Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold107
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: 2327068
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 25 characters in sequence are not A, C, G, or T
File 13 of 15
Found at i:1875795 original size:15 final size:15
Alignment explanation
Indices: 1875772--1875802 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1875762 ATCAAAGATA
1875772 ATGAAGATAATGATG
1 ATGAAGATAATGATG
*
1875787 ATGATGATAATGATG
1 ATGAAGATAATGATG
1875802 A
1 A
1875803 AGTTGACTCG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.45, C:0.00, G:0.26, T:0.29
Consensus pattern (15 bp):
ATGAAGATAATGATG
Found at i:1880401 original size:13 final size:13
Alignment explanation
Indices: 1880383--1880422 Score: 62
Period size: 13 Copynumber: 3.1 Consensus size: 13
1880373 ACAATGTTCT
1880383 TTGTATCGATACA
1 TTGTATCGATACA
*
1880396 TTGTATCGATATA
1 TTGTATCGATACA
*
1880409 ATGTATCGATACA
1 TTGTATCGATACA
1880422 T
1 T
1880423 GGGATACTAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.33, C:0.12, G:0.15, T:0.40
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:1881953 original size:79 final size:79
Alignment explanation
Indices: 1881771--1881989 Score: 189
Period size: 79 Copynumber: 2.8 Consensus size: 79
1881761 ACAACGGGGC
* * * * * * *
1881771 TGGAGTATCCCCGATTATGGAAAATTGATG-TTCTGGAAATAAAATCGGGGTTGGAGTATCCCCT
1 TGGAGAATCCCTGACTATAGAAAATCGATGATT-TAGAAATAAAATCGGGGTTGAAGTATCCCCT
*
1881835 CGAAAATAATAGGGT
65 CGAAAATAACAGGGT
* *
1881850 TGGAGAATCCCTGACTATAGAAAATC-A-GTATTTTGAAAATAAAATCGAGGTTGAAGTATCCCC
1 TGGAGAATCCCTGACTATAGAAAATCGATG-ATTTAG-AAATAAAATCGGGGTTGAAGTATCCCC
*
1881913 TCGAAAATAACGGGGT
64 TCGAAAATAACAGGGT
* * * * **
1881929 TGTA-ATAT-TCTCGATTGT-GAAAAATCGATGATTTAGAAATAAGGTCGGGGTTGAAGTATCC
1 TGGAGA-ATCCCT-GACTATAG-AAAATCGATGATTTAGAAATAAAATCGGGGTTGAAGTATCC
1881990 TTGATTGTGA
Statistics
Matches: 114, Mismatches: 18, Indels: 16
0.77 0.12 0.11
Matches are distributed among these distances:
77 1 0.01
78 7 0.06
79 99 0.87
80 6 0.05
81 1 0.01
ACGTcount: A:0.34, C:0.13, G:0.24, T:0.28
Consensus pattern (79 bp):
TGGAGAATCCCTGACTATAGAAAATCGATGATTTAGAAATAAAATCGGGGTTGAAGTATCCCCTC
GAAAATAACAGGGT
Found at i:1881996 original size:51 final size:51
Alignment explanation
Indices: 1881923--1882040 Score: 132
Period size: 51 Copynumber: 2.3 Consensus size: 51
1881913 TCGAAAATAA
* * *
1881923 CGGGGTTGTAA-TATTCTCGATTGTGAAAAATCGATGA-TTTAGAAATAAGGT
1 CGGGGTTG-AAGTATCCTCGATTGTGAAAAATCAAT-ATTTTAGAAATAAAGT
* * *
1881974 CGGGGTTGAAGTATCCTTGATTGTGAAAAATCAATATTTTGGGAATAAAGT
1 CGGGGTTGAAGTATCCTCGATTGTGAAAAATCAATATTTTAGAAATAAAGT
* *
1882025 CGGGTTTGGAGTATCC
1 CGGGGTTGAAGTATCC
1882041 CCTCAGAAAT
Statistics
Matches: 57, Mismatches: 8, Indels: 4
0.83 0.12 0.06
Matches are distributed among these distances:
50 3 0.05
51 54 0.95
ACGTcount: A:0.31, C:0.09, G:0.27, T:0.33
Consensus pattern (51 bp):
CGGGGTTGAAGTATCCTCGATTGTGAAAAATCAATATTTTAGAAATAAAGT
Found at i:1882057 original size:79 final size:77
Alignment explanation
Indices: 1881974--1882201 Score: 231
Period size: 80 Copynumber: 2.9 Consensus size: 77
1881964 GAAATAAGGT
* * *
1881974 CGGGGTTGAAGTATCCTTGATTGTGAAAAATCAATATTTTGGGAATAAAGTCGGGTTTGGAGTAT
1 CGGGGTTGGAGTATCC-TGATTGTGAAAAATCAATGTTTTGGGAATAAAATCGGG-TTGGAGTAT
*
1882039 CCCCTCAGAAATGA
64 CCCCTCAGAAATAA
* * * * **
1882053 CGGGGTTGGAGTATTCCTAACTGTAAAAAAACTGGTGTTTTGGGAATAAAATCTGGGTTGGAGTA
1 CGGGGTTGGAGTA-TCCTGATTGTGAAAAATC-AATGTTTTGGGAATAAAATC-GGGTTGGAGTA
* *
1882118 TCTCCTCGGAAATAA
63 TCCCCTCAGAAATAA
* * * * * *
1882133 CGGGATTGGAGTATCCCTGATTATGAAAAATTAATGTTTTTGAAATAAAACCGGGGTTGGAGTAT
1 CGGGGTTGGAGTAT-CCTGATTGTGAAAAATCAATGTTTTGGGAATAAAATC-GGGTTGGAGTAT
1882198 CCCC
64 CCCC
1882202 GAGATGAAGA
Statistics
Matches: 119, Mismatches: 26, Indels: 8
0.78 0.17 0.05
Matches are distributed among these distances:
79 54 0.45
80 62 0.52
81 3 0.03
ACGTcount: A:0.30, C:0.13, G:0.26, T:0.30
Consensus pattern (77 bp):
CGGGGTTGGAGTATCCTGATTGTGAAAAATCAATGTTTTGGGAATAAAATCGGGTTGGAGTATCC
CCTCAGAAATAA
Found at i:1882180 original size:210 final size:209
Alignment explanation
Indices: 1881808--1882199 Score: 448
Period size: 210 Copynumber: 1.9 Consensus size: 209
1881798 ATGTTCTGGA
* * *
1881808 AATAAAATCGGGGTTGGAGTATCCCCTCGAAAATAATAGGGTTGGAGAATCCCTGACTATAGAAA
1 AATAAAATCGGGGTTGGAGTATCCCCTCGAAAATAACAGGGTTGGAGAATCCCTAACTATAAAAA
* * * *
1881873 ATCAGTATTTTGAAAATAAAATCGAGGTTGAAGTATCCCCTCGAAAATAACGGGGTTGTAATATT
66 AACAGTATTTTGAAAATAAAATCGAGGTTGAAGTATCCCCTCGAAAATAACGGGATTGGAATATC
* * ***
1881938 CTCGATTGTGAAAAATCGATGATTTAGAAATAAGGTCGGGGTTGAAGTATCCTTGATTGTGAAAA
131 CTCGATTATGAAAAATCAATGATTTAGAAATAAAACCGGGGTTGAAGTATCCTTGATTGTGAAAA
1882003 ATCAATATTTTGGG
196 ATCAATATTTTGGG
* * * * * * *
1882017 AATAAAGTCGGGTTTGGAGTATCCCCTC-AGAAATGACGGGGTTGGAGTATTCCTAACTGTAAAA
1 AATAAAATCGGGGTTGGAGTATCCCCTCGA-AAATAACAGGGTTGGAGAATCCCTAACTATAAAA
* * ** * * * *
1882081 AAACTGGTGTTTTGGGAATAAAATCTG-GGTTGGAGTATCTCCTCGGAAATAACGGGATTGGAGT
65 AAAC-AGTATTTTGAAAATAAAATC-GAGGTTGAAGTATCCCCTCGAAAATAACGGGATTGGAAT
* * * *
1882145 ATCC-CTGATTATGAAAAATTAATGTTTTTGAAATAAAACCGGGGTTGGAGTATCC
128 ATCCTC-GATTATGAAAAATCAATGATTTAGAAATAAAACCGGGGTTGAAGTATCC
1882200 CCGAGATGAA
Statistics
Matches: 148, Mismatches: 31, Indels: 7
0.80 0.17 0.04
Matches are distributed among these distances:
208 1 0.01
209 56 0.38
210 90 0.61
211 1 0.01
ACGTcount: A:0.33, C:0.12, G:0.25, T:0.29
Consensus pattern (209 bp):
AATAAAATCGGGGTTGGAGTATCCCCTCGAAAATAACAGGGTTGGAGAATCCCTAACTATAAAAA
AACAGTATTTTGAAAATAAAATCGAGGTTGAAGTATCCCCTCGAAAATAACGGGATTGGAATATC
CTCGATTATGAAAAATCAATGATTTAGAAATAAAACCGGGGTTGAAGTATCCTTGATTGTGAAAA
ATCAATATTTTGGG
Found at i:1885193 original size:40 final size:39
Alignment explanation
Indices: 1885149--1885247 Score: 99
Period size: 41 Copynumber: 2.4 Consensus size: 39
1885139 GTCCCACTTT
* * * *
1885149 TTGAGGACAAAGGAAAAGAGAATGAAATGGGTCTTGCTCC
1 TTGAGGACAAAGGAAAAGAAAAGGAAA-GGGTCCTACTCC
* * *
1885189 TTGAGGAGAAAGGAAGAAAGAAAAGGAAAGTGTCCTACTTC
1 TTGAGGACAAAGG-A-AAAGAAAAGGAAAGGGTCCTACTCC
1885230 TTGAGGACAAAGTGAAAA
1 TTGAGGACAAAG-GAAAA
1885248 AGAGTACGTC
Statistics
Matches: 48, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
40 15 0.31
41 21 0.44
42 12 0.25
ACGTcount: A:0.42, C:0.10, G:0.29, T:0.18
Consensus pattern (39 bp):
TTGAGGACAAAGGAAAAGAAAAGGAAAGGGTCCTACTCC
Found at i:1885326 original size:42 final size:42
Alignment explanation
Indices: 1885254--1885620 Score: 322
Period size: 43 Copynumber: 8.5 Consensus size: 42
1885244 AAAAAGAGTA
*
1885254 CGTCCTACT-TTTCGAGGACAAAGGAAAAAAGGAAAATGAAA-TG
1 CGTCCTGCTCTTT-GAGGACAAAGGAAAAAAGG-AAAT-AAAGTG
* *
1885297 CGTCCTGCTCTTTGAGGACAAAAG-AAAAAGGAAAATAAAGTA
1 CGTCCTGCTCTTTGAGGACAAAGGAAAAAAGG-AAATAAAGTG
*
1885339 CGTCCTGCTCTTTGAGGACAAAAGGGGAAAATAAGGAAATGGAACGT-
1 CGTCCTGCTCTTTGAGGAC-AAA--GGAAAA-AAGGAAAT--AAAGTG
*
1885386 -GTCCTGCTCTTTGAGGACAAAGGAGAAAAGGAAAATAAAGTG
1 CGTCCTGCTCTTTGAGGACAAAGGAAAAAAGG-AAATAAAGTG
* * *
1885428 CGTCCTGCTCTTTAAGGACAAGGGGAAAAGAAGGGAATGGAACA-T-
1 CGTCCTGCTCTTTGAGGACAA-AGGAAAA-AAGGAAAT--AA-AGTG
* * *
1885473 -GTCCTACTCTTTGAGGACAAATGAGAAAAGGAAATAGAACGT-
1 CGTCCTGCTCTTTGAGGACAAAGGAAAAAAGGAAATA-AA-GTG
* * * *
1885515 -GTCCTGCTCTTTAAGGATAAAGGAGAAAAGAAAAATAAAGTG
1 CGTCCTGCTCTTTGAGGACAAAGGAAAAAAG-GAAATAAAGTG
*
1885557 TGTCCTGCTCTTTGAGGACAAAAGGGAAAAGAAGGAAATAAAGTG
1 CGTCCTGCTCTTTGAGGAC-AAA-GGAAAA-AAGGAAATAAAGTG
1885602 CGTCCTGCTCTTTGAGGAC
1 CGTCCTGCTCTTTGAGGAC
1885621 TAGGAGGTGC
Statistics
Matches: 271, Mismatches: 27, Indels: 50
0.78 0.08 0.14
Matches are distributed among these distances:
40 2 0.01
41 10 0.04
42 72 0.27
43 74 0.27
44 32 0.12
45 41 0.15
46 31 0.11
47 5 0.02
48 4 0.01
ACGTcount: A:0.39, C:0.14, G:0.26, T:0.20
Consensus pattern (42 bp):
CGTCCTGCTCTTTGAGGACAAAGGAAAAAAGGAAATAAAGTG
Found at i:1885490 original size:87 final size:87
Alignment explanation
Indices: 1885268--1885620 Score: 384
Period size: 87 Copynumber: 4.1 Consensus size: 87
1885258 CTACTTTTCG
* * * * *
1885268 AGGACAA-AGGAAAA-AAGGAAAATGAAATGCGTCCTGCTCTTTGAGGACAAAAGA-AAAAGGAA
1 AGGACAAGGGGAAAAGAAGG-AAATGGAACGTGTCCTGCTCTTTGAGGACAAAGGAGAAAAGGAA
* *
1885330 AATAAAGTACGTCCTGCTCTTTG
65 AATAAAGTGCGTCCTGCTCTTTA
*
1885353 AGGACAAAAGGGGAAAATAAGGAAATGGAACGTGTCCTGCTCTTTGAGGACAAAGGAGAAAAGGA
1 AGGAC--AAGGGGAAAAGAAGGAAATGGAACGTGTCCTGCTCTTTGAGGACAAAGGAGAAAAGGA
1885418 AAATAAAGTGCGTCCTGCTCTTTA
64 AAATAAAGTGCGTCCTGCTCTTTA
* * * *
1885442 AGGACAAGGGGAAAAGAAGGGAATGGAACATGTCCTACTCTTTGAGGACAAATGAGAAAAGG-AA
1 AGGACAAGGGGAAAAGAAGGAAATGGAACGTGTCCTGCTCTTTGAGGACAAAGGAGAAAAGGAAA
1885506 ATAGAACGT--GTCCTGCTCTTTA
66 ATA-AA-GTGCGTCCTGCTCTTTA
* * * *
1885528 AGGATAAAGGAGAAAAGAA--AAAT-AAAGTGTGTCCTGCTCTTTGAGGACAAAAGG-GAAAAGA
1 AGGA-CAAGGGGAAAAGAAGGAAATGGAA-CGTGTCCTGCTCTTTGAGGAC-AAAGGAGAAAAG-
* *
1885589 AGGAAATAAAGTGCGTCCTGCTCTTTG
62 -GAAAATAAAGTGCGTCCTGCTCTTTA
1885616 AGGAC
1 AGGAC
1885621 TAGGAGGTGC
Statistics
Matches: 231, Mismatches: 22, Indels: 28
0.82 0.08 0.10
Matches are distributed among these distances:
84 2 0.01
85 32 0.14
86 28 0.12
87 71 0.31
88 60 0.26
89 38 0.16
ACGTcount: A:0.41, C:0.13, G:0.27, T:0.19
Consensus pattern (87 bp):
AGGACAAGGGGAAAAGAAGGAAATGGAACGTGTCCTGCTCTTTGAGGACAAAGGAGAAAAGGAAA
ATAAAGTGCGTCCTGCTCTTTA
Found at i:1885544 original size:129 final size:132
Alignment explanation
Indices: 1885268--1885620 Score: 418
Period size: 129 Copynumber: 2.7 Consensus size: 132
1885258 CTACTTTTCG
* **
1885268 AGGACAAAGGAAAAAAGGAAAATGAAA-TGCGTCCTGCTCTTTGAGGACAAAAG-AAA-AAGGAA
1 AGGACAAAGGAGAAAAGGAAAAT-AAAGTGCGTCCTGCTCTTTGAGGACAAGGGAAAAGAAGGAA
* * *
1885330 AATAAAGTACGTCCTGCTCTTTGAGGACAAAAGGGGAAAATAAGGAAATGGAACGTGTCCTGCTC
65 AATAAAGCACGTCCTACTCTTTGAGGACAAAA-GGGAAAATAAGGAAATAGAACGTGTCCTGCTC
*
1885395 TTTG
129 TTTA
* *
1885399 AGGACAAAGGAGAAAAGGAAAATAAAGTGCGTCCTGCTCTTTAAGGACAAGGGGAAAAGAAGG-G
1 AGGACAAAGGAGAAAAGGAAAATAAAGTGCGTCCTGCTCTTTGAGGACAA-GGGAAAAGAAGGAA
* * * *
1885463 AATGGAA-CATGTCCTACTCTTTGAGGAC-AAA-TGAGAA-AAGGAAATAGAACGTGTCCTGCTC
65 AAT-AAAGCACGTCCTACTCTTTGAGGACAAAAGGGAAAATAAGGAAATAGAACGTGTCCTGCTC
1885524 TTTA
129 TTTA
* * *
1885528 AGGATAAAGGAGAAAAGAAAAATAAAGTGTGTCCTGCTCTTTGAGGACAAAAGGGAAAAGAAGG-
1 AGGACAAAGGAGAAAAGGAAAATAAAGTGCGTCCTGCTCTTTGAGGAC--AAGGGAAAAGAAGGA
** *
1885592 AAATAAAGTGCGTCCTGCTCTTTGAGGAC
64 AAATAAAGCACGTCCTACTCTTTGAGGAC
1885621 TAGGAGGTGC
Statistics
Matches: 191, Mismatches: 23, Indels: 17
0.83 0.10 0.07
Matches are distributed among these distances:
129 72 0.38
130 39 0.20
131 46 0.24
132 4 0.02
133 24 0.13
134 6 0.03
ACGTcount: A:0.41, C:0.13, G:0.27, T:0.19
Consensus pattern (132 bp):
AGGACAAAGGAGAAAAGGAAAATAAAGTGCGTCCTGCTCTTTGAGGACAAGGGAAAAGAAGGAAA
ATAAAGCACGTCCTACTCTTTGAGGACAAAAGGGAAAATAAGGAAATAGAACGTGTCCTGCTCTT
TA
Found at i:1885748 original size:105 final size:105
Alignment explanation
Indices: 1885559--1885785 Score: 400
Period size: 105 Copynumber: 2.2 Consensus size: 105
1885549 ATAAAGTGTG
1885559 TCCTGCTCTTTGAGGACAAAAGGGAAAAGAAGGAAATAAAGTGCGTCCTGCTCTTTGAGGACTAG
1 TCCTGCTCTTTGAGGACAAAAGGGAAAAGAAGGAAATAAAGTGCGTCCTGCTCTTTGAGGACTAG
* * *
1885624 GAGGTGCCACCAGCTTGTGTGGGCTTTGAAGGAGAAGGCA
66 GAGGTGCCACCAACCTGTGTGGGCTTTAAAGGAGAAGGCA
*
1885664 TCCTGCTCTTTGAGGACAAAAGGGAAAAGAAGGAAATGAAGTGCGTCCTGCTCTTTGAGGACTAG
1 TCCTGCTCTTTGAGGACAAAAGGGAAAAGAAGGAAATAAAGTGCGTCCTGCTCTTTGAGGACTAG
*
1885729 GAGGTGCCACCAACCTGTGTGGGCTTTAAAGGAGAAGGCG
66 GAGGTGCCACCAACCTGTGTGGGCTTTAAAGGAGAAGGCA
*
1885769 TCCTGCTCCTTGAGGAC
1 TCCTGCTCTTTGAGGAC
1885786 TAGAAGGTGC
Statistics
Matches: 116, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
105 116 1.00
ACGTcount: A:0.27, C:0.19, G:0.32, T:0.22
Consensus pattern (105 bp):
TCCTGCTCTTTGAGGACAAAAGGGAAAAGAAGGAAATAAAGTGCGTCCTGCTCTTTGAGGACTAG
GAGGTGCCACCAACCTGTGTGGGCTTTAAAGGAGAAGGCA
Found at i:1885799 original size:60 final size:60
Alignment explanation
Indices: 1885701--1885845 Score: 218
Period size: 60 Copynumber: 2.4 Consensus size: 60
1885691 AGAAGGAAAT
*
1885701 GAAGTGCGTCCTGCTCTTTGAGGACTAGGAGGTGCCACCAACCTGTGTGGGCTTTAAAGGA
1 GAAG-GCGTCCTGCTCTTTGAGGACTAGAAGGTGCCACCAACCTGTGTGGGCTTTAAAGGA
* ** * *
1885762 GAAGGCGTCCTGCTCCTTGAGGACTAGAAGGTGCCACCGGCTTGTGTGGGCTTTGAAGGA
1 GAAGGCGTCCTGCTCTTTGAGGACTAGAAGGTGCCACCAACCTGTGTGGGCTTTAAAGGA
*
1885822 GAAAGCGTCCTGCTCTTTGAGGAC
1 GAAGGCGTCCTGCTCTTTGAGGAC
1885846 AAAAGGAAAA
Statistics
Matches: 76, Mismatches: 8, Indels: 1
0.89 0.09 0.01
Matches are distributed among these distances:
60 72 0.95
61 4 0.05
ACGTcount: A:0.20, C:0.22, G:0.34, T:0.24
Consensus pattern (60 bp):
GAAGGCGTCCTGCTCTTTGAGGACTAGAAGGTGCCACCAACCTGTGTGGGCTTTAAAGGA
Found at i:1886032 original size:94 final size:94
Alignment explanation
Indices: 1885871--1886059 Score: 333
Period size: 94 Copynumber: 2.0 Consensus size: 94
1885861 GAAATGAAGT
1885871 GCGTCATGCTCTTTAAGGACTAAAGGGCAAAAGGAGAGAGCGTCCTGCTCTTTGAGGACTGGGAA
1 GCGTCATGCTCTTTAAGGACTAAAGGGCAAAAGGAGAGAGCGTCCTGCTCTTTGAGGACTGGGAA
1885936 GTGCCACCAACTTGTGTGGGCTTTAAAAG
66 GTGCCACCAACTTGTGTGGGCTTTAAAAG
* * * *
1885965 GCGTCCTGCTCTTTAAGGACTAAAGGGCGAAAGGAGAGAGCGTCTTGCTCTTTGAGGATTGGGAA
1 GCGTCATGCTCTTTAAGGACTAAAGGGCAAAAGGAGAGAGCGTCCTGCTCTTTGAGGACTGGGAA
*
1886030 GTGCCACCAACTTGTGTGGGCTTTTAAAG
66 GTGCCACCAACTTGTGTGGGCTTTAAAAG
1886059 G
1 G
1886060 AGTAGGCGTC
Statistics
Matches: 90, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
94 90 1.00
ACGTcount: A:0.25, C:0.19, G:0.32, T:0.25
Consensus pattern (94 bp):
GCGTCATGCTCTTTAAGGACTAAAGGGCAAAAGGAGAGAGCGTCCTGCTCTTTGAGGACTGGGAA
GTGCCACCAACTTGTGTGGGCTTTAAAAG
Found at i:1886093 original size:61 final size:62
Alignment explanation
Indices: 1886010--1887154 Score: 1258
Period size: 61 Copynumber: 18.9 Consensus size: 62
1886000 GAGAGCGTCT
* * * * ** * *
1886010 TGCTCTTTGAGGATTGGGAA-GTGCCACCAACTTGTGTGGGCTTT-TAAAGGAGTAGGCGTCT
1 TGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGGTGTCC
1886071 TGCTCTTTGAGGACTGGAAA-GTGCCACCAACTTGTGTGGGCTTT---AAG----AGGTGTCC
1 TGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGGTGTCC
* * ** * * * **
1886126 TACTCTTTGAGGATTGGGAGGTGCCAGCAACTTGTGTGGGCTTTG--AAGGAGAAGGCATCC
1 TGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGGTGTCC
* * *
1886186 TGCTCTTTGAGGACT-AGAAGGTGCCAACAACTTGTGTGGGCTTTGTAAAGAAAAAAGTGTCC
1 TGCTCTTTGAGGACTGA-AAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGGTGTCC
* * * * *
1886248 TGCTCTTTGAGGACTAGAAATGTGCCACCAACTTGTGTGGGC-ATCAAAAGGAAAAGGTGTCT
1 TGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGGTGTCC
* *
1886310 TGCTCTTTGAGGACT-AAAGGGTGCCACTAGCTTGTGTGGGCTTTGAAAAGAAAAAGGTGTCC
1 TGCTCTTTGAGGACTGAAA-GGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGGTGTCC
* *
1886372 TGCTCTTTGAGGACT-AAAGGTGCCACCAACTCGTGTGGGCTTTAAAAAGAAAAAGGTGTCC
1 TGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGGTGTCC
* * * * * *
1886433 TACTCTTTGAGGACT-AAATGTGCCACCAACTCGTGTGGGCTTTAAAAAGAAAAAAGTATCC
1 TGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGGTGTCC
**
1886494 TGCTCTTTGAGGACT-AAAGGTGCCACCAACTCATGTGGGCTTTGAAAAGAAAAAGGTGTCC
1 TGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGGTGTCC
* ** **
1886555 TGCTCTTTGAGGACT-AAAAGTGCCACCAACTCATGTGGGCTTTGAAAAGAAAAAGGCATCC
1 TGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGGTGTCC
* * * * *
1886616 TGCTCTTTGTGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGGACAAGGCGTCC
1 TGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGGTGTCC
* * *
1886678 TGCTCTTTGAGGACTAGAAA-GTGCCACCAACTTGTATGGGCTTT-------AAAAGGCGTCA
1 TGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGGTGTCC
** *
1886733 TGCTCTTTGAGGACTGGGAGGTGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAAGGTGTCC
1 TGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGGTGTCC
* * * * **
1886795 TACTCTTTAAAGACT-AAAGGTGCCACCAACTCGTGT-GGCTTTGAAAAGAAAAAGGCATCC
1 TGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGGTGTCC
* * * * *
1886855 TGCTCTTTGAGTACTAAAAGGTGCCACCAACTTGTGTGGGCTTTG--AAGGAGAAGGCGTCC
1 TGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGGTGTCC
* * * * * *
1886915 TACTTTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAAGATATCC
1 TGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGGTGTCC
* * * **
1886977 TGCTCTTTAAGGACTGGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAAGACGTCC
1 TGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGGTGTCC
* *
1887039 TGCTCTTTAAGGACT-AAAGGGTGCCACCAACTTGTGTGGGCTTT-AAAAGGAAAAGGTGTCC
1 TGCTCTTTGAGGACTGAAA-GGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGGTGTCC
** * *
1887100 TGCTCTTTGAGGACTGAAAAATGCCACCAACTTGTGTAGACTTTGAAAAAGAAAA
1 TGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTG-AAAAGAAAA
1887155 TGATGCCACT
Statistics
Matches: 940, Mismatches: 113, Indels: 60
0.84 0.10 0.05
Matches are distributed among these distances:
54 4 0.00
55 89 0.09
56 3 0.00
59 3 0.00
60 133 0.14
61 373 0.40
62 301 0.32
63 33 0.04
64 1 0.00
ACGTcount: A:0.28, C:0.19, G:0.27, T:0.26
Consensus pattern (62 bp):
TGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGGTGTCC
Found at i:1888200 original size:12 final size:11
Alignment explanation
Indices: 1888170--1888208 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
1888160 TCTCACCAAG
1888170 GTTTTTTGTTT
1 GTTTTTTGTTT
*
1888181 TTTTTTTGTTT
1 GTTTTTTGTTT
1888192 GTTTGTTTGTTT
1 GTTT-TTTGTTT
1888204 -TTTTT
1 GTTTTT
1888209 AGAAGAGAAC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
10 2 0.08
11 16 0.64
12 7 0.28
ACGTcount: A:0.00, C:0.00, G:0.15, T:0.85
Consensus pattern (11 bp):
GTTTTTTGTTT
Found at i:1893550 original size:79 final size:79
Alignment explanation
Indices: 1893344--1893551 Score: 237
Period size: 79 Copynumber: 2.6 Consensus size: 79
1893334 TGGAGATAAC
* * * * * * *
1893344 AACGGGGCTGGAGTATCCCCGATTATGGAAAATTGATG-TTCTGGAAATAAAATCGGGGTTGGAG
1 AACGGGGTTGAAGTATCCTCGATTATGAAAAATCGATGATT-TAGAAATAAAATCAGGGTTGGAG
1893408 TATCCCCTCAAAAAT
65 TATCCCCTCAAAAAT
* *
1893423 AACAGGGTT-AGAGTAT-CTCTGATTAT-AGAAAATCGAT-ATTTTGAAAATAAAATCAGGGTTG
1 AACGGGGTTGA-AGTATCCTC-GATTATGA-AAAATCGATGATTTAG-AAATAAAATCAGGGTTG
*
1893484 GAGTATCTCCTCAAAAAT
62 GAGTATCCCCTCAAAAAT
*
1893502 AACGGGGTTGAAGTATCCTCGATTGTGAAAAATCGATGATTTAGAAATAA
1 AACGGGGTTGAAGTATCCTCGATTATGAAAAATCGATGATTTAGAAATAA
1893552 GGCCGGGATT
Statistics
Matches: 108, Mismatches: 12, Indels: 18
0.78 0.09 0.13
Matches are distributed among these distances:
78 4 0.04
79 94 0.87
80 10 0.09
ACGTcount: A:0.36, C:0.13, G:0.23, T:0.28
Consensus pattern (79 bp):
AACGGGGTTGAAGTATCCTCGATTATGAAAAATCGATGATTTAGAAATAAAATCAGGGTTGGAGT
ATCCCCTCAAAAAT
Found at i:1893576 original size:51 final size:51
Alignment explanation
Indices: 1893504--1893623 Score: 179
Period size: 51 Copynumber: 2.4 Consensus size: 51
1893494 TCAAAAATAA
* * *
1893504 CGGGGTTGAAGTATCCTCGATTGTGAAAAATCGATGA-TTTAGAAATAAGGC
1 CGGGGTTGAAGTATCCCCGATTGTGAAAAATCAAT-ATTTTAGAAATAAAGC
* *
1893555 CGGGATTGAAGTATCCCCGATTGTGAAAAATTAATATTTTAGAAATAAAGC
1 CGGGGTTGAAGTATCCCCGATTGTGAAAAATCAATATTTTAGAAATAAAGC
1893606 CGGGGTTGAAGTATCCCC
1 CGGGGTTGAAGTATCCCC
1893624 TCGGAAATGA
Statistics
Matches: 62, Mismatches: 6, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
50 1 0.02
51 61 0.98
ACGTcount: A:0.33, C:0.14, G:0.25, T:0.28
Consensus pattern (51 bp):
CGGGGTTGAAGTATCCCCGATTGTGAAAAATCAATATTTTAGAAATAAAGC
Found at i:1893702 original size:80 final size:79
Alignment explanation
Indices: 1893555--1893782 Score: 294
Period size: 80 Copynumber: 2.9 Consensus size: 79
1893545 GAAATAAGGC
* * * * *
1893555 CGGGATTGAAGTATCCCCGATTGTGAAAAATTAATATTTTAGAAATAAAGCCGGGGTTGAAGTAT
1 CGGGATTGGAGTATCCCCGATTGTGAAAAATTAATGTTTTGGAAATAAAACCGGGGTTGGAGTAT
*
1893620 CCCCTCGGAAATGA
66 CCCCTCGGAAATAA
** * * * *
1893634 CGGGATTGGAGTATCCCTAATTGTGAAAAAACTAGTGTTTTGGGAATAAAATCGGGGTTGGAGTA
1 CGGGATTGGAGTATCCCCGATTGTG-AAAAATTAATGTTTTGGAAATAAAACCGGGGTTGGAGTA
1893699 TCCCCTCGGAAATAA
65 TCCCCTCGGAAATAA
* * * * *
1893714 CGAGATTAGAGTATCCCCGATTATGAAAAATTAATGTTTTGGAAATAAAACCGAGGTTAGAGTAT
1 CGGGATTGGAGTATCCCCGATTGTGAAAAATTAATGTTTTGGAAATAAAACCGGGGTTGGAGTAT
1893779 CCCC
66 CCCC
1893783 GAGATGAAGA
Statistics
Matches: 125, Mismatches: 23, Indels: 2
0.83 0.15 0.01
Matches are distributed among these distances:
79 60 0.48
80 65 0.52
ACGTcount: A:0.34, C:0.15, G:0.24, T:0.27
Consensus pattern (79 bp):
CGGGATTGGAGTATCCCCGATTGTGAAAAATTAATGTTTTGGAAATAAAACCGGGGTTGGAGTAT
CCCCTCGGAAATAA
Found at i:1893780 original size:210 final size:207
Alignment explanation
Indices: 1893318--1893784 Score: 463
Period size: 210 Copynumber: 2.2 Consensus size: 207
1893308 ATCTCCCGAC
* * * * * * *
1893318 GAAAAATTTAATATTTTGGAGATAACAACGGGGCTGGAGTATCCCCGATTATGGAAAATTGATGT
1 GAAAAA-TTAATGTTTTGGAAATAA-AACCGGG-TTGAGTATCCCCGATTATGAAAAATTAATAT
* * * * *
1893383 TCTGGAAATAAAATCGGGGTTGGAGTATCCCCTCAAAAATAACAGGGTTAGAGTATCTCTGATTA
63 TCTAGAAATAAAACCGGGGTTGAAGTATCCCCTCAAAAATAACAGGGTTAGAGTATCCCTAATTA
* * * * *
1893448 TAGAAAATCGATATTTTGAAAATAAAATCAGGGTTGGAGTATCTCCTCAAAAATAACGGGGTTGA
128 TAAAAAATAGATATTTTGAAAATAAAATCAGGGTTGGAGTATCCCCTCAAAAATAACGAGATTGA
* *
1893513 AGTATCCTCGATTGT
193 AGTATCCCCGATTAT
** * * ** *
1893528 GAAAAATCGATGATTTAGAAATAAGGCCGGGATTGAAGTATCCCCGATTGTGAAAAATTAATATT
1 GAAAAATTAATGTTTTGGAAATAAAACCGGG-TTG-AGTATCCCCGATTATGAAAAATTAATATT
* * ** * * *
1893593 TTAGAAATAAAGCCGGGGTTGAAGTATCCCCTCGGAAATGAC-GGGATTGGAGTATCCCTAATTG
64 CTAGAAATAAAACCGGGGTTGAAGTATCCCCTCAAAAATAACAGGG-TTAGAGTATCCCTAATTA
* ** * **
1893657 TGAAAAAACTAG-TGTTTTGGGAATAAAATCGGGGTTGGAGTATCCCCTCGGAAATAACGAGATT
128 T-AAAAAA-TAGATATTTTGAAAATAAAATCAGGGTTGGAGTATCCCCTCAAAAATAACGAGATT
1893721 -AGAGTATCCCCGATTAT
191 GA-AGTATCCCCGATTAT
1893738 GAAAAATTAATGTTTTGGAAATAAAACCGAGGTTAGAGTATCCCCGA
1 GAAAAATTAATGTTTTGGAAATAAAACCG-GGTT-GAGTATCCCCGA
1893785 GATGAAGAAT
Statistics
Matches: 204, Mismatches: 46, Indels: 14
0.77 0.17 0.05
Matches are distributed among these distances:
208 9 0.04
209 87 0.43
210 103 0.50
211 5 0.02
ACGTcount: A:0.35, C:0.13, G:0.24, T:0.28
Consensus pattern (207 bp):
GAAAAATTAATGTTTTGGAAATAAAACCGGGTTGAGTATCCCCGATTATGAAAAATTAATATTCT
AGAAATAAAACCGGGGTTGAAGTATCCCCTCAAAAATAACAGGGTTAGAGTATCCCTAATTATAA
AAAATAGATATTTTGAAAATAAAATCAGGGTTGGAGTATCCCCTCAAAAATAACGAGATTGAAGT
ATCCCCGATTAT
Found at i:1896065 original size:20 final size:20
Alignment explanation
Indices: 1896040--1896095 Score: 112
Period size: 20 Copynumber: 2.8 Consensus size: 20
1896030 ATGTATCGAT
1896040 ACAATGTATCGATACAATGA
1 ACAATGTATCGATACAATGA
1896060 ACAATGTATCGATACAATGA
1 ACAATGTATCGATACAATGA
1896080 ACAATGTATCGATACA
1 ACAATGTATCGATACA
1896096 TCTAGGTAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.45, C:0.16, G:0.14, T:0.25
Consensus pattern (20 bp):
ACAATGTATCGATACAATGA
Found at i:1896078 original size:13 final size:13
Alignment explanation
Indices: 1896029--1896058 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
1896019 AAAATACCTG
1896029 AATGTATCGATAC
1 AATGTATCGATAC
1896042 AATGTATCGATAC
1 AATGTATCGATAC
1896055 AATG
1 AATG
1896059 AACAATGTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.40, C:0.13, G:0.17, T:0.30
Consensus pattern (13 bp):
AATGTATCGATAC
Found at i:1898649 original size:23 final size:20
Alignment explanation
Indices: 1898618--1898674 Score: 71
Period size: 23 Copynumber: 2.7 Consensus size: 20
1898608 CTACCACTGT
1898618 TTGTATCGATACA-AATCGATA
1 TTGTATCGATACATAA-CGA-A
1898639 TAATGTATCGATACATAACGAA
1 T--TGTATCGATACATAACGAA
1898661 TTGTATCGATACAT
1 TTGTATCGATACAT
1898675 TATCCCAAAC
Statistics
Matches: 33, Mismatches: 0, Indels: 7
0.82 0.00 0.17
Matches are distributed among these distances:
20 13 0.39
21 1 0.03
22 2 0.06
23 15 0.45
24 2 0.06
ACGTcount: A:0.39, C:0.14, G:0.14, T:0.33
Consensus pattern (20 bp):
TTGTATCGATACATAACGAA
Found at i:1901379 original size:22 final size:20
Alignment explanation
Indices: 1901334--1901379 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
1901324 ACTTTAGGAC
* *
1901334 TTTTATGTTATTTTATGCTT
1 TTTTATATTATTTTATACTT
1901354 TTTTATATTATTTTAGTTACTT
1 TTTTATATTATTTTA--TACTT
1901376 TTTT
1 TTTT
1901380 TAAGTATAGA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 14 0.64
22 8 0.36
ACGTcount: A:0.17, C:0.04, G:0.07, T:0.72
Consensus pattern (20 bp):
TTTTATATTATTTTATACTT
Found at i:1901524 original size:57 final size:58
Alignment explanation
Indices: 1901440--1901599 Score: 141
Period size: 57 Copynumber: 2.8 Consensus size: 58
1901430 CCATAATTTG
* * * * *
1901440 GGATCATTTATGC-ATTCTTATTTATTTTAGGGTCATT-TTATAATTTGTCATGAGTT-A
1 GGATCATTTATGCAATT-TCA-TGATTTTAAGGTCATTCTAATAATTTGCCATGAGTTAA
* **
1901497 GGATCATTTATGCAATTTCATAGATTTTAAGGTCATTCTAATTATTTGCCATGTTTTAA
1 GGATCATTTATGCAATTTCAT-GATTTTAAGGTCATTCTAATAATTTGCCATGAGTTAA
* * * * *
1901556 GGAT-TTTTATGTAATTTCATGATTTTGAGATCATT-TAGTAATTT
1 GGATCATTTATGCAATTTCATGATTTTAAGGTCATTCTAATAATTT
1901600 ACTTGCATTT
Statistics
Matches: 85, Mismatches: 14, Indels: 9
0.79 0.13 0.08
Matches are distributed among these distances:
56 8 0.09
57 41 0.48
58 31 0.36
59 5 0.06
ACGTcount: A:0.27, C:0.09, G:0.15, T:0.49
Consensus pattern (58 bp):
GGATCATTTATGCAATTTCATGATTTTAAGGTCATTCTAATAATTTGCCATGAGTTAA
Found at i:1902858 original size:15 final size:15
Alignment explanation
Indices: 1902835--1902864 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1902825 AGTACTTCCT
*
1902835 ATTTCCTAGTTACTA
1 ATTTACTAGTTACTA
1902850 ATTTACTAGTTACTA
1 ATTTACTAGTTACTA
1902865 CTAATAACAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.30, C:0.17, G:0.07, T:0.47
Consensus pattern (15 bp):
ATTTACTAGTTACTA
Found at i:1905121 original size:15 final size:14
Alignment explanation
Indices: 1905098--1905215 Score: 61
Period size: 15 Copynumber: 8.3 Consensus size: 14
1905088 ATGACTTAAA
1905098 ATTATATTAAATAT
1 ATTATATTAAATAT
1905112 ATTAATATTAAAATTAT
1 ATT-ATATT-AAA-TAT
1905129 ATTATA-T-AATAT
1 ATTATATTAAATAT
*
1905141 A-T-T-TTAAATAA
1 ATTATATTAAATAT
* *
1905152 ATTATAATACATTAT
1 ATTATATTA-AATAT
1905167 ATT-TA-TAAATAAT
1 ATTATATTAAAT-AT
*
1905180 ATAATAATTAAATAT
1 ATTAT-ATTAAATAT
*
1905195 TTTATATCTGATAATAT
1 ATTATAT-T-A-AATAT
1905212 ATTA
1 ATTA
1905216 AAAATAATAT
Statistics
Matches: 79, Mismatches: 9, Indels: 29
0.68 0.08 0.25
Matches are distributed among these distances:
10 2 0.03
11 6 0.08
12 7 0.09
13 9 0.11
14 10 0.13
15 19 0.24
16 12 0.15
17 14 0.18
ACGTcount: A:0.50, C:0.02, G:0.01, T:0.47
Consensus pattern (14 bp):
ATTATATTAAATAT
Found at i:1905168 original size:28 final size:27
Alignment explanation
Indices: 1905122--1905198 Score: 79
Period size: 28 Copynumber: 2.9 Consensus size: 27
1905112 ATTAATATTA
* *
1905122 AAATTATATTATATAATATATTTTAAAT
1 AAATTATAATA-ATTATATATTTTAAAT
*
1905150 AAATTATAATACATTATAT-TTATAAAT
1 AAATTATAATA-ATTATATATTTTAAAT
*
1905177 -AA-TATAATAATTAAATATTTTA
1 AAATTATAATAATTATATATTTTA
1905199 TATCTGATAA
Statistics
Matches: 42, Mismatches: 6, Indels: 5
0.79 0.11 0.09
Matches are distributed among these distances:
24 6 0.14
25 11 0.26
26 2 0.05
27 7 0.17
28 16 0.38
ACGTcount: A:0.52, C:0.01, G:0.00, T:0.47
Consensus pattern (27 bp):
AAATTATAATAATTATATATTTTAAAT
Found at i:1905182 original size:25 final size:25
Alignment explanation
Indices: 1905129--1905198 Score: 76
Period size: 26 Copynumber: 2.8 Consensus size: 25
1905119 TTAAAATTAT
1905129 ATTAT-ATAA-TATATTTTAAATAA
1 ATTATAATAATTATATTTTAAATAA
1905152 ATTATAATACATTATATTTATAAAT-A
1 ATTATAATA-ATTATATTT-TAAATAA
1905178 A-TATAATAATTAAATATTTTA
1 ATTATAATAATT--ATATTTTA
1905199 TATCTGATAA
Statistics
Matches: 41, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
23 5 0.12
24 6 0.15
25 10 0.24
26 15 0.37
27 5 0.12
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.47
Consensus pattern (25 bp):
ATTATAATAATTATATTTTAAATAA
Found at i:1906887 original size:22 final size:23
Alignment explanation
Indices: 1906846--1906892 Score: 55
Period size: 22 Copynumber: 2.1 Consensus size: 23
1906836 AGATGTAATT
1906846 AAAATATTAAATTTTTATAT-TA
1 AAAATATTAAATTTTTATATATA
1906868 AAAATA-T-AATTATTTAATATATA
1 AAAATATTAAATT-TTT-ATATATA
1906891 AA
1 AA
1906893 TATGTTTTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
20 4 0.18
21 4 0.18
22 10 0.45
23 4 0.18
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (23 bp):
AAAATATTAAATTTTTATATATA
Found at i:1913182 original size:20 final size:20
Alignment explanation
Indices: 1913141--1913180 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
1913131 CATAATTTAC
*
1913141 ATAAAAATATATTATAATAA
1 ATAAAAATATAATATAATAA
*
1913161 ATAAAAATTTAATAT-ATAA
1 ATAAAAATATAATATAATAA
1913180 A
1 A
1913181 ATTACGTGTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 5 0.28
20 13 0.72
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (20 bp):
ATAAAAATATAATATAATAA
Found at i:1914427 original size:20 final size:19
Alignment explanation
Indices: 1914386--1914429 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
1914376 TAAATAAAAT
* *
1914386 ATAAAAAAATTTAATTTTA
1 ATAAAAAAATTTAACTTGA
*
1914405 ATAAAAAAATTATCACTTGA
1 ATAAAAAAATT-TAACTTGA
1914425 ATAAA
1 ATAAA
1914430 CTTTTTAACA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 11 0.52
20 10 0.48
ACGTcount: A:0.59, C:0.05, G:0.02, T:0.34
Consensus pattern (19 bp):
ATAAAAAAATTTAACTTGA
Found at i:1915367 original size:7 final size:7
Alignment explanation
Indices: 1915343--1915378 Score: 54
Period size: 7 Copynumber: 4.9 Consensus size: 7
1915333 ATCATTAATT
1915343 TTAAAATA
1 TTAAAA-A
1915351 TTATAAAA
1 TTA-AAAA
1915359 TTAAAAA
1 TTAAAAA
1915366 TTAAAAA
1 TTAAAAA
1915373 TTAAAA
1 TTAAAA
1915379 GTTTTATGAT
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
7 17 0.63
8 7 0.26
9 3 0.11
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (7 bp):
TTAAAAA
Found at i:1915625 original size:15 final size:16
Alignment explanation
Indices: 1915604--1915654 Score: 61
Period size: 15 Copynumber: 3.2 Consensus size: 16
1915594 TAAATATTAT
*
1915604 TTTTAAAATAATACTA
1 TTTTAAAATAATAATA
*
1915620 -TTTAAAATATTAATA
1 TTTTAAAATAATAATA
1915635 TTTTAAAATGAATAAT-
1 TTTTAAAAT-AATAATA
1915651 TTTT
1 TTTT
1915655 GATAATTAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
15 13 0.43
16 12 0.40
17 5 0.17
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (16 bp):
TTTTAAAATAATAATA
Found at i:1915999 original size:9 final size:10
Alignment explanation
Indices: 1915985--1916016 Score: 50
Period size: 9 Copynumber: 3.4 Consensus size: 10
1915975 TAGTATATCA
1915985 TTTTAAAT-T
1 TTTTAAATAT
1915994 TTTT-AATAT
1 TTTTAAATAT
1916003 TTTTAAATAT
1 TTTTAAATAT
1916013 TTTT
1 TTTT
1916017 GTATATATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
8 3 0.14
9 9 0.43
10 9 0.43
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (10 bp):
TTTTAAATAT
Found at i:1916022 original size:20 final size:21
Alignment explanation
Indices: 1915969--1916024 Score: 64
Period size: 18 Copynumber: 2.8 Consensus size: 21
1915959 TGGTATTGAT
*
1915969 ATATTTTAGTATATCATTTTAA
1 ATATTTTTGTATAT-ATTTTAA
*
1915991 AT-TTTTT-AATAT-TTTTAA
1 ATATTTTTGTATATATTTTAA
1916009 ATATTTTTGTATATAT
1 ATATTTTTGTATATAT
1916025 ATATATATAT
Statistics
Matches: 28, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
18 8 0.29
19 5 0.18
20 8 0.29
21 5 0.18
22 2 0.07
ACGTcount: A:0.34, C:0.02, G:0.04, T:0.61
Consensus pattern (21 bp):
ATATTTTTGTATATATTTTAA
Found at i:1918821 original size:13 final size:13
Alignment explanation
Indices: 1918803--1918843 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
1918793 AATAAAAAAT
*
1918803 AATTTAATATTTA
1 AATTTAATATATA
1918816 AATTTAAT-TATA
1 AATTTAATATATA
1918828 AATATTAATATA-A
1 AAT-TTAATATATA
1918841 AAT
1 AAT
1918844 ATTTTTAATA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
12 6 0.24
13 17 0.68
14 2 0.08
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (13 bp):
AATTTAATATATA
Found at i:1919115 original size:28 final size:29
Alignment explanation
Indices: 1919077--1919131 Score: 76
Period size: 28 Copynumber: 1.9 Consensus size: 29
1919067 TATGACCCAA
*
1919077 TTTTATAAAAATAGTATATTAAATATTAT
1 TTTTATAAAAATAATATATTAAATATTAT
* *
1919106 TTTTA-AAAAATAATATTTTAATTATT
1 TTTTATAAAAATAATATATTAAATATT
1919132 TTTAATCAGC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 18 0.78
29 5 0.22
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (29 bp):
TTTTATAAAAATAATATATTAAATATTAT
Found at i:1919215 original size:2 final size:2
Alignment explanation
Indices: 1919208--1919240 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1919198 GGTAAACGAA
1919208 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1919241 AATAAATGCA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1919625 original size:3 final size:3
Alignment explanation
Indices: 1919617--1919641 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
1919607 AGAAAAATGA
1919617 ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT A
1919642 ATTAATTAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:1920122 original size:2 final size:2
Alignment explanation
Indices: 1920115--1920139 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1920105 AAATTTAAAC
1920115 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
1920140 CACATACTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1920767 original size:5 final size:5
Alignment explanation
Indices: 1920757--1920834 Score: 56
Period size: 5 Copynumber: 15.2 Consensus size: 5
1920747 TTAATTTTTA
*
1920757 TATAT TATATT TAATAT TA-AT T-T-T TTTAT T-TAT TAATAT TATAT
1 TATAT TATA-T T-ATAT TATAT TATAT TATAT TATAT T-ATAT TATAT
*
1920801 TATAT TATAAT TATTTT TATAT TATATT TATAT T
1 TATAT TAT-AT TA-TAT TATAT TATA-T TATAT T
1920835 TTATAATTAA
Statistics
Matches: 61, Mismatches: 2, Indels: 20
0.73 0.02 0.24
Matches are distributed among these distances:
3 2 0.03
4 8 0.13
5 27 0.44
6 20 0.33
7 4 0.07
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (5 bp):
TATAT
Found at i:1920796 original size:34 final size:36
Alignment explanation
Indices: 1920737--1920834 Score: 111
Period size: 34 Copynumber: 2.8 Consensus size: 36
1920727 CAGACATGAT
1920737 TTAATTTTTTTTAATTT-TTATATATTATATT-TAATA
1 TTAA-TTTTTTT-ATTTATTATATATTATATTATAATA
*
1920773 TTAATTTTTTTATTTATTA-ATATTATATTATATTA
1 TTAATTTTTTTATTTATTATATATTATATTATAATA
1920808 -TAATTATTTTTA--TATTATAT-TTATATT
1 TTAATT-TTTTTATTTATTATATATTATATT
1920835 TTATAATTAA
Statistics
Matches: 57, Mismatches: 1, Indels: 11
0.83 0.01 0.16
Matches are distributed among these distances:
33 12 0.21
34 21 0.37
35 20 0.35
36 4 0.07
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (36 bp):
TTAATTTTTTTATTTATTATATATTATATTATAATA
Found at i:1920836 original size:19 final size:21
Alignment explanation
Indices: 1920746--1920830 Score: 74
Period size: 22 Copynumber: 4.2 Consensus size: 21
1920736 TTTAATTTTT
*
1920746 TTTAATT-TTTATATATTATA
1 TTTAATTATTTTTATATTATA
1920766 TTTAA-TATTAATTT-T-TT-TA
1 TTTAATTATT--TTTATATTATA
* *
1920785 TTT-ATTAATATTATATTATA
1 TTTAATTATTTTTATATTATA
1920805 TTATAATTATTTTTATATTATA
1 TT-TAATTATTTTTATATTATA
1920827 TTTA
1 TTTA
1920831 TATTTTATAA
Statistics
Matches: 51, Mismatches: 5, Indels: 17
0.70 0.07 0.23
Matches are distributed among these distances:
17 2 0.04
18 2 0.04
19 11 0.22
20 13 0.25
21 4 0.08
22 19 0.37
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (21 bp):
TTTAATTATTTTTATATTATA
Found at i:1922264 original size:54 final size:54
Alignment explanation
Indices: 1922196--1922340 Score: 254
Period size: 54 Copynumber: 2.7 Consensus size: 54
1922186 AATTGGGTTG
* * *
1922196 TTTTTAATTATTTAATTTGTAGCCAAGTGATTCTTATTTGGGTTTTTAATTTACC
1 TTTTTTATT-TTTAACTTGTAGTCAAGTGATTCTTATTTGGGTTTTTAATTTACC
1922251 TTTTTTATTTTTAACTTGTAGTCAAGTGATTCTTATTTGGGTTTTTAATTTACC
1 TTTTTTATTTTTAACTTGTAGTCAAGTGATTCTTATTTGGGTTTTTAATTTACC
1922305 TTTTTTATTTTTAACTTGTAGTCAAGTGATTCTTAT
1 TTTTTTATTTTTAACTTGTAGTCAAGTGATTCTTAT
1922341 GTGAGTTCAC
Statistics
Matches: 87, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
54 79 0.91
55 8 0.09
ACGTcount: A:0.22, C:0.09, G:0.12, T:0.57
Consensus pattern (54 bp):
TTTTTTATTTTTAACTTGTAGTCAAGTGATTCTTATTTGGGTTTTTAATTTACC
Found at i:1927702 original size:57 final size:58
Alignment explanation
Indices: 1927518--1927768 Score: 202
Period size: 57 Copynumber: 4.5 Consensus size: 58
1927508 GAAAATAACC
** * * * * *
1927518 AAAATGA-TCTTAAAATTTATGAAATTACATAAAAATCCT-TAGCATAGAAAATTATT
1 AAAATGACTCTTAAAATACATGAAATTACATAAAGATCCTAAATCATGGCAAATTATT
* * * * *
1927574 AAAATGACTC-TAAAATATATGATATTGCATAAATGATCTTAAATTATGGC-AA--A-T
1 AAAATGACTCTTAAAATACATGAAATTACATAAA-GATCCTAAATCATGGCAAATTATT
* * *
1927628 AAAATAAC-CTTAAAATGCATGAAATTACATAAAGGTCCTAAATCATGGCAAATTATT
1 AAAATGACTCTTAAAATACATGAAATTACATAAAGATCCTAAATCATGGCAAATTATT
* * ** * *
1927685 AAAATGACTC-TAAAATGCATGAAATTGCATGATTG-TCCTCAAA-CATGGTAAATTACT
1 AAAATGACTCTTAAAATACATGAAATTACAT-AAAGATCCT-AAATCATGGCAAATTATT
1927742 AAAATGAC-CTTAAAATACATGAAATTA
1 AAAATGACTCTTAAAATACATGAAATTA
1927769 TACAAATGGT
Statistics
Matches: 157, Mismatches: 26, Indels: 23
0.76 0.13 0.11
Matches are distributed among these distances:
53 14 0.09
54 29 0.18
55 1 0.01
56 29 0.18
57 74 0.47
58 10 0.06
ACGTcount: A:0.47, C:0.12, G:0.10, T:0.31
Consensus pattern (58 bp):
AAAATGACTCTTAAAATACATGAAATTACATAAAGATCCTAAATCATGGCAAATTATT
Found at i:1928089 original size:20 final size:20
Alignment explanation
Indices: 1928064--1928130 Score: 57
Period size: 20 Copynumber: 3.3 Consensus size: 20
1928054 CATTTCTATT
1928064 GATACACATGAAAATGTATC
1 GATACACATGAAAATGTATC
* * *
1928084 GATACATATTG-CAATGCATC
1 GATACACA-TGAAAATGTATC
*
1928104 TATACATCATGTAAAA-GTATC
1 GATACA-CATG-AAAATGTATC
1928125 GATACA
1 GATACA
1928131 TTTCATTGGC
Statistics
Matches: 35, Mismatches: 8, Indels: 7
0.70 0.16 0.14
Matches are distributed among these distances:
20 21 0.60
21 12 0.34
22 2 0.06
ACGTcount: A:0.42, C:0.16, G:0.13, T:0.28
Consensus pattern (20 bp):
GATACACATGAAAATGTATC
Found at i:1928184 original size:21 final size:21
Alignment explanation
Indices: 1928155--1928209 Score: 85
Period size: 21 Copynumber: 2.6 Consensus size: 21
1928145 ACTAACTCTC
*
1928155 AATTGTATCGATATAATTTGTA
1 AATTGTATCGATATAATTT-CA
1928177 AA-TGTATCGATATAATTTCA
1 AATTGTATCGATATAATTTCA
1928197 AATTGTATCGATA
1 AATTGTATCGATA
1928210 CATCCATACT
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
20 3 0.10
21 26 0.84
22 2 0.06
ACGTcount: A:0.38, C:0.07, G:0.13, T:0.42
Consensus pattern (21 bp):
AATTGTATCGATATAATTTCA
Found at i:1929392 original size:16 final size:16
Alignment explanation
Indices: 1929371--1929401 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
1929361 TGGGAGATGC
1929371 ATGGACATAGAAATAT
1 ATGGACATAGAAATAT
1929387 ATGGACATAGAAATA
1 ATGGACATAGAAATA
1929402 ATTAGCATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.52, C:0.06, G:0.19, T:0.23
Consensus pattern (16 bp):
ATGGACATAGAAATAT
Found at i:1937996 original size:28 final size:28
Alignment explanation
Indices: 1937944--1938306 Score: 442
Period size: 28 Copynumber: 12.9 Consensus size: 28
1937934 CTACAGCTCC
* *
1937944 GTGGCATCCTTTT-AAGTCCACAAGTCA
1 GTGGCACCCTTTTAAAGCCCACAAGTCA
* *
1937971 AT-GCTACCCTTTTAAAGCCCACAAGTTA
1 GTGGC-ACCCTTTTAAAGCCCACAAGTCA
* *
1937999 GTGGCACCCTTTCAAAGCCCACAAGTTA
1 GTGGCACCCTTTTAAAGCCCACAAGTCA
** *
1938027 GTGGCACTTTTTTCAAAGCCCATAAGTCA
1 GTGGCACCCTTTT-AAAGCCCACAAGTCA
* *
1938056 ATGGCACCCTTTCAAAGCCCACAAGTCA
1 GTGGCACCCTTTTAAAGCCCACAAGTCA
*
1938084 GTGGCACACTTTTAAAGCCCACAAGTCA
1 GTGGCACCCTTTTAAAGCCCACAAGTCA
* *
1938112 GTGGCACCCTTTCAAAGCCCACAAGTTA
1 GTGGCACCCTTTTAAAGCCCACAAGTCA
*
1938140 GTGGCACTCTTTTCAAAGCCCACAAGTCA
1 GTGGCACCCTTTT-AAAGCCCACAAGTCA
*
1938169 GTGGCACCCTTTCAAAGCCCACAAGTCA
1 GTGGCACCCTTTTAAAGCCCACAAGTCA
* ** *
1938197 GTGACTTCCTTTTAAAGCTCACAAGTCA
1 GTGGCACCCTTTTAAAGCCCACAAGTCA
*
1938225 GTGGCACCCTTTTAAAGCCCACAAGTTA
1 GTGGCACCCTTTTAAAGCCCACAAGTCA
* * *
1938253 GTGGCACCCTTTCAAAGTCCACAAGTTA
1 GTGGCACCCTTTTAAAGCCCACAAGTCA
* *
1938281 GTGGCACTCTTTTCAAGGCCCACAAG
1 GTGGCACCCTTTT-AAAGCCCACAAG
1938307 CTAGTGGTAA
Statistics
Matches: 287, Mismatches: 43, Indels: 10
0.84 0.13 0.03
Matches are distributed among these distances:
26 2 0.01
27 8 0.03
28 218 0.76
29 59 0.21
ACGTcount: A:0.29, C:0.30, G:0.17, T:0.25
Consensus pattern (28 bp):
GTGGCACCCTTTTAAAGCCCACAAGTCA
Found at i:1938096 original size:113 final size:113
Alignment explanation
Indices: 1937944--1938306 Score: 518
Period size: 113 Copynumber: 3.2 Consensus size: 113
1937934 CTACAGCTCC
* * * * *
1937944 GTGGCATCCTTT-TAAGTCCACAAGTCAAT-GCTACCCTTTTAAAGCCCACAAGTTAGTGGCACC
1 GTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCTA-CCTTTTAAAGCCCACAAGTCAGTGGCACC
* *
1938007 CTTTCAAAGCCCACAAGTTAGTGGCACTTTTTTCAAAGCCCATAAGTCA
65 CTTTCAAAGCCCACAAGTTAGTGGCACTCTTTTCAAAGCCCACAAGTCA
*
1938056 ATGGCACCCTTTCAAAGCCCACAAGTCAGTGGC-ACACTTTTAAAGCCCACAAGTCAGTGGCACC
1 GTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCTAC-CTTTTAAAGCCCACAAGTCAGTGGCACC
1938120 CTTTCAAAGCCCACAAGTTAGTGGCACTCTTTTCAAAGCCCACAAGTCA
65 CTTTCAAAGCCCACAAGTTAGTGGCACTCTTTTCAAAGCCCACAAGTCA
* * *
1938169 GTGGCACCCTTTCAAAGCCCACAAGTCAGTGACTTCCTTTTAAAGCTCACAAGTCAGTGGCACCC
1 GTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCTACCTTTTAAAGCCCACAAGTCAGTGGCACCC
* * * *
1938234 TTTTAAAGCCCACAAGTTAGTGGCAC-CCTTTCAAAGTCCACAAGTTA
66 TTTCAAAGCCCACAAGTTAGTGGCACTCTTTTCAAAGCCCACAAGTCA
* *
1938281 GTGGCACTCTTTTCAAGGCCCACAAG
1 GTGGCAC-CCTTTCAAAGCCCACAAG
1938307 CTAGTGGTAA
Statistics
Matches: 228, Mismatches: 18, Indels: 9
0.89 0.07 0.04
Matches are distributed among these distances:
112 36 0.16
113 189 0.83
114 3 0.01
ACGTcount: A:0.29, C:0.30, G:0.17, T:0.25
Consensus pattern (113 bp):
GTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCTACCTTTTAAAGCCCACAAGTCAGTGGCACCC
TTTCAAAGCCCACAAGTTAGTGGCACTCTTTTCAAAGCCCACAAGTCA
Found at i:1938182 original size:141 final size:141
Alignment explanation
Indices: 1937944--1938334 Score: 513
Period size: 141 Copynumber: 2.8 Consensus size: 141
1937934 CTACAGCTCC
* * *
1937944 GTGGCATCCTTTT-AAGTCCACAAGTCAAT-GCTACCCTTTTAAAGCCCACAAGTTAGTGGCAC-
1 GTGGCA-CCTTTTAAAGCCCACAAGTCAGTGGC-ACCCTTTCAAAGCCCACAAGTTAGTGGCACT
* * ** * *
1938006 CCTTTCAAAGCCCACAAGTTAGTGGCACTTTTTTCAAAGCCCATAAGTCAATGGCACCCTTTCAA
64 CTTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAATGACACCCTTTCAA
1938071 AGCCCACAAGTCA
129 AGCCCACAAGTCA
1938084 GTGGCACACTTTTAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTTAGTGGCACTC
1 GTGGCAC-CTTTTAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTTAGTGGCACTC
* ** *
1938149 TTTTCAAAGCCCACAAGTCAGTGGCAC-CCTTTCAAAGCCCACAAGTCAGTGACTTCCTTTTAAA
65 TTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAATGACACCCTTTCAAA
*
1938213 GCTCACAAGTCA
130 GCCCACAAGTCA
* *
1938225 GTGGCACCCTTTTAAAGCCCACAAGTTAGTGGCACCCTTTCAAAGTCCACAAGTTAGTGGCACTC
1 GTGGCA-CCTTTTAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTTAGTGGCACTC
* * * *
1938290 TTTTCAAGGCCCACAAG-CTAGTGGTAACTCTTTTCAAAACCCACA
65 TTTTCAAAGCCCACAAGTC-AGTGG-CACTCCTTTCAAAGCCCACA
1938335 CGAGTCGGAG
Statistics
Matches: 223, Mismatches: 20, Indels: 13
0.87 0.08 0.05
Matches are distributed among these distances:
139 1 0.00
140 12 0.05
141 165 0.74
142 31 0.14
143 14 0.06
ACGTcount: A:0.29, C:0.30, G:0.17, T:0.25
Consensus pattern (141 bp):
GTGGCACCTTTTAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTTAGTGGCACTCT
TTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAATGACACCCTTTCAAAG
CCCACAAGTCA
Found at i:1938540 original size:49 final size:45
Alignment explanation
Indices: 1938444--1938567 Score: 149
Period size: 49 Copynumber: 2.7 Consensus size: 45
1938434 TTGTCTCACA
* * *
1938444 TCGCTAGCCTTGAATCAGCATATTAGCACTTTTATTAGCCCAATG
1 TCGCTGGCCTTGAATCAGCACATTGGCACTTTTATTAGCCCAATG
*
1938489 TCGCTGGCCTTGAATCAGCACATTGGTCCACTTTTCCCTTAGCCCAATG
1 TCGCTGGCCTTGAATCAGCACATTGG--CACTTTT--ATTAGCCCAATG
* **
1938538 TCGCTGACCTTGAATTGGCACATTGGCACT
1 TCGCTGGCCTTGAATCAGCACATTGGCACT
1938568 CCTCTCATCT
Statistics
Matches: 68, Mismatches: 7, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
45 23 0.34
47 11 0.16
49 34 0.50
ACGTcount: A:0.22, C:0.28, G:0.19, T:0.31
Consensus pattern (45 bp):
TCGCTGGCCTTGAATCAGCACATTGGCACTTTTATTAGCCCAATG
Found at i:1938966 original size:20 final size:20
Alignment explanation
Indices: 1938941--1939015 Score: 105
Period size: 20 Copynumber: 3.8 Consensus size: 20
1938931 TTTTACTTAG
1938941 ATGTATCGATACATTTTTTA
1 ATGTATCGATACATTTTTTA
* * *
1938961 ATGTATCGATACATATATGA
1 ATGTATCGATACATTTTTTA
*
1938981 ATGTATCGATACATTATTTA
1 ATGTATCGATACATTTTTTA
*
1939001 ACGTATCGATACATT
1 ATGTATCGATACATT
1939016 CTGTCTTTTT
Statistics
Matches: 47, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 47 1.00
ACGTcount: A:0.35, C:0.12, G:0.12, T:0.41
Consensus pattern (20 bp):
ATGTATCGATACATTTTTTA
Found at i:1942721 original size:19 final size:20
Alignment explanation
Indices: 1942687--1942750 Score: 64
Period size: 19 Copynumber: 3.4 Consensus size: 20
1942677 AGAAACCTTA
*
1942687 TCTTTTCC-TT-TGTTTTTC
1 TCTTTTCCTTTCTATTTTTC
**
1942705 TCTTTTTTTTTCT-TTTTTC
1 TCTTTTCCTTTCTATTTTTC
1942724 TTCTTTTCCTTTCTATTTTT-
1 -TCTTTTCCTTTCTATTTTTC
1942744 TCTTTTC
1 TCTTTTC
1942751 TAGTTTTTTC
Statistics
Matches: 38, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
18 6 0.16
19 15 0.39
20 12 0.32
21 5 0.13
ACGTcount: A:0.02, C:0.20, G:0.02, T:0.77
Consensus pattern (20 bp):
TCTTTTCCTTTCTATTTTTC
Found at i:1942722 original size:20 final size:20
Alignment explanation
Indices: 1942687--1942746 Score: 54
Period size: 20 Copynumber: 3.0 Consensus size: 20
1942677 AGAAACCTTA
*
1942687 TCTTTTCCTTT--GTTTTTC
1 TCTTTTCCTTTCATTTTTTC
**
1942705 TCTTTTTTTTTC-TTTTTTC
1 TCTTTTCCTTTCATTTTTTC
1942724 TTCTTTTCCTTTCTATTTTTTC
1 -TCTTTTCCTTTC-ATTTTTTC
1942746 T
1 T
1942747 TTTCTAGTTT
Statistics
Matches: 33, Mismatches: 5, Indels: 5
0.77 0.12 0.12
Matches are distributed among these distances:
18 9 0.27
19 6 0.18
20 10 0.30
21 1 0.03
22 7 0.21
ACGTcount: A:0.02, C:0.20, G:0.02, T:0.77
Consensus pattern (20 bp):
TCTTTTCCTTTCATTTTTTC
Found at i:1942759 original size:15 final size:14
Alignment explanation
Indices: 1942710--1942762 Score: 61
Period size: 15 Copynumber: 3.6 Consensus size: 14
1942700 TTTTCTCTTT
* *
1942710 TTTTTTCTTTTTTC
1 TTTTTTCTTTTCTA
*
1942724 TTCTTTTCCTTTCTA
1 TT-TTTTCTTTTCTA
1942739 TTTTTTCTTTTCTA
1 TTTTTTCTTTTCTA
1942753 GTTTTTTCTT
1 -TTTTTTCTT
1942763 GCTAAAAACC
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
14 13 0.39
15 20 0.61
ACGTcount: A:0.04, C:0.17, G:0.02, T:0.77
Consensus pattern (14 bp):
TTTTTTCTTTTCTA
Found at i:1943519 original size:2 final size:2
Alignment explanation
Indices: 1943512--1943538 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1943502 CCTGATGATG
1943512 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1943539 CTTTGTGAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1944901 original size:22 final size:22
Alignment explanation
Indices: 1944876--1944960 Score: 84
Period size: 22 Copynumber: 3.8 Consensus size: 22
1944866 TAATGATAAT
1944876 TTTTTTAATTCT-TTAAATATTA
1 TTTTTTAATT-TATTAAATATTA
* *
1944898 TTTTTTAATTTGTTAATGTAATT-
1 TTTTTTAATTTATTAA-AT-ATTA
*
1944921 TTTTTAAATTTAATTAAATATTA
1 TTTTTTAATTT-ATTAAATATTA
*
1944944 TTTTTTATTTTATTAAA
1 TTTTTTAATTTATTAAA
1944961 AAATAATAAT
Statistics
Matches: 52, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
21 1 0.02
22 23 0.44
23 21 0.40
24 7 0.13
ACGTcount: A:0.33, C:0.01, G:0.02, T:0.64
Consensus pattern (22 bp):
TTTTTTAATTTATTAAATATTA
Found at i:1944921 original size:21 final size:21
Alignment explanation
Indices: 1944866--1944924 Score: 57
Period size: 21 Copynumber: 2.7 Consensus size: 21
1944856 TTTATTTAAA
1944866 TAATGATAATTTTTTTAATTCTT
1 TAATG-TAA-TTTTTTAATTCTT
* *
1944889 TAAATATTATTTTTTAATT-TGT
1 T-AATGTAATTTTTTAATTCT-T
1944911 TAATGTAATTTTTT
1 TAATGTAATTTTTT
1944925 TAAATTTAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
21 12 0.40
22 12 0.40
23 3 0.10
24 3 0.10
ACGTcount: A:0.31, C:0.02, G:0.05, T:0.63
Consensus pattern (21 bp):
TAATGTAATTTTTTAATTCTT
Found at i:1944938 original size:46 final size:45
Alignment explanation
Indices: 1944853--1944959 Score: 130
Period size: 46 Copynumber: 2.4 Consensus size: 45
1944843 GAATAGAAAG
*
1944853 TTTTTT-ATTTAAATAATGATAATTTTTTTAATTCTTTAAATATTA
1 TTTTTTAATTT-ATTAATGATAATTTTTTTAATTCTTTAAATATTA
*
1944898 TTTTTTAATTTGTTAATG-TAATTTTTTTAAATT-TAATTAAATATTA
1 TTTTTTAATTTATTAATGATAATTTTTTT-AATTCT--TTAAATATTA
*
1944944 TTTTTTATTTTATTAA
1 TTTTTTAATTTATTAA
1944960 AAAATAATAA
Statistics
Matches: 54, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
44 11 0.20
45 15 0.28
46 28 0.52
ACGTcount: A:0.34, C:0.01, G:0.03, T:0.63
Consensus pattern (45 bp):
TTTTTTAATTTATTAATGATAATTTTTTTAATTCTTTAAATATTA
Found at i:1945101 original size:25 final size:23
Alignment explanation
Indices: 1945073--1945120 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
1945063 TTTTAAAAAA
1945073 TTATAATAAAAACTTTTTTATTTTT
1 TTATAAT-AAAA-TTTTTTATTTTT
**
1945098 TTATTCTAAAATTTTTTATTTTT
1 TTATAATAAAATTTTTTATTTTT
1945121 ATGAAAACAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 12 0.57
24 4 0.19
25 5 0.24
ACGTcount: A:0.31, C:0.04, G:0.00, T:0.65
Consensus pattern (23 bp):
TTATAATAAAATTTTTTATTTTT
Found at i:1945180 original size:16 final size:15
Alignment explanation
Indices: 1945161--1945192 Score: 55
Period size: 16 Copynumber: 2.1 Consensus size: 15
1945151 ATTAATGTAA
1945161 TTTTTTAAACTTGAAT
1 TTTTTTAAACTT-AAT
1945177 TTTTTTAAACTTAAT
1 TTTTTTAAACTTAAT
1945192 T
1 T
1945193 AAATATAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.25
16 12 0.75
ACGTcount: A:0.31, C:0.06, G:0.03, T:0.59
Consensus pattern (15 bp):
TTTTTTAAACTTAAT
Found at i:1945716 original size:6 final size:6
Alignment explanation
Indices: 1945705--1945736 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
1945695 TATGAAAAAT
1945705 AATTTA AATTT- AATTT- AATTTA AATTTA AATT
1 AATTTA AATTTA AATTTA AATTTA AATTTA AATT
1945737 AATCTGATTC
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 10 0.40
6 15 0.60
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (6 bp):
AATTTA
Found at i:1945725 original size:16 final size:16
Alignment explanation
Indices: 1945704--1945739 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
1945694 ATATGAAAAA
*
1945704 TAATTTAAATTTAATT
1 TAATTTAAATTTAAAT
1945720 TAATTTAAATTTAAAT
1 TAATTTAAATTTAAAT
1945736 TAAT
1 TAAT
1945740 CTGATTCAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
TAATTTAAATTTAAAT
Found at i:1945738 original size:11 final size:11
Alignment explanation
Indices: 1945705--1945738 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
1945695 TATGAAAAAT
*
1945705 AATTTAAATTT
1 AATTTAAATTA
*
1945716 AATTTAATTTA
1 AATTTAAATTA
1945727 AATTTAAATTA
1 AATTTAAATTA
1945738 A
1 A
1945739 TCTGATTCAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (11 bp):
AATTTAAATTA
Found at i:1945826 original size:14 final size:15
Alignment explanation
Indices: 1945806--1945844 Score: 53
Period size: 16 Copynumber: 2.6 Consensus size: 15
1945796 AATACTTAAA
1945806 ATAATTTAATTT-TT
1 ATAATTTAATTTATT
*
1945820 TTAATTTAAATTTATT
1 ATAATTT-AATTTATT
1945836 ATAATTTAA
1 ATAATTTAA
1945845 AATTTTTACT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
14 6 0.29
15 7 0.33
16 8 0.38
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (15 bp):
ATAATTTAATTTATT
Found at i:1946430 original size:2 final size:2
Alignment explanation
Indices: 1946425--1946457 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1946415 TTTTTTCATT
1946425 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1946458 TATGCTTAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1946799 original size:25 final size:26
Alignment explanation
Indices: 1946749--1946803 Score: 85
Period size: 25 Copynumber: 2.2 Consensus size: 26
1946739 TTAATTAAAA
* *
1946749 ATTTATTTTAATTGATTTATATAATT
1 ATTTAATTCAATTGATTTATATAATT
1946775 ATTTAATTCAATTGA-TTATATAATT
1 ATTTAATTCAATTGATTTATATAATT
1946800 ATTT
1 ATTT
1946804 TTAAAAAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
25 14 0.52
26 13 0.48
ACGTcount: A:0.36, C:0.02, G:0.04, T:0.58
Consensus pattern (26 bp):
ATTTAATTCAATTGATTTATATAATT
Found at i:1949724 original size:2 final size:2
Alignment explanation
Indices: 1949717--1949750 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
1949707 AGGAAAAATA
* *
1949717 AT AT AT AT GT TT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1949751 TTTTAGAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (2 bp):
AT
Found at i:1950385 original size:30 final size:30
Alignment explanation
Indices: 1950349--1950407 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
1950339 GGTTCTATGA
*
1950349 AGAGAGA-GAAATGAGTTTTTGGAGAGAGAG
1 AGAGAGAGGAAA-GAGATTTTGGAGAGAGAG
*
1950379 AGAGAGAGGAAAGAGATTTTGGGGAGAGA
1 AGAGAGAGGAAAGAGATTTTGGAGAGAGA
1950408 ACCTAGAGGG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
30 22 0.85
31 4 0.15
ACGTcount: A:0.41, C:0.00, G:0.42, T:0.17
Consensus pattern (30 bp):
AGAGAGAGGAAAGAGATTTTGGAGAGAGAG
Found at i:1960582 original size:19 final size:18
Alignment explanation
Indices: 1960544--1960583 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
1960534 CGTTCAATGT
* *
1960544 ATAAAGTTTTCTTAATAA
1 ATAAAGTTTTATAAATAA
1960562 ATAAAGTTTTATAATATAA
1 ATAAAGTTTTATAA-ATAA
1960581 ATA
1 ATA
1960584 TTCTATATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 12 0.63
19 7 0.37
ACGTcount: A:0.50, C:0.03, G:0.05, T:0.42
Consensus pattern (18 bp):
ATAAAGTTTTATAAATAA
Found at i:1960640 original size:13 final size:11
Alignment explanation
Indices: 1960614--1960647 Score: 50
Period size: 13 Copynumber: 2.9 Consensus size: 11
1960604 AGTAATAAGA
1960614 TTTATTTTATT
1 TTTATTTTATT
1960625 TTTATTTATGATT
1 TTTATTT-T-ATT
1960638 TTTATTTTAT
1 TTTATTTTAT
1960648 AAATATTATT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
11 9 0.43
12 2 0.10
13 10 0.48
ACGTcount: A:0.21, C:0.00, G:0.03, T:0.76
Consensus pattern (11 bp):
TTTATTTTATT
Found at i:1960684 original size:15 final size:14
Alignment explanation
Indices: 1960651--1960685 Score: 61
Period size: 14 Copynumber: 2.4 Consensus size: 14
1960641 ATTTTATAAA
1960651 TATTATTAAAAATT
1 TATTATTAAAAATT
1960665 TATTATTAAAAATT
1 TATTATTAAAAATT
1960679 TCATTAT
1 T-ATTAT
1960686 AACAATAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 15 0.75
15 5 0.25
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (14 bp):
TATTATTAAAAATT
Found at i:1960747 original size:26 final size:28
Alignment explanation
Indices: 1960717--1960778 Score: 83
Period size: 26 Copynumber: 2.3 Consensus size: 28
1960707 AATTACTAAA
*
1960717 AAATTTTAAATAATACTTTT-AATAATT
1 AAATTTTAAATAAAACTTTTAAATAATT
* *
1960744 -AATTATAATTAAAACTTTTAAATAATT
1 AAATTTTAAATAAAACTTTTAAATAATT
1960771 AAATTTTA
1 AAATTTTA
1960779 TCGAATAACA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
26 16 0.55
27 7 0.24
28 6 0.21
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (28 bp):
AAATTTTAAATAAAACTTTTAAATAATT
Found at i:1961641 original size:9 final size:9
Alignment explanation
Indices: 1961627--1961682 Score: 69
Period size: 9 Copynumber: 6.1 Consensus size: 9
1961617 GAAAGGAACG
1961627 AGAAAAAAA
1 AGAAAAAAA
1961636 AGAAAAAAA
1 AGAAAAAAA
1961645 AGAAAAAAA
1 AGAAAAAAA
*
1961654 A-AAAGAAA
1 AGAAAAAAA
1961662 AGAAAGAAAGA
1 AGAAA-AAA-A
*
1961673 GGAAAAAAA
1 AGAAAAAAA
1961682 A
1 A
1961683 AAGGAAGGAG
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
8 7 0.17
9 23 0.57
10 5 0.12
11 5 0.12
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (9 bp):
AGAAAAAAA
Found at i:1961655 original size:21 final size:21
Alignment explanation
Indices: 1961629--1961670 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
1961619 AAGGAACGAG
1961629 AAAAAAAAGAAAAAAAAGAAA
1 AAAAAAAAGAAAAAAAAGAAA
*
1961650 AAAAAAAAGAAAAGAAAGAAA
1 AAAAAAAAGAAAAAAAAGAAA
1961671 GAGGAAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (21 bp):
AAAAAAAAGAAAAAAAAGAAA
Found at i:1961678 original size:21 final size:20
Alignment explanation
Indices: 1961633--1961704 Score: 56
Period size: 21 Copynumber: 3.5 Consensus size: 20
1961623 AACGAGAAAA
* **
1961633 AAAAGAAAAAAAAGAAAAAAA
1 AAAAG-AAAAAAAGAAAGAGG
1961654 AAAAGAAAAGAAAGAAAGAGG
1 AAAAGAAAA-AAAGAAAGAGG
* *
1961675 AAAA-AAAAAAGGAAGGAGAG
1 AAAAGAAAAAAAGAAAGAG-G
1961695 AAAAGTAAAA
1 AAAAG-AAAA
1961705 TTATATACAT
Statistics
Matches: 42, Mismatches: 5, Indels: 7
0.78 0.09 0.13
Matches are distributed among these distances:
19 8 0.19
20 13 0.31
21 17 0.40
22 4 0.10
ACGTcount: A:0.78, C:0.00, G:0.21, T:0.01
Consensus pattern (20 bp):
AAAAGAAAAAAAGAAAGAGG
Found at i:1961789 original size:11 final size:11
Alignment explanation
Indices: 1961775--1961823 Score: 57
Period size: 11 Copynumber: 4.5 Consensus size: 11
1961765 GTGTATTTGG
1961775 ATTATATTTAT
1 ATTATATTTAT
*
1961786 ATTATATTTTAAA
1 ATTATA-TTT-AT
1961799 ATT-T-TTTAT
1 ATTATATTTAT
1961808 ATTATATTTAT
1 ATTATATTTAT
1961819 ATTAT
1 ATTAT
1961824 TTTTTGTATA
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
9 4 0.12
10 4 0.12
11 16 0.50
12 4 0.12
13 4 0.12
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (11 bp):
ATTATATTTAT
Found at i:1961844 original size:20 final size:22
Alignment explanation
Indices: 1961781--1961844 Score: 62
Period size: 22 Copynumber: 3.0 Consensus size: 22
1961771 TTGGATTATA
*
1961781 TTTATATTATATTTTAAAAT-TT
1 TTTATAGTATA-TTTAAAATATT
* * *
1961803 TTTATATTATATTTATATTATT
1 TTTATAGTATATTTAAAATATT
1961825 TTT-T-GTATATTTAAAATATT
1 TTTATAGTATATTTAAAATATT
1961845 GTAAATTTAT
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
20 13 0.36
21 7 0.19
22 16 0.44
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (22 bp):
TTTATAGTATATTTAAAATATT
Found at i:1962661 original size:17 final size:18
Alignment explanation
Indices: 1962639--1962694 Score: 62
Period size: 17 Copynumber: 3.2 Consensus size: 18
1962629 TAAAACTTTA
1962639 AAATAAAAAAT-ATATTT
1 AAATAAAAAATAATATTT
* *
1962656 AAATAAATAATAATTTTT
1 AAATAAAAAATAATATTT
* *
1962674 TAATAAAAATTAAT-TTT
1 AAATAAAAAATAATATTT
1962691 AAAT
1 AAAT
1962695 TATATAATTA
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
17 16 0.50
18 16 0.50
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (18 bp):
AAATAAAAAATAATATTT
Found at i:1962725 original size:20 final size:22
Alignment explanation
Indices: 1962682--1962725 Score: 56
Period size: 20 Copynumber: 2.1 Consensus size: 22
1962672 TTTAATAAAA
*
1962682 ATTAATTTTAAATTATATAATT
1 ATTAATTTTAAATTAAATAATT
*
1962704 ATTAA-TTT-AATTAAATATTT
1 ATTAATTTTAAATTAAATAATT
1962724 AT
1 AT
1962726 AAATAATAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 12 0.60
21 3 0.15
22 5 0.25
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (22 bp):
ATTAATTTTAAATTAAATAATT
Found at i:1962898 original size:30 final size:29
Alignment explanation
Indices: 1962864--1962929 Score: 80
Period size: 30 Copynumber: 2.2 Consensus size: 29
1962854 TTAATTTACA
*
1962864 TTTAACTTTTAATTTATATAC-GAATAAATC
1 TTTAAC-TTTAATTTATA-ACTAAATAAATC
*
1962894 TTTAAACTTTAATTTATAACTAAATAAATT
1 TTT-AACTTTAATTTATAACTAAATAAATC
1962924 TTTAAC
1 TTTAAC
1962930 AAAATTCAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
29 5 0.16
30 24 0.75
31 3 0.09
ACGTcount: A:0.42, C:0.09, G:0.02, T:0.47
Consensus pattern (29 bp):
TTTAACTTTAATTTATAACTAAATAAATC
Found at i:1963212 original size:22 final size:21
Alignment explanation
Indices: 1963178--1963222 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 21
1963168 ATTAAAAAAT
1963178 TATTTTGATATTAATATTTAAA
1 TATTTTGATATTAA-ATTTAAA
*
1963200 TATTTT-ATAATTAAATTTTAA
1 TATTTTGAT-ATTAAATTTAAA
1963221 TA
1 TA
1963223 AAAATATATT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 10 0.48
22 11 0.52
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (21 bp):
TATTTTGATATTAAATTTAAA
Found at i:1963720 original size:35 final size:35
Alignment explanation
Indices: 1963650--1963725 Score: 109
Period size: 35 Copynumber: 2.2 Consensus size: 35
1963640 TTAATTGTTC
* ***
1963650 AAAAC-ATTTTTTTTATAAATAAAAAAACCCCAAT
1 AAAACAATATTTTTTATAAATAAAAAAACAAAAAT
1963684 AAAACAATATTTTTTATAAATAAAAAAACAAAAAT
1 AAAACAATATTTTTTATAAATAAAAAAACAAAAAT
1963719 AAAACAA
1 AAAACAA
1963726 ATGTTTCGAT
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
34 5 0.14
35 32 0.86
ACGTcount: A:0.62, C:0.11, G:0.00, T:0.28
Consensus pattern (35 bp):
AAAACAATATTTTTTATAAATAAAAAAACAAAAAT
Found at i:1966015 original size:16 final size:16
Alignment explanation
Indices: 1965966--1966015 Score: 50
Period size: 16 Copynumber: 3.1 Consensus size: 16
1965956 ATTCGTGTTT
1965966 AATTTAAA--AAATAAA
1 AATTTAAATTAAA-AAA
* *
1965981 AATTTTAATTTTAAAAA
1 AA-TTTAAATTAAAAAA
1965998 AATTTAAATTAAAAAA
1 AATTTAAATTAAAAAA
1966014 AA
1 AA
1966016 GTTAGAACTT
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
15 2 0.07
16 19 0.68
17 5 0.18
18 2 0.07
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (16 bp):
AATTTAAATTAAAAAA
Found at i:1966309 original size:23 final size:24
Alignment explanation
Indices: 1966262--1966314 Score: 65
Period size: 23 Copynumber: 2.2 Consensus size: 24
1966252 AAAACTATAT
* *
1966262 ATAAT-TATTATACAATTATATTA
1 ATAATATATTATACAATTAAAGTA
1966285 ATAATATATTAT-CAATTAAAGTA
1 ATAATATATTATACAATTAAAGTA
1966308 ATTAATA
1 A-TAATA
1966315 GTGAATCTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
23 15 0.58
24 11 0.42
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.43
Consensus pattern (24 bp):
ATAATATATTATACAATTAAAGTA
Found at i:1967358 original size:17 final size:16
Alignment explanation
Indices: 1967319--1967362 Score: 54
Period size: 15 Copynumber: 2.8 Consensus size: 16
1967309 ATATGATTAC
* *
1967319 ATATTTGAAATGTATA
1 ATATTTTAAATTTATA
1967335 A-ATTTTAAATTTATAA
1 ATATTTTAAATTTAT-A
1967351 ATATTTTAAATT
1 ATATTTTAAATT
1967363 CACCACTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 11 0.46
16 3 0.12
17 10 0.42
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (16 bp):
ATATTTTAAATTTATA
Found at i:1967526 original size:5 final size:4
Alignment explanation
Indices: 1967506--1967562 Score: 50
Period size: 4 Copynumber: 14.5 Consensus size: 4
1967496 TCATTAAAAA
*
1967506 AAAT ATAAT AAAT AAACT AAA- ACAAT -AAT AAA- ACA- AAAT AAAT AAAT
1 AAAT A-AAT AAAT AAA-T AAAT A-AAT AAAT AAAT AAAT AAAT AAAT AAAT
1967553 AAAT AAAT AA
1 AAAT AAAT AA
1967563 TTTTTGGACT
Statistics
Matches: 45, Mismatches: 2, Indels: 12
0.76 0.03 0.20
Matches are distributed among these distances:
3 8 0.18
4 29 0.64
5 8 0.18
ACGTcount: A:0.74, C:0.05, G:0.00, T:0.21
Consensus pattern (4 bp):
AAAT
Found at i:1968023 original size:12 final size:12
Alignment explanation
Indices: 1968008--1968036 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
1967998 ATAAAATTAT
1968008 ATATTTATATAA
1 ATATTTATATAA
1968020 ATATTTATATAA
1 ATATTTATATAA
1968032 ATATT
1 ATATT
1968037 AATTAATTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (12 bp):
ATATTTATATAA
Found at i:1968035 original size:18 final size:17
Alignment explanation
Indices: 1967990--1968041 Score: 52
Period size: 18 Copynumber: 3.1 Consensus size: 17
1967980 TTAATACTCA
1967990 ATATATAAATA-AAATT
1 ATATATAAATATAAATT
**
1968006 ATATATTTATATAAATAT
1 ATATATAAATATAAAT-T
* *
1968024 TTATATAAATATTAATT
1 ATATATAAATATAAATT
1968041 A
1 A
1968042 ATTTTGCCTT
Statistics
Matches: 27, Mismatches: 7, Indels: 3
0.73 0.19 0.08
Matches are distributed among these distances:
16 9 0.33
17 5 0.19
18 13 0.48
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATATAAATATAAATT
Found at i:1968269 original size:17 final size:17
Alignment explanation
Indices: 1968249--1968323 Score: 98
Period size: 17 Copynumber: 4.4 Consensus size: 17
1968239 ATCTAAATCT
1968249 AAAAATTTAAATTTAAA
1 AAAAATTTAAATTTAAA
* *
1968266 AAAAATTAAAATTCAAA
1 AAAAATTTAAATTTAAA
* *
1968283 ATAAATATAAATTT-AA
1 AAAAATTTAAATTTAAA
1968299 AAAAATTTAAATTTAAA
1 AAAAATTTAAATTTAAA
1968316 AATAAATT
1 AA-AAATT
1968324 GATCTAAATC
Statistics
Matches: 48, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
16 14 0.29
17 29 0.60
18 5 0.10
ACGTcount: A:0.65, C:0.01, G:0.00, T:0.33
Consensus pattern (17 bp):
AAAAATTTAAATTTAAA
Found at i:1968294 original size:34 final size:34
Alignment explanation
Indices: 1968251--1968322 Score: 108
Period size: 34 Copynumber: 2.1 Consensus size: 34
1968241 CTAAATCTAA
* *
1968251 AAATTTAAATTTAAAAAAAATTAAAATTCAAAAT
1 AAATATAAATTTAAAAAAAATTAAAATTAAAAAT
* *
1968285 AAATATAAATTTAAAAAAATTTAAATTTAAAAAT
1 AAATATAAATTTAAAAAAAATTAAAATTAAAAAT
1968319 AAAT
1 AAAT
1968323 TGATCTAAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.65, C:0.01, G:0.00, T:0.33
Consensus pattern (34 bp):
AAATATAAATTTAAAAAAAATTAAAATTAAAAAT
Found at i:1968994 original size:16 final size:16
Alignment explanation
Indices: 1968966--1969092 Score: 58
Period size: 16 Copynumber: 8.2 Consensus size: 16
1968956 CATAATATTC
1968966 TAAAATA-AA-ATAAT
1 TAAAATATAATATAAT
*
1968980 TAAAATATAATATAAA
1 TAAAATATAATATAAT
*
1968996 T-ATATATTAA-A-AAT
1 TAAAATA-TAATATAAT
* *
1969010 TATAAATATAAAATATTT
1 TA-AAATATAATATA-AT
1969028 TAAAATATAATTATAA-
1 TAAAATATAA-TATAAT
* *
1969044 TATAATAAAATAT-A-
1 TAAAATATAATATAAT
*
1969058 TAAATATATAA-ATTAT
1 TAAA-ATATAATATAAT
*
1969074 T-AAATTTAAATATAAT
1 TAAAATAT-AATATAAT
1969090 TAA
1 TAA
1969093 TTTTAATTCA
Statistics
Matches: 85, Mismatches: 13, Indels: 27
0.68 0.10 0.22
Matches are distributed among these distances:
14 19 0.22
15 23 0.27
16 27 0.32
17 10 0.12
18 6 0.07
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (16 bp):
TAAAATATAATATAAT
Found at i:1969005 original size:23 final size:21
Alignment explanation
Indices: 1968970--1969077 Score: 90
Period size: 23 Copynumber: 4.7 Consensus size: 21
1968960 ATATTCTAAA
1968970 ATAAAATAATTAAAATATAAT
1 ATAAAATAATTAAAATATAAT
1968991 ATAAATATATATTAAAAATTATAAAT
1 ATAAA-ATA-ATT-AAAA-TAT-AAT
*
1969017 ATAAAATATTTTAAAATATAATT
1 ATAAAATA-ATTAAAATATAA-T
* *
1969040 ATAATATAATAAAATATATAAAT
1 ATAAAATAATTAAA-ATAT-AAT
*
1969063 ATATAAATTATTAAA
1 ATA-AAATAATTAAA
1969078 TTTAAATATA
Statistics
Matches: 71, Mismatches: 7, Indels: 15
0.76 0.08 0.16
Matches are distributed among these distances:
21 5 0.07
22 9 0.13
23 22 0.31
24 18 0.25
25 9 0.13
26 8 0.11
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (21 bp):
ATAAAATAATTAAAATATAAT
Found at i:1969062 original size:8 final size:8
Alignment explanation
Indices: 1968989--1969087 Score: 60
Period size: 8 Copynumber: 13.4 Consensus size: 8
1968979 TTAAAATATA
1968989 ATATAAAT
1 ATATAAAT
1968997 ATAT--AT
1 ATATAAAT
*
1969003 -TAAAAAT
1 ATATAAAT
1969010 -TATAAAT
1 ATATAAAT
1969017 ATA-AAAT
1 ATATAAAT
*
1969024 ATTTTAAA-
1 A-TATAAAT
1969032 ATAT-AAT
1 ATATAAAT
1969039 -TAT-AAT
1 ATATAAAT
1969045 ATAATAAAAT
1 AT-AT-AAAT
1969055 ATATAAAT
1 ATATAAAT
1969063 ATATAAAT
1 ATATAAAT
1969071 -TATTAAAT
1 ATA-TAAAT
1969079 -T-TAAAT
1 ATATAAAT
1969085 ATA
1 ATA
1969088 ATTAATTTTA
Statistics
Matches: 74, Mismatches: 4, Indels: 26
0.71 0.04 0.25
Matches are distributed among these distances:
5 2 0.03
6 15 0.20
7 19 0.26
8 28 0.38
9 5 0.07
10 5 0.07
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (8 bp):
ATATAAAT
Found at i:1969063 original size:46 final size:47
Alignment explanation
Indices: 1968966--1969077 Score: 135
Period size: 46 Copynumber: 2.4 Consensus size: 47
1968956 CATAATATTC
1968966 TAAA-ATAAAATAATTAAAATATAATATAAATATATATTAAAAATTA
1 TAAATATAAAATAATTAAAATATAATATAAATATATATTAAAAATTA
*
1969012 TAAATATAAAATATTTTAAAATATAAT-TATAATATA-A-T-AAAATATA
1 TAAATATAAAATA-ATTAAAATATAATATA-AATATATATTAAAAAT-TA
*
1969058 TAAATATATAAATTATTAAA
1 TAAATATA-AAATAATTAAA
1969078 TTTAAATATA
Statistics
Matches: 58, Mismatches: 3, Indels: 10
0.82 0.04 0.14
Matches are distributed among these distances:
45 5 0.09
46 20 0.34
47 15 0.26
48 18 0.31
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (47 bp):
TAAATATAAAATAATTAAAATATAATATAAATATATATTAAAAATTA
Found at i:1969335 original size:27 final size:28
Alignment explanation
Indices: 1969295--1969350 Score: 80
Period size: 27 Copynumber: 2.0 Consensus size: 28
1969285 TTTATACAAT
*
1969295 TTAATCTTTGTATTAAAAATTAA-ATAAA
1 TTAATCTTTATATTAAAAA-TAATATAAA
1969323 TTAAT-TTTATATTAAAAATAATATAAA
1 TTAATCTTTATATTAAAAATAATATAAA
1969350 T
1 T
1969351 AAAAAATGTA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
26 3 0.12
27 18 0.69
28 5 0.19
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (28 bp):
TTAATCTTTATATTAAAAATAATATAAA
Found at i:1969375 original size:13 final size:13
Alignment explanation
Indices: 1969331--1969375 Score: 51
Period size: 13 Copynumber: 3.6 Consensus size: 13
1969321 AATTAATTTT
*
1969331 ATATTAAA-AATA
1 ATATTAAATAAAA
1969343 ATA-TAAATAAAA
1 ATATTAAATAAAA
1969355 A-ATGTAAATAAAA
1 ATAT-TAAATAAAA
1969368 ATATTAAA
1 ATATTAAA
1969376 ATATAAACGT
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
11 5 0.18
12 7 0.25
13 14 0.50
14 2 0.07
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (13 bp):
ATATTAAATAAAA
Found at i:1970060 original size:26 final size:27
Alignment explanation
Indices: 1970012--1970062 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
1970002 TGCAACAAGG
*
1970012 TTTATTTTTATTTTATCTTAAAATTTA
1 TTTATTTTTATTTTATCTGAAAATTTA
1970039 TTTATTTTATATTTT-T-TGAAAATT
1 TTTATTTT-TATTTTATCTGAAAATT
1970063 AAAATTTTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
26 7 0.32
27 9 0.41
28 6 0.27
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.67
Consensus pattern (27 bp):
TTTATTTTTATTTTATCTGAAAATTTA
Found at i:1976594 original size:43 final size:43
Alignment explanation
Indices: 1976533--1976623 Score: 164
Period size: 43 Copynumber: 2.1 Consensus size: 43
1976523 TGACTTCAAT
1976533 GTTTATATCAATTTGATTTGTTTTACTTTCAATAATAATCATA
1 GTTTATATCAATTTGATTTGTTTTACTTTCAATAATAATCATA
*
1976576 GTTTATATCAATTTGATTTGTTTTACTTTCAGTAATAATCATA
1 GTTTATATCAATTTGATTTGTTTTACTTTCAATAATAATCATA
*
1976619 CTTTA
1 GTTTA
1976624 GAGATCCAAA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
43 46 1.00
ACGTcount: A:0.31, C:0.10, G:0.08, T:0.52
Consensus pattern (43 bp):
GTTTATATCAATTTGATTTGTTTTACTTTCAATAATAATCATA
Found at i:1981952 original size:2 final size:2
Alignment explanation
Indices: 1981945--1981970 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1981935 CTTCGTTGAT
1981945 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
1981971 CACACACACA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1991063 original size:1 final size:1
Alignment explanation
Indices: 1991053--1991145 Score: 78
Period size: 1 Copynumber: 93.0 Consensus size: 1
1991043 TGGCAATTGG
* * * ** * * * **
1991053 AAAAAGAAAAAAACAAAACAAAAAAAAAGGAAAAAGAAAAAAAAAACAAAACAAAAAAAAAGGAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* *
1991118 AAAGAAAAAAAAAAAAACAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAA
1991146 GTGAAGATTT
Statistics
Matches: 72, Mismatches: 20, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
1 72 1.00
ACGTcount: A:0.87, C:0.05, G:0.08, T:0.00
Consensus pattern (1 bp):
A
Found at i:1991101 original size:33 final size:32
Alignment explanation
Indices: 1991051--1991144 Score: 158
Period size: 33 Copynumber: 3.0 Consensus size: 32
1991041 CATGGCAATT
1991051 GGAAAAAG--AAAAAAACAAAACAAAAAAAAA
1 GGAAAAAGAAAAAAAAACAAAACAAAAAAAAA
1991081 GGAAAAAGAAAAAAAAAACAAAACAAAAAAAAA
1 GGAAAAAG-AAAAAAAAACAAAACAAAAAAAAA
1991114 GGAAAAAGAAAAAAAAA-AAAACAAAAAAAAA
1 GGAAAAAGAAAAAAAAACAAAACAAAAAAAAA
1991145 AGTGAAGATT
Statistics
Matches: 61, Mismatches: 0, Indels: 5
0.92 0.00 0.08
Matches are distributed among these distances:
30 8 0.13
31 14 0.23
32 9 0.15
33 30 0.49
ACGTcount: A:0.85, C:0.05, G:0.10, T:0.00
Consensus pattern (32 bp):
GGAAAAAGAAAAAAAAACAAAACAAAAAAAAA
Found at i:2001695 original size:39 final size:39
Alignment explanation
Indices: 2001584--2001696 Score: 93
Period size: 39 Copynumber: 2.9 Consensus size: 39
2001574 AATGGCTTAG
* * * *
2001584 TTTTGGTATGAAAATGCTAACACTACCTTAAAGGGTTCAT
1 TTTTGATATGAAAATGCTAACACAACCTTAAA-GATTCAA
* ** * * * * *
2001624 TTTTAACCTAAAAATACCAA-ATCAGCCCTAAAGATTCAA
1 TTTTGATATGAAAATGCTAACA-CAACCTTAAAGATTCAA
2001663 TTTTGATATGAAAATGCTAACACAACCTTAAAGA
1 TTTTGATATGAAAATGCTAACACAACCTTAAAGA
2001697 CCCAGTTTTG
Statistics
Matches: 51, Mismatches: 20, Indels: 5
0.67 0.26 0.07
Matches are distributed among these distances:
39 30 0.59
40 21 0.41
ACGTcount: A:0.41, C:0.18, G:0.12, T:0.30
Consensus pattern (39 bp):
TTTTGATATGAAAATGCTAACACAACCTTAAAGATTCAA
Found at i:2003261 original size:26 final size:26
Alignment explanation
Indices: 2003231--2003311 Score: 78
Period size: 26 Copynumber: 3.1 Consensus size: 26
2003221 ACGTAAAATG
*
2003231 TTCATATATAAAAGTTTAATTAATAA
1 TTCATATGTAAAAGTTTAATTAATAA
*
2003257 TTCAT-TGTATAAAGTTCAATT-ATAAA
1 TTCATATGTA-AAAGTTTAATTAAT-AA
*
2003283 TTCTATATGTGAAAA-TTTAATTAACAA
1 TTC-ATATGT-AAAAGTTTAATTAATAA
2003310 TT
1 TT
2003312 TTACATGCAC
Statistics
Matches: 45, Mismatches: 4, Indels: 11
0.75 0.07 0.18
Matches are distributed among these distances:
25 5 0.11
26 20 0.44
27 12 0.27
28 7 0.16
29 1 0.02
ACGTcount: A:0.44, C:0.06, G:0.06, T:0.43
Consensus pattern (26 bp):
TTCATATGTAAAAGTTTAATTAATAA
Found at i:2003492 original size:27 final size:27
Alignment explanation
Indices: 2003455--2003531 Score: 93
Period size: 27 Copynumber: 2.9 Consensus size: 27
2003445 CTTGTTGGTG
* *
2003455 AAAAGTTTAATTAGAAATTTTATACGT
1 AAAAGTTTAATTAAAAATTCTATACGT
*
2003482 AAAAGTTTAATTAAAAATTCTATACAT
1 AAAAGTTTAATTAAAAATTCTATACGT
* *
2003509 GAAAAG-ATACTTAAAAATTCTAT
1 -AAAAGTTTAATTAAAAATTCTAT
2003532 TTTTAATAAA
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
27 39 0.89
28 5 0.11
ACGTcount: A:0.49, C:0.06, G:0.08, T:0.36
Consensus pattern (27 bp):
AAAAGTTTAATTAAAAATTCTATACGT
Found at i:2005214 original size:21 final size:20
Alignment explanation
Indices: 2005190--2005256 Score: 73
Period size: 20 Copynumber: 3.3 Consensus size: 20
2005180 GTCAATGACT
2005190 TGTATCGATAC-TTTTATATAA
1 TGTATCGATACATTTTA-AT-A
**
2005211 TGTATCGATACATTGCAATA
1 TGTATCGATACATTTTAATA
* *
2005231 TGTATCGATACATTTTCATG
1 TGTATCGATACATTTTAATA
2005251 TGTATC
1 TGTATC
2005257 AATAGAAATA
Statistics
Matches: 39, Mismatches: 6, Indels: 3
0.81 0.12 0.06
Matches are distributed among these distances:
20 23 0.59
21 13 0.33
22 3 0.08
ACGTcount: A:0.30, C:0.13, G:0.13, T:0.43
Consensus pattern (20 bp):
TGTATCGATACATTTTAATA
Found at i:2009217 original size:19 final size:20
Alignment explanation
Indices: 2009174--2009226 Score: 90
Period size: 19 Copynumber: 2.7 Consensus size: 20
2009164 AATTCAACGA
2009174 TTTGTATCGATACATAAAGT
1 TTTGTATCGATACATAAAGT
*
2009194 GTTGTATCGATACAT-AAGT
1 TTTGTATCGATACATAAAGT
2009213 TTTGTATCGATACA
1 TTTGTATCGATACA
2009227 ATTTAAGCTA
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 17 0.55
20 14 0.45
ACGTcount: A:0.32, C:0.11, G:0.17, T:0.40
Consensus pattern (20 bp):
TTTGTATCGATACATAAAGT
Found at i:2009358 original size:52 final size:52
Alignment explanation
Indices: 2009302--2009426 Score: 232
Period size: 52 Copynumber: 2.4 Consensus size: 52
2009292 CACTGATCTT
*
2009302 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
*
2009354 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
2009406 TGTATCGATACATGCAGGCAA
1 TGTATCGATACATGCAGGCAA
2009427 CTTTTCATAT
Statistics
Matches: 71, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
52 71 1.00
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.28
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:2015612 original size:3 final size:3
Alignment explanation
Indices: 2015604--2015634 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
2015594 CAAACTCTTG
*
2015604 ATC ATC ATC GTC ATC ATC ATC ATC ATC ATC A
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC A
2015635 CTTTGAGTGG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.32, C:0.32, G:0.03, T:0.32
Consensus pattern (3 bp):
ATC
Found at i:2017349 original size:20 final size:20
Alignment explanation
Indices: 2017324--2017361 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
2017314 TTTCACATAA
*
2017324 TGTATCGATAGATTGTAAGG
1 TGTATCGATACATTGTAAGG
2017344 TGTATCGATACATTGTAA
1 TGTATCGATACATTGTAA
2017362 TATGTGTTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.32, C:0.08, G:0.24, T:0.37
Consensus pattern (20 bp):
TGTATCGATACATTGTAAGG
Found at i:2032762 original size:12 final size:12
Alignment explanation
Indices: 2032745--2032895 Score: 50
Period size: 12 Copynumber: 12.6 Consensus size: 12
2032735 TTGTATAATA
2032745 TTTATATTATAT
1 TTTATATTATAT
2032757 TTTATA-TA-AT
1 TTTATATTATAT
*
2032767 TATTATATTTAAAAT
1 T-TTATA-TT-ATAT
*
2032782 ATTATA-TAT-T
1 TTTATATTATAT
* *
2032792 TTTATA-AATTT
1 TTTATATTATAT
*
2032803 TATTATATTAAATAA
1 T-TTATATT--ATAT
2032818 TTTAT-TATATAAT
1 TTTATAT-TAT-AT
* *
2032831 TTTTTAATATAT
1 TTTATATTATAT
*
2032843 TTATAAATT-T-T
1 TT-TATATTATAT
* *
2032854 ATTATTTTATAT
1 TTTATATTATAT
*
2032866 ATTATATTATAT
1 TTTATATTATAT
*
2032878 TTTATTTTA-AT
1 TTTATATTATAT
2032889 TTTATAT
1 TTTATAT
2032896 ATAAGCAAAA
Statistics
Matches: 103, Mismatches: 20, Indels: 33
0.66 0.13 0.21
Matches are distributed among these distances:
10 15 0.15
11 21 0.20
12 38 0.37
13 13 0.13
14 11 0.11
15 5 0.05
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (12 bp):
TTTATATTATAT
Found at i:2032785 original size:17 final size:17
Alignment explanation
Indices: 2032749--2032827 Score: 70
Period size: 18 Copynumber: 4.5 Consensus size: 17
2032739 ATAATATTTA
* *
2032749 TATTATATTTTATATAAT
1 TATTATATTTAAAAT-AT
2032767 TATTATATTTAAAATAT
1 TATTATATTTAAAATAT
* *
2032784 TATATATTTTTATAAATTT
1 TAT-TATATTTA-AAATAT
*
2032803 TATTATATTAAATAAT-T
1 TATTATATTTAA-AATAT
2032820 TATTATAT
1 TATTATAT
2032828 AATTTTTTAA
Statistics
Matches: 52, Mismatches: 6, Indels: 7
0.80 0.09 0.11
Matches are distributed among these distances:
17 15 0.29
18 29 0.56
19 8 0.15
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
TATTATATTTAAAATAT
Found at i:2032804 original size:27 final size:30
Alignment explanation
Indices: 2032774--2032833 Score: 72
Period size: 27 Copynumber: 2.1 Consensus size: 30
2032764 AATTATTATA
*
2032774 TTTAAAATATTATAT-ATTT-TTATA-AAT
1 TTTAAAATATTAAATAATTTATTATATAAT
**
2032801 TTTATTATATTAAATAATTTATTATATAAT
1 TTTAAAATATTAAATAATTTATTATATAAT
2032831 TTT
1 TTT
2032834 TTAATATATT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
27 12 0.44
28 4 0.15
29 5 0.19
30 6 0.22
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (30 bp):
TTTAAAATATTAAATAATTTATTATATAAT
Found at i:2032816 original size:34 final size:38
Alignment explanation
Indices: 2032741--2032827 Score: 98
Period size: 34 Copynumber: 2.4 Consensus size: 38
2032731 TTATTTGTAT
2032741 AATATTTATATTATATTTTATATAATTATTATATTTAA
1 AATATTTATATTATATTTTATATAATTATTATATTTAA
2032779 AATA-TTATA-TAT-TTTTATA-AATT-TTATTATATT-A
1 AATATTTATATTATATTTTATATAATTATTA-TAT-TTAA
*
2032813 AATAATT-TATTATAT
1 AATATTTATATTATAT
2032828 AATTTTTTAA
Statistics
Matches: 44, Mismatches: 0, Indels: 12
0.79 0.00 0.21
Matches are distributed among these distances:
33 3 0.07
34 14 0.32
35 14 0.32
36 4 0.09
37 5 0.11
38 4 0.09
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (38 bp):
AATATTTATATTATATTTTATATAATTATTATATTTAA
Found at i:2032864 original size:17 final size:17
Alignment explanation
Indices: 2032731--2032875 Score: 70
Period size: 17 Copynumber: 8.2 Consensus size: 17
2032721 ACAATCTCAT
2032731 TTATTTGTATAATATTTATA
1 TTATTT-TATAA-ATTT-TA
2032751 TTATATTTTATATAA--TTA
1 -T-TATTTTATA-AATTTTA
*
2032769 TTATATTTA-AAATATTA
1 TTAT-TTTATAAATTTTA
2032786 TATATTTTTATAAATTTTA
1 T-TA-TTTTATAAATTTTA
* *
2032805 TTATATTA-AATAATTTA
1 TTATTTTATAA-ATTTTA
*
2032822 TTA---TATAATTTTTTA
1 TTATTTTATAA-ATTTTA
*
2032837 ATATATTTATAAATTTTA
1 TTAT-TTTATAAATTTTA
* *
2032855 TTATTTTATATATTATA
1 TTATTTTATAAATTTTA
2032872 TTAT
1 TTAT
2032876 ATTTTATTTT
Statistics
Matches: 100, Mismatches: 10, Indels: 32
0.70 0.07 0.23
Matches are distributed among these distances:
14 2 0.02
15 11 0.11
16 6 0.06
17 36 0.36
18 18 0.18
19 15 0.15
21 6 0.06
22 6 0.06
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.60
Consensus pattern (17 bp):
TTATTTTATAAATTTTA
Found at i:2032886 original size:50 final size:49
Alignment explanation
Indices: 2032754--2032888 Score: 146
Period size: 50 Copynumber: 2.7 Consensus size: 49
2032744 ATTTATATTA
* * * *
2032754 TATTTTATATAATTATTATATTTAAAATATTATATATTTTTATAAATTTTAT
1 TATTTTATATATTTATTATATTT--TATTTTA-ATATATTTATAAATTTTAT
* * *
2032806 TATATTAAATAATTTATTATATAATT-TTTTAATATATTTATAAATTTTAT
1 TATTTTATAT-ATTTATTATAT-TTTATTTTAATATATTTATAAATTTTAT
2032856 TATTTTATATATTATATTATATTTTATTTTAAT
1 TATTTTATATATT-TATTATATTTTATTTTAAT
2032889 TTTATATATA
Statistics
Matches: 69, Mismatches: 10, Indels: 10
0.78 0.11 0.11
Matches are distributed among these distances:
49 5 0.07
50 41 0.59
51 4 0.06
52 8 0.12
53 10 0.14
54 1 0.01
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (49 bp):
TATTTTATATATTTATTATATTTTATTTTAATATATTTATAAATTTTAT
Found at i:2033323 original size:22 final size:22
Alignment explanation
Indices: 2033286--2033345 Score: 81
Period size: 22 Copynumber: 2.8 Consensus size: 22
2033276 TGTGTTTTTC
*
2033286 ATAATATTATTAATTATAAAAAT
1 ATAATAATA-TAATTATAAAAAT
2033309 ATAATAATATAATTATAAAAAT
1 ATAATAATATAATTATAAAAAT
2033331 -TAATAAT-T-ATTATAA
1 ATAATAATATAATTATAA
2033346 TATTTTATGA
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
19 7 0.19
20 1 0.03
21 7 0.19
22 13 0.36
23 8 0.22
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (22 bp):
ATAATAATATAATTATAAAAAT
Found at i:2035366 original size:48 final size:49
Alignment explanation
Indices: 2035274--2035369 Score: 117
Period size: 48 Copynumber: 2.0 Consensus size: 49
2035264 GAAATAGTTA
* **
2035274 TTTTAAATTAAAATATATTTTTATTCAAATTATGATATGTAATTAAATT
1 TTTTAAAATAAAATATATTTTTATTCAAATTATGATATAAAATTAAATT
*
2035323 TTTTAAAAT-AAATA-ATTATTTATTACATATTAT-ATATAAAATTAAAT
1 TTTTAAAATAAAATATATT-TTTATT-CAAATTATGATATAAAATTAAAT
2035370 AATAAATATT
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
47 3 0.07
48 23 0.56
49 15 0.37
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (49 bp):
TTTTAAAATAAAATATATTTTTATTCAAATTATGATATAAAATTAAATT
Found at i:2036739 original size:19 final size:20
Alignment explanation
Indices: 2036702--2036742 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
2036692 GATCATATTA
*
2036702 TTATAATAAATTCAATAAAT
1 TTATAATAAAATCAATAAAT
2036722 TTATAATAAAAT-AATAAAT
1 TTATAATAAAATCAATAAAT
2036741 TT
1 TT
2036743 GATTTTATTC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 9 0.45
20 11 0.55
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.41
Consensus pattern (20 bp):
TTATAATAAAATCAATAAAT
Done.