Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005847.1 Hibiscus syriacus cultivar Beakdansim tig00013722_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: 100044
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:1609 original size:44 final size:48
Alignment explanation
Indices: 1549--1639 Score: 118
Period size: 44 Copynumber: 2.0 Consensus size: 48
1539 CTAATAAACT
* * *
1549 ATTTTTTAATTATAATATAACTTAAACTAATAAAT-T-ACTTAACTAA
1 ATTTTTTAATTATAATATAAATTAAACAAACAAATATAACTTAACTAA
*
1595 ATTTTTT-A-TATAATATAAATTCAACAAACAAATATAACTTAACTA
1 ATTTTTTAATTATAATATAAATTAAACAAACAAATATAACTTAACTA
1640 TTTAACTAAC
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
44 21 0.54
45 2 0.05
46 16 0.41
ACGTcount: A:0.49, C:0.10, G:0.00, T:0.41
Consensus pattern (48 bp):
ATTTTTTAATTATAATATAAATTAAACAAACAAATATAACTTAACTAA
Found at i:1727 original size:34 final size:38
Alignment explanation
Indices: 1642--1746 Score: 133
Period size: 38 Copynumber: 2.8 Consensus size: 38
1632 CTTAACTATT
1642 TAACTAAC--ACAAACTAATTAAATATTTTTATATATA
1 TAACTAACTAACAAACTAATTAAATATTTTTATATATA
* * *
1678 TAACTAACTAACAAACTAATTAATTATTTTTAAATACA
1 TAACTAACTAACAAACTAATTAAATATTTTTATATATA
* * * *
1716 TAACTATCAAACAAATTAACTAAATATTTTT
1 TAACTAACTAACAAACTAATTAAATATTTTT
1747 TTATTTATGT
Statistics
Matches: 59, Mismatches: 8, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
36 8 0.14
38 51 0.86
ACGTcount: A:0.50, C:0.12, G:0.00, T:0.38
Consensus pattern (38 bp):
TAACTAACTAACAAACTAATTAAATATTTTTATATATA
Found at i:1813 original size:21 final size:21
Alignment explanation
Indices: 1760--1799 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
1750 TTTATGTATG
1760 ATATAACTTAAACTAACAATA
1 ATATAACTTAAACTAACAATA
1781 ATATAACTTAAACTAACAA
1 ATATAACTTAAACTAACAA
1800 ACTAATTAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.57, C:0.15, G:0.00, T:0.28
Consensus pattern (21 bp):
ATATAACTTAAACTAACAATA
Found at i:1880 original size:17 final size:18
Alignment explanation
Indices: 1851--1884 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
1841 AACAAACTAA
1851 TAATTTAAAATAATAAAC
1 TAATTTAAAATAATAAAC
1869 TAATTT-AAATAATAAA
1 TAATTTAAAATAATAAA
1885 AAATTACCTC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (18 bp):
TAATTTAAAATAATAAAC
Found at i:10925 original size:23 final size:22
Alignment explanation
Indices: 10899--10947 Score: 89
Period size: 23 Copynumber: 2.2 Consensus size: 22
10889 TTATTAAGTG
10899 GGGATATATATGGGTTACACGT
1 GGGATATATATGGGTTACACGT
10921 AGGGATATATATGGGTTACACGT
1 -GGGATATATATGGGTTACACGT
10944 GGGA
1 GGGA
10948 ATGAAGGAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
22 4 0.15
23 22 0.85
ACGTcount: A:0.29, C:0.08, G:0.35, T:0.29
Consensus pattern (22 bp):
GGGATATATATGGGTTACACGT
Found at i:12278 original size:22 final size:22
Alignment explanation
Indices: 12253--12300 Score: 78
Period size: 22 Copynumber: 2.2 Consensus size: 22
12243 GGGTCTACGC
*
12253 GGTCCTTCGGGACATATACAGA
1 GGTCCTTCGGGACAAATACAGA
*
12275 GGTCCTTCGGGACAAATACATA
1 GGTCCTTCGGGACAAATACAGA
12297 GGTC
1 GGTC
12301 TTTATGGACA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.27, C:0.23, G:0.27, T:0.23
Consensus pattern (22 bp):
GGTCCTTCGGGACAAATACAGA
Found at i:12449 original size:8 final size:8
Alignment explanation
Indices: 12436--12462 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
12426 TATGAAAAGA
12436 GTTTGTAT
1 GTTTGTAT
12444 GTTTGTAT
1 GTTTGTAT
12452 GTTTGTAT
1 GTTTGTAT
12460 GTT
1 GTT
12463 ATCATGTTAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.11, C:0.00, G:0.26, T:0.63
Consensus pattern (8 bp):
GTTTGTAT
Found at i:20025 original size:15 final size:15
Alignment explanation
Indices: 20002--20048 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
19992 GATATTTAGT
* *
20002 GGGCGGGCGGATGTG
1 GGGCAGGCGGATGCG
*
20017 GGGCAGGCGAATGCG
1 GGGCAGGCGGATGCG
*
20032 GGGCAGGCGGATACG
1 GGGCAGGCGGATGCG
20047 GG
1 GG
20049 ACGGATGCGA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.15, C:0.17, G:0.60, T:0.09
Consensus pattern (15 bp):
GGGCAGGCGGATGCG
Found at i:21016 original size:15 final size:16
Alignment explanation
Indices: 20996--21036 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
20986 GTTTACTTCA
*
20996 GAATGATT-AAGCGCT
1 GAATGATTCAAACGCT
*
21011 GAATGATTCAAATGCT
1 GAATGATTCAAACGCT
21027 GAATGATTCA
1 GAATGATTCA
21037 GAGGCTCTGT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 8 0.35
16 15 0.65
ACGTcount: A:0.37, C:0.12, G:0.22, T:0.29
Consensus pattern (16 bp):
GAATGATTCAAACGCT
Found at i:22098 original size:20 final size:21
Alignment explanation
Indices: 22073--22119 Score: 55
Period size: 19 Copynumber: 2.4 Consensus size: 21
22063 ATATATGCAA
22073 AAAAAATTAAT-ATATAAAGT
1 AAAAAATTAATGATATAAAGT
*
22093 AAAAAA--AATGATATTAAGT
1 AAAAAATTAATGATATAAAGT
*
22112 TAAAAATT
1 AAAAAATT
22120 TAATTTTTTG
Statistics
Matches: 22, Mismatches: 2, Indels: 5
0.76 0.07 0.17
Matches are distributed among these distances:
18 3 0.14
19 13 0.59
20 6 0.27
ACGTcount: A:0.64, C:0.00, G:0.06, T:0.30
Consensus pattern (21 bp):
AAAAAATTAATGATATAAAGT
Found at i:22877 original size:18 final size:19
Alignment explanation
Indices: 22854--22896 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 19
22844 CAGTAATCCT
22854 ATTCC-CTGATAATCTTAC
1 ATTCCACTGATAATCTTAC
*
22872 ATTCCCACTGATAATCTTAT
1 ATT-CCACTGATAATCTTAC
22892 ATTCC
1 ATTCC
22897 GTGAACCAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 3 0.14
19 4 0.18
20 15 0.68
ACGTcount: A:0.28, C:0.28, G:0.05, T:0.40
Consensus pattern (19 bp):
ATTCCACTGATAATCTTAC
Found at i:22884 original size:20 final size:20
Alignment explanation
Indices: 22859--22896 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
22849 ATCCTATTCC
22859 CTGATAATCTTACATTCCCA
1 CTGATAATCTTACATTCCCA
*
22879 CTGATAATCTTATATTCC
1 CTGATAATCTTACATTCC
22897 GTGAACCAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.29, C:0.26, G:0.05, T:0.39
Consensus pattern (20 bp):
CTGATAATCTTACATTCCCA
Found at i:26368 original size:36 final size:36
Alignment explanation
Indices: 26306--26445 Score: 217
Period size: 36 Copynumber: 3.9 Consensus size: 36
26296 TAGTGAGTAT
* * *
26306 TATCAGCTTTGATACAATCGTATATCAATGTTATCA
1 TATCAGCTTTGGTACATTCGTGTATCAATGTTATCA
* **
26342 TATCAGCTTTAGTACATTCACGTATCAATGTTATCA
1 TATCAGCTTTGGTACATTCGTGTATCAATGTTATCA
26378 TATCAGCTTTGGTACATTCGTGTATCAATGTTATCA
1 TATCAGCTTTGGTACATTCGTGTATCAATGTTATCA
*
26414 TATCATCTTTGGTACATTCGTGTATCAATGTT
1 TATCAGCTTTGGTACATTCGTGTATCAATGTT
26446 CAGCACCGTT
Statistics
Matches: 94, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
36 94 1.00
ACGTcount: A:0.28, C:0.17, G:0.14, T:0.41
Consensus pattern (36 bp):
TATCAGCTTTGGTACATTCGTGTATCAATGTTATCA
Found at i:27610 original size:20 final size:20
Alignment explanation
Indices: 27585--27655 Score: 124
Period size: 20 Copynumber: 3.5 Consensus size: 20
27575 CCAATAAGCA
27585 GTATCGCTACTGCTATGAGG
1 GTATCGCTACTGCTATGAGG
27605 GTATCGCTACTGCTATGAGG
1 GTATCGCTACTGCTATGAGG
*
27625 GTATCGCTACTGTTATGAGG
1 GTATCGCTACTGCTATGAGG
*
27645 GTATCGATACT
1 GTATCGCTACT
27656 TTCCTTACCT
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 49 1.00
ACGTcount: A:0.21, C:0.18, G:0.28, T:0.32
Consensus pattern (20 bp):
GTATCGCTACTGCTATGAGG
Found at i:32034 original size:28 final size:30
Alignment explanation
Indices: 32002--32068 Score: 84
Period size: 31 Copynumber: 2.3 Consensus size: 30
31992 AAACCCGACA
*
32002 CGACCCGAA-C-AGTATATTTAAAAAAATC
1 CGACCCGAACCGAATATATTTAAAAAAATC
* *
32030 CGACCCGAACCCGAATTTTTTTAAAAAAATC
1 CGACCCGAA-CCGAATATATTTAAAAAAATC
32061 CGACCCGA
1 CGACCCGA
32069 TCGAGTCGGG
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
28 9 0.27
30 1 0.03
31 23 0.70
ACGTcount: A:0.40, C:0.27, G:0.12, T:0.21
Consensus pattern (30 bp):
CGACCCGAACCGAATATATTTAAAAAAATC
Found at i:34115 original size:2 final size:2
Alignment explanation
Indices: 34108--34133 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
34098 TTATAAGGAT
34108 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
34134 ATTTTATTGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:35450 original size:19 final size:19
Alignment explanation
Indices: 35426--35471 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
35416 TCCTACCGCC
*
35426 TGCTCCTCTCATGCTCGCA
1 TGCTCCCCTCATGCTCGCA
35445 TGCTCCCCTCATGCTCGCA
1 TGCTCCCCTCATGCTCGCA
*
35464 TGTTCCCC
1 TGCTCCCC
35472 GCTGCTCCCA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.09, C:0.46, G:0.15, T:0.30
Consensus pattern (19 bp):
TGCTCCCCTCATGCTCGCA
Found at i:35483 original size:18 final size:19
Alignment explanation
Indices: 35435--35484 Score: 66
Period size: 19 Copynumber: 2.7 Consensus size: 19
35425 CTGCTCCTCT
* *
35435 CATGCTCGCATGCTCCCCT
1 CATGCTCGCATGTTCCCCG
35454 CATGCTCGCATGTTCCCCG
1 CATGCTCGCATGTTCCCCG
*
35473 C-TGCTCCCATGT
1 CATGCTCGCATGT
35485 AGCTTTAATA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
18 10 0.36
19 18 0.64
ACGTcount: A:0.10, C:0.44, G:0.18, T:0.28
Consensus pattern (19 bp):
CATGCTCGCATGTTCCCCG
Found at i:35547 original size:22 final size:23
Alignment explanation
Indices: 35505--35554 Score: 75
Period size: 22 Copynumber: 2.2 Consensus size: 23
35495 GCTGCATTAT
*
35505 TGCAGCATCATTTTTGTTGCTTCA
1 TGCAGCATCA-TTTTGCTGCTTCA
35529 TGCAGCATCA-TTTGCTGCTTCA
1 TGCAGCATCATTTTGCTGCTTCA
35551 TGCA
1 TGCA
35555 TCAATTATTG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
22 15 0.60
24 10 0.40
ACGTcount: A:0.18, C:0.24, G:0.18, T:0.40
Consensus pattern (23 bp):
TGCAGCATCATTTTGCTGCTTCA
Found at i:35565 original size:22 final size:21
Alignment explanation
Indices: 35509--35568 Score: 66
Period size: 22 Copynumber: 2.8 Consensus size: 21
35499 CATTATTGCA
* *
35509 GCATCATTTTTGTTGCTTCAT
1 GCATCATTATTGCTGCTTCAT
* *
35530 GCAGCATCATTTGCTGCTTCAT
1 GCATCATTA-TTGCTGCTTCAT
35552 GCATCAATTATTGCTGC
1 GCATC-ATTATTGCTGC
35569 GTTGAATGAT
Statistics
Matches: 31, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
21 6 0.19
22 22 0.71
23 3 0.10
ACGTcount: A:0.18, C:0.23, G:0.17, T:0.42
Consensus pattern (21 bp):
GCATCATTATTGCTGCTTCAT
Found at i:35931 original size:44 final size:44
Alignment explanation
Indices: 35813--35964 Score: 116
Period size: 47 Copynumber: 3.3 Consensus size: 44
35803 GGGTTTAGGG
* * * *
35813 TAAAAAATTTAGTTAATTAGTTTGTTAGTTT-A-AGTTATATCAT
1 TAAAAAAATTAATTAATTAATTTGTTTGTTTGATAGTTATAT-AT
* *
35856 ACATAAATAAAA--AATTATTTAATTAGTTTGTTTGATAGTTATATAT
1 ---TAAA-AAAATTAATTAATTAATTTGTTTGTTTGATAGTTATATAT
*
35902 TAAAAAAATTAATTAATTAATTTGTTTGTTAGTTGTTAGTTATATA-
1 TAAAAAAATTAATTAATTAATTTGTTTG-T--TTGATAGTTATATAT
35948 TAAAAAATATTTAATTA
1 TAAAAAA-A-TTAATTA
35965 GTTTGTAGTT
Statistics
Matches: 87, Mismatches: 9, Indels: 18
0.76 0.08 0.16
Matches are distributed among these distances:
42 4 0.05
43 4 0.05
44 16 0.18
45 17 0.20
46 14 0.16
47 25 0.29
48 7 0.08
ACGTcount: A:0.42, C:0.01, G:0.09, T:0.47
Consensus pattern (44 bp):
TAAAAAAATTAATTAATTAATTTGTTTGTTTGATAGTTATATAT
Found at i:40146 original size:22 final size:22
Alignment explanation
Indices: 40121--40170 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 22
40111 GGGGTATCAA
*
40121 TTCCCTCCAAAGGGGGAATCGG
1 TTCCCTCCAAAGGGGAAATCGG
* *
40143 TTCCTATTCAAAGGGGAAATCGG
1 TTCC-CTCCAAAGGGGAAATCGG
40166 TTCCC
1 TTCCC
40171 CTTTAAGGGG
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
22 4 0.17
23 19 0.83
ACGTcount: A:0.24, C:0.26, G:0.26, T:0.24
Consensus pattern (22 bp):
TTCCCTCCAAAGGGGAAATCGG
Found at i:40181 original size:23 final size:22
Alignment explanation
Indices: 40130--40191 Score: 61
Period size: 23 Copynumber: 2.8 Consensus size: 22
40120 ATTCCCTCCA
*
40130 AAGGGGGAATCGGTTCCTATTC
1 AAGGGGGAATCGGTTCCCATTC
* * *
40152 AAAGGGGAAATCGGTTCCCCTTT
1 -AAGGGGGAATCGGTTCCCATTC
* *
40175 AAGGGGGTATCGATTCC
1 AAGGGGGAATCGGTTCC
40192 TCCTGCCAGA
Statistics
Matches: 32, Mismatches: 7, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
22 14 0.44
23 18 0.56
ACGTcount: A:0.24, C:0.19, G:0.31, T:0.26
Consensus pattern (22 bp):
AAGGGGGAATCGGTTCCCATTC
Found at i:47645 original size:21 final size:20
Alignment explanation
Indices: 47624--47807 Score: 85
Period size: 18 Copynumber: 9.5 Consensus size: 20
47614 TAAATATTTA
47624 ATAATTATTAAATCATTA-T
1 ATAATTATTAAATCATTATT
*
47643 -TAATGATTAAATCATTATT
1 ATAATTATTAAATCATTATT
*
47662 ATAATT-TT--ATTATTATT
1 ATAATTATTAAATCATTATT
* *
47679 AGTCATTACTT-AATCATTAAT
1 A-TAATTA-TTAAATCATTATT
*
47700 ATCAAATCATTAAAT-ATTA--
1 AT--AATTATTAAATCATTATT
47719 AT-A--A-TAAATCATTATT
1 ATAATTATTAAATCATTATT
*
47735 AGTAATCATTACTAAATCATTATT
1 A-T-A--ATTATTAAATCATTATT
**
47759 ATAATT-TTAAAT-A-TAAA
1 ATAATTATTAAATCATTATT
*
47776 ATTATTATTAAATCATTATT
1 ATAATTATTAAATCATTATT
47796 ATCAAATTATTA
1 AT--AATTATTA
47808 CTAAATCAAA
Statistics
Matches: 125, Mismatches: 15, Indels: 47
0.67 0.08 0.25
Matches are distributed among these distances:
13 5 0.04
14 5 0.04
16 2 0.02
17 17 0.14
18 27 0.22
19 11 0.09
20 14 0.11
21 15 0.12
22 14 0.11
23 2 0.02
24 13 0.10
ACGTcount: A:0.45, C:0.07, G:0.02, T:0.46
Consensus pattern (20 bp):
ATAATTATTAAATCATTATT
Found at i:47741 original size:13 final size:12
Alignment explanation
Indices: 47725--47834 Score: 54
Period size: 11 Copynumber: 9.2 Consensus size: 12
47715 ATTAATAATA
47725 AATCATTATTAGT
1 AATCATTATTA-T
*
47738 AATCATTACTA-
1 AATCATTATTAT
47749 AATCATTATTAT
1 AATCATTATTAT
* *
47761 AAT-TTTAAATAT
1 AATCATT-ATTAT
*
47773 AA-AATTATTATT
1 AATCATTATTA-T
47785 AAATCATTATTAT
1 -AATCATTATTAT
47798 CAA--ATTATTACT
1 -AATCATTATTA-T
* *
47810 AAATCA-AATCAT
1 -AATCATTATTAT
47822 -ATCATTATTAT
1 AATCATTATTAT
47833 AA
1 AA
47835 ACCAAACCAG
Statistics
Matches: 73, Mismatches: 13, Indels: 23
0.67 0.12 0.21
Matches are distributed among these distances:
10 4 0.05
11 26 0.36
12 17 0.23
13 18 0.25
14 8 0.11
ACGTcount: A:0.46, C:0.09, G:0.01, T:0.44
Consensus pattern (12 bp):
AATCATTATTAT
Found at i:48436 original size:59 final size:59
Alignment explanation
Indices: 48351--48648 Score: 447
Period size: 59 Copynumber: 5.0 Consensus size: 59
48341 AATTATTATT
*
48351 ATAATTTCATTATTACTAATCATTACTAAATCATTACTATCAAATCATTAAATATTAATG
1 ATAA-TTCATTATTACTAATCATTACTAAATCATTACTATCAAATCATTAAATATTAATA
*
48411 ATAATTTCATTATT-CTAATCATTACTAAATCATTACTATTAAATCATTAAATATTAATA
1 ATAA-TTCATTATTACTAATCATTACTAAATCATTACTATCAAATCATTAAATATTAATA
48470 ATAAATT-ATTATTACTAATCATTACTAAATCATTACTATCAAATCATTAAATATTAATA
1 AT-AATTCATTATTACTAATCATTACTAAATCATTACTATCAAATCATTAAATATTAATA
* * * * *
48529 ATAAATCATTATTAGTAACCATTACTAAATCATTACTATTAAATAATTAAATATTAATA
1 ATAATTCATTATTACTAATCATTACTAAATCATTACTATCAAATCATTAAATATTAATA
* * * *
48588 ATAAATCATTACTATCAAATCATTACTAAATCATTACTATCAAATAATTAAATATTAATA
1 ATAATTCATTATTA-CTAATCATTACTAAATCATTACTATCAAATCATTAAATATTAATA
48648 A
1 A
48649 ACTAATTACC
Statistics
Matches: 221, Mismatches: 13, Indels: 8
0.91 0.05 0.03
Matches are distributed among these distances:
58 9 0.04
59 154 0.70
60 58 0.26
ACGTcount: A:0.47, C:0.12, G:0.01, T:0.40
Consensus pattern (59 bp):
ATAATTCATTATTACTAATCATTACTAAATCATTACTATCAAATCATTAAATATTAATA
Found at i:48455 original size:14 final size:14
Alignment explanation
Indices: 48322--48637 Score: 59
Period size: 14 Copynumber: 22.9 Consensus size: 14
48312 TAGTAATAAT
*
48322 TATTAAATCATTAA
1 TATTAAATCATTAC
* * *
48336 TATCAAATTATTAT
1 TATTAAATCATTAC
* *
48350 TA-TAATTTCATTAT
1 TATTAA-ATCATTAC
*
48364 TACT-AATCATTAC
1 TATTAAATCATTAC
48377 ---TAAATCATTAC
1 TATTAAATCATTAC
* *
48388 TATCAAATCATTAAA
1 TATTAAATCATT-AC
* *
48403 TATTAATGATAATTTCAT
1 TATTAA--ATCA-TT-AC
*
48421 TATTCTAATCATTAC
1 TATT-AAATCATTAC
48436 ---TAAATCATTAC
1 TATTAAATCATTAC
*
48447 TATTAAATCATTAAA
1 TATTAAATCATT-AC
* *
48462 TATTAATAATAAATTAT
1 TATT-A-AAT-CATTAC
48479 TATTACTAATCATTAC
1 TATTA--AATCATTAC
48495 ---TAAATCATTAC
1 TATTAAATCATTAC
* *
48506 TATCAAATCATTAAA
1 TATTAAATCATT-AC
* * *
48521 TATTAATAATAAATCAT
1 TATT-A-AAT-CATTAC
*
48538 TATTAGTAACCATTAC
1 TATTA--AATCATTAC
48554 ---TAAATCATTAC
1 TATTAAATCATTAC
48565 TATT-AA--A-TA-
1 TATTAAATCATTAC
*
48574 -ATTAAAT-ATTAA
1 TATTAAATCATTAC
*
48586 TAATAAATCATTAC
1 TATTAAATCATTAC
*
48600 TATCAAATCATTAC
1 TATTAAATCATTAC
48614 ---TAAATCATTAC
1 TATTAAATCATTAC
* *
48625 TATCAAATAATTA
1 TATTAAATCATTA
48638 AATATTAATA
Statistics
Matches: 222, Mismatches: 41, Indels: 78
0.65 0.12 0.23
Matches are distributed among these distances:
8 3 0.01
9 2 0.01
10 4 0.02
11 48 0.22
12 1 0.00
13 20 0.09
14 72 0.32
15 17 0.08
16 13 0.06
17 29 0.13
18 12 0.05
19 1 0.00
ACGTcount: A:0.46, C:0.12, G:0.01, T:0.41
Consensus pattern (14 bp):
TATTAAATCATTAC
Found at i:48474 original size:21 final size:21
Alignment explanation
Indices: 48436--48480 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
48426 TAATCATTAC
*
48436 TAAATCATTACTATTAAATCAT
1 TAAAT-ATTACTAATAAATCAT
* *
48458 TAAATATTAATAATAAATTAT
1 TAAATATTACTAATAAATCAT
48479 TA
1 TA
48481 TTACTAATCA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 15 0.75
22 5 0.25
ACGTcount: A:0.51, C:0.07, G:0.00, T:0.42
Consensus pattern (21 bp):
TAAATATTACTAATAAATCAT
Found at i:48525 original size:21 final size:22
Alignment explanation
Indices: 48495--48539 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
48485 TAATCATTAC
*
48495 TAAATCATTACT-ATCAAATCAT
1 TAAATCATTAATAAT-AAATCAT
48517 TAAAT-ATTAATAATAAATCAT
1 TAAATCATTAATAATAAATCAT
48538 TA
1 TA
48540 TTAGTAACCA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 14 0.67
22 7 0.33
ACGTcount: A:0.51, C:0.11, G:0.00, T:0.38
Consensus pattern (22 bp):
TAAATCATTAATAATAAATCAT
Found at i:48821 original size:21 final size:23
Alignment explanation
Indices: 48780--48821 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
48770 AATGTAAAAA
48780 ATAAATTCGACATATTTATAAAG
1 ATAAATTCGACATATTTATAAAG
48803 ATAAATTCGAC-TA-TTATAA
1 ATAAATTCGACATATTTATAA
48822 TCATTATTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 6 0.32
22 2 0.11
23 11 0.58
ACGTcount: A:0.48, C:0.10, G:0.07, T:0.36
Consensus pattern (23 bp):
ATAAATTCGACATATTTATAAAG
Found at i:48987 original size:15 final size:15
Alignment explanation
Indices: 48967--49005 Score: 69
Period size: 15 Copynumber: 2.6 Consensus size: 15
48957 TATTATTACT
*
48967 AAATCATTAAATATA
1 AAATCATTAAAAATA
48982 AAATCATTAAAAATA
1 AAATCATTAAAAATA
48997 AAATCATTA
1 AAATCATTA
49006 TTAAATCATT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.62, C:0.08, G:0.00, T:0.31
Consensus pattern (15 bp):
AAATCATTAAAAATA
Found at i:49059 original size:28 final size:28
Alignment explanation
Indices: 48990--49058 Score: 75
Period size: 28 Copynumber: 2.3 Consensus size: 28
48980 TAAAATCATT
48990 AAAAATAAAATCATTATTAAATCATTAGTAC
1 AAAAATAAAATC---ATTAAATCATTAGTAC
* * *
49021 ATAAATAAAATCATTAAATCATTATTAT
1 AAAAATAAAATCATTAAATCATTAGTAC
49049 AAAACATAAA
1 AAAA-ATAAA
49059 TTCAACTTCA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
28 17 0.52
29 5 0.15
31 11 0.33
ACGTcount: A:0.58, C:0.09, G:0.01, T:0.32
Consensus pattern (28 bp):
AAAAATAAAATCATTAAATCATTAGTAC
Found at i:52067 original size:26 final size:25
Alignment explanation
Indices: 52038--52097 Score: 68
Period size: 26 Copynumber: 2.3 Consensus size: 25
52028 ATTATTAATC
52038 TAATAATTTGATATT-TAATGATTTAA
1 TAATAATTTGAT-TTATAATGA-TTAA
* *
52064 TAATAATATGATTTAGTAATGATTAC
1 TAATAATTTGATTTA-TAATGATTAA
52090 TAATAATT
1 TAATAATT
52098 ATTTATTATA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
25 2 0.07
26 21 0.72
27 6 0.21
ACGTcount: A:0.43, C:0.02, G:0.08, T:0.47
Consensus pattern (25 bp):
TAATAATTTGATTTATAATGATTAA
Found at i:64961 original size:28 final size:30
Alignment explanation
Indices: 64913--64975 Score: 112
Period size: 28 Copynumber: 2.2 Consensus size: 30
64903 TATTTTTATA
64913 TAATATAATATATAACTTAAACTAACAAAC
1 TAATATAATATATAACTTAAACTAACAAAC
64943 TAATAT-A-ATATAACTTAAACTAACAAAC
1 TAATATAATATATAACTTAAACTAACAAAC
64971 TAATA
1 TAATA
64976 ATTTATACTA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
28 26 0.79
29 1 0.03
30 6 0.18
ACGTcount: A:0.57, C:0.13, G:0.00, T:0.30
Consensus pattern (30 bp):
TAATATAATATATAACTTAAACTAACAAAC
Found at i:64982 original size:28 final size:28
Alignment explanation
Indices: 64917--64982 Score: 107
Period size: 28 Copynumber: 2.4 Consensus size: 28
64907 TTTATATAAT
64917 ATAATATATAACTTAAACTAACAAACTA
1 ATAATATATAACTTAAACTAACAAACTA
64945 AT-ATAATATAACTTAAACTAACAAACTA
1 ATAAT-ATATAACTTAAACTAACAAACTA
*
64973 ATAATTTATA
1 ATAATATATA
64983 CTAACAAACT
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
27 2 0.06
28 31 0.89
29 2 0.06
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.32
Consensus pattern (28 bp):
ATAATATATAACTTAAACTAACAAACTA
Found at i:64985 original size:21 final size:21
Alignment explanation
Indices: 64952--65000 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
64942 CTAATATAAT
64952 ATAACTTAAACTAACAAACTA
1 ATAACTTAAACTAACAAACTA
* *
64973 ATAATTTATACTAACAAACTA
1 ATAACTTAAACTAACAAACTA
64994 ATTAACT
1 A-TAACT
65001 AAATTTTAGT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.53, C:0.16, G:0.00, T:0.31
Consensus pattern (21 bp):
ATAACTTAAACTAACAAACTA
Found at i:70677 original size:14 final size:15
Alignment explanation
Indices: 70660--70688 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
70650 GAATAAAATG
70660 AGTGGAAAA-ATGAA
1 AGTGGAAAAGATGAA
70674 AGTGGAAAAGATGAA
1 AGTGGAAAAGATGAA
70689 GGAAAAAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.55, C:0.00, G:0.31, T:0.14
Consensus pattern (15 bp):
AGTGGAAAAGATGAA
Found at i:71315 original size:24 final size:24
Alignment explanation
Indices: 71248--71308 Score: 79
Period size: 24 Copynumber: 2.5 Consensus size: 24
71238 TTTTGGAGGA
* *
71248 CCAAAATATGTGAT-ACTTAAAGTT
1 CCAAAAGATGTG-TCACTTGAAGTT
71272 CCAAAAGATGTGTCACTTGAAGTT
1 CCAAAAGATGTGTCACTTGAAGTT
*
71296 CCAAATGATGTGT
1 CCAAAAGATGTGT
71309 TCTTTGATAT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
23 1 0.03
24 32 0.97
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.31
Consensus pattern (24 bp):
CCAAAAGATGTGTCACTTGAAGTT
Found at i:95764 original size:15 final size:15
Alignment explanation
Indices: 95744--95797 Score: 76
Period size: 15 Copynumber: 3.7 Consensus size: 15
95734 TTTAACTCAT
95744 GAGTCAACTCAGACA
1 GAGTCAACTCAGACA
**
95759 GAGTCAACTC--ATT
1 GAGTCAACTCAGACA
95772 GAGTCAACTCAGACA
1 GAGTCAACTCAGACA
95787 GAGTCAACTCA
1 GAGTCAACTCA
95798 TTGACTTTGA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
13 11 0.33
15 22 0.67
ACGTcount: A:0.37, C:0.26, G:0.19, T:0.19
Consensus pattern (15 bp):
GAGTCAACTCAGACA
Found at i:95777 original size:13 final size:13
Alignment explanation
Indices: 95737--95797 Score: 52
Period size: 15 Copynumber: 4.5 Consensus size: 13
95727 AAGAACCTTT
95737 AACTCA-TGAGTC
1 AACTCACTGAGTC
*
95749 AACTCAGACAGAGTC
1 AACTC--ACTGAGTC
*
95764 AACTCATTGAGTC
1 AACTCACTGAGTC
*
95777 AACTCAGACAGAGTC
1 AACTC--ACTGAGTC
95792 AACTCA
1 AACTCA
95798 TTGACTTTGA
Statistics
Matches: 39, Mismatches: 5, Indels: 9
0.74 0.09 0.17
Matches are distributed among these distances:
12 5 0.13
13 12 0.31
14 1 0.03
15 21 0.54
ACGTcount: A:0.38, C:0.26, G:0.16, T:0.20
Consensus pattern (13 bp):
AACTCACTGAGTC
Found at i:95777 original size:28 final size:28
Alignment explanation
Indices: 95737--95801 Score: 123
Period size: 28 Copynumber: 2.4 Consensus size: 28
95727 AAGAACCTTT
95737 AACTCA-TGAGTCAACTCAGACAGAGTC
1 AACTCATTGAGTCAACTCAGACAGAGTC
95764 AACTCATTGAGTCAACTCAGACAGAGTC
1 AACTCATTGAGTCAACTCAGACAGAGTC
95792 AACTCATTGA
1 AACTCATTGA
95802 CTTTGACCTG
Statistics
Matches: 37, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
27 6 0.16
28 31 0.84
ACGTcount: A:0.37, C:0.25, G:0.17, T:0.22
Consensus pattern (28 bp):
AACTCATTGAGTCAACTCAGACAGAGTC
Done.