Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004779.1 Hibiscus syriacus cultivar Beakdansim tig00010778_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: 82068
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
Found at i:2637 original size:23 final size:23
Alignment explanation
Indices: 2611--2666 Score: 85
Period size: 23 Copynumber: 2.4 Consensus size: 23
2601 TAACATATGA
2611 GTAATAGGTAGCCCTTATATAAT
1 GTAATAGGTAGCCCTTATATAAT
* **
2634 GTAATAGGTATCGTTTATATAAT
1 GTAATAGGTAGCCCTTATATAAT
2657 GTAATAGGTA
1 GTAATAGGTA
2667 ATGGTTATAT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.36, C:0.07, G:0.20, T:0.38
Consensus pattern (23 bp):
GTAATAGGTAGCCCTTATATAAT
Found at i:2674 original size:23 final size:23
Alignment explanation
Indices: 2611--2676 Score: 80
Period size: 23 Copynumber: 2.9 Consensus size: 23
2601 TAACATATGA
* **
2611 GTAATAGGTAGCCCTTATATAAT
1 GTAATAGGTATCGGTTATATAAT
*
2634 GTAATAGGTATCGTTTATATAAT
1 GTAATAGGTATCGGTTATATAAT
2657 GTAATAGGTAAT-GGTTATAT
1 GTAATAGGT-ATCGGTTATAT
2677 TGTAAAGTGT
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
23 36 0.95
24 2 0.05
ACGTcount: A:0.35, C:0.06, G:0.20, T:0.39
Consensus pattern (23 bp):
GTAATAGGTATCGGTTATATAAT
Found at i:2715 original size:18 final size:19
Alignment explanation
Indices: 2680--2716 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
2670 GTTATATTGT
* *
2680 AAAGTGTCTATCCTTTTTA
1 AAAGTGTCCATACTTTTTA
2699 AAAGTGTCCATACTTTTT
1 AAAGTGTCCATACTTTTT
2717 TCACTGTGGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.27, C:0.16, G:0.11, T:0.46
Consensus pattern (19 bp):
AAAGTGTCCATACTTTTTA
Found at i:3060 original size:23 final size:23
Alignment explanation
Indices: 3029--3091 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
3019 ATAGGTAAAC
*
3029 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGCCCTT
* **
3052 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCCCTT
3075 ATATAATGTAATAGGTA
1 ATATAATGTAATAGGTA
3092 ATGGTTATAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.37, C:0.06, G:0.19, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCCCTT
Found at i:3099 original size:23 final size:23
Alignment explanation
Indices: 3029--3101 Score: 85
Period size: 23 Copynumber: 3.2 Consensus size: 23
3019 ATAGGTAAAC
* * **
3029 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTATCGGTT
*
3052 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTATCGGTT
3075 ATATAATGTAATAGGTAAT-GGTT
1 ATATAATGTAATAGGT-ATCGGTT
3098 ATAT
1 ATAT
3102 TGTAAAGTGT
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
23 42 0.95
24 2 0.05
ACGTcount: A:0.36, C:0.05, G:0.19, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTATCGGTT
Found at i:3412 original size:418 final size:424
Alignment explanation
Indices: 2508--3507 Score: 1823
Period size: 418 Copynumber: 2.4 Consensus size: 424
2498 AATTCGCAGT
2508 ACACTGTTAAAAAAATTGAAACAT-AATTACATAAGTTTTAAAAAAAGTATCGATCCTTTTTATA
1 ACACTGTT-AAAAAATTGAAACATAAATTACATAAGTTTTAAAAAAAGTATCGATCCTTTTTATA
2572 AAAAGTATGGACACTTTCAATATAATAGGT-AACATATGA-GTAATAGGTAGCCCTTATATAATG
65 AAAAGTATGGACACTTTCAATATAATAGGTAAACATATGATGTAATAGGTAGCCCTTATATAATG
2635 TAATAGGTATCGTTTATATAATGTAATAGGTAATGGTTATATTGTAAAGTGTCTATCCTTTTTAA
130 TAATAGGTATCGTTTATATAATGTAATAGGTAATGGTTATATTGTAAAGTGTCTATCCTTTTTAA
2700 AAGTGTCCATACTTTTTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAA
195 AAGTGTCCATACTTTTTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGT-AGTTTTAA
2765 GATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTACGTTACGGTATATATTATTAT
259 GATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTACGTTACGG-ATATATTATTAT
2830 TAAATTAAAAATTCTAAATAATATTTTAAAATATAAAAACAATCAAATAATTTTTTGTGCAAATG
323 TAAATTAAAAATTCTAAATAATATTTTAAAATATAAAAACAATCAAATAATTTTTTGTGCAAATG
2895 AAATTATTAAATCAATATTGTAGGTGGAAAACATGAA
388 AAATTATTAAATCAATATTGTAGGTGGAAAACATGAA
2932 ACACTGTTAAAAAATTGAAACATAAATTACATAAGTTTTAAAAAAAGTATCGATCC-TTTTATAA
1 ACACTGTTAAAAAATTGAAACATAAATTACATAAGTTTTAAAAAAAGTATCGATCCTTTTTATAA
2996 AAAGTATGGACACTTTCAATATAATAGGTAAACATATGATGTAATAGGTAGCCCTTATATAATGT
66 AAAGTATGGACACTTTCAATATAATAGGTAAACATATGATGTAATAGGTAGCCCTTATATAATGT
3061 AATAGGTATCGTTTATATAATGTAATAGGTAATGGTTATATTGTAAAGTGTCTATCCTTTTATAA
131 AATAGGTATCGTTTATATAATGTAATAGGTAATGGTTATATTGTAAAGTGTCTATCCTTTT-TAA
3126 AAGTGTCCATACTTTTTTCACTGTGGAAAACATTAATTTAAGGTTAT-TTTTGAGT-GTTTTAAG
195 AAGTGTCCATACTTTTTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTAGTTTTAAG
3189 ATATTAATTTAGTAATTAT-GGCGTCTAATGATTTA-TTTTTACGTTACGG-TATATTA-TATTA
260 ATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTACGTTACGGATATATTATTATTA
*
3250 AATTAAAAATTCTAAATAATATTTTATAAAATATAAAAACAATC-AATATTTTTTTGTGCAAATG
325 AATTAAAAATTCTAAATAATA-TTT-TAAAATATAAAAACAATCAAATAATTTTTTGTGCAAATG
3314 -AATTATTAAATCAATATTGTAGGTGGAAAACATGAA
388 AAATTATTAAATCAATATTGTAGGTGGAAAACATGAA
3350 ACACTGTTAAAAAATTG-AACATAAATTACATAAGTTTTAAAAAAAGTATCGATCCTTTTTATAA
1 ACACTGTTAAAAAATTGAAACATAAATTACATAAGTTTTAAAAAAAGTATCGATCCTTTTTATAA
3414 AAAGTATGGACACTTTCAATATAATAGGTAAACATATGATGTAATAGGTAGCCCTTATAT-ATGT
66 AAAGTATGGACACTTTCAATATAATAGGTAAACATATGATGTAATAGGTAGCCCTTATATAATGT
*
3478 AATATGTATCGTTTATAT-ATGTAATAGGTA
131 AATAGGTATCGTTTATATAATGTAATAGGTA
3508 TCTATCTCGC
Statistics
Matches: 567, Mismatches: 2, Indels: 22
0.96 0.00 0.04
Matches are distributed among these distances:
416 12 0.02
417 59 0.10
418 147 0.26
419 29 0.05
420 18 0.03
421 14 0.02
422 16 0.03
423 79 0.14
424 49 0.09
425 94 0.17
426 50 0.09
ACGTcount: A:0.40, C:0.08, G:0.13, T:0.39
Consensus pattern (424 bp):
ACACTGTTAAAAAATTGAAACATAAATTACATAAGTTTTAAAAAAAGTATCGATCCTTTTTATAA
AAAGTATGGACACTTTCAATATAATAGGTAAACATATGATGTAATAGGTAGCCCTTATATAATGT
AATAGGTATCGTTTATATAATGTAATAGGTAATGGTTATATTGTAAAGTGTCTATCCTTTTTAAA
AGTGTCCATACTTTTTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTAGTTTTAAGA
TATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTACGTTACGGATATATTATTATTAA
ATTAAAAATTCTAAATAATATTTTAAAATATAAAAACAATCAAATAATTTTTTGTGCAAATGAAA
TTATTAAATCAATATTGTAGGTGGAAAACATGAA
Found at i:3508 original size:22 final size:22
Alignment explanation
Indices: 3447--3509 Score: 81
Period size: 22 Copynumber: 2.8 Consensus size: 22
3437 ATAGGTAAAC
*
3447 ATATGATGTAATAGGTAGCCCTT
1 ATAT-ATGTAATAGGTATCCCTT
* **
3470 ATATATGTAATATGTATCGTTT
1 ATATATGTAATAGGTATCCCTT
3492 ATATATGTAATAGGTATC
1 ATATATGTAATAGGTATC
3510 TATCTCGCAT
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
22 31 0.89
23 4 0.11
ACGTcount: A:0.33, C:0.08, G:0.17, T:0.41
Consensus pattern (22 bp):
ATATATGTAATAGGTATCCCTT
Found at i:3733 original size:18 final size:18
Alignment explanation
Indices: 3712--3748 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
3702 GTAATTGGAG
3712 TTTGAATTTAAATTTCAA
1 TTTGAATTTAAATTTCAA
* *
3730 TTTGAGTTTGAATTTCAA
1 TTTGAATTTAAATTTCAA
3748 T
1 T
3749 ATATATTCGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.32, C:0.05, G:0.11, T:0.51
Consensus pattern (18 bp):
TTTGAATTTAAATTTCAA
Found at i:11075 original size:24 final size:24
Alignment explanation
Indices: 11048--11099 Score: 104
Period size: 24 Copynumber: 2.2 Consensus size: 24
11038 TCAAATAATT
11048 AACAAGTAAATGTTCTCAATTTAG
1 AACAAGTAAATGTTCTCAATTTAG
11072 AACAAGTAAATGTTCTCAATTTAG
1 AACAAGTAAATGTTCTCAATTTAG
11096 AACA
1 AACA
11100 CTCATCACAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.44, C:0.13, G:0.12, T:0.31
Consensus pattern (24 bp):
AACAAGTAAATGTTCTCAATTTAG
Found at i:26423 original size:35 final size:36
Alignment explanation
Indices: 26377--26457 Score: 119
Period size: 35 Copynumber: 2.3 Consensus size: 36
26367 AACACAGCCA
* * *
26377 TCAATTACATTCTAAACCCCAAATTTC-AAAATATT
1 TCAATTACATTCTAAACACCAAATTCCAAAAATAAT
*
26412 TCAATTACATTCTAAACAGCAAATTCCAAAAATAAT
1 TCAATTACATTCTAAACACCAAATTCCAAAAATAAT
26448 TCAATTACAT
1 TCAATTACAT
26458 GACCAACCCC
Statistics
Matches: 41, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
35 24 0.59
36 17 0.41
ACGTcount: A:0.46, C:0.21, G:0.01, T:0.32
Consensus pattern (36 bp):
TCAATTACATTCTAAACACCAAATTCCAAAAATAAT
Found at i:26471 original size:36 final size:35
Alignment explanation
Indices: 26377--26473 Score: 106
Period size: 36 Copynumber: 2.7 Consensus size: 35
26367 AACACAGCCA
* * *
26377 TCAATTACATTCTAAACCCCAAATTTCAAAATATT
1 TCAATTACATACTAAACCCCAAATTCCAAAATAAT
* **
26412 TCAATTACATTCTAAACAGCAAATTCCAAAAATAAT
1 TCAATTACATACTAAACCCCAAATTCC-AAAATAAT
*
26448 TCAATTACATGAC-CAACCCCAAATTC
1 TCAATTACAT-ACTAAACCCCAAATTC
26474 ATAATCCATT
Statistics
Matches: 52, Mismatches: 8, Indels: 3
0.83 0.13 0.05
Matches are distributed among these distances:
35 24 0.46
36 27 0.52
37 1 0.02
ACGTcount: A:0.44, C:0.25, G:0.02, T:0.29
Consensus pattern (35 bp):
TCAATTACATACTAAACCCCAAATTCCAAAATAAT
Found at i:27220 original size:148 final size:148
Alignment explanation
Indices: 26948--27234 Score: 468
Period size: 148 Copynumber: 1.9 Consensus size: 148
26938 AAACTATTTG
* *
26948 ATTAGAATCAAATAATATTATAGTATAATAAATATTTATAATTAAATTTAAACAGAAACTCAAAA
1 ATTAGAATAAAATAATATTATAATATAATAAATATTTATAATTAAATTTAAACAGAAACTCAAAA
* *** *
27013 ATTCAATTCAATTCGACTTGATTTAAATTTTATAAATTCAAATCGAAATTTTTTTGAGTCAACTA
66 ATTCAATTCAATTCGACTTGATTTAAATTTTATAAACTCAAATCGAAATAAATTCGAGTCAACTA
27078 TTTTATAAACTAAACTGA
131 TTTTATAAACTAAACTGA
* * *
27096 ATTAGAATAAAATAATATTATAATATGATAAATATTTATAATTAAATTTAAATAGAAACTCGAAA
1 ATTAGAATAAAATAATATTATAATATAATAAATATTTATAATTAAATTTAAACAGAAACTCAAAA
27161 ATTCAATTCAATTCGACTTGATTTAAATTTTATAAACTCAAATCGGAAA-AAATTCGAGTCAACT
66 ATTCAATTCAATTCGACTTGATTTAAATTTTATAAACTCAAATC-GAAATAAATTCGAGTCAACT
27225 ATTTTATAAA
130 ATTTTATAAA
27235 TTGAATTGAG
Statistics
Matches: 128, Mismatches: 10, Indels: 2
0.91 0.07 0.01
Matches are distributed among these distances:
148 124 0.97
149 4 0.03
ACGTcount: A:0.47, C:0.09, G:0.07, T:0.37
Consensus pattern (148 bp):
ATTAGAATAAAATAATATTATAATATAATAAATATTTATAATTAAATTTAAACAGAAACTCAAAA
ATTCAATTCAATTCGACTTGATTTAAATTTTATAAACTCAAATCGAAATAAATTCGAGTCAACTA
TTTTATAAACTAAACTGA
Found at i:27437 original size:35 final size:35
Alignment explanation
Indices: 27392--27492 Score: 114
Period size: 35 Copynumber: 2.9 Consensus size: 35
27382 TTGAGATTTG
** * **
27392 ATTTT-GAATTTGGGGTTGGGCATGTAATTGAAGT
1 ATTTTGGAATTTGGGGTTTAGAATGTAATTGAAAC
** *
27426 ATTTTGGAATTTGATGTTTAGAATGTAATTAAAAC
1 ATTTTGGAATTTGGGGTTTAGAATGTAATTGAAAC
*
27461 ATTTTGGATTTTGGGGTTTAGAATGTAATTGA
1 ATTTTGGAATTTGGGGTTTAGAATGTAATTGA
27493 TGATTGTGTT
Statistics
Matches: 54, Mismatches: 12, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
34 5 0.09
35 49 0.91
ACGTcount: A:0.29, C:0.02, G:0.26, T:0.44
Consensus pattern (35 bp):
ATTTTGGAATTTGGGGTTTAGAATGTAATTGAAAC
Found at i:33267 original size:21 final size:21
Alignment explanation
Indices: 33241--33285 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
33231 GATTTCTGGG
* *
33241 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
33262 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
33283 CAA
1 CAA
33286 ACGACATAAT
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:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:34422 original size:31 final size:31
Alignment explanation
Indices: 34364--34441 Score: 79
Period size: 31 Copynumber: 2.5 Consensus size: 31
34354 AGAGTCGAGG
*
34364 GTTTACCTATGTCTTTCGAGACATATGGAAA
1 GTTTACCTAGGTCTTTCGAGACATATGGAAA
* * *
34395 GTTTACCTAGGT-TCTTCGGGACCTATGGACA
1 GTTTACCTAGGTCT-TTCGAGACATATGGAAA
*
34426 G-TTACCGAGGATCTTT
1 GTTTACCTAGG-TCTTT
34442 ATGACCTCTG
Statistics
Matches: 39, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
30 9 0.23
31 29 0.74
32 1 0.03
ACGTcount: A:0.23, C:0.19, G:0.23, T:0.35
Consensus pattern (31 bp):
GTTTACCTAGGTCTTTCGAGACATATGGAAA
Found at i:34448 original size:30 final size:30
Alignment explanation
Indices: 34414--34632 Score: 386
Period size: 30 Copynumber: 7.3 Consensus size: 30
34404 GGTTCTTCGG
*
34414 GACCTATGGACAGTTACCGAGGATCTTTAT
1 GACCTCTGGACAGTTACCGAGGATCTTTAT
*
34444 GACCTCTGGACAGTTACCGATGATCTTTAT
1 GACCTCTGGACAGTTACCGAGGATCTTTAT
34474 GACCTCTGGACAGTTACCGAGGATCTTTAT
1 GACCTCTGGACAGTTACCGAGGATCTTTAT
34504 GACCTCTGGACAGTTACCGAGGATCTTTAT
1 GACCTCTGGACAGTTACCGAGGATCTTTAT
34534 GACCTCTGGACAGTTACCGAGGATCTTTAT
1 GACCTCTGGACAGTTACCGAGGATCTTTAT
34564 GACCTCTGGACAGTTACCGAGGATCTTTAT
1 GACCTCTGGACAGTTACCGAGGATCTTTAT
* * *
34594 GACCTCTGGATAGTTACCG-GGGTCTTTGT
1 GACCTCTGGACAGTTACCGAGGATCTTTAT
34623 GACCTCTGGA
1 GACCTCTGGA
34633 TAGGTCCTTC
Statistics
Matches: 183, Mismatches: 6, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
29 18 0.10
30 165 0.90
ACGTcount: A:0.22, C:0.23, G:0.24, T:0.31
Consensus pattern (30 bp):
GACCTCTGGACAGTTACCGAGGATCTTTAT
Found at i:37989 original size:14 final size:13
Alignment explanation
Indices: 37902--37986 Score: 50
Period size: 13 Copynumber: 6.2 Consensus size: 13
37892 TTATTATTTA
37902 TTTATTTTATTAT
1 TTTATTTTATTAT
37915 TTTATATCCTTA-TAT
1 TTTAT-T--TTATTAT
** *
37930 TCCATTTTAAACTAT
1 TTTATTTT--ATTAT
*
37945 TTATATTTAATTA-
1 TT-TATTTTATTAT
37958 TTTATTTTATTAT
1 TTTATTTTATTAT
37971 TTTATTCTTA-TAT
1 TTTATT-TTATTAT
37984 TTT
1 TTT
37987 TATCTTTATC
Statistics
Matches: 56, Mismatches: 7, Indels: 18
0.69 0.09 0.22
Matches are distributed among these distances:
12 11 0.20
13 19 0.34
14 9 0.16
15 10 0.18
16 7 0.12
ACGTcount: A:0.27, C:0.07, G:0.00, T:0.66
Consensus pattern (13 bp):
TTTATTTTATTAT
Found at i:46496 original size:29 final size:29
Alignment explanation
Indices: 46425--46483 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
46415 ATTTTCACCT
46425 AACTAAATTGATGTAAGCAATGACATCAA
1 AACTAAATTGATGTAAGCAATGACATCAA
*
46454 AACTAAATTGATGTAAGTAATGACATCAA
1 AACTAAATTGATGTAAGCAATGACATCAA
46483 A
1 A
46484 TTAATTTAGA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.49, C:0.12, G:0.14, T:0.25
Consensus pattern (29 bp):
AACTAAATTGATGTAAGCAATGACATCAA
Found at i:53496 original size:5 final size:5
Alignment explanation
Indices: 53486--53511 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
53476 TATTATTATT
53486 TCGGG TCGGG TCGGG TCGGG TCGGG T
1 TCGGG TCGGG TCGGG TCGGG TCGGG T
53512 TTCTAAGTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.00, C:0.19, G:0.58, T:0.23
Consensus pattern (5 bp):
TCGGG
Found at i:64735 original size:2 final size:2
Alignment explanation
Indices: 64725--64771 Score: 85
Period size: 2 Copynumber: 23.0 Consensus size: 2
64715 TATGAAAATA
64725 AT AT GAT 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
64768 AT AT
1 AT AT
64772 GTTGTATATG
Statistics
Matches: 44, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 42 0.95
3 2 0.05
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:66341 original size:23 final size:25
Alignment explanation
Indices: 66297--66342 Score: 62
Period size: 23 Copynumber: 1.9 Consensus size: 25
66287 ATTTGGCCGT
66297 TTTCTATTTTGAATAAAATTAATGA
1 TTTCTATTTTGAATAAAATTAATGA
66322 TTTCT-TTTT-AA-AAAAGTTAAT
1 TTTCTATTTTGAATAAAA-TTAAT
66343 ATCAATATTC
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
22 4 0.20
23 7 0.35
24 4 0.20
25 5 0.25
ACGTcount: A:0.39, C:0.04, G:0.07, T:0.50
Consensus pattern (25 bp):
TTTCTATTTTGAATAAAATTAATGA
Found at i:66913 original size:12 final size:13
Alignment explanation
Indices: 66888--66916 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
66878 ATATTTATTT
66888 ATATAAAAATATA
1 ATATAAAAATATA
66901 ATATAAAAA-ATA
1 ATATAAAAATATA
66913 ATAT
1 ATAT
66917 TATAATTTCG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 7 0.44
13 9 0.56
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (13 bp):
ATATAAAAATATA
Found at i:78351 original size:3 final size:3
Alignment explanation
Indices: 78345--78435 Score: 136
Period size: 3 Copynumber: 31.3 Consensus size: 3
78335 CATACAACAA
78345 ATT ATT ATT ATT A-T ATT ATT ATT ATT ATT -TT ATT ATT ATT ATT ATAT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT-T
*
78392 ACT ATT A-T ATT ATT ATT ATT A-T ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
78436 GTTTTGGCCC
Statistics
Matches: 81, Mismatches: 2, Indels: 10
0.87 0.02 0.11
Matches are distributed among these distances:
2 8 0.10
3 71 0.88
4 2 0.02
ACGTcount: A:0.35, C:0.01, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:78364 original size:14 final size:14
Alignment explanation
Indices: 78345--78435 Score: 132
Period size: 14 Copynumber: 6.5 Consensus size: 14
78335 CATACAACAA
78345 ATTATTATTATTAT
1 ATTATTATTATTAT
78359 ATTATTATTATTAT
1 ATTATTATTATTAT
*
78373 TTTATTATTA-T-T
1 ATTATTATTATTAT
*
78385 ATTATATACTATTAT
1 ATTAT-TATTATTAT
78400 ATTATTATTATTAT
1 ATTATTATTATTAT
78414 ATTATTATTATTATT
1 ATTATTATTATTA-T
78429 ATTATTA
1 ATTATTA
78436 GTTTTGGCCC
Statistics
Matches: 69, Mismatches: 4, Indels: 7
0.86 0.05 0.09
Matches are distributed among these distances:
12 5 0.07
13 5 0.07
14 45 0.65
15 14 0.20
ACGTcount: A:0.35, C:0.01, G:0.00, T:0.64
Consensus pattern (14 bp):
ATTATTATTATTAT
Found at i:80290 original size:2 final size:2
Alignment explanation
Indices: 80283--80324 Score: 66
Period size: 2 Copynumber: 21.0 Consensus size: 2
80273 AACTTGAGCA
* *
80283 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT GT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
80325 GTATTGCCTC
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (2 bp):
AT
Done.