Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr3
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: 100348136
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 3062571 characters in sequence are not A, C, G, or T
File 138 of 290
Found at i:46838047 original size:64 final size:67
Alignment explanation
Indices: 46837966--46838175 Score: 232
Period size: 67 Copynumber: 3.2 Consensus size: 67
46837956 AGACATTATG
* * *
46837966 ATGTAGCTAGGTCGCATG-G-GTGATACTA-TG-TGTACACCATGTAGACAAGAGAGCTACGGGA
1 ATGTAGCTAGGTCGCATGCGCG-GATACAAGTGAAGGACACCATGTAGACAAGAGAGCTACGGGA
46838027 TAT
65 TAT
* *
46838030 ATGTAGCTAGGTCGCATGCGCGGTTCCAAGTGAAGGACACCATGTAGACAAGAGAGCTACGGGAT
1 ATGTAGCTAGGTCGCATGCGCGGATACAAGTGAAGGACACCATGTAGACAAGAGAGCTACGGGAT
46838095 AT
66 AT
* * * * ** * * *
46838097 ATGTAACTAGGTCGCATGCGTGGTTCCTTGTGAAGGACACCATCTAGACAAGGGAGCTACGAGAT
1 ATGTAGCTAGGTCGCATGCGCGGATACAAGTGAAGGACACCATGTAGACAAGAGAGCTACGGGAT
*
46838162 AA
66 AT
*
46838164 AT-TGGCTAGGTC
1 ATGTAGCTAGGTC
46838176 ATGAATCAGA
Statistics
Matches: 127, Mismatches: 15, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
64 18 0.14
65 5 0.04
66 11 0.09
67 93 0.73
ACGTcount: A:0.29, C:0.18, G:0.30, T:0.23
Consensus pattern (67 bp):
ATGTAGCTAGGTCGCATGCGCGGATACAAGTGAAGGACACCATGTAGACAAGAGAGCTACGGGAT
AT
Found at i:46838083 original size:67 final size:67
Alignment explanation
Indices: 46837999--46838175 Score: 266
Period size: 67 Copynumber: 2.7 Consensus size: 67
46837989 TACTATGTGT
46837999 ACACCATGTAGACAAGAGAGCTACGGGATATATGTAGCTAGGTCGCATGCGCGGTTCCAAGTGAA
1 ACACCATGTAGACAAGAGAGCTACGGGATATATGTAGCTAGGTCGCATGCGCGGTTCCAAGTGAA
46838064 GG
66 GG
* * **
46838066 ACACCATGTAGACAAGAGAGCTACGGGATATATGTAACTAGGTCGCATGCGTGGTTCCTTGTGAA
1 ACACCATGTAGACAAGAGAGCTACGGGATATATGTAGCTAGGTCGCATGCGCGGTTCCAAGTGAA
46838131 GG
66 GG
* * * * *
46838133 ACACCATCTAGACAAGGGAGCTACGAGATAAAT-TGGCTAGGTC
1 ACACCATGTAGACAAGAGAGCTACGGGATATATGTAGCTAGGTC
46838176 ATGAATCAGA
Statistics
Matches: 100, Mismatches: 10, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
66 8 0.08
67 92 0.92
ACGTcount: A:0.31, C:0.19, G:0.29, T:0.21
Consensus pattern (67 bp):
ACACCATGTAGACAAGAGAGCTACGGGATATATGTAGCTAGGTCGCATGCGCGGTTCCAAGTGAA
GG
Found at i:46841743 original size:93 final size:93
Alignment explanation
Indices: 46841584--46841768 Score: 343
Period size: 93 Copynumber: 2.0 Consensus size: 93
46841574 TTCCAAGATT
46841584 TTTGTAAGTTCTCGGTTTAGTCCCGAACCCTTTCTAAAGTATGTTTTGGGTTTCGTAGACTCAAA
1 TTTGTAAGTTCTCGGTTTAGTCCCGAACCCTTTCTAAAGTATGTTTTGGGTTTCGTAGACTCAAA
* *
46841649 TAAGGGACTATTTGTAAGTGAATGAACG
66 TAAGGGACTATGTGCAAGTGAATGAACG
46841677 TTTGTAAGTTCTCGGTTTAGTCCCGAACCCTTTCTAAAGTATGTTTTGGGTTTCGTAGACTCAAA
1 TTTGTAAGTTCTCGGTTTAGTCCCGAACCCTTTCTAAAGTATGTTTTGGGTTTCGTAGACTCAAA
*
46841742 TATGGGACTATGTGCAAGTGAATGAAC
66 TAAGGGACTATGTGCAAGTGAATGAAC
46841769 ATTTTGAAAT
Statistics
Matches: 89, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
93 89 1.00
ACGTcount: A:0.25, C:0.16, G:0.23, T:0.36
Consensus pattern (93 bp):
TTTGTAAGTTCTCGGTTTAGTCCCGAACCCTTTCTAAAGTATGTTTTGGGTTTCGTAGACTCAAA
TAAGGGACTATGTGCAAGTGAATGAACG
Found at i:46842275 original size:24 final size:24
Alignment explanation
Indices: 46842243--46842289 Score: 94
Period size: 24 Copynumber: 2.0 Consensus size: 24
46842233 TAATAAGATA
46842243 TTCATAACAAAGGGTACTTTTTTT
1 TTCATAACAAAGGGTACTTTTTTT
46842267 TTCATAACAAAGGGTACTTTTTT
1 TTCATAACAAAGGGTACTTTTTT
46842290 ATTTTATTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.30, C:0.13, G:0.13, T:0.45
Consensus pattern (24 bp):
TTCATAACAAAGGGTACTTTTTTT
Found at i:46857016 original size:43 final size:42
Alignment explanation
Indices: 46856969--46857094 Score: 119
Period size: 43 Copynumber: 3.0 Consensus size: 42
46856959 GCCTCGATTG
* *
46856969 TGATTTACGTATAAGACCATGTCTGGGACATTGGCATTGTAT
1 TGATTTACATGTAAGACCATGTCTGGGACATTGGCATTGTAT
* * ** * *
46857011 CTGATTT-CATGTAAGGCCCTGTCTGGGACAGAGACATCGATAT
1 -TGATTTACATGTAAGACCATGTCTGGGACATTGGCATTG-TAT
* ** *
46857054 TGAATTACATGTAAGACCACATCTGGGACGTTGGCATTGTA
1 TGATTTACATGTAAGACCATGTCTGGGACATTGGCATTGTA
46857095 CTTGTTTGTG
Statistics
Matches: 63, Mismatches: 18, Indels: 5
0.73 0.21 0.06
Matches are distributed among these distances:
42 31 0.49
43 32 0.51
ACGTcount: A:0.27, C:0.17, G:0.25, T:0.31
Consensus pattern (42 bp):
TGATTTACATGTAAGACCATGTCTGGGACATTGGCATTGTAT
Found at i:46857079 original size:85 final size:85
Alignment explanation
Indices: 46856935--46857094 Score: 205
Period size: 85 Copynumber: 1.9 Consensus size: 85
46856925 TGAAATATCG
* * * * * **
46856935 TGTAAGACCGTGTCTGGGACACAGGCCTCGATTGTGATTTACGTATAAGACCATGTCTGGGACAT
1 TGTAAGACCCTGTCTGGGACACAGACATCGATTGTGAATTACATATAAGACCACATCTGGGACAT
46857000 TGGCATTGTATCTGATTTCA
66 TGGCATTGTATCTGATTTCA
* * * *
46857020 TGTAAGGCCCTGTCTGGGACAGAGACATCGATAT-TGAATTACATGTAAGACCACATCTGGGACG
1 TGTAAGACCCTGTCTGGGACACAGACATCGAT-TGTGAATTACATATAAGACCACATCTGGGACA
46857084 TTGGCATTGTA
65 TTGGCATTGTA
46857095 CTTGTTTGTG
Statistics
Matches: 63, Mismatches: 11, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
85 62 0.98
86 1 0.02
ACGTcount: A:0.26, C:0.19, G:0.26, T:0.29
Consensus pattern (85 bp):
TGTAAGACCCTGTCTGGGACACAGACATCGATTGTGAATTACATATAAGACCACATCTGGGACAT
TGGCATTGTATCTGATTTCA
Found at i:46875606 original size:29 final size:29
Alignment explanation
Indices: 46875546--46875608 Score: 108
Period size: 29 Copynumber: 2.2 Consensus size: 29
46875536 AAGATCACAG
*
46875546 ATGTTCTCTGGTATAAAAAAGAAAGATAA
1 ATGTTCTCTGGTATAAAAAAGAAAGACAA
*
46875575 ATGTTCTCTGGTATAAAAAAGAAAGACGA
1 ATGTTCTCTGGTATAAAAAAGAAAGACAA
46875604 ATGTT
1 ATGTT
46875609 GGGAGTTCCA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.44, C:0.08, G:0.19, T:0.29
Consensus pattern (29 bp):
ATGTTCTCTGGTATAAAAAAGAAAGACAA
Found at i:46879580 original size:61 final size:61
Alignment explanation
Indices: 46879485--46879606 Score: 235
Period size: 61 Copynumber: 2.0 Consensus size: 61
46879475 AATACACCTC
*
46879485 ATCAAGGGGCAACACTTTGCATGGTTATAATCAACTCTCTTTTAGATGACCTGGACATGAT
1 ATCAAGGGGCAACACTTTGCATGGCTATAATCAACTCTCTTTTAGATGACCTGGACATGAT
46879546 ATCAAGGGGCAACACTTTGCATGGCTATAATCAACTCTCTTTTAGATGACCTGGACATGAT
1 ATCAAGGGGCAACACTTTGCATGGCTATAATCAACTCTCTTTTAGATGACCTGGACATGAT
46879607 CAAATTGCTA
Statistics
Matches: 60, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
61 60 1.00
ACGTcount: A:0.30, C:0.20, G:0.20, T:0.30
Consensus pattern (61 bp):
ATCAAGGGGCAACACTTTGCATGGCTATAATCAACTCTCTTTTAGATGACCTGGACATGAT
Found at i:46891954 original size:46 final size:45
Alignment explanation
Indices: 46891858--46892074 Score: 181
Period size: 46 Copynumber: 4.7 Consensus size: 45
46891848 GTATATTTTT
* * ** *
46891858 GCCGATGCCATGTCCCAGACATGGTCTTACACTGAC-ACACCTC-ATA
1 GCCGATG-CATGTCCCAGACAT-GTCTTACACTGGCTTCGTCTCGA-G
46891904 GCCGATGCATGTCCCAGACATGTCTTACACTGGCTTACGTCTCGAG
1 GCCGATGCATGTCCCAGACATGTCTTACACTGGCTT-CGTCTCGAG
* * * *
46891950 GCCGATGCATGTCCCAGACATGTCTTACACTAGCACTCGTCTCAAT
1 GCCGATGCATGTCCCAGACATGTCTTACACTGGC-TTCGTCTCGAG
* * * *
46891996 GTCGATGCCATGTCCCAGACATGGTCTTACATTGG-TTC-TCATAATGTG
1 GCCGATG-CATGTCCCAGACAT-GTCTTACACTGGCTTCGTC-T--CGAG
* *
46892044 GCCAACGCATGTCCCAGACATGTCTTACACT
1 GCCGATGCATGTCCCAGACATGTCTTACACT
46892075 AGCTCACACA
Statistics
Matches: 141, Mismatches: 21, Indels: 18
0.78 0.12 0.10
Matches are distributed among these distances:
44 12 0.09
45 16 0.11
46 69 0.49
47 30 0.21
48 14 0.10
ACGTcount: A:0.23, C:0.31, G:0.20, T:0.26
Consensus pattern (45 bp):
GCCGATGCATGTCCCAGACATGTCTTACACTGGCTTCGTCTCGAG
Found at i:46892056 original size:94 final size:90
Alignment explanation
Indices: 46891866--46892077 Score: 236
Period size: 94 Copynumber: 2.3 Consensus size: 90
46891856 TTGCCGATGC
46891866 CATGTCCCAGACATGGTCTTACACT-GACACACCTCATAGCCGATGCATGTCCCAGACATGTCTT
1 CATGTCCCAGACAT-GTCTTACACTAG-CACACCTCATAGCCGATGCATGTCCCAGACATGTCTT
* *
46891930 ACACTGGCTTACGTCTCGAGGCCGATG
64 ACACTGGCTTACGTCTCGAGGCCAACG
* *
46891957 CATGTCCCAGACATGTCTTACACTAGCACTCGTCTCA-ATGTCGATGCCATGTCCCAGACATGGT
1 CATGTCCCAGACATGTCTTACACTAGCACAC--CTCATA-GCCGATG-CATGTCCCAGACAT-GT
* * *
46892021 CTTACATTGG-TT-C-TCATAATGTGGCCAACG
61 CTTACACTGGCTTACGTC-T--CGAGGCCAACG
46892051 CATGTCCCAGACATGTCTTACACTAGC
1 CATGTCCCAGACATGTCTTACACTAGC
46892078 TCACACAAGT
Statistics
Matches: 105, Mismatches: 7, Indels: 15
0.83 0.06 0.12
Matches are distributed among these distances:
90 14 0.13
91 18 0.17
92 12 0.11
93 16 0.15
94 45 0.43
ACGTcount: A:0.24, C:0.31, G:0.19, T:0.26
Consensus pattern (90 bp):
CATGTCCCAGACATGTCTTACACTAGCACACCTCATAGCCGATGCATGTCCCAGACATGTCTTAC
ACTGGCTTACGTCTCGAGGCCAACG
Found at i:46900639 original size:40 final size:42
Alignment explanation
Indices: 46900595--46900675 Score: 112
Period size: 41 Copynumber: 2.0 Consensus size: 42
46900585 CCGGGTTTTT
46900595 GGACACGGGCGA-TGACACAGGCGTGT-CTAGGCTATGTGAG
1 GGACACGGGCGAGTGACACAGGCGTGTGCTAGGCTATGTGAG
* * * *
46900635 GGACACGGGCTAGTGACACAGGTGTGTGCTTGGCTGTGTGA
1 GGACACGGGCGAGTGACACAGGCGTGTGCTAGGCTATGTGA
46900676 AAACCCCTGT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
40 11 0.31
41 13 0.37
42 11 0.31
ACGTcount: A:0.20, C:0.19, G:0.41, T:0.21
Consensus pattern (42 bp):
GGACACGGGCGAGTGACACAGGCGTGTGCTAGGCTATGTGAG
Found at i:46901323 original size:2 final size:2
Alignment explanation
Indices: 46901316--46901352 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
46901306 GAGCAAATAA
*
46901316 AC AC AC AC AC AC AG AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
46901353 TATATATAAC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.46, G:0.03, T:0.00
Consensus pattern (2 bp):
AC
Found at i:46902343 original size:20 final size:19
Alignment explanation
Indices: 46902295--46902343 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 19
46902285 TAGTTCGTCT
*
46902295 GTATAAACAATAGTTCATCA
1 GTAT-AACAATAATTCATCA
*
46902315 GTAATAACAATAATTCATCC
1 GT-ATAACAATAATTCATCA
46902335 GTATCAACA
1 GTAT-AACA
46902344 CATATGATTG
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
19 2 0.08
20 21 0.84
21 2 0.08
ACGTcount: A:0.45, C:0.18, G:0.08, T:0.29
Consensus pattern (19 bp):
GTATAACAATAATTCATCA
Found at i:46902596 original size:24 final size:24
Alignment explanation
Indices: 46902490--46902613 Score: 112
Period size: 24 Copynumber: 5.2 Consensus size: 24
46902480 AAGGTCCTCC
* *
46902490 TGAGCTGATAAACAATAAGCT-TTA
1 TGAGCTGA-AAACAGTAAGCTCTAA
46902514 TCGAGCTG-AAACAGTAAGCTCTAA
1 T-GAGCTGAAAACAGTAAGCTCTAA
* * * *
46902538 CT-AACTGAGAACAGTAAACTCCAA
1 -TGAGCTGAAAACAGTAAGCTCTAA
*
46902562 TGAGCTAAAAACTA-TAAGCTCTAA
1 TGAGCTGAAAAC-AGTAAGCTCTAA
*
46902586 TGAGCTGAAAACAGTAAGCTCTTA
1 TGAGCTGAAAACAGTAAGCTCTAA
46902610 TGAG
1 TGAG
46902614 TTGATATATC
Statistics
Matches: 80, Mismatches: 13, Indels: 14
0.75 0.12 0.13
Matches are distributed among these distances:
23 17 0.21
24 55 0.69
25 8 0.10
ACGTcount: A:0.41, C:0.18, G:0.18, T:0.23
Consensus pattern (24 bp):
TGAGCTGAAAACAGTAAGCTCTAA
Found at i:46909454 original size:30 final size:30
Alignment explanation
Indices: 46909370--46909459 Score: 114
Period size: 29 Copynumber: 3.0 Consensus size: 30
46909360 CCAGACGGGT
*
46909370 AACCTCGATATAATGTCAACTTGTGTGAGC
1 AACCTTGATATAATGTCAACTTGTGTGAGC
*
46909400 AA-CTATGTTA-AATGT-AAGCTTGTGTGAGC
1 AACCT-TGATATAATGTCAA-CTTGTGTGAGC
*
46909429 AACCTTGATATATTGTCAACTTGTGTGAGC
1 AACCTTGATATAATGTCAACTTGTGTGAGC
46909459 A
1 A
46909460 TTATATTCTG
Statistics
Matches: 51, Mismatches: 4, Indels: 10
0.78 0.06 0.15
Matches are distributed among these distances:
28 2 0.04
29 24 0.47
30 23 0.45
31 2 0.04
ACGTcount: A:0.30, C:0.16, G:0.21, T:0.33
Consensus pattern (30 bp):
AACCTTGATATAATGTCAACTTGTGTGAGC
Found at i:46923166 original size:3 final size:3
Alignment explanation
Indices: 46923158--46923185 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
46923148 TTGATAAAAT
46923158 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
46923186 ATAAATAAAT
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:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:46930601 original size:19 final size:21
Alignment explanation
Indices: 46930577--46930620 Score: 56
Period size: 20 Copynumber: 2.1 Consensus size: 21
46930567 CTAATTTCTC
*
46930577 CTTTTTCTTT-TCTTTT-TTT
1 CTTTTTCTTTCTATTTTGTTT
46930596 CTTTTTTCTTTCTATTTTGTTT
1 C-TTTTTCTTTCTATTTTGTTT
46930618 CTT
1 CTT
46930621 CTCTGTAACT
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
19 1 0.05
20 9 0.43
21 7 0.33
22 4 0.19
ACGTcount: A:0.02, C:0.16, G:0.02, T:0.80
Consensus pattern (21 bp):
CTTTTTCTTTCTATTTTGTTT
Found at i:46930820 original size:3 final size:3
Alignment explanation
Indices: 46930805--46930835 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
46930795 TTAATTATTG
*
46930805 ATA ATA ATT ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
46930836 ATTAATAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:46933450 original size:25 final size:25
Alignment explanation
Indices: 46933421--46933470 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
46933411 TGGTTTGCTA
46933421 GATGAAGATCTGAATGCTTATTTGG
1 GATGAAGATCTGAATGCTTATTTGG
*
46933446 GATGAAGATCTGAATTCTTATTTGG
1 GATGAAGATCTGAATGCTTATTTGG
46933471 CTAATTTCTA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.28, C:0.08, G:0.26, T:0.38
Consensus pattern (25 bp):
GATGAAGATCTGAATGCTTATTTGG
Found at i:46941283 original size:6 final size:6
Alignment explanation
Indices: 46941274--46941317 Score: 56
Period size: 6 Copynumber: 7.7 Consensus size: 6
46941264 TTTTGTCTTA
* *
46941274 AAAAAT AAAAA- AAAATT AAATA- AAAAAT AAAAAT AAAAAT AAAA
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAA
46941318 TAATATTTTA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
5 8 0.25
6 24 0.75
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (6 bp):
AAAAAT
Found at i:46941300 original size:22 final size:23
Alignment explanation
Indices: 46941272--46941316 Score: 74
Period size: 22 Copynumber: 2.0 Consensus size: 23
46941262 TCTTTTGTCT
*
46941272 TAAAAAATAAAAA-AAAATTAAA
1 TAAAAAATAAAAATAAAAATAAA
46941294 TAAAAAATAAAAATAAAAATAAA
1 TAAAAAATAAAAATAAAAATAAA
46941317 ATAATATTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
22 13 0.62
23 8 0.38
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (23 bp):
TAAAAAATAAAAATAAAAATAAA
Found at i:46941313 original size:12 final size:11
Alignment explanation
Indices: 46941273--46941317 Score: 63
Period size: 11 Copynumber: 4.0 Consensus size: 11
46941263 CTTTTGTCTT
46941273 AAAAAATAAAA
1 AAAAAATAAAA
* *
46941284 AAAAATTAAAT
1 AAAAAATAAAA
46941295 AAAAAATAAAA
1 AAAAAATAAAA
46941306 ATAAAAATAAAA
1 A-AAAAATAAAA
46941318 TAATATTTTA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
11 19 0.66
12 10 0.34
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (11 bp):
AAAAAATAAAA
Found at i:46942920 original size:6 final size:6
Alignment explanation
Indices: 46942902--46942991 Score: 60
Period size: 6 Copynumber: 14.7 Consensus size: 6
46942892 AAGAAACATT
* * *
46942902 ATCAGA A-CTAGA ATCAGA ATCAGA ATCAGA ATTAG- GTGAGAGA ATCAGA
1 ATCAGA ATC-AGA ATCAGA ATCAGA ATCAGA ATCAGA AT--CAGA ATCAGA
* * *
46942951 ATCAGA ATCAGT ATAAGGTA A-CAGA ATCAAA ATCAGA ATCA
1 ATCAGA ATCAGA ATCA-G-A ATCAGA ATCAGA ATCAGA ATCA
46942992 TTATTAGGTA
Statistics
Matches: 65, Mismatches: 11, Indels: 16
0.71 0.12 0.17
Matches are distributed among these distances:
5 4 0.06
6 54 0.83
7 5 0.08
8 2 0.03
ACGTcount: A:0.49, C:0.13, G:0.19, T:0.19
Consensus pattern (6 bp):
ATCAGA
Found at i:46942947 original size:31 final size:31
Alignment explanation
Indices: 46942911--46943021 Score: 150
Period size: 31 Copynumber: 3.5 Consensus size: 31
46942901 TATCAGAACT
* * * *
46942911 AGAATCAGAATCAGAATCAGAATTAGGTGAG
1 AGAATCAAAATCAGAATCAGTATTAGGTAAC
* *
46942942 AGAATCAGAATCAGAATCAGTATAAGGTAAC
1 AGAATCAAAATCAGAATCAGTATTAGGTAAC
*
46942973 AGAATCAAAATCAGAATCATTATTAGGTAAC
1 AGAATCAAAATCAGAATCAGTATTAGGTAAC
46943004 AGAATCAAAAATCAGAAT
1 AGAATC-AAAATCAGAAT
46943022 TTGAATGCAA
Statistics
Matches: 72, Mismatches: 7, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
31 61 0.85
32 11 0.15
ACGTcount: A:0.50, C:0.12, G:0.18, T:0.21
Consensus pattern (31 bp):
AGAATCAAAATCAGAATCAGTATTAGGTAAC
Found at i:46943200 original size:27 final size:26
Alignment explanation
Indices: 46943158--46943259 Score: 132
Period size: 27 Copynumber: 3.8 Consensus size: 26
46943148 GCTCAGTTAT
* *
46943158 CAGATATTGTGACAGAGTCACCAGATA
1 CAGATATTGTGGCAGAGCCACCAGA-A
46943185 CAGATATTGTGGCAGAGCCACCAGAA
1 CAGATATTGTGGCAGAGCCACCAGAA
*
46943211 CAGATATTTGTGGCATAGCCACCAGAAA
1 CAGATA-TTGTGGCAGAGCCACCAG-AA
* *
46943239 CAGATAATGTGGCAAAGCCAC
1 CAGATATTGTGGCAGAGCCAC
46943260 TTAACAGAAT
Statistics
Matches: 68, Mismatches: 5, Indels: 4
0.88 0.06 0.05
Matches are distributed among these distances:
26 7 0.10
27 53 0.78
28 8 0.12
ACGTcount: A:0.36, C:0.22, G:0.24, T:0.19
Consensus pattern (26 bp):
CAGATATTGTGGCAGAGCCACCAGAA
Found at i:46943737 original size:27 final size:27
Alignment explanation
Indices: 46943706--46943825 Score: 154
Period size: 27 Copynumber: 4.4 Consensus size: 27
46943696 AAACAATCAN
*
46943706 GTAATTTTACAAATCGAGGGTATTTCA
1 GTAATTTTACAAATCGAGGGTATTTCG
* *
46943733 ATAATTTTACAAA-CTGAGGGTATTTCT
1 GTAATTTTACAAATC-GAGGGTATTTCG
* *
46943760 GTAATTTTACAAATCGAGGATATTTGG
1 GTAATTTTACAAATCGAGGGTATTTCG
*
46943787 GTAATTTTATAAATCGAGGGTACTTT-G
1 GTAATTTTACAAATCGAGGGTA-TTTCG
46943814 GTAATTTTACAA
1 GTAATTTTACAA
46943826 GNNNNNNNNN
Statistics
Matches: 81, Mismatches: 9, Indels: 6
0.84 0.09 0.06
Matches are distributed among these distances:
26 1 0.01
27 76 0.94
28 4 0.05
ACGTcount: A:0.33, C:0.09, G:0.18, T:0.39
Consensus pattern (27 bp):
GTAATTTTACAAATCGAGGGTATTTCG
Found at i:46949832 original size:47 final size:47
Alignment explanation
Indices: 46949727--46949907 Score: 147
Period size: 47 Copynumber: 3.9 Consensus size: 47
46949717 GAGTAAGCTA
* * **
46949727 CCAATGACATGTCCCAAACATGGTCTTATACTGGCTCAT-ATCTCAAG
1 CCAATGACATGTCCCAGACATGGTCTTACACTGGCT-ATCATCTTGAG
* * * *
46949774 TCGATGCCATGTCCCAGACATGGTCTTACACTGACTATCATCTTGTAG
1 CCAATGACATGTCCCAGACATGGTCTTACACTGGCTATCATCTTG-AG
** * * *
46949822 CCAATG-CATGTCTTAGACAT-GTTTTACACTGGCT-TACGTCTCGAGG
1 CCAATGACATGTCCCAGACATGGTCTTACACTGGCTAT-CATCTTGA-G
* * *
46949868 CCGATG-CATGTCCCAGACATGGTCTTACACTAGCTCTCAT
1 CCAATGACATGTCCCAGACATGGTCTTACACTGGCTATCAT
46949908 AATGTGGCAG
Statistics
Matches: 106, Mismatches: 22, Indels: 12
0.76 0.16 0.09
Matches are distributed among these distances:
45 2 0.02
46 37 0.35
47 60 0.57
48 7 0.07
ACGTcount: A:0.24, C:0.28, G:0.18, T:0.30
Consensus pattern (47 bp):
CCAATGACATGTCCCAGACATGGTCTTACACTGGCTATCATCTTGAG
Found at i:46949922 original size:47 final size:44
Alignment explanation
Indices: 46949776--46949947 Score: 114
Period size: 47 Copynumber: 3.7 Consensus size: 44
46949766 ATCTCAAGTC
* *
46949776 GATGCCATGTCCCAGACATGGTCTTACACT-GACTATCATCTTGTAGCCA
1 GATG-CATGTCCCAGACAT-GTCTTACACTAG-CT-TCAT-ATGT-GGCA
** * * * * * *
46949825 -ATGCATGTCTTAGACATGTTTTACACTGGCTTACGTCTCGAGGCC
1 GATGCATGTCCCAGACATGTCTTACACTAGCTT-CATAT-GTGGCA
46949870 GATGCATGTCCCAGACATGGTCTTACACTAGCTCTCATAATGTGGCA
1 GATGCATGTCCCAGACAT-GTCTTACACTAGCT-TCAT-ATGTGGCA
* * *
46949917 GATGCATGTCCTAGATATTTCTTACACTAGC
1 GATGCATGTCCCAGACATGTCTTACACTAGC
46949948 CCACACACAA
Statistics
Matches: 97, Mismatches: 19, Indels: 17
0.73 0.14 0.13
Matches are distributed among these distances:
45 4 0.04
46 41 0.42
47 47 0.48
48 5 0.05
ACGTcount: A:0.24, C:0.26, G:0.20, T:0.31
Consensus pattern (44 bp):
GATGCATGTCCCAGACATGTCTTACACTAGCTTCATATGTGGCA
Found at i:46949922 original size:93 final size:94
Alignment explanation
Indices: 46949775--46949944 Score: 231
Period size: 93 Copynumber: 1.8 Consensus size: 94
46949765 TATCTCAAGT
** *
46949775 CGATGCCATGTCCCAGACATGGTCTTACACTGACTATCATCTTGTAGCCAATGCATGTCTTAGAC
1 CGATGCCATGTCCCAGACATGGTCTTACACTGACTATCATAATGTAGCCAATGCATGTCCTAGAC
46949840 ATGTT-TTACACTGGCTTACGTCTCGAGGC
66 AT-TTCTTACACTGGCTTACGTCTCGAGGC
* *
46949869 CGATG-CATGTCCCAGACATGGTCTTACACT-AGCTCTCATAATGT-GGCAGATGCATGTCCTAG
1 CGATGCCATGTCCCAGACATGGTCTTACACTGA-CTATCATAATGTAGCCA-ATGCATGTCCTAG
*
46949931 ATATTTCTTACACT
64 ACATTTCTTACACT
46949945 AGCCCACACA
Statistics
Matches: 67, Mismatches: 6, Indels: 7
0.84 0.08 0.09
Matches are distributed among these distances:
92 6 0.09
93 56 0.84
94 5 0.07
ACGTcount: A:0.24, C:0.26, G:0.19, T:0.31
Consensus pattern (94 bp):
CGATGCCATGTCCCAGACATGGTCTTACACTGACTATCATAATGTAGCCAATGCATGTCCTAGAC
ATTTCTTACACTGGCTTACGTCTCGAGGC
Found at i:46961270 original size:47 final size:48
Alignment explanation
Indices: 46961200--46961462 Score: 231
Period size: 47 Copynumber: 5.6 Consensus size: 48
46961190 GTAAGCTGCT
*
46961200 GATGCCATGTCCCAGACATGGTCTTACACTGGCTCAT-ATCTCAA-GTC
1 GATGCCATGTCCCAGACATGGTCTTACACTGGCT-ATCATCTCAAGGCC
* * *
46961247 AATGCCATGTCCCAGACATGGTCTTACTCTGACTATCATCTCATA-GCC
1 GATGCCATGTCCCAGACATGGTCTTACACTGGCTATCATCTCA-AGGCC
* * * * * * **
46961295 GATG-CATGTTCCAGACA-CGTATTACACTGGCTTTCGTCTTAAGGTG
1 GATGCCATGTCCCAGACATGGTCTTACACTGGCTATCATCTCAAGGCC
* * * * *
46961341 GATG-CATGCCCCAGACAT-GTCTTACACTAGCTTTCGTCTCAATGCC
1 GATGCCATGTCCCAGACATGGTCTTACACTGGCTATCATCTCAAGGCC
* * * **
46961387 GATGCCATGCCCCAGACATGGTCTTACACTGGCTCTCATAAT-GTGGCC
1 GATGCCATGTCCCAGACATGGTCTTACACTGGCTATCAT-CTCAAGGCC
46961435 GATG-CATGTCCCAGACAT-GTCTTACACT
1 GATGCCATGTCCCAGACATGGTCTTACACT
46961463 ATCTCGCACA
Statistics
Matches: 178, Mismatches: 31, Indels: 15
0.79 0.14 0.07
Matches are distributed among these distances:
45 1 0.01
46 71 0.40
47 76 0.43
48 29 0.16
49 1 0.01
ACGTcount: A:0.23, C:0.29, G:0.19, T:0.29
Consensus pattern (48 bp):
GATGCCATGTCCCAGACATGGTCTTACACTGGCTATCATCTCAAGGCC
Found at i:46961448 original size:94 final size:93
Alignment explanation
Indices: 46961200--46961463 Score: 258
Period size: 94 Copynumber: 2.8 Consensus size: 93
46961190 GTAAGCTGCT
*
46961200 GATGCCATGTCCCAGACATGGTCTTACACTGGCTCAT-ATCTCAA-GT-CAATGCCATGTCCCAG
1 GATGCCATGTCCCAGACATGGTCTTACACTGGCTC-TCA--T-AATGTGCGATG-CATGTCCCAG
*
46961262 ACATGGTCTTACTCT-GACTATCATCTCATAGCC
61 ACAT-GTCTTACACTAGACTATCATCTCATAGCC
* * * * * *
46961295 GATG-CATGTTCCAGACA-CGTATTACACTGGCTTTCGTCTTAAGGTG-GATGCATGCCCCAGAC
1 GATGCCATGTCCCAGACATGGTCTTACACTGGC--TC-TCATAATGTGCGATGCATGTCCCAGAC
* *
46961357 ATGTCTTACACTAG-CTTTCGTCTCA-ATGCC
63 ATGTCTTACACTAGACTATCATCTCATA-GCC
*
46961387 GATGCCATGCCCCAGACATGGTCTTACACTGGCTCTCATAATGTGGCCGATGCATGTCCCAGACA
1 GATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATAATGT-G-CGATGCATGTCCCAGACA
46961452 TGTCTTACACTA
64 TGTCTTACACTA
46961464 TCTCGCACAC
Statistics
Matches: 140, Mismatches: 17, Indels: 25
0.77 0.09 0.14
Matches are distributed among these distances:
91 8 0.06
92 28 0.20
93 39 0.28
94 58 0.41
95 7 0.05
ACGTcount: A:0.23, C:0.29, G:0.19, T:0.28
Consensus pattern (93 bp):
GATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATAATGTGCGATGCATGTCCCAGACATG
TCTTACACTAGACTATCATCTCATAGCC
Found at i:46961462 original size:140 final size:141
Alignment explanation
Indices: 46961200--46961462 Score: 327
Period size: 140 Copynumber: 1.9 Consensus size: 141
46961190 GTAAGCTGCT
* * * *
46961200 GATGCCATGTCCCAGACATGGTCTTACACTGGCTCATATCTCAAGTCAATGCCATGTCCCAGACA
1 GATGCCATGCCCCAGACATGGTCTTACACTAGCTCATATCTCAAGCCAATGCCATGCCCCAGACA
* * *
46961265 TGGTCTTACTCTGACTATCATCTCATAGCCGATGCATGTTCCAGACACGTATTACACTGGCTTTC
66 TGGTCTTACACTGACTATCATATCATAGCCGATGCATGTCCCAGACACGTATTACACTGGCTTTC
46961330 GTCTTAAGGTG
131 GTCTTAAGGTG
* * *
46961341 GATG-CATGCCCCAGACAT-GTCTTACACTAGCT-TTCGTCTCAATGCCGATGCCATGCCCCAGA
1 GATGCCATGCCCCAGACATGGTCTTACACTAGCTCAT-ATCTCAA-GCCAATGCCATGCCCCAGA
* * * * * *
46961403 CATGGTCTTACACTGGCTCTCATAAT-GTGGCCGATGCATGTCCCAGACATGTCTTACACT
64 CATGGTCTTACACTGACTATCAT-ATCATAGCCGATGCATGTCCCAGACACGTATTACACT
46961463 ATCTCGCACA
Statistics
Matches: 103, Mismatches: 16, Indels: 7
0.82 0.13 0.06
Matches are distributed among these distances:
138 1 0.01
139 19 0.18
140 78 0.76
141 5 0.05
ACGTcount: A:0.23, C:0.29, G:0.19, T:0.29
Consensus pattern (141 bp):
GATGCCATGCCCCAGACATGGTCTTACACTAGCTCATATCTCAAGCCAATGCCATGCCCCAGACA
TGGTCTTACACTGACTATCATATCATAGCCGATGCATGTCCCAGACACGTATTACACTGGCTTTC
GTCTTAAGGTG
Found at i:46963168 original size:49 final size:49
Alignment explanation
Indices: 46963113--46963288 Score: 198
Period size: 49 Copynumber: 3.6 Consensus size: 49
46963103 ACATTAAAGT
* * *
46963113 CGATGCCATGTTCC-AGACAGGTCTTACAGTGACTTTCATATATCGAGGG
1 CGATGCCATG-TCCTAGACAGGTCTTACACTGACTTTCATATATTGAGGC
* * * *
46963162 CGATGCCATGTCCTAGACAGGTCTTACACTGGCTCTCATCTATTG-GTGT
1 CGATGCCATGTCCTAGACAGGTCTTACACTGACTTTCATATATTGAG-GC
* * *
46963211 CGATGCCATGTCCCAGACAGGTCTTACACTAACTTGT-ATATTTTGAGGC
1 CGATGCCATGTCCTAGACAGGTCTTACACTGACTT-TCATATATTGAGGC
*
46963260 CGATG-CATGTCCTAGACATGTCTTACACT
1 CGATGCCATGTCCTAGACAGGTCTTACACT
46963289 AGCTCTCGTC
Statistics
Matches: 108, Mismatches: 15, Indels: 9
0.82 0.11 0.07
Matches are distributed among these distances:
48 26 0.24
49 80 0.74
50 2 0.02
ACGTcount: A:0.23, C:0.25, G:0.22, T:0.31
Consensus pattern (49 bp):
CGATGCCATGTCCTAGACAGGTCTTACACTGACTTTCATATATTGAGGC
Found at i:46963264 original size:98 final size:97
Alignment explanation
Indices: 46963111--46963295 Score: 273
Period size: 98 Copynumber: 1.9 Consensus size: 97
46963101 GCACATTAAA
* * * *
46963111 GTCGATGCCATGTTCCAGACAGGTCTTACAGTGACTTTCATATATCGAGGGCGATGCCATGTCCT
1 GTCGATGCCATGTCCCAGACAGGTCTTACACTAACTTTCATATATCGAGGCCGATG-CATGTCCT
*
46963176 AGACAGGTCTTACACTGGCTCTCATCTATTGGT
65 AGACAGGTCTTACACTAGCTCTCATCTATTGGT
* *
46963209 GTCGATGCCATGTCCCAGACAGGTCTTACACTAACTTGT-ATATTTTGAGGCCGATGCATGTCCT
1 GTCGATGCCATGTCCCAGACAGGTCTTACACTAACTT-TCATATATCGAGGCCGATGCATGTCCT
*
46963273 AGACATGTCTTACACTAGCTCTC
65 AGACAGGTCTTACACTAGCTCTC
46963296 GTCTCAATGT
Statistics
Matches: 78, Mismatches: 8, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
97 29 0.37
98 48 0.62
99 1 0.01
ACGTcount: A:0.22, C:0.25, G:0.22, T:0.31
Consensus pattern (97 bp):
GTCGATGCCATGTCCCAGACAGGTCTTACACTAACTTTCATATATCGAGGCCGATGCATGTCCTA
GACAGGTCTTACACTAGCTCTCATCTATTGGT
Found at i:46965255 original size:56 final size:56
Alignment explanation
Indices: 46965169--46965400 Score: 437
Period size: 56 Copynumber: 4.1 Consensus size: 56
46965159 ACAAGGGATG
46965169 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
*
46965225 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAGAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
46965281 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
* *
46965337 ATGGGCAAAACATGTCATCAAACATGTTGTGTTAATGGAAGAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
46965393 ATGGGCAA
1 ATGGGCAA
46965401 TAAACTAATA
Statistics
Matches: 172, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 172 1.00
ACGTcount: A:0.45, C:0.09, G:0.22, T:0.23
Consensus pattern (56 bp):
ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
Found at i:46969442 original size:25 final size:24
Alignment explanation
Indices: 46969409--46969495 Score: 106
Period size: 24 Copynumber: 3.6 Consensus size: 24
46969399 TTGAAAGTCT
46969409 GCACACATAGTGCTCTTAC-TTAT-TC
1 GCACACATAGTGC-C--ACGTTATCTC
*
46969434 GCACACATAGTGCCACGTTTTCTC
1 GCACACATAGTGCCACGTTATCTC
* *
46969458 GCACACATAGTGCCATGTAATCTC
1 GCACACATAGTGCCACGTTATCTC
46969482 GCACACATAGTGCC
1 GCACACATAGTGCC
46969496 GCATAGCCTT
Statistics
Matches: 56, Mismatches: 4, Indels: 5
0.86 0.06 0.08
Matches are distributed among these distances:
22 2 0.04
23 3 0.05
24 38 0.68
25 13 0.23
ACGTcount: A:0.25, C:0.31, G:0.16, T:0.28
Consensus pattern (24 bp):
GCACACATAGTGCCACGTTATCTC
Found at i:46975544 original size:28 final size:28
Alignment explanation
Indices: 46975504--46975560 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
46975494 ACTTAACCGC
46975504 ATGCATACAATCATTTCCAAGTTGTGAA
1 ATGCATACAATCATTTCCAAGTTGTGAA
46975532 ATGCATACAATCATTTCCAAGTTGTGAA
1 ATGCATACAATCATTTCCAAGTTGTGAA
46975560 A
1 A
46975561 ACTAGGTCAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.37, C:0.18, G:0.14, T:0.32
Consensus pattern (28 bp):
ATGCATACAATCATTTCCAAGTTGTGAA
Found at i:46975737 original size:21 final size:20
Alignment explanation
Indices: 46975703--46975742 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
46975693 CACTTGAAGT
*
46975703 AGGGCACACGCCCGTGTGGA
1 AGGGCACACACCCGTGTGGA
46975723 AGGGCAACACACCCGTGTGG
1 AGGGC-ACACACCCGTGTGG
46975743 CCATTATGAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.23, C:0.30, G:0.38, T:0.10
Consensus pattern (20 bp):
AGGGCACACACCCGTGTGGA
Found at i:46977045 original size:50 final size:50
Alignment explanation
Indices: 46976983--46977203 Score: 171
Period size: 50 Copynumber: 4.6 Consensus size: 50
46976973 ACATTATAGT
*
46976983 CGATGCCGTGTCCCAGACAGGTCTTACACTGA-CTTTCATATATCGAGGCC
1 CGATGCCATGTCCCAGACAGGTCTTACACTGAGCTTTCATATATCGAGG-C
* * * * *
46977033 CGATGCCATGTCCCAGACAAGTCTTACACT-AGCTCTCATCTATTG-GTGT
1 CGATGCCATGTCCCAGACAGGTCTTACACTGAGCTTTCATATATCGAG-GC
* * * * * *
46977082 CAATTCCATGTCCCAAACAGGTCTTACACTGA-C--ACATA-A-CAAAGC
1 CGATGCCATGTCCCAGACAGGTCTTACACTGAGCTTTCATATATCGAGGC
* * *
46977127 TGATGCCATGTCCCGGAC--GTCTTACACT-AGCTTGT-ATATCTCGAGGC
1 CGATGCCATGTCCCAGACAGGTCTTACACTGAGCTT-TCATATATCGAGGC
* *
46977174 GGATG-CATGTCCCAGACATGTCTTACACTG
1 CGATGCCATGTCCCAGACAGGTCTTACACTG
46977204 GCTCATATAC
Statistics
Matches: 131, Mismatches: 27, Indels: 27
0.71 0.15 0.15
Matches are distributed among these distances:
42 1 0.01
43 11 0.08
45 17 0.13
46 12 0.09
47 11 0.08
48 10 0.08
49 29 0.22
50 40 0.31
ACGTcount: A:0.25, C:0.29, G:0.19, T:0.27
Consensus pattern (50 bp):
CGATGCCATGTCCCAGACAGGTCTTACACTGAGCTTTCATATATCGAGGC
Found at i:46980293 original size:3 final size:3
Alignment explanation
Indices: 46980287--46980345 Score: 118
Period size: 3 Copynumber: 19.7 Consensus size: 3
46980277 ATTATTATTA
46980287 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG
46980335 TTG TTG TTG TT
1 TTG TTG TTG TT
46980346 TAATCTTATT
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 56 1.00
ACGTcount: A:0.00, C:0.00, G:0.32, T:0.68
Consensus pattern (3 bp):
TTG
Found at i:46982154 original size:17 final size:18
Alignment explanation
Indices: 46982132--46982165 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
46982122 AAAGTGATCT
46982132 TGAATTG-GAAATAAAAG
1 TGAATTGAGAAATAAAAG
*
46982149 TGAATTGAGAATTAAAA
1 TGAATTGAGAAATAAAA
46982166 TACCCTATTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.53, C:0.00, G:0.21, T:0.26
Consensus pattern (18 bp):
TGAATTGAGAAATAAAAG
Found at i:46982298 original size:21 final size:21
Alignment explanation
Indices: 46982250--46982335 Score: 100
Period size: 21 Copynumber: 4.0 Consensus size: 21
46982240 AGCTTTGCCG
*
46982250 ATCAGGCACTTTATGTGTCGT
1 ATCAGGCACCTTATGTGTCGT
*
46982271 ATTTCAGGCACCTTGTGTGTCGT
1 A--TCAGGCACCTTATGTGTCGT
**
46982294 ATCAGGCACCTCCTGTGTCGT
1 ATCAGGCACCTTATGTGTCGT
* *
46982315 TTCAGGCACTTTATGTGTCGT
1 ATCAGGCACCTTATGTGTCGT
46982336 GTACTGCTTC
Statistics
Matches: 55, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
21 36 0.65
23 19 0.35
ACGTcount: A:0.15, C:0.23, G:0.24, T:0.37
Consensus pattern (21 bp):
ATCAGGCACCTTATGTGTCGT
Found at i:46982641 original size:13 final size:13
Alignment explanation
Indices: 46982625--46982661 Score: 65
Period size: 13 Copynumber: 2.8 Consensus size: 13
46982615 TCAGTTGAAT
46982625 AAATCAAATGAGA
1 AAATCAAATGAGA
*
46982638 AAATCAAAAGAGA
1 AAATCAAATGAGA
46982651 AAATCAAATGA
1 AAATCAAATGA
46982662 ATTTAACCGA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.65, C:0.08, G:0.14, T:0.14
Consensus pattern (13 bp):
AAATCAAATGAGA
Found at i:46982715 original size:13 final size:13
Alignment explanation
Indices: 46982697--46982729 Score: 66
Period size: 13 Copynumber: 2.5 Consensus size: 13
46982687 TATGAGAAAG
46982697 TGAAATTATGAAT
1 TGAAATTATGAAT
46982710 TGAAATTATGAAT
1 TGAAATTATGAAT
46982723 TGAAATT
1 TGAAATT
46982730 GAGATATCGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.45, C:0.00, G:0.15, T:0.39
Consensus pattern (13 bp):
TGAAATTATGAAT
Found at i:46990523 original size:42 final size:42
Alignment explanation
Indices: 46990400--46990545 Score: 129
Period size: 43 Copynumber: 3.4 Consensus size: 42
46990390 TTCAGAGATG
* *
46990400 TGATTTCGTGTAAGACCAC-GTCTGGGAT-GTTGGCATCG-ATT
1 TGATTTCGTGTAAGACC-CTGTTTAGGATAG-TGGCATCGTATT
* * * *
46990441 TGAGATTTACGTGTAAGACCATGTTTAGGACA-TCGACATCGTATA
1 T--GATTT-CGTGTAAGACCCTGTTTAGGATAGT-GGCATCGTATT
46990486 TGATTTCGTGTAAGACCCTGTTTAGGATAGTGGCATCGATATT
1 TGATTTCGTGTAAGACCCTGTTTAGGATAGTGGCATCG-TATT
* *
46990529 TGATTACATGTAAGACC
1 TGATTTCGTGTAAGACC
46990546 ACGTTTGGGA
Statistics
Matches: 84, Mismatches: 12, Indels: 16
0.75 0.11 0.14
Matches are distributed among these distances:
41 1 0.01
42 27 0.32
43 30 0.36
44 23 0.27
45 3 0.04
ACGTcount: A:0.26, C:0.16, G:0.25, T:0.34
Consensus pattern (42 bp):
TGATTTCGTGTAAGACCCTGTTTAGGATAGTGGCATCGTATT
Found at i:46990545 original size:43 final size:42
Alignment explanation
Indices: 46990430--46990564 Score: 130
Period size: 43 Copynumber: 3.1 Consensus size: 42
46990420 TCTGGGATGT
*
46990430 TGGCATCGAT-TTGAGATTTACGTGTAAGACCATGTTTAGGACA
1 TGGCATCGATATT-TGA-TTACGTGTAAGACCATGTTTAGGACA
* * * * *
46990473 TCGACATCG-TATATGATTTCGTGTAAGACCCTGTTTAGGATA
1 T-GGCATCGATATTTGATTACGTGTAAGACCATGTTTAGGACA
* * *
46990515 GTGGCATCGATATTTGATTACATGTAAGACCACGTTTGGGACA
1 -TGGCATCGATATTTGATTACGTGTAAGACCATGTTTAGGACA
46990558 TTGGCAT
1 -TGGCAT
46990565 TGTACGAGCT
Statistics
Matches: 73, Mismatches: 15, Indels: 8
0.76 0.16 0.08
Matches are distributed among these distances:
42 29 0.40
43 37 0.51
44 7 0.10
ACGTcount: A:0.27, C:0.16, G:0.24, T:0.33
Consensus pattern (42 bp):
TGGCATCGATATTTGATTACGTGTAAGACCATGTTTAGGACA
Found at i:46997246 original size:7 final size:6
Alignment explanation
Indices: 46997214--46997274 Score: 65
Period size: 6 Copynumber: 10.5 Consensus size: 6
46997204 ATTGAGTCCA
* *
46997214 TTTTA- TTTTA- TTTTA- TTTTAT TTTTAGT TTTTAT TTTTAT ATTAAT
1 TTTTAT TTTTAT TTTTAT TTTTAT TTTTA-T TTTTAT TTTTAT TTTTAT
*
46997260 TTTTAT TTGTAT TTT
1 TTTTAT TTTTAT TTT
46997275 CCTAGACTTT
Statistics
Matches: 48, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
5 15 0.31
6 27 0.56
7 6 0.12
ACGTcount: A:0.20, C:0.00, G:0.03, T:0.77
Consensus pattern (6 bp):
TTTTAT
Found at i:47001659 original size:17 final size:18
Alignment explanation
Indices: 47001637--47001676 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
47001627 TTTGGGTCGT
47001637 GTGGG-CCACACGGGCGC
1 GTGGGCCCACACGGGCGC
*
47001654 GTGGGCCCACACGGGCGT
1 GTGGGCCCACACGGGCGC
47001672 GTGGG
1 GTGGG
47001677 ATTCTGGGCC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
17 5 0.24
18 16 0.76
ACGTcount: A:0.10, C:0.30, G:0.50, T:0.10
Consensus pattern (18 bp):
GTGGGCCCACACGGGCGC
Found at i:47004305 original size:23 final size:24
Alignment explanation
Indices: 47004279--47004334 Score: 60
Period size: 26 Copynumber: 2.3 Consensus size: 24
47004269 CCAGCACACC
* *
47004279 AATAT-CGCAGCATAGCTGCTAGA
1 AATATACGCAGCAAAGCTGCCAGA
47004302 AATAATAACGCAGCAAAGCTGCCAGA
1 AAT-AT-ACGCAGCAAAGCTGCCAGA
*
47004328 TATATAC
1 AATATAC
47004335 ACGACTTACA
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
23 3 0.11
24 4 0.15
25 2 0.07
26 18 0.67
ACGTcount: A:0.41, C:0.21, G:0.18, T:0.20
Consensus pattern (24 bp):
AATATACGCAGCAAAGCTGCCAGA
Found at i:47004920 original size:26 final size:27
Alignment explanation
Indices: 47004891--47004946 Score: 96
Period size: 26 Copynumber: 2.1 Consensus size: 27
47004881 AAACATTCAT
*
47004891 TTTACCCTACAGGGGTATTTGGGA-AA
1 TTTACACTACAGGGGTATTTGGGATAA
47004917 TTTACACTACAGGGGTATTTGGGATAA
1 TTTACACTACAGGGGTATTTGGGATAA
47004944 TTT
1 TTT
47004947 TACAATCTGA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
26 23 0.82
27 5 0.18
ACGTcount: A:0.27, C:0.12, G:0.25, T:0.36
Consensus pattern (27 bp):
TTTACACTACAGGGGTATTTGGGATAA
Found at i:47004961 original size:54 final size:54
Alignment explanation
Indices: 47004903--47005084 Score: 153
Period size: 54 Copynumber: 3.4 Consensus size: 54
47004893 TACCCTACAG
*
47004903 GGGTATTTGGGA-AA-TTTACACTACAG-GGGTATTTGGGATAATTTTAC-AATCTGA
1 GGGTATTT-GGATAATTTTACAAT-CAGAGGGTATTTGGG-TAATTTTACGAA-CTGA
* * *
47004957 GGGTATTTTGATAATTTTACAATCCGAGGGTATTTTGGTAATTTTACGAACTGA
1 GGGTATTTGGATAATTTTACAATCAGAGGGTATTTGGGTAATTTTACGAACTGA
** * * * * *
47005011 GGGTATTTCAACAATTTTACAATTC-GGGGGTATTTCGAT-ATTTTACAAACTG-
1 GGGTATTTGGATAATTTTACAA-TCAGAGGGTATTTGGGTAATTTTACGAACTGA
* *
47005063 GGGTATCTCGATAATTTTACAA
1 GGGTATTTGGATAATTTTACAA
47005085 ATCGGGGTCT
Statistics
Matches: 109, Mismatches: 14, Indels: 12
0.81 0.10 0.09
Matches are distributed among these distances:
52 19 0.17
53 14 0.13
54 55 0.50
55 21 0.19
ACGTcount: A:0.29, C:0.11, G:0.22, T:0.38
Consensus pattern (54 bp):
GGGTATTTGGATAATTTTACAATCAGAGGGTATTTGGGTAATTTTACGAACTGA
Found at i:47004969 original size:27 final size:27
Alignment explanation
Indices: 47004929--47005084 Score: 167
Period size: 27 Copynumber: 5.8 Consensus size: 27
47004919 TACACTACAG
*
47004929 GGGTATTTGGGATAATTTTACAATCTGA
1 GGGTATTT-CGATAATTTTACAATCTGA
* *
47004957 GGGTATTTTGATAATTTTACAATCCGA
1 GGGTATTTCGATAATTTTACAATCTGA
* *
47004984 GGGTATTTTGGTAATTTTACGAA-CTGA
1 GGGTATTTCGATAATTTTAC-AATCTGA
* * *
47005011 GGGTATTTCAACAATTTTACAAT-TCGG
1 GGGTATTTCGATAATTTTACAATCT-GA
*
47005038 GGGTATTTCGAT-ATTTTACAAACTG-
1 GGGTATTTCGATAATTTTACAATCTGA
*
47005063 GGGTATCTCGATAATTTTACAA
1 GGGTATTTCGATAATTTTACAA
47005085 ATCGGGGTCT
Statistics
Matches: 110, Mismatches: 13, Indels: 12
0.81 0.10 0.09
Matches are distributed among these distances:
25 11 0.10
26 22 0.20
27 67 0.61
28 10 0.09
ACGTcount: A:0.29, C:0.11, G:0.21, T:0.39
Consensus pattern (27 bp):
GGGTATTTCGATAATTTTACAATCTGA
Found at i:47006625 original size:21 final size:21
Alignment explanation
Indices: 47006599--47006638 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
47006589 CTATTCCACA
47006599 AATTGAACCTTAGACCTCACG
1 AATTGAACCTTAGACCTCACG
47006620 AATTGAACCTTAGACCTCA
1 AATTGAACCTTAGACCTCA
47006639 TGCACACCAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.35, C:0.28, G:0.12, T:0.25
Consensus pattern (21 bp):
AATTGAACCTTAGACCTCACG
Found at i:47012841 original size:15 final size:15
Alignment explanation
Indices: 47012821--47012851 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
47012811 AATTATGAAA
47012821 GATATGTTTTGGATT
1 GATATGTTTTGGATT
*
47012836 GATATGTTTTGTATT
1 GATATGTTTTGGATT
47012851 G
1 G
47012852 GAATTTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.19, C:0.00, G:0.26, T:0.55
Consensus pattern (15 bp):
GATATGTTTTGGATT
Found at i:47014139 original size:25 final size:25
Alignment explanation
Indices: 47014101--47014156 Score: 85
Period size: 25 Copynumber: 2.2 Consensus size: 25
47014091 TTATTTATTT
* *
47014101 GCTTATGACCTACTAAGCTATGATA
1 GCTTACGACCTACTAAGCAATGATA
*
47014126 GCTTACGACTTACTAAGCAATGATA
1 GCTTACGACCTACTAAGCAATGATA
47014151 GCTTAC
1 GCTTAC
47014157 TATGTGTATA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.32, C:0.21, G:0.16, T:0.30
Consensus pattern (25 bp):
GCTTACGACCTACTAAGCAATGATA
Found at i:47015868 original size:19 final size:21
Alignment explanation
Indices: 47015834--47015989 Score: 79
Period size: 21 Copynumber: 7.5 Consensus size: 21
47015824 GTACATTGTT
47015834 AACAGAAGCTCGTAAG-C-TG
1 AACAGAAGCTCGTAAGACTTG
47015853 AACAGAAGCT-GTTAAGACTTG
1 AACAGAAGCTCG-TAAGACTTG
* ***
47015874 AACAGGAGCTTACAAGAGC-TG
1 AACAGAAGCTCGTAAGA-CTTG
* * * ** *
47015895 AACAAAAACTCATAAGTGTTC
1 AACAGAAGCTCGTAAGACTTG
*
47015916 AACAGAAGCTCGTAAGAGC-TA
1 AACAGAAGCTCGTAAGA-CTTG
* * * * *
47015937 AACAGAAACTTGTATGAGTTA
1 AACAGAAGCTCGTAAGACTTG
* * *
47015958 AACAGAAACTCATAAGAGTTG
1 AACAGAAGCTCGTAAGACTTG
47015979 AACAGAAGCTC
1 AACAGAAGCTC
47015990 AATAGAGCTG
Statistics
Matches: 103, Mismatches: 26, Indels: 14
0.72 0.18 0.10
Matches are distributed among these distances:
18 1 0.01
19 14 0.14
20 1 0.01
21 86 0.83
22 1 0.01
ACGTcount: A:0.42, C:0.17, G:0.21, T:0.19
Consensus pattern (21 bp):
AACAGAAGCTCGTAAGACTTG
Found at i:47015931 original size:21 final size:21
Alignment explanation
Indices: 47015895--47016049 Score: 114
Period size: 21 Copynumber: 7.4 Consensus size: 21
47015885 ACAAGAGCTG
* * * *
47015895 AACAAAAACTCATAAGTGTTC
1 AACAGAAACTCGTAAGAGTTA
* *
47015916 AACAGAAGCTCGTAAGAGCTA
1 AACAGAAACTCGTAAGAGTTA
* *
47015937 AACAGAAACTTGTATGAGTTA
1 AACAGAAACTCGTAAGAGTTA
* *
47015958 AACAGAAACTCATAAGAGTTG
1 AACAGAAACTCGTAAGAGTTA
* * * *
47015979 AACAGAAGCTC-AATAGAGCTG
1 AACAGAAACTCGTA-AGAGTTA
** *
47016000 AATGGAAACTCATAAGAGTTA
1 AACAGAAACTCGTAAGAGTTA
* * *
47016021 AACATAAGCTCGTAAGAGCTA
1 AACAGAAACTCGTAAGAGTTA
47016042 AACAGAAA
1 AACAGAAA
47016050 GTAAAACACG
Statistics
Matches: 101, Mismatches: 31, Indels: 4
0.74 0.23 0.03
Matches are distributed among these distances:
20 1 0.01
21 99 0.98
22 1 0.01
ACGTcount: A:0.46, C:0.15, G:0.19, T:0.19
Consensus pattern (21 bp):
AACAGAAACTCGTAAGAGTTA
Found at i:47015997 original size:63 final size:63
Alignment explanation
Indices: 47015895--47016048 Score: 157
Period size: 63 Copynumber: 2.4 Consensus size: 63
47015885 ACAAGAGCTG
* * * ** *
47015895 AACAAAAACTCATAAGTGTTCAACAGAAGCTCGTAAGAGCTAAACAGAAACTTGTATGAGTTA
1 AACAAAAACTCATAAGAGTTAAACAGAAGCTCATAAGAGCTAAACAGAAACTCATAAGAGTTA
* * * **
47015958 AACAGAAACTCATAAGAGTTGAACAGAAGCTCA-ATAGAGCTGAATGGAAACTCATAAGAGTTA
1 AACAAAAACTCATAAGAGTTAAACAGAAGCTCATA-AGAGCTAAACAGAAACTCATAAGAGTTA
* * * *
47016021 AACATAAGCTCGTAAGAGCTAAACAGAA
1 AACAAAAACTCATAAGAGTTAAACAGAA
47016049 AGTAAAACAC
Statistics
Matches: 75, Mismatches: 15, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
62 1 0.01
63 74 0.99
ACGTcount: A:0.46, C:0.16, G:0.19, T:0.19
Consensus pattern (63 bp):
AACAAAAACTCATAAGAGTTAAACAGAAGCTCATAAGAGCTAAACAGAAACTCATAAGAGTTA
Found at i:47022142 original size:18 final size:20
Alignment explanation
Indices: 47022095--47022146 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 20
47022085 CTAAGATTAA
47022095 ACTTAATTAATTACTTTAATC
1 ACTTAATTAA-TACTTTAATC
47022116 ATGCTTAATTAA-ACTTTAATC
1 A--CTTAATTAATACTTTAATC
47022137 -CTTAATTAAT
1 ACTTAATTAAT
47022147 TAAATCTAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
18 9 0.32
21 10 0.36
23 9 0.32
ACGTcount: A:0.38, C:0.13, G:0.02, T:0.46
Consensus pattern (20 bp):
ACTTAATTAATACTTTAATC
Found at i:47030601 original size:10 final size:10
Alignment explanation
Indices: 47030586--47030644 Score: 84
Period size: 10 Copynumber: 5.9 Consensus size: 10
47030576 AATTTTAGCT
47030586 TTTATCTTTA
1 TTTATCTTTA
*
47030596 TTTATCCTTA
1 TTTATCTTTA
47030606 TTTATCTTTA
1 TTTATCTTTA
*
47030616 ATTATCTTTA
1 TTTATCTTTA
47030626 TTTAT-TTGTA
1 TTTATCTT-TA
47030636 TTTATCTTT
1 TTTATCTTT
47030645 TAGAATTTAA
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
9 2 0.05
10 39 0.91
11 2 0.05
ACGTcount: A:0.20, C:0.10, G:0.02, T:0.68
Consensus pattern (10 bp):
TTTATCTTTA
Found at i:47033223 original size:15 final size:15
Alignment explanation
Indices: 47033203--47033235 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
47033193 ACAATCCACT
47033203 TTACTATGGTCTTTA
1 TTACTATGGTCTTTA
*
47033218 TTACTATGTTCTTTA
1 TTACTATGGTCTTTA
47033233 TTA
1 TTA
47033236 GTATATTGTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.21, C:0.12, G:0.09, T:0.58
Consensus pattern (15 bp):
TTACTATGGTCTTTA
Found at i:47033695 original size:15 final size:15
Alignment explanation
Indices: 47033671--47033700 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
47033661 GTGCCATCAA
*
47033671 AAGTGTCCACTTTCG
1 AAGTGCCCACTTTCG
47033686 AAGTGCCCACTTTCG
1 AAGTGCCCACTTTCG
47033701 CTATCACTTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.20, C:0.30, G:0.20, T:0.30
Consensus pattern (15 bp):
AAGTGCCCACTTTCG
Found at i:47034314 original size:16 final size:16
Alignment explanation
Indices: 47034292--47034349 Score: 50
Period size: 16 Copynumber: 3.7 Consensus size: 16
47034282 GAATGTAAAA
47034292 CAAACTCAAAAAAGCT
1 CAAACTCAAAAAAGCT
* *
47034308 TAAACTC-GAAAAGCT
1 CAAACTCAAAAAAGCT
47034323 CAAA-TCCAAAAAAGAC-
1 CAAACT-CAAAAAAG-CT
*
47034339 CAAACCCAAAA
1 CAAACTCAAAA
47034350 TGCTCGAGCT
Statistics
Matches: 33, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
14 1 0.03
15 11 0.33
16 20 0.61
17 1 0.03
ACGTcount: A:0.57, C:0.26, G:0.07, T:0.10
Consensus pattern (16 bp):
CAAACTCAAAAAAGCT
Found at i:47037005 original size:21 final size:21
Alignment explanation
Indices: 47036981--47037021 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
47036971 AAAACTATTT
* *
47036981 TATATTTATATTTATATAAAC
1 TATATTTAAATTTAAATAAAC
47037002 TATATTTAAATTTAAATAAA
1 TATATTTAAATTTAAATAAA
47037022 TAGTGAAGTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (21 bp):
TATATTTAAATTTAAATAAAC
Found at i:47042148 original size:14 final size:15
Alignment explanation
Indices: 47042116--47042146 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
47042106 GCATACCTCC
47042116 TTGGTTTTTTCTGTT
1 TTGGTTTTTTCTGTT
47042131 TTGGTTTTTTCTGTT
1 TTGGTTTTTTCTGTT
47042146 T
1 T
47042147 GGGGACCATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.00, C:0.06, G:0.19, T:0.74
Consensus pattern (15 bp):
TTGGTTTTTTCTGTT
Found at i:47042315 original size:25 final size:24
Alignment explanation
Indices: 47042277--47042343 Score: 66
Period size: 25 Copynumber: 2.8 Consensus size: 24
47042267 GGGAAAAAGA
*
47042277 AGAAAGA-AAAAGAAAAAGAGAAGG
1 AGAAAGAGAAGAGAAAAAG-GAAGG
* *
47042301 AGAGAATAG-AGAGAAAGAAGGTAGG
1 AGA-AAGAGAAGAGAAA-AAGGAAGG
47042326 AGAAAGAGAAGAGAAAAA
1 AGAAAGAGAAGAGAAAAA
47042344 ATAATAATAG
Statistics
Matches: 35, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
24 9 0.26
25 23 0.66
26 3 0.09
ACGTcount: A:0.64, C:0.00, G:0.33, T:0.03
Consensus pattern (24 bp):
AGAAAGAGAAGAGAAAAAGGAAGG
Found at i:47043028 original size:22 final size:21
Alignment explanation
Indices: 47042978--47043028 Score: 50
Period size: 22 Copynumber: 2.4 Consensus size: 21
47042968 TTTTAATAGT
*
47042978 TAATTTTAATATAATTATTCA
1 TAATTATAATATAATTATTCA
* *
47042999 -AATATATATATATTATTATTTA
1 TAAT-TATA-ATATAATTATTCA
47043021 TAATTATA
1 TAATTATA
47043029 CTCAAACTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 5
0.75 0.09 0.16
Matches are distributed among these distances:
20 3 0.12
21 3 0.12
22 15 0.62
23 3 0.12
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (21 bp):
TAATTATAATATAATTATTCA
Found at i:47049318 original size:14 final size:14
Alignment explanation
Indices: 47049299--47049325 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
47049289 ACACGCTCGT
47049299 GTGTCCTCAGGCCC
1 GTGTCCTCAGGCCC
47049313 GTGTCCTCAGGCC
1 GTGTCCTCAGGCC
47049326 GTATAACTCT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.07, C:0.41, G:0.30, T:0.22
Consensus pattern (14 bp):
GTGTCCTCAGGCCC
Found at i:47050888 original size:191 final size:191
Alignment explanation
Indices: 47050564--47050950 Score: 729
Period size: 191 Copynumber: 2.0 Consensus size: 191
47050554 TTGCTTACAC
* *
47050564 CATTTCCTTTATCTGAAACTAGATTTGATAAGCTTTCATTTAATATTTTACTCAACCTCTATTCA
1 CATTTCCTTTATCTGAAACTAGACTTGATAAGCTTTCATTTAATATTTTACTCAACCTCTACTCA
*
47050629 ATTTCCACTATTTTTGGTGGGTTTTCACAGTCGGATCTCTGGTATTGTACTAATCTGTCTTTGTG
66 ATTTCCACTATTTTTGGTAGGTTTTCACAGTCGGATCTCTGGTATTGTACTAATCTGTCTTTGTG
*
47050694 CAACAGGATGATAACCATTACAAATTTGTCATAGAAATTATTCTCATAAATATCACTCATT
131 CAACAGGATGATAACCATCACAAATTTGTCATAGAAATTATTCTCATAAATATCACTCATT
*
47050755 CATTTCCTTTATCTGAAACTAGACTTGATAAGCTTTCATTTAATATTTTACTCAGCCTCTACTCA
1 CATTTCCTTTATCTGAAACTAGACTTGATAAGCTTTCATTTAATATTTTACTCAACCTCTACTCA
47050820 ATTTCCACTATTTTTGGTAGGTTTTCACAGTCGGATCTCTGGTATTGTACTAATCTGTCTTTGTG
66 ATTTCCACTATTTTTGGTAGGTTTTCACAGTCGGATCTCTGGTATTGTACTAATCTGTCTTTGTG
47050885 CAACAGGATGATAACCATCACAAATTTGTCATAGAAATTATTCTCATAAATATCACTCATT
131 CAACAGGATGATAACCATCACAAATTTGTCATAGAAATTATTCTCATAAATATCACTCATT
47050946 CATTT
1 CATTT
47050951 GCACTCTTAT
Statistics
Matches: 191, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
191 191 1.00
ACGTcount: A:0.28, C:0.19, G:0.12, T:0.41
Consensus pattern (191 bp):
CATTTCCTTTATCTGAAACTAGACTTGATAAGCTTTCATTTAATATTTTACTCAACCTCTACTCA
ATTTCCACTATTTTTGGTAGGTTTTCACAGTCGGATCTCTGGTATTGTACTAATCTGTCTTTGTG
CAACAGGATGATAACCATCACAAATTTGTCATAGAAATTATTCTCATAAATATCACTCATT
Found at i:47075276 original size:16 final size:16
Alignment explanation
Indices: 47075255--47075304 Score: 54
Period size: 16 Copynumber: 3.4 Consensus size: 16
47075245 AAGGTTTTAC
47075255 TATTTTTATTCTCTAT
1 TATTTTTATTCTCTAT
* *
47075271 TA---TT-TTCTTTAC
1 TATTTTTATTCTCTAT
47075283 TATTTTTATTCTCTAT
1 TATTTTTATTCTCTAT
47075299 TATTTT
1 TATTTT
47075305 CTTTCTTTTT
Statistics
Matches: 26, Mismatches: 4, Indels: 8
0.68 0.11 0.21
Matches are distributed among these distances:
12 8 0.31
13 2 0.08
15 2 0.08
16 14 0.54
ACGTcount: A:0.18, C:0.12, G:0.00, T:0.70
Consensus pattern (16 bp):
TATTTTTATTCTCTAT
Found at i:47075310 original size:16 final size:16
Alignment explanation
Indices: 47075263--47075310 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 16
47075253 ACTATTTTTA
47075263 TTCTCTATTATTTTCT
1 TTCTCTATTATTTTCT
* *
47075279 TT-ACTA-T-TTTT-A
1 TTCTCTATTATTTTCT
47075291 TTCTCTATTATTTTCT
1 TTCTCTATTATTTTCT
47075307 TTCT
1 TTCT
47075311 TTTTTTTATT
Statistics
Matches: 24, Mismatches: 4, Indels: 8
0.67 0.11 0.22
Matches are distributed among these distances:
12 2 0.08
13 7 0.29
14 2 0.08
15 7 0.29
16 6 0.25
ACGTcount: A:0.15, C:0.17, G:0.00, T:0.69
Consensus pattern (16 bp):
TTCTCTATTATTTTCT
Found at i:47075320 original size:28 final size:28
Alignment explanation
Indices: 47075250--47075316 Score: 118
Period size: 28 Copynumber: 2.4 Consensus size: 28
47075240 ATTCAAAGGT
47075250 TTTACTATTTTTATTCTCTATTATTTTC
1 TTTACTATTTTTATTCTCTATTATTTTC
47075278 TTTACTATTTTTATTCTCTATTATTTTC
1 TTTACTATTTTTATTCTCTATTATTTTC
*
47075306 TTT-CTTTTTTT
1 TTTACTATTTTT
47075317 TATTATATAC
Statistics
Matches: 38, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
27 7 0.18
28 31 0.82
ACGTcount: A:0.15, C:0.13, G:0.00, T:0.72
Consensus pattern (28 bp):
TTTACTATTTTTATTCTCTATTATTTTC
Found at i:47087078 original size:25 final size:24
Alignment explanation
Indices: 47087045--47087103 Score: 66
Period size: 26 Copynumber: 2.4 Consensus size: 24
47087035 GAGATGTTTC
* *
47087045 AAAAA-AAAAGAGAAAAATAGAGAA
1 AAAAATAAAAGAAAAAAATA-AAAA
*
47087069 AAAAATAAAAATAAAAAAATAAAAA
1 AAAAAT-AAAAGAAAAAAATAAAAA
47087094 AAAAATAAAA
1 AAAAATAAAA
47087104 AAATGGAGAG
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
24 9 0.30
25 9 0.30
26 12 0.40
ACGTcount: A:0.85, C:0.00, G:0.07, T:0.08
Consensus pattern (24 bp):
AAAAATAAAAGAAAAAAATAAAAA
Found at i:47087086 original size:14 final size:14
Alignment explanation
Indices: 47087067--47087107 Score: 59
Period size: 14 Copynumber: 3.0 Consensus size: 14
47087057 AAAAATAGAG
47087067 AAAAAAATAAAAAT
1 AAAAAAATAAAAAT
47087081 AAAAAAATAAAAA-
1 AAAAAAATAAAAAT
47087094 AAAAATAA-AAAAAT
1 AAAAA-AATAAAAAT
47087108 GGAGAGGCCA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
13 10 0.40
14 15 0.60
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (14 bp):
AAAAAAATAAAAAT
Found at i:47087092 original size:19 final size:19
Alignment explanation
Indices: 47087069--47087107 Score: 69
Period size: 19 Copynumber: 2.0 Consensus size: 19
47087059 AAATAGAGAA
47087069 AAAAATAAAAATAAAAAAAT
1 AAAAA-AAAAATAAAAAAAT
47087089 AAAAAAAAAATAAAAAAAT
1 AAAAAAAAAATAAAAAAAT
47087108 GGAGAGGCCA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.87, C:0.00, G:0.00, T:0.13
Consensus pattern (19 bp):
AAAAAAAAAATAAAAAAAT
Found at i:47088123 original size:119 final size:119
Alignment explanation
Indices: 47087941--47088268 Score: 593
Period size: 119 Copynumber: 2.8 Consensus size: 119
47087931 AGACAATTAG
* *
47087941 ACTGAAGCAGATCCAAGATAATTTGGTATTCTTGTGTTTACAAGGAACAAACCGAGGACATAGTA
1 ACTGAAGCAGATCCAAGATCATTTGGTGTTCTTGTGTTTACAAGGAACAAACCGAGGACATAGTA
47088006 GATTTGACTCTCAGACGTTCTCAAATATAGCAGATCTAACCTTCAGATGTTTAT
66 GATTTGACTCTCAGACGTTCTCAAATATAGCAGATCTAACCTTCAGATGTTTAT
47088060 ACTGAAGCAGATCCAAGATCATTTGGTGTTCTTGTGTTTACAAGGAACAAACCGAGGACATAGTA
1 ACTGAAGCAGATCCAAGATCATTTGGTGTTCTTGTGTTTACAAGGAACAAACCGAGGACATAGTA
47088125 GATTTGACTCTCAGACGTTCTCAAATATAGCAGATCTAACCTTCAGATGTTTAT
66 GATTTGACTCTCAGACGTTCTCAAATATAGCAGATCTAACCTTCAGATGTTTAT
* * *
47088179 ACTGAAGCAGATCCAAGATCATTTGGTGTTCTTGTGTTTACAAGAAACAAATCGAGGACATAGCA
1 ACTGAAGCAGATCCAAGATCATTTGGTGTTCTTGTGTTTACAAGGAACAAACCGAGGACATAGTA
* *
47088244 GATTGGACTCTCAGATGTTCTCAAA
66 GATTTGACTCTCAGACGTTCTCAAA
47088269 CAAACTCAAG
Statistics
Matches: 202, Mismatches: 7, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
119 202 1.00
ACGTcount: A:0.33, C:0.18, G:0.20, T:0.30
Consensus pattern (119 bp):
ACTGAAGCAGATCCAAGATCATTTGGTGTTCTTGTGTTTACAAGGAACAAACCGAGGACATAGTA
GATTTGACTCTCAGACGTTCTCAAATATAGCAGATCTAACCTTCAGATGTTTAT
Found at i:47088295 original size:83 final size:82
Alignment explanation
Indices: 47088191--47088388 Score: 256
Period size: 83 Copynumber: 2.4 Consensus size: 82
47088181 TGAAGCAGAT
* **
47088191 CCAAGATCATTTGGTGTTCTTGTGTTTACAAGAAACAAATCGAGGACATAGCAGA-TTGGACTCT
1 CCAAGATGATTTGGCATTCTTGTGTTTACAAGAAACAAATCGAGGACATAGCAGATTTGG-CTCT
47088255 -CAGATGTTCTCAAACAAA
65 CCAG-TGTTCTCAAACAAA
*
47088273 CTCAAGATGATTTGGCATTCTTGTGTTTACAAGAAACAAATCGAGGACGTAGCAGATTTGGCTCT
1 C-CAAGATGATTTGGCATTCTTGTGTTTACAAGAAACAAATCGAGGACATAGCAGATTTGGCTCT
**
47088338 CCAGTGTTCTCAAACAGT
65 CCAGTGTTCTCAAACAAA
* * **
47088356 CCTAAGATGGTTTGGCATCCTTGTACTTACAAG
1 CC-AAGATGATTTGGCATTCTTGTGTTTACAAG
47088389 GAGAAAATCA
Statistics
Matches: 102, Mismatches: 10, Indels: 7
0.86 0.08 0.06
Matches are distributed among these distances:
82 2 0.02
83 93 0.91
84 7 0.07
ACGTcount: A:0.30, C:0.19, G:0.21, T:0.30
Consensus pattern (82 bp):
CCAAGATGATTTGGCATTCTTGTGTTTACAAGAAACAAATCGAGGACATAGCAGATTTGGCTCTC
CAGTGTTCTCAAACAAA
Found at i:47088397 original size:83 final size:83
Alignment explanation
Indices: 47088216--47088418 Score: 236
Period size: 83 Copynumber: 2.4 Consensus size: 83
47088206 GTTCTTGTGT
*
47088216 TTACAAGAAACAAATCGAGGACATAGCAGA-TTGGACTCTCAGATGTTCTCAAACAAACTCAAGA
1 TTACAAGAAACAAATCGAGGACGTAGCAGATTTGG-CTCTCAGATGTTCTCAAACAAACTCAAGA
* **
47088280 TGATTTGGCATTCTTGTGT
65 TGATTTGGCATCCTTGTAC
**
47088299 TTACAAGAAACAAATCGAGGACGTAGCAGATTTGGCTCTCCAG-TGTTCTCAAACAGTC-CTAAG
1 TTACAAGAAACAAATCGAGGACGTAGCAGATTTGGCTCT-CAGATGTTCTCAAACAAACTC-AAG
*
47088362 ATGGTTTGGCATCCTTGTAC
64 ATGATTTGGCATCCTTGTAC
* * *
47088382 TTACAAGGAGA-AAATC-AGAGATGTAGCTGATTTGGCT
1 TTACAA-GAAACAAATCGAG-GACGTAGCAGATTTGGCT
47088419 TTCACGTGCT
Statistics
Matches: 105, Mismatches: 10, Indels: 10
0.84 0.08 0.08
Matches are distributed among these distances:
82 3 0.03
83 92 0.88
84 10 0.10
ACGTcount: A:0.33, C:0.18, G:0.22, T:0.28
Consensus pattern (83 bp):
TTACAAGAAACAAATCGAGGACGTAGCAGATTTGGCTCTCAGATGTTCTCAAACAAACTCAAGAT
GATTTGGCATCCTTGTAC
Found at i:47091160 original size:42 final size:42
Alignment explanation
Indices: 47091113--47091196 Score: 159
Period size: 42 Copynumber: 2.0 Consensus size: 42
47091103 TCCCTCATGC
*
47091113 ATCATCTTCAAAAAAGACAAGGCTCCAAAATTTTCAAAAAAA
1 ATCATCTTCAAAAAAGACAAGGCCCCAAAATTTTCAAAAAAA
47091155 ATCATCTTCAAAAAAGACAAGGCCCCAAAATTTTCAAAAAAA
1 ATCATCTTCAAAAAAGACAAGGCCCCAAAATTTTCAAAAAAA
47091197 TATAAAGGCA
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.52, C:0.20, G:0.07, T:0.20
Consensus pattern (42 bp):
ATCATCTTCAAAAAAGACAAGGCCCCAAAATTTTCAAAAAAA
Found at i:47092484 original size:14 final size:15
Alignment explanation
Indices: 47092460--47092490 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
47092450 TAAATAATTT
47092460 AAAATTATTAAATAA
1 AAAATTATTAAATAA
47092475 AAAATT-TTAAATAA
1 AAAATTATTAAATAA
47092489 AA
1 AA
47092491 TATTGAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.62
15 6 0.38
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (15 bp):
AAAATTATTAAATAA
Found at i:47093708 original size:3 final size:3
Alignment explanation
Indices: 47093700--47093724 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
47093690 GTATGTCCAT
47093700 TTC TTC TTC TTC TTC TTC TTC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC T
47093725 CCTCCTCCTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:47094871 original size:24 final size:24
Alignment explanation
Indices: 47094808--47094859 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
47094798 TTTCTAGAAG
* * *
47094808 ATTTAGTATTTATGAGTATAATAT
1 ATTTAGCATTTATTAGCATAATAT
47094832 ATTTAGCATTTATTAGCATAATAT
1 ATTTAGCATTTATTAGCATAATAT
47094856 ATTT
1 ATTT
47094860 GACTTTGATT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.37, C:0.04, G:0.10, T:0.50
Consensus pattern (24 bp):
ATTTAGCATTTATTAGCATAATAT
Found at i:47101654 original size:40 final size:40
Alignment explanation
Indices: 47101577--47101713 Score: 163
Period size: 40 Copynumber: 3.5 Consensus size: 40
47101567 ACCCAAGTAT
47101577 CTTCGGGAT-TTAG-CCGGATATAACAACTCGCACAAATGC
1 CTTCGGG-TCTTAGCCCGGATATAACAACTCGCACAAATGC
* *
47101616 CTTCGGGTCTTAGCCCGGATATAATC-ACTAGCATAAATGC
1 CTTCGGGTCTTAGCCCGGATATAA-CAACTCGCACAAATGC
* * * *
47101656 CTTCGGGACATAGCCCGGATATAGCAACTCGCACGAATGC
1 CTTCGGGTCTTAGCCCGGATATAACAACTCGCACAAATGC
* *
47101696 CTTCGGATCTTAGTCCGG
1 CTTCGGGTCTTAGCCCGG
47101714 TTATCATCCG
Statistics
Matches: 82, Mismatches: 12, Indels: 7
0.81 0.12 0.07
Matches are distributed among these distances:
38 1 0.01
39 12 0.15
40 68 0.83
41 1 0.01
ACGTcount: A:0.26, C:0.27, G:0.23, T:0.24
Consensus pattern (40 bp):
CTTCGGGTCTTAGCCCGGATATAACAACTCGCACAAATGC
Found at i:47110865 original size:10 final size:10
Alignment explanation
Indices: 47110852--47110879 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
47110842 CTATTCAAAT
47110852 ATCAAATATC
1 ATCAAATATC
47110862 ATCAAATATC
1 ATCAAATATC
47110872 ATCAAATA
1 ATCAAATA
47110880 AATCAATTTC
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:0.54, C:0.18, G:0.00, T:0.29
Consensus pattern (10 bp):
ATCAAATATC
Found at i:47111605 original size:19 final size:20
Alignment explanation
Indices: 47111565--47111606 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
47111555 TTGATTCATG
47111565 TTTTCAATCTCATATCTCAA
1 TTTTCAATCTCATATCTCAA
47111585 TTTTCAATTCTCA-AT-TCAA
1 TTTTCAA-TCTCATATCTCAA
47111604 TTT
1 TTT
47111607 CTCGTTTCAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 7 0.33
20 9 0.43
21 5 0.24
ACGTcount: A:0.29, C:0.21, G:0.00, T:0.50
Consensus pattern (20 bp):
TTTTCAATCTCATATCTCAA
Found at i:47121760 original size:15 final size:15
Alignment explanation
Indices: 47121734--47121788 Score: 76
Period size: 15 Copynumber: 3.7 Consensus size: 15
47121724 CATATATATT
*
47121734 ATATAA-TTCAATTA
1 ATATAATTTCAATCA
47121748 ATATAATTTCAATCA
1 ATATAATTTCAATCA
*
47121763 AAATAATTTCAATCA
1 ATATAATTTCAATCA
*
47121778 ATATAAATTCA
1 ATATAATTTCA
47121789 GTAAATTCAT
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
14 6 0.17
15 30 0.83
ACGTcount: A:0.51, C:0.11, G:0.00, T:0.38
Consensus pattern (15 bp):
ATATAATTTCAATCA
Found at i:47122967 original size:9 final size:9
Alignment explanation
Indices: 47122953--47122979 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
47122943 ACTTGTCTTT
47122953 TTTTATTTA
1 TTTTATTTA
47122962 TTTTATTTA
1 TTTTATTTA
47122971 TTTTATTTA
1 TTTTATTTA
47122980 CCATGCAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (9 bp):
TTTTATTTA
Found at i:47127267 original size:42 final size:43
Alignment explanation
Indices: 47127148--47127301 Score: 127
Period size: 43 Copynumber: 3.6 Consensus size: 43
47127138 ACATAGGATC
* * * * * *
47127148 CGATATTTGTTTTTGTGTAAGACTACGTCTTGGAC-GTTGACAT
1 CGATATTTGATTTCGTGTAAGACCATGTCTGGGACAG-TGGCAT
* *
47127191 CGACT-TATGATTTACGTGTAAGACCATGTTTGGGACA-TCGGCAT
1 CGA-TATTTGATTT-CGTGTAAGACCATGTCTGGGACAGT-GGCAT
* *
47127235 CG-TATTTGATTTCGTGTAAGACCCTGTCTGGGATAGTGGCAT
1 CGATATTTGATTTCGTGTAAGACCATGTCTGGGACAGTGGCAT
* * *
47127277 TGATATTTGATTACATGTAAGACCA
1 CGATATTTGATTTCGTGTAAGACCA
47127302 CATCAAGGAC
Statistics
Matches: 88, Mismatches: 16, Indels: 14
0.75 0.14 0.12
Matches are distributed among these distances:
42 27 0.31
43 37 0.42
44 24 0.27
ACGTcount: A:0.24, C:0.16, G:0.24, T:0.36
Consensus pattern (43 bp):
CGATATTTGATTTCGTGTAAGACCATGTCTGGGACAGTGGCAT
Found at i:47127284 original size:43 final size:42
Alignment explanation
Indices: 47127198--47127301 Score: 120
Period size: 42 Copynumber: 2.4 Consensus size: 42
47127188 CATCGACTTA
*
47127198 TGATTTACGTGTAAGACCATGTTTGGGACATCGGCATCGTATT
1 TGATTT-CGTGTAAGACCATGTCTGGGACATCGGCATCGTATT
* * *
47127241 TGATTTCGTGTAAGACCCTGTCTGGGATAGT-GGCATTGATATT
1 TGATTTCGTGTAAGACCATGTCTGGGACA-TCGGCATCG-TATT
* *
47127284 TGATTACATGTAAGACCA
1 TGATTTCGTGTAAGACCA
47127302 CATCAAGGAC
Statistics
Matches: 52, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
42 26 0.50
43 26 0.50
ACGTcount: A:0.25, C:0.15, G:0.25, T:0.35
Consensus pattern (42 bp):
TGATTTCGTGTAAGACCATGTCTGGGACATCGGCATCGTATT
Found at i:47135871 original size:31 final size:31
Alignment explanation
Indices: 47135835--47135896 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
47135825 ACATGTAAGA
47135835 AAGTCTCGTATAAAAATTTAATCATTTGTGT
1 AAGTCTCGTATAAAAATTTAATCATTTGTGT
47135866 AAGTCTCGTATAAAAATTTAATCATTTGTGT
1 AAGTCTCGTATAAAAATTTAATCATTTGTGT
47135897 GCTTAATTTG
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:0.35, C:0.10, G:0.13, T:0.42
Consensus pattern (31 bp):
AAGTCTCGTATAAAAATTTAATCATTTGTGT
Found at i:47136947 original size:44 final size:42
Alignment explanation
Indices: 47136863--47136990 Score: 132
Period size: 44 Copynumber: 3.0 Consensus size: 42
47136853 ATGTGTTTTT
* * * *
47136863 GTGTAAGACCACATTTGGGACGTTGGCATCGACTTATGATTTAC
1 GTGTAAGACCATATCTGGGACATTGGCATCGA-TTTTGATTT-C
47136907 GTGTAAGACCATATCTGGGACATTGGCATCGTATTTTGATTTC
1 GTGTAAGACCATATCTGGGACATTGGCATCG-ATTTTGATTTC
* * * *
47136950 ATGTAAAACCCTATC-GAGGACAATGGCATCGATATTTGATT
1 GTGTAAGACCATATCTG-GGACATTGGCATCGAT-TTTGATT
47136991 ACATCTATGT
Statistics
Matches: 73, Mismatches: 8, Indels: 7
0.83 0.09 0.08
Matches are distributed among these distances:
42 3 0.04
43 33 0.45
44 36 0.49
45 1 0.01
ACGTcount: A:0.27, C:0.17, G:0.23, T:0.33
Consensus pattern (42 bp):
GTGTAAGACCATATCTGGGACATTGGCATCGATTTTGATTTC
Found at i:47137459 original size:42 final size:43
Alignment explanation
Indices: 47137340--47137511 Score: 145
Period size: 43 Copynumber: 4.0 Consensus size: 43
47137330 TTATAGGATC
* * * * * *
47137340 CGATATTTGTTTTTGTGTAAGACTACGTCTTGGAC-GTTGACAT
1 CGATATTTGATTTCGTGTAAGACCATGTCTGGGACAG-TGGCAT
* *
47137383 CGACT-TATGATTTACGTGTAAGACCATGTTTGGGACA-TCGGCAT
1 CGA-TATTTGATTT-CGTGTAAGACCATGTCTGGGACAGT-GGCAT
*
47137427 CG-TATTTGATTTCGTGTAAGACCCTGTCTGGGACAGTGGCAT
1 CGATATTTGATTTCGTGTAAGACCATGTCTGGGACAGTGGCAT
* * * ** *
47137469 CGATATTTGATTACATGTAAGACCACGTCAAGGACATTGGCAT
1 CGATATTTGATTTCGTGTAAGACCATGTCTGGGACAGTGGCAT
47137512 TGTACGAGCT
Statistics
Matches: 104, Mismatches: 18, Indels: 14
0.76 0.13 0.10
Matches are distributed among these distances:
42 29 0.28
43 51 0.49
44 24 0.23
ACGTcount: A:0.24, C:0.17, G:0.24, T:0.34
Consensus pattern (43 bp):
CGATATTTGATTTCGTGTAAGACCATGTCTGGGACAGTGGCAT
Found at i:47137775 original size:496 final size:491
Alignment explanation
Indices: 47136841--47137788 Score: 1542
Period size: 496 Copynumber: 1.9 Consensus size: 491
47136831 ATGTCATGAC
*
47136841 ATAGGATCCGATATGTGTTTTTGTGTAAGACCACATTTGGGACGTTGGCATCGACTTATGATTTA
1 ATAGGATCCGATATGTGTTTTTGTGTAAGACCACATTTGGGACGTTGACATCGACTTATGATTTA
*
47136906 CGTGTAAGACCATATCTGGGACATTGGCATCGTATTTTGATTTCATGTAAAACCCTATCGAGGAC
66 CGTGTAAGACCATATCTGGGACATCGGCATCGTATTTTGATTTCATGTAAAACCCTATCGAGGAC
* * **
47136971 AATGGCATCGATATTTGATTACATCTATGTCTGGGACATTGGCATTGTACGAGCTTTTCGAGTTA
131 AATGGCATCGATATTTGATTACATCCACGTCAAGGACATTGGCATTGTACGAGCTTTTCGAGTTA
** * *
47137036 TCCGTGTATCCTTATGATTCCGAATGGTTCAACGAGCGTTCTAAGAAACGAATGATTATATGAAA
196 TCCGCATATCCTTATGATTCCGAATGGTTCAACGAGCATTCCAAGAAACGAATGATTATATGAAA
*
47137101 TGTGTATCCGATTCAGGTACGTTTGAAATTGTATATCATATTTGATGTTGAAAGGTGAGTATATG
261 TGTGTATCCGATTCAGGTACGTTTGAAATTGTATATCATATTTGATGTTGAAAGGTAAGTATATG
*
47137166 TATCTTTGTGATCAAGTGATTATATATGACAAAAGTATGATAAAATATGCTATATGTGAAAATGA
326 TATCTTTGTGATCAAGTGATTATATATGACAAAAGTATGAGAAAATATGCTATATGTGAAAATGA
* *
47137231 ATGGGGAATATGTGAAATGTATTTGAGCTATGTGGTTTGTGGTAGCATTTGGCTAAGGAGTAGTT
391 ATGGGGAATATGTGAAATGTATTTGAGCTATGTGGTTTGTGATAGCATTTGGCTAAAGAGTAGTT
47137296 TATATGCTTTTGAATAAACAAACCATAGGAATAGTT
456 TATATGCTTTTGAATAAACAAACCATAGGAATAGTT
* * *
47137332 ATAGGATCCGATATTTGTTTTTGTGTAAGACTACGTCTT-GGACGTTGACATCGACTTATGATTT
1 ATAGGATCCGATATGTGTTTTTGTGTAAGACCACAT-TTGGGACGTTGACATCGACTTATGATTT
* * * * *
47137396 ACGTGTAAGACCATGTTTGGGACATCGGCATCGTA-TTTGATTTCGTGTAAGACCCTGTCTG-GG
65 ACGTGTAAGACCATATCTGGGACATCGGCATCGTATTTTGATTTCATGTAAAACCCTATC-GAGG
*
47137459 ACAGTGGCATCGATATTTGATTACATGTAAGACCACGTCAAGGACATTGGCATTGTACGAGCTTT
129 ACAATGGCATCGATATTTGATTACA--T----CCACGTCAAGGACATTGGCATTGTACGAGCTTT
* *
47137524 TCGAGTTATCCGCATATCCTTATGATTCTGAATGGTTCAACGGGCATTCCAAGAAACGAATGATT
188 TCGAGTTATCCGCATATCCTTATGATTCCGAATGGTTCAACGAGCATTCCAAGAAACGAATGATT
*
47137589 ATATGAAATGTGTATCCGATTCAGGTACGTTTGAAATTGTCTATCATATTTGATGTTGAAAGGTA
253 ATATGAAATGTGTATCCGATTCAGGTACGTTTGAAATTGTATATCATATTTGATGTTGAAAGGTA
* *
47137654 AGTATATGTATCTTTGTGATCAAGTGATTGTATGTGACAAAAGTATGAGAAAATATGCTATATGT
318 AGTATATGTATCTTTGTGATCAAGTGATTATATATGACAAAAGTATGAGAAAATATGCTATATGT
*
47137719 GCAAATGAATGGGGAATATGTGAAATGTATTTGAGCTATGTGGTTTGTGATAGCATTTGGCTAAA
383 GAAAATGAATGGGGAATATGTGAAATGTATTTGAGCTATGTGGTTTGTGATAGCATTTGGCTAAA
47137784 GAGTA
448 GAGTA
47137789 TATGTATATT
Statistics
Matches: 420, Mismatches: 29, Indels: 11
0.91 0.06 0.02
Matches are distributed among these distances:
490 47 0.11
491 90 0.21
492 3 0.01
496 280 0.67
ACGTcount: A:0.29, C:0.13, G:0.23, T:0.35
Consensus pattern (491 bp):
ATAGGATCCGATATGTGTTTTTGTGTAAGACCACATTTGGGACGTTGACATCGACTTATGATTTA
CGTGTAAGACCATATCTGGGACATCGGCATCGTATTTTGATTTCATGTAAAACCCTATCGAGGAC
AATGGCATCGATATTTGATTACATCCACGTCAAGGACATTGGCATTGTACGAGCTTTTCGAGTTA
TCCGCATATCCTTATGATTCCGAATGGTTCAACGAGCATTCCAAGAAACGAATGATTATATGAAA
TGTGTATCCGATTCAGGTACGTTTGAAATTGTATATCATATTTGATGTTGAAAGGTAAGTATATG
TATCTTTGTGATCAAGTGATTATATATGACAAAAGTATGAGAAAATATGCTATATGTGAAAATGA
ATGGGGAATATGTGAAATGTATTTGAGCTATGTGGTTTGTGATAGCATTTGGCTAAAGAGTAGTT
TATATGCTTTTGAATAAACAAACCATAGGAATAGTT
Found at i:47138273 original size:21 final size:22
Alignment explanation
Indices: 47138242--47138282 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
47138232 TATGTTTTTG
47138242 TATGTCTTTGGCTTATGAATGT
1 TATGTCTTTGGCTTATGAATGT
* *
47138264 TATGT-TTTGGTTTGTGAAT
1 TATGTCTTTGGCTTATGAAT
47138283 TATGAATAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.17, C:0.05, G:0.24, T:0.54
Consensus pattern (22 bp):
TATGTCTTTGGCTTATGAATGT
Found at i:47140812 original size:24 final size:24
Alignment explanation
Indices: 47140749--47140800 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
47140739 TTTCTAGAAG
* * *
47140749 ATTTAGTATTTATGAGTATAATAT
1 ATTTAGCATTTATTAGCATAATAT
47140773 ATTTAGCATTTATTAGCATAATAT
1 ATTTAGCATTTATTAGCATAATAT
47140797 ATTT
1 ATTT
47140801 GACTTTGATT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.37, C:0.04, G:0.10, T:0.50
Consensus pattern (24 bp):
ATTTAGCATTTATTAGCATAATAT
Found at i:47141167 original size:14 final size:14
Alignment explanation
Indices: 47141148--47141176 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
47141138 TTATTAAATG
47141148 TTGCAAAATAATTT
1 TTGCAAAATAATTT
47141162 TTGCAAAATAATTT
1 TTGCAAAATAATTT
47141176 T
1 T
47141177 CTTAACAATC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.41, C:0.07, G:0.07, T:0.45
Consensus pattern (14 bp):
TTGCAAAATAATTT
Found at i:47141296 original size:18 final size:17
Alignment explanation
Indices: 47141275--47141334 Score: 68
Period size: 17 Copynumber: 3.5 Consensus size: 17
47141265 TATTATTTAA
47141275 ATAATTTTTTGAATTTTT
1 ATAATTTTTT-AATTTTT
**
47141293 ATAAGATTTTAATTTTT
1 ATAATTTTTTAATTTTT
*
47141310 -TAATTTTTTTAAATTTT
1 ATAA-TTTTTTAATTTTT
47141327 ATAATTTT
1 ATAATTTT
47141335 ATATTATTTA
Statistics
Matches: 35, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
16 3 0.09
17 21 0.60
18 11 0.31
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (17 bp):
ATAATTTTTTAATTTTT
Found at i:47141310 original size:8 final size:8
Alignment explanation
Indices: 47141276--47141334 Score: 55
Period size: 9 Copynumber: 6.9 Consensus size: 8
47141266 ATTATTTAAA
47141276 TAATTTTT
1 TAATTTTT
47141284 TGAATTTTT
1 T-AATTTTT
**
47141293 ATAAGATTT
1 -TAATTTTT
47141302 TAATTTTT
1 TAATTTTT
47141310 TAATTTTTT
1 TAA-TTTTT
*
47141319 TAAATTTTA
1 T-AATTTTT
47141328 TAATTTT
1 TAATTTT
47141335 ATATTATTTA
Statistics
Matches: 42, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
8 16 0.38
9 23 0.55
10 3 0.07
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.66
Consensus pattern (8 bp):
TAATTTTT
Found at i:47145798 original size:68 final size:67
Alignment explanation
Indices: 47145726--47145875 Score: 171
Period size: 67 Copynumber: 2.2 Consensus size: 67
47145716 CATCATGTGT
* * * *
47145726 ACAAGAGAGCTACAAGACATTATGATGTAGCTAGGTCGCATGGGT-GATACTA-TG-TGTACACC
1 ACAAGAGAGCTAC--GACA-TAT-ATGTAGCTAGGTCGCATGCGTGGATACAAGTGAAGGACACC
47145788 ATGTAG
62 ATGTAG
** * *
47145794 ACAAGAGAGCTACGGGATATATGTAGCTAGGTCGCATGCGTGGTTCCAAGTGAAGGACACCATGT
1 ACAAGAGAGCTACGACATATATGTAGCTAGGTCGCATGCGTGGATACAAGTGAAGGACACCATGT
47145859 AG
66 AG
47145861 ACAAGAGAGCTACGA
1 ACAAGAGAGCTACGA
47145876 GATAAACTGG
Statistics
Matches: 70, Mismatches: 9, Indels: 7
0.81 0.10 0.08
Matches are distributed among these distances:
64 20 0.29
65 7 0.10
66 4 0.06
67 26 0.37
68 13 0.19
ACGTcount: A:0.33, C:0.17, G:0.29, T:0.21
Consensus pattern (67 bp):
ACAAGAGAGCTACGACATATATGTAGCTAGGTCGCATGCGTGGATACAAGTGAAGGACACCATGT
AG
Found at i:47145831 original size:64 final size:64
Alignment explanation
Indices: 47145750--47145933 Score: 194
Period size: 67 Copynumber: 2.8 Consensus size: 64
47145740 AGACATTATG
* *
47145750 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGGGATAT
1 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
* * * * * *
47145814 ATGTAGCTAGGTCGCATGCGTGGTTCCAAGTGAAGGACACCATGTAGACAAGAGAGCTACGAGAT
1 ATGTAGCTAGGTCGCATGGGT-GATACTA-TG-TGTACACCATGTAGACAAGAGAGCTACGAGAT
47145879 AA
63 AA
* * * *
47145881 ACTG--GCTAGGTCACATGGGTGGTACTAAGTGTTCACCATGT-GTACAAGAGAGC
1 A-TGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAG-ACAAGAGAGC
47145934 CGAACTATAT
Statistics
Matches: 98, Mismatches: 17, Indels: 11
0.78 0.13 0.09
Matches are distributed among these distances:
62 1 0.01
63 19 0.19
64 21 0.21
65 8 0.08
66 16 0.16
67 31 0.32
68 2 0.02
ACGTcount: A:0.30, C:0.17, G:0.30, T:0.23
Consensus pattern (64 bp):
ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
Found at i:47149148 original size:16 final size:15
Alignment explanation
Indices: 47149109--47149151 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 15
47149099 CCCTAAAATA
47149109 ATAAAATTTTAATTT
1 ATAAAATTTTAATTT
*
47149124 A-AACCATTTATAATTT
1 ATAA-AATTT-TAATTT
47149140 ATAAAATTTTAA
1 ATAAAATTTTAA
47149152 ATTAATAGTA
Statistics
Matches: 23, Mismatches: 2, Indels: 6
0.74 0.06 0.19
Matches are distributed among these distances:
14 2 0.09
15 8 0.35
16 11 0.48
17 2 0.09
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.47
Consensus pattern (15 bp):
ATAAAATTTTAATTT
Found at i:47159940 original size:43 final size:43
Alignment explanation
Indices: 47159881--47159962 Score: 128
Period size: 43 Copynumber: 1.9 Consensus size: 43
47159871 GAGATATGTG
* *
47159881 GCATCCAAGCTCGTTGAGAGGTCCGATTTCATTATGGATGCGA
1 GCATCCAAGCTCGTTGAGAGGTCCGAGTTCATAATGGATGCGA
* *
47159924 GCATCCAAGCTTGTTGAGAGGTCTGAGTTCATAATGGAT
1 GCATCCAAGCTCGTTGAGAGGTCCGAGTTCATAATGGAT
47159963 ACAATTCATG
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
43 35 1.00
ACGTcount: A:0.24, C:0.18, G:0.28, T:0.29
Consensus pattern (43 bp):
GCATCCAAGCTCGTTGAGAGGTCCGAGTTCATAATGGATGCGA
Found at i:47167896 original size:43 final size:43
Alignment explanation
Indices: 47167848--47167929 Score: 119
Period size: 43 Copynumber: 1.9 Consensus size: 43
47167838 GAGATATGTG
*
47167848 GCATCCAAGCTCGTTAAGAGGTCCGAGTCCATTATGGATACGA
1 GCATCCAAGCTCGTTAAGAGGTCCGAGTCCATAATGGATACGA
* * * *
47167891 GCATCCGATCTCGTTGAGAGGTCCGAGTTCATAATGGAT
1 GCATCCAAGCTCGTTAAGAGGTCCGAGTCCATAATGGAT
47167930 GCGATTCATG
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
43 34 1.00
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.26
Consensus pattern (43 bp):
GCATCCAAGCTCGTTAAGAGGTCCGAGTCCATAATGGATACGA
Found at i:47171100 original size:40 final size:40
Alignment explanation
Indices: 47170995--47171119 Score: 173
Period size: 40 Copynumber: 3.1 Consensus size: 40
47170985 CGGATGATAA
* *
47170995 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTA-ATT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA-T
* * *
47171035 CTGGGCTAAG-CCCGAAGGCAATTGTGCGAGTTATTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
*
47171074 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
47171114 CCGGGC
1 CCGGGC
47171120 NNNNNNNNTG
Statistics
Matches: 74, Mismatches: 9, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
39 32 0.43
40 42 0.57
ACGTcount: A:0.23, C:0.22, G:0.29, T:0.26
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
Found at i:47185023 original size:58 final size:58
Alignment explanation
Indices: 47184961--47185099 Score: 185
Period size: 58 Copynumber: 2.4 Consensus size: 58
47184951 TTGATTCATA
*
47184961 TAATAATAATTATATTAAGAATTTTATTAAATT-TTATATTA-TTTTATTAAATTATATT
1 TAATAATAATTATATTAA-AATTTGATTAAATTATT-TATTATTTTTATTAAATTATATT
* * * *
47185019 TAATAATAATTATGTTAAAATATGCTTAAATTATTTATTATTTTTATTAAATTATTTT
1 TAATAATAATTATATTAAAATTTGATTAAATTATTTATTATTTTTATTAAATTATATT
47185077 TAATAATAATCT-TATTAAAATTT
1 TAATAATAAT-TATATTAAAATTT
47185100 AATAACAATA
Statistics
Matches: 71, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
57 16 0.23
58 54 0.76
59 1 0.01
ACGTcount: A:0.42, C:0.01, G:0.02, T:0.54
Consensus pattern (58 bp):
TAATAATAATTATATTAAAATTTGATTAAATTATTTATTATTTTTATTAAATTATATT
Found at i:47188117 original size:15 final size:15
Alignment explanation
Indices: 47188097--47188148 Score: 50
Period size: 15 Copynumber: 3.2 Consensus size: 15
47188087 ACTATAAAAC
47188097 ATTTATTATTAATAT
1 ATTTATTATTAATAT
*
47188112 ATTTATAATTGTAATAAAT
1 ATTTATTA-T-TAAT--AT
*
47188131 ATTTATTATTAAAAT
1 ATTTATTATTAATAT
47188146 ATT
1 ATT
47188149 AATATTGAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 8
0.73 0.07 0.20
Matches are distributed among these distances:
15 12 0.40
16 1 0.03
17 7 0.23
18 1 0.03
19 9 0.30
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
ATTTATTATTAATAT
Found at i:47188212 original size:16 final size:16
Alignment explanation
Indices: 47188181--47188217 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
47188171 ATGTGAATAA
47188181 TATTATTTAAAATTAT
1 TATTATTTAAAATTAT
47188197 TATT-TTTAAAATTTAT
1 TATTATTTAAAA-TTAT
47188213 TATTA
1 TATTA
47188218 AAATAAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 7 0.37
16 12 0.63
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
TATTATTTAAAATTAT
Found at i:47188269 original size:22 final size:22
Alignment explanation
Indices: 47188229--47188284 Score: 62
Period size: 22 Copynumber: 2.6 Consensus size: 22
47188219 AATAAAATTG
*
47188229 AAATATTAAA-TA-ATTTATTA
1 AAATAATAAATTATATTTATTA
47188249 AAATAATAAATTATATTTATTA
1 AAATAATAAATTATATTTATTA
* * *
47188271 TATTAATAATTTAT
1 AAATAATAAATTAT
47188285 TATATGACTA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
20 9 0.30
21 2 0.07
22 19 0.63
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
AAATAATAAATTATATTTATTA
Found at i:47190240 original size:20 final size:19
Alignment explanation
Indices: 47190215--47190279 Score: 60
Period size: 20 Copynumber: 3.4 Consensus size: 19
47190205 GGTATCACCA
47190215 TAAAAATTTTGATATTGAGT
1 TAAAAATTTTGATATT-AGT
* * *
47190235 TAAAAATATTGGTATTCGT
1 TAAAAATTTTGATATTAGT
* *
47190254 T-AAAATTTTTAGTATTAAT
1 TAAAAATTTTGA-TATTAGT
47190273 TAAAAAT
1 TAAAAAT
47190280 CTGTATTGTC
Statistics
Matches: 35, Mismatches: 8, Indels: 4
0.74 0.17 0.09
Matches are distributed among these distances:
18 7 0.20
19 9 0.26
20 19 0.54
ACGTcount: A:0.43, C:0.02, G:0.11, T:0.45
Consensus pattern (19 bp):
TAAAAATTTTGATATTAGT
Found at i:47190772 original size:23 final size:23
Alignment explanation
Indices: 47190720--47190787 Score: 59
Period size: 23 Copynumber: 2.9 Consensus size: 23
47190710 AGCAATTTAA
47190720 TTTTTTT-TCTTTTTTGTTCTTT
1 TTTTTTTATCTTTTTTGTTCTTT
***
47190742 TAACTTTATCTTTTTT-TTCTGTT
1 TTTTTTTATCTTTTTTGTTCT-TT
*
47190765 TTTTTTTATTCTCTTTTGCTTCT
1 TTTTTTTA-TCTTTTTTG-TTCT
47190788 CCCTCCATTT
Statistics
Matches: 34, Mismatches: 7, Indels: 6
0.72 0.15 0.13
Matches are distributed among these distances:
22 8 0.24
23 15 0.44
24 7 0.21
26 4 0.12
ACGTcount: A:0.06, C:0.13, G:0.04, T:0.76
Consensus pattern (23 bp):
TTTTTTTATCTTTTTTGTTCTTT
Found at i:47193091 original size:15 final size:15
Alignment explanation
Indices: 47193071--47193122 Score: 54
Period size: 15 Copynumber: 3.5 Consensus size: 15
47193061 ACAACATAAT
47193071 AATGTAAATGACTAA
1 AATGTAAATGACTAA
**
47193086 AATGTAACATTTCTAA
1 AATGTAA-ATGACTAA
*
47193102 CA--TAAATGACTAA
1 AATGTAAATGACTAA
47193115 AATGTAAA
1 AATGTAAA
47193123 CTGAGACATA
Statistics
Matches: 28, Mismatches: 6, Indels: 6
0.70 0.15 0.15
Matches are distributed among these distances:
13 7 0.25
14 3 0.11
15 11 0.39
16 7 0.25
ACGTcount: A:0.52, C:0.10, G:0.10, T:0.29
Consensus pattern (15 bp):
AATGTAAATGACTAA
Found at i:47193728 original size:20 final size:20
Alignment explanation
Indices: 47193705--47193742 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
47193695 TGGTATCTCG
47193705 TTAGAAATCTTGATATTATA
1 TTAGAAATCTTGATATTATA
* *
47193725 TTAGAAATTTTGTTATTA
1 TTAGAAATCTTGATATTA
47193743 ATTTATAATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.37, C:0.03, G:0.11, T:0.50
Consensus pattern (20 bp):
TTAGAAATCTTGATATTATA
Found at i:47195093 original size:29 final size:29
Alignment explanation
Indices: 47195029--47195094 Score: 87
Period size: 29 Copynumber: 2.3 Consensus size: 29
47195019 AAATGACCCT
**
47195029 AAAAATAATTATAAAAATAACTTAAGTTA
1 AAAAATAATTATAAAAATAACTTAAAATA
* *
47195058 AAAAATAATTATATAAATAACTTAAAATG
1 AAAAATAATTATAAAAATAACTTAAAATA
*
47195087 AATAATAA
1 AAAAATAA
47195095 AATTAAATTA
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.64, C:0.03, G:0.03, T:0.30
Consensus pattern (29 bp):
AAAAATAATTATAAAAATAACTTAAAATA
Found at i:47196456 original size:5 final size:5
Alignment explanation
Indices: 47196446--47196474 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
47196436 TGAAATTTTT
47196446 TCGAA TCGAA TCGAA TCGAA TCGAA TCGA
1 TCGAA TCGAA TCGAA TCGAA TCGAA TCGA
47196475 GTCAAAAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.38, C:0.21, G:0.21, T:0.21
Consensus pattern (5 bp):
TCGAA
Found at i:47196816 original size:31 final size:31
Alignment explanation
Indices: 47196776--47196834 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
47196766 GTGTAATTCA
47196776 TATTCGAGTTAAACCGAAAAACTTAATTTTT
1 TATTCGAGTTAAACCGAAAAACTTAATTTTT
* * * *
47196807 TATTTGAGTTGATCCGAATAACTTAATT
1 TATTCGAGTTAAACCGAAAAACTTAATT
47196835 AACTCAAATA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.36, C:0.12, G:0.12, T:0.41
Consensus pattern (31 bp):
TATTCGAGTTAAACCGAAAAACTTAATTTTT
Found at i:47197145 original size:19 final size:19
Alignment explanation
Indices: 47197121--47197157 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
47197111 ATCATCAAGC
*
47197121 AATAATTGAGTTAAAAATT
1 AATAATTGAGTCAAAAATT
*
47197140 AATAATTGGGTCAAAAAT
1 AATAATTGAGTCAAAAAT
47197158 CAATGTGGGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.51, C:0.03, G:0.14, T:0.32
Consensus pattern (19 bp):
AATAATTGAGTCAAAAATT
Found at i:47197987 original size:45 final size:43
Alignment explanation
Indices: 47197924--47198012 Score: 124
Period size: 45 Copynumber: 2.0 Consensus size: 43
47197914 GATAATTTGA
* *
47197924 TATATTATTTAGCTAAATTACATAGTATTTATTATAAATTATT
1 TATATTATTTAACTAAATTACATAATATTTATTATAAATTATT
* *
47197967 TATATTAATTTTAACTAAATTATATAATATTTATTATTAATTATT
1 TATATT-A-TTTAACTAAATTACATAATATTTATTATAAATTATT
47198012 T
1 T
47198013 GTACTTTGAC
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
43 6 0.15
44 1 0.03
45 33 0.82
ACGTcount: A:0.40, C:0.03, G:0.02, T:0.54
Consensus pattern (43 bp):
TATATTATTTAACTAAATTACATAATATTTATTATAAATTATT
Found at i:47199782 original size:108 final size:108
Alignment explanation
Indices: 47199582--47200041 Score: 651
Period size: 109 Copynumber: 4.3 Consensus size: 108
47199572 CAAAAAATTT
* **
47199582 TTTTTTACTCTCCGAAAATACGAGTTTT-AAAAAAAAATTTTGGGTGCTGGCCTGTCAATGGTAG
1 TTTTTTACTCTCCGAAAATACGAGTTTTAAAAAAAAAATTTTGGGTACTGGCCTGTCAATGGCCG
*
47199646 GCACCCAGTACAAAAAAAAATTCAAAATTTTTCTCAAAAAAAA
66 GCACCCAGTACAAAAAAAAATTCAAAATTTTTTTCAAAAAAAA
* *
47199689 ATTTTTACTCTCCGAAAATACGAGTTTTAAAAAAAAAATTTTTGGGTACTAGCCTGTCAATGGCC
1 TTTTTTACTCTCCGAAAATACGAGTTTTAAAAAAAAAA-TTTTGGGTACTGGCCTGTCAATGGCC
* *
47199754 GACACCCAGTAC-AAAAAAAATTCAAAATTTTTTTTAAAAAGAAA
65 GGCACCCAGTACAAAAAAAAATTCAAAATTTTTTTCAAAAA-AAA
* *
47199798 TTTTTTACTCCCCGAAAATACGAGTTTTAAAAAAAAAATTTCGGGTACTGGCCTGTCAATGGCCG
1 TTTTTTACTCTCCGAAAATACGAGTTTTAAAAAAAAAATTTTGGGTACTGGCCTGTCAATGGCCG
* * *
47199863 GCATCCAGTACAAAAAAAAATTCAAAATTTGTTTCAAAAAAATTT
66 GCACCCAGTACAAAAAAAAATTCAAAATTTTTTTCAAAAAAA--A
* * * *
47199908 TTTTTTACTCTCTGAAAATACGAGTTTTTAAAAAAAAAATTTTGGTTGCTGGCCTGTCAATTGCC
1 TTTTTTACTCTCCGAAAATACGAG-TTTTAAAAAAAAAATTTTGGGTACTGGCCTGTCAATGGCC
* * *
47199973 GGCACCCAGTAC-AAAAAAAATT--AATTTTTTTTTAAAAAACA
65 GGCACCCAGTACAAAAAAAAATTCAAAATTTTTTTCAAAAAAAA
*
47200014 TTTTTTGCTCTCCGAAAATACGAGTTTT
1 TTTTTTACTCTCCGAAAATACGAGTTTT
47200042 TTTTAAAAAA
Statistics
Matches: 315, Mismatches: 31, Indels: 16
0.87 0.09 0.04
Matches are distributed among these distances:
105 4 0.01
106 22 0.07
107 27 0.09
108 85 0.27
109 98 0.31
110 32 0.10
111 47 0.15
ACGTcount: A:0.38, C:0.16, G:0.13, T:0.32
Consensus pattern (108 bp):
TTTTTTACTCTCCGAAAATACGAGTTTTAAAAAAAAAATTTTGGGTACTGGCCTGTCAATGGCCG
GCACCCAGTACAAAAAAAAATTCAAAATTTTTTTCAAAAAAAA
Found at i:47206389 original size:14 final size:14
Alignment explanation
Indices: 47206370--47206399 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
47206360 TTTGTTGACT
47206370 GTTTGATCATTTTA
1 GTTTGATCATTTTA
47206384 GTTTGATCATTTTA
1 GTTTGATCATTTTA
47206398 GT
1 GT
47206400 AATTTATCAA
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:0.20, C:0.07, G:0.17, T:0.57
Consensus pattern (14 bp):
GTTTGATCATTTTA
Found at i:47207429 original size:16 final size:16
Alignment explanation
Indices: 47207396--47207429 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
47207386 GCCTGTTGTT
* *
47207396 AACATTAATGGGAGAC
1 AACATTAATGGCAAAC
47207412 AACATTAATGGCAAAC
1 AACATTAATGGCAAAC
47207428 AA
1 AA
47207430 TACAAAGTGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.15, G:0.18, T:0.18
Consensus pattern (16 bp):
AACATTAATGGCAAAC
Done.