Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007953.1 Hibiscus syriacus cultivar Beakdansim tig00110378_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: 794529
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
File 2 of 4
Found at i:247432 original size:33 final size:32
Alignment explanation
Indices: 247389--247481 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 32
247379 CACGAAACTT
**
247389 AAATCGCAACGCGAAATGAAAATCGCAACGAC
1 AAATCGCAACGCGAAACCAAAATCGCAACGAC
247421 AGAATCGCAACGCGAAACCAAAATCGCAACGAC
1 A-AATCGCAACGCGAAACCAAAATCGCAACGAC
247454 AAGATCGCAACGCGAAACCAAAATCGCA
1 AA-ATCGCAACGCGAAACCAAAATCGCA
247482 TTGCGATTTT
Statistics
Matches: 57, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
32 2 0.04
33 55 0.96
ACGTcount: A:0.46, C:0.28, G:0.18, T:0.08
Consensus pattern (32 bp):
AAATCGCAACGCGAAACCAAAATCGCAACGAC
Found at i:247481 original size:19 final size:19
Alignment explanation
Indices: 247373--247481 Score: 85
Period size: 19 Copynumber: 6.3 Consensus size: 19
247363 TAGTTTACTT
* **
247373 TCGCAACACGAAACTTAAA
1 TCGCAACGCGAAACCAAAA
**
247392 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
*
247411 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAACCAAAA
247425 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
*
247444 TCGCAA--CG--A-CAAGA
1 TCGCAACGCGAAACCAAAA
247458 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
247477 TCGCA
1 TCGCA
247482 TTGCGATTTT
Statistics
Matches: 71, Mismatches: 9, Indels: 20
0.71 0.09 0.20
Matches are distributed among these distances:
14 19 0.27
15 2 0.03
16 4 0.06
17 4 0.06
18 2 0.03
19 40 0.56
ACGTcount: A:0.45, C:0.28, G:0.17, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:247499 original size:19 final size:19
Alignment explanation
Indices: 247477--247611 Score: 128
Period size: 19 Copynumber: 7.6 Consensus size: 19
247467 GAAACCAAAA
*
247477 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
247496 TCGCGTTGCGA--TTC-TT
1 TCGCGTTGCGATTTTCATT
247512 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
247529 TCGCATTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
247545 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
247562 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
*
247581 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
247601 TCGTGTTGCGA
1 TCGCGTTGCGA
247612 AAGTAAACTA
Statistics
Matches: 95, Mismatches: 10, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 15 0.16
16 11 0.12
17 11 0.12
19 46 0.48
20 12 0.13
ACGTcount: A:0.11, C:0.19, G:0.24, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:247518 original size:14 final size:14
Alignment explanation
Indices: 247499--247555 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
247489 TTTCATTTCG
247499 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
247513 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TTT
*
247530 CGCATTGCGATTCTGT
1 CG--TTGCGATTCTTT
247546 CGTTGCGATT
1 CGTTGCGATT
247556 TTCATTTCGC
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 16 0.43
16 7 0.19
17 8 0.22
19 6 0.16
ACGTcount: A:0.11, C:0.21, G:0.23, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:247524 original size:33 final size:33
Alignment explanation
Indices: 247482--247574 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
247472 CAAAATCGCA
*
247482 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
*
247515 TTGCGATTTTCATTTCGCATTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
247548 TTGCGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
247575 TTGGTTTCGC
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.11, C:0.20, G:0.22, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
Found at i:249544 original size:14 final size:14
Alignment explanation
Indices: 249525--249560 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
249515 ATTGTTTAAT
249525 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
249539 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
249553 TGATTTGT
1 TGATTTGT
249561 GTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:249683 original size:19 final size:19
Alignment explanation
Indices: 249667--249764 Score: 143
Period size: 19 Copynumber: 5.4 Consensus size: 19
249657 AAAAATGACT
249667 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
249686 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
249705 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
249719 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
249738 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
249758 ATCGCAA
1 ATCGCAA
249765 CGAGAGAATC
Statistics
Matches: 71, Mismatches: 2, Indels: 11
0.85 0.02 0.13
Matches are distributed among these distances:
14 10 0.14
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 39 0.55
20 16 0.23
ACGTcount: A:0.46, C:0.17, G:0.22, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:249796 original size:53 final size:53
Alignment explanation
Indices: 249667--249782 Score: 225
Period size: 53 Copynumber: 2.2 Consensus size: 53
249657 AAAAATGACT
249667 ATCGCAATGCGAAATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
249719 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
249772 ATCGCAATGCG
1 ATCGCAATGCG
249783 TTTATAATTT
Statistics
Matches: 63, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
52 29 0.46
53 34 0.54
ACGTcount: A:0.44, C:0.18, G:0.24, T:0.14
Consensus pattern (53 bp):
ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
Found at i:249801 original size:19 final size:19
Alignment explanation
Indices: 249789--250012 Score: 247
Period size: 19 Copynumber: 12.8 Consensus size: 19
249779 TGCGTTTATA
249789 ATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTTTC
249808 ATTTCGCATTGCGA--TTC
1 ATTTCGCATTGCGATTTTC
*
249825 -TCTCG--TTGCGATTTTC
1 ATTTCGCATTGCGATTTTC
249841 ATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTTTC
249860 ATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTTTC
249879 ATTTCGCATTGCGA--TTC
1 ATTTCGCATTGCGATTTTC
*
249896 -TCTCG--TTGCGATTTTC
1 ATTTCGCATTGCGATTTTC
249912 ATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTTTC
*
249931 ATTTCGCATTGTGA--TTC
1 ATTTCGCATTGCGATTTTC
*
249948 -TCTCG--TTGCGATTTTC
1 ATTTCGCATTGCGATTTTC
249964 ATTTCCGCATTGCGATTTTC
1 ATTT-CGCATTGCGATTTTC
*
249984 A--T-G--TTGGGA-TTTC
1 ATTTCGCATTGCGATTTTC
249997 ATTTCGCATTGCGATT
1 ATTTCGCATTGCGATT
250013 CTCTCGTTGC
Statistics
Matches: 173, Mismatches: 10, Indels: 44
0.76 0.04 0.19
Matches are distributed among these distances:
13 5 0.03
14 22 0.13
15 1 0.01
16 23 0.13
17 19 0.11
18 8 0.05
19 83 0.48
20 12 0.07
ACGTcount: A:0.14, C:0.21, G:0.18, T:0.46
Consensus pattern (19 bp):
ATTTCGCATTGCGATTTTC
Found at i:249839 original size:33 final size:33
Alignment explanation
Indices: 249797--249927 Score: 208
Period size: 33 Copynumber: 3.8 Consensus size: 33
249787 TAATTTCGCA
249797 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
*
249830 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCG
1 TTGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG
249866 CATTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1 --TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
249901 TTGCGATTTTCATTTCGCATTGCGATT
1 TTGCGATTTTCATTTCGCATTGCGATT
249928 TTCATTTCGC
Statistics
Matches: 91, Mismatches: 2, Indels: 10
0.88 0.02 0.10
Matches are distributed among these distances:
33 52 0.57
35 7 0.08
36 7 0.08
38 25 0.27
ACGTcount: A:0.14, C:0.22, G:0.18, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
Found at i:249846 original size:52 final size:50
Alignment explanation
Indices: 249789--250012 Score: 254
Period size: 52 Copynumber: 4.3 Consensus size: 50
249779 TGCGTTTATA
*
249789 ATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCG-ATTTTC
1 ATTTCGCATTGCGATTTTCATTTCGCATTGCGATT-T-TCATTGCGCA-TTTC
* *
249841 ATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGC
1 ATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTGCGCATTTC
* * * *
249891 GATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGTG
1 -ATT-TCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTGCGCATT-TC
* * *
249944 ATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATGTTG-GGATTTC
1 ATT-TCGCATTGCGATTTTCATTT-CGCATTGCGATTTTCA--TTGCGCATTTC
249997 ATTTCGCATTGCGATT
1 ATTTCGCATTGCGATT
250013 CTCTCGTTGC
Statistics
Matches: 153, Mismatches: 12, Indels: 14
0.85 0.07 0.08
Matches are distributed among these distances:
50 9 0.06
51 5 0.03
52 113 0.74
53 20 0.13
54 4 0.03
55 2 0.01
ACGTcount: A:0.14, C:0.21, G:0.18, T:0.46
Consensus pattern (50 bp):
ATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTGCGCATTTC
Found at i:249868 original size:71 final size:71
Alignment explanation
Indices: 249789--249946 Score: 307
Period size: 71 Copynumber: 2.2 Consensus size: 71
249779 TGCGTTTATA
249789 ATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCG
1 ATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCG
249854 ATTTTC
66 ATTTTC
249860 ATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCG
1 ATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCG
249925 ATTTTC
66 ATTTTC
*
249931 ATTTCGCATTGTGATT
1 ATTTCGCATTGCGATT
249947 CTCTCGTTGC
Statistics
Matches: 86, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
71 86 1.00
ACGTcount: A:0.15, C:0.22, G:0.17, T:0.47
Consensus pattern (71 bp):
ATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCG
ATTTTC
Found at i:249995 original size:34 final size:33
Alignment explanation
Indices: 249920--250026 Score: 155
Period size: 33 Copynumber: 3.2 Consensus size: 33
249910 TCATTTCGCA
*
249920 TTGCGATTTTCATTTCGCATTGTGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
*
249953 TTGCGATTTTCATTTCCGCATTGCGATTTTCAT-G
1 TTGCGATTTTCATTT-CGCATTGCGATTCTC-TCG
*
249987 TTGGGA-TTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
250019 TTGCGATT
1 TTGCGATT
250027 GTAATTTCCG
Statistics
Matches: 65, Mismatches: 5, Indels: 8
0.83 0.06 0.10
Matches are distributed among these distances:
31 1 0.02
32 20 0.31
33 24 0.37
34 19 0.29
35 1 0.02
ACGTcount: A:0.13, C:0.21, G:0.20, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
Found at i:252313 original size:12 final size:12
Alignment explanation
Indices: 252296--252320 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
252286 TCTTCGGGGA
252296 CTTTTTCTTCTT
1 CTTTTTCTTCTT
252308 CTTTTTCTTCTT
1 CTTTTTCTTCTT
252320 C
1 C
252321 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:252528 original size:24 final size:24
Alignment explanation
Indices: 252494--252540 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
252484 CTGAAACATC
252494 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
252518 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
252541 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:253246 original size:20 final size:20
Alignment explanation
Indices: 253237--253447 Score: 255
Period size: 20 Copynumber: 10.6 Consensus size: 20
253227 TACAGATTAT
* *
253237 CGTTGCGATTTACGGATTCT
1 CGTTGCGATTTACGGATACG
*
253257 CGTTGCGATTTACGGATTA-T
1 CGTTGCGATTTACGGA-TACG
253277 CGTTGCGATTTACGGATACG
1 CGTTGCGATTTACGGATACG
*
253297 CGTTGCGATATACGGATACG
1 CGTTGCGATTTACGGATACG
* **
253317 CATTGCGATTTACCCATACG
1 CGTTGCGATTTACGGATACG
*
253337 CGTTGCGATTTACGGATACA
1 CGTTGCGATTTACGGATACG
*
253357 CGTTGCGATTTACGGATACA
1 CGTTGCGATTTACGGATACG
253377 CGTTGCGATTTACGGATACG
1 CGTTGCGATTTACGGATACG
* *
253397 CGTTGCGATTTATGTG-TTCG
1 CGTTGCGATTTACG-GATACG
* ** *
253417 CGTTGCGATTTTCATATTCG
1 CGTTGCGATTTACGGATACG
253437 CGTTGCGATTT
1 CGTTGCGATTT
253448 TGGAAAATCG
Statistics
Matches: 169, Mismatches: 18, Indels: 8
0.87 0.09 0.04
Matches are distributed among these distances:
19 2 0.01
20 165 0.98
21 2 0.01
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.35
Consensus pattern (20 bp):
CGTTGCGATTTACGGATACG
Found at i:253464 original size:21 final size:21
Alignment explanation
Indices: 253434--253516 Score: 78
Period size: 21 Copynumber: 4.0 Consensus size: 21
253424 ATTTTCATAT
*
253434 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTTGGAAAA
* * * **
253455 TCGCAATGCGAATTTGTACTA
1 TCGCATTGCGATTTTGGAAAA
*
253476 TCGCATTGCGATTTT-CAAGAA
1 TCGCATTGCGATTTTGGAA-AA
*
253497 TCGCGTTGCGATTTTGGAAA
1 TCGCATTGCGATTTTGGAAA
253517 CTGATTTGCG
Statistics
Matches: 47, Mismatches: 13, Indels: 4
0.73 0.20 0.06
Matches are distributed among these distances:
20 1 0.02
21 44 0.94
22 2 0.04
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTTGGAAAA
Found at i:253507 original size:42 final size:43
Alignment explanation
Indices: 253414--253512 Score: 100
Period size: 42 Copynumber: 2.4 Consensus size: 43
253404 ATTTATGTGT
* *
253414 TCGCGTTGCG-ATTT-TCATATTCGCGTTGCGATTTTGGAAAA
1 TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
**
253455 TCGCAATGCGAATTTGT-ACTA-TCGCATTGCGATTTT-CAAGAA
1 TCGCGTTGCGAATTTGTCA-TATTCGCATTGCGATTTTGCAA-AA
*
253497 TCGCGTTGCGATTTTG
1 TCGCGTTGCGAATTTG
253513 GAAACTGATT
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
41 10 0.21
42 34 0.72
43 3 0.06
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.37
Consensus pattern (43 bp):
TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
Found at i:253886 original size:51 final size:51
Alignment explanation
Indices: 253812--253970 Score: 147
Period size: 60 Copynumber: 2.9 Consensus size: 51
253802 TACATCGTTC
* * * *
253812 CTCACTGAACTTTATTTTATCTCTTATTTTCCTCATTCAACTTTCAATTTG
1 CTCACTGAATTTTACTCTCTCTCTTATTTTCCTCATTCAACTTTCAATTTG
*
253863 CTCACTGAATTTTACTCTCTCTCTTATTTTTCTTTCTCAACTTTCAATTTGTTCAATTTG
1 CTCACTGAATTTTACTCTCTCTCTTA-TTTTC---CTC-A--TTCAA-CT-TTCAATTTG
* * * **
253923 CTCATTGAATTTTACTCTCTCTCCTATTTTCATCACCCAACTTTCAAT
1 CTCACTGAATTTTACTCTCTCTCTTATTTTCCTCATTCAACTTTCAAT
253971 ATATGATTCA
Statistics
Matches: 88, Mismatches: 11, Indels: 18
0.75 0.09 0.15
Matches are distributed among these distances:
51 28 0.32
52 6 0.07
53 3 0.03
55 4 0.05
56 3 0.03
58 5 0.06
59 6 0.07
60 33 0.38
ACGTcount: A:0.21, C:0.26, G:0.04, T:0.50
Consensus pattern (51 bp):
CTCACTGAATTTTACTCTCTCTCTTATTTTCCTCATTCAACTTTCAATTTG
Found at i:253964 original size:60 final size:60
Alignment explanation
Indices: 253854--253970 Score: 173
Period size: 60 Copynumber: 1.9 Consensus size: 60
253844 TCATTCAACT
* ** *
253854 TTCAATTTGCTCACTGAATTTTACTCTCTCTCTTATTTTTCTTTCTCAACTTTCAATTTG
1 TTCAATTTGCTCACTGAATTTTACTCTCTCTCCTATTTTTCTCACCCAACTTTCAATTTG
*
253914 TTCAATTTGCTCATTGAATTTTACTCTCTCTCCTA-TTTTCATCACCCAACTTTCAAT
1 TTCAATTTGCTCACTGAATTTTACTCTCTCTCCTATTTTTC-TCACCCAACTTTCAAT
253971 ATATGATTCA
Statistics
Matches: 51, Mismatches: 5, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
59 5 0.10
60 46 0.90
ACGTcount: A:0.21, C:0.26, G:0.04, T:0.50
Consensus pattern (60 bp):
TTCAATTTGCTCACTGAATTTTACTCTCTCTCCTATTTTTCTCACCCAACTTTCAATTTG
Found at i:256380 original size:2 final size:2
Alignment explanation
Indices: 256373--256405 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
256363 TTTTCCAACA
*
256373 AT AT AT AT AT AT AT AT AT AT -T AT AA AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
256406 TATTTATTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:256412 original size:17 final size:19
Alignment explanation
Indices: 256374--256415 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
256364 TTTCCAACAA
*
256374 TATATATATATATATATAT
1 TATAAATATATATATATAT
*
256393 TATAAATATATATTATTTAT
1 TATAAATATATA-TATATAT
256413 TAT
1 TAT
256416 TAACTATTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 11 0.55
20 9 0.45
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (19 bp):
TATAAATATATATATATAT
Found at i:282427 original size:4 final size:4
Alignment explanation
Indices: 282418--282461 Score: 52
Period size: 4 Copynumber: 11.0 Consensus size: 4
282408 AGGACAACTC
* * * *
282418 TATG TATG TATG TAAG TATG TATG CATG CATG CATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
282462 AATTTGTTGC
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
4 36 1.00
ACGTcount: A:0.27, C:0.07, G:0.25, T:0.41
Consensus pattern (4 bp):
TATG
Found at i:285458 original size:29 final size:29
Alignment explanation
Indices: 285393--285459 Score: 116
Period size: 29 Copynumber: 2.3 Consensus size: 29
285383 TTGATTCACC
**
285393 TTCTTTGAAACTACCAATCAAATATATAT
1 TTCTTTGTTACTACCAATCAAATATATAT
285422 TTCTTTGTTACTACCAATCAAATATATAT
1 TTCTTTGTTACTACCAATCAAATATATAT
285451 TTCTTTGTT
1 TTCTTTGTT
285460 GAATGCTTCA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 36 1.00
ACGTcount: A:0.33, C:0.16, G:0.04, T:0.46
Consensus pattern (29 bp):
TTCTTTGTTACTACCAATCAAATATATAT
Found at i:289207 original size:2 final size:2
Alignment explanation
Indices: 289200--289225 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
289190 CAAAAATGTG
289200 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
289226 ATTTCATGGC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:291535 original size:15 final size:15
Alignment explanation
Indices: 291515--291545 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
291505 TAGGAACACC
291515 AAAAGTGTCATGTTT
1 AAAAGTGTCATGTTT
291530 AAAAGTGTCATGTTT
1 AAAAGTGTCATGTTT
291545 A
1 A
291546 TCAGAGTCAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.35, C:0.06, G:0.19, T:0.39
Consensus pattern (15 bp):
AAAAGTGTCATGTTT
Found at i:291896 original size:29 final size:29
Alignment explanation
Indices: 291855--291913 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
291845 AGTTTGATAG
291855 TAGTTTTGAGCAAATTAGATGAACTCTTA
1 TAGTTTTGAGCAAATTAGATGAACTCTTA
291884 TAGTTTTGAGCAAATTAGATGAACTCTTA
1 TAGTTTTGAGCAAATTAGATGAACTCTTA
291913 T
1 T
291914 TCGCATTTAC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.34, C:0.10, G:0.17, T:0.39
Consensus pattern (29 bp):
TAGTTTTGAGCAAATTAGATGAACTCTTA
Found at i:293497 original size:22 final size:22
Alignment explanation
Indices: 293469--293512 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
293459 TCAATTATAA
*
293469 ATGTATTT-ATTTTTATAATTAT
1 ATGTATTTGATTATTAT-ATTAT
293491 ATGTATTTGATTATTATATTAT
1 ATGTATTTGATTATTATATTAT
293513 TAATTCAGAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 13 0.65
23 7 0.35
ACGTcount: A:0.32, C:0.00, G:0.07, T:0.61
Consensus pattern (22 bp):
ATGTATTTGATTATTATATTAT
Found at i:294088 original size:2 final size:2
Alignment explanation
Indices: 294078--294136 Score: 79
Period size: 2 Copynumber: 30.5 Consensus size: 2
294068 TTTTATTTTT
*
294078 TA TA T- TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TG
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
294119 TA TA TA GTA -A TA TA -A TA T
1 TA TA TA -TA TA TA TA TA TA T
294137 TGTCGGAACC
Statistics
Matches: 51, Mismatches: 2, Indels: 8
0.84 0.03 0.13
Matches are distributed among these distances:
1 3 0.06
2 46 0.90
3 2 0.04
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
TA
Found at i:294470 original size:39 final size:39
Alignment explanation
Indices: 294411--294540 Score: 158
Period size: 41 Copynumber: 3.3 Consensus size: 39
294401 TAGTTTAAAA
*
294411 TATATATTATATATATATTTTAAAAGCGTTTTGAAAACATT
1 TATATATTATATA-A-ATTTTAAAAACGTTTTGAAAACATT
*
294452 TATATATTATATAAATTTTTAAAAATCATTTT-AAAA-ATT
1 TATATATTATATAAA-TTTTAAAAA-CGTTTTGAAAACATT
* * *
294491 TATATAATATAT-AGTTTTGAAAACGTTTTGAAAACATT
1 TATATATTATATAAATTTTAAAAACGTTTTGAAAACATT
294529 TATATATTATAT
1 TATATATTATAT
294541 GGTTTTTAAA
Statistics
Matches: 78, Mismatches: 7, Indels: 11
0.81 0.07 0.11
Matches are distributed among these distances:
36 5 0.06
37 12 0.15
38 15 0.19
39 15 0.19
40 13 0.17
41 18 0.23
ACGTcount: A:0.44, C:0.04, G:0.05, T:0.47
Consensus pattern (39 bp):
TATATATTATATAAATTTTAAAAACGTTTTGAAAACATT
Found at i:294495 original size:37 final size:36
Alignment explanation
Indices: 294407--294626 Score: 138
Period size: 37 Copynumber: 5.8 Consensus size: 36
294397 TTTATAGTTT
* * *
294407 AAAATATATATTATATATATATTTTAAAAGCGTTTTGA
1 AAAATATATATTATATAAAT-TTTTAAAAACATTTT-A
294445 AAACATTTATATATTATATAAATTTTTAAAAATCATTTTA
1 AAA-A--TATATATTATATAAATTTTTAAAAA-CATTTTA
* * * * * *
294485 AAAATTTATATAATATATAGTTTTGAAAACGTTTTGA
1 AAAATATATATTATATAAATTTTTAAAAACATTTT-A
** *
294522 AAACATTTATATATTATAT-GGTTTTTAAAAATATTTTTA
1 AAA-A--TATATATTATATAAATTTTTAAAAACA-TTTTA
* * ** *
294561 AGATATATATAATATATAGTTTTTTTAAAACATTTTTA
1 A-AAATATATATTATATAAATTTTTAAAAACA-TTTTA
* *
294599 AAAATATATATTGTAT-AGTTTTTAAAAA
1 AAAATATATATTATATAAATTTTTAAAAA
294627 AAATCATTTT
Statistics
Matches: 143, Mismatches: 28, Indels: 24
0.73 0.14 0.12
Matches are distributed among these distances:
36 14 0.10
37 47 0.33
38 22 0.15
39 13 0.09
40 27 0.19
41 20 0.14
ACGTcount: A:0.45, C:0.03, G:0.06, T:0.47
Consensus pattern (36 bp):
AAAATATATATTATATAAATTTTTAAAAACATTTTA
Found at i:294523 original size:77 final size:75
Alignment explanation
Indices: 294407--294583 Score: 250
Period size: 77 Copynumber: 2.3 Consensus size: 75
294397 TTTATAGTTT
294407 AAAATATATATTATATATATA-TTTTAAAAGCGTTTTGAAAACATTTATATATTATATAAATTTT
1 AAAATATATA-TA-ATATATAGTTTTAAAAGCGTTTTGAAAACATTTATATATTATAT-AATTTT
294471 TAAAAATCATTTTA
63 TAAAAAT-ATTTTA
* **
294485 AAAATTTATATAATATATAGTTTTGAAAA-CGTTTTGAAAACATTTATATATTATATGGTTTTTA
1 AAAATATATATAATATATAGTTTT-AAAAGCGTTTTGAAAACATTTATATATTATATAATTTTTA
*
294549 AAAATATTTTT
65 AAAATATTTTA
*
294560 AAGATATATATAATATATAGTTTT
1 AAAATATATATAATATATAGTTTT
294584 TTTAAAACAT
Statistics
Matches: 91, Mismatches: 6, Indels: 7
0.88 0.06 0.07
Matches are distributed among these distances:
75 27 0.30
76 18 0.20
77 33 0.36
78 13 0.14
ACGTcount: A:0.44, C:0.03, G:0.06, T:0.47
Consensus pattern (75 bp):
AAAATATATATAATATATAGTTTTAAAAGCGTTTTGAAAACATTTATATATTATATAATTTTTAA
AAATATTTTA
Found at i:294588 original size:39 final size:38
Alignment explanation
Indices: 294467--294662 Score: 118
Period size: 37 Copynumber: 5.1 Consensus size: 38
294457 ATTATATAAA
294467 TTTTTAAAAATCA-TTTTAAAAATTTATATAATATATAG--
1 TTTTTAAAAAT-ATTTTTAAAAA--TATATAATATATAGTT
* ** * * *
294505 -TTTTGAAAACGTTTTGAAAACATTTAT-ATATTATA-TGG
1 TTTTTAAAAATATTTTTAAAA-ATATATAATA-TATAGT-T
*
294543 TTTTTAAAAATATTTTTAAGATATATATAATATATAGTT
1 TTTTTAAAAATATTTTTAA-AAATATATAATATATAGTT
* * *
294582 TTTTT-AAAACATTTTTAAAAATATATATTGTATAGTT
1 TTTTTAAAAATATTTTTAAAAATATATAATATATAGTT
** **
294619 TTTAAAAAAAATCATTTTTGAAAACACGTATAATATATAGTT
1 TTT-TTAAAAAT-ATTTTT-AAAA-ATATATAATATATAGTT
294661 TT
1 TT
294663 GAAATTTATA
Statistics
Matches: 120, Mismatches: 23, Indels: 26
0.71 0.14 0.15
Matches are distributed among these distances:
35 3 0.03
36 8 0.07
37 34 0.28
38 13 0.11
39 32 0.27
40 11 0.09
41 4 0.03
42 15 0.12
ACGTcount: A:0.43, C:0.04, G:0.07, T:0.47
Consensus pattern (38 bp):
TTTTTAAAAATATTTTTAAAAATATATAATATATAGTT
Found at i:294731 original size:18 final size:18
Alignment explanation
Indices: 294704--294738 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
294694 TTTTTATAAC
*
294704 ATATTGTTATTATTATTT
1 ATATTATTATTATTATTT
294722 ATATTATTATTATTATT
1 ATATTATTATTATTATT
294739 ATTTATTTCC
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:0.31, C:0.00, G:0.03, T:0.66
Consensus pattern (18 bp):
ATATTATTATTATTATTT
Found at i:294756 original size:21 final size:21
Alignment explanation
Indices: 294705--294744 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
294695 TTTTATAACA
*
294705 TATTGTTATTATTATTTATAT
1 TATTATTATTATTATTTATAT
294726 TATTATTATTATTATTTAT
1 TATTATTATTATTATTTAT
294745 TTCCCTTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.68
Consensus pattern (21 bp):
TATTATTATTATTATTTATAT
Found at i:295777 original size:21 final size:21
Alignment explanation
Indices: 295733--295777 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
295723 CAAATTCTTA
* * *
295733 TTTTATTTATTATTATCATGG
1 TTTTAATTATTACTAGCATGG
*
295754 TTTTAATTATTACTAGCATTG
1 TTTTAATTATTACTAGCATGG
295775 TTT
1 TTT
295778 ATTTTTACTT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.24, C:0.07, G:0.09, T:0.60
Consensus pattern (21 bp):
TTTTAATTATTACTAGCATGG
Found at i:295836 original size:13 final size:12
Alignment explanation
Indices: 295820--295870 Score: 57
Period size: 13 Copynumber: 4.0 Consensus size: 12
295810 TTTTGAAATA
295820 ATTTTTTTGATTT
1 ATTTTTTT-ATTT
295833 ATTTTTTTATATT
1 ATTTTTTTAT-TT
295846 ATTTATTTTATTT
1 ATTT-TTTTATTT
**
295859 CCTTTTTTATTT
1 ATTTTTTTATTT
295871 TTATTTCATT
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
12 10 0.29
13 18 0.53
14 6 0.18
ACGTcount: A:0.18, C:0.04, G:0.02, T:0.76
Consensus pattern (12 bp):
ATTTTTTTATTT
Found at i:295960 original size:20 final size:22
Alignment explanation
Indices: 295937--295983 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
295927 TTTTCTTTCA
* *
295937 TTTTATTCCT-TTTT-TATGTT
1 TTTTATTACTATTTTATATATT
295957 TTTTATTACTATTTTATATATT
1 TTTTATTACTATTTTATATATT
295979 TTTTA
1 TTTTA
295984 ATTTATGTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 9 0.39
21 4 0.17
22 10 0.43
ACGTcount: A:0.19, C:0.06, G:0.02, T:0.72
Consensus pattern (22 bp):
TTTTATTACTATTTTATATATT
Found at i:307996 original size:16 final size:15
Alignment explanation
Indices: 307960--308001 Score: 66
Period size: 16 Copynumber: 2.7 Consensus size: 15
307950 TATATATATA
307960 TTGAAAATATAATTT
1 TTGAAAATATAATTT
*
307975 TCGAAAATATAATTTT
1 TTGAAAATATAA-TTT
307991 TTGAAAATATA
1 TTGAAAATATA
308002 TATGGTATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
15 11 0.46
16 13 0.54
ACGTcount: A:0.48, C:0.02, G:0.07, T:0.43
Consensus pattern (15 bp):
TTGAAAATATAATTT
Found at i:308158 original size:52 final size:52
Alignment explanation
Indices: 308058--308164 Score: 132
Period size: 51 Copynumber: 2.1 Consensus size: 52
308048 ATGTTTAATA
308058 TATATAATTTTTGAAATCATACAGGTTTTGAAAATATAATATATATTATATAT
1 TATATAATTTTTGAAATCATACAGGTTTTGAAAATATAATATATATTAT-TAT
* *
308111 TATATAATTTTT-AAGAT-ATATA-GTTTT-AATATATATATAGTATATTATTAT
1 TATATAATTTTTGAA-ATCATACAGGTTTTGAAAATATA-ATA-TATATTATTAT
308162 TAT
1 TAT
308165 CATCATCTTC
Statistics
Matches: 49, Mismatches: 2, Indels: 8
0.83 0.03 0.14
Matches are distributed among these distances:
50 7 0.14
51 14 0.29
52 14 0.29
53 14 0.29
ACGTcount: A:0.42, C:0.02, G:0.07, T:0.50
Consensus pattern (52 bp):
TATATAATTTTTGAAATCATACAGGTTTTGAAAATATAATATATATTATTAT
Found at i:310424 original size:17 final size:17
Alignment explanation
Indices: 310402--310436 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
310392 TCTCACTAAC
*
310402 TTGTTTCCTTTCATTTT
1 TTGTTTCATTTCATTTT
*
310419 TTGTTTTATTTCATTTT
1 TTGTTTCATTTCATTTT
310436 T
1 T
310437 ATCATTTGCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.09, C:0.11, G:0.06, T:0.74
Consensus pattern (17 bp):
TTGTTTCATTTCATTTT
Found at i:311652 original size:23 final size:25
Alignment explanation
Indices: 311615--311663 Score: 66
Period size: 23 Copynumber: 2.0 Consensus size: 25
311605 ATAATTATGA
*
311615 AAAATATATTAATTTATATATAAAT
1 AAAATATATTAATTTATATAGAAAT
*
311640 AAAATAT-TT-ATTTATTTAGAAAT
1 AAAATATATTAATTTATATAGAAAT
311663 A
1 A
311664 TCAGAAAAGG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 13 0.59
24 2 0.09
25 7 0.32
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (25 bp):
AAAATATATTAATTTATATAGAAAT
Found at i:311994 original size:13 final size:13
Alignment explanation
Indices: 311976--312027 Score: 59
Period size: 13 Copynumber: 3.7 Consensus size: 13
311966 ATTAAAAGTA
311976 AACATATAAAATT
1 AACATATAAAATT
*
311989 AACATATAACTAAAGTA
1 AACATAT-A--AAA-TT
312006 AACATATAAAATT
1 AACATATAAAATT
312019 AACATATAA
1 AACATATAA
312028 CTAAACAATG
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
13 17 0.52
14 4 0.12
16 4 0.12
17 8 0.24
ACGTcount: A:0.62, C:0.10, G:0.02, T:0.27
Consensus pattern (13 bp):
AACATATAAAATT
Found at i:312006 original size:30 final size:30
Alignment explanation
Indices: 311970--312032 Score: 126
Period size: 30 Copynumber: 2.1 Consensus size: 30
311960 ATAATAATTA
311970 AAAGTAAACATATAAAATTAACATATAACT
1 AAAGTAAACATATAAAATTAACATATAACT
312000 AAAGTAAACATATAAAATTAACATATAACT
1 AAAGTAAACATATAAAATTAACATATAACT
312030 AAA
1 AAA
312033 CAATGAACAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.62, C:0.10, G:0.03, T:0.25
Consensus pattern (30 bp):
AAAGTAAACATATAAAATTAACATATAACT
Found at i:312009 original size:17 final size:15
Alignment explanation
Indices: 311969--312016 Score: 55
Period size: 17 Copynumber: 3.2 Consensus size: 15
311959 AATAATAATT
311969 AAAAGTAAACATAT-
1 AAAAGTAAACATATA
*
311983 AAAA-TTAACATATA
1 AAAAGTAAACATATA
311997 ACTAAAGTAAACATATA
1 A--AAAGTAAACATATA
312014 AAA
1 AAA
312017 TTAACATATA
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
13 8 0.29
14 5 0.18
15 2 0.07
16 3 0.11
17 10 0.36
ACGTcount: A:0.65, C:0.08, G:0.04, T:0.23
Consensus pattern (15 bp):
AAAAGTAAACATATA
Found at i:312032 original size:17 final size:17
Alignment explanation
Indices: 311982--312032 Score: 56
Period size: 14 Copynumber: 3.2 Consensus size: 17
311972 AGTAAACATA
311982 TAAAATTAACATATAAC
1 TAAAATTAACATATAAC
* *
311999 T-AAAGTAA-ACAT-A-
1 TAAAATTAACATATAAC
312012 TAAAATTAACATATAAC
1 TAAAATTAACATATAAC
312029 TAAA
1 TAAA
312033 CAATGAACAA
Statistics
Matches: 26, Mismatches: 4, Indels: 8
0.68 0.11 0.21
Matches are distributed among these distances:
13 1 0.04
14 7 0.27
15 6 0.23
16 7 0.27
17 5 0.19
ACGTcount: A:0.61, C:0.10, G:0.02, T:0.27
Consensus pattern (17 bp):
TAAAATTAACATATAAC
Found at i:313309 original size:3 final size:3
Alignment explanation
Indices: 313301--313363 Score: 87
Period size: 3 Copynumber: 21.7 Consensus size: 3
313291 TAAAATTATT
*
313301 TAA TAA TAA TAA TAA T-A TAA TAA TTA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
313348 TAA -AA T-A TAAA TAA TA
1 TAA TAA TAA T-AA TAA TA
313364 TTCGAATGAA
Statistics
Matches: 54, Mismatches: 2, Indels: 8
0.84 0.03 0.12
Matches are distributed among these distances:
2 6 0.11
3 46 0.85
4 2 0.04
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:313921 original size:113 final size:114
Alignment explanation
Indices: 313668--314229 Score: 814
Period size: 113 Copynumber: 5.0 Consensus size: 114
313658 TAGAGTTATG
* *
313668 CAAAAGGTTGAACAAGTTCTTTTCATTATGAACTTCCTCTTCCTTCTTCAGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
** * * * *
313733 TTATGAACACT-TCTGGCAATGCTGATCCATCAAATGAT-GAATTCAAA
66 TTATGAACTTTCTCTGGAAATGCTGATCCATCAAGTGATGGATTTGAAA
* *
313780 CAAAAGGTTGAACAAATTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
* *
313845 TTATGAACTTTCTCTGGAAATGCTGATCCATCAGGTGATGGATTTGAGA
66 TTATGAACTTTCTCTGGAAATGCTGATCCATCAAGTGATGGATTTGAAA
*
313894 -AAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
* *
313958 TTATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTTG-AG
66 TTATGAACTTTCTCTGGAAATGCTGATCCATCAAGTGATGGATTTGAAA
*
314006 CAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
* ** * * *
314071 TTATGAAC-TT-TCTGGCAATATTGATCCATCAAATGAT-GAATTCAAA
66 TTATGAACTTTCTCTGGAAATGCTGATCCATCAAGTGATGGATTTGAAA
* * *
314117 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTATTA
1 CAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
* * * *
314182 TTATGAACTTTCTCTTGAAAAGCTAATCCATCGAGTGATGGATTTGAA
66 TTATGAACTTTCTCTGGAAATGCTGATCCATCAAGTGATGGATTTGAA
314230 TCTTTGCTAA
Statistics
Matches: 402, Mismatches: 41, Indels: 12
0.88 0.09 0.03
Matches are distributed among these distances:
110 4 0.01
111 92 0.23
112 74 0.18
113 220 0.55
114 12 0.03
ACGTcount: A:0.28, C:0.20, G:0.15, T:0.37
Consensus pattern (114 bp):
CAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
TTATGAACTTTCTCTGGAAATGCTGATCCATCAAGTGATGGATTTGAAA
Found at i:314194 original size:224 final size:227
Alignment explanation
Indices: 313668--314229 Score: 828
Period size: 224 Copynumber: 2.5 Consensus size: 227
313658 TAGAGTTATG
* *
313668 CAAAAGGTTGAACAAGTTCTTTTCATTATGAACTTCCTCTTCCTTCTTCAGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
** * * * * ** *
313733 TTATGAACACT-TCTGGCAATGCTGATCCATCAAATGATGAATTCAAACAAAAGGTTGAACAAAT
66 TTATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTTGAACAAAAGGTTGAACAAAC
*
313797 TCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGG
131 TCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGG
* ** * * *
313862 AAATGCTGATCCATCAGGTGATGGATTTGAGA
196 AAATACTGATCCATCAAATGATGGAATTCAAA
*
313894 -AAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
* *
313958 TTATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTTGAGCAAAAGGTTGAACAAGC
66 TTATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTTGAACAAAAGGTTGAACAAAC
314023 TCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAAC-TT-TCTGG
131 TCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGG
* *
314086 CAATATTGATCCATCAAATGAT-GAATTCAAA
196 AAATACTGATCCATCAAATGATGGAATTCAAA
* * *
314117 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTATTA
1 CAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
* * *
314182 TTATGAACTTTCTCTTGAAAAGCTAATCCATCGAGTGATGGATTTGAA
66 TTATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTTGAA
314230 TCTTTGCTAA
Statistics
Matches: 303, Mismatches: 31, Indels: 6
0.89 0.09 0.02
Matches are distributed among these distances:
223 6 0.02
224 126 0.42
225 72 0.24
226 99 0.33
ACGTcount: A:0.28, C:0.20, G:0.15, T:0.37
Consensus pattern (227 bp):
CAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
TTATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTTGAACAAAAGGTTGAACAAAC
TCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGG
AAATACTGATCCATCAAATGATGGAATTCAAA
Found at i:315758 original size:12 final size:12
Alignment explanation
Indices: 315741--315787 Score: 62
Period size: 11 Copynumber: 4.0 Consensus size: 12
315731 ATCTTGACCC
315741 TTCTTTTTTCTT
1 TTCTTTTTTCTT
315753 TTC-TTTTT-TT
1 TTCTTTTTTCTT
*
315763 TTCTTTTTTCAT
1 TTCTTTTTTCTT
315775 TTCATTTTTTCTT
1 TTC-TTTTTTCTT
315788 CAAGCATAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
10 5 0.17
11 10 0.33
12 7 0.23
13 8 0.27
ACGTcount: A:0.04, C:0.15, G:0.00, T:0.81
Consensus pattern (12 bp):
TTCTTTTTTCTT
Found at i:315766 original size:22 final size:22
Alignment explanation
Indices: 315741--315784 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
315731 ATCTTGACCC
* *
315741 TTCTTTTTTCTTTTCTTTTTTT
1 TTCTTTTTTCATTTCATTTTTT
315763 TTCTTTTTTCATTTCATTTTTT
1 TTCTTTTTTCATTTCATTTTTT
315785 CTTCAAGCAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.05, C:0.14, G:0.00, T:0.82
Consensus pattern (22 bp):
TTCTTTTTTCATTTCATTTTTT
Found at i:319330 original size:9 final size:9
Alignment explanation
Indices: 319307--319337 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
319297 GAAAAATAAT
319307 GAATGTAAA
1 GAATGTAAA
319316 -AATGTAAA
1 GAATGTAAA
319324 GAATGTAAA
1 GAATGTAAA
319333 GAATG
1 GAATG
319338 ATTGCCATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
8 8 0.38
9 13 0.62
ACGTcount: A:0.55, C:0.00, G:0.23, T:0.23
Consensus pattern (9 bp):
GAATGTAAA
Found at i:323132 original size:15 final size:15
Alignment explanation
Indices: 323109--323140 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
323099 AAAATAATGC
323109 AATGAATGTATGCAA
1 AATGAATGTATGCAA
*
323124 AATGCATGTATGCAA
1 AATGAATGTATGCAA
323139 AA
1 AA
323141 GGTATTGATC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.47, C:0.09, G:0.19, T:0.25
Consensus pattern (15 bp):
AATGAATGTATGCAA
Found at i:326508 original size:28 final size:27
Alignment explanation
Indices: 326447--326510 Score: 74
Period size: 28 Copynumber: 2.3 Consensus size: 27
326437 TGAAAGTAAA
* *
326447 ATGAAATATTAATAATATATATAAATACT
1 ATGAAA-A-TAATAATATATATAAAAAAT
326476 ATGAAAATAATAAGTATATATAAAAAAT
1 ATGAAAATAATAA-TATATATAAAAAAT
*
326504 TTGAAAA
1 ATGAAAA
326511 GAAAGAATTA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
27 6 0.19
28 19 0.61
29 6 0.19
ACGTcount: A:0.59, C:0.02, G:0.06, T:0.33
Consensus pattern (27 bp):
ATGAAAATAATAATATATATAAAAAAT
Found at i:327028 original size:23 final size:25
Alignment explanation
Indices: 326991--327039 Score: 66
Period size: 23 Copynumber: 2.0 Consensus size: 25
326981 ATAATTATGA
*
326991 AAAATATATTAATTTATATATAAAT
1 AAAATATATTAATTTATATAGAAAT
*
327016 AAAATAT-TT-ATTTATTTAGAAAT
1 AAAATATATTAATTTATATAGAAAT
327039 A
1 A
327040 TCAGAAAAGG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 13 0.59
24 2 0.09
25 7 0.32
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (25 bp):
AAAATATATTAATTTATATAGAAAT
Found at i:328653 original size:3 final size:3
Alignment explanation
Indices: 328645--328722 Score: 72
Period size: 3 Copynumber: 26.7 Consensus size: 3
328635 TAAAATTATT
* * * *
328645 TAA TAA TAA TAA TAA TAA T-A TAA TAA TTA TAA TTA TAA TTA TAA TTA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* *
328692 TAT TTA TAA TAA TAA TAA -AA T-A TAAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TA
328723 TTCAAATGAA
Statistics
Matches: 59, Mismatches: 12, Indels: 8
0.75 0.15 0.10
Matches are distributed among these distances:
2 6 0.10
3 51 0.86
4 2 0.03
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (3 bp):
TAA
Found at i:332160 original size:10 final size:10
Alignment explanation
Indices: 332113--332141 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
332103 AACTGTTGAC
332113 CGTTGACCAG
1 CGTTGACCAG
332123 CGTTGACCAG
1 CGTTGACCAG
332133 CGTTGACCA
1 CGTTGACCA
332142 AAACTTTGAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.21, C:0.31, G:0.28, T:0.21
Consensus pattern (10 bp):
CGTTGACCAG
Found at i:334429 original size:24 final size:24
Alignment explanation
Indices: 334402--334520 Score: 150
Period size: 24 Copynumber: 5.0 Consensus size: 24
334392 TTCGATTTAA
*
334402 ATTCTGATCTGACACTTGACATGG
1 ATTCTGATCTGATACTTGACATGG
* *
334426 ATTCTGATATGATA-TCTGAAATGG
1 ATTCTGATCTGATACT-TGACATGG
* *
334450 ATTTTGATCTGATACTTGACTTGG
1 ATTCTGATCTGATACTTGACATGG
*
334474 ATTCTGATCTGATACTTGACCTGG
1 ATTCTGATCTGATACTTGACATGG
* *
334498 ATTTTGATATGATACTTGACATG
1 ATTCTGATCTGATACTTGACATG
334521 AATTATGTTT
Statistics
Matches: 81, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
23 1 0.01
24 79 0.98
25 1 0.01
ACGTcount: A:0.26, C:0.14, G:0.20, T:0.39
Consensus pattern (24 bp):
ATTCTGATCTGATACTTGACATGG
Found at i:337167 original size:32 final size:32
Alignment explanation
Indices: 337126--337189 Score: 119
Period size: 32 Copynumber: 2.0 Consensus size: 32
337116 GAGATGAGTC
337126 AGCCCATCACTCATACCATCCCACACTCTAAG
1 AGCCCATCACTCATACCATCCCACACTCTAAG
*
337158 AGCCCATCACTCCTACCATCCCACACTCTAAG
1 AGCCCATCACTCATACCATCCCACACTCTAAG
337190 TGAAAAAGAG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.30, C:0.45, G:0.06, T:0.19
Consensus pattern (32 bp):
AGCCCATCACTCATACCATCCCACACTCTAAG
Found at i:337184 original size:16 final size:17
Alignment explanation
Indices: 337128--337185 Score: 59
Period size: 16 Copynumber: 3.6 Consensus size: 17
337118 GATGAGTCAG
*
337128 CCCATCACTCATACCAT
1 CCCATCACTCCTACCAT
** *
337145 CCCA-CACT-CTAAGAG
1 CCCATCACTCCTACCAT
337160 CCCATCACTCCTACCAT
1 CCCATCACTCCTACCAT
337177 CCCA-CACTC
1 CCCATCACTC
337186 TAAGTGAAAA
Statistics
Matches: 32, Mismatches: 7, Indels: 5
0.73 0.16 0.11
Matches are distributed among these distances:
15 7 0.22
16 13 0.41
17 12 0.38
ACGTcount: A:0.28, C:0.50, G:0.03, T:0.19
Consensus pattern (17 bp):
CCCATCACTCCTACCAT
Found at i:346627 original size:19 final size:20
Alignment explanation
Indices: 346584--346631 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
346574 TCTAAATCCT
*
346584 TTTTCAAAATTTCATTTTGG
1 TTTTCAAAATCTCATTTTGG
* *
346604 CTTTCAAAATCT-ATTTTTG
1 TTTTCAAAATCTCATTTTGG
346623 TTTTCAAAA
1 TTTTCAAAA
346632 GAAAATCGTT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.29, C:0.12, G:0.06, T:0.52
Consensus pattern (20 bp):
TTTTCAAAATCTCATTTTGG
Found at i:347799 original size:21 final size:21
Alignment explanation
Indices: 347773--347814 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
347763 CCAGAATGGG
*
347773 GGGAATCGGTACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
347794 GGGAATCGATACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
347815 ATATTCAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.26, C:0.29, G:0.21, T:0.24
Consensus pattern (21 bp):
GGGAATCGATACCCCTTCATA
Found at i:348002 original size:21 final size:20
Alignment explanation
Indices: 347978--348039 Score: 79
Period size: 21 Copynumber: 3.0 Consensus size: 20
347968 ATCTGTTCAC
347978 GGGGAATCGATACCCCCTGGG
1 GGGGAATCG-TACCCCCTGGG
*
347999 GGGGAATCTGTTCCCCCTGGG
1 GGGGAATC-GTACCCCCTGGG
*
348020 GGGGAATTTGTACCCCCTGG
1 GGGGAA-TCGTACCCCCTGG
348040 ACAATCTGAT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
21 34 0.94
22 2 0.06
ACGTcount: A:0.15, C:0.27, G:0.37, T:0.21
Consensus pattern (20 bp):
GGGGAATCGTACCCCCTGGG
Found at i:348008 original size:36 final size:34
Alignment explanation
Indices: 347928--348011 Score: 123
Period size: 34 Copynumber: 2.4 Consensus size: 34
347918 AAACCATGCA
* *
347928 GGGGGAATCTGTACCCGGGGAATCGATACCCCTG
1 GGGGGAATCTGTTCACGGGGAATCGATACCCCTG
*
347962 GGGGAAATCTGTTCACGGGGAATCGATACCCCCTGG
1 GGGGGAATCTGTTCACGGGGAATCGATA-CCCCT-G
347998 GGGGGAATCTGTTC
1 GGGGGAATCTGTTC
348012 CCCCTGGGGG
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
34 25 0.57
35 5 0.11
36 14 0.32
ACGTcount: A:0.20, C:0.24, G:0.36, T:0.20
Consensus pattern (34 bp):
GGGGGAATCTGTTCACGGGGAATCGATACCCCTG
Found at i:358120 original size:40 final size:40
Alignment explanation
Indices: 358035--358152 Score: 132
Period size: 40 Copynumber: 3.0 Consensus size: 40
358025 CTCGAAAAAT
* ** ** *
358035 TATATTAGATTTTTTTTTATCAAAACTAACAAATTTAAAAT
1 TATATTATA-TTTTTTTTATTGAAACTAACAAATTTGCAAG
358076 TATATTATATTTTTTTTATTGAAACTAACAAATTTGCAAG
1 TATATTATATTTTTTTTATTGAAACTAACAAATTTGCAAG
* * *
358116 TATATT-T-TATATTTTATTGAAACTAACAATTTTGCAA
1 TATATTATATTTTTTTTATTGAAACTAACAAATTTGCAA
358153 CAAAAATCGT
Statistics
Matches: 68, Mismatches: 9, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
38 27 0.40
39 1 0.01
40 32 0.47
41 8 0.12
ACGTcount: A:0.40, C:0.08, G:0.05, T:0.47
Consensus pattern (40 bp):
TATATTATATTTTTTTTATTGAAACTAACAAATTTGCAAG
Found at i:358140 original size:38 final size:40
Alignment explanation
Indices: 358057--358152 Score: 124
Period size: 38 Copynumber: 2.5 Consensus size: 40
358047 TTTTTTATCA
** * * *
358057 AAACTAACAAATTTAAAATTATATTATATTTTTTTTATTG
1 AAACTAACAAATTTGCAAGTATATTATATATATTTTATTG
358097 AAACTAACAAATTTGCAAGTATATT-T-TATATTTTATTG
1 AAACTAACAAATTTGCAAGTATATTATATATATTTTATTG
*
358135 AAACTAACAATTTTGCAA
1 AAACTAACAAATTTGCAA
358153 CAAAAATCGT
Statistics
Matches: 50, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
38 27 0.54
39 1 0.02
40 22 0.44
ACGTcount: A:0.43, C:0.08, G:0.05, T:0.44
Consensus pattern (40 bp):
AAACTAACAAATTTGCAAGTATATTATATATATTTTATTG
Found at i:359003 original size:25 final size:23
Alignment explanation
Indices: 358960--359012 Score: 70
Period size: 25 Copynumber: 2.2 Consensus size: 23
358950 TTTGTGGTTA
* *
358960 TTTAAAAAAATTATGTTTTCTTT
1 TTTAAAAAAATTATATTTTATTT
358983 TTTAAAAAAATATATAATTTTATTT
1 TTTAAAAAAAT-TAT-ATTTTATTT
359008 TTTAA
1 TTTAA
359013 TTTTAAATAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
23 11 0.42
24 3 0.12
25 12 0.46
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.55
Consensus pattern (23 bp):
TTTAAAAAAATTATATTTTATTT
Found at i:359008 original size:24 final size:23
Alignment explanation
Indices: 358960--359009 Score: 57
Period size: 23 Copynumber: 2.1 Consensus size: 23
358950 TTTGTGGTTA
* *
358960 TTTAAAAAAATTATGTTTTCTTT
1 TTTAAAAAAATTATATTTTCATT
358983 TTTAAAAAAATATATAATTTT-ATT
1 TTTAAAAAAAT-TAT-ATTTTCATT
359007 TTT
1 TTT
359010 TAATTTTAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
23 11 0.48
24 8 0.35
25 4 0.17
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (23 bp):
TTTAAAAAAATTATATTTTCATT
Found at i:359149 original size:28 final size:29
Alignment explanation
Indices: 359105--359164 Score: 86
Period size: 28 Copynumber: 2.1 Consensus size: 29
359095 CATTTTGAGT
*
359105 AACGAAATGAAATGTTAGGCACCAAATTGA
1 AACGAAA-GAAATGTTAGGCACCAAACTGA
*
359135 AACGAAA-AAATGTTAGGCACTAAACTGA
1 AACGAAAGAAATGTTAGGCACCAAACTGA
359163 AA
1 AA
359165 AAACGAGCAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
28 21 0.75
30 7 0.25
ACGTcount: A:0.50, C:0.13, G:0.18, T:0.18
Consensus pattern (29 bp):
AACGAAAGAAATGTTAGGCACCAAACTGA
Found at i:360536 original size:21 final size:21
Alignment explanation
Indices: 360487--360527 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
360477 GAACTGTTTT
360487 TGTATCAATGTCTGCCATAGA
1 TGTATCAATGTCTGCCATAGA
360508 TGTATCAATGTCTGCCATAG
1 TGTATCAATGTCTGCCATAG
360528 TACTTTCAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.27, C:0.20, G:0.20, T:0.34
Consensus pattern (21 bp):
TGTATCAATGTCTGCCATAGA
Found at i:362738 original size:19 final size:20
Alignment explanation
Indices: 362695--362738 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
362685 TAGTTCTTAT
362695 GTTTTCTCCATTATTATTCA
1 GTTTTCTCCATTATTATTCA
* * *
362715 CTTTTCTGCTTTATT-TTCA
1 GTTTTCTCCATTATTATTCA
362734 GTTTT
1 GTTTT
362739 GAAAAGGGAA
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
19 8 0.40
20 12 0.60
ACGTcount: A:0.14, C:0.18, G:0.07, T:0.61
Consensus pattern (20 bp):
GTTTTCTCCATTATTATTCA
Found at i:363810 original size:11 final size:11
Alignment explanation
Indices: 363794--363828 Score: 61
Period size: 11 Copynumber: 3.1 Consensus size: 11
363784 ATATGAATTG
363794 AGTCATTGCTA
1 AGTCATTGCTA
363805 AGTCATTGCTA
1 AGTCATTGCTA
363816 AGTCATTGGCTA
1 AGTCATT-GCTA
363828 A
1 A
363829 ATGAAAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
11 18 0.78
12 5 0.22
ACGTcount: A:0.29, C:0.17, G:0.20, T:0.34
Consensus pattern (11 bp):
AGTCATTGCTA
Found at i:365951 original size:22 final size:22
Alignment explanation
Indices: 365926--365970 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
365916 ATTGTTCATG
* *
365926 TGGTATTGATACTGTAAGAACA
1 TGGTATCGATACTATAAGAACA
365948 TGGTATCGATACTATAAGAACA
1 TGGTATCGATACTATAAGAACA
365970 T
1 T
365971 TATCGGTACT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.38, C:0.11, G:0.20, T:0.31
Consensus pattern (22 bp):
TGGTATCGATACTATAAGAACA
Found at i:365980 original size:20 final size:21
Alignment explanation
Indices: 365928--365980 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 21
365918 TGTTCATGTG
* *
365928 GTATTGATACTGTAAGAACAT
1 GTATCGATACTATAAGAACAT
365949 GGTATCGATACTATAAGAACAT
1 -GTATCGATACTATAAGAACAT
*
365971 -TATCGGTACT
1 GTATCGATACT
365981 TCTTTTCTAG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
20 9 0.32
22 19 0.68
ACGTcount: A:0.36, C:0.13, G:0.19, T:0.32
Consensus pattern (21 bp):
GTATCGATACTATAAGAACAT
Found at i:368296 original size:13 final size:13
Alignment explanation
Indices: 368278--368308 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
368268 AAAATTAATG
368278 AAAATAAATAAAT
1 AAAATAAATAAAT
368291 AAAATAAATAAAT
1 AAAATAAATAAAT
368304 AAAAT
1 AAAAT
368309 TTCTCTTCGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (13 bp):
AAAATAAATAAAT
Found at i:368866 original size:17 final size:14
Alignment explanation
Indices: 368821--368873 Score: 65
Period size: 13 Copynumber: 3.7 Consensus size: 14
368811 AGCATTGTGA
368821 AAAGAAAAT-AATG
1 AAAGAAAATAAATG
368834 AAAGAAAATAAA-G
1 AAAGAAAATAAATG
368847 AAAGAAAGATGAAGATG
1 AAAGAAA-AT-AA-ATG
368864 AAAGAAAATA
1 AAAGAAAATA
368874 GAACTTCAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
13 17 0.49
14 4 0.11
15 3 0.09
16 3 0.09
17 8 0.23
ACGTcount: A:0.70, C:0.00, G:0.19, T:0.11
Consensus pattern (14 bp):
AAAGAAAATAAATG
Found at i:371421 original size:21 final size:21
Alignment explanation
Indices: 371392--371444 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
371382 ATTCTGACTA
371392 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTCCAAAT
* *
371413 TCGCGTTGCGATTTTCCTAAT
1 TCGCATTGCGATTTTCCAAAT
*
371434 TCGCAATGCGA
1 TCGCATTGCGA
371445 ATACGTAAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.21, C:0.25, G:0.19, T:0.36
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCAAAT
Found at i:371459 original size:20 final size:20
Alignment explanation
Indices: 371434--371601 Score: 176
Period size: 20 Copynumber: 8.3 Consensus size: 20
371424 TTTTCCTAAT
371434 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
** ** *
371454 TCGCAACACGAATTTGGAAAA
1 TCGCAATGCGAA-TACGTAAA
*
371475 TCGCAATGCGATTACGTAAA
1 TCGCAATGCGAATACGTAAA
** ** *
371495 TCGCAACACGAATTTGGAAAA
1 TCGCAATGCGAA-TACGTAAA
*
371516 TCGCAATGCGATTACGTAAA
1 TCGCAATGCGAATACGTAAA
371536 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
371556 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
* *
371576 TCGCAACGCTAAT-CTGTAAA
1 TCGCAATGCGAATAC-GTAAA
371596 TCGCAA
1 TCGCAA
371602 CACGAATCTA
Statistics
Matches: 119, Mismatches: 26, Indels: 6
0.79 0.17 0.04
Matches are distributed among these distances:
19 1 0.01
20 90 0.76
21 28 0.24
ACGTcount: A:0.39, C:0.21, G:0.19, T:0.21
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:371477 original size:21 final size:21
Alignment explanation
Indices: 371451--371521 Score: 90
Period size: 21 Copynumber: 3.4 Consensus size: 21
371441 GCGAATACGT
371451 AAATCGCAACACGAATTTGGA
1 AAATCGCAACACGAATTTGGA
** ** *
371472 AAATCGCAATGCG-ATTACGT
1 AAATCGCAACACGAATTTGGA
371492 AAATCGCAACACGAATTTGGA
1 AAATCGCAACACGAATTTGGA
371513 AAATCGCAA
1 AAATCGCAA
371522 TGCGATTACG
Statistics
Matches: 39, Mismatches: 10, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
20 15 0.38
21 24 0.62
ACGTcount: A:0.42, C:0.20, G:0.18, T:0.20
Consensus pattern (21 bp):
AAATCGCAACACGAATTTGGA
Found at i:371480 original size:41 final size:41
Alignment explanation
Indices: 371434--371582 Score: 228
Period size: 41 Copynumber: 3.7 Consensus size: 41
371424 TTTTCCTAAT
371434 TCGCAATGCGAATACGTAAATCGCAACACGAATTTGGAAAA
1 TCGCAATGCGAATACGTAAATCGCAACACGAATTTGGAAAA
*
371475 TCGCAATGCGATTACGTAAATCGCAACACGAATTTGGAAAA
1 TCGCAATGCGAATACGTAAATCGCAACACGAATTTGGAAAA
* ** ** *
371516 TCGCAATGCGATTACGTAAATCGCAATGCGAA-TACGTAAA
1 TCGCAATGCGAATACGTAAATCGCAACACGAATTTGGAAAA
371556 TCGCAATGCGAATACGTAAATCGCAAC
1 TCGCAATGCGAATACGTAAATCGCAAC
371583 GCTAATCTGT
Statistics
Matches: 100, Mismatches: 8, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
40 30 0.30
41 70 0.70
ACGTcount: A:0.39, C:0.21, G:0.19, T:0.21
Consensus pattern (41 bp):
TCGCAATGCGAATACGTAAATCGCAACACGAATTTGGAAAA
Found at i:371608 original size:40 final size:41
Alignment explanation
Indices: 371434--371601 Score: 216
Period size: 41 Copynumber: 4.1 Consensus size: 41
371424 TTTTCCTAAT
*
371434 TCGCAATGCGAATACGTAAATCGCAACACGAATTTGGAAAA
1 TCGCAATGCGAATACGTAAATCGCAACACGAATCTGGAAAA
* *
371475 TCGCAATGCGATTACGTAAATCGCAACACGAATTTGGAAAA
1 TCGCAATGCGAATACGTAAATCGCAACACGAATCTGGAAAA
* ** *
371516 TCGCAATGCGATTACGTAAATCGCAATGCGAATAC--GTAAA
1 TCGCAATGCGAATACGTAAATCGCAACACGAAT-CTGGAAAA
* * *
371556 TCGCAATGCGAATACGTAAATCGCAACGCTAATCT-GTAAA
1 TCGCAATGCGAATACGTAAATCGCAACACGAATCTGGAAAA
371596 TCGCAA
1 TCGCAA
371602 CACGAATCTA
Statistics
Matches: 117, Mismatches: 8, Indels: 5
0.90 0.06 0.04
Matches are distributed among these distances:
39 1 0.01
40 45 0.38
41 71 0.61
ACGTcount: A:0.39, C:0.21, G:0.19, T:0.21
Consensus pattern (41 bp):
TCGCAATGCGAATACGTAAATCGCAACACGAATCTGGAAAA
Found at i:371618 original size:20 final size:20
Alignment explanation
Indices: 371595--371641 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
371585 TAATCTGTAA
371595 ATCGCAAC-ACGAATCTAACT
1 ATCGCAACGA-GAATCTAACT
* *
371615 ATCGCAACGAGATTCTGACT
1 ATCGCAACGAGAATCTAACT
371635 ATCGCAA
1 ATCGCAA
371642 TACTGAATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 23 0.96
21 1 0.04
ACGTcount: A:0.36, C:0.28, G:0.15, T:0.21
Consensus pattern (20 bp):
ATCGCAACGAGAATCTAACT
Found at i:372515 original size:24 final size:24
Alignment explanation
Indices: 372483--372536 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
372473 GTATTCAAAA
* *
372483 TTTGATCTTGGTTAATACCCGGAC
1 TTTGATCTTAGTCAATACCCGGAC
* *
372507 TTTGATCTTAGTCAATACTCGGAT
1 TTTGATCTTAGTCAATACCCGGAC
372531 TTTGAT
1 TTTGAT
372537 GATGTTTCAG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.22, C:0.17, G:0.19, T:0.43
Consensus pattern (24 bp):
TTTGATCTTAGTCAATACCCGGAC
Found at i:374993 original size:20 final size:21
Alignment explanation
Indices: 374968--375056 Score: 105
Period size: 20 Copynumber: 4.4 Consensus size: 21
374958 CAACGCGGAA
*
374968 ATCGCAACGC-AAATATGATT
1 ATCGCAACGCGAAATATGACT
* *
374988 ATCGCAACACGGAA-ATGACT
1 ATCGCAACGCGAAATATGACT
*
375008 ATCGCAACGCGAAAT-TAACT
1 ATCGCAACGCGAAATATGACT
*
375028 ATCGCAACGC-AAAAATGACT
1 ATCGCAACGCGAAATATGACT
375048 ATCGCAACG
1 ATCGCAACG
375057 AGAGAATCGC
Statistics
Matches: 58, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
19 3 0.05
20 53 0.91
21 2 0.03
ACGTcount: A:0.40, C:0.25, G:0.17, T:0.18
Consensus pattern (21 bp):
ATCGCAACGCGAAATATGACT
Found at i:375031 original size:40 final size:40
Alignment explanation
Indices: 374968--375056 Score: 117
Period size: 40 Copynumber: 2.2 Consensus size: 40
374958 CAACGCGGAA
* * **
374968 ATCGCAACGCAAATATGATTATCGCAACACGGAAATGACT
1 ATCGCAACGCAAATATAACTATCGCAACACAAAAATGACT
*
375008 ATCGCAACGCGAAAT-TAACTATCGCAACGCAAAAATGACT
1 ATCGCAACGC-AAATATAACTATCGCAACACAAAAATGACT
375048 ATCGCAACG
1 ATCGCAACG
375057 AGAGAATCGC
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
40 39 0.91
41 4 0.09
ACGTcount: A:0.40, C:0.25, G:0.17, T:0.18
Consensus pattern (40 bp):
ATCGCAACGCAAATATAACTATCGCAACACAAAAATGACT
Found at i:375116 original size:34 final size:34
Alignment explanation
Indices: 375028--375117 Score: 128
Period size: 33 Copynumber: 2.7 Consensus size: 34
375018 GAAATTAACT
* * **
375028 ATCGCAACGCAAAAATGACTATCGCAACGAGAGA
1 ATCGCAATGCGAAAATGAAAATCGCAACGAGAGA
*
375062 ATCGCAATGCG-AAATGAAAATCGCAACGAGTGA
1 ATCGCAATGCGAAAATGAAAATCGCAACGAGAGA
375095 ATCGCAATGCGAAAATGAAAATC
1 ATCGCAATGCGAAAATGAAAATC
375118 CCTATGCAAA
Statistics
Matches: 50, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
33 30 0.60
34 20 0.40
ACGTcount: A:0.44, C:0.20, G:0.21, T:0.14
Consensus pattern (34 bp):
ATCGCAATGCGAAAATGAAAATCGCAACGAGAGA
Found at i:375179 original size:14 final size:14
Alignment explanation
Indices: 375160--375213 Score: 54
Period size: 14 Copynumber: 3.5 Consensus size: 14
375150 CATTTTCGCA
375160 TTGCGATTCTCTCG
1 TTGCGATTCTCTCG
*
375174 TTGCGATTTTCATTTCG
1 TTGCGA--TTC-TCTCG
375191 CATTGCGATTCTCTCG
1 --TTGCGATTCTCTCG
375207 TTGCGAT
1 TTGCGAT
375214 AGTCATTTCC
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
14 13 0.39
16 7 0.21
17 7 0.21
19 6 0.18
ACGTcount: A:0.11, C:0.24, G:0.20, T:0.44
Consensus pattern (14 bp):
TTGCGATTCTCTCG
Found at i:375183 original size:34 final size:34
Alignment explanation
Indices: 375138--375233 Score: 149
Period size: 33 Copynumber: 2.9 Consensus size: 34
375128 TTTAGTTTCG
*
375138 CGTTGCAATTTTCATTTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTTCGCATTGCGATTCTCT
375172 CGTTGCGATTTTCA-TTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTTCGCATTGCGATTCTCT
** *
375205 CGTTGCGATAGTCATTTCCGCATTGCGAT
1 CGTTGCGATTTTCATTTTCGCATTGCGAT
375234 AGTCTATTTT
Statistics
Matches: 57, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
33 31 0.54
34 26 0.46
ACGTcount: A:0.15, C:0.24, G:0.19, T:0.43
Consensus pattern (34 bp):
CGTTGCGATTTTCATTTTCGCATTGCGATTCTCT
Found at i:375358 original size:14 final size:14
Alignment explanation
Indices: 375339--375375 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
375329 CATCAATTAA
375339 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
375353 ACAAATCATCTTTT
1 ACAAATCAACATTT
375367 ACAAATCAA
1 ACAAATCAA
375376 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:376813 original size:21 final size:22
Alignment explanation
Indices: 376789--376865 Score: 65
Period size: 21 Copynumber: 3.7 Consensus size: 22
376779 TGACATTGGC
376789 CTCTTGAACGG-TGAGAGGGGA
1 CTCTTGAACGGATGAGAGGGGA
* * *
376810 CTCTTG-AGGGATGATAGGGGC
1 CTCTTGAACGGATGAGAGGGGA
* *
376831 CTCTTGAAC-GAT-AGGGGAGGC
1 CTCTTGAACGGATGAGAGG-GGA
376852 CTCTTGAAC-GATGA
1 CTCTTGAACGGATGA
376866 CAGGTGAGTC
Statistics
Matches: 46, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
20 6 0.13
21 38 0.83
22 2 0.04
ACGTcount: A:0.23, C:0.17, G:0.38, T:0.22
Consensus pattern (22 bp):
CTCTTGAACGGATGAGAGGGGA
Found at i:376865 original size:42 final size:42
Alignment explanation
Indices: 376762--376869 Score: 110
Period size: 42 Copynumber: 2.5 Consensus size: 42
376752 AGAATGTTGG
* ** *
376762 GGGGACCTCTTCAACGATGACATTGGCCTCTTGAACGGTGAGA
1 GGGG-CCTCTTGAACGATGACAGGGGCCTCTTGAACGATGAGA
* ** * *
376805 GGGGACTCTTGAGGGATGATAGGGGCCTCTTGAACGAT-AGG
1 GGGGCCTCTTGAACGATGACAGGGGCCTCTTGAACGATGAGA
376846 GGAGGCCTCTTGAACGATGACAGG
1 GG-GGCCTCTTGAACGATGACAGG
376870 TGAGTCAGGC
Statistics
Matches: 51, Mismatches: 13, Indels: 3
0.76 0.19 0.04
Matches are distributed among these distances:
41 4 0.08
42 43 0.84
43 4 0.08
ACGTcount: A:0.23, C:0.19, G:0.36, T:0.21
Consensus pattern (42 bp):
GGGGCCTCTTGAACGATGACAGGGGCCTCTTGAACGATGAGA
Found at i:377376 original size:20 final size:20
Alignment explanation
Indices: 377353--377391 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
377343 CTTAAAATCG
377353 CAACGTGAAAATGACTATCA
1 CAACGTGAAAATGACTATCA
377373 CAACGTGAAAATGACTATC
1 CAACGTGAAAATGACTATC
377392 GTAATACAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.44, C:0.21, G:0.15, T:0.21
Consensus pattern (20 bp):
CAACGTGAAAATGACTATCA
Found at i:377487 original size:20 final size:20
Alignment explanation
Indices: 377462--377565 Score: 163
Period size: 20 Copynumber: 5.2 Consensus size: 20
377452 GATTCTTTCG
**
377462 TTGCGATAGTCAAATTCGCA
1 TTGCGATAGTCATTTTCGCA
*
377482 TTGCGATAGTCATTTTCGTA
1 TTGCGATAGTCATTTTCGCA
*
377502 TTGCGATAGTCATTTTCGTA
1 TTGCGATAGTCATTTTCGCA
377522 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
*
377542 TTGCGATAGTCATTTTCGCG
1 TTGCGATAGTCATTTTCGCA
377562 TTGC
1 TTGC
377566 AATTTTGTTG
Statistics
Matches: 79, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 79 1.00
ACGTcount: A:0.20, C:0.18, G:0.21, T:0.40
Consensus pattern (20 bp):
TTGCGATAGTCATTTTCGCA
Found at i:377554 original size:40 final size:40
Alignment explanation
Indices: 377424--377565 Score: 163
Period size: 40 Copynumber: 3.7 Consensus size: 40
377414 AACGAGAGAA
* **
377424 TCGCAATGCGATTTTCA-TTTCGCATTGCGAT--TC--TT
1 TCGCATTGCGATAGTCATTTTCGCATTGCGATAGTCATTT
**
377459 TCG--TTGCGATAGTCAAATTCGCATTGCGATAGTCATTT
1 TCGCATTGCGATAGTCATTTTCGCATTGCGATAGTCATTT
* *
377497 TCGTATTGCGATAGTCATTTTCGTATTGCGATAGTCATTT
1 TCGCATTGCGATAGTCATTTTCGCATTGCGATAGTCATTT
*
377537 TCGCATTGCGATAGTCATTTTCGCGTTGC
1 TCGCATTGCGATAGTCATTTTCGCATTGC
377566 AATTTTGTTG
Statistics
Matches: 90, Mismatches: 10, Indels: 9
0.83 0.09 0.08
Matches are distributed among these distances:
33 9 0.10
34 13 0.14
35 3 0.03
36 2 0.02
38 5 0.06
40 58 0.64
ACGTcount: A:0.19, C:0.20, G:0.20, T:0.41
Consensus pattern (40 bp):
TCGCATTGCGATAGTCATTTTCGCATTGCGATAGTCATTT
Found at i:379566 original size:19 final size:20
Alignment explanation
Indices: 379496--379565 Score: 97
Period size: 20 Copynumber: 3.5 Consensus size: 20
379486 TCTGAAACTT
379496 AAAATCGCAACACGAAAATG
1 AAAATCGCAACACGAAAATG
379516 AAAATCGCAACACGAAAATG
1 AAAATCGCAACACGAAAATG
** * *
379536 ACTATCGTAACGCG-AAATG
1 AAAATCGCAACACGAAAATG
379555 AAAATCGCAAC
1 AAAATCGCAAC
379566 GACGGAATCG
Statistics
Matches: 43, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
19 13 0.30
20 30 0.70
ACGTcount: A:0.50, C:0.21, G:0.16, T:0.13
Consensus pattern (20 bp):
AAAATCGCAACACGAAAATG
Found at i:379964 original size:22 final size:22
Alignment explanation
Indices: 379902--379967 Score: 105
Period size: 22 Copynumber: 3.0 Consensus size: 22
379892 TGACCATGAA
* *
379902 TGATTTCGCCGGAGATGGAGAC
1 TGATTTCGTCGGAGATGGGGAC
*
379924 TGATATCGTCGGAGATGGGGAC
1 TGATTTCGTCGGAGATGGGGAC
379946 TGATTTCGTCGGAGATGGGGAC
1 TGATTTCGTCGGAGATGGGGAC
379968 GGATGTTGCC
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 40 1.00
ACGTcount: A:0.21, C:0.15, G:0.39, T:0.24
Consensus pattern (22 bp):
TGATTTCGTCGGAGATGGGGAC
Found at i:380195 original size:20 final size:20
Alignment explanation
Indices: 380165--380258 Score: 98
Period size: 20 Copynumber: 4.7 Consensus size: 20
380155 CGATAGTTAG
*
380165 ATTCGCGTTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
*
380185 ATTTGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
* * **
380205 AATCGCATTGCGATTTTCCAA
1 ATTCGCATTGCGA-TTTACGT
* * *
380226 ATTTGCGTTGCGATTTATGT
1 ATTCGCATTGCGATTTACGT
380246 ATTCGCATTGCGA
1 ATTCGCATTGCGA
380259 ATTAGGAAAA
Statistics
Matches: 57, Mismatches: 16, Indels: 2
0.76 0.21 0.03
Matches are distributed among these distances:
20 43 0.75
21 14 0.25
ACGTcount: A:0.20, C:0.18, G:0.21, T:0.40
Consensus pattern (20 bp):
ATTCGCATTGCGATTTACGT
Found at i:380295 original size:61 final size:60
Alignment explanation
Indices: 380144--380299 Score: 154
Period size: 61 Copynumber: 2.6 Consensus size: 60
380134 GGCGCTATGT
* * * *
380144 AAATCGC-ATAGCGATAGTTAGATTCGCGTTGCGATTTACGTATTTGCATTGCGATTTACG
1 AAATCGCAAT-GCGATAGTCAGAATCGCGTTGCGATTTACGTATTCGCATTGCGAATTACG
* * ** * * *
380204 TAATCGCATTGCGATTTTCCA-AATTTGCGTTGCGATTTATGTATTCGCATTGCGAATTAGG
1 AAATCGCAATGCGATAGT-CAGAA-TCGCGTTGCGATTTACGTATTCGCATTGCGAATTACG
*
380265 AAAATCGCAATGCAATAGTCAGAATCGCGTTGCGA
1 -AAATCGCAATGCGATAGTCAGAATCGCGTTGCGA
380300 ATCTGGAAAT
Statistics
Matches: 74, Mismatches: 17, Indels: 9
0.74 0.17 0.09
Matches are distributed among these distances:
60 13 0.18
61 46 0.62
62 15 0.20
ACGTcount: A:0.27, C:0.17, G:0.22, T:0.33
Consensus pattern (60 bp):
AAATCGCAATGCGATAGTCAGAATCGCGTTGCGATTTACGTATTCGCATTGCGAATTACG
Found at i:381220 original size:39 final size:40
Alignment explanation
Indices: 381177--381410 Score: 145
Period size: 42 Copynumber: 5.8 Consensus size: 40
381167 AAGAGTGCAA
* *
381177 GATTATTGTGGCGTTTAT-AAAAATGCCGCTAAAGTCCAT
1 GATTATTGTGGCGTTTATCAAAAACGCCACTAAAGTCCAT
* * * *
381216 GATTATTGTTGCATTTATCAAAAACGTCACTAAAGTGCAT
1 GATTATTGTGGCGTTTATCAAAAACGCCACTAAAGTCCAT
* * * *
381256 AATTA-TGTGGCGTTT-T-AATAAACCCCGC-AAAGGTGCAT
1 GATTATTGTGGCGTTTATCAA-AAACGCCACTAAA-GTCCAT
* * * * * *
381294 AACTATTGCGGCCTTTATTGCAAAAACACCACTAAAGTGCAT
1 GATTATTGTGGCGTTTA-T-CAAAAACGCCACTAAAGTCCAT
* * * * * *
381336 GACTATTGCGACGTTTATTACAAAAACACCACTAAGGTTCAT
1 GATTATTGTGGCGTTTA-T-CAAAAACGCCACTAAAGTCCAT
* * * *
381378 GACTGTTGCGGCGTTTATAAAAAACGCCACTAA
1 GATTATTGTGGCGTTTATCAAAAACGCCACTAA
381411 GCTAAATTAC
Statistics
Matches: 159, Mismatches: 27, Indels: 17
0.78 0.13 0.08
Matches are distributed among these distances:
37 5 0.03
38 17 0.11
39 32 0.20
40 34 0.21
41 2 0.01
42 64 0.40
43 5 0.03
ACGTcount: A:0.34, C:0.19, G:0.18, T:0.29
Consensus pattern (40 bp):
GATTATTGTGGCGTTTATCAAAAACGCCACTAAAGTCCAT
Found at i:381353 original size:42 final size:42
Alignment explanation
Indices: 381288--381484 Score: 186
Period size: 42 Copynumber: 4.8 Consensus size: 42
381278 CCCCGCAAAG
* * *
381288 GTGCATAACTATTGCGGCCTTTATTGCAAAAACACCACTAAA
1 GTGCATGACTATTGCGGCGTTTATTACAAAAACACCACTAAA
* *
381330 GTGCATGACTATTGCGACGTTTATTACAAAAACACCACTAAG
1 GTGCATGACTATTGCGGCGTTTATTACAAAAACACCACTAAA
* * *
381372 GTTCATGACTGTTGCGGCGTTTA-TA-AAAAACGCCACT-AA
1 GTGCATGACTATTGCGGCGTTTATTACAAAAACACCACTAAA
** * * * * * *
381411 GCTAAATTACTATTGCGGTGTTTATTACAAGAACGCCGCTAAG
1 G-TGCATGACTATTGCGGCGTTTATTACAAAAACACCACTAAA
* * *
381454 GTGCATGACTGTTGTGGC-ATTATTACAAAAA
1 GTGCATGACTATTGCGGCGTTTATTACAAAAA
381485 TGCGCTAAGG
Statistics
Matches: 125, Mismatches: 26, Indels: 9
0.78 0.16 0.06
Matches are distributed among these distances:
39 2 0.02
40 28 0.22
41 15 0.12
42 78 0.62
43 2 0.02
ACGTcount: A:0.33, C:0.20, G:0.19, T:0.28
Consensus pattern (42 bp):
GTGCATGACTATTGCGGCGTTTATTACAAAAACACCACTAAA
Found at i:387449 original size:21 final size:21
Alignment explanation
Indices: 387424--387471 Score: 96
Period size: 21 Copynumber: 2.3 Consensus size: 21
387414 TTATCTTTGT
387424 AGAAGATAAACTACAAAGAAA
1 AGAAGATAAACTACAAAGAAA
387445 AGAAGATAAACTACAAAGAAA
1 AGAAGATAAACTACAAAGAAA
387466 AGAAGA
1 AGAAGA
387472 CGATGATAGC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.67, C:0.08, G:0.17, T:0.08
Consensus pattern (21 bp):
AGAAGATAAACTACAAAGAAA
Found at i:391408 original size:15 final size:15
Alignment explanation
Indices: 391388--391418 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
391378 AGAAAAGGAA
391388 ACATTCGGGAGAGAC
1 ACATTCGGGAGAGAC
391403 ACATTCGGGAGAGAC
1 ACATTCGGGAGAGAC
391418 A
1 A
391419 GGAGACGGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.35, C:0.19, G:0.32, T:0.13
Consensus pattern (15 bp):
ACATTCGGGAGAGAC
Found at i:404857 original size:12 final size:12
Alignment explanation
Indices: 404842--404900 Score: 52
Period size: 12 Copynumber: 5.1 Consensus size: 12
404832 ATAAAAATTA
*
404842 AATTTTAAGTAT
1 AATTTTAAATAT
404854 AATTTTAAATAT
1 AATTTTAAATAT
**
404866 -A-TAAAAAT-T
1 AATTTTAAATAT
*
404875 AAATTTTAAGTAT
1 -AATTTTAAATAT
404888 AATTTTAAATAT
1 AATTTTAAATAT
404900 A
1 A
404901 TACAAGTTTA
Statistics
Matches: 36, Mismatches: 7, Indels: 8
0.71 0.14 0.16
Matches are distributed among these distances:
9 1 0.03
10 5 0.14
11 2 0.06
12 27 0.75
13 1 0.03
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (12 bp):
AATTTTAAATAT
Found at i:404874 original size:34 final size:34
Alignment explanation
Indices: 404832--404902 Score: 142
Period size: 34 Copynumber: 2.1 Consensus size: 34
404822 CTAAAATAAA
404832 ATAAAAATTAAATTTTAAGTATAATTTTAAATAT
1 ATAAAAATTAAATTTTAAGTATAATTTTAAATAT
404866 ATAAAAATTAAATTTTAAGTATAATTTTAAATAT
1 ATAAAAATTAAATTTTAAGTATAATTTTAAATAT
404900 ATA
1 ATA
404903 CAAGTTTAAG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 37 1.00
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.44
Consensus pattern (34 bp):
ATAAAAATTAAATTTTAAGTATAATTTTAAATAT
Found at i:411580 original size:30 final size:30
Alignment explanation
Indices: 411544--411601 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
411534 TCTGGAGATA
*
411544 TGATCGGATGTCTATTAGCTTTCCAACGGT
1 TGATCGGATATCTATTAGCTTTCCAACGGT
* *
411574 TGATCGGATATCTCTTAGTTTTCCAACG
1 TGATCGGATATCTATTAGCTTTCCAACG
411602 ATTCTTGAAT
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:0.21, C:0.21, G:0.21, T:0.38
Consensus pattern (30 bp):
TGATCGGATATCTATTAGCTTTCCAACGGT
Found at i:412586 original size:142 final size:142
Alignment explanation
Indices: 412295--412579 Score: 430
Period size: 142 Copynumber: 2.0 Consensus size: 142
412285 TTGTTCTTTC
412295 ACACAAAACCATCAAGGTACCCCAACGGATCTAGTTTGTAAAAGATTCACCGTTTCATGTTCTTC
1 ACACAAAACCATCAAGGTACCCCAACGGATCTAGTTTGTAAAAGATTCACCGTTTCATGTTCTTC
* *
412360 TTGTTTAATTTTAATTAGATTCAAATTTCCTTGTTAGTTTGTTGTTTTTCATTAAAAAAGATCTT
66 TTGTTTAATTTTAATTAGATTCAAATTTCCTTGTTAGTTTGTTGTTTTTCATTAAAAAAGAGCTC
***** *****
412425 GCTTGTTCTTTC
131 GAAAAATAAAAA
412437 ACACAAAACCATCAAGGTACCCCAACGGATCTAGTTTGTAAAAGATTCACCGTTTCATGTTCTTC
1 ACACAAAACCATCAAGGTACCCCAACGGATCTAGTTTGTAAAAGATTCACCGTTTCATGTTCTTC
412502 TTGTTTAATTTTAATTTAGATTCAAATCTTCCTTGTTAGTTTGTTGTTTTTCATTAAAAAAG-GC
66 TTGTTTAATTTTAA-TTAGATTCAAAT-TTCCTTGTTAGTTTGTTGTTTTTCATTAAAAAAGAGC
412566 -CGAAAAATAAAAA
129 TCGAAAAATAAAAA
412579 A
1 A
412580 GCCAAAAAAA
Statistics
Matches: 129, Mismatches: 12, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
142 82 0.64
143 13 0.10
144 34 0.26
ACGTcount: A:0.31, C:0.17, G:0.13, T:0.39
Consensus pattern (142 bp):
ACACAAAACCATCAAGGTACCCCAACGGATCTAGTTTGTAAAAGATTCACCGTTTCATGTTCTTC
TTGTTTAATTTTAATTAGATTCAAATTTCCTTGTTAGTTTGTTGTTTTTCATTAAAAAAGAGCTC
GAAAAATAAAAA
Found at i:412587 original size:16 final size:17
Alignment explanation
Indices: 412556--412588 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
412546 TGTTTTTCAT
*
412556 TAAAAAAGGCCGAAAAA
1 TAAAAAAGGCCAAAAAA
412573 TAAAAAA-GCCAAAAAA
1 TAAAAAAGGCCAAAAAA
412589 ATCACAAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.70, C:0.12, G:0.12, T:0.06
Consensus pattern (17 bp):
TAAAAAAGGCCAAAAAA
Found at i:413219 original size:19 final size:19
Alignment explanation
Indices: 413195--413239 Score: 81
Period size: 19 Copynumber: 2.4 Consensus size: 19
413185 GACTAAAGAG
413195 TTTGCATACTTCTTCATTC
1 TTTGCATACTTCTTCATTC
*
413214 TTTGCATACTTCTTCCTTC
1 TTTGCATACTTCTTCATTC
413233 TTTGCAT
1 TTTGCAT
413240 TCTTGTTCTC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.13, C:0.27, G:0.07, T:0.53
Consensus pattern (19 bp):
TTTGCATACTTCTTCATTC
Found at i:417675 original size:2 final size:2
Alignment explanation
Indices: 417668--417696 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
417658 TGTATTTTAA
417668 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
417697 CACATTTAAA
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:426450 original size:20 final size:19
Alignment explanation
Indices: 426389--426450 Score: 52
Period size: 20 Copynumber: 3.1 Consensus size: 19
426379 ATAATAAATT
426389 ATATTAATTAATATGATTAA
1 ATATTAATT-ATATGATTAA
* * * * *
426409 TTTTTAAATATTATAATAAA
1 ATATTAATTA-TATGATTAA
426429 ATATTAATTATGATGATTAA
1 ATATTAATTAT-ATGATTAA
426449 AT
1 AT
426451 TAATAAATAG
Statistics
Matches: 30, Mismatches: 10, Indels: 4
0.68 0.23 0.09
Matches are distributed among these distances:
19 2 0.07
20 28 0.93
ACGTcount: A:0.48, C:0.00, G:0.05, T:0.47
Consensus pattern (19 bp):
ATATTAATTATATGATTAA
Found at i:427540 original size:18 final size:18
Alignment explanation
Indices: 427517--427567 Score: 75
Period size: 18 Copynumber: 2.8 Consensus size: 18
427507 GCGTAGAATT
*
427517 TGTCCCGTAGGACCACTA
1 TGTCCCGAAGGACCACTA
* *
427535 TGTCCCAAAGGACCACTG
1 TGTCCCGAAGGACCACTA
427553 TGTCCCGAAGGACCA
1 TGTCCCGAAGGACCA
427568 TTGATAATCC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.25, C:0.33, G:0.24, T:0.18
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:431766 original size:14 final size:14
Alignment explanation
Indices: 431728--431766 Score: 60
Period size: 14 Copynumber: 2.8 Consensus size: 14
431718 ATTTTAAATA
*
431728 ATTTACATTTACAT
1 ATTTACATTTGCAT
*
431742 TTTTACATTTGCAT
1 ATTTACATTTGCAT
431756 ATTTACATTTG
1 ATTTACATTTG
431767 GAATCTTTGC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.28, C:0.13, G:0.05, T:0.54
Consensus pattern (14 bp):
ATTTACATTTGCAT
Found at i:440003 original size:114 final size:113
Alignment explanation
Indices: 439501--440059 Score: 734
Period size: 112 Copynumber: 5.0 Consensus size: 113
439491 GCAAAGATTT
* * * * * *
439501 GAATCCATTACTCAATGGATCAACA-TGCCAG-GTAGAGTTCATAATAAGAAGAACTCATCTGAA
1 GAATTCATCACTCGATGGATCAACATTTCCAGAG-AAAGTTCATAATGAGAAGAACTCATCTG-A
*
439564 AGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTTAACCTTTTGCTC
64 AGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTC
* * *
439614 GAATTCATCACTTGATGGATCAACATTTCCAGAGAAAGTTCATAATGGGAAGAACTTATCTGAAG
1 GAATTCATCACTCGATGGATCAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
* * *
439679 -AGGAAGAAGAAATTCATAATAAGAAGAATTTGTTCAACCTTTTGC-C
66 AAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTC
* * * * * *
439725 TGAATTCATCACTTGATGGATTAACTTTTCTAGAGGAAGTTCATAATGAGAAGAACTCATCTAAA
1 -GAATTCATCACTCGATGGATCAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAA
439790 GAAGG-AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTC
65 GAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTC
* * *
439838 GAATTCATCACTCGATGGATCAGCATTGCCAG-GTAGAGTTCATAATGAGAAGAACTCATCTGAA
1 GAATTCATCACTCGATGGATCAACATTTCCAGAG-AAAGTTCATAATGAGAAGAACTCATCTGAA
* * * * *
439902 GAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACTTTTTTGTTT
65 GAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAAC-CTTTTGCTC
* * * * *
439952 GAACTCATCACTCAATGGATCAACTTTTCTAGAGAAAGTTCATAATGAGAAGAACTCGTCTGAAG
1 GAATTCATCACTCGATGGATCAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
*
440017 AAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTT
66 AAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTT
440060 GTTTGATACT
Statistics
Matches: 388, Mismatches: 49, Indels: 18
0.85 0.11 0.04
Matches are distributed among these distances:
111 2 0.01
112 195 0.50
113 63 0.16
114 126 0.32
115 2 0.01
ACGTcount: A:0.38, C:0.15, G:0.20, T:0.28
Consensus pattern (113 bp):
GAATTCATCACTCGATGGATCAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
AAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTC
Found at i:440402 original size:3 final size:3
Alignment explanation
Indices: 440394--440437 Score: 51
Period size: 3 Copynumber: 16.0 Consensus size: 3
440384 TTTGTTTTAT
*
440394 TTA TTA TTA TTA TT- TTG TT- TTA TTA TTA -TA TTA -TA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
440438 AATAATTAAT
Statistics
Matches: 37, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
2 8 0.22
3 29 0.78
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:440418 original size:16 final size:16
Alignment explanation
Indices: 440391--440437 Score: 60
Period size: 16 Copynumber: 3.0 Consensus size: 16
440381 TCATTTGTTT
440391 TATT-TATTATTATTA
1 TATTATATTATTATTA
* * *
440406 TTTTGTTTTATTATTA
1 TATTATATTATTATTA
440422 TATTATATTATTATTA
1 TATTATATTATTATTA
440438 AATAATTAAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
15 3 0.12
16 23 0.88
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (16 bp):
TATTATATTATTATTA
Found at i:440430 original size:23 final size:23
Alignment explanation
Indices: 440384--440427 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
440374 TTTTATTTCA
440384 TTTGTTTTATTTATTATTATTAT
1 TTTGTTTTATTTATTATTATTAT
440407 TTTGTTTTA-TTATTA-TATTAT
1 TTTGTTTTATTTATTATTATTAT
440428 ATTATTATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 6 0.29
22 6 0.29
23 9 0.43
ACGTcount: A:0.23, C:0.00, G:0.05, T:0.73
Consensus pattern (23 bp):
TTTGTTTTATTTATTATTATTAT
Found at i:442166 original size:2 final size:2
Alignment explanation
Indices: 442159--442203 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
442149 TTTACAAAAC
442159 TA TA TA TA TA 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 TA TA TA TA TA
442201 TA T
1 TA T
442204 TTAATATTCT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:443318 original size:20 final size:20
Alignment explanation
Indices: 443293--443330 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
443283 TTTCCATTGA
443293 AGTGCATCGATACATTCTAT
1 AGTGCATCGATACATTCTAT
443313 AGTGCATCGATACATTCT
1 AGTGCATCGATACATTCT
443331 TTAACATGTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.29, C:0.21, G:0.16, T:0.34
Consensus pattern (20 bp):
AGTGCATCGATACATTCTAT
Found at i:444356 original size:2 final size:2
Alignment explanation
Indices: 444349--444378 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
444339 TCGATACTCA
444349 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
444379 TTCTTACTCA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:446716 original size:18 final size:18
Alignment explanation
Indices: 446693--446755 Score: 90
Period size: 18 Copynumber: 3.5 Consensus size: 18
446683 TTTGTCTCGT
* *
446693 AGGACCACTATATCCCAA
1 AGGACCACTATGTCCCGA
*
446711 AGGACCACTGTGTCCCGA
1 AGGACCACTATGTCCCGA
*
446729 AGGTCCACTATGTCCCGA
1 AGGACCACTATGTCCCGA
446747 AGGACCACT
1 AGGACCACT
446756 GATAATCCCT
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 39 1.00
ACGTcount: A:0.29, C:0.33, G:0.21, T:0.17
Consensus pattern (18 bp):
AGGACCACTATGTCCCGA
Done.