Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002364.1 Hibiscus syriacus cultivar Beakdansim tig00004826_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: 69113
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:5596 original size:36 final size:37
Alignment explanation
Indices: 5529--5601 Score: 112
Period size: 36 Copynumber: 2.0 Consensus size: 37
5519 TATGTGCAGG
**
5529 GGGAACAGATTCCCCCTTGGGGGGGTATCGATTCCCC
1 GGGAACAGATTCCCCCTTAAGGGGGTATCGATTCCCC
*
5566 GGGAATAGATTCCCCC-TAAGGGGGTATCGATTCCCC
1 GGGAACAGATTCCCCCTTAAGGGGGTATCGATTCCCC
5602 CCTAGTGGTC
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
36 18 0.55
37 15 0.45
ACGTcount: A:0.19, C:0.29, G:0.30, T:0.22
Consensus pattern (37 bp):
GGGAACAGATTCCCCCTTAAGGGGGTATCGATTCCCC
Found at i:6069 original size:20 final size:20
Alignment explanation
Indices: 6044--6082 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
6034 CAGTATGTGC
6044 AGGGGG-AACAGATTCCCCCT
1 AGGGGGTAAC-GATTCCCCCT
*
6064 AGGGGGTATCGATTCCCCC
1 AGGGGGTAACGATTCCCCC
6083 CTAAATGAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 15 0.88
21 2 0.12
ACGTcount: A:0.21, C:0.31, G:0.31, T:0.18
Consensus pattern (20 bp):
AGGGGGTAACGATTCCCCCT
Found at i:6675 original size:15 final size:15
Alignment explanation
Indices: 6655--6690 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
6645 TTGAGGGTAT
*
6655 TGTAGTCTTTCGGGA
1 TGTAGTCCTTCGGGA
6670 TGTAGTCCTTCGGGA
1 TGTAGTCCTTCGGGA
*
6685 CGTAGT
1 TGTAGT
6691 GGTCTTACGG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.14, C:0.17, G:0.33, T:0.36
Consensus pattern (15 bp):
TGTAGTCCTTCGGGA
Found at i:7381 original size:22 final size:21
Alignment explanation
Indices: 7356--7403 Score: 62
Period size: 21 Copynumber: 2.2 Consensus size: 21
7346 AGAATCGATA
7356 CCCTCATG-AGGGAACCGATTCC
1 CCCT-ATGAAGGG-ACCGATTCC
*
7378 CCCTTTGAAGGGACCGATTCC
1 CCCTATGAAGGGACCGATTCC
7399 CCCTA
1 CCCTA
7404 GGGGAATCGA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
21 15 0.65
22 8 0.35
ACGTcount: A:0.21, C:0.38, G:0.21, T:0.21
Consensus pattern (21 bp):
CCCTATGAAGGGACCGATTCC
Found at i:12650 original size:85 final size:85
Alignment explanation
Indices: 12549--12714 Score: 210
Period size: 85 Copynumber: 2.0 Consensus size: 85
12539 ATACAATCAC
* * * * * *
12549 GACACACGAATGTGTGTCATCTTT-TTTAATGATGTGTGATTCAATGACACGTAATGTAA-TTCA
1 GACACACAAATGTGTGTCATCTTTATTT-ATGACGGGAGATTCAATGACACGCAATG-AACGTCA
*
12612 TAAATGCGTGTCATAAATTTAT
64 TAAATGCGCGTCATAAATTTAT
* * *
12634 GACACACAAATGTGTGTCGTCTTTATTTATGACGGGAGCTTCAATGACGCGCAATGAACGTCATA
1 GACACACAAATGTGTGTCATCTTTATTTATGACGGGAGATTCAATGACACGCAATGAACGTCATA
12699 AATGCGCGTCATAAAT
66 AATGCGCGTCATAAAT
12715 ACGTGTCATA
Statistics
Matches: 69, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
84 2 0.03
85 64 0.93
86 3 0.04
ACGTcount: A:0.31, C:0.16, G:0.20, T:0.33
Consensus pattern (85 bp):
GACACACAAATGTGTGTCATCTTTATTTATGACGGGAGATTCAATGACACGCAATGAACGTCATA
AATGCGCGTCATAAATTTAT
Found at i:12708 original size:13 final size:13
Alignment explanation
Indices: 12692--12737 Score: 65
Period size: 13 Copynumber: 3.5 Consensus size: 13
12682 GCGCAATGAA
12692 CGTCATAAATGCG
1 CGTCATAAATGCG
*
12705 CGTCATAAATACG
1 CGTCATAAATGCG
* *
12718 TGTCATAAATGCA
1 CGTCATAAATGCG
12731 CGTCATA
1 CGTCATA
12738 GATTTATGAC
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
13 28 1.00
ACGTcount: A:0.35, C:0.22, G:0.17, T:0.26
Consensus pattern (13 bp):
CGTCATAAATGCG
Found at i:12962 original size:32 final size:32
Alignment explanation
Indices: 12921--12992 Score: 101
Period size: 32 Copynumber: 2.2 Consensus size: 32
12911 ACTTCAAATG
*
12921 AATAATTTGACT-AGTGAATAAGGTTATTTTAA
1 AATAATTTGACTCA-TGAATAAGATTATTTTAA
*
12953 AATAATTTGATTCATGAATAAGATTATTTTAA
1 AATAATTTGACTCATGAATAAGATTATTTTAA
*
12985 TATAATTT
1 AATAATTT
12993 AATATATATA
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
32 35 0.97
33 1 0.03
ACGTcount: A:0.42, C:0.03, G:0.11, T:0.44
Consensus pattern (32 bp):
AATAATTTGACTCATGAATAAGATTATTTTAA
Found at i:15595 original size:3 final size:3
Alignment explanation
Indices: 15587--15619 Score: 50
Period size: 3 Copynumber: 11.0 Consensus size: 3
15577 TTAAATAAAA
15587 AAT AAT AAT AAT AAT AAT -AT AATT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AA-T AAT AAT AAT
15620 TTTTAAATCC
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
2 2 0.07
3 23 0.82
4 3 0.11
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
AAT
Found at i:24752 original size:23 final size:24
Alignment explanation
Indices: 24726--24779 Score: 60
Period size: 22 Copynumber: 2.3 Consensus size: 24
24716 TATATATATT
* *
24726 ATAAATATTTTTTATT-GAAATTA
1 ATAAATATCTTTGATTGGAAATTA
24749 AT-AA-ATCTTTGATTGGAAATTA
1 ATAAATATCTTTGATTGGAAATTA
24771 ATATAATAT
1 ATA-AATAT
24780 ATAAAAATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
21 8 0.32
22 11 0.44
23 2 0.08
24 2 0.08
25 2 0.08
ACGTcount: A:0.44, C:0.02, G:0.07, T:0.46
Consensus pattern (24 bp):
ATAAATATCTTTGATTGGAAATTA
Found at i:34315 original size:20 final size:20
Alignment explanation
Indices: 34303--34359 Score: 105
Period size: 20 Copynumber: 2.9 Consensus size: 20
34293 TTATTAGTGA
34303 GAATAAAAAATTATCAGTAG
1 GAATAAAAAATTATCAGTAG
34323 GAATAAAAAATTATCAGTAG
1 GAATAAAAAATTATCAGTAG
*
34343 GAATAAAAGATTATCAG
1 GAATAAAAAATTATCAG
34360 AGAATATTAT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.54, C:0.05, G:0.16, T:0.25
Consensus pattern (20 bp):
GAATAAAAAATTATCAGTAG
Found at i:34885 original size:17 final size:19
Alignment explanation
Indices: 34863--34898 Score: 58
Period size: 17 Copynumber: 2.0 Consensus size: 19
34853 AAACGGGAGA
34863 ATGTGAAT-T-ACATTCTC
1 ATGTGAATCTCACATTCTC
34880 ATGTGAATCTCACATTCTC
1 ATGTGAATCTCACATTCTC
34899 CAAACCAAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 8 0.47
18 1 0.06
19 8 0.47
ACGTcount: A:0.28, C:0.22, G:0.11, T:0.39
Consensus pattern (19 bp):
ATGTGAATCTCACATTCTC
Found at i:37305 original size:24 final size:24
Alignment explanation
Indices: 37278--37325 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
37268 CGTTCATTTA
*
37278 CGTTCGTGAACGTTCGGTTATGTT
1 CGTTCATGAACGTTCGGTTATGTT
* **
37302 CGTTTATGTTCGTTCGGTTATGTT
1 CGTTCATGAACGTTCGGTTATGTT
37326 AGTTTATGTT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.10, C:0.15, G:0.27, T:0.48
Consensus pattern (24 bp):
CGTTCATGAACGTTCGGTTATGTT
Found at i:37330 original size:24 final size:24
Alignment explanation
Indices: 37288--37336 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
37278 CGTTCGTGAA
*
37288 CGTTCGGTTATGTTCGTTTATGTT
1 CGTTCGGTTATGTTAGTTTATGTT
37312 CGTTCGGTTATGTTAGTTTATGTT
1 CGTTCGGTTATGTTAGTTTATGTT
37336 C
1 C
37337 ATTCATTTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.10, C:0.12, G:0.24, T:0.53
Consensus pattern (24 bp):
CGTTCGGTTATGTTAGTTTATGTT
Found at i:37346 original size:24 final size:24
Alignment explanation
Indices: 37294--37349 Score: 76
Period size: 24 Copynumber: 2.3 Consensus size: 24
37284 TGAACGTTCG
* * *
37294 GTTATGTTCGTTTATGTTCGTTCG
1 GTTATGTTAGTTTATGTTCATTCA
37318 GTTATGTTAGTTTATGTTCATTCA
1 GTTATGTTAGTTTATGTTCATTCA
*
37342 TTTATGTT
1 GTTATGTT
37350 TAACTCAATC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.14, C:0.09, G:0.20, T:0.57
Consensus pattern (24 bp):
GTTATGTTAGTTTATGTTCATTCA
Found at i:37377 original size:14 final size:14
Alignment explanation
Indices: 37349--37389 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
37339 TCATTTATGT
* *
37349 TTAACTCAATCTTC
1 TTAAATCAATTTTC
*
37363 TTATATCAATTTTC
1 TTAAATCAATTTTC
37377 TTAAATCAATTTT
1 TTAAATCAATTTT
37390 GGTGACCAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.32, C:0.17, G:0.00, T:0.51
Consensus pattern (14 bp):
TTAAATCAATTTTC
Found at i:38464 original size:16 final size:16
Alignment explanation
Indices: 38443--38485 Score: 68
Period size: 16 Copynumber: 2.7 Consensus size: 16
38433 CCAACGTTTA
*
38443 TGTTCGTTTATATTTG
1 TGTTCGTTTATATTCG
*
38459 TGTTCGTTTATGTTCG
1 TGTTCGTTTATATTCG
38475 TGTTCGTTTAT
1 TGTTCGTTTAT
38486 TTATTAAATG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.09, C:0.09, G:0.21, T:0.60
Consensus pattern (16 bp):
TGTTCGTTTATATTCG
Found at i:44371 original size:158 final size:158
Alignment explanation
Indices: 44078--44395 Score: 435
Period size: 158 Copynumber: 2.0 Consensus size: 158
44068 ACTCGCAACC
* * * *
44078 CACCTGCAACAATCAAATTCCGAATTCATTCGAACCGAAAAAGGCTCGAAAAAAGTTATGAACTT
1 CACCTGCAACAACCAAATTCCGAATTCATTCCAACCGAAAAAAGCTCGAAAAAAGTTATAAACTT
*
44143 TCAAGCTTGTAGATTTACGATTCATTCCAAGATTATAGCTTTGATGATTAACAAGTACTCAAAAG
66 TCAAGCTTGTAGATTTACAATTCATTCCAAGATTATAGCTTTGATGATTAACAAGTACTCAAAAG
*
44208 CAATGGACA-CATGACAGTAAAGCGAATA
131 AAATGGA-ATCATGACAGTAAAGCGAATA
* * *
44236 CACCTGCAACAGCCAAATTCCGAATT-ATTCCAATCGAAAAAAGTTCGAAAAAAAGTTATAAACT
1 CACCTGCAACAACCAAATTCCGAATTCATTCCAACCGAAAAAAGCTCG-AAAAAAGTTATAAACT
* * * ** *
44300 TTCAAGTTTGTAGATTTACAATTCCTTCCAAGTTTATAG-TTGTGATGATTAATTAGTTCTCAAA
65 TTCAAGCTTGTAGATTTACAATTCATTCCAAGATTATAGCTT-TGATGATTAACAAGTACTCAAA
* *
44364 AGAAATGGAATCATGATAGTAAAGCTAATA
129 AGAAATGGAATCATGACAGTAAAGCGAATA
44394 CA
1 CA
44396 GTTTTTTTTC
Statistics
Matches: 140, Mismatches: 17, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
157 20 0.14
158 120 0.86
ACGTcount: A:0.40, C:0.17, G:0.15, T:0.28
Consensus pattern (158 bp):
CACCTGCAACAACCAAATTCCGAATTCATTCCAACCGAAAAAAGCTCGAAAAAAGTTATAAACTT
TCAAGCTTGTAGATTTACAATTCATTCCAAGATTATAGCTTTGATGATTAACAAGTACTCAAAAG
AAATGGAATCATGACAGTAAAGCGAATA
Found at i:46502 original size:15 final size:15
Alignment explanation
Indices: 46482--46530 Score: 71
Period size: 15 Copynumber: 3.3 Consensus size: 15
46472 TTTAGCTAGA
46482 CGGGCGGATGCGGGG
1 CGGGCGGATGCGGGG
*
46497 CGGGCGGATGCGAGG
1 CGGGCGGATGCGGGG
* *
46512 CGGACGGATGCGGGA
1 CGGGCGGATGCGGGG
46527 CGGG
1 CGGG
46531 TAATGACTCA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 29 1.00
ACGTcount: A:0.12, C:0.20, G:0.61, T:0.06
Consensus pattern (15 bp):
CGGGCGGATGCGGGG
Found at i:47531 original size:2 final size:2
Alignment explanation
Indices: 47524--47566 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
47514 ATATTATCAA
47524 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
47565 AT
1 AT
47567 GCAAGGGTAA
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 39 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:48578 original size:20 final size:21
Alignment explanation
Indices: 48555--48593 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
48545 TGATTCAACA
48555 CCGAAAA-ATAAAATAAAAAT
1 CCGAAAACATAAAATAAAAAT
*
48575 CCGAAAACATAAAGTAAAA
1 CCGAAAACATAAAATAAAA
48594 TCTTGAGAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.67, C:0.13, G:0.08, T:0.13
Consensus pattern (21 bp):
CCGAAAACATAAAATAAAAAT
Found at i:48915 original size:24 final size:24
Alignment explanation
Indices: 48888--48938 Score: 84
Period size: 24 Copynumber: 2.1 Consensus size: 24
48878 TTTATGTTCA
48888 TTCATTTATGTTCATTCATTTATG
1 TTCATTTATGTTCATTCATTTATG
* *
48912 TTCATTTATTTTCGTTCATTTATG
1 TTCATTTATGTTCATTCATTTATG
48936 TTC
1 TTC
48939 GAACAGAGGG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.18, C:0.14, G:0.08, T:0.61
Consensus pattern (24 bp):
TTCATTTATGTTCATTCATTTATG
Found at i:48934 original size:14 final size:14
Alignment explanation
Indices: 48878--48931 Score: 83
Period size: 14 Copynumber: 3.9 Consensus size: 14
48868 TATATGTTCG
48878 TTTATGTTCATTCA
1 TTTATGTTCATTCA
48892 TTTATGTTCATTCA
1 TTTATGTTCATTCA
*
48906 TTTATGTTCATTTA
1 TTTATGTTCATTCA
48920 TTT-TCGTTCATT
1 TTTAT-GTTCATT
48932 TATGTTCGAA
Statistics
Matches: 38, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
13 1 0.03
14 37 0.97
ACGTcount: A:0.19, C:0.13, G:0.07, T:0.61
Consensus pattern (14 bp):
TTTATGTTCATTCA
Found at i:48939 original size:14 final size:14
Alignment explanation
Indices: 48873--48939 Score: 70
Period size: 14 Copynumber: 5.1 Consensus size: 14
48863 TCGATTATAT
*
48873 GTTCGTTTATGTTC
1 GTTCATTTATGTTC
*
48887 ATTCATTTATGTTC
1 GTTCATTTATGTTC
*
48901 ATTCATTTA---T-
1 GTTCATTTATGTTC
*
48911 GTTCATTTATTTTC
1 GTTCATTTATGTTC
48925 GTTCATTTATGTTC
1 GTTCATTTATGTTC
48939 G
1 G
48940 AACAGAGGGC
Statistics
Matches: 45, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
10 8 0.18
11 1 0.02
13 1 0.02
14 35 0.78
ACGTcount: A:0.16, C:0.13, G:0.12, T:0.58
Consensus pattern (14 bp):
GTTCATTTATGTTC
Found at i:49224 original size:14 final size:14
Alignment explanation
Indices: 49196--49264 Score: 52
Period size: 14 Copynumber: 4.9 Consensus size: 14
49186 TGTTTTTTGT
*
49196 GTTTGTGTT-GTTC
1 GTTTATGTTCGTTC
49209 GTTTATGTTCGTTC
1 GTTTATGTTCGTTC
* ** *
49223 GTTTGTGTTTTTTGT
1 GTTTATGTTCGTT-C
49238 GTTTAT-TTACGTTC
1 GTTTATGTT-CGTTC
*
49252 ATTTATGTTCGTT
1 GTTTATGTTCGTT
49265 TATATTTAAA
Statistics
Matches: 42, Mismatches: 10, Indels: 7
0.71 0.17 0.12
Matches are distributed among these distances:
13 8 0.19
14 25 0.60
15 9 0.21
ACGTcount: A:0.07, C:0.09, G:0.22, T:0.62
Consensus pattern (14 bp):
GTTTATGTTCGTTC
Found at i:49250 original size:29 final size:33
Alignment explanation
Indices: 49191--49260 Score: 78
Period size: 29 Copynumber: 2.2 Consensus size: 33
49181 AAGTTTGTTT
*
49191 TTTGTGTTTGTGTTGTTCGTTTATGTTCGTTCG
1 TTTGTGTTTGTGTTGTTCGTTTATGTTCGTTCA
49224 TTTGTGTTT-T-TTG-T-GTTTAT-TTACGTTCA
1 TTTGTGTTTGTGTTGTTCGTTTATGTT-CGTTCA
*
49253 TTTATGTT
1 TTTGTGTT
49261 CGTTTATATT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
28 2 0.06
29 18 0.53
30 1 0.03
31 3 0.09
32 1 0.03
33 9 0.26
ACGTcount: A:0.07, C:0.07, G:0.21, T:0.64
Consensus pattern (33 bp):
TTTGTGTTTGTGTTGTTCGTTTATGTTCGTTCA
Found at i:59523 original size:2 final size:2
Alignment explanation
Indices: 59516--59578 Score: 126
Period size: 2 Copynumber: 31.5 Consensus size: 2
59506 ATGACTTCTC
59516 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
59558 AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT A
59579 GCTTGTATTC
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 61 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:60447 original size:64 final size:64
Alignment explanation
Indices: 60376--60556 Score: 190
Period size: 65 Copynumber: 2.8 Consensus size: 64
60366 TTGGACCCTT
* * *
60376 AGTGCATCGGTGCACTAAG-AGTGCATCGATGCATGAAGTGCATTCGATG-TTTCA-AAATAGCC
1 AGTGCATCGATGCA-T-AGCAGTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAA-AGCC
60438 TG
63 TG
* * *
60440 AGTGCATCGATGCATGGCTTGTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAAGGCCTG
1 AGTGCATCGATGCATAGC-AGTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAAAGCCTG
* * * *
60505 AGTGCATCGATGCATGGTATGCGCATCGATGCATAAAATGCA-TCTGATGTTT
1 AGTGCATCGATGCATAGCA-GTGCATCGATGCATCAAATGCATTC-GATGTTT
60557 AATTTATTCC
Statistics
Matches: 101, Mismatches: 10, Indels: 11
0.83 0.08 0.09
Matches are distributed among these distances:
62 1 0.01
63 1 0.01
64 42 0.42
65 54 0.53
66 3 0.03
ACGTcount: A:0.27, C:0.19, G:0.25, T:0.29
Consensus pattern (64 bp):
AGTGCATCGATGCATAGCAGTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAAAGCCTG
Found at i:60531 original size:65 final size:65
Alignment explanation
Indices: 60398--60556 Score: 218
Period size: 65 Copynumber: 2.5 Consensus size: 65
60388 CACTAAGAGT
* * *
60398 GCATCGATGCATGAAGTGCATTCGATG-TTTCAAAATAGCCTGAGTGCATCGATGCATGGCTTGT
1 GCATCGATGCATAAAATGCATTCGATGTTTTCAAAATAGCCTGAGTGCATCGATGCATGGCTTGC
* *
60462 GCATCGATGCATCAAATGCATTCGATGTTTTCATAAA-GGCCTGAGTGCATCGATGCATGG-TAT
1 GCATCGATGCATAAAATGCATTCGATGTTTTCA-AAATAGCCTGAGTGCATCGATGCATGGCT-T
60525 GC
64 GC
60527 GCATCGATGCATAAAATGCA-TCTGATGTTT
1 GCATCGATGCATAAAATGCATTC-GATGTTT
60557 AATTTATTCC
Statistics
Matches: 86, Mismatches: 5, Indels: 7
0.88 0.05 0.07
Matches are distributed among these distances:
64 28 0.33
65 55 0.64
66 3 0.03
ACGTcount: A:0.26, C:0.19, G:0.25, T:0.30
Consensus pattern (65 bp):
GCATCGATGCATAAAATGCATTCGATGTTTTCAAAATAGCCTGAGTGCATCGATGCATGGCTTGC
Found at i:62763 original size:25 final size:26
Alignment explanation
Indices: 62717--62766 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 26
62707 CAAAAACATT
62717 AATAAATTTCGAAAATAACAAAAAAA
1 AATAAATTTCGAAAATAACAAAAAAA
* * *
62743 AATAATTTTTGAAAAT-TCAAAAAA
1 AATAAATTTCGAAAATAACAAAAAA
62767 TTCTTGAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
25 7 0.33
26 14 0.67
ACGTcount: A:0.64, C:0.06, G:0.04, T:0.26
Consensus pattern (26 bp):
AATAAATTTCGAAAATAACAAAAAAA
Found at i:63226 original size:21 final size:22
Alignment explanation
Indices: 63167--63242 Score: 75
Period size: 21 Copynumber: 3.5 Consensus size: 22
63157 TGTCCTTGTA
63167 CATCGATGCACATTCAAGGAGTG
1 CATCGATGCACATTC-AGGAGTG
* *
63190 CATC-AGTGCACCTTCATG-GTG
1 CATCGA-TGCACATTCAGGAGTG
* * *
63211 TATCGATGCACATTCAAGAATG
1 CATCGATGCACATTCAGGAGTG
63233 CATCGATGCA
1 CATCGATGCA
63243 TTGTTAAGTG
Statistics
Matches: 43, Mismatches: 7, Indels: 7
0.75 0.12 0.12
Matches are distributed among these distances:
21 16 0.37
22 15 0.35
23 12 0.28
ACGTcount: A:0.29, C:0.24, G:0.22, T:0.25
Consensus pattern (22 bp):
CATCGATGCACATTCAGGAGTG
Done.