Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr6
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: 56482370
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1659275 characters in sequence are not A, C, G, or T
File 92 of 172
Found at i:30893987 original size:73 final size:73
Alignment explanation
Indices: 30893905--30894231 Score: 329
Period size: 73 Copynumber: 4.5 Consensus size: 73
30893895 TTAAATAATA
* * * * * *
30893905 TCTATCCCAACCTTTTTAAGGTTGCTTTAAACAGGTCAATCCCAACCTTTTTTAAAAGATACCTC
1 TCTATCCCAACCTTTTTAAGGTTGCCTTAGACAGGTCTATCCCAACCTTTTTTAAAAGTTGCCTT
30893970 AGACATGG
66 AGACATGG
* * *
30893978 TCTATCCCAACCTTTTTAAGGTTGCCTTAGAC-GAGTCTATTCCGACCTTTTTTAAAGGTTGCCT
1 TCTATCCCAACCTTTTTAAGGTTGCCTTAGACAG-GTCTATCCCAACCTTTTTTAAAAGTTGCCT
*
30894042 TAGAAATGG
65 TAGACATGG
* * * **
30894051 TCTATCCTAACC--ATTAAGGTTGCCTTAGACAGGTCTATCCCAACCTTTTTTAATAGGTTGTTT
1 TCTATCCCAACCTTTTTAAGGTTGCCTTAGACAGGTCTATCCCAACCTTTTTTAA-AAGTTGCCT
30894114 TAGACAAT-G
65 TAGAC-ATGG
* * * * * *
30894123 TCGATCCCAACCTTTTTAAGGTTGCTTTAGACTGCTCTATCCCAATCGTTTTTAAAAGTTGCCTT
1 TCTATCCCAACCTTTTTAAGGTTGCCTTAGACAGGTCTATCCCAACCTTTTTTAAAAGTTGCCTT
* * *
30894188 AAACAAGA
66 AGACATGG
* ** * * *
30894196 ACTATATCGACCTTTTTAACGTTGTCTTAGACAGGT
1 TCTATCCCAACCTTTTTAAGGTTGCCTTAGACAGGT
30894232 AACAACCTTT
Statistics
Matches: 206, Mismatches: 41, Indels: 14
0.79 0.16 0.05
Matches are distributed among these distances:
71 36 0.17
72 25 0.12
73 110 0.53
74 35 0.17
ACGTcount: A:0.27, C:0.22, G:0.15, T:0.36
Consensus pattern (73 bp):
TCTATCCCAACCTTTTTAAGGTTGCCTTAGACAGGTCTATCCCAACCTTTTTTAAAAGTTGCCTT
AGACATGG
Found at i:30894045 original size:37 final size:35
Alignment explanation
Indices: 30893905--30894188 Score: 186
Period size: 36 Copynumber: 7.8 Consensus size: 35
30893895 TTAAATAATA
* *
30893905 TCTATCCCAACCTTTTTAAGGTTGCTTTAAAC-AGG
1 TCTATCCCAACCTTTTTAAGGTTGCCTTAGACGA-G
* * * * *
30893940 TCAATCCCAACCTTTTTTAAAAGATACCTCAGAC-ATGG
1 TCTATCCCAACC-TTTTT-AAGGTTGCCTTAGACGA--G
30893978 TCTATCCCAACCTTTTTAAGGTTGCCTTAGACGAG
1 TCTATCCCAACCTTTTTAAGGTTGCCTTAGACGAG
* * *
30894013 TCTATTCCGACCTTTTTTAAAGGTTGCCTTAGA-AATGG
1 TCTATCCCAACC-TTTTT-AAGGTTGCCTTAGACGA--G
* *
30894051 TCTATCCTAACC--ATTAAGGTTGCCTTAGAC-AGG
1 TCTATCCCAACCTTTTTAAGGTTGCCTTAGACGA-G
** *
30894084 TCTATCCCAACCTTTTTTAATAGGTTGTTTTAGACAATG
1 TCTATCCCAACC-TTTTT-A-AGGTTGCCTTAGACGA-G
* * *
30894123 TCGATCCCAACCTTTTTAAGGTTGCTTTAGACTG-C
1 TCTATCCCAACCTTTTTAAGGTTGCCTTAGAC-GAG
* *
30894158 TCTATCCCAATCGTTTTTAAAAGTTGCCTTA
1 TCTATCCCAA-CCTTTTT-AAGGTTGCCTTA
30894189 AACAAGAACT
Statistics
Matches: 199, Mismatches: 32, Indels: 34
0.75 0.12 0.13
Matches are distributed among these distances:
33 13 0.07
34 15 0.08
35 33 0.17
36 43 0.22
37 42 0.21
38 40 0.20
39 13 0.07
ACGTcount: A:0.26, C:0.23, G:0.15, T:0.37
Consensus pattern (35 bp):
TCTATCCCAACCTTTTTAAGGTTGCCTTAGACGAG
Found at i:30894075 original size:34 final size:33
Alignment explanation
Indices: 30894032--30894095 Score: 101
Period size: 34 Copynumber: 1.9 Consensus size: 33
30894022 ACCTTTTTTA
*
30894032 AAGGTTGCCTTAGAAATGGTCTATCCTAACCATT
1 AAGGTTGCCTTAGAAA-GGTCTATCCCAACCATT
*
30894066 AAGGTTGCCTTAGACAGGTCTATCCCAACC
1 AAGGTTGCCTTAGAAAGGTCTATCCCAACC
30894096 TTTTTTAATA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
33 13 0.46
34 15 0.54
ACGTcount: A:0.28, C:0.25, G:0.19, T:0.28
Consensus pattern (33 bp):
AAGGTTGCCTTAGAAAGGTCTATCCCAACCATT
Found at i:30894162 original size:145 final size:144
Alignment explanation
Indices: 30893920--30894188 Score: 344
Period size: 145 Copynumber: 1.9 Consensus size: 144
30893910 CCCAACCTTT
* *
30893920 TTAAGGTTGCTTTAAACAGGTCAATCCCAACCTTTTTTAAAAGATACCTCAGACATGGTCTATCC
1 TTAAGGTTGCCTTAAACAGGTCAATCCCAACCTTTTTTAAAAGATACCTCAGACATGGTCGATCC
* * * * *
30893985 CAACCTTTTTAAGGTTGCCTTAGACGAGTCTATTCCGACCTTTTTTAAAGGTTGCCTTAGAAATG
66 CAACCTTTTTAAGGTTGCCTTAGACGACTCTATCCCAACCGTTTTTAAAAGTTGCCTTAGAAATG
30894050 GTCTATCCTAACCA
131 GTCTATCCTAACCA
* * * * *** *
30894064 TTAAGGTTGCCTTAGACAGGTCTATCCCAACCTTTTTTAATAGGTTGTTTTAGACAAT-GTCGAT
1 TTAAGGTTGCCTTAAACAGGTCAATCCCAACCTTTTTTAA-AAGATACCTCAGAC-ATGGTCGAT
* *
30894128 CCCAACCTTTTTAAGGTTGCTTTAGACTG-CTCTATCCCAATCGTTTTTAAAAGTTGCCTTA
64 CCCAACCTTTTTAAGGTTGCCTTAGAC-GACTCTATCCCAACCGTTTTTAAAAGTTGCCTTA
30894189 AACAAGAACT
Statistics
Matches: 105, Mismatches: 17, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
144 37 0.35
145 65 0.62
146 3 0.03
ACGTcount: A:0.26, C:0.22, G:0.16, T:0.36
Consensus pattern (144 bp):
TTAAGGTTGCCTTAAACAGGTCAATCCCAACCTTTTTTAAAAGATACCTCAGACATGGTCGATCC
CAACCTTTTTAAGGTTGCCTTAGACGACTCTATCCCAACCGTTTTTAAAAGTTGCCTTAGAAATG
GTCTATCCTAACCA
Found at i:30898563 original size:6 final size:6
Alignment explanation
Indices: 30898552--30898582 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
30898542 CAAATCTAAA
*
30898552 AGGCAT AGGCAT AGGCAT AGGCAT ATGCAT A
1 AGGCAT AGGCAT AGGCAT AGGCAT AGGCAT A
30898583 CATGTATAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.35, C:0.16, G:0.29, T:0.19
Consensus pattern (6 bp):
AGGCAT
Found at i:30910298 original size:37 final size:37
Alignment explanation
Indices: 30910225--30910303 Score: 104
Period size: 37 Copynumber: 2.1 Consensus size: 37
30910215 TTATTACGAA
* * * * *
30910225 GTCTTACCCGGGCATAATCTCCACACGAAGTTATCGG
1 GTCTTACCCGGACAAAATCCCCAAACGAAGTCATCGG
*
30910262 GTCTTACCCGGACAAAATCCCCAAACGTAGTCATCGG
1 GTCTTACCCGGACAAAATCCCCAAACGAAGTCATCGG
30910299 GTCTT
1 GTCTT
30910304 TAGAGCTCGG
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.25, C:0.30, G:0.20, T:0.24
Consensus pattern (37 bp):
GTCTTACCCGGACAAAATCCCCAAACGAAGTCATCGG
Found at i:30910572 original size:47 final size:47
Alignment explanation
Indices: 30910422--30910623 Score: 280
Period size: 47 Copynumber: 4.3 Consensus size: 47
30910412 CCCTTCGAGA
* * * * * * * *
30910422 CTTATCACATTTATGCACTTTCACATCCATCACGTTGGGCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
30910469 CCTGTCACATATATACACTTTCACATTCA-CACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
30910515 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
30910562 CTTATTACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
30910609 CTTATCACCTATATA
1 CTTATCACATATATA
30910624 TATTCGAATA
Statistics
Matches: 138, Mismatches: 16, Indels: 2
0.88 0.10 0.01
Matches are distributed among these distances:
46 39 0.28
47 99 0.72
ACGTcount: A:0.28, C:0.30, G:0.10, T:0.33
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:30910581 original size:93 final size:94
Alignment explanation
Indices: 30910422--30910623 Score: 280
Period size: 93 Copynumber: 2.2 Consensus size: 94
30910412 CCCTTCGAGA
* * * * * * *
30910422 CTTATCACATTTATGCACTTTCACATCCATCACGTTGGGCACTCGGCCCTGTCACATATATACAC
1 CTTATCACATATATACACTTTCACATCCATCACATCGGCCACTAGGCCCTATCACATATATACAC
30910487 TTTCACATTCA-CACATCGGCCATTAGGC
66 TTTCACATTCATCACATCGGCCATTAGGC
* * * *
30910515 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATTACATATATACAC
1 CTTATCACATATATACACTTTCACATCCATCACATCGGCCACTAGGCCCTATCACATATATACAC
*
30910580 TTTCACATTCATCACATCGGCTATTAGGC
66 TTTCACATTCATCACATCGGCCATTAGGC
*
30910609 CTTATCACCTATATA
1 CTTATCACATATATA
30910624 TATTCGAATA
Statistics
Matches: 95, Mismatches: 13, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
93 65 0.68
94 30 0.32
ACGTcount: A:0.28, C:0.30, G:0.10, T:0.33
Consensus pattern (94 bp):
CTTATCACATATATACACTTTCACATCCATCACATCGGCCACTAGGCCCTATCACATATATACAC
TTTCACATTCATCACATCGGCCATTAGGC
Found at i:30910803 original size:23 final size:23
Alignment explanation
Indices: 30910777--30910852 Score: 59
Period size: 23 Copynumber: 3.3 Consensus size: 23
30910767 GTCACTAAAT
30910777 TCACATATACACTTTCACATTCA
1 TCACATATACACTTTCACATTCA
*** *
30910800 TCACATCGGC-CATTTGGC-CTTATCA
1 TCACATATACAC-TTT--CACAT-TCA
30910825 -CACATATACACTTTCACATTCA
1 TCACATATACACTTTCACATTCA
30910847 TCACAT
1 TCACAT
30910853 CGACCATTTG
Statistics
Matches: 38, Mismatches: 8, Indels: 14
0.63 0.13 0.23
Matches are distributed among these distances:
22 5 0.13
23 17 0.45
24 11 0.29
25 5 0.13
ACGTcount: A:0.30, C:0.32, G:0.05, T:0.33
Consensus pattern (23 bp):
TCACATATACACTTTCACATTCA
Found at i:30910844 original size:47 final size:47
Alignment explanation
Indices: 30910778--30910868 Score: 173
Period size: 47 Copynumber: 1.9 Consensus size: 47
30910768 TCACTAAATT
*
30910778 CACATATACACTTTCACATTCATCACATCGGCCATTTGGCCTTATCA
1 CACATATACACTTTCACATTCATCACATCGACCATTTGGCCTTATCA
30910825 CACATATACACTTTCACATTCATCACATCGACCATTTGGCCTTA
1 CACATATACACTTTCACATTCATCACATCGACCATTTGGCCTTA
30910869 CTATCATTTC
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 43 1.00
ACGTcount: A:0.29, C:0.32, G:0.08, T:0.32
Consensus pattern (47 bp):
CACATATACACTTTCACATTCATCACATCGACCATTTGGCCTTATCA
Found at i:30910980 original size:256 final size:256
Alignment explanation
Indices: 30910525--30911033 Score: 914
Period size: 256 Copynumber: 2.0 Consensus size: 256
30910515 CTTATCACAT
* *
30910525 ATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATTACATATATACACTTTCACATTC
1 ATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACACATATACACTTTCACATTC
* *
30910590 ATCACATCGGCTATTAGGCCTTATCACCTATATATATTCGAATACTCATAACTTACAATATCATG
66 ATCACATCGACCATTAGGCCTTATCACCTATATATATTCGAATACTCATAACTTACAATATCATG
30910655 ATTTAGAATTCAAGTATGGGTTTAATCAATAGCTTATGAGCAACTAAAACAAGTTTATCAAGGTT
131 ATTTAGAATTCAAGTATGGGTTTAATCAATAGCTTATGAGCAACTAAAACAAGTTTATCAAGGTT
30910720 CACAACATAATCTCAAATTCAGCACAAGCTGTTTTTCCTGAGCAATAGTCACTAAATTCAC
196 CACAACATAATCTCAAATTCAGCACAAGCTGTTTTTCCTGAGCAATAGTCACTAAATTCAC
*
30910781 ATATACACTTTCACATTCATCACATCGGCCATTTGGCCTTATCACACATATACACTTTCACATTC
1 ATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACACATATACACTTTCACATTC
* * *
30910846 ATCACATCGACCATTTGGCCTTA-CTATC-ATTTCATATTCGAATACTCATAACTTACAATATCA
66 ATCACATCGACCATTAGGCCTTATC-ACCTATAT-ATATTCGAATACTCATAACTTACAATATCA
30910909 TGATTTAGAATTCAAGTATGGGTTTAATCAATAGCTTATGAGCAACTAAAACAAGTTTATCAAGG
129 TGATTTAGAATTCAAGTATGGGTTTAATCAATAGCTTATGAGCAACTAAAACAAGTTTATCAAGG
30910974 TTCACAACATAATCTCAAATTCAGCACAAGCTGTTTTTCCTGAGCAATAGTCACTAAATT
194 TTCACAACATAATCTCAAATTCAGCACAAGCTGTTTTTCCTGAGCAATAGTCACTAAATT
30911034 ATTTATAACT
Statistics
Matches: 243, Mismatches: 8, Indels: 4
0.95 0.03 0.02
Matches are distributed among these distances:
255 4 0.02
256 239 0.98
ACGTcount: A:0.34, C:0.22, G:0.10, T:0.33
Consensus pattern (256 bp):
ATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACACATATACACTTTCACATTC
ATCACATCGACCATTAGGCCTTATCACCTATATATATTCGAATACTCATAACTTACAATATCATG
ATTTAGAATTCAAGTATGGGTTTAATCAATAGCTTATGAGCAACTAAAACAAGTTTATCAAGGTT
CACAACATAATCTCAAATTCAGCACAAGCTGTTTTTCCTGAGCAATAGTCACTAAATTCAC
Found at i:30913611 original size:46 final size:46
Alignment explanation
Indices: 30913544--30913672 Score: 213
Period size: 46 Copynumber: 2.8 Consensus size: 46
30913534 TGTAACCCGC
* * * * *
30913544 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGTAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
30913590 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
30913636 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
30913673 TGCTCAACCA
Statistics
Matches: 78, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
46 78 1.00
ACGTcount: A:0.29, C:0.29, G:0.22, T:0.20
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
Found at i:30919884 original size:43 final size:43
Alignment explanation
Indices: 30919794--30919961 Score: 126
Period size: 43 Copynumber: 3.9 Consensus size: 43
30919784 ACCGAGATGT
* * * * * *
30919794 GATTACATGTAAGACCATGTCTAGAACATTGGCATTGTATTTT
1 GATTACGTGTAAGACCATGTCTGGGACATTGGCATCGTATATC
30919837 GATTACGTGTAAGACCATGTCTGGGACATTGGCATCGT-TAATC
1 GATTACGTGTAAGACCATGTCTGGGACATTGGCATCGTAT-ATC
* * * * * * * *
30919880 GATTATGTATAAGACCCTGTCGGGGACAGTGACATTG-ATATGT
1 GATTACGTGTAAGACCATGTCTGGGACATTGGCATCGTATAT-C
* * * * *
30919923 GATAACATGTAAGACCATATCTGGGATA-TGGCATTGTAT
1 GATTACGTGTAAGACCATGTCTGGGACATTGGCATCGTAT
30919962 GAGTTATGTA
Statistics
Matches: 98, Mismatches: 23, Indels: 8
0.76 0.18 0.06
Matches are distributed among these distances:
42 10 0.10
43 88 0.90
ACGTcount: A:0.29, C:0.15, G:0.24, T:0.32
Consensus pattern (43 bp):
GATTACGTGTAAGACCATGTCTGGGACATTGGCATCGTATATC
Found at i:30922537 original size:6 final size:6
Alignment explanation
Indices: 30922526--30922556 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
30922516 AACATCTCAA
*
30922526 AGGCAT AGGCAT AGGCAT AGGCAT ATGCAT A
1 AGGCAT AGGCAT AGGCAT AGGCAT AGGCAT A
30922557 CATGTATAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.35, C:0.16, G:0.29, T:0.19
Consensus pattern (6 bp):
AGGCAT
Found at i:30926013 original size:25 final size:25
Alignment explanation
Indices: 30925966--30926014 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
30925956 GTCAAGGCAC
* **
30925966 CAGAATTGTAGTTAAGCTGCTAGAA
1 CAGAATTGTAGTTAAACCACTAGAA
*
30925991 CAGATTTGTAGTTAAACCACTAGA
1 CAGAATTGTAGTTAAACCACTAGA
30926015 TAAGGCAACT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.37, C:0.14, G:0.20, T:0.29
Consensus pattern (25 bp):
CAGAATTGTAGTTAAACCACTAGAA
Found at i:30950524 original size:20 final size:19
Alignment explanation
Indices: 30950470--30950550 Score: 75
Period size: 20 Copynumber: 4.4 Consensus size: 19
30950460 TATTTTAATA
30950470 AATTTAATA-T-AA-TATT
1 AATTTAATATTAAATTATT
**
30950486 AGATTTAATATTATTTTATT
1 A-ATTTAATATTAAATTATT
30950506 AATTTAATATTAAAGTTATT
1 AATTTAATATTAAA-TTATT
30950526 -ATATTAATATTAAA-T-TT
1 AAT-TTAATATTAAATTATT
30950543 AATTTAAT
1 AATTTAAT
30950551 GTTTTTCTTG
Statistics
Matches: 54, Mismatches: 4, Indels: 13
0.76 0.06 0.18
Matches are distributed among these distances:
16 1 0.02
17 15 0.28
18 4 0.07
19 13 0.24
20 21 0.39
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.53
Consensus pattern (19 bp):
AATTTAATATTAAATTATT
Found at i:30950859 original size:18 final size:18
Alignment explanation
Indices: 30950818--30950860 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
30950808 AAACTTGGTC
**
30950818 CAAAATTTTAAAAAAATTT
1 CAAAA-TTTAAAAAAAAAT
30950837 C-AAATTTAAAAAAAAAT
1 CAAAATTTAAAAAAAAAT
30950854 CAAAATT
1 CAAAATT
30950861 ACCCCACTGG
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
17 12 0.57
18 8 0.38
19 1 0.05
ACGTcount: A:0.63, C:0.07, G:0.00, T:0.30
Consensus pattern (18 bp):
CAAAATTTAAAAAAAAAT
Found at i:30964154 original size:21 final size:20
Alignment explanation
Indices: 30964126--30964165 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 20
30964116 AGATATAATA
30964126 GCCAAGCTTA-ATCATATTCG
1 GCCAAGCTTATAT-ATATTCG
30964146 GCCATAGCTTATATATATTC
1 GCCA-AGCTTATATATATTC
30964166 ACACATTTCG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 4 0.22
21 12 0.67
22 2 0.11
ACGTcount: A:0.30, C:0.23, G:0.12, T:0.35
Consensus pattern (20 bp):
GCCAAGCTTATATATATTCG
Found at i:30969033 original size:40 final size:40
Alignment explanation
Indices: 30968973--30969156 Score: 241
Period size: 40 Copynumber: 4.6 Consensus size: 40
30968963 TATTCGAATG
*
30968973 ATATCCGGGCTAAG-TCCCGAAGGCTTTTATGCTAGTGACT
1 ATATCCGGGCTAAGAT-CCGAAGGCATTTATGCTAGTGACT
*
30969013 ATATCCGGGCTAAGATCCGAAGGCATTTGTG-TGAGTTG-CT
1 ATATCCGGGCTAAGATCCGAAGGCATTTATGCT-AG-TGACT
* * *
30969053 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGCGACT
1 ATATCCGGGCTAAGATCCGAAGGCATTTATGCTAGTGACT
*
30969093 ATATCCGGGCTAAG-TCCCGAAGGCATTTATGCTAGTGACC
1 ATATCCGGGCTAAGAT-CCGAAGGCATTTATGCTAGTGACT
*
30969133 ATATCCGGGCTAAGACCCGAAGGC
1 ATATCCGGGCTAAGATCCGAAGGC
30969157 CTTGTGCGAG
Statistics
Matches: 128, Mismatches: 9, Indels: 14
0.85 0.06 0.09
Matches are distributed among these distances:
39 2 0.02
40 122 0.95
41 4 0.03
ACGTcount: A:0.24, C:0.23, G:0.27, T:0.25
Consensus pattern (40 bp):
ATATCCGGGCTAAGATCCGAAGGCATTTATGCTAGTGACT
Found at i:30969106 original size:80 final size:80
Alignment explanation
Indices: 30968973--30969156 Score: 266
Period size: 80 Copynumber: 2.3 Consensus size: 80
30968963 TATTCGAATG
* * *
30968973 ATATCCGGGCTAAGTCCCGAAGGCTTTTATGCTAGTGACTATATCCGGGCTAAGAT-CCGAAGGC
1 ATATCCGGGCTAAGACCCGAAGGCATTTATGCTAGCGACTATATCCGGGCTAAG-TCCCGAAGGC
* *
30969037 ATTTGTG-TGAGTTG-CT
65 ATTTATGCT-AG-TGACC
*
30969053 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGCGACTATATCCGGGCTAAGTCCCGAAGGCA
1 ATATCCGGGCTAAGACCCGAAGGCATTTATGCTAGCGACTATATCCGGGCTAAGTCCCGAAGGCA
30969118 TTTATGCTAGTGACC
66 TTTATGCTAGTGACC
30969133 ATATCCGGGCTAAGACCCGAAGGC
1 ATATCCGGGCTAAGACCCGAAGGC
30969157 CTTGTGCGAG
Statistics
Matches: 95, Mismatches: 6, Indels: 6
0.89 0.06 0.06
Matches are distributed among these distances:
79 3 0.03
80 91 0.96
81 1 0.01
ACGTcount: A:0.24, C:0.23, G:0.27, T:0.25
Consensus pattern (80 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTATGCTAGCGACTATATCCGGGCTAAGTCCCGAAGGCA
TTTATGCTAGTGACC
Found at i:30987080 original size:17 final size:18
Alignment explanation
Indices: 30987051--30987085 Score: 63
Period size: 17 Copynumber: 2.0 Consensus size: 18
30987041 TTTATGGACT
30987051 TAATTTAGTAAAAAGTAC
1 TAATTTAGTAAAAAGTAC
30987069 TAATTT-GTAAAAAGTAC
1 TAATTTAGTAAAAAGTAC
30987086 AAAACTTAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 11 0.65
18 6 0.35
ACGTcount: A:0.49, C:0.06, G:0.11, T:0.34
Consensus pattern (18 bp):
TAATTTAGTAAAAAGTAC
Found at i:30995963 original size:47 final size:47
Alignment explanation
Indices: 30995894--30995986 Score: 159
Period size: 47 Copynumber: 2.0 Consensus size: 47
30995884 ACAACTTTTA
* *
30995894 CTAAGTGATTTTTCATGAAAATACCTAAAAAGGACCTATTTGTAAAT
1 CTAAGTAATTTTTCATGAAAATACCTAAAAAGGACCTATTTATAAAT
*
30995941 CTAAGTAATTTTTCATGAAAATACCTAAAAGGGACCTATTTATAAA
1 CTAAGTAATTTTTCATGAAAATACCTAAAAAGGACCTATTTATAAA
30995987 AAGTTATAAA
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
47 43 1.00
ACGTcount: A:0.42, C:0.13, G:0.12, T:0.33
Consensus pattern (47 bp):
CTAAGTAATTTTTCATGAAAATACCTAAAAAGGACCTATTTATAAAT
Found at i:31000617 original size:37 final size:36
Alignment explanation
Indices: 31000557--31000629 Score: 119
Period size: 37 Copynumber: 2.0 Consensus size: 36
31000547 AGTCGACTCT
* *
31000557 TTCCGTACGAAATCCGTCTGAGGTAAGTCAAATTAC
1 TTCCCTACGAAATCCGTCCGAGGTAAGTCAAATTAC
31000593 NTTCCCTACGAAATCCGTCCGAGGTAAGTCAAATTAC
1 -TTCCCTACGAAATCCGTCCGAGGTAAGTCAAATTAC
31000630 AATTACGTGT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.30, C:0.25, G:0.18, T:0.26
Consensus pattern (36 bp):
TTCCCTACGAAATCCGTCCGAGGTAAGTCAAATTAC
Found at i:31000876 original size:43 final size:43
Alignment explanation
Indices: 31000829--31000949 Score: 120
Period size: 43 Copynumber: 2.8 Consensus size: 43
31000819 CCTGAATTGA
* *
31000829 GATTTACGTATAAGACCATGTCTGGGACATCGGCATC-ATATCT
1 GATTTACATGTAAGACCATGTCTGGGACATCGGCATCGATAT-T
* * * **
31000872 GATTT-CATGTAAGACCCTATCTGGGATAGAGGCATCGATATT
1 GATTTACATGTAAGACCATGTCTGGGACATCGGCATCGATATT
* * * *
31000914 GAGTTACATGTAAGACCACGTCCGGGACGTCGGCAT
1 GATTTACATGTAAGACCATGTCTGGGACATCGGCAT
31000950 TGTACTTGTT
Statistics
Matches: 60, Mismatches: 16, Indels: 4
0.75 0.20 0.05
Matches are distributed among these distances:
42 29 0.48
43 31 0.52
ACGTcount: A:0.27, C:0.21, G:0.25, T:0.27
Consensus pattern (43 bp):
GATTTACATGTAAGACCATGTCTGGGACATCGGCATCGATATT
Found at i:31000896 original size:42 final size:43
Alignment explanation
Indices: 31000839--31000931 Score: 109
Period size: 42 Copynumber: 2.2 Consensus size: 43
31000829 GATTTACGTA
* ** *
31000839 TAAGACCATGTCTGGGACATCGGCATC-ATATCTGA-TTTCATG
1 TAAGACCATATCTGGGACAGAGGCATCGATAT-TGAGTTACATG
* *
31000881 TAAGACCCTATCTGGGATAGAGGCATCGATATTGAGTTACATG
1 TAAGACCATATCTGGGACAGAGGCATCGATATTGAGTTACATG
31000924 TAAGACCA
1 TAAGACCA
31000932 CGTCCGGGAC
Statistics
Matches: 42, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
42 25 0.60
43 17 0.40
ACGTcount: A:0.30, C:0.19, G:0.23, T:0.28
Consensus pattern (43 bp):
TAAGACCATATCTGGGACAGAGGCATCGATATTGAGTTACATG
Found at i:31009157 original size:40 final size:40
Alignment explanation
Indices: 31009102--31009288 Score: 311
Period size: 40 Copynumber: 4.7 Consensus size: 40
31009092 AGCATTGGAT
31009102 TATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGA
1 TATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGA
*
31009142 TATATCCGGGCTAAGACCCGAAGGCAACTATGCGAGTTGA
1 TATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGA
* ** *
31009182 TATATTCGGGCTGTGACCCGAAGGCAATTATGCGAGATGA
1 TATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGA
31009222 TATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGA
1 TATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGA
* *
31009262 TATGTCCGGGTTAAGACCCGAAGGCAA
1 TATATCCGGGCTAAGACCCGAAGGCAA
31009289 ATGTGTTTGC
Statistics
Matches: 135, Mismatches: 12, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 135 1.00
ACGTcount: A:0.29, C:0.20, G:0.28, T:0.22
Consensus pattern (40 bp):
TATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGA
Found at i:31024517 original size:30 final size:30
Alignment explanation
Indices: 31024474--31024562 Score: 92
Period size: 30 Copynumber: 3.0 Consensus size: 30
31024464 CAAAGATGAC
31024474 AAGAAAACC-GAATAAAGAAATCCAAGATA
1 AAGAAAACCAGAATAAAGAAATCCAAGATA
* * *
31024503 GAGAAACCCAGAATAAAGAAAT-CTAGAATA
1 AAGAAAACCAGAATAAAGAAATCCAAG-ATA
* * * *
31024533 AAGAGATCCAGGATAAAGAAACCCAAGATA
1 AAGAAAACCAGAATAAAGAAATCCAAGATA
31024563 CGATACTATG
Statistics
Matches: 48, Mismatches: 9, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
29 10 0.21
30 35 0.73
31 3 0.06
ACGTcount: A:0.57, C:0.15, G:0.17, T:0.11
Consensus pattern (30 bp):
AAGAAAACCAGAATAAAGAAATCCAAGATA
Found at i:31024522 original size:15 final size:15
Alignment explanation
Indices: 31024474--31024553 Score: 83
Period size: 15 Copynumber: 5.4 Consensus size: 15
31024464 CAAAGATGAC
*
31024474 AAGAAAACC-GAATA
1 AAGAAATCCAGAATA
31024488 AAGAAATCCA-AGATA
1 AAGAAATCCAGA-ATA
* *
31024503 GAGAAACCCAGAATA
1 AAGAAATCCAGAATA
*
31024518 AAGAAATCTAGAATA
1 AAGAAATCCAGAATA
* *
31024533 AAGAGATCCAGGATA
1 AAGAAATCCAGAATA
31024548 AAGAAA
1 AAGAAA
31024554 CCCAAGATAC
Statistics
Matches: 53, Mismatches: 10, Indels: 5
0.78 0.15 0.07
Matches are distributed among these distances:
14 9 0.17
15 43 0.81
16 1 0.02
ACGTcount: A:0.59, C:0.12, G:0.17, T:0.11
Consensus pattern (15 bp):
AAGAAATCCAGAATA
Found at i:31024562 original size:15 final size:15
Alignment explanation
Indices: 31024485--31024562 Score: 61
Period size: 15 Copynumber: 5.2 Consensus size: 15
31024475 AGAAAACCGA
*
31024485 ATAAAGAAATCCAAG
1 ATAAAGAAACCCAAG
*
31024500 ATAGAGAAACCC-AG
1 ATAAAGAAACCCAAG
* *
31024514 AATAAAGAAA-TCTAG
1 -ATAAAGAAACCCAAG
* * *
31024529 AATAAAGAGATCCAGG
1 -ATAAAGAAACCCAAG
31024545 ATAAAGAAACCCAAG
1 ATAAAGAAACCCAAG
31024560 ATA
1 ATA
31024563 CGATACTATG
Statistics
Matches: 49, Mismatches: 11, Indels: 6
0.74 0.17 0.09
Matches are distributed among these distances:
14 3 0.06
15 44 0.90
16 2 0.04
ACGTcount: A:0.56, C:0.14, G:0.17, T:0.13
Consensus pattern (15 bp):
ATAAAGAAACCCAAG
Found at i:31028716 original size:27 final size:28
Alignment explanation
Indices: 31028679--31028791 Score: 135
Period size: 27 Copynumber: 4.2 Consensus size: 28
31028669 AGCATGGCTG
* *
31028679 CCAGA-ACAGATA-TTGTGACAGAGTCA
1 CCAGATACAGATATTTGTGGCAGAGCCA
*
31028705 CCAGATACAGATA-TTGTGGTAGAGCCA
1 CCAGATACAGATATTTGTGGCAGAGCCA
* *
31028732 CCGGAAACAGATATTTGTGGCAGAGCCA
1 CCAGATACAGATATTTGTGGCAGAGCCA
* *
31028760 CCAGAT-CGGATATTTGTGGCAGAGCCG
1 CCAGATACAGATATTTGTGGCAGAGCCA
31028787 CCAGA
1 CCAGA
31028792 AATGCTTCCT
Statistics
Matches: 75, Mismatches: 10, Indels: 3
0.85 0.11 0.03
Matches are distributed among these distances:
26 5 0.07
27 53 0.71
28 17 0.23
ACGTcount: A:0.32, C:0.21, G:0.27, T:0.19
Consensus pattern (28 bp):
CCAGATACAGATATTTGTGGCAGAGCCA
Found at i:31034833 original size:15 final size:15
Alignment explanation
Indices: 31034785--31034863 Score: 83
Period size: 15 Copynumber: 5.4 Consensus size: 15
31034775 CAAAGATAAC
*
31034785 AAGAAAACCA-AATA
1 AAGAAATCCAGAATA
31034799 AAGAAATCCA-AGATA
1 AAGAAATCCAGA-ATA
* *
31034814 GAGAAACCCAGAATA
1 AAGAAATCCAGAATA
31034829 AAGAAATCCAGAATA
1 AAGAAATCCAGAATA
* *
31034844 AAG-AGTCCAGGATA
1 AAGAAATCCAGAATA
31034858 AAGAAA
1 AAGAAA
31034864 CCCAAGATAC
Statistics
Matches: 54, Mismatches: 8, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
14 22 0.41
15 31 0.57
16 1 0.02
ACGTcount: A:0.59, C:0.14, G:0.16, T:0.10
Consensus pattern (15 bp):
AAGAAATCCAGAATA
Found at i:31048431 original size:43 final size:42
Alignment explanation
Indices: 31048383--31048542 Score: 164
Period size: 43 Copynumber: 3.8 Consensus size: 42
31048373 TGTGTTTACA
31048383 TGTAAGACCATGTCTGGGACATTGGCATTGTATCGTGATTATG
1 TGTAAGACCATGTCTGGGACATTGGCATTGTAT-GTGATTATG
* *
31048426 TGTAAGACCATGTCTAGGACATTGGCATCAT-TATATGATT-TCG
1 TGTAAGACCATGTCTGGGACATTGGCAT--TGTATGTGATTAT-G
* * * **
31048469 TGTAAGACAATGTCTGGGACATTGGCATCGATATGTGATAACA
1 TGTAAGACCATGTCTGGGACATTGGCATTG-TATGTGATTATG
* * *
31048512 TGTAAAACCATATCTGGGATA-TGGCATTGTA
1 TGTAAGACCATGTCTGGGACATTGGCATTGTA
31048543 CGGGCAAAGT
Statistics
Matches: 97, Mismatches: 14, Indels: 14
0.78 0.11 0.11
Matches are distributed among these distances:
41 2 0.02
42 8 0.08
43 83 0.86
44 3 0.03
45 1 0.01
ACGTcount: A:0.29, C:0.14, G:0.24, T:0.33
Consensus pattern (42 bp):
TGTAAGACCATGTCTGGGACATTGGCATTGTATGTGATTATG
Found at i:31051355 original size:20 final size:20
Alignment explanation
Indices: 31051330--31051385 Score: 85
Period size: 20 Copynumber: 2.8 Consensus size: 20
31051320 GCCCATAAGT
31051330 GAACTCGGACTCAACTCAAC
1 GAACTCGGACTCAACTCAAC
31051350 GAACTCGGACTCAACTCAAC
1 GAACTCGGACTCAACTCAAC
**
31051370 GAGTTCGGAACTCAAC
1 GAACTCGG-ACTCAAC
31051386 CATCCTAGTC
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
20 26 0.79
21 7 0.21
ACGTcount: A:0.34, C:0.32, G:0.18, T:0.16
Consensus pattern (20 bp):
GAACTCGGACTCAACTCAAC
Found at i:31053724 original size:10 final size:10
Alignment explanation
Indices: 31053700--31053729 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
31053690 GATGGTTTAA
31053700 ATATATGTG-
1 ATATATGTGT
31053709 ATATATGTGT
1 ATATATGTGT
31053719 ATATATGTGT
1 ATATATGTGT
31053729 A
1 A
31053730 ATAAATCAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 9 0.45
10 11 0.55
ACGTcount: A:0.33, C:0.00, G:0.20, T:0.47
Consensus pattern (10 bp):
ATATATGTGT
Found at i:31054100 original size:32 final size:33
Alignment explanation
Indices: 31054064--31054127 Score: 78
Period size: 32 Copynumber: 2.0 Consensus size: 33
31054054 ACAAGTAAGG
* *
31054064 ATGAACGTCC-AAGTACATGTATTAC-AAGGGAC
1 ATGAACATCCTAA-TACATGTATGACAAAGGGAC
*
31054096 ATGAACATCCTTATACATGTATGACAAAGGGA
1 ATGAACATCCTAATACATGTATGACAAAGGGA
31054128 GATGCTAGTT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
32 20 0.74
33 7 0.26
ACGTcount: A:0.39, C:0.17, G:0.20, T:0.23
Consensus pattern (33 bp):
ATGAACATCCTAATACATGTATGACAAAGGGAC
Found at i:31054622 original size:32 final size:33
Alignment explanation
Indices: 31054560--31054623 Score: 78
Period size: 32 Copynumber: 2.0 Consensus size: 33
31054550 AACTAACATC
* *
31054560 TCCCTTTGTCATACATGTATAAGGATGTTCATG
1 TCCCTTTGTAATACATGTATAAGGACGTTCATG
*
31054593 TCCC-TTGTAATACATGTACT-TGGACGTTCAT
1 TCCCTTTGTAATACATGTA-TAAGGACGTTCAT
31054624 CCTTACTTGT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
32 22 0.81
33 5 0.19
ACGTcount: A:0.23, C:0.20, G:0.17, T:0.39
Consensus pattern (33 bp):
TCCCTTTGTAATACATGTATAAGGACGTTCATG
Found at i:31055777 original size:50 final size:50
Alignment explanation
Indices: 31055640--31055784 Score: 141
Period size: 50 Copynumber: 2.9 Consensus size: 50
31055630 GACGTTTCAA
* * ** *
31055640 GCATGAAGCATGAATGATTTCAATGCATGGAGATGTTCTTTATCA-TTCAAAT
1 GCATG-AGCATGAATGATTTCAATGAAAGGAGA-CAT-TTTCTCATTTCAAAT
* * * * *
31055692 ACATGAGCATGGATGGTTTCAACTCATAGGA-ACATTTTCTCATTTCAAAT
1 GCATGAGCATGAATGATTTCAA-TGAAAGGAGACATTTTCTCATTTCAAAT
*
31055742 GCATGAGCATGAATGATTTCAAAGAAAGGAGACATTTTCTCAT
1 GCATGAGCATGAATGATTTCAATGAAAGGAGACATTTTCTCAT
31055785 CCAAATACAT
Statistics
Matches: 74, Mismatches: 16, Indels: 8
0.76 0.16 0.08
Matches are distributed among these distances:
49 11 0.15
50 39 0.53
51 16 0.22
52 8 0.11
ACGTcount: A:0.34, C:0.15, G:0.19, T:0.32
Consensus pattern (50 bp):
GCATGAGCATGAATGATTTCAATGAAAGGAGACATTTTCTCATTTCAAAT
Found at i:31064972 original size:25 final size:25
Alignment explanation
Indices: 31064944--31065028 Score: 111
Period size: 26 Copynumber: 3.4 Consensus size: 25
31064934 CTGGAGGCCT
*
31064944 AGCCTCTTTTAAT-AACTGGGGCAAA
1 AGCC-CTTTTGATAAACTGGGGCAAA
31064969 AGCCCTTTTTGATAAACTGGGGCAAA
1 AGCCC-TTTTGATAAACTGGGGCAAA
*
31064995 AGCCCTTTTCGGTAAACTGGGGC-AA
1 AGCCCTTTT-GATAAACTGGGGCAAA
31065020 AGCCCTTTT
1 AGCCCTTTT
31065029 CTGTAACTAG
Statistics
Matches: 55, Mismatches: 2, Indels: 6
0.87 0.03 0.10
Matches are distributed among these distances:
24 1 0.02
25 25 0.45
26 29 0.53
ACGTcount: A:0.27, C:0.22, G:0.22, T:0.28
Consensus pattern (25 bp):
AGCCCTTTTGATAAACTGGGGCAAA
Found at i:31065029 original size:25 final size:26
Alignment explanation
Indices: 31064957--31065052 Score: 126
Period size: 26 Copynumber: 3.8 Consensus size: 26
31064947 CTCTTTTAAT
* *
31064957 AACTGGGGCAAAAGCCCTTTTTGATA
1 AACTGGGGCAAAAGCCCTTTTCGGTA
31064983 AACTGGGGCAAAAGCCCTTTTCGGTA
1 AACTGGGGCAAAAGCCCTTTTCGGTA
*
31065009 AACTGGGGC-AAAGCCCTTTTCTGT-
1 AACTGGGGCAAAAGCCCTTTTCGGTA
* *
31065033 AACTAGGGC-ATAGCCCTTTT
1 AACTGGGGCAAAAGCCCTTTT
31065053 GAAGTTCCTC
Statistics
Matches: 65, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
24 18 0.28
25 14 0.22
26 33 0.51
ACGTcount: A:0.26, C:0.23, G:0.24, T:0.27
Consensus pattern (26 bp):
AACTGGGGCAAAAGCCCTTTTCGGTA
Found at i:31071530 original size:34 final size:34
Alignment explanation
Indices: 31071492--31071564 Score: 83
Period size: 34 Copynumber: 2.1 Consensus size: 34
31071482 TTAGCCCCTC
* *
31071492 TTTCAATAGCAGTAGCAGTCTGGGCCTGAGCCCA
1 TTTCAATAACAGTAGCAGTCTAGGCCTGAGCCCA
* * * * *
31071526 TTTCAGTAATAGTGGTAGTCTAGGCCTTAGCCCA
1 TTTCAATAACAGTAGCAGTCTAGGCCTGAGCCCA
31071560 TTTCA
1 TTTCA
31071565 CTATAGTATG
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.23, C:0.23, G:0.23, T:0.30
Consensus pattern (34 bp):
TTTCAATAACAGTAGCAGTCTAGGCCTGAGCCCA
Found at i:31074329 original size:21 final size:21
Alignment explanation
Indices: 31074287--31074329 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
31074277 TATCGTGGTA
*
31074287 GTGGTAGTAAAAGAGGTCATG
1 GTGGTAGTAAAAGAGGGCATG
31074308 GTGGTAG-AAAAGAGGGCGATG
1 GTGGTAGTAAAAGAGGGC-ATG
31074329 G
1 G
31074330 GACTAGATCT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 9 0.45
21 11 0.55
ACGTcount: A:0.33, C:0.05, G:0.44, T:0.19
Consensus pattern (21 bp):
GTGGTAGTAAAAGAGGGCATG
Found at i:31076074 original size:40 final size:40
Alignment explanation
Indices: 31075992--31076213 Score: 308
Period size: 40 Copynumber: 5.6 Consensus size: 40
31075982 AACCCAAGTA
* * *
31075992 CCTTCGGGATTTAG-CCGGATATAG-CAACTCGCAGAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCAA-TAGCACAAATG
* *
31076031 CCTTCGGGTCTTAGCCCGGATATAGTCAATAGCACAAAAG
1 CCTTCGGGACTTAGCCCGGATATAGTCAATAGCACAAATG
31076071 CCTTCGGGACTTAGCCCGGATATAG-CAACTCA-CACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCAA-T-AGCACAAATG
31076111 CCTTCGGGACTTAGCCCGGATATAGTCAATAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCAATAGCACAAATG
* * * *
31076151 CCTTCGGTACTTAGCCCGCATATAGTTACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCAATAGCACAAATG
31076191 CCTTCGGGACTTAGCCCGGATAT
1 CCTTCGGGACTTAGCCCGGATAT
31076214 CATTCGAATA
Statistics
Matches: 164, Mismatches: 13, Indels: 11
0.87 0.07 0.06
Matches are distributed among these distances:
39 16 0.10
40 141 0.86
41 7 0.04
ACGTcount: A:0.28, C:0.27, G:0.22, T:0.23
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTCAATAGCACAAATG
Found at i:31076100 original size:80 final size:80
Alignment explanation
Indices: 31075992--31076213 Score: 347
Period size: 80 Copynumber: 2.8 Consensus size: 80
31075982 AACCCAAGTA
* * *
31075992 CCTTCGGGATTTAG-CCGGATATAGCAACTCGCAGAAATGCCTTCGGGTCTTAGCCCGGATATAG
1 CCTTCGGGACTTAGCCCGGATATAGCAACTCGCACAAATGCCTTCGGGACTTAGCCCGGATATAG
31076056 TCAATAGCACAAAAG
66 TCAATAGCACAAAAG
*
31076071 CCTTCGGGACTTAGCCCGGATATAGCAACTCACACAAATGCCTTCGGGACTTAGCCCGGATATAG
1 CCTTCGGGACTTAGCCCGGATATAGCAACTCGCACAAATGCCTTCGGGACTTAGCCCGGATATAG
*
31076136 TCAATAGCACAAATG
66 TCAATAGCACAAAAG
* * ** *
31076151 CCTTCGGTACTTAGCCCGCATATAGTTACTAGCACAAATGCCTTCGGGACTTAGCCCGGATAT
1 CCTTCGGGACTTAGCCCGGATATAGCAACTCGCACAAATGCCTTCGGGACTTAGCCCGGATAT
31076214 CATTCGAATA
Statistics
Matches: 131, Mismatches: 11, Indels: 1
0.92 0.08 0.01
Matches are distributed among these distances:
79 13 0.10
80 118 0.90
ACGTcount: A:0.28, C:0.27, G:0.22, T:0.23
Consensus pattern (80 bp):
CCTTCGGGACTTAGCCCGGATATAGCAACTCGCACAAATGCCTTCGGGACTTAGCCCGGATATAG
TCAATAGCACAAAAG
Found at i:31080137 original size:43 final size:43
Alignment explanation
Indices: 31080087--31080244 Score: 176
Period size: 43 Copynumber: 3.7 Consensus size: 43
31080077 ATGATTTGTG
*
31080087 TAAGACCACATCTGGGACGTTGGCATCGATTTGAGATATCGTC
1 TAAGACCACGTCTGGGACGTTGGCATCGATTTGAGATATCGTC
* * *
31080130 TAAGACCACGTCTGGGACGTTGGCATTGATTTCAGATATCGTG
1 TAAGACCACGTCTGGGACGTTGGCATCGATTTGAGATATCGTC
* * * * * *
31080173 TAAGACCACGTCTGGCACATTGGCATCAATTAGAGATTTTGT-
1 TAAGACCACGTCTGGGACGTTGGCATCGATTTGAGATATCGTC
* **
31080215 TGAAGACCATGTCT-GGACAATGGCATCGAT
1 T-AAGACCACGTCTGGGACGTTGGCATCGAT
31080245 ATGTAATTAC
Statistics
Matches: 98, Mismatches: 16, Indels: 3
0.84 0.14 0.03
Matches are distributed among these distances:
42 14 0.14
43 84 0.86
ACGTcount: A:0.27, C:0.20, G:0.25, T:0.28
Consensus pattern (43 bp):
TAAGACCACGTCTGGGACGTTGGCATCGATTTGAGATATCGTC
Found at i:31098001 original size:17 final size:17
Alignment explanation
Indices: 31097979--31098020 Score: 77
Period size: 16 Copynumber: 2.5 Consensus size: 17
31097969 GTTTACCAGT
31097979 GTGGGGCCCGCATGCTC
1 GTGGGGCCCGCATGCTC
31097996 GTGGGG-CCGCATGCTC
1 GTGGGGCCCGCATGCTC
31098012 GTGGGGCCC
1 GTGGGGCCC
31098021 ACACAGCCCA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
16 16 0.67
17 8 0.33
ACGTcount: A:0.05, C:0.33, G:0.45, T:0.17
Consensus pattern (17 bp):
GTGGGGCCCGCATGCTC
Found at i:31127462 original size:127 final size:127
Alignment explanation
Indices: 31127236--31127489 Score: 445
Period size: 127 Copynumber: 2.0 Consensus size: 127
31127226 GAATTAATAA
31127236 TGTAACATCCTGATTTTCGGATTTATTCGCGATTTTCAATATTTTGTAAAGACTTTAAAATTTAG
1 TGTAACATCCTGATTTTCGGATTTATTCGCGATTTTCAATATTTTGTAAAGACTTTAAAATTTAG
*
31127301 TATTTGGATGTGGAACTAATATTTTGAGTAGGTAAATGGGGTTATAGAAGGCCCATGTGTTG
66 TATTTGGATGTGGAACTAATATTTTGAGTAGGTAAATGGGCTTATAGAAGGCCCATGTGTTG
* * *
31127363 TGTAACATCCTGATTTTCGGATTTATTCGCGGTTTTCAATATTTTGTAAAGATTTTAAAATTTTG
1 TGTAACATCCTGATTTTCGGATTTATTCGCGATTTTCAATATTTTGTAAAGACTTTAAAATTTAG
* * *
31127428 TATTTGGATGTGGAATTTATCTTTTGAGTAGGTAAATGGGCTTATAGAAGGCCCATGTGTTG
66 TATTTGGATGTGGAACTAATATTTTGAGTAGGTAAATGGGCTTATAGAAGGCCCATGTGTTG
31127490 GCCAAAACCC
Statistics
Matches: 120, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
127 120 1.00
ACGTcount: A:0.27, C:0.09, G:0.22, T:0.42
Consensus pattern (127 bp):
TGTAACATCCTGATTTTCGGATTTATTCGCGATTTTCAATATTTTGTAAAGACTTTAAAATTTAG
TATTTGGATGTGGAACTAATATTTTGAGTAGGTAAATGGGCTTATAGAAGGCCCATGTGTTG
Found at i:31138510 original size:27 final size:27
Alignment explanation
Indices: 31138480--31138657 Score: 178
Period size: 27 Copynumber: 6.6 Consensus size: 27
31138470 ATATTGAGTC
* *
31138480 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAATCAACT
* *
31138507 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
*
31138534 CGCACACTTAGTGCTACATAGTCAACCT
1 CGCACACTTAGTGCTACATAATCAA-CT
** ** *
31138562 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAATCAACT
* **
31138589 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAATCAACT
* * * *
31138616 CGCGCACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
31138643 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
31138658 GTACAATTTA
Statistics
Matches: 127, Mismatches: 21, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
27 103 0.81
28 24 0.19
ACGTcount: A:0.29, C:0.29, G:0.16, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAACT
Found at i:31138624 original size:82 final size:81
Alignment explanation
Indices: 31138501--31138656 Score: 215
Period size: 82 Copynumber: 1.9 Consensus size: 81
31138491 TGCTATATAA
* * *
31138501 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAACCTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAA-ATCGCA
31138566 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * ** *
31138583 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCGCACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
31138647 CACTTAGTGC
65 CACTTAGTGC
31138657 TGTACAATTT
Statistics
Matches: 65, Mismatches: 8, Indels: 3
0.86 0.11 0.04
Matches are distributed among these distances:
81 16 0.25
82 49 0.75
ACGTcount: A:0.28, C:0.29, G:0.16, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:31138640 original size:54 final size:54
Alignment explanation
Indices: 31138480--31138656 Score: 196
Period size: 54 Copynumber: 3.3 Consensus size: 54
31138470 ATATTGAGTC
* * * *
31138480 CGCACACTCAGTGCTAT-ATAATCAACTCGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGC-ATCATAATCAACTCGCACACTTAGTGCAACATAGTCAAAT
* ** * *
31138534 CGCACACTTAGTGC-TACATAGTCAACCTCGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCAT-CATAATCAA-CTCGCACACTTAGTGCAACATAGTCAAAT
* ** *
31138589 CGCACACTTAGTGCATCATATTCATTTCGCGCACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCATCATAATCAACTCGCACACTTAGTGCAACATAGTCAAAT
31138643 CGCACACTTAGTGC
1 CGCACACTTAGTGC
31138657 TGTACAATTT
Statistics
Matches: 103, Mismatches: 16, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
52 1 0.01
54 57 0.55
55 44 0.43
56 1 0.01
ACGTcount: A:0.29, C:0.29, G:0.16, T:0.27
Consensus pattern (54 bp):
CGCACACTTAGTGCATCATAATCAACTCGCACACTTAGTGCAACATAGTCAAAT
Found at i:31153551 original size:44 final size:44
Alignment explanation
Indices: 31153485--31153573 Score: 151
Period size: 44 Copynumber: 2.0 Consensus size: 44
31153475 AATCGTTGAG
* *
31153485 TTGAGTCCGAGTTCACTTATGGGTGGGTTACATGGTAGCTTGGC
1 TTGAGTCCGAGTTCACTCATGGGTGCGTTACATGGTAGCTTGGC
*
31153529 TTGAGTCCGAGTTCACTCATGGGTGCGTTACGTGGTAGCTTGGC
1 TTGAGTCCGAGTTCACTCATGGGTGCGTTACATGGTAGCTTGGC
31153573 T
1 T
31153574 ACACATATAT
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
44 42 1.00
ACGTcount: A:0.15, C:0.18, G:0.34, T:0.34
Consensus pattern (44 bp):
TTGAGTCCGAGTTCACTCATGGGTGCGTTACATGGTAGCTTGGC
Found at i:31160685 original size:42 final size:44
Alignment explanation
Indices: 31160589--31160698 Score: 136
Period size: 42 Copynumber: 2.5 Consensus size: 44
31160579 TTATTATGTC
* *
31160589 AGACCACGTCTAGGACGTTGGCATCGACTTATGATTTACGTGTA
1 AGACCATGTCTAGGACATTGGCATCGACTTATGATTTACGTGTA
* *
31160633 AGACCATGTCTGGGACATTGGCATCGTA-TT-TGATTT-CGTTTA
1 AGACCATGTCTAGGACATTGGCATCG-ACTTATGATTTACGTGTA
* *
31160675 AGACCCTGTCTAGGACAGTGGCAT
1 AGACCATGTCTAGGACATTGGCAT
31160699 TGAAATTTGG
Statistics
Matches: 58, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
42 26 0.45
43 6 0.10
44 25 0.43
45 1 0.02
ACGTcount: A:0.24, C:0.20, G:0.25, T:0.31
Consensus pattern (44 bp):
AGACCATGTCTAGGACATTGGCATCGACTTATGATTTACGTGTA
Found at i:31160707 original size:43 final size:43
Alignment explanation
Indices: 31160589--31160733 Score: 134
Period size: 42 Copynumber: 3.4 Consensus size: 43
31160579 TTATTATGTC
* *
31160589 AGACCACGTCTAGGAC-GTTGGCATCGACTTATGATTTACGTGTA
1 AGACCATGTCTAGGACAG-TGGCATCGAATT-TGATTTACGTGTA
* * * *
31160633 AGACCATGTCTGGGACATTGGCATCGTATTTGATTT-CGTTTA
1 AGACCATGTCTAGGACAGTGGCATCGAATTTGATTTACGTGTA
* * * *
31160675 AGACCCTGTCTAGGACAGTGGCATTGAAATTTG-GTTACATGTA
1 AGACCATGTCTAGGACAGTGGCATCG-AATTTGATTTACGTGTA
* *
31160718 AGACCACGTCTGGGAC
1 AGACCATGTCTAGGAC
31160734 GTTGCATTGT
Statistics
Matches: 81, Mismatches: 17, Indels: 7
0.77 0.16 0.07
Matches are distributed among these distances:
42 29 0.36
43 28 0.35
44 24 0.30
ACGTcount: A:0.25, C:0.19, G:0.26, T:0.30
Consensus pattern (43 bp):
AGACCATGTCTAGGACAGTGGCATCGAATTTGATTTACGTGTA
Found at i:31164961 original size:62 final size:62
Alignment explanation
Indices: 31164857--31164980 Score: 203
Period size: 62 Copynumber: 2.0 Consensus size: 62
31164847 CATTGTTACT
* * * *
31164857 CTTTTCCACTTCCATAGCGGAATTTTCACAGGTTGCAATAATCCCGAAGGCAATTGGTGCTC
1 CTTTCCCACTTCCATAGCGGAATTTTCACAAGTTACAATAATCCCAAAGGCAATTGGTGCTC
*
31164919 CTTTCCCACTTCCATAGCGGAATTTTCACAAGTTACAGTAATCCCAAAGGCAATTGGTGCTC
1 CTTTCCCACTTCCATAGCGGAATTTTCACAAGTTACAATAATCCCAAAGGCAATTGGTGCTC
31164981 AGCCTTAACC
Statistics
Matches: 57, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
62 57 1.00
ACGTcount: A:0.26, C:0.27, G:0.18, T:0.30
Consensus pattern (62 bp):
CTTTCCCACTTCCATAGCGGAATTTTCACAAGTTACAATAATCCCAAAGGCAATTGGTGCTC
Found at i:31170166 original size:70 final size:70
Alignment explanation
Indices: 31170048--31170186 Score: 251
Period size: 70 Copynumber: 2.0 Consensus size: 70
31170038 AGGGTATTTC
* * *
31170048 GGTAGTTATGTTCTTTAGGGGTAATTTCGTACTTACGCAACTACACACGTTATTTCAGAAATTTT
1 GGTAATTATGCTCTTTAAGGGTAATTTCGTACTTACGCAACTACACACGTTATTTCAGAAATTTT
31170113 TAGCT
66 TAGCT
31170118 GGTAATTATGCTCTTTAAGGGTAATTTCGTACTTACGCAACTACACACGTTATTTCAGAAATTTT
1 GGTAATTATGCTCTTTAAGGGTAATTTCGTACTTACGCAACTACACACGTTATTTCAGAAATTTT
31170183 TAGC
66 TAGC
31170187 CGTTTTATGC
Statistics
Matches: 66, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
70 66 1.00
ACGTcount: A:0.27, C:0.17, G:0.17, T:0.39
Consensus pattern (70 bp):
GGTAATTATGCTCTTTAAGGGTAATTTCGTACTTACGCAACTACACACGTTATTTCAGAAATTTT
TAGCT
Found at i:31171832 original size:83 final size:83
Alignment explanation
Indices: 31171693--31171857 Score: 303
Period size: 83 Copynumber: 2.0 Consensus size: 83
31171683 TCAAAAATTC
*
31171693 AACTGGGTTTTGGCCAACACATGGGCCTTCTATAAGCCCATTTACTTACTCAAAATATAAATTTC
1 AACTGGGTTTTGGCCAACACATGGGCCTTCTATAAGCCCATTTACCTACTCAAAATATAAATTTC
31171758 ACATCCAAATACAAAATA
66 ACATCCAAATACAAAATA
* *
31171776 AACTGGGTTTTGGGCAACAGATGGGCCTTCTATAAGCCCATTTACCTACTCAAAATATAAATTTC
1 AACTGGGTTTTGGCCAACACATGGGCCTTCTATAAGCCCATTTACCTACTCAAAATATAAATTTC
31171841 ACATCCAAATACAAAAT
66 ACATCCAAATACAAAAT
31171858 TTTAAAATCT
Statistics
Matches: 79, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
83 79 1.00
ACGTcount: A:0.37, C:0.22, G:0.12, T:0.28
Consensus pattern (83 bp):
AACTGGGTTTTGGCCAACACATGGGCCTTCTATAAGCCCATTTACCTACTCAAAATATAAATTTC
ACATCCAAATACAAAATA
Found at i:31175939 original size:46 final size:45
Alignment explanation
Indices: 31175889--31176064 Score: 221
Period size: 46 Copynumber: 3.8 Consensus size: 45
31175879 TGGTTGAGCA
31175889 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-G
*** * *
31175935 TCCGAACTCGTTGAGTTGAGTCCGAGTTCGAGAAATGTAACTAG-GCA-
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-ACTTATG-GA-T-GCGAAG
31175982 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-G
* *
31176028 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
31176065 GCGGGTTACA
Statistics
Matches: 111, Mismatches: 12, Indels: 14
0.81 0.09 0.10
Matches are distributed among these distances:
43 1 0.01
44 3 0.03
45 1 0.01
46 68 0.61
47 33 0.30
48 1 0.01
49 3 0.03
50 1 0.01
ACGTcount: A:0.22, C:0.21, G:0.28, T:0.28
Consensus pattern (45 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAG
Found at i:31176045 original size:93 final size:93
Alignment explanation
Indices: 31175886--31176056 Score: 315
Period size: 93 Copynumber: 1.8 Consensus size: 93
31175876 GGATGGTTGA
* *
31175886 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
31175951 TGAGTCCGAGTTCGAGAAATGTAACTAG
66 TGAGTCCGAGTTCGAGAAATGTAACTAG
*
31175979 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
31176044 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
31176057 ACTTATGGGC
Statistics
Matches: 75, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.22, C:0.22, G:0.29, T:0.27
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGAGAAATGTAACTAG
Found at i:31178042 original size:39 final size:39
Alignment explanation
Indices: 31177985--31178077 Score: 134
Period size: 39 Copynumber: 2.4 Consensus size: 39
31177975 TGCATGGTAT
* * *
31177985 TGGAAAAATATCCAGACTTGAAGTCCGCAGGCTTTA-TGC
1 TGGAAAAATATCCGGACTTAAAGTCCGCAGGC-TAAGTGC
*
31178024 TGGAAATATATCCGGACTTAAAGTCCGCAGGCTAAGTGC
1 TGGAAAAATATCCGGACTTAAAGTCCGCAGGCTAAGTGC
31178063 TGGAAAAATATCCGG
1 TGGAAAAATATCCGG
31178078 GCTAAGTCCC
Statistics
Matches: 48, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
38 2 0.04
39 46 0.96
ACGTcount: A:0.32, C:0.19, G:0.25, T:0.24
Consensus pattern (39 bp):
TGGAAAAATATCCGGACTTAAAGTCCGCAGGCTAAGTGC
Found at i:31178102 original size:39 final size:39
Alignment explanation
Indices: 31178070--31178246 Score: 282
Period size: 39 Copynumber: 4.5 Consensus size: 39
31178060 TGCTGGAAAA
31178070 ATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTATT
1 ATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTATT
* * **
31178109 ATATCTGGGCTAAGTCCTGAAGGCATTCGTGCTGGTGCT
1 ATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTATT
**
31178148 ATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGCGTT
1 ATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTATT
31178187 ATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTATT
1 ATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTATT
31178226 ATATCCGGGCTTAAAGTCCCG
1 ATATCCGGGC-T-AAGTCCCG
31178247 CATGCTTTGT
Statistics
Matches: 126, Mismatches: 10, Indels: 2
0.91 0.07 0.01
Matches are distributed among these distances:
39 117 0.93
40 1 0.01
41 8 0.06
ACGTcount: A:0.20, C:0.24, G:0.29, T:0.28
Consensus pattern (39 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTATT
Found at i:31185951 original size:201 final size:200
Alignment explanation
Indices: 31185607--31186007 Score: 775
Period size: 201 Copynumber: 2.0 Consensus size: 200
31185597 CATGCCATTT
*
31185607 CGAAGTTCAACCAAAATTGTACCAGAAGGGGGGGCTTTGATAGTGTGGGCGACTTTGACCTCAAG
1 CGAAGTTCAACCAAAATTGTACCAAAAGGGGGGGCTTTGATAGTGTGGGCGACTTTGACCTCAAG
31185672 ATCCCGAGTCCGATAGCTGGAGAACCAAATCTATAAAACAGAGGAGCAATGAAACGGAGTAAGCA
66 ATCCCGAGTCCGATAGCTGGAGAACCAAATCTATAAAACAGAGGAGCAATGAAACGGAGTAAGCA
*
31185737 ATTTATGCTTAGTAAGTTTTGAGCAAGGAATTCCAGCACAACAAAAGTATAGCATTCATATAGTT
131 ATTTATGCTTAGTAAGTTTTGAGCAAGGAATTCCAGCACAACAAAAGTATAGCATTCATATAGCT
31185802 AAACG
196 AAACG
31185807 CGAAGTTCAACCAAAATTGTACCAAAAGGGGGGGGCTTTGATAGTGTGGGCGACTTTGACCTCAA
1 CGAAGTTCAACCAAAATTGTACCAAAA-GGGGGGGCTTTGATAGTGTGGGCGACTTTGACCTCAA
31185872 GATCCCGAGTCCGATAGCTGGAGAACCAAATCTATAAAACAGAGGAGCAATGAAACGGAGTAAGC
65 GATCCCGAGTCCGATAGCTGGAGAACCAAATCTATAAAACAGAGGAGCAATGAAACGGAGTAAGC
31185937 AATTTATGCTTAGTAAGTTTTGAGCAAGGAATTCCAGCACAACAAAAGTATAGCATTCATATAGC
130 AATTTATGCTTAGTAAGTTTTGAGCAAGGAATTCCAGCACAACAAAAGTATAGCATTCATATAGC
31186002 TAAACG
195 TAAACG
31186008 GATAATTCCA
Statistics
Matches: 198, Mismatches: 2, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
200 26 0.13
201 172 0.87
ACGTcount: A:0.36, C:0.18, G:0.24, T:0.22
Consensus pattern (200 bp):
CGAAGTTCAACCAAAATTGTACCAAAAGGGGGGGCTTTGATAGTGTGGGCGACTTTGACCTCAAG
ATCCCGAGTCCGATAGCTGGAGAACCAAATCTATAAAACAGAGGAGCAATGAAACGGAGTAAGCA
ATTTATGCTTAGTAAGTTTTGAGCAAGGAATTCCAGCACAACAAAAGTATAGCATTCATATAGCT
AAACG
Found at i:31186154 original size:69 final size:69
Alignment explanation
Indices: 31186043--31186181 Score: 269
Period size: 69 Copynumber: 2.0 Consensus size: 69
31186033 GATATCGTAC
*
31186043 TTGCTTCACATTATCAACTCTTATGTACATACACAAAAGATCAACTCAGCCAAAGGCCGGTAGCT
1 TTGCTTCACATTATCAACCCTTATGTACATACACAAAAGATCAACTCAGCCAAAGGCCGGTAGCT
31186108 CGTT
66 CGTT
31186112 TTGCTTCACATTATCAACCCTTATGTACATACACAAAAGATCAACTCAGCCAAAGGCCGGTAGCT
1 TTGCTTCACATTATCAACCCTTATGTACATACACAAAAGATCAACTCAGCCAAAGGCCGGTAGCT
31186177 CGTT
66 CGTT
31186181 T
1 T
31186182 ATCAACTGAG
Statistics
Matches: 69, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
69 69 1.00
ACGTcount: A:0.32, C:0.27, G:0.14, T:0.27
Consensus pattern (69 bp):
TTGCTTCACATTATCAACCCTTATGTACATACACAAAAGATCAACTCAGCCAAAGGCCGGTAGCT
CGTT
Found at i:31186450 original size:79 final size:78
Alignment explanation
Indices: 31186348--31186570 Score: 256
Period size: 79 Copynumber: 2.8 Consensus size: 78
31186338 GCTCCTCGTT
* *
31186348 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAATTCGCACAAATGCCTTCGGGACTTAACCCGG
1 CAAATGCCTTCGGG-CTTAGCCCGG-TATAGTAATTCGCACAAATGCCTTCGGGACTTAGCCCGG
*
31186413 ATTTAGTAACTCGCA
64 AATTAGTAACTCGCA
*
31186428 CAAATGCCTTCGGGCTTAGCCCGGAATTAGT-ATCTCGCACAAATGCCTTCGGG-CTTAGCCCGG
1 CAAATGCCTTCGGGCTTAGCCCGGTA-TAGTAAT-TCGCACAAATGCCTTCGGGACTTAGCCCGG
*
31186491 AATTAGTATCTCGCA
64 AATTAGTAACTCGCA
* * * * * *
31186506 CAAATGCCTTCGGATCTTAGTCCGGATATTGTCACTTAGCAC-AA-GCCTTCAGGACTTAGCCCG
1 CAAATGCCTTCGG-GCTTAGCCCGG-TATAGT-AATTCGCACAAATGCCTTCGGGACTTAGCCCG
31186569 GA
63 GA
31186571 CATCATTCAA
Statistics
Matches: 124, Mismatches: 12, Indels: 15
0.82 0.08 0.10
Matches are distributed among these distances:
78 46 0.37
79 57 0.46
80 20 0.16
81 1 0.01
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26
Consensus pattern (78 bp):
CAAATGCCTTCGGGCTTAGCCCGGTATAGTAATTCGCACAAATGCCTTCGGGACTTAGCCCGGAA
TTAGTAACTCGCA
Found at i:31186465 original size:39 final size:40
Alignment explanation
Indices: 31186348--31186570 Score: 257
Period size: 39 Copynumber: 5.7 Consensus size: 40
31186338 GCTCCTCGTT
* *
31186348 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAAT-TCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAAT-TAGT-ATCTCGCA
* * *
31186388 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
31186428 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
31186467 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
* *
31186506 CAAATGCCTTC-GGATCTTAGTCCGGATATT-GTCA-CTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGA-ATTAGT-ATC-TCGCA
*
31186547 C-AA-GCCTTCAGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
31186571 CATCATTCAA
Statistics
Matches: 166, Mismatches: 9, Indels: 17
0.86 0.05 0.09
Matches are distributed among these distances:
38 2 0.01
39 89 0.54
40 64 0.39
41 11 0.07
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
Found at i:31190127 original size:94 final size:91
Alignment explanation
Indices: 31189962--31190227 Score: 263
Period size: 94 Copynumber: 2.8 Consensus size: 91
31189952 ATATGTGTGC
** ** *
31189962 TAGTGTAAGACATGTCTGGGACATGCATCAGCCTCAAGATATTTAAGCCAGTGTAAGA-CATGTC
1 TAGTGTAAGACATGTCTGGGACATGCATCAGCCTCGCGATA-GAAAGCTAGTGTAAGACCATGTC
*
31190026 T-AGGACATGCAGT-GGCATTGA-GACTAGAGT
65 TGA-GACATGC-GTCAGC-TTGACG--T-GAGT
* *
31190056 TAGTGTAAGACATGTCTGGGACATGCATCAGCCTCGCGGTAGACATGCTAGTGTAAGACCA-GTC
1 TAGTGTAAGACATGTCTGGGACATGCATCAGCCTCGCGATAGA-AAGCTAGTGTAAGACCATGTC
* *
31190120 TGAGACATGGCGTCAGCTTGTCGTGTGT
65 TGAGACAT-GCGTCAGCTTGACGTGAGT
* * *
31190148 TAGTGTAAGACCTGTCTGGGACATGGCATCGGCCTCGCTATATGAAAGCTAGTGTAAGACCATGT
1 TAGTGTAAGACATGTCTGGGACAT-GCATCAGCCTCGCGATA-GAAAGCTAGTGTAAGACCATGT
*
31190213 CTGGGACATGGCGTC
64 CTGAGACAT-GCGTC
31190228 GGCATCTTAA
Statistics
Matches: 147, Mismatches: 16, Indels: 18
0.81 0.09 0.10
Matches are distributed among these distances:
92 26 0.18
93 31 0.21
94 82 0.56
95 8 0.05
ACGTcount: A:0.26, C:0.20, G:0.29, T:0.26
Consensus pattern (91 bp):
TAGTGTAAGACATGTCTGGGACATGCATCAGCCTCGCGATAGAAAGCTAGTGTAAGACCATGTCT
GAGACATGCGTCAGCTTGACGTGAGT
Found at i:31192935 original size:40 final size:40
Alignment explanation
Indices: 31192903--31193093 Score: 276
Period size: 40 Copynumber: 4.8 Consensus size: 40
31192893 CCAGCATGAT
* * *
31192903 TGCTCTTCGGGACCTAGCCCGGATATAACACCAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAA
** *
31192943 TGCT-TTCGGGGTTTAGCACGGATATATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAA
* *
31192982 TGCTCTTCGGAACTTAGTCCGGATATATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAA
* *
31193022 TGCTCTTCGAGACTTAGCCCGGATACATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAA
*
31193062 TGCTCTTCGGGACTTAGCCCGGATACATCACT
1 TGCTCTTCGGGACTTAGCCCGGATATATCACT
31193094 CTCAATTCTC
Statistics
Matches: 134, Mismatches: 16, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
39 33 0.25
40 101 0.75
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.25
Consensus pattern (40 bp):
TGCTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAA
Found at i:31194681 original size:49 final size:48
Alignment explanation
Indices: 31194507--31194819 Score: 438
Period size: 47 Copynumber: 6.6 Consensus size: 48
31194497 CCCTTCGGGA
* * * * * * *
31194507 CTTATCAC-ATTTATACACTTTCATATCCATCACGTTGGCCACTCGGC
1 CTTATCACTATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * *
31194554 CCTATCACT-TATATACACTTTCACATTCATCACATTGGCCGTTAGGC
1 CTTATCACTATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
31194601 CTTATCAC-ATATATACACTTTCACATTCATCACATCGGCTATTATGC
1 CTTATCACTATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
31194648 CTTATCACATATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCAC-TATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
31194697 CTTATCAC-ATATATACACTTTCACATTCATCACATCGGCTATTATGC
1 CTTATCACTATATATACACTTTCACATTCATCACATCGGCCATTAGGC
31194744 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC-TATATATACACTTTCACATTCATCACATCGGCCATTAGGC
31194793 CTTATCAC-ATATATACACTTTCACATT
1 CTTATCACTATATATACACTTTCACATT
31194820 TATTCAAATA
Statistics
Matches: 243, Mismatches: 17, Indels: 12
0.89 0.06 0.04
Matches are distributed among these distances:
47 152 0.63
49 91 0.37
ACGTcount: A:0.29, C:0.28, G:0.08, T:0.35
Consensus pattern (48 bp):
CTTATCACTATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:31194704 original size:96 final size:96
Alignment explanation
Indices: 31194507--31194819 Score: 495
Period size: 96 Copynumber: 3.3 Consensus size: 96
31194497 CCCTTCGGGA
* * * * * * * ** *
31194507 CTTATCACATTTATACACTTTCATATCCATCACGTTGGCCACTCGGCCCTATCAC-T-TATATAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTATGCCTTATCACATATATATAC
* *
31194570 ACTTTCACATTCATCACATTGGCCGTTAGGC
66 ACTTTCACATTCATCACATCGGCCATTAGGC
31194601 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTATGCCTTATCACATATATATAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTATGCCTTATCACATATATATAC
*
31194666 ACTTTCACATTCATCACATCGGCTATTAGGC
66 ACTTTCACATTCATCACATCGGCCATTAGGC
31194697 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTATGCCTTATCACATATATATAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTATGCCTTATCACATATATATAC
31194762 ACTTTCACATTCATCACATCGGCCATTAGGC
66 ACTTTCACATTCATCACATCGGCCATTAGGC
31194793 CTTATCACATATATACACTTTCACATT
1 CTTATCACATATATACACTTTCACATT
31194820 TATTCAAATA
Statistics
Matches: 203, Mismatches: 14, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
94 45 0.22
95 1 0.00
96 157 0.77
ACGTcount: A:0.29, C:0.28, G:0.08, T:0.35
Consensus pattern (96 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTATGCCTTATCACATATATATAC
ACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:31200953 original size:39 final size:41
Alignment explanation
Indices: 31200858--31201041 Score: 208
Period size: 40 Copynumber: 4.6 Consensus size: 41
31200848 TTGAATGATG
*
31200858 TCCGGGCTAAGTCCCGAAGGC--TTGTGCTAAGTGAC-AATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAAGT-ACTAATA
*
31200897 TCCGGACTAAGAT-CCGAAGGCATTTGTGCG-AGATACTAAT-
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAAG-TACTAATA
31200937 TCCGGGCTAAG-CCCGAAGGCATTTGTGCG-AGATACTAA-A
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAAG-TACTAATA
* *
31200976 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAATTACT-ATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAAGTACTAATA
* *
31201016 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
31201042 AACGAGGAGC
Statistics
Matches: 127, Mismatches: 8, Indels: 19
0.82 0.05 0.12
Matches are distributed among these distances:
39 55 0.43
40 61 0.48
41 11 0.09
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.24
Consensus pattern (41 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAAGTACTAATA
Found at i:31201063 original size:79 final size:79
Alignment explanation
Indices: 31200910--31201074 Score: 194
Period size: 79 Copynumber: 2.1 Consensus size: 79
31200900 GGACTAAGAT
* **
31200910 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTGTGCGAGATACTAA
1 CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGATACTAA
*
31200975 ATCCGGGTTAAGTC
66 ATCCGGGTTAAATC
* *
31200989 CCGAAGGCATTTGTGCGA-ATTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAGGA-G
1 CCGAAGGCATTTGTGCGAGA-TACTAAT-ACCGGGCTAAG-CCCGAAGGCATTTGAACGA-GATA
* *
31201051 CTATATCC-GGTTAAATT
62 CTAAATCCGGGTTAAATC
31201068 CCGAAGG
1 CCGAAGG
31201075 TACGTGATTT
Statistics
Matches: 74, Mismatches: 8, Indels: 8
0.82 0.09 0.09
Matches are distributed among these distances:
78 3 0.04
79 45 0.61
80 24 0.32
81 2 0.03
ACGTcount: A:0.27, C:0.21, G:0.27, T:0.24
Consensus pattern (79 bp):
CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGATACTAA
ATCCGGGTTAAATC
Found at i:31208946 original size:79 final size:81
Alignment explanation
Indices: 31208810--31208994 Score: 229
Period size: 79 Copynumber: 2.3 Consensus size: 81
31208800 TTGAATGATG
*
31208810 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
31208874 TGTGCGAGA-TACTA-A
66 TGTGCGA-ATTACTATA
* * * **
31208889 TTCCGGGCTAAG-CCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCA
1 -TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCA
31208951 TTTGTGCGAATTACTATA
64 TTTGTGCGAATTACTATA
* *
31208969 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
31208995 AACGAGGAGC
Statistics
Matches: 92, Mismatches: 8, Indels: 10
0.84 0.07 0.09
Matches are distributed among these distances:
78 2 0.02
79 57 0.62
80 33 0.36
ACGTcount: A:0.25, C:0.23, G:0.27, T:0.25
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
TGTGCGAATTACTATA
Found at i:31209008 original size:40 final size:39
Alignment explanation
Indices: 31208811--31208994 Score: 189
Period size: 40 Copynumber: 4.6 Consensus size: 39
31208801 TGAATGATGT
* * *
31208811 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGT-ACTATAA
* *
31208851 CCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTA-ATT
1 CCGGGCTAAG-TCCCGAAGGCATTTGTGCGAG-TACTATA-A
31208891 CCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTA-AA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAG-TACTATAA
* *
31208929 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAATTACTATAA
1 -CCGGGCTAAGTCCCGAAGGCATTTGTGCG-AGTACTATAA
*
31208970 CCGGGCTATGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTG
31208995 AACGAGGAGC
Statistics
Matches: 125, Mismatches: 10, Indels: 18
0.82 0.07 0.12
Matches are distributed among these distances:
39 35 0.28
40 78 0.62
41 12 0.10
ACGTcount: A:0.25, C:0.23, G:0.27, T:0.25
Consensus pattern (39 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTACTATAA
Found at i:31209016 original size:79 final size:79
Alignment explanation
Indices: 31208811--31209027 Score: 194
Period size: 79 Copynumber: 2.7 Consensus size: 79
31208801 TGAATGATGT
** * * * **
31208811 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGAT-CCGAAGGCATT
1 CCGGGCTAAG-CCCGAAGGCATTTGAAC-GAGTGACTAAATCCGGGTTAA-ATCCCGAAGGCATT
*
31208874 TGTGCGAGATACTAATT
63 TGTGCGAGATACTAATA
** * *
31208891 CCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCATTTGT
1 CCGGGCTAAGCCCGAAGGCATTTGAACGAGTGACTAAATCCGGGTTAAATCCCGAAGGCATTTGT
31208956 GCGA-ATTACT-ATAA
66 GCGAGA-TACTAAT-A
* * *
31208970 CCGGGCTATGTCCCGAAGGCATTTGAACGAG-GAGCTATATCC-GGTTAAATTCCGAAGG
1 CCGGGCTAAG-CCCGAAGGCATTTGAACGAGTGA-CTAAATCCGGGTTAAATCCCGAAGG
31209028 TACGTGATTT
Statistics
Matches: 116, Mismatches: 15, Indels: 13
0.81 0.10 0.09
Matches are distributed among these distances:
78 4 0.03
79 70 0.60
80 42 0.36
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.24
Consensus pattern (79 bp):
CCGGGCTAAGCCCGAAGGCATTTGAACGAGTGACTAAATCCGGGTTAAATCCCGAAGGCATTTGT
GCGAGATACTAATA
Found at i:31216979 original size:54 final size:54
Alignment explanation
Indices: 31216918--31217143 Score: 294
Period size: 54 Copynumber: 4.2 Consensus size: 54
31216908 CCTAAATTGA
* *
31216918 TAAAATGACTATTTTGCCCTTATGGGGTAAAATGATTATTTTTCCCTTATCGGG
1 TAAAATGACTATTTTGCCCTTATGGGGTAAAATGATTGTTTTGCCCTTATCGGG
* * * * *
31216972 TAAAATGACTGTTTTTCTCTTATGGGGTAAAATGATTGTTTTGCCTTTATGGGG
1 TAAAATGACTATTTTGCCCTTATGGGGTAAAATGATTGTTTTGCCCTTATCGGG
* * *
31217026 TAAAATGACTATTTTGCCCTTATGTGGTAAAGTGAATGTTTTGCCCTTAT-GAGG
1 TAAAATGACTATTTTGCCCTTATGGGGTAAAATGATTGTTTTGCCCTTATCG-GG
* * * *
31217080 TAAAATGAC-AGTTTTGCCCTTATGTGGTAAAATGATTGTTTTGCCCTTAACTGA
1 TAAAATGACTA-TTTTGCCCTTATGGGGTAAAATGATTGTTTTGCCCTTATCGGG
31217134 TAAAATGACT
1 TAAAATGACT
31217144 GTTGTACCCC
Statistics
Matches: 149, Mismatches: 19, Indels: 7
0.85 0.11 0.04
Matches are distributed among these distances:
53 2 0.01
54 147 0.99
ACGTcount: A:0.27, C:0.13, G:0.20, T:0.40
Consensus pattern (54 bp):
TAAAATGACTATTTTGCCCTTATGGGGTAAAATGATTGTTTTGCCCTTATCGGG
Found at i:31217055 original size:81 final size:81
Alignment explanation
Indices: 31216918--31217146 Score: 298
Period size: 81 Copynumber: 2.8 Consensus size: 81
31216908 CCTAAATTGA
* *
31216918 TAAAATGACTATTTTGCCCTTATGGGGTAAAATGATTATTTTTCCCTTATCG-GGTAAAATGACT
1 TAAAATGACTGTTTTGCCCTTATGGGGTAAAATGATTATTTTGCCCTTAT-GTGGTAAAATGACT
* * *
31216982 GTTTTTCTCTTATGGGG
65 GTTTTGCCCTTATGAGG
* * * * *
31216999 TAAAATGATTGTTTTGCCTTTATGGGGTAAAATGACTATTTTGCCCTTATGTGGTAAAGTGAATG
1 TAAAATGACTGTTTTGCCCTTATGGGGTAAAATGATTATTTTGCCCTTATGTGGTAAAATGACTG
31217064 TTTTGCCCTTATGAGG
66 TTTTGCCCTTATGAGG
* * * ** *
31217080 TAAAATGACAGTTTTGCCCTTATGTGGTAAAATGATTGTTTTGCCCTTAACTGATAAAATGACTG
1 TAAAATGACTGTTTTGCCCTTATGGGGTAAAATGATTATTTTGCCCTTATGTGGTAAAATGACTG
31217145 TT
66 TT
31217147 GTACCCCTAT
Statistics
Matches: 126, Mismatches: 21, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
80 1 0.01
81 125 0.99
ACGTcount: A:0.26, C:0.13, G:0.21, T:0.41
Consensus pattern (81 bp):
TAAAATGACTGTTTTGCCCTTATGGGGTAAAATGATTATTTTGCCCTTATGTGGTAAAATGACTG
TTTTGCCCTTATGAGG
Found at i:31217162 original size:27 final size:27
Alignment explanation
Indices: 31216918--31217146 Score: 262
Period size: 27 Copynumber: 8.5 Consensus size: 27
31216908 CCTAAATTGA
* *
31216918 TAAAATGACTATTTTGCCCTTATGGGG
1 TAAAATGACTGTTTTGCCCTTATGTGG
* * *
31216945 TAAAATGATTATTTTTCCCTTATCG-GG
1 TAAAATGACTGTTTTGCCCTTAT-GTGG
* * *
31216972 TAAAATGACTGTTTTTCTCTTATGGGG
1 TAAAATGACTGTTTTGCCCTTATGTGG
* * *
31216999 TAAAATGATTGTTTTGCCTTTATGGGG
1 TAAAATGACTGTTTTGCCCTTATGTGG
*
31217026 TAAAATGACTATTTTGCCCTTATGTGG
1 TAAAATGACTGTTTTGCCCTTATGTGG
* * *
31217053 TAAAGTGAATGTTTTGCCCTTATGAGG
1 TAAAATGACTGTTTTGCCCTTATGTGG
*
31217080 TAAAATGACAGTTTTGCCCTTATGTGG
1 TAAAATGACTGTTTTGCCCTTATGTGG
* ** *
31217107 TAAAATGATTGTTTTGCCCTTAACTGA
1 TAAAATGACTGTTTTGCCCTTATGTGG
31217134 TAAAATGACTGTT
1 TAAAATGACTGTT
31217147 GTACCCCTAT
Statistics
Matches: 173, Mismatches: 27, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
26 1 0.01
27 171 0.99
28 1 0.01
ACGTcount: A:0.26, C:0.13, G:0.21, T:0.41
Consensus pattern (27 bp):
TAAAATGACTGTTTTGCCCTTATGTGG
Found at i:31221098 original size:43 final size:43
Alignment explanation
Indices: 31221035--31221135 Score: 141
Period size: 43 Copynumber: 2.3 Consensus size: 43
31221025 TTCAACGAAC
*
31221035 TCGCACACGTAGTGCTAATTAATTAACTGAAGCTATAATTGTA
1 TCGCACACTTAGTGCTAATTAATTAACTGAAGCTATAATTGTA
* **
31221078 TTGCACACTTAGTG-TCAATTAATTAGTTGAAGCTATAATTGTA
1 TCGCACACTTAGTGCT-AATTAATTAACTGAAGCTATAATTGTA
*
31221121 TCACACACTTAGTGC
1 TCGCACACTTAGTGC
31221136 CATTACATTA
Statistics
Matches: 50, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
42 1 0.02
43 49 0.98
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.35
Consensus pattern (43 bp):
TCGCACACTTAGTGCTAATTAATTAACTGAAGCTATAATTGTA
Found at i:31224916 original size:94 final size:92
Alignment explanation
Indices: 31224751--31225016 Score: 265
Period size: 94 Copynumber: 2.8 Consensus size: 92
31224741 ATATGTGTGC
** ** *
31224751 TAGTGTAAGACATGTCTGGGACATGCATCAGCCTCAAGATATTTAAGCCAGTGTAAGA-CATGTC
1 TAGTGTAAGACATGTCTGGGACATGCATCAGCCTCGCGATA-GAAAGCTAGTGTAAGACCATGTC
*
31224815 TAGGACAT-GCAGT-GGCATTGA-GACTAGAGT
65 TAGGACATGGC-GTCAGC-TTGACG--T-GAGT
* *
31224845 TAGTGTAAGACATGTCTGGGACATGCATCAGCCTCGCGGTAGACATGCTAGTGTAAGACCA-GTC
1 TAGTGTAAGACATGTCTGGGACATGCATCAGCCTCGCGATAGA-AAGCTAGTGTAAGACCATGTC
* *
31224909 T-GAGACATGGCGTCAGCTTGTCGTGTGT
65 TAG-GACATGGCGTCAGCTTGACGTGAGT
* * *
31224937 TAGTGTAAGACCTGTCTGGGACATGGCATCGGCCTCGCTATATGAAAGCTAGTGTAAGACCATGT
1 TAGTGTAAGACATGTCTGGGACAT-GCATCAGCCTCGCGATA-GAAAGCTAGTGTAAGACCATGT
* *
31225002 TTGGGACATGGCGTC
64 CTAGGACATGGCGTC
31225017 GTCATCTTAA
Statistics
Matches: 146, Mismatches: 16, Indels: 20
0.80 0.09 0.11
Matches are distributed among these distances:
92 26 0.18
93 32 0.22
94 80 0.55
95 8 0.05
ACGTcount: A:0.26, C:0.19, G:0.29, T:0.26
Consensus pattern (92 bp):
TAGTGTAAGACATGTCTGGGACATGCATCAGCCTCGCGATAGAAAGCTAGTGTAAGACCATGTCT
AGGACATGGCGTCAGCTTGACGTGAGT
Found at i:31229238 original size:27 final size:27
Alignment explanation
Indices: 31229208--31229378 Score: 141
Period size: 27 Copynumber: 6.3 Consensus size: 27
31229198 ATATTGAGCC
* *
31229208 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAATCAACT
* * *
31229235 CGCACACTTAGTGCCACGTAATCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
* *
31229262 CGCACACTTAGTGCTACATAGTTAGACT
1 CGCACACTTAGTGCTACATAATCA-ACT
** ** *
31229290 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAATCAACT
* **
31229317 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAATCAACT
*
31229344 CGCACACTTAGTGCAACA-AAGTCGAA-T
1 CGCACACTTAGTGCTACATAA-TC-AACT
31229371 CGCACACT
1 CGCACACT
31229379 CTTACCGAGC
Statistics
Matches: 118, Mismatches: 21, Indels: 10
0.79 0.14 0.07
Matches are distributed among these distances:
26 1 0.01
27 93 0.79
28 24 0.20
ACGTcount: A:0.30, C:0.29, G:0.16, T:0.26
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAACT
Found at i:31229301 original size:55 final size:54
Alignment explanation
Indices: 31229208--31229378 Score: 175
Period size: 54 Copynumber: 3.1 Consensus size: 54
31229198 ATATTGAGCC
* * *
31229208 CGCACACTCAGTGCTATATAATCAACTCGCACACTTAGTGCCACGTAATCAAAT
1 CGCACACTTAGTGCTACATAATCAACTCGCACACTTAGTGCCACATAATCAAAT
* * * ** *
31229262 CGCACACTTAGTGCTACATAGTTAGACTCGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAATCA-ACTCGCACACTTAGTGCCACATAATCAAAT
* ** * *
31229317 CGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACA-AAGTCGAAT
1 CGCACACTTAGTGCTA-CATAATCAACTCGCACACTTAGTGCCACATAA-TCAAAT
31229371 CGCACACT
1 CGCACACT
31229379 CTTACCGAGC
Statistics
Matches: 95, Mismatches: 19, Indels: 6
0.79 0.16 0.05
Matches are distributed among these distances:
54 50 0.53
55 45 0.47
ACGTcount: A:0.30, C:0.29, G:0.16, T:0.26
Consensus pattern (54 bp):
CGCACACTTAGTGCTACATAATCAACTCGCACACTTAGTGCCACATAATCAAAT
Found at i:31229549 original size:27 final size:27
Alignment explanation
Indices: 31229519--31229696 Score: 178
Period size: 27 Copynumber: 6.6 Consensus size: 27
31229509 ATATTGAGCC
* * * *
31229519 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* * *
31229546 CGCACACTTAGTGCCACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
31229573 CGCACACTTAGTGCTACATAGTTAGACT
1 CGCACACTTAGTGCTACATAGTCA-AAT
** * *
31229601 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
31229628 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
31229655 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
31229682 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
31229697 GTACAATTTA
Statistics
Matches: 125, Mismatches: 23, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
27 102 0.82
28 23 0.18
ACGTcount: A:0.29, C:0.28, G:0.16, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:31229631 original size:311 final size:311
Alignment explanation
Indices: 31229068--31229689 Score: 1210
Period size: 311 Copynumber: 2.0 Consensus size: 311
31229058 ATAGGTTCAA
31229068 CTTACCGAGCTCAACACCAAGTATACGCATAGCACATATTAGCCATGTACTCAAGACACTTACCC
1 CTTACCGAGCTCAACACCAAGTATACGCATAGCACATATTAGCCATGTACTCAAGACACTTACCC
31229133 GATCCGCTGTCCGCGATCGACTCAATAGTGTCGCACACATAGTGTCCATAATGATTCACGAATGT
66 GATCCGCTGTCCGCGATCGACTCAATAGTGTCGCACACATAGTGTCCATAATGATTCACGAATGT
31229198 ATATTGAGCCCGCACACTCAGTGCTATATAATCAACTCGCACACTTAGTGCCACGTAATCAAATC
131 ATATTGAGCCCGCACACTCAGTGCTATATAATCAACTCGCACACTTAGTGCCACGTAATCAAATC
31229263 GCACACTTAGTGCTACATAGTTAGACTCGCACACTTAGTGCCGCATGGTCAATTCGCACACTTAG
196 GCACACTTAGTGCTACATAGTTAGACTCGCACACTTAGTGCCGCATGGTCAATTCGCACACTTAG
*
31229328 TGCATCATATTCATTTCGCACACTTAGTGCAACAAAGTCGAATCGCACACT
261 TGCATCATATTCATTTCGCACACTTAGTGCAACAAAGTCAAATCGCACACT
31229379 CTTACCGAGCTCAACACCAAGTATACGCATAGCACATATTAGCCATGTACTCAAGACACTTACCC
1 CTTACCGAGCTCAACACCAAGTATACGCATAGCACATATTAGCCATGTACTCAAGACACTTACCC
31229444 GATCCGCTGTCCGCGATC-AGCTCAATAGTGTCGCACACATAGTGTCCATAATGATTCACGAATG
66 GATCCGCTGTCCGCGATCGA-CTCAATAGTGTCGCACACATAGTGTCCATAATGATTCACGAATG
31229508 TATATTGAGCCCGCACACTCAGTGCTATATAATCAACTCGCACACTTAGTGCCACGTAATCAAAT
130 TATATTGAGCCCGCACACTCAGTGCTATATAATCAACTCGCACACTTAGTGCCACGTAATCAAAT
31229573 CGCACACTTAGTGCTACATAGTTAGACTCGCACACTTAGTGCCGCATGGTCAATTCGCACACTTA
195 CGCACACTTAGTGCTACATAGTTAGACTCGCACACTTAGTGCCGCATGGTCAATTCGCACACTTA
*
31229638 GTGCATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCACACT
260 GTGCATCATATTCATTTCGCACACTTAGTGCAACAAAGTCAAATCGCACACT
31229690 TAGTGCTGTA
Statistics
Matches: 308, Mismatches: 2, Indels: 2
0.99 0.01 0.01
Matches are distributed among these distances:
310 1 0.00
311 307 1.00
ACGTcount: A:0.30, C:0.29, G:0.16, T:0.25
Consensus pattern (311 bp):
CTTACCGAGCTCAACACCAAGTATACGCATAGCACATATTAGCCATGTACTCAAGACACTTACCC
GATCCGCTGTCCGCGATCGACTCAATAGTGTCGCACACATAGTGTCCATAATGATTCACGAATGT
ATATTGAGCCCGCACACTCAGTGCTATATAATCAACTCGCACACTTAGTGCCACGTAATCAAATC
GCACACTTAGTGCTACATAGTTAGACTCGCACACTTAGTGCCGCATGGTCAATTCGCACACTTAG
TGCATCATATTCATTTCGCACACTTAGTGCAACAAAGTCAAATCGCACACT
Found at i:31229658 original size:82 final size:81
Alignment explanation
Indices: 31229540--31229695 Score: 215
Period size: 82 Copynumber: 1.9 Consensus size: 81
31229530 TGCTATATAA
* * * *
31229540 TCAACTCGCACACTTAGTGCCACGTAATCAAATCGCACACTTAGTGCTACATAGTTAGACTCGCA
1 TCAACTCGCACACTTAGTGCCACATAATCAAATCGCACACTTAGTGCAACATAGTCA-AATCGCA
31229605 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
31229622 TCAATTCGCACACTTAGTG-CATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCCA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
31229686 CACTTAGTGC
65 CACTTAGTGC
31229696 TGTACAATTT
Statistics
Matches: 65, Mismatches: 8, Indels: 3
0.86 0.11 0.04
Matches are distributed among these distances:
81 18 0.28
82 47 0.72
ACGTcount: A:0.29, C:0.28, G:0.16, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCCACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:31235596 original size:27 final size:27
Alignment explanation
Indices: 31235572--31235651 Score: 97
Period size: 27 Copynumber: 3.0 Consensus size: 27
31235562 CTTCGCCAAG
*
31235572 CCTACTGGCGAACACTAACTTGCCAGA
1 CCTACTAGCGAACACTAACTTGCCAGA
* * * *
31235599 CCAACTATCGAACACTAGCTCGCCAGA
1 CCTACTAGCGAACACTAACTTGCCAGA
* *
31235626 CCTACTAGCGTACACTATCTTGCCAG
1 CCTACTAGCGAACACTAACTTGCCAG
31235652 TCTTGTTGGC
Statistics
Matches: 43, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
27 43 1.00
ACGTcount: A:0.29, C:0.35, G:0.16, T:0.20
Consensus pattern (27 bp):
CCTACTAGCGAACACTAACTTGCCAGA
Found at i:31235672 original size:27 final size:27
Alignment explanation
Indices: 31235617--31235694 Score: 68
Period size: 27 Copynumber: 2.9 Consensus size: 27
31235607 CGAACACTAG
* * * * *
31235617 CTCGCCAGACCTACTAGCGTACACTAT
1 CTCGCCAGATCTGCTGGCGTATACCAT
* *
31235644 CTTGCCAG-TCTTGTTGGCGTATACCAT
1 CTCGCCAGATC-TGCTGGCGTATACCAT
*
31235671 CTCGTCAGATCTGCTGGCGTATAC
1 CTCGCCAGATCTGCTGGCGTATAC
31235695 TAGCTCTGTA
Statistics
Matches: 39, Mismatches: 10, Indels: 4
0.74 0.19 0.08
Matches are distributed among these distances:
26 1 0.03
27 36 0.92
28 2 0.05
ACGTcount: A:0.19, C:0.31, G:0.21, T:0.29
Consensus pattern (27 bp):
CTCGCCAGATCTGCTGGCGTATACCAT
Found at i:31236809 original size:20 final size:20
Alignment explanation
Indices: 31236786--31236823 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
31236776 TAATTTTTGA
31236786 AAAATAA-AAATAAAAATTAG
1 AAAATAATAAA-AAAAATTAG
31236806 AAAATAATAAAAAAAATT
1 AAAATAATAAAAAAAATT
31236824 TCATTGTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 14 0.82
21 3 0.18
ACGTcount: A:0.76, C:0.00, G:0.03, T:0.21
Consensus pattern (20 bp):
AAAATAATAAAAAAAATTAG
Found at i:31236864 original size:22 final size:22
Alignment explanation
Indices: 31236839--31236883 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
31236829 GTTTTTTACT
*
31236839 AAAAAATATTTTC-TAAATTATA
1 AAAAAAT-TTTTCAAAAATTATA
*
31236861 AAAATATTTTTCAAAAATTATA
1 AAAAAATTTTTCAAAAATTATA
31236883 A
1 A
31236884 TAATCCAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 5 0.25
22 15 0.75
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (22 bp):
AAAAAATTTTTCAAAAATTATA
Found at i:31237647 original size:27 final size:27
Alignment explanation
Indices: 31237602--31237654 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 27
31237592 CAGAATTTTT
** *
31237602 CATATTTCCAAAATGTATATCATTTAC
1 CATATTTCCAAAACATATAACATTTAC
*
31237629 CATATTTTCAAAACATATAACATTTA
1 CATATTTCCAAAACATATAACATTTA
31237655 AAAATAAATC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.42, C:0.17, G:0.02, T:0.40
Consensus pattern (27 bp):
CATATTTCCAAAACATATAACATTTAC
Found at i:31243938 original size:6 final size:6
Alignment explanation
Indices: 31243927--31243951 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
31243917 AAGTTCATAA
31243927 TTAACT TTAACT TTAACT TTAACT T
1 TTAACT TTAACT TTAACT TTAACT T
31243952 ACCATAAATG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.32, C:0.16, G:0.00, T:0.52
Consensus pattern (6 bp):
TTAACT
Found at i:31244307 original size:13 final size:13
Alignment explanation
Indices: 31244289--31244331 Score: 52
Period size: 13 Copynumber: 3.3 Consensus size: 13
31244279 TTGTATAATT
31244289 ATTTCATTTAAAC
1 ATTTCATTTAAAC
*
31244302 ATTTCATCTT-ACC
1 ATTTCAT-TTAAAC
*
31244315 ATTTCATTTACAC
1 ATTTCATTTAAAC
31244328 ATTT
1 ATTT
31244332 AACACATAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
12 2 0.08
13 21 0.84
14 2 0.08
ACGTcount: A:0.30, C:0.21, G:0.00, T:0.49
Consensus pattern (13 bp):
ATTTCATTTAAAC
Found at i:31247279 original size:46 final size:46
Alignment explanation
Indices: 31247204--31247378 Score: 178
Period size: 46 Copynumber: 3.8 Consensus size: 46
31247194 TGTAACCCTC
* *
31247204 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGGCGTTCACAT
*
31247250 CCATGAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGG--G-C--GTTCACAT
* * * * *
31247300 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGGCGTTCACAT
* * *
31247343 CCATAAGTGAACTCAGACTCAAATCAACGCGTTCGG
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGG
31247379 ATGCCCAAAT
Statistics
Matches: 107, Mismatches: 13, Indels: 18
0.78 0.09 0.13
Matches are distributed among these distances:
42 2 0.02
43 3 0.03
44 2 0.02
45 2 0.02
46 58 0.54
47 28 0.26
48 3 0.03
49 2 0.02
50 4 0.04
51 3 0.03
ACGTcount: A:0.29, C:0.30, G:0.21, T:0.21
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGGCGTTCACAT
Found at i:31247370 original size:93 final size:93
Alignment explanation
Indices: 31247211--31247383 Score: 274
Period size: 93 Copynumber: 1.9 Consensus size: 93
31247201 CTCCCATAAG
* * * * *
31247211 CGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCACATCCATGAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCACATCCATAAGTGAACTCAGACTCAAATCA
31247276 ACGAGTTCGGATGCCTAGTTACATCTCA
66 ACGAGTTCGGATGCCTAGTTACATCTCA
* *
31247304 CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCAGACTCAAATCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCACATCCATAAGTGAACTCAGACTCAAATCA
*
31247369 ACGCGTTCGGATGCC
66 ACGAGTTCGGATGCC
31247384 CAAATATCCT
Statistics
Matches: 72, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
93 72 1.00
ACGTcount: A:0.28, C:0.30, G:0.21, T:0.21
Consensus pattern (93 bp):
CGAACTCGGACTCAACTCAACGAGCTCGGACATTCACATCCATAAGTGAACTCAGACTCAAATCA
ACGAGTTCGGATGCCTAGTTACATCTCA
Found at i:31251613 original size:14 final size:15
Alignment explanation
Indices: 31251582--31251614 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
31251572 TATTTACTAA
31251582 TTTTCTTATAGAATT
1 TTTTCTTATAGAATT
31251597 TTTTCTTATAGAATT
1 TTTTCTTATAGAATT
31251612 TTT
1 TTT
31251615 GGTCTAGTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.24, C:0.06, G:0.06, T:0.64
Consensus pattern (15 bp):
TTTTCTTATAGAATT
Found at i:31252753 original size:46 final size:46
Alignment explanation
Indices: 31252678--31252852 Score: 196
Period size: 46 Copynumber: 3.8 Consensus size: 46
31252668 TGTAACCCGC
* *
31252678 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGGCGTTCGCAT
* *
31252724 CCATGAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGG--G-C--GTTCGCAT
* * * * *
31252774 -C-TCA-CGAACTCGGACTCAACTCAACAAGTTCGGACATTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGGCGTTCGCAT
31252817 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGG
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGG
31252853 TTGCCCAAAT
Statistics
Matches: 107, Mismatches: 13, Indels: 18
0.78 0.09 0.13
Matches are distributed among these distances:
42 2 0.02
43 3 0.03
44 2 0.02
45 2 0.02
46 60 0.56
47 27 0.25
48 3 0.03
49 2 0.02
50 3 0.03
51 3 0.03
ACGTcount: A:0.29, C:0.30, G:0.21, T:0.21
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGGCGTTCGCAT
Found at i:31252844 original size:93 final size:93
Alignment explanation
Indices: 31252685--31252857 Score: 292
Period size: 93 Copynumber: 1.9 Consensus size: 93
31252675 CGCCCATAAG
* * * *
31252685 CGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATGAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACAAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
31252750 ACGAGTTCGGATGCCTAGTTACATCTCA
66 ACGAGTTCGGATGCCTAGTTACATCTCA
*
31252778 CGAACTCGGACTCAACTCAACAAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACAAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
*
31252843 ACGAGTTCGGTTGCC
66 ACGAGTTCGGATGCC
31252858 CAAATATCCT
Statistics
Matches: 74, Mismatches: 6, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
93 74 1.00
ACGTcount: A:0.27, C:0.30, G:0.21, T:0.21
Consensus pattern (93 bp):
CGAACTCGGACTCAACTCAACAAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
ACGAGTTCGGATGCCTAGTTACATCTCA
Found at i:31252872 original size:46 final size:45
Alignment explanation
Indices: 31252681--31252872 Score: 108
Period size: 46 Copynumber: 4.2 Consensus size: 45
31252671 AACCCGCCCA
* * ** ** **
31252681 TAAGCGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCC
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGTTGCCCATATCC
* * *
31252726 ATGAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGT-TACATC
1 -TAAGTGAACTCGGACTCAACTCAACGAGTTCGGTTGCCCA-TAT-C--C
* * * *
31252775 TCA-CGAACTCGGACTCAACTCAACAAGTTCGGACATT-CGC--ATCC
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGG---TTGCCCATATCC
31252819 ATAAGTGAACTCGGACTCAACTCAACGAGTTCGGTTGCCCAAATATCC
1 -TAAGTGAACTCGGACTCAACTCAACGAGTTCGGTTGCCC--ATATCC
31252867 T-AGTGA
1 TAAGTGA
31252873 CATGTCACTT
Statistics
Matches: 111, Mismatches: 20, Indels: 30
0.69 0.12 0.19
Matches are distributed among these distances:
43 2 0.02
44 3 0.03
45 2 0.02
46 65 0.59
47 30 0.27
48 6 0.05
49 2 0.02
50 1 0.01
ACGTcount: A:0.29, C:0.29, G:0.21, T:0.22
Consensus pattern (45 bp):
TAAGTGAACTCGGACTCAACTCAACGAGTTCGGTTGCCCATATCC
Found at i:31254413 original size:32 final size:32
Alignment explanation
Indices: 31254373--31254435 Score: 126
Period size: 32 Copynumber: 2.0 Consensus size: 32
31254363 CATCTATGTG
31254373 ACTTGATTGATATGAAGATTTTGGTGACTAAA
1 ACTTGATTGATATGAAGATTTTGGTGACTAAA
31254405 ACTTGATTGATATGAAGATTTTGGTGACTAA
1 ACTTGATTGATATGAAGATTTTGGTGACTAA
31254436 CATGTTTGAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.33, C:0.06, G:0.22, T:0.38
Consensus pattern (32 bp):
ACTTGATTGATATGAAGATTTTGGTGACTAAA
Found at i:31262763 original size:48 final size:48
Alignment explanation
Indices: 31262683--31263397 Score: 721
Period size: 48 Copynumber: 14.9 Consensus size: 48
31262673 ACTAAGGTAG
* * *
31262683 TGAGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCAGCCTCGATA
1 TGAGAGCCAGTGTAAGACCATGTTTGGGACATAGCATCAGCCTCGATA
* * * * * * **
31262731 TGTGAGCCAGTATAAGACCATGTTTGGAACATGGCATCAACATTTATA
1 TGAGAGCCAGTGTAAGACCATGTTTGGGACATAGCATCAGCCTCGATA
* * *
31262779 TGAGAGCTAGTGTAAGACCATGTCTGGGACATAGCATCAACCTCGATA
1 TGAGAGCCAGTGTAAGACCATGTTTGGGACATAGCATCAGCCTCGATA
* * * * **
31262827 TGTGAGCCAGTGTAAGACCATGTTTGGAACATAGCATTAGCATTTATA
1 TGAGAGCCAGTGTAAGACCATGTTTGGGACATAGCATCAGCCTCGATA
* * * *
31262875 TGAGAGCTAGTGTAACACCATGTCTGGGACATAGCATCAACCTCGATA
1 TGAGAGCCAGTGTAAGACCATGTTTGGGACATAGCATCAGCCTCGATA
* * * * * **
31262923 TGTGAGCCTGTGTAAGACCATGTTTGGAACATAGCATTAGCATTTATA
1 TGAGAGCCAGTGTAAGACCATGTTTGGGACATAGCATCAGCCTCGATA
* * * *
31262971 TGAGAGCTAGTGTAACACCATGTCTGGGACATAGCATCAACCTCGATA
1 TGAGAGCCAGTGTAAGACCATGTTTGGGACATAGCATCAGCCTCGATA
* * * * * **
31263019 TGTGAGCCTGTGTAAGACCATGTTTGGAACATAGCATTAGCATTTATA
1 TGAGAGCCAGTGTAAGACCATGTTTGGGACATAGCATCAGCCTCGATA
* * * *
31263067 TGAGAGCTAGTGTAACACCATGTCTGGGACATAGCATCAACCTCGATA
1 TGAGAGCCAGTGTAAGACCATGTTTGGGACATAGCATCAGCCTCGATA
* * * * ** **
31263115 TGTGAGCCAGTGTAAGACCATGTTTGGAACATGGCATCGGTATTTATA
1 TGAGAGCCAGTGTAAGACCATGTTTGGGACATAGCATCAGCCTCGATA
* * * *
31263163 TGAGAGCTAGTGTAAGACCATGTTTGGGACATGGCATCGGCCTCGAAA
1 TGAGAGCCAGTGTAAGACCATGTTTGGGACATAGCATCAGCCTCGATA
* * * * ** * **
31263211 TGTGATCCAATGTAAGACCATGTTTGGAACATAGCATTGGCATTTATA
1 TGAGAGCCAGTGTAAGACCATGTTTGGGACATAGCATCAGCCTCGATA
* * * *
31263259 TGAGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCAGCCTCGACA
1 TGAGAGCCAGTGTAAGACCATGTTTGGGACATAGCATCAGCCTCGATA
* *
31263307 TGTGAGCCAGTGTAAGACCATGTTTGGAACATAGCATCAGCAC-CGATATA
1 TGAGAGCCAGTGTAAGACCATGTTTGGGACATAGCATCAGC-CTCG--ATA
* *
31263357 TGAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCAGC
1 TGAGAGCCAGTGTAAGACCATGTTTGGGACATAGCATCAGC
31263398 ATCTTACCCT
Statistics
Matches: 529, Mismatches: 135, Indels: 4
0.79 0.20 0.01
Matches are distributed among these distances:
48 489 0.92
49 1 0.00
50 39 0.07
ACGTcount: A:0.30, C:0.19, G:0.25, T:0.26
Consensus pattern (48 bp):
TGAGAGCCAGTGTAAGACCATGTTTGGGACATAGCATCAGCCTCGATA
Found at i:31262847 original size:96 final size:96
Alignment explanation
Indices: 31262683--31263395 Score: 1129
Period size: 96 Copynumber: 7.4 Consensus size: 96
31262673 ACTAAGGTAG
* * *
31262683 TGAGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCAGCCTCGATATGTGAGCCAGTATAAGA
1 TGAGAGCTAGTGTAAGACCATGTCTGGGACATAGCATCAACCTCGATATGTGAGCCAGTGTAAGA
* * *
31262748 CCATGTTTGGAACATGGCATCAACATTTATA
66 CCATGTTTGGAACATAGCATTAGCATTTATA
31262779 TGAGAGCTAGTGTAAGACCATGTCTGGGACATAGCATCAACCTCGATATGTGAGCCAGTGTAAGA
1 TGAGAGCTAGTGTAAGACCATGTCTGGGACATAGCATCAACCTCGATATGTGAGCCAGTGTAAGA
31262844 CCATGTTTGGAACATAGCATTAGCATTTATA
66 CCATGTTTGGAACATAGCATTAGCATTTATA
* *
31262875 TGAGAGCTAGTGTAACACCATGTCTGGGACATAGCATCAACCTCGATATGTGAGCCTGTGTAAGA
1 TGAGAGCTAGTGTAAGACCATGTCTGGGACATAGCATCAACCTCGATATGTGAGCCAGTGTAAGA
31262940 CCATGTTTGGAACATAGCATTAGCATTTATA
66 CCATGTTTGGAACATAGCATTAGCATTTATA
* *
31262971 TGAGAGCTAGTGTAACACCATGTCTGGGACATAGCATCAACCTCGATATGTGAGCCTGTGTAAGA
1 TGAGAGCTAGTGTAAGACCATGTCTGGGACATAGCATCAACCTCGATATGTGAGCCAGTGTAAGA
31263036 CCATGTTTGGAACATAGCATTAGCATTTATA
66 CCATGTTTGGAACATAGCATTAGCATTTATA
*
31263067 TGAGAGCTAGTGTAACACCATGTCTGGGACATAGCATCAACCTCGATATGTGAGCCAGTGTAAGA
1 TGAGAGCTAGTGTAAGACCATGTCTGGGACATAGCATCAACCTCGATATGTGAGCCAGTGTAAGA
* ** *
31263132 CCATGTTTGGAACATGGCATCGGTATTTATA
66 CCATGTTTGGAACATAGCATTAGCATTTATA
* * ** * * *
31263163 TGAGAGCTAGTGTAAGACCATGTTTGGGACATGGCATCGGCCTCGAAATGTGATCCAATGTAAGA
1 TGAGAGCTAGTGTAAGACCATGTCTGGGACATAGCATCAACCTCGATATGTGAGCCAGTGTAAGA
*
31263228 CCATGTTTGGAACATAGCATTGGCATTTATA
66 CCATGTTTGGAACATAGCATTAGCATTTATA
* * *
31263259 TGAGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCAGCCTCGACATGTGAGCCAGTGTAAGA
1 TGAGAGCTAGTGTAAGACCATGTCTGGGACATAGCATCAACCTCGATATGTGAGCCAGTGTAAGA
* **
31263324 CCATGTTTGGAACATAGCATCAGCACCGATATA
66 CCATGTTTGGAACATAGCATTAGCA--TTTATA
* *
31263357 TGAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCA
1 TGAGAGCTAGTGTAAGACCATGTCTGGGACATAGCATCA
31263396 GCATCTTACC
Statistics
Matches: 581, Mismatches: 34, Indels: 2
0.94 0.06 0.00
Matches are distributed among these distances:
96 539 0.93
98 42 0.07
ACGTcount: A:0.30, C:0.19, G:0.25, T:0.26
Consensus pattern (96 bp):
TGAGAGCTAGTGTAAGACCATGTCTGGGACATAGCATCAACCTCGATATGTGAGCCAGTGTAAGA
CCATGTTTGGAACATAGCATTAGCATTTATA
Found at i:31263874 original size:10 final size:9
Alignment explanation
Indices: 31263846--31263871 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
31263836 ATTCATTTAT
31263846 TTTTAGTTA
1 TTTTAGTTA
31263855 TTTTAGTTA
1 TTTTAGTTA
31263864 TTTTAGTT
1 TTTTAGTT
31263872 TATGTCTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.19, C:0.00, G:0.12, T:0.69
Consensus pattern (9 bp):
TTTTAGTTA
Found at i:31263972 original size:50 final size:53
Alignment explanation
Indices: 31263909--31264025 Score: 172
Period size: 50 Copynumber: 2.3 Consensus size: 53
31263899 TAATAAAGTT
*
31263909 ATGCATTATGTAACT-CTCATGTAAGTT-AAGTTTGCATCA-TAAATTATG-AC
1 ATGCATTATGTAACTCCT-ATGTAAGTTAAAGTTTGCATCATTAAATTAAGTAC
31263959 ATGCATTATGTAACTCCTATGTAAGTTAAAGTTTGCATCATTAAATTAAGTAC
1 ATGCATTATGTAACTCCTATGTAAGTTAAAGTTTGCATCATTAAATTAAGTAC
*
31264012 -TGCATTAAGTAACT
1 ATGCATTATGTAACT
31264026 TATTTGTTCA
Statistics
Matches: 61, Mismatches: 2, Indels: 6
0.88 0.03 0.09
Matches are distributed among these distances:
50 24 0.39
51 14 0.23
52 21 0.34
53 2 0.03
ACGTcount: A:0.35, C:0.14, G:0.14, T:0.38
Consensus pattern (53 bp):
ATGCATTATGTAACTCCTATGTAAGTTAAAGTTTGCATCATTAAATTAAGTAC
Found at i:31266493 original size:6 final size:6
Alignment explanation
Indices: 31266484--31266542 Score: 57
Period size: 6 Copynumber: 9.3 Consensus size: 6
31266474 AAAAGCATGT
* *
31266484 GAAAAA GAAAAA GAAATA GAAAAA GAAAAAA GGAATGAAA G-AAAA CAAAAA
1 GAAAAA GAAAAA GAAAAA GAAAAA G-AAAAA -GAA--AAA GAAAAA GAAAAA
31266535 GAAAAA GA
1 GAAAAA GA
31266543 GAATGAAAGA
Statistics
Matches: 44, Mismatches: 4, Indels: 10
0.76 0.07 0.17
Matches are distributed among these distances:
5 3 0.07
6 28 0.64
7 8 0.18
8 2 0.05
9 3 0.07
ACGTcount: A:0.76, C:0.02, G:0.19, T:0.03
Consensus pattern (6 bp):
GAAAAA
Found at i:31266540 original size:27 final size:28
Alignment explanation
Indices: 31266493--31266563 Score: 101
Period size: 27 Copynumber: 2.6 Consensus size: 28
31266483 TGAAAAAGAA
*
31266493 AAAGAAATAGAAAAAGAAAAAAG-GAATG
1 AAAGAAA-ACAAAAAGAAAAAAGAGAATG
31266521 AAAGAAAACAAAAAG-AAAAAGAGAATG
1 AAAGAAAACAAAAAGAAAAAAGAGAATG
*
31266548 AAAGAGAACAAAAAGA
1 AAAGAAAACAAAAAGA
31266564 GATTGAGAGC
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
26 6 0.15
27 26 0.67
28 7 0.18
ACGTcount: A:0.73, C:0.03, G:0.20, T:0.04
Consensus pattern (28 bp):
AAAGAAAACAAAAAGAAAAAAGAGAATG
Found at i:31266581 original size:21 final size:21
Alignment explanation
Indices: 31266536--31266581 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
31266526 AAACAAAAAG
*
31266536 AAAAAGAGAATGAAAGAGAAC
1 AAAAAGAGAATGAAAGAGAAA
* * *
31266557 AAAAAGAGATTGAGAGCGAAA
1 AAAAAGAGAATGAAAGAGAAA
31266578 AAAA
1 AAAA
31266582 TGTGAGAAAG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.65, C:0.04, G:0.24, T:0.07
Consensus pattern (21 bp):
AAAAAGAGAATGAAAGAGAAA
Found at i:31266905 original size:13 final size:13
Alignment explanation
Indices: 31266887--31266913 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
31266877 AAGCAAGGTA
31266887 AGGGTTTCATGTT
1 AGGGTTTCATGTT
31266900 AGGGTTTCATGTT
1 AGGGTTTCATGTT
31266913 A
1 A
31266914 TCTGAGTCTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.19, C:0.07, G:0.30, T:0.44
Consensus pattern (13 bp):
AGGGTTTCATGTT
Found at i:31268341 original size:52 final size:51
Alignment explanation
Indices: 31268212--31268343 Score: 176
Period size: 50 Copynumber: 2.6 Consensus size: 51
31268202 ATGTGTTCTG
* * *
31268212 CATTTAATAAAGTCATGCATTATGTAACTCTCATATAAGTTAAGTTTGCAT
1 CATTAAATTAAGTCATGCATTATGTAACTCCCATATAAGTTAAGTTTGCAT
* * * *
31268263 CA-TAAATTATGACATGCATTATGTAACTCCCATGTTAGTTAAAGTTTGCAT
1 CATTAAATTAAGTCATGCATTATGTAACTCCCATATAAGTT-AAGTTTGCAT
*
31268314 CATTAAATTAAGTCATGCATTAAGTAACTC
1 CATTAAATTAAGTCATGCATTATGTAACTC
31268344 ATTTGTTCAT
Statistics
Matches: 69, Mismatches: 10, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
50 31 0.45
51 14 0.20
52 24 0.35
ACGTcount: A:0.36, C:0.15, G:0.12, T:0.37
Consensus pattern (51 bp):
CATTAAATTAAGTCATGCATTATGTAACTCCCATATAAGTTAAGTTTGCAT
Found at i:31268985 original size:12 final size:12
Alignment explanation
Indices: 31268968--31268996 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
31268958 AAAGGTCACA
31268968 AATAGGCATTTG
1 AATAGGCATTTG
31268980 AATAGGCATTTG
1 AATAGGCATTTG
31268992 AATAG
1 AATAG
31268997 TCATAATAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.38, C:0.07, G:0.24, T:0.31
Consensus pattern (12 bp):
AATAGGCATTTG
Found at i:31270504 original size:21 final size:20
Alignment explanation
Indices: 31270480--31270518 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
31270470 GTTAAGAGGA
31270480 CACACGAGCATGTCGCCCTTC
1 CACACGAGCATGT-GCCCTTC
* *
31270501 CACATGAGCGTGTGCCCT
1 CACACGAGCATGTGCCCT
31270519 CGGTTGCATT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 5 0.31
21 11 0.69
ACGTcount: A:0.18, C:0.38, G:0.23, T:0.21
Consensus pattern (20 bp):
CACACGAGCATGTGCCCTTC
Found at i:31272647 original size:50 final size:50
Alignment explanation
Indices: 31272582--31272875 Score: 297
Period size: 50 Copynumber: 5.8 Consensus size: 50
31272572 ACCGAAGCTC
* * * * * *
31272582 TCTGGTACGCATAGTAGCCTGCACTTAGTTCTACACATGCGACCCAACAA
1 TCTGGTACACGTAGTAGCCTACACTTAGTACTACACATGTGACCTAACAA
* * *
31272632 TCTGGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGACCTAACCA
1 TCTGGTACACGTAGTAGCCTACACTTAGTACTACACATGTGACCTAACAA
* * * * *
31272682 T-TGGATACACGTAGTAGCCTACACTTACTACTACACACGTGATCAAAGCTA
1 TCTGG-TACACGTAGTAGCCTACACTTAGTACTACACATGTGACCTAA-CAA
* * * *
31272733 TCGGGTACGCATAGTAGCCTACACTTAGTA-TAACACATGCGACCTAACAA
1 TCTGGTACACGTAGTAGCCTACACTTAGTACT-ACACATGTGACCTAACAA
*
31272783 TCTGGTACACGTAGTAGCCTACACTTAGTACTACACATGTGACCTGA-AA
1 TCTGGTACACGTAGTAGCCTACACTTAGTACTACACATGTGACCTAACAA
** * * *
31272832 TCGTCTTAAACACATAGTAGCCTGCACATAGTACTACACATGTG
1 TC-TGGT--ACACGTAGTAGCCTACACTTAGTACTACACATGTG
31272876 TTCTCACAAC
Statistics
Matches: 205, Mismatches: 31, Indels: 14
0.82 0.12 0.06
Matches are distributed among these distances:
49 7 0.03
50 127 0.62
51 37 0.18
52 34 0.17
ACGTcount: A:0.31, C:0.27, G:0.17, T:0.25
Consensus pattern (50 bp):
TCTGGTACACGTAGTAGCCTACACTTAGTACTACACATGTGACCTAACAA
Found at i:31272769 original size:101 final size:101
Alignment explanation
Indices: 31272643--31272824 Score: 278
Period size: 101 Copynumber: 1.8 Consensus size: 101
31272633 CTGGTACACG
* * *
31272643 TAGTAGCCTGCACTTAGTACTACACACGTGACCTAACCAT-TGGATACACGTAGTAGCCTACACT
1 TAGTAGCCTACACTTAGTACTACACACGCGACCTAACAATCTGG-TACACGTAGTAGCCTACACT
31272707 TACTACTACACACGTGATCAAAGCTATCGGGTACGCA
65 TACTACTACACACGTGATCAAAGCTATCGGGTACGCA
*
31272744 TAGTAGCCTACACTTAGTA-TAACACATGCGACCTAACAATCTGGTACACGTAGTAGCCTACACT
1 TAGTAGCCTACACTTAGTACT-ACACACGCGACCTAACAATCTGGTACACGTAGTAGCCTACACT
* *
31272808 TAGTACTACACATGTGA
65 TACTACTACACACGTGA
31272825 CCTGAAATCG
Statistics
Matches: 73, Mismatches: 6, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
100 1 0.01
101 69 0.95
102 3 0.04
ACGTcount: A:0.32, C:0.26, G:0.17, T:0.25
Consensus pattern (101 bp):
TAGTAGCCTACACTTAGTACTACACACGCGACCTAACAATCTGGTACACGTAGTAGCCTACACTT
ACTACTACACACGTGATCAAAGCTATCGGGTACGCA
Found at i:31279731 original size:50 final size:50
Alignment explanation
Indices: 31279637--31279924 Score: 242
Period size: 50 Copynumber: 5.7 Consensus size: 50
31279627 ACCAAAGCTC
* * * **
31279637 TCTGGTACACATA-TAGCCTGCACTTAGTATTAAACAAGCAACCTAACAA
1 TCTGGTACACATAGTAGCCTGCACTTAGTACTACACACGTGACCTAACAA
* * * *
31279686 TCTTGTACACGTAGTAGCCTGCACTTAGTACTACACATGTGACCTAACCA
1 TCTGGTACACATAGTAGCCTGCACTTAGTACTACACACGTGACCTAACAA
* * ** * * * * * *
31279736 TCAGATACATGTAGTAGCCTACGCTTACTACTACACACGTGATCGAAGCTA
1 TCTGGTACACATAGTAGCCTGCACTTAGTACTACACACGTGACCTAA-CAA
** * *
31279787 TC-GGATATGCATAGTAGCCTGCACTTAGTACTACACATGCGACCTAACAA
1 TCTGG-TACACATAGTAGCCTGCACTTAGTACTACACACGTGACCTAACAA
*
31279837 TCTGGTACACGA-ATTAGCCTGCACTTAGTACTACACACGTGACCTAA-AA
1 TCTGGTACAC-ATAGTAGCCTGCACTTAGTACTACACACGTGACCTAACAA
** * *
31279886 TCGTCTTAAACACATAGTAGCCTACACATAGTACTACAC
1 TC-TGGT--ACACATAGTAGCCTGCACTTAGTACTACAC
31279925 GTGTTCTCAC
Statistics
Matches: 188, Mismatches: 42, Indels: 15
0.77 0.17 0.06
Matches are distributed among these distances:
49 15 0.08
50 109 0.58
51 39 0.21
52 25 0.13
ACGTcount: A:0.33, C:0.26, G:0.15, T:0.25
Consensus pattern (50 bp):
TCTGGTACACATAGTAGCCTGCACTTAGTACTACACACGTGACCTAACAA
Found at i:31279872 original size:101 final size:101
Alignment explanation
Indices: 31279697--31279878 Score: 274
Period size: 101 Copynumber: 1.8 Consensus size: 101
31279687 CTTGTACACG
* * * * *
31279697 TAGTAGCCTGCACTTAGTACTACACATGTGACCTAACCATCAGATACATGTAGTAGCCTACGCTT
1 TAGTAGCCTGCACTTAGTACTACACATGCGACCTAACAATCAGATACACGAAGTAGCCTACACTT
31279762 ACTACTACACACGTGATCGAAGCTATCGGATATGCA
66 ACTACTACACACGTGATCGAAGCTATCGGATATGCA
* * * *
31279798 TAGTAGCCTGCACTTAGTACTACACATGCGACCTAACAATCTGGTACACGAATTAGCCTGCACTT
1 TAGTAGCCTGCACTTAGTACTACACATGCGACCTAACAATCAGATACACGAAGTAGCCTACACTT
*
31279863 AGTACTACACACGTGA
66 ACTACTACACACGTGA
31279879 CCTAAAATCG
Statistics
Matches: 71, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
101 71 1.00
ACGTcount: A:0.31, C:0.26, G:0.18, T:0.25
Consensus pattern (101 bp):
TAGTAGCCTGCACTTAGTACTACACATGCGACCTAACAATCAGATACACGAAGTAGCCTACACTT
ACTACTACACACGTGATCGAAGCTATCGGATATGCA
Found at i:31279925 original size:151 final size:149
Alignment explanation
Indices: 31279646--31279927 Score: 359
Period size: 151 Copynumber: 1.9 Consensus size: 149
31279636 CTCTGGTACA
* * *
31279646 CATATAGCCTGCACTTAGTATTAAACAAGCAACCTAACAATCTTGTACACGTAGTAGCCTGCACT
1 CATATAGCCTGCACTTAGTACTAAACAAGCAACCTAACAATCTGGTACACGAAGTAGCCTGCACT
* * ** * *
31279711 TAGTACTACACATGTGACCTAACCATCAGATACATGTAGTAGCCTACGCTTACTACTACACACGT
66 TAGTACTACACACGTGACCTAACCATCAGAAACACATAGTAGCCTACACATACTACTA-ACACGT
31279776 GATCGAAGCTATCGGATATG
130 GATCGAAGCTATCGGATATG
* * * *
31279796 CATAGTAGCCTGCACTTAGTACTACACATGCGACCTAACAATCTGGTACACGAATTAGCCTGCAC
1 CATA-TAGCCTGCACTTAGTACTAAACAAGCAACCTAACAATCTGGTACACGAAGTAGCCTGCAC
* * ** *
31279861 TTAGTACTACACACGTGACCTAAAATCGTCTTAAACACATAGTAGCCTACACATAGTACT-ACAC
65 TTAGTACTACACACGTGACCT--AACCATCAGAAACACATAGTAGCCTACACATACTACTAACAC
31279925 GTG
128 GTG
31279928 TTCTCACAAC
Statistics
Matches: 111, Mismatches: 18, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
150 4 0.04
151 80 0.72
153 27 0.24
ACGTcount: A:0.33, C:0.26, G:0.16, T:0.25
Consensus pattern (149 bp):
CATATAGCCTGCACTTAGTACTAAACAAGCAACCTAACAATCTGGTACACGAAGTAGCCTGCACT
TAGTACTACACACGTGACCTAACCATCAGAAACACATAGTAGCCTACACATACTACTAACACGTG
ATCGAAGCTATCGGATATG
Found at i:31282863 original size:27 final size:25
Alignment explanation
Indices: 31282802--31282896 Score: 79
Period size: 26 Copynumber: 3.7 Consensus size: 25
31282792 CATAAATGTG
31282802 CCACAAAGGCTTTCATTTT-ATATTT
1 CCACAAAGGCTTTC-TTTTCATATTT
* *
31282827 CCACAGAGGCTTTCTTTTCATGGTTT
1 CCACAAAGGCTTTCTTTTCAT-ATTT
*
31282853 GGCACAAAGGCTTT-TTTTCAT-TTT
1 -CCACAAAGGCTTTCTTTTCATATTT
*
31282877 AAACCACAAATGCTTTCTTT
1 ---CCACAAAGGCTTTCTTT
31282897 ATCTGTTGTG
Statistics
Matches: 57, Mismatches: 7, Indels: 10
0.77 0.09 0.14
Matches are distributed among these distances:
24 7 0.12
25 15 0.26
26 21 0.37
27 14 0.25
ACGTcount: A:0.24, C:0.21, G:0.13, T:0.42
Consensus pattern (25 bp):
CCACAAAGGCTTTCTTTTCATATTT
Found at i:31288236 original size:41 final size:41
Alignment explanation
Indices: 31288179--31288342 Score: 328
Period size: 41 Copynumber: 4.0 Consensus size: 41
31288169 TTCTTGTATG
31288179 ACTTTAGATTTTTGGCAAGTCCAGTGAGAATCATTTTCATT
1 ACTTTAGATTTTTGGCAAGTCCAGTGAGAATCATTTTCATT
31288220 ACTTTAGATTTTTGGCAAGTCCAGTGAGAATCATTTTCATT
1 ACTTTAGATTTTTGGCAAGTCCAGTGAGAATCATTTTCATT
31288261 ACTTTAGATTTTTGGCAAGTCCAGTGAGAATCATTTTCATT
1 ACTTTAGATTTTTGGCAAGTCCAGTGAGAATCATTTTCATT
31288302 ACTTTAGATTTTTGGCAAGTCCAGTGAGAATCATTTTCATT
1 ACTTTAGATTTTTGGCAAGTCCAGTGAGAATCATTTTCATT
31288343 CTGCAAACAA
Statistics
Matches: 123, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 123 1.00
ACGTcount: A:0.27, C:0.15, G:0.17, T:0.41
Consensus pattern (41 bp):
ACTTTAGATTTTTGGCAAGTCCAGTGAGAATCATTTTCATT
Found at i:31292027 original size:24 final size:24
Alignment explanation
Indices: 31291982--31292027 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
31291972 TACTAATAGT
* * *
31291982 TTAAATATTGAATTATATTTTATA
1 TTAAATATTAAATTAAAATTTATA
31292006 TTAAATATTAAATTAAAATTTA
1 TTAAATATTAAATTAAAATTTA
31292028 ATTGTAATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (24 bp):
TTAAATATTAAATTAAAATTTATA
Found at i:31296862 original size:33 final size:34
Alignment explanation
Indices: 31296820--31296883 Score: 103
Period size: 33 Copynumber: 1.9 Consensus size: 34
31296810 GCATGTTGTA
* *
31296820 ACAGTCTGGGCTTGAGCCCTATTCAG-AATCAGT
1 ACAGTCTGGGCCTGAGCCCTATACAGTAATCAGT
31296853 ACAGTCTGGGCCTGAGCCCTATACAGTAATC
1 ACAGTCTGGGCCTGAGCCCTATACAGTAATC
31296884 GTGTGGCCTA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
33 24 0.86
34 4 0.14
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25
Consensus pattern (34 bp):
ACAGTCTGGGCCTGAGCCCTATACAGTAATCAGT
Found at i:31296879 original size:27 final size:29
Alignment explanation
Indices: 31296849--31296912 Score: 73
Period size: 27 Copynumber: 2.3 Consensus size: 29
31296839 TATTCAGAAT
* *
31296849 CAGTACAGTC-TG-GGCCTGAGCCCTATA
1 CAGTACAGTCGTGTGGCCTAAGCCCAATA
31296876 CAGTA-A-TCGTGTGGCCTAAGCCCAATA
1 CAGTACAGTCGTGTGGCCTAAGCCCAATA
31296903 CAGTATCAGT
1 CAGTA-CAGT
31296913 ACAGTGTAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
25 2 0.07
26 3 0.10
27 23 0.77
29 1 0.03
30 1 0.03
ACGTcount: A:0.27, C:0.27, G:0.23, T:0.23
Consensus pattern (29 bp):
CAGTACAGTCGTGTGGCCTAAGCCCAATA
Found at i:31297102 original size:27 final size:27
Alignment explanation
Indices: 31297072--31297149 Score: 102
Period size: 27 Copynumber: 2.9 Consensus size: 27
31297062 GCTAGAAATT
* *
31297072 GTAAATGTGGCAAAGCCACCAGTATCA
1 GTAAATGTGGCATAGCCACCAGTAACA
*
31297099 GTAATTGTGGCATAGCCACCAGTAACA
1 GTAAATGTGGCATAGCCACCAGTAACA
* * *
31297126 GTGAATGTGACATAGTCACCAGTA
1 GTAAATGTGGCATAGCCACCAGTA
31297150 CTTCCTCCAT
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 44 1.00
ACGTcount: A:0.35, C:0.21, G:0.23, T:0.22
Consensus pattern (27 bp):
GTAAATGTGGCATAGCCACCAGTAACA
Found at i:31297316 original size:27 final size:27
Alignment explanation
Indices: 31297286--31297448 Score: 143
Period size: 27 Copynumber: 6.1 Consensus size: 27
31297276 GGCATAATCA
* *
31297286 TCATTTTACCATACAAGGGTATTACGG
1 TCATTTTACCCTACAAGGGCATTACGG
* * * *
31297313 TCATTTTACCTTACAGGGGTATTA-TG
1 TCATTTTACCCTACAAGGGCATTACGG
* *** * *
31297339 -AATTTTACCCTTTTAGGGTATTACAG
1 TCATTTTACCCTACAAGGGCATTACGG
*
31297365 TCATTTTACCCTACAGGGGCATTACGG
1 TCATTTTACCCTACAAGGGCATTACGG
* * * *
31297392 TCATTTAACCCTATAGGGGCATTACGC
1 TCATTTTACCCTACAAGGGCATTACGG
31297419 TCATTTTACCCTA-AAGGGGCATTACGG
1 TCATTTTACCCTACAA-GGGCATTACGG
31297446 TCA
1 TCA
31297449 AATAACGACC
Statistics
Matches: 110, Mismatches: 23, Indels: 6
0.79 0.17 0.04
Matches are distributed among these distances:
25 17 0.15
26 3 0.03
27 90 0.82
ACGTcount: A:0.26, C:0.21, G:0.19, T:0.34
Consensus pattern (27 bp):
TCATTTTACCCTACAAGGGCATTACGG
Found at i:31297426 original size:54 final size:53
Alignment explanation
Indices: 31297301--31297448 Score: 158
Period size: 54 Copynumber: 2.8 Consensus size: 53
31297291 TTACCATACA
* * * * * * *
31297301 AGGGTATTACGGTCATTTTACCTTACAGGGGTATTA-TG-AATTTTACCCTTTT
1 AGGGCATTAC-GTCATTTTACCCTACAGGGGCATTACGGTCATTTAACCCTTAT
*
31297353 AGGGTATTACAGTCATTTTACCCTACAGGGGCATTACGGTCATTTAACCC-TAT
1 AGGGCATTAC-GTCATTTTACCCTACAGGGGCATTACGGTCATTTAACCCTTAT
*
31297406 AGGGGCATTACGCTCATTTTACCCTAAAGGGGCATTACGGTCA
1 A-GGGCATTACG-TCATTTTACCCTACAGGGGCATTACGGTCA
31297449 AATAACGACC
Statistics
Matches: 83, Mismatches: 9, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
52 33 0.40
53 5 0.06
54 45 0.54
ACGTcount: A:0.25, C:0.20, G:0.21, T:0.34
Consensus pattern (53 bp):
AGGGCATTACGTCATTTTACCCTACAGGGGCATTACGGTCATTTAACCCTTAT
Done.