Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004935.1 Hibiscus syriacus cultivar Beakdansim tig00011102_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: 77409
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:3766 original size:14 final size:14
Alignment explanation
Indices: 3729--3783 Score: 56
Period size: 14 Copynumber: 3.9 Consensus size: 14
3719 TTGACCCGAC
*
3729 GAGTCAACTCGGACT
1 GAGTCAACTCGTA-T
* *
3744 GAGTAAACTCATAT
1 GAGTCAACTCGTAT
**
3758 GAGTCAACTCGTCC
1 GAGTCAACTCGTAT
3772 GAGTCAACTCGT
1 GAGTCAACTCGT
3784 TGACTTTGAC
Statistics
Matches: 33, Mismatches: 7, Indels: 1
0.80 0.17 0.02
Matches are distributed among these distances:
14 23 0.70
15 10 0.30
ACGTcount: A:0.29, C:0.25, G:0.22, T:0.24
Consensus pattern (14 bp):
GAGTCAACTCGTAT
Found at i:20022 original size:36 final size:36
Alignment explanation
Indices: 19955--20024 Score: 97
Period size: 36 Copynumber: 1.9 Consensus size: 36
19945 TCTTAGGTAC
*
19955 ATAAGGAATTACCAGCTTGATCAATGTTGAACCTCT
1 ATAAGGAATTACCAGCTTGATCAATGATGAACCTCT
* *
19991 ATAAGGAATTACCATCTTGATTGAA-GATGAACCT
1 ATAAGGAATTACCAGCTTGA-TCAATGATGAACCT
20025 GTAGAGACTT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
36 27 0.90
37 3 0.10
ACGTcount: A:0.36, C:0.17, G:0.17, T:0.30
Consensus pattern (36 bp):
ATAAGGAATTACCAGCTTGATCAATGATGAACCTCT
Found at i:20781 original size:21 final size:21
Alignment explanation
Indices: 20756--20795 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
20746 TTGACTTTTT
20756 GGTCAAA-GTCAACAGTCAACG
1 GGTCAAAGGTCAA-AGTCAACG
20777 GGTCAAAGGTCAAAGTCAA
1 GGTCAAAGGTCAAAGTCAA
20796 AGTCAACATG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.40, C:0.20, G:0.25, T:0.15
Consensus pattern (21 bp):
GGTCAAAGGTCAAAGTCAACG
Found at i:21455 original size:19 final size:19
Alignment explanation
Indices: 21431--21467 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
21421 GGGGTTAGGG
21431 AATTGG-GATTATTTTGGGA
1 AATTGGAGATT-TTTTGGGA
21450 AATTGGAGATTTTTTGGG
1 AATTGGAGATTTTTTGGG
21468 TTTGGGAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.24, C:0.00, G:0.32, T:0.43
Consensus pattern (19 bp):
AATTGGAGATTTTTTGGGA
Found at i:30759 original size:18 final size:19
Alignment explanation
Indices: 30738--30782 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
30728 ATTTAGACAT
30738 TTTGCATTTT-TTAGTTTC
1 TTTGCATTTTGTTAGTTTC
*
30756 TTTGCATTTTGTTATTTTC
1 TTTGCATTTTGTTAGTTTC
30775 TTTGCATT
1 TTTGCATT
30783 CACATTAACT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
18 10 0.40
19 15 0.60
ACGTcount: A:0.11, C:0.11, G:0.11, T:0.67
Consensus pattern (19 bp):
TTTGCATTTTGTTAGTTTC
Found at i:34149 original size:106 final size:106
Alignment explanation
Indices: 33962--34865 Score: 1567
Period size: 106 Copynumber: 8.5 Consensus size: 106
33952 TTCAAGCCAG
* *
33962 AGTTCAACTTCACGACGAAGGGACCGCTAGTTGTCAACAAACAACTTCTCAATTTTAGAGCCAAT
1 AGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCAAT
34027 TTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCA
66 TTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCA
* * * *
34068 ATTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACGACTTCTCAATTTCAGAGCTAAT
1 AGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCAAT
34133 TTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCA
66 TTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCA
*
34174 AGTTCAACTTCACGACGAAGGGATCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCAAT
1 AGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCAAT
*
34239 TTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCA
66 TTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCA
* *
34280 TGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTTAATTTCAGAGCCAAT
1 AGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCAAT
*
34345 TTCAACTTCACAACGAAGGATATTGGACTCCAGAAAACGCA
66 TTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCA
*
34386 AGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTTAGAGCCAAT
1 AGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCAAT
* *
34451 TTCAACTTCACAACGAAGGATATTGGACTCCAGAAAACACA
66 TTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCA
*
34492 TGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCAAT
1 AGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCAAT
* *
34557 TTCAACTTCACAGCGAAGGATATTGTACTCCAGACAACGCA
66 TTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCA
34598 AGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCAAT
1 AGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCAAT
34663 TTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCA
66 TTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCA
* * *
34704 AGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCTCAATTTCAGAGTCAAT
1 AGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCAAT
* * *
34769 TTCAACTTCATAGCGAAGGATATTGGACTCAAGACAACGCA
66 TTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCA
* * *
34810 AGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAATAACTT-TCAACTTCA
1 AGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCA
34866 CGACGAAGGG
Statistics
Matches: 759, Mismatches: 39, Indels: 1
0.95 0.05 0.00
Matches are distributed among these distances:
105 8 0.01
106 751 0.99
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.24
Consensus pattern (106 bp):
AGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCAAT
TTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCA
Found at i:34864 original size:44 final size:44
Alignment explanation
Indices: 34812--34914 Score: 197
Period size: 44 Copynumber: 2.3 Consensus size: 44
34802 ACAACGCAAG
*
34812 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAATAACT
1 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACT
34856 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACT
1 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACT
34900 TTCAACTTCACGACG
1 TTCAACTTCACGACG
34915 GAGGATATTG
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 58 1.00
ACGTcount: A:0.31, C:0.25, G:0.19, T:0.24
Consensus pattern (44 bp):
TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACT
Found at i:35157 original size:71 final size:71
Alignment explanation
Indices: 35031--35170 Score: 183
Period size: 71 Copynumber: 2.0 Consensus size: 71
35021 ACTCAGCTCT
* * * * *
35031 GAGGGCATATCATTTGCAGTATAACTTAAGTCGAGAGGGTTATCTGCCAACCAAAGACCTTCGAG
1 GAGGGCACATCATTTGCAGCATAACTCAAGGCGAGAGGGTTATCCGCCAACCAAAGACCTTCGAG
35096 TTCGTC
66 TTCGTC
* * * *
35102 GAGGGCACGTCATTTGTAGCATAACTCAAGGCTAGAAGGGTTATCCGCCAA-CAAAGACCTTTGA
1 GAGGGCACATCATTTGCAGCATAACTCAAGGCGAG-AGGGTTATCCGCCAACCAAAGACCTTCGA
35166 GTTCG
65 GTTCG
35171 ACTACGCTCA
Statistics
Matches: 59, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
71 45 0.76
72 14 0.24
ACGTcount: A:0.29, C:0.21, G:0.25, T:0.25
Consensus pattern (71 bp):
GAGGGCACATCATTTGCAGCATAACTCAAGGCGAGAGGGTTATCCGCCAACCAAAGACCTTCGAG
TTCGTC
Found at i:36675 original size:5 final size:5
Alignment explanation
Indices: 36665--36732 Score: 58
Period size: 5 Copynumber: 14.4 Consensus size: 5
36655 CCTTTTACTT
* *
36665 TTTTA TTTTA -TTCA TTTTA TTTTA -TTTA TTTTA TTTTTA TTTT- TATT-
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA -TTTTA TTTTA TTTTA
36712 TTTTA TTTTCA --TTA TTTTA TT
1 TTTTA TTTT-A TTTTA TTTTA TT
36733 ATTTTTGTTT
Statistics
Matches: 52, Mismatches: 4, Indels: 14
0.74 0.06 0.20
Matches are distributed among these distances:
3 1 0.02
4 15 0.29
5 30 0.58
6 6 0.12
ACGTcount: A:0.19, C:0.03, G:0.00, T:0.78
Consensus pattern (5 bp):
TTTTA
Found at i:36692 original size:9 final size:9
Alignment explanation
Indices: 36680--36737 Score: 56
Period size: 9 Copynumber: 6.9 Consensus size: 9
36670 TTTTATTCAT
36680 TTTATTTTA
1 TTTATTTTA
36689 TTTATTTTA
1 TTTATTTTA
36698 TTT-TTATT-
1 TTTATT-TTA
36706 TTTA-TTT-
1 TTTATTTTA
36713 TTTATTTTCA
1 TTTATTTT-A
36723 -TTATTTTA
1 TTTATTTTA
36731 -TTATTTT
1 TTTATTTT
36738 TGTTTATTAT
Statistics
Matches: 44, Mismatches: 0, Indels: 11
0.80 0.00 0.20
Matches are distributed among these distances:
7 6 0.14
8 17 0.39
9 21 0.48
ACGTcount: A:0.19, C:0.02, G:0.00, T:0.79
Consensus pattern (9 bp):
TTTATTTTA
Found at i:36715 original size:14 final size:13
Alignment explanation
Indices: 36657--36738 Score: 76
Period size: 14 Copynumber: 5.9 Consensus size: 13
36647 AAACTAACCC
*
36657 TTTTACTTTTTTA
1 TTTTATTTTTTTA
*
36670 TTTTATTCATTTTA
1 TTTTATT-TTTTTA
36684 TTTTATTTATTTTA
1 TTTTATTT-TTTTA
36698 TTTTTATTTTTATT-
1 -TTTTATTTTT-TTA
*
36712 TTTTATTTTCATTA
1 TTTTATTTT-TTTA
36726 TTTTATTATTTTT
1 TTTTATT-TTTTT
36739 GTTTATTATC
Statistics
Matches: 57, Mismatches: 5, Indels: 13
0.76 0.07 0.17
Matches are distributed among these distances:
13 17 0.30
14 28 0.49
15 12 0.21
ACGTcount: A:0.18, C:0.04, G:0.00, T:0.78
Consensus pattern (13 bp):
TTTTATTTTTTTA
Found at i:36738 original size:9 final size:9
Alignment explanation
Indices: 36670--36738 Score: 52
Period size: 9 Copynumber: 7.4 Consensus size: 9
36660 TACTTTTTTA
36670 TTTTATTCAT
1 TTTTATT-AT
*
36680 TTTATTTTAT
1 TTT-TATTAT
36690 TTATT-TTAT
1 TT-TTATTAT
*
36699 TTTTATTTT
1 TTTTATTAT
*
36708 TATTTTTTAT
1 T-TTTATTAT
*
36718 TTTCATTA-
1 TTTTATTAT
36726 TTTTATTAT
1 TTTTATTAT
36735 TTTT
1 TTTT
36739 GTTTATTATC
Statistics
Matches: 47, Mismatches: 7, Indels: 11
0.72 0.11 0.17
Matches are distributed among these distances:
8 9 0.19
9 19 0.40
10 15 0.32
11 4 0.09
ACGTcount: A:0.19, C:0.03, G:0.00, T:0.78
Consensus pattern (9 bp):
TTTTATTAT
Found at i:37682 original size:186 final size:186
Alignment explanation
Indices: 37368--37748 Score: 753
Period size: 186 Copynumber: 2.0 Consensus size: 186
37358 ATAATAATTA
37368 TTATATTTTGTTTAACTTGTGACATTTTAGGGTTCATATGTAAATGTAAATTTCTAAAGGTTATA
1 TTATATTTTGTTTAACTTGTGACATTTTAGGGTTCATATGTAAATGTAAATTTCTAAAGGTTATA
37433 AATTGAAATTAGATTAAACAGATATCTTTAAACAATCAGGAATGGACCTACATGTATAATAAGAG
66 AATTGAAATTAGATTAAACAGATATCTTTAAACAATCAGGAATGGACCTACATGTATAATAAGAG
37498 AGATCCAGCCTCTTCCCATAAAAAATGGTTTAGTCACATTTTTAGTCCCTAATAGT
131 AGATCCAGCCTCTTCCCATAAAAAATGGTTTAGTCACATTTTTAGTCCCTAATAGT
37554 TTATATTTTGTTTAACTTGTGACATTTTAGGGTTCATATGTAAATGTAAATTTCTAAAGGTTATA
1 TTATATTTTGTTTAACTTGTGACATTTTAGGGTTCATATGTAAATGTAAATTTCTAAAGGTTATA
37619 AATTGAAATTAGATTAAACAGATATCTTTAAACAATCAGGAATGGACCTACATGTATAATAAGAG
66 AATTGAAATTAGATTAAACAGATATCTTTAAACAATCAGGAATGGACCTACATGTATAATAAGAG
*
37684 AGATCCGGCCTCTTCCCATAAAAAATGGTTTAGTCACATTTTTAGTCCCTAATAGT
131 AGATCCAGCCTCTTCCCATAAAAAATGGTTTAGTCACATTTTTAGTCCCTAATAGT
37740 TTATATTTT
1 TTATATTTT
37749 ATTCAACTAA
Statistics
Matches: 194, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
186 194 1.00
ACGTcount: A:0.35, C:0.13, G:0.14, T:0.38
Consensus pattern (186 bp):
TTATATTTTGTTTAACTTGTGACATTTTAGGGTTCATATGTAAATGTAAATTTCTAAAGGTTATA
AATTGAAATTAGATTAAACAGATATCTTTAAACAATCAGGAATGGACCTACATGTATAATAAGAG
AGATCCAGCCTCTTCCCATAAAAAATGGTTTAGTCACATTTTTAGTCCCTAATAGT
Found at i:46237 original size:13 final size:13
Alignment explanation
Indices: 46219--46257 Score: 60
Period size: 13 Copynumber: 2.9 Consensus size: 13
46209 ATGGTCAAAT
*
46219 TTTGAAAACTATG
1 TTTGAAAACAATG
46232 TTTGAAAACAATG
1 TTTGAAAACAATG
46245 TTTGAAAATCAAT
1 TTTGAAAA-CAAT
46258 ATGTAGTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
13 20 0.83
14 4 0.17
ACGTcount: A:0.44, C:0.08, G:0.13, T:0.36
Consensus pattern (13 bp):
TTTGAAAACAATG
Found at i:46770 original size:23 final size:21
Alignment explanation
Indices: 46719--46794 Score: 75
Period size: 23 Copynumber: 3.6 Consensus size: 21
46709 GTCTTGACAG
* *
46719 GGGGTATCGGTAC-CCTT-AA
1 GGGGTATCGATACACATTAAA
*
46738 GGGGTTTCGATACACATTCAAA
1 GGGGTATCGATACACATT-AAA
* *
46760 TGGGGTATCGATACACGTTGAA
1 -GGGGTATCGATACACATTAAA
46782 GGGGTATCGATAC
1 GGGGTATCGATAC
46795 CTAGTGCACA
Statistics
Matches: 47, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
19 11 0.23
20 3 0.06
21 13 0.28
22 4 0.09
23 16 0.34
ACGTcount: A:0.26, C:0.17, G:0.30, T:0.26
Consensus pattern (21 bp):
GGGGTATCGATACACATTAAA
Found at i:50640 original size:22 final size:21
Alignment explanation
Indices: 50599--50647 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
50589 GAGATTATTT
*
50599 TCATTTTTCAATTTTGAAATA
1 TCATTTTTCAATTTTAAAATA
50620 TCATTTTT-ATATTTTAAAA-A
1 TCATTTTTCA-ATTTTAAAATA
*
50640 TAATTTTT
1 TCATTTTT
50648 TCATAATCCG
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 9 0.36
21 16 0.64
ACGTcount: A:0.35, C:0.06, G:0.02, T:0.57
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAATA
Found at i:54493 original size:22 final size:22
Alignment explanation
Indices: 54467--54509 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
54457 GCAATAGGTA
*
54467 TTGATATTTAGCAATGTTTGTG
1 TTGATATTTAGCAACGTTTGTG
*
54489 TTGATATTTAGCGACGTTTGT
1 TTGATATTTAGCAACGTTTGT
54510 CAAAAAAACA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.21, C:0.07, G:0.23, T:0.49
Consensus pattern (22 bp):
TTGATATTTAGCAACGTTTGTG
Found at i:54550 original size:43 final size:43
Alignment explanation
Indices: 54489--54587 Score: 128
Period size: 43 Copynumber: 2.3 Consensus size: 43
54479 AATGTTTGTG
*
54489 TTGATATTTAGCGACGTTTGTCAAAAAAACACTGCAGTAAGTA
1 TTGATATTTAGCGACGTTTGTCAAAAAAACACTGCAATAAGTA
* ** * *
54532 TTGATATTTAGC-AGCGTTTGTCATAAAAATGCTGCAATAGGTG
1 TTGATATTTAGCGA-CGTTTGTCAAAAAAACACTGCAATAAGTA
54575 TTGATATTTAGCG
1 TTGATATTTAGCG
54588 GCATTTTTTA
Statistics
Matches: 48, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
42 1 0.02
43 47 0.98
ACGTcount: A:0.32, C:0.12, G:0.21, T:0.34
Consensus pattern (43 bp):
TTGATATTTAGCGACGTTTGTCAAAAAAACACTGCAATAAGTA
Found at i:54648 original size:43 final size:41
Alignment explanation
Indices: 54558--54765 Score: 161
Period size: 42 Copynumber: 4.9 Consensus size: 41
54548 TTTGTCATAA
* * * ***
54558 AAATGCTGCAATAGGTGTTGATATTTAGCGGCATTTTTTAGAC
1 AAATGCCGCAGTAGGT-TTGATGTTTAGCGGC-TTTTTCCCAC
* *
54601 AAATGCCGCAATAGGTTATGATGTTTAGCGGCGTTTTTCTCTA-
1 AAATGCCGCAGTAGGTT-TGATGTTTAGCGGC-TTTTTC-CCAC
* * *
54644 AAATGCCGCAGTAGGTGATAATGTTTTA-CGGCATTTTCCCAC
1 AAATGCCGCAGTAGGT-TTGATG-TTTAGCGGCTTTTTCCCAC
* * *
54686 AAACGCCGCAGTAGGTGTTGATGTTTTA-CGACATTTTCCCAC
1 AAATGCCGCAGTAGGT-TTGATG-TTTAGCGGCTTTTTCCCAC
*
54728 AAATGCCGCAGTAGGTTTTGATGTTTTGCGGCGTTTTT
1 AAATGCCGCAGTAGG-TTTGATGTTTAGCGGC-TTTTT
54766 GCTAAAAATA
Statistics
Matches: 138, Mismatches: 19, Indels: 16
0.80 0.11 0.09
Matches are distributed among these distances:
41 5 0.04
42 67 0.49
43 61 0.44
44 5 0.04
ACGTcount: A:0.24, C:0.17, G:0.24, T:0.36
Consensus pattern (41 bp):
AAATGCCGCAGTAGGTTTGATGTTTAGCGGCTTTTTCCCAC
Found at i:54749 original size:42 final size:42
Alignment explanation
Indices: 54599--54764 Score: 183
Period size: 42 Copynumber: 3.9 Consensus size: 42
54589 CATTTTTTAG
* * * *
54599 ACAAATGCCGCAATAGGTTATGATG-TTTAGCGGCGTTTTTCTCT
1 ACAAATGCCGCAGTAGGTGATGATGTTTTA-CGGC-ATTTTC-CC
*
54643 A-AAATGCCGCAGTAGGTGATAATGTTTTACGGCATTTTCCC
1 ACAAATGCCGCAGTAGGTGATGATGTTTTACGGCATTTTCCC
* * *
54684 ACAAACGCCGCAGTAGGTGTTGATGTTTTACGACATTTTCCC
1 ACAAATGCCGCAGTAGGTGATGATGTTTTACGGCATTTTCCC
** * *
54726 ACAAATGCCGCAGTAGGTTTTGATGTTTTGCGGCGTTTT
1 ACAAATGCCGCAGTAGGTGATGATGTTTTACGGCATTTT
54765 TGCTAAAAAT
Statistics
Matches: 106, Mismatches: 14, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
41 2 0.02
42 75 0.71
43 24 0.23
44 5 0.05
ACGTcount: A:0.23, C:0.19, G:0.23, T:0.34
Consensus pattern (42 bp):
ACAAATGCCGCAGTAGGTGATGATGTTTTACGGCATTTTCCC
Found at i:55196 original size:21 final size:21
Alignment explanation
Indices: 55172--55231 Score: 75
Period size: 21 Copynumber: 2.9 Consensus size: 21
55162 CTGTTGATAT
*
55172 GCTGCTTCTCTCTATGTTGCC
1 GCTGCTTCTCTCTATGCTGCC
* *
55193 GCTGCTTCTCTCTGTGCTGTC
1 GCTGCTTCTCTCTATGCTGCC
* *
55214 GCTGCTTCTTTCTCTGCT
1 GCTGCTTCTCTCTATGCT
55232 TCCACTACTG
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.02, C:0.33, G:0.20, T:0.45
Consensus pattern (21 bp):
GCTGCTTCTCTCTATGCTGCC
Found at i:55251 original size:21 final size:21
Alignment explanation
Indices: 55227--55266 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
55217 GCTTCTTTCT
*
55227 CTGCTTCCACTACTGCTCTGG
1 CTGCTTCAACTACTGCTCTGG
*
55248 CTGCTTCAACTGCTGCTCT
1 CTGCTTCAACTACTGCTCT
55267 CTCTTCTTTC
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:0.10, C:0.38, G:0.17, T:0.35
Consensus pattern (21 bp):
CTGCTTCAACTACTGCTCTGG
Found at i:66647 original size:82 final size:83
Alignment explanation
Indices: 66436--66661 Score: 224
Period size: 83 Copynumber: 2.7 Consensus size: 83
66426 TTTGTGGGAT
* * * * * * *
66436 AAACGCCGCTAAATTATTACTCTATTACGGCGTTTTTTGCATAAATGCCACTATAAACAACCTTT
1 AAACGCCGCTAAATTACTACTCTATTACGACGTTTATTGAAAAAACGCCACTATAAACAACCTTA
* * *
66501 TTGCGACATTTGTTTGAT
66 TTACGACATTTGTATGAA
* * * * * * * *
66519 AAACACCGCTAAATTACTTCT-TAATAGCGTCATTTGTTGAACAAACGACACTATAAACAACAC-
1 AAACGCCGCTAAATTACTACTCTATTA-CGACGTTTATTGAAAAAACGCCACTATAAACAAC-CT
* *
66582 TATTACGGCGTTTGTAT-AA
64 TATTACGACATTTGTATGAA
*
66601 AAACGCCGCTAAATTACCACTCTATTACGACGTTTATTGAAAAAACGCCACTATAAACAAC
1 AAACGCCGCTAAATTACTACTCTATTACGACGTTTATTGAAAAAACGCCACTATAAACAAC
66662 TCTAAATTAC
Statistics
Matches: 114, Mismatches: 26, Indels: 7
0.78 0.18 0.05
Matches are distributed among these distances:
82 52 0.46
83 61 0.54
84 1 0.01
ACGTcount: A:0.35, C:0.22, G:0.12, T:0.31
Consensus pattern (83 bp):
AAACGCCGCTAAATTACTACTCTATTACGACGTTTATTGAAAAAACGCCACTATAAACAACCTTA
TTACGACATTTGTATGAA
Found at i:66664 original size:41 final size:40
Alignment explanation
Indices: 66555--66665 Score: 109
Period size: 41 Copynumber: 2.7 Consensus size: 40
66545 GCGTCATTTG
* * * *
66555 TTGAACAAACGACACTATAAACAACACTATTACGGCGTTT
1 TTGAAAAAACGCCACTATAAACAACTCTATTACGACGTTT
* * *
66595 GT-ATAAAAACGCCGCTA-AATTACCACTCTATTACGACGTTT
1 TTGA-AAAAACGCCACTATAA--ACAACTCTATTACGACGTTT
66636 ATTGAAAAAACGCCACTATAAACAACTCTA
1 -TTGAAAAAACGCCACTATAAACAACTCTA
66666 AATTACCATT
Statistics
Matches: 55, Mismatches: 10, Indels: 11
0.72 0.13 0.14
Matches are distributed among these distances:
39 3 0.05
40 11 0.20
41 25 0.45
42 13 0.24
43 3 0.05
ACGTcount: A:0.41, C:0.23, G:0.11, T:0.25
Consensus pattern (40 bp):
TTGAAAAAACGCCACTATAAACAACTCTATTACGACGTTT
Found at i:71690 original size:13 final size:13
Alignment explanation
Indices: 71672--71706 Score: 54
Period size: 13 Copynumber: 2.7 Consensus size: 13
71662 TACAATCACT
71672 CAAAAAGAAGAAA
1 CAAAAAGAAGAAA
71685 CAAAAAGAAGAAA
1 CAAAAAGAAGAAA
71698 -AGAAAAGAA
1 CA-AAAAGAA
71707 ATTGCAAAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 1 0.05
13 20 0.95
ACGTcount: A:0.77, C:0.06, G:0.17, T:0.00
Consensus pattern (13 bp):
CAAAAAGAAGAAA
Done.