Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011224.1 Kokia drynarioides strain JFW-HI SEQ_126202, 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: 83373
ACGTcount: A:0.33, C:0.17, G:0.15, T:0.35
Warning! 128 characters in sequence are not A, C, G, or T
Found at i:4062 original size:20 final size:20
Alignment explanation
Indices: 4037--4110 Score: 58
Period size: 20 Copynumber: 3.6 Consensus size: 20
4027 ATGAGCCTTT
*
4037 AAATCAATTTGAATAGAATC
1 AAATCAAATTGAATAGAATC
** *
4057 AAATCAAATCAAATTGAATC
1 AAATCAAATTGAATAGAATC
* * * *
4077 GAAAATCAATTTGATTATAATA
1 --AAATCAAATTGAATAGAATC
4099 AAATCAAATTGA
1 AAATCAAATTGA
4111 GATATTTGTA
Statistics
Matches: 40, Mismatches: 12, Indels: 4
0.71 0.21 0.07
Matches are distributed among these distances:
20 27 0.68
22 13 0.32
ACGTcount: A:0.53, C:0.09, G:0.08, T:0.30
Consensus pattern (20 bp):
AAATCAAATTGAATAGAATC
Found at i:5363 original size:27 final size:27
Alignment explanation
Indices: 5316--5390 Score: 71
Period size: 27 Copynumber: 2.8 Consensus size: 27
5306 GGATTTAGAC
* * * *
5316 ATTTA-AAAAAAGATTGGGAATTAAGA
1 ATTTAGAAAAAAAATCGAGAATTAACA
*
5342 ATTTAGAAAAAAAATCGAGAATTGACA
1 ATTTAGAAAAAAAATCGAGAATTAACA
* *
5369 ATTGAGAATAATAAATCGAGAA
1 ATTTAGAA-AAAAAATCGAGAA
5391 CAATAAGTTG
Statistics
Matches: 40, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
26 5 0.12
27 23 0.57
28 12 0.30
ACGTcount: A:0.55, C:0.04, G:0.17, T:0.24
Consensus pattern (27 bp):
ATTTAGAAAAAAAATCGAGAATTAACA
Found at i:5934 original size:23 final size:23
Alignment explanation
Indices: 5879--5926 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 23
5869 TTCATTTTTT
*
5879 AAATACTATTATTTTTAATATAA
1 AAATACTATTATTTTAAATATAA
*
5902 AAATACTATTATTTTAAATTTAA
1 AAATACTATTATTTTAAATATAA
5925 AA
1 AA
5927 GTATTATTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (23 bp):
AAATACTATTATTTTAAATATAA
Found at i:8663 original size:661 final size:661
Alignment explanation
Indices: 7313--9242 Score: 3324
Period size: 663 Copynumber: 2.9 Consensus size: 661
7303 CTCATATACT
* * *
7313 TCTCATTTTTTTCCCCAAATATTGGCATAGGATTTACATGTGTTTATGGTGTTAAAGTATTTTTT
1 TCTCA-TTTTTTCCCCAAATATTGGCATAGGATTTACATGTTTTTATGGTATTAAAGTA--CTTT
* * *
7378 CCTTTTGGTTTTGTGTTGGTGAATTTTACTCTTGATTACAAGGTCTTCTCATGT-TTATCAAAAT
63 --ATTTGGTTCTGTGTTGGTGAATTTTACTCTTGTTTACAAGGTCTTCTCATGTCTT-TCAAAAT
* * ** *
7442 TTACTTGTTAATTTAGGAGTTTGTGAAGAACTGAGAGAATTTTTCTTGTAATTCCATTAACTTAG
125 TTACTTGTTAATTTAGGAGTTCGTGAAGAATTGAGAGAATTTTTCAAGAAATTCCATTAACTTAG
* *
7507 CTTGTAATACCTCAGGTTTACAAAGATAGTACCTGAAAACTAGGCT-A---ACT----TG----C
190 CTTGTAATACCTCAGGTTTACAAAGATAATAACTGAAAACTAGGCTAACTTACTAAACTGACTAC
* *
7560 ---T-AAAACCTCTAACTGGCATTGCAGTTTGGATTAATTTTGCTGCTGGCTCTTCCTTGGGTGC
255 TATTAAAAACCTCTAACTGGCATTGCAGTTTGGACTAATTCTGCTGCTGGCTCTTCCTTGGGTGC
* * * *
7621 AAGTCATAACTTGCCAGAGTGTGATGCCATAAACAATCACAATAACCTTTGCAACGGAGACCTTG
320 AAGTCATAACTTGCCAGAGTATGGTGCCATGAACAATCACAATAACCTTTGCAACAGAGACCTTG
7686 CTGCTGGTAATAAATTGAGTATTTTGCATATATTACTTTGGTTTATCTTGTTTATTGTATTTTCT
385 CTGCTGGTAATAAATTGAGTATTTTGCATATATTACTTTGGTTTATCTTGTTTATTGTATTTTCT
7751 TTAATTCCCCCCTCCATTTGGCAAAGAAATTACATGTTTGTTTTTTTTGGTCTTTTATGTTGGTT
450 TTAATTCCCCCCTCCATTTGGCAAAGAAATTACATG--T-TTTTTTTTGGTCTTTTATGTTGGTT
*
7816 AATTTCACTCTTGATTGCAAGACAAGGTAATCATCATATTGGTTCATCTTGTTTTGTGATTCTTT
512 AATTTCACTCTTGATTACAAGACAAGGTAATCATCATATTGGTTCATCTTGTTTTGTGATTCTTT
7881 TTAAATTCCTCCCTCCAATTGGTAACAATATTTCATGTTTTGTGATTCTTTCATGTTTGCTCTCA
577 TTAAATTCCTCCCTCCAATTGGTAACAATATTTCATGTTTTGTGATTCTTTCATGTTTGCTCTCA
7946 TCAGCATATATTCTGGTTCA
642 TCAGCATATATTCTGGTTCA
*
7966 TCTCGTTTTTTCCCCAAATATTGGCATAGGATTTACATGTTTTTATGGTATTAAAGTACTTTATT
1 TCTCATTTTTTCCCCAAATATTGGCATAGGATTTACATGTTTTTATGGTATTAAAGTACTTTATT
*
8031 TGGTTCTGTGTTGGTGAATTCTACTCTTGTTTACAAGGTCTTCTCATGTCTTTCAAAATTTACTT
66 TGGTTCTGTGTTGGTGAATTTTACTCTTGTTTACAAGGTCTTCTCATGTCTTTCAAAATTTACTT
8096 GTTAATTTAGGAGTTCGTGAAGAATTGAGAGAATTTTTCAAGAAATTCCATTAACTTAGCTTGTA
131 GTTAATTTAGGAGTTCGTGAAGAATTGAGAGAATTTTTCAAGAAATTCCATTAACTTAGCTTGTA
8161 ATACCTCAGGTTTACAAAGATAATAACTGAAAACTAGGCTAACTTACTAAACTGACTACTATTAA
196 ATACCTCAGGTTTACAAAGATAATAACTGAAAACTAGGCTAACTTACTAAACTGACTACTATTAA
8226 AAACCTCTAACTGGCATTGCAGTTTGGACTAATTCTGCTGCTGGCTCTTCCTTGGGTGCAAGTCA
261 AAACCTCTAACTGGCATTGCAGTTTGGACTAATTCTGCTGCTGGCTCTTCCTTGGGTGCAAGTCA
8291 TAACTTGCCAGAGTATGGTGCCATGAACAATCACAATAACCTTTGCAACAGAGACCTTGCTGCTG
326 TAACTTGCCAGAGTATGGTGCCATGAACAATCACAATAACCTTTGCAACAGAGACCTTGCTGCTG
8356 GTAATAAATTGAGTATTTTGCATATATTACTTTGGTTTATCTTGTTTATTGTATTTTCTTTAATT
391 GTAATAAATTGAGTATTTTGCATATATTACTTTGGTTTATCTTGTTTATTGTATTTTCTTTAATT
8421 CCCCCCTCCATTTGGCAAAGAAATTACATGTTTTTTTTTGGTCTTTTATGTTGGTTAATTTCACT
456 CCCCCCTCCATTTGGCAAAGAAATTACATGTTTTTTTTTGGTCTTTTATGTTGGTTAATTTCACT
8486 CTTGATTACAAGACAAGGTAATCATCATATTGGTTCATCTTGTTTTGTGATTCTTTTTAAATTCC
521 CTTGATTACAAGACAAGGTAATCATCATATTGGTTCATCTTGTTTTGTGATTCTTTTTAAATTCC
8551 TCCCTCCAATTGGTAACAATATTTCATGTTTTGTGATTCTTTCATGTTTGCTCTCATCAGCATAT
586 TCCCTCCAATTGGTAACAATATTTCATGTTTTGTGATTCTTTCATGTTTGCTCTCATCAGCATAT
8616 ATTCTGGTTCA
651 ATTCTGGTTCA
8627 TCTCATTTTTTCCCCAAATATTGGCATAGGATTTACATGTTTTTATGGTATTAAAGTACTTTATT
1 TCTCATTTTTTCCCCAAATATTGGCATAGGATTTACATGTTTTTATGGTATTAAAGTACTTTATT
*
8692 TGGGTCTGTGTTGGTGAAAATTTTACTCTTGTTTACAAGGTCTTCTCATGTCTTTCAAAATTTAC
66 TGGTTCTGTGTTGGTG--AATTTTACTCTTGTTTACAAGGTCTTCTCATGTCTTTCAAAATTTAC
*
8757 TTGTTAATTTAGGAGTTCGTGAAGAATTGAGAGAACTTTTCAAGAAATTCCATTAACTTAGCTTG
129 TTGTTAATTTAGGAGTTCGTGAAGAATTGAGAGAATTTTTCAAGAAATTCCATTAACTTAGCTTG
8822 TAATACCTCAGGTTTACAAAGATAATAACTGAAAACTAGGCTAACTTACTAAACTGACTACTATT
194 TAATACCTCAGGTTTACAAAGATAATAACTGAAAACTAGGCTAACTTACTAAACTGACTACTATT
* *
8887 AACAACCTCTACCTGGCATTGCAGTTTGGACTAATTCTGCTGCTGGCTCTTCCTTGGGTGCAAGT
259 AAAAACCTCTAACTGGCATTGCAGTTTGGACTAATTCTGCTGCTGGCTCTTCCTTGGGTGCAAGT
* *
8952 CATAACTTGCCAGAGAATGGTGCCATGAACAACCACAATAACCTTTGCAACAGAGACCTTGCTGC
324 CATAACTTGCCAGAGTATGGTGCCATGAACAATCACAATAACCTTTGCAACAGAGACCTTGCTGC
9017 TGGTAATAAATTGAGTATTTTGCATATATTACTTTGGTTTATCTTGTTTATTGTATTTTCTTTAA
389 TGGTAATAAATTGAGTATTTTGCATATATTACTTTGGTTTATCTTGTTTATTGTATTTTCTTTAA
*
9082 TTCCCCCCTCCATTTGGCAAAGAAGTTACATG-TTTTTTTTGGTC-TTT-TGTTGGTTAATTTCA
454 TTCCCCCCTCCATTTGGCAAAGAAATTACATGTTTTTTTTTGGTCTTTTATGTTGGTTAATTTCA
** * *
9144 CTCTTGATTACAAGACAAGGTAATCATCATAACGGTTCATTTTGTTTTGTGATTCTTTTTTAATT
519 CTCTTGATTACAAGACAAGGTAATCATCATATTGGTTCATCTTGTTTTGTGATTCTTTTTAAATT
9209 CCTCCCTCCAATTGGTAACAATATTTCATGTTTT
584 CCTCCCTCCAATTGGTAACAATATTTCATGTTTT
9243 TATCATTGTA
Statistics
Matches: 1223, Mismatches: 35, Indels: 31
0.95 0.03 0.02
Matches are distributed among these distances:
648 159 0.13
649 3 0.00
650 3 0.00
652 54 0.04
653 4 0.00
656 2 0.00
660 111 0.09
661 256 0.21
662 13 0.01
663 398 0.33
664 220 0.18
ACGTcount: A:0.26, C:0.17, G:0.16, T:0.41
Consensus pattern (661 bp):
TCTCATTTTTTCCCCAAATATTGGCATAGGATTTACATGTTTTTATGGTATTAAAGTACTTTATT
TGGTTCTGTGTTGGTGAATTTTACTCTTGTTTACAAGGTCTTCTCATGTCTTTCAAAATTTACTT
GTTAATTTAGGAGTTCGTGAAGAATTGAGAGAATTTTTCAAGAAATTCCATTAACTTAGCTTGTA
ATACCTCAGGTTTACAAAGATAATAACTGAAAACTAGGCTAACTTACTAAACTGACTACTATTAA
AAACCTCTAACTGGCATTGCAGTTTGGACTAATTCTGCTGCTGGCTCTTCCTTGGGTGCAAGTCA
TAACTTGCCAGAGTATGGTGCCATGAACAATCACAATAACCTTTGCAACAGAGACCTTGCTGCTG
GTAATAAATTGAGTATTTTGCATATATTACTTTGGTTTATCTTGTTTATTGTATTTTCTTTAATT
CCCCCCTCCATTTGGCAAAGAAATTACATGTTTTTTTTTGGTCTTTTATGTTGGTTAATTTCACT
CTTGATTACAAGACAAGGTAATCATCATATTGGTTCATCTTGTTTTGTGATTCTTTTTAAATTCC
TCCCTCCAATTGGTAACAATATTTCATGTTTTGTGATTCTTTCATGTTTGCTCTCATCAGCATAT
ATTCTGGTTCA
Found at i:10621 original size:42 final size:40
Alignment explanation
Indices: 10546--10638 Score: 107
Period size: 43 Copynumber: 2.2 Consensus size: 40
10536 TGTATAAAAA
*
10546 AAATATCTTTTTTTACAATTTTAAAATAATTTTAACAATATTT
1 AAATATTTTTTTTTACAATTTT-AAATAATTTTAA-AA-ATTT
* * *
10589 AATTATTTTTTTTTACAAATTTT-AATAGTTTTAATAATTT
1 AAATATTTTTTTTTAC-AATTTTAAATAATTTTAAAAATTT
10629 AAATATTTTT
1 AAATATTTTT
10639 AATATGATTT
Statistics
Matches: 44, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
40 13 0.30
41 1 0.02
42 10 0.23
43 14 0.32
44 6 0.14
ACGTcount: A:0.39, C:0.04, G:0.01, T:0.56
Consensus pattern (40 bp):
AAATATTTTTTTTTACAATTTTAAATAATTTTAAAAATTT
Found at i:10627 original size:18 final size:18
Alignment explanation
Indices: 10606--10642 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
10596 TTTTTTTACA
*
10606 AATTTTAATAGTTTTAAT
1 AATTTAAATAGTTTTAAT
*
10624 AATTTAAATATTTTTAAT
1 AATTTAAATAGTTTTAAT
10642 A
1 A
10643 TGATTTTTAA
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:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (18 bp):
AATTTAAATAGTTTTAAT
Found at i:15059 original size:17 final size:17
Alignment explanation
Indices: 15039--15071 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
15029 TTTAAATAAG
15039 TTTTATTAAT-TTTATAT
1 TTTTA-TAATATTTATAT
15056 TTTTATAATATTTATA
1 TTTTATAATATTTATA
15072 AGTTTATATC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (17 bp):
TTTTATAATATTTATAT
Found at i:15355 original size:97 final size:97
Alignment explanation
Indices: 15172--15357 Score: 282
Period size: 97 Copynumber: 1.9 Consensus size: 97
15162 TTGGCTTGTC
* * *
15172 AATTTCTTTTACCAATCAACACAGTCAATGACGAAAATCGTTAACGAAGGGGCTTAATTGATTAT
1 AATTTATTTTACCAATCAACACAGTCAATGACGAAAATCGTTAACGAAAGAGCTTAATTGATTAT
*
15237 TTTAGTTAACGATAGACGCTTAATTGGGTGCT
66 TTTAGTTAACGACAGACGCTTAATTGGGTGCT
* * *
15269 AATTTATTTTACCAGTCAACATAGTCAATGATGAAAATCGTTAACGAAAGAGCTTAATTGATTAT
1 AATTTATTTTACCAATCAACACAGTCAATGACGAAAATCGTTAACGAAAGAGCTTAATTGATTAT
* **
15334 TTTAGTTAATGACAGGTGCTTAAT
66 TTTAGTTAACGACAGACGCTTAAT
15358 AGGCATGAGA
Statistics
Matches: 79, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
97 79 1.00
ACGTcount: A:0.35, C:0.13, G:0.17, T:0.34
Consensus pattern (97 bp):
AATTTATTTTACCAATCAACACAGTCAATGACGAAAATCGTTAACGAAAGAGCTTAATTGATTAT
TTTAGTTAACGACAGACGCTTAATTGGGTGCT
Found at i:21292 original size:21 final size:21
Alignment explanation
Indices: 21259--21312 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
21249 AGAGTTTTTA
*
21259 GTATCGATAGAAG-CATAACTT
1 GTATCGGTAGAAGTCA-AACTT
* *
21280 GTTTCGGTAGAAGTCACACTT
1 GTATCGGTAGAAGTCAAACTT
21301 GTATCGGTAGAA
1 GTATCGGTAGAA
21313 CTATCACAAC
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 26 0.93
22 2 0.07
ACGTcount: A:0.31, C:0.15, G:0.24, T:0.30
Consensus pattern (21 bp):
GTATCGGTAGAAGTCAAACTT
Found at i:24074 original size:11 final size:11
Alignment explanation
Indices: 24058--24109 Score: 54
Period size: 11 Copynumber: 4.7 Consensus size: 11
24048 TGATATGTCA
24058 AGAAAACAATG
1 AGAAAACAATG
*
24069 AGAAAACAATA
1 AGAAAACAATG
*
24080 ATAAAACAATTG
1 AGAAAACAA-TG
24092 -GAAAACAAT-
1 AGAAAACAATG
24101 AGGAAAACA
1 A-GAAAACA
24110 TCATTTTTTT
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
10 1 0.03
11 32 0.94
12 1 0.03
ACGTcount: A:0.65, C:0.10, G:0.13, T:0.12
Consensus pattern (11 bp):
AGAAAACAATG
Found at i:24107 original size:22 final size:22
Alignment explanation
Indices: 24057--24109 Score: 72
Period size: 22 Copynumber: 2.4 Consensus size: 22
24047 GTGATATGTC
24057 AAGAAAACAATGAGAAAACAAT
1 AAGAAAACAATGAGAAAACAAT
*
24079 AATAAAACAATTG-GAAAACAAT
1 AAGAAAACAA-TGAGAAAACAAT
*
24101 AGGAAAACA
1 AAGAAAACA
24110 TCATTTTTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
22 25 0.93
23 2 0.07
ACGTcount: A:0.66, C:0.09, G:0.13, T:0.11
Consensus pattern (22 bp):
AAGAAAACAATGAGAAAACAAT
Found at i:26809 original size:18 final size:19
Alignment explanation
Indices: 26775--26810 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
26765 TTTAATTATT
*
26775 TTTTAAAATTATAAAAATA
1 TTTTAAAACTATAAAAATA
26794 TTTTAAAACT-TAAAAAT
1 TTTTAAAACTATAAAAAT
26811 TATCAAAAAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.42
Consensus pattern (19 bp):
TTTTAAAACTATAAAAATA
Found at i:29023 original size:2 final size:2
Alignment explanation
Indices: 29013--29059 Score: 58
Period size: 2 Copynumber: 23.5 Consensus size: 2
29003 GACATGTGTG
* * * *
29013 TA TA AA TA TA TA TA TA TA TA TA TA TA TT TA CA CA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
29055 TA TA T
1 TA TA T
29060 TAGTTATTAG
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:31022 original size:6 final size:6
Alignment explanation
Indices: 31011--31056 Score: 55
Period size: 6 Copynumber: 8.3 Consensus size: 6
31001 GATAATAAAT
*
31011 TGTTTA TGTTTA --TTTA TGTTTA TG--TA TGTTTA TGTTTA TGCTTA
1 TGTTTA TGTTTA TGTTTA TGTTTA TGTTTA TGTTTA TGTTTA TGTTTA
31055 TG
1 TG
31057 AAACCTAATT
Statistics
Matches: 35, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
4 8 0.23
6 27 0.77
ACGTcount: A:0.17, C:0.02, G:0.17, T:0.63
Consensus pattern (6 bp):
TGTTTA
Found at i:31032 original size:16 final size:16
Alignment explanation
Indices: 31011--31055 Score: 63
Period size: 16 Copynumber: 2.8 Consensus size: 16
31001 GATAATAAAT
31011 TGTTTATGTTTATTTA
1 TGTTTATGTTTATTTA
* *
31027 TGTTTATGTATGTTTA
1 TGTTTATGTTTATTTA
*
31043 TGTTTATGCTTAT
1 TGTTTATGTTTAT
31056 GAAACCTAAT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.18, C:0.02, G:0.16, T:0.64
Consensus pattern (16 bp):
TGTTTATGTTTATTTA
Found at i:31044 original size:10 final size:10
Alignment explanation
Indices: 31015--31045 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
31005 ATAAATTGTT
*
31015 TATGTTTATT
1 TATGTTTATG
31025 TATGTTTATG
1 TATGTTTATG
31035 TATGTTTATG
1 TATGTTTATG
31045 T
1 T
31046 TTATGCTTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.19, C:0.00, G:0.16, T:0.65
Consensus pattern (10 bp):
TATGTTTATG
Found at i:33251 original size:16 final size:16
Alignment explanation
Indices: 33230--33290 Score: 59
Period size: 16 Copynumber: 3.5 Consensus size: 16
33220 ATTCACCGAT
33230 ACAAAGCCTACTAGGC
1 ACAAAGCCTACTAGGC
*
33246 ACAAAGCCTGCATACACTGGC
1 ACAAAGCCTAC-T--A--GGC
33267 ACAAAGCCTACTAGGC
1 ACAAAGCCTACTAGGC
*
33283 ACATAGCC
1 ACAAAGCC
33291 CGAATATACC
Statistics
Matches: 37, Mismatches: 3, Indels: 10
0.74 0.06 0.20
Matches are distributed among these distances:
16 20 0.54
17 1 0.03
18 1 0.03
19 1 0.03
20 1 0.03
21 13 0.35
ACGTcount: A:0.36, C:0.33, G:0.18, T:0.13
Consensus pattern (16 bp):
ACAAAGCCTACTAGGC
Found at i:33322 original size:38 final size:37
Alignment explanation
Indices: 33230--33405 Score: 217
Period size: 37 Copynumber: 4.7 Consensus size: 37
33220 ATTCACCGAT
* * * *
33230 ACAAAGCCTACTAGGCACAAAGCCTGCATACACTGGC
1 ACAAAGCCTACTAGGCACATAGCCCGAATACACCGGC
*
33267 ACAAAGCCTACTAGGCACATAGCCCGAATATACCGGC
1 ACAAAGCCTACTAGGCACATAGCCCGAATACACCGGC
* *
33304 ACAAAAGCCTACTTGGCACATAACCCGAATACACCGGC
1 AC-AAAGCCTACTAGGCACATAGCCCGAATACACCGGC
* * *
33342 ACAAAGCTTACTAGACACATAGCCCGAATACACTGGC
1 ACAAAGCCTACTAGGCACATAGCCCGAATACACCGGC
* * * *
33379 TCAAAGCTTTCTAGGCACAAAGCCCGA
1 ACAAAGCCTACTAGGCACATAGCCCGA
33406 TTATTTAAAT
Statistics
Matches: 121, Mismatches: 17, Indels: 2
0.86 0.12 0.01
Matches are distributed among these distances:
37 87 0.72
38 34 0.28
ACGTcount: A:0.36, C:0.32, G:0.18, T:0.15
Consensus pattern (37 bp):
ACAAAGCCTACTAGGCACATAGCCCGAATACACCGGC
Found at i:33355 original size:75 final size:75
Alignment explanation
Indices: 33232--33405 Score: 226
Period size: 75 Copynumber: 2.3 Consensus size: 75
33222 TCACCGATAC
* * * *
33232 AAAGCCTACTAGGCACAAAGCCTGCATACACTGGCACAAAGCCTACTAGGCACATAGCCCGAATA
1 AAAGCCTACTAGGCACAAAGCCCGAATACACCGGCACAAAGCCTACTAGACACATAGCCCGAATA
33297 TACCGGCACA
66 TACCGGCACA
* *
33307 AAAGCCTACTTGGCACATAA-CCCGAATACACCGGCACAAAGCTTACTAGACACATAGCCCGAAT
1 AAAGCCTACTAGGCACA-AAGCCCGAATACACCGGCACAAAGCCTACTAGACACATAGCCCGAAT
* * *
33371 ACACTGGCTC-
65 ATACCGGCACA
* *
33381 AAAGCTTTCTAGGCACAAAGCCCGA
1 AAAGCCTACTAGGCACAAAGCCCGA
33406 TTATTTAAAT
Statistics
Matches: 85, Mismatches: 12, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
73 2 0.02
74 19 0.22
75 62 0.73
76 2 0.02
ACGTcount: A:0.36, C:0.32, G:0.18, T:0.15
Consensus pattern (75 bp):
AAAGCCTACTAGGCACAAAGCCCGAATACACCGGCACAAAGCCTACTAGACACATAGCCCGAATA
TACCGGCACA
Found at i:35772 original size:24 final size:24
Alignment explanation
Indices: 35745--35845 Score: 121
Period size: 24 Copynumber: 4.2 Consensus size: 24
35735 GCAAGTTCAT
* *
35745 TACGTTTACGCTCGTCAGTATGAA
1 TACGTTTACGCTCGCCAGCATGAA
*
35769 TACGTTTACACTCGCCAGCATGAA
1 TACGTTTACGCTCGCCAGCATGAA
** *
35793 TACGTTTTTTGCTTGCCAGCATGAA
1 TACG-TTTACGCTCGCCAGCATGAA
* *
35818 TACGTTTACGCTCGTCATCATGAA
1 TACGTTTACGCTCGCCAGCATGAA
35842 TACG
1 TACG
35846 AGAAACATTG
Statistics
Matches: 64, Mismatches: 12, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
24 44 0.69
25 20 0.31
ACGTcount: A:0.25, C:0.24, G:0.19, T:0.33
Consensus pattern (24 bp):
TACGTTTACGCTCGCCAGCATGAA
Found at i:39544 original size:43 final size:43
Alignment explanation
Indices: 39444--39857 Score: 446
Period size: 43 Copynumber: 9.7 Consensus size: 43
39434 TTATTACGAA
*
39444 AAACGCCGCTATAGAACATGGTCTTTAGCGGCGCTTTCC-CAC
1 AAACGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTTCCTCAC
* *
39486 AAATGCCGCTAAAGAACATTGTCTTTAGCGGCGCTTTCCTCAC
1 AAACGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTTCCTCAC
*
39529 AAACGCCGCTAAAGAACATGGTCTTTAGTGGCGCTTT--TACAC
1 AAACGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTTCCT-CAC
* * *
39571 AAATGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTTCCCCAA
1 AAACGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTTCCTCAC
* *
39614 AAACGCCGCTAAAGAACATGATCTTTAGTGGCGCTTTACC-CAC
1 AAACGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTT-CCTCAC
* * * *
39657 AAACACCGCAAAAGAACATGGTCTTTAGCGGTGCTTTCAC-CAA
1 AAACGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTTC-CTCAC
* * * * * *
39700 AAACGTCACTAAAAAACATGGTCTTTAGCCGCACTTT-CTCCGC
1 AAACGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTTCCT-CAC
* * * ** * * **
39743 AAACGCTGCCAAAGAACATGGTATTTAGCAACGTTTTTCTCGT
1 AAACGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTTCCTCAC
* *
39786 AAACACCGCTAAAGAACATGGTCTTTAGCGGCGC-TTCTCTCAA
1 AAACGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTTC-CTCAC
* *
39829 AAACGCCGCTAAAGACCATGTTCTTTAGC
1 AAACGCCGCTAAAGAACATGGTCTTTAGC
39858 AAATTTTAAC
Statistics
Matches: 308, Mismatches: 54, Indels: 19
0.81 0.14 0.05
Matches are distributed among these distances:
41 2 0.01
42 77 0.25
43 225 0.73
44 4 0.01
ACGTcount: A:0.29, C:0.27, G:0.19, T:0.25
Consensus pattern (43 bp):
AAACGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTTCCTCAC
Found at i:39938 original size:15 final size:15
Alignment explanation
Indices: 39918--39950 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
39908 TTTTCTTGTA
39918 AATTCAAATCCAACC
1 AATTCAAATCCAACC
*
39933 AATTCAAATCCATCC
1 AATTCAAATCCAACC
39948 AAT
1 AAT
39951 AACTTCAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.45, C:0.30, G:0.00, T:0.24
Consensus pattern (15 bp):
AATTCAAATCCAACC
Found at i:41433 original size:173 final size:171
Alignment explanation
Indices: 41060--41561 Score: 789
Period size: 173 Copynumber: 2.9 Consensus size: 171
41050 ATTTTAACCT
* * * * *
41060 CACGCGAATTAGCTTATCCACCCCCTGAACAATACTATAAGAATCAGTACTGAACATCCCTCCTG
1 CACGAGAATTAGCTTATCGACCCCCCGAACAGTACTATAAGAATCAGTATTGAACATCCCTCCTG
*
41125 TAATTGTACACGCGCCCATAGCAATAACATATTTAGGTT-GATGCATTTGTC-CATATATAATCT
66 TAATTGTACACGCGCCCATAGCAATAACATATTTAGGTTCG-GGCATTTGTCTCATATATAATCT
* *
41188 CACTAAAGAGGGCGCCATTTTCATTGTTACTTTATAGACATC
130 CACTAAAAAGGGCGCCATTTTCATTGTTACTGTATAGACATC
*
41230 CACGGGAATTAGCTTATCGACCCCCCGAACAGTACTATAAGAATCAGTATTGAACATCCCTCCTG
1 CACGAGAATTAGCTTATCGACCCCCCGAACAGTACTATAAGAATCAGTATTGAACATCCCTCCTG
* *
41295 TAATTGTACACGCGCCCATTGCAATAACATATTTAGATTCGGGCATTTGTTCATCATATATAATC
66 TAATTGTACACGCGCCCATAGCAATAACATATTTAGGTTCGGGCATTTG-TC-TCATATATAATC
* *
41360 TCACTAAAAAGGGTGTCATTTTCATTGTTACTGTATAGACATC
129 TCACTAAAAAGGGCGCCATTTTCATTGTTACTGTATAGACATC
*
41403 CACGAGAATTAGCTTATCGACCCCCCGAACAGTACTATAAGAATCATTATTGAACATCCCTCCTG
1 CACGAGAATTAGCTTATCGACCCCCCGAACAGTACTATAAGAATCAGTATTGAACATCCCTCCTG
* * *
41468 TAATTGTACACGTGCCCATAGCAATAACATTTTTAGGTTCGGGCATTTGT-TC--GTATAATCTC
66 TAATTGTACACGCGCCCATAGCAATAACATATTTAGGTTCGGGCATTTGTCTCATATATAATCTC
41530 ACTAAAAAGGGCGCCATTTTCATTGTTACTGT
131 ACTAAAAAGGGCGCCATTTTCATTGTTACTGT
41562 TCCAACTGTT
Statistics
Matches: 307, Mismatches: 21, Indels: 10
0.91 0.06 0.03
Matches are distributed among these distances:
168 39 0.13
170 106 0.35
171 3 0.01
172 1 0.00
173 158 0.51
ACGTcount: A:0.30, C:0.24, G:0.15, T:0.31
Consensus pattern (171 bp):
CACGAGAATTAGCTTATCGACCCCCCGAACAGTACTATAAGAATCAGTATTGAACATCCCTCCTG
TAATTGTACACGCGCCCATAGCAATAACATATTTAGGTTCGGGCATTTGTCTCATATATAATCTC
ACTAAAAAGGGCGCCATTTTCATTGTTACTGTATAGACATC
Found at i:42147 original size:41 final size:41
Alignment explanation
Indices: 42085--42462 Score: 476
Period size: 41 Copynumber: 9.3 Consensus size: 41
42075 TTTAAATATA
* * * * *
42085 TTAGTGGCGCTTATGGGAAAGCGTCACTAATACTCTGACCT
1 TTAGCGGCGCTTATGGGAAAGCGCCGCTAATGCCCTGACCT
*
42126 TTAGCGGCGCTTATGGGAAAGCGCCGC---TGCCCTAACCT
1 TTAGCGGCGCTTATGGGAAAGCGCCGCTAATGCCCTGACCT
* *
42164 TTAGCGGCACTTATGGGAAAGCGCCGCTAATGCCCTAACCT
1 TTAGCGGCGCTTATGGGAAAGCGCCGCTAATGCCCTGACCT
* ** *
42205 TTAGTGAAGCTTATGGGAAAGCGCCGCTAATGCCTTGACCT
1 TTAGCGGCGCTTATGGGAAAGCGCCGCTAATGCCCTGACCT
* * *
42246 TTAGCGGCGCTTATGGGAAAGTGCCCCGAATGCCCTGACCT
1 TTAGCGGCGCTTATGGGAAAGCGCCGCTAATGCCCTGACCT
* * * **
42287 TTAGCGGTGCTTATGAGAAAGCGCCACTAATGCTTTGACCT
1 TTAGCGGCGCTTATGGGAAAGCGCCGCTAATGCCCTGACCT
*
42328 TTAGCGGCGCTTATGAGAAAGCGCCGCTAATGCCCTGACCT
1 TTAGCGGCGCTTATGGGAAAGCGCCGCTAATGCCCTGACCT
* *
42369 TTAGCAGTGCTTATGGGAAAGCGCCGCTAATGCCCTGACCT
1 TTAGCGGCGCTTATGGGAAAGCGCCGCTAATGCCCTGACCT
* ** *
42410 TTAGCGGCGCTT-CGACATAAACGCCGCTAATGCCCTGACCT
1 TTAGCGGCGCTTATGGGA-AAGCGCCGCTAATGCCCTGACCT
42451 TTAGCGGCGCTT
1 TTAGCGGCGCTT
42463 CGACATAAAC
Statistics
Matches: 293, Mismatches: 40, Indels: 8
0.86 0.12 0.02
Matches are distributed among these distances:
38 34 0.12
40 2 0.01
41 257 0.88
ACGTcount: A:0.22, C:0.27, G:0.26, T:0.25
Consensus pattern (41 bp):
TTAGCGGCGCTTATGGGAAAGCGCCGCTAATGCCCTGACCT
Found at i:42496 original size:41 final size:41
Alignment explanation
Indices: 42390--42521 Score: 151
Period size: 41 Copynumber: 3.2 Consensus size: 41
42380 TATGGGAAAG
* *
42390 CGCCGCTAATGCCCTGACCTTTAGCGGCGCTTCGACATAAA
1 CGCCGCTAAAGCCCTGACCATTAGCGGCGCTTCGACATAAA
* *
42431 CGCCGCTAATGCCCTGACCTTTAGCGGCGCTTCGACATAAA
1 CGCCGCTAAAGCCCTGACCATTAGCGGCGCTTCGACATAAA
** * *
42472 CGCCGCTAAAG-GTTAGAGCATTAGCGGCGCTTTC-TCTATAAA
1 CGCCGCTAAAGCCCT-GACCATTAGCGGCGC-TTCGAC-ATAAA
42514 CGCCGCTA
1 CGCCGCTA
42522 TTGCTTTTCC
Statistics
Matches: 82, Mismatches: 6, Indels: 5
0.88 0.06 0.05
Matches are distributed among these distances:
40 1 0.01
41 65 0.79
42 16 0.20
ACGTcount: A:0.23, C:0.32, G:0.23, T:0.23
Consensus pattern (41 bp):
CGCCGCTAAAGCCCTGACCATTAGCGGCGCTTCGACATAAA
Found at i:42618 original size:40 final size:40
Alignment explanation
Indices: 42511--42618 Score: 144
Period size: 40 Copynumber: 2.7 Consensus size: 40
42501 CTTTCTCTAT
* * *
42511 AAACGCCGCTATTGCTTTTCCTTTTGCAGCACTTATGGAA
1 AAACGCCGCTATTGCTTTACCTTTTGCGGCACTTATGAAA
***
42551 AAACGCCGCTATTGCTTTACCTTTTGCGGTGTTTATGAAA
1 AAACGCCGCTATTGCTTTACCTTTTGCGGCACTTATGAAA
* *
42591 AAACCCCGCTATTGCTTTACTTTTTGCG
1 AAACGCCGCTATTGCTTTACCTTTTGCG
42619 ACGTTTTCTT
Statistics
Matches: 60, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
40 60 1.00
ACGTcount: A:0.21, C:0.24, G:0.18, T:0.37
Consensus pattern (40 bp):
AAACGCCGCTATTGCTTTACCTTTTGCGGCACTTATGAAA
Found at i:44935 original size:24 final size:24
Alignment explanation
Indices: 44907--44965 Score: 73
Period size: 24 Copynumber: 2.5 Consensus size: 24
44897 TAGACTAATA
* *
44907 AGAGTTTGACTCAAACAAATAAAT
1 AGAGTTTAACTCAAACAAATAAAC
* * *
44931 AGAGTTTAATTTAAACAATTAAAC
1 AGAGTTTAACTCAAACAAATAAAC
44955 AGAGTTTAACT
1 AGAGTTTAACT
44966 GAAAGATTAT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.47, C:0.10, G:0.12, T:0.31
Consensus pattern (24 bp):
AGAGTTTAACTCAAACAAATAAAC
Found at i:58620 original size:127 final size:128
Alignment explanation
Indices: 58446--58685 Score: 302
Period size: 127 Copynumber: 1.9 Consensus size: 128
58436 TATATTTATG
* * * * * * *
58446 TTACAATATAATCAAACACATTACATTCAATGGGACGTAACGAAAATGCCATCATCATTATTGGA
1 TTACAACATAATCAAACACAATACATTCAATGGAACATAACGAAAATGCCACCATCATCATTCGA
* ** *
58511 AAGTTGCCTCCGAAGATGGA-TTTTCACAAAGCTGAAATTCCAAATTAACAAGGGAACATATC
66 AAGTTACCTCCGAAGATAAATTTTTCACAAAGCTAAAATTCCAAATTAACAAGGGAACATATC
* * * *
58573 TTACAACATATTCAAACACAATACATTCAATGGAACATGACGTAAATGGCACCATCATCATTCGA
1 TTACAACATAATCAAACACAATACATTCAATGGAACATAACGAAAATGCCACCATCATCATTCGA
* * * *
58638 AAGTTATCTCTGAAGATAAATTTTTCACATAGCTAAAATTTCAAATTA
66 AAGTTACCTCCGAAGATAAATTTTTCACAAAGCTAAAATTCCAAATTA
58686 GAAAAAAAAA
Statistics
Matches: 93, Mismatches: 19, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
127 69 0.74
128 24 0.26
ACGTcount: A:0.41, C:0.19, G:0.12, T:0.28
Consensus pattern (128 bp):
TTACAACATAATCAAACACAATACATTCAATGGAACATAACGAAAATGCCACCATCATCATTCGA
AAGTTACCTCCGAAGATAAATTTTTCACAAAGCTAAAATTCCAAATTAACAAGGGAACATATC
Found at i:59618 original size:5 final size:5
Alignment explanation
Indices: 59599--59632 Score: 50
Period size: 5 Copynumber: 6.6 Consensus size: 5
59589 ACATTTAAGG
*
59599 CTCGA GCTCGG CTCGA CTCGA CTCGA CTCGA CTC
1 CTCGA -CTCGA CTCGA CTCGA CTCGA CTCGA CTC
59633 ATTTTAAGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
5 22 0.85
6 4 0.15
ACGTcount: A:0.15, C:0.41, G:0.24, T:0.21
Consensus pattern (5 bp):
CTCGA
Found at i:61084 original size:3 final size:3
Alignment explanation
Indices: 61078--61123 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
61068 GCAGTAGTAC
61078 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT G
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT G
61124 TTGTTGTTAA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.33, C:0.00, G:0.35, T:0.33
Consensus pattern (3 bp):
GAT
Found at i:61154 original size:19 final size:19
Alignment explanation
Indices: 61130--61168 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
61120 GATGTTGTTG
*
61130 TTAAAATATGTCATAAGTT
1 TTAAAATATGCCATAAGTT
61149 TTAAAATATGCCATAAGTT
1 TTAAAATATGCCATAAGTT
61168 T
1 T
61169 ATATACTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.41, C:0.08, G:0.10, T:0.41
Consensus pattern (19 bp):
TTAAAATATGCCATAAGTT
Found at i:62053 original size:61 final size:61
Alignment explanation
Indices: 61983--62105 Score: 246
Period size: 61 Copynumber: 2.0 Consensus size: 61
61973 TAGTAAAAAA
61983 TCGCATCTGGGGGGAAACTTTGGAGATTTGTTTTACCAATACTCTACTAGCTAGAGAGCTC
1 TCGCATCTGGGGGGAAACTTTGGAGATTTGTTTTACCAATACTCTACTAGCTAGAGAGCTC
62044 TCGCATCTGGGGGGAAACTTTGGAGATTTGTTTTACCAATACTCTACTAGCTAGAGAGCTC
1 TCGCATCTGGGGGGAAACTTTGGAGATTTGTTTTACCAATACTCTACTAGCTAGAGAGCTC
62105 T
1 T
62106 TTGGGAAACA
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
61 62 1.00
ACGTcount: A:0.24, C:0.20, G:0.24, T:0.32
Consensus pattern (61 bp):
TCGCATCTGGGGGGAAACTTTGGAGATTTGTTTTACCAATACTCTACTAGCTAGAGAGCTC
Found at i:63515 original size:25 final size:25
Alignment explanation
Indices: 63449--63516 Score: 100
Period size: 25 Copynumber: 2.7 Consensus size: 25
63439 TCTCAAAATT
*
63449 TTACCAAGGATAAAATCGTCATAATA
1 TTACCAAGG-TAAAATTGTCATAATA
* *
63475 TTACTAGGGTAAAATTGTCATAATA
1 TTACCAAGGTAAAATTGTCATAATA
63500 TTACCAAGGTAAAATTG
1 TTACCAAGGTAAAATTG
63517 GGATGAGAAA
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
25 30 0.81
26 7 0.19
ACGTcount: A:0.43, C:0.12, G:0.15, T:0.31
Consensus pattern (25 bp):
TTACCAAGGTAAAATTGTCATAATA
Found at i:66598 original size:19 final size:19
Alignment explanation
Indices: 66547--66598 Score: 52
Period size: 19 Copynumber: 2.7 Consensus size: 19
66537 TAAATAATAA
66547 ATTTTGTAATTTTTATAAAT
1 ATTTTGT-ATTTTTATAAAT
** *
66567 ATTTTAAAATTTTA-AAATT
1 ATTTTGTATTTTTATAAA-T
66586 ATTTTGTATTTTT
1 ATTTTGTATTTTT
66599 TTGTTGAGAG
Statistics
Matches: 25, Mismatches: 6, Indels: 3
0.74 0.18 0.09
Matches are distributed among these distances:
18 3 0.12
19 17 0.68
20 5 0.20
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.62
Consensus pattern (19 bp):
ATTTTGTATTTTTATAAAT
Found at i:67091 original size:22 final size:22
Alignment explanation
Indices: 67066--67135 Score: 54
Period size: 22 Copynumber: 3.2 Consensus size: 22
67056 AGTTACCTCC
67066 GAAGATAAATTTTCACAGAGTT
1 GAAGATAAATTTTCACAGAGTT
* ** **
67088 GAAGTTCCAAATTAACA-AGA-AA
1 GAAGAT--AAATTTTCACAGAGTT
*
67110 AAAGATAAATTTTCACAGAGTT
1 GAAGATAAATTTTCACAGAGTT
67132 GAAG
1 GAAG
67136 TTCCAAATTA
Statistics
Matches: 32, Mismatches: 12, Indels: 8
0.62 0.23 0.15
Matches are distributed among these distances:
20 7 0.22
21 3 0.09
22 12 0.38
23 3 0.09
24 7 0.22
ACGTcount: A:0.47, C:0.10, G:0.17, T:0.26
Consensus pattern (22 bp):
GAAGATAAATTTTCACAGAGTT
Found at i:67096 original size:127 final size:127
Alignment explanation
Indices: 66863--67106 Score: 344
Period size: 127 Copynumber: 1.9 Consensus size: 127
66853 TCTATTTATG
* * * * *
66863 TTACAACATAATCAAACACACTACATTCGATGGGACGTGACGAAAATGCCATCATCATTATTGGA
1 TTACAACATAATCAAACACAATACATTCAATGGGACATGACGAAAATGACATCATCATCATTGGA
* **
66928 AAGTTGCCTCCGAAGATGGATTTTCACAAAACTGAAATTCCAAATTAACAAGGGAGCATATC
66 AAGTTACCTCCGAAGATAAATTTTCACAAAACTGAAATTCCAAATTAACAAGGGAGCATATC
* * * *
66990 TTACAACATATTTAAACACAATACATTCAATGGGACATGACGTAAATGACATCATCATCATTTGA
1 TTACAACATAATCAAACACAATACATTCAATGGGACATGACGAAAATGACATCATCATCATTGGA
* ** *
67055 AAGTTACCTCCGAAGATAAATTTTCACAGAGTTGAAGTTCCAAATTAACAAG
66 AAGTTACCTCCGAAGATAAATTTTCACAAAACTGAAATTCCAAATTAACAAG
67107 AAAAAAGATA
Statistics
Matches: 101, Mismatches: 16, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
127 101 1.00
ACGTcount: A:0.40, C:0.19, G:0.15, T:0.26
Consensus pattern (127 bp):
TTACAACATAATCAAACACAATACATTCAATGGGACATGACGAAAATGACATCATCATCATTGGA
AAGTTACCTCCGAAGATAAATTTTCACAAAACTGAAATTCCAAATTAACAAGGGAGCATATC
Found at i:67099 original size:24 final size:24
Alignment explanation
Indices: 67072--67144 Score: 64
Period size: 24 Copynumber: 3.2 Consensus size: 24
67062 CTCCGAAGAT
67072 AAATTTTCACAGAGTTGAAGTTCC
1 AAATTTTCACAGAGTTGAAGTTCC
** *** *
67096 AAATTAACA-AGA-AAAAAGAT--
1 AAATTTTCACAGAGTTGAAGTTCC
67116 AAATTTTCACAGAGTTGAAGTTCC
1 AAATTTTCACAGAGTTGAAGTTCC
67140 AAATT
1 AAATT
67145 AACAAGAAAA
Statistics
Matches: 33, Mismatches: 12, Indels: 8
0.62 0.23 0.15
Matches are distributed among these distances:
20 7 0.21
21 3 0.09
22 8 0.24
23 3 0.09
24 12 0.36
ACGTcount: A:0.45, C:0.12, G:0.14, T:0.29
Consensus pattern (24 bp):
AAATTTTCACAGAGTTGAAGTTCC
Found at i:67130 original size:44 final size:44
Alignment explanation
Indices: 67067--67156 Score: 180
Period size: 44 Copynumber: 2.0 Consensus size: 44
67057 GTTACCTCCG
67067 AAGATAAATTTTCACAGAGTTGAAGTTCCAAATTAACAAGAAAA
1 AAGATAAATTTTCACAGAGTTGAAGTTCCAAATTAACAAGAAAA
67111 AAGATAAATTTTCACAGAGTTGAAGTTCCAAATTAACAAGAAAA
1 AAGATAAATTTTCACAGAGTTGAAGTTCCAAATTAACAAGAAAA
67155 AA
1 AA
67157 TAATCAAAGG
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 46 1.00
ACGTcount: A:0.51, C:0.11, G:0.13, T:0.24
Consensus pattern (44 bp):
AAGATAAATTTTCACAGAGTTGAAGTTCCAAATTAACAAGAAAA
Found at i:68391 original size:20 final size:20
Alignment explanation
Indices: 68353--68390 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
68343 AAAAATTACA
68353 AAAAATTCAAATTAATTTTC
1 AAAAATTCAAATTAATTTTC
*
68373 AAAAATTTAAATT-ATTTT
1 AAAAATTCAAATTAATTTT
68391 TTAAATTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (20 bp):
AAAAATTCAAATTAATTTTC
Found at i:68398 original size:18 final size:18
Alignment explanation
Indices: 68374--68418 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
68364 TTAATTTTCA
* *
68374 AAAATTTAAATTATTTTTT
1 AAAATTTAAAATA-TTTAT
*
68393 AAATTTTAAAATATTTAT
1 AAAATTTAAAATATTTAT
68411 AAAATTTA
1 AAAATTTA
68419 TACTTTTATA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
18 11 0.50
19 11 0.50
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
AAAATTTAAAATATTTAT
Found at i:68415 original size:19 final size:19
Alignment explanation
Indices: 68373--68417 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 19
68363 ATTAATTTTC
* * *
68373 AAAAATTTAAATTATTTTT
1 AAAATTTTAAAATATTTAT
*
68392 TAAATTTTAAAATATTTAT
1 AAAATTTTAAAATATTTAT
68411 AAAATTT
1 AAAATTT
68418 ATACTTTTAT
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (19 bp):
AAAATTTTAAAATATTTAT
Found at i:68448 original size:32 final size:31
Alignment explanation
Indices: 68373--68458 Score: 79
Period size: 33 Copynumber: 2.8 Consensus size: 31
68363 ATTAATTTTC
* *
68373 AAAAATT-TAAA-TTATTTTTTAAATTTTAA
1 AAAAATTATAAATTTATCTTTTAAATTTAAA
* * *
68402 AATATTTATAAAATTTATACTTTTATATTTAAA
1 AAAAATTAT-AAATTTAT-CTTTTAAATTTAAA
*
68435 AAAAATTATAAATTT-TTTTTTAAA
1 AAAAATTATAAATTTATCTTTTAAA
68459 AAAAAATCTA
Statistics
Matches: 44, Mismatches: 9, Indels: 7
0.73 0.15 0.12
Matches are distributed among these distances:
29 5 0.11
30 7 0.16
31 4 0.09
32 10 0.23
33 18 0.41
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (31 bp):
AAAAATTATAAATTTATCTTTTAAATTTAAA
Found at i:68718 original size:31 final size:31
Alignment explanation
Indices: 68680--68900 Score: 126
Period size: 31 Copynumber: 7.4 Consensus size: 31
68670 TTAATATAAT
68680 ATTTGGTACCTGAACTTGACATTTTTTCCTA
1 ATTTGGTACCTGAACTTGACATTTTTTCCTA
* * *
68711 ATTTGGTACCT-AAATT----TTTTTAACCCA
1 ATTTGGTACCTGAACTTGACATTTTT-TCCTA
* *
68738 ATTTGGTACCTGAACTTGACACTTTTTCTTA
1 ATTTGGTACCTGAACTTGACATTTTTTCCTA
** * * *
68769 ATTCAGTA-CTTAAATT----TTTTTTGACCCA
1 ATTTGGTACCTGAACTTGACATTTTTT--CCTA
* *
68797 ATTTGGTACTTGAACTTGACACTTTTTCCTA
1 ATTTGGTACCTGAACTTGACATTTTTTCCTA
** * * *
68828 ATTCAGTACCTAAACTT---TTTTTTTGAACCCA
1 ATTTGGTACCTGAACTTGACATTTTTT---CCTA
*
68859 ATTTGGTACTTGAACTTGACATTTTTTCCTA
1 ATTTGGTACCTGAACTTGACATTTTTTCCTA
*
68890 ATTTGATACCT
1 ATTTGGTACCT
68901 AAGCTTTTTT
Statistics
Matches: 134, Mismatches: 37, Indels: 38
0.64 0.18 0.18
Matches are distributed among these distances:
26 10 0.07
27 14 0.10
28 17 0.13
29 5 0.04
30 10 0.07
31 63 0.47
32 4 0.03
33 5 0.04
34 6 0.04
ACGTcount: A:0.25, C:0.19, G:0.10, T:0.45
Consensus pattern (31 bp):
ATTTGGTACCTGAACTTGACATTTTTTCCTA
Found at i:68902 original size:62 final size:60
Alignment explanation
Indices: 68680--68892 Score: 315
Period size: 59 Copynumber: 3.6 Consensus size: 60
68670 TTAATATAAT
* **
68680 ATTTGGTACCTGAACTTGACATTTTTTCCTAATTTGGTACCTAAA-TTTTTTT-AACCCA
1 ATTTGGTACCTGAACTTGACACTTTTTCCTAATTCAGTACCTAAATTTTTTTTGAACCCA
* *
68738 ATTTGGTACCTGAACTTGACACTTTTTCTTAATTCAGTACTTAAATTTTTTTTG-ACCCA
1 ATTTGGTACCTGAACTTGACACTTTTTCCTAATTCAGTACCTAAATTTTTTTTGAACCCA
*
68797 ATTTGGTACTTGAACTTGACACTTTTTCCTAATTCAGTACCTAAACTTTTTTTTTGAACCCA
1 ATTTGGTACCTGAACTTGACACTTTTTCCTAATTCAGTACCTAAA--TTTTTTTTGAACCCA
* *
68859 ATTTGGTACTTGAACTTGACATTTTTTCCTAATT
1 ATTTGGTACCTGAACTTGACACTTTTTCCTAATT
68893 TGATACCTAA
Statistics
Matches: 141, Mismatches: 9, Indels: 6
0.90 0.06 0.04
Matches are distributed among these distances:
58 40 0.28
59 54 0.38
61 9 0.06
62 38 0.27
ACGTcount: A:0.25, C:0.19, G:0.10, T:0.46
Consensus pattern (60 bp):
ATTTGGTACCTGAACTTGACACTTTTTCCTAATTCAGTACCTAAATTTTTTTTGAACCCA
Found at i:69194 original size:58 final size:59
Alignment explanation
Indices: 69072--69194 Score: 140
Period size: 59 Copynumber: 2.1 Consensus size: 59
69062 AATTAATATT
* * * ***
69072 AAAAAAGATTAAGTATCAAATTAAGAAAAAGAGTCAAGTTCAGGTACCAAATTGGACCC
1 AAAAAAGATTAAGTACCAAATTAAAAAAAAGAGTCAAGTTCAGGTACCAAATTAGAAAA
* * * * *
69131 CAAAAAGTTTAAGTACCAACTTAAAAAAAAGTGTCATGTT-AGGTACCAAATTAGAAAA
1 AAAAAAGATTAAGTACCAAATTAAAAAAAAGAGTCAAGTTCAGGTACCAAATTAGAAAA
69189 AAAAAA
1 AAAAAA
69195 AACATGTCAA
Statistics
Matches: 52, Mismatches: 12, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
58 19 0.37
59 33 0.63
ACGTcount: A:0.52, C:0.12, G:0.15, T:0.21
Consensus pattern (59 bp):
AAAAAAGATTAAGTACCAAATTAAAAAAAAGAGTCAAGTTCAGGTACCAAATTAGAAAA
Found at i:69203 original size:37 final size:37
Alignment explanation
Indices: 69153--69233 Score: 92
Period size: 38 Copynumber: 2.2 Consensus size: 37
69143 GTACCAACTT
* *
69153 AAAAAAAAGTGTCATGTTAG-GTACCAAATTAGAAAA
1 AAAAAAAAATGTCAAGTTAGAGTACCAAATTAGAAAA
* * * *
69189 AAAAAAAACATGTCAAGTTTGAGTATCAAATTGGATAA
1 AAAAAAAA-ATGTCAAGTTAGAGTACCAAATTAGAAAA
69227 AAAAAAA
1 AAAAAAA
69234 TTAGATACCA
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
36 8 0.22
37 9 0.24
38 20 0.54
ACGTcount: A:0.56, C:0.07, G:0.15, T:0.22
Consensus pattern (37 bp):
AAAAAAAAATGTCAAGTTAGAGTACCAAATTAGAAAA
Found at i:77744 original size:81 final size:81
Alignment explanation
Indices: 77609--77768 Score: 311
Period size: 81 Copynumber: 2.0 Consensus size: 81
77599 GGGTCCGAGT
77609 CTTTTATTTATTTCTTGTTGTCCTGAGGGTGTCTTGTTCCCCCCATTGGTTGCTGCAACTTTGTA
1 CTTTTATTTATTTCTTGTTGTCCTGAGGGTGTCTTGTTCCCCCCATTGGTTGCTGCAACTTTGTA
77674 TGTTGAATGCGTGTGA
66 TGTTGAATGCGTGTGA
*
77690 CTTTTATTTATTTCTTGTTGTCCTGAGGGTGTCTTGTTCCCCCCATTGGTTGCTGCAACTTTGTG
1 CTTTTATTTATTTCTTGTTGTCCTGAGGGTGTCTTGTTCCCCCCATTGGTTGCTGCAACTTTGTA
77755 TGTTGAATGCGTGT
66 TGTTGAATGCGTGT
77769 TTTGATTATG
Statistics
Matches: 78, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
81 78 1.00
ACGTcount: A:0.11, C:0.19, G:0.24, T:0.46
Consensus pattern (81 bp):
CTTTTATTTATTTCTTGTTGTCCTGAGGGTGTCTTGTTCCCCCCATTGGTTGCTGCAACTTTGTA
TGTTGAATGCGTGTGA
Found at i:79129 original size:14 final size:15
Alignment explanation
Indices: 79105--79135 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
79095 CCTATTTTAT
79105 TAATGGCTAAAGTTG
1 TAATGGCTAAAGTTG
79120 TAAT-GCTAAAGTTG
1 TAATGGCTAAAGTTG
79134 TA
1 TA
79136 TTAATGGCTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 12 0.75
15 4 0.25
ACGTcount: A:0.35, C:0.06, G:0.23, T:0.35
Consensus pattern (15 bp):
TAATGGCTAAAGTTG
Found at i:79429 original size:6 final size:6
Alignment explanation
Indices: 79420--79452 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
79410 TTAATTTTGA
*
79420 TTGAGG TTGAGG TTGAGG TTGAGG TTGACG TTG
1 TTGAGG TTGAGG TTGAGG TTGAGG TTGAGG TTG
79453 GATAAGAACT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.15, C:0.03, G:0.45, T:0.36
Consensus pattern (6 bp):
TTGAGG
Found at i:82271 original size:30 final size:29
Alignment explanation
Indices: 82240--82515 Score: 210
Period size: 29 Copynumber: 9.4 Consensus size: 29
82230 GTCCCTAAAC
* * *
82240 CTTCTAAAAATTACCATTTTACCCCCAAA
1 CTTCCAAAAATTACCATTTTACCCTCGAA
* *
82269 CCTCCCAAAA-TACCATTTTTGA-CCTCGAA
1 CTTCCAAAAATTACCA-TTTT-ACCCTCGAA
* * *
82298 CCTTCTAAAAATTACCATTTTACCCCCAAA
1 -CTTCCAAAAATTACCATTTTACCCTCGAA
* *
82328 CTTCCAAAAA-TCCCATTTTTGA-CCTCGAGC
1 CTTCCAAAAATTACCA-TTTT-ACCCTCGA-A
*
82358 CTTCTAAAAATTACCATTTTACCCTCGAA
1 CTTCCAAAAATTACCATTTTACCCTCGAA
*
82387 CTTCCAAAAATCTGA--TTTTTGA-CCTCGAA
1 CTTCCAAAAAT-T-ACCATTTT-ACCCTCGAA
* *
82416 CCTTCTAAAAAGTACCATTTTACCCTCGAA
1 -CTTCCAAAAATTACCATTTTACCCTCGAA
* *
82446 CTTCCAAAAA-TCCCATTTTTGACCC-CAAA
1 CTTCCAAAAATTACCA-TTTT-ACCCTCGAA
* *
82475 CTTTTCAAAAATTACCATTTTACCCCCGAA
1 C-TTCCAAAAATTACCATTTTACCCTCGAA
82505 CTTCCAAAAAT
1 CTTCCAAAAAT
82516 CTCATTTTTG
Statistics
Matches: 195, Mismatches: 30, Indels: 44
0.72 0.11 0.16
Matches are distributed among these distances:
28 14 0.07
29 88 0.45
30 79 0.41
31 14 0.07
ACGTcount: A:0.34, C:0.31, G:0.05, T:0.31
Consensus pattern (29 bp):
CTTCCAAAAATTACCATTTTACCCTCGAA
Found at i:82338 original size:59 final size:58
Alignment explanation
Indices: 82237--82558 Score: 416
Period size: 59 Copynumber: 5.5 Consensus size: 58
82227 GAGGTCCCTA
* * *
82237 AACCTTCTAAAAATTACCATTTTACCCCCAAACCTCCCAAAATACCATTTTTGACCTCG
1 AACCTTCTAAAAATTACCATTTTACCCCCGAACTTCCAAAAAT-CCATTTTTGACCTCG
*
82296 AACCTTCTAAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCTCG
1 AACCTTCTAAAAATTACCATTTTACCCCCGAACTTCCAAAAAT-CCATTTTTGACCTCG
* * *
82355 AGCCTTCTAAAAATTACCATTTTACCCTCGAACTTCCAAAAATCTGATTTTTGACCTCG
1 AACCTTCTAAAAATTACCATTTTACCCCCGAACTTCCAAAAATC-CATTTTTGACCTCG
* * *
82414 AACCTTCTAAAAAGTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACC-CC
1 AACCTTCTAAAAATTACCATTTTACCCCCGAACTTCCAAAAAT-CCATTTTTGACCTCG
* *
82472 AAACTTTTCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCTCATTTTTGA-CTCCG
1 AACCTTCT-AAAAATTACCATTTTACCCCCGAACTTCCAAAAATC-CATTTTTGACCT-CG
* * * *
82532 AACCCTC-CAAAACTACCATTTTGCCCC
1 AACCTTCTAAAAATTACCATTTTACCCC
82559 TTGCATCCGA
Statistics
Matches: 235, Mismatches: 22, Indels: 13
0.87 0.08 0.05
Matches are distributed among these distances:
58 27 0.11
59 202 0.86
60 6 0.03
ACGTcount: A:0.33, C:0.32, G:0.05, T:0.30
Consensus pattern (58 bp):
AACCTTCTAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCATTTTTGACCTCG
Done.