Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003730.1 Hibiscus syriacus cultivar Beakdansim tig00007974_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: 45329
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:1414 original size:30 final size:31
Alignment explanation
Indices: 1371--1441 Score: 117
Period size: 30 Copynumber: 2.3 Consensus size: 31
1361 ATGAGGGCAG
*
1371 AGTGACTATTTTGTTATAAATCGATAATATT
1 AGTGACTAATTTGTTATAAATCGATAATATT
1402 AGTGA-TAATTTGTTATAAATCGATAATATT
1 AGTGACTAATTTGTTATAAATCGATAATATT
*
1432 AATGACTAAT
1 AGTGACTAAT
1442 ATTTTATTTT
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
30 28 0.76
31 9 0.24
ACGTcount: A:0.39, C:0.06, G:0.13, T:0.42
Consensus pattern (31 bp):
AGTGACTAATTTGTTATAAATCGATAATATT
Found at i:5696 original size:40 final size:40
Alignment explanation
Indices: 5573--5699 Score: 125
Period size: 45 Copynumber: 3.0 Consensus size: 40
5563 AATTAAGTAG
* *
5573 AGATGTTACACTTTCATACAAATTCCTACTCATTTCCACCAATC
1 AGATATTACACTTT-ATA-AAATCCCTACTC-TTT-CACCAATC
*
5617 ATGATATTACACTTTTATACAAATCCCT-CTCATTCACCAAT-
1 A-GATATTACAC-TTTATA-AAATCCCTACTCTTTCACCAATC
5658 AGATATTACACTTTAT-AAATCCCTACTCTTTTCTACCAATC
1 AGATATTACACTTTATAAAATCCCTACTC-TTTC-ACCAATC
5699 A
1 A
5700 TGTGACACTC
Statistics
Matches: 73, Mismatches: 4, Indels: 15
0.79 0.04 0.16
Matches are distributed among these distances:
37 8 0.11
38 3 0.04
39 8 0.11
40 16 0.22
41 2 0.03
42 7 0.10
43 2 0.03
44 4 0.05
45 20 0.27
46 3 0.04
ACGTcount: A:0.33, C:0.28, G:0.03, T:0.36
Consensus pattern (40 bp):
AGATATTACACTTTATAAAATCCCTACTCTTTCACCAATC
Found at i:15499 original size:3 final size:3
Alignment explanation
Indices: 15491--15524 Score: 52
Period size: 3 Copynumber: 11.3 Consensus size: 3
15481 TCTGAAACAT
15491 TTA TTA TTA TTA -TA TTTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA T
15525 AAAAAGTATG
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
2 2 0.07
3 25 0.86
4 2 0.07
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:15509 original size:15 final size:15
Alignment explanation
Indices: 15489--15518 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
15479 ATTCTGAAAC
15489 ATTTATTATTATTAT
1 ATTTATTATTATTAT
15504 ATTTATTATTATTAT
1 ATTTATTATTATTAT
15519 TATTATAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (15 bp):
ATTTATTATTATTAT
Found at i:17990 original size:58 final size:58
Alignment explanation
Indices: 17883--17993 Score: 136
Period size: 58 Copynumber: 1.9 Consensus size: 58
17873 AATAGTTAGG
*
17883 TGATCATTTATAACTTTTAATAGTTCAGGGATTCAACAAAGCAACATTCTATAATCGA
1 TGATCATTTATAACTTTTAATAGTTCAGAGATTCAACAAAGCAACATTCTATAATCGA
* * * * *
17941 TGATCATTTTGTAATTTTTAATA-TTCAGAGACTT-AATAAAGTAATATTCTATA
1 TGATCA-TTTATAACTTTTAATAGTTCAGAGA-TTCAACAAAGCAACATTCTATA
17994 GTTGGGGACT
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
58 29 0.64
59 16 0.36
ACGTcount: A:0.38, C:0.12, G:0.11, T:0.40
Consensus pattern (58 bp):
TGATCATTTATAACTTTTAATAGTTCAGAGATTCAACAAAGCAACATTCTATAATCGA
Found at i:27949 original size:9 final size:9
Alignment explanation
Indices: 27937--27970 Score: 50
Period size: 9 Copynumber: 3.6 Consensus size: 9
27927 TATTGTCCTT
27937 ATTAATTAA
1 ATTAATTAA
27946 ATTAATTAA
1 ATTAATTAA
27955 ATATAATTAA
1 AT-TAATTAA
27965 AGTTAA
1 A-TTAA
27971 GTTGCTTACG
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
9 11 0.48
10 11 0.48
11 1 0.04
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (9 bp):
ATTAATTAA
Found at i:28544 original size:16 final size:16
Alignment explanation
Indices: 28506--28536 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
28496 AGTTCGAAAT
*
28506 ATAAAATAAATAATTC
1 ATAATATAAATAATTC
28522 ATAATATAAATAATT
1 ATAATATAAATAATT
28537 TATTATATTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.35
Consensus pattern (16 bp):
ATAATATAAATAATTC
Found at i:29201 original size:19 final size:20
Alignment explanation
Indices: 29161--29208 Score: 62
Period size: 19 Copynumber: 2.4 Consensus size: 20
29151 TTGATTAAAT
*
29161 ATTTAATATTTTTTATTTTAA
1 ATTTAA-ATTTTTTATTATAA
29182 ATTTAAATTTTTTA-TATAA
1 ATTTAAATTTTTTATTATAA
*
29201 ATTAAAAT
1 ATTTAAAT
29209 ACTATTAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 11 0.44
20 8 0.32
21 6 0.24
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (20 bp):
ATTTAAATTTTTTATTATAA
Found at i:30487 original size:2 final size:2
Alignment explanation
Indices: 30480--30514 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
30470 TTATTTAATT
30480 TA TA TA TA TA TA TA TA TA TA 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 T
30515 TTAAATATAG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:30743 original size:40 final size:40
Alignment explanation
Indices: 30691--30799 Score: 148
Period size: 40 Copynumber: 2.8 Consensus size: 40
30681 TTGAATTTGG
**
30691 ATACTAAAATAAAATAAAAACTAAAATTTTTAACGATGAA
1 ATACTAAAATAAAATAAAAACTAAAATTTTTAACGAAAAA
*
30731 ATACTAAAATAAAATAAAAACTAAATTTTTTAACGAAAAA
1 ATACTAAAATAAAATAAAAACTAAAATTTTTAACGAAAAA
* ** *
30771 ATATTAAAACGAATTAAAAACT-AAATTTT
1 ATACTAAAATAAAATAAAAACTAAAATTTT
30800 AAGTATCAAC
Statistics
Matches: 61, Mismatches: 8, Indels: 1
0.87 0.11 0.01
Matches are distributed among these distances:
39 6 0.10
40 55 0.90
ACGTcount: A:0.60, C:0.07, G:0.04, T:0.29
Consensus pattern (40 bp):
ATACTAAAATAAAATAAAAACTAAAATTTTTAACGAAAAA
Found at i:38290 original size:17 final size:19
Alignment explanation
Indices: 38262--38296 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
38252 TTGAAATATT
38262 AATGTGTAATTT-ACCCAA
1 AATGTGTAATTTGACCCAA
38280 AATGT-TAATTTGACCCA
1 AATGTGTAATTTGACCCA
38297 CTGCGTCCTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.37, C:0.17, G:0.11, T:0.34
Consensus pattern (19 bp):
AATGTGTAATTTGACCCAA
Found at i:38772 original size:20 final size:20
Alignment explanation
Indices: 38749--38958 Score: 246
Period size: 20 Copynumber: 10.5 Consensus size: 20
38739 GCGAATATGA
* *
38749 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
38769 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
38789 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
38809 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
38829 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
38849 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
38869 AAATCGCAACG-ATAATCCGT
1 AAATCGCAACGCGT-ATCCGT
* * *
38889 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGTATCCGT
*
38909 AAATCGCAACG-ATAATCCGT
1 AAATCGCAACGCGT-ATCCGT
* * *
38929 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGTATCCGT
*
38949 AAATCACAAC
1 AAATCGCAAC
38959 ACTTAAATTT
Statistics
Matches: 166, Mismatches: 19, Indels: 10
0.85 0.10 0.05
Matches are distributed among these distances:
19 1 0.01
20 163 0.98
21 2 0.01
ACGTcount: A:0.36, C:0.26, G:0.18, T:0.20
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:38798 original size:60 final size:59
Alignment explanation
Indices: 38670--38939 Score: 195
Period size: 60 Copynumber: 4.5 Consensus size: 59
38660 ATGACCAACA
* ** ** * *
38670 AAATCGCAACGCGAAATA--AAAATCGCAACGCGATCCCCAGAATCGCAAATCAGTTTCC-A
1 AAATCGCAACGCG-AATACGAAAATCGCAACGCGAACCATA-AATCGCAACGC-GTATCCGT
* *
38729 AAATTGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGAATACGAAAATCGCAACGCGAAC-CATAAATCGCAACGCGTATCCGT
* * * * * * *
38789 AAATCGCAACGTGTATCCGTAAATCGCAACGCGTATCCGTAAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGAATACGAAAATCGCAACGCG-AACCATAAATCGCAACGCGTATCCGT
* * * * ** * * * *
38849 ATATCGCAACGCGTATCCGTAAATCGCAACGATAATCCGTAAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGAATACGAAAATCGCAACGCGAA-CCATAAATCGCAACGCGTATCCGT
** * *
38909 AAATCGCAACGATAATCCGTAAATCGCAACG
1 AAATCGCAACGCGAATACGAAAATCGCAACG
38940 AGAATCTGTA
Statistics
Matches: 175, Mismatches: 30, Indels: 11
0.81 0.14 0.05
Matches are distributed among these distances:
58 4 0.02
59 18 0.10
60 149 0.85
61 4 0.02
ACGTcount: A:0.37, C:0.26, G:0.18, T:0.19
Consensus pattern (59 bp):
AAATCGCAACGCGAATACGAAAATCGCAACGCGAACCATAAATCGCAACGCGTATCCGT
Found at i:39690 original size:24 final size:24
Alignment explanation
Indices: 39651--39697 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
39641 AAATTTGGTC
39651 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
39675 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
39698 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:39889 original size:12 final size:12
Alignment explanation
Indices: 39872--39896 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
39862 ATTTAATCCT
39872 GAAGAAGAAAAA
1 GAAGAAGAAAAA
39884 GAAGAAGAAAAA
1 GAAGAAGAAAAA
39896 G
1 G
39897 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:42230 original size:33 final size:33
Alignment explanation
Indices: 42179--42430 Score: 247
Period size: 33 Copynumber: 7.2 Consensus size: 33
42169 CGGAAATTAC
* *
42179 AATCGCAACGAGAGAATCGCAATGCGAAATGAA
1 AATCGCAACAAGAAAATCGCAATGCGAAATGAA
*
42212 AATCCCAACAAGAAAATCGCAATGCGGAAATGAA
1 AATCGCAACAAGAAAATCGCAATGC-GAAATGAA
42246 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAA--C--AA-GAAAATCGCAATGCGAAATGAA
* * *
42284 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCG-C
1 AATCGCAA--C--AA-GAAAATCGCAATGCGA-AAT-GAA
* *
42323 AATGCGGAA-ATGAAAATCGCAATGCGAAATGAA
1 AAT-CGCAACAAGAAAATCGCAATGCGAAATGAA
* *
42356 AATCGCAACGAGAGAATCGCAATGCGAAATGAA
1 AATCGCAACAAGAAAATCGCAATGCGAAATGAA
* *
42389 AATCGCAACGAGAGAATCGCAATGCGGAAATGAA
1 AATCGCAACAAGAAAATCGCAATGC-GAAATGAA
42423 AATCGCAA
1 AATCGCAA
42431 TGCGAAATGA
Statistics
Matches: 191, Mismatches: 16, Indels: 23
0.83 0.07 0.10
Matches are distributed among these distances:
32 5 0.03
33 74 0.39
34 45 0.24
35 1 0.01
36 1 0.01
38 40 0.21
39 20 0.10
40 5 0.03
ACGTcount: A:0.46, C:0.18, G:0.23, T:0.13
Consensus pattern (33 bp):
AATCGCAACAAGAAAATCGCAATGCGAAATGAA
Found at i:42262 original size:19 final size:19
Alignment explanation
Indices: 42193--42454 Score: 312
Period size: 19 Copynumber: 14.7 Consensus size: 19
42183 GCAACGAGAG
42193 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
42212 AATCCCAA--C--AA-GAA
1 AATCGCAATGCGAAATGAA
42226 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
42246 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
42265 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
42284 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
42303 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
42317 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
42337 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
42356 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
42370 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
42389 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
42403 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
42423 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
42442 AATCGCATTGCGA
1 AATCGCAATGCGA
42455 TTCTCTCGTT
Statistics
Matches: 211, Mismatches: 9, Indels: 46
0.79 0.03 0.17
Matches are distributed among these distances:
14 40 0.19
15 5 0.02
16 5 0.02
17 9 0.04
18 1 0.00
19 111 0.53
20 40 0.19
ACGTcount: A:0.46, C:0.18, G:0.23, T:0.14
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:42364 original size:53 final size:52
Alignment explanation
Indices: 42223--42454 Score: 281
Period size: 53 Copynumber: 4.3 Consensus size: 52
42213 ATCCCAACAA
*
42223 GAAAATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGC-GAAATGAAAATCGCAA--CG--A-GAGAATCGCAATGCGAAAT
42281 GAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGGAAAT
1 GAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGC-GAAAT
42334 GAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAAT
* * * * *
42386 GAAAATCGCAACGAGAGAATCG-CAATGCGGAA--ATGAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGA-AAT-GAAAAT-CGCAACGA-GAGAATCGCAATGCGAAAT
*
42439 GAAAATCGCATTGCGA
1 GAAAATCGCAATGCGA
42455 TTCTCTCGTT
Statistics
Matches: 160, Mismatches: 9, Indels: 15
0.87 0.05 0.08
Matches are distributed among these distances:
52 33 0.21
53 90 0.56
54 5 0.03
55 2 0.01
57 16 0.10
58 14 0.09
ACGTcount: A:0.45, C:0.17, G:0.24, T:0.14
Consensus pattern (52 bp):
GAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAAT
Found at i:42375 original size:14 final size:14
Alignment explanation
Indices: 42356--42410 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
42346 GCGAAATGAA
42356 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
42370 AATCGCAATGCGAAATGAA
1 AATCGCAA--CG--A-GAG
42389 AATCGCAACGAGAG
1 AATCGCAACGAGAG
42403 AATCGCAA
1 AATCGCAA
42411 TGCGGAAATG
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.29
ACGTcount: A:0.45, C:0.20, G:0.24, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:42416 original size:86 final size:86
Alignment explanation
Indices: 42179--42448 Score: 459
Period size: 86 Copynumber: 3.1 Consensus size: 86
42169 CGGAAATTAC
* * *
42179 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCCCAACAAGAAAATCGCAATGCGGAAATG
1 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGGAAATG
42244 AAAATCGCAATGCGAAATGAA
66 AAAATCGCAATGCGAAATGAA
*
42265 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGG
1 AATCGCAA--CG--A-GAGAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGG
42330 AAATGAAAATCGCAATGCGAAATGAA
61 AAATGAAAATCGCAATGCGAAATGAA
42356 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGGAAATG
1 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGGAAATG
42421 AAAATCGCAATGCGAAATGAA
66 AAAATCGCAATGCGAAATGAA
42442 AATCGCA
1 AATCGCA
42449 TTGCGATTCT
Statistics
Matches: 174, Mismatches: 5, Indels: 10
0.92 0.03 0.05
Matches are distributed among these distances:
86 89 0.51
87 1 0.01
88 2 0.01
89 2 0.01
90 1 0.01
91 79 0.45
ACGTcount: A:0.46, C:0.18, G:0.23, T:0.13
Consensus pattern (86 bp):
AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGGAAATG
AAAATCGCAATGCGAAATGAA
Found at i:42488 original size:53 final size:52
Alignment explanation
Indices: 42425--42540 Score: 160
Period size: 53 Copynumber: 2.2 Consensus size: 52
42415 GAAATGAAAA
*
42425 TCGCAATGCGAAATGAAAATCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 TCGCATTGCGAAATGAAAATCGCATTGCGATTCTCTCGTTGCGATTTTCATT
** ** **
42477 TCCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 T-CGCATTGCGAAATGAAAATCGCATTGCGATTCTCTCGTTGCGATTTTCATT
42530 TCGCATTGCGA
1 TCGCATTGCGA
42541 TTTTCATTTC
Statistics
Matches: 56, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
52 11 0.20
53 45 0.80
ACGTcount: A:0.19, C:0.23, G:0.19, T:0.39
Consensus pattern (52 bp):
TCGCATTGCGAAATGAAAATCGCATTGCGATTCTCTCGTTGCGATTTTCATT
Found at i:42503 original size:19 final size:19
Alignment explanation
Indices: 42463--42550 Score: 123
Period size: 19 Copynumber: 4.8 Consensus size: 19
42453 GATTCTCTCG
42463 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
42483 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
42502 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
42516 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
42535 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
42551 AACATAATGC
Statistics
Matches: 61, Mismatches: 2, Indels: 11
0.82 0.03 0.15
Matches are distributed among these distances:
14 6 0.10
16 7 0.11
17 7 0.11
19 26 0.43
20 15 0.25
ACGTcount: A:0.14, C:0.23, G:0.16, T:0.48
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:42660 original size:14 final size:14
Alignment explanation
Indices: 42641--42677 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
42631 CATCAATTAC
42641 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
42655 ACAAATCATCTTTT
1 ACAAATCAACTTTT
42669 ACAAATCAA
1 ACAAATCAA
42678 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:44649 original size:19 final size:19
Alignment explanation
Indices: 44623--44779 Score: 136
Period size: 19 Copynumber: 8.8 Consensus size: 19
44613 CACGAAACTT
*
44623 AAAATCGCAACGCGAAATG
1 AAAATCGCAACGCGAAACG
* * *
44642 AGAATCGCAACGAGAAACC
1 AAAATCGCAACGCGAAACG
*
44661 AAAATCGCAACGCGAAACC
1 AAAATCGCAACGCGAAACG
*
44680 AAAATCGCAACGCGAAATG
1 AAAATCGCAACGCGAAACG
44699 AAAATCGCAA--CG--AC-
1 AAAATCGCAACGCGAAACG
* *
44713 AGAATCGCAACGCGAAACA
1 AAAATCGCAACGCGAAACG
44732 AAAATCGCAA--CG--A-G
1 AAAATCGCAACGCGAAACG
* * *
44746 AGAATCGCAACGCAAAATG
1 AAAATCGCAACGCGAAACG
*
44765 AAAATCGCAATGCGA
1 AAAATCGCAACGCGA
44780 TTTTGGTTTC
Statistics
Matches: 111, Mismatches: 17, Indels: 20
0.75 0.11 0.14
Matches are distributed among these distances:
14 18 0.16
15 2 0.02
16 3 0.03
17 4 0.04
18 3 0.03
19 81 0.73
ACGTcount: A:0.48, C:0.24, G:0.20, T:0.08
Consensus pattern (19 bp):
AAAATCGCAACGCGAAACG
Found at i:44686 original size:57 final size:52
Alignment explanation
Indices: 44623--44743 Score: 170
Period size: 52 Copynumber: 2.2 Consensus size: 52
44613 CACGAAACTT
* *
44623 AAAATCGCAACGCGAAATGAGAATCGCAACGAGAAACCAAAATCGCAACGCGAAACC
1 AAAATCGCAACGCGAAATGAAAATCGCAAC--G--A-CAAAATCGCAACGCGAAACA
*
44680 AAAATCGCAACGCGAAATGAAAATCGCAACGACAGAATCGCAACGCGAAACA
1 AAAATCGCAACGCGAAATGAAAATCGCAACGACAAAATCGCAACGCGAAACA
44732 AAAATCGCAACG
1 AAAATCGCAACG
44744 AGAGAATCGC
Statistics
Matches: 61, Mismatches: 3, Indels: 5
0.88 0.04 0.07
Matches are distributed among these distances:
52 30 0.49
53 1 0.02
55 1 0.02
57 29 0.48
ACGTcount: A:0.48, C:0.26, G:0.19, T:0.07
Consensus pattern (52 bp):
AAAATCGCAACGCGAAATGAAAATCGCAACGACAAAATCGCAACGCGAAACA
Found at i:44720 original size:14 final size:14
Alignment explanation
Indices: 44701--44757 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
44691 GCGAAATGAA
44701 AATCGCAACGACAG
1 AATCGCAACGACAG
*
44715 AATCGCAACGCGAAACAAA
1 AATCGCAA--CG--AC-AG
*
44734 AATCGCAACGAGAG
1 AATCGCAACGACAG
44748 AATCGCAACG
1 AATCGCAACG
44758 CAAAATGAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
14 19 0.54
15 1 0.03
16 2 0.06
17 2 0.06
18 2 0.06
19 9 0.26
ACGTcount: A:0.46, C:0.26, G:0.21, T:0.07
Consensus pattern (14 bp):
AATCGCAACGACAG
Found at i:44724 original size:33 final size:33
Alignment explanation
Indices: 44682--44774 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 33
44672 GCGAAACCAA
44682 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGACAG
** *
44715 AATCGCAACGCGAAACAAAAATCGCAACGAGAG
1 AATCGCAACGCGAAATGAAAATCGCAACGACAG
*
44748 AATCGCAACGCAAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
44775 TGCGATTTTG
Statistics
Matches: 54, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 54 1.00
ACGTcount: A:0.48, C:0.24, G:0.19, T:0.09
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGACAG
Found at i:44771 original size:52 final size:52
Alignment explanation
Indices: 44641--44779 Score: 144
Period size: 52 Copynumber: 2.7 Consensus size: 52
44631 AACGCGAAAT
* * *
44641 GAGAATCGCAACG-AGAAACCAAAATCGCAACGCGAAACCAAAATCGCAACGC
1 GAGAATCGCAACGCA-AAACGAAAATCGCAACGCGAAACAAAAATCGCAACGA
*
44693 GA-AAT-GAAAATCGC--AACGACAGAATCGCAACGCGAAACAAAAATCGCAACGA
1 GAGAATCG-CAA-CGCAAAACGA-A-AATCGCAACGCGAAACAAAAATCGCAACGA
* *
44745 GAGAATCGCAACGCAAAATGAAAATCGCAATGCGA
1 GAGAATCGCAACGCAAAACGAAAATCGCAACGCGA
44780 TTTTGGTTTC
Statistics
Matches: 71, Mismatches: 7, Indels: 18
0.74 0.07 0.19
Matches are distributed among these distances:
50 5 0.07
51 6 0.08
52 49 0.69
53 6 0.08
54 5 0.07
ACGTcount: A:0.47, C:0.24, G:0.20, T:0.08
Consensus pattern (52 bp):
GAGAATCGCAACGCAAAACGAAAATCGCAACGCGAAACAAAAATCGCAACGA
Found at i:44791 original size:19 final size:19
Alignment explanation
Indices: 44775--44852 Score: 103
Period size: 19 Copynumber: 4.4 Consensus size: 19
44765 AAAATCGCAA
44775 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
44794 TGCGATTTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
44808 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
**
44827 TGCGATTTTCATTTCGCGT
1 TGCGATTTTGGTTTCGCGT
44846 TGCGATT
1 TGCGATT
44853 CTCTCGTTTT
Statistics
Matches: 52, Mismatches: 2, Indels: 10
0.81 0.03 0.16
Matches are distributed among these distances:
14 12 0.23
15 1 0.02
16 1 0.02
17 1 0.02
18 1 0.02
19 36 0.69
ACGTcount: A:0.08, C:0.17, G:0.28, T:0.47
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:44836 original size:14 final size:14
Alignment explanation
Indices: 44791--44817 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
44781 TTTGGTTTCG
44791 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
44805 CGTTGCGATTTTG
1 CGTTGCGATTTTG
44818 GTTTCGCGTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.07, C:0.15, G:0.30, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:44860 original size:52 final size:53
Alignment explanation
Indices: 44775--44884 Score: 141
Period size: 52 Copynumber: 2.1 Consensus size: 53
44765 AAAATCGCAA
** * * *
44775 TGCGATTTTGGTTTCGCGTTGCGATTTTGTCGTTGCGATTTT-GGTTTCGCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGTTGCGATTTTAAGTTTCGCGT
** *
44827 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGTTTTGATTTTAAGTTTCGTGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGTTGCGATTTTAAGTTTCGCGT
44880 TGCGA
1 TGCGA
44885 AAGTAAACTA
Statistics
Matches: 49, Mismatches: 8, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
52 36 0.73
53 13 0.27
ACGTcount: A:0.09, C:0.16, G:0.26, T:0.48
Consensus pattern (53 bp):
TGCGATTTTCATTTCGCGTTGCGATTCTCTCGTTGCGATTTTAAGTTTCGCGT
Found at i:45048 original size:83 final size:87
Alignment explanation
Indices: 44932--45204 Score: 324
Period size: 93 Copynumber: 3.1 Consensus size: 87
44922 ATGGATTGCA
* * **
44932 TTAC-TTCAACCAATATACAAAACAAAGACAAATACTGACTT-CAG-G-G-TA-TTAGTTTAGCA
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACT-ACTTACAGTGAGATACACAGTTTAGCA
44991 GAATTGGCAGCAACCGAACAAAT
65 GAATTGGCAGCAACCGAACAAAT
*
45014 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTACTT-ACAGTG----AG-ATACACAGTT
45079 TAGCAGAATTGGCAGCAACCGAACAAAT
60 TAGCAGAATTGGCAGCAACCGAACAAAT
*
45107 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTACTT-ACAGTG----AG-ATACACAGTT
*
45172 TAGCAGAATTGGCAGCAACCGAATAAAT
60 TAGCAGAATTGGCAGCAACCGAACAAAT
45200 TTACT
1 TTACT
45205 AAGCAATCTA
Statistics
Matches: 173, Mismatches: 6, Indels: 13
0.90 0.03 0.07
Matches are distributed among these distances:
82 7 0.04
83 30 0.17
84 3 0.02
85 1 0.01
90 1 0.01
92 2 0.01
93 129 0.75
ACGTcount: A:0.45, C:0.19, G:0.13, T:0.23
Consensus pattern (87 bp):
TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTACTTACAGTGAGATACACAGTTTAGCAG
AATTGGCAGCAACCGAACAAAT
Found at i:45141 original size:93 final size:93
Alignment explanation
Indices: 44982--45204 Score: 437
Period size: 93 Copynumber: 2.4 Consensus size: 93
44972 TCAGGGTATT
44982 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
1 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
45047 TACTATTTCACAGTGTTAAAGAATACAC
66 TACTATTTCACAGTGTTAAAGAATACAC
45075 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
1 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
45140 TACTATTTCACAGTGTTAAAGAATACAC
66 TACTATTTCACAGTGTTAAAGAATACAC
*
45168 AGTTTAGCAGAATTGGCAGCAACCGAATAAATTTACT
1 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACT
45205 AAGCAATCTA
Statistics
Matches: 129, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
93 129 1.00
ACGTcount: A:0.45, C:0.19, G:0.14, T:0.22
Consensus pattern (93 bp):
AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
TACTATTTCACAGTGTTAAAGAATACAC
Done.