Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001652.1 Hibiscus syriacus cultivar Beakdansim tig00003305_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: 56924
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Found at i:4230 original size:17 final size:17
Alignment explanation
Indices: 4190--4232 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
4180 TGGTTCATAA
4190 ATTAAACTAGTTAATTC
1 ATTAAACTAGTTAATTC
* *
4207 ATCAAACTAGTTTATTTC
1 ATTAAACTAG-TTAATTC
4225 -TTAAACTA
1 ATTAAACTA
4233 ACTCTTAATT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
17 16 0.73
18 6 0.27
ACGTcount: A:0.40, C:0.14, G:0.05, T:0.42
Consensus pattern (17 bp):
ATTAAACTAGTTAATTC
Found at i:9501 original size:20 final size:19
Alignment explanation
Indices: 9467--9513 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
9457 AATGATTTGG
*
9467 TTTTGAAAGCAAAATCTAA
1 TTTTGAAAGCAAAATCAAA
* *
9486 TTTTGAGAATCAAAATGAAA
1 TTTTGA-AAGCAAAATCAAA
9506 TTTTGAAA
1 TTTTGAAA
9514 AAAATTATTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 8 0.33
20 16 0.67
ACGTcount: A:0.47, C:0.06, G:0.13, T:0.34
Consensus pattern (19 bp):
TTTTGAAAGCAAAATCAAA
Found at i:13135 original size:13 final size:13
Alignment explanation
Indices: 13113--13147 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
13103 TGATTGTGGC
*
13113 CGGCGTCGGTGTT
1 CGGCGCCGGTGTT
13126 CGGCGCCGGTGTT
1 CGGCGCCGGTGTT
*
13139 CGACGCCGG
1 CGGCGCCGG
13148 AGTGCGGCTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.03, C:0.31, G:0.46, T:0.20
Consensus pattern (13 bp):
CGGCGCCGGTGTT
Found at i:13732 original size:16 final size:18
Alignment explanation
Indices: 13710--13750 Score: 61
Period size: 16 Copynumber: 2.4 Consensus size: 18
13700 ATTACTTTTA
13710 AATTTATTTTA-AATATT
1 AATTTATTTTATAATATT
13727 -ATTTA-TTTATAATATT
1 AATTTATTTTATAATATT
13743 AATTTATT
1 AATTTATT
13751 ATTACTTTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
15 4 0.19
16 11 0.52
17 5 0.24
18 1 0.05
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (18 bp):
AATTTATTTTATAATATT
Found at i:13752 original size:20 final size:18
Alignment explanation
Indices: 13723--13774 Score: 50
Period size: 20 Copynumber: 2.6 Consensus size: 18
13713 TTATTTTAAA
13723 TATTATTTATTTATAATAT
1 TATTA-TTATTTATAATAT
*
13742 TAATTTATTATTACTTTAATAT
1 T-A-TTATTATT--TATAATAT
13764 TATTATTATTT
1 TATTATTATTT
13775 CATATTAGTC
Statistics
Matches: 28, Mismatches: 1, Indels: 9
0.74 0.03 0.24
Matches are distributed among these distances:
18 1 0.04
19 1 0.04
20 14 0.50
21 4 0.14
22 8 0.29
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (18 bp):
TATTATTATTTATAATAT
Found at i:13794 original size:2 final size:2
Alignment explanation
Indices: 13789--13844 Score: 103
Period size: 2 Copynumber: 28.0 Consensus size: 2
13779 TTAGTCACAC
13789 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
*
13831 TT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT
13845 TTTAAATAAT
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:14201 original size:12 final size:13
Alignment explanation
Indices: 14181--14220 Score: 55
Period size: 12 Copynumber: 3.1 Consensus size: 13
14171 TATTTCTAAA
14181 TAAATAAATATTT
1 TAAATAAATATTT
*
14194 T-TATAAATATATT
1 TAAATAAATAT-TT
14207 TAAATAAATATTT
1 TAAATAAATATTT
14220 T
1 T
14221 CTTAAAAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
12 8 0.35
13 7 0.30
14 8 0.35
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (13 bp):
TAAATAAATATTT
Found at i:14746 original size:8 final size:9
Alignment explanation
Indices: 14707--14771 Score: 53
Period size: 9 Copynumber: 7.0 Consensus size: 9
14697 TTTCTTTCAA
14707 ATTTTA-TT
1 ATTTTATTT
14715 ACTTTTATATT
1 A-TTTTAT-TT
*
14726 ATTTTATTA
1 ATTTTATTT
14735 ATTTT-TTT
1 ATTTTATTT
*
14743 ATTTTATTCAG
1 ATTTTATT--T
*
14754 ATATTATTT
1 ATTTTATTT
14763 ATTTTATTT
1 ATTTTATTT
14772 GTCTGTTAGA
Statistics
Matches: 45, Mismatches: 6, Indels: 11
0.73 0.10 0.18
Matches are distributed among these distances:
8 8 0.18
9 21 0.47
10 6 0.13
11 10 0.22
ACGTcount: A:0.26, C:0.03, G:0.02, T:0.69
Consensus pattern (9 bp):
ATTTTATTT
Found at i:14763 original size:20 final size:17
Alignment explanation
Indices: 14707--14770 Score: 65
Period size: 20 Copynumber: 3.5 Consensus size: 17
14697 TTTCTTTCAA
*
14707 ATTTTATTACTTTTATATT
1 ATTTTATTA-ATTTAT-TT
*
14726 ATTTTATTAATTTTTTT
1 ATTTTATTAATTTATTT
14743 ATTTTATTCAGATATTATTT
1 ATTTTATT-A-AT-TTATTT
14763 ATTTTATT
1 ATTTTATT
14771 TGTCTGTTAG
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
17 10 0.26
18 5 0.13
19 11 0.28
20 13 0.33
ACGTcount: A:0.27, C:0.03, G:0.02, T:0.69
Consensus pattern (17 bp):
ATTTTATTAATTTATTT
Found at i:19695 original size:7 final size:7
Alignment explanation
Indices: 19680--19763 Score: 68
Period size: 7 Copynumber: 12.3 Consensus size: 7
19670 TCCAACAAAG
19680 AAAGAAA
1 AAAGAAA
19687 AAAGGAAA
1 AAA-GAAA
** *
19695 AATCCAAC
1 AA-AGAAA
19703 AAAGAAA
1 AAAGAAA
*
19710 GAAGAAA
1 AAAGAAA
*
19717 GAA-AAA
1 AAAGAAA
19723 AAAGAAA
1 AAAGAAA
19730 AAAGAAA
1 AAAGAAA
19737 AAAG-AA
1 AAAGAAA
19743 AAA-AAA
1 AAAGAAA
*
19749 AGA-AAA
1 AAAGAAA
19755 AAAGAAA
1 AAAGAAA
19762 AA
1 AA
19764 TGGGAGAAAT
Statistics
Matches: 62, Mismatches: 10, Indels: 10
0.76 0.12 0.12
Matches are distributed among these distances:
6 19 0.31
7 33 0.53
8 10 0.16
ACGTcount: A:0.81, C:0.04, G:0.14, T:0.01
Consensus pattern (7 bp):
AAAGAAA
Found at i:19700 original size:27 final size:27
Alignment explanation
Indices: 19669--19746 Score: 92
Period size: 27 Copynumber: 3.0 Consensus size: 27
19659 TCTTATACTC
19669 ATCCAACAAAGAAAGAAAAAAGGAAAA
1 ATCCAACAAAGAAAGAAAAAAGGAAAA
*
19696 ATCCAACAAAGAAAGAAGAAA-GAAAA
1 ATCCAACAAAGAAAGAAAAAAGGAAAA
* * *
19722 A--AAAGAAA-AAAGAAAAAAGAAAAA
1 ATCCAACAAAGAAAGAAAAAAGGAAAA
19746 A
1 A
19747 AAAGAAAAAA
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
23 9 0.20
24 10 0.22
26 6 0.13
27 20 0.44
ACGTcount: A:0.76, C:0.08, G:0.14, T:0.03
Consensus pattern (27 bp):
ATCCAACAAAGAAAGAAAAAAGGAAAA
Found at i:19728 original size:16 final size:16
Alignment explanation
Indices: 19707--19763 Score: 80
Period size: 16 Copynumber: 3.6 Consensus size: 16
19697 TCCAACAAAG
*
19707 AAAGAAGAAAGAAAAA
1 AAAGAAAAAAGAAAAA
19723 AAAGAAAAAAGAAAAA
1 AAAGAAAAAAGAAAAA
*
19739 AGAAAAAAAAAG-AAAA
1 A-AAGAAAAAAGAAAAA
19755 AAAGAAAAA
1 AAAGAAAAA
19764 TGGGAGAAAT
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
15 7 0.19
16 21 0.57
17 9 0.24
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (16 bp):
AAAGAAAAAAGAAAAA
Found at i:19732 original size:8 final size:8
Alignment explanation
Indices: 19714--19763 Score: 66
Period size: 8 Copynumber: 6.1 Consensus size: 8
19704 AAGAAAGAAG
19714 AAAGAAAA
1 AAAGAAAA
19722 AAA-AGAAA
1 AAAGA-AAA
19730 AAAGAAAA
1 AAAGAAAA
*
19738 AAGAAAAAA
1 AA-AGAAAA
19747 AAAGAAAA
1 AAAGAAAA
19755 AAAGAAAA
1 AAAGAAAA
19763 A
1 A
19764 TGGGAGAAAT
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
7 1 0.03
8 28 0.76
9 8 0.22
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (8 bp):
AAAGAAAA
Found at i:19740 original size:23 final size:23
Alignment explanation
Indices: 19680--19763 Score: 87
Period size: 24 Copynumber: 3.4 Consensus size: 23
19670 TCCAACAAAG
* *
19680 AAAGAAAAAAGGAAAAATCCAACAAA
1 AAAGAAAAAA-GAAAAA--AAAGAAA
*
19706 GAAAGAAGAAAGAAAAAAAAGAAA
1 -AAAGAAAAAAGAAAAAAAAGAAA
19730 AAAGAAAAAAGAAAAAAAAAGAAAA
1 AAAGAAAAAAG-AAAAAAAAG-AAA
19755 AAAGAAAAA
1 AAAGAAAAA
19764 TGGGAGAAAT
Statistics
Matches: 51, Mismatches: 4, Indels: 6
0.84 0.07 0.10
Matches are distributed among these distances:
23 10 0.20
24 14 0.27
25 12 0.24
26 6 0.12
27 9 0.18
ACGTcount: A:0.81, C:0.04, G:0.14, T:0.01
Consensus pattern (23 bp):
AAAGAAAAAAGAAAAAAAAGAAA
Found at i:22031 original size:114 final size:114
Alignment explanation
Indices: 21831--22052 Score: 336
Period size: 114 Copynumber: 1.9 Consensus size: 114
21821 CACATTCTCG
*
21831 TAGCAGAAATAAGGAAACCCAATAGCATCTTCTGGAAATGTTCTTTGAGTTATCTGATCTGATTT
1 TAGCAGAAATAAGGAAACCCAATAGCATCTTCTGGAAATGTTCTTTGAGTTATCTGATCTGATTC
* * * *
21896 GGTATGAACCCTAAAACCAATCATTGGATTTAAAAGATGAATTTGCTCA
66 GGTAGGAACCCCAAAACCAATCATTAGAATTAAAAGATGAATTTGCTCA
* * * * *
21945 TAGCAGAAATAAGGAGACCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATTTGATCTGGTTC
1 TAGCAGAAATAAGGAAACCCAATAGCATCTTCTGGAAATGTTCTTTGAGTTATCTGATCTGATTC
* *
22010 GGTAGGAACCCCAGAACCAATCATTAGAATTGAAAGATGAATT
66 GGTAGGAACCCCAAAACCAATCATTAGAATTAAAAGATGAATT
22053 GCATGATTGT
Statistics
Matches: 96, Mismatches: 12, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
114 96 1.00
ACGTcount: A:0.34, C:0.15, G:0.20, T:0.31
Consensus pattern (114 bp):
TAGCAGAAATAAGGAAACCCAATAGCATCTTCTGGAAATGTTCTTTGAGTTATCTGATCTGATTC
GGTAGGAACCCCAAAACCAATCATTAGAATTAAAAGATGAATTTGCTCA
Found at i:23114 original size:74 final size:75
Alignment explanation
Indices: 22988--23165 Score: 207
Period size: 74 Copynumber: 2.4 Consensus size: 75
22978 ATTAACAATA
* * **
22988 AGCAAATGTTGGGGCATGCTGAAAACCCTTTTCAATCCGAATCAGAAATGTTGAAATATTCTGAA
1 AGCAAATGTTGGGGCATGCTGAAAGCCCATTTCAATCAAAATCAGAAATGTTGAAATATTCTGAA
*
23053 TA-TT-TATC
66 CACTTGTATC
* * * ** *
23061 AGCAAAATGCTGGGGCATGCTGAAAGCCCATTTCAATCAAAATTAGAACTGTTGATGTATTTTGA
1 AGC-AAATGTTGGGGCATGCTGAAAGCCCATTTCAATCAAAATCAGAAATGTTGAAATATTCTGA
*
23126 ACACTTGTATT
65 ACACTTGTATC
* *
23137 AGCCAATGTTGGGGCATGCTGAAGGCCCA
1 AGCAAATGTTGGGGCATGCTGAAAGCCCA
23166 CAACATCCTG
Statistics
Matches: 87, Mismatches: 15, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
73 3 0.03
74 53 0.61
75 25 0.29
76 6 0.07
ACGTcount: A:0.32, C:0.17, G:0.21, T:0.29
Consensus pattern (75 bp):
AGCAAATGTTGGGGCATGCTGAAAGCCCATTTCAATCAAAATCAGAAATGTTGAAATATTCTGAA
CACTTGTATC
Found at i:24125 original size:54 final size:55
Alignment explanation
Indices: 24043--24197 Score: 233
Period size: 54 Copynumber: 2.9 Consensus size: 55
24033 GAAATCTTGG
* *
24043 CAGAAGCCATAGGAAAGGATGAATGTGTTGTCAAATGTTTTACGAACATTTGA-A
1 CAGAAGCCACAGGAAAGGATGAATGTGTTGTCAAATGTTTTACGAACATCTGAGA
* *
24097 CAGAAACCACAGGAAATGATGAATGTGTTGTCAAATGTTTTACGAACATCTGAGA
1 CAGAAGCCACAGGAAAGGATGAATGTGTTGTCAAATGTTTTACGAACATCTGAGA
* * *
24152 -AGAAGCCACAGGAAAGGATGAATGCGCTGTCAAATGTTTTATGAAC
1 CAGAAGCCACAGGAAAGGATGAATGTGTTGTCAAATGTTTTACGAAC
24198 CTGCTATTCT
Statistics
Matches: 91, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
54 90 0.99
55 1 0.01
ACGTcount: A:0.37, C:0.14, G:0.24, T:0.25
Consensus pattern (55 bp):
CAGAAGCCACAGGAAAGGATGAATGTGTTGTCAAATGTTTTACGAACATCTGAGA
Found at i:24593 original size:22 final size:22
Alignment explanation
Indices: 24564--24618 Score: 85
Period size: 22 Copynumber: 2.5 Consensus size: 22
24554 ATCTACACTC
24564 TTCAAAGATGATA-AGTTCTCTT
1 TTCAAAGATGATAGA-TTCTCTT
*
24586 TTTAAAGATGATAGATTCTCTT
1 TTCAAAGATGATAGATTCTCTT
24608 TTCAAAGATGA
1 TTCAAAGATGA
24619 AAGCTTTATT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
22 29 0.97
23 1 0.03
ACGTcount: A:0.35, C:0.11, G:0.15, T:0.40
Consensus pattern (22 bp):
TTCAAAGATGATAGATTCTCTT
Found at i:25424 original size:76 final size:76
Alignment explanation
Indices: 25293--25665 Score: 737
Period size: 76 Copynumber: 4.9 Consensus size: 76
25283 CTATTTCCTA
*
25293 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTCTTTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
25358 AGCCTTAGGGT
66 AGCCTTAGGGT
25369 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
25434 AGCCTTAGGGT
66 AGCCTTAGGGT
25445 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
25510 AGCCTTAGGGT
66 AGCCTTAGGGT
25521 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
25586 AGCCTTAGGGT
66 AGCCTTAGGGT
25597 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
25662 AGCC
66 AGCC
25666 ATTCAGTGCA
Statistics
Matches: 296, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
76 296 1.00
ACGTcount: A:0.23, C:0.20, G:0.23, T:0.34
Consensus pattern (76 bp):
CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
AGCCTTAGGGT
Found at i:25913 original size:3 final size:3
Alignment explanation
Indices: 25838--25902 Score: 67
Period size: 3 Copynumber: 20.3 Consensus size: 3
25828 TTTTACTTAA
** *
25838 ATT ATT ATT AAA ATT ATT ATT ATT ATT ATT AAAT ATT ATT ATT ATAT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT -ATT ATT ATT ATT AT-T
25885 ATAT ATAT ATT ATT ATT A
1 AT-T AT-T ATT ATT ATT A
25903 AATAATTATT
Statistics
Matches: 54, Mismatches: 6, Indels: 4
0.84 0.09 0.06
Matches are distributed among these distances:
3 41 0.76
4 13 0.24
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (3 bp):
ATT
Found at i:27323 original size:16 final size:16
Alignment explanation
Indices: 27302--27343 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 16
27292 TCACTTTTAA
27302 ATTTATTT-TAAATATT
1 ATTTATTTAT-AATATT
27318 ATTTATTTATAATATT
1 ATTTATTTATAATATT
27334 AATTT-TTTAT
1 -ATTTATTTAT
27344 TACTTTTATA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
16 19 0.79
17 5 0.21
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (16 bp):
ATTTATTTATAATATT
Found at i:27362 original size:17 final size:17
Alignment explanation
Indices: 27340--27373 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
27330 TATTAATTTT
27340 TTATTACTTTT-ATATTA
1 TTATTA-TTTTCATATTA
27357 TTATTATTTTCATATTA
1 TTATTATTTTCATATTA
27374 GTCACATAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.29, C:0.06, G:0.00, T:0.65
Consensus pattern (17 bp):
TTATTATTTTCATATTA
Found at i:27398 original size:2 final size:2
Alignment explanation
Indices: 27391--27434 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
27381 AAATAAATAA
*
27391 AT AT AT AT AT AT AT AT AT AT AT TT 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
27433 AT
1 AT
27435 TTTAAATAAT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:32315 original size:21 final size:21
Alignment explanation
Indices: 32289--32347 Score: 91
Period size: 21 Copynumber: 2.8 Consensus size: 21
32279 ATTTACCGTG
32289 ATTGCGGCCGTCGCGGGCGCT
1 ATTGCGGCCGTCGCGGGCGCT
* *
32310 ATTGCGGCCGTCGCGGACGTT
1 ATTGCGGCCGTCGCGGGCGCT
*
32331 ATTGCGGCCGTCTCGGG
1 ATTGCGGCCGTCGCGGG
32348 TAACTCGGAC
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.07, C:0.31, G:0.41, T:0.22
Consensus pattern (21 bp):
ATTGCGGCCGTCGCGGGCGCT
Found at i:45978 original size:12 final size:12
Alignment explanation
Indices: 45952--46030 Score: 106
Period size: 12 Copynumber: 6.7 Consensus size: 12
45942 ATATACAAAT
45952 ACCTAACTC-TC
1 ACCTAACTCTTC
45963 ACCTAACTCTTC
1 ACCTAACTCTTC
*
45975 ACCTAATTCTTC
1 ACCTAACTCTTC
45987 ACCTAACTCTTC
1 ACCTAACTCTTC
* **
45999 TCCTATTTCTTC
1 ACCTAACTCTTC
*
46011 ACCTAAATCTTC
1 ACCTAACTCTTC
46023 ACCTAACT
1 ACCTAACT
46031 AAATTGATGT
Statistics
Matches: 58, Mismatches: 9, Indels: 1
0.85 0.13 0.01
Matches are distributed among these distances:
11 9 0.16
12 49 0.84
ACGTcount: A:0.25, C:0.38, G:0.00, T:0.37
Consensus pattern (12 bp):
ACCTAACTCTTC
Found at i:47691 original size:2 final size:2
Alignment explanation
Indices: 47686--47721 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
47676 GTAGACACAC
*
47686 AT AT AT AT AT AT AT AT AT AT AT -T AC AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
47722 AATTATTTTC
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:47716 original size:17 final size:17
Alignment explanation
Indices: 47694--47726 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
47684 ACATATATAT
*
47694 ATATATATATATATTAC
1 ATATATATATAAATTAC
47711 ATATATATATAAATTA
1 ATATATATATAAATTA
47727 TTTTCGTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (17 bp):
ATATATATATAAATTAC
Found at i:48884 original size:2 final size:2
Alignment explanation
Indices: 48877--48929 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
48867 CCTTATTATT
48877 TA TA TA TA TA TA TA TA 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 TA TA TA TA TA TA TA TA
48919 TA TA TA TA TA T
1 TA TA TA TA TA T
48930 TATTACTTAA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:49032 original size:12 final size:12
Alignment explanation
Indices: 49015--49065 Score: 52
Period size: 12 Copynumber: 4.2 Consensus size: 12
49005 CTACCTTTGT
49015 TATTATTATTTA
1 TATTATTATTTA
49027 TATTA-TATTT-
1 TATTATTATTTA
49037 TATTATATATTTCA
1 TATTAT-TATTT-A
* *
49051 TGTCATTATTTA
1 TATTATTATTTA
49063 TAT
1 TAT
49066 ATAGGTATGT
Statistics
Matches: 32, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
10 5 0.16
11 5 0.16
12 13 0.41
13 5 0.16
14 4 0.12
ACGTcount: A:0.31, C:0.04, G:0.02, T:0.63
Consensus pattern (12 bp):
TATTATTATTTA
Found at i:50251 original size:16 final size:16
Alignment explanation
Indices: 50230--50263 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
50220 TCCTTTGCCA
*
50230 TTTATTTATTTTTATT
1 TTTATTTATTTTCATT
50246 TTTATTTATTTTCATT
1 TTTATTTATTTTCATT
50262 TT
1 TT
50264 ACTAACTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.18, C:0.03, G:0.00, T:0.79
Consensus pattern (16 bp):
TTTATTTATTTTCATT
Found at i:52549 original size:23 final size:23
Alignment explanation
Indices: 52523--52566 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
52513 ATATTTTGCA
52523 TTTTTATATTT-CAAGTTTTTATT
1 TTTTTAT-TTTCCAAGTTTTTATT
*
52546 TTTTTATTTTCCATGTTTTTA
1 TTTTTATTTTCCAAGTTTTTA
52567 CATTTGTATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 3 0.16
23 16 0.84
ACGTcount: A:0.18, C:0.07, G:0.05, T:0.70
Consensus pattern (23 bp):
TTTTTATTTTCCAAGTTTTTATT
Done.