Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005521.1 Hibiscus syriacus cultivar Beakdansim tig00012754_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: 72851
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.33
Found at i:7588 original size:18 final size:18
Alignment explanation
Indices: 7567--7612 Score: 51
Period size: 18 Copynumber: 2.7 Consensus size: 18
7557 TATTAATGGA
7567 GTAAAAAAAATACAAAAG
1 GTAAAAAAAATACAAAAG
* *
7585 GTAAAAGAAAT-TAAAAG
1 GTAAAAAAAATACAAAAG
*
7602 G-AATAAAAATA
1 GTAAAAAAAATA
7613 ATGTGTACAT
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
16 7 0.30
17 6 0.26
18 10 0.43
ACGTcount: A:0.70, C:0.02, G:0.13, T:0.15
Consensus pattern (18 bp):
GTAAAAAAAATACAAAAG
Found at i:7826 original size:2 final size:2
Alignment explanation
Indices: 7819--7859 Score: 66
Period size: 2 Copynumber: 21.0 Consensus size: 2
7809 TTAATACATC
*
7819 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A GA 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
7860 AAATAAAAAT
Statistics
Matches: 37, Mismatches: 1, Indels: 2
0.93 0.03 0.05
Matches are distributed among these distances:
1 1 0.03
2 36 0.97
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.46
Consensus pattern (2 bp):
TA
Found at i:10338 original size:67 final size:65
Alignment explanation
Indices: 10222--10404 Score: 215
Period size: 65 Copynumber: 2.8 Consensus size: 65
10212 AAGATATCTG
* * * **
10222 TTGTTTCATGA-AAACGGTCTCAAGGGAAAAAAAATTTTGTTTTAAGGGAAATAAATTTGAAGAT
1 TTGTTTCAAGAGAAACTGTCTCAAGGGAGAAAAAA-TTTGTTTTAAGGGAAATAAATTCAAAGA-
10286 TT
64 TT
* *
10288 TGTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTTAGGGGAAATAAATTCAAAGAT
1 T-TGTTTCAAGAGAAACTGTCTCAAGGGAGAAAAAATTTGTTTTAAGGGAAATAAATTCAAAGAT
10353 T
65 T
* * ** * *
10354 TTGTTTCAAGGGAAACTGTCTCAAGAGAGATGAAATTTGTTTCAAGAGAAA
1 TTGTTTCAAGAGAAACTGTCTCAAGGGAGAAAAAATTTGTTTTAAGGGAAA
10405 CTGTCTCAAG
Statistics
Matches: 101, Mismatches: 14, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
65 43 0.43
66 4 0.04
67 34 0.34
68 20 0.20
ACGTcount: A:0.38, C:0.08, G:0.22, T:0.32
Consensus pattern (65 bp):
TTGTTTCAAGAGAAACTGTCTCAAGGGAGAAAAAATTTGTTTTAAGGGAAATAAATTCAAAGATT
Found at i:10405 original size:36 final size:36
Alignment explanation
Indices: 10353--10577 Score: 175
Period size: 36 Copynumber: 6.4 Consensus size: 36
10343 ATTCAAAGAT
*
10353 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGATGAAA
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGATGAAA
**
10389 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGATGAAA
* * *
10425 CTTAGTTCCAAAAGAAACTGTCTCAAG-GAAGATGAAA
1 -TTTGTTTCAAGAGAAACTGTCTCAAGAG-AGATGAAA
* *
10462 TTTGTTTCAA-ATAAAACATAT-TC---A-A-AT--AA
1 TTTGTTTCAAGA-GAAAC-TGTCTCAAGAGAGATGAAA
* *
10491 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGATAAAA
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGATGAAA
* * * * * * *
10527 TTTATTGCAAGGGAAACTTTCTTAAGAGAAACGAAA
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGATGAAA
*
10563 TTTATTTCAAG-GAAA
1 TTTGTTTCAAGAGAAA
10578 TGTTTTCAAT
Statistics
Matches: 152, Mismatches: 23, Indels: 29
0.75 0.11 0.14
Matches are distributed among these distances:
28 2 0.01
29 18 0.12
31 2 0.01
32 2 0.01
33 1 0.01
34 2 0.01
35 5 0.03
36 89 0.59
37 31 0.20
ACGTcount: A:0.41, C:0.12, G:0.18, T:0.28
Consensus pattern (36 bp):
TTTGTTTCAAGAGAAACTGTCTCAAGAGAGATGAAA
Found at i:10450 original size:37 final size:36
Alignment explanation
Indices: 10365--10451 Score: 120
Period size: 37 Copynumber: 2.4 Consensus size: 36
10355 TGTTTCAAGG
** * * *
10365 GAAACTGTCTCAAGAGAGATGAAATTTGTTTCAAGA
1 GAAACTGTCTCAAGAGAGACAAAATTAGTTCCAAAA
10401 GAAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAAA
1 GAAACTGTCTCAAGAGAGACAAAA-TTAGTTCCAAAA
10438 GAAACTGTCTCAAG
1 GAAACTGTCTCAAG
10452 GAAGATGAAA
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
36 22 0.49
37 23 0.51
ACGTcount: A:0.41, C:0.16, G:0.20, T:0.23
Consensus pattern (36 bp):
GAAACTGTCTCAAGAGAGACAAAATTAGTTCCAAAA
Found at i:10451 original size:138 final size:138
Alignment explanation
Indices: 10299--10555 Score: 352
Period size: 138 Copynumber: 1.9 Consensus size: 138
10289 GTGTTTCAAG
* * ** * * *
10299 AGAAACTGTCTCAAGGGAGACAAAATTTGTTTTAGGGGAAATAAATTCAAAGATTTTGTTTCAAG
1 AGAAACTGTCTCAAGGAAGACAAAATTTGTTTCAAAGAAAACAAATTCAAAGAATTTGTTTCAAG
* * *
10364 GGAAACTGTCTCAAGAGAGATGAAATTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTA
66 GGAAACTGTCTCAAGAGAGATAAAATTTATTGCAAGAGAAACTGTCTCAAGAGAGACAAAACTTA
10429 GTTCCAAA
131 GTTCCAAA
** * * *
10437 AGAAACTGTCTCAAGGAAGATGAAATTTGTTTCAAATAAAACATATTCAAATAATTTGTTTCAAG
1 AGAAACTGTCTCAAGGAAGACAAAATTTGTTTCAAAGAAAACAAATTCAAAGAATTTGTTTCAAG
* * *
10502 GGAAACTGTCTCAAGAGAGATAAAATTTATTGCAAGGGAAACTTTCTTAAGAGA
66 GGAAACTGTCTCAAGAGAGATAAAATTTATTGCAAGAGAAACTGTCTCAAGAGA
10556 AACGAAATTT
Statistics
Matches: 101, Mismatches: 18, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
138 101 1.00
ACGTcount: A:0.41, C:0.12, G:0.19, T:0.28
Consensus pattern (138 bp):
AGAAACTGTCTCAAGGAAGACAAAATTTGTTTCAAAGAAAACAAATTCAAAGAATTTGTTTCAAG
GGAAACTGTCTCAAGAGAGATAAAATTTATTGCAAGAGAAACTGTCTCAAGAGAGACAAAACTTA
GTTCCAAA
Found at i:10607 original size:100 final size:101
Alignment explanation
Indices: 10387--10653 Score: 288
Period size: 101 Copynumber: 2.6 Consensus size: 101
10377 AGAGAGATGA
* **
10387 AATTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAACTGTCTCAAG
1 AATTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTA-TTCCAAGGGAAACTGTCTCAAG
* * *
10452 GAAGATGAAATTTGTTTCAAATAAAACATATTCAAAT
65 GAAGACGAAATTTATTTCAAAGAAAACATATTCAAAT
* * * * *
10489 AATTTGTTTCAAGGGAAACTGTCTCAAGAGAGATAAAATTTATTGCAAGGGAAACTTTCTTAAGA
1 AATTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTATTCCAAGGGAAACTGTCTCAAG-
* ** *
10554 GAA-ACGAAATTTATTTC-AAGGAAATGTTTTC-AAT
65 GAAGACGAAATTTATTTCAAAGAAAACATATTCAAAT
** * * * *
10588 GTTTATGTTTCAAGAGAAACTCTCTCAAGGGAGACAAAATTTTATTTCAAGGGAAACTATCTCAA
1 AATT-TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TTTATTCCAAGGGAAACTGTCTCAA
10653 G
64 G
10654 CGAGATAAAA
Statistics
Matches: 138, Mismatches: 24, Indels: 7
0.82 0.14 0.04
Matches are distributed among these distances:
99 5 0.04
100 39 0.28
101 52 0.38
102 42 0.30
ACGTcount: A:0.40, C:0.13, G:0.17, T:0.30
Consensus pattern (101 bp):
AATTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTATTCCAAGGGAAACTGTCTCAAGG
AAGACGAAATTTATTTCAAAGAAAACATATTCAAAT
Found at i:12334 original size:13 final size:12
Alignment explanation
Indices: 12314--12374 Score: 72
Period size: 12 Copynumber: 5.1 Consensus size: 12
12304 TTTTCTTCAA
*
12314 TTTTTCT-TTGT
1 TTTTTCTCTTTT
12325 TTTTTCTCTTTT
1 TTTTTCTCTTTT
12337 TATTTTCTCTTTT
1 T-TTTTCTCTTTT
*
12350 CTTTTT-TCTCTT
1 -TTTTTCTCTTTT
12362 TTTTTCTCTTTT
1 TTTTTCTCTTTT
12374 T
1 T
12375 GTTCTGATTG
Statistics
Matches: 43, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
11 12 0.28
12 15 0.35
13 15 0.35
14 1 0.02
ACGTcount: A:0.02, C:0.16, G:0.02, T:0.80
Consensus pattern (12 bp):
TTTTTCTCTTTT
Found at i:12356 original size:14 final size:13
Alignment explanation
Indices: 12314--12366 Score: 72
Period size: 13 Copynumber: 4.1 Consensus size: 13
12304 TTTTCTTCAA
*
12314 TTTT-TCTTTGTT
1 TTTTCTCTTTTTT
*
12326 TTTTCTCTTTTTA
1 TTTTCTCTTTTTT
12339 TTTTCTCTTTTCTT
1 TTTTCTCTTTT-TT
12353 TTTTCTCTTTTTT
1 TTTTCTCTTTTTT
12366 T
1 T
12367 CTCTTTTTGT
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
12 4 0.11
13 20 0.56
14 12 0.33
ACGTcount: A:0.02, C:0.15, G:0.02, T:0.81
Consensus pattern (13 bp):
TTTTCTCTTTTTT
Found at i:12366 original size:24 final size:24
Alignment explanation
Indices: 12297--12373 Score: 77
Period size: 24 Copynumber: 3.2 Consensus size: 24
12287 ATGCATCTTG
**
12297 TTTTCTTTTTTCTTCAATTTTTCT-
1 TTTTCTTTTTTC-TCTTTTTTTCTC
* *
12321 TTGTT-TTTTCTCTTTTTATTTTCTC
1 TT-TTCTTTTTTCTCTTT-TTTTCTC
12346 TTTTCTTTTTTCTCTTTTTTTCTC
1 TTTTCTTTTTTCTCTTTTTTTCTC
12370 TTTT
1 TTTT
12374 TGTTCTGATT
Statistics
Matches: 43, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
23 2 0.05
24 27 0.63
25 14 0.33
ACGTcount: A:0.04, C:0.17, G:0.01, T:0.78
Consensus pattern (24 bp):
TTTTCTTTTTTCTCTTTTTTTCTC
Found at i:12373 original size:7 final size:7
Alignment explanation
Indices: 12326--12363 Score: 51
Period size: 7 Copynumber: 5.6 Consensus size: 7
12316 TTTCTTTGTT
12326 TTTTCTC
1 TTTTCTC
*
12333 TTTT-TA
1 TTTTCTC
12339 TTTTCTC
1 TTTTCTC
*
12346 TTTTCTT
1 TTTTCTC
12353 TTTTCTC
1 TTTTCTC
12360 TTTT
1 TTTT
12364 TTTCTCTTTT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
6 5 0.19
7 21 0.81
ACGTcount: A:0.03, C:0.18, G:0.00, T:0.79
Consensus pattern (7 bp):
TTTTCTC
Found at i:15442 original size:22 final size:23
Alignment explanation
Indices: 15417--15477 Score: 56
Period size: 22 Copynumber: 2.6 Consensus size: 23
15407 CAAACGTGAG
15417 AATAATAAATAAAACAAG-AAAA
1 AATAATAAATAAAACAAGTAAAA
*
15439 AATAGA-AAATAACAAAACACGTAAAA
1 AATA-ATAAAT---AAAACAAGTAAAA
15465 AATAATAAA-AAAA
1 AATAATAAATAAAA
15478 TTAAAATAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 12
0.71 0.02 0.27
Matches are distributed among these distances:
22 12 0.38
23 1 0.03
25 8 0.25
26 11 0.34
ACGTcount: A:0.75, C:0.07, G:0.05, T:0.13
Consensus pattern (23 bp):
AATAATAAATAAAACAAGTAAAA
Found at i:15699 original size:13 final size:13
Alignment explanation
Indices: 15681--15705 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
15671 CATGATATTA
15681 AGAAAAAAATAAT
1 AGAAAAAAATAAT
15694 AGAAAAAAATAA
1 AGAAAAAAATAA
15706 AATAAAATAA
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:0.80, C:0.00, G:0.08, T:0.12
Consensus pattern (13 bp):
AGAAAAAAATAAT
Found at i:15724 original size:31 final size:31
Alignment explanation
Indices: 15683--15756 Score: 78
Period size: 31 Copynumber: 2.4 Consensus size: 31
15673 TGATATTAAG
* *
15683 AAAAAAATAATAGAAAAAAATAAA-ATAAAAT
1 AAAAATATAATAGAAAAAAATAAATA-AAAAC
* * *
15714 AAAAATATAATATATATAAATAAATAAAAAC
1 AAAAATATAATAGAAAAAAATAAATAAAAAC
*
15745 AAAAATAGAATA
1 AAAAATATAATA
15757 TTAAGAAAAT
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
31 35 0.97
32 1 0.03
ACGTcount: A:0.76, C:0.01, G:0.03, T:0.20
Consensus pattern (31 bp):
AAAAATATAATAGAAAAAAATAAATAAAAAC
Found at i:15777 original size:36 final size:37
Alignment explanation
Indices: 15737--15811 Score: 100
Period size: 38 Copynumber: 2.0 Consensus size: 37
15727 ATATAAATAA
*
15737 ATAAAAAC-A-AAAATAGAATATTAAGAAAATATATAT
1 ATAAAAACGATAAAATAGAATACT-AGAAAATATATAT
*
15773 ATAAAAACGTATAAAATATAATACTAGAAAATATATAT
1 ATAAAAACG-ATAAAATAGAATACTAGAAAATATATAT
15811 A
1 A
15812 CATAGTAAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
36 8 0.24
38 15 0.44
39 11 0.32
ACGTcount: A:0.64, C:0.04, G:0.05, T:0.27
Consensus pattern (37 bp):
ATAAAAACGATAAAATAGAATACTAGAAAATATATAT
Found at i:15856 original size:2 final size:2
Alignment explanation
Indices: 15849--15921 Score: 107
Period size: 2 Copynumber: 37.5 Consensus size: 2
15839 CTATACATAC
15849 AT AT AT AT AT AT AT AT AT 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 AT AT AT AT AT
*
15891 AT AT AT AT A- AT A- AT GAT AT A- AG AT AT AT AT A
1 AT AT AT AT AT AT AT AT -AT AT AT AT AT AT AT AT A
15922 ATAAAAATAA
Statistics
Matches: 66, Mismatches: 1, Indels: 8
0.88 0.01 0.11
Matches are distributed among these distances:
1 3 0.05
2 61 0.92
3 2 0.03
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (2 bp):
AT
Found at i:15911 original size:11 final size:10
Alignment explanation
Indices: 15832--15925 Score: 66
Period size: 12 Copynumber: 8.6 Consensus size: 10
15822 GGAGAAAAAT
*
15832 TAATAATCTA
1 TAATAATATA
15842 TACATACATATA
1 TA-ATA-ATATA
15854 T-AT-ATATA
1 TAATAATATA
15862 TATATATATATA
1 TA-ATA-ATATA
15874 TATATATATATA
1 TA-ATA-ATATA
15886 TATATATATATA
1 TA-ATA-ATATA
15898 TAATAATGATA
1 TAATAAT-ATA
*
15909 TAAGATATATA
1 TAATA-ATATA
15920 TAATAA
1 TAATAA
15926 AAATAATATA
Statistics
Matches: 73, Mismatches: 3, Indels: 16
0.79 0.03 0.17
Matches are distributed among these distances:
8 6 0.08
10 9 0.12
11 20 0.27
12 38 0.52
ACGTcount: A:0.52, C:0.03, G:0.02, T:0.43
Consensus pattern (10 bp):
TAATAATATA
Found at i:15931 original size:20 final size:20
Alignment explanation
Indices: 15891--15969 Score: 72
Period size: 20 Copynumber: 3.8 Consensus size: 20
15881 ATATATATAT
*
15891 ATATATATAATAATGATATAAG
1 ATATATATAATAA--AAATAAG
*
15913 ATATATATAATAAAAATAAT
1 ATATATATAATAAAAATAAG
15933 ATA-ATATAAATAAAAA-AAGG
1 ATATATAT-AATAAAAATAA-G
*
15953 AATATAAATAATAAAAA
1 -ATATATATAATAAAAA
15970 AATATAATTA
Statistics
Matches: 49, Mismatches: 4, Indels: 9
0.79 0.06 0.15
Matches are distributed among these distances:
19 6 0.12
20 16 0.33
21 11 0.22
22 16 0.33
ACGTcount: A:0.66, C:0.00, G:0.05, T:0.29
Consensus pattern (20 bp):
ATATATATAATAAAAATAAG
Found at i:15934 original size:14 final size:14
Alignment explanation
Indices: 15917--15991 Score: 64
Period size: 14 Copynumber: 5.4 Consensus size: 14
15907 TATAAGATAT
15917 ATATAATAAAAATA
1 ATATAATAAAAATA
*
15931 ATATAATATAAATA
1 ATATAATAAAAATA
* * ** *
15945 AAAAAAGGAATATA
1 ATATAATAAAAATA
15959 A-ATAATAAAAA-A
1 ATATAATAAAAATA
15971 ATATAATTAAAAATA
1 ATATAA-TAAAAATA
15986 TATATA
1 -ATATA
15992 TAGGGGACAA
Statistics
Matches: 46, Mismatches: 11, Indels: 6
0.73 0.17 0.10
Matches are distributed among these distances:
12 2 0.04
13 10 0.22
14 28 0.61
15 1 0.02
16 5 0.11
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.28
Consensus pattern (14 bp):
ATATAATAAAAATA
Found at i:15948 original size:21 final size:19
Alignment explanation
Indices: 15915--15993 Score: 67
Period size: 18 Copynumber: 4.3 Consensus size: 19
15905 GATATAAGAT
15915 ATATATAATAAAAATAATATA
1 ATATA-AATAAAAA-AATATA
**
15936 ATATAAATAAAAAAA-GGA
1 ATATAAATAAAAAAATATA
*
15954 ATATAAATAATAAAA-A-A
1 ATATAAATAAAAAAATATA
* *
15971 ATATAATTAAAAATATAT-
1 ATATAAATAAAAAAATATA
15989 ATATA
1 ATATA
15994 GGGGACAAAA
Statistics
Matches: 49, Mismatches: 7, Indels: 7
0.78 0.11 0.11
Matches are distributed among these distances:
17 13 0.27
18 21 0.43
19 2 0.04
20 8 0.16
21 5 0.10
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.29
Consensus pattern (19 bp):
ATATAAATAAAAAAATATA
Found at i:15985 original size:20 final size:20
Alignment explanation
Indices: 15921--15985 Score: 62
Period size: 20 Copynumber: 3.2 Consensus size: 20
15911 AGATATATAT
*
15921 AATAAAAATAATATAA-TATA
1 AATAAAAA-AATATAATTAAA
**
15941 AATAAAAAAA-GGAATATAAA
1 AATAAAAAAATATAAT-TAAA
15961 TAATAAAAAAATATAATTAAA
1 -AATAAAAAAATATAATTAAA
15982 AATA
1 AATA
15986 TATATATAGG
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
18 2 0.06
19 2 0.06
20 15 0.42
21 14 0.39
22 3 0.08
ACGTcount: A:0.72, C:0.00, G:0.03, T:0.25
Consensus pattern (20 bp):
AATAAAAAAATATAATTAAA
Found at i:15993 original size:35 final size:34
Alignment explanation
Indices: 15913--15993 Score: 83
Period size: 35 Copynumber: 2.3 Consensus size: 34
15903 ATGATATAAG
* *
15913 ATATATATAATAAAAATAATATAATATAAATAAAA
1 ATATATAT-ATAAAAATAAAAAAATATAAATAAAA
* * *
15948 AAAGGA-ATATAAATAATAAAAAAATATAATTAAAA
1 ATA-TATATATAAA-AATAAAAAAATATAAATAAAA
15983 ATATATATATA
1 ATATATATATA
15994 GGGGACAAAA
Statistics
Matches: 36, Mismatches: 7, Indels: 6
0.73 0.14 0.12
Matches are distributed among these distances:
34 6 0.17
35 29 0.81
36 1 0.03
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (34 bp):
ATATATATATAAAAATAAAAAAATATAAATAAAA
Found at i:23175 original size:14 final size:14
Alignment explanation
Indices: 23156--23186 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
23146 TTCTTCTGCT
23156 AAACGAGATAAAGA
1 AAACGAGATAAAGA
23170 AAACGAGATAAAGA
1 AAACGAGATAAAGA
23184 AAA
1 AAA
23187 TGAAAAAAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.68, C:0.06, G:0.19, T:0.06
Consensus pattern (14 bp):
AAACGAGATAAAGA
Found at i:23936 original size:15 final size:15
Alignment explanation
Indices: 23916--23956 Score: 73
Period size: 15 Copynumber: 2.7 Consensus size: 15
23906 CTAAAGGTAA
23916 TAAAGAAAGTAATTT
1 TAAAGAAAGTAATTT
23931 TAAAGAAAGTAATTT
1 TAAAGAAAGTAATTT
*
23946 TAAATAAAGTA
1 TAAAGAAAGTA
23957 GAGATGAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.56, C:0.00, G:0.12, T:0.32
Consensus pattern (15 bp):
TAAAGAAAGTAATTT
Found at i:27488 original size:23 final size:23
Alignment explanation
Indices: 27462--27506 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
27452 AAATTTGAAA
*
27462 TAATTTATTATTT-TGACTAAATT
1 TAATATATT-TTTGTGACTAAATT
*
27485 TAATATGTTTTTGTGACTAAAT
1 TAATATATTTTTGTGACTAAAT
27507 AAATGTTTCA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 3 0.16
23 16 0.84
ACGTcount: A:0.33, C:0.04, G:0.09, T:0.53
Consensus pattern (23 bp):
TAATATATTTTTGTGACTAAATT
Found at i:27638 original size:32 final size:33
Alignment explanation
Indices: 27564--27638 Score: 80
Period size: 32 Copynumber: 2.3 Consensus size: 33
27554 ATTTTTATAT
* * * *
27564 TGAGAAATTAGAATTTTTTATAAAGTGTTATTA
1 TGAGAAAATAGAATTTGTCATAAAGTATTATTA
** *
27597 TGATTAAATA-AATTTGTCATAATGTATTATTA
1 TGAGAAAATAGAATTTGTCATAAAGTATTATTA
27629 TGAGAAAATA
1 TGAGAAAATA
27639 TTGTAACTAC
Statistics
Matches: 33, Mismatches: 9, Indels: 1
0.77 0.21 0.02
Matches are distributed among these distances:
32 26 0.79
33 7 0.21
ACGTcount: A:0.43, C:0.01, G:0.13, T:0.43
Consensus pattern (33 bp):
TGAGAAAATAGAATTTGTCATAAAGTATTATTA
Found at i:27688 original size:198 final size:195
Alignment explanation
Indices: 27253--27724 Score: 558
Period size: 198 Copynumber: 2.4 Consensus size: 195
27243 TTTGGTGACG
* * * * * *
27253 AAATAAATTTTACATAATTTCTTATTTTGAATAAATTTAATATGTTATTGTGACTAAATAATTTT
1 AAATAAATTTAAAATAATTTATTATTTTGACTAAATTTAATATGTTATTGTGACTAAATAAATGT
* * *
27318 TTTACAATTTATTATTTTGAAAAGATTATTATTTATCATAATTTTATATTGATATTTAATATTTA
66 TTCACAATTTATTATTTTGAAAAGATTATTATTTATCATAATTTTATATTGAAAATTAATATTTA
* * * *
27383 TTATAAATAGTTATTATGATTAAGTAATGTATCAAAAAAAATTATTTTGAAAAAATGTTGTCACT
131 TTATAAATAGTTATTATGATTAAATAATGTATCAAAAAAAATTATTATGAAAAAATATTGTAACT
* *
27448 AAATAAATTTGAAATAATTTATTATTTTGACTAAATTTAATATGTTTTTGTGACTAAATAAATGT
1 AAATAAATTTAAAATAATTTATTATTTTGACTAAATTTAATATGTTATTGTGACTAAATAAATGT
* * *
27513 TTCACAATTT-TTTTTATTGTGAAAGA-TATTATTTTTCATAAATTTTTATATTGAGAAATTAGA
66 TTCACAATTTATTATT-TTG-AAAAGATTATTATTTATCAT-AA-TTTTATATTGA-AAATTA-A
* * * * *** *
27576 -ATTTTTTATAAAGT-GTTATTATGATTAAATAAATTTGTCATAATGTATTATTATGAGAAAATA
125 TATTTATTATAAA-TAGTTATTATGATTAAAT-AATGTATCAAAAAAAATTATTATGAAAAAATA
27639 TTGTAACT
188 TTGTAACT
* * *
27647 ACATAAATTTAAAAT-ATTTTTTATTTTGACTAAATTTAATATATTATTGTGACTAAATAAATGT
1 AAATAAATTTAAAATAATTTATTATTTTGACTAAATTTAATATGTTATTGTGACTAAATAAATGT
* *
27711 GTCATAATTTATTA
66 TTCACAATTTATTA
27725 ATTAAAAAAT
Statistics
Matches: 235, Mismatches: 33, Indels: 14
0.83 0.12 0.05
Matches are distributed among these distances:
194 4 0.02
195 82 0.35
196 7 0.03
197 11 0.05
198 84 0.36
199 47 0.20
ACGTcount: A:0.40, C:0.04, G:0.08, T:0.48
Consensus pattern (195 bp):
AAATAAATTTAAAATAATTTATTATTTTGACTAAATTTAATATGTTATTGTGACTAAATAAATGT
TTCACAATTTATTATTTTGAAAAGATTATTATTTATCATAATTTTATATTGAAAATTAATATTTA
TTATAAATAGTTATTATGATTAAATAATGTATCAAAAAAAATTATTATGAAAAAATATTGTAACT
Found at i:29269 original size:2 final size:2
Alignment explanation
Indices: 29262--29293 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
29252 ATAGATTTTA
29262 AT AT AT AT 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
29294 TTATTATAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:32627 original size:192 final size:193
Alignment explanation
Indices: 32369--32752 Score: 499
Period size: 192 Copynumber: 2.0 Consensus size: 193
32359 ACATTTATAT
* **
32369 ATAACGTCACTATATAATTAATATTCAATGACAACTAATTATGTCACTAAATTATGTAAAATTTC
1 ATAACGTCACTATATAATTAATATTCAATGACAACTAATTAAGTCACTAAATTAAATAAAATTTC
* * *
32434 GTTATTGATGATTGATATCATCAC-GGATAATACATTAAAATTAACCTATATGTGACG-AAAGAG
66 GTTATTGATCATTGATATCATCACAAG-TAATACATTAAAATCAACCTATATGTGA-GAAAAGAG
32497 ATATTGTCAAATTTTTAGTGACA-ATATAAAT-GTTACCTAATAATATTATAAAT-GACGATTAT
129 ATATTGTCAAATTTTTAGTGACATA-ATAAATCGTTACCTAATAATATTATAAATGGA-GATTAT
32559 GC
192 GC
* * * ** ** *
32561 ATAACGTCACTTTATAATTTATATTCTATGACAGTTGGTTAAGTCACTAAATTAAATAAGATTTC
1 ATAACGTCACTATATAATTAATATTCAATGACAACTAATTAAGTCACTAAATTAAATAAAATTTC
* ** * *
32626 GTTATTGATCATTTATATTGTCACAAGTAATGCATTAAAATCAACTTATATGTGAGAAAAGAGAT
66 GTTATTGATCATTGATATCATCACAAGTAATACATTAAAATCAACCTATATGTGAGAAAAGAGAT
* * *
32691 ATTGTCACATTTTTAGTGACATAATATATCGTTACCTAATAATATTATGAATGGAGATTATG
131 ATTGTCAAATTTTTAGTGACATAATAAATCGTTACCTAATAATATTATAAATGGAGATTATG
32753 AAGGGAAATA
Statistics
Matches: 165, Mismatches: 22, Indels: 9
0.84 0.11 0.05
Matches are distributed among these distances:
191 1 0.01
192 132 0.80
193 30 0.18
194 2 0.01
ACGTcount: A:0.39, C:0.11, G:0.12, T:0.37
Consensus pattern (193 bp):
ATAACGTCACTATATAATTAATATTCAATGACAACTAATTAAGTCACTAAATTAAATAAAATTTC
GTTATTGATCATTGATATCATCACAAGTAATACATTAAAATCAACCTATATGTGAGAAAAGAGAT
ATTGTCAAATTTTTAGTGACATAATAAATCGTTACCTAATAATATTATAAATGGAGATTATGC
Found at i:33543 original size:19 final size:18
Alignment explanation
Indices: 33517--33616 Score: 78
Period size: 18 Copynumber: 5.4 Consensus size: 18
33507 ATAATTATTA
33517 AAAATTAGAAAAATATAG
1 AAAATTAGAAAAATATAG
*
33535 AAAATTTAGATAAATATATCG
1 AAAA-TTAGA-AAA-ATATAG
*** *
33556 CAGGGTTAGAAATAT-TAG
1 -AAAATTAGAAAAATATAG
33574 AAAATTAGAAAAATATTA-
1 AAAATTAGAAAAATA-TAG
* *
33592 AAAATTAGAAAAATTTAT
1 AAAATTAGAAAAATATAG
33610 AAAATTA
1 AAAATTA
33617 CCTCCAAGTT
Statistics
Matches: 64, Mismatches: 11, Indels: 14
0.72 0.12 0.16
Matches are distributed among these distances:
17 12 0.19
18 27 0.42
19 9 0.14
20 5 0.08
21 10 0.16
22 1 0.02
ACGTcount: A:0.58, C:0.02, G:0.11, T:0.29
Consensus pattern (18 bp):
AAAATTAGAAAAATATAG
Found at i:33604 original size:9 final size:9
Alignment explanation
Indices: 33561--33606 Score: 51
Period size: 9 Copynumber: 5.2 Consensus size: 9
33551 TATCGCAGGG
*
33561 TTAGAAATA
1 TTAGAAAAA
33570 TTAG-AAAA
1 TTAGAAAAA
33578 TTAGAAAAA
1 TTAGAAAAA
*
33587 -TATTAAAAA
1 TTA-GAAAAA
33596 TTAGAAAAA
1 TTAGAAAAA
33605 TT
1 TT
33607 TATAAAATTA
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
8 9 0.29
9 20 0.65
10 2 0.06
ACGTcount: A:0.61, C:0.00, G:0.09, T:0.30
Consensus pattern (9 bp):
TTAGAAAAA
Found at i:34446 original size:16 final size:16
Alignment explanation
Indices: 34425--34469 Score: 90
Period size: 16 Copynumber: 2.8 Consensus size: 16
34415 AACTTATTGT
34425 TTTTATAATTTAAGAG
1 TTTTATAATTTAAGAG
34441 TTTTATAATTTAAGAG
1 TTTTATAATTTAAGAG
34457 TTTTATAATTTAA
1 TTTTATAATTTAA
34470 TTTTTTATGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 29 1.00
ACGTcount: A:0.38, C:0.00, G:0.09, T:0.53
Consensus pattern (16 bp):
TTTTATAATTTAAGAG
Found at i:36025 original size:14 final size:14
Alignment explanation
Indices: 36006--36033 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
35996 TATATTGCAG
36006 TTAGTTTTAAAATA
1 TTAGTTTTAAAATA
36020 TTAGTTTTAAAATA
1 TTAGTTTTAAAATA
36034 AGTTATGATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (14 bp):
TTAGTTTTAAAATA
Found at i:38831 original size:100 final size:100
Alignment explanation
Indices: 38700--38880 Score: 245
Period size: 100 Copynumber: 1.8 Consensus size: 100
38690 ATTGTTAAGA
*
38700 TTATATGTTTGAAACCTACTTAATAAAGAAAAAGTAAGAGAAAACATGTTTATATGAATAAAAAT
1 TTATATGTTTGAAACCTACTTAATAAAGAAAAAGTAAGAGAAAACATGTTTAGATGAATAAAAAT
*
38765 ATAGGTAGTGCCTTTTATATTGACAACTGTTGACG
66 ATAGGTAGTGCATTTTATATTGACAACTGTTGACG
** * * * ** ** * *
38800 TTATATGTTTGAAACCTTTTTATTTATGAAAATTTAAGATTAAACATGTTTAGATGTATAACAAT
1 TTATATGTTTGAAACCTACTTAATAAAGAAAAAGTAAGAGAAAACATGTTTAGATGAATAAAAAT
38865 ATAGGTAGTGCATTTT
66 ATAGGTAGTGCATTTT
38881 TAAAAGGTTC
Statistics
Matches: 68, Mismatches: 13, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
100 68 1.00
ACGTcount: A:0.39, C:0.08, G:0.15, T:0.38
Consensus pattern (100 bp):
TTATATGTTTGAAACCTACTTAATAAAGAAAAAGTAAGAGAAAACATGTTTAGATGAATAAAAAT
ATAGGTAGTGCATTTTATATTGACAACTGTTGACG
Found at i:48735 original size:60 final size:60
Alignment explanation
Indices: 48630--48747 Score: 166
Period size: 60 Copynumber: 2.0 Consensus size: 60
48620 AATGAAGAAA
* * * *
48630 AGTTAAATGCCTAATTGTGCATATTGGTATAAAGGTGCCATTAATGTAAGTTAGATGATT
1 AGTTAAATGCCTAATTGTGCATATTAGCAGAAAGGTGCCAATAATGTAAGTTAGATGATT
* *
48690 AGTTAAATGTCTAATTGTGCATATTAGCAGAAATGG-GTCAATAATGTAAGTTAGATGA
1 AGTTAAATGCCTAATTGTGCATATTAGCAGAAA-GGTGCCAATAATGTAAGTTAGATGA
48748 AAGGTCTAAC
Statistics
Matches: 51, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
60 49 0.96
61 2 0.04
ACGTcount: A:0.36, C:0.08, G:0.22, T:0.35
Consensus pattern (60 bp):
AGTTAAATGCCTAATTGTGCATATTAGCAGAAAGGTGCCAATAATGTAAGTTAGATGATT
Found at i:48853 original size:52 final size:52
Alignment explanation
Indices: 48700--49070 Score: 404
Period size: 52 Copynumber: 6.9 Consensus size: 52
48690 AGTTAAATGT
* * * * *
48700 CTAATTGTGCATATTAGCAGAAATGG-GTCAATAATGTAAGTTAGATGAAAGGT
1 CTAACTGTGCA-ATTGGCAGAAA-GGTGCCAATAATGCAAGTTAGATGAAAGGC
* * * *
48753 CTAACTGTGCATGTTGGAAGAAAGGTGTCAATAATTG-AAGTTATATGAAAGGC
1 CTAACTGTGCA-ATTGGCAGAAAGGTGCCAATAA-TGCAAGTTAGATGAAAGGC
* *
48806 CTAACTGTGTAATTGGGAGAAAGGTGCCAATAATGCAAGTTAGATGAAAGGC
1 CTAACTGTGCAATTGGCAGAAAGGTGCCAATAATGCAAGTTAGATGAAAGGC
* * **
48858 CTAACTGTGCATATTGGCAAAAAGGTGTCAATAATATAAGTTAGATGAAAGGC
1 CTAACTGTGCA-ATTGGCAGAAAGGTGCCAATAATGCAAGTTAGATGAAAGGC
* *
48911 CTAACTGTGCAATTGGCAGAAATGTGCCAATAATACAAGTTAGATGAAAGGC
1 CTAACTGTGCAATTGGCAGAAAGGTGCCAATAATGCAAGTTAGATGAAAGGC
* * *
48963 CTAACTGTGCATTTGGTAGAAAGGTACCAATAATGCAAGTTAGATGAAATGTTAAATGC
1 CTAACTGTGCAATTGGCAGAAAGGTGCCAATAATGCAAGTTAGATGAAA-G------GC
* * * *
49022 CTAACTGTGCATTTGGTAGAAAAGTGCCACTAATGCAAGTTAGATGAAA
1 CTAACTGTGCAATTGGCAGAAAGGTGCCAATAATGCAAGTTAGATGAAA
49071 AACATTGTAT
Statistics
Matches: 278, Mismatches: 29, Indels: 16
0.86 0.09 0.05
Matches are distributed among these distances:
51 2 0.01
52 127 0.46
53 99 0.36
54 2 0.01
59 48 0.17
ACGTcount: A:0.37, C:0.12, G:0.24, T:0.27
Consensus pattern (52 bp):
CTAACTGTGCAATTGGCAGAAAGGTGCCAATAATGCAAGTTAGATGAAAGGC
Found at i:48900 original size:105 final size:102
Alignment explanation
Indices: 48700--49070 Score: 409
Period size: 105 Copynumber: 3.5 Consensus size: 102
48690 AGTTAAATGT
* * * * * * *
48700 CTAATTGTGCATATTAGCAGAAATGGGTCAATAATGTAAGTTAGATGAAAGGTCTAACTGTGCAT
1 CTAACTGTGCA-ATTGGCAGAAAAGTGCCAATAATGCAAGTTAGATGAAAGGCCTAACTGTGCAT
48765 GTTGGAAGAAAGGTGTCAATAATTGAAGTTATATGAAAGGC
65 -TTGGAA-AAAGGTGTCAATAATT-AAGTTATATGAAAGGC
* * *
48806 CTAACTGTGTAATTGGGAGAAAGGTGCCAATAATGCAAGTTAGATGAAAGGCCTAACTGTGCATA
1 CTAACTGTGCAATTGGCAGAAAAGTGCCAATAATGCAAGTTAGATGAAAGGCCTAACTGTGCAT-
*
48871 TTGGCAAAAAGGTGTCAATAATATAAGTTAGATGAAAGGC
65 TTGG-AAAAAGGTGTCAATAAT-TAAGTTATATGAAAGGC
* *
48911 CTAACTGTGCAATTGGCAGAAATGTGCCAATAATACAAGTTAGATGAAAGGCCTAACTGTGCATT
1 CTAACTGTGCAATTGGCAGAAAAGTGCCAATAATGCAAGTTAGATGAAAGGCCTAACTGTGCATT
* ** * *
48976 TGGTAGAAAGGTACCAATAATGCAAGTTAGATGAAATGTTAAATGC
66 TGG-AAAAAGGTGTCAATAAT-TAAGTT--AT---ATG--AAAGGC
* * *
49022 CTAACTGTGCATTTGGTAGAAAAGTGCCACTAATGCAAGTTAGATGAAA
1 CTAACTGTGCAATTGGCAGAAAAGTGCCAATAATGCAAGTTAGATGAAA
49071 AACATTGTAT
Statistics
Matches: 228, Mismatches: 28, Indels: 13
0.85 0.10 0.05
Matches are distributed among these distances:
104 23 0.10
105 140 0.61
106 13 0.06
109 3 0.01
111 49 0.21
ACGTcount: A:0.37, C:0.12, G:0.24, T:0.27
Consensus pattern (102 bp):
CTAACTGTGCAATTGGCAGAAAAGTGCCAATAATGCAAGTTAGATGAAAGGCCTAACTGTGCATT
TGGAAAAAGGTGTCAATAATTAAGTTATATGAAAGGC
Found at i:50641 original size:21 final size:21
Alignment explanation
Indices: 50609--50663 Score: 103
Period size: 21 Copynumber: 2.7 Consensus size: 21
50599 TTTAAATAGT
50609 TTTAAG-TGTTTTAATTAGGA
1 TTTAAGATGTTTTAATTAGGA
50629 TTTAAGATGTTTTAATTAGGA
1 TTTAAGATGTTTTAATTAGGA
50650 TTTAAGATGTTTTA
1 TTTAAGATGTTTTA
50664 GCTTGTTTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
20 6 0.18
21 28 0.82
ACGTcount: A:0.31, C:0.00, G:0.18, T:0.51
Consensus pattern (21 bp):
TTTAAGATGTTTTAATTAGGA
Found at i:51287 original size:22 final size:22
Alignment explanation
Indices: 51247--51294 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
51237 CTTTAATTTG
*
51247 TTTATTTAATTAATTTTTTTCT
1 TTTATTTAATTAATTTTTTTAT
*
51269 TTTATTTAATT-CTTATTTTTAT
1 TTTATTTAATTAATT-TTTTTAT
51291 TTTA
1 TTTA
51295 ACCACAACTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 2 0.09
22 21 0.91
ACGTcount: A:0.23, C:0.04, G:0.00, T:0.73
Consensus pattern (22 bp):
TTTATTTAATTAATTTTTTTAT
Found at i:51368 original size:13 final size:12
Alignment explanation
Indices: 51336--51375 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 12
51326 TTACTATTAC
51336 TATTATTATTATAT
1 TATTATT-TTAT-T
51350 TATTATTTTATT
1 TATTATTTTATT
51362 TATTTATTTTATT
1 TA-TTATTTTATT
51375 T
1 T
51376 TAATATATCT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
12 3 0.12
13 15 0.60
14 7 0.28
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (12 bp):
TATTATTTTATT
Found at i:55138 original size:20 final size:20
Alignment explanation
Indices: 55115--55187 Score: 58
Period size: 20 Copynumber: 3.3 Consensus size: 20
55105 TGGTTTGCAT
55115 ACATGGTTAATTATTTGGCC
1 ACATGGTTAATTATTTGGCC
*
55135 ACATGTAAGTTACCATTAGGTTT-GCAG
1 ACATG---GTTA--ATTA--TTTGGC-C
55162 ACATGGTTAATTATTTGGCC
1 ACATGGTTAATTATTTGGCC
55182 ACATGG
1 ACATGG
55188 AAGAACTGCT
Statistics
Matches: 42, Mismatches: 2, Indels: 18
0.68 0.03 0.29
Matches are distributed among these distances:
20 14 0.33
21 2 0.05
22 4 0.10
23 4 0.10
24 4 0.10
25 4 0.10
26 2 0.05
27 8 0.19
ACGTcount: A:0.27, C:0.15, G:0.22, T:0.36
Consensus pattern (20 bp):
ACATGGTTAATTATTTGGCC
Found at i:58330 original size:74 final size:74
Alignment explanation
Indices: 58241--58400 Score: 241
Period size: 74 Copynumber: 2.2 Consensus size: 74
58231 TTGAACTCAA
*
58241 ATTTAGGATAATATTTTAAACATATAT-TTTATCTTTGTATTTTAGTTTAAATAGGTTTTAGTAT
1 ATTTAGGATATTATTTT-AACATATATCTTTATCTTTGTATTTTAGTTTAAATAGGTTTTAGTAT
58305 TTTAATTAAG
65 TTTAATTAAG
* * * *
58315 TTTTAGGATATTATTTTTATATTTATCTTTATCTTTGTATTTTAGTTTAAATAGGTTTTAGTATT
1 ATTTAGGATATTATTTTAACATATATCTTTATCTTTGTATTTTAGTTTAAATAGGTTTTAGTATT
*
58380 TTAATTAGG
66 TTAATTAAG
*
58389 ATTTAGAATATT
1 ATTTAGGATATT
58401 TATTATTTTA
Statistics
Matches: 77, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
73 6 0.08
74 71 0.92
ACGTcount: A:0.31, C:0.03, G:0.11, T:0.56
Consensus pattern (74 bp):
ATTTAGGATATTATTTTAACATATATCTTTATCTTTGTATTTTAGTTTAAATAGGTTTTAGTATT
TTAATTAAG
Found at i:58388 original size:19 final size:19
Alignment explanation
Indices: 58360--58419 Score: 54
Period size: 19 Copynumber: 3.2 Consensus size: 19
58350 TGTATTTTAG
*
58360 TTTAAATAGGTTTTAGTAT
1 TTTAATTAGGTTTTAGTAT
* *
58379 TTTAATTAGGATTTAGAAT
1 TTTAATTAGGTTTTAGTAT
58398 ATTT-ATTA--TTTTAGGTAT
1 -TTTAATTAGGTTTTA-GTAT
58416 TTTA
1 TTTA
58420 GTTTAAATAG
Statistics
Matches: 33, Mismatches: 5, Indels: 7
0.73 0.11 0.16
Matches are distributed among these distances:
17 7 0.21
18 3 0.09
19 20 0.61
20 3 0.09
ACGTcount: A:0.32, C:0.00, G:0.13, T:0.55
Consensus pattern (19 bp):
TTTAATTAGGTTTTAGTAT
Found at i:59027 original size:21 final size:22
Alignment explanation
Indices: 59003--59043 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
58993 TAATTTATTA
59003 TTTATTTAATTATT-TTTTTCT
1 TTTATTTAATTATTATTTTTCT
*
59024 TTTATTTAATTCTTATTTTT
1 TTTATTTAATTATTATTTTT
59044 ATTTAACCAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.20, C:0.05, G:0.00, T:0.76
Consensus pattern (22 bp):
TTTATTTAATTATTATTTTTCT
Found at i:64865 original size:60 final size:56
Alignment explanation
Indices: 64760--65189 Score: 383
Period size: 52 Copynumber: 8.0 Consensus size: 56
64750 AATTAAGAAA
* * *
64760 AGTTAAATGTCTAACTGTGCATATTGGCAGAAAGGTATCATTAATGCAAGTTAGATAAT
1 AGTTAAATGCCTAACTGTGCATATTGGCAGAAAGGTGTCAATAATGCAAGTTAG---AT
* *
64819 CAGTTAAATGCCTAACTGTGCATATTGGCAAAAATGTGTCAATAATGCAAGTTAGAT
1 -AGTTAAATGCCTAACTGTGCATATTGGCAGAAAGGTGTCAATAATGCAAGTTAGAT
*
64876 -G--AAAGGCCTAACTGTGCATATTGGCAGAAAGGTGTCAATAAT----G-T--A-
1 AGTTAAATGCCTAACTGTGCATATTGGCAGAAAGGTGTCAATAATGCAAGTTAGAT
* *
64921 AGTTAAATGGCCTAACTGTACA-AGTGGCAGAAAGGTGTCAATAATGCAAGTTAGAT
1 AGTTAAAT-GCCTAACTGTGCATATTGGCAGAAAGGTGTCAATAATGCAAGTTAGAT
* * * *
64977 -G--AAAGGCCTAACTGTGC--ATTGGTAGAAAAGTGTCAATAATGTAAGTTAGAT
1 AGTTAAATGCCTAACTGTGCATATTGGCAGAAAGGTGTCAATAATGCAAGTTAGAT
* * * * *
65028 -G--AAAGGCATAACTGTGCA-GTTGGTAGAAAGGTATCAATAATGCAAGTTAGAT
1 AGTTAAATGCCTAACTGTGCATATTGGCAGAAAGGTGTCAATAATGCAAGTTAGAT
* * *
65080 -G--AAAGGCCTAACTGTGAAT-TTGGCAGAAAGGTGCCAA-AATGCAAGTTAGAT
1 AGTTAAATGCCTAACTGTGCATATTGGCAGAAAGGTGTCAATAATGCAAGTTAGAT
* * *
65131 GAAATGTTAAGTGCCTAACTGTGCAT-TTGGCAGAAAGGTGTCACTAATGCCAGTTAGAT
1 ---A-GTTAAATGCCTAACTGTGCATATTGGCAGAAAGGTGTCAATAATGCAAGTTAGAT
65190 GAAAAAATAG
Statistics
Matches: 315, Mismatches: 33, Indels: 45
0.80 0.08 0.11
Matches are distributed among these distances:
46 2 0.01
48 26 0.08
49 13 0.04
51 60 0.19
52 73 0.23
53 42 0.13
55 3 0.01
56 1 0.00
57 2 0.01
58 31 0.10
59 13 0.04
60 49 0.16
ACGTcount: A:0.36, C:0.12, G:0.24, T:0.27
Consensus pattern (56 bp):
AGTTAAATGCCTAACTGTGCATATTGGCAGAAAGGTGTCAATAATGCAAGTTAGAT
Found at i:65075 original size:52 final size:52
Alignment explanation
Indices: 64828--65193 Score: 422
Period size: 52 Copynumber: 7.0 Consensus size: 52
64818 TCAGTTAAAT
* * *
64828 GCCTAACTGTGCATATTGGCAAAAATGTGTCAATAATGCAAGTTAGATGAAAG
1 GCCTAACTGTGCA-GTTGGCAGAAAGGTGTCAATAATGCAAGTTAGATGAAAG
* * *
64881 GCCTAACTGTGCATATTGGCAGAAAGGTGTCAATAATGTAAGTT--A--AATG
1 GCCTAACTGTGCA-GTTGGCAGAAAGGTGTCAATAATGCAAGTTAGATGAAAG
*
64930 GCCTAACTGTACAAG-TGGCAGAAAGGTGTCAATAATGCAAGTTAGATGAAAG
1 GCCTAACTGTGC-AGTTGGCAGAAAGGTGTCAATAATGCAAGTTAGATGAAAG
* * *
64982 GCCTAACTGTGCA-TTGGTAGAAAAGTGTCAATAATGTAAGTTAGATGAAAG
1 GCCTAACTGTGCAGTTGGCAGAAAGGTGTCAATAATGCAAGTTAGATGAAAG
* * *
65033 GCATAACTGTGCAGTTGGTAGAAAGGTATCAATAATGCAAGTTAGATGAAAG
1 GCCTAACTGTGCAGTTGGCAGAAAGGTGTCAATAATGCAAGTTAGATGAAAG
* * *
65085 GCCTAACTGTGAATTTGGCAGAAAGGTGCCAA-AATGCAAGTTAGATGAAATGTTAAG
1 GCCTAACTGTGCAGTTGGCAGAAAGGTGTCAATAATGCAAGTTAGATG--A----AAG
* * *
65142 TGCCTAACTGTGCATTTGGCAGAAAGGTGTCACTAATGCCAGTTAGATGAAA
1 -GCCTAACTGTGCAGTTGGCAGAAAGGTGTCAATAATGCAAGTTAGATGAAA
65194 AAATAGTGTA
Statistics
Matches: 272, Mismatches: 26, Indels: 30
0.83 0.08 0.09
Matches are distributed among these distances:
48 27 0.10
49 14 0.05
50 2 0.01
51 63 0.23
52 75 0.28
53 44 0.16
57 4 0.01
58 29 0.11
59 14 0.05
ACGTcount: A:0.36, C:0.13, G:0.25, T:0.26
Consensus pattern (52 bp):
GCCTAACTGTGCAGTTGGCAGAAAGGTGTCAATAATGCAAGTTAGATGAAAG
Found at i:65086 original size:103 final size:103
Alignment explanation
Indices: 64828--65193 Score: 438
Period size: 103 Copynumber: 3.5 Consensus size: 103
64818 TCAGTTAAAT
* * *
64828 GCCTAACTGTGCATATTGGCAAAAATGTGTCAATAATGCAAGTTAGATGAAAGGCCTAACTGTGC
1 GCCTAACTGTGCA-GTTGGCAGAAAGGTGTCAATAATGCAAGTTAGATGAAAGGCCTAACTGTGC
*
64893 ATATTGGCAGAAAGGTGTCAATAATGTAAGTT--A--AATG
65 --ATTGGCAGAAAGGTGTCAATAATGTAAGTTAGATGAAAG
*
64930 GCCTAACTGTACAAG-TGGCAGAAAGGTGTCAATAATGCAAGTTAGATGAAAGGCCTAACTGTGC
1 GCCTAACTGTGC-AGTTGGCAGAAAGGTGTCAATAATGCAAGTTAGATGAAAGGCCTAACTGTGC
* *
64994 ATTGGTAGAAAAGTGTCAATAATGTAAGTTAGATGAAAG
65 ATTGGCAGAAAGGTGTCAATAATGTAAGTTAGATGAAAG
* * * *
65033 GCATAACTGTGCAGTTGGTAGAAAGGTATCAATAATGCAAGTTAGATGAAAGGCCTAACTGTGAA
1 GCCTAACTGTGCAGTTGGCAGAAAGGTGTCAATAATGCAAGTTAGATGAAAGGCCTAACTGTGCA
* *
65098 TTTGGCAGAAAGGTGCCAA-AATGCAAGTTAGATGAAATGTTAAG
66 -TTGGCAGAAAGGTGTCAATAATGTAAGTTAGATG--A----AAG
* * *
65142 TGCCTAACTGTGCATTTGGCAGAAAGGTGTCACTAATGCCAGTTAGATGAAA
1 -GCCTAACTGTGCAGTTGGCAGAAAGGTGTCAATAATGCAAGTTAGATGAAA
65194 AAATAGTGTA
Statistics
Matches: 228, Mismatches: 22, Indels: 20
0.84 0.08 0.07
Matches are distributed among these distances:
99 28 0.12
101 48 0.21
102 13 0.06
103 75 0.33
104 15 0.07
105 1 0.00
109 3 0.01
110 45 0.20
ACGTcount: A:0.36, C:0.13, G:0.25, T:0.26
Consensus pattern (103 bp):
GCCTAACTGTGCAGTTGGCAGAAAGGTGTCAATAATGCAAGTTAGATGAAAGGCCTAACTGTGCA
TTGGCAGAAAGGTGTCAATAATGTAAGTTAGATGAAAG
Done.