Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr12 ID=Chr12-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 35429946
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 509281 characters in sequence are not A, C, G, or T
File 1 of 120
Found at i:5072 original size:31 final size:31
Alignment explanation
Indices: 5037--5114 Score: 95
Period size: 30 Copynumber: 2.5 Consensus size: 31
5027 CAAACCCTAG
5037 ATCCCAAGCCGGGATATACCTACAATAAGAT
1 ATCCCAAGCCGGGATATACCTACAATAAGAT
** * * *
5068 ATCCCAAGCCGGGAT-GCCCTAGAGTAGGAT
1 ATCCCAAGCCGGGATATACCTACAATAAGAT
*
5098 ATCTCAAGCCGGGATAT
1 ATCCCAAGCCGGGATAT
5115 TCCTGGAATG
Statistics
Matches: 39, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
30 24 0.62
31 15 0.38
ACGTcount: A:0.32, C:0.26, G:0.23, T:0.19
Consensus pattern (31 bp):
ATCCCAAGCCGGGATATACCTACAATAAGAT
Found at i:20619 original size:5 final size:5
Alignment explanation
Indices: 20598--20632 Score: 56
Period size: 5 Copynumber: 7.4 Consensus size: 5
20588 GTAAAATGGT
20598 AATT- AATTA AA-TA AATTA AATTA AATTA AATTA AA
1 AATTA AATTA AATTA AATTA AATTA AATTA AATTA AA
20633 CCAAAATATT
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
4 8 0.28
5 21 0.72
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (5 bp):
AATTA
Found at i:27899 original size:16 final size:18
Alignment explanation
Indices: 27862--27899 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
27852 TTTCGGAATT
*
27862 TTCAAGATTTTTTTATAC
1 TTCAAGATTTTTTAATAC
27880 TTCAA-ATTTTTTAATA-
1 TTCAAGATTTTTTAATAC
27896 TTCA
1 TTCA
27900 TTTTAAAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 4 0.21
17 10 0.53
18 5 0.26
ACGTcount: A:0.32, C:0.11, G:0.03, T:0.55
Consensus pattern (18 bp):
TTCAAGATTTTTTAATAC
Found at i:54881 original size:30 final size:29
Alignment explanation
Indices: 54802--54940 Score: 136
Period size: 30 Copynumber: 4.7 Consensus size: 29
54792 AGCCGAAGCT
* * *
54802 ATCCCTTTTCATATTTTAATGGTTGTCA-C
1 ATCCCTTTTCATA-TTTGATAGTCGTCACC
*
54831 ATCCCTTTTCATAGTTGATAGTCGTCACC
1 ATCCCTTTTCATATTTGATAGTCGTCACC
* ** *
54860 ATCCCTTTTCATGATTTGATAGCCGAAACT
1 ATCCCTTTTCAT-ATTTGATAGTCGTCACC
* *
54890 ATCCCTTTTCATAGTTCGATGGTCGTCACC
1 ATCCCTTTTCATA-TTTGATAGTCGTCACC
*
54920 ATCCATTTTCATAATTTGATA
1 ATCCCTTTTCAT-ATTTGATA
54941 TCCCAAGCTA
Statistics
Matches: 88, Mismatches: 18, Indels: 7
0.78 0.16 0.06
Matches are distributed among these distances:
28 10 0.11
29 27 0.31
30 50 0.57
31 1 0.01
ACGTcount: A:0.23, C:0.24, G:0.12, T:0.41
Consensus pattern (29 bp):
ATCCCTTTTCATATTTGATAGTCGTCACC
Found at i:54918 original size:88 final size:89
Alignment explanation
Indices: 54766--54932 Score: 237
Period size: 88 Copynumber: 1.9 Consensus size: 89
54756 CACGATGGTT
* * * * *
54766 GTCACCATTCCTTCTCATAATTCGATAGCCGAAGCTATCCCTTTTCATATTTTAATGGTTGTCA-
1 GTCACCATCCCTTCTCATAATTCGATAGCCGAAACTATCCCTTTTCATAGTTCAATGGTCGTCAC
*
54830 CATCCCTTTTCATAGTTGATAGTC
66 CATCCATTTTCATAGTTGATAGTC
* * * *
54854 GTCACCATCCCTTTTCATGATTTGATAGCCGAAACTATCCCTTTTCATAGTTCGATGGTCGTCAC
1 GTCACCATCCCTTCTCATAATTCGATAGCCGAAACTATCCCTTTTCATAGTTCAATGGTCGTCAC
54919 CATCCATTTTCATA
66 CATCCATTTTCATA
54933 ATTTGATATC
Statistics
Matches: 68, Mismatches: 10, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
88 55 0.81
89 13 0.19
ACGTcount: A:0.23, C:0.26, G:0.13, T:0.38
Consensus pattern (89 bp):
GTCACCATCCCTTCTCATAATTCGATAGCCGAAACTATCCCTTTTCATAGTTCAATGGTCGTCAC
CATCCATTTTCATAGTTGATAGTC
Found at i:54929 original size:60 final size:59
Alignment explanation
Indices: 54831--54958 Score: 184
Period size: 60 Copynumber: 2.2 Consensus size: 59
54821 TGGTTGTCAC
* * *
54831 ATCCCTTTTCATAGTTGATAGTCGTCACCATCCCTTTTCATGATTTGATAGCCGAAACT
1 ATCCCTTTTCATAGTTGATAGTCGTCACCATCCATTTTCATAATTTGATAGCCCAAACT
* * *
54890 ATCCCTTTTCATAGTTCGATGGTCGTCACCATCCATTTTCATAATTTGATATCCCAAGCT
1 ATCCCTTTTCATAGTT-GATAGTCGTCACCATCCATTTTCATAATTTGATAGCCCAAACT
*
54950 ATCTCTTTT
1 ATCCCTTTT
54959 TACAAGTTGA
Statistics
Matches: 61, Mismatches: 7, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
59 16 0.26
60 45 0.74
ACGTcount: A:0.23, C:0.26, G:0.12, T:0.40
Consensus pattern (59 bp):
ATCCCTTTTCATAGTTGATAGTCGTCACCATCCATTTTCATAATTTGATAGCCCAAACT
Found at i:54981 original size:30 final size:30
Alignment explanation
Indices: 54860--55047 Score: 173
Period size: 30 Copynumber: 6.3 Consensus size: 30
54850 AGTCGTCACC
* * *
54860 ATCCCTTTTCATGATTTGATAGCCGAAACT
1 ATCCCTTTTTATAATTTGATAGCCGAAGCT
* * * * * * *
54890 ATCCCTTTTCATAGTTCGATGGTCGTCA-CC
1 ATCCCTTTTTATAATTTGATAGCCG-AAGCT
* * * *
54920 ATCCATTTTCATAATTTGATATCCCAAGCT
1 ATCCCTTTTTATAATTTGATAGCCGAAGCT
* * * * *
54950 ATCTCTTTTTACAAGTTGACAGCTGAAGCT
1 ATCCCTTTTTATAATTTGATAGCCGAAGCT
54980 ATCCCTTTTTATAATTTGATAGCCGAAGCT
1 ATCCCTTTTTATAATTTGATAGCCGAAGCT
55010 AT-CCTTTTTCATAATTTGATAGCCGAAGCT
1 ATCCCTTTTT-ATAATTTGATAGCCGAAGCT
55040 ATCCCTTT
1 ATCCCTTT
55048 CCATTGGTCG
Statistics
Matches: 124, Mismatches: 30, Indels: 7
0.77 0.19 0.04
Matches are distributed among these distances:
29 8 0.06
30 110 0.89
31 6 0.05
ACGTcount: A:0.25, C:0.23, G:0.13, T:0.39
Consensus pattern (30 bp):
ATCCCTTTTTATAATTTGATAGCCGAAGCT
Found at i:56918 original size:178 final size:178
Alignment explanation
Indices: 56616--56967 Score: 614
Period size: 178 Copynumber: 2.0 Consensus size: 178
56606 ATTCTTAGGT
* * * *
56616 CTTATTTAGCCTTTTATCGTGAGAATTAAACTTCTTTTTATAAACATGCATGAAGGTTTAAGTTC
1 CTTATTTAGCCTTTTACCATGAAAATTAAACTTCTTTTTATAAACATGCATGAAGATTTAAGTTC
* ** * *
56681 TTAGATTTGACTTAGTAACTTTTTTGAGGCGAAATCTTAGGAGGCATAAGAATCTAAACATGATT
66 TTAGAATCAACTTAGTAACTTTCTTGAGGCGAAATCTTAGGAGGCATAAGAACCTAAACATGATT
56746 TAGGCACATTTTATTTGGACCATTTGAGCCTTTCAAGCCTACCCTAAG
131 TAGGCACATTTTATTTGGACCATTTGAGCCTTTCAAGCCTACCCTAAG
56794 CTTATTTAGCCTTTTACCATGAAAATTAAACTTCTTTTTATAAACATGCATGAAGATTTAAGTTC
1 CTTATTTAGCCTTTTACCATGAAAATTAAACTTCTTTTTATAAACATGCATGAAGATTTAAGTTC
56859 TTAGAATCAACTTAGTAACTTTCTTGAGGCGAAATCTTAGGAGGCATAAGAACCTAAACATGATT
66 TTAGAATCAACTTAGTAACTTTCTTGAGGCGAAATCTTAGGAGGCATAAGAACCTAAACATGATT
*
56924 TAGGCACATTTTATTTGGATCATTTGAGCCTTTCAAGCCTACCC
131 TAGGCACATTTTATTTGGACCATTTGAGCCTTTCAAGCCTACCC
56968 CATATAAATT
Statistics
Matches: 164, Mismatches: 10, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
178 164 1.00
ACGTcount: A:0.31, C:0.17, G:0.16, T:0.37
Consensus pattern (178 bp):
CTTATTTAGCCTTTTACCATGAAAATTAAACTTCTTTTTATAAACATGCATGAAGATTTAAGTTC
TTAGAATCAACTTAGTAACTTTCTTGAGGCGAAATCTTAGGAGGCATAAGAACCTAAACATGATT
TAGGCACATTTTATTTGGACCATTTGAGCCTTTCAAGCCTACCCTAAG
Found at i:60835 original size:15 final size:15
Alignment explanation
Indices: 60815--60844 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
60805 TTAAATGTAT
60815 TCATTAACAATTTCA
1 TCATTAACAATTTCA
60830 TCATTAACAATTTCA
1 TCATTAACAATTTCA
60845 CGTGGGTTGC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.40, C:0.20, G:0.00, T:0.40
Consensus pattern (15 bp):
TCATTAACAATTTCA
Found at i:67022 original size:19 final size:19
Alignment explanation
Indices: 66985--67024 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
66975 CTTTAAATCA
* * *
66985 AATTTAACTCCTTATTTTC
1 AATTAAACTCCTAAATTTC
67004 AATTAAACTCCTAAATTTC
1 AATTAAACTCCTAAATTTC
67023 AA
1 AA
67025 AATTTTCACA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.38, C:0.20, G:0.00, T:0.42
Consensus pattern (19 bp):
AATTAAACTCCTAAATTTC
Found at i:67325 original size:19 final size:20
Alignment explanation
Indices: 67298--67335 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
67288 TAGCCATGCG
67298 TTCTCTCATTT-CTTTCTTT
1 TTCTCTCATTTCCTTTCTTT
*
67317 TTCTTTCATTTCCTTTCTT
1 TTCTCTCATTTCCTTTCTT
67336 AGTTTGCATG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.05, C:0.26, G:0.00, T:0.68
Consensus pattern (20 bp):
TTCTCTCATTTCCTTTCTTT
Found at i:67476 original size:2 final size:2
Alignment explanation
Indices: 67456--67496 Score: 57
Period size: 2 Copynumber: 21.0 Consensus size: 2
67446 TAATGAAAAC
* *
67456 AT AT TT AT A- AT AC AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
67497 TAGAATAACA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:75089 original size:25 final size:25
Alignment explanation
Indices: 75026--75138 Score: 99
Period size: 25 Copynumber: 4.6 Consensus size: 25
75016 AAATATCGAA
*
75026 AAGCTCATACGAGCCATAAAT-GGG
1 AAGCTCATAAGAGCCATAAATCGGG
* * *
75050 AAGCTCA-AGAAAGCCATTAATCAGG
1 AAGCTCATA-AGAGCCATAAATCGGG
75075 AAGCTCATAAGAGCCA-AATATCGGG
1 AAGCTCATAAGAGCCATAA-ATCGGG
* *
75100 AAGCTCAAAAGAGTCATATAA-CGGG
1 AAGCTCATAAGAGCCATA-AATCGGG
**
75125 GTGCTCATAAGAGC
1 AAGCTCATAAGAGC
75139 TAAATAGCGG
Statistics
Matches: 70, Mismatches: 13, Indels: 11
0.74 0.14 0.12
Matches are distributed among these distances:
23 1 0.01
24 17 0.24
25 48 0.69
26 3 0.04
27 1 0.01
ACGTcount: A:0.40, C:0.19, G:0.24, T:0.17
Consensus pattern (25 bp):
AAGCTCATAAGAGCCATAAATCGGG
Found at i:75149 original size:25 final size:25
Alignment explanation
Indices: 75073--75165 Score: 80
Period size: 25 Copynumber: 3.7 Consensus size: 25
75063 CCATTAATCA
* *
75073 GGAAGCTCATAAGAGCCAAATATCG
1 GGAAGCTCATAAGAGCTAAATAACG
* *
75098 GGAAGCTCAAAAGAG-TCATATAACG
1 GGAAGCTCATAAGAGCT-AAATAACG
** *
75123 GGGTGCTCATAAGAGCTAAATAGCG
1 GGAAGCTCATAAGAGCTAAATAACG
* * *
75148 GGACGCTCTTACGAGCTA
1 GGAAGCTCATAAGAGCTA
75166 TGGTGTGTCC
Statistics
Matches: 53, Mismatches: 13, Indels: 4
0.76 0.19 0.06
Matches are distributed among these distances:
25 52 0.98
26 1 0.02
ACGTcount: A:0.35, C:0.19, G:0.27, T:0.18
Consensus pattern (25 bp):
GGAAGCTCATAAGAGCTAAATAACG
Found at i:77112 original size:50 final size:50
Alignment explanation
Indices: 77002--77300 Score: 282
Period size: 50 Copynumber: 5.9 Consensus size: 50
76992 ACATTAAGAG
* *
77002 GATGAGA--TCCCATGTAAAACCATGTCTGGGACATGGCATTGGCATCATTGA
1 GATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-C--CGA
* *
77053 GATTATGAGAGGTCCCATGTAAGACCATGTCTGAGACATGGCGTTGGCACCGA
1 G---ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGA
*
77106 GATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGA
1 GATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGA
** * *
77156 GATGAGAGGTCCCCCGTAAGACCATGTCTGGGACATGGCATGGGCACCTA
1 GATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGA
* * ** * * * *
77206 TATGTGAATTCCCATGTAATACCATATCTGGGATATGACATTGGCA--GTA
1 GATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCG-A
* * * ** * * *
77255 CAAGAAACATCCCATGTAAGACTATGTCTGGGACATAGCTTTGGCA
1 GATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
77301 TGTTATATTC
Statistics
Matches: 207, Mismatches: 35, Indels: 14
0.81 0.14 0.05
Matches are distributed among these distances:
49 34 0.16
50 128 0.62
51 1 0.00
53 3 0.01
54 6 0.03
55 1 0.00
56 34 0.16
ACGTcount: A:0.28, C:0.21, G:0.27, T:0.24
Consensus pattern (50 bp):
GATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGA
Found at i:88232 original size:44 final size:44
Alignment explanation
Indices: 88169--88383 Score: 259
Period size: 51 Copynumber: 4.6 Consensus size: 44
88159 TTTGAGTACT
88169 TCTGATCAGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTA
1 TCTGATCAGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTA
*
88213 TCTGATCAGTGACAAGTGATAAGTGATAGCTTTAGCTACACTTA
1 TCTGATCAGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTA
*
88257 TCTGATCAGTGACAAGAGACAAGTGATGAGTGGTAGCTTTAGCTACACTTA
1 TCTGATCAGT-------GACAAGTGATAAGTGGTAGCTTTAGCTACACTTA
*
88308 TCTGATCAGTGACAAGTGACAAGTGATGAGGTGTAGCTTTAGCTACACTTA
1 TCTGATCAGTGACAAGTGATAA--G-T---G-GTAGCTTTAGCTACACTTA
* *
88359 TCTGATCAGGGACAAGTGACAAGTG
1 TCTGATCAGTGACAAGTGATAAGTG
88384 ATAAATGTGA
Statistics
Matches: 151, Mismatches: 6, Indels: 27
0.82 0.03 0.15
Matches are distributed among these distances:
44 63 0.42
45 1 0.01
46 1 0.01
47 1 0.01
48 1 0.01
49 1 0.01
50 1 0.01
51 82 0.54
ACGTcount: A:0.31, C:0.16, G:0.25, T:0.29
Consensus pattern (44 bp):
TCTGATCAGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTA
Found at i:88278 original size:51 final size:50
Alignment explanation
Indices: 88220--88387 Score: 273
Period size: 51 Copynumber: 3.3 Consensus size: 50
88210 TTATCTGATC
88220 AGTGACAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAGTGACA
1 AGTGACAAGTGATAAGTG-TAGCTTTAGCTACACTTATCTGATCAGTGACA
* *
88271 AGAGACAAGTGATGAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACA
1 AGTGACAAGTGATAAGT-GTAGCTTTAGCTACACTTATCTGATCAGTGACA
* *
88322 AGTGACAAGTGATGAGGTGTAGCTTTAGCTACACTTATCTGATCAGGGACA
1 AGTGACAAGTGAT-AAGTGTAGCTTTAGCTACACTTATCTGATCAGTGACA
88373 AGTGACAAGTGATAA
1 AGTGACAAGTGATAA
88388 ATGTGATCCG
Statistics
Matches: 108, Mismatches: 7, Indels: 5
0.90 0.06 0.04
Matches are distributed among these distances:
50 1 0.01
51 104 0.96
52 3 0.03
ACGTcount: A:0.33, C:0.15, G:0.25, T:0.27
Consensus pattern (50 bp):
AGTGACAAGTGATAAGTGTAGCTTTAGCTACACTTATCTGATCAGTGACA
Found at i:88325 original size:95 final size:98
Alignment explanation
Indices: 88179--88387 Score: 325
Period size: 95 Copynumber: 2.1 Consensus size: 98
88169 TCTGATCAGT
*
88179 GACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACAAGTGATAA-G-TGA-TA
1 GACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACAAGTGACAAGGATGAGTA
*
88241 GCTTTAGCTACACTTATCTGATCAGTGACAAGA
66 GCTTTAGCTACACTTATCTGATCAGGGACAAGA
*
88274 GACAAGTGATGAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACAAGTGACAAGTGATGAGG
1 GACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACAAGTGACAAG-GATGA--
*
88339 TGTAGCTTTAGCTACACTTATCTGATCAGGGACAAGT
63 -GTAGCTTTAGCTACACTTATCTGATCAGGGACAAGA
88376 GACAAGTGATAA
1 GACAAGTGATAA
88388 ATGTGATCCG
Statistics
Matches: 102, Mismatches: 5, Indels: 7
0.89 0.04 0.06
Matches are distributed among these distances:
95 54 0.53
97 1 0.01
98 3 0.03
102 44 0.43
ACGTcount: A:0.32, C:0.15, G:0.24, T:0.28
Consensus pattern (98 bp):
GACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACAAGTGACAAGGATGAGTA
GCTTTAGCTACACTTATCTGATCAGGGACAAGA
Found at i:100380 original size:111 final size:111
Alignment explanation
Indices: 100260--100481 Score: 435
Period size: 111 Copynumber: 2.0 Consensus size: 111
100250 ATATCCGAAA
100260 TCCATTCAGGCAAGAAAAAAAAACGATTAACCCCAGATAAAATGTTTTGATTCATATGCTCCAAT
1 TCCATTCAGGCAAGAAAAAAAAACGATTAACCCCAGATAAAATGTTTTGATTCATATGCTCCAAT
100325 TCATAGACGCCGAATGCTTCCCACAAAATGATAAAAGGGTGCTCTC
66 TCATAGACGCCGAATGCTTCCCACAAAATGATAAAAGGGTGCTCTC
*
100371 TCCATTCAGGCAAGAAAAAAAAAGGATTAACCCCAGATAAAATGTTTTGATTCATATGCTCCAAT
1 TCCATTCAGGCAAGAAAAAAAAACGATTAACCCCAGATAAAATGTTTTGATTCATATGCTCCAAT
100436 TCATAGACGCCGAATGCTTCCCACAAAATGATAAAAGGGTGCTCTC
66 TCATAGACGCCGAATGCTTCCCACAAAATGATAAAAGGGTGCTCTC
100482 GAATTTCTAC
Statistics
Matches: 110, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
111 110 1.00
ACGTcount: A:0.38, C:0.22, G:0.16, T:0.24
Consensus pattern (111 bp):
TCCATTCAGGCAAGAAAAAAAAACGATTAACCCCAGATAAAATGTTTTGATTCATATGCTCCAAT
TCATAGACGCCGAATGCTTCCCACAAAATGATAAAAGGGTGCTCTC
Found at i:105258 original size:135 final size:135
Alignment explanation
Indices: 105112--105380 Score: 434
Period size: 135 Copynumber: 2.0 Consensus size: 135
105102 TTACAGAAAC
* *
105112 ATTAGATTTTTTTTAATTTCTGAAAATGAAAAACTTATTTATTAAATATATATTTTT-TAAGGAG
1 ATTAGAATTTTTTTAATTTCTGAAAATGAAAAACTTATTTATTAAA-ATATATTTTTCGAAGGAG
105176 TATCTCGACACTCATGGGTGTCGAGTTTAATAT-AGAGTTTTTAACTATTGAACTTTTTCGAGAA
65 TATCTCGACACTCATGGGTGTCGAGTTTAATATAAGA-TTTTTAACTATTGAACTTTTTCGAGAA
105240 TAGGAAT
129 TAGGAAT
* * *
105247 ATTAGAATTTTTTTAATTTCTGACAATGGAAAACTTATTTATTAAAATATGTTTTTCGAAGGAGT
1 ATTAGAATTTTTTTAATTTCTGAAAATGAAAAACTTATTTATTAAAATATATTTTTCGAAGGAGT
* * *
105312 ATCTCGGCACTCATGGGTGTTGAGTTTAGTATAAGATTTTTAACTATTGAACTTTTTCGAGAATA
66 ATCTCGACACTCATGGGTGTCGAGTTTAATATAAGATTTTTAACTATTGAACTTTTTCGAGAATA
105377 GGAA
131 GGAA
105381 GAAACAAAAA
Statistics
Matches: 124, Mismatches: 8, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
134 9 0.07
135 112 0.90
136 3 0.02
ACGTcount: A:0.33, C:0.09, G:0.16, T:0.42
Consensus pattern (135 bp):
ATTAGAATTTTTTTAATTTCTGAAAATGAAAAACTTATTTATTAAAATATATTTTTCGAAGGAGT
ATCTCGACACTCATGGGTGTCGAGTTTAATATAAGATTTTTAACTATTGAACTTTTTCGAGAATA
GGAAT
Found at i:106079 original size:31 final size:31
Alignment explanation
Indices: 106037--106120 Score: 87
Period size: 32 Copynumber: 2.6 Consensus size: 31
106027 GCTAAAGCCA
*
106037 CAAATTAGTACCTAAACTATATCATTTTTCT
1 CAAATTGGTACCTAAACTATATCATTTTTCT
* ** *
106068 CAAATTGGTACCTAAACCTTTATTTTTTTTGT
1 CAAATTGGTACCTAAA-CTATATCATTTTTCT
* *
106100 CACAAGTGGTACCTAAGCTAT
1 CA-AATTGGTACCTAAACTAT
106121 TCTTTTAGTA
Statistics
Matches: 43, Mismatches: 8, Indels: 3
0.80 0.15 0.06
Matches are distributed among these distances:
31 15 0.35
32 16 0.37
33 12 0.28
ACGTcount: A:0.31, C:0.19, G:0.10, T:0.40
Consensus pattern (31 bp):
CAAATTGGTACCTAAACTATATCATTTTTCT
Found at i:112866 original size:31 final size:32
Alignment explanation
Indices: 112830--112891 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
112820 CTTAGATAAT
112830 TTTAAAGAG-TTTTATTAGGATTCAATTACTC
1 TTTAAAGAGTTTTTATTAGGATTCAATTACTC
112861 TTTAAAGAGTTTTTATTAGGATTCAATTACT
1 TTTAAAGAGTTTTTATTAGGATTCAATTACT
112892 GTTGTAATTT
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 9 0.30
32 21 0.70
ACGTcount: A:0.32, C:0.08, G:0.13, T:0.47
Consensus pattern (32 bp):
TTTAAAGAGTTTTTATTAGGATTCAATTACTC
Found at i:113487 original size:14 final size:13
Alignment explanation
Indices: 113427--113515 Score: 67
Period size: 13 Copynumber: 6.5 Consensus size: 13
113417 CTTATTCTTT
113427 AAAAAAACAGCAAA
1 AAAAAAAC-GCAAA
113441 AAGAAAAA-G-AAA
1 AA-AAAAACGCAAA
*
113453 AAGAAAAAAG-AAGA
1 AA-AAAAACGCAA-A
*
113467 AGCAAAAAGCGCAAA
1 A--AAAAAACGCAAA
113482 AAAAAAACGCAAA
1 AAAAAAACGCAAA
*
113495 AAAAAACCCGCAAA
1 AAAAAA-ACGCAAA
113509 AAAAAAA
1 AAAAAAA
113516 ACAAAAAGTT
Statistics
Matches: 63, Mismatches: 5, Indels: 15
0.76 0.06 0.18
Matches are distributed among these distances:
12 11 0.17
13 21 0.33
14 16 0.25
15 12 0.19
16 3 0.05
ACGTcount: A:0.75, C:0.12, G:0.12, T:0.00
Consensus pattern (13 bp):
AAAAAAACGCAAA
Found at i:117072 original size:22 final size:22
Alignment explanation
Indices: 117044--117196 Score: 225
Period size: 22 Copynumber: 7.0 Consensus size: 22
117034 TTTATTGTTC
*
117044 AAACATGAGAGCTTAGTACGTG
1 AAACATGAGAGCTTAGTACGTT
117066 AAACATGAGAGCTTAGTACGTT
1 AAACATGAGAGCTTAGTACGTT
**
117088 AGCCATGAGAGCTTAGTACGTT
1 AAACATGAGAGCTTAGTACGTT
** * * *
117110 AGCCATGAGGGTTTAGTTCGTT
1 AAACATGAGAGCTTAGTACGTT
117132 AAACATGAGAGCTTAGTACGTT
1 AAACATGAGAGCTTAGTACGTT
*
117154 AAACATGAGAGCTTAGTACGTG
1 AAACATGAGAGCTTAGTACGTT
117176 AAACATGAGAGCTTAGTACGT
1 AAACATGAGAGCTTAGTACGT
117197 ACTATCAACA
Statistics
Matches: 119, Mismatches: 12, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 119 1.00
ACGTcount: A:0.33, C:0.14, G:0.26, T:0.27
Consensus pattern (22 bp):
AAACATGAGAGCTTAGTACGTT
Found at i:119093 original size:31 final size:32
Alignment explanation
Indices: 119057--119121 Score: 123
Period size: 32 Copynumber: 2.1 Consensus size: 32
119047 CTTAAATAAT
119057 TTTAAAGAG-TTTTATTAGGATTCAATTACTC
1 TTTAAAGAGTTTTTATTAGGATTCAATTACTC
119088 TTTAAAGAGTTTTTATTAGGATTCAATTACTC
1 TTTAAAGAGTTTTTATTAGGATTCAATTACTC
119120 TT
1 TT
119122 GTAATTTGCC
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 9 0.27
32 24 0.73
ACGTcount: A:0.31, C:0.09, G:0.12, T:0.48
Consensus pattern (32 bp):
TTTAAAGAGTTTTTATTAGGATTCAATTACTC
Found at i:123741 original size:3 final size:3
Alignment explanation
Indices: 123735--123762 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
123725 GGAGGAGGAG
123735 GAA GAA GAA GAA GAA GAA GAA GAA GAA G
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA G
123763 CCTGGGTGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:127980 original size:29 final size:30
Alignment explanation
Indices: 127947--128005 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
127937 CTAAATGACC
127947 AGAAAAGGCTCATTTT-TTAAAAAAATTAT
1 AGAAAAGGCTCATTTTGTTAAAAAAATTAT
* * **
127976 AGAAATGGGTTGTTTTGTTAAAAAAATTAT
1 AGAAAAGGCTCATTTTGTTAAAAAAATTAT
128006 TGGAAAGGGC
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
29 12 0.48
30 13 0.52
ACGTcount: A:0.44, C:0.03, G:0.15, T:0.37
Consensus pattern (30 bp):
AGAAAAGGCTCATTTTGTTAAAAAAATTAT
Found at i:128899 original size:13 final size:13
Alignment explanation
Indices: 128881--128905 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
128871 TAATATTTTA
128881 ATTTTTCGTGTTG
1 ATTTTTCGTGTTG
128894 ATTTTTCGTGTT
1 ATTTTTCGTGTT
128906 TTGAATTTTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.08, C:0.08, G:0.20, T:0.64
Consensus pattern (13 bp):
ATTTTTCGTGTTG
Found at i:134641 original size:27 final size:28
Alignment explanation
Indices: 134602--134655 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 28
134592 TAAGTACCTA
* *
134602 TTATTATAATTAATTATCTATTTAAATT
1 TTATTATAATTAAATATCTATCTAAATT
*
134630 TTATT-TAATTAAATATTTATCTAAAT
1 TTATTATAATTAAATATCTATCTAAAT
134656 AAATATTGTC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
27 18 0.78
28 5 0.22
ACGTcount: A:0.41, C:0.04, G:0.00, T:0.56
Consensus pattern (28 bp):
TTATTATAATTAAATATCTATCTAAATT
Found at i:134658 original size:16 final size:16
Alignment explanation
Indices: 134624--134662 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
134614 ATTATCTATT
* *
134624 TAAAT-TTTATTTAAT
1 TAAATATTTATCTAAA
134639 TAAATATTTATCTAAA
1 TAAATATTTATCTAAA
134655 TAAATATT
1 TAAATATT
134663 GTCATCCCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 5 0.24
16 16 0.76
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (16 bp):
TAAATATTTATCTAAA
Found at i:144266 original size:58 final size:58
Alignment explanation
Indices: 144176--144294 Score: 238
Period size: 58 Copynumber: 2.1 Consensus size: 58
144166 GAATAACCGT
144176 TATTCATACACATACATTTTTCATCATTTACAAAGAAAGAATACTTACCTTATACAAA
1 TATTCATACACATACATTTTTCATCATTTACAAAGAAAGAATACTTACCTTATACAAA
144234 TATTCATACACATACATTTTTCATCATTTACAAAGAAAGAATACTTACCTTATACAAA
1 TATTCATACACATACATTTTTCATCATTTACAAAGAAAGAATACTTACCTTATACAAA
144292 TAT
1 TAT
144295 AAAATAAAAA
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
58 61 1.00
ACGTcount: A:0.43, C:0.18, G:0.03, T:0.35
Consensus pattern (58 bp):
TATTCATACACATACATTTTTCATCATTTACAAAGAAAGAATACTTACCTTATACAAA
Found at i:145043 original size:17 final size:17
Alignment explanation
Indices: 144998--145044 Score: 53
Period size: 17 Copynumber: 2.8 Consensus size: 17
144988 ATGCTTAACA
144998 AAAGAGTTCGCC-AACC
1 AAAGAGTTCGCCAAACC
* *
145014 ATAGA-TCTCGCCAAAGC
1 AAAGAGT-TCGCCAAACC
145031 AAAGAGTTCGCCAA
1 AAAGAGTTCGCCAA
145045 TTGGCATAAC
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
15 1 0.04
16 9 0.36
17 14 0.56
18 1 0.04
ACGTcount: A:0.38, C:0.28, G:0.19, T:0.15
Consensus pattern (17 bp):
AAAGAGTTCGCCAAACC
Found at i:145858 original size:12 final size:13
Alignment explanation
Indices: 145839--145870 Score: 57
Period size: 12 Copynumber: 2.5 Consensus size: 13
145829 AAGAGAGAGA
145839 GAGAGGGGGAGGG
1 GAGAGGGGGAGGG
145852 G-GAGGGGGAGGG
1 GAGAGGGGGAGGG
145864 GAGAGGG
1 GAGAGGG
145871 AGAGAGATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 12 0.67
13 6 0.33
ACGTcount: A:0.22, C:0.00, G:0.78, T:0.00
Consensus pattern (13 bp):
GAGAGGGGGAGGG
Found at i:145859 original size:7 final size:6
Alignment explanation
Indices: 145841--145870 Score: 51
Period size: 6 Copynumber: 4.8 Consensus size: 6
145831 GAGAGAGAGA
145841 GAGGGG GAGGGG GAGGGG GAGGGG AGAGGG
1 GAGGGG GAGGGG GAGGGG GAGGGG -GAGGG
145871 AGAGAGATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 18 0.78
7 5 0.22
ACGTcount: A:0.20, C:0.00, G:0.80, T:0.00
Consensus pattern (6 bp):
GAGGGG
Found at i:146665 original size:27 final size:27
Alignment explanation
Indices: 146627--146683 Score: 114
Period size: 27 Copynumber: 2.1 Consensus size: 27
146617 ATGTACCAGT
146627 TTGCAAATGAGTCTCTGAAAACTCCTA
1 TTGCAAATGAGTCTCTGAAAACTCCTA
146654 TTGCAAATGAGTCTCTGAAAACTCCTA
1 TTGCAAATGAGTCTCTGAAAACTCCTA
146681 TTG
1 TTG
146684 ACACGCCATT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.32, C:0.21, G:0.16, T:0.32
Consensus pattern (27 bp):
TTGCAAATGAGTCTCTGAAAACTCCTA
Found at i:148861 original size:43 final size:42
Alignment explanation
Indices: 148792--148878 Score: 156
Period size: 43 Copynumber: 2.0 Consensus size: 42
148782 AAAGTAATGG
148792 CAGAATTGACAGCTAAACTAAAACTGATTCCACAAATCAAGT
1 CAGAATTGACAGCTAAACTAAAACTGATTCCACAAATCAAGT
*
148834 CAGAATTGACAGGCTTAACTAAAACTGATTCCACAAATCAAGT
1 CAGAATTGACA-GCTAAACTAAAACTGATTCCACAAATCAAGT
148877 CA
1 CA
148879 AAGGGGAATA
Statistics
Matches: 43, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
42 11 0.26
43 32 0.74
ACGTcount: A:0.44, C:0.22, G:0.13, T:0.22
Consensus pattern (42 bp):
CAGAATTGACAGCTAAACTAAAACTGATTCCACAAATCAAGT
Found at i:150562 original size:29 final size:30
Alignment explanation
Indices: 150506--150562 Score: 73
Period size: 29 Copynumber: 1.9 Consensus size: 30
150496 CAAGTTGACT
* *
150506 TAAATTTTGAAATATGAAAAGTACAAAGGC
1 TAAATTTTCAAATATGAAAAGGACAAAGGC
150536 TAAA-TTTCAAATATGTAAAAGGA-AAAG
1 TAAATTTTCAAATATG-AAAAGGACAAAG
150563 CTAGAAAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 14 0.58
30 10 0.42
ACGTcount: A:0.53, C:0.05, G:0.16, T:0.26
Consensus pattern (30 bp):
TAAATTTTCAAATATGAAAAGGACAAAGGC
Found at i:153284 original size:20 final size:20
Alignment explanation
Indices: 153259--153298 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
153249 GACTATATCA
* *
153259 GAAAAATTTGGAAATTTTAG
1 GAAAAATTTGAAAAATTTAG
153279 GAAAAATTTGAAAAATTTAG
1 GAAAAATTTGAAAAATTTAG
153299 ACTGCAAGGG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.50, C:0.00, G:0.17, T:0.33
Consensus pattern (20 bp):
GAAAAATTTGAAAAATTTAG
Found at i:159804 original size:15 final size:16
Alignment explanation
Indices: 159784--159814 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
159774 ATCTCGCTTC
159784 CTTTTCTTT-TTTTCT
1 CTTTTCTTTATTTTCT
159799 CTTTTCTTTATTTTCT
1 CTTTTCTTTATTTTCT
159815 GTCGATTTCT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.60
16 6 0.40
ACGTcount: A:0.03, C:0.19, G:0.00, T:0.77
Consensus pattern (16 bp):
CTTTTCTTTATTTTCT
Found at i:161469 original size:31 final size:31
Alignment explanation
Indices: 161431--161499 Score: 111
Period size: 31 Copynumber: 2.2 Consensus size: 31
161421 CTTAACAACC
*
161431 CAGTAACTTAAATAAAAACTTTTAAATAATT
1 CAGTAACTTAAATAAAAACTTTCAAATAATT
* *
161462 CAGTAACTTAAATGAAAACTTTCAAATAGTT
1 CAGTAACTTAAATAAAAACTTTCAAATAATT
161493 CAGTAAC
1 CAGTAAC
161500 CATTTTGTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.48, C:0.13, G:0.07, T:0.32
Consensus pattern (31 bp):
CAGTAACTTAAATAAAAACTTTCAAATAATT
Found at i:170792 original size:71 final size:72
Alignment explanation
Indices: 170712--170844 Score: 182
Period size: 70 Copynumber: 1.9 Consensus size: 72
170702 TTATATGTTT
* *
170712 TTTAATTAAAAGTATGTTTATGATATTTA-GGTTTAGGTG-TGTGTCTTTATTTA-TTATTTTAC
1 TTTAATT-AAAGTATCTTTATGATA-TTAGGGTTTAGGTGTTGTGTCTTTATTTACTTAGTTTAC
170774 TAAGAGATC
64 TAAGAGATC
* * *
170783 TTTAATTAAAGTATCTTTATGGTATTAGGGTTTAGGTGTTTTTTCTTTATTTACTTAGTTTA
1 TTTAATTAAAGTATCTTTATGATATTAGGGTTTAGGTGTTGTGTCTTTATTTACTTAGTTTA
170845 AGACTCGATC
Statistics
Matches: 54, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
69 3 0.06
70 25 0.46
71 19 0.35
72 7 0.13
ACGTcount: A:0.26, C:0.05, G:0.17, T:0.53
Consensus pattern (72 bp):
TTTAATTAAAGTATCTTTATGATATTAGGGTTTAGGTGTTGTGTCTTTATTTACTTAGTTTACTA
AGAGATC
Found at i:173040 original size:2 final size:2
Alignment explanation
Indices: 173035--173073 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
173025 TGCTTGTGTG
173035 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
173074 GTACATGAGG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:177684 original size:2 final size:2
Alignment explanation
Indices: 177677--177702 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
177667 ATTAGCATTA
177677 TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG
177703 ATAAGTCTGC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:185720 original size:8 final size:8
Alignment explanation
Indices: 185707--185739 Score: 66
Period size: 8 Copynumber: 4.1 Consensus size: 8
185697 TTTTAATCTG
185707 ATGTATTT
1 ATGTATTT
185715 ATGTATTT
1 ATGTATTT
185723 ATGTATTT
1 ATGTATTT
185731 ATGTATTT
1 ATGTATTT
185739 A
1 A
185740 AGTTTTGTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 25 1.00
ACGTcount: A:0.27, C:0.00, G:0.12, T:0.61
Consensus pattern (8 bp):
ATGTATTT
Found at i:202209 original size:15 final size:16
Alignment explanation
Indices: 202189--202229 Score: 54
Period size: 15 Copynumber: 2.8 Consensus size: 16
202179 TTCGGATTTT
202189 TTTTTAAATATTAG-A
1 TTTTTAAATATTAGTA
202204 TTTTT--ATATTAGTA
1 TTTTTAAATATTAGTA
202218 TTTTTAAA-ATTA
1 TTTTTAAATATTA
202230 AAAAAATTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
13 7 0.30
14 6 0.26
15 9 0.39
16 1 0.04
ACGTcount: A:0.37, C:0.00, G:0.05, T:0.59
Consensus pattern (16 bp):
TTTTTAAATATTAGTA
Found at i:207792 original size:9 final size:9
Alignment explanation
Indices: 207778--207814 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
207768 TATAGTTTGA
207778 TATTCGAAT
1 TATTCGAAT
207787 TATTCGAAT
1 TATTCGAAT
*
207796 TATTCGAGT
1 TATTCGAAT
207805 TATTCGAAT
1 TATTCGAAT
207814 T
1 T
207815 CGAAAATTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:216240 original size:22 final size:22
Alignment explanation
Indices: 216212--216324 Score: 154
Period size: 22 Copynumber: 5.1 Consensus size: 22
216202 TTTATTGTTC
*
216212 AAACATGAGAGCTTAGTACGTG
1 AAACATGAGAGCTTAGTACGTT
216234 AAACATGAGAGCTTAGTACGTT
1 AAACATGAGAGCTTAGTACGTT
**
216256 AGCCATGAGAGCTTAGTACGTT
1 AAACATGAGAGCTTAGTACGTT
** * * *
216278 AGCCATGAGGGTTTAGTTCGTT
1 AAACATGAGAGCTTAGTACGTT
216300 AAACATGAGAGCTTAGTACGTT
1 AAACATGAGAGCTTAGTACGTT
216322 AAA
1 AAA
216325 GTCTGTGTAT
Statistics
Matches: 80, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 80 1.00
ACGTcount: A:0.33, C:0.14, G:0.26, T:0.27
Consensus pattern (22 bp):
AAACATGAGAGCTTAGTACGTT
Found at i:217586 original size:19 final size:18
Alignment explanation
Indices: 217562--217603 Score: 66
Period size: 19 Copynumber: 2.3 Consensus size: 18
217552 TATTAAACCC
217562 TTTTAAAATTTAAAAATT
1 TTTTAAAATTTAAAAATT
*
217580 ATTTTAAAATTTATAAATT
1 -TTTTAAAATTTAAAAATT
217599 TTTTA
1 TTTTA
217604 TTAAAAAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 5 0.23
19 17 0.77
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (18 bp):
TTTTAAAATTTAAAAATT
Found at i:223197 original size:21 final size:21
Alignment explanation
Indices: 223173--223214 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
223163 GCAACCATCA
*
223173 ACGCATCACCACCGTGAACCG
1 ACGCATCACCACCATGAACCG
223194 ACGCATCACCACCATGAACCG
1 ACGCATCACCACCATGAACCG
223215 CTACCTCCCT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.31, C:0.43, G:0.17, T:0.10
Consensus pattern (21 bp):
ACGCATCACCACCATGAACCG
Found at i:225054 original size:2 final size:2
Alignment explanation
Indices: 225047--225076 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
225037 GAAGTAACTA
225047 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
225077 GGAAGGGAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:228572 original size:19 final size:20
Alignment explanation
Indices: 228545--228592 Score: 64
Period size: 19 Copynumber: 2.5 Consensus size: 20
228535 GTTGGTAAAT
*
228545 ACATGTGTA-ATAATAATAA
1 ACATATGTATATAATAATAA
*
228564 ACATATGTATTTAATAATAA
1 ACATATGTATATAATAATAA
228584 A-ATATGTAT
1 ACATATGTAT
228593 TGCTTATTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
19 16 0.62
20 10 0.38
ACGTcount: A:0.50, C:0.04, G:0.08, T:0.38
Consensus pattern (20 bp):
ACATATGTATATAATAATAA
Found at i:228593 original size:19 final size:20
Alignment explanation
Indices: 228555--228593 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
228545 ACATGTGTAA
228555 TAATAATAAACATATGTATT
1 TAATAATAAACATATGTATT
228575 TAATAATAAA-ATATGTATT
1 TAATAATAAACATATGTATT
228594 GCTTATTAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 9 0.47
20 10 0.53
ACGTcount: A:0.51, C:0.03, G:0.05, T:0.41
Consensus pattern (20 bp):
TAATAATAAACATATGTATT
Found at i:229443 original size:24 final size:24
Alignment explanation
Indices: 229407--229453 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
229397 ATTCAAATGG
229407 ATTGATTTAATATGTGA-TGAATTT
1 ATTGATTTAATAT-TGATTGAATTT
229431 ATTGAATTT-ATATTGATTGAATT
1 ATTG-ATTTAATATTGATTGAATT
229454 GGTATATATA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
23 3 0.14
24 14 0.67
25 4 0.19
ACGTcount: A:0.34, C:0.00, G:0.15, T:0.51
Consensus pattern (24 bp):
ATTGATTTAATATTGATTGAATTT
Found at i:229505 original size:2 final size:2
Alignment explanation
Indices: 229456--229496 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
229446 ATTGAATTGG
229456 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
229497 TGAATATATT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:229763 original size:40 final size:40
Alignment explanation
Indices: 229644--229781 Score: 140
Period size: 40 Copynumber: 3.5 Consensus size: 40
229634 CTTTGAGTCA
* *
229644 ATGAGACACTGGGTGTCAATTTATTACTT-AGGATTAATTCG
1 ATGAGACACTGGGTGTCAAATTATTACTTCA-GATTAA-CCG
* * * * *
229685 ATGAGGCATTGGGTGTC-AA-T-TTACTTCGGTTTAGCCG
1 ATGAGACACTGGGTGTCAAATTATTACTTCAGATTAACCG
*
229722 ATGAGACACTGGGTGTCAAATTATTACTTCAAATTAACCG
1 ATGAGACACTGGGTGTCAAATTATTACTTCAGATTAACCG
* *
229762 ATGAGGCACTGGGTGCCAAA
1 ATGAGACACTGGGTGTCAAA
229782 CTGGTGTGTT
Statistics
Matches: 78, Mismatches: 15, Indels: 9
0.76 0.15 0.09
Matches are distributed among these distances:
37 17 0.22
38 12 0.15
39 2 0.03
40 32 0.41
41 15 0.19
ACGTcount: A:0.28, C:0.16, G:0.25, T:0.31
Consensus pattern (40 bp):
ATGAGACACTGGGTGTCAAATTATTACTTCAGATTAACCG
Found at i:235588 original size:19 final size:19
Alignment explanation
Indices: 235540--235595 Score: 69
Period size: 19 Copynumber: 2.9 Consensus size: 19
235530 AAAGAATAAA
*
235540 TAATGATTTTTCAGAATTTT
1 TAAT-ATTTTTTAGAATTTT
235560 TAATATTTTTTAGAATTTT
1 TAATATTTTTTAGAATTTT
*
235579 TTAT-TCTTTTTAGAATT
1 TAATAT-TTTTTAGAATT
235596 ATTGTTAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
18 1 0.03
19 28 0.85
20 4 0.12
ACGTcount: A:0.29, C:0.04, G:0.07, T:0.61
Consensus pattern (19 bp):
TAATATTTTTTAGAATTTT
Found at i:236256 original size:25 final size:25
Alignment explanation
Indices: 236210--236258 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
236200 ATTATATATT
**
236210 AAATATATATTTTTTATTTTTAATC
1 AAATATATATTTTTTAAATTTAATC
236235 AAATATA-ATTTTTTAAAATTTAAT
1 AAATATATATTTTTT-AAATTTAAT
236259 ATGCTATTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 7 0.33
25 14 0.67
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (25 bp):
AAATATATATTTTTTAAATTTAATC
Found at i:244667 original size:21 final size:21
Alignment explanation
Indices: 244637--244684 Score: 78
Period size: 21 Copynumber: 2.2 Consensus size: 21
244627 AACAAGCTCT
*
244637 AATACCAATTGTTAGGCTTAAA
1 AATA-CAATTGTTAGGCCTAAA
244659 AATACAATTGTTAGGCCTAAA
1 AATACAATTGTTAGGCCTAAA
244680 AATAC
1 AATAC
244685 TAAGATAGGG
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
21 21 0.84
22 4 0.16
ACGTcount: A:0.44, C:0.15, G:0.12, T:0.29
Consensus pattern (21 bp):
AATACAATTGTTAGGCCTAAA
Found at i:245343 original size:22 final size:21
Alignment explanation
Indices: 245318--245361 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
245308 TTTATTTCAC
*
245318 ACATTTAACAATATGTCTCGAG
1 ACATATAACAAT-TGTCTCGAG
**
245340 ACATATAACCCTTGTCTCGAG
1 ACATATAACAATTGTCTCGAG
245361 A
1 A
245362 TAGGAAGAAC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 10 0.53
22 9 0.47
ACGTcount: A:0.34, C:0.23, G:0.14, T:0.30
Consensus pattern (21 bp):
ACATATAACAATTGTCTCGAG
Found at i:245806 original size:11 final size:11
Alignment explanation
Indices: 245790--245824 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
245780 AATTTAAACA
*
245790 TTTTATAACTT
1 TTTTATAAATT
*
245801 TTTTATAATTT
1 TTTTATAAATT
245812 TTTTATAAATT
1 TTTTATAAATT
245823 TT
1 TT
245825 ATGATATTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.69
Consensus pattern (11 bp):
TTTTATAAATT
Found at i:245833 original size:22 final size:22
Alignment explanation
Indices: 245790--245835 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
245780 AATTTAAACA
* *
245790 TTTTATAACTTTTTTATAATTT
1 TTTTATAAATTTTTGATAATTT
245812 TTTTATAAATTTTATGAT-ATTT
1 TTTTATAAATTTT-TGATAATTT
245834 TT
1 TT
245836 AAATTTTTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 18 0.86
23 3 0.14
ACGTcount: A:0.28, C:0.02, G:0.02, T:0.67
Consensus pattern (22 bp):
TTTTATAAATTTTTGATAATTT
Found at i:279185 original size:2 final size:2
Alignment explanation
Indices: 279178--279209 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
279168 AGAAGAATAC
279178 AT AT AT AT AT AT AT AT AT AT AT AT -T AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
279210 TTACAACAAC
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.07
2 26 0.93
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:281406 original size:8 final size:8
Alignment explanation
Indices: 281393--281423 Score: 55
Period size: 8 Copynumber: 4.0 Consensus size: 8
281383 AGACCCCCCC
281393 TTCTTTTT
1 TTCTTTTT
281401 TTCTTTTT
1 TTCTTTTT
281409 TTCTTTTT
1 TTCTTTTT
281417 TT-TTTTT
1 TTCTTTTT
281424 CATATAAGTC
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 5 0.22
8 18 0.78
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (8 bp):
TTCTTTTT
Found at i:283123 original size:12 final size:12
Alignment explanation
Indices: 283106--283144 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
283096 AAGATGACCA
*
283106 TTAGAGTTAGAG
1 TTAGAGTTAAAG
*
283118 TTAGAGATAAAG
1 TTAGAGTTAAAG
*
283130 TTAAAGTTAAAG
1 TTAGAGTTAAAG
283142 TTA
1 TTA
283145 AGGTTTTCTA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.44, C:0.00, G:0.23, T:0.33
Consensus pattern (12 bp):
TTAGAGTTAAAG
Found at i:284445 original size:25 final size:25
Alignment explanation
Indices: 284417--284468 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
284407 CATAACTTAC
284417 CTCAATAACAATTTAATATGATAAG
1 CTCAATAACAATTTAATATGATAAG
284442 CTCAATAACAATTTAATATGATAAG
1 CTCAATAACAATTTAATATGATAAG
284467 CT
1 CT
284469 ACTAGCTTGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.46, C:0.13, G:0.08, T:0.33
Consensus pattern (25 bp):
CTCAATAACAATTTAATATGATAAG
Found at i:286223 original size:19 final size:19
Alignment explanation
Indices: 286177--286234 Score: 55
Period size: 19 Copynumber: 3.0 Consensus size: 19
286167 AGATTAATCA
* *
286177 TTAATTAATCAATAATTAGC
1 TTAATTAA-CTATAATTAAC
286197 TTAATTAACTATAATTAAC
1 TTAATTAACTATAATTAAC
* *
286216 -TAACTTAATTATACTTAAC
1 TTAA-TTAACTATAATTAAC
286235 AAAGTTTAGT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
18 3 0.09
19 22 0.67
20 8 0.24
ACGTcount: A:0.45, C:0.12, G:0.02, T:0.41
Consensus pattern (19 bp):
TTAATTAACTATAATTAAC
Found at i:306949 original size:160 final size:161
Alignment explanation
Indices: 306649--306957 Score: 485
Period size: 160 Copynumber: 1.9 Consensus size: 161
306639 TGGTCTTTTC
* * * *
306649 GTTCATTAGTTAAGTCATTAGTTCTCTGTGGCTTGATGTTCGAATTAGGCTTCTTGCCTATAGTC
1 GTTCATTAGTTAAGTCATTAGTTCTCTGTGGCTCGATATTCAAATTAGGCTTCTTGCC-ATAGTA
* * * *
306714 TATTGGTTCTTGCTTGGATGCTTAACATTTTGTACCGTAGCTATCACTTTTACTTTGGTTTTATC
65 TATTGGTTCTTGCTTGGATGCTTAACATTATGTACCATAGCTAGCACTTTTACTTTGGTTTTACC
306779 ATTATAACTGTGATAATTTAACTGGTCCCACT
130 ATTATAACTGTGATAATTTAACTGGTCCCACT
* *
306811 GTTCATTAGTTAAGTCTTTAGTTCTCTGTGGCTCGATATTCAAATTAGGTTTCTTGCC-TAGTAT
1 GTTCATTAGTTAAGTCATTAGTTCTCTGTGGCTCGATATTCAAATTAGGCTTCTTGCCATAGTAT
* * *
306875 ATTGGTTCTTGCTTGGGTGCTTAACATTATGTACCATTGCTAGCACTTTTTCTTTGGTTTTACCA
66 ATTGGTTCTTGCTTGGATGCTTAACATTATGTACCATAGCTAGCACTTTTACTTTGGTTTTACCA
306940 TTATAACTGTGATAATTT
131 TTATAACTGTGATAATTT
306958 GCTTACTAAA
Statistics
Matches: 134, Mismatches: 13, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
160 81 0.60
162 53 0.40
ACGTcount: A:0.20, C:0.17, G:0.18, T:0.45
Consensus pattern (161 bp):
GTTCATTAGTTAAGTCATTAGTTCTCTGTGGCTCGATATTCAAATTAGGCTTCTTGCCATAGTAT
ATTGGTTCTTGCTTGGATGCTTAACATTATGTACCATAGCTAGCACTTTTACTTTGGTTTTACCA
TTATAACTGTGATAATTTAACTGGTCCCACT
Found at i:322287 original size:17 final size:17
Alignment explanation
Indices: 322265--322298 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
322255 TTACAAAATT
*
322265 AAATCTTATAGGATTAC
1 AAATCTTATAAGATTAC
*
322282 AAATCTTCTAAGATTAC
1 AAATCTTATAAGATTAC
322299 TTTCCTTATT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.41, C:0.15, G:0.09, T:0.35
Consensus pattern (17 bp):
AAATCTTATAAGATTAC
Found at i:333622 original size:8 final size:9
Alignment explanation
Indices: 333609--333725 Score: 92
Period size: 8 Copynumber: 13.4 Consensus size: 9
333599 TGTTAAAAAA
333609 ATATTAT-T
1 ATATTATAT
333617 ATATTATAGT
1 ATATTATA-T
*
333627 AATGATTATGT
1 -AT-ATTATAT
*
333638 -TTTTATAT
1 ATATTATAT
333646 -TA-TAT-T
1 ATATTATAT
333652 ATTATTA-AT
1 A-TATTATAT
333661 ATATTATATT
1 ATATTATA-T
333671 ATATTATAT
1 ATATTATAT
333680 ATA-TATAT
1 ATATTATAT
333688 ATA-TATAT
1 ATATTATAT
333696 ATA-TATAT
1 ATATTATAT
333704 ATA-TATAT
1 ATATTATAT
333712 ATATATATAT
1 ATAT-TATAT
333722 ATAT
1 ATAT
333726 CAAAAGAAAG
Statistics
Matches: 93, Mismatches: 4, Indels: 22
0.78 0.03 0.18
Matches are distributed among these distances:
6 1 0.01
7 3 0.03
8 52 0.56
9 10 0.11
10 19 0.20
11 3 0.03
12 5 0.05
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.55
Consensus pattern (9 bp):
ATATTATAT
Found at i:333675 original size:10 final size:10
Alignment explanation
Indices: 333613--333725 Score: 83
Period size: 12 Copynumber: 10.8 Consensus size: 10
333603 AAAAAAATAT
333613 TATTATATTA
1 TATTATATTA
*
333623 TAGTAATGATTA
1 TA-TTAT-ATTA
*
333635 TGTT-T-TTA
1 TATTATATTA
333643 TATTATATTA
1 TATTATATTA
333653 TTATTA-A-TA
1 -TATTATATTA
333662 TATTATATTA
1 TATTATATTA
333672 TATTATA-TA
1 TATTATATTA
333681 TATATATATATA
1 TAT-TATAT-TA
333693 TATATATATATA
1 TAT-TATAT-TA
333705 TATATATATATA
1 TAT-TATAT-TA
333717 TATATATAT
1 TAT-TATAT
333726 CAAAAGAAAG
Statistics
Matches: 89, Mismatches: 4, Indels: 18
0.80 0.04 0.16
Matches are distributed among these distances:
8 11 0.12
9 9 0.10
10 20 0.22
11 9 0.10
12 40 0.45
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (10 bp):
TATTATATTA
Found at i:333680 original size:2 final size:2
Alignment explanation
Indices: 333641--333725 Score: 114
Period size: 2 Copynumber: 46.5 Consensus size: 2
333631 ATTATGTTTT
333641 TA TA T- TA TA T- TA T- TA T- TA -A TA TA T- TA TA T- TA TA T-
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
333675 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
333717 TA TA TA TA T
1 TA TA TA TA T
333726 CAAAAGAAAG
Statistics
Matches: 75, Mismatches: 0, Indels: 16
0.82 0.00 0.18
Matches are distributed among these distances:
1 8 0.11
2 67 0.89
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (2 bp):
TA
Found at i:333751 original size:16 final size:16
Alignment explanation
Indices: 333730--333773 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
333720 ATATATCAAA
*
333730 AGAAAGAATAGAAA-TG
1 AGAAAGAA-AGAAACGG
333746 AGAAAGAAAGAAACGG
1 AGAAAGAAAGAAACGG
333762 AGAAAG-AAGAAA
1 AGAAAGAAAGAAA
333774 AAGAAAGGGA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
15 11 0.42
16 15 0.58
ACGTcount: A:0.66, C:0.02, G:0.27, T:0.05
Consensus pattern (16 bp):
AGAAAGAAAGAAACGG
Found at i:333779 original size:6 final size:7
Alignment explanation
Indices: 333746--333802 Score: 55
Period size: 8 Copynumber: 8.0 Consensus size: 7
333736 AATAGAAATG
333746 AGAAAGAA
1 AGAAAG-A
*
333754 AGAAACGG
1 AGAAA-GA
333762 AGAAAGA
1 AGAAAGA
333769 AGAAA-A
1 AGAAAGA
*
333775 AGAAAGGG
1 AGAAA-GA
333783 AGAAAGA
1 AGAAAGA
333790 AGAAA-A
1 AGAAAGA
333796 AGAAAGA
1 AGAAAGA
333803 GAGCGACGCT
Statistics
Matches: 41, Mismatches: 4, Indels: 9
0.76 0.07 0.17
Matches are distributed among these distances:
6 12 0.29
7 13 0.32
8 15 0.37
9 1 0.02
ACGTcount: A:0.68, C:0.02, G:0.30, T:0.00
Consensus pattern (7 bp):
AGAAAGA
Found at i:333801 original size:21 final size:21
Alignment explanation
Indices: 333752--333801 Score: 91
Period size: 21 Copynumber: 2.4 Consensus size: 21
333742 AATGAGAAAG
*
333752 AAAGAAACGGAGAAAGAAGAA
1 AAAGAAAGGGAGAAAGAAGAA
333773 AAAGAAAGGGAGAAAGAAGAA
1 AAAGAAAGGGAGAAAGAAGAA
333794 AAAGAAAG
1 AAAGAAAG
333802 AGAGCGACGC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.68, C:0.02, G:0.30, T:0.00
Consensus pattern (21 bp):
AAAGAAAGGGAGAAAGAAGAA
Found at i:333802 original size:25 final size:23
Alignment explanation
Indices: 333746--333794 Score: 75
Period size: 21 Copynumber: 2.2 Consensus size: 23
333736 AATAGAAATG
333746 AGAAAGAAAGAAACGGAGAAAGA
1 AGAAAGAAAGAAACGGAGAAAGA
*
333769 AG-AA-AAAGAAAGGGAGAAAGA
1 AGAAAGAAAGAAACGGAGAAAGA
333790 AGAAA
1 AGAAA
333795 AAGAAAGAGA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
21 18 0.75
22 4 0.17
23 2 0.08
ACGTcount: A:0.67, C:0.02, G:0.31, T:0.00
Consensus pattern (23 bp):
AGAAAGAAAGAAACGGAGAAAGA
Found at i:335265 original size:6 final size:6
Alignment explanation
Indices: 335254--335295 Score: 57
Period size: 6 Copynumber: 6.8 Consensus size: 6
335244 GTGTGTTGAA
* *
335254 TACTGT TACTGT TACTGT TACTGC TACCGT TACTGTT TACTG
1 TACTGT TACTGT TACTGT TACTGT TACTGT TACTG-T TACTG
335296 ATCAGGTACT
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
6 25 0.81
7 6 0.19
ACGTcount: A:0.17, C:0.21, G:0.17, T:0.45
Consensus pattern (6 bp):
TACTGT
Found at i:348449 original size:28 final size:28
Alignment explanation
Indices: 348413--348544 Score: 113
Period size: 28 Copynumber: 4.7 Consensus size: 28
348403 GAATTCGCAT
* * *
348413 GTAAAAGTTTGTATGAATTATCTTTCAA
1 GTAAGAGTTTGTATGGATTATCTTCCAA
* * * * *
348441 GCACGAGTTTGTATGGATTTTCATCCAG
1 GTAAGAGTTTGTATGGATTATCTTCCAA
* ** ** *
348469 GTAAGAGTCTACATAAATTATCTTTCAA
1 GTAAGAGTTTGTATGGATTATCTTCCAA
*
348497 G-AACGAGTTTGTATGGATTTTCTTCCAA
1 GTAA-GAGTTTGTATGGATTATCTTCCAA
348525 GTAAGAGTTTGTATGGATTA
1 GTAAGAGTTTGTATGGATTA
348545 GATTTCGAAC
Statistics
Matches: 75, Mismatches: 27, Indels: 4
0.71 0.25 0.04
Matches are distributed among these distances:
27 2 0.03
28 71 0.95
29 2 0.03
ACGTcount: A:0.30, C:0.11, G:0.20, T:0.39
Consensus pattern (28 bp):
GTAAGAGTTTGTATGGATTATCTTCCAA
Found at i:351563 original size:3 final size:3
Alignment explanation
Indices: 351555--351620 Score: 73
Period size: 3 Copynumber: 22.3 Consensus size: 3
351545 TAAGTAAATG
* *
351555 ATA ATA ATA ATA ATA ATA ATA AT- ACA ATA ATA ATA ATA CTA ATTA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A-TA
* *
351600 GTT A-A ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA A
351621 GGGACTAAAT
Statistics
Matches: 52, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
2 2 0.04
3 48 0.92
4 2 0.04
ACGTcount: A:0.62, C:0.03, G:0.02, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:353729 original size:46 final size:44
Alignment explanation
Indices: 353366--353864 Score: 196
Period size: 43 Copynumber: 11.5 Consensus size: 44
353356 TAATCCGCTT
* * * *
353366 CACTGTAACTTCAGGGAGATAGGA-T-AGTATCTTCGATCTGCTC
1 CACTGTAACCTCAGGGAGATAAGACTGAAT-TCTTCGATCTACTC
** * * ** * * *
353409 CGTTGTAATCTCAGGAAGATAAGATCTCTA-GCTTCAATCT-GTAC
1 CACTGTAACCTCAGGGAGATAAGA-CTGAATTCTTCGATCTACT-C
* *
353453 CACTGTAACCTCAGGGAGATGAGATCTGAAATTCTTCGGTCTACTC
1 CACTGTAACCTCAGGGAGATAAGA-CTG-AATTCTTCGATCTACTC
* *
353499 CACTGTAACCCCAGGGAGATAAGACATG-A---TGCGATCTACTC
1 CACTGTAACCTCAGGGAGATAAGAC-TGAATTCTTCGATCTACTC
** * * ** * *
353540 TGCTGTAACTTCAGAGAGATAAGATCCTTTATT-TT-AATCCACTC
1 CACTGTAACCTCAGGGAGATAAGA--CTGAATTCTTCGATCTACTC
* * * * *
353584 TACTGTAACTTCAGGGAGATAGGA-T-AGTGTCTTCGATCTGCTC
1 CACTGTAACCTCAGGGAGATAAGACTGAAT-TCTTCGATCTACTC
* * * * * * *
353627 CGCTGCAATCTCAGGGAGAT-AGAAT-AGTGTCTTCGATATGCTC
1 CACTGTAACCTCAGGGAGATAAGACTGAAT-TCTTCGATCTACTC
* * *
353670 CGCTGTAATCTCAGGGAGATAAGATCTGAAATTCTTCGGTCTACTC
1 CACTGTAACCTCAGGGAGATAAGA-CTG-AATTCTTCGATCTACTC
* *
353716 CACTGTAACCTCAGAGAGATAAGACCTG-A-T-GT-GATCTACTC
1 CACTGTAACCTCAGGGAGATAAGA-CTGAATTCTTCGATCTACTC
** * * ** * *
353757 TGCTGTAACTTCAGAGAGATAAGATCCTTTATT-TT-AATCCACTC
1 CACTGTAACCTCAGGGAGATAAGA--CTGAATTCTTCGATCTACTC
* * * *
353801 CACTGTAACTTCAGGGAGATAGGA-T-AATGTCTTTGATCTGCTC
1 CACTGTAACCTCAGGGAGATAAGACTGAAT-TCTTCGATCTACTC
* *
353844 CGCTGTAATCTCAGGGAGATA
1 CACTGTAACCTCAGGGAGATA
353865 GGATCTCTAA
Statistics
Matches: 349, Mismatches: 80, Indels: 54
0.72 0.17 0.11
Matches are distributed among these distances:
40 3 0.01
41 62 0.18
42 11 0.03
43 105 0.30
44 93 0.27
45 5 0.01
46 67 0.19
47 3 0.01
ACGTcount: A:0.28, C:0.21, G:0.21, T:0.30
Consensus pattern (44 bp):
CACTGTAACCTCAGGGAGATAAGACTGAATTCTTCGATCTACTC
Found at i:353766 original size:217 final size:218
Alignment explanation
Indices: 353273--353873 Score: 829
Period size: 217 Copynumber: 2.8 Consensus size: 218
353263 TGTGGTTTTA
* * * * * ** * *
353273 GTCTGCTCTACTGTAACTTCAGGGAGATAAGA-CTGGATGAGATCTGCTCTACTACATCTTTAGA
1 GTCTACTCCACTGTAACCTCAGGGAGATAAGACCT-GATGAGATCTACTCTGCTGTAACTTCAGA
* * * *
353337 GAGATAAGATCTTTTGTTTTAATCCGCT-TCACTGTAACTTCAGGGAGATAGGATAGTATCTTCG
65 GAGATAAGATCCTTTATTTTAATCCACTCT-ACTGTAACTTCAGGGAGATAGGATAGTGTCTTCG
* * *
353401 ATCTGCTCCGTTGTAATCTCAGGAAGATA-AGATCTCTAGCTTCAATCTGTACCACTGTAACCTC
129 ATCTGCTCCGCTGTAATCTCAGGGAGATAGAGATCTCTA-CTTCAATATGTACCACTGTAACCTC
*
353465 AGGGAGATGAGATCTGAAATTCTTCG
193 AGGGAGATAAGATCTGAAATTCTTCG
* * *
353491 GTCTACTCCACTGTAACCCCAGGGAGATAAGACATGATGCGATCTACTCTGCTGTAACTTCAGAG
1 GTCTACTCCACTGTAACCTCAGGGAGATAAGACCTGATGAGATCTACTCTGCTGTAACTTCAGAG
353556 AGATAAGATCCTTTATTTTAATCCACTCTACTGTAACTTCAGGGAGATAGGATAGTGTCTTCGAT
66 AGATAAGATCCTTTATTTTAATCCACTCTACTGTAACTTCAGGGAGATAGGATAGTGTCTTCGAT
* * * * * *
353621 CTGCTCCGCTGCAATCTCAGGGAGATAGA-ATAGTGT-CTTCGATATGCT-CCGCTGTAATCTCA
131 CTGCTCCGCTGTAATCTCAGGGAGATAGAGAT-CTCTACTTCAATATG-TACCACTGTAACCTCA
353683 GGGAGATAAGATCTGAAATTCTTCG
194 GGGAGATAAGATCTGAAATTCTTCG
* *
353708 GTCTACTCCACTGTAACCTCAGAGAGATAAGACCTGATGTGATCTACTCTGCTGTAACTTCAGAG
1 GTCTACTCCACTGTAACCTCAGGGAGATAAGACCTGATGAGATCTACTCTGCTGTAACTTCAGAG
* * *
353773 AGATAAGATCCTTTATTTTAATCCACTCCACTGTAACTTCAGGGAGATAGGATAATGTCTTTGAT
66 AGATAAGATCCTTTATTTTAATCCACTCTACTGTAACTTCAGGGAGATAGGATAGTGTCTTCGAT
353838 CTGCTCCGCTGTAATCTCAGGGAGATAG-GATCTCTA
131 CTGCTCCGCTGTAATCTCAGGGAGATAGAGATCTCTA
353874 ATATTCATTA
Statistics
Matches: 340, Mismatches: 36, Indels: 15
0.87 0.09 0.04
Matches are distributed among these distances:
216 2 0.01
217 196 0.58
218 137 0.40
219 5 0.01
ACGTcount: A:0.27, C:0.21, G:0.21, T:0.31
Consensus pattern (218 bp):
GTCTACTCCACTGTAACCTCAGGGAGATAAGACCTGATGAGATCTACTCTGCTGTAACTTCAGAG
AGATAAGATCCTTTATTTTAATCCACTCTACTGTAACTTCAGGGAGATAGGATAGTGTCTTCGAT
CTGCTCCGCTGTAATCTCAGGGAGATAGAGATCTCTACTTCAATATGTACCACTGTAACCTCAGG
GAGATAAGATCTGAAATTCTTCG
Found at i:353820 original size:44 final size:41
Alignment explanation
Indices: 353712--353821 Score: 121
Period size: 44 Copynumber: 2.6 Consensus size: 41
353702 TCTTCGGTCT
* * *
353712 ACTCCACTGTAACCTCAGAGAGATAAGACCTGATGTGATCT
1 ACTCCACTGTAACTTCAGAGAGATAAGACCTGATGTAATCC
** * *
353753 ACTCTGCTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCC
1 ACTCCACTGTAACTTCAGAGAGATAAGA-CC-TGA-TGTAATCC
*
353797 ACTCCACTGTAACTTCAGGGAGATA
1 ACTCCACTGTAACTTCAGAGAGATA
353822 GGATAATGTC
Statistics
Matches: 56, Mismatches: 10, Indels: 3
0.81 0.14 0.04
Matches are distributed among these distances:
41 25 0.45
42 2 0.04
43 2 0.04
44 27 0.48
ACGTcount: A:0.31, C:0.23, G:0.17, T:0.29
Consensus pattern (41 bp):
ACTCCACTGTAACTTCAGAGAGATAAGACCTGATGTAATCC
Found at i:354022 original size:3 final size:3
Alignment explanation
Indices: 354014--354051 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
354004 ATGCAGAATT
354014 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
354052 TTGAGAATGA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:366719 original size:3 final size:3
Alignment explanation
Indices: 366711--366741 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
366701 TTGTATGTAG
*
366711 AAT AAT AAT AAT AAT AGT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
366742 TAGAAACAGT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:368996 original size:28 final size:28
Alignment explanation
Indices: 368938--368996 Score: 66
Period size: 28 Copynumber: 2.1 Consensus size: 28
368928 ATTAATAATT
****
368938 ATAAAATTATATTTTTTTTTTCAAAATA
1 ATAAAATTATATTTTTACGATCAAAATA
368966 ATAAAATTATATTTTTACGATCATAAA-A
1 ATAAAATTATATTTTTACGATCA-AAATA
368994 ATA
1 ATA
368997 TATAATTAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
28 23 0.88
29 3 0.12
ACGTcount: A:0.47, C:0.05, G:0.02, T:0.46
Consensus pattern (28 bp):
ATAAAATTATATTTTTACGATCAAAATA
Found at i:378558 original size:2 final size:2
Alignment explanation
Indices: 378551--378587 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
378541 ACTAGATCTT
378551 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
378588 CAGTGTTAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:380363 original size:6 final size:6
Alignment explanation
Indices: 380352--380376 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
380342 GGCAAATCTC
380352 TTTTCT TTTTCT TTTTCT TTTTCT T
1 TTTTCT TTTTCT TTTTCT TTTTCT T
380377 CTAAGCACTT
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:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (6 bp):
TTTTCT
Found at i:385354 original size:24 final size:24
Alignment explanation
Indices: 385327--385378 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
385317 TTAGTAAGTC
*
385327 AAATAAACTATACTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
385351 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
385375 AAAT
1 AAAT
385379 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:387320 original size:24 final size:24
Alignment explanation
Indices: 387293--387344 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
387283 TTAGTAAGTC
*
387293 AAATAAACTATACTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
387317 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
387341 AAAT
1 AAAT
387345 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:388259 original size:26 final size:26
Alignment explanation
Indices: 388230--388281 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
388220 TGGTCTACAC
388230 CCTTTCGATTATATGGAAATTGAAAA
1 CCTTTCGATTATATGGAAATTGAAAA
*
388256 CCTTTCTATTATATGGAAATTGAAAA
1 CCTTTCGATTATATGGAAATTGAAAA
388282 ATGAACTCAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.38, C:0.12, G:0.13, T:0.37
Consensus pattern (26 bp):
CCTTTCGATTATATGGAAATTGAAAA
Found at i:399149 original size:44 final size:43
Alignment explanation
Indices: 399079--399271 Score: 180
Period size: 44 Copynumber: 4.5 Consensus size: 43
399069 TGATTTCATA
* * *
399079 TAAGACCATAGCTGGGGTA-TGACATCGATATATGGGACTTTGTG
1 TAAGACCATAGCTGGGATATTGGCATCGATATAT-GGA-TTCGTG
* *
399123 TAAGACCATATCTAGGATA-TGGCATCGATATATGTGATTACGTG
1 TAAGACCATAGCTGGGATATTGGCATCGATATATG-GATT-CGTG
** *
399167 TAAGACCATATATGGGACATTGGCATCGATATAT-GATTCGTG
1 TAAGACCATAGCTGGGATATTGGCATCGATATATGGATTCGTG
* * * * *
399209 TAAGATCATAGCTGGGCTATTGGCATCGATATGT-GATAACATG
1 TAAGACCATAGCTGGGATATTGGCATCGATATATGGAT-TCGTG
399252 TAAGACCATATG-TGGGATAT
1 TAAGACCATA-GCTGGGATAT
399272 GGAATTGTAT
Statistics
Matches: 126, Mismatches: 18, Indels: 11
0.81 0.12 0.07
Matches are distributed among these distances:
42 35 0.28
43 26 0.21
44 51 0.40
45 14 0.11
ACGTcount: A:0.31, C:0.13, G:0.25, T:0.31
Consensus pattern (43 bp):
TAAGACCATAGCTGGGATATTGGCATCGATATATGGATTCGTG
Found at i:399254 original size:85 final size:87
Alignment explanation
Indices: 399101--399268 Score: 216
Period size: 85 Copynumber: 1.9 Consensus size: 87
399091 TGGGGTATGA
* * * *
399101 CATCGATATATGGGACTTTGTGTAAGACCATATCTAGGATATGGCATCGATATATGTGATTACGT
1 CATCGATATAT-GGACTTCGTGTAAGACCATAGCTAGGATATGGCATCGA-ATATGTGATAACAT
399166 GTAAGACCATATATGGGACATTGG
64 GTAAGACCATATATGGGACATTGG
* * *
399190 CATCGATATAT-GA-TTCGTGTAAGATCATAGCTGGGCTATTGGCATCG-ATATGTGATAACATG
1 CATCGATATATGGACTTCGTGTAAGACCATAGCTAGGATA-TGGCATCGAATATGTGATAACATG
*
399252 TAAGACCATATGTGGGA
65 TAAGACCATATATGGGA
399269 TATGGAATTG
Statistics
Matches: 70, Mismatches: 8, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
85 29 0.41
86 20 0.29
87 10 0.14
89 11 0.16
ACGTcount: A:0.30, C:0.14, G:0.25, T:0.31
Consensus pattern (87 bp):
CATCGATATATGGACTTCGTGTAAGACCATAGCTAGGATATGGCATCGAATATGTGATAACATGT
AAGACCATATATGGGACATTGG
Found at i:406476 original size:38 final size:38
Alignment explanation
Indices: 406433--406509 Score: 100
Period size: 38 Copynumber: 2.0 Consensus size: 38
406423 CTTTTACTTA
* * **
406433 CGAGATTTTATTAATCTCACGGTCCGCTAATTTACGAT
1 CGAGATTTAATGAATCTCACAATCCGCTAATTTACGAT
* *
406471 CGAGATTTAATGAATCTCGCAATTCGCTAATTTACGAT
1 CGAGATTTAATGAATCTCACAATCCGCTAATTTACGAT
406509 C
1 C
406510 ACAACCTTTA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
38 33 1.00
ACGTcount: A:0.29, C:0.21, G:0.16, T:0.35
Consensus pattern (38 bp):
CGAGATTTAATGAATCTCACAATCCGCTAATTTACGAT
Found at i:415020 original size:84 final size:84
Alignment explanation
Indices: 414873--415034 Score: 288
Period size: 84 Copynumber: 1.9 Consensus size: 84
414863 AAGGGAATAC
* *
414873 AGTTCATGACGAATACGGGACAACTTCGTATCGGTTACTGCTGCAAAGAGGGGAGTGGCAGTATT
1 AGTTCATGACGAATACGGGACAACTTCGCACCGGTTACTGCTGCAAAGAGGGGAGTGGCAGTATT
414938 CCAAAAATCACTTACCATT
66 CCAAAAATCACTTACCATT
* *
414957 AGTTTATGACGAATACGGGACAACTTCGCACCGGTTACTGCTGCAAAGAGGGGAGTGGTAGTATT
1 AGTTCATGACGAATACGGGACAACTTCGCACCGGTTACTGCTGCAAAGAGGGGAGTGGCAGTATT
415022 CCAAAAATCACTT
66 CCAAAAATCACTT
415035 GCCGTTCGAA
Statistics
Matches: 74, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
84 74 1.00
ACGTcount: A:0.31, C:0.20, G:0.25, T:0.25
Consensus pattern (84 bp):
AGTTCATGACGAATACGGGACAACTTCGCACCGGTTACTGCTGCAAAGAGGGGAGTGGCAGTATT
CCAAAAATCACTTACCATT
Found at i:415987 original size:33 final size:33
Alignment explanation
Indices: 415916--415991 Score: 89
Period size: 33 Copynumber: 2.3 Consensus size: 33
415906 ACAGGGGAAA
*
415916 GTGATGTTGAAAGAGTAGAAGTTGATAGAAAGG
1 GTGATGTTGAAAGAGTAAAAGTTGATAGAAAGG
* * * * **
415949 ATGATGTTGAAGGGGTAAAAGTTGATGGGGAGG
1 GTGATGTTGAAAGAGTAAAAGTTGATAGAAAGG
415982 GTGATGTTGA
1 GTGATGTTGA
415992 TGGGAAGGGT
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.33, C:0.00, G:0.41, T:0.26
Consensus pattern (33 bp):
GTGATGTTGAAAGAGTAAAAGTTGATAGAAAGG
Found at i:415992 original size:18 final size:18
Alignment explanation
Indices: 415969--416014 Score: 74
Period size: 18 Copynumber: 2.6 Consensus size: 18
415959 AGGGGTAAAA
*
415969 GTTGATGGGGAGGGTGAT
1 GTTGATGGGGAGGGTAAT
*
415987 GTTGATGGGAAGGGTAAT
1 GTTGATGGGGAGGGTAAT
416005 GTTGATGGGG
1 GTTGATGGGG
416015 TAGGTTTAGA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.20, C:0.00, G:0.52, T:0.28
Consensus pattern (18 bp):
GTTGATGGGGAGGGTAAT
Found at i:416062 original size:33 final size:33
Alignment explanation
Indices: 416023--416144 Score: 102
Period size: 33 Copynumber: 3.7 Consensus size: 33
416013 GGTAGGTTTA
*
416023 GATGGGGAAGGTGTTGTAGAAGGGGTACAAGCT
1 GATGGGGAAGGTGATGTAGAAGGGGTACAAGCT
* * * * *
416056 GCTGGGGAATGCGATGCT-GAAAGGGTAGAAGCT
1 GATGGGGAAGGTGATG-TAGAAGGGGTACAAGCT
* * * *
416089 GATGGGTAGGGTGATGTAGAAGGCGTACAAACT
1 GATGGGGAAGGTGATGTAGAAGGGGTACAAGCT
* ** *
416122 TATGAAGAGGGTGATGTAGAAGG
1 GATGGGGAAGGTGATGTAGAAGG
416145 TGTAAAAGTT
Statistics
Matches: 68, Mismatches: 19, Indels: 4
0.75 0.21 0.04
Matches are distributed among these distances:
32 1 0.01
33 66 0.97
34 1 0.01
ACGTcount: A:0.30, C:0.07, G:0.43, T:0.20
Consensus pattern (33 bp):
GATGGGGAAGGTGATGTAGAAGGGGTACAAGCT
Found at i:416797 original size:11 final size:11
Alignment explanation
Indices: 416781--416820 Score: 71
Period size: 11 Copynumber: 3.6 Consensus size: 11
416771 TACACAAGGC
*
416781 TGCCTTTGCAT
1 TGCCTTCGCAT
416792 TGCCTTCGCAT
1 TGCCTTCGCAT
416803 TGCCTTCGCAT
1 TGCCTTCGCAT
416814 TGCCTTC
1 TGCCTTC
416821 ATTCTTAAAG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
11 28 1.00
ACGTcount: A:0.07, C:0.35, G:0.17, T:0.40
Consensus pattern (11 bp):
TGCCTTCGCAT
Found at i:423546 original size:4 final size:4
Alignment explanation
Indices: 423532--423563 Score: 55
Period size: 4 Copynumber: 8.0 Consensus size: 4
423522 ATGATTCACA
*
423532 ACAT GCAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
423564 CCATCCATCC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.47, C:0.25, G:0.03, T:0.25
Consensus pattern (4 bp):
ACAT
Found at i:427897 original size:22 final size:23
Alignment explanation
Indices: 427863--427906 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 23
427853 ACCATCAATG
427863 TATTTAAATAA-TTAATTTTATA
1 TATTTAAATAATTTAATTTTATA
427885 TATTTATAA-AATTTTAATTTTA
1 TATTTA-AATAA-TTTAATTTTA
427907 ATTTTCAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
22 8 0.42
23 2 0.11
24 9 0.47
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (23 bp):
TATTTAAATAATTTAATTTTATA
Found at i:433880 original size:196 final size:196
Alignment explanation
Indices: 433541--433930 Score: 595
Period size: 196 Copynumber: 2.0 Consensus size: 196
433531 CCTTGTAGGA
* *
433541 CTTTCTGTATAAAAAGACACTCTTGTGGTTGAGTTTGATTCACTTAAAACTTCTTTGTGCTCTAG
1 CTTTCTGTATAAAAAGACACTCTTGTGGTTGAGTTTAATTCACTTAAAACTTCTTTGTGCTCAAG
* *
433606 GGATGGAGAGGGAACACATACTAAATGCACCATGACGTAATTTCTTGGAAGGATATCTTATATTA
66 GGATGGAGAGAGAACACATACTAAATGCACCATGACATAATTTCTTGGAAGGATATCTTATATTA
* *
433671 CTAATTATTATAGGTCAAGTTGTGTCGGATTGAAACCACTTGAGAA-GAAAATGGAATGTGCTTG
131 CTAATTATTATAGGTCAAATTGCGTCGGATTGAAACCACTTGA-AATGAAAATGGAATGTGCTTG
433735 TG
195 TG
* * * * * *
433737 CTTTTTGTATAAAAGGACATTCTTGTGGTTGTGTTTAATTCACTTTAAGCTTAC-TTGTGCTCAA
1 CTTTCTGTATAAAAAGACACTCTTGTGGTTGAGTTTAATTCACTTAAAACTT-CTTTGTGCTCAA
* * * *
433801 GGGATGGAGAGATAACACATACTAAATGTACCTTGACATGATTTCTTGGAAGGATATCTTATATT
65 GGGATGGAGAGAGAACACATACTAAATGCACCATGACATAATTTCTTGGAAGGATATCTTATATT
*
433866 ACTAATTATTATAGGTCAAATTGCGTTGGATTGAAACCACTTGAAATGAAAATGGAATGTGCTTG
130 ACTAATTATTATAGGTCAAATTGCGTCGGATTGAAACCACTTGAAATGAAAATGGAATGTGCTTG
433931 CACTTTTTAA
Statistics
Matches: 175, Mismatches: 17, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
195 2 0.01
196 172 0.98
197 1 0.01
ACGTcount: A:0.31, C:0.13, G:0.21, T:0.35
Consensus pattern (196 bp):
CTTTCTGTATAAAAAGACACTCTTGTGGTTGAGTTTAATTCACTTAAAACTTCTTTGTGCTCAAG
GGATGGAGAGAGAACACATACTAAATGCACCATGACATAATTTCTTGGAAGGATATCTTATATTA
CTAATTATTATAGGTCAAATTGCGTCGGATTGAAACCACTTGAAATGAAAATGGAATGTGCTTGT
G
Found at i:440927 original size:18 final size:17
Alignment explanation
Indices: 440904--440952 Score: 53
Period size: 19 Copynumber: 2.7 Consensus size: 17
440894 ATAGTACAAC
*
440904 AAAATTGAAAGAGAATGA
1 AAAATTGAAA-AGAAAGA
440922 AAAATTGTAACAAGAAAGA
1 AAAATTG-AA-AAGAAAGA
*
440941 AAAATAGAAAAG
1 AAAATTGAAAAG
440953 GAGGGATTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
17 3 0.11
18 9 0.33
19 14 0.52
20 1 0.04
ACGTcount: A:0.65, C:0.02, G:0.18, T:0.14
Consensus pattern (17 bp):
AAAATTGAAAAGAAAGA
Found at i:441823 original size:3 final size:3
Alignment explanation
Indices: 441815--441887 Score: 69
Period size: 3 Copynumber: 25.0 Consensus size: 3
441805 TTTGTTACTG
* * *
441815 TTA TTA TTA TCA TTA TAA TTA -AA TT- TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * * *
441861 TTA CTA TTG TTA CTA TTA TTA CTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA
441888 CCGCTTTGTG
Statistics
Matches: 54, Mismatches: 14, Indels: 4
0.75 0.19 0.06
Matches are distributed among these distances:
2 3 0.06
3 51 0.94
ACGTcount: A:0.34, C:0.05, G:0.01, T:0.59
Consensus pattern (3 bp):
TTA
Found at i:443610 original size:20 final size:19
Alignment explanation
Indices: 443579--443637 Score: 57
Period size: 20 Copynumber: 2.9 Consensus size: 19
443569 ACTTGTTTAA
*
443579 AAACAATTTTAACATGATTG
1 AAACAGTTTTAAC-TGATTG
*
443599 AAA-ATGTTTTAACTCAATTG
1 AAACA-GTTTTAACT-GATTG
443619 AAACAGTTTTAACTTGATT
1 AAACAGTTTTAAC-TGATT
443638 TTATCATTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
19 2 0.06
20 28 0.88
21 2 0.06
ACGTcount: A:0.41, C:0.10, G:0.10, T:0.39
Consensus pattern (19 bp):
AAACAGTTTTAACTGATTG
Found at i:443689 original size:22 final size:24
Alignment explanation
Indices: 443662--443705 Score: 74
Period size: 22 Copynumber: 1.9 Consensus size: 24
443652 ATTTTGTTCA
443662 ACTTTAATTT-TTAT-TCAAAAAC
1 ACTTTAATTTGTTATATCAAAAAC
443684 ACTTTAATTTGTTATATCAAAA
1 ACTTTAATTTGTTATATCAAAA
443706 CATATTATCA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 10 0.50
23 4 0.20
24 6 0.30
ACGTcount: A:0.41, C:0.11, G:0.02, T:0.45
Consensus pattern (24 bp):
ACTTTAATTTGTTATATCAAAAAC
Found at i:446238 original size:31 final size:29
Alignment explanation
Indices: 446203--446287 Score: 91
Period size: 31 Copynumber: 2.9 Consensus size: 29
446193 CAACAAATAC
* *
446203 TTATAATTTAAGAACTCAATTAAAACATTAT
1 TTATAATTTAAAAACTCAATTAAAA-AAT-T
* *
446234 TTATAGTTCAAAAACTCAATTAAAAAATT
1 TTATAATTTAAAAACTCAATTAAAAAATT
*
446263 TTAAAATTTAAAAACT-AAGTTAAAA
1 TTATAATTTAAAAACTCAA-TTAAAA
446288 TTTTTTAGAG
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
28 2 0.04
29 20 0.43
30 2 0.04
31 22 0.48
ACGTcount: A:0.53, C:0.08, G:0.04, T:0.35
Consensus pattern (29 bp):
TTATAATTTAAAAACTCAATTAAAAAATT
Found at i:449727 original size:16 final size:17
Alignment explanation
Indices: 449693--449743 Score: 52
Period size: 16 Copynumber: 3.1 Consensus size: 17
449683 TAGAAATTAT
*
449693 ATAAAAA-ATAAATATAA
1 ATAAAAATATTAATA-AA
449710 ATAAAAATATTAA-AAA
1 ATAAAAATATTAATAAA
* *
449726 ATAATAATCTTAATAAA
1 ATAAAAATATTAATAAA
449743 A
1 A
449744 ATAACAAACT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
16 13 0.45
17 12 0.41
18 4 0.14
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (17 bp):
ATAAAAATATTAATAAA
Found at i:449731 original size:13 final size:14
Alignment explanation
Indices: 449690--449731 Score: 54
Period size: 13 Copynumber: 3.1 Consensus size: 14
449680 TTCTAGAAAT
449690 TATATAAAAAATAA
1 TATATAAAAAATAA
449704 -ATATAAATAAA-AA
1 TATATAAA-AAATAA
449717 TAT-TAAAAAATAA
1 TATATAAAAAATAA
449730 TA
1 TA
449732 ATCTTAATAA
Statistics
Matches: 25, Mismatches: 0, Indels: 7
0.78 0.00 0.22
Matches are distributed among these distances:
12 3 0.12
13 17 0.68
14 5 0.20
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (14 bp):
TATATAAAAAATAA
Found at i:455410 original size:38 final size:38
Alignment explanation
Indices: 455359--455435 Score: 154
Period size: 38 Copynumber: 2.0 Consensus size: 38
455349 TATTAGAAAA
455359 TATGATTTTGAACTAAATAAGTCCTTATGTGGTAATTT
1 TATGATTTTGAACTAAATAAGTCCTTATGTGGTAATTT
455397 TATGATTTTGAACTAAATAAGTCCTTATGTGGTAATTT
1 TATGATTTTGAACTAAATAAGTCCTTATGTGGTAATTT
455435 T
1 T
455436 TCCAAGGATG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.31, C:0.08, G:0.16, T:0.45
Consensus pattern (38 bp):
TATGATTTTGAACTAAATAAGTCCTTATGTGGTAATTT
Found at i:472922 original size:14 final size:14
Alignment explanation
Indices: 472903--472932 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
472893 TTACTCTTTG
472903 GGCCTCCTGGTACA
1 GGCCTCCTGGTACA
472917 GGCCTCCTGGTACA
1 GGCCTCCTGGTACA
472931 GG
1 GG
472933 GAAAACAATG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.13, C:0.33, G:0.33, T:0.20
Consensus pattern (14 bp):
GGCCTCCTGGTACA
Found at i:486742 original size:2 final size:2
Alignment explanation
Indices: 486731--486767 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
486721 GTGGGCAACA
486731 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
486768 TTAAGGGGTC
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:487566 original size:13 final size:12
Alignment explanation
Indices: 487548--487620 Score: 62
Period size: 13 Copynumber: 6.1 Consensus size: 12
487538 TGGCCTGAAT
487548 TATATATTAAATA
1 TATATATT-AATA
* *
487561 TATATATTTATT
1 TATATATTAATA
* *
487573 TTTA-ATCAA-A
1 TATATATTAATA
487583 TATATATT-ATA
1 TATATATTAATA
487594 TATATATTAAATA
1 TATATATT-AATA
487607 TATATATTTAATA
1 TATATA-TTAATA
487620 T
1 T
487621 GAGTCAGGTC
Statistics
Matches: 47, Mismatches: 8, Indels: 10
0.72 0.12 0.15
Matches are distributed among these distances:
10 4 0.09
11 14 0.30
12 5 0.11
13 22 0.47
14 2 0.04
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.52
Consensus pattern (12 bp):
TATATATTAATA
Found at i:487620 original size:11 final size:11
Alignment explanation
Indices: 487548--487611 Score: 56
Period size: 11 Copynumber: 5.6 Consensus size: 11
487538 TGGCCTGAAT
487548 TATATATTAAA
1 TATATATTAAA
**
487559 TATATATATTTA
1 TATATAT-TAAA
* * *
487571 TTTTTAATCAAA
1 TATAT-ATTAAA
*
487583 TATATATTATA
1 TATATATTAAA
487594 TATATATTAAA
1 TATATATTAAA
487605 TATATAT
1 TATATAT
487612 ATTTAATATG
Statistics
Matches: 39, Mismatches: 12, Indels: 4
0.71 0.22 0.07
Matches are distributed among these distances:
11 28 0.72
12 9 0.23
13 2 0.05
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.52
Consensus pattern (11 bp):
TATATATTAAA
Found at i:491810 original size:37 final size:36
Alignment explanation
Indices: 491761--491836 Score: 143
Period size: 37 Copynumber: 2.1 Consensus size: 36
491751 ATAAGAAAGA
491761 AAAATAAAACACAGATTTTACGTGGAAACCCTTTAGG
1 AAAATAAAACACAGATTTTACGTGGAAA-CCTTTAGG
491798 AAAATAAAACACAGATTTTACGTGGAAACCTTTAGG
1 AAAATAAAACACAGATTTTACGTGGAAACCTTTAGG
491834 AAA
1 AAA
491837 GAAATACAGG
Statistics
Matches: 39, Mismatches: 0, Indels: 1
0.98 0.00 0.03
Matches are distributed among these distances:
36 11 0.28
37 28 0.72
ACGTcount: A:0.46, C:0.14, G:0.16, T:0.24
Consensus pattern (36 bp):
AAAATAAAACACAGATTTTACGTGGAAACCTTTAGG
Found at i:493141 original size:290 final size:288
Alignment explanation
Indices: 492493--493110 Score: 628
Period size: 290 Copynumber: 2.1 Consensus size: 288
492483 TGGTAAATTA
* * * ** * ** *
492493 AAAG-TTTTACTAATGCAATTGGCATGGGTTCAAATATCACCATATGCATATTTTTATTAGTTTT
1 AAAGATTTTATTAATGCACTTGGCATGGGCTCAAATCCCACTATATG-A-A-TAATATTA-TTTA
** * *
492557 TTTTAAAGTAAAAGACTAACGTACCCTAAAATAATATTAATTGTTTTGATTATGGAAGGACATTC
62 TTTTAAAGTAAAAGACTAAAATACCCTAAAATAATATTAATTATTTTAATTATGGAAGGACATTC
* * * * * * *
492622 CCGTAACTTCCTAACCGAGTTGGTGACCCAGTTGAGGGTGACACCGATTCAATCAGGAACTTAAA
127 CCGTAACTTCATAACCGAGTTGGCGACACAGTTGAGGGCGACACCAACTCAATCAAGAACTTAAA
* * * * * *
492687 TAATAGTATATATATACAATTGATGGTCATGAAGTGTATATAATAAAATTAAAATATATAAATAT
192 TAATAGTATAGATAGACAATTGAAGGTCATAAAGTGTACATAATAAAATTAAAATATATAAAAAT
* *
492752 ATTAAAAGAAAAAGCTTTAGCTGAAAGGTAAATT
257 ATTAAAAGAAAAAGCTTTAGATG-AA-GTAAACT
* ** * * * * *
492786 AAAGTTTTTATTAATGCACTTGGTGTGGGTTCAAATTCCACTTTATGCATATTATTA-TTATTTT
1 AAAGATTTTATTAATGCACTTGGCATGGGCTCAAATCCCACTATATGAATAATATTATTTATTTT
* * *
492850 AAAGTGAAAAGACTAAAATACTCC-CAAATAATATTACTTATTTTAATTATGGAATGACATTCCC
66 AAAGT-AAAAGACTAAAATAC-CCTAAAATAATATTAATTATTTTAATTATGGAAGGACATTCCC
* * * * *
492914 TTAATTTCATAACCGAGTTGGCGACACAGTTGAGGGCGGCATCAACTCAATCAAGAGCTTAAATA
129 GTAACTTCATAACCGAGTTGGCGACACAGTTGAGGGCGACACCAACTCAATCAAGAACTTAAATA
** * * *
492979 ATAGTATAGATAGATGA-TGAAGG-CACTAAAGTGTGCATGATAAAATTAAAATGTATAAAAATA
194 ATAGTATAGATAGACAATTGAAGGTCA-TAAAGTGTACATAATAAAATTAAAATATATAAAAATA
493042 -TAAAA-AAAATAG-TTTA-ATG-A-TAAACT
258 TTAAAAGAAAA-AGCTTTAGATGAAGTAAACT
493068 AAAGATTTTATTAATGCACTTGGCATGGGCTCAAATCCCACTA
1 AAAGATTTTATTAATGCACTTGGCATGGGCTCAAATCCCACTA
493111 AAATACCTTC
Statistics
Matches: 271, Mismatches: 49, Indels: 21
0.79 0.14 0.06
Matches are distributed among these distances:
282 42 0.15
284 1 0.00
286 2 0.01
287 8 0.03
288 9 0.03
289 47 0.17
290 114 0.42
291 9 0.03
292 1 0.00
293 4 0.01
294 34 0.13
ACGTcount: A:0.39, C:0.13, G:0.16, T:0.33
Consensus pattern (288 bp):
AAAGATTTTATTAATGCACTTGGCATGGGCTCAAATCCCACTATATGAATAATATTATTTATTTT
AAAGTAAAAGACTAAAATACCCTAAAATAATATTAATTATTTTAATTATGGAAGGACATTCCCGT
AACTTCATAACCGAGTTGGCGACACAGTTGAGGGCGACACCAACTCAATCAAGAACTTAAATAAT
AGTATAGATAGACAATTGAAGGTCATAAAGTGTACATAATAAAATTAAAATATATAAAAATATTA
AAAGAAAAAGCTTTAGATGAAGTAAACT
Found at i:495609 original size:21 final size:20
Alignment explanation
Indices: 495583--495626 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 20
495573 TATCTGAAAT
495583 CTTAAACCCCGAACTCTAAAC
1 CTTAAACCCCGAACT-TAAAC
* *
495604 CTTAAACTCCGACCTTAAAC
1 CTTAAACCCCGAACTTAAAC
495624 CTT
1 CTT
495627 GACCTCTGAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 8 0.38
21 13 0.62
ACGTcount: A:0.34, C:0.36, G:0.05, T:0.25
Consensus pattern (20 bp):
CTTAAACCCCGAACTTAAAC
Found at i:496078 original size:21 final size:21
Alignment explanation
Indices: 496054--496123 Score: 79
Period size: 21 Copynumber: 3.4 Consensus size: 21
496044 GCGGTCAAGA
*
496054 TTTAGGTTTAGAGTTCAGCAT
1 TTTAGGTTTAGAGTTCAGAAT
* *
496075 TTTAGGTTCAGAGTTCA-AAA
1 TTTAGGTTTAGAGTTCAGAAT
* **
496095 TTCAGGTTTAGAGTTCAGTGT
1 TTTAGGTTTAGAGTTCAGAAT
496116 TTTAGGTT
1 TTTAGGTT
496124 CGAGGTTCAG
Statistics
Matches: 39, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
20 16 0.41
21 23 0.59
ACGTcount: A:0.24, C:0.09, G:0.24, T:0.43
Consensus pattern (21 bp):
TTTAGGTTTAGAGTTCAGAAT
Found at i:496119 original size:41 final size:41
Alignment explanation
Indices: 496048--496132 Score: 118
Period size: 41 Copynumber: 2.1 Consensus size: 41
496038 AGGTCTGCGG
* *
496048 TCAAGATTTAGGTTTAGAGTTCAGCATTTTAGGTTC-AGAGT
1 TCAAAATTCAGGTTTAGAGTTCAGCATTTTAGGTTCGAG-GT
**
496089 TCAAAATTCAGGTTTAGAGTTCAGTGTTTTAGGTTCGAGGT
1 TCAAAATTCAGGTTTAGAGTTCAGCATTTTAGGTTCGAGGT
496130 TCA
1 TCA
496133 GGTAAAAAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
41 37 0.95
42 2 0.05
ACGTcount: A:0.26, C:0.11, G:0.25, T:0.39
Consensus pattern (41 bp):
TCAAAATTCAGGTTTAGAGTTCAGCATTTTAGGTTCGAGGT
Found at i:497883 original size:29 final size:30
Alignment explanation
Indices: 497826--497887 Score: 76
Period size: 29 Copynumber: 2.1 Consensus size: 30
497816 ATACATTTTA
497826 ATCACAATCAAAGTTTCATGCCTATAATTGC
1 ATCACAATCAAAGTTTCATG-CTATAATTGC
497857 ATCA-AATCAAAG-TTCATG-TATCCAATTGC
1 ATCACAATCAAAGTTTCATGCTAT--AATTGC
497886 AT
1 AT
497888 ATTAAATCGA
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
27 3 0.10
29 14 0.48
30 8 0.28
31 4 0.14
ACGTcount: A:0.37, C:0.21, G:0.10, T:0.32
Consensus pattern (30 bp):
ATCACAATCAAAGTTTCATGCTATAATTGC
Found at i:500172 original size:6 final size:6
Alignment explanation
Indices: 500161--500204 Score: 52
Period size: 6 Copynumber: 7.2 Consensus size: 6
500151 TTAATAATTT
* * *
500161 AATATA AATATA AATATA AATATA ATTATA TATAATT AATATA A
1 AATATA AATATA AATATA AATATA AATATA AAT-ATA AATATA A
500205 TATTTTTATA
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
6 27 0.87
7 4 0.13
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (6 bp):
AATATA
Found at i:507124 original size:2 final size:2
Alignment explanation
Indices: 507117--507147 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
507107 TTCTTTTTGG
*
507117 TA TA TA TA TA AA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
507148 TGGATTTCAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Done.