Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr12
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: 101062743
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 4026412 characters in sequence are not A, C, G, or T
File 1 of 297
Found at i:608 original size:27 final size:26
Alignment explanation
Indices: 568--708 Score: 174
Period size: 27 Copynumber: 5.2 Consensus size: 26
558 AGGAAGCGTC
*
568 CTGGTGGCTATGCCACAATTATCTGAT
1 CTGGTGGCTCTGCCAC-ATTATCTGAT
*
595 CTGGTGGCTCTGCCACATATATCTGTT
1 CTGGTGGCTCTGCCACAT-TATCTGAT
*
622 CTGGTGGCTATGCCACGATTATCTGAT
1 CTGGTGGCTCTGCCAC-ATTATCTGAT
*
649 CTGGTGGCTCTGCCACATATATCTGTT
1 CTGGTGGCTCTGCCACAT-TATCTGAT
* *
676 CTGGTGGCTCTACCACAATATCTGTAT
1 CTGGTGGCTCTGCCACATTATCTG-AT
*
703 GTGGTG
1 CTGGTG
709 ACTTCGTCAC
Statistics
Matches: 100, Mismatches: 10, Indels: 8
0.85 0.08 0.07
Matches are distributed among these distances:
26 10 0.10
27 88 0.88
28 2 0.02
ACGTcount: A:0.18, C:0.23, G:0.24, T:0.35
Consensus pattern (26 bp):
CTGGTGGCTCTGCCACATTATCTGAT
Found at i:650 original size:54 final size:54
Alignment explanation
Indices: 568--708 Score: 230
Period size: 54 Copynumber: 2.6 Consensus size: 54
558 AGGAAGCGTC
568 CTGGTGGCTATGCCACAATTATCTGATCTGGTGGCTCTGCCACATATATCTGTT
1 CTGGTGGCTATGCCACAATTATCTGATCTGGTGGCTCTGCCACATATATCTGTT
*
622 CTGGTGGCTATGCCACGATTATCTGATCTGGTGGCTCTGCCACATATATCTGTT
1 CTGGTGGCTATGCCACAATTATCTGATCTGGTGGCTCTGCCACATATATCTGTT
* * *
676 CTGGTGGCTCTACCACAA-TATCTGTATGTGGTG
1 CTGGTGGCTATGCCACAATTATCTG-ATCTGGTG
709 ACTTCGTCAC
Statistics
Matches: 81, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
53 6 0.07
54 75 0.93
ACGTcount: A:0.18, C:0.23, G:0.24, T:0.35
Consensus pattern (54 bp):
CTGGTGGCTATGCCACAATTATCTGATCTGGTGGCTCTGCCACATATATCTGTT
Found at i:7525 original size:54 final size:54
Alignment explanation
Indices: 7443--8357 Score: 1735
Period size: 54 Copynumber: 17.0 Consensus size: 54
7433 AGGAAGCGTC
*
7443 CTGGTGGCTATGCCACAATTATCTGATCTGGTGGCTCTGCCACATATATCTGTT
1 CTGGTGGCTATGCCACGATTATCTGATCTGGTGGCTCTGCCACATATATCTGTT
7497 CTGGTGGCTATGCCACGATTATCTGATCTGGTGGCTCTGCCACATATATCTGTT
1 CTGGTGGCTATGCCACGATTATCTGATCTGGTGGCTCTGCCACATATATCTGTT
7551 CTGGTGGCTATGCCACGATTATCTGATCTGGTGGCTCTGCCACATATATCTGTT
1 CTGGTGGCTATGCCACGATTATCTGATCTGGTGGCTCTGCCACATATATCTGTT
7605 CTGGTGGCTATGCCACGATTATCTGATCTGGTGGCTCTGCCACATATATCTGTT
1 CTGGTGGCTATGCCACGATTATCTGATCTGGTGGCTCTGCCACATATATCTGTT
7659 CTGGTGGCTATGCCACGATTATCTGATCTGGTGGCTCTGCCACATATATCTGTT
1 CTGGTGGCTATGCCACGATTATCTGATCTGGTGGCTCTGCCACATATATCTGTT
7713 CTGGTGGCTATGCCACGATTATCTGATCTGGTGGCTCTGCCACATATATCTGTT
1 CTGGTGGCTATGCCACGATTATCTGATCTGGTGGCTCTGCCACATATATCTGTT
7767 CTGGTGGCTATGCCACGATTATCTGATCTGGTGGCTCTGCCACATATATCTGTT
1 CTGGTGGCTATGCCACGATTATCTGATCTGGTGGCTCTGCCACATATATCTGTT
7821 CTGGTGGCTATGCCACGATTATCTGATCTGGTGGCTCTGCCACATATATCTGTT
1 CTGGTGGCTATGCCACGATTATCTGATCTGGTGGCTCTGCCACATATATCTGTT
7875 CTGGTGGCTATGCCACGATTATCTGATCTGGTGGCTCTGCCACATATATCTGTT
1 CTGGTGGCTATGCCACGATTATCTGATCTGGTGGCTCTGCCACATATATCTGTT
7929 CTGGTGGCTATGCCACGATTATCTGATCTGGTGGCTCTGCCACATATATCTGTT
1 CTGGTGGCTATGCCACGATTATCTGATCTGGTGGCTCTGCCACATATATCTGTT
7983 CTGGTGGCTATGCCACGATTATCTGATCTGGTGGCTCTGCCACATATATCTGTT
1 CTGGTGGCTATGCCACGATTATCTGATCTGGTGGCTCTGCCACATATATCTGTT
8037 CTGGTGGCTATGCCACGATTATCTGATCTGGTGGCTCTGCCACATATATCTGTT
1 CTGGTGGCTATGCCACGATTATCTGATCTGGTGGCTCTGCCACATATATCTGTT
8091 CTGGTGGCTATGCCACGATTATCTGATCTGGTGGCTCTGCCACATATATCTGTT
1 CTGGTGGCTATGCCACGATTATCTGATCTGGTGGCTCTGCCACATATATCTGTT
8145 CTGGTGGCTATGCCACGATTATCTGATCTGGTGGCTCTGCCACATATATCTGTT
1 CTGGTGGCTATGCCACGATTATCTGATCTGGTGGCTCTGCCACATATATCTGTT
8199 CTGGTGGCTATGCCACGATTATCTGATCTGGTGGCTCTGCCACATATATCTGTT
1 CTGGTGGCTATGCCACGATTATCTGATCTGGTGGCTCTGCCACATATATCTGTT
8253 CTGGTGGCTATGCCACGATTATCTGATCTGGTGGCTCTGCCACATATATCTGTT
1 CTGGTGGCTATGCCACGATTATCTGATCTGGTGGCTCTGCCACATATATCTGTT
* * * * * * *
8307 TTGGTGGCTCTACCAC-AATATCTGTATCTGGTGACTTTGTCACA-ATATCTG
1 CTGGTGGCTATGCCACGATTATCTG-ATCTGGTGGCTCTGCCACATATATCTG
8358 GCAGCCTCGG
Statistics
Matches: 852, Mismatches: 8, Indels: 3
0.99 0.01 0.00
Matches are distributed among these distances:
53 14 0.02
54 838 0.98
ACGTcount: A:0.17, C:0.24, G:0.24, T:0.35
Consensus pattern (54 bp):
CTGGTGGCTATGCCACGATTATCTGATCTGGTGGCTCTGCCACATATATCTGTT
Found at i:17993 original size:48 final size:48
Alignment explanation
Indices: 17922--18157 Score: 224
Period size: 48 Copynumber: 4.9 Consensus size: 48
17912 CCATTTGGGT
* * *
17922 GATATGTGTGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCCAC
1 GATATGAGAGCCAGTGTAAGACCATGTTTGGGACATGGCATCGGCCAC
* * ** *
17970 GATATGAGAGCCAGTGTAAGACCATGTTTGGAACATGGCATTGGTGAT
1 GATATGAGAGCCAGTGTAAGACCATGTTTGGGACATGGCATCGGCCAC
* * * * * * * *
18018 GTTGTGAGAGCTAGTGTAAAACCATGTCTGGGACATATGCATAGG-CATT
1 GATATGAGAGCCAGTGTAAGACCATGTTTGGGACAT-GGCATCGGCCA-C
* * * * *
18067 GAGATGAGAGCTAGTGTAATACCATGTTTGGGACCTGGCATCGGCCTC
1 GATATGAGAGCCAGTGTAAGACCATGTTTGGGACATGGCATCGGCCAC
* *
18115 GACATGTA-AGCCAGTGTAAGACCATGTTTGGAACATGGCATCG
1 GATATG-AGAGCCAGTGTAAGACCATGTTTGGGACATGGCATCG
18158 ACAATTCACC
Statistics
Matches: 152, Mismatches: 32, Indels: 8
0.79 0.17 0.04
Matches are distributed among these distances:
48 113 0.74
49 39 0.26
ACGTcount: A:0.27, C:0.18, G:0.30, T:0.25
Consensus pattern (48 bp):
GATATGAGAGCCAGTGTAAGACCATGTTTGGGACATGGCATCGGCCAC
Found at i:18131 original size:97 final size:96
Alignment explanation
Indices: 17931--18155 Score: 242
Period size: 97 Copynumber: 2.3 Consensus size: 96
17921 TGATATGTGT
* *
17931 GCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCCACGATATGAGAGCCAGTGTAAGACCATG
1 GCCAGTGTAAGACCATGTCTGGGACATGGCATAGGCCACGAGATGAGAGCCAGTGTAAGACCATG
* **
17996 TTTGGAACATGGCATTGGTGATGTTGTGAGA
66 TTTGGAACATGGCATCGGTGATCATGTGAGA
* * * * * *
18027 GCTAGTGTAAAACCATGTCTGGGACATATGCATAGG-CATTGAGATGAGAGCTAGTGTAATACCA
1 GCCAGTGTAAGACCATGTCTGGGACAT-GGCATAGGCCA-CGAGATGAGAGCCAGTGTAAGACCA
* *
18091 TGTTTGGGACCTGGCATCGGCCTCGA-CATGT-A-A
64 TGTTTGGAACATGGCATCGG--T-GATCATGTGAGA
* *
18124 GCCAGTGTAAGACCATGTTTGGAACATGGCAT
1 GCCAGTGTAAGACCATGTCTGGGACATGGCAT
18156 CGACAATTCA
Statistics
Matches: 106, Mismatches: 18, Indels: 10
0.79 0.13 0.07
Matches are distributed among these distances:
96 31 0.29
97 68 0.64
98 1 0.01
99 4 0.04
100 2 0.02
ACGTcount: A:0.27, C:0.18, G:0.30, T:0.25
Consensus pattern (96 bp):
GCCAGTGTAAGACCATGTCTGGGACATGGCATAGGCCACGAGATGAGAGCCAGTGTAAGACCATG
TTTGGAACATGGCATCGGTGATCATGTGAGA
Found at i:19378 original size:21 final size:21
Alignment explanation
Indices: 19352--19399 Score: 96
Period size: 21 Copynumber: 2.3 Consensus size: 21
19342 TGTTAGGAAG
19352 ACACGGGCGTGTCGCCCTTTC
1 ACACGGGCGTGTCGCCCTTTC
19373 ACACGGGCGTGTCGCCCTTTC
1 ACACGGGCGTGTCGCCCTTTC
19394 ACACGG
1 ACACGG
19400 ACTTGTGGCC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.12, C:0.38, G:0.29, T:0.21
Consensus pattern (21 bp):
ACACGGGCGTGTCGCCCTTTC
Found at i:19410 original size:21 final size:21
Alignment explanation
Indices: 19352--19411 Score: 84
Period size: 21 Copynumber: 2.9 Consensus size: 21
19342 TGTTAGGAAG
*
19352 ACACGGGCGTGTCGCCCTTTC
1 ACACGGACGTGTCGCCCTTTC
*
19373 ACACGGGCGTGTCGCCCTTTC
1 ACACGGACGTGTCGCCCTTTC
* *
19394 ACACGGACTTGTGGCCCT
1 ACACGGACGTGTCGCCCT
19412 ATCAGCTTGA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.12, C:0.37, G:0.28, T:0.23
Consensus pattern (21 bp):
ACACGGACGTGTCGCCCTTTC
Found at i:25015 original size:44 final size:42
Alignment explanation
Indices: 24952--25108 Score: 165
Period size: 43 Copynumber: 3.7 Consensus size: 42
24942 TGTGTTTTTG
* *
24952 TGTAAGACCACGTCTGGGACGTTGGCATCGACTTATAATTTACA
1 TGTAAGACCACGTCTGGGACATTGGCATCGA-TT-TGATTTACA
* *
24996 TGTAAGACCATGTCTGGGACATTGGCATCGTATTTGATTT-CG
1 TGTAAGACCACGTCTGGGACATTGGCATCG-ATTTGATTTACA
** * *
25038 TGTAAGACCTTGTCTGGGACAATGGCATCTATATTTGA-TTACA
1 TGTAAGACCACGTCTGGGACATTGGCATC--GATTTGATTTACA
* *
25081 TGTAAGACCACATCTGGGAGATTGGCAT
1 TGTAAGACCACGTCTGGGACATTGGCAT
25109 TGTACGAGCT
Statistics
Matches: 96, Mismatches: 13, Indels: 9
0.81 0.11 0.08
Matches are distributed among these distances:
42 30 0.31
43 35 0.36
44 30 0.31
45 1 0.01
ACGTcount: A:0.26, C:0.18, G:0.24, T:0.32
Consensus pattern (42 bp):
TGTAAGACCACGTCTGGGACATTGGCATCGATTTGATTTACA
Found at i:26608 original size:27 final size:27
Alignment explanation
Indices: 26578--26663 Score: 127
Period size: 27 Copynumber: 3.2 Consensus size: 27
26568 AATACACCAA
*
26578 AAAGGCAATCCATACAGAGTATGCCAC
1 AAAGGCAATCCATACAAAGTATGCCAC
26605 AAAGGCAATCCATACAAAGTATGCCAC
1 AAAGGCAATCCATACAAAGTATGCCAC
* * * *
26632 AAAGGCGATTCATACATAGTACGCCAC
1 AAAGGCAATCCATACAAAGTATGCCAC
26659 AAAGG
1 AAAGG
26664 TTAATAGGAT
Statistics
Matches: 54, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 54 1.00
ACGTcount: A:0.42, C:0.24, G:0.19, T:0.15
Consensus pattern (27 bp):
AAAGGCAATCCATACAAAGTATGCCAC
Found at i:29334 original size:46 final size:46
Alignment explanation
Indices: 29284--29409 Score: 225
Period size: 46 Copynumber: 2.7 Consensus size: 46
29274 TGGTTGAGCA
*
29284 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
29330 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
* *
29376 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTA
29410 GGGGCGGGTT
Statistics
Matches: 77, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 77 1.00
ACGTcount: A:0.21, C:0.22, G:0.28, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
Found at i:30968 original size:17 final size:19
Alignment explanation
Indices: 30934--30972 Score: 64
Period size: 17 Copynumber: 2.2 Consensus size: 19
30924 AAAAAATGCT
30934 AAAAGAAAATAGACGAGAG
1 AAAAGAAAATAGACGAGAG
30953 AAAAGAAAA-A-ACGAGAG
1 AAAAGAAAATAGACGAGAG
30970 AAA
1 AAA
30973 TATTGTTGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 10 0.50
18 1 0.05
19 9 0.45
ACGTcount: A:0.69, C:0.05, G:0.23, T:0.03
Consensus pattern (19 bp):
AAAAGAAAATAGACGAGAG
Found at i:33105 original size:19 final size:19
Alignment explanation
Indices: 33078--33115 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
33068 GGTTAACCTC
33078 AAAAAATTTTAAAAATTAT
1 AAAAAATTTTAAAAATTAT
* *
33097 AAAATATTTTCAAAATTAT
1 AAAAAATTTTAAAAATTAT
33116 TTTTATTAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (19 bp):
AAAAAATTTTAAAAATTAT
Found at i:33428 original size:20 final size:20
Alignment explanation
Indices: 33412--33450 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
33402 CAATAAACTC
33412 TAAACCCTAAAC-TTAAACCT
1 TAAA-CCTAAACATTAAACCT
33432 TAAACCTAAACATTAAACC
1 TAAACCTAAACATTAAACC
33451 ATGAATCTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 7 0.39
20 11 0.61
ACGTcount: A:0.49, C:0.28, G:0.00, T:0.23
Consensus pattern (20 bp):
TAAACCTAAACATTAAACCT
Found at i:33447 original size:13 final size:13
Alignment explanation
Indices: 33405--33470 Score: 60
Period size: 13 Copynumber: 4.8 Consensus size: 13
33395 ACCTTACCAA
*
33405 TAAACTCTAAACCC
1 TAAAC-CTAAACCT
*
33419 TAAACTTAAACCT
1 TAAACCTAAACCT
*
33432 TAAACCTAAACAT
1 TAAACCTAAACCT
* *
33445 TAAACCATGAATCT
1 TAAACC-TAAACCT
33459 TAAACCATAAAC
1 TAAACC-TAAAC
33471 TCCAAACTCC
Statistics
Matches: 42, Mismatches: 9, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
13 23 0.55
14 19 0.45
ACGTcount: A:0.48, C:0.26, G:0.02, T:0.24
Consensus pattern (13 bp):
TAAACCTAAACCT
Found at i:36553 original size:40 final size:39
Alignment explanation
Indices: 36490--36571 Score: 110
Period size: 40 Copynumber: 2.1 Consensus size: 39
36480 TAACGACTTA
*
36490 TCGGCTAAAATGGCACTTAGTGTGCAGTTCGAAATAGCT
1 TCGGCTAAAATGGCACTTAGTGTGCAATTCGAAATAGCT
* * * *
36529 TCGGTTAAAAGTGGCACTTGGTGTGCAATTTGAGATAGCT
1 TCGGCTAAAA-TGGCACTTAGTGTGCAATTCGAAATAGCT
36569 TCG
1 TCG
36572 ACTATATATA
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
39 9 0.24
40 28 0.76
ACGTcount: A:0.26, C:0.16, G:0.28, T:0.30
Consensus pattern (39 bp):
TCGGCTAAAATGGCACTTAGTGTGCAATTCGAAATAGCT
Found at i:39377 original size:45 final size:47
Alignment explanation
Indices: 39314--39438 Score: 137
Period size: 50 Copynumber: 2.6 Consensus size: 47
39304 CATGTGAACT
* *
39314 AGTGTAAGACCATGTCTGGGACATGGCATCAG-CTTGATAT-GTGTC
1 AGTGTAAGACCATATCTGGGACATGGCATCAGCCTTGATATAGAGTC
* * * **
39359 AGTGTAAGAGCATATCTGGGATATGGCTTTGGCCTTGATATAAGAGAGTC
1 AGTGTAAGACCATATCTGGGACATGGCATCAGCCTTGATAT---AGAGTC
*
39409 AGTGTAAGACCATATATGGGACATGGCATC
1 AGTGTAAGACCATATCTGGGACATGGCATC
39439 GACTCTATAT
Statistics
Matches: 63, Mismatches: 12, Indels: 5
0.79 0.15 0.06
Matches are distributed among these distances:
45 26 0.41
46 8 0.13
50 29 0.46
ACGTcount: A:0.28, C:0.15, G:0.29, T:0.28
Consensus pattern (47 bp):
AGTGTAAGACCATATCTGGGACATGGCATCAGCCTTGATATAGAGTC
Found at i:39509 original size:43 final size:43
Alignment explanation
Indices: 39445--39554 Score: 141
Period size: 43 Copynumber: 2.6 Consensus size: 43
39435 CATCGACTCT
* *
39445 ATATGTGATTACATGTAAGACCATGTCTGGGACATTGACATTG
1 ATATGTGATTACATGTAAGACCATGTCTGGGACAGTGACATCG
* * * *
39488 -TATTGTGATTTCATGTAAGACCCTGTGTGGGACAGTGGCATCG
1 ATA-TGTGATTACATGTAAGACCATGTCTGGGACAGTGACATCG
*
39531 ATATGTGATAACATGTAAGACCAT
1 ATATGTGATTACATGTAAGACCAT
39555 ATCTAGGATA
Statistics
Matches: 56, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
42 2 0.04
43 52 0.93
44 2 0.04
ACGTcount: A:0.29, C:0.15, G:0.25, T:0.32
Consensus pattern (43 bp):
ATATGTGATTACATGTAAGACCATGTCTGGGACAGTGACATCG
Found at i:41552 original size:6 final size:5
Alignment explanation
Indices: 41543--41617 Score: 60
Period size: 6 Copynumber: 13.0 Consensus size: 5
41533 GATGATGATG
41543 TTTAGT TTTAT TTTAT CTTTATT TTTATT TTTATT TTTAT TTTCATT TTTAT
1 TTTA-T TTTAT TTTAT -TTTA-T TTTA-T TTTA-T TTTAT TTT-A-T TTTAT
41595 TTTCAT TTTCAT TTTCAT TTTAT
1 TTT-AT TTT-AT TTT-AT TTTAT
41618 GTTTTTATTA
Statistics
Matches: 64, Mismatches: 0, Indels: 11
0.85 0.00 0.15
Matches are distributed among these distances:
5 16 0.25
6 43 0.67
7 5 0.08
ACGTcount: A:0.17, C:0.07, G:0.01, T:0.75
Consensus pattern (5 bp):
TTTAT
Found at i:41570 original size:12 final size:11
Alignment explanation
Indices: 41543--41615 Score: 76
Period size: 12 Copynumber: 6.2 Consensus size: 11
41533 GATGATGATG
41543 TTTAGTTTTA-T
1 TTTA-TTTTATT
41554 TTTATCTTTATT
1 TTTAT-TTTATT
41566 TTTATTTTTATT
1 TTTA-TTTTATT
41578 TTTATTTTCATT
1 TTTATTTT-ATT
41590 TTTATTTTCATT
1 TTTATTTT-ATT
*
41602 TTCATTTTCATT
1 TTTATTTT-ATT
41614 TT
1 TT
41616 ATGTTTTTAT
Statistics
Matches: 57, Mismatches: 1, Indels: 7
0.88 0.02 0.11
Matches are distributed among these distances:
10 1 0.02
11 12 0.21
12 43 0.75
13 1 0.02
ACGTcount: A:0.16, C:0.07, G:0.01, T:0.75
Consensus pattern (11 bp):
TTTATTTTATT
Found at i:41576 original size:18 final size:17
Alignment explanation
Indices: 41543--41622 Score: 81
Period size: 18 Copynumber: 4.5 Consensus size: 17
41533 GATGATGATG
*
41543 TTTAGTTTTA-TTTTAT
1 TTTATTTTTATTTTTAT
41559 CTTTATTTTTATTTTTATT
1 -TTTATTTTTATTTTTA-T
*
41578 TTTATTTTCATTTTTAT
1 TTTATTTTTATTTTTAT
* *
41595 TTTCATTTTCATTTTCAT
1 TTT-ATTTTTATTTTTAT
41613 TTTATGTTTT
1 TTTAT-TTTT
41623 TATTAATTTT
Statistics
Matches: 55, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
17 15 0.27
18 39 0.71
19 1 0.02
ACGTcount: A:0.16, C:0.06, G:0.03, T:0.75
Consensus pattern (17 bp):
TTTATTTTTATTTTTAT
Found at i:48676 original size:43 final size:43
Alignment explanation
Indices: 48575--48722 Score: 145
Period size: 43 Copynumber: 3.4 Consensus size: 43
48565 TTTTCATGAC
* * **
48575 CTTTAGCGACGATTT-TGGGAAAAGTGCCGCTAAAGGTCATGTT
1 CTTTAGCGGCG-TTTGTGGGGAAAGCACCGCTAAAGGTCATGTT
* *
48618 CTTTAGCGGCATTTGTGGGGAAAGCACCGTTAAAGGTCATGTT
1 CTTTAGCGGCGTTTGTGGGGAAAGCACCGCTAAAGGTCATGTT
* ** * * * * *
48661 CTTTAGCGGTGTTTGTAAGGTAAGCGCCGCTAAAGATTATATT
1 CTTTAGCGGCGTTTGTGGGGAAAGCACCGCTAAAGGTCATGTT
*
48704 CTATAGCGGCGTTTGTGGG
1 CTTTAGCGGCGTTTGTGGG
48723 AAGGTCATGT
Statistics
Matches: 84, Mismatches: 20, Indels: 2
0.79 0.19 0.02
Matches are distributed among these distances:
42 3 0.04
43 81 0.96
ACGTcount: A:0.23, C:0.16, G:0.30, T:0.32
Consensus pattern (43 bp):
CTTTAGCGGCGTTTGTGGGGAAAGCACCGCTAAAGGTCATGTT
Found at i:67109 original size:29 final size:26
Alignment explanation
Indices: 67067--67129 Score: 74
Period size: 29 Copynumber: 2.3 Consensus size: 26
67057 TATTAAAGAG
*
67067 AAATAAAATAAAAAGTAATTTAAAAATAT
1 AAATAAAATAAAAAGTAA---AAAAATAA
67096 AAATAAAGAT-AAAAGTAAAAAAATAA
1 AAATAAA-ATAAAAAGTAAAAAAATAA
67122 AAATAAAA
1 AAATAAAA
67130 AATATAAGTC
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
25 1 0.03
26 14 0.44
29 15 0.47
30 2 0.06
ACGTcount: A:0.75, C:0.00, G:0.05, T:0.21
Consensus pattern (26 bp):
AAATAAAATAAAAAGTAAAAAAATAA
Found at i:67123 original size:14 final size:15
Alignment explanation
Indices: 67089--67136 Score: 53
Period size: 14 Copynumber: 3.1 Consensus size: 15
67079 AAGTAATTTA
*
67089 AAAATATAAATAAAGAT
1 AAAA-ATAAA-AAATAT
*
67106 AAAAGTAAAAAA-AT
1 AAAAATAAAAAATAT
67120 AAAAATAAAAAATAT
1 AAAAATAAAAAATAT
67135 AA
1 AA
67137 GTCTTCAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
14 13 0.46
15 7 0.25
16 4 0.14
17 4 0.14
ACGTcount: A:0.77, C:0.00, G:0.04, T:0.19
Consensus pattern (15 bp):
AAAAATAAAAAATAT
Found at i:68956 original size:55 final size:55
Alignment explanation
Indices: 68854--68957 Score: 136
Period size: 55 Copynumber: 1.9 Consensus size: 55
68844 ACGGATGGTA
* * * **
68854 GGCACGGGCGTGTCACATGCCCATGTCATTTTTATAGTTTTGACCACGGGTAGTG
1 GGCACGGGCGTGTCACACGCCCATGTCATTTTGACAGGATTGACCACGGGTAGTG
* * *
68909 GGCACGGGCGTGTCACACGCCCGTGTTATTTTGACAGGATTGCCCACGG
1 GGCACGGGCGTGTCACACGCCCATGTCATTTTGACAGGATTGACCACGG
68958 CCATGTCACA
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
55 41 1.00
ACGTcount: A:0.17, C:0.25, G:0.31, T:0.27
Consensus pattern (55 bp):
GGCACGGGCGTGTCACACGCCCATGTCATTTTGACAGGATTGACCACGGGTAGTG
Found at i:71700 original size:34 final size:34
Alignment explanation
Indices: 71655--71723 Score: 129
Period size: 34 Copynumber: 2.0 Consensus size: 34
71645 TACTCGATTT
71655 AGCTCCAGTTAAAGTAGGTTTAGCATAATCATAC
1 AGCTCCAGTTAAAGTAGGTTTAGCATAATCATAC
*
71689 AGCTCCTGTTAAAGTAGGTTTAGCATAATCATAC
1 AGCTCCAGTTAAAGTAGGTTTAGCATAATCATAC
71723 A
1 A
71724 TAGTACGAGG
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.30
Consensus pattern (34 bp):
AGCTCCAGTTAAAGTAGGTTTAGCATAATCATAC
Found at i:75391 original size:26 final size:25
Alignment explanation
Indices: 75317--75391 Score: 105
Period size: 26 Copynumber: 2.9 Consensus size: 25
75307 TTGAGTTTCG
* *
75317 TTGGGCTTGTTTGGGTTTTGGGGAA
1 TTGGGTTTGTTTGGGTTTTGGGTAA
75342 TTGGGTTTGTTTTGGGTTTTGGGTAA
1 TTGGGTTTG-TTTGGGTTTTGGGTAA
*
75368 TTGGGGTTTGTTTGGGTGTTGGGT
1 TT-GGGTTTGTTTGGGTTTTGGGT
75392 TGGTATTAGG
Statistics
Matches: 45, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
25 8 0.18
26 30 0.67
27 7 0.16
ACGTcount: A:0.05, C:0.01, G:0.44, T:0.49
Consensus pattern (25 bp):
TTGGGTTTGTTTGGGTTTTGGGTAA
Found at i:78664 original size:48 final size:48
Alignment explanation
Indices: 78612--78705 Score: 170
Period size: 48 Copynumber: 2.0 Consensus size: 48
78602 AAATAAATGG
78612 TAAAAGCTTAGTTTGTGAATGAGACAATTCAAAAGTTTTACCTGAATT
1 TAAAAGCTTAGTTTGTGAATGAGACAATTCAAAAGTTTTACCTGAATT
* *
78660 TAAAAGCTTAGTTTGTGAATGAGACAATTCAAAATTTTTATCTGAA
1 TAAAAGCTTAGTTTGTGAATGAGACAATTCAAAAGTTTTACCTGAA
78706 CTTTTTTGTA
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
48 44 1.00
ACGTcount: A:0.38, C:0.10, G:0.16, T:0.36
Consensus pattern (48 bp):
TAAAAGCTTAGTTTGTGAATGAGACAATTCAAAAGTTTTACCTGAATT
Found at i:82013 original size:24 final size:24
Alignment explanation
Indices: 81981--82028 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
81971 GATAACTTAA
81981 CCTATGAACCCGTTTCGTGGGTTC
1 CCTATGAACCCGTTTCGTGGGTTC
82005 CCTATGAACCCGTTTCGTGGGTTC
1 CCTATGAACCCGTTTCGTGGGTTC
82029 TATAGCTGGT
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:0.12, C:0.29, G:0.25, T:0.33
Consensus pattern (24 bp):
CCTATGAACCCGTTTCGTGGGTTC
Found at i:83012 original size:16 final size:17
Alignment explanation
Indices: 82981--83013 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
82971 TTCATAAGTA
82981 TATATCAATCATTTCAT
1 TATATCAATCATTTCAT
82998 TATATCAAT-ATTTCAT
1 TATATCAATCATTTCAT
83014 GCTCCATCAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.36, C:0.15, G:0.00, T:0.48
Consensus pattern (17 bp):
TATATCAATCATTTCAT
Found at i:83355 original size:46 final size:46
Alignment explanation
Indices: 83298--83563 Score: 274
Period size: 46 Copynumber: 5.8 Consensus size: 46
83288 TTTGACATGA
* * *
83298 TGCCATAGTATCTTTCAACTATGGTCTTACTCATTTTCTGTCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTTCTGTCACGT
** * *
83344 TGCCATGGTATCTTTCAACCATGGTCTTGTTCA-TTTCATGTTACAT
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTTC-TGTCACGT
* * *
83390 TGCCACGGTATCTTTCAACCATGGTCTTACAT-ATTTTATATC-CTGT
1 TGCCATGGTATCTTTCAACCATGGTCTTAC-TCATTTTCTGTCAC-GT
** * *
83436 TGCCATGGTATCTTTCAACCATGGTCTTGTTCA-TTTCATGTTACAT
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTTC-TGTCACGT
* * *
83482 TGCCACGGTATCTTTCAACCATGGTCTTACAT-ATTTTATATC-CTGT
1 TGCCATGGTATCTTTCAACCATGGTCTTAC-TCATTTTCTGTCAC-GT
*
83528 TGCCATGGTATCTTTCAACCATGGTCTTACACATTT
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCATTT
83564 CATTTCAGAA
Statistics
Matches: 179, Mismatches: 30, Indels: 22
0.77 0.13 0.10
Matches are distributed among these distances:
45 10 0.06
46 160 0.89
47 9 0.05
ACGTcount: A:0.21, C:0.23, G:0.14, T:0.42
Consensus pattern (46 bp):
TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTTCTGTCACGT
Found at i:83546 original size:138 final size:138
Alignment explanation
Indices: 83298--83563 Score: 340
Period size: 138 Copynumber: 1.9 Consensus size: 138
83288 TTTGACATGA
* ** *
83298 TGCCATAGTATCTTTCAACTATGGTCTTACTCATTTTCTGTCAGGTTGCCATGGTATCTTTCAAC
1 TGCCATAGTATCTTTCAACCATGGTCTTACTCATTTTCTGTCACATTGCCACGGTATCTTTCAAC
** * *
83363 CATGGTCTTGTTCATTTCATGTTACATTGCCACGGTATCTTTCAACCATGGTCTTACATATTTTA
66 CATGGTCTTCATCATTTCATGATACATTGCCACGGTATCTTTCAACCATGGTCTTACACATTTTA
83428 TATCCTGT
131 TATCCTGT
* ** *
83436 TGCCATGGTATCTTTCAACCATGGTCTTGTTCA-TTTCATGTTACATTGCCACGGTATCTTTCAA
1 TGCCATAGTATCTTTCAACCATGGTCTTACTCATTTTC-TGTCACATTGCCACGGTATCTTTCAA
* * * *
83500 CCATGGTCTTACAT-ATTTTAT-ATCCTGTTGCCATGGTATCTTTCAACCATGGTCTTACACATT
65 CCATGGTCTT-CATCATTTCATGATAC-ATTGCCACGGTATCTTTCAACCATGGTCTTACACATT
83563 T
128 T
83564 CATTTCAGAA
Statistics
Matches: 109, Mismatches: 16, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
137 6 0.06
138 102 0.94
139 1 0.01
ACGTcount: A:0.21, C:0.23, G:0.14, T:0.42
Consensus pattern (138 bp):
TGCCATAGTATCTTTCAACCATGGTCTTACTCATTTTCTGTCACATTGCCACGGTATCTTTCAAC
CATGGTCTTCATCATTTCATGATACATTGCCACGGTATCTTTCAACCATGGTCTTACACATTTTA
TATCCTGT
Found at i:83566 original size:92 final size:92
Alignment explanation
Indices: 83305--83555 Score: 441
Period size: 92 Copynumber: 2.7 Consensus size: 92
83295 TGATGCCATA
* * * **
83305 GTATCTTTCAACTATGGTCTTAC-TCATTTTCTGTCAGGTTGCCATGGTATCTTTCAACCATGGT
1 GTATCTTTCAACCATGGTCTTACAT-ATTTTATATCCTGTTGCCATGGTATCTTTCAACCATGGT
83369 CTTGTTCATTTCATGTTACATTGCCACG
65 CTTGTTCATTTCATGTTACATTGCCACG
83397 GTATCTTTCAACCATGGTCTTACATATTTTATATCCTGTTGCCATGGTATCTTTCAACCATGGTC
1 GTATCTTTCAACCATGGTCTTACATATTTTATATCCTGTTGCCATGGTATCTTTCAACCATGGTC
83462 TTGTTCATTTCATGTTACATTGCCACG
66 TTGTTCATTTCATGTTACATTGCCACG
83489 GTATCTTTCAACCATGGTCTTACATATTTTATATCCTGTTGCCATGGTATCTTTCAACCATGGTC
1 GTATCTTTCAACCATGGTCTTACATATTTTATATCCTGTTGCCATGGTATCTTTCAACCATGGTC
83554 TT
66 TT
83556 ACACATTTCA
Statistics
Matches: 153, Mismatches: 5, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
92 152 0.99
93 1 0.01
ACGTcount: A:0.20, C:0.23, G:0.15, T:0.43
Consensus pattern (92 bp):
GTATCTTTCAACCATGGTCTTACATATTTTATATCCTGTTGCCATGGTATCTTTCAACCATGGTC
TTGTTCATTTCATGTTACATTGCCACG
Found at i:85666 original size:8 final size:8
Alignment explanation
Indices: 85653--85677 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
85643 ATATATACTA
85653 AATAAAAT
1 AATAAAAT
85661 AATAAAAT
1 AATAAAAT
85669 AATAAAAT
1 AATAAAAT
85677 A
1 A
85678 TCATTTAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (8 bp):
AATAAAAT
Found at i:94881 original size:28 final size:29
Alignment explanation
Indices: 94810--94889 Score: 99
Period size: 28 Copynumber: 2.8 Consensus size: 29
94800 ATCCACCATC
* *
94810 GGTACATAGTACATGGAACTGTAAACACC
1 GGTACATAGTACCTGGAACTGTAAACACA
* * *
94839 GGCACAGAGTGCCTGGAACTG-AAACACA
1 GGTACATAGTACCTGGAACTGTAAACACA
*
94867 GGTACATAGCACCTGGAACTGTA
1 GGTACATAGTACCTGGAACTGTA
94890 GTCATCGATG
Statistics
Matches: 41, Mismatches: 9, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
28 23 0.56
29 18 0.44
ACGTcount: A:0.35, C:0.23, G:0.25, T:0.17
Consensus pattern (29 bp):
GGTACATAGTACCTGGAACTGTAAACACA
Found at i:108387 original size:18 final size:18
Alignment explanation
Indices: 108364--108399 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
108354 CCATTTCTAC
108364 CCATATTTTGAGTTAGGG
1 CCATATTTTGAGTTAGGG
108382 CCATATTTTGAGTTAGGG
1 CCATATTTTGAGTTAGGG
108400 TTTATGTATG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.22, C:0.11, G:0.28, T:0.39
Consensus pattern (18 bp):
CCATATTTTGAGTTAGGG
Found at i:115128 original size:38 final size:38
Alignment explanation
Indices: 115076--115150 Score: 123
Period size: 38 Copynumber: 2.0 Consensus size: 38
115066 ATTGATTCAT
* * *
115076 TAACGTGGTTCTAAGTGGATATACCACGGTTATACATG
1 TAACGTGGTGCTAAGTGGATATACCACGATTACACATG
115114 TAACGTGGTGCTAAGTGGATATACCACGATTACACAT
1 TAACGTGGTGCTAAGTGGATATACCACGATTACACAT
115151 ATTGATACAT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
38 34 1.00
ACGTcount: A:0.31, C:0.17, G:0.23, T:0.29
Consensus pattern (38 bp):
TAACGTGGTGCTAAGTGGATATACCACGATTACACATG
Found at i:135148 original size:42 final size:42
Alignment explanation
Indices: 134995--135148 Score: 143
Period size: 42 Copynumber: 3.6 Consensus size: 42
134985 TATTATACCA
* * *
134995 ATGCCATATCCTAGAAATGGTCTTACATG-GGATCTCGTATCG
1 ATGCCATATCCTAGATATGGTCTTACATGAAG-TCTCATATCG
* * * * * *
135037 ATGCTAATAGCCTAGCTATGGTTTTACACGAAATCTCATATCG
1 ATGC-CATATCCTAGATATGGTCTTACATGAAGTCTCATATCG
* *
135080 ATGCCATATTCC-AAATATGGTATTACATGAAGTCTCATAAT-G
1 ATGCCATA-TCCTAGATATGGTCTTACATGAAGTCTCAT-ATCG
*
135122 ATGCCATATCCTAGATATGATCTTACA
1 ATGCCATATCCTAGATATGGTCTTACA
135149 CATAGCCTTG
Statistics
Matches: 88, Mismatches: 19, Indels: 10
0.75 0.16 0.09
Matches are distributed among these distances:
41 3 0.03
42 49 0.56
43 36 0.41
ACGTcount: A:0.31, C:0.20, G:0.16, T:0.32
Consensus pattern (42 bp):
ATGCCATATCCTAGATATGGTCTTACATGAAGTCTCATATCG
Found at i:138211 original size:25 final size:25
Alignment explanation
Indices: 138159--138250 Score: 76
Period size: 25 Copynumber: 3.7 Consensus size: 25
138149 TCCTATACAT
* * * * *
138159 GTATGCTCATACGAGCTATGAATAG
1 GTATGCTCACACAAGCTGTAAATCG
* *
138184 GTATGCTCACTCAAGCTGTAGATCG
1 GTATGCTCACACAAGCTGTAAATCG
* * *
138209 GTATGCTCTCACGAGTTGTAAATCG
1 GTATGCTCACACAAGCTGTAAATCG
* *
138234 GAATGCTCACACGAGCT
1 GTATGCTCACACAAGCT
138251 ATGGGTCAGA
Statistics
Matches: 52, Mismatches: 15, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
25 52 1.00
ACGTcount: A:0.27, C:0.22, G:0.24, T:0.27
Consensus pattern (25 bp):
GTATGCTCACACAAGCTGTAAATCG
Found at i:138333 original size:41 final size:41
Alignment explanation
Indices: 138237--138336 Score: 146
Period size: 41 Copynumber: 2.4 Consensus size: 41
138227 TAAATCGGAA
* * * *
138237 TGCTCACACGAGCTATGGGTCAGAACGTAGATGCAAGATGC
1 TGCTCACACGAGCTGTGGGTCAGAACATAGATACAAGATAC
**
138278 TGCTCACACGAGCTGTGGGTCAGAACATAGATACACTATAC
1 TGCTCACACGAGCTGTGGGTCAGAACATAGATACAAGATAC
138319 TGCTCACACGAGCTGTGG
1 TGCTCACACGAGCTGTGG
138337 AATATCTGAA
Statistics
Matches: 53, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 53 1.00
ACGTcount: A:0.28, C:0.24, G:0.27, T:0.21
Consensus pattern (41 bp):
TGCTCACACGAGCTGTGGGTCAGAACATAGATACAAGATAC
Found at i:143022 original size:42 final size:42
Alignment explanation
Indices: 142975--143078 Score: 154
Period size: 42 Copynumber: 2.5 Consensus size: 42
142965 ACTGAGGTTA
* *
142975 CGTGTAAGACTATATCTGGGATATGGCGTCAGTATGAGACTT
1 CGTGTAAGACCATATCTGGGATATGGCGTCAATATGAGACTT
* *
143017 CGTGTAAGACCATATTTGGGATATGGCGTCAATATGAGATTT
1 CGTGTAAGACCATATCTGGGATATGGCGTCAATATGAGACTT
* *
143059 CATGTAAGACCATAACTGGG
1 CGTGTAAGACCATATCTGGG
143079 CTATTGGCAT
Statistics
Matches: 55, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
42 55 1.00
ACGTcount: A:0.29, C:0.14, G:0.27, T:0.30
Consensus pattern (42 bp):
CGTGTAAGACCATATCTGGGATATGGCGTCAATATGAGACTT
Found at i:145758 original size:31 final size:31
Alignment explanation
Indices: 145723--145784 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
145713 GGAGTATTGT
145723 TCCTCCACTACTCAACCGTTAAAAGTCCACC
1 TCCTCCACTACTCAACCGTTAAAAGTCCACC
145754 TCCTCCACTACTCAACCGTTAAAAGTCCACC
1 TCCTCCACTACTCAACCGTTAAAAGTCCACC
145785 CGTTAGCCTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.29, C:0.42, G:0.06, T:0.23
Consensus pattern (31 bp):
TCCTCCACTACTCAACCGTTAAAAGTCCACC
Found at i:152866 original size:5 final size:5
Alignment explanation
Indices: 152856--152907 Score: 68
Period size: 5 Copynumber: 9.6 Consensus size: 5
152846 ATTAAGTCCG
152856 TTTAT TTTAT TTTAT TTTAT TTTATT TTTATT TTTAT GTTTAT TGTTAT
1 TTTAT TTTAT TTTAT TTTAT TTTA-T TTTA-T TTTAT -TTTAT T-TTAT
152905 TTT
1 TTT
152908 TTTAAACTTC
Statistics
Matches: 44, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
5 23 0.52
6 21 0.48
ACGTcount: A:0.17, C:0.00, G:0.04, T:0.79
Consensus pattern (5 bp):
TTTAT
Found at i:152886 original size:6 final size:6
Alignment explanation
Indices: 152856--152908 Score: 60
Period size: 6 Copynumber: 9.5 Consensus size: 6
152846 ATTAAGTCCG
*
152856 TTTA-T TTTA-T TTTA-T TTTA-T TTTATT TTTATT TTTATG TTTATT
1 TTTATT TTTATT TTTATT TTTATT TTTATT TTTATT TTTATT TTTATT
*
152900 GTTATT TTT
1 TTTATT TTT
152909 TTAAACTTCT
Statistics
Matches: 43, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
5 19 0.44
6 24 0.56
ACGTcount: A:0.17, C:0.00, G:0.04, T:0.79
Consensus pattern (6 bp):
TTTATT
Found at i:155437 original size:17 final size:17
Alignment explanation
Indices: 155415--155448 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
155405 CAATTAATCA
155415 ACCTAGAGTCAGTTATT
1 ACCTAGAGTCAGTTATT
155432 ACCTAGAGTCAGTTATT
1 ACCTAGAGTCAGTTATT
155449 CTTGCTCTCG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.35
Consensus pattern (17 bp):
ACCTAGAGTCAGTTATT
Found at i:158139 original size:10 final size:10
Alignment explanation
Indices: 158117--158149 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
158107 CTAAGCTAAC
158117 AAAACATAA-T
1 AAAA-ATAATT
158127 AAAAATAATT
1 AAAAATAATT
158137 AAAAATAATT
1 AAAAATAATT
158147 AAA
1 AAA
158150 GCAGCCTTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
9 4 0.18
10 18 0.82
ACGTcount: A:0.73, C:0.03, G:0.00, T:0.24
Consensus pattern (10 bp):
AAAAATAATT
Found at i:158538 original size:60 final size:60
Alignment explanation
Indices: 158399--158550 Score: 168
Period size: 60 Copynumber: 2.5 Consensus size: 60
158389 CTATTCAGAA
* *
158399 ATCAGAGT-TAACTGGGCCTTAGCCCATATCAATATTAATCTGGGCCATAGCCCCTTACAAT
1 ATCAGAGTAT-ACTGGGCC-TAGCCCATATCAATATCAATCTAGGCCATAGCCCCTTACAAT
* *
158460 ATCAGAGTATACTAGGCCTAGCCCATATCAGTATCAATCTAGGCCATAG-CCCTATAACAA-
1 ATCAGAGTATACTGGGCCTAGCCCATATCAATATCAATCTAGGCCATAGCCCCT-T-ACAAT
* * *
158520 GTC-GAGATATATTGGGCCTTGCCCATATCAA
1 ATCAGAG-TATACTGGGCCTAGCCCATATCAA
158551 CACAGTTGGC
Statistics
Matches: 78, Mismatches: 9, Indels: 9
0.81 0.09 0.09
Matches are distributed among these distances:
59 7 0.09
60 51 0.65
61 19 0.24
62 1 0.01
ACGTcount: A:0.31, C:0.26, G:0.17, T:0.26
Consensus pattern (60 bp):
ATCAGAGTATACTGGGCCTAGCCCATATCAATATCAATCTAGGCCATAGCCCCTTACAAT
Found at i:162446 original size:17 final size:19
Alignment explanation
Indices: 162424--162466 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 19
162414 TCTAAATGGG
*
162424 ATTAAAATAAA-TT-CTTA
1 ATTAAAATAAATTTAATTA
162441 ATTAAAA-AAATTTAATTA
1 ATTAAAATAAATTTAATTA
162459 ATTAAAAT
1 ATTAAAAT
162467 TTTCAAACCT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
16 3 0.14
17 9 0.41
18 10 0.45
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (19 bp):
ATTAAAATAAATTTAATTA
Found at i:162675 original size:16 final size:17
Alignment explanation
Indices: 162654--162686 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
162644 AGGTTTAGGT
162654 TTAAAA-TTTTAATTAA
1 TTAAAATTTTTAATTAA
162670 TTAAAATTTTTAATTAA
1 TTAAAATTTTTAATTAA
162687 AAATCTATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (17 bp):
TTAAAATTTTTAATTAA
Found at i:165740 original size:34 final size:34
Alignment explanation
Indices: 165699--165770 Score: 126
Period size: 34 Copynumber: 2.1 Consensus size: 34
165689 TTATGTCATG
*
165699 GATCTCTTCAGGCAAACCCCCGCCTCTACTATAT
1 GATCTCTTCAGGAAAACCCCCGCCTCTACTATAT
*
165733 GATCTCTTCAGGAAAACCCTCGCCTCTACTATAT
1 GATCTCTTCAGGAAAACCCCCGCCTCTACTATAT
165767 GATC
1 GATC
165771 ATATTAAATG
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.25, C:0.35, G:0.12, T:0.28
Consensus pattern (34 bp):
GATCTCTTCAGGAAAACCCCCGCCTCTACTATAT
Found at i:167419 original size:15 final size:15
Alignment explanation
Indices: 167399--167434 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
167389 TCTTTCACAA
*
167399 TCAAATATTTTTCTT
1 TCAAATATTTTGCTT
167414 TCAAATATTTTGCTT
1 TCAAATATTTTGCTT
167429 TCAAAT
1 TCAAAT
167435 CTTTAATGGG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.31, C:0.14, G:0.03, T:0.53
Consensus pattern (15 bp):
TCAAATATTTTGCTT
Found at i:173839 original size:27 final size:26
Alignment explanation
Indices: 173818--173923 Score: 140
Period size: 27 Copynumber: 3.9 Consensus size: 26
173808 ACGGTCATTT
173818 TACCCTACGAGGGTATTTCGGTAATCC
1 TACCCTAC-AGGGTATTTCGGTAATCC
*
173845 TACCCTACAAGGGTATTTCGATAATCC
1 TACCCTAC-AGGGTATTTCGGTAATCC
*
173872 TACCCTACAGGGGTATTTCGATAATCC
1 TACCCTACA-GGGTATTTCGGTAATCC
* *
173899 TACCCTATAGGGGTATTTTGGTAAT
1 TACCCTACA-GGGTATTTCGGTAAT
173924 TTCACAAATC
Statistics
Matches: 73, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
26 1 0.01
27 72 0.99
ACGTcount: A:0.25, C:0.23, G:0.20, T:0.32
Consensus pattern (26 bp):
TACCCTACAGGGTATTTCGGTAATCC
Found at i:173950 original size:27 final size:27
Alignment explanation
Indices: 173907--174101 Score: 187
Period size: 27 Copynumber: 7.2 Consensus size: 27
173897 CCTACCCTAT
** *
173907 AGGGGTATTTTGGTAATTTCACAAATC
1 AGGGGTATTTCAGTAATTTTACAAATC
* * *
173934 AAGGGTATTTCAATAATTTTAC-AACC
1 AGGGGTATTTCAGTAATTTTACAAATC
* * * *
173960 CGGGGATATTTTAGTAATTTTAAAAATT
1 AGGGG-TATTTCAGTAATTTTACAAATC
* *
173988 AGGGGTAATTT-AATAATTTTACAAATT
1 AGGGGT-ATTTCAGTAATTTTACAAATC
* *
174015 AGGGGTATTTCAGTAATGTTACAAGTC
1 AGGGGTATTTCAGTAATTTTACAAATC
* **
174042 AGGGGTATTTCGGTAATTTTACAACCC
1 AGGGGTATTTCAGTAATTTTACAAATC
* *
174069 GGGGGTATTTCAGTAATTTTACAAACC
1 AGGGGTATTTCAGTAATTTTACAAATC
174096 AGGGGT
1 AGGGGT
174102 CTTAACAACC
Statistics
Matches: 136, Mismatches: 28, Indels: 8
0.79 0.16 0.05
Matches are distributed among these distances:
26 10 0.07
27 116 0.85
28 10 0.07
ACGTcount: A:0.32, C:0.11, G:0.21, T:0.36
Consensus pattern (27 bp):
AGGGGTATTTCAGTAATTTTACAAATC
Found at i:173970 original size:54 final size:53
Alignment explanation
Indices: 173908--174101 Score: 210
Period size: 54 Copynumber: 3.6 Consensus size: 53
173898 CTACCCTATA
** * *
173908 GGGGTATTTTGGTAATTTCACAAATCAAGGGTATTTCAATAATTTTACAACCC
1 GGGGTATTTCAGTAATTTTACAAATCAGGGGTATTTCAATAATTTTACAACCC
* * * ***
173961 GGGGATATTTTAGTAATTTTAAAAATTAGGGGTAATTT-AATAATTTTACAAATTA
1 GGGG-TATTTCAGTAATTTTACAAATCAGGGGT-ATTTCAATAATTTTAC-AACCC
* * **
174016 GGGGTATTTCAGTAATGTTACAAGTCAGGGGTATTTCGGTAATTTTACAACCC
1 GGGGTATTTCAGTAATTTTACAAATCAGGGGTATTTCAATAATTTTACAACCC
*
174069 GGGGGTATTTCAGTAATTTTACAAACCAGGGGT
1 -GGGGTATTTCAGTAATTTTACAAATCAGGGGT
174102 CTTAACAACC
Statistics
Matches: 115, Mismatches: 21, Indels: 9
0.79 0.14 0.06
Matches are distributed among these distances:
53 10 0.09
54 95 0.83
55 10 0.09
ACGTcount: A:0.32, C:0.11, G:0.21, T:0.36
Consensus pattern (53 bp):
GGGGTATTTCAGTAATTTTACAAATCAGGGGTATTTCAATAATTTTACAACCC
Found at i:175749 original size:17 final size:17
Alignment explanation
Indices: 175727--175768 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
175717 TCACACTCAT
*
175727 TTTCTCTAGCCTTT-CTC
1 TTTCTCTAG-ATTTCCTC
*
175744 TTTCTCTCGATTTCCTC
1 TTTCTCTAGATTTCCTC
175761 TTTCTCTA
1 TTTCTCTA
175769 CTTCACATTT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
16 3 0.14
17 18 0.86
ACGTcount: A:0.07, C:0.33, G:0.05, T:0.55
Consensus pattern (17 bp):
TTTCTCTAGATTTCCTC
Found at i:177592 original size:15 final size:17
Alignment explanation
Indices: 177574--177605 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
177564 TAGCATAATT
177574 TACCAAA-TCA-ATTCA
1 TACCAAACTCACATTCA
177589 TACCAAACTCACATTCA
1 TACCAAACTCACATTCA
177606 CAAGTATCAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 7 0.47
16 3 0.20
17 5 0.33
ACGTcount: A:0.44, C:0.31, G:0.00, T:0.25
Consensus pattern (17 bp):
TACCAAACTCACATTCA
Found at i:182718 original size:18 final size:18
Alignment explanation
Indices: 182695--182731 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
182685 AGATATGGGA
182695 ATGTCACCTGGCCGTGTG
1 ATGTCACCTGGCCGTGTG
182713 ATGTCACCTGGCCGTGTG
1 ATGTCACCTGGCCGTGTG
182731 A
1 A
182732 GCCACACGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.14, C:0.27, G:0.32, T:0.27
Consensus pattern (18 bp):
ATGTCACCTGGCCGTGTG
Found at i:187160 original size:17 final size:17
Alignment explanation
Indices: 187138--187172 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
187128 ATACAAAAGC
187138 AAAGTAACTAATATGGA
1 AAAGTAACTAATATGGA
187155 AAAGTAACTAATATGGA
1 AAAGTAACTAATATGGA
187172 A
1 A
187173 CATGTACATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.54, C:0.06, G:0.17, T:0.23
Consensus pattern (17 bp):
AAAGTAACTAATATGGA
Found at i:189926 original size:43 final size:43
Alignment explanation
Indices: 189811--189927 Score: 139
Period size: 43 Copynumber: 2.7 Consensus size: 43
189801 CTAATATCTT
*
189811 AGACGTGGTCTTACATGTAATCACATATCGATGCCACTGTCCC
1 AGACGTGGTCTTACATGTAATCACATATCGATGCCACTATCCC
** * *
189854 AGACAAGGTCTAACATGTAATCACTTATCGATGCCAAC-ATCCC
1 AGACGTGGTCTTACATGTAATCACATATCGATGCC-ACTATCCC
* *
189897 AGACGTGGTCTTATATG-AGAACACATATCGA
1 AGACGTGGTCTTACATGTA-ATCACATATCGA
189928 AAATCCTATG
Statistics
Matches: 61, Mismatches: 11, Indels: 4
0.80 0.14 0.05
Matches are distributed among these distances:
42 1 0.02
43 58 0.95
44 2 0.03
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.26
Consensus pattern (43 bp):
AGACGTGGTCTTACATGTAATCACATATCGATGCCACTATCCC
Found at i:194890 original size:9 final size:9
Alignment explanation
Indices: 194876--194908 Score: 57
Period size: 9 Copynumber: 3.7 Consensus size: 9
194866 GTTAAACGAA
194876 TCGAGTTAT
1 TCGAGTTAT
*
194885 TCGAGTTAA
1 TCGAGTTAT
194894 TCGAGTTAT
1 TCGAGTTAT
194903 TCGAGT
1 TCGAGT
194909 CAACTCGAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.24, C:0.12, G:0.24, T:0.39
Consensus pattern (9 bp):
TCGAGTTAT
Found at i:194897 original size:18 final size:18
Alignment explanation
Indices: 194874--194908 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
194864 AAGTTAAACG
194874 AATCGAGTTATTCGAGTT
1 AATCGAGTTATTCGAGTT
194892 AATCGAGTTATTCGAGT
1 AATCGAGTTATTCGAGT
194909 CAACTCGAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.29, C:0.11, G:0.23, T:0.37
Consensus pattern (18 bp):
AATCGAGTTATTCGAGTT
Found at i:195063 original size:21 final size:21
Alignment explanation
Indices: 195022--195064 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
195012 ACCCCAAACT
* *
195022 CTCAAACCTTTTTACTTTTCC
1 CTCAAAACTTTTTACTCTTCC
195043 CTCAAAAC-TTTTACTCCTTCC
1 CTCAAAACTTTTTACT-CTTCC
195064 C
1 C
195065 ACTTTCCCCC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 7 0.37
21 12 0.63
ACGTcount: A:0.21, C:0.37, G:0.00, T:0.42
Consensus pattern (21 bp):
CTCAAAACTTTTTACTCTTCC
Found at i:197493 original size:3 final size:3
Alignment explanation
Indices: 197485--197514 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
197475 AGTCATGCTT
197485 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
197515 CAACGATCAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:203897 original size:23 final size:22
Alignment explanation
Indices: 203809--203885 Score: 124
Period size: 21 Copynumber: 3.6 Consensus size: 22
203799 CATAAGTGTA
203809 TGAA-ACGACACACGAGGTGCC
1 TGAATACGACACACGAGGTGCC
203830 TG-ATACGACACACGAGGTGCC
1 TGAATACGACACACGAGGTGCC
203851 T-AATACGACACACGAGGTGCC
1 TGAATACGACACACGAGGTGCC
203872 TGAAATACGACACA
1 TG-AATACGACACA
203886 TAAAGTGCCT
Statistics
Matches: 52, Mismatches: 0, Indels: 6
0.90 0.00 0.10
Matches are distributed among these distances:
20 1 0.02
21 40 0.77
23 11 0.21
ACGTcount: A:0.35, C:0.27, G:0.25, T:0.13
Consensus pattern (22 bp):
TGAATACGACACACGAGGTGCC
Found at i:204039 original size:24 final size:24
Alignment explanation
Indices: 203991--204045 Score: 62
Period size: 24 Copynumber: 2.3 Consensus size: 24
203981 TATTCAATTT
203991 TCATA-TTTCAATTCAATCACTTTC
1 TCATATTTTCAATTCAATCAC-TTC
*
204015 TCATATTTTCCATTCAAATCA-TTC
1 TCATATTTTCAATTC-AATCACTTC
204039 TCA-ATTT
1 TCATATTT
204046 AAATCACAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
23 4 0.14
24 11 0.39
25 8 0.29
26 5 0.18
ACGTcount: A:0.29, C:0.24, G:0.00, T:0.47
Consensus pattern (24 bp):
TCATATTTTCAATTCAATCACTTC
Found at i:207200 original size:157 final size:156
Alignment explanation
Indices: 206906--207206 Score: 394
Period size: 157 Copynumber: 1.9 Consensus size: 156
206896 ATCTATGCCG
* * *
206906 AAAATCAAAGAATGTCTACCCATAAATGTTTCGAGGAATCATAGTAGGAGTTTTGTAACAAGCTA
1 AAAATCAAAGAATGTCTACCCATAAATGTCTAGAGGAATCATAGTAGGAGTTTTGTAACAAGCCA
* ** * * * *
206971 GTGAGCCCATTGTACAACAGTGTAGTAGGACTTTCTACTTCAGTTTTGGTTTCAACATTAGTCAC
66 GTGAACCCACCGCACAACAGTGTAGTAGGACTTTCTACTTCAGCTTTGGTTCCAACATTAGCCAC
*
207036 AACGGTGGCTGAAGGTGGACCTATCA
131 AAAGGTGGCTGAAGGTGGACCTATCA
*
207062 AAAATCGAAGAATGTCTACCCATAGACAT-TCTAG-GGACATCATAGTAGGAGTTTTGTAACAAG
1 AAAATCAAAGAATGTCTACCCATA-A-ATGTCTAGAGGA-ATCATAGTAGGAGTTTTGTAACAAG
* *
207125 CCAGT-ATATCCACCGCGCAATC-GTGTAGTAGGACTTTCTACTTCAGCTTTGGTTCCAACATTA
63 CCAGTGA-ACCCACCGCACAA-CAGTGTAGTAGGACTTTCTACTTCAGCTTTGGTTCCAACATTA
*
207188 GCCGCAAAGGTGGCTGAAG
126 GCCACAAAGGTGGCTGAAG
207207 ATAGACTTGG
Statistics
Matches: 125, Mismatches: 15, Indels: 9
0.84 0.10 0.06
Matches are distributed among these distances:
156 27 0.22
157 95 0.76
158 3 0.02
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.28
Consensus pattern (156 bp):
AAAATCAAAGAATGTCTACCCATAAATGTCTAGAGGAATCATAGTAGGAGTTTTGTAACAAGCCA
GTGAACCCACCGCACAACAGTGTAGTAGGACTTTCTACTTCAGCTTTGGTTCCAACATTAGCCAC
AAAGGTGGCTGAAGGTGGACCTATCA
Found at i:211446 original size:20 final size:20
Alignment explanation
Indices: 211421--211458 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
211411 AAATAGTTGA
211421 CTTGAC-GATTGAATCAATTG
1 CTTGACTGA-TGAATCAATTG
211441 CTTGACTGATGAATCAAT
1 CTTGACTGATGAATCAAT
211459 GACTTAACCG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 15 0.88
21 2 0.12
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Consensus pattern (20 bp):
CTTGACTGATGAATCAATTG
Found at i:213800 original size:3 final size:3
Alignment explanation
Indices: 213786--213814 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
213776 TCTTTCTTAT
213786 CTA CTA -TA CTA CTA CTA CTA CTA CTA CTA
1 CTA CTA CTA CTA CTA CTA CTA CTA CTA CTA
213815 TTATTATTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.08
3 23 0.92
ACGTcount: A:0.34, C:0.31, G:0.00, T:0.34
Consensus pattern (3 bp):
CTA
Found at i:216535 original size:16 final size:16
Alignment explanation
Indices: 216514--216544 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
216504 TTCACTATTA
*
216514 TGTCTTTTGTATTTTC
1 TGTCTTTTATATTTTC
216530 TGTCTTTTATATTTT
1 TGTCTTTTATATTTT
216545 ACATGCATAG
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:0.10, C:0.10, G:0.10, T:0.71
Consensus pattern (16 bp):
TGTCTTTTATATTTTC
Found at i:218247 original size:48 final size:48
Alignment explanation
Indices: 218168--218361 Score: 166
Period size: 48 Copynumber: 4.1 Consensus size: 48
218158 AGATCCCGCA
* * ** * *
218168 TAAGACCATATCTGGGATATGGCATCAGCATCGTTATGTGATCCCATA
1 TAAGACCATGTCTGGGACATGGCATTGGCATCGATATGTGATCCCATG
* * *
218216 TAAGACCATGTCTGGGACATGGCATTGGCATCGATATGAGAACATCATG
1 TAAGACCATGTCTGGGACATGGCATTGGCATCGATATGTGATC-CCATG
* * * *
218265 TAAGACCATAG-CTAGG-CTATCGGC-TTCG-AT--ATGTGTGATCTCATG
1 TAAGACCAT-GTCTGGGAC-AT-GGCATTGGCATCGATATGTGATCCCATG
* * *
218310 TAATACCATGTCTGGGACATGGCATTGGCATCGATAAGTGGTCCCATG
1 TAAGACCATGTCTGGGACATGGCATTGGCATCGATATGTGATCCCATG
218358 TAAG
1 TAAG
218362 TGTAATATCC
Statistics
Matches: 114, Mismatches: 22, Indels: 20
0.73 0.14 0.13
Matches are distributed among these distances:
44 4 0.04
45 22 0.19
46 10 0.09
48 53 0.46
49 21 0.18
50 4 0.04
ACGTcount: A:0.28, C:0.20, G:0.25, T:0.28
Consensus pattern (48 bp):
TAAGACCATGTCTGGGACATGGCATTGGCATCGATATGTGATCCCATG
Found at i:219694 original size:46 final size:46
Alignment explanation
Indices: 219644--219819 Score: 216
Period size: 46 Copynumber: 3.8 Consensus size: 46
219634 TGGTTGAGCA
219644 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
219690 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
*
219735 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
219783 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
219820 GCGGGTTACA
Statistics
Matches: 111, Mismatches: 10, Indels: 18
0.80 0.07 0.13
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
45 3 0.03
46 63 0.57
47 29 0.26
48 3 0.03
50 4 0.04
51 2 0.02
ACGTcount: A:0.20, C:0.21, G:0.30, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:219800 original size:93 final size:93
Alignment explanation
Indices: 219641--219812 Score: 317
Period size: 93 Copynumber: 1.8 Consensus size: 93
219631 GGATGGTTGA
* *
219641 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
219706 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
*
219734 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
219799 TGAGTCCGAGTTCG
66 TGAGTCCGAGTTCG
219813 CTTATGGGCG
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 76 1.00
ACGTcount: A:0.21, C:0.22, G:0.30, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:229053 original size:42 final size:42
Alignment explanation
Indices: 228990--229087 Score: 151
Period size: 42 Copynumber: 2.3 Consensus size: 42
228980 ATAGCCCAGT
* *
228990 TATGGTCTTACATGAAATCTCATATTGACGCCATATCCCAAA
1 TATGGTCTTACACGAAATCTCATACTGACGCCATATCCCAAA
* *
229032 TATGGTCTTACACGAAGTCTCATACTGACGCCATATCCCAGA
1 TATGGTCTTACACGAAATCTCATACTGACGCCATATCCCAAA
*
229074 TATAGTCTTACACG
1 TATGGTCTTACACG
229088 TAACCTCAGT
Statistics
Matches: 51, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 51 1.00
ACGTcount: A:0.31, C:0.26, G:0.14, T:0.30
Consensus pattern (42 bp):
TATGGTCTTACACGAAATCTCATACTGACGCCATATCCCAAA
Found at i:230258 original size:81 final size:81
Alignment explanation
Indices: 230123--230284 Score: 315
Period size: 81 Copynumber: 2.0 Consensus size: 81
230113 AATCGTTCCA
*
230123 TAAAATTGTAGACTATAAAAATATAATAAAAATAAATTTTCTACGTTAGATTCGTGGTCACAAAT
1 TAAAATTGTAGACTATAAAAATATAATAAAAATAAATTTTCTACGTTAGATTCGTGGTCACAAAA
230188 CCACTGTTCTGATTAG
66 CCACTGTTCTGATTAG
230204 TAAAATTGTAGACTATAAAAATATAATAAAAATAAATTTTCTACGTTAGATTCGTGGTCACAAAA
1 TAAAATTGTAGACTATAAAAATATAATAAAAATAAATTTTCTACGTTAGATTCGTGGTCACAAAA
230269 CCACTGTTCTGATTAG
66 CCACTGTTCTGATTAG
230285 ACCCAAAATC
Statistics
Matches: 80, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
81 80 1.00
ACGTcount: A:0.41, C:0.12, G:0.12, T:0.34
Consensus pattern (81 bp):
TAAAATTGTAGACTATAAAAATATAATAAAAATAAATTTTCTACGTTAGATTCGTGGTCACAAAA
CCACTGTTCTGATTAG
Found at i:235258 original size:26 final size:26
Alignment explanation
Indices: 235222--235281 Score: 93
Period size: 26 Copynumber: 2.3 Consensus size: 26
235212 GAAGCTCCGG
235222 AGAGCCATTAATCAGGAAGCTCACAA
1 AGAGCCATTAATCAGGAAGCTCACAA
* * *
235248 AGAGCCTTTAATTAGGAAGCTCACGA
1 AGAGCCATTAATCAGGAAGCTCACAA
235274 AGAGCCAT
1 AGAGCCAT
235282 ATATAGGTAT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.38, C:0.22, G:0.22, T:0.18
Consensus pattern (26 bp):
AGAGCCATTAATCAGGAAGCTCACAA
Found at i:236433 original size:46 final size:47
Alignment explanation
Indices: 236377--236498 Score: 138
Period size: 50 Copynumber: 2.6 Consensus size: 47
236367 GGGTTGACAG
* *
236377 GACAGAAATGAGTCATGTAAGTCCATATCAG-ATATATGGCTTTGGA
1 GACAGGAATGAGTCATGTAAGTCCATATCAGAATATATGGCATTGGA
* * *
236423 GACAGGAATGAGCCATGTAAGCCCATATTAGATATATATATGGCATTGGA
1 GACAGGAATGAGTCATGTAAGTCCATATCAG--A-ATATATGGCATTGGA
* * *
236473 GATAGGAATAATTCATGTAAGTCCAT
1 GACAGGAATGAGTCATGTAAGTCCAT
236499 GTTGAAGACA
Statistics
Matches: 62, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
46 27 0.44
50 35 0.56
ACGTcount: A:0.36, C:0.13, G:0.23, T:0.28
Consensus pattern (47 bp):
GACAGGAATGAGTCATGTAAGTCCATATCAGAATATATGGCATTGGA
Found at i:238904 original size:15 final size:15
Alignment explanation
Indices: 238884--238961 Score: 88
Period size: 15 Copynumber: 5.2 Consensus size: 15
238874 CATAGTATCG
*
238884 TATCTTGGGTTTCTT
1 TATCTTGGATTTCTT
*
238899 TATCTTGGATCTCTT
1 TATCTTGGATTTCTT
238914 TAT-TCTGGATTTCTT
1 TATCT-TGGATTTCTT
* *
238929 TAT-TCTGGGTTTCTC
1 TATCT-TGGATTTCTT
238944 TATCTTGGATTTCTT
1 TATCTTGGATTTCTT
238959 TAT
1 TAT
238962 TCGGTTTTCT
Statistics
Matches: 54, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
14 1 0.02
15 52 0.96
16 1 0.02
ACGTcount: A:0.12, C:0.15, G:0.15, T:0.58
Consensus pattern (15 bp):
TATCTTGGATTTCTT
Found at i:244039 original size:46 final size:45
Alignment explanation
Indices: 243986--244201 Score: 213
Period size: 46 Copynumber: 4.7 Consensus size: 45
243976 AGATTTGTGT
243986 GCCAGTGTAAGACATGTCTGGGACATGCATCGGTCGTATTATGATA
1 GCCAGTGTAAGACATGTCTGGGACATGCATCGGTCGTA-TATGATA
* * ** *
244032 GCCAGTGTAAGACCATGTCTGGGACATGCATCAGCCACAGTATGAGA
1 GCCAGTGTAAGA-CATGTCTGGGACATGCATCGGTCGTA-TATGATA
* * *
244079 GCCAGTGTAAGACATGTCTGGGACATGCATTGGCCTCG-AGATGTTA
1 GCCAGTGTAAGACATGTCTGGGACATGCATCGG--TCGTATATGATA
* * * * *
244125 GCCAGTGTCAGACATGTCTGGGACATGCGTCGG-C-TACAAGATGT
1 GCCAGTGTAAGACATGTCTGGGACATGCATCGGTCGTATATGAT-A
* * *
244169 GCTAGTGTATGACATGTCTAGGACATGCATCGG
1 GCCAGTGTAAGACATGTCTGGGACATGCATCGG
244202 CACGGTTACA
Statistics
Matches: 140, Mismatches: 25, Indels: 12
0.79 0.14 0.07
Matches are distributed among these distances:
43 5 0.04
44 28 0.20
46 65 0.46
47 41 0.29
48 1 0.01
ACGTcount: A:0.25, C:0.20, G:0.30, T:0.25
Consensus pattern (45 bp):
GCCAGTGTAAGACATGTCTGGGACATGCATCGGTCGTATATGATA
Found at i:244106 original size:93 final size:89
Alignment explanation
Indices: 243986--244202 Score: 258
Period size: 93 Copynumber: 2.4 Consensus size: 89
243976 AGATTTGTGT
*
243986 GCCAGTGTAAGACATGTCTGGGACATGCATCGG-TCGTATTATGATAGCCAGTGTAAGACCATGT
1 GCCAGTGTAAGACATGTCTGGGACATGCATCGGCTCG-A-GATGATAGCCAGTGTAAGA-CATGT
244050 CTGGGACATGCATCAGCCAC-AGTATGAGA
63 CTGGGACATGCATCAGCCACAAG-AT--GA
* * *
244079 GCCAGTGTAAGACATGTCTGGGACATGCATTGGCCTCGAGATGTTAGCCAGTGTCAGACATGTCT
1 GCCAGTGTAAGACATGTCTGGGACATGCATCGG-CTCGAGATGATAGCCAGTGTAAGACATGTCT
* * * *
244144 GGGACATGCGTCGGCTACAAGATGT
65 GGGACATGCATCAGCCACAAGATGA
* * *
244169 GCTAGTGTATGACATGTCTAGGACATGCATCGGC
1 GCCAGTGTAAGACATGTCTGGGACATGCATCGGC
244203 ACGGTTACAT
Statistics
Matches: 109, Mismatches: 12, Indels: 10
0.83 0.09 0.08
Matches are distributed among these distances:
89 1 0.01
90 30 0.28
92 24 0.22
93 50 0.46
94 1 0.01
95 3 0.03
ACGTcount: A:0.25, C:0.21, G:0.29, T:0.24
Consensus pattern (89 bp):
GCCAGTGTAAGACATGTCTGGGACATGCATCGGCTCGAGATGATAGCCAGTGTAAGACATGTCTG
GGACATGCATCAGCCACAAGATGA
Found at i:250126 original size:48 final size:48
Alignment explanation
Indices: 250062--250370 Score: 537
Period size: 48 Copynumber: 6.4 Consensus size: 48
250052 TATATATGTG
250062 TGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATGTATA
1 TGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATGTATA
*
250110 TGTGGTAAAGCGGAATGGCTAATGTGAAATATGTATGAGATATGTATA
1 TGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATGTATA
*
250158 TGTGGTAAAGCCGAGTGGCTAATGTGAAATATGTATGAGATATGTATA
1 TGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATGTATA
* *
250206 TGTGGTAAAGCCGAATGGCTAGTGTGAACTATGTATGAGATATGTATA
1 TGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATGTATA
* * * *
250254 CGTGGTAAAGCTGAATGACTAGTGTGAAATATGTATGAGATATGTATA
1 TGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATGTATA
*
250302 TGTGGTAAAGCCGAATGGCTAATGCGAAATATGTATGAGATATGTATA
1 TGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATGTATA
250350 TGTGGTAAAGCCGAATGGCTA
1 TGTGGTAAAGCCGAATGGCTA
250371 GTGATTCGGC
Statistics
Matches: 246, Mismatches: 15, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
48 246 1.00
ACGTcount: A:0.34, C:0.07, G:0.28, T:0.30
Consensus pattern (48 bp):
TGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATGTATA
Found at i:250593 original size:37 final size:37
Alignment explanation
Indices: 250543--250645 Score: 188
Period size: 37 Copynumber: 2.8 Consensus size: 37
250533 GGAAATATAT
250543 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
*
250580 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
*
250617 TCCGGGTAAGACCCGATAACTACGTGTGG
1 TCCGGGTAAGACCCGATGACTACGTGTGG
250646 GGACTATCCG
Statistics
Matches: 64, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 64 1.00
ACGTcount: A:0.23, C:0.20, G:0.32, T:0.24
Consensus pattern (37 bp):
TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
Found at i:253055 original size:12 final size:12
Alignment explanation
Indices: 253038--253069 Score: 64
Period size: 12 Copynumber: 2.7 Consensus size: 12
253028 TGTAATTGTC
253038 CACACGGGTAGA
1 CACACGGGTAGA
253050 CACACGGGTAGA
1 CACACGGGTAGA
253062 CACACGGG
1 CACACGGG
253070 CGTGTGTCTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.31, C:0.28, G:0.34, T:0.06
Consensus pattern (12 bp):
CACACGGGTAGA
Found at i:260266 original size:21 final size:21
Alignment explanation
Indices: 260242--260288 Score: 94
Period size: 21 Copynumber: 2.2 Consensus size: 21
260232 TCGAGTAGTA
260242 TTTTCCAGCCAGAATTCAGCT
1 TTTTCCAGCCAGAATTCAGCT
260263 TTTTCCAGCCAGAATTCAGCT
1 TTTTCCAGCCAGAATTCAGCT
260284 TTTTC
1 TTTTC
260289 TAGATCATCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.21, C:0.28, G:0.13, T:0.38
Consensus pattern (21 bp):
TTTTCCAGCCAGAATTCAGCT
Found at i:262430 original size:40 final size:40
Alignment explanation
Indices: 262359--262603 Score: 352
Period size: 40 Copynumber: 6.2 Consensus size: 40
262349 CGAATGATAA
* *
262359 CGAAGGCATTTGTGCTAGTGACTA-ATCCCGGGCTAAGTCC
1 CGAAGGCATTTGTGCGAGTTACTATAT-CCGGGCTAAGTCC
*
262399 CGAAGGCATTTGTGCGAGTTACTAGATCCGGGCTAAGTCC
1 CGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCC
*
262439 CGAAGGCATTTGTGCAAGTTACTATATCCGGGCTAAGTCC
1 CGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCC
262479 CGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCC
1 CGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCC
* * *
262519 CAAAGGCATTGGTGCGAGCTACTATATCCGGGCTAAGTCC
1 CGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCC
* * * *
262559 CGATGGCATTTGAGCGAG-TAGCTATATCC-GGTTAAATCC
1 CGAAGGCATTTGTGCGAGTTA-CTATATCCGGGCTAAGTCC
262598 CGAAGG
1 CGAAGG
262604 TACTTGGTTT
Statistics
Matches: 188, Mismatches: 15, Indels: 5
0.90 0.07 0.02
Matches are distributed among these distances:
39 15 0.08
40 171 0.91
41 2 0.01
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (40 bp):
CGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCC
Found at i:264662 original size:13 final size:14
Alignment explanation
Indices: 264644--264676 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
264634 TATCAAAGGA
264644 GCACACGA-CCAGG
1 GCACACGATCCAGG
264657 GCACAC-ATCCAGG
1 GCACACGATCCAGG
264670 GCACACG
1 GCACACG
264677 CCCATATGGC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 1 0.06
13 17 0.94
ACGTcount: A:0.30, C:0.39, G:0.27, T:0.03
Consensus pattern (14 bp):
GCACACGATCCAGG
Found at i:265706 original size:33 final size:33
Alignment explanation
Indices: 265668--265781 Score: 133
Period size: 33 Copynumber: 3.5 Consensus size: 33
265658 GGTGTACATT
**
265668 CCTTTTCAAGTGGTACACACAAAGTATACCTTT
1 CCTTTTCAAGTGGTACACACAAAGTATACCTAA
*
265701 CCTTTTCATA-TGGTATACACAAAGTATACCTAA
1 CCTTTTCA-AGTGGTACACACAAAGTATACCTAA
** * *
265734 CCTTACCAAGT-GTACACACAAAGTGTACATAA
1 CCTTTTCAAGTGGTACACACAAAGTATACCTAA
*
265766 CCTTTTCAAGTTGTAC
1 CCTTTTCAAGTGGTAC
265782 CACTTGGGTA
Statistics
Matches: 68, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
32 28 0.41
33 39 0.57
34 1 0.01
ACGTcount: A:0.33, C:0.24, G:0.11, T:0.32
Consensus pattern (33 bp):
CCTTTTCAAGTGGTACACACAAAGTATACCTAA
Found at i:272288 original size:51 final size:51
Alignment explanation
Indices: 272223--272617 Score: 681
Period size: 51 Copynumber: 7.8 Consensus size: 51
272213 TGAAGATGCG
* *
272223 TATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACCCGTATATA
1 TATGTGTGCTAAGGCCGAATGGCCAATGTGATCAATGTGAACCCGTATATA
*
272274 TATGTGTGATAAGGCCGAATGGCCAATGTGATCAATGTGAACCCGTATATA
1 TATGTGTGCTAAGGCCGAATGGCCAATGTGATCAATGTGAACCCGTATATA
272325 TATGTGTGCTAAGGCCGAATGGCCAATGTGATCAATGTGAACCCGTATATA
1 TATGTGTGCTAAGGCCGAATGGCCAATGTGATCAATGTGAACCCGTATATA
272376 TATGTGTGCTAAGGCCGAATGGCCAATGTGATCAATGTGAACCCGTATATA
1 TATGTGTGCTAAGGCCGAATGGCCAATGTGATCAATGTGAACCCGTATATA
272427 TATGTGTGCTAAGGCCGAATGGCCAATGTGATCAATGTGAACCCGTATATA
1 TATGTGTGCTAAGGCCGAATGGCCAATGTGATCAATGTGAACCCGTATATA
272478 TATGTGTGCTAAGGCCGAATGGCCAATGTGATCAATGTGAACCCGTATATA
1 TATGTGTGCTAAGGCCGAATGGCCAATGTGATCAATGTGAACCCGTATATA
* ***
272529 TATGTGTGCTAAGGCCGAATGGCCAATGTGATGAATGTGAA--C--ATGCG
1 TATGTGTGCTAAGGCCGAATGGCCAATGTGATCAATGTGAACCCGTATATA
* *
272576 TATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAC
1 TATGTGTGCTAAGGCCGAATGGCCAATGTGATCAATGTGAAC
272618 ATGCATATAT
Statistics
Matches: 336, Mismatches: 7, Indels: 5
0.97 0.02 0.01
Matches are distributed among these distances:
47 42 0.12
49 1 0.00
51 293 0.87
ACGTcount: A:0.30, C:0.16, G:0.27, T:0.27
Consensus pattern (51 bp):
TATGTGTGCTAAGGCCGAATGGCCAATGTGATCAATGTGAACCCGTATATA
Found at i:272972 original size:37 final size:37
Alignment explanation
Indices: 272854--272965 Score: 188
Period size: 37 Copynumber: 3.0 Consensus size: 37
272844 AACTTGGAAA
*
272854 TATGTCCGGGTAAGACCCGATGACTACGTGTGGAGAT
1 TATGTCTGGGTAAGACCCGATGACTACGTGTGGAGAT
272891 TATGTCTGGGTAAGACCCGATGACTACGTGTGGAGAT
1 TATGTCTGGGTAAGACCCGATGACTACGTGTGGAGAT
* * *
272928 TATGTCTGGGTAAGACCCGATAACTTCATGTGGAGAT
1 TATGTCTGGGTAAGACCCGATGACTACGTGTGGAGAT
272965 T
1 T
272966 TCGTCTGAGC
Statistics
Matches: 71, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 71 1.00
ACGTcount: A:0.25, C:0.17, G:0.30, T:0.28
Consensus pattern (37 bp):
TATGTCTGGGTAAGACCCGATGACTACGTGTGGAGAT
Found at i:276404 original size:43 final size:42
Alignment explanation
Indices: 276297--276407 Score: 116
Period size: 43 Copynumber: 2.6 Consensus size: 42
276287 ATAGGATTTA
*
276297 CGATATGTGATTGCGTGTAAGACCATGTCTGGGACATCGACAT
1 CGATATGTGATT-CGTGTAAGACCATATCTGGGACATCGACAT
* * * * *
276340 CGTATACGTGATTCGTCTAAGACCCTATCTGGGATAGT-GGCAT
1 CG-ATATGTGATTCGTGTAAGACCATATCTGGGACA-TCGACAT
*
276383 CGATATGTGATTACATGTAAGACCA
1 CGATATGTGATT-CGTGTAAGACCA
276408 CGTCTAGGAC
Statistics
Matches: 55, Mismatches: 10, Indels: 6
0.77 0.14 0.08
Matches are distributed among these distances:
42 9 0.16
43 36 0.65
44 10 0.18
ACGTcount: A:0.27, C:0.19, G:0.25, T:0.29
Consensus pattern (42 bp):
CGATATGTGATTCGTGTAAGACCATATCTGGGACATCGACAT
Found at i:277964 original size:28 final size:22
Alignment explanation
Indices: 277912--277958 Score: 94
Period size: 22 Copynumber: 2.1 Consensus size: 22
277902 TTGATTTAGT
277912 TATTTTATTAAGGTTAAGGTAA
1 TATTTTATTAAGGTTAAGGTAA
277934 TATTTTATTAAGGTTAAGGTAA
1 TATTTTATTAAGGTTAAGGTAA
277956 TAT
1 TAT
277959 ATATATATGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.36, C:0.00, G:0.17, T:0.47
Consensus pattern (22 bp):
TATTTTATTAAGGTTAAGGTAA
Found at i:279686 original size:29 final size:28
Alignment explanation
Indices: 279606--279698 Score: 154
Period size: 29 Copynumber: 3.3 Consensus size: 28
279596 AGAACCCAAG
279606 TTTTGCAATTTATTCAATTTGGTCCCTAA
1 TTTT-CAATTTATTCAATTTGGTCCCTAA
279635 TTTTCAA-TT-TTCAATTTGGTCCCTAA
1 TTTTCAATTTATTCAATTTGGTCCCTAA
279661 TTTTGCAATTTATTCAATTTGGTCCCTAA
1 TTTT-CAATTTATTCAATTTGGTCCCTAA
279690 TTTTCAATT
1 TTTTCAATT
279699 GGACACCTTA
Statistics
Matches: 61, Mismatches: 0, Indels: 7
0.90 0.00 0.10
Matches are distributed among these distances:
26 21 0.34
27 5 0.08
28 10 0.16
29 25 0.41
ACGTcount: A:0.24, C:0.17, G:0.09, T:0.51
Consensus pattern (28 bp):
TTTTCAATTTATTCAATTTGGTCCCTAA
Found at i:283637 original size:27 final size:27
Alignment explanation
Indices: 283599--283650 Score: 95
Period size: 27 Copynumber: 1.9 Consensus size: 27
283589 GATAATAGTC
*
283599 CATTTCTAACAATATCAAATTTATTGT
1 CATTTCTAACAATATCAAATATATTGT
283626 CATTTCTAACAATATCAAATATATT
1 CATTTCTAACAATATCAAATATATT
283651 AAAAAATTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.40, C:0.15, G:0.02, T:0.42
Consensus pattern (27 bp):
CATTTCTAACAATATCAAATATATTGT
Found at i:283759 original size:25 final size:23
Alignment explanation
Indices: 283704--283748 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
283694 ACTTACTAAC
* *
283704 AAATCACAATAAACAAAATATAA
1 AAATAACACTAAACAAAATATAA
*
283727 AAATAACACTAAACAAACTATA
1 AAATAACACTAAACAAAATATA
283749 TAATACTAAC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.67, C:0.16, G:0.00, T:0.18
Consensus pattern (23 bp):
AAATAACACTAAACAAAATATAA
Found at i:283835 original size:41 final size:41
Alignment explanation
Indices: 283790--283873 Score: 150
Period size: 41 Copynumber: 2.0 Consensus size: 41
283780 ATCTATTATA
*
283790 TTTGAAAAAAACAATAAGAAAATTACATTTTCTTTTCTTTC
1 TTTGAAAAAAACAATAAGAAAAATACATTTTCTTTTCTTTC
*
283831 TTTGAAAATAACAATAAGAAAAATACATTTTCTTTTCTTTC
1 TTTGAAAAAAACAATAAGAAAAATACATTTTCTTTTCTTTC
283872 TT
1 TT
283874 CTCTTTTCTT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.40, C:0.12, G:0.05, T:0.43
Consensus pattern (41 bp):
TTTGAAAAAAACAATAAGAAAAATACATTTTCTTTTCTTTC
Found at i:283887 original size:18 final size:18
Alignment explanation
Indices: 283858--283901 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
283848 GAAAAATACA
283858 TTTTCTTTTCTTTCTTCTC
1 TTTTC-TTTCTTTCTTCTC
283877 TTTTCTTTCTTTCTTCTC
1 TTTTCTTTCTTTCTTCTC
*
283895 TTCTCTT
1 TTTTCTT
283902 CTCTCTCTCT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 19 0.79
19 5 0.21
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (18 bp):
TTTTCTTTCTTTCTTCTC
Found at i:283902 original size:5 final size:5
Alignment explanation
Indices: 283861--283912 Score: 56
Period size: 5 Copynumber: 10.8 Consensus size: 5
283851 AAATACATTT
* *
283861 TCTTT TCTT- TCTTC TCTTT TCTT- TCTT- TCTTC TCTTC TCTTC TCTCTC
1 TCTTC TCTTC TCTTC TCTTC TCTTC TCTTC TCTTC TCTTC TCTTC TCT-TC
283909 TCTT
1 TCTT
283913 GTTCTGTAAT
Statistics
Matches: 43, Mismatches: 1, Indels: 6
0.86 0.02 0.12
Matches are distributed among these distances:
4 12 0.28
5 26 0.60
6 5 0.12
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (5 bp):
TCTTC
Found at i:306975 original size:13 final size:13
Alignment explanation
Indices: 306957--306984 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
306947 TTACTGCAGC
306957 TTTTCATATAAAA
1 TTTTCATATAAAA
306970 TTTTCATATAAAA
1 TTTTCATATAAAA
306983 TT
1 TT
306985 ATTTAACATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.43, C:0.07, G:0.00, T:0.50
Consensus pattern (13 bp):
TTTTCATATAAAA
Found at i:334110 original size:20 final size:19
Alignment explanation
Indices: 334085--334127 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
334075 ATAAGGGACA
*
334085 TTTTAAATATGAATGAATAT
1 TTTTAAATATGAACGAA-AT
*
334105 TTTT-AATTTGAACGAAAT
1 TTTTAAATATGAACGAAAT
334123 TTTTA
1 TTTTA
334128 TGGCCTGATT
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
18 6 0.30
19 10 0.50
20 4 0.20
ACGTcount: A:0.40, C:0.02, G:0.09, T:0.49
Consensus pattern (19 bp):
TTTTAAATATGAACGAAAT
Found at i:334858 original size:36 final size:36
Alignment explanation
Indices: 334818--334890 Score: 146
Period size: 36 Copynumber: 2.0 Consensus size: 36
334808 ATGTGTTTGA
334818 TATGTTTGATTAAGTGAATGTGATGAGAAAAGACAT
1 TATGTTTGATTAAGTGAATGTGATGAGAAAAGACAT
334854 TATGTTTGATTAAGTGAATGTGATGAGAAAAGACAT
1 TATGTTTGATTAAGTGAATGTGATGAGAAAAGACAT
334890 T
1 T
334891 TGAAATTCAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.38, C:0.03, G:0.25, T:0.34
Consensus pattern (36 bp):
TATGTTTGATTAAGTGAATGTGATGAGAAAAGACAT
Found at i:338215 original size:46 final size:46
Alignment explanation
Indices: 338165--338532 Score: 280
Period size: 46 Copynumber: 7.7 Consensus size: 46
338155 TGAGCATCCA
338165 AACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGAGAATGTCCG
1 AACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGAGAATGTCCG
*** * *
338211 AACTCGTTGAGTTGAGTCCGAGTTCGAGAGATGTAACT-AGGCA--TCCG
1 AACTCGTTGAGTTGAGTCCGAGTTC-ACTTATG-GA-TGA-GAATGTCCG
* * * * *
338258 AGCTCGTTGAGTTGAGTTCGAGTTCACTTATGGATGCGAACGCCCG
1 AACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGAGAATGTCCG
* * **
338304 AGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGGGCGACTAGGATGGTTGAGCATCCG
1 AACTCGTTGAGTTGAGTCCGAGTTCACTTAT--G-GA-T--GA-GAAT--G--TCCG
*
338361 AACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCG
1 AACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGAGAATGTCCG
*** * *
338407 AACTCGTTGAGTTGAGTCCGAGTTCGAGAGATGTAACT-AGGCA--TCCG
1 AACTCGTTGAGTTGAGTCCGAGTTC-ACTTATG-GA-TGA-GAATGTCCG
* * * * *
338454 AGCTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGCGAACGCCCG
1 AACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGAGAATGTCCG
* *
338500 AGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 AACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
338533 GCAGATTACA
Statistics
Matches: 254, Mismatches: 43, Indels: 50
0.73 0.12 0.14
Matches are distributed among these distances:
44 6 0.02
45 2 0.01
46 128 0.50
47 62 0.24
48 5 0.02
49 8 0.03
50 3 0.01
51 1 0.00
52 1 0.00
53 2 0.01
54 2 0.01
55 2 0.01
57 32 0.13
ACGTcount: A:0.21, C:0.20, G:0.31, T:0.29
Consensus pattern (46 bp):
AACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGAGAATGTCCG
Found at i:338317 original size:93 final size:93
Alignment explanation
Indices: 338158--338525 Score: 493
Period size: 93 Copynumber: 3.8 Consensus size: 93
338148 GGATGGTTGA
* * * *
338158 GCATCCAAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGAGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
338223 TGAGTCCGAGTTCGAGAGATGTAACTAG
66 TGAGTCCGAGTTCGAGAGATGTAACTAG
* * *
338251 GCATCCGAGCTCGTTGAGTTGAGTTCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
* * ** *
338316 TGAGTCCGAGTTCGCTTATGGGCGACTAGGATGGTTG
66 TGAGTCCGAGTTCG---A---GAGA-T-GTA-ACTAG
* *
338353 AGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAG
1 -GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
338418 TTGAGTCCGAGTTCGAGAGATGTAACTAG
65 TTGAGTCCGAGTTCGAGAGATGTAACTAG
* * *
338447 GCATCCGAGCTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
338512 TGAGTCCGAGTTCG
66 TGAGTCCGAGTTCG
338526 CTTATGGGCA
Statistics
Matches: 238, Mismatches: 27, Indels: 20
0.84 0.09 0.07
Matches are distributed among these distances:
93 146 0.61
94 2 0.01
95 2 0.01
96 2 0.01
97 3 0.01
99 3 0.01
100 2 0.01
101 2 0.01
102 2 0.01
103 74 0.31
ACGTcount: A:0.21, C:0.20, G:0.30, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGAGAGATGTAACTAG
Found at i:338479 original size:196 final size:196
Alignment explanation
Indices: 338144--338534 Score: 748
Period size: 196 Copynumber: 2.0 Consensus size: 196
338134 GTGACATGTC
338144 ACTAGGATGGTTGAGCATCCAAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGAGAATGTC
1 ACTAGGATGGTTGAGCATCCAAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGAGAATGTC
338209 CGAACTCGTTGAGTTGAGTCCGAGTTCGAGAGATGTAACTAGGCATCCGAGCTCGTTGAGTTGAG
66 CGAACTCGTTGAGTTGAGTCCGAGTTCGAGAGATGTAACTAGGCATCCGAGCTCGTTGAGTTGAG
338274 TTCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGGGC
131 TTCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGGGC
338339 G
196 G
* *
338340 ACTAGGATGGTTGAGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTC
1 ACTAGGATGGTTGAGCATCCAAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGAGAATGTC
338405 CGAACTCGTTGAGTTGAGTCCGAGTTCGAGAGATGTAACTAGGCATCCGAGCTCGTTGAGTTGAG
66 CGAACTCGTTGAGTTGAGTCCGAGTTCGAGAGATGTAACTAGGCATCCGAGCTCGTTGAGTTGAG
338470 -TCTGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGGG
131 TTC-GAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGGG
338534 C
195 C
338535 AGATTACATG
Statistics
Matches: 192, Mismatches: 2, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
195 2 0.01
196 190 0.99
ACGTcount: A:0.21, C:0.20, G:0.31, T:0.28
Consensus pattern (196 bp):
ACTAGGATGGTTGAGCATCCAAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGAGAATGTC
CGAACTCGTTGAGTTGAGTCCGAGTTCGAGAGATGTAACTAGGCATCCGAGCTCGTTGAGTTGAG
TTCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGGGC
G
Found at i:338880 original size:194 final size:194
Alignment explanation
Indices: 338547--338933 Score: 729
Period size: 194 Copynumber: 2.0 Consensus size: 194
338537 ATTACATGGT
*
338547 AGCTTGGCTACATATGTGGCACTTATGTGCAAAGTTTCTATGTATCCGAATTATATTCCGATGTG
1 AGCTTGGCTACATATGTGGCACTTATGTGCAAAGTTTCCATGTATCCGAATTATATTCCGATGTG
338612 TTCAACGGGTAAAGTTCTACTGAAATGGAGGAATACTCAAGAAGAAAGGGACGTATTGTTAAGTG
66 TTCAACGGGTAAAGTTCTACTGAAATGGAGGAATACTCAAGAAGAAAGGGACGTATTGTTAAGTG
338677 TTATGAAATGGGTACTTTGAACAGGTATGTACTTAACCCTCGGGTTGAAAAATCGATATAACAA
131 TTATGAAATGGGTACTTTGAACAGGTATGTACTTAACCCTCGGGTTGAAAAATCGATATAACAA
*
338741 AGCTTGGCTACATATGTGGCACTTATGTGCAAAGTTTCCATGTATCCGAATTATATTCTGATGTG
1 AGCTTGGCTACATATGTGGCACTTATGTGCAAAGTTTCCATGTATCCGAATTATATTCCGATGTG
* *
338806 TTCAACGGGTAAAGTTCTACTGAAATGGAGGAATACTCCAGAAGAAAGGGATGTATTGTTAAGTG
66 TTCAACGGGTAAAGTTCTACTGAAATGGAGGAATACTCAAGAAGAAAGGGACGTATTGTTAAGTG
*
338871 TTGTGAAATGGGTACTTTGAACAGGTATGTACTTAACCCTCGGGTTGAAAAATCGATATAACA
131 TTATGAAATGGGTACTTTGAACAGGTATGTACTTAACCCTCGGGTTGAAAAATCGATATAACA
338934 GACTAGGATG
Statistics
Matches: 188, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
194 188 1.00
ACGTcount: A:0.32, C:0.14, G:0.24, T:0.31
Consensus pattern (194 bp):
AGCTTGGCTACATATGTGGCACTTATGTGCAAAGTTTCCATGTATCCGAATTATATTCCGATGTG
TTCAACGGGTAAAGTTCTACTGAAATGGAGGAATACTCAAGAAGAAAGGGACGTATTGTTAAGTG
TTATGAAATGGGTACTTTGAACAGGTATGTACTTAACCCTCGGGTTGAAAAATCGATATAACAA
Found at i:339002 original size:46 final size:46
Alignment explanation
Indices: 338952--339121 Score: 172
Period size: 46 Copynumber: 3.7 Consensus size: 46
338942 TGGTTGAGCA
* *
338952 TCCGAACTCGTTGAGTTGAGTTCAAGTTCACCTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACCTATGGATGCGAATG
* *
338998 TCCGAACTCGTTGAGTTGAGTCCGAGTT---C-GTGAGATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACCTATG-GATGCGAA-T--G
* *
339043 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACCTATGGATGCGAATG
*
339091 -CCCAAGCTCGTTGAGTTGAGTCCGAGTTCAC
1 TCCGAA-CTCGTTGAGTTGAGTCCGAGTTCAC
339122 TTAGGGGCGG
Statistics
Matches: 103, Mismatches: 9, Indels: 24
0.76 0.07 0.18
Matches are distributed among these distances:
42 4 0.04
43 6 0.06
45 5 0.05
46 51 0.50
47 28 0.27
48 1 0.01
50 4 0.04
51 4 0.04
ACGTcount: A:0.22, C:0.22, G:0.28, T:0.28
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACCTATGGATGCGAATG
Found at i:339073 original size:93 final size:93
Alignment explanation
Indices: 338949--339119 Score: 281
Period size: 93 Copynumber: 1.8 Consensus size: 93
338939 GGATGGTTGA
* * *
338949 GCATCCGAACTCGTTGAGTTGAGTTCAAGTTCACCTATGGATGCGAATGTCCGAA-CTCGTTGAG
1 GCATCCGAACTCGTTGAGTTGAGTCCAAGTTCACCTATGGATGCGAACG-CCCAAGCTCGTTGAG
339013 TTGAGTCCGAGTTCGTGAGATGTAACTAG
65 TTGAGTCCGAGTTCGTGAGATGTAACTAG
* *
339042 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCAAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCAAGTTCACCTATGGATGCGAACGCCCAAGCTCGTTGAGT
339107 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
339120 ACTTAGGGGC
Statistics
Matches: 72, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
92 4 0.06
93 68 0.94
ACGTcount: A:0.22, C:0.22, G:0.28, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCAAGTTCACCTATGGATGCGAACGCCCAAGCTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:354893 original size:27 final size:26
Alignment explanation
Indices: 354792--354903 Score: 125
Period size: 27 Copynumber: 4.2 Consensus size: 26
354782 AGGAAGCGTC
* *
354792 CTGGTGGCTATGCCACAATTATCTGAT
1 CTGGTGGCTCTGCCAC-ATTATCTGTT
*
354819 CTGGTGGCACTGCCACATATATCTGTT
1 CTGGTGGCTCTGCCACAT-TATCTGTT
354846 CTGGTGGCTCTGCCACGATTATCTGTAT
1 CTGGTGGCTCTGCCAC-ATTATCTGT-T
* * * *
354874 CTGGTGACTCCGTCACATTATTTGTT
1 CTGGTGGCTCTGCCACATTATCTGTT
354900 CTGG
1 CTGG
354904 CAGCCATGCT
Statistics
Matches: 74, Mismatches: 8, Indels: 7
0.83 0.09 0.08
Matches are distributed among these distances:
26 7 0.09
27 51 0.69
28 16 0.22
ACGTcount: A:0.17, C:0.24, G:0.23, T:0.36
Consensus pattern (26 bp):
CTGGTGGCTCTGCCACATTATCTGTT
Found at i:354900 original size:54 final size:54
Alignment explanation
Indices: 354792--354903 Score: 145
Period size: 54 Copynumber: 2.1 Consensus size: 54
354782 AGGAAGCGTC
* *
354792 CTGGTGGCTATGCCACAATTATCTGATCTGGTGGCACTGCCACATATATCTGTT
1 CTGGTGGCTATGCCACAATTATCTGATCTGGTGACACCGCCACATATATCTGTT
* * * * *
354846 CTGGTGGCTCTGCCACGATTATCTGTATCTGGTGACTCCGTCACAT-TATTTGTT
1 CTGGTGGCTATGCCACAATTATCTG-ATCTGGTGACACCGCCACATATATCTGTT
354900 CTGG
1 CTGG
354904 CAGCCATGCT
Statistics
Matches: 50, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
54 34 0.68
55 16 0.32
ACGTcount: A:0.17, C:0.24, G:0.23, T:0.36
Consensus pattern (54 bp):
CTGGTGGCTATGCCACAATTATCTGATCTGGTGACACCGCCACATATATCTGTT
Found at i:355898 original size:15 final size:15
Alignment explanation
Indices: 355863--355898 Score: 54
Period size: 16 Copynumber: 2.3 Consensus size: 15
355853 TGTGGAATGG
*
355863 GTTTACAAAAACAAA
1 GTTTTCAAAAACAAA
355878 GATTTTCAAAAACAAA
1 G-TTTTCAAAAACAAA
355894 GTTTT
1 GTTTT
355899 ATAAAGATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
15 5 0.26
16 14 0.74
ACGTcount: A:0.50, C:0.11, G:0.08, T:0.31
Consensus pattern (15 bp):
GTTTTCAAAAACAAA
Found at i:358742 original size:39 final size:39
Alignment explanation
Indices: 358578--358760 Score: 170
Period size: 40 Copynumber: 4.6 Consensus size: 39
358568 TTGAATGCTG
* * * * * * *
358578 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGAATATA
1 TCCGGGTTATGTCCCGAAGGCATTGTGC-GAGTTACTAAA
* * * *
358618 TCCGGATTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAAA
1 TCCGGGTTATG-TCCCGAAGG-CATTGTGCGAGTTACTAAA
* **
358658 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAA
1 TCCGGGTTATGTCCCGAAGGCATT-GTGCGAGTTACTAAA
*
358698 TCCGGGTTATGTCCCGAAGGCATTGTGTGAGTTACTAAA
1 TCCGGGTTATGTCCCGAAGGCATTGTGCGAGTTACTAAA
* *
358737 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTATGTCCCGAAGGCATT
358761 TGAACGAGGA
Statistics
Matches: 121, Mismatches: 18, Indels: 9
0.82 0.12 0.06
Matches are distributed among these distances:
39 38 0.31
40 74 0.61
41 9 0.07
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.27
Consensus pattern (39 bp):
TCCGGGTTATGTCCCGAAGGCATTGTGCGAGTTACTAAA
Found at i:358780 original size:79 final size:80
Alignment explanation
Indices: 358614--358795 Score: 190
Period size: 79 Copynumber: 2.3 Consensus size: 80
358604 GCTAAGTGAA
* * * *
358614 TATATCCGGATTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTCCCGAAGG
1 TATATCCGGGTTAAG-TCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGG
** ** *
358678 CATTCGTGCGAGTTGT
65 CATTCGAACGAGGAGC
* * * * *
358694 TAAATCCGGGTTATGTCCCGAAGG-CATTGTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGC
1 TATATCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGC
*
358758 ATTTGAACGAGGAGC
66 ATTCGAACGAGGAGC
*
358773 TATATCC-GGTTAAATCCCGAAGG
1 TATATCCGGGTTAAGTCCCGAAGG
358796 TACGTGATTT
Statistics
Matches: 83, Mismatches: 18, Indels: 4
0.79 0.17 0.04
Matches are distributed among these distances:
78 14 0.17
79 50 0.60
80 19 0.23
ACGTcount: A:0.26, C:0.20, G:0.27, T:0.26
Consensus pattern (80 bp):
TATATCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGC
ATTCGAACGAGGAGC
Found at i:374167 original size:27 final size:26
Alignment explanation
Indices: 374136--374313 Score: 169
Period size: 27 Copynumber: 6.6 Consensus size: 26
374126 TAAATTGTAC
374136 AGCACTAAGTGTGCGATTCGACTATGT
1 AGCACTAAGTGTGCGATT-GACTATGT
* * *
374163 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCG-ATTGACTATGT
* *
374189 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCG-ATTGACTATGT
*
374217 GGCACTAAGTGTGCGAGTCTGACTATGT
1 AGCACTAAGTGTGCGA-T-TGACTATGT
* *
374245 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGA-TTGACTATGT
* * *
374272 GGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGA-TTGACTATGT
*
374299 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
374314 GGCTCAATAT
Statistics
Matches: 126, Mismatches: 20, Indels: 10
0.81 0.13 0.06
Matches are distributed among these distances:
26 1 0.01
27 100 0.79
28 25 0.20
ACGTcount: A:0.26, C:0.16, G:0.29, T:0.29
Consensus pattern (26 bp):
AGCACTAAGTGTGCGATTGACTATGT
Found at i:374252 original size:82 final size:81
Alignment explanation
Indices: 374137--374292 Score: 224
Period size: 82 Copynumber: 1.9 Consensus size: 81
374127 AAATTGTACA
* * *
374137 GCACTAAGTGTGCGATTCGACTATGTTGCACTAAGTGTGCGAAATGAATATGAT-GCACTAAGTG
1 GCACTAAGTGTGCGAGTCGACTATGTAGCACTAAGTGTGCGAAATGAATACG-TGGCACTAAGTG
374201 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
374218 GCACTAAGTGTGCGAGTCTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTGGCACTAAGTG
1 GCACTAAGTGTGCGAGTC-GACTATGTAGCACTAAGTGTGCGAAATGAATACGTGGCACTAAGTG
*
374283 TGCGAGTTGA
65 TGCGAATTGA
374293 TTATATAGCA
Statistics
Matches: 66, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
81 18 0.27
82 48 0.73
ACGTcount: A:0.26, C:0.17, G:0.29, T:0.28
Consensus pattern (81 bp):
GCACTAAGTGTGCGAGTCGACTATGTAGCACTAAGTGTGCGAAATGAATACGTGGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:374304 original size:82 final size:81
Alignment explanation
Indices: 374133--374313 Score: 220
Period size: 82 Copynumber: 2.2 Consensus size: 81
374123 GATTAAATTG
* * *
374133 TACAGCACTAAGTGTGCGATTCGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGAGTCGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
374198 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
374214 TGCGGCACTAAGTGTGCGAGTCTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TGGCACT
1 TACAGCACTAAGTGTGCGAGTC-GACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
374278 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
374296 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
374314 GGCTCAATAT
Statistics
Matches: 83, Mismatches: 15, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
81 20 0.24
82 63 0.76
ACGTcount: A:0.27, C:0.17, G:0.28, T:0.29
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGAGTCGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Found at i:376303 original size:29 final size:29
Alignment explanation
Indices: 376269--376341 Score: 94
Period size: 29 Copynumber: 2.5 Consensus size: 29
376259 AATCAACCAT
* *
376269 GCACACTTAGTGCCATGTACTTT-AAACTC
1 GCACACTTAGTGCCATGCA-TTTCAAACCC
*
376298 GCACACTTAGTGCCATGCATTTCAAGCCC
1 GCACACTTAGTGCCATGCATTTCAAACCC
*
376327 GTACACTTAGTGCCA
1 GCACACTTAGTGCCA
376342 ATCTTACAAC
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
28 3 0.08
29 36 0.92
ACGTcount: A:0.26, C:0.30, G:0.16, T:0.27
Consensus pattern (29 bp):
GCACACTTAGTGCCATGCATTTCAAACCC
Found at i:388941 original size:29 final size:29
Alignment explanation
Indices: 388899--388971 Score: 103
Period size: 29 Copynumber: 2.5 Consensus size: 29
388889 GTTGGTTTTC
* *
388899 GGCACTAAGTGTGCGGGCTTGAAA-TGCAT
1 GGCACTAAGTGTGCGAG-TTGAAAGTACAT
*
388928 GGCACTAAGTGTGCGAGTTTAAAGTACAT
1 GGCACTAAGTGTGCGAGTTGAAAGTACAT
388957 GGCACTAAGTGTGCG
1 GGCACTAAGTGTGCG
388972 TGGTTGATTA
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
28 5 0.12
29 35 0.88
ACGTcount: A:0.26, C:0.16, G:0.33, T:0.25
Consensus pattern (29 bp):
GGCACTAAGTGTGCGAGTTGAAAGTACAT
Found at i:393057 original size:22 final size:22
Alignment explanation
Indices: 393032--393075 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
393022 ATTGGTGCTA
393032 ATATTTGACCGCTCAATGCTTC
1 ATATTTGACCGCTCAATGCTTC
393054 ATATTTGACCGCTCAATGCTTC
1 ATATTTGACCGCTCAATGCTTC
393076 CTTGAACTAC
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:0.23, C:0.27, G:0.14, T:0.36
Consensus pattern (22 bp):
ATATTTGACCGCTCAATGCTTC
Found at i:407555 original size:40 final size:40
Alignment explanation
Indices: 407511--407749 Score: 349
Period size: 40 Copynumber: 6.0 Consensus size: 40
407501 AATTTAACCA
* *
407511 GATATAGCT-ACTCGCTCAAATGCCTTCAGGACTTAGCCCG
1 GATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGCCCG
** *
407551 GATATAGTAGTTCGCACAAATGCCTTTGGGACTTAGCCCG
1 GATATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCG
407591 GATATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCG
1 GATATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCG
*
407631 GATATAGTAACTCGCACAAATGCCTTCGGGGCTTAGCCCG
1 GATATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCG
*
407671 GA-ATTAGTAACTAGCACAAATGCCTTCGGGACTTAGCCCG
1 GATA-TAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCG
* *
407711 GA-ATTAGTCACTAGCACAAATGCCTTCGGGACTTAGCCC
1 GATA-TAGTAACTCGCACAAATGCCTTCGGGACTTAGCCC
407750 CGTTATCATC
Statistics
Matches: 185, Mismatches: 12, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
39 2 0.01
40 183 0.99
ACGTcount: A:0.27, C:0.27, G:0.23, T:0.24
Consensus pattern (40 bp):
GATATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCG
Found at i:412927 original size:55 final size:55
Alignment explanation
Indices: 412816--412929 Score: 138
Period size: 55 Copynumber: 2.1 Consensus size: 55
412806 CTGCCAAAAC
* ** * *
412816 AACACGGGCGTGCGACATGCCCGTGCCTTGAAACCGTGGCCAAACCTGTCAAATT
1 AACACGGGCGTGCGACACGCCCGTGCCAAGAAACCATGGCCAAACCTATCAAATT
* * * * *
412871 AACACGGGCGTGCGACACGCCCGTGCCAAGCAACTATGGTCAAACCTATTAGATT
1 AACACGGGCGTGCGACACGCCCGTGCCAAGAAACCATGGCCAAACCTATCAAATT
412926 AACA
1 AACA
412930 TAGGCGTGGG
Statistics
Matches: 49, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
55 49 1.00
ACGTcount: A:0.29, C:0.30, G:0.24, T:0.18
Consensus pattern (55 bp):
AACACGGGCGTGCGACACGCCCGTGCCAAGAAACCATGGCCAAACCTATCAAATT
Found at i:418705 original size:26 final size:27
Alignment explanation
Indices: 418650--418719 Score: 65
Period size: 26 Copynumber: 2.6 Consensus size: 27
418640 CCCATATTGA
*
418650 TAAAATGA-TGATTAGACCCCTAAGAGG
1 TAAAATGACTGATTTGA-CCCTAAGAGG
* *
418677 TAAAATGACTGATTTG-CCCTATGATG
1 TAAAATGACTGATTTGACCCTAAGAGG
*
418703 T-AATTGACTGTATTTGA
1 TAAAATGACTG-ATTTGA
418720 GCATGATATT
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
25 8 0.22
26 14 0.39
27 8 0.22
28 6 0.17
ACGTcount: A:0.34, C:0.13, G:0.20, T:0.33
Consensus pattern (27 bp):
TAAAATGACTGATTTGACCCTAAGAGG
Found at i:440392 original size:39 final size:40
Alignment explanation
Indices: 440297--440558 Score: 337
Period size: 39 Copynumber: 6.7 Consensus size: 40
440287 TTGAATGATG
*
440297 TCCGGGCTAAGTCCCGAAGGC--TTGTGCTA-AGTGAC-AAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-T-ACTAAT
*
440335 ATCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 -TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGATACTAAT
440376 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
440415 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
* *
440454 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
*
440493 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGA-ATTACT-AT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-TACTAAT
* *
440532 AACCGGGCTATGTCCCGAAGGCATTTG
1 -TCCGGGCTAAGTCCCGAAGGCATTTG
440559 AACGAGGAGC
Statistics
Matches: 203, Mismatches: 11, Indels: 17
0.88 0.05 0.07
Matches are distributed among these distances:
39 132 0.65
40 59 0.29
41 11 0.05
42 1 0.00
ACGTcount: A:0.26, C:0.23, G:0.27, T:0.24
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
Found at i:442782 original size:49 final size:49
Alignment explanation
Indices: 442706--442820 Score: 133
Period size: 49 Copynumber: 2.3 Consensus size: 49
442696 ACGACTAAGA
* ** * * * *
442706 AACATAAAATATGTTCTTGCACTTAACACATTTATGAGAATGGCTAAAG
1 AACATTAAATATGTTCACGAACCTAACACACTTATCAGAATGGCTAAAG
* *
442755 AACATTAAATATGTTCACGAACCTAACACACTTATCAGAATGGCTGAGG
1 AACATTAAATATGTTCACGAACCTAACACACTTATCAGAATGGCTAAAG
442804 AACA-TAAGATATGTTCA
1 AACATTAA-ATATGTTCA
442821 AGCTTACCCT
Statistics
Matches: 56, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
48 3 0.05
49 53 0.95
ACGTcount: A:0.41, C:0.17, G:0.15, T:0.28
Consensus pattern (49 bp):
AACATTAAATATGTTCACGAACCTAACACACTTATCAGAATGGCTAAAG
Done.