Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006067.1 Hibiscus syriacus cultivar Beakdansim tig00014346_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: 91984
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:417 original size:20 final size:21
Alignment explanation
Indices: 394--436 Score: 70
Period size: 20 Copynumber: 2.1 Consensus size: 21
384 AACCCTAAAC
394 AAGCCCAAAATC-TATCTGCT
1 AAGCCCAAAATCGTATCTGCT
*
414 AAGCCCAAAATCGTATCTTCT
1 AAGCCCAAAATCGTATCTGCT
435 AA
1 AA
437 ACTCGCAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 12 0.57
21 9 0.43
ACGTcount: A:0.37, C:0.28, G:0.09, T:0.26
Consensus pattern (21 bp):
AAGCCCAAAATCGTATCTGCT
Found at i:3720 original size:33 final size:33
Alignment explanation
Indices: 3682--3758 Score: 95
Period size: 32 Copynumber: 2.4 Consensus size: 33
3672 TTTATATATT
* *
3682 TTGAATTTTTTTTGAC-TTTATATTCTTTTTGTA
1 TTGAATTTTTATTCACTTTTA-ATTCTTTTTGTA
*
3715 TTGAA-TTTTATTCACTTTTAATTCTTTTTTTA
1 TTGAATTTTTATTCACTTTTAATTCTTTTTGTA
*
3747 TTGCATTTTTAT
1 TTGAATTTTTAT
3759 ACTTTAAATT
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
32 23 0.61
33 15 0.39
ACGTcount: A:0.19, C:0.08, G:0.06, T:0.66
Consensus pattern (33 bp):
TTGAATTTTTATTCACTTTTAATTCTTTTTGTA
Found at i:3763 original size:22 final size:22
Alignment explanation
Indices: 3720--3763 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
3710 TTGTATTGAA
*
3720 TTTTATTCACTTTTAATTCTTT
1 TTTTATTCACTTTTAATACTTT
*
3742 TTTTATTGCA-TTTTTATACTTT
1 TTTTATT-CACTTTTAATACTTT
3764 AAATTACAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 17 0.89
23 2 0.11
ACGTcount: A:0.18, C:0.11, G:0.02, T:0.68
Consensus pattern (22 bp):
TTTTATTCACTTTTAATACTTT
Found at i:5585 original size:14 final size:13
Alignment explanation
Indices: 5572--5615 Score: 52
Period size: 13 Copynumber: 3.3 Consensus size: 13
5562 GGATGTAAAT
5572 TTTATATTAAAAA
1 TTTATATTAAAAA
* *
5585 TATAAATTTAAAAA
1 TTTATA-TTAAAAA
*
5599 ATTATATTAAAAA
1 TTTATATTAAAAA
5612 TTTA
1 TTTA
5616 AGAGATTCGA
Statistics
Matches: 24, Mismatches: 6, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
13 14 0.58
14 10 0.42
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (13 bp):
TTTATATTAAAAA
Found at i:8068 original size:2 final size:2
Alignment explanation
Indices: 8061--8102 Score: 75
Period size: 2 Copynumber: 20.5 Consensus size: 2
8051 GAAGGTTCAC
8061 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AGT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT A
8103 GTCTACTTTA
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 37 0.95
3 2 0.05
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (2 bp):
AT
Found at i:14714 original size:62 final size:62
Alignment explanation
Indices: 14570--14723 Score: 159
Period size: 62 Copynumber: 2.5 Consensus size: 62
14560 GAAGATGTAT
* *** *
14570 CGATGCACAGGTAGTGCATCGATGCACTCTTTTAATCTAAAAACATCGAATGCAATTGGTGCAT
1 CGATGCACAAGTAGTGCATCGATGCA-TCCAGTAA-CTAAAAACATCGAATGCAATTGGTGCAC
* * * * *
14634 CGATGCATAAGGCA-TGCATCGATGCATCCAGTAA-TAAATAACATCGAATGTATTTTGTGCAC
1 CGATGCACAA-GTAGTGCATCGATGCATCCAGTAACTAAA-AACATCGAATGCAATTGGTGCAC
*
14696 CGATGCACAAGTAGTGCATCGATTCATC
1 CGATGCACAAGTAGTGCATCGATGCATC
14724 GGTAGGGAAT
Statistics
Matches: 74, Mismatches: 13, Indels: 8
0.78 0.14 0.08
Matches are distributed among these distances:
61 6 0.08
62 41 0.55
63 5 0.07
64 20 0.27
65 2 0.03
ACGTcount: A:0.32, C:0.21, G:0.20, T:0.27
Consensus pattern (62 bp):
CGATGCACAAGTAGTGCATCGATGCATCCAGTAACTAAAAACATCGAATGCAATTGGTGCAC
Found at i:15689 original size:101 final size:102
Alignment explanation
Indices: 15507--15722 Score: 371
Period size: 101 Copynumber: 2.1 Consensus size: 102
15497 GTCGAGGGTC
15507 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACA-ATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
* *
15572 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
65 TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
* *
15610 TATGTGGTCCTTCGGGAC-ATATGTATTCTTTGGAATATGTGTGAAGTTTGGTGAGACACATACT
1 TATGTGGTCCTTCGGGACAATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACT
*
15674 TGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
66 TGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
15711 TATGTGGTCCTT
1 TATGTGGTCCTT
15723 ATGGACATTA
Statistics
Matches: 108, Mismatches: 5, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
101 90 0.83
103 18 0.17
ACGTcount: A:0.25, C:0.13, G:0.24, T:0.38
Consensus pattern (102 bp):
TATGTGGTCCTTCGGGACAATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACT
TGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
Found at i:15789 original size:23 final size:23
Alignment explanation
Indices: 15763--15806 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
15753 ATTCTACGCG
15763 GCACTCCAGTGCAATTATATGTA
1 GCACTCCAGTGCAATTATATGTA
* *
15786 GCACTTCGGTGCAATTATATG
1 GCACTCCAGTGCAATTATATG
15807 AGCTGTGGTG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.27, C:0.20, G:0.20, T:0.32
Consensus pattern (23 bp):
GCACTCCAGTGCAATTATATGTA
Found at i:21547 original size:103 final size:103
Alignment explanation
Indices: 21322--21539 Score: 409
Period size: 103 Copynumber: 2.1 Consensus size: 103
21312 GTCGAGGGTC
21322 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
* *
21387 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
21425 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
*
21490 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
21528 TATGTGGTCCTT
1 TATGTGGTCCTT
21540 ATGGACATTA
Statistics
Matches: 112, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
103 112 1.00
ACGTcount: A:0.26, C:0.14, G:0.24, T:0.37
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
Found at i:21607 original size:23 final size:23
Alignment explanation
Indices: 21546--21623 Score: 75
Period size: 23 Copynumber: 3.3 Consensus size: 23
21536 CCTTATGGAC
*
21546 ATTATTATATGGCACTACGGTGTA
1 ATTA-TATGTGGCACTACGGTGTA
* * * * *
21570 ATTCTACGCGACACTCCGGTGTA
1 ATTATATGTGGCACTACGGTGTA
* *
21593 ATTATATGTGGCACTTCGGTGCA
1 ATTATATGTGGCACTACGGTGTA
21616 ATTATATG
1 ATTATATG
21624 AGTTGTGGTG
Statistics
Matches: 42, Mismatches: 12, Indels: 1
0.76 0.22 0.02
Matches are distributed among these distances:
23 39 0.93
24 3 0.07
ACGTcount: A:0.26, C:0.18, G:0.22, T:0.35
Consensus pattern (23 bp):
ATTATATGTGGCACTACGGTGTA
Found at i:22780 original size:40 final size:40
Alignment explanation
Indices: 22725--22957 Score: 242
Period size: 40 Copynumber: 5.8 Consensus size: 40
22715 AAATGACTAA
* *
22725 CAAATTCGCAACGCGAACTCCAATTTCGCAACACAAAAGT
1 CAAATTCGCAACGCGAATTCCAAATTCGCAACACAAAAGT
*
22765 CAAATTCGCAACGCGATAGT-CAAA-TCTGCAACACAAAAGT
1 CAAATTCGCAACGCGA-ATTCCAAATTC-GCAACACAAAAGT
* ** *
22805 CAAATTCGCAATGCGAATTTGTAAA-TCGCAACACAGAAGT
1 CAAATTCGCAACGCGAA-TTCCAAATTCGCAACACAAAAGT
* * **
22845 CAAATTCACAACGCG-ATAGCCAAATTCGCAACGTAAAAGT
1 CAAATTCGCAACGCGAAT-TCCAAATTCGCAACACAAAAGT
* * *
22885 CAAATTCGCAACACTGAATTTCAAATTCGCAACATAAAAGT
1 CAAATTCGCAACGC-GAATTCCAAATTCGCAACACAAAAGT
*
22926 CAAATTCGCAACGCGAAAGT-CAAATTCGCAAC
1 CAAATTCGCAACGCG-AATTCCAAATTCGCAAC
22958 GCGAAATACA
Statistics
Matches: 163, Mismatches: 21, Indels: 18
0.81 0.10 0.09
Matches are distributed among these distances:
38 1 0.01
39 7 0.04
40 110 0.67
41 43 0.26
42 2 0.01
ACGTcount: A:0.42, C:0.25, G:0.14, T:0.19
Consensus pattern (40 bp):
CAAATTCGCAACGCGAATTCCAAATTCGCAACACAAAAGT
Found at i:22858 original size:80 final size:81
Alignment explanation
Indices: 22725--22957 Score: 294
Period size: 80 Copynumber: 2.9 Consensus size: 81
22715 AAATGACTAA
* * * *
22725 CAAATTCGCAACGC-GAACTCCAATTTCGCAACACAAAAGTCAAATTCGCAACGCGATAGTCAAA
1 CAAATTCGCAACACTGAATTTCAAATTCGCAACACAAAAGTCAAATTCGCAACGCGATAGTCAAA
22789 -TCTGCAACACAAAAGT
66 TTC-GCAACACAAAAGT
** * * * *
22805 CAAATTCGCAATGC-GAATTTGTAAA-TCGCAACACAGAAGTCAAATTCACAACGCGATAGCCAA
1 CAAATTCGCAACACTGAATTT-CAAATTCGCAACACAAAAGTCAAATTCGCAACGCGATAGTCAA
**
22868 ATTCGCAACGTAAAAGT
65 ATTCGCAACACAAAAGT
* *
22885 CAAATTCGCAACACTGAATTTCAAATTCGCAACATAAAAGTCAAATTCGCAACGCGAAAGTCAAA
1 CAAATTCGCAACACTGAATTTCAAATTCGCAACACAAAAGTCAAATTCGCAACGCGATAGTCAAA
22950 TTCGCAAC
66 TTCGCAAC
22958 GCGAAATACA
Statistics
Matches: 131, Mismatches: 18, Indels: 7
0.84 0.12 0.04
Matches are distributed among these distances:
80 79 0.60
81 52 0.40
ACGTcount: A:0.42, C:0.25, G:0.14, T:0.19
Consensus pattern (81 bp):
CAAATTCGCAACACTGAATTTCAAATTCGCAACACAAAAGTCAAATTCGCAACGCGATAGTCAAA
TTCGCAACACAAAAGT
Found at i:22958 original size:20 final size:20
Alignment explanation
Indices: 22725--22963 Score: 200
Period size: 20 Copynumber: 11.9 Consensus size: 20
22715 AAATGACTAA
*
22725 CAAATTCGCAACGCG-AACT
1 CAAATTCGCAACGCGAAAGT
* * *
22744 CCAATTTCGCAACACAAAAGT
1 -CAAATTCGCAACGCGAAAGT
*
22765 CAAATTCGCAACGCGATAGT
1 CAAATTCGCAACGCGAAAGT
* *
22785 CAAA-TCTGCAACACAAAAGT
1 CAAATTC-GCAACGCGAAAGT
* *
22805 CAAATTCGCAATGCGAATTTGT
1 CAAATTCGCAACGCGAA--AGT
*
22827 -AAA-TCGCAACAC-AGAAGT
1 CAAATTCGCAACGCGA-AAGT
* * *
22845 CAAATTCACAACGCGATAGC
1 CAAATTCGCAACGCGAAAGT
**
22865 CAAATTCGCAACGTAAAAGT
1 CAAATTCGCAACGCGAAAGT
* **
22885 CAAATTCGCAACACTGAATTT
1 CAAATTCGCAACGC-GAAAGT
***
22906 CAAATTCGCAACATAAAAGT
1 CAAATTCGCAACGCGAAAGT
22926 CAAATTCGCAACGCGAAAGT
1 CAAATTCGCAACGCGAAAGT
22946 CAAATTCGCAACGCGAAA
1 CAAATTCGCAACGCGAAA
22964 TACAATATTA
Statistics
Matches: 170, Mismatches: 39, Indels: 20
0.74 0.17 0.09
Matches are distributed among these distances:
18 2 0.01
19 6 0.04
20 135 0.79
21 25 0.15
22 2 0.01
ACGTcount: A:0.42, C:0.25, G:0.15, T:0.19
Consensus pattern (20 bp):
CAAATTCGCAACGCGAAAGT
Found at i:23098 original size:22 final size:22
Alignment explanation
Indices: 23073--23123 Score: 75
Period size: 22 Copynumber: 2.3 Consensus size: 22
23063 CTACGGTGAC
23073 ATCCGTCCCCATCTCCAACGAA
1 ATCCGTCCCCATCTCCAACGAA
* **
23095 ATCCATCCCCATCTCCGGCGAA
1 ATCCGTCCCCATCTCCAACGAA
23117 ATCCGTC
1 ATCCGTC
23124 TATCTCCATC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.24, C:0.45, G:0.12, T:0.20
Consensus pattern (22 bp):
ATCCGTCCCCATCTCCAACGAA
Found at i:23547 original size:20 final size:20
Alignment explanation
Indices: 23509--23556 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
23499 AAATCGCAAC
23509 GCGATTTT-AGTTTCGCGTT
1 GCGATTTTCAGTTTCGCGTT
23528 GCGATTTTCA-TTTCCGCGTT
1 GCGATTTTCAGTTT-CGCGTT
*
23548 GCAATTTTC
1 GCGATTTTC
23557 TCGTTGCGAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
19 11 0.42
20 15 0.58
ACGTcount: A:0.12, C:0.21, G:0.21, T:0.46
Consensus pattern (20 bp):
GCGATTTTCAGTTTCGCGTT
Found at i:27268 original size:65 final size:65
Alignment explanation
Indices: 27131--27306 Score: 255
Period size: 66 Copynumber: 2.6 Consensus size: 65
27121 GGGTACACTT
*
27131 TTTTTTTGCTTGTTTAATTGAATTTTACATTAAAAGTTGATTTGTTTAATTGATGAGGAAATAAG
1 TTTTTTTGCTTGTTTAATTG-A-TTT---GTAAAAGTTGATTTGTTTAATTGATGAGGAAATAAG
27196 AATTA
61 AATTA
* *
27201 -TTTTTTGCTTGTTTAATTGATTTGTAAAAGTTGATTTGTTTAATTTGATGTGTAAATAAGAATT
1 TTTTTTTGCTTGTTTAATTGATTTGTAAAAGTTGATTTGTTTAA-TTGATGAGGAAATAAGAATT
27265 A
65 A
*
27266 TTTTTTTTCTTGTTTAATTGATTTGTAAAAGTTGATTTGTT
1 TTTTTTTGCTTGTTTAATTGATTTGTAAAAGTTGATTTGTT
27307 GTTTTAAATT
Statistics
Matches: 100, Mismatches: 4, Indels: 8
0.89 0.04 0.07
Matches are distributed among these distances:
64 19 0.19
65 19 0.19
66 39 0.39
67 3 0.03
68 1 0.01
69 19 0.19
ACGTcount: A:0.28, C:0.02, G:0.16, T:0.53
Consensus pattern (65 bp):
TTTTTTTGCTTGTTTAATTGATTTGTAAAAGTTGATTTGTTTAATTGATGAGGAAATAAGAATTA
Found at i:27385 original size:20 final size:20
Alignment explanation
Indices: 27360--27408 Score: 98
Period size: 20 Copynumber: 2.5 Consensus size: 20
27350 GTTGAAGGTA
27360 CAAATTCGCAACGCGAAAGT
1 CAAATTCGCAACGCGAAAGT
27380 CAAATTCGCAACGCGAAAGT
1 CAAATTCGCAACGCGAAAGT
27400 CAAATTCGC
1 CAAATTCGC
27409 GTTACGATTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.39, C:0.27, G:0.18, T:0.16
Consensus pattern (20 bp):
CAAATTCGCAACGCGAAAGT
Found at i:27754 original size:18 final size:18
Alignment explanation
Indices: 27731--27766 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
27721 AAGCCGGTTG
27731 TGATTGAGATTTTGATTT
1 TGATTGAGATTTTGATTT
*
27749 TGATTGCGATTTTGATTT
1 TGATTGAGATTTTGATTT
27767 CCTTTTGCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.19, C:0.03, G:0.22, T:0.56
Consensus pattern (18 bp):
TGATTGAGATTTTGATTT
Found at i:30225 original size:12 final size:12
Alignment explanation
Indices: 30204--30237 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
30194 TGGTGTGGGT
*
30204 TTTGAGATTGTG
1 TTTGATATTGTG
30216 TTTGATATTGTG
1 TTTGATATTGTG
*
30228 TTTGGTATTG
1 TTTGATATTG
30238 GAAATGTGGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.29, T:0.56
Consensus pattern (12 bp):
TTTGATATTGTG
Found at i:30854 original size:16 final size:16
Alignment explanation
Indices: 30832--30871 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
30822 GAAATCATTG
*
30832 AAAAATTATATAGAAA
1 AAAAATTATATAAAAA
* *
30848 TAAAATTATGTAAAAA
1 AAAAATTATATAAAAA
30864 AAAAATTA
1 AAAAATTA
30872 GAGATGAGGA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.68, C:0.00, G:0.05, T:0.28
Consensus pattern (16 bp):
AAAAATTATATAAAAA
Found at i:31069 original size:20 final size:19
Alignment explanation
Indices: 31044--31092 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 19
31034 TTAAATTCGT
31044 GTTGCGAATTCAAAAATCTA
1 GTTGCGAATTCAAAAATC-A
** *
31064 GTTGCGAATTTGAAATTCA
1 GTTGCGAATTCAAAAATCA
31083 GTTGCGAATT
1 GTTGCGAATT
31093 TGAAATTCAG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
19 11 0.42
20 15 0.58
ACGTcount: A:0.33, C:0.12, G:0.20, T:0.35
Consensus pattern (19 bp):
GTTGCGAATTCAAAAATCA
Found at i:31085 original size:19 final size:19
Alignment explanation
Indices: 31044--31119 Score: 98
Period size: 19 Copynumber: 3.9 Consensus size: 19
31034 TTAAATTCGT
** *
31044 GTTGCGAATTCAAAAATCTA
1 GTTGCGAATTTGAAATTC-A
31064 GTTGCGAATTTGAAATTCA
1 GTTGCGAATTTGAAATTCA
31083 GTTGCGAATTTGAAATTCA
1 GTTGCGAATTTGAAATTCA
* *
31102 GTTACAAATTTGAAATTC
1 GTTGCGAATTTGAAATTC
31120 CGCGTTGTGA
Statistics
Matches: 51, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
19 36 0.71
20 15 0.29
ACGTcount: A:0.36, C:0.12, G:0.17, T:0.36
Consensus pattern (19 bp):
GTTGCGAATTTGAAATTCA
Found at i:31164 original size:40 final size:41
Alignment explanation
Indices: 31114--31234 Score: 158
Period size: 40 Copynumber: 3.0 Consensus size: 41
31104 TACAAATTTG
* *
31114 AAATTCCGCGTTGTGAATTTGACTTTTGTGTTGCAAATTTGAC
1 AAATT-CGCGTTGCGAATTTGACTTCTGTGTTGC-AATTTGAC
* *
31157 -TA-TCGCGTTGCGAATTTGACTTCTGTGTTGCGATTT-AC
1 AAATTCGCGTTGCGAATTTGACTTCTGTGTTGCAATTTGAC
31195 AAATTCGCGTTGCGAATTTGACTTCTGTGTTGCGAATTTG
1 AAATTCGCGTTGCGAATTTGACTTCTGTGTTGC-AATTTG
31235 GAAAATCGCA
Statistics
Matches: 68, Mismatches: 6, Indels: 9
0.82 0.07 0.11
Matches are distributed among these distances:
38 2 0.03
39 5 0.07
40 55 0.81
41 5 0.07
42 1 0.01
ACGTcount: A:0.20, C:0.16, G:0.23, T:0.41
Consensus pattern (41 bp):
AAATTCGCGTTGCGAATTTGACTTCTGTGTTGCAATTTGAC
Found at i:31188 original size:20 final size:20
Alignment explanation
Indices: 31123--31234 Score: 115
Period size: 20 Copynumber: 5.6 Consensus size: 20
31113 GAAATTCCGC
* *
31123 GTTGTGAATTTGACTTTTGT
1 GTTGCGAATTTGACTTCTGT
* *
31143 GTTGCAAATTTGACTATC-GC
1 GTTGCGAATTTGACT-TCTGT
31163 GTTGCGAATTTGACTTCTGT
1 GTTGCGAATTTGACTTCTGT
*
31183 GTTGCG-ATTT-ACAAATTC-GC
1 GTTGCGAATTTGAC---TTCTGT
31203 GTTGCGAATTTGACTTCTGT
1 GTTGCGAATTTGACTTCTGT
31223 GTTGCGAATTTG
1 GTTGCGAATTTG
31235 GAAAATCGCA
Statistics
Matches: 76, Mismatches: 8, Indels: 16
0.76 0.08 0.16
Matches are distributed among these distances:
18 2 0.03
19 9 0.12
20 55 0.72
21 8 0.11
22 2 0.03
ACGTcount: A:0.19, C:0.14, G:0.24, T:0.43
Consensus pattern (20 bp):
GTTGCGAATTTGACTTCTGT
Found at i:33142 original size:20 final size:20
Alignment explanation
Indices: 33114--33210 Score: 176
Period size: 20 Copynumber: 4.8 Consensus size: 20
33104 CACCCAATAA
* *
33114 TATCACTTAAGGTGTCTTAT
1 TATCCCTTAAGGTCTCTTAT
33134 TATCCCTTAAGGTCTCTTAT
1 TATCCCTTAAGGTCTCTTAT
33154 TATCCCTTAAGGTCTCTTAT
1 TATCCCTTAAGGTCTCTTAT
33174 TATCCCTTAAGGTCTCTTAT
1 TATCCCTTAAGGTCTCTTAT
33194 TATCCCTTAAGGTCTCT
1 TATCCCTTAAGGTCTCT
33211 GTTGATTGAT
Statistics
Matches: 75, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 75 1.00
ACGTcount: A:0.21, C:0.24, G:0.11, T:0.44
Consensus pattern (20 bp):
TATCCCTTAAGGTCTCTTAT
Found at i:34173 original size:15 final size:15
Alignment explanation
Indices: 34149--34220 Score: 51
Period size: 15 Copynumber: 4.8 Consensus size: 15
34139 ACATCATTAA
*
34149 ATTAATTTATAAAAT
1 ATTAAATTATAAAAT
*
34164 ATTAAATTATAAAGT
1 ATTAAATTATAAAAT
* *
34179 ACTAAA-TATATAAT
1 ATTAAATTATAAAAT
34193 -TATAAATTAGTTAAAA-
1 AT-TAAATTA--TAAAAT
*
34209 ATTAAAATATAA
1 ATTAAATTATAA
34221 TATTTATAAA
Statistics
Matches: 44, Mismatches: 8, Indels: 11
0.70 0.13 0.17
Matches are distributed among these distances:
14 13 0.30
15 20 0.45
16 6 0.14
17 5 0.11
ACGTcount: A:0.57, C:0.01, G:0.03, T:0.39
Consensus pattern (15 bp):
ATTAAATTATAAAAT
Found at i:35171 original size:2 final size:2
Alignment explanation
Indices: 35164--35267 Score: 208
Period size: 2 Copynumber: 52.0 Consensus size: 2
35154 CAGCATTTTG
35164 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
35206 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
35248 AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT
35268 GTCAAGTCTC
Statistics
Matches: 102, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 102 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:35710 original size:34 final size:34
Alignment explanation
Indices: 35667--35735 Score: 138
Period size: 34 Copynumber: 2.0 Consensus size: 34
35657 GAGCTTTTCT
35667 TGTTGAGGGGAATGTTATCTGGTTCAAGACCAAC
1 TGTTGAGGGGAATGTTATCTGGTTCAAGACCAAC
35701 TGTTGAGGGGAATGTTATCTGGTTCAAGACCAAC
1 TGTTGAGGGGAATGTTATCTGGTTCAAGACCAAC
35735 T
1 T
35736 TCTTTTTTCA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.26, C:0.14, G:0.29, T:0.30
Consensus pattern (34 bp):
TGTTGAGGGGAATGTTATCTGGTTCAAGACCAAC
Found at i:50752 original size:55 final size:54
Alignment explanation
Indices: 50639--50760 Score: 156
Period size: 55 Copynumber: 2.2 Consensus size: 54
50629 TGCATCTGTT
** * *
50639 GTGTATCGGTATACAAAATGCATTTGATGTTGGGGTGTATCAGTACATCAAAGA
1 GTGTATCGGTACCCAAAATACATTTGATATTGGGGTGTATCAGTACATCAAAGA
* *
50693 GTGTATCGGTACCCAAATTACATTTGATATTGGGGGTGTATC-GATACATCCAAGA
1 GTGTATCGGTACCCAAAATACATTTGATATT-GGGGTGTATCAG-TACATCAAAGA
*
50748 GTGTATCAGTACC
1 GTGTATCGGTACC
50761 TCCCTTTGTA
Statistics
Matches: 59, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
54 27 0.46
55 32 0.54
ACGTcount: A:0.30, C:0.15, G:0.25, T:0.31
Consensus pattern (54 bp):
GTGTATCGGTACCCAAAATACATTTGATATTGGGGTGTATCAGTACATCAAAGA
Found at i:51094 original size:13 final size:13
Alignment explanation
Indices: 51063--51094 Score: 57
Period size: 12 Copynumber: 2.5 Consensus size: 13
51053 GATTTTCTTG
51063 TGAAAATCATTTT
1 TGAAAATCATTTT
51076 TG-AAATCATTTT
1 TGAAAATCATTTT
51088 TGAAAAT
1 TGAAAAT
51095 TACTCCACCT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 12 0.67
13 6 0.33
ACGTcount: A:0.41, C:0.06, G:0.09, T:0.44
Consensus pattern (13 bp):
TGAAAATCATTTT
Found at i:52863 original size:12 final size:13
Alignment explanation
Indices: 52846--52878 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
52836 ATGGGCAAAA
*
52846 TTTGAAAACTAT-
1 TTTGAAAACAATG
52858 TTTGAAAACAATG
1 TTTGAAAACAATG
52871 TTTGAAAA
1 TTTGAAAA
52879 ATCATATTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 11 0.58
13 8 0.42
ACGTcount: A:0.45, C:0.06, G:0.12, T:0.36
Consensus pattern (13 bp):
TTTGAAAACAATG
Found at i:53406 original size:21 final size:22
Alignment explanation
Indices: 53348--53430 Score: 64
Period size: 21 Copynumber: 3.8 Consensus size: 22
53338 AAAACCGGAC
*
53348 GAGTGTATCGATACAC-ATTCAA
1 GAGTGTATCGATACACTAGTC-A
* * *
53370 GGAATGCATCGGTACACTA-TCA
1 -GAGTGTATCGATACACTAGTCA
* *
53392 TAGTGTATCGATACA-TAGTGA
1 GAGTGTATCGATACACTAGTCA
*
53413 GGGTGTATCGATACACTA
1 GAGTGTATCGATACACTA
53431 CGCACAAAAA
Statistics
Matches: 47, Mismatches: 10, Indels: 7
0.73 0.16 0.11
Matches are distributed among these distances:
20 2 0.04
21 26 0.55
22 3 0.06
23 15 0.32
24 1 0.02
ACGTcount: A:0.33, C:0.17, G:0.23, T:0.28
Consensus pattern (22 bp):
GAGTGTATCGATACACTAGTCA
Found at i:61105 original size:18 final size:18
Alignment explanation
Indices: 61082--61159 Score: 138
Period size: 18 Copynumber: 4.3 Consensus size: 18
61072 TGGAATGTAA
*
61082 GATTACCAGCGGGAATAT
1 GATTACCGGCGGGAATAT
61100 GATTACCGGCGGGAATAT
1 GATTACCGGCGGGAATAT
61118 GATTACCGGCGGGAATAT
1 GATTACCGGCGGGAATAT
*
61136 GATTACCGGCGGGAATAA
1 GATTACCGGCGGGAATAT
61154 GATTAC
1 GATTAC
61160 TGAGAATGTT
Statistics
Matches: 58, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 58 1.00
ACGTcount: A:0.31, C:0.17, G:0.31, T:0.22
Consensus pattern (18 bp):
GATTACCGGCGGGAATAT
Found at i:63161 original size:21 final size:21
Alignment explanation
Indices: 63132--63184 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
63122 ATTCTGACTA
63132 TCGCATTGCGATTTCCCAAAT
1 TCGCATTGCGATTTCCCAAAT
* * *
63153 TCGCGTTGCGATTTTCCTAAT
1 TCGCATTGCGATTTCCCAAAT
*
63174 TCGCAATGCGA
1 TCGCATTGCGA
63185 ATACGTAAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.21, C:0.26, G:0.19, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTCCCAAAT
Found at i:63199 original size:20 final size:20
Alignment explanation
Indices: 63174--63307 Score: 196
Period size: 20 Copynumber: 6.7 Consensus size: 20
63164 TTTTCCTAAT
63174 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
* ** *
63194 TCGCAACGCGAATTTGGAAAA
1 TCGCAATGCGAA-TACGTAAA
*
63215 TCGCAATGCGATTACGTAAA
1 TCGCAATGCGAATACGTAAA
63235 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
*
63255 TCGCAATGCGATTACGTAAA
1 TCGCAATGCGAATACGTAAA
*
63275 TCGCAATGCGAATACATAAA
1 TCGCAATGCGAATACGTAAA
63295 TCGCAATGCGAAT
1 TCGCAATGCGAAT
63308 CTGACTATCG
Statistics
Matches: 100, Mismatches: 13, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
20 85 0.85
21 15 0.15
ACGTcount: A:0.38, C:0.20, G:0.20, T:0.22
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:63528 original size:22 final size:22
Alignment explanation
Indices: 63503--63564 Score: 62
Period size: 18 Copynumber: 3.0 Consensus size: 22
63493 GGCAACATCC
63503 GTCCCCATCTCCGACGAAATCA
1 GTCCCCATCTCCGACGAAATCA
63525 GTCCCCA----CGACGATAA-CA
1 GTCCCCATCTCCGACGA-AATCA
* *
63543 GTCTCCATCTCCGGCGAAATCA
1 GTCCCCATCTCCGACGAAATCA
63565 TTCATGGTCA
Statistics
Matches: 32, Mismatches: 2, Indels: 12
0.70 0.04 0.26
Matches are distributed among these distances:
18 14 0.44
19 2 0.06
21 2 0.06
22 14 0.44
ACGTcount: A:0.27, C:0.39, G:0.16, T:0.18
Consensus pattern (22 bp):
GTCCCCATCTCCGACGAAATCA
Found at i:63957 original size:20 final size:20
Alignment explanation
Indices: 63932--63981 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
63922 TGCGATTCTT
63932 GCGTTGCGATAGTCAAATTC
1 GCGTTGCGATAGTCAAATTC
**
63952 GCGTTGCGATAGTCATTTTC
1 GCGTTGCGATAGTCAAATTC
*
63972 GTGTTGCGAT
1 GCGTTGCGAT
63982 TTTCATTTTC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.18, C:0.18, G:0.28, T:0.36
Consensus pattern (20 bp):
GCGTTGCGATAGTCAAATTC
Found at i:63987 original size:20 final size:20
Alignment explanation
Indices: 63949--64003 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
63939 GATAGTCAAA
* **
63949 TTCGCGTTGCGATAGTCATT
1 TTCGTGTTGCGATTTTCATT
63969 TTCGTGTTGCGATTTTCATT
1 TTCGTGTTGCGATTTTCATT
63989 TTCGTGTTGCGATTT
1 TTCGTGTTGCGATTT
64004 AAAGTTTCAG
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.11, C:0.16, G:0.24, T:0.49
Consensus pattern (20 bp):
TTCGTGTTGCGATTTTCATT
Found at i:64011 original size:20 final size:20
Alignment explanation
Indices: 63968--64011 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
63958 CGATAGTCAT
** *
63968 TTTCGTGTTGCGATTTTCAT
1 TTTCGTGTTGCGATTTAAAG
63988 TTTCGTGTTGCGATTTAAAG
1 TTTCGTGTTGCGATTTAAAG
64008 TTTC
1 TTTC
64012 AGAAACTATT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.14, C:0.14, G:0.20, T:0.52
Consensus pattern (20 bp):
TTTCGTGTTGCGATTTAAAG
Found at i:65901 original size:20 final size:20
Alignment explanation
Indices: 65876--65965 Score: 153
Period size: 20 Copynumber: 4.5 Consensus size: 20
65866 AGAATAGTTT
65876 ACTATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
65896 ACTATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
*
65916 ACTATCGCAATGCGAATATG
1 ACTATCGCAATGCGAAAATG
**
65936 ACTATCGCAATGCGAATTTG
1 ACTATCGCAATGCGAAAATG
65956 ACTATCGCAA
1 ACTATCGCAA
65966 CGAAAGAATC
Statistics
Matches: 68, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 68 1.00
ACGTcount: A:0.37, C:0.21, G:0.19, T:0.23
Consensus pattern (20 bp):
ACTATCGCAATGCGAAAATG
Found at i:66037 original size:20 final size:20
Alignment explanation
Indices: 66012--66058 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
66002 GATTCTCTCG
66012 TTGCGATAGTCAAATTCGCA
1 TTGCGATAGTCAAATTCGCA
** *
66032 TTGCGATAGTCATTTTCGCG
1 TTGCGATAGTCAAATTCGCA
66052 TTGCGAT
1 TTGCGAT
66059 TTTGTTGTTG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.21, C:0.19, G:0.23, T:0.36
Consensus pattern (20 bp):
TTGCGATAGTCAAATTCGCA
Found at i:66071 original size:87 final size:87
Alignment explanation
Indices: 65980--66145 Score: 199
Period size: 87 Copynumber: 1.9 Consensus size: 87
65970 AGAATCACAA
*
65980 TGCGAAATGAAAATCGCATTGCGATTCTCTCGTTGCGATAGTCAAATTCG-CATTGCGATAGTCA
1 TGCGAAATGAAAATCACATTGCGATTCTCTCGTTGCGATAGTCAAATTCGTCA-TGCGATAGTCA
*
66044 TTTTCGCGTTGCGATTTTGTTGT
65 TTTTCGCGTTACGATTTTGTTGT
** ** ** * ** * *
66067 TGCGATTTTCATTTCATATTGCGATTCTCTCGTTGCGATAGTCATTTTTGTGATGCGATAGTCAT
1 TGCGAAATGAAAATCACATTGCGATTCTCTCGTTGCGATAGTCAAATTCGTCATGCGATAGTCAT
66132 TTTCGCGTTACGAT
66 TTTCGCGTTACGAT
66146 AGTCATTTTC
Statistics
Matches: 65, Mismatches: 13, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
87 64 0.98
88 1 0.02
ACGTcount: A:0.20, C:0.18, G:0.22, T:0.40
Consensus pattern (87 bp):
TGCGAAATGAAAATCACATTGCGATTCTCTCGTTGCGATAGTCAAATTCGTCATGCGATAGTCAT
TTTCGCGTTACGATTTTGTTGT
Found at i:66112 original size:33 final size:33
Alignment explanation
Indices: 66032--66113 Score: 83
Period size: 33 Copynumber: 2.5 Consensus size: 33
66022 CAAATTCGCA
* * * * *
66032 TTGCGATAGTCATTTTCGCGTTGCGATTTTGTTG
1 TTGCGATAGTCA-TTTCACATTGCGATTCTCTCG
** *
66066 TTGCGATTTTCATTTCATATTGCGATTCTCTCG
1 TTGCGATAGTCATTTCACATTGCGATTCTCTCG
66099 TTGCGATAGTCATTT
1 TTGCGATAGTCATTT
66114 TTGTGATGCG
Statistics
Matches: 38, Mismatches: 10, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
33 28 0.74
34 10 0.26
ACGTcount: A:0.15, C:0.17, G:0.21, T:0.48
Consensus pattern (33 bp):
TTGCGATAGTCATTTCACATTGCGATTCTCTCG
Found at i:66125 original size:20 final size:20
Alignment explanation
Indices: 66097--66185 Score: 133
Period size: 20 Copynumber: 4.5 Consensus size: 20
66087 GCGATTCTCT
*
66097 CGTTGCGATAGTCATTTTTG
1 CGTTGCGATAGTCATTTTCG
* *
66117 TGATGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
*
66137 CGTTACGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
*
66157 CGTTGTGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
66177 CGTTGCGAT
1 CGTTGCGAT
66186 TTTAAGTTTC
Statistics
Matches: 60, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 60 1.00
ACGTcount: A:0.17, C:0.17, G:0.25, T:0.42
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTTCG
Found at i:68383 original size:33 final size:33
Alignment explanation
Indices: 68319--68398 Score: 97
Period size: 33 Copynumber: 2.4 Consensus size: 33
68309 AATCACATTA
**
68319 CGATTTTCATTTTCACATTGTGATTCACTCGTTG
1 CGATTTTCA-TTTCACATTCCGATTCACTCGTTG
* *
68353 CGATTTTCATTTCGCATTCCGATTCTCTCGTTG
1 CGATTTTCATTTCACATTCCGATTCACTCGTTG
**
68386 CGATAGTCATTTC
1 CGATTTTCATTTC
68399 CGCGTTGCGA
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
33 31 0.77
34 9 0.22
ACGTcount: A:0.16, C:0.24, G:0.15, T:0.45
Consensus pattern (33 bp):
CGATTTTCATTTCACATTCCGATTCACTCGTTG
Found at i:68406 original size:20 final size:20
Alignment explanation
Indices: 68381--68469 Score: 119
Period size: 20 Copynumber: 4.5 Consensus size: 20
68371 CCGATTCTCT
68381 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTTCCG
*
68401 CGTTGCGATAGTCAATTCCG
1 CGTTGCGATAGTCATTTCCG
*
68421 CATTGC-AGTAGTCATTTCCG
1 CGTTGCGA-TAGTCATTTCCG
*
68441 TGTTGCGATAGTCATATT-CG
1 CGTTGCGATAGTCAT-TTCCG
68461 CGTTGCGAT
1 CGTTGCGAT
68470 TTCTGCGTTG
Statistics
Matches: 60, Mismatches: 6, Indels: 6
0.83 0.08 0.08
Matches are distributed among these distances:
19 1 0.02
20 56 0.93
21 3 0.05
ACGTcount: A:0.18, C:0.22, G:0.25, T:0.35
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTCCG
Found at i:70930 original size:24 final size:24
Alignment explanation
Indices: 70903--70956 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
70893 TTGAAAAATC
70903 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
70927 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
70951 ATCAAA
1 ATCAAA
70957 TTTTGAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:71843 original size:20 final size:20
Alignment explanation
Indices: 71820--71918 Score: 79
Period size: 20 Copynumber: 5.3 Consensus size: 20
71810 CAGAATCTCG
71820 TTGCGATTTACATATTCGCA
1 TTGCGATTTACATATTCGCA
71840 TTGCGA-TT---TA--CG--
1 TTGCGATTTACATATTCGCA
* *
71852 TTGCGATTTACGTAATCGCA
1 TTGCGATTTACATATTCGCA
* * *
71872 TTGCGATTTTCCAAATTCGCG
1 TTGCGA-TTTACATATTCGCA
*
71893 TTGCGATTTACGTATTCGCA
1 TTGCGATTTACATATTCGCA
71913 TTGCGA
1 TTGCGA
71919 ATTAGGAAAA
Statistics
Matches: 61, Mismatches: 9, Indels: 18
0.69 0.10 0.20
Matches are distributed among these distances:
12 6 0.10
13 2 0.03
14 2 0.03
16 4 0.07
18 2 0.03
19 2 0.03
20 28 0.46
21 15 0.25
ACGTcount: A:0.21, C:0.20, G:0.20, T:0.38
Consensus pattern (20 bp):
TTGCGATTTACATATTCGCA
Found at i:71857 original size:12 final size:12
Alignment explanation
Indices: 71840--71864 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
71830 CATATTCGCA
71840 TTGCGATTTACG
1 TTGCGATTTACG
71852 TTGCGATTTACG
1 TTGCGATTTACG
71864 T
1 T
71865 AATCGCATTG
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:0.16, C:0.16, G:0.24, T:0.44
Consensus pattern (12 bp):
TTGCGATTTACG
Found at i:71859 original size:32 final size:32
Alignment explanation
Indices: 71818--71880 Score: 108
Period size: 32 Copynumber: 2.0 Consensus size: 32
71808 GTCAGAATCT
*
71818 CGTTGCGATTTACATATTCGCATTGCGATTTA
1 CGTTGCGATTTACATAATCGCATTGCGATTTA
*
71850 CGTTGCGATTTACGTAATCGCATTGCGATTT
1 CGTTGCGATTTACATAATCGCATTGCGATTT
71881 TCCAAATTCG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.21, C:0.19, G:0.21, T:0.40
Consensus pattern (32 bp):
CGTTGCGATTTACATAATCGCATTGCGATTTA
Found at i:71896 original size:21 final size:20
Alignment explanation
Indices: 71850--71903 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 20
71840 TTGCGATTTA
**
71850 CGTTGCGATTTACGTAATCG
1 CGTTGCGATTTACCAAATCG
* *
71870 CATTGCGATTTTCCAAATTCG
1 CGTTGCGATTTACCAAA-TCG
71891 CGTTGCGATTTAC
1 CGTTGCGATTTAC
71904 GTATTCGCAT
Statistics
Matches: 27, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
20 13 0.48
21 14 0.52
ACGTcount: A:0.20, C:0.22, G:0.20, T:0.37
Consensus pattern (20 bp):
CGTTGCGATTTACCAAATCG
Found at i:80893 original size:21 final size:21
Alignment explanation
Indices: 80850--80893 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
80840 AATATAAATT
*
80850 GTGTATCGATGCACTGCTACA
1 GTGTATCGATGCACTACTACA
*
80871 GTGTATCGATGCACTACTGCA
1 GTGTATCGATGCACTACTACA
80892 GT
1 GT
80894 AACTTCGGAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.23, C:0.23, G:0.25, T:0.30
Consensus pattern (21 bp):
GTGTATCGATGCACTACTACA
Done.