Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr9
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: 91122320
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2661692 characters in sequence are not A, C, G, or T
File 151 of 279
Found at i:49039132 original size:54 final size:55
Alignment explanation
Indices: 49039032--49039137 Score: 144
Period size: 54 Copynumber: 1.9 Consensus size: 55
49039022 GTCCTGAGGC
* *
49039032 TCAACTCACCTCTCGCAATATGAGTTGATTTTGAAAAAGTAGAAATT-AAAAGGT
1 TCAACCCACCTCTCGCAATATGAGTTGATTTTGAAAAAGCAGAAATTGAAAAGGT
* * *
49039086 TCAACCCACCTCTCGCAATATGAGTTGGTTCTTGAACAA-CATAAATTGAAAA
1 TCAACCCACCTCTCGCAATATGAGTTGATT-TTGAAAAAGCAGAAATTGAAAA
49039138 TAGAAATTGA
Statistics
Matches: 45, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
54 34 0.76
55 11 0.24
ACGTcount: A:0.38, C:0.19, G:0.15, T:0.28
Consensus pattern (55 bp):
TCAACCCACCTCTCGCAATATGAGTTGATTTTGAAAAAGCAGAAATTGAAAAGGT
Found at i:49039146 original size:13 final size:13
Alignment explanation
Indices: 49039128--49039152 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
49039118 TGAACAACAT
49039128 AAATTGAAAATAG
1 AAATTGAAAATAG
49039141 AAATTGAAAATA
1 AAATTGAAAATA
49039153 CCTCAGCGTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.64, C:0.00, G:0.12, T:0.24
Consensus pattern (13 bp):
AAATTGAAAATAG
Found at i:49039222 original size:14 final size:14
Alignment explanation
Indices: 49039203--49039238 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
49039193 AAGCTAATTT
* *
49039203 TTGAAAAGTAGGAA
1 TTGAAAAGCAGAAA
49039217 TTGAAAAGCAGAAA
1 TTGAAAAGCAGAAA
49039231 TTGAAAAG
1 TTGAAAAG
49039239 ACCTCAGCGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.53, C:0.03, G:0.25, T:0.19
Consensus pattern (14 bp):
TTGAAAAGCAGAAA
Found at i:49039401 original size:73 final size:70
Alignment explanation
Indices: 49039234--49039534 Score: 298
Period size: 73 Copynumber: 4.2 Consensus size: 70
49039224 GCAGAAATTG
* * * * *
49039234 AAAAGACCTCAGCGTGCCCCGAAGCTTGACTCACCTCTCGCAATATGAGT-ATTTTCTAAACATA
1 AAAATACCTCAGCGTGACCCGAGGCTCGACTCACCTCTCGCAATATGAGTGATTTTTTAAACATA
49039298 AACTA
66 AACTA
* * * *
49039303 AAAATACCTTAGCGTGCCCCGAGGCTCGACTCACCCCTCGCAATATGAGCTGATTTTTTAAACAA
1 AAAATACCTCAGCGTGACCCGAGGCTCGACTCACCTCTCGCAATATGAG-TGATTTTTTAAACAT
* *
49039368 AAGGATTT
65 AA--ACTA
* * * *
49039376 AAAATACCTCAGCGTGACCTGAGGCTTGACTCACCTCTCGCAATATGAGTCAATTTTTGAAACAT
1 AAAATACCTCAGCGTGACCCGAGGCTCGACTCACCTCTCGCAATATGAGT-GATTTTTTAAACAT
49039441 AAACTA
65 AAACTA
* * ** *
49039447 AAAATACCTCAGCGTGTGACCTGAGGCTCAACTCATTTCTCACAATATGAGTTGATTTTTTTGAA
1 AAAATACCTCAGC--GTGACCCGAGGCTCGACTCACCTCTCGCAATATGAG-TGA-TTTTTT--A
* *
49039512 AACATGAATTA
60 AACATAAACTA
*
49039523 AAGATACCTCAG
1 AAAATACCTCAG
49039535 AGTACCCAAA
Statistics
Matches: 192, Mismatches: 29, Indels: 15
0.81 0.12 0.06
Matches are distributed among these distances:
69 44 0.23
70 1 0.01
71 28 0.15
72 1 0.01
73 91 0.47
74 6 0.03
76 21 0.11
ACGTcount: A:0.33, C:0.24, G:0.16, T:0.27
Consensus pattern (70 bp):
AAAATACCTCAGCGTGACCCGAGGCTCGACTCACCTCTCGCAATATGAGTGATTTTTTAAACATA
AACTA
Found at i:49040502 original size:44 final size:44
Alignment explanation
Indices: 49040439--49040526 Score: 158
Period size: 44 Copynumber: 2.0 Consensus size: 44
49040429 TCGACAACTC
* *
49040439 TTTCCTATCCATCTCGGTAAGGATCAAAGCTCTTCCTGAGAATG
1 TTTCCCATCCATCTCGGTAAGGATCAAAGCTCCTCCTGAGAATG
49040483 TTTCCCATCCATCTCGGTAAGGATCAAAGCTCCTCCTGAGAATG
1 TTTCCCATCCATCTCGGTAAGGATCAAAGCTCCTCCTGAGAATG
49040527 CCTTCTTTAC
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
44 42 1.00
ACGTcount: A:0.25, C:0.27, G:0.18, T:0.30
Consensus pattern (44 bp):
TTTCCCATCCATCTCGGTAAGGATCAAAGCTCCTCCTGAGAATG
Found at i:49057329 original size:10 final size:10
Alignment explanation
Indices: 49057295--49057335 Score: 52
Period size: 10 Copynumber: 4.3 Consensus size: 10
49057285 AAATTATTAA
49057295 TAAATATTTT
1 TAAATATTTT
49057305 TAACA-ATTTT
1 TAA-ATATTTT
49057315 T--ATATTTT
1 TAAATATTTT
49057323 TAAATATTTT
1 TAAATATTTT
49057333 TAA
1 TAA
49057336 TTTTTAAAAC
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
7 1 0.04
8 6 0.22
10 19 0.70
11 1 0.04
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (10 bp):
TAAATATTTT
Found at i:49057332 original size:17 final size:17
Alignment explanation
Indices: 49057298--49057344 Score: 69
Period size: 18 Copynumber: 2.7 Consensus size: 17
49057288 TTATTAATAA
49057298 ATATTTTTAACAATTTTT
1 ATATTTTTAA-AATTTTT
49057316 ATATTTTTAAATATTTTT
1 ATATTTTTAAA-ATTTTT
49057334 A-ATTTTTAAAA
1 ATATTTTTAAAA
49057345 CTTCATTTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
16 1 0.04
17 10 0.36
18 17 0.61
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (17 bp):
ATATTTTTAAAATTTTT
Found at i:49058502 original size:32 final size:32
Alignment explanation
Indices: 49058459--49058535 Score: 91
Period size: 32 Copynumber: 2.4 Consensus size: 32
49058449 CAAAATAAAT
** *
49058459 TATGAAAAGTTACGAATGTGAAGAGGCTTGAA
1 TATGAAAAGTTACGAATGCAAAGAGACTTGAA
* **
49058491 TATGAAGAGTTAATAATGCAAAGAGACTTGAA
1 TATGAAAAGTTACGAATGCAAAGAGACTTGAA
*
49058523 GATGAAAAGTTAC
1 TATGAAAAGTTAC
49058536 ACACATGCAT
Statistics
Matches: 36, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
32 36 1.00
ACGTcount: A:0.44, C:0.06, G:0.25, T:0.25
Consensus pattern (32 bp):
TATGAAAAGTTACGAATGCAAAGAGACTTGAA
Found at i:49063011 original size:32 final size:32
Alignment explanation
Indices: 49062968--49063044 Score: 100
Period size: 32 Copynumber: 2.4 Consensus size: 32
49062958 CAAAATAAAT
**
49062968 TATGAAAAGTTACGAATGTGAAGAGACTTGAA
1 TATGAAAAGTTACGAATGCAAAGAGACTTGAA
* **
49063000 TATGAAGAGTTAATAATGCAAAGAGACTTGAA
1 TATGAAAAGTTACGAATGCAAAGAGACTTGAA
*
49063032 GATGAAAAGTTAC
1 TATGAAAAGTTAC
49063045 ACACATGCAT
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
32 37 1.00
ACGTcount: A:0.45, C:0.06, G:0.23, T:0.25
Consensus pattern (32 bp):
TATGAAAAGTTACGAATGCAAAGAGACTTGAA
Found at i:49065428 original size:27 final size:27
Alignment explanation
Indices: 49065353--49065429 Score: 75
Period size: 27 Copynumber: 2.9 Consensus size: 27
49065343 CCCACCATTT
* * *
49065353 GCGCCTCTGAGATATAGACAATTAGTT
1 GCGCCTCTGAGATATGGACAACTAGTC
* *
49065380 GCGCCTCTGAGA-AAGGCTCAACTAGTC
1 GCGCCTCTGAGATATGG-ACAACTAGTC
* *
49065407 GCGGCTCTGAGATATGGGCAACT
1 GCGCCTCTGAGATATGGACAACT
49065430 TGTATTCGTA
Statistics
Matches: 40, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
26 2 0.05
27 35 0.88
28 3 0.08
ACGTcount: A:0.26, C:0.23, G:0.27, T:0.23
Consensus pattern (27 bp):
GCGCCTCTGAGATATGGACAACTAGTC
Found at i:49065500 original size:27 final size:30
Alignment explanation
Indices: 49065465--49065526 Score: 85
Period size: 27 Copynumber: 2.1 Consensus size: 30
49065455 TACTGATCCG
*
49065465 AAAATAAAAAAATAAT-ATTTT-AT-TAAA
1 AAAATAAAAAAAAAATAATTTTAATATAAA
49065492 AAAATAAAAAAAAAATAAATTTTAATATAAA
1 AAAATAAAAAAAAAAT-AATTTTAATATAAA
49065523 AAAA
1 AAAA
49065527 GAGTCTCATC
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
27 15 0.50
29 5 0.17
30 2 0.07
31 8 0.27
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (30 bp):
AAAATAAAAAAAAAATAATTTTAATATAAA
Found at i:49071636 original size:9 final size:9
Alignment explanation
Indices: 49071622--49071651 Score: 60
Period size: 9 Copynumber: 3.3 Consensus size: 9
49071612 ATAATACCAT
49071622 AAACAAACA
1 AAACAAACA
49071631 AAACAAACA
1 AAACAAACA
49071640 AAACAAACA
1 AAACAAACA
49071649 AAA
1 AAA
49071652 TAATCCTGAA
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:0.80, C:0.20, G:0.00, T:0.00
Consensus pattern (9 bp):
AAACAAACA
Found at i:49073158 original size:3 final size:3
Alignment explanation
Indices: 49073150--49073176 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
49073140 TTGTTATTCC
49073150 CAT CAT CAT CAT CAT CAT CAT CAT CAT
1 CAT CAT CAT CAT CAT CAT CAT CAT CAT
49073177 ATTTCACCCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (3 bp):
CAT
Found at i:49077413 original size:13 final size:13
Alignment explanation
Indices: 49077381--49077406 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
49077371 AGCCATTTTC
49077381 CCATAAAAGTTGA
1 CCATAAAAGTTGA
49077394 CCATAAAAGTTGA
1 CCATAAAAGTTGA
49077407 GTATAAATTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.15, G:0.15, T:0.23
Consensus pattern (13 bp):
CCATAAAAGTTGA
Found at i:49085784 original size:21 final size:21
Alignment explanation
Indices: 49085758--49085799 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
49085748 CCTATAAATA
49085758 GACATAGTCTATTCCTCTTGT
1 GACATAGTCTATTCCTCTTGT
49085779 GACATAGTCTATTCCTCTTGT
1 GACATAGTCTATTCCTCTTGT
49085800 ATTGATTCAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.19, C:0.24, G:0.14, T:0.43
Consensus pattern (21 bp):
GACATAGTCTATTCCTCTTGT
Found at i:49085905 original size:5 final size:5
Alignment explanation
Indices: 49085889--49085922 Score: 50
Period size: 5 Copynumber: 6.6 Consensus size: 5
49085879 TTGTGTGTTC
*
49085889 TTTAT CTTTAT TTTAT TTTAT TTTAT TCTAT TTT
1 TTTAT -TTTAT TTTAT TTTAT TTTAT TTTAT TTT
49085923 TCACAGAAGC
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
5 21 0.81
6 5 0.19
ACGTcount: A:0.18, C:0.06, G:0.00, T:0.76
Consensus pattern (5 bp):
TTTAT
Found at i:49089949 original size:72 final size:72
Alignment explanation
Indices: 49089832--49089979 Score: 260
Period size: 72 Copynumber: 2.1 Consensus size: 72
49089822 CAATTTCTTC
* *
49089832 CAAACTTGACATACTCCCCATCCACCTTGGTATGTCCCCAGAAAGCTCGTTATTGCTTAAATCCA
1 CAAACTTGACATACTCCCCATCCACCTTGGTATCTCCCCAGAAAGCACGTTATTGCTTAAATCCA
49089897 ATGTTGA
66 ATGTTGA
* *
49089904 CAAACTTGACATATTCTCCATCCACCTTGGTATCTCCCCAGAAAGCACGTTATTGCTTAAATCCA
1 CAAACTTGACATACTCCCCATCCACCTTGGTATCTCCCCAGAAAGCACGTTATTGCTTAAATCCA
49089969 ATGTTGA
66 ATGTTGA
49089976 CAAA
1 CAAA
49089980 AAGGAGCAAT
Statistics
Matches: 72, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
72 72 1.00
ACGTcount: A:0.30, C:0.28, G:0.13, T:0.29
Consensus pattern (72 bp):
CAAACTTGACATACTCCCCATCCACCTTGGTATCTCCCCAGAAAGCACGTTATTGCTTAAATCCA
ATGTTGA
Found at i:49094932 original size:14 final size:14
Alignment explanation
Indices: 49094913--49094942 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
49094903 AACACTTATA
49094913 ATTGAGGTAAAAGT
1 ATTGAGGTAAAAGT
49094927 ATTGAGGTAAAAGT
1 ATTGAGGTAAAAGT
49094941 AT
1 AT
49094943 CATGCGGTCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.43, C:0.00, G:0.27, T:0.30
Consensus pattern (14 bp):
ATTGAGGTAAAAGT
Found at i:49113290 original size:25 final size:23
Alignment explanation
Indices: 49113228--49113291 Score: 62
Period size: 24 Copynumber: 2.8 Consensus size: 23
49113218 TCTTTCAATT
*
49113228 TAATTTATTTAAAT-TTGAAAAA
1 TAATTTTTTTAAATATTGAAAAA
*
49113250 T-ATCTTTTTT-ATTATTGATAAAAA
1 TAAT-TTTTTTAAATATTG--AAAAA
49113274 TAATTTTTTTAAATATTG
1 TAATTTTTTTAAATATTG
49113292 TTTTTGTTAG
Statistics
Matches: 33, Mismatches: 3, Indels: 9
0.73 0.07 0.20
Matches are distributed among these distances:
21 4 0.12
22 9 0.27
24 12 0.36
25 8 0.24
ACGTcount: A:0.41, C:0.02, G:0.05, T:0.53
Consensus pattern (23 bp):
TAATTTTTTTAAATATTGAAAAA
Found at i:49130578 original size:18 final size:19
Alignment explanation
Indices: 49130534--49130579 Score: 51
Period size: 18 Copynumber: 2.5 Consensus size: 19
49130524 ACTTTTTAAA
49130534 AATATTATTATATTAATAT
1 AATATTATTATATTAATAT
* * *
49130553 AA-AATATTATATT-TTTT
1 AATATTATTATATTAATAT
49130570 AATATTATTA
1 AATATTATTA
49130580 AACATACATA
Statistics
Matches: 22, Mismatches: 4, Indels: 3
0.76 0.14 0.10
Matches are distributed among these distances:
17 4 0.18
18 16 0.73
19 2 0.09
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (19 bp):
AATATTATTATATTAATAT
Found at i:49130700 original size:15 final size:14
Alignment explanation
Indices: 49130675--49130714 Score: 57
Period size: 13 Copynumber: 2.9 Consensus size: 14
49130665 TTTTAACTTT
49130675 ATTTT-AATAATAA
1 ATTTTAAATAATAA
49130688 ATTTTAAAATAAT-A
1 ATTTT-AAATAATAA
49130702 ATTTTAAATAATA
1 ATTTTAAATAATA
49130715 TTCTTCACAT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
13 12 0.50
14 6 0.25
15 6 0.25
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (14 bp):
ATTTTAAATAATAA
Found at i:49131088 original size:25 final size:26
Alignment explanation
Indices: 49131055--49131105 Score: 77
Period size: 25 Copynumber: 2.0 Consensus size: 26
49131045 TTCAATTTTT
* *
49131055 TATATTATTTTTTTGTTTTT-TTAAA
1 TATAATATTTTTTTATTTTTATTAAA
49131080 TATAATATTTTTTTATTTTTATTAAA
1 TATAATATTTTTTTATTTTTATTAAA
49131106 AATATTTAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 18 0.78
26 5 0.22
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (26 bp):
TATAATATTTTTTTATTTTTATTAAA
Found at i:49131704 original size:33 final size:33
Alignment explanation
Indices: 49131667--49131763 Score: 109
Period size: 33 Copynumber: 3.1 Consensus size: 33
49131657 GTTTTTTATA
49131667 ATTATTTTAAAATTAATTTGTTAGTAATTTAGG
1 ATTATTTTAAAATTAATTTGTTAGTAATTTAGG
* *
49131700 ATTATGTTAAAATT-TTTTG-T-GT--TTGTA--
1 ATTATTTTAAAATTAATTTGTTAGTAATT-TAGG
*
49131727 ATTATTTTAAAATTAATTTATTAGTAATTTAGG
1 ATTATTTTAAAATTAATTTGTTAGTAATTTAGG
49131760 ATTA
1 ATTA
49131764 AGTTATAAAT
Statistics
Matches: 51, Mismatches: 5, Indels: 16
0.71 0.07 0.22
Matches are distributed among these distances:
27 13 0.25
28 5 0.10
29 3 0.06
30 4 0.08
31 3 0.06
32 6 0.12
33 17 0.33
ACGTcount: A:0.35, C:0.00, G:0.11, T:0.54
Consensus pattern (33 bp):
ATTATTTTAAAATTAATTTGTTAGTAATTTAGG
Found at i:49131743 original size:60 final size:61
Alignment explanation
Indices: 49131651--49131784 Score: 200
Period size: 60 Copynumber: 2.2 Consensus size: 61
49131641 TGAATGTAAT
* * *
49131651 TTTTTTGTTTTTTATAATTATTTTAAAATTAATTTGTTAGTAATTTAGGATTATGTTA-AAA
1 TTTTTTG-TGTTTATAATTATTTTAAAATTAATTTATTAGTAATTTAGGATTAAGTTATAAA
*
49131712 TTTTTTGTGTTTGTAATTATTTTAAAATTAATTTATTAGTAATTTAGGATTAAGTTATAAA
1 TTTTTTGTGTTTATAATTATTTTAAAATTAATTTATTAGTAATTTAGGATTAAGTTATAAA
*
49131773 -TTGTTGTGTTTA
1 TTTTTTGTGTTTA
49131785 GTTTAGTATT
Statistics
Matches: 66, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
60 56 0.85
61 10 0.15
ACGTcount: A:0.31, C:0.00, G:0.12, T:0.57
Consensus pattern (61 bp):
TTTTTTGTGTTTATAATTATTTTAAAATTAATTTATTAGTAATTTAGGATTAAGTTATAAA
Found at i:49132107 original size:27 final size:27
Alignment explanation
Indices: 49132064--49132116 Score: 90
Period size: 27 Copynumber: 2.0 Consensus size: 27
49132054 CCCACCATTT
49132064 GCGCCTCAGAGATAGGCTCGACTAGTC
1 GCGCCTCAGAGATAGGCTCGACTAGTC
49132091 GCGCCTCAGAGGA-AGGCTCGACTAGT
1 GCGCCTCAGA-GATAGGCTCGACTAGT
49132117 AACGCCCCTA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
27 23 0.92
28 2 0.08
ACGTcount: A:0.23, C:0.28, G:0.32, T:0.17
Consensus pattern (27 bp):
GCGCCTCAGAGATAGGCTCGACTAGTC
Found at i:49132122 original size:27 final size:27
Alignment explanation
Indices: 49132065--49132122 Score: 82
Period size: 27 Copynumber: 2.1 Consensus size: 27
49132055 CCACCATTTG
**
49132065 CGCCTCAGAGATAGGCTCGACTAGTCG
1 CGCCTCAGAGATAGGCTCGACTAGTAA
49132092 CGCCTCAGAGGA-AGGCTCGACTAGTAA
1 CGCCTCAGA-GATAGGCTCGACTAGTAA
49132119 CGCC
1 CGCC
49132123 CCTAACCCGA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
27 26 0.93
28 2 0.07
ACGTcount: A:0.24, C:0.31, G:0.29, T:0.16
Consensus pattern (27 bp):
CGCCTCAGAGATAGGCTCGACTAGTAA
Found at i:49137946 original size:29 final size:30
Alignment explanation
Indices: 49137883--49137956 Score: 87
Period size: 29 Copynumber: 2.5 Consensus size: 30
49137873 AATAATGCTT
* * * *
49137883 ATAGGTCGATTTTGAAATTTATTTAGGTAT
1 ATAGGCCGATTTTGAAAATTATTTAGGGAA
*
49137913 TTAGGCCGATTTT-AAAATTATTTAGGGAA
1 ATAGGCCGATTTTGAAAATTATTTAGGGAA
*
49137942 ATAGGCTGATTTTGA
1 ATAGGCCGATTTTGA
49137957 GGGAAAGCTA
Statistics
Matches: 36, Mismatches: 7, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
29 24 0.67
30 12 0.33
ACGTcount: A:0.31, C:0.05, G:0.22, T:0.42
Consensus pattern (30 bp):
ATAGGCCGATTTTGAAAATTATTTAGGGAA
Found at i:49138774 original size:23 final size:21
Alignment explanation
Indices: 49138715--49138780 Score: 60
Period size: 22 Copynumber: 3.0 Consensus size: 21
49138705 TTCAAATATT
*
49138715 TTTATATGTGAAATATTTTAA
1 TTTATATGTGAAATATATTAA
* * *
49138736 TTAATTATTTGAAATATCATTATG
1 TTTA-TATGTGAAATAT-ATTA-A
*
49138760 TTTATATGTGAAATATTTTAA
1 TTTATATGTGAAATATATTAA
49138781 ATACACGTAT
Statistics
Matches: 34, Mismatches: 8, Indels: 6
0.71 0.17 0.12
Matches are distributed among these distances:
21 3 0.09
22 14 0.41
23 14 0.41
24 3 0.09
ACGTcount: A:0.38, C:0.02, G:0.09, T:0.52
Consensus pattern (21 bp):
TTTATATGTGAAATATATTAA
Found at i:49139445 original size:5 final size:5
Alignment explanation
Indices: 49139435--49139471 Score: 51
Period size: 5 Copynumber: 7.8 Consensus size: 5
49139425 AATTATTTGA
*
49139435 AAAAT AAAAT AAAAT AAAAT TAAA- AAAAT AAAA- AAAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAA
49139472 CTCTAAATTC
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
4 7 0.24
5 22 0.76
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (5 bp):
AAAAT
Found at i:49153784 original size:17 final size:16
Alignment explanation
Indices: 49153754--49153800 Score: 51
Period size: 17 Copynumber: 2.9 Consensus size: 16
49153744 AACATGTCAA
* *
49153754 TTTGTGTGTATTTTAT
1 TTTGTTTGTTTTTTAT
49153770 GTTTGTTTGTTTTTTAT
1 -TTTGTTTGTTTTTTAT
49153787 TTT-TTTGATTTTTT
1 TTTGTTTG-TTTTTT
49153801 TTGAATGTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
15 4 0.15
16 9 0.33
17 14 0.52
ACGTcount: A:0.09, C:0.00, G:0.15, T:0.77
Consensus pattern (16 bp):
TTTGTTTGTTTTTTAT
Found at i:49153793 original size:15 final size:18
Alignment explanation
Indices: 49153764--49153800 Score: 53
Period size: 16 Copynumber: 2.2 Consensus size: 18
49153754 TTTGTGTGTA
49153764 TTTTATGTTTGTTTG-TT
1 TTTTATGTTTGTTTGATT
49153781 TTTTAT-TTT-TTTGATT
1 TTTTATGTTTGTTTGATT
49153797 TTTT
1 TTTT
49153801 TTGAATGTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 4 0.21
16 9 0.47
17 6 0.32
ACGTcount: A:0.08, C:0.00, G:0.11, T:0.81
Consensus pattern (18 bp):
TTTTATGTTTGTTTGATT
Found at i:49159874 original size:12 final size:12
Alignment explanation
Indices: 49159859--49159903 Score: 54
Period size: 12 Copynumber: 3.6 Consensus size: 12
49159849 TAAAAATGGC
*
49159859 ATTAAAATTAGT
1 ATTAAAATTAAT
49159871 ATTAAAATTAAT
1 ATTAAAATTAAT
*
49159883 AATAAAATTTAAT
1 ATTAAAA-TTAAT
49159896 ATCTAAAA
1 AT-TAAAA
49159904 ATATCTTTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
12 17 0.61
13 6 0.21
14 5 0.18
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.38
Consensus pattern (12 bp):
ATTAAAATTAAT
Found at i:49161320 original size:28 final size:29
Alignment explanation
Indices: 49161280--49161356 Score: 111
Period size: 28 Copynumber: 2.7 Consensus size: 29
49161270 GAATTAACCG
*
49161280 AAAAAGTTCGGTTCGGTTA-TTTTTTTGA
1 AAAAAATTCGGTTCGGTTATTTTTTTTGA
*
49161308 AAAAAATTTGGTTCGGTTATTTTTTTTGA
1 AAAAAATTCGGTTCGGTTATTTTTTTTGA
*
49161337 AAACAAATTCAGTTCGGTTA
1 AAA-AAATTCGGTTCGGTTA
49161357 ACGGTTAAGG
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
28 17 0.40
29 12 0.28
30 14 0.33
ACGTcount: A:0.30, C:0.08, G:0.18, T:0.44
Consensus pattern (29 bp):
AAAAAATTCGGTTCGGTTATTTTTTTTGA
Found at i:49161580 original size:19 final size:20
Alignment explanation
Indices: 49161552--49161591 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
49161542 TTAATCCATT
*
49161552 TTTAATATTTT-CAAAAAAA
1 TTTAACATTTTACAAAAAAA
49161571 TTTAACATTTTAACAAAAAAA
1 TTTAACATTTT-ACAAAAAAA
49161592 ATTATTAACT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 10 0.56
21 8 0.44
ACGTcount: A:0.55, C:0.07, G:0.00, T:0.38
Consensus pattern (20 bp):
TTTAACATTTTACAAAAAAA
Found at i:49168177 original size:15 final size:15
Alignment explanation
Indices: 49168159--49168193 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
49168149 ATATCGACTC
49168159 AAAAAAGAAGAAAAG
1 AAAAAAGAAGAAAAG
*
49168174 AAAAAATAAGAAAAG
1 AAAAAAGAAGAAAAG
49168189 AAAAA
1 AAAAA
49168194 CCCTTTCCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.83, C:0.00, G:0.14, T:0.03
Consensus pattern (15 bp):
AAAAAAGAAGAAAAG
Found at i:49179599 original size:13 final size:14
Alignment explanation
Indices: 49179572--49179605 Score: 52
Period size: 13 Copynumber: 2.4 Consensus size: 14
49179562 CTCCCTCTTG
49179572 TTTTCTCCCCTTCTC
1 TTTTC-CCCCTTCTC
49179587 TTTTCCCCC-TCTC
1 TTTTCCCCCTTCTC
49179600 TTTTCC
1 TTTTCC
49179606 ATTTTAAGGG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 10 0.53
14 4 0.21
15 5 0.26
ACGTcount: A:0.00, C:0.47, G:0.00, T:0.53
Consensus pattern (14 bp):
TTTTCCCCCTTCTC
Found at i:49182018 original size:11 final size:11
Alignment explanation
Indices: 49182002--49182026 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
49181992 TGTCTTTTTT
49182002 AGTCAAATGAG
1 AGTCAAATGAG
49182013 AGTCAAATGAG
1 AGTCAAATGAG
49182024 AGT
1 AGT
49182027 TGCAATTATT
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:0.44, C:0.08, G:0.28, T:0.20
Consensus pattern (11 bp):
AGTCAAATGAG
Found at i:49192728 original size:41 final size:41
Alignment explanation
Indices: 49192671--49192753 Score: 157
Period size: 41 Copynumber: 2.0 Consensus size: 41
49192661 TCATTGCACG
49192671 ACGCTACTTGACAAATGAAGGCTTTATCTTGTCCTTTAGAT
1 ACGCTACTTGACAAATGAAGGCTTTATCTTGTCCTTTAGAT
*
49192712 ACGCTCCTTGACAAATGAAGGCTTTATCTTGTCCTTTAGAT
1 ACGCTACTTGACAAATGAAGGCTTTATCTTGTCCTTTAGAT
49192753 A
1 A
49192754 ATCAATCTTT
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.27, C:0.20, G:0.17, T:0.36
Consensus pattern (41 bp):
ACGCTACTTGACAAATGAAGGCTTTATCTTGTCCTTTAGAT
Found at i:49208756 original size:13 final size:13
Alignment explanation
Indices: 49208740--49208766 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
49208730 GACAAATCAA
49208740 CTCGACACTAACT
1 CTCGACACTAACT
49208753 CTCGACACTAACT
1 CTCGACACTAACT
49208766 C
1 C
49208767 ACAATTGATG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.41, G:0.07, T:0.22
Consensus pattern (13 bp):
CTCGACACTAACT
Found at i:49218782 original size:28 final size:28
Alignment explanation
Indices: 49218730--49218813 Score: 125
Period size: 28 Copynumber: 3.0 Consensus size: 28
49218720 CACTTTGTGC
49218730 TATTCTGGTGTGTTTTGGATGGATTATAT
1 TATTCTGGTGTGTTTTGGA-GGATTATAT
49218759 TATTCTGGTGT-TTTTGGGAGGATTATAT
1 TATTCTGGTGTGTTTT-GGAGGATTATAT
* *
49218787 GATACTGGTGTGTTTTGGAGGATTATA
1 TATTCTGGTGTGTTTTGGAGGATTATA
49218814 CTGGTGTGTT
Statistics
Matches: 51, Mismatches: 2, Indels: 5
0.88 0.03 0.09
Matches are distributed among these distances:
28 33 0.65
29 18 0.35
ACGTcount: A:0.19, C:0.04, G:0.30, T:0.48
Consensus pattern (28 bp):
TATTCTGGTGTGTTTTGGAGGATTATAT
Found at i:49218783 original size:23 final size:24
Alignment explanation
Indices: 49218757--49218827 Score: 74
Period size: 23 Copynumber: 2.8 Consensus size: 24
49218747 GATGGATTAT
49218757 ATTATTCTGGTGT-TTTTGGGAGG
1 ATTATTCTGGTGTGTTTTGGGAGG
49218780 ATTATATGATACTGGTGTGTTTT-GGAGG
1 A-T-TAT--T-CTGGTGTGTTTTGGGAGG
*
49218808 ATTATACTGGTGTGTTTTGG
1 ATTATTCTGGTGTGTTTTGG
49218828 TTGGACATTT
Statistics
Matches: 40, Mismatches: 1, Indels: 13
0.74 0.02 0.24
Matches are distributed among these distances:
23 13 0.32
24 2 0.05
25 3 0.08
26 3 0.08
27 2 0.05
28 13 0.32
29 4 0.10
ACGTcount: A:0.17, C:0.04, G:0.32, T:0.46
Consensus pattern (24 bp):
ATTATTCTGGTGTGTTTTGGGAGG
Found at i:49219065 original size:21 final size:21
Alignment explanation
Indices: 49219017--49219103 Score: 104
Period size: 21 Copynumber: 4.1 Consensus size: 21
49219007 GGCTATACTG
*
49219017 ATCAGGCACTTTATGTGTCGT
1 ATCAGGCACCTTATGTGTCGT
*
49219038 ATTTCAGGCACCTTGTGTGTCGT
1 A--TCAGGCACCTTATGTGTCGT
**
49219061 ATCAGGCACCTCGTGTGTCGT
1 ATCAGGCACCTTATGTGTCGT
*
49219082 TTCAGGCA-CTTATGTGTCGT
1 ATCAGGCACCTTATGTGTCGT
49219102 AT
1 AT
49219104 ACTGATCAGG
Statistics
Matches: 57, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
20 11 0.19
21 27 0.47
23 19 0.33
ACGTcount: A:0.16, C:0.22, G:0.25, T:0.37
Consensus pattern (21 bp):
ATCAGGCACCTTATGTGTCGT
Found at i:49220343 original size:46 final size:48
Alignment explanation
Indices: 49220185--49220371 Score: 163
Period size: 46 Copynumber: 3.9 Consensus size: 48
49220175 TGGTTGGACC
49220185 ATGGCATCA-A-TGTGATATGTGA-TCTGTGTAAGACCATAGCTGGGCT
1 ATGGCATCAGAGTGTGATATGTGATTC-GTGTAAGACCATAGCTGGGCT
* * * *
49220231 ATGGCATCAGAGATATGTGATTATGTGCTTCCGTATAAGACCATATCTGGGAT
1 ATGGCATCAGAG---TGTGA-TATGTGATT-CGTGTAAGACCATAGCTGGGCT
* *
49220284 ATGGCATC--AGTGTGATATGTGATTCGTGTAATACCATGGCTGGGCT
1 ATGGCATCAGAGTGTGATATGTGATTCGTGTAAGACCATAGCTGGGCT
* * *
49220330 ATGGC-TACGGTGTGTGATATGTGACTAT-GTGCAAGACCATAG
1 ATGGCAT-CAGAGTGTGATATGTGA-T-TCGTGTAAGACCATAG
49220372 TTTTACTATG
Statistics
Matches: 114, Mismatches: 14, Indels: 23
0.75 0.09 0.15
Matches are distributed among these distances:
45 1 0.01
46 32 0.28
47 9 0.08
48 18 0.16
49 12 0.11
50 1 0.01
51 7 0.06
52 6 0.05
53 27 0.24
54 1 0.01
ACGTcount: A:0.26, C:0.15, G:0.28, T:0.31
Consensus pattern (48 bp):
ATGGCATCAGAGTGTGATATGTGATTCGTGTAAGACCATAGCTGGGCT
Found at i:49231420 original size:12 final size:12
Alignment explanation
Indices: 49231405--49231429 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
49231395 TTAATTTTCA
49231405 TTTTATTAATTT
1 TTTTATTAATTT
49231417 TTTTATTAATTT
1 TTTTATTAATTT
49231429 T
1 T
49231430 ACTGATTCAA
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:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (12 bp):
TTTTATTAATTT
Found at i:49236223 original size:13 final size:14
Alignment explanation
Indices: 49236175--49236222 Score: 51
Period size: 14 Copynumber: 3.2 Consensus size: 14
49236165 TATAACTAAA
*
49236175 AAAATAACATTGTAAT
1 AAAATAA-ATT-TAAC
49236191 AAACATAAATTTAAC
1 AAA-ATAAATTTAAC
*
49236206 AAAATAATTTTAAC
1 AAAATAAATTTAAC
49236220 AAA
1 AAA
49236223 TGAACTTGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
14 13 0.45
15 6 0.21
16 6 0.21
17 4 0.14
ACGTcount: A:0.60, C:0.08, G:0.02, T:0.29
Consensus pattern (14 bp):
AAAATAAATTTAAC
Found at i:49236307 original size:29 final size:31
Alignment explanation
Indices: 49236253--49236321 Score: 83
Period size: 31 Copynumber: 2.3 Consensus size: 31
49236243 TGAGAAATAG
49236253 AGGGACTAAATTCCTAGAAAT-AAA-AGTAT
1 AGGGACTAAATTCCTAGAAATAAAAGAGTAT
*
49236282 AGGGACTAAATT-CTA-AATTTACAAAGAGTAT
1 AGGGACTAAATTCCTAGAA-ATA-AAAGAGTAT
49236313 AGGGACTAA
1 AGGGACTAA
49236322 TGTCATGTTT
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
27 2 0.06
28 4 0.11
29 12 0.34
30 3 0.09
31 14 0.40
ACGTcount: A:0.46, C:0.10, G:0.19, T:0.25
Consensus pattern (31 bp):
AGGGACTAAATTCCTAGAAATAAAAGAGTAT
Found at i:49247113 original size:16 final size:16
Alignment explanation
Indices: 49247092--49247122 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
49247082 AGGAGTAATA
*
49247092 TATCTATATCTATATC
1 TATCTATATATATATC
49247108 TATCTATATATATAT
1 TATCTATATATATAT
49247123 ATAATGAGCT
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:0.35, C:0.13, G:0.00, T:0.52
Consensus pattern (16 bp):
TATCTATATATATATC
Found at i:49249243 original size:21 final size:21
Alignment explanation
Indices: 49249219--49249269 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
49249209 GACACCGTCC
49249219 GTGACGGCGATGACTCACCTT
1 GTGACGGCGATGACTCACCTT
* *
49249240 GTGACGTCGATGTCTCACCTT
1 GTGACGGCGATGACTCACCTT
**
49249261 CCGACGGCG
1 GTGACGGCG
49249270 GAGAATCCAT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.16, C:0.31, G:0.29, T:0.24
Consensus pattern (21 bp):
GTGACGGCGATGACTCACCTT
Found at i:49250059 original size:15 final size:16
Alignment explanation
Indices: 49250039--49250068 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
49250029 GTTTTAGAGA
49250039 AATGGAAA-ATAATTG
1 AATGGAAATATAATTG
49250054 AATGGAAATATAATT
1 AATGGAAATATAATT
49250069 ATAAATTCTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.53, C:0.00, G:0.17, T:0.30
Consensus pattern (16 bp):
AATGGAAATATAATTG
Found at i:49254327 original size:11 final size:11
Alignment explanation
Indices: 49254311--49254335 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
49254301 CGGGGAACAG
49254311 TTTTTTATTTT
1 TTTTTTATTTT
49254322 TTTTTTATTTT
1 TTTTTTATTTT
49254333 TTT
1 TTT
49254336 GAGGAAAATG
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:0.08, C:0.00, G:0.00, T:0.92
Consensus pattern (11 bp):
TTTTTTATTTT
Found at i:49256686 original size:24 final size:25
Alignment explanation
Indices: 49256636--49256689 Score: 74
Period size: 24 Copynumber: 2.2 Consensus size: 25
49256626 ATTATATACA
* *
49256636 AATAAATTTAACAAAAATAAAACAC
1 AATAAATTCAACAAAAAGAAAACAC
*
49256661 AATAAATTCAAC-ATAAGAAAACAC
1 AATAAATTCAACAAAAAGAAAACAC
49256685 AATAA
1 AATAA
49256690 CCAATCAAAG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
24 15 0.58
25 11 0.42
ACGTcount: A:0.67, C:0.13, G:0.02, T:0.19
Consensus pattern (25 bp):
AATAAATTCAACAAAAAGAAAACAC
Found at i:49258160 original size:39 final size:38
Alignment explanation
Indices: 49258117--49258205 Score: 101
Period size: 39 Copynumber: 2.3 Consensus size: 38
49258107 ATATTTAATC
* * * *
49258117 AATAATTAAAATCTATT-AAAA-TTATTTATATTAGATTA
1 AATAATTAAAA--AATTAAAAATTTATTTATACTAAAATA
49258155 TAATAATTAAAAAATTAAAAATTTATTTATACTAAAATA
1 -AATAATTAAAAAATTAAAAATTTATTTATACTAAAATA
49258194 AATAATTAAAAA
1 AATAATTAAAAA
49258206 TATAAATATA
Statistics
Matches: 44, Mismatches: 4, Indels: 5
0.83 0.08 0.09
Matches are distributed among these distances:
37 3 0.07
38 16 0.36
39 25 0.57
ACGTcount: A:0.57, C:0.02, G:0.01, T:0.39
Consensus pattern (38 bp):
AATAATTAAAAAATTAAAAATTTATTTATACTAAAATA
Found at i:49258210 original size:16 final size:18
Alignment explanation
Indices: 49258191--49258223 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
49258181 TTATACTAAA
49258191 ATAAATA-AT-TAAAAAT
1 ATAAATATATATAAAAAT
49258207 ATAAATATATATAAAAA
1 ATAAATATATATAAAAA
49258224 AAAGCTTTGG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
17 2 0.13
18 6 0.40
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (18 bp):
ATAAATATATATAAAAAT
Found at i:49259640 original size:3 final size:3
Alignment explanation
Indices: 49259632--49259659 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
49259622 TTATATTGAT
49259632 ATC ATC ATC ATC ATC ATC ATC ATC ATC A
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC A
49259660 GTAGTTATGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.36, C:0.32, G:0.00, T:0.32
Consensus pattern (3 bp):
ATC
Found at i:49263434 original size:16 final size:16
Alignment explanation
Indices: 49263415--49263451 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
49263405 TGGAAAGATG
49263415 GAAAACT-GAAGGGATA
1 GAAAACTAGAA-GGATA
49263431 GAAAACTAGAAGGATA
1 GAAAACTAGAAGGATA
49263447 GAAAA
1 GAAAA
49263452 TATAACTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 17 0.85
17 3 0.15
ACGTcount: A:0.57, C:0.05, G:0.27, T:0.11
Consensus pattern (16 bp):
GAAAACTAGAAGGATA
Found at i:49267802 original size:75 final size:75
Alignment explanation
Indices: 49267681--49267821 Score: 196
Period size: 75 Copynumber: 1.9 Consensus size: 75
49267671 CCAGGCTATG
* *
49267681 CTCCTCCAAGGCCAAGTCCTCAAGCGCCACCACCAGGACCTCGTCATCCTCC-GAGTCCACCACA
1 CTCCTCCAAGGCCAAGTCCTCAAGCGCCACCACCAAGACCACGTCATCCTCCAG-GTCCACCACA
49267745 TGCTGAGCATC
65 TGCTGAGCATC
* * * *
49267756 CTCCTCCAAGGCCAAGT-CTCTATGTGCCACCACCAAGACCAGGTCATCCTCCAGGTCCACTACA
1 CTCCTCCAAGGCCAAGTCCTC-AAGCGCCACCACCAAGACCACGTCATCCTCCAGGTCCACCACA
49267820 TG
65 TG
49267822 AGCATCCTCC
Statistics
Matches: 58, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
74 3 0.05
75 54 0.93
76 1 0.02
ACGTcount: A:0.23, C:0.42, G:0.17, T:0.18
Consensus pattern (75 bp):
CTCCTCCAAGGCCAAGTCCTCAAGCGCCACCACCAAGACCACGTCATCCTCCAGGTCCACCACAT
GCTGAGCATC
Found at i:49267842 original size:99 final size:99
Alignment explanation
Indices: 49267725--49267919 Score: 275
Period size: 99 Copynumber: 2.0 Consensus size: 99
49267715 AGGACCTCGT
* * * *
49267725 CATCCTCCGAGTCCACCACATGCTGAGCATCCTCCTCCAAGGCCA-AGTCTCTATGTGCCACCAC
1 CATCCTCCAAGTCCACCACATGCTGAGCATCCTCCTCCAAGGCCAGA-TCCCCATGCGCCACCAC
* *
49267789 CAAGACCAGGTCATCCTCCAGGTCCACTACATGAG
65 CAAGACCAGGTCATCCTCCAAGTCCACCACATGAG
* ***
49267824 CATCCTCCAAGTCCACCACATGTTGAGCATCCTCCTCCAAGGCCAGATCCCCATGCGCCACCGTT
1 CATCCTCCAAGTCCACCACATGCTGAGCATCCTCCTCCAAGGCCAGATCCCCATGCGCCACCACC
*
49267889 AGGACCAGGTCATCCTCCAAGTCCACCACAT
66 AAGACCAGGTCATCCTCCAAGTCCACCACAT
49267920 AATAATCATC
Statistics
Matches: 84, Mismatches: 11, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
99 83 0.99
100 1 0.01
ACGTcount: A:0.24, C:0.41, G:0.16, T:0.19
Consensus pattern (99 bp):
CATCCTCCAAGTCCACCACATGCTGAGCATCCTCCTCCAAGGCCAGATCCCCATGCGCCACCACC
AAGACCAGGTCATCCTCCAAGTCCACCACATGAG
Found at i:49267858 original size:27 final size:24
Alignment explanation
Indices: 49267800--49267845 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
49267790 AAGACCAGGT
* *
49267800 CATCCTCCAGGTCCACTACATGAG
1 CATCCTCCAAGTCCACCACATGAG
49267824 CATCCTCCAAGTCCACCACATG
1 CATCCTCCAAGTCCACCACATG
49267846 TTGAGCATCC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.26, C:0.41, G:0.13, T:0.20
Consensus pattern (24 bp):
CATCCTCCAAGTCCACCACATGAG
Found at i:49267977 original size:93 final size:93
Alignment explanation
Indices: 49267853--49268183 Score: 319
Period size: 93 Copynumber: 3.6 Consensus size: 93
49267843 ATGTTGAGCA
* * ***
49267853 TCCTCCTCCAAGGCCAGATCCCCATGCGCCACCGTTAGGACCAGGTCATCCTCCAAGTCCACCAC
1 TCCTCCTCCAAGGCCAGGTCCCCATGTGCCACCACCAGGACCAGGTCATCCTCCAAGTCCACCAC
*
49267918 ATAATAATCATCTTCATCCAGACCATGC
66 ATAATAATCATCTTCATCCAGGCCATGC
* * * * * *
49267946 TCCTCCTCCAGGGCCAGGTCCCCATGTGCCACCACCAAGACCTGGACATCCTCCAAGTGCATCAC
1 TCCTCCTCCAAGGCCAGGTCCCCATGTGCCACCACCAGGACCAGGTCATCCTCCAAGTCCACCAC
**
49268011 ATGCTGAA-CAT-TCTCATCCAGGCCATGC
66 ATAAT-AATCATCT-TCATCCAGGCCATGC
* * * *
49268039 TCCTCCTCC-AGGACCAAGTCCCCATGCT-CCACCACCAGAACCAGGTCATCTTCCAAGTCAACC
1 TCCTCCTCCAAGG-CCAGGTCCCCATG-TGCCACCACCAGGACCAGGTCATCCTCCAAGTCCACC
** ** * * *
49268102 ACATCTTGGTCATCCTCATCCAGGCCACGG
64 ACATAATAATCATCTTCATCCAGGCCATGC
* ** * * *
49268132 TCCCCCTCCAAGGCCAGGTCCCCATGCACCACTACCAGGTCTAGGTCATCCT
1 TCCTCCTCCAAGGCCAGGTCCCCATGTGCCACCACCAGGACCAGGTCATCCT
49268184 TCTGAGCCAC
Statistics
Matches: 191, Mismatches: 39, Indels: 16
0.78 0.16 0.07
Matches are distributed among these distances:
92 3 0.02
93 182 0.95
94 6 0.03
ACGTcount: A:0.23, C:0.41, G:0.16, T:0.20
Consensus pattern (93 bp):
TCCTCCTCCAAGGCCAGGTCCCCATGTGCCACCACCAGGACCAGGTCATCCTCCAAGTCCACCAC
ATAATAATCATCTTCATCCAGGCCATGC
Found at i:49279435 original size:17 final size:19
Alignment explanation
Indices: 49279410--49279450 Score: 50
Period size: 17 Copynumber: 2.3 Consensus size: 19
49279400 GCTAATAATT
*
49279410 TATTGTAATATT-ATA-TA
1 TATTTTAATATTAATAGTA
*
49279427 TATTTTAATTTTAATAGTA
1 TATTTTAATATTAATAGTA
49279446 TATTT
1 TATTT
49279451 AATTTGTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
17 10 0.50
18 3 0.15
19 7 0.35
ACGTcount: A:0.37, C:0.00, G:0.05, T:0.59
Consensus pattern (19 bp):
TATTTTAATATTAATAGTA
Found at i:49280590 original size:20 final size:21
Alignment explanation
Indices: 49280565--49280603 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
49280555 TTGGTTTGAT
49280565 TTTTTTTATCT-AAATATAGA
1 TTTTTTTATCTGAAATATAGA
*
49280585 TTTTTTTATTTGAAATATA
1 TTTTTTTATCTGAAATATA
49280604 TTAATAATGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.33, C:0.03, G:0.05, T:0.59
Consensus pattern (21 bp):
TTTTTTTATCTGAAATATAGA
Found at i:49285292 original size:58 final size:58
Alignment explanation
Indices: 49285189--49285301 Score: 136
Period size: 58 Copynumber: 1.9 Consensus size: 58
49285179 CAATTTGTTC
* * *
49285189 AAGCCTTAATATAGGTACAACTGCCAAATTCAAATATTAACTTGGAAAAAAAAAAGTT
1 AAGCCCTAATATAGGTACAACTGCCAAATTCAAAGACTAACTTGGAAAAAAAAAAGTT
* * * * * * *
49285247 AAGCCCTACTATAGGTACAATTGTCAAGTTCAGAGACTAATTTGGACAAAAAAAA
1 AAGCCCTAATATAGGTACAACTGCCAAATTCAAAGACTAACTTGGAAAAAAAAAA
49285302 TTCAAACCTT
Statistics
Matches: 45, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
58 45 1.00
ACGTcount: A:0.46, C:0.15, G:0.14, T:0.25
Consensus pattern (58 bp):
AAGCCCTAATATAGGTACAACTGCCAAATTCAAAGACTAACTTGGAAAAAAAAAAGTT
Found at i:49285627 original size:5 final size:5
Alignment explanation
Indices: 49285617--49285641 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
49285607 AGTGAGAATT
49285617 TAAAA TAAAA TAAAA TAAAA TAAAA
1 TAAAA TAAAA TAAAA TAAAA TAAAA
49285642 AAAGAATGTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
TAAAA
Found at i:49288511 original size:16 final size:18
Alignment explanation
Indices: 49288490--49288522 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
49288480 TTATTTTAAA
49288490 TTTTTTC-AA-ATTTTTG
1 TTTTTTCTAATATTTTTG
49288506 TTTTTTCTAATATTTTT
1 TTTTTTCTAATATTTTT
49288523 TTTAGAATCA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
17 2 0.13
18 6 0.40
ACGTcount: A:0.18, C:0.06, G:0.03, T:0.73
Consensus pattern (18 bp):
TTTTTTCTAATATTTTTG
Found at i:49294558 original size:5 final size:5
Alignment explanation
Indices: 49294548--49294584 Score: 65
Period size: 5 Copynumber: 7.2 Consensus size: 5
49294538 ATGCGACAGC
49294548 ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT CATTTT A
1 ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT -ATTTT A
49294585 AGTTCGGACA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
5 26 0.84
6 5 0.16
ACGTcount: A:0.22, C:0.03, G:0.00, T:0.76
Consensus pattern (5 bp):
ATTTT
Found at i:49300260 original size:24 final size:24
Alignment explanation
Indices: 49300212--49300261 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
49300202 TTTAAATTAA
* *
49300212 TAAAAATAAATTTATATTTTGATT
1 TAAAAATAAATTTAGATTTTAATT
49300236 TAAAAATAAAATTTAGA-TTTAATT
1 TAAAAAT-AAATTTAGATTTTAATT
49300260 TA
1 TA
49300262 TTAAATTTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 15 0.65
25 8 0.35
ACGTcount: A:0.50, C:0.00, G:0.04, T:0.46
Consensus pattern (24 bp):
TAAAAATAAATTTAGATTTTAATT
Found at i:49309793 original size:10 final size:10
Alignment explanation
Indices: 49309780--49309835 Score: 64
Period size: 10 Copynumber: 5.8 Consensus size: 10
49309770 TTTTGATACA
49309780 TTTTATAAAT
1 TTTTATAAAT
49309790 TTTTACT--AT
1 TTTTA-TAAAT
*
49309799 TTTTATAAAA
1 TTTTATAAAT
*
49309809 TTTTA-CAAT
1 TTTTATAAAT
49309818 TTTTATAAAT
1 TTTTATAAAT
49309828 TTTTATAA
1 TTTTATAA
49309836 TTCTTAATAC
Statistics
Matches: 38, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
8 1 0.03
9 14 0.37
10 22 0.58
11 1 0.03
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.59
Consensus pattern (10 bp):
TTTTATAAAT
Found at i:49309802 original size:19 final size:19
Alignment explanation
Indices: 49309780--49309837 Score: 89
Period size: 19 Copynumber: 3.1 Consensus size: 19
49309770 TTTTGATACA
*
49309780 TTTTATAAATTTTTACTAT
1 TTTTATAAATTTTTACAAT
*
49309799 TTTTATAAAATTTTACAAT
1 TTTTATAAATTTTTACAAT
*
49309818 TTTTATAAATTTTTATAAT
1 TTTTATAAATTTTTACAAT
49309837 T
1 T
49309838 CTTAATACTT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 35 1.00
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.60
Consensus pattern (19 bp):
TTTTATAAATTTTTACAAT
Found at i:49309811 original size:29 final size:28
Alignment explanation
Indices: 49309779--49309835 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 28
49309769 TTTTTGATAC
49309779 ATTTTATAAATTTTTACT-ATTTTTATAAA
1 ATTTTA-AAATTTTTA-TAATTTTTATAAA
*
49309808 ATTTTACAATTTTTATAAATTTTTATAA
1 ATTTTAAAATTTTTAT-AATTTTTATAA
49309836 TTCTTAATAC
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
27 1 0.04
28 8 0.32
29 16 0.64
ACGTcount: A:0.39, C:0.04, G:0.00, T:0.58
Consensus pattern (28 bp):
ATTTTAAAATTTTTATAATTTTTATAAA
Found at i:49318621 original size:15 final size:15
Alignment explanation
Indices: 49318596--49318639 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
49318586 TAATTTTCTC
49318596 TAATTTAATTTAAATT
1 TAATTT-ATTTAAATT
* *
49318612 TAGTTTATTTAGATT
1 TAATTTATTTAAATT
*
49318627 TAATTTACTTAAA
1 TAATTTATTTAAA
49318640 ATACTTAATA
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
15 18 0.78
16 5 0.22
ACGTcount: A:0.39, C:0.02, G:0.05, T:0.55
Consensus pattern (15 bp):
TAATTTATTTAAATT
Found at i:49322252 original size:94 final size:93
Alignment explanation
Indices: 49322089--49322282 Score: 343
Period size: 94 Copynumber: 2.1 Consensus size: 93
49322079 GAAATATTAA
49322089 TATAAAAAAAATTTAGATTACATGAACTCAACAAAAACAAACCTTTATATCAGATTCACATGCAT
1 TATAAAAAAAATTTAGATTACATGAACTCAACAAAAACAAACCTTTATATCAGATTCACATGCAT
49322154 TTTTGAATGAGCATGATTCAACTTTCCC
66 TTTTGAATGAGCATGATTCAACTTTCCC
*
49322182 TANTAAAAAAAATTTAGATTACATGAACTCAACAAGAACAAACCTTTATATCAGATTCACATGCA
1 TA-TAAAAAAAATTTAGATTACATGAACTCAACAAAAACAAACCTTTATATCAGATTCACATGCA
* *
49322247 TTTTTGAATGTGCATGGTTCAACTTTCCC
65 TTTTTGAATGAGCATGATTCAACTTTCCC
*
49322276 TACAAAA
1 TATAAAA
49322283 GAAAGAAAGA
Statistics
Matches: 96, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
93 6 0.06
94 90 0.94
ACGTcount: A:0.41, C:0.18, G:0.09, T:0.31
Consensus pattern (93 bp):
TATAAAAAAAATTTAGATTACATGAACTCAACAAAAACAAACCTTTATATCAGATTCACATGCAT
TTTTGAATGAGCATGATTCAACTTTCCC
Found at i:49334816 original size:24 final size:24
Alignment explanation
Indices: 49334756--49334816 Score: 65
Period size: 21 Copynumber: 2.7 Consensus size: 24
49334746 TTAATTTTTT
* *
49334756 TAAAAATATATAATATTAAAATTA
1 TAAAAATATATAATTTTAAAATCA
**
49334780 T-AAAAT-TAT-ATTTTATTATCA
1 TAAAAATATATAATTTTAAAATCA
49334801 TAAAAATATATAATTT
1 TAAAAATATATAATTT
49334817 AATTTTCACC
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
21 9 0.30
22 8 0.27
23 8 0.27
24 5 0.17
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (24 bp):
TAAAAATATATAATTTTAAAATCA
Found at i:49340216 original size:6 final size:6
Alignment explanation
Indices: 49340201--49340231 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
49340191 TTCGCCCGGG
49340201 AAAA-A AAAAGA AAAAGA AAAAGA AAAAGA AA
1 AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA AA
49340232 TGGTCACTGT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 4 0.16
6 21 0.84
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (6 bp):
AAAAGA
Found at i:49347487 original size:61 final size:61
Alignment explanation
Indices: 49347392--49347576 Score: 325
Period size: 61 Copynumber: 3.0 Consensus size: 61
49347382 AGCTGAGACA
* * * *
49347392 CACGACCGTGTCTCTACTCATGTGTTTACTATCATGCATACTGACTTGAAACTTTTACGTG
1 CACGACCGTATCTCTGCCCGTGTGTTTACTATCATGCATACTGACTTGAAACTTTTACGTG
49347453 CACGACCGTATCTCTGCCCGTGTGTTTACTATCATGCATACTGACTTGAAACTTTTACGTG
1 CACGACCGTATCTCTGCCCGTGTGTTTACTATCATGCATACTGACTTGAAACTTTTACGTG
*
49347514 CACGACCGTATCTCTGCCCGTGTGTTTACTATCATGCATACTGACTTGAAATTTTTACGTG
1 CACGACCGTATCTCTGCCCGTGTGTTTACTATCATGCATACTGACTTGAAACTTTTACGTG
49347575 CA
1 CA
49347577 GAGGGCACAC
Statistics
Matches: 119, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
61 119 1.00
ACGTcount: A:0.22, C:0.25, G:0.17, T:0.35
Consensus pattern (61 bp):
CACGACCGTATCTCTGCCCGTGTGTTTACTATCATGCATACTGACTTGAAACTTTTACGTG
Found at i:49348781 original size:18 final size:18
Alignment explanation
Indices: 49348750--49348861 Score: 107
Period size: 18 Copynumber: 6.2 Consensus size: 18
49348740 AATTTCATTT
*
49348750 AGTAACATTCAATTATTC
1 AGTAACAATCAATTATTC
* *
49348768 AGTAGCAATTAATTATTC
1 AGTAACAATCAATTATTC
* **
49348786 AGTAACAATCATTTGCTC
1 AGTAACAATCAATTATTC
* * *
49348804 AGTAGCAATTAGTTATTC
1 AGTAACAATCAATTATTC
* *
49348822 AGTAACGATCAATTATTT
1 AGTAACAATCAATTATTC
* *
49348840 AGTAACAATCAGTCATTC
1 AGTAACAATCAATTATTC
49348858 AGTA
1 AGTA
49348862 CTTTTATTTA
Statistics
Matches: 72, Mismatches: 22, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
18 72 1.00
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.36
Consensus pattern (18 bp):
AGTAACAATCAATTATTC
Found at i:49348858 original size:36 final size:35
Alignment explanation
Indices: 49348744--49348861 Score: 119
Period size: 36 Copynumber: 3.3 Consensus size: 35
49348734 TTTATCAATT
* *
49348744 TCATTTAGTAACATTCAATTATTCAGTAGCAATTAA
1 TCATTCAGTAACA-TCAATTATTCAGTAGCAATTAG
* * **
49348780 TTATTCAGTAACAATCATTTGCTCAGTAGCAATTAG
1 TCATTCAGTAAC-ATCAATTATTCAGTAGCAATTAG
* * * *
49348816 TTATTCAGTAACGATCAATTATTTAGTAACAATCAG
1 TCATTCAGTAAC-ATCAATTATTCAGTAGCAATTAG
49348852 TCATTCAGTA
1 TCATTCAGTA
49348862 CTTTTATTTA
Statistics
Matches: 67, Mismatches: 14, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
36 66 0.99
37 1 0.01
ACGTcount: A:0.36, C:0.15, G:0.11, T:0.37
Consensus pattern (35 bp):
TCATTCAGTAACATCAATTATTCAGTAGCAATTAG
Found at i:49349080 original size:44 final size:44
Alignment explanation
Indices: 49349026--49349117 Score: 123
Period size: 44 Copynumber: 2.1 Consensus size: 44
49349016 CTGAAGTAAT
* *
49349026 AGTAACAGTACGACACATA-AGGTGCCTCATCGACTTAAAGTCGA
1 AGTAACAGTACGACACATATA-GTGCCTCATCAACTCAAAGTCGA
* * *
49349070 AGTAATAGTACGACACTTATAGTGCCTCATCAACTCAAGGTCGA
1 AGTAACAGTACGACACATATAGTGCCTCATCAACTCAAAGTCGA
49349114 AGTA
1 AGTA
49349118 TCCCTAAACA
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
44 41 0.98
45 1 0.02
ACGTcount: A:0.36, C:0.22, G:0.20, T:0.23
Consensus pattern (44 bp):
AGTAACAGTACGACACATATAGTGCCTCATCAACTCAAAGTCGA
Found at i:49349851 original size:12 final size:11
Alignment explanation
Indices: 49349811--49349851 Score: 55
Period size: 12 Copynumber: 3.5 Consensus size: 11
49349801 TTAATATTTA
49349811 AATTTCTTATTC
1 AATTTC-TATTC
49349823 AATTTCTATTC
1 AATTTCTATTC
*
49349834 AATTTCTACTTT
1 AATTTCTA-TTC
49349846 AATTTC
1 AATTTC
49349852 AATTTTAATA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
11 13 0.48
12 14 0.52
ACGTcount: A:0.27, C:0.17, G:0.00, T:0.56
Consensus pattern (11 bp):
AATTTCTATTC
Found at i:49350377 original size:13 final size:13
Alignment explanation
Indices: 49350351--49350394 Score: 52
Period size: 13 Copynumber: 3.2 Consensus size: 13
49350341 CATTTACTTT
49350351 ATATATATTATAATA
1 ATATA-ATT-TAATA
49350366 ATATAATTTAATA
1 ATATAATTTAATA
* *
49350379 ATATACTTAAATA
1 ATATAATTTAATA
49350392 ATA
1 ATA
49350395 AGTAAACATA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
13 19 0.70
14 3 0.11
15 5 0.19
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (13 bp):
ATATAATTTAATA
Found at i:49353082 original size:46 final size:44
Alignment explanation
Indices: 49352957--49353166 Score: 149
Period size: 46 Copynumber: 4.6 Consensus size: 44
49352947 GGTGTTACAT
* * * * **
49352957 CATGTCCTAGACATGGTCTTACACT-GACACATCTCGTAGCTAATG
1 CATGTCCCAGACAT-GTCTTACACTAGTCTCGTCTCG-AGCCGATG
* * *
49353002 CATGTCCCAAACATGTCTTACACT-GGCTTACGTCTCGAGGCCGAAG
1 CATGTCCCAGACATGTCTTACACTAGTC-T-CGTCTCGA-GCCGATG
*
49353048 CATGTCCCAGACATGTCTTACACTAGTACTCGTCTCAATGCCGATG
1 CATGTCCCAGACATGTCTTACACTAGT-CTCGTCTCGA-GCCGATG
* * *
49353094 CCATG-CCCTAGACAGGGTCTTACACTAGCTCTCATAAT-GTAGCCGATG
1 -CATGTCCC-AGACA-TGTCTTACACTAG-TCTCGT-CTCG-AGCCGATG
*
49353142 CATGCCCCAGACATGTCTTACACTA
1 CATGTCCCAGACATGTCTTACACTA
49353167 ACTCATACAA
Statistics
Matches: 135, Mismatches: 18, Indels: 23
0.77 0.10 0.13
Matches are distributed among these distances:
44 12 0.09
45 13 0.10
46 60 0.44
47 20 0.15
48 27 0.20
49 3 0.02
ACGTcount: A:0.25, C:0.30, G:0.19, T:0.26
Consensus pattern (44 bp):
CATGTCCCAGACATGTCTTACACTAGTCTCGTCTCGAGCCGATG
Found at i:49356236 original size:22 final size:22
Alignment explanation
Indices: 49356211--49356254 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
49356201 AATGTTTTAT
49356211 TATGAAAATATTATGATTACTA
1 TATGAAAATATTATGATTACTA
49356233 TATGAAAATATTATGATTACTA
1 TATGAAAATATTATGATTACTA
49356255 AGTTATCTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.45, C:0.05, G:0.09, T:0.41
Consensus pattern (22 bp):
TATGAAAATATTATGATTACTA
Found at i:49356466 original size:52 final size:52
Alignment explanation
Indices: 49356388--49356519 Score: 219
Period size: 52 Copynumber: 2.5 Consensus size: 52
49356378 ACAGAATAGA
* *
49356388 TGTGATATGTGCGCCTGTATAAGACCATAGCTGGGCTATGACATCGGTGCAT
1 TGTGATATGTGCGCCCGTATAAGACCATAGCTGGGCAATGACATCGGTGCAT
*
49356440 TGTGATATGTGCGCCCGTATAAGACCATAGCTGGGCAATGGCATCGGTGCAT
1 TGTGATATGTGCGCCCGTATAAGACCATAGCTGGGCAATGACATCGGTGCAT
* *
49356492 TGTGATATGTACTCCCGTATAAGACCAT
1 TGTGATATGTGCGCCCGTATAAGACCAT
49356520 TGGCATTGGT
Statistics
Matches: 75, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 75 1.00
ACGTcount: A:0.24, C:0.20, G:0.27, T:0.28
Consensus pattern (52 bp):
TGTGATATGTGCGCCCGTATAAGACCATAGCTGGGCAATGACATCGGTGCAT
Found at i:49367200 original size:70 final size:70
Alignment explanation
Indices: 49367116--49367255 Score: 271
Period size: 70 Copynumber: 2.0 Consensus size: 70
49367106 AATTTGGTTG
*
49367116 GGGGGGGGGGGGGTCCCATAGAATATAACTTTAAAATTTATTTTTTGAAGTCTCACCATCAATAA
1 GGGGGGGGGAGGGTCCCATAGAATATAACTTTAAAATTTATTTTTTGAAGTCTCACCATCAATAA
49367181 ATAGT
66 ATAGT
49367186 GGGGGGGGGAGGGTCCCATAGAATATAACTTTAAAATTTATTTTTTGAAGTCTCACCATCAATAA
1 GGGGGGGGGAGGGTCCCATAGAATATAACTTTAAAATTTATTTTTTGAAGTCTCACCATCAATAA
49367251 ATAGT
66 ATAGT
49367256 TACTCTCTGT
Statistics
Matches: 69, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
70 69 1.00
ACGTcount: A:0.32, C:0.13, G:0.24, T:0.31
Consensus pattern (70 bp):
GGGGGGGGGAGGGTCCCATAGAATATAACTTTAAAATTTATTTTTTGAAGTCTCACCATCAATAA
ATAGT
Found at i:49375926 original size:4 final size:4
Alignment explanation
Indices: 49375917--49375951 Score: 56
Period size: 4 Copynumber: 9.2 Consensus size: 4
49375907 GAGCAAACGT
49375917 GAAA GAAA G-AA GAAA GAAA GAAA GAAA GAAA -AAA G
1 GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA G
49375952 GGAAATTTGA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
3 6 0.21
4 23 0.79
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (4 bp):
GAAA
Found at i:49378486 original size:13 final size:13
Alignment explanation
Indices: 49378468--49378492 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
49378458 AATTCTTTCT
49378468 AGAAAATTTCTCA
1 AGAAAATTTCTCA
49378481 AGAAAATTTCTC
1 AGAAAATTTCTC
49378493 TTCTGGCACT
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:0.44, C:0.16, G:0.08, T:0.32
Consensus pattern (13 bp):
AGAAAATTTCTCA
Found at i:49380593 original size:46 final size:44
Alignment explanation
Indices: 49380541--49380628 Score: 131
Period size: 46 Copynumber: 2.0 Consensus size: 44
49380531 AGAACAGAAA
* *
49380541 TGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAGACAGGAT
1 TGAGCCATCTAAGTCCATATT--AAATATGGCATTGGAGACAGGAT
*
49380587 TGAGCCATCTAAGTCCATATTATATATGGCATTGGAGACAGG
1 TGAGCCATCTAAGTCCATATTAAATATGGCATTGGAGACAGG
49380629 GATAATTCAT
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
44 19 0.49
46 20 0.51
ACGTcount: A:0.32, C:0.15, G:0.25, T:0.28
Consensus pattern (44 bp):
TGAGCCATCTAAGTCCATATTAAATATGGCATTGGAGACAGGAT
Found at i:49380644 original size:44 final size:45
Alignment explanation
Indices: 49380543--49380667 Score: 128
Period size: 44 Copynumber: 2.8 Consensus size: 45
49380533 AACAGAAATG
* *
49380543 AGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAGACAGGATTG
1 AGCCATGTAAGTCCATATTA-AAATATGGCATTGGAGACAGGATTA
* *
49380589 AGCCATCTAAGTCCATATT-ATATATGGCATTGGAGACAGGGA-TA
1 AGCCATGTAAGTCCATATTAAAATATGGCATTGGAGACA-GGATTA
** * * *
49380633 ATTCATGTAAGTCCATGTCAAAGACATGGCATTGG
1 AGCCATGTAAGTCCATATTAAA-ATATGGCATTGG
49380668 CAGGGTATCC
Statistics
Matches: 65, Mismatches: 11, Indels: 6
0.79 0.13 0.07
Matches are distributed among these distances:
44 32 0.49
45 4 0.06
46 29 0.45
ACGTcount: A:0.33, C:0.15, G:0.24, T:0.28
Consensus pattern (45 bp):
AGCCATGTAAGTCCATATTAAAATATGGCATTGGAGACAGGATTA
Found at i:49381659 original size:77 final size:77
Alignment explanation
Indices: 49381562--49381717 Score: 294
Period size: 77 Copynumber: 2.0 Consensus size: 77
49381552 CTACTTGAAG
*
49381562 AAACATGGTTCGTAGCAAGAAGAGGTTAGTGCAGTCAAGTTTTGAAACAAGGGAAACTTTAACTA
1 AAACATGGTTCGTACCAAGAAGAGGTTAGTGCAGTCAAGTTTTGAAACAAGGGAAACTTTAACTA
49381627 ATAAACTGTACT
66 ATAAACTGTACT
49381639 AAACATGGTTCGTACCAAGAAGAGGTTAGTGCAGTCAAGTTTTGAAACAAGGGAAACTTTAACTA
1 AAACATGGTTCGTACCAAGAAGAGGTTAGTGCAGTCAAGTTTTGAAACAAGGGAAACTTTAACTA
*
49381704 ATAAATTGTACT
66 ATAAACTGTACT
49381716 AA
1 AA
49381718 TTGGCCAAGT
Statistics
Matches: 77, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
77 77 1.00
ACGTcount: A:0.40, C:0.13, G:0.21, T:0.26
Consensus pattern (77 bp):
AAACATGGTTCGTACCAAGAAGAGGTTAGTGCAGTCAAGTTTTGAAACAAGGGAAACTTTAACTA
ATAAACTGTACT
Found at i:49384046 original size:68 final size:68
Alignment explanation
Indices: 49383966--49384103 Score: 276
Period size: 68 Copynumber: 2.0 Consensus size: 68
49383956 GTCTCGATAC
49383966 CTCATTTTTGACCCGTTTGACCTAATAAATTCTTTTAATTCACTAATTTCACCATTTCACAAATT
1 CTCATTTTTGACCCGTTTGACCTAATAAATTCTTTTAATTCACTAATTTCACCATTTCACAAATT
49384031 CTT
66 CTT
49384034 CTCATTTTTGACCCGTTTGACCTAATAAATTCTTTTAATTCACTAATTTCACCATTTCACAAATT
1 CTCATTTTTGACCCGTTTGACCTAATAAATTCTTTTAATTCACTAATTTCACCATTTCACAAATT
49384099 CTT
66 CTT
49384102 CT
1 CT
49384104 AAATTCTTAC
Statistics
Matches: 70, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
68 70 1.00
ACGTcount: A:0.28, C:0.24, G:0.04, T:0.44
Consensus pattern (68 bp):
CTCATTTTTGACCCGTTTGACCTAATAAATTCTTTTAATTCACTAATTTCACCATTTCACAAATT
CTT
Found at i:49384098 original size:34 final size:34
Alignment explanation
Indices: 49383992--49384101 Score: 91
Period size: 34 Copynumber: 3.2 Consensus size: 34
49383982 TTGACCTAAT
49383992 AAATTCTTTTAATTCACTAATTTCACCATTTCAC
1 AAATTCTTTTAATTCACTAATTTCACCATTTCAC
** * *** * * *
49384026 AAATTCTTCTCATTTTTGACCCGTTTGACC---TAAT
1 AAATTCTT-T--TAATTCACTAATTTCACCATTTCAC
49384060 AAATTCTTTTAATTCACTAATTTCACCATTTCAC
1 AAATTCTTTTAATTCACTAATTTCACCATTTCAC
49384094 AAATTCTT
1 AAATTCTT
49384102 CTAAATTCTT
Statistics
Matches: 52, Mismatches: 18, Indels: 12
0.63 0.22 0.15
Matches are distributed among these distances:
31 11 0.21
33 1 0.02
34 28 0.54
35 1 0.02
37 11 0.21
ACGTcount: A:0.30, C:0.23, G:0.03, T:0.45
Consensus pattern (34 bp):
AAATTCTTTTAATTCACTAATTTCACCATTTCAC
Found at i:49389879 original size:53 final size:53
Alignment explanation
Indices: 49389798--49389948 Score: 196
Period size: 53 Copynumber: 2.8 Consensus size: 53
49389788 CTTACACGGT
* * *
49389798 TCACATATCATACCGAAGCCATATCCCAGAC-ATGGTCTTATACGGAATCGCATTA
1 TCACAT-T-ATACCGATGCCATAGCCCAG-CTATGGTCTTATACGGAATCACATTA
* *
49389853 TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGGAGTCATATTA
1 TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGGAATCACATTA
** *
49389906 TCACATTGCACCGATGCCATAGCCCAGCTATGGTCTTAAACGG
1 TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGG
49389949 GCACACTTAT
Statistics
Matches: 87, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
52 1 0.01
53 79 0.91
54 1 0.01
55 6 0.07
ACGTcount: A:0.29, C:0.27, G:0.17, T:0.26
Consensus pattern (53 bp):
TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGGAATCACATTA
Found at i:49391677 original size:42 final size:42
Alignment explanation
Indices: 49391614--49391740 Score: 145
Period size: 42 Copynumber: 3.0 Consensus size: 42
49391604 CTTCGTTTTC
** *
49391614 TCGATGCCATAGTTCAACTATGGTCTTACACATC-TTCACATAA
1 TCGATGCCATAGCCCAGCTATGGTCTTACACA-CATTCACAT-A
* *
49391657 T-GATGCCATAGCCCGGCTATGGTCTTACACACATTCATATA
1 TCGATGCCATAGCCCAGCTATGGTCTTACACACATTCACATA
*
49391698 TCGATGCCATAGCCTAGCTATGGTCTTACACGA-A-TCACATA
1 TCGATGCCATAGCCCAGCTATGGTCTTACAC-ACATTCACATA
49391739 TC
1 TC
49391741 TCACTGATGC
Statistics
Matches: 73, Mismatches: 8, Indels: 8
0.82 0.09 0.09
Matches are distributed among these distances:
41 11 0.15
42 60 0.82
43 2 0.03
ACGTcount: A:0.28, C:0.27, G:0.15, T:0.30
Consensus pattern (42 bp):
TCGATGCCATAGCCCAGCTATGGTCTTACACACATTCACATA
Found at i:49391800 original size:47 final size:46
Alignment explanation
Indices: 49391699--49391822 Score: 158
Period size: 47 Copynumber: 2.7 Consensus size: 46
49391689 ATTCATATAT
* * * * * *
49391699 CGATGCCATAGCCTAGCTATGGTCTTACACGAATCACATATCTCAC
1 CGATGCCATATCCCAGATATGGTCTTATACGAAGCACATATCACAC
* * *
49391745 TGATGCCATATCCCAGATATGGTCTTATACAGTAGCATATATCACAC
1 CGATGCCATATCCCAGATATGGTCTTATAC-GAAGCACATATCACAC
49391792 CGATGCCATATCCCAGATATGGTCTTATACG
1 CGATGCCATATCCCAGATATGGTCTTATACG
49391823 GAAATCACTT
Statistics
Matches: 67, Mismatches: 10, Indels: 2
0.85 0.13 0.03
Matches are distributed among these distances:
46 26 0.39
47 41 0.61
ACGTcount: A:0.29, C:0.27, G:0.16, T:0.28
Consensus pattern (46 bp):
CGATGCCATATCCCAGATATGGTCTTATACGAAGCACATATCACAC
Found at i:49391875 original size:31 final size:31
Alignment explanation
Indices: 49391840--49392019 Score: 265
Period size: 31 Copynumber: 5.8 Consensus size: 31
49391830 CTTGTCACTT
*
49391840 GTAGCCGAAGCTACCACTATTCACTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
**
49391871 GTAGCC-AGAGCTACCGTTTTTCACTGATCAG
1 GTAGCCGA-AGCTACCACTTTTCACTGATCAG
*
49391902 GTAGCCGGAGCTACCACTTTTCACTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
49391933 GTAGCCAGAA-CTACCACTTTTCACTGATCAG
1 GTAGCC-GAAGCTACCACTTTTCACTGATCAG
* *
49391964 GTAGCAGAAGCTACCACTTTTCACTGATTAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
*
49391995 GTAGCTGAAGCTACCACTTTTCACT
1 GTAGCCGAAGCTACCACTTTTCACT
49392020 TGTCATTTGT
Statistics
Matches: 135, Mismatches: 10, Indels: 8
0.88 0.07 0.05
Matches are distributed among these distances:
30 4 0.03
31 129 0.96
32 2 0.01
ACGTcount: A:0.26, C:0.27, G:0.19, T:0.27
Consensus pattern (31 bp):
GTAGCCGAAGCTACCACTTTTCACTGATCAG
Found at i:49399333 original size:13 final size:13
Alignment explanation
Indices: 49399315--49399341 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
49399305 GCAAGTAGAC
49399315 TATGGTTCAAGCT
1 TATGGTTCAAGCT
49399328 TATGGTTCAAGCT
1 TATGGTTCAAGCT
49399341 T
1 T
49399342 CTTTCATGGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.22, C:0.15, G:0.22, T:0.41
Consensus pattern (13 bp):
TATGGTTCAAGCT
Found at i:49399711 original size:20 final size:20
Alignment explanation
Indices: 49399686--49399725 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
49399676 AATTTTTGTG
49399686 TAAAACTAAAAGGAAAATAC
1 TAAAACTAAAAGGAAAATAC
49399706 TAAAACTAAAAGGAAAATAC
1 TAAAACTAAAAGGAAAATAC
49399726 ACTATCTTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.65, C:0.10, G:0.10, T:0.15
Consensus pattern (20 bp):
TAAAACTAAAAGGAAAATAC
Found at i:49403363 original size:23 final size:23
Alignment explanation
Indices: 49403314--49403372 Score: 82
Period size: 23 Copynumber: 2.5 Consensus size: 23
49403304 TTAATATATT
*
49403314 TATTTAGTTTGAATATTAATTTGG
1 TATTTAGTTT-AATATTAATTTAG
*
49403338 TATTTAGTTTAATTTTAATTTAG
1 TATTTAGTTTAATATTAATTTAG
49403361 TATTTGAGTTTA
1 TATTT-AGTTTA
49403373 GTATCTAAAC
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
23 16 0.50
24 16 0.50
ACGTcount: A:0.29, C:0.00, G:0.14, T:0.58
Consensus pattern (23 bp):
TATTTAGTTTAATATTAATTTAG
Found at i:49419815 original size:10 final size:10
Alignment explanation
Indices: 49419800--49419827 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
49419790 GTCTCTTTCT
49419800 TCTCTCTCCC
1 TCTCTCTCCC
49419810 TCTCTCTCCC
1 TCTCTCTCCC
49419820 TCTCTCTC
1 TCTCTCTC
49419828 TCTCCCCGTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.00, C:0.57, G:0.00, T:0.43
Consensus pattern (10 bp):
TCTCTCTCCC
Found at i:49421040 original size:24 final size:24
Alignment explanation
Indices: 49420995--49421041 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
49420985 TTTGTTTGTT
*
49420995 TAATTTTAAAATTCAGATATCAAA
1 TAATTTTAAAATTCAGAAATCAAA
*
49421019 TAATTTTAACAATT-TGAAATCAA
1 TAATTTTAA-AATTCAGAAATCAA
49421042 TCTATTTATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 16 0.80
25 4 0.20
ACGTcount: A:0.49, C:0.09, G:0.04, T:0.38
Consensus pattern (24 bp):
TAATTTTAAAATTCAGAAATCAAA
Found at i:49421151 original size:21 final size:22
Alignment explanation
Indices: 49421116--49421158 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 22
49421106 ATAACCACCT
*
49421116 AATAATTTGAATAATTTTTTTA
1 AATAATTTGAATAATTATTTTA
49421138 AATAATTT-AATAATTATTTTA
1 AATAATTTGAATAATTATTTTA
49421159 TAACTATTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 12 0.60
22 8 0.40
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.53
Consensus pattern (22 bp):
AATAATTTGAATAATTATTTTA
Found at i:49421634 original size:28 final size:28
Alignment explanation
Indices: 49421576--49421634 Score: 68
Period size: 28 Copynumber: 2.1 Consensus size: 28
49421566 ACATGAATCG
* *
49421576 ATTATTTAATTAGTAAACGAAGTATAAA
1 ATTATTTAACTAATAAACGAAGTATAAA
49421604 ATTATTTAACTACATAAAC-AA-TATAATA
1 ATTATTTAACTA-ATAAACGAAGTATAA-A
49421632 ATT
1 ATT
49421635 TTACCTTTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
27 5 0.19
28 17 0.63
29 5 0.19
ACGTcount: A:0.51, C:0.07, G:0.05, T:0.37
Consensus pattern (28 bp):
ATTATTTAACTAATAAACGAAGTATAAA
Found at i:49422039 original size:27 final size:27
Alignment explanation
Indices: 49422009--49422062 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 27
49421999 ATTAACTGTT
49422009 TTTTAACAATTTTATTATAA-ATTTAAA
1 TTTTAACAATTTTA-TATAATATTTAAA
* **
49422036 TTTTATCTTTTTTATATAATATTTAAA
1 TTTTAACAATTTTATATAATATTTAAA
49422063 ACTATTTATA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
26 5 0.22
27 18 0.78
ACGTcount: A:0.39, C:0.04, G:0.00, T:0.57
Consensus pattern (27 bp):
TTTTAACAATTTTATATAATATTTAAA
Found at i:49424434 original size:9 final size:9
Alignment explanation
Indices: 49424409--49424438 Score: 51
Period size: 9 Copynumber: 3.2 Consensus size: 9
49424399 ATCATTAGCC
49424409 TAAGTTAAT
1 TAAGTTAAT
49424418 TAAGGTTAAT
1 TAA-GTTAAT
49424428 TAAGTTAAT
1 TAAGTTAAT
49424437 TA
1 TA
49424439 TGATTTATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
9 11 0.55
10 9 0.45
ACGTcount: A:0.43, C:0.00, G:0.13, T:0.43
Consensus pattern (9 bp):
TAAGTTAAT
Found at i:49424448 original size:19 final size:19
Alignment explanation
Indices: 49424409--49424448 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
49424399 ATCATTAGCC
*
49424409 TAAGTTAATTAAGGTTAAT
1 TAAGTTAATTAAGATTAAT
* *
49424428 TAAGTTAATTATGATTTAT
1 TAAGTTAATTAAGATTAAT
49424447 TA
1 TA
49424449 TATATTAATC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.40, C:0.00, G:0.12, T:0.47
Consensus pattern (19 bp):
TAAGTTAATTAAGATTAAT
Found at i:49424987 original size:24 final size:24
Alignment explanation
Indices: 49424958--49425005 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
49424948 AATGAAAAAG
49424958 TTTAAGGAACATTTGAAAATTGAA
1 TTTAAGGAACATTTGAAAATTGAA
49424982 TTTAAGGAACATTTGAAAATTGAA
1 TTTAAGGAACATTTGAAAATTGAA
49425006 ATTGAACTGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.46, C:0.04, G:0.17, T:0.33
Consensus pattern (24 bp):
TTTAAGGAACATTTGAAAATTGAA
Found at i:49428047 original size:19 final size:17
Alignment explanation
Indices: 49428012--49428053 Score: 50
Period size: 19 Copynumber: 2.4 Consensus size: 17
49428002 CTTATTTTAA
49428012 TATTTATATTAGAGTAG
1 TATTTATATTAGAGTAG
*
49428029 TATTATATATTTAGTGTAG
1 TATT-TATA-TTAGAGTAG
49428048 -ATTTAT
1 TATTTAT
49428054 TTTATTAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
17 7 0.32
18 7 0.32
19 8 0.36
ACGTcount: A:0.33, C:0.00, G:0.14, T:0.52
Consensus pattern (17 bp):
TATTTATATTAGAGTAG
Found at i:49431912 original size:6 final size:6
Alignment explanation
Indices: 49431901--49431928 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
49431891 TCCCAATATC
49431901 AGCCTT AGCCTT AGCCTT AGCCTT AGCC
1 AGCCTT AGCCTT AGCCTT AGCCTT AGCC
49431929 ATTTCACTAT
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:0.18, C:0.36, G:0.18, T:0.29
Consensus pattern (6 bp):
AGCCTT
Found at i:49433551 original size:38 final size:38
Alignment explanation
Indices: 49433500--49433576 Score: 136
Period size: 38 Copynumber: 2.0 Consensus size: 38
49433490 CAATTCGACA
* *
49433500 ATCAATATAGTAGATTAATAGTCATTGATAAGTAGAAG
1 ATCAATACAGTAGATTAATACTCATTGATAAGTAGAAG
49433538 ATCAATACAGTAGATTAATACTCATTGATAAGTAGAAG
1 ATCAATACAGTAGATTAATACTCATTGATAAGTAGAAG
49433576 A
1 A
49433577 GCATACCTTA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.45, C:0.08, G:0.17, T:0.30
Consensus pattern (38 bp):
ATCAATACAGTAGATTAATACTCATTGATAAGTAGAAG
Found at i:49440639 original size:26 final size:25
Alignment explanation
Indices: 49440586--49440645 Score: 61
Period size: 26 Copynumber: 2.4 Consensus size: 25
49440576 TTAGAATCTA
*
49440586 TTTTTAA-AATAATTAAATTTAACTT
1 TTTTTAATAAAAATTAAATTTAAC-T
49440611 TTTTTAATAAAAATTAAACTATTAA-T
1 TTTTTAATAAAAATTAAA-T-TTAACT
*
49440637 TTTGTAATA
1 TTTTTAATA
49440646 CATATTAATT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
25 7 0.23
26 18 0.60
27 1 0.03
28 4 0.13
ACGTcount: A:0.45, C:0.03, G:0.02, T:0.50
Consensus pattern (25 bp):
TTTTTAATAAAAATTAAATTTAACT
Found at i:49441958 original size:21 final size:23
Alignment explanation
Indices: 49441928--49441978 Score: 70
Period size: 23 Copynumber: 2.3 Consensus size: 23
49441918 TTTTTTAAGT
*
49441928 TAAATTTAAAAT-A-AAAAAATA
1 TAAATATAAAATGAGAAAAAATA
*
49441949 TAAATATAAATTGAGAAAAAATA
1 TAAATATAAAATGAGAAAAAATA
49441972 TAAATAT
1 TAAATAT
49441979 TAAGAACTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
21 10 0.38
22 1 0.04
23 15 0.58
ACGTcount: A:0.67, C:0.00, G:0.04, T:0.29
Consensus pattern (23 bp):
TAAATATAAAATGAGAAAAAATA
Found at i:49444100 original size:2 final size:2
Alignment explanation
Indices: 49444093--49444132 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
49444083 CTTATCTAAA
49444093 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
49444133 ATGCCATACT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:49447249 original size:15 final size:16
Alignment explanation
Indices: 49447220--49447265 Score: 58
Period size: 15 Copynumber: 2.8 Consensus size: 16
49447210 TAATAAAGTC
49447220 TCATTCTTTTCATTTTA
1 TCATT-TTTTCATTTTA
49447237 TCATTTTTT-ATTTTA
1 TCATTTTTTCATTTTA
*
49447252 TTATTTTATTCATT
1 TCATTTT-TTCATT
49447266 CAAAAAATAG
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
15 12 0.46
16 6 0.23
17 8 0.31
ACGTcount: A:0.20, C:0.11, G:0.00, T:0.70
Consensus pattern (16 bp):
TCATTTTTTCATTTTA
Found at i:49450163 original size:17 final size:17
Alignment explanation
Indices: 49450141--49450199 Score: 63
Period size: 16 Copynumber: 3.6 Consensus size: 17
49450131 AAAAAATATA
49450141 AAATTAATAATGTTAAC
1 AAATTAATAATGTTAAC
49450158 AAATTAATAATG--AATC
1 AAATTAATAATGTTAA-C
* *
49450174 TAATTAA-AAT-TTAAA
1 AAATTAATAATGTTAAC
49450189 AAATTAATAAT
1 AAATTAATAAT
49450200 ATTTTTCTTA
Statistics
Matches: 35, Mismatches: 3, Indels: 9
0.74 0.06 0.19
Matches are distributed among these distances:
15 11 0.31
16 12 0.34
17 12 0.34
ACGTcount: A:0.58, C:0.03, G:0.03, T:0.36
Consensus pattern (17 bp):
AAATTAATAATGTTAAC
Found at i:49451272 original size:48 final size:48
Alignment explanation
Indices: 49451211--49452098 Score: 1776
Period size: 48 Copynumber: 18.5 Consensus size: 48
49451201 ATTACAAACA
49451211 TCAATTATTTACCCTATTAACAAATAATCTCATTTTCAAAATTTCATT
1 TCAATTATTTACCCTATTAACAAATAATCTCATTTTCAAAATTTCATT
49451259 TCAATTATTTACCCTATTAACAAATAATCTCATTTTCAAAATTTCATT
1 TCAATTATTTACCCTATTAACAAATAATCTCATTTTCAAAATTTCATT
49451307 TCAATTATTTACCCTATTAACAAATAATCTCATTTTCAAAATTTCATT
1 TCAATTATTTACCCTATTAACAAATAATCTCATTTTCAAAATTTCATT
49451355 TCAATTATTTACCCTATTAACAAATAATCTCATTTTCAAAATTTCATT
1 TCAATTATTTACCCTATTAACAAATAATCTCATTTTCAAAATTTCATT
49451403 TCAATTATTTACCCTATTAACAAATAATCTCATTTTCAAAATTTCATT
1 TCAATTATTTACCCTATTAACAAATAATCTCATTTTCAAAATTTCATT
49451451 TCAATTATTTACCCTATTAACAAATAATCTCATTTTCAAAATTTCATT
1 TCAATTATTTACCCTATTAACAAATAATCTCATTTTCAAAATTTCATT
49451499 TCAATTATTTACCCTATTAACAAATAATCTCATTTTCAAAATTTCATT
1 TCAATTATTTACCCTATTAACAAATAATCTCATTTTCAAAATTTCATT
49451547 TCAATTATTTACCCTATTAACAAATAATCTCATTTTCAAAATTTCATT
1 TCAATTATTTACCCTATTAACAAATAATCTCATTTTCAAAATTTCATT
49451595 TCAATTATTTACCCTATTAACAAATAATCTCATTTTCAAAATTTCATT
1 TCAATTATTTACCCTATTAACAAATAATCTCATTTTCAAAATTTCATT
49451643 TCAATTATTTACCCTATTAACAAATAATCTCATTTTCAAAATTTCATT
1 TCAATTATTTACCCTATTAACAAATAATCTCATTTTCAAAATTTCATT
49451691 TCAATTATTTACCCTATTAACAAATAATCTCATTTTCAAAATTTCATT
1 TCAATTATTTACCCTATTAACAAATAATCTCATTTTCAAAATTTCATT
49451739 TCAATTATTTACCCTATTAACAAATAATCTCATTTTCAAAATTTCATT
1 TCAATTATTTACCCTATTAACAAATAATCTCATTTTCAAAATTTCATT
49451787 TCAATTATTTACCCTATTAACAAATAATCTCATTTTCAAAATTTCATT
1 TCAATTATTTACCCTATTAACAAATAATCTCATTTTCAAAATTTCATT
49451835 TCAATTATTTACCCTATTAACAAATAATCTCATTTTCAAAATTTCATT
1 TCAATTATTTACCCTATTAACAAATAATCTCATTTTCAAAATTTCATT
49451883 TCAATTATTTACCCTATTAACAAATAATCTCATTTTCAAAATTTCATT
1 TCAATTATTTACCCTATTAACAAATAATCTCATTTTCAAAATTTCATT
49451931 TCAATTATTTACCCTATTAACAAATAATCTCATTTTCAAAATTTCATT
1 TCAATTATTTACCCTATTAACAAATAATCTCATTTTCAAAATTTCATT
49451979 TCAATTATTTACCCTATTAACAAATAATCTCATTTTCAAAATTTCATT
1 TCAATTATTTACCCTATTAACAAATAATCTCATTTTCAAAATTTCATT
49452027 TCAATTATTTACCCTATTAACAAATAATCTCATTTTCAAAATTTCATT
1 TCAATTATTTACCCTATTAACAAATAATCTCATTTTCAAAATTTCATT
49452075 TCAATTATTTACCCTATTAACAAA
1 TCAATTATTTACCCTATTAACAAA
49452099 GCTCGGACTA
Statistics
Matches: 840, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 840 1.00
ACGTcount: A:0.38, C:0.19, G:0.00, T:0.44
Consensus pattern (48 bp):
TCAATTATTTACCCTATTAACAAATAATCTCATTTTCAAAATTTCATT
Found at i:49453706 original size:5 final size:5
Alignment explanation
Indices: 49453696--49453723 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
49453686 TATATATATA
49453696 ATAAT ATAAT ATAAT ATAAT ATAAT ATA
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATA
49453724 CTTAATTATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (5 bp):
ATAAT
Found at i:49456425 original size:31 final size:31
Alignment explanation
Indices: 49456351--49456411 Score: 113
Period size: 31 Copynumber: 2.0 Consensus size: 31
49456341 GTTAACACTC
*
49456351 TTAAAATTACTTTATCAAATTCAGGTTCATA
1 TTAAAATTATTTTATCAAATTCAGGTTCATA
49456382 TTAAAATTATTTTATCAAATTCAGGTTCAT
1 TTAAAATTATTTTATCAAATTCAGGTTCAT
49456412 TATAGCATTA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.38, C:0.11, G:0.07, T:0.44
Consensus pattern (31 bp):
TTAAAATTATTTTATCAAATTCAGGTTCATA
Found at i:49458279 original size:20 final size:20
Alignment explanation
Indices: 49458254--49458295 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
49458244 TACTATTAAT
49458254 ATTATTTTAATATTAATA-TA
1 ATTATTTTAA-ATTAATACTA
*
49458274 ATTATTTTTAATTAATACTA
1 ATTATTTTAAATTAATACTA
49458294 AT
1 AT
49458296 ATAATATTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 7 0.35
20 13 0.65
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (20 bp):
ATTATTTTAAATTAATACTA
Found at i:49458288 original size:25 final size:25
Alignment explanation
Indices: 49458260--49458317 Score: 82
Period size: 25 Copynumber: 2.3 Consensus size: 25
49458250 TAATATTATT
49458260 TTAATATTAATATAAT-TATTTTTAA
1 TTAATATTAATATAATAT-TTTTTAA
*
49458285 TTAATACTAATATAATATTTTTTAA
1 TTAATATTAATATAATATTTTTTAA
49458310 TTATATAT
1 TTA-ATAT
49458318 AGATTATTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
25 25 0.86
26 4 0.14
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (25 bp):
TTAATATTAATATAATATTTTTTAA
Found at i:49459441 original size:25 final size:25
Alignment explanation
Indices: 49459413--49459462 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
49459403 TAGCTGTTTA
* *
49459413 TTTAATTTTATGTTT-TTTTTAAATT
1 TTTAAATTTAT-TTTCTTGTTAAATT
49459438 TTTAAATTTATTTTCTTGTTAAATT
1 TTTAAATTTATTTTCTTGTTAAATT
49459463 ACTAAAAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 3 0.14
25 19 0.86
ACGTcount: A:0.26, C:0.02, G:0.04, T:0.68
Consensus pattern (25 bp):
TTTAAATTTATTTTCTTGTTAAATT
Found at i:49459782 original size:150 final size:150
Alignment explanation
Indices: 49459581--49459940 Score: 634
Period size: 150 Copynumber: 2.4 Consensus size: 150
49459571 AAAAATTCAA
*
49459581 AAAAATATAAAAAATATTTTTTATATTTTTTTGAATTTTTTAAAATTTAAAAAATTAATTAAGTG
1 AAAAATATAAAAAATATTTTTTATATATTTTTGAATTTTTTAAAATTTAAAAAATTAATTAAGTG
49459646 ATGACATGTTATCTATGTGACAATCTTACATGTGGATTTTTTGGTGGATGGCATTTTAATATTTA
66 ATGACATGTTATCTATGTGACAATCTTACATGTGGATTTTTTGGTGGATGGCATTTTAATATTTA
49459711 ATTAATTCTTTTAAAATATT
131 ATTAATTCTTTTAAAATATT
****
49459731 AAAAATATATTTTTATATTTTTT-TGA-ATTTTTGAATTTTTTAAAATTTAAAAAATTAATTAAG
1 AAAAATATA-AAAAATATTTTTTAT-ATATTTTTGAATTTTTTAAAATTTAAAAAATTAATTAAG
49459794 TGATGACATGTTATCTATGTGACAATCTTACATGTGGATTTTTTGGTGGATGGCATTTTAATATT
64 TGATGACATGTTATCTATGTGACAATCTTACATGTGGATTTTTTGGTGGATGGCATTTTAATATT
49459859 TAATTAATTCTTTTAAAATATT
129 TAATTAATTCTTTTAAAATATT
*
49459881 AAAAATATAAAAAATATTTTTTATATTTTTTTGAATTTTTTAAAATTTAAAAAATTAATT
1 AAAAATATAAAAAATATTTTTTATATATTTTTGAATTTTTTAAAATTTAAAAAATTAATT
49459941 CAATCGTTTT
Statistics
Matches: 196, Mismatches: 10, Indels: 8
0.92 0.05 0.04
Matches are distributed among these distances:
149 10 0.05
150 176 0.90
151 10 0.05
ACGTcount: A:0.38, C:0.04, G:0.09, T:0.49
Consensus pattern (150 bp):
AAAAATATAAAAAATATTTTTTATATATTTTTGAATTTTTTAAAATTTAAAAAATTAATTAAGTG
ATGACATGTTATCTATGTGACAATCTTACATGTGGATTTTTTGGTGGATGGCATTTTAATATTTA
ATTAATTCTTTTAAAATATT
Done.