Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015095.1 Kokia drynarioides strain JFW-HI SEQ_130139, 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: 310183
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.34
Warning! 548 characters in sequence are not A, C, G, or T
Found at i:732 original size:13 final size:14
Alignment explanation
Indices: 704--741 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
694 ACGATACGAA
*
704 AATATGACATATAC
1 AATATGACAAATAC
718 AATATGA-AAATAC
1 AATATGACAAATAC
*
731 AACATGACAAA
1 AATATGACAAA
742 CTGTAAATGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
13 11 0.52
14 10 0.48
ACGTcount: A:0.58, C:0.13, G:0.08, T:0.21
Consensus pattern (14 bp):
AATATGACAAATAC
Found at i:735 original size:22 final size:22
Alignment explanation
Indices: 692--735 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
682 AACACAGCAA
* **
692 ATACGATACGAAAATATGACAT
1 ATACAATACGAAAATACAACAT
*
714 ATACAATATGAAAATACAACAT
1 ATACAATACGAAAATACAACAT
736 GACAAACTGT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.55, C:0.14, G:0.09, T:0.23
Consensus pattern (22 bp):
ATACAATACGAAAATACAACAT
Found at i:1698 original size:136 final size:136
Alignment explanation
Indices: 1454--1698 Score: 350
Period size: 136 Copynumber: 1.8 Consensus size: 136
1444 GCCACGAAGA
* * * **
1454 AAATCATTTCAAATATGGAAATCCCTTTTAGGCCTGGTCTTGTTCATAAATTTATAAACATGATG
1 AAATCATTTCAAAAATGGAAATCCCTTTCAGGCCTGGCCTCATTCATAAATTTATAAACATGATG
1519 TAATTAACGCACGCCACGAAGAAAATCATTTCAAAATGGAAATCCCTTTCAGGCTTGGGCTCGCA
66 TAATTAACGCACGCCACGAAGAAAATCATTTCAAAATGGAAATCCCTTTCAGGCTTGGGCTCGCA
1584 ACAAAG
131 ACAAAG
* * ** *
1590 AAATCATTTCAAAAATGGAAATCCCTTTCGGGCTTGGCCTCATTTGTAAATTTATAAACGTGATG
1 AAATCATTTCAAAAATGGAAATCCCTTTCAGGCCTGGCCTCATTCATAAATTTATAAACATGATG
* *
1655 TAAGTT-AC-CACGCGATGAAGAAAATCATTTCAAAAATGGAAATC
66 TAA-TTAACGCACGCCACGAAGAAAATCATTTC-AAAATGGAAATC
1699 AGGTTAACAG
Statistics
Matches: 95, Mismatches: 12, Indels: 4
0.86 0.11 0.04
Matches are distributed among these distances:
135 21 0.22
136 72 0.76
137 2 0.02
ACGTcount: A:0.36, C:0.18, G:0.16, T:0.29
Consensus pattern (136 bp):
AAATCATTTCAAAAATGGAAATCCCTTTCAGGCCTGGCCTCATTCATAAATTTATAAACATGATG
TAATTAACGCACGCCACGAAGAAAATCATTTCAAAATGGAAATCCCTTTCAGGCTTGGGCTCGCA
ACAAAG
Found at i:3955 original size:20 final size:22
Alignment explanation
Indices: 3930--3972 Score: 72
Period size: 20 Copynumber: 2.0 Consensus size: 22
3920 AAATATCGTG
3930 AAAAAATAT-TTTTAAAA-AAT
1 AAAAAATATATTTTAAAATAAT
3950 AAAAAATATATTTTAAAATAAT
1 AAAAAATATATTTTAAAATAAT
3972 A
1 A
3973 TATATATATA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 9 0.43
21 8 0.38
22 4 0.19
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (22 bp):
AAAAAATATATTTTAAAATAAT
Found at i:3960 original size:22 final size:21
Alignment explanation
Indices: 3930--3972 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
3920 AAATATCGTG
3930 AAAAAATATTTTTAAAA-AATA
1 AAAAAATA-TTTTAAAATAATA
3951 AAAAATATATTTTAAAATAATA
1 AAAAA-ATATTTTAAAATAATA
3973 TATATATATA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
21 13 0.65
22 7 0.35
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (21 bp):
AAAAAATATTTTAAAATAATA
Found at i:6100 original size:13 final size:14
Alignment explanation
Indices: 6075--6102 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
6065 GTTATTTTAA
6075 TTTTACTTTTTTTT
1 TTTTACTTTTTTTT
6089 TTTTACTTTTTTTT
1 TTTTACTTTTTTTT
6103 AGTTCTTGAA
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:0.07, C:0.07, G:0.00, T:0.86
Consensus pattern (14 bp):
TTTTACTTTTTTTT
Found at i:7825 original size:20 final size:20
Alignment explanation
Indices: 7800--7837 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
7790 AATCATTAAA
7800 TTATTAATAAATTTAGAATT
1 TTATTAATAAATTTAGAATT
* *
7820 TTATTATTCAATTTAGAA
1 TTATTAATAAATTTAGAA
7838 AAATTATAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.42, C:0.03, G:0.05, T:0.50
Consensus pattern (20 bp):
TTATTAATAAATTTAGAATT
Found at i:7878 original size:13 final size:13
Alignment explanation
Indices: 7860--7884 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
7850 GGTTATTAAA
7860 TTATTTAAATTTT
1 TTATTTAAATTTT
7873 TTATTTAAATTT
1 TTATTTAAATTT
7885 CTATGTTGTT
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:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (13 bp):
TTATTTAAATTTT
Found at i:9453 original size:9 final size:9
Alignment explanation
Indices: 9439--9464 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
9429 ATTGGGAACA
9439 GTTGAGAAT
1 GTTGAGAAT
9448 GTTGAGAAT
1 GTTGAGAAT
9457 GTTGAGAA
1 GTTGAGAA
9465 AGCAACGTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.35, C:0.00, G:0.35, T:0.31
Consensus pattern (9 bp):
GTTGAGAAT
Found at i:10891 original size:39 final size:39
Alignment explanation
Indices: 10847--10923 Score: 120
Period size: 39 Copynumber: 2.0 Consensus size: 39
10837 TGTACTCTTA
*
10847 TTTTTATAAAATTA-TTTTTTAATAAAAAGATATAAATTT
1 TTTTTATAAAAGTATTTTTTTAAT-AAAAGATATAAATTT
*
10886 TTTTTATAAAAGTATTTTTTTAATAAAAGATATTAATT
1 TTTTTATAAAAGTATTTTTTTAATAAAAGATATAAATT
10924 ATTTGAATTA
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
39 26 0.74
40 9 0.26
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.52
Consensus pattern (39 bp):
TTTTTATAAAAGTATTTTTTTAATAAAAGATATAAATTT
Found at i:10905 original size:16 final size:18
Alignment explanation
Indices: 10882--10919 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 18
10872 AAAGATATAA
*
10882 ATTTTTTTTATAAAAG-T
1 ATTTTTTTAATAAAAGAT
10899 ATTTTTTTAATAAAAGAT
1 ATTTTTTTAATAAAAGAT
10917 ATT
1 ATT
10920 AATTATTTGA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 15 0.79
18 4 0.21
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.55
Consensus pattern (18 bp):
ATTTTTTTAATAAAAGAT
Found at i:28154 original size:53 final size:53
Alignment explanation
Indices: 28074--28180 Score: 187
Period size: 53 Copynumber: 2.0 Consensus size: 53
28064 GCAGGCAGAA
*
28074 GCTTATTTATCTTTGAAAGAAAGCAACCAATGTTGCATGTTGTACTAAACCTT
1 GCTTATTTATCTTTGAAAGAAAGCAACCAATGTTGCATGTTGTACAAAACCTT
* *
28127 GCTTATTTATCTTTGCAAGAAAGCAACCAATGTTGCATGTTGTACAAAATCTT
1 GCTTATTTATCTTTGAAAGAAAGCAACCAATGTTGCATGTTGTACAAAACCTT
28180 G
1 G
28181 TTTGCAACTA
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
53 51 1.00
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.36
Consensus pattern (53 bp):
GCTTATTTATCTTTGAAAGAAAGCAACCAATGTTGCATGTTGTACAAAACCTT
Found at i:35369 original size:20 final size:19
Alignment explanation
Indices: 35344--35381 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
35334 AATTCTCTAA
*
35344 AAATAAAATATTAAAATATT
1 AAATAAAAT-TGAAAATATT
35364 AAATAAAATTGAAAATAT
1 AAATAAAATTGAAAATAT
35382 GAATATGAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.32
Consensus pattern (19 bp):
AAATAAAATTGAAAATATT
Found at i:35619 original size:15 final size:16
Alignment explanation
Indices: 35599--35632 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
35589 ATATTATTAA
35599 TTTCAATTA-ATATGT
1 TTTCAATTATATATGT
*
35614 TTTCAATTATCTATGT
1 TTTCAATTATATATGT
35630 TTT
1 TTT
35633 TGTAAATTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 9 0.53
16 8 0.47
ACGTcount: A:0.26, C:0.09, G:0.06, T:0.59
Consensus pattern (16 bp):
TTTCAATTATATATGT
Found at i:35677 original size:20 final size:20
Alignment explanation
Indices: 35654--35692 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
35644 TCATTATAAA
* *
35654 TTTTTTTTATAATTTATATG
1 TTTTTTCTAGAATTTATATG
35674 TTTTTTCTAGAATTTATAT
1 TTTTTTCTAGAATTTATAT
35693 ATATCTTCTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.26, C:0.03, G:0.05, T:0.67
Consensus pattern (20 bp):
TTTTTTCTAGAATTTATATG
Found at i:35707 original size:19 final size:20
Alignment explanation
Indices: 35664--35715 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
35654 TTTTTTTTAT
* * *
35664 AATTTATATGTTTTTTCTAG
1 AATTTATATATATCTTCTAG
35684 AATTTATATATATCTTCT-G
1 AATTTATATATATCTTCTAG
*
35703 AATTTTTATATAT
1 AATTTATATATAT
35716 TTATTTATGT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
19 13 0.46
20 15 0.54
ACGTcount: A:0.31, C:0.06, G:0.06, T:0.58
Consensus pattern (20 bp):
AATTTATATATATCTTCTAG
Found at i:35728 original size:19 final size:19
Alignment explanation
Indices: 35706--35757 Score: 52
Period size: 19 Copynumber: 2.7 Consensus size: 19
35696 TCTTCTGAAT
*
35706 TTTTATATATTTATTTATG
1 TTTTATATATTTATTAATG
*
35725 TTTTCTTATATTT-TTAATG
1 TTTT-ATATATTTATTAATG
*
35744 TGTTTATACATTTA
1 T-TTTATATATTTA
35758 ATAAAAGAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 5
0.74 0.11 0.14
Matches are distributed among these distances:
19 16 0.62
20 10 0.38
ACGTcount: A:0.25, C:0.04, G:0.06, T:0.65
Consensus pattern (19 bp):
TTTTATATATTTATTAATG
Found at i:36328 original size:16 final size:18
Alignment explanation
Indices: 36291--36331 Score: 52
Period size: 16 Copynumber: 2.4 Consensus size: 18
36281 GATAAAAAAT
*
36291 TATTAATAATATTTTTAA
1 TATTAATAATATTATTAA
36309 -ATTAA-AATA-TATTAA
1 TATTAATAATATTATTAA
36324 TATTAATA
1 TATTAATA
36332 TTCAAATCAT
Statistics
Matches: 20, Mismatches: 1, Indels: 5
0.77 0.04 0.19
Matches are distributed among these distances:
15 5 0.25
16 9 0.45
17 6 0.30
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (18 bp):
TATTAATAATATTATTAA
Found at i:36378 original size:15 final size:15
Alignment explanation
Indices: 36358--36389 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
36348 TTTTTTATAT
*
36358 TATTTTAATATTAAA
1 TATTTTAAAATTAAA
36373 TATTTTAAAATTAAA
1 TATTTTAAAATTAAA
36388 TA
1 TA
36390 ACGTTAATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
TATTTTAAAATTAAA
Found at i:38269 original size:12 final size:12
Alignment explanation
Indices: 38252--38276 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
38242 GAGCTTATTG
38252 AAAAGAAGAAAT
1 AAAAGAAGAAAT
38264 AAAAGAAGAAAT
1 AAAAGAAGAAAT
38276 A
1 A
38277 TCAGTACGTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.76, C:0.00, G:0.16, T:0.08
Consensus pattern (12 bp):
AAAAGAAGAAAT
Found at i:40350 original size:13 final size:13
Alignment explanation
Indices: 40332--40361 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
40322 TATTTTGTAG
*
40332 TACAAATTGTAAT
1 TACAAATCGTAAT
40345 TACAAATCGTAAT
1 TACAAATCGTAAT
40358 TACA
1 TACA
40362 CGATTACATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.47, C:0.13, G:0.07, T:0.33
Consensus pattern (13 bp):
TACAAATCGTAAT
Found at i:46650 original size:40 final size:40
Alignment explanation
Indices: 46604--46688 Score: 125
Period size: 40 Copynumber: 2.1 Consensus size: 40
46594 TTTTTAGGGT
* * *
46604 TAAAACGACTCATAATCCTATACGAATTTAACTTATATAG
1 TAAAACGACTCATAATCCAATACAAATTCAACTTATATAG
* *
46644 TAAAACGACTCATAATCCAATATAAATTCAACTTGTATAG
1 TAAAACGACTCATAATCCAATACAAATTCAACTTATATAG
46684 TAAAA
1 TAAAA
46689 TCTATATCTC
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.46, C:0.16, G:0.07, T:0.31
Consensus pattern (40 bp):
TAAAACGACTCATAATCCAATACAAATTCAACTTATATAG
Found at i:47872 original size:2 final size:2
Alignment explanation
Indices: 47865--47905 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
47855 CCCTTAAATT
47865 TA TA TA 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 TA TA TA T
47906 TAGTGCCAGT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:47955 original size:21 final size:20
Alignment explanation
Indices: 47916--47956 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
47906 TAGTGCCAGT
*
47916 GGGTCATAATTTAAGATTGA
1 GGGTCATAATTTAAAATTGA
*
47936 GGGTCCTAATTTTAAAATTGA
1 GGGTCATAA-TTTAAAATTGA
47957 ATAAATGATC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.34, C:0.07, G:0.22, T:0.37
Consensus pattern (20 bp):
GGGTCATAATTTAAAATTGA
Found at i:55284 original size:67 final size:67
Alignment explanation
Indices: 55132--55260 Score: 249
Period size: 67 Copynumber: 1.9 Consensus size: 67
55122 GTTGAGCCCA
*
55132 ACATGTCTCCCCCACAAATGCACTCCTTCAAAGAAAGCGACATGGGACAAATATCAAAATGCCCA
1 ACATGTCTCCCCCACAAATGCACTCCTCCAAAGAAAGCGACATGGGACAAATATCAAAATGCCCA
55197 AC
66 AC
55199 ACATGTCTCCCCCACAAATGCACTCCTCCAAAGAAAGCGACATGGGACAAATATCAAAATGC
1 ACATGTCTCCCCCACAAATGCACTCCTCCAAAGAAAGCGACATGGGACAAATATCAAAATGC
55261 ATTCAACTAC
Statistics
Matches: 61, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
67 61 1.00
ACGTcount: A:0.39, C:0.31, G:0.14, T:0.16
Consensus pattern (67 bp):
ACATGTCTCCCCCACAAATGCACTCCTCCAAAGAAAGCGACATGGGACAAATATCAAAATGCCCA
AC
Found at i:58571 original size:118 final size:118
Alignment explanation
Indices: 58360--58666 Score: 463
Period size: 118 Copynumber: 2.6 Consensus size: 118
58350 ACAAATTGAA
* * * *
58360 ATCCAGACTTAGAACACCCATT-AGAAAAAAAATCCAGACTTAGAACACCCATCAATTCATTAAA
1 ATCCAAACTTAGAACACCCATTAAAAAAAAAAATCCAAACTTAGAACACCCATCAATCCATT---
* *
58424 AAAAAAATCAAAAACTTAACAGCACAAATAAAACCCTAAAAAGTAACATATCAAAC
63 AAAAAAATAAAAAACTTAACAGCACAAATAAAACCCTAAAAAGTAACAGATCAAAC
* * * *
58480 ATCCAAACTTAAAACACCCATTAAAAAAAAAAATCCAAACATAAAACGCCCATCAATCCATTAAA
1 ATCCAAACTTAGAACACCCATTAAAAAAAAAAATCCAAACTTAGAACACCCATCAATCCATTAAA
*
58545 AAAATAAAAAACTTAACATCACAAATAAAACCCTAAAAAGTAACAGATCAAAC
66 AAAATAAAAAACTTAACAGCACAAATAAAACCCTAAAAAGTAACAGATCAAAC
*
58598 ATCCAAACTTAGAACACCCATTAGAAAAAAAAAATTCAAACTTAGAACACCCATCAATCCATTAA
1 ATCCAAACTTAGAACACCCATTA-AAAAAAAAAATCCAAACTTAGAACACCCATCAATCCATTAA
58663 AAAA
65 AAAA
58667 CCTAGAATGT
Statistics
Matches: 169, Mismatches: 16, Indels: 5
0.89 0.08 0.03
Matches are distributed among these distances:
118 75 0.44
119 41 0.24
120 20 0.12
121 33 0.20
ACGTcount: A:0.56, C:0.23, G:0.04, T:0.17
Consensus pattern (118 bp):
ATCCAAACTTAGAACACCCATTAAAAAAAAAAATCCAAACTTAGAACACCCATCAATCCATTAAA
AAAATAAAAAACTTAACAGCACAAATAAAACCCTAAAAAGTAACAGATCAAAC
Found at i:63210 original size:21 final size:24
Alignment explanation
Indices: 63161--63218 Score: 77
Period size: 21 Copynumber: 2.5 Consensus size: 24
63151 CAAGTATGCA
*
63161 AACTACCGATACATCTATACATAC
1 AACTACCGATACATCTACACATAC
*
63185 AACTACCGATAC-TC-ACA-ATTC
1 AACTACCGATACATCTACACATAC
63206 AACTACCGATACA
1 AACTACCGATACA
63219 ACTCAAGTCA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
21 15 0.48
22 2 0.06
23 2 0.06
24 12 0.39
ACGTcount: A:0.41, C:0.31, G:0.05, T:0.22
Consensus pattern (24 bp):
AACTACCGATACATCTACACATAC
Found at i:63910 original size:52 final size:52
Alignment explanation
Indices: 63800--64041 Score: 224
Period size: 52 Copynumber: 4.6 Consensus size: 52
63790 TCACTTCATT
* * * * *
63800 CATATACTCACGATGACACATAGCCATCGGACCT-TATAATCCACG--AGGGATT
1 CATATACTCACGATGATACTTAGTCATCGGACCTCT-TAAT-CA-GTAAAGGATC
* * ** *
63852 CGTATACTCACGATTATACAAAGTTATCGGACCTCTTAATCAGTAAAGGATC
1 CATATACTCACGATGATACTTAGTCATCGGACCTCTTAATCAGTAAAGGATC
* *
63904 CATATACTCACGATGACACTTAGTCATCGGACCT-TTAAAACCA-TAAAGGATC
1 CATATACTCACGATGATACTTAGTCATCGGACCTCTT--AATCAGTAAAGGATC
* * * *
63956 TCATATACTCACGATGATACTTAGTCATCTGACCTCATAATCTGTAAAGGATT
1 -CATATACTCACGATGATACTTAGTCATCGGACCTCTTAATCAGTAAAGGATC
* * *
64009 CATTTACTCATGATGACACTTAGTCATCGGACC
1 CATATACTCACGATGATACTTAGTCATCGGACC
64042 CTTTTTCATT
Statistics
Matches: 157, Mismatches: 25, Indels: 16
0.79 0.13 0.08
Matches are distributed among these distances:
50 1 0.01
51 4 0.03
52 106 0.68
53 45 0.29
54 1 0.01
ACGTcount: A:0.33, C:0.24, G:0.15, T:0.28
Consensus pattern (52 bp):
CATATACTCACGATGATACTTAGTCATCGGACCTCTTAATCAGTAAAGGATC
Found at i:64005 original size:105 final size:104
Alignment explanation
Indices: 63800--64041 Score: 306
Period size: 105 Copynumber: 2.3 Consensus size: 104
63790 TCACTTCATT
* * * * * *
63800 CATATACTCACGATGACACATAGCCATCGGACCTTATAATCCACGAGGGATTCGTATACTCACGA
1 CATATACTCACGATGACACTTAGTCATCGGACCTTATAAACCACAAAGGATTCATATACTCACGA
* * *
63865 TTATACAAAGTTATCGGACCTCTTAATCAGTAAAGGATC
66 TGATACAAAGTCATCGGACCTCATAATCAGTAAAGGATC
*
63904 CATATACTCACGATGACACTTAGTCATCGGACCTT-TAAAACCATAAAGGATCTCATATACTCAC
1 CATATACTCACGATGACACTTAGTCATCGGACCTTAT-AAACCACAAAGGAT-TCATATACTCAC
** * * *
63968 GATGATACTTAGTCATCTGACCTCATAATCTGTAAAGGATT
64 GATGATACAAAGTCATCGGACCTCATAATCAGTAAAGGATC
* *
64009 CATTTACTCATGATGACACTTAGTCATCGGACC
1 CATATACTCACGATGACACTTAGTCATCGGACC
64042 CTTTTTCATT
Statistics
Matches: 119, Mismatches: 17, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
103 1 0.01
104 43 0.36
105 75 0.63
ACGTcount: A:0.33, C:0.24, G:0.15, T:0.28
Consensus pattern (104 bp):
CATATACTCACGATGACACTTAGTCATCGGACCTTATAAACCACAAAGGATTCATATACTCACGA
TGATACAAAGTCATCGGACCTCATAATCAGTAAAGGATC
Found at i:64934 original size:22 final size:22
Alignment explanation
Indices: 64901--64952 Score: 63
Period size: 22 Copynumber: 2.4 Consensus size: 22
64891 TAGACTTTCT
64901 TTATTAA-CTTAATTAA-TCATA
1 TTATTAACCTTAA-TAATTCATA
* *
64922 TTTTTAACCTTAATAATTCCTA
1 TTATTAACCTTAATAATTCATA
64944 TTATTAACC
1 TTATTAACC
64953 AATATTTGTC
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
21 9 0.35
22 17 0.65
ACGTcount: A:0.37, C:0.15, G:0.00, T:0.48
Consensus pattern (22 bp):
TTATTAACCTTAATAATTCATA
Found at i:79106 original size:25 final size:24
Alignment explanation
Indices: 79047--79107 Score: 61
Period size: 26 Copynumber: 2.4 Consensus size: 24
79037 ATAAAACAAC
79047 AAAAGTAAAAACTAAGTCTAAAAAG
1 AAAAG-AAAAACTAAGTCTAAAAAG
*
79072 AAAATGGAAAACCTAA-TCTAAAAAATG
1 AAAA--GAAAAACTAAGTCT-AAAAA-G
79099 AAAAGAAAA
1 AAAAGAAAA
79108 TAAAACCTAA
Statistics
Matches: 31, Mismatches: 1, Indels: 8
0.77 0.03 0.20
Matches are distributed among these distances:
25 12 0.39
26 13 0.42
27 6 0.19
ACGTcount: A:0.66, C:0.08, G:0.11, T:0.15
Consensus pattern (24 bp):
AAAAGAAAAACTAAGTCTAAAAAG
Found at i:81982 original size:79 final size:79
Alignment explanation
Indices: 81842--82047 Score: 340
Period size: 79 Copynumber: 2.6 Consensus size: 79
81832 ACTGACGATT
* *
81842 CTGGTACCCAGTGCCTAGCGGATAAACTGCAAAAGTGAACCCAGCTCTAGTTGGATTAACCAACA
1 CTGGCACCCAGTGCCTAGCGGATAAACCGCAAAAGTGAACCCAGCTCTAGTTGGATTAACCAACA
81907 ATATCCGTCAAATC
66 ATATCCGTCAAATC
*
81921 CTGGCACCTAGTGCCTAGCGGATAAACCGCAAAAGTGAACCCAGCTCTAGTTGGATTAACCAACA
1 CTGGCACCCAGTGCCTAGCGGATAAACCGCAAAAGTGAACCCAGCTCTAGTTGGATTAACCAACA
*
81986 ATATGCGTCAAATC
66 ATATCCGTCAAATC
* * * *
82000 CTGGCACCCAGTGCCAAGCGGATAAATCGCAAATGTGAGCCCAGCTCT
1 CTGGCACCCAGTGCCTAGCGGATAAACCGCAAAAGTGAACCCAGCTCT
82048 GACAAAATAA
Statistics
Matches: 118, Mismatches: 9, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
79 118 1.00
ACGTcount: A:0.32, C:0.28, G:0.21, T:0.20
Consensus pattern (79 bp):
CTGGCACCCAGTGCCTAGCGGATAAACCGCAAAAGTGAACCCAGCTCTAGTTGGATTAACCAACA
ATATCCGTCAAATC
Found at i:84994 original size:27 final size:27
Alignment explanation
Indices: 84934--85001 Score: 77
Period size: 26 Copynumber: 2.6 Consensus size: 27
84924 TGATTTTTTT
* *
84934 TTTGAAATTTTATAGTTTTTTAAAAAA
1 TTTGAAATTTTAAAATTTTTTAAAAAA
* *
84961 TAT-AAATTTTAAAA-TTTTTATAAATA
1 TTTGAAATTTTAAAATTTTTTA-AAAAA
84987 TTTGAAATTTTAAAA
1 TTTGAAATTTTAAAA
85002 ACTATTTTGA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
25 6 0.18
26 15 0.44
27 13 0.38
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (27 bp):
TTTGAAATTTTAAAATTTTTTAAAAAA
Found at i:84998 original size:18 final size:19
Alignment explanation
Indices: 84961--84997 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
84951 TTTTAAAAAA
84961 TATAAAT-TTTAAAATTTT
1 TATAAATATTTAAAATTTT
*
84979 TATAAATATTTGAAATTTT
1 TATAAATATTTAAAATTTT
84998 AAAAACTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (19 bp):
TATAAATATTTAAAATTTT
Found at i:85012 original size:20 final size:19
Alignment explanation
Indices: 84966--85017 Score: 52
Period size: 20 Copynumber: 2.7 Consensus size: 19
84956 AAAAATATAA
* *
84966 ATTTTAAAATTTTTATAAAT
1 ATTTTGAAA-TTTTAAAAAT
84986 A-TTTGAAATTTTAAAAACT
1 ATTTTGAAATTTTAAAAA-T
*
85005 ATTTTGAACTTTT
1 ATTTTGAAATTTT
85018 TGTAATTTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
18 8 0.30
19 8 0.30
20 11 0.41
ACGTcount: A:0.40, C:0.04, G:0.04, T:0.52
Consensus pattern (19 bp):
ATTTTGAAATTTTAAAAAT
Found at i:95423 original size:21 final size:22
Alignment explanation
Indices: 95357--95423 Score: 75
Period size: 21 Copynumber: 3.0 Consensus size: 22
95347 TCTCATATTT
95357 TTTTTGGAAAATTTATAATTTATA-
1 TTTTT-GAAAA-TTATAA-TTATAC
**
95381 TTTTTGAAAATTATAAAAATAC
1 TTTTTGAAAATTATAATTATAC
95403 TTTTT-AAAATTATAATTATAC
1 TTTTTGAAAATTATAATTATAC
95424 AAAGAATTTA
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
21 17 0.45
22 11 0.29
23 5 0.13
24 5 0.13
ACGTcount: A:0.43, C:0.03, G:0.04, T:0.49
Consensus pattern (22 bp):
TTTTTGAAAATTATAATTATAC
Found at i:120705 original size:6 final size:6
Alignment explanation
Indices: 120696--120720 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
120686 TTTAACTACT
120696 ACTTAA ACTTAA ACTTAA ACTTAA A
1 ACTTAA ACTTAA ACTTAA ACTTAA A
120721 AATAATAAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.52, C:0.16, G:0.00, T:0.32
Consensus pattern (6 bp):
ACTTAA
Found at i:121711 original size:14 final size:13
Alignment explanation
Indices: 121690--121723 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
121680 TTAAATATTT
*
121690 TAAAATATAATTA
1 TAAAATATAAATA
121703 TAAATATATAAATA
1 TAAA-ATATAAATA
121717 TAAAATA
1 TAAAATA
121724 ATATTTTATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
13 7 0.37
14 12 0.63
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (13 bp):
TAAAATATAAATA
Found at i:124165 original size:18 final size:18
Alignment explanation
Indices: 124142--124177 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
124132 GTTACATCTC
124142 CTTGGTTATTGACAAATA
1 CTTGGTTATTGACAAATA
124160 CTTGGTTATTGACAAATA
1 CTTGGTTATTGACAAATA
124178 ATTATGACTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.33, C:0.11, G:0.17, T:0.39
Consensus pattern (18 bp):
CTTGGTTATTGACAAATA
Found at i:125752 original size:25 final size:22
Alignment explanation
Indices: 125713--125757 Score: 63
Period size: 25 Copynumber: 1.9 Consensus size: 22
125703 ATTCCAAAGC
125713 AAAAAAAATGATTTTTATAATA
1 AAAAAAAATGATTTTTATAATA
125735 AAAAAAAAGTTGAGTTTTTATAA
1 AAAAAAAA--TGA-TTTTTATAA
125758 AAATCATTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
22 8 0.40
24 3 0.15
25 9 0.45
ACGTcount: A:0.56, C:0.00, G:0.09, T:0.36
Consensus pattern (22 bp):
AAAAAAAATGATTTTTATAATA
Found at i:126179 original size:14 final size:14
Alignment explanation
Indices: 126162--126202 Score: 64
Period size: 14 Copynumber: 2.9 Consensus size: 14
126152 ATGAATTATT
126162 ATATTAAAATTAAA
1 ATATTAAAATTAAA
*
126176 ATATTATAATTAAA
1 ATATTAAAATTAAA
126190 ATATTCAAAATTA
1 ATATT-AAAATTA
126203 TTTAAATTCA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
14 18 0.75
15 6 0.25
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (14 bp):
ATATTAAAATTAAA
Found at i:126784 original size:64 final size:64
Alignment explanation
Indices: 126683--126810 Score: 247
Period size: 64 Copynumber: 2.0 Consensus size: 64
126673 TTATTAAAAA
126683 AATTTAACGGGACGTTTGAACCGATTGTCAAGTATGGAACTTGGCCCAGTCTGCTCGGCTTATG
1 AATTTAACGGGACGTTTGAACCGATTGTCAAGTATGGAACTTGGCCCAGTCTGCTCGGCTTATG
*
126747 AATTTGACGGGACGTTTGAACCGATTGTCAAGTATGGAACTTGGCCCAGTCTGCTCGGCTTATG
1 AATTTAACGGGACGTTTGAACCGATTGTCAAGTATGGAACTTGGCCCAGTCTGCTCGGCTTATG
126811 CAGTTACTGT
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
64 63 1.00
ACGTcount: A:0.23, C:0.20, G:0.27, T:0.30
Consensus pattern (64 bp):
AATTTAACGGGACGTTTGAACCGATTGTCAAGTATGGAACTTGGCCCAGTCTGCTCGGCTTATG
Found at i:132814 original size:9 final size:9
Alignment explanation
Indices: 132800--132827 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
132790 AATAGAGGCT
132800 GATGTTGAA
1 GATGTTGAA
132809 GATGTTGAA
1 GATGTTGAA
132818 GATGTTGAA
1 GATGTTGAA
132827 G
1 G
132828 GAAGTGAGCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.36, T:0.32
Consensus pattern (9 bp):
GATGTTGAA
Found at i:135808 original size:27 final size:28
Alignment explanation
Indices: 135778--135833 Score: 105
Period size: 27 Copynumber: 2.0 Consensus size: 28
135768 ATGATTCAAG
135778 GTTCAAGGGTTTGAGGTTAAGGG-ATGA
1 GTTCAAGGGTTTGAGGTTAAGGGCATGA
135805 GTTCAAGGGTTTGAGGTTAAGGGCATGA
1 GTTCAAGGGTTTGAGGTTAAGGGCATGA
135833 G
1 G
135834 GTTTAGGGTT
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
27 23 0.82
28 5 0.18
ACGTcount: A:0.25, C:0.05, G:0.41, T:0.29
Consensus pattern (28 bp):
GTTCAAGGGTTTGAGGTTAAGGGCATGA
Found at i:135826 original size:14 final size:14
Alignment explanation
Indices: 135776--135843 Score: 68
Period size: 14 Copynumber: 4.9 Consensus size: 14
135766 TTATGATTCA
135776 AGGTTCAAGGGTTTG
1 AGGTT-AAGGGTTTG
*
135791 AGGTTAAGGG-ATG
1 AGGTTAAGGGTTTG
135804 A-GTTCAAGGGTTTG
1 AGGTT-AAGGGTTTG
**
135818 AGGTTAAGGGCATG
1 AGGTTAAGGGTTTG
*
135832 AGGTTTAGGGTT
1 AGGTTAAGGGTT
135844 CAAGATTTTA
Statistics
Matches: 43, Mismatches: 7, Indels: 7
0.75 0.12 0.12
Matches are distributed among these distances:
12 3 0.07
13 8 0.19
14 24 0.56
15 8 0.19
ACGTcount: A:0.24, C:0.04, G:0.41, T:0.31
Consensus pattern (14 bp):
AGGTTAAGGGTTTG
Found at i:143827 original size:25 final size:25
Alignment explanation
Indices: 143794--143848 Score: 103
Period size: 25 Copynumber: 2.2 Consensus size: 25
143784 TTTATTTAGA
143794 CCTG-TGTTTTTGGTTGGTGTTTGT
1 CCTGTTGTTTTTGGTTGGTGTTTGT
143818 CCTGTTGTTTTTGGTTGGTGTTTGT
1 CCTGTTGTTTTTGGTTGGTGTTTGT
143843 CCTGTT
1 CCTGTT
143849 AGCCTTAATT
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
24 4 0.13
25 26 0.87
ACGTcount: A:0.00, C:0.11, G:0.31, T:0.58
Consensus pattern (25 bp):
CCTGTTGTTTTTGGTTGGTGTTTGT
Found at i:149125 original size:15 final size:15
Alignment explanation
Indices: 149105--149135 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
149095 TATTTTGTTG
149105 GATTCAGAAAGAGTA
1 GATTCAGAAAGAGTA
*
149120 GATTCAGATAGAGTA
1 GATTCAGAAAGAGTA
149135 G
1 G
149136 GAAGAGACAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.42, C:0.06, G:0.29, T:0.23
Consensus pattern (15 bp):
GATTCAGAAAGAGTA
Found at i:163830 original size:15 final size:17
Alignment explanation
Indices: 163810--163848 Score: 55
Period size: 15 Copynumber: 2.4 Consensus size: 17
163800 AATTCTTTAA
163810 AAATTATGAAAAT-AT-
1 AAATTATGAAAATGATG
*
163825 AAATTATTAAAATGATG
1 AAATTATGAAAATGATG
163842 AAATTAT
1 AAATTAT
163849 ATATTTACTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 12 0.57
16 2 0.10
17 7 0.33
ACGTcount: A:0.56, C:0.00, G:0.08, T:0.36
Consensus pattern (17 bp):
AAATTATGAAAATGATG
Found at i:167007 original size:21 final size:21
Alignment explanation
Indices: 166967--167007 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
166957 TTTATTCCCG
* **
166967 AAAATTTTAATTTTTTATTTT
1 AAAATTTAAATTTTAAATTTT
166988 AAAATTTAAATTTTAAATTT
1 AAAATTTAAATTTTAAATTT
167008 CAACCATCAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (21 bp):
AAAATTTAAATTTTAAATTTT
Found at i:167418 original size:26 final size:26
Alignment explanation
Indices: 167389--167441 Score: 88
Period size: 26 Copynumber: 2.0 Consensus size: 26
167379 AACTCTATTT
* *
167389 ATCTTCTCTTAATCTTAATGTGATGA
1 ATCTTCTCTTAATCCTAACGTGATGA
167415 ATCTTCTCTTAATCCTAACGTGATGA
1 ATCTTCTCTTAATCCTAACGTGATGA
167441 A
1 A
167442 GATATCAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.28, C:0.19, G:0.11, T:0.42
Consensus pattern (26 bp):
ATCTTCTCTTAATCCTAACGTGATGA
Found at i:167640 original size:27 final size:27
Alignment explanation
Indices: 167602--167653 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
167592 GCCTTGTCAC
*
167602 AATAAGTAATTTAACCCAGTTTACCCA
1 AATAAGTAATTTAACCCAATTTACCCA
*
167629 AATAAGTAATTTAATCCAATTTACC
1 AATAAGTAATTTAACCCAATTTACC
167654 TCTCGATTAC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.42, C:0.19, G:0.06, T:0.33
Consensus pattern (27 bp):
AATAAGTAATTTAACCCAATTTACCCA
Found at i:181368 original size:19 final size:19
Alignment explanation
Indices: 181346--181383 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
181336 GATTTAAACT
181346 TTCAAAATGCATTTTCAAA
1 TTCAAAATGCATTTTCAAA
181365 TTCAAAATGCATTTTCAAA
1 TTCAAAATGCATTTTCAAA
181384 AATGTAATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.42, C:0.16, G:0.05, T:0.37
Consensus pattern (19 bp):
TTCAAAATGCATTTTCAAA
Found at i:181453 original size:20 final size:19
Alignment explanation
Indices: 181429--181475 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
181419 AAAAAACAAG
181429 TAAAAATAAATAAATTTTA
1 TAAAAATAAATAAATTTTA
* * *
181448 GAAAAATTATTAAATTTTAA
1 TAAAAATAAATAAATTTT-A
181468 TAAAAATA
1 TAAAAATA
181476 TAAAAACTAT
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
19 15 0.68
20 7 0.32
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (19 bp):
TAAAAATAAATAAATTTTA
Found at i:181819 original size:19 final size:19
Alignment explanation
Indices: 181797--181876 Score: 58
Period size: 19 Copynumber: 4.3 Consensus size: 19
181787 TTTTTACGAC
*
181797 TTTATAAAATTTTATAAAT
1 TTTATAAAATTTTACAAAT
* *
181816 TTTAT---ATTTATATATAT
1 TTTATAAAATTT-TACAAAT
** * *
181833 TTTATAATTTTTTACGATT
1 TTTATAAAATTTTACAAAT
*
181852 TTTATAAAATTTTACAATT
1 TTTATAAAATTTTACAAAT
181871 TTTATA
1 TTTATA
181877 TTTTTTCTAT
Statistics
Matches: 48, Mismatches: 9, Indels: 8
0.74 0.14 0.12
Matches are distributed among these distances:
16 4 0.08
17 11 0.23
19 30 0.62
20 3 0.06
ACGTcount: A:0.38, C:0.03, G:0.01, T:0.59
Consensus pattern (19 bp):
TTTATAAAATTTTACAAAT
Found at i:181827 original size:15 final size:17
Alignment explanation
Indices: 181805--181838 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
181795 ACTTTATAAA
*
181805 ATTT-TATAAATTTTAT
1 ATTTATATATATTTTAT
181821 ATTTATATATATTTTAT
1 ATTTATATATATTTTAT
181838 A
1 A
181839 ATTTTTTACG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (17 bp):
ATTTATATATATTTTAT
Found at i:181831 original size:10 final size:9
Alignment explanation
Indices: 181805--181941 Score: 58
Period size: 9 Copynumber: 15.6 Consensus size: 9
181795 ACTTTATAAA
*
181805 ATTTTATAA
1 ATTTTATAT
181814 ATTTTATAT
1 ATTTTATAT
*
181823 -TTATATAT
1 ATTTTATAT
181831 ATTTTATA-
1 ATTTTATAT
* *
181839 ATTTTTTACG
1 ATTTTATA-T
*
181849 ATTTTTATAAA
1 A-TTTTAT-AT
*
181860 ATTTTACA-
1 ATTTTATAT
181868 ATTTT-TAT
1 ATTTTATAT
* *
181876 ATTTTTTCT
1 ATTTTATAT
181885 ATTTTAATAT
1 ATTTT-ATAT
* *
181895 TTTTTATAA
1 ATTTTATAT
*
181904 ACTTTAT-T
1 ATTTTATAT
181912 GATTTTA-AT
1 -ATTTTATAT
181921 -TTTTGATA-
1 ATTTT-ATAT
181929 A-TTTATAT
1 ATTTTATAT
181937 ATTTT
1 ATTTT
181942 TTAATAAAAG
Statistics
Matches: 96, Mismatches: 17, Indels: 30
0.67 0.12 0.21
Matches are distributed among these distances:
7 8 0.08
8 29 0.30
9 40 0.42
10 12 0.12
11 6 0.06
12 1 0.01
ACGTcount: A:0.32, C:0.03, G:0.02, T:0.63
Consensus pattern (9 bp):
ATTTTATAT
Found at i:181834 original size:17 final size:16
Alignment explanation
Indices: 181805--181843 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 16
181795 ACTTTATAAA
181805 ATTTTATAAATTTTAT
1 ATTTTATAAATTTTAT
*
181821 ATTTATATATATTTTAT
1 ATTT-TATAAATTTTAT
181838 AATTTT
1 -ATTTT
181844 TTACGATTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
16 4 0.20
17 12 0.60
18 4 0.20
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (16 bp):
ATTTTATAAATTTTAT
Found at i:181856 original size:55 final size:54
Alignment explanation
Indices: 181734--181900 Score: 176
Period size: 55 Copynumber: 3.0 Consensus size: 54
181724 TGGTACGATA
* *
181734 ATTTTTATAAATATTTTTTATGAATTTTATTTTTCTTTATATTCTGTATAATTTTTTTACG
1 ATTTTTATAAA-A--TTTTATAAATTTTATATTT-TTTATATT-T-TATAA-TTTTTTACG
* *
181795 A-CTTTATAAAATTTTATAAATTTTATATTTATATATATTTTATAATTTTTTACG
1 ATTTTTATAAAATTTTATAAATTTTATATTT-TTTATATTTTATAATTTTTTACG
* * *
181849 ATTTTTATAAAATTTTACAATTTTTATATTTTTTCTATTTTA-ATATTTTTTA
1 ATTTTTATAAAATTTTATAAATTTTATATTTTTTATATTTTATA-ATTTTTTA
181901 TAAACTTTAT
Statistics
Matches: 94, Mismatches: 10, Indels: 11
0.82 0.09 0.10
Matches are distributed among these distances:
53 1 0.01
54 27 0.29
55 31 0.33
56 1 0.01
57 24 0.26
59 1 0.01
60 8 0.09
61 1 0.01
ACGTcount: A:0.31, C:0.04, G:0.02, T:0.62
Consensus pattern (54 bp):
ATTTTTATAAAATTTTATAAATTTTATATTTTTTATATTTTATAATTTTTTACG
Found at i:182078 original size:31 final size:30
Alignment explanation
Indices: 182021--182098 Score: 77
Period size: 31 Copynumber: 2.6 Consensus size: 30
182011 TTAGTATAAC
* * *
182021 ATTTGGTACCTGAATTTGAAATTTTTTCCTA
1 ATTTGGTACCTAAACTTGAAACTTTTT-CTA
*
182052 ATTTGGTACCTAAACTT-AACACTTTTTTTA
1 ATTTGGTACCTAAACTTGAA-ACTTTTTCTA
* *
182082 AGTTGGTACTTAAACTT
1 ATTTGGTACCTAAACTT
182099 TTTGGGTTCC
Statistics
Matches: 40, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
30 19 0.47
31 21 0.52
ACGTcount: A:0.28, C:0.14, G:0.12, T:0.46
Consensus pattern (30 bp):
ATTTGGTACCTAAACTTGAAACTTTTTCTA
Found at i:182433 original size:31 final size:30
Alignment explanation
Indices: 182398--182491 Score: 99
Period size: 31 Copynumber: 3.1 Consensus size: 30
182388 TTTAAGTACT
182398 AAATTAAGAAAAAGTGTCAAGTTCAGATATC
1 AAATTAAGAAAAA-TGTCAAGTTCAGATATC
*
182429 AAATTAAGTCAAAAA----AAGTTTAGATATC
1 AAATTAAG--AAAAATGTCAAGTTCAGATATC
182457 AAATTAAGAAAAAATGTCAAGTTC-GAATATC
1 AAATTAAG-AAAAATGTCAAGTTCAG-ATATC
182488 AAAT
1 AAAT
182492 ATTATATTTT
Statistics
Matches: 53, Mismatches: 3, Indels: 14
0.76 0.04 0.20
Matches are distributed among these distances:
27 5 0.09
28 20 0.38
30 1 0.02
31 22 0.42
33 5 0.09
ACGTcount: A:0.52, C:0.09, G:0.13, T:0.27
Consensus pattern (30 bp):
AAATTAAGAAAAATGTCAAGTTCAGATATC
Found at i:182465 original size:59 final size:58
Alignment explanation
Indices: 182308--182491 Score: 167
Period size: 59 Copynumber: 3.1 Consensus size: 58
182298 ATTTAGGTAC
* * * * * ** *
182308 CAAATTAAATCTAAAAAAAGATTAGGTATCAAATTAGGGAAAATACCAAGTTCAGATAC
1 CAAATTAAGTC-AAAAAAAGTTTAGATATCAAATTAAGAAAAATGTCAAGTTCAGATAT
** * *
182367 CAAATTGGGCCCAAAAAAGTTTTTA-AGTA-CTAAATTAAGAAAAAGTGTCAAGTTCAGATAT
1 CAAATTAAGTCAAAAAAAG--TTTAGA-TATC-AAATTAAGAAAAA-TGTCAAGTTCAGATAT
182428 CAAATTAAGTCAAAAAAAGTTTAGATATCAAATTAAGAAAAAATGTCAAGTTC-GAATAT
1 CAAATTAAGTCAAAAAAAGTTTAGATATCAAATTAAG-AAAAATGTCAAGTTCAG-ATAT
182487 CAAAT
1 CAAAT
182492 ATTATATTTT
Statistics
Matches: 100, Mismatches: 16, Indels: 18
0.75 0.12 0.13
Matches are distributed among these distances:
58 8 0.08
59 41 0.41
60 23 0.23
61 28 0.28
ACGTcount: A:0.49, C:0.11, G:0.14, T:0.26
Consensus pattern (58 bp):
CAAATTAAGTCAAAAAAAGTTTAGATATCAAATTAAGAAAAATGTCAAGTTCAGATAT
Found at i:182470 original size:28 final size:28
Alignment explanation
Indices: 182416--182470 Score: 83
Period size: 28 Copynumber: 2.0 Consensus size: 28
182406 AAAAAGTGTC
**
182416 AAGTTCAGATATCAAATTAAGTCAAAAA
1 AAGTTCAGATATCAAATTAAGAAAAAAA
*
182444 AAGTTTAGATATCAAATTAAGAAAAAA
1 AAGTTCAGATATCAAATTAAGAAAAAA
182471 TGTCAAGTTC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.56, C:0.07, G:0.11, T:0.25
Consensus pattern (28 bp):
AAGTTCAGATATCAAATTAAGAAAAAAA
Found at i:184742 original size:17 final size:17
Alignment explanation
Indices: 184687--184734 Score: 51
Period size: 17 Copynumber: 2.6 Consensus size: 17
184677 ATTAATGAAT
*
184687 TAAATTTTACAATTTTTTAA
1 TAAATTTTA-AA-TATTT-A
184707 TATAATTTTAAATATTTA
1 TA-AATTTTAAATATTTA
184725 TAAATTTTAA
1 TAAATTTTAA
184735 TAATTTATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
17 8 0.31
18 3 0.12
19 4 0.15
20 4 0.15
21 7 0.27
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (17 bp):
TAAATTTTAAATATTTA
Found at i:188561 original size:20 final size:20
Alignment explanation
Indices: 188536--188575 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
188526 GCCAAAGGCT
188536 GCTCTTATCTATGCACTGGC
1 GCTCTTATCTATGCACTGGC
188556 GCTCTTATCTATGCACTGGC
1 GCTCTTATCTATGCACTGGC
188576 CGCCAAGAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.15, C:0.30, G:0.20, T:0.35
Consensus pattern (20 bp):
GCTCTTATCTATGCACTGGC
Found at i:194311 original size:20 final size:20
Alignment explanation
Indices: 194274--194339 Score: 64
Period size: 19 Copynumber: 3.4 Consensus size: 20
194264 TACAAAATAA
* *
194274 TCAAAATAAATTTCAAAAAT
1 TCAAAATAATTTTTAAAAAT
*
194294 TGAAAATAATTTTT-AAAAT
1 TCAAAATAATTTTTAAAAAT
* *
194313 TCAAAAT-GTTTATAAAAAT
1 TCAAAATAATTTTTAAAAAT
194332 TCTAAAAT
1 TC-AAAAT
194340 TTGTGAATAT
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
18 4 0.11
19 18 0.47
20 16 0.42
ACGTcount: A:0.55, C:0.06, G:0.03, T:0.36
Consensus pattern (20 bp):
TCAAAATAATTTTTAAAAAT
Found at i:200764 original size:22 final size:22
Alignment explanation
Indices: 200738--200789 Score: 104
Period size: 22 Copynumber: 2.4 Consensus size: 22
200728 TTACATTGGA
200738 TGGATTTCAATTCTCAGTGAAG
1 TGGATTTCAATTCTCAGTGAAG
200760 TGGATTTCAATTCTCAGTGAAG
1 TGGATTTCAATTCTCAGTGAAG
200782 TGGATTTC
1 TGGATTTC
200790 CACTTCACCT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.25, C:0.13, G:0.23, T:0.38
Consensus pattern (22 bp):
TGGATTTCAATTCTCAGTGAAG
Found at i:202034 original size:18 final size:19
Alignment explanation
Indices: 201992--202034 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
201982 AAATTGTGAT
* *
201992 AAAATTTTAATTTGTATAT
1 AAAATTTTAATTTGTAAAA
*
202011 AAAATTTTGATTT-TAAAA
1 AAAATTTTAATTTGTAAAA
202029 AAAATT
1 AAAATT
202035 ATATTTATAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
18 9 0.43
19 12 0.57
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.47
Consensus pattern (19 bp):
AAAATTTTAATTTGTAAAA
Found at i:202062 original size:44 final size:43
Alignment explanation
Indices: 202000--202088 Score: 99
Period size: 43 Copynumber: 2.0 Consensus size: 43
201990 ATAAAATTTT
202000 AATTTGTATATAAAATTTTGA-TTTTAAAAAAAATTATATTTATA
1 AATTTGTATATAAAATTTTGAGTTTT--AAAAAATTATATTTATA
* ** * * *
202044 AATTTTTATATATTATTTTTAGTTTTTAAAATTTATATTTATA
1 AATTTGTATATAAAATTTTGAGTTTTAAAAAATTATATTTATA
202087 AA
1 AA
202089 CCACAGGAGT
Statistics
Matches: 38, Mismatches: 6, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
43 17 0.45
44 17 0.45
45 4 0.11
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (43 bp):
AATTTGTATATAAAATTTTGAGTTTTAAAAAATTATATTTATA
Found at i:203465 original size:32 final size:32
Alignment explanation
Indices: 203416--203483 Score: 109
Period size: 32 Copynumber: 2.1 Consensus size: 32
203406 ATTTCCAACA
* *
203416 TTAATTGCATCATATAAAACACGAATATAATT
1 TTAACTGCATCACATAAAACACGAATATAATT
*
203448 TTAACTGCATCACATAAAACATGAATATAATT
1 TTAACTGCATCACATAAAACACGAATATAATT
203480 TTAA
1 TTAA
203484 TTAAATTTTA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.47, C:0.13, G:0.06, T:0.34
Consensus pattern (32 bp):
TTAACTGCATCACATAAAACACGAATATAATT
Found at i:210153 original size:23 final size:24
Alignment explanation
Indices: 210127--210171 Score: 74
Period size: 23 Copynumber: 1.9 Consensus size: 24
210117 CCAATTAAAG
210127 AATTATTGTTTAG-ATTTAATTCT
1 AATTATTGTTTAGAATTTAATTCT
*
210150 AATTATTTTTTAGAATTTAATT
1 AATTATTGTTTAGAATTTAATT
210172 TGGATCCAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 12 0.60
24 8 0.40
ACGTcount: A:0.33, C:0.02, G:0.07, T:0.58
Consensus pattern (24 bp):
AATTATTGTTTAGAATTTAATTCT
Found at i:221837 original size:51 final size:51
Alignment explanation
Indices: 221761--221938 Score: 241
Period size: 51 Copynumber: 3.5 Consensus size: 51
221751 CGAAAGAGTT
* * *
221761 CGATGACTAAGTGTTATCGTGAGTAAATGAATCCTTTACGGATTAAAGGTC
1 CGATGACTAAATGTCATCGTGAGTAAATGAATCCTTTACAGATTAAAGGTC
*
221812 CGATGACTAAATGTCATCATGAGTAAATGAATCCTTTACAGATTAAAGGTC
1 CGATGACTAAATGTCATCGTGAGTAAATGAATCCTTTACAGATTAAAGGTC
* * * * * *
221863 TGATAACTAAGTGTCATCGTGAGTAAATGAATCCATGACAAATTAAAGGTC
1 CGATGACTAAATGTCATCGTGAGTAAATGAATCCTTTACAGATTAAAGGTC
*
221914 CAATGAC-AATATGTCATCGTGAGTA
1 CGATGACTAA-ATGTCATCGTGAGTA
221939 TTAAATGAAA
Statistics
Matches: 111, Mismatches: 15, Indels: 2
0.87 0.12 0.02
Matches are distributed among these distances:
50 2 0.02
51 109 0.98
ACGTcount: A:0.36, C:0.15, G:0.20, T:0.29
Consensus pattern (51 bp):
CGATGACTAAATGTCATCGTGAGTAAATGAATCCTTTACAGATTAAAGGTC
Found at i:236956 original size:37 final size:38
Alignment explanation
Indices: 236915--236996 Score: 157
Period size: 37 Copynumber: 2.2 Consensus size: 38
236905 ATAAAACCAT
236915 GAGAAGGAAGAATGGTTTGGTGGATTTACC-AAAAAAA
1 GAGAAGGAAGAATGGTTTGGTGGATTTACCAAAAAAAA
236952 GAGAAGGAAGAATGGTTTGGTGGATTTACCAAAAAAAA
1 GAGAAGGAAGAATGGTTTGGTGGATTTACCAAAAAAAA
236990 GAGAAGG
1 GAGAAGG
236997 TGGGTTACAT
Statistics
Matches: 44, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
37 30 0.68
38 14 0.32
ACGTcount: A:0.44, C:0.05, G:0.32, T:0.20
Consensus pattern (38 bp):
GAGAAGGAAGAATGGTTTGGTGGATTTACCAAAAAAAA
Found at i:237452 original size:18 final size:20
Alignment explanation
Indices: 237408--237463 Score: 71
Period size: 20 Copynumber: 2.9 Consensus size: 20
237398 TAATATTGAT
237408 TTTTAAAAGATAAAAATAAA
1 TTTTAAAAGATAAAAATAAA
* *
237428 TTTTAAAATATAAAAA-ATA
1 TTTTAAAAGATAAAAATAAA
*
237447 -TTTAAAAGTTAAAAATA
1 TTTTAAAAGATAAAAATA
237464 CATAAGATTT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
18 13 0.42
19 3 0.10
20 15 0.48
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.34
Consensus pattern (20 bp):
TTTTAAAAGATAAAAATAAA
Found at i:237499 original size:20 final size:20
Alignment explanation
Indices: 237417--237499 Score: 57
Period size: 20 Copynumber: 4.2 Consensus size: 20
237407 TTTTTAAAAG
* *
237417 ATAAAAATAAATTTTAAAA-T
1 ATAAAAATACA-TATAAAATT
* * *
237437 ATAAAAA-ATATTTAAAAGT
1 ATAAAAATACATATAAAATT
* *
237456 -TAAAAATACATA-AGATTT
1 ATAAAAATACATATAAAATT
237474 ATTAAAAATACATATAAAATT
1 A-TAAAAATACATATAAAATT
237495 ATAAA
1 ATAAA
237500 TAAATGAATA
Statistics
Matches: 50, Mismatches: 8, Indels: 10
0.74 0.12 0.15
Matches are distributed among these distances:
18 16 0.32
19 6 0.12
20 23 0.46
21 5 0.10
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (20 bp):
ATAAAAATACATATAAAATT
Found at i:237697 original size:7 final size:7
Alignment explanation
Indices: 237685--237709 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
237675 CTTTCACCTA
237685 CAACCAC
1 CAACCAC
237692 CAACCAC
1 CAACCAC
237699 CAACCAC
1 CAACCAC
237706 CAAC
1 CAAC
237710 ACTAATAACT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.44, C:0.56, G:0.00, T:0.00
Consensus pattern (7 bp):
CAACCAC
Found at i:238611 original size:4 final size:4
Alignment explanation
Indices: 238602--238637 Score: 72
Period size: 4 Copynumber: 9.0 Consensus size: 4
238592 TGCCCCCACC
238602 CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT
1 CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT
238638 TTGCCCTAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 32 1.00
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (4 bp):
CTTT
Found at i:238982 original size:18 final size:18
Alignment explanation
Indices: 238956--239002 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 18
238946 AAAATAACAT
238956 TAAAGATAAAATTA-AATA
1 TAAA-ATAAAATTATAATA
* *
238974 CTATAATAATATTATAATA
1 -TAAAATAAAATTATAATA
238993 TAAAATAAAA
1 TAAAATAAAA
239003 AAACAAATTA
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
18 16 0.70
19 7 0.30
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.32
Consensus pattern (18 bp):
TAAAATAAAATTATAATA
Found at i:240632 original size:19 final size:19
Alignment explanation
Indices: 240608--240644 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
240598 GTTTTAGGAT
240608 TTTGAATCAAATTAGTTAA
1 TTTGAATCAAATTAGTTAA
**
240627 TTTGAATTGAATTAGTTA
1 TTTGAATCAAATTAGTTA
240645 TTTATATGAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.38, C:0.03, G:0.14, T:0.46
Consensus pattern (19 bp):
TTTGAATCAAATTAGTTAA
Found at i:247378 original size:2 final size:2
Alignment explanation
Indices: 247371--247395 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
247361 TTAGGCTATT
247371 GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA G
247396 CAGCTATAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:248808 original size:3 final size:3
Alignment explanation
Indices: 248800--248824 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
248790 CAACTAGTTC
248800 TAG TAG TAG TAG TAG TAG TAG TAG T
1 TAG TAG TAG TAG TAG TAG TAG TAG T
248825 TAAACTGATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.32, T:0.36
Consensus pattern (3 bp):
TAG
Found at i:250744 original size:2 final size:2
Alignment explanation
Indices: 250737--250769 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
250727 ACTATGTATA
250737 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
250770 ATAATCATAC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:251943 original size:2 final size:2
Alignment explanation
Indices: 251938--251977 Score: 62
Period size: 2 Copynumber: 20.0 Consensus size: 2
251928 CACACAACAG
* *
251938 GA GA GA GA GG GA GA GA GA GA GA CA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
251978 TGTGACCCTA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.47, C:0.03, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:256784 original size:2 final size:2
Alignment explanation
Indices: 256777--256801 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
256767 TATCATACAT
256777 GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA G
256802 GGGGGGTTCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:257977 original size:25 final size:25
Alignment explanation
Indices: 257905--257985 Score: 100
Period size: 23 Copynumber: 3.4 Consensus size: 25
257895 ACACTAGCGC
257905 GCTCTCTG--ATTAGCACTGTGTGT
1 GCTCTCTGTTATTAGCACTGTGTGT
*
257928 GCTCTCTG-T-TTAGCAC-GTCTCGT
1 GCTCTCTGTTATTAGCACTGTGT-GT
*
257951 GCTGTCTGTTATTAGCACTGTGTGT
1 GCTCTCTGTTATTAGCACTGTGTGT
257976 GCTCTCTGTT
1 GCTCTCTGTT
257986 GCCCAGCACT
Statistics
Matches: 49, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
22 3 0.06
23 24 0.49
24 1 0.02
25 18 0.37
26 3 0.06
ACGTcount: A:0.10, C:0.23, G:0.25, T:0.42
Consensus pattern (25 bp):
GCTCTCTGTTATTAGCACTGTGTGT
Found at i:258902 original size:503 final size:493
Alignment explanation
Indices: 257955--258951 Score: 1904
Period size: 503 Copynumber: 2.0 Consensus size: 493
257945 TCTCGTGCTG
257955 TCTGTTATTAGCACTGTGTGTGCTCTCTGTTGCCCAGCACTTATGTGCTCTCTGTTTGTTCCATA
1 TCTGTTATTAGCACTGTGTGTGCTCTCTGTTGCCCAGCACTTATGTGCTCTCTGTTTGTTCCATA
258020 TATCCTAACGGTTCTATGAAAGTCTACTAAGGGCTAAACTACAGAAAGTGGATAAAAGTGTAAGT
66 TATCCTAACGGTTCTATGAAAGTCTACTAAGGGCTAAACTACAGAAAGTGGATAAAAGTGTAAGT
258085 TGTACCATTGTGGTAAGTTACAGGTTACATGTAAGAAAAGCAAGAAGTTTATATGCATGAGTACT
131 TGTACCATTGTGGTAAGTTACAGGTTACATGTAAGAAAAGCAAGAAGTTTATATGCATGAGTACT
258150 TAAATGATCATTCATTACTTTTGTAGTGCTTACTAAGCCTTCACCGGCTTAACGCGTTTATTTTA
196 TAAATGATCATTCATTACTTTTGTAGTGCTTACTAAGCCTTCACCGGCTTAACGCGTTTATTTTA
258215 ACGCGTAGGTACAAGGAATACAAGAAGGTAGATCGGGACCTCTCATTACATCACATCACTTGGAG
261 ACGCGTAGGTACAAGGAATACAAGAAGGTAGATCGGGACCTCTCATTACATCACATCACTTGGAG
258280 CTCAAATTTTGGTATATTTCTTTTGATGTAAAATGACATGTACTATGGAACTTATATGTGTACTT
326 CTCAAATTTTGGTATATTTCTTTTGATGTAAAATGACATGTACTATGGAACTTATATGTGTACTT
258345 ATTAGATAAACAAAAATGTTGTTTTGTGTGACGAAATGAAATGAGGTATTTTGGATAAAAAAAAA
391 ATTAGATAAACAAAAATGTTGTTTTGTGTGACGAAATGAAATGAGGTATTTTGGATAAAAAAAAA
258410 AGTTGCATGACTCGGTTTATTTTAATGTAATACTTTTA
456 AGTTGCATGACTCGGTTTATTTTAATGTAATACTTTTA
258448 NNNNNNNNNNTCTGTTATTAGCACTGTGTGTGCTCTCTGTTGCCCAGCACTTATGTGCTCTCTGT
1 ----------TCTGTTATTAGCACTGTGTGTGCTCTCTGTTGCCCAGCACTTATGTGCTCTCTGT
258513 TTGTTCCATATATCCTAACGGTTCTATGAAAGTCTACTAAGGGCTAAACTACAGAAAGTGGATAA
56 TTGTTCCATATATCCTAACGGTTCTATGAAAGTCTACTAAGGGCTAAACTACAGAAAGTGGATAA
258578 AAGTGTAAGTTGTACCATTGTGGTAAGTTACAGGTTACATGTAAGAAAAGCAAGAAGTTTATATG
121 AAGTGTAAGTTGTACCATTGTGGTAAGTTACAGGTTACATGTAAGAAAAGCAAGAAGTTTATATG
258643 CATGAGTACTTAAATGATCATTCATTACTTTTGTAGTGCTTACTAAGCCTTCACCGGCTTAACGC
186 CATGAGTACTTAAATGATCATTCATTACTTTTGTAGTGCTTACTAAGCCTTCACCGGCTTAACGC
258708 GTTTATTTTAACGCGTAGGTACAAGGAATACAAGAAGGTAGATCGGGACCTCTCATTACATCACA
251 GTTTATTTTAACGCGTAGGTACAAGGAATACAAGAAGGTAGATCGGGACCTCTCATTACATCACA
258773 TCACTTGGAGCTCAAATTTTGGTATATTTCTTTTGATGTAAAATGACATGTACTATGGAACTTAT
316 TCACTTGGAGCTCAAATTTTGGTATATTTCTTTTGATGTAAAATGACATGTACTATGGAACTTAT
258838 ATGTGTACTTATTAGATAAACAAAAATGTTGTTTTGTGTGACGAAATGAAATGAGGTATTTTGGA
381 ATGTGTACTTATTAGATAAACAAAAATGTTGTTTTGTGTGACGAAATGAAATGAGGTATTTTGGA
258903 TAAAAAAAAAAGTTGCATGACTCGGTTTATTTTAATGTAATACTTTTA
446 TAAAAAAAAAAGTTGCATGACTCGGTTTATTTTAATGTAATACTTTTA
258951 T
1 T
258952 ATCGGGTTTA
Statistics
Matches: 494, Mismatches: 0, Indels: 10
0.98 0.00 0.02
Matches are distributed among these distances:
493 1 0.00
503 493 1.00
ACGTcount: A:0.31, C:0.14, G:0.19, T:0.35
Consensus pattern (493 bp):
TCTGTTATTAGCACTGTGTGTGCTCTCTGTTGCCCAGCACTTATGTGCTCTCTGTTTGTTCCATA
TATCCTAACGGTTCTATGAAAGTCTACTAAGGGCTAAACTACAGAAAGTGGATAAAAGTGTAAGT
TGTACCATTGTGGTAAGTTACAGGTTACATGTAAGAAAAGCAAGAAGTTTATATGCATGAGTACT
TAAATGATCATTCATTACTTTTGTAGTGCTTACTAAGCCTTCACCGGCTTAACGCGTTTATTTTA
ACGCGTAGGTACAAGGAATACAAGAAGGTAGATCGGGACCTCTCATTACATCACATCACTTGGAG
CTCAAATTTTGGTATATTTCTTTTGATGTAAAATGACATGTACTATGGAACTTATATGTGTACTT
ATTAGATAAACAAAAATGTTGTTTTGTGTGACGAAATGAAATGAGGTATTTTGGATAAAAAAAAA
AGTTGCATGACTCGGTTTATTTTAATGTAATACTTTTA
Found at i:259017 original size:17 final size:17
Alignment explanation
Indices: 258992--259024 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
258982 GGGTGTTACA
258992 TCTTCTTTCTTTCATTC
1 TCTTCTTTCTTTCATTC
*
259009 TCTTTTTTCTTTCATT
1 TCTTCTTTCTTTCATT
259025 TTTCCTTCAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.06, C:0.24, G:0.00, T:0.70
Consensus pattern (17 bp):
TCTTCTTTCTTTCATTC
Found at i:260240 original size:24 final size:23
Alignment explanation
Indices: 260213--260258 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
260203 TCAGTCCGAC
*
260213 TAGTTAATAGGGACTTTCAATTTA
1 TAGTTAATA-GCACTTTCAATTTA
* *
260237 TAGTTCATATCACTTTCAATTT
1 TAGTTAATAGCACTTTCAATTT
260259 CAATTTCACT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 11 0.58
24 8 0.42
ACGTcount: A:0.30, C:0.13, G:0.11, T:0.46
Consensus pattern (23 bp):
TAGTTAATAGCACTTTCAATTTA
Found at i:260962 original size:16 final size:16
Alignment explanation
Indices: 260940--260985 Score: 56
Period size: 16 Copynumber: 2.9 Consensus size: 16
260930 CTGTTCTTCC
* *
260940 TTCTTTTGTTTCTTTT
1 TTCTTTTATTTCTTTA
* *
260956 TTTTTTTTTTTCTTTA
1 TTCTTTTATTTCTTTA
260972 TTCTTTTATTTCTT
1 TTCTTTTATTTCTT
260986 ATATATATAT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.04, C:0.11, G:0.02, T:0.83
Consensus pattern (16 bp):
TTCTTTTATTTCTTTA
Found at i:261482 original size:27 final size:27
Alignment explanation
Indices: 261447--261502 Score: 67
Period size: 27 Copynumber: 2.1 Consensus size: 27
261437 GGAAAAACAC
* *
261447 CCTTTAGTGCCGCCACTTTAAGTCCCT
1 CCTTCAGTGACGCCACTTTAAGTCCCT
* **
261474 CCTTCAGTGACGTCACTTTGTGTCCCT
1 CCTTCAGTGACGCCACTTTAAGTCCCT
261501 CC
1 CC
261503 ATTAGATGTC
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.12, C:0.38, G:0.16, T:0.34
Consensus pattern (27 bp):
CCTTCAGTGACGCCACTTTAAGTCCCT
Found at i:263394 original size:21 final size:21
Alignment explanation
Indices: 263368--263407 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
263358 CTTAATTGAA
* *
263368 AATTAAAATATATTTAAATTT
1 AATTAAAATAAATATAAATTT
263389 AATTAAAATAAATATAAAT
1 AATTAAAATAAATATAAAT
263408 AAAAAATTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (21 bp):
AATTAAAATAAATATAAATTT
Found at i:267590 original size:2 final size:2
Alignment explanation
Indices: 267583--267617 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
267573 CCATTATTCT
267583 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
267618 TATGTAAAGA
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:269096 original size:24 final size:24
Alignment explanation
Indices: 269064--269113 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
269054 TTATTAGACC
269064 TACTACTGAATACCCCCATATAAA
1 TACTACTGAATACCCCCATATAAA
269088 TACTACTGAATACCCCCATATAAA
1 TACTACTGAATACCCCCATATAAA
269112 TA
1 TA
269114 TATGTTAATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.42, C:0.28, G:0.04, T:0.26
Consensus pattern (24 bp):
TACTACTGAATACCCCCATATAAA
Found at i:269193 original size:17 final size:19
Alignment explanation
Indices: 269171--269205 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
269161 TTGTTCATCT
269171 GTCTTTTT-TTT-TTTTTG
1 GTCTTTTTCTTTGTTTTTG
269188 GTCTTTTTCTTTGTTTTT
1 GTCTTTTTCTTTGTTTTT
269206 TTTTTCTCCC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 8 0.50
18 3 0.19
19 5 0.31
ACGTcount: A:0.00, C:0.09, G:0.11, T:0.80
Consensus pattern (19 bp):
GTCTTTTTCTTTGTTTTTG
Found at i:275293 original size:16 final size:17
Alignment explanation
Indices: 275258--275292 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
275248 CACATAATAT
275258 AATAAACATATTTAAAA
1 AATAAACATATTTAAAA
275275 AATAAACAT-TTATAAAA
1 AATAAACATATT-TAAAA
275292 A
1 A
275293 TTTAATTTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 2 0.12
17 15 0.88
ACGTcount: A:0.66, C:0.06, G:0.00, T:0.29
Consensus pattern (17 bp):
AATAAACATATTTAAAA
Found at i:284206 original size:21 final size:21
Alignment explanation
Indices: 284180--284220 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
284170 TACAACAAAC
*
284180 AACAATCTTTAAAATTAACAA
1 AACAATATTTAAAATTAACAA
* *
284201 AACAATATTTCAACTTAACA
1 AACAATATTTAAAATTAACA
284221 CATTTTTAGG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.54, C:0.17, G:0.00, T:0.29
Consensus pattern (21 bp):
AACAATATTTAAAATTAACAA
Found at i:290829 original size:2 final size:2
Alignment explanation
Indices: 290824--290852 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
290814 TGTATGTATG
290824 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 T
290853 CTGAATAAAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:306741 original size:22 final size:20
Alignment explanation
Indices: 306715--306770 Score: 58
Period size: 22 Copynumber: 2.6 Consensus size: 20
306705 ATTTTTAAAG
*
306715 AATTAAAATATAATTTTATCA
1 AATTAAAATAAAATTTTAT-A
**
306736 ATATTAATTTAAAATTTTATA
1 A-ATTAAAATAAAATTTTATA
306757 AATTATAAATAAAA
1 AATTA-AAATAAAA
306771 AAATTCCATT
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
20 4 0.14
21 9 0.32
22 15 0.54
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (20 bp):
AATTAAAATAAAATTTTATA
Found at i:308768 original size:65 final size:65
Alignment explanation
Indices: 308684--308810 Score: 245
Period size: 65 Copynumber: 2.0 Consensus size: 65
308674 GTTAAAAATG
*
308684 GTAAATAGTTATCCTAAGGACCTTTATTATGGTATCAAGTAATAACATTGTGTAAGCTTTTAGAT
1 GTAAATAGTTATCCCAAGGACCTTTATTATGGTATCAAGTAATAACATTGTGTAAGCTTTTAGAT
308749 GTAAATAGTTATCCCAAGGACCTTTATTATGGTATCAAGTAATAACATTGTGTAAGCTTTTA
1 GTAAATAGTTATCCCAAGGACCTTTATTATGGTATCAAGTAATAACATTGTGTAAGCTTTTA
308811 AATCAGGATG
Statistics
Matches: 61, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
65 61 1.00
ACGTcount: A:0.34, C:0.12, G:0.17, T:0.38
Consensus pattern (65 bp):
GTAAATAGTTATCCCAAGGACCTTTATTATGGTATCAAGTAATAACATTGTGTAAGCTTTTAGAT
Done.