Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000259.1 Hibiscus syriacus cultivar Beakdansim tig00000472_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: 68245
ACGTcount: A:0.33, C:0.15, G:0.18, T:0.34
Found at i:1805 original size:2 final size:2
Alignment explanation
Indices: 1798--1843 Score: 85
Period size: 2 Copynumber: 23.5 Consensus size: 2
1788 AAGCTTATCT
1798 TA TA TA TA TA TA TA TA TA TA TA T- TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1839 TA TA T
1 TA TA T
1844 TCAATATTTT
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 42 0.98
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1850 original size:23 final size:23
Alignment explanation
Indices: 1797--1844 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
1787 TAAGCTTATC
1797 TTATATATATATATATATATATA
1 TTATATATATATATATATATATA
1820 TTATATATATATATATATATATA
1 TTATATATATATATATATATATA
1843 TT
1 TT
1845 CAATATTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (23 bp):
TTATATATATATATATATATATA
Found at i:4106 original size:10 final size:9
Alignment explanation
Indices: 4069--4161 Score: 53
Period size: 9 Copynumber: 9.8 Consensus size: 9
4059 CTAAATTACG
*
4069 AAAACAAAT
1 AAAAAAAAT
*
4078 CAAATAAAAT
1 -AAAAAAAAT
*
4088 AAAGAAAAT
1 AAAAAAAAT
4097 AAAAAGAAAT
1 AAAAA-AAAT
*
4107 AAAAAACGAT
1 AAAAAA-AAT
* *
4117 AACTAAAAAC
1 AA-AAAAAAT
*
4127 AAAAAACA-
1 AAAAAAAAT
*
4135 AAAAATAAT
1 AAAAAAAAT
4144 AATGAAAAAAT
1 AA--AAAAAAT
4155 AAAAAAA
1 AAAAAAA
4162 TATATATATA
Statistics
Matches: 64, Mismatches: 13, Indels: 13
0.71 0.14 0.14
Matches are distributed among these distances:
8 6 0.09
9 24 0.38
10 23 0.36
11 11 0.17
ACGTcount: A:0.77, C:0.06, G:0.04, T:0.12
Consensus pattern (9 bp):
AAAAAAAAT
Found at i:4478 original size:30 final size:27
Alignment explanation
Indices: 4428--4491 Score: 69
Period size: 30 Copynumber: 2.3 Consensus size: 27
4418 ACATTAGGAA
4428 AAAT-ATAATAAAATAAATAAATAA-AT
1 AAATAATAATAAAATAAATAAA-AACAT
4454 AAATAATAATAAGAATAAAAATAAAAACAT
1 AAATAATAATAA-AAT--AAATAAAAACAT
*
4484 AAAAAATA
1 AAATAATA
4492 TGTATAATAT
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
26 4 0.12
27 7 0.22
28 3 0.09
29 2 0.06
30 16 0.50
ACGTcount: A:0.75, C:0.02, G:0.02, T:0.22
Consensus pattern (27 bp):
AAATAATAATAAAATAAATAAAAACAT
Found at i:5516 original size:5 final size:5
Alignment explanation
Indices: 5506--5535 Score: 51
Period size: 5 Copynumber: 5.8 Consensus size: 5
5496 ACCTGTAACT
5506 AAATA AAATA AAATA AAATA AAATA TAAAT
1 AAATA AAATA AAATA AAATA AAATA -AAAT
5536 TAATATAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 20 0.83
6 4 0.17
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (5 bp):
AAATA
Found at i:5526 original size:15 final size:16
Alignment explanation
Indices: 5506--5549 Score: 54
Period size: 17 Copynumber: 2.8 Consensus size: 16
5496 ACCTGTAACT
5506 AAATAAAATA-AAATA
1 AAATAAAATATAAATA
5521 AAATAAAATATAAATTA
1 AAATAAAATATAAA-TA
* *
5538 ATATAATATATA
1 AAATAAAATATA
5550 TAGATATTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
15 10 0.40
16 3 0.12
17 12 0.48
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (16 bp):
AAATAAAATATAAATA
Found at i:6444 original size:85 final size:85
Alignment explanation
Indices: 6285--6610 Score: 422
Period size: 86 Copynumber: 3.8 Consensus size: 85
6275 ATGTGCCATC
* *
6285 GAGCTGAATGGAATCGAACTCGACA-GT-TTTGTTGACAAATAACCCTTCTCGCCTTGAGCTATG
1 GAGCTGAATGTAATCGAACTCGA-AGGTCTTTGTTGACAGATAACCCTTCTCGCCTTGAGCTATG
* * *
6348 CTGTAAATTTGATGTTCCTTT
65 ATGTAAATTTGATATGCCTTT
* * * *
6369 GAGCTGAATGTAATCGAACTCGAAGGTCTTTGCTGACAGATAACTCTTCTCTCCTTGAGTTATGA
1 GAGCTGAATGTAATCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTCGCCTTGAGCTATGA
*
6434 TGTAAGTTTGATATGCCTTT
66 TGTAAATTTGATATGCCTTT
* * * * *
6454 GAGCTAAATGTAATCTAACTCGAAGGTCTTTTGTTAACAGATAGCCCTTCTCGCTTTGAGCTATG
1 GAGCTGAATGTAATCGAACTCGAAGGTC-TTTGTTGACAGATAACCCTTCTCGCCTTGAGCTATG
**
6519 CCGTAAATTTGATATGCCTTT
65 ATGTAAATTTGATATGCCTTT
* * * *
6540 GAGCTGAATGTAATCGAACTCGAAGGTTTTTGGTCGATAGATAGCCCTTCTCGCCTTGAGCTATG
1 GAGCTGAATGTAATCGAACTCGAAGGTCTTT-GTTGACAGATAACCCTTCTCGCCTTGAGCTATG
6605 ATGTAA
65 ATGTAA
6611 TTGGCTGGGA
Statistics
Matches: 207, Mismatches: 31, Indels: 6
0.85 0.13 0.02
Matches are distributed among these distances:
83 1 0.00
84 24 0.12
85 77 0.37
86 105 0.51
ACGTcount: A:0.25, C:0.19, G:0.21, T:0.35
Consensus pattern (85 bp):
GAGCTGAATGTAATCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTCGCCTTGAGCTATGA
TGTAAATTTGATATGCCTTT
Found at i:6889 original size:65 final size:64
Alignment explanation
Indices: 6783--7143 Score: 478
Period size: 65 Copynumber: 5.8 Consensus size: 64
6773 TCCAATATTG
* *
6783 TTTGGCTTTGAGTTGGATATCCTTCGTTGTGAAGTTAAAATCCAATCATGTATAAATTTCACCGA
1 TTTGGCTTTGAGTTGGATATCCTTCGTTGTGAAGTTGAAATCCAATCTTG-ATAAATTTCACCGA
* *
6848 TTTGGTTTTGAGTTGGATATCCTTCGTTGTGAAGTTGAAATCCAATCTTGA-ATA-TT-----A
1 TTTGGCTTTGAGTTGGATATCCTTCGTTGTGAAGTTGAAATCCAATCTTGATAAATTTCACCGA
* *
6905 TTTGGCTTTGGGTTAGATATCCTTCGTTGTGAAGTTGAAATCCAATCTTGTATAAATTTCACCGA
1 TTTGGCTTTGAGTTGGATATCCTTCGTTGTGAAGTTGAAATCCAATCTTG-ATAAATTTCACCGA
* * * *
6970 ATTGGCTTTGAGTTGGATATACTTCGTTGTGAAGTTGAAAACCAATCTTGA-ATATTT-----A
1 TTTGGCTTTGAGTTGGATATCCTTCGTTGTGAAGTTGAAATCCAATCTTGATAAATTTCACCGA
* *
7028 TTTGGCTTTGGGTTGGATATCCTTCGTTATGAAGTTGAAATCCAATCTTGCATAAATTTCACCGA
1 TTTGGCTTTGAGTTGGATATCCTTCGTTGTGAAGTTGAAATCCAATCTTG-ATAAATTTCACCGA
* *
7093 ATTGGCTTTGGGTTGGATATCCTTCGTTGTGAAGTTGAAATCCAATCTTGA
1 TTTGGCTTTGAGTTGGATATCCTTCGTTGTGAAGTTGAAATCCAATCTTGA
7144 ATATGTTGCG
Statistics
Matches: 259, Mismatches: 22, Indels: 31
0.83 0.07 0.10
Matches are distributed among these distances:
57 48 0.19
58 47 0.18
59 3 0.01
60 7 0.03
62 2 0.01
63 7 0.03
64 3 0.01
65 142 0.55
ACGTcount: A:0.25, C:0.14, G:0.21, T:0.40
Consensus pattern (64 bp):
TTTGGCTTTGAGTTGGATATCCTTCGTTGTGAAGTTGAAATCCAATCTTGATAAATTTCACCGA
Found at i:6949 original size:122 final size:122
Alignment explanation
Indices: 6737--7147 Score: 647
Period size: 122 Copynumber: 3.4 Consensus size: 122
6727 ATGAAGTTGA
* * *
6737 GCTTTGAATTGGATATCCTTCGTTGTGAAGTTGAAAT-C---C---AATATTGTTTGGCTTTGAG
1 GCTTTGAGTTGGATATCCTTCGTTGTGAAGTTGAAATCCAATCTTGAATATTATTTGGCTTTGGG
* * *
6795 TTGGATATCCTTCGTTGTGAAGTTAAAATCCAATCATGTATAAATTTCACCGATTTG
66 TTGGATATCCTTCGTTGTGAAGTTGAAATCCAATCTTGTATAAATTTCACCGAATTG
*
6852 GTTTTGAGTTGGATATCCTTCGTTGTGAAGTTGAAATCCAATCTTGAATATTATTTGGCTTTGGG
1 GCTTTGAGTTGGATATCCTTCGTTGTGAAGTTGAAATCCAATCTTGAATATTATTTGGCTTTGGG
*
6917 TTAGATATCCTTCGTTGTGAAGTTGAAATCCAATCTTGTATAAATTTCACCGAATTG
66 TTGGATATCCTTCGTTGTGAAGTTGAAATCCAATCTTGTATAAATTTCACCGAATTG
* *
6974 GCTTTGAGTTGGATATACTTCGTTGTGAAGTTGAAAACCAATCTTGAATATTTATTTGGCTTTGG
1 GCTTTGAGTTGGATATCCTTCGTTGTGAAGTTGAAATCCAATCTTGAATA-TTATTTGGCTTTGG
* *
7039 GTTGGATATCCTTCGTTATGAAGTTGAAATCCAATCTTGCATAAATTTCACCGAATTG
65 GTTGGATATCCTTCGTTGTGAAGTTGAAATCCAATCTTGTATAAATTTCACCGAATTG
*
7097 GCTTTGGGTTGGATATCCTTCGTTGTGAAGTTGAAATCCAATCTTGAATAT
1 GCTTTGAGTTGGATATCCTTCGTTGTGAAGTTGAAATCCAATCTTGAATAT
7148 GTTGCGTTAT
Statistics
Matches: 271, Mismatches: 17, Indels: 9
0.91 0.06 0.03
Matches are distributed among these distances:
115 35 0.13
116 1 0.00
119 1 0.00
122 118 0.44
123 116 0.43
ACGTcount: A:0.26, C:0.14, G:0.21, T:0.40
Consensus pattern (122 bp):
GCTTTGAGTTGGATATCCTTCGTTGTGAAGTTGAAATCCAATCTTGAATATTATTTGGCTTTGGG
TTGGATATCCTTCGTTGTGAAGTTGAAATCCAATCTTGTATAAATTTCACCGAATTG
Found at i:7191 original size:123 final size:120
Alignment explanation
Indices: 6737--7147 Score: 573
Period size: 123 Copynumber: 3.4 Consensus size: 120
6727 ATGAAGTTGA
* * *
6737 GCTTTGAATTGGATATCCTTCGTTGTGAAGTTGAAATCCAA---T--AT-TGTTTGGCTTTGAGT
1 GCTTTGAGTTGGATATCCTTCGTTGTGAAGTTGAAATCCAATCTTGAATATTTTTGGCTTTG-GG
** * * *
6796 TGGATATCCTTCGTTGTGAAGTTAAAATCCAATCATGTATAAATTTCACCGATTTG
65 TCAATATCCTTCGTTGTGAAGTTGAAATCCAATCTTGTATAAATTTCACCGAATTG
*
6852 GTTTTGAGTTGGATATCCTTCGTTGTGAAGTTGAAATCCAATCTTGAATATTATTTGGCTTTGGG
1 GCTTTGAGTTGGATATCCTTCGTTGTGAAGTTGAAATCCAATCTTGAATATT-TTTGGCTTTGGG
*
6917 TTAGATATCCTTCGTTGTGAAGTTGAAATCCAATCTTGTATAAATTTCACCGAATTG
65 TCA-ATATCCTTCGTTGTGAAGTTGAAATCCAATCTTGTATAAATTTCACCGAATTG
* *
6974 GCTTTGAGTTGGATATACTTCGTTGTGAAGTTGAAAACCAATCTTGAATATTTATTTGGCTTTGG
1 GCTTTGAGTTGGATATCCTTCGTTGTGAAGTTGAAATCCAATCTTGAATA-TT-TTTGGCTTTGG
** * *
7039 GTTGGATATCCTTCGTTATGAAGTTGAAATCCAATCTTGCATAAATTTCACCGAATTG
64 G-TCAATATCCTTCGTTGTGAAGTTGAAATCCAATCTTGTATAAATTTCACCGAATTG
*
7097 GCTTTGGGTTGGATATCCTTCGTTGTGAAGTTGAAATCCAATCTTGAATAT
1 GCTTTGAGTTGGATATCCTTCGTTGTGAAGTTGAAATCCAATCTTGAATAT
7148 GTTGCGTTAT
Statistics
Matches: 267, Mismatches: 19, Indels: 13
0.89 0.06 0.04
Matches are distributed among these distances:
115 39 0.15
118 1 0.00
120 2 0.01
121 3 0.01
122 108 0.40
123 113 0.42
124 1 0.00
ACGTcount: A:0.26, C:0.14, G:0.21, T:0.40
Consensus pattern (120 bp):
GCTTTGAGTTGGATATCCTTCGTTGTGAAGTTGAAATCCAATCTTGAATATTTTTGGCTTTGGGT
CAATATCCTTCGTTGTGAAGTTGAAATCCAATCTTGTATAAATTTCACCGAATTG
Found at i:13673 original size:74 final size:74
Alignment explanation
Indices: 13585--13730 Score: 213
Period size: 74 Copynumber: 2.0 Consensus size: 74
13575 AAACTCAAAT
*
13585 TTAGGATAATATTTTAAACATTATAT-TTTATCTTTGTATTTTAGTTTAAATAGTTCTTTAGTAT
1 TTAGGATAATATTTTAAACATTATATCTTTATCTTTGTATTTTAGTTTAAATAGAT-TTTAGTAT
13649 TTTAATTAAG
65 TTTAATTAAG
* ** ** *
13659 TTAGGATATTATTTTTTATTTTTTATCTTTATCTTTGTATTTTAGTTTAAATAGATTTTAGTATT
1 TTAGGATAATATTTTAAACATTATATCTTTATCTTTGTATTTTAGTTTAAATAGATTTTAGTATT
13724 TTAATTA
66 TTAATTA
13731 GGTTTTAAAA
Statistics
Matches: 64, Mismatches: 7, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
74 36 0.56
75 28 0.44
ACGTcount: A:0.29, C:0.03, G:0.09, T:0.58
Consensus pattern (74 bp):
TTAGGATAATATTTTAAACATTATATCTTTATCTTTGTATTTTAGTTTAAATAGATTTTAGTATT
TTAATTAAG
Found at i:13754 original size:75 final size:75
Alignment explanation
Indices: 13611--13754 Score: 211
Period size: 75 Copynumber: 1.9 Consensus size: 75
13601 AACATTATAT
* ** *
13611 TTTATCTTTGTATTTTAGTTTAAATAGTTCTTTAGTATTTTAATTAAGTTAGGATATTATTTTTT
1 TTTATCTTTGTATTTTAGTTTAAATAGATCTTTAGTATTTTAATTAAGTTAAAATATTATTTTAT
13676 ATTTTTTATC
66 ATTTTTTATC
*
13686 TTTATCTTTGTATTTTAGTTTAAATAGAT-TTTAGTATTTTAATTAGGTTTTAAAATATTA-TTT
1 TTTATCTTTGTATTTTAGTTTAAATAGATCTTTAGTATTTTAATTAAG--TTAAAATATTATTTT
13749 ATATTT
64 ATATTT
13755 ATTTTAGTTT
Statistics
Matches: 62, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
74 17 0.27
75 36 0.58
76 9 0.15
ACGTcount: A:0.28, C:0.03, G:0.09, T:0.60
Consensus pattern (75 bp):
TTTATCTTTGTATTTTAGTTTAAATAGATCTTTAGTATTTTAATTAAGTTAAAATATTATTTTAT
ATTTTTTATC
Found at i:14394 original size:16 final size:17
Alignment explanation
Indices: 14370--14415 Score: 58
Period size: 16 Copynumber: 2.7 Consensus size: 17
14360 AATCTCTTTA
*
14370 ATTTGTTTATTTAATT-
1 ATTTTTTTATTTAATTC
14386 ATTTTTTTATTTAATTC
1 ATTTTTTTATTTAATTC
*
14403 TTATTTTTTATTT
1 AT-TTTTTTATTT
14416 TAACCACAAC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
16 15 0.58
17 1 0.04
18 10 0.38
ACGTcount: A:0.22, C:0.02, G:0.02, T:0.74
Consensus pattern (17 bp):
ATTTTTTTATTTAATTC
Found at i:14467 original size:16 final size:15
Alignment explanation
Indices: 14446--14480 Score: 52
Period size: 16 Copynumber: 2.3 Consensus size: 15
14436 TCCCCCTTTT
14446 ATATTTATTACTATTA
1 ATATTTATTA-TATTA
*
14462 ATATTTATTATTTTA
1 ATATTTATTATATTA
14477 ATAT
1 ATAT
14481 ATCTTTTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 8 0.44
16 10 0.56
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (15 bp):
ATATTTATTATATTA
Found at i:14479 original size:15 final size:16
Alignment explanation
Indices: 14441--14480 Score: 57
Period size: 15 Copynumber: 2.6 Consensus size: 16
14431 AAAAATCCCC
14441 CTTTT-ATATTTATTA
1 CTTTTAATATTTATTA
*
14456 CTATTAATATTTATTA
1 CTTTTAATATTTATTA
14472 -TTTTAATAT
1 CTTTTAATAT
14481 ATCTTTTTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
15 12 0.55
16 10 0.45
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.62
Consensus pattern (16 bp):
CTTTTAATATTTATTA
Found at i:20076 original size:20 final size:20
Alignment explanation
Indices: 20044--20090 Score: 78
Period size: 19 Copynumber: 2.4 Consensus size: 20
20034 CATTTCGTTA
20044 TATTTTTGTTTTTATTTTTTT
1 TATTTTTGTTTTTA-TTTTTT
20065 TATTTTTG-TTTTATTTTTT
1 TATTTTTGTTTTTATTTTTT
20084 TATTTTT
1 TATTTTT
20091 TTAGCGAACT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
19 13 0.50
20 5 0.19
21 8 0.31
ACGTcount: A:0.11, C:0.00, G:0.04, T:0.85
Consensus pattern (20 bp):
TATTTTTGTTTTTATTTTTT
Found at i:20091 original size:21 final size:22
Alignment explanation
Indices: 20041--20092 Score: 81
Period size: 21 Copynumber: 2.5 Consensus size: 22
20031 ACCCATTTCG
20041 TTATATTTTTGTTTTTATTTTT
1 TTATATTTTTGTTTTTATTTTT
20063 TT-TATTTTTG-TTTTATTTTT
1 TTATATTTTTGTTTTTATTTTT
*
20083 TTATTTTTTT
1 TTATATTTTT
20093 AGCGAACTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
20 12 0.43
21 14 0.50
22 2 0.07
ACGTcount: A:0.12, C:0.00, G:0.04, T:0.85
Consensus pattern (22 bp):
TTATATTTTTGTTTTTATTTTT
Found at i:20093 original size:8 final size:9
Alignment explanation
Indices: 20052--20092 Score: 57
Period size: 9 Copynumber: 4.4 Consensus size: 9
20042 TATATTTTTG
20052 TTTTTATTT
1 TTTTTATTT
20061 TTTTTATTT
1 TTTTTATTT
20070 TTGTTT-TATT
1 TT-TTTAT-TT
20080 TTTTTATTT
1 TTTTTATTT
20089 TTTT
1 TTTT
20093 AGCGAACTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
9 21 0.72
10 8 0.28
ACGTcount: A:0.10, C:0.00, G:0.02, T:0.88
Consensus pattern (9 bp):
TTTTTATTT
Found at i:21849 original size:76 final size:75
Alignment explanation
Indices: 21759--21906 Score: 210
Period size: 76 Copynumber: 2.0 Consensus size: 75
21749 TAAACTGAAA
*
21759 TTTAGGATAATA-TTTTAAGCATTATAT-TTTATCTTTGTATTTTAGTTTAAATAGTTCTTTAGT
1 TTTAGGATAATATTTTTAA-CATTATATCTTTATCTTTGTA-TTTAGTTTAAATAGGT-TTTAGT
21822 ATTTTAATTAAGT
63 ATTTTAATTAAGT
* * * *
21835 TTTAGGATATTATTTTTTATATTTTATCTTTATCTTTGTATTTAGTTTAAATAGGTTTTAGTATT
1 TTTAGGATAATATTTTTAACATTATATCTTTATCTTTGTATTTAGTTTAAATAGGTTTTAGTATT
21900 TTAATTA
66 TTAATTA
21907 GGATTTAAAA
Statistics
Matches: 65, Mismatches: 5, Indels: 5
0.87 0.07 0.07
Matches are distributed among these distances:
75 16 0.25
76 32 0.49
77 17 0.26
ACGTcount: A:0.28, C:0.03, G:0.10, T:0.58
Consensus pattern (75 bp):
TTTAGGATAATATTTTTAACATTATATCTTTATCTTTGTATTTAGTTTAAATAGGTTTTAGTATT
TTAATTAAGT
Found at i:22589 original size:16 final size:16
Alignment explanation
Indices: 22568--22599 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
22558 AATCTCTTTA
22568 ATTTGTTTATTTAATT
1 ATTTGTTTATTTAATT
22584 ATTTGTTTATTTAATT
1 ATTTGTTTATTTAATT
22600 CTTATTTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.25, C:0.00, G:0.06, T:0.69
Consensus pattern (16 bp):
ATTTGTTTATTTAATT
Found at i:24436 original size:18 final size:18
Alignment explanation
Indices: 24413--24449 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
24403 TTTGCACTCG
24413 TAGCAAATAATAGGGTCT
1 TAGCAAATAATAGGGTCT
24431 TAGCAAATAATAGGGTCT
1 TAGCAAATAATAGGGTCT
24449 T
1 T
24450 TCTCATTCGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.38, C:0.11, G:0.22, T:0.30
Consensus pattern (18 bp):
TAGCAAATAATAGGGTCT
Found at i:27561 original size:99 final size:99
Alignment explanation
Indices: 27390--27598 Score: 303
Period size: 99 Copynumber: 2.1 Consensus size: 99
27380 GGACAACTCA
* * * * *
27390 ATATTATAATCACCTTTATTAGGTTAGCTGAATCTTATCCATAGATACGGGGCGTTTAACCAATT
1 ATATTATAATCACCTTTATCAGGCTAGCTGAATCTTATCCATAAATACGGGGAGGTTAACCAATT
* * *
27455 GCTCTAGAGGGATAGCTCAAGCTTTATTGTATAG
66 ACTCTAGAGGGACAACTCAAGCTTTATTGTATAG
*
27489 ATATTATAATCGCCTTTATCAGGCTAGCTGAATCTTATCCATAAAGT-CGGGGAGGTTAACCAAT
1 ATATTATAATCACCTTTATCAGGCTAGCTGAATCTTATCCATAAA-TACGGGGAGGTTAACCAAT
*
27553 TACTCTAGAGGGACAACTCAAGCTTTATTGTATAT
65 TACTCTAGAGGGACAACTCAAGCTTTATTGTATAG
*
27588 ATAATATAATC
1 ATATTATAATC
27599 TGGGAATACG
Statistics
Matches: 98, Mismatches: 11, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
99 97 0.99
100 1 0.01
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.34
Consensus pattern (99 bp):
ATATTATAATCACCTTTATCAGGCTAGCTGAATCTTATCCATAAATACGGGGAGGTTAACCAATT
ACTCTAGAGGGACAACTCAAGCTTTATTGTATAG
Found at i:31599 original size:5 final size:5
Alignment explanation
Indices: 31589--31644 Score: 57
Period size: 5 Copynumber: 11.6 Consensus size: 5
31579 TTATGGAAAC
*
31589 AAATA AAATA AAAT- AAAGA AAATA AAATA AAA-A GAAATA AAA-A ACAAT-
1 AAATA AAATA AAATA AAATA AAATA AAATA AAATA -AAATA AAATA A-AATA
31637 AAATA AAA
1 AAATA AAA
31645 ACAAAAACAA
Statistics
Matches: 43, Mismatches: 2, Indels: 12
0.75 0.04 0.21
Matches are distributed among these distances:
4 9 0.21
5 33 0.77
6 1 0.02
ACGTcount: A:0.80, C:0.02, G:0.04, T:0.14
Consensus pattern (5 bp):
AAATA
Found at i:31612 original size:14 final size:14
Alignment explanation
Indices: 31593--31667 Score: 62
Period size: 15 Copynumber: 5.1 Consensus size: 14
31583 GGAAACAAAT
*
31593 AAAATAAAATAAAG
1 AAAATAAAATAAAA
31607 AAAATAAAATAAAA
1 AAAATAAAATAAAA
31621 AGAAATAAAA-AACAA
1 A-AAATAAAATAA-AA
* *
31636 TAAATAAAAACAAAA
1 AAAAT-AAAATAAAA
* *
31651 ACAAAAAAAAGAAAA
1 A-AAATAAAATAAAA
31666 AA
1 AA
31668 GGAAAAACTA
Statistics
Matches: 51, Mismatches: 5, Indels: 10
0.77 0.08 0.15
Matches are distributed among these distances:
14 21 0.41
15 25 0.49
16 5 0.10
ACGTcount: A:0.83, C:0.04, G:0.04, T:0.09
Consensus pattern (14 bp):
AAAATAAAATAAAA
Found at i:31645 original size:15 final size:14
Alignment explanation
Indices: 31594--31650 Score: 53
Period size: 14 Copynumber: 3.9 Consensus size: 14
31584 GAAACAAATA
*
31594 AAAT-AAAATAAAG
1 AAATAAAAAAAAAG
31607 AAAATAAAATAAAAAG
1 -AAATAAAA-AAAAAG
* *
31623 AAATAAAAAACAAT
1 AAATAAAAAAAAAG
31637 AAATAAAAACAAAA
1 AAATAAAAA-AAAA
31651 ACAAAAAAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
14 17 0.47
15 14 0.39
16 5 0.14
ACGTcount: A:0.81, C:0.04, G:0.04, T:0.12
Consensus pattern (14 bp):
AAATAAAAAAAAAG
Found at i:31645 original size:24 final size:23
Alignment explanation
Indices: 31589--31667 Score: 74
Period size: 24 Copynumber: 3.4 Consensus size: 23
31579 TTATGGAAAC
*
31589 AAATAAAATAAAATAAAGAAAATA
1 AAATAAAA-AAAATAAAAAAAATA
31613 AAATAAAAAGAAATAAAAAACAAT-
1 AAATAAAAA-AAATAAAAAA-AATA
* *
31637 AAATAAAAACAA-AAACAAAA-A
1 AAATAAAAAAAATAAAAAAAATA
*
31658 AAAGAAAAAA
1 AAATAAAAAA
31668 GGAAAAACTA
Statistics
Matches: 47, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
21 10 0.21
22 5 0.11
23 3 0.06
24 26 0.55
25 3 0.06
ACGTcount: A:0.82, C:0.04, G:0.04, T:0.10
Consensus pattern (23 bp):
AAATAAAAAAAATAAAAAAAATA
Found at i:31646 original size:13 final size:12
Alignment explanation
Indices: 31598--31657 Score: 50
Period size: 12 Copynumber: 4.8 Consensus size: 12
31588 CAAATAAAAT
*
31598 AAAATAAAGAAAA
1 AAAATAAA-AACA
*
31611 TAAAATAAAAAGA
1 -AAAATAAAAACA
*
31624 AATA-AAAAACA
1 AAAATAAAAACA
31635 ATAAATAAAAACA
1 A-AAATAAAAACA
*
31648 AAAACAAAAA
1 AAAATAAAAA
31658 AAAGAAAAAA
Statistics
Matches: 39, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
11 7 0.18
12 13 0.33
13 11 0.28
14 8 0.21
ACGTcount: A:0.82, C:0.05, G:0.03, T:0.10
Consensus pattern (12 bp):
AAAATAAAAACA
Found at i:31667 original size:10 final size:10
Alignment explanation
Indices: 31593--31666 Score: 53
Period size: 10 Copynumber: 7.4 Consensus size: 10
31583 GGAAACAAAT
31593 AAAAT-AAAA
1 AAAATAAAAA
* * *
31602 TAAAGAAAAT
1 AAAATAAAAA
31612 AAAATAAAAA
1 AAAATAAAAA
*
31622 GAAATAAAAA
1 AAAATAAAAA
* *
31632 ACAATAAATA
1 AAAATAAAAA
*
31642 AAAACAAAAA
1 AAAATAAAAA
31652 CAAAA-AAAAGA
1 -AAAATAAAA-A
31663 AAAA
1 AAAA
31667 AGGAAAAACT
Statistics
Matches: 49, Mismatches: 13, Indels: 5
0.73 0.19 0.07
Matches are distributed among these distances:
9 3 0.06
10 41 0.84
11 5 0.10
ACGTcount: A:0.82, C:0.04, G:0.04, T:0.09
Consensus pattern (10 bp):
AAAATAAAAA
Found at i:32075 original size:4 final size:4
Alignment explanation
Indices: 32066--32111 Score: 51
Period size: 4 Copynumber: 11.5 Consensus size: 4
32056 AGGAAAAACA
*
32066 AAAT AAAT AAAT AAAAT AAAT -AAT AAAA ATAAT AAAT -AAT AAAT AA
1 AAAT AAAT AAAT -AAAT AAAT AAAT AAAT A-AAT AAAT AAAT AAAT AA
32112 TAGTAAAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
3 6 0.17
4 23 0.64
5 7 0.19
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AAAT
Found at i:32083 original size:13 final size:13
Alignment explanation
Indices: 32065--32104 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
32055 TAGGAAAAAC
32065 AAAATAAATAAAT
1 AAAATAAATAAAT
32078 AAAATAAAT-AAT
1 AAAATAAATAAAT
32090 AAAA-ATAATAAAT
1 AAAATA-AATAAAT
32103 AA
1 AA
32105 TAAATAATAG
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
11 1 0.04
12 10 0.40
13 14 0.56
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.23
Consensus pattern (13 bp):
AAAATAAATAAAT
Found at i:32098 original size:9 final size:9
Alignment explanation
Indices: 32065--32154 Score: 66
Period size: 9 Copynumber: 10.3 Consensus size: 9
32055 TAGGAAAAAC
32065 AAAATAA-A
1 AAAATAATA
*
32073 TAAATAA-A
1 AAAATAATA
32081 ATAAATAATA
1 A-AAATAATA
32091 AAAATAAT-
1 AAAATAATA
32099 -AAATAATA
1 AAAATAATA
*
32107 AATAATAGTAA
1 AA-AATAAT-A
*
32118 AAAAGAATA
1 AAAATAATA
*
32127 AAAAGAATA
1 AAAATAATA
32136 AAAATAA-A
1 AAAATAATA
*
32144 AACATAA-A
1 AAAATAATA
32152 AAA
1 AAA
32155 TATGTATAAT
Statistics
Matches: 68, Mismatches: 8, Indels: 12
0.77 0.09 0.14
Matches are distributed among these distances:
7 7 0.10
8 17 0.25
9 30 0.44
10 11 0.16
11 3 0.04
ACGTcount: A:0.77, C:0.01, G:0.03, T:0.19
Consensus pattern (9 bp):
AAAATAATA
Found at i:32145 original size:16 final size:17
Alignment explanation
Indices: 32066--32145 Score: 60
Period size: 16 Copynumber: 4.7 Consensus size: 17
32056 AGGAAAAACA
*
32066 AAATAAATAAATAA-AAT
1 AAAT-AATAAAAAAGAAT
*
32083 AAATAAT-AAAAATAAT
1 AAATAATAAAAAAGAAT
*
32099 AAATAATAAATAATAGTAAA
1 AAATAATAAA-AA-AG-AAT
*
32119 AAAGAAT-AAAAAGAAT
1 AAATAATAAAAAAGAAT
32135 AAA-AATAAAAA
1 AAATAATAAAAA
32146 CATAAAAAAT
Statistics
Matches: 52, Mismatches: 5, Indels: 13
0.74 0.07 0.19
Matches are distributed among these distances:
15 7 0.13
16 22 0.42
17 8 0.15
18 4 0.08
19 3 0.06
20 8 0.15
ACGTcount: A:0.76, C:0.00, G:0.04, T:0.20
Consensus pattern (17 bp):
AAATAATAAAAAAGAAT
Found at i:32150 original size:8 final size:7
Alignment explanation
Indices: 32065--32156 Score: 50
Period size: 7 Copynumber: 12.9 Consensus size: 7
32055 TAGGAAAAAC
32065 AAAATAA
1 AAAATAA
32072 ATAAAT--
1 A-AAATAA
32078 AAAATAA
1 AAAATAA
*
32085 ATAAT-A
1 AAAATAA
32091 AAAATAA
1 AAAATAA
*
32098 TAAATAA
1 AAAATAA
*
32105 TAAATAA
1 AAAATAA
32112 TAGTAAA-AA
1 -A--AAATAA
*
32121 AGAATAA
1 AAAATAA
32128 AAAGA-ATA
1 AAA-ATA-A
32136 AAAATAA
1 AAAATAA
32143 AAACATAA
1 AAA-ATAA
32151 AAAATA
1 AAAATA
32157 TGTATAATAT
Statistics
Matches: 67, Mismatches: 6, Indels: 24
0.69 0.06 0.25
Matches are distributed among these distances:
5 4 0.06
6 8 0.12
7 32 0.48
8 18 0.27
9 2 0.03
10 3 0.04
ACGTcount: A:0.76, C:0.01, G:0.03, T:0.20
Consensus pattern (7 bp):
AAAATAA
Found at i:38633 original size:22 final size:22
Alignment explanation
Indices: 38607--38652 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
38597 TTATCAGTTG
38607 CGATTTTGCTCTATCCGATAGC
1 CGATTTTGCTCTATCCGATAGC
38629 CGATTTTGCTCTATCCGATAGC
1 CGATTTTGCTCTATCCGATAGC
38651 CG
1 CG
38653 TCTTCCGCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.17, C:0.28, G:0.20, T:0.35
Consensus pattern (22 bp):
CGATTTTGCTCTATCCGATAGC
Found at i:44295 original size:7 final size:7
Alignment explanation
Indices: 44283--44324 Score: 57
Period size: 7 Copynumber: 5.9 Consensus size: 7
44273 TAAACCAAAA
44283 AATATTT
1 AATATTT
44290 AATATTT
1 AATATTT
44297 AATATTT
1 AATATTT
*
44304 AATATAT
1 AATATTT
*
44311 ATTATTT
1 AATATTT
44318 ATATATT
1 A-ATATT
44325 ATTTATAAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
7 26 0.87
8 4 0.13
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (7 bp):
AATATTT
Found at i:44320 original size:11 final size:11
Alignment explanation
Indices: 44306--44331 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
44296 TAATATTTAA
44306 TATATATTATT
1 TATATATTATT
44317 TATATATTATT
1 TATATATTATT
44328 TATA
1 TATA
44332 AATTTGGTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (11 bp):
TATATATTATT
Found at i:47139 original size:5 final size:5
Alignment explanation
Indices: 47126--47338 Score: 354
Period size: 5 Copynumber: 42.6 Consensus size: 5
47116 TTATTAAACG
* * * * * * *
47126 GATAT GATAG GATAT GATAG GATAT GATAG GATAG GATAG GATAG GATAG
1 GATAT GATAT GATAT GATAT GATAT GATAT GATAT GATAT GATAT GATAT
*
47176 GATAG GATAT GATAT GATAT GATAT GATAT GATAT GATAT GATAT GATAT
1 GATAT GATAT GATAT GATAT GATAT GATAT GATAT GATAT GATAT GATAT
47226 GATAT GATAT GATAT GATAT GATAT GATAT GATAT GATAT GATAT GATAT
1 GATAT GATAT GATAT GATAT GATAT GATAT GATAT GATAT GATAT GATAT
47276 GATAT GATAT GATAT GATAT GATAT GATAT GATAT GATAT GATAT GATAT
1 GATAT GATAT GATAT GATAT GATAT GATAT GATAT GATAT GATAT GATAT
47326 GATAT GATAT GAT
1 GATAT GATAT GAT
47339 TGTATGTTGT
Statistics
Matches: 202, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
5 202 1.00
ACGTcount: A:0.40, C:0.00, G:0.24, T:0.36
Consensus pattern (5 bp):
GATAT
Found at i:47666 original size:36 final size:36
Alignment explanation
Indices: 47597--47668 Score: 99
Period size: 36 Copynumber: 2.0 Consensus size: 36
47587 TAAAATTTAA
* * *
47597 AATAAGTATGTAAGTTATGGTAAATACGGAAGTTAT
1 AATAAGTATGAAAGTTATGATAAATACGAAAGTTAT
* *
47633 AATAAGTATGAAAGTTATGATACATATGAAAGTTAT
1 AATAAGTATGAAAGTTATGATAAATACGAAAGTTAT
47669 GAAATATGTA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.44, C:0.03, G:0.19, T:0.33
Consensus pattern (36 bp):
AATAAGTATGAAAGTTATGATAAATACGAAAGTTAT
Found at i:47669 original size:18 final size:17
Alignment explanation
Indices: 47598--47676 Score: 70
Period size: 18 Copynumber: 4.5 Consensus size: 17
47588 AAAATTTAAA
*
47598 ATAAGTATGTAAGTTATG
1 ATAA-TATGAAAGTTATG
* * * *
47616 GTAAATACGGAAGTTATA
1 AT-AATATGAAAGTTATG
47634 ATAAGTATGAAAGTTATG
1 ATAA-TATGAAAGTTATG
47652 ATACATATGAAAGTTATG
1 ATA-ATATGAAAGTTATG
47670 A-AATATG
1 ATAATATG
47677 TACGAATGGA
Statistics
Matches: 50, Mismatches: 8, Indels: 8
0.76 0.12 0.12
Matches are distributed among these distances:
16 5 0.10
17 3 0.06
18 39 0.78
19 3 0.06
ACGTcount: A:0.44, C:0.03, G:0.20, T:0.33
Consensus pattern (17 bp):
ATAATATGAAAGTTATG
Found at i:50222 original size:27 final size:27
Alignment explanation
Indices: 50190--50253 Score: 119
Period size: 27 Copynumber: 2.4 Consensus size: 27
50180 TGAAGTTGTC
*
50190 TAGAAATTTAAATTCGAACAGTTAGTT
1 TAGAAATTTAAATTCGAACAATTAGTT
50217 TAGAAATTTAAATTCGAACAATTAGTT
1 TAGAAATTTAAATTCGAACAATTAGTT
50244 TAGAAATTTA
1 TAGAAATTTA
50254 CCATAAATTA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.44, C:0.06, G:0.12, T:0.38
Consensus pattern (27 bp):
TAGAAATTTAAATTCGAACAATTAGTT
Found at i:50984 original size:17 final size:16
Alignment explanation
Indices: 50947--51007 Score: 61
Period size: 17 Copynumber: 3.6 Consensus size: 16
50937 TCTTTATAGA
50947 TATCAGATGATTATA-AT
1 TATCAGAT-ATT-TACAT
50964 TATCAGATATTTACAT
1 TATCAGATATTTACAT
*
50980 ATATCAAATATTTTACAGT
1 -TATCAGATA-TTTACA-T
50999 TATCAGATA
1 TATCAGATA
51008 CATGTTAATA
Statistics
Matches: 38, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
15 2 0.05
16 5 0.13
17 16 0.42
18 14 0.37
19 1 0.03
ACGTcount: A:0.41, C:0.10, G:0.08, T:0.41
Consensus pattern (16 bp):
TATCAGATATTTACAT
Found at i:51003 original size:35 final size:36
Alignment explanation
Indices: 50912--51007 Score: 101
Period size: 35 Copynumber: 2.8 Consensus size: 36
50902 TGTTTATAGT
* * * *
50912 TATCATATGATTTT-CAGTTATAAGATCTTTATAGA
1 TATCAAATGATTTTACAGTTATCAGATATTTACAGA
* * *
50947 TATCAGATGATTATA-A-TTATCAGATATTTACATA
1 TATCAAATGATTTTACAGTTATCAGATATTTACAGA
50981 TATCAAAT-ATTTTACAGTTATCAGATA
1 TATCAAATGATTTTACAGTTATCAGATA
51008 CATGTTAATA
Statistics
Matches: 50, Mismatches: 8, Indels: 6
0.78 0.12 0.09
Matches are distributed among these distances:
33 5 0.10
34 22 0.44
35 23 0.46
ACGTcount: A:0.39, C:0.09, G:0.09, T:0.43
Consensus pattern (36 bp):
TATCAAATGATTTTACAGTTATCAGATATTTACAGA
Found at i:51170 original size:43 final size:42
Alignment explanation
Indices: 51108--51195 Score: 122
Period size: 43 Copynumber: 2.1 Consensus size: 42
51098 GTGCTTATCC
* *
51108 GTTATCAATTATCAAATCAGCTTTGGTACATTCTTGTATCAAT
1 GTTATCAACTATCAAATCAGCTTTGGTA-ATTCGTGTATCAAT
* * *
51151 GTTATCAGCTATCATATCAGCTTTGGTAATTCGTGTATTAAT
1 GTTATCAACTATCAAATCAGCTTTGGTAATTCGTGTATCAAT
51193 GTT
1 GTT
51196 TAGTACCGTT
Statistics
Matches: 40, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
42 15 0.38
43 25 0.62
ACGTcount: A:0.27, C:0.15, G:0.15, T:0.43
Consensus pattern (42 bp):
GTTATCAACTATCAAATCAGCTTTGGTAATTCGTGTATCAAT
Found at i:57502 original size:3 final size:3
Alignment explanation
Indices: 57494--57519 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
57484 TTGATTTAAA
57494 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
57520 AGTGTTAGAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:57780 original size:34 final size:34
Alignment explanation
Indices: 57742--57818 Score: 93
Period size: 34 Copynumber: 2.2 Consensus size: 34
57732 TATGGTTTTT
*
57742 AGTTATCAGATCTTTACATATATCAGATGA-TTAC
1 AGTTATCAGATATTTACATATATCAGAT-ATTTAC
* * *
57776 AGTTATAAGCTATTTACATATATTAGATATTTTAC
1 AGTTATCAGATATTTACATATATCAGATA-TTTAC
57811 AGTTATCA
1 AGTTATCA
57819 TATACAAATT
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
33 1 0.03
34 24 0.67
35 11 0.31
ACGTcount: A:0.36, C:0.12, G:0.10, T:0.42
Consensus pattern (34 bp):
AGTTATCAGATATTTACATATATCAGATATTTAC
Found at i:59455 original size:44 final size:44
Alignment explanation
Indices: 59392--59481 Score: 180
Period size: 44 Copynumber: 2.0 Consensus size: 44
59382 AAAGATGAAC
59392 ACAGGTGCCTCTGGCAATGGCATTTACTTGAAGAAACATCATTA
1 ACAGGTGCCTCTGGCAATGGCATTTACTTGAAGAAACATCATTA
59436 ACAGGTGCCTCTGGCAATGGCATTTACTTGAAGAAACATCATTA
1 ACAGGTGCCTCTGGCAATGGCATTTACTTGAAGAAACATCATTA
59480 AC
1 AC
59482 CAATGAATAC
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 46 1.00
ACGTcount: A:0.32, C:0.21, G:0.20, T:0.27
Consensus pattern (44 bp):
ACAGGTGCCTCTGGCAATGGCATTTACTTGAAGAAACATCATTA
Found at i:59957 original size:37 final size:36
Alignment explanation
Indices: 59884--59987 Score: 111
Period size: 37 Copynumber: 2.8 Consensus size: 36
59874 GTATGTAGCG
*
59884 GCAACAAACATAACACAACGAAA-AAGCGATCTCAACC
1 GCAACAAACATAACACAAC-AAATAAGTGA-CTCAACC
59921 GCAACAAACATAACACAACAAATAAGTGACTGCAACC
1 GCAACAAACATAACACAACAAATAAGTGACT-CAACC
* * * * * *
59958 ACAATAAACACAGCACATCGAATAAGTGAC
1 GCAACAAACATAACACAACAAATAAGTGAC
59988 CACAAATACA
Statistics
Matches: 58, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
36 5 0.09
37 53 0.91
ACGTcount: A:0.51, C:0.27, G:0.12, T:0.11
Consensus pattern (36 bp):
GCAACAAACATAACACAACAAATAAGTGACTCAACC
Found at i:62203 original size:12 final size:10
Alignment explanation
Indices: 62162--62202 Score: 57
Period size: 10 Copynumber: 4.1 Consensus size: 10
62152 TTTATCACAC
62162 CAAATTCTCT
1 CAAATTCTCT
62172 CAAATTCTCT
1 CAAATTCTCT
62182 -AAATTTCTCT
1 CAAA-TTCTCT
*
62192 CAAATACTCT
1 CAAATTCTCT
62202 C
1 C
62203 TTTTTAAGGT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
9 3 0.11
10 22 0.79
11 3 0.11
ACGTcount: A:0.32, C:0.29, G:0.00, T:0.39
Consensus pattern (10 bp):
CAAATTCTCT
Found at i:62251 original size:13 final size:14
Alignment explanation
Indices: 62223--62251 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
62213 ATATTTTATA
62223 ATATTTTTACTATT
1 ATATTTTTACTATT
62237 ATATTTTTACT-TT
1 ATATTTTTACTATT
62250 AT
1 AT
62252 TTAATATTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 4 0.27
14 11 0.73
ACGTcount: A:0.28, C:0.07, G:0.00, T:0.66
Consensus pattern (14 bp):
ATATTTTTACTATT
Done.