Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397257.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_95.0, 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: 12062019
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 103452 characters in sequence are not A, C, G, or T
File 7 of 26
Found at i:2356161 original size:21 final size:21
Alignment explanation
Indices: 2356137--2356206 Score: 77
Period size: 21 Copynumber: 3.3 Consensus size: 21
2356127 AATCCATTAC
2356137 ATTTAAATTTAATTTATTTAA
1 ATTTAAATTTAATTTATTTAA
** * * *
2356158 ATTTAAATAAAAATTAATTAC
1 ATTTAAATTTAATTTATTTAA
* *
2356179 ATTTAAATTTAATTTATGTAG
1 ATTTAAATTTAATTTATTTAA
2356200 ATTTAAA
1 ATTTAAA
2356207 AAACATATAC
Statistics
Matches: 38, Mismatches: 11, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
21 38 1.00
ACGTcount: A:0.47, C:0.01, G:0.03, T:0.49
Consensus pattern (21 bp):
ATTTAAATTTAATTTATTTAA
Found at i:2357756 original size:53 final size:51
Alignment explanation
Indices: 2357652--2357788 Score: 136
Period size: 53 Copynumber: 2.7 Consensus size: 51
2357642 GGCGTGGGAG
** * ** *
2357652 ACTGAGGAAGAGGGTCGGGTGCTTTGGGGCGTGAAGGTGGGGGTGGGAGAT
1 ACTGAGGAAGAGAATTGGGTGCTTTGGGGCGTGAAGGTGGGCATGGAAGAT
*
2357703 CAACTGAGGAAGAGAATTGGGTGCTTTGGGGCGTGACGCG-GGGCATGGAAGAT
1 --ACTGAGGAAGAGAATTGGGTGCTTTGGGGCGTGAAG-GTGGGCATGGAAGAT
* * *
2357756 -C-GAGGAAGAGCAGTGGGTGCTTGGGGGCGTGAA
1 ACTGAGGAAGAGAATTGGGTGCTTTGGGGCGTGAA
2357789 AGACTGAGGA
Statistics
Matches: 72, Mismatches: 11, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
49 28 0.39
50 1 0.01
53 42 0.58
54 1 0.01
ACGTcount: A:0.21, C:0.11, G:0.50, T:0.18
Consensus pattern (51 bp):
ACTGAGGAAGAGAATTGGGTGCTTTGGGGCGTGAAGGTGGGCATGGAAGAT
Found at i:2367682 original size:27 final size:26
Alignment explanation
Indices: 2367646--2367707 Score: 81
Period size: 26 Copynumber: 2.3 Consensus size: 26
2367636 TCTTCCTAAA
2367646 TTTTTAAAATTTAATAAT-TTTTTTTAT
1 TTTTTAAAATTT--TAATGTTTTTTTAT
* *
2367673 TTTTTTAAATTTTATTGTTTTTTTAT
1 TTTTTAAAATTTTAATGTTTTTTTAT
2367699 TTTTTAAAA
1 TTTTTAAAA
2367708 CTAAAATCAT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
25 3 0.10
26 17 0.55
27 11 0.35
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (26 bp):
TTTTTAAAATTTTAATGTTTTTTTAT
Found at i:2367703 original size:18 final size:18
Alignment explanation
Indices: 2367662--2367704 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
2367652 AAATTTAATA
2367662 ATTTTTT-TTATTTTTTT
1 ATTTTTTATTATTTTTTT
** *
2367679 AAATTTTATTGTTTTTTT
1 ATTTTTTATTATTTTTTT
2367697 ATTTTTTA
1 ATTTTTTA
2367705 AAACTAAAAT
Statistics
Matches: 20, Mismatches: 5, Indels: 1
0.77 0.19 0.04
Matches are distributed among these distances:
17 5 0.25
18 15 0.75
ACGTcount: A:0.19, C:0.00, G:0.02, T:0.79
Consensus pattern (18 bp):
ATTTTTTATTATTTTTTT
Found at i:2370305 original size:79 final size:78
Alignment explanation
Indices: 2370181--2370342 Score: 218
Period size: 79 Copynumber: 2.1 Consensus size: 78
2370171 TGATTGGTTG
* * * *
2370181 AAATTTAGTTTTATCTCTAAATTATCTTAATTTATTTATAGATAAATTGGATGACTAAT-AAGTG
1 AAATTTAGATTTATCTCTAAAATATCTTAATTTATTTAAAAATAAATTGGATGACTAATGAA-TG
*
2370245 AATCTTAATTGGTC
65 AATCTTAATTGGCC
* * *
2370259 AAATTTAAGATTTATCTTTAAAATATCTTAATTTATTTAAAAATAAATTGGATGATTCATGAATG
1 AAATTT-AGATTTATCTCTAAAATATCTTAATTTATTTAAAAATAAATTGGATGACTAATGAATG
*
2370324 AATTTTAATTGGCC
65 AATCTTAATTGGCC
2370338 AAATT
1 AAATT
2370343 ATGTTATTTT
Statistics
Matches: 73, Mismatches: 9, Indels: 3
0.86 0.11 0.04
Matches are distributed among these distances:
78 6 0.08
79 65 0.89
80 2 0.03
ACGTcount: A:0.39, C:0.07, G:0.10, T:0.44
Consensus pattern (78 bp):
AAATTTAGATTTATCTCTAAAATATCTTAATTTATTTAAAAATAAATTGGATGACTAATGAATGA
ATCTTAATTGGCC
Found at i:2381905 original size:19 final size:17
Alignment explanation
Indices: 2381881--2381926 Score: 56
Period size: 19 Copynumber: 2.6 Consensus size: 17
2381871 GTAAATAAAC
*
2381881 ATAAAATTAAAATAAGTTT
1 ATAAAAATAAAATAA--TT
*
2381900 ATAAAAATAAACTAATT
1 ATAAAAATAAAATAATT
2381917 ATAAAAATAA
1 ATAAAAATAA
2381927 TTAAAAATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 12 0.48
19 13 0.52
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.30
Consensus pattern (17 bp):
ATAAAAATAAAATAATT
Found at i:2387236 original size:28 final size:28
Alignment explanation
Indices: 2387174--2387261 Score: 90
Period size: 28 Copynumber: 3.2 Consensus size: 28
2387164 ATTTTTTTAT
** * * *
2387174 TATTCATCCTCTCCTAGCAG-TAAAAAA
1 TATTCATCCAATCCTAGTAGATTAAAAG
*
2387201 TATTCATCCAATCGTAGT-GAGTTAAAAG
1 TATTCATCCAATCCTAGTAGA-TTAAAAG
*
2387229 TATTCATCCAGTCCTAGTAGATTAAAAG
1 TATTCATCCAATCCTAGTAGATTAAAAG
2387257 TATTC
1 TATTC
2387262 TTATTATTAG
Statistics
Matches: 50, Mismatches: 8, Indels: 5
0.79 0.13 0.08
Matches are distributed among these distances:
26 1 0.02
27 14 0.28
28 33 0.66
29 2 0.04
ACGTcount: A:0.35, C:0.19, G:0.12, T:0.33
Consensus pattern (28 bp):
TATTCATCCAATCCTAGTAGATTAAAAG
Found at i:2393291 original size:29 final size:28
Alignment explanation
Indices: 2393218--2393364 Score: 150
Period size: 29 Copynumber: 5.1 Consensus size: 28
2393208 CCACGTGTGA
* * * *
2393218 TAAGGCACGTAGCCAAATCCAAAGGTGT
1 TAAGGCACCTAACCAAATCCAAAAGTGC
* * * *
2393246 TATGGTACCGAACCCAAATCCAAAAGTTC
1 TAAGGCACCTAA-CCAAATCCAAAAGTGC
*
2393275 TAAGGCACTTGAACCAAATCCAAAAGTGC
1 TAAGGCACCT-AACCAAATCCAAAAGTGC
2393304 TAAGGCACCTAAACCAAATCCAAAAGTGC
1 TAAGGCACCT-AACCAAATCCAAAAGTGC
* ** *
2393333 TAACGCACCTAACCAAATTAAAAAATGC
1 TAAGGCACCTAACCAAATCCAAAAGTGC
2393361 TAAG
1 TAAG
2393365 TCACTTACAA
Statistics
Matches: 97, Mismatches: 20, Indels: 4
0.80 0.17 0.03
Matches are distributed among these distances:
28 25 0.26
29 70 0.72
30 2 0.02
ACGTcount: A:0.42, C:0.24, G:0.16, T:0.18
Consensus pattern (28 bp):
TAAGGCACCTAACCAAATCCAAAAGTGC
Found at i:2406817 original size:191 final size:190
Alignment explanation
Indices: 2406470--2406972 Score: 672
Period size: 191 Copynumber: 2.6 Consensus size: 190
2406460 TAGATTTTTG
* * *
2406470 AAATAAAAATTCTTAATATT-AAAA-TTTTCTAAAATCTCCCAAATGCTTATGGTAAAATTTTAG
1 AAATAGAAATCCTCAATATTGAAAATTTTTC-AAAATCTCCCAAATGCTTATGGTAAAATTTTAG
* * * ** *
2406533 AAAATTCTCTTACCTAGAAATTCCCAAAAAACCACTTTTAGTTTTCTTGAGATTTCATCATTTGA
65 AAAATTCTCTCACC-AAAAATTCCCAAGAAGTCACTTTTGGTTTTCTTGAGATTTCATCATTTGA
* * * *
2406598 GAATTTATTAATTTAATTCTATTCTAGTTCAATATTCAATTTTTATTTTCCTTATATCTTAT
129 GAACTTATTAATTTAATTATAGTCTAGTTCAATATTCAATTTTTATTTTCCTTATATATTAT
* *
2406660 AAATAGAAATCCTCAATATTGAAAATTTTTCAAAATCTTCCAAATGTTTATGGTAAAATTTTAGA
1 AAATAGAAATCCTCAATATTGAAAATTTTTCAAAATCTCCCAAATGCTTATGGTAAAATTTTAGA
*
2406725 AAATTCTCTCACCAAAATATTCCCAAGAAGTCACTTTTGGTTTTCTTGATATTTCATCA-TTGAA
66 AAATTCTCTCACCAAAA-ATTCCCAAGAAGTCACTTTTGGTTTTCTTGAGATTTCATCATTTG-A
*
2406789 GAACTTATTTATTTAATTATAGTCTAGTTCAATATTCAATTTTTATTTTCCTTATATATTAT
129 GAACTTATTAATTTAATTATAGTCTAGTTCAATATTCAATTTTTATTTTCCTTATATATTAT
* * * * *
2406851 AAAT-GAAAAACCTCGATATTGAGAATTTCTCAAAATCTCCCAAACGCTTATGGTAAAATTTTAG
1 AAATAG-AAATCCTCAATATTGAAAATTTTTCAAAATCTCCCAAATGCTTATGGTAAAATTTTAG
** *** *
2406915 AAAATTCTCTCATGTAAAAATTCTTGAGAAGTCACTTTGGGTTTTCTTGAGATTTCAT
65 AAAATTCTCTCA-CCAAAAATTCCCAAGAAGTCACTTTTGGTTTTCTTGAGATTTCAT
2406973 TACTGGAGAA
Statistics
Matches: 276, Mismatches: 31, Indels: 11
0.87 0.10 0.03
Matches are distributed among these distances:
190 24 0.09
191 243 0.88
192 9 0.03
ACGTcount: A:0.35, C:0.14, G:0.09, T:0.42
Consensus pattern (190 bp):
AAATAGAAATCCTCAATATTGAAAATTTTTCAAAATCTCCCAAATGCTTATGGTAAAATTTTAGA
AAATTCTCTCACCAAAAATTCCCAAGAAGTCACTTTTGGTTTTCTTGAGATTTCATCATTTGAGA
ACTTATTAATTTAATTATAGTCTAGTTCAATATTCAATTTTTATTTTCCTTATATATTAT
Found at i:2407054 original size:16 final size:16
Alignment explanation
Indices: 2407028--2407060 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
2407018 AAAACAAAAT
2407028 AAATAAATAAAAGTAAA
1 AAATAAATAAAAG-AAA
2407045 AAAT-AATAAAAGAAA
1 AAATAAATAAAAGAAA
2407060 A
1 A
2407061 TAATTCAGAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.25
16 8 0.50
17 4 0.25
ACGTcount: A:0.79, C:0.00, G:0.06, T:0.15
Consensus pattern (16 bp):
AAATAAATAAAAGAAA
Found at i:2407968 original size:26 final size:26
Alignment explanation
Indices: 2407939--2407989 Score: 93
Period size: 26 Copynumber: 2.0 Consensus size: 26
2407929 TCAAATTCTT
2407939 AAAAGAAAAAACTTGATTTTTAAATG
1 AAAAGAAAAAACTTGATTTTTAAATG
*
2407965 AAAAGAAAAGACTTGATTTTTAAAT
1 AAAAGAAAAAACTTGATTTTTAAAT
2407990 TCTTTGTAAC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.53, C:0.04, G:0.12, T:0.31
Consensus pattern (26 bp):
AAAAGAAAAAACTTGATTTTTAAATG
Found at i:2408025 original size:21 final size:21
Alignment explanation
Indices: 2408011--2408054 Score: 67
Period size: 18 Copynumber: 2.2 Consensus size: 21
2408001 GGAAGAATCG
2408011 ATTCTGCAAAAGGAAAAGTCA
1 ATTCTGCAAAAGGAAAAGTCA
2408032 ATTCTGCAAAA-G--AAGTCA
1 ATTCTGCAAAAGGAAAAGTCA
2408050 ATTCT
1 ATTCT
2408055 TGGAAAATAG
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 11 0.48
20 1 0.04
21 11 0.48
ACGTcount: A:0.43, C:0.16, G:0.16, T:0.25
Consensus pattern (21 bp):
ATTCTGCAAAAGGAAAAGTCA
Found at i:2409050 original size:35 final size:34
Alignment explanation
Indices: 2408972--2409040 Score: 93
Period size: 34 Copynumber: 2.0 Consensus size: 34
2408962 CAATGTCTTG
* * *
2408972 ATAGAGGTTATGCTTGATCCTACAAAAGTATGTT
1 ATAGAAGTTACGCTTGATCCTACAAAAGCATGTT
*
2409006 ATAGAAGTTACGCTTGATCCTGCAAAAGGCATGTT
1 ATAGAAGTTACGCTTGATCCTACAAAA-GCATGTT
2409041 GTGAAAGTTA
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
34 24 0.80
35 6 0.20
ACGTcount: A:0.32, C:0.14, G:0.22, T:0.32
Consensus pattern (34 bp):
ATAGAAGTTACGCTTGATCCTACAAAAGCATGTT
Found at i:2409953 original size:28 final size:28
Alignment explanation
Indices: 2409922--2410012 Score: 92
Period size: 28 Copynumber: 3.2 Consensus size: 28
2409912 ATCAAGCAAT
* *
2409922 AACCCATGGTTTTAGTGGGTTCACCACA
1 AACCCATGGTTTTAATGGGATCACCACA
* ** * *
2409950 AACCCATGATTTTTCTAGGCTCACCACA
1 AACCCATGGTTTTAATGGGATCACCACA
* * *
2409978 AACCCAAGGTTTTAATGAGATCACCATA
1 AACCCATGGTTTTAATGGGATCACCACA
2410006 AACCCAT
1 AACCCAT
2410013 ACAATGGCTT
Statistics
Matches: 49, Mismatches: 14, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
28 49 1.00
ACGTcount: A:0.32, C:0.27, G:0.14, T:0.26
Consensus pattern (28 bp):
AACCCATGGTTTTAATGGGATCACCACA
Found at i:2410164 original size:30 final size:30
Alignment explanation
Indices: 2410123--2410191 Score: 129
Period size: 30 Copynumber: 2.3 Consensus size: 30
2410113 TTTTGCTGAA
*
2410123 TGGGTACAATGGAGGAAAAATTCCTAACAT
1 TGGGTATAATGGAGGAAAAATTCCTAACAT
2410153 TGGGTATAATGGAGGAAAAATTCCTAACAT
1 TGGGTATAATGGAGGAAAAATTCCTAACAT
2410183 TGGGTATAA
1 TGGGTATAA
2410192 AGATTGGATA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 38 1.00
ACGTcount: A:0.39, C:0.10, G:0.25, T:0.26
Consensus pattern (30 bp):
TGGGTATAATGGAGGAAAAATTCCTAACAT
Found at i:2413671 original size:21 final size:20
Alignment explanation
Indices: 2413617--2413676 Score: 61
Period size: 21 Copynumber: 3.0 Consensus size: 20
2413607 CAATCAAAAG
* *
2413617 CACAAAAAT-GTTGACTTTA
1 CACAAACATAGTTGACTATA
*
2413636 CACAAACATAATTGACTATA
1 CACAAACATAGTTGACTATA
2413656 CA-AGAAGCATAGTTGACTATA
1 CACA-AA-CATAGTTGACTATA
2413677 GCAACTCAGA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
19 9 0.26
20 12 0.35
21 13 0.38
ACGTcount: A:0.45, C:0.17, G:0.12, T:0.27
Consensus pattern (20 bp):
CACAAACATAGTTGACTATA
Found at i:2417218 original size:24 final size:23
Alignment explanation
Indices: 2417177--2417221 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 23
2417167 AGACAGGACC
2417177 CAACACCATACAAACTCAAAGTT
1 CAACACCATACAAACTCAAAGTT
2417200 CAACACC-TACACAAGCTCAAAG
1 CAACACCATACA-AA-CTCAAAG
2417222 CCAAATGTCC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
22 4 0.20
23 9 0.45
24 7 0.35
ACGTcount: A:0.47, C:0.33, G:0.07, T:0.13
Consensus pattern (23 bp):
CAACACCATACAAACTCAAAGTT
Found at i:2423237 original size:15 final size:16
Alignment explanation
Indices: 2423219--2423253 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
2423209 AAAATATGAA
2423219 AAAAAAAGAAA-AAAC
1 AAAAAAAGAAATAAAC
*
2423234 AAAAAAATAAATAAAC
1 AAAAAAAGAAATAAAC
2423250 AAAA
1 AAAA
2423254 GATGAACAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 10 0.56
16 8 0.44
ACGTcount: A:0.86, C:0.06, G:0.03, T:0.06
Consensus pattern (16 bp):
AAAAAAAGAAATAAAC
Found at i:2429341 original size:22 final size:22
Alignment explanation
Indices: 2429298--2429341 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
2429288 CTTATCAATA
**
2429298 AAACCATTCCAAGAGAGTATTC
1 AAACCATTCCAAGAGAAAATTC
**
2429320 AAACCATTCCAAGTTAAAATTC
1 AAACCATTCCAAGAGAAAATTC
2429342 TCTAATGACA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.43, C:0.23, G:0.09, T:0.25
Consensus pattern (22 bp):
AAACCATTCCAAGAGAAAATTC
Found at i:2434416 original size:2 final size:2
Alignment explanation
Indices: 2434411--2434437 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2434401 TGTGTGTGTC
2434411 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
2434438 CTCTGAGGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2434918 original size:38 final size:38
Alignment explanation
Indices: 2434876--2434951 Score: 152
Period size: 38 Copynumber: 2.0 Consensus size: 38
2434866 GCTATTTTTT
2434876 CCCGTTCTGTTTATGGGTATCTCATCAGGAGATTAAGG
1 CCCGTTCTGTTTATGGGTATCTCATCAGGAGATTAAGG
2434914 CCCGTTCTGTTTATGGGTATCTCATCAGGAGATTAAGG
1 CCCGTTCTGTTTATGGGTATCTCATCAGGAGATTAAGG
2434952 GTAGAAAAGT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.21, C:0.18, G:0.26, T:0.34
Consensus pattern (38 bp):
CCCGTTCTGTTTATGGGTATCTCATCAGGAGATTAAGG
Found at i:2434964 original size:38 final size:38
Alignment explanation
Indices: 2434884--2434964 Score: 99
Period size: 38 Copynumber: 2.1 Consensus size: 38
2434874 TTCCCGTTCT
* ****
2434884 GTTTATGGGTATCTCATCAGGAGATTAAGGCCCGTTCT
1 GTTTATGGGTATCTCATCAGGAGATTAAGGCCAGAAAA
**
2434922 GTTTATGGGTATCTCATCAGGAGATTAAGGGTAGAAAA
1 GTTTATGGGTATCTCATCAGGAGATTAAGGCCAGAAAA
2434960 GTTTA
1 GTTTA
2434965 GGAAGGATGC
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
38 36 1.00
ACGTcount: A:0.27, C:0.12, G:0.27, T:0.33
Consensus pattern (38 bp):
GTTTATGGGTATCTCATCAGGAGATTAAGGCCAGAAAA
Found at i:2444611 original size:14 final size:14
Alignment explanation
Indices: 2444592--2444626 Score: 70
Period size: 14 Copynumber: 2.5 Consensus size: 14
2444582 AAGTTTCATC
2444592 TCTATCATTCTTCT
1 TCTATCATTCTTCT
2444606 TCTATCATTCTTCT
1 TCTATCATTCTTCT
2444620 TCTATCA
1 TCTATCA
2444627 CTGTCAAACT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.17, C:0.29, G:0.00, T:0.54
Consensus pattern (14 bp):
TCTATCATTCTTCT
Found at i:2444993 original size:52 final size:52
Alignment explanation
Indices: 2444915--2445018 Score: 199
Period size: 52 Copynumber: 2.0 Consensus size: 52
2444905 ATAGATTATC
*
2444915 GATGTGTTGTTTGAAAAAGTCCTTAGTCTGGTTATTATGCTTGGATCTTCTT
1 GATGTGTTGTTTGAAAAAGTCCTTAGTCTGGTTATTATGCTTGGAACTTCTT
2444967 GATGTGTTGTTTGAAAAAGTCCTTAGTCTGGTTATTATGCTTGGAACTTCTT
1 GATGTGTTGTTTGAAAAAGTCCTTAGTCTGGTTATTATGCTTGGAACTTCTT
2445019 TTGATGTCTG
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 51 1.00
ACGTcount: A:0.20, C:0.12, G:0.23, T:0.45
Consensus pattern (52 bp):
GATGTGTTGTTTGAAAAAGTCCTTAGTCTGGTTATTATGCTTGGAACTTCTT
Found at i:2448615 original size:14 final size:14
Alignment explanation
Indices: 2448574--2448616 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
2448564 AAAATTGAGC
*
2448574 AAAAAACCCAAAATA
1 AAAAAACACAAAA-A
* *
2448589 AACAAAGACAAAAA
1 AAAAAACACAAAAA
2448603 AAAAAACACAAAAA
1 AAAAAACACAAAAA
2448617 GCCAGAAACA
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
14 13 0.57
15 10 0.43
ACGTcount: A:0.79, C:0.16, G:0.02, T:0.02
Consensus pattern (14 bp):
AAAAAACACAAAAA
Found at i:2458431 original size:25 final size:25
Alignment explanation
Indices: 2458397--2458462 Score: 80
Period size: 25 Copynumber: 2.6 Consensus size: 25
2458387 AAAAAAATAA
*
2458397 AATCTCTATAATTATGATGATTT-T
1 AATCCCTATAATTATGATGATTTCT
*
2458421 CAATCCCTATAATTATGGTGATTTCT
1 -AATCCCTATAATTATGATGATTTCT
* *
2458447 AATTCCTATAAATATG
1 AATCCCTATAATTATG
2458463 TTTATTAATA
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
25 35 0.97
26 1 0.03
ACGTcount: A:0.33, C:0.14, G:0.09, T:0.44
Consensus pattern (25 bp):
AATCCCTATAATTATGATGATTTCT
Found at i:2461085 original size:15 final size:17
Alignment explanation
Indices: 2461065--2461096 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
2461055 AGCCCAAACA
2461065 TCAAAA-TGGAC-TAAC
1 TCAAAAGTGGACATAAC
2461080 TCAAAAGTGGACATAAC
1 TCAAAAGTGGACATAAC
2461097 CTGTTTATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 6 0.40
16 5 0.33
17 4 0.27
ACGTcount: A:0.47, C:0.19, G:0.16, T:0.19
Consensus pattern (17 bp):
TCAAAAGTGGACATAAC
Found at i:2469252 original size:21 final size:22
Alignment explanation
Indices: 2469217--2469263 Score: 69
Period size: 21 Copynumber: 2.2 Consensus size: 22
2469207 CTCTTAAAGT
2469217 AATTTAAAATAAAATAACTTAA
1 AATTTAAAATAAAATAACTTAA
* *
2469239 AATTT-AACTAAAATAACTTTA
1 AATTTAAAATAAAATAACTTAA
2469260 AATT
1 AATT
2469264 AATCACTTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 18 0.78
22 5 0.22
ACGTcount: A:0.57, C:0.06, G:0.00, T:0.36
Consensus pattern (22 bp):
AATTTAAAATAAAATAACTTAA
Found at i:2475043 original size:21 final size:21
Alignment explanation
Indices: 2475017--2475059 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
2475007 ACCTTAAAGT
2475017 AATTTAAAT-AAAATAACTTAA
1 AATTTAAATAAAAAT-ACTTAA
*
2475038 AATTTAACTAAAAATACTTAA
1 AATTTAAATAAAAATACTTAA
2475059 A
1 A
2475060 TTAATCACTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 15 0.75
22 5 0.25
ACGTcount: A:0.60, C:0.07, G:0.00, T:0.33
Consensus pattern (21 bp):
AATTTAAATAAAAATACTTAA
Found at i:2478457 original size:7 final size:7
Alignment explanation
Indices: 2478447--2478472 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
2478437 CCTTTGGCAT
2478447 TTGAAAG
1 TTGAAAG
2478454 TTGAAAG
1 TTGAAAG
2478461 TTGAAAG
1 TTGAAAG
2478468 TTGAA
1 TTGAA
2478473 TGAAGCTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.42, C:0.00, G:0.27, T:0.31
Consensus pattern (7 bp):
TTGAAAG
Found at i:2490443 original size:18 final size:18
Alignment explanation
Indices: 2490394--2490445 Score: 62
Period size: 18 Copynumber: 3.2 Consensus size: 18
2490384 TTCTTAAAAG
2490394 TTAGCTAAGTTCTTGAAT
1 TTAGCTAAGTTCTTGAAT
2490412 TTAG----GTTC--GAAT
1 TTAGCTAAGTTCTTGAAT
2490424 TTAGCTAAGTTCTTGAAT
1 TTAGCTAAGTTCTTGAAT
2490442 TTAG
1 TTAG
2490446 GTTAAGATTT
Statistics
Matches: 28, Mismatches: 0, Indels: 12
0.70 0.00 0.30
Matches are distributed among these distances:
12 8 0.29
14 4 0.14
16 4 0.14
18 12 0.43
ACGTcount: A:0.27, C:0.10, G:0.19, T:0.44
Consensus pattern (18 bp):
TTAGCTAAGTTCTTGAAT
Found at i:2490456 original size:30 final size:30
Alignment explanation
Indices: 2490394--2490457 Score: 103
Period size: 30 Copynumber: 2.1 Consensus size: 30
2490384 TTCTTAAAAG
*
2490394 TTAGCTAAGTTCTTGAATTTAGGTTCGAAT
1 TTAGCTAAGTTCTTGAATTTAGGTTAGAAT
2490424 TTAGCTAAGTTCTTGAATTTAGGTTA-AGAT
1 TTAGCTAAGTTCTTGAATTTAGGTTAGA-AT
2490454 TTAG
1 TTAG
2490458 TTACATTTAG
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
29 1 0.03
30 31 0.97
ACGTcount: A:0.28, C:0.08, G:0.20, T:0.44
Consensus pattern (30 bp):
TTAGCTAAGTTCTTGAATTTAGGTTAGAAT
Found at i:2491748 original size:6 final size:6
Alignment explanation
Indices: 2491735--2491763 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
2491725 TTTGTATTAA
2491735 TTAG-T TTAGTT TTAGTT TTAGTT TTAGTT
1 TTAGTT TTAGTT TTAGTT TTAGTT TTAGTT
2491764 GATTAATTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 4 0.17
6 19 0.83
ACGTcount: A:0.17, C:0.00, G:0.17, T:0.66
Consensus pattern (6 bp):
TTAGTT
Found at i:2493951 original size:14 final size:15
Alignment explanation
Indices: 2493934--2493966 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
2493924 AAATTAACAT
*
2493934 AAAATAATTTAA-TA
1 AAAATAAATTAATTA
2493948 AAAATAAATTAATTA
1 AAAATAAATTAATTA
2493963 AAAA
1 AAAA
2493967 ATAACTAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 11 0.65
15 6 0.35
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (15 bp):
AAAATAAATTAATTA
Found at i:2493957 original size:15 final size:14
Alignment explanation
Indices: 2493914--2493966 Score: 52
Period size: 15 Copynumber: 3.6 Consensus size: 14
2493904 AATTAAGATA
*
2493914 AATAAATATAAAATT
1 AATAAAAAT-AAATT
* *
2493929 AACATAAAATAATTT
1 AATA-AAAATAAATT
2493944 AATAAAAATAAATT
1 AATAAAAATAAATT
2493958 AATTAAAAA
1 AA-TAAAAA
2493967 ATAACTAAAT
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
14 11 0.35
15 16 0.52
16 4 0.13
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (14 bp):
AATAAAAATAAATT
Found at i:2521666 original size:68 final size:68
Alignment explanation
Indices: 2521587--2521850 Score: 282
Period size: 68 Copynumber: 3.9 Consensus size: 68
2521577 GCATGTTGGT
* * * * ** *
2521587 ATGATGAATGCCATAAGATTATGTATTTGATGTAAATTTTATATACCATATGAGATGATTAAGTA
1 ATGATTAATGCCATGAGAATATGTATATGATGTAAATTCCATATACTATATGAGATGATTAAGTA
2521652 TGC
66 TGC
* * * * *
2521655 ATGATTAATGCCATGAGAATATGTATATGACGTATATTCCATATATTACATGAAATGATTAAGTA
1 ATGATTAATGCCATGAGAATATGTATATGATGTAAATTCCATATACTATATGAGATGATTAAGTA
*
2521720 TGG
66 TGC
* * * * * * *
2521723 ATGATTAATACCATGAGAATATGTATATGTTGTATATTCCATATACTAGATGAGATTATTGAGCA
1 ATGATTAATGCCATGAGAATATGTATATGATGTAAATTCCATATACTATATGAGATGATTAAGTA
*
2521788 AGC
66 TGC
* * * *
2521791 AT-A--AATGCCATGAGATTATGTATATGATGTAAATTTCATATACTTTATGAGATGAGTAAG
1 ATGATTAATGCCATGAGAATATGTATATGATGTAAATTCCATATACTATATGAGATGATTAAG
2521851 CATTTATGTG
Statistics
Matches: 162, Mismatches: 34, Indels: 3
0.81 0.17 0.02
Matches are distributed among these distances:
65 47 0.29
67 1 0.01
68 114 0.70
ACGTcount: A:0.38, C:0.08, G:0.18, T:0.36
Consensus pattern (68 bp):
ATGATTAATGCCATGAGAATATGTATATGATGTAAATTCCATATACTATATGAGATGATTAAGTA
TGC
Found at i:2522025 original size:30 final size:30
Alignment explanation
Indices: 2521982--2522039 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
2521972 GCTCAAGGAT
*
2521982 AATAAGGACATACGTTGCTAGCCCAAGGGC
1 AATAAGGACATACGTTGCCAGCCCAAGGGC
* *
2522012 AATAGGGATATACGTTGCCAGCCCAAGG
1 AATAAGGACATACGTTGCCAGCCCAAGG
2522040 TTGACAGGGA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.33, C:0.22, G:0.28, T:0.17
Consensus pattern (30 bp):
AATAAGGACATACGTTGCCAGCCCAAGGGC
Found at i:2535081 original size:18 final size:18
Alignment explanation
Indices: 2535060--2535094 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
2535050 GGCAACAGTG
2535060 CTGGTGGGTATGCTGGTT
1 CTGGTGGGTATGCTGGTT
*
2535078 CTGGTGGGTATGGTGGT
1 CTGGTGGGTATGCTGGT
2535095 GGCAGCGGCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.06, C:0.09, G:0.49, T:0.37
Consensus pattern (18 bp):
CTGGTGGGTATGCTGGTT
Found at i:2538606 original size:27 final size:27
Alignment explanation
Indices: 2538538--2538738 Score: 129
Period size: 27 Copynumber: 7.5 Consensus size: 27
2538528 ACTTTTAGGA
*
2538538 GCTTTTGTACTTGGAA--CACCCTGGGT
1 GCTTCTGTACTTGGAATGC-CCCTGGGT
* * * *
2538564 GTTTTTGTGCTTGGAATGCCCCTGGAT
1 GCTTCTGTACTTGGAATGCCCCTGGGT
* * * *
2538591 ACTTCTGTACTGGGAATGCCCTTGGGC
1 GCTTCTGTACTTGGAATGCCCCTGGGT
*
2538618 GCTTCTGTACTTGGAACGCCCCTGGGT
1 GCTTCTGTACTTGGAATGCCCCTGGGT
* ** * *
2538645 GCTTCTGCACTTGGAACCCCCCTAGGC
1 GCTTCTGTACTTGGAATGCCCCTGGGT
* * * * *
2538672 GCTTCTGCACTTGAAACT-CCACTAGGC
1 GCTTCTGTACTTGGAA-TGCCCCTGGGT
* * **
2538699 GCTTCTGCACTTGGAACGCCTATGGGT
1 GCTTCTGTACTTGGAATGCCCCTGGGT
**
2538726 ATTTCTGTACTTG
1 GCTTCTGTACTTG
2538739 AAACACCACT
Statistics
Matches: 139, Mismatches: 32, Indels: 7
0.78 0.18 0.04
Matches are distributed among these distances:
26 14 0.10
27 124 0.89
28 1 0.01
ACGTcount: A:0.15, C:0.27, G:0.26, T:0.32
Consensus pattern (27 bp):
GCTTCTGTACTTGGAATGCCCCTGGGT
Found at i:2538677 original size:81 final size:81
Alignment explanation
Indices: 2538592--2538785 Score: 212
Period size: 81 Copynumber: 2.4 Consensus size: 81
2538582 CCCCTGGATA
* * * *
2538592 CTTCTGTACTGGGAA-TGCCCTTGGGCGCTTCTGTACTTGGAACGCCCCTGGGTGCTTCTGCACT
1 CTTCTGTACTAGGAACT-CCCTTGGGCGCTTCTGCACTTGGAACGCCCATGGGTACTTCTGCACT
* * *
2538656 TGGAACCCCCCTAGGCG
65 TGAAACACCACTAGGCG
* * * * * * *
2538673 CTTCTGCACTTGAAACTCCAC-TAGGCGCTTCTGCACTTGGAACGCCTATGGGTATTTCTGTACT
1 CTTCTGTACTAGGAACTCC-CTTGGGCGCTTCTGCACTTGGAACGCCCATGGGTACTTCTGCACT
2538737 TGAAACACCACTAGGCG
65 TGAAACACCACTAGGCG
* *
2538754 CTTCTATACTAGGAACTCCCTTGGGCGTTTCT
1 CTTCTGTACTAGGAACTCCCTTGGGCGCTTCT
2538786 ATAATTAGAA
Statistics
Matches: 91, Mismatches: 19, Indels: 6
0.78 0.16 0.05
Matches are distributed among these distances:
80 1 0.01
81 88 0.97
82 2 0.02
ACGTcount: A:0.17, C:0.30, G:0.24, T:0.29
Consensus pattern (81 bp):
CTTCTGTACTAGGAACTCCCTTGGGCGCTTCTGCACTTGGAACGCCCATGGGTACTTCTGCACTT
GAAACACCACTAGGCG
Found at i:2538763 original size:27 final size:27
Alignment explanation
Indices: 2538615--2538758 Score: 137
Period size: 27 Copynumber: 5.3 Consensus size: 27
2538605 AATGCCCTTG
* * *
2538615 GGCGCTTCTGTACTTGGAACGCCCCTG
1 GGCGCTTCTGCACTTGGAACGCCACTA
* * *
2538642 GGTGCTTCTGCACTTGGAACCCCCCTA
1 GGCGCTTCTGCACTTGGAACGCCACTA
* *
2538669 GGCGCTTCTGCACTTGAAACTCCACTA
1 GGCGCTTCTGCACTTGGAACGCCACTA
*
2538696 GGCGCTTCTGCACTTGGAACGCCTA-TG
1 GGCGCTTCTGCACTTGGAACGCC-ACTA
*** * * *
2538723 GGTATTTCTGTACTTGAAACACCACTA
1 GGCGCTTCTGCACTTGGAACGCCACTA
2538750 GGCGCTTCT
1 GGCGCTTCT
2538759 ATACTAGGAA
Statistics
Matches: 94, Mismatches: 21, Indels: 4
0.79 0.18 0.03
Matches are distributed among these distances:
26 1 0.01
27 92 0.98
28 1 0.01
ACGTcount: A:0.17, C:0.31, G:0.24, T:0.28
Consensus pattern (27 bp):
GGCGCTTCTGCACTTGGAACGCCACTA
Found at i:2538785 original size:54 final size:54
Alignment explanation
Indices: 2538592--2538785 Score: 176
Period size: 54 Copynumber: 3.6 Consensus size: 54
2538582 CCCCTGGATA
* * * * * * *
2538592 CTTCTGTACTGGGAA-TGCCCTTGGGCGCTTCTGTACTTGGAACGCCCCTGGGTG
1 CTTCTGCACTTGGAACT-CCCTTGGGCGCTTCTGTACTTGAAACACCACTAGGCG
* * * * *
2538646 CTTCTGCACTTGGAACCCCCCTAGGCGCTTCTGCACTTGAAACTCCACTAGGCG
1 CTTCTGCACTTGGAACTCCCTTGGGCGCTTCTGTACTTGAAACACCACTAGGCG
* ***
2538700 CTTCTGCACTTGGAAC-GCCTATGGGTATTTCTGTACTTGAAACACCACTAGGCG
1 CTTCTGCACTTGGAACTCCCT-TGGGCGCTTCTGTACTTGAAACACCACTAGGCG
** * *
2538754 CTTCTATACTAGGAACTCCCTTGGGCGTTTCT
1 CTTCTGCACTTGGAACTCCCTTGGGCGCTTCT
2538786 ATAATTAGAA
Statistics
Matches: 112, Mismatches: 25, Indels: 6
0.78 0.17 0.04
Matches are distributed among these distances:
53 2 0.02
54 107 0.96
55 3 0.03
ACGTcount: A:0.17, C:0.30, G:0.24, T:0.29
Consensus pattern (54 bp):
CTTCTGCACTTGGAACTCCCTTGGGCGCTTCTGTACTTGAAACACCACTAGGCG
Found at i:2539011 original size:2 final size:2
Alignment explanation
Indices: 2539004--2539035 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
2538994 AGACAATGCT
2539004 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2539036 AATCCCAAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2541948 original size:33 final size:33
Alignment explanation
Indices: 2541911--2542021 Score: 134
Period size: 33 Copynumber: 3.4 Consensus size: 33
2541901 TTAATGATGG
* *
2541911 TGATGTGGATGCTACTACTAGAGTTGGTGGTGA
1 TGATGTGAATGCTGCTACTAGAGTTGGTGGTGA
* * *
2541944 TGATGTCAATGTTGCTACTAGAGTTGGTGATGA
1 TGATGTGAATGCTGCTACTAGAGTTGGTGGTGA
* * *
2541977 CGATGT-AGGTGTTGCTACTAGAGTTGGTGGTGA
1 TGATGTGA-ATGCTGCTACTAGAGTTGGTGGTGA
2542010 TGATGTGAATGC
1 TGATGTGAATGC
2542022 CATTAACCAA
Statistics
Matches: 65, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
32 1 0.02
33 63 0.97
34 1 0.02
ACGTcount: A:0.22, C:0.09, G:0.35, T:0.34
Consensus pattern (33 bp):
TGATGTGAATGCTGCTACTAGAGTTGGTGGTGA
Found at i:2543247 original size:92 final size:92
Alignment explanation
Indices: 2543101--2543320 Score: 298
Period size: 92 Copynumber: 2.4 Consensus size: 92
2543091 CCTTTTTGTA
* *
2543101 AATAGCAAACTATGGCCAAGAAGTGAGCGATAAAGCTTGCGGCCAACAACATAAAGCCAGATTAT
1 AATAGCAAACTATGGCCAAGAAGTGAGCGATAAAGCCTACGGCCAACAACATAAAGCCAGATTAT
*
2543166 AAGCGTTAAAGCTTGCAGCTTTTAATG
66 AAACGTTAAAGCTTGCAGCTTTTAATG
* * * * * * * *
2543193 GATAGCAAACTATGG-CTAGAAAGTGAGCGGTAAAGCCTACGGCTAATAATATAAAGCTATATTA
1 AATAGCAAACTATGGCCAAG-AAGTGAGCGATAAAGCCTACGGCCAACAACATAAAGCCAGATTA
**
2543257 TAAACGTTAAAGCTTGCAGCTTTTTGTG
65 TAAACGTTAAAGCTTGCAGCTTTTAATG
*
2543285 AATAGCAAACTATGGCCAAGTAGTGAGCGATAAAGC
1 AATAGCAAACTATGGCCAAGAAGTGAGCGATAAAGC
2543321 TTGCAGCCAA
Statistics
Matches: 109, Mismatches: 17, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
91 3 0.03
92 103 0.94
93 3 0.03
ACGTcount: A:0.38, C:0.16, G:0.22, T:0.24
Consensus pattern (92 bp):
AATAGCAAACTATGGCCAAGAAGTGAGCGATAAAGCCTACGGCCAACAACATAAAGCCAGATTAT
AAACGTTAAAGCTTGCAGCTTTTAATG
Found at i:2543469 original size:101 final size:101
Alignment explanation
Indices: 2543261--2543473 Score: 345
Period size: 101 Copynumber: 2.1 Consensus size: 101
2543251 ATATTATAAA
* * *
2543261 CGTTAAAGCTTGCAGCTTTTTGTGAATAGCAAACTATGGCCAAGTAGTGAGCGATAAAGCTTGCA
1 CGTTAAAGCTTGCAACTTTTTGTGAATAGCAAACTATGGCCAAGAAGTGAGCGATAAAGCTTACA
* *
2543326 GCCAATAGCGTAATATTATTACAACTAGATTATGGG
66 ACCAATAGCGTAATATTATTACAACTAGATTATGAG
* *
2543362 CATTAAAGCTTGCAACTTTTTGTGAATAGCAAACTATGGTCAAGAAGTGAGCGATAAAGCTTACA
1 CGTTAAAGCTTGCAACTTTTTGTGAATAGCAAACTATGGCCAAGAAGTGAGCGATAAAGCTTACA
*
2543427 ACCAATAGCGTAATATTATTACAGCTAGATTATGAG
66 ACCAATAGCGTAATATTATTACAACTAGATTATGAG
*
2543463 TGTTAAAGCTT
1 CGTTAAAGCTT
2543474 ACAGTTGAAA
Statistics
Matches: 102, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
101 102 1.00
ACGTcount: A:0.35, C:0.15, G:0.21, T:0.30
Consensus pattern (101 bp):
CGTTAAAGCTTGCAACTTTTTGTGAATAGCAAACTATGGCCAAGAAGTGAGCGATAAAGCTTACA
ACCAATAGCGTAATATTATTACAACTAGATTATGAG
Found at i:2544690 original size:78 final size:78
Alignment explanation
Indices: 2544589--2544757 Score: 207
Period size: 78 Copynumber: 2.2 Consensus size: 78
2544579 GGAGCTTTGT
* *
2544589 TACTTGGAACACCCTGGGCCTTCTGCACTTGGAACACTCTT-GCTGCTTCTGTACTTGGAACACC
1 TACTTGGAACACCCTGGGCCTTCTGCACTTGGAACAC-CTTAGCTGATTCTGTACTTAGAACACC
2544653 T-TGGGCGTTTCTG
65 TATGGGCGTTTCTG
* * * * * * **
2544666 TACTTGGAACACCTTGGGTGCTTCTGTACTTGGAAGACCTTAGGTGATTCTGTGCTTAGAACGGC
1 TACTTGGAACACCCTGGG-CCTTCTGCACTTGGAACACCTTAGCTGATTCTGTACTTAGAACACC
2544731 TATGGGCGTTTCTG
65 TATGGGCGTTTCTG
*
2544745 TACTTGAAACACC
1 TACTTGGAACACC
2544758 ACTAGGCGCT
Statistics
Matches: 78, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
77 20 0.26
78 34 0.44
79 24 0.31
ACGTcount: A:0.18, C:0.24, G:0.25, T:0.33
Consensus pattern (78 bp):
TACTTGGAACACCCTGGGCCTTCTGCACTTGGAACACCTTAGCTGATTCTGTACTTAGAACACCT
ATGGGCGTTTCTG
Found at i:2544711 original size:26 final size:26
Alignment explanation
Indices: 2544549--2544757 Score: 172
Period size: 26 Copynumber: 8.0 Consensus size: 26
2544539 GTAACGCCCT
*** *
2544549 TTGGGTGCTTCTACGCTTGGAACACTT
1 TTGGGTGCTTCTGTACTTGGAACAC-C
*
2544576 TTGGGAGCTT-TGTTACTTGGAACACC
1 TTGGGTGCTTCTG-TACTTGGAACACC
* * *
2544602 CTGGG-CCTTCTGCACTTGGAACACTC
1 TTGGGTGCTTCTGTACTTGGAACAC-C
*
2544628 TT-GCTGCTTCTGTACTTGGAACACC
1 TTGGGTGCTTCTGTACTTGGAACACC
* *
2544653 TTGGGCGTTTCTGTACTTGGAACACC
1 TTGGGTGCTTCTGTACTTGGAACACC
*
2544679 TTGGGTGCTTCTGTACTTGGAAGACC
1 TTGGGTGCTTCTGTACTTGGAACACC
* * * * **
2544705 TTAGGTGATTCTGTGCTTAGAACGGC
1 TTGGGTGCTTCTGTACTTGGAACACC
* * *
2544731 TATGGGCGTTTCTGTACTTGAAACACC
1 T-TGGGTGCTTCTGTACTTGGAACACC
2544758 ACTAGGCGCT
Statistics
Matches: 143, Mismatches: 33, Indels: 12
0.76 0.18 0.06
Matches are distributed among these distances:
25 18 0.13
26 89 0.62
27 36 0.25
ACGTcount: A:0.17, C:0.23, G:0.26, T:0.34
Consensus pattern (26 bp):
TTGGGTGCTTCTGTACTTGGAACACC
Found at i:2544717 original size:52 final size:52
Alignment explanation
Indices: 2544564--2544797 Score: 177
Period size: 52 Copynumber: 4.4 Consensus size: 52
2544554 TGCTTCTACG
* * * * * *
2544564 CTTGGAACACTTTTGGGAGCTT-TGTTACTTGGAACACCCTGGGC-CTTCTGCA
1 CTTGGAACAC-CTTGGGTGCTTCTG-TACTTGGAACACCTTAGGCGATTCTGTA
* * *
2544616 CTTGGAACACTCTT-GCTGCTTCTGTACTTGGAACACCTTGGGCGTTTCTGTA
1 CTTGGAACAC-CTTGGGTGCTTCTGTACTTGGAACACCTTAGGCGATTCTGTA
* * *
2544668 CTTGGAACACCTTGGGTGCTTCTGTACTTGGAAGACCTTAGGTGATTCTGTG
1 CTTGGAACACCTTGGGTGCTTCTGTACTTGGAACACCTTAGGCGATTCTGTA
* ** * * * * * *
2544720 CTTAGAACGGCTATGGGCGTTTCTGTACTTGAAACACCACTAGGCGCTTCTATA
1 CTTGGAACACCT-TGGGTGCTTCTGTACTTGGAACACC-TTAGGCGATTCTGTA
* * *
2544774 CTAGGAACGCTCTTGGGCGCTTCT
1 CTTGGAACAC-CTTGGGTGCTTCT
2544798 ATGATTAGAA
Statistics
Matches: 148, Mismatches: 28, Indels: 10
0.80 0.15 0.05
Matches are distributed among these distances:
51 26 0.18
52 72 0.49
53 21 0.14
54 27 0.18
55 2 0.01
ACGTcount: A:0.18, C:0.24, G:0.25, T:0.33
Consensus pattern (52 bp):
CTTGGAACACCTTGGGTGCTTCTGTACTTGGAACACCTTAGGCGATTCTGTA
Found at i:2564221 original size:73 final size:73
Alignment explanation
Indices: 2564097--2564281 Score: 255
Period size: 73 Copynumber: 2.5 Consensus size: 73
2564087 TAGACAGAAT
** *
2564097 GCTCTTAGTCGACTAACATTACTATTTAGTCGATTAAGTCATCTCTATCTCTGAAC-CTAGTTTT
1 GCTCTTAGTCGACTAACAAAACTTTTTAGTCGATTAAGTCATCTCTATCTCTGAACTC-AGTTTT
*
2564161 TGGTAGTAA
65 TGGCAGTAA
* * * * *
2564170 GCTCTTAGTTGATTAACAAAACTTTTTAGTTGATTAAGTCATTTCTGTCTCTGAACTCAGTTTTT
1 GCTCTTAGTCGACTAACAAAACTTTTTAGTCGATTAAGTCATCTCTATCTCTGAACTCAGTTTTT
2564235 GGCAGTAA
66 GGCAGTAA
* *
2564243 GCTCTTAGTCGACTAACAAAACTTCTTAGTCAATTAAGT
1 GCTCTTAGTCGACTAACAAAACTTTTTAGTCGATTAAGT
2564282 GTTCTCTGTC
Statistics
Matches: 97, Mismatches: 14, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
73 96 0.99
74 1 0.01
ACGTcount: A:0.28, C:0.18, G:0.15, T:0.39
Consensus pattern (73 bp):
GCTCTTAGTCGACTAACAAAACTTTTTAGTCGATTAAGTCATCTCTATCTCTGAACTCAGTTTTT
GGCAGTAA
Found at i:2568203 original size:38 final size:38
Alignment explanation
Indices: 2568107--2568204 Score: 106
Period size: 38 Copynumber: 2.6 Consensus size: 38
2568097 TCATCATGTC
2568107 TTCAATGTATCTTTCTTGACTAATAAAGATGCCCTCCT
1 TTCAATGTATCTTTCTTGACTAATAAAGATGCCCTCCT
**********
2568145 TTCAATNNNNNNNNNNTGACTAATAAAGATGCCCTCCT
1 TTCAATGTATCTTTCTTGACTAATAAAGATGCCCTCCT
2568183 TTCAATGTATCTTTCTTGACTA
1 TTCAATGTATCTTTCTTGACTA
2568205 GTTTTTAGGC
Statistics
Matches: 40, Mismatches: 20, Indels: 0
0.67 0.33 0.00
Matches are distributed among these distances:
38 40 1.00
ACGTcount: A:0.24, C:0.20, G:0.09, T:0.36
Consensus pattern (38 bp):
TTCAATGTATCTTTCTTGACTAATAAAGATGCCCTCCT
Found at i:2577746 original size:71 final size:71
Alignment explanation
Indices: 2577655--2577786 Score: 210
Period size: 71 Copynumber: 1.9 Consensus size: 71
2577645 TCTCTGTTTT
* * **
2577655 TGAACCCAGTTTCTAGCAGTAGGCTCTTAATTGACTAACAAAACTTCTTAGTCGATTAAGTTGTT
1 TGAACCCAATTTCTAACAGTAGGCTCTTAATCAACTAACAAAACTTCTTAGTCGATTAAGTTGTT
2577720 TGTCTC
66 TGTCTC
* *
2577726 TGAACCCAATTTCTAACAGTATGCTCTTAGTCAACTAACAAAACTTCTTAGTCGATTAAGT
1 TGAACCCAATTTCTAACAGTAGGCTCTTAATCAACTAACAAAACTTCTTAGTCGATTAAGT
2577787 GTTCTTTGTC
Statistics
Matches: 55, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
71 55 1.00
ACGTcount: A:0.30, C:0.20, G:0.14, T:0.35
Consensus pattern (71 bp):
TGAACCCAATTTCTAACAGTAGGCTCTTAATCAACTAACAAAACTTCTTAGTCGATTAAGTTGTT
TGTCTC
Found at i:2581885 original size:20 final size:20
Alignment explanation
Indices: 2581848--2581903 Score: 78
Period size: 20 Copynumber: 2.9 Consensus size: 20
2581838 TTAGTGACTT
*
2581848 TTGGGCATTGTG-AAGACAC
1 TTGGACATTGTGAAAGACAC
**
2581867 TTGGATGTTGTGAAAGACAC
1 TTGGACATTGTGAAAGACAC
2581887 TTGGACATTGTGAAAGA
1 TTGGACATTGTGAAAGA
2581904 TACCAATCAT
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
19 9 0.29
20 22 0.71
ACGTcount: A:0.30, C:0.11, G:0.30, T:0.29
Consensus pattern (20 bp):
TTGGACATTGTGAAAGACAC
Found at i:2581957 original size:40 final size:40
Alignment explanation
Indices: 2581921--2582022 Score: 159
Period size: 40 Copynumber: 2.5 Consensus size: 40
2581911 CATGGTGATA
2581921 TTGAAAACCCCACTAAGGTGAATCACCAATATTGGTGAGG
1 TTGAAAACCCCACTAAGGTGAATCACCAATATTGGTGAGG
* * * **
2581961 TTAAAAACCCCACTAAGGTGAATCACTAATCTTGGCAAGG
1 TTGAAAACCCCACTAAGGTGAATCACCAATATTGGTGAGG
2582001 TTGAAAACCCCACTAAGGTGAA
1 TTGAAAACCCCACTAAGGTGAA
2582023 AAATAACCAA
Statistics
Matches: 56, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 56 1.00
ACGTcount: A:0.37, C:0.22, G:0.20, T:0.22
Consensus pattern (40 bp):
TTGAAAACCCCACTAAGGTGAATCACCAATATTGGTGAGG
Found at i:2590371 original size:21 final size:22
Alignment explanation
Indices: 2590342--2590385 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
2590332 AAGTGATTAA
2590342 TTTAAGTTATTTTA-GTTAAAT
1 TTTAAGTTATTTTATGTTAAAT
* *
2590363 TTTAGGTTATTTTATTTTAAAT
1 TTTAAGTTATTTTATGTTAAAT
2590385 T
1 T
2590386 ACTTTAAGAG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 13 0.65
22 7 0.35
ACGTcount: A:0.30, C:0.00, G:0.09, T:0.61
Consensus pattern (22 bp):
TTTAAGTTATTTTATGTTAAAT
Found at i:2591059 original size:12 final size:12
Alignment explanation
Indices: 2591035--2591081 Score: 71
Period size: 12 Copynumber: 4.0 Consensus size: 12
2591025 AGAGATTTTT
2591035 GAGGCAG-AAGA
1 GAGGCAGCAAGA
2591046 GAGGCAGCAAGA
1 GAGGCAGCAAGA
2591058 GAGGCAGCAA-A
1 GAGGCAGCAAGA
2591069 GGAGGCAGCAAGA
1 -GAGGCAGCAAGA
2591082 AACTATTCTG
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
11 8 0.24
12 24 0.73
13 1 0.03
ACGTcount: A:0.43, C:0.15, G:0.43, T:0.00
Consensus pattern (12 bp):
GAGGCAGCAAGA
Found at i:2597637 original size:36 final size:36
Alignment explanation
Indices: 2597592--2597675 Score: 114
Period size: 36 Copynumber: 2.3 Consensus size: 36
2597582 AGTGTCTCGA
* *
2597592 TAAAGGTTACGCTTGATCGTGATAAAAGACATATTG
1 TAAAGGTTACACTTGATCCTGATAAAAGACATATTG
* * * *
2597628 TGAAGGTTACACTTGATCCTGTTAAAAGGCATGTTG
1 TAAAGGTTACACTTGATCCTGATAAAAGACATATTG
2597664 TAAAGGTTACAC
1 TAAAGGTTACAC
2597676 CTAATTCTAT
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
36 41 1.00
ACGTcount: A:0.33, C:0.13, G:0.23, T:0.31
Consensus pattern (36 bp):
TAAAGGTTACACTTGATCCTGATAAAAGACATATTG
Found at i:2598261 original size:26 final size:25
Alignment explanation
Indices: 2598230--2598279 Score: 82
Period size: 26 Copynumber: 2.0 Consensus size: 25
2598220 CCATTCTACA
*
2598230 ACCAACATCAAACAAACACATCAACC
1 ACCAACATAAAACAAACA-ATCAACC
2598256 ACCAACATAAAACAAACAATCAAC
1 ACCAACATAAAACAAACAATCAAC
2598280 ATAAGTGCAC
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 6 0.26
26 17 0.74
ACGTcount: A:0.58, C:0.34, G:0.00, T:0.08
Consensus pattern (25 bp):
ACCAACATAAAACAAACAATCAACC
Found at i:2598359 original size:44 final size:44
Alignment explanation
Indices: 2598309--2598397 Score: 178
Period size: 44 Copynumber: 2.0 Consensus size: 44
2598299 TAGCCAAATG
2598309 ACATCAAACAAGTAGTGCACCAGCTTATAATTTTGAAACAAACA
1 ACATCAAACAAGTAGTGCACCAGCTTATAATTTTGAAACAAACA
2598353 ACATCAAACAAGTAGTGCACCAGCTTATAATTTTGAAACAAACA
1 ACATCAAACAAGTAGTGCACCAGCTTATAATTTTGAAACAAACA
2598397 A
1 A
2598398 ATAGCCAAAT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 45 1.00
ACGTcount: A:0.46, C:0.20, G:0.11, T:0.22
Consensus pattern (44 bp):
ACATCAAACAAGTAGTGCACCAGCTTATAATTTTGAAACAAACA
Found at i:2604837 original size:39 final size:39
Alignment explanation
Indices: 2604751--2604882 Score: 153
Period size: 39 Copynumber: 3.4 Consensus size: 39
2604741 ACATAAGTTA
* * *
2604751 AAGCACAACTTTTAC--AAGTAACTACCTT-TCAAGGATC
1 AAGCACAACCTTTACAAAAGTCACTACCTTCT-TAGGATC
* * *
2604788 AAGCACAACCTTTAGAAAAGTTACTAGCTTCTTAGGATC
1 AAGCACAACCTTTACAAAAGTCACTACCTTCTTAGGATC
* * *
2604827 AGGCATAACCTTTACAAAAGTCACTACCTTTTTAGGATC
1 AAGCACAACCTTTACAAAAGTCACTACCTTCTTAGGATC
2604866 AAGCACAACCTTTACAA
1 AAGCACAACCTTTACAA
2604883 CCAATTTCCT
Statistics
Matches: 79, Mismatches: 13, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
37 13 0.16
39 65 0.82
40 1 0.01
ACGTcount: A:0.37, C:0.23, G:0.12, T:0.27
Consensus pattern (39 bp):
AAGCACAACCTTTACAAAAGTCACTACCTTCTTAGGATC
Found at i:2612974 original size:20 final size:20
Alignment explanation
Indices: 2612941--2612988 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
2612931 ATGTTTCGTA
* *
2612941 ATATAAAATGTTATGAATAT
1 ATATATAATGTTATAAATAT
*
2612961 ATATATAATTTTATAAATAT
1 ATATATAATGTTATAAATAT
2612981 ATTATATA
1 A-TATATA
2612989 TACATATATN
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
20 18 0.75
21 6 0.25
ACGTcount: A:0.50, C:0.00, G:0.04, T:0.46
Consensus pattern (20 bp):
ATATATAATGTTATAAATAT
Found at i:2613481 original size:218 final size:214
Alignment explanation
Indices: 2613017--2613619 Score: 668
Period size: 218 Copynumber: 2.8 Consensus size: 214
2613007 NCATAAATAT
* * * * *
2613017 TACTATAATTTATAATAAACTTTATTTATATGATCACACTAAATAACTTTATTAGTTATCGCCTT
1 TACTATAACTTATAATAAACTTTATTTATATGATTACACTTAATAACTTTATTAGTTATCACTTT
* * *
2613082 AGATTTTATAATACATTATTTATAATTAATTATTATTTATACAAACTTTGATATAAAACATTATG
66 AGATTTTATAACACATTGTTTATAATTAATTATTATTTATACAAACTTTGATATAAAACATTATA
* *
2613147 ACATATAAATTATGTCACTAATTTCATATATATATAATAAAGTCATATATTACATATACATATAT
131 ACATATAAATTATATCACTAATTTCATATATATATAAAAAAGTCATATATTACATATACATATAT
* *
2613212 TTAATTTGTATATAAGCAT
196 TTAATTTATATATAAGCAA
** * * * * *
2613231 TACTATAACTTACGATAGATTTTATTTATATGATTGCATTTAATAATTTTATTAGTTATCACTTT
1 TACTATAACTTATAATAAACTTTATTTATATGATTACACTTAATAACTTTATTAGTTATCACTTT
* * ** * *
2613296 AGATTTTATAACACATTGTTTATAATTAGTTATTGTTTATATGAATTTTGATATAAAACATTTTA
66 AGATTTTATAACACATTGTTTATAATTAATTATTATTTATACAAACTTTGATATAAAACATTATA
* * * * *
2613361 ACATATAATTTGTATCATTAATTTTATACATATTTATATAAAAAAG-CAATATATTATATATACA
131 ACATATAAATTATATCACTAA--TT-T-CATATATATATAAAAAAGTC-ATATATTACATATACA
*
2613425 TATATTTAATTTATATATAAGTAA
191 TATATTTAATTTATATATAAGCAA
* * * * **
2613449 TACTATAACTTATAATAAACTTTATGTATATGATTACACATAATAAGTTTATTAGCTATTTCTTT
1 TACTATAACTTATAATAAACTTTATTTATATGATTACACTTAATAACTTTATTAGTTATCACTTT
* * ********** *
2613514 AGATTTTATAACATATTGCTTNNNNNNNNNNATTATTTATACAAACTTTGATATAAAACATTAGA
66 AGATTTTATAACACATTGTTTATAATTAATTATTATTTATACAAACTTTGATATAAAACATTATA
* * * *
2613579 ACATATAAGTTATATTATTAATTTCATATATATATATAAAA
131 ACATATAAATTATATCACTAATTTCATATATATATAAAAAA
2613620 TTATGAATGA
Statistics
Matches: 318, Mismatches: 66, Indels: 10
0.81 0.17 0.03
Matches are distributed among these distances:
214 141 0.44
215 1 0.00
216 4 0.01
217 2 0.01
218 170 0.53
ACGTcount: A:0.40, C:0.08, G:0.05, T:0.45
Consensus pattern (214 bp):
TACTATAACTTATAATAAACTTTATTTATATGATTACACTTAATAACTTTATTAGTTATCACTTT
AGATTTTATAACACATTGTTTATAATTAATTATTATTTATACAAACTTTGATATAAAACATTATA
ACATATAAATTATATCACTAATTTCATATATATATAAAAAAGTCATATATTACATATACATATAT
TTAATTTATATATAAGCAA
Found at i:2618370 original size:35 final size:35
Alignment explanation
Indices: 2618331--2618397 Score: 125
Period size: 35 Copynumber: 1.9 Consensus size: 35
2618321 TTAAAGTCCT
*
2618331 TTATATACACCTTAAAGTTATGCACGATAAGCCCC
1 TTATATACACCTTAAAGGTATGCACGATAAGCCCC
2618366 TTATATACACCTTAAAGGTATGCACGATAAGC
1 TTATATACACCTTAAAGGTATGCACGATAAGC
2618398 AGAGCATTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 31 1.00
ACGTcount: A:0.36, C:0.22, G:0.13, T:0.28
Consensus pattern (35 bp):
TTATATACACCTTAAAGGTATGCACGATAAGCCCC
Found at i:2634974 original size:23 final size:23
Alignment explanation
Indices: 2634948--2635011 Score: 71
Period size: 23 Copynumber: 2.8 Consensus size: 23
2634938 ATTAATATAT
*
2634948 TTTATTTTAATTTCTTTTTTTTC
1 TTTATTTTAATTTCTTTTTTGTC
*
2634971 TTTATTTTCATTT-TTCCTTTTGTC
1 TTTATTTTAATTTCTT--TTTTGTC
2634995 -TT-TTTTAATTTCTTTTT
1 TTTATTTTAATTTCTTTTT
2635012 ATTAAAATAT
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
21 3 0.09
22 10 0.29
23 16 0.46
24 6 0.17
ACGTcount: A:0.11, C:0.11, G:0.02, T:0.77
Consensus pattern (23 bp):
TTTATTTTAATTTCTTTTTTGTC
Found at i:2639467 original size:16 final size:16
Alignment explanation
Indices: 2639446--2639477 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
2639436 ATAGAATGAC
*
2639446 GATGATGTGCGTCAAA
1 GATGATGTGCATCAAA
2639462 GATGATGTGCATCAAA
1 GATGATGTGCATCAAA
2639478 ATACATCCAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.34, C:0.12, G:0.28, T:0.25
Consensus pattern (16 bp):
GATGATGTGCATCAAA
Found at i:2642690 original size:52 final size:52
Alignment explanation
Indices: 2642626--2642742 Score: 191
Period size: 52 Copynumber: 2.2 Consensus size: 52
2642616 ACTCCCTAGG
* * *
2642626 CAATTCTATCAGTAATTGCTGAAATCTGTCATTGATAGATGAACTTTGTCGA
1 CAATTCTATCAGTAACTGATGAAATCTGTCATTGATAGATGAACTTTGTCAA
2642678 CAATTCTATCAGTAACTGATGAAATCTGTCATTGATAGATGAACTTTGTCAA
1 CAATTCTATCAGTAACTGATGAAATCTGTCATTGATAGATGAACTTTGTCAA
2642730 CAATT-TCATCAGT
1 CAATTCT-ATCAGT
2642743 GTTATAGATA
Statistics
Matches: 61, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
51 1 0.02
52 60 0.98
ACGTcount: A:0.32, C:0.16, G:0.15, T:0.36
Consensus pattern (52 bp):
CAATTCTATCAGTAACTGATGAAATCTGTCATTGATAGATGAACTTTGTCAA
Found at i:2646386 original size:9 final size:9
Alignment explanation
Indices: 2646372--2646412 Score: 57
Period size: 9 Copynumber: 4.7 Consensus size: 9
2646362 AACTATGAAT
2646372 AAAAAATGA
1 AAAAAATGA
2646381 AAAAAATG-
1 AAAAAATGA
*
2646389 AAAAAATGG
1 AAAAAATGA
*
2646398 GAAAAATGA
1 AAAAAATGA
2646407 AAAAAA
1 AAAAAA
2646413 ATAAACTCAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
8 8 0.29
9 20 0.71
ACGTcount: A:0.76, C:0.00, G:0.15, T:0.10
Consensus pattern (9 bp):
AAAAAATGA
Found at i:2646394 original size:17 final size:17
Alignment explanation
Indices: 2646372--2646411 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
2646362 AACTATGAAT
2646372 AAAAAATGAAAAAAATG
1 AAAAAATGAAAAAAATG
**
2646389 AAAAAATGGGAAAAATG
1 AAAAAATGAAAAAAATG
2646406 AAAAAA
1 AAAAAA
2646412 AATAAACTCA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.75, C:0.00, G:0.15, T:0.10
Consensus pattern (17 bp):
AAAAAATGAAAAAAATG
Found at i:2650795 original size:251 final size:251
Alignment explanation
Indices: 2650511--2650967 Score: 707
Period size: 251 Copynumber: 1.8 Consensus size: 251
2650501 GCCAAATTAA
* * *
2650511 TTAATTTAAAAATTTTTTAAATTAAATAATATTACTAATTTTGTTACTTGCTTAATTACTAAAAG
1 TTAATTTAAAAATTTTTAAAATTAAATAATATTACTAATTTTGTTAATTGCTTAATTACTAAAAA
* * * * * **
2650576 ATTTTATTCATTTGGTTAGTTAAATTATTTAATTATTTATGTATATATGTTAATTCATTTAAATA
66 ACTTTATTCATTTCGTTAGTCAAATTATTTAATTATTTATGTAAAAACCTTAATTCATTTAAATA
* * * * *
2650641 ATTTTTAATTATCTTCAATTAATTATTTTAGTTATTTGATTAATGACTAATACTTATAATTAATA
131 ATCTTTAATTATCTTCAATTAACTAATTTAGTTATATGATTAATAACTAATACTTATAATTAATA
*
2650706 CATTGCATTACTTAATTAGCTTAGTCATTGAACCATGTTATTAACACCTTAAGTCG
196 CATTACATTACTTAATTAGCTTAGTCATTGAACCATGTTATTAACACCTTAAGTCG
* * *
2650762 TTAATTTAAATATTTTTAAAATTCAATAATATTAGTAATTTTGTTAATTGCTTAATTACTAAAAA
1 TTAATTTAAAAATTTTTAAAATTAAATAATATTACTAATTTTGTTAATTGCTTAATTACTAAAAA
* * *
2650827 ACTTTATTTATTTCGTTTGTCAAATTATTTAATTATTTATGTAAAAACCTTAATTTATTTAAATA
66 ACTTTATTCATTTCGTTAGTCAAATTATTTAATTATTTATGTAAAAACCTTAATTCATTTAAATA
*
2650892 ATCTTTGATTATCTTCAATTAACTAATTTAGTTATATGATTAATAACTAATACTTATAATTAATA
131 ATCTTTAATTATCTTCAATTAACTAATTTAGTTATATGATTAATAACTAATACTTATAATTAATA
2650957 CATTACATTAC
196 CATTACATTAC
2650968 ATTATTTGTT
Statistics
Matches: 183, Mismatches: 23, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
251 183 1.00
ACGTcount: A:0.37, C:0.08, G:0.06, T:0.48
Consensus pattern (251 bp):
TTAATTTAAAAATTTTTAAAATTAAATAATATTACTAATTTTGTTAATTGCTTAATTACTAAAAA
ACTTTATTCATTTCGTTAGTCAAATTATTTAATTATTTATGTAAAAACCTTAATTCATTTAAATA
ATCTTTAATTATCTTCAATTAACTAATTTAGTTATATGATTAATAACTAATACTTATAATTAATA
CATTACATTACTTAATTAGCTTAGTCATTGAACCATGTTATTAACACCTTAAGTCG
Found at i:2651467 original size:24 final size:24
Alignment explanation
Indices: 2651407--2651459 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
2651397 CTAAATCCAC
* *
2651407 AACAACCAAAACCTCAAATATTCA
1 AACAACAAAAACCTCAAATATACA
* *
2651431 AACAACAAAAACCTTAATTATACA
1 AACAACAAAAACCTCAAATATACA
2651455 AACAA
1 AACAA
2651460 TTAAAACCAC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.58, C:0.25, G:0.00, T:0.17
Consensus pattern (24 bp):
AACAACAAAAACCTCAAATATACA
Found at i:2651705 original size:19 final size:18
Alignment explanation
Indices: 2651680--2651733 Score: 54
Period size: 19 Copynumber: 2.9 Consensus size: 18
2651670 CAAGTAGGGT
2651680 GAAGAGAGAGAAAAGAAA
1 GAAGAGAGAGAAAAGAAA
* * *
2651698 GCAAGAGAGTGAAGAGAGA
1 G-AAGAGAGAGAAAAGAAA
*
2651717 GAAGAAGGGAGAAAAGA
1 GAAG-AGAGAGAAAAGA
2651734 GTAAATGGAG
Statistics
Matches: 28, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
18 4 0.14
19 24 0.86
ACGTcount: A:0.57, C:0.02, G:0.39, T:0.02
Consensus pattern (18 bp):
GAAGAGAGAGAAAAGAAA
Found at i:2654673 original size:16 final size:16
Alignment explanation
Indices: 2654649--2654699 Score: 84
Period size: 16 Copynumber: 3.2 Consensus size: 16
2654639 TAAAAATATA
* *
2654649 AAAAAAATCCAAATCT
1 AAAACAATCAAAATCT
2654665 AAAACAATCAAAATCT
1 AAAACAATCAAAATCT
2654681 AAAACAATCAAAATCT
1 AAAACAATCAAAATCT
2654697 AAA
1 AAA
2654700 TTTTGGTTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 33 1.00
ACGTcount: A:0.65, C:0.18, G:0.00, T:0.18
Consensus pattern (16 bp):
AAAACAATCAAAATCT
Found at i:2656262 original size:2 final size:2
Alignment explanation
Indices: 2656255--2656283 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2656245 CTATCAAGAC
2656255 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
2656284 AGGTGACATC
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:2657667 original size:83 final size:83
Alignment explanation
Indices: 2657549--2657768 Score: 244
Period size: 83 Copynumber: 2.7 Consensus size: 83
2657539 AATCACAACA
* * * * *
2657549 AAATCGTGTGAAGTGGAGACCTACTCAATCAACTTTACAACAAAAATATGGTAAATGGACACCTA
1 AAATCATGAGAAGTGGAGACATACTCAATCCACTTTACAACAAAAATATGGGAAATGGACACCTA
* *
2657614 CTTAATCTATTTTACCAC
66 CTTAATCCACTTTACCAC
* * * * * * * *
2657632 AAATCATGGGAAGTGGGGACATACTCAATCCACTTTATAACAAAATTATGGGAAGTGGAGACTTG
1 AAATCATGAGAAGTGGAGACATACTCAATCCACTTTACAACAAAAATATGGGAAATGGACACCTA
* *
2657697 TTTAATCCACTTTACCAT
66 CTTAATCCACTTTACCAC
* * *
2657715 AAATCATGAGAAATGGAGACATACTCAATCCGCTTTTCAAC-AAAATCATGGGAA
1 AAATCATGAGAAGTGGAGACATACTCAATCCACTTTACAACAAAAAT-ATGGGAA
2657769 TACGGAGAAC
Statistics
Matches: 113, Mismatches: 23, Indels: 2
0.82 0.17 0.01
Matches are distributed among these distances:
82 4 0.04
83 109 0.96
ACGTcount: A:0.38, C:0.19, G:0.16, T:0.27
Consensus pattern (83 bp):
AAATCATGAGAAGTGGAGACATACTCAATCCACTTTACAACAAAAATATGGGAAATGGACACCTA
CTTAATCCACTTTACCAC
Found at i:2657675 original size:41 final size:42
Alignment explanation
Indices: 2657545--2657768 Score: 172
Period size: 42 Copynumber: 5.4 Consensus size: 42
2657535 AGCCAATCAC
* * * * *
2657545 AACAAAATCGTGTGAAGTGGAGACCTACTCAATCAACTTTAC
1 AACAAAATCATGGGAAGTGGAGACATACTCAATCCACTTTAT
* * * * * *
2657587 AACAAAAAT-ATGGTAAATGGACACCTACTTAATCTA-TTT-T
1 AAC-AAAATCATGGGAAGTGGAGACATACTCAATCCACTTTAT
* *
2657627 ACCACAAATCATGGGAAGTGGGGACATACTCAATCCACTTTAT
1 AACA-AAATCATGGGAAGTGGAGACATACTCAATCCACTTTAT
* * ** *
2657670 AACAAAATTATGGGAAGTGGAGACTTGTTTAATCCAC-TT-T
1 AACAAAATCATGGGAAGTGGAGACATACTCAATCCACTTTAT
* * * *
2657710 ACCATAAATCATGAGAAATGGAGACATACTCAATCCGCTTT-T
1 AACA-AAATCATGGGAAGTGGAGACATACTCAATCCACTTTAT
2657752 CAACAAAATCATGGGAA
1 -AACAAAATCATGGGAA
2657769 TACGGAGAAC
Statistics
Matches: 140, Mismatches: 34, Indels: 16
0.74 0.18 0.08
Matches are distributed among these distances:
39 1 0.01
40 10 0.07
41 50 0.36
42 67 0.48
43 12 0.09
ACGTcount: A:0.39, C:0.19, G:0.16, T:0.26
Consensus pattern (42 bp):
AACAAAATCATGGGAAGTGGAGACATACTCAATCCACTTTAT
Found at i:2658610 original size:106 final size:105
Alignment explanation
Indices: 2658422--2658633 Score: 300
Period size: 106 Copynumber: 2.0 Consensus size: 105
2658412 NNNNNNNGCT
* * * **
2658422 ATAGCAAGTGAGAAAATCCACCTAAATCCTCTAGTTCGCTGACATCAATAATTCTAGAACAATAA
1 ATAGCAAGTGAGAAAATCCACCCAAATCCTCTAATTCACAAACATCAATAATTCTAGAACAATAA
* * *
2658487 ACCATATTTTCATAATAAAAAATCCAAGGTTTAAAGATTC
66 ACCACATTTTCAGAATAAAAAAGCCAAGGTTTAAAGATTC
2658527 ATAGCAAGTGAGAAAATCCACCCCAAATCCTCTAATTCACAAACATCAATAATT-TAGGAACAAT
1 ATAGCAAGTGAGAAAATCCA-CCCAAATCCTCTAATTCACAAACATCAATAATTCTA-GAACAAT
** *
2658591 AAACCACATTTTCAGAATAAGCAGGCCAAGGTTTAAAGATTC
64 AAACCACATTTTCAGAATAAAAAAGCCAAGGTTTAAAGATTC
2658633 A
1 A
2658634 ATAGTGGAAA
Statistics
Matches: 94, Mismatches: 11, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
105 22 0.23
106 72 0.77
ACGTcount: A:0.43, C:0.20, G:0.11, T:0.25
Consensus pattern (105 bp):
ATAGCAAGTGAGAAAATCCACCCAAATCCTCTAATTCACAAACATCAATAATTCTAGAACAATAA
ACCACATTTTCAGAATAAAAAAGCCAAGGTTTAAAGATTC
Found at i:2667149 original size:27 final size:27
Alignment explanation
Indices: 2667091--2667150 Score: 66
Period size: 27 Copynumber: 2.2 Consensus size: 27
2667081 CCCAAAGTTG
* * *
2667091 CCTAAAGTTGCTAAAGTCCTAAGATTG
1 CCTAAAGTTGCTAAAGTCCCAAGACTA
* * *
2667118 GCTAAAGTTGTTAGAGTCCCAAGACTA
1 CCTAAAGTTGCTAAAGTCCCAAGACTA
2667145 CCTAAA
1 CCTAAA
2667151 AGAGTGTTTT
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.35, C:0.20, G:0.18, T:0.27
Consensus pattern (27 bp):
CCTAAAGTTGCTAAAGTCCCAAGACTA
Found at i:2672004 original size:18 final size:19
Alignment explanation
Indices: 2671965--2672010 Score: 51
Period size: 18 Copynumber: 2.5 Consensus size: 19
2671955 ATAATTAATT
*
2671965 AAAACTAAATTTAATC-AA
1 AAAACTAAATCTAATCAAA
*
2671983 AAAACTAAA-CTAATTAACA
1 AAAACTAAATCTAATCAA-A
2672002 AAAACTAAA
1 AAAACTAAA
2672011 AATCCTTTAG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 4 0.17
18 10 0.42
19 10 0.42
ACGTcount: A:0.65, C:0.13, G:0.00, T:0.22
Consensus pattern (19 bp):
AAAACTAAATCTAATCAAA
Found at i:2678967 original size:21 final size:21
Alignment explanation
Indices: 2678943--2678982 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
2678933 TAAACTAATT
*
2678943 TAAAGTAAAATAACATAAAAA
1 TAAACTAAAATAACATAAAAA
* *
2678964 TAAACTAAGATAACTTAAA
1 TAAACTAAAATAACATAAA
2678983 CTAACTAAAC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.65, C:0.07, G:0.05, T:0.23
Consensus pattern (21 bp):
TAAACTAAAATAACATAAAAA
Found at i:2680023 original size:35 final size:35
Alignment explanation
Indices: 2679976--2680070 Score: 163
Period size: 35 Copynumber: 2.7 Consensus size: 35
2679966 ATCATTGTTG
2679976 GTTATACCTTAACCATTTAAAAGGTAGTTAAATTA
1 GTTATACCTTAACCATTTAAAAGGTAGTTAAATTA
*
2680011 GTTATACTTTAACCATTTAAAAGGTAGTTAAATTA
1 GTTATACCTTAACCATTTAAAAGGTAGTTAAATTA
**
2680046 GTTATACCTTAACCATAGAAAAGGT
1 GTTATACCTTAACCATTTAAAAGGT
2680071 GGAAGGGTTA
Statistics
Matches: 56, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
35 56 1.00
ACGTcount: A:0.40, C:0.12, G:0.13, T:0.36
Consensus pattern (35 bp):
GTTATACCTTAACCATTTAAAAGGTAGTTAAATTA
Found at i:2682890 original size:28 final size:28
Alignment explanation
Indices: 2682838--2683001 Score: 197
Period size: 28 Copynumber: 5.6 Consensus size: 28
2682828 TCTTGTTTGT
2682838 AATTAAGACAAAAATAT-TTTATCTTGTCTA
1 AATTAAGAC--AAATATGTTT-TCTTGTCTA
*
2682868 AATTGAGACAAATATGTTTTCTTGTCTA
1 AATTAAGACAAATATGTTTTCTTGTCTA
2682896 AATTAAGACCAAAAATAT-TTTTCTTGTCTTA
1 AATTAAGA-C--AAATATGTTTTCTTGTC-TA
* * *
2682927 AATTAAGACAAACATATTTTCTTATCTA
1 AATTAAGACAAATATGTTTTCTTGTCTA
2682955 AATTAAGACCAAATATGTTTTCTTGTCTA
1 AATTAAGA-CAAATATGTTTTCTTGTCTA
*
2682984 AATTAAGACAAACATGTT
1 AATTAAGACAAATATGTT
2683002 AAAGCTACCA
Statistics
Matches: 119, Mismatches: 8, Indels: 16
0.83 0.06 0.11
Matches are distributed among these distances:
28 46 0.39
29 38 0.32
30 19 0.16
31 16 0.13
ACGTcount: A:0.40, C:0.12, G:0.09, T:0.40
Consensus pattern (28 bp):
AATTAAGACAAATATGTTTTCTTGTCTA
Found at i:2682909 original size:59 final size:58
Alignment explanation
Indices: 2682838--2683001 Score: 244
Period size: 59 Copynumber: 2.8 Consensus size: 58
2682828 TCTTGTTTGT
* * *
2682838 AATTAAGA-CAAAAATATTTTATCTTGTCTAAATTGAGACAAATATGTTTTCTTGTCTA
1 AATTAAGACCAAAAATATTTT-TCTTGTCTAAATTAAGACAAACATGTTTTCTTATCTA
*
2682896 AATTAAGACCAAAAATATTTTTCTTGTCTTAAATTAAGACAAACATATTTTCTTATCTA
1 AATTAAGACCAAAAATATTTTTCTTGTC-TAAATTAAGACAAACATGTTTTCTTATCTA
2682955 AATTAAGACC--AAATATGTTTTCTTGTCTAAATTAAGACAAACATGTT
1 AATTAAGACCAAAAATAT-TTTTCTTGTCTAAATTAAGACAAACATGTT
2683002 AAAGCTACCA
Statistics
Matches: 98, Mismatches: 5, Indels: 7
0.89 0.05 0.06
Matches are distributed among these distances:
57 25 0.26
58 25 0.26
59 48 0.49
ACGTcount: A:0.40, C:0.12, G:0.09, T:0.40
Consensus pattern (58 bp):
AATTAAGACCAAAAATATTTTTCTTGTCTAAATTAAGACAAACATGTTTTCTTATCTA
Found at i:2682967 original size:29 final size:28
Alignment explanation
Indices: 2682838--2682995 Score: 199
Period size: 29 Copynumber: 5.4 Consensus size: 28
2682828 TCTTGTTTGT
2682838 AATTAAGACAAAAATATTTTATCTTGTCTA
1 AATTAAGACAAAAATA-TTT-TCTTGTCTA
* * *
2682868 AATTGAGACAAATATGTTTTCTTGTCTA
1 AATTAAGACAAAAATATTTTCTTGTCTA
2682896 AATTAAGACCAAAAATATTTTTCTTGTCTTA
1 AATTAAGA-CAAAAATA-TTTTCTTGTC-TA
* *
2682927 AATTAAGACAAACATATTTTCTTATCTA
1 AATTAAGACAAAAATATTTTCTTGTCTA
* *
2682955 AATTAAGACCAAATATGTTTTCTTGTCTA
1 AATTAAGA-CAAAAATATTTTCTTGTCTA
2682984 AATTAAGACAAA
1 AATTAAGACAAA
2682996 CATGTTAAAG
Statistics
Matches: 113, Mismatches: 11, Indels: 10
0.84 0.08 0.07
Matches are distributed among these distances:
28 30 0.27
29 43 0.38
30 30 0.27
31 10 0.09
ACGTcount: A:0.41, C:0.12, G:0.08, T:0.39
Consensus pattern (28 bp):
AATTAAGACAAAAATATTTTCTTGTCTA
Found at i:2686988 original size:29 final size:30
Alignment explanation
Indices: 2686953--2687022 Score: 97
Period size: 29 Copynumber: 2.4 Consensus size: 30
2686943 AATTCTTATC
* *
2686953 AAATTTTTATATTTTTATTTT-AATTAAAT
1 AAATTTTTATAGTTTTATTTTGAATCAAAT
* *
2686982 AATTTTTTTTAGTTTTATTTTGAATCAAAT
1 AAATTTTTATAGTTTTATTTTGAATCAAAT
2687012 AAATTTTTATA
1 AAATTTTTATA
2687023 ACTAATGGTT
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
29 18 0.53
30 16 0.47
ACGTcount: A:0.36, C:0.01, G:0.03, T:0.60
Consensus pattern (30 bp):
AAATTTTTATAGTTTTATTTTGAATCAAAT
Found at i:2700503 original size:25 final size:24
Alignment explanation
Indices: 2700475--2700537 Score: 74
Period size: 24 Copynumber: 2.6 Consensus size: 24
2700465 ATATCATTAT
*
2700475 CAACCAAGAA-TATTCAAAATAATAC
1 CAACCAA-AAGTATTC-AAATAACAC
*
2700500 CAACTAAAAGTATTCAAATAACAC
1 CAACCAAAAGTATTCAAATAACAC
*
2700524 CAACTAAAAGTATT
1 CAACCAAAAGTATT
2700538 TTTCCAACAA
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
24 24 0.69
25 11 0.31
ACGTcount: A:0.54, C:0.19, G:0.05, T:0.22
Consensus pattern (24 bp):
CAACCAAAAGTATTCAAATAACAC
Found at i:2700525 original size:24 final size:25
Alignment explanation
Indices: 2700485--2700537 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 25
2700475 CAACCAAGAA
*
2700485 TATTCAAAATAATACCAACTAAAAG
1 TATTCAAAATAACACCAACTAAAAG
2700510 TATTC-AAATAACACCAACTAAAAG
1 TATTCAAAATAACACCAACTAAAAG
2700534 TATT
1 TATT
2700538 TTTCCAACAA
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
24 22 0.81
25 5 0.19
ACGTcount: A:0.53, C:0.17, G:0.04, T:0.26
Consensus pattern (25 bp):
TATTCAAAATAACACCAACTAAAAG
Found at i:2700636 original size:26 final size:27
Alignment explanation
Indices: 2700600--2700652 Score: 90
Period size: 26 Copynumber: 2.0 Consensus size: 27
2700590 AAATGCAAGT
*
2700600 AAGATTCTCAACCAAGC-TTTCAAACC
1 AAGATCCTCAACCAAGCTTTTCAAACC
2700626 AAGATCCTCAACCAAGCTTTTCAAACC
1 AAGATCCTCAACCAAGCTTTTCAAACC
2700653 TTAGCTTCAA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
26 16 0.64
27 9 0.36
ACGTcount: A:0.38, C:0.32, G:0.08, T:0.23
Consensus pattern (27 bp):
AAGATCCTCAACCAAGCTTTTCAAACC
Found at i:2706856 original size:2 final size:2
Alignment explanation
Indices: 2706849--2706881 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
2706839 CCAATTAGAA
2706849 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
2706882 ATTGATCGAG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2710787 original size:31 final size:31
Alignment explanation
Indices: 2710749--2710807 Score: 118
Period size: 31 Copynumber: 1.9 Consensus size: 31
2710739 GCTTCAAGGG
2710749 TCTTAACGACTTAATCTTGATCACGAATGCT
1 TCTTAACGACTTAATCTTGATCACGAATGCT
2710780 TCTTAACGACTTAATCTTGATCACGAAT
1 TCTTAACGACTTAATCTTGATCACGAAT
2710808 ACTTGATCTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.31, C:0.22, G:0.12, T:0.36
Consensus pattern (31 bp):
TCTTAACGACTTAATCTTGATCACGAATGCT
Found at i:2710812 original size:80 final size:80
Alignment explanation
Indices: 2710707--2710856 Score: 255
Period size: 80 Copynumber: 1.9 Consensus size: 80
2710697 GAGTCTTCAT
* *
2710707 GACTTAATCTTGATCATAAACACTTGATCTTTGCTTCAAGGGTCTTAACGACTTAATCTTGATCA
1 GACTTAATCTTGATCACAAACACTTGATCTTCGCTTCAAGGGTCTTAACGACTTAATCTTGATCA
2710772 CGAATGCTTCTTAAC
66 CGAATGCTTCTTAAC
* * *
2710787 GACTTAATCTTGATCACGAATACTTGATCTTCGCTTCAAGGGTCTTCACGACTTAATCTTGATCA
1 GACTTAATCTTGATCACAAACACTTGATCTTCGCTTCAAGGGTCTTAACGACTTAATCTTGATCA
2710852 CGAAT
66 CGAAT
2710857 ACTTGATCAC
Statistics
Matches: 65, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
80 65 1.00
ACGTcount: A:0.28, C:0.22, G:0.15, T:0.35
Consensus pattern (80 bp):
GACTTAATCTTGATCACAAACACTTGATCTTCGCTTCAAGGGTCTTAACGACTTAATCTTGATCA
CGAATGCTTCTTAAC
Found at i:2710861 original size:14 final size:14
Alignment explanation
Indices: 2710844--2710878 Score: 70
Period size: 14 Copynumber: 2.5 Consensus size: 14
2710834 ACGACTTAAT
2710844 CTTGATCACGAATA
1 CTTGATCACGAATA
2710858 CTTGATCACGAATA
1 CTTGATCACGAATA
2710872 CTTGATC
1 CTTGATC
2710879 TTCGCTTCAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.31, C:0.23, G:0.14, T:0.31
Consensus pattern (14 bp):
CTTGATCACGAATA
Found at i:2710865 original size:63 final size:63
Alignment explanation
Indices: 2710795--2710926 Score: 237
Period size: 63 Copynumber: 2.1 Consensus size: 63
2710785 ACGACTTAAT
* *
2710795 CTTGATCACGAATACTTGATCTTCGCTTCAAGGGTCTTCACGACTTAATCTTGATCACGAATA
1 CTTGATCACGAATACTTGATCTTCGCTTCAAGGGTCATCACGACTTAATCTTGATCACGAACA
*
2710858 CTTGATCACGAATACTTGATCTTCGCTTCAAGGGTCATCACGACTTAATCTTGATCATGAACA
1 CTTGATCACGAATACTTGATCTTCGCTTCAAGGGTCATCACGACTTAATCTTGATCACGAACA
2710921 CTTGAT
1 CTTGAT
2710927 TTTCGCTTCA
Statistics
Matches: 66, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
63 66 1.00
ACGTcount: A:0.27, C:0.23, G:0.16, T:0.33
Consensus pattern (63 bp):
CTTGATCACGAATACTTGATCTTCGCTTCAAGGGTCATCACGACTTAATCTTGATCACGAACA
Found at i:2710911 original size:49 final size:49
Alignment explanation
Indices: 2710858--2710975 Score: 184
Period size: 49 Copynumber: 2.4 Consensus size: 49
2710848 ATCACGAATA
2710858 CTTGATCACGAATACTTGATCTTCGCTTCAAGGGTCA-TCACGACTTAAT
1 CTTGATCACGAATACTTGATCTTCGCTTCAAGGGT-ATTCACGACTTAAT
* * * *
2710907 CTTGATCATGAACACTTGATTTTCGCTTCAAGGGTATTCATGACTTAAT
1 CTTGATCACGAATACTTGATCTTCGCTTCAAGGGTATTCACGACTTAAT
2710956 CTTGATCACGAATACTTGAT
1 CTTGATCACGAATACTTGAT
2710976 ATCTTAATCA
Statistics
Matches: 62, Mismatches: 6, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
48 1 0.02
49 61 0.98
ACGTcount: A:0.27, C:0.21, G:0.16, T:0.36
Consensus pattern (49 bp):
CTTGATCACGAATACTTGATCTTCGCTTCAAGGGTATTCACGACTTAAT
Found at i:2711047 original size:26 final size:26
Alignment explanation
Indices: 2710997--2711049 Score: 88
Period size: 26 Copynumber: 2.0 Consensus size: 26
2710987 AAACTTCGTT
*
2710997 GTCGCTTGATCACGAACTTCGCCGCC
1 GTCGCTTGATCACGAACTTCACCGCC
*
2711023 GTCGCTTGATCACGAACTTTACCGCC
1 GTCGCTTGATCACGAACTTCACCGCC
2711049 G
1 G
2711050 CTTATCTTCA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.17, C:0.36, G:0.23, T:0.25
Consensus pattern (26 bp):
GTCGCTTGATCACGAACTTCACCGCC
Found at i:2713294 original size:246 final size:247
Alignment explanation
Indices: 2712618--2714147 Score: 1394
Period size: 249 Copynumber: 6.1 Consensus size: 247
2712608 ACATCAATGC
* *
2712618 TTTTT-AATGACAATTTTTAACAATAATTATTTTTATCCTTATTATTATTTATTTTTAAATTAAG
1 TTTTTCAATGACAA-CTTTAACAATAATTATTTTTATCCTTATTATTATATATTTTTAAATTAA-
* * ** * *
2712682 GA-TTGTAAA-TAGTTAAATCCTTTTAGCCTGAGAATGCAAATTCAAATGTTTTTTTTTTCATTA
64 AATTTGTAAATTA-TTAAATACTTTTAGCC-GAGAATATAAATTTAAA---TATTTTTTTCATTA
* * * ** *
2712745 AAGTTAGATTTTTATGATTTAATTGACCTGTTATATTAACTCTCACATATTTATGTTAAAATTTT
124 AAATTAGATTTTTGTGACTTAATTGACCTGTTACGTTAACTCTCACATATTTATGTTAAGA-TTT
* * ** * *
2712810 AAATATGATTGTTTCACTTTTACGAGAGTTTATATCAATTCTTATAACTTTACGTCAAGG
188 AAATATGCTTGTTTCACTTTTATGAGTTTTTATATTAATTCTTATAGCTTTACGTCAAGG
* * * * * *
2712870 CTTTTCAATAACAACTTTTAACAATAGTGATTTTTATTCTTATTATTA-ATTATTTTAAAATTAA
1 TTTTTCAATGACAAC-TTTAACAATAATTATTTTTATCCTTATTATTATA-TATTTTTAAATTAA
* * * * * *
2712934 ATTTTGTAAATTGTGAAATATTTTTAACCCGAGAATATAAATTTAAAT-GTTTTTTCATTAAAAT
64 AATTTGTAAATTATTAAATACTTTT-AGCCGAGAATATAAATTTAAATATTTTTTTCATTAAAAT
* * * * *
2712998 TAGATTTTTGTGACGTAATTGACCTATTACATTAACCCTCACATATTTATGTTAAGA-TTAGATA
128 TAGATTTTTGTGACTTAATTGACCTGTTACGTTAACTCTCACATATTTATGTTAAGATTTAAATA
* * * * * *
2713062 TGCTTGTTTAACTTTTATGAGATTTTATATTAATTTTTACAGTTTTACGTTAAGG
193 TGCTTGTTTCACTTTTATGAGTTTTTATATTAATTCTTATAGCTTTACGTCAAGG
* * *
2713117 TTTTTCAATGTCAAC-TTAACTATAATTATTTTTATCTTTATTATTATATATTTTTAAATTAAAA
1 TTTTTCAATGACAACTTTAACAATAATTATTTTTATCCTTATTATTATATATTTTTAAATTAAAA
* * * *
2713181 TTTATAAATTGTTAAACACTTTTAGCCGGAGAGTATAAATTTAAATATTTTTTTCATTAAAATTA
66 TTTGTAAATTATTAAATACTTTTAGCC-GAGAATATAAATTTAAATATTTTTTTCATTAAAATTA
* * * * *
2713246 GATTTTTGTAACTTAATTGACCTGTTATGTTAAGTATCACACATTTATGTTAAGA-TTAAATATG
130 GATTTTTGTGACTTAATTGACCTGTTACGTTAACTCTCACATATTTATGTTAAGATTTAAATATG
* *
2713310 CTTGTTTCACTTTTATGAGTTTTTACATTAATTCTTACAGCTTTACGTCAAGG
195 CTTGTTTCACTTTTATGAGTTTTTATATTAATTCTTATAGCTTTACGTCAAGG
* * *
2713363 CTTTTCAATGTA-AACTTTTAACTATAATTA-TTTTATCCTTATTATTATTTA-TTTTAAATTAA
1 TTTTTCAATG-ACAAC-TTTAACAATAATTATTTTTATCCTTATTATTATATATTTTTAAATTAA
* * * * *
2713425 AATTTGTAAATCATTAAATACTTATGGCCAGAGAATATAAATTTAAATGTTTATTTTTTATTAAA
64 AATTTGTAAATTATTAAATACTTTTAGCC-GAGAATATAAATTTAAAT-ATT-TTTTTCATTAAA
* * *
2713490 ATTAGATTTTTTGTGACTTAATTAACTTGTTACGTTAACTCTTACATATTTACT-TTAAGATTTT
126 ATTAGA-TTTTTGTGACTTAATTGACCTGTTACGTTAACTCTCACATATTTA-TGTTAAGA-TTT
* * * * * * * *
2713554 AAATATACTCGTTCCAAC-TTTCTGA-TTTTTTTTTTCAATTTTTATAGCTTAACGTCAAGG
188 AAATATGCTTGTTTC-ACTTTTATGAGTTTTTATATT-AATTCTTATAGCTTTACGTCAAGG
* * * * *
2713614 TCTTTCAATGACAACTTTTAACAATAATTATTTTAATCTTTATTGTTATTTATTTTTAAATTAAA
1 TTTTTCAATGACAAC-TTTAACAATAATTATTTTTATCCTTATTATTATATATTTTTAAATTAAA
* * * * *
2713679 ATTTATAAATTATTAAATAATTTTGGCCTAGAATATAAATTTAAAAATTTATTTTCATTAAAATT
65 ATTTGTAAATTATTAAATACTTTTAGCCGAGAATATAAATTTAAATATTT-TTTTCATTAAAATT
* * * * * * * *
2713744 AGAGTTTTGTGACTTAATTGGCGTGTTACGTTAACTCTTATACATTCATCTT-AGAATTTTAAAT
129 AGATTTTTGTGACTTAATTGACCTGTTACGTTAACTCTCACATATTTATGTTAAG-A-TTTAAAT
* * ** * * * * * *
2713808 ATGCTGGTTCCACCCTAATGAGTTTTTATGTCAATTCTTATAACTTTACATCAAAG
192 ATGCTTGTTTCACTTTTATGAGTTTTTATATTAATTCTTATAGCTTTACGTCAAGG
* *
2713864 TTTTTCAATGACAACTTTAACAATATTTATTTTTATCCTTATTATTATACATTTTTAAATTAAAA
1 TTTTTCAATGACAACTTTAACAATAATTATTTTTATCCTTATTATTATATATTTTTAAATTAAAA
* * * * * * * *
2713929 TTTGTATATCATTAAATACTTTTGGCTCAAGAATATAAAGTTAAATGTTTGTTTCCA-CAAAATT
66 TTTGTAAATTATTAAATACTTTTAGC-CGAGAATATAAATTTAAATATTT-TTTTCATTAAAA-T
* * * * * * * *
2713993 TAGATTTTT-TTACTTAATTGACATATTA-GTTAACTCTCATACATTCATATTAGGATTTTAAAC
128 TAGATTTTTGTGACTTAATTGACCTGTTACGTTAACTCTCACATATTTATGTTAAGA-TTTAAA-
* ** * * * ** *
2714056 T-TACTCATTTTA-TCTTTATAAATTTTTACGTTAATTCTTATAGTTTTACGTCAA-G
191 TATGCTTGTTTCACT-TTTATGAGTTTTTATATTAATTCTTATAGCTTTACGTCAAGG
* **
2714111 CTTTTCAATAGTA-ATTTTTAACAATAATTATTTTTAT
1 TTTTTCAAT-G-ACAACTTTAACAATAATTATTTTTAT
2714148 TTTTATTTTT
Statistics
Matches: 1061, Mismatches: 182, Indels: 74
0.81 0.14 0.06
Matches are distributed among these distances:
244 3 0.00
245 76 0.07
246 182 0.17
247 93 0.09
248 118 0.11
249 200 0.19
250 139 0.13
251 91 0.09
252 40 0.04
253 115 0.11
254 4 0.00
ACGTcount: A:0.33, C:0.10, G:0.08, T:0.48
Consensus pattern (247 bp):
TTTTTCAATGACAACTTTAACAATAATTATTTTTATCCTTATTATTATATATTTTTAAATTAAAA
TTTGTAAATTATTAAATACTTTTAGCCGAGAATATAAATTTAAATATTTTTTTCATTAAAATTAG
ATTTTTGTGACTTAATTGACCTGTTACGTTAACTCTCACATATTTATGTTAAGATTTAAATATGC
TTGTTTCACTTTTATGAGTTTTTATATTAATTCTTATAGCTTTACGTCAAGG
Found at i:2717317 original size:251 final size:249
Alignment explanation
Indices: 2716812--2717374 Score: 614
Period size: 251 Copynumber: 2.3 Consensus size: 249
2716802 GATTTTGTTT
* * * * * * * *
2716812 TCAATTTTTATAGCTTAACGTCAAGATCTTTCAATGACAACTTTTAACAATAATTATTTTAATCT
1 TCAATTATTATAACTTTACATCAAGCTTTTTCAATGACAACTTTTAACAATAATTATTTTTATCC
* ** * *
2716877 TTATTGTTATTTATTTTTAAATTAAAATTTATAAATATTAAATAATTTTGGCCTAGAATATAAAT
66 TTATTATTATACATTTTTAAATTAAAATTTATAAATATTAAATAATTTTGGCCAAGAATATAAAG
* * * * ** *
2716942 TTAAAAATTTATTTTCATTAAAATTAGAGTTTTGTGACTTAATTGACGTGTTACGTTAACTCTTA
131 TTAAAAATTTATTTCCATCAAAATTAGAGTTTTGTGACTTAATTGACATATTAAATTAACTCTCA
* * ** * * *
2717007 TACATTCATCTTAAGATTTTAAATATACTGGTTCCACCTTAATGAGTTTTTATG
196 CACATTCATATTAAGATTTTAAATATACTCATTCCACCTTAATAAATTTTTACG
* *
2717061 TCAATTCTTATAACTTTACATCAAAG-TTTTTCAATGACAAC-TTTAACAATATTTATTTTTATC
1 TCAATTATTATAACTTTACATC-AAGCTTTTTCAATGACAACTTTTAACAATAATTATTTTTATC
* *
2717124 CTTATTATTATACATTTTTAAATTAAAATTTGTAAATCATTAAATACTTTTGGCTCAAGAATATA
65 CTTATTATTATACATTTTTAAATTAAAATTTATAAAT-ATTAAATAATTTTGGC-CAAGAATATA
** * * * *
2717189 AAGTTAAATGTTTGTGTTCCA-CAAAATTTAGATTTTTTTTACTTAATTGACATATTAAATTAAC
128 AAGTTAAAAATTTAT-TTCCATCAAAA-TTAGAGTTTTGTGACTTAATTGACATATTAAATTAAC
* ** * *
2717253 TCTCACACATTCATATT-AGAATTTTAAATTTACTCATTTTATCTTTATAAATTTTTACG
191 TCTCACACATTCATATTAAG-ATTTTAAATATACTCATTCCACCTTAATAAATTTTTACG
** * *
2717312 TCAATTATTATAGTTTTACGTCAAGCTTTTTCAAT-AGTAACTTTTAACAATAATTATTTTTAT
1 TCAATTATTATAACTTTACATCAAGCTTTTTCAATGA-CAACTTTTAACAATAATTATTTTTAT
2717375 TTTTATTTTT
Statistics
Matches: 259, Mismatches: 46, Indels: 15
0.81 0.14 0.05
Matches are distributed among these distances:
248 52 0.20
249 47 0.18
250 33 0.13
251 107 0.41
252 20 0.08
ACGTcount: A:0.35, C:0.11, G:0.07, T:0.46
Consensus pattern (249 bp):
TCAATTATTATAACTTTACATCAAGCTTTTTCAATGACAACTTTTAACAATAATTATTTTTATCC
TTATTATTATACATTTTTAAATTAAAATTTATAAATATTAAATAATTTTGGCCAAGAATATAAAG
TTAAAAATTTATTTCCATCAAAATTAGAGTTTTGTGACTTAATTGACATATTAAATTAACTCTCA
CACATTCATATTAAGATTTTAAATATACTCATTCCACCTTAATAAATTTTTACG
Found at i:2717395 original size:7 final size:6
Alignment explanation
Indices: 2717365--2717394 Score: 51
Period size: 6 Copynumber: 4.8 Consensus size: 6
2717355 TTAACAATAA
2717365 TTATTT TTATTT TTATTT TTATTAT TTATT
1 TTATTT TTATTT TTATTT TTATT-T TTATT
2717395 AGAGAGTCCT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 17 0.74
7 6 0.26
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (6 bp):
TTATTT
Found at i:2725215 original size:53 final size:55
Alignment explanation
Indices: 2725158--2725377 Score: 159
Period size: 54 Copynumber: 4.1 Consensus size: 55
2725148 ATTTCTTGTC
* *
2725158 GAATTCT-GTTGGAAATGCTTTTTCAATGGAAAA-TTCATTGAAAATTTCCAACA
1 GAATTCTCGTAGGAAATGCTTTTTCAATGAAAAATTTCATTGAAAATTTCCAACA
* * * ** * *
2725211 GAATT-TCATAGGACATGC-TTTTCTAACGAAAAATTTTGTTAAAAATTTCTAAC-
1 GAATTCTCGTAGGAAATGCTTTTTC-AATGAAAAATTTCATTGAAAATTTCCAACA
* * * ** *** *
2725264 GAAATTC-CGTGGGAAATACTTTTACAATGAAAAATTTCATTGGCAATTTTTGATA
1 G-AATTCTCGTAGGAAATGCTTTTTCAATGAAAAATTTCATTGAAAATTTCCAACA
* * * * *
2725319 GAATT-TCGTAGGAAATGCTTTTCCAATG-GAATTTTCATTGGAAATTTCCAACG
1 GAATTCTCGTAGGAAATGCTTTTTCAATGAAAAATTTCATTGAAAATTTCCAACA
2725372 GAATTC
1 GAATTC
2725378 CATTTCAAAA
Statistics
Matches: 124, Mismatches: 34, Indels: 17
0.71 0.19 0.10
Matches are distributed among these distances:
52 6 0.05
53 43 0.35
54 70 0.56
55 5 0.04
ACGTcount: A:0.35, C:0.13, G:0.15, T:0.36
Consensus pattern (55 bp):
GAATTCTCGTAGGAAATGCTTTTTCAATGAAAAATTTCATTGAAAATTTCCAACA
Found at i:2725270 original size:107 final size:108
Alignment explanation
Indices: 2725116--2725341 Score: 269
Period size: 107 Copynumber: 2.1 Consensus size: 108
2725106 AATTTCGTGT
* * ** * * *
2725116 GAAATGC-TTTCTAACGGAAAATTTTGTTTAAAATTTCTTGTCGAATTCTGTTGGAAATGCTTTT
1 GAAATGCTTTTCTAACGAAAAATTTTGTTAAAAATTTCTTAACGAATTCCGTGGGAAATACTTTT
* *
2725180 TCAATGGAAAA-TTCATTGAAAATTTCCAACAGAATTTCATAG
66 ACAATGAAAAATTTCATTGAAAATTTCCAACAGAATTTCATAG
*
2725222 GACATGCTTTTCTAACGAAAAATTTTGTTAAAAATTTC-TAACGAAATTCCGTGGGAAATACTTT
1 GAAATGCTTTTCTAACGAAAAATTTTGTTAAAAATTTCTTAACG-AATTCCGTGGGAAATACTTT
** *** * *
2725286 TACAATGAAAAATTTCATTGGCAATTTTTGATAGAATTTCGTAG
65 TACAATGAAAAATTTCATTGAAAATTTCCAACAGAATTTCATAG
2725330 GAAATGCTTTTC
1 GAAATGCTTTTC
2725342 CAATGGAATT
Statistics
Matches: 99, Mismatches: 18, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
106 9 0.09
107 55 0.56
108 35 0.35
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (108 bp):
GAAATGCTTTTCTAACGAAAAATTTTGTTAAAAATTTCTTAACGAATTCCGTGGGAAATACTTTT
ACAATGAAAAATTTCATTGAAAATTTCCAACAGAATTTCATAG
Found at i:2726279 original size:17 final size:17
Alignment explanation
Indices: 2726245--2726283 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
2726235 AATTTTATTA
* * *
2726245 GAGCATATATTTATGGG
1 GAGCATATACTCACGGG
2726262 GAGCATATACTCACGGG
1 GAGCATATACTCACGGG
2726279 GAGCA
1 GAGCA
2726284 ATCCCAAAAC
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:0.31, C:0.15, G:0.31, T:0.23
Consensus pattern (17 bp):
GAGCATATACTCACGGG
Found at i:2733376 original size:188 final size:188
Alignment explanation
Indices: 2733044--2733422 Score: 483
Period size: 188 Copynumber: 2.0 Consensus size: 188
2733034 AAATTCAATA
* ** * * * *
2733044 GATTCTCTCCTCGACGGTTGATGCCTCTGACCTCTGAAGGTGGGGTTTTGGTCAAACTCAAGGCC
1 GATTCTCTCCTCCACGGTTGACACCTCTAACCTCTGAAGGTGGGGTTTCGATCAAACTCAAGGAC
* * *
2733109 TATCAGTAGCTGTTCTGTCACCAAAACTAAAATAGAAACTTCTTCCCCGACAACCCAGACCAGCG
66 TATCAGCAGCTGGTCTGTCACCAAAACTAAAACAGAAACTTCTTCCCCGACAACCCAGACCAGCG
* * * * * *
2733174 ACGTCTTTGTCAATCCGGTTAATGTCCCATCG-TGGACTAATCAAGACACTCATACTCT
131 ACATCCTCGTCAATCCAGTTAATGTCCCATCGCCGG-CTAATCAAGACACTCAGACTCT
*
2733232 GATTCTCTCCTCCACGGTTGACACCT-TCAACCTCTGAAGGTGGGGTTTCGATCGAACTCAAGGA
1 GATTCTCTCCTCCACGGTTGACACCTCT-AACCTCTGAAGGTGGGGTTTCGATCAAACTCAAGGA
* * * * * * * *
2733296 CTATCGGCAGCTGGTCTGTCACCGAAACTGAAACGGGAACTTCTTCCCTGACAGCCCAGACCAGT
65 CTATCAGCAGCTGGTCTGTCACCAAAACTAAAACAGAAACTTCTTCCCCGACAACCCAGACCAGC
* *
2733361 GCCATCCTCGTCAATCCAGTTAATGTCCCATCGCCGGCTAATCGAGACACTCAGACTCT
130 GACATCCTCGTCAATCCAGTTAATGTCCCATCGCCGGCTAATCAAGACACTCAGACTCT
2733420 GAT
1 GAT
2733423 ACTCCTCAGT
Statistics
Matches: 162, Mismatches: 27, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
187 1 0.01
188 159 0.98
189 2 0.01
ACGTcount: A:0.25, C:0.30, G:0.20, T:0.25
Consensus pattern (188 bp):
GATTCTCTCCTCCACGGTTGACACCTCTAACCTCTGAAGGTGGGGTTTCGATCAAACTCAAGGAC
TATCAGCAGCTGGTCTGTCACCAAAACTAAAACAGAAACTTCTTCCCCGACAACCCAGACCAGCG
ACATCCTCGTCAATCCAGTTAATGTCCCATCGCCGGCTAATCAAGACACTCAGACTCT
Found at i:2735397 original size:101 final size:101
Alignment explanation
Indices: 2735222--2735423 Score: 359
Period size: 101 Copynumber: 2.0 Consensus size: 101
2735212 TTTTCAGCAG
2735222 CAACCATTGCCCATTCACCGTAAACTTTTTGCTAGTCATACCATCAACAAGTTCCACAGCACCAT
1 CAACCATTGCCCATTCACCGTAAACTTTTTGCTAGTCATACCATCAACAAGTTCCACAGCACCAT
* *
2735287 GTGGGAATACTCTTAAAACAAGAAAAGGTTCTGACC
66 GTAGGAATACTCTCAAAACAAGAAAAGGTTCTGACC
* *
2735323 CAACCGTTGCCCATTCACCTTAAACTTTTTGCTAGTCATACCATCAACAAGTTCCACAGCACCAT
1 CAACCATTGCCCATTCACCGTAAACTTTTTGCTAGTCATACCATCAACAAGTTCCACAGCACCAT
*
2735388 GTAGGAATACTCTCGAAACAAGAAAAGGTTCTGACC
66 GTAGGAATACTCTCAAAACAAGAAAAGGTTCTGACC
2735424 ACCTTAATTT
Statistics
Matches: 96, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
101 96 1.00
ACGTcount: A:0.33, C:0.28, G:0.14, T:0.25
Consensus pattern (101 bp):
CAACCATTGCCCATTCACCGTAAACTTTTTGCTAGTCATACCATCAACAAGTTCCACAGCACCAT
GTAGGAATACTCTCAAAACAAGAAAAGGTTCTGACC
Found at i:2745566 original size:116 final size:116
Alignment explanation
Indices: 2745435--2745666 Score: 446
Period size: 116 Copynumber: 2.0 Consensus size: 116
2745425 TAAAGAAAGA
2745435 AAAAAAAAACTTAGACTAAAATCAATCTATTTTGTATTAATATTAGCAAAACAAATAAAAAAAAC
1 AAAAAAAAACTTAGACTAAAATCAATCTATTTTGTATTAATATTAGCAAAACAAATAAAAAAAAC
2745500 AAATCCTCAGCAATGGTGCCAAAAACTTGTCGCAAAGCTAATACCTGCAAG
66 AAATCCTCAGCAATGGTGCCAAAAACTTGTCGCAAAGCTAATACCTGCAAG
2745551 AAAAAAAAACTTAGACTAAAATCAATCTATTTTGTATTAATATTAGCAAAACAAATAAAAAAAAC
1 AAAAAAAAACTTAGACTAAAATCAATCTATTTTGTATTAATATTAGCAAAACAAATAAAAAAAAC
* *
2745616 AAATCCTCAGCAATGGTGCTAAAAACTTGTTGCAAAGCTAATACCTGCAAG
66 AAATCCTCAGCAATGGTGCCAAAAACTTGTCGCAAAGCTAATACCTGCAAG
2745667 TATACATATT
Statistics
Matches: 114, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
116 114 1.00
ACGTcount: A:0.49, C:0.16, G:0.10, T:0.24
Consensus pattern (116 bp):
AAAAAAAAACTTAGACTAAAATCAATCTATTTTGTATTAATATTAGCAAAACAAATAAAAAAAAC
AAATCCTCAGCAATGGTGCCAAAAACTTGTCGCAAAGCTAATACCTGCAAG
Found at i:2747228 original size:40 final size:40
Alignment explanation
Indices: 2747168--2747243 Score: 116
Period size: 40 Copynumber: 1.9 Consensus size: 40
2747158 CTTGGCTATT
*
2747168 CAAAATTGTAAGAAATAAAAGGTTACACCTTAGCCTATAA
1 CAAAATTGTAAGAAAGAAAAGGTTACACCTTAGCCTATAA
* * *
2747208 CAAAATTGTGAGAGAGAAAAGGTTATACCTTAGCCT
1 CAAAATTGTAAGAAAGAAAAGGTTACACCTTAGCCT
2747244 CCAAAAGGTA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 32 1.00
ACGTcount: A:0.43, C:0.14, G:0.17, T:0.25
Consensus pattern (40 bp):
CAAAATTGTAAGAAAGAAAAGGTTACACCTTAGCCTATAA
Found at i:2747423 original size:34 final size:34
Alignment explanation
Indices: 2747350--2747423 Score: 103
Period size: 34 Copynumber: 2.2 Consensus size: 34
2747340 TCAAGCCCAT
* **
2747350 AAAAAGGCATTGTAAAGGTTATGCTTGATTCTAG
1 AAAAAGGCATTGTAAAGGTTATGCCTGAGCCTAG
* *
2747384 TAAAAGGCATTGTAAAGGTTATGCCTGAGCCTTG
1 AAAAAGGCATTGTAAAGGTTATGCCTGAGCCTAG
2747418 AAAAAG
1 AAAAAG
2747424 TATTTTTCAT
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.36, C:0.11, G:0.24, T:0.28
Consensus pattern (34 bp):
AAAAAGGCATTGTAAAGGTTATGCCTGAGCCTAG
Found at i:2752269 original size:3 final size:3
Alignment explanation
Indices: 2752255--2752304 Score: 91
Period size: 3 Copynumber: 16.7 Consensus size: 3
2752245 CTTTCCTTTC
*
2752255 ATT ATG ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
2752303 AT
1 AT
2752305 GGTGTGCCTA
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:2759153 original size:17 final size:17
Alignment explanation
Indices: 2759131--2759163 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
2759121 ATCAAATGAA
2759131 TTTCATTAAAAATATTT
1 TTTCATTAAAAATATTT
*
2759148 TTTCATTATAAATATT
1 TTTCATTAAAAATATT
2759164 AATAATATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.39, C:0.06, G:0.00, T:0.55
Consensus pattern (17 bp):
TTTCATTAAAAATATTT
Found at i:2759171 original size:26 final size:28
Alignment explanation
Indices: 2759135--2759188 Score: 85
Period size: 26 Copynumber: 2.0 Consensus size: 28
2759125 AATGAATTTC
2759135 ATTAAAAATATTT-TTTCA-TTATAAAT
1 ATTAAAAATATTTGTTTCATTTATAAAT
*
2759161 ATTAATAATATTTGTTTCATTTATAAAT
1 ATTAAAAATATTTGTTTCATTTATAAAT
2759189 TAGAATTCTA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
26 12 0.48
27 5 0.20
28 8 0.32
ACGTcount: A:0.43, C:0.04, G:0.02, T:0.52
Consensus pattern (28 bp):
ATTAAAAATATTTGTTTCATTTATAAAT
Found at i:2760784 original size:22 final size:23
Alignment explanation
Indices: 2760754--2760800 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 23
2760744 ATATTCAACA
*
2760754 TTTAGATACTATTAT-TTTAAAT
1 TTTACATACTATTATATTTAAAT
* *
2760776 TTTACATACTTTTTTATTTAAAT
1 TTTACATACTATTATATTTAAAT
2760799 TT
1 TT
2760801 AGAATTTATA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
22 12 0.57
23 9 0.43
ACGTcount: A:0.32, C:0.06, G:0.02, T:0.60
Consensus pattern (23 bp):
TTTACATACTATTATATTTAAAT
Found at i:2762117 original size:3 final size:3
Alignment explanation
Indices: 2762109--2762138 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
2762099 ATTTTTAAAA
2762109 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
2762139 ATGTTATGTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:2767453 original size:14 final size:15
Alignment explanation
Indices: 2767415--2767455 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 15
2767405 AATTAACTTC
*
2767415 AAAA-CATAAACATG
1 AAAAGCATAAACATA
*
2767429 AAAATCATAAACATA
1 AAAAGCATAAACATA
2767444 AAAAGC-TAAACA
1 AAAAGCATAAACA
2767456 CTTCCCCCTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
14 10 0.42
15 14 0.58
ACGTcount: A:0.66, C:0.15, G:0.05, T:0.15
Consensus pattern (15 bp):
AAAAGCATAAACATA
Found at i:2775096 original size:26 final size:26
Alignment explanation
Indices: 2775067--2775153 Score: 61
Period size: 28 Copynumber: 3.2 Consensus size: 26
2775057 CATGTTCAGT
2775067 CTTTACATACTGCTGCAGTGGTCCGA
1 CTTTACATACTGCTGCAGTGGTCCGA
** * *
2775093 CTTTGACAAATA-TTTTGACCA-TGATCCAAGT
1 CTTT-AC--ATACTGCTG--CAGTGGTCC--GA
2775124 CTTTACATACTGCTGCAGTGGTCCGA
1 CTTTACATACTGCTGCAGTGGTCCGA
2775150 CTTT
1 CTTT
2775154 GACAAATATT
Statistics
Matches: 44, Mismatches: 8, Indels: 18
0.63 0.11 0.26
Matches are distributed among these distances:
26 9 0.20
27 4 0.09
28 11 0.25
29 11 0.25
30 4 0.09
31 5 0.11
ACGTcount: A:0.23, C:0.24, G:0.18, T:0.34
Consensus pattern (26 bp):
CTTTACATACTGCTGCAGTGGTCCGA
Found at i:2775131 original size:57 final size:57
Alignment explanation
Indices: 2775064--2775174 Score: 222
Period size: 57 Copynumber: 1.9 Consensus size: 57
2775054 CATCATGTTC
2775064 AGTCTTTACATACTGCTGCAGTGGTCCGACTTTGACAAATATTTTGACCATGATCCA
1 AGTCTTTACATACTGCTGCAGTGGTCCGACTTTGACAAATATTTTGACCATGATCCA
2775121 AGTCTTTACATACTGCTGCAGTGGTCCGACTTTGACAAATATTTTGACCATGAT
1 AGTCTTTACATACTGCTGCAGTGGTCCGACTTTGACAAATATTTTGACCATGAT
2775175 TCAATCAGAA
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
57 54 1.00
ACGTcount: A:0.26, C:0.22, G:0.18, T:0.34
Consensus pattern (57 bp):
AGTCTTTACATACTGCTGCAGTGGTCCGACTTTGACAAATATTTTGACCATGATCCA
Found at i:2775443 original size:20 final size:19
Alignment explanation
Indices: 2775418--2775455 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
2775408 TAATTTAAAA
2775418 TAAAATAACCTAAAATTAAC
1 TAAAATAA-CTAAAATTAAC
*
2775438 TAAAATAACTTAAATTAA
1 TAAAATAACTAAAATTAA
2775456 TCACTTAACA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.61, C:0.11, G:0.00, T:0.29
Consensus pattern (19 bp):
TAAAATAACTAAAATTAAC
Found at i:2779136 original size:18 final size:21
Alignment explanation
Indices: 2779096--2779138 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 21
2779086 AAACTAAGAC
2779096 AAATAAATATAAAATTAGCATA
1 AAATAAATATAAAATTA-CATA
2779118 AAATAAA-AT-AAATTA-ATA
1 AAATAAATATAAAATTACATA
2779136 AAA
1 AAA
2779139 ACAAACTAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
18 6 0.29
20 6 0.29
21 2 0.10
22 7 0.33
ACGTcount: A:0.70, C:0.02, G:0.02, T:0.26
Consensus pattern (21 bp):
AAATAAATATAAAATTACATA
Found at i:2779899 original size:14 final size:14
Alignment explanation
Indices: 2779880--2779915 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
2779870 TCACTTCCTG
2779880 TCTCTCTTTCTCTT
1 TCTCTCTTTCTCTT
*
2779894 TCTCTCTCTCTCTT
1 TCTCTCTTTCTCTT
*
2779908 TCTTTCTT
1 TCTCTCTT
2779916 AAATCTACCT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (14 bp):
TCTCTCTTTCTCTT
Found at i:2783497 original size:11 final size:11
Alignment explanation
Indices: 2783481--2783510 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
2783471 CACATGTAAA
2783481 AGAAGGAAAAT
1 AGAAGGAAAAT
2783492 AGAAGGAAAAT
1 AGAAGGAAAAT
2783503 AGAAGGAA
1 AGAAGGAA
2783511 TTGGAATGTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.63, C:0.00, G:0.30, T:0.07
Consensus pattern (11 bp):
AGAAGGAAAAT
Found at i:2784622 original size:15 final size:15
Alignment explanation
Indices: 2784578--2784631 Score: 67
Period size: 15 Copynumber: 3.7 Consensus size: 15
2784568 TAGGAAGCAA
*
2784578 AGGAA-AAAGGGAGAA
1 AGGAAGAAA-GGAGAG
*
2784593 AGAAAGAAAGGAGAG
1 AGGAAGAAAGGAGAG
2784608 AGGAAGAAAGGAGAG
1 AGGAAGAAAGGAGAG
2784623 AGG-AGAAAG
1 AGGAAGAAAG
2784632 AAGAAAAGAG
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
14 6 0.17
15 26 0.74
16 3 0.09
ACGTcount: A:0.57, C:0.00, G:0.43, T:0.00
Consensus pattern (15 bp):
AGGAAGAAAGGAGAG
Found at i:2805446 original size:10 final size:11
Alignment explanation
Indices: 2805427--2805456 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
2805417 GAGGTTTATT
2805427 AAAAATTTTTC
1 AAAAATTTTTC
2805438 AAAAATTTTTC
1 AAAAATTTTTC
2805449 AAAAATTT
1 AAAAATTT
2805457 CCTAATATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (11 bp):
AAAAATTTTTC
Found at i:2808205 original size:36 final size:36
Alignment explanation
Indices: 2808158--2808234 Score: 120
Period size: 36 Copynumber: 2.1 Consensus size: 36
2808148 CAGAATAGTT
*
2808158 TCTTCCTGCCTC-CTTTGCTGCCTCTCTTGCTACCTC
1 TCTTCCTGCCTCTC-TTGCTGCCTCTCTTCCTACCTC
*
2808194 TCTTCCTGCCTCTCTTGCTGCCTCTCTTCCTGCCTC
1 TCTTCCTGCCTCTCTTGCTGCCTCTCTTCCTACCTC
2808230 TCTTC
1 TCTTC
2808235 TCTGAAAAAG
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
36 37 0.97
37 1 0.03
ACGTcount: A:0.01, C:0.45, G:0.10, T:0.43
Consensus pattern (36 bp):
TCTTCCTGCCTCTCTTGCTGCCTCTCTTCCTACCTC
Done.