Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168492.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_9, 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: 25814696
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 122000 characters in sequence are not A, C, G, or T
File 107 of 126
Found at i:21178454 original size:22 final size:24
Alignment explanation
Indices: 21178437--21178494 Score: 70
Period size: 24 Copynumber: 2.5 Consensus size: 24
21178427 AATATTAATT
21178437 TAATAAAAATATTATATTTATATA
1 TAATAAAAATATTATATTTATATA
*
21178461 TAATAAAGATA-TA-ATTTATAT-
1 TAATAAAAATATTATATTTATATA
21178482 TAA-AAATAATATT
1 TAATAAA-AATATT
21178495 TTAGGAATAT
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
20 3 0.10
21 6 0.20
22 9 0.30
23 2 0.07
24 10 0.33
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (24 bp):
TAATAAAAATATTATATTTATATA
Found at i:21178495 original size:18 final size:18
Alignment explanation
Indices: 21178411--21178495 Score: 50
Period size: 18 Copynumber: 4.4 Consensus size: 18
21178401 AAATTATTTT
*
21178411 TAATATTT-TAATTTAAAA
1 TAATATTTAT-ATTAAAAA
*
21178429 TATTAATTTA-A-TAAAAA
1 TAAT-ATTTATATTAAAAA
21178446 TATTATATTTATATATAATAAA
1 TA--ATATTTATAT-TAA-AAA
*
21178468 GATATAATTTATATTAAAAA
1 TA-AT-ATTTATATTAAAAA
21178488 TAATATTT
1 TAATATTT
21178496 TAGGAATATA
Statistics
Matches: 53, Mismatches: 5, Indels: 18
0.70 0.07 0.24
Matches are distributed among these distances:
17 7 0.13
18 13 0.25
19 8 0.15
20 4 0.08
21 9 0.17
22 12 0.23
ACGTcount: A:0.52, C:0.00, G:0.01, T:0.47
Consensus pattern (18 bp):
TAATATTTATATTAAAAA
Found at i:21185523 original size:11 final size:11
Alignment explanation
Indices: 21185443--21185513 Score: 63
Period size: 11 Copynumber: 6.5 Consensus size: 11
21185433 TAATTTAAAA
*
21185443 AAAAAAATTTCA
1 AAAAAAA-TTCT
21185455 AAAAAAATTCT
1 AAAAAAATTCT
21185466 AAAAAAATTCT
1 AAAAAAATTCT
* * *
21185477 TAAAAAGTTTT
1 AAAAAAATTCT
*
21185488 TAAAAAA-TCT
1 AAAAAAATTCT
* *
21185498 AAACAAATTTT
1 AAAAAAATTCT
21185509 AAAAA
1 AAAAA
21185514 TTATAAAAAA
Statistics
Matches: 48, Mismatches: 10, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
10 7 0.15
11 34 0.71
12 7 0.15
ACGTcount: A:0.62, C:0.07, G:0.01, T:0.30
Consensus pattern (11 bp):
AAAAAAATTCT
Found at i:21185524 original size:19 final size:20
Alignment explanation
Indices: 21185485--21185531 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
21185475 CTTAAAAAGT
*
21185485 TTTTAAAAAATCTAAACAAA
1 TTTTAAAAAATATAAACAAA
*
21185505 TTTTAAAAATTATAAA-AAA
1 TTTTAAAAAATATAAACAAA
*
21185524 TTTCAAAA
1 TTTTAAAA
21185532 TATTTCAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
19 10 0.42
20 14 0.58
ACGTcount: A:0.60, C:0.06, G:0.00, T:0.34
Consensus pattern (20 bp):
TTTTAAAAAATATAAACAAA
Found at i:21185594 original size:19 final size:20
Alignment explanation
Indices: 21185567--21185607 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
21185557 TAAAATTAAA
21185567 AACAAA-TTT-AAGAAATTCT
1 AACAAATTTTGAA-AAATTCT
*
21185586 AACACATTTTGAAAAATTCT
1 AACAAATTTTGAAAAATTCT
21185606 AA
1 AA
21185608 AATAATTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
19 5 0.26
20 12 0.63
21 2 0.11
ACGTcount: A:0.51, C:0.12, G:0.05, T:0.32
Consensus pattern (20 bp):
AACAAATTTTGAAAAATTCT
Found at i:21185688 original size:28 final size:28
Alignment explanation
Indices: 21185631--21185690 Score: 84
Period size: 28 Copynumber: 2.1 Consensus size: 28
21185621 ATTTTTTTTG
* * **
21185631 AAAATTATAAAAATTTGAAATAAACTAA
1 AAAATTATAAAAATTTCAAAAAAAAAAA
21185659 AAAATTATAAAAATTTCAAAAAAAAAAA
1 AAAATTATAAAAATTTCAAAAAAAAAAA
21185687 AAAA
1 AAAA
21185691 CTATGAGCAT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.72, C:0.03, G:0.02, T:0.23
Consensus pattern (28 bp):
AAAATTATAAAAATTTCAAAAAAAAAAA
Found at i:21185749 original size:18 final size:17
Alignment explanation
Indices: 21185726--21185774 Score: 59
Period size: 15 Copynumber: 2.9 Consensus size: 17
21185716 ATAATTTCAA
21185726 AAAAAAAATT-AGAAAATT
1 AAAAAAAATTCA-AAAA-T
21185744 AAAAAAAATTCAAAAAT
1 AAAAAAAATTCAAAAAT
21185761 --AAAAAATTCAAAAA
1 AAAAAAAATTCAAAAA
21185775 AATTTTAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
15 14 0.47
17 1 0.03
18 14 0.47
19 1 0.03
ACGTcount: A:0.76, C:0.04, G:0.02, T:0.18
Consensus pattern (17 bp):
AAAAAAAATTCAAAAAT
Found at i:21185758 original size:17 final size:18
Alignment explanation
Indices: 21185726--21185766 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
21185716 ATAATTTCAA
* *
21185726 AAAAAAAATTAGAAAATT
1 AAAAAAAATTACAAAAAT
21185744 AAAAAAAATT-CAAAAAT
1 AAAAAAAATTACAAAAAT
21185761 AAAAAA
1 AAAAAA
21185767 TTCAAAAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 11 0.52
18 10 0.48
ACGTcount: A:0.78, C:0.02, G:0.02, T:0.17
Consensus pattern (18 bp):
AAAAAAAATTACAAAAAT
Found at i:21185785 original size:26 final size:26
Alignment explanation
Indices: 21185729--21185778 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 26
21185719 ATTTCAAAAA
*
21185729 AAAAATTAGAAAATTAAAAAAAATTC
1 AAAAATTAAAAAATTAAAAAAAATTC
*
21185755 AAAAA-TAAAAAATTCAAAAAAATT
1 AAAAATTAAAAAATTAAAAAAAATT
21185779 TTAAAAAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 17 0.77
26 5 0.23
ACGTcount: A:0.72, C:0.04, G:0.02, T:0.22
Consensus pattern (26 bp):
AAAAATTAAAAAATTAAAAAAAATTC
Found at i:21185787 original size:21 final size:21
Alignment explanation
Indices: 21185761--21185804 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
21185751 ATTCAAAAAT
21185761 AAAAAATTCAAAAAAATTTTA
1 AAAAAATTCAAAAAAATTTTA
*
21185782 AAAAAATTCAAAAAACTTTTA
1 AAAAAATTCAAAAAAATTTTA
21185803 AA
1 AA
21185805 TTTTTTTAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.66, C:0.07, G:0.00, T:0.27
Consensus pattern (21 bp):
AAAAAATTCAAAAAAATTTTA
Found at i:21185839 original size:9 final size:10
Alignment explanation
Indices: 21185826--21185913 Score: 60
Period size: 9 Copynumber: 9.0 Consensus size: 10
21185816 ATAAAATATA
21185826 AAAAATTTCT
1 AAAAATTTCT
21185836 AAAAATTTCT
1 AAAAATTTCT
*
21185846 AAAAATTT-A
1 AAAAATTTCT
*
21185855 AAAAACGTAT-T
1 AAAAA--TTTCT
*
21185866 AAAAA-TTAT
1 AAAAATTTCT
21185875 AAAAATTT-T
1 AAAAATTTCT
* *
21185884 GAAAATTTTT
1 AAAAATTTCT
21185894 GAAAAATTT-T
1 -AAAAATTTCT
*
21185904 AAAAAATTCT
1 AAAAATTTCT
21185914 TAAAGAATTA
Statistics
Matches: 64, Mismatches: 7, Indels: 14
0.75 0.08 0.16
Matches are distributed among these distances:
8 1 0.02
9 26 0.41
10 23 0.36
11 14 0.22
ACGTcount: A:0.55, C:0.05, G:0.03, T:0.38
Consensus pattern (10 bp):
AAAAATTTCT
Found at i:21185841 original size:10 final size:9
Alignment explanation
Indices: 21185826--21185922 Score: 77
Period size: 10 Copynumber: 9.8 Consensus size: 9
21185816 ATAAAATATA
21185826 AAAAATTTCT
1 AAAAATTT-T
21185836 AAAAATTTCT
1 AAAAATTT-T
*
21185846 AAAAATTTA
1 AAAAATTTT
*
21185855 AAAAACGTATT
1 AAAAA--TTTT
*
21185866 AAAAATTAT
1 AAAAATTTT
21185875 AAAAATTTT
1 AAAAATTTT
*
21185884 GAAAATTTTT
1 -AAAAATTTT
21185894 GAAAAATTTT
1 -AAAAATTTT
21185904 AAAAAATTCTT
1 -AAAAATT-TT
21185915 AAAGAATT
1 AAA-AATT
21185923 AAGGAAACTT
Statistics
Matches: 73, Mismatches: 9, Indels: 9
0.80 0.10 0.10
Matches are distributed among these distances:
9 15 0.21
10 45 0.62
11 13 0.18
ACGTcount: A:0.55, C:0.04, G:0.04, T:0.37
Consensus pattern (9 bp):
AAAAATTTT
Found at i:21185856 original size:29 final size:27
Alignment explanation
Indices: 21185818--21185908 Score: 83
Period size: 29 Copynumber: 3.1 Consensus size: 27
21185808 TTTTAAAAAT
*
21185818 AAAATATAAAAAATTTCTAAAAATTTCTA
1 AAAATTTAAAAAATTT-TAAAAATTT-TA
* *
21185847 AAAATTTAAAAAACGTATTAAAAATTATA
1 AAAATTTAAAAAA--TTTTAAAAATTTTA
* *
21185876 AAAATTTTGAAAATTTTTGAAAAATTTTA
1 AAAA-TTTAAAAAATTTT-AAAAATTTTA
21185905 AAAA
1 AAAA
21185909 ATTCTTAAAG
Statistics
Matches: 51, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
28 3 0.06
29 31 0.61
30 15 0.29
31 2 0.04
ACGTcount: A:0.58, C:0.03, G:0.03, T:0.35
Consensus pattern (27 bp):
AAAATTTAAAAAATTTTAAAAATTTTA
Found at i:21185916 original size:11 final size:10
Alignment explanation
Indices: 21185760--21185922 Score: 75
Period size: 10 Copynumber: 15.9 Consensus size: 10
21185750 AATTCAAAAA
*
21185760 TAAAAAATTC
1 TAAAAAATTT
*
21185770 AAAAAAATTT
1 TAAAAAATTT
*
21185780 TAAAAAAATT
1 TAAAAAATTT
*
21185790 CAAAAAACTTT
1 TAAAAAA-TTT
***
21185801 TAAATTTTTT
1 TAAAAAATTT
* *
21185811 TAAAAATAAAATA
1 T--AAA-AAATTT
21185824 TAAAAAATTT
1 TAAAAAATTT
21185834 CT-AAAAATTT
1 -TAAAAAATTT
21185844 CT-AAAAA-TT
1 -TAAAAAATTT
*
21185853 TAAAAAACGTAT
1 TAAAAAA--TTT
*
21185865 T-AAAAATTA
1 TAAAAAATTT
21185874 T-AAAAATTT
1 TAAAAAATTT
* *
21185883 TGAAAATTTT
1 TAAAAAATTT
*
21185893 TGAAAAATTT
1 TAAAAAATTT
21185903 TAAAAAATTCT
1 TAAAAAATT-T
*
21185914 TAAAGAATT
1 TAAAAAATT
21185923 AAGGAAACTT
Statistics
Matches: 117, Mismatches: 25, Indels: 21
0.72 0.15 0.13
Matches are distributed among these distances:
8 1 0.01
9 17 0.15
10 69 0.59
11 23 0.20
12 5 0.04
13 2 0.02
ACGTcount: A:0.57, C:0.04, G:0.02, T:0.36
Consensus pattern (10 bp):
TAAAAAATTT
Found at i:21185993 original size:9 final size:9
Alignment explanation
Indices: 21185981--21186075 Score: 50
Period size: 9 Copynumber: 10.7 Consensus size: 9
21185971 AAAAGAATTT
*
21185981 TTTTTTAGA
1 TTTTTTAAA
21185990 TTTTTTAAA
1 TTTTTTAAA
**
21185999 TTTTAAAGAA
1 TTTTTTA-AA
* *
21186009 TGTTTCAAA
1 TTTTTTAAA
* *
21186018 ATTTTGAAA
1 TTTTTTAAA
*
21186027 TTTCTT-AA
1 TTTTTTAAA
*
21186035 TTTCTT-AA
1 TTTTTTAAA
21186043 TTTTTTAAA
1 TTTTTTAAA
**
21186052 ACTTTTAAA
1 TTTTTTAAA
* *
21186061 CTTTTTATA
1 TTTTTTAAA
21186070 TTTTTT
1 TTTTTT
21186076 CTTATTTTCA
Statistics
Matches: 65, Mismatches: 19, Indels: 4
0.74 0.22 0.05
Matches are distributed among these distances:
8 15 0.23
9 44 0.68
10 6 0.09
ACGTcount: A:0.32, C:0.05, G:0.04, T:0.59
Consensus pattern (9 bp):
TTTTTTAAA
Found at i:21186186 original size:18 final size:18
Alignment explanation
Indices: 21186165--21186215 Score: 57
Period size: 18 Copynumber: 2.8 Consensus size: 18
21186155 CTTTTTTATT
*
21186165 TTTTAAAAAAATTTAGAA
1 TTTTAAAAATATTTAGAA
* * *
21186183 TTTTTAAAATTTTTATAA
1 TTTTAAAAATATTTAGAA
21186201 TTTATAAAAATATTT
1 TTT-TAAAAATATTT
21186216 CATATTTTTA
Statistics
Matches: 26, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
18 17 0.65
19 9 0.35
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (18 bp):
TTTTAAAAATATTTAGAA
Found at i:21186193 original size:9 final size:9
Alignment explanation
Indices: 21186176--21186260 Score: 55
Period size: 9 Copynumber: 9.3 Consensus size: 9
21186166 TTTAAAAAAA
*
21186176 TTTAGAATT
1 TTTAAAATT
21186185 TTTAAAATT
1 TTTAAAATT
*
21186194 TTTATAATT
1 TTTAAAATT
* *
21186203 TATAAAAATA
1 T-TTAAAATT
* *
21186213 TTTCATATT
1 TTTAAAATT
*
21186222 TTT-AATTT
1 TTTAAAATT
*
21186230 TTTAGAATT
1 TTTAAAATT
* *
21186239 GTTTAGATTT
1 -TTTAAAATT
21186249 TTTAAAATT
1 TTTAAAATT
21186258 TTT
1 TTT
21186261 TGAGAAATTT
Statistics
Matches: 57, Mismatches: 16, Indels: 6
0.72 0.20 0.08
Matches are distributed among these distances:
8 6 0.11
9 37 0.65
10 14 0.25
ACGTcount: A:0.35, C:0.01, G:0.05, T:0.59
Consensus pattern (9 bp):
TTTAAAATT
Found at i:21186250 original size:19 final size:18
Alignment explanation
Indices: 21186222--21186257 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
21186212 ATTTCATATT
*
21186222 TTTAATTTTTTAGAATTG
1 TTTAATTTTTTAAAATTG
21186240 TTTAGATTTTTTAAAATT
1 TTTA-ATTTTTTAAAATT
21186258 TTTTGAGAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 4 0.25
19 12 0.75
ACGTcount: A:0.31, C:0.00, G:0.08, T:0.61
Consensus pattern (18 bp):
TTTAATTTTTTAAAATTG
Found at i:21186365 original size:18 final size:19
Alignment explanation
Indices: 21186342--21186398 Score: 55
Period size: 18 Copynumber: 3.1 Consensus size: 19
21186332 ATTTTTTAAA
21186342 TTAAAATTTTTTATA-AAT
1 TTAAAATTTTTTATAGAAT
** * *
21186360 TTAAAAAATTTTAAATAAT
1 TTAAAATTTTTTATAGAAT
*
21186379 TT-GAATTTTTTATAGAAT
1 TTAAAATTTTTTATAGAAT
21186397 TT
1 TT
21186399 TTTTTAAAAA
Statistics
Matches: 30, Mismatches: 8, Indels: 2
0.75 0.20 0.05
Matches are distributed among these distances:
18 25 0.83
19 5 0.17
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.53
Consensus pattern (19 bp):
TTAAAATTTTTTATAGAAT
Found at i:21186429 original size:32 final size:32
Alignment explanation
Indices: 21186368--21186432 Score: 80
Period size: 32 Copynumber: 2.0 Consensus size: 32
21186358 ATTTAAAAAA
* *
21186368 TTTTAAATAATTTGAATTTTTTATAGAATTTT
1 TTTTAAAAAATTTGAATTGTTTATAGAATTTT
21186400 TTTTAAAAAAATTTAGAATTGTTT-T-GAATTTT
1 TTTT-AAAAAATTT-GAATTGTTTATAGAATTTT
21186432 T
1 T
21186433 ATAAGTTTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
32 12 0.41
33 9 0.31
34 8 0.28
ACGTcount: A:0.35, C:0.00, G:0.08, T:0.57
Consensus pattern (32 bp):
TTTTAAAAAATTTGAATTGTTTATAGAATTTT
Found at i:21186450 original size:9 final size:9
Alignment explanation
Indices: 21186426--21186643 Score: 112
Period size: 9 Copynumber: 21.8 Consensus size: 9
21186416 AATTGTTTTG
21186426 AATTTTTATA
1 AATTTTTA-A
*
21186436 AGTTTTTAA
1 AATTTTTAA
**
21186445 AATTTTTTG
1 AATTTTTAA
21186454 AATTTTTAAAA
1 AATTTTT--AA
*
21186465 ATATTTTTGA
1 A-ATTTTTAA
*
21186475 AATTTTTTA
1 AATTTTTAA
21186484 AATTTTTAAAA
1 AATTTTT--AA
*
21186495 AAATTTTAA
1 AATTTTTAA
21186504 AATTTCTTTTATA
1 AA--T-TTTTA-A
21186517 AATTTTTCAA
1 AATTTTT-AA
*
21186527 TATTTTTTGAA
1 -AATTTTT-AA
21186538 AATTTTTTAA
1 AA-TTTTTAA
21186548 ATATTTTTTAAA
1 A-A-TTTTT-AA
*
21186560 AATTTTTAT
1 AATTTTTAA
21186569 AATTTTTAAA
1 AATTTTT-AA
*
21186579 AAATTTTAA
1 AATTTTTAA
21186588 AATCTTTTTAAA
1 AA--TTTTT-AA
*
21186600 AATGTTTAA
1 AATTTTTAA
*
21186609 AATTTTTAG
1 AATTTTTAA
*
21186618 AATTTTTTA
1 AATTTTTAA
* *
21186627 GATTTTATAG
1 AATTTT-TAA
21186637 AATTTTT
1 AATTTTT
21186644 TATTAAATTT
Statistics
Matches: 162, Mismatches: 27, Indels: 39
0.71 0.12 0.17
Matches are distributed among these distances:
9 66 0.41
10 40 0.25
11 35 0.22
12 18 0.11
13 3 0.02
ACGTcount: A:0.39, C:0.01, G:0.04, T:0.56
Consensus pattern (9 bp):
AATTTTTAA
Found at i:21186451 original size:10 final size:10
Alignment explanation
Indices: 21186428--21186656 Score: 162
Period size: 10 Copynumber: 22.5 Consensus size: 10
21186418 TTGTTTTGAA
* *
21186428 TTTTTATAAG
1 TTTTTAAAAT
21186438 TTTTTAAAAT
1 TTTTTAAAAT
*
21186448 TTTTT-GAAT
1 TTTTTAAAAT
*
21186457 TTTTAAAAAT
1 TTTTTAAAAT
*
21186467 ATTTTTGAAAT
1 -TTTTTAAAAT
21186478 TTTTT-AAAT
1 TTTTTAAAAT
* *
21186487 TTTTAAAAAA
1 TTTTTAAAAT
*
21186497 ATTTTAAAATT
1 TTTTTAAAA-T
21186508 TCTTTTATAAAT
1 T-TTTTA-AAAT
* *
21186520 TTTTCAATAT
1 TTTTTAAAAT
21186530 TTTTTGAAAAT
1 TTTTT-AAAAT
21186541 TTTTTAAATAT
1 TTTTTAAA-AT
*
21186552 TTTTTAAAAA
1 TTTTTAAAAT
*
21186562 TTTTTATAA-
1 TTTTTAAAAT
*
21186571 TTTTTAAAAA
1 TTTTTAAAAT
*
21186581 ATTTTAAAAT
1 TTTTTAAAAT
*
21186591 CTTTTTAAAAA
1 -TTTTTAAAAT
*
21186602 TGTTTAAAA-
1 TTTTTAAAAT
*
21186611 TTTTTAGAAT
1 TTTTTAAAAT
*
21186621 TTTTT-AGAT
1 TTTTTAAAAT
* *
21186630 TTTATAGAAT
1 TTTTTAAAAT
21186640 TTTTTATTAAAT
1 TTTTTA--AAAT
21186652 TTTTT
1 TTTTT
21186657 CTGAAATTTT
Statistics
Matches: 171, Mismatches: 34, Indels: 26
0.74 0.15 0.11
Matches are distributed among these distances:
9 36 0.21
10 78 0.46
11 39 0.23
12 15 0.09
13 3 0.02
ACGTcount: A:0.38, C:0.01, G:0.03, T:0.57
Consensus pattern (10 bp):
TTTTTAAAAT
Found at i:21186478 original size:30 final size:29
Alignment explanation
Indices: 21186399--21186575 Score: 117
Period size: 30 Copynumber: 5.9 Consensus size: 29
21186389 TATAGAATTT
* *
21186399 TTTTTAAAAAAATTTAG-AATTGTTTTGAA
1 TTTTTAAAAAATTTTTGAAATT-TTTTGAA
* * *
21186428 TTTTT-ATAAGTTTTTAAAATTTTTTGAA
1 TTTTTAAAAAATTTTTGAAATTTTTTGAA
*
21186456 TTTTTAAAAATATTTTTGAAATTTTTTAAA
1 TTTTTAAAAA-ATTTTTGAAATTTTTTGAA
* * *
21186486 TTTTTAAAAAAATTTTAAAATTTCTTTTATAAA
1 TTTTTAAAAAATTTTTGAAA--T-TTTT-TGAA
* * * *
21186519 TTTTTCAATATTTTTTGAAAATTTTTTAAATA
1 TTTTTAAAAAATTTTTG-AAATTTTTT-GA-A
*
21186551 TTTTTTAAAAATTTTT-ATAATTTTT
1 TTTTTAAAAAATTTTTGA-AATTTTT
21186576 AAAAAATTTT
Statistics
Matches: 118, Mismatches: 19, Indels: 20
0.75 0.12 0.13
Matches are distributed among these distances:
28 18 0.15
29 20 0.17
30 28 0.24
31 14 0.12
32 19 0.16
33 16 0.14
34 3 0.03
ACGTcount: A:0.38, C:0.01, G:0.04, T:0.57
Consensus pattern (29 bp):
TTTTTAAAAAATTTTTGAAATTTTTTGAA
Found at i:21186498 original size:21 final size:20
Alignment explanation
Indices: 21186428--21186615 Score: 159
Period size: 21 Copynumber: 9.2 Consensus size: 20
21186418 TTGTTTTGAA
* *
21186428 TTTTTATAAGTTTTTAAAAT
1 TTTTTAAAAATTTTTAAAAT
*
21186448 TTTTT--GAATTTTTAAAAAT
1 TTTTTAAAAATTTTT-AAAAT
* *
21186467 ATTTTT-GAAATTTTTTAAAT
1 -TTTTTAAAAATTTTTAAAAT
* *
21186487 TTTTAAAAAAATTTTAAAATT
1 TTTTTAAAAATTTTTAAAA-T
* *
21186508 TCTTTTATAAATTTTTCAATAT
1 T-TTTTAAAAATTTTT-AAAAT
*
21186530 TTTTTGAAAATTTTTTAAATAT
1 TTTTT-AAAAATTTTTAAA-AT
*
21186552 TTTTTAAAAATTTTTATAA-
1 TTTTTAAAAATTTTTAAAAT
*
21186571 TTTTTAAAAAATTTTAAAAT
1 TTTTTAAAAATTTTTAAAAT
*
21186591 CTTTTTAAAAATGTTTAAAAT
1 -TTTTTAAAAATTTTTAAAAT
21186612 TTTT
1 TTTT
21186616 AGAATTTTTT
Statistics
Matches: 136, Mismatches: 21, Indels: 22
0.76 0.12 0.12
Matches are distributed among these distances:
18 6 0.04
19 26 0.19
20 29 0.21
21 44 0.32
22 28 0.21
23 3 0.02
ACGTcount: A:0.39, C:0.02, G:0.03, T:0.56
Consensus pattern (20 bp):
TTTTTAAAAATTTTTAAAAT
Found at i:21186637 original size:19 final size:18
Alignment explanation
Indices: 21186610--21186645 Score: 63
Period size: 19 Copynumber: 1.9 Consensus size: 18
21186600 AATGTTTAAA
21186610 ATTTTTAGAATTTTTTAG
1 ATTTTTAGAATTTTTTAG
21186628 ATTTTATAGAATTTTTTA
1 ATTTT-TAGAATTTTTTA
21186646 TTAAATTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.31, C:0.00, G:0.08, T:0.61
Consensus pattern (18 bp):
ATTTTTAGAATTTTTTAG
Found at i:21188792 original size:20 final size:20
Alignment explanation
Indices: 21188767--21188805 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
21188757 CAATATATTC
*
21188767 ATCAATATTAAAACATCATT
1 ATCAATATCAAAACATCATT
21188787 ATCAATATCAAAACATCAT
1 ATCAATATCAAAACATCAT
21188806 CTGATTTTCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.51, C:0.18, G:0.00, T:0.31
Consensus pattern (20 bp):
ATCAATATCAAAACATCATT
Found at i:21188822 original size:18 final size:18
Alignment explanation
Indices: 21188799--21188836 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
21188789 CAATATCAAA
**
21188799 ACATCATCTGATTTTCAT
1 ACATCATCAAATTTTCAT
21188817 ACATCATCAAATTTTCAT
1 ACATCATCAAATTTTCAT
21188835 AC
1 AC
21188837 CATTGTTTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.34, C:0.24, G:0.03, T:0.39
Consensus pattern (18 bp):
ACATCATCAAATTTTCAT
Found at i:21189094 original size:6 final size:6
Alignment explanation
Indices: 21189083--21189108 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
21189073 GGCTTTAGTG
21189083 AGGTGA AGGTGA AGGTGA AGGTGA AG
1 AGGTGA AGGTGA AGGTGA AGGTGA AG
21189109 AATGAAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.35, C:0.00, G:0.50, T:0.15
Consensus pattern (6 bp):
AGGTGA
Found at i:21196838 original size:11 final size:11
Alignment explanation
Indices: 21196822--21196862 Score: 55
Period size: 11 Copynumber: 3.7 Consensus size: 11
21196812 GTATTATTAT
*
21196822 AAATGAATAGC
1 AAATGAATAAC
21196833 AAATGAATAAC
1 AAATGAATAAC
* *
21196844 AAATGAACAAT
1 AAATGAATAAC
21196855 AAATGAAT
1 AAATGAAT
21196863 GAACTTTAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
11 26 1.00
ACGTcount: A:0.61, C:0.07, G:0.12, T:0.20
Consensus pattern (11 bp):
AAATGAATAAC
Found at i:21197518 original size:6 final size:6
Alignment explanation
Indices: 21197507--21197567 Score: 59
Period size: 6 Copynumber: 9.5 Consensus size: 6
21197497 TTTAGCTGTG
* * *
21197507 TTTTAT TTTTAT TTTCTAA TTTTAT ATTTATT TATTTAT TTTTGGT TTTTAT
1 TTTTAT TTTTAT TTT-TAT TTTTAT TTTTA-T T-TTTAT TTTT-AT TTTTAT
21197559 TTTTAT TTT
1 TTTTAT TTT
21197568 ACCAATTATG
Statistics
Matches: 45, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
6 28 0.62
7 13 0.29
8 4 0.09
ACGTcount: A:0.18, C:0.02, G:0.03, T:0.77
Consensus pattern (6 bp):
TTTTAT
Found at i:21197718 original size:43 final size:40
Alignment explanation
Indices: 21197648--21197732 Score: 125
Period size: 43 Copynumber: 2.0 Consensus size: 40
21197638 ATTTATTTGC
*
21197648 ATGATATTTTGCATAAATTTTATTTATTTGCATGATTTCTT
1 ATGATATTTTACATAAATTTTATTTATTTGCATGATTT-TT
*
21197689 ATGATATTTTTACATAATTATTTATTTATTTGCATGATTTTT
1 ATGATA-TTTTACATAAAT-TTTATTTATTTGCATGATTTTT
21197731 AT
1 AT
21197733 TTTTTGCCTA
Statistics
Matches: 40, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
41 6 0.15
42 14 0.35
43 20 0.50
ACGTcount: A:0.28, C:0.06, G:0.08, T:0.58
Consensus pattern (40 bp):
ATGATATTTTACATAAATTTTATTTATTTGCATGATTTTT
Found at i:21197732 original size:23 final size:23
Alignment explanation
Indices: 21197666--21197734 Score: 58
Period size: 23 Copynumber: 3.1 Consensus size: 23
21197656 TTGCATAAAT
21197666 TTTATTTATTTGCATGATTTCTTA
1 TTTATTTATTTGCATGATTT-TTA
* * *
21197690 -TGATATT-TTTACAT-A--ATTA
1 TTTAT-TTATTTGCATGATTTTTA
21197709 TTTATTTATTTGCATGATTTTTA
1 TTTATTTATTTGCATGATTTTTA
21197732 TTT
1 TTT
21197735 TTTGCCTATT
Statistics
Matches: 33, Mismatches: 6, Indels: 13
0.63 0.12 0.25
Matches are distributed among these distances:
19 5 0.15
20 9 0.27
21 1 0.03
22 1 0.03
23 15 0.45
24 2 0.06
ACGTcount: A:0.25, C:0.06, G:0.07, T:0.62
Consensus pattern (23 bp):
TTTATTTATTTGCATGATTTTTA
Found at i:21198342 original size:10 final size:10
Alignment explanation
Indices: 21198329--21198404 Score: 50
Period size: 10 Copynumber: 7.4 Consensus size: 10
21198319 ACAAAAAAAC
21198329 AAAAAACATA
1 AAAAAACATA
21198339 AAAAAA-A-A
1 AAAAAACATA
*
21198347 TAAAAACA-A
1 AAAAAACATA
*
21198356 AACAAAACAAAA
1 AA-AAAAC-ATA
*
21198368 AATAAAAAATAA
1 AA-AAAACAT-A
*
21198380 AAAAAACTTA
1 AAAAAACATA
21198390 ACAAAAACATA
1 A-AAAAACATA
21198401 AAAA
1 AAAA
21198405 TTGGATCAAG
Statistics
Matches: 52, Mismatches: 8, Indels: 12
0.72 0.11 0.17
Matches are distributed among these distances:
8 6 0.12
9 4 0.08
10 16 0.31
11 16 0.31
12 10 0.19
ACGTcount: A:0.82, C:0.09, G:0.00, T:0.09
Consensus pattern (10 bp):
AAAAAACATA
Found at i:21198345 original size:11 final size:11
Alignment explanation
Indices: 21198329--21198404 Score: 63
Period size: 11 Copynumber: 7.3 Consensus size: 11
21198319 ACAAAAAAAC
21198329 AAAAAACATAA
1 AAAAAACATAA
21198340 AAAAAA-AT--
1 AAAAAACATAA
21198348 -AAAAACA-AA
1 AAAAAACATAA
* *
21198357 ACAAAACAAAA
1 AAAAAACATAA
*
21198368 AATAAAAAATAA
1 AA-AAAACATAA
*
21198380 AAAAAACTTAA
1 AAAAAACATAA
*
21198391 CAAAAACATAA
1 AAAAAACATAA
21198402 AAA
1 AAA
21198405 TTGGATCAAG
Statistics
Matches: 50, Mismatches: 9, Indels: 12
0.70 0.13 0.17
Matches are distributed among these distances:
7 5 0.10
8 1 0.02
10 8 0.16
11 27 0.54
12 9 0.18
ACGTcount: A:0.82, C:0.09, G:0.00, T:0.09
Consensus pattern (11 bp):
AAAAAACATAA
Found at i:21198356 original size:33 final size:33
Alignment explanation
Indices: 21198319--21198404 Score: 88
Period size: 33 Copynumber: 2.5 Consensus size: 33
21198309 AAGTTATGAC
21198319 ACAAAAAAACA-AAAAACATAAAAAA-AAATAAAA
1 ACAAAAAAACACAAAAA-ATAAAAAATAAA-AAAA
21198352 ACAAAACAAA-ACAAAAAATAAAAAATAAAAAAA
1 ACAAAA-AAACACAAAAAATAAAAAATAAAAAAA
*
21198385 ACTTAACAAAAACATAAAAA
1 AC--AA-AAAAACACAAAAA
21198405 TTGGATCAAG
Statistics
Matches: 45, Mismatches: 1, Indels: 11
0.79 0.02 0.19
Matches are distributed among these distances:
33 21 0.47
34 11 0.24
35 5 0.11
36 8 0.18
ACGTcount: A:0.81, C:0.10, G:0.00, T:0.08
Consensus pattern (33 bp):
ACAAAAAAACACAAAAAATAAAAAATAAAAAAA
Found at i:21198385 original size:23 final size:23
Alignment explanation
Indices: 21198323--21198386 Score: 76
Period size: 23 Copynumber: 2.7 Consensus size: 23
21198313 TATGACACAA
*
21198323 AAAAACAAAAAACATAAAAAAAAAT
1 AAAAACAAAAAA-A-AACAAAAAAT
*
21198348 AAAAACAAAACAAAACAAAAAAT
1 AAAAACAAAAAAAAACAAAAAAT
21198371 AAAAA-ATAAAAAAAAC
1 AAAAACA-AAAAAAAAC
21198387 TTAACAAAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
22 1 0.03
23 22 0.63
24 1 0.03
25 11 0.31
ACGTcount: A:0.84, C:0.09, G:0.00, T:0.06
Consensus pattern (23 bp):
AAAAACAAAAAAAAACAAAAAAT
Found at i:21198385 original size:28 final size:29
Alignment explanation
Indices: 21198321--21198404 Score: 93
Period size: 29 Copynumber: 2.9 Consensus size: 29
21198311 GTTATGACAC
21198321 AAAAAAACAAAA-AACATAAA-AAAAAATAA
1 AAAAAAACAAAACAA-A-AAATAAAAAATAA
21198350 AAACAAAACAAAACAAAAAATAAAAAAT-A
1 AAA-AAAACAAAACAAAAAATAAAAAATAA
**
21198379 AAAAAAACTTAACAAAAACATAAAAA
1 AAAAAAACAAAACAAAAA-ATAAAAA
21198405 TTGGATCAAG
Statistics
Matches: 49, Mismatches: 2, Indels: 8
0.83 0.03 0.14
Matches are distributed among these distances:
28 13 0.27
29 17 0.35
30 17 0.35
31 2 0.04
ACGTcount: A:0.82, C:0.10, G:0.00, T:0.08
Consensus pattern (29 bp):
AAAAAAACAAAACAAAAAATAAAAAATAA
Found at i:21198405 original size:28 final size:30
Alignment explanation
Indices: 21198324--21198404 Score: 89
Period size: 30 Copynumber: 2.7 Consensus size: 30
21198314 ATGACACAAA
21198324 AAAACAAAA-AACATAAA-AAAAAATAAAAAC
1 AAAACAAAACAA-A-AAATAAAAAATAAAAAC
21198354 AAAACAAAACAAAAAATAAAAAAT-AAAA-
1 AAAACAAAACAAAAAATAAAAAATAAAAAC
**
21198382 AAAACTTAACAAAAACATAAAAA
1 AAAACAAAACAAAAA-ATAAAAA
21198405 TTGGATCAAG
Statistics
Matches: 46, Mismatches: 2, Indels: 7
0.84 0.04 0.13
Matches are distributed among these distances:
28 13 0.28
29 14 0.30
30 17 0.37
31 2 0.04
ACGTcount: A:0.81, C:0.10, G:0.00, T:0.09
Consensus pattern (30 bp):
AAAACAAAACAAAAAATAAAAAATAAAAAC
Found at i:21199172 original size:278 final size:278
Alignment explanation
Indices: 21198668--21199182 Score: 811
Period size: 278 Copynumber: 1.9 Consensus size: 278
21198658 AGCAAAAACA
*
21198668 TCATGTAGTTTAAGGGACTTACGAGGTTTAAAATCTAACACTTAACTACCATGAGATTTGATTTA
1 TCATGTAGTTTAAGGGACTCACGAGGTTTAAAATCTAACACTTAACTACCATGAGATTTGATTTA
* *
21198733 TTATTTTTTCTTAAAACCGTTACCTTTGTTGTTGTCCATTGCTATTTTGGTAACAAACCATTTGA
66 TTATTTTTTCTTAAAACCGTTACCTTTGTTGTTGTCCATTGCTATTTTAGTAACAAACCATCTGA
*
21198798 TTAGTTCTTTCTTAAATAATTGATGAGCTTAGAAGTTTTTCATCAGGTAATTGAAGTGCTTCTTC
131 TTAGTTCTTTCTTAAATAATTAATGAGCTTAGAAGTTTTTCATCAGGTAATTGAAGTGCTTCTTC
* * * *
21198863 TAATTATAGAGATGGGAAACTAGCTTAATTCAGGCACTCACTAGCTATATTTGTTTAATGTCGTT
196 TAATTATAAAGATGAGAAACTAGCCTAATTCAAGCACTCACTAGCTATATTTGTTTAATGTCGTT
21198928 GGATTGATTATGGAGATG
261 GGATTGATTATGGAGATG
* * *
21198946 TCATGTAGTTTGAGGGACTCACGAGGTTTAAAATGTAACACTTAACTACCCTGAGATTTGATTTA
1 TCATGTAGTTTAAGGGACTCACGAGGTTTAAAATCTAACACTTAACTACCATGAGATTTGATTTA
* *
21199011 TTATTATTTT-TTTAAATCGTTACCTTT-TCTGTTGTCCATTGCTATTTTAGTAACAAACCATCT
66 TTATT-TTTTCTTAAAACCGTTACCTTTGT-TGTTGTCCATTGCTATTTTAGTAACAAACCATCT
* *
21199074 GATTAGTTCTTTCTTAAATAATTAATGAGCTTAGAAGTTTTTCGTCAGGTAATTGAAGTG-TTTT
129 GATTAGTTCTTTCTTAAATAATTAATGAGCTTAGAAGTTTTTCATCAGGTAATTGAAGTGCTTCT
* * * *
21199138 TATTAATTATAAAGGTGAGATACTGGCCTAATTCAAGCACTCACT
194 T-CTAATTATAAAGATGAGAAACTAGCCTAATTCAAGCACTCACT
21199183 TTGATATATT
Statistics
Matches: 215, Mismatches: 19, Indels: 6
0.90 0.08 0.03
Matches are distributed among these distances:
277 5 0.02
278 206 0.96
279 4 0.02
ACGTcount: A:0.29, C:0.14, G:0.17, T:0.41
Consensus pattern (278 bp):
TCATGTAGTTTAAGGGACTCACGAGGTTTAAAATCTAACACTTAACTACCATGAGATTTGATTTA
TTATTTTTTCTTAAAACCGTTACCTTTGTTGTTGTCCATTGCTATTTTAGTAACAAACCATCTGA
TTAGTTCTTTCTTAAATAATTAATGAGCTTAGAAGTTTTTCATCAGGTAATTGAAGTGCTTCTTC
TAATTATAAAGATGAGAAACTAGCCTAATTCAAGCACTCACTAGCTATATTTGTTTAATGTCGTT
GGATTGATTATGGAGATG
Found at i:21204854 original size:3 final size:3
Alignment explanation
Indices: 21204848--21204884 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
21204838 AGTAGTAGCA
21204848 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG A
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG A
21204885 GGAGGAGGAG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.35, C:0.00, G:0.32, T:0.32
Consensus pattern (3 bp):
ATG
Found at i:21206468 original size:18 final size:18
Alignment explanation
Indices: 21206447--21206489 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
21206437 TCTGGTGAGA
21206447 ATGATGAGGAGTTGTCAG
1 ATGATGAGGAGTTGTCAG
** *
21206465 ATGATGCTGAGTTTTCAG
1 ATGATGAGGAGTTGTCAG
21206483 ATGATGA
1 ATGATGA
21206490 AAAGGAGGCT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.28, C:0.07, G:0.33, T:0.33
Consensus pattern (18 bp):
ATGATGAGGAGTTGTCAG
Found at i:21209550 original size:13 final size:13
Alignment explanation
Indices: 21209527--21209582 Score: 67
Period size: 13 Copynumber: 4.3 Consensus size: 13
21209517 AAAAAACCAG
*
21209527 CAGCGCCCTCCTT
1 CAGCACCCTCCTT
*
21209540 TAGCACCCTCCTT
1 CAGCACCCTCCTT
*
21209553 CAGCACTCTCCTT
1 CAGCACCCTCCTT
* *
21209566 CAGCACTCTCTTT
1 CAGCACCCTCCTT
21209579 CAGC
1 CAGC
21209583 TACTCCCTCC
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 38 1.00
ACGTcount: A:0.14, C:0.46, G:0.11, T:0.29
Consensus pattern (13 bp):
CAGCACCCTCCTT
Found at i:21209563 original size:26 final size:27
Alignment explanation
Indices: 21209534--21209587 Score: 74
Period size: 26 Copynumber: 2.0 Consensus size: 27
21209524 CAGCAGCGCC
*
21209534 CTCCTTTAGCACCCTCCTTCAGC-ACT
1 CTCCTTCAGCACCCTCCTTCAGCTACT
* *
21209560 CTCCTTCAGCACTCTCTTTCAGCTACT
1 CTCCTTCAGCACCCTCCTTCAGCTACT
21209587 C
1 C
21209588 CCTCCTAAAG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
26 20 0.83
27 4 0.17
ACGTcount: A:0.15, C:0.44, G:0.07, T:0.33
Consensus pattern (27 bp):
CTCCTTCAGCACCCTCCTTCAGCTACT
Found at i:21209662 original size:25 final size:24
Alignment explanation
Indices: 21209632--21209682 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 24
21209622 GCTCTCGGAC
21209632 CTTCCTCTTTCCTTCTT-ATTTTTTT
1 CTTCCT-TTT-CTTCTTCATTTTTTT
*
21209657 CTTCCTTTTTTTCTTCATTTTTTT
1 CTTCCTTTTCTTCTTCATTTTTTT
21209681 CT
1 CT
21209683 ACCCCCGCGT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
23 5 0.21
24 13 0.54
25 6 0.25
ACGTcount: A:0.04, C:0.25, G:0.00, T:0.71
Consensus pattern (24 bp):
CTTCCTTTTCTTCTTCATTTTTTT
Found at i:21209668 original size:13 final size:12
Alignment explanation
Indices: 21209644--21209682 Score: 62
Period size: 12 Copynumber: 3.3 Consensus size: 12
21209634 TCCTCTTTCC
21209644 TTCTT-ATTTTT
1 TTCTTCATTTTT
*
21209655 TTCTTCCTTTTT
1 TTCTTCATTTTT
21209667 TTCTTCATTTTT
1 TTCTTCATTTTT
21209679 TTCT
1 TTCT
21209683 ACCCCCGCGT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
11 5 0.20
12 20 0.80
ACGTcount: A:0.05, C:0.18, G:0.00, T:0.77
Consensus pattern (12 bp):
TTCTTCATTTTT
Found at i:21211487 original size:41 final size:42
Alignment explanation
Indices: 21211441--21211520 Score: 110
Period size: 41 Copynumber: 1.9 Consensus size: 42
21211431 TCAAACTCAA
*
21211441 TGTTTTCTATTTTTT-TTGTTGATTTTTTT-TACAATTTTTGT
1 TGTTTTCTATTTTTTATT-TTGATTTTTTTATAAAATTTTTGT
* *
21211482 TGTTTTTTATTTTTTATTTTTATTTTTTTATAAAATTTT
1 TGTTTTCTATTTTTTATTTTGATTTTTTTATAAAATTTT
21211521 CATATGAAGA
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
41 24 0.71
42 10 0.29
ACGTcount: A:0.16, C:0.03, G:0.06, T:0.75
Consensus pattern (42 bp):
TGTTTTCTATTTTTTATTTTGATTTTTTTATAAAATTTTTGT
Found at i:21211512 original size:14 final size:13
Alignment explanation
Indices: 21211485--21211509 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
21211475 TTTTTGTTGT
21211485 TTTTTATTTTTTA
1 TTTTTATTTTTTA
21211498 TTTTTATTTTTT
1 TTTTTATTTTTT
21211510 TATAAAATTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (13 bp):
TTTTTATTTTTTA
Found at i:21211703 original size:46 final size:47
Alignment explanation
Indices: 21211584--21211703 Score: 113
Period size: 46 Copynumber: 2.6 Consensus size: 47
21211574 AAGAATTGAG
*** *
21211584 ATTCACAT-TTAAAAATAAAAAATTTGCATTCGAAAAAATCTTTAAAG
1 ATTCACATCTTAAAAATAAAAAATTCAAATTC-AAAAAATCTTTAAAC
* *
21211631 ATTCACATC-TAAGAAATCAAAGATTCAAATTC-AAAAA-CTTTAAAAC
1 ATTCACATCTTAA-AAATAAAAAATTCAAATTCAAAAAATCTTT-AAAC
* *
21211677 ATTTATATCTTAAAAATAAAAAATTCA
1 ATTCACATCTTAAAAATAAAAAATTCA
21211704 TTTGAAAAAG
Statistics
Matches: 59, Mismatches: 10, Indels: 9
0.76 0.13 0.12
Matches are distributed among these distances:
45 4 0.07
46 27 0.46
47 14 0.24
48 14 0.24
ACGTcount: A:0.53, C:0.12, G:0.04, T:0.31
Consensus pattern (47 bp):
ATTCACATCTTAAAAATAAAAAATTCAAATTCAAAAAATCTTTAAAC
Found at i:21212083 original size:21 final size:22
Alignment explanation
Indices: 21212059--21212112 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 22
21212049 TGAGATTCCC
* *
21212059 ATCGAGGGTTTT-TAGATTTAA
1 ATCGAAGGTTTTCGAGATTTAA
*
21212080 ATCGAAGGTTTTCGAGATTTAT
1 ATCGAAGGTTTTCGAGATTTAA
*
21212102 ATTGAAGGTTT
1 ATCGAAGGTTT
21212113 CAAGATTCAC
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
21 11 0.39
22 17 0.61
ACGTcount: A:0.28, C:0.06, G:0.24, T:0.43
Consensus pattern (22 bp):
ATCGAAGGTTTTCGAGATTTAA
Found at i:21212100 original size:22 final size:21
Alignment explanation
Indices: 21212043--21212112 Score: 68
Period size: 21 Copynumber: 3.3 Consensus size: 21
21212033 TTCACATAAG
***
21212043 AGGTTTTGAGATTCCCATCGA
1 AGGTTTTGAGATTTAAATCGA
* *
21212064 GGGTTTTTAGATTTAAATCGA
1 AGGTTTTGAGATTTAAATCGA
* *
21212085 AGGTTTTCGAGATTTATATTGA
1 AGGTTTT-GAGATTTAAATCGA
21212107 AGGTTT
1 AGGTTT
21212113 CAAGATTCAC
Statistics
Matches: 39, Mismatches: 9, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
21 22 0.56
22 17 0.44
ACGTcount: A:0.26, C:0.09, G:0.24, T:0.41
Consensus pattern (21 bp):
AGGTTTTGAGATTTAAATCGA
Found at i:21212118 original size:21 final size:22
Alignment explanation
Indices: 21212059--21212119 Score: 63
Period size: 21 Copynumber: 2.9 Consensus size: 22
21212049 TGAGATTCCC
* *
21212059 ATCGAGGGTTTT-TAGATTTAA
1 ATCGAAGGTTTTCAAGATTTAA
* *
21212080 ATCGAAGGTTTTCGAGATTTAT
1 ATCGAAGGTTTTCAAGATTTAA
*
21212102 ATTGAAGG-TTTCAAGATT
1 ATCGAAGGTTTTCAAGATT
21212120 CACATCGAGG
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
21 20 0.59
22 14 0.41
ACGTcount: A:0.30, C:0.07, G:0.23, T:0.41
Consensus pattern (22 bp):
ATCGAAGGTTTTCAAGATTTAA
Found at i:21212508 original size:177 final size:177
Alignment explanation
Indices: 21212182--21212510 Score: 453
Period size: 177 Copynumber: 1.9 Consensus size: 177
21212172 ATCTAAAACT
* *
21212182 TCTCAAATAAAAGGTCATTCTCTCAAAATCTAATCTTGAAAAGAGCTTATTTAATTTAAGACTTA
1 TCTCAAATAAAAAGTCATTCTCTCAAAATCTAATCTTGAAAAGAGCTTATTTAATCTAAGACTTA
* *
21212247 ACAATTTTAAAAATCATTCTCATAACGTATTACTTCAGAGATTCAATCACTAAACAAAAAAAATT
66 ACAACTTTAAAAATCATTCTCATAACGTATCACTTCAGAGATTCAATCACTAAACAAAAAAAATT
** *
21212312 AAAAGTCATTACCAATTTTTTTTCATTAAGGTGCCATTATCTCAAAA
131 AAAAGTCACCACAAATTTTTTTTCATTAAGGTGCCATTATCTCAAAA
* * * **
21212359 TCTCAAATAAAAAGTCATTCTTTCAAAATCTAATCTTGAAAATAGCTTCTTTAATCTAAGGTTTA
1 TCTCAAATAAAAAGTCATTCTCTCAAAATCTAATCTTGAAAAGAGCTTATTTAATCTAAGACTTA
** ** * * * * *
21212424 ATGACTTTAAAAATTGTTGTCATAACGTGTCGCTTTAGAGATTCAATCACTAGAC-AAAAAAATT
66 ACAACTTTAAAAATCATTCTCATAACGTATCACTTCAGAGATTCAATCACTAAACAAAAAAAATT
21212488 AAAAGTCACCATCAAATTTTTTT
131 AAAAGTCACCA-CAAATTTTTTT
21212511 GTTGAGGTGC
Statistics
Matches: 130, Mismatches: 21, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
176 18 0.14
177 112 0.86
ACGTcount: A:0.40, C:0.16, G:0.09, T:0.35
Consensus pattern (177 bp):
TCTCAAATAAAAAGTCATTCTCTCAAAATCTAATCTTGAAAAGAGCTTATTTAATCTAAGACTTA
ACAACTTTAAAAATCATTCTCATAACGTATCACTTCAGAGATTCAATCACTAAACAAAAAAAATT
AAAAGTCACCACAAATTTTTTTTCATTAAGGTGCCATTATCTCAAAA
Found at i:21213237 original size:26 final size:26
Alignment explanation
Indices: 21213211--21213261 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 26
21213201 TTATTAAATA
21213211 TTTTATGCA-TTTTTTATCATTTTATAT
1 TTTTAT-CATTTTTTTAT-ATTTTATAT
*
21213238 TTTTATTATTTTTTTATATTTTAT
1 TTTTATCATTTTTTTATATTTTAT
21213262 TGAAAAGGTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
26 8 0.36
27 14 0.64
ACGTcount: A:0.22, C:0.04, G:0.02, T:0.73
Consensus pattern (26 bp):
TTTTATCATTTTTTTATATTTTATAT
Found at i:21213246 original size:19 final size:18
Alignment explanation
Indices: 21213220--21213259 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
21213210 ATTTTATGCA
21213220 TTTTTTATCATTTTATAT
1 TTTTTTATCATTTTATAT
**
21213238 TTTTATTATTTTTTTATAT
1 TTTT-TTATCATTTTATAT
21213257 TTT
1 TTT
21213260 ATTGAAAAGG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 4 0.21
19 15 0.79
ACGTcount: A:0.20, C:0.03, G:0.00, T:0.78
Consensus pattern (18 bp):
TTTTTTATCATTTTATAT
Found at i:21213394 original size:3 final size:3
Alignment explanation
Indices: 21213386--21213447 Score: 124
Period size: 3 Copynumber: 20.7 Consensus size: 3
21213376 AAACTTCACT
21213386 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
21213434 TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TT
21213448 CTAAAATATT
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 59 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:21213489 original size:20 final size:20
Alignment explanation
Indices: 21213452--21213489 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
21213442 ATTATTCTAA
* *
21213452 AATATTTTTAACATTTTTAG
1 AATATTTTTAAAAATTTTAG
21213472 AATATTTTTAAAAATTTT
1 AATATTTTTAAAAATTTT
21213490 CTTGCATATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.39, C:0.03, G:0.03, T:0.55
Consensus pattern (20 bp):
AATATTTTTAAAAATTTTAG
Found at i:21213756 original size:20 final size:18
Alignment explanation
Indices: 21213707--21213762 Score: 53
Period size: 20 Copynumber: 2.9 Consensus size: 18
21213697 TTATTTCATC
21213707 ATTTTATTTAT-TTTTTAA
1 ATTTTATTT-TGTTTTTAA
21213725 A-TTTATTATTGTTTATTAAA
1 ATTTTATT-TTGTTT-TT-AA
21213745 ATTTTATTTTGTCTTTTA
1 ATTTTATTTTGT-TTTTA
21213763 TTGAAAATTT
Statistics
Matches: 32, Mismatches: 0, Indels: 11
0.74 0.00 0.26
Matches are distributed among these distances:
17 7 0.22
18 5 0.16
19 3 0.09
20 9 0.28
21 8 0.25
ACGTcount: A:0.27, C:0.02, G:0.04, T:0.68
Consensus pattern (18 bp):
ATTTTATTTTGTTTTTAA
Found at i:21216733 original size:52 final size:53
Alignment explanation
Indices: 21216677--21216782 Score: 169
Period size: 52 Copynumber: 2.0 Consensus size: 53
21216667 TTCCAAAATT
*
21216677 TGCTCCCTAATATAAAGGGTGATCTTTGGTT-GAATTTTTTTCAAAGAAATCA
1 TGCTCCCTAATATAAAGGGTGATCTTTAGTTGGAATTTTTTTCAAAGAAATCA
* * *
21216729 TGCTCCCTAATGTAAATGGTGATCTTTAGTTGGATTTTTTTTCAAAGAAATCA
1 TGCTCCCTAATATAAAGGGTGATCTTTAGTTGGAATTTTTTTCAAAGAAATCA
21216782 T
1 T
21216783 AATAGGCTTA
Statistics
Matches: 49, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
52 28 0.57
53 21 0.43
ACGTcount: A:0.29, C:0.13, G:0.17, T:0.41
Consensus pattern (53 bp):
TGCTCCCTAATATAAAGGGTGATCTTTAGTTGGAATTTTTTTCAAAGAAATCA
Found at i:21219464 original size:26 final size:26
Alignment explanation
Indices: 21219433--21219486 Score: 81
Period size: 26 Copynumber: 2.1 Consensus size: 26
21219423 TATATGCTTC
* * *
21219433 TTTTAGAAAAATAAAAAGCTCTCTTT
1 TTTTAGAAAAACAAAAAACTATCTTT
21219459 TTTTAGAAAAACAAAAAACTATCTTT
1 TTTTAGAAAAACAAAAAACTATCTTT
21219485 TT
1 TT
21219487 AAAAGAAAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.44, C:0.11, G:0.06, T:0.39
Consensus pattern (26 bp):
TTTTAGAAAAACAAAAAACTATCTTT
Found at i:21219872 original size:14 final size:14
Alignment explanation
Indices: 21219850--21219879 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
21219840 ATATTATCAG
*
21219850 AAAATTTATTCCCT
1 AAAAATTATTCCCT
21219864 AAAAATTATTCCCT
1 AAAAATTATTCCCT
21219878 AA
1 AA
21219880 TGTGTCATAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.43, C:0.20, G:0.00, T:0.37
Consensus pattern (14 bp):
AAAAATTATTCCCT
Found at i:21223799 original size:21 final size:22
Alignment explanation
Indices: 21223753--21223804 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 22
21223743 TAAATTATTA
21223753 TTTTTGTTTAAAAACACATG-G
1 TTTTTGTTTAAAAACACATGTG
* ** *
21223774 CTTTTGTTTAAAAACTTATGTT
1 TTTTTGTTTAAAAACACATGTG
21223796 TTTTTGTTT
1 TTTTTGTTT
21223805 CAGTTCGTAA
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
21 17 0.68
22 8 0.32
ACGTcount: A:0.25, C:0.08, G:0.12, T:0.56
Consensus pattern (22 bp):
TTTTTGTTTAAAAACACATGTG
Found at i:21234384 original size:12 final size:12
Alignment explanation
Indices: 21234367--21234394 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
21234357 CCACAGCCAA
21234367 TTCATTAGCAGT
1 TTCATTAGCAGT
21234379 TTCATTAGCAGT
1 TTCATTAGCAGT
21234391 TTCA
1 TTCA
21234395 AAAGTAAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.25, C:0.18, G:0.14, T:0.43
Consensus pattern (12 bp):
TTCATTAGCAGT
Found at i:21235428 original size:16 final size:15
Alignment explanation
Indices: 21235407--21235462 Score: 58
Period size: 16 Copynumber: 3.5 Consensus size: 15
21235397 ATGCTATGAT
*
21235407 GATTTTTTTTTTTTGG
1 GATTTTTTGTTTTT-G
21235423 GATTTTGTTGTTTTTG
1 GATTTT-TTGTTTTTG
* *
21235439 GATTTGTTGGTTTTAG
1 GATTT-TTTGTTTTTG
21235455 GATTTTTT
1 GATTTTTT
21235463 TTAGGGTTTT
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
15 2 0.06
16 24 0.71
17 8 0.24
ACGTcount: A:0.09, C:0.00, G:0.23, T:0.68
Consensus pattern (15 bp):
GATTTTTTGTTTTTG
Found at i:21236218 original size:8 final size:8
Alignment explanation
Indices: 21236207--21236235 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
21236197 TTGTTTTTTT
21236207 TTTTTGGA
1 TTTTTGGA
21236215 TTTTTGGA
1 TTTTTGGA
21236223 TTTTTGGA
1 TTTTTGGA
21236231 TTTTT
1 TTTTT
21236236 TATTTAATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.10, C:0.00, G:0.21, T:0.69
Consensus pattern (8 bp):
TTTTTGGA
Found at i:21236219 original size:16 final size:16
Alignment explanation
Indices: 21236207--21236240 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
21236197 TTGTTTTTTT
*
21236207 TTTTTGGATTTTTGGA
1 TTTTTGGATTTTTTGA
21236223 TTTTTGGATTTTTT-A
1 TTTTTGGATTTTTTGA
21236238 TTT
1 TTT
21236241 AATTTTTCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 4 0.24
16 13 0.76
ACGTcount: A:0.12, C:0.00, G:0.18, T:0.71
Consensus pattern (16 bp):
TTTTTGGATTTTTTGA
Found at i:21236839 original size:114 final size:113
Alignment explanation
Indices: 21236708--21237019 Score: 358
Period size: 114 Copynumber: 2.7 Consensus size: 113
21236698 CGAGTGGATG
* * ** * * *
21236708 CAAATGACTTC-GATATCACCATTGAAAGAAACTTGAATATCGCCATCAAAAAAATACAAATGAC
1 CAAATGATTTCGGATATCACCATTGAAA-AAAATTGAATATAACCATCAAGAAAATATAGATGAC
* * * * * *
21236772 TTCGGATATCACCATCGAAGAGAACTCGGATATTGTCATC-GAGAAAATA
65 TTCGAATATCACCACCAAAAAGAACTCGGATATTGCCA-CAAAGAAAATA
* * * *
21236821 CAAATGATTTCGGATATCACTATTGAAAAAAATTTAGATATAACCACCAAGAAAATTTAGATGAC
1 CAAATGATTTCGGATATCACCATTGAAAAAAATTGA-ATATAACCATCAAGAAAATATAGATGAC
*
21236886 TTCAAATATCACCACCAAAAAGAACTCGGATATTGCCACAAAGAAAATA
65 TTCGAATATCACCACCAAAAAGAACTCGGATATTGCCACAAAGAAAATA
* * ** *
21236935 TAAATGATTTCGGATATTACCGCTGAAAAAAATTTGGATATAACCATCAAGAAAATATAGATGAC
1 CAAATGATTTCGGATATCACCATTGAAAAAAA-TTGAATATAACCATCAAGAAAATATAGATGAC
*
21237000 TTCGAATATCGCCACCAAAA
65 TTCGAATATCACCACCAAAA
21237020 GAAACAAAAA
Statistics
Matches: 166, Mismatches: 29, Indels: 7
0.82 0.14 0.03
Matches are distributed among these distances:
113 17 0.10
114 147 0.89
115 2 0.01
ACGTcount: A:0.45, C:0.18, G:0.13, T:0.24
Consensus pattern (113 bp):
CAAATGATTTCGGATATCACCATTGAAAAAAATTGAATATAACCATCAAGAAAATATAGATGACT
TCGAATATCACCACCAAAAAGAACTCGGATATTGCCACAAAGAAAATA
Found at i:21236861 original size:57 final size:56
Alignment explanation
Indices: 21236708--21237009 Score: 187
Period size: 57 Copynumber: 5.3 Consensus size: 56
21236698 CGAGTGGATG
*
21236708 CAAATGACTTC-GATATCACCATTGAAAGAAACTTGAATATCGCCATCAAAAAAATA
1 CAAATGACTTCGGATATCACCATTGAAAAAAACTTG-ATATCGCCATCAAAAAAATA
* * * * * * * *
21236764 CAAATGACTTCGGATATCACCATCGAAGAGAACTCGGATATTGTCATCGAGAAAATA
1 CAAATGACTTCGGATATCACCATTGAAAAAAACT-TGATATCGCCATCAAAAAAATA
* * * ** * * *
21236821 CAAATGATTTCGGATATCACTATTGAAAAAAATTTAGATATAACCACCAAGAAAATT
1 CAAATGACTTCGGATATCACCATTGAAAAAAACTT-GATATCGCCATCAAAAAAATA
* * ** ** * *
21236878 TAGATGACTTCAAATATCACCA-CCAAAAAGAACTCGGATATTGCCA-CAAAGAAAATA
1 CAAATGACTTCGGATATCACCATTGAAAAA-AACT-TGATATCGCCATCAAA-AAAATA
* * * ** * ** *
21236935 TAAATGATTTCGGATATTACCGCTGAAAAAAATTTGGATATAACCATCAAGAAAATA
1 CAAATGACTTCGGATATCACCATTGAAAAAAACTT-GATATCGCCATCAAAAAAATA
* * *
21236992 TAGATGACTTCGAATATC
1 CAAATGACTTCGGATATC
21237010 GCCACCAAAA
Statistics
Matches: 184, Mismatches: 53, Indels: 17
0.72 0.21 0.07
Matches are distributed among these distances:
56 19 0.10
57 156 0.85
58 9 0.05
ACGTcount: A:0.44, C:0.17, G:0.14, T:0.25
Consensus pattern (56 bp):
CAAATGACTTCGGATATCACCATTGAAAAAAACTTGATATCGCCATCAAAAAAATA
Found at i:21237441 original size:21 final size:22
Alignment explanation
Indices: 21237416--21237464 Score: 66
Period size: 21 Copynumber: 2.3 Consensus size: 22
21237406 TTTTATGATA
21237416 CAAATGT-CTCTTACAAAAATG
1 CAAATGTCCTCTTACAAAAATG
* *
21237437 CAAAT-TCCTTTTACAAATATG
1 CAAATGTCCTCTTACAAAAATG
21237458 CAAATGT
1 CAAATGT
21237465 GTACTTCTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 1 0.04
21 22 0.92
22 1 0.04
ACGTcount: A:0.41, C:0.18, G:0.08, T:0.33
Consensus pattern (22 bp):
CAAATGTCCTCTTACAAAAATG
Found at i:21237589 original size:57 final size:56
Alignment explanation
Indices: 21237501--21237610 Score: 166
Period size: 57 Copynumber: 1.9 Consensus size: 56
21237491 TTAATGATGT
21237501 AAAAGCAAAGTCAAAAGAAGCAAATGCTCAAAATCTTCATTTCTTAAATCTTTCAAA
1 AAAAGCAAAGTCAAAAGAAGCAAATGCTCAAAATCTTCATTTCTTAAAT-TTTCAAA
* * * * *
21237558 AAAAGCCAAGTCAAAATATGTAAATGCTCAAAATCTTCTTTTCTTAAATTTTC
1 AAAAGCAAAGTCAAAAGAAGCAAATGCTCAAAATCTTCATTTCTTAAATTTTC
21237611 CAAATTTTTT
Statistics
Matches: 48, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
56 4 0.08
57 44 0.92
ACGTcount: A:0.44, C:0.17, G:0.08, T:0.31
Consensus pattern (56 bp):
AAAAGCAAAGTCAAAAGAAGCAAATGCTCAAAATCTTCATTTCTTAAATTTTCAAA
Found at i:21239350 original size:18 final size:17
Alignment explanation
Indices: 21239317--21239349 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
21239307 CCATTGATAT
21239317 TTTTTCTTTTTTTTTTG
1 TTTTTCTTTTTTTTTTG
21239334 TTTTTCTTTTTTTTTT
1 TTTTTCTTTTTTTTTT
21239350 TTTCATATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.00, C:0.06, G:0.03, T:0.91
Consensus pattern (17 bp):
TTTTTCTTTTTTTTTTG
Found at i:21239361 original size:17 final size:15
Alignment explanation
Indices: 21239316--21239352 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 15
21239306 ACCATTGATA
21239316 TTTTTTCTTTTTTTTT
1 TTTTTTC-TTTTTTTT
21239332 TGTTTTTCTTTTTTTT
1 T-TTTTTCTTTTTTTT
21239348 TTTTT
1 TTTTT
21239353 CATATTTTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
15 4 0.20
16 10 0.50
17 6 0.30
ACGTcount: A:0.00, C:0.05, G:0.03, T:0.92
Consensus pattern (15 bp):
TTTTTTCTTTTTTTT
Found at i:21242925 original size:31 final size:30
Alignment explanation
Indices: 21242888--21242950 Score: 74
Period size: 30 Copynumber: 2.1 Consensus size: 30
21242878 TTAATTTTTG
*
21242888 TTGGTTTCAAGGGAGATAAATG-GATTAAGAT
1 TTGGTTT-AAGAGAGATAAATGAG-TTAAGAT
**
21242919 TTGGTTTTTGAGAGATAAATGAGTTAAGAT
1 TTGGTTTAAGAGAGATAAATGAGTTAAGAT
21242949 TT
1 TT
21242951 TATTTATTAG
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
30 20 0.71
31 8 0.29
ACGTcount: A:0.33, C:0.02, G:0.27, T:0.38
Consensus pattern (30 bp):
TTGGTTTAAGAGAGATAAATGAGTTAAGAT
Found at i:21244899 original size:18 final size:17
Alignment explanation
Indices: 21244873--21244931 Score: 57
Period size: 18 Copynumber: 3.4 Consensus size: 17
21244863 TATATCTTAT
*
21244873 TATATTTATAAAAATTA
1 TATAATTATAAAAATTA
**
21244890 TATCAATTATTTAAATTA
1 TAT-AATTATAAAAATTA
*
21244908 TATAAATATTAAAAATTA
1 TATAATTA-TAAAAATTA
21244926 -ATAATT
1 TATAATT
21244932 TTGATCAATA
Statistics
Matches: 33, Mismatches: 7, Indels: 4
0.75 0.16 0.09
Matches are distributed among these distances:
17 12 0.36
18 21 0.64
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.46
Consensus pattern (17 bp):
TATAATTATAAAAATTA
Found at i:21246391 original size:2 final size:2
Alignment explanation
Indices: 21246384--21246412 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
21246374 GGAATATTAC
21246384 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
21246413 TACTAGAAGA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:21248191 original size:13 final size:13
Alignment explanation
Indices: 21248173--21248200 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
21248163 GACATAAATT
21248173 TTCAAAAATCAAG
1 TTCAAAAATCAAG
21248186 TTCAAAAATCAAG
1 TTCAAAAATCAAG
21248199 TT
1 TT
21248201 ATTTTTTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.50, C:0.14, G:0.07, T:0.29
Consensus pattern (13 bp):
TTCAAAAATCAAG
Found at i:21249815 original size:20 final size:20
Alignment explanation
Indices: 21249792--21249833 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
21249782 CTTTAAAAAC
*
21249792 CTTTCATTTCCTTTCTTTTA
1 CTTTCATTTCCTTTCCTTTA
* *
21249812 CTTTCTTTTTCTTTCCTTTA
1 CTTTCATTTCCTTTCCTTTA
21249832 CT
1 CT
21249834 AATACTATCC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.07, C:0.26, G:0.00, T:0.67
Consensus pattern (20 bp):
CTTTCATTTCCTTTCCTTTA
Found at i:21251715 original size:18 final size:19
Alignment explanation
Indices: 21251670--21251715 Score: 53
Period size: 18 Copynumber: 2.5 Consensus size: 19
21251660 AGCTCACGAG
*
21251670 TTTAATTA-AGTTTTTTAT
1 TTTAATTATAGTTTATTAT
21251688 TTT-ATATATA-TTTATTAT
1 TTTAAT-TATAGTTTATTAT
21251706 TTTAATTATA
1 TTTAATTATA
21251716 AAATTACAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 6
0.77 0.03 0.19
Matches are distributed among these distances:
17 2 0.08
18 19 0.79
19 3 0.12
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (19 bp):
TTTAATTATAGTTTATTAT
Found at i:21267159 original size:16 final size:16
Alignment explanation
Indices: 21267138--21267168 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
21267128 CATTAGGAAG
21267138 ATAGTTTCGATGAATC
1 ATAGTTTCGATGAATC
*
21267154 ATAGTTTTGATGAAT
1 ATAGTTTCGATGAAT
21267169 TAGAATAGTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.32, C:0.06, G:0.19, T:0.42
Consensus pattern (16 bp):
ATAGTTTCGATGAATC
Found at i:21269275 original size:14 final size:14
Alignment explanation
Indices: 21269256--21269282 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
21269246 TTTTTATGTT
21269256 ATTTTAATTTAATA
1 ATTTTAATTTAATA
21269270 ATTTTAATTTAAT
1 ATTTTAATTTAAT
21269283 CATTAATTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (14 bp):
ATTTTAATTTAATA
Found at i:21270307 original size:2 final size:2
Alignment explanation
Indices: 21270302--21270328 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
21270292 ATATATATAT
21270302 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 A
21270329 CTGTAAAATT
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:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:21270355 original size:13 final size:12
Alignment explanation
Indices: 21270332--21270358 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
21270322 AGAGAGACTG
21270332 TAAAATTTTTTT
1 TAAAATTTTTTT
21270344 TAAAATTTTTTT
1 TAAAATTTTTTT
21270356 TAA
1 TAA
21270359 TTATTAATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (12 bp):
TAAAATTTTTTT
Found at i:21270367 original size:7 final size:7
Alignment explanation
Indices: 21270355--21270386 Score: 57
Period size: 7 Copynumber: 4.7 Consensus size: 7
21270345 AAAATTTTTT
21270355 TTAATTA
1 TTAATTA
21270362 TTAATTA
1 TTAATTA
21270369 TTAATTA
1 TTAATTA
21270376 TTAATT-
1 TTAATTA
21270382 TTAAT
1 TTAAT
21270387 AGATTAAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 5 0.20
7 20 0.80
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (7 bp):
TTAATTA
Found at i:21273502 original size:17 final size:18
Alignment explanation
Indices: 21273476--21273510 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
21273466 AATTTTATGA
21273476 TAAATATTTATTTAAATT
1 TAAATATTTATTTAAATT
*
21273494 TAAAT-TTTATTTTAATT
1 TAAATATTTATTTAAATT
21273511 CAGATATATC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (18 bp):
TAAATATTTATTTAAATT
Found at i:21273988 original size:2 final size:2
Alignment explanation
Indices: 21273976--21274006 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
21273966 GTATATTGTA
21273976 AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
21274007 GATTGTCAAC
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
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:21279048 original size:16 final size:16
Alignment explanation
Indices: 21279027--21279057 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
21279017 TGACATATCT
21279027 TTAACAATTGGTATGC
1 TTAACAATTGGTATGC
21279043 TTAACAATTGGTATG
1 TTAACAATTGGTATG
21279058 AGCTTGTATG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.32, C:0.10, G:0.19, T:0.39
Consensus pattern (16 bp):
TTAACAATTGGTATGC
Found at i:21281997 original size:3 final size:3
Alignment explanation
Indices: 21281982--21282045 Score: 101
Period size: 3 Copynumber: 21.3 Consensus size: 3
21281972 CAAAAAGAAT
* * *
21281982 TAA TAA TAT TAA TAA TAA TAG TAA TAA TAA TGA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
21282030 TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA T
21282046 CTTTTAAGAA
Statistics
Matches: 55, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 55 1.00
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:21282551 original size:130 final size:128
Alignment explanation
Indices: 21282357--21282818 Score: 413
Period size: 130 Copynumber: 3.6 Consensus size: 128
21282347 ACATTAAAAA
* * * * * *
21282357 AATCCCTTACTAAATTACAAAATTACCTATTTC-ATTATTTGATGAGAAAGTAACATGTATCCAA
1 AATCTCTTA-TAAATTACAAAA-TACCT-TTTCTATTATATGATAAGAAATTGACATGTAGCCAA
* *
21282421 ATGCACTATTATGCCCTTATATCATAATTATAAAAATACCCATTTTCTTATAATTATTTAT-TAA
63 ATGAACTATTATGCCCTTATACCATAATTATAAAAATACCCATTTTCTTATAATTATTT-TCTAA
21282485 AT
127 AT
*
21282487 AATCT-TTCAATAAATTATGAAAATACCTTTTCTATTATATGATAAGAAATTGACATGTAGCCAA
1 AATCTCTT--ATAAATTA-CAAAATACCTTTTCTATTATATGATAAGAAATTGACATGTAGCCAA
* * * * * * *
21282551 ATAAACTATTATGCTCTCATGCCATAAATATGAAAATACCCATTTTCTTATAATTATTTTCTAAG
63 ATGAACTATTATGCCCTTATACCATAATTATAAAAATACCCATTTTCTTATAATTATTTTCTAAA
21282616 T
128 T
* ** *
21282617 AATCTCTTATAAAATTACCAAAATATCGTTTT-TATTACGTGATAAGAAATTGACATGT-GATCA
1 AATCTCTTAT-AAATTA-CAAAATA-CCTTTTCTATTATATGATAAGAAATTGACATGTAG-CCA
* * * * *
21282680 AATGGACTATTATG-CCTTATACCATAATTAAAAAAAATTCTC-TTCTT-TTATAATTATTTAC-
62 AATGAACTATTATGCCCTTATACCATAATT-ATAAAAATACCCATT-TTCTTATAATTATTTTCT
21282741 AAAT
125 AAAT
* * * * * * * *
21282745 AAACCCTTATAAATTACCAATTATCC-CTTATATTATATAATAAGAAATTGACATGTGGCCAAAT
1 AATCTCTTATAAATTACAAAATA-CCTTTTCTATTATATGATAAGAAATTGACATGTAGCCAAAT
* *
21282809 GGATTATTAT
65 GAACTATTAT
21282819 TATCTCATTC
Statistics
Matches: 274, Mismatches: 45, Indels: 30
0.79 0.13 0.09
Matches are distributed among these distances:
125 2 0.01
126 44 0.16
127 7 0.03
128 11 0.04
129 36 0.13
130 162 0.59
131 12 0.04
ACGTcount: A:0.40, C:0.15, G:0.07, T:0.38
Consensus pattern (128 bp):
AATCTCTTATAAATTACAAAATACCTTTTCTATTATATGATAAGAAATTGACATGTAGCCAAATG
AACTATTATGCCCTTATACCATAATTATAAAAATACCCATTTTCTTATAATTATTTTCTAAAT
Found at i:21286221 original size:8 final size:8
Alignment explanation
Indices: 21286208--21286246 Score: 69
Period size: 8 Copynumber: 4.9 Consensus size: 8
21286198 GGGTATTGTA
21286208 AGTGGCTG
1 AGTGGCTG
21286216 AGTGGCTG
1 AGTGGCTG
*
21286224 AGTGGTTG
1 AGTGGCTG
21286232 AGTGGCTG
1 AGTGGCTG
21286240 AGTGGCT
1 AGTGGCT
21286247 TTGTTACCAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
8 29 1.00
ACGTcount: A:0.13, C:0.10, G:0.49, T:0.28
Consensus pattern (8 bp):
AGTGGCTG
Found at i:21304036 original size:78 final size:78
Alignment explanation
Indices: 21303951--21304107 Score: 278
Period size: 78 Copynumber: 2.0 Consensus size: 78
21303941 TACTTTAAGC
21303951 TCTTGCAAGTTACTTTAAAACTCTTAATTTTAAGTTCAAGTTCTTTAAATTATTGTTCAAATTCT
1 TCTTGCAAGTTACTTTAAAACTCTTAATTTTAAGTTCAAGTTCTTTAAATTATTGTTCAAATTCT
21304016 GTAAGTTTCAATT
66 GTAAGTTTCAATT
* * *
21304029 TCTTGCAATTTCCTTTGAAACTCTTAATTTTAAGTTCAAGTTCTTTAAATTATTGTTCAAATTCT
1 TCTTGCAAGTTACTTTAAAACTCTTAATTTTAAGTTCAAGTTCTTTAAATTATTGTTCAAATTCT
*
21304094 TTAAGTTTCAATT
66 GTAAGTTTCAATT
21304107 T
1 T
21304108 AACCTTTGTT
Statistics
Matches: 75, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
78 75 1.00
ACGTcount: A:0.29, C:0.13, G:0.08, T:0.49
Consensus pattern (78 bp):
TCTTGCAAGTTACTTTAAAACTCTTAATTTTAAGTTCAAGTTCTTTAAATTATTGTTCAAATTCT
GTAAGTTTCAATT
Found at i:21304619 original size:10 final size:10
Alignment explanation
Indices: 21304603--21304658 Score: 71
Period size: 10 Copynumber: 5.7 Consensus size: 10
21304593 CACATTAACA
21304603 TTAAAAAATT
1 TTAAAAAATT
*
21304613 AT-AAAAA-T
1 TTAAAAAATT
*
21304621 TTATAAAAGTT
1 TTA-AAAAATT
21304632 TTAAAAAATT
1 TTAAAAAATT
21304642 TTAAAAAATT
1 TTAAAAAATT
21304652 TTAAAAA
1 TTAAAAA
21304659 TTCAAAAAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
8 2 0.05
9 5 0.13
10 28 0.72
11 4 0.10
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.38
Consensus pattern (10 bp):
TTAAAAAATT
Found at i:21304666 original size:9 final size:9
Alignment explanation
Indices: 21304603--21304667 Score: 60
Period size: 10 Copynumber: 6.9 Consensus size: 9
21304593 CACATTAACA
21304603 TTAAAAAA-
1 TTAAAAAAT
21304611 TTATAAAAAT
1 TTA-AAAAAT
*
21304621 TTATAAAAGTT
1 TTA-AAAA-AT
21304632 TTAAAAAATT
1 TTAAAAAA-T
21304642 TTAAAAAAT
1 TTAAAAAAT
*
21304651 TTTAAAAAT
1 TTAAAAAAT
*
21304660 TCAAAAAA
1 TTAAAAAA
21304668 AAAAATCTAA
Statistics
Matches: 48, Mismatches: 5, Indels: 7
0.80 0.08 0.12
Matches are distributed among these distances:
8 3 0.06
9 20 0.42
10 21 0.44
11 4 0.08
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.35
Consensus pattern (9 bp):
TTAAAAAAT
Found at i:21305856 original size:10 final size:10
Alignment explanation
Indices: 21305843--21305938 Score: 72
Period size: 10 Copynumber: 9.6 Consensus size: 10
21305833 TTTTAGTATA
21305843 TTTTTAAA-T
1 TTTTTAAATT
21305852 TTTTTAGAATT
1 TTTTTA-AATT
* *
21305863 ATTTTAGA-T
1 TTTTTAAATT
21305872 TTTTTAAATT
1 TTTTTAAATT
* *
21305882 ATTTTAGAA-A
1 TTTTTA-AATT
21305892 TTTTTATAATT
1 TTTTTA-AATT
**
21305903 TTTCAAAATT
1 TTTTTAAATT
*
21305913 TTTTTGAATT
1 TTTTTAAATT
*
21305923 TTTTAAAATT
1 TTTTTAAATT
21305933 TTTTTA
1 TTTTTA
21305939 TTATACTTAC
Statistics
Matches: 65, Mismatches: 17, Indels: 9
0.71 0.19 0.10
Matches are distributed among these distances:
9 13 0.20
10 40 0.62
11 12 0.18
ACGTcount: A:0.32, C:0.01, G:0.04, T:0.62
Consensus pattern (10 bp):
TTTTTAAATT
Found at i:21305857 original size:20 final size:19
Alignment explanation
Indices: 21305832--21305936 Score: 95
Period size: 20 Copynumber: 5.3 Consensus size: 19
21305822 TCCTCGAGTA
*
21305832 TTTTTAGTATATTTTTAAAT
1 TTTTTAGAAT-TTTTTAAAT
*
21305852 TTTTTAGAATTATTTTAGAT
1 TTTTTAGAATT-TTTTAAAT
*
21305872 TTTTTA-AATTATTTTAGAAA
1 TTTTTAGAATT-TTTTA-AAT
* *
21305892 TTTTTATAATTTTTCAAAAT
1 TTTTTAGAATTTTT-TAAAT
*
21305912 TTTTTTGAATTTTTTAAAAT
1 TTTTTAGAATTTTTT-AAAT
21305932 TTTTT
1 TTTTT
21305937 TATTATACTT
Statistics
Matches: 71, Mismatches: 9, Indels: 10
0.79 0.10 0.11
Matches are distributed among these distances:
19 11 0.15
20 55 0.77
21 5 0.07
ACGTcount: A:0.31, C:0.01, G:0.05, T:0.63
Consensus pattern (19 bp):
TTTTTAGAATTTTTTAAAT
Found at i:21305895 original size:19 final size:20
Alignment explanation
Indices: 21305853--21305895 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 20
21305843 TTTTTAAATT
**
21305853 TTTTAGAATTATTTTAGATT
1 TTTTAGAATTATTTTAGAAA
21305873 TTTTA-AATTATTTTAGAAA
1 TTTTAGAATTATTTTAGAAA
21305892 TTTT
1 TTTT
21305896 TATAATTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 16 0.76
20 5 0.24
ACGTcount: A:0.33, C:0.00, G:0.07, T:0.60
Consensus pattern (20 bp):
TTTTAGAATTATTTTAGAAA
Found at i:21309118 original size:21 final size:24
Alignment explanation
Indices: 21309092--21309137 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 24
21309082 AAAATTCAAC
21309092 AAAAATG-AT-ATT-TTAAAAATA
1 AAAAATGAATCATTGTTAAAAATA
21309113 AAAAATGCAATCATTGTTAAAAATA
1 AAAAATG-AATCATTGTTAAAAATA
21309138 TGAAAACAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
21 7 0.33
23 2 0.10
24 3 0.14
25 9 0.43
ACGTcount: A:0.59, C:0.04, G:0.07, T:0.30
Consensus pattern (24 bp):
AAAAATGAATCATTGTTAAAAATA
Found at i:21309203 original size:73 final size:73
Alignment explanation
Indices: 21309038--21309219 Score: 215
Period size: 73 Copynumber: 2.5 Consensus size: 73
21309028 TGCTATGATT
* * *
21309038 AAAAATACAATTTTTGCTGAAAATATGAGATAAAATTATTTTTTAAAATTCAACAAAAATGATAT
1 AAAAATACAATTTTTGTTGAAAATATGA-A-AAAAATATTTTTTAAAATTCAACAAAAATGACAT
21309103 TTTAAAAATA
64 TTTAAAAATA
* ** * * *
21309113 AAAAATGCAATCATTGTTAAAAATATGAAAACAAATATTTTTTAGAATTTAAC-AAAATGACATT
1 AAAAATACAATTTTTGTTGAAAATATGAAAA-AAATATTTTTTAAAATTCAACAAAAATGACATT
21309177 TCT-AAAATA
65 T-TAAAAATA
* *
21309186 AAAAATACATTTTTTGTTGAAAATATTAAAAAAA
1 AAAAATACAATTTTTGTTGAAAATATGAAAAAAA
21309220 ATTAGAATTC
Statistics
Matches: 90, Mismatches: 15, Indels: 7
0.80 0.13 0.06
Matches are distributed among these distances:
72 3 0.03
73 44 0.49
74 20 0.22
75 23 0.26
ACGTcount: A:0.53, C:0.06, G:0.07, T:0.35
Consensus pattern (73 bp):
AAAAATACAATTTTTGTTGAAAATATGAAAAAAATATTTTTTAAAATTCAACAAAAATGACATTT
TAAAAATA
Found at i:21309815 original size:2 final size:2
Alignment explanation
Indices: 21309797--21309842 Score: 67
Period size: 2 Copynumber: 23.5 Consensus size: 2
21309787 TCACCAGTTC
* *
21309797 TA TA TA AA TA TA AA TA TA TA TA T- 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
21309838 TA TA T
1 TA TA T
21309843 TTGATTTGGT
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
1 1 0.03
2 38 0.97
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:21313283 original size:16 final size:17
Alignment explanation
Indices: 21313259--21313328 Score: 54
Period size: 16 Copynumber: 4.2 Consensus size: 17
21313249 TTGAATATGA
*
21313259 AAAAATAAA-AAAATTT
1 AAAATTAAATAAAATTT
*
21313275 AAAATTAAATCAAATTT
1 AAAATTAAATAAAATTT
* * *
21313292 -AAATTTAATAATATAT
1 AAAATTAAATAAAATTT
* * *
21313308 AAAATCAAATCAAATTC
1 AAAATTAAATAAAATTT
21313325 AAAA
1 AAAA
21313329 CGAGTAAAAC
Statistics
Matches: 40, Mismatches: 12, Indels: 3
0.73 0.22 0.05
Matches are distributed among these distances:
16 20 0.50
17 20 0.50
ACGTcount: A:0.64, C:0.06, G:0.00, T:0.30
Consensus pattern (17 bp):
AAAATTAAATAAAATTT
Found at i:21313289 original size:17 final size:17
Alignment explanation
Indices: 21313269--21313328 Score: 61
Period size: 17 Copynumber: 3.6 Consensus size: 17
21313259 AAAAATAAAA
21313269 AAATTTAAAATTAAATC
1 AAATTTAAAATTAAATC
*
21313286 AAATTT-AAATTTAAT-
1 AAATTTAAAATTAAATC
* *
21313301 AATATATAAAATCAAATC
1 AA-ATTTAAAATTAAATC
*
21313319 AAATTCAAAA
1 AAATTTAAAA
21313329 CGAGTAAAAC
Statistics
Matches: 34, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
15 2 0.06
16 11 0.32
17 19 0.56
18 2 0.06
ACGTcount: A:0.60, C:0.07, G:0.00, T:0.33
Consensus pattern (17 bp):
AAATTTAAAATTAAATC
Found at i:21313312 original size:23 final size:23
Alignment explanation
Indices: 21313269--21313312 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
21313259 AAAAATAAAA
*
21313269 AAATTTAAAATTAAATCAAATTT
1 AAATTTAAAATTAAATAAAATTT
*
21313292 AAATTTAATAA-TATATAAAAT
1 AAATTTAA-AATTAAATAAAAT
21313313 CAAATCAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
23 16 0.89
24 2 0.11
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (23 bp):
AAATTTAAAATTAAATAAAATTT
Found at i:21313475 original size:21 final size:22
Alignment explanation
Indices: 21313435--21313475 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
21313425 ACCCTATTCT
* *
21313435 TTTCTCTTCTTTCTTCTTTTTA
1 TTTCTCTTCTTTCCTATTTTTA
21313457 TTTC-CTTCTTTCCTATTTT
1 TTTCTCTTCTTTCCTATTTT
21313476 CCTTTTTTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.05, C:0.24, G:0.00, T:0.71
Consensus pattern (22 bp):
TTTCTCTTCTTTCCTATTTTTA
Found at i:21315041 original size:2 final size:2
Alignment explanation
Indices: 21315034--21315071 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
21315024 TCCACCCAAG
*
21315034 AT AT AT AT AT AT AT AT AT TT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
21315072 CTTAGGTTTC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:21317466 original size:15 final size:15
Alignment explanation
Indices: 21317458--21317488 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
21317448 TATTATATTT
21317458 TATTATATTAAGTTA
1 TATTATATTAAGTTA
*
21317473 TATTATATTACGTTA
1 TATTATATTAAGTTA
21317488 T
1 T
21317489 GTATATATAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.35, C:0.03, G:0.06, T:0.55
Consensus pattern (15 bp):
TATTATATTAAGTTA
Found at i:21321928 original size:25 final size:25
Alignment explanation
Indices: 21321900--21321952 Score: 63
Period size: 25 Copynumber: 2.1 Consensus size: 25
21321890 AACAATGTGC
*
21321900 TCATACACACC-TTTCAGCAAACCAT
1 TCATAAACACCATTT-AGCAAACCAT
* *
21321925 TCATAAACACCATTTAGCATACGAT
1 TCATAAACACCATTTAGCAAACCAT
21321950 TCA
1 TCA
21321953 GCCCCTCAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 21 0.88
26 3 0.12
ACGTcount: A:0.38, C:0.30, G:0.06, T:0.26
Consensus pattern (25 bp):
TCATAAACACCATTTAGCAAACCAT
Found at i:21323076 original size:14 final size:14
Alignment explanation
Indices: 21323057--21323083 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
21323047 CCTTTAATAA
21323057 TTTAAAAAAAATTT
1 TTTAAAAAAAATTT
21323071 TTTAAAAAAAATT
1 TTTAAAAAAAATT
21323084 ATTGAAGACG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (14 bp):
TTTAAAAAAAATTT
Found at i:21323671 original size:356 final size:353
Alignment explanation
Indices: 21322720--21323903 Score: 1539
Period size: 356 Copynumber: 3.3 Consensus size: 353
21322710 AGTTTATAGC
* * * *
21322720 AAATTATTGAAGGCATTGTTATTTGCAACCGTATTTACTAATTATCTACAAATTGTGATAAAAAT
1 AAATTATTGAAGGCATTGTTATCTGCAACCGCATTCACTAATTATCTACAAACTGTGATAAAAAT
* * **
21322785 TATTAAAGGCATCTTTCTTAGATATACACCTTCAATAACCATGTTAAAATTTGTGTGGTGGTATA
66 TATTAAAAGCATTTTTCTTAGATATACACCTTCAATAACCATGTTAAAATTTGTGTGACGGTATA
* * * *
21322850 TAAAAGGTATTTTACAGTAAAAGACGCCTTTTAATAATTCTTAAAATTTTTAGTGAAAAAATTTT
131 TAAAAGGTATTTTACAATAGAAGATG-CTTTTAATAA-TCCTAAAATTTTTAGTGAAAAAATTTT
* *
21322915 GAAGGTGTCTGTTATTAACAAACGCCTTCAGTAATGGATTACTAAGTTTAAAAGTATATTGAAGG
194 GAAGGCGTCTGTTATTAACAAACGCCTTCAGTAATGGATTACTAAGTTTAAAGGTATATTGAAGG
* * **
21322980 AGCTTTTTTGAATAAATGCCTTCTATAACCATTATGGTATATTCAAGGTATTTCATAATAAAAGA
259 A-CTTTTTTGAATAAATGCCTTCCATAACCATCATGGTATATTCAAGGCGTTTCATAATAAAAGA
**
21323045 CGCCTTTAATAATTTAAAAAAAATTTTTTAAAAA
323 CGCCTTTAATAA--T-CCAAAAATTTTTTAAAAA
* * * * * **
21323079 AAATTATTGAAGACGTTGTTATCTACAATCGCCTTCACTAATTATCTACAAGTTGTGATAAAAAT
1 AAATTATTGAAGGCATTGTTATCTGCAACCGCATTCACTAATTATCTACAAACTGTGATAAAAAT
* *
21323144 TATTAAAAGCATTTTTCTTAGATATACACCTTCAATAACCATATTAAAATTTATGTGACGGTATA
66 TATTAAAAGCATTTTTCTTAGATATACACCTTCAATAACCATGTTAAAATTTGTGTGACGGTATA
* * * * *
21323209 TAAAATGTATTTTACAATAGAATATGCTTTTAATGATTCCTAAAATATTTAGTGAGAAAATTTTG
131 TAAAAGGTATTTTACAATAGAAGATGCTTTTAAT-AATCCTAAAATTTTTAGTGAAAAAATTTTG
* * *
21323274 AAGGCGTCTGATATTAACAAACGCCTTCAGTAATAGATTACTATGTTTAAAGGTATATTGAAGGC
195 AAGGCGTCTGTTATTAACAAACGCCTTCAGTAATGGATTACTAAGTTTAAAGGTATATTGAAGG-
* * *
21323339 ACTTTTTTGAATAAATGCCTTCCATAACCATCGTGGTATATTGAAGGCGTTTCATAATAAAAAAC
259 ACTTTTTTGAATAAATGCCTTCCATAACCATCATGGTATATTCAAGGCGTTTCATAATAAAAGAC
*
21323404 ACCTTTAATAATCCAAAAATTTTTTTAAAAA
324 GCCTTTAATAATCCAAAAA-TTTTTTAAAAA
* * * * * *
21323435 AAATTATTAAAGGTATTGTTATCTGCAACTGTATTAACTAATTATCTACAAACTGTGATAGAAAT
1 AAATTATTGAAGGCATTGTTATCTGCAACCGCATTCACTAATTATCTACAAACTGTGATAAAAAT
* ** * * *
21323500 TATTAAAAAACATTTTTCTTAGATATATGCTTTCAATAACCGTGTTAAAATTTGTGTGACAGTAT
66 TATT-AAAAGCATTTTTCTTAGATATACACCTTCAATAACCATGTTAAAATTTGTGTGACGGTAT
*
21323565 ATAAAAGGTATTTTACAATAGAAGATGCTTTTAATAATCCTCAAAATTTTTAAT-AAAAAATTTT
130 ATAAAAGGTATTTTACAATAGAAGATGCTTTTAATAATCCT-AAAATTTTTAGTGAAAAAATTTT
* *
21323629 GAAGGCGTCTGTTATTAACAAATGCCTTCAGTAATGGATTACTAAGTTTAAAGGTATATTAAATG
194 GAAGGCGTCTGTTATTAACAAACGCCTTCAGTAATGGATTACTAAGTTTAAAGGTATATTGAA-G
* * ** * * * *
21323694 TATTTTTTTGAATAAACACCTTTCATAACCATCTTGGTATATTTAAGACGTTTCATAATAAAAGA
258 GACTTTTTTGAATAAATGCCTTCCATAACCATCATGGTATATTCAAGGCGTTTCATAATAAAAGA
* **
21323759 TGCCTTTAATAATCC-AAAA--TTAAAAAAA
323 CGCCTTTAATAATCCAAAAATTTTTTAAAAA
* * *
21323787 AAATTATTGAAGGCATTGTTATCTGTAACCGCCTTCACTAATTATCTACAAACTATGATAAAAAT
1 AAATTATTGAAGGCATTGTTATCTGCAACCGCATTCACTAATTATCTACAAACTGTGATAAAAAT
* * * * * **
21323852 TATTAAAGGTATTTTTTTTGGATATACGCCTTCAATAACTGTGTTAAAATTT
66 TATTAAAAGCATTTTTCTTAGATATACACCTTCAATAACCATGTTAAAATTT
21323904 ATTTGGCGAT
Statistics
Matches: 718, Mismatches: 101, Indels: 20
0.86 0.12 0.02
Matches are distributed among these distances:
351 40 0.06
352 67 0.09
355 9 0.01
356 209 0.29
357 96 0.13
358 159 0.22
359 138 0.19
ACGTcount: A:0.38, C:0.12, G:0.12, T:0.37
Consensus pattern (353 bp):
AAATTATTGAAGGCATTGTTATCTGCAACCGCATTCACTAATTATCTACAAACTGTGATAAAAAT
TATTAAAAGCATTTTTCTTAGATATACACCTTCAATAACCATGTTAAAATTTGTGTGACGGTATA
TAAAAGGTATTTTACAATAGAAGATGCTTTTAATAATCCTAAAATTTTTAGTGAAAAAATTTTGA
AGGCGTCTGTTATTAACAAACGCCTTCAGTAATGGATTACTAAGTTTAAAGGTATATTGAAGGAC
TTTTTTGAATAAATGCCTTCCATAACCATCATGGTATATTCAAGGCGTTTCATAATAAAAGACGC
CTTTAATAATCCAAAAATTTTTTAAAAA
Found at i:21331540 original size:134 final size:133
Alignment explanation
Indices: 21331282--21331530 Score: 372
Period size: 134 Copynumber: 1.9 Consensus size: 133
21331272 GTTAGGTGGC
* * * *
21331282 ATTTTTTATAGAAATGCCACTAAAGCAACGACATTTTTCTCATAAACATACCATTGAATTAGCGA
1 ATTTTTTATACAAATGCCACTAAAGCAACGACATTTTTATCATAAAAATACCACTGAATTAGCGA
** * *
21331347 AGACTAAAAGATACAAACGTCGTTAATATTGAGGTATTTTTATATTCAAACACCTCTAAAATAAC
66 AGACTAAAAGATACAAACACCGCTAATATTAAGGTATTTTTATATTCAAACACCTCTAAAATAAC
21331412 GGT
131 GGT
* * * *
21331415 ATTTTTTATTACAAATGCCCCTAAAGCAACGGCGTTTTTATCTTAAAAATACCACTGAATTAGCG
1 ATTTTTTA-TACAAATGCCACTAAAGCAACGACATTTTTATCATAAAAATACCACTGAATTAGCG
*
21331480 ATGACTAAAAGATACAAACACCGCTAATATTAAGGTATTTTTATATTCAAA
65 AAGACTAAAAGATACAAACACCGCTAATATTAAGGTATTTTTATATTCAAA
21331531 TGTCTCTAAA
Statistics
Matches: 102, Mismatches: 13, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
133 8 0.08
134 94 0.92
ACGTcount: A:0.39, C:0.17, G:0.12, T:0.32
Consensus pattern (133 bp):
ATTTTTTATACAAATGCCACTAAAGCAACGACATTTTTATCATAAAAATACCACTGAATTAGCGA
AGACTAAAAGATACAAACACCGCTAATATTAAGGTATTTTTATATTCAAACACCTCTAAAATAAC
GGT
Found at i:21331560 original size:134 final size:133
Alignment explanation
Indices: 21331280--21331577 Score: 343
Period size: 134 Copynumber: 2.2 Consensus size: 133
21331270 TAGTTAGGTG
* * * * * *
21331280 GCATTTTTTA-TAGAAATGCCACTAAAGCAACGACATTTTTCTCATAAACATACCATTGAATTAG
1 GCATTTTTAATTACAAATGCCCCTAAAGCAACGACATTTTTATCATAAAAATACCACTGAATTAG
** * *
21331344 CGAAGACTAAAAGATACAAACGTCGTTAATATTGAGGTATTTTTATATTCAAACACCTCTAAAAT
66 CGAAGACTAAAAGATACAAACACCGCTAATATTAAGGTATTTTTATATTCAAACACCTCTAAAAT
21331409 AAC
131 AAC
* * * * *
21331412 GGTATTTTTTATTACAAATGCCCCTAAAGCAACGGCGTTTTTATCTTAAAAATACCACTGAATTA
1 -GCATTTTTAATTACAAATGCCCCTAAAGCAACGACATTTTTATCATAAAAATACCACTGAATTA
* ***
21331477 GCGATGACTAAAAGATACAAACACCGCTAATATTAAGGTATTTTTATATTCAAATGTCTCTAAAG
65 GCGAAGACTAAAAGATACAAACACCGCTAATATTAAGGTATTTTTATATTCAAACACCTCTAAA-
21331542 TAGTAAC
129 -A-TAAC
*
21331549 -CA-TTTTAATTACAAACGCCACC-AAAGCAA
1 GCATTTTTAATTACAAATGCC-CCTAAAGCAA
21331578 GGTATTTTTT
Statistics
Matches: 140, Mismatches: 20, Indels: 9
0.83 0.12 0.05
Matches are distributed among these distances:
133 9 0.06
134 123 0.88
135 3 0.02
136 1 0.01
137 4 0.03
ACGTcount: A:0.39, C:0.18, G:0.12, T:0.31
Consensus pattern (133 bp):
GCATTTTTAATTACAAATGCCCCTAAAGCAACGACATTTTTATCATAAAAATACCACTGAATTAG
CGAAGACTAAAAGATACAAACACCGCTAATATTAAGGTATTTTTATATTCAAACACCTCTAAAAT
AAC
Found at i:21331823 original size:22 final size:22
Alignment explanation
Indices: 21331781--21331823 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
21331771 TGACGGTAAT
* *
21331781 AAACGTCGCTAAACGATAAAAA
1 AAACGTCACTAAACAATAAAAA
*
21331803 AAACGTCACTAAA-AATCAAAA
1 AAACGTCACTAAACAATAAAAA
21331824 CCCCTATAGT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.58, C:0.19, G:0.09, T:0.14
Consensus pattern (22 bp):
AAACGTCACTAAACAATAAAAA
Found at i:21333098 original size:12 final size:11
Alignment explanation
Indices: 21333080--21333129 Score: 52
Period size: 12 Copynumber: 4.6 Consensus size: 11
21333070 GGCAAATTTA
21333080 TTTATATATAT
1 TTTATATATAT
21333091 TGTTATATA-A-
1 T-TTATATATAT
*
21333101 TATATATATA-
1 TTTATATATAT
21333111 TTTATATATAT
1 TTTATATATAT
21333122 ATTTATAT
1 -TTTATAT
21333130 TAGATGAGGG
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
9 6 0.18
10 11 0.33
11 2 0.06
12 14 0.42
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (11 bp):
TTTATATATAT
Found at i:21334821 original size:2 final size:2
Alignment explanation
Indices: 21334814--21334839 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
21334804 CTGTCCTATT
21334814 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
21334840 AATAAAAGAC
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:21336056 original size:14 final size:14
Alignment explanation
Indices: 21336019--21336050 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
21336009 ATTTTTTTCT
*
21336019 TTTTTCTTTTGGTA
1 TTTTTATTTTGGTA
21336033 TTTTTATTTTGGTA
1 TTTTTATTTTGGTA
21336047 TTTT
1 TTTT
21336051 GTTTTTCTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.09, C:0.03, G:0.12, T:0.75
Consensus pattern (14 bp):
TTTTTATTTTGGTA
Found at i:21336086 original size:15 final size:16
Alignment explanation
Indices: 21336066--21336098 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
21336056 TCTTTCTTGT
*
21336066 TTTATTTATTTG-TTA
1 TTTATTGATTTGCTTA
21336081 TTTATTGATTTGCTTA
1 TTTATTGATTTGCTTA
21336097 TT
1 TT
21336099 GACTTGTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 11 0.69
16 5 0.31
ACGTcount: A:0.18, C:0.03, G:0.09, T:0.70
Consensus pattern (16 bp):
TTTATTGATTTGCTTA
Found at i:21337761 original size:35 final size:33
Alignment explanation
Indices: 21337712--21337795 Score: 136
Period size: 35 Copynumber: 2.5 Consensus size: 33
21337702 TATATTTTAA
21337712 TTTTTAA-TATTTTTATAATATTTTGTTTGCCTTT
1 TTTTTAATTATTTTTATAATATTTTGTTTGCC--T
21337746 TTTTTAATTATTTTTATAATATTTTGTTTGCCT
1 TTTTTAATTATTTTTATAATATTTTGTTTGCCT
21337779 TTTTT-ATTATTTTTATA
1 TTTTTAATTATTTTTATA
21337796 TTAAAATAAT
Statistics
Matches: 49, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
32 12 0.24
33 6 0.12
34 7 0.14
35 24 0.49
ACGTcount: A:0.21, C:0.05, G:0.05, T:0.69
Consensus pattern (33 bp):
TTTTTAATTATTTTTATAATATTTTGTTTGCCT
Found at i:21337814 original size:15 final size:15
Alignment explanation
Indices: 21337794--21337822 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
21337784 ATTATTTTTA
21337794 TATTAAAATAATTAG
1 TATTAAAATAATTAG
21337809 TATTAAAATAATTA
1 TATTAAAATAATTA
21337823 ATCTACCCTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.41
Consensus pattern (15 bp):
TATTAAAATAATTAG
Found at i:21338430 original size:21 final size:19
Alignment explanation
Indices: 21338382--21338432 Score: 57
Period size: 21 Copynumber: 2.5 Consensus size: 19
21338372 ATAATAATGA
*
21338382 AATAAAATAACAAACGAAT
1 AATAAAACAACAAACGAAT
*
21338401 AATAAAAACAATAAACAGAAT
1 AAT-AAAACAACAAAC-GAAT
21338422 AAGTAAAACAA
1 AA-TAAAACAA
21338433 GAAAAAGAGA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
19 3 0.11
20 10 0.37
21 13 0.48
22 1 0.04
ACGTcount: A:0.71, C:0.10, G:0.06, T:0.14
Consensus pattern (19 bp):
AATAAAACAACAAACGAAT
Found at i:21340536 original size:21 final size:22
Alignment explanation
Indices: 21340498--21340538 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
21340488 ATCCTTTTTA
*
21340498 GTTTAAGCTCTTTATATCAAAT
1 GTTTAAGCTCTCTATATCAAAT
21340520 GTTTAAGCTC-CTATATCAA
1 GTTTAAGCTCTCTATATCAA
21340539 TTGACATAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.32, C:0.17, G:0.10, T:0.41
Consensus pattern (22 bp):
GTTTAAGCTCTCTATATCAAAT
Found at i:21347530 original size:16 final size:16
Alignment explanation
Indices: 21347511--21347544 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
21347501 ATTTTTTTGT
21347511 ATAAA-AAATATAAAAA
1 ATAAATAAA-ATAAAAA
21347527 ATAAATAAAATAAAAA
1 ATAAATAAAATAAAAA
21347543 AT
1 AT
21347545 GTCTATAGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 14 0.82
17 3 0.18
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (16 bp):
ATAAATAAAATAAAAA
Found at i:21359003 original size:2 final size:2
Alignment explanation
Indices: 21358996--21359023 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
21358986 TGCTTTTGGA
21358996 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
21359024 GATTGCATGG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:21362288 original size:14 final size:14
Alignment explanation
Indices: 21362239--21362288 Score: 52
Period size: 13 Copynumber: 3.7 Consensus size: 14
21362229 AGGATTTGAA
*
21362239 TTTAGGGTTTCA-T
1 TTTAGGGTTTTATT
*
21362252 TTTAAGGTTTTATT
1 TTTAGGGTTTTATT
21362266 TTGTA--GTTTTATT
1 TT-TAGGGTTTTATT
21362279 TTTAGGGTTT
1 TTTAGGGTTT
21362289 CAAGTTTCAC
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
12 2 0.06
13 20 0.65
14 7 0.23
15 2 0.06
ACGTcount: A:0.16, C:0.02, G:0.20, T:0.62
Consensus pattern (14 bp):
TTTAGGGTTTTATT
Done.