Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002226.1 Hibiscus syriacus cultivar Beakdansim tig00004531_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: 67429
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:263 original size:67 final size:64
Alignment explanation
Indices: 174--895 Score: 440
Period size: 56 Copynumber: 11.7 Consensus size: 64
164 GAAGCTTCAA
* *
174 CTTGACTTTCTCGTGAAGAGAAGTCAATCTTTGTTATTCCTGACTCCCCTGTGAAGAGGAACCAA
1 CTTGACTTCCTCATGAAGAGAAGTCAATCTTTGTTATTCCTGA-T-CCCT-TGAAGAGGAACCAA
239 TC
63 TC
* * * * **
241 CTTGAATTCATCATAAAGAGAAGTTAATCTTTGTTA----T--T-CC-TGAAGA-GAAGTTAATC
1 CTTGACTTCCTCATGAAGAGAAGTCAATCTTTGTTATTCCTGATCCCTTGAAGAGGAA-CCAATC
* * *
297 ATTGACTTCCTCGTGAAGAGAAGTCAATCTTTGTTATTCCTGACACCCTCATGAAGAGGAACCAA
1 CTTGACTTCCTCATGAAGAGAAGTCAATCTTTGTTATTCCTGA-TCCCT--TGAAGAGGAACCAA
362 TC
63 TC
* * * * ** *
364 CTTCACTTCTTCATAAAGAGAAGTTAATCTTTGTTATT-C--A-----TGAAGAGGAGTCGATC
1 CTTGACTTCCTCATGAAGAGAAGTCAATCTTTGTTATTCCTGATCCCTTGAAGAGGAACCAATC
* * * *
420 CTTGAATTCCTCGTGAAGAGAAGTCAATCTTTGTTATTCTTGAATCCTTCGTGATA-AGGAACCA
1 CTTGACTTCCTCATGAAGAGAAGTCAATCTTTGTTATTCCTG-ATCC--CTTGA-AGAGGAACCA
484 ATC
62 ATC
* * * **
487 CTTGACTTCTTCATGAAGAGAAGTCAATCTATGTTATT-C--A-----TGAAGAAGATTCAATC
1 CTTGACTTCCTCATGAAGAGAAGTCAATCTTTGTTATTCCTGATCCCTTGAAGAGGAACCAATC
* * *
543 CTTGACTTCCTCGTGAAGAGAAGTCAATCTCTGTTATTCCTGACTCCCTCTCGAAGAGGAACAAA
1 CTTGACTTCCTCATGAAGAGAAGTCAATCTTTGTTATTCCTGA-TCCCT-T-GAAGAGGAACCAA
608 TC
63 TC
* * *
610 CTTGATTTTCTCATGAAGAGAAGTCAATCTTTGTTATTCCTGA-------AA-AGG-ACTTAATC
1 CTTGACTTCCTCATGAAGAGAAGTCAATCTTTGTTATTCCTGATCCCTTGAAGAGGAAC-CAATC
* * * * * *
666 ATTGACTTCCTCGTGAAAAGAAGTCAATCTTTTTTATTCCTGACTCCCTCGTAAAGAGAAACCAA
1 CTTGACTTCCTCATGAAGAGAAGTCAATCTTTGTTATTCCTGA-TCCCT--TGAAGAGGAACCAA
731 TC
63 TC
* * * ** * *
733 CTTGACTTACT-ATTGAAGGGAAGTAAATCTTAATTA-T--T--T--C-TGAAGATGAGCCAATC
1 CTTGACTTCCTCA-TGAAGAGAAGTCAATCTTTGTTATTCCTGATCCCTTGAAGAGGAACCAATC
* * * * *
789 ATTGACTTTCTCGTGAAGAAAAGTCAATC-TT-TTATTCCTGA-CTCCTTCGTGAGAGGAACCAA
1 CTTGACTTCCTCATGAAGAGAAGTCAATCTTTGTTATTCCTGATC-CCTT-G-AAGAGGAACCAA
851 TC
63 TC
* *
853 CTTGACTTCCTCGTGGAGAGAAGTCAATCTTTGTTATTCCTGA
1 CTTGACTTCCTCATGAAGAGAAGTCAATCTTTGTTATTCCTGA
896 AGAGGAGTTA
Statistics
Matches: 500, Mismatches: 90, Indels: 131
0.69 0.12 0.18
Matches are distributed among these distances:
54 3 0.01
55 8 0.02
56 209 0.42
57 4 0.01
58 2 0.00
59 2 0.00
60 3 0.01
61 2 0.00
62 1 0.00
63 3 0.01
64 40 0.08
65 2 0.00
66 15 0.03
67 200 0.40
68 6 0.01
ACGTcount: A:0.30, C:0.20, G:0.17, T:0.33
Consensus pattern (64 bp):
CTTGACTTCCTCATGAAGAGAAGTCAATCTTTGTTATTCCTGATCCCTTGAAGAGGAACCAATC
Found at i:269 original size:29 final size:28
Alignment explanation
Indices: 237--325 Score: 74
Period size: 29 Copynumber: 3.1 Consensus size: 28
227 AAGAGGAACC
* *
237 AATCCTTGAATTCATCATAAAGAGAAGTT
1 AATCATTG-ATTCATCATGAAGAGAAGTT
* *
266 AATCTTTG-TT-ATTCCTGAAGAGAAGTT
1 AATCATTGATTCA-TCATGAAGAGAAGTT
* * *
293 AATCATTGACTTCCTCGTGAAGAGAAGTC
1 AATCATTGA-TTCATCATGAAGAGAAGTT
322 AATC
1 AATC
326 TTTGTTATTC
Statistics
Matches: 49, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
26 1 0.02
27 22 0.45
29 26 0.53
ACGTcount: A:0.35, C:0.16, G:0.17, T:0.33
Consensus pattern (28 bp):
AATCATTGATTCATCATGAAGAGAAGTT
Found at i:289 original size:27 final size:27
Alignment explanation
Indices: 256--339 Score: 105
Period size: 27 Copynumber: 3.0 Consensus size: 27
246 ATTCATCATA
256 AAGAGAAGTTAATCTTTGTTATTCCTG
1 AAGAGAAGTTAATCTTTGTTATTCCTG
* ** *
283 AAGAGAAGTTAATCATTGACTTCCTCGTG
1 AAGAGAAGTTAATCTTTG--TTATTCCTG
*
312 AAGAGAAGTCAATCTTTGTTATTCCTG
1 AAGAGAAGTTAATCTTTGTTATTCCTG
339 A
1 A
340 CACCCTCATG
Statistics
Matches: 46, Mismatches: 9, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
27 24 0.52
29 22 0.48
ACGTcount: A:0.31, C:0.14, G:0.19, T:0.36
Consensus pattern (27 bp):
AAGAGAAGTTAATCTTTGTTATTCCTG
Found at i:394 original size:123 final size:123
Alignment explanation
Indices: 175--908 Score: 921
Period size: 123 Copynumber: 6.0 Consensus size: 123
165 AAGCTTCAAC
*
175 TTGACTTTCTCGTGAAGAGAAGTCAATCTTTGTTATTCCTGACTCCC-CTGTGAAGAGGAACCAA
1 TTGACTTCCTCGTGAAGAGAAGTCAATCTTTGTTATTCCTGACTCCCTC-GTGAAGAGGAACCAA
* * * * *
239 TCCTTGAATTCATCATAAAGAGAAGTTAATCTTTGTTATTCCTGAAGAGAAGTTAATCA
65 TCCTTGACTTCTTCATGAAGAGAAGTCAATCTTTGTTATTCCTGAAGAGGAGTTAATCA
* *
298 TTGACTTCCTCGTGAAGAGAAGTCAATCTTTGTTATTCCTGACACCCTCATGAAGAGGAACCAAT
1 TTGACTTCCTCGTGAAGAGAAGTCAATCTTTGTTATTCCTGACTCCCTCGTGAAGAGGAACCAAT
* * * * ** *
363 CCTTCACTTCTTCATAAAGAGAAGTTAATCTTTGTTATTCATGAAGAGGAGTCGATCC
66 CCTTGACTTCTTCATGAAGAGAAGTCAATCTTTGTTATTCCTGAAGAGGAGTTAATCA
* * * *
421 TTGAATTCCTCGTGAAGAGAAGTCAATCTTTGTTATTCTTGAATCCTTCGTGATA-AGGAACCAA
1 TTGACTTCCTCGTGAAGAGAAGTCAATCTTTGTTATTCCTGACTCCCTCGTGA-AGAGGAACCAA
* * * *
485 TCCTTGACTTCTTCATGAAGAGAAGTCAATCTATGTTATTCATGAAGAAGA-TTCAATCC
65 TCCTTGACTTCTTCATGAAGAGAAGTCAATCTTTGTTATTCCTGAAGAGGAGTT-AATCA
* *
544 TTGACTTCCTCGTGAAGAGAAGTCAATCTCTGTTATTCCTGACTCCCTC-TCGAAGAGGAACAAA
1 TTGACTTCCTCGTGAAGAGAAGTCAATCTTTGTTATTCCTGACTCCCTCGT-GAAGAGGAACCAA
* * *
608 TCCTTGA-TTTTCTCATGAAGAGAAGTCAATCTTTGTTATTCCTGAAAAGGACTTAATCA
65 TCCTTGACTTCT-TCATGAAGAGAAGTCAATCTTTGTTATTCCTGAAGAGGAGTTAATCA
* * * *
667 TTGACTTCCTCGTGAAAAGAAGTCAATCTTTTTTATTCCTGACTCCCTCGTAAAGAGAAACCAAT
1 TTGACTTCCTCGTGAAGAGAAGTCAATCTTTGTTATTCCTGACTCCCTCGTGAAGAGGAACCAAT
* * ** * * **
732 CCTTGACTTAC-T-ATTGAAGGGAAGTAAATCTTAATTATTTCTGAAGATGAGCCAATCA
66 CCTTGACTT-CTTCA-TGAAGAGAAGTCAATCTTTGTTATTCCTGAAGAGGAGTTAATCA
* * *
790 TTGACTTTCTCGTGAAGAAAAGTCAATC-TT-TTATTCCTGACTCCTTCGTG-AGAGGAACCAAT
1 TTGACTTCCTCGTGAAGAGAAGTCAATCTTTGTTATTCCTGACTCCCTCGTGAAGAGGAACCAAT
* * *
852 CCTTGACTTCCTCGTGGAGAGAAGTCAATCTTTGTTATTCCTGAAGAGGAGTTAATC
66 CCTTGACTTCTTCATGAAGAGAAGTCAATCTTTGTTATTCCTGAAGAGGAGTTAATC
909 TTTCATATTT
Statistics
Matches: 529, Mismatches: 69, Indels: 29
0.84 0.11 0.05
Matches are distributed among these distances:
119 1 0.00
120 55 0.10
121 18 0.03
122 9 0.02
123 439 0.83
124 7 0.01
ACGTcount: A:0.30, C:0.20, G:0.18, T:0.33
Consensus pattern (123 bp):
TTGACTTCCTCGTGAAGAGAAGTCAATCTTTGTTATTCCTGACTCCCTCGTGAAGAGGAACCAAT
CCTTGACTTCTTCATGAAGAGAAGTCAATCTTTGTTATTCCTGAAGAGGAGTTAATCA
Found at i:409 original size:27 final size:27
Alignment explanation
Indices: 373--463 Score: 83
Period size: 27 Copynumber: 3.3 Consensus size: 27
363 CCTTCACTTC
* *
373 TTCATAAAGAGAAGTTAATCTTTGTTA
1 TTCATGAAGAGAAGTCAATCTTTGTTA
* * * *
400 TTCATGAAGAGGAGTCGATCCTTGAATTC
1 TTCATGAAGAGAAGTCAATCTTTG--TTA
* *
429 CTCGTGAAGAGAAGTCAATCTTTGTTA
1 TTCATGAAGAGAAGTCAATCTTTGTTA
*
456 TTCTTGAA
1 TTCATGAA
464 TCCTTCGTGA
Statistics
Matches: 48, Mismatches: 14, Indels: 4
0.73 0.21 0.06
Matches are distributed among these distances:
27 27 0.56
29 21 0.44
ACGTcount: A:0.31, C:0.13, G:0.20, T:0.36
Consensus pattern (27 bp):
TTCATGAAGAGAAGTCAATCTTTGTTA
Found at i:514 original size:29 final size:29
Alignment explanation
Indices: 482--571 Score: 98
Period size: 29 Copynumber: 3.2 Consensus size: 29
472 GATAAGGAAC
482 CAATCCTTGACTTCTTCATGAAGAGAAGT
1 CAATCCTTGACTTCTTCATGAAGAGAAGT
* *
511 CAAT-CTATG--TTATTCATGAAGA-AGATT
1 CAATCCT-TGACTTCTTCATGAAGAGA-AGT
* *
538 CAATCCTTGACTTCCTCGTGAAGAGAAGT
1 CAATCCTTGACTTCTTCATGAAGAGAAGT
567 CAATC
1 CAATC
572 TCTGTTATTC
Statistics
Matches: 49, Mismatches: 6, Indels: 12
0.73 0.09 0.18
Matches are distributed among these distances:
26 1 0.02
27 20 0.41
28 4 0.08
29 23 0.47
30 1 0.02
ACGTcount: A:0.32, C:0.20, G:0.17, T:0.31
Consensus pattern (29 bp):
CAATCCTTGACTTCTTCATGAAGAGAAGT
Found at i:527 original size:27 final size:26
Alignment explanation
Indices: 496--581 Score: 75
Period size: 27 Copynumber: 3.1 Consensus size: 26
486 CCTTGACTTC
496 TTCATGAAGAGAAGTCAATCTATGTTA
1 TTCATGAAGAGAAGTCAATCT-TGTTA
* *
523 TTCATGAAGA-AGATTCAATCCTTGACTTC
1 TTCATGAAGAGA-AGTCAAT-CTTG--TTA
* *
552 CTCGTGAAGAGAAGTCAATCTCTGTTA
1 TTCATGAAGAGAAGTCAATCT-TGTTA
579 TTC
1 TTC
582 CTGACTCCCT
Statistics
Matches: 46, Mismatches: 7, Indels: 12
0.71 0.11 0.18
Matches are distributed among these distances:
26 1 0.02
27 22 0.48
28 4 0.09
29 18 0.39
30 1 0.02
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.34
Consensus pattern (26 bp):
TTCATGAAGAGAAGTCAATCTTGTTA
Found at i:1214 original size:134 final size:135
Alignment explanation
Indices: 925--1215 Score: 383
Period size: 134 Copynumber: 2.2 Consensus size: 135
915 ATTTTGTCTT
* * *
925 CCTGAAGAATAGAGAAGCAAATCAAGTTCGATTCAATCTTCCCTGAAGAACAATGAAGTGGATCA
1 CCTGAAGAACA-AGAAGCAAATCAAGTTCGATTCAATCATCCCTAAAGAACAATGAAGTGGATCA
** * * *
990 AAGATTTTTCGAGTATGATATCCCCTAAAGAAGAGTGGAGTAGATTCTTTTTTTTCTTCAGATTT
65 AAGATTTTTCGAGTATGATATCCCCTAAAGAAGAGTGGAACAGATTCTTTCTTCTCTTCAGAATT
* * *
1055 GGTCTT
130 GATATC
* * * *
1061 CCTGAAG-ACAACAATCAAATCAAGTTCGATTCCAT-ATCCCTAAAGAACAGTGAAGTGGATCAA
1 CCTGAAGAACAAGAAGCAAATCAAGTTCGATTCAATCATCCCTAAAGAACAATGAAGTGGATCAA
*
1124 AGATTTTCTCGAGTATGATCTCCCCTAAAGAAGAGTGGAACAGATTC-TTCTTCT-TTCAGAATT
66 AGATTTT-TCGAGTATGATATCCCCTAAAGAAGAGTGGAACAGATTCTTTCTTCTCTTCAGAATT
1187 GATATC
130 GATATC
1193 CCTGAAGAACAATGAAGCAAATC
1 CCTGAAGAACAA-GAAGCAAATC
1216 CTCGTTTTAA
Statistics
Matches: 134, Mismatches: 18, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
132 18 0.13
133 41 0.31
134 66 0.49
135 2 0.01
136 7 0.05
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.29
Consensus pattern (135 bp):
CCTGAAGAACAAGAAGCAAATCAAGTTCGATTCAATCATCCCTAAAGAACAATGAAGTGGATCAA
AGATTTTTCGAGTATGATATCCCCTAAAGAAGAGTGGAACAGATTCTTTCTTCTCTTCAGAATTG
ATATC
Found at i:1505 original size:3 final size:3
Alignment explanation
Indices: 1497--1536 Score: 57
Period size: 3 Copynumber: 13.7 Consensus size: 3
1487 TCATCCCTAA
1497 TAT TAT TA- TAT TA- TAT TAT TAT TATT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT TA
1537 ACTTTTATTG
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
2 4 0.12
3 27 0.79
4 3 0.09
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:1514 original size:13 final size:14
Alignment explanation
Indices: 1496--1536 Score: 68
Period size: 13 Copynumber: 3.1 Consensus size: 14
1486 TTCATCCCTA
1496 ATATTATTA-TATT
1 ATATTATTATTATT
1509 ATATTATTATTATT
1 ATATTATTATTATT
1523 -TATTATTATTATT
1 ATATTATTATTATT
1536 A
1 A
1537 ACTTTTATTG
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
13 22 0.85
14 4 0.15
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (14 bp):
ATATTATTATTATT
Found at i:1518 original size:16 final size:16
Alignment explanation
Indices: 1497--1536 Score: 64
Period size: 16 Copynumber: 2.5 Consensus size: 16
1487 TCATCCCTAA
1497 TATTATTATATTA-TAT
1 TATTATTAT-TTATTAT
1513 TATTATTATTTATTAT
1 TATTATTATTTATTAT
1529 TATTATTA
1 TATTATTA
1537 ACTTTTATTG
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
15 3 0.13
16 20 0.87
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (16 bp):
TATTATTATTTATTAT
Found at i:1544 original size:16 final size:15
Alignment explanation
Indices: 1497--1545 Score: 53
Period size: 16 Copynumber: 3.1 Consensus size: 15
1487 TCATCCCTAA
*
1497 TATTATTATATTATAT
1 TATTATTA-ATTTTAT
*
1513 TATTATTATTTATTAT
1 TATTATTAATT-TTAT
1529 TATTATTAACTTTTAT
1 TATTATTAA-TTTTAT
1545 T
1 T
1546 GTAGGCCCAA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
15 2 0.07
16 24 0.86
17 2 0.07
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (15 bp):
TATTATTAATTTTAT
Found at i:6516 original size:23 final size:23
Alignment explanation
Indices: 6469--6522 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
6459 GGTGACTAAA
* * **
6469 ATAAAATTATATTAAATTAGCAC
1 ATAAAATTAAAATAAATTAAAAC
*
6492 ATTAAATTAAAATAAATTAAAAC
1 ATAAAATTAAAATAAATTAAAAC
6515 ATAAAATT
1 ATAAAATT
6523 CAGGGTTTAA
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.59, C:0.06, G:0.02, T:0.33
Consensus pattern (23 bp):
ATAAAATTAAAATAAATTAAAAC
Found at i:7696 original size:22 final size:22
Alignment explanation
Indices: 7644--7697 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 22
7634 GGGCATGTAA
*
7644 AAATGTAATAATAATAAATTAT
1 AAATATAATAATAATAAATTAT
** *
7666 TTATTTAATAATAAT-AATATAT
1 AAATATAATAATAATAAAT-TAT
7688 AAATATAATA
1 AAATATAATA
7698 TTAAACAAAT
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
21 3 0.12
22 22 0.88
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (22 bp):
AAATATAATAATAATAAATTAT
Found at i:7735 original size:27 final size:30
Alignment explanation
Indices: 7675--7728 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
7665 TTTATTTAAT
*
7675 AATAATAATATATAAATATAATATTAAACA
1 AATAATAATATATAAATATAATACTAAACA
7705 AATAATAATA-ATAAATA-AA-ACTAA
1 AATAATAATATATAAATATAATACTAA
7729 TGAAATAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
27 4 0.17
28 2 0.09
29 7 0.30
30 10 0.43
ACGTcount: A:0.67, C:0.04, G:0.00, T:0.30
Consensus pattern (30 bp):
AATAATAATATATAAATATAATACTAAACA
Found at i:8191 original size:113 final size:114
Alignment explanation
Indices: 8046--8570 Score: 644
Period size: 113 Copynumber: 4.7 Consensus size: 114
8036 TGTGATAGAG
* * *
8046 TCAAAC-AAAGGTTGAACAAATTCTTCTTATTATGAACTTCTTCTT-CATCTTCAGATAAGTTCT
1 TCAAACAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCT
* *
8109 TCTCATTATGAACTCTTCTTTGGAAAAT-TTGATCCATCGAGTGATGAAT
66 TCTCATTATGAACTCTTCTTTGG-AAATGTTAATCCATCAAGTGATGAAT
* * * * *
8158 TCAAATAAAAAGTTGAACAAATTCTTCTCATTATGAATTTCTTCCTCTTTCTTCAGATGAGTTCT
1 TCAAACAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCT
*
8223 TCTCATTATGAACTC-TCTTTGGAAAAGTTAATCCATCAAGTGATGAAT
66 TCTCATTATGAACTCTTCTTTGGAAATGTTAATCCATCAAGTGATGAAT
* * * *
8271 TCGAGA-AAAAGGTTAAACAAGTTCTTCTCATTATGAACTTCTTTTTCCTTCTTCAGATGAG---
1 TC-AAACAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTC
** * *
8332 TTCTCATTATGAACAATTC--TGGAAATGTTGATCCATCAAGTGATGGAT
65 TTCTCATTATGAACTCTTCTTTGGAAATGTTAATCCATCAAGTGATGAAT
** * ** *
8380 TTGAGCAAAAGGTTGAACACGTTCTTCTCATTATGAACTTCCTCTTCCTTCTTCAGATGAGTTCT
1 TCAAACAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCT
* * * ** *
8445 TCTCATTATGAACT-TTCTCTGGTAATGCTAATCCATCGGGTGATAAAT
66 TCTCATTATGAACTCTTCTTTGGAAATGTTAATCCATCAAGTGATGAAT
*
8493 T-AAAGCAAAAGGTTGAACAAAAT-TTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTC
1 TCAAA-CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTC
8556 TTCTCATTATGAACT
65 TTCTCATTATGAACT
8571 TTACCTGGCA
Statistics
Matches: 355, Mismatches: 46, Indels: 24
0.84 0.11 0.06
Matches are distributed among these distances:
109 78 0.22
110 14 0.04
111 5 0.01
112 77 0.22
113 149 0.42
114 32 0.09
ACGTcount: A:0.30, C:0.18, G:0.14, T:0.38
Consensus pattern (114 bp):
TCAAACAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCT
TCTCATTATGAACTCTTCTTTGGAAATGTTAATCCATCAAGTGATGAAT
Found at i:8442 original size:222 final size:222
Alignment explanation
Indices: 8052--8608 Score: 656
Period size: 222 Copynumber: 2.5 Consensus size: 222
8042 AGAGTCAAAC
* * *
8052 AAAGGTTGAACAAATTCTTCTTATTATGAACTTCTTCTT-CATCTTCAGATAAGTTCTTCTCATT
1 AAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAG-T-TTCTCATT
* * * * *
8116 ATGAACTCTTCTTTGGAAAAT-TTGATCCATCGAGTGATGAATTCAAATAAAAAGTTGAACAAAT
64 ATGAAC-ATTC--TGG-AAATGTTGATCCATCAAGTGATGGATTTAAACAAAAAGTTGAACAAAT
* * * *
8180 TCTTCTCATTATGAATTTCTTCCTCTTTCTTCAGATGAGTTCTTCTCATTATGAACTCTCTTTGG
125 TCTTCTCATTATGAACTTCCTCCTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTCTCTGG
* * **
8245 AAAAGTTAATCCATCAAGTGATGAATTCGAGAA
190 AAAAGCTAATCCATCAAGTGATAAATTAAAGAA
* * *
8278 AAAGGTTAAACAAGTTCTTCTCATTATGAACTTCTTTTTCCTTCTTCAGATGAG-TTCTCATTAT
1 AAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTTCTCATTAT
* * * **
8342 GAACAATTCTGGAAATGTTGATCCATCAAGTGATGGATTTGAGCAAAAGGTTGAACACGTTCTTC
66 GAAC-ATTCTGGAAATGTTGATCCATCAAGTGATGGATTTAAACAAAAAGTTGAACAAATTCTTC
* * * *
8407 TCATTATGAACTTCCTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGTAATG
130 TCATTATGAACTTCCTCCTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTCTCTGGAAAAG
** *
8472 CTAATCCATCGGGTGATAAATTAAAGCA
195 CTAATCCATCAAGTGATAAATTAAAGAA
*
8500 AAAGGTTGAACAAAAT-TTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAG-T-TTCTCATT
* * * *
8564 ATGAACTTTACCTGG-CATGTTGATCCATTAAGTAATGGATTTAAA
64 ATGAACATT--CTGGAAATGTTGATCCATCAAGTGATGGATTTAAA
8609 TCTTTGCTAA
Statistics
Matches: 282, Mismatches: 42, Indels: 16
0.83 0.12 0.05
Matches are distributed among these distances:
221 40 0.14
222 133 0.47
223 2 0.01
224 56 0.20
225 4 0.01
226 35 0.12
227 12 0.04
ACGTcount: A:0.29, C:0.18, G:0.14, T:0.38
Consensus pattern (222 bp):
AAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTTCTCATTAT
GAACATTCTGGAAATGTTGATCCATCAAGTGATGGATTTAAACAAAAAGTTGAACAAATTCTTCT
CATTATGAACTTCCTCCTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTCTCTGGAAAAGC
TAATCCATCAAGTGATAAATTAAAGAA
Found at i:16901 original size:43 final size:44
Alignment explanation
Indices: 16839--16923 Score: 127
Period size: 43 Copynumber: 2.0 Consensus size: 44
16829 GTGCATCAAA
* *
16839 CAAAACTTTTACATATAGGGGACATCTTTCAGTCCTAACTTCAG
1 CAAAACTTTTACATATAGGGGACAACTTTCACTCCTAACTTCAG
* *
16883 CAAAAC-TTTACATATAGGGGATAACTTTCCCTCCTAACTTC
1 CAAAACTTTTACATATAGGGGACAACTTTCACTCCTAACTTC
16924 TCTAAAGCCA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
43 31 0.84
44 6 0.16
ACGTcount: A:0.32, C:0.25, G:0.12, T:0.32
Consensus pattern (44 bp):
CAAAACTTTTACATATAGGGGACAACTTTCACTCCTAACTTCAG
Found at i:18920 original size:28 final size:28
Alignment explanation
Indices: 18864--18921 Score: 66
Period size: 28 Copynumber: 2.1 Consensus size: 28
18854 TAATATTAAT
* *
18864 AAATAAATAAATATAAAATATTATCTAA
1 AAATAAATAAAAATAAAATATTATATAA
18892 AAAT-AATAAAAATAAATATAATT-TATAA
1 AAATAAATAAAAATAAA-AT-ATTATATAA
18920 AA
1 AA
18922 GTAAGATATT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
27 11 0.42
28 12 0.46
29 3 0.12
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (28 bp):
AAATAAATAAAAATAAAATATTATATAA
Found at i:20890 original size:3 final size:3
Alignment explanation
Indices: 20884--20936 Score: 60
Period size: 3 Copynumber: 19.0 Consensus size: 3
20874 ATTATTTATT
* *
20884 TAA TAA TAA TAA T-A TAA T-A TAA TAA TAA TAT TAA -AA CAA -AA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
20928 TAA TAA TAA
1 TAA TAA TAA
20937 ATAAAACTAA
Statistics
Matches: 44, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
2 8 0.18
3 36 0.82
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:20906 original size:19 final size:18
Alignment explanation
Indices: 20884--20939 Score: 67
Period size: 19 Copynumber: 3.0 Consensus size: 18
20874 ATTATTTATT
20884 TAATAATAATAATATAATA
1 TAATAATAATAATA-AATA
* *
20903 TAATAATAATATTAAAACA
1 TAATAATAATAAT-AAATA
*
20922 AAATAATAATAATAAATA
1 TAATAATAATAATAAATA
20940 AAACTAATGA
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
18 4 0.13
19 26 0.84
20 1 0.03
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (18 bp):
TAATAATAATAATAAATA
Found at i:20909 original size:22 final size:21
Alignment explanation
Indices: 20862--20940 Score: 74
Period size: 22 Copynumber: 3.8 Consensus size: 21
20852 TGTAAAAATG
* * *
20862 TAATAATAATAAATTATTTATT
1 TAATAATAATAAATAATATA-A
20884 TAATAATAATAATATAATATAA
1 TAATAATAATAA-ATAATATAA
*
20906 TAATAATATTAAA-ACA-A-AA
1 TAATAATAATAAATA-ATATAA
20925 TAATAATAATAAATAA
1 TAATAATAATAAATAA
20941 AACTAATGAA
Statistics
Matches: 49, Mismatches: 5, Indels: 9
0.78 0.08 0.14
Matches are distributed among these distances:
19 15 0.31
20 3 0.06
21 2 0.04
22 23 0.47
23 6 0.12
ACGTcount: A:0.62, C:0.01, G:0.00, T:0.37
Consensus pattern (21 bp):
TAATAATAATAAATAATATAA
Found at i:20947 original size:19 final size:18
Alignment explanation
Indices: 20887--20962 Score: 66
Period size: 19 Copynumber: 4.1 Consensus size: 18
20877 ATTTATTTAA
*
20887 TAATAATAATATAATATAA-
1 TAATAATAATA-AA-AAAAC
* *
20906 TAATAATATTAAAACAAAA
1 TAATAATAATAAAA-AAAC
20925 TAATAATAATAAATAAAAC
1 TAATAATAATAAA-AAAAC
*
20944 TAATGA-AATAAAAAAAC
1 TAATAATAATAAAAAAAC
20961 TA
1 TA
20963 GTGTCTTCAA
Statistics
Matches: 49, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
17 8 0.16
18 10 0.20
19 30 0.61
20 1 0.02
ACGTcount: A:0.67, C:0.04, G:0.01, T:0.28
Consensus pattern (18 bp):
TAATAATAATAAAAAAAC
Found at i:30794 original size:43 final size:44
Alignment explanation
Indices: 30732--30816 Score: 127
Period size: 43 Copynumber: 2.0 Consensus size: 44
30722 GTGCATCAAA
* *
30732 CAAAACTTTTACATATAGGGGACATCTTTCAGTCCTAACTTCAG
1 CAAAACTTTTACATATAGGGGACAACTTTCACTCCTAACTTCAG
* *
30776 CAAAAC-TTTACATATAGGGGATAACTTTCCCTCCTAACTTC
1 CAAAACTTTTACATATAGGGGACAACTTTCACTCCTAACTTC
30817 TCTAAAGCCA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
43 31 0.84
44 6 0.16
ACGTcount: A:0.32, C:0.25, G:0.12, T:0.32
Consensus pattern (44 bp):
CAAAACTTTTACATATAGGGGACAACTTTCACTCCTAACTTCAG
Found at i:32818 original size:29 final size:28
Alignment explanation
Indices: 32760--32819 Score: 68
Period size: 29 Copynumber: 2.1 Consensus size: 28
32750 TAATATTAAT
*
32760 AAATAAATAAATATAAAATATTTATCTAA
1 AAATAAATAAAAATAAAATATTTA-CTAA
*
32789 AAATAATTAAAAATAAATATAATTTA-TAA
1 AAATAAATAAAAATAAA-AT-ATTTACTAA
32818 AA
1 AA
32820 GTAAGATATT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
29 20 0.74
30 2 0.07
31 5 0.19
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (28 bp):
AAATAAATAAAAATAAAATATTTACTAA
Found at i:34791 original size:3 final size:3
Alignment explanation
Indices: 34785--34837 Score: 60
Period size: 3 Copynumber: 19.0 Consensus size: 3
34775 ATTATTTATT
* *
34785 TAA TAA TAA TAA T-A TAA T-A TAA TAA TAA TAT TAA -AA CAA -AA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
34829 TAA TAA TAA
1 TAA TAA TAA
34838 ATAAAACTAA
Statistics
Matches: 44, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
2 8 0.18
3 36 0.82
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:34807 original size:19 final size:18
Alignment explanation
Indices: 34785--34840 Score: 67
Period size: 19 Copynumber: 3.0 Consensus size: 18
34775 ATTATTTATT
34785 TAATAATAATAATATAATA
1 TAATAATAATAATA-AATA
* *
34804 TAATAATAATATTAAAACA
1 TAATAATAATAAT-AAATA
*
34823 AAATAATAATAATAAATA
1 TAATAATAATAATAAATA
34841 AAACTAATGA
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
18 4 0.13
19 26 0.84
20 1 0.03
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (18 bp):
TAATAATAATAATAAATA
Found at i:34810 original size:22 final size:21
Alignment explanation
Indices: 34763--34841 Score: 74
Period size: 22 Copynumber: 3.8 Consensus size: 21
34753 TGTAAAAATG
* * *
34763 TAATAATAATAAATTATTTATT
1 TAATAATAATAAATAATATA-A
34785 TAATAATAATAATATAATATAA
1 TAATAATAATAA-ATAATATAA
*
34807 TAATAATATTAAA-ACA-A-AA
1 TAATAATAATAAATA-ATATAA
34826 TAATAATAATAAATAA
1 TAATAATAATAAATAA
34842 AACTAATGAA
Statistics
Matches: 49, Mismatches: 5, Indels: 9
0.78 0.08 0.14
Matches are distributed among these distances:
19 15 0.31
20 3 0.06
21 2 0.04
22 23 0.47
23 6 0.12
ACGTcount: A:0.62, C:0.01, G:0.00, T:0.37
Consensus pattern (21 bp):
TAATAATAATAAATAATATAA
Found at i:34848 original size:19 final size:18
Alignment explanation
Indices: 34788--34863 Score: 66
Period size: 19 Copynumber: 4.1 Consensus size: 18
34778 ATTTATTTAA
*
34788 TAATAATAATATAATATAA-
1 TAATAATAATA-AA-AAAAC
* *
34807 TAATAATATTAAAACAAAA
1 TAATAATAATAAAA-AAAC
34826 TAATAATAATAAATAAAAC
1 TAATAATAATAAA-AAAAC
*
34845 TAATGA-AATAAAAAAAC
1 TAATAATAATAAAAAAAC
34862 TA
1 TA
34864 GTGTCTTCAA
Statistics
Matches: 49, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
17 8 0.16
18 10 0.20
19 30 0.61
20 1 0.02
ACGTcount: A:0.67, C:0.04, G:0.01, T:0.28
Consensus pattern (18 bp):
TAATAATAATAAAAAAAC
Found at i:48616 original size:23 final size:21
Alignment explanation
Indices: 48588--48645 Score: 62
Period size: 23 Copynumber: 2.7 Consensus size: 21
48578 ACATAGCAGA
48588 GTGCATCGATGCACATTCAAGG
1 GTGCATCGATGCACATTC-AGG
* * *
48610 CGTGCATCGGTGCACCTTCATG
1 -GTGCATCGATGCACATTCAGG
*
48632 GTGAATCGATGCAC
1 GTGCATCGATGCAC
48646 TAGGTAGTGT
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
21 12 0.40
22 2 0.07
23 16 0.53
ACGTcount: A:0.22, C:0.26, G:0.28, T:0.24
Consensus pattern (21 bp):
GTGCATCGATGCACATTCAGG
Found at i:48644 original size:21 final size:23
Alignment explanation
Indices: 48592--48645 Score: 58
Period size: 21 Copynumber: 2.4 Consensus size: 23
48582 AGCAGAGTGC
*
48592 ATCGATGCACATTCAAGGCGTGC
1 ATCGATGCACATTCAAGGCGTGA
* * *
48615 ATCGGTGCACCTTC-ATG-GTGA
1 ATCGATGCACATTCAAGGCGTGA
48636 ATCGATGCAC
1 ATCGATGCAC
48646 TAGGTAGTGT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
21 12 0.46
22 2 0.08
23 12 0.46
ACGTcount: A:0.24, C:0.26, G:0.26, T:0.24
Consensus pattern (23 bp):
ATCGATGCACATTCAAGGCGTGA
Found at i:57222 original size:14 final size:14
Alignment explanation
Indices: 57174--57222 Score: 55
Period size: 14 Copynumber: 3.6 Consensus size: 14
57164 GGTCAAAGGA
57174 GGTCAACGATC-AC
1 GGTCAACGATCAAC
* *
57187 GGTCAACGGTCAAT
1 GGTCAACGATCAAC
* *
57201 AGTAAACGATCAAC
1 GGTCAACGATCAAC
57215 GGTCAACG
1 GGTCAACG
57223 TCGGTTGGTC
Statistics
Matches: 27, Mismatches: 8, Indels: 1
0.75 0.22 0.03
Matches are distributed among these distances:
13 10 0.37
14 17 0.63
ACGTcount: A:0.35, C:0.24, G:0.24, T:0.16
Consensus pattern (14 bp):
GGTCAACGATCAAC
Found at i:57278 original size:10 final size:10
Alignment explanation
Indices: 57258--57318 Score: 56
Period size: 9 Copynumber: 6.2 Consensus size: 10
57248 GTCAAACTGC
*
57258 TTCAGACCGG
1 TTCAAACCGG
*
57268 TTCGAACCGG
1 TTCAAACCGG
57278 -TCAAACCGG
1 TTCAAACCGG
*
57287 -TCAAAACCGA
1 TTC-AAACCGG
57297 TTCAAAACCGG
1 TTC-AAACCGG
57308 -TCAAACCGG
1 TTCAAACCGG
57317 TT
1 TT
57319 TTCCAGCTGC
Statistics
Matches: 43, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
9 17 0.40
10 17 0.40
11 9 0.21
ACGTcount: A:0.31, C:0.30, G:0.21, T:0.18
Consensus pattern (10 bp):
TTCAAACCGG
Found at i:57286 original size:9 final size:10
Alignment explanation
Indices: 57272--57317 Score: 60
Period size: 9 Copynumber: 4.7 Consensus size: 10
57262 GACCGGTTCG
57272 AACCGGTC-A
1 AACCGGTCAA
57281 AACCGGTCAA
1 AACCGGTCAA
*
57291 AACCGATTCAA
1 AACCG-GTCAA
57302 AACCGGTC-A
1 AACCGGTCAA
57311 AACCGGT
1 AACCGGT
57318 TTTCCAGCTG
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
9 16 0.48
10 8 0.24
11 9 0.27
ACGTcount: A:0.37, C:0.30, G:0.20, T:0.13
Consensus pattern (10 bp):
AACCGGTCAA
Found at i:65905 original size:27 final size:27
Alignment explanation
Indices: 65875--65960 Score: 88
Period size: 27 Copynumber: 3.2 Consensus size: 27
65865 CATTGAAACT
*
65875 TCAA-CTTGAGTTCCTCGTGAAGAGAAG
1 TCAATCTTGAGTT-TTCGTGAAGAGAAG
* * *
65902 TCAATCTT-TGTTATTCCTGAAGAGGAG
1 TCAATCTTGAGTT-TTCGTGAAGAGAAG
65929 TCAATCCTTGA-TTTTCGTGAAGAGAAG
1 TCAAT-CTTGAGTTTTCGTGAAGAGAAG
65956 TCAAT
1 TCAAT
65961 TTTGTTATTC
Statistics
Matches: 48, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
27 40 0.83
28 8 0.17
ACGTcount: A:0.29, C:0.16, G:0.22, T:0.33
Consensus pattern (27 bp):
TCAATCTTGAGTTTTCGTGAAGAGAAG
Found at i:66045 original size:26 final size:28
Alignment explanation
Indices: 65995--66083 Score: 83
Period size: 29 Copynumber: 3.2 Consensus size: 28
65985 AAAAAGGAAC
* **
65995 CAATCCTTGACTTCCTCGTGAAGAGAAGT
1 CAATCCTTGA-TTACTAATGAAGAGAAGT
*
66024 CAATCC-TG-TTACTAATGAAGAGGAGT
1 CAATCCTTGATTACTAATGAAGAGAAGT
* **
66050 CAATCCTTGACTTCCTCGTGAAGAGAAGT
1 CAATCCTTGA-TTACTAATGAAGAGAAGT
66079 CAATC
1 CAATC
66084 TTTATTATTC
Statistics
Matches: 49, Mismatches: 8, Indels: 6
0.78 0.13 0.10
Matches are distributed among these distances:
26 20 0.41
27 2 0.04
28 2 0.04
29 25 0.51
ACGTcount: A:0.30, C:0.22, G:0.20, T:0.27
Consensus pattern (28 bp):
CAATCCTTGATTACTAATGAAGAGAAGT
Found at i:66115 original size:120 final size:122
Alignment explanation
Indices: 65879--66269 Score: 559
Period size: 120 Copynumber: 3.3 Consensus size: 122
65869 GAAACTTCAA
* *
65879 CTTGAGTTCCTCGTGAAGAGAAGTCAATCTTTGTTATTCCTGAAGAGGAGTCAATCCTTGATT-T
1 CTTGACTTCCTCGTGAAGAGAAGTCAATCTTTGTTATTCCTGAAGAGGAGTCAATCCTTGATTCC
* *
65943 TCGTGAAGAGAAGTCAAT-TTTGTTATTCCTGACTCCCTCGTGAAAAAGGAACCAATC
66 TCGTGAAGAGAAGTCAATCTTTATTATTCCTGACTCCCTCGTGAAGAA-GAACCAATC
* * **
66000 CTTGACTTCCTCGTGAAGAGAAGTCAATC-CTGTTACTAATGAAGAGGAGTCAATCCTTGACTTC
1 CTTGACTTCCTCGTGAAGAGAAGTCAATCTTTGTTATTCCTGAAGAGGAGTCAATCCTTGA-TTC
66064 CTCGTGAAGAGAAGTCAATCTTTATTATT-CTGACTCCCTCGT-AAGAAGAACCAATC
65 CTCGTGAAGAGAAGTCAATCTTTATTATTCCTGACTCCCTCGTGAAGAAGAACCAATC
*
66120 C-TGACTTCCTCGTGAAGAGAAGTCAATCTTTGTTATTCCTGAAGAGGATTCAATCCTTGATTTC
1 CTTGACTTCCTCGTGAAGAGAAGTCAATCTTTGTTATTCCTGAAGAGGAGTCAATCCTTGA-TTC
* * * *
66184 CTCGT-AA-AGAGGTCAATCTTTTTTATTCCTGACTCCCTTGTGAAGATGAACCAATC
65 CTCGTGAAGAGAAGTCAATCTTTATTATTCCTGACTCCCTCGTGAAGAAGAACCAATC
*
66240 CTTGACTTCCTCGT-AA-AGAGGTCAATCTTT
1 CTTGACTTCCTCGTGAAGAGAAGTCAATCTTT
66270 ATTTTTCATG
Statistics
Matches: 244, Mismatches: 19, Indels: 16
0.87 0.07 0.06
Matches are distributed among these distances:
118 18 0.07
119 54 0.22
120 87 0.36
121 46 0.19
122 31 0.13
123 8 0.03
ACGTcount: A:0.28, C:0.21, G:0.19, T:0.32
Consensus pattern (122 bp):
CTTGACTTCCTCGTGAAGAGAAGTCAATCTTTGTTATTCCTGAAGAGGAGTCAATCCTTGATTCC
TCGTGAAGAGAAGTCAATCTTTATTATTCCTGACTCCCTCGTGAAGAAGAACCAATC
Found at i:66162 original size:27 final size:27
Alignment explanation
Indices: 66132--66215 Score: 82
Period size: 27 Copynumber: 3.1 Consensus size: 27
66122 GACTTCCTCG
66132 TGAAGAGAAGTCAATCTTTGTTATTCC
1 TGAAGAGAAGTCAATCTTTGTTATTCC
* * * *
66159 TGAAGAGGATTCAATCCTTGAT-TTCC
1 TGAAGAGAAGTCAATCTTTGTTATTCC
* *
66185 TCGTAA-AGAGGTCAATCTTTTTTATTCC
1 T-G-AAGAGAAGTCAATCTTTGTTATTCC
66213 TGA
1 TGA
66216 CTCCCTTGTG
Statistics
Matches: 44, Mismatches: 10, Indels: 7
0.72 0.16 0.11
Matches are distributed among these distances:
26 6 0.14
27 31 0.70
28 7 0.16
ACGTcount: A:0.27, C:0.17, G:0.18, T:0.38
Consensus pattern (27 bp):
TGAAGAGAAGTCAATCTTTGTTATTCC
Found at i:66263 original size:65 final size:65
Alignment explanation
Indices: 66159--66318 Score: 241
Period size: 65 Copynumber: 2.5 Consensus size: 65
66149 TTGTTATTCC
** * *
66159 TGAAGAGGATTCAATCCTTGATTTCCTCGTAAAGAGGTCAATCTTT-TTTATTCCTGACTCCCTT
1 TGAAGAGGAACCAATCCTTGACTTCCTCGTAAAGAGGTCAATCTTTATTT-TTCATGACTCCCTT
66223 G
65 G
* *
66224 TGAAGATGAACCAATCCTTGACTTCCTCGTAAAGAGGTCAATCTTTATTTTTCATGACTCCCTTT
1 TGAAGAGGAACCAATCCTTGACTTCCTCGTAAAGAGGTCAATCTTTATTTTTCATGACTCCCTTG
*
66289 TTAAGAGGAACCAATCCTTGACTTCCTCGT
1 TGAAGAGGAACCAATCCTTGACTTCCTCGT
66319 GGAGAGATGA
Statistics
Matches: 86, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
65 83 0.97
66 3 0.03
ACGTcount: A:0.25, C:0.23, G:0.16, T:0.36
Consensus pattern (65 bp):
TGAAGAGGAACCAATCCTTGACTTCCTCGTAAAGAGGTCAATCTTTATTTTTCATGACTCCCTTG
Found at i:66627 original size:133 final size:129
Alignment explanation
Indices: 66342--66633 Score: 345
Period size: 131 Copynumber: 2.2 Consensus size: 129
66332 CTTTAGATCA
* * * ***
66342 GGTCTTCCTGAAGAACATCGAAGC-AATCAAGTTTGATCAATCTTCTCTGAAGAATGGCGAAGGG
1 GGTCTTCCTGAAGAACAACGAAGCAAATCAAGTTTGATCAATATTCCCTGAAGAACAACGAAGGG
* * * * *
66406 ATCAAATATTTCTCGAGTCTGATCTCCCCTAAGAAGAGTGTATCAGATTCTTCTTTTCATATTT
66 ATCAAATATTTCTCGAGTCTGATATCCCCTAAGAAGAGTGGAGCAAATTATTCTTTTCATATTT
* * ** * *
66470 TGTCTTCCTAAAGAACAGTGAAGCAAATCATGTTTGATTCAATATTCCCTGAAGAACAATGAAGT
1 GGTCTTCCTGAAGAACAACGAAGCAAATCAAGTTTGA-TCAATATTCCCTGAAGAACAACGAAG-
* * *
66535 GGATCAAATATTTGTCTAGTCTGATAT-CCCTAAAGAATAGTGGAGCAAATTATTCTTCTTTCAT
64 GGATCAAATATTTCTCGAGTCTGATATCCCCT-AAGAAGAGTGGAGCAAATTATTC-T-TTTCAT
66599 ATTT
126 ATTT
66603 GGTCTTCCTGAAGAACAACGAAGCAAATCAA
1 GGTCTTCCTGAAGAACAACGAAGCAAATCAA
66634 CCTCGGTTCA
Statistics
Matches: 134, Mismatches: 24, Indels: 7
0.81 0.15 0.04
Matches are distributed among these distances:
128 20 0.15
129 11 0.08
130 24 0.18
131 42 0.31
132 1 0.01
133 36 0.27
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Consensus pattern (129 bp):
GGTCTTCCTGAAGAACAACGAAGCAAATCAAGTTTGATCAATATTCCCTGAAGAACAACGAAGGG
ATCAAATATTTCTCGAGTCTGATATCCCCTAAGAAGAGTGGAGCAAATTATTCTTTTCATATTT
Found at i:66644 original size:133 final size:129
Alignment explanation
Indices: 66342--66653 Score: 313
Period size: 133 Copynumber: 2.4 Consensus size: 129
66332 CTTTAGATCA
* * * * * * ***
66342 GGTCTTCCTGAAGAACATCGAAGC-AATCAAGTTTGATCAATCTTCTCTGAAGAATGGCGAAGGG
1 GGTCTTCCTGAAGAACAACGAAGCAAATCAACTTGGTTCAATATTCCCTGAAGAACAACGAAGGG
* * * * *
66406 ATCAAATATTTCTCGAGTCTGATCTCCCCTAAGAAGAGTGTATCAGATTCTTCTTTTCATATTT
66 ATCAAATATTTCTCGAGTCTGATATCCCCTAAGAAGAGTGGAGCAAATTATTCTTTTCATATTT
* * ** ** * *
66470 TGTCTTCCTAAAGAACAGTGAAGCAAATCATGTTTGATTCAATATTCCCTGAAGAACAATGAAGT
1 GGTCTTCCTGAAGAACAACGAAGCAAATCA-ACTTGGTTCAATATTCCCTGAAGAACAACGAAG-
* * *
66535 GGATCAAATATTTGTCTAGTCTGATAT-CCCTAAAGAATAGTGGAGCAAATTATTCTTCTTTCAT
64 GGATCAAATATTTCTCGAGTCTGATATCCCCT-AAGAAGAGTGGAGCAAATTATTC-T-TTTCAT
66599 ATTT
126 ATTT
* *
66603 GGTCTTCCTGAAGAACAACGAAGCAAATCAACCTCGGTTCAACATTCCCTG
1 GGTCTTCCTGAAGAACAACGAAGCAAATCAA-CTTGGTTCAATATTCCCTG
66654 GAAAATAGTG
Statistics
Matches: 145, Mismatches: 32, Indels: 9
0.78 0.17 0.05
Matches are distributed among these distances:
128 20 0.14
129 5 0.03
130 26 0.18
131 42 0.29
132 1 0.01
133 51 0.35
ACGTcount: A:0.31, C:0.20, G:0.17, T:0.32
Consensus pattern (129 bp):
GGTCTTCCTGAAGAACAACGAAGCAAATCAACTTGGTTCAATATTCCCTGAAGAACAACGAAGGG
ATCAAATATTTCTCGAGTCTGATATCCCCTAAGAAGAGTGGAGCAAATTATTCTTTTCATATTT
Found at i:66921 original size:3 final size:3
Alignment explanation
Indices: 66908--66953 Score: 78
Period size: 3 Copynumber: 16.0 Consensus size: 3
66898 TTTTCGTCCC
66908 TAT TA- TAT TAT TAT TAT TAT TAT TA- TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
66954 CTTATTTCTT
Statistics
Matches: 41, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
2 4 0.10
3 37 0.90
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:66930 original size:17 final size:17
Alignment explanation
Indices: 66916--66950 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
66906 CCTATTATAT
66916 TATTATTATTATTATTA
1 TATTATTATTATTATTA
66933 TATTATTATTATTATTA
1 TATTATTATTATTATTA
66950 T
1 T
66951 TATCTTATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (17 bp):
TATTATTATTATTATTA
Found at i:66933 original size:20 final size:20
Alignment explanation
Indices: 66908--66959 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
66898 TTTTCGTCCC
66908 TATTATATTATTATTATTAT
1 TATTATATTATTATTATTAT
66928 TATTATATTATTATTATTAT
1 TATTATATTATTATTATTAT
*
66948 TATTATCTTATT
1 TATTATATTATT
66960 TCTTAAATGT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (20 bp):
TATTATATTATTATTATTAT
Done.