAAGAACAAGACCTTTAGATTCGCTTTACCCACA
1 AACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCCCACA
* * *
44013244 AACGCCGCTAAAAACCAAGACCTTTAGCGGCGCTTTACACACA
1 AACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCCCACA
44013287 AACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCCCA-A
1 AACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCCCACA
* * * **
44013329 GAATGTCGCTATAGACCTTGACCTTTAGCGGCGCTTTTCCCACA
1 -AACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCCCACA
* * * * * *
44013373 AACGCCGCTAAAGACTATGACCTTTACCGACACTTTTTCCACA
1 AACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCCCACA
* ** * * **
44013416 AACGCTGCTAAAGATTATGAACTTTTAGCGGCGCTTTTATCACA
1 AACGCCGCTAAAGACCAAG-ACCTTTAGCGGCGCTTTTCCCACA
* * * *
44013460 AACGCCGCTAAAGAACAA-ACCTTTAGCGGCGCTTCTCACAAA
1 AACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCCCACA
44013502 AACGCCGCTAAA
1 AACGCCGCTAAA
44013514 AATATAACCT
Statistics
Matches: 262, Mismatches: 48, Indels: 7
0.83 0.15 0.02
Matches are distributed among these distances:
42 32 0.12
43 197 0.75
44 33 0.13
ACGTcount: A:0.31, C:0.30, G:0.16, T:0.22
Consensus pattern (43 bp):
AACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCCCACA
Found at i:44016149 original size:21 final size:21
Alignment explanation
Indices: 44016123--44016168 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
44016113 TCTTGGATGT
44016123 GGGAAA-TTAGGGATTTTAGGG
1 GGGAAAGTTAGGGA-TTTAGGG
* *
44016144 GGGAAAGTTGGGGATTTCGGG
1 GGGAAAGTTAGGGATTTAGGG
44016165 GGGA
1 GGGA
44016169 GGGGGGAGGG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 16 0.73
22 6 0.27
ACGTcount: A:0.24, C:0.02, G:0.50, T:0.24
Consensus pattern (21 bp):
GGGAAAGTTAGGGATTTAGGG
Found at i:44017425 original size:33 final size:33
Alignment explanation
Indices: 44017353--44017425 Score: 101
Period size: 33 Copynumber: 2.2 Consensus size: 33
44017343 TAATCTAAAT
* * *
44017353 CCTAAACCCTAACTCGACCCTAAATCCCTAATC
1 CCTAAACCCTAACCCGACCCTAAATCCATAACC
* *
44017386 CTTAAACCCTAACCCGACCCTGAATCCATAACC
1 CCTAAACCCTAACCCGACCCTAAATCCATAACC
44017419 CCTAAAC
1 CCTAAAC
44017426 ATTATTTAAT
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.34, C:0.42, G:0.04, T:0.19
Consensus pattern (33 bp):
CCTAAACCCTAACCCGACCCTAAATCCATAACC
Found at i:44018291 original size:41 final size:41
Alignment explanation
Indices: 44018232--44018555 Score: 450
Period size: 41 Copynumber: 7.9 Consensus size: 41
44018222 TTTTATTATT
* * * *
44018232 ATTAGCGGCGCTCTTTCAAAAACGCAGCTAAAGGCCTGATC
1 ATTAGCGGCGCTTTTTCAAAAACGCCGCTAAAGGCCCGAGC
* *
44018273 ATTAGCGGCGCTTATTCAAAAACGCTGCTAAAGGCCCGAGC
1 ATTAGCGGCGCTTTTTCAAAAACGCCGCTAAAGGCCCGAGC
* * * *
44018314 ATTAGCGGCGCTTATTCAAAAACGCTGCTAAAGGCCCAAGA
1 ATTAGCGGCGCTTTTTCAAAAACGCCGCTAAAGGCCCGAGC
* * *
44018355 ATTAGCGGCTCTTATTCAAAAACGCCGCTAAAGGCACGAGC
1 ATTAGCGGCGCTTTTTCAAAAACGCCGCTAAAGGCCCGAGC
* *
44018396 ATTAGTGGCGCTTTTTCAAAAACGCCGCTAAAGGCCCAAGC
1 ATTAGCGGCGCTTTTTCAAAAACGCCGCTAAAGGCCCGAGC
*
44018437 ATTAGCGGCACTTTTTCAAAAACGCCGCTAAAGGCCCGAGC
1 ATTAGCGGCGCTTTTTCAAAAACGCCGCTAAAGGCCCGAGC
* * * *
44018478 ATTAACAGCGCTTTTTCAAAATCACCGCTAAAGGCCCGAGC
1 ATTAGCGGCGCTTTTTCAAAAACGCCGCTAAAGGCCCGAGC
* *
44018519 ATTAGCGGCGCTTTTTCAAAAATGCCGCTAAATGCCC
1 ATTAGCGGCGCTTTTTCAAAAACGCCGCTAAAGGCCC
44018556 CAAAAACTCA
Statistics
Matches: 252, Mismatches: 31, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 252 1.00
ACGTcount: A:0.30, C:0.27, G:0.21, T:0.21
Consensus pattern (41 bp):
ATTAGCGGCGCTTTTTCAAAAACGCCGCTAAAGGCCCGAGC
Found at i:44018725 original size:40 final size:39
Alignment explanation
Indices: 44018591--44018725 Score: 148
Period size: 40 Copynumber: 3.4 Consensus size: 39
44018581 GGGCTTAGGC
* *
44018591 TTTTT-GCGGCGCTTTTAAAAAAACGCCGCTAATGCTT-A
1 TTTTTAGCGGCG-TTTTTAAAAAGCGCCGCTAATGCTTGA
* *
44018629 TTTTTAGCGGCGTTTTCCAAAAAGCGCCGCTAATGCTCGA
1 TTTTTAGCGGCGTTTT-TAAAAAGCGCCGCTAATGCTTGA
** * *
44018669 CCTTTAGCGGTGTTTTTATAGAAGCGCCGCTAATGCTTGA
1 TTTTTAGCGGCGTTTTTA-AAAAGCGCCGCTAATGCTTGA
*
44018709 TTTTTAGTGGCGTTTTT
1 TTTTTAGCGGCGTTTTT
44018726 TGTCCAAATG
Statistics
Matches: 80, Mismatches: 13, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
38 9 0.11
39 25 0.31
40 46 0.57
ACGTcount: A:0.21, C:0.20, G:0.22, T:0.37
Consensus pattern (39 bp):
TTTTTAGCGGCGTTTTTAAAAAGCGCCGCTAATGCTTGA
Found at i:44025534 original size:25 final size:24
Alignment explanation
Indices: 44025506--44025576 Score: 72
Period size: 25 Copynumber: 2.8 Consensus size: 24
44025496 ATCGATTGCG
*
44025506 GCTCTTGAGAGCTTACTGATTCTCA
1 GCTCTT-AGAGCTTACCGATTCTCA
44025531 GCTCGTATA-AGCTTACCGATTCTCA
1 GCTC-T-TAGAGCTTACCGATTCTCA
* *
44025556 ACTCATATGAGCTTACCGATT
1 GCTCTTA-GAGCTTACCGATT
44025577 TACAGCCCGT
Statistics
Matches: 39, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
23 2 0.05
25 34 0.87
26 2 0.05
27 1 0.03
ACGTcount: A:0.24, C:0.25, G:0.17, T:0.34
Consensus pattern (24 bp):
GCTCTTAGAGCTTACCGATTCTCA
Found at i:44025617 original size:25 final size:25
Alignment explanation
Indices: 44025529--44025621 Score: 73
Period size: 25 Copynumber: 3.7 Consensus size: 25
44025519 TACTGATTCT
* * *
44025529 CAGCTCGTATAAGCTTACCGATTCT-
1 CAGCTCATATGAGCATACCGATT-TA
* *
44025554 CAACTCATATGAGCTTACCGATTTA
1 CAGCTCATATGAGCATACCGATTTA
* * *
44025579 CAGCCCGTGA-GAGCATACTGATTTA
1 CAGCTCAT-ATGAGCATACCGATTTA
*
44025604 TAGCTCATATGAGCATAC
1 CAGCTCATATGAGCATAC
44025622 ATGTATAGGA
Statistics
Matches: 54, Mismatches: 11, Indels: 6
0.76 0.15 0.08
Matches are distributed among these distances:
24 2 0.04
25 51 0.94
26 1 0.02
ACGTcount: A:0.29, C:0.25, G:0.17, T:0.29
Consensus pattern (25 bp):
CAGCTCATATGAGCATACCGATTTA
Found at i:44026754 original size:15 final size:16
Alignment explanation
Indices: 44026734--44026763 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
44026724 TGGTGCCTTG
44026734 TTGAT-ATGTGTTAAT
1 TTGATAATGTGTTAAT
44026749 TTGATAATGTGTTAA
1 TTGATAATGTGTTAA
44026764 AGTATGCTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.30, C:0.00, G:0.20, T:0.50
Consensus pattern (16 bp):
TTGATAATGTGTTAAT
Found at i:44034896 original size:11 final size:11
Alignment explanation
Indices: 44034880--44034904 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
44034870 TGTAGAGTGA
44034880 TGTGAGCGATG
1 TGTGAGCGATG
44034891 TGTGAGCGATG
1 TGTGAGCGATG
44034902 TGT
1 TGT
44034905 TCTCGAAGGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.16, C:0.08, G:0.44, T:0.32
Consensus pattern (11 bp):
TGTGAGCGATG
Found at i:44034967 original size:11 final size:11
Alignment explanation
Indices: 44034943--44035001 Score: 95
Period size: 11 Copynumber: 5.5 Consensus size: 11
44034933 TTTTTAAGTA
44034943 GTGAGCGA--T
1 GTGAGCGATGT
44034952 GTGAGCGATGT
1 GTGAGCGATGT
44034963 GTGAGCGATGT
1 GTGAGCGATGT
*
44034974 GTGACCGATGT
1 GTGAGCGATGT
44034985 GTGAGCGATGT
1 GTGAGCGATGT
44034996 GTGAGC
1 GTGAGC
44035002 TCACCCATTC
Statistics
Matches: 46, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
9 8 0.17
11 38 0.83
ACGTcount: A:0.19, C:0.12, G:0.44, T:0.25
Consensus pattern (11 bp):
GTGAGCGATGT
Found at i:44040333 original size:48 final size:48
Alignment explanation
Indices: 44040262--44040362 Score: 184
Period size: 48 Copynumber: 2.1 Consensus size: 48
44040252 TGTAAGGAGC
*
44040262 AATTGATATCGACGATGTTCCCGGTACTAACTCAATGGTAGCCTCTCT
1 AATTGATATCGACGATGTTCCCGGTACTAACTCAATGGCAGCCTCTCT
*
44040310 AATTGATATCGATGATGTTCCCGGTACTAACTCAATGGCAGCCTCTCT
1 AATTGATATCGACGATGTTCCCGGTACTAACTCAATGGCAGCCTCTCT
44040358 AATTG
1 AATTG
44040363 GCGGTAACCC
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
48 51 1.00
ACGTcount: A:0.26, C:0.24, G:0.19, T:0.32
Consensus pattern (48 bp):
AATTGATATCGACGATGTTCCCGGTACTAACTCAATGGCAGCCTCTCT
Found at i:44041872 original size:20 final size:20
Alignment explanation
Indices: 44041847--44041894 Score: 71
Period size: 20 Copynumber: 2.4 Consensus size: 20
44041837 TCCATGTGGT
44041847 TCAGCTCAC-TCGAGCTCAAG
1 TCAGCTCACAT-GAGCTCAAG
*
44041867 TCAGCTCACATGAGCTCAAT
1 TCAGCTCACATGAGCTCAAG
44041887 TCAGCTCA
1 TCAGCTCA
44041895 TTGAGCTCGT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
20 25 0.96
21 1 0.04
ACGTcount: A:0.27, C:0.33, G:0.17, T:0.23
Consensus pattern (20 bp):
TCAGCTCACATGAGCTCAAG
Found at i:44043591 original size:262 final size:262
Alignment explanation
Indices: 44043126--44043651 Score: 928
Period size: 262 Copynumber: 2.0 Consensus size: 262
44043116 CTCGTCGATG
* *
44043126 ATCGGGCAACTACGTGAAACGACTAGATCAACTCGGGCCAGTTCGCATCAAATACACTCCCTCAA
1 ATCGGGCAACTACATGAAACGACTAGATCAACCCGGGCCAGTTCGCATCAAATACACTCCCTCAA
*
44043191 CACAACTAAAACCAAATATGAATCTTTTAATAGAGATACGACACATTTTAAACACTCTGGCGATG
66 CACAACTAAAACCAAAGATGAATCTTTTAATAGAGATACGACACATTTTAAACACTCTGGCGATG
* * *
44043256 AACAAGATAACTCGTCGAAAACTATGATAGTATTTTTTAACTAGAATTCTCCTCGGATCATCATC
131 AACAAGATAACTCATCGAAAACTATAATAGTATTTTTTAACCAGAATTCTCCTCGGATCATCATC
*
44043321 AACTATAGCTCTAAATATTTCAGCTCCATATTTGTGAATTTTATCAACTGGCGGTTTATTAATTC
196 AACTATAGCTCTAAATATTTCAGCTCCATATTTGTGAATTTTATCAACTGGCAGTTTATTAATTC
44043386 GC
261 GC
*
44043388 ATCGGGCAACTACATGAAACGACTCA-ATCAACCCGGGCCAGTTGGCATCAAATACACTCCCTCA
1 ATCGGGCAACTACATGAAACGACT-AGATCAACCCGGGCCAGTTCGCATCAAATACACTCCCTCA
* *
44043452 ACACAACTAAAACCAAAGATGAATCTTTTAATAGAGATACGGCACATTTTACACACTCTGGCGAT
65 ACACAACTAAAACCAAAGATGAATCTTTTAATAGAGATACGACACATTTTAAACACTCTGGCGAT
* *
44043517 GAATAAGATAACTCATCGAAAACTCTAATAGTATTTTTTAACCAGAATTCTCCTCGGATCATCAT
130 GAACAAGATAACTCATCGAAAACTATAATAGTATTTTTTAACCAGAATTCTCCTCGGATCATCAT
44043582 CAACTATAGCTCTAAATATTTCAGCTCCATATTTGTGAATTTTATCAACTGGCAGTTTATTAATT
195 CAACTATAGCTCTAAATATTTCAGCTCCATATTTGTGAATTTTATCAACTGGCAGTTTATTAATT
44043647 CGC
260 CGC
44043650 AT
1 AT
44043652 TGGATCCAAA
Statistics
Matches: 251, Mismatches: 12, Indels: 2
0.95 0.05 0.01
Matches are distributed among these distances:
262 250 1.00
263 1 0.00
ACGTcount: A:0.35, C:0.23, G:0.14, T:0.29
Consensus pattern (262 bp):
ATCGGGCAACTACATGAAACGACTAGATCAACCCGGGCCAGTTCGCATCAAATACACTCCCTCAA
CACAACTAAAACCAAAGATGAATCTTTTAATAGAGATACGACACATTTTAAACACTCTGGCGATG
AACAAGATAACTCATCGAAAACTATAATAGTATTTTTTAACCAGAATTCTCCTCGGATCATCATC
AACTATAGCTCTAAATATTTCAGCTCCATATTTGTGAATTTTATCAACTGGCAGTTTATTAATTC
GC
Found at i:44045122 original size:15 final size:15
Alignment explanation
Indices: 44045090--44045127 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
44045080 TAAAGGACTT
44045090 AAGGATTAATGCATGA
1 AAGG-TTAATGCATGA
44045106 AAGGTTAATCGCA-GA
1 AAGGTTAAT-GCATGA
44045121 AAGGTTA
1 AAGGTTA
44045128 TGTCGAATCA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 14 0.67
16 7 0.33
ACGTcount: A:0.42, C:0.08, G:0.26, T:0.24
Consensus pattern (15 bp):
AAGGTTAATGCATGA
Found at i:44045994 original size:30 final size:30
Alignment explanation
Indices: 44045958--44046021 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 30
44045948 TTCCCAACAT
*
44045958 GTGTGACACACACAACTGAAACACACGACC
1 GTGTGACACACACAACTGAAACACACAACC
* ** *
44045988 GTGTGACTCACACGGCTGAGACACACAACC
1 GTGTGACACACACAACTGAAACACACAACC
44046018 GTGT
1 GTGT
44046022 CTTAAGCCGT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.33, C:0.31, G:0.22, T:0.14
Consensus pattern (30 bp):
GTGTGACACACACAACTGAAACACACAACC
Found at i:44047201 original size:29 final size:29
Alignment explanation
Indices: 44047158--44047325 Score: 171
Period size: 29 Copynumber: 5.8 Consensus size: 29
44047148 AGTGTGTTAA
* *
44047158 CGATGGTCGTAACCACCCCTTTTCATATT
1 CGATGGTCGTCACCATCCCTTTTCATATT
*
44047187 CGATGGTCGTCACCATCCCTTTTCATTAAT
1 CGATGGTCGTCACCATCCCTTTTCA-TATT
* *
44047217 CGATGATCGTCACTATCCCTTTTCATAGTT
1 CGATGGTCGTCACCATCCCTTTTCATA-TT
*
44047247 -GATGGTCATCACCATCCCTTTTCATAGTT
1 CGATGGTCGTCACCATCCCTTTTCATA-TT
* * *
44047276 -AATGGTC-TCACCATCCCTTTTTATAGT
1 CGATGGTCGTCACCATCCCTTTTCATATT
* ** *
44047303 CGATAGTCGAAACTATCCCTTTT
1 CGATGGTCGTCACCATCCCTTTT
44047326 AGCATTTAGT
Statistics
Matches: 118, Mismatches: 17, Indels: 8
0.83 0.12 0.06
Matches are distributed among these distances:
27 1 0.01
28 22 0.19
29 68 0.58
30 27 0.23
ACGTcount: A:0.21, C:0.28, G:0.13, T:0.38
Consensus pattern (29 bp):
CGATGGTCGTCACCATCCCTTTTCATATT
Found at i:44048683 original size:11 final size:11
Alignment explanation
Indices: 44048660--44048693 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
44048650 TTACTATTAT
44048660 TATAACTATATA
1 TATAAC-ATATA
44048672 TATAACATATA
1 TATAACATATA
*
44048683 TATAATATATA
1 TATAACATATA
44048694 CATACACATT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
11 15 0.71
12 6 0.29
ACGTcount: A:0.53, C:0.06, G:0.00, T:0.41
Consensus pattern (11 bp):
TATAACATATA
Found at i:44051280 original size:38 final size:40
Alignment explanation
Indices: 44051247--44051328 Score: 114
Period size: 39 Copynumber: 2.0 Consensus size: 40
44051237 TATAAAAAAC
44051247 TAAAATAAATAACA-ATAAAACA-ATTTAAAATAAATAATA
1 TAAAA-AAATAACATATAAAACAGATTTAAAATAAATAATA
* *
44051286 TAAAAAAATAACATATAAAACAGTTTTAAAATATATATATA
1 TAAAAAAATAACATATAAAACAGATTTAAAATAAATA-ATA
44051327 TA
1 TA
44051329 TATATAAAAT
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
38 8 0.21
39 13 0.34
40 12 0.32
41 5 0.13
ACGTcount: A:0.65, C:0.05, G:0.01, T:0.29
Consensus pattern (40 bp):
TAAAAAAATAACATATAAAACAGATTTAAAATAAATAATA
Found at i:44051291 original size:25 final size:24
Alignment explanation
Indices: 44051173--44051294 Score: 81
Period size: 24 Copynumber: 5.0 Consensus size: 24
44051163 TAAATAATAG
* *
44051173 TTTAAAATAAATGACTTATAAGAACAA
1 TTTAAAATAAAT-A-ATATAA-AAAAA
* *
44051200 TTCAAAATAAAT-A-AT-AAAAAT
1 TTTAAAATAAATAATATAAAAAAA
* * *
44051221 TTTCAAATAAACAAAATATAAAAAA
1 TTTAAAATAAATAATATA-AAAAAA
* * *
44051246 -CTAAAATAAATAACAATAAAACAA
1 TTTAAAATAAATAA-TATAAAAAAA
44051270 TTTAAAATAAATAATATAAAAAAA
1 TTTAAAATAAATAATATAAAAAAA
44051294 T
1 T
44051295 AACATATAAA
Statistics
Matches: 74, Mismatches: 15, Indels: 15
0.71 0.14 0.14
Matches are distributed among these distances:
21 12 0.16
22 2 0.03
23 4 0.05
24 24 0.32
25 21 0.28
27 11 0.15
ACGTcount: A:0.66, C:0.07, G:0.02, T:0.26
Consensus pattern (24 bp):
TTTAAAATAAATAATATAAAAAAA
Found at i:44051304 original size:39 final size:39
Alignment explanation
Indices: 44051137--44051328 Score: 125
Period size: 38 Copynumber: 4.9 Consensus size: 39
44051127 AAAACGAAAC
* *
44051137 AAAATAATATATAAAACAATTTAAAGTAAATAATAGTTTAAA
1 AAAATAACATATAAAACAATTTAAAATAAATAATA---TAAA
* * *
44051179 ATAAATGACTTATAAGAACAATTCAAAATAAAT-A-AT-AA
1 A-AAATAACATATAA-AACAATTTAAAATAAATAATATAAA
* ** * *
44051217 AAATTTTCAAAT-AAACAA---AATATAAA-AA-ACTAAA
1 AAAATAACATATAAAACAATTTAAAATAAATAATA-TAAA
44051251 ATAAATAACA-ATAAAACAATTTAAAATAAATAATATAAA
1 A-AAATAACATATAAAACAATTTAAAATAAATAATATAAA
* *
44051290 AAAATAACATATAAAACAGTTTTAAAATATATATATATA
1 AAAATAACATATAAAACA-ATTTAAAATAAATA-ATATA
44051329 TATATAAAAT
Statistics
Matches: 118, Mismatches: 17, Indels: 31
0.71 0.10 0.19
Matches are distributed among these distances:
32 9 0.08
33 1 0.01
34 5 0.04
35 16 0.14
36 1 0.01
37 6 0.05
38 18 0.15
39 16 0.14
40 13 0.11
41 5 0.04
42 2 0.02
43 11 0.09
44 15 0.13
ACGTcount: A:0.64, C:0.06, G:0.03, T:0.28
Consensus pattern (39 bp):
AAAATAACATATAAAACAATTTAAAATAAATAATATAAA
Found at i:44051375 original size:26 final size:25
Alignment explanation
Indices: 44051359--44051448 Score: 108
Period size: 26 Copynumber: 3.4 Consensus size: 25
44051349 TATATAATAG
44051359 TTTACAATAAATAATATATAAAAGAAA
1 TTTA-AATAAATAATATATAAAA-AAA
*
44051386 TTTAAATAAATAATATGTAAAACAAA
1 TTTAAATAAATAATATATAAAA-AAA
* *
44051412 TTAAAATAAATAATATATATAAAAAC
1 TTTAAATAAATAATATATA-AAAAAA
*
44051438 TTAAAATAAAT
1 TTTAAATAAAT
44051449 GATGATAAAA
Statistics
Matches: 57, Mismatches: 5, Indels: 3
0.88 0.08 0.05
Matches are distributed among these distances:
26 50 0.88
27 7 0.12
ACGTcount: A:0.63, C:0.03, G:0.02, T:0.31
Consensus pattern (25 bp):
TTTAAATAAATAATATATAAAAAAA
Found at i:44053035 original size:44 final size:44
Alignment explanation
Indices: 44052946--44053141 Score: 153
Period size: 44 Copynumber: 4.5 Consensus size: 44
44052936 AATCCGACCT
* * * * *
44052946 ACTGCAACTTCAGAGATATAGGATTCA-TCGTTTTAATCCGATCC
1 ACTGCAACTTCAGAGAGATAGGATT-AGTAGCTTCAATCTGATCC
* *
44052990 ACTGCAACTTCACAGAGATAGGATTAGTAGCTTCAATCTGCTCC
1 ACTGCAACTTCAGAGAGATAGGATTAGTAGCTTCAATCTGATCC
* ** * * * * * *
44053034 ACTACAACTTTTGGGAGATAAGATTGGTATCTTCAACCTGCTCC
1 ACTGCAACTTCAGAGAGATAGGATTAGTAGCTTCAATCTGATCC
* * * * *
44053078 ACTACAACTTCAGGGAGATAAGG-TTTGTGGCTTCGATCTGATCC
1 ACTGCAACTTCAGAGAGAT-AGGATTAGTAGCTTCAATCTGATCC
* *
44053122 ACTGTAACTTCAGGGAGATA
1 ACTGCAACTTCAGAGAGATA
44053142 AGATCTGCAA
Statistics
Matches: 123, Mismatches: 27, Indels: 5
0.79 0.17 0.03
Matches are distributed among these distances:
43 2 0.02
44 119 0.97
45 2 0.02
ACGTcount: A:0.29, C:0.22, G:0.20, T:0.30
Consensus pattern (44 bp):
ACTGCAACTTCAGAGAGATAGGATTAGTAGCTTCAATCTGATCC
Done.