Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014093.1 Kokia drynarioides strain JFW-HI SEQ_129124, whole genome shotgun sequence
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: 310132
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 176 characters in sequence are not A, C, G, or T
File 1 of 2
Found at i:109 original size:37 final size:38
Alignment explanation
Indices: 9--111 Score: 100
Period size: 37 Copynumber: 2.7 Consensus size: 38
1 CCTTGAGT
* *
9 CGATGAGACACTGGGTGTCATTATTTTACTTCGGATAGATT
1 CGATGAGACACTGGGTGTC---ACTTTACTTCGGATAGATC
** * ** *
50 CGATGAGGTACTAGGTACCACTTTACTTCGGCTAG-TC
1 CGATGAGACACTGGGTGTCACTTTACTTCGGATAGATC
87 CGATGAGACACTGGGTGTCACTTTA
1 CGATGAGACACTGGGTGTCACTTTA
112 TTGCTTCGAA
Statistics
Matches: 49, Mismatches: 13, Indels: 4
0.74 0.20 0.06
Matches are distributed among these distances:
37 21 0.43
38 14 0.29
41 14 0.29
ACGTcount: A:0.23, C:0.19, G:0.25, T:0.32
Consensus pattern (38 bp):
CGATGAGACACTGGGTGTCACTTTACTTCGGATAGATC
Found at i:9879 original size:16 final size:16
Alignment explanation
Indices: 9860--9898 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
9850 ATATTTAATA
*
9860 ATTTAATACATTTTTT
1 ATTTAATAAATTTTTT
*
9876 ATTTATTAAATTTTTT
1 ATTTAATAAATTTTTT
*
9892 ATATAAT
1 ATTTAAT
9899 TATCTTAATA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.62
Consensus pattern (16 bp):
ATTTAATAAATTTTTT
Found at i:17467 original size:19 final size:20
Alignment explanation
Indices: 17434--17490 Score: 75
Period size: 19 Copynumber: 3.0 Consensus size: 20
17424 TTTAAAAATA
17434 TTAAAAATATTTTTATAATT
1 TTAAAAATATTTTTATAATT
*
17454 TTAATAAT-TTTTTAT--TT
1 TTAAAAATATTTTTATAATT
17471 TTAAAAATAGTTTTTATAAT
1 TTAAAAATA-TTTTTATAAT
17491 GTTTTTCTTA
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
17 9 0.29
19 14 0.45
20 7 0.23
21 1 0.03
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (20 bp):
TTAAAAATATTTTTATAATT
Found at i:23342 original size:16 final size:18
Alignment explanation
Indices: 23303--23336 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
23293 TAAGTTTATA
23303 ATATTT-TATATTATGTT
1 ATATTTATATATTATGTT
*
23320 ATTTTTATATATTATGT
1 ATATTTATATATTATGT
23337 AATTTAGAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (18 bp):
ATATTTATATATTATGTT
Found at i:44820 original size:127 final size:126
Alignment explanation
Indices: 44594--44840 Score: 422
Period size: 127 Copynumber: 2.0 Consensus size: 126
44584 GGCCATAGAT
* *
44594 CTTAACGTGGCTCCGCCACTGCTAATAATATAAGTAATTTTCCTATTAATCCTTCATTGTTTTGC
1 CTTAACGTGACTCCGCCACTGCTAATAATATAAGTAAATTTCCTATTAATCCTTCATTGTTTTGC
44659 CATCTTTTCCATATATTCACAAAACTTCCATATTTCCTACTTTTTGCCACAATGATGAAGGC
66 CATCTTTTCCATATATTCACAAAACTTCCATATTTCCTAC-TTTTGCCACAATGATGAAGGC
* *
44721 CTTAACTTGACTCCGCCACTGCTAATAATATGAGTAAATTTCCTATTAATCCTTCATTGTTTTGC
1 CTTAACGTGACTCCGCCACTGCTAATAATATAAGTAAATTTCCTATTAATCCTTCATTGTTTTGC
* * *
44786 CATGTTTTCCATATATTCACATAACTTCCATATTTCCTACTTTTGCCACAGTGAT
66 CATCTTTTCCATATATTCACAAAACTTCCATATTTCCTACTTTTGCCACAATGAT
44841 TTCTATACTC
Statistics
Matches: 113, Mismatches: 7, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
126 14 0.12
127 99 0.88
ACGTcount: A:0.26, C:0.24, G:0.10, T:0.40
Consensus pattern (126 bp):
CTTAACGTGACTCCGCCACTGCTAATAATATAAGTAAATTTCCTATTAATCCTTCATTGTTTTGC
CATCTTTTCCATATATTCACAAAACTTCCATATTTCCTACTTTTGCCACAATGATGAAGGC
Found at i:45833 original size:25 final size:25
Alignment explanation
Indices: 45780--45826 Score: 62
Period size: 23 Copynumber: 1.9 Consensus size: 25
45770 TCACCTCTTC
*
45780 TTAAATATAATTATATTTTTAAATA
1 TTAAATATAATTATATTTCTAAATA
45805 TTAAAT-T-ATTATATTTACTAAA
1 TTAAATATAATTATATTT-CTAAA
45827 CTTTTAACTT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 9 0.45
24 5 0.25
25 6 0.30
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (25 bp):
TTAAATATAATTATATTTCTAAATA
Found at i:48212 original size:21 final size:21
Alignment explanation
Indices: 48170--48229 Score: 68
Period size: 22 Copynumber: 2.7 Consensus size: 21
48160 TGATGGTGTT
48170 ATGATTAAAAAATTAATTAATTA
1 ATGA-TAAAAAATT-ATTAATTA
48193 ATGATAAAAAATT-TTAAATTA
1 ATGATAAAAAATTATT-AATTA
*
48214 ATAATAATAAAATTAT
1 ATGATAA-AAAATTAT
48230 ACTTTAATCT
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
20 2 0.06
21 11 0.33
22 15 0.45
23 5 0.15
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.38
Consensus pattern (21 bp):
ATGATAAAAAATTATTAATTA
Found at i:48263 original size:17 final size:17
Alignment explanation
Indices: 48241--48275 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
48231 CTTTAATCTC
48241 TTAAAA-AATATAAATTA
1 TTAAAATAATA-AAATTA
48258 TTAAAATAATAAAATTA
1 TTAAAATAATAAAATTA
48275 T
1 T
48276 ATTTTTATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 13 0.76
18 4 0.24
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (17 bp):
TTAAAATAATAAAATTA
Found at i:49071 original size:29 final size:29
Alignment explanation
Indices: 49033--49094 Score: 90
Period size: 29 Copynumber: 2.1 Consensus size: 29
49023 TTTTGAAATT
*
49033 AAAAATAATAATT-TATAAATAAATCAATG
1 AAAAATAATACTTAT-TAAATAAATCAATG
*
49062 AAAATTAATACTTATTAAATAAATCAATG
1 AAAAATAATACTTATTAAATAAATCAATG
49091 AAAA
1 AAAA
49095 CCATAAAAAC
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 29 0.97
30 1 0.03
ACGTcount: A:0.61, C:0.05, G:0.03, T:0.31
Consensus pattern (29 bp):
AAAAATAATACTTATTAAATAAATCAATG
Found at i:49167 original size:26 final size:27
Alignment explanation
Indices: 49121--49171 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
49111 TCTTTCACTC
49121 TCTTTTTTTCTTGAAACATTTTTTCTT
1 TCTTTTTTTCTTGAAACATTTTTTCTT
*
49148 TCTTTTTTTCTT-AAATATTTTTTC
1 TCTTTTTTTCTTGAAACATTTTTTC
49172 CATATAAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
26 11 0.48
27 12 0.52
ACGTcount: A:0.16, C:0.14, G:0.02, T:0.69
Consensus pattern (27 bp):
TCTTTTTTTCTTGAAACATTTTTTCTT
Found at i:50316 original size:23 final size:23
Alignment explanation
Indices: 50272--50317 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
50262 TGTAATAAGA
***
50272 TTTTAATTTAACATGTTTAATTT
1 TTTTAATTTAACATGAACAATTT
*
50295 TTTTAATTTAACTTGAACAATTT
1 TTTTAATTTAACATGAACAATTT
50318 CAATCGATTC
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.33, C:0.07, G:0.04, T:0.57
Consensus pattern (23 bp):
TTTTAATTTAACATGAACAATTT
Found at i:65846 original size:18 final size:17
Alignment explanation
Indices: 65823--65866 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
65813 TTTTATAAAA
65823 TATAAATTTTGGAATATT
1 TATAAATTTTGGAAT-TT
*
65841 TATAAATATTTTGAATTT
1 TATAAAT-TTTGGAATTT
*
65859 TAAAAATT
1 TATAAATT
65867 ATTTTTATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
17 1 0.04
18 15 0.65
19 7 0.30
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (17 bp):
TATAAATTTTGGAATTT
Found at i:65869 original size:19 final size:20
Alignment explanation
Indices: 65828--65871 Score: 56
Period size: 19 Copynumber: 2.2 Consensus size: 20
65818 TAAAATATAA
*
65828 ATTTTGGAATATTTATAAAT
1 ATTTTGGAATATTTAAAAAT
65848 ATTTT-GAAT-TTTAAAAATT
1 ATTTTGGAATATTTAAAAA-T
65867 ATTTT
1 ATTTT
65872 TATTTTTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 7 0.32
19 10 0.45
20 5 0.23
ACGTcount: A:0.39, C:0.00, G:0.07, T:0.55
Consensus pattern (20 bp):
ATTTTGGAATATTTAAAAAT
Found at i:66833 original size:30 final size:30
Alignment explanation
Indices: 66769--66886 Score: 116
Period size: 31 Copynumber: 3.9 Consensus size: 30
66759 TTAAACGGTG
* * * *
66769 AAAAGAAATTTAAATCTCTTAAAAATTGATA
1 AAAAAAAATTTAAACCT-TTAAAAATTAAAA
* * *
66800 AAAAAAAATTTGAATCTTTAAAAGTTAAAA
1 AAAAAAAATTTAAACCTTTAAAAATTAAAA
66830 AAAATAAAA-TTAAACCCTTTAAAAATT-AAA
1 AAAA-AAAATTTAAA-CCTTTAAAAATTAAAA
*
66860 TAAAAAAATTT-AACCTTTAAAAATTAA
1 AAAAAAAATTTAAACCTTTAAAAATTAA
66887 TTTTTTGAGC
Statistics
Matches: 74, Mismatches: 9, Indels: 10
0.80 0.10 0.11
Matches are distributed among these distances:
28 12 0.16
29 7 0.09
30 26 0.35
31 29 0.39
ACGTcount: A:0.59, C:0.07, G:0.03, T:0.31
Consensus pattern (30 bp):
AAAAAAAATTTAAACCTTTAAAAATTAAAA
Found at i:73830 original size:2 final size:2
Alignment explanation
Indices: 73825--73857 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
73815 AAGATGTGTG
73825 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 T
73858 CTGAAGTTAG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:74817 original size:28 final size:30
Alignment explanation
Indices: 74756--74819 Score: 114
Period size: 28 Copynumber: 2.2 Consensus size: 30
74746 TTATTTCAAA
74756 AAAAATAGAGCAATTTAATCTATCAATTTT
1 AAAAATAGAGCAATTTAATCTATCAATTTT
74786 AAAAATA-AGCAATTTAATC-ATCAATTTT
1 AAAAATAGAGCAATTTAATCTATCAATTTT
74814 AAAAAT
1 AAAAAT
74820 TAAATATTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
28 15 0.44
29 12 0.35
30 7 0.21
ACGTcount: A:0.52, C:0.09, G:0.05, T:0.34
Consensus pattern (30 bp):
AAAAATAGAGCAATTTAATCTATCAATTTT
Found at i:78664 original size:23 final size:22
Alignment explanation
Indices: 78634--78730 Score: 107
Period size: 23 Copynumber: 4.5 Consensus size: 22
78624 GATGGGGAAA
78634 CAGTAAGCACACACAGTGCAAT
1 CAGTAAGCACACACAGTGCAAT
78656 CCAGTAAGCACACACAGTGCAAT
1 -CAGTAAGCACACACAGTGCAAT
78679 CCAGTAAG------CAGTGCAAT
1 -CAGTAAGCACACACAGTGCAAT
* *
78696 CAGTAGGCACACACAGCGCAAAT
1 CAGTAAGCACACACAGTGC-AAT
78719 CAGTAAGCACAC
1 CAGTAAGCACAC
78731 GAAGTGCGAA
Statistics
Matches: 64, Mismatches: 3, Indels: 14
0.79 0.04 0.17
Matches are distributed among these distances:
16 6 0.09
17 9 0.14
22 5 0.08
23 44 0.69
ACGTcount: A:0.39, C:0.29, G:0.20, T:0.12
Consensus pattern (22 bp):
CAGTAAGCACACACAGTGCAAT
Found at i:78706 original size:39 final size:40
Alignment explanation
Indices: 78647--78727 Score: 121
Period size: 39 Copynumber: 2.0 Consensus size: 40
78637 TAAGCACACA
*
78647 CAGTGCAATCCAGTAAGCACACACAGTGC-AATCCAGTAAG
1 CAGTGCAATCCAGTAAGCACACACAGCGCAAAT-CAGTAAG
*
78687 CAGTGCAAT-CAGTAGGCACACACAGCGCAAATCAGTAAG
1 CAGTGCAATCCAGTAAGCACACACAGCGCAAATCAGTAAG
78726 CA
1 CA
78728 CACGAAGTGC
Statistics
Matches: 38, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
39 26 0.68
40 12 0.32
ACGTcount: A:0.38, C:0.27, G:0.21, T:0.14
Consensus pattern (40 bp):
CAGTGCAATCCAGTAAGCACACACAGCGCAAATCAGTAAG
Found at i:78747 original size:62 final size:60
Alignment explanation
Indices: 78634--78753 Score: 147
Period size: 62 Copynumber: 1.9 Consensus size: 60
78624 GATGGGGAAA
*
78634 CAGTAAGCACACACAGTGCAATCCAGTAAGCACACACAGTGCAATCCAGTAAGCAGTGCAAT
1 CAGTAAGCACACACAGCGCAATCCAGTAAGCACACACAGTGCAAT-CAGTAAGC-GTGCAAT
*
78696 CAGTAGGCACACACAGCGCAAAT-CAGTAAGCACACGA-AGTGCGAAAT-AGTAAGCGTGC
1 CAGTAAGCACACACAGCGC-AATCCAGTAAGCACAC-ACAGTGC--AATCAGTAAGCGTGC
78754 TAGCGTTCCT
Statistics
Matches: 52, Mismatches: 2, Indels: 9
0.83 0.03 0.14
Matches are distributed among these distances:
61 4 0.08
62 41 0.79
63 4 0.08
64 3 0.06
ACGTcount: A:0.38, C:0.26, G:0.23, T:0.13
Consensus pattern (60 bp):
CAGTAAGCACACACAGCGCAATCCAGTAAGCACACACAGTGCAATCAGTAAGCGTGCAAT
Found at i:84032 original size:60 final size:60
Alignment explanation
Indices: 83950--84394 Score: 324
Period size: 59 Copynumber: 7.5 Consensus size: 60
83940 AAAAAAATTT
* *
83950 GGTGTTGGTCATTGC-ATAGCCGACACCCCTTTTTAATTTGATAAAAAAAATCAAA-TTTTG
1 GGTGTTGGTCA-TGCAATGGCCGACACCCCTTTTT-ATCTGATAAAAAAAATCAAATTTTTG
* * * * *
84010 GGTATTGGTCATGCAATGGCCGACACCCTTTTTTGT-TAGATAAAAAAATTC-AATTTTTT
1 GGTGTTGGTCATGCAATGGCCGACACCCCTTTTTATCT-GATAAAAAAAATCAAATTTTTG
* * * *
84069 TGTGTTGGTCATGCCATGGCCGACACCCCTATTTATCTGATAAAAAAAATCAAATTTTTTT
1 GGTGTTGGTCATGCAATGGCCGACACCCCTTTTTATCTGATAAAAAAAATCAAA-TTTTTG
* * * *
84130 GGTGTT-GCCAT-TACATGGTCGACACCCCTTTTTATCTGA-ATAAAAAATCAAATTTTTG
1 GGTGTTGGTCATGCA-ATGGCCGACACCCCTTTTTATCTGATAAAAAAAATCAAATTTTTG
* * * * * * *** * * *
84188 GGTGCTGGCCATGCCATGGCCGACAAACCCTTTTTGTCAGATAAAAATTTTGAATTTTTTTT
1 GGTGTTGGTCATGCAATGGCCGAC-ACCCCTTTTTATCTGATAAAAAAAATCAA-ATTTTTG
* * * *
84250 GGTGTTGGTCATGCCATGGTCGACACCCCCTTTTTTATCTGGT---AAAAATC-AATTTTTT
1 GGTGTTGGTCATGCAATGGCCGACA-CCCC-TTTTTATCTGATAAAAAAAATCAAATTTTTG
* * * * *
84308 TGTGTTGGTCATGCAATGGTCGACACTTCCTTTTTTATCTGGT--AAAAAATC-AATTTTGTT
1 GGTGTTGGTCATGCAATGGCCGACAC--CCCTTTTTATCTGATAAAAAAAATCAAATTTT-TG
** * *
84368 TATGTTGGTCATGCAATGACCAACACC
1 GGTGTTGGTCATGCAATGGCCGACACC
84395 AACTTTCCCT
Statistics
Matches: 313, Mismatches: 54, Indels: 38
0.77 0.13 0.09
Matches are distributed among these distances:
57 1 0.00
58 55 0.18
59 103 0.33
60 97 0.31
61 19 0.06
62 29 0.09
63 9 0.03
ACGTcount: A:0.27, C:0.18, G:0.17, T:0.37
Consensus pattern (60 bp):
GGTGTTGGTCATGCAATGGCCGACACCCCTTTTTATCTGATAAAAAAAATCAAATTTTTG
Found at i:84162 original size:119 final size:118
Alignment explanation
Indices: 83951--84379 Score: 358
Period size: 119 Copynumber: 3.6 Consensus size: 118
83941 AAAAAATTTG
* * *
83951 GTGTTGGTCATTG-CATAGCCGACACCCCTTTTTAATTTGATAAAAAAAATCAAA--TTTTGGGT
1 GTGTTGGTCA-TGCCATGGCCGACACCCCTTTTT-ATCTGATAAAAAAAATCAAATTTTTTTGGT
* * * *
84013 ATTGGTCA-TGCAATGGCCGACACCCTTTTTTGTTAGATAAAAAAATTCAATTTTTTT
64 GTTGGTCATTAC-ATGGTCGACACCCCTTTTT-TTAGATAAAAAAA-TCAATTTTTTT
*
84070 GTGTTGGTCATGCCATGGCCGACACCCCTATTTATCTGATAAAAAAAATCAAATTTTTTTGGTGT
1 GTGTTGGTCATGCCATGGCCGACACCCCTTTTTATCTGATAAAAAAAATCAAATTTTTTTGGTGT
* **
84135 T-GCCATTACATGGTCGACACCCCTTTTTATCT-GA-ATAAAAAATCAAATTTTTGG
66 TGGTCATTACATGGTCGACACCCCTTTTT-T-TAGATA-AAAAAATC-AATTTTTTT
* * * * * *** * *
84189 GTGCTGGCCATGCCATGGCCGACAAACCCTTTTTGTCAGATAAAAATTTTGAATTTTTTTTGGTG
1 GTGTTGGTCATGCCATGGCCGAC-ACCCCTTTTTATCTGATAAAAAAAATCAAATTTTTTTGGTG
** * ** **
84254 TTGGTCATGCCATGGTCGACACCCCCTTTTTTATCTGGTAAAAATCAATTTTTTT
65 TTGGTCATTACATGGTCGACACCCCTTTTTTTAGAT-AAAAAAATCAATTTTTTT
* * * * *
84309 GTGTTGGTCATGCAATGGTCGACACTTCCTTTTTTATCTGGT--AAAAAATC-AATTTTGTTT-A
1 GTGTTGGTCATGCCATGGCCGACAC--CCCTTTTTATCTGATAAAAAAAATCAAATTTT-TTTGG
84370 TGTTGGTCAT
63 TGTTGGTCAT
84380 GCAATGACCA
Statistics
Matches: 247, Mismatches: 48, Indels: 31
0.76 0.15 0.10
Matches are distributed among these distances:
118 39 0.16
119 94 0.38
120 73 0.30
121 41 0.17
ACGTcount: A:0.27, C:0.18, G:0.17, T:0.38
Consensus pattern (118 bp):
GTGTTGGTCATGCCATGGCCGACACCCCTTTTTATCTGATAAAAAAAATCAAATTTTTTTGGTGT
TGGTCATTACATGGTCGACACCCCTTTTTTTAGATAAAAAAATCAATTTTTTT
Found at i:84340 original size:120 final size:118
Alignment explanation
Indices: 83951--84356 Score: 351
Period size: 120 Copynumber: 3.4 Consensus size: 118
83941 AAAAAATTTG
* ** *
83951 GTGTTGGTCATTG-CATAGCCGACACCCCTTTTTAATTTGATAAAAAAAATCAAA--TTTTGGGT
1 GTGTTGGTCA-TGCCATGGCCGACACCCCTTTTT-ATCAGATAAAAAAAATCAAATTTTTTTGGT
* * * * *
84013 ATTGGTCATG-CAATGGCCGACA-CCCTTTTT-TGTTAGATAAAAAAATTCAATTTTTTT
64 GTT-GCCATGAC-ATGGTCGACACCCCTTTTTATCTGA-AT-AAAAAA-TCAATTTTTTT
* *
84070 GTGTTGGTCATGCCATGGCCGACACCCCTATTTATCTGATAAAAAAAATCAAATTTTTTTGGTGT
1 GTGTTGGTCATGCCATGGCCGACACCCCTTTTTATCAGATAAAAAAAATCAAATTTTTTTGGTGT
* **
84135 TGCCATTACATGGTCGACACCCCTTTTTATCTGAATAAAAAATCAAATTTTTGG
66 TGCCATGACATGGTCGACACCCCTTTTTATCTGAATAAAAAATC-AATTTTTTT
* * * * *** * *
84189 GTGCTGGCCATGCCATGGCCGACAAACCCTTTTTGTCAGATAAAAATTTTGAATTTTTTTTGGTG
1 GTGTTGGTCATGCCATGGCCGAC-ACCCCTTTTTATCAGATAAAAAAAATCAAATTTTTTTGGTG
* * *
84254 TTGGTCATGCCATGGTCGACACCCCCTTTTTTATCTG-GT-AAAAATCAATTTTTTT
65 TT-GCCATGACATGGTCGACA-CCCC-TTTTTATCTGAATAAAAAATCAATTTTTTT
* * * * *
84309 GTGTTGGTCATGCAATGGTCGACACTTCCTTTTTTATCTGGTAAAAAA
1 GTGTTGGTCATGCCATGGCCGACAC--CCCTTTTTATCAGATAAAAAA
84357 TCAATTTTGT
Statistics
Matches: 235, Mismatches: 39, Indels: 24
0.79 0.13 0.08
Matches are distributed among these distances:
118 23 0.10
119 76 0.32
120 80 0.34
121 41 0.17
122 5 0.02
123 10 0.04
ACGTcount: A:0.27, C:0.18, G:0.17, T:0.37
Consensus pattern (118 bp):
GTGTTGGTCATGCCATGGCCGACACCCCTTTTTATCAGATAAAAAAAATCAAATTTTTTTGGTGT
TGCCATGACATGGTCGACACCCCTTTTTATCTGAATAAAAAATCAATTTTTTT
Found at i:85020 original size:18 final size:18
Alignment explanation
Indices: 84978--85029 Score: 58
Period size: 17 Copynumber: 3.0 Consensus size: 18
84968 TAACAATTAA
84978 TTATAATTT-ATTTTATC
1 TTATAATTTAATTTTATC
84995 TGTA-AATTTAATTTGTAT-
1 T-TATAATTTAATTT-TATC
85013 TTATAATTT-ATTTTATC
1 TTATAATTTAATTTTATC
85030 GTATTGCATG
Statistics
Matches: 30, Mismatches: 0, Indels: 10
0.75 0.00 0.25
Matches are distributed among these distances:
16 3 0.10
17 12 0.40
18 12 0.40
19 3 0.10
ACGTcount: A:0.31, C:0.04, G:0.04, T:0.62
Consensus pattern (18 bp):
TTATAATTTAATTTTATC
Found at i:85213 original size:59 final size:57
Alignment explanation
Indices: 85082--85409 Score: 212
Period size: 58 Copynumber: 5.4 Consensus size: 57
85072 AAAAAAGGGG
* * * * * *
85082 GTGTCGACCATGGTATGGCCAACACAAAAAAGAAATTCGAATTTTTTATCTGACAAAA-AA
1 GTGTCGGCCATGGCATGGCCAACAC--CAAA-AAATTTG-ATTTTTTATCAGATAAAAGAA
* * *
85142 TGAATGTCGGCCATGGTATGGCCAACACCCAAAAATTTGATTTTTTATTCAGATAATAAGAT
1 -G--TGTCGGCCATGGCATGGCCAACACCAAAAAATTTGATTTTTTA-TCAGATAA-AAGAA
* *
85204 GTGTCGGCCAT-GCAATGGCCAACACCAAAAAAATTTGAAAATTTTTTATCTGAAAAAAGGAA
1 GTGTCGGCCATGGC-ATGGCCAACACC-AAAAAATTTG---ATTTTTTATCAGATAAAA-GAA
** * * * * * **
85266 GTGTCGATCATTGCATGGCTAATACAAAAAAATTTAATTTTTTATCAGATAAATAGGG
1 GTGTCGGCCATGGCATGGCCAACACCAAAAAATTTGATTTTTTATCAGATAAA-AGAA
* * * *
85324 GTGTCGGCTATTGCATGGCCAACACCCAAAAATTTGATTTTTTTTATCAGATTAAAAGAGG
1 GTGTCGGCCATGGCATGGCCAACACCAAAAAATTTGA--TTTTTTATCAGA-TAAAAGA-A
* *
85385 GTGCCGGCCAT-GCAATGGCGAACAC
1 GTGTCGGCCATGGC-ATGGCCAACAC
85410 AATTTTTTTT
Statistics
Matches: 215, Mismatches: 34, Indels: 36
0.75 0.12 0.13
Matches are distributed among these distances:
58 46 0.21
59 31 0.14
60 37 0.17
61 41 0.19
62 27 0.13
63 33 0.15
ACGTcount: A:0.36, C:0.16, G:0.19, T:0.28
Consensus pattern (57 bp):
GTGTCGGCCATGGCATGGCCAACACCAAAAAATTTGATTTTTTATCAGATAAAAGAA
Found at i:85222 original size:122 final size:118
Alignment explanation
Indices: 85035--85348 Score: 276
Period size: 122 Copynumber: 2.6 Consensus size: 118
85025 TTATCGTATT
* * * * * * * * *
85035 GCATGACCAACACAAAAAAAATTGA-TTTTTACCATATAAAAAAGGGGGTGTCGACCATGGTATG
1 GCATGGCCAACACAAAAAAATTTAATTTTTTATCAGAT-AAATA-GAGGTGTCGGCCAT-GCATG
* *
85099 GCCAACACAAAAAAGAAATTCG-AATTTTTTATCTGACAAAAAATGAA-TGTCGGCCATG
63 GCCAACAC-AAAAA-AAATTCGAAATTTTTTATCTG--AAAAAAGGAAGTGTCGACCATG
* ** * *
85157 GTATGGCCAACACCCAAAAATTTGATTTTTTATTCAGAT-AATAAGATGTGTCGGCCATGCAATG
1 GCATGGCCAACACAAAAAAATTTAATTTTTTA-TCAGATAAAT-AGAGGTGTCGGCCATGC-ATG
* * * *
85221 GCCAACACCAAAAAAATTTGAAAATTTTTTATCTGAAAAAAGGAAGTGTCGATCATT
63 GCCAACACAAAAAAAATTCG-AAATTTTTTATCTGAAAAAAGGAAGTGTCGACCATG
* * * *
85278 GCATGGCTAATACAAAAAAATTTAATTTTTTATCAGATAAATAGGGGTGTCGGCTATTGCATGGC
1 GCATGGCCAACACAAAAAAATTTAATTTTTTATCAGATAAATAGAGGTGTCGGCCA-TGCATGGC
85343 CAACAC
65 CAACAC
85349 CCAAAAATTT
Statistics
Matches: 156, Mismatches: 27, Indels: 20
0.77 0.13 0.10
Matches are distributed among these distances:
120 43 0.28
121 45 0.29
122 57 0.37
123 7 0.04
124 4 0.03
ACGTcount: A:0.39, C:0.16, G:0.18, T:0.27
Consensus pattern (118 bp):
GCATGGCCAACACAAAAAAATTTAATTTTTTATCAGATAAATAGAGGTGTCGGCCATGCATGGCC
AACACAAAAAAAATTCGAAATTTTTTATCTGAAAAAAGGAAGTGTCGACCATG
Found at i:85329 original size:58 final size:58
Alignment explanation
Indices: 85032--85375 Score: 171
Period size: 59 Copynumber: 5.7 Consensus size: 58
85022 ATTTTATCGT
* * * * * * *
85032 ATTGCATGACCAACACAAAAAAAATT-GA-TTTTTACCATATAAAAAAGGGGGTGTCGACC
1 ATTGCATGGCCAACACAAAAAAATTTAAATTTTTTATCAGAT-AAATA-GGAGTGTCG-CC
* * ** * * * * *
85091 ATGGTATGGCCAACACAAAAAAGAAATTCGAATTTTTTATCTGACAAAAAATGAATGTCGGCC
1 ATTGCATGGCCAACAC--AAAA-AAATTTAAATTTTTTATCAGA-TAAATAGGAGTGTC-GCC
* * ** * *
85154 ATGGTATGGCCAACACCCAAAAATTT-GATTTTTTATTCAGAT-AATAAGATGTGTCGGCC
1 ATTGCATGGCCAACACAAAAAAATTTAAATTTTTTA-TCAGATAAATAGGA-GTGTC-GCC
* * *
85213 A-TGCAATGGCCAACACCAAAAAAATTTGAAAATTTTTTATCTGA-AAAAAGGAAGTGTCGATC
1 ATTGC-ATGGCCAACA-CAAAAAAATTT--AAATTTTTTATCAGATAAATAGG-AGTGTCG-CC
* * * *
85275 ATTGCATGGCTAATACAAAAAAATTT-AATTTTTTATCAGATAAATAGGGGTGTCGGCT
1 ATTGCATGGCCAACACAAAAAAATTTAAATTTTTTATCAGATAAATAGGAGTGTC-GCC
** **
85333 ATTGCATGGCCAACACCCAAAAATTTGATTTTTTTTATCAGAT
1 ATTGCATGGCCAACACAAAAAAATTT-AAATTTTTTATCAGAT
85376 TAAAAGAGGG
Statistics
Matches: 219, Mismatches: 44, Indels: 43
0.72 0.14 0.14
Matches are distributed among these distances:
58 46 0.21
59 47 0.21
60 31 0.14
61 18 0.08
62 27 0.12
63 36 0.16
64 14 0.06
ACGTcount: A:0.38, C:0.15, G:0.17, T:0.29
Consensus pattern (58 bp):
ATTGCATGGCCAACACAAAAAAATTTAAATTTTTTATCAGATAAATAGGAGTGTCGCC
Found at i:85409 original size:61 final size:59
Alignment explanation
Indices: 85074--85409 Score: 222
Period size: 60 Copynumber: 5.5 Consensus size: 59
85064 TACCATATAA
* * * * * * *
85074 AAAAGGGGGTGTCGACCATGGTATGGCCAACACAAAAAAGAAATTCGA-ATTTTTTATCTGAC
1 AAAAGAGGGTGTCGGCCAT-GCATGGCCAACAC--CAAA-AAATTTGATATTTTTTATCAGAT
* ** * *
85136 AAAAAATGAATGTCGGCCATGGTATGGCCAACACCCAAAAATTTG--ATTTTTTATTCAGAT
1 AAAAGA-GGGTGTCGGCCAT-GCATGGCCAACACCAAAAAATTTGATATTTTTTA-TCAGAT
* * *
85196 AATAAGA-TGTGTCGGCCATGCAATGGCCAACACCAAAAAAATTTGAAAATTTTTTATCTGA-
1 AA-AAGAGGGTGTCGGCCATGC-ATGGCCAACACC-AAAAAATTTG-ATATTTTTTATCAGAT
** * * *
85257 AAAA-AGGAAGTGTCGATCATTGCATGGCTAATACAAAAAAATTT-A-ATTTTTTATCAGAT
1 AAAAGAGG--GTGTCGGCCA-TGCATGGCCAACACCAAAAAATTTGATATTTTTTATCAGAT
* * *
85316 AAATAG-GGGTGTCGGCTATTGCATGGCCAACACCCAAAAATTTGATTTTTTTTATCAGATT
1 AAA-AGAGGGTGTCGGCCA-TGCATGGCCAACACCAAAAAATTTGATATTTTTTATCAGA-T
* *
85377 AAAAGAGGGTGCCGGCCATGCAATGGCGAACAC
1 AAAAGAGGGTGTCGGCCATGC-ATGGCCAACAC
85410 AATTTTTTTT
Statistics
Matches: 220, Mismatches: 34, Indels: 41
0.75 0.12 0.14
Matches are distributed among these distances:
58 41 0.19
59 36 0.16
60 43 0.20
61 40 0.18
62 25 0.11
63 35 0.16
ACGTcount: A:0.37, C:0.16, G:0.20, T:0.28
Consensus pattern (59 bp):
AAAAGAGGGTGTCGGCCATGCATGGCCAACACCAAAAAATTTGATATTTTTTATCAGAT
Found at i:88021 original size:2 final size:2
Alignment explanation
Indices: 87969--88007 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
87959 TATAGTTTCT
87969 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
88008 AACAAGTTTA
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:89106 original size:30 final size:30
Alignment explanation
Indices: 89065--89141 Score: 84
Period size: 31 Copynumber: 2.6 Consensus size: 30
89055 CCAAAACTAC
** * *
89065 ACATG-AACTTTGATTTGGTGCACTTGTGT
1 ACATGAAACTTTGATTTGGTGCAAATATAT
*
89094 ACATGAAACTTTGATTGTGGTTCAAATATAT
1 ACATGAAACTTTGATT-TGGTGCAAATATAT
*
89125 ACATTAAACTTTGATTT
1 ACATGAAACTTTGATTT
89142 TGATTCAATT
Statistics
Matches: 40, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
29 5 0.12
30 11 0.28
31 24 0.60
ACGTcount: A:0.30, C:0.12, G:0.17, T:0.42
Consensus pattern (30 bp):
ACATGAAACTTTGATTTGGTGCAAATATAT
Found at i:89134 original size:31 final size:31
Alignment explanation
Indices: 89093--89163 Score: 88
Period size: 31 Copynumber: 2.3 Consensus size: 31
89083 TGCACTTGTG
* *
89093 TACATGAAACTTTGATTGTGGTTCAAATATA
1 TACATTAAACTTTGATTGTGATTCAAATATA
* * *
89124 TACATTAAACTTTGATTTTGATTCAATTGTA
1 TACATTAAACTTTGATTGTGATTCAAATATA
*
89155 TACTTTAAA
1 TACATTAAA
89164 GAAATGAATA
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.35, C:0.10, G:0.11, T:0.44
Consensus pattern (31 bp):
TACATTAAACTTTGATTGTGATTCAAATATA
Found at i:91372 original size:2 final size:2
Alignment explanation
Indices: 91365--91390 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
91355 TGAGATGAGA
91365 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
91391 TGTATTGCGG
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:95883 original size:18 final size:17
Alignment explanation
Indices: 95856--95907 Score: 50
Period size: 18 Copynumber: 2.8 Consensus size: 17
95846 TTTTTATAAA
*
95856 AATTTATAATTTTTAATT
1 AATTT-TAATTTTTAATG
*
95874 AACTTTTAATTATTTTATG
1 AA-TTTTAATT-TTTAATG
95893 AATTTTAAGTTTTTA
1 AATTTTAA-TTTTTA
95908 TTTTTTATAA
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
18 16 0.57
19 12 0.43
ACGTcount: A:0.35, C:0.02, G:0.04, T:0.60
Consensus pattern (17 bp):
AATTTTAATTTTTAATG
Found at i:99129 original size:46 final size:46
Alignment explanation
Indices: 99073--99160 Score: 124
Period size: 46 Copynumber: 1.9 Consensus size: 46
99063 AAGGAAAATA
* *
99073 AAAACATAATATAATAAAGAGAA-TAAGTAAAACTAAAACTCTTAAT
1 AAAACATAATATAATAAA-AAAATTAAATAAAACTAAAACTCTTAAT
* *
99119 AAAACCTAATATAATAAAAAAATTAAATAAATCTAAAACTCT
1 AAAACATAATATAATAAAAAAATTAAATAAAACTAAAACTCT
99161 AATTGCAATA
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
45 3 0.08
46 34 0.92
ACGTcount: A:0.61, C:0.10, G:0.03, T:0.25
Consensus pattern (46 bp):
AAAACATAATATAATAAAAAAATTAAATAAAACTAAAACTCTTAAT
Found at i:102132 original size:47 final size:47
Alignment explanation
Indices: 102041--102183 Score: 180
Period size: 47 Copynumber: 3.0 Consensus size: 47
102031 CGATTTTTAC
* * * * *
102041 GATTTTTTATCAATATAATACAAAAAATAATAATTAAATACCAAAATG
1 GATTATTTATCAAAATAGTACAAAAAA-AATATTTATATACCAAAATG
102089 GATTATTTATCAAAATAGTACAAAAAAAATATTTATATACCAAAAT-
1 GATTATTTATCAAAATAGTACAAAAAAAATATTTATATACCAAAATG
* * * *
102135 GAGTTATTTACCAAAATGGTACAAAATAAATATTTATATATCAAAATG
1 GA-TTATTTATCAAAATAGTACAAAAAAAATATTTATATACCAAAATG
102183 G
1 G
102184 TATCCACACC
Statistics
Matches: 84, Mismatches: 9, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
46 2 0.02
47 57 0.68
48 25 0.30
ACGTcount: A:0.52, C:0.08, G:0.07, T:0.33
Consensus pattern (47 bp):
GATTATTTATCAAAATAGTACAAAAAAAATATTTATATACCAAAATG
Found at i:102269 original size:30 final size:29
Alignment explanation
Indices: 102221--102278 Score: 80
Period size: 30 Copynumber: 2.0 Consensus size: 29
102211 GTGGTGGAGA
*
102221 TACCAATTTAGTATATAAATATTTATTTTG
1 TACCAATTTAGTAAATAAATATTT-TTTTG
* *
102251 TACCATTTTGGTAAATAAATATTTTTTT
1 TACCAATTTAGTAAATAAATATTTTTTT
102279 ATATTAAATT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
29 4 0.16
30 21 0.84
ACGTcount: A:0.34, C:0.07, G:0.07, T:0.52
Consensus pattern (29 bp):
TACCAATTTAGTAAATAAATATTTTTTTG
Found at i:102352 original size:35 final size:35
Alignment explanation
Indices: 102306--102379 Score: 121
Period size: 35 Copynumber: 2.1 Consensus size: 35
102296 ATCCATTTAC
* *
102306 ATTACTTACTTATTTACTACTACTAACAAAATAAA
1 ATTACTTACTTACTAACTACTACTAACAAAATAAA
*
102341 ATTACTTACTTACTAACTACTACTAACAAAATAGA
1 ATTACTTACTTACTAACTACTACTAACAAAATAAA
102376 ATTA
1 ATTA
102380 TTTTAATAAC
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.46, C:0.18, G:0.01, T:0.35
Consensus pattern (35 bp):
ATTACTTACTTACTAACTACTACTAACAAAATAAA
Found at i:105012 original size:99 final size:96
Alignment explanation
Indices: 104701--105096 Score: 666
Period size: 96 Copynumber: 4.1 Consensus size: 96
104691 CATGCTCAAG
104701 ATCATTCCTCAACTTCTCAATCTCTTTTTCTTGATCTCTCAAAGTTTGACTCATCAAAGAATAAT
1 ATCATTCCTCAACTTCTCAATCTCTTTTTCTTGATCTCTCAAAGTTTGACTCATCAAAGAATAAT
*
104766 CCTTTAAGGACACAATCTCCTTCTTTAAAGA
66 CCTTTAAGGACGCAATCTCCTTCTTTAAAGA
*
104797 ATCATTCCTCAACTTCTCAATCTCCTTTTCTTGATCTCTCAAAGTTTGACTCATCAAAGAATAAT
1 ATCATTCCTCAACTTCTCAATCTCTTTTTCTTGATCTCTCAAAGTTTGACTCATCAAAGAATAAT
104862 CCTTTAAGGACGCAATCTCCTTCTTTAAAGA
66 CCTTTAAGGACGCAATCTCCTTCTTTAAAGA
*
104893 ATCATTCCTCAACTTCTCAATCTCTTTTTCTTGATCTCTCAAAGTTTGATTCATCAAAGAATAAA
1 ATCATTCCTCAACTTCTCAATCTCTTTTTCTTGATCTCTCAAAGTTTGACTCATCAAAGAAT--A
**
104958 ACTTTTTTAAGGACGCAATCTCCTTCTTTAAAGA
64 A-TCCTTTAAGGACGCAATCTCCTTCTTTAAAGA
*
104992 ATCATTCCTCAACTTCTCAATCTCTTTTTCTTGATCTCTCAAAGTTTGATTCATCAAAGAATAAT
1 ATCATTCCTCAACTTCTCAATCTCTTTTTCTTGATCTCTCAAAGTTTGACTCATCAAAGAATAAT
* *
105057 CCTTTTTTAAGGACGCATTCTCCTTCTTTAAAAA
66 CC---TTTAAGGACGCAATCTCCTTCTTTAAAGA
105091 ATCATT
1 ATCATT
105097 TTCTTCATGA
Statistics
Matches: 284, Mismatches: 10, Indels: 9
0.94 0.03 0.03
Matches are distributed among these distances:
96 155 0.55
97 2 0.01
98 2 0.01
99 125 0.44
ACGTcount: A:0.30, C:0.24, G:0.08, T:0.39
Consensus pattern (96 bp):
ATCATTCCTCAACTTCTCAATCTCTTTTTCTTGATCTCTCAAAGTTTGACTCATCAAAGAATAAT
CCTTTAAGGACGCAATCTCCTTCTTTAAAGA
Found at i:105030 original size:195 final size:193
Alignment explanation
Indices: 104701--105096 Score: 668
Period size: 195 Copynumber: 2.0 Consensus size: 193
104691 CATGCTCAAG
104701 ATCATTCCTCAACTTCTCAATCTCTTTTTCTTGATCTCTCAAAGTTTGACTCATCAAAGAATAAT
1 ATCATTCCTCAACTTCTCAATCTCTTTTTCTTGATCTCTCAAAGTTTGACTCATCAAAGAATAAT
104766 CCTTTAAGGACACAATCTCCTTCTTTAAAGAATCATTCCTCAACTTCTCAATCTCCTTTTCTTGA
66 CCTTTAAGGACACAATCTCCTTCTTTAAAGAATCATTCCTCAACTTCTCAATCTCCTTTTCTTGA
*
104831 TCTCTCAAAGTTTGACTCATCAAAGAATAATCC-TTTAAGGACGCAATCTCCTTCTTTAAAGA
131 TCTCTCAAAGTTTGACTCATCAAAGAATAATCCTTTTAAGGACGCAATCTCCTTCTTTAAAAA
*
104893 ATCATTCCTCAACTTCTCAATCTCTTTTTCTTGATCTCTCAAAGTTTGATTCATCAAAGAATAAA
1 ATCATTCCTCAACTTCTCAATCTCTTTTTCTTGATCTCTCAAAGTTTGACTCATCAAAGAAT--A
** * *
104958 ACTTTTTTAAGGACGCAATCTCCTTCTTTAAAGAATCATTCCTCAACTTCTCAATCTCTTTTTCT
64 A-TCCTTTAAGGACACAATCTCCTTCTTTAAAGAATCATTCCTCAACTTCTCAATCTCCTTTTCT
* *
105023 TGATCTCTCAAAGTTTGATTCATCAAAGAATAATCCTTTTTTAAGGACGCATTCTCCTTCTTTAA
128 TGATCTCTCAAAGTTTGACTCATCAAAGAATAATCC--TTTTAAGGACGCAATCTCCTTCTTTAA
105088 AAA
191 AAA
105091 ATCATT
1 ATCATT
105097 TTCTTCATGA
Statistics
Matches: 190, Mismatches: 8, Indels: 6
0.93 0.04 0.03
Matches are distributed among these distances:
192 61 0.32
194 2 0.01
195 94 0.49
198 33 0.17
ACGTcount: A:0.30, C:0.24, G:0.08, T:0.39
Consensus pattern (193 bp):
ATCATTCCTCAACTTCTCAATCTCTTTTTCTTGATCTCTCAAAGTTTGACTCATCAAAGAATAAT
CCTTTAAGGACACAATCTCCTTCTTTAAAGAATCATTCCTCAACTTCTCAATCTCCTTTTCTTGA
TCTCTCAAAGTTTGACTCATCAAAGAATAATCCTTTTAAGGACGCAATCTCCTTCTTTAAAAA
Found at i:107375 original size:3 final size:3
Alignment explanation
Indices: 107369--107416 Score: 69
Period size: 3 Copynumber: 16.0 Consensus size: 3
107359 CAACAACAGC
* * *
107369 AAG AAG AAG AAG AAG AAG ATG ATG AAG AAG AAG AAG AAG AAA AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
107417 GGCCAAAACT
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.65, C:0.00, G:0.31, T:0.04
Consensus pattern (3 bp):
AAG
Found at i:108375 original size:2 final size:2
Alignment explanation
Indices: 108368--108392 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
108358 TATGGTAGAC
108368 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
108393 AGTATGTCTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:108471 original size:18 final size:18
Alignment explanation
Indices: 108448--108487 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
108438 TCAGGGACTT
108448 ATGATGATAATAATAATA
1 ATGATGATAATAATAATA
* *
108466 ATGATGATGATGATAATA
1 ATGATGATAATAATAATA
108484 ATGA
1 ATGA
108488 CAACGGACGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.17, T:0.33
Consensus pattern (18 bp):
ATGATGATAATAATAATA
Found at i:108788 original size:2 final size:2
Alignment explanation
Indices: 108781--108811 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
108771 ATACTTTAGA
108781 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
108812 AAAAAAAACC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:110161 original size:5 final size:6
Alignment explanation
Indices: 110143--110169 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
110133 CATATATTTA
110143 TTGTTT TTGTTT TTGTTT TTGTTT TTG
1 TTGTTT TTGTTT TTGTTT TTGTTT TTG
110170 CTTAAAATAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.00, C:0.00, G:0.19, T:0.81
Consensus pattern (6 bp):
TTGTTT
Found at i:112323 original size:24 final size:24
Alignment explanation
Indices: 112293--112379 Score: 138
Period size: 24 Copynumber: 3.6 Consensus size: 24
112283 TAGATTAATA
*
112293 AGAGTTTAACTCAAACAAATAAAC
1 AGAGTTTAACTGAAACAAATAAAC
* *
112317 AAAGTTTAATTGAAACAAATAAAC
1 AGAGTTTAACTGAAACAAATAAAC
*
112341 AGAGTTTAATTGAAACAAATAAAC
1 AGAGTTTAACTGAAACAAATAAAC
112365 AGAGTTTAACTGAAA
1 AGAGTTTAACTGAAA
112380 GATTATTTCT
Statistics
Matches: 58, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 58 1.00
ACGTcount: A:0.54, C:0.10, G:0.11, T:0.24
Consensus pattern (24 bp):
AGAGTTTAACTGAAACAAATAAAC
Found at i:114349 original size:24 final size:24
Alignment explanation
Indices: 114288--114350 Score: 90
Period size: 24 Copynumber: 2.6 Consensus size: 24
114278 TAGATTAATA
* *
114288 AGAGTTTGACTCAAACAAATAAAC
1 AGAGTTTAACTGAAACAAATAAAC
* *
114312 ATAGTTTAATTGAAACAAATAAAC
1 AGAGTTTAACTGAAACAAATAAAC
114336 AGAGTTTAACTGAAA
1 AGAGTTTAACTGAAA
114351 GATTATTTCT
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.51, C:0.11, G:0.13, T:0.25
Consensus pattern (24 bp):
AGAGTTTAACTGAAACAAATAAAC
Found at i:115563 original size:24 final size:22
Alignment explanation
Indices: 115523--115613 Score: 81
Period size: 18 Copynumber: 4.4 Consensus size: 22
115513 ATTATATTGT
*
115523 TGTTTTGATGCTTTTTTTTTTAC
1 TGTTTTGATGC-TGTTTTTTTAC
*
115546 TGTTTTGATTGCTGTTTTTTTAT
1 TGTTTTGA-TGCTGTTTTTTTAC
*
115569 TGTTTT--TG-T-ATTTTTTAC
1 TGTTTTGATGCTGTTTTTTTAC
115587 TGTTTTGA---T-TTTTTTTAC
1 TGTTTTGATGCTGTTTTTTTAC
115605 TGTTTTGAT
1 TGTTTTGAT
115614 TGTTATTTTC
Statistics
Matches: 59, Mismatches: 5, Indels: 12
0.78 0.07 0.16
Matches are distributed among these distances:
18 30 0.51
19 1 0.02
20 2 0.03
23 23 0.39
24 3 0.05
ACGTcount: A:0.10, C:0.05, G:0.14, T:0.70
Consensus pattern (22 bp):
TGTTTTGATGCTGTTTTTTTAC
Found at i:115657 original size:23 final size:23
Alignment explanation
Indices: 115607--115677 Score: 76
Period size: 23 Copynumber: 3.1 Consensus size: 23
115597 TTTTTTACTG
115607 TTTTGATTGTTATTTTCATGTTGT
1 TTTTGATTGTTATTTT-ATGTTGT
115631 TTTTG-TTGTTATTTT-TGTTGCT
1 TTTTGATTGTTATTTTATGTTG-T
* *
115653 ATTTTTATTGTT-TTTAATGTTGT
1 -TTTTGATTGTTATTTTATGTTGT
115676 TT
1 TT
115678 ACTATTATTT
Statistics
Matches: 41, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
21 5 0.12
22 3 0.07
23 18 0.44
24 15 0.37
ACGTcount: A:0.11, C:0.03, G:0.15, T:0.70
Consensus pattern (23 bp):
TTTTGATTGTTATTTTATGTTGT
Found at i:115657 original size:59 final size:58
Alignment explanation
Indices: 115525--115658 Score: 137
Period size: 59 Copynumber: 2.3 Consensus size: 58
115515 TATATTGTTG
* * * **
115525 TTTTGATGCTTTTTTTTTTACTGTTTTGATTGCTGTTTTTTTATTGTTTTTGTATTTT
1 TTTTGTTGCTATTTTTTTTACTGTTTTGATTGCTATTTTCATATTGTTTTTGTATTTT
* * * *
115583 TTACTGTT-TTGATTTTTTTTACTGTTTTGATTGTTATTTTCATGTTGTTTTTGT-TGTTAT
1 TT-TTGTTGCT-ATTTTTTTTACTGTTTTGATTGCTATTTTCATATTGTTTTTGTAT-TT-T
115643 TTTTGTTGCTATTTTT
1 TTTTGTTGCTATTTTT
115659 ATTGTTTTTA
Statistics
Matches: 60, Mismatches: 11, Indels: 9
0.75 0.14 0.11
Matches are distributed among these distances:
58 4 0.07
59 52 0.87
60 4 0.07
ACGTcount: A:0.10, C:0.05, G:0.14, T:0.71
Consensus pattern (58 bp):
TTTTGTTGCTATTTTTTTTACTGTTTTGATTGCTATTTTCATATTGTTTTTGTATTTT
Found at i:120002 original size:24 final size:24
Alignment explanation
Indices: 119956--120002 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
119946 TTAATATACA
* *
119956 TAGATTAATTTTTAACAGTAAAGT
1 TAGATTAATATTTAACAGAAAAGT
119980 TAGATTAAATATTTAACA-AAAAG
1 TAGATT-AATATTTAACAGAAAAG
120003 ATTCATTTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 10 0.50
25 10 0.50
ACGTcount: A:0.49, C:0.04, G:0.11, T:0.36
Consensus pattern (24 bp):
TAGATTAATATTTAACAGAAAAGT
Found at i:121491 original size:22 final size:22
Alignment explanation
Indices: 121430--121493 Score: 92
Period size: 22 Copynumber: 2.9 Consensus size: 22
121420 GAGTGTGGGT
* * **
121430 TCTATTTGCGAACCGATAGAGT
1 TCTATTTGTGAACCGATGGAAA
121452 TCTATTTGTGAACCGATGGAAA
1 TCTATTTGTGAACCGATGGAAA
121474 TCTATTTGTGAACCGATGGA
1 TCTATTTGTGAACCGATGGA
121494 CACAATGAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 38 1.00
ACGTcount: A:0.28, C:0.16, G:0.23, T:0.33
Consensus pattern (22 bp):
TCTATTTGTGAACCGATGGAAA
Found at i:122043 original size:16 final size:18
Alignment explanation
Indices: 122004--122045 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 18
121994 ATAGTTTGTA
122004 ATGTTT-TATATTATGTT
1 ATGTTTATATATTATGTT
*
122021 ATTTTTATATATTATG-T
1 ATGTTTATATATTATGTT
122038 A-GTTTATA
1 ATGTTTATA
122046 ACATACAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
16 6 0.27
17 7 0.32
18 9 0.41
ACGTcount: A:0.29, C:0.00, G:0.10, T:0.62
Consensus pattern (18 bp):
ATGTTTATATATTATGTT
Found at i:122171 original size:23 final size:22
Alignment explanation
Indices: 122134--122178 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 22
122124 AAAATTTTAA
122134 TAAATAAAAAATATAAAAATAT
1 TAAATAAAAAATATAAAAATAT
* *
122156 TAAATTAAAAATTATATAAATAT
1 TAAA-TAAAAAATATAAAAATAT
122179 GTTTTTTTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 4 0.20
23 16 0.80
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (22 bp):
TAAATAAAAAATATAAAAATAT
Found at i:124440 original size:9 final size:8
Alignment explanation
Indices: 124423--124454 Score: 55
Period size: 8 Copynumber: 3.9 Consensus size: 8
124413 TTTAAATACC
124423 TTAAATTT
1 TTAAATTT
124431 TTAAATTT
1 TTAAATTT
124439 TTAAAATTT
1 TT-AAATTT
124448 TTAAATT
1 TTAAATT
124455 ACATTTGAGC
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
8 15 0.65
9 8 0.35
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (8 bp):
TTAAATTT
Found at i:126626 original size:5 final size:6
Alignment explanation
Indices: 126610--126634 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
126600 TTTTTAAGTT
126610 TAAAAA TAAAAA TAAAAA TAAAAA T
1 TAAAAA TAAAAA TAAAAA TAAAAA T
126635 TATTATCAAT
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:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (6 bp):
TAAAAA
Found at i:128328 original size:3 final size:3
Alignment explanation
Indices: 128320--128346 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
128310 AGAAATATGA
128320 AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT
128347 TTCTTGTGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:134096 original size:91 final size:90
Alignment explanation
Indices: 133938--134119 Score: 269
Period size: 91 Copynumber: 2.0 Consensus size: 90
133928 GCTGACTGTA
* * *
133938 AAGAAAAAGAGCAAAGAAGGATAGAAGCAAGTAACTTAGAGTAAGATGAATAAATATCTAGTTAT
1 AAGAAAAAGAGCAAAGAAGGATAAAAGCAAGGAACTTAGAGTAAGATGAATAAATATCTAG-CAT
*
134003 CCTCTGGAGAATAAATTAGAAATTCT
65 CCTCTAGAGAATAAATTAGAAATTCT
*
134029 AAGAAAAAGCA-CAAAGAAGGTATAAAAGCAAGGAACTTAGAGTGAAGATGAATACATATCTA-C
1 AAGAAAAAG-AGCAAAGAAGG-ATAAAAGCAAGGAACTTAGAGT-AAGATGAATAAATATCTAGC
134092 ATCCTCTAGAGAATAAATTAGAAATTCT
63 ATCCTCTAGAGAATAAATTAGAAATTCT
134120 TAGTCAATAA
Statistics
Matches: 83, Mismatches: 5, Indels: 6
0.88 0.05 0.06
Matches are distributed among these distances:
91 45 0.54
92 21 0.25
93 17 0.20
ACGTcount: A:0.49, C:0.10, G:0.19, T:0.22
Consensus pattern (90 bp):
AAGAAAAAGAGCAAAGAAGGATAAAAGCAAGGAACTTAGAGTAAGATGAATAAATATCTAGCATC
CTCTAGAGAATAAATTAGAAATTCT
Found at i:142795 original size:30 final size:30
Alignment explanation
Indices: 142761--142825 Score: 85
Period size: 30 Copynumber: 2.2 Consensus size: 30
142751 CAACTTAACA
* * * *
142761 AACAAATATCTTTAAAATAATAATAAAATT
1 AACAAATACCTCTAAAAAAATAACAAAATT
*
142791 AACAAATGCCTCTAAAAAAATAACAAAATT
1 AACAAATACCTCTAAAAAAATAACAAAATT
142821 AACAA
1 AACAA
142826 TAAAATAAGT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.62, C:0.12, G:0.02, T:0.25
Consensus pattern (30 bp):
AACAAATACCTCTAAAAAAATAACAAAATT
Found at i:146376 original size:21 final size:21
Alignment explanation
Indices: 146347--146386 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
146337 TCGAAACCTC
* *
146347 AAATTAATTTATAAAATTTTA
1 AAATAAATTTAAAAAATTTTA
146368 AAATAAATTTAAAAAATTT
1 AAATAAATTTAAAAAATTT
146387 AGAACTTTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (21 bp):
AAATAAATTTAAAAAATTTTA
Found at i:149206 original size:6 final size:6
Alignment explanation
Indices: 149195--149224 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
149185 CATAAGCAAC
149195 CATGGG CATGGG CATGGG CATGGG CATGGG
1 CATGGG CATGGG CATGGG CATGGG CATGGG
149225 ATTTTTGTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.17, C:0.17, G:0.50, T:0.17
Consensus pattern (6 bp):
CATGGG
Found at i:149536 original size:9 final size:9
Alignment explanation
Indices: 149522--149547 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
149512 TTTAAATCGC
149522 ATATAAAAA
1 ATATAAAAA
149531 ATATAAAAA
1 ATATAAAAA
149540 ATATAAAA
1 ATATAAAA
149548 TCTTATATTA
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:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (9 bp):
ATATAAAAA
Found at i:150867 original size:60 final size:58
Alignment explanation
Indices: 150420--151036 Score: 488
Period size: 60 Copynumber: 10.3 Consensus size: 58
150410 GTTGGCCATG
* * * *
150420 TTGTCAGATAAAAAGTTCAAATTTTTTTTTTGTTGGTCATGTCATTGCCGACACCCCCTTT
1 TTGTCAGATAAAAAATTCAAA-TTTTTTTGTGTTGGCCATG-CATGGCCGACA-CCCCTTT
* * * ***
150481 TTGTCAAAT-AAAAATTCAAATTTTTTGGCGTTAATCATGCTATGGCCGACACTCCCTTT
1 TTGTCAGATAAAAAATTCAAATTTTTTTGTGTTGGCCATGC-ATGGCCGACAC-CCCTTT
* * * * *
150540 TAGTTAGATAAAAAAATC-AATTTTTTTGGTGTTGGTCATGCCATGACCGACACCCCTTTT
1 TTGTCAGATAAAAAATTCAAATTTTTTT-GTGTTGGCCATG-CATGGCCGACACCCC-TTT
* * * * * * *
150600 TTATCTGATAAAAAAATCAATTTTTTTTATGTTAGCCATGTCATGACCGACACCCCCTTT
1 TTGTCAGATAAAAAATTCAAATTTTTTTGTGTTGGCCATG-CATGGCCGACA-CCCCTTT
* * * * *
150660 TTATCTGACAAAAAATTTAAATTTTTTTGGTGTTGGCCATTGCATGGCTGACACCCCATTT
1 TTGTCAGATAAAAAATTCAAATTTTTTT-GTGTTGGCCA-TGCATGGCCGACACCCC-TTT
* * * * *
150721 TTGTCAGATAAAAAATTTAAATTTTTTGGTGTTGGTCATACCATGGTCGACACCCCCTTT
1 TTGTCAGATAAAAAATTCAAATTTTTTTGTGTTGGCCAT-GCATGGCCGACA-CCCCTTT
* * * * *
150781 TTATCTGACAAAAAAATCAATTTTTTTTGTGTTGGCCATTGCATGGCCGACACCCTCTTT
1 TTGTCAGATAAAAAATTCAAATTTTTTTGTGTTGGCCA-TGCATGGCCGACACCC-CTTT
* * ** ***
150841 TTGTCAGATAAAAAATTCAAAATTTTTAGTGTTATCCATGTCATGATTGACACCCCTTT
1 TTGTCAGATAAAAAATTCAAATTTTTTTGTGTTGGCCATG-CATGGCCGACACCCCTTT
* * * * * *
150900 TTATCTGACAAAAAATTCAAATTTTTTTGTGTTGGTCATTGCATGG-CAACACCATCTTT
1 TTGTCAGATAAAAAATTCAAATTTTTTTGTGTTGGCCA-TGCATGGCCGACACC-CCTTT
* * *
150959 TTATCTGATAAAAAAATT--AATTTTTTTGTTGTTGGCCATTGCATGGCCGACACCACTATT
1 TTGTCAGAT-AAAAAATTCAAATTTTTTTG-TGTTGGCCA-TGCATGGCCGACACCCCT-TT
151019 AGTTGTCAGATAAAAAAT
1 --TTGTCAGATAAAAAAT
151037 ATTTTTTTTT
Statistics
Matches: 450, Mismatches: 82, Indels: 48
0.78 0.14 0.08
Matches are distributed among these distances:
58 17 0.04
59 120 0.27
60 227 0.50
61 77 0.17
62 9 0.02
ACGTcount: A:0.28, C:0.18, G:0.14, T:0.39
Consensus pattern (58 bp):
TTGTCAGATAAAAAATTCAAATTTTTTTGTGTTGGCCATGCATGGCCGACACCCCTTT
Found at i:153135 original size:20 final size:20
Alignment explanation
Indices: 153101--153166 Score: 73
Period size: 20 Copynumber: 3.4 Consensus size: 20
153091 GGTGTAAGAT
* * *
153101 ATATTTTTGAAATTTTTATA
1 ATATTTTTTATATTTTCATA
*
153121 ATATTTTTTTTATTTTCATA
1 ATATTTTTTATATTTTCATA
*
153141 ATGTTTTTTATATTTTCA-A
1 ATATTTTTTATATTTTCATA
153160 AT-TTTTT
1 ATATTTTT
153167 AAAAAATAAA
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
18 5 0.12
19 3 0.08
20 32 0.80
ACGTcount: A:0.27, C:0.03, G:0.03, T:0.67
Consensus pattern (20 bp):
ATATTTTTTATATTTTCATA
Found at i:153165 original size:18 final size:18
Alignment explanation
Indices: 153123--153166 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 18
153113 TTTTTATAAT
153123 ATTTTTTTTATTTTCATA
1 ATTTTTTTTATTTTCATA
153141 ATGTTTTTTATATTTTCA-A
1 AT-TTTTTT-TATTTTCATA
153160 ATTTTTT
1 ATTTTTT
153167 AAAAAATAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
18 7 0.29
19 9 0.38
20 8 0.33
ACGTcount: A:0.23, C:0.05, G:0.02, T:0.70
Consensus pattern (18 bp):
ATTTTTTTTATTTTCATA
Found at i:153201 original size:13 final size:13
Alignment explanation
Indices: 153183--153207 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
153173 TAAAATTTTG
153183 ATATTTTTTACAA
1 ATATTTTTTACAA
153196 ATATTTTTTACA
1 ATATTTTTTACA
153208 TTTTCAAAAT
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:0.36, C:0.08, G:0.00, T:0.56
Consensus pattern (13 bp):
ATATTTTTTACAA
Found at i:153347 original size:13 final size:13
Alignment explanation
Indices: 153329--153353 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
153319 TAAAAATTTG
153329 ATATTTTTTACAA
1 ATATTTTTTACAA
153342 ATATTTTTTACA
1 ATATTTTTTACA
153354 CTTTCAAAAT
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:0.36, C:0.08, G:0.00, T:0.56
Consensus pattern (13 bp):
ATATTTTTTACAA
Found at i:154338 original size:30 final size:30
Alignment explanation
Indices: 154304--154422 Score: 152
Period size: 30 Copynumber: 4.0 Consensus size: 30
154294 ATTTTTTTTC
* *
154304 CGTTTACT-TTTTAAATTTAATTTGTAACTT
1 CGTTTA-TATTTTAAATTTAATTTCTAATTT
* *
154334 CGTTTTTATTTTAAATTTAATTTTTAATTT
1 CGTTTATATTTTAAATTTAATTTCTAATTT
*
154364 C-TTGTATATTTTAATTTTAATTTCTAATTT
1 CGTT-TATATTTTAAATTTAATTTCTAATTT
*
154394 CGTTTATATTTTAAATTTCATTTCTAATT
1 CGTTTATATTTTAAATTTAATTTCTAATT
154423 ATTATTTTTT
Statistics
Matches: 78, Mismatches: 8, Indels: 6
0.85 0.09 0.07
Matches are distributed among these distances:
29 3 0.04
30 73 0.94
31 2 0.03
ACGTcount: A:0.27, C:0.08, G:0.04, T:0.61
Consensus pattern (30 bp):
CGTTTATATTTTAAATTTAATTTCTAATTT
Found at i:155494 original size:120 final size:119
Alignment explanation
Indices: 155306--155857 Score: 497
Period size: 120 Copynumber: 4.7 Consensus size: 119
155296 GTGATATCGA
** * * * ** *
155306 CCATGCAATAACCAACACCAAAAAATTTGATTATTTTTTATCATATAAAAAGGTAGTGTCGACAA
1 CCATGCAATGGCCAACACAAAAAAATTTGA--ATTTTTTATCAGACAAAAAGGGGGTGTCGACCA
* *
155371 TGGCATGACCAACACCAAAATATTTAATTTTTTTATCAAACAAAAAGGTGGTGTCGG
64 TGGCATGACCAACACCAAAAAATTTAATTTTTTTATCAGACAAAAAGG-GGTGTCGG
* * * *
155428 CCATGCAATGGTCAACACAAAAAAAATTGAATTTTTTGTCAGATAAAAAGGGGGTGTCGACCATG
1 CCATGCAATGGCCAACACAAAAAAATTTGAATTTTTTATCAGACAAAAAGGGGGTGTCGACCATG
* *
155493 GCATGACCAACACCAAAAAATTTTATTTTTTTATCAGATAAAAAGGGAGTGTCGG
66 GCATGACCAACACCAAAAAATTTAATTTTTTTATCAGACAAAAAGGG-GTGTCGG
* * ** ***
155548 CAATGGC-ATGGCCAACACTAAAAAATTTGAATTTTTTATTTGACAAAAAGGGGGTGTCGGTTAT
1 CCAT-GCAATGGCCAACACAAAAAAATTTGAATTTTTTATCAGACAAAAAGGGGGTGTCGACCAT
* * * **
155612 GCCATGGCCAACACCAAAAAATTTGAA-TTTTTTATCTGACAAAAAGGGGATGTCAA
65 GGCATGACCAACACCAAAAAATTT-AATTTTTTTATCAGACAAAAAGGGG-TGTCGG
* * * * * * *
155668 TCATGCAATAGCCAACATAAAAAAATTTTAA-TTTTTATCTGACAAACAGGGGGTGTCGGCCAT-
1 CCATGCAATGGCCAACACAAAAAAATTTGAATTTTTTATCAGACAAAAAGGGGGTGTCGACCATG
* * * **
155731 GCAATGACCAACACTCAAAAAA---AA--ATTTTATCTGAAAAAAAGGGGTGTTTG
66 GC-ATGACCAACAC-CAAAAAATTTAATTTTTTTATCAGACAAAAAGGGGTGTCGG
* * *
155782 CCATGCAATGGCCAACACCAAAAAA----AA--TTTTATCTGACAAAAAGGTGGTGTCGACCAT-
1 CCATGCAATGGCCAACACAAAAAAATTTGAATTTTTTATCAGACAAAAAGGGGGTGTCGACCATG
* *
155840 GCAATAACCAATACCAAA
66 GC-ATGACCAACACCAAA
155858 TTTTTTTTTT
Statistics
Matches: 365, Mismatches: 58, Indels: 28
0.81 0.13 0.06
Matches are distributed among these distances:
108 4 0.01
109 40 0.11
110 2 0.01
114 24 0.07
115 19 0.05
116 2 0.01
118 1 0.00
119 42 0.12
120 203 0.56
121 3 0.01
122 25 0.07
ACGTcount: A:0.39, C:0.17, G:0.17, T:0.26
Consensus pattern (119 bp):
CCATGCAATGGCCAACACAAAAAAATTTGAATTTTTTATCAGACAAAAAGGGGGTGTCGACCATG
GCATGACCAACACCAAAAAATTTAATTTTTTTATCAGACAAAAAGGGGTGTCGG
Found at i:155554 original size:180 final size:177
Alignment explanation
Indices: 155235--155857 Score: 566
Period size: 180 Copynumber: 3.5 Consensus size: 177
155225 GATAAATGAA
* * *
155235 AAAAAGTTGGTGTCAGTCATGCAATGGCCAACACAAAAAAATTTG-ATTTTTTT-A-AAATAAGG
1 AAAAAGGTGGTGTCGGTCATGCAATGGCCAACACAAAAAAATTTGAATTTTTTTCAGAAAAAAGG
* * * * *
155297 TGATATCGACCATGCAATAACCAACACCAAAAAATTTGATTATTTTTTATCATATAAAAAGGTAG
66 GGATGTCGACCATGCAAT-ACCAACACCAAAAAATTTTA-T-TTTTTTATCAGATAAAAAGGGAG
* *
155362 TGTCGACAATGGCATGACCAACACCAAAATATTT-AATTTTTTTATCAAAC
128 TGTCGGCAATGGCATGACCAACACCAAAAAATTTGAA-TTTTTTATCAAAC
* * *
155412 AAAAAGGTGGTGTCGGCCATGCAATGGTCAACACAAAAAAAATTGAATTTTTTGTCAGATAAAAA
1 AAAAAGGTGGTGTCGGTCATGCAATGGCCAACACAAAAAAATTTGAATTTTTT-TCAGA-AAAAA
*
155477 GGGGGTGTCGACCATGGC-ATGACCAACACCAAAAAATTTTATTTTTTTATCAGATAAAAAGGGA
64 GGGGATGTCGACCAT-GCAAT-ACCAACACCAAAAAATTTTATTTTTTTATCAGATAAAAAGGGA
* * ***
155541 GTGTCGGCAATGGCATGGCCAACACTAAAAAATTTGAATTTTTTATTTGAC
127 GTGTCGGCAATGGCATGACCAACACCAAAAAATTTGAATTTTTTATCAAAC
* * * * *
155592 AAAAAGGGGGTGTCGGTTATGCCATGGCCAACACCAAAAAATTTGAATTTTTTATCTGACAAAAA
1 AAAAAGGTGGTGTCGGTCATGCAATGGCCAACACAAAAAAATTTGAATTTTTT-TCAGA-AAAAA
* * ** * * * * *
155657 GGGGATGTCAATCATGCAATAGCCAACATAAAAAAATTTTA-ATTTTTATCTGACAAACAGGGGG
64 GGGGATGTCGACCATGCAATA-CCAACACCAAAAAATTTTATTTTTTTATCAGATAAAAAGGGAG
* * *
155721 TGTCGGCCAT-GCAATGACCAACACTCAAAAAA----AA-ATTTTATCTGAA-
128 TGTCGGCAATGGC-ATGACCAACAC-CAAAAAATTTGAATTTTTTATC-AAAC
** * * * *
155767 AAAAAGG-GGTGTTTGCCATGCAATGGCCAACACCAAAAAA----AA-TTTTATCTGACAAAAAG
1 AAAAAGGTGGTGTCGGTCATGCAATGGCCAACACAAAAAAATTTGAATTTTTTTCAGA-AAAAAG
*
155826 GTGG-TGTCGACCATGCAATAACCAATACCAAA
65 G-GGATGTCGACCATGCAAT-ACCAACACCAAA
155858 TTTTTTTTTT
Statistics
Matches: 374, Mismatches: 58, Indels: 37
0.80 0.12 0.08
Matches are distributed among these distances:
168 34 0.09
169 7 0.02
170 2 0.01
174 28 0.07
175 13 0.03
176 3 0.01
177 40 0.11
178 9 0.02
179 41 0.11
180 154 0.41
181 4 0.01
182 37 0.10
183 2 0.01
ACGTcount: A:0.40, C:0.16, G:0.17, T:0.27
Consensus pattern (177 bp):
AAAAAGGTGGTGTCGGTCATGCAATGGCCAACACAAAAAAATTTGAATTTTTTTCAGAAAAAAGG
GGATGTCGACCATGCAATACCAACACCAAAAAATTTTATTTTTTTATCAGATAAAAAGGGAGTGT
CGGCAATGGCATGACCAACACCAAAAAATTTGAATTTTTTATCAAAC
Found at i:155732 original size:59 final size:59
Alignment explanation
Indices: 155243--155844 Score: 418
Period size: 60 Copynumber: 10.3 Consensus size: 59
155233 AAAAAAAGTT
* * *
155243 GGTGTCAGTCATGCAATGGCCAACACAAAAAAATTTG-ATTTTT-T-T-A-AAATAAGGT
1 GGTGTCGGCCATGCAATGGCCAACACAAAAAAATTTGAATTTTTATCTGACAAA-AAGGG
* * * ** * * *
155298 GATATCGACCATGCAATAACCAACACCAAAAAATTTGATTATTTTTTATCAT-ATAAAAAGGT
1 GGTGTCGGCCATGCAATGGCCAACACAAAAAAATTTGA--A-TTTTTATC-TGACAAAAAGGG
* * * * * * ** *
155360 AGTGTCGACAATGGC-ATGACCAACACCAAAATATTT-AATTTTTTTATCAAACAAAAAGGT
1 GGTGTCGGCCAT-GCAATGGCCAACACAAAAAAATTTGAA--TTTTTATCTGACAAAAAGGG
* * * * *
155420 GGTGTCGGCCATGCAATGGTCAACACAAAAAAAATTGAATTTTTTGTCAGATAAAAAGGG
1 GGTGTCGGCCATGCAATGGCCAACACAAAAAAATTTGAA-TTTTTATCTGACAAAAAGGG
* * * * * * *
155480 GGTGTCGACCATGGC-ATGACCAACACCAAAAAATTTTATTTTTTTATCAGATAAAAAGGG
1 GGTGTCGGCCAT-GCAATGGCCAACACAAAAAAATTTGA-ATTTTTATCTGACAAAAAGGG
* * * *
155540 AGTGTCGGCAATGGC-ATGGCCAACACTAAAAAATTTGAATTTTTTATTTGACAAAAAGGG
1 GGTGTCGGCCAT-GCAATGGCCAACACAAAAAAATTTGAA-TTTTTATCTGACAAAAAGGG
** * *
155600 GGTGTCGGTTATGCCATGGCCAACACCAAAAAATTTGAATTTTTTATCTGACAAAAAGGG
1 GGTGTCGGCCATGCAATGGCCAACACAAAAAAATTTGAA-TTTTTATCTGACAAAAAGGG
* *** * * * *
155660 GATGTCAATCATGCAATAGCCAACATAAAAAAATTTTAATTTTTATCTGACAAACAGGG
1 GGTGTCGGCCATGCAATGGCCAACACAAAAAAATTTGAATTTTTATCTGACAAAAAGGG
* *
155719 GGTGTCGGCCATGCAATGACCAACACTCAAAAAAA----AA-TTTTATCTGA-AAAAAAGG
1 GGTGTCGGCCATGCAATGGCCAACA--CAAAAAAATTTGAATTTTTATCTGACAAAAAGGG
** * *
155774 GGTGTTTGCCATGCAATGGCCAACACCAAAAAA----AA-TTTTATCTGACAAAAAGGT
1 GGTGTCGGCCATGCAATGGCCAACACAAAAAAATTTGAATTTTTATCTGACAAAAAGGG
*
155828 GGTGTCGACCATGCAAT
1 GGTGTCGGCCATGCAAT
155845 AACCAATACC
Statistics
Matches: 448, Mismatches: 79, Indels: 41
0.79 0.14 0.07
Matches are distributed among these distances:
53 19 0.04
54 20 0.04
55 57 0.13
56 10 0.02
57 2 0.00
58 1 0.00
59 48 0.11
60 240 0.54
61 12 0.03
62 34 0.08
63 5 0.01
ACGTcount: A:0.39, C:0.16, G:0.18, T:0.27
Consensus pattern (59 bp):
GGTGTCGGCCATGCAATGGCCAACACAAAAAAATTTGAATTTTTATCTGACAAAAAGGG
Found at i:155797 original size:55 final size:53
Alignment explanation
Indices: 155700--155857 Score: 199
Period size: 55 Copynumber: 2.9 Consensus size: 53
155690 AAATTTTAAT
* *
155700 TTTTATCTGACAAACAGGGGGTGTCGGCCATGCAATGACCAACACTCAAAAAAAAA
1 TTTTATCTGA-AAAAAAGGGGTGTCGGCCATGCAATGACCAACAC-C-AAAAAAAA
** *
155756 TTTTATCTGAAAAAAAGGGGTGTTTGCCATGCAATGGCCAACACCAAAAAAAA
1 TTTTATCTGAAAAAAAGGGGTGTCGGCCATGCAATGACCAACACCAAAAAAAA
* * * *
155809 TTTTATCTGACAAAAAGGTGGTGTCGACCATGCAATAACCAATACCAAA
1 TTTTATCTGAAAAAAAGG-GGTGTCGGCCATGCAATGACCAACACCAAA
155858 TTTTTTTTTT
Statistics
Matches: 89, Mismatches: 12, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
53 25 0.28
54 25 0.28
55 29 0.33
56 10 0.11
ACGTcount: A:0.40, C:0.20, G:0.18, T:0.22
Consensus pattern (53 bp):
TTTTATCTGAAAAAAAGGGGTGTCGGCCATGCAATGACCAACACCAAAAAAAA
Found at i:156362 original size:27 final size:26
Alignment explanation
Indices: 156312--156398 Score: 68
Period size: 27 Copynumber: 3.2 Consensus size: 26
156302 AATTTGATAA
* *
156312 AATTTTAACATTTTATATAGTTTTTAT
1 AATTTTAAAATTTTA-ATAATTTTTAT
* *
156339 AATTTCTAAAATTTTAATACTTTTCCAT
1 AATTT-TAAAATTTTAATAATTTT-TAT
** *
156367 -ATTTTTTAATATTTAATAAATTTTAT
1 AATTTTAAAAT-TTTAATAATTTTTAT
156393 AATTTT
1 AATTTT
156399 CTATATTTTT
Statistics
Matches: 48, Mismatches: 8, Indels: 8
0.75 0.12 0.12
Matches are distributed among these distances:
26 6 0.12
27 31 0.65
28 11 0.23
ACGTcount: A:0.36, C:0.06, G:0.01, T:0.57
Consensus pattern (26 bp):
AATTTTAAAATTTTAATAATTTTTAT
Found at i:156380 original size:28 final size:27
Alignment explanation
Indices: 156314--156398 Score: 66
Period size: 28 Copynumber: 3.1 Consensus size: 27
156304 TTTGATAAAA
* * *
156314 TTTTAACATTTTATATAGTTTTTATAAT
1 TTTTAAAATTTTA-ATACTTTTCATAAT
* *
156342 TTCTAAAATTTTAATACTTTTCCATATT
1 TTTTAAAATTTTAATACTTTT-CATAAT
* *
156370 TTTTAATA-TTTAATAAATTTT-ATAAT
1 TTTTAAAATTTTAAT-ACTTTTCATAAT
156396 TTT
1 TTT
156399 CTATATTTTT
Statistics
Matches: 46, Mismatches: 9, Indels: 6
0.75 0.15 0.10
Matches are distributed among these distances:
26 7 0.15
27 13 0.28
28 26 0.57
ACGTcount: A:0.34, C:0.06, G:0.01, T:0.59
Consensus pattern (27 bp):
TTTTAAAATTTTAATACTTTTCATAAT
Found at i:156414 original size:37 final size:37
Alignment explanation
Indices: 156278--156431 Score: 119
Period size: 36 Copynumber: 4.2 Consensus size: 37
156268 TAACAAAATT
* * *
156278 TTTTAT-ATTTT-TATCTTTTAAATAA-ATTTGATAAAA
1 TTTTATAATTTTCTATATTTT-TATAATATTTAAT-AAA
*
156314 TTTTA-ACATTTTATATAGTTTTTATAAT-TTCT-A-AAA
1 TTTTATA-ATTTTCTATA-TTTTTATAATATT-TAATAAA
* *
156350 TTTTAATACTTTTCCATATTTTT-TAATATTTAATAAA
1 TTTT-ATAATTTTCTATATTTTTATAATATTTAATAAA
156387 TTTTATAATTTTCTATATTTTTATAATATGTTAAT-AA
1 TTTTATAATTTTCTATATTTTTATAATAT-TTAATAAA
156424 TCTTTATA
1 T-TTTATA
156432 TTTAAATGCT
Statistics
Matches: 97, Mismatches: 7, Indels: 26
0.75 0.05 0.20
Matches are distributed among these distances:
35 5 0.05
36 36 0.37
37 29 0.30
38 22 0.23
39 5 0.05
ACGTcount: A:0.36, C:0.05, G:0.02, T:0.57
Consensus pattern (37 bp):
TTTTATAATTTTCTATATTTTTATAATATTTAATAAA
Found at i:157999 original size:37 final size:37
Alignment explanation
Indices: 157958--158030 Score: 130
Period size: 37 Copynumber: 2.0 Consensus size: 37
157948 ATCTCCTTTG
157958 GCTTCTTGTCTTTCTTCCCCC-TCTAATCAAACGTGTT
1 GCTTCTTGTC-TTCTTCCCCCTTCTAATCAAACGTGTT
157995 GCTTCTTGTCTTCTTCCCCCTTCTAATCAAACGTGT
1 GCTTCTTGTCTTCTTCCCCCTTCTAATCAAACGTGT
158031 AACTTCCATG
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
36 10 0.29
37 25 0.71
ACGTcount: A:0.14, C:0.33, G:0.11, T:0.42
Consensus pattern (37 bp):
GCTTCTTGTCTTCTTCCCCCTTCTAATCAAACGTGTT
Found at i:160619 original size:16 final size:16
Alignment explanation
Indices: 160598--160631 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
160588 AATAAATTAT
160598 TAAAAAT-TTATAAAAA
1 TAAAAATATTA-AAAAA
160614 TAAAAATATTAAAAAA
1 TAAAAATATTAAAAAA
160630 TA
1 TA
160632 GCTCAATTCC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 14 0.82
17 3 0.18
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (16 bp):
TAAAAATATTAAAAAA
Found at i:167892 original size:21 final size:20
Alignment explanation
Indices: 167849--167893 Score: 54
Period size: 21 Copynumber: 2.2 Consensus size: 20
167839 GGTTAAACCT
* *
167849 AAAACAAACAAATCCTAAAG
1 AAAACAAACAAAGCATAAAG
*
167869 AAAACAAACCAAAGCATAATG
1 AAAACAAA-CAAAGCATAAAG
167890 AAAA
1 AAAA
167894 AGAAGGGCAC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 8 0.38
21 13 0.62
ACGTcount: A:0.67, C:0.18, G:0.07, T:0.09
Consensus pattern (20 bp):
AAAACAAACAAAGCATAAAG
Found at i:171188 original size:18 final size:20
Alignment explanation
Indices: 171154--171199 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
171144 CTAAAAATAA
*
171154 TCAAAATAATTT-TTAAAAT
1 TCAAAATAATTTATAAAAAT
171173 TCAAAAT-ATTTATAAAAAT
1 TCAAAATAATTTATAAAAAT
171192 TCCAAAAT
1 T-CAAAAT
171200 CTAAAGAATA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
18 4 0.17
19 14 0.58
20 6 0.25
ACGTcount: A:0.54, C:0.09, G:0.00, T:0.37
Consensus pattern (20 bp):
TCAAAATAATTTATAAAAAT
Found at i:174229 original size:19 final size:19
Alignment explanation
Indices: 174205--174241 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
174195 ATTGATCAGA
174205 TTGATTCATATTTTATTAT
1 TTGATTCATATTTTATTAT
*
174224 TTGATTCGTATTTTATTA
1 TTGATTCATATTTTATTA
174242 GACAATCACG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.24, C:0.05, G:0.08, T:0.62
Consensus pattern (19 bp):
TTGATTCATATTTTATTAT
Found at i:181068 original size:11 final size:10
Alignment explanation
Indices: 181043--181067 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
181033 ATTGATTCTT
181043 AAAAATTTAA
1 AAAAATTTAA
181053 AAAAATTTAA
1 AAAAATTTAA
181063 AAAAA
1 AAAAA
181068 AAAAATTGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (10 bp):
AAAAATTTAA
Found at i:183381 original size:30 final size:31
Alignment explanation
Indices: 183345--183407 Score: 101
Period size: 30 Copynumber: 2.1 Consensus size: 31
183335 TGTTAATTCT
* *
183345 AATTTTTAACAAGGAAGAA-ATAGAGAGCAA
1 AATTTTTAACAAGGAAGAAGATAAAGAGAAA
183375 AATTTTTAACAAGGAAGAAGATAAAGAGAAA
1 AATTTTTAACAAGGAAGAAGATAAAGAGAAA
183406 AA
1 AA
183408 GGTAGTTGAG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
30 19 0.63
31 11 0.37
ACGTcount: A:0.57, C:0.05, G:0.19, T:0.19
Consensus pattern (31 bp):
AATTTTTAACAAGGAAGAAGATAAAGAGAAA
Found at i:188028 original size:2 final size:2
Alignment explanation
Indices: 188021--188063 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
188011 CTATAAATGA
188021 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
188063 T
1 T
188064 TTTTCGTATA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:194791 original size:3 final size:3
Alignment explanation
Indices: 194783--194814 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
194773 GATAGCCCTA
*
194783 CAG CAG CAG CAG CAG CAG CAG CAG CAG AAG CA
1 CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CA
194815 AAGGGTTTAG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.38, C:0.31, G:0.31, T:0.00
Consensus pattern (3 bp):
CAG
Found at i:201868 original size:12 final size:13
Alignment explanation
Indices: 201832--201869 Score: 51
Period size: 12 Copynumber: 2.8 Consensus size: 13
201822 AATTATATCT
201832 AAATAATTTTGAATA
1 AAATAA-TTT-AATA
201847 AAATAATTTAATA
1 AAATAATTTAATA
201860 AAA-AATTTAA
1 AAATAATTTAA
201870 AAGGTTGGTC
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 7 0.30
13 7 0.30
14 3 0.13
15 6 0.26
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.37
Consensus pattern (13 bp):
AAATAATTTAATA
Found at i:207846 original size:21 final size:20
Alignment explanation
Indices: 207804--207843 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
207794 AATTTTTTTT
207804 ATTTAAAAATAAATAAATTA
1 ATTTAAAAATAAATAAATTA
*
207824 ATTTATAAATTAAATCAAAT
1 ATTTA-AAAATAAAT-AAAT
207844 AATAAATTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 5 0.29
21 8 0.47
22 4 0.24
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.38
Consensus pattern (20 bp):
ATTTAAAAATAAATAAATTA
Found at i:211016 original size:9 final size:8
Alignment explanation
Indices: 210964--211023 Score: 50
Period size: 8 Copynumber: 7.0 Consensus size: 8
210954 ACTTTTATCC
210964 TTTAGTTTT
1 TTTA-TTTT
210973 TTT-TTTCT
1 TTTATTT-T
*
210981 TTTCAATTT
1 TTT-ATTTT
210990 TTTATTTT
1 TTTATTTT
*
210998 TTTATATT
1 TTTATTTT
211006 TTTAGTTTT
1 TTTA-TTTT
211015 TTTACTTTT
1 TTTA-TTTT
211024 AAAATTTATA
Statistics
Matches: 42, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
7 3 0.07
8 19 0.45
9 18 0.43
10 2 0.05
ACGTcount: A:0.13, C:0.05, G:0.03, T:0.78
Consensus pattern (8 bp):
TTTATTTT
Found at i:218111 original size:16 final size:17
Alignment explanation
Indices: 218087--218119 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
218077 ATGGTAAATA
218087 TATATACTACTATTTTT
1 TATATACTACTATTTTT
*
218104 TATA-ACTATTATTTTT
1 TATATACTACTATTTTT
218120 GAAAAACTCA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.30, C:0.09, G:0.00, T:0.61
Consensus pattern (17 bp):
TATATACTACTATTTTT
Found at i:218925 original size:30 final size:29
Alignment explanation
Indices: 218891--218948 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 29
218881 TTTTTATAAC
*
218891 TTTTAAACTTATTTCATTTTTTA-TAATTTA
1 TTTTAAACTT-TCT-ATTTTTTAGTAATTTA
218921 TTTTAAACTTTCTATTTTTTAGTAATTT
1 TTTTAAACTTTCTATTTTTTAGTAATTT
218949 TCTACAATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
28 8 0.31
29 8 0.31
30 10 0.38
ACGTcount: A:0.28, C:0.07, G:0.02, T:0.64
Consensus pattern (29 bp):
TTTTAAACTTTCTATTTTTTAGTAATTTA
Found at i:219683 original size:22 final size:20
Alignment explanation
Indices: 219642--219684 Score: 52
Period size: 20 Copynumber: 2.0 Consensus size: 20
219632 AAATAAATTC
219642 TTTTAAACAAAATATTTAAA
1 TTTTAAACAAAATATTTAAA
219662 TTTTATAA-AAAATCATTCTAAA
1 TTTTA-AACAAAAT-ATT-TAAA
219684 T
1 T
219685 AATATATAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
20 10 0.50
21 5 0.25
22 5 0.25
ACGTcount: A:0.51, C:0.07, G:0.00, T:0.42
Consensus pattern (20 bp):
TTTTAAACAAAATATTTAAA
Found at i:225913 original size:21 final size:21
Alignment explanation
Indices: 225870--225913 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
225860 ATAAAATAAA
*
225870 AAATAAAATTAATTATAAATT
1 AAATAAAATAAATTATAAATT
*
225891 AAATAAAAATAAATT-TAATTT
1 AAAT-AAAATAAATTATAAATT
225912 AA
1 AA
225914 CTCCGAATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 11 0.55
22 9 0.45
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (21 bp):
AAATAAAATAAATTATAAATT
Found at i:231697 original size:31 final size:31
Alignment explanation
Indices: 231643--231701 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
231633 TAATTCGATT
* *
231643 ACTTAAATAAAAACTTTCGAATAGTTTATCG
1 ACTTAAATAAAAAATTTCAAATAGTTTATCG
231674 ACTTAAATAAAAAAATTT-AAATAGTTTA
1 ACTTAAAT-AAAAAATTTCAAATAGTTTA
231702 ATAATCGTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
31 17 0.68
32 8 0.32
ACGTcount: A:0.49, C:0.08, G:0.07, T:0.36
Consensus pattern (31 bp):
ACTTAAATAAAAAATTTCAAATAGTTTATCG
Found at i:233343 original size:26 final size:26
Alignment explanation
Indices: 233307--233359 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
233297 AAGAAGAGGA
233307 TATGATAACTCATGTGATATATGTGG
1 TATGATAACTCATGTGATATATGTGG
233333 TATGATAACTCATGTGATATATGTGG
1 TATGATAACTCATGTGATATATGTGG
233359 T
1 T
233360 TATCAATCTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.30, C:0.08, G:0.23, T:0.40
Consensus pattern (26 bp):
TATGATAACTCATGTGATATATGTGG
Found at i:235551 original size:22 final size:23
Alignment explanation
Indices: 235526--235572 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
235516 AATTGACACC
*
235526 TAGTTTCTCTT-TTTTTTTTTTT
1 TAGTTTCTCTTGCTTTTTTTTTT
*
235548 TAGTTTGTCTTGCTTTTTTTTTT
1 TAGTTTCTCTTGCTTTTTTTTTT
235571 TA
1 TA
235573 ACATTCAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 10 0.45
23 12 0.55
ACGTcount: A:0.06, C:0.09, G:0.09, T:0.77
Consensus pattern (23 bp):
TAGTTTCTCTTGCTTTTTTTTTT
Found at i:237833 original size:16 final size:16
Alignment explanation
Indices: 237789--237833 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
237779 GTTTGGTTCG
*
237789 TTGTAATGAAATGGAA
1 TTGTAATGAAATAGAA
* *
237805 TTGAAATAAAATAGAA
1 TTGTAATGAAATAGAA
*
237821 TTGTAATGGAATA
1 TTGTAATGAAATA
237834 AAGTTATAAA
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.49, C:0.00, G:0.20, T:0.31
Consensus pattern (16 bp):
TTGTAATGAAATAGAA
Found at i:246064 original size:20 final size:20
Alignment explanation
Indices: 246035--246075 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
246025 CTGTTCAGTC
246035 AATTTAATCCTTTAAAAATT
1 AATTTAATCCTTTAAAAATT
*
246055 AATTTTATCCTTTAAAAATT
1 AATTTAATCCTTTAAAAATT
246075 A
1 A
246076 TAAAATATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.44, C:0.10, G:0.00, T:0.46
Consensus pattern (20 bp):
AATTTAATCCTTTAAAAATT
Found at i:262058 original size:382 final size:381
Alignment explanation
Indices: 261351--262116 Score: 1433
Period size: 382 Copynumber: 2.0 Consensus size: 381
261341 GAAGTCCTCA
261351 TTTCCAAACAATCATTTTCTAGGTGGATGTCTGTATGTCTCGAACTTATATGCTTCAAATGAGTT
1 TTTCCAAACAATCATTTTCTAGGTGGATGTCTGTATGTCTCGAACTTATATGCTTCAAATGAGTT
*
261416 GACTTCTTACTCTTTGGCCTTTTTTCAGTTTTTTTTTCTTTTCTTTTACAACATTTGAATGAATT
66 GACTTCTTACTCTTTGGCCTTTTTGCAGTTTTTTTTTCTTTTCTTTTACAACATTTGAATGAATT
*
261481 AGACCATCTTTTCAGTCAGTGCATCCATGTAGACGGAGTAATGCTCCTTATTATGGCCTATACAA
131 AGACCATCTTTTCACTCAGTGCATCCATGTAGACGGAGTAATGCTCCTTATTATGGCCTATACAA
*
261546 ATTTGTTTTCTGTAGTTCCAAGTAAGAACAATAAATGAAAAGTCCAAATGGTGGTTGTCTTCTTG
196 ATTTGTTTTCTGTAGTTCCAAGTAAGAACAATAAATGAAAAGTCCAAATGGTGGGTGTCTTCTTG
* * * *
261611 TGTATTTATTGCATTATTAAATTATTTTATAGGGAGCCTGTACTTAGTGCTTTGGTAATTACATT
261 TGTATTTATTGCATTATTAAATTATTTTACAGGGAGCCAGTACTTAGAGCTTTGGTAACTACATT
261676 TTTGTTTTCAAAAGCTTTAGGTTCAAGACGTTGATTGCTCTGAAAAGCCCTTGTAG
326 TTTGTTTTCAAAAGCTTTAGGTTCAAGACGTTGATTGCTCTGAAAAGCCCTTGTAG
*
261732 TTTCCAAACAATCATTTTCTAGGTGGATGTCTGTATGTCTCGAACTTGTATGCTTCAAATGAGTT
1 TTTCCAAACAATCATTTTCTAGGTGGATGTCTGTATGTCTCGAACTTATATGCTTCAAATGAGTT
*
261797 GACTTCTTGCTCTTTGGCCTTTTTGCAGTTTTTCTTTTCTTTTCTTTTACAACATTTGAATGAAT
66 GACTTCTTACTCTTTGGCCTTTTTGCAGTTTTT-TTTTCTTTTCTTTTACAACATTTGAATGAAT
*
261862 TAGACCATCTTTTCACTCAGTGCATCCATGTGGACGGAGTAATGCTCCTTATTATGGCCTATACA
130 TAGACCATCTTTTCACTCAGTGCATCCATGTAGACGGAGTAATGCTCCTTATTATGGCCTATACA
261927 AATTTGTTTTCTGTAGTTCCAAGTAAGAACAATAAATGAAAAGTCCAAATGGTGGGTGTCTTCTT
195 AATTTGTTTTCTGTAGTTCCAAGTAAGAACAATAAATGAAAAGTCCAAATGGTGGGTGTCTTCTT
261992 GTGTATTTATTGCATTATTAAATTATTTTACAGGGAGCCAGTACTTAGAGCTTTGGTAACTACAT
260 GTGTATTTATTGCATTATTAAATTATTTTACAGGGAGCCAGTACTTAGAGCTTTGGTAACTACAT
262057 TTTTGTTTTCAAAAGCTTTAGGTTCAAGACGTTGATTGCTCTGAAAAGCCCTTGTAG
325 TTTTGTTTTCAAAAGCTTTAGGTTCAAGACGTTGATTGCTCTGAAAAGCCCTTGTAG
262114 TTT
1 TTT
262117 GGATTTCTTT
Statistics
Matches: 374, Mismatches: 10, Indels: 1
0.97 0.03 0.00
Matches are distributed among these distances:
381 95 0.25
382 279 0.75
ACGTcount: A:0.25, C:0.16, G:0.17, T:0.41
Consensus pattern (381 bp):
TTTCCAAACAATCATTTTCTAGGTGGATGTCTGTATGTCTCGAACTTATATGCTTCAAATGAGTT
GACTTCTTACTCTTTGGCCTTTTTGCAGTTTTTTTTTCTTTTCTTTTACAACATTTGAATGAATT
AGACCATCTTTTCACTCAGTGCATCCATGTAGACGGAGTAATGCTCCTTATTATGGCCTATACAA
ATTTGTTTTCTGTAGTTCCAAGTAAGAACAATAAATGAAAAGTCCAAATGGTGGGTGTCTTCTTG
TGTATTTATTGCATTATTAAATTATTTTACAGGGAGCCAGTACTTAGAGCTTTGGTAACTACATT
TTTGTTTTCAAAAGCTTTAGGTTCAAGACGTTGATTGCTCTGAAAAGCCCTTGTAG
Found at i:264712 original size:51 final size:51
Alignment explanation
Indices: 264637--264739 Score: 197
Period size: 51 Copynumber: 2.0 Consensus size: 51
264627 TAAAATTTCC
*
264637 TTTCATTCTTATTGTTAAAAACTGCCCTTGTACATCAATATGAAATGCACA
1 TTTCATTCTTATTGTTAAAAACTGCCCTTATACATCAATATGAAATGCACA
264688 TTTCATTCTTATTGTTAAAAACTGCCCTTATACATCAATATGAAATGCACA
1 TTTCATTCTTATTGTTAAAAACTGCCCTTATACATCAATATGAAATGCACA
264739 T
1 T
264740 CGTCTGTTTG
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 51 1.00
ACGTcount: A:0.34, C:0.19, G:0.09, T:0.38
Consensus pattern (51 bp):
TTTCATTCTTATTGTTAAAAACTGCCCTTATACATCAATATGAAATGCACA
Found at i:268330 original size:15 final size:15
Alignment explanation
Indices: 268310--268360 Score: 52
Period size: 15 Copynumber: 3.5 Consensus size: 15
268300 ATAAAGAGAT
268310 AACATAAATAATTAA
1 AACATAAATAATTAA
*
268325 AACATAACAT--TTTA
1 AACATAA-ATAATTAA
*
268339 AACCTAAATAATTAA
1 AACATAAATAATTAA
*
268354 AATATAA
1 AACATAA
268361 TATGAGAGAA
Statistics
Matches: 28, Mismatches: 5, Indels: 6
0.72 0.13 0.15
Matches are distributed among these distances:
13 2 0.07
14 9 0.32
15 15 0.54
16 2 0.07
ACGTcount: A:0.61, C:0.10, G:0.00, T:0.29
Consensus pattern (15 bp):
AACATAAATAATTAA
Found at i:268916 original size:13 final size:14
Alignment explanation
Indices: 268894--268924 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
268884 AAAATTTTAA
268894 AATAATTTTTTTGG
1 AATAATTTTTTTGG
268908 AATAATTTTTTT-G
1 AATAATTTTTTTGG
268921 AATA
1 AATA
268925 TTAAAATTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.29
14 12 0.71
ACGTcount: A:0.35, C:0.00, G:0.10, T:0.55
Consensus pattern (14 bp):
AATAATTTTTTTGG
Found at i:271533 original size:26 final size:26
Alignment explanation
Indices: 271478--271534 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 26
271468 TCTAGACCTT
**
271478 ATTAAATAAATTCAAACATAAAAATT
1 ATTAAATAAATTCAAACATAAAAAGA
** *
271504 ATTAAATAAATTCAAATTTAAACAGA
1 ATTAAATAAATTCAAACATAAAAAGA
271530 ATTAA
1 ATTAA
271535 TTCCAAATTC
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.60, C:0.07, G:0.02, T:0.32
Consensus pattern (26 bp):
ATTAAATAAATTCAAACATAAAAAGA
Found at i:275058 original size:10 final size:10
Alignment explanation
Indices: 275043--275075 Score: 66
Period size: 10 Copynumber: 3.3 Consensus size: 10
275033 TTTCTTTTTT
275043 AATATAAAAA
1 AATATAAAAA
275053 AATATAAAAA
1 AATATAAAAA
275063 AATATAAAAA
1 AATATAAAAA
275073 AAT
1 AAT
275076 TAGCACCACT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 23 1.00
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (10 bp):
AATATAAAAA
Found at i:284851 original size:18 final size:18
Alignment explanation
Indices: 284817--284852 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
284807 TATTACAATC
**
284817 TATGTAATACTTTTTTTT
1 TATGTAATACTCATTTTT
284835 TATGTAATACTCATTTTT
1 TATGTAATACTCATTTTT
284853 ATCATTTACA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.25, C:0.08, G:0.06, T:0.61
Consensus pattern (18 bp):
TATGTAATACTCATTTTT
Found at i:286497 original size:9 final size:9
Alignment explanation
Indices: 286485--286510 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
286475 AAAAATAAAT
286485 TTAATAATA
1 TTAATAATA
286494 TTAATAATA
1 TTAATAATA
286503 TTAATAAT
1 TTAATAAT
286511 TGAACGTAAA
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:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (9 bp):
TTAATAATA
Found at i:293672 original size:25 final size:25
Alignment explanation
Indices: 293644--293725 Score: 58
Period size: 25 Copynumber: 3.1 Consensus size: 25
293634 TTTGAGATCT
293644 TTAAGCTTTCAAAATAATATAAAGA
1 TTAAGCTTTCAAAATAATATAAAGA
** ***
293669 TTAAATTTATCGTTATAATA-AAAGGA
1 TTAAGCTT-TCAAAATAATATAAA-GA
*
293695 TTTTTAAGCTTTCAAAATAATATAGAGA
1 ---TTAAGCTTTCAAAATAATATAAAGA
293723 TTA
1 TTA
293726 TATTTATCGC
Statistics
Matches: 40, Mismatches: 11, Indels: 12
0.63 0.17 0.19
Matches are distributed among these distances:
25 12 0.30
26 10 0.25
28 10 0.25
29 8 0.20
ACGTcount: A:0.46, C:0.06, G:0.10, T:0.38
Consensus pattern (25 bp):
TTAAGCTTTCAAAATAATATAAAGA
Found at i:293707 original size:54 final size:54
Alignment explanation
Indices: 293643--293749 Score: 187
Period size: 54 Copynumber: 2.0 Consensus size: 54
293633 ATTTGAGATC
*
293643 TTTAAGCTTTCAAAATAATATAAAGATTAAATTTATCGTTATAATAAAAGGATT
1 TTTAAGCTTTCAAAATAATATAAAGATTAAATTTATCGCTATAATAAAAGGATT
* *
293697 TTTAAGCTTTCAAAATAATATAGAGATTATATTTATCGCTATAATAAAAGGAT
1 TTTAAGCTTTCAAAATAATATAAAGATTAAATTTATCGCTATAATAAAAGGAT
293750 CAGCTAAGTG
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
54 50 1.00
ACGTcount: A:0.45, C:0.07, G:0.10, T:0.38
Consensus pattern (54 bp):
TTTAAGCTTTCAAAATAATATAAAGATTAAATTTATCGCTATAATAAAAGGATT
Found at i:293724 original size:28 final size:28
Alignment explanation
Indices: 293637--293724 Score: 69
Period size: 28 Copynumber: 3.2 Consensus size: 28
293627 GTATCAATTT
*
293637 GAGATCTTTAAGCTTTCAAAATAATATA
1 GAGATTTTTAAGCTTTCAAAATAATATA
* * * *
293665 AAGATTAAATTT-ATCGTT-ATAATAA-A-A
1 GAGATT---TTTAAGCTTTCAAAATAATATA
293692 G-GATTTTTAAGCTTTCAAAATAATATA
1 GAGATTTTTAAGCTTTCAAAATAATATA
293719 GAGATT
1 GAGATT
293725 ATATTTATCG
Statistics
Matches: 43, Mismatches: 9, Indels: 16
0.63 0.13 0.24
Matches are distributed among these distances:
23 3 0.07
24 4 0.09
25 6 0.14
26 5 0.12
27 3 0.07
28 9 0.21
29 6 0.14
30 4 0.09
31 3 0.07
ACGTcount: A:0.44, C:0.07, G:0.11, T:0.38
Consensus pattern (28 bp):
GAGATTTTTAAGCTTTCAAAATAATATA
Found at i:294221 original size:12 final size:12
Alignment explanation
Indices: 294181--294236 Score: 58
Period size: 12 Copynumber: 4.7 Consensus size: 12
294171 TGCGGCAGGT
*
294181 GCTGAAGCTGAA
1 GCTGGAGCTGAA
* *
294193 GCTGAAGCTGCA
1 GCTGGAGCTGAA
*
294205 CCTGGAGCTGAA
1 GCTGGAGCTGAA
* *
294217 GCTGGAGATGGA
1 GCTGGAGCTGAA
294229 GCTGGAGC
1 GCTGGAGC
294237 GGCGCCAGCA
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
12 36 1.00
ACGTcount: A:0.25, C:0.20, G:0.39, T:0.16
Consensus pattern (12 bp):
GCTGGAGCTGAA
Found at i:294228 original size:18 final size:18
Alignment explanation
Indices: 294192--294232 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
294182 CTGAAGCTGA
*
294192 AGCTGAAGCTGCACCTGG
1 AGCTGAAGCTGCACATGG
* *
294210 AGCTGAAGCTGGAGATGG
1 AGCTGAAGCTGCACATGG
294228 AGCTG
1 AGCTG
294233 GAGCGGCGCC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.24, C:0.20, G:0.39, T:0.17
Consensus pattern (18 bp):
AGCTGAAGCTGCACATGG
Found at i:294236 original size:6 final size:6
Alignment explanation
Indices: 294181--294220 Score: 53
Period size: 6 Copynumber: 6.7 Consensus size: 6
294171 TGCGGCAGGT
* * *
294181 GCTGAA GCTGAA GCTGAA GCTGCA CCTGGA GCTGAA GCTG
1 GCTGAA GCTGAA GCTGAA GCTGAA GCTGAA GCTGAA GCTG
294221 GAGATGGAGC
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.25, C:0.23, G:0.35, T:0.17
Consensus pattern (6 bp):
GCTGAA
Found at i:295153 original size:11 final size:11
Alignment explanation
Indices: 295124--295165 Score: 50
Period size: 11 Copynumber: 3.8 Consensus size: 11
295114 TATCACATTA
295124 TTATTTTTATT
1 TTATTTTTATT
*
295135 CTT-GTTTTATT
1 -TTATTTTTATT
295146 TTATTTTTATT
1 TTATTTTTATT
*
295157 TTATCTTTA
1 TTATTTTTA
295166 ATAAATTCAA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
10 2 0.08
11 22 0.85
12 2 0.08
ACGTcount: A:0.17, C:0.05, G:0.02, T:0.76
Consensus pattern (11 bp):
TTATTTTTATT
Found at i:295165 original size:22 final size:22
Alignment explanation
Indices: 295124--295165 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
295114 TATCACATTA
*
295124 TTATTTTTATTCTTGTTTTATT
1 TTATTTTTATTCTTATTTTATT
295146 TTATTTTTATT-TTATCTTTA
1 TTATTTTTATTCTTAT-TTTA
295166 ATAAATTCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 3 0.17
22 15 0.83
ACGTcount: A:0.17, C:0.05, G:0.02, T:0.76
Consensus pattern (22 bp):
TTATTTTTATTCTTATTTTATT
Found at i:295437 original size:30 final size:31
Alignment explanation
Indices: 295401--295459 Score: 86
Period size: 30 Copynumber: 1.9 Consensus size: 31
295391 GTTTTACATT
295401 AAAAATTTAATC-CATCT-TCTTTTATTTTCA
1 AAAAATTTAATCTC-TCTCTCTTTTATTTTCA
*
295431 AAAAATTTAATCTCTCTCTCTTTTTTTTT
1 AAAAATTTAATCTCTCTCTCTTTTATTTT
295460 TTTTTACAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
30 15 0.58
31 11 0.42
ACGTcount: A:0.29, C:0.17, G:0.00, T:0.54
Consensus pattern (31 bp):
AAAAATTTAATCTCTCTCTCTTTTATTTTCA
Found at i:303591 original size:22 final size:23
Alignment explanation
Indices: 303537--303592 Score: 60
Period size: 22 Copynumber: 2.5 Consensus size: 23
303527 TCGCACTTCG
** *
303537 TGTGCTTACTGATTTGTGCTATG
1 TGTGCTTACTGATTTGCACTATA
* *
303560 TGCGCCTACTGA-TTGCACTATA
1 TGTGCTTACTGATTTGCACTATA
303582 TGTGCTTACTG
1 TGTGCTTACTG
303593 TTTCCCCAGC
Statistics
Matches: 26, Mismatches: 7, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
22 16 0.62
23 10 0.38
ACGTcount: A:0.16, C:0.20, G:0.23, T:0.41
Consensus pattern (23 bp):
TGTGCTTACTGATTTGCACTATA
Found at i:304871 original size:30 final size:30
Alignment explanation
Indices: 304828--304901 Score: 100
Period size: 29 Copynumber: 2.5 Consensus size: 30
304818 TTTTTTACTA
*
304828 TTGTTTT-CTGTTTTTTGCTATTTTGGTG-T
1 TTGTTTTACTGTTTTGTGCTATTTT-GTGCT
*
304857 TTGTTTTACTGTTTTGTGCTGTTTTGTGCT
1 TTGTTTTACTGTTTTGTGCTATTTTGTGCT
304887 TT-TTTTACTGTTTTG
1 TTGTTTTACTGTTTTG
304902 ATGTTGTTAT
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
29 23 0.56
30 18 0.44
ACGTcount: A:0.04, C:0.08, G:0.20, T:0.68
Consensus pattern (30 bp):
TTGTTTTACTGTTTTGTGCTATTTTGTGCT
Found at i:304879 original size:22 final size:21
Alignment explanation
Indices: 304806--304881 Score: 70
Period size: 20 Copynumber: 3.7 Consensus size: 21
304796 TATATTGTTG
304806 TTTTAGTGCTGTTTTTTTACTA
1 TTTT-GTGCTGTTTTTTTACTA
* *
304828 TTGTT-TTCTG-TTTTTTGCTA
1 TT-TTGTGCTGTTTTTTTACTA
*
304848 TTTTG-G-TGTTTGTTTTACTG
1 TTTTGTGCTGTTT-TTTTACTA
304868 TTTTGTGCTGTTTT
1 TTTTGTGCTGTTTT
304882 GTGCTTTTTT
Statistics
Matches: 43, Mismatches: 5, Indels: 13
0.70 0.08 0.21
Matches are distributed among these distances:
18 2 0.05
19 4 0.09
20 22 0.51
21 6 0.14
22 7 0.16
23 2 0.05
ACGTcount: A:0.07, C:0.08, G:0.18, T:0.67
Consensus pattern (21 bp):
TTTTGTGCTGTTTTTTTACTA
Found at i:304926 original size:12 final size:12
Alignment explanation
Indices: 304903--305015 Score: 127
Period size: 12 Copynumber: 9.4 Consensus size: 12
304893 ACTGTTTTGA
*
304903 TGTTGTTATTTT
1 TGTTGCTATTTT
* *
304915 TGTTACTGTTTT
1 TGTTGCTATTTT
*
304927 TATTGCTATTTT
1 TGTTGCTATTTT
* *
304939 TGCTGTTATTTT
1 TGTTGCTATTTT
* *
304951 TGTTACTGTTTT
1 TGTTGCTATTTT
304963 TGTTGCTATTTT
1 TGTTGCTATTTT
*
304975 TGTTGTTATTTT
1 TGTTGCTATTTT
* *
304987 TGCTGCTGTTTT
1 TGTTGCTATTTT
304999 TGTTGCTATTTT
1 TGTTGCTATTTT
305011 TGTTG
1 TGTTG
305016 TTTTGCTGTT
Statistics
Matches: 80, Mismatches: 21, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
12 80 1.00
ACGTcount: A:0.08, C:0.07, G:0.18, T:0.67
Consensus pattern (12 bp):
TGTTGCTATTTT
Found at i:304936 original size:24 final size:24
Alignment explanation
Indices: 304868--305015 Score: 128
Period size: 24 Copynumber: 6.3 Consensus size: 24
304858 TGTTTTACTG
304868 TTTTG-TGCTG-TTTTG-TGC--T
1 TTTTGTTGCTGTTTTTGTTGCTAT
* *
304887 TTTT-TTACTGTTTTGATGTTGTTAT
1 TTTTGTTGCTGTTTT--TGTTGCTAT
* *
304912 TTTTGTTACTGTTTTTATTGCTAT
1 TTTTGTTGCTGTTTTTGTTGCTAT
* * * * *
304936 TTTTGCTGTTATTTTTGTTACTGT
1 TTTTGTTGCTGTTTTTGTTGCTAT
* *
304960 TTTTGTTGCTATTTTTGTTGTTAT
1 TTTTGTTGCTGTTTTTGTTGCTAT
*
304984 TTTTGCTGCTGTTTTTGTTGCTAT
1 TTTTGTTGCTGTTTTTGTTGCTAT
305008 TTTTGTTG
1 TTTTGTTG
305016 TTTTGCTGTT
Statistics
Matches: 101, Mismatches: 20, Indels: 11
0.77 0.15 0.08
Matches are distributed among these distances:
19 8 0.08
20 3 0.03
22 2 0.02
23 2 0.02
24 71 0.70
25 5 0.05
26 10 0.10
ACGTcount: A:0.07, C:0.07, G:0.18, T:0.67
Consensus pattern (24 bp):
TTTTGTTGCTGTTTTTGTTGCTAT
Found at i:304946 original size:36 final size:36
Alignment explanation
Indices: 304903--305017 Score: 194
Period size: 36 Copynumber: 3.2 Consensus size: 36
304893 ACTGTTTTGA
*
304903 TGTTGTTATTTTTGTTACTGTTTTTATTGCTATTTT
1 TGTTGTTATTTTTGTTACTGTTTTTGTTGCTATTTT
*
304939 TGCTGTTATTTTTGTTACTGTTTTTGTTGCTATTTT
1 TGTTGTTATTTTTGTTACTGTTTTTGTTGCTATTTT
* *
304975 TGTTGTTATTTTTGCTGCTGTTTTTGTTGCTATTTT
1 TGTTGTTATTTTTGTTACTGTTTTTGTTGCTATTTT
305011 TGTTGTT
1 TGTTGTT
305018 TTGCTGTTAT
Statistics
Matches: 74, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 74 1.00
ACGTcount: A:0.08, C:0.07, G:0.17, T:0.68
Consensus pattern (36 bp):
TGTTGTTATTTTTGTTACTGTTTTTGTTGCTATTTT
Found at i:305033 original size:29 final size:32
Alignment explanation
Indices: 304990--305049 Score: 83
Period size: 29 Copynumber: 2.0 Consensus size: 32
304980 TTATTTTTGC
304990 TGCTGTTTTTGTTGCTA-T-TTTT-GTTGTTT
1 TGCTGTTTTTGTTGCTACTGTTTTGGTTGTTT
305019 TGCTGTTATTT-TTGCTACTGTTTTGGTTGTT
1 TGCTGTT-TTTGTTGCTACTGTTTTGGTTGTT
305050 ATTTTGGTTG
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
29 13 0.48
30 4 0.15
31 4 0.15
32 6 0.22
ACGTcount: A:0.05, C:0.08, G:0.22, T:0.65
Consensus pattern (32 bp):
TGCTGTTTTTGTTGCTACTGTTTTGGTTGTTT
Found at i:305040 original size:44 final size:44
Alignment explanation
Indices: 304972--305075 Score: 145
Period size: 44 Copynumber: 2.4 Consensus size: 44
304962 TTGTTGCTAT
* * * *
304972 TTTTGTTGTTATTTTTGCTGCTGTTTTTGTTGCTATTTTTGTTG
1 TTTTGATGTTATTTTTGCTACTGTTTTGGTTGCTATTTTGGTTG
* *
305016 TTTTGCTGTTATTTTTGCTACTGTTTTGGTTGTTATTTTGGTTG
1 TTTTGATGTTATTTTTGCTACTGTTTTGGTTGCTATTTTGGTTG
*
305060 TTTTGATGTTTTTTTT
1 TTTTGATGTTATTTTT
305076 ATGTGTTTTT
Statistics
Matches: 53, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
44 53 1.00
ACGTcount: A:0.06, C:0.06, G:0.20, T:0.68
Consensus pattern (44 bp):
TTTTGATGTTATTTTTGCTACTGTTTTGGTTGCTATTTTGGTTG
Found at i:305052 original size:24 final size:24
Alignment explanation
Indices: 304892--305054 Score: 136
Period size: 24 Copynumber: 6.9 Consensus size: 24
304882 GTGCTTTTTT
*
304892 TACTGTTTTGATGTTGTTATTTTTGT
1 TACTGTTTT--TGTTGTTATTTTTGC
* *
304918 TACTGTTTTTATTGCTATTTTTGC
1 TACTGTTTTTGTTGTTATTTTTGC
** * ** * *
304942 TGTTATTTTTGTTACTGTTTTTGT
1 TACTGTTTTTGTTGTTATTTTTGC
* *
304966 TGCTATTTTTGTTGTTATTTTTGC
1 TACTGTTTTTGTTGTTATTTTTGC
* *
304990 TGCTGTTTTTGTTGCTATTTTTG-
1 TACTGTTTTTGTTGTTATTTTTGC
*
305013 T--TG-TTTTGCTGTTATTTTTGC
1 TACTGTTTTTGTTGTTATTTTTGC
*
305034 TACTGTTTTGGTTGTTATTTT
1 TACTGTTTTTGTTGTTATTTT
305055 GGTTGTTTTG
Statistics
Matches: 112, Mismatches: 21, Indels: 10
0.78 0.15 0.07
Matches are distributed among these distances:
20 15 0.13
21 3 0.03
23 3 0.03
24 82 0.73
26 9 0.08
ACGTcount: A:0.09, C:0.07, G:0.18, T:0.66
Consensus pattern (24 bp):
TACTGTTTTTGTTGTTATTTTTGC
Done.