Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032252.1 Gossypioides kirkii chromosome KI_10
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: 47257441
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 3600 characters in sequence are not A, C, G, or T
File 8 of 163
Found at i:2469494 original size:59 final size:60
Alignment explanation
Indices: 2469251--2469558 Score: 191
Period size: 59 Copynumber: 5.2 Consensus size: 60
2469241 GGTGAAATCG
** * *
2469251 GGGTTAAAAATGGAATTTTA--AAAGATTAGGGGGT-AAAATGGTAATTTTTGGTGAAA--TTG
1 GGGTTAAAAATGGAATTTTAGGAAAG-TTTTGGGGTCAAAAT-GTAA-TTTTGG-AAAAGTTTT
** * **
2469310 GGGTTAAAAATGGAATTTTA-G-AAGCTTCGGGGGT-AAAATGGTAATTTTTGGCAAA-TTCG
1 GGGTTAAAAATGGAATTTTAGGAAAG-TTTTGGGGTCAAAAT-GTAA-TTTTGGAAAAGTTTT
* ** * *
2469369 GGGTTAAAAATAGAATTTTA-G-AAGCTTCGGGGGGGGT-AAAATGGTAATTTTGGTGAAA--TC
1 GGGTTAAAAATGGAATTTTAGGAAAG-TT---TTGGGGTCAAAAT-GTAATTTTGG-AAAAGTTT
*
2469429 G
60 T
* * *
2469430 GGGTTAAAAATGGGA-TTTAGGAAAGTTTTGGGGTCAAAATGTATTTTTTG-AAAGTTTT
1 GGGTTAAAAATGGAATTTTAGGAAAGTTTTGGGGTCAAAATGTAATTTTGGAAAAGTTTT
*
2469488 GAGGTT-AAAATGTAATTTTAGGAAAGTTTTGGGGTCAAAATGTAATTTTGGAAAAGTTTT
1 G-GGTTAAAAATGGAATTTTAGGAAAGTTTTGGGGTCAAAATGTAATTTTGGAAAAGTTTT
*
2469548 GGGGTAAAAAT
1 GGGTTAAAAAT
2469559 ATAATTTTGG
Statistics
Matches: 214, Mismatches: 20, Indels: 29
0.81 0.08 0.11
Matches are distributed among these distances:
56 3 0.01
58 25 0.12
59 121 0.57
60 18 0.08
61 25 0.12
62 22 0.10
ACGTcount: A:0.34, C:0.03, G:0.29, T:0.34
Consensus pattern (60 bp):
GGGTTAAAAATGGAATTTTAGGAAAGTTTTGGGGTCAAAATGTAATTTTGGAAAAGTTTT
Found at i:2469538 original size:19 final size:18
Alignment explanation
Indices: 2469514--2469584 Score: 55
Period size: 19 Copynumber: 4.2 Consensus size: 18
2469504 TTTAGGAAAG
2469514 TTTTGGGGTCAAAATGTAA
1 TTTT-GGGTCAAAATGTAA
2469533 TTTT-GG--AAAA-GT--
1 TTTTGGGTCAAAATGTAA
* * *
2469545 TTTGGGGTAAAAATATAA
1 TTTTGGGTCAAAATGTAA
2469563 TTTTGGGTCAAAAATGTAA
1 TTTTGGGTC-AAAATGTAA
2469582 TTT
1 TTT
2469585 CTGGACAATT
Statistics
Matches: 40, Mismatches: 5, Indels: 14
0.68 0.08 0.24
Matches are distributed among these distances:
12 3 0.08
13 2 0.05
14 2 0.05
15 8 0.20
16 1 0.03
17 2 0.05
18 7 0.17
19 15 0.38
ACGTcount: A:0.35, C:0.03, G:0.23, T:0.39
Consensus pattern (18 bp):
TTTTGGGTCAAAATGTAA
Found at i:2469564 original size:30 final size:29
Alignment explanation
Indices: 2469444--2469568 Score: 169
Period size: 30 Copynumber: 4.2 Consensus size: 29
2469434 TAAAAATGGG
*
2469444 ATTTAGGAAAGTTTTGGGGTCAAAATGTA
1 ATTTTGGAAAGTTTTGGGGTCAAAATGTA
* * * *
2469473 TTTTTTGAAAGTTTTGAGGTTAAAATGTA
1 ATTTTGGAAAGTTTTGGGGTCAAAATGTA
2469502 ATTTTAGGAAAGTTTTGGGGTCAAAATGTA
1 ATTTT-GGAAAGTTTTGGGGTCAAAATGTA
* *
2469532 ATTTTGGAAAAGTTTTGGGGTAAAAATATA
1 ATTTTGG-AAAGTTTTGGGGTCAAAATGTA
2469562 ATTTTGG
1 ATTTTGG
2469569 GTCAAAAATG
Statistics
Matches: 83, Mismatches: 11, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
29 30 0.36
30 53 0.64
ACGTcount: A:0.34, C:0.02, G:0.25, T:0.40
Consensus pattern (29 bp):
ATTTTGGAAAGTTTTGGGGTCAAAATGTA
Found at i:2470852 original size:12 final size:12
Alignment explanation
Indices: 2470832--2470861 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
2470822 GTTATTATTG
2470832 TAATATATTTAT
1 TAATATATTTAT
*
2470844 TAATGTATTTAT
1 TAATATATTTAT
2470856 TAATAT
1 TAATAT
2470862 CATTCACCGT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (12 bp):
TAATATATTTAT
Found at i:2471369 original size:20 final size:20
Alignment explanation
Indices: 2471337--2471396 Score: 93
Period size: 20 Copynumber: 3.0 Consensus size: 20
2471327 CAGGGCATGG
2471337 TGGAGCTTGGTGGTCAGCAGA
1 TGGAGC-TGGTGGTCAGCAGA
2471358 TGGAGCTGGTGGTCAGCAGA
1 TGGAGCTGGTGGTCAGCAGA
* *
2471378 TGGAGCAGGTGGCCAGCAG
1 TGGAGCTGGTGGTCAGCAG
2471397 CAGTAGGCAC
Statistics
Matches: 37, Mismatches: 2, Indels: 1
0.93 0.05 0.03
Matches are distributed among these distances:
20 31 0.84
21 6 0.16
ACGTcount: A:0.20, C:0.17, G:0.45, T:0.18
Consensus pattern (20 bp):
TGGAGCTGGTGGTCAGCAGA
Found at i:2471458 original size:14 final size:14
Alignment explanation
Indices: 2471441--2471467 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
2471431 ATTTGGACTA
2471441 TTGTAATTGGGCCT
1 TTGTAATTGGGCCT
2471455 TTGTAATTGGGCC
1 TTGTAATTGGGCC
2471468 CTGGGCCATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.15, C:0.15, G:0.30, T:0.41
Consensus pattern (14 bp):
TTGTAATTGGGCCT
Found at i:2471564 original size:48 final size:48
Alignment explanation
Indices: 2471504--2471610 Score: 119
Period size: 48 Copynumber: 2.2 Consensus size: 48
2471494 ATTTGGACTT
* * ** *
2471504 TTAAATGTTAAAT-TTAATATTTTAATTTTTATTTAAATTTAAATTCAAA
1 TTAAAT-TTAAATATTAA-ATTTTAAATTTAAAATAAATCTAAATTCAAA
* *
2471553 TTAAATTTAAATATTTAATTTTAAATTTAAAATAAATCTAAATTTAAA
1 TTAAATTTAAATATTAAATTTTAAATTTAAAATAAATCTAAATTCAAA
2471601 -TAAATTTAAA
1 TTAAATTTAAA
2471611 ATCAATTTAA
Statistics
Matches: 50, Mismatches: 7, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
47 10 0.20
48 31 0.62
49 9 0.18
ACGTcount: A:0.49, C:0.02, G:0.01, T:0.49
Consensus pattern (48 bp):
TTAAATTTAAATATTAAATTTTAAATTTAAAATAAATCTAAATTCAAA
Found at i:2471568 original size:31 final size:31
Alignment explanation
Indices: 2471533--2471595 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 31
2471523 TTTTAATTTT
* *
2471533 TATTTAAATTTAAATTCAAATTAAATTTAAA
1 TATTTAAATTTAAATTCAAAATAAATCTAAA
* *
2471564 TATTTAATTTTAAATTTAAAATAAATCTAAA
1 TATTTAAATTTAAATTCAAAATAAATCTAAA
2471595 T
1 T
2471596 TTAAATAAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (31 bp):
TATTTAAATTTAAATTCAAAATAAATCTAAA
Found at i:2471583 original size:6 final size:6
Alignment explanation
Indices: 2471503--2471610 Score: 89
Period size: 6 Copynumber: 18.0 Consensus size: 6
2471493 CATTTGGACT
* ** *
2471503 TTTAAA TGTTAAA TTTAATA TTTTAA TTTTTA TTTAAA TTTAAA TTCAAA
1 TTTAAA T-TTAAA TTTAA-A TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* * *
2471553 -TTAAA TTTAAATA TTTAAT TTTAAA TTTAAA -ATAAA TCTAAA TTTAAA
1 TTTAAA TTT-AA-A TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
2471601 --TAAA TTTAAA
1 TTTAAA TTTAAA
2471611 ATCAATTTAA
Statistics
Matches: 83, Mismatches: 11, Indels: 16
0.75 0.10 0.15
Matches are distributed among these distances:
4 4 0.05
5 8 0.10
6 52 0.63
7 15 0.18
8 4 0.05
ACGTcount: A:0.48, C:0.02, G:0.01, T:0.49
Consensus pattern (6 bp):
TTTAAA
Found at i:2471596 original size:42 final size:43
Alignment explanation
Indices: 2471506--2471601 Score: 110
Period size: 42 Copynumber: 2.2 Consensus size: 43
2471496 TTGGACTTTT
* *
2471506 AAATGTTAAATTTAATATTTTAATTTTTATTTAAATTTAAATTC
1 AAAT-TTAAATTTAATATTTTAATTTTAATTTAAATATAAATTC
2471550 AAA-TTAAATTTAA-ATATTTAATTTTAAATTTAAA-ATAAA-TC
1 AAATTTAAATTTAATAT-TTTAATTTT-AATTTAAATATAAATTC
2471591 TAAATTTAAAT
1 -AAATTTAAAT
2471602 AAATTTAAAA
Statistics
Matches: 46, Mismatches: 2, Indels: 9
0.81 0.04 0.16
Matches are distributed among these distances:
41 4 0.09
42 26 0.57
43 13 0.28
44 3 0.07
ACGTcount: A:0.48, C:0.02, G:0.01, T:0.49
Consensus pattern (43 bp):
AAATTTAAATTTAATATTTTAATTTTAATTTAAATATAAATTC
Found at i:2472892 original size:69 final size:69
Alignment explanation
Indices: 2472775--2472917 Score: 223
Period size: 69 Copynumber: 2.1 Consensus size: 69
2472765 AATATCATGG
* * * *
2472775 AAGTCTTTGTATTAAGAGTTGAATTGCAAGTTACAAGATGGTATCTAAACTATTCAAAAGTTTTT
1 AAGTTTTTGTATTAAGAGTCGAATTGCAAGTTACAAGATGGTAACTAAACTACTCAAAAGTTTTT
*
2472840 ATTT
66 ACTT
* *
2472844 AAGTTTTTGTATTAGGAGTCGGATTGCAAGTTACAAGATGGTAACTAAACTACTCAAAAGTTTTT
1 AAGTTTTTGTATTAAGAGTCGAATTGCAAGTTACAAGATGGTAACTAAACTACTCAAAAGTTTTT
2472909 ACTT
66 ACTT
2472913 AAGTT
1 AAGTT
2472918 ATTGGGCTGG
Statistics
Matches: 67, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
69 67 1.00
ACGTcount: A:0.34, C:0.10, G:0.17, T:0.38
Consensus pattern (69 bp):
AAGTTTTTGTATTAAGAGTCGAATTGCAAGTTACAAGATGGTAACTAAACTACTCAAAAGTTTTT
ACTT
Found at i:2479247 original size:2 final size:2
Alignment explanation
Indices: 2479240--2479278 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
2479230 GAAGACTACT
2479240 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2479279 TGCATTTTAG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2483829 original size:17 final size:17
Alignment explanation
Indices: 2483807--2483845 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
2483797 AGGTGGAGAA
* *
2483807 CTTGTTCGTTGAGACTT
1 CTTGTTCGTAGAGAATT
2483824 CTTGTTCGTAGAGAATT
1 CTTGTTCGTAGAGAATT
2483841 CTTGT
1 CTTGT
2483846 CAAGGTGGAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.15, C:0.15, G:0.23, T:0.46
Consensus pattern (17 bp):
CTTGTTCGTAGAGAATT
Found at i:2483987 original size:28 final size:28
Alignment explanation
Indices: 2483947--2484057 Score: 114
Period size: 28 Copynumber: 3.8 Consensus size: 28
2483937 TAGACCTTTT
2483947 TATTTTATTTTAATTAGAGTAAGTCATC
1 TATTTTATTTTAATTAGAGTAAGTCATC
* * * ** *
2483975 TATTTTATTTTAATAAATAAACTAGACTTTTT
1 TATTTTATTTTAAT---TAGAGTA-AGTCATC
*
2484007 TATTTTATTTTAATTAGAGTAAATCATC
1 TATTTTATTTTAATTAGAGTAAGTCATC
*
2484035 TATTTTATTTTAATTAGAATAAG
1 TATTTTATTTTAATTAGAGTAAG
2484058 GTGTTTCAAC
Statistics
Matches: 65, Mismatches: 14, Indels: 8
0.75 0.16 0.09
Matches are distributed among these distances:
28 38 0.58
29 5 0.08
31 5 0.08
32 17 0.26
ACGTcount: A:0.36, C:0.05, G:0.07, T:0.51
Consensus pattern (28 bp):
TATTTTATTTTAATTAGAGTAAGTCATC
Found at i:2484019 original size:60 final size:60
Alignment explanation
Indices: 2483929--2484048 Score: 222
Period size: 60 Copynumber: 2.0 Consensus size: 60
2483919 AGTAAAGTCC
*
2483929 AAATAAACTAGACCTTTTTATTTTATTTTAATTAGAGTAAGTCATCTATTTTATTTTAAT
1 AAATAAACTAGACCTTTTTATTTTATTTTAATTAGAGTAAATCATCTATTTTATTTTAAT
*
2483989 AAATAAACTAGACTTTTTTATTTTATTTTAATTAGAGTAAATCATCTATTTTATTTTAAT
1 AAATAAACTAGACCTTTTTATTTTATTTTAATTAGAGTAAATCATCTATTTTATTTTAAT
2484049 TAGAATAAGG
Statistics
Matches: 58, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
60 58 1.00
ACGTcount: A:0.36, C:0.07, G:0.06, T:0.51
Consensus pattern (60 bp):
AAATAAACTAGACCTTTTTATTTTATTTTAATTAGAGTAAATCATCTATTTTATTTTAAT
Found at i:2485843 original size:6 final size:6
Alignment explanation
Indices: 2485829--2485859 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
2485819 GATTTCATGA
*
2485829 TTTAAT TTTATT TTTATT TTTATT TTTATT T
1 TTTATT TTTATT TTTATT TTTATT TTTATT T
2485860 AATCCTTGAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (6 bp):
TTTATT
Found at i:2487266 original size:30 final size:30
Alignment explanation
Indices: 2487231--2487292 Score: 124
Period size: 30 Copynumber: 2.1 Consensus size: 30
2487221 AAAATATCTA
2487231 TTAATCATATGTTATCAAATGAAAATAATC
1 TTAATCATATGTTATCAAATGAAAATAATC
2487261 TTAATCATATGTTATCAAATGAAAATAATC
1 TTAATCATATGTTATCAAATGAAAATAATC
2487291 TT
1 TT
2487293 CAATGAGGGG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.45, C:0.10, G:0.06, T:0.39
Consensus pattern (30 bp):
TTAATCATATGTTATCAAATGAAAATAATC
Found at i:2487402 original size:4 final size:4
Alignment explanation
Indices: 2487393--2487421 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
2487383 CAATAACTCA
2487393 TAAT TAAT TAAT TAAT TAAT TAAT TAAT T
1 TAAT TAAT TAAT TAAT TAAT TAAT TAAT T
2487422 TGATAAGTGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (4 bp):
TAAT
Found at i:2487727 original size:19 final size:19
Alignment explanation
Indices: 2487703--2487739 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
2487693 ATAACAGGGA
*
2487703 GTGGTTGGTTGATTTTCAT
1 GTGGTTGGTTGACTTTCAT
2487722 GTGGTTGGTTGACTTTCA
1 GTGGTTGGTTGACTTTCA
2487740 AATTAGGTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.11, C:0.08, G:0.32, T:0.49
Consensus pattern (19 bp):
GTGGTTGGTTGACTTTCAT
Found at i:2489880 original size:18 final size:18
Alignment explanation
Indices: 2489857--2489894 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 18
2489847 TAATATAATT
2489857 TTATTTG-GTTTATTCGAA
1 TTATTTGAG-TTATTCGAA
2489875 TTATTTGAGTTATTCGAA
1 TTATTTGAGTTATTCGAA
2489893 TT
1 TT
2489895 CAAAAATTCA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 18 0.95
19 1 0.05
ACGTcount: A:0.24, C:0.05, G:0.16, T:0.55
Consensus pattern (18 bp):
TTATTTGAGTTATTCGAA
Found at i:2497267 original size:20 final size:20
Alignment explanation
Indices: 2497242--2497283 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
2497232 TGATTTGGTA
2497242 TAATTATATATACAAAATTT
1 TAATTATATATACAAAATTT
* **
2497262 TAATTATTTATGTAAAATTT
1 TAATTATATATACAAAATTT
2497282 TA
1 TA
2497284 TATATAAAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.50
Consensus pattern (20 bp):
TAATTATATATACAAAATTT
Found at i:2501407 original size:12 final size:12
Alignment explanation
Indices: 2501390--2501415 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
2501380 ATACCATAAA
2501390 TTACATGTTAAT
1 TTACATGTTAAT
2501402 TTACATGTTAAT
1 TTACATGTTAAT
2501414 TT
1 TT
2501416 TTTAAAATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.31, C:0.08, G:0.08, T:0.54
Consensus pattern (12 bp):
TTACATGTTAAT
Found at i:2501907 original size:19 final size:18
Alignment explanation
Indices: 2501854--2501907 Score: 63
Period size: 18 Copynumber: 2.9 Consensus size: 18
2501844 TAAAAAGAAT
*
2501854 ATATTTTTATATTTATTTA
1 ATATTTTTATATTT-TTAA
* *
2501873 ATAATTTTAATATTTTAAA
1 AT-ATTTTTATATTTTTAA
2501892 ATATTTTTATATTTTT
1 ATATTTTTATATTTTT
2501908 TAACTTTTAA
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
18 12 0.41
19 6 0.21
20 11 0.38
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (18 bp):
ATATTTTTATATTTTTAA
Found at i:2502430 original size:29 final size:30
Alignment explanation
Indices: 2502398--2502456 Score: 86
Period size: 29 Copynumber: 2.0 Consensus size: 30
2502388 AAAAAGAAAG
2502398 AAAATTATATTTA-ATCTCTTC-AAAATAAT
1 AAAATTATATTTAGAT-TCTTCAAAAATAAT
*
2502427 AAAATTATATTTAGATTTTTCAAAAATAAT
1 AAAATTATATTTAGATTCTTCAAAAATAAT
2502457 TAATATTCAA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
29 17 0.63
30 10 0.37
ACGTcount: A:0.49, C:0.07, G:0.02, T:0.42
Consensus pattern (30 bp):
AAAATTATATTTAGATTCTTCAAAAATAAT
Found at i:2504466 original size:161 final size:158
Alignment explanation
Indices: 2504146--2504630 Score: 751
Period size: 161 Copynumber: 3.0 Consensus size: 158
2504136 TTTGTAAAAT
* *
2504146 TTTTAGATTTTCACAATAAAATCAAACGTCATAATCACATAATATATTGATAGATATTGATAAAT
1 TTTTAAATTTTCACAATAAAATCAAACGTCATAATCTCATAATATATTGATAGATATTGATAAAT
* *
2504211 AATCATATATATATATATATACACACTTAGTACTAAATACACTGTATGTTAGTAAAAGAAACATA
66 AATCACATATATATATATA-ACACACTTAGTACTAAATACACTATATGTTAGTAAAAGAAACATA
*
2504276 AAAGTTATTGTATTAAGATTTAGATTGCA
130 AAAGTTATTGTATTAAGATTCAGATTGCA
*
2504305 TTTTAAATTTTCACAATAAAATCAAACGACATAATCTCATAATATATTGATAGATATTGATAAAT
1 TTTTAAATTTTCACAATAAAATCAAACGTCATAATCTCATAATATATTGATAGATATTGATAAAT
2504370 AATCACACATATATATATATACACACACTTAGTACTAAATACACTATATGTTAGTAAAAGAAACA
66 AAT--CACATATATATATATA-ACACACTTAGTACTAAATACACTATATGTTAGTAAAAGAAACA
*
2504435 TAAAAGTTCTTGTATTAAGATTCAGATTGCA
128 TAAAAGTTATTGTATTAAGATTCAGATTGCA
* *
2504466 TTTTAAATTTTCACAATAAAATCAAATGTTATAATCTCATAATATATTGATAGATATTGATAAAT
1 TTTTAAATTTTCACAATAAAATCAAACGTCATAATCTCATAATATATTGATAGATATTGATAAAT
* * *
2504531 AATCAC--ATGTATATAT-ACACACTTAGTACTAAATACACTACATGTTATATAGTAAAAGTAAC
66 AATCACATATATATATATAACACACTTAGTACTAAATACACTATATG---T-TAGTAAAAGAAAC
* *
2504593 ATAAAAGGTATTGTATTAAGATTCAAATTGCA
127 ATAAAAGTTATTGTATTAAGATTCAGATTGCA
2504625 TTTTAA
1 TTTTAA
2504631 TTTCTTTGCT
Statistics
Matches: 303, Mismatches: 17, Indels: 12
0.91 0.05 0.04
Matches are distributed among these distances:
155 27 0.09
157 9 0.03
158 1 0.00
159 115 0.38
161 151 0.50
ACGTcount: A:0.45, C:0.11, G:0.09, T:0.35
Consensus pattern (158 bp):
TTTTAAATTTTCACAATAAAATCAAACGTCATAATCTCATAATATATTGATAGATATTGATAAAT
AATCACATATATATATATAACACACTTAGTACTAAATACACTATATGTTAGTAAAAGAAACATAA
AAGTTATTGTATTAAGATTCAGATTGCA
Found at i:2506233 original size:18 final size:18
Alignment explanation
Indices: 2506212--2506248 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
2506202 CAGATAATTT
2506212 AAATATAA-AATATTTTAA
1 AAATATAATAAT-TTTTAA
2506230 AAATATAATAATTTTTAA
1 AAATATAATAATTTTTAA
2506248 A
1 A
2506249 TTATTTTTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 15 0.83
19 3 0.17
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (18 bp):
AAATATAATAATTTTTAA
Found at i:2509255 original size:20 final size:19
Alignment explanation
Indices: 2509220--2509257 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
2509210 TTACATTCTG
2509220 TGTAGTTTGGTCTTTTTTT
1 TGTAGTTTGGTCTTTTTTT
* *
2509239 TGTAGTTTTGTGTTTTTTT
1 TGTAGTTTGGTCTTTTTTT
2509258 GTGACATTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.05, C:0.03, G:0.21, T:0.71
Consensus pattern (19 bp):
TGTAGTTTGGTCTTTTTTT
Found at i:2521113 original size:19 final size:16
Alignment explanation
Indices: 2521066--2521113 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 16
2521056 TTCCTATTTT
2521066 TTAAATATTTTTATAA
1 TTAAATATTTTTATAA
*
2521082 TTAGATAATTTTTATACA
1 TTAAAT-ATTTTTATA-A
2521100 TTATTAATATTTTT
1 TTA--AATATTTTT
2521114 TTATATCAAG
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
16 5 0.19
17 9 0.35
18 4 0.15
19 6 0.23
20 2 0.08
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.58
Consensus pattern (16 bp):
TTAAATATTTTTATAA
Found at i:2522097 original size:12 final size:12
Alignment explanation
Indices: 2522080--2522104 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2522070 AAACTACGAT
2522080 GCTCATCGATCC
1 GCTCATCGATCC
2522092 GCTCATCGATCC
1 GCTCATCGATCC
2522104 G
1 G
2522105 TTCTACAGGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.40, G:0.20, T:0.24
Consensus pattern (12 bp):
GCTCATCGATCC
Found at i:2525478 original size:142 final size:143
Alignment explanation
Indices: 2525242--2525506 Score: 408
Period size: 142 Copynumber: 1.9 Consensus size: 143
2525232 GCACAGCATG
**
2525242 TAGTATGAATTGAACCTATGCCCTATAATATACAGATAAGGCATTTGTCGATGAACTAGCCTAAG
1 TAGTATGAATCAAACCTATGCCCTATAATATACAGATAAGGCATTTGTCGATGAACTAGCCTAAG
*
2525307 TAGTACTCAACTTATACTTATGCCTCATTTAAGGTACAAGTTTAAACCCTACTAATGGTGAACTA
66 TAGTACTCAACATATACTTATGCCTCATTTAAGGTACAAGTTTAAACCCTACTAATGGTGAACTA
2525372 TTCGCATAGCGCA
131 TTCGCATAGCGCA
* * ** *
2525385 TAGTATGAATCAAACCTA-GTCCTATAATATA-GGTATAAGGCATTTGTCGATGAGTTAGCTTAA
1 TAGTATGAATCAAACCTATGCCCTATAATATACAG-ATAAGGCATTTGTCGATGAACTAGCCTAA
* * *
2525448 GTAGTATTCAACATATACTTATGCCTCATTTAATGTACAAGTTTAAACTCTACTAATGG
65 GTAGTACTCAACATATACTTATGCCTCATTTAAGGTACAAGTTTAAACCCTACTAATGG
2525507 CGAATTTTTT
Statistics
Matches: 110, Mismatches: 11, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
141 1 0.01
142 93 0.85
143 16 0.15
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Consensus pattern (143 bp):
TAGTATGAATCAAACCTATGCCCTATAATATACAGATAAGGCATTTGTCGATGAACTAGCCTAAG
TAGTACTCAACATATACTTATGCCTCATTTAAGGTACAAGTTTAAACCCTACTAATGGTGAACTA
TTCGCATAGCGCA
Found at i:2531841 original size:15 final size:16
Alignment explanation
Indices: 2531823--2531858 Score: 56
Period size: 15 Copynumber: 2.3 Consensus size: 16
2531813 ATATTTTAAC
2531823 AAATAAAATTAA-AAA
1 AAATAAAATTAACAAA
*
2531838 AAATGAAATTAACAAA
1 AAATAAAATTAACAAA
2531854 AAATA
1 AAATA
2531859 TAGTGAGAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
15 11 0.61
16 7 0.39
ACGTcount: A:0.75, C:0.03, G:0.03, T:0.19
Consensus pattern (16 bp):
AAATAAAATTAACAAA
Found at i:2544754 original size:21 final size:21
Alignment explanation
Indices: 2544706--2544755 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 21
2544696 TTGCTGTTGT
* *
2544706 CTCCGCTTGCCTCTCTATTGC
1 CTCCGCTTGCCTCACTACTGC
* * *
2544727 TTTCGCTTGCCTCACTGCTGC
1 CTCCGCTTGCCTCACTACTGC
2544748 CTCCGCTT
1 CTCCGCTT
2544756 TATGTTGTAG
Statistics
Matches: 22, Mismatches: 7, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.04, C:0.42, G:0.16, T:0.38
Consensus pattern (21 bp):
CTCCGCTTGCCTCACTACTGC
Found at i:2550325 original size:32 final size:32
Alignment explanation
Indices: 2550256--2550322 Score: 116
Period size: 33 Copynumber: 2.1 Consensus size: 32
2550246 TTGATTTAAA
2550256 TTTAAAAATACATATTAGTGACAACATTTTAC
1 TTTAAAAATACATATTAGTGACAACATTTTAC
*
2550288 TTTAAAATATATATATTAGTGACAACATTTTAC
1 TTTAAAA-ATACATATTAGTGACAACATTTTAC
2550321 TT
1 TT
2550323 AAATATTTAG
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
32 7 0.21
33 26 0.79
ACGTcount: A:0.42, C:0.10, G:0.06, T:0.42
Consensus pattern (32 bp):
TTTAAAAATACATATTAGTGACAACATTTTAC
Found at i:2550357 original size:8 final size:8
Alignment explanation
Indices: 2550344--2550437 Score: 65
Period size: 8 Copynumber: 11.8 Consensus size: 8
2550334 CTGTTTTTAT
2550344 TAATTAAA
1 TAATTAAA
2550352 TAATTAAA
1 TAATTAAA
*
2550360 T-ATTTAA
1 TAATTAAA
2550367 T--TTAATA
1 TAATTAA-A
2550374 TAATTAAA
1 TAATTAAA
2550382 TAATTAAA
1 TAATTAAA
*
2550390 T-ATT--T
1 TAATTAAA
2550395 TCAATTAAA
1 T-AATTAAA
*
2550404 TATTTAAA
1 TAATTAAA
2550412 TAAAATTAAA
1 T--AATTAAA
2550422 TAATTATATA
1 TAATTA-A-A
2550432 TAATTA
1 TAATTA
2550438 TTTACGAAAA
Statistics
Matches: 69, Mismatches: 6, Indels: 20
0.73 0.06 0.21
Matches are distributed among these distances:
5 1 0.01
6 3 0.04
7 14 0.20
8 31 0.45
9 6 0.09
10 14 0.20
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.45
Consensus pattern (8 bp):
TAATTAAA
Found at i:2550364 original size:34 final size:30
Alignment explanation
Indices: 2550344--2550582 Score: 107
Period size: 30 Copynumber: 7.7 Consensus size: 30
2550334 CTGTTTTTAT
2550344 TAATTAAATAATTAAATATTTAATTTAATA
1 TAATTAAATAATTAAATATTTAATTTAATA
2550374 TAATTAAATAATTAAATATTTTCAA-TTAA-A
1 TAATTAAATAATTAAATA-TTT-AATTTAATA
* *
2550404 TATTTAAATAAAATTAAATAATT-A--T-ATA
1 TAATTAAAT--AATTAAATATTTAATTTAATA
** *** *
2550432 TAATTATTTACGAAAATATTTTAAATTAAATA
1 TAATTAAATAATTAAATA-TTT-AATTTAATA
* **
2550464 GTTAATTAAATATAATTAAATAATTAA-TCGATA
1 --TAATT-AA-ATAATTAAATATTTAATTTAATA
** * ** * *
2550497 TTGTT-TATAATTAAATACATAATTAAACA
1 TAATTAAATAATTAAATATTTAATTTAATA
*
2550526 TAATTAAATAATTTAATATAATTATTTACTTTAATA
1 TAATTAAATAA--T--TA-AA-TATTTAATTTAATA
2550562 TAATTAAATAATTAAATATTT
1 TAATTAAATAATTAAATATTT
2550583 TAACGTAAAT
Statistics
Matches: 152, Mismatches: 34, Indels: 46
0.66 0.15 0.20
Matches are distributed among these distances:
26 6 0.04
27 3 0.02
28 22 0.14
29 8 0.05
30 36 0.24
31 14 0.09
32 17 0.11
33 4 0.03
34 10 0.07
35 5 0.03
36 27 0.18
ACGTcount: A:0.51, C:0.03, G:0.02, T:0.44
Consensus pattern (30 bp):
TAATTAAATAATTAAATATTTAATTTAATA
Found at i:2550379 original size:22 final size:21
Alignment explanation
Indices: 2550343--2550410 Score: 75
Period size: 22 Copynumber: 3.2 Consensus size: 21
2550333 ACTGTTTTTA
2550343 TTAATTAA-ATAATTAAATAT
1 TTAATTAATATAATTAAATAT
*
2550363 TTAATTTAATATAATTAAATAA
1 TTAA-TTAATATAATTAAATAT
* * *
2550385 TTAAATATTTTCAATTAAATAT
1 TTAATTAATAT-AATTAAATAT
2550407 TTAA
1 TTAA
2550411 ATAAAATTAA
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
20 4 0.10
21 8 0.20
22 28 0.70
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.47
Consensus pattern (21 bp):
TTAATTAATATAATTAAATAT
Found at i:2550391 original size:18 final size:18
Alignment explanation
Indices: 2550344--2550580 Score: 95
Period size: 18 Copynumber: 13.1 Consensus size: 18
2550334 CTGTTTTTAT
2550344 TAATTAAATAATTAAATA
1 TAATTAAATAATTAAATA
2550362 T--TT-AAT--TT-AATA
1 TAATTAAATAATTAAATA
2550374 TAATTAAATAATTAAATA
1 TAATTAAATAATTAAATA
*
2550392 TTTTCAATTAAATATTTAAATA
1 ---T-AATTAAATAATTAAATA
* *
2550414 AAATTAAATAATTATATA
1 TAATTAAATAATTAAATA
** ***
2550432 TAATTATTTACGAAAATA
1 TAATTAAATAATTAAATA
2550450 TTTTAAATTAAATAGTTAATTAAATA
1 ---T-AATT-AA-A--TAATTAAATA
2550476 TAATTAAATAATT-AATCGA
1 TAATTAAATAATTAAAT--A
*
2550495 T-ATT--GT--TTATAAT-
1 TAATTAAATAATTA-AATA
* * *
2550508 TAAATACATAATTAAACA
1 TAATTAAATAATTAAATA
*
2550526 TAATTAAATAATTTAATA
1 TAATTAAATAATTAAATA
** * *
2550544 TAATTATTTACTTTAATA
1 TAATTAAATAATTAAATA
2550562 TAATTAAATAATTAAATA
1 TAATTAAATAATTAAATA
2550580 T
1 T
2550581 TTTAACGTAA
Statistics
Matches: 160, Mismatches: 31, Indels: 56
0.65 0.13 0.23
Matches are distributed among these distances:
12 5 0.03
13 3 0.02
14 6 0.04
15 6 0.04
16 7 0.04
17 7 0.04
18 86 0.54
19 2 0.01
20 1 0.01
21 4 0.03
22 24 0.15
23 2 0.01
26 7 0.04
ACGTcount: A:0.52, C:0.03, G:0.02, T:0.44
Consensus pattern (18 bp):
TAATTAAATAATTAAATA
Found at i:2550534 original size:112 final size:110
Alignment explanation
Indices: 2550415--2551081 Score: 854
Period size: 112 Copynumber: 6.0 Consensus size: 110
2550405 ATTTAAATAA
*** * * *
2550415 AATTAAATAA-TTATATATAATTATTTACGAAAATAT-TTTAAATTAAATAGTTAATTAAATATA
1 AATTAAATAATTTA-ATATAATTATTTACTTTAATATAATTAAA-TAATTAATT-ATTAAAT-TA
* * *
2550478 ATTAAATAATTAATCGATATTGTTTATAATTAAATACATAATTAAACAT
62 AATAATTAATTAATCGATACTGTTTATAATTAAATACATAATTAAACAT
* **
2550527 AATTAAATAATTTAATATAATTATTTACTTTAATATAATTAAATAATTAAATATTTTAACGTAAA
1 AATTAAATAATTTAATATAATTATTTACTTTAATATAATTAAATAATT-AAT-TATTAAATTAAA
* *
2550592 TAGTTAATTAATCGATACTGTTTATAATTAAATACATAGTTAAACAT
64 TAATTAATTAATCGATACTGTTTATAATTAAATACATAATTAAACAT
* * *
2550639 GATTAAATAATTTAATATAATTATTTACTTTAATATAATTAAATAATTAAATATTTTTAATTAAA
1 AATTAAATAATTTAATATAATTATTTACTTTAATATAATTAAATAATT-AAT-TATTAAATTAAA
*
2550704 TAATTAGTTAATCGATACTGTTTATAATTAAATACATAATTAAACAT
64 TAATTAATTAATCGATACTGTTTATAATTAAATACATAATTAAACAT
* * *
2550751 GATTAAATAATTTAATACAATTATTTACTTTAATATAATTAAATAATTGAATCTATTAACTTAAA
1 AATTAAATAATTTAATATAATTATTTACTTTAATATAATTAAATAATT-AAT-TATTAAATTAAA
* * *
2550816 T-TTGTAATTAATCGATACTTTTTATAATTAAATACATAATTAAATAT
64 TAAT-TAATTAATCGATACTGTTTATAATTAAATACATAATTAAACAT
* * * *
2550863 GATTAAATAATTTAATATACTTATTTAATTTAATATAATTAAATAATTAAATCTATTAACTTAAA
1 AATTAAATAATTTAATATAATTATTTACTTTAATATAATTAAATAATT-AAT-TATTAAATTAAA
*
2550928 TATTTAATTAATCGATACTGTTTATAATTAAATACATAATTAAACAT
64 TAATTAATTAATCGATACTGTTTATAATTAAATACATAATTAAACAT
* * * *
2550975 AATTAAAAAATTTAATATAATTATTTACTTTAATATAATTGAATAATTAAATCTTTTAACTTAAA
1 AATTAAATAATTTAATATAATTATTTACTTTAATATAATTAAATAATT-AAT-TATTAAATTAAA
* * *
2551040 TATTTAATTAATTGATACGGTTTATAATTAAATACATAATTA
64 TAATTAATTAATCGATACTGTTTATAATTAAATACATAATTA
2551082 TTTAATTATT
Statistics
Matches: 504, Mismatches: 45, Indels: 12
0.90 0.08 0.02
Matches are distributed among these distances:
111 1 0.00
112 486 0.96
113 16 0.03
114 1 0.00
ACGTcount: A:0.48, C:0.05, G:0.04, T:0.44
Consensus pattern (110 bp):
AATTAAATAATTTAATATAATTATTTACTTTAATATAATTAAATAATTAATTATTAAATTAAATA
ATTAATTAATCGATACTGTTTATAATTAAATACATAATTAAACAT
Found at i:2550620 original size:54 final size:52
Alignment explanation
Indices: 2550560--2551073 Score: 187
Period size: 54 Copynumber: 9.2 Consensus size: 52
2550550 TTTACTTTAA
*
2550560 TATAATTAAATAATTAAATATTTTAACGTAAATAGTTAATTAATCGATACTGTT
1 TATAATTAAATAATTAAATATTTTAA-ATAAATA-TTAATTAATCGATACTGTT
* * *
2550614 TATAATTAAATACATAGTTAAACATGATTAAAT-AAT-TTAATATAAT-TATTTACT-TT
1 TATAATTAAAT--A-A-TTAAATAT-TTTAAATAAATATTAAT-TAATCGA--TACTGTT
* *
2550670 AATATAATTAAATAATTAAATATTTTTAATTAAATAATTAGTTAATCGATACTGTT
1 --TATAATTAAATAATTAAATA-TTTTAAATAAAT-ATTAATTAATCGATACTGTT
* * * *
2550726 TATAATTAAATACATAATTAAACATGATTAAAT-AAT-TTAATACAAT-TATTTACT-TT
1 TATAATT--A-A-ATAATTAAATAT-TTTAAATAAATATTAAT-TAATCGA--TACTGTT
* * * * * *
2550782 AATATAATTAAATAATTGAATCTATTAACTTAAATTTGTAATTAATCGATACTTTT
1 --TATAATTAAATAATTAAATATTTTAA-ATAAATAT-TAATTAATCGATACTGTT
* * * *
2550838 TATAATTAAATACATAATTAAATATGATTAAAT-AAT-TTAATATACT-TATTTAAT-TT
1 TATAATT--A-A-ATAATTAAATAT-TTTAAATAAATATTAAT-TAATCGA--TACTGTT
* * *
2550894 AATATAATTAAATAATTAAATCTATTAACTTAAATATTTAATTAATCGATACTGTT
1 --TATAATTAAATAATTAAATATTTTAA-ATAAATA-TTAATTAATCGATACTGTT
* * *
2550950 TATAATTAAATACATAATTAAACATAATTAAA-AAAT-TTAATATAAT-TATTTACT-TT
1 TATAATT--A-A-ATAATTAAATAT-TTTAAATAAATATTAAT-TAATCGA--TACTGTT
* * * * *
2551006 AATATAATTGAATAATTAAATCTTTTAACTTAAATATTTAATTAATTGATACGGTT
1 --TATAATTAAATAATTAAATATTTTAA-ATAAATA-TTAATTAATCGATACTGTT
2551062 TATAATTAAATA
1 TATAATTAAATA
2551074 CATAATTATT
Statistics
Matches: 352, Mismatches: 44, Indels: 128
0.67 0.08 0.24
Matches are distributed among these distances:
53 14 0.04
54 86 0.24
55 54 0.15
56 53 0.15
57 55 0.16
58 76 0.22
59 14 0.04
ACGTcount: A:0.47, C:0.05, G:0.04, T:0.44
Consensus pattern (52 bp):
TATAATTAAATAATTAAATATTTTAAATAAATATTAATTAATCGATACTGTT
Found at i:2550691 original size:18 final size:18
Alignment explanation
Indices: 2550515--2551022 Score: 138
Period size: 18 Copynumber: 27.3 Consensus size: 18
2550505 AATTAAATAC
* *
2550515 ATAATTAAACATAATTAA
1 ATAATTTAATATAATTAA
*
2550533 ATAATTTAATATAATTAT
1 ATAATTTAATATAATTAA
* *
2550551 TTACTTTAATATAATTAA
1 ATAATTTAATATAATTAA
* *
2550569 ATAATTAAATATTTTAACGTAA
1 ATAATTTAATA---TAA-TTAA
* **
2550591 AT-AGTTAAT-TAA-TCG
1 ATAATTTAATATAATTAA
*
2550606 ATACTGTT--TATAATTAA
1 ATAAT-TTAATATAATTAA
* *
2550623 ATACATAGTTAAACATGATTAA
1 ATA-AT--TT-AATATAATTAA
*
2550645 ATAATTTAATATAATTAT
1 ATAATTTAATATAATTAA
* *
2550663 TTACTTTAATATAATTAA
1 ATAATTTAATATAATTAA
*
2550681 ATAATTAAATATTTTTAATTAA
1 ATAATTTAATA----TAATTAA
* **
2550703 ATAA-TTAGT-TAA-TCG
1 ATAATTTAATATAATTAA
*
2550718 ATACTGTT--TATAATTAA
1 ATAAT-TTAATATAATTAA
* *
2550735 ATACATAATTAAACATGATTAA
1 ATA-AT--TT-AATATAATTAA
* *
2550757 ATAATTTAATACAATTAT
1 ATAATTTAATATAATTAA
* *
2550775 TTACTTTAATATAATTAA
1 ATAATTTAATATAATTAA
*
2550793 ATAATTGAATCTATTAACTTAA
1 ATAATTTAA--TA-TAA-TTAA
**
2550815 AT--TTGTAAT-TAA-TCG
1 ATAATT-TAATATAATTAA
* *
2550830 ATACTTT-TTATAATTAA
1 ATAATTTAATATAATTAA
*
2550847 ATACATAATTAAATATGATTAA
1 ATA-AT--TT-AATATAATTAA
* *
2550869 ATAATTTAATATACTTAT
1 ATAATTTAATATAATTAA
*
2550887 TTAATTTAATATAATTAA
1 ATAATTTAATATAATTAA
*
2550905 ATAATTAAATCTATTAACTTAA
1 ATAATTTAA--TA-TAA-TTAA
**
2550927 AT-ATTTAAT-TAA-TCG
1 ATAATTTAATATAATTAA
*
2550942 ATACTGTT--TATAATTAA
1 ATAAT-TTAATATAATTAA
*
2550959 ATACATAATTAAACATAATTAA
1 ATA-AT--TT-AATATAATTAA
* *
2550981 AAAATTTAATATAATTAT
1 ATAATTTAATATAATTAA
* * *
2550999 TTACTTTAATATAATTGA
1 ATAATTTAATATAATTAA
2551017 ATAATT
1 ATAATT
2551023 AAATCTTTTA
Statistics
Matches: 349, Mismatches: 88, Indels: 106
0.64 0.16 0.20
Matches are distributed among these distances:
15 17 0.05
16 17 0.05
17 33 0.09
18 156 0.45
19 17 0.05
20 8 0.02
21 32 0.09
22 69 0.20
ACGTcount: A:0.47, C:0.05, G:0.03, T:0.44
Consensus pattern (18 bp):
ATAATTTAATATAATTAA
Found at i:2551109 original size:112 final size:111
Alignment explanation
Indices: 2550484--2551082 Score: 887
Period size: 112 Copynumber: 5.4 Consensus size: 111
2550474 TATAATTAAA
* * *
2550484 TAATTAATCGATATTGTTTATAATTAAATACATAATTAAACATAATTAAATAATTTAATATAATT
1 TAATTAATCGATACTGTTTATAATTAAATACATAATTATA-ATGATTAAATAATTTAATATAATT
* * *
2550549 ATTTACTTTAATATAATTAAATAATTAAATATTTTAACGTAAATAGT
65 ATTTACTTTAATATAATTAAATAATTAAATCTTTTAACTTAAATATT
* *
2550596 TAATTAATCGATACTGTTTATAATTAAATACATAGTTAAACATGATTAAATAATTTAATATAATT
1 TAATTAATCGATACTGTTTATAATTAAATACATAATTATA-ATGATTAAATAATTTAATATAATT
* *
2550661 ATTTACTTTAATATAATTAAATAATTAAATATTTTTAA-TTAAATAAT
65 ATTTACTTTAATATAATTAAATAATTAAAT-CTTTTAACTTAAATATT
* * *
2550708 TAGTTAATCGATACTGTTTATAATTAAATACATAATTAAACATGATTAAATAATTTAATACAATT
1 TAATTAATCGATACTGTTTATAATTAAATACATAATTATA-ATGATTAAATAATTTAATATAATT
* *
2550773 ATTTACTTTAATATAATTAAATAATTGAATCTATTAACTTAAAT-TT
65 ATTTACTTTAATATAATTAAATAATTAAATCTTTTAACTTAAATATT
* * *
2550819 GTAATTAATCGATACTTTTTATAATTAAATACATAATTAAATATGATTAAATAATTTAATATACT
1 -TAATTAATCGATACTGTTTATAATTAAATACATAATTATA-ATGATTAAATAATTTAATATAAT
* *
2550884 TATTTAATTTAATATAATTAAATAATTAAATCTATTAACTTAAATATT
64 TATTTACTTTAATATAATTAAATAATTAAATCTTTTAACTTAAATATT
* * *
2550932 TAATTAATCGATACTGTTTATAATTAAATACATAATTAAACATAATTAAAAAATTTAATATAATT
1 TAATTAATCGATACTGTTTATAATTAAATACATAATTATA-ATGATTAAATAATTTAATATAATT
*
2550997 ATTTACTTTAATATAATTGAATAATTAAATCTTTTAACTTAAATATT
65 ATTTACTTTAATATAATTAAATAATTAAATCTTTTAACTTAAATATT
* *
2551044 TAATTAATTGATACGGTTTATAATTAAATACATAATTAT
1 TAATTAATCGATACTGTTTATAATTAAATACATAATTAT
2551083 TTAATTATTT
Statistics
Matches: 452, Mismatches: 31, Indels: 8
0.92 0.06 0.02
Matches are distributed among these distances:
111 6 0.01
112 438 0.97
113 8 0.02
ACGTcount: A:0.47, C:0.06, G:0.04, T:0.44
Consensus pattern (111 bp):
TAATTAATCGATACTGTTTATAATTAAATACATAATTATAATGATTAAATAATTTAATATAATTA
TTTACTTTAATATAATTAAATAATTAAATCTTTTAACTTAAATATT
Found at i:2552410 original size:29 final size:31
Alignment explanation
Indices: 2552370--2552532 Score: 108
Period size: 29 Copynumber: 5.5 Consensus size: 31
2552360 ACCCGGGGGC
*
2552370 AAAATGGTAATTTT-GGTGTAATCGGGGTTA
1 AAAATGGTAATTTTAGGTGAAATCGGGGTTA
*** * * *
2552400 AAAATGG-AATTTTAAAAG-ATTTGGGGAT-
1 AAAATGGTAATTTTAGGTGAAATCGGGGTTA
* *
2552428 AAAATGGTAATTTTCGGTGAAATTGGGGTTA
1 AAAATGGTAATTTTAGGTGAAATCGGGGTTA
* ** ** *
2552459 AAAACGG-AATTTTAGAAG-TTTCGGGGGT-
1 AAAATGGTAATTTTAGGTGAAATCGGGGTTA
* *
2552487 AAAATGGTAATTTTCGGTGAAATCAGGGTTAA
1 AAAATGGTAATTTTAGGTGAAATCGGGGTT-A
2552519 AAAATGG-AATTTTA
1 AAAATGGTAATTTTA
2552533 AAAGATTCGG
Statistics
Matches: 96, Mismatches: 29, Indels: 15
0.69 0.21 0.11
Matches are distributed among these distances:
28 13 0.14
29 34 0.35
30 30 0.31
31 12 0.12
32 7 0.07
ACGTcount: A:0.36, C:0.04, G:0.27, T:0.33
Consensus pattern (31 bp):
AAAATGGTAATTTTAGGTGAAATCGGGGTTA
Found at i:2552551 original size:60 final size:59
Alignment explanation
Indices: 2552363--2552560 Score: 299
Period size: 59 Copynumber: 3.4 Consensus size: 59
2552353 TATGGATACC
* *
2552363 CGGGGGCAAAATGGTAATTTT-GGTGTAATCGGGGTTAAAAATGGAATTTTAAAAGATT
1 CGGGGGTAAAATGGTAATTTTCGGTGAAATCGGGGTTAAAAATGGAATTTTAAAAGATT
* * * * * *
2552421 TGGGGATAAAATGGTAATTTTCGGTGAAATTGGGGTTAAAAACGGAATTTTAGAAGTTT
1 CGGGGGTAAAATGGTAATTTTCGGTGAAATCGGGGTTAAAAATGGAATTTTAAAAGATT
*
2552480 CGGGGGTAAAATGGTAATTTTCGGTGAAATCAGGGTTAAAAAATGGAATTTTAAAAGATT
1 CGGGGGTAAAATGGTAATTTTCGGTGAAATCGGGGTT-AAAAATGGAATTTTAAAAGATT
2552540 CGGGGGTAAAATGGTAATTTT
1 CGGGGGTAAAATGGTAATTTT
2552561 TGAAAGTTTT
Statistics
Matches: 123, Mismatches: 15, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
58 18 0.15
59 65 0.53
60 40 0.33
ACGTcount: A:0.35, C:0.05, G:0.29, T:0.32
Consensus pattern (59 bp):
CGGGGGTAAAATGGTAATTTTCGGTGAAATCGGGGTTAAAAATGGAATTTTAAAAGATT
Found at i:2552596 original size:60 final size:60
Alignment explanation
Indices: 2552532--2552738 Score: 267
Period size: 60 Copynumber: 3.5 Consensus size: 60
2552522 ATGGAATTTT
* * * *
2552532 AAAAGATTCGGGGGT-AAAATGGTAATTTTTG-AAAGTTTTGGGATCAAAATATAATTTTGG
1 AAAAG-TTTGGGGGTCAAAAT-ATAATTTTGGAAAAGTTTTGGGGTCAAAATATAATTTTGG
* * *
2552592 AAAAGTTTTGGGGTCAAAATATAATTTTGGAAAAGTTTTGGGGCCAAAATGTAATTTTGG
1 AAAAGTTTGGGGGTCAAAATATAATTTTGGAAAAGTTTTGGGGTCAAAATATAATTTTGG
*
2552652 AAAAGTTTTGGGGTCAAAATATAATTTTGGAAAAG-TTTGGGGTCAAAATATAATTTTGG
1 AAAAGTTTGGGGGTCAAAATATAATTTTGGAAAAGTTTTGGGGTCAAAATATAATTTTGG
* * * *
2552711 AAAAGTTTTGGCGTTAAAATGTAATTTT
1 AAAAGTTTGGGGGTCAAAATATAATTTT
2552739 TGGATAATTT
Statistics
Matches: 133, Mismatches: 12, Indels: 5
0.89 0.08 0.03
Matches are distributed among these distances:
59 62 0.47
60 71 0.53
ACGTcount: A:0.36, C:0.04, G:0.24, T:0.36
Consensus pattern (60 bp):
AAAAGTTTGGGGGTCAAAATATAATTTTGGAAAAGTTTTGGGGTCAAAATATAATTTTGG
Found at i:2552597 original size:30 final size:30
Alignment explanation
Indices: 2552554--2552738 Score: 293
Period size: 30 Copynumber: 6.2 Consensus size: 30
2552544 GGTAAAATGG
* *
2552554 TAATTTTTG-AAAGTTTTGGGATCAAAATA
1 TAATTTTGGAAAAGTTTTGGGGTCAAAATA
2552583 TAATTTTGGAAAAGTTTTGGGGTCAAAATA
1 TAATTTTGGAAAAGTTTTGGGGTCAAAATA
* *
2552613 TAATTTTGGAAAAGTTTTGGGGCCAAAATG
1 TAATTTTGGAAAAGTTTTGGGGTCAAAATA
2552643 TAATTTTGGAAAAGTTTTGGGGTCAAAATA
1 TAATTTTGGAAAAGTTTTGGGGTCAAAATA
2552673 TAATTTTGGAAAAG-TTTGGGGTCAAAATA
1 TAATTTTGGAAAAGTTTTGGGGTCAAAATA
* * *
2552702 TAATTTTGGAAAAGTTTTGGCGTTAAAATG
1 TAATTTTGGAAAAGTTTTGGGGTCAAAATA
2552732 TAATTTT
1 TAATTTT
2552739 TGGATAATTT
Statistics
Matches: 145, Mismatches: 9, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
29 37 0.26
30 108 0.74
ACGTcount: A:0.36, C:0.04, G:0.22, T:0.38
Consensus pattern (30 bp):
TAATTTTGGAAAAGTTTTGGGGTCAAAATA
Found at i:2554634 original size:6 final size:6
Alignment explanation
Indices: 2554602--2554695 Score: 70
Period size: 6 Copynumber: 15.8 Consensus size: 6
2554592 TTTTAAATTG
** ** *
2554602 TTAAAT TTAATAT TTTTAT TTTTAT TTAAAT TTAAAT TCAAA- TTAAAT
1 TTAAAT TTAA-AT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT
* *
2554650 TTAAATAT TTAAAT TTAAA- ATAAAT CTAAAT TTAAA- -TAAAT TTAAA
1 TT-AA-AT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAA
2554696 ATCAATTTAA
Statistics
Matches: 72, Mismatches: 9, Indels: 14
0.76 0.09 0.15
Matches are distributed among these distances:
4 4 0.06
5 8 0.11
6 48 0.67
7 8 0.11
8 4 0.06
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (6 bp):
TTAAAT
Found at i:2554659 original size:25 final size:25
Alignment explanation
Indices: 2554631--2554680 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
2554621 TTTTATTTAA
* *
2554631 ATTTAAATTCAAATTAAATTTAAAT
1 ATTTAAATTCAAAATAAATCTAAAT
*
2554656 ATTTAAATTTAAAATAAATCTAAAT
1 ATTTAAATTCAAAATAAATCTAAAT
2554681 TTAAATAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (25 bp):
ATTTAAATTCAAAATAAATCTAAAT
Found at i:2554659 original size:31 final size:31
Alignment explanation
Indices: 2554624--2554687 Score: 103
Period size: 31 Copynumber: 2.1 Consensus size: 31
2554614 TTTTTATTTT
*
2554624 TATTTAAATTTAAATTCAAAT-TAAATTTAAA
1 TATTTAAATTTAAAAT-AAATCTAAATTTAAA
2554655 TATTTAAATTTAAAATAAATCTAAATTTAAA
1 TATTTAAATTTAAAATAAATCTAAATTTAAA
2554686 TA
1 TA
2554688 AATTTAAAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
30 4 0.13
31 27 0.87
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (31 bp):
TATTTAAATTTAAAATAAATCTAAATTTAAA
Found at i:2554697 original size:17 final size:16
Alignment explanation
Indices: 2554625--2554695 Score: 85
Period size: 17 Copynumber: 4.4 Consensus size: 16
2554615 TTTTATTTTT
2554625 ATTTAAATTTAAATTCAA
1 ATTTAAATTTAAA-T-AA
2554643 A-TTAAATTTAAAT--
1 ATTTAAATTTAAATAA
2554656 ATTTAAATTTAAAATAA
1 ATTTAAATTT-AAATAA
*
2554673 ATCTAAATTTAAATAA
1 ATTTAAATTTAAATAA
2554689 ATTTAAA
1 ATTTAAA
2554696 ATCAATTTAA
Statistics
Matches: 47, Mismatches: 2, Indels: 10
0.80 0.03 0.17
Matches are distributed among these distances:
13 1 0.02
14 8 0.17
15 4 0.09
16 13 0.28
17 20 0.43
18 1 0.02
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (16 bp):
ATTTAAATTTAAATAA
Found at i:2555068 original size:68 final size:68
Alignment explanation
Indices: 2554981--2555281 Score: 557
Period size: 68 Copynumber: 4.4 Consensus size: 68
2554971 AAGACTTTGC
* *
2554981 TATCCAACTTTACTTCAATTTCAAGAGGATGACGTTGCTCTTACTTCAATTTCAGAGATGAAGAC
1 TATCC-ACTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTACTTCAATTTCAGAGATGAAGAC
2555046 GTGT
65 GTGT
*
2555050 TATCCACTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTACTTCAATTTCAGAGATTAAGACG
1 TATCCACTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTACTTCAATTTCAGAGATGAAGACG
2555115 TGT
66 TGT
*
2555118 TATCCACTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTACTTCAATTTCAGAGATTAAGACG
1 TATCCACTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTACTTCAATTTCAGAGATGAAGACG
2555183 TGT
66 TGT
2555186 TATCCACTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTACTTCAATTTCAGAGATGAAGACG
1 TATCCACTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTACTTCAATTTCAGAGATGAAGACG
2555251 TGT
66 TGT
2555254 TATCCACTCTACTTCAATTTCAAGGGGA
1 TATCCACTCTACTTCAATTTCAAGGGGA
2555282 CGTGTTATCC
Statistics
Matches: 228, Mismatches: 4, Indels: 1
0.98 0.02 0.00
Matches are distributed among these distances:
68 223 0.98
69 5 0.02
ACGTcount: A:0.27, C:0.21, G:0.18, T:0.35
Consensus pattern (68 bp):
TATCCACTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTACTTCAATTTCAGAGATGAAGACG
TGT
Found at i:2555306 original size:169 final size:170
Alignment explanation
Indices: 2555022--2555454 Score: 542
Period size: 169 Copynumber: 2.5 Consensus size: 170
2555012 ACGTTGCTCT
** * * *
2555022 TACTTCAATTTCAGAGATGA-AGACGTGTTATCCACTCTACTTCAATTTCAAGGGGATGACG-T-
1 TACTTCAATTTCA-AGGGGATAGACG-GTTATCCACTCTACTTCAATTTCAAGGAGACG-TGTTA
* * **
2555084 TGCTCT-TACTTCAATTTCAGAGATTAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGGATG
63 TCCACTCTACTTCAATTTCA-AG---GGGACGTGTTATCCACTCTACTTCAATTTCAAGGGGATG
* * *
2555148 ACGTTGCTCTTACTTCAATTTCAGAGATTAAGACGTGTTATCCACTC
124 ACATTGCTCTTACTTCAATTTCAGAGATGAAGACCTGTTATCCACTC
* *
2555195 TACTTCAATTTCAAGGGGAT-GAC-G-T-TGCTCT-TACTTCAATTTCAGAGATGAAGACGTGTT
1 TACTTCAATTTCAAGGGGATAGACGGTTATCCACTCTACTTCAATTTCA-AG--G-AGACGTGTT
2555255 ATCCACTCTACTTCAATTTCAAGGGGACGTGTTATCCACTCTACTTCAATTTCAAGGGGATGACA
62 ATCCACTCTACTTCAATTTCAAGGGGACGTGTTATCCACTCTACTTCAATTTCAAGGGGATGACA
2555320 TTGCTCTTACTTCAATTTCAGAGATGAAGACCTGTTATCCACTC
127 TTGCTCTTACTTCAATTTCAGAGATGAAGACCTGTTATCCACTC
*
2555364 TACTTCAATTTCAAGGGGATGAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGGACGTGTTA
1 TACTTCAATTTCAAGGGGAT--AGACG-GTTATCCACTCTACTTCAATTTCAAGGAGACGTGTTA
2555429 TCCACTCTACTTCAATTTCAAGGGGA
63 TCCACTCTACTTCAATTTCAAGGGGA
2555455 TGACATTGCT
Statistics
Matches: 227, Mismatches: 17, Indels: 32
0.82 0.06 0.12
Matches are distributed among these distances:
167 13 0.06
168 6 0.03
169 102 0.45
170 3 0.01
171 4 0.02
172 16 0.07
173 61 0.27
174 2 0.01
175 1 0.00
176 6 0.03
177 13 0.06
ACGTcount: A:0.27, C:0.21, G:0.18, T:0.34
Consensus pattern (170 bp):
TACTTCAATTTCAAGGGGATAGACGGTTATCCACTCTACTTCAATTTCAAGGAGACGTGTTATCC
ACTCTACTTCAATTTCAAGGGGACGTGTTATCCACTCTACTTCAATTTCAAGGGGATGACATTGC
TCTTACTTCAATTTCAGAGATGAAGACCTGTTATCCACTC
Found at i:2555364 original size:68 final size:68
Alignment explanation
Indices: 2555284--2555526 Score: 341
Period size: 68 Copynumber: 3.5 Consensus size: 68
2555274 CAAGGGGACG
2555284 TGTTATCCACTCTACTTCAATTTCAAGGGGATGACATTGCTCTTACTTCAATTTCAGAGATGAAG
1 TGTTATCCACTCTACTTCAATTTCAAGGGGATGACATTGCTCTTACTTCAATTTCAGAGATGAAG
2555349 ACC
66 ACC
* * *
2555352 TGTTATCCACTCTACTTCAATTTCAAGGGGATGAAGACGTGTTATCCACTCTACTTCAATTTCA-
1 TGTTATCCACTCTACTTCAATTTCAAGGGGAT---GAC---AT-TGCTCT-TACTTCAATTTCAG
* *
2555416 AG--G-GGACG
58 AGATGAAGACC
2555424 TGTTATCCACTCTACTTCAATTTCAAGGGGATGACATTGCTCTTACTTCAATTTCAGAGATGAAG
1 TGTTATCCACTCTACTTCAATTTCAAGGGGATGACATTGCTCTTACTTCAATTTCAGAGATGAAG
2555489 ACC
66 ACC
2555492 TGTTATCCACTCTACTTCAATTTCAAGGGGATGAC
1 TGTTATCCACTCTACTTCAATTTCAAGGGGATGAC
2555527 GTTGAGACCT
Statistics
Matches: 153, Mismatches: 10, Indels: 24
0.82 0.05 0.13
Matches are distributed among these distances:
64 13 0.08
65 6 0.04
66 1 0.01
67 1 0.01
68 70 0.46
69 3 0.02
71 3 0.02
72 35 0.23
73 1 0.01
74 1 0.01
75 6 0.04
76 13 0.08
ACGTcount: A:0.27, C:0.22, G:0.17, T:0.33
Consensus pattern (68 bp):
TGTTATCCACTCTACTTCAATTTCAAGGGGATGACATTGCTCTTACTTCAATTTCAGAGATGAAG
ACC
Found at i:2555395 original size:39 final size:38
Alignment explanation
Indices: 2555327--2555525 Score: 210
Period size: 39 Copynumber: 5.6 Consensus size: 38
2555317 ACATTGCTCT
*
2555327 TACTTCAATTTC-AGAGATGAAGACCTGTTATCCACTC
1 TACTTCAATTTCAAGGGATGAAGACCTGTTATCCACTC
*
2555364 TACTTCAATTTCAAGGGGATGAAGACGTGTTATCCACTC
1 TACTTCAATTTCAA-GGGATGAAGACCTGTTATCCACTC
*
2555403 TACTTCAATTTCAA-GG--G--GACGTGTTATCCACTC
1 TACTTCAATTTCAAGGGATGAAGACCTGTTATCCACTC
* * * *
2555436 TACTTCAATTTCAAGGG--GATGA-C--AT-TGCTCT-
1 TACTTCAATTTCAAGGGATGAAGACCTGTTATCCACTC
*
2555467 TACTTCAATTTC-AGAGATGAAGACCTGTTATCCACTC
1 TACTTCAATTTCAAGGGATGAAGACCTGTTATCCACTC
2555504 TACTTCAATTTCAAGGGGATGA
1 TACTTCAATTTCAA-GGGATGA
2555526 CGTTGAGACC
Statistics
Matches: 136, Mismatches: 12, Indels: 26
0.78 0.07 0.15
Matches are distributed among these distances:
30 3 0.02
31 12 0.09
32 8 0.06
33 32 0.24
34 3 0.02
35 2 0.01
36 6 0.04
37 26 0.19
38 2 0.01
39 42 0.31
ACGTcount: A:0.28, C:0.22, G:0.18, T:0.33
Consensus pattern (38 bp):
TACTTCAATTTCAAGGGATGAAGACCTGTTATCCACTC
Found at i:2555417 original size:140 final size:140
Alignment explanation
Indices: 2555226--2555525 Score: 577
Period size: 140 Copynumber: 2.2 Consensus size: 140
2555216 ACGTTGCTCT
*
2555226 TACTTCAATTTC-A-GAGATGAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGGACGTGTTA
1 TACTTCAATTTCAAGGGGATGAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGGACGTGTTA
2555289 TCCACTCTACTTCAATTTCAAGGGGATGACATTGCTCTTACTTCAATTTCAGAGATGAAGACCTG
66 TCCACTCTACTTCAATTTCAAGGGGATGACATTGCTCTTACTTCAATTTCAGAGATGAAGACCTG
2555354 TTATCCACTC
131 TTATCCACTC
2555364 TACTTCAATTTCAAGGGGATGAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGGACGTGTTA
1 TACTTCAATTTCAAGGGGATGAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGGACGTGTTA
2555429 TCCACTCTACTTCAATTTCAAGGGGATGACATTGCTCTTACTTCAATTTCAGAGATGAAGACCTG
66 TCCACTCTACTTCAATTTCAAGGGGATGACATTGCTCTTACTTCAATTTCAGAGATGAAGACCTG
2555494 TTATCCACTC
131 TTATCCACTC
2555504 TACTTCAATTTCAAGGGGATGA
1 TACTTCAATTTCAAGGGGATGA
2555526 CGTTGAGACC
Statistics
Matches: 159, Mismatches: 1, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
138 12 0.08
139 1 0.01
140 146 0.92
ACGTcount: A:0.28, C:0.22, G:0.18, T:0.33
Consensus pattern (140 bp):
TACTTCAATTTCAAGGGGATGAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGGACGTGTTA
TCCACTCTACTTCAATTTCAAGGGGATGACATTGCTCTTACTTCAATTTCAGAGATGAAGACCTG
TTATCCACTC
Found at i:2555517 original size:101 final size:105
Alignment explanation
Indices: 2555022--2555522 Score: 429
Period size: 101 Copynumber: 4.9 Consensus size: 105
2555012 ACGTTGCTCT
* ** *
2555022 TACTTCAATTTCAGAGATGAAGACGTGTTATCCACTCTACTTCAATTTCA-AGGGGATGAC--G-
1 TACTTCAATTTCAGAGAGGAAGAC--GTTATCCACTCTACTTCAATTTCAGAGATGAAGACGTGT
* * **
2555083 T-TGCTCT-TACTTCAATTTCAGAGATTAAGACGTGTTATCCACTC
64 TATCCACTCTACTTCAATTTCA-AG---GGGACGTGTTATCCACTC
* * * * *
2555127 TACTTCAATTTCA-AGGGGATGACG-T-TGCTCT-TACTTCAATTTCAGAGATTAAGACGTGTTA
1 TACTTCAATTTCAGAGAGGAAGACGTTATCCACTCTACTTCAATTTCAGAGATGAAGACGTGTTA
* * * *
2555188 TCCACTCTACTTCAATTTCAAGGGGATGACG-T-TGCTCT-
66 TCCACTCTACTTCAATTTCAAGGGGACG-TGTTATCCACTC
* *
2555226 TACTTCAATTTCAGAGATGAAGACGTGTTATCCACTCTACTTCAATTTCA-AG--G-GGACGTGT
1 TACTTCAATTTCAGAGAGGAAGAC--GTTATCCACTCTACTTCAATTTCAGAGATGAAGACGTGT
** **
2555287 TATCCACTCTACTTCAATTTCAAGGGGA--TGACAT-TGCTC
64 TATCCACTCTACTTCAATTTCAAGGGGACGTGTTATCCACTC
* *
2555326 TTACTTCAATTTCAGAGATGAAGACCTGTTATCCACTCTACTTCAATTTCAAGGGGATGAAGACG
1 -TACTTCAATTTCAGAGAGGAAGA-C-GTTATCCACTCTACTTCAATTTC-A-GAGATGAAGACG
2555391 TGTTATCCACTCTACTTCAATTTCAAGGGGACGTGTTATCCACTC
61 TGTTATCCACTCTACTTCAATTTCAAGGGGACGTGTTATCCACTC
* * * * * *
2555436 TACTTCAATTTCA-AGGGGATGAC-AT-TGCTCT-TACTTCAATTTCAGAGATGAAGACCTGTTA
1 TACTTCAATTTCAGAGAGGAAGACGTTATCCACTCTACTTCAATTTCAGAGATGAAGACGTGTTA
2555497 TCCACTCTACTTCAATTTCAAGGGGA
66 TCCACTCTACTTCAATTTCAAGGGGA
2555523 TGACGTTGAG
Statistics
Matches: 327, Mismatches: 42, Indels: 58
0.77 0.10 0.14
Matches are distributed among these distances:
98 1 0.00
99 28 0.09
100 22 0.07
101 128 0.39
102 7 0.02
103 14 0.04
104 24 0.07
105 40 0.12
106 1 0.00
107 36 0.11
108 6 0.02
109 17 0.05
110 3 0.01
ACGTcount: A:0.27, C:0.21, G:0.18, T:0.34
Consensus pattern (105 bp):
TACTTCAATTTCAGAGAGGAAGACGTTATCCACTCTACTTCAATTTCAGAGATGAAGACGTGTTA
TCCACTCTACTTCAATTTCAAGGGGACGTGTTATCCACTC
Found at i:2567447 original size:29 final size:30
Alignment explanation
Indices: 2567405--2567614 Score: 146
Period size: 29 Copynumber: 7.1 Consensus size: 30
2567395 ACCCGAGGGC
* *
2567405 AAAATGGTAATTTT-GGTGTAATCGGGGTT
1 AAAATGGTAATTTTAGATGAAATCGGGGTT
* * *
2567434 AAAAATGG-AATTTTAAATG-ATTCGGGGAT
1 -AAAATGGTAATTTTAGATGAAATCGGGGTT
* *
2567463 AAAATGGTAATTTTTGATGAAATTGGGGTT
1 AAAATGGTAATTTTAGATGAAATCGGGGTT
* * ** *
2567493 GAAAACGG-AATTTTAGAAG-TTTCGGGGGT
1 -AAAATGGTAATTTTAGATGAAATCGGGGTT
2567522 AAAATGGTAATTTTCAG-TGAAATCGGGGTT
1 AAAATGGTAATTTT-AGATGAAATCGGGGTT
** * ** * *
2567552 AAAAACGTAATTTTAGAAG-TTTTGGGGGT
1 AAAATGGTAATTTTAGATGAAATCGGGGTT
* * *
2567581 AAAATGGTAATTTTCGGTGAAATTGGGGTT
1 AAAATGGTAATTTTAGATGAAATCGGGGTT
2567611 AAAA
1 AAAA
2567615 AATGGAACTT
Statistics
Matches: 135, Mismatches: 36, Indels: 18
0.71 0.19 0.10
Matches are distributed among these distances:
28 13 0.10
29 58 0.43
30 58 0.43
31 6 0.04
ACGTcount: A:0.34, C:0.04, G:0.28, T:0.34
Consensus pattern (30 bp):
AAAATGGTAATTTTAGATGAAATCGGGGTT
Found at i:2567503 original size:59 final size:59
Alignment explanation
Indices: 2567405--2567658 Score: 298
Period size: 59 Copynumber: 4.3 Consensus size: 59
2567395 ACCCGAGGGC
* * * *
2567405 AAAATGGTAA-TTTTGGTGTAATCGGGGTTAAAAATGGAATTTTA-AATGATTCGGGGAT
1 AAAATGGTAATTTTTGATGAAATCGGGGTTAAAAACGGAATTTTAGAA-GATTCGGGGGT
* * *
2567463 AAAATGGTAATTTTTGATGAAATTGGGGTTGAAAACGGAATTTTAGAAGTTTCGGGGGT
1 AAAATGGTAATTTTTGATGAAATCGGGGTTAAAAACGGAATTTTAGAAGATTCGGGGGT
* * * *
2567522 AAAATGGTAA-TTTTCAGTGAAATCGGGGTTAAAAACGTAATTTTAGAAGTTTTGGGGGT
1 AAAATGGTAATTTTTGA-TGAAATCGGGGTTAAAAACGGAATTTTAGAAGATTCGGGGGT
* * * * * *
2567581 AAAATGGTAATTTTCGGTGAAATTGGGGTTAAAAAATGGAACTTTAAAAGATTCGAGGGGT
1 AAAATGGTAATTTTTGATGAAATCGGGGTT-AAAAACGGAATTTTAGAAGATTCG-GGGGT
2567642 AAAATGGTAATTTTTGA
1 AAAATGGTAATTTTTGA
2567659 AAGTTTTGGG
Statistics
Matches: 166, Mismatches: 24, Indels: 9
0.83 0.12 0.05
Matches are distributed among these distances:
58 15 0.09
59 108 0.65
60 23 0.14
61 20 0.12
ACGTcount: A:0.35, C:0.04, G:0.28, T:0.33
Consensus pattern (59 bp):
AAAATGGTAATTTTTGATGAAATCGGGGTTAAAAACGGAATTTTAGAAGATTCGGGGGT
Found at i:2567692 original size:30 final size:30
Alignment explanation
Indices: 2567649--2567808 Score: 250
Period size: 30 Copynumber: 5.3 Consensus size: 30
2567639 GGTAAAATGG
* *
2567649 TAATTTTTG-AAAGTTTTGGGATTAAAATA
1 TAATTTTGGAAAAGTTTTGGGGTTAAAATA
*
2567678 TAATTTTGGAAAAGTTTTGGGGTCAAAATA
1 TAATTTTGGAAAAGTTTTGGGGTTAAAATA
* *
2567708 TAATTTTGGAAAAGTTTTGGGGTCAAAATG
1 TAATTTTGGAAAAGTTTTGGGGTTAAAATA
2567738 TAATTTTGGAAAAGTTTTGGGGTTAAAATA
1 TAATTTTGGAAAAGTTTTGGGGTTAAAATA
*
2567768 TAATTTTGGAAAAGTTTTGGGGTTAAAATG
1 TAATTTTGGAAAAGTTTTGGGGTTAAAATA
2567798 TAATTTCTGGA
1 TAATTT-TGGA
2567809 CAATTTAGGG
Statistics
Matches: 122, Mismatches: 7, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
29 8 0.07
30 110 0.90
31 4 0.03
ACGTcount: A:0.35, C:0.02, G:0.23, T:0.40
Consensus pattern (30 bp):
TAATTTTGGAAAAGTTTTGGGGTTAAAATA
Found at i:2567764 original size:90 final size:90
Alignment explanation
Indices: 2567637--2567808 Score: 276
Period size: 90 Copynumber: 1.9 Consensus size: 90
2567627 AAAGATTCGA
*
2567637 GGGGTAAAATGGTAATTTTTGAAAGTTTTGGGATTAAAATATAATTTTGGAAAAGTTTTGGGGTC
1 GGGGTAAAATGGTAATTTTGGAAAGTTTTGGGATTAAAATATAATTTTGGAAAAGTTTTGGGGTC
2567702 AAAATATAATTT-TGGAAAAGTTTT
66 AAAATATAATTTCTGGAAAAGTTTT
*
2567726 GGGGTCAAAAT-GTAATTTTGGAAAAGTTTTGGGGTTAAAATATAATTTTGGAAAAGTTTTGGGG
1 GGGGT-AAAATGGTAATTTTGG-AAAGTTTTGGGATTAAAATATAATTTTGGAAAAGTTTTGGGG
* *
2567790 TTAAAATGTAATTTCTGGA
64 TCAAAATATAATTTCTGGA
2567809 CAATTTAGGG
Statistics
Matches: 76, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
89 14 0.18
90 58 0.76
91 4 0.05
ACGTcount: A:0.35, C:0.02, G:0.25, T:0.38
Consensus pattern (90 bp):
GGGGTAAAATGGTAATTTTGGAAAGTTTTGGGATTAAAATATAATTTTGGAAAAGTTTTGGGGTC
AAAATATAATTTCTGGAAAAGTTTT
Found at i:2568265 original size:14 final size:15
Alignment explanation
Indices: 2568240--2568272 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
2568230 TAAATAACAT
*
2568240 TTTCAGATTTTTTTA
1 TTTCAGATTTTTTCA
2568255 TTTCA-ATTTTTTCA
1 TTTCAGATTTTTTCA
2568269 TTTC
1 TTTC
2568273 TTAAAAATTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 12 0.71
15 5 0.29
ACGTcount: A:0.18, C:0.12, G:0.03, T:0.67
Consensus pattern (15 bp):
TTTCAGATTTTTTCA
Found at i:2568372 original size:23 final size:21
Alignment explanation
Indices: 2568318--2568372 Score: 56
Period size: 23 Copynumber: 2.5 Consensus size: 21
2568308 TCTTTTCTCT
*
2568318 CCCCTTGTCCAAGTCCGGCAC
1 CCCCTTGGCCAAGTCCGGCAC
*
2568339 CCCCTCCGGCCAAGCTCCGGCAGC
1 CCCCT-TGGCCAAG-TCCGGCA-C
*
2568363 CGCCTTGGCC
1 CCCCTTGGCC
2568373 GCGCGTGGGG
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
21 5 0.19
22 6 0.22
23 11 0.41
24 5 0.19
ACGTcount: A:0.11, C:0.51, G:0.24, T:0.15
Consensus pattern (21 bp):
CCCCTTGGCCAAGTCCGGCAC
Found at i:2569688 original size:6 final size:6
Alignment explanation
Indices: 2569668--2569761 Score: 79
Period size: 6 Copynumber: 15.8 Consensus size: 6
2569658 TTTTAAATTG
* ** *
2569668 TTAAAT TTAATAT TTTAAT TTTTAT TTAAAT TTAAAT TCAAA- TTAAAT
1 TTAAAT TTAA-AT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT
* *
2569716 TTAAATAT TTAAAT TTAAA- ATAAAT CTAAAT TTAAA- -TAAAT TTAAA
1 TT-AA-AT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAA
2569762 ATCAATTTAA
Statistics
Matches: 72, Mismatches: 9, Indels: 14
0.76 0.09 0.15
Matches are distributed among these distances:
4 4 0.06
5 8 0.11
6 47 0.65
7 9 0.12
8 4 0.06
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (6 bp):
TTAAAT
Found at i:2569725 original size:25 final size:25
Alignment explanation
Indices: 2569697--2569746 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
2569687 TTTTATTTAA
* *
2569697 ATTTAAATTCAAATTAAATTTAAAT
1 ATTTAAATTCAAAATAAATCTAAAT
*
2569722 ATTTAAATTTAAAATAAATCTAAAT
1 ATTTAAATTCAAAATAAATCTAAAT
2569747 TTAAATAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (25 bp):
ATTTAAATTCAAAATAAATCTAAAT
Found at i:2569725 original size:31 final size:31
Alignment explanation
Indices: 2569690--2569753 Score: 103
Period size: 31 Copynumber: 2.1 Consensus size: 31
2569680 TTTTAATTTT
*
2569690 TATTTAAATTTAAATTCAAAT-TAAATTTAAA
1 TATTTAAATTTAAAAT-AAATCTAAATTTAAA
2569721 TATTTAAATTTAAAATAAATCTAAATTTAAA
1 TATTTAAATTTAAAATAAATCTAAATTTAAA
2569752 TA
1 TA
2569754 AATTTAAAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
30 4 0.13
31 27 0.87
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (31 bp):
TATTTAAATTTAAAATAAATCTAAATTTAAA
Found at i:2569740 original size:42 final size:43
Alignment explanation
Indices: 2569668--2569761 Score: 113
Period size: 42 Copynumber: 2.3 Consensus size: 43
2569658 TTTTAAATTG
* * ** *
2569668 TTAAATTT-AATATTTTAATTTTTATTTAAATTTAAATTCAAA
1 TTAAATTTAAATATTTTAAATTTAAAATAAATCTAAATTCAAA
*
2569710 TTAAATTTAAATA-TTTAAATTTAAAATAAATCTAAATTTAAA
1 TTAAATTTAAATATTTTAAATTTAAAATAAATCTAAATTCAAA
2569752 -TAAATTTAAA
1 TTAAATTTAAA
2569762 ATCAATTTAA
Statistics
Matches: 45, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
41 10 0.22
42 31 0.69
43 4 0.09
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (43 bp):
TTAAATTTAAATATTTTAAATTTAAAATAAATCTAAATTCAAA
Found at i:2569763 original size:17 final size:16
Alignment explanation
Indices: 2569691--2569761 Score: 85
Period size: 17 Copynumber: 4.4 Consensus size: 16
2569681 TTTAATTTTT
2569691 ATTTAAATTTAAATTCAA
1 ATTTAAATTTAAA-T-AA
2569709 A-TTAAATTTAAAT--
1 ATTTAAATTTAAATAA
2569722 ATTTAAATTTAAAATAA
1 ATTTAAATTT-AAATAA
*
2569739 ATCTAAATTTAAATAA
1 ATTTAAATTTAAATAA
2569755 ATTTAAA
1 ATTTAAA
2569762 ATCAATTTAA
Statistics
Matches: 47, Mismatches: 2, Indels: 10
0.80 0.03 0.17
Matches are distributed among these distances:
13 1 0.02
14 8 0.17
15 4 0.09
16 13 0.28
17 20 0.43
18 1 0.02
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (16 bp):
ATTTAAATTTAAATAA
Found at i:2570494 original size:34 final size:34
Alignment explanation
Indices: 2570456--2570548 Score: 123
Period size: 34 Copynumber: 2.7 Consensus size: 34
2570446 TGTTTTCAAT
* *
2570456 ATTTAAATAAATAAATAAATAAATAATTGGGTTG
1 ATTTAAATAATTAAATAATTAAATAATTGGGTTG
* * *
2570490 ATTTAAGTAATTAAATAATTAAGTATTTGGGTTG
1 ATTTAAATAATTAAATAATTAAATAATTGGGTTG
* *
2570524 TTTTTAATAATTAAATAATTAAATA
1 ATTTAAATAATTAAATAATTAAATA
2570549 TTTTGAATTG
Statistics
Matches: 50, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
34 50 1.00
ACGTcount: A:0.47, C:0.00, G:0.11, T:0.42
Consensus pattern (34 bp):
ATTTAAATAATTAAATAATTAAATAATTGGGTTG
Found at i:2570604 original size:34 final size:34
Alignment explanation
Indices: 2570559--2570655 Score: 106
Period size: 34 Copynumber: 2.8 Consensus size: 34
2570549 TTTTGAATTG
2570559 AATATTTGGGTTGTTTTTAATATTTAAATAAATA
1 AATATTTGGGTTGTTTTTAATATTTAAATAAATA
* * * *
2570593 AATAATTGGGTTG-ATTTAAGTAATTAAATAATTA
1 AATATTTGGGTTGTTTTTAA-TATTTAAATAAATA
* * *
2570627 AGTATTTGGGTTTTTTTTACTAATTTAAA
1 AATATTTGGGTTGTTTTTAAT-ATTTAAA
2570656 ATTTAAAAAA
Statistics
Matches: 50, Mismatches: 10, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
33 5 0.10
34 35 0.70
35 10 0.20
ACGTcount: A:0.37, C:0.01, G:0.13, T:0.48
Consensus pattern (34 bp):
AATATTTGGGTTGTTTTTAATATTTAAATAAATA
Found at i:2570662 original size:124 final size:119
Alignment explanation
Indices: 2570366--2570651 Score: 461
Period size: 124 Copynumber: 2.4 Consensus size: 119
2570356 CGGTCAAGCA
*
2570366 ATTTAAATAATTAAATAATTAAGTATTTGGGTTGTTTTTAATAATTAAATAATTAAATATTTTGA
1 ATTTAAGTAATTAAATAATTAAGTATTTGGGTTGTTTTTAATAATTAAATAATTAAATATTTTGA
2570431 ATTAAATATTTGGGTTGTTTTCAATATTTAAATAAATAAATAAATAAATAATTGGGTTG
66 ATTAAATATTTGGGTTGTTTTCAATA-TT--AT--ATAAATAAATAAATAATTGGGTTG
2570490 ATTTAAGTAATTAAATAATTAAGTATTTGGGTTGTTTTTAATAATTAAATAATTAAATATTTTGA
1 ATTTAAGTAATTAAATAATTAAGTATTTGGGTTGTTTTTAATAATTAAATAATTAAATATTTTGA
* *
2570555 ATTGAATATTTGGGTTGTTTTTAATA-T-T-TAAATAAATAAATAATTGGGTTG
66 ATTAAATATTTGGGTTGTTTTCAATATTATATAAATAAATAAATAATTGGGTTG
* *
2570606 ATTTAAGTAATTAAATAATTAAGTATTTGGGTTTTTTTTACTAATT
1 ATTTAAGTAATTAAATAATTAAGTATTTGGGTTGTTTTTAATAATT
2570652 TAAAATTTAA
Statistics
Matches: 157, Mismatches: 5, Indels: 8
0.92 0.03 0.05
Matches are distributed among these distances:
116 67 0.43
119 1 0.01
122 1 0.01
124 88 0.56
ACGTcount: A:0.40, C:0.01, G:0.12, T:0.47
Consensus pattern (119 bp):
ATTTAAGTAATTAAATAATTAAGTATTTGGGTTGTTTTTAATAATTAAATAATTAAATATTTTGA
ATTAAATATTTGGGTTGTTTTCAATATTATATAAATAAATAAATAATTGGGTTG
Found at i:2570828 original size:10 final size:10
Alignment explanation
Indices: 2570813--2570839 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
2570803 TTCCTATGTT
2570813 GAATTTATTA
1 GAATTTATTA
2570823 GAATTTATTA
1 GAATTTATTA
2570833 GAATTTA
1 GAATTTA
2570840 AAAGATTCCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.41, C:0.00, G:0.11, T:0.48
Consensus pattern (10 bp):
GAATTTATTA
Found at i:2572422 original size:15 final size:15
Alignment explanation
Indices: 2572402--2572445 Score: 61
Period size: 15 Copynumber: 2.9 Consensus size: 15
2572392 GGAGGAGGAG
2572402 AGGGATTTAGAAATT
1 AGGGATTTAGAAATT
*
2572417 AGGGATTTAGAATTT
1 AGGGATTTAGAAATT
* *
2572432 AGGAATTTCGAAAT
1 AGGGATTTAGAAAT
2572446 CTGTTTTTAG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.39, C:0.02, G:0.25, T:0.34
Consensus pattern (15 bp):
AGGGATTTAGAAATT
Found at i:2572542 original size:41 final size:41
Alignment explanation
Indices: 2572497--2572900 Score: 542
Period size: 41 Copynumber: 9.9 Consensus size: 41
2572487 CAGTAAAAAT
* *
2572497 TTTAGCGGCGCTTTCCCATAAGCGCAGCTATTTCTCCGACC
1 TTTAGCGGCGCTTTCCCATAAGCGCCGCTATTGCTCCGACC
*
2572538 TTTAGCGGCGATTTCCCATAAGCGCCGCTATTGCTCCGACC
1 TTTAGCGGCGCTTTCCCATAAGCGCCGCTATTGCTCCGACC
* ** * * *
2572579 TTTGGCGGCGCTTTCTTATAAGCGTCGCTATTTCTCAGACC
1 TTTAGCGGCGCTTTCCCATAAGCGCCGCTATTGCTCCGACC
*
2572620 TTTAGCGGCGCTTTCCCATAAGCGCCGCTATTGCTCTGACC
1 TTTAGCGGCGCTTTCCCATAAGCGCCGCTATTGCTCCGACC
* * * ** *
2572661 TTTAGTGGTGATTTCTTATAAGCGCCGCTATTGCTCCGACT
1 TTTAGCGGCGCTTTCCCATAAGCGCCGCTATTGCTCCGACC
*
2572702 TTTAGTGGCGCTTTCCCATAAGCGCCGCTATTGCTCCGACC
1 TTTAGCGGCGCTTTCCCATAAGCGCCGCTATTGCTCCGACC
* ** *
2572743 TTTAGCGGCGCATTCTTATAAGCGCCGCTATTGCTCCGATC
1 TTTAGCGGCGCTTTCCCATAAGCGCCGCTATTGCTCCGACC
**
2572784 TTTA-CGGCGCTTTTACATAAGCGCCGCTATTGCTCCGACC
1 TTTAGCGGCGCTTTCCCATAAGCGCCGCTATTGCTCCGACC
* ** *
2572824 TTTAGCGGCGCTATCATATAAGCGCCGCTATTGCTCCGATC
1 TTTAGCGGCGCTTTCCCATAAGCGCCGCTATTGCTCCGACC
2572865 TTTAGCGGCG-TTTCTCCATAAGCGCCGCTATTGCTC
1 TTTAGCGGCGCTTTC-CCATAAGCGCCGCTATTGCTC
2572901 AATCTTTTGC
Statistics
Matches: 316, Mismatches: 45, Indels: 4
0.87 0.12 0.01
Matches are distributed among these distances:
40 38 0.12
41 278 0.88
ACGTcount: A:0.16, C:0.31, G:0.22, T:0.31
Consensus pattern (41 bp):
TTTAGCGGCGCTTTCCCATAAGCGCCGCTATTGCTCCGACC
Found at i:2572931 original size:40 final size:41
Alignment explanation
Indices: 2572683--2572939 Score: 161
Period size: 41 Copynumber: 6.3 Consensus size: 41
2572673 TTCTTATAAG
* * * * *
2572683 CGCCGCTATTGCTCCGA-CTTTTAGTGGCGCTTT-CCCATAAG
1 CGCCGCTATTGCTCCAATC-TTTAGCGGCG-TTTATCCAAAAA
* * ** * * *
2572724 CGCCGCTATTGCTCCGACCTTTAGCGGCGCAT-TCTTATAAG
1 CGCCGCTATTGCTCCAATCTTTAGCGGCGTTTATC-CAAAAA
* * * *
2572765 CGCCGCTATTGCTCCGATCTTTA-CGGCGCTTT-TACATAAG
1 CGCCGCTATTGCTCCAATCTTTAGCGGCG-TTTATCCAAAAA
* * * *
2572805 CGCCGCTATTGCTCCGACCTTTAGCGGCG-CTAT-CATATAAG
1 CGCCGCTATTGCTCCAATCTTTAGCGGCGTTTATCCA-A-AAA
* * * *
2572846 CGCCGCTATTGCTCCGATCTTTAGCGGCGTTTCTCCATAAG
1 CGCCGCTATTGCTCCAATCTTTAGCGGCGTTTATCCAAAAA
* **
2572887 CGCCGCTATTGCT-CAATCTTTTGCGGCGTTTATGTAAAAA
1 CGCCGCTATTGCTCCAATCTTTAGCGGCGTTTATCCAAAAA
2572927 CGCCGCTATTGCT
1 CGCCGCTATTGCT
2572940 TTAACATTTG
Statistics
Matches: 183, Mismatches: 24, Indels: 19
0.81 0.11 0.08
Matches are distributed among these distances:
39 3 0.02
40 68 0.37
41 107 0.58
42 3 0.02
43 2 0.01
ACGTcount: A:0.17, C:0.30, G:0.21, T:0.31
Consensus pattern (41 bp):
CGCCGCTATTGCTCCAATCTTTAGCGGCGTTTATCCAAAAA
Found at i:2572955 original size:40 final size:41
Alignment explanation
Indices: 2572887--2572975 Score: 101
Period size: 40 Copynumber: 2.2 Consensus size: 41
2572877 TCTCCATAAG
*
2572887 CGCCGCTATTGCTCAATCTTTTGCGGCG-TTTATGTAAAAA
1 CGCCGCTATTGCTCAATCATTTGCGGCGTTTTATGTAAAAA
* * * **
2572927 CGCCGCTATTGCTTTAA-CATTTGTGGCGTTTTCTGTCCAAA
1 CGCCGCTATTGC-TCAATCATTTGCGGCGTTTTATGTAAAAA
2572968 CGCCGCTA
1 CGCCGCTA
2572976 ATAACCTATT
Statistics
Matches: 41, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
40 21 0.51
41 20 0.49
ACGTcount: A:0.19, C:0.26, G:0.20, T:0.35
Consensus pattern (41 bp):
CGCCGCTATTGCTCAATCATTTGCGGCGTTTTATGTAAAAA
Found at i:2572972 original size:122 final size:121
Alignment explanation
Indices: 2572497--2572975 Score: 416
Period size: 123 Copynumber: 3.9 Consensus size: 121
2572487 CAGTAAAAAT
* * * * ** *
2572497 TTTAGCGGCGCTTTC-CCATAAGCGCAGCTATTTCTCCGACCTTTAGCGGCGATTTCCCATAAGC
1 TTTAGCGGCGCTTTCTCCATAAGCGCCGCTATTGCT-CGATCTTTTGCGGCG-TTT-TTAAAAGC
* * * ** * * * *
2572561 GCCGCTATTGCTCCGACCTTTGGCGGCGCTTTCTTATAAGCGTCGCTATTTCTCAGACC
63 GCCGCTATTGCTCCGACATTTAGTGGCGCTTTCTTCCAAACGCCGCTATTGCTCCGACC
* * * * *
2572620 TTTAGCGGCGCTTTC-CCATAAGCGCCGCTATTGCTCTGACCTTTAGTGGTGATTTCTTATAAGC
1 TTTAGCGGCGCTTTCTCCATAAGCGCCGCTATTGCTC-GATCTTTTGCGGCG-TTT-TTAAAAGC
*
2572684 GCCGCTATTGCTCCGACTTTTAGTGGCGCTTTC--CCATAAGCGCCGCTATTGCTCCGACC
63 GCCGCTATTGCTCCGACATTTAGTGGCGCTTTCTTCCA-AA-CGCCGCTATTGCTCCGACC
* * * *
2572743 TTTAGCGGCGCATTCT-TATAAGCGCCGCTATTGCTCCGATC-TTTACGGCGCTTTTACATAAGC
1 TTTAGCGGCGCTTTCTCCATAAGCGCCGCTATTGCT-CGATCTTTTGCGGCGTTTTTA-A-AAGC
* * * * ** * *
2572806 GCCGCTATTGCTCCGACCTTTAGCGGCGCTATCATATAAGCGCCGCTATTGCTCCGATC
63 GCCGCTATTGCTCCGACATTTAGTGGCGCTTTCTTCCAAACGCCGCTATTGCTCCGACC
* *
2572865 TTTAGCGGCG-TTTCTCCATAAGCGCCGCTATTGCTCAATCTTTTGCGGCGTTTATGTAAAAACG
1 TTTAGCGGCGCTTTCTCCATAAGCGCCGCTATTGCTCGATCTTTTGCGGCGTTT-T-TAAAAGCG
*** *
2572929 CCGCTATTGCTTTAACATTT-GTGGCGTTTTCTGTCCAAACGCCGCTA
64 CCGCTATTGCTCCGACATTTAGTGGCGCTTTCT-TCCAAACGCCGCTA
2572976 ATAACCTATT
Statistics
Matches: 294, Mismatches: 48, Indels: 29
0.79 0.13 0.08
Matches are distributed among these distances:
120 3 0.01
121 19 0.06
122 128 0.44
123 140 0.48
124 4 0.01
ACGTcount: A:0.17, C:0.29, G:0.21, T:0.32
Consensus pattern (121 bp):
TTTAGCGGCGCTTTCTCCATAAGCGCCGCTATTGCTCGATCTTTTGCGGCGTTTTTAAAAGCGCC
GCTATTGCTCCGACATTTAGTGGCGCTTTCTTCCAAACGCCGCTATTGCTCCGACC
Found at i:2585817 original size:32 final size:32
Alignment explanation
Indices: 2585776--2585840 Score: 112
Period size: 32 Copynumber: 2.0 Consensus size: 32
2585766 ATAACAATCG
2585776 ATTTAAATATATAAACAATCAATTCAAAATAA
1 ATTTAAATATATAAACAATCAATTCAAAATAA
* *
2585808 ATTTAAATATATATACAATCGATTCAAAATAA
1 ATTTAAATATATAAACAATCAATTCAAAATAA
2585840 A
1 A
2585841 CAATATTTCA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.57, C:0.09, G:0.02, T:0.32
Consensus pattern (32 bp):
ATTTAAATATATAAACAATCAATTCAAAATAA
Found at i:2592013 original size:30 final size:32
Alignment explanation
Indices: 2591960--2592026 Score: 93
Period size: 31 Copynumber: 2.2 Consensus size: 32
2591950 TTAATAATTT
* *
2591960 ATTTTTTATTATTTTTAAAGGGTTAAATTA-A
1 ATTTTTTATCATTTTTAAAGGGTTAAAGTATA
*
2591991 ATTTTTTATCATTTTT-AGGGGTTAAAGTATA
1 ATTTTTTATCATTTTTAAAGGGTTAAAGTATA
2592022 ATTTT
1 ATTTT
2592027 ACCATTATTA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
30 11 0.34
31 21 0.66
ACGTcount: A:0.31, C:0.01, G:0.12, T:0.55
Consensus pattern (32 bp):
ATTTTTTATCATTTTTAAAGGGTTAAAGTATA
Found at i:2592062 original size:23 final size:23
Alignment explanation
Indices: 2592021--2592070 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
2592011 GTTAAAGTAT
* *
2592021 AATTTTACCATTATTAATT-TAA
1 AATTTTACAATTATAAATTGTAA
2592043 AATTTTACAAATTATAAATTGTAA
1 AATTTTAC-AATTATAAATTGTAA
2592067 AATT
1 AATT
2592071 AAAAATTTAC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 8 0.33
23 9 0.38
24 7 0.29
ACGTcount: A:0.46, C:0.06, G:0.02, T:0.46
Consensus pattern (23 bp):
AATTTTACAATTATAAATTGTAA
Found at i:2603616 original size:8 final size:8
Alignment explanation
Indices: 2603603--2603627 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
2603593 CACAACTGAG
2603603 TCATACTA
1 TCATACTA
2603611 TCATACTA
1 TCATACTA
2603619 TCATACTA
1 TCATACTA
2603627 T
1 T
2603628 GTTTTCTTTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.36, C:0.24, G:0.00, T:0.40
Consensus pattern (8 bp):
TCATACTA
Found at i:2609605 original size:16 final size:17
Alignment explanation
Indices: 2609584--2609624 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
2609574 GCGACTCGCT
2609584 AACAAAGGAAAA-AAAA
1 AACAAAGGAAAATAAAA
*
2609600 AACAAA-GAAAATAAAT
1 AACAAAGGAAAATAAAA
*
2609616 TACAAAGGA
1 AACAAAGGA
2609625 TTAGTTAATG
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
15 5 0.24
16 14 0.67
17 2 0.10
ACGTcount: A:0.73, C:0.07, G:0.12, T:0.07
Consensus pattern (17 bp):
AACAAAGGAAAATAAAA
Found at i:2619824 original size:17 final size:17
Alignment explanation
Indices: 2619802--2619840 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
2619792 AGGTGGAGAA
* * *
2619802 CTTGTTCGTTGAGAGTT
1 CTTGTTCATAGAGAATT
2619819 CTTGTTCATAGAGAATT
1 CTTGTTCATAGAGAATT
2619836 CTTGT
1 CTTGT
2619841 CAAGGTGGAG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.18, C:0.13, G:0.23, T:0.46
Consensus pattern (17 bp):
CTTGTTCATAGAGAATT
Found at i:2620367 original size:148 final size:148
Alignment explanation
Indices: 2620094--2620375 Score: 519
Period size: 148 Copynumber: 1.9 Consensus size: 148
2620084 TTGATTCAAT
*
2620094 TTTTAGACATTAGTGAATCTTCTTCTCCTCTGCCCGTGGTTTTTTCCCGAAAGGGTTTCCACGTA
1 TTTTAGACATTAGTGAATCTTCTTCTCCTCTGCCCGTGATTTTTTCCCGAAAGGGTTTCCACGTA
2620159 AAATCCGTGTGTTCTTTCTTTTCATTTTCTTTGCGATATTTATTCATTATCGTCATTTAAATCTT
66 AAATCCGTGTGTTCTTTCTTTTCATTTTCTTTGCGATATTTATTCATTATCGTCATTTAAATCTT
2620224 ATCAAATATAGTATTCCA
131 ATCAAATATAGTATTCCA
* * *
2620242 TTTTCGACATTAGTGAATCTTCTTCTCCTCTGCCTGTGATTTTTTCCCGAAAGGGTTTTCACGTA
1 TTTTAGACATTAGTGAATCTTCTTCTCCTCTGCCCGTGATTTTTTCCCGAAAGGGTTTCCACGTA
*
2620307 AAATCTGTGTGTTCTTTCTTTTCATTTTCTTTGCGATATTTATTCATTATCGTCATTTAAATCTT
66 AAATCCGTGTGTTCTTTCTTTTCATTTTCTTTGCGATATTTATTCATTATCGTCATTTAAATCTT
2620372 ATCA
131 ATCA
2620376 GCGAGTTTTC
Statistics
Matches: 129, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
148 129 1.00
ACGTcount: A:0.21, C:0.20, G:0.13, T:0.47
Consensus pattern (148 bp):
TTTTAGACATTAGTGAATCTTCTTCTCCTCTGCCCGTGATTTTTTCCCGAAAGGGTTTCCACGTA
AAATCCGTGTGTTCTTTCTTTTCATTTTCTTTGCGATATTTATTCATTATCGTCATTTAAATCTT
ATCAAATATAGTATTCCA
Found at i:2620480 original size:17 final size:17
Alignment explanation
Indices: 2620454--2620513 Score: 50
Period size: 17 Copynumber: 3.5 Consensus size: 17
2620444 ACATAGATCG
*
2620454 CAAAGATGCAAACTCTC
1 CAAAGGTGCAAACTCTC
*
2620471 CAAAGGTGCAAGCTCAT-
1 CAAAGGTGCAAACTC-TC
* * *
2620488 CAAAGCTGCAAAGTCAC
1 CAAAGGTGCAAACTCTC
*
2620505 CAAAAGTGC
1 CAAAGGTGC
2620514 GAGCTTATAT
Statistics
Matches: 33, Mismatches: 8, Indels: 4
0.73 0.18 0.09
Matches are distributed among these distances:
17 32 0.97
18 1 0.03
ACGTcount: A:0.40, C:0.27, G:0.18, T:0.15
Consensus pattern (17 bp):
CAAAGGTGCAAACTCTC
Found at i:2620492 original size:34 final size:34
Alignment explanation
Indices: 2620454--2620518 Score: 85
Period size: 34 Copynumber: 1.9 Consensus size: 34
2620444 ACATAGATCG
* *
2620454 CAAAGATGCAAACTCTCCAAAGGTGCAAGCTCAT
1 CAAAGATGCAAACTCACCAAAAGTGCAAGCTCAT
* * *
2620488 CAAAGCTGCAAAGTCACCAAAAGTGCGAGCT
1 CAAAGATGCAAACTCACCAAAAGTGCAAGCT
2620519 TATATGTGCG
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
34 26 1.00
ACGTcount: A:0.38, C:0.26, G:0.20, T:0.15
Consensus pattern (34 bp):
CAAAGATGCAAACTCACCAAAAGTGCAAGCTCAT
Found at i:2621388 original size:21 final size:21
Alignment explanation
Indices: 2621363--2621402 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
2621353 GATTTATGAG
2621363 AAAAACTAAATATAAATTATA
1 AAAAACTAAATATAAATTATA
*
2621384 AAAAATTAAATATAAATTA
1 AAAAACTAAATATAAATTA
2621403 AAATTTTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.30
Consensus pattern (21 bp):
AAAAACTAAATATAAATTATA
Found at i:2631468 original size:70 final size:69
Alignment explanation
Indices: 2631356--2631493 Score: 231
Period size: 70 Copynumber: 2.0 Consensus size: 69
2631346 CAACTCAATA
* * *
2631356 ACTTAAATAAAAACTTTTGAGTAGTTTAGTTACCATCGTGTAACTTGCAATCTAACTCCTAATAC
1 ACTTAAATAAAAACTTTTGAATAGTTTAATTACCATCGTGTAACTTGCAATCCAACTCCTAATAC
2631421 AAAG
66 AAAG
*
2631425 ACTTAAATAAAAAACTTTTGAATAGTTTAATTACCATCTTGTAACTTGCAATCCAACTCCTAATA
1 ACTTAAAT-AAAAACTTTTGAATAGTTTAATTACCATCGTGTAACTTGCAATCCAACTCCTAATA
2631490 CAAA
65 CAAA
2631494 AACCTTCATA
Statistics
Matches: 64, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
69 8 0.12
70 56 0.88
ACGTcount: A:0.40, C:0.18, G:0.09, T:0.33
Consensus pattern (69 bp):
ACTTAAATAAAAACTTTTGAATAGTTTAATTACCATCGTGTAACTTGCAATCCAACTCCTAATAC
AAAG
Found at i:2636986 original size:25 final size:23
Alignment explanation
Indices: 2636958--2637003 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 23
2636948 GTTGGATCCA
2636958 AATTAAATTCTAAAAAGATAATTAG
1 AATTAAA-TCTAAAAA-ATAATTAG
*
2636983 AATTAAATCTAAACAATAATT
1 AATTAAATCTAAAAAATAATT
2637004 CTTTAATTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 7 0.35
25 7 0.35
ACGTcount: A:0.57, C:0.07, G:0.04, T:0.33
Consensus pattern (23 bp):
AATTAAATCTAAAAAATAATTAG
Found at i:2637967 original size:11 final size:11
Alignment explanation
Indices: 2637951--2637991 Score: 57
Period size: 11 Copynumber: 3.7 Consensus size: 11
2637941 AATAGTCCAT
2637951 AATTAAAATAA
1 AATTAAAATAA
2637962 AATTAAAAATAA
1 AATT-AAAATAA
2637974 AA-TAAAATAA
1 AATTAAAATAA
*
2637984 AACTAAAA
1 AATTAAAA
2637992 AATGAAAATG
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
10 9 0.32
11 10 0.36
12 9 0.32
ACGTcount: A:0.76, C:0.02, G:0.00, T:0.22
Consensus pattern (11 bp):
AATTAAAATAA
Found at i:2637974 original size:6 final size:6
Alignment explanation
Indices: 2637955--2638009 Score: 51
Period size: 6 Copynumber: 9.3 Consensus size: 6
2637945 GTCCATAATT
* * * *
2637955 AAAATA AAATTA AAAAT- AAAAT- AAAATA AAACTAA AAAATG AAAATG
1 AAAATA AAAATA AAAATA AAAATA AAAATA AAAAT-A AAAATA AAAATA
2638002 AAAATA AA
1 AAAATA AA
2638010 TATACTAATT
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
5 10 0.24
6 26 0.63
7 5 0.12
ACGTcount: A:0.76, C:0.02, G:0.04, T:0.18
Consensus pattern (6 bp):
AAAATA
Found at i:2637992 original size:17 final size:16
Alignment explanation
Indices: 2637954--2637991 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
2637944 AGTCCATAAT
2637954 TAAAATAAAATTAAAAA
1 TAAAATAAAA-TAAAAA
*
2637971 TAAAATAAAATAAAAC
1 TAAAATAAAATAAAAA
2637987 TAAAA
1 TAAAA
2637992 AATGAAAATG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
16 10 0.50
17 10 0.50
ACGTcount: A:0.76, C:0.03, G:0.00, T:0.21
Consensus pattern (16 bp):
TAAAATAAAATAAAAA
Found at i:2640931 original size:19 final size:19
Alignment explanation
Indices: 2640869--2640931 Score: 56
Period size: 19 Copynumber: 3.3 Consensus size: 19
2640859 CAAAAGCAAA
* *
2640869 AAAAATTAAAATAGAAAAAT
1 AAAAATAAAAATA-AATAAT
* * *
2640889 TAAATTAAAAAGCAAATAAT
1 AAAAATAAAAA-TAAATAAT
2640909 -AAAATAAAAATAAATAAT
1 AAAAATAAAAATAAATAAT
2640927 AAAAA
1 AAAAA
2640932 AAGGCTAAAG
Statistics
Matches: 34, Mismatches: 7, Indels: 5
0.74 0.15 0.11
Matches are distributed among these distances:
18 7 0.21
19 13 0.38
20 13 0.38
21 1 0.03
ACGTcount: A:0.75, C:0.02, G:0.03, T:0.21
Consensus pattern (19 bp):
AAAAATAAAAATAAATAAT
Found at i:2648008 original size:19 final size:22
Alignment explanation
Indices: 2647985--2648035 Score: 72
Period size: 22 Copynumber: 2.4 Consensus size: 22
2647975 TTATTTTCAT
2647985 TTTATTTTTTTT-A-TAAATTA
1 TTTATTTTTTTTGATTAAATTA
2648005 -TTATTTTCTTTTGATTAAATTA
1 TTTATTTT-TTTTGATTAAATTA
2648027 TTTATTTTT
1 TTTATTTTT
2648036 AGCAAATGGG
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
19 7 0.26
20 4 0.15
21 1 0.04
22 8 0.30
23 7 0.26
ACGTcount: A:0.25, C:0.02, G:0.02, T:0.71
Consensus pattern (22 bp):
TTTATTTTTTTTGATTAAATTA
Found at i:2650163 original size:31 final size:31
Alignment explanation
Indices: 2650094--2650166 Score: 137
Period size: 31 Copynumber: 2.4 Consensus size: 31
2650084 TTGGTGTTTA
*
2650094 GATTGCTCTGTTGAGATTGATGTGTAATTGG
1 GATTGCTTTGTTGAGATTGATGTGTAATTGG
2650125 GATTGCTTTGTTGAGATTGATGTGTAATTGG
1 GATTGCTTTGTTGAGATTGATGTGTAATTGG
2650156 GATTGCTTTGT
1 GATTGCTTTGT
2650167 GAATTGGTTC
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
31 41 1.00
ACGTcount: A:0.18, C:0.05, G:0.32, T:0.45
Consensus pattern (31 bp):
GATTGCTTTGTTGAGATTGATGTGTAATTGG
Found at i:2653206 original size:22 final size:23
Alignment explanation
Indices: 2653175--2653217 Score: 79
Period size: 22 Copynumber: 1.9 Consensus size: 23
2653165 TGTTTGATTA
2653175 ATAAGAAAAAGTAAATATAAATT
1 ATAAGAAAAAGTAAATATAAATT
2653198 ATAA-AAAAAGTAAATATAAA
1 ATAAGAAAAAGTAAATATAAA
2653218 AAATTATTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
22 16 0.80
23 4 0.20
ACGTcount: A:0.70, C:0.00, G:0.07, T:0.23
Consensus pattern (23 bp):
ATAAGAAAAAGTAAATATAAATT
Found at i:2666944 original size:6 final size:6
Alignment explanation
Indices: 2666922--2666988 Score: 55
Period size: 6 Copynumber: 10.7 Consensus size: 6
2666912 TTCAATGAAT
* * * *
2666922 AAAAAG AAGAAG AAAAAAG AAAAA- AGAAAAG CAAAAG AAGAAG AAGAAG
1 AAAAAG AAAAAG -AAAAAG AAAAAG A-AAAAG AAAAAG AAAAAG AAAAAG
2666971 AAACAGAG AAAAAG AAAA
1 AAA-A-AG AAAAAG AAAA
2666989 GGAGAGGTCG
Statistics
Matches: 50, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
5 1 0.02
6 37 0.74
7 7 0.14
8 5 0.10
ACGTcount: A:0.76, C:0.03, G:0.21, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:2668139 original size:49 final size:49
Alignment explanation
Indices: 2668066--2668160 Score: 120
Period size: 49 Copynumber: 1.9 Consensus size: 49
2668056 GTGTACCTCA
* * **
2668066 GAAGACAAGAAGGTAAAGATTTAAGCCGT-AACGGCGAATCCAATACAAT
1 GAAGACAAGAAGGGAAAAATTTAAGCC-TCAACGGAAAATCCAATACAAT
* *
2668115 GAAGACATGACGGGAAAAATTTAAGCCTCAACGGAAAATCCAATAC
1 GAAGACAAGAAGGGAAAAATTTAAGCCTCAACGGAAAATCCAATAC
2668161 TACGAAGATT
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
48 1 0.03
49 38 0.97
ACGTcount: A:0.45, C:0.18, G:0.21, T:0.16
Consensus pattern (49 bp):
GAAGACAAGAAGGGAAAAATTTAAGCCTCAACGGAAAATCCAATACAAT
Found at i:2668775 original size:167 final size:165
Alignment explanation
Indices: 2668477--2668809 Score: 486
Period size: 167 Copynumber: 2.0 Consensus size: 165
2668467 CTCAACGCTC
* *
2668477 AATGTGAGCAAACCTTCGAACCCAGCTTCCTGATGAGACACTAAGAAACAGGTCGAAGCAATAAA
1 AATGCGAGCAAACCTTCGAACCCAGCTTCCTGATGAGACACTAAGAAACAGGTCAAAGCAATAAA
* * * * *
2668542 TGGTTAGCTTCCTGATGAGACACTGAGAAGTGGACCAAATTTGTCTTCCTGAGGCGATCCAGAGA
66 TGGTTAGCTTCCTGATGACACACTGAGAAGCGGACAAAATTCGTCTTCCTGAGGAGATCCAGAGA
* *
2668607 AGCTAATTAAAACAAGTGATGCGGTCATCTTCCTG
131 AGCAAATTAAAACAAGTGATACGGTCATCTTCCTG
* * * * * *
2668642 AATGCGAGCAAATCTTTGAACCCTAGCTTCCTGATGAGATATTGAGAAGCAGGTCAAAGCAATAA
1 AATGCGAGCAAACCTTCGAACCC-AGCTTCCTGATGAGACACTAAGAAACAGGTCAAAGCAAT-A
* *
2668707 AATGGTTAGCTTCCTGATGACATACTGAGAAGCGGACAAAATTCGTCTTCCTGAGGAGATCTAGA
64 AATGGTTAGCTTCCTGATGACACACTGAGAAGCGGACAAAATTCGTCTTCCTGAGGAGATCCAGA
*
2668772 GAAGCAAATTAAAATAAGTGATACGGTCATCTTCCTG
129 GAAGCAAATTAAAACAAGTGATACGGTCATCTTCCTG
2668809 A
1 A
2668810 TGAGACACAG
Statistics
Matches: 148, Mismatches: 18, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
165 20 0.14
166 34 0.23
167 94 0.64
ACGTcount: A:0.34, C:0.20, G:0.23, T:0.24
Consensus pattern (165 bp):
AATGCGAGCAAACCTTCGAACCCAGCTTCCTGATGAGACACTAAGAAACAGGTCAAAGCAATAAA
TGGTTAGCTTCCTGATGACACACTGAGAAGCGGACAAAATTCGTCTTCCTGAGGAGATCCAGAGA
AGCAAATTAAAACAAGTGATACGGTCATCTTCCTG
Found at i:2669006 original size:204 final size:203
Alignment explanation
Indices: 2668642--2669508 Score: 1213
Period size: 204 Copynumber: 4.2 Consensus size: 203
2668632 CATCTTCCTG
* * *
2668642 AATGCGAGCAAATCTTTGAACCCTAGCTTCCTGATGAGATATTGAGAAGCAGGTCAAAGCAATAA
1 AATGCGAGCAAATCTTCGAACCC-AGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAAT-A
* * * *
2668707 AATGGTTAGCTTCCTGATGACATACTGAGAAGCGGA-CAAAATTCGTCTTCCTGAGGAGATCTAG
64 AATGGTTAGCTTCCTGATGAGACACTGAGAAGTGGACCAAAA-TCGTCTTCCTGAGGAGATCCAG
* *
2668771 AGAAGCAAATTAAAATAAGTGAT-ACGGTCATCTTCCTGATGAGACACAGAGAAGAAGACCAAAT
128 AGAAGCGAATTAAAACAAGTGATGA-GGTCATCTTCCTGATGAGACACAGAGAAGAAGACCAAAT
2668835 CAAACCAGGCTC
192 CAAACCAGGCTC
* *
2668847 AATGCAAGCAAATCTTCGAACCCTAGCTTCCTGATGAGATACTGAGAAGCAGGTTGAAGCAATAA
1 AATGCGAGCAAATCTTCGAACCC-AGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAA
*
2668912 ATGGTTAGCTTCCTGATGAGACAGTGAGAAGTGGACCAAAATCGTCTTCCTGAGGAGATCCAGAG
65 ATGGTTAGCTTCCTGATGAGACACTGAGAAGTGGACCAAAATCGTCTTCCTGAGGAGATCCAGAG
* * * *
2668977 AAACGAATTAAAATAAGGGATGAGGTCATCTTCCTGATGAGACACTGAGAAGAAGACCAAATCAA
130 AAGCGAATTAAAACAAGTGATGAGGTCATCTTCCTGATGAGACACAGAGAAGAAGACCAAATCAA
*
2669042 GCCCAGGCTC
195 -ACCAGGCTC
* *
2669052 AATACG-GCAAATCTTCGAATCCCAGCTTCCTGATGAGATAATGAGAAGCAGGTCGAAGCAATAA
1 AATGCGAGCAAATCTTCGAA-CCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAA
* * * *
2669116 ATGGTTAGCTTCCTGATGAGACACTGAGAAGTGGACCAAATTCGTCTTCGTTAGGAGATCTAGAG
65 ATGGTTAGCTTCCTGATGAGACACTGAGAAGTGGACCAAAATCGTCTTCCTGAGGAGATCCAGAG
* * * * *
2669181 AAGTGAATTAAAACAAGTGATGCGGTCATCTTTCTGATGAGACACTGAGAAGAAGACCAAATAAA
130 AAGCGAATTAAAACAAGTGATGAGGTCATCTTCCTGATGAGACACAGAGAAGAAGACCAAATCAA
* *
2669246 ACCTAAGCTA
195 ACC-AGGCTC
*
2669256 AATGCGAGCAAATCTTCGAACCCCAGCTTCTTGATGAGATACTGAGAAGCAGGTCGAAGCAATAA
1 AATGCGAGCAAATCTTCGAA-CCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAA
* * *
2669321 ATGGTTAGCTT-CTGATGAGACACTAAGAAGTGGACCAAATTCATCTTCCTGAGGAGATCCAGAG
65 ATGGTTAGCTTCCTGATGAGACACTGAGAAGTGGACCAAAATCGTCTTCCTGAGGAGATCCAGAG
* *
2669385 AAGCGAATTGAAACAAGTGATGCGGTCATCTTCCTGATGAGACACTA-AGAAGAAGACCAAATCA
130 AAGCGAATTAAAACAAGTGATGAGGTCATCTTCCTGATGAGACAC-AGAGAAGAAGACCAAATCA
2669449 AACCCAGGCTC
194 AA-CCAGGCTC
** * * * *
2669460 AATATGAGCGAATCTTCGAATCCCAACTTCCTGATGAGACACTAAGAAG
1 AATGCGAGCAAATCTTCGAA-CCCAGCTTCCTGATGAGATACTGAGAAG
2669509 TGGACCAATT
Statistics
Matches: 596, Mismatches: 58, Indels: 17
0.89 0.09 0.03
Matches are distributed among these distances:
203 2 0.00
204 447 0.75
205 147 0.25
ACGTcount: A:0.36, C:0.19, G:0.23, T:0.22
Consensus pattern (203 bp):
AATGCGAGCAAATCTTCGAACCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAA
TGGTTAGCTTCCTGATGAGACACTGAGAAGTGGACCAAAATCGTCTTCCTGAGGAGATCCAGAGA
AGCGAATTAAAACAAGTGATGAGGTCATCTTCCTGATGAGACACAGAGAAGAAGACCAAATCAAA
CCAGGCTC
Found at i:2669338 original size:408 final size:410
Alignment explanation
Indices: 2668646--2669498 Score: 1336
Period size: 408 Copynumber: 2.1 Consensus size: 410
2668636 TTCCTGAATG
* *
2668646 CGAGCAAATCTTTGAA-CCCTAGCTTCCTGATGAGATATTGAGAAGCAGGTCAAAGCAATAAAAT
1 CGAGCAAATCTTCGAATCCC-AGCTTCCTGATGAGATAATGAGAAGCAGGTCAAAGCAATAAAAT
*
2668710 GGTTAGCTTCCTGATGACATACTGAGAAGCGGACAAAATTCGTCTTCCTGAGGAGATCTAGAGAA
65 GGTTAGCTTCCTGATGACACACTGAGAAGCGGACAAAATTCGTCTTCCTGAGGAGATCTAGAGAA
* *
2668775 GCAAATTAAAATAAGTGATACGGTCATCTTCCTGATGAGACACAGAGAAGAAGACCAAATCAAAC
130 GCAAATTAAAACAAGTGATACGGTCATCTTCCTGATGAGACACAGAGAAGAAGACCAAATAAAAC
* * * *
2668840 CAGGCTCAATGCAAGCAAATCTTCGAACCCTAGCTTCCTGATGAGATACTGAGAAGCAGGTTGAA
195 CAAGCTAAATGCAAGCAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAA
* * *
2668905 GCAATAAATGGTTAGCTTCCTGATGAGACAGTGAGAAGTGGACCAAAATCGTCTTCCTGAGGAGA
260 GCAATAAATGGTTAGCTTCCTGATGAGACACTAAGAAGTGGACCAAAATCATCTTCCTGAGGAGA
* *
2668970 TCCAGAGAAACGAATTAAAATAAGGGATGAGGTCATCTTCCTGATGAGACACTGAGAAGAAGACC
325 TCCAGAGAAACGAATTAAAACAAGGGATGAGGTCATCTTCCTGATGAGACACTAAGAAGAAGACC
*
2669035 AAATCAAGCCCAGGCTCAATA
390 AAATCAAACCCAGGCTCAATA
*
2669056 CG-GCAAATCTTCGAATCCCAGCTTCCTGATGAGATAATGAGAAGCAGGTCGAAGCAAT-AAATG
1 CGAGCAAATCTTCGAATCCCAGCTTCCTGATGAGATAATGAGAAGCAGGTCAAAGCAATAAAATG
* * * * *
2669119 GTTAGCTTCCTGATGAGACACTGAGAAGTGGACCAAATTCGTCTTCGTTAGGAGATCTAGAGAAG
66 GTTAGCTTCCTGATGACACACTGAGAAGCGGACAAAATTCGTCTTCCTGAGGAGATCTAGAGAAG
** * * *
2669184 TGAATTAAAACAAGTGATGCGGTCATCTTTCTGATGAGACACTGAGAAGAAGACCAAATAAAACC
131 CAAATTAAAACAAGTGATACGGTCATCTTCCTGATGAGACACAGAGAAGAAGACCAAATAAAACC
* *
2669249 TAAGCTAAATGCGAGCAAATCTTCGAACCCCAGCTTCTTGATGAGATACTGAGAAGCAGGTCGAA
196 -AAGCTAAATGCAAGCAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAA
*
2669314 GCAATAAATGGTTAGCTT-CTGATGAGACACTAAGAAGTGGACCAAATTCATCTTCCTGAGGAGA
260 GCAATAAATGGTTAGCTTCCTGATGAGACACTAAGAAGTGGACCAAAATCATCTTCCTGAGGAGA
* * * *
2669378 TCCAGAGAAGCGAATTGAAACAAGTGATGCGGTCATCTTCCTGATGAGACACTAAGAAGAAGACC
325 TCCAGAGAAACGAATTAAAACAAGGGATGAGGTCATCTTCCTGATGAGACACTAAGAAGAAGACC
2669443 AAATCAAACCCAGGCTCAATA
390 AAATCAAACCCAGGCTCAATA
* * *
2669464 TGAGCGAATCTTCGAATCCCAACTTCCTGATGAGA
1 CGAGCAAATCTTCGAATCCCAGCTTCCTGATGAGA
2669499 CACTAAGAAG
Statistics
Matches: 404, Mismatches: 36, Indels: 7
0.90 0.08 0.02
Matches are distributed among these distances:
408 244 0.60
409 155 0.38
410 5 0.01
ACGTcount: A:0.36, C:0.20, G:0.23, T:0.22
Consensus pattern (410 bp):
CGAGCAAATCTTCGAATCCCAGCTTCCTGATGAGATAATGAGAAGCAGGTCAAAGCAATAAAATG
GTTAGCTTCCTGATGACACACTGAGAAGCGGACAAAATTCGTCTTCCTGAGGAGATCTAGAGAAG
CAAATTAAAACAAGTGATACGGTCATCTTCCTGATGAGACACAGAGAAGAAGACCAAATAAAACC
AAGCTAAATGCAAGCAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAG
CAATAAATGGTTAGCTTCCTGATGAGACACTAAGAAGTGGACCAAAATCATCTTCCTGAGGAGAT
CCAGAGAAACGAATTAAAACAAGGGATGAGGTCATCTTCCTGATGAGACACTAAGAAGAAGACCA
AATCAAACCCAGGCTCAATA
Found at i:2669619 original size:157 final size:158
Alignment explanation
Indices: 2669332--2669665 Score: 492
Period size: 157 Copynumber: 2.1 Consensus size: 158
2669322 TGGTTAGCTT
* * *
2669332 CTGATGAGACACTAAGAAGTGGACCAAATTCATCTTCCTGAGGAGATCCAGAGAAGCGAATTGAA
1 CTGATGAGACACTAAGAAGTGGACCAAATTCATCTTCCTGAGGAGATCCAAAGAAGCAAATTAAA
* *
2669397 ACAAGTGATGCGGTCATCTTCCTGATGAGACACTAAGAAGAAGACCAAATCAAACCCAGGCTCAA
66 ACAAGTGATGCGGTCATCTTCCTGATGAGACACTAAGAAAAAGACCAAATCAAACCCAGACTCAA
* *
2669462 TATGAGCGAATCTTCGAATCCC-AACTTC
131 TACGAGCAAATCTTCGAA-CCCTAACTTC
*
2669490 CTGATGAGACACTAAGAAGTGGACC-AATTCGTCTTCCTGAGGAGATCCAAAGAAGCAAATTAAA
1 CTGATGAGACACTAAGAAGTGGACCAAATTCATCTTCCTGAGGAGATCCAAAGAAGCAAATTAAA
* * * *
2669554 ACAAGTGATGCGGTCATCTTCCTGATGAGACATTGAGAAAAAGAGCAAATCAAAGCCAGACTCAA
66 ACAAGTGATGCGGTCATCTTCCTGATGAGACACTAAGAAAAAGACCAAATCAAACCCAGACTCAA
* * *
2669619 TGCGAGCAAATCTTTGAACCCTAGCTTC
131 TACGAGCAAATCTTCGAACCCTAACTTC
* *
2669647 CTGATGAGATACTGAGAAG
1 CTGATGAGACACTAAGAAG
2669666 CAGGTCAAAG
Statistics
Matches: 158, Mismatches: 17, Indels: 3
0.89 0.10 0.02
Matches are distributed among these distances:
156 3 0.02
157 130 0.82
158 25 0.16
ACGTcount: A:0.37, C:0.21, G:0.22, T:0.21
Consensus pattern (158 bp):
CTGATGAGACACTAAGAAGTGGACCAAATTCATCTTCCTGAGGAGATCCAAAGAAGCAAATTAAA
ACAAGTGATGCGGTCATCTTCCTGATGAGACACTAAGAAAAAGACCAAATCAAACCCAGACTCAA
TACGAGCAAATCTTCGAACCCTAACTTC
Found at i:2670129 original size:17 final size:16
Alignment explanation
Indices: 2670073--2670127 Score: 74
Period size: 16 Copynumber: 3.4 Consensus size: 16
2670063 TTGAACTGAT
2670073 TTTAAATTTATTTAAA
1 TTTAAATTTATTTAAA
* *
2670089 TTTAAATTTGTTTTGAA
1 TTTAAATTT-ATTTAAA
*
2670106 TTTAAATTTAATTAAA
1 TTTAAATTTATTTAAA
2670122 TTTAAA
1 TTTAAA
2670128 ATGGTTTTAA
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
16 19 0.58
17 14 0.42
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.55
Consensus pattern (16 bp):
TTTAAATTTATTTAAA
Found at i:2670135 original size:33 final size:33
Alignment explanation
Indices: 2670073--2670135 Score: 99
Period size: 33 Copynumber: 1.9 Consensus size: 33
2670063 TTGAACTGAT
* * *
2670073 TTTAAATTTATTTAAATTTAAATTTGTTTTGAA
1 TTTAAATTTAATTAAATTTAAAATGGTTTTGAA
2670106 TTTAAATTTAATTAAATTTAAAATGGTTTT
1 TTTAAATTTAATTAAATTTAAAATGGTTTT
2670136 AAACTTAAGA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 27 1.00
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.56
Consensus pattern (33 bp):
TTTAAATTTAATTAAATTTAAAATGGTTTTGAA
Found at i:2672038 original size:29 final size:28
Alignment explanation
Indices: 2671959--2672106 Score: 102
Period size: 29 Copynumber: 5.1 Consensus size: 28
2671949 CCCTAGAGGT
**
2671959 CCCTAAACTATCCAAAAATTGTATTTTAAC
1 CCCTAAACT-TCCAAAAATTACATTTT-AC
* *
2671989 CCCTAAACTTCTCCAAGATTACATTTTAC
1 CCCTAAACTTC-CAAAAATTACATTTTAC
*
2672018 CCCTAAAACTTCCAAAAATTACTTTTTAC
1 CCCT-AAACTTCCAAAAATTACATTTTAC
** * * * *
2672047 CCCCGAATTTCTAAAAATTCCATTTTTAA
1 CCCTAAACTTCCAAAAATTACA-TTTTAC
* *
2672076 CCTTAAAAATT--AAAAATTACCATTTTAC
1 CCCT-AAACTTCCAAAAATTA-CATTTTAC
2672104 CCC
1 CCC
2672107 GACTGTCCAA
Statistics
Matches: 92, Mismatches: 21, Indels: 12
0.74 0.17 0.10
Matches are distributed among these distances:
28 27 0.29
29 34 0.37
30 31 0.34
ACGTcount: A:0.37, C:0.26, G:0.02, T:0.34
Consensus pattern (28 bp):
CCCTAAACTTCCAAAAATTACATTTTAC
Found at i:2682284 original size:73 final size:71
Alignment explanation
Indices: 2682142--2682286 Score: 200
Period size: 73 Copynumber: 2.0 Consensus size: 71
2682132 ATGCATATCG
* * * *
2682142 TCTAGCTTATTCATTGGGGCAATATGACTTTCTTTATGGGGATTCATCCAAAAATCACGCCAAAT
1 TCTAGCGTATTCATTGGGGCAATATAACTTTCTTAATGGGGATTCATCCAAAAATCACGCCAAAG
2682207 AATCCT
66 AATCCT
* * **
2682213 TCTAGCGTATTCATTGGGGGCCATATAACTTTCTTAATGGGGAATTCATTCAAAAATCACGTTAA
1 TCTAGCGTATTCATT-GGGGCAATATAACTTTCTTAATGGGG-ATTCATCCAAAAATCACGCCAA
2682278 AGAATCCT
64 AGAATCCT
2682286 T
1 T
2682287 TGTTAGTTTA
Statistics
Matches: 64, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
71 14 0.22
72 23 0.36
73 27 0.42
ACGTcount: A:0.30, C:0.19, G:0.17, T:0.34
Consensus pattern (71 bp):
TCTAGCGTATTCATTGGGGCAATATAACTTTCTTAATGGGGATTCATCCAAAAATCACGCCAAAG
AATCCT
Found at i:2691006 original size:28 final size:26
Alignment explanation
Indices: 2690973--2691035 Score: 90
Period size: 28 Copynumber: 2.3 Consensus size: 26
2690963 TAAATATATT
*
2690973 TTTATATTTACGTTTTAAATTTTTATAA
1 TTTATATTTAAGTTTTAAA-TTTT-TAA
*
2691001 TTTATATTTAATTTTTAAATTTTTAA
1 TTTATATTTAAGTTTTAAATTTTTAA
2691027 TTTATATTT
1 TTTATATTT
2691036 TTTTTCTCAT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
26 12 0.36
27 4 0.12
28 17 0.52
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.65
Consensus pattern (26 bp):
TTTATATTTAAGTTTTAAATTTTTAA
Found at i:2691013 original size:20 final size:20
Alignment explanation
Indices: 2690990--2691037 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
2690980 TTACGTTTTA
2690990 AATTTTTATAATTTAT-ATTT
1 AATTTTTA-AATTTATAATTT
*
2691010 AATTTTTAAATTTTTAATTT
1 AATTTTTAAATTTATAATTT
2691030 ATATTTTT
1 A-ATTTTT
2691038 TTTCTCATCA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
19 6 0.24
20 13 0.52
21 6 0.24
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (20 bp):
AATTTTTAAATTTATAATTT
Found at i:2707353 original size:23 final size:25
Alignment explanation
Indices: 2707327--2707372 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
2707317 CCAATTAGGG
2707327 AATTAT-TGTTTAG-ATTTAATTCT
1 AATTATCTGTTTAGAATTTAATTCT
*
2707350 AATTATCTTTTTAGAATTTAATT
1 AATTATCTGTTTAGAATTTAATT
2707373 TGAATCCAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 6 0.30
25 8 0.40
ACGTcount: A:0.33, C:0.04, G:0.07, T:0.57
Consensus pattern (25 bp):
AATTATCTGTTTAGAATTTAATTCT
Found at i:2708466 original size:14 final size:14
Alignment explanation
Indices: 2708439--2708490 Score: 52
Period size: 14 Copynumber: 3.8 Consensus size: 14
2708429 TTTAGCCATT
*
2708439 TTTTTATTAT-TTA
1 TTTTTATTTTATTA
2708452 TTTTTATTTTATTA
1 TTTTTATTTTATTA
* **
2708466 TTTTTAGTTTAAAA
1 TTTTTATTTTATTA
*
2708480 TTTCTATTTTA
1 TTTTTATTTTA
2708491 ATTTTTCCTT
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
13 9 0.28
14 23 0.72
ACGTcount: A:0.25, C:0.02, G:0.02, T:0.71
Consensus pattern (14 bp):
TTTTTATTTTATTA
Found at i:2713983 original size:11 final size:11
Alignment explanation
Indices: 2713967--2714011 Score: 67
Period size: 11 Copynumber: 4.3 Consensus size: 11
2713957 TCATGTTTTT
2713967 AAAAAAATTGA
1 AAAAAAATTGA
2713978 AAAAAAATT--
1 AAAAAAATTGA
2713987 AAAAAAATTGA
1 AAAAAAATTGA
*
2713998 AAAAAATTTGA
1 AAAAAAATTGA
2714009 AAA
1 AAA
2714012 GTTCAAAAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
9 9 0.29
11 22 0.71
ACGTcount: A:0.73, C:0.00, G:0.07, T:0.20
Consensus pattern (11 bp):
AAAAAAATTGA
Found at i:2713990 original size:20 final size:20
Alignment explanation
Indices: 2713965--2714026 Score: 81
Period size: 20 Copynumber: 3.1 Consensus size: 20
2713955 TTTCATGTTT
2713965 TTAAAAAAATTGAAAAAAAA
1 TTAAAAAAATTGAAAAAAAA
2713985 TTAAAAAAATTG-AAAAAAA
1 TTAAAAAAATTGAAAAAAAA
** * *
2714004 TTTGAAAAGTTCAAAAAAAA
1 TTAAAAAAATTGAAAAAAAA
2714024 TTA
1 TTA
2714027 GTTTTTTTTA
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
19 15 0.42
20 21 0.58
ACGTcount: A:0.68, C:0.02, G:0.06, T:0.24
Consensus pattern (20 bp):
TTAAAAAAATTGAAAAAAAA
Found at i:2714064 original size:11 final size:10
Alignment explanation
Indices: 2714028--2714087 Score: 59
Period size: 11 Copynumber: 5.5 Consensus size: 10
2714018 AAAAAATTAG
2714028 TTTT-TTTTA
1 TTTTATTTTA
2714037 TTTTCATTTTCA
1 TTTT-ATTTT-A
2714049 CTTTTAGTTTTA
1 -TTTTA-TTTTA
2714061 TTTTATTTTA
1 TTTTATTTTA
2714071 TTTTTATTTTTA
1 -TTTTA-TTTTA
2714083 TTTTA
1 TTTTA
2714088 ATTATGCACT
Statistics
Matches: 44, Mismatches: 0, Indels: 12
0.79 0.00 0.21
Matches are distributed among these distances:
9 4 0.09
10 5 0.11
11 19 0.43
12 8 0.18
13 8 0.18
ACGTcount: A:0.17, C:0.05, G:0.02, T:0.77
Consensus pattern (10 bp):
TTTTATTTTA
Found at i:2714066 original size:5 final size:5
Alignment explanation
Indices: 2714028--2714087 Score: 59
Period size: 6 Copynumber: 11.0 Consensus size: 5
2714018 AAAAAATTAG
2714028 TTTT- TTTTA TTTTCA TTTTCA CTTTTA GTTTTA TTTTA TTTTA TTTTTA
1 TTTTA TTTTA TTTT-A TTTT-A -TTTTA -TTTTA TTTTA TTTTA -TTTTA
2714077 TTTTTA TTTTA
1 -TTTTA TTTTA
2714088 ATTATGCACT
Statistics
Matches: 51, Mismatches: 1, Indels: 7
0.86 0.02 0.12
Matches are distributed among these distances:
4 4 0.08
5 19 0.37
6 24 0.47
7 4 0.08
ACGTcount: A:0.17, C:0.05, G:0.02, T:0.77
Consensus pattern (5 bp):
TTTTA
Found at i:2714081 original size:28 final size:29
Alignment explanation
Indices: 2714024--2714087 Score: 89
Period size: 28 Copynumber: 2.3 Consensus size: 29
2714014 TCAAAAAAAA
2714024 TTAGTTTT-TTTTATTTTCATTTTCACTT
1 TTAGTTTTATTTTATTTTCATTTTCACTT
* *
2714052 TTAGTTTTATTTTATTTT-ATTTTTATTT
1 TTAGTTTTATTTTATTTTCATTTTCACTT
2714080 TTA-TTTTA
1 TTAGTTTTA
2714088 ATTATGCACT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
27 5 0.15
28 19 0.58
29 9 0.27
ACGTcount: A:0.17, C:0.05, G:0.03, T:0.75
Consensus pattern (29 bp):
TTAGTTTTATTTTATTTTCATTTTCACTT
Found at i:2715066 original size:14 final size:13
Alignment explanation
Indices: 2715034--2715068 Score: 54
Period size: 14 Copynumber: 2.7 Consensus size: 13
2715024 AAAAAAATCG
2715034 AAAAAA-AATTAA
1 AAAAAAGAATTAA
2715046 AAAAAAGAATTGAA
1 AAAAAAGAATT-AA
2715060 AAAAAAGAA
1 AAAAAAGAA
2715069 AAAGAAAGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 6 0.29
13 4 0.19
14 11 0.52
ACGTcount: A:0.80, C:0.00, G:0.09, T:0.11
Consensus pattern (13 bp):
AAAAAAGAATTAA
Found at i:2715071 original size:24 final size:24
Alignment explanation
Indices: 2715024--2715078 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 24
2715014 AAAAAAAGGC
**
2715024 AAAAA-AATCGAAAAAAAATTAAA
1 AAAAAGAATCGAAAAAAAAGAAAA
*
2715047 AAAAAGAATTGAAAAAAAAGAAAA
1 AAAAAGAATCGAAAAAAAAGAAAA
*
2715071 AGAAAGAA
1 AAAAAGAA
2715079 AAAGAAAAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
23 5 0.19
24 22 0.81
ACGTcount: A:0.78, C:0.02, G:0.11, T:0.09
Consensus pattern (24 bp):
AAAAAGAATCGAAAAAAAAGAAAA
Found at i:2715080 original size:16 final size:15
Alignment explanation
Indices: 2715044--2715087 Score: 54
Period size: 16 Copynumber: 2.9 Consensus size: 15
2715034 AAAAAAAATT
**
2715044 AAAAAAAAG-AATTG
1 AAAAAAAAGAAAAAG
2715058 AAAAAAAAGAAAAAG
1 AAAAAAAAGAAAAAG
2715073 AAAGAAAAAGAAAAA
1 AAA-AAAAAGAAAAA
2715088 AGTGTGTTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
14 9 0.35
15 6 0.23
16 11 0.42
ACGTcount: A:0.82, C:0.00, G:0.14, T:0.05
Consensus pattern (15 bp):
AAAAAAAAGAAAAAG
Found at i:2720783 original size:20 final size:20
Alignment explanation
Indices: 2720760--2720798 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
2720750 AAAAAAAATA
2720760 TAAATTAAAAATT-TAAAAAG
1 TAAA-TAAAAATTATAAAAAG
*
2720780 TAAATATAAATTATAAAAA
1 TAAATAAAAATTATAAAAA
2720799 TTTAAAACGT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.31
Consensus pattern (20 bp):
TAAATAAAAATTATAAAAAG
Found at i:2720804 original size:28 final size:26
Alignment explanation
Indices: 2720755--2720817 Score: 99
Period size: 28 Copynumber: 2.3 Consensus size: 26
2720745 ATGAGAAAAA
2720755 AAATATAAATTAAAAATTTAAAAAGT
1 AAATATAAATTAAAAATTTAAAAAGT
*
2720781 AAATATAAATTATAAAAATTTAAAACGT
1 AAATATAAA-T-TAAAAATTTAAAAAGT
2720809 AAATATAAA
1 AAATATAAA
2720818 AATATATTTA
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
26 9 0.26
27 1 0.03
28 24 0.71
ACGTcount: A:0.65, C:0.02, G:0.03, T:0.30
Consensus pattern (26 bp):
AAATATAAATTAAAAATTTAAAAAGT
Found at i:2728802 original size:20 final size:21
Alignment explanation
Indices: 2728774--2728816 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
2728764 TACATGATTG
2728774 ATGAGAAAAAG-TAAATATAA
1 ATGAGAAAAAGTTAAATATAA
*
2728794 ATGATAAAAAGTTAAATATAA
1 ATGAGAAAAAGTTAAATATAA
2728815 AT
1 AT
2728817 TAAAATTTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 10 0.48
21 11 0.52
ACGTcount: A:0.63, C:0.00, G:0.12, T:0.26
Consensus pattern (21 bp):
ATGAGAAAAAGTTAAATATAA
Found at i:2734861 original size:23 final size:23
Alignment explanation
Indices: 2734831--2734885 Score: 74
Period size: 23 Copynumber: 2.4 Consensus size: 23
2734821 ACGTGGCGTC
* *
2734831 CAGTCAGCAGTTTCTAGAAGATT
1 CAGTCAGCAGCTTCCAGAAGATT
*
2734854 CAGTCAGCAGCTTCCAGAAGGTT
1 CAGTCAGCAGCTTCCAGAAGATT
*
2734877 TAGTCAGCA
1 CAGTCAGCA
2734886 AGGATGGACG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.29, C:0.22, G:0.24, T:0.25
Consensus pattern (23 bp):
CAGTCAGCAGCTTCCAGAAGATT
Done.