Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000108.1 Hibiscus syriacus cultivar Beakdansim tig00000192_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: 112330
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:208 original size:17 final size:16
Alignment explanation
Indices: 173--219 Score: 58
Period size: 17 Copynumber: 2.8 Consensus size: 16
163 AATATGAATT
*
173 AGATTCTAATTCCTGAC
1 AGATTC-AATTCCTCAC
190 AGATTCAATTCCTTCAC
1 AGATTCAATTCC-TCAC
207 AGATTTCAATTCC
1 AGA-TTCAATTCC
220 CTCATAAACA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
16 6 0.22
17 12 0.44
18 9 0.33
ACGTcount: A:0.30, C:0.26, G:0.09, T:0.36
Consensus pattern (16 bp):
AGATTCAATTCCTCAC
Found at i:489 original size:20 final size:21
Alignment explanation
Indices: 465--524 Score: 79
Period size: 20 Copynumber: 3.0 Consensus size: 21
455 TCTGACTATT
465 TAATTATTGTATATTTTAATA
1 TAATTATTGTATATTTTAATA
* *
486 -AATTATGGTATTTTTTAATA
1 TAATTATTGTATATTTTAATA
*
506 TAATTATTG-ATGTTTTAAT
1 TAATTATTGTATATTTTAAT
525 TTTATTTAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
20 27 0.79
21 7 0.21
ACGTcount: A:0.35, C:0.00, G:0.08, T:0.57
Consensus pattern (21 bp):
TAATTATTGTATATTTTAATA
Found at i:2728 original size:15 final size:16
Alignment explanation
Indices: 2704--2737 Score: 61
Period size: 15 Copynumber: 2.2 Consensus size: 16
2694 ATTAAATAAA
2704 TATATATTTAATCAAC
1 TATATATTTAATCAAC
2720 TATAT-TTTAATCAAC
1 TATATATTTAATCAAC
2735 TAT
1 TAT
2738 TTCTTAAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 13 0.72
16 5 0.28
ACGTcount: A:0.41, C:0.12, G:0.00, T:0.47
Consensus pattern (16 bp):
TATATATTTAATCAAC
Found at i:12175 original size:28 final size:28
Alignment explanation
Indices: 12135--12188 Score: 99
Period size: 28 Copynumber: 1.9 Consensus size: 28
12125 TTTACATCTA
12135 GTAGTTCACTTGATCACTATATTCTGGT
1 GTAGTTCACTTGATCACTATATTCTGGT
*
12163 GTAGTTCACTTGATCATTATATTCTG
1 GTAGTTCACTTGATCACTATATTCTG
12189 TCCAATTAAC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.22, C:0.17, G:0.17, T:0.44
Consensus pattern (28 bp):
GTAGTTCACTTGATCACTATATTCTGGT
Found at i:22516 original size:64 final size:63
Alignment explanation
Indices: 22443--22605 Score: 170
Period size: 64 Copynumber: 2.5 Consensus size: 63
22433 ATTGTTCAAG
* * *
22443 GTGTTTCGATGCATATGAGGTGTATCGATGCACTCCT-TTAAAATAAAAACATCGAATGTCA-TT
1 GTGTATCGATGCATA-GA-GTGAATCGATGCAC-CCTCTTAAAATAAAAACATCGAATGGCATTT
22506 A
63 A
* * *
22507 GTGTATCGATGCACAAGTAGTGAATCGATGCACCCTCTTAAAATACAAACATCGAATGGGATTTA
1 GTGTATCGATGCA-TAG-AGTGAATCGATGCACCCTCTTAAAATAAAAACATCGAATGGCATTTA
* *
22572 -TGTACCGATGCATAGATTGTGCATCGATGCACCC
1 GTGTATCGATGCATAGA--GTGAATCGATGCACCC
22606 GTCAAGGTAT
Statistics
Matches: 84, Mismatches: 9, Indels: 12
0.80 0.09 0.11
Matches are distributed among these distances:
62 1 0.01
63 5 0.06
64 73 0.87
65 5 0.06
ACGTcount: A:0.32, C:0.19, G:0.20, T:0.29
Consensus pattern (63 bp):
GTGTATCGATGCATAGAGTGAATCGATGCACCCTCTTAAAATAAAAACATCGAATGGCATTTA
Found at i:23200 original size:18 final size:18
Alignment explanation
Indices: 23177--23245 Score: 75
Period size: 18 Copynumber: 3.7 Consensus size: 18
23167 AGGGATTATC
*
23177 AGTGGTCCTTCGGGACAT
1 AGTGGTCCTTCGGAACAT
* *
23195 AGTGGTTCTTCAGAACAAT
1 AGTGGTCCTTCGGAAC-AT
*
23214 CAATGGTCCTTCGGAACAT
1 -AGTGGTCCTTCGGAACAT
*
23233 AGTGGTCATTCGG
1 AGTGGTCCTTCGG
23246 GACAAATATT
Statistics
Matches: 41, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
18 24 0.59
19 4 0.10
20 13 0.32
ACGTcount: A:0.23, C:0.20, G:0.28, T:0.29
Consensus pattern (18 bp):
AGTGGTCCTTCGGAACAT
Found at i:28255 original size:64 final size:64
Alignment explanation
Indices: 28170--28330 Score: 186
Period size: 64 Copynumber: 2.5 Consensus size: 64
28160 TTGTTTAAGG
* * * *
28170 TGCATCGATTCACA-TGCAGTGCATCGATGCAT-TAATTTAAAAAGAAAACATCGAATAGGATTT
1 TGCATCGATGCATAGTGTAGTGCATCGATGCATCCAA-TTAAAAA-AAAACATCGAATAGGATTT
28233 A
64 A
* * *
28234 TGCATCGATGCATAAG-G-AGTGCATCGATGCATCCCCATTAAATACAAACATCGAATAGGATTT
1 TGCATCGATGCAT-AGTGTAGTGCATCGATGCAT-CCAATTAAAAAAAAACATCGAATAGGATTT
28297 A
64 A
*
28298 TGCATCGATGCATGGTGTAGTGCATCGATGCAT
1 TGCATCGATGCATAGTGTAGTGCATCGATGCAT
28331 ACCTTCATTA
Statistics
Matches: 84, Mismatches: 7, Indels: 11
0.82 0.07 0.11
Matches are distributed among these distances:
63 1 0.01
64 59 0.70
65 23 0.27
66 1 0.01
ACGTcount: A:0.34, C:0.18, G:0.20, T:0.27
Consensus pattern (64 bp):
TGCATCGATGCATAGTGTAGTGCATCGATGCATCCAATTAAAAAAAAACATCGAATAGGATTTA
Found at i:29543 original size:31 final size:31
Alignment explanation
Indices: 29505--29578 Score: 87
Period size: 31 Copynumber: 2.4 Consensus size: 31
29495 TCGAGGGTTT
**
29505 TACCTATG-TCTTTCGAGACATATAGACAGTA
1 TACCTATGTTCTAACGA-ACATATAGACAGTA
* *
29536 TACCTATGTTCTAACGAACATATGGACAGTT
1 TACCTATGTTCTAACGAACATATAGACAGTA
*
29567 TACCTAGGTTCT
1 TACCTATGTTCT
29579 TTGGGACCTA
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
31 31 0.84
32 6 0.16
ACGTcount: A:0.30, C:0.20, G:0.16, T:0.34
Consensus pattern (31 bp):
TACCTATGTTCTAACGAACATATAGACAGTA
Found at i:29617 original size:30 final size:31
Alignment explanation
Indices: 29556--29617 Score: 90
Period size: 30 Copynumber: 2.0 Consensus size: 31
29546 CTAACGAACA
*
29556 TATGGACAGTTTACCTAGGTTCTTTGGGACC
1 TATGGACAGTTTACCTAGGTTCTTTAGGACC
* *
29587 TATGGACAG-TTGCCTAGGTTCTTTATGACC
1 TATGGACAGTTTACCTAGGTTCTTTAGGACC
29617 T
1 T
29618 CTAGATAGTT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
30 19 0.68
31 9 0.32
ACGTcount: A:0.19, C:0.19, G:0.24, T:0.37
Consensus pattern (31 bp):
TATGGACAGTTTACCTAGGTTCTTTAGGACC
Found at i:32788 original size:18 final size:18
Alignment explanation
Indices: 32765--32799 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
32755 AGGGATTATC
32765 AGTGGTCCTTCGGGACAT
1 AGTGGTCCTTCGGGACAT
32783 AGTGGTCCTTCGGGACA
1 AGTGGTCCTTCGGGACA
32800 AATATTCAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.17, C:0.23, G:0.34, T:0.26
Consensus pattern (18 bp):
AGTGGTCCTTCGGGACAT
Found at i:35257 original size:21 final size:21
Alignment explanation
Indices: 35205--35259 Score: 69
Period size: 21 Copynumber: 2.6 Consensus size: 21
35195 ATTTCCACAA
35205 TATCAATACTAGAGCCTCTAG
1 TATCAATACTAGAGCCTCTAG
*
35226 TATTGAA-ACTAGAGCC-CTCAG
1 TA-TCAATACTAGAGCCTCT-AG
35247 TATCAATACTAGA
1 TATCAATACTAGA
35260 TGAGCGGTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
20 5 0.17
21 21 0.72
22 3 0.10
ACGTcount: A:0.36, C:0.22, G:0.15, T:0.27
Consensus pattern (21 bp):
TATCAATACTAGAGCCTCTAG
Found at i:35878 original size:24 final size:24
Alignment explanation
Indices: 35850--35912 Score: 99
Period size: 24 Copynumber: 2.6 Consensus size: 24
35840 ACTTGCTATG
35850 AAAGAGGGGGAAAGAAGAGAGAAA
1 AAAGAGGGGGAAAGAAGAGAGAAA
*
35874 AAAGAGGGGGAAAGAATAGAGAAA
1 AAAGAGGGGGAAAGAAGAGAGAAA
* *
35898 AAAGATGAGGAAAGA
1 AAAGAGGGGGAAAGA
35913 GGATAAGAAG
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 36 1.00
ACGTcount: A:0.59, C:0.00, G:0.38, T:0.03
Consensus pattern (24 bp):
AAAGAGGGGGAAAGAAGAGAGAAA
Found at i:44369 original size:31 final size:31
Alignment explanation
Indices: 44287--44369 Score: 96
Period size: 31 Copynumber: 2.6 Consensus size: 31
44277 AAGTACTTAA
*
44287 AATATTTTTTTATCAAAATAAATTTATAAAGT
1 AATA-TTTTTTATCAAAATAGATTTATAAAGT
* **
44319 TATATTTTTCCTCAAAATAGATATT-TAAAGT
1 AATATTTTTTATCAAAATAGAT-TTATAAAGT
*
44350 AATATTTTTTGTCAAAATAG
1 AATATTTTTTATCAAAATAG
44370 GTACCCAAAA
Statistics
Matches: 43, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
31 38 0.88
32 5 0.12
ACGTcount: A:0.42, C:0.06, G:0.06, T:0.46
Consensus pattern (31 bp):
AATATTTTTTATCAAAATAGATTTATAAAGT
Found at i:56654 original size:85 final size:85
Alignment explanation
Indices: 56511--56675 Score: 305
Period size: 85 Copynumber: 1.9 Consensus size: 85
56501 AGTTAAAAAA
*
56511 ATAAGTGCATTTGGTCCTTTATATTATCAATCTGTTTGGTTTTAATCTATTAGTCATTGACTTTC
1 ATAAGTGCATTTGGTCCTTTATATTATCAATCTGTTTGGTTTTAATCTATCAGTCATTGACTTTC
56576 GTTAACACCTTAATAAGAGC
66 GTTAACACCTTAATAAGAGC
56596 ATAAGTGCATTTGGTCCTTTATATTATCAAT-TCGTTTGGTTTTAATCTATCAGTCATTGACTTT
1 ATAAGTGCATTTGGTCCTTTATATTATCAATCT-GTTTGGTTTTAATCTATCAGTCATTGACTTT
56660 CGTTAACACCTTAATA
65 CGTTAACACCTTAATA
56676 GGAGTATTAT
Statistics
Matches: 78, Mismatches: 1, Indels: 2
0.96 0.01 0.02
Matches are distributed among these distances:
84 1 0.01
85 77 0.99
ACGTcount: A:0.27, C:0.16, G:0.13, T:0.44
Consensus pattern (85 bp):
ATAAGTGCATTTGGTCCTTTATATTATCAATCTGTTTGGTTTTAATCTATCAGTCATTGACTTTC
GTTAACACCTTAATAAGAGC
Found at i:56861 original size:2 final size:2
Alignment explanation
Indices: 56854--56891 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
56844 TATTTCAAAG
56854 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
56892 AGTTTTTAGA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:61532 original size:17 final size:16
Alignment explanation
Indices: 61510--61562 Score: 63
Period size: 17 Copynumber: 3.2 Consensus size: 16
61500 GATTTCTCGG
61510 CCCGGATGTTCCGGGTA
1 CCCGGATGTT-CGGGTA
*
61527 CCCGGATTTTACGGGTA
1 CCCGGATGTT-CGGGTA
*
61544 CCCGTATG-TCGGGTA
1 CCCGGATGTTCGGGTA
61559 CCCG
1 CCCG
61563 AATACTCGGA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
15 10 0.31
16 1 0.03
17 21 0.66
ACGTcount: A:0.13, C:0.30, G:0.32, T:0.25
Consensus pattern (16 bp):
CCCGGATGTTCGGGTA
Found at i:65639 original size:172 final size:172
Alignment explanation
Indices: 65353--65696 Score: 652
Period size: 172 Copynumber: 2.0 Consensus size: 172
65343 ATATCCTTGT
* *
65353 TGTTGAAACATTTTGATATTTTGATATAACAAATTAAGTTAAATGGATTTTAAGATTTTCCAAAT
1 TGTTGAAACATTTTAATATTTCGATATAACAAATTAAGTTAAATGGATTTTAAGATTTTCCAAAT
*
65418 GATTTTCTAAGTATATTCGATATAACTATTCGAATATCAAAACATTACTCCAAATATTTCAAAAA
66 GATTTTCTAAGAATATTCGATATAACTATTCGAATATCAAAACATTACTCCAAATATTTCAAAAA
65483 TCATTTTTAATCCTTACTTAAGTGTAAAATTAAGTTTTAATC
131 TCATTTTTAATCCTTACTTAAGTGTAAAATTAAGTTTTAATC
65525 TGTTGAAACATTTTAATATTTCGATATAACAAATTAAGTTAAATGGATTTTAAGATTTTCCAAAT
1 TGTTGAAACATTTTAATATTTCGATATAACAAATTAAGTTAAATGGATTTTAAGATTTTCCAAAT
65590 GATTTTCTAAGAATATTCGATATAACTATTCGAATATCAAAACATTACTCCAAATATTTCAAAAA
66 GATTTTCTAAGAATATTCGATATAACTATTCGAATATCAAAACATTACTCCAAATATTTCAAAAA
*
65655 TCATTTTTGATCCTTACTTAAGTGTAAAATTAAGTTTTAATC
131 TCATTTTTAATCCTTACTTAAGTGTAAAATTAAGTTTTAATC
65697 ATAAAACAAT
Statistics
Matches: 168, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
172 168 1.00
ACGTcount: A:0.39, C:0.11, G:0.09, T:0.41
Consensus pattern (172 bp):
TGTTGAAACATTTTAATATTTCGATATAACAAATTAAGTTAAATGGATTTTAAGATTTTCCAAAT
GATTTTCTAAGAATATTCGATATAACTATTCGAATATCAAAACATTACTCCAAATATTTCAAAAA
TCATTTTTAATCCTTACTTAAGTGTAAAATTAAGTTTTAATC
Found at i:71716 original size:21 final size:21
Alignment explanation
Indices: 71690--71729 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
71680 CCCCCTTTGA
*
71690 AGGGGAACCGATTCCCCCCAC
1 AGGGGAACCGATACCCCCCAC
*
71711 AGGGGAATCGATACCCCCC
1 AGGGGAACCGATACCCCCC
71730 TGGGGTTCTG
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:0.25, C:0.40, G:0.25, T:0.10
Consensus pattern (21 bp):
AGGGGAACCGATACCCCCCAC
Found at i:81046 original size:21 final size:21
Alignment explanation
Indices: 81020--81082 Score: 63
Period size: 21 Copynumber: 2.9 Consensus size: 21
81010 TTTTGGTGCA
*
81020 GAGGGAATCGATCCCCCCCCT
1 GAGGGAACCGATCCCCCCCCT
* **
81041 GAGGGAACCGATTCCCCCTTT
1 GAGGGAACCGATCCCCCCCCT
*
81062 GAAGGGGAACCGATTCCCCCC
1 G-A-GGGAACCGATCCCCCCC
81083 ACAGGGGAAT
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
21 18 0.51
22 1 0.03
23 16 0.46
ACGTcount: A:0.21, C:0.38, G:0.25, T:0.16
Consensus pattern (21 bp):
GAGGGAACCGATCCCCCCCCT
Found at i:81090 original size:21 final size:21
Alignment explanation
Indices: 81064--81103 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
81054 CCCCCTTTGA
*
81064 AGGGGAACCGATTCCCCCCAC
1 AGGGGAACCGATACCCCCCAC
*
81085 AGGGGAATCGATACCCCCC
1 AGGGGAACCGATACCCCCC
81104 TGGGGTTCTG
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:0.25, C:0.40, G:0.25, T:0.10
Consensus pattern (21 bp):
AGGGGAACCGATACCCCCCAC
Found at i:81513 original size:21 final size:21
Alignment explanation
Indices: 81465--81517 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
81455 AAAACACAAG
* *
81465 AATTTTTCAAAAAAAATTTTT
1 AATTTTTCAAAAAAAAATGTT
*
81486 AAATTTTCGAAAAAAAAATGTT
1 AATTTTTC-AAAAAAAAATGTT
81508 -ATTTTTCAAA
1 AATTTTTCAAA
81518 TTATTGTGTT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
20 3 0.11
21 13 0.48
22 11 0.41
ACGTcount: A:0.49, C:0.06, G:0.04, T:0.42
Consensus pattern (21 bp):
AATTTTTCAAAAAAAAATGTT
Found at i:83064 original size:9 final size:8
Alignment explanation
Indices: 83042--83092 Score: 52
Period size: 9 Copynumber: 6.2 Consensus size: 8
83032 TGTTTCAACA
83042 TTTTGGAT
1 TTTTGGAT
83050 ATTTTGGAT
1 -TTTTGGAT
83059 TGTTT-GAT
1 T-TTTGGAT
83067 TTTGTGGAT
1 TTT-TGGAT
*
83076 TGTTGGA-
1 TTTTGGAT
83083 TTTTGGAT
1 TTTTGGAT
83091 TT
1 TT
83093 ATGAATGGTG
Statistics
Matches: 36, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
7 8 0.22
8 12 0.33
9 16 0.44
ACGTcount: A:0.14, C:0.00, G:0.27, T:0.59
Consensus pattern (8 bp):
TTTTGGAT
Found at i:83076 original size:17 final size:17
Alignment explanation
Indices: 83044--83087 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
83034 TTTCAACATT
83044 TTGGATATTT-TGGATTG
1 TTGGAT-TTTGTGGATTG
*
83061 TTTGATTTTGTGGATTG
1 TTGGATTTTGTGGATTG
83078 TTGGATTTTG
1 TTGGATTTTG
83088 GATTTATGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 3 0.12
17 21 0.88
ACGTcount: A:0.14, C:0.00, G:0.30, T:0.57
Consensus pattern (17 bp):
TTGGATTTTGTGGATTG
Found at i:83822 original size:75 final size:74
Alignment explanation
Indices: 83692--83898 Score: 236
Period size: 75 Copynumber: 2.8 Consensus size: 74
83682 CAAAGCCAAA
* * * * ***
83692 AATTCCAGATTGCTCAGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCTGAATGGTT
1 AATTCCAGAATGCTCGGAGGGAACCGATT-CCCCCATAGGAGGAACCGATCCCCCCTAAACAATT
83757 TGGCTCCGAG
65 TGGCTCCGAG
* *
83767 ATTTCCAGAATGCTCGGAGGGAACCGATTCCCCCATTGGAGGAACCGATCCCCCCCTAAACAATT
1 AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCATAGGAGGAACCGAT-CCCCCCTAAACAATT
* *
83832 TTGTTCCGAG
65 TGGCTCCGAG
* * * *
83842 AATTCCAGTATGCTCGGAGGGAACCGATCCCCCCCA-AGGGGGTACCGATTCCCCCCT
1 AATTCCAGAATGCTCGGAGGGAACCGAT-TCCCCCATAGGAGGAACCGA-TCCCCCCT
83899 TGTACAACGG
Statistics
Matches: 112, Mismatches: 17, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
74 19 0.17
75 86 0.77
76 7 0.06
ACGTcount: A:0.24, C:0.32, G:0.24, T:0.21
Consensus pattern (74 bp):
AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCATAGGAGGAACCGATCCCCCCTAAACAATTT
GGCTCCGAG
Found at i:90479 original size:21 final size:21
Alignment explanation
Indices: 90455--90515 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 21
90445 TTCAAAGAAA
90455 CATTTACCAAACTTTGAAAAC
1 CATTTACCAAACTTTGAAAAC
*
90476 CATTT-TCAAA----G-AAA-
1 CATTTACCAAACTTTGAAAAC
90490 CATTTACCAAACTTTGAAAAC
1 CATTTACCAAACTTTGAAAAC
90511 CATTT
1 CATTT
90516 TCAAAGTTGG
Statistics
Matches: 31, Mismatches: 2, Indels: 14
0.66 0.04 0.30
Matches are distributed among these distances:
14 5 0.16
15 7 0.23
16 1 0.03
19 1 0.03
20 7 0.23
21 10 0.32
ACGTcount: A:0.43, C:0.21, G:0.05, T:0.31
Consensus pattern (21 bp):
CATTTACCAAACTTTGAAAAC
Found at i:90489 original size:35 final size:35
Alignment explanation
Indices: 90406--90521 Score: 171
Period size: 35 Copynumber: 3.3 Consensus size: 35
90396 ACCCATTCCT
* * **
90406 ATTTTC-AACAAACATCTACCAAACTTTGAAAAAAT
1 ATTTTCAAAGAAACATTTACCAAACTTTG-AAAACC
90441 ATTTTTCAAAGAAACATTTACCAAACTTTGAAAACC
1 A-TTTTCAAAGAAACATTTACCAAACTTTGAAAACC
90477 ATTTTCAAAGAAACATTTACCAAACTTTGAAAACC
1 ATTTTCAAAGAAACATTTACCAAACTTTGAAAACC
90512 ATTTTCAAAG
1 ATTTTCAAAG
90522 TTGGTTGTCA
Statistics
Matches: 75, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
35 45 0.60
36 10 0.13
37 20 0.27
ACGTcount: A:0.46, C:0.19, G:0.05, T:0.30
Consensus pattern (35 bp):
ATTTTCAAAGAAACATTTACCAAACTTTGAAAACC
Found at i:96173 original size:26 final size:26
Alignment explanation
Indices: 96137--96195 Score: 109
Period size: 26 Copynumber: 2.3 Consensus size: 26
96127 ACCGATTAAA
96137 GGAAAATCTCCCTTCCTCCAAACGAC
1 GGAAAATCTCCCTTCCTCCAAACGAC
96163 GGAAAATCTCCCTTCCTCCAAACGAC
1 GGAAAATCTCCCTTCCTCCAAACGAC
*
96189 AGAAAAT
1 GGAAAAT
96196 TCTTTTTCCA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 32 1.00
ACGTcount: A:0.36, C:0.34, G:0.12, T:0.19
Consensus pattern (26 bp):
GGAAAATCTCCCTTCCTCCAAACGAC
Found at i:96425 original size:29 final size:29
Alignment explanation
Indices: 96390--96471 Score: 137
Period size: 29 Copynumber: 2.8 Consensus size: 29
96380 AAACTAAATT
*
96390 GATGTCATTACTTACATCATTTAATTAAA
1 GATGTCATTGCTTACATCATTTAATTAAA
*
96419 GATGTCATTGCTTACATCATTTAATTAAT
1 GATGTCATTGCTTACATCATTTAATTAAA
96448 GATGTCATTGCTTACATCAATTTA
1 GATGTCATTGCTTACATC-ATTTA
96472 GTTAGGTGAG
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
29 45 0.90
30 5 0.10
ACGTcount: A:0.33, C:0.15, G:0.10, T:0.43
Consensus pattern (29 bp):
GATGTCATTGCTTACATCATTTAATTAAA
Found at i:97774 original size:15 final size:15
Alignment explanation
Indices: 97751--97780 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
97741 ACGAGGCTGG
97751 AATTACAACAATAAC
1 AATTACAACAATAAC
*
97766 AATTCCAACAATAAC
1 AATTACAACAATAAC
97781 TATGAGAAGG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.57, C:0.23, G:0.00, T:0.20
Consensus pattern (15 bp):
AATTACAACAATAAC
Found at i:101180 original size:29 final size:29
Alignment explanation
Indices: 101145--101226 Score: 137
Period size: 29 Copynumber: 2.8 Consensus size: 29
101135 AAACTAAATT
*
101145 GATGTCATTACTTACATCATTTAATTAAA
1 GATGTCATTGCTTACATCATTTAATTAAA
*
101174 GATGTCATTGCTTACATCATTTAATTAAT
1 GATGTCATTGCTTACATCATTTAATTAAA
101203 GATGTCATTGCTTACATCAATTTA
1 GATGTCATTGCTTACATC-ATTTA
101227 GTTAGGTGAG
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
29 45 0.90
30 5 0.10
ACGTcount: A:0.33, C:0.15, G:0.10, T:0.43
Consensus pattern (29 bp):
GATGTCATTGCTTACATCATTTAATTAAA
Found at i:101632 original size:17 final size:16
Alignment explanation
Indices: 101607--101647 Score: 55
Period size: 17 Copynumber: 2.5 Consensus size: 16
101597 CAAATATATA
*
101607 TATATATATATATAAG
1 TATATATATATAAAAG
*
101623 TATCATATATGTAAAAG
1 TAT-ATATATATAAAAG
101640 TATATATA
1 TATATATA
101648 ATTATTTATG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
16 8 0.36
17 14 0.64
ACGTcount: A:0.49, C:0.02, G:0.07, T:0.41
Consensus pattern (16 bp):
TATATATATATAAAAG
Found at i:104061 original size:17 final size:17
Alignment explanation
Indices: 104020--104064 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
104010 CACTATTTGA
104020 TTAAATATTTAATAAAT
1 TTAAATATTTAATAAAT
** **
104037 TTTTATATTTTTTAAAT
1 TTAAATATTTAATAAAT
104054 TTAAATATTTA
1 TTAAATATTTA
104065 TTTTTACATG
Statistics
Matches: 21, Mismatches: 7, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
TTAAATATTTAATAAAT
Found at i:104199 original size:2 final size:2
Alignment explanation
Indices: 104192--104220 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
104182 GGCGTCAATT
104192 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
104221 TTCCCATACA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Done.