Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005881.1 Hibiscus syriacus cultivar Beakdansim tig00013813_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: 77784
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Found at i:472 original size:14 final size:14
Alignment explanation
Indices: 437--482 Score: 53
Period size: 14 Copynumber: 3.4 Consensus size: 14
427 AATAAACAAA
*
437 TAATTA-TTAAGAT
1 TAATTATTTATGAT
450 TAA-TATTTAT-ATT
1 TAATTATTTATGA-T
463 TAATTATTTATGAT
1 TAATTATTTATGAT
477 TAATTA
1 TAATTA
483 AAGAGTGTCA
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
12 3 0.11
13 10 0.36
14 14 0.50
15 1 0.04
ACGTcount: A:0.41, C:0.00, G:0.04, T:0.54
Consensus pattern (14 bp):
TAATTATTTATGAT
Found at i:1892 original size:42 final size:41
Alignment explanation
Indices: 1845--1925 Score: 110
Period size: 42 Copynumber: 2.0 Consensus size: 41
1835 TTGGCTTTTG
* *
1845 GGTTAAGTAGATTGAATATC-TAAAAATATCTTTTTAAAATTA
1 GGTTAAGTAGATCGAATA-CATAAAAACAT-TTTTTAAAATTA
*
1887 GGTTAAGTAGGTCGAATACATAAAAACATTTTTTAAAAT
1 GGTTAAGTAGATCGAATACATAAAAACATTTTTTAAAAT
1926 AATTTTAAGA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
41 11 0.31
42 24 0.69
ACGTcount: A:0.43, C:0.06, G:0.14, T:0.37
Consensus pattern (41 bp):
GGTTAAGTAGATCGAATACATAAAAACATTTTTTAAAATTA
Found at i:1945 original size:15 final size:15
Alignment explanation
Indices: 1921--1952 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
1911 AACATTTTTT
1921 AAAATAATTTTAAGA
1 AAAATAATTTTAAGA
*
1936 AAAATCATTTTAAGA
1 AAAATAATTTTAAGA
1951 AA
1 AA
1953 TTAGTTTGTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.59, C:0.03, G:0.06, T:0.31
Consensus pattern (15 bp):
AAAATAATTTTAAGA
Found at i:3963 original size:13 final size:14
Alignment explanation
Indices: 3933--3977 Score: 58
Period size: 14 Copynumber: 3.4 Consensus size: 14
3923 AAAGGAAAAG
3933 AAAAAGAAAATAAC
1 AAAAAGAAAATAAC
*
3947 AAAAAGAAAGTAA-
1 AAAAAGAAAATAAC
*
3960 AAAAA-ATAATAAC
1 AAAAAGAAAATAAC
3973 AAAAA
1 AAAAA
3978 CCAAAAAACA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
12 5 0.19
13 10 0.37
14 12 0.44
ACGTcount: A:0.80, C:0.04, G:0.07, T:0.09
Consensus pattern (14 bp):
AAAAAGAAAATAAC
Found at i:13082 original size:21 final size:20
Alignment explanation
Indices: 13056--13100 Score: 54
Period size: 21 Copynumber: 2.2 Consensus size: 20
13046 TTCAATTAAG
*
13056 AATCAAAGAGCTTTACTTCA
1 AATCAAAGAGCCTTACTTCA
* *
13076 TAATCAAGGCGCCTTACTTCA
1 -AATCAAAGAGCCTTACTTCA
13097 AATC
1 AATC
13101 CATAGCTTGT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 4 0.19
21 17 0.81
ACGTcount: A:0.36, C:0.24, G:0.11, T:0.29
Consensus pattern (20 bp):
AATCAAAGAGCCTTACTTCA
Found at i:16418 original size:81 final size:80
Alignment explanation
Indices: 16309--16475 Score: 208
Period size: 81 Copynumber: 2.1 Consensus size: 80
16299 TTGGGCCTAT
* * *
16309 GGCCTACCCAAGGATATCCTTAGATCCGTAGAGTTACCTTAAGCACACAAAAAAAGAAACCAACC
1 GGCCTACCCAAGGATACCCTTAGATCCGTAGAGTTACCCTAACCACACAAAAAAAGAAACCAACC
*
16374 TAAGGATATGCCTTGG
66 TAAGGATATACCTT-G
* * * ** ** * *
16390 GGCCTACCCAAGGGTACCCTTAGGTCCGTAGGGTTACCCTGTCCACACAGCAAAGGGAACCAACC
1 GGCCTACCCAAGGATACCCTTAGATCCGTAGAGTTACCCTAACCACACAAAAAAAGAAACCAACC
16455 TAAGGATATACCTTG
66 TAAGGATATACCTTG
16470 GGCCTA
1 GGCCTA
16476 TGGGCCTACC
Statistics
Matches: 73, Mismatches: 13, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
80 7 0.10
81 66 0.90
ACGTcount: A:0.32, C:0.28, G:0.22, T:0.19
Consensus pattern (80 bp):
GGCCTACCCAAGGATACCCTTAGATCCGTAGAGTTACCCTAACCACACAAAAAAAGAAACCAACC
TAAGGATATACCTTG
Found at i:27292 original size:38 final size:38
Alignment explanation
Indices: 27250--27326 Score: 118
Period size: 38 Copynumber: 2.0 Consensus size: 38
27240 TCTTGTTGAG
* * * *
27250 GATGACTAGTCATATTCTGAATACAACATTGTTCTTTC
1 GATGACTAGTCATATTCTAAAGACAAAATTGTTCCTTC
27288 GATGACTAGTCATATTCTAAAGACAAAATTGTTCCTTC
1 GATGACTAGTCATATTCTAAAGACAAAATTGTTCCTTC
27326 G
1 G
27327 TGTTGAGGAT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
38 35 1.00
ACGTcount: A:0.31, C:0.18, G:0.14, T:0.36
Consensus pattern (38 bp):
GATGACTAGTCATATTCTAAAGACAAAATTGTTCCTTC
Found at i:27357 original size:46 final size:46
Alignment explanation
Indices: 27288--27378 Score: 137
Period size: 46 Copynumber: 2.0 Consensus size: 46
27278 TTGTTCTTTC
*
27288 GATGACTAGTCATATTCTAAAGACAAAATTGTTCCTTCGTGTTGAG
1 GATGACTAGTCATATTCTAAAGACAAAATTGTTCCTTCGCGTTGAG
* * * *
27334 GATGACTAGTCGTATTCTGAAGACAACATTGTTTCTTCGCGTTGA
1 GATGACTAGTCATATTCTAAAGACAAAATTGTTCCTTCGCGTTGA
27379 TTAAGTTTGA
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
46 40 1.00
ACGTcount: A:0.27, C:0.16, G:0.21, T:0.35
Consensus pattern (46 bp):
GATGACTAGTCATATTCTAAAGACAAAATTGTTCCTTCGCGTTGAG
Found at i:32281 original size:21 final size:18
Alignment explanation
Indices: 32257--32298 Score: 50
Period size: 18 Copynumber: 2.2 Consensus size: 18
32247 ATAACACTTT
32257 TTTTTAAAACGAAATTATTGA
1 TTTTTAAAA--AAATTA-TGA
32278 -TTTTAAAAAAATTATGA
1 TTTTTAAAAAAATTATGA
32295 TTTT
1 TTTT
32299 AATTTGGAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 5
0.80 0.00 0.20
Matches are distributed among these distances:
17 3 0.15
18 9 0.45
20 8 0.40
ACGTcount: A:0.43, C:0.02, G:0.07, T:0.48
Consensus pattern (18 bp):
TTTTTAAAAAAATTATGA
Found at i:32297 original size:17 final size:19
Alignment explanation
Indices: 32258--32300 Score: 63
Period size: 17 Copynumber: 2.3 Consensus size: 19
32248 TAACACTTTT
32258 TTTTAAAACGAAATTATTGA
1 TTTTAAAAC-AAATTATTGA
32278 TTTTAAAA-AAATTA-TGA
1 TTTTAAAACAAATTATTGA
32295 TTTTAA
1 TTTTAA
32301 TTTGGAAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 9 0.39
18 6 0.26
20 8 0.35
ACGTcount: A:0.47, C:0.02, G:0.07, T:0.44
Consensus pattern (19 bp):
TTTTAAAACAAATTATTGA
Found at i:36766 original size:31 final size:31
Alignment explanation
Indices: 36731--36823 Score: 96
Period size: 31 Copynumber: 3.0 Consensus size: 31
36721 TCCACCATTT
*
36731 TGTGTCACATTATTACTTTCAACACGTGATA
1 TGTGTCACATTATTACTTTCGACACGTGATA
* * * * *
36762 TGTGTTACATTATCATTTTTGACCCGTGATA
1 TGTGTCACATTATTACTTTCGACACGTGATA
** * *
36793 TGTGTCATGTCATTACTTTCGACACATGATA
1 TGTGTCACATTATTACTTTCGACACGTGATA
36824 GTCTCGTATT
Statistics
Matches: 47, Mismatches: 15, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
31 47 1.00
ACGTcount: A:0.26, C:0.18, G:0.15, T:0.41
Consensus pattern (31 bp):
TGTGTCACATTATTACTTTCGACACGTGATA
Found at i:38338 original size:6 final size:6
Alignment explanation
Indices: 38327--38365 Score: 51
Period size: 6 Copynumber: 6.3 Consensus size: 6
38317 CTGTCAAAGG
* *
38327 TATACA TATACA TATACA TATTCA TTATAAA TATACA TA
1 TATACA TATACA TATACA TATACA -TATACA TATACA TA
38366 CATTCTTATA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
6 24 0.86
7 4 0.14
ACGTcount: A:0.49, C:0.13, G:0.00, T:0.38
Consensus pattern (6 bp):
TATACA
Found at i:39865 original size:3 final size:3
Alignment explanation
Indices: 39857--39885 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
39847 TTGGGACTAT
39857 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
39886 TCCTATAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:41181 original size:28 final size:28
Alignment explanation
Indices: 41113--41182 Score: 72
Period size: 27 Copynumber: 2.5 Consensus size: 28
41103 AAATTTAAAT
41113 TAAATAAATATTAAAAATTAATTTTATCA
1 TAAAT-AATATTAAAAATTAATTTTATCA
* * *
41142 TAAATAAT-TTAAAATTTTATATTTAT-T
1 TAAATAATATTAAAAATTAAT-TTTATCA
*
41169 TAATTAATATTAAA
1 TAAATAATATTAAA
41183 CTAATAGAAG
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
27 17 0.49
28 13 0.37
29 5 0.14
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.47
Consensus pattern (28 bp):
TAAATAATATTAAAAATTAATTTTATCA
Found at i:41337 original size:14 final size:14
Alignment explanation
Indices: 41300--41346 Score: 53
Period size: 14 Copynumber: 3.4 Consensus size: 14
41290 TGATTATACA
41300 ATTATATAAATTAA-
1 ATTATAT-AATTAAT
*
41314 A-TATAAAATTAAT
1 ATTATATAATTAAT
41327 ATTATATAATTAAT
1 ATTATATAATTAAT
*
41341 TTTATA
1 ATTATA
41347 GACTAGCTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
12 6 0.21
13 5 0.18
14 17 0.61
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (14 bp):
ATTATATAATTAAT
Found at i:49750 original size:117 final size:117
Alignment explanation
Indices: 49601--49822 Score: 281
Period size: 117 Copynumber: 1.9 Consensus size: 117
49591 TAAAAATGAT
* *
49601 CTTCTTTTGAAAACTAAAATAGACTTGGAAAATCAAAATGAAATGTTG-AGAA-ATGAGTTAGAG
1 CTTCTTTTGAAAACGAAAATAGACTTGGAAAATCAAAATGAAATCTTGAAGAAGA--AGTTAGAG
*
49664 CTTTCAAAAATAAAATCTGAAAACT-TTGAAAAAGAAATTTTCAAATTAAACAAA
64 CTTTCAAAAATAAAATCTG-AAACTATTGAAAAAGAAAATTTCAAATTAAACAAA
* * * *
49718 CTTCTTCTTG-AAACGAAAATGGATTTTGAAAATCAAAATGAAATCTTGAAGAAGAATTTAGAGC
1 CTTCTT-TTGAAAACGAAAATAGACTTGGAAAATCAAAATGAAATCTTGAAGAAGAAGTTAGAGC
* * * *
49782 TTTCAAAAATGAATTTTGAAAGTATTGAAAAAGAAAATTTC
65 TTTCAAAAATAAAATCTGAAACTATTGAAAAAGAAAATTTC
49823 GATTTGAAAG
Statistics
Matches: 90, Mismatches: 11, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
116 4 0.04
117 78 0.87
118 7 0.08
119 1 0.01
ACGTcount: A:0.47, C:0.09, G:0.14, T:0.30
Consensus pattern (117 bp):
CTTCTTTTGAAAACGAAAATAGACTTGGAAAATCAAAATGAAATCTTGAAGAAGAAGTTAGAGCT
TTCAAAAATAAAATCTGAAACTATTGAAAAAGAAAATTTCAAATTAAACAAA
Found at i:54246 original size:15 final size:16
Alignment explanation
Indices: 54226--54266 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
54216 GTTTACTTCA
*
54226 GAATGATT-AAGCGTT
1 GAATGATTCAAACGTT
*
54241 GAATGATTCAAATGTT
1 GAATGATTCAAACGTT
54257 GAATGATTCA
1 GAATGATTCA
54267 GAGGCTTTGT
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:0.07, G:0.22, T:0.34
Consensus pattern (16 bp):
GAATGATTCAAACGTT
Found at i:54459 original size:20 final size:20
Alignment explanation
Indices: 54434--54480 Score: 94
Period size: 20 Copynumber: 2.4 Consensus size: 20
54424 AACGGTTCAA
54434 CATTCAGCGCTAAATGGTTC
1 CATTCAGCGCTAAATGGTTC
54454 CATTCAGCGCTAAATGGTTC
1 CATTCAGCGCTAAATGGTTC
54474 CATTCAG
1 CATTCAG
54481 AGCCAAACAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.26, C:0.26, G:0.19, T:0.30
Consensus pattern (20 bp):
CATTCAGCGCTAAATGGTTC
Found at i:58159 original size:13 final size:14
Alignment explanation
Indices: 58126--58156 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
58116 CATTTTAAGT
58126 AAAATATTTTCTAA
1 AAAATATTTTCTAA
*
58140 AAAATATTTTTTAA
1 AAAATATTTTCTAA
58154 AAA
1 AAA
58157 TATAATTCAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (14 bp):
AAAATATTTTCTAA
Found at i:58520 original size:20 final size:20
Alignment explanation
Indices: 58497--58548 Score: 86
Period size: 20 Copynumber: 2.6 Consensus size: 20
58487 CGCGATTTAA
*
58497 AAAATCGCAACGTTAAAAAG
1 AAAATCGCAACGGTAAAAAG
*
58517 AAAATCGCAACGGTCAAAAG
1 AAAATCGCAACGGTAAAAAG
58537 AAAATCGCAACG
1 AAAATCGCAACG
58549 CAATCTTCCA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.52, C:0.19, G:0.17, T:0.12
Consensus pattern (20 bp):
AAAATCGCAACGGTAAAAAG
Found at i:58583 original size:20 final size:19
Alignment explanation
Indices: 58555--58938 Score: 336
Period size: 20 Copynumber: 18.7 Consensus size: 19
58545 AACGCAATCT
58555 TCCAAGAATCGCAATGCGA
1 TCCAAGAATCGCAATGCGA
58574 TCCAAAGAATCGCAATGCGA
1 TCC-AAGAATCGCAATGCGA
58594 TTCCAAGAATCGCAATGCGA
1 -TCCAAGAATCGCAATGCGA
*
58614 GCCAAAGAATCGCAATGCGA
1 TCC-AAGAATCGCAATGCGA
58634 TTCCAAGAATCGCAATGCGA
1 -TCCAAGAATCGCAATGCGA
58654 TTCCAAGAATCGCAATGCGA
1 -TCCAAGAATCGCAATGCGA
58674 TCTTCGAAGAATCGCAATGCGA
1 TC--C-AAGAATCGCAATGCGA
58696 TCTTCGAAGAATCGCAATGCGA
1 TC--C-AAGAATCGCAATGCGA
58718 TCTTCGAAGAATCGCAATGCGA
1 TC--C-AAGAATCGCAATGCGA
58740 TCTTCGAAGAATCGCAATGCGA
1 TC--C-AAGAATCGCAATGCGA
58762 TCTTCGAAGAATCGCAATGCGA
1 TC--C-AAGAATCGCAATGCGA
* *
58784 TTCAAAGAATCGCAACGCGA
1 -TCCAAGAATCGCAATGCGA
** * *
58804 TTGAGAAAATCGCAACGCGA
1 TCCA-AGAATCGCAATGCGA
* *
58824 TTCCAATAATCGCAACGCGA
1 -TCCAAGAATCGCAATGCGA
* *
58844 TTCCAATAATCGCAACGCGA
1 -TCCAAGAATCGCAATGCGA
** * *
58864 TTGAGAAAATCGCAACGCGA
1 TCCA-AGAATCGCAATGCGA
* *
58884 TTTCAAGAATCGCAACGCGA
1 -TCCAAGAATCGCAATGCGA
** *
58904 TTGAGAAAATCGCAATGCGA
1 TCCA-AGAATCGCAATGCGA
58924 TTCCAAGAATCGCAA
1 -TCCAAGAATCGCAA
58939 AACGGCAAAA
Statistics
Matches: 330, Mismatches: 21, Indels: 27
0.87 0.06 0.07
Matches are distributed among these distances:
19 14 0.04
20 197 0.60
21 13 0.04
22 104 0.32
23 2 0.01
ACGTcount: A:0.36, C:0.24, G:0.21, T:0.19
Consensus pattern (19 bp):
TCCAAGAATCGCAATGCGA
Found at i:58609 original size:40 final size:40
Alignment explanation
Indices: 58554--58938 Score: 402
Period size: 40 Copynumber: 9.4 Consensus size: 40
58544 CAACGCAATC
58554 TTCCAAGAATCGCAATGCGATCCAAAGAATCGCAATGCGA
1 TTCCAAGAATCGCAATGCGATCCAAAGAATCGCAATGCGA
*
58594 TTCCAAGAATCGCAATGCGAGCCAAAGAATCGCAATGCGA
1 TTCCAAGAATCGCAATGCGATCCAAAGAATCGCAATGCGA
58634 TTCCAAGAATCGCAATGCGATTCC-AAGAATCGCAATGCGA
1 TTCCAAGAATCGCAATGCGA-TCCAAAGAATCGCAATGCGA
* *
58674 TCTTCGAAGAATCGCAATGCGATCTTCGAAGAATCGCAATGCGA
1 --TTCCAAGAATCGCAATGCGATC--CAAAGAATCGCAATGCGA
* *
58718 TCTTCGAAGAATCGCAATGCGATCTTCGAAGAATCGCAATGCGA
1 --TTCCAAGAATCGCAATGCGATC--CAAAGAATCGCAATGCGA
* * *
58762 TCTTCGAAGAATCGCAATGCGATTCAAAGAATCGCAACGCGA
1 --TTCCAAGAATCGCAATGCGATCCAAAGAATCGCAATGCGA
* * * * *
58804 TT-GAGAAAATCGCAACGCGATTCC-AATAATCGCAACGCGA
1 TTCCA-AGAATCGCAATGCGA-TCCAAAGAATCGCAATGCGA
* * ** *
58844 TTCCAATAATCGCAACGCGATTGAGAA-AATCGCAACGCGA
1 TTCCAAGAATCGCAATGCGATCCA-AAGAATCGCAATGCGA
* * **
58884 TTTCAAGAATCGCAACGCGATTGAGAA-AATCGCAATGCGA
1 TTCCAAGAATCGCAATGCGATCCA-AAGAATCGCAATGCGA
58924 TTCCAAGAATCGCAA
1 TTCCAAGAATCGCAA
58939 AACGGCAAAA
Statistics
Matches: 316, Mismatches: 18, Indels: 22
0.89 0.05 0.06
Matches are distributed among these distances:
39 3 0.01
40 185 0.59
41 9 0.03
42 35 0.11
43 1 0.00
44 83 0.26
ACGTcount: A:0.36, C:0.24, G:0.21, T:0.19
Consensus pattern (40 bp):
TTCCAAGAATCGCAATGCGATCCAAAGAATCGCAATGCGA
Found at i:58633 original size:60 final size:60
Alignment explanation
Indices: 58558--58938 Score: 394
Period size: 60 Copynumber: 6.2 Consensus size: 60
58548 GCAATCTTCC
*
58558 AAGAATCGCAATGCGA-TCCAAAGAATCGCAATGCGATTCCAAGAATCGCAATGCGAGCCA
1 AAGAATCGCAATGCGATTCC-AAGAATCGCAATGCGATTCCAAGAATCGCAATGCGATCCA
*
58618 AAGAATCGCAATGCGATTCCAAGAATCGCAATGCGATTCCAAGAATCGCAATGCGATCTTCG
1 AAGAATCGCAATGCGATTCCAAGAATCGCAATGCGATTCCAAGAATCGCAATGCGATC--CA
* *
58680 AAGAATCGCAATGCGATCTTCGAAGAATCGCAATGCGATCTTCGAAGAATCGCAATGCGATCTTC
1 AAGAATCGCAATGCGA--TTCCAAGAATCGCAATGCGA--TTCCAAGAATCGCAATGCGATC--C
*
58745 G
60 A
* * * **
58746 AAGAATCGCAATGCGATCTTCGAAGAATCGCAATGCGATTCAAAGAATCGCAACGCGATTGA
1 AAGAATCGCAATGCGA--TTCCAAGAATCGCAATGCGATTCCAAGAATCGCAATGCGATCCA
* * * * * **
58808 GAA-AATCGCAACGCGATTCCAATAATCGCAACGCGATTCCAATAATCGCAACGCGATTGA
1 -AAGAATCGCAATGCGATTCCAAGAATCGCAATGCGATTCCAAGAATCGCAATGCGATCCA
* * * * *
58868 GAA-AATCGCAACGCGATTTCAAGAATCGCAACGCGATT-GAGAAAATCGCAATGCGATTCC-
1 -AAGAATCGCAATGCGATTCCAAGAATCGCAATGCGATTCCA-AGAATCGCAATGCGA-TCCA
58928 AAGAATCGCAA
1 AAGAATCGCAA
58939 AACGGCAAAA
Statistics
Matches: 288, Mismatches: 22, Indels: 22
0.87 0.07 0.07
Matches are distributed among these distances:
59 3 0.01
60 149 0.52
61 4 0.01
62 29 0.10
63 2 0.01
64 38 0.13
66 63 0.22
ACGTcount: A:0.36, C:0.24, G:0.21, T:0.19
Consensus pattern (60 bp):
AAGAATCGCAATGCGATTCCAAGAATCGCAATGCGATTCCAAGAATCGCAATGCGATCCA
Found at i:59060 original size:6 final size:6
Alignment explanation
Indices: 59049--59087 Score: 78
Period size: 6 Copynumber: 6.5 Consensus size: 6
59039 GACACGTATT
59049 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACC
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACC
59088 CGAGACGAGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.33, C:0.51, G:0.15, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:62120 original size:21 final size:21
Alignment explanation
Indices: 62095--62137 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
62085 CAATGGATTC
62095 AACTAAGAAAACATACTACAG
1 AACTAAGAAAACATACTACAG
62116 AACTAAGAAAACATACTACAG
1 AACTAAGAAAACATACTACAG
62137 A
1 A
62138 GCCGAAAAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.58, C:0.19, G:0.09, T:0.14
Consensus pattern (21 bp):
AACTAAGAAAACATACTACAG
Found at i:64036 original size:45 final size:45
Alignment explanation
Indices: 63963--64048 Score: 120
Period size: 45 Copynumber: 1.9 Consensus size: 45
63953 TGATAATTTA
* * *
63963 ATTCAAATATTATTTATTTTATATTTTATTTTAT-AATATATCAT
1 ATTCAAATATTATTAATCTTATATTTTATGTTATAAATATATCAT
*
64007 ATTCAAGTATTAATTAATCTTATATTTTATGTTATAAATATA
1 ATTCAAATATT-ATTAATCTTATATTTTATGTTATAAATATA
64049 ATTAGAGTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
44 10 0.28
45 20 0.56
46 6 0.17
ACGTcount: A:0.38, C:0.05, G:0.02, T:0.55
Consensus pattern (45 bp):
ATTCAAATATTATTAATCTTATATTTTATGTTATAAATATATCAT
Found at i:64926 original size:31 final size:31
Alignment explanation
Indices: 64891--64955 Score: 103
Period size: 31 Copynumber: 2.1 Consensus size: 31
64881 TGCAACACAA
*
64891 TCCCCCAACATTTAGTATGTTTGCAATATGG
1 TCCCCCAACATTTAATATGTTTGCAATATGG
* *
64922 TCCCCTAACATTTAATCTGTTTGCAATATGG
1 TCCCCCAACATTTAATATGTTTGCAATATGG
64953 TCC
1 TCC
64956 TCAACGTAAC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.25, C:0.25, G:0.14, T:0.37
Consensus pattern (31 bp):
TCCCCCAACATTTAATATGTTTGCAATATGG
Found at i:66945 original size:35 final size:35
Alignment explanation
Indices: 66815--66954 Score: 147
Period size: 36 Copynumber: 3.9 Consensus size: 35
66805 TGAATAAGAA
* * *
66815 GAACGAAATGAAGCATCATCACTTTCGATTCAAAGT
1 GAACGGAAGGAAGCATC-GCACTTTCGATTCAAAGT
**
66851 GAACGGAAGGAAGCATCGGCACTTTCGATTCAAAAA
1 GAACGGAAGGAAGCATC-GCACTTTCGATTCAAAGT
* * *
66887 GAATGAAAGGAAGCATCGACACTTTTGATTC-AAGT
1 GAACGGAAGGAAGCATCG-CACTTTCGATTCAAAGT
**
66922 GAACGGAAGGACTCATCTGCACTTTCGATTCAA
1 GAACGGAAGGAAGCATC-GCACTTTCGATTCAA
66955 TTGTTTATCT
Statistics
Matches: 85, Mismatches: 16, Indels: 6
0.79 0.15 0.06
Matches are distributed among these distances:
35 27 0.32
36 58 0.68
ACGTcount: A:0.36, C:0.19, G:0.21, T:0.23
Consensus pattern (35 bp):
GAACGGAAGGAAGCATCGCACTTTCGATTCAAAGT
Found at i:66950 original size:71 final size:72
Alignment explanation
Indices: 66813--66954 Score: 207
Period size: 71 Copynumber: 2.0 Consensus size: 72
66803 GGTGAATAAG
*
66813 AAGAACGAAATGAAGCATCATCACTTTCGATTCAAAGTGAACGGAAGGAAGCATCGGCACTTTCG
1 AAGAACGAAAGGAAGCATCATCACTTTCGATTCAAAGTGAACGGAAGGAAGCATCGGCACTTTCG
66878 ATTCAAA
66 ATTCAAA
* * ** *
66885 AAGAATGAAAGGAAGCATCGA-CACTTTTGATTC-AAGTGAACGGAAGGACTCATCTGCACTTTC
1 AAGAACGAAAGGAAGCATC-ATCACTTTCGATTCAAAGTGAACGGAAGGAAGCATCGGCACTTTC
66948 GATTCAA
65 GATTCAA
66955 TTGTTTATCT
Statistics
Matches: 63, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
71 34 0.54
72 28 0.44
73 1 0.02
ACGTcount: A:0.37, C:0.19, G:0.21, T:0.23
Consensus pattern (72 bp):
AAGAACGAAAGGAAGCATCATCACTTTCGATTCAAAGTGAACGGAAGGAAGCATCGGCACTTTCG
ATTCAAA
Found at i:68228 original size:36 final size:36
Alignment explanation
Indices: 68181--68320 Score: 162
Period size: 36 Copynumber: 3.9 Consensus size: 36
68171 TGAATAAGAA
*
68181 GAACGAAAGGAAGCATCATCACTTTTGATTCAAAGT
1 GAACGAAAGGAAGCATCATCACTTTCGATTCAAAGT
* ** *
68217 GAACGGAAGGAAGCATCGGCACTTTCGATTCAAAAAT
1 GAACGAAAGGAAGCATCATCACTTTCGATTC-AAAGT
*
68254 -AACGAAAGGAAGCATCGA-CACTTTTGATTC-AAGT
1 GAACGAAAGGAAGCATC-ATCACTTTCGATTCAAAGT
*
68288 GAACGGAAGGAAGCAT-ATGCACTTTCGATTCAA
1 GAACGAAAGGAAGCATCAT-CACTTTCGATTCAA
68321 TTGTTCATCT
Statistics
Matches: 87, Mismatches: 11, Indels: 12
0.79 0.10 0.11
Matches are distributed among these distances:
33 1 0.01
34 3 0.03
35 25 0.29
36 54 0.62
37 4 0.05
ACGTcount: A:0.38, C:0.18, G:0.22, T:0.22
Consensus pattern (36 bp):
GAACGAAAGGAAGCATCATCACTTTCGATTCAAAGT
Found at i:68315 original size:71 final size:72
Alignment explanation
Indices: 68182--68320 Score: 237
Period size: 71 Copynumber: 1.9 Consensus size: 72
68172 GAATAAGAAG
*
68182 AACGAAAGGAAGCATCATCACTTTTGATTCAAAGTGAACGGAAGGAAGCATCGGCACTTTCGATT
1 AACGAAAGGAAGCATCATCACTTTTGATTCAAAGTGAACGGAAGGAAGCATAGGCACTTTCGATT
68247 CAAAAAT
66 CAAAAAT
*
68254 AACGAAAGGAAGCATCGA-CACTTTTGATTC-AAGTGAACGGAAGGAAGCATATGCACTTTCGAT
1 AACGAAAGGAAGCATC-ATCACTTTTGATTCAAAGTGAACGGAAGGAAGCATAGGCACTTTCGAT
68317 TCAA
65 TCAA
68321 TTGTTCATCT
Statistics
Matches: 64, Mismatches: 2, Indels: 3
0.93 0.03 0.04
Matches are distributed among these distances:
71 35 0.55
72 28 0.44
73 1 0.02
ACGTcount: A:0.38, C:0.18, G:0.22, T:0.22
Consensus pattern (72 bp):
AACGAAAGGAAGCATCATCACTTTTGATTCAAAGTGAACGGAAGGAAGCATAGGCACTTTCGATT
CAAAAAT
Found at i:69667 original size:35 final size:36
Alignment explanation
Indices: 69549--69688 Score: 169
Period size: 36 Copynumber: 3.9 Consensus size: 36
69539 TGAATAAGAA
*
69549 GAACGAAATGAAGCATC-ATCACTTTCGATTCAAAGT
1 GAACGAAAGGAAGCATCGA-CACTTTCGATTCAAAGT
* * **
69585 GAACGGAAGGAAGCATCGGCACTTTCGATTCAAAAA
1 GAACGAAAGGAAGCATCGACACTTTCGATTCAAAGT
*
69621 GAACGAAAGGAAGCATCGACACTTTTGATTC-AAGT
1 GAACGAAAGGAAGCATCGACACTTTCGATTCAAAGT
* *
69656 GAACGGAAGGAAGCATCTG-CACTTTTGATTCAA
1 GAACGAAAGGAAGCATC-GACACTTTCGATTCAA
69689 TTGTTCATCT
Statistics
Matches: 90, Mismatches: 11, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
35 30 0.33
36 60 0.67
ACGTcount: A:0.37, C:0.19, G:0.22, T:0.22
Consensus pattern (36 bp):
GAACGAAAGGAAGCATCGACACTTTCGATTCAAAGT
Found at i:69686 original size:71 final size:72
Alignment explanation
Indices: 69547--69688 Score: 225
Period size: 71 Copynumber: 2.0 Consensus size: 72
69537 GGTGAATAAG
*
69547 AAGAACGAAATGAAGCATCATCACTTTCGATTCAAAGTGAACGGAAGGAAGCATCGGCACTTTCG
1 AAGAACGAAAGGAAGCATCATCACTTTCGATTCAAAGTGAACGGAAGGAAGCATCGGCACTTTCG
69612 ATTCAAA
66 ATTCAAA
* * *
69619 AAGAACGAAAGGAAGCATCGA-CACTTTTGATTC-AAGTGAACGGAAGGAAGCATCTGCACTTTT
1 AAGAACGAAAGGAAGCATC-ATCACTTTCGATTCAAAGTGAACGGAAGGAAGCATCGGCACTTTC
69682 GATTCAA
65 GATTCAA
69689 TTGTTCATCT
Statistics
Matches: 65, Mismatches: 4, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
71 35 0.54
72 29 0.45
73 1 0.02
ACGTcount: A:0.38, C:0.18, G:0.22, T:0.22
Consensus pattern (72 bp):
AAGAACGAAAGGAAGCATCATCACTTTCGATTCAAAGTGAACGGAAGGAAGCATCGGCACTTTCG
ATTCAAA
Found at i:71001 original size:72 final size:71
Alignment explanation
Indices: 70915--71056 Score: 214
Period size: 71 Copynumber: 2.0 Consensus size: 71
70905 GGTGAATAAG
70915 AAGAACGAAAGGAAGCATC-ATCACTTTCGATTCAAAGTGAACAGAAGGAAACATCGGCACTTTC
1 AAGAACGAAAGGAAGCATCGA-CACTTTCGATTC-AAGTGAACAGAAGGAAACATCGGCACTTTC
70979 GATTCAAA
64 GATTCAAA
* * * * *
70987 AAGAACGAAAGGAAGCATCGACACTTTTGATTCAAGTGAACGGAAGGAAGCATCTGTACTTTCGA
1 AAGAACGAAAGGAAGCATCGACACTTTCGATTCAAGTGAACAGAAGGAAACATCGGCACTTTCGA
71052 TTCAA
66 TTCAA
71057 TTGTTCATCT
Statistics
Matches: 64, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
71 33 0.52
72 30 0.47
73 1 0.02
ACGTcount: A:0.39, C:0.18, G:0.21, T:0.21
Consensus pattern (71 bp):
AAGAACGAAAGGAAGCATCGACACTTTCGATTCAAGTGAACAGAAGGAAACATCGGCACTTTCGA
TTCAAA
Found at i:71035 original size:35 final size:36
Alignment explanation
Indices: 70917--71056 Score: 162
Period size: 36 Copynumber: 3.9 Consensus size: 36
70907 TGAATAAGAA
70917 GAACGAAAGGAAGCATC-ATCACTTTCGATTCAAAGT
1 GAACGAAAGGAAGCATCGA-CACTTTCGATTCAAAGT
* * **
70953 GAAC-AGAAGGAAACATCGGCACTTTCGATTCAAAAA
1 GAACGA-AAGGAAGCATCGACACTTTCGATTCAAAGT
*
70989 GAACGAAAGGAAGCATCGACACTTTTGATTC-AAGT
1 GAACGAAAGGAAGCATCGACACTTTCGATTCAAAGT
* *
71024 GAACGGAAGGAAGCATCTG-TACTTTCGATTCAA
1 GAACGAAAGGAAGCATC-GACACTTTCGATTCAA
71057 TTGTTCATCT
Statistics
Matches: 87, Mismatches: 12, Indels: 10
0.80 0.11 0.09
Matches are distributed among these distances:
35 29 0.33
36 57 0.66
37 1 0.01
ACGTcount: A:0.39, C:0.19, G:0.21, T:0.21
Consensus pattern (36 bp):
GAACGAAAGGAAGCATCGACACTTTCGATTCAAAGT
Done.