Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold194
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: 3945165
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 1023 characters in sequence are not A, C, G, or T
File 2 of 24
Found at i:160330 original size:56 final size:56
Alignment explanation
Indices: 160176--160717 Score: 319
Period size: 56 Copynumber: 9.5 Consensus size: 56
160166 GTGCCAACGA
* * * * * * **
160176 CACCTCTTTTAAAGCCCACGAGTTAATGGCATCTTTCCAAAG-CCACGAGTCAGTGG
1 CACC-CTTTCAAAGCCCACAAGTCAGTGGCACCTTTTCAAAGCCCATAAGTCAGTGG
* ** * * * ** ** *
160232 CATCCTTTCAAAAATCCACCAGTTAGTAGCATTTTTTCAAAGCCCACGAGTTAGTGG
1 CACCCTTTC-AAAGCCCACAAGTCAGTGGCACCTTTTCAAAGCCCATAAGTCAGTGG
*
160289 CA-CCTTCTCAAAGCCCACAAGTCAGCGGCACCTTTTCAAAGCCCATAAGTCAGTGG
1 CACCCTT-TCAAAGCCCACAAGTCAGTGGCACCTTTTCAAAGCCCATAAGTCAGTGG
* * * ** *
160345 CACCCTTTGAATGCTCATGAGTCAGTGGCACCTTCTT-AAAGCCCATAAGTCAATGG
1 CACCCTTTCAAAGCCCACAAGTCAGTGGCACCTT-TTCAAAGCCCATAAGTCAGTGG
* * **
160401 CACCCTTTCAAAGCCCACGAA-TTAGTGGCACCTTCTCAAAGCCCAGGAGTCAGTGG
1 CACCCTTTCAAAGCCCAC-AAGTCAGTGGCACCTTTTCAAAGCCCATAAGTCAGTGG
** * * * **
160457 CACCC-TTCTAAAGCCCATGAGTTAGTGGCACCCTTT-AAAACCCCCAAGTCAGTGG
1 CACCCTTTC-AAAGCCCACAAGTCAGTGGCACCTTTTCAAAGCCCATAAGTCAGTGG
* *** ** * *
160512 CACCCTTTTGACTCCCACACAAGAGAGTGGCAACCTCTCTT-AAAGCCCACAAGTCGGTGG
1 CACCC-TTTCAAAGCC-CACAAGTCAGTGGC-ACCT-T-TTCAAAGCCCATAAGTCAGTGG
* * * * *
160572 TAACCCCTT-ACAGCCTACACAAGTC-GTTGGCAACCTCTCTCAAAGCCCATAAGCCAGTGG
1 -CACCCTTTCAAAGCC--CACAAGTCAG-TGGC-ACCT-TTTCAAAGCCCATAAGTCAGTGG
* * * * * *
160632 CACCCTTTCAAAGGCCACAAGTTAGTGGCACCCTTTCGAAGCCCACAAATCAGTGG
1 CACCCTTTCAAAGCCCACAAGTCAGTGGCACCTTTTCAAAGCCCATAAGTCAGTGG
* * * * *
160688 CATCTTTTTAAAGCACACAAGTTAGTGGCA
1 CACCCTTTCAAAGCCCACAAGTCAGTGGCA
160718 ACCCTCCTAA
Statistics
Matches: 381, Mismatches: 84, Indels: 42
0.75 0.17 0.08
Matches are distributed among these distances:
55 29 0.08
56 223 0.59
57 39 0.10
58 14 0.04
59 14 0.04
60 58 0.15
61 4 0.01
ACGTcount: A:0.28, C:0.30, G:0.19, T:0.23
Consensus pattern (56 bp):
CACCCTTTCAAAGCCCACAAGTCAGTGGCACCTTTTCAAAGCCCATAAGTCAGTGG
Found at i:160372 original size:84 final size:83
Alignment explanation
Indices: 160266--160689 Score: 302
Period size: 84 Copynumber: 5.0 Consensus size: 83
160256 AGTAGCATTT
* * * * *
160266 TTTCAAAGCCCACGAGTTAGTGGCACCTTCTCAAAGCCCACAAGTCAGCGGCACCTTTTCAAAGC
1 TTTCAAAGCCCAGGAGTCAGTGGCACCTTCT-AAAGCCCATAAGTCAGTGGCACCCTTTCAAAGC
*
160331 CCATAAGTCAGTGGCACCC
65 CCACAAGTCAGTGGCACCC
* * * * *
160350 TTTGAATGCTCATGAGTCAGTGGCACCTTCTTAAAGCCCATAAGTCAATGGCACCCTTTCAAAGC
1 TTTCAAAGCCCAGGAGTCAGTGGCACCTTC-TAAAGCCCATAAGTCAGTGGCACCCTTTCAAAGC
*
160415 CCACGAA-TTAGTGGCA-CC
65 CCAC-AAGTCAGTGGCACCC
* * *
160433 TTCTCAAAGCCCAGGAGTCAGTGGCACCCTTCTAAAGCCCATGAGTTAGTGGCACCCTTT-AAAA
1 TT-TCAAAGCCCAGGAGTCAGTGGCA-CCTTCTAAAGCCCATAAGTCAGTGGCACCCTTTCAAAG
*
160497 CCCCCAAGTCAGTGGCACCC
64 CCCACAAGTCAGTGGCACCC
* *** ** ** * * * *
160517 TTTTGACTCCCACACAAGAGAGTGGCAACCTCTCTTAAAGCCCACAAGTCGGTGGTAACCCCTT-
1 -TTTCAAAGCC-CAGGAGTCAGTGGC-ACCT-TC-TAAAGCCCATAAGTCAGTGG-CACCCTTTC
*
160581 ACAGCCTACACAAGTC-GTTGGCAACCTC
60 AAAGCC--CACAAGTCAG-TGGC-ACC-C
* ** * * * * *
160609 TCTCAAAGCCCATAAGCCAGTGGCACCCTT-TCAAAGGCCACAAGTTAGTGGCACCCTTTCGAAG
1 TTTCAAAGCCCAGGAGTCAGTGGCA-CCTTCT-AAAGCCCATAAGTCAGTGGCACCCTTTCAAAG
*
160673 CCCACAAATCAGTGGCA
64 CCCACAAGTCAGTGGCA
160690 TCTTTTTAAA
Statistics
Matches: 265, Mismatches: 54, Indels: 41
0.74 0.15 0.11
Matches are distributed among these distances:
82 2 0.01
83 19 0.07
84 115 0.43
85 24 0.09
86 14 0.05
87 24 0.09
88 30 0.11
89 3 0.01
90 25 0.09
91 8 0.03
92 1 0.00
ACGTcount: A:0.28, C:0.32, G:0.19, T:0.21
Consensus pattern (83 bp):
TTTCAAAGCCCAGGAGTCAGTGGCACCTTCTAAAGCCCATAAGTCAGTGGCACCCTTTCAAAGCC
CACAAGTCAGTGGCACCC
Found at i:160487 original size:28 final size:29
Alignment explanation
Indices: 160186--160734 Score: 265
Period size: 28 Copynumber: 19.3 Consensus size: 29
160176 CACCTCTTTT
* * * *
160186 AAAGCCCACGAGTTAATGGCATCTTTC-C
1 AAAGCCCACGAGTCAGTGGCACCCTTCTC
*
160214 AAAG-CCACGAGTCAGTGGCATCCTT-TC
1 AAAGCCCACGAGTCAGTGGCACCCTTCTC
** * * * ** *
160241 AAAAATCCACCAGTTAGTAGCA-TTTTTTC
1 -AAAGCCCACGAGTCAGTGGCACCCTTCTC
*
160270 AAAGCCCACGAGTTAGTGGCA-CCTTCTC
1 AAAGCCCACGAGTCAGTGGCACCCTTCTC
* * *
160298 AAAGCCCACAAGTCAGCGGCA-CCTTTTC
1 AAAGCCCACGAGTCAGTGGCACCCTTCTC
** *
160326 AAAGCCCATAAGTCAGTGGCACCCTT-TG
1 AAAGCCCACGAGTCAGTGGCACCCTTCTC
* * * *
160354 AATGCTCATGAGTCAGTGGCA-CCTTCTT
1 AAAGCCCACGAGTCAGTGGCACCCTTCTC
** *
160382 AAAGCCCATAAGTCAATGGCACCCTT-TC
1 AAAGCCCACGAGTCAGTGGCACCCTTCTC
* *
160410 AAAGCCCACGAATTAGTGGCA-CCTTCTC
1 AAAGCCCACGAGTCAGTGGCACCCTTCTC
*
160438 AAAGCCCAGGAGTCAGTGGCACCCTTCT-
1 AAAGCCCACGAGTCAGTGGCACCCTTCTC
* *
160466 AAAGCCCATGAGTTAGTGGCACCCTT-T-
1 AAAGCCCACGAGTCAGTGGCACCCTTCTC
* * * * *
160493 AAAACCCCCAAGTCAGTGGCACCCTTTTG
1 AAAGCCCACGAGTCAGTGGCACCCTTCTC
*** * ** * *
160522 ACTCCCACACAAGAGAGTGGCAACCTCTCTT
1 AAAGCC-CACGAGTCAGTGGCACCCT-TCTC
* * * *
160553 AAAGCCCACAAGTCGGTGGTAACCC--CTT
1 AAAGCCCACGAGTCAGTGG-CACCCTTCTC
* * *
160581 ACAGCCTACACAAGTC-GTTGGCAACCTCTCTC
1 AAAGCC--CACGAGTCAG-TGGCACCCT-TCTC
** *
160613 AAAGCCCATAAGCCAGTGGCACCCTT-TC
1 AAAGCCCACGAGTCAGTGGCACCCTTCTC
* * *
160641 AAAGGCCACAAGTTAGTGGCACCCTT-TC
1 AAAGCCCACGAGTCAGTGGCACCCTTCTC
* * * * * *
160669 GAAGCCCACAAATCAGTGGCA-TCTTTTT
1 AAAGCCCACGAGTCAGTGGCACCCTTCTC
* * * *
160697 AAAGCACACAAGTTAGTGGCAACCCTCCT-
1 AAAGCCCACGAGTCAGTGGC-ACCCTTCTC
160726 AAAGCCCAC
1 AAAGCCCAC
160735 ACAAGTTGGT
Statistics
Matches: 407, Mismatches: 90, Indels: 47
0.75 0.17 0.09
Matches are distributed among these distances:
27 52 0.13
28 240 0.59
29 46 0.11
30 53 0.13
31 9 0.02
32 7 0.02
ACGTcount: A:0.28, C:0.31, G:0.19, T:0.22
Consensus pattern (29 bp):
AAAGCCCACGAGTCAGTGGCACCCTTCTC
Found at i:160740 original size:175 final size:173
Alignment explanation
Indices: 160426--160751 Score: 390
Period size: 175 Copynumber: 1.9 Consensus size: 173
160416 CACGAATTAG
* * **
160426 TGGCACCTTCTCAAAGCCCAGGAGTCAGTGGCACCCTTCTAAAGCCCATGAGTTAGTGGCACCCT
1 TGGCACCTTCTCAAAGCCCAGAAGCCAGTGGCACCCTTCTAAAGCCCACAAGTTAGTGGCACCCT
* * ** *
160491 TTAAAACCCCCAAGTCAGTGGCACCCTTTTGACTCCCACACAAGAGAGTGGCAACCTCTCTTAAA
66 TTAAAACCCACAAATCAGTGGCACCCTTTTGACAACCACACAAGAGAGTGGCAACCTCTCCTAAA
*
160556 GCCCACAAGTCGGTGGTAACCCCTTACAGCCTACACAAGTCGT
131 GCCCACAAGTCGGTGGCAACCCCTTACAGCCTACACAAGTCGT
* *
160599 TGGCAACCTCTCTCAAAGCCCATAAGCCAGTGGCACCCTT-TCAAAGGCCACAAGTTAGTGGCAC
1 TGGC-ACCT-TCTCAAAGCCCAGAAGCCAGTGGCACCCTTCT-AAAGCCCACAAGTTAGTGGCAC
* * * * * **
160663 CCTTTCGAAGCCCACAAATCAGTGGCA-TCTTTTTA-AAGCACACAAGTTAGTGGCAACC-CTCC
63 CCTTT-AAAACCCACAAATCAGTGGCACCCTTTTGACAACCACACAAGAGAGTGGCAACCTCTCC
*
160725 TAAAGCCCACACAAGTTGGTGGCAACC
127 TAAAG-CC-CACAAGTCGGTGGCAACC
160752 TTTCTGAACC
Statistics
Matches: 127, Mismatches: 20, Indels: 10
0.81 0.13 0.06
Matches are distributed among these distances:
173 12 0.09
174 25 0.20
175 73 0.57
176 17 0.13
ACGTcount: A:0.28, C:0.32, G:0.19, T:0.21
Consensus pattern (173 bp):
TGGCACCTTCTCAAAGCCCAGAAGCCAGTGGCACCCTTCTAAAGCCCACAAGTTAGTGGCACCCT
TTAAAACCCACAAATCAGTGGCACCCTTTTGACAACCACACAAGAGAGTGGCAACCTCTCCTAAA
GCCCACAAGTCGGTGGCAACCCCTTACAGCCTACACAAGTCGT
Found at i:165741 original size:96 final size:96
Alignment explanation
Indices: 165620--165839 Score: 291
Period size: 96 Copynumber: 2.3 Consensus size: 96
165610 ATTAAAAAAT
* * * *
165620 AGGGTTGGAGTATCCCCTCGAAGGAATGGGGTTATAGTGTCGCCC-ATGATGATAATTTAAATAA
1 AGGGTTGGAGTATCCCTTAG-AGGAATGGGGTTAGAGTGTC-CCCAATGATGACAATTTAAATAA
165684 GAATAAGATTTAAACTTTGATGTGTTTAAAA-C
64 GAATAAGATTTAAACTTTGATGTGTTTAAAAGC
* * * *
165716 GGGGTTGGAGTATCCCTTTAGAGGAATGGGGTTGGAGTGTCCCCAATGATGACAATTTAAGTGAG
1 AGGGTTGGAGTATCCC-TTAGAGGAATGGGGTTAGAGTGTCCCCAATGATGACAATTTAAATAAG
165781 AATAAGATTTAAACTTTGATGTGTTTAAAAGC
65 AATAAGATTTAAACTTTGATGTGTTTAAAAGC
* * *
165813 AGGATTAGAGTATCCCCTCAGAGGAAT
1 AGGGTTGGAGTAT-CCCTTAGAGGAAT
165840 AAGATTGGAG
Statistics
Matches: 108, Mismatches: 12, Indels: 7
0.85 0.09 0.06
Matches are distributed among these distances:
95 3 0.03
96 80 0.74
97 22 0.20
98 3 0.03
ACGTcount: A:0.32, C:0.12, G:0.26, T:0.30
Consensus pattern (96 bp):
AGGGTTGGAGTATCCCTTAGAGGAATGGGGTTAGAGTGTCCCCAATGATGACAATTTAAATAAGA
ATAAGATTTAAACTTTGATGTGTTTAAAAGC
Found at i:166245 original size:196 final size:196
Alignment explanation
Indices: 165910--166301 Score: 599
Period size: 196 Copynumber: 2.0 Consensus size: 196
165900 ACAAGGATGG
* * *
165910 TAATGATGTAAAAGTATTTAGGTCTTGATATGGCATGATGGAGGTCTAAAAAAAGGTTTCAAGAC
1 TAATGATGTAAAAGTATTTAGGCCTTGACATGGCATGAGGGAGGTCTAAAAAAAGGTTTCAAGAC
* * * *
165975 TGATTGGGGTTATACGAAGACATCCCAATGTCTCGGGATGAAACCTTGGAAGATGAATCAATTTT
66 TGATTGGGGTTATACGAAGACATCCCAATGTCTCCGGATGAAACCTGGGAAAATGAACCAATTTT
* * *
166040 GGTAGCAACCAAAAACAAG-GGACAACATCGCGCTGTCCCTCTTCCCAAATTTATTTTAGGTTGA
131 GGCAGCAACCAAAAA-AAGTGGACAACATCGCGCTGTCCCACTTCCCAAATTTATTTCAGGTTGA
166104 TT
195 TT
* **
166106 TAATGATGTAAAAGTATTT-GTGCCTTGACATGGCCTGAGGGAGGTCTAAAAAAAGGTTTTGAGA
1 TAATGATGTAAAAGTATTTAG-GCCTTGACATGGCATGAGGGAGGTCTAAAAAAAGGTTTCAAGA
166170 CTGATTGGGGTTATACGAAGACATCCCAATGTCTCCGGATGAAACCTGGGAAAATGAACCAATTT
65 CTGATTGGGGTTATACGAAGACATCCCAATGTCTCCGGATGAAACCTGGGAAAATGAACCAATTT
* * * *
166235 TGGCAGCAACCAAATATAGTGGACAGCATCGCGCTGTCCCACTTCCTAAATTTATTTCAGGTTGA
130 TGGCAGCAACCAAAAAAAGTGGACAACATCGCGCTGTCCCACTTCCCAAATTTATTTCAGGTTGA
166300 TT
195 TT
166302 CGAAGGTTCT
Statistics
Matches: 177, Mismatches: 17, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
195 3 0.02
196 174 0.98
ACGTcount: A:0.32, C:0.17, G:0.23, T:0.29
Consensus pattern (196 bp):
TAATGATGTAAAAGTATTTAGGCCTTGACATGGCATGAGGGAGGTCTAAAAAAAGGTTTCAAGAC
TGATTGGGGTTATACGAAGACATCCCAATGTCTCCGGATGAAACCTGGGAAAATGAACCAATTTT
GGCAGCAACCAAAAAAAGTGGACAACATCGCGCTGTCCCACTTCCCAAATTTATTTCAGGTTGAT
T
Found at i:166929 original size:16 final size:16
Alignment explanation
Indices: 166908--166939 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
166898 GTGATACGAG
166908 CATCACAAACTCATTT
1 CATCACAAACTCATTT
166924 CATCACAAACTCATTT
1 CATCACAAACTCATTT
166940 ACATAGCCCC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.38, C:0.31, G:0.00, T:0.31
Consensus pattern (16 bp):
CATCACAAACTCATTT
Found at i:167771 original size:13 final size:12
Alignment explanation
Indices: 167749--167796 Score: 62
Period size: 13 Copynumber: 3.9 Consensus size: 12
167739 TTTGTTTTTA
167749 TTTTTTTCTCTC
1 TTTTTTTCTCTC
167761 TTTTCTTTCTC-C
1 TTTT-TTTCTCTC
*
167773 CTTTTTTCTCTC
1 TTTTTTTCTCTC
167785 ATTTTTTTCTCT
1 -TTTTTTTCTCT
167797 TTCTTCAGTT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
11 6 0.19
12 9 0.29
13 16 0.52
ACGTcount: A:0.02, C:0.27, G:0.00, T:0.71
Consensus pattern (12 bp):
TTTTTTTCTCTC
Found at i:167777 original size:24 final size:24
Alignment explanation
Indices: 167750--167795 Score: 76
Period size: 24 Copynumber: 1.9 Consensus size: 24
167740 TTGTTTTTAT
167750 TTTTTTCTCTC-TTTTCTTTCTCCC
1 TTTTTTCTCTCATTTT-TTTCTCCC
167774 TTTTTTCTCTCATTTTTTTCTC
1 TTTTTTCTCTCATTTTTTTCTC
167796 TTTCTTCAGT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
24 17 0.81
25 4 0.19
ACGTcount: A:0.02, C:0.28, G:0.00, T:0.70
Consensus pattern (24 bp):
TTTTTTCTCTCATTTTTTTCTCCC
Found at i:170931 original size:23 final size:22
Alignment explanation
Indices: 170912--170953 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
170902 TTACTTTTCG
170912 TTTT-CTTCTAGTTCTCCTTTT
1 TTTTCCTTCTAGTTCTCCTTTT
*
170933 TTTTCCCTTCTGGTTCTCCTT
1 TTTT-CCTTCTAGTTCTCCTT
170954 CTTGTGCTCT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 4 0.22
23 14 0.78
ACGTcount: A:0.02, C:0.29, G:0.07, T:0.62
Consensus pattern (22 bp):
TTTTCCTTCTAGTTCTCCTTTT
Found at i:172837 original size:32 final size:30
Alignment explanation
Indices: 172786--172846 Score: 79
Period size: 32 Copynumber: 2.0 Consensus size: 30
172776 TTGCATTGGA
*
172786 AGAAACTAAAAATATAGCTAAGGACACAAAAT
1 AGAAACTAAAAATAAAGCTAA-GACA-AAAAT
172818 AGAAACCTAAAAA-AAAGCTAAGACAAAAA
1 AGAAA-CTAAAAATAAAGCTAAGACAAAAA
172847 CATGCCTATT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
30 4 0.15
31 4 0.15
32 12 0.44
33 7 0.26
ACGTcount: A:0.64, C:0.13, G:0.11, T:0.11
Consensus pattern (30 bp):
AGAAACTAAAAATAAAGCTAAGACAAAAAT
Found at i:180381 original size:28 final size:28
Alignment explanation
Indices: 180235--181033 Score: 763
Period size: 28 Copynumber: 27.5 Consensus size: 28
180225 CATTAACTTG
* * *
180235 TGTGGGCTTTGAAAAGAGTCACCACCGACTT
1 TGTGGGCTTTG-AAAGGGT-GCCACTGAC-T
* * *
180266 GTGTGGGCTTTGAAAAGAGTTACCACCGACT
1 -TGTGGGCTTTG-AAAG-GGTGCCACTGACT
* * *
180297 CGTGTGGGCTTTGAAAAGAGTTACCACTGGCT
1 --TGTGGGCTTTG-AAAG-GGTGCCACTGACT
*
180329 TGTGGGCTTTGAAAAGAGTGCCACTGACT
1 TGTGGGCTTTG-AAAGGGTGCCACTGACT
180358 TGTGGGCTTTGAAAGGGTGCCACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
*
180386 TGTGGGCTTTGAAAGGGTGCCACTAACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* *
180414 TGTGGGCTTTGAAAGGATGCCACTGGCT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* *
180442 TGTGGGCTTTGAAAAGAGTGCCACTAACT
1 TGTGGGCTTTG-AAAGGGTGCCACTGACT
* *
180471 TGTAGGCTTTGAAAGGGTGCCACTAACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
*
180499 TGTGGGCTTTGAAAGGGTGCCACTAACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* *
180527 TGTGGGCTTTGAAAGGGTGCCATTAACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* *
180555 TCTGGGCTTTGAAAAGAGTGCCACTGACT
1 TGTGGGCTTTG-AAAGGGTGCCACTGACT
180584 TGTGGGCTTTGAAAGGGTGCCACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* * * *
180612 TGTGGGCTTTAAAAGGATGCCATTAACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* *
180640 TGTGGGCTTTGAAAGGATGCCACTAACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* * *
180668 TATGGGCTTTGAAACGATGCCACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* * *
180696 TGTGGGCTTTGAAATGATGCCATTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
*
180724 TGTGGGCTTTGAAAGGGTGCCACTAACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* *
180752 TGTGGGCTTTGAAAGGATGCCAATGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* * * *
180780 TGTAGGCTTTGAAACGATGCCACCGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
** * *
180808 TGTGAAC-TTGAAAGGATGCCACTGAGT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* *
180835 TGTGGGCTTTGAAAGGATGCCACTAACTT
1 TGTGGGCTTTGAAAGGGTGCCACTGAC-T
* **
180864 GTGTGGGCTTTGAAATGGGTTACCACCAACTT
1 -TGTGGGCTTTGAAA-GGG-TGCCACTGAC-T
* *
180896 GTGTGGGCTTTGAAATGAGTTGCCACCGACT
1 -TGTGGGCTTTGAAA-G-GGTGCCACTGACT
** *
180927 TGTATGGGCTTTGAATTGATGCCACTGACTT
1 TG--TGGGCTTTGAAAGGGTGCCACTGAC-T
* * ** *
180958 GTGTGGGCTTTCAAATGAGTTAACACCGACTT
1 -TGTGGGCTTTGAAA-G-GGTGCCACTGAC-T
*
180990 GTGTGGGCTTTGAAAAGAGTTGCCACTGACT
1 -TGTGGGCTTTG-AAAG-GGTGCCACTGACT
181021 TGTGGGCTTTGAA
1 TGTGGGCTTTGAA
181034 GAGATGAACG
Statistics
Matches: 669, Mismatches: 81, Indels: 37
0.85 0.10 0.05
Matches are distributed among these distances:
27 22 0.03
28 369 0.55
29 70 0.10
30 63 0.09
31 6 0.01
32 134 0.20
33 5 0.01
ACGTcount: A:0.23, C:0.18, G:0.30, T:0.29
Consensus pattern (28 bp):
TGTGGGCTTTGAAAGGGTGCCACTGACT
Found at i:180472 original size:113 final size:113
Alignment explanation
Indices: 180299--181033 Score: 873
Period size: 113 Copynumber: 6.4 Consensus size: 113
180289 CACCGACTCG
* * *
180299 TGTGGGCTTTGAAAAGAGTTACCACTGGCTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGG
1 TGTGGGCTTTG-AAAG-GATGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGG
*
180364 CTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTAACT
64 CTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTAACT
* * *
180414 TGTGGGCTTTGAAAGGATGCCACTGGCTTGTGGGCTTTGAAAAGAGTGCCACTAACTTGTAGGCT
1 TGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCT
* *
180479 TTGAAAGGGTGCCACTAACTTGTGGGCTTTGAAAGGGTGCCACTAACT
66 TTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTAACT
* * * *
180527 TGTGGGCTTTGAAAGGGTGCCATTAACTTCTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCT
1 TGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCT
* * * *
180592 TTGAAAGGGTGCCACTGACTTGTGGGCTTTAAAAGGATGCCATTAACT
66 TTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTAACT
* * *
180640 TGTGGGCTTTGAAAGGATGCCACTAACTTATGGGCTTTGAAACGA-TGCCACTGACTTGTGGGCT
1 TGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCT
* *
180704 TTGAAATGATGCCATTGACTTGTGGGCTTTGAAAGGGTGCCACTAACT
66 TTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTAACT
* * * * **
180752 TGTGGGCTTTGAAAGGATGCCAATGACTTGTAGGCTTTGAAACGA-TGCCACCGACTTGTGAAC-
1 TGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCT
* *
180815 TTGAAAGGATGCCACTGAGTTGTGGGCTTTGAAAGGATGCCACTAACTT
66 TTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTAAC-T
* * ** * *
180864 GTGTGGGCTTTGAAATGGGTTACCACCAACTTGTGTGGGCTTTGAAATGAGTTGCCACCGACTTG
1 -TGTGGGCTTTGAAA--GGATGCCACTGAC-T-TGTGGGCTTTGAAAAGAG-TGCCACTGACTTG
** * * ** **
180929 TATGGGCTTTGAATTGATGCCACTGACTTGTGTGGGCTTTCAAATGAGTTAACACCGACTT
60 --TGGGCTTTGAAAGGATGCCACTGAC-T-TGTGGGCTTTGAAA-G-GGTGCCACTAAC-T
*
180990 GTGTGGGCTTTGAAAAGAGTTGCCACTGACTTGTGGGCTTTGAA
1 -TGTGGGCTTTG-AAAG-GATGCCACTGACTTGTGGGCTTTGAA
181034 GAGATGAACG
Statistics
Matches: 545, Mismatches: 58, Indels: 25
0.87 0.09 0.04
Matches are distributed among these distances:
111 43 0.08
112 118 0.22
113 250 0.46
114 4 0.01
115 19 0.03
116 1 0.00
117 15 0.03
119 13 0.02
121 3 0.01
122 16 0.03
123 1 0.00
124 26 0.05
125 3 0.01
126 30 0.06
127 3 0.01
ACGTcount: A:0.23, C:0.17, G:0.30, T:0.30
Consensus pattern (113 bp):
TGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCT
TTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTAACT
Found at i:180998 original size:94 final size:92
Alignment explanation
Indices: 180235--181033 Score: 432
Period size: 85 Copynumber: 9.1 Consensus size: 92
180225 CATTAACTTG
* * ** * * * * *
180235 TGTGGGCTTTGAAAAGAGTCACCACCGACTTGTGTGGGCTTTGAAAAGAGTTACCACCGACTCGT
1 TGTGGGCTTTGAAAGGA-T-GCCACTAACTTGTGTGGGCTTTCAAATGAGTTAACACCAACTTGT
* * *
180300 GTGGGCTTTGAAAAGAGTTACCACTGGCT
64 GTGGGCTTTGAAAAGAGTTGCCACCGACT
* * * * ** **
180329 TGTGGGCTTTGAAAAGAGTGCCACTGAC-T-TGTGGGCTTTGAAA-G-GGTGCCACTGAC-T-TG
1 TGTGGGCTTTGAAAGGA-TGCCACTAACTTGTGTGGGCTTTCAAATGAGTTAACACCAACTTGTG
* **
180388 TGGGCTTTG-AAAG-GGTGCCACTAACT
65 TGGGCTTTGAAAAGAGTTGCCACCGACT
** * * ** *
180414 TGTGGGCTTTGAAAGGATGCCACTGGC-T-TGTGGGCTTTGAAAAGAG-TGCCACTAAC-T-TGT
1 TGTGGGCTTTGAAAGGATGCCACTAACTTGTGTGGGCTTTCAAATGAGTTAACACCAACTTGTGT
* * **
180474 AGGCTTTG-AAAG-GGTGCCACTAACT
66 GGGCTTTGAAAAGAGTTGCCACCGACT
* * * ** ** *
180499 TGTGGGCTTTGAAAGGGTGCCACTAAC-T-TGTGGGCTTTGAAA-G-GGTGCCATTAAC-T-TCT
1 TGTGGGCTTTGAAAGGATGCCACTAACTTGTGTGGGCTTTCAAATGAGTTAACACCAACTTGTGT
*
180558 GGGCTTTGAAAAGAG-TGCCACTGACT
66 GGGCTTTGAAAAGAGTTGCCACCGACT
* * * * ** **
180584 TGTGGGCTTTGAAAGGGTGCCACTGAC-T-TGTGGGCTTT-AAAAG-GATGCCATTAAC-T-TGT
1 TGTGGGCTTTGAAAGGATGCCACTAACTTGTGTGGGCTTTCAAATGAGTTAACACCAACTTGTGT
* **
180643 GGGCTTTG-AAAG-GATGCCACTAACT
66 GGGCTTTGAAAAGAGTTGCCACCGACT
* * * * ** ***
180668 TATGGGCTTTGAAACGATGCCACTGAC-T-TGTGGGCTTTGAAATGA--TGCCATTGAC-T-TGT
1 TGTGGGCTTTGAAAGGATGCCACTAACTTGTGTGGGCTTTCAAATGAGTTAACACCAACTTGTGT
* **
180727 GGGCTTTG-AAAG-GGTGCCACTAACT
66 GGGCTTTGAAAAGAGTTGCCACCGACT
* * * * * ** *
180752 TGTGGGCTTTGAAAGGATGCCAATGAC-T-TGTAGGCTTTGAAACGA--TGCCACCGAC-T-TGT
1 TGTGGGCTTTGAAAGGATGCCACTAACTTGTGTGGGCTTTCAAATGAGTTAACACCAACTTGTGT
** * * *
180811 GAAC-TTG-AAAG-GATGCCACTGAGT
66 GGGCTTTGAAAAGAGTTGCCACCGACT
* * *
180835 TGTGGGCTTTGAAAGGATGCCACTAACTTGTGTGGGCTTTGAAATGGGTTACCACCAACTTGTGT
1 TGTGGGCTTTGAAAGGATGCCACTAACTTGTGTGGGCTTTCAAATGAGTTAACACCAACTTGTGT
*
180900 GGGCTTTGAAATGAGTTGCCACCGACT
66 GGGCTTTGAAAAGAGTTGCCACCGACT
** * *
180927 TGTATGGGCTTTGAATTGATGCCACTGACTTGTGTGGGCTTTCAAATGAGTTAACACCGACTTGT
1 TG--TGGGCTTTGAAAGGATGCCACTAACTTGTGTGGGCTTTCAAATGAGTTAACACCAACTTGT
*
180992 GTGGGCTTTGAAAAGAGTTGCCACTGACT
64 GTGGGCTTTGAAAAGAGTTGCCACCGACT
181021 TGTGGGCTTTGAA
1 TGTGGGCTTTGAA
181034 GAGATGAACG
Statistics
Matches: 620, Mismatches: 65, Indels: 42
0.85 0.09 0.06
Matches are distributed among these distances:
83 44 0.07
84 188 0.30
85 194 0.31
86 6 0.01
87 19 0.03
88 1 0.00
89 14 0.02
90 4 0.01
91 17 0.03
92 24 0.04
93 7 0.01
94 102 0.16
ACGTcount: A:0.23, C:0.18, G:0.30, T:0.29
Consensus pattern (92 bp):
TGTGGGCTTTGAAAGGATGCCACTAACTTGTGTGGGCTTTCAAATGAGTTAACACCAACTTGTGT
GGGCTTTGAAAAGAGTTGCCACCGACT
Found at i:182279 original size:23 final size:21
Alignment explanation
Indices: 182253--182299 Score: 67
Period size: 21 Copynumber: 2.1 Consensus size: 21
182243 GACCCCTTTC
182253 TGTTTTTTTTGCTATTTTTTCTT
1 TGTTTTTTTTG-T-TTTTTTCTT
*
182276 TGTTTTTTTTGTTTTTTTTTT
1 TGTTTTTTTTGTTTTTTTCTT
182297 TGT
1 TGT
182300 GCAAAGGACG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 11 0.48
22 1 0.04
23 11 0.48
ACGTcount: A:0.02, C:0.04, G:0.11, T:0.83
Consensus pattern (21 bp):
TGTTTTTTTTGTTTTTTTCTT
Found at i:182296 original size:12 final size:13
Alignment explanation
Indices: 182267--182299 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
182257 TTTTTTGCTA
*
182267 TTTTTTCTTTGTT
1 TTTTTTGTTTGTT
182280 TTTTTTGTTT-TT
1 TTTTTTGTTTGTT
182292 TTTTTTGT
1 TTTTTTGT
182300 GCAAAGGACG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 10 0.53
13 9 0.47
ACGTcount: A:0.00, C:0.03, G:0.09, T:0.88
Consensus pattern (13 bp):
TTTTTTGTTTGTT
Found at i:193522 original size:20 final size:20
Alignment explanation
Indices: 193497--193623 Score: 110
Period size: 20 Copynumber: 5.8 Consensus size: 20
193487 AATTTTAACT
193497 AAATGTATCGATACATTGAA
1 AAATGTATCGATACATTGAA
193517 AAATGTATCGATACATCTGGGTAGAAAGA
1 AAATGTATCGATACA--T---T-G--A-A
193546 CAGAATGTATCGATACATTGAA
1 -A-AATGTATCGATACATTGAA
* * *
193568 GAATGTATCGATACATTCAT
1 AAATGTATCGATACATTGAA
* *
193588 ACATGTATCGATCCATTGAA
1 AAATGTATCGATACATTGAA
193608 AAATGTATCGATACAT
1 AAATGTATCGATACAT
193624 CTGGTACTTT
Statistics
Matches: 86, Mismatches: 10, Indels: 22
0.73 0.08 0.19
Matches are distributed among these distances:
20 61 0.71
22 2 0.02
23 1 0.01
25 2 0.02
26 2 0.02
28 1 0.01
29 2 0.02
30 1 0.01
31 14 0.16
ACGTcount: A:0.40, C:0.13, G:0.17, T:0.29
Consensus pattern (20 bp):
AAATGTATCGATACATTGAA
Found at i:194444 original size:14 final size:14
Alignment explanation
Indices: 194427--194455 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
194417 TTTTTCCTTG
194427 TTTTT-TTTTTTGT
1 TTTTTATTTTTTGT
194440 TTTTTATTTTTTGT
1 TTTTTATTTTTTGT
194454 TT
1 TT
194456 GGTTTTTTTC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.33
14 10 0.67
ACGTcount: A:0.03, C:0.00, G:0.07, T:0.90
Consensus pattern (14 bp):
TTTTTATTTTTTGT
Found at i:194449 original size:19 final size:19
Alignment explanation
Indices: 194427--194463 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
194417 TTTTTCCTTG
* *
194427 TTTTTTTTTTTGTTTTTTA
1 TTTTTTGTTTGGTTTTTTA
194446 TTTTTTGTTTGGTTTTTT
1 TTTTTTGTTTGGTTTTTT
194464 TCTATTTCTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.03, C:0.00, G:0.11, T:0.86
Consensus pattern (19 bp):
TTTTTTGTTTGGTTTTTTA
Found at i:208368 original size:28 final size:28
Alignment explanation
Indices: 208326--208379 Score: 99
Period size: 28 Copynumber: 1.9 Consensus size: 28
208316 AGATGTATCG
208326 ATACATTGAAAAATGTATCGATACATTC
1 ATACATTGAAAAATGTATCGATACATTC
*
208354 ATACATTGAAGAATGTATCGATACAT
1 ATACATTGAAAAATGTATCGATACAT
208380 CTGGGTACCT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.43, C:0.13, G:0.13, T:0.31
Consensus pattern (28 bp):
ATACATTGAAAAATGTATCGATACATTC
Found at i:210703 original size:37 final size:37
Alignment explanation
Indices: 210634--210706 Score: 92
Period size: 37 Copynumber: 2.0 Consensus size: 37
210624 GTAAAAACGA
***
210634 GGTTGGAGTATCCACTCAGAAATGGTGGGGTTGGAGG
1 GGTTGGAGTATCCACTCAGAAATGGCAAGGTTGGAGG
* * *
210671 GGTTGGAGTATCCCCTCGGAGATGGCAAGGTTGGAG
1 GGTTGGAGTATCCACTCAGAAATGGCAAGGTTGGAG
210707 CATCCCTAAA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
37 30 1.00
ACGTcount: A:0.21, C:0.14, G:0.42, T:0.23
Consensus pattern (37 bp):
GGTTGGAGTATCCACTCAGAAATGGCAAGGTTGGAGG
Found at i:210791 original size:118 final size:118
Alignment explanation
Indices: 210600--210829 Score: 365
Period size: 118 Copynumber: 1.9 Consensus size: 118
210590 ACCCTTGAAG
*
210600 ATGGAAAATTGGATATCTTTAGAAGTAAAAACGAGGTTGGAGTATCCACTCAGAAATGGTGGGGT
1 ATGGAAAATTGGATATCTTTAGAAGTAAAAACGAGGTTGGAGTATCCACTCAAAAATGGTGGGGT
*
210665 TGGAGGGGTTGGAGTATCCCCTCGGAGATGGCAAGGTTGGAGCATCCCTAAAA
66 TGGAGGGGTTGGAGTATCCCCTCGAAGATGGCAAGGTTGGAGCATCCCTAAAA
* *
210718 ATGGAAAATTGGATATTTTTAGAAGTGAAAACGAGGTTGGAGTATTCC-CTCAAAAATGGTGGGG
1 ATGGAAAATTGGATATCTTTAGAAGTAAAAACGAGGTTGGAGTA-TCCACTCAAAAATGGTGGGG
* * *
210782 TTGTG-GGGGTTGGAGTATCCCCTCGAAGTTGGCGAGGTTGGAGTATCC
65 TTG-GAGGGGTTGGAGTATCCCCTCGAAGATGGCAAGGTTGGAGCATCC
210830 TTGATCAGAT
Statistics
Matches: 103, Mismatches: 7, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
118 99 0.96
119 4 0.04
ACGTcount: A:0.28, C:0.13, G:0.33, T:0.26
Consensus pattern (118 bp):
ATGGAAAATTGGATATCTTTAGAAGTAAAAACGAGGTTGGAGTATCCACTCAAAAATGGTGGGGT
TGGAGGGGTTGGAGTATCCCCTCGAAGATGGCAAGGTTGGAGCATCCCTAAAA
Found at i:211071 original size:37 final size:37
Alignment explanation
Indices: 211002--211074 Score: 94
Period size: 37 Copynumber: 2.0 Consensus size: 37
210992 GTAAAAACGA
* *
211002 GGTTGGAGTATCCACTCAGAAATGGTGGGGTTGGAGG
1 GGTTGGAGTATCCACTCAGAAATGGCGAGGTTGGAGG
* *
211039 GGTTGGAGTATTCC-CTCGGAGATGGCGAGGTTGGAG
1 GGTTGGAGTA-TCCACTCAGAAATGGCGAGGTTGGAG
211075 CATCCCCAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
37 28 0.90
38 3 0.10
ACGTcount: A:0.19, C:0.12, G:0.44, T:0.25
Consensus pattern (37 bp):
GGTTGGAGTATCCACTCAGAAATGGCGAGGTTGGAGG
Found at i:211158 original size:117 final size:117
Alignment explanation
Indices: 210948--211272 Score: 408
Period size: 117 Copynumber: 2.8 Consensus size: 117
210938 TAAAAAAAAT
* ** * *
210948 GAGGTTGGAGTACCCTTGAAGATGGAAAATTGGATATCTTTA-AAGTAAAAACGAGGTTGGAGTA
1 GAGGTTGGAGCACCCTCAAAAATGGAAAATTGGATATTTTTAGAAGT-AAAACGAGGTTGGAGTA
* * *
211012 -TCCACTCAGAAATGGTGGGGTTGGAGGGGTTGGAGTATTCCCTCGGAGATGGC
65 TTCC-CTCAAAAATGGTGGGGTTGGAGGGGTTGGAGTATCCCCTCGAAGATGGC
211065 GAGGTTGGAGCATCCC-CAAAAATGGAAAATTGGAT-TTTTTAGAAGTGAAAACGAGGTTGGAGT
1 GAGGTTGGAGCA-CCCTCAAAAATGGAAAATTGGATATTTTTAGAAGT-AAAACGAGGTTGGAGT
211128 ATTCCCTCAAAAATGGTGGGGTTGTG-GGGGTTGGAGTATCCCCTCGAAGATGGC
64 ATTCCCTCAAAAATGGTGGGGTTG-GAGGGGTTGGAGTATCCCCTCGAAGATGGC
* * * ** *
211182 GAGGTTGGAGTACCCTCGAAGATGGAAAATTGGATATTTTTAGAAGTAAAAATAGAGTTGGAATA
1 GAGGTTGGAGCACCCTCAAAAATGGAAAATTGGATATTTTTAGAAGTAAAACGAG-GTTGGAGTA
* * *
211247 TCCCCTTAAAAATAGTGGGGTTGGAG
65 TTCCCTCAAAAATGGTGGGGTTGGAG
211273 TATTTTGATG
Statistics
Matches: 182, Mismatches: 18, Indels: 15
0.85 0.08 0.07
Matches are distributed among these distances:
116 8 0.04
117 127 0.70
118 47 0.26
ACGTcount: A:0.30, C:0.12, G:0.32, T:0.26
Consensus pattern (117 bp):
GAGGTTGGAGCACCCTCAAAAATGGAAAATTGGATATTTTTAGAAGTAAAACGAGGTTGGAGTAT
TCCCTCAAAAATGGTGGGGTTGGAGGGGTTGGAGTATCCCCTCGAAGATGGC
Found at i:211604 original size:199 final size:199
Alignment explanation
Indices: 211200--211580 Score: 504
Period size: 199 Copynumber: 1.9 Consensus size: 199
211190 AGTACCCTCG
* *
211200 AAGATGGAAAATTGGATATTTTTAGAAGTAAAAATAGAGTTGGAATATCCCCTTAAAAATAGTGG
1 AAGATGGAAAATTGGATATTTTTAGAAGTAAAAATAGAGTTGGAATATACCCTCAAAAATAGTGG
* * *
211265 GGTTGGAGTATTTTGATGTTTTTGGAAGTAAATATGGGGTTGGAGTATCCCCGTAAATGAAAATT
66 GGTTGGAGTATTTCGATGTTTTTGGAAGTAAAGACGGGGTTGGAGTATCCCCGTAAATGAAAATT
* * * * ** ** ** *
211330 TTTTATTTTTTAGAAGTAAAAACAGGGTTGGAGTATCTCCTTGGCGATAGTGAGGTTGGAGTATC
131 TTATATTTTTTAAAAGTAAAAACAGGGTTCGAGTATCTCCTCGAAGATAGAAAAATTGGAGTATA
* *
211395 CCTG
196 ACTA
* * * *
211399 AAGATGGAAAATTGGATATTTTTAGAAGTAAAAATGGAGTTGGAGTATAGCCTCAAAAATGGTGG
1 AAGATGGAAAATTGGATATTTTTAGAAGTAAAAATAGAGTTGGAATATACCCTCAAAAATAGTGG
211464 GGTTGGAGTA-TTCGATGTTTTTGGAAGTAAAGACGGGGTT-GAGTATCCCCGTAAATGAAAATT
66 GGTTGGAGTATTTCGATGTTTTTGGAAGTAAAGACGGGGTTGGAGTATCCCCGTAAATGAAAATT
*
211527 TTGATA-TTTTTAAAAGTAAAAATAGGGTTCGAGTATC-CC-CGAAGATA-AAAAATT
131 TT-ATATTTTTTAAAAGTAAAAACAGGGTTCGAGTATCTCCTCGAAGATAGAAAAATT
211581 TGATGTTTTT
Statistics
Matches: 161, Mismatches: 20, Indels: 7
0.86 0.11 0.04
Matches are distributed among these distances:
194 3 0.02
195 5 0.03
196 2 0.01
197 53 0.33
198 29 0.18
199 69 0.43
ACGTcount: A:0.34, C:0.08, G:0.26, T:0.32
Consensus pattern (199 bp):
AAGATGGAAAATTGGATATTTTTAGAAGTAAAAATAGAGTTGGAATATACCCTCAAAAATAGTGG
GGTTGGAGTATTTCGATGTTTTTGGAAGTAAAGACGGGGTTGGAGTATCCCCGTAAATGAAAATT
TTATATTTTTTAAAAGTAAAAACAGGGTTCGAGTATCTCCTCGAAGATAGAAAAATTGGAGTATA
ACTA
Found at i:211618 original size:53 final size:51
Alignment explanation
Indices: 211477--211619 Score: 153
Period size: 53 Copynumber: 2.7 Consensus size: 51
211467 TGGAGTATTC
* * *
211477 GATGTTTTTGGAAGTAAAGACGGGGTTGAGTATCCCCGTAAATGAAAATTTT
1 GATGTTTTTGGAAGTAAAGA-TGGGTTGAGTATCCCCGTAAATAAAAAATTT
* ** *
211529 GATATTTTTAAAAGTAAAAATAGGGTTCGAGTATCCCCG-AAGATAAAAAATTT
1 GATGTTTTTGGAAGTAAAGAT-GGGTT-GAGTATCCCCGTAA-ATAAAAAATTT
*
211582 GATGTTTTTGGAAGTAAAGATGGGATTGGAGAATCCCC
1 GATGTTTTTGGAAGTAAAGATGGG-TT-GAGTATCCCC
211620 ATAATTGACG
Statistics
Matches: 74, Mismatches: 13, Indels: 7
0.79 0.14 0.07
Matches are distributed among these distances:
52 26 0.35
53 48 0.65
ACGTcount: A:0.35, C:0.10, G:0.24, T:0.31
Consensus pattern (51 bp):
GATGTTTTTGGAAGTAAAGATGGGTTGAGTATCCCCGTAAATAAAAAATTT
Found at i:211982 original size:70 final size:70
Alignment explanation
Indices: 211867--212012 Score: 249
Period size: 70 Copynumber: 2.1 Consensus size: 70
211857 ACCTTGATCT
*
211867 AAGCCTACATGAGTTGATGTGTGTTCATTTCAACTACAAGGATTGATC-GAGATCACACGGAGGT
1 AAGCCTACATGAGTTGATGCGTGTTCATTTCAACTACAAGGATTGATCAG-GATCACACGGAGGT
211931 ATTTGA
65 ATTTGA
* *
211937 ATGCCTACGTGAGTTGATGCGTGTTCATTTCAACTACAAGGATTGATCAGGATCACACGGAGGTA
1 AAGCCTACATGAGTTGATGCGTGTTCATTTCAACTACAAGGATTGATCAGGATCACACGGAGGTA
212002 TTTGA
66 TTTGA
212007 AAGCCT
1 AAGCCT
212013 CGGAGTGGGA
Statistics
Matches: 71, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
70 70 0.99
71 1 0.01
ACGTcount: A:0.29, C:0.17, G:0.25, T:0.29
Consensus pattern (70 bp):
AAGCCTACATGAGTTGATGCGTGTTCATTTCAACTACAAGGATTGATCAGGATCACACGGAGGTA
TTTGA
Found at i:218049 original size:13 final size:13
Alignment explanation
Indices: 218031--218057 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
218021 ACAATGTTCT
218031 TTGTATCGATACA
1 TTGTATCGATACA
218044 TTGTATCGATACA
1 TTGTATCGATACA
218057 T
1 T
218058 GGGTTACTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:222384 original size:40 final size:38
Alignment explanation
Indices: 222326--222403 Score: 120
Period size: 40 Copynumber: 2.0 Consensus size: 38
222316 AAGCATCCTT
* *
222326 CTCTTTGAGGACTGAAAGGATAAGAGGTGCTACCAGCTTG
1 CTCTTTAAGGACTAAAAGGATAAGAGGTGC--CCAGCTTG
222366 CTCTTTAAGGACTAAAAGGATAAGAGGTGCCCAGCTTG
1 CTCTTTAAGGACTAAAAGGATAAGAGGTGCCCAGCTTG
222404 TGTGGGCTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
38 8 0.22
40 28 0.78
ACGTcount: A:0.29, C:0.18, G:0.28, T:0.24
Consensus pattern (38 bp):
CTCTTTAAGGACTAAAAGGATAAGAGGTGCCCAGCTTG
Found at i:222555 original size:69 final size:69
Alignment explanation
Indices: 222366--223340 Score: 885
Period size: 69 Copynumber: 14.2 Consensus size: 69
222356 TACCAGCTTG
* * *
222366 CTCTTTAAGGACTAAAAGGATAAGAGGTG-C-CCAGCTTGTGTGGGCTTT-AAAA-AAAAA-CGT
1 CTCTTTGAGGACTAAAAGGATAAAAGGTGCCACCAGCTTGTGTGGGCTTTAAAAAGAAAAAGCAT
* *
222426 CTTG
66 CCTA
* * * * **
222430 CTCTTTGAGGACTGAAAGGATAAGAGGTG-C-CCAGCTCGTGTGGCCTTTAAAAAGAAAAAGTGT
1 CTCTTTGAGGACTAAAAGGATAAAAGGTGCCACCAGCTTGTGTGGGCTTTAAAAAGAAAAAGCAT
222493 CCTA
66 CCTA
* * * *
222497 CTTTTTAAGGACTAAAAGGATAAGAGGTGCCACCAGCTTGTGTAGGCTTTAAAAAGAAAAAGCAT
1 CTCTTTGAGGACTAAAAGGATAAAAGGTGCCACCAGCTTGTGTGGGCTTTAAAAAGAAAAAGCAT
*
222562 CCTG
66 CCTA
* * * * * * * * *
222566 CTCTTTGAAGACTGAAAGGATAAGAGATGCCACCAGCTTGTGTGTGCTGTAGAAAGAAAAAACAC
1 CTCTTTGAGGACTAAAAGGATAAAAGGTGCCACCAGCTTGTGTGGGCTTTAAAAAGAAAAAGCAT
222631 CCTA
66 CCTA
* * * ** * * **
222635 TTCTTTGAGGACTGAAAGAATAAAAATTGCCACCAGCTTGTGTGAGCTTTAGAAAGAAAAAGTGT
1 CTCTTTGAGGACTAAAAGGATAAAAGGTGCCACCAGCTTGTGTGGGCTTTAAAAAGAAAAAGCAT
*
222700 CCTG
66 CCTA
* * * * * *
222704 CTCTTTAAGGACTGAAAGGATAAAAAGTGCCATCAACTTGTGTGGGCTTTAGAAAGAAAAA-CAT
1 CTCTTTGAGGACTAAAAGGATAAAAGGTGCCACCAGCTTGTGTGGGCTTTAAAAAGAAAAAGCAT
* *
222768 CTTG
66 CCTA
* * * *
222772 CT-TTTGAGGGCGAAAAGGATAAAAAGTGCCACTAGCTTGTGTGGGCTTTTAAAAAGAAAAAGGC
1 CTCTTTGAGGACTAAAAGGATAAAAGGTGCCACCAGCTTGTGTGGGC-TTTAAAAAGAAAAA-GC
* *
222836 ATCTTG
64 ATCCTA
* *
222842 CTCTTTGAGGACTAAAAGG-T-----GT--CACCAGTTTATGTGGGCTTTTAAAAGGAAAGAGAA
1 CTCTTTGAGGACTAAAAGGATAAAAGGTGCCACCAGCTTGTGTGGGC-TTT--AA--AAAGA-AA
*
222899 AAGCGTCCTA
60 AAGCATCCTA
* * * * *
222909 CTCTTTGAGGACTGAAAGGATAAAAGATACCACCAGCTTATGTAGGCTTTAAAAAGAAAAAGCAT
1 CTCTTTGAGGACTAAAAGGATAAAAGGTGCCACCAGCTTGTGTGGGCTTTAAAAAGAAAAAGCAT
222974 CCTA
66 CCTA
* * * **
222978 CTCGTTGAGGACTAAAAGGATAAGAGGTGCCACTAGCTTGTGTGGGCTTT--AAA-AAAAAGTTT
1 CTCTTTGAGGACTAAAAGGATAAAAGGTGCCACCAGCTTGTGTGGGCTTTAAAAAGAAAAAGCAT
223040 CCTA
66 CCTA
** * *
223044 CTACTTTTGAGGACTGGAAGGATAAAAAGTGCCACCAGCTTGTGTGGGCTTTAGAAAGAAAAAGC
1 CT-C-TTTGAGGACTAAAAGGATAAAAGGTGCCACCAGCTTGTGTGGGCTTTAAAAAGAAAAAGC
223109 ATCCTA
64 ATCCTA
* * * * *
223115 CTTTTTGAGGACTAAAAGGATAAAAAGTGCCACCAGCTTGTTTGGGCTTTAGAAAGAAAAAGTAT
1 CTCTTTGAGGACTAAAAGGATAAAAGGTGCCACCAGCTTGTGTGGGCTTTAAAAAGAAAAAGCAT
*
223180 TCTA
66 CCTA
* * * * * * *
223184 CTCTTTGAGGACTGAAAA-GATAAAAAGTGCCATCAGCTTGTATAGGCTTTAGAAAGAAAAAACT
1 CTCTTTGAGGACT-AAAAGGATAAAAGGTGCCACCAGCTTGTGTGGGCTTTAAAAAGAAAAAGCA
*
223248 TCCTG
65 TCCTA
* ** * * *
223253 CTTTTTGAGGACTAAAAGTTTAAAAGGTGCCACAAGCTTGTATGGGCTTTTAAAAAGAAAAAAGT
1 CTCTTTGAGGACTAAAAGGATAAAAGGTGCCACCAGCTTGTGTGGGC-TTTAAAAAG-AAAAAGC
* * *
223318 GTCTTG
64 ATCCTA
223324 CTCTTTGAGGACTAAAA
1 CTCTTTGAGGACTAAAA
223341 AGTGCCACTA
Statistics
Matches: 762, Mismatches: 118, Indels: 55
0.81 0.13 0.06
Matches are distributed among these distances:
63 18 0.02
64 44 0.06
65 8 0.01
66 18 0.02
67 99 0.13
68 70 0.09
69 402 0.53
70 30 0.04
71 52 0.07
72 2 0.00
73 1 0.00
74 3 0.00
75 15 0.02
ACGTcount: A:0.35, C:0.15, G:0.23, T:0.26
Consensus pattern (69 bp):
CTCTTTGAGGACTAAAAGGATAAAAGGTGCCACCAGCTTGTGTGGGCTTTAAAAAGAAAAAGCAT
CCTA
Found at i:223413 original size:67 final size:64
Alignment explanation
Indices: 223274--223477 Score: 195
Period size: 66 Copynumber: 3.1 Consensus size: 64
223264 CTAAAAGTTT
* * *
223274 AAAAGGTGCCACAAGCTTGTATGGGCTTTTAAA--AAGAAAAAAGTGTCTTGCTCTTTGAGGACT
1 AAAAGGTGCCACAAGCTTGTGTGGGCTTTTAAAGGAAGAAGAAAG-GTCCTGCTCTTTGAGGAC-
223337 A
64 A
* *
223338 AAAA-GTGCCACTAGCTTGTGTGGGC-TTTAATAGGCAAGAAGAAAGGCATCCTGCTCTTTGAAG
1 AAAAGGTGCCACAAGCTTGTGTGGGCTTTTAA-AGG-AAGAAGAAAGG--TCCTGCTCTTTGAGG
223401 ACA
62 ACA
* * *
223404 AAAAGGTGCCACCAA-CTTGCGTGGCCTTTTAAAAGGAA-AAGAAAAGTGTCCTACTCTTTGAGG
1 AAAAGGTGCCA-CAAGCTTGTGTGGGCTTTT-AAAGGAAGAAG-AAAG-GTCCTGCTCTTTGAGG
*
223467 ACT
62 ACA
223470 AAAAGGTG
1 AAAAGGTG
223478 TGTTAGGATC
Statistics
Matches: 117, Mismatches: 11, Indels: 22
0.78 0.07 0.15
Matches are distributed among these distances:
62 5 0.04
63 20 0.17
64 4 0.03
65 1 0.01
66 40 0.34
67 36 0.31
68 9 0.08
69 2 0.02
ACGTcount: A:0.34, C:0.17, G:0.25, T:0.25
Consensus pattern (64 bp):
AAAAGGTGCCACAAGCTTGTGTGGGCTTTTAAAGGAAGAAGAAAGGTCCTGCTCTTTGAGGACA
Found at i:223461 original size:66 final size:66
Alignment explanation
Indices: 223274--223477 Score: 204
Period size: 67 Copynumber: 3.1 Consensus size: 66
223264 CTAAAAGTTT
* * *
223274 AAAAGGTGCCA-CAAGCTTGTATGGGCTTTTAAAA--AGAA-AAAAGTGTCTTGCTCTTTGAGGA
1 AAAAGGTGCCACCAA-CTTGTGTGGGCTTTTAAAAGGAAAAGAAAAGTGTCCTGCTCTTTGAGGA
223335 CTA
65 C-A
* * * * ** *
223338 AAAA-GTGCCACTAGCTTGTGTGGGC-TTTAATAGGCAAGAAGAAAGGCATCCTGCTCTTTGAAG
1 AAAAGGTGCCACCAACTTGTGTGGGCTTTTAAAAGG-AA-AAGAAAAGTGTCCTGCTCTTTGAGG
223401 ACA
64 ACA
* * *
223404 AAAAGGTGCCACCAACTTGCGTGGCCTTTTAAAAGGAAAAGAAAAGTGTCCTACTCTTTGAGGAC
1 AAAAGGTGCCACCAACTTGTGTGGGCTTTTAAAAGGAAAAGAAAAGTGTCCTGCTCTTTGAGGAC
*
223469 T
66 A
223470 AAAAGGTG
1 AAAAGGTG
223478 TGTTAGGATC
Statistics
Matches: 111, Mismatches: 21, Indels: 14
0.76 0.14 0.10
Matches are distributed among these distances:
62 6 0.05
63 16 0.14
64 5 0.05
65 1 0.01
66 37 0.33
67 38 0.34
68 8 0.07
ACGTcount: A:0.34, C:0.17, G:0.25, T:0.25
Consensus pattern (66 bp):
AAAAGGTGCCACCAACTTGTGTGGGCTTTTAAAAGGAAAAGAAAAGTGTCCTGCTCTTTGAGGAC
A
Found at i:223870 original size:13 final size:13
Alignment explanation
Indices: 223852--223877 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
223842 ACACCAAAGT
223852 ATGTATCGATACA
1 ATGTATCGATACA
223865 ATGTATCGATACA
1 ATGTATCGATACA
223878 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:223894 original size:33 final size:33
Alignment explanation
Indices: 223833--223897 Score: 87
Period size: 33 Copynumber: 2.0 Consensus size: 33
223823 TAGCCAAACT
* *
223833 TGTATCGATACACCAAAGTATGTATCGATACAA
1 TGTATCGATACACAAAAATATGTATCGATACAA
*
223866 TGTATCGATACACAAAAA-ATTGTGTCGATACA
1 TGTATCGATACACAAAAATA-TGTATCGATACA
223898 TTGGCTTGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
32 1 0.04
33 27 0.96
ACGTcount: A:0.40, C:0.17, G:0.15, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACAAAAATATGTATCGATACAA
Found at i:230073 original size:13 final size:13
Alignment explanation
Indices: 230055--230093 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
230045 ACATTTTTCT
230055 TTGTATCGATACA
1 TTGTATCGATACA
230068 TTGTATCGATACA
1 TTGTATCGATACA
*
230081 CTGTATCGATACA
1 TTGTATCGATACA
230094 GGGGGATAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.36
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:234074 original size:20 final size:19
Alignment explanation
Indices: 234025--234074 Score: 55
Period size: 19 Copynumber: 2.6 Consensus size: 19
234015 ACATTATGTT
**
234025 TTGTATTGATACATGTTCA
1 TTGTATTGATACATACTCA
* *
234044 TTGCATCGATACATACTCAA
1 TTGTATTGATACATACTC-A
234064 TTGTATTGATA
1 TTGTATTGATA
234075 ATGAAACTGG
Statistics
Matches: 24, Mismatches: 6, Indels: 1
0.77 0.19 0.03
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.30, C:0.14, G:0.14, T:0.42
Consensus pattern (19 bp):
TTGTATTGATACATACTCA
Found at i:242831 original size:39 final size:40
Alignment explanation
Indices: 242762--242853 Score: 100
Period size: 39 Copynumber: 2.3 Consensus size: 40
242752 ACCCTAGAAA
** * *
242762 GTATCGATACACATTCAGATGTATCGATACATTA-TGC-TTT
1 GTATCGATACATGTTCAGATGTATCAATACA-TACT-CAATT
*
242802 GTATCGATACATGTTCA-TTGTATCAATACATACTCAATT
1 GTATCGATACATGTTCAGATGTATCAATACATACTCAATT
242841 GTATCGATACATG
1 GTATCGATACATG
242854 AAACCAGTAA
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
38 3 0.07
39 27 0.60
40 15 0.33
ACGTcount: A:0.32, C:0.17, G:0.14, T:0.37
Consensus pattern (40 bp):
GTATCGATACATGTTCAGATGTATCAATACATACTCAATT
Found at i:242843 original size:20 final size:19
Alignment explanation
Indices: 242762--242852 Score: 76
Period size: 20 Copynumber: 4.6 Consensus size: 19
242752 ACCCTAGAAA
* * *
242762 GTATCGATACACATTCAGAT
1 GTATCGATACATACTCA-TT
*
242782 GTATCGATACATTA-TGCTTT
1 GTATCGATACA-TACT-CATT
**
242802 GTATCGATACATGTTCATT
1 GTATCGATACATACTCATT
*
242821 GTATCAATACATACTCAATT
1 GTATCGATACATACTC-ATT
242841 GTATCGATACAT
1 GTATCGATACAT
242853 GAAACCAGTA
Statistics
Matches: 58, Mismatches: 9, Indels: 8
0.77 0.12 0.11
Matches are distributed among these distances:
19 17 0.29
20 39 0.67
21 2 0.03
ACGTcount: A:0.32, C:0.18, G:0.13, T:0.37
Consensus pattern (19 bp):
GTATCGATACATACTCATT
Found at i:242944 original size:32 final size:32
Alignment explanation
Indices: 242884--242947 Score: 85
Period size: 32 Copynumber: 2.0 Consensus size: 32
242874 AAGTAAAAAG
** *
242884 TATCGATACATGGGACATTGTATTGATACATT
1 TATCGATACATGGGACAAAGTATCGATACATT
242916 TATCGATACATGGTGA-AAAGTATCGATACATT
1 TATCGATACATGG-GACAAAGTATCGATACATT
242948 GTGGCCAACG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
32 26 0.93
33 2 0.07
ACGTcount: A:0.34, C:0.12, G:0.19, T:0.34
Consensus pattern (32 bp):
TATCGATACATGGGACAAAGTATCGATACATT
Found at i:246053 original size:25 final size:24
Alignment explanation
Indices: 246001--246058 Score: 80
Period size: 24 Copynumber: 2.3 Consensus size: 24
245991 TTACACAAAT
*
246001 AAAAGAGAAATGGATAGCTATAGCA
1 AAAAG-GAAATGGATAGCTACAGCA
*
246026 AAAAGGAAATGGATAGCTGCAGCAA
1 AAAAGGAAATGGATAGCTACAGC-A
246051 AAAAGGAA
1 AAAAGGAA
246059 TATAAAGCAA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
24 16 0.53
25 14 0.47
ACGTcount: A:0.53, C:0.09, G:0.26, T:0.12
Consensus pattern (24 bp):
AAAAGGAAATGGATAGCTACAGCA
Found at i:246086 original size:17 final size:19
Alignment explanation
Indices: 246064--246098 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
246054 AGGAATATAA
246064 AGCAAGA-AACAA-AAAAT
1 AGCAAGAGAACAAGAAAAT
246081 AGCAAGAGAACAAGAAAA
1 AGCAAGAGAACAAGAAAA
246099 AGAGAAAGTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.44
18 5 0.31
19 4 0.25
ACGTcount: A:0.69, C:0.11, G:0.17, T:0.03
Consensus pattern (19 bp):
AGCAAGAGAACAAGAAAAT
Found at i:246156 original size:30 final size:30
Alignment explanation
Indices: 246116--246195 Score: 135
Period size: 30 Copynumber: 2.7 Consensus size: 30
246106 GTAAGAAACG
*
246116 AAAA-AAATAAAAGGAAAAAATGAAACAGC
1 AAAAGAAATAAAAGAAAAAAATGAAACAGC
246145 AAAAGAAATAAAAGAAAAAAATGAAACAGC
1 AAAAGAAATAAAAGAAAAAAATGAAACAGC
*
246175 AAAAGAAAAAAAAGAAAAAAA
1 AAAAGAAATAAAAGAAAAAAA
246196 GCACTAAAGG
Statistics
Matches: 48, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
29 4 0.08
30 44 0.92
ACGTcount: A:0.78, C:0.05, G:0.12, T:0.05
Consensus pattern (30 bp):
AAAAGAAATAAAAGAAAAAAATGAAACAGC
Found at i:246192 original size:8 final size:9
Alignment explanation
Indices: 246145--246195 Score: 57
Period size: 9 Copynumber: 5.3 Consensus size: 9
246135 ATGAAACAGC
*
246145 AAAAGAAAT
1 AAAAGAAAA
246154 AAAAGAAAA
1 AAAAGAAAA
*
246163 AAATGAAACA
1 AAAAGAAA-A
246173 GCAAAAGAAAA
1 --AAAAGAAAA
246184 AAAAGAAAA
1 AAAAGAAAA
246193 AAA
1 AAA
246196 GCACTAAAGG
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
9 27 0.75
10 1 0.03
11 1 0.03
12 7 0.19
ACGTcount: A:0.80, C:0.04, G:0.12, T:0.04
Consensus pattern (9 bp):
AAAAGAAAA
Found at i:247301 original size:17 final size:18
Alignment explanation
Indices: 247269--247302 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
247259 TTCACTCTTG
*
247269 ATTTTGATGTATTTTTTA
1 ATTTTGATGGATTTTTTA
247287 ATTTTG-TGGATTTTTT
1 ATTTTGATGGATTTTTT
247303 TTGATGTAGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.18, C:0.00, G:0.15, T:0.68
Consensus pattern (18 bp):
ATTTTGATGGATTTTTTA
Found at i:252829 original size:25 final size:24
Alignment explanation
Indices: 252800--252847 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
252790 AAGAGTTCAA
*
252800 AATTTATGATTTTTTTTAAAAAAAT
1 AATTT-TGATTTGTTTTAAAAAAAT
*
252825 AATTTTTATTTGTTTTAAAAAAA
1 AATTTTGATTTGTTTTAAAAAAA
252848 AGTTTGTGCT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 16 0.76
25 5 0.24
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.52
Consensus pattern (24 bp):
AATTTTGATTTGTTTTAAAAAAAT
Found at i:256110 original size:20 final size:19
Alignment explanation
Indices: 256065--256117 Score: 63
Period size: 19 Copynumber: 2.8 Consensus size: 19
256055 GTATCGATAT
* **
256065 ATTGTATTGATACATGTTC
1 ATTGTATCGATACATACTC
256084 ATTGTATCGATACATACTC
1 ATTGTATCGATACATACTC
256103 AGTTGTATCGA-ACAT
1 A-TTGTATCGATACAT
256118 GAAACTGTAG
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
19 21 0.70
20 9 0.30
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.40
Consensus pattern (19 bp):
ATTGTATCGATACATACTC
Found at i:263551 original size:13 final size:13
Alignment explanation
Indices: 263533--263559 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
263523 AAATTATGCT
263533 TTGTATCAATACA
1 TTGTATCAATACA
263546 TTGTATCAATACA
1 TTGTATCAATACA
263559 T
1 T
263560 GTTCATTGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.15, G:0.07, T:0.41
Consensus pattern (13 bp):
TTGTATCAATACA
Found at i:263568 original size:19 final size:19
Alignment explanation
Indices: 263544--263599 Score: 76
Period size: 19 Copynumber: 2.9 Consensus size: 19
263534 TGTATCAATA
* *
263544 CATTGTATCAATACATGTT
1 CATTGTATCGATACATGCT
*
263563 CATTGTATCGATACATACT
1 CATTGTATCGATACATGCT
263582 CAATTGTATCGATACATG
1 C-ATTGTATCGATACATG
263600 AAACTACAGT
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
19 17 0.53
20 15 0.47
ACGTcount: A:0.32, C:0.18, G:0.12, T:0.38
Consensus pattern (19 bp):
CATTGTATCGATACATGCT
Found at i:263646 original size:13 final size:13
Alignment explanation
Indices: 263628--263652 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
263618 TATCACTGTT
263628 TGTATCGATACAG
1 TGTATCGATACAG
263641 TGTATCGATACA
1 TGTATCGATACA
263653 TGAAGAATTG
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:0.32, C:0.16, G:0.20, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAG
Found at i:274038 original size:1 final size:1
Alignment explanation
Indices: 274027--274107 Score: 54
Period size: 1 Copynumber: 81.0 Consensus size: 1
274017 TGTCCTTCCC
* * * * * * * * *
274027 AAAAAACAAAAAAACAAAAAAACAAAAAGAACAAAAAATAAGAAAAAAACAAAAAACAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* * *
274092 AACAACACAAAAAAAA
1 AAAAAAAAAAAAAAAA
274108 GAGAGGTCCA
Statistics
Matches: 56, Mismatches: 24, Indels: 0
0.70 0.30 0.00
Matches are distributed among these distances:
1 56 1.00
ACGTcount: A:0.85, C:0.11, G:0.02, T:0.01
Consensus pattern (1 bp):
A
Found at i:274046 original size:16 final size:16
Alignment explanation
Indices: 274027--274106 Score: 92
Period size: 16 Copynumber: 4.9 Consensus size: 16
274017 TGTCCTTCCC
274027 AAAAAACAAAAAAACA
1 AAAAAACAAAAAAACA
274043 AAAAAACAAAAAGAACAA
1 AAAAAACAAAAA-AAC-A
*
274061 AAAATAAGAAAAAAAC-
1 AAAA-AACAAAAAAACA
274077 AAAAAACAAAAAAA-A
1 AAAAAACAAAAAAACA
*
274092 AACAACACAAAAAAA
1 AA-AAAACAAAAAAA
274107 AGAGAGGTCC
Statistics
Matches: 56, Mismatches: 3, Indels: 10
0.81 0.04 0.14
Matches are distributed among these distances:
15 11 0.20
16 27 0.48
17 3 0.05
18 8 0.14
19 7 0.12
ACGTcount: A:0.85, C:0.11, G:0.03, T:0.01
Consensus pattern (16 bp):
AAAAAACAAAAAAACA
Found at i:274048 original size:18 final size:18
Alignment explanation
Indices: 274027--274096 Score: 83
Period size: 18 Copynumber: 3.9 Consensus size: 18
274017 TGTCCTTCCC
274027 AAAAAACAAAAAAAC--A
1 AAAAAACAAAAAAACAAA
274043 AAAAAACAAAAAGAACAAA
1 AAAAAACAAAAA-AACAAA
* *
274062 AAATAAGAAAAAAACAAA
1 AAAAAACAAAAAAACAAA
274080 AAACAAA-AAAAAAACAA
1 AAA-AAACAAAAAAACAA
274097 CACAAAAAAA
Statistics
Matches: 47, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
16 12 0.26
17 3 0.06
18 19 0.40
19 13 0.28
ACGTcount: A:0.86, C:0.10, G:0.03, T:0.01
Consensus pattern (18 bp):
AAAAAACAAAAAAACAAA
Found at i:274064 original size:11 final size:11
Alignment explanation
Indices: 274027--274106 Score: 70
Period size: 13 Copynumber: 6.5 Consensus size: 11
274017 TGTCCTTCCC
274027 AAAAAACAAAA
1 AAAAAACAAAA
*
274038 AAACAAAAAAACA
1 AAA-AAACAAA-A
274051 AAAAGAACAAAA
1 AAAA-AACAAAA
*
274063 AATAAGAAAAAAA
1 AA-AA-AACAAAA
274076 CAAAAAACAAAA
1 -AAAAAACAAAA
274088 AAAAAACAACACA
1 AAAAAACAA-A-A
274101 AAAAAA
1 AAAAAA
274107 AGAGAGGTCC
Statistics
Matches: 58, Mismatches: 4, Indels: 12
0.78 0.05 0.16
Matches are distributed among these distances:
11 12 0.21
12 17 0.29
13 27 0.47
14 2 0.03
ACGTcount: A:0.85, C:0.11, G:0.03, T:0.01
Consensus pattern (11 bp):
AAAAAACAAAA
Found at i:274090 original size:27 final size:26
Alignment explanation
Indices: 274029--274109 Score: 85
Period size: 27 Copynumber: 3.0 Consensus size: 26
274019 TCCTTCCCAA
274029 AAAACAAAAAAACAAAAAAACAAAAAG
1 AAAA-AAAAAAACAAAAAAACAAAAAG
* *
274056 AACAAAAAATAAGAAAAAAACAAAAA-
1 AA-AAAAAAAAACAAAAAAACAAAAAG
*
274082 ACAAAAAAAAAACAACACAAA-AAAAAG
1 A-AAAAAAAAAACAA-AAAAACAAAAAG
274109 A
1 A
274110 GAGGTCCAAA
Statistics
Matches: 45, Mismatches: 5, Indels: 8
0.78 0.09 0.14
Matches are distributed among these distances:
26 16 0.36
27 27 0.60
28 2 0.04
ACGTcount: A:0.84, C:0.11, G:0.04, T:0.01
Consensus pattern (26 bp):
AAAAAAAAAAACAAAAAAACAAAAAG
Found at i:274107 original size:16 final size:14
Alignment explanation
Indices: 274026--274107 Score: 76
Period size: 14 Copynumber: 5.6 Consensus size: 14
274016 GTGTCCTTCC
274026 CAAAAAACAAAAAAA
1 CAAAAAA-AAAAAAA
*
274041 CAAAAAAACAAAAA
1 CAAAAAAAAAAAAA
* * *
274055 GAACAAAAAATAAGA
1 CAA-AAAAAAAAAAA
*
274070 -AAAAAACAAAAAA
1 CAAAAAAAAAAAAA
274083 CAAAAAAAAAACAACA
1 CAAAAAAAAAA-AA-A
274099 CAAAAAAAA
1 CAAAAAAAA
274108 GAGAGGTCCA
Statistics
Matches: 54, Mismatches: 9, Indels: 7
0.77 0.13 0.10
Matches are distributed among these distances:
13 8 0.15
14 19 0.35
15 17 0.31
16 10 0.19
ACGTcount: A:0.84, C:0.12, G:0.02, T:0.01
Consensus pattern (14 bp):
CAAAAAAAAAAAAA
Found at i:275458 original size:28 final size:28
Alignment explanation
Indices: 275416--276081 Score: 185
Period size: 28 Copynumber: 23.5 Consensus size: 28
275406 AATACAACCT
**
275416 TTTTTAAAGTCCACAAGTCAGTAGCATC
1 TTTTTAAAACCCACAAGTCAGTAGCATC
* *
275444 TTTTTAAAACTCACAAGTCAGTGGCATC
1 TTTTTAAAACCCACAAGTCAGTAGCATC
* * * *
275472 TTTTTAAAGCCCACAAGTTAGT-GTAACC
1 TTTTTAAAACCCACAAGTCAGTAG-CATC
* * *
275500 TTTTTCAAAGCCCACAAGTTAGTAGCACC
1 TTTTT-AAAACCCACAAGTCAGTAGCATC
* * * * * *
275529 TTCTCAAAGCCCACAAGTTAGTGGCACC
1 TTTTTAAAACCCACAAGTCAGTAGCATC
* * * * *
275557 CTTTCAAAGCCCACAA-ACTAGTGGCATC
1 TTTTTAAAACCCACAAGTC-AGTAGCATC
* ** *
275585 TTTTCAAATTCCACAAGTCAGTGGCATC
1 TTTTTAAAACCCACAAGTCAGTAGCATC
* ** ** * *
275613 TTTTCAAAGTCCACAAGTCAGCGGTAACC
1 TTTTTAAAACCCACAAGTCAGTAG-CATC
* * * * *
275642 TTTTTCAAAGCCCATAAGTCAATGGCACC
1 TTTTT-AAAACCCACAAGTCAGTAGCATC
* * * * * * *
275671 TTCTCAAAGCCCATAAGTCAGTGGTACC
1 TTTTTAAAACCCACAAGTCAGTAGCATC
* * * *
275699 TTTTCAAAGCCTATAAGTCA--ACGACAACTC
1 TTTTTAAAACCCACAAGTCAGTA-G-C-A-TC
** * *
275729 TTTCCAAAGCCCACAAGTCAGTGGCATC
1 TTTTTAAAACCCACAAGTCAGTAGCATC
* * * *
275757 TTTTCAAAGCACACAAGTCAGTGGCA-C
1 TTTTTAAAACCCACAAGTCAGTAGCATC
* * * * *
275784 TTTCTAAAAGCCCACAAGTAAGTGGTACC
1 TTTTTAAAA-CCCACAAGTCAGTAGCATC
* * * *
275813 TTTTCAAAGCCCACAAGTCAATGGCA-C
1 TTTTTAAAACCCACAAGTCAGTAGCATC
* * *
275840 TTTCTAAAAGCCCACAAGTAAGTGGCA-C
1 TTTTTAAAA-CCCACAAGTCAGTAGCATC
* * * * *
275868 ATTTTCAAAGCCCACAAGTCAATGGCATA
1 -TTTTTAAAACCCACAAGTCAGTAGCATC
* * * *
275897 TTTTCAAAGCCCATAAGTCAGTGGCAACTC
1 TTTTTAAAACCCACAAGTCAGTAGC-A-TC
* * * *
275927 TTTTCAAAGCCCACAAGTTAGTGGCATC
1 TTTTTAAAACCCACAAGTCAGTAGCATC
* * * * * * *
275955 CTTTCAAAGCCTACAAGTTAGTGGCACC
1 TTTTTAAAACCCACAAGTCAGTAGCATC
* * * * * *
275983 TTTTCAAAGCTCAAAAGTCAGTGGCACC
1 TTTTTAAAACCCACAAGTCAGTAGCATC
* * * * * *
276011 CTTTCAAAGCCCACAAGTCAATGGCATA
1 TTTTTAAAACCCACAAGTCAGTAGCATC
* * * *
276039 TTTTCAAAGCCCGCAAGTCAGTGGCATC
1 TTTTTAAAACCCACAAGTCAGTAGCATC
* * *
276067 CTTTCAAAGCCCACA
1 TTTTTAAAACCCACA
276082 CAAGTCATTG
Statistics
Matches: 523, Mismatches: 95, Indels: 40
0.79 0.14 0.06
Matches are distributed among these distances:
27 16 0.03
28 394 0.75
29 53 0.10
30 59 0.11
31 1 0.00
ACGTcount: A:0.32, C:0.27, G:0.16, T:0.26
Consensus pattern (28 bp):
TTTTTAAAACCCACAAGTCAGTAGCATC
Found at i:275503 original size:56 final size:56
Alignment explanation
Indices: 275416--276113 Score: 659
Period size: 56 Copynumber: 12.3 Consensus size: 56
275406 AATACAACCT
* * * * * * * *
275416 TTTTTAAAGTCCACAAGTCAGTAGCATCTTTTTAAAACTCACAAGTCAGTGGCATC
1 TTTTCAAAGCCCACAAGTCAGTGGCACCTTTTCAAAGCCCACAAGTCAGTGGCACC
* * ** * *
275472 TTTTTAAAGCCCACAAGTTAGTGTAACCTTTTTCAAAGCCCACAAGTTAGTAGCACC
1 TTTTCAAAGCCCACAAGTCAGTGGCACC-TTTTCAAAGCCCACAAGTCAGTGGCACC
* * * * *
275529 TTCTCAAAGCCCACAAGTTAGTGGCACCCTTTCAAAGCCCACAA-ACTAGTGGCATC
1 TTTTCAAAGCCCACAAGTCAGTGGCACCTTTTCAAAGCCCACAAGTC-AGTGGCACC
** * * * *
275585 TTTTCAAATTCCACAAGTCAGTGGCATCTTTTCAAAGTCCACAAGTCAGCGGTAACC
1 TTTTCAAAGCCCACAAGTCAGTGGCACCTTTTCAAAGCCCACAAGTCAGTGG-CACC
* * * * *
275642 TTTTTCAAAGCCCATAAGTCAATGGCACCTTCTCAAAGCCCATAAGTCAGTGGTACC
1 -TTTTCAAAGCCCACAAGTCAGTGGCACCTTTTCAAAGCCCACAAGTCAGTGGCACC
* * ** * * *
275699 TTTTCAAAGCCTATAAGTCAACGACAACTCTTTCCAAAGCCCACAAGTCAGTGGCATC
1 TTTTCAAAGCCCACAAGTCAGTGGC-AC-CTTTTCAAAGCCCACAAGTCAGTGGCACC
* * * *
275757 TTTTCAAAGCACACAAGTCAGTGGCA-CTTTCTAAAAGCCCACAAGTAAGTGGTACC
1 TTTTCAAAGCCCACAAGTCAGTGGCACCTTT-TCAAAGCCCACAAGTCAGTGGCACC
* * * *
275813 TTTTCAAAGCCCACAAGTCAATGGCA-CTTTCTAAAAGCCCACAAGTAAGTGGCACA
1 TTTTCAAAGCCCACAAGTCAGTGGCACCTTT-TCAAAGCCCACAAGTCAGTGGCACC
* ** *
275869 TTTTCAAAGCCCACAAGTCAATGGCATATTTTCAAAGCCCATAAGTCAGTGGCAACTC
1 TTTTCAAAGCCCACAAGTCAGTGGCACCTTTTCAAAGCCCACAAGTCAGTGGC-AC-C
* * *
275927 TTTTCAAAGCCCACAAGTTAGTGGCATCC-TTTCAAAGCCTACAAGTTAGTGGCACC
1 TTTTCAAAGCCCACAAGTCAGTGGCA-CCTTTTCAAAGCCCACAAGTCAGTGGCACC
* * * * **
275983 TTTTCAAAGCTCAAAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAATGGCATA
1 TTTTCAAAGCCCACAAGTCAGTGGCACCTTTTCAAAGCCCACAAGTCAGTGGCACC
* * *
276039 TTTTCAAAGCCCGCAAGTCAGTGGCATCC-TTTCAAAGCCCACACAAGTCATTGGCAAC
1 TTTTCAAAGCCCACAAGTCAGTGGCA-CCTTTTCAAAG-CC-CACAAGTCAGTGGCACC
*
276097 TTTCTCTAACGCCCACA
1 TTT-TC-AAAGCCCACA
276114 TAAGTTGGTA
Statistics
Matches: 531, Mismatches: 93, Indels: 32
0.81 0.14 0.05
Matches are distributed among these distances:
55 6 0.01
56 301 0.57
57 66 0.12
58 148 0.28
59 2 0.00
60 8 0.02
ACGTcount: A:0.32, C:0.27, G:0.16, T:0.26
Consensus pattern (56 bp):
TTTTCAAAGCCCACAAGTCAGTGGCACCTTTTCAAAGCCCACAAGTCAGTGGCACC
Found at i:275705 original size:142 final size:141
Alignment explanation
Indices: 275416--276081 Score: 700
Period size: 142 Copynumber: 4.7 Consensus size: 141
275406 AATACAACCT
* * * * * * * *
275416 TTTTTAAAGTCCACAAGTCAGTAGCATCTTTTTAAAACTCACAAGTCAGTGGCATCTTTTTAAAG
1 TTTTCAAAGCCCAAAAGTCAGTGGCATCTTTTCAAAGCCCACAAGTCAGTGGCATCTTTTCAAAG
* * *
275481 CCCACAAGTTAGT-GTAACCTTTTTCAAAGCCCACAAGTTAGTAGCACCTTCTCAAAGCCCACAA
66 CCCACAAGTCAGTGGTAA-CTTTTTCAAAGCCCACAAGTTAATGGCACCTTCTCAAAGCCCACAA
*
275545 GTTAGTGGCACC
130 GTCAGTGGCACC
* * **
275557 CTTTCAAAGCCCACAAACT-AGTGGCATCTTTTCAAATTCCACAAGTCAGTGGCATCTTTTCAAA
1 TTTTCAAAGCCCA-AAAGTCAGTGGCATCTTTTCAAAGCCCACAAGTCAGTGGCATCTTTTCAAA
* * * * *
275621 GTCCACAAGTCAGCGGTAACCTTTTTCAAAGCCCATAAGTCAATGGCACCTTCTCAAAGCCCATA
65 GCCCACAAGTCAGTGGTAA-CTTTTTCAAAGCCCACAAGTTAATGGCACCTTCTCAAAGCCCACA
*
275686 AGTCAGTGGTACC
129 AGTCAGTGGCACC
* * ** * *
275699 TTTTCAAAGCCTATAAGTCAACGACAACTCTTTCCAAAGCCCACAAGTCAGTGGCATCTTTTCAA
1 TTTTCAAAGCCCAAAAGTCAGTGGC-A-TCTTTTCAAAGCCCACAAGTCAGTGGCATCTTTTCAA
* * * * * *
275764 AGCACACAAGTCAGTGG-CACTTTCTAAAAGCCCACAAG-TAAGTGGTACCTTTTCAAAGCCCAC
64 AGCCCACAAGTCAGTGGTAACTTTTTCAAAGCCCACAAGTTAA-TGGCACCTTCTCAAAGCCCAC
*
275827 AAGTCAATGGCA-C
128 AAGTCAGTGGCACC
* * * * *
275840 TTTCTAAAAGCCCACAAGTAAGTGGCA-CATTTTCAAAGCCCACAAGTCAATGGCATATTTTCAA
1 TTT-TCAAAGCCCAAAAGTCAGTGGCATC-TTTTCAAAGCCCACAAGTCAGTGGCATCTTTTCAA
* * * *
275904 AGCCCATAAGTCAGTGGCAACTCTTTTCAAAGCCCACAAGTTAGTGGCATCCTT-TCAAAGCCTA
64 AGCCCACAAGTCAGTGGTAACT-TTTTCAAAGCCCACAAGTTAATGGCA-CCTTCTCAAAGCCCA
*
275968 CAAGTTAGTGGCACC
127 CAAGTCAGTGGCACC
* * * * *
275983 TTTTCAAAGCTCAAAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAATGGCATATTTTCAAAG
1 TTTTCAAAGCCCAAAAGTCAGTGGCATCTTTTCAAAGCCCACAAGTCAGTGGCATCTTTTCAAAG
* * * *
276048 CCCGCAAGTCAGTGGCATC-CTTTCAAAGCCCACA
66 CCCACAAGTCAGTGGTAACTTTTTCAAAGCCCACA
276082 CAAGTCATTG
Statistics
Matches: 438, Mismatches: 73, Indels: 29
0.81 0.14 0.05
Matches are distributed among these distances:
139 1 0.00
140 61 0.14
141 73 0.17
142 242 0.55
143 13 0.03
144 48 0.11
ACGTcount: A:0.32, C:0.27, G:0.16, T:0.26
Consensus pattern (141 bp):
TTTTCAAAGCCCAAAAGTCAGTGGCATCTTTTCAAAGCCCACAAGTCAGTGGCATCTTTTCAAAG
CCCACAAGTCAGTGGTAACTTTTTCAAAGCCCACAAGTTAATGGCACCTTCTCAAAGCCCACAAG
TCAGTGGCACC
Found at i:279095 original size:24 final size:25
Alignment explanation
Indices: 279068--279116 Score: 64
Period size: 27 Copynumber: 1.9 Consensus size: 25
279058 ATCAAATTTT
279068 ATTCATCT-GGGATACTCCAACCCC
1 ATTCATCTAGGGATACTCCAACCCC
*
279092 ATTCTTCTGAAGGGATACTCCAACC
1 ATTCATCT--AGGGATACTCCAACC
279117 TTGTTTTTCA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 7 0.33
27 14 0.67
ACGTcount: A:0.27, C:0.33, G:0.14, T:0.27
Consensus pattern (25 bp):
ATTCATCTAGGGATACTCCAACCCC
Found at i:280208 original size:79 final size:79
Alignment explanation
Indices: 280077--280233 Score: 235
Period size: 79 Copynumber: 2.0 Consensus size: 79
280067 TTAGGGTATA
* ** *
280077 GGTGCAAACCACACATTTCCCAGTCATATCTTTTTTCGTTCAACTGTCAGATGATATTGATGCAT
1 GGTGCAAACCACACATTTCCCAATCATATCTTTTTTCGTTCAACTACCAGATGATATTGACGCAT
* *
280142 CCTAGAGCCTAATT
66 CCCAAAGCCTAATT
*
280156 GGTGCAGACCACACATTTCCCAATCATATCTTATTTTC-TTCAACTACCAGATGATATTGACGCA
1 GGTGCAAACCACACATTTCCCAATCATATCTT-TTTTCGTTCAACTACCAGATGATATTGACGCA
280220 TCCCAAAGCCTAAT
65 TCCCAAAGCCTAAT
280234 ACCTTGGGAC
Statistics
Matches: 70, Mismatches: 7, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
79 65 0.93
80 5 0.07
ACGTcount: A:0.29, C:0.26, G:0.13, T:0.32
Consensus pattern (79 bp):
GGTGCAAACCACACATTTCCCAATCATATCTTTTTTCGTTCAACTACCAGATGATATTGACGCAT
CCCAAAGCCTAATT
Found at i:280968 original size:42 final size:42
Alignment explanation
Indices: 280921--281009 Score: 124
Period size: 42 Copynumber: 2.1 Consensus size: 42
280911 AAACCTTCTT
* * *
280921 TTCTTTACCTTTTGTTTGCCTCTTGATTTTAACCTGGGAGAC
1 TTCTTTACCTTTTGTCTGCCTCTTGACTTTAACCTGGAAGAC
* * *
280963 TTCTTTACCTTTTGTCTGCCTGTTGACTTTGACCTGGAAGAT
1 TTCTTTACCTTTTGTCTGCCTCTTGACTTTAACCTGGAAGAC
281005 TTCTT
1 TTCTT
281010 CACCCATTGT
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.13, C:0.21, G:0.17, T:0.48
Consensus pattern (42 bp):
TTCTTTACCTTTTGTCTGCCTCTTGACTTTAACCTGGAAGAC
Found at i:281020 original size:42 final size:42
Alignment explanation
Indices: 280932--281021 Score: 99
Period size: 42 Copynumber: 2.1 Consensus size: 42
280922 TCTTTACCTT
* * * * **
280932 TTGTTTGCCTCTTGATTTTAACCTGGGAGACTTCTTTACCTT
1 TTGTCTGCCTCTTGACTTTAACCTGGAAGACTTCTTCACCCA
* * *
280974 TTGTCTGCCTGTTGACTTTGACCTGGAAGATTTCTTCACCCA
1 TTGTCTGCCTCTTGACTTTAACCTGGAAGACTTCTTCACCCA
281016 TTGTCT
1 TTGTCT
281022 ACTTGTCAAC
Statistics
Matches: 39, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
42 39 1.00
ACGTcount: A:0.14, C:0.23, G:0.18, T:0.44
Consensus pattern (42 bp):
TTGTCTGCCTCTTGACTTTAACCTGGAAGACTTCTTCACCCA
Found at i:281034 original size:42 final size:42
Alignment explanation
Indices: 280958--281221 Score: 165
Period size: 42 Copynumber: 6.3 Consensus size: 42
280948 TTTAACCTGG
* * * ** *
280958 GAGACTTCTTTACCTTTTGTCTGCCTGTTGACTTTGACCTGGA
1 GAGATTTCTTTACC-CTTGTCTACCTGTCAACTTTGACCTGAA
* * *
281001 -AGATTTCTTCACCCATTGTCTACTTGTCAACTTTGA-CTTAA
1 GAGATTTCTTTACCC-TTGTCTACCTGTCAACTTTGACCTGAA
* **
281042 GAGATTTCATTACCCCTTGTCTACTCT-TCGGCTTTGACCT-AA
1 GAGATTTCTTTA-CCCTTGTCTAC-CTGTCAACTTTGACCTGAA
* *
281084 GAGACTTCTTTA-CCTTATCTACCTGTCAACTTTGA-CTCG-A
1 GAGATTTCTTTACCCTTGTCTACCTGTCAACTTTGACCT-GAA
* *
281124 GAGACTTT-TTTACCCTTTGTCTGCCTGTCAGCTTTGACCTGAA
1 GAGA-TTTCTTTACCC-TTGTCTACCTGTCAACTTTGACCTGAA
* * * *
281167 -AGACTAT-TTTACCCTTTGTTTACCGGTCAATTTTGA-CTCG-A
1 GAGA-TTTCTTTACCC-TTGTCTACCTGTCAACTTTGACCT-GAA
*
281208 GAGACTTCTTTACC
1 GAGATTTCTTTACC
281222 TTTTGCTTGC
Statistics
Matches: 174, Mismatches: 31, Indels: 33
0.73 0.13 0.14
Matches are distributed among these distances:
39 4 0.02
40 26 0.15
41 11 0.06
42 124 0.71
43 9 0.05
ACGTcount: A:0.20, C:0.25, G:0.15, T:0.40
Consensus pattern (42 bp):
GAGATTTCTTTACCCTTGTCTACCTGTCAACTTTGACCTGAA
Found at i:281220 original size:84 final size:83
Alignment explanation
Indices: 280958--281400 Score: 323
Period size: 84 Copynumber: 5.3 Consensus size: 83
280948 TTTAACCTGG
* * * *
280958 GAGACTTCTTTACCTTTTGTCTGCCTGT-TGACTTTGACCTGGAAGA-TTTCTTCACCCATTGTC
1 GAGACTTCTTTACCCTTTGTCTGCCTGTCAG-CTTTGACCTGAAAGACTTT-TT-ACCCTTTGTC
* **
281021 TACTTGTCAACTTTGACTTAA
63 TACCTGTCAACTTTGACTCGA
* * * * * *
281042 GAGATTTCATTACCCCTTGTCTACTCT-TCGGCTTTGACCT-AAGAGACTTCTTTA-CC-TTATC
1 GAGACTTCTTTACCCTTTGTCTGC-CTGTCAGCTTTGACCTGAA-AGACTT-TTTACCCTTTGTC
281103 TACCTGTCAACTTTGACTCGA
63 TACCTGTCAACTTTGACTCGA
* *
281124 GAGACTTTTTTACCCTTTGTCTGCCTGTCAGCTTTGACCTGAAAGACTATTTTACCCTTTGTTTA
1 GAGACTTCTTTACCCTTTGTCTGCCTGTCAGCTTTGACCTGAAAGACT-TTTTACCCTTTGTCTA
* *
281189 CCGGTCAATTTTGACTCGA
65 CCTGTCAACTTTGACTCGA
* ** * * * * *
281208 GAGACTTCTTTACCTTTTG-CTTGCCCATCAGTTTTTAACCCGTAAGACTTTTTTACCCTTTGTT
1 GAGACTTCTTTACCCTTTGTC-TGCCTGTCAG-CTTTGACCTGAAAGAC-TTTTTACCCTTTGTC
* *
281272 TACCCGTCAGA-TTTGACCCGA
63 TACCTGTCA-ACTTTGACTCGA
* * * * * *
281293 GAGACTTTTTTACCCCTTG-CTTGCCTGTCTA-CTTTGA-CTCAAGAAACTTCTTTTCCTTTTGT
1 GAGACTTCTTTACCCTTTGTC-TGCCTGTC-AGCTTTGACCTGAA-AGACTT-TTTACCCTTTGT
* *
281355 CTACTTGTCGACTTTGACTCGA
62 CTACCTGTCAACTTTGACTCGA
* * **
281377 GAAACTTCTATACTTTTTGTCTGC
1 GAGACTTCTTTACCCTTTGTCTGC
281401 TCATCGGCTT
Statistics
Matches: 285, Mismatches: 55, Indels: 38
0.75 0.15 0.10
Matches are distributed among these distances:
81 2 0.01
82 62 0.22
83 14 0.05
84 128 0.45
85 75 0.26
86 4 0.01
ACGTcount: A:0.19, C:0.26, G:0.15, T:0.41
Consensus pattern (83 bp):
GAGACTTCTTTACCCTTTGTCTGCCTGTCAGCTTTGACCTGAAAGACTTTTTACCCTTTGTCTAC
CTGTCAACTTTGACTCGA
Found at i:281287 original size:85 final size:84
Alignment explanation
Indices: 281103--281317 Score: 263
Period size: 85 Copynumber: 2.5 Consensus size: 84
281093 TTACCTTATC
* * ** * *
281103 TACCTGTCAACTTTGACTCGAGAGACTTTTTTACCCTTTG-TCTGCCTGTCAGCTTTGACCTGAA
1 TACCCGTCAATTTTGACTCGAGAGACTTTTTTACCCTTTGCT-TGCCCATCAGCTTTAACCCGAA
281167 AGACTATTTTACCCTTTGTT
65 AGACTATTTTACCCTTTGTT
* * * * *
281187 TACCGGTCAATTTTGACTCGAGAGACTTCTTTACCTTTTGCTTGCCCATCAGTTTTTAACCCGTA
1 TACCCGTCAATTTTGACTCGAGAGACTTTTTTACCCTTTGCTTGCCCATCAG-CTTTAACCCGAA
*
281252 AGACTTTTTTACCCTTTGTT
65 AGACTATTTTACCCTTTGTT
* *
281272 TACCCGTCAGA-TTTGACCCGAGAGACTTTTTTACCCCTTGCTTGCC
1 TACCCGTCA-ATTTTGACTCGAGAGACTTTTTTACCCTTTGCTTGCC
281318 TGTCTACTTT
Statistics
Matches: 112, Mismatches: 16, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
84 44 0.39
85 67 0.60
86 1 0.01
ACGTcount: A:0.19, C:0.27, G:0.15, T:0.40
Consensus pattern (84 bp):
TACCCGTCAATTTTGACTCGAGAGACTTTTTTACCCTTTGCTTGCCCATCAGCTTTAACCCGAAA
GACTATTTTACCCTTTGTT
Found at i:281287 original size:127 final size:127
Alignment explanation
Indices: 281125--281353 Score: 314
Period size: 127 Copynumber: 1.8 Consensus size: 127
281115 TTGACTCGAG
* * * * * *
281125 AGACTTTTTTACCCTTTGTCTGCCTGTCAGCTTTGACCTGAAAGACTATTTTACCCTTTGTTTAC
1 AGACTTTTTTACCCTTTGTCTACCCGTCAGATTTGACCCGAAAGACTATTTTACCCCTTGCTTAC
* * *
281190 CGGTCAATTTTGACTCGAGAGACTTCTTTACCTTTTGCTTGCCCATCAGTTTTTAACCCGTA
66 CGGTCAACTTTGACTCAAGAAACTTCTTTACCTTTTGCTTGCCCATCAGTTTTTAACCCGTA
* * * *
281252 AGACTTTTTTACCCTTTGTTTACCCGTCAGATTTGACCCGAGAGACTTTTTTACCCCTTGCTTGC
1 AGACTTTTTTACCCTTTGTCTACCCGTCAGATTTGACCCGAAAGACTATTTTACCCCTTGCTTAC
* * *
281317 CTGTCTACTTTGACTCAAGAAACTTCTTTTCCTTTTG
66 CGGTCAACTTTGACTCAAGAAACTTCTTTACCTTTTG
281354 TCTACTTGTC
Statistics
Matches: 86, Mismatches: 16, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
127 86 1.00
ACGTcount: A:0.18, C:0.26, G:0.14, T:0.41
Consensus pattern (127 bp):
AGACTTTTTTACCCTTTGTCTACCCGTCAGATTTGACCCGAAAGACTATTTTACCCCTTGCTTAC
CGGTCAACTTTGACTCAAGAAACTTCTTTACCTTTTGCTTGCCCATCAGTTTTTAACCCGTA
Found at i:281329 original size:42 final size:42
Alignment explanation
Indices: 281072--281330 Score: 197
Period size: 42 Copynumber: 6.2 Consensus size: 42
281062 CTACTCTTCG
** * *
281072 GCTTTGACCTAAGAGACTTCTTTA-CCTTAT-C-TACCTGTCA
1 GCTTTGACCCGAGAGACTTTTTTACCCTT-TGCTTGCCTGTCA
* *
281112 ACTTTGACTCGAGAGACTTTTTTACCCTTTG-TCTGCCTGTCA
1 GCTTTGACCCGAGAGACTTTTTTACCCTTTGCT-TGCCTGTCA
* * * * * *
281154 GCTTTGACCTGAAAGACTATTTTACCCTTTGTTTACCGGTCA
1 GCTTTGACCCGAGAGACTTTTTTACCCTTTGCTTGCCTGTCA
** * * * **
281196 ATTTTGACTCGAGAGACTTCTTTACCTTTTGCTTGCCCATCA
1 GCTTTGACCCGAGAGACTTTTTTACCCTTTGCTTGCCTGTCA
* * * * *
281238 GTTTTTAACCCGTA-AGACTTTTTTACCCTTTGTTTACCCGTCA
1 G-CTTTGACCCG-AGAGACTTTTTTACCCTTTGCTTGCCTGTCA
* *
281281 GATTTGACCCGAGAGACTTTTTTACCCCTTGCTTGCCTGTCTA
1 GCTTTGACCCGAGAGACTTTTTTACCCTTTGCTTGCCTGTC-A
281324 -CTTTGAC
1 GCTTTGAC
281331 TCAAGAAACT
Statistics
Matches: 170, Mismatches: 40, Indels: 16
0.75 0.18 0.07
Matches are distributed among these distances:
40 20 0.12
41 5 0.03
42 109 0.64
43 35 0.21
44 1 0.01
ACGTcount: A:0.19, C:0.26, G:0.15, T:0.40
Consensus pattern (42 bp):
GCTTTGACCCGAGAGACTTTTTTACCCTTTGCTTGCCTGTCA
Found at i:281369 original size:42 final size:42
Alignment explanation
Indices: 281318--281430 Score: 136
Period size: 42 Copynumber: 2.7 Consensus size: 42
281308 CTTGCTTGCC
* *
281318 TGTCTACTTTGACTCAAGAAACTTCTTTTCCTTTTGTCTACT
1 TGTCGACTTTGACTCGAGAAACTTCTTTTCCTTTTGTCTACT
* * * *
281360 TGTCGACTTTGACTCGAGAAACTTCTATACTTTTTGTCTGCT
1 TGTCGACTTTGACTCGAGAAACTTCTTTTCCTTTTGTCTACT
** * *
281402 CATCGGCTTTGACTCGAGAGACTTCTTTT
1 TGTCGACTTTGACTCGAGAAACTTCTTTT
281431 GACTCGAGAA
Statistics
Matches: 59, Mismatches: 12, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
42 59 1.00
ACGTcount: A:0.19, C:0.23, G:0.15, T:0.43
Consensus pattern (42 bp):
TGTCGACTTTGACTCGAGAAACTTCTTTTCCTTTTGTCTACT
Found at i:281433 original size:19 final size:19
Alignment explanation
Indices: 281409--281447 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
281399 GCTCATCGGC
*
281409 TTTGACTCGAGAGACTTCT
1 TTTGACTCGAGAAACTTCT
281428 TTTGACTCGAGAAACTTCT
1 TTTGACTCGAGAAACTTCT
281447 T
1 T
281448 CACCTTTTGT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.23, C:0.21, G:0.18, T:0.38
Consensus pattern (19 bp):
TTTGACTCGAGAAACTTCT
Found at i:281441 original size:61 final size:61
Alignment explanation
Indices: 281367--281487 Score: 181
Period size: 61 Copynumber: 2.0 Consensus size: 61
281357 ACTTGTCGAC
* * * *
281367 TTTGACTCGAGAAACTTCTAT-ACTTTTTGTCTGCTCATCGGCTTTGACTCGAGAGACTTCT
1 TTTGACTCGAGAAACTTCT-TCACCTTTTGTCTACTCATCGACTTTGACCCGAGAGACTTCT
*
281428 TTTGACTCGAGAAACTTCTTCACCTTTTGTCTACTCGTCGACTTTGACCCGAGAGACTTC
1 TTTGACTCGAGAAACTTCTTCACCTTTTGTCTACTCATCGACTTTGACCCGAGAGACTTC
281488 ATTACCTTTT
Statistics
Matches: 54, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
60 1 0.02
61 53 0.98
ACGTcount: A:0.20, C:0.26, G:0.17, T:0.37
Consensus pattern (61 bp):
TTTGACTCGAGAAACTTCTTCACCTTTTGTCTACTCATCGACTTTGACCCGAGAGACTTCT
Found at i:281487 original size:42 final size:41
Alignment explanation
Indices: 281428--281518 Score: 112
Period size: 42 Copynumber: 2.2 Consensus size: 41
281418 AGAGACTTCT
* *
281428 TTTGACTCGAGAAACTTC-TTCACCTTTTGTCTACTCGTCGAC
1 TTTGACCCGAGAAACTTCATT-ACCTTTTGTCTACT-GTCAAC
* *
281470 TTTGACCCGAGAGACTTCATTACCTTTTGTCTCCTGTCAAC
1 TTTGACCCGAGAAACTTCATTACCTTTTGTCTACTGTCAAC
*
281511 TTTAACCC
1 TTTGACCC
281519 ATAAAACTTA
Statistics
Matches: 43, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
41 12 0.28
42 29 0.67
43 2 0.05
ACGTcount: A:0.20, C:0.30, G:0.13, T:0.37
Consensus pattern (41 bp):
TTTGACCCGAGAAACTTCATTACCTTTTGTCTACTGTCAAC
Found at i:282170 original size:8 final size:8
Alignment explanation
Indices: 282141--282224 Score: 57
Period size: 9 Copynumber: 9.9 Consensus size: 8
282131 GGTTATTAAA
282141 AAAATAA-
1 AAAATAAT
282148 AAAAT-AT
1 AAAATAAT
*
282155 AATCATAAT
1 AA-AATAAT
*
282164 TAAATAA-
1 AAAATAAT
282171 AAATATAAT
1 AAA-ATAAT
282180 AATAAAATAAT
1 -A--AAATAAT
282191 AAAATAAT
1 AAAATAAT
282199 AATAATAAT
1 AA-AATAAT
282208 AATAATAAT
1 AA-AATAAT
282217 AATAATAA
1 AA-AATAA
282225 AGAGATTAAT
Statistics
Matches: 64, Mismatches: 4, Indels: 16
0.76 0.05 0.19
Matches are distributed among these distances:
6 1 0.02
7 9 0.14
8 19 0.30
9 26 0.41
10 2 0.03
11 5 0.08
12 2 0.03
ACGTcount: A:0.70, C:0.01, G:0.00, T:0.29
Consensus pattern (8 bp):
AAAATAAT
Found at i:282175 original size:22 final size:23
Alignment explanation
Indices: 282142--282210 Score: 79
Period size: 22 Copynumber: 3.0 Consensus size: 23
282132 GTTATTAAAA
*
282142 AAATAAAAAATATAATCATAATT
1 AAATAAAAAATATAATAATAATT
*
282165 AAAT-AAAAATATAATAATAA-A
1 AAATAAAAAATATAATAATAATT
282186 ATAATAAAATAATAATAATAATAAT
1 A-AATAAAA-AAT-ATAATAATAAT
282211 AATAATAATA
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
21 1 0.03
22 18 0.46
23 7 0.18
24 3 0.08
25 10 0.26
ACGTcount: A:0.70, C:0.01, G:0.00, T:0.29
Consensus pattern (23 bp):
AAATAAAAAATATAATAATAATT
Found at i:282183 original size:3 final size:3
Alignment explanation
Indices: 282153--282224 Score: 89
Period size: 3 Copynumber: 25.3 Consensus size: 3
282143 AATAAAAAAT
* * *
282153 ATA ATC ATA ATT A-A ATA AAA AT- ATA ATA ATA A-A ATA ATA A-A ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
282197 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
282225 AGAGATTAAT
Statistics
Matches: 59, Mismatches: 6, Indels: 8
0.81 0.08 0.11
Matches are distributed among these distances:
2 7 0.12
3 52 0.88
ACGTcount: A:0.68, C:0.01, G:0.00, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:282207 original size:9 final size:9
Alignment explanation
Indices: 282153--282224 Score: 89
Period size: 8 Copynumber: 8.4 Consensus size: 9
282143 AATAAAAAAT
*
282153 ATAATCATA
1 ATAATAATA
*
282162 ATTA-AATA
1 ATAATAATA
*
282170 AAAAT-ATA
1 ATAATAATA
282178 ATAATAA-A
1 ATAATAATA
282186 ATAATAA-A
1 ATAATAATA
282194 ATAATAATA
1 ATAATAATA
282203 ATAATAATA
1 ATAATAATA
282212 ATAATAATA
1 ATAATAATA
282221 ATAA
1 ATAA
282225 AGAGATTAAT
Statistics
Matches: 55, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
8 28 0.51
9 27 0.49
ACGTcount: A:0.68, C:0.01, G:0.00, T:0.31
Consensus pattern (9 bp):
ATAATAATA
Found at i:282571 original size:67 final size:67
Alignment explanation
Indices: 282428--282579 Score: 207
Period size: 68 Copynumber: 2.3 Consensus size: 67
282418 AAATGGCTAT
** * * * *
282428 AACAAATAGGAGAGAAATGGCAAAAAGAAGAACAGCTGCTAAAAAAGGAAAAACGGACAAAGCAA
1 AACAAATAAAAGAGAAATGACAAAAAGAAAAACAACTACTAAAAAA-GAAAAACGGACAAAGCAA
282493 TTA
65 TTA
* *
282496 AACAAATAAAAGAGAAATGACAAAAAGAAAAACAACTACTAAAAAA-AAGAAATGGACAAAGCAG
1 AACAAATAAAAGAGAAATGACAAAAAGAAAAACAACTACTAAAAAAGAA-AAACGGACAAAGCAA
282560 TTA
65 TTA
282563 AACAAATAAAAGAGAAA
1 AACAAATAAAAGAGAAA
282580 CGAACAGCTA
Statistics
Matches: 75, Mismatches: 8, Indels: 3
0.87 0.09 0.03
Matches are distributed among these distances:
66 2 0.03
67 33 0.44
68 40 0.53
ACGTcount: A:0.63, C:0.11, G:0.17, T:0.09
Consensus pattern (67 bp):
AACAAATAAAAGAGAAATGACAAAAAGAAAAACAACTACTAAAAAAGAAAAACGGACAAAGCAAT
TA
Found at i:282693 original size:15 final size:15
Alignment explanation
Indices: 282666--282752 Score: 72
Period size: 15 Copynumber: 5.7 Consensus size: 15
282656 GACAATAAGA
* *
282666 AAAAGAGAAAACAAG
1 AAAAGAAAAAACAAC
*
282681 AAATGAAAAAACAAC
1 AAAAGAAAAAACAAC
282696 AAAAGAAAGAAACAA-
1 AAAAGAAA-AAACAAC
*
282711 AACAGTAAAAGAA-AA-
1 AAAAG-AAAA-AACAAC
*
282726 AAAAGAAAAAACATC
1 AAAAGAAAAAACAAC
282741 AAAAGAGAAAAA
1 AAAAGA-AAAAA
282753 AAAGAAAGCA
Statistics
Matches: 59, Mismatches: 7, Indels: 11
0.77 0.09 0.14
Matches are distributed among these distances:
13 2 0.03
14 5 0.08
15 36 0.61
16 16 0.27
ACGTcount: A:0.76, C:0.08, G:0.13, T:0.03
Consensus pattern (15 bp):
AAAAGAAAAAACAAC
Found at i:282731 original size:26 final size:26
Alignment explanation
Indices: 282696--282759 Score: 71
Period size: 26 Copynumber: 2.5 Consensus size: 26
282686 AAAAAACAAC
*
282696 AAAAGAAAGAAACAAAACAGT-AAA-AG
1 AAAAAAAAGAAA-AAAACA-TAAAAGAG
282722 AAAAAAAAG-AAAAAACATCAAAAGAG
1 AAAAAAAAGAAAAAAACAT-AAAAGAG
282748 AAAAAAAAGAAA
1 AAAAAAAAGAAA
282760 GCAGTAACCA
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
23 1 0.03
24 6 0.18
25 5 0.15
26 19 0.58
27 2 0.06
ACGTcount: A:0.78, C:0.06, G:0.12, T:0.03
Consensus pattern (26 bp):
AAAAAAAAGAAAAAAACATAAAAGAG
Found at i:294258 original size:20 final size:20
Alignment explanation
Indices: 294216--294277 Score: 63
Period size: 20 Copynumber: 3.0 Consensus size: 20
294206 TACCACTGTT
*
294216 CATGATTGATTTGTATC-AGTA
1 CATGA-TGAATTGTATCGA-TA
* *
294237 CATGGTGAATTGTATTGATA
1 CATGATGAATTGTATCGATA
*
294257 CATTATGAATTGTATCGATA
1 CATGATGAATTGTATCGATA
294277 C
1 C
294278 TTAGGGGCAT
Statistics
Matches: 34, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
20 29 0.85
21 5 0.15
ACGTcount: A:0.31, C:0.10, G:0.19, T:0.40
Consensus pattern (20 bp):
CATGATGAATTGTATCGATA
Found at i:301595 original size:36 final size:36
Alignment explanation
Indices: 301539--301652 Score: 174
Period size: 36 Copynumber: 3.2 Consensus size: 36
301529 GCTTGCTGTC
* * *
301539 GTTGTTGCTGCTATGATGTTGCTATTGGTGCTCGAT
1 GTTGCTGCTGCTGTGTTGTTGCTATTGGTGCTCGAT
*
301575 GTTGCTGCTGCTGTGTTGTTGCTGTTGGTGCTCGAT
1 GTTGCTGCTGCTGTGTTGTTGCTATTGGTGCTCGAT
* *
301611 GTTGCTGCTACTGTGTTGTTGCTATTGGTGGTCGAT
1 GTTGCTGCTGCTGTGTTGTTGCTATTGGTGCTCGAT
301647 GTTGCT
1 GTTGCT
301653 ACTTGCTTGC
Statistics
Matches: 71, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 71 1.00
ACGTcount: A:0.07, C:0.15, G:0.33, T:0.45
Consensus pattern (36 bp):
GTTGCTGCTGCTGTGTTGTTGCTATTGGTGCTCGAT
Found at i:302152 original size:14 final size:13
Alignment explanation
Indices: 302109--302158 Score: 50
Period size: 12 Copynumber: 3.9 Consensus size: 13
302099 GAGTAAACGC
*
302109 ATGCATG-AAGGT
1 ATGCATGAAATGT
*
302121 ATGCGTGAAA-GT
1 ATGCATGAAATGT
302133 ATGCATGAAATGT
1 ATGCATGAAATGT
*
302146 AATGCATGCAATG
1 -ATGCATGAAATG
302159 CATGAAACGA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
12 17 0.53
13 4 0.12
14 11 0.34
ACGTcount: A:0.36, C:0.10, G:0.28, T:0.26
Consensus pattern (13 bp):
ATGCATGAAATGT
Found at i:302175 original size:23 final size:23
Alignment explanation
Indices: 302133--302181 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
302123 GCGTGAAAGT
* * * *
302133 ATGCATGAAATGTAATGCATGCA
1 ATGCATGAAACGAAAAGCATGAA
302156 ATGCATGAAACGAAAAGCATGAA
1 ATGCATGAAACGAAAAGCATGAA
302179 ATG
1 ATG
302182 AACACTACGT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.45, C:0.12, G:0.22, T:0.20
Consensus pattern (23 bp):
ATGCATGAAACGAAAAGCATGAA
Found at i:302200 original size:25 final size:25
Alignment explanation
Indices: 302168--302228 Score: 88
Period size: 25 Copynumber: 2.5 Consensus size: 25
302158 GCATGAAACG
*
302168 AAAA-GCATGAAATGAACACTACGT
1 AAAATGCATGAAATGAAAACTACGT
* *
302192 TAAATGCATGAAATGAAAATTACGT
1 AAAATGCATGAAATGAAAACTACGT
302217 AAAATGCATGAA
1 AAAATGCATGAA
302229 TGTAATTCAT
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
24 3 0.09
25 29 0.91
ACGTcount: A:0.51, C:0.11, G:0.16, T:0.21
Consensus pattern (25 bp):
AAAATGCATGAAATGAAAACTACGT
Found at i:302243 original size:38 final size:38
Alignment explanation
Indices: 302194--302282 Score: 160
Period size: 38 Copynumber: 2.3 Consensus size: 38
302184 CACTACGTTA
302194 AATGCATGAAATGAAAATTACGTAAAATGCATGAATGT
1 AATGCATGAAATGAAAATTACGTAAAATGCATGAATGT
* *
302232 AATTCATGAAATGAAAATTACGTAAAATGCATGCATGT
1 AATGCATGAAATGAAAATTACGTAAAATGCATGAATGT
302270 AATGCATGAAATG
1 AATGCATGAAATG
302283 CATGCAATAT
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
38 48 1.00
ACGTcount: A:0.46, C:0.09, G:0.18, T:0.27
Consensus pattern (38 bp):
AATGCATGAAATGAAAATTACGTAAAATGCATGAATGT
Found at i:302969 original size:42 final size:41
Alignment explanation
Indices: 302922--303548 Score: 260
Period size: 42 Copynumber: 15.0 Consensus size: 41
302912 AACTAGATGA
* * *
302922 AAGGTGAAAAAGTCTCCAGGGTCAAAGCCGATAGGTAGACTT
1 AAGGT-AAAAAGTCTCCAAGGTCAAAGCCGACAGGCAGACTT
* *** * * *
302964 CAGGTGATGTAGTCTCTAAGGTCAAAGCCGACAAGCAGACTA
1 AAGGT-AAAAAGTCTCCAAGGTCAAAGCCGACAGGCAGACTT
*
303006 AAGGTAGGAAAGTCTCCAAGGTCAAAGCCGACAGGCAGACTT
1 AAGGTA-AAAAGTCTCCAAGGTCAAAGCCGACAGGCAGACTT
* * * * *
303048 TAGATAAGGCAA-TCTCTAGGGTCAAAGCCGACAGGCAGAC-T
1 AAGGTAA--AAAGTCTCCAAGGTCAAAGCCGACAGGCAGACTT
* * * *
303089 AAGGTAGGAAAGTTTCCAAGGTCAAAGCCAACAGGCAGACTA
1 AAGGTA-AAAAGTCTCCAAGGTCAAAGCCGACAGGCAGACTT
* * * *
303131 AAGGTCGAAAAGTCTCCAAGGTCAAAGCTGATAGGCAGATTT
1 AAGGT-AAAAAGTCTCCAAGGTCAAAGCCGACAGGCAGACTT
* * * * * * *
303173 TAGATAAGACAGTTTCCAGGGTCAAAGCCGATAGGTAGA-TT
1 AAGGTAA-AAAGTCTCCAAGGTCAAAGCCGACAGGCAGACTT
* * * * *
303214 GAGGGTAAGAGAGTCTCCAATGTCAAAGCCGACATGCGGACTT
1 -AAGGTAA-AAAGTCTCCAAGGTCAAAGCCGACAGGCAGACTT
* * *** * * * *
303257 TAGATGAGGTAGTCT-CTAGGATCAAAGCTGATAGGCAGACTG
1 AAGGT-AAAAAGTCTCCAAGG-TCAAAGCCGACAGGCAGACTT
* * **
303299 AAGGTAGGAGAGTCT-TTAGCGTCAAAGCCGACAGGCAGACTT
1 AAGGTA-AAAAGTCTCCAAG-GTCAAAGCCGACAGGCAGACTT
* * *** ** * * *
303341 TAGATGAGGCAGTCTTTAGGGTCAAAGTCGATAGGCAGAC-T
1 AAGGT-AAAAAGTCTCCAAGGTCAAAGCCGACAGGCAGACTT
* * * * *
303382 AAGGGTAGGAGAGTCTCCAGGGTCAAAGCTGATAGGCAGACTT
1 AA-GGTA-AAAAGTCTCCAAGGTCAAAGCCGACAGGCAGACTT
** ** * * *
303425 AA-ACAAGGCAGTCTCCAAGGTCAAAGCCGACAGGAAAACTA
1 AAGGTAA-AAAGTCTCCAAGGTCAAAGCCGACAGGCAGACTT
** * * * *
303466 AAGGTAGGGAAGTCTCTATGGTCAAAGCCGATAAGCAGACTT
1 AAGGTA-AAAAGTCTCCAAGGTCAAAGCCGACAGGCAGACTT
* * *** * * *
303508 TAGATGAGGCAGTCTCTAGGGTCAAAGCCGACAAGCAGACT
1 AAGGT-AAAAAGTCTCCAAGGTCAAAGCCGACAGGCAGACT
303549 GAGGGTAGGA
Statistics
Matches: 439, Mismatches: 123, Indels: 46
0.72 0.20 0.08
Matches are distributed among these distances:
40 2 0.00
41 69 0.16
42 355 0.81
43 13 0.03
ACGTcount: A:0.34, C:0.19, G:0.29, T:0.19
Consensus pattern (41 bp):
AAGGTAAAAAGTCTCCAAGGTCAAAGCCGACAGGCAGACTT
Found at i:303154 original size:83 final size:84
Alignment explanation
Indices: 302974--303201 Score: 253
Period size: 83 Copynumber: 2.7 Consensus size: 84
302964 CAGGTGATGT
* * *
302974 AGTCTCTAAGGTCAAAGCCGACAAGCAGACTAAAGGTAGGAAAGTCTCCAAGGTCAAAGCCGACA
1 AGTCTCTAAGGTCAAAGCCGACAGGCAGACT-AAGGTAGGAAAGTTTCCAAGGTCAAAGCCAACA
** **
303039 GGCAGACTTTAGATAAGGCA
65 GGCAGACTAAAGATAAGAAA
*
303059 A-TCTCTAGGGTCAAAGCCGACAGGCAGACTAAGGTAGGAAAGTTTCCAAGGTCAAAGCCAACAG
1 AGTCTCTAAGGTCAAAGCCGACAGGCAGACTAAGGTAGGAAAGTTTCCAAGGTCAAAGCCAACAG
* *
303123 GCAGACTAAAGGT-CGAAA
66 GCAGACTAAAGATAAGAAA
* * * * * * * * *
303141 AGTCTCCAAGGTCAAAGCTGATAGGCAGATTTTAGATAAGACAGTTTCCAGGGTCAAAGCC
1 AGTCTCTAAGGTCAAAGCCGACAGGCAGA-CTAAGGTAGGAAAGTTTCCAAGGTCAAAGCC
303202 GATAGGTAGA
Statistics
Matches: 121, Mismatches: 20, Indels: 5
0.83 0.14 0.03
Matches are distributed among these distances:
82 3 0.02
83 65 0.54
84 52 0.43
85 1 0.01
ACGTcount: A:0.36, C:0.21, G:0.26, T:0.17
Consensus pattern (84 bp):
AGTCTCTAAGGTCAAAGCCGACAGGCAGACTAAGGTAGGAAAGTTTCCAAGGTCAAAGCCAACAG
GCAGACTAAAGATAAGAAA
Found at i:303534 original size:293 final size:291
Alignment explanation
Indices: 302932--303548 Score: 663
Period size: 293 Copynumber: 2.1 Consensus size: 291
302922 AAGGTGAAAA
* * * *
302932 AGTCTCCAGGGTCAAAGCCGATAGGTAGACTTCAGGTGATGTAGTCTCTAAGGTCAAAGCCGACA
1 AGTCTCCAGGGTCAAAGCCGACAGGCAGACTTCAGATGAGGTAGTCTCTAAGGTCAAAGCCGACA
302997 AGCAGACTAAAGGTAGGAAAGTCTCCAAGGTCAAAGCCGACAGGCAGACTTTAGATAAGGCAATC
66 AGCAGACTAAAGGTAGGAAAGTCTCCAAGGTCAAAGCCGACAGGCAGACTTTAGATAAGGCAATC
*
303062 TCTAGGGTCAAAGCCGACAGGCAGACTAAGGTAGGAAAGTTTCCAAGGTCAAAGCCAACAGGCAG
131 TCTAGGGTCAAAGCCGACAGGCAGACTAAGGTAGGAAAGTCTCCAAGGTCAAAGCCAACAGGCAG
* * * * * ** *
303127 ACTAAAGGTCGAAAAGTCTCCAAGGTCAAAGCTGATAGGCAGATTTTAGATAAGACAGTTTCCAG
196 ACTAAA-G-CGAAAAGTCTCCAAGGTCAAAGCCGACAGGAAAACTAAAGATAAGACAGTCTCCAG
* * *
303192 GGTCAAAGCCGATAGGTAGATTGAGGGTAAGAG
259 GGTCAAAGCCGATAAGCAGATTGAGGATAAGAG
** * * * * *
303225 AGTCTCCAATGTCAAAGCCGACATGCGGACTTTAGATGAGGTAGTCTCT-AGGATCAAAGCTGAT
1 AGTCTCCAGGGTCAAAGCCGACAGGCAGACTTCAGATGAGGTAGTCTCTAAGG-TCAAAGCCGAC
* * * ** * *
303289 AGGCAGACTGAAGGTAGGAGAGTCT-TTAGCGTCAAAGCCGACAGGCAGACTTTAGATGAGGCAG
65 AAGCAGACTAAAGGTAGGAAAGTCTCCAAG-GTCAAAGCCGACAGGCAGACTTTAGATAAGGCAA
* * * * * ** *
303353 TCTTTAGGGTCAAAGTCGATAGGCAGACTAAGGGTAGGAGAGTCTCCAGGGTCAAAGCTGATAGG
129 TCTCTAGGGTCAAAGCCGACAGGCAGACTAA-GGTAGGAAAGTCTCCAAGGTCAAAGCCAACAGG
* * *
303418 CAGACTTAAA-C-AAGGCAGTCTCCAAGGTCAAAGCCGACAGGAAAACTAAAGGTAGGGA-AGTC
193 CAGAC-TAAAGCGAA--AAGTCTCCAAGGTCAAAGCCGACAGGAAAACTAAAGATA-AGACAGTC
* * * *
303480 TCTATGGTCAAAGCCGATAAGCAGACTTTA-GATGAG-G
254 TCCAGGGTCAAAGCCGATAAGCAGA-TTGAGGATAAGAG
* *
303517 CAGTCTCTAGGGTCAAAGCCGACAAGCAGACT
1 -AGTCTCCAGGGTCAAAGCCGACAGGCAGACT
303549 GAGGGTAGGA
Statistics
Matches: 265, Mismatches: 50, Indels: 18
0.80 0.15 0.05
Matches are distributed among these distances:
291 2 0.01
292 7 0.03
293 215 0.81
294 37 0.14
295 4 0.02
ACGTcount: A:0.34, C:0.19, G:0.29, T:0.19
Consensus pattern (291 bp):
AGTCTCCAGGGTCAAAGCCGACAGGCAGACTTCAGATGAGGTAGTCTCTAAGGTCAAAGCCGACA
AGCAGACTAAAGGTAGGAAAGTCTCCAAGGTCAAAGCCGACAGGCAGACTTTAGATAAGGCAATC
TCTAGGGTCAAAGCCGACAGGCAGACTAAGGTAGGAAAGTCTCCAAGGTCAAAGCCAACAGGCAG
ACTAAAGCGAAAAGTCTCCAAGGTCAAAGCCGACAGGAAAACTAAAGATAAGACAGTCTCCAGGG
TCAAAGCCGATAAGCAGATTGAGGATAAGAG
Found at i:303556 original size:84 final size:85
Alignment explanation
Indices: 302932--303557 Score: 463
Period size: 84 Copynumber: 7.5 Consensus size: 85
302922 AAGGTGAAAA
* * **
302932 AGTCTCCAGGGTCAAAGCCGATAGGTAGACTTCAGGT---GATGTAGTCTCTAAGGTCAAAGCCG
1 AGTCTCCAGGGTCAAAGCCGACAGGCAGACTAAAGGTAGGGA-G-AGTCTCTAAGGTCAAAGCCG
* ** * *
302994 ACAAGCAGACTAAAGGT-AGGAA
64 ACAGGCAGACTTTAGATGAGG-C
* ** * * *
303016 AGTCTCCAAGGTCAAAGCCGACAGGCAGACTTTAGATAAGGCA-A-TCTCTAGGGTCAAAGCCGA
1 AGTCTCCAGGGTCAAAGCCGACAGGCAGACTAAAGGT-AGGGAGAGTCTCTAAGGTCAAAGCCGA
* * *
303079 CAGGCAGAC-TAAGGT-AGGAA
65 CAGGCAGACTTTAGATGAGG-C
* * * * * * * * *
303099 AGTTTCCAAGGTCAAAGCCAACAGGCAGACTAAAGGT-CGAAAAGTCTCCAAGGTCAAAGCTGAT
1 AGTCTCCAGGGTCAAAGCCGACAGGCAGACTAAAGGTAGGGAGAGTCTCTAAGGTCAAAGCCGAC
* * *
303163 AGGCAGATTTTAGATAAGAC
66 AGGCAGACTTTAGATGAGGC
* * * * * * * * *
303183 AGTTTCCAGGGTCAAAGCCGATAGGTAGATTGAGGGTA-AGAGAGTCTCCAATGTCAAAGCCGAC
1 AGTCTCCAGGGTCAAAGCCGACAGGCAGACTAAAGGTAGGGAGAGTCTCTAAGGTCAAAGCCGAC
* * *
303247 ATGCGGACTTTAGATGAGGT
66 AGGCAGACTTTAGATGAGGC
* * * * * *
303267 AGTCTCTAGGATCAAAGCTGATAGGCAGACTGAAGGTA-GGAGAGTCT-TTAGCGTCAAAGCCGA
1 AGTCTCCAGGGTCAAAGCCGACAGGCAGACTAAAGGTAGGGAGAGTCTCTAAG-GTCAAAGCCGA
303330 CAGGCAGACTTTAGATGAGGC
65 CAGGCAGACTTTAGATGAGGC
** * * * * * * *
303351 AGTCTTTAGGGTCAAAGTCGATAGGCAGACTAAGGGTA-GGAGAGTCTCCAGGGTCAAAGCTGAT
1 AGTCTCCAGGGTCAAAGCCGACAGGCAGACTAAAGGTAGGGAGAGTCTCTAAGGTCAAAGCCGAC
* **
303415 AGGCAGAC-TTAAACAAGGC
66 AGGCAGACTTTAGATGAGGC
* * * * *
303434 AGTCTCCAAGGTCAAAGCCGACAGGAAAACTAAAGGTAGGGA-AGTCTCTATGGTCAAAGCCGAT
1 AGTCTCCAGGGTCAAAGCCGACAGGCAGACTAAAGGTAGGGAGAGTCTCTAAGGTCAAAGCCGAC
*
303498 AAGCAGACTTTAGATGAGGC
66 AGGCAGACTTTAGATGAGGC
* * * *
303518 AGTCTCTAGGGTCAAAGCCGACAAGCAGACTGAGGGTAGG
1 AGTCTCCAGGGTCAAAGCCGACAGGCAGACTAAAGGTAGG
303558 AAAATTCATA
Statistics
Matches: 435, Mismatches: 94, Indels: 26
0.78 0.17 0.05
Matches are distributed among these distances:
81 2 0.00
82 1 0.00
83 130 0.30
84 297 0.68
85 4 0.01
88 1 0.00
ACGTcount: A:0.33, C:0.19, G:0.29, T:0.19
Consensus pattern (85 bp):
AGTCTCCAGGGTCAAAGCCGACAGGCAGACTAAAGGTAGGGAGAGTCTCTAAGGTCAAAGCCGAC
AGGCAGACTTTAGATGAGGC
Found at i:305167 original size:14 final size:15
Alignment explanation
Indices: 305143--305171 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
305133 AGAAAGGAAG
305143 AAAAAGCAAAAAAAA
1 AAAAAGCAAAAAAAA
305158 AAAAAG-AAAAAAAA
1 AAAAAGCAAAAAAAA
305172 TATGAAATGG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.90, C:0.03, G:0.07, T:0.00
Consensus pattern (15 bp):
AAAAAGCAAAAAAAA
Found at i:318469 original size:20 final size:20
Alignment explanation
Indices: 318444--318518 Score: 87
Period size: 20 Copynumber: 3.8 Consensus size: 20
318434 TTTTACCCAG
* *
318444 ATGTATCGATATATTTTTCA
1 ATGTATCAATACATTTTTCA
* * *
318464 ATGTATCAATACATGTATGA
1 ATGTATCAATACATTTTTCA
*
318484 ATGTATCAATACATTCTTCA
1 ATGTATCAATACATTTTTCA
*
318504 ATGTATCGATACATT
1 ATGTATCAATACATT
318519 CTATCTTTCT
Statistics
Matches: 45, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 45 1.00
ACGTcount: A:0.35, C:0.13, G:0.11, T:0.41
Consensus pattern (20 bp):
ATGTATCAATACATTTTTCA
Found at i:319462 original size:20 final size:21
Alignment explanation
Indices: 319423--319462 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
319413 TAGCCTTTAA
* *
319423 CCATGCTTTTTTTACTATGTT
1 CCATGCATTTTTAACTATGTT
319444 CCATGCATTTTTAAC-ATGT
1 CCATGCATTTTTAACTATGT
319463 CTAGCATCTC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.20, C:0.20, G:0.10, T:0.50
Consensus pattern (21 bp):
CCATGCATTTTTAACTATGTT
Found at i:325373 original size:13 final size:13
Alignment explanation
Indices: 325355--325379 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
325345 CATAAAGTGT
325355 TGTATCGATACAA
1 TGTATCGATACAA
325368 TGTATCGATACA
1 TGTATCGATACA
325380 TAAGTTTTGT
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:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:325397 original size:32 final size:33
Alignment explanation
Indices: 325335--325400 Score: 107
Period size: 32 Copynumber: 2.0 Consensus size: 33
325325 TTCAATGATT
325335 TGTATCGATACATAAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAAGTGTTGTATCGATACAA
* *
325368 TGTATCGATACAT-AAGTTTTGTATTGATACAA
1 TGTATCGATACATAAAGTGTTGTATCGATACAA
325400 T
1 T
325401 TTAAGCTACT
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 18 0.58
33 13 0.42
ACGTcount: A:0.35, C:0.11, G:0.17, T:0.38
Consensus pattern (33 bp):
TGTATCGATACATAAAGTGTTGTATCGATACAA
Found at i:325459 original size:13 final size:13
Alignment explanation
Indices: 325441--325465 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
325431 ATTACTCAAA
325441 TGTATCGATACAT
1 TGTATCGATACAT
325454 TGTATCGATACA
1 TGTATCGATACA
325466 CTGATCTTTG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:325517 original size:52 final size:50
Alignment explanation
Indices: 325454--325602 Score: 217
Period size: 52 Copynumber: 2.9 Consensus size: 50
325444 ATCGATACAT
*
325454 TGTATCGATACACTGATCTTTGTATCGATACATGCAGGCAAATTTGCCCAGA
1 TGTATCGATACACT-AT-TATGTATCGATACATGCAGGCAAATTTGCCCAGA
* *
325506 TGTATCGATACATTATAAAATGTATCGATACATGCAGGCAAATTTGCCCAGA
1 TGTATCGATACACTAT--TATGTATCGATACATGCAGGCAAATTTGCCCAGA
325558 TGTATCGATACACTATTAAATGTATCGATACATGCAGGCAAATTT
1 TGTATCGATACACTATT--ATGTATCGATACATGCAGGCAAATTT
325603 TCATATTTTG
Statistics
Matches: 88, Mismatches: 6, Indels: 6
0.88 0.06 0.06
Matches are distributed among these distances:
51 2 0.02
52 86 0.98
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31
Consensus pattern (50 bp):
TGTATCGATACACTATTATGTATCGATACATGCAGGCAAATTTGCCCAGA
Found at i:332485 original size:5 final size:5
Alignment explanation
Indices: 332475--332529 Score: 64
Period size: 5 Copynumber: 11.6 Consensus size: 5
332465 GTAAACACAC
*
332475 AAACA AAACA AAA-A AAA-A AAGA-A AAAAA AAACA AAACA AAACA AAA-A
1 AAACA AAACA AAACA AAACA AA-ACA AAACA AAACA AAACA AAACA AAACA
332522 AAACA AAA
1 AAACA AAA
332530 TAGAAAAAAG
Statistics
Matches: 46, Mismatches: 1, Indels: 6
0.87 0.02 0.11
Matches are distributed among these distances:
4 12 0.26
5 34 0.74
ACGTcount: A:0.87, C:0.11, G:0.02, T:0.00
Consensus pattern (5 bp):
AAACA
Found at i:332503 original size:14 final size:14
Alignment explanation
Indices: 332484--332539 Score: 51
Period size: 14 Copynumber: 3.9 Consensus size: 14
332474 CAAACAAAAC
332484 AAAAAAAAAAAGAA
1 AAAAAAAAAAAGAA
332498 AAAAAAAACAAA-ACA
1 AAAAAAAA-AAAGA-A
*
332513 AAACAAAAAAAACAA
1 AAA-AAAAAAAAGAA
* *
332528 AATAGAAAAAAG
1 AAAAAAAAAAAG
332540 GTGCAAAGGC
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
14 16 0.46
15 13 0.37
16 6 0.17
ACGTcount: A:0.86, C:0.07, G:0.05, T:0.02
Consensus pattern (14 bp):
AAAAAAAAAAAGAA
Found at i:332798 original size:17 final size:16
Alignment explanation
Indices: 332776--332835 Score: 50
Period size: 17 Copynumber: 3.5 Consensus size: 16
332766 TGTTCTTTTC
332776 CAAAAAAAGAAACAAAA
1 CAAAAAAAGAAA-AAAA
*
332793 CAAAAAAGGAAAAAAA
1 CAAAAAAAGAAAAAAA
*
332809 -AAGAAGAAACAAAAAAAA
1 CAA-AA-AAA-GAAAAAAA
332827 CGAAAAAAA
1 C-AAAAAAA
332836 AACGAAAAAC
Statistics
Matches: 35, Mismatches: 3, Indels: 9
0.74 0.06 0.19
Matches are distributed among these distances:
15 2 0.06
16 6 0.17
17 13 0.37
18 10 0.29
19 2 0.06
20 2 0.06
ACGTcount: A:0.82, C:0.08, G:0.10, T:0.00
Consensus pattern (16 bp):
CAAAAAAAGAAAAAAA
Found at i:332806 original size:14 final size:12
Alignment explanation
Indices: 332777--332837 Score: 59
Period size: 13 Copynumber: 4.8 Consensus size: 12
332767 GTTCTTTTCC
* *
332777 AAAAAAAGAAAC
1 AAAAAAAAAAAG
*
332789 AAAACAAAAAAGG
1 AAAA-AAAAAAAG
332802 AAAAAAAAAGAAG
1 AAAAAAAAA-AAG
332815 AAACAAAAAAAACG
1 AAA-AAAAAAAA-G
332829 AAAAAAAAA
1 AAAAAAAAA
332838 CGAAAAACCC
Statistics
Matches: 41, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
12 9 0.22
13 22 0.54
14 10 0.24
ACGTcount: A:0.84, C:0.07, G:0.10, T:0.00
Consensus pattern (12 bp):
AAAAAAAAAAAG
Found at i:332813 original size:27 final size:26
Alignment explanation
Indices: 332777--332845 Score: 86
Period size: 27 Copynumber: 2.5 Consensus size: 26
332767 GTTCTTTTCC
*
332777 AAAAAAAGAAACAA-AACAAAAAAGGAA
1 AAAAAAAGAAA-AACAA-AAAAAACGAA
332804 AAAAAAAGAAGAAACAAAAAAAACGAA
1 AAAAAAAGAA-AAACAAAAAAAACGAA
332831 AAAAAAACGAAAAAC
1 AAAAAAA-GAAAAAC
332846 CCCTTTTCAC
Statistics
Matches: 38, Mismatches: 1, Indels: 6
0.84 0.02 0.13
Matches are distributed among these distances:
27 32 0.84
28 6 0.16
ACGTcount: A:0.81, C:0.09, G:0.10, T:0.00
Consensus pattern (26 bp):
AAAAAAAGAAAAACAAAAAAAACGAA
Found at i:332836 original size:30 final size:29
Alignment explanation
Indices: 332777--332837 Score: 81
Period size: 30 Copynumber: 2.1 Consensus size: 29
332767 GTTCTTTTCC
332777 AAAAAAAGAAACAAAACAAAAAAGGAAAAA
1 AAAAAAAGAAACAAAACAAAAAA-GAAAAA
* *
332807 AAAAGAAGAAAC-AAA-AAAAACGAAAAA
1 AAAAAAAGAAACAAAACAAAAAAGAAAAA
332834 AAAA
1 AAAA
332838 CGAAAAACCC
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
27 10 0.34
28 5 0.17
29 3 0.10
30 11 0.38
ACGTcount: A:0.84, C:0.07, G:0.10, T:0.00
Consensus pattern (29 bp):
AAAAAAAGAAACAAAACAAAAAAGAAAAA
Found at i:332842 original size:25 final size:24
Alignment explanation
Indices: 332777--332842 Score: 64
Period size: 25 Copynumber: 2.7 Consensus size: 24
332767 GTTCTTTTCC
* *
332777 AAAAAAAGAAACAAAACAAAAAAGG
1 AAAAAAAAAAACGAAACAAAAAA-G
332802 AAAAAAAAAGAA-GAAACAAAAAA-
1 AAAAAAAAA-AACGAAACAAAAAAG
332825 AACGAAAAAAAAACGAAA
1 AA--AAAAAAAAACGAAA
332843 AACCCCTTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
23 2 0.06
24 2 0.06
25 29 0.83
26 2 0.06
ACGTcount: A:0.82, C:0.08, G:0.11, T:0.00
Consensus pattern (24 bp):
AAAAAAAAAAACGAAACAAAAAAG
Found at i:333944 original size:34 final size:34
Alignment explanation
Indices: 333788--334079 Score: 309
Period size: 34 Copynumber: 8.8 Consensus size: 34
333778 TACCTTCTTA
* * *
333788 AAGTCCACGACTCCGTGGCAC-CTTCTT--TTCA
1 AAGTCCACAACTCCGTGGCACTCTTTTTCCTTCT
* *
333819 AAGCCCACAACTCCGTGGCACTCTTTTTCCCTTTT
1 AAGTCCACAACTCCGTGGCACTCTTTTT-CCTTCT
* *
333854 AAAGTCCACAACTCTGTGGCACTCTTTTTCCCTTTT
1 -AAGTCCACAACTCCGTGGCACTCTTTTT-CCTTCT
* * *
333890 AAAGCCCACAACTTCATGGCACTCTTTTTCCTTCT
1 -AAGTCCACAACTCCGTGGCACTCTTTTTCCTTCT
* *
333925 AAGTCCACAAATCCGTGGCA-TC-----CGTT-T
1 AAGTCCACAACTCCGTGGCACTCTTTTTCCTTCT
*
333952 AAGCCCACAACTCCGTGGCACTCTTTTTCCTTCT
1 AAGTCCACAACTCCGTGGCACTCTTTTTCCTTCT
* * *
333986 AAGTCCATAACTCCGTGGCAC-CTTTTTCTTTTT
1 AAGTCCACAACTCCGTGGCACTCTTTTTCCTTCT
*
334019 AAGTCCACAACTCCGTGGCACTCTTTCTCCTTCT
1 AAGTCCACAACTCCGTGGCACTCTTTTTCCTTCT
*
334053 AAGTCCACAACTCCGTGGCACCCTTTT
1 AAGTCCACAACTCCGTGGCACTCTTTT
334080 ACATCCATAG
Statistics
Matches: 218, Mismatches: 30, Indels: 23
0.80 0.11 0.08
Matches are distributed among these distances:
27 19 0.09
28 5 0.02
31 19 0.09
32 5 0.02
33 35 0.16
34 70 0.32
35 7 0.03
36 58 0.27
ACGTcount: A:0.20, C:0.34, G:0.13, T:0.33
Consensus pattern (34 bp):
AAGTCCACAACTCCGTGGCACTCTTTTTCCTTCT
Found at i:334036 original size:94 final size:97
Alignment explanation
Indices: 333859--334038 Score: 258
Period size: 94 Copynumber: 1.9 Consensus size: 97
333849 CTTTTAAAGT
* * *
333859 CCACAACTCTGTGGCACTCTTTTTCCCTTTTAAAGCCCACAACTTCATGGCACTCTTTTTCCTTC
1 CCACAACTCCGTGGCACTCTTTTTCCCTTCTAAAGCCCACAACTCCATGGCACTCTTTTTCCTTC
333924 TAAGTCCACAAATCCGTGGCATCCGTTTAAGC
66 TAAGTCCACAAATCCGTGGCATCCGTTTAAGC
* * * * *
333956 CCACAACTCCGTGGCACTCTTTTT-CCTTCT-AAGTCCATAACTCCGTGGCAC-CTTTTTCTTTT
1 CCACAACTCCGTGGCACTCTTTTTCCCTTCTAAAGCCCACAACTCCATGGCACTCTTTTTCCTTC
*
334018 TAAGTCCACAACTCCGTGGCA
66 TAAGTCCACAAATCCGTGGCA
334039 CTCTTTCTCC
Statistics
Matches: 74, Mismatches: 9, Indels: 3
0.86 0.10 0.03
Matches are distributed among these distances:
94 29 0.39
95 17 0.23
96 5 0.07
97 23 0.31
ACGTcount: A:0.21, C:0.33, G:0.13, T:0.33
Consensus pattern (97 bp):
CCACAACTCCGTGGCACTCTTTTTCCCTTCTAAAGCCCACAACTCCATGGCACTCTTTTTCCTTC
TAAGTCCACAAATCCGTGGCATCCGTTTAAGC
Found at i:334057 original size:67 final size:66
Alignment explanation
Indices: 333788--334079 Score: 346
Period size: 67 Copynumber: 4.4 Consensus size: 66
333778 TACCTTCTTA
*
333788 AAGTCCACGACTCCGTGGCACC--TTCTTTTCAAAGCCCACAACTCCGTGGCACTCTTTTTCCCT
1 AAGTCCACAACTCCGTGGCACCTTTTCTTTT-AAAGCCCACAACTCCGTGGCACTCTTTTT-CCT
*
333851 TTT
64 TCT
* * *
333854 AAAGTCCACAACTCTGTGGCACTCTTTTTCCCTTTTAAAGCCCACAACTTCATGGCACTCTTTTT
1 -AAGTCCACAACTCCGTGGCAC-C-TTTT--CTTTTAAAGCCCACAACTCCGTGGCACTCTTTTT
333919 CCTTCT
61 CCTTCT
* * *
333925 AAGTCCACAAATCCGTGGCA----TCCGTTT-AAGCCCACAACTCCGTGGCACTCTTTTTCCTTC
1 AAGTCCACAACTCCGTGGCACCTTTTCTTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCCTTC
333985 T
66 T
* * * *
333986 AAGTCCATAACTCCGTGGCACCTTTTTCTTTTTAAGTCCACAACTCCGTGGCACTCTTTCTCCTT
1 AAGTCCACAACTCCGTGGCACC-TTTTCTTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCCTT
334051 CT
65 CT
334053 AAGTCCACAACTCCGTGGCACCCTTTT
1 AAGTCCACAACTCCGTGGCA-CCTTTT
334080 ACATCCATAG
Statistics
Matches: 194, Mismatches: 18, Indels: 26
0.82 0.08 0.11
Matches are distributed among these distances:
61 50 0.26
62 4 0.02
64 1 0.01
66 5 0.03
67 74 0.38
68 3 0.02
70 18 0.09
71 7 0.04
72 27 0.14
73 5 0.03
ACGTcount: A:0.20, C:0.34, G:0.13, T:0.33
Consensus pattern (66 bp):
AAGTCCACAACTCCGTGGCACCTTTTCTTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCCTTC
T
Found at i:334077 original size:27 final size:27
Alignment explanation
Indices: 334047--334099 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 27
334037 CACTCTTTCT
334047 CCTTCTA-AGTCCACAACTCCGTGGCAC
1 CCTTCTACA-TCCACAACTCCGTGGCAC
* * *
334074 CCTTTTACATCCATAGCTCCGTGGCA
1 CCTTCTACATCCACAACTCCGTGGCA
334100 TCTTTCTCCT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
27 21 0.95
28 1 0.05
ACGTcount: A:0.21, C:0.38, G:0.15, T:0.26
Consensus pattern (27 bp):
CCTTCTACATCCACAACTCCGTGGCAC
Found at i:334144 original size:32 final size:32
Alignment explanation
Indices: 334115--334445 Score: 427
Period size: 32 Copynumber: 10.2 Consensus size: 32
334105 CTCCTTTTTC
* *
334115 AAAGCCCACACAAGTCGGTGGCAACCTTTTTCC
1 AAAGCCCACACAAGTCGGTGGCAACC-TTCTCT
*
334148 AAAGCCCACACAAGTCGGTGGCAACCCTTCCCT
1 AAAGCCCACACAAGTCGGTGGCAA-CCTTCTCT
334181 AAAGCCCACACAAGTCGGTGGCAACCTTCTTCT
1 AAAGCCCACACAAGTCGGTGGCAACCTTC-TCT
*
334214 CAAAGCCCACACAAGTCGGTGGCAACCCTCTCT
1 -AAAGCCCACACAAGTCGGTGGCAACCTTCTCT
334247 AAAGCCCACACAAGTCGGTGGCAATCCTTCTC-
1 AAAGCCCACACAAGTCGGTGGCAA-CCTTCTCT
* * * *
334279 AAAGCCCATACAAGTCGATGGTAACCCTCTCT
1 AAAGCCCACACAAGTCGGTGGCAACCTTCTCT
* *
334311 AAAGCCCACACATGTCGGTGGCAACCCTTTTC-
1 AAAGCCCACACAAGTCGGTGGCAA-CCTTCTCT
** *
334343 AAAGCCCACACAAGTTAGTGGCAACCCTCTCT
1 AAAGCCCACACAAGTCGGTGGCAACCTTCTCT
* *
334375 AAAGCCCACACAAGTTGGTGGTAACCATTCTCT
1 AAAGCCCACACAAGTCGGTGGCAACC-TTCTCT
*
334408 AAAGCCCACACAAGTCGGTGGCAACCCT-TCT
1 AAAGCCCACACAAGTCGGTGGCAACCTTCTCT
334439 -AAGCCCA
1 AAAGCCCA
334446 ATATAGCTGG
Statistics
Matches: 263, Mismatches: 27, Indels: 19
0.85 0.09 0.06
Matches are distributed among these distances:
30 7 0.03
31 14 0.05
32 116 0.44
33 96 0.37
34 30 0.11
ACGTcount: A:0.29, C:0.34, G:0.18, T:0.19
Consensus pattern (32 bp):
AAAGCCCACACAAGTCGGTGGCAACCTTCTCT
Found at i:334549 original size:43 final size:43
Alignment explanation
Indices: 334487--334755 Score: 286
Period size: 43 Copynumber: 6.0 Consensus size: 43
334477 CCTTCATCTT
*
334487 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTC
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTC
* * *
334530 CAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATC
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACC----TC
* * *
334577 TTTAAGTCCAATGTAGCTGGCTTTGAATCAGCACATTGGCACCTT
1 --TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTC
* *
334622 TAAGTCCAATATAGCTGGCCTTGAATAAGCATATTGGCATCTTCTTC
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCA-C--C-TC
* * * * *
334669 TTTAAGTTCAATGTAGCTGGCCTTGATTCAGCACACTGGCACCTT
1 --TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTC
* *
334714 TAAGTCCAATATAGCTAGCCTTGAATCAGCATATTGGCACCT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCT
334756 TTTCTATCTT
Statistics
Matches: 186, Mismatches: 28, Indels: 24
0.78 0.12 0.10
Matches are distributed among these distances:
43 108 0.58
44 1 0.01
45 2 0.01
46 2 0.01
47 3 0.02
48 1 0.01
49 69 0.37
ACGTcount: A:0.26, C:0.25, G:0.19, T:0.31
Consensus pattern (43 bp):
TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTC
Found at i:334603 original size:92 final size:93
Alignment explanation
Indices: 334433--334810 Score: 557
Period size: 92 Copynumber: 4.1 Consensus size: 93
334423 CGGTGGCAAC
*
334433 CCTTCTAAGCCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTC-ATCTTTAAGTCCAAT
1 CCTT-TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCTATCTTTAAGTCCAAT
334497 GTAGCTGGCCTTGAATCAGCACATTGGCA
65 GTAGCTGGCCTTGAATCAGCACATTGGCA
** *
334526 CCTCCAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTT-TATCTTTAAGTCCAATG
1 CCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCTATCTTTAAGTCCAATG
*
334590 TAGCTGGCTTTGAATCAGCACATTGGCA
66 TAGCTGGCCTTGAATCAGCACATTGGCA
* * *
334618 CCTTTAAGTCCAATATAGCTGGCCTTGAATAAGCATATTGGCATCTTCT-TCTTTAAGTTCAATG
1 CCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCTATCTTTAAGTCCAATG
* *
334682 TAGCTGGCCTTGATTCAGCACACTGGCA
66 TAGCTGGCCTTGAATCAGCACATTGGCA
* *
334710 CCTTTAAGTCCAATATAGCTAGCCTTGAATCAGCATATTGGCACCTTTTCTATCTTTAAGTTCAA
1 CCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACC--TTCTATCTTTAAGTCCAA
* *
334775 TGTAGCTAGCCTTGAATC-GACACATTGACA
64 TGTAGCTGGCCTTGAATCAG-CACATTGGCA
334805 TCCTTT
1 -CCTTT
334811 TTCTCATCTT
Statistics
Matches: 257, Mismatches: 21, Indels: 11
0.89 0.07 0.04
Matches are distributed among these distances:
92 206 0.80
93 4 0.02
94 5 0.02
95 37 0.14
96 5 0.02
ACGTcount: A:0.26, C:0.25, G:0.17, T:0.32
Consensus pattern (93 bp):
CCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCTATCTTTAAGTCCAATG
TAGCTGGCCTTGAATCAGCACATTGGCA
Found at i:334789 original size:52 final size:55
Alignment explanation
Indices: 334711--334832 Score: 153
Period size: 52 Copynumber: 2.3 Consensus size: 55
334701 ACACTGGCAC
* *
334711 CTTTAAGTCCAATATAGCTAGCCTTGAATC-AGCATATTGGCA-CC-TTTTCT-AT
1 CTTTAAGTCCAATATAGCTAGCCTTGAATCGA-CACATTGACATCCTTTTTCTCAT
* *
334763 CTTTAAGTTCAATGTAGCTAGCCTTGAATCGACACATTGACATCCTTTTTCTCAT
1 CTTTAAGTCCAATATAGCTAGCCTTGAATCGACACATTGACATCCTTTTTCTCAT
**
334818 CTTTAAACCCAATAT
1 CTTTAAGTCCAATAT
334833 CGTTGGCCGT
Statistics
Matches: 58, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
52 36 0.62
53 3 0.05
54 6 0.10
55 13 0.22
ACGTcount: A:0.28, C:0.24, G:0.11, T:0.37
Consensus pattern (55 bp):
CTTTAAGTCCAATATAGCTAGCCTTGAATCGACACATTGACATCCTTTTTCTCAT
Found at i:344342 original size:19 final size:21
Alignment explanation
Indices: 344297--344350 Score: 76
Period size: 21 Copynumber: 2.7 Consensus size: 21
344287 TTTCAACAAT
344297 TTGTATCGATACAAATAGTAA
1 TTGTATCGATACAAATAGTAA
* *
344318 TTGTATCGATACATA-AGT-G
1 TTGTATCGATACAAATAGTAA
344337 TTGTATCGATACAA
1 TTGTATCGATACAA
344351 TGTATCGCTA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
19 13 0.43
20 3 0.10
21 14 0.47
ACGTcount: A:0.37, C:0.11, G:0.17, T:0.35
Consensus pattern (21 bp):
TTGTATCGATACAAATAGTAA
Found at i:345052 original size:15 final size:15
Alignment explanation
Indices: 345024--345056 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
345014 AAATAAATCA
345024 AAATTTGTTGAAAATG
1 AAATTTGTTGAAAA-G
345040 AAATTTG-TGAAAAG
1 AAATTTGTTGAAAAG
345054 AAA
1 AAA
345057 ATTTTCAAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 4 0.24
15 6 0.35
16 7 0.41
ACGTcount: A:0.52, C:0.00, G:0.18, T:0.30
Consensus pattern (15 bp):
AAATTTGTTGAAAAG
Found at i:345058 original size:15 final size:17
Alignment explanation
Indices: 345018--345060 Score: 56
Period size: 15 Copynumber: 2.7 Consensus size: 17
345008 GGAAGAAAAT
*
345018 AAATCAAAATTTGTTGA
1 AAATGAAAATTTGTTGA
345035 AAATG-AAATTTG-TGA
1 AAATGAAAATTTGTTGA
345050 AAA-GAAAATTT
1 AAATGAAAATTT
345061 TCAAACTAGA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
14 1 0.04
15 12 0.50
16 7 0.29
17 4 0.17
ACGTcount: A:0.51, C:0.02, G:0.14, T:0.33
Consensus pattern (17 bp):
AAATGAAAATTTGTTGA
Found at i:347199 original size:20 final size:20
Alignment explanation
Indices: 347174--347227 Score: 67
Period size: 20 Copynumber: 2.7 Consensus size: 20
347164 GTTACAAGCA
347174 ATGTATCAATACAAT-TCAAC-
1 ATGTATCAATACAATGTC--CT
*
347194 ATGTATCGATACAATGTCCT
1 ATGTATCAATACAATGTCCT
347214 ATGTATCAATACAA
1 ATGTATCAATACAA
347228 ACAGTGATAG
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
19 1 0.03
20 27 0.90
21 2 0.07
ACGTcount: A:0.41, C:0.19, G:0.09, T:0.31
Consensus pattern (20 bp):
ATGTATCAATACAATGTCCT
Found at i:347299 original size:19 final size:18
Alignment explanation
Indices: 347250--347339 Score: 100
Period size: 19 Copynumber: 5.1 Consensus size: 18
347240 ACTGCTAGTT
347250 TCATGTATCGATACAATTG
1 TCATGTATCGATACAA-TG
347269 TCCATGTATCGATACAATG
1 T-CATGTATCGATACAATG
*
347288 ATCATCTATCGATAC-A--
1 -TCATGTATCGATACAATG
347304 --ATGTATCGATACAATG
1 TCATGTATCGATACAATG
347320 ATCATGTATCGATACAATG
1 -TCATGTATCGATACAATG
347339 T
1 T
347340 ATCGATACTT
Statistics
Matches: 61, Mismatches: 2, Indels: 17
0.76 0.03 0.21
Matches are distributed among these distances:
13 11 0.18
14 1 0.02
18 2 0.03
19 31 0.51
20 16 0.26
ACGTcount: A:0.34, C:0.18, G:0.14, T:0.33
Consensus pattern (18 bp):
TCATGTATCGATACAATG
Found at i:347312 original size:13 final size:12
Alignment explanation
Indices: 347271--347347 Score: 57
Period size: 13 Copynumber: 7.1 Consensus size: 12
347261 TACAATTGTC
347271 CATGTATCGATA
1 CATGTATCGATA
347283 CA---AT-GAT-
1 CATGTATCGATA
*
347290 CATCTATCGATA
1 CATGTATCGATA
347302 CAATGTATCGATA
1 C-ATGTATCGATA
347315 CA---AT-GAT-
1 CATGTATCGATA
347322 CATGTATCGATA
1 CATGTATCGATA
347334 CAATGTATCGATA
1 C-ATGTATCGATA
347347 C
1 C
347348 TTCTGGGTGT
Statistics
Matches: 52, Mismatches: 1, Indels: 23
0.68 0.01 0.30
Matches are distributed among these distances:
7 4 0.08
8 6 0.12
9 4 0.08
10 4 0.08
11 6 0.12
12 5 0.10
13 23 0.44
ACGTcount: A:0.36, C:0.18, G:0.14, T:0.31
Consensus pattern (12 bp):
CATGTATCGATA
Found at i:347313 original size:32 final size:32
Alignment explanation
Indices: 347272--347347 Score: 143
Period size: 32 Copynumber: 2.4 Consensus size: 32
347262 ACAATTGTCC
347272 ATGTATCGATACAATGATCATCTATCGATACA
1 ATGTATCGATACAATGATCATCTATCGATACA
*
347304 ATGTATCGATACAATGATCATGTATCGATACA
1 ATGTATCGATACAATGATCATCTATCGATACA
347336 ATGTATCGATAC
1 ATGTATCGATAC
347348 TTCTGGGTGT
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
32 43 1.00
ACGTcount: A:0.37, C:0.17, G:0.14, T:0.32
Consensus pattern (32 bp):
ATGTATCGATACAATGATCATCTATCGATACA
Found at i:353855 original size:52 final size:52
Alignment explanation
Indices: 353707--353835 Score: 222
Period size: 52 Copynumber: 2.5 Consensus size: 52
353697 CGAAATATGA
353707 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
* *
353759 AAATTTGCCTGGATGTATCGATACATTTTATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
* *
353811 AAATTTGCCTACATGTATTGATACA
1 AAATTTGCCTGCATGTATCGATACA
353836 AAGATCAGTG
Statistics
Matches: 72, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 72 1.00
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.36
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
Found at i:353935 original size:19 final size:18
Alignment explanation
Indices: 353911--354008 Score: 90
Period size: 19 Copynumber: 5.8 Consensus size: 18
353901 TAGCTTATAT
353911 TGTATCGATACAAAACTTA
1 TGTATCGATAC-AAACTTA
353930 TGTATCGATAC--A--T-
1 TGTATCGATACAAACTTA
353943 TGTATCGATACAACACTTA
1 TGTATCGATACAA-ACTTA
353962 TGTATCGATAC--A--T-
1 TGTATCGATACAAACTTA
353975 TGTATCGATACAACACTTTA
1 TGTATCGATACAA-AC-TTA
353995 TGTATCGATACAAA
1 TGTATCGATACAAA
354009 TCATTGAAAT
Statistics
Matches: 66, Mismatches: 0, Indels: 26
0.72 0.00 0.28
Matches are distributed among these distances:
13 22 0.33
14 2 0.03
16 4 0.06
18 1 0.02
19 24 0.36
20 13 0.20
ACGTcount: A:0.37, C:0.17, G:0.12, T:0.34
Consensus pattern (18 bp):
TGTATCGATACAAACTTA
Found at i:353948 original size:13 final size:13
Alignment explanation
Indices: 353930--353986 Score: 60
Period size: 13 Copynumber: 3.9 Consensus size: 13
353920 ACAAAACTTA
353930 TGTATCGATACAT
1 TGTATCGATACAT
353943 TGTATCGATACAACACTT
1 TGTATCGAT---ACA--T
353961 ATGTATCGATACAT
1 -TGTATCGATACAT
353975 TGTATCGATACA
1 TGTATCGATACA
353987 ACACTTTATG
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 21 0.55
14 1 0.03
16 6 0.16
18 1 0.03
19 9 0.24
ACGTcount: A:0.33, C:0.18, G:0.14, T:0.35
Consensus pattern (13 bp):
TGTATCGATACAT
Done.