Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007834.1 Hibiscus syriacus cultivar Beakdansim tig00110183_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 925658
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 5
Found at i:7004 original size:41 final size:40
Alignment explanation
Indices: 6954--7053 Score: 101
Period size: 41 Copynumber: 2.5 Consensus size: 40
6944 CATTTACAAT
* * * * *
6954 AAAACGCCACTAAGGTATAGGTCATTCGTGACGTTTACGA
1 AAAAAGCCACTAAGGTACAGGACAGTCATGACGTTTACGA
** *
6994 AAAAGAGCCACTAAATTACAGGACAGTCATGGCGTTTACGA
1 AAAA-AGCCACTAAGGTACAGGACAGTCATGACGTTTACGA
* *
7035 AAAACGCCGCTAAGGTACA
1 AAAAAGCCACTAAGGTACA
7054 TACATATTGC
Statistics
Matches: 47, Mismatches: 12, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
40 15 0.32
41 32 0.68
ACGTcount: A:0.37, C:0.21, G:0.22, T:0.20
Consensus pattern (40 bp):
AAAAAGCCACTAAGGTACAGGACAGTCATGACGTTTACGA
Found at i:9607 original size:14 final size:15
Alignment explanation
Indices: 9589--9629 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 15
9579 CATATTAAAT
9589 AATAAATATAATT-A
1 AATAAATATAATTAA
* *
9603 TATAACTATAATTAA
1 AATAAATATAATTAA
9618 AATAAATA-AATT
1 AATAAATATAATT
9630 TGGGGCTAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
14 15 0.68
15 7 0.32
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (15 bp):
AATAAATATAATTAA
Found at i:11860 original size:14 final size:13
Alignment explanation
Indices: 11836--11873 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 13
11826 ATAGTACGAA
11836 ACTAGTATATATAT
1 ACTA-TATATATAT
11850 ACATATATATATAT
1 AC-TATATATATAT
11864 ACTAT-TATAT
1 ACTATATATAT
11874 CGTATGTATA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
12 5 0.22
13 3 0.13
14 13 0.57
15 2 0.09
ACGTcount: A:0.45, C:0.08, G:0.03, T:0.45
Consensus pattern (13 bp):
ACTATATATATAT
Found at i:14617 original size:24 final size:24
Alignment explanation
Indices: 14581--14626 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
14571 ACCAACCGTG
* *
14581 TCAGAGGGTATAGTTGAACTTGAA
1 TCAGAAGGCATAGTTGAACTTGAA
14605 TCAGAAGGCATAGTTGAACTTG
1 TCAGAAGGCATAGTTGAACTTG
14627 CATCCTCGTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.33, C:0.11, G:0.28, T:0.28
Consensus pattern (24 bp):
TCAGAAGGCATAGTTGAACTTGAA
Found at i:20321 original size:23 final size:23
Alignment explanation
Indices: 20290--20333 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
20280 TATGTTTAAA
* *
20290 TTGTGAAGACATGGATTAAATAT
1 TTGTAAAGACAAGGATTAAATAT
*
20313 TTGTAAAGATAAGGATTAAAT
1 TTGTAAAGACAAGGATTAAAT
20334 TAAACATAAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.43, C:0.02, G:0.20, T:0.34
Consensus pattern (23 bp):
TTGTAAAGACAAGGATTAAATAT
Found at i:25269 original size:15 final size:15
Alignment explanation
Indices: 25251--25282 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
25241 GCTGATGATG
25251 GGGGAGGGGAGAGGA
1 GGGGAGGGGAGAGGA
25266 GGGGAGGGGAGAGGA
1 GGGGAGGGGAGAGGA
25281 GG
1 GG
25283 AATAAGGTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.25, C:0.00, G:0.75, T:0.00
Consensus pattern (15 bp):
GGGGAGGGGAGAGGA
Found at i:29075 original size:16 final size:17
Alignment explanation
Indices: 29048--29080 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
29038 TTTTTAGTTA
29048 CTTTGTAAAAGTAAATG
1 CTTTGTAAAAGTAAATG
*
29065 CTTTG-AAAAGTCAATG
1 CTTTGTAAAAGTAAATG
29081 TGACACCTCG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.39, C:0.09, G:0.18, T:0.33
Consensus pattern (17 bp):
CTTTGTAAAAGTAAATG
Found at i:53497 original size:26 final size:26
Alignment explanation
Indices: 53469--53578 Score: 102
Period size: 27 Copynumber: 4.2 Consensus size: 26
53459 TTAATTTAGT
53469 TATATTTTT-AATAAATTAAAATAAA
1 TATATTTTTAAATAAATTAAAATAAA
*
53494 TTATATATTTTAAATGAAAATAAAATAAA
1 -TATAT-TTTTAAAT-AAATTAAAATAAA
* *
53523 -ATATTTTTAAATTAAGTTAATAGTAAA
1 TATATTTTTAAA-TAAATTAA-AATAAA
* *
53550 T-TATTTTT-AATAAATTAATATATA
1 TATATTTTTAAATAAATTAAAATAAA
53574 TATAT
1 TATAT
53579 ATATAATTAT
Statistics
Matches: 69, Mismatches: 8, Indels: 15
0.75 0.09 0.16
Matches are distributed among these distances:
24 4 0.06
25 10 0.14
26 19 0.28
27 21 0.30
28 3 0.04
29 12 0.17
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (26 bp):
TATATTTTTAAATAAATTAAAATAAA
Found at i:53871 original size:39 final size:39
Alignment explanation
Indices: 53823--53928 Score: 119
Period size: 39 Copynumber: 2.7 Consensus size: 39
53813 TTTTAAAAAT
*
53823 AATTCAGAACGTTAATGTGAAATAATTTAAGAAATTAAG
1 AATTTAGAACGTTAATGTGAAATAATTTAAGAAATTAAG
*
53862 AATTTAGAACGTT-ATGGTGTCAA-AATTTAAGAAATTAAG
1 AATTTAGAACGTTAAT-GTG-AAATAATTTAAGAAATTAAG
* * *
53901 ATTTTAAAATGTTAGA-GTGAAATAATTT
1 AATTTAGAACGTTA-ATGTGAAATAATTT
53929 GAGGATTATG
Statistics
Matches: 56, Mismatches: 6, Indels: 10
0.78 0.08 0.14
Matches are distributed among these distances:
38 4 0.07
39 49 0.88
40 2 0.04
41 1 0.02
ACGTcount: A:0.45, C:0.04, G:0.16, T:0.35
Consensus pattern (39 bp):
AATTTAGAACGTTAATGTGAAATAATTTAAGAAATTAAG
Found at i:61285 original size:150 final size:149
Alignment explanation
Indices: 61116--61398 Score: 413
Period size: 150 Copynumber: 1.9 Consensus size: 149
61106 AAACCCTACC
* *
61116 AAAACATTACTTCTTCTATACGAAACACCCGGATTATAAAAAGTACGTCAACAATCAACCAATTA
1 AAAACATTACTTCTTCTATACGAAACACCCAGATTATAAAAAGAACGTCAACAATCAACCAATTA
* * * ** * *
61181 AAATCTGCGTAAACTGAAGAATTATCGGAATGAATAAGCAAACCAAAGAATTTATTTGAATGCTG
66 AAATCTGAGCAAACTG-AGAATAATAAGAATGAATAAACAAACAAAAGAATTTATTTGAATGCTG
61246 AAAATTAAAAACCCAAACCA
130 AAAATTAAAAACCCAAACCA
* * * *
61266 AAAACCTTACTTCTTCTATACGGAACACCCAGATTATAAAAAGAACGTCAACAATCAGCCGATTA
1 AAAACATTACTTCTTCTATACGAAACACCCAGATTATAAAAAGAACGTCAACAATCAACCAATTA
* * *
61331 AAATCTGAGCAAATTGATAATAATAAGAATGGATAAACAAACAAAAGAATTTATTTGAATGCTGA
66 AAATCTGAGCAAACTGAGAATAATAAGAATGAATAAACAAACAAAAGAATTTATTTGAATGCTGA
61396 AAA
131 AAA
61399 AAAAAACTGT
Statistics
Matches: 117, Mismatches: 16, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
149 45 0.38
150 72 0.62
ACGTcount: A:0.47, C:0.17, G:0.12, T:0.24
Consensus pattern (149 bp):
AAAACATTACTTCTTCTATACGAAACACCCAGATTATAAAAAGAACGTCAACAATCAACCAATTA
AAATCTGAGCAAACTGAGAATAATAAGAATGAATAAACAAACAAAAGAATTTATTTGAATGCTGA
AAATTAAAAACCCAAACCA
Found at i:64228 original size:3 final size:3
Alignment explanation
Indices: 64220--64264 Score: 54
Period size: 3 Copynumber: 14.3 Consensus size: 3
64210 AATTAAAAAT
* *
64220 ATA ATA ATA ATA ATA ATAA ATA ATA TTA ATA TTA ATA TATA ATA A
1 ATA ATA ATA ATA ATA AT-A ATA ATA ATA ATA ATA ATA -ATA ATA A
64265 AACTATATAA
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
3 30 0.83
4 6 0.17
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (3 bp):
ATA
Found at i:64244 original size:19 final size:19
Alignment explanation
Indices: 64220--64264 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 19
64210 AATTAAAAAT
64220 ATAATAATAATAATAATAA
1 ATAATAATAATAATAATAA
* * *
64239 ATAATATTAATATTAATAT
1 ATAATAATAATAATAATAA
64258 ATAATAA
1 ATAATAA
64265 AACTATATAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (19 bp):
ATAATAATAATAATAATAA
Found at i:64271 original size:13 final size:12
Alignment explanation
Indices: 64213--64276 Score: 53
Period size: 13 Copynumber: 5.2 Consensus size: 12
64203 AAAATAAAAT
64213 TAAAA-ATATAA
1 TAAAATATATAA
64224 TAATAATA-ATAA
1 TAA-AATATATAA
64236 T-AAATAATATTAA
1 TAAAAT-ATA-TAA
*
64249 TATTAATATATAA
1 TA-AAATATATAA
64262 TAAAACTATATAA
1 TAAAA-TATATAA
64275 TA
1 TA
64277 TTATGTTTTC
Statistics
Matches: 43, Mismatches: 2, Indels: 14
0.73 0.03 0.24
Matches are distributed among these distances:
10 3 0.07
11 5 0.12
12 10 0.23
13 19 0.44
14 3 0.07
15 3 0.07
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (12 bp):
TAAAATATATAA
Found at i:64298 original size:17 final size:17
Alignment explanation
Indices: 64273--64314 Score: 66
Period size: 17 Copynumber: 2.5 Consensus size: 17
64263 AAAACTATAT
*
64273 AATATTATGTTTTCAAA
1 AATAATATGTTTTCAAA
64290 AATAATATGTTTTCAAA
1 AATAATATGTTTTCAAA
*
64307 AATTATAT
1 AATAATAT
64315 ATTATATATG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.45, C:0.05, G:0.05, T:0.45
Consensus pattern (17 bp):
AATAATATGTTTTCAAA
Found at i:65665 original size:23 final size:23
Alignment explanation
Indices: 65639--65697 Score: 75
Period size: 23 Copynumber: 2.6 Consensus size: 23
65629 TCTACTTTCA
*
65639 TGGCACGTTTTTCTCCGTC-TTTG
1 TGGCACATTTTTCTCCG-CATTTG
*
65662 TGGCACATTTTTCTCTGCATTTG
1 TGGCACATTTTTCTCCGCATTTG
*
65685 TGGCATATTTTTC
1 TGGCACATTTTTC
65698 GTTTTCTTTC
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
22 1 0.03
23 31 0.97
ACGTcount: A:0.10, C:0.22, G:0.19, T:0.49
Consensus pattern (23 bp):
TGGCACATTTTTCTCCGCATTTG
Found at i:66210 original size:23 final size:23
Alignment explanation
Indices: 66168--66218 Score: 61
Period size: 23 Copynumber: 2.2 Consensus size: 23
66158 AAATAATAAT
*
66168 AAAATTTATATTAAATTATTTTA
1 AAAATTTATATTAAATTATTATA
66191 AAAAGTTTAT-TTATAA-TATTATA
1 AAAA-TTTATATTA-AATTATTATA
66214 AAAAT
1 AAAAT
66219 ATTTTAAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
22 1 0.04
23 17 0.68
24 7 0.28
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (23 bp):
AAAATTTATATTAAATTATTATA
Found at i:66451 original size:23 final size:23
Alignment explanation
Indices: 66415--66465 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 23
66405 GATAATTTTA
**
66415 AAATAATATTATTTCAATTAAAT
1 AAATAATATTATTTCAAAAAAAT
*
66438 AAATAAT-TTGATTTTAAAAAAAT
1 AAATAATATT-ATTTCAAAAAAAT
66461 AAATA
1 AAATA
66466 TTTTTATAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 2 0.08
23 22 0.92
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (23 bp):
AAATAATATTATTTCAAAAAAAT
Found at i:80583 original size:2 final size:2
Alignment explanation
Indices: 80578--80624 Score: 69
Period size: 2 Copynumber: 24.0 Consensus size: 2
80568 ACACACTATT
**
80578 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA CG TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
80619 TA TA TA
1 TA TA TA
80625 AATTATTTTC
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
1 1 0.03
2 39 0.98
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (2 bp):
TA
Found at i:81936 original size:28 final size:29
Alignment explanation
Indices: 81885--81941 Score: 73
Period size: 28 Copynumber: 2.0 Consensus size: 29
81875 TTCGTCGTTG
* *
81885 TATATATATATTTTATTACTATT-ATTAT
1 TATATATATATTATATCACTATTAATTAT
81913 TATATATATATTATACTCAC-ATTAATTAT
1 TATATATATATTATA-TCACTATTAATTAT
81942 ATCTATCTAC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 17 0.68
29 8 0.32
ACGTcount: A:0.39, C:0.07, G:0.00, T:0.54
Consensus pattern (29 bp):
TATATATATATTATATCACTATTAATTAT
Found at i:83179 original size:10 final size:10
Alignment explanation
Indices: 83160--83192 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
83150 TTCCTTTACC
83160 ATTT-TTTTT
1 ATTTATTTTT
83169 ATTTATTTTT
1 ATTTATTTTT
*
83179 ATTTATTTCT
1 ATTTATTTTT
83189 ATTT
1 ATTT
83193 TACTAACCTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
9 4 0.18
10 18 0.82
ACGTcount: A:0.18, C:0.03, G:0.00, T:0.79
Consensus pattern (10 bp):
ATTTATTTTT
Found at i:93649 original size:105 final size:105
Alignment explanation
Indices: 93467--94241 Score: 1424
Period size: 105 Copynumber: 7.4 Consensus size: 105
93457 CAGGTTTTAC
*
93467 CAGAGTCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACACAAGTTCAACTTCACG
1 CAGAGTCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* *
93532 AAGAAGGGACCGCAGGTTGTCAACAAACATTTCTCAAATT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
*
93572 CAGAGTCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACG
1 CAGAGTCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
93637 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
*
93677 CAGAGTCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACG
1 CAGAGTCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* *
93742 ATGAAGGGACCGTTGGTTGTCAACAAACATTTCTCAAATT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
*
93782 CAGAGTCAATTTTAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGTCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
93847 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
93887 CAGAGTCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGTCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
93952 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
* *
93992 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACG
1 CAGAGTCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
94057 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
*
94097 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGTCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
94162 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
*
94202 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTC
1 CAGAGTCAATTTCAACTTCACAACGAAGGATATTGGACTC
94242 GGAACAATAC
Statistics
Matches: 655, Mismatches: 15, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
105 655 1.00
ACGTcount: A:0.34, C:0.24, G:0.18, T:0.23
Consensus pattern (105 bp):
CAGAGTCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
Found at i:94529 original size:2 final size:2
Alignment explanation
Indices: 94524--94566 Score: 61
Period size: 2 Copynumber: 22.0 Consensus size: 2
94514 ACACACTATT
**
94524 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA CG TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
94565 TA
1 TA
94567 AATTATTTTC
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (2 bp):
TA
Found at i:95795 original size:23 final size:23
Alignment explanation
Indices: 95725--95795 Score: 58
Period size: 21 Copynumber: 3.1 Consensus size: 23
95715 TGTTACGTAA
* * *
95725 TTTATTTATTTATTAATATTATGT
1 TTTATATATTT-TTACTATTATAT
*
95749 ATATATATATTTTT-C-ATT-TAAT
1 -TTTATATATTTTTACTATTAT-AT
95771 TTTATATATTTTTACTATTATAT
1 TTTATATATTTTTACTATTATAT
95794 TT
1 TT
95796 ATTCTCTATT
Statistics
Matches: 37, Mismatches: 5, Indels: 10
0.71 0.10 0.19
Matches are distributed among these distances:
21 13 0.35
22 5 0.14
23 7 0.19
24 3 0.08
25 9 0.24
ACGTcount: A:0.31, C:0.03, G:0.01, T:0.65
Consensus pattern (23 bp):
TTTATATATTTTTACTATTATAT
Found at i:95877 original size:28 final size:29
Alignment explanation
Indices: 95826--95882 Score: 73
Period size: 28 Copynumber: 2.0 Consensus size: 29
95816 TTCGTCGTTG
* *
95826 TATATATATATTTTATTACTATT-ATTAT
1 TATATATATATTATATCACTATTAATTAT
95854 TATATATATATTATACTCAC-ATTAATTAT
1 TATATATATATTATA-TCACTATTAATTAT
95883 ATCTATCTAC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 17 0.68
29 8 0.32
ACGTcount: A:0.39, C:0.07, G:0.00, T:0.54
Consensus pattern (29 bp):
TATATATATATTATATCACTATTAATTAT
Found at i:97527 original size:24 final size:24
Alignment explanation
Indices: 97495--97556 Score: 79
Period size: 24 Copynumber: 2.6 Consensus size: 24
97485 GTGACATATG
*
97495 TTCTCTTTGTTCTTGCGGCACACA
1 TTCTCTTTGTTCTTGCGACACACA
* *
97519 TTCTCTTTGTTCTTGTGACACTCA
1 TTCTCTTTGTTCTTGCGACACACA
* *
97543 TTTTCTTTGCTCTT
1 TTCTCTTTGTTCTT
97557 ATGATATGAT
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.10, C:0.26, G:0.13, T:0.52
Consensus pattern (24 bp):
TTCTCTTTGTTCTTGCGACACACA
Found at i:115030 original size:17 final size:19
Alignment explanation
Indices: 115008--115045 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
114998 TATCGACAAC
115008 ACCATG-CA-AGTATCGAT
1 ACCATGTCACAGTATCGAT
115025 ACCATGTCATCAGTATCGAT
1 ACCATGTCA-CAGTATCGAT
115045 A
1 A
115046 TCATATGAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 6 0.33
18 2 0.11
20 10 0.56
ACGTcount: A:0.34, C:0.24, G:0.16, T:0.26
Consensus pattern (19 bp):
ACCATGTCACAGTATCGAT
Found at i:119448 original size:21 final size:20
Alignment explanation
Indices: 119395--119448 Score: 58
Period size: 18 Copynumber: 2.7 Consensus size: 20
119385 ATTCTTCTAC
*
119395 TTTATTTATTTTC-TCATTA
1 TTTATTTATTTTCAACATTA
*
119414 -TTATTTTTTATTCAACATTTA
1 TTTATTTATT-TTCAACA-TTA
119435 TTTATTTATTTTCA
1 TTTATTTATTTTCA
119449 TTAATTTTAA
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
18 8 0.29
19 3 0.11
20 2 0.07
21 7 0.25
22 8 0.29
ACGTcount: A:0.24, C:0.09, G:0.00, T:0.67
Consensus pattern (20 bp):
TTTATTTATTTTCAACATTA
Found at i:119565 original size:4 final size:4
Alignment explanation
Indices: 119546--119582 Score: 56
Period size: 4 Copynumber: 8.8 Consensus size: 4
119536 ATCCTACTTC
119546 TTTA TTTTA CTTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA -TTTA -TTTA TTTA TTTA TTTA TTTA TTTA TTT
119583 GAGAATTATC
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
4 23 0.74
5 8 0.26
ACGTcount: A:0.22, C:0.03, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTA
Found at i:130978 original size:60 final size:60
Alignment explanation
Indices: 130862--130978 Score: 153
Period size: 60 Copynumber: 1.9 Consensus size: 60
130852 CATTTGACAT
* * * * * * *
130862 GATGCCTTCAAGTTCCAAGGGGAGGCATTCAATTGCGAGCTTCTTCGACCTCAATGTCGA
1 GATGCCTTCAAGTTCAAAGGGAAGGCATTCAACTACCAGCTTCTTCCACCTAAATGTCGA
* *
130922 GATGCCTTCAAGTTCAAAGGGAAGGCATTCAACTACCAGCTTGTTCCACTTAAATGT
1 GATGCCTTCAAGTTCAAAGGGAAGGCATTCAACTACCAGCTTCTTCCACCTAAATGT
130979 TGGCATCATG
Statistics
Matches: 48, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
60 48 1.00
ACGTcount: A:0.26, C:0.24, G:0.22, T:0.27
Consensus pattern (60 bp):
GATGCCTTCAAGTTCAAAGGGAAGGCATTCAACTACCAGCTTCTTCCACCTAAATGTCGA
Found at i:133354 original size:19 final size:19
Alignment explanation
Indices: 133316--133354 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
133306 ACAAACAAAA
* *
133316 TAAATAAAAAGTATATAAT
1 TAAATAAAAAATATACAAT
*
133335 TAAATAAAAAATTTACAAT
1 TAAATAAAAAATATACAAT
133354 T
1 T
133355 GTTGGTAAAC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.62, C:0.03, G:0.03, T:0.33
Consensus pattern (19 bp):
TAAATAAAAAATATACAAT
Found at i:133825 original size:21 final size:20
Alignment explanation
Indices: 133783--133834 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 20
133773 CCTACAGCGA
133783 TGGCATCTGAACCAGCTACGG
1 TGGCATCTG-ACCAGCTACGG
* *
133804 TGGCATCTGACCTGGCTGCGG
1 TGGCATCTGACC-AGCTACGG
*
133825 TGACATCTGA
1 TGGCATCTGA
133835 TATGGAAGTG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
20 3 0.11
21 24 0.89
ACGTcount: A:0.19, C:0.27, G:0.31, T:0.23
Consensus pattern (20 bp):
TGGCATCTGACCAGCTACGG
Found at i:133886 original size:21 final size:21
Alignment explanation
Indices: 133862--133907 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
133852 TTAACTCAGC
*
133862 TGCGGTGCCATTTGATAA-GGT
1 TGCGGTGCCATCTGA-AACGGT
133883 TGCGGTGCCATCTGAAACGGT
1 TGCGGTGCCATCTGAAACGGT
133904 TGCG
1 TGCG
133908 AAATGTACAC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 2 0.09
21 21 0.91
ACGTcount: A:0.17, C:0.20, G:0.35, T:0.28
Consensus pattern (21 bp):
TGCGGTGCCATCTGAAACGGT
Found at i:146265 original size:37 final size:36
Alignment explanation
Indices: 146190--146265 Score: 100
Period size: 36 Copynumber: 2.1 Consensus size: 36
146180 TTTTATATTT
*
146190 TTTAATTTTGTAAAAAAATTATATAAATATTATGAA
1 TTTAATTTTGTAAAAAAATTATATAAATATTATCAA
* *
146226 TTTAATTTTTTAAAGAAAA-TATATAAATATTTTACAA
1 TTTAATTTTGTAAA-AAAATTATATAAATATTAT-CAA
146263 TTT
1 TTT
146266 GTAATATTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
36 26 0.74
37 9 0.26
ACGTcount: A:0.47, C:0.01, G:0.04, T:0.47
Consensus pattern (36 bp):
TTTAATTTTGTAAAAAAATTATATAAATATTATCAA
Found at i:146428 original size:18 final size:19
Alignment explanation
Indices: 146404--146448 Score: 56
Period size: 20 Copynumber: 2.4 Consensus size: 19
146394 CCCAGTAATC
146404 ATATTCC-CTGGTAATATT
1 ATATTCCACTGGTAATATT
* *
146422 TTATTCCCACTGGTAATCTT
1 ATATT-CCACTGGTAATATT
146442 ATATTCC
1 ATATTCC
146449 GTGAACCAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
18 4 0.18
19 4 0.18
20 14 0.64
ACGTcount: A:0.24, C:0.22, G:0.09, T:0.44
Consensus pattern (19 bp):
ATATTCCACTGGTAATATT
Found at i:146436 original size:20 final size:20
Alignment explanation
Indices: 146411--146448 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
146401 ATCATATTCC
*
146411 CTGGTAATATTTTATTCCCA
1 CTGGTAATATTATATTCCCA
*
146431 CTGGTAATCTTATATTCC
1 CTGGTAATATTATATTCC
146449 GTGAACCAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.24, C:0.21, G:0.11, T:0.45
Consensus pattern (20 bp):
CTGGTAATATTATATTCCCA
Found at i:146584 original size:2 final size:2
Alignment explanation
Indices: 146577--146605 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
146567 TTTGTCCTCC
146577 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
146606 AACATTGAGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:148954 original size:13 final size:13
Alignment explanation
Indices: 148938--148971 Score: 54
Period size: 12 Copynumber: 2.8 Consensus size: 13
148928 AAATTAAAGT
148938 ATTAAAAAATATA
1 ATTAAAAAATATA
148951 ATT-AAAAA-ATA
1 ATTAAAAAATATA
148962 ATTAAAAAAT
1 ATTAAAAAAT
148972 TAAAAATTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
11 6 0.32
12 10 0.53
13 3 0.16
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (13 bp):
ATTAAAAAATATA
Found at i:148962 original size:11 final size:11
Alignment explanation
Indices: 148942--148971 Score: 51
Period size: 11 Copynumber: 2.6 Consensus size: 11
148932 TAAAGTATTA
148942 AAAAATATAATT
1 AAAAA-ATAATT
148954 AAAAAATAATT
1 AAAAAATAATT
148965 AAAAAAT
1 AAAAAAT
148972 TAAAAATTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 13 0.72
12 5 0.28
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (11 bp):
AAAAAATAATT
Found at i:148987 original size:24 final size:25
Alignment explanation
Indices: 148927--148987 Score: 69
Period size: 24 Copynumber: 2.6 Consensus size: 25
148917 TTAAAAGACT
148927 AAAATTAAAGT-ATTAAAAAATATA
1 AAAATTAAAGTAATTAAAAAATATA
148951 ATTAAA--AAA-TAATTAAAAAAT-TA
1 A--AAATTAAAGTAATTAAAAAATATA
148974 AAAATTAAAGTAAT
1 AAAATTAAAGTAAT
148988 GAAATTAAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 12
0.72 0.00 0.28
Matches are distributed among these distances:
21 3 0.10
23 7 0.23
24 18 0.58
26 3 0.10
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.30
Consensus pattern (25 bp):
AAAATTAAAGTAATTAAAAAATATA
Found at i:148994 original size:14 final size:14
Alignment explanation
Indices: 148974--149019 Score: 58
Period size: 14 Copynumber: 3.3 Consensus size: 14
148964 TAAAAAATTA
148974 AAAATTAAAGTAA-T
1 AAAATTAAA-TAACT
*
148988 GAAATTAAATAACT
1 AAAATTAAATAACT
*
149002 AAAATTAAATAAAT
1 AAAATTAAATAACT
149016 AAAA
1 AAAA
149020 AGTAAATGGC
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
13 3 0.11
14 25 0.89
ACGTcount: A:0.67, C:0.02, G:0.04, T:0.26
Consensus pattern (14 bp):
AAAATTAAATAACT
Found at i:149073 original size:33 final size:33
Alignment explanation
Indices: 149036--149099 Score: 112
Period size: 33 Copynumber: 1.9 Consensus size: 33
149026 TGGCATAAAT
149036 TTAAAATATAAAGTAAA-AGACTAAAATAAAAGA
1 TTAAAATATAAAGTAAAGA-ACTAAAATAAAAGA
149069 TTAAAATATAAAGTAAAGAACTAAAATAAAA
1 TTAAAATATAAAGTAAAGAACTAAAATAAAA
149100 AAATATCATA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
33 29 0.97
34 1 0.03
ACGTcount: A:0.67, C:0.03, G:0.08, T:0.22
Consensus pattern (33 bp):
TTAAAATATAAAGTAAAGAACTAAAATAAAAGA
Found at i:149709 original size:13 final size:12
Alignment explanation
Indices: 149682--149730 Score: 55
Period size: 12 Copynumber: 4.1 Consensus size: 12
149672 TTCGAAAAAC
*
149682 AAAATTAAATGA
1 AAAATAAAATGA
149694 AAAATAAAACTGA
1 AAAATAAAA-TGA
*
149707 AAAATAAACT-A
1 AAAATAAAATGA
*
149718 AAAACAAAATGA
1 AAAATAAAATGA
149730 A
1 A
149731 GAGAACCTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
11 9 0.29
12 11 0.35
13 11 0.35
ACGTcount: A:0.71, C:0.06, G:0.06, T:0.16
Consensus pattern (12 bp):
AAAATAAAATGA
Found at i:150823 original size:42 final size:42
Alignment explanation
Indices: 150776--150860 Score: 107
Period size: 42 Copynumber: 2.0 Consensus size: 42
150766 CTCATTTGAA
* * ** * *
150776 AACATCATGCATTGAAGGTCTTATGGATGACTCGAAGGCTTT
1 AACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGATTT
*
150818 AACATCTTGCACTGAAGGGCTTACAGATGACCCGAAGGATTT
1 AACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGATTT
150860 A
1 A
150861 TAGATTAAAA
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
42 36 1.00
ACGTcount: A:0.31, C:0.19, G:0.24, T:0.27
Consensus pattern (42 bp):
AACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGATTT
Found at i:150903 original size:132 final size:132
Alignment explanation
Indices: 150755--150992 Score: 404
Period size: 132 Copynumber: 1.8 Consensus size: 132
150745 GAAAGGCTTG
* * *
150755 GTTTCTAAAATCTCATTTGAAAACATCATGCATTGAAGGTCTTATGGATGACTCGAAGGCTTTAA
1 GTTTCTAAAATCTCATTTGAAAACATCATGCACTGAAGGTCTTATGGATGACCCGAACGCTTTAA
150820 CATCTTGCACTGAAGGGCTTACAGATGACCCGAAGGATTTATAGATTAAAAAACCCTCTAAGGAT
66 CATCTTGCACTGAAGGGCTTACAGATGACCCGAAGGATTTATAGATTAAAAAACCCTCTAAGGAT
150885 TA
131 TA
*
150887 GTTTCTAAAATCTCATTTGAAAACATCCTGCACTGAAGGTCTTATGGATGACCCGAACGCTTTAA
1 GTTTCTAAAATCTCATTTGAAAACATCATGCACTGAAGGTCTTATGGATGACCCGAACGCTTTAA
* ** *
150952 CATCTTGCACTGAAGGTCTTATGGATGACCCGAAGGCTTTA
66 CATCTTGCACTGAAGGGCTTACAGATGACCCGAAGGATTTA
150993 ACATCTTGCA
Statistics
Matches: 98, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
132 98 1.00
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.30
Consensus pattern (132 bp):
GTTTCTAAAATCTCATTTGAAAACATCATGCACTGAAGGTCTTATGGATGACCCGAACGCTTTAA
CATCTTGCACTGAAGGGCTTACAGATGACCCGAAGGATTTATAGATTAAAAAACCCTCTAAGGAT
TA
Found at i:151238 original size:86 final size:86
Alignment explanation
Indices: 150908--151937 Score: 1376
Period size: 86 Copynumber: 12.0 Consensus size: 86
150898 CTCATTTGAA
* * ** * * * *
150908 AACATCCTGCACTGAAGGTCTTATGGATGACCCGAACG-CTTT-AACATCTTGCACTGAAGGTCT
1 AACATCTTGCACTGGAGGTCTTACAGATGACCCGAAGGATTTTAAACATCCTGCACTGGAGGTCT
*
150971 TATGGATGACCCGAAGGCTTT
66 TATGGATGACCCGAAGGATTT
* * * * * * *
150992 AACATCTTGCACTGAAGGGCTTACAGATGACCAGAAGGA-TTTCAACATCTTGTACTGAAGGTCT
1 AACATCTTGCACTGGAGGTCTTACAGATGACCCGAAGGATTTTAAACATCCTGCACTGGAGGTCT
**
151056 TACAGATGACCCGAAGGATTT
66 TATGGATGACCCGAAGGATTT
* ** *
151077 AAACATCTTGCACTGAAGGTCTTATGGATGACCCGAAGGA-TTT-AACATCTTGCACTGGAGGTC
1 -AACATCTTGCACTGGAGGTCTTACAGATGACCCGAAGGATTTTAAACATCCTGCACTGGAGGTC
** *
151140 TTACAGATGACCCAAAGGATTT
65 TTATGGATGACCCGAAGGATTT
* * * *
151162 AACATCTTGCACTGGAGGTCTTACAGATAACCCGAAGAATTTTAAACATCCTGCACCGGAGGGCT
1 AACATCTTGCACTGGAGGTCTTACAGATGACCCGAAGGATTTTAAACATCCTGCACTGGAGGTCT
**
151227 TACAGATGACCCGAAGGATTT
66 TATGGATGACCCGAAGGATTT
* * * **
151248 CAACATCTTGCACTGAAGGTCTTACAGATGATCCGAAGGA-TTTAAACATCTTGCACTAAAGGTC
1 -AACATCTTGCACTGGAGGTCTTACAGATGACCCGAAGGATTTTAAACATCCTGCACTGGAGGTC
*
151312 TTATGGATGACCTGAAGGATTT
65 TTATGGATGACCCGAAGGATTT
* *
151334 AACATCTTGCATTGGAGGTCTTATAGATGACCCGAAGGATTTTAAACATCCTGCACTGGAGGTCT
1 AACATCTTGCACTGGAGGTCTTACAGATGACCCGAAGGATTTTAAACATCCTGCACTGGAGGTCT
151399 TATGGATGACCC-AGAGGATTT
66 TATGGATGACCCGA-AGGATTT
* * *
151420 AACATCTTGCACTTGAGGTCTTACAGAAGACCCGAAGGATTTTAAACATCCTGCATTGGAGGTCT
1 AACATCTTGCACTGGAGGTCTTACAGATGACCCGAAGGATTTTAAACATCCTGCACTGGAGGTCT
*
151485 TATGGATGACCCGGAGGATTT
66 TATGGATGACCCGAAGGATTT
* * * *
151506 AACATCTTACAGTGGAGGTCTTACAGATGACCCGAAGGATTTTAAACATCCTACACTAGAGGTCT
1 AACATCTTGCACTGGAGGTCTTACAGATGACCCGAAGGATTTTAAACATCCTGCACTGGAGGTCT
*
151571 TTTGGATGACCC-AGAGGATTT
66 TATGGATGACCCGA-AGGATTT
* *
151592 AACATCTTGCACTGGAGGTCTTACAAATGACCCGAAAGATTTTAAACATCCTGCACTGGAGGTCT
1 AACATCTTGCACTGGAGGTCTTACAGATGACCCGAAGGATTTTAAACATCCTGCACTGGAGGTCT
*
151657 TATGGATGACCCGGAGGATTT
66 TATGGATGACCCGAAGGATTT
*
151678 AACATCTTGCACTGGAGGTCTTACAGATGACCCGAAGGATTTTAAATATCCTGCACTGGAGGTCT
1 AACATCTTGCACTGGAGGTCTTACAGATGACCCGAAGGATTTTAAACATCCTGCACTGGAGGTCT
** *
151743 TATGGATGAACATG-ATGATTT
66 TATGGATG-ACCCGAAGGATTT
*
151764 AACATCTTGCACTGGAGGTCTTACAGATGACCCGAAGAATTTTAAACATCCTGCACTGGAGGTCT
1 AACATCTTGCACTGGAGGTCTTACAGATGACCCGAAGGATTTTAAACATCCTGCACTGGAGGTCT
*
151829 TATGGATGACCCGGAGGATTT
66 TATGGATGACCCGAAGGATTT
* * * ** *
151850 AACATCTTCCACTGGAGGTCTTACAGATGACCTGAATGATTTTAAATGTCCTGCTCTGGAGGTCT
1 AACATCTTGCACTGGAGGTCTTACAGATGACCCGAAGGATTTTAAACATCCTGCACTGGAGGTCT
*
151915 TATGGATGATCCGAAGGATTT
66 TATGGATGACCCGAAGGATTT
151936 AA
1 AA
151938 AAATTTGAGA
Statistics
Matches: 844, Mismatches: 89, Indels: 24
0.88 0.09 0.03
Matches are distributed among these distances:
84 69 0.08
85 119 0.14
86 618 0.73
87 38 0.05
ACGTcount: A:0.29, C:0.20, G:0.23, T:0.28
Consensus pattern (86 bp):
AACATCTTGCACTGGAGGTCTTACAGATGACCCGAAGGATTTTAAACATCCTGCACTGGAGGTCT
TATGGATGACCCGAAGGATTT
Found at i:152611 original size:22 final size:22
Alignment explanation
Indices: 152586--152682 Score: 135
Period size: 22 Copynumber: 4.5 Consensus size: 22
152576 AATAAAGCTT
*
152586 TCATTTTTGAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
* *
152608 TCATCTTTGAAGAGAGATTCTA
1 TCATCTTTGAAAAGAGAATCTA
*
152630 TCATCTTTGAAGAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
152652 TCATCTTTG--AAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
*
152672 TTATCTTTGAA
1 TCATCTTTGAA
152683 GAATGTAGAT
Statistics
Matches: 67, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
20 18 0.27
22 49 0.73
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.37
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATCTA
Found at i:152622 original size:20 final size:20
Alignment explanation
Indices: 152597--152684 Score: 131
Period size: 20 Copynumber: 4.2 Consensus size: 20
152587 CATTTTTGAA
152597 AAGAGAATCTATCATCTTTG
1 AAGAGAATCTATCATCTTTG
152617 AAGAGAGATTCTATCATCTTTG
1 AAGAGA-A-TCTATCATCTTTG
152639 AAGAGAGAATCTATCATCTTTG
1 -A-AGAGAATCTATCATCTTTG
*
152661 AAGAGAATCTATTATCTTTG
1 AAGAGAATCTATCATCTTTG
152681 AAGA
1 AAGA
152685 ATGTAGATGT
Statistics
Matches: 63, Mismatches: 1, Indels: 8
0.88 0.01 0.11
Matches are distributed among these distances:
20 28 0.44
21 2 0.03
22 26 0.41
23 2 0.03
24 5 0.08
ACGTcount: A:0.36, C:0.12, G:0.17, T:0.34
Consensus pattern (20 bp):
AAGAGAATCTATCATCTTTG
Found at i:152654 original size:44 final size:42
Alignment explanation
Indices: 152586--152684 Score: 153
Period size: 44 Copynumber: 2.3 Consensus size: 42
152576 AATAAAGCTT
* *
152586 TCATTTTTGAAAAGAGAATCTATCATCTTTGAAGAGAGATTCTA
1 TCATCTTTGAAGAGAGAATCTATCATCTTTGAAGAGA-A-TCTA
152630 TCATCTTTGAAGAGAGAATCTATCATCTTTGAAGAGAATCTA
1 TCATCTTTGAAGAGAGAATCTATCATCTTTGAAGAGAATCTA
*
152672 TTATCTTTGAAGA
1 TCATCTTTGAAGA
152685 ATGTAGATGT
Statistics
Matches: 52, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
42 16 0.31
43 1 0.02
44 35 0.67
ACGTcount: A:0.35, C:0.12, G:0.16, T:0.36
Consensus pattern (42 bp):
TCATCTTTGAAGAGAGAATCTATCATCTTTGAAGAGAATCTA
Found at i:153505 original size:40 final size:40
Alignment explanation
Indices: 153461--153547 Score: 104
Period size: 40 Copynumber: 2.2 Consensus size: 40
153451 GATATGAATA
* * * *
153461 TTCAAAATGCATTCAA-AATTGTTTCTTGTTGATGTGAGCC
1 TTCAAAATGC-TTCAACAATTGCTTCCTGATGATATGAGCC
* *
153501 TTCAAAATGCTTCAACATTTGCTTCCTGATGATATGAGCT
1 TTCAAAATGCTTCAACAATTGCTTCCTGATGATATGAGCC
153541 TTCAAAA
1 TTCAAAA
153548 ATGCCCAAAT
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
39 5 0.12
40 35 0.88
ACGTcount: A:0.30, C:0.17, G:0.15, T:0.38
Consensus pattern (40 bp):
TTCAAAATGCTTCAACAATTGCTTCCTGATGATATGAGCC
Found at i:155244 original size:16 final size:16
Alignment explanation
Indices: 155223--155273 Score: 75
Period size: 16 Copynumber: 3.1 Consensus size: 16
155213 TGATTCAATT
*
155223 TTTTTTTTTTTTTTTC
1 TTTTTTTTCTTTTTTC
*
155239 TTTTTTTTCTTTTCTC
1 TTTTTTTTCTTTTTTC
155255 TTTTTTTTCCTTTTTTC
1 TTTTTTTT-CTTTTTTC
155272 TT
1 TT
155274 ATGATGAATG
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
16 22 0.71
17 9 0.29
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (16 bp):
TTTTTTTTCTTTTTTC
Found at i:155244 original size:17 final size:17
Alignment explanation
Indices: 155222--155273 Score: 70
Period size: 17 Copynumber: 3.1 Consensus size: 17
155212 TTGATTCAAT
*
155222 TTTTTTTTTTTTTTTTC
1 TTTTTTTTTCTTTTTTC
*
155239 -TTTTTTTTCTTTTCTC
1 TTTTTTTTTCTTTTTTC
*
155255 TTTTTTTTCCTTTTTTC
1 TTTTTTTTTCTTTTTTC
155272 TT
1 TT
155274 ATGATGAATG
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
16 14 0.47
17 16 0.53
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (17 bp):
TTTTTTTTTCTTTTTTC
Found at i:159586 original size:29 final size:29
Alignment explanation
Indices: 159532--159600 Score: 70
Period size: 28 Copynumber: 2.4 Consensus size: 29
159522 ATGTAATGCA
159532 AGCAAAAT-AAATCAATATAAACAAATTAG
1 AGCAAAATAAAATCAATATAAACAAA-TAG
** *
159561 AGCAAAATAAAATGTATATACA-AAATAG
1 AGCAAAATAAAATCAATATAAACAAATAG
**
159589 ATAAAAATAAAA
1 AGCAAAATAAAA
159601 GAAAAAAAAT
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
28 13 0.38
29 11 0.32
30 10 0.29
ACGTcount: A:0.65, C:0.07, G:0.07, T:0.20
Consensus pattern (29 bp):
AGCAAAATAAAATCAATATAAACAAATAG
Found at i:159589 original size:28 final size:28
Alignment explanation
Indices: 159547--159600 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 28
159537 AATAAATCAA
* *
159547 TATAAACAAATTAGAGCAAAATAAAATG
1 TATAAACAAAATAGAGAAAAATAAAATG
* *
159575 TATATACAAAATAGATAAAAATAAAA
1 TATAAACAAAATAGAGAAAAATAAAA
159601 GAAAAAAAAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 22 1.00
ACGTcount: A:0.65, C:0.06, G:0.07, T:0.22
Consensus pattern (28 bp):
TATAAACAAAATAGAGAAAAATAAAATG
Found at i:160268 original size:26 final size:26
Alignment explanation
Indices: 160221--160277 Score: 64
Period size: 26 Copynumber: 2.2 Consensus size: 26
160211 TAAGGATATA
160221 AAATAATAAAGAATAAAGAATTGAAAG
1 AAATAATAAAGAATAAAGAATT-AAAG
* *
160248 AAATAA-AAAGAATCATA-AATTAAAT
1 AAATAATAAAGAAT-AAAGAATTAAAG
160273 AAATA
1 AAATA
160278 TGAATTCTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
25 8 0.30
26 11 0.41
27 8 0.30
ACGTcount: A:0.68, C:0.02, G:0.09, T:0.21
Consensus pattern (26 bp):
AAATAATAAAGAATAAAGAATTAAAG
Found at i:161197 original size:22 final size:21
Alignment explanation
Indices: 161172--161250 Score: 52
Period size: 22 Copynumber: 3.6 Consensus size: 21
161162 TGAAATGAAC
*
161172 AAAAAAATAAAACGAAATAGTT
1 AAAAAAATAAAACAAAATA-TT
* * * *
161194 AAAAGACTAAAATTAAAGTATT
1 AAAAAAATAAAA-CAAAATATT
*
161216 AAAAAATATAAAGCAAAAATAATT
1 AAAAAA-ATAAAAC-AAAAT-ATT
161240 -AAAAAATAAAA
1 AAAAAAATAAAA
161251 ATTAAAGTAA
Statistics
Matches: 42, Mismatches: 11, Indels: 8
0.69 0.18 0.13
Matches are distributed among these distances:
22 22 0.52
23 17 0.40
24 3 0.07
ACGTcount: A:0.70, C:0.04, G:0.06, T:0.20
Consensus pattern (21 bp):
AAAAAAATAAAACAAAATATT
Found at i:161253 original size:14 final size:14
Alignment explanation
Indices: 161236--161293 Score: 66
Period size: 14 Copynumber: 4.1 Consensus size: 14
161226 AAGCAAAAAT
161236 AATTAAA-AAATAAA
1 AATTAAATAAAT-AA
*
161250 AATTAAAGT-AATGA
1 AATTAAA-TAAATAA
*
161264 AATTAAATAACTAA
1 AATTAAATAAATAA
161278 AATTAAATAAATAA
1 AATTAAATAAATAA
161292 AA
1 AA
161294 AGTAAACGGC
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
13 1 0.03
14 33 0.89
15 3 0.08
ACGTcount: A:0.69, C:0.02, G:0.03, T:0.26
Consensus pattern (14 bp):
AATTAAATAAATAA
Found at i:161261 original size:23 final size:24
Alignment explanation
Indices: 161201--161294 Score: 77
Period size: 23 Copynumber: 3.9 Consensus size: 24
161191 GTTAAAAGAC
161201 TAAAATTAAAGT-ATTAAAAAATA
1 TAAAATTAAAGTAATTAAAAAATA
*** *
161224 TAAAGCAAAAATAATTAAAAAATA
1 TAAAATTAAAGTAATTAAAAAATA
*
161248 -AAAATTAAAGTAATGAAATTAAATAA
1 TAAAATTAAAGTAATTAAA--AAAT-A
*
161274 CTAAAATTAAA-TAAATAAAAA
1 -TAAAATTAAAGTAATTAAAAA
161295 GTAAACGGCA
Statistics
Matches: 54, Mismatches: 11, Indels: 10
0.72 0.15 0.13
Matches are distributed among these distances:
23 21 0.39
24 11 0.20
25 6 0.11
26 1 0.02
27 6 0.11
28 9 0.17
ACGTcount: A:0.68, C:0.02, G:0.04, T:0.26
Consensus pattern (24 bp):
TAAAATTAAAGTAATTAAAAAATA
Found at i:161351 original size:33 final size:32
Alignment explanation
Indices: 161306--161373 Score: 102
Period size: 33 Copynumber: 2.1 Consensus size: 32
161296 TAAACGGCAT
161306 AAATTTAAAATATAAAGTAAA-AGACTAAAATA
1 AAATTTAAAATATAAAGTAAAGA-ACTAAAATA
*
161338 AAATATTATAATATAAAGTAAAGAACTAAAATA
1 AAAT-TTAAAATATAAAGTAAAGAACTAAAATA
161371 AAA
1 AAA
161374 GATATCAGAA
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
32 4 0.12
33 28 0.85
34 1 0.03
ACGTcount: A:0.66, C:0.03, G:0.06, T:0.25
Consensus pattern (32 bp):
AAATTTAAAATATAAAGTAAAGAACTAAAATA
Found at i:161985 original size:24 final size:23
Alignment explanation
Indices: 161953--162001 Score: 62
Period size: 24 Copynumber: 2.1 Consensus size: 23
161943 TTAGAAAAAC
* * *
161953 AAAATTAAATGAAAAATAAAACTG
1 AAAAATAAACGAAAAACAAAA-TG
161977 AAAAATAAACGAAAAACAAAATG
1 AAAAATAAACGAAAAACAAAATG
162000 AA
1 AA
162002 GAGAACATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
23 4 0.18
24 18 0.82
ACGTcount: A:0.71, C:0.06, G:0.08, T:0.14
Consensus pattern (23 bp):
AAAAATAAACGAAAAACAAAATG
Found at i:168677 original size:16 final size:16
Alignment explanation
Indices: 168653--168698 Score: 83
Period size: 16 Copynumber: 2.9 Consensus size: 16
168643 TCCTAAATTT
*
168653 TTTTTGAGTTCAAGCC
1 TTTTCGAGTTCAAGCC
168669 TTTTCGAGTTCAAGCC
1 TTTTCGAGTTCAAGCC
168685 TTTTCGAGTTCAAG
1 TTTTCGAGTTCAAG
168699 TTTCAATATT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
16 29 1.00
ACGTcount: A:0.20, C:0.20, G:0.20, T:0.41
Consensus pattern (16 bp):
TTTTCGAGTTCAAGCC
Found at i:171215 original size:30 final size:30
Alignment explanation
Indices: 171181--171250 Score: 70
Period size: 30 Copynumber: 2.3 Consensus size: 30
171171 TGGAGTGATT
171181 TGATTGTAATAATTAATAAATTA-AGTGACC
1 TGATTGTAATAATTAATAAA-TAGAGTGACC
* ** ** *
171211 TGATTATTGTAATTGTTAAATAGAGTGATC
1 TGATTGTAATAATTAATAAATAGAGTGACC
171241 TGATTGTAAT
1 TGATTGTAAT
171251 TAAATAATTA
Statistics
Matches: 30, Mismatches: 9, Indels: 2
0.73 0.22 0.05
Matches are distributed among these distances:
29 2 0.07
30 28 0.93
ACGTcount: A:0.37, C:0.04, G:0.17, T:0.41
Consensus pattern (30 bp):
TGATTGTAATAATTAATAAATAGAGTGACC
Found at i:174543 original size:11 final size:10
Alignment explanation
Indices: 174498--174548 Score: 57
Period size: 11 Copynumber: 4.7 Consensus size: 10
174488 TTGATATCAC
174498 GAGAGGGAGG
1 GAGAGGGAGG
174508 GAGGGAGGGAGG
1 GA--GAGGGAGG
*
174520 GGGAGGGATGG
1 GAGAGGGA-GG
174531 GAGAGGGTAGG
1 GAGAGGG-AGG
174542 GAGAGGG
1 GAGAGGG
174549 GAGGACGCAT
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
10 8 0.23
11 17 0.49
12 10 0.29
ACGTcount: A:0.25, C:0.00, G:0.71, T:0.04
Consensus pattern (10 bp):
GAGAGGGAGG
Found at i:175942 original size:21 final size:21
Alignment explanation
Indices: 175916--175960 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
175906 GATTTCTGGG
* *
175916 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
175937 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
175958 CAA
1 CAA
175961 ACGACAGAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:176470 original size:2 final size:2
Alignment explanation
Indices: 176463--176491 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
176453 CATGAGTTAG
176463 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
176492 GGAATTGTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:177025 original size:31 final size:31
Alignment explanation
Indices: 176987--177064 Score: 95
Period size: 31 Copynumber: 2.5 Consensus size: 31
176977 AGAGTCGAGG
*
176987 GTTTACCTATG-TCTTTCGAGACATATGGACA
1 GTTTACCTAGGTTC-TTCGAGACATATGGACA
* *
177018 GTTTACCTAGGTTCTTCGGGACCTATGGACA
1 GTTTACCTAGGTTCTTCGAGACATATGGACA
* *
177049 GTTTACCGAGGATCTT
1 GTTTACCTAGGTTCTT
177065 TATGACCTCT
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
31 39 0.95
32 2 0.05
ACGTcount: A:0.22, C:0.21, G:0.23, T:0.35
Consensus pattern (31 bp):
GTTTACCTAGGTTCTTCGAGACATATGGACA
Found at i:177139 original size:29 final size:30
Alignment explanation
Indices: 177037--177136 Score: 148
Period size: 30 Copynumber: 3.3 Consensus size: 30
177027 GGTTCTTCGG
*
177037 GACCTATGGACAGTTTACCGAGGATCTTTAT
1 GACCTCTGGACAG-TTACCGAGGATCTTTAT
177068 GACCTCTGGACAGTTACCGAGGATCTTTAT
1 GACCTCTGGACAGTTACCGAGGATCTTTAT
* * *
177098 GACCTCTGGATAGTTACCG-GGGTCTTTGT
1 GACCTCTGGACAGTTACCGAGGATCTTTAT
177127 GACCTCTGGA
1 GACCTCTGGA
177137 TAGGTCCTTC
Statistics
Matches: 65, Mismatches: 4, Indels: 2
0.92 0.06 0.03
Matches are distributed among these distances:
29 18 0.28
30 35 0.54
31 12 0.18
ACGTcount: A:0.21, C:0.22, G:0.26, T:0.31
Consensus pattern (30 bp):
GACCTCTGGACAGTTACCGAGGATCTTTAT
Found at i:180468 original size:21 final size:21
Alignment explanation
Indices: 180442--180486 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
180432 GATTTCTGGG
* *
180442 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
180463 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
180484 CAA
1 CAA
180487 ACGACAGAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:181545 original size:31 final size:31
Alignment explanation
Indices: 181507--181585 Score: 97
Period size: 31 Copynumber: 2.5 Consensus size: 31
181497 AGAGTCGAGG
181507 GTTTACCTATGTCTTTCGAGACATATGGACA
1 GTTTACCTATGTCTTTCGAGACATATGGACA
* * *
181538 GTTTACCTAGGT-TCTTCGGGACCTATGGACA
1 GTTTACCTATGTCT-TTCGAGACATATGGACA
*
181569 GTTTACCGATGATCTTT
1 GTTTACCTATG-TCTTT
181586 ATGACCTCTG
Statistics
Matches: 40, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
30 1 0.03
31 35 0.88
32 3 0.08
33 1 0.03
ACGTcount: A:0.22, C:0.20, G:0.22, T:0.37
Consensus pattern (31 bp):
GTTTACCTATGTCTTTCGAGACATATGGACA
Found at i:181592 original size:31 final size:30
Alignment explanation
Indices: 181530--181656 Score: 112
Period size: 31 Copynumber: 4.2 Consensus size: 30
181520 TTTCGAGACA
* * ***
181530 TATGGACAGTTTACCTAGGTTCTTCGGGACC
1 TATGGACAG-TTACCGAGGATCTTTATGACC
*
181561 TATGGACAGTTTACCGATGATCTTTATGACC
1 TATGGACAG-TTACCGAGGATCTTTATGACC
* *
181592 TCTGGACAGTTACTGAGGATCTTTATGACC
1 TATGGACAGTTACCGAGGATCTTTATGACC
* * * *
181622 TCTGGATAGTTACCG-GGGTCTTTGTGACC
1 TATGGACAGTTACCGAGGATCTTTATGACC
*
181651 TCTGGA
1 TATGGA
181657 TAGGTCCTTC
Statistics
Matches: 83, Mismatches: 13, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
29 18 0.22
30 32 0.39
31 33 0.40
ACGTcount: A:0.20, C:0.20, G:0.25, T:0.34
Consensus pattern (30 bp):
TATGGACAGTTACCGAGGATCTTTATGACC
Found at i:181615 original size:30 final size:30
Alignment explanation
Indices: 181557--181656 Score: 130
Period size: 30 Copynumber: 3.3 Consensus size: 30
181547 GGTTCTTCGG
* *
181557 GACCTATGGACAGTTTACCGATGATCTTTAT
1 GACCTCTGGACAG-TTACCGAGGATCTTTAT
*
181588 GACCTCTGGACAGTTACTGAGGATCTTTAT
1 GACCTCTGGACAGTTACCGAGGATCTTTAT
* * *
181618 GACCTCTGGATAGTTACCG-GGGTCTTTGT
1 GACCTCTGGACAGTTACCGAGGATCTTTAT
181647 GACCTCTGGA
1 GACCTCTGGA
181657 TAGGTCCTTC
Statistics
Matches: 62, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
29 18 0.29
30 32 0.52
31 12 0.19
ACGTcount: A:0.21, C:0.21, G:0.25, T:0.33
Consensus pattern (30 bp):
GACCTCTGGACAGTTACCGAGGATCTTTAT
Found at i:190586 original size:12 final size:12
Alignment explanation
Indices: 190569--190597 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
190559 TATCATCTTT
190569 TCCCTTCTTATA
1 TCCCTTCTTATA
190581 TCCCTTCTTATA
1 TCCCTTCTTATA
190593 TCCCT
1 TCCCT
190598 GCCTTTCGGC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.14, C:0.38, G:0.00, T:0.48
Consensus pattern (12 bp):
TCCCTTCTTATA
Found at i:191352 original size:20 final size:20
Alignment explanation
Indices: 191329--191368 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
191319 TTCATTGAAA
*
191329 ACATGTTCAGAAAATGAATT
1 ACATGTTCAGAAAATCAATT
* *
191349 ACATTTTCTGAAAATCAATT
1 ACATGTTCAGAAAATCAATT
191369 TTAAAAAACT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.42, C:0.12, G:0.10, T:0.35
Consensus pattern (20 bp):
ACATGTTCAGAAAATCAATT
Found at i:192231 original size:29 final size:29
Alignment explanation
Indices: 192189--192260 Score: 135
Period size: 29 Copynumber: 2.5 Consensus size: 29
192179 TTAGGATTAA
192189 TCATCTTGTGTTCATTACCTCCTTCATAC
1 TCATCTTGTGTTCATTACCTCCTTCATAC
*
192218 TCATCTTGTGTTCATTGCCTCCTTCATAC
1 TCATCTTGTGTTCATTACCTCCTTCATAC
192247 TCATCTTGTGTTCA
1 TCATCTTGTGTTCA
192261 GTCGTGAAAC
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
29 42 1.00
ACGTcount: A:0.15, C:0.29, G:0.10, T:0.46
Consensus pattern (29 bp):
TCATCTTGTGTTCATTACCTCCTTCATAC
Found at i:196831 original size:2 final size:2
Alignment explanation
Indices: 196820--196879 Score: 111
Period size: 2 Copynumber: 30.0 Consensus size: 2
196810 AAAGGAAAAA
*
196820 AT AT AA AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
196862 AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT
196880 CAAAGTATTA
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 56 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:197105 original size:26 final size:24
Alignment explanation
Indices: 197067--197116 Score: 64
Period size: 26 Copynumber: 2.0 Consensus size: 24
197057 ATTTTTTTTT
* *
197067 AAAAAAAATATAATAATAATGAATA
1 AAAAAAAAAATAATAAAAAT-AATA
197092 AAAAAACAAAATAATAAAAATAATA
1 AAAAAA-AAAATAATAAAAATAATA
197117 TAAATATATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 10 0.45
26 12 0.55
ACGTcount: A:0.76, C:0.02, G:0.02, T:0.20
Consensus pattern (24 bp):
AAAAAAAAAATAATAAAAATAATA
Found at i:197352 original size:47 final size:47
Alignment explanation
Indices: 197258--197349 Score: 116
Period size: 47 Copynumber: 2.0 Consensus size: 47
197248 GATAATTACA
* * * * *
197258 ATATATATATAGTAATATTAAACTTATAAGTAAAATATTAAAGAAAT
1 ATATATATATAATAATAATAAACATATAAGTAAAAAAATAAAGAAAT
197305 ATATATATATAATAATAATAAA-ATAT-AGTAAAAAAATAAATGAAA
1 ATATATATATAATAATAATAAACATATAAGTAAAAAAATAAA-GAAA
197350 ATAATTTAAT
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
45 12 0.31
46 7 0.18
47 20 0.51
ACGTcount: A:0.61, C:0.01, G:0.05, T:0.33
Consensus pattern (47 bp):
ATATATATATAATAATAATAAACATATAAGTAAAAAAATAAAGAAAT
Found at i:197409 original size:17 final size:18
Alignment explanation
Indices: 197376--197411 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
197366 ATATATATAT
*
197376 ATAATAATAACATGAATA
1 ATAAAAATAACATGAATA
197394 ATAAAAATAA-ATGAATA
1 ATAAAAATAACATGAATA
197411 A
1 A
197412 AATATCCATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.67, C:0.03, G:0.06, T:0.25
Consensus pattern (18 bp):
ATAAAAATAACATGAATA
Found at i:197416 original size:55 final size:56
Alignment explanation
Indices: 197303--197416 Score: 137
Period size: 60 Copynumber: 2.0 Consensus size: 56
197293 TATTAAAGAA
197303 ATATATATATATAATAATAATAAAATATAGTAAAAAAATAAATGAAAATAATTTAATAT
1 ATATATATATATAATAATAATAAAATATAGTAAAAAAATAAATG-AAATAA--TAATAT
*
197362 ATATATATATATATATAATAATAACATGA-A-TAATAAAAATAAATG-AATAA-AATAT
1 ATATATATATATA-ATAATAATAAAAT-ATAGTAA-AAAAATAAATGAAATAATAATAT
197417 CCATATAATA
Statistics
Matches: 51, Mismatches: 1, Indels: 10
0.82 0.02 0.16
Matches are distributed among these distances:
55 5 0.10
58 5 0.10
59 16 0.31
60 24 0.47
61 1 0.02
ACGTcount: A:0.62, C:0.01, G:0.04, T:0.33
Consensus pattern (56 bp):
ATATATATATATAATAATAATAAAATATAGTAAAAAAATAAATGAAATAATAATAT
Found at i:197423 original size:55 final size:58
Alignment explanation
Indices: 197303--197431 Score: 135
Period size: 60 Copynumber: 2.2 Consensus size: 58
197293 TATTAAAGAA
*
197303 ATATATATATATAATAATAATAAAATATAGTAAAAAAATAAATGAAAATAATTTAATATAT
1 ATATATATATATAATAATAATAAAATATAGTAAAAAAATAAATG-AAATAA--TAATATAC
* *
197364 ATATATATATAT-ATAATAATAACATGA-A-TAATAAAAATAAATG-AATAA-AATATCC
1 ATATATATATATAATAATAATAAAAT-ATAGTAA-AAAAATAAATGAAATAATAATATAC
*
197419 ATATA-ATAAATAA
1 ATATATATATATAA
197432 AGGGACTAAT
Statistics
Matches: 61, Mismatches: 4, Indels: 12
0.79 0.05 0.16
Matches are distributed among these distances:
54 5 0.08
55 11 0.18
58 5 0.08
59 3 0.05
60 24 0.39
61 13 0.21
ACGTcount: A:0.62, C:0.02, G:0.03, T:0.33
Consensus pattern (58 bp):
ATATATATATATAATAATAATAAAATATAGTAAAAAAATAAATGAAATAATAATATAC
Found at i:197824 original size:37 final size:37
Alignment explanation
Indices: 197774--197877 Score: 136
Period size: 37 Copynumber: 2.8 Consensus size: 37
197764 GTGCTTGTGG
* * * * *
197774 ATCCTATCTTTAGGAATTTAAATCTTAGTAGAACTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAAAACTCT
* * *
197811 ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAATTTT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAAAACTCT
197848 ATCCTATTTTTAGGAGTTTGAATCCTAGTA
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTA
197878 TGACGAAAAT
Statistics
Matches: 58, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
37 58 1.00
ACGTcount: A:0.30, C:0.14, G:0.13, T:0.42
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTGAATCCTAGTAAAACTCT
Found at i:198719 original size:105 final size:105
Alignment explanation
Indices: 198415--199044 Score: 896
Period size: 105 Copynumber: 6.0 Consensus size: 105
198405 GCATTGTTCC
* * * ** * *
198415 GAGTCCAATATCCTCCGTCGTGAAGTTGAAATTGGTTCTG-GAACCGGGAAATTATTTGTTGACA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAG-ATTGGGAAGTT-GTTGTTGACA
* * * * *
198479 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTC
64 AGCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
198521 GAGTCCAATATCCTTCGCTGTGAAATTGAAATTGACTCTGA-A-T--GAAATT-TTGTTGACAAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAG
* *
198581 CAGCGCTCCCTTCGTCGTGGAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
198621 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAGGTTGTTGTTGACAAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAG
198686 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
198726 AAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGACTGGGAAGTTGTTGTTGACAAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAG
*
198791 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTA
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
198831 AAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAG
198896 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
198936 GAGTCCAATAT-CTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTG-TTGTTGACAA
* * * * *
199000 CCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTC
65 GCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
199041 GAGT
1 GAGT
199045 GTCACGATAT
Statistics
Matches: 482, Mismatches: 35, Indels: 15
0.91 0.07 0.03
Matches are distributed among these distances:
100 82 0.17
101 1 0.00
102 7 0.01
104 46 0.10
105 312 0.65
106 34 0.07
ACGTcount: A:0.22, C:0.18, G:0.27, T:0.33
Consensus pattern (105 bp):
GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAG
CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:199288 original size:36 final size:36
Alignment explanation
Indices: 199241--199316 Score: 116
Period size: 36 Copynumber: 2.1 Consensus size: 36
199231 TGTTTGGAGA
* * *
199241 GAAACTGTCTCAAGGGAGACAAAATTCGTTTCAAGG
1 GAAACTATCTCAAGCGAGACAAAATTCATTTCAAGG
*
199277 GAAACTATCTCAAGCGAGATAAAATTCATTTCAAGG
1 GAAACTATCTCAAGCGAGACAAAATTCATTTCAAGG
199313 GAAA
1 GAAA
199317 TGTTTTCAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.41, C:0.16, G:0.21, T:0.22
Consensus pattern (36 bp):
GAAACTATCTCAAGCGAGACAAAATTCATTTCAAGG
Found at i:199309 original size:86 final size:85
Alignment explanation
Indices: 199152--199310 Score: 196
Period size: 86 Copynumber: 1.8 Consensus size: 85
199142 TGTCGTTTCA
* *** *
199152 AGAGAAACTGTCTCAAGGGAGACAAAATTGTTTGAAGGAAAACATATTCAAGATTTCGTTAAATT
1 AGAGAAACTGTCTCAAGGGAGACAAAATTGTTTCAAGGAAAACATATTCAAGA-CGAGTAAAATT
**
199217 GTTTTCAAAGTTTATGTTTGG
65 CATTTCAAAGTTTATGTTTGG
*
199238 AGAGAAACTGTCTCAAGGGAGACAAAATTCGTTTCAAGGGAAAC-TATCTCAAG-CGAGATAAAA
1 AGAGAAACTGTCTCAAGGGAGACAAAATT-GTTTCAAGGAAAACATAT-TCAAGACGAG-TAAAA
199301 TTCATTTCAA
63 TTCATTTCAA
199311 GGGAAATGTT
Statistics
Matches: 62, Mismatches: 8, Indels: 6
0.82 0.11 0.08
Matches are distributed among these distances:
85 1 0.02
86 44 0.71
87 17 0.27
ACGTcount: A:0.38, C:0.13, G:0.20, T:0.29
Consensus pattern (85 bp):
AGAGAAACTGTCTCAAGGGAGACAAAATTGTTTCAAGGAAAACATATTCAAGACGAGTAAAATTC
ATTTCAAAGTTTATGTTTGG
Found at i:199491 original size:39 final size:39
Alignment explanation
Indices: 199437--199511 Score: 98
Period size: 39 Copynumber: 1.9 Consensus size: 39
199427 TCAATGTTTA
* *
199437 TGTTTCAAGAGAAACTGTCTCAAGG-GAGACAAAATTTTC
1 TGTTTCAAGAGAAACTATCTC-AGGAGAGAAAAAATTTTC
* *
199476 TGTTTCGAGGGAAACTATCTCAGGAGAGAAAAAATT
1 TGTTTCAAGAGAAACTATCTCAGGAGAGAAAAAATT
199512 AATTTCAAGG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
38 3 0.10
39 28 0.90
ACGTcount: A:0.37, C:0.13, G:0.23, T:0.27
Consensus pattern (39 bp):
TGTTTCAAGAGAAACTATCTCAGGAGAGAAAAAATTTTC
Found at i:199550 original size:105 final size:104
Alignment explanation
Indices: 199216--199534 Score: 518
Period size: 105 Copynumber: 3.1 Consensus size: 104
199206 TTCGTTAAAT
* ** *
199216 TGTTTTCAAAGTTTATGTTTGGAGAGAAACTGTCTCAAGGGAGACAAAA--TTC-GTTTCAAGGG
1 TGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTCTGTTTCGAGGG
* *
199278 AAACTATCTCAAGCGAGATAAAATTCATTTCAAGGGAAA
66 AAACTATCTCAAGAGAGAAAAAATTCATTTCAAGGGAAA
*
199317 TGTTTTCAATGTTTATGTTTCAAGAGAAACTCTCTCAAGGGAGACAAAATTTTCTGTTTCGAGGG
1 TGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTCTGTTTCGAGGG
*
199382 AAACTATCTCAAGAGAGAAAAAAAATCATTTCAAGGGAAA
66 AAACTATCTCAAGAGAG-AAAAAATTCATTTCAAGGGAAA
199422 TGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTCTGTTTCGAGGG
1 TGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTCTGTTTCGAGGG
* *
199487 AAACTATCTCAGGAGAGAAAAAATTAATTTCAAGGGAAA
66 AAACTATCTCAAGAGAGAAAAAATTCATTTCAAGGGAAA
199526 TGTTTTCAA
1 TGTTTTCAA
199535 GAGAAACTCT
Statistics
Matches: 202, Mismatches: 12, Indels: 5
0.92 0.05 0.02
Matches are distributed among these distances:
101 45 0.22
103 3 0.01
104 54 0.27
105 100 0.50
ACGTcount: A:0.37, C:0.13, G:0.20, T:0.30
Consensus pattern (104 bp):
TGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTCTGTTTCGAGGG
AAACTATCTCAAGAGAGAAAAAATTCATTTCAAGGGAAA
Found at i:199711 original size:36 final size:36
Alignment explanation
Indices: 199666--199780 Score: 99
Period size: 36 Copynumber: 3.2 Consensus size: 36
199656 GGTCTCACGA
*
199666 GAGACAAATCTTGTTTTAAGAAAAACAATATTGAGT
1 GAGATAAATCTTGTTTTAAGAAAAACAATATTGAGT
* * ** * * **
199702 GAAATAAATCTTCTTTCGAGAAAAACAGTCTCAAGT
1 GAGATAAATCTTGTTTTAAGAAAAACAATATTGAGT
* *
199738 GAGACAAAGT-ATGTTTTAAGAAAAACAA-ATTTGAGT
1 GAGATAAA-TCTTGTTTTAAGAAAAACAATA-TTGAGT
199774 GAGATAA
1 GAGATAA
199781 TCATATGCAT
Statistics
Matches: 57, Mismatches: 20, Indels: 4
0.70 0.25 0.05
Matches are distributed among these distances:
36 56 0.98
37 1 0.02
ACGTcount: A:0.45, C:0.10, G:0.17, T:0.28
Consensus pattern (36 bp):
GAGATAAATCTTGTTTTAAGAAAAACAATATTGAGT
Found at i:199744 original size:72 final size:74
Alignment explanation
Indices: 199620--199780 Score: 204
Period size: 72 Copynumber: 2.2 Consensus size: 74
199610 AAAAACAGCC
* * * *
199620 TTGAGTGAAATGAAATGTCTTCTTTCGAGTGAAAACGGTCTCACGAGAGACAAA-TCTTGTTTTA
1 TTGAGTGAAAT-AAA-GTCTTCTTTCGAGTAAAAACAGTCTCAAGAGAGACAAAGT-ATGTTTTA
199684 AGAAAAAC-AAT
63 AGAAAAACAAAT
*
199695 ATTGAGTGAAATAAA-TCTTCTTTCGAG-AAAAACAGTCTCAAGTGAGACAAAGTATGTTTTAAG
1 -TTGAGTGAAATAAAGTCTTCTTTCGAGTAAAAACAGTCTCAAGAGAGACAAAGTATGTTTTAAG
199758 AAAAACAAAT
65 AAAAACAAAT
*
199768 TTGAGTGAGATAA
1 TTGAGTGAAATAA
199781 TCATATGCAT
Statistics
Matches: 77, Mismatches: 6, Indels: 8
0.85 0.07 0.09
Matches are distributed among these distances:
72 47 0.61
73 16 0.21
75 3 0.04
76 11 0.14
ACGTcount: A:0.41, C:0.11, G:0.19, T:0.29
Consensus pattern (74 bp):
TTGAGTGAAATAAAGTCTTCTTTCGAGTAAAAACAGTCTCAAGAGAGACAAAGTATGTTTTAAGA
AAAACAAAT
Found at i:201186 original size:183 final size:183
Alignment explanation
Indices: 200923--201456 Score: 977
Period size: 183 Copynumber: 2.9 Consensus size: 183
200913 ATCAGGTTTA
*
200923 ACTGAAGGGTTCATCTCATCACAAAGTCTTTGACCTGACAAAAGCAGTGGAGCAAACACCGAATT
1 ACTGAAGGGTTCATCTCATCACAAAGTCTTTGGCCTGACAAAAGCAGTGGAGCAAACACCGAATT
*
200988 GCCAAGTGTCCGAGCAATGTCAT-GATTTGAATGTAATCTATTCATAAAGCCAGGGCTTTCGAGT
66 GCCAAGTGTCCGAGCAATGTCATAG-TTTGAATATAATCTATTCATAAAGCCAGGGCTTTCGAGT
201052 TTCCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTAGAGGGACAAATC
130 TTCCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTAGAGGGACAAATC
*
201106 ACTGAAGGGTTCGTCTCATCACAAAGTCTTTGGCCTGACAAAAGCAGTGGAGCAAACACCGAATT
1 ACTGAAGGGTTCATCTCATCACAAAGTCTTTGGCCTGACAAAAGCAGTGGAGCAAACACCGAATT
* *
201171 GCCAAGTGTCCGAGCAGTGTCATAGTTTGAATATAATCTATTCATAAAGTCAGGGCTTTCGAGTT
66 GCCAAGTGTCCGAGCAATGTCATAGTTTGAATATAATCTATTCATAAAGCCAGGGCTTTCGAGTT
201236 TCCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTAGAGGGACAAATC
131 TCCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTAGAGGGACAAATC
201289 ACTGAAGGGTTCATCTCATCACAAAGTCTTTGGCCTGACAAAAGC-GTGGAGCAAACACCGAATT
1 ACTGAAGGGTTCATCTCATCACAAAGTCTTTGGCCTGACAAAAGCAGTGGAGCAAACACCGAATT
*
201353 GCCAA--GTCCGAGCAATGTCATAGTTTGAACATAATCTATTCATAAAGCCAGGGCTTTCGAGTT
66 GCCAAGTGTCCGAGCAATGTCATAGTTTGAATATAATCTATTCATAAAGCCAGGGCTTTCGAGTT
201416 TCCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTA
131 TCCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTA
201457 CGGATTTAAT
Statistics
Matches: 341, Mismatches: 9, Indels: 5
0.96 0.03 0.01
Matches are distributed among these distances:
180 96 0.28
182 24 0.07
183 220 0.65
184 1 0.00
ACGTcount: A:0.31, C:0.22, G:0.21, T:0.27
Consensus pattern (183 bp):
ACTGAAGGGTTCATCTCATCACAAAGTCTTTGGCCTGACAAAAGCAGTGGAGCAAACACCGAATT
GCCAAGTGTCCGAGCAATGTCATAGTTTGAATATAATCTATTCATAAAGCCAGGGCTTTCGAGTT
TCCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTAGAGGGACAAATC
Found at i:204983 original size:19 final size:19
Alignment explanation
Indices: 204959--205013 Score: 101
Period size: 19 Copynumber: 2.8 Consensus size: 19
204949 AGATGATAGA
204959 AAAAAAAATAAAAGAGAGG
1 AAAAAAAATAAAAGAGAGG
204978 AAAAAAAATAAAAGAGAGG
1 AAAAAAAATAAAAGAGAGG
204997 AAAAAAAATGAAAAGAG
1 AAAAAAAAT-AAAAGAG
205014 TTAGTAAGGT
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
19 28 0.80
20 7 0.20
ACGTcount: A:0.75, C:0.00, G:0.20, T:0.05
Consensus pattern (19 bp):
AAAAAAAATAAAAGAGAGG
Found at i:206010 original size:19 final size:19
Alignment explanation
Indices: 205988--206027 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
205978 AAATAACAAG
205988 TTAAATTAAAAGGTAAAGT
1 TTAAATTAAAAGGTAAAGT
206007 TTAAATTAAAAGGTAAAGT
1 TTAAATTAAAAGGTAAAGT
206026 TT
1 TT
206028 CGATCATAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.50, C:0.00, G:0.15, T:0.35
Consensus pattern (19 bp):
TTAAATTAAAAGGTAAAGT
Found at i:206213 original size:38 final size:38
Alignment explanation
Indices: 206157--206229 Score: 94
Period size: 38 Copynumber: 1.9 Consensus size: 38
206147 AGATAAGAAA
* * * *
206157 AAAAAATAGTAAAGTAATAATTATATATAGTAATATTTG
1 AAAAAATAGAAAAATAATAAATATAAATA-TAATATTTG
206196 AAAAAAT-GAAAAATAATAAATATAAATATAATAT
1 AAAAAATAGAAAAATAATAAATATAAATATAATAT
206230 ATATATATAT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
37 6 0.20
38 17 0.57
39 7 0.23
ACGTcount: A:0.62, C:0.00, G:0.07, T:0.32
Consensus pattern (38 bp):
AAAAAATAGAAAAATAATAAATATAAATATAATATTTG
Found at i:206220 original size:6 final size:6
Alignment explanation
Indices: 206206--206279 Score: 51
Period size: 6 Copynumber: 11.8 Consensus size: 6
206196 AAAAAATGAA
* * * *
206206 AAATAAT AAATAT AAATAT AATATAT ATATAT ATATAT ATATAT ATATAT
1 AAAT-AT AAATAT AAATAT AA-ATAT AAATAT AAATAT AAATAT AAATAT
* *
206256 ATATAT CAAAGTAT TAATA- AAATA
1 AAATAT -AAA-TAT AAATAT AAATA
206280 AATAAACTAT
Statistics
Matches: 60, Mismatches: 4, Indels: 8
0.83 0.06 0.11
Matches are distributed among these distances:
5 4 0.07
6 40 0.67
7 13 0.22
8 3 0.05
ACGTcount: A:0.58, C:0.01, G:0.01, T:0.39
Consensus pattern (6 bp):
AAATAT
Found at i:206233 original size:2 final size:2
Alignment explanation
Indices: 206215--206261 Score: 78
Period size: 2 Copynumber: 24.0 Consensus size: 2
206205 AAAATAATAA
*
206215 AT AT AA AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
206256 AT AT AT
1 AT AT AT
206262 CAAAGTATTA
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
1 1 0.02
2 41 0.98
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:206780 original size:52 final size:51
Alignment explanation
Indices: 206691--206789 Score: 114
Period size: 52 Copynumber: 1.9 Consensus size: 51
206681 TATTAAAGAT
*
206691 ATATATATATATAATAATAAAATATAGTAAAAAAATAAATGAAAATAATTTA
1 ATATATATATATAATAATAAAATATAGTAAAAAAAT-AATAAAAATAATTTA
**
206743 ATATATATATATACAT-ATAATAATA-A-TAACATGAATAATAAAAATAA
1 ATATATATATATA-ATAATAA-AATATAGTAA-AAAAATAATAAAAATAA
206790 ATGAATAAAA
Statistics
Matches: 41, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
51 13 0.32
52 22 0.54
53 6 0.15
ACGTcount: A:0.63, C:0.02, G:0.03, T:0.32
Consensus pattern (51 bp):
ATATATATATATAATAATAAAATATAGTAAAAAAATAATAAAAATAATTTA
Found at i:206782 original size:18 final size:17
Alignment explanation
Indices: 206759--206806 Score: 64
Period size: 18 Copynumber: 2.9 Consensus size: 17
206749 ATATATACAT
206759 ATAATAATAATAACATGA
1 ATAATAATAATAA-ATGA
*
206777 ATAATAAAAATAAATGA
1 ATAATAATAATAAATGA
206794 ATAA-AAT-ATAAAT
1 ATAATAATAATAAAT
206807 ATAAATAAAG
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
15 6 0.21
16 2 0.07
17 8 0.29
18 12 0.43
ACGTcount: A:0.67, C:0.02, G:0.04, T:0.27
Consensus pattern (17 bp):
ATAATAATAATAAATGA
Found at i:206809 original size:58 final size:57
Alignment explanation
Indices: 206677--206809 Score: 141
Period size: 58 Copynumber: 2.3 Consensus size: 57
206667 ACTTATAAGT
* * * *
206677 AAAAT-ATTAA-AGATATATATATATATAATAATAAAATATAGTAAAAAAATAAATG
1 AAAATAATTAATAAATATATATACATATAATAATAAAACATAATAAAAAAATAAATG
*
206732 AAAATAATTTAATATATATATATACATATAATAATAATAACATGAATAATAAAAATAAATG
1 AAAATAA-TTAATAAATATATATACATATAATAATAA-AACAT-AATAA-AAAAATAAATG
206793 AATAA-AA-T-ATAAATATA
1 AA-AATAATTAATAAATATA
206810 AATAAAGGGA
Statistics
Matches: 66, Mismatches: 5, Indels: 11
0.80 0.06 0.13
Matches are distributed among these distances:
55 5 0.08
56 1 0.02
57 4 0.06
58 30 0.45
59 5 0.08
60 4 0.06
61 15 0.23
62 2 0.03
ACGTcount: A:0.63, C:0.02, G:0.04, T:0.32
Consensus pattern (57 bp):
AAAATAATTAATAAATATATATACATATAATAATAAAACATAATAAAAAAATAAATG
Found at i:206810 original size:13 final size:13
Alignment explanation
Indices: 206761--206811 Score: 50
Period size: 15 Copynumber: 3.7 Consensus size: 13
206751 ATATACATAT
*
206761 AATAATAATAACATG
1 AATAATAA-AA-ATA
206776 AATAATAAAAATA
1 AATAATAAAAATA
206789 AATGAATAAAATATA
1 AAT-AATAAAA-ATA
206804 AAT-ATAAA
1 AATAATAAA
206812 TAAAGGGACT
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
13 10 0.30
14 9 0.27
15 14 0.42
ACGTcount: A:0.69, C:0.02, G:0.04, T:0.25
Consensus pattern (13 bp):
AATAATAAAAATA
Found at i:228279 original size:60 final size:61
Alignment explanation
Indices: 228207--228335 Score: 165
Period size: 60 Copynumber: 2.1 Consensus size: 61
228197 AATATTTCAT
**
228207 TTTCATCCTTAAACTATGA-CTATCATTCTAAATTAA-TCTTTAAACTTT-TGAACATTCCAA
1 TTTCATCCTTAAACTATGACCT-TCATTCTAAATTAATTC-CCAAACTTTATGAACATTCCAA
* * *
228267 TTTCATCCTTAAATTATGACCTTCATTCTAATTTAATTCCCAAACTTTATGAACATTTCAA
1 TTTCATCCTTAAACTATGACCTTCATTCTAAATTAATTCCCAAACTTTATGAACATTCCAA
*
228328 TTTTATCC
1 TTTCATCC
228336 CAAACTACAT
Statistics
Matches: 60, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
60 38 0.63
61 22 0.37
ACGTcount: A:0.33, C:0.21, G:0.03, T:0.43
Consensus pattern (61 bp):
TTTCATCCTTAAACTATGACCTTCATTCTAAATTAATTCCCAAACTTTATGAACATTCCAA
Found at i:231161 original size:16 final size:18
Alignment explanation
Indices: 231129--231163 Score: 56
Period size: 16 Copynumber: 2.1 Consensus size: 18
231119 ATATAAAAAC
231129 ATAAAATATAGGATAAAT
1 ATAAAATATAGGATAAAT
231147 ATAAAA-ATA-GATAAAT
1 ATAAAATATAGGATAAAT
231163 A
1 A
231164 AATGAGTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.47
17 3 0.18
18 6 0.35
ACGTcount: A:0.66, C:0.00, G:0.09, T:0.26
Consensus pattern (18 bp):
ATAAAATATAGGATAAAT
Found at i:231199 original size:20 final size:20
Alignment explanation
Indices: 231174--231211 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
231164 AATGAGTAAA
231174 ATATATAAAAAAGTAAAAGC
1 ATATATAAAAAAGTAAAAGC
* *
231194 ATATATATATAAGTAAAA
1 ATATATAAAAAAGTAAAA
231212 TAATAATAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.63, C:0.03, G:0.08, T:0.26
Consensus pattern (20 bp):
ATATATAAAAAAGTAAAAGC
Found at i:231784 original size:37 final size:36
Alignment explanation
Indices: 231741--231842 Score: 172
Period size: 34 Copynumber: 2.9 Consensus size: 36
231731 AAAGTAGAAC
231741 TCTATCCTATTTTTAGGAGTTTGAATCCTAGCAAAAT
1 TCTATCCTATTTTTAGGAGTTTGAATCCTAG-AAAAT
*
231778 TTTATCCTATTTTTAGGAGTTTGAATCCT--AAAAT
1 TCTATCCTATTTTTAGGAGTTTGAATCCTAGAAAAT
231812 TCTATCCTATTTTTAGGAGTTTGAATCCTAG
1 TCTATCCTATTTTTAGGAGTTTGAATCCTAG
231843 TAGGACGAAA
Statistics
Matches: 61, Mismatches: 2, Indels: 5
0.90 0.03 0.07
Matches are distributed among these distances:
34 33 0.54
37 28 0.46
ACGTcount: A:0.27, C:0.15, G:0.14, T:0.44
Consensus pattern (36 bp):
TCTATCCTATTTTTAGGAGTTTGAATCCTAGAAAAT
Found at i:232698 original size:105 final size:105
Alignment explanation
Indices: 232388--233321 Score: 1463
Period size: 105 Copynumber: 9.0 Consensus size: 105
232378 CATTGTTCCA
* * * ** *
232388 AGTCCAATATCCTCCGTCGTGAAGTTGAAATTGGCTCTGGAACCGGGATA-TTGTTTGTTGACAA
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGA-AGTTG-TTGTTGACAA
* * * * * *
232452 CCAGCCGTCCCTTCGTTGTGACGTTGAACTTGTGTTGTCTCG
64 GCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
**
232494 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGAATCTG-AA-TGA-AA-TT-TTGTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGC
*
232554 AGCGGTCCCTTCGTCATGAAGTTGAACTTGCGTTGTCTGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* *
232594 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGC
* *
232659 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTTTCTGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* *
232699 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGC
* *
232764 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCTGA
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
232804 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGC
232869 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
232909 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGC
*
232974 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGA
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * *
233014 AGTCCAATATCCTTCATTGTGAAGTTGAAATTGGTTCTGAAATTGAGAA---GTTGTTGACAGGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGC
*
233076 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGA
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* *
233116 AGTCCAATATCCTTCATTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAGGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGC
233181 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
*
233221 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTG-TTGTTGACAAG
** * *
233286 CAGTTGTCCCTTCGTTGTGAAGTTGAACTTGTGTTG
65 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTG
233322 CCTCGAGTGC
Statistics
Matches: 778, Mismatches: 41, Indels: 18
0.93 0.05 0.02
Matches are distributed among these distances:
100 82 0.11
101 1 0.00
102 105 0.13
103 3 0.00
104 3 0.00
105 508 0.65
106 76 0.10
ACGTcount: A:0.22, C:0.17, G:0.27, T:0.34
Consensus pattern (105 bp):
AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGC
AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
Found at i:234099 original size:67 final size:66
Alignment explanation
Indices: 233964--234121 Score: 194
Period size: 68 Copynumber: 2.4 Consensus size: 66
233954 AAGATATCTG
* * **
233964 TTGTTTCATGAGAAACGGTCTCAAGGGAAACAAAATTATGTTTTAAGGGAAATAAATTTGAAGAT
1 TTGTTTCAAGAGAAACTGTCTCAAGGGAAACAAAATTATGTTTTAAGGGAAATAAATTCAAAGA-
234029 TT
65 TT
* *
234031 TGTGTTTCAAGAGTAACTGTCTCAAGGGAGAA-AAAATT-TGTTTTAGGGGAAATAAATTCAAAG
1 T-TGTTTCAAGAGAAACTGTCTCAAGGGA-AACAAAATTATGTTTTAAGGGAAATAAATTCAAAG
*
234094 GTT
64 ATT
* *
234097 TTGTTTCAAGGGGAACTGTCTCAAG
1 TTGTTTCAAGAGAAACTGTCTCAAG
234122 ATAGACGAAA
Statistics
Matches: 80, Mismatches: 9, Indels: 6
0.84 0.09 0.06
Matches are distributed among these distances:
65 22 0.28
66 3 0.04
67 23 0.29
68 30 0.38
69 2 0.03
ACGTcount: A:0.35, C:0.09, G:0.23, T:0.32
Consensus pattern (66 bp):
TTGTTTCAAGAGAAACTGTCTCAAGGGAAACAAAATTATGTTTTAAGGGAAATAAATTCAAAGAT
T
Found at i:234150 original size:36 final size:36
Alignment explanation
Indices: 234097--234219 Score: 142
Period size: 36 Copynumber: 3.4 Consensus size: 36
234087 TTCAAAGGTT
* * *
234097 TTGTTTCAAGGGGAACTGTCTCAAGATAGACGAAAA
1 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACGAAAA
234133 TTGTTTCAAGAGAAACTGTCTCAAGAGAGAC-AAAA
1 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACGAAAA
* * * * *
234168 CTTAGTTCCAAAAGAAACTGTCTCAAGGGAGACGGAAT
1 -TT-GTTTCAAGAGAAACTGTCTCAAGAGAGACGAAAA
234206 TTGTTTCAA-AGAAA
1 TTGTTTCAAGAGAAA
234220 ACATATTCAA
Statistics
Matches: 75, Mismatches: 9, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
35 9 0.12
36 36 0.48
37 28 0.37
38 2 0.03
ACGTcount: A:0.39, C:0.15, G:0.22, T:0.24
Consensus pattern (36 bp):
TTGTTTCAAGAGAAACTGTCTCAAGAGAGACGAAAA
Found at i:234192 original size:37 final size:36
Alignment explanation
Indices: 234110--234219 Score: 125
Period size: 37 Copynumber: 3.1 Consensus size: 36
234100 TTTCAAGGGG
* * *
234110 AACTGTCTCAAGATAGACGAAAATTGTTTCAAGAGA
1 AACTGTCTCAAGAGAGACGAAAATTGTTCCAAAAGA
234146 AACTGTCTCAAGAGAGAC-AAAACTTAGTTCCAAAAGA
1 AACTGTCTCAAGAGAGACGAAAA-TT-GTTCCAAAAGA
* * * *
234183 AACTGTCTCAAGGGAGACGGAATTTGTTTC-AAAGA
1 AACTGTCTCAAGAGAGACGAAAATTGTTCCAAAAGA
234218 AA
1 AA
234220 ACATATTCAA
Statistics
Matches: 64, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
35 11 0.17
36 23 0.36
37 28 0.44
38 2 0.03
ACGTcount: A:0.42, C:0.15, G:0.20, T:0.23
Consensus pattern (36 bp):
AACTGTCTCAAGAGAGACGAAAATTGTTCCAAAAGA
Found at i:234776 original size:18 final size:18
Alignment explanation
Indices: 234749--234784 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
234739 TGTTGAATCC
* *
234749 CCAAAGATGCCTCAATAT
1 CCAAAAATGCCCCAATAT
234767 CCAAAAATGCCCCAATAT
1 CCAAAAATGCCCCAATAT
234785 TTGATGTTGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.42, C:0.31, G:0.08, T:0.19
Consensus pattern (18 bp):
CCAAAAATGCCCCAATAT
Found at i:235922 original size:16 final size:17
Alignment explanation
Indices: 235903--235948 Score: 51
Period size: 16 Copynumber: 2.8 Consensus size: 17
235893 TCTTTTTGAT
*
235903 TTTTGCTCTTTTTTC-C
1 TTTTGCTCTTGTTTCTC
*
235919 TTTTGTTCTTGTTTCTC
1 TTTTGCTCTTGTTTCTC
*
235936 TTTTTCT-TTGTTT
1 TTTTGCTCTTGTTT
235949 TTTTTTTTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
16 19 0.76
17 6 0.24
ACGTcount: A:0.00, C:0.17, G:0.09, T:0.74
Consensus pattern (17 bp):
TTTTGCTCTTGTTTCTC
Found at i:235959 original size:14 final size:15
Alignment explanation
Indices: 235936--235988 Score: 54
Period size: 16 Copynumber: 3.5 Consensus size: 15
235926 CTTGTTTCTC
235936 TTTTTCTTTG-TTTT
1 TTTTTCTTTGCTTTT
*
235950 TTTTTTTTTGCTTTT
1 TTTTTCTTTGCTTTT
* *
235965 TTGCTTCTTTTCTTTT
1 TT-TTTCTTTGCTTTT
*
235981 TTGTTCTT
1 TTTTTCTT
235989 GATTGGATCT
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
14 9 0.28
15 11 0.34
16 12 0.38
ACGTcount: A:0.00, C:0.11, G:0.08, T:0.81
Consensus pattern (15 bp):
TTTTTCTTTGCTTTT
Found at i:235979 original size:16 final size:16
Alignment explanation
Indices: 235942--235988 Score: 55
Period size: 15 Copynumber: 3.1 Consensus size: 16
235932 TCTCTTTTTC
*
235942 TTTG-TTTTTT-TTTT
1 TTTGCTTTTTTGTTCT
235956 TTTGCTTTTTTGCTTCT
1 TTTGCTTTTTTG-TTCT
235973 TTT-CTTTTTTGTTCT
1 TTTGCTTTTTTGTTCT
235988 T
1 T
235989 GATTGGATCT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
14 4 0.14
15 11 0.38
16 8 0.28
17 6 0.21
ACGTcount: A:0.00, C:0.11, G:0.09, T:0.81
Consensus pattern (16 bp):
TTTGCTTTTTTGTTCT
Found at i:239196 original size:24 final size:22
Alignment explanation
Indices: 239149--239197 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 22
239139 CAGTAAAAGA
*
239149 ATATAAAAAATAAATGATAAAT
1 ATATAAAAAATAAAAGATAAAT
*
239171 ATATAAAAAAGTAAAAGCATATAT
1 ATATAAAAAA-TAAAAG-ATAAAT
239195 ATA
1 ATA
239198 AGTAAAATAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 10 0.43
23 5 0.22
24 8 0.35
ACGTcount: A:0.65, C:0.02, G:0.06, T:0.27
Consensus pattern (22 bp):
ATATAAAAAATAAAAGATAAAT
Found at i:239217 original size:40 final size:39
Alignment explanation
Indices: 239124--239225 Score: 109
Period size: 40 Copynumber: 2.6 Consensus size: 39
239114 TGATAATGCA
*
239124 AATAAATAAATAAAACAGTAAAAGAATATAAAAAATAAAT
1 AATAAAT-AATAAAAAAGTAAAAGAATATAAAAAATAAAT
* * * *
239164 GATAAATATATAAAAAAGTAAAAGCATATATATAAGTAAAAT
1 AATAAATA-ATAAAAAAGTAAAAGAATATA-AAAAAT-AAAT
239206 AAT-AATAATAAAAAAG-AAAA
1 AATAAATAATAAAAAAGTAAAA
239226 TCAAAAGTAA
Statistics
Matches: 53, Mismatches: 6, Indels: 7
0.80 0.09 0.11
Matches are distributed among these distances:
39 5 0.09
40 34 0.64
41 8 0.15
42 6 0.11
ACGTcount: A:0.70, C:0.02, G:0.07, T:0.22
Consensus pattern (39 bp):
AATAAATAATAAAAAAGTAAAAGAATATAAAAAATAAAT
Found at i:239771 original size:37 final size:36
Alignment explanation
Indices: 239728--239829 Score: 172
Period size: 34 Copynumber: 2.9 Consensus size: 36
239718 ATAGTAGAAC
239728 TCTATCCTATTTTTAGGAGTTTGAATCCTAGCAAAAT
1 TCTATCCTATTTTTAGGAGTTTGAATCCTAG-AAAAT
*
239765 TTTATCCTATTTTTAGGAGTTTGAATCCT--AAAAT
1 TCTATCCTATTTTTAGGAGTTTGAATCCTAGAAAAT
239799 TCTATCCTATTTTTAGGAGTTTGAATCCTAG
1 TCTATCCTATTTTTAGGAGTTTGAATCCTAG
239830 TAGGACGAAA
Statistics
Matches: 61, Mismatches: 2, Indels: 5
0.90 0.03 0.07
Matches are distributed among these distances:
34 33 0.54
37 28 0.46
ACGTcount: A:0.27, C:0.15, G:0.14, T:0.44
Consensus pattern (36 bp):
TCTATCCTATTTTTAGGAGTTTGAATCCTAGAAAAT
Found at i:240983 original size:18 final size:18
Alignment explanation
Indices: 240962--240997 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
240952 ATGAAAAAAA
*
240962 GGAAATAAATATGTATAT
1 GGAAATAAATATATATAT
*
240980 GGAAATATATATATATAT
1 GGAAATAAATATATATAT
240998 ATATATATAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.14, T:0.36
Consensus pattern (18 bp):
GGAAATAAATATATATAT
Found at i:240991 original size:2 final size:2
Alignment explanation
Indices: 240984--241020 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
240974 GTATATGGAA
240984 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
241021 ATGTCATACG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:244532 original size:14 final size:14
Alignment explanation
Indices: 244515--244541 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
244505 ATTATGTTAT
244515 TAAAAAATTAATTG
1 TAAAAAATTAATTG
244529 TAAAAAATTAATT
1 TAAAAAATTAATT
244542 TTTAATTAGA
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:0.59, C:0.00, G:0.04, T:0.37
Consensus pattern (14 bp):
TAAAAAATTAATTG
Found at i:244611 original size:14 final size:15
Alignment explanation
Indices: 244577--244608 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
244567 ATGAAATTAA
244577 AAATTAATTTTTATG
1 AAATTAATTTTTATG
244592 AAATTAATTTTTATG
1 AAATTAATTTTTATG
244607 AA
1 AA
244609 TTATAATATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (15 bp):
AAATTAATTTTTATG
Found at i:252510 original size:29 final size:29
Alignment explanation
Indices: 252477--252543 Score: 134
Period size: 29 Copynumber: 2.3 Consensus size: 29
252467 TTGCATTTCG
252477 CGTTGCGATAATTGAAAATCGCAACTTGT
1 CGTTGCGATAATTGAAAATCGCAACTTGT
252506 CGTTGCGATAATTGAAAATCGCAACTTGT
1 CGTTGCGATAATTGAAAATCGCAACTTGT
252535 CGTTGCGAT
1 CGTTGCGAT
252544 TTTCCAAATT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 38 1.00
ACGTcount: A:0.28, C:0.18, G:0.22, T:0.31
Consensus pattern (29 bp):
CGTTGCGATAATTGAAAATCGCAACTTGT
Found at i:252562 original size:19 final size:19
Alignment explanation
Indices: 252534--252600 Score: 116
Period size: 19 Copynumber: 3.5 Consensus size: 19
252524 TCGCAACTTG
*
252534 TCGTTGCGATTTTCCAAAT
1 TCGTTACGATTTTCCAAAT
252553 TCGTTACGATTTTCCAAAT
1 TCGTTACGATTTTCCAAAT
252572 TCGTTACGATTTTCCAAAT
1 TCGTTACGATTTTCCAAAT
*
252591 TCGTTGCGAT
1 TCGTTACGAT
252601 AGTCTACATT
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 46 1.00
ACGTcount: A:0.22, C:0.21, G:0.15, T:0.42
Consensus pattern (19 bp):
TCGTTACGATTTTCCAAAT
Found at i:252616 original size:22 final size:22
Alignment explanation
Indices: 252591--252666 Score: 134
Period size: 22 Copynumber: 3.5 Consensus size: 22
252581 TTTTCCAAAT
*
252591 TCGTTGCGATAGTCTACATTTG
1 TCGTTGCGATAGTCTACAGTTG
252613 TCGTTGCGATAGTCTACAGTTG
1 TCGTTGCGATAGTCTACAGTTG
*
252635 TCGTTGCGGTAGTCTACAGTTG
1 TCGTTGCGATAGTCTACAGTTG
252657 TCGTTGCGAT
1 TCGTTGCGAT
252667 TTTCCAAATT
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 51 1.00
ACGTcount: A:0.16, C:0.18, G:0.28, T:0.38
Consensus pattern (22 bp):
TCGTTGCGATAGTCTACAGTTG
Found at i:252789 original size:6 final size:6
Alignment explanation
Indices: 252778--252810 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
252768 GACACGTATT
252778 ACCACG ACCACG ACCACG ACCACG ACCACG ACC
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACC
252811 CGAGACGAGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.33, C:0.52, G:0.15, T:0.00
Consensus pattern (6 bp):
ACCACG
Done.