Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168048.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_3, 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: 33276047
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 139000 characters in sequence are not A, C, G, or T
File 33 of 190
Found at i:5775531 original size:23 final size:23
Alignment explanation
Indices: 5775497--5775543 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
5775487 ATTAGTTGAC
*
5775497 AATTTGAAATTTGAATTCCAAAA
1 AATTTGAAATTTGAATCCCAAAA
*
5775520 AATTTGAGATTTGAATCCCAAAA
1 AATTTGAAATTTGAATCCCAAAA
5775543 A
1 A
5775544 CTATAAATAG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.47, C:0.11, G:0.11, T:0.32
Consensus pattern (23 bp):
AATTTGAAATTTGAATCCCAAAA
Found at i:5776922 original size:44 final size:45
Alignment explanation
Indices: 5776802--5776938 Score: 222
Period size: 45 Copynumber: 3.1 Consensus size: 45
5776792 GTATTCCGAG
* * *
5776802 TATAAATGCTTTAAGAAATCCTTAGATGATAAGATTTTTTATAAA
1 TATAGATGCTTTAAGAAATCCTTAGGTGAAAAGATTTTTTATAAA
*
5776847 TATAGATGCTTTAAGAAATCCTTAAGTGAAAAGATTTTTTATAAA
1 TATAGATGCTTTAAGAAATCCTTAGGTGAAAAGATTTTTTATAAA
*
5776892 TATAGATGATTTAAGAAAT-CTTAGGTGAAAAGATTTTTTATAAA
1 TATAGATGCTTTAAGAAATCCTTAGGTGAAAAGATTTTTTATAAA
5776936 TAT
1 TAT
5776939 TACCAGTGTA
Statistics
Matches: 86, Mismatches: 6, Indels: 1
0.92 0.06 0.01
Matches are distributed among these distances:
44 27 0.31
45 59 0.69
ACGTcount: A:0.42, C:0.05, G:0.13, T:0.39
Consensus pattern (45 bp):
TATAGATGCTTTAAGAAATCCTTAGGTGAAAAGATTTTTTATAAA
Found at i:5777007 original size:3 final size:3
Alignment explanation
Indices: 5776999--5777029 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
5776989 CTCTTTTCTT
5776999 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
5777030 TCAATAAATC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:5778113 original size:17 final size:17
Alignment explanation
Indices: 5778076--5778123 Score: 53
Period size: 17 Copynumber: 2.6 Consensus size: 17
5778066 ATAAAATATT
5778076 AAAATACTAAAATTAAAATC
1 AAAATA-TAAAA-T-AAATC
5778096 AATAA-ATAAAATAAATC
1 AA-AATATAAAATAAATC
5778113 AAAATATAAAA
1 AAAATATAAAA
5778124 AATAAAAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
16 2 0.08
17 13 0.50
18 1 0.04
19 5 0.19
20 3 0.12
21 2 0.08
ACGTcount: A:0.71, C:0.06, G:0.00, T:0.23
Consensus pattern (17 bp):
AAAATATAAAATAAATC
Found at i:5778715 original size:3 final size:3
Alignment explanation
Indices: 5778707--5778731 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
5778697 TAGTTTAAAA
5778707 TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT T
5778732 GTTGTTGTTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:5778736 original size:3 final size:3
Alignment explanation
Indices: 5778730--5778761 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
5778720 ATTATTATTA
*
5778730 TTG TTG TTG TTG TTG TTA TTG TTG TTG TTG TT
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
5778762 ATTTACTGTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.03, C:0.00, G:0.28, T:0.69
Consensus pattern (3 bp):
TTG
Found at i:5778753 original size:15 final size:15
Alignment explanation
Indices: 5778733--5778764 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
5778723 ATTATTATTG
5778733 TTGTTGTTGTTGTTA
1 TTGTTGTTGTTGTTA
5778748 TTGTTGTTGTTGTTA
1 TTGTTGTTGTTGTTA
5778763 TT
1 TT
5778765 TACTGTTATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.06, C:0.00, G:0.25, T:0.69
Consensus pattern (15 bp):
TTGTTGTTGTTGTTA
Found at i:5784679 original size:1 final size:1
Alignment explanation
Indices: 5784673--5784698 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
5784663 CTTACATACC
5784673 AAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAA
5784699 CTACTCACTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:5786308 original size:30 final size:29
Alignment explanation
Indices: 5786274--5786377 Score: 120
Period size: 30 Copynumber: 3.5 Consensus size: 29
5786264 TCTTACACTA
5786274 AAATAAACTCTTAATTTATAATTTGTAT-T
1 AAATAAACTCTTAATTT-TAATTTGTATCT
*
5786303 CAAATAAACTCTTAAAATTTAATTTGTATCT
1 -AAATAAACTCTT-AATTTTAATTTGTATCT
* * *
5786334 TAATAAACCCTTAATTTTTAATTTATATCT
1 AAATAAACTCTTAA-TTTTAATTTGTATCT
*
5786364 AAATAAATTCTTAA
1 AAATAAACTCTTAA
5786378 CATAAATTAA
Statistics
Matches: 63, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
29 2 0.03
30 56 0.89
31 5 0.08
ACGTcount: A:0.42, C:0.11, G:0.02, T:0.45
Consensus pattern (29 bp):
AAATAAACTCTTAATTTTAATTTGTATCT
Found at i:5786473 original size:28 final size:28
Alignment explanation
Indices: 5786415--5786473 Score: 66
Period size: 28 Copynumber: 2.1 Consensus size: 28
5786405 TAATTTATTT
* *
5786415 TAATATAAATAAAAAAAATATTTGAATA
1 TAATAAAAATAAAAAAAATATTTGAACA
**
5786443 TAATAAAAATATAAAAACTTATTT-AACA
1 TAATAAAAATA-AAAAAAATATTTGAACA
5786471 TAA
1 TAA
5786474 ATAGAATAGT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
28 16 0.62
29 10 0.38
ACGTcount: A:0.63, C:0.03, G:0.02, T:0.32
Consensus pattern (28 bp):
TAATAAAAATAAAAAAAATATTTGAACA
Found at i:5787284 original size:29 final size:29
Alignment explanation
Indices: 5787252--5787310 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
5787242 AGTTAACATA
* *
5787252 TTTATAATTCATATATCATATTAAAAATT
1 TTTAAAATTCAAATATCATATTAAAAATT
* * *
5787281 TTTAAAATTTAAATATTATATTAAACATT
1 TTTAAAATTCAAATATCATATTAAAAATT
5787310 T
1 T
5787311 CACTATAGTT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.46, C:0.05, G:0.00, T:0.49
Consensus pattern (29 bp):
TTTAAAATTCAAATATCATATTAAAAATT
Found at i:5787682 original size:20 final size:20
Alignment explanation
Indices: 5787637--5787676 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
5787627 TAAAAAATTT
*
5787637 AAAATAGATTTTTTGGATAA
1 AAAATAGATTTTTTGAATAA
5787657 AAAATAGA-TTTTTGAATAA
1 AAAATAGATTTTTTGAATAA
5787676 A
1 A
5787677 TTAATAAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 11 0.58
20 8 0.42
ACGTcount: A:0.50, C:0.00, G:0.12, T:0.38
Consensus pattern (20 bp):
AAAATAGATTTTTTGAATAA
Found at i:5787722 original size:32 final size:31
Alignment explanation
Indices: 5787685--5787801 Score: 121
Period size: 32 Copynumber: 3.7 Consensus size: 31
5787675 AATTAATAAA
*
5787685 TAAAATGATATA-AATTTTTTTACTTAATATTT
1 TAAAATGATATAGAA-TTTTTTATTTAAT-TTT
* *
5787717 TAAAATGATATTGAATTGTTTATTTAATTTT
1 TAAAATGATATAGAATTTTTTATTTAATTTT
* * *
5787748 T-AAGTAGAAATAGAAATTTTTATTTAATTTTT
1 TAAAAT-GATATAGAATTTTTTATTTAA-TTTT
*
5787780 TATAATGATATAGAATTTTTTA
1 TAAAATGATATAGAATTTTTTA
5787802 AAAAGGATTT
Statistics
Matches: 69, Mismatches: 12, Indels: 8
0.78 0.13 0.09
Matches are distributed among these distances:
30 3 0.04
31 21 0.30
32 41 0.59
33 4 0.06
ACGTcount: A:0.39, C:0.01, G:0.08, T:0.52
Consensus pattern (31 bp):
TAAAATGATATAGAATTTTTTATTTAATTTT
Found at i:5787924 original size:29 final size:30
Alignment explanation
Indices: 5787880--5787942 Score: 78
Period size: 29 Copynumber: 2.1 Consensus size: 30
5787870 TTACTAATAA
*
5787880 ATAATGTTATGATAAAAAATATTT-T-AAATT
1 ATAATATTATGAT--AAAATATTTATGAAATT
5787910 ATAATATTAT-ATAAAATATTTATGAAATT
1 ATAATATTATGATAAAATATTTATGAAATT
5787939 ATAA
1 ATAA
5787943 AATCAATTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
27 9 0.30
28 1 0.03
29 11 0.37
30 9 0.30
ACGTcount: A:0.52, C:0.00, G:0.05, T:0.43
Consensus pattern (30 bp):
ATAATATTATGATAAAATATTTATGAAATT
Found at i:5787980 original size:21 final size:22
Alignment explanation
Indices: 5787948--5787998 Score: 52
Period size: 21 Copynumber: 2.4 Consensus size: 22
5787938 TATAAAATCA
5787948 ATTTTT-TCTTTAATTATTTTT
1 ATTTTTATCTTTAATTATTTTT
* *
5787969 ATTTTTAT-TTTACTTTTTTTT
1 ATTTTTATCTTTAATTATTTTT
*
5787990 CTTCTTTAT
1 ATT-TTTAT
5787999 AAAATATATT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
21 19 0.76
22 6 0.24
ACGTcount: A:0.16, C:0.08, G:0.00, T:0.76
Consensus pattern (22 bp):
ATTTTTATCTTTAATTATTTTT
Found at i:5788094 original size:19 final size:19
Alignment explanation
Indices: 5788047--5788094 Score: 51
Period size: 20 Copynumber: 2.5 Consensus size: 19
5788037 AAAAGATATT
*
5788047 TAATATTTTTAATAGAAAA
1 TAATATTTTGAATAGAAAA
* * *
5788066 TAAATTTTTTGGATAGAAGA
1 T-AATATTTTGAATAGAAAA
5788086 TAATATTTT
1 TAATATTTT
5788095 CTATTATAAT
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
19 8 0.35
20 15 0.65
ACGTcount: A:0.44, C:0.00, G:0.10, T:0.46
Consensus pattern (19 bp):
TAATATTTTGAATAGAAAA
Found at i:5789836 original size:12 final size:13
Alignment explanation
Indices: 5789817--5789850 Score: 54
Period size: 12 Copynumber: 2.8 Consensus size: 13
5789807 TTAAAGAGAA
5789817 GAAAAATTTTTTT
1 GAAAAATTTTTTT
5789830 G-AAAA-TTTTTT
1 GAAAAATTTTTTT
5789841 GAAAAATTTT
1 GAAAAATTTT
5789851 CAGATTCTGG
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
11 7 0.37
12 8 0.42
13 4 0.21
ACGTcount: A:0.41, C:0.00, G:0.09, T:0.50
Consensus pattern (13 bp):
GAAAAATTTTTTT
Found at i:5790483 original size:58 final size:58
Alignment explanation
Indices: 5790418--5790533 Score: 196
Period size: 58 Copynumber: 2.0 Consensus size: 58
5790408 AAAAAAATAT
* *
5790418 AAAATAAAATTTTTAAAAAGCATTTTTGAGGAAAAGTTGAAAGTATCAATATTTCTTG
1 AAAATAAAATTTTTAAAAAACATTTTTGAGAAAAAGTTGAAAGTATCAATATTTCTTG
* *
5790476 AAAATAAAATTTTTAAAAAATATTTTTGAGAAAAAGTTGAAAGTATCAATTTTTCTTG
1 AAAATAAAATTTTTAAAAAACATTTTTGAGAAAAAGTTGAAAGTATCAATATTTCTTG
5790534 TATAAAAGCA
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
58 54 1.00
ACGTcount: A:0.46, C:0.04, G:0.12, T:0.38
Consensus pattern (58 bp):
AAAATAAAATTTTTAAAAAACATTTTTGAGAAAAAGTTGAAAGTATCAATATTTCTTG
Found at i:5794538 original size:23 final size:24
Alignment explanation
Indices: 5794511--5794603 Score: 66
Period size: 23 Copynumber: 3.8 Consensus size: 24
5794501 AAAATAAAAA
* *
5794511 AAAAGAGAAAAA-AAAGAAAGAGA
1 AAAAGAGAAAAAGAAAAAAAAAGA
*
5794534 GAAAGA-AAAAAGAAAAAAAAAGA
1 AAAAGAGAAAAAGAAAAAAAAAGA
* *
5794557 AAAAGATGAAAGAATGGAAAAAAGATGAA
1 AAAAGA-GAAA-AA--GAAAAAAAAAG-A
5794586 AAGAAGAGAAAAA-AAAAA
1 AA-AAGAGAAAAAGAAAAA
5794604 GAAATACTCA
Statistics
Matches: 56, Mismatches: 6, Indels: 14
0.74 0.08 0.18
Matches are distributed among these distances:
22 5 0.09
23 19 0.34
25 8 0.14
26 2 0.04
28 11 0.20
29 7 0.12
30 4 0.07
ACGTcount: A:0.76, C:0.00, G:0.20, T:0.03
Consensus pattern (24 bp):
AAAAGAGAAAAAGAAAAAAAAAGA
Found at i:5794550 original size:38 final size:36
Alignment explanation
Indices: 5794488--5794601 Score: 108
Period size: 38 Copynumber: 3.1 Consensus size: 36
5794478 AGAAAAAATT
5794488 AAAA-AAA-AAGAAAAAAATAA-AAAAAAAGAGAAAA
1 AAAAGAAAGAAGAAAAAAA-AAGAAAAAAAGAGAAAA
*
5794522 AAAAGAAAGAGAGAAAGAAAAAAGAAAAAAAAAGAAAA
1 AAAAGAAAGA-AGAAA-AAAAAAGAAAAAAAGAGAAAA
* * * * *
5794560 AGATGAAAGAATGGAAAAAAGATGAAAAGAAGAGAAAA
1 AAAAGAAAGAA--GAAAAAAAAAGAAAAAAAGAGAAAA
5794598 AAAA
1 AAAA
5794602 AAGAAATACT
Statistics
Matches: 64, Mismatches: 9, Indels: 10
0.77 0.11 0.12
Matches are distributed among these distances:
34 4 0.06
35 3 0.05
36 1 0.02
37 8 0.12
38 44 0.69
39 4 0.06
ACGTcount: A:0.79, C:0.00, G:0.18, T:0.04
Consensus pattern (36 bp):
AAAAGAAAGAAGAAAAAAAAAGAAAAAAAGAGAAAA
Found at i:5794567 original size:19 final size:18
Alignment explanation
Indices: 5794477--5794567 Score: 85
Period size: 19 Copynumber: 4.8 Consensus size: 18
5794467 AGAAAAGATG
*
5794477 AAGAAAAAATTAAAAAAA
1 AAGAAAAAATGAAAAAAA
*
5794495 AAGAAAAAAATAAAAAAAA
1 AAG-AAAAAATGAAAAAAA
* *
5794514 AGAGAAAAAAAAGAAAGAGAGA
1 A-AG-AAAAAATGAAA-A-AAA
5794536 AAGAAAAAA-GAAAAAAA
1 AAGAAAAAATGAAAAAAA
5794553 AAGAAAAAGATGAAA
1 AAGAAAAA-ATGAAA
5794568 GAATGGAAAA
Statistics
Matches: 62, Mismatches: 5, Indels: 11
0.79 0.06 0.14
Matches are distributed among these distances:
17 10 0.16
18 5 0.08
19 23 0.37
20 18 0.29
21 3 0.05
22 3 0.05
ACGTcount: A:0.81, C:0.00, G:0.14, T:0.04
Consensus pattern (18 bp):
AAGAAAAAATGAAAAAAA
Found at i:5794568 original size:30 final size:30
Alignment explanation
Indices: 5794469--5794570 Score: 131
Period size: 29 Copynumber: 3.5 Consensus size: 30
5794459 ACTGGATGAG
*
5794469 AAAAGATG-AAGAAAAAATTAAAAAAAAAGA
1 AAAAGATGAAAGAAAAAA-GAAAAAAAAAGA
*
5794499 AAAAAAT-AAA-AAAAAAGAGAAAAAAAAGA
1 AAAAGATGAAAGAAAAAAGA-AAAAAAAAGA
*
5794528 AAGAGA-GAAAGAAAAAAGAAAAAAAAAGA
1 AAAAGATGAAAGAAAAAAGAAAAAAAAAGA
5794557 AAAAGATGAAAGAA
1 AAAAGATGAAAGAA
5794571 TGGAAAAAAG
Statistics
Matches: 62, Mismatches: 5, Indels: 10
0.81 0.06 0.13
Matches are distributed among these distances:
28 1 0.02
29 38 0.61
30 23 0.37
ACGTcount: A:0.79, C:0.00, G:0.16, T:0.05
Consensus pattern (30 bp):
AAAAGATGAAAGAAAAAAGAAAAAAAAAGA
Found at i:5794578 original size:19 final size:20
Alignment explanation
Indices: 5794508--5794599 Score: 72
Period size: 20 Copynumber: 4.8 Consensus size: 20
5794498 AAAAAAATAA
* *
5794508 AAAAAAAGAGAAAAAA-AAG
1 AAAAGAAGAGAAAAAAGATG
*
5794527 AAAGAGAGAAAGAAAAAAGA--
1 AAA-AGA-AGAGAAAAAAGATG
*
5794547 AAAA-AAAAG-AAAAAGATG
1 AAAAGAAGAGAAAAAAGATG
5794565 -AAAGAATG-GAAAAAAGATG
1 AAAAGAA-GAGAAAAAAGATG
5794584 AAAAGAAGAGAAAAAA
1 AAAAGAAGAGAAAAAA
5794600 AAAAGAAATA
Statistics
Matches: 60, Mismatches: 3, Indels: 19
0.73 0.04 0.23
Matches are distributed among these distances:
16 7 0.12
17 7 0.12
18 4 0.07
19 14 0.23
20 18 0.30
21 9 0.15
22 1 0.02
ACGTcount: A:0.76, C:0.00, G:0.21, T:0.03
Consensus pattern (20 bp):
AAAAGAAGAGAAAAAAGATG
Found at i:5795725 original size:46 final size:46
Alignment explanation
Indices: 5795650--5796159 Score: 582
Period size: 46 Copynumber: 11.0 Consensus size: 46
5795640 GTTTTGATTT
* *
5795650 TTAAATGAGAATTCTTTAAGATGTTTTCAAATAAGAATCTTTGAGTC
1 TTAAATGAGAA-TCTTTAAGACGTTTTCAAATGAGAATCTTTGAGTC
5795697 TTAAATGAGAATCTTTAAGACGTTTTCAAATGAGAATCTTTGAGTC
1 TTAAATGAGAATCTTTAAGACGTTTTCAAATGAGAATCTTTGAGTC
* * * * *
5795743 TTAAATGAGAATCTTTAAGACATTTTCAAATAAAAATCTTTAAGTT
1 TTAAATGAGAATCTTTAAGACGTTTTCAAATGAGAATCTTTGAGTC
*
5795789 TTCAATGAGAATCTTTAAGACG-TTTCAAAATGAGAATCTTTGAGTC
1 TTAAATGAGAATCTTTAAGACGTTTTC-AAATGAGAATCTTTGAGTC
* *
5795835 TTAAATGAAAATCTTTAAGACATTTTCAAATGAGAATCTTTGAGTC
1 TTAAATGAGAATCTTTAAGACGTTTTCAAATGAGAATCTTTGAGTC
* * * * *
5795881 TTAAATGAGAATTTTTAAGACGTTTTCAAATGAAAATTTTTAAGATATT
1 TTAAATGAGAATCTTTAAGACGTTTTCAAATGAGAATCTTT--GA-GTC
* *
5795930 TTCAAATGAGAATCTTT--GA-GTCTT-AAATGAGAATCTTTAAGACGTT
1 TT-AAATGAGAATCTTTAAGACGTTTTCAAATGAGAATCTTT--GA-GTC
* *
5795976 TTCAAATGAGAATATTTAAGATGTTTTCAAATGAGAATCTTTGAGTC
1 TT-AAATGAGAATCTTTAAGACGTTTTCAAATGAGAATCTTTGAGTC
* * * *
5796023 TCAAATGAGAATCTTTAAGACATTTTTAAATTACGAATCTTTGAGT-
1 TTAAATGAGAATCTTTAAGACGTTTTCAAATGA-GAATCTTTGAGTC
* * * *
5796069 TTCAAATAAGAATCTTTAAGATGTTTTCAAATGAGTAGCTTTGAGTC
1 TT-AAATGAGAATCTTTAAGACGTTTTCAAATGAGAATCTTTGAGTC
* * ** *
5796116 TTAAGTGAGAACCTTTAAGATATTTTCAAATGAGAATATTTGAG
1 TTAAATGAGAATCTTTAAGACGTTTTCAAATGAGAATCTTTGAG
5796160 ATATAAAACC
Statistics
Matches: 397, Mismatches: 53, Indels: 27
0.83 0.11 0.06
Matches are distributed among these distances:
45 4 0.01
46 289 0.73
47 62 0.16
48 8 0.02
49 7 0.02
50 27 0.07
ACGTcount: A:0.37, C:0.09, G:0.15, T:0.38
Consensus pattern (46 bp):
TTAAATGAGAATCTTTAAGACGTTTTCAAATGAGAATCTTTGAGTC
Found at i:5795781 original size:71 final size:70
Alignment explanation
Indices: 5795699--5796085 Score: 463
Period size: 71 Copynumber: 5.5 Consensus size: 70
5795689 TTTGAGTCTT
*
5795699 AAATGAGAATCTTTAAGACGTTTTCAAATGAGAATCTTTGAGTCTTAAATGAGAATCTTTAAGAC
1 AAATGAAAATCTTTAAGA-GTTTTCAAATGAGAATCTTTGAGTCTTAAATGAGAATCTTTAAGAC
*
5795764 ATTTTC
65 GTTTTC
*
5795770 AAATAAAAATCTTT-A-AGTTTTC-AATGAGAATCTTTAAGACGT-TTCAAAATGAGAATCTTT-
1 AAATGAAAATCTTTAAGAGTTTTCAAATGAGAATCTTT--GA-GTCTT--AAATGAGAATCTTTA
*
5795830 -GA-GTCTT-
61 AGACGTTTTC
* *
5795837 AAATGAAAATCTTTAAGACATTTTCAAATGAGAATCTTTGAGTCTTAAATGAGAATTTTTAAGAC
1 AAATGAAAATCTTTAAGA-GTTTTCAAATGAGAATCTTTGAGTCTTAAATGAGAATCTTTAAGAC
5795902 GTTTTC
65 GTTTTC
* *
5795908 AAATGAAAATTTTTAAGATATTTTCAAATGAGAATCTTTGAGTCTTAAATGAGAATCTTTAAGAC
1 AAATGAAAATCTTTAAGA-GTTTTCAAATGAGAATCTTTGAGTCTTAAATGAGAATCTTTAAGAC
5795973 GTTTTC
65 GTTTTC
* * *
5795979 AAATGAGAATATTTAAGATGTTTTCAAATGAGAATCTTTGAGTCTCAAATGAGAATCTTTAAGAC
1 AAATGAAAATCTTTAAGA-GTTTTCAAATGAGAATCTTTGAGTCTTAAATGAGAATCTTTAAGAC
* *
5796044 ATTTTT
65 GTTTTC
* * *
5796050 AAATTACGAATCTTT--GAG-TTTCAAATAAGAATCTTT
1 AAATGA-AAATCTTTAAGAGTTTTCAAATGAGAATCTTT
5796086 AAGATGTTTT
Statistics
Matches: 281, Mismatches: 20, Indels: 33
0.84 0.06 0.10
Matches are distributed among these distances:
67 39 0.14
68 29 0.10
69 15 0.05
70 14 0.05
71 177 0.63
72 7 0.02
ACGTcount: A:0.38, C:0.10, G:0.14, T:0.38
Consensus pattern (70 bp):
AAATGAAAATCTTTAAGAGTTTTCAAATGAGAATCTTTGAGTCTTAAATGAGAATCTTTAAGACG
TTTTC
Found at i:5796152 original size:71 final size:69
Alignment explanation
Indices: 5795646--5796159 Score: 430
Period size: 71 Copynumber: 7.3 Consensus size: 69
5795636 TGAAGTTTTG
* * *
5795646 ATTTTTAAATGAGAATTCTTTAAGATGTTTTCAAATAAGAATCTTT-GAGTCTTAAATGAGAATC
1 ATTTTCAAATGAGAA-TCTTT--GA-GTTTTCAAATGAGAATCTTTAGAGTTTTAAATGAGAATC
*
5795710 TTTAAGAC
62 TTTAAGAT
* * * * *
5795718 GTTTTCAAATGAGAATCTTTGAGTCTT-AAATGAGAATCTTTAAGACATTTTCAAATAAAAATCT
1 ATTTTCAAATGAGAATCTTTGAGTTTTCAAATGAGAATCTTT-AGA-GTTTT-AAATGAGAATCT
5795782 TTAAG--
63 TTAAGAT
* *
5795787 -TTTTC-AATGAGAATCTTTAAGACG-TTTCAAAATGAGAATCTTT-GAGTCTTAAATGAAAATC
1 ATTTTCAAATGAGAATCTTT--GA-GTTTTC-AAATGAGAATCTTTAGAGTTTTAAATGAGAATC
*
5795848 TTTAAGAC
62 TTTAAGAT
* * * *
5795856 ATTTTCAAATGAGAATCTTTGAGTCTT-AAATGAGAATTTTTAAGACGTTTTCAAATGAAAATTT
1 ATTTTCAAATGAGAATCTTTGAGTTTTCAAATGAGAATCTTT-AGA-GTTTT-AAATGAGAATCT
5795920 TTAAGAT
63 TTAAGAT
* *
5795927 ATTTTCAAATGAGAATCTTTGAGTCTT-AAATGAGAATCTTTAAGACGTTTTCAAATGAGAATAT
1 ATTTTCAAATGAGAATCTTTGAGTTTTCAAATGAGAATCTTT-AGA-GTTTT-AAATGAGAATCT
5795991 TTAAGAT
63 TTAAGAT
* * * *
5795998 GTTTTCAAATGAGAATCTTTGAG-TCTCAAATGAGAATCTTTAAGACATTTTTAAATTACGAATC
1 ATTTTCAAATGAGAATCTTTGAGTTTTCAAATGAGAATCTTT-AG--AGTTTTAAATGA-GAATC
5796062 TTT--G--
62 TTTAAGAT
* * * * * * *
5796066 AGTTTCAAATAAGAATCTTTAAGATGTTTTCAAATGAGTAGCTTT-GAGTCTTAAGTGAGAACCT
1 ATTTTCAAATGAGAATCTTT--GA-GTTTTCAAATGAGAATCTTTAGAGTTTTAAATGAGAATCT
5796130 TTAAGAT
63 TTAAGAT
*
5796137 ATTTTCAAATGAGAATATTTGAG
1 ATTTTCAAATGAGAATCTTTGAG
5796160 ATATAAAACC
Statistics
Matches: 372, Mismatches: 40, Indels: 64
0.78 0.08 0.13
Matches are distributed among these distances:
67 62 0.17
68 39 0.10
69 19 0.05
70 18 0.05
71 194 0.52
72 39 0.10
73 1 0.00
ACGTcount: A:0.37, C:0.09, G:0.15, T:0.39
Consensus pattern (69 bp):
ATTTTCAAATGAGAATCTTTGAGTTTTCAAATGAGAATCTTTAGAGTTTTAAATGAGAATCTTTA
AGAT
Found at i:5796527 original size:41 final size:41
Alignment explanation
Indices: 5796470--5796619 Score: 158
Period size: 41 Copynumber: 3.6 Consensus size: 41
5796460 ATGATTGTCA
*
5796470 AGGAGCAATTTACTTTTCAAAGTTGTAGTACCCT-TGTTTAG
1 AGGAGCAATTTACTTTTCAAAGTTGTAGT-CCCTCTATTTAG
* * *
5796511 AGGAGTAATTTACTTTTCAAAGTTGTGGTGCCTCTATTTAG
1 AGGAGCAATTTACTTTTCAAAGTTGTAGTCCCTCTATTTAG
* * * * * *
5796552 AGGAGCAATTTACTTTTTAAAGTTATGGTTGCCTCTGTTTAA
1 AGGAGCAATTTACTTTTCAAAGTTGTAG-TCCCTCTATTTAG
* * *
5796594 AGGGGCATTTTATTTTTCAAAGTTGT
1 AGGAGCAATTTACTTTTCAAAGTTGT
5796620 GATTCTTTTA
Statistics
Matches: 93, Mismatches: 14, Indels: 3
0.85 0.13 0.03
Matches are distributed among these distances:
40 3 0.03
41 58 0.62
42 32 0.34
ACGTcount: A:0.25, C:0.12, G:0.21, T:0.42
Consensus pattern (41 bp):
AGGAGCAATTTACTTTTCAAAGTTGTAGTCCCTCTATTTAG
Found at i:5796632 original size:83 final size:82
Alignment explanation
Indices: 5796470--5796646 Score: 201
Period size: 83 Copynumber: 2.1 Consensus size: 82
5796460 ATGATTGTCA
* * *
5796470 AGGAGCAATTTACTTTTCAAAGTTGTAGTACCCTTGTTTAGAGGAGTAATTTACTTTTCAAAGTT
1 AGGAGCAATTTACTTTTCAAAGTTATAGTACCCTTGTTTAAAGGAGCAATTTACTTTTCAAAGTT
*
5796535 GTGGTGCCTCTATTTAG
66 GTGATGCCTCTATTTAG
* * ** * * *
5796552 AGGAGCAATTTACTTTTTAAAGTTATGGTTGCCTCTGTTTAAAGGGGCATTTTATTTTTCAAAGT
1 AGGAGCAATTTACTTTTCAAAGTTATAGTACCCT-TGTTTAAAGGAGCAATTTACTTTTCAAAGT
* * *
5796617 TGTGATTCTTTTATTTAG
65 TGTGATGCCTCTATTTAG
* *
5796635 AGAAGCATTTTA
1 AGGAGCAATTTA
5796647 TTAAAGTAGT
Statistics
Matches: 78, Mismatches: 16, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
82 29 0.37
83 49 0.63
ACGTcount: A:0.26, C:0.11, G:0.20, T:0.43
Consensus pattern (82 bp):
AGGAGCAATTTACTTTTCAAAGTTATAGTACCCTTGTTTAAAGGAGCAATTTACTTTTCAAAGTT
GTGATGCCTCTATTTAG
Found at i:5797952 original size:24 final size:24
Alignment explanation
Indices: 5797925--5797971 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
5797915 TTTTAAAAAA
5797925 TATATTTTGAGAAAAAGTTGAAAT
1 TATATTTTGAGAAAAAGTTGAAAT
*
5797949 TATATTTTGAGGAAAAGTTGAAA
1 TATATTTTGAGAAAAAGTTGAAA
5797972 GTATTAATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.45, C:0.00, G:0.19, T:0.36
Consensus pattern (24 bp):
TATATTTTGAGAAAAAGTTGAAAT
Found at i:5798039 original size:58 final size:58
Alignment explanation
Indices: 5797953--5798083 Score: 192
Period size: 58 Copynumber: 2.3 Consensus size: 58
5797943 TGAAATTATA
* * *
5797953 TTTTGAGGAAAAGTTGAAAGTATTAATTTTCCTTGAAAATAAAATTTCT-AAAAAATAT
1 TTTTGAGGAAAAGTTAAAAATATTAATTTTCCTCGAAAATAAAATTT-TAAAAAAATAT
* *
5798011 TTTTGAGAAAAAGTTAAAAATATTAATTTTTCTCGAAAATAAAATTTTAAAAAAATAT
1 TTTTGAGGAAAAGTTAAAAATATTAATTTTCCTCGAAAATAAAATTTTAAAAAAATAT
*
5798069 TTTTTAGGAAAAGTT
1 TTTTGAGGAAAAGTT
5798084 GAAGGAAAAG
Statistics
Matches: 65, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
57 1 0.02
58 64 0.98
ACGTcount: A:0.47, C:0.04, G:0.11, T:0.39
Consensus pattern (58 bp):
TTTTGAGGAAAAGTTAAAAATATTAATTTTCCTCGAAAATAAAATTTTAAAAAAATAT
Found at i:5798040 original size:84 final size:84
Alignment explanation
Indices: 5797869--5798033 Score: 271
Period size: 84 Copynumber: 2.0 Consensus size: 84
5797859 TAAAAAGCAT
* *
5797869 TTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTGAAAATAAAATTTTTTAAAAAATATATTTTG
1 TTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATAAAATTTTCTAAAAAATATATTTTG
* *
5797934 AGAAAAAGTTGAAATTATA
66 AGAAAAAGTTAAAAATATA
*
5797953 TTTTGAGGAAAAGTTGAAAGTATTAATTTTCCTTGAAAATAAAA-TTTCTAAAAAATAT-TTTTG
1 TTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATAAAATTTTCTAAAAAATATATTTTG
5798016 AGAAAAAGTTAAAAATAT
66 AGAAAAAGTTAAAAATAT
5798034 TAATTTTTCT
Statistics
Matches: 76, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
82 21 0.28
83 13 0.17
84 42 0.55
ACGTcount: A:0.46, C:0.03, G:0.13, T:0.38
Consensus pattern (84 bp):
TTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATAAAATTTTCTAAAAAATATATTTTG
AGAAAAAGTTAAAAATATA
Found at i:5798091 original size:12 final size:12
Alignment explanation
Indices: 5798074--5798098 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
5798064 AATATTTTTT
5798074 AGGAAAAGTTGA
1 AGGAAAAGTTGA
5798086 AGGAAAAGTTGA
1 AGGAAAAGTTGA
5798098 A
1 A
5798099 AGTATCAATT
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:0.52, C:0.00, G:0.32, T:0.16
Consensus pattern (12 bp):
AGGAAAAGTTGA
Found at i:5811304 original size:251 final size:255
Alignment explanation
Indices: 5810853--5811575 Score: 841
Period size: 251 Copynumber: 2.8 Consensus size: 255
5810843 AGTTTTTAGG
* * * * *
5810853 ATCAAGCGCTTACCACTGCACTAAAAGCTATAACTGATAGTGAAGGTGCAACTCTATTTCGTTAT
1 ATCAAGCACTTACCACTACACCAAAAGCTATAGCTGATAGTGAAGGTGCAACTCTATTTCCTTAT
* * *
5810918 TCTCTTTTGATAGCGTAGAGCCTGGTGCTAAGCGACAAGTGAACATAA-AGGGCTTCATAAAGCC
66 TCTCTTTTGATAGTGTAGAGCC-GGTGCTAAGCGACAAGTGAACATAAGA-GGCTTCGTAAAGAC
* * *
5810982 TTCATGAGATACCTCACTCAGATGAATTGACATACCGAGTCTCTAAAGGAGATCGTTGGACCCCA
129 TTCATGAGATACCTCACTCAGATGAATTGACATACCAAGTCCCTAAAGGAGACCGTTGGACCCCA
* * * *
5811047 TAATCCAATAATCTCTCCTCCAGTAGCACTTGGGGGACTCGAACCTGTAA-C-CTC-G-C-TC
194 TAATCCAACAATCTCCCCTCC-GTAGCACTTGAGGGACTCGAACCTGCAATCGCTCTGACTTC
* * * * *
5811105 -TGAGGCACTTACCACTACACCAAAAGCTATAGCTGATAATGAAAGTGCAACTCTATTTCCTTTT
1 ATCAAGCACTTACCACTACACCAAAAGCTATAGCTGATAGTGAAGGTGCAACTCTATTTCCTTAT
** * * *
5811169 TCTCTTTTGATAGTGTAGAGTCCGGTGCTAAATGACAAGTGGACATAAGAGGTTTCGTAAAGTCT
66 TCTCTTTTGATAGTGTAGAG-CCGGTGCTAAGCGACAAGTGAACATAAGAGGCTTCGTAAAGACT
* * **
5811234 TCATGAGATACCTCACTCAAATGAATTGATATACCAAGTCCCTAAAGGAGACCGTTGGAGTCCAT
130 TCATGAGATACCTCACTCAGATGAATTGACATACCAAGTCCCTAAAGGAGACCGTTGGACCCCAT
* *
5811299 AATCCAACAATCTCCCCTCCGTGGCACTTGAGGGACTCGAACCTGCAATTTCGTTCTGATATCAA
195 AATCCAACAATCTCCCCTCCGTAGCACTTGAGGGACTCGAACCTGCAA--TCGCTCTG--A-C--
5811364 TTTTC
253 --TTC
* *
5811369 AAGATCAAGCGCTTACCACTACACCAAAAGCTATAGCTGATAGTGAAGGTGTAACTCTATTTCCT
1 ---ATCAAGCACTTACCACTACACCAAAAGCTATAGCTGATAGTGAAGGTGCAACTCTATTTCCT
* * * *
5811434 TATTCTCTTTTGATAGTGTAGAGCCAGTGCTAAGCGACAAGTAAACATAAGGGGCTTCGCAAA-A
63 TATTCTCTTTTGATAGTGTAGAGCCGGTGCTAAGCGACAAGTGAACATAAGAGGCTTCGTAAAGA
* * * * * * *
5811498 CTTTTATGAGATACCTCACTCAGATGAATTGACATACCAAGTCCCTAAAAGAGATCGCTAGAACT
128 C-TTCATGAGATACCTCACTCAGATGAATTGACATACCAAGTCCCTAAAGGAGACCGTTGGACCC
5811563 CATAATCCAACAA
192 CATAATCCAACAA
5811576 GTGCCTTGTT
Statistics
Matches: 394, Mismatches: 56, Indels: 27
0.83 0.12 0.06
Matches are distributed among these distances:
250 25 0.06
251 183 0.46
252 3 0.01
253 1 0.00
254 2 0.01
255 1 0.00
259 1 0.00
264 2 0.01
266 1 0.00
267 98 0.25
268 77 0.20
ACGTcount: A:0.31, C:0.23, G:0.19, T:0.27
Consensus pattern (255 bp):
ATCAAGCACTTACCACTACACCAAAAGCTATAGCTGATAGTGAAGGTGCAACTCTATTTCCTTAT
TCTCTTTTGATAGTGTAGAGCCGGTGCTAAGCGACAAGTGAACATAAGAGGCTTCGTAAAGACTT
CATGAGATACCTCACTCAGATGAATTGACATACCAAGTCCCTAAAGGAGACCGTTGGACCCCATA
ATCCAACAATCTCCCCTCCGTAGCACTTGAGGGACTCGAACCTGCAATCGCTCTGACTTC
Found at i:5818520 original size:3 final size:3
Alignment explanation
Indices: 5818507--5818542 Score: 56
Period size: 3 Copynumber: 12.0 Consensus size: 3
5818497 ATAAAATTTT
5818507 TTA TT- TTA TTA TTA TTA TTA TTA TTA TTA TTTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA
5818543 ATGCCAAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
2 2 0.06
3 26 0.84
4 3 0.10
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:5820340 original size:39 final size:37
Alignment explanation
Indices: 5820261--5820341 Score: 90
Period size: 39 Copynumber: 2.1 Consensus size: 37
5820251 TGTGAAAACA
*
5820261 ATTTATTTTCAAAAATATCTTCCAATATATTAGTAAG
1 ATTTTTTTTCAAAAATATCTTCCAATATATTAGTAAG
* * * * *
5820298 ATTTTTTTATCAAAAATTATTTTTCAATATGTTGGTAGG
1 ATTTTTTT-TCAAAAA-TATCTTCCAATATATTAGTAAG
5820337 ATTTT
1 ATTTT
5820342 AATAATAATT
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
37 7 0.19
38 7 0.19
39 22 0.61
ACGTcount: A:0.35, C:0.07, G:0.09, T:0.49
Consensus pattern (37 bp):
ATTTTTTTTCAAAAATATCTTCCAATATATTAGTAAG
Found at i:5820570 original size:20 final size:22
Alignment explanation
Indices: 5820523--5820572 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 22
5820513 CAAATAATAC
5820523 CATGCAAAAATAATATAATATA
1 CATGCAAAAATAATATAATATA
5820545 CAATGCAAAAAT-AT-TAAT-TA
1 C-ATGCAAAAATAATATAATATA
5820565 TCATGCAA
1 -CATGCAA
5820573 TTAAATATAA
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
20 8 0.31
21 5 0.19
22 3 0.12
23 10 0.38
ACGTcount: A:0.54, C:0.12, G:0.06, T:0.28
Consensus pattern (22 bp):
CATGCAAAAATAATATAATATA
Found at i:5821553 original size:14 final size:15
Alignment explanation
Indices: 5821536--5821571 Score: 65
Period size: 14 Copynumber: 2.5 Consensus size: 15
5821526 CTTAATTTCA
5821536 TTGATTTTTGG-GAT
1 TTGATTTTTGGAGAT
5821550 TTGATTTTTGGAGAT
1 TTGATTTTTGGAGAT
5821565 TTGATTT
1 TTGATTT
5821572 CTTGTATCTT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 11 0.52
15 10 0.48
ACGTcount: A:0.17, C:0.00, G:0.25, T:0.58
Consensus pattern (15 bp):
TTGATTTTTGGAGAT
Found at i:5822572 original size:15 final size:14
Alignment explanation
Indices: 5822547--5822580 Score: 59
Period size: 15 Copynumber: 2.4 Consensus size: 14
5822537 TATCATTTTC
5822547 AAATTTGGCTTGTG
1 AAATTTGGCTTGTG
5822561 AAATTATGGCTTGTG
1 AAATT-TGGCTTGTG
5822576 AAATT
1 AAATT
5822581 GGTATATTGC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 5 0.26
15 14 0.74
ACGTcount: A:0.29, C:0.06, G:0.24, T:0.41
Consensus pattern (14 bp):
AAATTTGGCTTGTG
Found at i:5822760 original size:36 final size:36
Alignment explanation
Indices: 5822712--5822832 Score: 181
Period size: 36 Copynumber: 3.4 Consensus size: 36
5822702 GGAGAGATAA
5822712 TGGTATGAAAAATTTTTATTTGATTGATGATCTTGG
1 TGGTATGAAAAATTTTTATTTGATTGATGATCTTGG
* * *
5822748 TGGTATGCAAAATTTCTATTTGATTGATGATCTTAG
1 TGGTATGAAAAATTTTTATTTGATTGATGATCTTGG
* *
5822784 TGGTATGAAAAATTTTTCTTTGATTGATGA-CTTGA
1 TGGTATGAAAAATTTTTATTTGATTGATGATCTTGG
*
5822819 TGGTATGCAAAATT
1 TGGTATGAAAAATT
5822833 CCTACTTGAT
Statistics
Matches: 76, Mismatches: 9, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
35 16 0.21
36 60 0.79
ACGTcount: A:0.29, C:0.06, G:0.21, T:0.45
Consensus pattern (36 bp):
TGGTATGAAAAATTTTTATTTGATTGATGATCTTGG
Found at i:5825720 original size:60 final size:59
Alignment explanation
Indices: 5825592--5825937 Score: 412
Period size: 60 Copynumber: 5.7 Consensus size: 59
5825582 TGCTTTTGTA
* * *
5825592 CAAGAAAAATTGATACTTTCAACTTTTTCTAAAAAAAAAAACTCTTTTTTG--AAAACTTATTTT
1 CAAGAAAAATTGATACTTTCAAC-TTTTCT---CAAAAATA-T-TTTTTAGAAAAAACTTATTTT
* * *
5825655 TAAGAAAAATGGATACTTTCAACTTTTTCCCAAAAATATTTTTTAGAAAAAACTTATTTT
1 CAAGAAAAATTGATACTTTCAAC-TTTTCTCAAAAATATTTTTTAGAAAAAACTTATTTT
* * *
5825715 CAAGAAAAATTGATACTTTAAACTTTTCTTCAAAAATATTTTTCAAAAAAAACTTATTTT
1 CAAGAAAAATTGATACTTTCAACTTTTC-TCAAAAATATTTTTTAGAAAAAACTTATTTT
* * *
5825775 CAAGAAAAATTAATACTTTCAACTTTTTCTCAAAAATATTTTTTTA-AAAACATTTATTTT
1 CAAGAAAAATTGATACTTTCAAC-TTTTCTCAAAAATA-TTTTTTAGAAAAAACTTATTTT
* *
5825835 CAAGGAAAATTGATACTTTCAACTTTTCTTCAAAAAAATTTTTTAG-AAAAACTTATTTT
1 CAAGAAAAATTGATACTTTCAACTTTTC-TCAAAAATATTTTTTAGAAAAAACTTATTTT
* *
5825894 CAAGGAAAATTGATACTTTCAACTTTTCCTTAAAAATATTTTTT
1 CAAGAAAAATTGATACTTTCAACTTTT-CTCAAAAATATTTTTT
5825938 TTGAATTTTA
Statistics
Matches: 251, Mismatches: 24, Indels: 20
0.85 0.08 0.07
Matches are distributed among these distances:
58 6 0.02
59 69 0.27
60 138 0.55
61 11 0.04
63 27 0.11
ACGTcount: A:0.42, C:0.12, G:0.05, T:0.41
Consensus pattern (59 bp):
CAAGAAAAATTGATACTTTCAACTTTTCTCAAAAATATTTTTTAGAAAAAACTTATTTT
Found at i:5825974 original size:6 final size:5
Alignment explanation
Indices: 5825960--5826014 Score: 83
Period size: 5 Copynumber: 10.4 Consensus size: 5
5825950 TAAAGAAAAT
5825960 AATAA AATAAA AATAAA AATAAA AATAA AATAA AATAA AATAA AATAA
1 AATAA AAT-AA AAT-AA AAT-AA AATAA AATAA AATAA AATAA AATAA
5826008 AATAA AA
1 AATAA AA
5826015 AGTACTAAAC
Statistics
Matches: 49, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
5 32 0.65
6 17 0.35
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (5 bp):
AATAA
Found at i:5826074 original size:12 final size:10
Alignment explanation
Indices: 5825957--5826079 Score: 71
Period size: 10 Copynumber: 12.2 Consensus size: 10
5825947 ATTTAAAGAA
5825957 AATAATAAAAT
1 AATAAT-AAAT
*
5825968 AAAAATAAA-
1 AATAATAAAT
5825977 AATAA-AAAT
1 AATAATAAAT
5825986 AA-AATAAAAT
1 AATAAT-AAAT
5825996 AA-AATAAAAT
1 AATAAT-AAAT
5826006 AA-AATAAA-
1 AATAATAAAT
* *
5826014 AAGTACTAAAC
1 AA-TAATAAAT
** *
5826025 AATTCTAATGT
1 AATAATAA-AT
5826036 AATCAATAAAT
1 AAT-AATAAAT
5826047 AATAAT-AAT
1 AATAATAAAT
5826056 AATAATAAAT
1 AATAATAAAT
5826066 AAATAAATAAAT
1 -AAT-AATAAAT
5826078 AA
1 AA
5826080 CCTGGGAACG
Statistics
Matches: 92, Mismatches: 9, Indels: 22
0.75 0.07 0.18
Matches are distributed among these distances:
8 7 0.08
9 18 0.20
10 38 0.41
11 19 0.21
12 10 0.11
ACGTcount: A:0.71, C:0.03, G:0.02, T:0.24
Consensus pattern (10 bp):
AATAATAAAT
Found at i:5826491 original size:19 final size:19
Alignment explanation
Indices: 5826469--5826505 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
5826459 TAGATAATTG
*
5826469 GTCGAAAAGTTCAACCGAT
1 GTCGAAAAATTCAACCGAT
5826488 GTCGAAAAATTCAACCGA
1 GTCGAAAAATTCAACCGA
5826506 AATCTGGAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.41, C:0.22, G:0.19, T:0.19
Consensus pattern (19 bp):
GTCGAAAAATTCAACCGAT
Found at i:5826817 original size:3 final size:3
Alignment explanation
Indices: 5826811--5826964 Score: 59
Period size: 3 Copynumber: 48.7 Consensus size: 3
5826801 AGAAAGAAAA
* * * *
5826811 AAT AAT AAA AAT AAT AA- AAT AAT AAA AAA AGAT AAT -AT ATT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT AAT AAT AAT AAT
* *
5826855 AAAT AAA AAT AAT AAT AGAT AAAT AAT AAT AA- AGT ATAT ATAT CAAT
1 -AAT AAT AAT AAT AAT A-AT -AAT AAT AAT AAT AAT A-AT A-AT -AAT
* * *
5826902 AGAT AAAT AAT AAAT AAA AAT -AT ATAT ATT AA- AA- AAT AGT AAT AAT
1 A-AT -AAT AAT -AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT
5826948 AAAT AAAT AAAT AAT AA
1 -AAT -AAT -AAT AAT AA
5826965 ATAAGATACA
Statistics
Matches: 119, Mismatches: 16, Indels: 32
0.71 0.10 0.19
Matches are distributed among these distances:
2 11 0.09
3 68 0.57
4 37 0.31
5 3 0.03
ACGTcount: A:0.68, C:0.01, G:0.03, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:5826847 original size:21 final size:20
Alignment explanation
Indices: 5826807--5826869 Score: 74
Period size: 21 Copynumber: 3.1 Consensus size: 20
5826797 AAAAAGAAAG
*
5826807 AAAA-AATAATAAAAATAAT
1 AAAATAATAAAAAAAATAAT
5826826 AAAATAATAAAAAAAGATAAT
1 AAAATAATAAAAAAA-ATAAT
* *
5826847 ATATTAATAAATAAAAATAAT
1 AAAATAATAAA-AAAAATAAT
5826868 AA
1 AA
5826870 TAGATAAATA
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
19 4 0.11
20 9 0.24
21 20 0.54
22 4 0.11
ACGTcount: A:0.75, C:0.00, G:0.02, T:0.24
Consensus pattern (20 bp):
AAAATAATAAAAAAAATAAT
Found at i:5826855 original size:24 final size:24
Alignment explanation
Indices: 5826827--5826985 Score: 80
Period size: 25 Copynumber: 6.5 Consensus size: 24
5826817 AAAAATAATA
5826827 AAATAATAAAAAAAGATAATATAT
1 AAATAATAAAAAAAGATAATATAT
* * *
5826851 TAATAAATAAAAATA-ATAATAGAT
1 AAAT-AATAAAAAAAGATAATATAT
*
5826875 AAATAAT-AATAAAG-TATATATAT
1 AAATAATAAAAAAAGATA-ATATAT
* *
5826898 CAATAGATAAATAATAA-ATAAAAATAT
1 AAATA-ATAAA-AA-AAGAT-AATATAT
* *
5826925 ATATATTAAAAAATAG-TAATA-AT
1 AAATAATAAAAAA-AGATAATATAT
* *
5826948 AAATAAATAAATAATAA-ATAAGATAC
1 AAAT-AATAAA-AA-AAGATAATATAT
*
5826974 AAAAAATAAAAA
1 AAATAATAAAAA
5826986 CACAAGATAC
Statistics
Matches: 100, Mismatches: 19, Indels: 32
0.66 0.13 0.21
Matches are distributed among these distances:
22 6 0.06
23 17 0.17
24 27 0.27
25 28 0.28
26 10 0.10
27 11 0.11
28 1 0.01
ACGTcount: A:0.68, C:0.01, G:0.04, T:0.27
Consensus pattern (24 bp):
AAATAATAAAAAAAGATAATATAT
Found at i:5826861 original size:4 final size:4
Alignment explanation
Indices: 5826852--5826983 Score: 57
Period size: 4 Copynumber: 33.5 Consensus size: 4
5826842 ATAATATATT
* * * * *
5826852 AATA AATA AAAA TAAT- AATA GATA AAT- AAT- AATA AAGTA TATA TATC
1 AATA AATA AATA -AATA AATA AATA AATA AATA AATA AA-TA AATA AATA
* * *
5826899 AATA GATA AAT- AATA AAT- AA-A AATA TATA TATTA AA-A AATA GTAAT-
1 AATA AATA AATA AATA AATA AATA AATA AATA -AATA AATA AATA --AATA
*
5826945 AATA AATA AATA AAT- AATA AATA AGATA CAAAA AATA AA
1 AATA AATA AATA AATA AATA AATA A-ATA -AATA AATA AA
5826984 AACACAAGAT
Statistics
Matches: 97, Mismatches: 16, Indels: 30
0.68 0.11 0.21
Matches are distributed among these distances:
3 25 0.26
4 56 0.58
5 12 0.12
6 4 0.04
ACGTcount: A:0.67, C:0.02, G:0.04, T:0.27
Consensus pattern (4 bp):
AATA
Found at i:5826875 original size:31 final size:29
Alignment explanation
Indices: 5826842--5826985 Score: 82
Period size: 31 Copynumber: 4.7 Consensus size: 29
5826832 ATAAAAAAAG
5826842 ATAATATATTAATAAATAAAAATAATAATAG
1 ATAA-ATA-TAATAAATAAAAATAATAATAG
* *
5826873 ATAAATAATAATAAAGTATATAT-ATCAATAG
1 ATAAAT-ATAATAAA-TAAAAATAAT-AATAG
5826904 AT-AA-ATAATAAATAAAAATATATATATTA-
1 ATAAATATAATAAATAAAAATA-ATA-A-TAG
* *
5826933 AAAAATAGTAAT-AATAAATAAATAAATAATAA
1 ATAAATA-TAATAAAT-AA-AAAT-AATAATAG
* *
5826965 ATAAGATACAAAAAATAAAAA
1 ATAA-ATATAATAAATAAAAA
5826986 CACAAGATAC
Statistics
Matches: 89, Mismatches: 8, Indels: 32
0.69 0.06 0.25
Matches are distributed among these distances:
27 5 0.06
28 9 0.10
29 4 0.04
30 17 0.19
31 26 0.29
32 14 0.16
33 13 0.15
34 1 0.01
ACGTcount: A:0.67, C:0.01, G:0.03, T:0.28
Consensus pattern (29 bp):
ATAAATATAATAAATAAAAATAATAATAG
Found at i:5826923 original size:21 final size:20
Alignment explanation
Indices: 5826814--5826968 Score: 106
Period size: 21 Copynumber: 7.5 Consensus size: 20
5826804 AAGAAAAAAT
5826814 AATAAAAATAATAAAATAATA
1 AATAAAAATAAT-AAATAATA
*
5826835 AA-AAAAGATAATATATTAATA
1 AATAAAA-ATAATA-AATAATA
5826856 AATAAAAATAAT-AATAGATA
1 AATAAAAATAATAAATA-ATA
5826876 AAT---AATAATAAAGT-ATA
1 AATAAAAATAATAAA-TAATA
* **
5826893 TATATCAATAGATAAATAATA
1 AATAAAAATA-ATAAATAATA
* *
5826914 AATAAAAATATATATATTAAAA
1 AATAAAAATA-ATA-AATAATA
**
5826936 AATAGTAATAATAAATAAATA
1 AATAAAAATAATAAAT-AATA
5826957 AATAATAAATAA
1 AATAA-AAATAA
5826969 GATACAAAAA
Statistics
Matches: 105, Mismatches: 15, Indels: 27
0.71 0.10 0.18
Matches are distributed among these distances:
17 11 0.10
18 2 0.02
19 4 0.04
20 18 0.17
21 48 0.46
22 22 0.21
ACGTcount: A:0.68, C:0.01, G:0.03, T:0.28
Consensus pattern (20 bp):
AATAAAAATAATAAATAATA
Found at i:5826928 original size:35 final size:31
Alignment explanation
Indices: 5826811--5826930 Score: 101
Period size: 31 Copynumber: 4.0 Consensus size: 31
5826801 AGAAAGAAAA
*
5826811 AATA-ATAAA-AATAATAAAATA-ATA-A-A
1 AATAGATAAATAATAATAAAATATATATATC
* * * *
5826837 AAAAGATAATATATTAAT-AAATAAAAATAAT-
1 AATAGATAA-ATAATAATAAAATATATAT-ATC
*
5826868 AATAGATAAATAATAATAAAGTATATATATC
1 AATAGATAAATAATAATAAAATATATATATC
5826899 AATAGATAAATAATAAATAAAAATATATATAT
1 AATAGATAAATAAT-AAT-AAAATATATATAT
5826931 TAAAAAATAG
Statistics
Matches: 74, Mismatches: 9, Indels: 15
0.76 0.09 0.15
Matches are distributed among these distances:
26 3 0.04
27 4 0.05
28 6 0.08
29 7 0.09
30 9 0.12
31 30 0.41
32 3 0.04
33 12 0.16
ACGTcount: A:0.67, C:0.01, G:0.03, T:0.29
Consensus pattern (31 bp):
AATAGATAAATAATAATAAAATATATATATC
Found at i:5826950 original size:16 final size:15
Alignment explanation
Indices: 5826807--5826965 Score: 78
Period size: 16 Copynumber: 10.2 Consensus size: 15
5826797 AAAAAGAAAG
*
5826807 AAAAAATAATAAAAAT
1 AAAAAAT-ATAATAAT
5826823 AATAAAATAATAA-AA-
1 AA-AAAAT-ATAATAAT
*
5826838 AAAGATAATATATTAAT
1 AAA-A-AATATAATAAT
*
5826855 AAATAAAAATAATAAT
1 AAA-AAATATAATAAT
* *
5826871 AGATAA-ATAATAAT
1 AAAAAATATAATAAT
**
5826885 AAAGTATATATATCAAT
1 AAAAAATATA-AT-AAT
* *
5826902 AGATAA-ATAATAA-
1 AAAAAATATAATAAT
*
5826915 ATAAAAATATATATATT
1 A-AAAAATATA-ATAAT
5826932 AAAAAATAGTAATAAT
1 AAAAAATA-TAATAAT
5826948 AAATAAATA-AATAAT
1 AAA-AAATATAATAAT
5826963 AAA
1 AAA
5826966 TAAGATACAA
Statistics
Matches: 113, Mismatches: 16, Indels: 29
0.72 0.10 0.18
Matches are distributed among these distances:
13 1 0.01
14 17 0.15
15 25 0.22
16 42 0.37
17 28 0.25
ACGTcount: A:0.69, C:0.01, G:0.03, T:0.28
Consensus pattern (15 bp):
AAAAAATATAATAAT
Found at i:5827335 original size:83 final size:83
Alignment explanation
Indices: 5827185--5827408 Score: 260
Period size: 83 Copynumber: 2.7 Consensus size: 83
5827175 TTTGATCAAG
* * * *
5827185 GCTCTTCTAAGTAGAGCCTCAACAAC-TTTAAAAATAAGTAAAGCTCCTCTAAACAGAGGCTCGA
1 GCTCTTCTAAGTAGAGGCTCAACAACTTTTAAAAATAA--AAAGCTCCTCTAATCAGAGACTCAA
5827249 CGAC-TTTGAAAA-TAAGCAAA
64 CGACTTTTGAAAAGTAA--AAA
* *
5827269 GCTCCTCTAAGTAGAGGCTTAACAACTTTTAAAAATAAAAAGCTCCTCTAATCAGAGACTCAACG
1 GCTCTTCTAAGTAGAGGCTCAACAACTTTTAAAAATAAAAAGCTCCTCTAATCAGAGACTCAACG
*
5827334 ACTTTTGAAAAGTAAATA
66 ACTTTTGAAAAGTAAAAA
* * **
5827352 GCTCTTCTGAA-CAGAGGCTCAACAACTTTTGAAAAGTAAATTGCT-CTCTAATCAGAG
1 GCTCTTCT-AAGTAGAGGCTCAACAACTTTT-AAAAATAAAAAGCTCCTCTAATCAGAG
5827409 GCATCACAAC
Statistics
Matches: 122, Mismatches: 13, Indels: 11
0.84 0.09 0.08
Matches are distributed among these distances:
83 64 0.52
84 44 0.36
85 14 0.11
ACGTcount: A:0.39, C:0.21, G:0.15, T:0.25
Consensus pattern (83 bp):
GCTCTTCTAAGTAGAGGCTCAACAACTTTTAAAAATAAAAAGCTCCTCTAATCAGAGACTCAACG
ACTTTTGAAAAGTAAAAA
Found at i:5827338 original size:41 final size:41
Alignment explanation
Indices: 5827197--5827419 Score: 197
Period size: 42 Copynumber: 5.4 Consensus size: 41
5827187 TCTTCTAAGT
* *
5827197 AGAGCCTCAACAAC-TTTAAAAATAAGTAAAGCTCCTCTAAAC
1 AGAGGCTCAACAACTTTTAAAAATAA--AAAGCTCCTCTAATC
* * *
5827239 AGAGGCTCGACGAC-TTTGAAAATAAGCAAAGCTCCTCTAAGT-
1 AGAGGCTCAACAACTTTTAAAAATAA--AAAGCTCCTCTAA-TC
*
5827281 AGAGGCTTAACAACTTTTAAAAATAAAAAGCTCCTCTAATC
1 AGAGGCTCAACAACTTTTAAAAATAAAAAGCTCCTCTAATC
* * * * *
5827322 AGAGACTCAACGACTTTTGAAAAGTAAATAGCTCTTCTGAA-C
1 AGAGGCTCAACAACTTTT-AAAAATAAAAAGCTCCTCT-AATC
* **
5827364 AGAGGCTCAACAACTTTTGAAAAGTAAATTGCT-CTCTAATC
1 AGAGGCTCAACAACTTTT-AAAAATAAAAAGCTCCTCTAATC
5827405 AGAGGCATC-ACAACT
1 AGAGGC-TCAACAACT
5827420 AGATTACTCC
Statistics
Matches: 154, Mismatches: 20, Indels: 15
0.81 0.11 0.08
Matches are distributed among these distances:
40 3 0.02
41 44 0.29
42 95 0.62
43 12 0.08
ACGTcount: A:0.40, C:0.21, G:0.15, T:0.24
Consensus pattern (41 bp):
AGAGGCTCAACAACTTTTAAAAATAAAAAGCTCCTCTAATC
Found at i:5828492 original size:13 final size:12
Alignment explanation
Indices: 5828474--5828535 Score: 54
Period size: 13 Copynumber: 4.9 Consensus size: 12
5828464 TGAGTCTTTC
5828474 TTTTTTATTCACT
1 TTTTTTATTCA-T
*
5828487 TTTTTTTTTCATT
1 TTTTTTATTCA-T
*
5828500 TTTTTTCTTTCAT
1 TTTTTT-ATTCAT
*
5828513 TTTTTCATTTCAT
1 TTTTTTA-TTCAT
5828526 TTTTTT-TTCA
1 TTTTTTATTCA
5828536 AGCATAATAT
Statistics
Matches: 42, Mismatches: 5, Indels: 6
0.79 0.09 0.11
Matches are distributed among these distances:
11 4 0.10
13 33 0.79
14 5 0.12
ACGTcount: A:0.11, C:0.13, G:0.00, T:0.76
Consensus pattern (12 bp):
TTTTTTATTCAT
Found at i:5828510 original size:14 final size:14
Alignment explanation
Indices: 5828481--5828532 Score: 65
Period size: 13 Copynumber: 3.9 Consensus size: 14
5828471 TTCTTTTTTA
*
5828481 TTCACTTTTTTT-T
1 TTCATTTTTTTTCT
5828494 TTCATTTTTTTTCT
1 TTCATTTTTTTTCT
5828508 TTCA--TTTTTTCAT
1 TTCATTTTTTTTC-T
5828521 TTCATTTTTTTT
1 TTCATTTTTTTT
5828533 TCAAGCATAA
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
12 7 0.21
13 16 0.47
14 5 0.15
15 6 0.18
ACGTcount: A:0.10, C:0.13, G:0.00, T:0.77
Consensus pattern (14 bp):
TTCATTTTTTTTCT
Found at i:5839221 original size:58 final size:55
Alignment explanation
Indices: 5839014--5839222 Score: 183
Period size: 58 Copynumber: 3.6 Consensus size: 55
5839004 TTTGTACAAA
* *
5839014 GAAAATTGATACTTTCAACTTTTTCCCAAAATATTTTTTAG-AAACTTTAATTTTGAG
1 GAAAATTAATACTTTCAACTTTTT-CCAAAATATTTTTTAGAAAAC-TT-ATTTTAAG
* **
5839071 GAAAATTGATACTTTCAACTTTTCTTAAAAAAAAATCATTTTTT-GAAAACTTATTTTTAAG
1 GAAAATTAATACTTTCAAC-TTT-TT---CCAAAAT-ATTTTTTAGAAAACTTA-TTTTAAG
* *
5839132 GAAAATGAATACTTT--ACTTTTCCCCAAAAATATTTTTTAGAAAAAACTTATTTTCAAG
1 GAAAATTAATACTTTCAACTTTT-TCC-AAAATATTTTTTAG--AAAACTTATTTT-AAG
*
5839190 GAAAATTAATACTTTCAACTTTTTCCTAAATAT
1 GAAAATTAATACTTTCAACTTTTTCCAAAATAT
5839223 ATATATTTTC
Statistics
Matches: 125, Mismatches: 12, Indels: 29
0.75 0.07 0.17
Matches are distributed among these distances:
55 7 0.06
56 6 0.05
57 24 0.19
58 37 0.30
59 6 0.05
60 7 0.06
61 27 0.22
62 11 0.09
ACGTcount: A:0.39, C:0.12, G:0.07, T:0.42
Consensus pattern (55 bp):
GAAAATTAATACTTTCAACTTTTTCCAAAATATTTTTTAGAAAACTTATTTTAAG
Found at i:5839231 original size:119 final size:118
Alignment explanation
Indices: 5839014--5839237 Score: 271
Period size: 119 Copynumber: 1.9 Consensus size: 118
5839004 TTTGTACAAA
* * *
5839014 GAAAATTGATACTTTCAACTTTTTCCCAAAATATTTTTTAGAAACTTTAATTTTGAGGAAAATTG
1 GAAAATTGATACTTT-AACTTTTCCCCAAAATATTTTTTAGAAACTTTAATTTTAAGGAAAATTA
*
5839079 ATACTTTCAACTTTTCTTAAAAAAAAATCATTTT-TTGAAAACTTATTTTTAAG
65 ATACTTTCAACTTTTCCTAAAAAAAAATCATTTTCTTGAAAACTTATTTTTAAG
5839132 GAAAA-TGAATACTTT-ACTTTTCCCCAAAAATATTTTTTAGAAAAAAC-TT-ATTTTCAAGGAA
1 GAAAATTG-ATACTTTAACTTTTCCCC-AAAATATTTTTTAG---AAACTTTAATTTT-AAGGAA
* * *
5839193 AATTAATACTTTCAACTTTTTCCTAAATATATAT-ATTTTCTTGAA
60 AATTAATACTTTCAAC-TTTTCCTAAAAAAAAATCATTTTCTTGAA
5839238 TTTTATTTAA
Statistics
Matches: 91, Mismatches: 7, Indels: 14
0.81 0.06 0.12
Matches are distributed among these distances:
116 9 0.10
117 16 0.18
118 17 0.19
119 27 0.30
120 22 0.24
ACGTcount: A:0.39, C:0.12, G:0.07, T:0.42
Consensus pattern (118 bp):
GAAAATTGATACTTTAACTTTTCCCCAAAATATTTTTTAGAAACTTTAATTTTAAGGAAAATTAA
TACTTTCAACTTTTCCTAAAAAAAAATCATTTTCTTGAAAACTTATTTTTAAG
Found at i:5839263 original size:5 final size:5
Alignment explanation
Indices: 5839255--5839287 Score: 57
Period size: 5 Copynumber: 6.4 Consensus size: 5
5839245 TAAAGAAAAT
5839255 AATAA AATAAA AATAA AATAA AATAA AATAA AA
1 AATAA AAT-AA AATAA AATAA AATAA AATAA AA
5839288 AAGTACTAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 22 0.81
6 5 0.19
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (5 bp):
AATAA
Found at i:5839333 original size:16 final size:16
Alignment explanation
Indices: 5839251--5839338 Score: 53
Period size: 15 Copynumber: 5.4 Consensus size: 16
5839241 TATTTAAAGA
5839251 AAATAATAA-AATAA-
1 AAATAATAATAATAAT
5839265 AAATAA-AATAA-AAT
1 AAATAATAATAATAAT
*
5839279 AAAATAA-AA-AAGTACT
1 -AAATAATAATAA-TAAT
5839295 AAATAATTCTAATCTAATCAAT
1 AAATAA---TAA--TAAT-AAT
5839317 AAATAATAATAATAAT
1 AAATAATAATAATAAT
5839333 AAATAA
1 AAATAA
5839339 ATAAACTGAG
Statistics
Matches: 59, Mismatches: 2, Indels: 24
0.69 0.02 0.28
Matches are distributed among these distances:
13 4 0.07
14 10 0.17
15 14 0.24
16 11 0.19
17 4 0.07
19 5 0.08
21 1 0.02
22 10 0.17
ACGTcount: A:0.68, C:0.05, G:0.01, T:0.26
Consensus pattern (16 bp):
AAATAATAATAATAAT
Found at i:5839337 original size:10 final size:10
Alignment explanation
Indices: 5839252--5839342 Score: 50
Period size: 10 Copynumber: 9.2 Consensus size: 10
5839242 ATTTAAAGAA
5839252 AATAAT-AA-
1 AATAATAAAT
5839260 AATAA-AAAT
1 AATAATAAAT
5839269 AA-AATAAAAT
1 AATAAT-AAAT
*
5839279 AA-AATAAAA
1 AATAATAAAT
*
5839288 AAGTACTAAAT
1 AA-TAATAAAT
** *
5839299 AATTCTAATCT
1 AATAATAA-AT
5839310 AATCAATAAAT
1 AAT-AATAAAT
5839321 AATAAT-AAT
1 AATAATAAAT
5839330 AATAAATAAAT
1 AAT-AATAAAT
5839341 AA
1 AA
5839343 ACTGAGAACA
Statistics
Matches: 65, Mismatches: 8, Indels: 17
0.72 0.09 0.19
Matches are distributed among these distances:
8 9 0.14
9 13 0.20
10 20 0.31
11 20 0.31
12 3 0.05
ACGTcount: A:0.68, C:0.04, G:0.01, T:0.26
Consensus pattern (10 bp):
AATAATAAAT
Found at i:5839446 original size:11 final size:11
Alignment explanation
Indices: 5839430--5839454 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
5839420 AAACTGCTCG
5839430 CACTCGAGTCA
1 CACTCGAGTCA
5839441 CACTCGAGTCA
1 CACTCGAGTCA
5839452 CAC
1 CAC
5839455 GTGGGTCGCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.28, C:0.40, G:0.16, T:0.16
Consensus pattern (11 bp):
CACTCGAGTCA
Found at i:5840201 original size:16 final size:17
Alignment explanation
Indices: 5840182--5840271 Score: 75
Period size: 16 Copynumber: 5.5 Consensus size: 17
5840172 TAAAGATAAT
5840182 ATATTAATAGATAAA-A
1 ATATTAATAGATAAATA
5840198 ATATTAATAGATAAATA
1 ATATTAATAGATAAATA
* * *
5840215 ATAATAATAAAGTATAT-
1 ATATTAATAGA-TAAATA
* *
5840232 ATATCAACAGATAAATA
1 ATATTAATAGATAAATA
5840249 ATA--AATA-A-AAATA
1 ATATTAATAGATAAATA
5840262 TATATTAATA
1 -ATATTAATA
5840272 AATAGTAATA
Statistics
Matches: 59, Mismatches: 9, Indels: 12
0.74 0.11 0.15
Matches are distributed among these distances:
13 5 0.08
14 4 0.07
15 3 0.05
16 23 0.39
17 20 0.34
18 4 0.07
ACGTcount: A:0.61, C:0.02, G:0.04, T:0.32
Consensus pattern (17 bp):
ATATTAATAGATAAATA
Found at i:5840216 original size:27 final size:28
Alignment explanation
Indices: 5840163--5840302 Score: 94
Period size: 27 Copynumber: 4.9 Consensus size: 28
5840153 AAAAGAAAAA
* *
5840163 AATAAA-AAATAA-AGATAATATATTAAT
1 AATAAATATATAATAGATAA-ATAATAAT
*
5840190 AGATAAAAATATTAATAGATAAATAATAAT
1 A-ATAAATATA-TAATAGATAAATAATAAT
5840220 AATAAAGTATATATATCAACAGATAAATAATAAAT
1 AATAAA-TATATA-AT----AGATAAATAAT-AAT
* *
5840255 AA-AAATATATATTA-ATAAATAGTAAT
1 AATAAATATATAATAGATAAATAATAAT
*
5840281 AATAAATAAATAA-A-ATAAATAA
1 AATAAATATATAATAGATAAATAA
5840303 ATAAGATACA
Statistics
Matches: 93, Mismatches: 8, Indels: 25
0.74 0.06 0.20
Matches are distributed among these distances:
26 13 0.14
27 17 0.18
28 6 0.06
29 9 0.10
30 16 0.17
31 6 0.06
32 1 0.01
33 6 0.06
34 14 0.15
35 5 0.05
ACGTcount: A:0.65, C:0.01, G:0.04, T:0.29
Consensus pattern (28 bp):
AATAAATATATAATAGATAAATAATAAT
Found at i:5840220 original size:20 final size:18
Alignment explanation
Indices: 5840177--5840284 Score: 60
Period size: 16 Copynumber: 6.5 Consensus size: 18
5840167 AAAAATAAAG
5840177 ATAAT-ATATTAATAGAT
1 ATAATAATATTAATAGAT
5840194 A-AA-AATATTAATAGAT
1 ATAATAATATTAATAGAT
* *
5840210 A-AATAATAATAATAAAGT
1 ATAATAATATTAATAGA-T
* *
5840228 AT-AT-ATATCAACAGAT
1 ATAATAATATTAATAGAT
5840244 A-AATAATA--AATA-A-
1 ATAATAATATTAATAGAT
*
5840257 A-AATATATATTAATAAAT
1 ATAATA-ATATTAATAGAT
5840275 AGTAATAATA
1 A-TAATAATA
5840285 AATAAATAAA
Statistics
Matches: 71, Mismatches: 7, Indels: 24
0.70 0.07 0.24
Matches are distributed among these distances:
13 5 0.07
14 4 0.06
15 3 0.04
16 25 0.35
17 22 0.31
18 5 0.07
19 3 0.04
20 4 0.06
ACGTcount: A:0.61, C:0.02, G:0.05, T:0.32
Consensus pattern (18 bp):
ATAATAATATTAATAGAT
Found at i:5840285 original size:13 final size:13
Alignment explanation
Indices: 5840163--5840302 Score: 72
Period size: 13 Copynumber: 9.9 Consensus size: 13
5840153 AAAAGAAAAA
*
5840163 AATAAAAAATAA-
1 AATAATAAATAAT
*
5840175 AGATAATATATTAAT
1 A-ATAATA-AATAAT
*
5840190 AGATAA-AAATATT
1 A-ATAATAAATAAT
5840203 AATAGATAAATAAT
1 AATA-ATAAATAAT
5840217 AATAATAAAGTATAT
1 AATAATAAA-TA-AT
5840232 ATATCAACAGATAAATAAT
1 A-AT----A-ATAAATAAT
5840251 AAATAA-AAATATAT
1 -AATAATAAATA-AT
* *
5840265 ATTAATAAATAGT
1 AATAATAAATAAT
5840278 AATAATAAATAAAT
1 AATAATAAAT-AAT
5840292 AA-AATAAATAA
1 AATAATAAATAA
5840303 ATAAGATACA
Statistics
Matches: 102, Mismatches: 9, Indels: 34
0.70 0.06 0.23
Matches are distributed among these distances:
12 6 0.06
13 42 0.41
14 29 0.28
15 10 0.10
16 2 0.02
19 4 0.04
20 4 0.04
21 5 0.05
ACGTcount: A:0.65, C:0.01, G:0.04, T:0.29
Consensus pattern (13 bp):
AATAATAAATAAT
Found at i:5840301 original size:17 final size:18
Alignment explanation
Indices: 5840242--5840321 Score: 69
Period size: 17 Copynumber: 4.5 Consensus size: 18
5840232 ATATCAACAG
*
5840242 ATAAAT-AATAAATAAAA
1 ATAAATAAATAAATACAA
* **
5840259 ATATATATTAATAAATAGTA
1 ATA-A-ATAAATAAATACAA
5840279 AT-AATAAATAAATA-AA
1 ATAAATAAATAAATACAA
5840295 ATAAATAAATAAGATACAA
1 ATAAATAAATAA-ATACAA
5840314 A-AAATAAA
1 ATAAATAAA
5840322 AACACAAGAT
Statistics
Matches: 53, Mismatches: 4, Indels: 11
0.78 0.06 0.16
Matches are distributed among these distances:
16 3 0.06
17 22 0.42
18 12 0.23
19 5 0.09
20 11 0.21
ACGTcount: A:0.70, C:0.01, G:0.03, T:0.26
Consensus pattern (18 bp):
ATAAATAAATAAATACAA
Found at i:5840303 original size:13 final size:13
Alignment explanation
Indices: 5840268--5840322 Score: 58
Period size: 13 Copynumber: 4.2 Consensus size: 13
5840258 AATATATATT
*
5840268 AATAAAT-AGTAA
1 AATAAATAAATAA
5840280 TAATAAATAAATAA
1 -AATAAATAAATAA
5840294 AATAAATAAATAA
1 AATAAATAAATAA
* *
5840307 GATACAAAAAATAA
1 AATA-AATAAATAA
5840321 AA
1 AA
5840323 ACACAAGATA
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
13 23 0.64
14 13 0.36
ACGTcount: A:0.73, C:0.02, G:0.04, T:0.22
Consensus pattern (13 bp):
AATAAATAAATAA
Found at i:5840317 original size:22 final size:22
Alignment explanation
Indices: 5840292--5840348 Score: 71
Period size: 22 Copynumber: 2.5 Consensus size: 22
5840282 ATAAATAAAT
*
5840292 AAAATAAATAAATAAGATACAA
1 AAAATAAATAAACAAGATACAA
5840314 AAAATAAA-AACACAAGATACAA
1 AAAATAAATAA-ACAAGATACAA
*
5840336 AATAAAAAATAAA
1 AA-AATAAATAAA
5840349 AAATAAAATG
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
21 2 0.07
22 20 0.67
23 6 0.20
24 2 0.07
ACGTcount: A:0.75, C:0.07, G:0.04, T:0.14
Consensus pattern (22 bp):
AAAATAAATAAACAAGATACAA
Found at i:5840344 original size:7 final size:7
Alignment explanation
Indices: 5840278--5840356 Score: 52
Period size: 7 Copynumber: 11.0 Consensus size: 7
5840268 AATAAATAGT
*
5840278 AATAATA
1 AATAAAA
5840285 AATAAATAA
1 AAT-AA-AA
5840294 AATAAATA
1 AATAAA-A
*
5840302 AATAAGA
1 AATAAAA
* *
5840309 TACAAAA
1 AATAAAA
5840316 AAT-AAA
1 AATAAAA
* *
5840322 AACACAA
1 AATAAAA
* *
5840329 GATACAA
1 AATAAAA
5840336 AATAAAA
1 AATAAAA
5840343 AATAAAA
1 AATAAAA
5840350 AATAAAA
1 AATAAAA
5840357 TGGTCATACC
Statistics
Matches: 55, Mismatches: 13, Indels: 8
0.72 0.17 0.11
Matches are distributed among these distances:
6 5 0.09
7 36 0.65
8 10 0.18
9 4 0.07
ACGTcount: A:0.76, C:0.05, G:0.03, T:0.16
Consensus pattern (7 bp):
AATAAAA
Found at i:5840356 original size:13 final size:13
Alignment explanation
Indices: 5840244--5840356 Score: 57
Period size: 14 Copynumber: 8.1 Consensus size: 13
5840234 ATCAACAGAT
5840244 AAATAATAAATAAA
1 AAATAA-AAATAAA
*
5840258 AATATATATTAATAAA
1 AA-ATA-A-AAATAAA
* * *
5840274 TAGTAATAATAAA
1 AAATAAAAATAAA
5840287 TAAAT-AAAATAAA
1 -AAATAAAAATAAA
* *
5840300 TAAATAAGATACAAA
1 -AAATAA-AAATAAA
* *
5840315 AAATAAAAACACA
1 AAATAAAAATAAA
*
5840328 AGATACAAAATAAA
1 AAATA-AAAATAAA
5840342 AAATAAAAAATAAA
1 AAAT-AAAAATAAA
5840356 A
1 A
5840357 TGGTCATACC
Statistics
Matches: 78, Mismatches: 14, Indels: 14
0.74 0.13 0.13
Matches are distributed among these distances:
13 28 0.36
14 30 0.38
15 11 0.14
16 9 0.12
ACGTcount: A:0.73, C:0.04, G:0.03, T:0.21
Consensus pattern (13 bp):
AAATAAAAATAAA
Found at i:5842672 original size:20 final size:21
Alignment explanation
Indices: 5842629--5842671 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
5842619 ATACATGTGC
*
5842629 AAATGAAT-AACAAATATATA
1 AAATGAATAAACAAATAAATA
*
5842649 AAATGAATAAATAAATAAATA
1 AAATGAATAAACAAATAAATA
5842670 AA
1 AA
5842672 TAATACAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 8 0.40
21 12 0.60
ACGTcount: A:0.70, C:0.02, G:0.05, T:0.23
Consensus pattern (21 bp):
AAATGAATAAACAAATAAATA
Found at i:5843265 original size:37 final size:38
Alignment explanation
Indices: 5843216--5843293 Score: 97
Period size: 38 Copynumber: 2.1 Consensus size: 38
5843206 TATGAAAGCA
*
5843216 ATTTATTTTCAAA-AATATCTTCCAATATGTTGGTAAG
1 ATTTATTTTCAAAGAATATCCTCCAATATGTTGGTAAG
* * *
5843253 ATTT-TTTGTCAAAGATTATCCTCTAATATGTTGGTAGG
1 ATTTATTT-TCAAAGAATATCCTCCAATATGTTGGTAAG
5843291 ATT
1 ATT
5843294 GAAAATTTAT
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
36 3 0.09
37 9 0.26
38 23 0.66
ACGTcount: A:0.31, C:0.10, G:0.14, T:0.45
Consensus pattern (38 bp):
ATTTATTTTCAAAGAATATCCTCCAATATGTTGGTAAG
Found at i:5843709 original size:20 final size:19
Alignment explanation
Indices: 5843671--5843709 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
5843661 TTTAATAGAT
*
5843671 CATACAATAAATATGAAAA
1 CATACAATAAATATAAAAA
*
5843690 CATACAATTAGATATAAAAA
1 CATACAA-TAAATATAAAAA
5843710 AATGCAAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.62, C:0.10, G:0.05, T:0.23
Consensus pattern (19 bp):
CATACAATAAATATAAAAA
Found at i:5843779 original size:14 final size:14
Alignment explanation
Indices: 5843760--5843798 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
5843750 AACAACCATA
*
5843760 ATAAATATTAAAAT
1 ATAAATATAAAAAT
5843774 ATAAATATAAAAAT
1 ATAAATATAAAAAT
5843788 A-AAATA-AAAAA
1 ATAAATATAAAAA
5843799 CAAAATTATT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
12 5 0.21
13 5 0.21
14 14 0.58
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (14 bp):
ATAAATATAAAAAT
Found at i:5843798 original size:12 final size:13
Alignment explanation
Indices: 5843762--5843804 Score: 52
Period size: 14 Copynumber: 3.3 Consensus size: 13
5843752 CAACCATAAT
*
5843762 AAATATTAAAATA
1 AAATATAAAAATA
5843775 TAAATATAAAAATA
1 -AAATATAAAAATA
*
5843789 AAATA-AAAAACA
1 AAATATAAAAATA
5843801 AAAT
1 AAAT
5843805 TATTTTTAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
12 10 0.37
13 5 0.19
14 12 0.44
ACGTcount: A:0.74, C:0.02, G:0.00, T:0.23
Consensus pattern (13 bp):
AAATATAAAAATA
Found at i:5844436 original size:22 final size:22
Alignment explanation
Indices: 5844405--5844447 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
5844395 TTATTTAAAA
5844405 ATTATGATATAATAAATAAATT
1 ATTATGATATAATAAATAAATT
* *
5844427 ATTATTATATAATTAATAAAT
1 ATTATGATATAATAAATAAAT
5844448 AAAATTTAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.44
Consensus pattern (22 bp):
ATTATGATATAATAAATAAATT
Found at i:5845257 original size:2 final size:2
Alignment explanation
Indices: 5845250--5845278 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
5845240 CCTTTCGAGC
5845250 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
5845279 CATTTTTTGT
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:5846568 original size:18 final size:18
Alignment explanation
Indices: 5846545--5846585 Score: 82
Period size: 18 Copynumber: 2.3 Consensus size: 18
5846535 ATACTTTATT
5846545 TTGTTATTGCTATAAATA
1 TTGTTATTGCTATAAATA
5846563 TTGTTATTGCTATAAATA
1 TTGTTATTGCTATAAATA
5846581 TTGTT
1 TTGTT
5846586 TTTGTATATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.29, C:0.05, G:0.12, T:0.54
Consensus pattern (18 bp):
TTGTTATTGCTATAAATA
Found at i:5849626 original size:39 final size:39
Alignment explanation
Indices: 5849582--5849659 Score: 113
Period size: 39 Copynumber: 2.0 Consensus size: 39
5849572 CGGCTCTATG
* **
5849582 ACTGAGCCGTGTTCAATTAACATTTC-TACAGTTTGGTTT
1 ACTGAGCCGAGTTCAAACAACATTTCTTA-AGTTTGGTTT
5849621 ACTGAGCCGAGTTCAAACAACATTTCTTAAGTTTGGTTT
1 ACTGAGCCGAGTTCAAACAACATTTCTTAAGTTTGGTTT
5849660 GAGCTCAGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
39 33 0.94
40 2 0.06
ACGTcount: A:0.26, C:0.18, G:0.18, T:0.38
Consensus pattern (39 bp):
ACTGAGCCGAGTTCAAACAACATTTCTTAAGTTTGGTTT
Found at i:5866639 original size:22 final size:22
Alignment explanation
Indices: 5866614--5866657 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
5866604 TGTATATTTA
*
5866614 TATTTGTATCTCTAGAATTAAG
1 TATTTGTATCCCTAGAATTAAG
5866636 TATTTGTATCCCTAGAATTAAG
1 TATTTGTATCCCTAGAATTAAG
5866658 GAAGATTTAG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.32, C:0.11, G:0.14, T:0.43
Consensus pattern (22 bp):
TATTTGTATCCCTAGAATTAAG
Found at i:5866833 original size:23 final size:26
Alignment explanation
Indices: 5866807--5866867 Score: 78
Period size: 25 Copynumber: 2.5 Consensus size: 26
5866797 AATTTTCAGT
*
5866807 CTTCATTGCT-GACT-CT-TTTAGGC
1 CTTCATTGCTCGAATCCTGTTTAGGC
5866830 CTTCATTG-TCGAATCCTGTTTAGGC
1 CTTCATTGCTCGAATCCTGTTTAGGC
5866855 CTTCATTGC-CGAA
1 CTTCATTGCTCGAA
5866868 CCCTTTCAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
22 1 0.03
23 11 0.33
24 2 0.06
25 19 0.58
ACGTcount: A:0.16, C:0.26, G:0.18, T:0.39
Consensus pattern (26 bp):
CTTCATTGCTCGAATCCTGTTTAGGC
Found at i:5870537 original size:22 final size:22
Alignment explanation
Indices: 5870511--5870553 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
5870501 TGTATATTTA
*
5870511 TATTTGTATCTCTAAAATTAAG
1 TATTTGTATCCCTAAAATTAAG
5870533 TATTTGTATCCCTAAAATTAA
1 TATTTGTATCCCTAAAATTAA
5870554 AGAAGATTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.37, C:0.12, G:0.07, T:0.44
Consensus pattern (22 bp):
TATTTGTATCCCTAAAATTAAG
Found at i:5884275 original size:18 final size:18
Alignment explanation
Indices: 5884252--5884313 Score: 61
Period size: 18 Copynumber: 3.2 Consensus size: 18
5884242 CTTTTAGGGT
5884252 TTTGGTTAGGGTTTAAGG
1 TTTGGTTAGGGTTTAAGG
* *
5884270 TTTGGTTGGGGTTCAGAGG
1 TTTGGTTAGGGTTTA-AGG
*
5884289 TTTGGCATTAGTGTTTAAGGG
1 TTTGG--TTAGGGTTTAA-GG
5884310 TTTG
1 TTTG
5884314 ATTTGGTTTA
Statistics
Matches: 35, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
18 13 0.37
19 8 0.23
20 1 0.03
21 13 0.37
ACGTcount: A:0.15, C:0.03, G:0.39, T:0.44
Consensus pattern (18 bp):
TTTGGTTAGGGTTTAAGG
Found at i:5886127 original size:146 final size:144
Alignment explanation
Indices: 5885977--5886303 Score: 345
Period size: 146 Copynumber: 2.2 Consensus size: 144
5885967 TTTAAAAGTT
* **
5885977 AAATTATAAAAATACCCCTAAAAGATATTTTAGTAATTTCAACTC-TTTTGAGGTGTGATCCGAG
1 AAATTATAAAAATACCCCTAAAAGATATTTT-GTAATTTCAA-TCATTTTGAGGTGCGATAAGAG
* * * * *
5886041 TTTTTTA-ATATATCAAAATCATGAAATAATATCAAAACATAATTTAAAGCTTTTTCACAAAAAA
64 TTCTCTATACAT-TAAAAAGCATGAAATAATATCAAAACATAATTTAAAGCTTTTTCAC-AAAAA
* * * *
5886105 AATGATATCGAAAGGGTC
127 AATAACATCAAAAAGGTC
** * * *
5886123 AAATTACGAAAATA-CCTTTAAAGAGTATTTTGGTAATTTCAATCATTTTGGGGTGCGATAAGAG
1 AAATTATAAAAATACCCCTAAAAGA-TATTTT-GTAATTTCAATCATTTTGAGGTGCGATAAGAG
* * * * *
5886187 TTCTCTATACATTAAAAAGCATGAAATAATATTAAAACATAATTTGAAGTTTTTTCACGAAAAAC
64 TTCTCTATACATTAAAAAGCATGAAATAATATCAAAACATAATTTAAAGCTTTTTCACAAAAAAA
* *
5886252 TAACATTAAAAAGGTT
129 TAACATCAAAAAGGTC
* *
5886268 AAATTATAAAAATACCCCTAAATGTTATTTTGTAAT
1 AAATTATAAAAATACCCCTAAAAGATATTTTGTAAT
5886304 CTTATTCTTC
Statistics
Matches: 146, Mismatches: 31, Indels: 10
0.78 0.17 0.05
Matches are distributed among these distances:
144 5 0.03
145 43 0.29
146 95 0.65
147 3 0.02
ACGTcount: A:0.43, C:0.11, G:0.12, T:0.34
Consensus pattern (144 bp):
AAATTATAAAAATACCCCTAAAAGATATTTTGTAATTTCAATCATTTTGAGGTGCGATAAGAGTT
CTCTATACATTAAAAAGCATGAAATAATATCAAAACATAATTTAAAGCTTTTTCACAAAAAAATA
ACATCAAAAAGGTC
Found at i:5889249 original size:52 final size:52
Alignment explanation
Indices: 5889193--5889301 Score: 134
Period size: 52 Copynumber: 2.1 Consensus size: 52
5889183 TAATATAATA
*
5889193 TAATAAAAA-ATTTATTTGATAT-ATTACTTTTTATTAA-TTTTTAATTATTTAT
1 TAATAAAAATA-TTATTTGATATAATTAC--TTTAATAATTTTTTAATTATTTAT
* *
5889245 TAATAAAATTATTATTTGATATAAATTACTTTAATAATTTTTTAGTTATTTAT
1 TAATAAAAATATTATTTGATAT-AATTACTTTAATAATTTTTTAATTATTTAT
5889298 TAAT
1 TAAT
5889302 TTTATAAATG
Statistics
Matches: 50, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
52 26 0.52
53 19 0.38
54 5 0.10
ACGTcount: A:0.39, C:0.02, G:0.03, T:0.56
Consensus pattern (52 bp):
TAATAAAAATATTATTTGATATAATTACTTTAATAATTTTTTAATTATTTAT
Found at i:5891601 original size:26 final size:26
Alignment explanation
Indices: 5891572--5891628 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 26
5891562 AAAAAATAAA
* * *
5891572 AAAAATCCAAAATAATTGAAATTTTG
1 AAAAATCCAAAAAAAATAAAATTTTG
* *
5891598 AAAAATCTAAAAAAAATAAAATTTTT
1 AAAAATCCAAAAAAAATAAAATTTTG
5891624 AAAAA
1 AAAAA
5891629 ATGAGGGAAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.63, C:0.05, G:0.04, T:0.28
Consensus pattern (26 bp):
AAAAATCCAAAAAAAATAAAATTTTG
Found at i:5893473 original size:19 final size:19
Alignment explanation
Indices: 5893440--5893478 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
5893430 TATTTTTATA
*
5893440 AAAAAATTTATAATC-TAC
1 AAAAAATTTAAAATCATAC
5893458 AAAAAATTTAAAAATCATAC
1 AAAAAATTT-AAAATCATAC
5893478 A
1 A
5893479 TTTTAATCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 9 0.50
19 5 0.28
20 4 0.22
ACGTcount: A:0.62, C:0.10, G:0.00, T:0.28
Consensus pattern (19 bp):
AAAAAATTTAAAATCATAC
Found at i:5898536 original size:24 final size:24
Alignment explanation
Indices: 5898509--5898555 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
5898499 GATTTAAAAT
*
5898509 TAAT-TTAATAATTTTAAGTTAATA
1 TAATATTAAT-ATTATAAGTTAATA
*
5898533 TAATATTTATATTATAAGTTAAT
1 TAATATTAATATTATAAGTTAAT
5898556 CAGTGTATAG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 16 0.80
25 4 0.20
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (24 bp):
TAATATTAATATTATAAGTTAATA
Found at i:5898783 original size:13 final size:13
Alignment explanation
Indices: 5898740--5898784 Score: 56
Period size: 13 Copynumber: 3.4 Consensus size: 13
5898730 CTTCATGAGC
5898740 AAATTT-TTTTAA
1 AAATTTATTTTAA
*
5898752 AAATATTACTTTTAT
1 AAAT-TTA-TTTTAA
5898767 AAATTTATTTTAA
1 AAATTTATTTTAA
5898780 AAATT
1 AAATT
5898785 AATATTTATT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
12 4 0.14
13 12 0.43
14 3 0.11
15 9 0.32
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.53
Consensus pattern (13 bp):
AAATTTATTTTAA
Found at i:5898792 original size:27 final size:26
Alignment explanation
Indices: 5898740--5898793 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 26
5898730 CTTCATGAGC
*
5898740 AAATTTTTTTAAAAATATTACTTTTAT
1 AAATTTTTTTAAAAATAATAC-TTTAT
5898767 AAATTTATTTTAAAAATTAATA-TTTAT
1 AAATTT-TTTTAAAAA-TAATACTTTAT
5898794 TTATTAATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
27 11 0.46
28 9 0.38
29 4 0.17
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (26 bp):
AAATTTTTTTAAAAATAATACTTTAT
Found at i:5907063 original size:3 final size:3
Alignment explanation
Indices: 5907020--5907048 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
5907010 AGATCTCTAC
5907020 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
5907049 AGCTCATTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:5908983 original size:62 final size:62
Alignment explanation
Indices: 5908886--5909011 Score: 234
Period size: 62 Copynumber: 2.0 Consensus size: 62
5908876 TTACTTAACT
*
5908886 ATGATAATATTTCTAAGTTTTAATGTAAGAATTGACTTTTTATTTAATTACTTGATATGATA
1 ATGATAATATTTCTAAGTTTTAATGTAAGAATTGACTTTTTATTTAATTAATTGATATGATA
*
5908948 ATGATCATATTTCTAAGTTTTAATGTAAGAATTGACTTTTTATTTAATTAATTGATATGATA
1 ATGATAATATTTCTAAGTTTTAATGTAAGAATTGACTTTTTATTTAATTAATTGATATGATA
5909010 AT
1 AT
5909012 ATTTGTTTCA
Statistics
Matches: 62, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
62 62 1.00
ACGTcount: A:0.36, C:0.05, G:0.11, T:0.48
Consensus pattern (62 bp):
ATGATAATATTTCTAAGTTTTAATGTAAGAATTGACTTTTTATTTAATTAATTGATATGATA
Found at i:5909921 original size:15 final size:14
Alignment explanation
Indices: 5909901--5909959 Score: 54
Period size: 13 Copynumber: 4.3 Consensus size: 14
5909891 TCCATTTTGT
*
5909901 TTTTGTTTTTTATTA
1 TTTTGTATTTTA-TA
5909916 TTTTGTATTTTATA
1 TTTTGTATTTTATA
5909930 TTTT-TATTTT-TAA
1 TTTTGTATTTTAT-A
5909943 TTTT-TAATTTT-TA
1 TTTTGT-ATTTTATA
5909956 TTTT
1 TTTT
5909960 TTTTCTTCTT
Statistics
Matches: 41, Mismatches: 1, Indels: 6
0.85 0.02 0.12
Matches are distributed among these distances:
12 1 0.02
13 17 0.41
14 12 0.29
15 11 0.27
ACGTcount: A:0.19, C:0.00, G:0.03, T:0.78
Consensus pattern (14 bp):
TTTTGTATTTTATA
Found at i:5909924 original size:7 final size:6
Alignment explanation
Indices: 5909913--5909960 Score: 60
Period size: 7 Copynumber: 7.3 Consensus size: 6
5909903 TTGTTTTTTA
5909913 TTATTT TGTATTT TATATTT TTATTT TTAATTT TTAATTT TTATTT TT
1 TTATTT T-TATTT T-TATTT TTATTT TT-ATTT TT-ATTT TTATTT TT
5909961 TTTCTTCTTT
Statistics
Matches: 39, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
6 14 0.36
7 25 0.64
ACGTcount: A:0.21, C:0.00, G:0.02, T:0.77
Consensus pattern (6 bp):
TTATTT
Found at i:5909931 original size:17 final size:15
Alignment explanation
Indices: 5909901--5909933 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
5909891 TCCATTTTGT
5909901 TTTTGTTTTTTATTA
1 TTTTGTTTTTTATTA
*
5909916 TTTTGTATTTTA-TA
1 TTTTGTTTTTTATTA
5909930 TTTT
1 TTTT
5909934 TATTTTTAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 6 0.35
15 11 0.65
ACGTcount: A:0.15, C:0.00, G:0.06, T:0.79
Consensus pattern (15 bp):
TTTTGTTTTTTATTA
Found at i:5909961 original size:7 final size:7
Alignment explanation
Indices: 5909900--5909961 Score: 54
Period size: 7 Copynumber: 8.7 Consensus size: 7
5909890 ATCCATTTTG
*
5909900 TTTTTGT
1 TTTTTAT
5909907 TTTTTAT
1 TTTTTAT
*
5909914 TATTTTGT
1 T-TTTTAT
*
5909922 ATTTTAT
1 TTTTTAT
5909929 ATTTTTA-
1 -TTTTTAT
*
5909936 TTTTTAA
1 TTTTTAT
*
5909943 TTTTTAA
1 TTTTTAT
5909950 TTTTTAT
1 TTTTTAT
5909957 TTTTT
1 TTTTT
5909962 TTCTTCTTTG
Statistics
Matches: 46, Mismatches: 6, Indels: 6
0.79 0.10 0.10
Matches are distributed among these distances:
6 6 0.13
7 30 0.65
8 10 0.22
ACGTcount: A:0.18, C:0.00, G:0.03, T:0.79
Consensus pattern (7 bp):
TTTTTAT
Found at i:5909961 original size:14 final size:13
Alignment explanation
Indices: 5909908--5910006 Score: 65
Period size: 13 Copynumber: 7.2 Consensus size: 13
5909898 TGTTTTTGTT
5909908 TTTTATTATTTTGTA
1 TTTT-TTATTTT-TA
*
5909923 TTTTATATTTTTA
1 TTTTTTATTTTTA
*
5909936 TTTTTAATTTTTA
1 TTTTTTATTTTTA
*
5909949 ATTTTTATTTTT-
1 TTTTTTATTTTTA
* * *
5909961 TTTCTTCTTTGTA
1 TTTTTTATTTTTA
*
5909974 TCTTATGTATTATTTA
1 T-TT-TTTATT-TTTA
5909990 TTTATTTATTTATTA
1 TTT-TTTATTT-TTA
5910005 TT
1 TT
5910007 ATTATTTATT
Statistics
Matches: 65, Mismatches: 14, Indels: 10
0.73 0.16 0.11
Matches are distributed among these distances:
12 8 0.12
13 24 0.37
14 9 0.14
15 20 0.31
16 4 0.06
ACGTcount: A:0.20, C:0.03, G:0.03, T:0.74
Consensus pattern (13 bp):
TTTTTTATTTTTA
Found at i:5909992 original size:4 final size:4
Alignment explanation
Indices: 5909983--5910144 Score: 69
Period size: 4 Copynumber: 42.0 Consensus size: 4
5909973 ATCTTATGTA
* *
5909983 TTAT TTAT TTAT TTAT TTA- TTA- TTA- TTAT TTAT TAAT ATAT ATT-T
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT -TTAT
* * * * * *
5910028 TTAT GTTAAT ATAT ATAT TTA- TTA- TTAC TTAG CTAT TTAT ATA- TTAT
1 TTAT -TT-AT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT
* * * *
5910075 TATAT ATAT GTAT TTA- TTA- TTAT TTAT CTAT TTAT ATAT TATAAT TTAT
1 T-TAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT T-T-AT TTAT
*
5910124 CTA- TTAT TTA- TT-T TTAT TTAT
1 TTAT TTAT TTAT TTAT TTAT TTAT
5910145 CTGTTAATAT
Statistics
Matches: 123, Mismatches: 21, Indels: 28
0.72 0.12 0.16
Matches are distributed among these distances:
3 31 0.25
4 78 0.63
5 9 0.07
6 5 0.04
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.64
Consensus pattern (4 bp):
TTAT
Found at i:5910009 original size:22 final size:22
Alignment explanation
Indices: 5909976--5910146 Score: 143
Period size: 22 Copynumber: 7.7 Consensus size: 22
5909966 TCTTTGTATC
*
5909976 TTATGTATTATTTATTTATTTAT
1 TTAT-TATTATTTATCTATTTAT
*
5909999 TTATTATTA-TTATTTATTAATAT
1 TTATTATTATTTATCTATT--TAT
* * * *
5910022 ATATTTTTATGTTAATATATATAT
1 TTATTATTAT-TT-ATCTATTTAT
* *
5910046 TTATTATTACTTAGCTATTTAT
1 TTATTATTATTTATCTATTTAT
* * *
5910068 ATATTATTA--TATATATGTAT
1 TTATTATTATTTATCTATTTAT
5910088 TTATTATTATTTATCTATTTAT
1 TTATTATTATTTATCTATTTAT
* *
5910110 ATATTATAATTTATCTA-TTAT
1 TTATTATTATTTATCTATTTAT
*
5910131 TTATTTTTATTTATCT
1 TTATTATTATTTATCT
5910147 GTTAATATTT
Statistics
Matches: 119, Mismatches: 22, Indels: 16
0.76 0.14 0.10
Matches are distributed among these distances:
20 16 0.13
21 26 0.22
22 44 0.37
23 16 0.13
24 10 0.08
25 2 0.02
26 5 0.04
ACGTcount: A:0.32, C:0.03, G:0.02, T:0.63
Consensus pattern (22 bp):
TTATTATTATTTATCTATTTAT
Found at i:5910038 original size:18 final size:18
Alignment explanation
Indices: 5910015--5910049 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
5910005 TTATTATTTA
*
5910015 TTAATATATATTTTTATG
1 TTAATATATATATTTATG
5910033 TTAATATATATATTTAT
1 TTAATATATATATTTAT
5910050 TATTACTTAG
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:0.37, C:0.00, G:0.03, T:0.60
Consensus pattern (18 bp):
TTAATATATATATTTATG
Found at i:5910092 original size:42 final size:42
Alignment explanation
Indices: 5910036--5910135 Score: 137
Period size: 42 Copynumber: 2.4 Consensus size: 42
5910026 TTTTATGTTA
5910036 ATATATATATTTATTATTACTTAGCTATTTATATATTATTAT
1 ATATATATATTTATTATTACTTAGCTATTTATATATTATTAT
* * * *
5910078 ATATATGTATTTATTATTATTTATCTATTTATATATTATAAT
1 ATATATATATTTATTATTACTTAGCTATTTATATATTATTAT
* *
5910120 TTATCTATTATTTATT
1 ATATATA-TATTTATT
5910136 TTTATTTATC
Statistics
Matches: 50, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
42 42 0.84
43 8 0.16
ACGTcount: A:0.34, C:0.04, G:0.02, T:0.60
Consensus pattern (42 bp):
ATATATATATTTATTATTACTTAGCTATTTATATATTATTAT
Found at i:5910144 original size:14 final size:14
Alignment explanation
Indices: 5909909--5910144 Score: 60
Period size: 14 Copynumber: 16.4 Consensus size: 14
5909899 GTTTTTGTTT
5909909 TTTA-TTATTTTGTA
1 TTTATTTATTTT-TA
*
5909923 TTT-TATATTTTTA
1 TTTATTTATTTTTA
*
5909936 TTT-TTAATTTTTA
1 TTTATTTATTTTTA
*
5909949 ATT-TTTATTTTT-
1 TTTATTTATTTTTA
* * *
5909961 TTT-CTTCTTTGTA
1 TTTATTTATTTTTA
*
5909974 TCTTATGTATTATTTA
1 T-TTATTTATT-TTTA
5909990 TTTATTTATTTATTA
1 TTTATTTATTT-TTA
*
5910005 TTATTATTTATTAATATA
1 -T-TTATTTATT--TTTA
5910023 TATT-TTTATGTTAATATA
1 T-TTATTTAT-TT--T-TA
* *
5910041 TATATTTATTATTA
1 TTTATTTATTTTTA
* ** *
5910055 CTTAGCTATTTATA
1 TTTATTTATTTTTA
* *
5910069 TATTA-TTATATATA
1 T-TTATTTATTTTTA
* *
5910083 TGTATTTATTATTA
1 TTTATTTATTTTTA
* *
5910097 TTTATCTATTTATA
1 TTTATTTATTTTTA
*
5910111 TATTA-TAATTTATCTA
1 T-TTATTTATTT-T-TA
5910127 -TTATTTATTTTTA
1 TTTATTTATTTTTA
5910140 TTTAT
1 TTTAT
5910145 CTGTTAATAT
Statistics
Matches: 161, Mismatches: 39, Indels: 44
0.66 0.16 0.18
Matches are distributed among these distances:
12 8 0.05
13 28 0.17
14 59 0.37
15 27 0.17
16 12 0.07
17 16 0.10
18 10 0.06
19 1 0.01
ACGTcount: A:0.28, C:0.03, G:0.03, T:0.67
Consensus pattern (14 bp):
TTTATTTATTTTTA
Found at i:5910175 original size:18 final size:19
Alignment explanation
Indices: 5910131--5910175 Score: 56
Period size: 20 Copynumber: 2.4 Consensus size: 19
5910121 TATCTATTAT
*
5910131 TTATTTTTATTTATCTGTTA
1 TTATTTTGATTTATCTG-TA
*
5910151 ATATTTTGATTTATCTG-A
1 TTATTTTGATTTATCTGTA
5910169 TTATTTT
1 TTATTTT
5910176 CTTTTAATTA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 7 0.32
20 15 0.68
ACGTcount: A:0.22, C:0.04, G:0.07, T:0.67
Consensus pattern (19 bp):
TTATTTTGATTTATCTGTA
Found at i:5910199 original size:42 final size:41
Alignment explanation
Indices: 5910118--5910204 Score: 104
Period size: 42 Copynumber: 2.1 Consensus size: 41
5910108 ATATATTATA
* * * *
5910118 ATTTATCTATTATTTATTTTTATTTATCTGTTAATATTTTG
1 ATTTATCTATTATTTATTTTTAATTATCTATCAACATTTTG
*
5910159 ATTTATCTGATTATTT-TCTTTTAATTATCTATCAACATTTTT
1 ATTTATCT-ATTATTTAT-TTTTAATTATCTATCAACATTTTG
5910201 ATTT
1 ATTT
5910205 GATTTTTTTC
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
41 9 0.23
42 30 0.77
ACGTcount: A:0.25, C:0.08, G:0.03, T:0.63
Consensus pattern (41 bp):
ATTTATCTATTATTTATTTTTAATTATCTATCAACATTTTG
Found at i:5911148 original size:10 final size:10
Alignment explanation
Indices: 5911133--5911173 Score: 52
Period size: 10 Copynumber: 4.3 Consensus size: 10
5911123 TTAATACTTT
5911133 TTTATTTTTA
1 TTTATTTTTA
5911143 TTTATTTTTA
1 TTTATTTTTA
5911153 TTT-TATTTTA
1 TTTAT-TTTTA
5911163 -TTA-TTTTA
1 TTTATTTTTA
5911171 TTT
1 TTT
5911174 TCTTTAAATA
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
8 5 0.18
9 5 0.18
10 18 0.64
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (10 bp):
TTTATTTTTA
Found at i:5911463 original size:58 final size:58
Alignment explanation
Indices: 5911191--5911460 Score: 370
Period size: 57 Copynumber: 4.7 Consensus size: 58
5911181 ATAAAATTCA
*
5911191 AAAAAATATTTTTGAGAAAAAGTTGAAAGTATCAATTTTCCTTGAAAATAAGCTTTTT
1 AAAAAATATTTTTGAGAAAAAGTTGAAAGTATCAATTTTCCTTGAAAATAAGCTTTCT
*
5911249 AAAAAATA-TTTTGAGAAAAAGTTGAAAGTATCAATTTTCCTTGAAAATAAGCTTTCCA
1 AAAAAATATTTTTGAGAAAAAGTTGAAAGTATCAATTTTCCTTGAAAATAAGCTTT-CT
* *
5911307 AAAAAATATTTTTGAAAAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAG-TTT-T
1 AAAAAATATTTTTGAGAAAAAGTTGAAAGTATCAATTTTCCTTGAAAATAAGCTTTCT
* * * * * *
5911363 CAAAAGTGGATTTTTGAGGAAAAGTTAAAAGTATCAATTTTCCTCGAAATTAAAG-TTTCT
1 AAAAAAT--ATTTTTGAGAAAAAGTTGAAAGTATCAATTTTCCTTGAAAAT-AAGCTTTCT
*
5911423 AAAAAATA-TTTTGGGAAAAAGTTGAAAGTATCAATTTT
1 AAAAAATATTTTTGAGAAAAAGTTGAAAGTATCAATTTT
5911461 TCCTGTACAA
Statistics
Matches: 188, Mismatches: 18, Indels: 13
0.86 0.08 0.06
Matches are distributed among these distances:
56 5 0.03
57 74 0.39
58 56 0.30
59 47 0.25
60 6 0.03
ACGTcount: A:0.44, C:0.07, G:0.13, T:0.36
Consensus pattern (58 bp):
AAAAAATATTTTTGAGAAAAAGTTGAAAGTATCAATTTTCCTTGAAAATAAGCTTTCT
Found at i:5911464 original size:116 final size:116
Alignment explanation
Indices: 5911189--5911460 Score: 383
Period size: 116 Copynumber: 2.4 Consensus size: 116
5911179 AAATAAAATT
* *
5911189 CAAAAAAATATTTTTGAGAAAAAGTTGAAAGTATCAATTTTCCTTGAAAATAAGCTTTTTAAAAA
1 CAAAAAAATATTTTTGAGAAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAGCTTTTCAAAAA
* *
5911254 ATATTTTGAGAAAAAGTTGAAAGTATCAATTTTCCTTGAAAATAAGCTTTC
66 ATATTTTGAGAAAAAGTTAAAAGTATCAATTTTCCTCGAAAATAAGCTTTC
*
5911305 CAAAAAAATATTTTTGAAAAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAG-TTTTC-AAAA
1 CAAAAAAATATTTTTGAGAAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAGCTTTTCAAAAA
* * *
5911368 GTGGATTTTTGAGGAAAAGTTAAAAGTATCAATTTTCCTCGAAATTAAAG-TTT-
66 AT--A-TTTTGAGAAAAAGTTAAAAGTATCAATTTTCCTCGAAAAT-AAGCTTTC
* *
5911421 CTAAAAAATA-TTTTGGGAAAAAGTTGAAAGTATCAATTTT
1 CAAAAAAATATTTTTGAGAAAAAGTTGAAAGTATCAATTTT
5911461 TCCTGTACAA
Statistics
Matches: 141, Mismatches: 11, Indels: 9
0.88 0.07 0.06
Matches are distributed among these distances:
114 5 0.04
115 32 0.23
116 62 0.44
117 39 0.28
118 3 0.02
ACGTcount: A:0.44, C:0.08, G:0.13, T:0.35
Consensus pattern (116 bp):
CAAAAAAATATTTTTGAGAAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAGCTTTTCAAAAA
ATATTTTGAGAAAAAGTTAAAAGTATCAATTTTCCTCGAAAATAAGCTTTC
Found at i:5915420 original size:18 final size:17
Alignment explanation
Indices: 5915395--5915445 Score: 59
Period size: 18 Copynumber: 2.9 Consensus size: 17
5915385 AGTAACGGAT
5915395 AAAAAATGAGAAAAAAA
1 AAAAAATGAGAAAAAAA
* *
5915412 AAGAAAATGATGGAAAAAG
1 AA-AAAATGA-GAAAAAAA
5915431 AAAAAATGA-AAAAAA
1 AAAAAATGAGAAAAAA
5915446 TGGAGAAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
16 5 0.17
17 2 0.07
18 14 0.48
19 8 0.28
ACGTcount: A:0.76, C:0.00, G:0.16, T:0.08
Consensus pattern (17 bp):
AAAAAATGAGAAAAAAA
Found at i:5915445 original size:9 final size:9
Alignment explanation
Indices: 5915431--5915483 Score: 54
Period size: 9 Copynumber: 5.8 Consensus size: 9
5915421 ATGGAAAAAG
5915431 AAAAAATGA
1 AAAAAATGA
5915440 AAAAAATGGA
1 AAAAAAT-GA
*
5915450 GAAAAAAAGA
1 -AAAAAATGA
* *
5915460 AAGAAA-GG
1 AAAAAATGA
5915468 AAAAAATGA
1 AAAAAATGA
5915477 AAAAAAT
1 AAAAAAT
5915484 TTAAATTGAA
Statistics
Matches: 36, Mismatches: 5, Indels: 6
0.77 0.11 0.13
Matches are distributed among these distances:
8 6 0.17
9 20 0.56
10 4 0.11
11 6 0.17
ACGTcount: A:0.75, C:0.00, G:0.17, T:0.08
Consensus pattern (9 bp):
AAAAAATGA
Found at i:5915453 original size:36 final size:37
Alignment explanation
Indices: 5915395--5915483 Score: 94
Period size: 36 Copynumber: 2.4 Consensus size: 37
5915385 AGTAACGGAT
* * *
5915395 AAAAAATGAGAAAAAA-AAAGAAAATGATGGAA-AAA-G
1 AAAAAATGA-AAAAAATAAAGAAAA-AAAGAAAGAAAGG
**
5915431 AAAAAATGAAAAAAATGGAGAAAAAAAGAAAGAAAGG
1 AAAAAATGAAAAAAATAAAGAAAAAAAGAAAGAAAGG
5915468 AAAAAATGAAAAAAAT
1 AAAAAATGAAAAAAAT
5915484 TTAAATTGAA
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
35 10 0.22
36 18 0.40
37 17 0.38
ACGTcount: A:0.74, C:0.00, G:0.18, T:0.08
Consensus pattern (37 bp):
AAAAAATGAAAAAAATAAAGAAAAAAAGAAAGAAAGG
Found at i:5915474 original size:28 final size:26
Alignment explanation
Indices: 5915425--5915482 Score: 73
Period size: 28 Copynumber: 2.2 Consensus size: 26
5915415 AAAATGATGG
5915425 AAAAAGAAAAAATGAAAAAAATGGAGAA
1 AAAAAGAAAAAATGAAAAAAAT-GA-AA
*
5915453 AAAAAGAAAGAAA-GGAAAAAATGAAA
1 AAAAAGAAA-AAATGAAAAAAATGAAA
5915479 AAAA
1 AAAA
5915483 TTTAAATTGA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
26 6 0.21
27 2 0.07
28 17 0.61
29 3 0.11
ACGTcount: A:0.78, C:0.00, G:0.17, T:0.05
Consensus pattern (26 bp):
AAAAAGAAAAAATGAAAAAAATGAAA
Found at i:5916293 original size:63 final size:63
Alignment explanation
Indices: 5916166--5916302 Score: 168
Period size: 63 Copynumber: 2.2 Consensus size: 63
5916156 ATGAAACTGA
* * ** * *
5916166 TGCTGAAAAACTTATGAATGATGACCAAGTGACAAATGATGAAATTTGTTTTGAAATGGCTAG
1 TGCTGAGAAGCTTATGAATGATGACCAAGTGACAAAACATGAAATTTATTTTGAAATGACTAG
* * *
5916229 TGTTGAGAAGCTTATGAGTGATGACCAAGTGA-AAGAACATGAAATTTATTTTGAAATGATTAG
1 TGCTGAGAAGCTTATGAATGATGACCAAGTGACAA-AACATGAAATTTATTTTGAAATGACTAG
*
5916292 TGCTGATAAGC
1 TGCTGAGAAGC
5916303 CTGGCATGTA
Statistics
Matches: 62, Mismatches: 11, Indels: 2
0.83 0.15 0.03
Matches are distributed among these distances:
62 2 0.03
63 60 0.97
ACGTcount: A:0.37, C:0.09, G:0.23, T:0.31
Consensus pattern (63 bp):
TGCTGAGAAGCTTATGAATGATGACCAAGTGACAAAACATGAAATTTATTTTGAAATGACTAG
Found at i:5916741 original size:21 final size:22
Alignment explanation
Indices: 5916706--5916763 Score: 66
Period size: 21 Copynumber: 2.7 Consensus size: 22
5916696 GAATATTTTG
*
5916706 ATGAGAATTTTTGAGAACTC-AA
1 ATGAGAATCTTTGAG-ACTCAAA
**
5916728 ATGAGAA-CTTTGAGTTTCAAA
1 ATGAGAATCTTTGAGACTCAAA
5916749 ATGAGAATCTTTGAG
1 ATGAGAATCTTTGAG
5916764 GAGTGAAACC
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
20 2 0.06
21 15 0.48
22 14 0.45
ACGTcount: A:0.38, C:0.09, G:0.21, T:0.33
Consensus pattern (22 bp):
ATGAGAATCTTTGAGACTCAAA
Found at i:5917014 original size:43 final size:42
Alignment explanation
Indices: 5916947--5917028 Score: 128
Period size: 43 Copynumber: 1.9 Consensus size: 42
5916937 GCCTTTGAAC
* *
5916947 TCAAATGAAAAGCTTTAAATTTTTGGATGTGAATCTCCAAAAT
1 TCAAATGAAAAGCTTTAAACTTTTGGATATGAAT-TCCAAAAT
*
5916990 TCAAATGAAAAGCTTTAGACTTTTGGATATGAATTCCAA
1 TCAAATGAAAAGCTTTAAACTTTTGGATATGAATTCCAA
5917029 GTTTGCCAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
42 5 0.14
43 31 0.86
ACGTcount: A:0.39, C:0.12, G:0.15, T:0.34
Consensus pattern (42 bp):
TCAAATGAAAAGCTTTAAACTTTTGGATATGAATTCCAAAAT
Found at i:5917402 original size:42 final size:42
Alignment explanation
Indices: 5917340--5917754 Score: 304
Period size: 42 Copynumber: 9.8 Consensus size: 42
5917330 AGTAATTTAC
* *
5917340 TTTTCAAAAGTCGTTGAGCCTCTGATTAGAAGAGCTTTAGTCA
1 TTTTC-AAAGTTGTTGAGCCTCTGATTAGAGGAGCTTTAGTCA
* * * * *
5917383 TTTTCAGAGTTTTTAAGCCTCTAATTAGAGGAGTCATTTA--CT
1 TTTTCAAAGTTGTTGAGCCTCTGATTAGAGGAG-C-TTTAGTCA
* * * *
5917425 TTTTAAAAGTTGTTAAGCCTTTGATTAGAAGAGCCATTTA--C-
1 TTTTCAAAGTTGTTGAGCCTCTGATTAGAGGAG-C-TTTAGTCA
* * *
5917466 TTTTCAAAAGTCGTTGAGCCTCTGATTAGATGAGCTTTAGTTA
1 TTTTC-AAAGTTGTTGAGCCTCTGATTAGAGGAGCTTTAGTCA
* *
5917509 TTTTCAAAATTGTTGAGCCTCTGATTAGAGGAGC--TAGTTA
1 TTTTCAAAGTTGTTGAGCCTCTGATTAGAGGAGCTTTAGTCA
* *
5917549 CTTTTCAAAAGTTGTTAAGCCTCTAATTAGAGGAGCCATTTA--C-
1 -TTTTC-AAAGTTGTTGAGCCTCTGATTAGAGGAG-C-TTTAGTCA
* ** *
5917592 TTTTCAAAAGTTGTTGAGCCTTTGATTCTAGGAGCTTTAGTTA
1 TTTTC-AAAGTTGTTGAGCCTCTGATTAGAGGAGCTTTAGTCA
*
5917635 TTTTCAAAGTTGTTGAGCCTCTGATTAGAAGAGCCATTTA--C-
1 TTTTCAAAGTTGTTGAGCCTCTGATTAGAGGAG-C-TTTAGTCA
**
5917676 TTTTCAAAAGTCATTGAGCCTCTGATTAGAGGAGCATTGTTTA-T-A
1 TTTTC-AAAGTTGTTGAGCCTCTGATTAGAGGAGC----TTTAGTCA
*
5917721 TTTTTCAAAGTCGTTGAGCCTCT-ACTTAGAGGAG
1 -TTTTCAAAGTTGTTGAGCCTCTGA-TTAGAGGAG
5917755 TTTTGATCAA
Statistics
Matches: 304, Mismatches: 43, Indels: 48
0.77 0.11 0.12
Matches are distributed among these distances:
40 14 0.05
41 17 0.06
42 210 0.69
43 18 0.06
44 13 0.04
45 25 0.08
46 7 0.02
ACGTcount: A:0.27, C:0.15, G:0.20, T:0.38
Consensus pattern (42 bp):
TTTTCAAAGTTGTTGAGCCTCTGATTAGAGGAGCTTTAGTCA
Found at i:5917444 original size:84 final size:85
Alignment explanation
Indices: 5917334--5917710 Score: 421
Period size: 84 Copynumber: 4.5 Consensus size: 85
5917324 TTAAAGAGTA
* * * *
5917334 ATTTACTTTTCAAAAGTCGTTGAGCCTCTGATTAGAAGAGCTTTAGTCATTTTC-AGAGTTTTTA
1 ATTTACTTTTCAAAAGTTGTTGAGCCTCTGATTAGAGGAGCTTTAGTCATTTTCAAAAGTTGTTA
*
5917398 AGCCTCTAATTAGAGGAGTC
66 AGCCTCTAATTAGAGGAGCC
* * * * *
5917418 ATTTACTTTTTAAAAGTTGTTAAGCCTTTGATTAGAAGAGCCATTTA--C-TTTTCAAAAGTCGT
1 ATTTACTTTTCAAAAGTTGTTGAGCCTCTGATTAGAGGAG-C-TTTAGTCATTTTCAAAAGTTGT
* * * *
5917480 TGAGCCTCTGATTAGATGAGCTTT
64 TAAGCCTCTAATTAGAGGAGC--C
* *
5917504 AGTTA-TTTTCAAAA-TTGTTGAGCCTCTGATTAGAGGAGC--TAGTTACTTTTCAAAAGTTGTT
1 ATTTACTTTTCAAAAGTTGTTGAGCCTCTGATTAGAGGAGCTTTAGTCA-TTTTCAAAAGTTGTT
5917565 AAGCCTCTAATTAGAGGAGCC
65 AAGCCTCTAATTAGAGGAGCC
* ** * *
5917586 ATTTACTTTTCAAAAGTTGTTGAGCCTTTGATTCTAGGAGCTTTAGTTATTTTC-AAAGTTGTTG
1 ATTTACTTTTCAAAAGTTGTTGAGCCTCTGATTAGAGGAGCTTTAGTCATTTTCAAAAGTTGTTA
* *
5917650 AGCCTCTGATTAGAAGAGCC
66 AGCCTCTAATTAGAGGAGCC
**
5917670 ATTTACTTTTCAAAAGTCATTGAGCCTCTGATTAGAGGAGC
1 ATTTACTTTTCAAAAGTTGTTGAGCCTCTGATTAGAGGAGC
5917711 ATTGTTTATA
Statistics
Matches: 245, Mismatches: 35, Indels: 26
0.80 0.11 0.08
Matches are distributed among these distances:
80 2 0.01
82 4 0.02
83 15 0.06
84 196 0.80
85 14 0.06
86 14 0.06
ACGTcount: A:0.28, C:0.15, G:0.19, T:0.38
Consensus pattern (85 bp):
ATTTACTTTTCAAAAGTTGTTGAGCCTCTGATTAGAGGAGCTTTAGTCATTTTCAAAAGTTGTTA
AGCCTCTAATTAGAGGAGCC
Found at i:5917552 original size:126 final size:126
Alignment explanation
Indices: 5917334--5917710 Score: 540
Period size: 126 Copynumber: 3.0 Consensus size: 126
5917324 TTAAAGAGTA
* * * *
5917334 ATTTACTTTTCAAAAGTCGTTGAGCCTCTGATTAGAAGAGCTTTAGTCATTTTCAGAGTTTTTAA
1 ATTTACTTTTCAAAAGTCGTTGAGCCTCTGATTAGAAGAGCTTTAGTTATTTTCAAAGTTGTTGA
* * * *
5917399 GCCTCTAATTAGAGGAG-TCATTTACTTTTTAAAAGTTGTTAAGCCTTTGATTAGAAGAGCC
66 GCCTCTGATTAGAGGAGCT-ATTTACTTTTCAAAAGTTGTTAAGCCTCTGATTAGAGGAGCC
* *
5917460 ATTTACTTTTCAAAAGTCGTTGAGCCTCTGATTAGATGAGCTTTAGTTATTTTCAAAATTGTTGA
1 ATTTACTTTTCAAAAGTCGTTGAGCCTCTGATTAGAAGAGCTTTAGTTATTTTCAAAGTTGTTGA
* *
5917525 GCCTCTGATTAGAGGAGCTAGTTACTTTTCAAAAGTTGTTAAGCCTCTAATTAGAGGAGCC
66 GCCTCTGATTAGAGGAGCTATTTACTTTTCAAAAGTTGTTAAGCCTCTGATTAGAGGAGCC
* * ** *
5917586 ATTTACTTTTCAAAAGTTGTTGAGCCTTTGATTCTAGGAGCTTTAGTTATTTTCAAAGTTGTTGA
1 ATTTACTTTTCAAAAGTCGTTGAGCCTCTGATTAGAAGAGCTTTAGTTATTTTCAAAGTTGTTGA
* * ** *
5917651 GCCTCTGATTAGAAGAGCCATTTACTTTTCAAAAGTCATTGAGCCTCTGATTAGAGGAGC
66 GCCTCTGATTAGAGGAGCTATTTACTTTTCAAAAGTTGTTAAGCCTCTGATTAGAGGAGC
5917711 ATTGTTTATA
Statistics
Matches: 225, Mismatches: 25, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
126 224 1.00
127 1 0.00
ACGTcount: A:0.28, C:0.15, G:0.19, T:0.38
Consensus pattern (126 bp):
ATTTACTTTTCAAAAGTCGTTGAGCCTCTGATTAGAAGAGCTTTAGTTATTTTCAAAGTTGTTGA
GCCTCTGATTAGAGGAGCTATTTACTTTTCAAAAGTTGTTAAGCCTCTGATTAGAGGAGCC
Found at i:5917967 original size:30 final size:32
Alignment explanation
Indices: 5917933--5917996 Score: 78
Period size: 34 Copynumber: 2.0 Consensus size: 32
5917923 GTAGGCCCAT
*
5917933 TTTG-TTTTTGT-TTTTTTTTTTATTTTTTAT
1 TTTGTTTTTTGTATTTTTTTTTTATTCTTTAT
*
5917963 TTTGTATTTTTTGTATTTTTTTTTTCTTCTTTAT
1 TTTG--TTTTTTGTATTTTTTTTTTATTCTTTAT
5917997 ATCTTATGTA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
30 4 0.14
33 7 0.25
34 17 0.61
ACGTcount: A:0.08, C:0.03, G:0.06, T:0.83
Consensus pattern (32 bp):
TTTGTTTTTTGTATTTTTTTTTTATTCTTTAT
Found at i:5918016 original size:4 final size:4
Alignment explanation
Indices: 5918007--5918167 Score: 66
Period size: 4 Copynumber: 39.5 Consensus size: 4
5917997 ATCTTATGTA
*
5918007 TTAT TTAT TTAT TTAT TTA- TTAT TACTAT TTAT TAATAT ATAT TTAT
1 TTAT TTAT TTAT TTAT TTAT TTAT T--TAT TTAT T--TAT TTAT TTAT
* * * * * * *
5918054 TTTT TTAAT GTTAAT ATAT ATAT TTA- TTA- TTAC TTAG CTAT TTAT ATA-
1 TTAT TT-AT -TT-AT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT
* * * *
5918102 TTAT TATAT ATAT GTAT TTA- TTA- TTAT TTAT CTAT TTAT ATAT TATAAT
1 TTAT T-TAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT T-T-AT
*
5918151 TTAT CTA- TTAT TTAT TT
1 TTAT TTAT TTAT TTAT TT
5918168 TTATTTTTTT
Statistics
Matches: 122, Mismatches: 21, Indels: 28
0.71 0.12 0.16
Matches are distributed among these distances:
3 19 0.16
4 81 0.66
5 7 0.06
6 15 0.12
ACGTcount: A:0.32, C:0.03, G:0.02, T:0.63
Consensus pattern (4 bp):
TTAT
Found at i:5918030 original size:22 final size:22
Alignment explanation
Indices: 5917992--5918236 Score: 92
Period size: 22 Copynumber: 11.5 Consensus size: 22
5917982 TTTTTTCTTC
*
5917992 TTTA-TATCTTATGTATTATTTA
1 TTTATTAT-TTATCTATTATTTA
*
5918014 TTTATTTATTTAT-TATTA-CTA
1 TTTA-TTATTTATCTATTATTTA
* * *
5918035 TTTATTA-ATATATATTTATTTT
1 TTTATTATTTATCTA-TTATTTA
* * * *
5918057 TTTAATGTTAATATATATATTTA
1 TTTATTATTTATCTAT-TATTTA
* *
5918080 -TTATTACTTAGC---TATTTA
1 TTTATTATTTATCTATTATTTA
* *
5918098 TATATTATTATATATATGTATTTA
1 TTTATTATT-TATCTAT-TATTTA
*
5918122 -TTATTATTTATCTATT-TATA
1 TTTATTATTTATCTATTATTTA
*
5918142 TATTATAATTTATCTATTATTTA
1 T-TTATTATTTATCTATTATTTA
* * * *
5918165 TTT-TTATTTTTTTGTTA-ATA
1 TTTATTATTTATCTATTATTTA
*
5918185 TTT-TGATTTATCTGATTATTT-
1 TTTATTATTTATCT-ATTATTTA
* *
5918206 TATT-TTAATTATCTATTA-ATA
1 T-TTATTATTTATCTATTATTTA
5918227 TTT-TTATTTA
1 TTTATTATTTA
5918237 ATTTTTATTT
Statistics
Matches: 165, Mismatches: 38, Indels: 42
0.67 0.16 0.17
Matches are distributed among these distances:
18 6 0.04
19 9 0.05
20 31 0.19
21 29 0.18
22 56 0.34
23 25 0.15
24 9 0.05
ACGTcount: A:0.30, C:0.03, G:0.03, T:0.64
Consensus pattern (22 bp):
TTTATTATTTATCTATTATTTA
Done.