Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000752.1 Hibiscus syriacus cultivar Beakdansim tig00001455_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: 122949
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Found at i:6731 original size:30 final size:30
Alignment explanation
Indices: 6695--6758 Score: 128
Period size: 30 Copynumber: 2.1 Consensus size: 30
6685 ATGTTGGATA
6695 ATAGTACAAATTATCAAGGGATGTCCGATT
1 ATAGTACAAATTATCAAGGGATGTCCGATT
6725 ATAGTACAAATTATCAAGGGATGTCCGATT
1 ATAGTACAAATTATCAAGGGATGTCCGATT
6755 ATAG
1 ATAG
6759 CTTTTATTTG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.38, C:0.12, G:0.20, T:0.30
Consensus pattern (30 bp):
ATAGTACAAATTATCAAGGGATGTCCGATT
Found at i:11182 original size:21 final size:21
Alignment explanation
Indices: 11143--11187 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
11133 ATTTGGTTGA
***
11143 CCTTTGCCTGATGTTTGCTGT
1 CCTTTGCCTGATAAATGCTGT
11164 CCTTTGCCTGATAAATGCTGT
1 CCTTTGCCTGATAAATGCTGT
11185 CCT
1 CCT
11188 CTTGATGGAG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.11, C:0.27, G:0.20, T:0.42
Consensus pattern (21 bp):
CCTTTGCCTGATAAATGCTGT
Found at i:15518 original size:18 final size:18
Alignment explanation
Indices: 15495--15529 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
15485 AGTTTTGTTG
15495 TTGCGAACCTTTAAATGC
1 TTGCGAACCTTTAAATGC
* *
15513 TTGCGAGCTTTTAAATG
1 TTGCGAACCTTTAAATG
15530 TAATACAAAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.26, C:0.17, G:0.20, T:0.37
Consensus pattern (18 bp):
TTGCGAACCTTTAAATGC
Found at i:16456 original size:29 final size:29
Alignment explanation
Indices: 16428--16517 Score: 74
Period size: 31 Copynumber: 3.0 Consensus size: 29
16418 TTAGATTATA
* *
16428 TTTTTAATTAATTGAGTGATTTATTTATAAC
1 TTTTTAA--AATTGAATGATCTATTTATAAC
**
16459 TTTTTAAAATTGAATGATCTATTGGTAATC
1 TTTTTAAAATTGAATGATCTATTTATAA-C
* *
16489 TTATTAATAATT-AGATAATCTATTTATAA
1 TTTTTAA-AATTGA-ATGATCTATTTATAA
16518 TCTTACTAAT
Statistics
Matches: 48, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
29 17 0.35
30 8 0.17
31 23 0.48
ACGTcount: A:0.37, C:0.04, G:0.09, T:0.50
Consensus pattern (29 bp):
TTTTTAAAATTGAATGATCTATTTATAAC
Found at i:16519 original size:31 final size:31
Alignment explanation
Indices: 16449--16537 Score: 96
Period size: 31 Copynumber: 3.0 Consensus size: 31
16439 TTGAGTGATT
* *
16449 TATTTATAA-CTTTTTAA-AATT-GAATGATC
1 TATTTATAATCTTATTAATAATTAG-ATAATC
**
16478 TATTGGTAATCTTATTAATAATTAGATAATC
1 TATTTATAATCTTATTAATAATTAGATAATC
*
16509 TATTTATAATCTTACTAATAATTAG-TAAT
1 TATTTATAATCTTATTAATAATTAGATAAT
16538 TAGATATAGT
Statistics
Matches: 50, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
29 7 0.14
30 11 0.22
31 31 0.62
32 1 0.02
ACGTcount: A:0.39, C:0.07, G:0.07, T:0.47
Consensus pattern (31 bp):
TATTTATAATCTTATTAATAATTAGATAATC
Found at i:17355 original size:31 final size:31
Alignment explanation
Indices: 17297--17355 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 31
17287 GTAGTAGTTA
* *
17297 GACTGTTACACTGATTATGATGATATAATTT
1 GACTGTTACACTGATAATCATGATATAATTT
*
17328 GACTGTTA-ACTGATAATCCATGTTATAA
1 GACTGTTACACTGATAAT-CATGATATAA
17356 ACTTATAATG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 8 0.33
31 16 0.67
ACGTcount: A:0.34, C:0.12, G:0.15, T:0.39
Consensus pattern (31 bp):
GACTGTTACACTGATAATCATGATATAATTT
Found at i:18546 original size:21 final size:21
Alignment explanation
Indices: 18520--18562 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
18510 TTCAGTTCTG
18520 TACAAAGCATTGTCATAGGCT
1 TACAAAGCATTGTCATAGGCT
18541 TACAAAGCATTGTCATAGGCT
1 TACAAAGCATTGTCATAGGCT
18562 T
1 T
18563 GTTTCCTTCG
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:0.33, C:0.19, G:0.19, T:0.30
Consensus pattern (21 bp):
TACAAAGCATTGTCATAGGCT
Found at i:30728 original size:2 final size:2
Alignment explanation
Indices: 30721--30761 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
30711 ATTCCCATAC
30721 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
30762 CATACTTTTT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:30981 original size:4 final size:4
Alignment explanation
Indices: 30972--31422 Score: 881
Period size: 4 Copynumber: 113.5 Consensus size: 4
30962 TTATGCTACA
30972 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
31020 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
31068 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
31116 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
31164 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TA-- TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
31210 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
31258 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
31306 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
31354 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
31402 TATG TATG TATG TATG T-TG TA
1 TATG TATG TATG TATG TATG TA
31423 GTTGATGAGT
Statistics
Matches: 444, Mismatches: 0, Indels: 6
0.99 0.00 0.01
Matches are distributed among these distances:
2 2 0.00
3 3 0.01
4 439 0.99
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.50
Consensus pattern (4 bp):
TATG
Found at i:33782 original size:14 final size:15
Alignment explanation
Indices: 33763--33798 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
33753 CACATAATAT
33763 AAAAATTA-ATTTTA
1 AAAAATTACATTTTA
*
33777 AAAAATGACATTTTA
1 AAAAATTACATTTTA
33792 AAAAATT
1 AAAAATT
33799 TATATATTAG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
14 7 0.37
15 12 0.63
ACGTcount: A:0.58, C:0.03, G:0.03, T:0.36
Consensus pattern (15 bp):
AAAAATTACATTTTA
Found at i:35493 original size:10 final size:10
Alignment explanation
Indices: 35478--35516 Score: 53
Period size: 10 Copynumber: 3.9 Consensus size: 10
35468 TTATCACATT
35478 AAATTCTCTC
1 AAATTCTCTC
35488 AAATTCTCT-
1 AAATTCTCTC
35497 AAATTTCTCTC
1 AAA-TTCTCTC
*
35508 AAATACTCT
1 AAATTCTCT
35517 ATCTTTTTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
9 3 0.12
10 20 0.77
11 3 0.12
ACGTcount: A:0.33, C:0.26, G:0.00, T:0.41
Consensus pattern (10 bp):
AAATTCTCTC
Found at i:35506 original size:20 final size:19
Alignment explanation
Indices: 35477--35517 Score: 64
Period size: 20 Copynumber: 2.1 Consensus size: 19
35467 TTTATCACAT
*
35477 TAAATTCTCTCAAATTCTC
1 TAAATTCTCTCAAATACTC
35496 TAAATTTCTCTCAAATACTC
1 TAAA-TTCTCTCAAATACTC
35516 TA
1 TA
35518 TCTTTTTAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 4 0.20
20 16 0.80
ACGTcount: A:0.34, C:0.24, G:0.00, T:0.41
Consensus pattern (19 bp):
TAAATTCTCTCAAATACTC
Found at i:35837 original size:111 final size:111
Alignment explanation
Indices: 35643--35851 Score: 382
Period size: 111 Copynumber: 1.9 Consensus size: 111
35633 TGGAAATCAT
* *
35643 ATATCTCTACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
1 ATATCTCGACACTTTGATGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
*
35708 TATTTAGTTGATTTATTTAATACATGATTATTATATTAAAAATTAA
66 TAATTAGTTGATTTATTTAATACATGATTATTATATTAAAAATTAA
35754 ATATCTCGACACTTTGATGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
1 ATATCTCGACACTTTGATGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
*
35819 TAATTAGTTGATTTATTTAATGCATGATTATTA
66 TAATTAGTTGATTTATTTAATACATGATTATTA
35852 GAGTAAGAAT
Statistics
Matches: 94, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
111 94 1.00
ACGTcount: A:0.36, C:0.08, G:0.10, T:0.46
Consensus pattern (111 bp):
ATATCTCGACACTTTGATGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
TAATTAGTTGATTTATTTAATACATGATTATTATATTAAAAATTAA
Found at i:37397 original size:18 final size:18
Alignment explanation
Indices: 37371--37405 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
37361 CAGCAGCCAC
*
37371 CGCATCCATATATGATGT
1 CGCAGCCATATATGATGT
37389 CGCAGCCATATATGATG
1 CGCAGCCATATATGATG
37406 CCGCCATCGC
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:0.29, C:0.23, G:0.20, T:0.29
Consensus pattern (18 bp):
CGCAGCCATATATGATGT
Found at i:37756 original size:3 final size:3
Alignment explanation
Indices: 37748--37791 Score: 52
Period size: 3 Copynumber: 14.7 Consensus size: 3
37738 ACATGCTCAG
* * **
37748 GAC GAC GAC GAC GAC GAC GAT GAC GAT GGT GAC GAC GAC GAC GA
1 GAC GAC GAC GAC GAC GAC GAC GAC GAC GAC GAC GAC GAC GAC GA
37792 TGATGACAGC
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.32, C:0.25, G:0.36, T:0.07
Consensus pattern (3 bp):
GAC
Found at i:37781 original size:18 final size:18
Alignment explanation
Indices: 37748--37798 Score: 66
Period size: 18 Copynumber: 2.8 Consensus size: 18
37738 ACATGCTCAG
* *
37748 GACGACGACGACGACGAC
1 GACGACGATGATGACGAC
* *
37766 GATGACGATGGTGACGAC
1 GACGACGATGATGACGAC
37784 GACGACGATGATGAC
1 GACGACGATGATGAC
37799 AGCGAGGAGT
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.31, C:0.24, G:0.35, T:0.10
Consensus pattern (18 bp):
GACGACGATGATGACGAC
Found at i:37796 original size:21 final size:21
Alignment explanation
Indices: 37757--37796 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
37747 GGACGACGAC
*
37757 GACGACGACGATGACGATGGT
1 GACGACGACGACGACGATGGT
*
37778 GACGACGACGACGATGATG
1 GACGACGACGACGACGATG
37797 ACAGCGAGGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.30, C:0.20, G:0.38, T:0.12
Consensus pattern (21 bp):
GACGACGACGACGACGATGGT
Found at i:45351 original size:2 final size:2
Alignment explanation
Indices: 45344--45377 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
45334 AATCAAAATA
45344 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
45378 GTTAAATTAC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:50094 original size:33 final size:33
Alignment explanation
Indices: 50052--50182 Score: 199
Period size: 33 Copynumber: 4.0 Consensus size: 33
50042 ATATTTTTTA
* * *
50052 TTAAGAAGATAAACTTTGCCTTAAATTGTAGGT
1 TTAAGAAGATAAACTTAGCTTTAAATTGTAGGC
*
50085 TTAAGAAGATAAGCTTAGCTTTAAATTGTAGGC
1 TTAAGAAGATAAACTTAGCTTTAAATTGTAGGC
* *
50118 TTAAGAAGATAAGCTTAGCTTTAATTTGTAGGC
1 TTAAGAAGATAAACTTAGCTTTAAATTGTAGGC
*
50151 TTAAGAATATAAACTTAGCTTTAAATTGTAGG
1 TTAAGAAGATAAACTTAGCTTTAAATTGTAGG
50183 ATTTAGGGGA
Statistics
Matches: 90, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 90 1.00
ACGTcount: A:0.37, C:0.08, G:0.19, T:0.36
Consensus pattern (33 bp):
TTAAGAAGATAAACTTAGCTTTAAATTGTAGGC
Found at i:73770 original size:45 final size:45
Alignment explanation
Indices: 73678--73770 Score: 116
Period size: 45 Copynumber: 2.1 Consensus size: 45
73668 GGTGGCATTC
* * *
73678 CCACAATTGCCCCACTACCCTCTTGCAAGGCATTATACGAAGTCT
1 CCACAATTGCCCCACTACCCTCCTACAAGGCATTATACGAAGCCT
* * *
73723 CCACAATTGCCTCACTACCCTCCTACAAGTCTTTA-ACTGAAGCCT
1 CCACAATTGCCCCACTACCCTCCTACAAGGCATTATAC-GAAGCCT
73768 CCA
1 CCA
73771 TAGAAGTACC
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
44 2 0.05
45 39 0.95
ACGTcount: A:0.27, C:0.38, G:0.11, T:0.25
Consensus pattern (45 bp):
CCACAATTGCCCCACTACCCTCCTACAAGGCATTATACGAAGCCT
Found at i:74620 original size:64 final size:63
Alignment explanation
Indices: 74552--74781 Score: 212
Period size: 64 Copynumber: 3.6 Consensus size: 63
74542 TTGGAACACT
* ***
74552 TGATGCATCGGTGCACCAAGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAAATAGCC
1 TGATGCATCGATGCATGGAGTGTGCATCGATGCATGAAATGCATTCGATGTTTG-AAAATAGCC
** * **
74616 TGATGCATCGATGCATGGCTTGTGCATCGATGCATCAAATGCATTCGATGTTTTGAAAATATTC
1 TGATGCATCGATGCATGGAGTGTGCATCGATGCATGAAATGCATTCGATG-TTTGAAAATAGCC
* * * * * * *
74680 AGAGTGCATCGATGCATGGAGAGTGCATCGGTGCATGGAATACATTCGATG-TTCAATTAAT-TC
1 TGA-TGCATCGATGCATGGAGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAA--AATAGC
*
74743 A
63 C
* *
74744 TCGATGCATCGATGCATGGACTGATGCATCGGTGCATG
1 T-GATGCATCGATGCATGGAGTG-TGCATCGATGCATG
74782 CCTTTGAATA
Statistics
Matches: 137, Mismatches: 23, Indels: 11
0.80 0.13 0.06
Matches are distributed among these distances:
63 4 0.03
64 70 0.51
65 63 0.46
ACGTcount: A:0.27, C:0.18, G:0.26, T:0.29
Consensus pattern (63 bp):
TGATGCATCGATGCATGGAGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAATAGCC
Found at i:74704 original size:19 final size:19
Alignment explanation
Indices: 74680--74718 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
74670 GAAAATATTC
74680 AGAGTGCATCGATGCATGG
1 AGAGTGCATCGATGCATGG
*
74699 AGAGTGCATCGGTGCATGG
1 AGAGTGCATCGATGCATGG
74718 A
1 A
74719 ATACATTCGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.26, C:0.15, G:0.38, T:0.21
Consensus pattern (19 bp):
AGAGTGCATCGATGCATGG
Found at i:74706 original size:65 final size:65
Alignment explanation
Indices: 74573--74732 Score: 207
Period size: 65 Copynumber: 2.5 Consensus size: 65
74563 TGCACCAAGT
* ***
74573 GTGCATCGATGCATGAAATGCATTCGATG-TTTGAAAAATAGCCTGATGCATCGATGCATGGCTT
1 GTGCATCGATGCATGAAATGCATTCGATGTTTTGAAAAATAGCCAGATGCATCGATGCATGGAGA
* **
74637 GTGCATCGATGCATCAAATGCATTCGATGTTTTG-AAAATATTCAGAGTGCATCGATGCATGGAG
1 GTGCATCGATGCATGAAATGCATTCGATGTTTTGAAAAATAGCCAGA-TGCATCGATGCATGGAG
74701 A
65 A
* * *
74702 GTGCATCGGTGCATGGAATACATTCGATGTT
1 GTGCATCGATGCATGAAATGCATTCGATGTT
74733 CAATTAATTC
Statistics
Matches: 83, Mismatches: 11, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
64 37 0.45
65 46 0.55
ACGTcount: A:0.28, C:0.16, G:0.26, T:0.30
Consensus pattern (65 bp):
GTGCATCGATGCATGAAATGCATTCGATGTTTTGAAAAATAGCCAGATGCATCGATGCATGGAGA
Found at i:74772 original size:65 final size:64
Alignment explanation
Indices: 74574--74781 Score: 194
Period size: 65 Copynumber: 3.2 Consensus size: 64
74564 GCACCAAGTG
* * * ** *
74574 TGCATCGATGCATGAAATGCATTCGATGTTTGAAAAATAGCCTGATGCATCGATGCATGG-CTTG
1 TGCATCGGTGCATGAAATACATTCGATGTTT-CAAAATATTCAGATGCATCGATGCATGGAC-TG
74638 -
64 A
* * * *
74638 TGCATCGATGCATCAAATGCATTCGATGTTTTGAAAATATTCAGAGTGCATCGATGCATGGA--G
1 TGCATCGGTGCATGAAATACATTCGATG-TTTCAAAATATTCAGA-TGCATCGATGCATGGACTG
74701 A
64 A
* *
74702 GTGCATCGGTGCATGGAATACATTCGATG-TTC-AATTAATTCATCGATGCATCGATGCATGGAC
1 -TGCATCGGTGCATGAAATACATTCGATGTTTCAAAAT-ATTCA--GATGCATCGATGCATGGAC
74765 TGA
62 TGA
74768 TGCATCGGTGCATG
1 TGCATCGGTGCATG
74782 CCTTTGAATA
Statistics
Matches: 123, Mismatches: 11, Indels: 19
0.80 0.07 0.12
Matches are distributed among these distances:
62 3 0.02
63 8 0.07
64 52 0.42
65 58 0.47
66 2 0.02
ACGTcount: A:0.28, C:0.17, G:0.25, T:0.30
Consensus pattern (64 bp):
TGCATCGGTGCATGAAATACATTCGATGTTTCAAAATATTCAGATGCATCGATGCATGGACTGA
Found at i:80858 original size:22 final size:21
Alignment explanation
Indices: 80816--80855 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
80806 GAGTTTGTTT
*
80816 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
80837 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
80856 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:82848 original size:64 final size:63
Alignment explanation
Indices: 82780--83009 Score: 212
Period size: 64 Copynumber: 3.6 Consensus size: 63
82770 TTGGAACACT
* ***
82780 TGATGCATCGGTGCACCAAGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAAATAGCC
1 TGATGCATCGATGCATGGAGTGTGCATCGATGCATGAAATGCATTCGATGTTTG-AAAATAGCC
** * **
82844 TGATGCATCGATGCATGGCTTGTGCATCGATGCATCAAATGCATTCGATGTTTTGAAAATATTC
1 TGATGCATCGATGCATGGAGTGTGCATCGATGCATGAAATGCATTCGATG-TTTGAAAATAGCC
* * * * * * *
82908 AGAGTGCATCGATGCATGGAGAGTGTATCGGTGCATGGAATGCATTCGATG-TTCAATTAAT-TC
1 TGA-TGCATCGATGCATGGAGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAA--AATAGC
*
82971 A
63 C
* *
82972 TCGATGCATCGATGCATGGACTGATGCATCGGTGCATG
1 T-GATGCATCGATGCATGGAGTG-TGCATCGATGCATG
83010 CCTTTGAATA
Statistics
Matches: 136, Mismatches: 24, Indels: 11
0.80 0.14 0.06
Matches are distributed among these distances:
63 4 0.03
64 70 0.51
65 62 0.46
ACGTcount: A:0.27, C:0.17, G:0.26, T:0.30
Consensus pattern (63 bp):
TGATGCATCGATGCATGGAGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAATAGCC
Found at i:82932 original size:19 final size:19
Alignment explanation
Indices: 82908--82958 Score: 61
Period size: 19 Copynumber: 2.7 Consensus size: 19
82898 GAAAATATTC
82908 AGAGTGCATCGATGCATGG
1 AGAGTGCATCGATGCATGG
* *
82927 AGAGTGTATCGGTGCATGG
1 AGAGTGCATCGATGCATGG
82946 A-A-TGCATTCGATG
1 AGAGTGCA-TCGATG
82959 TTCAATTAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
17 3 0.11
18 6 0.22
19 18 0.67
ACGTcount: A:0.25, C:0.14, G:0.35, T:0.25
Consensus pattern (19 bp):
AGAGTGCATCGATGCATGG
Found at i:83003 original size:65 final size:64
Alignment explanation
Indices: 82802--83009 Score: 221
Period size: 65 Copynumber: 3.2 Consensus size: 64
82792 GCACCAAGTG
* *
82802 TGCATCGATGCATGAAATGCATTCGATGTTTGAAAAATAGCCTGATGCATCGATGCATGG-CTTG
1 TGCATCGATGCATGAAATGCATTCGATGTTTGAAAAAT-TCATGATGCATCGATGCATGGAC-TG
82866 -
64 A
*
82866 TGCATCGATGCATCAAATGCATTCGATGTTTTGAAAATATTCA-GAGTGCATCGATGCATGGA--
1 TGCATCGATGCATGAAATGCATTCGATG-TTTGAAAA-ATTCATGA-TGCATCGATGCATGGACT
82928 GA
63 GA
* * * * *
82930 GTGTATCGGTGCATGGAATGCATTCGATG-TTCAATTAATTCATCGATGCATCGATGCATGGACT
1 -TGCATCGATGCATGAAATGCATTCGATGTTTGAA-AAATTCAT-GATGCATCGATGCATGGACT
82994 GA
63 GA
*
82996 TGCATCGGTGCATG
1 TGCATCGATGCATG
83010 CCTTTGAATA
Statistics
Matches: 123, Mismatches: 10, Indels: 21
0.80 0.06 0.14
Matches are distributed among these distances:
63 10 0.08
64 46 0.37
65 63 0.51
66 4 0.03
ACGTcount: A:0.27, C:0.17, G:0.25, T:0.30
Consensus pattern (64 bp):
TGCATCGATGCATGAAATGCATTCGATGTTTGAAAAATTCATGATGCATCGATGCATGGACTGA
Found at i:93435 original size:55 final size:55
Alignment explanation
Indices: 92665--93444 Score: 918
Period size: 55 Copynumber: 14.3 Consensus size: 55
92655 ATACTTGAAA
* * * *
92665 AATCTTCA-AATAACGGGTCTGCTCCCTTTTCTTTCA-AGGAGTATA-AGACTCGAAC
1 AATCTTCATAA-AACGGGTCCGCTCTCTATTCCTTCAGA-GAGTATAGA-ACTCGAAC
*** * * * * * *
92720 AATCATT-GGCAAACGTGTCTGCTCCCTATTCATTCAGGGAGTATA-AGACTCAAAC
1 AATC-TTCATAAAACGGGTCCGCTCTCTATTCCTTCAGAGAGTATAGA-ACTCGAAC
** ** * * * *
92775 AATCTTCA-ACAAACATGTTTGCTCCCTATTCGTTCAGGGAGTATA-AGACTCGAAT
1 AATCTTCATA-AAACGGGTCCGCTCTCTATTCCTTCAGAGAGTATAGA-ACTCGAAC
* * * * *
92830 AATCTTCA-ACAAACGTGTCTGCTCCCTATTCGTTCAGGGAGTATA-AGACTCG---
1 AATCTTCATA-AAACGGGTCCGCTCTCTATTCCTTCAGAGAGTATAGA-ACTCGAAC
* ** * * *
92882 -ATCTTCA-ACAAACGTGTCTACTCCCTATTCGTTCAGGGAGTATA-AGACTCG---
1 AATCTTCATA-AAACGGGTCCGCTCTCTATTCCTTCAGAGAGTATAGA-ACTCGAAC
* * * *
92933 -ATCTTCA-ATAAA-GGTGTTCGCTCCCTATTCCTTCAGAGAGTATAGGACTCAAAC
1 AATCTTCATA-AAACGG-GTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAAC
* * * *
92987 AATCTTCAAAAAACAGGTCCGCTCTCTATTCTTTCAGAGAGTATAGAACTCAAAC
1 AATCTTCATAAAACGGGTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAAC
93042 AATCTTCATAAAACGGGTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAAC
1 AATCTTCATAAAACGGGTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAAC
93097 AATCTTCATAAAACGGGTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAAC
1 AATCTTCATAAAACGGGTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAAC
93152 AATCTTCATAAAACGGGTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAAC
1 AATCTTCATAAAACGGGTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAAC
93207 AATCTTCATAAAACGGGTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAAC
1 AATCTTCATAAAACGGGTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAAC
*
93262 AATCTTCATAAAACGGGTCCGCTCTCTATTCCTTCGGAGAGTATAGAACTCGAAC
1 AATCTTCATAAAACGGGTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAAC
*
93317 AATCTTCATAAAACGGGTCCGCTCTCTATTCCTACAGAGAGTATAGAACTCGAAC
1 AATCTTCATAAAACGGGTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAAC
93372 AATCTTCATAAAACGGGTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAAC
1 AATCTTCATAAAACGGGTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAAC
93427 AATCTTCATAAAACGGGT
1 AATCTTCATAAAACGGGT
93445 TTGCTTCACT
Statistics
Matches: 673, Mismatches: 39, Indels: 26
0.91 0.05 0.04
Matches are distributed among these distances:
50 1 0.00
51 89 0.13
54 2 0.00
55 576 0.86
56 5 0.01
ACGTcount: A:0.31, C:0.24, G:0.17, T:0.28
Consensus pattern (55 bp):
AATCTTCATAAAACGGGTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAAC
Found at i:93498 original size:37 final size:37
Alignment explanation
Indices: 93444--93526 Score: 132
Period size: 37 Copynumber: 2.2 Consensus size: 37
93434 ATAAAACGGG
*
93444 TTTGCTTCACTATTCTTCCGTGAAGGCTTATAGA-TGA
1 TTTGCTTCACTACTCTTCCGTGAAGGCTTA-AGATTGA
93481 TTTGCTTCACTACTCTTCCGTGAAGGCTTAAGATTGA
1 TTTGCTTCACTACTCTTCCGTGAAGGCTTAAGATTGA
*
93518 TTTGTTTCA
1 TTTGCTTCA
93527 AAGATCCAAC
Statistics
Matches: 43, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
36 3 0.07
37 40 0.93
ACGTcount: A:0.20, C:0.19, G:0.18, T:0.42
Consensus pattern (37 bp):
TTTGCTTCACTACTCTTCCGTGAAGGCTTAAGATTGA
Found at i:94828 original size:16 final size:16
Alignment explanation
Indices: 94800--94927 Score: 82
Period size: 16 Copynumber: 7.6 Consensus size: 16
94790 CCTCCTTTTA
94800 TTTCTCTTTTTTTCATT
1 TTTCTC-TTTTTTCATT
94817 TTTCTCTTTTTTCATT
1 TTTCTCTTTTTTCATT
* **
94833 TTTCATTTTTTCTTCCCT
1 TTTC-TCTTTT-TTCATT
94851 TTTC-CATTTTTTC-TT
1 TTTCTC-TTTTTTCATT
* *
94866 CTTT-TTTTCTTTTCGTT
1 -TTTCTCTT-TTTTCATT
* *
94883 TTTCCATCATTTTTCTTT
1 TTT-C-TCTTTTTTCATT
*
94901 TTTCTCATTTTTCATTT
1 TTTCTCTTTTTTCA-TT
94918 TTTCTCTTTT
1 TTTCTCTTTT
94928 ATTTCTTCTT
Statistics
Matches: 89, Mismatches: 11, Indels: 22
0.73 0.09 0.18
Matches are distributed among these distances:
15 3 0.03
16 37 0.42
17 29 0.33
18 18 0.20
19 2 0.02
ACGTcount: A:0.06, C:0.20, G:0.01, T:0.73
Consensus pattern (16 bp):
TTTCTCTTTTTTCATT
Found at i:94872 original size:19 final size:18
Alignment explanation
Indices: 94806--94871 Score: 59
Period size: 19 Copynumber: 3.8 Consensus size: 18
94796 TTTATTTCTC
*
94806 TTTTT-TTCATTTTTC-T
1 TTTTTCTTCCTTTTTCAT
* *
94822 CTTTT-TTCATTTTTCAT
1 TTTTTCTTCCTTTTTCAT
*
94839 TTTTTCTTCCCTTTTCCAT
1 TTTTTCTT-CCTTTTTCAT
94858 TTTTTCTT-CTTTTT
1 TTTTTCTTCCTTTTT
94872 TTCTTTTCGT
Statistics
Matches: 42, Mismatches: 5, Indels: 5
0.81 0.10 0.10
Matches are distributed among these distances:
16 14 0.33
17 10 0.24
18 2 0.05
19 16 0.38
ACGTcount: A:0.06, C:0.20, G:0.00, T:0.74
Consensus pattern (18 bp):
TTTTTCTTCCTTTTTCAT
Found at i:99959 original size:9 final size:9
Alignment explanation
Indices: 99945--99970 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
99935 TCAAACAATT
99945 TTTTTTTTC
1 TTTTTTTTC
99954 TTTTTTTTC
1 TTTTTTTTC
99963 TTTTTTTT
1 TTTTTTTT
99971 TTTCGTATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (9 bp):
TTTTTTTTC
Found at i:100828 original size:31 final size:31
Alignment explanation
Indices: 100790--100914 Score: 189
Period size: 31 Copynumber: 4.0 Consensus size: 31
100780 CCCGAAGGAC
* * *
100790 CAGTCCATA-GATTCCGAAGAACCTAGGTAAT
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
*
100821 CAGTCCATATGTCCCGAAGGACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
*
100852 CAGTCCATATGTTCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
100883 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
100914 C
1 C
100915 CCTCGACCCT
Statistics
Matches: 86, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
31 85 0.99
32 1 0.01
ACGTcount: A:0.37, C:0.22, G:0.20, T:0.21
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:101696 original size:21 final size:20
Alignment explanation
Indices: 101652--101692 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
101642 AATTCTGTCG
* *
101652 CTTGAAGGGGTATCGGTTCC
1 CTTGAAGGGGTACCGATTCC
*
101672 CTTGAATGGGTACCGATTCC
1 CTTGAAGGGGTACCGATTCC
101692 C
1 C
101693 CTTGCCCAGA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.17, C:0.24, G:0.29, T:0.29
Consensus pattern (20 bp):
CTTGAAGGGGTACCGATTCC
Found at i:104035 original size:9 final size:9
Alignment explanation
Indices: 104021--104046 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
104011 TCAAACAATT
104021 TTTTTTTTC
1 TTTTTTTTC
104030 TTTTTTTTC
1 TTTTTTTTC
104039 TTTTTTTT
1 TTTTTTTT
104047 TCGTATAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (9 bp):
TTTTTTTTC
Found at i:104035 original size:10 final size:10
Alignment explanation
Indices: 104020--104048 Score: 51
Period size: 9 Copynumber: 3.0 Consensus size: 10
104010 TTCAAACAAT
104020 TTTTTTTTTC
1 TTTTTTTTTC
104030 -TTTTTTTTC
1 TTTTTTTTTC
104039 TTTTTTTTTC
1 TTTTTTTTTC
104049 GTATAAAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
9 9 0.50
10 9 0.50
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (10 bp):
TTTTTTTTTC
Found at i:104905 original size:31 final size:31
Alignment explanation
Indices: 104867--104991 Score: 189
Period size: 31 Copynumber: 4.0 Consensus size: 31
104857 CCCGAAGGAC
* * *
104867 CAGTCCATA-GATTCCGAAGAACCTAGGTAAT
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
*
104898 CAGTCCATATGTCCCGAAGGACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
*
104929 CAGTCCATATGTTCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
104960 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
104991 C
1 C
104992 CCTCGACCCT
Statistics
Matches: 86, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
31 85 0.99
32 1 0.01
ACGTcount: A:0.37, C:0.22, G:0.20, T:0.21
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:105752 original size:21 final size:21
Alignment explanation
Indices: 105726--105771 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
105716 AATTCTGTCG
* *
105726 CTTGAAGGGGTATCGGTTCCC
1 CTTGAAGGGGTACCGATTCCC
*
105747 CTTGAATGGGTACCGATTCCC
1 CTTGAAGGGGTACCGATTCCC
105768 CTTG
1 CTTG
105772 CCCAGAACTC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.15, C:0.26, G:0.28, T:0.30
Consensus pattern (21 bp):
CTTGAAGGGGTACCGATTCCC
Found at i:111254 original size:45 final size:47
Alignment explanation
Indices: 111186--111274 Score: 155
Period size: 45 Copynumber: 1.9 Consensus size: 47
111176 TGCTTTGTTA
111186 TTCACAAAAATAAATCCTAACCGCATGATATCTAATTCGCATGCTTG
1 TTCACAAAAATAAATCCTAACCGCATGATATCTAATTCGCATGCTTG
*
111233 TTCA-AAAAATAAA-CCTAACCGCATGATATCTAGTTCGCATGC
1 TTCACAAAAATAAATCCTAACCGCATGATATCTAATTCGCATGC
111275 ATTTATTCGA
Statistics
Matches: 41, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
45 28 0.68
46 9 0.22
47 4 0.10
ACGTcount: A:0.37, C:0.24, G:0.11, T:0.28
Consensus pattern (47 bp):
TTCACAAAAATAAATCCTAACCGCATGATATCTAATTCGCATGCTTG
Found at i:114763 original size:33 final size:33
Alignment explanation
Indices: 114721--114787 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
114711 TGTTCTGGAT
114721 ATAGTAATGTTACTAACGGAAATCATTCTCTCA
1 ATAGTAATGTTACTAACGGAAATCATTCTCTCA
114754 ATAGTAATGTTACTAACGGAAATCATTCTCTCA
1 ATAGTAATGTTACTAACGGAAATCATTCTCTCA
114787 A
1 A
114788 GCCTCCAACA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.37, C:0.18, G:0.12, T:0.33
Consensus pattern (33 bp):
ATAGTAATGTTACTAACGGAAATCATTCTCTCA
Found at i:119205 original size:29 final size:29
Alignment explanation
Indices: 119172--119343 Score: 246
Period size: 29 Copynumber: 6.0 Consensus size: 29
119162 ATCTGATCTA
119172 GTGATATTTTGAG-AATTATTTTTAAAACG
1 GTGATATTTTG-GTAATTATTTTTAAAACG
119201 GTGATATTTTGAG-AATTA-TTTTAAAACG
1 GTGATATTTTG-GTAATTATTTTTAAAACG
*
119229 GTGATATTTTGGTAATTATTTTTAAAATG
1 GTGATATTTTGGTAATTATTTTTAAAACG
119258 GTGATATTTTGGTAATTATTTTTAAAACG
1 GTGATATTTTGGTAATTATTTTTAAAACG
*
119287 ATGATATTTTGGTAATTATTTTTAAAGA-G
1 GTGATATTTTGGTAATTATTTTTAAA-ACG
*
119316 GTGATATTGTT-GTAAATATTTTTAAAAC
1 GTGATATT-TTGGTAATTATTTTTAAAAC
119344 AATGCTATTT
Statistics
Matches: 133, Mismatches: 5, Indels: 10
0.90 0.03 0.07
Matches are distributed among these distances:
27 1 0.01
28 27 0.20
29 102 0.77
30 3 0.02
ACGTcount: A:0.34, C:0.02, G:0.17, T:0.47
Consensus pattern (29 bp):
GTGATATTTTGGTAATTATTTTTAAAACG
Done.