Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003130.1 Hibiscus syriacus cultivar Beakdansim tig00006566_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: 95527
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:450 original size:13 final size:13
Alignment explanation
Indices: 432--457 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
422 TTACAGACGC
432 GCATATGAAGATT
1 GCATATGAAGATT
445 GCATATGAAGATT
1 GCATATGAAGATT
458 TTCAACTATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.08, G:0.23, T:0.31
Consensus pattern (13 bp):
GCATATGAAGATT
Found at i:802 original size:18 final size:18
Alignment explanation
Indices: 757--801 Score: 74
Period size: 18 Copynumber: 2.6 Consensus size: 18
747 GGCTAGTTCG
*
757 AAAGGAAAAATCAAAGGA
1 AAAGGAAAAATCAAAGAA
775 AAAGGAAAAATCAAA-AA
1 AAAGGAAAAATCAAAGAA
792 AAAGGAAAAA
1 AAAGGAAAAA
802 AAAGTGGAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
17 11 0.42
18 15 0.58
ACGTcount: A:0.73, C:0.04, G:0.18, T:0.04
Consensus pattern (18 bp):
AAAGGAAAAATCAAAGAA
Found at i:2975 original size:18 final size:18
Alignment explanation
Indices: 2954--2994 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
2944 ACTTTTATAT
*
2954 TATATAATATATACATAG
1 TATATAATATATACATAC
*
2972 TATATAATATATATATAC
1 TATATAATATATACATAC
2990 TATAT
1 TATAT
2995 TATAGTGGGT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.49, C:0.05, G:0.02, T:0.44
Consensus pattern (18 bp):
TATATAATATATACATAC
Found at i:7105 original size:59 final size:60
Alignment explanation
Indices: 7004--7140 Score: 154
Period size: 59 Copynumber: 2.3 Consensus size: 60
6994 AATTAAGGGT
* * * * * *
7004 AAAG-TATACAAATGTTCCTCCAACTATGAGGTGTTATTTTGTTGAGTCATC-GACTATTA
1 AAAGTTATA-AAATGGTCATCCAACTATGAGGTATTACTTTGTTGAATCACCTGACTATTA
* *
7063 AAATTTATAAAATGGTCATCCAACTAT-AGAGTATTACTTTGTTGAATCCCCTGACTATTA
1 AAAGTTATAAAATGGTCATCCAACTATGAG-GTATTACTTTGTTGAATCACCTGACTATTA
*
7123 AAAGTTACAAAATGGTCA
1 AAAGTTATAAAATGGTCA
7141 CCTGACTATT
Statistics
Matches: 65, Mismatches: 10, Indels: 5
0.81 0.12 0.06
Matches are distributed among these distances:
58 2 0.03
59 35 0.54
60 28 0.43
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Consensus pattern (60 bp):
AAAGTTATAAAATGGTCATCCAACTATGAGGTATTACTTTGTTGAATCACCTGACTATTA
Found at i:10383 original size:17 final size:17
Alignment explanation
Indices: 10361--10395 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
10351 TATGGCATCC
10361 CCATATAT-GCATGTATG
1 CCATATATGGCA-GTATG
10378 CCATATATGGCAGTATG
1 CCATATATGGCAGTATG
10395 C
1 C
10396 TTTCCTTTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 14 0.82
18 3 0.18
ACGTcount: A:0.29, C:0.20, G:0.20, T:0.31
Consensus pattern (17 bp):
CCATATATGGCAGTATG
Found at i:11332 original size:31 final size:29
Alignment explanation
Indices: 11282--11351 Score: 81
Period size: 30 Copynumber: 2.4 Consensus size: 29
11272 TATTTTATGA
*
11282 ATTTTA-T-ATTAATAAAATATTTTAATAT
1 ATTTTATTAATTAATAAAATA-TTTAAAAT
*
11310 CATTTTATTAATTATTAAAATATTTAAAAT
1 -ATTTTATTAATTAATAAAATATTTAAAAT
11340 ATATTTATTAAT
1 AT-TTTATTAAT
11352 ATTTCTAATA
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
29 8 0.22
30 17 0.47
31 11 0.31
ACGTcount: A:0.46, C:0.01, G:0.00, T:0.53
Consensus pattern (29 bp):
ATTTTATTAATTAATAAAATATTTAAAAT
Found at i:11347 original size:30 final size:31
Alignment explanation
Indices: 11282--11351 Score: 85
Period size: 31 Copynumber: 2.4 Consensus size: 31
11272 TATTTTATGA
*
11282 ATTTTA-T-ATTAATAAAATATTTTAATATC
1 ATTTTATTAATTAATAAAATATTTAAATATC
*
11311 ATTTTATTAATTATTAAAATATTTAAA-AT-
1 ATTTTATTAATTAATAAAATATTTAAATATC
11340 ATATTTATTAAT
1 AT-TTTATTAAT
11352 ATTTCTAATA
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
29 8 0.22
30 12 0.33
31 16 0.44
ACGTcount: A:0.46, C:0.01, G:0.00, T:0.53
Consensus pattern (31 bp):
ATTTTATTAATTAATAAAATATTTAAATATC
Found at i:11395 original size:31 final size:35
Alignment explanation
Indices: 11338--11408 Score: 96
Period size: 31 Copynumber: 2.1 Consensus size: 35
11328 AATATTTAAA
*
11338 ATATATTTATTAATATTTCTAATAAAATAAT-ATT
1 ATATATTTATTAACATTTCTAATAAAATAATAATT
11372 ATATA-TT-TTAACATTT-TAATAAAATAATCAATT
1 ATATATTTATTAACATTTCTAATAAAATAAT-AATT
11405 ATAT
1 ATAT
11409 TATAATAATA
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
31 12 0.35
32 8 0.24
33 9 0.26
34 5 0.15
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (35 bp):
ATATATTTATTAACATTTCTAATAAAATAATAATT
Found at i:14288 original size:23 final size:23
Alignment explanation
Indices: 14226--14300 Score: 80
Period size: 23 Copynumber: 3.3 Consensus size: 23
14216 AAATGAGTTG
* *
14226 ATAAACAAGTTTCAAATGAGCCA
1 ATAAACAAATTTTAAATGAGCCA
* **
14249 AGAAA-TGATTTTCAAATGAGCCA
1 ATAAACAAATTTT-AAATGAGCCA
*
14272 ATAAACAAATTTTAAATGAGTCA
1 ATAAACAAATTTTAAATGAGCCA
14295 ATAAAC
1 ATAAAC
14301 GAGCCAAGAA
Statistics
Matches: 41, Mismatches: 9, Indels: 4
0.76 0.17 0.07
Matches are distributed among these distances:
22 3 0.07
23 33 0.80
24 5 0.12
ACGTcount: A:0.49, C:0.13, G:0.12, T:0.25
Consensus pattern (23 bp):
ATAAACAAATTTTAAATGAGCCA
Found at i:25893 original size:13 final size:13
Alignment explanation
Indices: 25875--25922 Score: 62
Period size: 13 Copynumber: 3.8 Consensus size: 13
25865 AAATAATAAA
25875 AAAAAAGTACAAT
1 AAAAAAGTACAAT
*
25888 AAAAAAGTCCAAT
1 AAAAAAGTACAAT
* *
25901 AAATAACTACAAT
1 AAAAAAGTACAAT
25914 -AAAAAGTAC
1 AAAAAAGTAC
25923 TAAATACAAA
Statistics
Matches: 29, Mismatches: 6, Indels: 1
0.81 0.17 0.03
Matches are distributed among these distances:
12 7 0.24
13 22 0.76
ACGTcount: A:0.65, C:0.12, G:0.06, T:0.17
Consensus pattern (13 bp):
AAAAAAGTACAAT
Found at i:26085 original size:24 final size:24
Alignment explanation
Indices: 26058--26105 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
26048 ACCATCATCA
26058 TCGTCATCATCATCATCGTCGTCG
1 TCGTCATCATCATCATCGTCGTCG
* *
26082 TCGTCCTCATCGTCATCGTCGTCG
1 TCGTCATCATCATCATCGTCGTCG
26106 CCCTGGGCAG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.12, C:0.35, G:0.19, T:0.33
Consensus pattern (24 bp):
TCGTCATCATCATCATCGTCGTCG
Found at i:26091 original size:18 final size:18
Alignment explanation
Indices: 26070--26104 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
26060 GTCATCATCA
*
26070 TCATCGTCGTCGTCGTCC
1 TCATCGTCATCGTCGTCC
26088 TCATCGTCATCGTCGTC
1 TCATCGTCATCGTCGTC
26105 GCCCTGGGCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.09, C:0.37, G:0.20, T:0.34
Consensus pattern (18 bp):
TCATCGTCATCGTCGTCC
Found at i:28168 original size:9 final size:9
Alignment explanation
Indices: 28138--28189 Score: 56
Period size: 9 Copynumber: 6.1 Consensus size: 9
28128 TATGCAAAAA
*
28138 AAATTAATT
1 AAATTAAAT
28147 AAA-TAAA-
1 AAATTAAAT
*
28154 ATATTAAAT
1 AAATTAAAT
28163 AAATTAAAT
1 AAATTAAAT
*
28172 -ACTTAAAT
1 AAATTAAAT
28180 AAATTAAAT
1 AAATTAAAT
28189 A
1 A
28190 CAAAATATTA
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
7 2 0.06
8 14 0.40
9 19 0.54
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (9 bp):
AAATTAAAT
Found at i:28170 original size:17 final size:17
Alignment explanation
Indices: 28135--28187 Score: 65
Period size: 16 Copynumber: 3.2 Consensus size: 17
28125 ATATATGCAA
* *
28135 AAAAAATTAATTAAA-T
1 AAAATATTAAATAAATT
28151 AAAATATTAAATAAATT
1 AAAATATTAAATAAATT
28168 -AAATACTTAAATAAATT
1 AAAATA-TTAAATAAATT
28185 AAA
1 AAA
28188 TACAAAATAT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
16 18 0.56
17 12 0.38
18 2 0.06
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (17 bp):
AAAATATTAAATAAATT
Found at i:28188 original size:17 final size:17
Alignment explanation
Indices: 28141--28190 Score: 75
Period size: 17 Copynumber: 3.0 Consensus size: 17
28131 GCAAAAAAAA
* *
28141 TTAATTAAATAAAATA-
1 TTAAATAAATTAAATAC
28157 TTAAATAAATTAAATAC
1 TTAAATAAATTAAATAC
28174 TTAAATAAATTAAATAC
1 TTAAATAAATTAAATAC
28191 AAAATATTAG
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
16 14 0.45
17 17 0.55
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.36
Consensus pattern (17 bp):
TTAAATAAATTAAATAC
Found at i:28210 original size:38 final size:37
Alignment explanation
Indices: 28138--28210 Score: 85
Period size: 38 Copynumber: 1.9 Consensus size: 37
28128 TATGCAAAAA
* * *
28138 AAATTAATTAAATAAAATATTAAATAAATTAAATACTT
1 AAATAAATTAAATAAAATATT-AAGAAATAAAATACTT
28176 AAATAAATTAAATACAAAATATT-AGAAATAAAATA
1 AAATAAATTAAAT--AAAATATTAAGAAATAAAATA
28211 AAATATACCT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
38 22 0.73
40 8 0.27
ACGTcount: A:0.64, C:0.03, G:0.01, T:0.32
Consensus pattern (37 bp):
AAATAAATTAAATAAAATATTAAGAAATAAAATACTT
Found at i:32080 original size:17 final size:18
Alignment explanation
Indices: 32049--32085 Score: 51
Period size: 17 Copynumber: 2.1 Consensus size: 18
32039 ACTTCTTTTG
32049 AAAACAATTTTAAGA-AA
1 AAAACAATTTTAAGACAA
32066 AAAAC-ATTTTAAAGACAA
1 AAAACAATTTT-AAGACAA
32084 AA
1 AA
32086 TTTGATCTGC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 5 0.28
17 9 0.50
18 4 0.22
ACGTcount: A:0.65, C:0.08, G:0.05, T:0.22
Consensus pattern (18 bp):
AAAACAATTTTAAGACAA
Found at i:38153 original size:27 final size:30
Alignment explanation
Indices: 38096--38200 Score: 96
Period size: 27 Copynumber: 3.5 Consensus size: 30
38086 ATATAATCAA
* * *
38096 TTATATTATAATAATATAAGATATTAGATTTT
1 TTATATT-TAATAATATATGA-ATAATATTTT
38128 TTAT-TTTAATAATATAT-AATAA-ATTTT
1 TTATATTTAATAATATATGAATAATATTTT
38155 TTATATATT--TAATA-ATGAATAATATTTT
1 TTATAT-TTAATAATATATGAATAATATTTT
38183 TATATATTTAAATAATAT
1 T-TATATTT-AATAATAT
38201 TTTAGTAAAG
Statistics
Matches: 62, Mismatches: 2, Indels: 18
0.76 0.02 0.22
Matches are distributed among these distances:
26 2 0.03
27 19 0.31
28 12 0.19
29 8 0.13
30 10 0.16
31 7 0.11
32 4 0.06
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (30 bp):
TTATATTTAATAATATATGAATAATATTTT
Found at i:38374 original size:19 final size:17
Alignment explanation
Indices: 38342--38377 Score: 54
Period size: 19 Copynumber: 2.0 Consensus size: 17
38332 TAATAAAATT
38342 ATAAAAAATATTTAATA
1 ATAAAAAATATTTAATA
38359 ATAAATAAATTATTTAATA
1 ATAAA-AAA-TATTTAATA
38378 TTTTAAAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.29
18 3 0.18
19 9 0.53
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (17 bp):
ATAAAAAATATTTAATA
Found at i:38536 original size:20 final size:20
Alignment explanation
Indices: 38513--38562 Score: 91
Period size: 20 Copynumber: 2.5 Consensus size: 20
38503 TCATAAAACG
38513 TTTTCCAGAAATATAATTCA
1 TTTTCCAGAAATATAATTCA
*
38533 TTTTCCAGAAATGTAATTCA
1 TTTTCCAGAAATATAATTCA
38553 TTTTCCAGAA
1 TTTTCCAGAA
38563 TTCAAATTCC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.36, C:0.16, G:0.08, T:0.40
Consensus pattern (20 bp):
TTTTCCAGAAATATAATTCA
Found at i:38597 original size:30 final size:30
Alignment explanation
Indices: 38545--38626 Score: 139
Period size: 30 Copynumber: 2.8 Consensus size: 30
38535 TTCCAGAAAT
38545 GTAATTCATTTTCCAG-AATTCAAATTCCA
1 GTAATTCATTTTCCAGTAATTCAAATTCCA
38574 GTAATTCATTTTCCAGTAATTCAAATTCCA
1 GTAATTCATTTTCCAGTAATTCAAATTCCA
**
38604 GTAATTCAAATTCCAGTAATTCA
1 GTAATTCATTTTCCAGTAATTCA
38627 TTTTCCGAAA
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
29 16 0.32
30 34 0.68
ACGTcount: A:0.35, C:0.20, G:0.07, T:0.38
Consensus pattern (30 bp):
GTAATTCATTTTCCAGTAATTCAAATTCCA
Found at i:38620 original size:45 final size:44
Alignment explanation
Indices: 38545--38632 Score: 149
Period size: 45 Copynumber: 2.0 Consensus size: 44
38535 TTCCAGAAAT
**
38545 GTAATTCATTTTCCAGAATTCAAATTCCAGTAATTCATTTTCCA
1 GTAATTCAAATTCCAGAATTCAAATTCCAGTAATTCATTTTCCA
38589 GTAATTCAAATTCCAGTAATTCAAATTCCAGTAATTCATTTTCC
1 GTAATTCAAATTCCAG-AATTCAAATTCCAGTAATTCATTTTCC
38633 GAAAAATCAA
Statistics
Matches: 41, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
44 14 0.34
45 27 0.66
ACGTcount: A:0.33, C:0.20, G:0.07, T:0.40
Consensus pattern (44 bp):
GTAATTCAAATTCCAGAATTCAAATTCCAGTAATTCATTTTCCA
Found at i:38632 original size:15 final size:15
Alignment explanation
Indices: 38545--38626 Score: 121
Period size: 15 Copynumber: 5.5 Consensus size: 15
38535 TTCCAGAAAT
**
38545 GTAATTCATTTTCCA
1 GTAATTCAAATTCCA
38560 G-AATTCAAATTCCA
1 GTAATTCAAATTCCA
**
38574 GTAATTCATTTTCCA
1 GTAATTCAAATTCCA
38589 GTAATTCAAATTCCA
1 GTAATTCAAATTCCA
38604 GTAATTCAAATTCCA
1 GTAATTCAAATTCCA
38619 GTAATTCA
1 GTAATTCA
38627 TTTTCCGAAA
Statistics
Matches: 60, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
14 12 0.20
15 48 0.80
ACGTcount: A:0.35, C:0.20, G:0.07, T:0.38
Consensus pattern (15 bp):
GTAATTCAAATTCCA
Found at i:40542 original size:20 final size:19
Alignment explanation
Indices: 40505--40542 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
40495 AAGAATTGGG
*
40505 AAAATAAAAAAAATAGAAC
1 AAAATAAAAAAAAAAGAAC
40524 AAAATAAAATAAAAAAGAA
1 AAAATAAAA-AAAAAAGAA
40543 GTGTTAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.82, C:0.03, G:0.05, T:0.11
Consensus pattern (19 bp):
AAAATAAAAAAAAAAGAAC
Found at i:40672 original size:16 final size:18
Alignment explanation
Indices: 40637--40675 Score: 55
Period size: 16 Copynumber: 2.3 Consensus size: 18
40627 GTTGTTTTTA
40637 AAATAAAAGATAAGAATT
1 AAATAAAAGATAAGAATT
*
40655 AAATAAAA-A-AATAATT
1 AAATAAAAGATAAGAATT
40671 AAATA
1 AAATA
40676 TATAATCTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 11 0.55
17 1 0.05
18 8 0.40
ACGTcount: A:0.72, C:0.00, G:0.05, T:0.23
Consensus pattern (18 bp):
AAATAAAAGATAAGAATT
Found at i:41904 original size:51 final size:50
Alignment explanation
Indices: 41835--41935 Score: 157
Period size: 51 Copynumber: 2.0 Consensus size: 50
41825 TTAAAAAATA
* *
41835 ATATTATATATATTTTCAAAATGTTTTCAAAAACTATATAATATATATAT
1 ATATTATATATATTTTCAAAATGTTTTCAAAAACTAAATAATAAATATAT
* *
41885 ATATATATATATGTTTTCAAAATGTTTTCAAAAACTAAATATTAAATATAT
1 ATAT-TATATATATTTTCAAAATGTTTTCAAAAACTAAATAATAAATATAT
41936 GTTTTCAAAA
Statistics
Matches: 46, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
50 4 0.09
51 42 0.91
ACGTcount: A:0.47, C:0.06, G:0.03, T:0.45
Consensus pattern (50 bp):
ATATTATATATATTTTCAAAATGTTTTCAAAAACTAAATAATAAATATAT
Found at i:43814 original size:2 final size:2
Alignment explanation
Indices: 43803--43842 Score: 64
Period size: 2 Copynumber: 20.5 Consensus size: 2
43793 TTTCAAAAAC
*
43803 TA TA -A TA TA TA TA TA TA TA TA TA CA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
43843 GTTTTCAAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:52371 original size:18 final size:18
Alignment explanation
Indices: 52350--52392 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
52340 GTTGTTTTTA
52350 AAATAAAAGATAAG-AATT
1 AAATAAAAGA-AAGTAATT
52368 AAATAAAAGAAAGTAATT
1 AAATAAAAGAAAGTAATT
52386 AAATAAA
1 AAATAAA
52393 TAATCTAAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
17 3 0.12
18 21 0.88
ACGTcount: A:0.70, C:0.00, G:0.09, T:0.21
Consensus pattern (18 bp):
AAATAAAAGAAAGTAATT
Found at i:53326 original size:38 final size:38
Alignment explanation
Indices: 53272--53344 Score: 105
Period size: 38 Copynumber: 1.9 Consensus size: 38
53262 TAGATTTATA
53272 TTTTAAAAAATAATATTATATAT-A-TTTTCAAAATGT
1 TTTTAAAAAATAATATTATATATAAGTTTTCAAAATGT
*
53308 TTTTCAAAAACTATATATTATATATAAGTTTTCAAAA
1 TTTT-AAAAAATA-ATATTATATATAAGTTTTCAAAA
53345 ACTATTCTAT
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
36 4 0.12
37 7 0.22
38 11 0.34
39 1 0.03
40 9 0.28
ACGTcount: A:0.47, C:0.05, G:0.03, T:0.45
Consensus pattern (38 bp):
TTTTAAAAAATAATATTATATATAAGTTTTCAAAATGT
Found at i:59306 original size:22 final size:22
Alignment explanation
Indices: 59279--59334 Score: 103
Period size: 22 Copynumber: 2.5 Consensus size: 22
59269 ACCATCCTAA
59279 GGGTATCGATACCACCCTTCAG
1 GGGTATCGATACCACCCTTCAG
59301 GGGTATCGATACCACCCTTCAG
1 GGGTATCGATACCACCCTTCAG
*
59323 GGTTATCGATAC
1 GGGTATCGATAC
59335 TTACGCATGT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.23, C:0.29, G:0.23, T:0.25
Consensus pattern (22 bp):
GGGTATCGATACCACCCTTCAG
Found at i:65749 original size:21 final size:21
Alignment explanation
Indices: 65720--65769 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
65710 ATAGAGTATA
* *
65720 TTCACATTCAC-TGATTCTAAG
1 TTCATATTCACATG-TTCAAAG
65741 TTCATATTCACATGTTCAAAG
1 TTCATATTCACATGTTCAAAG
65762 TTCATATT
1 TTCATATT
65770 TTCATAACAC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
21 24 0.92
22 2 0.08
ACGTcount: A:0.30, C:0.20, G:0.08, T:0.42
Consensus pattern (21 bp):
TTCATATTCACATGTTCAAAG
Found at i:66132 original size:20 final size:22
Alignment explanation
Indices: 66107--66157 Score: 79
Period size: 22 Copynumber: 2.4 Consensus size: 22
66097 GTTTGGAGAC
66107 ATCGATACCACCC-T-AAGGGT
1 ATCGATACCACCCTTCAAGGGT
*
66127 ATCGATACCACCCTTCAGGGGT
1 ATCGATACCACCCTTCAAGGGT
66149 ATCGATACC
1 ATCGATACC
66158 TACGCATGTA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
20 13 0.46
21 1 0.04
22 14 0.50
ACGTcount: A:0.27, C:0.31, G:0.20, T:0.22
Consensus pattern (22 bp):
ATCGATACCACCCTTCAAGGGT
Found at i:93174 original size:17 final size:17
Alignment explanation
Indices: 93154--93192 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
93144 AATTAAGGTG
93154 TATAAAAAATA-ATCAAA
1 TATAAAAAATATAT-AAA
*
93171 TATAAAAACTATATAAA
1 TATAAAAAATATATAAA
93188 TATAA
1 TATAA
93193 TATTATAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 18 0.90
18 2 0.10
ACGTcount: A:0.67, C:0.05, G:0.00, T:0.28
Consensus pattern (17 bp):
TATAAAAAATATATAAA
Found at i:93327 original size:14 final size:15
Alignment explanation
Indices: 93294--93326 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
93284 TTTCACTCTT
93294 ATTTTAATTA-TTAA
1 ATTTTAATTATTTAA
*
93308 ATTTTAATTATTTCA
1 ATTTTAATTATTTAA
93323 ATTT
1 ATTT
93327 ACTTATTGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 10 0.59
15 7 0.41
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (15 bp):
ATTTTAATTATTTAA
Done.