Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006628.1 Hibiscus syriacus cultivar Beakdansim tig00016286_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: 65204
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Found at i:5630 original size:22 final size:22
Alignment explanation
Indices: 5578--5630 Score: 97
Period size: 22 Copynumber: 2.4 Consensus size: 22
5568 ATTCCACTCT
*
5578 AACTGCCAATTTCTGATGAGTA
1 AACTGCCATTTTCTGATGAGTA
5600 AACTGCCATTTTCTGATGAGTA
1 AACTGCCATTTTCTGATGAGTA
5622 AACTGCCAT
1 AACTGCCAT
5631 AGAAATGTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.30, C:0.21, G:0.17, T:0.32
Consensus pattern (22 bp):
AACTGCCATTTTCTGATGAGTA
Found at i:14801 original size:31 final size:31
Alignment explanation
Indices: 14726--14802 Score: 93
Period size: 32 Copynumber: 2.5 Consensus size: 31
14716 TTGAGGCCTG
*
14726 AGAGCCTACCCAAGAAAGTTCTCGGGGTCAC
1 AGAGCCTACCCAAGAAAGTTCTCGGGGCCAC
* *
14757 GGAGGCCTACCCAAGAAA-TATCTCGGTGCCAC
1 AGA-GCCTACCCAAGAAAGT-TCTCGGGGCCAC
*
14789 AGAGACTACCCAAG
1 AGAGCCTACCCAAG
14803 GGTCACCTTA
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
31 13 0.33
32 26 0.67
ACGTcount: A:0.31, C:0.30, G:0.25, T:0.14
Consensus pattern (31 bp):
AGAGCCTACCCAAGAAAGTTCTCGGGGCCAC
Found at i:16175 original size:18 final size:19
Alignment explanation
Indices: 16136--16172 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
16126 GAGTCTTATA
*
16136 CAATGTTTCGTCTTTAATC
1 CAATGTTTCGTCTTGAATC
16155 CAAT-TTTCGTC-TGAATC
1 CAATGTTTCGTCTTGAATC
16172 C
1 C
16173 CAAGATAGCT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
17 6 0.35
18 7 0.41
19 4 0.24
ACGTcount: A:0.22, C:0.24, G:0.11, T:0.43
Consensus pattern (19 bp):
CAATGTTTCGTCTTGAATC
Found at i:16551 original size:30 final size:30
Alignment explanation
Indices: 16517--16585 Score: 75
Period size: 30 Copynumber: 2.3 Consensus size: 30
16507 ACTTTTTGGT
* * *
16517 CAAAGTCAAAGGTCAACATGTTGATTCGGC
1 CAAAGTCAAAGATCAACAGGTTGACTCGGC
* * * *
16547 CAAAGTGAACGATCAACGGGTTGACTCGGT
1 CAAAGTCAAAGATCAACAGGTTGACTCGGC
16577 CAAAGTCAA
1 CAAAGTCAA
16586 CGGGTTGACT
Statistics
Matches: 31, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.35, C:0.20, G:0.25, T:0.20
Consensus pattern (30 bp):
CAAAGTCAAAGATCAACAGGTTGACTCGGC
Found at i:16589 original size:23 final size:23
Alignment explanation
Indices: 16559--16610 Score: 95
Period size: 23 Copynumber: 2.3 Consensus size: 23
16549 AAGTGAACGA
*
16559 TCAACGGGTTGACTCGGTCAAAG
1 TCAACGGGTTGACTAGGTCAAAG
16582 TCAACGGGTTGACTAGGTCAAAG
1 TCAACGGGTTGACTAGGTCAAAG
16605 TCAACG
1 TCAACG
16611 AGTTTACCCT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.29, C:0.21, G:0.29, T:0.21
Consensus pattern (23 bp):
TCAACGGGTTGACTAGGTCAAAG
Found at i:17447 original size:65 final size:64
Alignment explanation
Indices: 17373--17527 Score: 145
Period size: 65 Copynumber: 2.4 Consensus size: 64
17363 AATATTTTTT
* * *
17373 ACAACTTTTTTACTGTGACTAAATAAT-TTTGTTACAATTTGTTATTTTGA-AAGAATATTATTT
1 ACAA-TTTTTTA-TATGACTAAATAATATTTGTTACAAATTGTTATTTTGATAA-AATA-AATTT
17436 GCC
62 GCC
* * * * *
17439 ACCATTTTTTATAATGA-GAAATTAATATTTGTTATAAATTGTTATTTTGATTAAATAAATTTGT
1 ACAATTTTTTAT-ATGACTAAA-TAATATTTGTTACAAATTGTTATTTTGATAAAATAAATTTGC
17503 C
64 C
*
17504 ACAATTTTTTATTTTGACTAAATA
1 ACAATTTTTTA-TATGACTAAATA
17528 TTGGGACGAA
Statistics
Matches: 72, Mismatches: 11, Indels: 13
0.75 0.11 0.14
Matches are distributed among these distances:
64 4 0.06
65 35 0.49
66 32 0.44
67 1 0.01
ACGTcount: A:0.35, C:0.08, G:0.09, T:0.48
Consensus pattern (64 bp):
ACAATTTTTTATATGACTAAATAATATTTGTTACAAATTGTTATTTTGATAAAATAAATTTGCC
Found at i:17502 original size:32 final size:32
Alignment explanation
Indices: 17465--17527 Score: 81
Period size: 32 Copynumber: 2.0 Consensus size: 32
17455 AGAAATTAAT
* * *
17465 ATTTGTTATAAATTGTTATTTTGATTAAATAA
1 ATTTGTCACAAATTGTTATTTTGACTAAATAA
* *
17497 ATTTGTCACAATTTTTTATTTTGACTAAATA
1 ATTTGTCACAAATTGTTATTTTGACTAAATA
17528 TTGGGACGAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.35, C:0.05, G:0.08, T:0.52
Consensus pattern (32 bp):
ATTTGTCACAAATTGTTATTTTGACTAAATAA
Found at i:21466 original size:19 final size:19
Alignment explanation
Indices: 21428--21467 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
21418 ATAATATATG
* *
21428 TTATAACTATAATTAAAAT
1 TTATAACTACAAGTAAAAT
*
21447 TTATAACTACAAGTATAAT
1 TTATAACTACAAGTAAAAT
21466 TT
1 TT
21468 CTCACAAAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.47, C:0.07, G:0.03, T:0.42
Consensus pattern (19 bp):
TTATAACTACAAGTAAAAT
Found at i:21993 original size:418 final size:414
Alignment explanation
Indices: 21194--22036 Score: 1137
Period size: 418 Copynumber: 2.0 Consensus size: 414
21184 ACTATAAAAC
* * * *
21194 TTTTACTATATAACATTTTTGGCACCAAAAAATAGGGATAATTTTTTATAGTATAATTTTTCATA
1 TTTTACTATATAACATTTTTGACACAAAAAAATAGGGAAAATTTTTGATAGTATAATTTTTCATA
* * *
21259 ATGATTAAAATATATAAATACAAAATAATTGATTACAAAAAACTTGAATTTTATTATCTGATGTG
66 ATGATTAAAATATATAAATAAAAAATAATTGAATACAAAAAACTTGAA-TTTATTATCTGATATG
* * *
21324 ATAATTTTTTCTATAACAATTACTATAAATTATAATTACAAAACTTATCAATATAGCTTTTTGAA
130 ATAATTTTTTCTATAACAATAACTATAAATTATAATTACAAAAATTATCAATATAACTTTTTGAA
* * *
21389 ACAAAAAAAAGTTGAAAAAAATATTTATCATAATATATGTTATAACTATAATTAAAATTTATAAC
195 ACAAAAAAAAGTGGAAAAAAATAATTATCATAATATATGCTATAACTATAATTAAAATTTATAAC
* * *
21454 TACAAGTATAATTTCTCACAAAAATGTGAATACCATTATTTTTTGTGACAATGTTTTCTGTAATA
260 TACAAATATAATTTCTCACAAAAACGTGAATACCATTATTTTTTGTGACAATGTTTTATGTAATA
* *
21519 ATTATAAACACTTATAGTTACAAAAATTATTACAATATGATTTTTCTAGTGCAAAAAAATATAGA
325 ATTATAAACACTTATAGTTACAAAAATTATCACAATATGATTTTTCTAGCGCAAAAAAATATAGA
21584 -GGAAAATCTTTATGAAAATAT-ATT
390 TGG-AAATCTTTATGAAAATATAATT
*
21608 TTGTTACTATATAACATTTTTGACATTAAAAAAATAGGGAGAAATAATTTTGATAGTATAATTTT
1 TT-TTACTATATAACATTTTTGACA-CAAAAAAATAGGGA-AAAT--TTTTGATAGTATAATTTT
* *
21673 TCATAATGATTAAAATATATAAGTAAAAAAATAATTTAATACAAAAAACTTGAA-TT-TTAT-TG
61 TCATAATGATTAAAATATATAAAT-AAAAAATAATTGAATACAAAAAACTTGAATTTATTATCTG
* * *
21735 ATATGAT-ATTTTTTCTATAACAATAATTATAAATTATAATTATAAAAATTGTCAATATAAC-TT
125 ATATGATAATTTTTTCTATAACAATAACTATAAATTATAATTACAAAAATTATCAATATAACTTT
* * *
21798 TTGAAAC-AAAAAAAGTGGAGAAAAATAATTATGACGATTAATATATGCTATCACTATAGTTAAA
190 TTGAAACAAAAAAAAGTGGAAAAAAATAATTAT--C-A-TAATATATGCTATAACTATAATTAAA
* *
21862 ATTTATAACTACAAATATAATTTGTCACAAAAAACGTGAATATCATTATTTTTTGTGACAATGTT
251 ATTTATAACTACAAATATAATTTCTCAC-AAAAACGTGAATACCATTATTTTTTGTGACAATGTT
* * * * ** *
21927 TTATGTAATAATTATTAACATTTATAGTTACAAAATTTGTCATTATATGACTTTTT-TTGCGCAA
315 TTATGTAATAATTATAAACACTTATAGTTACAAAAATTATCACAATATGA-TTTTTCTAGCGCAA
* * *
21991 AAAAATATGGATGGAAATCTTTGTGACAATATAATT
379 AAAAATATAGATGGAAATCTTTATGAAAATATAATT
*
22027 TTTCACTATA
1 TTTTACTATA
22037 ATTAAAACAT
Statistics
Matches: 375, Mismatches: 40, Indels: 24
0.85 0.09 0.05
Matches are distributed among these distances:
413 22 0.06
414 11 0.03
415 70 0.19
416 21 0.06
417 56 0.15
418 117 0.31
419 52 0.14
420 26 0.07
ACGTcount: A:0.44, C:0.08, G:0.09, T:0.39
Consensus pattern (414 bp):
TTTTACTATATAACATTTTTGACACAAAAAAATAGGGAAAATTTTTGATAGTATAATTTTTCATA
ATGATTAAAATATATAAATAAAAAATAATTGAATACAAAAAACTTGAATTTATTATCTGATATGA
TAATTTTTTCTATAACAATAACTATAAATTATAATTACAAAAATTATCAATATAACTTTTTGAAA
CAAAAAAAAGTGGAAAAAAATAATTATCATAATATATGCTATAACTATAATTAAAATTTATAACT
ACAAATATAATTTCTCACAAAAACGTGAATACCATTATTTTTTGTGACAATGTTTTATGTAATAA
TTATAAACACTTATAGTTACAAAAATTATCACAATATGATTTTTCTAGCGCAAAAAAATATAGAT
GGAAATCTTTATGAAAATATAATT
Found at i:22135 original size:181 final size:178
Alignment explanation
Indices: 21848--22290 Score: 432
Period size: 181 Copynumber: 2.5 Consensus size: 178
21838 ATATATGCTA
* ** * * * * *
21848 TCACTATAGTTAAAATTTATAACTACAAATATAATTTGTCACAAAAAACGTGAATATCATTATTT
1 TCACTATAATTAAAACATATAACGACAAACAAAATTTGTCAC-AAAAACTTGAATCTCATTATTT
** * * * * ** **
21913 TTTGTGACAATGTTTTATGTAATAATTATTAACATTTATAGTTACAAAATTTGTCATTATATGAC
65 GCTGTGACAATTTTTTTTGTAACAATAATTAACA-TTATAGTTACAAAACATGTCACCATATGAC
*
21978 TTT-TTTTGCGCAAAAAAATATGGATGGA-AATC-TTTGTGACAATATA-ATTTT-
129 TTTGTTTTGCAC-AAAAAAT-TGGA--GATAATCATTTGTGAC--TATACATTTTG
* ** * *
22029 TCACTATAATTAAAACATATCACGACAAACATTATTTTTTACTAAAAACTTGAATCTCATTATTT
1 TCACTATAATTAAAACATATAACGACAAACAAAATTTGTCAC-AAAAACTTGAATCTCATTATTT
*
22094 GCTGTGACAATTTTTTTTGTAACAATAATTATAGC-TTATAGTTACAAAACATGTGACCATATGA
65 GCTGTGACAATTTTTTTTGTAACAATAATTA-A-CATTATAGTTACAAAACATGTCACCATATGA
* ** *
22158 TTTTGTTTTTTACCAAAAATTGGAGATAATCATTTGTGACTATACATTTTG
128 CTTTGTTTTGCACAAAAAATTGGAGATAATCATTTGTGACTATACATTTTG
** *
22209 TCACTATAATTAAAACATATAATTACAAACAAAATTTGTCACAACAAA-TCTAAATCTCATTATT
1 TCACTATAATTAAAACATATAACGACAAACAAAATTTGTCACAA-AAACT-TGAATCTCATTATT
22273 TGCTGTGACAATTTTTTT
64 TGCTGTGACAATTTTTTT
22291 CATAGTTACT
Statistics
Matches: 217, Mismatches: 36, Indels: 19
0.80 0.13 0.07
Matches are distributed among these distances:
178 6 0.03
179 12 0.06
180 81 0.37
181 111 0.51
182 6 0.03
183 1 0.00
ACGTcount: A:0.38, C:0.12, G:0.09, T:0.40
Consensus pattern (178 bp):
TCACTATAATTAAAACATATAACGACAAACAAAATTTGTCACAAAAACTTGAATCTCATTATTTG
CTGTGACAATTTTTTTTGTAACAATAATTAACATTATAGTTACAAAACATGTCACCATATGACTT
TGTTTTGCACAAAAAATTGGAGATAATCATTTGTGACTATACATTTTG
Found at i:26105 original size:30 final size:30
Alignment explanation
Indices: 26069--26143 Score: 78
Period size: 30 Copynumber: 2.5 Consensus size: 30
26059 AATTTAACTT
*
26069 TTCGGTCAAAGTCAAAGGTAAACGGGTTGA
1 TTCGGTCAAAGTCAAAGGTAAACAGGTTGA
* * ** * *
26099 TTCGGTCATAGTGATTGGTCAATAGGTTGA
1 TTCGGTCAAAGTCAAAGGTAAACAGGTTGA
*
26129 CTCGGTCAAAGTCAA
1 TTCGGTCAAAGTCAA
26144 CGAGTTGACC
Statistics
Matches: 34, Mismatches: 11, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.29, C:0.15, G:0.28, T:0.28
Consensus pattern (30 bp):
TTCGGTCAAAGTCAAAGGTAAACAGGTTGA
Found at i:28574 original size:14 final size:13
Alignment explanation
Indices: 28534--28576 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
28524 TCGGTCAAAG
*
28534 TCAACGAGTTGAC
1 TCAATGAGTTGAC
*
28547 CCAATGAGTTGAC
1 TCAATGAGTTGAC
*
28560 TCAACTGATTTGAC
1 TCAA-TGAGTTGAC
28574 TCA
1 TCA
28577 GTGTGGGTTG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
13 14 0.56
14 11 0.44
ACGTcount: A:0.30, C:0.23, G:0.19, T:0.28
Consensus pattern (13 bp):
TCAATGAGTTGAC
Found at i:32820 original size:330 final size:330
Alignment explanation
Indices: 32219--32881 Score: 1317
Period size: 330 Copynumber: 2.0 Consensus size: 330
32209 AGGCCATTTC
32219 TCTGTAGCATGATGCTATGGTTGGGGTTTGCAACACTTGGGTTGAGCTTATCTTATCTTCTGTCT
1 TCTGTAGCATGATGCTATGGTTGGGGTTTGCAACACTTGGGTTGAGCTTATCTTATCTTCTGTCT
32284 CCACTATTACATACCGAGTTCGGATCAATAGTAGCCTTACTAATGCTTTCGCTCTACAACAAGGC
66 CCACTATTACATACCGAGTTCGGATCAATAGTAGCCTTACTAATGCTTTCGCTCTACAACAAGGC
32349 CTTCGTTAAGGGGATTCCATATCGCCATTTTTGTCTGTTATATGCGCTCAGGGGCTATCATACTT
131 CTTCGTTAAGGGGATTCCATATCGCCATTTTTGTCTGTTATATGCGCTCAGGGGCTATCATACTT
32414 TCTCCATATTGAACAACAACGAGGAAGTATTTGTGGCCTTCGCATTTGTCGTGGTGGACCTCGCC
196 TCTCCATATTGAACAACAACGAGGAAGTATTTGTGGCCTTCGCATTTGTCGTGGTGGACCTCGCC
*
32479 GTGCACATTTATTTAATGTCGATGATTGTATCATTTTCCTGCATATTTCAGATGAGGAGTTCCTG
261 GTGCACATTTATTTAATGTCGATGATTGTATCATTTTCCTGCATATTTCAGATGAGGAATTCCTG
32544 CATAT
326 CATAT
32549 TCTGTAGCATGATGCTATGGTTGGGGTTTGCAACACTTGGGTTGAGCTTATCTTATCTTCTGTCT
1 TCTGTAGCATGATGCTATGGTTGGGGTTTGCAACACTTGGGTTGAGCTTATCTTATCTTCTGTCT
32614 CCACTATTACATACCGAGTTCGGATCAATAGTAGCCTTACTAATGCTTTCGCTCTACAACAAGGC
66 CCACTATTACATACCGAGTTCGGATCAATAGTAGCCTTACTAATGCTTTCGCTCTACAACAAGGC
32679 CTTCGTTAAGGGGATTCCATATCGCCATTTTTGTCTGTTATATGCGCTCAGGGGCTATCATACTT
131 CTTCGTTAAGGGGATTCCATATCGCCATTTTTGTCTGTTATATGCGCTCAGGGGCTATCATACTT
32744 TCTCCATATTGAACAACAACGAGGAAGTATTTGTGGCCTTCGCATTTGTCGTGGTGGACCTCGCC
196 TCTCCATATTGAACAACAACGAGGAAGTATTTGTGGCCTTCGCATTTGTCGTGGTGGACCTCGCC
32809 GTGCACATTTATTTAATGTCGATGATTGTATCATTTTCCTGCATATTTCAGATGAGGAATTCCTG
261 GTGCACATTTATTTAATGTCGATGATTGTATCATTTTCCTGCATATTTCAGATGAGGAATTCCTG
32874 CATAT
326 CATAT
32879 TCT
1 TCT
32882 AACCATGTTG
Statistics
Matches: 332, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
330 332 1.00
ACGTcount: A:0.22, C:0.21, G:0.21, T:0.36
Consensus pattern (330 bp):
TCTGTAGCATGATGCTATGGTTGGGGTTTGCAACACTTGGGTTGAGCTTATCTTATCTTCTGTCT
CCACTATTACATACCGAGTTCGGATCAATAGTAGCCTTACTAATGCTTTCGCTCTACAACAAGGC
CTTCGTTAAGGGGATTCCATATCGCCATTTTTGTCTGTTATATGCGCTCAGGGGCTATCATACTT
TCTCCATATTGAACAACAACGAGGAAGTATTTGTGGCCTTCGCATTTGTCGTGGTGGACCTCGCC
GTGCACATTTATTTAATGTCGATGATTGTATCATTTTCCTGCATATTTCAGATGAGGAATTCCTG
CATAT
Found at i:59523 original size:25 final size:24
Alignment explanation
Indices: 59478--59524 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 24
59468 GAAAAAATGG
*
59478 AAAAATAACAAAATACGTAAAAAA
1 AAAAATAACAAAATACATAAAAAA
59502 AAAAATAAACAAAATGA-ATAAAA
1 AAAAAT-AACAAAAT-ACATAAAA
59525 TGTTAAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
24 6 0.30
25 13 0.65
26 1 0.05
ACGTcount: A:0.77, C:0.06, G:0.04, T:0.13
Consensus pattern (24 bp):
AAAAATAACAAAATACATAAAAAA
Found at i:59725 original size:5 final size:5
Alignment explanation
Indices: 59702--59760 Score: 59
Period size: 5 Copynumber: 11.8 Consensus size: 5
59692 TGATATTAAG
* * *
59702 AAAA- AAAAT AAAAA AAAAT AAAAT AAAGT AAAAT ATATAT ATAAAT -AAAT
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT A-AAAT A-AAAT AAAAT
59752 AAAAT AAAA
1 AAAAT AAAA
59761 GAATATTAAG
Statistics
Matches: 46, Mismatches: 6, Indels: 5
0.81 0.11 0.09
Matches are distributed among these distances:
4 8 0.17
5 30 0.65
6 8 0.17
ACGTcount: A:0.78, C:0.00, G:0.02, T:0.20
Consensus pattern (5 bp):
AAAAT
Found at i:61469 original size:110 final size:109
Alignment explanation
Indices: 61325--61527 Score: 289
Period size: 110 Copynumber: 1.9 Consensus size: 109
61315 AACTGGGAAA
* * * **
61325 TTATTTGTTGACAGCCAGCCGCCCTTTCGCTGTGAAGTTGAGCTTGTGTTATCTCGAGTTTAATA
1 TTATTTGTTGACAACCAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTATTATCT-GAGTCCAATA
*
61390 TCCTTCACTGTGAAGTTGAAATTGACTCTAAATGAAACTGAAAAG
65 TCCCTCACTGTGAAGTTGAAATTGACTCTAAATGAAACTGAAAAG
* * * *
61435 TTATTTGTTGACAATCAGTCGCCCCTTCGTTGTGAAGTTGAGCTTGTATTGTCTGAGTCCAATAT
1 TTATTTGTTGACAACCAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTATTATCTGAGTCCAATAT
* *
61500 CCCTCGCTGTGAAGTTGAAATTGGCTCT
66 CCCTCACTGTGAAGTTGAAATTGACTCT
61528 GAAACTGGAA
Statistics
Matches: 81, Mismatches: 12, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
109 34 0.42
110 47 0.58
ACGTcount: A:0.23, C:0.19, G:0.22, T:0.36
Consensus pattern (109 bp):
TTATTTGTTGACAACCAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTATTATCTGAGTCCAATAT
CCCTCACTGTGAAGTTGAAATTGACTCTAAATGAAACTGAAAAG
Found at i:62337 original size:50 final size:49
Alignment explanation
Indices: 62268--62363 Score: 133
Period size: 50 Copynumber: 1.9 Consensus size: 49
62258 AAGGAAAACA
**
62268 AAATTTTGTTTTAAGGGAAATAAATTTGAAGATTTTGTGTTTCAAGGGAGAT
1 AAATTTTGTTTTAAGGGAAATAAATTCAAAGA--TT-TGTTTCAAGGGAGAT
62320 AAATTTT-TTTT-AGGGAAATAAATTCAAAGATTTGTTTCAAGGGA
1 AAATTTTGTTTTAAGGGAAATAAATTCAAAGATTTGTTTCAAGGGA
62364 AACTGTCTCA
Statistics
Matches: 42, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
47 12 0.29
48 2 0.05
50 17 0.40
51 4 0.10
52 7 0.17
ACGTcount: A:0.36, C:0.03, G:0.21, T:0.40
Consensus pattern (49 bp):
AAATTTTGTTTTAAGGGAAATAAATTCAAAGATTTGTTTCAAGGGAGAT
Found at i:62421 original size:25 final size:25
Alignment explanation
Indices: 62365--62430 Score: 97
Period size: 21 Copynumber: 2.8 Consensus size: 25
62355 TTCAAGGGAA
62365 ACTGTCTCAAGAGAGACGAAATTTG
1 ACTGTCTCAAGAGAGACGAAATTTG
62390 --T-T-TCAAGAGAGACGAAATTTG
1 ACTGTCTCAAGAGAGACGAAATTTG
62411 ACTGTCTCAAGAGAGA-GAAA
1 ACTGTCTCAAGAGAGACGAAA
62431 ACTAAGTTCC
Statistics
Matches: 37, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
21 19 0.51
22 1 0.03
23 2 0.05
24 5 0.14
25 10 0.27
ACGTcount: A:0.39, C:0.14, G:0.24, T:0.23
Consensus pattern (25 bp):
ACTGTCTCAAGAGAGACGAAATTTG
Found at i:62558 original size:65 final size:67
Alignment explanation
Indices: 62444--62626 Score: 194
Period size: 65 Copynumber: 2.7 Consensus size: 67
62434 AAGTTCCAAA
* ***
62444 AGAAACTGTCTCAAGAGAGATGAAATTTGTTTCAAATAAAACATATTCAAATAATT-TGTTTCAA
1 AGAAACTGTCTCAAGAGAGACGAAATTTGTTTCAAGGGAAACATATTC-AATAATTATGTTTCAA
62508 G-G
65 GAG
* * ** * **
62510 -GAAACTGTCTCAAAAGAGACGAAATTTATTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAG
1 AGAAACTGTCTCAAGAGAGACGAAATTTGTTTCAAGGGAAACATATTCAATAATTATGTTTCAAG
62574 AG
66 AG
* *
62576 AGAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGGGAAAC-TATCTCAA
1 AGAAACTGTCTCAAGAGAGACGAAA-TTTGTTTCAAGGGAAACATAT-TCAA
62627 GAGAGACAAA
Statistics
Matches: 95, Mismatches: 17, Indels: 8
0.79 0.14 0.07
Matches are distributed among these distances:
64 5 0.05
65 47 0.49
66 1 0.01
67 23 0.24
68 19 0.20
ACGTcount: A:0.39, C:0.12, G:0.18, T:0.31
Consensus pattern (67 bp):
AGAAACTGTCTCAAGAGAGACGAAATTTGTTTCAAGGGAAACATATTCAATAATTATGTTTCAAG
AG
Found at i:62625 original size:37 final size:37
Alignment explanation
Indices: 62565--62734 Score: 119
Period size: 37 Copynumber: 4.8 Consensus size: 37
62555 TCAATGTTTA
*
62565 TGTTTCAAGAGAGAAACTGTCTCAAGGGAGACAAAATTT
1 TGTTTCAAG-G-GAAACTATCTCAAGGGAGACAAAATTT
*
62604 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAA-TT
1 TGTTTCAAGGGAAACTATCTCAAGGGAGACAAAATTT
** * * * *
62640 CATTTCAAGAGAAA-TGTTTTCAA---TG------TTT
1 TGTTTCAAGGGAAACT-ATCTCAAGGGAGACAAAATTT
* * *
62668 ATGTTTCAAGAGAAACTGTCTCAAGGGAGACAATATTT
1 -TGTTTCAAGGGAAACTATCTCAAGGGAGACAAAATTT
*
62706 TGTTTCAAGGGAAACTATCTCAAGCGAGA
1 TGTTTCAAGGGAAACTATCTCAAGGGAGA
62735 TAAATCTTCT
Statistics
Matches: 102, Mismatches: 16, Indels: 28
0.70 0.11 0.19
Matches are distributed among these distances:
28 2 0.02
29 17 0.17
30 1 0.01
32 1 0.01
33 1 0.01
35 1 0.01
36 18 0.18
37 48 0.47
38 4 0.04
39 9 0.09
ACGTcount: A:0.37, C:0.14, G:0.21, T:0.29
Consensus pattern (37 bp):
TGTTTCAAGGGAAACTATCTCAAGGGAGACAAAATTT
Found at i:62710 original size:102 final size:104
Alignment explanation
Indices: 62493--62734 Score: 398
Period size: 104 Copynumber: 2.3 Consensus size: 104
62483 AACATATTCA
* * * * * *
62493 AATAATTTGTTTCAAGGGAAACTGTCTCAAAAGAGACGAAATTTATTTCAAGGGAAATGTTTTCA
1 AATATTTTGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGAGAAATGTTTTCA
62558 ATGTTTATGTTTCAAGAGAGAAACTGTCTCAAGGGAGAC
66 ATGTTTATGTTTCAAGAGAGAAACTGTCTCAAGGGAGAC
*
62597 AAAATTTTGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGAGAAATGTTTTCA
1 AATATTTTGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGAGAAATGTTTTCA
62662 ATGTTTATGTTTC-A-AGAGAAACTGTCTCAAGGGAGAC
66 ATGTTTATGTTTCAAGAGAGAAACTGTCTCAAGGGAGAC
*
62699 AATATTTTGTTTCAAGGGAAACTATCTCAAGCGAGA
1 AATATTTTGTTTCAAGGGAAACTATCTCAAGAGAGA
62735 TAAATCTTCT
Statistics
Matches: 129, Mismatches: 9, Indels: 2
0.92 0.06 0.01
Matches are distributed among these distances:
102 57 0.44
103 1 0.01
104 71 0.55
ACGTcount: A:0.37, C:0.12, G:0.20, T:0.31
Consensus pattern (104 bp):
AATATTTTGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGAGAAATGTTTTCA
ATGTTTATGTTTCAAGAGAGAAACTGTCTCAAGGGAGAC
Found at i:64250 original size:69 final size:69
Alignment explanation
Indices: 64147--64284 Score: 231
Period size: 69 Copynumber: 2.0 Consensus size: 69
64137 TGTCTCTCTC
* * * *
64147 TTGATGCTCTATGATCTTCGAGTGGAGTGATTCAGTTATTCATAAATGGTTGTGCTTGATCAATC
1 TTGATGCTCTATGATCTTCGAGTGAAGTGATTCAGTGATTCAGAAATGATTGTGCTTGATCAATC
64212 TCAT
66 TCAT
*
64216 TTGATGCTCTATGATCTTCGAGTGAAGTGGTTCAGTGATTCAGAAATGATTGTGCTTGATCAATC
1 TTGATGCTCTATGATCTTCGAGTGAAGTGATTCAGTGATTCAGAAATGATTGTGCTTGATCAATC
64281 TCAT
66 TCAT
64285 AGTTTGAATC
Statistics
Matches: 64, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
69 64 1.00
ACGTcount: A:0.24, C:0.14, G:0.22, T:0.39
Consensus pattern (69 bp):
TTGATGCTCTATGATCTTCGAGTGAAGTGATTCAGTGATTCAGAAATGATTGTGCTTGATCAATC
TCAT
Done.