Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016549.1 Corchorus olitorius cultivar O-4 contig16582, 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: 197447
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:5758 original size:34 final size:33
Alignment explanation
Indices: 5713--5778 Score: 96
Period size: 34 Copynumber: 2.0 Consensus size: 33
5703 ATCATGCTTA
*
5713 TTTTTTTTTGGCCAAAAACATCATGCTTATCTT
1 TTTTTTTTTGGCCAAAAACATAATGCTTATCTT
**
5746 TTTTTTTCTTGGCTGAAAACATAATGCTTATCT
1 TTTTTTT-TTGGCCAAAAACATAATGCTTATCT
5779 AAACGCAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
33 7 0.24
34 22 0.76
ACGTcount: A:0.24, C:0.17, G:0.11, T:0.48
Consensus pattern (33 bp):
TTTTTTTTTGGCCAAAAACATAATGCTTATCTT
Found at i:10485 original size:13 final size:13
Alignment explanation
Indices: 10467--10493 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
10457 AAATATAATA
10467 AATATGATTTATG
1 AATATGATTTATG
10480 AATATGATTTATG
1 AATATGATTTATG
10493 A
1 A
10494 GGTTATAGAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.00, G:0.15, T:0.44
Consensus pattern (13 bp):
AATATGATTTATG
Found at i:14342 original size:2 final size:2
Alignment explanation
Indices: 14335--14410 Score: 55
Period size: 2 Copynumber: 43.0 Consensus size: 2
14325 TTTAATAATC
* *
14335 AT AT AT AT -T AT -T AT AT AT A- AT -T AT AT TT AT CT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
14372 -T AT -T AT AT AT AT A- AT AT AT AT TT A- AT -T 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
14409 AT
1 AT
14411 TAATAAACGG
Statistics
Matches: 58, Mismatches: 6, Indels: 20
0.69 0.07 0.24
Matches are distributed among these distances:
1 10 0.17
2 48 0.83
ACGTcount: A:0.45, C:0.01, G:0.00, T:0.54
Consensus pattern (2 bp):
AT
Found at i:14351 original size:10 final size:10
Alignment explanation
Indices: 14336--14404 Score: 70
Period size: 10 Copynumber: 6.7 Consensus size: 10
14326 TTAATAATCA
14336 TATATATTAT
1 TATATATTAT
*
14346 TATATATAAT
1 TATATATTAT
14356 TATAT-TTAT
1 TATATATTAT
14365 CTA-ATATTAT
1 -TATATATTAT
*
14375 TATATATATAA
1 TATATAT-TAT
14386 TATATATTTAAT
1 TATATA-TT-AT
14398 TATATAT
1 TATATAT
14405 ATATATTAAT
Statistics
Matches: 49, Mismatches: 4, Indels: 11
0.77 0.06 0.17
Matches are distributed among these distances:
9 7 0.14
10 24 0.49
11 10 0.20
12 8 0.16
ACGTcount: A:0.43, C:0.01, G:0.00, T:0.55
Consensus pattern (10 bp):
TATATATTAT
Found at i:14371 original size:19 final size:20
Alignment explanation
Indices: 14336--14404 Score: 70
Period size: 19 Copynumber: 3.4 Consensus size: 20
14326 TTAATAATCA
14336 TATATATTATTATATATAAT
1 TATATATTATTATATATAAT
*
14356 TATAT-TTATCTA-ATATTAT
1 TATATATTAT-TATATATAAT
*
14375 TATATATATAATATATATTTAAT
1 TATATAT-T-AT-TATATATAAT
14398 TATATAT
1 TATATAT
14405 ATATATTAAT
Statistics
Matches: 40, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
19 15 0.38
20 8 0.20
21 1 0.03
22 4 0.10
23 12 0.30
ACGTcount: A:0.43, C:0.01, G:0.00, T:0.55
Consensus pattern (20 bp):
TATATATTATTATATATAAT
Found at i:29241 original size:19 final size:19
Alignment explanation
Indices: 29213--29257 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
29203 AGAAGGTGGA
* *
29213 TTAATATTTG-AATAATGAT
1 TTAATTTTTGTAAAAATG-T
29232 TTAATTTTTGTAAAAATGT
1 TTAATTTTTGTAAAAATGT
29251 TTAATTT
1 TTAATTT
29258 AGGATGCAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 17 0.74
20 6 0.26
ACGTcount: A:0.38, C:0.00, G:0.09, T:0.53
Consensus pattern (19 bp):
TTAATTTTTGTAAAAATGT
Found at i:29712 original size:29 final size:30
Alignment explanation
Indices: 29650--29712 Score: 74
Period size: 32 Copynumber: 2.1 Consensus size: 30
29640 TGATGATTTT
* * *
29650 TGTTTATTATATAAATCATTTTTTTGGGTACA
1 TGTTTATTATATAAATCA--TTGTGGGGCACA
29682 TGTTTATTATATAAATCA-TGTGGGGCACA
1 TGTTTATTATATAAATCATTGTGGGGCACA
29711 TG
1 TG
29713 ATGTTAACAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
29 10 0.36
32 18 0.64
ACGTcount: A:0.29, C:0.08, G:0.17, T:0.46
Consensus pattern (30 bp):
TGTTTATTATATAAATCATTGTGGGGCACA
Found at i:41707 original size:28 final size:29
Alignment explanation
Indices: 41674--41747 Score: 105
Period size: 30 Copynumber: 2.6 Consensus size: 29
41664 ACTTGTAGCG
*
41674 TTTGGACGTTTTACCCACGAACT-TCAAT
1 TTTGGACATTTTACCCACGAACTCTCAAT
**
41702 TTTGGACATTTTACCTCTTGAACTCTCAAT
1 TTTGGACATTTTACC-CACGAACTCTCAAT
41732 TTTGGACATTTTACCC
1 TTTGGACATTTTACCC
41748 CTAAACTTTC
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
28 14 0.34
29 7 0.17
30 20 0.49
ACGTcount: A:0.23, C:0.24, G:0.12, T:0.41
Consensus pattern (29 bp):
TTTGGACATTTTACCCACGAACTCTCAAT
Found at i:41910 original size:31 final size:29
Alignment explanation
Indices: 41874--41955 Score: 112
Period size: 28 Copynumber: 2.8 Consensus size: 29
41864 GAACTTGTAC
*
41874 ATTTTGGACGTTTTGCCCCCTAAATTTATA
1 ATTTTGGACATTTTGCCCCCTAAATTT-TA
* *
41904 CGTTTTGGACATTTT-ACCCCTAAATTTTA
1 -ATTTTGGACATTTTGCCCCCTAAATTTTA
41933 ATTTTGGACATTTTGCCCCCTAA
1 ATTTTGGACATTTTGCCCCCTAA
41956 GCAACAAGAA
Statistics
Matches: 45, Mismatches: 5, Indels: 4
0.83 0.09 0.07
Matches are distributed among these distances:
28 13 0.29
29 9 0.20
30 11 0.24
31 12 0.27
ACGTcount: A:0.23, C:0.22, G:0.12, T:0.43
Consensus pattern (29 bp):
ATTTTGGACATTTTGCCCCCTAAATTTTA
Found at i:42057 original size:29 final size:30
Alignment explanation
Indices: 42017--42077 Score: 81
Period size: 29 Copynumber: 2.1 Consensus size: 30
42007 ACAAAGGCTC
*
42017 AAATTGAGAATTCAA-AGGGCAAAATGTCCA
1 AAATTGAGAATTCAAGA-GGCAAAACGTCCA
*
42047 AAATTGA-AATTCAGGAGGCAAAACGTCCA
1 AAATTGAGAATTCAAGAGGCAAAACGTCCA
42076 AA
1 AA
42078 TGCTACAACT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
29 20 0.71
30 8 0.29
ACGTcount: A:0.48, C:0.15, G:0.20, T:0.18
Consensus pattern (30 bp):
AAATTGAGAATTCAAGAGGCAAAACGTCCA
Found at i:42785 original size:21 final size:21
Alignment explanation
Indices: 42761--42805 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 21
42751 TGAGGTATTC
*
42761 ATATTT-TTTTAATAAAATAAT
1 ATATTTATTATAA-AAAATAAT
42782 ATATTTAATTATAAAAAATAAT
1 ATATTT-ATTATAAAAAATAAT
42804 AT
1 AT
42806 TAGAAGAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 6 0.29
22 10 0.48
23 5 0.24
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (21 bp):
ATATTTATTATAAAAAATAAT
Found at i:55475 original size:25 final size:25
Alignment explanation
Indices: 55435--55483 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
55425 ATTATTTAAG
*
55435 ATATTATTAAACATGTTATATAGTAA
1 ATATTATTAAAAATGTTATA-AGTAA
55461 ATATTA-TAAAAATGTTATAAGTA
1 ATATTATTAAAAATGTTATAAGTA
55484 TCAAGAAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 4 0.18
25 12 0.55
26 6 0.27
ACGTcount: A:0.49, C:0.02, G:0.08, T:0.41
Consensus pattern (25 bp):
ATATTATTAAAAATGTTATAAGTAA
Found at i:59463 original size:19 final size:19
Alignment explanation
Indices: 59439--59481 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
59429 TATTTTGTAT
*
59439 ATATAAAATATATATATAA
1 ATATAAAATATACATATAA
* *
59458 ATATAACATATACATATAT
1 ATATAAAATATACATATAA
59477 ATATA
1 ATATA
59482 TACTAGTTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (19 bp):
ATATAAAATATACATATAA
Found at i:59685 original size:22 final size:21
Alignment explanation
Indices: 59660--60163 Score: 306
Period size: 22 Copynumber: 23.0 Consensus size: 21
59650 AAATTTTTTT
59660 TAACCTCCTTATGAAATTTTGA
1 TAACCTCC-TATGAAATTTTGA
* * *
59682 TAACCTCCCTAAGGAATTTTAA
1 TAACCT-CCTATGAAATTTTGA
*
59704 AAACCTCACTATGAAATTTTGA
1 TAACCTC-CTATGAAATTTTGA
* *
59726 TAACTTCCGAATGAAATTTTGA
1 TAACCTCC-TATGAAATTTTGA
* * *
59748 TAACCAACACTATGAGATGTTGA
1 TAACC-TC-CTATGAAATTTTGA
*
59771 TAACCTCCATATGATATATTGATGA
1 TAACCTCC-TATGA-A-ATT-TTGA
* * * *
59796 TAACCACGTTATGAAAATTTAA
1 TAACCTC-CTATGAAATTTTGA
* *
59818 GAACCTCCATTTG-AATTGTT-A
1 TAACCTCC-TATGAAATT-TTGA
* * *
59839 GTAATCACACTCTGAAATTTTGA
1 -TAACCTC-CTATGAAATTTTGA
* * *
59862 TAATCACACTATGAAATTGTGA
1 TAACCTC-CTATGAAATTTTGA
* *
59884 TAACCTTGCTATAAAATTTTGA
1 TAACC-TCCTATGAAATTTTGA
*
59906 TAAACCTCCTTATAAAATTTTGA
1 T-AACCTCC-TATGAAATTTTGA
59929 TAACCTCCTTATGAAATTTTGA
1 TAACCTCC-TATGAAATTTTGA
*
59951 TAACCTCCTTATGAAATCTTGA
1 TAACCTCC-TATGAAATTTTGA
*
59973 TAA----CTA-CAAATTTTGA
1 TAACCTCCTATGAAATTTTGA
**
59989 TAACCTCCCTATGATTTTTTGA
1 TAACCT-CCTATGAAATTTTGA
* *
60011 TAACCTCATTATGAAATTTTGT
1 TAACCTC-CTATGAAATTTTGA
*
60033 TAATCTCCCTATGAAATTTTGA
1 TAACCT-CCTATGAAATTTTGA
* * *
60055 TCTACATACTATGAAATTTTGA
1 T-AACCTCCTATGAAATTTTGA
* *
60077 TAACCCTCTTATGAAAATTTGA
1 TAA-CCTCCTATGAAATTTTGA
* *
60099 -AAACTAAACTATGAAATTTTGA
1 TAACCT--CCTATGAAATTTTGA
*
60121 TAACCTTCATATGAAATTTTGA
1 TAACC-TCCTATGAAATTTTGA
* *
60143 TATCCTCC-CTGAAATTTTGA
1 TAACCTCCTATGAAATTTTGA
60163 T
1 T
60164 TACTCCATAG
Statistics
Matches: 375, Mismatches: 74, Indels: 68
0.73 0.14 0.13
Matches are distributed among these distances:
16 11 0.03
17 2 0.01
18 1 0.00
20 14 0.04
21 16 0.04
22 262 0.70
23 50 0.13
24 5 0.01
25 14 0.04
ACGTcount: A:0.36, C:0.17, G:0.10, T:0.37
Consensus pattern (21 bp):
TAACCTCCTATGAAATTTTGA
Found at i:59973 original size:44 final size:43
Alignment explanation
Indices: 59660--60599 Score: 342
Period size: 44 Copynumber: 21.7 Consensus size: 43
59650 AAATTTTTTT
* * * *
59660 TAACCTCCTTATGAAATTTTGATAACCTCCCTAAGGAATTTTAA
1 TAACCTCC-TATGAAATTTTGATAACCTCCTTATGAAATTTTGA
* * **
59704 AAACCTCACTATGAAATTTTGATAACTTCCGAATGAAATTTTGA
1 TAACCTC-CTATGAAATTTTGATAACCTCCTTATGAAATTTTGA
* * * * *
59748 TAACCAACACTATGAGATGTTGATAACCTCCATATGATATATTGATGA
1 TAACC-TC-CTATGAAATTTTGATAACCTCCTTATGA-A-ATT-TTGA
* * * * *
59796 TAACCACGTTATGAAAATTTAAGAACCTCCATT-TG-AATTGTT-A
1 TAACCTC-CTATGAAATTTTGATAACCTCC-TTATGAAATT-TTGA
* * * * * *
59839 GTAATCACACTCTGAAATTTTGATAATCACAC-TATGAAATTGTGA
1 -TAACCTC-CTATGAAATTTTGATAACCTC-CTTATGAAATTTTGA
* * *
59884 TAACCTTGCTATAAAATTTTGATAAACCTCCTTATAAAATTTTGA
1 TAACC-TCCTATGAAATTTTGAT-AACCTCCTTATGAAATTTTGA
*
59929 TAACCTCCTTATGAAATTTTGATAACCTCCTTATGAAATCTTGA
1 TAACCTCC-TATGAAATTTTGATAACCTCCTTATGAAATTTTGA
* * **
59973 TAA----CTA-CAAATTTTGATAACCTCCCTATGATTTTTTGA
1 TAACCTCCTATGAAATTTTGATAACCTCCTTATGAAATTTTGA
* * * *
60011 TAACCTCATTATGAAATTTTGTTAATCTCCCTATGAAATTTTGA
1 TAACCTC-CTATGAAATTTTGATAACCTCCTTATGAAATTTTGA
* * * *
60055 TCTACATACTATGAAATTTTGATAACC-CTCTTATGAAAATTTGA
1 T-AACCTCCTATGAAATTTTGATAACCTC-CTTATGAAATTTTGA
* * * *
60099 -AAACTAAACTATGAAATTTTGATAACCTTCATATGAAATTTTGA
1 TAACCT--CCTATGAAATTTTGATAACCTCCTTATGAAATTTTGA
* * * * * * *
60143 TATCCTCC-CTGAAATTTTGATTA-CTCCATAGTAAAAGTTTAA
1 TAACCTCCTATGAAATTTTGATAACCTCCTTA-TGAAATTTTGA
* *
60185 TAACCTTCC--T--AA-TTTGGTAACCATAC-TATGAAATTTTGA
1 TAACC-TCCTATGAAATTTTGATAACC-TCCTTATGAAATTTTGA
* * * *
60224 TAACTTCCCCAT--AA-----AT-ACC-AC-TATGAAATTTTGG
1 TAACCT-CCTATGAAATTTTGATAACCTCCTTATGAAATTTTGA
* * * * * *
60258 TAATCACATTTTGAAAATTTGATAACCTCTTTATGAAATTTTGA
1 TAACCTC-CTATGAAATTTTGATAACCTCCTTATGAAATTTTGA
* * * * *
60302 TAACCTCTTTATAAAATGTTGTTGACC-CCTCTATGAAATTTTGA
1 TAACCTC-CTATGAAATTTTGATAACCTCCT-TATGAAATTTTGA
*** * * * *
60346 TATTTTCATTATGTAATTTGGATAACCTCGCTT-TGAAATATTGA
1 TAACCTC-CTATGAAATTTTGATAACCTC-CTTATGAAATTTTGA
** *
60390 TAACAACACTATGAAATTTTGATAATCTTCC-TAT-AAATTTCT-A
1 TAACCTC-CTATGAAATTTTGATAA-CCTCCTTATGAAATTT-TGA
*
60433 TAATCCGATCTCTATGAAATTTTGATAA--TCACTCTATGAGA-TTTGA
1 TAA-CC--TC-CTATGAAATTTTGATAACCTC-CT-TATGAAATTTTGA
* * * *
60479 TAACTTTCTATCAAATTTTTG-T-A-CTCCTTATGAAATTAAGGATTTTA
1 TAACCTCCTATGAAA-TTTTGATAACCTCCTTATGAAA-T-----TTTGA
* * * ** *
60526 TAACCTTCATATGAAATTTTGATAACCACATTAAAAAATTTTAA
1 TAACC-TCCTATGAAATTTTGATAACCTCCTTATGAAATTTTGA
*
60570 TAACCACACTATGACAA-TTTGATAACCTCC
1 TAACCTC-CTATGA-AATTTTGATAACCTCC
60600 CAACCTCCTT
Statistics
Matches: 670, Mismatches: 152, Indels: 148
0.69 0.16 0.15
Matches are distributed among these distances:
33 1 0.00
34 18 0.03
36 5 0.01
37 1 0.00
38 31 0.05
39 22 0.03
40 12 0.02
41 16 0.02
42 41 0.06
43 30 0.04
44 317 0.47
45 81 0.12
46 30 0.04
47 38 0.06
48 17 0.03
49 2 0.00
50 8 0.01
ACGTcount: A:0.36, C:0.17, G:0.10, T:0.38
Consensus pattern (43 bp):
TAACCTCCTATGAAATTTTGATAACCTCCTTATGAAATTTTGA
Found at i:60046 original size:82 final size:83
Alignment explanation
Indices: 59897--60144 Score: 234
Period size: 82 Copynumber: 2.9 Consensus size: 83
59887 CCTTGCTATA
* * *
59897 AAATTTTGATAAACCTCCTTATAAAATTTTGATAACCTCCTTATGAAATTTTGATAACCTCCTTA
1 AAATTTTGATAAACCTCCCTATAAAATTTTGATAACCTCATTATGAAATTTTGATAACCTCCCTA
59962 TGAAATCTTGATAACTAC
66 TGAAATCTTGATAACTAC
* ** * *
59980 AAATTTTGAT-AACCTCCCTATGATTTTTTGATAACCTCATTATGAAATTTTGTTAATCTCCCTA
1 AAATTTTGATAAACCTCCCTATAAAATTTTGATAACCTCATTATGAAATTTTGATAACCTCCCTA
* *
60044 TGAAATTTTGATCTACATACTATG
66 TGAAATCTTGA--T--A-ACTA-C
* * * * * * *
60068 AAATTTTGATAACCCT-CTTATGAAAA-TTTGA-AAACTAAACTATGAAATTTTGATAACCTTCA
1 AAATTTTGATAAACCTCCCTAT-AAAATTTTGATAACCT-CATTATGAAATTTTGATAACCTCCC
*
60130 TATGAAATTTTGATA
64 TATGAAATCTTGATA
60145 TCCTCCCTGA
Statistics
Matches: 134, Mismatches: 22, Indels: 17
0.77 0.13 0.10
Matches are distributed among these distances:
82 56 0.42
83 10 0.07
84 2 0.01
86 2 0.01
87 8 0.06
88 51 0.38
89 5 0.04
ACGTcount: A:0.36, C:0.16, G:0.08, T:0.40
Consensus pattern (83 bp):
AAATTTTGATAAACCTCCCTATAAAATTTTGATAACCTCATTATGAAATTTTGATAACCTCCCTA
TGAAATCTTGATAACTAC
Found at i:60429 original size:21 final size:24
Alignment explanation
Indices: 60398--60481 Score: 83
Period size: 21 Copynumber: 3.7 Consensus size: 24
60388 GATAACAACA
*
60398 CTATGAAATTTTGATAATC-TTC-
1 CTATGAAATTTTGATAATCGATCT
60420 CTAT-AAATTTCT-ATAATCCGATCT
1 CTATGAAATTT-TGATAAT-CGATCT
60444 CTATGAAATTTTGATAATC-A-CT
1 CTATGAAATTTTGATAATCGATCT
*
60466 CTATGAGA-TTTGATAA
1 CTATGAAATTTTGATAA
60482 CTTTCTATCA
Statistics
Matches: 54, Mismatches: 2, Indels: 13
0.78 0.03 0.19
Matches are distributed among these distances:
21 19 0.35
22 15 0.28
23 3 0.06
24 6 0.11
25 11 0.20
ACGTcount: A:0.35, C:0.14, G:0.10, T:0.42
Consensus pattern (24 bp):
CTATGAAATTTTGATAATCGATCT
Found at i:60470 original size:22 final size:22
Alignment explanation
Indices: 60244--60481 Score: 105
Period size: 22 Copynumber: 10.8 Consensus size: 22
60234 ATAAATACCA
*
60244 CTATGAAATTTTGGTAATCACAT
1 CTATGAAATTTTGATAATCAC-T
* * * *
60267 -TTTGAAAATTTGATAACCTCT
1 CTATGAAATTTTGATAATCACT
* * *
60288 TTATGAAATTTTGATAACCTCT
1 CTATGAAATTTTGATAATCACT
* * * * * * *
60310 TTATAAAATGTTGTTGACCCCT
1 CTATGAAATTTTGATAATCACT
*
60332 CTATGAAATTTTGATATTTTCA-T
1 CTATGAAATTTTGATA--ATCACT
* * * * *
60355 -TATGTAATTTGGATAACCTCG
1 CTATGAAATTTTGATAATCACT
* * *
60376 CTTTGAAATATTGATAA-CAACA
1 CTATGAAATTTTGATAATC-ACT
*
60398 CTATGAAATTTTGATAATC-TT
1 CTATGAAATTTTGATAATCACT
60419 CCTAT-AAATTTCT-ATAATCCGATCT
1 -CTATGAAATTT-TGATAAT-C-A-CT
60444 CTATGAAATTTTGATAATCACT
1 CTATGAAATTTTGATAATCACT
*
60466 CTATGAGA-TTTGATAA
1 CTATGAAATTTTGATAA
60482 CTTTCTATCA
Statistics
Matches: 162, Mismatches: 38, Indels: 32
0.70 0.16 0.14
Matches are distributed among these distances:
20 1 0.01
21 21 0.13
22 118 0.73
23 3 0.02
24 7 0.04
25 12 0.07
ACGTcount: A:0.34, C:0.14, G:0.11, T:0.42
Consensus pattern (22 bp):
CTATGAAATTTTGATAATCACT
Found at i:60594 original size:22 final size:22
Alignment explanation
Indices: 60535--60596 Score: 72
Period size: 22 Copynumber: 2.8 Consensus size: 22
60525 ATAACCTTCA
*
60535 TATGAAATTTTGATAACCACAT
1 TATGAAATTTTGATAACCACAC
** *
60557 TAAAAAATTTTAATAACCACAC
1 TATGAAATTTTGATAACCACAC
60579 TATGACAA-TTTGATAACC
1 TATGA-AATTTTGATAACC
60597 TCCCAACCTC
Statistics
Matches: 32, Mismatches: 7, Indels: 2
0.78 0.17 0.05
Matches are distributed among these distances:
22 30 0.94
23 2 0.06
ACGTcount: A:0.45, C:0.16, G:0.06, T:0.32
Consensus pattern (22 bp):
TATGAAATTTTGATAACCACAC
Found at i:60726 original size:22 final size:23
Alignment explanation
Indices: 60701--60814 Score: 85
Period size: 22 Copynumber: 5.1 Consensus size: 23
60691 AAATTGTGAA
*
60701 AACC-ACACTATGAAATTTCAAT
1 AACCTACACTATGAAATTTTAAT
* **
60723 AACCTTCA-TAAAAAATTTTAAT
1 AACCTACACTATGAAATTTTAAT
**
60745 AACCTGATC-CTATGAAATTTTGGT
1 AACCT-A-CACTATGAAATTTTAAT
*
60769 AACC-ACACTATGAAATTTTGAT
1 AACCTACACTATGAAATTTTAAT
* * *
60791 AACCTTC-CCATGAAATTTTGAT
1 AACCTACACTATGAAATTTTAAT
60813 AA
1 AA
60815 TTTCCATGTG
Statistics
Matches: 74, Mismatches: 12, Indels: 12
0.76 0.12 0.12
Matches are distributed among these distances:
21 1 0.01
22 55 0.74
23 3 0.04
24 15 0.20
ACGTcount: A:0.40, C:0.18, G:0.08, T:0.33
Consensus pattern (23 bp):
AACCTACACTATGAAATTTTAAT
Found at i:60772 original size:46 final size:44
Alignment explanation
Indices: 60708--60814 Score: 108
Period size: 46 Copynumber: 2.4 Consensus size: 44
60698 GAAAACCACA
** *
60708 CTATGAAATTTCAATAACCTTCA-TAAAAAATTTTAATAACCTGATC
1 CTATGAAATTTTGATAACC-ACACTAAAAAATTTTAATAACCT--TC
* ** *
60754 CTATGAAATTTTGGTAACCACACTATGAAATTTTGATAACCTTC
1 CTATGAAATTTTGATAACCACACTAAAAAATTTTAATAACCTTC
*
60798 CCATGAAATTTTGATAA
1 CTATGAAATTTTGATAA
60815 TTTCCATGTG
Statistics
Matches: 51, Mismatches: 9, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
44 17 0.33
45 2 0.04
46 32 0.63
ACGTcount: A:0.39, C:0.17, G:0.08, T:0.36
Consensus pattern (44 bp):
CTATGAAATTTTGATAACCACACTAAAAAATTTTAATAACCTTC
Found at i:60807 original size:68 final size:66
Alignment explanation
Indices: 60701--60840 Score: 165
Period size: 68 Copynumber: 2.1 Consensus size: 66
60691 AAATTGTGAA
*
60701 AACCACACTATGAAATTTCAATAACCTTCATAAAAAATTTTAATAACCTGATCC-TATGAAATTT
1 AACCACACTATGAAATTTCAATAACCTTCACAAAAAATTTTAATAA--T-ATCCATATGAAATTT
60765 TGGT
63 TGGT
** * ** * * *
60769 AACCACACTATGAAATTTTGATAACCTTCCCATGAAATTTTGATAATTTCCATGTGAAATTTTGG
1 AACCACACTATGAAATTTCAATAACCTTCACAAAAAATTTTAATAATATCCATATGAAATTTTGG
60834 T
66 T
60835 AACCAC
1 AACCAC
60841 CCTCCTCATG
Statistics
Matches: 62, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
65 3 0.05
66 20 0.32
68 39 0.63
ACGTcount: A:0.38, C:0.19, G:0.09, T:0.34
Consensus pattern (66 bp):
AACCACACTATGAAATTTCAATAACCTTCACAAAAAATTTTAATAATATCCATATGAAATTTTGG
T
Found at i:60826 original size:22 final size:21
Alignment explanation
Indices: 60778--60837 Score: 68
Period size: 22 Copynumber: 2.8 Consensus size: 21
60768 TAACCACACT
60778 ATGAAATTTTGATAACCTTCCC
1 ATGAAATTTTGATAA-CTTCCC
*
60800 ATGAAATTTTGATAA-TTTCC
1 ATGAAATTTTGATAACTTCCC
*
60820 ATGTGAAATTTTGGTAAC
1 A--TGAAATTTTGATAAC
60838 CACCCTCCTC
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
20 5 0.15
22 28 0.85
ACGTcount: A:0.33, C:0.13, G:0.13, T:0.40
Consensus pattern (21 bp):
ATGAAATTTTGATAACTTCCC
Found at i:60874 original size:70 final size:66
Alignment explanation
Indices: 60757--60884 Score: 166
Period size: 70 Copynumber: 1.9 Consensus size: 66
60747 CCTGATCCTA
* * *
60757 TGAAATTTTGGTAACCACACTATGAAATTTTGATAACCTTCCCATGAAATTTTGATAATTTCCAT
1 TGAAATTTTGGTAACCACACTATGAAATTATAATAACCATCCCATGAAATTTTGATAATTTCCAT
60822 G
66 G
* **
60823 TGAAATTTTGGTAACCACCCTCCTCATGAAATTATAATAACCATCTTATGAAATTTTGATAA
1 TGAAATTTTGGTAACCA--C-ACT-ATGAAATTATAATAACCATCCCATGAAATTTTGATAA
60885 CCACACAGAG
Statistics
Matches: 52, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
66 17 0.33
68 1 0.02
69 2 0.04
70 32 0.62
ACGTcount: A:0.35, C:0.17, G:0.11, T:0.37
Consensus pattern (66 bp):
TGAAATTTTGGTAACCACACTATGAAATTATAATAACCATCCCATGAAATTTTGATAATTTCCAT
G
Found at i:61084 original size:19 final size:20
Alignment explanation
Indices: 61053--61090 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
61043 TATTGACATT
61053 TAAAAATTGAAATT-AAAAG
1 TAAAAATTGAAATTCAAAAG
61072 TAAAATATT-AAATTCAAAA
1 TAAAA-ATTGAAATTCAAAA
61091 AATAATAGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.63, C:0.03, G:0.05, T:0.29
Consensus pattern (20 bp):
TAAAAATTGAAATTCAAAAG
Found at i:61970 original size:19 final size:17
Alignment explanation
Indices: 61937--61974 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 17
61927 AATTTCCATT
61937 ATTAAAATAATTAAATA
1 ATTAAAATAATTAAATA
61954 ATTAAAATATTATTAAATA
1 ATTAAAATA--ATTAAATA
61973 AT
1 AT
61975 GACAATTTAG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 9 0.47
19 10 0.53
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (17 bp):
ATTAAAATAATTAAATA
Found at i:62701 original size:89 final size:89
Alignment explanation
Indices: 62550--62733 Score: 307
Period size: 89 Copynumber: 2.1 Consensus size: 89
62540 GTCACCCCGG
* *
62550 TCAACTAGCAAAAAGGGTTATTTATGCAATAATCTTCGGACATTTCAACTTTATGCTTTTAAGTC
1 TCAACTAGCAAAAAGAGTTATTTATGCAATAATCTTCAGACATTTCAACTTTATGCTTTTAAGTC
* *
62615 TCCATTAAATTTCTTATAAGTCCT
66 CCCATTAAATTTCTTATAAATCCT
62639 TCAACTAGCAAAAAGAGTTATTTATGCAATAA-CTCTCAGACATTTCAACTTTATGCTTTTAAGT
1 TCAACTAGCAAAAAGAGTTATTTATGCAATAATCT-TCAGACATTTCAACTTTATGCTTTTAAGT
*
62703 CCCCATTATATTTCTTATAAATCCT
65 CCCCATTAAATTTCTTATAAATCCT
62728 TCAACT
1 TCAACT
62734 TAATCTATTT
Statistics
Matches: 89, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
88 2 0.02
89 87 0.98
ACGTcount: A:0.33, C:0.20, G:0.09, T:0.39
Consensus pattern (89 bp):
TCAACTAGCAAAAAGAGTTATTTATGCAATAATCTTCAGACATTTCAACTTTATGCTTTTAAGTC
CCCATTAAATTTCTTATAAATCCT
Found at i:75875 original size:8 final size:8
Alignment explanation
Indices: 75843--75876 Score: 50
Period size: 8 Copynumber: 4.1 Consensus size: 8
75833 ACATGCCTGA
75843 TTTCTTTT
1 TTTCTTTT
*
75851 CTTTCTTTC
1 -TTTCTTTT
75860 TTTCTTTT
1 TTTCTTTT
75868 TTTCTTTT
1 TTTCTTTT
75876 T
1 T
75877 CCTAAATGCA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
8 16 0.70
9 7 0.30
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (8 bp):
TTTCTTTT
Found at i:76623 original size:21 final size:19
Alignment explanation
Indices: 76597--76652 Score: 60
Period size: 21 Copynumber: 2.9 Consensus size: 19
76587 CGCTGCTCTA
76597 CTAATCTCATCTGTACAAT
1 CTAATCTCATCTGTACAAT
* *
76616 ACCTAATCTAATCTGTA-AGT
1 --CTAATCTCATCTGTACAAT
*
76636 GTAATCTCATCTGTACA
1 CTAATCTCATCTGTACA
76653 GTTGCTAAAC
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
18 13 0.43
19 1 0.03
20 2 0.07
21 14 0.47
ACGTcount: A:0.32, C:0.23, G:0.09, T:0.36
Consensus pattern (19 bp):
CTAATCTCATCTGTACAAT
Found at i:78130 original size:83 final size:83
Alignment explanation
Indices: 77991--78159 Score: 338
Period size: 83 Copynumber: 2.0 Consensus size: 83
77981 TAAGTAATCT
77991 TATGCCCTTAGTAATTTTAGAAGCATTTTGTTAATAATGACGGGTGTTAATCTTCTTATCTAATG
1 TATGCCCTTAGTAATTTTAGAAGCATTTTGTTAATAATGACGGGTGTTAATCTTCTTATCTAATG
78056 TCTCAATAAGCAAAATTA
66 TCTCAATAAGCAAAATTA
78074 TATGCCCTTAGTAATTTTAGAAGCATTTTGTTAATAATGACGGGTGTTAATCTTCTTATCTAATG
1 TATGCCCTTAGTAATTTTAGAAGCATTTTGTTAATAATGACGGGTGTTAATCTTCTTATCTAATG
78139 TCTCAATAAGCAAAATTA
66 TCTCAATAAGCAAAATTA
78157 TAT
1 TAT
78160 ATAGGTTATG
Statistics
Matches: 86, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
83 86 1.00
ACGTcount: A:0.33, C:0.13, G:0.14, T:0.40
Consensus pattern (83 bp):
TATGCCCTTAGTAATTTTAGAAGCATTTTGTTAATAATGACGGGTGTTAATCTTCTTATCTAATG
TCTCAATAAGCAAAATTA
Found at i:84959 original size:99 final size:99
Alignment explanation
Indices: 84788--84984 Score: 358
Period size: 99 Copynumber: 2.0 Consensus size: 99
84778 TTTACCAACC
* *
84788 TGCGTAAACAAATTATTAGAAAAAGTCTTACATTCCTACTTAATTTAATTAATTCTTAAATAAAC
1 TGCGTAAACAAATTATTAGAAAAAGTCTTACATTCATACTTAATTTAATTAATTCTAAAATAAAC
84853 CCTTAAAGTAAATTAAAAGGAAAAGAAGAAAGAA
66 CCTTAAAGTAAATTAAAAGGAAAAGAAGAAAGAA
*
84887 TGCGTAAACAAATTATTAGAAAAAGTCTTACATTCATACTTAATTTAATTAATTCTAAAATAAAT
1 TGCGTAAACAAATTATTAGAAAAAGTCTTACATTCATACTTAATTTAATTAATTCTAAAATAAAC
*
84952 TCTTAAAGTAAATTAAAAGGAAAAGAAGAAAGA
66 CCTTAAAGTAAATTAAAAGGAAAAGAAGAAAGA
84985 GATAAATATG
Statistics
Matches: 94, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
99 94 1.00
ACGTcount: A:0.50, C:0.10, G:0.10, T:0.30
Consensus pattern (99 bp):
TGCGTAAACAAATTATTAGAAAAAGTCTTACATTCATACTTAATTTAATTAATTCTAAAATAAAC
CCTTAAAGTAAATTAAAAGGAAAAGAAGAAAGAA
Found at i:85031 original size:67 final size:67
Alignment explanation
Indices: 84955--85088 Score: 241
Period size: 67 Copynumber: 2.0 Consensus size: 67
84945 AATAAATTCT
*
84955 TAAAGTAAATTAAAAGGAAAAGAAGAAAGAGATAAATATGCTACAAAATAGCCTACATAATAATC
1 TAAAGTAAATTAAAAGGAAAAGAAGAAAGAAATAAATATGCTACAAAATAGCCTACATAATAATC
85020 GG
66 GG
* *
85022 TAAAGTAAATTAAAAGGAAAAGAAGAAAGAAATAAATTTGCTGCAAAATAGCCTACATAATAATC
1 TAAAGTAAATTAAAAGGAAAAGAAGAAAGAAATAAATATGCTACAAAATAGCCTACATAATAATC
85087 GG
66 GG
85089 CTTAGAAATC
Statistics
Matches: 64, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
67 64 1.00
ACGTcount: A:0.54, C:0.09, G:0.16, T:0.20
Consensus pattern (67 bp):
TAAAGTAAATTAAAAGGAAAAGAAGAAAGAAATAAATATGCTACAAAATAGCCTACATAATAATC
GG
Found at i:87112 original size:5 final size:5
Alignment explanation
Indices: 87102--87141 Score: 50
Period size: 5 Copynumber: 8.4 Consensus size: 5
87092 TATATCTTAG
87102 TATCT TATCT TA-C- TAT-T GTATCT TATCT TATCT TATCT TA
1 TATCT TATCT TATCT TATCT -TATCT TATCT TATCT TATCT TA
87142 CTATATATAC
Statistics
Matches: 31, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
3 2 0.06
4 1 0.03
5 27 0.87
6 1 0.03
ACGTcount: A:0.23, C:0.17, G:0.03, T:0.57
Consensus pattern (5 bp):
TATCT
Found at i:87112 original size:13 final size:13
Alignment explanation
Indices: 87094--87145 Score: 61
Period size: 13 Copynumber: 3.8 Consensus size: 13
87084 GGACTTCATA
*
87094 TATCTTAGTATCT
1 TATCTTACTATCT
87107 TATCTTACTAT-T
1 TATCTTACTATCT
87119 GTATCTTATCTTATCT
1 -TATCTTA-C-TATCT
87135 TATCTTACTAT
1 TATCTTACTAT
87146 ATATACTATA
Statistics
Matches: 34, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
12 1 0.03
13 20 0.59
14 2 0.06
15 10 0.29
16 1 0.03
ACGTcount: A:0.23, C:0.17, G:0.04, T:0.56
Consensus pattern (13 bp):
TATCTTACTATCT
Found at i:89211 original size:44 final size:44
Alignment explanation
Indices: 89148--89247 Score: 110
Period size: 44 Copynumber: 2.3 Consensus size: 44
89138 TGACAATAAA
* * * *
89148 ACCAAAATTACATAGGAAGGCTATCTAAATTTAATAGTGTTGAT
1 ACCAAAATTTCATAGGAAGGCTATCAAAACTTAATAGTGTAGAT
* * * * *
89192 ACCAAAATTTCGTATGAAGGTTATCAAAACTTCATAGTGTAGTT
1 ACCAAAATTTCATAGGAAGGCTATCAAAACTTAATAGTGTAGAT
*
89236 ATCAAAATTTCA
1 ACCAAAATTTCA
89248 CATAGAGGTT
Statistics
Matches: 45, Mismatches: 11, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
44 45 1.00
ACGTcount: A:0.40, C:0.13, G:0.14, T:0.33
Consensus pattern (44 bp):
ACCAAAATTTCATAGGAAGGCTATCAAAACTTAATAGTGTAGAT
Found at i:89219 original size:22 final size:22
Alignment explanation
Indices: 89194--89381 Score: 166
Period size: 22 Copynumber: 8.5 Consensus size: 22
89184 GTGTTGATAC
*
89194 CAAAATTTCGTATGAAGGTTAT
1 CAAAATTTCATATGAAGGTTAT
* *
89216 CAAAACTTCATAGTGTA-GTTAT
1 CAAAATTTCATA-TGAAGGTTAT
* *
89238 CAAAATTTCACAT-AGAGGTTAC
1 CAAAATTTCATATGA-AGGTTAT
* **
89260 CAATATTTCATAAAAAGGTTAT
1 CAAAATTTCATATGAAGGTTAT
* * * *
89282 CAAAATTTCTTAGGGAGGTTAA
1 CAAAATTTCATATGAAGGTTAT
* *
89304 CAAAATTTCATACGAATGTTAT
1 CAAAATTTCATATGAAGGTTAT
* *
89326 CAAAATTTTATAGTG-TGGTTAT
1 CAAAATTTCATA-TGAAGGTTAT
* *
89348 CAAAATTTCATAAGAAGGTTAA
1 CAAAATTTCATATGAAGGTTAT
89370 CAAAATTTCATA
1 CAAAATTTCATA
89382 GGGAGGAAAT
Statistics
Matches: 130, Mismatches: 30, Indels: 12
0.76 0.17 0.07
Matches are distributed among these distances:
21 3 0.02
22 122 0.94
23 5 0.04
ACGTcount: A:0.40, C:0.11, G:0.14, T:0.35
Consensus pattern (22 bp):
CAAAATTTCATATGAAGGTTAT
Found at i:89645 original size:22 final size:22
Alignment explanation
Indices: 89553--89727 Score: 135
Period size: 22 Copynumber: 8.1 Consensus size: 22
89543 AGTTTCATTA
* * *
89553 TCATAGGGAGGTTATCAAAACT
1 TCATAGTGTGGTTATCAAAATT
*
89575 TCA-AGGTATGGTTATCAAAATTT
1 TCATA-GTGTGGTTATCAAAA-TT
**
89598 TCATAGTGCAGTTATC--AATT
1 TCATAGTGTGGTTATCAAAATT
* *
89618 TTATAGTGTGATTATCAAAATT
1 TCATAGTGTGGTTATCAAAATT
* * * *
89640 CCATAGGGAGATTATCAAAATT
1 TCATAGTGTGGTTATCAAAATT
* * **
89662 TCACACTAAGGTTATCAAAATT
1 TCATAGTGTGGTTATCAAAATT
89684 TC-T-GTGTGGTTATCAAAATT
1 TCATAGTGTGGTTATCAAAATT
* *
89704 TCACAGTGTGGTTATCCAAATT
1 TCATAGTGTGGTTATCAAAATT
89726 TC
1 TC
89728 TATGTTGGAG
Statistics
Matches: 119, Mismatches: 27, Indels: 14
0.74 0.17 0.09
Matches are distributed among these distances:
20 30 0.25
21 3 0.03
22 73 0.61
23 12 0.10
24 1 0.01
ACGTcount: A:0.34, C:0.13, G:0.17, T:0.37
Consensus pattern (22 bp):
TCATAGTGTGGTTATCAAAATT
Found at i:89719 original size:64 final size:63
Alignment explanation
Indices: 89562--89727 Score: 147
Period size: 64 Copynumber: 2.6 Consensus size: 63
89552 ATCATAGGGA
* * * * * *
89562 GGTTATCAAAACTTCAAGGTATGGTTATCAAAATTTTCATAGTGCAGTTATCAATTTTATAGTGT
1 GGTTATCAAAATTTCAA-GTGTGGTTATCAAAA-TTTCACACTGAAGTTATCAAATTTATAGTGT
* * * * * *
89627 GATTATCAAAATTCCATAGGGAGATTATCAAAATTTCACACT-AAGGTTATCAAAATTTCT-GTG
1 GGTTATCAAAATTTCA-AGTGTGGTTATCAAAATTTCACACTGAA-GTTATC-AAATTTATAGTG
89690 T
63 T
*
89691 GGTTATCAAAATTTCACAGTGTGGTTATCCAAATTTC
1 GGTTATCAAAATTTCA-AGTGTGGTTATCAAAATTTC
89728 TATGTTGGAG
Statistics
Matches: 79, Mismatches: 19, Indels: 7
0.75 0.18 0.07
Matches are distributed among these distances:
63 1 0.01
64 47 0.59
65 30 0.38
66 1 0.01
ACGTcount: A:0.34, C:0.13, G:0.16, T:0.37
Consensus pattern (63 bp):
GGTTATCAAAATTTCAAGTGTGGTTATCAAAATTTCACACTGAAGTTATCAAATTTATAGTGT
Found at i:90643 original size:38 final size:38
Alignment explanation
Indices: 90592--90665 Score: 121
Period size: 38 Copynumber: 1.9 Consensus size: 38
90582 TTGACAAATG
* *
90592 ATATAATGAATGGTTTTAAATTTTTTCTTAAATATACA
1 ATATAATAAATGGTTTTAAATTTTTTCATAAATATACA
*
90630 ATATAATAAATGGTTTTAAATTTTTTGATAAATATA
1 ATATAATAAATGGTTTTAAATTTTTTCATAAATATA
90666 TAACTTTTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
38 33 1.00
ACGTcount: A:0.42, C:0.03, G:0.08, T:0.47
Consensus pattern (38 bp):
ATATAATAAATGGTTTTAAATTTTTTCATAAATATACA
Found at i:96493 original size:30 final size:29
Alignment explanation
Indices: 96422--96499 Score: 86
Period size: 29 Copynumber: 2.7 Consensus size: 29
96412 GAAATTACAC
*
96422 AAAACGGCCAAATAAGCCCCTGAACTCTA
1 AAAAAGGCCAAATAAGCCCCTGAACTCTA
***
96451 ATTGCA-GCCAAATAAGCCCCTGAACTCTTA
1 A-AAAAGGCCAAATAAGCCCCTGAACTC-TA
*
96481 AAAAAGGCCAAATATGCCC
1 AAAAAGGCCAAATAAGCCC
96500 TTTTCTGATG
Statistics
Matches: 38, Mismatches: 8, Indels: 5
0.75 0.16 0.10
Matches are distributed among these distances:
29 23 0.61
30 15 0.39
ACGTcount: A:0.40, C:0.29, G:0.14, T:0.17
Consensus pattern (29 bp):
AAAAAGGCCAAATAAGCCCCTGAACTCTA
Found at i:102497 original size:41 final size:41
Alignment explanation
Indices: 102441--102525 Score: 111
Period size: 41 Copynumber: 2.1 Consensus size: 41
102431 TCATGTTTTT
* *
102441 TTTCTTTTTATCTCACCTAGGGTTTA-ATGTGTTTTTTGAGGG
1 TTTCTTTTCATCTCACCTAGGGTTTATAT-TGTTTGTT-AGGG
*
102483 TTTC-TTTCATCTCACTTAGGGTTTATATTGTTTGTTAGGG
1 TTTCTTTTCATCTCACCTAGGGTTTATATTGTTTGTTAGGG
102523 TTT
1 TTT
102526 GGATTTCATA
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
40 7 0.18
41 26 0.67
42 6 0.15
ACGTcount: A:0.14, C:0.12, G:0.20, T:0.54
Consensus pattern (41 bp):
TTTCTTTTCATCTCACCTAGGGTTTATATTGTTTGTTAGGG
Found at i:103250 original size:38 final size:38
Alignment explanation
Indices: 103201--103317 Score: 143
Period size: 38 Copynumber: 3.1 Consensus size: 38
103191 ATTATTATAT
103201 TTTTTTTTGTGATTGATTTTGCTTGATAAATTGATTTA
1 TTTTTTTTGTGATTGATTTTGCTTGATAAATTGATTTA
* * *
103239 TTTTTTTTGTGATCCTTA-CTTGC-TCAT-AATT-ATTATA
1 TTTTTTTTGTGAT--TGATTTTGCTTGATAAATTGATT-TA
103276 TTTTATTTTGTGATTGATTTTGCTTGATAAATTGATTTA
1 TTTT-TTTTGTGATTGATTTTGCTTGATAAATTGATTTA
103315 TTT
1 TTT
103318 ATATTAGCAC
Statistics
Matches: 65, Mismatches: 6, Indels: 15
0.76 0.07 0.17
Matches are distributed among these distances:
36 5 0.08
37 14 0.22
38 28 0.43
39 13 0.20
40 5 0.08
ACGTcount: A:0.21, C:0.06, G:0.13, T:0.60
Consensus pattern (38 bp):
TTTTTTTTGTGATTGATTTTGCTTGATAAATTGATTTA
Found at i:103252 original size:76 final size:76
Alignment explanation
Indices: 103172--103317 Score: 283
Period size: 76 Copynumber: 1.9 Consensus size: 76
103162 ATTGATTAGT
*
103172 TGATCCTTACTTGCTCATAATTATTATATTTTTTTTTGTGATTGATTTTGCTTGATAAATTGATT
1 TGATCCTTACTTGCTCATAATTATTATATTTTATTTTGTGATTGATTTTGCTTGATAAATTGATT
103237 TATTTTTTTTG
66 TATTTTTTTTG
103248 TGATCCTTACTTGCTCATAATTATTATATTTTATTTTGTGATTGATTTTGCTTGATAAATTGATT
1 TGATCCTTACTTGCTCATAATTATTATATTTTATTTTGTGATTGATTTTGCTTGATAAATTGATT
103313 TATTT
66 TATTT
103318 ATATTAGCAC
Statistics
Matches: 69, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
76 69 1.00
ACGTcount: A:0.23, C:0.08, G:0.12, T:0.58
Consensus pattern (76 bp):
TGATCCTTACTTGCTCATAATTATTATATTTTATTTTGTGATTGATTTTGCTTGATAAATTGATT
TATTTTTTTTG
Found at i:111429 original size:59 final size:60
Alignment explanation
Indices: 111360--111547 Score: 162
Period size: 59 Copynumber: 3.3 Consensus size: 60
111350 GGAAATATGT
*
111360 TTACCCTTACA-TTAAACCTAGACAAATGATAGCTCATTACACCTTGGGATAATATTGAG
1 TTACCATTACACTTAAACCTAGACAAATGATAGCTCATTACACCTTGGGATAATATTGAG
* ***** * * *** *
111419 TTACCATTACACTT-AA--T-GA-TAATCCCCCCTAGATTGAAAAAATGGGA-AATA-TG-T
1 TTACCATTACACTTAAACCTAGACAAATGATAGCT-CATT-ACACCTTGGGATAATATTGAG
*
111473 TTACCCTTACA-TTAAACCTAGACAAATGATAGCTCATTACACCTTGGGATAATATTGAG
1 TTACCATTACACTTAAACCTAGACAAATGATAGCTCATTACACCTTGGGATAATATTGAG
111532 TTACCATTACACTTAA
1 TTACCATTACACTTAA
111548 TGATAATCCC
Statistics
Matches: 90, Mismatches: 27, Indels: 23
0.64 0.19 0.16
Matches are distributed among these distances:
53 2 0.02
54 12 0.13
55 7 0.08
56 17 0.19
57 17 0.19
58 7 0.08
59 22 0.24
60 6 0.07
ACGTcount: A:0.37, C:0.20, G:0.12, T:0.31
Consensus pattern (60 bp):
TTACCATTACACTTAAACCTAGACAAATGATAGCTCATTACACCTTGGGATAATATTGAG
Found at i:111546 original size:113 final size:113
Alignment explanation
Indices: 111348--111571 Score: 448
Period size: 113 Copynumber: 2.0 Consensus size: 113
111338 TTACACTTAG
111348 TGGGAAATATGTTTACCCTTACATTAAACCTAGACAAATGATAGCTCATTACACCTTGGGATAAT
1 TGGGAAATATGTTTACCCTTACATTAAACCTAGACAAATGATAGCTCATTACACCTTGGGATAAT
111413 ATTGAGTTACCATTACACTTAATGATAATCCCCCCTAGATTGAAAAAA
66 ATTGAGTTACCATTACACTTAATGATAATCCCCCCTAGATTGAAAAAA
111461 TGGGAAATATGTTTACCCTTACATTAAACCTAGACAAATGATAGCTCATTACACCTTGGGATAAT
1 TGGGAAATATGTTTACCCTTACATTAAACCTAGACAAATGATAGCTCATTACACCTTGGGATAAT
111526 ATTGAGTTACCATTACACTTAATGATAATCCCCCCTAGATTGAAAA
66 ATTGAGTTACCATTACACTTAATGATAATCCCCCCTAGATTGAAAA
111572 GACAACAGGT
Statistics
Matches: 111, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
113 111 1.00
ACGTcount: A:0.37, C:0.20, G:0.13, T:0.30
Consensus pattern (113 bp):
TGGGAAATATGTTTACCCTTACATTAAACCTAGACAAATGATAGCTCATTACACCTTGGGATAAT
ATTGAGTTACCATTACACTTAATGATAATCCCCCCTAGATTGAAAAAA
Found at i:113581 original size:132 final size:132
Alignment explanation
Indices: 113343--113779 Score: 775
Period size: 132 Copynumber: 3.3 Consensus size: 132
113333 TTTGTTGGCC
* *
113343 AAAAATAGAGTTTTTAGTTTAATAAAACTATAAAAATATATTTAAAAAATTCTAATATATATAAT
1 AAAAATAGAGTTTTTAGTTGAGTAAAACTAT-AAAATATATTTAAAAAATTCTAATATATATAAT
*
113408 TTTTTTAATTAAAATAGTAAAATGGTAAAAATTAAATAGTTATAAGGATATATTATATTTAATTA
65 TTTTCTAATTAAAATAGTAAAATGGTAAAAATTAAATAGTTATAAGGATATATTATATTTAATTA
113473 AAT
130 AAT
113476 AAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAATATATTTAAAAAATTCTAATATATATAATT
1 AAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAATATATTTAAAAAATTCTAATATATATAATT
113541 TTTCTAATTAAAATAGTAAAATGGTAAAAATTAAATAGTTATAAGGATATATTATATTTAATTAA
66 TTTCTAATTAAAATAGTAAAATGGTAAAAATTAAATAGTTATAAGGATATATTATATTTAATTAA
113606 AT
131 AT
*
113608 AAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAATATATTTAAAAAATTATAATATATATAATT
1 AAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAATATATTTAAAAAATTCTAATATATATAATT
*
113673 TTTCTAATTAAAATAGTAAAATGGTAAAAATTAAATAGTTATAAGGATATTTTATATTTAATTAA
66 TTTCTAATTAAAATAGTAAAATGGTAAAAATTAAATAGTTATAAGGATATATTATA--T--TT-A
113738 ATTAAAT
126 ATTAAAT
113745 AAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAA
1 AAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAA
113780 GTCTAAACAA
Statistics
Matches: 294, Mismatches: 5, Indels: 6
0.96 0.02 0.02
Matches are distributed among these distances:
132 219 0.74
133 29 0.10
134 1 0.00
136 2 0.01
137 43 0.15
ACGTcount: A:0.51, C:0.02, G:0.08, T:0.39
Consensus pattern (132 bp):
AAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAATATATTTAAAAAATTCTAATATATATAATT
TTTCTAATTAAAATAGTAAAATGGTAAAAATTAAATAGTTATAAGGATATATTATATTTAATTAA
AT
Found at i:116986 original size:2 final size:2
Alignment explanation
Indices: 116979--117010 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
116969 GATTTTGTGA
116979 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
117011 GCACTAGTAT
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:117865 original size:54 final size:54
Alignment explanation
Indices: 117801--117909 Score: 218
Period size: 54 Copynumber: 2.0 Consensus size: 54
117791 ACCGGGTAAA
117801 AACCGGTTGGACCGGCGGTTGAATCGGGTTTTGACCGGATAAAACCGGTTTGAT
1 AACCGGTTGGACCGGCGGTTGAATCGGGTTTTGACCGGATAAAACCGGTTTGAT
117855 AACCGGTTGGACCGGCGGTTGAATCGGGTTTTGACCGGATAAAACCGGTTTGAT
1 AACCGGTTGGACCGGCGGTTGAATCGGGTTTTGACCGGATAAAACCGGTTTGAT
117909 A
1 A
117910 GTTAAGAAAA
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 55 1.00
ACGTcount: A:0.23, C:0.18, G:0.33, T:0.26
Consensus pattern (54 bp):
AACCGGTTGGACCGGCGGTTGAATCGGGTTTTGACCGGATAAAACCGGTTTGAT
Found at i:120560 original size:438 final size:436
Alignment explanation
Indices: 119623--120573 Score: 1270
Period size: 438 Copynumber: 2.2 Consensus size: 436
119613 ATAATTACCC
* * * * * *
119623 TAAGAAAATATTTGTTAATGGAGATCTTGAAACATAAAAATTTCCTTTTGAACCCTTCATGAAAC
1 TAAGAAAATGTTCGTCAATGAAGATCTTGAAACATAAAAATTTTCTTTTGAA--CTTCATGAAAA
** *** *
119688 TCGTAGATCAAATTTAACTTTTGGGTTTTTCATGAAAGTCGTAGATCATACAATAACCTTTTAAC
64 TCGTAGATCAAATTTAACTTTCAGGTCCGTCATGAAAGTCGTAAATCATACAATAACCTTTTAAC
**
119753 CAACACTTGAATAACTTTAATCGGACATGTGGATCGAAAATTATATGGTATTAAATAGACCAGCA
129 CAACACTTGAATAACTTTAATCGGACATGTGGATCGAAAACCATATGGTATTAAATAGACCAGCA
* *
119818 ATCGAAACGACCAAATTTAGAAAGCATTTTTTGAATTGAAACATAAAAATTTGCTTTTGAGTCCT
194 ATCGAAACCAACAAATTTAGAAAGCATTTTTTGAATTGAAACATAAAAATTTGCTTTTGAGTCCT
* * *
119883 TCATGAAAGTTGTAGATCATGAAATTACCTTTTCATAGACACATGAATCAACTTAATCGGACAAA
259 TCATGAAAGTTGTAGATAATGAAATTACCTTGTAATAGACACATGAATCAACTTAATCGGACAAA
* ** *
119948 TAAAACAAAGAATAAAAAAAATAAAGCTTAAACGTTAGATAAAGATAGAATTTGTAAAGTACTAA
324 TAAAACAAAGAATAAAAAAAATAAAGCTGAAACGTTAGATAAAGATAGAATTAATAAAGAACTAA
*
120013 GCAGTATAAAGTAGAAAAGTATGAGGGTCATTCGATAAATAATCCAAA
389 GCAGTATAAAGTAGAAAAATATGAGGGTCATTCGATAAATAATCCAAA
* * * * *
120061 TAAGAAAATGTTTGTTAATGGAGATCTTGAAACATAAAAATTCTCTTTTCAACCCTTCATGAAAA
1 TAAGAAAATGTTCGTCAATGAAGATCTTGAAACATAAAAATTTTCTTTTGAA--CTTCATGAAAA
*
120126 TCGTAGATCAAATTTAGCTTTCAGGTCCGTCATGAAAGTCGTAAATCATGA-AATAACCTTTTAA
64 TCGTAGATCAAATTTAACTTTCAGGTCCGTCATGAAAGTCGTAAATCAT-ACAATAACCTTTTAA
**
120190 CTGACACTTGAATAACTTTAATCGGACATGTGGATCGAAAACCATATGGTATTAAATAGACC-GA
128 CCAACACTTGAATAACTTTAATCGGACATGTGGATCGAAAACCATATGGTATTAAATAGACCAG-
* * * *
120254 CAATCGAACCCAACAAATTTGGGAAGCATTTTCTTTAATTGAAACATAAAAA-TTGACTTTTGAG
192 CAATCGAAACCAACAAATTTAGAAAGCATTTT-TTGAATTGAAACATAAAAATTTG-CTTTTGAG
* * * * *
120318 TCCTTTATGAAAGTTGTAGATAATGAAATTACCTTGTAATAGGCACCTGAATCACCTTGATCGGA
255 TCCTTCATGAAAGTTGTAGATAATGAAATTACCTTGTAATAGACACATGAATCAACTTAATCGGA
* *
120383 CAAATAGAACAAA-AA-AAAAAAAACTAAAGCTGAAGCGTTAAATTGATTAAA-ATAGAATTAAT
320 CAAATAAAACAAAGAATAAAAAAAA-TAAAGCTGAAACGTT--A--GA-TAAAGATAGAATTAAT
* ** * *
120445 AACGAACTAAGTTGTAT-AAGTAGAAAAATATGAGGGTCATTTGATAAATAATCCAAT
379 AAAGAACTAAGCAGTATAAAGTAGAAAAATATGAGGGTCATTCGATAAATAATCCAAA
* *
120502 TAAGAAAATGTTCGTCGATGAAGATCTTGAAACATAAAAATTTTCTTTTGAA-TTCATGAAAGTC
1 TAAGAAAATGTTCGTCAATGAAGATCTTGAAACATAAAAATTTTCTTTTGAACTTCATGAAAATC
120566 GTAGATCA
66 GTAGATCA
120574 TGCAGTAACC
Statistics
Matches: 454, Mismatches: 49, Indels: 20
0.87 0.09 0.04
Matches are distributed among these distances:
437 9 0.02
438 237 0.52
439 96 0.21
440 1 0.00
441 83 0.18
442 24 0.05
443 4 0.01
ACGTcount: A:0.41, C:0.13, G:0.15, T:0.30
Consensus pattern (436 bp):
TAAGAAAATGTTCGTCAATGAAGATCTTGAAACATAAAAATTTTCTTTTGAACTTCATGAAAATC
GTAGATCAAATTTAACTTTCAGGTCCGTCATGAAAGTCGTAAATCATACAATAACCTTTTAACCA
ACACTTGAATAACTTTAATCGGACATGTGGATCGAAAACCATATGGTATTAAATAGACCAGCAAT
CGAAACCAACAAATTTAGAAAGCATTTTTTGAATTGAAACATAAAAATTTGCTTTTGAGTCCTTC
ATGAAAGTTGTAGATAATGAAATTACCTTGTAATAGACACATGAATCAACTTAATCGGACAAATA
AAACAAAGAATAAAAAAAATAAAGCTGAAACGTTAGATAAAGATAGAATTAATAAAGAACTAAGC
AGTATAAAGTAGAAAAATATGAGGGTCATTCGATAAATAATCCAAA
Found at i:122276 original size:12 final size:10
Alignment explanation
Indices: 122253--122288 Score: 54
Period size: 10 Copynumber: 3.6 Consensus size: 10
122243 ATACCTTGAT
122253 ATATCCGTAA
1 ATATCCGTAA
122263 ATATCCGTAA
1 ATATCCGTAA
* *
122273 AAATTCGTAA
1 ATATCCGTAA
122283 ATATCC
1 ATATCC
122289 ATATTAAATT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.42, C:0.19, G:0.08, T:0.31
Consensus pattern (10 bp):
ATATCCGTAA
Found at i:122830 original size:17 final size:17
Alignment explanation
Indices: 122808--122862 Score: 60
Period size: 17 Copynumber: 3.2 Consensus size: 17
122798 CAAAATAAGT
122808 GTTTCAATTAAGTCTGG
1 GTTTCAATTAAGTCTGG
*
122825 GTTTCAACTTAATATCT--
1 GTTTCAA-TTAA-GTCTGG
*
122842 GTTTCAAATAAGTCTGG
1 GTTTCAATTAAGTCTGG
122859 GTTT
1 GTTT
122863 TGCATTTAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
15 3 0.10
16 3 0.10
17 18 0.58
18 4 0.13
19 3 0.10
ACGTcount: A:0.25, C:0.13, G:0.18, T:0.44
Consensus pattern (17 bp):
GTTTCAATTAAGTCTGG
Found at i:127883 original size:16 final size:14
Alignment explanation
Indices: 127851--127884 Score: 50
Period size: 16 Copynumber: 2.3 Consensus size: 14
127841 ACAAACTTAG
127851 ATATGAATTATGAA
1 ATATGAATTATGAA
127865 ATATGTAATTATGGAA
1 ATATG-AATTAT-GAA
127881 ATAT
1 ATAT
127885 TATCAACTGA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 5 0.28
15 6 0.33
16 7 0.39
ACGTcount: A:0.47, C:0.00, G:0.15, T:0.38
Consensus pattern (14 bp):
ATATGAATTATGAA
Found at i:129706 original size:2 final size:2
Alignment explanation
Indices: 129695--129753 Score: 93
Period size: 2 Copynumber: 29.5 Consensus size: 2
129685 TCGGTCCTTT
*
129695 TA TA TA -A TA TA TA TA TA TA TGA TA TA TA TA TA TA TG TA TA TA
1 TA TA TA TA TA TA TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA
129737 TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA T
129754 TTTGTTTTAG
Statistics
Matches: 53, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
1 1 0.02
2 50 0.94
3 2 0.04
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
TA
Found at i:130060 original size:101 final size:100
Alignment explanation
Indices: 129881--130685 Score: 925
Period size: 101 Copynumber: 8.0 Consensus size: 100
129871 TTGCTATAAA
* * * * * **
129881 TACGAACATTGTCGTTCTCATAAAGAGTTCAAGGTTTACGTTTAGCCACAACTTAGTTTCGATGT
1 TACGAACA-TGCCGTTCTCACAAAGAGTCCAGGGCTTACGTTCGGCCACAACTTAGTTTCGATGT
* ** * *
129946 TCTCACGGGGAGTCCGGATCGAAATCTAAGGTCCAT
65 TCTCATGACGAGTCCAGATCGAAATCTAAGGTCAAT
* *
129982 TACGAACTATGTCGTTCTCACAAAGAGTCCAGGGCTTACGTTCGGCCAGAACTTAGTTTCGATGT
1 TACGAAC-ATGCCGTTCTCACAAAGAGTCCAGGGCTTACGTTCGGCCACAACTTAGTTTCGATGT
* * *
130047 TCTCATGACGAGTCCGGATCAAAATCTAAGGTCAGT
65 TCTCATGACGAGTCCAGATCGAAATCTAAGGTCAAT
* * * * * *
130083 TTCGAACTTAGCCATTCTCATAAAGAGTCCAGGGATTACGTTCGGCCACAACTTAGTTTTGATGT
1 TACGAACAT-GCCGTTCTCACAAAGAGTCCAGGGCTTACGTTCGGCCACAACTTAGTTTCGATGT
* ** * * *
130148 TCTCACGGGGAGTCCGGATCGAAATCAAAGGTCCAT
65 TCTCATGACGAGTCCAGATCGAAATCTAAGGTCAAT
* *
130184 TACGAACATTGTCGTTCTCACAAAGAGTCCAGGGCTCACGTTCGGCCACAACTTAGTTTCGATGT
1 TACGAACA-TGCCGTTCTCACAAAGAGTCCAGGGCTTACGTTCGGCCACAACTTAGTTTCGATGT
* **
130249 TCTCACGGGGAGTCCAGATCGAAATCTAAGGTCAAT
65 TCTCATGACGAGTCCAGATCGAAATCTAAGGTCAAT
* * *
130285 TACGAACATTGCCGTTCTCACAAAGAGTCAAGGGCTTACGTCCGGCCACAACTTATTTTCGATGT
1 TACGAACA-TGCCGTTCTCACAAAGAGTCCAGGGCTTACGTTCGGCCACAACTTAGTTTCGATGT
* * *
130350 TCTCA-CAGGGAGTCCGGATCGAAATCTCAA-GTCAAT
65 TCTCATGA-CGAGTCCAGATCGAAATCT-AAGGTCAAT
* * * **
130386 TACGAACATTACGGTTCTCACAAAGCGTCCAGGGCTTACGTTCGGCCACAACTTAGTTTCCTTGT
1 TACGAACA-TGCCGTTCTCACAAAGAGTCCAGGGCTTACGTTCGGCCACAACTTAGTTTCGATGT
* *
130451 TCTCATGACGAGTTCAAATCGAAATCTAAGGTCAAT
65 TCTCATGACGAGTCCAGATCGAAATCTAAGGTCAAT
* * * * *
130487 TACGAAC-TGAGCCATTCTCACAAAGAGTCCAAGGCATACGTTCGACCACAACTTAGTTTTGATG
1 TACGAACAT--GCCGTTCTCACAAAGAGTCCAGGGCTTACGTTCGGCCACAACTTAGTTTCGATG
* *
130551 TTC-CTATGACGAGTCCAGATCGAAATCAAAGGTCAAA
64 TTCTC-ATGACGAGTCCAGATCGAAATCTAAGGTCAAT
* * * *
130588 TACGAACTTAACCGTTCTCACAAAAAGTCCAGGGCTTACGTTCGGCCACAACTTAGTTTTGATGT
1 TACGAACAT-GCCGTTCTCACAAAGAGTCCAGGGCTTACGTTCGGCCACAACTTAGTTTCGATGT
* * *
130653 TTTCATGACGAGTCTAGAGCGAAATCTAAGGTC
65 TCTCATGACGAGTCCAGATCGAAATCTAAGGTC
130686 TCTCCGAAAT
Statistics
Matches: 608, Mismatches: 84, Indels: 24
0.85 0.12 0.03
Matches are distributed among these distances:
99 1 0.00
100 4 0.01
101 596 0.98
102 7 0.01
ACGTcount: A:0.28, C:0.23, G:0.21, T:0.27
Consensus pattern (100 bp):
TACGAACATGCCGTTCTCACAAAGAGTCCAGGGCTTACGTTCGGCCACAACTTAGTTTCGATGTT
CTCATGACGAGTCCAGATCGAAATCTAAGGTCAAT
Found at i:130241 original size:202 final size:201
Alignment explanation
Indices: 129895--130685 Score: 1027
Period size: 202 Copynumber: 3.9 Consensus size: 201
129885 AACATTGTCG
* * * * ** *
129895 TTCTCATAAAGAGTTCAAGGTTTACGTTTAGCCACAACTTAGTTTCGATGTTCTCACGGGGAGTC
1 TTCTCACAAAGAGTCCAGGGATTACGTTCGGCCACAACTTAGTTTTGATGTTCTCACGGGGAGTC
* *
129960 CGGATCGAAATCTAAGGTCCATTACGAACTATGTCGTTCTCACAAAGAGTCCAGGGCTTACGTTC
66 CGGATCGAAATCAAAGGTCAATTACGAACT-TGTCGTTCTCACAAAGAGTCCAGGGCTTACGTTC
* * * * *
130025 GGCCAGAACTTAGTTTCGATGTTCTCATGACGAGTCCGGATCAAAATCTAAGGTCAGTTTCGAAC
130 GGCCACAACTTAGTTTCGATGTTCTCATGACGAGTCCAGATCGAAATCTAAGGTCAATTACGAAC
130090 TTAGCCA
195 TTAGCCA
*
130097 TTCTCATAAAGAGTCCAGGGATTACGTTCGGCCACAACTTAGTTTTGATGTTCTCACGGGGAGTC
1 TTCTCACAAAGAGTCCAGGGATTACGTTCGGCCACAACTTAGTTTTGATGTTCTCACGGGGAGTC
* *
130162 CGGATCGAAATCAAAGGTCCATTACGAACATTGTCGTTCTCACAAAGAGTCCAGGGCTCACGTTC
66 CGGATCGAAATCAAAGGTCAATTACGAAC-TTGTCGTTCTCACAAAGAGTCCAGGGCTTACGTTC
* **
130227 GGCCACAACTTAGTTTCGATGTTCTCACGGGGAGTCCAGATCGAAATCTAAGGTCAATTACGAAC
130 GGCCACAACTTAGTTTCGATGTTCTCATGACGAGTCCAGATCGAAATCTAAGGTCAATTACGAAC
*
130292 ATT-GCCG
195 -TTAGCCA
* * * *
130299 TTCTCACAAAGAGTCAAGGGCTTACGTCCGGCCACAACTTA-TTTTCGATGTTCTCACAGGGAGT
1 TTCTCACAAAGAGTCCAGGGATTACGTTCGGCCACAACTTAGTTTT-GATGTTCTCACGGGGAGT
* * *
130363 CCGGATCGAAATCTCAA-GTCAATTACGAACATT-ACGGTTCTCACAAAGCGTCCAGGGCTTACG
65 CCGGATCGAAATC-AAAGGTCAATTACGAAC-TTGTC-GTTCTCACAAAGAGTCCAGGGCTTACG
** * *
130426 TTCGGCCACAACTTAGTTTCCTTGTTCTCATGACGAGTTCAAATCGAAATCTAAGGTCAATTACG
127 TTCGGCCACAACTTAGTTTCGATGTTCTCATGACGAGTCCAGATCGAAATCTAAGGTCAATTACG
*
130491 AACTGAGCCA
192 AACTTAGCCA
* * * **
130501 TTCTCACAAAGAGTCCAAGGCA-TACGTTCGACCACAACTTAGTTTTGATGTTC-CTATGACGAG
1 TTCTCACAAAGAGTCC-AGGGATTACGTTCGGCCACAACTTAGTTTTGATGTTCTC-ACGGGGAG
* * ** *
130564 TCCAGATCGAAATCAAAGGTCAAATACGAACTTAACCGTTCTCACAAAAAGTCCAGGGCTTACGT
64 TCCGGATCGAAATCAAAGGTCAATTACGAACTT-GTCGTTCTCACAAAGAGTCCAGGGCTTACGT
* * * *
130629 TCGGCCACAACTTAGTTTTGATGTTTTCATGACGAGTCTAGAGCGAAATCTAAGGTC
128 TCGGCCACAACTTAGTTTCGATGTTCTCATGACGAGTCCAGATCGAAATCTAAGGTC
130686 TCTCCGAAAT
Statistics
Matches: 518, Mismatches: 59, Indels: 24
0.86 0.10 0.04
Matches are distributed among these distances:
201 11 0.02
202 494 0.95
203 13 0.03
ACGTcount: A:0.28, C:0.24, G:0.21, T:0.27
Consensus pattern (201 bp):
TTCTCACAAAGAGTCCAGGGATTACGTTCGGCCACAACTTAGTTTTGATGTTCTCACGGGGAGTC
CGGATCGAAATCAAAGGTCAATTACGAACTTGTCGTTCTCACAAAGAGTCCAGGGCTTACGTTCG
GCCACAACTTAGTTTCGATGTTCTCATGACGAGTCCAGATCGAAATCTAAGGTCAATTACGAACT
TAGCCA
Found at i:131481 original size:233 final size:233
Alignment explanation
Indices: 131065--131493 Score: 610
Period size: 233 Copynumber: 1.8 Consensus size: 233
131055 TTGCCACATA
* * * *
131065 CACCTTCGTGGATCTCCCTCAACATATAGTCGGCTTCATCTGGGTCTACACATTTCAACAAAGGA
1 CACCTTCGTGGATCTCCCTCAACACATAGTCAGCTTCATCTAGGTCTACACACTTCAACAAAGGA
* * *
131130 AAGGTGAAGGATTTCTTATATAGTTCATCATCAATCAACACATACCTTGACGTTCTCATTTGTTT
66 AAGGTGAAGGATTTCTTATAGAGTTCATCATCAATCAACACATACCTTGACGCTCTCATTTGTCT
* * * * *
131195 AGTTGTCGCCACTTTTGGACTAAAGGGAGGATTGATCCCTTTCAAATACTCCACTATCTCGATCA
131 AGCTATCGCAACTTTTGGACTAAAGGGAGGATTGATCCCTTTCAAACACTCCACTATCTCAATCA
131260 TCCACCTTCGTGGATCGGGCTTACGTTCGGGGGTCTTC
196 TCCACCTTCGTGGATCGGGCTTACGTTCGGGGGTCTTC
* * * * * *
131298 CACCTTTGTGGATCTCCCTTAACACATAGTCAGCTTCATTTAGGTCTATATACTTCAACAATGGA
1 CACCTTCGTGGATCTCCCTCAACACATAGTCAGCTTCATCTAGGTCTACACACTTCAACAAAGGA
* * *
131363 AGGGTGAAGGATTTCTTATAGAGTTCATCATCAATCAATACATACCTTGCCGCTCTTCA-TTGTC
66 AAGGTGAAGGATTTCTTATAGAGTTCATCATCAATCAACACATACCTTGACGCTC-TCATTTGTC
** *
131427 TAGCTATCGCAACTTTTGGA-TCGGAGGGAGGATTGATCCCTTTCAAGCACTCCACTATCTCAAT
130 TAGCTATCGCAACTTTTGGACT-AAAGGGAGGATTGATCCCTTTCAAACACTCCACTATCTCAAT
131491 CAT
194 CAT
131494 TTAGTTAGAG
Statistics
Matches: 170, Mismatches: 24, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
232 1 0.01
233 166 0.98
234 3 0.02
ACGTcount: A:0.25, C:0.24, G:0.18, T:0.32
Consensus pattern (233 bp):
CACCTTCGTGGATCTCCCTCAACACATAGTCAGCTTCATCTAGGTCTACACACTTCAACAAAGGA
AAGGTGAAGGATTTCTTATAGAGTTCATCATCAATCAACACATACCTTGACGCTCTCATTTGTCT
AGCTATCGCAACTTTTGGACTAAAGGGAGGATTGATCCCTTTCAAACACTCCACTATCTCAATCA
TCCACCTTCGTGGATCGGGCTTACGTTCGGGGGTCTTC
Found at i:133125 original size:99 final size:99
Alignment explanation
Indices: 133017--133477 Score: 300
Period size: 99 Copynumber: 4.7 Consensus size: 99
133007 TCGATGTTGT
* * *
133017 CGTTCTTCCATGTTTAGGTTCTATC-ACCATCAAATCTTTCAAGTCTGTAATCAACGTAAGGATC
1 CGTTCTTCCATGTTCAGGTTCTA-CGGCCATTAAATCTTTCAAGTCTGTAATCAACGTAAGGATC
*
133081 TCCATATATAACACACTT-CCGATCTACGATGTATC
65 TCCATATATAACAC-CTTGCCAATCTACGATGTATC
* * * ** * *
133116 CGTTCTTCCACGTTCGGGTACTACGGTGATTAAATCTTTCAAGTTTGTAATCAACGTAAGTATCT
1 CGTTCTTCCATGTTCAGGTTCTACGGCCATTAAATCTTTCAAGTCTGTAATCAACGTAAGGATCT
* * * * *
133181 ACATATTTGACACTTTGCCAATCTACGATGTTTC
66 CCATATATAACACCTTGCCAATCTACGATGTATC
* * * * * *
133215 CATTCTCCCATGTTCA-GTTCTACGGCCATTAAACCTTTCAAATCTGTAACCAACGCAAGGAT-T
1 CGTTCTTCCATGTTCAGGTTCTACGGCCATTAAATCTTTCAAGTCTGTAATCAACGTAAGGATCT
* ** * * ** *
133278 CGCATATCTAACATTTTTGTCGATCTTTGATGT-TGT
66 C-CATATATAACA-CCTTGCCAATCTACGATGTAT-C
* * * * * ** * * *
133314 CGTACTACCATGTTCGGGTACTACAGCGTTTAAATCTTTCAAGTTTGTAATCAACGCAAGGATTT
1 CGTTCTTCCATGTTCAGGTTCTACGGCCATTAAATCTTTCAAGTCTGTAATCAACGTAAGGATCT
* * * * * *
133379 CCAAATCTAACACTTCTGCCGATCTTCGATGTTTC
66 CCATATATAACACCT-TGCCAATCTACGATGTATC
* * * * **
133414 TGTTC-TCCTATGTTCGGGTTCCAC-G--ATTGAATCTTTCAA---T-TAATCAACACAAGGATC
1 CGTTCTTCC-ATGTTCAGGTTCTACGGCCATTAAATCTTTCAAGTCTGTAATCAACGTAAGGATC
133471 TCCATAT
65 TCCATAT
133478 TTGACACTTC
Statistics
Matches: 287, Mismatches: 65, Indels: 26
0.76 0.17 0.07
Matches are distributed among these distances:
93 21 0.07
94 1 0.00
97 13 0.05
98 50 0.17
99 121 0.42
100 78 0.27
101 3 0.01
ACGTcount: A:0.26, C:0.24, G:0.15, T:0.36
Consensus pattern (99 bp):
CGTTCTTCCATGTTCAGGTTCTACGGCCATTAAATCTTTCAAGTCTGTAATCAACGTAAGGATCT
CCATATATAACACCTTGCCAATCTACGATGTATC
Found at i:135101 original size:17 final size:17
Alignment explanation
Indices: 135079--135111 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
135069 ACCGTGAACT
*
135079 TAACATCCTCAGGTACG
1 TAACATCCTCAAGTACG
135096 TAACATCCTCAAGTAC
1 TAACATCCTCAAGTAC
135112 TTGTTTGATC
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:0.33, C:0.30, G:0.12, T:0.24
Consensus pattern (17 bp):
TAACATCCTCAAGTACG
Found at i:142438 original size:11 final size:11
Alignment explanation
Indices: 142424--142461 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
142414 ATTCATAACA
142424 AATTTATAATT
1 AATTTATAATT
142435 AATTTATAATT
1 AATTTATAATT
142446 -ATTTGATAATT
1 AATTT-ATAATT
*
142457 TATTT
1 AATTT
142462 TATATAGAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
10 4 0.16
11 17 0.68
12 4 0.16
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (11 bp):
AATTTATAATT
Found at i:143029 original size:3 final size:3
Alignment explanation
Indices: 143021--143084 Score: 128
Period size: 3 Copynumber: 21.3 Consensus size: 3
143011 AATTAAACTT
143021 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
143069 TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA T
143085 CCAATAGAAA
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 61 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:148890 original size:19 final size:19
Alignment explanation
Indices: 148870--148906 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
148860 AATTAATTAT
148870 TTTA-ATATTATATTTTTA
1 TTTATATATTATATTTTTA
148888 TTTATATATTATATTTTTA
1 TTTATATATTATATTTTTA
148907 CTTAAAAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 4 0.22
19 14 0.78
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (19 bp):
TTTATATATTATATTTTTA
Found at i:148917 original size:19 final size:19
Alignment explanation
Indices: 148876--148917 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
148866 TTATTTTAAT
* * *
148876 ATTATATTTTTATTTATAT
1 ATTATATTTTTACTTAAAA
148895 ATTATATTTTTACTTAAAA
1 ATTATATTTTTACTTAAAA
148914 ATTA
1 ATTA
148918 CTCGTAATTA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (19 bp):
ATTATATTTTTACTTAAAA
Found at i:149786 original size:31 final size:30
Alignment explanation
Indices: 149710--149786 Score: 93
Period size: 29 Copynumber: 2.6 Consensus size: 30
149700 TGATACCAAA
* * *
149710 TTGTAAGTAGAGGGACTAGATTGACAGTTT
1 TTGTAAGTAGAGGGACTAAATTGACACTCT
* *
149740 TTGT-AGTAGATGGACTAAATTGATCCCTCT
1 TTGTAAGTAGAGGGACTAAATTGA-CACTCT
149770 TTGTAAGTAGAGGGACT
1 TTGTAAGTAGAGGGACT
149787 TGTAGGTATT
Statistics
Matches: 39, Mismatches: 6, Indels: 3
0.81 0.12 0.06
Matches are distributed among these distances:
29 17 0.44
30 11 0.28
31 11 0.28
ACGTcount: A:0.29, C:0.10, G:0.27, T:0.34
Consensus pattern (30 bp):
TTGTAAGTAGAGGGACTAAATTGACACTCT
Found at i:154279 original size:91 final size:91
Alignment explanation
Indices: 154162--154337 Score: 343
Period size: 91 Copynumber: 1.9 Consensus size: 91
154152 AAGCTACATC
154162 TTAATTTCAACTCCATTTCCTCAAAAAAGTATAGAATAAATTACATTCTATCGTATTATCATTGT
1 TTAATTTCAACTCCATTTCCTCAAAAAAGTATAGAATAAATTACATTCTATCGTATTATCATTGT
154227 GGCATGCAGGAGTGGGATTAATCAAT
66 GGCATGCAGGAGTGGGATTAATCAAT
*
154253 TTAATTTCAACTCCATTTCCTCAAAAAAGTATAGAATAGATTACATTCTATCGTATTATCATTGT
1 TTAATTTCAACTCCATTTCCTCAAAAAAGTATAGAATAAATTACATTCTATCGTATTATCATTGT
154318 GGCATGCAGGAGTGGGATTA
66 GGCATGCAGGAGTGGGATTA
154338 TTCTGCAGTA
Statistics
Matches: 84, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
91 84 1.00
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.35
Consensus pattern (91 bp):
TTAATTTCAACTCCATTTCCTCAAAAAAGTATAGAATAAATTACATTCTATCGTATTATCATTGT
GGCATGCAGGAGTGGGATTAATCAAT
Found at i:158349 original size:78 final size:79
Alignment explanation
Indices: 158208--158355 Score: 219
Period size: 78 Copynumber: 1.9 Consensus size: 79
158198 TACGACTATC
* **
158208 GGGAAACTTTTAAAAATTGATGATAATATCCTTACTTTCTAAAAAATATTTCCGACATGCCATTA
1 GGGAAACTTTT-AAAATTGACGATAATATCCTTACTTTCTAAAAAATATTTCCGACACACCATTA
158273 CTTAAGACGAATGTT
65 CTTAAGACGAATGTT
* *
158288 GGGAAACTTTT-AAATTGACGATAATA-CCATTATTTTCTAAAAAATATTTCTGACACACCATTA
1 GGGAAACTTTTAAAATTGACGATAATATCC-TTACTTTCTAAAAAATATTTCCGACACACCATTA
158351 CTTAA
65 CTTAA
158356 AAGAGTTACT
Statistics
Matches: 62, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
77 2 0.03
78 49 0.79
80 11 0.18
ACGTcount: A:0.39, C:0.16, G:0.11, T:0.35
Consensus pattern (79 bp):
GGGAAACTTTTAAAATTGACGATAATATCCTTACTTTCTAAAAAATATTTCCGACACACCATTAC
TTAAGACGAATGTT
Found at i:163360 original size:21 final size:21
Alignment explanation
Indices: 163334--163381 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
163324 TGAAATTATG
*
163334 AGATTAAATACTATACAGATC
1 AGATTAAATAATATACAGATC
* * *
163355 AGATTAGATAATGTACAGATG
1 AGATTAAATAATATACAGATC
163376 AGATTA
1 AGATTA
163382 TAATCAGCGG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.46, C:0.08, G:0.17, T:0.29
Consensus pattern (21 bp):
AGATTAAATAATATACAGATC
Found at i:163550 original size:21 final size:20
Alignment explanation
Indices: 163520--163568 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 20
163510 TTCTAAAAAA
163520 AATTATTTTATTT-TCTTATT
1 AATTATTTTATTTAT-TTATT
163540 AATTAATTTTATTTATTTATT
1 AATT-ATTTTATTTATTTATT
163561 AAATTATT
1 -AATTATT
163569 ATATATGTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
20 4 0.15
21 17 0.65
22 5 0.19
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (20 bp):
AATTATTTTATTTATTTATT
Found at i:163696 original size:20 final size:20
Alignment explanation
Indices: 163671--163723 Score: 58
Period size: 20 Copynumber: 2.6 Consensus size: 20
163661 TTATTTAACT
163671 TATAAATCAAATAAGA-T-AAA
1 TATAAAT-AAATAA-ATTAAAA
163691 TATAAAATAAATAAATTAAAA
1 TAT-AAATAAATAAATTAAAA
163712 TATAAA-AAATAA
1 TATAAATAAATAA
163724 TAGAAGACGT
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
19 7 0.23
20 13 0.43
21 10 0.33
ACGTcount: A:0.70, C:0.02, G:0.02, T:0.26
Consensus pattern (20 bp):
TATAAATAAATAAATTAAAA
Found at i:168133 original size:27 final size:27
Alignment explanation
Indices: 168054--168126 Score: 137
Period size: 27 Copynumber: 2.7 Consensus size: 27
168044 TATAAAAACC
168054 AAGAGAAAAAACCCTAATTTTTTTTATA
1 AAGAG-AAAAACCCTAATTTTTTTTATA
168082 AAGAGAAAAACCCTAATTTTTTTTATA
1 AAGAGAAAAACCCTAATTTTTTTTATA
168109 AAGAGAAAAACCCTAATT
1 AAGAGAAAAACCCTAATT
168127 AAATTTAGGA
Statistics
Matches: 45, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
27 40 0.89
28 5 0.11
ACGTcount: A:0.48, C:0.12, G:0.08, T:0.32
Consensus pattern (27 bp):
AAGAGAAAAACCCTAATTTTTTTTATA
Found at i:169724 original size:30 final size:30
Alignment explanation
Indices: 169690--169749 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
169680 TTGCCATGAT
* *
169690 AACAGAGGAGTATGGA-ATAATATCATGTGA
1 AACAGAGGAGGA-GGATAGAATATCATGTGA
169720 AACAGAGGAGGAGGATAGAATATCATGTGA
1 AACAGAGGAGGAGGATAGAATATCATGTGA
169750 TGAAGTCCTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
29 3 0.11
30 24 0.89
ACGTcount: A:0.43, C:0.07, G:0.30, T:0.20
Consensus pattern (30 bp):
AACAGAGGAGGAGGATAGAATATCATGTGA
Found at i:172412 original size:178 final size:177
Alignment explanation
Indices: 172143--172469 Score: 469
Period size: 178 Copynumber: 1.8 Consensus size: 177
172133 CCGATTAGGG
* * *
172143 TGATTTAAGTGTCTATTAAAAGATTGTTCCATTATCTACAACTTTCATGAAGGACTCAAAAACTA
1 TGATTCAAGTGTCTATTAAAAGATTGTTCCATGATCTACAACTTTCATGAAGAACTCAAAAACTA
* * * * * *
172208 AATTTAATGTTTCAAGTATCAAAAATGCTTCCGAAA-TATTTGTTGTTTCGGTTAACGGGAATAG
66 AATTTAATGATTCAAGTATAAAAAATGATTCC-AAAGAATTAGTTGTTTCGGTTAACGGAAATAG
*
172272 ACGGTCCACTTAATATTATATAAATTTCACTCCAAATGTTTGATTGAGA
130 ACAGTCCACTTAATA-TATATAAATTTCACTCCAAATGTTTGATTGAGA
* * * *
172321 TGATTCAAGTGTCTCTTGAAAGGTTGTTCCATGATCTACAACTTTCATGAAGAACTCGAAAACTA
1 TGATTCAAGTGTCTATTAAAAGATTGTTCCATGATCTACAACTTTCATGAAGAACTCAAAAACTA
172386 AATTTAAT-ATTCAAGGTATAAAAAATGATTCCAAAGAATTAGTTGTTTCGGTTAACGGAAATAG
66 AATTTAATGATTCAA-GTATAAAAAATGATTCCAAAGAATTAGTTGTTTCGGTTAACGGAAATAG
* *
172450 ATAGTCTACTTAATATATAT
130 ACAGTCCACTTAATATATAT
172470 TACATAATTT
Statistics
Matches: 131, Mismatches: 16, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
177 13 0.10
178 118 0.90
ACGTcount: A:0.36, C:0.13, G:0.15, T:0.35
Consensus pattern (177 bp):
TGATTCAAGTGTCTATTAAAAGATTGTTCCATGATCTACAACTTTCATGAAGAACTCAAAAACTA
AATTTAATGATTCAAGTATAAAAAATGATTCCAAAGAATTAGTTGTTTCGGTTAACGGAAATAGA
CAGTCCACTTAATATATATAAATTTCACTCCAAATGTTTGATTGAGA
Found at i:175340 original size:27 final size:27
Alignment explanation
Indices: 175290--175342 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
175280 AATTCATCAC
* **
175290 AAATCTTAATGCTTTTTTTTTGAAGGA
1 AAATCTTAATGCTTATTTGATGAAGGA
175317 AAATCTTAATGCTTATTTGATGAAGG
1 AAATCTTAATGCTTATTTGATGAAGG
175343 TTACTTTCTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.32, C:0.08, G:0.17, T:0.43
Consensus pattern (27 bp):
AAATCTTAATGCTTATTTGATGAAGGA
Found at i:175747 original size:3 final size:3
Alignment explanation
Indices: 175733--175817 Score: 81
Period size: 3 Copynumber: 29.7 Consensus size: 3
175723 AGGTAATATG
175733 TAA TATA TAA TAA TAA TAA TAA TAA T-A TAA TAA TAA TAA TAA T-A
1 TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
** ** *
175777 TAA TGG TAA T-A TTT TAA -AA -AA TAA TAA TAA TAA TAG TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
175818 GATGTTAGTA
Statistics
Matches: 68, Mismatches: 9, Indels: 10
0.78 0.10 0.11
Matches are distributed among these distances:
2 10 0.15
3 55 0.81
4 3 0.04
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:175760 original size:20 final size:20
Alignment explanation
Indices: 175733--175776 Score: 81
Period size: 20 Copynumber: 2.2 Consensus size: 20
175723 AGGTAATATG
175733 TAAT-ATATAATAATAATAA
1 TAATAATATAATAATAATAA
175752 TAATAATATAATAATAATAA
1 TAATAATATAATAATAATAA
175772 TAATA
1 TAATA
175777 TAATGGTAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 4 0.17
20 20 0.83
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (20 bp):
TAATAATATAATAATAATAA
Found at i:185367 original size:14 final size:14
Alignment explanation
Indices: 185348--185374 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
185338 GTTGATTCAG
185348 ATTTTATTATTATT
1 ATTTTATTATTATT
185362 ATTTTATTATTAT
1 ATTTTATTATTAT
185375 GCATAAAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (14 bp):
ATTTTATTATTATT
Found at i:185600 original size:19 final size:19
Alignment explanation
Indices: 185576--185621 Score: 58
Period size: 21 Copynumber: 2.4 Consensus size: 19
185566 ATTTATTCAA
*
185576 TAAATTTTA-TATTATTAT
1 TAAATTTTACTATTATGAT
185594 TATAATTTTACCTATTATGAT
1 TA-AATTTTA-CTATTATGAT
185615 TAAATTT
1 TAAATTT
185622 GTTAAACTTC
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
18 2 0.08
19 7 0.29
20 5 0.21
21 10 0.42
ACGTcount: A:0.37, C:0.04, G:0.02, T:0.57
Consensus pattern (19 bp):
TAAATTTTACTATTATGAT
Found at i:186845 original size:129 final size:129
Alignment explanation
Indices: 186673--186940 Score: 380
Period size: 131 Copynumber: 2.1 Consensus size: 129
186663 ATAATGTCAT
* * *
186673 TTATGAAATATATTTTAAAAATTCTAATATATCTAAGTTTTTT-AATTAAATTAGTAAAATGGT-
1 TTAT-AAAAATATATTAAAAATTCTAATATA-CTAAGTTTTTTAAATTAAAATAGTAAAATGGTA
* *
186736 AAAATAAAATAGGTATAAAGATATTAGATATGATTAAATAGAAATAGAGTTTTTAGTTGAGTAAA
64 AAAATAAAATAGGTATAAAGATATTAGATATAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAA
186801 A
129 A
186802 TTATAAAAATATATTAAAAAGTTCTAATATA-TAAGTTTTTTTTAAATTAAAATAGTAAAATGGT
1 TTATAAAAATATATTAAAAA-TTCTAATATACTAAG--TTTTTTAAATTAAAATAGTAAAATGGT
* * * *
186866 AAAAATAAAATAGTTATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTGGTTGAGTAA
63 AAAAATAAAATAGGTATAAAGATATTAGATATAATTAAATAAAAATAGAGTTTTTAGTTGAGTAA
186931 AA
128 AA
*
186933 CTATAAAA
1 TTATAAAA
186941 GTTTAAACAA
Statistics
Matches: 124, Mismatches: 10, Indels: 8
0.87 0.07 0.06
Matches are distributed among these distances:
127 4 0.03
128 14 0.11
129 20 0.16
130 19 0.15
131 67 0.54
ACGTcount: A:0.49, C:0.01, G:0.12, T:0.38
Consensus pattern (129 bp):
TTATAAAAATATATTAAAAATTCTAATATACTAAGTTTTTTAAATTAAAATAGTAAAATGGTAAA
AATAAAATAGGTATAAAGATATTAGATATAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAA
Found at i:193713 original size:12 final size:12
Alignment explanation
Indices: 193696--193721 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
193686 AATATTTGGA
193696 ATCATTATTATT
1 ATCATTATTATT
193708 ATCATTATTATT
1 ATCATTATTATT
193720 AT
1 AT
193722 TATGTATATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.35, C:0.08, G:0.00, T:0.58
Consensus pattern (12 bp):
ATCATTATTATT
Found at i:195468 original size:42 final size:43
Alignment explanation
Indices: 195413--195507 Score: 131
Period size: 45 Copynumber: 2.2 Consensus size: 43
195403 AGTGCATTAC
*
195413 CTAA-ATTATA-CTCCATCTCTAGGTAATTCATCAAAATAAAG
1 CTAATATTATACCTCCATCTCTAGATAATTCATCAAAATAAAG
* *
195454 CTAATATTCTACTCCTCCATCTCTTGATAATTCATCAAAATAAAG
1 CTAATATTATA--CCTCCATCTCTAGATAATTCATCAAAATAAAG
195499 CTAATATTA
1 CTAATATTA
195508 ATTGTTGCTT
Statistics
Matches: 46, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
41 4 0.09
42 5 0.11
45 37 0.80
ACGTcount: A:0.39, C:0.21, G:0.05, T:0.35
Consensus pattern (43 bp):
CTAATATTATACCTCCATCTCTAGATAATTCATCAAAATAAAG
Done.