Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006599.1 Hibiscus syriacus cultivar Beakdansim tig00016187_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: 72479
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.33
Found at i:8399 original size:6 final size:6
Alignment explanation
Indices: 8383--8411 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
8373 TCATAATTTC
8383 AATAT- AATATA AATATA AATATA AATATA
1 AATATA AATATA AATATA AATATA AATATA
8412 CTTTTAATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 5 0.22
6 18 0.78
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (6 bp):
AATATA
Found at i:24637 original size:31 final size:31
Alignment explanation
Indices: 24580--24638 Score: 77
Period size: 31 Copynumber: 1.9 Consensus size: 31
24570 CAAACTAACT
24580 TACTAACTTTTATTTATTCACTTTATTATTG
1 TACTAACTTTTATTTATTCACTTTATTATTG
*
24611 TACTAATTTTTCATTT-TT-ACTGTTATTA
1 TACTAACTTTT-ATTTATTCACT-TTATTA
24639 CTAACATTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
30 3 0.12
31 18 0.72
32 4 0.16
ACGTcount: A:0.25, C:0.12, G:0.03, T:0.59
Consensus pattern (31 bp):
TACTAACTTTTATTTATTCACTTTATTATTG
Found at i:26451 original size:115 final size:115
Alignment explanation
Indices: 26249--26469 Score: 388
Period size: 115 Copynumber: 1.9 Consensus size: 115
26239 ATGCACCACT
*
26249 TTGTTATTTGGACTAATTTTTGAAATGCATTTTTATATGTTTTTAAATATGGAACGAAATTTATA
1 TTGTTATTTGGACTAATTTTTGAAATGCATTTTTATATGTTTTTAAATATGGAAAGAAATTTATA
*
26314 TTTGATATGTGACCGTCTAGATTCGGTCATAACAACCATGCATAATAACC
66 TTTGATATGTGACCGTCTAGATTCAGTCATAACAACCATGCATAATAACC
*
26364 TTGTTATTTGGATTAATTTTTGAAATGCATTTTTATATGTTTTTAAATATGGAAAGAAATTTATA
1 TTGTTATTTGGACTAATTTTTGAAATGCATTTTTATATGTTTTTAAATATGGAAAGAAATTTATA
* * *
26429 TTTGATATGTGATCGTCTAGATTTAGTTATAACAACCATGC
66 TTTGATATGTGACCGTCTAGATTCAGTCATAACAACCATGC
26470 TGAATCTAGG
Statistics
Matches: 100, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
115 100 1.00
ACGTcount: A:0.32, C:0.10, G:0.15, T:0.43
Consensus pattern (115 bp):
TTGTTATTTGGACTAATTTTTGAAATGCATTTTTATATGTTTTTAAATATGGAAAGAAATTTATA
TTTGATATGTGACCGTCTAGATTCAGTCATAACAACCATGCATAATAACC
Found at i:27325 original size:21 final size:21
Alignment explanation
Indices: 27299--27341 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
27289 TTATGTCCAA
27299 TGTTGACAAAACATAAAGTTT
1 TGTTGACAAAACATAAAGTTT
27320 TGTTGACAAAACATAAAGTTT
1 TGTTGACAAAACATAAAGTTT
27341 T
1 T
27342 AAGAGAAAAG
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:0.42, C:0.09, G:0.14, T:0.35
Consensus pattern (21 bp):
TGTTGACAAAACATAAAGTTT
Found at i:29486 original size:13 final size:13
Alignment explanation
Indices: 29454--29500 Score: 60
Period size: 13 Copynumber: 3.5 Consensus size: 13
29444 TCAAATGATC
29454 ATTTTTATGTTTACT
1 ATTTTTAT-TTTA-T
29469 ATTTTT-TTTTAT
1 ATTTTTATTTTAT
29481 ATTTTTATTTTAT
1 ATTTTTATTTTAT
*
29494 ATGTTTA
1 ATTTTTA
29501 ACGTGAATTG
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
12 7 0.23
13 16 0.53
14 1 0.03
15 6 0.20
ACGTcount: A:0.21, C:0.02, G:0.04, T:0.72
Consensus pattern (13 bp):
ATTTTTATTTTAT
Found at i:31282 original size:24 final size:24
Alignment explanation
Indices: 31255--31334 Score: 151
Period size: 24 Copynumber: 3.3 Consensus size: 24
31245 TAGAAGTTCG
*
31255 ATTGAAGCCTAAAATTTGAGTTCA
1 ATTGAAGCCTAAAATTTGAGCTCA
31279 ATTGAAGCCTAAAATTTGAGCTCA
1 ATTGAAGCCTAAAATTTGAGCTCA
31303 ATTGAAGCCTAAAATTTGAGCTCA
1 ATTGAAGCCTAAAATTTGAGCTCA
31327 ATTGAAGC
1 ATTGAAGC
31335 GAAAGAATAG
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
24 55 1.00
ACGTcount: A:0.38, C:0.15, G:0.17, T:0.30
Consensus pattern (24 bp):
ATTGAAGCCTAAAATTTGAGCTCA
Found at i:31980 original size:20 final size:21
Alignment explanation
Indices: 31955--32088 Score: 139
Period size: 21 Copynumber: 6.5 Consensus size: 21
31945 TTTTCCCAAT
*
31955 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
31975 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
*
31996 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
32016 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
*
32037 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
32057 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
32078 TCGCAATGCGA
1 TCGCAATGCGA
32089 TACTGACTAT
Statistics
Matches: 90, Mismatches: 21, Indels: 5
0.78 0.18 0.04
Matches are distributed among these distances:
20 43 0.48
21 47 0.52
ACGTcount: A:0.40, C:0.18, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:32103 original size:41 final size:41
Alignment explanation
Indices: 31955--32088 Score: 268
Period size: 41 Copynumber: 3.3 Consensus size: 41
31945 TTTTCCCAAT
31955 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
31996 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
32037 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
32078 TCGCAATGCGA
1 TCGCAATGCGA
32089 TACTGACTAT
Statistics
Matches: 93, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 93 1.00
ACGTcount: A:0.40, C:0.18, G:0.25, T:0.17
Consensus pattern (41 bp):
TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
Found at i:32119 original size:41 final size:41
Alignment explanation
Indices: 32074--32171 Score: 133
Period size: 41 Copynumber: 2.4 Consensus size: 41
32064 GCGAATTGGG
*
32074 AAAATCGCAATGCGATACTGACTATCGCAATGCGATAATAA
1 AAAATCGCAATGCGATACTGACTATCGCAACGCGATAATAA
* * * * *
32115 AAAATCGCAACGAGATACTTACTTTCGCAACGCGATAATAC
1 AAAATCGCAATGCGATACTGACTATCGCAACGCGATAATAA
*
32156 ATAATCGCAATGCGAT
1 AAAATCGCAATGCGAT
32172 TTTCAAAGCG
Statistics
Matches: 48, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
41 48 1.00
ACGTcount: A:0.40, C:0.21, G:0.16, T:0.22
Consensus pattern (41 bp):
AAAATCGCAATGCGATACTGACTATCGCAACGCGATAATAA
Found at i:32123 original size:21 final size:20
Alignment explanation
Indices: 32074--32171 Score: 61
Period size: 20 Copynumber: 4.8 Consensus size: 20
32064 GCGAATTGGG
* *
32074 AAAATCGCAATGCGATACTG
1 AAAATCGCAATGCGATAATA
**
32094 ACTATCGCAATGCGATAATAA
1 AAAATCGCAATGCGATAAT-A
* * * *
32115 AAAATCGCAACGAGATACTT
1 AAAATCGCAATGCGATAATA
*** *
32135 ACTTTCGCAACGCGATAATA
1 AAAATCGCAATGCGATAATA
*
32155 CATAATCGCAATGCGAT
1 -AAAATCGCAATGCGAT
32172 TTTCAAAGCG
Statistics
Matches: 56, Mismatches: 20, Indels: 3
0.71 0.25 0.04
Matches are distributed among these distances:
20 30 0.54
21 26 0.46
ACGTcount: A:0.40, C:0.21, G:0.16, T:0.22
Consensus pattern (20 bp):
AAAATCGCAATGCGATAATA
Found at i:32367 original size:22 final size:22
Alignment explanation
Indices: 32339--32382 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
32329 CACTCTCTCA
32339 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
*
32361 CCCATCTCCGGCGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
32383 TATCTCCATC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.20, C:0.45, G:0.16, T:0.18
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:34004 original size:18 final size:18
Alignment explanation
Indices: 33983--34027 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
33973 TCCACTTCGG
*
33983 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCACCCA
* *
34001 GAGCTATTACCTCACCCA
1 GAGCCATCACCTCACCCA
34019 GAGCCATCA
1 GAGCCATCA
34028 TCTGATCGAA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.27, C:0.42, G:0.16, T:0.16
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:34494 original size:19 final size:20
Alignment explanation
Indices: 34440--34506 Score: 73
Period size: 20 Copynumber: 3.4 Consensus size: 20
34430 TAGTTTACTT
* *
34440 TCGCAACACGAAAATGACTA
1 TCGCAACGCGGAAATGACTA
*
34460 TCGCAACGCGGAAATGGCTA
1 TCGCAACGCGGAAATGACTA
* **
34480 TCGCAATGC-GAAATGAAAA
1 TCGCAACGCGGAAATGACTA
34499 TCGCAACG
1 TCGCAACG
34507 ACAAAATCGC
Statistics
Matches: 39, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
19 14 0.36
20 25 0.64
ACGTcount: A:0.39, C:0.24, G:0.22, T:0.15
Consensus pattern (20 bp):
TCGCAACGCGGAAATGACTA
Found at i:34514 original size:14 final size:14
Alignment explanation
Indices: 34495--34552 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
34485 ATGCGAAATG
34495 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
34509 AAAATCGCAACGCGAA
1 AAAATCGCAA--CGAC
34525 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
34541 AAAATCGCAACG
1 AAAATCGCAACG
34553 CGAAATGAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.48, C:0.26, G:0.17, T:0.09
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:34537 original size:32 final size:33
Alignment explanation
Indices: 34479--34569 Score: 166
Period size: 32 Copynumber: 2.8 Consensus size: 33
34469 GGAAATGGCT
*
34479 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
34512 ATCGCAACGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
34544 ATCGCAACGCGAAATGAAAATCGCAA
1 ATCGCAACGCGAAATGAAAATCGCAA
34570 TGCGATTTGT
Statistics
Matches: 56, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
32 32 0.57
33 24 0.43
ACGTcount: A:0.47, C:0.23, G:0.19, T:0.11
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGACAAA
Found at i:34563 original size:19 final size:19
Alignment explanation
Indices: 34440--34574 Score: 85
Period size: 19 Copynumber: 7.6 Consensus size: 19
34430 TAGTTTACTT
* **
34440 TCGCAACACGAAAATGACTA
1 TCGCAACGCG-AAATGAAAA
***
34460 TCGCAACGCGGAAATGGCTA
1 TCGCAACGC-GAAATGAAAA
*
34480 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
34499 TCGCAA--CG--A-CAAAA
1 TCGCAACGCGAAATGAAAA
34513 TCGCAACGCGAAATG-AAA
1 TCGCAACGCGAAATGAAAA
*
34531 TCGCAA--CG--A-CAAAA
1 TCGCAACGCGAAATGAAAA
34545 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
34564 TCGCAATGCGA
1 TCGCAACGCGA
34575 TTTGTGTTTC
Statistics
Matches: 92, Mismatches: 11, Indels: 25
0.72 0.09 0.20
Matches are distributed among these distances:
14 20 0.22
15 1 0.01
16 6 0.07
17 2 0.02
18 11 0.12
19 27 0.29
20 24 0.26
21 1 0.01
ACGTcount: A:0.43, C:0.24, G:0.21, T:0.13
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:34605 original size:14 final size:14
Alignment explanation
Indices: 34586--34643 Score: 62
Period size: 14 Copynumber: 3.9 Consensus size: 14
34576 TTGTGTTTCG
34586 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
34600 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
34616 CGCGTTGCGATTTTGT
1 --CGTTGCGATTTTGT
*
34632 CGTTGTGATTTT
1 CGTTGCGATTTT
34644 CATTTCGCAT
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
14 22 0.59
16 4 0.11
18 11 0.30
ACGTcount: A:0.09, C:0.16, G:0.26, T:0.50
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:34620 original size:32 final size:33
Alignment explanation
Indices: 34581--34659 Score: 133
Period size: 32 Copynumber: 2.4 Consensus size: 33
34571 GCGATTTGTG
34581 TTTCGCGTTGCGATTTTGTCGTTGCGA-TTTCA
1 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
*
34613 TTTCGCGTTGCGATTTTGTCGTTGTGATTTTCA
1 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
*
34646 TTTCGCATTGCGAT
1 TTTCGCGTTGCGAT
34660 AGCCATTTTC
Statistics
Matches: 44, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
32 26 0.59
33 18 0.41
ACGTcount: A:0.10, C:0.18, G:0.24, T:0.48
Consensus pattern (33 bp):
TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
Found at i:34690 original size:19 final size:19
Alignment explanation
Indices: 34643--34698 Score: 85
Period size: 20 Copynumber: 2.9 Consensus size: 19
34633 GTTGTGATTT
*
34643 TCATTTCGCATTGCGATAG
1 TCATTTCGCGTTGCGATAG
*
34662 CCATTTTCGCGTTGCGATAG
1 TCA-TTTCGCGTTGCGATAG
34682 TCATTTCGCGTTGCGAT
1 TCATTTCGCGTTGCGAT
34699 TTTAAGTTTC
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
19 16 0.48
20 17 0.52
ACGTcount: A:0.16, C:0.23, G:0.23, T:0.38
Consensus pattern (19 bp):
TCATTTCGCGTTGCGATAG
Found at i:34794 original size:27 final size:26
Alignment explanation
Indices: 34728--34797 Score: 79
Period size: 25 Copynumber: 2.7 Consensus size: 26
34718 AAGTAAACTA
* *
34728 TTCTTCTTCTGGAATGTTTATATATG
1 TTCTTCTTCTGAAATGTTTATATAAG
* * *
34754 TTGTCCTT-TTAAATGTTTATATAAG
1 TTCTTCTTCTGAAATGTTTATATAAG
34779 TTCTTACTTCTGAAATGTT
1 TTCTT-CTTCTGAAATGTT
34798 ATCTGAGCAT
Statistics
Matches: 34, Mismatches: 8, Indels: 3
0.76 0.18 0.07
Matches are distributed among these distances:
25 17 0.50
26 9 0.26
27 8 0.24
ACGTcount: A:0.23, C:0.11, G:0.13, T:0.53
Consensus pattern (26 bp):
TTCTTCTTCTGAAATGTTTATATAAG
Found at i:36731 original size:19 final size:19
Alignment explanation
Indices: 36716--36764 Score: 89
Period size: 19 Copynumber: 2.6 Consensus size: 19
36706 ATCGCAACGA
36716 GAAAATCGCAATGCAAAAT
1 GAAAATCGCAATGCAAAAT
*
36735 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCAAAAT
36754 GAAAATCGCAA
1 GAAAATCGCAA
36765 CGAGAAAATC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.51, C:0.16, G:0.18, T:0.14
Consensus pattern (19 bp):
GAAAATCGCAATGCAAAAT
Found at i:36771 original size:19 final size:19
Alignment explanation
Indices: 36716--36771 Score: 78
Period size: 19 Copynumber: 2.9 Consensus size: 19
36706 ATCGCAACGA
36716 GAAAATCGCAATGCA-AAAT
1 GAAAATCGCAATG-AGAAAT
*
36735 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGAGAAAT
*
36754 GAAAATCGCAACGAGAAA
1 GAAAATCGCAATGAGAAA
36772 ATCGCAATGC
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
19 33 1.00
ACGTcount: A:0.52, C:0.16, G:0.20, T:0.12
Consensus pattern (19 bp):
GAAAATCGCAATGAGAAAT
Found at i:36859 original size:20 final size:20
Alignment explanation
Indices: 36802--36859 Score: 98
Period size: 20 Copynumber: 2.9 Consensus size: 20
36792 TCGCATTGCG
* *
36802 ATTTTCTCGTTGCGATAACC
1 ATTTTCGCGTTGCGATAGCC
36822 ATTTTCGCGTTGCGATAGCC
1 ATTTTCGCGTTGCGATAGCC
36842 ATTTTCGCGTTGCGATAG
1 ATTTTCGCGTTGCGATAG
36860 TCAAATGAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.17, C:0.22, G:0.22, T:0.38
Consensus pattern (20 bp):
ATTTTCGCGTTGCGATAGCC
Found at i:37946 original size:24 final size:24
Alignment explanation
Indices: 37919--37972 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
37909 GTATTCGAAA
* *
37919 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATACACGGAC
*
37943 TTTGATATTGGTCAATACACGGAT
1 TTTGATATTGGTCAATACACGGAC
37967 TTTGAT
1 TTTGAT
37973 GATGTTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.24, C:0.17, G:0.20, T:0.39
Consensus pattern (24 bp):
TTTGATATTGGTCAATACACGGAC
Found at i:38989 original size:21 final size:21
Alignment explanation
Indices: 38923--38989 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
38913 GTGAATCGAG
*
38923 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * ** * *
38943 CCTCTTCAACGATGACAGTGGC
1 -CTCTTGAACGGTGGGAGGGGA
38965 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
38986 CTCT
1 CTCT
38990 CGAGGAATGA
Statistics
Matches: 32, Mismatches: 13, Indels: 2
0.68 0.28 0.04
Matches are distributed among these distances:
21 30 0.94
22 2 0.06
ACGTcount: A:0.19, C:0.21, G:0.36, T:0.24
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGA
Found at i:39008 original size:42 final size:41
Alignment explanation
Indices: 38923--39044 Score: 111
Period size: 42 Copynumber: 2.9 Consensus size: 41
38913 GTGAATCGAG
* * * * *
38923 CTCTTGAATGGTGGGA-GGGACCTCTTCAACGATGACAGTGGC
1 CTCTTGAACGGTGGGAGGGGA-CTC-TCGAGGATGATAGAGGC
38965 CTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGAGGC
1 CTCTTGAACGGTGGGAGGGGACTCTCGAGG-ATGATAGAGGC
* * * * *
39007 CTCTTCAACGATAGGAGTGGACTCTTGAGGGATGATAG
1 CTCTTGAACGGTGGGAGGGGACTCTCGA-GGATGATAG
39045 GCGAGTCGGG
Statistics
Matches: 67, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
41 4 0.06
42 57 0.85
43 6 0.09
ACGTcount: A:0.24, C:0.18, G:0.35, T:0.23
Consensus pattern (41 bp):
CTCTTGAACGGTGGGAGGGGACTCTCGAGGATGATAGAGGC
Found at i:41073 original size:20 final size:20
Alignment explanation
Indices: 41048--41107 Score: 68
Period size: 20 Copynumber: 3.0 Consensus size: 20
41038 CTTTTGGTTG
41048 TAATGAAAATCGCAACGAGA
1 TAATGAAAATCGCAACGAGA
* *
41068 TAATGAGAATCGCAACGCGGA
1 TAATGAAAATCGCAACG-AGA
**
41089 -AATGACTATCGCAACGAGA
1 TAATGAAAATCGCAACGAGA
41108 GAATCGCAAC
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
19 2 0.06
20 30 0.88
21 2 0.06
ACGTcount: A:0.43, C:0.18, G:0.23, T:0.15
Consensus pattern (20 bp):
TAATGAAAATCGCAACGAGA
Found at i:41129 original size:33 final size:33
Alignment explanation
Indices: 41072--41170 Score: 144
Period size: 33 Copynumber: 3.0 Consensus size: 33
41062 ACGAGATAAT
*
41072 GAGAATCGCAACGCGGAAATGACTATCGCAACGA
1 GAGAATCGCAACGC-GAAATGACTATCGCAACCA
*
41106 GAGAATCGCAACGCGAAATGACTATCGCGACCA
1 GAGAATCGCAACGCGAAATGACTATCGCAACCA
* **
41139 GACAATCGCAACGCGAAATGAAAATCGCAACC
1 GAGAATCGCAACGCGAAATGACTATCGCAACC
41171 GCGAAATAAA
Statistics
Matches: 59, Mismatches: 6, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
33 45 0.76
34 14 0.24
ACGTcount: A:0.39, C:0.26, G:0.23, T:0.11
Consensus pattern (33 bp):
GAGAATCGCAACGCGAAATGACTATCGCAACCA
Found at i:41164 original size:19 final size:19
Alignment explanation
Indices: 41049--41231 Score: 170
Period size: 19 Copynumber: 10.0 Consensus size: 19
41039 TTTTGGTTGT
*
41049 AATGAAAATCGCAACGAGA
1 AATGAAAATCGCAACGCGA
*
41068 TAATGAGAATCGCAACGCGGA
1 -AATGAAAATCGCAACGC-GA
**
41089 AATGACTATCGCAA--CG-
1 AATGAAAATCGCAACGCGA
*
41105 -A-GAGAATCGCAACGCGA
1 AATGAAAATCGCAACGCGA
** *
41122 AATGACTATCGCGAC-C--
1 AATGAAAATCGCAACGCGA
*
41138 -A-GACAATCGCAACGCGA
1 AATGAAAATCGCAACGCGA
41155 AATGAAAATCGCAACCGCGA
1 AATGAAAATCGCAA-CGCGA
*
41175 AATAAAAATCGCAACGCGA
1 AATGAAAATCGCAACGCGA
41194 AATGAAAATCGCAACGCGA
1 AATGAAAATCGCAACGCGA
*
41213 AATGAAAATCGCAATGCGA
1 AATGAAAATCGCAACGCGA
41232 TTTTGGTTTC
Statistics
Matches: 136, Mismatches: 15, Indels: 25
0.77 0.09 0.14
Matches are distributed among these distances:
14 19 0.14
15 3 0.02
16 2 0.01
17 1 0.01
18 4 0.03
19 60 0.44
20 45 0.33
21 2 0.01
ACGTcount: A:0.44, C:0.22, G:0.22, T:0.12
Consensus pattern (19 bp):
AATGAAAATCGCAACGCGA
Found at i:41185 original size:39 final size:38
Alignment explanation
Indices: 41142--41231 Score: 153
Period size: 39 Copynumber: 2.3 Consensus size: 38
41132 GCGACCAGAC
41142 AATCGCAACGCGAAATGAAAATCGCAACCGCGAAATAAA
1 AATCGCAACGCGAAATGAAAATCGCAA-CGCGAAATAAA
*
41181 AATCGCAACGCGAAATGAAAATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAAAATCGCAACGCGAAATAAA
*
41219 AATCGCAATGCGA
1 AATCGCAACGCGA
41232 TTTTGGTTTC
Statistics
Matches: 49, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
38 22 0.45
39 27 0.55
ACGTcount: A:0.47, C:0.22, G:0.20, T:0.11
Consensus pattern (38 bp):
AATCGCAACGCGAAATGAAAATCGCAACGCGAAATAAA
Found at i:41249 original size:19 final size:19
Alignment explanation
Indices: 41227--41271 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 19
41217 AAAATCGCAA
* *
41227 TGCGATTTTGGTTTCGTGT
1 TGCGATTTTGATTTCGCGT
*
41246 TGCGATTTTTATTTCGCGT
1 TGCGATTTTGATTTCGCGT
41265 TGCGATT
1 TGCGATT
41272 ATCTCGTTGC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.09, C:0.13, G:0.27, T:0.51
Consensus pattern (19 bp):
TGCGATTTTGATTTCGCGT
Found at i:41829 original size:20 final size:20
Alignment explanation
Indices: 41804--41843 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
41794 GCGCTATGTA
41804 AATCGCACTGCGAAAGTCAG
1 AATCGCACTGCGAAAGTCAG
**
41824 AATCGCGTTGCGAAAGTCAG
1 AATCGCACTGCGAAAGTCAG
41844 TATCTCGTTG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.33, C:0.23, G:0.28, T:0.17
Consensus pattern (20 bp):
AATCGCACTGCGAAAGTCAG
Found at i:41852 original size:20 final size:20
Alignment explanation
Indices: 41812--41856 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
41802 TAAATCGCAC
41812 TGCGAAAGTCAGAATCGCGT
1 TGCGAAAGTCAGAATCGCGT
* *
41832 TGCGAAAGTCAGTATCTCGT
1 TGCGAAAGTCAGAATCGCGT
41852 TGCGA
1 TGCGA
41857 TTTTGTATTA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.27, C:0.20, G:0.29, T:0.24
Consensus pattern (20 bp):
TGCGAAAGTCAGAATCGCGT
Found at i:41890 original size:20 final size:20
Alignment explanation
Indices: 41865--41918 Score: 99
Period size: 20 Copynumber: 2.7 Consensus size: 20
41855 GATTTTGTAT
41865 TATCGCATTGCGATAGTAAG
1 TATCGCATTGCGATAGTAAG
*
41885 TATCGCATTGCGATAGTCAG
1 TATCGCATTGCGATAGTAAG
41905 TATCGCATTGCGAT
1 TATCGCATTGCGAT
41919 TTTCCCAATT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.31
Consensus pattern (20 bp):
TATCGCATTGCGATAGTAAG
Found at i:41903 original size:61 final size:61
Alignment explanation
Indices: 41805--41921 Score: 162
Period size: 61 Copynumber: 1.9 Consensus size: 61
41795 CGCTATGTAA
* * * *
41805 ATCGCACTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGTATCTCGTTGCGATTTTGTATT
1 ATCGCACTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTGTATT
* * * *
41866 ATCGCATTGCGATAGTAAGTATCGCATTGCGATAGTCAGTATCGCATTGCGATTTT
1 ATCGCACTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTT
41922 CCCAATTCGC
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
61 48 1.00
ACGTcount: A:0.25, C:0.19, G:0.24, T:0.32
Consensus pattern (61 bp):
ATCGCACTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTGTATT
Found at i:41937 original size:61 final size:61
Alignment explanation
Indices: 41805--41939 Score: 146
Period size: 61 Copynumber: 2.2 Consensus size: 61
41795 CGCTATGTAA
* * * * * * * ** *
41805 ATCGCACTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGTATCTCGTTGCGATTTTGTATT
1 ATCGCATTGCGATAGTAAGTATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTCCAAT
*
41866 ATCGCATTGCGATAGTAAGTATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCCCAAT
1 ATCGCATTGCGATAGTAAGTATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTT-CCAAT
*
41928 -TCGCGTTGCGAT
1 ATCGCATTGCGAT
41940 TTACTTATTC
Statistics
Matches: 61, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
61 59 0.97
62 2 0.03
ACGTcount: A:0.24, C:0.21, G:0.24, T:0.32
Consensus pattern (61 bp):
ATCGCATTGCGATAGTAAGTATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTCCAAT
Found at i:48281 original size:16 final size:16
Alignment explanation
Indices: 48260--48290 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
48250 TTTTATTATT
48260 ATTATATTAATATTTA
1 ATTATATTAATATTTA
*
48276 ATTATATTATTATTT
1 ATTATATTAATATTT
48291 TTAGGTCATT
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:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
ATTATATTAATATTTA
Found at i:57942 original size:20 final size:20
Alignment explanation
Indices: 57919--57963 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
57909 AAAAGGTAGG
* *
57919 TATCGATACTCAAGGTTCAA
1 TATCAATACTCAAGGGTCAA
*
57939 TATCAATACTGAAGGGTCAA
1 TATCAATACTCAAGGGTCAA
57959 TATCA
1 TATCA
57964 GTACCATCAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.38, C:0.18, G:0.16, T:0.29
Consensus pattern (20 bp):
TATCAATACTCAAGGGTCAA
Found at i:61244 original size:20 final size:20
Alignment explanation
Indices: 61215--61252 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
61205 TTTCAAAGGG
61215 ATGCACCGATGCACCAATCC
1 ATGCACCGATGCACCAATCC
*
61235 ATGCATCGATGCACCAAT
1 ATGCACCGATGCACCAAT
61253 GAATAAATTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.32, C:0.34, G:0.16, T:0.18
Consensus pattern (20 bp):
ATGCACCGATGCACCAATCC
Found at i:61332 original size:65 final size:64
Alignment explanation
Indices: 61214--61358 Score: 159
Period size: 65 Copynumber: 2.2 Consensus size: 64
61204 TTTTCAAAGG
* * *
61214 GATGCACCGATGCACCAATCCATGCATCGATGCACCAATGAATAAATTGAACATCGAATGTAGTT
1 GATGCATCGATGCA-CAATCCATGCATCGATGCACCAATGAATAAATTGAACATCGAATGCA-CT
61279 T
64 T
* ** **
61280 GATGCATCGATGCACAATCCATGTATCGATGCACTC-A-GGCTATTTTGAAACATCGAATGCACT
1 GATGCATCGATGCACAATCCATGCATCGATGCAC-CAATGAATAAATTG-AACATCGAATGCACT
61343 T
64 T
*
61344 CATGCATCGATGCAC
1 GATGCATCGATGCAC
61359 TAAGGGCCCA
Statistics
Matches: 68, Mismatches: 9, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
64 22 0.32
65 32 0.47
66 14 0.21
ACGTcount: A:0.32, C:0.24, G:0.19, T:0.26
Consensus pattern (64 bp):
GATGCATCGATGCACAATCCATGCATCGATGCACCAATGAATAAATTGAACATCGAATGCACTT
Found at i:68825 original size:20 final size:20
Alignment explanation
Indices: 68796--68833 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
68786 TTTCAAAGGG
68796 ATGCACCGATGCACCAATCC
1 ATGCACCGATGCACCAATCC
*
68816 ATGCATCGATGCACCAAT
1 ATGCACCGATGCACCAAT
68834 GAATAAATTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.32, C:0.34, G:0.16, T:0.18
Consensus pattern (20 bp):
ATGCACCGATGCACCAATCC
Found at i:68932 original size:46 final size:44
Alignment explanation
Indices: 68879--68986 Score: 137
Period size: 45 Copynumber: 2.4 Consensus size: 44
68869 ATTCACTCTC
* * *
68879 CATGCATCGATTCACTCAGG-TTTTAATGAAAACATCGAATGCATTT
1 CATGCATCGATGCACTCAGGCATTT--TG-AAACATCGAATGCACTT
*
68925 GATGCATCGATGCACTCAGGCCATTTTGAAACATCGAATGCACTT
1 CATGCATCGATGCACTCAGG-CATTTTGAAACATCGAATGCACTT
68970 CATGCATCGATGCACTC
1 CATGCATCGATGCACTC
68987 TTAGTACAAC
Statistics
Matches: 55, Mismatches: 5, Indels: 5
0.85 0.08 0.08
Matches are distributed among these distances:
45 32 0.58
46 20 0.36
48 3 0.05
ACGTcount: A:0.30, C:0.24, G:0.18, T:0.29
Consensus pattern (44 bp):
CATGCATCGATGCACTCAGGCATTTTGAAACATCGAATGCACTT
Done.