Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000598.1 Hibiscus syriacus cultivar Beakdansim tig00001157_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: 67793
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:5830 original size:20 final size:21
Alignment explanation
Indices: 5805--5855 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 21
5795 ACTAGTGTGG
*
5805 AAATTACTCAAT-GGTAAAAT
1 AAATTACTCAATCAGTAAAAT
*
5825 AAATTATTCAATCAGTAAAAT
1 AAATTACTCAATCAGTAAAAT
* *
5846 GAATTTCTCA
1 AAATTACTCA
5856 TGCAATTCAT
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 11 0.44
21 14 0.56
ACGTcount: A:0.47, C:0.12, G:0.08, T:0.33
Consensus pattern (21 bp):
AAATTACTCAATCAGTAAAAT
Found at i:16223 original size:19 final size:19
Alignment explanation
Indices: 16199--16235 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
16189 TTATTTTGAA
16199 TTTTTCACTATCACAACAT
1 TTTTTCACTATCACAACAT
*
16218 TTTTTCACTATCGCAACA
1 TTTTTCACTATCACAACA
16236 ACACGTTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.30, C:0.27, G:0.03, T:0.41
Consensus pattern (19 bp):
TTTTTCACTATCACAACAT
Found at i:16275 original size:19 final size:19
Alignment explanation
Indices: 16248--16285 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
16238 ACGTTTTTCA
*
16248 AACTCTCGCAATACATTTT
1 AACTATCGCAATACATTTT
16267 AACTATCGCAATACATTTT
1 AACTATCGCAATACATTTT
16286 TCAAAATCGC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.34, C:0.24, G:0.05, T:0.37
Consensus pattern (19 bp):
AACTATCGCAATACATTTT
Found at i:16475 original size:18 final size:19
Alignment explanation
Indices: 16452--16494 Score: 61
Period size: 18 Copynumber: 2.3 Consensus size: 19
16442 ATTTTCTCTT
*
16452 ATAATTATTATA-TTTGTA
1 ATAATTATTATATTTTATA
*
16470 ATAATTTTTATATTTTATA
1 ATAATTATTATATTTTATA
16489 ATAATT
1 ATAATT
16495 TATACACATG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 11 0.50
19 11 0.50
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (19 bp):
ATAATTATTATATTTTATA
Found at i:16492 original size:19 final size:18
Alignment explanation
Indices: 16452--16495 Score: 61
Period size: 19 Copynumber: 2.4 Consensus size: 18
16442 ATTTTCTCTT
* *
16452 ATAATTATTATATTTGTA
1 ATAATTTTTATATTTATA
16470 ATAATTTTTATATTTTATA
1 ATAATTTTTATA-TTTATA
16489 ATAATTT
1 ATAATTT
16496 ATACACATGA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 11 0.48
19 12 0.52
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (18 bp):
ATAATTTTTATATTTATA
Found at i:18558 original size:23 final size:23
Alignment explanation
Indices: 18510--18573 Score: 69
Period size: 23 Copynumber: 2.7 Consensus size: 23
18500 TTATTATTGC
*
18510 AATTAATATATATAATTATGATTAA
1 AATTAAT-TA-ATAATTATGAATAA
18535 AATTAATTAATAA-TATGCAATAA
1 AATTAATTAATAATTATG-AATAA
*
18558 AATT-ATTAATATTTAT
1 AATTAATTAATAATTAT
18574 ATAATTATAT
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
22 11 0.31
23 15 0.43
24 2 0.06
25 7 0.20
ACGTcount: A:0.52, C:0.02, G:0.03, T:0.44
Consensus pattern (23 bp):
AATTAATTAATAATTATGAATAA
Found at i:20772 original size:2 final size:2
Alignment explanation
Indices: 20765--20833 Score: 131
Period size: 2 Copynumber: 35.0 Consensus size: 2
20755 ATTAATTCAA
20765 AT AT AT AT 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 AT AT AT AT
20807 AT AT A- 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
20834 GAATCAAACT
Statistics
Matches: 66, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.02
2 65 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:29094 original size:3 final size:3
Alignment explanation
Indices: 29086--29111 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
29076 CTTTTTACTT
29086 TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TT
29112 TTCATTTGTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:31979 original size:33 final size:33
Alignment explanation
Indices: 31933--31997 Score: 103
Period size: 33 Copynumber: 2.0 Consensus size: 33
31923 TAAGACTTAC
*
31933 AGAAAGATTATTTTCAACAATGAACAAATGAAT
1 AGAAAGATCATTTTCAACAATGAACAAATGAAT
**
31966 AGAAAGATCATTTTCAAGGATGAACAAATGAA
1 AGAAAGATCATTTTCAACAATGAACAAATGAA
31998 AAACCTTAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.51, C:0.09, G:0.15, T:0.25
Consensus pattern (33 bp):
AGAAAGATCATTTTCAACAATGAACAAATGAAT
Found at i:35901 original size:12 final size:14
Alignment explanation
Indices: 35871--35900 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
35861 AATCATTATA
35871 TTTTAATTTTATTT
1 TTTTAATTTTATTT
35885 TTTTAATTTT-TTT
1 TTTTAATTTTATTT
35898 TTT
1 TTT
35901 ATAAAAAATC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.38
14 10 0.62
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (14 bp):
TTTTAATTTTATTT
Found at i:36736 original size:2 final size:2
Alignment explanation
Indices: 36729--36761 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
36719 CCAAATTCAT
36729 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 T
36762 TAGTTGTTTG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:41431 original size:21 final size:21
Alignment explanation
Indices: 41389--41431 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
41379 TTTCTGGGCT
*
41389 AGGGGAATCGATACCCATTCA
1 AGGGGAATCGATACCCACTCA
*
41410 AGGGGAATCGATACCCCCTCA
1 AGGGGAATCGATACCCACTCA
41431 A
1 A
41432 CGAATATGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.33, C:0.28, G:0.23, T:0.16
Consensus pattern (21 bp):
AGGGGAATCGATACCCACTCA
Found at i:41483 original size:20 final size:20
Alignment explanation
Indices: 41458--41495 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
41448 GAATGCTAGA
*
41458 GGGGAATCGATACCCCCAGG
1 GGGGAACCGATACCCCCAGG
*
41478 GGGGAACCGATTCCCCCA
1 GGGGAACCGATACCCCCA
41496 TATATATATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.24, C:0.34, G:0.32, T:0.11
Consensus pattern (20 bp):
GGGGAACCGATACCCCCAGG
Found at i:42169 original size:23 final size:23
Alignment explanation
Indices: 42124--42169 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
42114 CATTATTATA
*
42124 TGGCACTACGGTGCAATTCTACG
1 TGGCACTACGGTGCAATTATACG
* *
42147 TGGCACTTCGGTGCATTTATACG
1 TGGCACTACGGTGCAATTATACG
42170 AGTTGTGGTG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.20, C:0.24, G:0.26, T:0.30
Consensus pattern (23 bp):
TGGCACTACGGTGCAATTATACG
Found at i:48459 original size:16 final size:16
Alignment explanation
Indices: 48438--48468 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
48428 TATTTATTCT
48438 CTCTCATACATAAACA
1 CTCTCATACATAAACA
48454 CTCTCATACATAAAC
1 CTCTCATACATAAAC
48469 GTATCTTTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.42, C:0.32, G:0.00, T:0.26
Consensus pattern (16 bp):
CTCTCATACATAAACA
Found at i:50420 original size:60 final size:60
Alignment explanation
Indices: 50262--50421 Score: 182
Period size: 60 Copynumber: 2.6 Consensus size: 60
50252 TAAGATATTA
* * * * * *
50262 TTTTGTTGAGTTCTTTAACTATTAAAAGTTATAAAATGATCATCTGATCGTAGGGAGTTGC
1 TTTTGTTGAGTT-TTTGACTATTAAAAGTTACAAAATGGTCATCTGATCATAAGGAATTGC
* * *
50323 TTTTG-TGAGTTTCTTGACTATTAAAGGTTACAAAATGGT-TTCCTGATTATAAGGAATTG-
1 TTTTGTTGAGTTT-TTGACTATTAAAAGTTACAAAATGGTCAT-CTGATCATAAGGAATTGC
50382 TTTTGTTGAGTCTTTTGACTATTAAAAGTTACAAAATGGT
1 TTTTGTTGAGT-TTTTGACTATTAAAAGTTACAAAATGGT
50422 AACCCAATTA
Statistics
Matches: 85, Mismatches: 10, Indels: 9
0.82 0.10 0.09
Matches are distributed among these distances:
59 7 0.08
60 71 0.84
61 7 0.08
ACGTcount: A:0.29, C:0.09, G:0.19, T:0.42
Consensus pattern (60 bp):
TTTTGTTGAGTTTTTGACTATTAAAAGTTACAAAATGGTCATCTGATCATAAGGAATTGC
Found at i:51854 original size:20 final size:20
Alignment explanation
Indices: 51793--51944 Score: 198
Period size: 20 Copynumber: 7.6 Consensus size: 20
51783 GATTTTCCAG
* ** *
51793 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
51813 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
*
51833 AATCGCAACGCTTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
51853 AATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
51873 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
51893 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
51913 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
51933 AATCGCAACGCG
1 AATCGCAACGCG
51945 ATTTTTAAAG
Statistics
Matches: 115, Mismatches: 15, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
19 1 0.01
20 112 0.97
21 2 0.02
ACGTcount: A:0.34, C:0.28, G:0.19, T:0.20
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:52486 original size:21 final size:20
Alignment explanation
Indices: 52460--52533 Score: 94
Period size: 21 Copynumber: 3.5 Consensus size: 20
52450 TGCAGAAGAG
52460 TCGCAACGAGATAAATGAAAA
1 TCGCAACGAGA-AAATGAAAA
* **
52481 TCGCAACGTGAAAATGACTA
1 TCGCAACGAGAAAATGAAAA
52501 TCTGCAACGAGAAAAATGAAAA
1 TC-GCAACGAG-AAAATGAAAA
52523 TCGCAACGAGA
1 TCGCAACGAGA
52534 GAATCGCAAC
Statistics
Matches: 45, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
20 10 0.22
21 25 0.56
22 10 0.22
ACGTcount: A:0.47, C:0.18, G:0.20, T:0.15
Consensus pattern (20 bp):
TCGCAACGAGAAAATGAAAA
Found at i:52620 original size:33 final size:37
Alignment explanation
Indices: 52578--52670 Score: 113
Period size: 41 Copynumber: 2.5 Consensus size: 37
52568 TTTCATTTCG
52578 CGTTGCGATTTTCATTTCACGTT-G-C-G-ATTCTCT
1 CGTTGCGATTTTCATTTCACGTTCGACAGCATTCTCT
*
52611 CGTTGCGATTTTCATTTCTCTCGTTGCGACAGTCATTCTCT
1 CGTTGCGATTTTCA-TT-TCACGTT-CGACAG-CATTCTCT
52652 CGTTGCGATTTTCATTTCA
1 CGTTGCGATTTTCATTTCA
52671 ACCAAAAGAC
Statistics
Matches: 50, Mismatches: 2, Indels: 10
0.81 0.03 0.16
Matches are distributed among these distances:
33 14 0.28
34 2 0.04
35 6 0.12
37 1 0.02
38 1 0.02
39 3 0.06
40 2 0.04
41 21 0.42
ACGTcount: A:0.13, C:0.25, G:0.17, T:0.45
Consensus pattern (37 bp):
CGTTGCGATTTTCATTTCACGTTCGACAGCATTCTCT
Found at i:52631 original size:21 final size:21
Alignment explanation
Indices: 52605--52669 Score: 96
Period size: 21 Copynumber: 3.1 Consensus size: 21
52595 CACGTTGCGA
52605 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
***
52626 TTCTCTCGTTGCGACAGTCA-
1 TTCTCTCGTTGCGATTTTCAT
52646 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
52667 TTC
1 TTC
52670 AACCAAAAGA
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
20 17 0.46
21 20 0.54
ACGTcount: A:0.11, C:0.26, G:0.15, T:0.48
Consensus pattern (21 bp):
TTCTCTCGTTGCGATTTTCAT
Found at i:52666 original size:20 final size:20
Alignment explanation
Indices: 52561--52667 Score: 104
Period size: 19 Copynumber: 5.7 Consensus size: 20
52551 CAAAATCGCA
*
52561 TTGCGATTTTCATT-TCGCG
1 TTGCGATTTTCATTCTCTCG
*
52580 TTGCGATTTTCATT-TCACG
1 TTGCGATTTTCATTCTCTCG
52599 TTGCG------ATTCTCTCG
1 TTGCGATTTTCATTCTCTCG
52613 TTGCGATTTTCATTTCTCTCG
1 TTGCGATTTTCA-TTCTCTCG
***
52634 TTGCGACAGTCATTCTCTCG
1 TTGCGATTTTCATTCTCTCG
52654 TTGCGATTTTCATT
1 TTGCGATTTTCATT
52668 TCAACCAAAA
Statistics
Matches: 72, Mismatches: 8, Indels: 15
0.76 0.08 0.16
Matches are distributed among these distances:
13 3 0.04
14 9 0.12
19 23 0.32
20 20 0.28
21 17 0.24
ACGTcount: A:0.12, C:0.23, G:0.18, T:0.47
Consensus pattern (20 bp):
TTGCGATTTTCATTCTCTCG
Found at i:54616 original size:93 final size:93
Alignment explanation
Indices: 54349--54816 Score: 895
Period size: 93 Copynumber: 5.1 Consensus size: 93
54339 TAGATTGCTT
*
54349 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
54414 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
54442 AGTAAATTTGTTCGG-TGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
54506 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
54534 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
54599 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
*
54627 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTATGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
54692 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
54720 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
*
54785 TTTGTCTTTGTTTTGTCTATTGGTTG-A
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
54812 AGTAA
1 AGTAA
54817 TGCAATCCAT
Statistics
Matches: 370, Mismatches: 4, Indels: 3
0.98 0.01 0.01
Matches are distributed among these distances:
92 98 0.26
93 272 0.74
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:54901 original size:14 final size:14
Alignment explanation
Indices: 54882--54938 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
54872 CGAAACTTAA
54882 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
54896 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
*
54915 AATCGCAACGACAG
1 AATCGCAACGAGAG
54929 AATCGCAACG
1 AATCGCAACG
54939 CGAAACCAAA
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 1 0.03
19 10 0.29
ACGTcount: A:0.44, C:0.25, G:0.23, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:54920 original size:19 final size:18
Alignment explanation
Indices: 54896--54987 Score: 65
Period size: 19 Copynumber: 5.4 Consensus size: 18
54886 GCAACGAGAG
54896 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAA-GAA
*
54915 AATCGCAA--CGACAG--
1 AATCGCAACGCGAAAGAA
*
54929 AATCGCAACGCGAAACCAA
1 AATCGCAACGCGAAA-GAA
*
54948 AATCGCAA--CG--ACAA
1 AATCGCAACGCGAAAGAA
*
54962 AATCGCAACGCGAAACCAA
1 AATCGCAACGCGAAA-GAA
54981 AATCGCA
1 AATCGCA
54988 TTGCGATTTT
Statistics
Matches: 60, Mismatches: 3, Indels: 20
0.72 0.04 0.24
Matches are distributed among these distances:
14 19 0.32
15 1 0.02
16 7 0.12
17 6 0.10
18 1 0.02
19 26 0.43
ACGTcount: A:0.47, C:0.28, G:0.17, T:0.08
Consensus pattern (18 bp):
AATCGCAACGCGAAAGAA
Found at i:54922 original size:33 final size:33
Alignment explanation
Indices: 54864--54987 Score: 185
Period size: 33 Copynumber: 3.7 Consensus size: 33
54854 TAGTTTACTT
* * *
54864 TCGCAACACGAAACTTAAAATCGCAACGAGAGAA
1 TCGCAACGCGAAAC-CAAAATCGCAACGACAGAA
**
54898 TCGCAACGCGAAATGAAAATCGCAACGACAGAA
1 TCGCAACGCGAAACCAAAATCGCAACGACAGAA
*
54931 TCGCAACGCGAAACCAAAATCGCAACGACAAAA
1 TCGCAACGCGAAACCAAAATCGCAACGACAGAA
54964 TCGCAACGCGAAACCAAAATCGCA
1 TCGCAACGCGAAACCAAAATCGCA
54988 TTGCGATTTT
Statistics
Matches: 83, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
33 71 0.86
34 12 0.14
ACGTcount: A:0.46, C:0.27, G:0.18, T:0.09
Consensus pattern (33 bp):
TCGCAACGCGAAACCAAAATCGCAACGACAGAA
Found at i:54964 original size:14 final size:14
Alignment explanation
Indices: 54913--54971 Score: 64
Period size: 14 Copynumber: 3.9 Consensus size: 14
54903 ACGCGAAATG
54913 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
54927 AGAATCGCAACGCGAAACC
1 AAAATCGCAA--CG--A-C
54946 AAAATCGCAACGAC
1 AAAATCGCAACGAC
54960 AAAATCGCAACG
1 AAAATCGCAACG
54972 CGAAACCAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
14 22 0.58
15 1 0.03
16 2 0.05
17 2 0.05
18 1 0.03
19 10 0.26
ACGTcount: A:0.47, C:0.29, G:0.17, T:0.07
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:55030 original size:33 final size:33
Alignment explanation
Indices: 54988--55101 Score: 147
Period size: 33 Copynumber: 3.3 Consensus size: 33
54978 CAAAATCGCA
*
54988 TTGCGATTTTCCTTTCGCGTTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
*
55021 TTGCGATTTTCATTTCGCGTTGCGATTTTGGTTTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCT-G----TCG
* *
55059 TTGCGATTCTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
55092 TTGCGATTTT
1 TTGCGATTTT
55102 AGAGACGAGA
Statistics
Matches: 70, Mismatches: 6, Indels: 10
0.81 0.07 0.12
Matches are distributed among these distances:
33 39 0.56
34 1 0.01
38 30 0.43
ACGTcount: A:0.08, C:0.22, G:0.23, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
Found at i:55088 original size:19 final size:19
Alignment explanation
Indices: 54983--55085 Score: 108
Period size: 19 Copynumber: 5.7 Consensus size: 19
54973 GAAACCAAAA
* *
54983 TCGCATTGCGATTTTCCTT
1 TCGCGTTGCGATTTTCATT
*
55002 TCGCGTTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
55018 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
55035 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
* *
55054 TCTCGTTGCGATTCTCATT
1 TCGCGTTGCGATTTTCATT
55073 TCGCGTTGCGATT
1 TCGCGTTGCGATT
55086 CTCTCGTTGC
Statistics
Matches: 69, Mismatches: 10, Indels: 10
0.78 0.11 0.11
Matches are distributed among these distances:
14 8 0.12
16 5 0.07
17 5 0.07
19 51 0.74
ACGTcount: A:0.09, C:0.22, G:0.23, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:55629 original size:14 final size:14
Alignment explanation
Indices: 55610--55645 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
55600 ATTGTTTAAT
55610 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
55624 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
55638 TGATTTGT
1 TGATTTGT
55646 GTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:55760 original size:19 final size:19
Alignment explanation
Indices: 55736--55823 Score: 114
Period size: 19 Copynumber: 4.8 Consensus size: 19
55726 GCATTATGTT
55736 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAATGC
55755 GAAATGAAAATCGCAA--C
1 GAAATGAAAATCGCAATGC
*
55772 G--A-GAGAATCGCAATGC
1 GAAATGAAAATCGCAATGC
*
55788 GAAATAAAAATCGCAATGC
1 GAAATGAAAATCGCAATGC
55807 GGAAATGAAAATCGCAA
1 -GAAATGAAAATCGCAA
55824 CGAGAGAATC
Statistics
Matches: 59, Mismatches: 4, Indels: 11
0.80 0.05 0.15
Matches are distributed among these distances:
14 10 0.17
15 1 0.02
16 2 0.03
17 2 0.03
18 1 0.02
19 28 0.47
20 15 0.25
ACGTcount: A:0.49, C:0.16, G:0.22, T:0.14
Consensus pattern (19 bp):
GAAATGAAAATCGCAATGC
Found at i:55855 original size:53 final size:53
Alignment explanation
Indices: 55736--55842 Score: 198
Period size: 53 Copynumber: 2.0 Consensus size: 53
55726 GCATTATGTT
*
55736 GAAATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGAATCGCAATGC
1 GAAATAAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGC
55788 GAAATAAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGC
1 GAAATAAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGC
55841 GA
1 GA
55843 TTTTCATTTC
Statistics
Matches: 53, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
52 18 0.34
53 35 0.66
ACGTcount: A:0.47, C:0.17, G:0.23, T:0.13
Consensus pattern (53 bp):
GAAATAAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGC
Found at i:55919 original size:72 final size:68
Alignment explanation
Indices: 55833--56125 Score: 249
Period size: 72 Copynumber: 4.2 Consensus size: 68
55823 ACGAGAGAAT
*
55833 CGCAATGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATT
1 CGCATTGCGA-TTTC-TTTCG--TTGCGATTTTCATTT-CGCATTGCGATTCTCTCGTTGCGATT
55898 TTCATTT-
61 TTCATTTC
* * * * *
55905 CGCATTGCGATTTTCATTTCGCATTGCGATTCTATCGTTGCG-ATTTTC-ATT-TCGCATTGCGA
1 CGCATTGCGA-TTTC-TTTCG--TTGCGATT-T-TCATTTCGCA-TTGCGATTCTCTCGTTGCGA
55967 TTTTCATTTC
59 TTTTCATTTC
* *
55977 CGCATTGCGA-TTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATT
1 CGCATTGCGATTTCTTTCGTTGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG--TTGCGATT
56041 TTCATTTC
61 TTCATTTC
* * * * *
56049 CGCATTGCGATTTC-TT-GTTGGGATTTTCATTTTGTATTGCGATTCTCTCGTTGCGATTGTAAT
1 CGCATTGCGATTTCTTTCGTTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCAT
56112 TTC
66 TTC
**
56115 CGTGTTGCGAT
1 CGCATTGCGAT
56126 AGTCAAATGC
Statistics
Matches: 186, Mismatches: 22, Indels: 32
0.77 0.09 0.13
Matches are distributed among these distances:
65 9 0.05
66 26 0.14
67 8 0.04
68 6 0.03
69 7 0.04
70 5 0.03
71 41 0.22
72 71 0.38
73 9 0.05
74 4 0.02
ACGTcount: A:0.14, C:0.22, G:0.18, T:0.46
Consensus pattern (68 bp):
CGCATTGCGATTTCTTTCGTTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCAT
TTC
Found at i:55958 original size:105 final size:105
Alignment explanation
Indices: 55838--56040 Score: 406
Period size: 105 Copynumber: 1.9 Consensus size: 105
55828 AGAATCGCAA
55838 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCAT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCAT
55903 TTCGCATTGCGATTTTCATTTCGCATTGCGATTCTATCGT
66 TTCGCATTGCGATTTTCATTTCGCATTGCGATTCTATCGT
55943 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCAT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCAT
56008 TTCGCATTGCGATTTTCATTTCGCATTGCGATT
66 TTCGCATTGCGATTTTCATTTCGCATTGCGATT
56041 TTCATTTCCG
Statistics
Matches: 98, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
105 98 1.00
ACGTcount: A:0.14, C:0.23, G:0.17, T:0.46
Consensus pattern (105 bp):
TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCAT
TTCGCATTGCGATTTTCATTTCGCATTGCGATTCTATCGT
Found at i:56062 original size:19 final size:19
Alignment explanation
Indices: 55832--56061 Score: 292
Period size: 19 Copynumber: 12.7 Consensus size: 19
55822 AACGAGAGAA
*
55832 TCGCAATGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
55851 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
55870 TCCGCATTGCGA--TTC-TC
1 T-CGCATTGCGATTTTCATT
55887 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
55904 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
55923 TCGCATTGCGA--TTC-TA
1 TCGCATTGCGATTTTCATT
55939 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
55956 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
55975 TCCGCATTGCGA--TTC-TC
1 T-CGCATTGCGATTTTCATT
55992 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
56009 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
56028 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
56047 TCCGCATTGCGATTT
1 T-CGCATTGCGATTT
56062 CTTGTTGGGA
Statistics
Matches: 186, Mismatches: 7, Indels: 35
0.82 0.03 0.15
Matches are distributed among these distances:
14 18 0.10
16 17 0.09
17 19 0.10
18 6 0.03
19 93 0.50
20 33 0.18
ACGTcount: A:0.15, C:0.23, G:0.17, T:0.45
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:56081 original size:39 final size:38
Alignment explanation
Indices: 55832--56061 Score: 292
Period size: 33 Copynumber: 6.4 Consensus size: 38
55822 AACGAGAGAA
*
55832 TCGCAATGCGATTTTCATTTCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATT
*
55870 TCCGCATTGCGA--TTC-TCTCG--TTGCGATTTTCATT
1 T-CGCATTGCGATTTTCATTTCGCATTGCGATTTTCATT
*
55904 TCGCATTGCGATTTTCATTTCGCATTGCGA--TTC-TA
1 TCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATT
55939 TCG--TTGCGATTTTCATTTCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATT
*
55975 TCCGCATTGCGA--TTC-TCTCG--TTGCGATTTTCATT
1 T-CGCATTGCGATTTTCATTTCGCATTGCGATTTTCATT
56009 TCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATT
56047 TCCGCATTGCGATTT
1 T-CGCATTGCGATTT
56062 CTTGTTGGGA
Statistics
Matches: 167, Mismatches: 7, Indels: 35
0.80 0.03 0.17
Matches are distributed among these distances:
33 45 0.27
34 30 0.18
35 13 0.08
36 21 0.13
37 8 0.05
38 22 0.13
39 28 0.17
ACGTcount: A:0.15, C:0.23, G:0.17, T:0.45
Consensus pattern (38 bp):
TCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATT
Found at i:56114 original size:52 final size:52
Alignment explanation
Indices: 55838--56106 Score: 382
Period size: 52 Copynumber: 5.1 Consensus size: 52
55828 AGAATCGCAA
55838 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTT-CGCATTGCGATTCTCTCGT
*
55891 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTATCGT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGT
55943 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTT-CGCATTGCGATTCTCTCGT
*
55996 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATT-T-TCATT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTC-GT
* * *** * * *
56047 TCCGCA-TTGCGATTTCTTGTTGGGATTTTCATTTTGTATTGCGATTCTCTCGT
1 TGCG-ATTTTC-ATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGT
56100 TGCGATT
1 TGCGATT
56107 GTAATTTCCG
Statistics
Matches: 196, Mismatches: 13, Indels: 14
0.88 0.06 0.06
Matches are distributed among these distances:
50 2 0.01
51 8 0.04
52 94 0.48
53 90 0.46
54 2 0.01
ACGTcount: A:0.14, C:0.22, G:0.18, T:0.47
Consensus pattern (52 bp):
TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGT
Found at i:56125 original size:105 final size:105
Alignment explanation
Indices: 55840--56106 Score: 389
Period size: 105 Copynumber: 2.6 Consensus size: 105
55830 AATCGCAATG
*
55840 CGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCATTT
1 CGATTTGCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCATTT
*
55905 CGCATTGCGATTTTCATTTCGCATTGCGATTCTATCGTTG
66 CGCATTGCGATTTTCATTTCGCATTGCGATTCTATCGTTC
*
55945 CGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCATTT
1 CGATTTGCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCATTT
*
56010 CGCATTGCGATTTTCATTTCGCATTGCGATT-T-TCATTTC
66 CGCATTGCGATTTTCATTTCGCATTGCGATTCTATC-GTTC
*** * * *
56049 CGCA-TTGCGATTTCTTGTTGGGATTTTCATTT-TGTATTGCGATTCTCTCGTTGCGATT
1 CG-ATTTGC-ATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATT
56107 GTAATTTCCG
Statistics
Matches: 150, Mismatches: 9, Indels: 7
0.90 0.05 0.04
Matches are distributed among these distances:
103 2 0.01
104 32 0.21
105 116 0.77
ACGTcount: A:0.14, C:0.22, G:0.18, T:0.47
Consensus pattern (105 bp):
CGATTTGCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCATTT
CGCATTGCGATTTTCATTTCGCATTGCGATTCTATCGTTC
Found at i:58405 original size:12 final size:12
Alignment explanation
Indices: 58388--58412 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
58378 TCTTCGGGGA
58388 CTTTTTCTTCTT
1 CTTTTTCTTCTT
58400 CTTTTTCTTCTT
1 CTTTTTCTTCTT
58412 C
1 C
58413 AGGATTATAT
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:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:58621 original size:24 final size:24
Alignment explanation
Indices: 58587--58633 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
58577 CTGAAACATC
58587 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
58611 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
58634 GACCAAATTT
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:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:59353 original size:20 final size:20
Alignment explanation
Indices: 59323--59552 Score: 210
Period size: 20 Copynumber: 11.5 Consensus size: 20
59313 AAATTTCAGT
* *
59323 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCTC
* *
59343 ATTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCTC
*
59363 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCTC
*
59383 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCTC
* *
59403 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCTC
* * *
59423 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATTCTC
* * *
59443 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCTC
* * *
59463 GTTGCTATTTACGGATACAC
1 GTTGCGATTTACGGATTCTC
* * *
59483 GTTGCGGTTTACGGATACGC
1 GTTGCGATTTACGGATTCTC
* *
59503 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATTCTC
* ** *
59523 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATTCTC
59543 GTTGCGATTT
1 GTTGCGATTT
59553 TGGAAACTGA
Statistics
Matches: 180, Mismatches: 28, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
20 179 0.99
21 1 0.01
ACGTcount: A:0.20, C:0.18, G:0.25, T:0.37
Consensus pattern (20 bp):
GTTGCGATTTACGGATTCTC
Found at i:59546 original size:60 final size:60
Alignment explanation
Indices: 59323--59552 Score: 239
Period size: 60 Copynumber: 3.8 Consensus size: 60
59313 AAATTTCAGT
* * * * * * * *
59323 GTTGTGATTTACAGATTCTCATTGCGATTTACGGATTA-TCGTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGCGTTGCGATTTACGGA-TACGCGTTGCGATTTACGGATACGC
** *
59383 GTTGCGATTTACGGATTATCGTTGCGATTTACGGATACGCGTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATTCGCGTTGCGATTTACGGATACGCGTTGCGATTTACGGATACGC
* * * * *
59443 ATTGCGATTTACGGATACGCGTTGCTATTTACGGATACACGTTGCGGTTTACGGATACGC
1 GTTGCGATTTACGGATTCGCGTTGCGATTTACGGATACGCGTTGCGATTTACGGATACGC
* * ** *
59503 GTTGCGATTTATGTG-TTCGCGTTGCGATTTTCATATTCGCGTTGCGATTT
1 GTTGCGATTTACG-GATTCGCGTTGCGATTTACGGATACGCGTTGCGATTT
59553 TGGAAACTGA
Statistics
Matches: 141, Mismatches: 27, Indels: 4
0.82 0.16 0.02
Matches are distributed among these distances:
59 2 0.01
60 138 0.98
61 1 0.01
ACGTcount: A:0.20, C:0.18, G:0.25, T:0.37
Consensus pattern (60 bp):
GTTGCGATTTACGGATTCGCGTTGCGATTTACGGATACGCGTTGCGATTTACGGATACGC
Found at i:67160 original size:54 final size:54
Alignment explanation
Indices: 67078--67188 Score: 213
Period size: 54 Copynumber: 2.1 Consensus size: 54
67068 TTTAATAAAA
67078 ATATTTTATTTATTGATTTGTTTTTTTAATTATAATAAAATATAATTTTATTAT
1 ATATTTTATTTATTGATTTGTTTTTTTAATTATAATAAAATATAATTTTATTAT
*
67132 ATATTTTATTTATTGATTTGTTTTTTTAATTATAATCAAATATAATTTTATTAT
1 ATATTTTATTTATTGATTTGTTTTTTTAATTATAATAAAATATAATTTTATTAT
67186 ATA
1 ATA
67189 CTACCATAAA
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
54 56 1.00
ACGTcount: A:0.35, C:0.01, G:0.04, T:0.60
Consensus pattern (54 bp):
ATATTTTATTTATTGATTTGTTTTTTTAATTATAATAAAATATAATTTTATTAT
Done.