Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005073.1 Hibiscus syriacus cultivar Beakdansim tig00011391_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 66545
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:11576 original size:19 final size:20
Alignment explanation
Indices: 11544--11581 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
11534 AATTAAACAA
*
11544 AAATTAAGATCAAATTTATT
1 AAATTAAGATCAAAATTATT
11564 AAATTAA-ATCAAAATTAT
1 AAATTAAGATCAAAATTAT
11582 AACCCCATGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.55, C:0.05, G:0.03, T:0.37
Consensus pattern (20 bp):
AAATTAAGATCAAAATTATT
Found at i:14488 original size:13 final size:13
Alignment explanation
Indices: 14470--14515 Score: 56
Period size: 13 Copynumber: 3.3 Consensus size: 13
14460 GTCATAACCC
14470 GACCCGACCCGTT
1 GACCCGACCCGTT
*
14483 GACCCGACCCATT
1 GACCCGACCCGTT
14496 GACCCGTTGACCCGTT
1 GACCC---GACCCGTT
14512 GACC
1 GACC
14516 GTTGACCGGC
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
13 17 0.61
16 11 0.39
ACGTcount: A:0.17, C:0.43, G:0.22, T:0.17
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:14523 original size:7 final size:8
Alignment explanation
Indices: 14475--14522 Score: 59
Period size: 8 Copynumber: 6.5 Consensus size: 8
14465 AACCCGACCC
14475 GACCCGTT
1 GACCCGTT
14483 GACCC---
1 GACCCGTT
*
14488 GACCCATT
1 GACCCGTT
14496 GACCCGTT
1 GACCCGTT
14504 GACCCGTT
1 GACCCGTT
14512 GA-CCGTT
1 GACCCGTT
14519 GACC
1 GACC
14523 GGCTTTGACC
Statistics
Matches: 35, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
5 5 0.14
7 7 0.20
8 23 0.66
ACGTcount: A:0.17, C:0.40, G:0.23, T:0.21
Consensus pattern (8 bp):
GACCCGTT
Found at i:17063 original size:24 final size:24
Alignment explanation
Indices: 17036--17151 Score: 137
Period size: 24 Copynumber: 4.8 Consensus size: 24
17026 TTTTATTTGA
17036 ATTCTGATCTGATACTTGACATGG
1 ATTCTGATCTGATACTTGACATGG
17060 ATTCTGATCTGATA-TCTGACATGG
1 ATTCTGATCTGATACT-TGACATGG
* * *
17084 ATTTTGATATGATACTTGACTTGG
1 ATTCTGATCTGATACTTGACATGG
* *
17108 ATTCTGATCTGTTACTTGACCT-G
1 ATTCTGATCTGATACTTGACATGG
* *
17131 ATTTATGATATGATACTTGAC
1 A-TTCTGATCTGATACTTGAC
17152 CTGATTTATG
Statistics
Matches: 79, Mismatches: 10, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
23 3 0.04
24 75 0.95
25 1 0.01
ACGTcount: A:0.25, C:0.15, G:0.19, T:0.41
Consensus pattern (24 bp):
ATTCTGATCTGATACTTGACATGG
Found at i:17097 original size:48 final size:48
Alignment explanation
Indices: 17040--17151 Score: 156
Period size: 48 Copynumber: 2.3 Consensus size: 48
17030 ATTTGAATTC
*
17040 TGATCTGATACTTGACATGGATTCTGATCTGATA-TCTGACATGGATTT-
1 TGATATGATACTTGACATGGATTCTGATCTGATACT-TGACAT-GATTTA
* * *
17088 TGATATGATACTTGACTTGGATTCTGATCTGTTACTTGACCTGATTTA
1 TGATATGATACTTGACATGGATTCTGATCTGATACTTGACATGATTTA
17136 TGATATGATACTTGAC
1 TGATATGATACTTGAC
17152 CTGATTTATG
Statistics
Matches: 58, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
47 5 0.09
48 52 0.90
49 1 0.02
ACGTcount: A:0.25, C:0.14, G:0.20, T:0.41
Consensus pattern (48 bp):
TGATATGATACTTGACATGGATTCTGATCTGATACTTGACATGATTTA
Found at i:19485 original size:22 final size:23
Alignment explanation
Indices: 19459--19507 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 23
19449 TCGAAATTCT
*
19459 TTTATTGTCTTTAAATTT-TATA
1 TTTATTGTATTTAAATTTATATA
* *
19481 TTTATTTTATTTTAATTTATATA
1 TTTATTGTATTTAAATTTATATA
19504 TTTA
1 TTTA
19508 AAGATTGGAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 15 0.65
23 8 0.35
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.67
Consensus pattern (23 bp):
TTTATTGTATTTAAATTTATATA
Found at i:21747 original size:15 final size:16
Alignment explanation
Indices: 21715--21747 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
21705 TCTAACATGA
*
21715 TAAAATTAAAATATAT
1 TAAAAATAAAATATAT
21731 TAAAAATAAAA-ATAT
1 TAAAAATAAAATATAT
21746 TA
1 TA
21748 TTTTGATCAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (16 bp):
TAAAAATAAAATATAT
Found at i:24398 original size:46 final size:47
Alignment explanation
Indices: 24339--24432 Score: 181
Period size: 46 Copynumber: 2.0 Consensus size: 47
24329 TTTAGCTTGA
24339 ATAGGAAGAGATGTGATGAATAAT-AGTGGAAACGTGGATTGAAATG
1 ATAGGAAGAGATGTGATGAATAATCAGTGGAAACGTGGATTGAAATG
24385 ATAGGAAGAGATGTGATGAATAATCAGTGGAAACGTGGATTGAAATG
1 ATAGGAAGAGATGTGATGAATAATCAGTGGAAACGTGGATTGAAATG
24432 A
1 A
24433 AAGCCATTTT
Statistics
Matches: 47, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
46 24 0.51
47 23 0.49
ACGTcount: A:0.41, C:0.03, G:0.32, T:0.23
Consensus pattern (47 bp):
ATAGGAAGAGATGTGATGAATAATCAGTGGAAACGTGGATTGAAATG
Found at i:29069 original size:17 final size:18
Alignment explanation
Indices: 29033--29070 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
29023 TAATATCTAA
*
29033 TATAATATGCAATGTTATT
1 TATAACATGCAA-GTTATT
29052 TATAACATGCAA-TTATT
1 TATAACATGCAAGTTATT
29069 TA
1 TA
29071 ATATGAAACT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 7 0.39
19 11 0.61
ACGTcount: A:0.39, C:0.08, G:0.08, T:0.45
Consensus pattern (18 bp):
TATAACATGCAAGTTATT
Found at i:29752 original size:43 final size:42
Alignment explanation
Indices: 29705--29820 Score: 151
Period size: 43 Copynumber: 2.7 Consensus size: 42
29695 AGTGGTTTTA
*
29705 ACTGATCCAACTCCTTCTCTGAAGAATCAAATGAAATATTGTT
1 ACTGATCCAACTCCTTCTCTGAAG-ATCAAATGAAACATTGTT
* * *
29748 ACTGATCTAACTCCTTTTTTGAATGATCAAATGAAACATTGTT
1 ACTGATCCAACTCCTTCTCTGAA-GATCAAATGAAACATTGTT
* *
29791 ACTGATCCAACTTCTTCTGTGAAGGATCAA
1 ACTGATCCAACTCCTTCTCTGAA-GATCAA
29821 GTAACATGAC
Statistics
Matches: 63, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
43 62 0.98
44 1 0.02
ACGTcount: A:0.33, C:0.20, G:0.13, T:0.34
Consensus pattern (42 bp):
ACTGATCCAACTCCTTCTCTGAAGATCAAATGAAACATTGTT
Found at i:30473 original size:13 final size:13
Alignment explanation
Indices: 30455--30479 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
30445 GTTCCACCTC
30455 ATGGTTTCATCTT
1 ATGGTTTCATCTT
30468 ATGGTTTCATCT
1 ATGGTTTCATCT
30480 CACGTTCGAA
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:0.16, C:0.16, G:0.16, T:0.52
Consensus pattern (13 bp):
ATGGTTTCATCTT
Found at i:30638 original size:14 final size:13
Alignment explanation
Indices: 30620--30721 Score: 87
Period size: 13 Copynumber: 7.2 Consensus size: 13
30610 CGGGTTTTCA
30620 CTTTTTTTTCTTT
1 CTTTTTTTTCTTT
*
30633 CATTTTTTTCTTCCT
1 CTTTTTTTTCTT--T
*
30648 CTTTGTTTTCTCTT
1 CTTTTTTTTCT-TT
*
30662 CTTTTTCTTGTTCTCT
1 C-TTTT-TT-TTCTTT
30678 CTTTATTTTTCTTT
1 CTTT-TTTTTCTTT
30692 CTTTTTCTTTCTTT
1 CTTTTT-TTTCTTT
* *
30706 CATTTCTTTCTTT
1 CTTTTTTTTCTTT
30719 CTT
1 CTT
30722 CCACTTTGTT
Statistics
Matches: 72, Mismatches: 9, Indels: 16
0.74 0.09 0.16
Matches are distributed among these distances:
13 22 0.31
14 22 0.31
15 18 0.25
16 6 0.08
17 4 0.06
ACGTcount: A:0.03, C:0.22, G:0.02, T:0.74
Consensus pattern (13 bp):
CTTTTTTTTCTTT
Found at i:30694 original size:4 final size:4
Alignment explanation
Indices: 30685--30721 Score: 51
Period size: 4 Copynumber: 9.5 Consensus size: 4
30675 TCTCTTTATT
30685 TTTC TTTC -TT- TTTC TTTC TTTC ATTTC TTTC TTTC TT
1 TTTC TTTC TTTC TTTC TTTC TTTC -TTTC TTTC TTTC TT
30722 CCACTTTGTT
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
3 4 0.13
4 22 0.73
5 4 0.13
ACGTcount: A:0.03, C:0.22, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTC
Found at i:30694 original size:30 final size:28
Alignment explanation
Indices: 30620--30721 Score: 102
Period size: 28 Copynumber: 3.6 Consensus size: 28
30610 CGGGTTTTCA
30620 CTTTTTTTTCTTTCATTTTT-TTCTTCCT
1 CTTTTTTTTCTTTC-TTTTTCTTCTTCCT
* *
30648 CTTTGTTTTCTCTTCTTTTTCTTGTTCTCT
1 CTTTTTTTTCT-TTCTTTTTCTTCTTC-CT
30678 CTTTATTTTTCTTTCTTTTTCTTTCTT--T
1 CTTT-TTTTTCTTTCTTTTTC-TTCTTCCT
* *
30706 CATTTCTTTCTTTCTT
1 CTTTTTTTTCTTTCTT
30722 CCACTTTGTT
Statistics
Matches: 63, Mismatches: 6, Indels: 11
0.79 0.08 0.14
Matches are distributed among these distances:
27 11 0.17
28 19 0.30
29 8 0.13
30 15 0.24
31 10 0.16
ACGTcount: A:0.03, C:0.22, G:0.02, T:0.74
Consensus pattern (28 bp):
CTTTTTTTTCTTTCTTTTTCTTCTTCCT
Found at i:30699 original size:24 final size:24
Alignment explanation
Indices: 30665--30784 Score: 77
Period size: 24 Copynumber: 5.0 Consensus size: 24
30655 TTCTCTTCTT
*
30665 TTTCTTGTTCTCTCTTTATTTTTC
1 TTTCTTTTTCTCTCTTTATTTTTC
*
30689 TTTCTTTTTCTTTCTTTCA--TTTC
1 TTTCTTTTTCTCTCTTT-ATTTTTC
* *
30712 TTTCTTTCTTC-CACTTT-GTTTTC
1 TTTCTTT-TTCTCTCTTTATTTTTC
* * *
30735 TCTTCTTTTTCTGTTTTTCTTTCTTC
1 T-TTCTTTTTCTCTCTTTATTT-TTC
* * *
30761 TTCTGTTTTTCTTTATTTATTTTT
1 TT-TCTTTTTCTCTCTTTATTTTT
30785 TTGAAAACTG
Statistics
Matches: 75, Mismatches: 12, Indels: 17
0.72 0.12 0.16
Matches are distributed among these distances:
23 23 0.31
24 27 0.36
25 6 0.08
26 19 0.25
ACGTcount: A:0.04, C:0.20, G:0.03, T:0.72
Consensus pattern (24 bp):
TTTCTTTTTCTCTCTTTATTTTTC
Found at i:30702 original size:10 final size:10
Alignment explanation
Indices: 30620--30705 Score: 63
Period size: 10 Copynumber: 8.8 Consensus size: 10
30610 CGGGTTTTCA
30620 CTTT-TTTTT
1 CTTTCTTTTT
*
30629 CTTTCATTTT
1 CTTTCTTTTT
**
30639 -TTTCTTCCT
1 CTTTCTTTTT
*
30648 CTTT-GTTTT
1 CTTTCTTTTT
30657 CTCTTCTTTTT
1 CT-TTCTTTTT
* *
30668 CTTGT-TCTCT
1 CTT-TCTTTTT
*
30678 CTTTATTTTT
1 CTTTCTTTTT
30688 CTTTCTTTTT
1 CTTTCTTTTT
30698 CTTTCTTT
1 CTTTCTTT
30706 CATTTCTTTC
Statistics
Matches: 58, Mismatches: 13, Indels: 11
0.71 0.16 0.13
Matches are distributed among these distances:
9 15 0.26
10 36 0.62
11 7 0.12
ACGTcount: A:0.02, C:0.21, G:0.02, T:0.74
Consensus pattern (10 bp):
CTTTCTTTTT
Found at i:30728 original size:23 final size:23
Alignment explanation
Indices: 30685--30746 Score: 63
Period size: 23 Copynumber: 2.7 Consensus size: 23
30675 TCTCTTTATT
**
30685 TTTCTTTCTTTTTCTTTCTTTCA
1 TTTCTTTCTTTTTCTCACTTTCA
**
30708 TTTCTTTCTTTCTTC-CACTTTGT
1 TTTCTTTCTTT-TTCTCACTTTCA
30731 TTTCTCTTCTTTTTCT
1 TTTCT-TTCTTTTTCT
30747 GTTTTTCTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
23 23 0.72
24 9 0.28
ACGTcount: A:0.03, C:0.24, G:0.02, T:0.71
Consensus pattern (23 bp):
TTTCTTTCTTTTTCTCACTTTCA
Found at i:30742 original size:14 final size:13
Alignment explanation
Indices: 30622--30744 Score: 55
Period size: 13 Copynumber: 9.4 Consensus size: 13
30612 GGTTTTCACT
30622 TTTTTTTCT-TTC
1 TTTTTTTCTCTTC
*
30634 ATTTTTTTCTTCCTC
1 -TTTTTTTC-TCTTC
30649 TTTGTTTTCTCTTC
1 TTT-TTTTCTCTTC
*
30663 TTTTTCTTGTTCTCTC
1 TTTTT-TT-CTCT-TC
30679 TTTATTTT-TCTT-
1 TTT-TTTTCTCTTC
*
30691 TCTTTTTCT-TTC
1 TTTTTTTCTCTTC
*
30703 TTTCATTTCT-TTC
1 TTT-TTTTCTCTTC
* *
30716 -TTTCTTC-C-AC
1 TTTTTTTCTCTTC
30726 TTTGTTTTCTCTTC
1 TTT-TTTTCTCTTC
30740 TTTTT
1 TTTTT
30745 CTGTTTTTCT
Statistics
Matches: 84, Mismatches: 11, Indels: 30
0.67 0.09 0.24
Matches are distributed among these distances:
10 1 0.01
11 11 0.13
12 11 0.13
13 22 0.26
14 20 0.24
15 10 0.12
16 7 0.08
17 2 0.02
ACGTcount: A:0.03, C:0.22, G:0.02, T:0.72
Consensus pattern (13 bp):
TTTTTTTCTCTTC
Found at i:30757 original size:23 final size:21
Alignment explanation
Indices: 30677--30759 Score: 62
Period size: 23 Copynumber: 3.7 Consensus size: 21
30667 TCTTGTTCTC
*
30677 TCTTTATT-TTTCTTTCTTTT
1 TCTTTTTTCTTTCTTTCTTTT
30697 TCTTTCTTTCATTTCTTTCTTTCT
1 TCTTT-TTTC-TTTCTTTCTTT-T
* *
30721 TCCACTTTGT-TTTCTCTTCTTTT
1 T-C-TTTTTTCTTTCT-TTCTTTT
30744 TCTGTTTTTCTTTCTT
1 TCT-TTTTTCTTTCTT
30760 CTTCTGTTTT
Statistics
Matches: 49, Mismatches: 5, Indels: 16
0.70 0.07 0.23
Matches are distributed among these distances:
20 5 0.10
21 2 0.04
22 6 0.12
23 23 0.47
24 8 0.16
25 3 0.06
26 2 0.04
ACGTcount: A:0.04, C:0.22, G:0.02, T:0.72
Consensus pattern (21 bp):
TCTTTTTTCTTTCTTTCTTTT
Found at i:31501 original size:6 final size:7
Alignment explanation
Indices: 31453--31510 Score: 62
Period size: 7 Copynumber: 7.7 Consensus size: 7
31443 TAAACCCTCA
*
31453 TTTTCAT
1 TTTTTAT
*
31460 TTTGTTTT
1 TTT-TTAT
31468 TTTTCTAT
1 TTTT-TAT
31476 TGTTTCTAT
1 T-TTT-TAT
31485 TTTTTAT
1 TTTTTAT
31492 TTTTTAT
1 TTTTTAT
31499 TTTTTAT
1 TTTTTAT
31506 TTTTT
1 TTTTT
31511 CTTCTTTCTT
Statistics
Matches: 45, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
7 26 0.58
8 11 0.24
9 8 0.18
ACGTcount: A:0.10, C:0.05, G:0.03, T:0.81
Consensus pattern (7 bp):
TTTTTAT
Found at i:31766 original size:5 final size:5
Alignment explanation
Indices: 31752--31827 Score: 54
Period size: 5 Copynumber: 15.6 Consensus size: 5
31742 TGGCGACATA
* * * *
31752 TTTC- TTTCT TTTCT TTTCT TTTAT TTT-T TTTCA TTTCA TTTCA TTTCAT
1 TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT TTTC-T
31801 TTT-T CTTT-T TTTCT TTT-T CTTTCT TTT
1 TTTCT -TTTCT TTTCT TTTCT -TTTCT TTT
31828 ATTCTTCAAG
Statistics
Matches: 62, Mismatches: 3, Indels: 13
0.79 0.04 0.17
Matches are distributed among these distances:
4 13 0.21
5 45 0.73
6 4 0.06
ACGTcount: A:0.07, C:0.16, G:0.00, T:0.78
Consensus pattern (5 bp):
TTTCT
Found at i:31813 original size:15 final size:15
Alignment explanation
Indices: 31752--31827 Score: 63
Period size: 14 Copynumber: 5.2 Consensus size: 15
31742 TGGCGACATA
*
31752 TTTCTTTCT-TTTCT
1 TTTCTTTTTCTTTCT
31766 TTTCTTTTAT-TTT-T
1 TTTCTTTT-TCTTTCT
* *
31780 TTTC-ATTTCATTTCA
1 TTTCTTTTTC-TTTCT
31795 TTTCATTTTTCTTT-T
1 TTTC-TTTTTCTTTCT
31810 TTTCTTTTTCTTTCT
1 TTTCTTTTTCTTTCT
31825 TTT
1 TTT
31828 ATTCTTCAAG
Statistics
Matches: 50, Mismatches: 5, Indels: 13
0.74 0.07 0.19
Matches are distributed among these distances:
12 1 0.02
13 2 0.04
14 24 0.48
15 16 0.32
16 3 0.06
17 4 0.08
ACGTcount: A:0.07, C:0.16, G:0.00, T:0.78
Consensus pattern (15 bp):
TTTCTTTTTCTTTCT
Found at i:32640 original size:16 final size:16
Alignment explanation
Indices: 32619--32660 Score: 59
Period size: 16 Copynumber: 2.6 Consensus size: 16
32609 AAAAATGAAG
*
32619 AATAAA-AATAAGTAAA
1 AATAAATAA-AAGGAAA
32635 AATAAATAAAAGGAAA
1 AATAAATAAAAGGAAA
32651 AATAAATAAA
1 AATAAATAAA
32661 TAAATGAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
16 22 0.92
17 2 0.08
ACGTcount: A:0.76, C:0.00, G:0.07, T:0.17
Consensus pattern (16 bp):
AATAAATAAAAGGAAA
Found at i:32676 original size:2 final size:2
Alignment explanation
Indices: 32669--32693 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
32659 AATAAATGAA
32669 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 A
32694 AATGAGTAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:33001 original size:19 final size:19
Alignment explanation
Indices: 32970--33007 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
32960 ATATATATAT
*
32970 ATATATATATAAATAATAA
1 ATATATATATAAAAAATAA
32989 ATATAGTAT-TAAAAAATAA
1 ATATA-TATATAAAAAATAA
33008 CCAAATGAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 14 0.82
20 3 0.18
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (19 bp):
ATATATATATAAAAAATAA
Found at i:34616 original size:106 final size:106
Alignment explanation
Indices: 34306--36521 Score: 3069
Period size: 106 Copynumber: 21.0 Consensus size: 106
34296 CATTGTTCCA
* * * **** * *
34306 AGTCCAATATCCTCCGTCGTGAAGTTTAAATTGGCTCTGAAACCAAGAAATTATTTGTTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAAC
* * * * * *
34371 CAGCCGTCCCTTCGTTGTGAAATTGAACTTGTGTTATCTCG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * * * * *
34412 AGTCCAATATCATTCGCTGTGAAGTTGAAATTGACTCTG-AA-T--GAAA-T-TTTGTTGATAAT
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAAC
* * * * *
34471 CAGCCGCCCCTTCATCGTGAAGTTGAGCTTGTGTTGTCTTGG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTC-TGG
* * *
34513 -GTCCAAGATCCTTCGTTGAGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAAC
*
34577 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* *
34618 AGTCCAATATCCTAT-GCTGTGAAGTTGAAATTGGCTCTAAAATTGGGAAATTGTTTATTGACAA
1 AGTCCAATATCCT-TCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
* * *
34682 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTATCTAG
65 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * * * * *
34724 AGTCCAATATCCTTTGTTGTGAAGTTGAAATTGACTCTAAAATTGAGAAGTTGTTTGTTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAAC
*
34789 CAGTGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* *
34830 AGTCCAATATTCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAAC
* *
34895 CAACGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * * *
34936 AGTCCAATATCCTTCGCTGTGAAATTGAAATTGGCTCTGAAATTAGGAAATTGTTTGTTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAAC
35001 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * * *
35042 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTGTGAAATTGAGAAGTTGTTTGTTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAAC
* *
35107 CAGTGGTCCCTTTGTCGTGAAGTTGAACTTGCGTTGTCTGG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * * *
35148 AGTTCAATATCCTTCGCTGTGAAGTTGAAATTGGTTCTGAAATTGGGAAGTTGTTTATTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAAC
* *
35213 CAGCGGTCCCTTTGTCGTGAA---G---TTGCGTTGTCTTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * *
35248 AGTCCAATATCCTACGCTGTGAAGTTGAAATTGGCTCTGAAATTAGGAAATTGTTTATTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAAC
* * *
35313 TAGAGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * *
35354 AGTCCAATATCCTTCGTTGTAAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTGTTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAAC
*
35419 CAGCGGTCCCTTCGTCATGAAGTTGAACTTGCGTTGTCTGG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * * * * *
35460 AGTCCAATATCCTTCGATGCGAAGTTGAAATTGGCTTTTAAATTGGGAAGTTGTTTATTGACAAT
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAAC
*
35525 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * * *
35566 AGTCTAATATCTTTCGCTGTGAAGTTAAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAAC
* * *
35631 CAGCGGCCCCTTCGTCGTGGAGTTGAATTTGCGTTGTCTGG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * *
35672 AGTCCAATATCCTTCGTTATGAAGTTGAAATTGGCTCTAAAATTGGGAAGTTGTTTATTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAAC
* *
35737 CAGCGGTCCCTTCTTCGTGAAGTTGAACTTGCGTTGTCTTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* *
35778 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTATTTATTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAAC
* * *
35843 CAGCGGTCCCTTCATCGTGAAGTTGAACTTGCATTGTCTAG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* ** * * *
35884 AGTCCAATATCCTTCGTTGTGAAGTTGGAATTGGCTCTGAAATTAAGAAGTTATTTGTTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAAC
*
35949 CAGCGGTCCCTTCGTTGTGAAGTTGAACTTGCGTTGTCTGG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* *
35990 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTATTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAAC
* *
36055 CAGTGGTCCCTTCATCGTGAAGTTGAACTTGCGTTGTCTGG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * * * *
36096 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTATAAAATTGAGAAGTTGTTTGTTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAAC
* *
36161 CAGCGGTCCTTTCGTCGTGAAGTTGAACTTACGTTGTCTGG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
*
36202 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATT-GGAAAGTTGTTTATTGACAA
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAA-TTGTTTATTGACAA
* * *** *
36266 GCAGCGTTTTTTTCGTCGTGAAGTTGAACTTGTGTTGTCTGG
65 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * *
36308 AGTCCAATATCCTTCGTTGTGAAGTAGAAATTGGCTATGAAATTGGGAAATTATTTATTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAAC
**
36373 CAGTAGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * * *
36414 AGTCCAATATCCTTCGATGTGAAGTTGAAATTGGCTCAGAAATTGGAAAATTG-TTGTTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAAC
* * * * * *
36478 TAGCCGTCGCTTCGTTGTGAAGTTGAACTTGTGTTGTCTTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
36519 AGT
1 AGT
36522 GGCACGATAT
Statistics
Matches: 1881, Mismatches: 211, Indels: 37
0.88 0.10 0.02
Matches are distributed among these distances:
100 165 0.09
101 5 0.00
102 5 0.00
103 2 0.00
104 3 0.00
105 56 0.03
106 1639 0.87
107 6 0.00
ACGTcount: A:0.24, C:0.17, G:0.24, T:0.35
Consensus pattern (106 bp):
AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAAC
CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
Found at i:37351 original size:22 final size:22
Alignment explanation
Indices: 37324--37444 Score: 197
Period size: 22 Copynumber: 5.5 Consensus size: 22
37314 TTATGTTTGA
37324 TCAAAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
37346 TCAAAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
*
37368 TCAAAGGTTTGGTATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
*
37390 TCAAAGGTTTGGCATTTGATAC
1 TCAAAGGTTTGGCATTTGATGC
* *
37412 TCATAGGTTTGGCATCTGATGC
1 TCAAAGGTTTGGCATTTGATGC
*
37434 TCAATGGTTTG
1 TCAAAGGTTTG
37445 ATGGGGTAGC
Statistics
Matches: 91, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 91 1.00
ACGTcount: A:0.22, C:0.13, G:0.26, T:0.38
Consensus pattern (22 bp):
TCAAAGGTTTGGCATTTGATGC
Found at i:38062 original size:22 final size:22
Alignment explanation
Indices: 38037--38117 Score: 83
Period size: 23 Copynumber: 3.5 Consensus size: 22
38027 CTTTTTCTCC
*
38037 CTTTTTCTTTTGATTTTTGCTT
1 CTTTTTTTTTTGATTTTTGCTT
* *
38059 CTTTTCTTTTTTG-TTCTTGATT
1 CTTTT-TTTTTTGATTTTTGCTT
38081 CTCTTTTTTATTTGATTTTTGCTT
1 CT-TTTTTT-TTTGATTTTTGCTT
*
38105 CTTTACTTTTTTG
1 CTTT-TTTTTTTG
38118 TTCTTGATTG
Statistics
Matches: 48, Mismatches: 6, Indels: 9
0.76 0.10 0.14
Matches are distributed among these distances:
22 17 0.35
23 19 0.40
24 12 0.25
ACGTcount: A:0.06, C:0.14, G:0.09, T:0.72
Consensus pattern (22 bp):
CTTTTTTTTTTGATTTTTGCTT
Found at i:38075 original size:15 final size:15
Alignment explanation
Indices: 38050--38122 Score: 51
Period size: 16 Copynumber: 4.7 Consensus size: 15
38040 TTTCTTTTGA
38050 TTTTTGCTTCTTTTCT
1 TTTTTG-TTCTTTTCT
38066 TTTTTGTTCTTGATTCT
1 TTTTTGTTCTT--TTCT
* * **
38083 CTTTT-TT-ATTTGA
1 TTTTTGTTCTTTTCT
*
38096 TTTTTGCTTCTTTACT
1 TTTTTG-TTCTTTTCT
38112 TTTTTGTTCTT
1 TTTTTGTTCTT
38123 GATTGGATCT
Statistics
Matches: 43, Mismatches: 9, Indels: 11
0.68 0.14 0.17
Matches are distributed among these distances:
13 6 0.14
15 13 0.30
16 16 0.37
17 8 0.19
ACGTcount: A:0.05, C:0.14, G:0.08, T:0.73
Consensus pattern (15 bp):
TTTTTGTTCTTTTCT
Found at i:38100 original size:46 final size:46
Alignment explanation
Indices: 38037--38126 Score: 155
Period size: 46 Copynumber: 2.0 Consensus size: 46
38027 CTTTTTCTCC
*
38037 CTTTTTCTTTTGATTTTTGCTTCTTTTCTTTTTTGTTCTTGATTCT
1 CTTTTTCTTTTGATTTTTGCTTCTTTACTTTTTTGTTCTTGATTCT
38083 CTTTTT-TATTTGATTTTTGCTTCTTTACTTTTTTGTTCTTGATT
1 CTTTTTCT-TTTGATTTTTGCTTCTTTACTTTTTTGTTCTTGATT
38127 GGATCTTCGC
Statistics
Matches: 42, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
45 1 0.02
46 41 0.98
ACGTcount: A:0.07, C:0.13, G:0.09, T:0.71
Consensus pattern (46 bp):
CTTTTTCTTTTGATTTTTGCTTCTTTACTTTTTTGTTCTTGATTCT
Found at i:41081 original size:16 final size:16
Alignment explanation
Indices: 41060--41101 Score: 59
Period size: 16 Copynumber: 2.6 Consensus size: 16
41050 AAAAATGAAG
*
41060 AATAAA-AATAAGTAAA
1 AATAAATAA-AAGGAAA
41076 AATAAATAAAAGGAAA
1 AATAAATAAAAGGAAA
41092 AATAAATAAA
1 AATAAATAAA
41102 TAAATAAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
16 22 0.92
17 2 0.08
ACGTcount: A:0.76, C:0.00, G:0.07, T:0.17
Consensus pattern (16 bp):
AATAAATAAAAGGAAA
Found at i:41210 original size:22 final size:22
Alignment explanation
Indices: 41168--41210 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
41158 AATCATAACA
* *
41168 ATAATAATAGTAATATGAAAAT
1 ATAATAATAGTAAAATAAAAAT
41190 ATAAT-ATAGTATAAATAAAAA
1 ATAATAATAGTA-AAATAAAAA
41211 AAACCAGAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.63, C:0.00, G:0.07, T:0.30
Consensus pattern (22 bp):
ATAATAATAGTAAAATAAAAAT
Found at i:41444 original size:19 final size:19
Alignment explanation
Indices: 41413--41450 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
41403 AAAAAAAAGT
*
41413 ATATATATATAAATAATAA
1 ATATATATATAAAAAATAA
41432 ATATAGTAT-TAAAAAATAA
1 ATATA-TATATAAAAAATAA
41451 CCAAATGAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 14 0.82
20 3 0.18
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (19 bp):
ATATATATATAAAAAATAA
Found at i:42017 original size:37 final size:37
Alignment explanation
Indices: 41976--42072 Score: 140
Period size: 37 Copynumber: 2.6 Consensus size: 37
41966 GGATCCTATC
* *
41976 TTTAGGAGTTTAAATCATAGTAGAACTCTATCATATT
1 TTTAGGAGTTTGAATCCTAGTAGAACTCTATCATATT
* * * *
42013 TTTAGGAGTTTGAATCCTAGCAAAATTCTATCCTATT
1 TTTAGGAGTTTGAATCCTAGTAGAACTCTATCATATT
42050 TTTAGGAGTTTGAATCCTAGTAG
1 TTTAGGAGTTTGAATCCTAGTAG
42073 GACGAAAAGG
Statistics
Matches: 52, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
37 52 1.00
ACGTcount: A:0.31, C:0.12, G:0.16, T:0.40
Consensus pattern (37 bp):
TTTAGGAGTTTGAATCCTAGTAGAACTCTATCATATT
Found at i:48479 original size:22 final size:22
Alignment explanation
Indices: 48454--48497 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
48444 TTTAATGAAT
48454 GAAAATGAATATAAATG-TAAAA
1 GAAAATGAATA-AAATGATAAAA
*
48476 GAAAATTAATAAAATGATAAAA
1 GAAAATGAATAAAATGATAAAA
48498 ATATAAAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 5 0.25
22 15 0.75
ACGTcount: A:0.66, C:0.00, G:0.11, T:0.23
Consensus pattern (22 bp):
GAAAATGAATAAAATGATAAAA
Found at i:49373 original size:22 final size:22
Alignment explanation
Indices: 49348--49393 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
49338 AAATTTAATG
49348 AATGAACATGAATATAAATG-TA
1 AATGAACATGAATA-AAATGATA
* *
49370 AATGAATATTAATAAAATGATA
1 AATGAACATGAATAAAATGATA
49392 AA
1 AA
49394 AATGCAAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 5 0.24
22 16 0.76
ACGTcount: A:0.59, C:0.02, G:0.11, T:0.28
Consensus pattern (22 bp):
AATGAACATGAATAAAATGATA
Found at i:50340 original size:21 final size:21
Alignment explanation
Indices: 50310--50360 Score: 93
Period size: 21 Copynumber: 2.4 Consensus size: 21
50300 ATTCCATCTC
*
50310 CTCAATCTCCTTACGCTGGCG
1 CTCAACCTCCTTACGCTGGCG
50331 CTCAACCTCCTTACGCTGGCG
1 CTCAACCTCCTTACGCTGGCG
50352 CTCAACCTC
1 CTCAACCTC
50361 TAGTTCTTAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.16, C:0.43, G:0.16, T:0.25
Consensus pattern (21 bp):
CTCAACCTCCTTACGCTGGCG
Found at i:51649 original size:36 final size:36
Alignment explanation
Indices: 51602--51701 Score: 119
Period size: 37 Copynumber: 2.7 Consensus size: 36
51592 TTTCGTCCTA
* *
51602 TAGGATTCAAACTCCTAAAATAGGATAAAATTTTGC
1 TAGGATTCAAACTCCTAAAATAGGATAAAATTCTAC
* *
51638 TAGGATTCAAACTCCTAAAAATAGAATAAAGTTCTAC
1 TAGGATTCAAACTCCT-AAAATAGGATAAAATTCTAC
* * *
51675 TAAGATTTAAATTCCTAAAGATAGGAT
1 TAGGATTCAAACTCCTAAA-ATAGGAT
51702 CCACAAGCAC
Statistics
Matches: 54, Mismatches: 8, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
36 19 0.35
37 35 0.65
ACGTcount: A:0.44, C:0.13, G:0.13, T:0.30
Consensus pattern (36 bp):
TAGGATTCAAACTCCTAAAATAGGATAAAATTCTAC
Found at i:52096 original size:18 final size:17
Alignment explanation
Indices: 52057--52099 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
52047 ATTATATGGA
52057 TATT-TTATTCATTTAT
1 TATTATTATTCATTTAT
*
52073 TTTTATTATTCATGTTAT
1 TATTATTATTCAT-TTAT
52091 TATTATTAT
1 TATTATTAT
52100 ATGTATATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 3 0.13
17 8 0.35
18 12 0.52
ACGTcount: A:0.26, C:0.05, G:0.02, T:0.67
Consensus pattern (17 bp):
TATTATTATTCATTTAT
Found at i:57000 original size:183 final size:183
Alignment explanation
Indices: 56684--57220 Score: 905
Period size: 183 Copynumber: 2.9 Consensus size: 183
56674 ATTAAATCCG
*
56684 TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCGGGCTTTATGA
1 TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
* * *
56749 ATAGATTATGTTCAAACTATGACACTGCTCGGACACTTGGTAATTCGGTGTTTGCTCTACTACTT
66 ATAGATTATGTTCAAACTATGACACTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTGCTT
*
56814 TTGTCAGGACAAAGACTTTGTGATGAGATGAACCGTTCAGTGATTTGTCCCTC
131 TTGTCAGGACAAAGACTTTGTGATGAGATGAACCCTTCAGTGATTTGTCCCTC
* *
56867 TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCAAAATCCCTGGCTTTATGA
1 TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
56932 ATAGATTATGTTCAAACTATGACACTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTGCTT
66 ATAGATTATGTTCAAACTATGACACTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTGCTT
* * *
56997 TTGTCAGGCCAAAGACTTTGTGATGAGACGTACCCTTCAGTGATTTGTCCCTC
131 TTGTCAGGACAAAGACTTTGTGATGAGATGAACCCTTCAGTGATTTGTCCCTC
* *
57050 TAAAGCTGAGCTATTCCACTAAGGCAATTGATTATAGAGGAAAATCGAAAGCCCTGGCTTTATGA
1 TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
** * *
57115 ATAGATTACATTCAAA-TCATGACATTGCTCTGACACTTGGCAATTCGGTGTTTGCTCCACTGCT
66 ATAGATTATGTTCAAACT-ATGACACTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTGCT
*
57179 TTTGTCAGGTCAAAGACTTTGTGATGAGATGAACCCTTCAGT
130 TTTGTCAGGACAAAGACTTTGTGATGAGATGAACCCTTCAGT
57221 TAAACCTGAT
Statistics
Matches: 332, Mismatches: 21, Indels: 2
0.94 0.06 0.01
Matches are distributed among these distances:
182 1 0.00
183 331 1.00
ACGTcount: A:0.28, C:0.20, G:0.21, T:0.31
Consensus pattern (183 bp):
TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
ATAGATTATGTTCAAACTATGACACTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTGCTT
TTGTCAGGACAAAGACTTTGTGATGAGATGAACCCTTCAGTGATTTGTCCCTC
Found at i:58385 original size:36 final size:35
Alignment explanation
Indices: 58342--58455 Score: 97
Period size: 36 Copynumber: 3.2 Consensus size: 35
58332 ATGCAGATGA
*
58342 TTATCTCACTCAAATTTGTTTTTCTTAAAACATACT
1 TTATCTCACTCAAATTTGTTTTTCTTAAAACAGA-T
* ** * * *
58378 TTGTCTCACTTGAA-CTGTTTTTCTCGAAAAAAGAT
1 TTATCTCACTCAAATTTGTTTTTCT-TAAAACAGAT
*
58413 TTATTTCACTCAAGATTT-TTTTTCTTAAAACAAGAT
1 TTATCTCACTCAA-ATTTGTTTTTCTTAAAAC-AGAT
*
58449 TTGTCTC
1 TTATCTC
58456 GCTTTAGACC
Statistics
Matches: 58, Mismatches: 16, Indels: 8
0.71 0.20 0.10
Matches are distributed among these distances:
35 23 0.40
36 34 0.59
37 1 0.02
ACGTcount: A:0.29, C:0.18, G:0.08, T:0.46
Consensus pattern (35 bp):
TTATCTCACTCAAATTTGTTTTTCTTAAAACAGAT
Found at i:58572 original size:39 final size:39
Alignment explanation
Indices: 58513--58670 Score: 104
Period size: 39 Copynumber: 3.8 Consensus size: 39
58503 GCTTTTTTTA
* **
58513 AGAAGATTTTATCTTGCTTGAGATAGTTTCCCTCGAAAC
1 AGAAAATTTTATCTCCCTTGAGATAGTTTCCCTCGAAAC
* * *
58552 AGAAAATTTTATCTCCCTTGAGACAGTTTCTCTTGAAAAC
1 AGAAAATTTTATCTCCCTTGAGATAGTTTCCCTCG-AAAC
* *
58592 ATTTCCTTTGAAATTAATTTTTTCTCTCC-TGAGATAGATTCCCTCGAAAC
1 A--------G-AA--AATTTTATCTC-CCTTGAGATAGTTTCCCTCGAAAC
*
58642 AGAAAATTTTGTCT-CCTTGAGATAGTTTC
1 AGAAAATTTTATCTCCCTTGAGATAGTTTC
58671 TCTTTAAACA
Statistics
Matches: 92, Mismatches: 13, Indels: 29
0.69 0.10 0.22
Matches are distributed among these distances:
37 2 0.02
38 11 0.12
39 38 0.41
40 5 0.05
41 2 0.02
42 1 0.01
48 1 0.01
49 2 0.02
50 5 0.05
51 23 0.25
52 2 0.02
ACGTcount: A:0.28, C:0.19, G:0.14, T:0.39
Consensus pattern (39 bp):
AGAAAATTTTATCTCCCTTGAGATAGTTTCCCTCGAAAC
Found at i:58805 original size:106 final size:105
Alignment explanation
Indices: 58584--58902 Score: 443
Period size: 106 Copynumber: 3.1 Consensus size: 105
58574 ACAGTTTCTC
* * * *
58584 TTGAAAACATTTCCTTTGAAATTA-ATTTTTTCTCTCCTGAGATAGATTCCCTCGAAACAGAAAA
1 TTGAAAACATTTCCCTTGAAATGATATTTTTTCTCTCTTGAGATAGTTTCCCTCGAAACAGAAAA
* *
58648 TTTTGTCT-CCTTGAGATAGTTTCTCTTTAAACATAAACA
66 TTTTGTCTCCCTTGAGACAGTTTCTCTTCAAACATAAACA
* * * *
58687 TTGAAAATATTTCCCTTAAAATGATTTTTTTTTCTCTCTTGAGATAGTTTCCCTCAAAACAGAAA
1 TTGAAAACATTTCCCTTGAAATGA-TATTTTTTCTCTCTTGAGATAGTTTCCCTCGAAACAGAAA
*
58752 ATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACA
65 ATTTTGTCTCCCTTGAGACAGTTTCTCTTCAAACATAAACA
* * *
58793 TTGAAAACATTTCCCTTGAAATGA-ATTTTATCTCGCTTGAGATAGTTTCCCTTGAAAC-G--AA
1 TTGAAAACATTTCCCTTGAAATGATATTTTTTCTCTCTTGAGATAGTTTCCCTCGAAACAGAAAA
* *
58854 TTTTGTCTCCCTTGAGACAGTTTCTCTCCAAACATAAACT
66 TTTTGTCTCCCTTGAGACAGTTTCTCTTCAAACATAAACA
58894 TTGAAAACA
1 TTGAAAACA
58903 ATTTAACGAA
Statistics
Matches: 193, Mismatches: 20, Indels: 8
0.87 0.09 0.04
Matches are distributed among these distances:
101 48 0.25
103 21 0.11
104 29 0.15
105 44 0.23
106 51 0.26
ACGTcount: A:0.31, C:0.19, G:0.11, T:0.38
Consensus pattern (105 bp):
TTGAAAACATTTCCCTTGAAATGATATTTTTTCTCTCTTGAGATAGTTTCCCTCGAAACAGAAAA
TTTTGTCTCCCTTGAGACAGTTTCTCTTCAAACATAAACA
Found at i:58849 original size:36 final size:36
Alignment explanation
Indices: 58802--58877 Score: 116
Period size: 36 Copynumber: 2.1 Consensus size: 36
58792 ATTGAAAACA
* * *
58802 TTTCCCTTGAAATGAATTTTATCTCGCTTGAGATAG
1 TTTCCCTTGAAACGAATTTTATCTCCCTTGAGACAG
*
58838 TTTCCCTTGAAACGAATTTTGTCTCCCTTGAGACAG
1 TTTCCCTTGAAACGAATTTTATCTCCCTTGAGACAG
58874 TTTC
1 TTTC
58878 TCTCCAAACA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.22, C:0.21, G:0.16, T:0.41
Consensus pattern (36 bp):
TTTCCCTTGAAACGAATTTTATCTCCCTTGAGACAG
Found at i:59278 original size:105 final size:105
Alignment explanation
Indices: 59044--59685 Score: 834
Period size: 105 Copynumber: 6.2 Consensus size: 105
59034 CAAACATCCG
* * * * * * *
59044 AATTTCAACTCCACGACGGAGGATATCGTGACACTCGAGACAACACAAGTTCAACTTCACAACGA
1 AATTTCAACTTCACAACGAAGGATAT--TG-GACTCCAGACAACGCAAGTTCAACTTCACGACGA
* *
59109 AGGGA----TG-TTGTCAACAAACAACATCTCAATTTCAGAGCC
63 AGGGACCGCTGCTTGTCAAC-AACAACTTCCCAATTTCAGAGCC
59148 AATTT-AACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
1 AATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
* **
59212 GACCGCTACTTGTCAACAACAACTTCTTAATTTCAGAGCC
66 GACCGCTGCTTGTCAACAACAACTTCCCAATTTCAGAGCC
* * *
59252 AATTTCAACTTCACAACGAAGGATATTAGACTTCAGACAATGCAAGTTCAACTTCACGACGAAGG
1 AATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
*
59317 GACCGCTGCTTGT---CAACAACTTCCCAATCTCAGAGCC
66 GACCGCTGCTTGTCAACAACAACTTCCCAATTTCAGAGCC
59354 AATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
1 AATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
*
59419 GACCGCTGCTTGTCAACAACAACTTCCCAATCTCAGAGCC
66 GACCGCTGCTTGTCAACAACAACTTCCCAATTTCAGAGCC
*
59459 AATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTCCACGACGAAGG
1 AATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
* *
59524 GACCGCTGCTTGTCAACAA-AA-TT-TC-A-TTCAGAGTC
66 GACCGCTGCTTGTCAACAACAACTTCCCAATTTCAGAGCC
* * * *
59559 AATTT-AACTTCACAGCGAAGGATATTGGACTCGAGAC-A--CAAGTTCAACTTGACAACGAAGG
1 AATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
* * * ** *
59620 GACGGCTGGTTGTCAACAAACAATTTCCCGGTTCCAGAGCC
66 GACCGCTGCTTGTCAAC-AACAACTTCCCAATTTCAGAGCC
*
59661 AATTTCAACTTCACGACGAAGGATA
1 AATTTCAACTTCACAACGAAGGATA
59686 CTCGGAACAA
Statistics
Matches: 485, Mismatches: 37, Indels: 33
0.87 0.07 0.06
Matches are distributed among these distances:
96 35 0.07
97 2 0.00
98 3 0.01
99 32 0.07
100 48 0.10
101 3 0.01
102 109 0.22
103 36 0.07
104 34 0.07
105 183 0.38
ACGTcount: A:0.34, C:0.26, G:0.18, T:0.22
Consensus pattern (105 bp):
AATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
GACCGCTGCTTGTCAACAACAACTTCCCAATTTCAGAGCC
Found at i:59400 original size:207 final size:205
Alignment explanation
Indices: 59125--59685 Score: 835
Period size: 207 Copynumber: 2.7 Consensus size: 205
59115 GTTGTCAACA
*
59125 AACAACATCTCAATTTCAGAGCCAATTTAACTTCACAACGAAGGATATTGGACTCCAGACAACGC
1 AACAACTTCTCAA-TTCAGAGCCAATTTAACTTCACAACGAAGGATATTGGACTCCAGACAACGC
* **
59190 AAGTTCAACTTCACGACGAAGGGACCGCTACTTGTCAACAACAACTTCTTAATTTCAGAGCCAAT
65 AAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCAATTTCAGAGCCAAT
* * *
59255 TTCAACTTCACAACGAAGGATATTAGACTTCAGACAATGCAAGTTCAACTTCACGACGAAGGGAC
130 TTCAACTTCACAACGAAGGATATTAGACTCCAGACAACGCAAGTTCAACTCCACGACGAAGGGAC
59320 CGCTGCTTGTC
195 CGCTGCTTGTC
*
59331 AACAACTTCCCAATCTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACG
1 AACAACTTCTCAAT-TCAGAGCCAATTT-AACTTCACAACGAAGGATATTGGACTCCAGACAACG
*
59396 CAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCAATCTCAGAGCCAA
64 CAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCAATTTCAGAGCCAA
*
59461 TTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTCCACGACGAAGGGA
129 TTTCAACTTCACAACGAAGGATATTAGACTCCAGACAACGCAAGTTCAACTCCACGACGAAGGGA
59526 CCGCTGCTTGTC
194 CCGCTGCTTGTC
* * * *
59538 AACAAAATT-TC-ATTCAGAGTCAATTTAACTTCACAGCGAAGGATATTGGACTCGAGAC-A--C
1 AAC-AACTTCTCAATTCAGAGCCAATTTAACTTCACAACGAAGGATATTGGACTCCAGACAACGC
* * * * * ** *
59598 AAGTTCAACTTGACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCCGGTTCCAGAGCCAA
65 AAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAAC-AACAACTTCCCAATTTCAGAGCCAA
*
59663 TTTCAACTTCACGACGAAGGATA
129 TTTCAACTTCACAACGAAGGATA
59686 CTCGGAACAA
Statistics
Matches: 326, Mismatches: 25, Indels: 12
0.90 0.07 0.03
Matches are distributed among these distances:
201 36 0.11
202 42 0.13
203 1 0.00
204 30 0.09
205 13 0.04
206 26 0.08
207 174 0.53
208 4 0.01
ACGTcount: A:0.34, C:0.26, G:0.18, T:0.22
Consensus pattern (205 bp):
AACAACTTCTCAATTCAGAGCCAATTTAACTTCACAACGAAGGATATTGGACTCCAGACAACGCA
AGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCAATTTCAGAGCCAATT
TCAACTTCACAACGAAGGATATTAGACTCCAGACAACGCAAGTTCAACTCCACGACGAAGGGACC
GCTGCTTGTC
Found at i:60272 original size:37 final size:37
Alignment explanation
Indices: 60218--60323 Score: 140
Period size: 37 Copynumber: 2.9 Consensus size: 37
60208 AACACATATG
60218 TCTACTAGGATTCAAACTCCTAAAAATAGGATAAAAT
1 TCTACTAGGATTCAAACTCCTAAAAATAGGATAAAAT
* * * *
60255 TTTGCTAGGATTCAAACTCCTAAAAATAGGATAGAGT
1 TCTACTAGGATTCAAACTCCTAAAAATAGGATAAAAT
* * * *
60292 TCTACTAAGATTTAAATTCCTAAAGATAGGAT
1 TCTACTAGGATTCAAACTCCTAAAAATAGGAT
60324 CCACAAGCAC
Statistics
Matches: 59, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
37 59 1.00
ACGTcount: A:0.42, C:0.14, G:0.14, T:0.30
Consensus pattern (37 bp):
TCTACTAGGATTCAAACTCCTAAAAATAGGATAAAAT
Found at i:60701 original size:17 final size:18
Alignment explanation
Indices: 60675--60714 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
60665 ATTATATGGA
60675 TATT-TTATTCAT-TTAT
1 TATTATTATTCATGTTAT
*
60691 TTTTATTATTCATGTTAT
1 TATTATTATTCATGTTAT
60709 TATTAT
1 TATTAT
60715 ATGTATATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
16 3 0.15
17 8 0.40
18 9 0.45
ACGTcount: A:0.25, C:0.05, G:0.03, T:0.68
Consensus pattern (18 bp):
TATTATTATTCATGTTAT
Found at i:60733 original size:55 final size:54
Alignment explanation
Indices: 60674--60787 Score: 126
Period size: 57 Copynumber: 2.0 Consensus size: 54
60664 TATTATATGG
* *
60674 ATATT-TTA-TTCATTTATTTTTATTATTCATGTTATTATTA-TATGTATATATATAT
1 ATATTATTATTTCATTTATTTTT-TTACT-ATATT-TTATTATTAT-TATATATATAT
60729 ATATTAAATTATTTTCATTTATTTTTTTACTATATTTTATTATTATTATATATATAT
1 ATATT--ATTA-TTTCATTTATTTTTTTACTATATTTTATTATTATTATATATATAT
60786 AT
1 AT
60788 TTCTTTAATA
Statistics
Matches: 51, Mismatches: 2, Indels: 10
0.81 0.03 0.16
Matches are distributed among these distances:
55 5 0.10
57 19 0.37
58 10 0.20
59 4 0.08
60 13 0.25
ACGTcount: A:0.32, C:0.04, G:0.02, T:0.62
Consensus pattern (54 bp):
ATATTATTATTTCATTTATTTTTTTACTATATTTTATTATTATTATATATATAT
Found at i:60880 original size:72 final size:74
Alignment explanation
Indices: 60781--60919 Score: 169
Period size: 72 Copynumber: 1.9 Consensus size: 74
60771 TTATTATATA
* * *
60781 TATATATTTCTTTAATATTTTACTTATA-AGTCTAATATTACTATATATATATT-GTAATTATCT
1 TATATATTTCTTTAATAGTTTACTTATATA-CCTAATATTA-AATATATATATTCGTAATTATCT
60844 TTATCTAGTCG
64 TTATCTAGTCG
* * * *
60855 TATATATTT-TTT-ATAGTTTATTTATATACCTATTATTAAATATATATATTCTTAATTATTTTT
1 TATATATTTCTTTAATAGTTTACTTATATACCTAATATTAAATATATATATTCGTAATTATCTTT
60918 AT
66 AT
60920 TTGATTATTT
Statistics
Matches: 56, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
71 11 0.20
72 32 0.57
73 4 0.07
74 9 0.16
ACGTcount: A:0.33, C:0.07, G:0.04, T:0.56
Consensus pattern (74 bp):
TATATATTTCTTTAATAGTTTACTTATATACCTAATATTAAATATATATATTCGTAATTATCTTT
ATCTAGTCG
Found at i:61019 original size:21 final size:20
Alignment explanation
Indices: 60965--61020 Score: 58
Period size: 21 Copynumber: 2.7 Consensus size: 20
60955 ACTTTATAAC
* *
60965 TTTATATTATTTTTTATTAT
1 TTTATATTATTATTCATTAT
* *
60985 TTTCATTTTTTTATTCATTAT
1 TTT-ATATTATTATTCATTAT
61006 TATTATATTATTATT
1 T-TTATATTATTATT
61021 TTAAAAAAAA
Statistics
Matches: 28, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
20 3 0.11
21 23 0.82
22 2 0.07
ACGTcount: A:0.25, C:0.04, G:0.00, T:0.71
Consensus pattern (20 bp):
TTTATATTATTATTCATTAT
Found at i:61197 original size:34 final size:36
Alignment explanation
Indices: 61150--61221 Score: 89
Period size: 36 Copynumber: 2.1 Consensus size: 36
61140 ATTGGGAGGG
*
61150 TAGCTTTTCTA-TTT-TTAAGTA-TTTGGTATATATA
1 TAGCTTTTCTATTTTATTAA-TACTTTGATATATATA
61184 TAGCTTATT-TATTTTATTAATACTTTGATATATATA
1 TAGCTT-TTCTATTTTATTAATACTTTGATATATATA
61220 TA
1 TA
61222 TATTTATATT
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
34 8 0.24
35 7 0.21
36 18 0.55
ACGTcount: A:0.31, C:0.06, G:0.08, T:0.56
Consensus pattern (36 bp):
TAGCTTTTCTATTTTATTAATACTTTGATATATATA
Found at i:63775 original size:19 final size:21
Alignment explanation
Indices: 63753--63792 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 21
63743 CTAAGGCTCT
*
63753 AACTAATAAC-TAAAG-CTAA
1 AACTAAGAACTTAAAGTCTAA
63772 AACTAAGAACTTAAAGTCTAA
1 AACTAAGAACTTAAAGTCTAA
63793 GGTTTAATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 9 0.50
20 5 0.28
21 4 0.22
ACGTcount: A:0.55, C:0.15, G:0.07, T:0.23
Consensus pattern (21 bp):
AACTAAGAACTTAAAGTCTAA
Found at i:65543 original size:67 final size:66
Alignment explanation
Indices: 65434--65563 Score: 197
Period size: 67 Copynumber: 2.0 Consensus size: 66
65424 ACTTAAAGAT
* * * *
65434 TGATTTTTGGATGATATTTGCCCCACTATGACAATTTTATTTGGTGTTGGATGACGCTTGAATGA
1 TGATTTTTGGATAATATTTGCCACACCATGACAATTTGATTTGGTG-TGGATGACGCTTGAATGA
65499 TA
65 TA
**
65501 TGATTTTTGGATAATATTTGCCACACCATGATTATTTGATTTGGTGTGGATGACGCTTGAATG
1 TGATTTTTGGATAATATTTGCCACACCATGACAATTTGATTTGGTGTGGATGACGCTTGAATG
65564 GTACTTTGTT
Statistics
Matches: 57, Mismatches: 6, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
66 17 0.30
67 40 0.70
ACGTcount: A:0.24, C:0.12, G:0.23, T:0.42
Consensus pattern (66 bp):
TGATTTTTGGATAATATTTGCCACACCATGACAATTTGATTTGGTGTGGATGACGCTTGAATGAT
A
Done.