Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012097.1 Kokia drynarioides strain JFW-HI SEQ_127096, 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: 105572
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Warning! 61 characters in sequence are not A, C, G, or T
Found at i:7 original size:2 final size:2
Alignment explanation
Indices: 1--35 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
36 TCTTTGTTTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3595 original size:39 final size:39
Alignment explanation
Indices: 3549--3630 Score: 121
Period size: 39 Copynumber: 2.1 Consensus size: 39
3539 CTATAATTAT
* *
3549 TACTAAAATTTTTATTAG-AAACCCAATTTTGTAACCAAA
1 TACTAAAATTCTTATT-GCAAACCAAATTTTGTAACCAAA
*
3588 TACTAAAATTCTTATTGCAAATCAAATTTTGTAACCAAA
1 TACTAAAATTCTTATTGCAAACCAAATTTTGTAACCAAA
3627 TACT
1 TACT
3631 TAGGTTTTTT
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
38 1 0.03
39 38 0.97
ACGTcount: A:0.43, C:0.16, G:0.05, T:0.37
Consensus pattern (39 bp):
TACTAAAATTCTTATTGCAAACCAAATTTTGTAACCAAA
Found at i:4169 original size:15 final size:15
Alignment explanation
Indices: 4137--4182 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
4127 AAAAAAAAAA
4137 AAGAAAGA-AAGAAGG
1 AAGAAAGAGAAGAA-G
*
4152 AAGAAGGAGAAGAAG
1 AAGAAAGAGAAGAAG
*
4167 AAGAAAGAGAAAAAG
1 AAGAAAGAGAAGAAG
4182 A
1 A
4183 TAATGTATTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
15 22 0.81
16 5 0.19
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (15 bp):
AAGAAAGAGAAGAAG
Found at i:4336 original size:18 final size:18
Alignment explanation
Indices: 4313--4347 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
4303 TGAAAAAATG
4313 TAAGTTTGATTAATTTTT
1 TAAGTTTGATTAATTTTT
*
4331 TAAGTTTGGTTAATTTT
1 TAAGTTTGATTAATTTT
4348 AAATTTAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.26, C:0.00, G:0.14, T:0.60
Consensus pattern (18 bp):
TAAGTTTGATTAATTTTT
Found at i:4409 original size:22 final size:21
Alignment explanation
Indices: 4384--4424 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
4374 TGTTAGTTAA
*
4384 TTTGATTATTTTAAGTTTTTGT
1 TTTGATTAATTTAA-TTTTTGT
*
4406 TTTGTTTAATTTAATTTTT
1 TTTGATTAATTTAATTTTT
4425 AATTGATTTG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 5 0.29
22 12 0.71
ACGTcount: A:0.20, C:0.00, G:0.10, T:0.71
Consensus pattern (21 bp):
TTTGATTAATTTAATTTTTGT
Found at i:5315 original size:16 final size:16
Alignment explanation
Indices: 5269--5317 Score: 61
Period size: 16 Copynumber: 3.2 Consensus size: 16
5259 TAAACCTAGG
5269 TAATTAATTACCAAAA
1 TAATTAATTACCAAAA
5285 T-A-TAATATA--AAAA
1 TAATTAAT-TACCAAAA
5298 TAATTAATTACCAAAA
1 TAATTAATTACCAAAA
5314 TAAT
1 TAAT
5318 ATCCCATCAC
Statistics
Matches: 28, Mismatches: 0, Indels: 10
0.74 0.00 0.26
Matches are distributed among these distances:
13 5 0.18
14 7 0.25
15 7 0.25
16 9 0.32
ACGTcount: A:0.59, C:0.08, G:0.00, T:0.33
Consensus pattern (16 bp):
TAATTAATTACCAAAA
Found at i:7288 original size:45 final size:45
Alignment explanation
Indices: 7199--7290 Score: 112
Period size: 45 Copynumber: 2.0 Consensus size: 45
7189 CCCTAGCTCA
* * * **
7199 TCAAGCCAAGGATATTAGCCTTAGTTTGACGAGTCACCGTAATAC
1 TCAAGCCAAGGATATCAGCCTGAGTTTGACGAGCCACCACAATAC
* * *
7244 TCAAGCCAAGGATATCAGGCTGAGTTTGATGAGCCACTACAATAC
1 TCAAGCCAAGGATATCAGCCTGAGTTTGACGAGCCACCACAATAC
7289 TC
1 TC
7291 TACTTCTCCC
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
45 39 1.00
ACGTcount: A:0.32, C:0.23, G:0.21, T:0.25
Consensus pattern (45 bp):
TCAAGCCAAGGATATCAGCCTGAGTTTGACGAGCCACCACAATAC
Found at i:7558 original size:7 final size:7
Alignment explanation
Indices: 7543--7640 Score: 56
Period size: 7 Copynumber: 14.0 Consensus size: 7
7533 TAAATTTCAT
*
7543 AACCTTA
1 AACCCTA
7550 AACCCTA
1 AACCCTA
*
7557 AAACCTA
1 AACCCTA
* **
7564 AATCAAA
1 AACCCTA
*
7571 AACCTTA
1 AACCCTA
*
7578 AA-CTTA
1 AACCCTA
7584 GAACCCTA
1 -AACCCTA
*
7592 AATCCTA
1 AACCCTA
7599 AACCCTA
1 AACCCTA
*
7606 AA-CTTAA
1 AACCCT-A
*
7613 AACCATA
1 AACCCTA
*
7620 AACCATA
1 AACCCTA
7627 AACCCTA
1 AACCCTA
*
7634 AATCCTA
1 AACCCTA
7641 TACATGAAAC
Statistics
Matches: 72, Mismatches: 15, Indels: 8
0.76 0.16 0.08
Matches are distributed among these distances:
6 6 0.08
7 61 0.85
8 5 0.07
ACGTcount: A:0.49, C:0.30, G:0.01, T:0.20
Consensus pattern (7 bp):
AACCCTA
Found at i:7591 original size:28 final size:27
Alignment explanation
Indices: 7555--7635 Score: 90
Period size: 28 Copynumber: 2.9 Consensus size: 27
7545 CCTTAAACCC
* * *
7555 TAAAACCTAAATCAAAAACCTTAAACT
1 TAAACCCTAAATCATAAACCCTAAACT
*
7582 TAGAACCCTAAATCCTAAACCCTAAACT
1 TA-AACCCTAAATCATAAACCCTAAACT
* *
7610 TAAAACCATAAACCATAAACCCTAAA
1 T-AAACCCTAAATCATAAACCCTAAA
7636 TCCTATACAT
Statistics
Matches: 45, Mismatches: 7, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
27 2 0.04
28 42 0.93
29 1 0.02
ACGTcount: A:0.52, C:0.27, G:0.01, T:0.20
Consensus pattern (27 bp):
TAAACCCTAAATCATAAACCCTAAACT
Found at i:7600 original size:42 final size:42
Alignment explanation
Indices: 7543--7640 Score: 110
Period size: 42 Copynumber: 2.3 Consensus size: 42
7533 TAAATTTCAT
* * * *
7543 AACCTTAAACCCTAAAACCTAAA-TCAAAAACCTTAAA-CTTA
1 AACCCTAAATCCTAAAACCTAAACT-AAAAACCATAAACCATA
* *
7584 GAACCCTAAATCCTAAACCCTAAACTTAAAACCATAAACCATA
1 -AACCCTAAATCCTAAAACCTAAACTAAAAACCATAAACCATA
7627 AACCCTAAATCCTA
1 AACCCTAAATCCTA
7641 TACATGAAAC
Statistics
Matches: 48, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
42 44 0.92
43 4 0.08
ACGTcount: A:0.49, C:0.30, G:0.01, T:0.20
Consensus pattern (42 bp):
AACCCTAAATCCTAAAACCTAAACTAAAAACCATAAACCATA
Found at i:10626 original size:4 final size:4
Alignment explanation
Indices: 10604--10662 Score: 57
Period size: 4 Copynumber: 14.2 Consensus size: 4
10594 AACAAATTAC
* * *
10604 CTTT CTCT CCTT C-TT CTTT CTTT CCTCTC CTTT CTTT CTTT CTTTT CTTT
1 CTTT CTTT CTTT CTTT CTTT CTTT -CT-TT CTTT CTTT CTTT C-TTT CTTT
10654 CTTT CTTT C
1 CTTT CTTT C
10663 CCGTTTATTT
Statistics
Matches: 46, Mismatches: 5, Indels: 8
0.78 0.08 0.14
Matches are distributed among these distances:
3 3 0.07
4 34 0.74
5 8 0.17
6 1 0.02
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (4 bp):
CTTT
Found at i:10652 original size:13 final size:13
Alignment explanation
Indices: 10620--10661 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
10610 CTCCTTCTTC
* *
10620 TTTCTTTCCTCTCC
1 TTTCTTT-CTTTCT
10634 TTTCTTTCTTTCT
1 TTTCTTTCTTTCT
10647 TTTCTTTCTTTCT
1 TTTCTTTCTTTCT
10660 TT
1 TT
10662 CCCGTTTATT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
13 19 0.73
14 7 0.27
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (13 bp):
TTTCTTTCTTTCT
Found at i:10655 original size:17 final size:17
Alignment explanation
Indices: 10604--10662 Score: 73
Period size: 17 Copynumber: 3.3 Consensus size: 17
10594 AACAAATTAC
10604 CTTTCTCTCCTTCTTCTTT
1 CTTTCTCTCC-T-TTCTTT
10623 CTTTCCTCTCCTTTCTTT
1 CTTT-CTCTCCTTTCTTT
* *
10641 CTTTCTTTTCTTTCTTT
1 CTTTCTCTCCTTTCTTT
10658 CTTTC
1 CTTTC
10663 CCGTTTATTT
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
17 16 0.43
18 10 0.27
19 5 0.14
20 6 0.16
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (17 bp):
CTTTCTCTCCTTTCTTT
Found at i:10776 original size:19 final size:19
Alignment explanation
Indices: 10752--10790 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
10742 TTTACAATTA
10752 AAATAAAATAAACACACAC
1 AAATAAAATAAACACACAC
10771 AAATAAAATAAACACACAC
1 AAATAAAATAAACACACAC
10790 A
1 A
10791 CATACGACAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.69, C:0.21, G:0.00, T:0.10
Consensus pattern (19 bp):
AAATAAAATAAACACACAC
Found at i:13276 original size:24 final size:24
Alignment explanation
Indices: 13249--13299 Score: 93
Period size: 24 Copynumber: 2.1 Consensus size: 24
13239 AATTTGACTC
*
13249 AAACAACTAAACAGAGTTTAATTG
1 AAACAAATAAACAGAGTTTAATTG
13273 AAACAAATAAACAGAGTTTAATTG
1 AAACAAATAAACAGAGTTTAATTG
13297 AAA
1 AAA
13300 TATTATTTCT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.55, C:0.10, G:0.12, T:0.24
Consensus pattern (24 bp):
AAACAAATAAACAGAGTTTAATTG
Found at i:19177 original size:17 final size:17
Alignment explanation
Indices: 19152--19185 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
19142 TTTTGACATT
*
19152 AATAAATTTATAGTAAA
1 AATAAATTTATAATAAA
*
19169 AATATATTTATAATAAA
1 AATAAATTTATAATAAA
19186 TAACATATGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (17 bp):
AATAAATTTATAATAAA
Found at i:20212 original size:3 final size:3
Alignment explanation
Indices: 20139--20193 Score: 110
Period size: 3 Copynumber: 18.3 Consensus size: 3
20129 TAACCATAGT
20139 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
20187 TAA TAA T
1 TAA TAA T
20194 TGTTTTTAAA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 52 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:21257 original size:30 final size:29
Alignment explanation
Indices: 21216--21479 Score: 293
Period size: 30 Copynumber: 9.0 Consensus size: 29
21206 GAAGGTCATT
*
21216 AAACTTTCCAAAAATCCCATTTTTAACCTCT
1 AAAC-TTCCAAAAATCCCATTTTTAACC-CA
21247 AAACTTCCAAAAAAT-CCA-TTTTAACCCCA
1 AAACTTCC-AAAAATCCCATTTTTAA-CCCA
* * *
21276 AAACATCCAAAAATCCCATTTTTACCCCT
1 AAACTTCCAAAAATCCCATTTTTAACCCA
* * * *
21305 ATACTACCAAAAATCCAATTTTTAACCTCG
1 AAACTTCCAAAAATCCCATTTTTAACC-CA
*
21335 AAACTTCCAAAAATTCCATTTTTAATCCCA
1 AAACTTCCAAAAATCCCATTTTTAA-CCCA
*
21365 AAACTTCCAAAAATCCCA-TTTTAACCCC
1 AAACTTCCAAAAATCCCATTTTTAACCCA
*
21393 AAACTTCCAAAAATTCCATTTTTAACCCCA
1 AAACTTCCAAAAATCCCATTTTTAA-CCCA
* * *
21423 AAACTTCTAAAAATCCTATTTTTAACCCC
1 AAACTTCCAAAAATCCCATTTTTAACCCA
* *
21452 AAACTTTCAAAAATTCCATTTTT-ACCCA
1 AAACTTCCAAAAATCCCATTTTTAACCCA
21480 CGAATGTCTA
Statistics
Matches: 197, Mismatches: 28, Indels: 19
0.81 0.11 0.08
Matches are distributed among these distances:
28 30 0.15
29 76 0.39
30 79 0.40
31 12 0.06
ACGTcount: A:0.39, C:0.30, G:0.00, T:0.31
Consensus pattern (29 bp):
AAACTTCCAAAAATCCCATTTTTAACCCA
Found at i:21269 original size:29 final size:28
Alignment explanation
Indices: 21216--21479 Score: 273
Period size: 29 Copynumber: 9.0 Consensus size: 28
21206 GAAGGTCATT
*
21216 AAACTTTCCAAAAATCCCATTTTTAACCTCT
1 AAAC-TTCCAAAAAT-CCATTTTTAACC-CA
21247 AAACTTCCAAAAAATCCA-TTTTAACCCCA
1 AAACTTCC-AAAAATCCATTTTTAA-CCCA
* * *
21276 AAACATCCAAAAATCCCATTTTTACCCCT
1 AAACTTCCAAAAAT-CCATTTTTAACCCA
* * *
21305 ATACTACCAAAAATCCAATTTTTAACCTCG
1 AAACTTCCAAAAATCC-ATTTTTAACC-CA
21335 AAACTTCCAAAAATTCCATTTTTAATCCCA
1 AAACTTCCAAAAA-TCCATTTTTAA-CCCA
*
21365 AAACTTCCAAAAATCCCA-TTTTAACCCC
1 AAACTTCCAAAAAT-CCATTTTTAACCCA
21393 AAACTTCCAAAAATTCCATTTTTAACCCCA
1 AAACTTCCAAAAA-TCCATTTTTAA-CCCA
* *
21423 AAACTTCTAAAAATCCTATTTTTAACCCC
1 AAACTTCCAAAAATCC-ATTTTTAACCCA
*
21452 AAACTTTCAAAAATTCCATTTTT-ACCCA
1 AAACTTCCAAAAA-TCCATTTTTAACCCA
21480 CGAATGTCTA
Statistics
Matches: 200, Mismatches: 19, Indels: 31
0.80 0.08 0.12
Matches are distributed among these distances:
28 31 0.16
29 77 0.38
30 77 0.38
31 15 0.08
ACGTcount: A:0.39, C:0.30, G:0.00, T:0.31
Consensus pattern (28 bp):
AAACTTCCAAAAATCCATTTTTAACCCA
Found at i:21387 original size:88 final size:85
Alignment explanation
Indices: 21223--21478 Score: 325
Period size: 88 Copynumber: 2.9 Consensus size: 85
21213 ATTAAACTTT
* *
21223 CCAAAAATCCCATTTTTAACCTCTAAACTTCCAAAAAATCCA-TTTTAACCCCAAAACATCCAAA
1 CCAAAAAT-CCATTTTTAACCTCAAAACTTCC-AAAAATCCATTTTTAA-CCCAAAACTTCCAAA
*
21287 AATCCCATTTTTACCCCTATACTA
63 AATCCCATTTTTACCCC-AAACTA
*
21311 CCAAAAATCCAATTTTTAACCTCGAAACTTCCAAAAATTCCATTTTTAATCCCAAAACTTCCAAA
1 CCAAAAATCC-ATTTTTAACCTCAAAACTTCCAAAAA-TCCATTTTTAA-CCCAAAACTTCCAAA
* *
21376 AATCCCATTTTAACCCCAAACTT
63 AATCCCATTTTTACCCCAAACTA
* * * *
21399 CCAAAAATTCCATTTTTAACCCCAAAACTTCTAAAAATCCTATTTTTAACCCCAAACTTTCAAAA
1 CCAAAAA-TCCATTTTTAACCTCAAAACTTCCAAAAATCC-ATTTTTAACCCAAAACTTCCAAAA
*
21464 ATTCCATTTTTACCC
64 ATCCCATTTTTACCC
21479 ACGAATGTCT
Statistics
Matches: 150, Mismatches: 13, Indels: 11
0.86 0.07 0.06
Matches are distributed among these distances:
87 37 0.25
88 74 0.49
89 39 0.26
ACGTcount: A:0.39, C:0.30, G:0.00, T:0.30
Consensus pattern (85 bp):
CCAAAAATCCATTTTTAACCTCAAAACTTCCAAAAATCCATTTTTAACCCAAAACTTCCAAAAAT
CCCATTTTTACCCCAAACTA
Found at i:32901 original size:17 final size:17
Alignment explanation
Indices: 32873--32942 Score: 106
Period size: 17 Copynumber: 4.2 Consensus size: 17
32863 TCAAAGACAG
32873 AATTTAAATTTATTTTA
1 AATTTAAATTTATTTTA
* *
32890 AAATTAAGTTTATTTTA
1 AATTTAAATTTATTTTA
*
32907 AATTTAAATTTATTTGA
1 AATTTAAATTTATTTTA
32924 AATTTAAATTTA-TTTA
1 AATTTAAATTTATTTTA
32940 AAT
1 AAT
32943 AATGTCCAAT
Statistics
Matches: 47, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
16 6 0.13
17 41 0.87
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (17 bp):
AATTTAAATTTATTTTA
Found at i:32928 original size:7 final size:6
Alignment explanation
Indices: 32873--32935 Score: 53
Period size: 6 Copynumber: 11.0 Consensus size: 6
32863 TCAAAGACAG
* * * *
32873 AATTTA AATTT- ATTTTA AAATTA AGTTT- ATTTTA AATTTA AATTT-
1 AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA
32918 -ATTTGA AATTTA AATTTA
1 AATTT-A AATTTA AATTTA
32936 TTTAAATAAT
Statistics
Matches: 45, Mismatches: 7, Indels: 10
0.73 0.11 0.16
Matches are distributed among these distances:
4 4 0.09
5 8 0.18
6 29 0.64
7 4 0.09
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (6 bp):
AATTTA
Found at i:32964 original size:13 final size:13
Alignment explanation
Indices: 32946--32971 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
32936 TTTAAATAAT
32946 GTCCAATTACAAA
1 GTCCAATTACAAA
32959 GTCCAATTACAAA
1 GTCCAATTACAAA
32972 TCAAGCCCAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.23, G:0.08, T:0.23
Consensus pattern (13 bp):
GTCCAATTACAAA
Found at i:34839 original size:29 final size:29
Alignment explanation
Indices: 34804--35000 Score: 177
Period size: 29 Copynumber: 7.1 Consensus size: 29
34794 CTAAACTGTT
*
34804 CAAAAATTACATTTTTACCCCAAAACTTC
1 CAAAAATTCCATTTTTACCCCAAAACTTC
*
34833 CAAAAATCCCATTTTTGA-CCC---A----
1 CAAAAATTCCATTTTT-ACCCCAAAACTTC
*
34855 -AAAA-TTCCATTTTTACTCCC-GAACTTC
1 CAAAAATTCCATTTTTAC-CCCAAAACTTC
34882 CAAAAATTCCATTTTTAACCCCAAAACTTC
1 CAAAAATTCCATTTTT-ACCCCAAAACTTC
* *
34912 CAAAAATCCCA-TTTTAACCCAAAACTTC
1 CAAAAATTCCATTTTTACCCCAAAACTTC
* *
34940 CAAAAATTCCATTTTTACCCTC-GAACCTC
1 CAAAAATTCCATTTTTACCC-CAAAACTTC
* *
34969 CAAAAGTTCCATTTTTGACCCCAAAAATTC
1 CAAAAATTCCATTTTT-ACCCCAAAACTTC
34999 CA
1 CA
35001 TTTTTACTCC
Statistics
Matches: 137, Mismatches: 14, Indels: 33
0.74 0.08 0.18
Matches are distributed among these distances:
19 1 0.01
20 9 0.07
21 7 0.05
23 1 0.01
26 1 0.01
28 26 0.19
29 62 0.45
30 30 0.22
ACGTcount: A:0.37, C:0.30, G:0.03, T:0.30
Consensus pattern (29 bp):
CAAAAATTCCATTTTTACCCCAAAACTTC
Found at i:34880 original size:49 final size:50
Alignment explanation
Indices: 34804--34913 Score: 152
Period size: 49 Copynumber: 2.2 Consensus size: 50
34794 CTAAACTGTT
* *
34804 CAAAAATTACATTTTTACCCCAAAACTTCCAAAAATCCCATTTTTGA-CC
1 CAAAAATTCCATTTTTACCCCAAAACTTCCAAAAATCCCATTTTTAACCC
* *
34853 CAAAAATTCCATTTTTACTCCC-GAACTTCCAAAAATTCCATTTTTAACCC
1 CAAAAATTCCATTTTTAC-CCCAAAACTTCCAAAAATCCCATTTTTAACCC
*
34903 CAAAACTTCCA
1 CAAAAATTCCA
34914 AAAATCCCAT
Statistics
Matches: 54, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
49 39 0.72
50 15 0.28
ACGTcount: A:0.37, C:0.30, G:0.02, T:0.31
Consensus pattern (50 bp):
CAAAAATTCCATTTTTACCCCAAAACTTCCAAAAATCCCATTTTTAACCC
Found at i:35015 original size:20 final size:21
Alignment explanation
Indices: 34968--35015 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
34958 CCTCGAACCT
34968 CCAAAAGTTCCATTTTTGACC
1 CCAAAAGTTCCATTTTTGACC
*
34989 CCAAAAATTCCATTTTT-ACTC
1 CCAAAAGTTCCATTTTTGAC-C
35010 CCAAAA
1 CCAAAA
35016 CGTCCAAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 2 0.08
21 23 0.92
ACGTcount: A:0.35, C:0.29, G:0.04, T:0.31
Consensus pattern (21 bp):
CCAAAAGTTCCATTTTTGACC
Found at i:35021 original size:21 final size:20
Alignment explanation
Indices: 34968--35021 Score: 56
Period size: 21 Copynumber: 2.5 Consensus size: 20
34958 CCTCGAACCT
34968 CCAAAAGTTCCATTTTTGACC
1 CCAAAAG-TCCATTTTTGACC
*
34989 CCAAAAATTCCATTTTT-ACTC
1 CC-AAAAGTCCATTTTTGAC-C
35010 CCAAAACGTCCA
1 CCAAAA-GTCCA
35022 AAAACTACCT
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
20 6 0.21
21 18 0.64
22 4 0.14
ACGTcount: A:0.33, C:0.31, G:0.06, T:0.30
Consensus pattern (20 bp):
CCAAAAGTCCATTTTTGACC
Found at i:43421 original size:49 final size:48
Alignment explanation
Indices: 43349--43446 Score: 126
Period size: 49 Copynumber: 2.0 Consensus size: 48
43339 TCAGGTACTA
* * * *
43349 GAAACTTTAAGGTTTTAAGTTTGAATTTCA-CTTCGTATAAAATGTTATT
1 GAAACTTTAAAGTTTCAAGTTTGAATCTCACCTT-GCAT-AAATGTTATT
*
43398 GAAACTTTAAAGTTTCAAGTTTGAGTCTCACCTTGCATAAATGTTATT
1 GAAACTTTAAAGTTTCAAGTTTGAATCTCACCTTGCATAAATGTTATT
43446 G
1 G
43447 GACCCGTTAT
Statistics
Matches: 43, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
48 11 0.26
49 29 0.67
50 3 0.07
ACGTcount: A:0.32, C:0.11, G:0.15, T:0.42
Consensus pattern (48 bp):
GAAACTTTAAAGTTTCAAGTTTGAATCTCACCTTGCATAAATGTTATT
Found at i:43794 original size:3 final size:3
Alignment explanation
Indices: 43786--43844 Score: 109
Period size: 3 Copynumber: 19.7 Consensus size: 3
43776 AGAAAAATGC
43786 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
43834 TAT CAT TAT TA
1 TAT TAT TAT TA
43845 AGTAAATGTG
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 54 1.00
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:49072 original size:35 final size:35
Alignment explanation
Indices: 49025--49095 Score: 124
Period size: 35 Copynumber: 2.0 Consensus size: 35
49015 TTGTTATACA
*
49025 CAAGTAAATTAAACTTTTGTCATATCACCTAACGC
1 CAAGTAAATTAAACTTTTGCCATATCACCTAACGC
*
49060 CAAGTAACTTAAACTTTTGCCATATCACCTAACGC
1 CAAGTAAATTAAACTTTTGCCATATCACCTAACGC
49095 C
1 C
49096 TAAAAAAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.35, C:0.27, G:0.08, T:0.30
Consensus pattern (35 bp):
CAAGTAAATTAAACTTTTGCCATATCACCTAACGC
Found at i:51477 original size:24 final size:24
Alignment explanation
Indices: 51423--51477 Score: 74
Period size: 24 Copynumber: 2.3 Consensus size: 24
51413 TTTTAATATA
* *
51423 TAAAATATAAATATTAAATATTTT
1 TAAAATTTAAATATTAAATATTTG
* *
51447 TAAAATTTTAATATTAATTATTTG
1 TAAAATTTAAATATTAAATATTTG
51471 TAAAATT
1 TAAAATT
51478 CAATTTAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (24 bp):
TAAAATTTAAATATTAAATATTTG
Found at i:51513 original size:19 final size:20
Alignment explanation
Indices: 51481--51518 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
51471 TAAAATTCAA
*
51481 TTTAAATCTATAAAATATAT
1 TTTAAATATATAAAATATAT
51501 TTTAAATAT-TAAAATATA
1 TTTAAATATATAAAATATA
51519 ATACAATTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.45
Consensus pattern (20 bp):
TTTAAATATATAAAATATAT
Found at i:60516 original size:7 final size:7
Alignment explanation
Indices: 60504--60532 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
60494 AATCGAGTTA
60504 GGTTTAG
1 GGTTTAG
60511 GGTTTAG
1 GGTTTAG
60518 GGTTTAG
1 GGTTTAG
60525 GGTTTAG
1 GGTTTAG
60532 G
1 G
60533 TTTTCAACCG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.14, C:0.00, G:0.45, T:0.41
Consensus pattern (7 bp):
GGTTTAG
Found at i:65620 original size:17 final size:18
Alignment explanation
Indices: 65583--65631 Score: 55
Period size: 18 Copynumber: 2.8 Consensus size: 18
65573 TATTCCTTCC
*
65583 TTTTAATTTTTTTTTATA
1 TTTTAATTTTCTTTTATA
*
65601 TTTTGATTTTCTTTTA-A
1 TTTTAATTTTCTTTTATA
* *
65618 TTTTTATTTGCTTT
1 TTTTAATTTTCTTT
65632 GTGGCACATT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
17 13 0.48
18 14 0.52
ACGTcount: A:0.16, C:0.04, G:0.04, T:0.76
Consensus pattern (18 bp):
TTTTAATTTTCTTTTATA
Found at i:65642 original size:22 final size:24
Alignment explanation
Indices: 65617--65662 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
65607 TTTTCTTTTA
65617 ATTTTT-ATTTGCT-TTGTGGCAC
1 ATTTTTCATTTGCTCTTGTGGCAC
* *
65639 ATTTTTCTTTTTCTCTTGTGGCAC
1 ATTTTTCATTTGCTCTTGTGGCAC
65663 GCTTTTGTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 6 0.30
23 5 0.25
24 9 0.45
ACGTcount: A:0.11, C:0.17, G:0.15, T:0.57
Consensus pattern (24 bp):
ATTTTTCATTTGCTCTTGTGGCAC
Found at i:69435 original size:17 final size:18
Alignment explanation
Indices: 69409--69442 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
69399 TATTAATTAA
*
69409 ATAAATATTA-AAAATTC
1 ATAAAAATTATAAAATTC
69426 ATAAAAATTATAAAATT
1 ATAAAAATTATAAAATT
69443 GGTTCAACCG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (18 bp):
ATAAAAATTATAAAATTC
Found at i:71081 original size:2 final size:2
Alignment explanation
Indices: 71069--71100 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
71059 AAGTCAATAC
*
71069 AT AT AT GT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
71101 GGGGTAAAAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:85930 original size:21 final size:20
Alignment explanation
Indices: 85906--85945 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
85896 ATAAAAAATA
85906 TATAATATTTTTATGAATATG
1 TATAATATTTTTAT-AATATG
*
85927 TATATTATTTTTATAATAT
1 TATAATATTTTTATAATAT
85946 ATAACATGGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.57
Consensus pattern (20 bp):
TATAATATTTTTATAATATG
Found at i:86063 original size:21 final size:23
Alignment explanation
Indices: 86023--86064 Score: 61
Period size: 21 Copynumber: 1.9 Consensus size: 23
86013 TATAACATTT
86023 TTATAACATGTTAAACTTTTTCG
1 TTATAACATGTTAAACTTTTTCG
*
86046 TTATAAC-T-TTAAATTTTTT
1 TTATAACATGTTAAACTTTTT
86065 TTGAGATTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 10 0.56
22 1 0.06
23 7 0.39
ACGTcount: A:0.31, C:0.10, G:0.05, T:0.55
Consensus pattern (23 bp):
TTATAACATGTTAAACTTTTTCG
Found at i:87300 original size:56 final size:55
Alignment explanation
Indices: 87184--87387 Score: 199
Period size: 50 Copynumber: 3.7 Consensus size: 55
87174 TGTAAAAAAA
* *
87184 TTTGATGTTGACCATTGCATGGTCGACACCACCTTTTTTTCAGAT--AA---TTT
1 TTTGGTGTTGGCCATTGCATGGTCGACACCACCTTTTTTTCAGATAAAATTTTTT
87234 TTTGGTGTTGGCCA-TGCAATGGTCGACACC-CCATTTTTTTCAGATAAAATTTTTT
1 TTTGGTGTTGGCCATTGC-ATGGTCGACACCACC-TTTTTTTCAGATAAAATTTTTT
* * * * *
87289 TTTGGGTGTTGGCCATTGCATGGTTGACACCTCCTTTTTATCTTATAAAAAAATTATTTTT
1 TTT-GGTGTTGGCCATTGCATGGTCGACACCACCTTTTT-T-TCA-GATAAAA-T-TTTTT
*
87350 TTTGGTGTTGGCCA-TGCCATGGCCGACACCACCTTTTT
1 TTTGGTGTTGGCCATTG-CATGGTCGACACCACCTTTTT
87388 ATATGATAAA
Statistics
Matches: 129, Mismatches: 9, Indels: 22
0.81 0.06 0.14
Matches are distributed among these distances:
49 5 0.04
50 36 0.28
52 2 0.02
55 6 0.05
56 27 0.21
57 6 0.05
58 2 0.02
59 7 0.05
60 30 0.23
61 8 0.06
ACGTcount: A:0.21, C:0.20, G:0.18, T:0.42
Consensus pattern (55 bp):
TTTGGTGTTGGCCATTGCATGGTCGACACCACCTTTTTTTCAGATAAAATTTTTT
Found at i:87371 original size:60 final size:57
Alignment explanation
Indices: 87231--87401 Score: 186
Period size: 60 Copynumber: 2.9 Consensus size: 57
87221 TTTCAGATAA
* * *
87231 TTTTTTGGTGTTGGCCATGCAATGGTCGACACCCCATTTTT-TTCA-GATAAAATTTT
1 TTTTTTGGTGTTGGCCATGCCATGGTCGACACCCC-TTTTTATTCATAAAAAAATTTT
* * *
87287 TTTTTGGGTGTTGGCCATTG-CATGGTTGACACCTCCTTTTTATCTTATAAAAAAATTATT
1 TTTTTTGGTGTTGGCCA-TGCCATGGTCGACACC-CCTTTTTAT-TCATAAAAAAATT-TT
* *
87347 TTTTTTGGTGTTGGCCATGCCATGGCCGACACCACCTTTTTATATGATAAAAAAA
1 TTTTTTGGTGTTGGCCATGCCATGGTCGACACC-CCTTTTTAT-TCATAAAAAAA
87402 AATCAAATTT
Statistics
Matches: 96, Mismatches: 12, Indels: 10
0.81 0.10 0.08
Matches are distributed among these distances:
56 32 0.33
57 5 0.05
58 2 0.02
59 9 0.09
60 48 0.50
ACGTcount: A:0.24, C:0.18, G:0.18, T:0.41
Consensus pattern (57 bp):
TTTTTTGGTGTTGGCCATGCCATGGTCGACACCCCTTTTTATTCATAAAAAAATTTT
Found at i:87422 original size:20 final size:21
Alignment explanation
Indices: 87396--87435 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
87386 TTATATGATA
87396 AAAAAAAATCAAATTTTTTTT
1 AAAAAAAATCAAATTTTTTTT
87417 AAAAAAAATCAAATTTTTT
1 AAAAAAAATCAAATTTTTT
87436 GGCCTTGTCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.40
Consensus pattern (21 bp):
AAAAAAAATCAAATTTTTTTT
Found at i:88356 original size:30 final size:30
Alignment explanation
Indices: 88293--88413 Score: 142
Period size: 30 Copynumber: 4.1 Consensus size: 30
88283 GAAATGAATT
*
88293 TTAAAATATAAACGAAATTATAAATTAAAAA
1 TTAAAATATAAACGAAATTAAAAATT-AAAA
88324 TTAAAATATACAA-GAAATTAAAAATTAAAA
1 TTAAAATATA-AACGAAATTAAAAATTAAAA
* * *
88354 TTAAAATAAAAACGAAATTACAAATTAAAT
1 TTAAAATATAAACGAAATTAAAAATTAAAA
*
88384 TTAAAA-AGTAAACGAAA--AAAAATCAAAA
1 TTAAAATA-TAAACGAAATTAAAAATTAAAA
88412 TT
1 TT
88414 TAGTAGATCC
Statistics
Matches: 79, Mismatches: 8, Indels: 9
0.82 0.08 0.09
Matches are distributed among these distances:
28 10 0.13
29 3 0.04
30 42 0.53
31 22 0.28
32 2 0.03
ACGTcount: A:0.65, C:0.05, G:0.04, T:0.26
Consensus pattern (30 bp):
TTAAAATATAAACGAAATTAAAAATTAAAA
Found at i:89527 original size:13 final size:13
Alignment explanation
Indices: 89511--89535 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
89501 ATTTCGAAAA
89511 TGTAAAAAATATT
1 TGTAAAAAATATT
89524 TGTAAAAAATAT
1 TGTAAAAAATAT
89536 AATATTTTTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.56, C:0.00, G:0.08, T:0.36
Consensus pattern (13 bp):
TGTAAAAAATATT
Found at i:90079 original size:59 final size:60
Alignment explanation
Indices: 89968--90443 Score: 407
Period size: 59 Copynumber: 8.0 Consensus size: 60
89958 AACTAGTCAC
* * * *
89968 CCATCGCATGACCGACAC-AAAAAA-TTGATTTTTTACCAGAAAAAAAAAGGGGTGTCGG
1 CCATTGCATGACCAACACAAAAAAATTTGATTTTTTACCAGATAAAAAAGGGGGTGTCGG
* * * * *
90026 CTATTGCATGGCTAACACAAAAAAATTTGTTTTTTTA-CAGATAAAAAAGGGGGTGTCGA
1 CCATTGCATGACCAACACAAAAAAATTTGATTTTTTACCAGATAAAAAAGGGGGTGTCGG
* ** * *
90085 CCATTGCATGACCAACACAAAAAAATTTGAATTTTTTATCTCA-CAAAAAGGGGGTGTCAG
1 CCATTGCATGACCAACACAAAAAAATTTG-ATTTTTTACCAGATAAAAAAGGGGGTGTCGG
* * ** * * * * * *
90145 CTATTACATGGGCAACACAAAAAAA-TTGATTTGTTACTAGATAAAAAAGAGAGTGTTGA
1 CCATTGCATGACCAACACAAAAAAATTTGATTTTTTACCAGATAAAAAAGGGGGTGTCGG
* * * * * *
90204 CCA-TGCAATGACCAACACCAAAAAATTTAAATTTTTTATCTG--ACAAAAGGGGATGTCGG
1 CCATTGC-ATGACCAACACAAAAAAATTT-GATTTTTTACCAGATAAAAAAGGGGGTGTCGG
* ** * *
90263 CCATTGCATGGCCAACACAAAAAAAAAATGATTTTTTACCAGATAAAAAAGGAGGTGTCAG
1 CCATTGCATGACCAACAC-AAAAAAATTTGATTTTTTACCAGATAAAAAAGGGGGTGTCGG
* * * * * *
90324 CCATTGTATGACCAACACCAAAAAATTTAAAATTTTTATCAGAT--AAAAGGGGGTATCGG
1 CCATTGCATGACCAACACAAAAAAATTT-GATTTTTTACCAGATAAAAAAGGGGGTGTCGG
* * * * * *
90383 CTATTGCATAACTAGCACAAAAAAAATTGATTTTTTACCAGATAAAAAA-GGAGTGTCGG
1 CCATTGCATGACCAACACAAAAAAATTTGATTTTTTACCAGATAAAAAAGGGGGTGTCGG
90442 CC
1 CC
90444 GTACAATGGA
Statistics
Matches: 319, Mismatches: 84, Indels: 29
0.74 0.19 0.07
Matches are distributed among these distances:
58 35 0.11
59 158 0.50
60 75 0.24
61 51 0.16
ACGTcount: A:0.41, C:0.16, G:0.18, T:0.26
Consensus pattern (60 bp):
CCATTGCATGACCAACACAAAAAAATTTGATTTTTTACCAGATAAAAAAGGGGGTGTCGG
Found at i:90139 original size:119 final size:120
Alignment explanation
Indices: 90010--90433 Score: 522
Period size: 119 Copynumber: 3.6 Consensus size: 120
90000 TTACCAGAAA
* * *
90010 AAAAAAGGGGTGTCGGCTATTGCATGGCTAACACAAAAAAATTTGTTTTTTTA-CAGATAAAAAA
1 AAAAAGGGGGTGTCGGCTATTGCATGGCTAACACAAAAAAAATTGATTTTTTACCAGATAAAAAA
* *
90074 GGGGGTGTCGACCATTGCATGACCAACACAAAAAAATTTGAATTTTTTATCTCAC
66 GGGGGTGTCGACCATTGCATGACCAACACCAAAAAATTTAAATTTTTTATCTCAC
* * * *
90129 AAAAAGGGGGTGTCAGCTATTACATGGGC-AACAC-AAAAAAATTGATTTGTTACTAGATAAAAA
1 AAAAAGGGGGTGTCGGCTATTGCAT-GGCTAACACAAAAAAAATTGATTTTTTACCAGATAAAAA
* * * *
90192 AGAGAGTGTTGACCA-TGCAATGACCAACACCAAAAAATTTAAATTTTTTATCTGAC
65 AGGGGGTGTCGACCATTGC-ATGACCAACACCAAAAAATTTAAATTTTTTATCTCAC
* * * *
90248 -AAAAGGGGATGTCGGCCATTGCATGGCCAACACAAAAAAAAAATGATTTTTTACCAGATAAAAA
1 AAAAAGGGGGTGTCGGCTATTGCATGGCTAACAC-AAAAAAAATTGATTTTTTACCAGATAAAAA
* * * *
90312 AGGAGGTGTC-AGCCATTGTATGACCAACACCAAAAAATTTAAAATTTTTA--TCAG
65 AGGGGGTGTCGA-CCATTGCATGACCAACACCAAAAAATTTAAATTTTTTATCTCAC
* ** *
90366 ATAAAAGGGGGTATCGGCTATTGCATAACTAGCACAAAAAAAATTGATTTTTTACCAGATAAAAA
1 A-AAAAGGGGGTGTCGGCTATTGCATGGCTAACACAAAAAAAATTGATTTTTTACCAGATAAAAA
90431 AGG
65 AGG
90434 AGTGTCGGCC
Statistics
Matches: 259, Mismatches: 36, Indels: 20
0.82 0.11 0.06
Matches are distributed among these distances:
117 3 0.01
118 45 0.17
119 115 0.44
120 94 0.36
121 2 0.01
ACGTcount: A:0.41, C:0.15, G:0.18, T:0.26
Consensus pattern (120 bp):
AAAAAGGGGGTGTCGGCTATTGCATGGCTAACACAAAAAAAATTGATTTTTTACCAGATAAAAAA
GGGGGTGTCGACCATTGCATGACCAACACCAAAAAATTTAAATTTTTTATCTCAC
Found at i:93173 original size:32 final size:33
Alignment explanation
Indices: 93134--93204 Score: 92
Period size: 32 Copynumber: 2.2 Consensus size: 33
93124 AATAATTAAA
* *
93134 TAATTAAATCATGCCTTAA-TATATCATTGA-TT
1 TAATTAAATCAAGCCTTAATTA-AGCATTGATTT
*
93166 TAATTAAATCAAGGCTTAATTAAGCATTGATTT
1 TAATTAAATCAAGCCTTAATTAAGCATTGATTT
93199 TAATTA
1 TAATTA
93205 CCAATATCTA
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
32 24 0.71
33 10 0.29
ACGTcount: A:0.39, C:0.10, G:0.08, T:0.42
Consensus pattern (33 bp):
TAATTAAATCAAGCCTTAATTAAGCATTGATTT
Found at i:94028 original size:21 final size:19
Alignment explanation
Indices: 94004--94047 Score: 52
Period size: 19 Copynumber: 2.2 Consensus size: 19
93994 TCAAATACAC
94004 TTAAAAACATTAAAACAAACA
1 TTAAAAA-ATTAAAA-AAACA
* *
94025 TTAAAAAATTTAAAATACA
1 TTAAAAAATTAAAAAAACA
94044 TTAA
1 TTAA
94048 TTTTTTTTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 8 0.38
20 6 0.29
21 7 0.33
ACGTcount: A:0.64, C:0.09, G:0.00, T:0.27
Consensus pattern (19 bp):
TTAAAAAATTAAAAAAACA
Found at i:94215 original size:44 final size:44
Alignment explanation
Indices: 94166--94324 Score: 151
Period size: 44 Copynumber: 3.6 Consensus size: 44
94156 CAAATGCATA
* * * *
94166 AAAAATAACATCCAAACAACAAAAATAATAACCAAAACAGTAGC
1 AAAAATAACATCAAAACAACAAAAATAACAACAAAAATAGTAGC
* * * **
94210 AAAAATAACAGCAAAATAACATTAAA-AACAACAAAAATAACAGC
1 AAAAATAACATCAAAACAACA-AAAATAACAACAAAAATAGTAGC
* * *
94254 -AAAATAACATTAAAAACAACAAAAATAGCAACAAAAATAGTAAC
1 AAAAATAACA-TCAAAACAACAAAAATAACAACAAAAATAGTAGC
*
94298 AAAAATAACAGCAAAAGCAACACAAAA
1 AAAAATAACATCAAAA-CAACA-AAAA
94325 ACATCAATCA
Statistics
Matches: 90, Mismatches: 19, Indels: 10
0.76 0.16 0.08
Matches are distributed among these distances:
43 12 0.13
44 57 0.63
45 17 0.19
46 4 0.04
ACGTcount: A:0.67, C:0.17, G:0.05, T:0.11
Consensus pattern (44 bp):
AAAAATAACATCAAAACAACAAAAATAACAACAAAAATAGTAGC
Found at i:94222 original size:12 final size:12
Alignment explanation
Indices: 94209--94313 Score: 64
Period size: 12 Copynumber: 9.4 Consensus size: 12
94199 AAAACAGTAG
*
94209 CAAAAATAACAG
1 CAAAAATAACAA
94221 C-AAAATAAC-A
1 CAAAAATAACAA
**
94231 TTAAAA--ACAA
1 CAAAAATAACAA
*
94241 CAAAAATAACAG
1 CAAAAATAACAA
94253 C-AAAATAAC-A
1 CAAAAATAACAA
**
94263 -TTAAA-AACAA
1 CAAAAATAACAA
*
94273 CAAAAATAGCAA
1 CAAAAATAACAA
**
94285 CAAAAATAGTAA
1 CAAAAATAACAA
*
94297 CAAAAATAACAG
1 CAAAAATAACAA
94309 CAAAA
1 CAAAA
94314 GCAACACAAA
Statistics
Matches: 71, Mismatches: 14, Indels: 16
0.70 0.14 0.16
Matches are distributed among these distances:
9 5 0.07
10 9 0.13
11 23 0.32
12 34 0.48
ACGTcount: A:0.69, C:0.15, G:0.05, T:0.11
Consensus pattern (12 bp):
CAAAAATAACAA
Found at i:94245 original size:32 final size:32
Alignment explanation
Indices: 94209--94289 Score: 144
Period size: 32 Copynumber: 2.5 Consensus size: 32
94199 AAAACAGTAG
94209 CAAAAATAACAGCAAAATAACATTAAAAACAA
1 CAAAAATAACAGCAAAATAACATTAAAAACAA
94241 CAAAAATAACAGCAAAATAACATTAAAAACAA
1 CAAAAATAACAGCAAAATAACATTAAAAACAA
* *
94273 CAAAAATAGCAACAAAA
1 CAAAAATAACAGCAAAA
94290 ATAGTAACAA
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
32 47 1.00
ACGTcount: A:0.69, C:0.16, G:0.04, T:0.11
Consensus pattern (32 bp):
CAAAAATAACAGCAAAATAACATTAAAAACAA
Found at i:94268 original size:11 final size:11
Alignment explanation
Indices: 94211--94262 Score: 54
Period size: 11 Copynumber: 4.8 Consensus size: 11
94201 AACAGTAGCA
94211 AAAATAACAGC
1 AAAATAACAGC
*
94222 AAAATAACA-T
1 AAAATAACAGC
* *
94232 TAAA-AACAAC
1 AAAATAACAGC
94242 AAAAATAACAGC
1 -AAAATAACAGC
94254 AAAATAACA
1 AAAATAACA
94263 TTAAAAACAA
Statistics
Matches: 33, Mismatches: 5, Indels: 6
0.75 0.11 0.14
Matches are distributed among these distances:
9 4 0.12
10 3 0.09
11 21 0.64
12 5 0.15
ACGTcount: A:0.69, C:0.15, G:0.04, T:0.12
Consensus pattern (11 bp):
AAAATAACAGC
Found at i:94302 original size:33 final size:33
Alignment explanation
Indices: 94182--94324 Score: 94
Period size: 32 Copynumber: 4.3 Consensus size: 33
94172 AACATCCAAA
* * *
94182 CAACAAAAATAATAACCAAAACAGTAGCAAAAATAA
1 CAACAAAAATAACAACAAAAACA--A-CAAAAATAG
* ** *
94218 CAGC-AAAATAACATTAAAAACAACAAAAATAA
1 CAACAAAAATAACAACAAAAACAACAAAAATAG
* **
94250 CAGC-AAAATAACATTAAAAACAACAAAAATAG
1 CAACAAAAATAACAACAAAAACAACAAAAATAG
** * *
94282 CAACAAAAATAGTAACAAAAATAACAGCAAA-AG
1 CAACAAAAATAACAACAAAAACAACA-AAAATAG
94315 CAACACAAAA
1 CAACA-AAAA
94325 ACATCAATCA
Statistics
Matches: 91, Mismatches: 13, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
32 43 0.47
33 24 0.26
34 7 0.08
35 14 0.15
36 3 0.03
ACGTcount: A:0.67, C:0.17, G:0.06, T:0.10
Consensus pattern (33 bp):
CAACAAAAATAACAACAAAAACAACAAAAATAG
Found at i:94366 original size:21 final size:20
Alignment explanation
Indices: 94333--94417 Score: 61
Period size: 21 Copynumber: 4.3 Consensus size: 20
94323 AAACATCAAT
* *
94333 CAAAATAGT-AAAAAAGCAC
1 CAAAACAGTAAAAAAAACAC
*
94352 CAAAACAGT-AAAAAAATA-
1 CAAAACAGTAAAAAAAACAC
* *
94370 -AAAACAGCAAAAAAAACAAT
1 CAAAACAGTAAAAAAAAC-AC
* *
94390 CAAAATAGTAAAAAATAGCAC
1 CAAAACAGTAAAAAA-AACAC
94411 CAAAACA
1 CAAAACA
94418 ACAATATAAT
Statistics
Matches: 51, Mismatches: 10, Indels: 8
0.74 0.14 0.12
Matches are distributed among these distances:
17 7 0.14
18 7 0.14
19 16 0.31
21 19 0.37
22 2 0.04
ACGTcount: A:0.68, C:0.15, G:0.07, T:0.09
Consensus pattern (20 bp):
CAAAACAGTAAAAAAAACAC
Found at i:94402 original size:19 final size:19
Alignment explanation
Indices: 94329--94404 Score: 59
Period size: 19 Copynumber: 4.0 Consensus size: 19
94319 ACAAAAACAT
*
94329 CAATCAAAATAGTAAAAAA
1 CAATCAAAACAGTAAAAAA
*
94348 GC-ACCAAAACAGT-AAAAA
1 -CAATCAAAACAGTAAAAAA
* *
94366 -AATAAAAACAGCAAAAAAAA
1 CAATCAAAACAG--TAAAAAA
*
94386 CAATCAAAATAGTAAAAAA
1 CAATCAAAACAGTAAAAAA
94405 TAGCACCAAA
Statistics
Matches: 43, Mismatches: 8, Indels: 11
0.69 0.13 0.18
Matches are distributed among these distances:
17 8 0.19
18 5 0.12
19 15 0.35
20 6 0.14
21 9 0.21
ACGTcount: A:0.70, C:0.13, G:0.07, T:0.11
Consensus pattern (19 bp):
CAATCAAAACAGTAAAAAA
Found at i:94918 original size:2 final size:2
Alignment explanation
Indices: 94911--94937 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
94901 CTAACTTACC
94911 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
94938 ATTGTTTTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:100134 original size:209 final size:209
Alignment explanation
Indices: 99768--100246 Score: 809
Period size: 209 Copynumber: 2.3 Consensus size: 209
99758 TTCTCAACAA
* * **
99768 ACAACCACAAGTTCCACAGCTTGAGCCAAAAAGCTTTGATGA-TTGCACATAACTCAAAAACCAC
1 ACAACCACAAGTTACACAGCTTGAGCCAAAAAGCTTTGAT-ATTTGCACATAATTTGAAAACCAC
** *
99832 ATTAAAATAAACTTTTGGTTGTTCTCATTCAACATGAAAATAGGATTGAAATGCTAGAAAACAAC
65 ATTAAAATAAACTTTTGGTCATTCTCATTCAACATGAAAATAGGATAGAAATGCTAGAAAACAAC
99897 TTAGGAACAACAAACAAGAACATAAAGGTATGCTACCATACTATTGGCACCAAAAGAAGCAACCA
130 TTAGGAACAACAAACAAGAACATAAAGGTATGCTACCATACTATTGGCACCAAAAGAAGCAACCA
99962 ACATAATATTATAAC
195 ACATAATATTATAAC
99977 ACAACCACAAGTTACACAGCTTGAG-CAAAAAGCTTTGATATTTGCACATAATTTGAAAACCACC
1 ACAACCACAAGTTACACAGCTTGAGCCAAAAAGCTTTGATATTTGCACATAATTTGAAAACCA-C
*
100041 ATTAAAATAAACTTTTGGTCATTTTCATTCAACATGAAAATAGGATAGAAATGCTAGAAAACAAC
65 ATTAAAATAAACTTTTGGTCATTCTCATTCAACATGAAAATAGGATAGAAATGCTAGAAAACAAC
* * *
100106 TTAGGAACAACAAACAAGAACGTAAAGGTATGCTACCATACTATTGGCATCAAAAGAAGCAACCG
130 TTAGGAACAACAAACAAGAACATAAAGGTATGCTACCATACTATTGGCACCAAAAGAAGCAACCA
100171 ACATAATATTATAAC
195 ACATAATATTATAAC
* *
100186 ACAACCACAAGTTACGCAGCTTGAGCCAAAAAGCTTTGCTATTTGCACATAATTTGAAAAC
1 ACAACCACAAGTTACACAGCTTGAGCCAAAAAGCTTTGATATTTGCACATAATTTGAAAAC
100247 TGCATCCAAC
Statistics
Matches: 254, Mismatches: 13, Indels: 5
0.93 0.05 0.02
Matches are distributed among these distances:
207 1 0.00
208 32 0.13
209 187 0.74
210 34 0.13
ACGTcount: A:0.44, C:0.20, G:0.13, T:0.23
Consensus pattern (209 bp):
ACAACCACAAGTTACACAGCTTGAGCCAAAAAGCTTTGATATTTGCACATAATTTGAAAACCACA
TTAAAATAAACTTTTGGTCATTCTCATTCAACATGAAAATAGGATAGAAATGCTAGAAAACAACT
TAGGAACAACAAACAAGAACATAAAGGTATGCTACCATACTATTGGCACCAAAAGAAGCAACCAA
CATAATATTATAAC
Done.