Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015311.1 Kokia drynarioides strain JFW-HI SEQ_130356, 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: 296063
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 393 characters in sequence are not A, C, G, or T
Found at i:1590 original size:15 final size:15
Alignment explanation
Indices: 1570--1615 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
1560 ACAATATATT
1570 AACATAAGTGATTAA
1 AACATAAGTGATTAA
*
1585 AACATAA-T-ATTTTA
1 AACATAAGTGA-TTAA
*
1599 AATATAAGTGATTAA
1 AACATAAGTGATTAA
1614 AA
1 AA
1616 TGTAATTTGA
Statistics
Matches: 25, Mismatches: 3, Indels: 6
0.74 0.09 0.18
Matches are distributed among these distances:
13 1 0.04
14 10 0.40
15 13 0.52
16 1 0.04
ACGTcount: A:0.54, C:0.04, G:0.09, T:0.33
Consensus pattern (15 bp):
AACATAAGTGATTAA
Found at i:12377 original size:23 final size:20
Alignment explanation
Indices: 12342--12385 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 20
12332 ACTATCAAAC
*
12342 ATATATAAATTTATAATTCAA
1 ATATATAAATTTA-AATACAA
12363 ATATATAACAGTTTAAATACAA
1 ATATATAA-A-TTTAAATACAA
12385 A
1 A
12386 CAAACCATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 8 0.40
22 8 0.40
23 4 0.20
ACGTcount: A:0.55, C:0.07, G:0.02, T:0.36
Consensus pattern (20 bp):
ATATATAAATTTAAATACAA
Found at i:20024 original size:19 final size:17
Alignment explanation
Indices: 19988--20021 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
19978 ATAAATACAA
*
19988 TATAATTACATGTATAT
1 TATAATTACATATATAT
*
20005 TATAATTACAAATATAT
1 TATAATTACATATATAT
20022 ATTTAAGAAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.47, C:0.06, G:0.03, T:0.44
Consensus pattern (17 bp):
TATAATTACATATATAT
Found at i:29811 original size:6 final size:6
Alignment explanation
Indices: 29800--29825 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
29790 ATCCTCAACA
29800 TCAGCC TCAGCC TCAGCC TCAGCC TC
1 TCAGCC TCAGCC TCAGCC TCAGCC TC
29826 GTGCTCACTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.15, C:0.50, G:0.15, T:0.19
Consensus pattern (6 bp):
TCAGCC
Found at i:35160 original size:15 final size:15
Alignment explanation
Indices: 35140--35169 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
35130 TTCAAAATGA
*
35140 AAAAAATTATTTTTT
1 AAAAAATAATTTTTT
35155 AAAAAATAATTTTTT
1 AAAAAATAATTTTTT
35170 TTTAAATAAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
AAAAAATAATTTTTT
Found at i:35165 original size:18 final size:18
Alignment explanation
Indices: 35139--35180 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
35129 ATTCAAAATG
35139 AAAAA-AATTATTTTTTA
1 AAAAATAATTATTTTTTA
*
35156 AAAAATAATTTTTTTTTA
1 AAAAATAATTATTTTTTA
*
35174 AATAATA
1 AAAAATA
35181 CACATGTGCT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 5 0.23
18 17 0.77
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (18 bp):
AAAAATAATTATTTTTTA
Found at i:35261 original size:17 final size:17
Alignment explanation
Indices: 35239--35271 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
35229 TTATATATTC
*
35239 TAATTAATTTTTATAGA
1 TAATTAATATTTATAGA
35256 TAATTAATATTTATAG
1 TAATTAATATTTATAG
35272 CTTAAAATTA
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:0.42, C:0.00, G:0.06, T:0.52
Consensus pattern (17 bp):
TAATTAATATTTATAGA
Found at i:36892 original size:29 final size:31
Alignment explanation
Indices: 36818--36895 Score: 124
Period size: 31 Copynumber: 2.6 Consensus size: 31
36808 TTTCTGATCC
*
36818 AATTTGGTACTCAAACTTGACACATTTTCTT
1 AATTTGGTACTTAAACTTGACACATTTTCTT
*
36849 AATTTGGTACCTAAACTTGACAC-TTTT-TT
1 AATTTGGTACTTAAACTTGACACATTTTCTT
36878 AATTTGGTACTTAAACTT
1 AATTTGGTACTTAAACTT
36896 TTTGGGGTCC
Statistics
Matches: 44, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
29 19 0.43
30 4 0.09
31 21 0.48
ACGTcount: A:0.29, C:0.17, G:0.10, T:0.44
Consensus pattern (31 bp):
AATTTGGTACTTAAACTTGACACATTTTCTT
Found at i:36911 original size:88 final size:90
Alignment explanation
Indices: 36760--36950 Score: 244
Period size: 88 Copynumber: 2.1 Consensus size: 90
36750 TTAATATATC
* * ** * *
36760 ATTTGGTACCTGAATTTGACACTTTTTCTTAATTTGGTGTTTAAATTTTTTCTGATCCAATTTGG
1 ATTTGGTACCTAAACTTGACACTTTTTCTTAATTTGGTACTTAAACTTTTTCGGATCCAATTTGG
*
36825 TAC-TCAAACTTGACACATTTTCTTA
66 TACAT-AAACTTGACACATTTTCCTA
* *
36850 ATTTGGTACCTAAACTTGACAC-TTTT-TTAATTTGGTACTTAAACTTTTTGGGGTCCAATTTGG
1 ATTTGGTACCTAAACTTGACACTTTTTCTTAATTTGGTACTTAAACTTTTTCGGATCCAATTTGG
* * *
36913 TACATGAACTTGACTCTTTTTCCTA
66 TACATAAACTTGACACATTTTCCTA
36938 ATTTGGTACCTAA
1 ATTTGGTACCTAA
36951 TTTTTTTTAA
Statistics
Matches: 88, Mismatches: 12, Indels: 4
0.85 0.12 0.04
Matches are distributed among these distances:
88 63 0.72
89 5 0.06
90 20 0.23
ACGTcount: A:0.25, C:0.16, G:0.14, T:0.46
Consensus pattern (90 bp):
ATTTGGTACCTAAACTTGACACTTTTTCTTAATTTGGTACTTAAACTTTTTCGGATCCAATTTGG
TACATAAACTTGACACATTTTCCTA
Found at i:39143 original size:23 final size:23
Alignment explanation
Indices: 39115--39165 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 23
39105 TTAAATTTAT
*
39115 ATTTAATAT-TTAATATAAACATG
1 ATTTAA-ATGTTAAGATAAACATG
* *
39138 ATTTAAATGTTAAGATAAATATT
1 ATTTAAATGTTAAGATAAACATG
39161 ATTTA
1 ATTTA
39166 TCTTTTTTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 2 0.08
23 22 0.92
ACGTcount: A:0.47, C:0.02, G:0.06, T:0.45
Consensus pattern (23 bp):
ATTTAAATGTTAAGATAAACATG
Found at i:39344 original size:30 final size:28
Alignment explanation
Indices: 39310--39365 Score: 76
Period size: 28 Copynumber: 1.9 Consensus size: 28
39300 TATATCTTCA
39310 ATATAAATAATACCCAAAAAATATATATGG
1 ATAT-AATAATA-CCAAAAAATATATATGG
* *
39340 ATATAATAATATCTAAAAATATATAT
1 ATATAATAATACCAAAAAATATATAT
39366 TGTGTACAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 13 0.54
29 7 0.29
30 4 0.17
ACGTcount: A:0.57, C:0.07, G:0.04, T:0.32
Consensus pattern (28 bp):
ATATAATAATACCAAAAAATATATATGG
Found at i:40166 original size:30 final size:30
Alignment explanation
Indices: 40130--40281 Score: 162
Period size: 30 Copynumber: 5.0 Consensus size: 30
40120 TCAATTTATC
* * *
40130 GATATGTGAAAGCCTTTGTAGTTGTTCTAT
1 GATATGTGAAAGCCTTTGTGGTTATTCTCT
* *
40160 GATATGT-AGAAGCCATTTGTGGCTGTTCTCT
1 GATATGTGA-AAGCC-TTTGTGGTTATTCTCT
* * *
40191 AATATGTGGAAGCCTTTGTGGTTATTATCT
1 GATATGTGAAAGCCTTTGTGGTTATTCTCT
* *
40221 GATATGTGAAAGCCTTTGTGATTATTCTTT
1 GATATGTGAAAGCCTTTGTGGTTATTCTCT
* * *
40251 GATATGTGGAAGCCTTTGTGGCTATTTTCT
1 GATATGTGAAAGCCTTTGTGGTTATTCTCT
40281 G
1 G
40282 TTACATGTGA
Statistics
Matches: 101, Mismatches: 18, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
29 1 0.01
30 76 0.75
31 24 0.24
ACGTcount: A:0.21, C:0.12, G:0.24, T:0.43
Consensus pattern (30 bp):
GATATGTGAAAGCCTTTGTGGTTATTCTCT
Found at i:54982 original size:40 final size:40
Alignment explanation
Indices: 54893--55046 Score: 132
Period size: 40 Copynumber: 3.9 Consensus size: 40
54883 CTTAATTCCA
* * * **
54893 ACACTGACTCATAGCCTGCTAAGCCATAGCTCGAGTTTAG
1 ACACTGGCTCATAGCCTGTTAAGCCATAGCTTGAAATTAG
* * *
54933 TCACCGGCTCGTAGCCTGTTAAGCCATAGCTTGAAATTAG
1 ACACTGGCTCATAGCCTGTTAAGCCATAGCTTGAAATTAG
* * * *
54973 ACACTGGCTCAAAGCCT-TCTAAGTCGTAGCTTGAAATTAA
1 ACACTGGCTCATAGCCTGT-TAAGCCATAGCTTGAAATTAG
* * * *
55013 ACACAT-ACTCAAAGCCTGCTAAGCCGTAGCTTGA
1 ACAC-TGGCTCATAGCCTGTTAAGCCATAGCTTGA
55047 GTTTATTCAA
Statistics
Matches: 93, Mismatches: 18, Indels: 6
0.79 0.15 0.05
Matches are distributed among these distances:
39 1 0.01
40 91 0.98
41 1 0.01
ACGTcount: A:0.29, C:0.26, G:0.19, T:0.25
Consensus pattern (40 bp):
ACACTGGCTCATAGCCTGTTAAGCCATAGCTTGAAATTAG
Found at i:61026 original size:36 final size:35
Alignment explanation
Indices: 60956--61026 Score: 81
Period size: 36 Copynumber: 2.0 Consensus size: 35
60946 GATGAGGAAC
* *
60956 ATGATGATGAAGAACCGAAAGTAGGGAATGATAGTG
1 ATGATGAGGAAGAA-CGAAAGGAGGGAATGATAGTG
*
60992 ATGATGAGGAAGAA-GAAATGGAGGGGATGAATAGT
1 ATGATGAGGAAGAACGAAA-GGAGGGAATG-ATAGT
61027 TGTTTAAGAC
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
34 4 0.13
35 8 0.27
36 18 0.60
ACGTcount: A:0.42, C:0.03, G:0.37, T:0.18
Consensus pattern (35 bp):
ATGATGAGGAAGAACGAAAGGAGGGAATGATAGTG
Found at i:61775 original size:24 final size:24
Alignment explanation
Indices: 61701--61775 Score: 57
Period size: 24 Copynumber: 3.2 Consensus size: 24
61691 AAAAAAAAGG
*
61701 AGAATTTTTTG-GAATTAGATTCAA
1 AGAATTTTTTGAGAA-TACATTCAA
* * * *
61725 AG-ATTTTTTTA-TATAGCACTCAG
1 AGAATTTTTTGAGAATA-CATTCAA
*
61748 AGAATTTTTTGAGCATACATTCAA
1 AGAATTTTTTGAGAATACATTCAA
61772 AGAA
1 AGAA
61776 AATTCAAAGC
Statistics
Matches: 38, Mismatches: 9, Indels: 8
0.69 0.16 0.15
Matches are distributed among these distances:
22 2 0.05
23 14 0.37
24 19 0.50
25 3 0.08
ACGTcount: A:0.37, C:0.09, G:0.15, T:0.39
Consensus pattern (24 bp):
AGAATTTTTTGAGAATACATTCAA
Found at i:62706 original size:29 final size:29
Alignment explanation
Indices: 62645--62709 Score: 89
Period size: 29 Copynumber: 2.2 Consensus size: 29
62635 GTTTTACGTC
62645 TATAATTGCACCAAATCAAAGTTCATATA
1 TATAATTGCACCAAATCAAAGTTCATATA
*
62674 TATAATTGCACATTAAATCAAAGTTCAT-T-
1 TATAATTGCAC--CAAATCAAAGTTCATATA
62703 TATAATT
1 TATAATT
62710 TTGAAATTTA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
29 18 0.55
30 1 0.03
31 14 0.42
ACGTcount: A:0.43, C:0.14, G:0.06, T:0.37
Consensus pattern (29 bp):
TATAATTGCACCAAATCAAAGTTCATATA
Found at i:62856 original size:24 final size:23
Alignment explanation
Indices: 62806--62863 Score: 70
Period size: 22 Copynumber: 2.7 Consensus size: 23
62796 TATTTACTCC
*
62806 TATTT-ATTAT-TTTTATTGTGT
1 TATTTAATTATATTTAATTGTGT
62827 TA-TTAATTATATTTAATTGTGT
1 TATTTAATTATATTTAATTGTGT
62849 TCATTTAATT-TATTT
1 T-ATTTAATTATATTT
62864 TATTCATGTA
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
20 2 0.06
21 7 0.22
22 11 0.34
23 6 0.19
24 6 0.19
ACGTcount: A:0.26, C:0.02, G:0.07, T:0.66
Consensus pattern (23 bp):
TATTTAATTATATTTAATTGTGT
Found at i:66410 original size:12 final size:12
Alignment explanation
Indices: 66393--66418 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
66383 AAATTTTAAA
66393 AATAAATAAATT
1 AATAAATAAATT
66405 AATAAATAAATT
1 AATAAATAAATT
66417 AA
1 AA
66419 AATAAAAATC
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:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (12 bp):
AATAAATAAATT
Found at i:66427 original size:16 final size:15
Alignment explanation
Indices: 66389--66427 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
66379 TATTAAATTT
*
66389 TAAAAATAAATAAAT
1 TAAAAATAAATAAAA
66404 TAATAAATAAATTAAAA
1 TAA-AAATAAA-TAAAA
66421 TAAAAAT
1 TAAAAAT
66428 CCTCACACAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
15 3 0.14
16 11 0.52
17 7 0.33
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (15 bp):
TAAAAATAAATAAAA
Found at i:70667 original size:24 final size:24
Alignment explanation
Indices: 70638--70816 Score: 211
Period size: 24 Copynumber: 7.5 Consensus size: 24
70628 TTTAACCCAC
*
70638 ACGAGCCCAGAATGATTAGTTCTT
1 ACGAGCCCAGAATGGTTAGTTCTT
* *
70662 ACGAGCCTAGAATGGTTAGCTCTT
1 ACGAGCCCAGAATGGTTAGTTCTT
* *
70686 ACGATCCCAAAATGGTTA-TCTCTT
1 ACGAGCCCAGAATGGTTAGT-TCTT
*
70710 ACGAGCCCAGAATGGTTAGCTCTT
1 ACGAGCCCAGAATGGTTAGTTCTT
* *
70734 ACGAGCCCAAAATGGTTAGCTCTT
1 ACGAGCCCAGAATGGTTAGTTCTT
*
70758 ACGAGCCTAGAATGGTTAGCTT-TT
1 ACGAGCCCAGAATGGTTAG-TTCTT
*
70782 ACGAGCCTAGAATGGTTAGCTT-TT
1 ACGAGCCCAGAATGGTTAG-TTCTT
*
70806 ACAAGCCCAGA
1 ACGAGCCCAGA
70817 CAAAGTTTAA
Statistics
Matches: 136, Mismatches: 16, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
24 135 0.99
25 1 0.01
ACGTcount: A:0.28, C:0.22, G:0.22, T:0.28
Consensus pattern (24 bp):
ACGAGCCCAGAATGGTTAGTTCTT
Found at i:70713 original size:48 final size:48
Alignment explanation
Indices: 70638--70812 Score: 251
Period size: 48 Copynumber: 3.6 Consensus size: 48
70628 TTTAACCCAC
* * *
70638 ACGAGCCCAGAATGATTAGTTCTTACGAGCCTAGAATGGTTAGCTCTT
1 ACGAGCCCAAAATGGTTAGCTCTTACGAGCCTAGAATGGTTAGCTCTT
* * *
70686 ACGATCCCAAAATGGTTATCTCTTACGAGCCCAGAATGGTTAGCTCTT
1 ACGAGCCCAAAATGGTTAGCTCTTACGAGCCTAGAATGGTTAGCTCTT
*
70734 ACGAGCCCAAAATGGTTAGCTCTTACGAGCCTAGAATGGTTAGCTTTT
1 ACGAGCCCAAAATGGTTAGCTCTTACGAGCCTAGAATGGTTAGCTCTT
* * * *
70782 ACGAGCCTAGAATGGTTAGCTTTTACAAGCC
1 ACGAGCCCAAAATGGTTAGCTCTTACGAGCC
70813 CAGACAAAGT
Statistics
Matches: 113, Mismatches: 14, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
48 113 1.00
ACGTcount: A:0.27, C:0.22, G:0.22, T:0.29
Consensus pattern (48 bp):
ACGAGCCCAAAATGGTTAGCTCTTACGAGCCTAGAATGGTTAGCTCTT
Found at i:70721 original size:72 final size:72
Alignment explanation
Indices: 70638--70814 Score: 246
Period size: 72 Copynumber: 2.5 Consensus size: 72
70628 TTTAACCCAC
* * * * *
70638 ACGAGCCCAGAATGATTAGTTCTTACGAGCCTAGAATGGTTAGCTCTTACGATCCCAAAATGGTT
1 ACGAGCCCAGAATGGTTAGCTCTTACGAGCCCAAAATGGTTAGCTCTTACGAGCCCAAAATGGTT
*
70703 ATCTCTT
66 AGCTCTT
* *
70710 ACGAGCCCAGAATGGTTAGCTCTTACGAGCCCAAAATGGTTAGCTCTTACGAGCCTAGAATGGTT
1 ACGAGCCCAGAATGGTTAGCTCTTACGAGCCCAAAATGGTTAGCTCTTACGAGCCCAAAATGGTT
*
70775 AGCTTTT
66 AGCTCTT
* * *
70782 ACGAGCCTAGAATGGTTAGCTTTTACAAGCCCA
1 ACGAGCCCAGAATGGTTAGCTCTTACGAGCCCA
70815 GACAAAGTTT
Statistics
Matches: 93, Mismatches: 12, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
72 93 1.00
ACGTcount: A:0.28, C:0.23, G:0.21, T:0.28
Consensus pattern (72 bp):
ACGAGCCCAGAATGGTTAGCTCTTACGAGCCCAAAATGGTTAGCTCTTACGAGCCCAAAATGGTT
AGCTCTT
Found at i:73464 original size:27 final size:26
Alignment explanation
Indices: 73427--73564 Score: 127
Period size: 26 Copynumber: 5.2 Consensus size: 26
73417 TTTTCAAGAT
* **
73427 TTGCCACAAAGGCTTCCGTTTTATGA
1 TTGCCACAAAGGCTTCCATTCCATGA
*
73453 TATGCCACAAAGGCTTTCATTCCATGA
1 T-TGCCACAAAGGCTTCCATTCCATGA
* *
73480 TTGCCACAAAGGCTTTCATTTCATGA
1 TTGCCACAAAGGCTTCCATTCCATGA
* *
73506 -T-CCACTATAATGGTTTCCATTTCATGA
1 TTGCCAC-A-AA-GGCTTCCATTCCATGA
* * *
73533 ATGCCATAAAGGCTTTCATTCCATGA
1 TTGCCACAAAGGCTTCCATTCCATGA
73559 TTGCCA
1 TTGCCA
73565 TAGAACTCAC
Statistics
Matches: 94, Mismatches: 12, Indels: 12
0.80 0.10 0.10
Matches are distributed among these distances:
24 4 0.04
25 2 0.02
26 45 0.48
27 38 0.40
28 2 0.02
29 3 0.03
ACGTcount: A:0.27, C:0.24, G:0.15, T:0.34
Consensus pattern (26 bp):
TTGCCACAAAGGCTTCCATTCCATGA
Found at i:73491 original size:26 final size:26
Alignment explanation
Indices: 73402--73564 Score: 152
Period size: 27 Copynumber: 6.1 Consensus size: 26
73392 TCATAATACA
* * *
73402 CCACGAAGGCTATTCTTTTCAAGATTTG
1 CCACAAAGGCT-TTCATTTCATGA-TTG
* * *
73430 CCACAAAGGCTTCCGTTTTATGATATG
1 CCACAAAGGCTTTCATTTCATGAT-TG
*
73457 CCACAAAGGCTTTCATTCCATGATTG
1 CCACAAAGGCTTTCATTTCATGATTG
73483 CCACAAAGGCTTTCATTTCATGA-T-
1 CCACAAAGGCTTTCATTTCATGATTG
*
73507 CCACTATAATGG-TTTCCATTTCATGAATG
1 CCAC-A-AA-GGCTTT-CATTTCATGATTG
* *
73536 CCATAAAGGCTTTCATTCCATGATTG
1 CCACAAAGGCTTTCATTTCATGATTG
73562 CCA
1 CCA
73565 TAGAACTCAC
Statistics
Matches: 114, Mismatches: 13, Indels: 18
0.79 0.09 0.12
Matches are distributed among these distances:
24 4 0.04
25 2 0.02
26 46 0.40
27 47 0.41
28 12 0.11
29 3 0.03
ACGTcount: A:0.27, C:0.24, G:0.15, T:0.34
Consensus pattern (26 bp):
CCACAAAGGCTTTCATTTCATGATTG
Found at i:73506 original size:53 final size:56
Alignment explanation
Indices: 73427--73564 Score: 148
Period size: 53 Copynumber: 2.6 Consensus size: 56
73417 TTTTCAAGAT
* * *
73427 TTGCCACAAAGGCTTCCGTTTTATGATATGCCAC-A-AA-GGCTTT-CATTCCATGA
1 TTGCCACAAAGGCTTTCATTTCATGATATGCCACTATAATGG-TTTCCATTCCATGA
*
73480 TTGCCACAAAGGCTTTCATTTCATG--AT-CCACTATAATGGTTTCCATTTCATGA
1 TTGCCACAAAGGCTTTCATTTCATGATATGCCACTATAATGGTTTCCATTCCATGA
* * *
73533 ATGCCATAAAGGCTTTCATTCCATGAT-TGCCA
1 TTGCCACAAAGGCTTTCATTTCATGATATGCCA
73565 TAGAACTCAC
Statistics
Matches: 71, Mismatches: 7, Indels: 12
0.79 0.08 0.13
Matches are distributed among these distances:
50 4 0.06
51 3 0.04
52 5 0.07
53 55 0.77
54 1 0.01
55 3 0.04
ACGTcount: A:0.27, C:0.24, G:0.15, T:0.34
Consensus pattern (56 bp):
TTGCCACAAAGGCTTTCATTTCATGATATGCCACTATAATGGTTTCCATTCCATGA
Found at i:75653 original size:73 final size:73
Alignment explanation
Indices: 75531--75678 Score: 260
Period size: 73 Copynumber: 2.0 Consensus size: 73
75521 TCTGATGATC
* * *
75531 TACAAGAAATCAAACATAACGAATGTAAGCAAATCTTTTCTTAATAAGTTCGTATTAAACTTTAA
1 TACAAGAAATCAAACACAACGAATGTAAGCAAATCTTTTCTTAAAAAGTTCGTATTAAACTTAAA
75596 CTTTAACT
66 CTTTAACT
*
75604 TACAAGAAATCAAACACAATGAATGTAAGCAAATCTTTTCTTAAAAAGTTCGTATTAAACTTAAA
1 TACAAGAAATCAAACACAACGAATGTAAGCAAATCTTTTCTTAAAAAGTTCGTATTAAACTTAAA
75669 CTTTAACT
66 CTTTAACT
75677 TA
1 TA
75679 TTGTAAAGGT
Statistics
Matches: 71, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
73 71 1.00
ACGTcount: A:0.44, C:0.15, G:0.08, T:0.33
Consensus pattern (73 bp):
TACAAGAAATCAAACACAACGAATGTAAGCAAATCTTTTCTTAAAAAGTTCGTATTAAACTTAAA
CTTTAACT
Found at i:75948 original size:27 final size:27
Alignment explanation
Indices: 75918--75997 Score: 90
Period size: 27 Copynumber: 3.0 Consensus size: 27
75908 AATGCTTTTA
*
75918 TGGAAAAATCTGAAAGAATTGCCTTCG
1 TGGAAAAATTTGAAAGAATTGCCTTCG
* * *
75945 TGGAAAACTTTGAAAGGAA-TGTCTTTG
1 TGGAAAAATTTGAAA-GAATTGCCTTCG
* *
75972 TGGCAAAATTTGAAATAATTGCCTTC
1 TGGAAAAATTTGAAAGAATTGCCTTC
75998 ATGGTGAACT
Statistics
Matches: 42, Mismatches: 9, Indels: 4
0.76 0.16 0.07
Matches are distributed among these distances:
26 2 0.05
27 37 0.88
28 3 0.07
ACGTcount: A:0.35, C:0.12, G:0.21, T:0.31
Consensus pattern (27 bp):
TGGAAAAATTTGAAAGAATTGCCTTCG
Found at i:79700 original size:100 final size:100
Alignment explanation
Indices: 79527--79725 Score: 362
Period size: 100 Copynumber: 2.0 Consensus size: 100
79517 ACTTTGCCTA
*
79527 TTTTAAGTCTCAAGAAAAGATGTAACACCCCTTGCCCAACTCAATCATCGGGTCCAAGCTACAAG
1 TTTTAAGTCTCAAGAAAAGATGTAACACCCCTTGCCCAACTCAATCATCAGGTCCAAGCTACAAG
*
79592 ATGCCACATTTATTGTCAAAGCAATTACAAAAATC
66 ATGCCACATTCATTGTCAAAGCAATTACAAAAATC
*
79627 TTTTAAGTCTCAAGAAAAGATGTAACACCCCTTGCCCAACTCAATCATCAGGTCCAAGCTAGAAG
1 TTTTAAGTCTCAAGAAAAGATGTAACACCCCTTGCCCAACTCAATCATCAGGTCCAAGCTACAAG
*
79692 ATGCCACATTCATTGTTAAAGCAATTACAAAAAT
66 ATGCCACATTCATTGTCAAAGCAATTACAAAAAT
79726 TTTCAATAAG
Statistics
Matches: 95, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
100 95 1.00
ACGTcount: A:0.38, C:0.24, G:0.13, T:0.25
Consensus pattern (100 bp):
TTTTAAGTCTCAAGAAAAGATGTAACACCCCTTGCCCAACTCAATCATCAGGTCCAAGCTACAAG
ATGCCACATTCATTGTCAAAGCAATTACAAAAATC
Found at i:82271 original size:51 final size:51
Alignment explanation
Indices: 82186--82425 Score: 268
Period size: 51 Copynumber: 4.6 Consensus size: 51
82176 GCTATAAACG
* * * * *
82186 AAAGAGTCTGATGACTGAGCGTCATCGTGAGTAAATGAATCCTTTACGGATT
1 AAAG-GTCTGATGACTAAGTGTCATCGTGAGTAAATGAATCCATGACGAATT
* *
82238 AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCATGATGAATT
1 AAAGGTCTGATGACTAAGTGTCATCGTGAGTAAATGAATCCATGACGAATT
* *
82289 AAAGTTTTGATGACTAAGTGTCATCGTGAGTAAATGAATCCATGACGAATT
1 AAAGGTCTGATGACTAAGTGTCATCGTGAGTAAATGAATCCATGACGAATT
* * * * **
82340 AAAGGTCTGATGACTCAGTGTTATCATGAGTATATGAATTCCTAT-ACGGAACA
1 AAAGGTCTGATGACTAAGTGTCATCGTGAGTAAATGAA-TCC-ATGAC-GAATT
*
82393 AAGAGGTCCGATGACTATA-TGTCATCGTGAGTA
1 AA-AGGTCTGATGACTA-AGTGTCATCGTGAGTA
82426 TTAAATGAAA
Statistics
Matches: 160, Mismatches: 23, Indels: 8
0.84 0.12 0.04
Matches are distributed among these distances:
51 119 0.74
52 9 0.06
53 7 0.04
54 24 0.15
55 1 0.01
ACGTcount: A:0.33, C:0.14, G:0.23, T:0.29
Consensus pattern (51 bp):
AAAGGTCTGATGACTAAGTGTCATCGTGAGTAAATGAATCCATGACGAATT
Found at i:89693 original size:22 final size:23
Alignment explanation
Indices: 89652--89704 Score: 65
Period size: 22 Copynumber: 2.3 Consensus size: 23
89642 ATAAGGTTTT
* *
89652 TAGTTATTATTATTTATTTGTGA
1 TAGTTAATATTATTTATTTGTCA
89675 TA-TTAATATT-TTTATTTTGTCA
1 TAGTTAATATTATTTA-TTTGTCA
89697 TAGTTAAT
1 TAGTTAAT
89705 TAAAATCAAC
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
21 4 0.15
22 15 0.58
23 7 0.27
ACGTcount: A:0.28, C:0.02, G:0.09, T:0.60
Consensus pattern (23 bp):
TAGTTAATATTATTTATTTGTCA
Found at i:92511 original size:18 final size:18
Alignment explanation
Indices: 92488--92524 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
92478 ATAGCTATGC
92488 ATATTTGCATTTGTTTGT
1 ATATTTGCATTTGTTTGT
92506 ATATTTGCATTTGTTTGT
1 ATATTTGCATTTGTTTGT
92524 A
1 A
92525 CTTGTGGAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.19, C:0.05, G:0.16, T:0.59
Consensus pattern (18 bp):
ATATTTGCATTTGTTTGT
Found at i:110248 original size:25 final size:24
Alignment explanation
Indices: 110220--110278 Score: 57
Period size: 24 Copynumber: 2.4 Consensus size: 24
110210 ATAAAAAACA
*
110220 CTAAAAATATTAAAAGAAATATTTT
1 CTAAAAATATGAAAA-AAATATTTT
* *
110245 CTAACAAAT-TGAAAATAATTTTTT
1 CTAA-AAATATGAAAAAAATATTTT
*
110269 TTAAAAATAT
1 CTAAAAATAT
110279 ATATTTAAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
23 4 0.14
24 11 0.39
25 9 0.32
26 4 0.14
ACGTcount: A:0.53, C:0.05, G:0.03, T:0.39
Consensus pattern (24 bp):
CTAAAAATATGAAAAAAATATTTT
Found at i:123860 original size:2 final size:2
Alignment explanation
Indices: 123853--123877 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
123843 GGTATTTTGT
123853 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 T
123878 TCTATTTATT
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:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:123925 original size:5 final size:5
Alignment explanation
Indices: 123915--123951 Score: 58
Period size: 5 Copynumber: 7.4 Consensus size: 5
123905 TCTTATTTCA
123915 AAAAT AAAAT -AAAT AAATAT AAAAT AAAAT AAAAT AA
1 AAAAT AAAAT AAAAT AAA-AT AAAAT AAAAT AAAAT AA
123952 CAAAAGTTAG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
4 4 0.13
5 21 0.70
6 5 0.17
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (5 bp):
AAAAT
Found at i:132643 original size:58 final size:59
Alignment explanation
Indices: 132561--132711 Score: 200
Period size: 58 Copynumber: 2.6 Consensus size: 59
132551 TTTTAATAAG
* * * *
132561 ATTATTATTAAATATAATTCAATAAAAATAATAAATAATTTAATTATA-TTTTAACATA
1 ATTATTATTAAATAAAATTTAATAAAAATAATAAATAATTTAATAACATTTTTAACATA
* *
132619 ATTATTATTAAATAAAATTTAAT-AAAATAATATATAATTTAATAACATTTTTAATATA
1 ATTATTATTAAATAAAATTTAATAAAAATAATAAATAATTTAATAACATTTTTAACATA
*
132677 ATTATTATTAAAATAAGAA-TTAATAAAAATCATAA
1 ATTATTATT-AAATAA-AATTTAATAAAAATAATAA
132712 TATATAATAT
Statistics
Matches: 81, Mismatches: 8, Indels: 6
0.85 0.08 0.06
Matches are distributed among these distances:
57 21 0.26
58 39 0.48
59 11 0.14
60 10 0.12
ACGTcount: A:0.55, C:0.03, G:0.01, T:0.42
Consensus pattern (59 bp):
ATTATTATTAAATAAAATTTAATAAAAATAATAAATAATTTAATAACATTTTTAACATA
Found at i:134330 original size:6 final size:7
Alignment explanation
Indices: 134295--134333 Score: 69
Period size: 7 Copynumber: 5.6 Consensus size: 7
134285 CAGGAAAAAG
134295 AAGGGGA
1 AAGGGGA
134302 AAGGGGA
1 AAGGGGA
134309 AAGGGGA
1 AAGGGGA
134316 AAGGGGA
1 AAGGGGA
*
134323 AAGGGAA
1 AAGGGGA
134330 AAGG
1 AAGG
134334 TTCTACAAGT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
7 31 1.00
ACGTcount: A:0.46, C:0.00, G:0.54, T:0.00
Consensus pattern (7 bp):
AAGGGGA
Found at i:138821 original size:53 final size:53
Alignment explanation
Indices: 138719--139028 Score: 372
Period size: 53 Copynumber: 5.6 Consensus size: 53
138709 TTCACATTTG
* * *
138719 ATAACTCACGATGACATAGAGTCATCAGACATTTTAATCCGTAATAGGATTCAT
1 ATAACTCACGATGACACAGAGTCATCGGAC-CTTTAATCCGTAATAGGATTCAT
* * *
138773 ATAACTCATGATAACACAGAGTCATCGGACCTTTAATCTGTAATAGGATTCAT
1 ATAACTCACGATGACACAGAGTCATCGGACCTTTAATCCGTAATAGGATTCAT
138826 ATAACTCACGATGACACAGAGTCATCGGACCTTTAATCCGTAATAGGATTCATAATAGGATTCAT
1 ATAACTCACGATGACACAGAGTCATCGGACCTTTAATCC-------G-----TAATAGGATTCAT
*
138891 ATAACTCACGATGACACAGAGTCATCGGACCTTTAATCCGTAATAAGATTCAT
1 ATAACTCACGATGACACAGAGTCATCGGACCTTTAATCCGTAATAGGATTCAT
* * * *
138944 ATAACACACAATGACACAGAATCATTGGACCTTTAATCCGTAATAGGATTCAT
1 ATAACTCACGATGACACAGAGTCATCGGACCTTTAATCCGTAATAGGATTCAT
* *
138997 ATAACTCACGATG--ACATAGTCATCGGATCTTT
1 ATAACTCACGATGACACAGAGTCATCGGACCTTT
139029 TTGCATTTAC
Statistics
Matches: 223, Mismatches: 21, Indels: 27
0.82 0.08 0.10
Matches are distributed among these distances:
51 15 0.07
53 128 0.57
54 26 0.12
58 1 0.00
60 1 0.00
65 52 0.23
ACGTcount: A:0.36, C:0.20, G:0.15, T:0.28
Consensus pattern (53 bp):
ATAACTCACGATGACACAGAGTCATCGGACCTTTAATCCGTAATAGGATTCAT
Found at i:138883 original size:12 final size:12
Alignment explanation
Indices: 138866--138891 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
138856 CTTTAATCCG
138866 TAATAGGATTCA
1 TAATAGGATTCA
138878 TAATAGGATTCA
1 TAATAGGATTCA
138890 TA
1 TA
138892 TAACTCACGA
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:0.42, C:0.08, G:0.15, T:0.35
Consensus pattern (12 bp):
TAATAGGATTCA
Found at i:138917 original size:65 final size:65
Alignment explanation
Indices: 138813--138944 Score: 255
Period size: 65 Copynumber: 2.0 Consensus size: 65
138803 CTTTAATCTG
*
138813 TAATAGGATTCATATAACTCACGATGACACAGAGTCATCGGACCTTTAATCCGTAATAGGATTCA
1 TAATAGGATTCATATAACTCACGATGACACAGAGTCATCGGACCTTTAATCCGTAATAAGATTCA
138878 TAATAGGATTCATATAACTCACGATGACACAGAGTCATCGGACCTTTAATCCGTAATAAGATTCA
1 TAATAGGATTCATATAACTCACGATGACACAGAGTCATCGGACCTTTAATCCGTAATAAGATTCA
138943 TA
1 TA
138945 TAACACACAA
Statistics
Matches: 66, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
65 66 1.00
ACGTcount: A:0.36, C:0.20, G:0.16, T:0.28
Consensus pattern (65 bp):
TAATAGGATTCATATAACTCACGATGACACAGAGTCATCGGACCTTTAATCCGTAATAAGATTCA
Found at i:138974 original size:118 final size:118
Alignment explanation
Indices: 138760--138997 Score: 404
Period size: 118 Copynumber: 2.0 Consensus size: 118
138750 TTTTAATCCG
* * *
138760 TAATAGGATTCATATAACTCATGATAACACAGAGTCATCGGACCTTTAATCTGTAATAGGATTCA
1 TAATAGGATTCATATAACTCACGATAACACAGAGTCATCGGACCTTTAATCCGTAATAAGATTCA
* * *
138825 TATAACTCACGATGACACAGAGTCATCGGACCTTTAATCCGTAATAGGATTCA
66 TATAACACACAATGACACAGAATCATCGGACCTTTAATCCGTAATAGGATTCA
*
138878 TAATAGGATTCATATAACTCACGATGACACAGAGTCATCGGACCTTTAATCCGTAATAAGATTCA
1 TAATAGGATTCATATAACTCACGATAACACAGAGTCATCGGACCTTTAATCCGTAATAAGATTCA
*
138943 TATAACACACAATGACACAGAATCATTGGACCTTTAATCCGTAATAGGATTCA
66 TATAACACACAATGACACAGAATCATCGGACCTTTAATCCGTAATAGGATTCA
138996 TA
1 TA
138998 TAACTCACGA
Statistics
Matches: 112, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
118 112 1.00
ACGTcount: A:0.37, C:0.20, G:0.15, T:0.28
Consensus pattern (118 bp):
TAATAGGATTCATATAACTCACGATAACACAGAGTCATCGGACCTTTAATCCGTAATAAGATTCA
TATAACACACAATGACACAGAATCATCGGACCTTTAATCCGTAATAGGATTCA
Found at i:139005 original size:171 final size:170
Alignment explanation
Indices: 138719--139028 Score: 478
Period size: 171 Copynumber: 1.8 Consensus size: 170
138709 TTCACATTTG
* * * * **
138719 ATAACTCACGATGACATAGAGTCATCAGACATTTTAATCCGTAATAGGATTCATATAACTCATGA
1 ATAACTCACGATGACACAGAGTCATCAGACACTTTAATCCGTAATAAGATTCATATAACACACAA
* *
138784 TAACACAGAGTCATCGGACCTTTAATCTGTAATAGGATTCATATAACTCACGATGACACAGAGTC
66 TAACACAGAATCATCGGACCTTTAATCCGTAATAGGATTCATATAACTCACGATG--ACAGAGTC
138849 ATCGGACCTTTAATCCGTAATAGGATTCATAATAGGATTCAT
129 ATCGGACCTTTAATCCGTAATAGGATTCATAATAGGATTCAT
*
138891 ATAACTCACGATGACACAGAGTCATCGGAC-CTTTAATCCGTAATAAGATTCATATAACACACAA
1 ATAACTCACGATGACACAGAGTCATCAGACACTTTAATCCGTAATAAGATTCATATAACACACAA
* * *
138955 TGACACAGAATCATTGGACCTTTAATCCGTAATAGGATTCATATAACTCACGATGACATAGTCAT
66 TAACACAGAATCATCGGACCTTTAATCCGTAATAGGATTCATATAACTCACGATGACAGAGTCAT
*
139020 CGGATCTTT
131 CGGACCTTT
139029 TTGCATTTAC
Statistics
Matches: 125, Mismatches: 13, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
169 17 0.14
171 80 0.64
172 28 0.22
ACGTcount: A:0.36, C:0.20, G:0.15, T:0.28
Consensus pattern (170 bp):
ATAACTCACGATGACACAGAGTCATCAGACACTTTAATCCGTAATAAGATTCATATAACACACAA
TAACACAGAATCATCGGACCTTTAATCCGTAATAGGATTCATATAACTCACGATGACAGAGTCAT
CGGACCTTTAATCCGTAATAGGATTCATAATAGGATTCAT
Found at i:139797 original size:16 final size:18
Alignment explanation
Indices: 139756--139794 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 18
139746 ATTTTCATCT
139756 TTTATTTTAATTAACCTCC
1 TTTATTTTAATTAA-CTCC
139775 TTTTATTTTAATTAA-TCC
1 -TTTATTTTAATTAACTCC
139793 TT
1 TT
139795 ATTATAAACA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 2 0.11
18 3 0.16
20 14 0.74
ACGTcount: A:0.26, C:0.15, G:0.00, T:0.59
Consensus pattern (18 bp):
TTTATTTTAATTAACTCC
Found at i:141394 original size:49 final size:49
Alignment explanation
Indices: 141304--141497 Score: 219
Period size: 50 Copynumber: 3.9 Consensus size: 49
141294 CATACTGTGA
* * * **
141304 AGATGTGAAGGGAAAGATATGAAGCCGCAAT-GACAAGTCTTGTACCTTAG
1 AGATATGATGGGAAAGAT-TGAAGCCGTAATGGTGAA-TCTTGTACCTTAG
* *
141354 AGATATGATGGGAAAAATTGAAGCCGTAATGGTGAATCTTGTACCCTAG
1 AGATATGATGGGAAAGATTGAAGCCGTAATGGTGAATCTTGTACCTTAG
* * * * * *
141403 AGATGTGAAGGGAAAGATATGAAACCGCAACGATGAATCTTGTACCTTAG
1 AGATATGATGGGAAAGAT-TGAAGCCGTAATGGTGAATCTTGTACCTTAG
* *
141453 AGATATGATGGGAAAGATTGAAGTCGTAATGGCGAATCTTGTACC
1 AGATATGATGGGAAAGATTGAAGCCGTAATGGTGAATCTTGTACC
141498 CTAAAGATTG
Statistics
Matches: 119, Mismatches: 23, Indels: 5
0.81 0.16 0.03
Matches are distributed among these distances:
49 59 0.50
50 60 0.50
ACGTcount: A:0.36, C:0.13, G:0.27, T:0.24
Consensus pattern (49 bp):
AGATATGATGGGAAAGATTGAAGCCGTAATGGTGAATCTTGTACCTTAG
Found at i:141448 original size:50 final size:49
Alignment explanation
Indices: 141304--141510 Score: 220
Period size: 49 Copynumber: 4.2 Consensus size: 49
141294 CATACTGTGA
* * *
141304 AGATGTGAAGGGAAAGATATGAAGCCGCAATGA-CAAGTCTTGTACCTTAG
1 AGATATGAAGGGAAAGAT-TGAAGCCGCAATGATGAA-TCTTGTACCCTAG
* * * *
141354 AGATATGATGGGAAAAATTGAAGCCGTAATGGTGAATCTTGTACCCTAG
1 AGATATGAAGGGAAAGATTGAAGCCGCAATGATGAATCTTGTACCCTAG
* * * *
141403 AGATGTGAAGGGAAAGATATGAAACCGCAACGATGAATCTTGTACCTTAG
1 AGATATGAAGGGAAAGAT-TGAAGCCGCAATGATGAATCTTGTACCCTAG
* * * ** *
141453 AGATATGATGGGAAAGATTGAAGTCGTAATGGCGAATCTTGTACCCTAA
1 AGATATGAAGGGAAAGATTGAAGCCGCAATGATGAATCTTGTACCCTAG
141502 AGAT-TGAAG
1 AGATATGAAG
141511 CCGTAGTGGT
Statistics
Matches: 129, Mismatches: 26, Indels: 6
0.80 0.16 0.04
Matches are distributed among these distances:
48 4 0.03
49 66 0.51
50 59 0.46
ACGTcount: A:0.36, C:0.13, G:0.27, T:0.24
Consensus pattern (49 bp):
AGATATGAAGGGAAAGATTGAAGCCGCAATGATGAATCTTGTACCCTAG
Found at i:141475 original size:99 final size:99
Alignment explanation
Indices: 141303--141510 Score: 330
Period size: 99 Copynumber: 2.1 Consensus size: 99
141293 CCATACTGTG
* *
141303 AAGATGTGAAGGGAAAGATATGAAGCCGCAATGACAAGTCTTGTACCTTAGAGATATGATGGGAA
1 AAGATGTGAAGGGAAAGATATGAAACCGCAACGACAAGTCTTGTACCTTAGAGATATGATGGGAA
*
141368 AAATTGAAGCCGTAATGGTGAATCTTGTACCCTA
66 AAATTGAAGCCGTAATGGCGAATCTTGTACCCTA
* *
141402 GAGATGTGAAGGGAAAGATATGAAACCGCAACGATGAA-TCTTGTACCTTAGAGATATGATGGGA
1 AAGATGTGAAGGGAAAGATATGAAACCGCAACGA-CAAGTCTTGTACCTTAGAGATATGATGGGA
* *
141466 AAGATTGAAGTCGTAATGGCGAATCTTGTACCCTA
65 AAAATTGAAGCCGTAATGGCGAATCTTGTACCCTA
141501 AAGAT-TGAAG
1 AAGATGTGAAG
141511 CCGTAGTGGT
Statistics
Matches: 100, Mismatches: 8, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
98 5 0.05
99 93 0.93
100 2 0.02
ACGTcount: A:0.37, C:0.12, G:0.27, T:0.24
Consensus pattern (99 bp):
AAGATGTGAAGGGAAAGATATGAAACCGCAACGACAAGTCTTGTACCTTAGAGATATGATGGGAA
AAATTGAAGCCGTAATGGCGAATCTTGTACCCTA
Found at i:142146 original size:4 final size:4
Alignment explanation
Indices: 142137--142171 Score: 52
Period size: 4 Copynumber: 8.2 Consensus size: 4
142127 ATTGTTTTTA
142137 TATT TATT TATT TATT TATT TATAT TATTT TATT T
1 TATT TATT TATT TATT TATT TAT-T TA-TT TATT T
142172 GTTTCATGTA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
4 22 0.76
5 6 0.21
6 1 0.03
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (4 bp):
TATT
Found at i:159615 original size:15 final size:14
Alignment explanation
Indices: 159590--159619 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
159580 CATTTCTTTA
159590 TTTCATTTTATTTG
1 TTTCATTTTATTTG
159604 TTTCACTTTTATTTG
1 TTTCA-TTTTATTTG
159619 T
1 T
159620 GTTGTTTCAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.33
15 10 0.67
ACGTcount: A:0.13, C:0.10, G:0.07, T:0.70
Consensus pattern (14 bp):
TTTCATTTTATTTG
Found at i:161442 original size:16 final size:16
Alignment explanation
Indices: 161421--161463 Score: 79
Period size: 16 Copynumber: 2.8 Consensus size: 16
161411 ATGATCAGTT
161421 GAAGGAGAAGGATCAA
1 GAAGGAGAAGGATCAA
161437 GAAGGAGAAGGATCAA
1 GAAGGAGAAGGATCAA
161453 GAAGG-GAAGGA
1 GAAGGAGAAGGA
161464 AAAAGAAATT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 6 0.22
16 21 0.78
ACGTcount: A:0.49, C:0.05, G:0.42, T:0.05
Consensus pattern (16 bp):
GAAGGAGAAGGATCAA
Found at i:163590 original size:13 final size:13
Alignment explanation
Indices: 163572--163605 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
163562 TTCTTCTTAA
*
163572 ATGATGATGGATT
1 ATGATGATGAATT
163585 ATGATGATGAATT
1 ATGATGATGAATT
*
163598 TTGATGAT
1 ATGATGAT
163606 ATTAAATGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.26, T:0.41
Consensus pattern (13 bp):
ATGATGATGAATT
Found at i:166330 original size:45 final size:45
Alignment explanation
Indices: 166275--166442 Score: 183
Period size: 45 Copynumber: 3.7 Consensus size: 45
166265 CATTGGCTAG
* * ***
166275 AAAAATGAGTAAGACCATAGTTGAAAGATGTTATGGCATCATGAT
1 AAAAATGAATAAGACCATAGCTGAAAGACACTATGGCATCATGAT
** * * * *
166320 TCAGATGAGTAAGACCATAGCTGAAAGACACTATGACATCAAGAT
1 AAAAATGAATAAGACCATAGCTGAAAGACACTATGGCATCATGAT
* * *
166365 AAAAATGAATAAGACCATGGCTGAAAGACACTGTGGCATCATGAC
1 AAAAATGAATAAGACCATAGCTGAAAGACACTATGGCATCATGAT
** *
166410 GGAAATGAATAAGACCATAGTTGAAAGACACTA
1 AAAAATGAATAAGACCATAGCTGAAAGACACTA
166443 GGGATTCATA
Statistics
Matches: 100, Mismatches: 23, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
45 100 1.00
ACGTcount: A:0.43, C:0.14, G:0.21, T:0.21
Consensus pattern (45 bp):
AAAAATGAATAAGACCATAGCTGAAAGACACTATGGCATCATGAT
Found at i:178873 original size:67 final size:66
Alignment explanation
Indices: 178802--179014 Score: 155
Period size: 67 Copynumber: 3.1 Consensus size: 66
178792 TTAATTCATA
*
178802 CAAAATATTAATTGTATATATTTTATCTAATTTATTAATATAAACAATTATATTAATTAATTTCG
1 CAAAATATTAATTGTATATATTTTA-CTAATTTATTAATATAAAAAATTATATTAATTAATTTCG
178867 GT
65 GT
** * ** * * * * *
178869 CAAAATA-TAAAAG-ACATGAAAATTAATATTTTTTTGAAAAAAATAAAATTAATATATGAATTT
1 CAAAATATTAATTGTATAT--ATTTTACTAATTTATT-AATATAA-AAAATT-ATAT-T-AA-TT
* *
178932 GA-TTC-AT
58 AATTTCGGT
* * *
178939 ACAAAATATTAATTGTATATATTTTACCAAATTTATTAATATAAATAGTTATATTAATTAATTTC
1 -CAAAATATTAATTGTATATATTTTA-CTAATTTATTAATATAAAAAATTATATTAATTAATTTC
179004 GGT
64 GGT
179007 CAAAATAT
1 CAAAATAT
179015 AAAATACATG
Statistics
Matches: 104, Mismatches: 28, Indels: 28
0.65 0.17 0.17
Matches are distributed among these distances:
65 3 0.03
66 14 0.13
67 29 0.28
68 7 0.07
69 8 0.08
70 6 0.06
71 21 0.20
72 13 0.12
73 3 0.03
ACGTcount: A:0.46, C:0.06, G:0.06, T:0.42
Consensus pattern (66 bp):
CAAAATATTAATTGTATATATTTTACTAATTTATTAATATAAAAAATTATATTAATTAATTTCGG
T
Found at i:179024 original size:138 final size:138
Alignment explanation
Indices: 178777--179330 Score: 853
Period size: 138 Copynumber: 4.0 Consensus size: 138
178767 ACATAGATAA
* * *
178777 AATTAATATATGAATTTAATTCATACAAAATATTAATTGTATATATTTTATCTAATTTATTAATA
1 AATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACCAAATTTATTAATA
* *
178842 TAAACAATTATATTAATTAATTTCGGTCAAAATATAAAAGACATGAAAATTAATATTTTTTTGAA
66 TAAACAGTTATATTAATTAATTTCGATCAAAATATAAAAGACATGAAAATTAATATTTTTTTGAA
* *
178907 AAAAATAA
131 AAGAATAT
178915 AATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACCAAATTTATTAATA
1 AATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACCAAATTTATTAATA
* * * *
178980 TAAATAGTTATATTAATTAATTTCGGTCAAAATATAAAATACATGAAAATTAATA--TTTTTGGA
66 TAAACAGTTATATTAATTAATTTCGATCAAAATATAAAAGACATGAAAATTAATATTTTTTTGAA
179043 AAGAATAT
131 AAGAATAT
* *
179051 AATTAATATATGAATTTGATTCATACAAAATATTAATTGTATTTATATTACCGAAA-TTATTAAT
1 AATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACC-AAATTTATTAAT
* * * * * *
179115 ATAAATAGTTTTATTAATTAATTTCGATAAAAATATAAAAGACATGAAAATTAATATTCTTTCGG
65 ATAAACAGTTATATTAATTAATTTCGATCAAAATATAAAAGACATGAAAATTAATATTTTTTTGA
179180 AAAGAATAT
130 AAAGAATAT
* * *
179189 AATTAATATATGAATTTGATTTATACAAAACATTAATTGTATATATTTTACCTAATTTATTAATA
1 AATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACCAAATTTATTAATA
* * *
179254 TAAACAGTTATATTAATTAATTTCGATCAAAATATAAAAGATATGGAAATTAATGTTTTTTTGAA
66 TAAACAGTTATATTAATTAATTTCGATCAAAATATAAAAGACATGAAAATTAATATTTTTTTGAA
179319 AAGAATAT
131 AAGAATAT
179327 AATT
1 AATT
179331 TATTTTTACA
Statistics
Matches: 381, Mismatches: 31, Indels: 8
0.91 0.07 0.02
Matches are distributed among these distances:
136 123 0.32
137 5 0.01
138 253 0.66
ACGTcount: A:0.47, C:0.05, G:0.07, T:0.41
Consensus pattern (138 bp):
AATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACCAAATTTATTAATA
TAAACAGTTATATTAATTAATTTCGATCAAAATATAAAAGACATGAAAATTAATATTTTTTTGAA
AAGAATAT
Found at i:179266 original size:274 final size:275
Alignment explanation
Indices: 178777--179330 Score: 858
Period size: 274 Copynumber: 2.0 Consensus size: 275
178767 ACATAGATAA
* * * *
178777 AATTAATATATGAATTTAATTCATACAAAATATTAATTGTATATATTTTATCTAATTTATTAATA
1 AATTAATATATGAATTTAATTCATACAAAATATTAATTGTATATATATTACCGAAATTATTAATA
* * * *
178842 TAAACAATTATATTAATTAATTTCGGTCAAAATATAAAAGACATGAAAATTAATATTTTTTTGAA
66 TAAACAATTATATTAATTAATTTCGATAAAAATATAAAAGACATGAAAATTAATATTCTTTCGAA
*
178907 AAAAATAAAATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACCAAATT
131 AAAAATAAAATTAATATATGAATTTGATTCATACAAAACATTAATTGTATATATTTTACCAAATT
* * *
178972 TATTAATATAAATAGTTATATTAATTAATTTCGGTCAAAATATAAAATACATGAAAATTAA-TAT
196 TATTAATATAAACAGTTATATTAATTAATTTCGATCAAAATATAAAAGACATGAAAATTAAGTAT
*
179036 TTTTGGAAAGAATAT
261 TTTTGAAAAGAATAT
* *
179051 AATTAATATATGAATTTGATTCATACAAAATATTAATTGTATTTATATTACCGAAATTATTAATA
1 AATTAATATATGAATTTAATTCATACAAAATATTAATTGTATATATATTACCGAAATTATTAATA
* * * *
179116 TAAATAGTTTTATTAATTAATTTCGATAAAAATATAAAAGACATGAAAATTAATATTCTTTCGGA
66 TAAACAATTATATTAATTAATTTCGATAAAAATATAAAAGACATGAAAATTAATATTCTTTCGAA
* * * *
179181 AAGAATATAATTAATATATGAATTTGATTTATACAAAACATTAATTGTATATATTTTACCTAATT
131 AAAAATAAAATTAATATATGAATTTGATTCATACAAAACATTAATTGTATATATTTTACCAAATT
* * *
179246 TATTAATATAAACAGTTATATTAATTAATTTCGATCAAAATATAAAAGATATGGAAATTAATGTT
196 TATTAATATAAACAGTTATATTAATTAATTTCGATCAAAATATAAAAGACATGAAAATTAA-GTA
179311 TTTTTGAAAAGAATAT
260 TTTTTGAAAAGAATAT
179327 AATT
1 AATT
179331 TATTTTTACA
Statistics
Matches: 252, Mismatches: 26, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
274 232 0.92
276 20 0.08
ACGTcount: A:0.47, C:0.05, G:0.07, T:0.41
Consensus pattern (275 bp):
AATTAATATATGAATTTAATTCATACAAAATATTAATTGTATATATATTACCGAAATTATTAATA
TAAACAATTATATTAATTAATTTCGATAAAAATATAAAAGACATGAAAATTAATATTCTTTCGAA
AAAAATAAAATTAATATATGAATTTGATTCATACAAAACATTAATTGTATATATTTTACCAAATT
TATTAATATAAACAGTTATATTAATTAATTTCGATCAAAATATAAAAGACATGAAAATTAAGTAT
TTTTGAAAAGAATAT
Found at i:179430 original size:62 final size:63
Alignment explanation
Indices: 179318--179442 Score: 173
Period size: 62 Copynumber: 2.0 Consensus size: 63
179308 GTTTTTTTGA
* *
179318 AAAGAATATAATTTATTTTTACAACTTTCCTTTTATCTTCTCTATTAATAAAAGAATAATCCT
1 AAAGAATATAATTTATTTTTACAACTTTCCATTTAGCTTCTCTATTAATAAAAGAATAATCCT
* * **
179381 AAAGAATATAATTTATTTTT-TAACTTTTCATTT-GCATTCTCTATTAATAAGGGAATAATCCT
1 AAAGAATATAATTTATTTTTACAACTTTCCATTTAGC-TTCTCTATTAATAAAAGAATAATCCT
179443 TATTTTCCTT
Statistics
Matches: 55, Mismatches: 6, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
61 1 0.02
62 34 0.62
63 20 0.36
ACGTcount: A:0.37, C:0.13, G:0.06, T:0.45
Consensus pattern (63 bp):
AAAGAATATAATTTATTTTTACAACTTTCCATTTAGCTTCTCTATTAATAAAAGAATAATCCT
Found at i:190839 original size:26 final size:26
Alignment explanation
Indices: 190803--190855 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
190793 TTTCCTTTGT
190803 TTTAATGTGATATTAAGGGGAAAAGC
1 TTTAATGTGATATTAAGGGGAAAAGC
190829 TTTAATGTGATATTAAGGGGAAAAGC
1 TTTAATGTGATATTAAGGGGAAAAGC
190855 T
1 T
190856 ACTAAGGAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.38, C:0.04, G:0.26, T:0.32
Consensus pattern (26 bp):
TTTAATGTGATATTAAGGGGAAAAGC
Found at i:193412 original size:2 final size:2
Alignment explanation
Indices: 193405--193439 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
193395 ATTGGCGCAA
193405 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
193440 ATTAACCCAA
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:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:201443 original size:63 final size:64
Alignment explanation
Indices: 201335--201462 Score: 172
Period size: 63 Copynumber: 2.0 Consensus size: 64
201325 TCTGAATGAA
*
201335 TTCATTTCCATTTTCATTTTGGAGAAAACCACATTAATTTCCAAATG-ATTTCACTTCTCCATT
1 TTCATTTCCATTTTCATTTTGGAGAAAACCACATTAATTTACAAATGTATTTCACTTCTCCATT
* * * *
201398 TTCATTTTCATTTTCATTTTGGAGAAAACCTTA-ATT-ATTTACAAATGTTTTTTATTTCTCCAT
1 TTCATTTCCATTTTCATTTTGGAGAAAACC--ACATTAATTTACAAATGTATTTCACTTCTCCAT
201461 T
64 T
201462 T
1 T
201463 CACCATTTCT
Statistics
Matches: 57, Mismatches: 5, Indels: 5
0.85 0.07 0.07
Matches are distributed among these distances:
63 39 0.68
64 17 0.30
65 1 0.02
ACGTcount: A:0.27, C:0.18, G:0.06, T:0.48
Consensus pattern (64 bp):
TTCATTTCCATTTTCATTTTGGAGAAAACCACATTAATTTACAAATGTATTTCACTTCTCCATT
Found at i:202663 original size:96 final size:96
Alignment explanation
Indices: 202491--202682 Score: 257
Period size: 96 Copynumber: 2.0 Consensus size: 96
202481 TTTTTGGGAA
** *
202491 AAGGATATTCGATTATCTCGATTTGAAGAAAGGTTGCACCTAGTAAGTTAAGGCGTAATATTTCA
1 AAGGATATTCGATTATCTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCGAAATATTTCA
*
202556 GAATCGAAGAT-AAGGAAACATTGCCTCGATT
66 GAATCGAAGATAAAAG-AACATTGCCTCGATT
* *
202587 AAGGGTATTCGATTATTTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCGCAAAT-TTTC
1 AAGGATATTCGATTATCTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCG-AAATATTTC
*
202651 -GAAATTCG-AGATAAAAGAATATTGCCTCGATT
65 AG-AA-TCGAAGATAAAAGAACATTGCCTCGATT
202683 TTAAAGTCTT
Statistics
Matches: 85, Mismatches: 7, Indels: 8
0.85 0.07 0.08
Matches are distributed among these distances:
95 1 0.01
96 75 0.88
97 9 0.11
ACGTcount: A:0.36, C:0.13, G:0.21, T:0.30
Consensus pattern (96 bp):
AAGGATATTCGATTATCTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCGAAATATTTCA
GAATCGAAGATAAAAGAACATTGCCTCGATT
Found at i:203415 original size:29 final size:29
Alignment explanation
Indices: 203383--203785 Score: 378
Period size: 29 Copynumber: 13.8 Consensus size: 29
203373 GAACATCCGG
203383 GGGT-AAAATGGTAATTTTTGGAAGTTTCA
1 GGGTAAAAATGG-AATTTTTGGAAGTTTCA
203412 GGGTCAAAAATGGAATTTTTGGAAG-TTCA
1 GGGT-AAAAATGGAATTTTTGGAAGTTTCA
203441 GGGCTAAAAATGGAATTTTTGGAAG-TTCA
1 GGG-TAAAAATGGAATTTTTGGAAGTTTCA
203470 GGGCTAAAAATGGAATTTTTGGAAG-TTCGA
1 GGG-TAAAAATGGAATTTTTGGAAGTTTC-A
* *
203500 GGGT-AAAATGGGATTTTTTGGAAGTTTGA
1 GGGTAAAAAT-GGAATTTTTGGAAGTTTCA
*
203529 GGGTAAAAATGGAATTTTTGGAAGTTTTA
1 GGGTAAAAATGGAATTTTTGGAAGTTTCA
* *
203558 GGGTTAAAAATGGGATTTTTGGAAG-TTCGGG
1 GGG-TAAAAATGGAATTTTTGGAAGTTTC--A
* * **
203589 GGGTAAAAATAGAATTTTTAGAAGTTTTG
1 GGGTAAAAATGGAATTTTTGGAAGTTTCA
* * *
203618 GGGTCAAAATGGGATTTTTAGAAGTTT-A
1 GGGTAAAAATGGAATTTTTGGAAGTTTCA
* * **
203646 GGGGT-AAAATAGAATTTTTAGAAGTTTTG
1 -GGGTAAAAATGGAATTTTTGGAAGTTTCA
*
203675 GGGTCAAAAATGGGATTTTTGGAAGTTT-A
1 GGGT-AAAAATGGAATTTTTGGAAGTTTCA
* * **
203704 GGGGTAAAAATAGAATTTTTAGAAGTTTTG
1 -GGGTAAAAATGGAATTTTTGGAAGTTTCA
* *
203734 GGGTTAAAAATGGGATTTTTGGAAG-TTCGT
1 GGG-TAAAAATGGAATTTTTGGAAGTTTC-A
*
203764 GGGTAAAAACT-AAATTTTTGGA
1 GGGTAAAAA-TGGAATTTTTGGA
203786 CAATTTAGGG
Statistics
Matches: 321, Mismatches: 33, Indels: 40
0.81 0.08 0.10
Matches are distributed among these distances:
28 29 0.09
29 173 0.54
30 107 0.33
31 12 0.04
ACGTcount: A:0.33, C:0.03, G:0.29, T:0.35
Consensus pattern (29 bp):
GGGTAAAAATGGAATTTTTGGAAGTTTCA
Found at i:203422 original size:58 final size:59
Alignment explanation
Indices: 203265--203790 Score: 287
Period size: 59 Copynumber: 9.0 Consensus size: 59
203255 TTGGATTCTT
* * ** * * * *
203265 GAGGGTGAAATGGTAATTTTGGGAAAATTCGGGGTTAAAAATAGAATTTTTAGATATTC
1 GAGGGTAAAATGGTAATTTTTGGAAGTTTCAGGGTCAAAAATAGAATTTTTGGAAATTC
* * * * *
203324 GAGGGTAAAAGGGTAA-TTTT-GAGAGTTTC-GAAGTCGAAAATAG-AGTTTT-GAACATCC
1 GAGGGTAAAATGGTAATTTTTGGA-AGTTTCAG-GGTCAAAAATAGAATTTTTGGAA-ATTC
* * *
203381 GGGGGTAAAATGGTAATTTTTGGAAGTTTCAGGGTCAAAAATGGAATTTTTGGAAGTTC
1 GAGGGTAAAATGGTAATTTTTGGAAGTTTCAGGGTCAAAAATAGAATTTTTGGAAATTC
* *
203440 -AGGGCTAAAAATGG-AATTTTTGGAAG-TTCAGGG-CTAAAAATGGAATTTTTGGAAGTTC
1 GAGGG-T-AAAATGGTAATTTTTGGAAGTTTCAGGGTC-AAAAATAGAATTTTTGGAAATTC
* * * * * *
203498 GAGGGTAAAATGGGATTTTTTGGAAGTTTGAGGGT-AAAAATGGAATTTTTGGAAGTTT
1 GAGGGTAAAATGGTAATTTTTGGAAGTTTCAGGGTCAAAAATAGAATTTTTGGAAATTC
* * * * * *
203556 TAGGGTTAAAAATGG-GATTTTTGGAAG-TTCGGGGGGT-AAAAATAGAATTTTTAGAAGTTTT
1 GAGGG-T-AAAATGGTAATTTTTGGAAGTTTC--AGGGTCAAAAATAGAATTTTTGGAA-ATTC
* * * * *
203617 G-GGGTCAAAATGG-GATTTTTAGAAGTTT-AGGGGT--AAAATAGAATTTTTAGAAGTTTT
1 GAGGGT-AAAATGGTAATTTTTGGAAGTTTCA-GGGTCAAAAATAGAATTTTTGGAA-ATTC
* * * *
203674 G-GGGTCAAAAATGG-GATTTTTGGAAGTTT-AGGGGT-AAAAATAGAATTTTTAGAAGTTTT
1 GAGGGT--AAAATGGTAATTTTTGGAAGTTTCA-GGGTCAAAAATAGAATTTTTGGAA-ATTC
* *
203733 G-GGGTTAAAAATGG-GATTTTTGGAAG-TTCGTGGGT-AAAAACTA-AATTTTTGGACAATT
1 GAGGG-T-AAAATGGTAATTTTTGGAAGTTTC-AGGGTCAAAAA-TAGAATTTTTGGA-AATT
203791 TAGGGACCTC
Statistics
Matches: 398, Mismatches: 40, Indels: 58
0.80 0.08 0.12
Matches are distributed among these distances:
56 2 0.01
57 61 0.15
58 141 0.35
59 144 0.36
60 47 0.12
61 3 0.01
ACGTcount: A:0.33, C:0.04, G:0.29, T:0.34
Consensus pattern (59 bp):
GAGGGTAAAATGGTAATTTTTGGAAGTTTCAGGGTCAAAAATAGAATTTTTGGAAATTC
Found at i:203449 original size:116 final size:116
Alignment explanation
Indices: 203265--203723 Score: 309
Period size: 117 Copynumber: 3.9 Consensus size: 116
203255 TTGGATTCTT
* * ** * * *
203265 GAGGGTGAAATGGTAATTTTGGGAAAATTCGGGGTTAAAAATAGAATTTTTAGATA-TTCGAGGG
1 GAGGGTAAAATGGTAATTTTTGGAAGTTTCAGGG-TAAAAATGGAATTTTTGGA-AGTTCGAGGG
* *
203329 T-AAAAGGGTAA-TTTT-GAGAGTTTCGAAGTC-GAAAATAG-AGTTTT-GAACATCC
64 TAAAAAGGG-AATTTTTGGA-AG-TTC-AAGGCTAAAAATAGAAGTTTTGGAA-ATCC
*
203381 GGGGGTAAAATGGTAATTTTTGGAAGTTTCAGGGTCAAAAATGGAATTTTTGGAAGTTC-AGGGC
1 GAGGGTAAAATGGTAATTTTTGGAAGTTTCAGGGT-AAAAATGGAATTTTTGGAAGTTCGAGGG-
* * * * * *
203445 TAAAAATGGAATTTTTGGAAGTTCAGGGCTAAAAATGGAATTTTTGGAAGTTC
64 TAAAAAGGGAATTTTTGGAAGTTCAAGGCTAAAAATAGAAGTTTTGGAAATCC
* * * **
203498 GAGGGTAAAATGGGATTTTTTGGAAGTTTGAGGGTAAAAATGGAATTTTTGGAAGTTTTAGGGTT
1 GAGGGTAAAATGGTAATTTTTGGAAGTTTCAGGGTAAAAATGGAATTTTTGGAAGTTCGAGGG-T
** * * * * **
203563 AAAAATGGG-ATTTTTGGAAGTTCGGGGGGTAAAAATAGAATTTTTAGAAGTTTT
65 AAAAA-GGGAATTTTTGGAAGTTC-AAGGCTAAAAATAGAAGTTTTGGAA-ATCC
* * * * *
203617 G-GGGTCAAAATGG-GATTTTTAGAAGTTT-AGGGGT-AAAATAGAATTTTTAGAAGTTTTG-GG
1 GAGGGT-AAAATGGTAATTTTTGGAAGTTTCA-GGGTAAAAATGGAATTTTTGGAAG-TTCGAGG
* * * *
203677 GTCAAAAATGGG-ATTTTTGGAAGTTTAGGGGTAAAAATAGAATTTTT
63 GT-AAAAA-GGGAATTTTTGGAAGTTCAAGGCTAAAAATAGAAGTTTT
203724 AGAAGTTTTG
Statistics
Matches: 289, Mismatches: 37, Indels: 34
0.80 0.10 0.09
Matches are distributed among these distances:
115 9 0.03
116 102 0.35
117 117 0.40
118 51 0.18
119 10 0.03
ACGTcount: A:0.33, C:0.04, G:0.29, T:0.34
Consensus pattern (116 bp):
GAGGGTAAAATGGTAATTTTTGGAAGTTTCAGGGTAAAAATGGAATTTTTGGAAGTTCGAGGGTA
AAAAGGGAATTTTTGGAAGTTCAAGGCTAAAAATAGAAGTTTTGGAAATCC
Found at i:203459 original size:59 final size:58
Alignment explanation
Indices: 203382--203782 Score: 426
Period size: 59 Copynumber: 6.8 Consensus size: 58
203372 TGAACATCCG
* * * *
203382 GGGGT-AAAATGGTAATTTTTGGAAGTTTCAGGGTCAAAAATGGAATTTTTGGAAGTTCA
1 GGGGTAAAAATGG-GATTTTTGGAAGTTTCAGGGT-AAAAATAGAATTTTTAGAAGTTTA
* * * * *
203441 GGGCTAAAAATGGAATTTTTGGAAG-TTCAGGGCTAAAAATGGAATTTTTGGAAG-TTC
1 GGGGTAAAAATGGGATTTTTGGAAGTTTCAGGG-TAAAAATAGAATTTTTAGAAGTTTA
* * *
203498 GAGGGT-AAAATGGGATTTTTTGGAAGTTTGAGGGTAAAAATGGAATTTTTGGAAGTTTTA
1 G-GGGTAAAAATGGGA-TTTTTGGAAGTTTCAGGGTAAAAATAGAATTTTTAGAAG-TTTA
* * *
203558 GGGTTAAAAATGGGATTTTTGGAAG-TTCGGGGGGTAAAAATAGAATTTTTAGAAGTTTT
1 GGGGTAAAAATGGGATTTTTGGAAGTTTC--AGGGTAAAAATAGAATTTTTAGAAGTTTA
* * *
203617 GGGGTCAAAATGGGATTTTTAGAAGTTT-AGGGGT-AAAATAGAATTTTTAGAAGTTTT
1 GGGGTAAAAATGGGATTTTTGGAAGTTTCA-GGGTAAAAATAGAATTTTTAGAAGTTTA
*
203674 GGGGTCAAAAATGGGATTTTTGGAAGTTT-AGGGGTAAAAATAGAATTTTTAGAAGTTTT
1 GGGGT-AAAAATGGGATTTTTGGAAGTTTCA-GGGTAAAAATAGAATTTTTAGAAGTTTA
*
203733 GGGGTTAAAAATGGGATTTTTGGAAG-TTCGTGGGTAAAAACTA-AATTTTT
1 GGGG-TAAAAATGGGATTTTTGGAAGTTTC-AGGGTAAAAA-TAGAATTTTT
203783 GGACAATTTA
Statistics
Matches: 304, Mismatches: 20, Indels: 36
0.84 0.06 0.10
Matches are distributed among these distances:
57 38 0.12
58 96 0.32
59 124 0.41
60 46 0.15
ACGTcount: A:0.33, C:0.03, G:0.29, T:0.35
Consensus pattern (58 bp):
GGGGTAAAAATGGGATTTTTGGAAGTTTCAGGGTAAAAATAGAATTTTTAGAAGTTTA
Found at i:204802 original size:6 final size:6
Alignment explanation
Indices: 204791--204878 Score: 53
Period size: 6 Copynumber: 15.3 Consensus size: 6
204781 AATTAAACAT
*
204791 TTTAAA TTTAAA TTTATAA --TAAA TTTAAA TTTCAAA --TAAA TTTAAT
1 TTTAAA TTTAAA TTTA-AA TTTAAA TTTAAA TTT-AAA TTTAAA TTTAAA
* * * * * *
204837 TTTAAA -ATAAA CTTAAT TTTAAA -ATAAA TTCAAA TTTCAA TT
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TT
204879 GGCCAGATAA
Statistics
Matches: 62, Mismatches: 12, Indels: 16
0.69 0.13 0.18
Matches are distributed among these distances:
4 5 0.08
5 11 0.18
6 41 0.66
7 5 0.08
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (6 bp):
TTTAAA
Found at i:204815 original size:17 final size:17
Alignment explanation
Indices: 204793--204873 Score: 108
Period size: 17 Copynumber: 4.8 Consensus size: 17
204783 TTAAACATTT
*
204793 TAAATTTAAATTTATAA
1 TAAATTTAAATTTAAAA
*
204810 TAAATTTAAATTTCAAA
1 TAAATTTAAATTTAAAA
*
204827 TAAATTTAATTTTAAAA
1 TAAATTTAAATTTAAAA
* *
204844 TAAACTTAATTTTAAAA
1 TAAATTTAAATTTAAAA
*
204861 TAAATTCAAATTT
1 TAAATTTAAATTT
204874 CAATTGGCCA
Statistics
Matches: 56, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 56 1.00
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.44
Consensus pattern (17 bp):
TAAATTTAAATTTAAAA
Found at i:207708 original size:2 final size:2
Alignment explanation
Indices: 207703--207730 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
207693 TATGTGTACT
207703 AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG
207731 TTACAAGTGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:209039 original size:46 final size:47
Alignment explanation
Indices: 208972--209064 Score: 152
Period size: 46 Copynumber: 2.0 Consensus size: 47
208962 GTCAGCTTAT
*
208972 CATTACATCGTTAACGGCAATTAACAACTCAGTGACT-AAATGTTAC
1 CATTACACCGTTAACGGCAATTAACAACTCAGTGACTAAAATGTTAC
* *
209018 CATTACACCGTTAACTGCAATTAACGACTCAGTGACTAAAATGTTAC
1 CATTACACCGTTAACGGCAATTAACAACTCAGTGACTAAAATGTTAC
209065 AATATGTTAA
Statistics
Matches: 43, Mismatches: 3, Indels: 1
0.91 0.06 0.02
Matches are distributed among these distances:
46 34 0.79
47 9 0.21
ACGTcount: A:0.37, C:0.23, G:0.13, T:0.28
Consensus pattern (47 bp):
CATTACACCGTTAACGGCAATTAACAACTCAGTGACTAAAATGTTAC
Found at i:209949 original size:19 final size:18
Alignment explanation
Indices: 209925--210001 Score: 57
Period size: 19 Copynumber: 4.1 Consensus size: 18
209915 TTTTAAAAAT
*
209925 AATTTTTATAATTCTTAAC
1 AATTTTTATAATT-TTAAA
*
209944 AATTTTAATAAATTTTAAA
1 AATTTTTAT-AATTTTAAA
***
209963 ATAGTTTTTATAATTTTTGG
1 A-A-TTTTTATAATTTTAAA
*
209983 ATTTTTTA-AATTTTAAA
1 AATTTTTATAATTTTAAA
210000 AA
1 AA
210002 ATCGTCACTA
Statistics
Matches: 44, Mismatches: 11, Indels: 8
0.70 0.17 0.13
Matches are distributed among these distances:
17 7 0.16
18 6 0.14
19 13 0.30
20 12 0.27
21 6 0.14
ACGTcount: A:0.40, C:0.03, G:0.04, T:0.53
Consensus pattern (18 bp):
AATTTTTATAATTTTAAA
Found at i:214673 original size:17 final size:17
Alignment explanation
Indices: 214633--214673 Score: 57
Period size: 17 Copynumber: 2.4 Consensus size: 17
214623 ACAAATGTTT
*
214633 GAACATGAGTTCAAATA
1 GAACATAAGTTCAAATA
214650 -AAGCATAAGTTCAAATA
1 GAA-CATAAGTTCAAATA
214667 GAACATA
1 GAACATA
214674 GGCAATAAGC
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
16 2 0.10
17 17 0.81
18 2 0.10
ACGTcount: A:0.51, C:0.12, G:0.15, T:0.22
Consensus pattern (17 bp):
GAACATAAGTTCAAATA
Found at i:216002 original size:24 final size:24
Alignment explanation
Indices: 215968--216017 Score: 82
Period size: 24 Copynumber: 2.1 Consensus size: 24
215958 ACGCTGAGCA
215968 ATAAAGCTCAGTGATACTTTCATG
1 ATAAAGCTCAGTGATACTTTCATG
* *
215992 ATAAAGTTCAGTGGTACTTTCATG
1 ATAAAGCTCAGTGATACTTTCATG
216016 AT
1 AT
216018 TCAAGATAAC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.32, C:0.14, G:0.18, T:0.36
Consensus pattern (24 bp):
ATAAAGCTCAGTGATACTTTCATG
Found at i:222737 original size:156 final size:156
Alignment explanation
Indices: 222480--222793 Score: 556
Period size: 156 Copynumber: 2.0 Consensus size: 156
222470 TGAACAGATG
*
222480 CAGCAGAGGGACTTTTATCCTCAGCTAGATGTGTTTCTACCTGCTCTTCAGGAATACTTCTGATT
1 CAGCAGAGGGACTTTTATCCTCAGCTAGAGGTGTTTCTACCTGCTCTTCAGGAATACTTCTGATT
* * *
222545 TCTTCCTCCTGAACTGATGCAGCAACCGTTGTTTCATCCTCAGCTAGGGGAGCTTCCTCTTGTAC
66 TCTTCCTCCTGAACTGATGCAGCAACCGATGTTTCATCCTCAGCTAGGGCAACTTCCTCTTGTAC
222610 TACACCTTTTTGTGTAGACTCTTCAT
131 TACACCTTTTTGTGTAGACTCTTCAT
* * *
222636 CAGCAGAGGGAGTTTTATCCTCAGCTAGAGGTGTTTCTACCTGCTGTTCGGGAATACTTCTGATT
1 CAGCAGAGGGACTTTTATCCTCAGCTAGAGGTGTTTCTACCTGCTCTTCAGGAATACTTCTGATT
222701 TCTTCCTCCTGAACTGATGCAGCAACCGATGTTTCATCCTCAGCTAGGGCAACTTCCTCTTGTAC
66 TCTTCCTCCTGAACTGATGCAGCAACCGATGTTTCATCCTCAGCTAGGGCAACTTCCTCTTGTAC
*
222766 TACATCTTTTTGTGTAGACTCTTCAT
131 TACACCTTTTTGTGTAGACTCTTCAT
222792 CA
1 CA
222794 ACTGAAATTT
Statistics
Matches: 150, Mismatches: 8, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
156 150 1.00
ACGTcount: A:0.20, C:0.26, G:0.19, T:0.35
Consensus pattern (156 bp):
CAGCAGAGGGACTTTTATCCTCAGCTAGAGGTGTTTCTACCTGCTCTTCAGGAATACTTCTGATT
TCTTCCTCCTGAACTGATGCAGCAACCGATGTTTCATCCTCAGCTAGGGCAACTTCCTCTTGTAC
TACACCTTTTTGTGTAGACTCTTCAT
Found at i:222906 original size:231 final size:228
Alignment explanation
Indices: 222636--223077 Score: 769
Period size: 231 Copynumber: 1.9 Consensus size: 228
222626 GACTCTTCAT
* * *
222636 CAGCAGAGGGAGTTTTATCCTCAGCTAGAGGTGTTTCTACCTGCTGTTCGGGAATACTTCTGATT
1 CAGCAGAGGGAGTTTTATCCTCAGCTAGAGGTGTTTCTACCTGCTCTTCAGGAATACTTCCGATT
*
222701 TCTTCCTCCTGAACTGATGCAGCAACCGATGTTTCATCCTCAGCTAGGGCAACTTCCTCTTGTAC
66 TCTTCCTCCTGAACTGATGCAGCAACCGATGTTTCATCCACAGCTAGGGCAACTTCCTCTTGTAC
*
222766 TACATCTTTTTGTGTAGACTCTTCATCAACTGAAATTTT-GGAAGTCACTTGGTCAACTACTTCT
131 TACATCTTTTAGTGTAGACTCTTCATCAACTG-AATTTTCGGAAGTCACTTGGTCAACTA---CT
*
222830 CCAGATGATCCAGCTATTTCTTCCTCTTCAACAGATC
192 CCAGATGATCCAGCAATTTCTTCCTCTTCAACAGATC
222867 CAGCAGAGGGAGTTTTATCCTCAGCTAGAGGTGTTTCTACCTGCTCTTCAGGAATACTTCCGATT
1 CAGCAGAGGGAGTTTTATCCTCAGCTAGAGGTGTTTCTACCTGCTCTTCAGGAATACTTCCGATT
* *
222932 TCTTCCTCCTGAACTGATGCAGCAACCGATGTTTCATCCACAGCTAGGGGAGCTTCCTCTTGTAC
66 TCTTCCTCCTGAACTGATGCAGCAACCGATGTTTCATCCACAGCTAGGGCAACTTCCTCTTGTAC
222997 TACATCTTTTAGTGTAGACTCTTCATCAACTGAATTTTCGGAAGTCACTTGGTCAACTACTCCAG
131 TACATCTTTTAGTGTAGACTCTTCATCAACTGAATTTTCGGAAGTCACTTGGTCAACTACTCCAG
223062 ATGATCCAGCAATTTC
196 ATGATCCAGCAATTTC
223078 ATCACTTCCC
Statistics
Matches: 202, Mismatches: 8, Indels: 5
0.94 0.04 0.02
Matches are distributed among these distances:
228 21 0.10
230 6 0.03
231 175 0.87
ACGTcount: A:0.23, C:0.26, G:0.18, T:0.33
Consensus pattern (228 bp):
CAGCAGAGGGAGTTTTATCCTCAGCTAGAGGTGTTTCTACCTGCTCTTCAGGAATACTTCCGATT
TCTTCCTCCTGAACTGATGCAGCAACCGATGTTTCATCCACAGCTAGGGCAACTTCCTCTTGTAC
TACATCTTTTAGTGTAGACTCTTCATCAACTGAATTTTCGGAAGTCACTTGGTCAACTACTCCAG
ATGATCCAGCAATTTCTTCCTCTTCAACAGATC
Found at i:228412 original size:30 final size:31
Alignment explanation
Indices: 228345--228417 Score: 94
Period size: 31 Copynumber: 2.4 Consensus size: 31
228335 TTTGTTCAAT
* * *
228345 TTGGTACTCAAACTTGATACTTTTCCCTAAT
1 TTGGTACTTAAACTTGACACTTTTCCCTAAG
**
228376 TTGGTACTTAAACTTGACACTTTT-TTTAAG
1 TTGGTACTTAAACTTGACACTTTTCCCTAAG
228406 TTGGTACTTAAA
1 TTGGTACTTAAA
228418 TTTTTTGGGA
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
30 15 0.41
31 22 0.59
ACGTcount: A:0.27, C:0.16, G:0.12, T:0.44
Consensus pattern (31 bp):
TTGGTACTTAAACTTGACACTTTTCCCTAAG
Found at i:228448 original size:89 final size:89
Alignment explanation
Indices: 228297--228471 Score: 205
Period size: 89 Copynumber: 2.0 Consensus size: 89
228287 TTAGTATCTG
* * ** * *
228297 AACTTGACACATTTTTTAATTTGGTATTTAAAATTTTTTTTGTTCAATTTGGTACTCAAACTTGA
1 AACTTGACACATTTTTTAAGTTGGTACTTAAAATTTTTTGGGTCCAATTTGATACTCAAACTTGA
*
228362 -TACTT-TTCCCTAATTTGGTACTTA
66 CT-CTTGTT-CCAAATTTGGTACTTA
* *
228386 AACTTGACACTTTTTTTAAGTTGGTACTT-AAATTTTTTGGGATCCAATTTGATAC-CTGAACTT
1 AACTTGACACATTTTTTAAGTTGGTACTTAAAATTTTTTGGG-TCCAATTTGATACTC-AAACTT
228449 GACTCTTGTTCCAAATTTGGTAC
64 GACTCTTGTTCCAAATTTGGTAC
228472 CTAATCTTTT
Statistics
Matches: 73, Mismatches: 9, Indels: 8
0.81 0.10 0.09
Matches are distributed among these distances:
88 11 0.15
89 59 0.81
90 3 0.04
ACGTcount: A:0.26, C:0.15, G:0.13, T:0.46
Consensus pattern (89 bp):
AACTTGACACATTTTTTAAGTTGGTACTTAAAATTTTTTGGGTCCAATTTGATACTCAAACTTGA
CTCTTGTTCCAAATTTGGTACTTA
Found at i:228742 original size:59 final size:60
Alignment explanation
Indices: 228610--228745 Score: 152
Period size: 59 Copynumber: 2.3 Consensus size: 60
228600 AATATTTAAT
* *
228610 AAATTTAGATACCAAATTGGATCTAAAAAAAGCTTAGGTACCAAATTAGGAAAAAAAGCC
1 AAATTTAGATACCAAATTGGATCAAAAAAAAGCTTAGGTACCAAATTAGGAAAAAAAACC
* * * * * * *
228670 AAGTTCAGGTACCAAATTGGGT-AAAAAAAAGTTTA-ATGACCAAATTA-GAAAAAAATATC
1 AAATTTAGATACCAAATTGGATCAAAAAAAAGCTTAGGT-ACCAAATTAGGAAAAAAA-ACC
228729 AAATTTAGATACCAAAT
1 AAATTTAGATACCAAAT
228746 ATTATATTAA
Statistics
Matches: 62, Mismatches: 12, Indels: 5
0.78 0.15 0.06
Matches are distributed among these distances:
58 9 0.15
59 35 0.56
60 18 0.29
ACGTcount: A:0.51, C:0.12, G:0.14, T:0.24
Consensus pattern (60 bp):
AAATTTAGATACCAAATTGGATCAAAAAAAAGCTTAGGTACCAAATTAGGAAAAAAAACC
Found at i:233984 original size:31 final size:28
Alignment explanation
Indices: 233936--234021 Score: 82
Period size: 31 Copynumber: 2.9 Consensus size: 28
233926 TCATATCATC
*
233936 AAAAATAATATTGAATTGTAAAATTTAATT
1 AAAAATAAAATT-AATTGTAAAATTTAA-T
*
233966 AAAAAATCAAAATTAATTGCAAAATTTAAT
1 -AAAAAT-AAAATTAATTGTAAAATTTAAT
* *
233996 AAAATTTAAAATTTAATAGTAAAATT
1 AAAA-ATAAAA-TTAATTGTAAAATT
234022 AAATCGCATA
Statistics
Matches: 47, Mismatches: 5, Indels: 7
0.80 0.08 0.12
Matches are distributed among these distances:
29 8 0.17
30 14 0.30
31 20 0.43
32 5 0.11
ACGTcount: A:0.57, C:0.02, G:0.05, T:0.36
Consensus pattern (28 bp):
AAAAATAAAATTAATTGTAAAATTTAAT
Found at i:235346 original size:23 final size:23
Alignment explanation
Indices: 235303--235360 Score: 55
Period size: 23 Copynumber: 2.4 Consensus size: 23
235293 TACATAAAAA
*
235303 AAAATATAATCAAAATTTATAAT
1 AAAATATAATCAAAATATATAAT
*
235326 AAAAT-TATTCAAACATATATATAT
1 AAAATATAATCAAA-ATATATA-AT
*
235350 ATATATATAAT
1 A-AAATATAAT
235361 TTTGGCATTA
Statistics
Matches: 27, Mismatches: 4, Indels: 5
0.75 0.11 0.14
Matches are distributed among these distances:
22 7 0.26
23 11 0.41
24 3 0.11
25 3 0.11
26 3 0.11
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.38
Consensus pattern (23 bp):
AAAATATAATCAAAATATATAAT
Found at i:240572 original size:24 final size:24
Alignment explanation
Indices: 240544--240602 Score: 82
Period size: 24 Copynumber: 2.5 Consensus size: 24
240534 TAGACTAATA
*
240544 AGAGTTTGACTCAAACAAATAAAC
1 AGAGTTTAACTCAAACAAATAAAC
* *
240568 AGAGTTTAATTGAAACAAATAAAC
1 AGAGTTTAACTCAAACAAATAAAC
*
240592 AAAGTTTAACT
1 AGAGTTTAACT
240603 AAAAGAATAT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.51, C:0.12, G:0.12, T:0.25
Consensus pattern (24 bp):
AGAGTTTAACTCAAACAAATAAAC
Found at i:244654 original size:21 final size:21
Alignment explanation
Indices: 244611--244654 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
244601 ATTTCTCAAT
* *
244611 TAAATTAATTATTATTAATTA
1 TAAATTAATAATTATTAAGTA
244632 TAAATTAATAATT-TGTAAGTA
1 TAAATTAATAATTAT-TAAGTA
244653 TA
1 TA
244655 TATGAGGAGA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 1 0.05
21 19 0.95
ACGTcount: A:0.48, C:0.00, G:0.05, T:0.48
Consensus pattern (21 bp):
TAAATTAATAATTATTAAGTA
Found at i:249546 original size:14 final size:14
Alignment explanation
Indices: 249527--249561 Score: 54
Period size: 14 Copynumber: 2.5 Consensus size: 14
249517 CAGGAAACCA
249527 AATTAATATTT-TTT
1 AATTAA-ATTTATTT
249541 AATTAAATTTATTT
1 AATTAAATTTATTT
249555 AATTAAA
1 AATTAAA
249562 AAAATTAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 4 0.20
14 16 0.80
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (14 bp):
AATTAAATTTATTT
Found at i:265515 original size:58 final size:58
Alignment explanation
Indices: 265438--265604 Score: 214
Period size: 58 Copynumber: 2.9 Consensus size: 58
265428 TATTATTGTT
*
265438 ATTAAATTTTAATAAAATTATTATTAAATATAATTTAATAAAAATAATAAATAATTTA
1 ATTAAATTTTAATATAATTATTATTAAATATAATTTAATAAAAATAATAAATAATTTA
* * * *
265496 ATTATATTTTAACATAATTATTATTAAATACAATTTAAT-AAAATAATAATTAATTTA
1 ATTAAATTTTAATATAATTATTATTAAATATAATTTAATAAAAATAATAAATAATTTA
* *
265553 A-TAACATTTTTAATATAATTATTATTAAAATATGAA-TTAGTAAAAATTATAA
1 ATTAA-A-TTTTAATATAATTATTATT-AAATAT-AATTTAATAAAAATAATAA
265605 TATATAATAT
Statistics
Matches: 94, Mismatches: 10, Indels: 8
0.84 0.09 0.07
Matches are distributed among these distances:
56 2 0.02
57 19 0.20
58 53 0.56
59 9 0.10
60 11 0.12
ACGTcount: A:0.53, C:0.02, G:0.01, T:0.44
Consensus pattern (58 bp):
ATTAAATTTTAATATAATTATTATTAAATATAATTTAATAAAAATAATAAATAATTTA
Found at i:265547 original size:26 final size:26
Alignment explanation
Indices: 265445--265548 Score: 75
Period size: 26 Copynumber: 3.8 Consensus size: 26
265435 GTTATTAAAT
* *
265445 TTTAATAAAATTATTATTAAATATAA
1 TTTAATAAAATAATAATTAAATATAA
* *
265471 TTTAATAAAAATAATAAAT-AATTTAA
1 TTTAAT-AAAATAATAATTAAATATAA
* * *
265497 TTATATTTTAACATAATTATTATTAAATACAA
1 TT-TA--ATAAAATAA-TA--ATTAAATATAA
265529 TTTAATAAAATAATAATTAA
1 TTTAATAAAATAATAATTAA
265549 TTTAATAACA
Statistics
Matches: 59, Mismatches: 11, Indels: 16
0.69 0.13 0.19
Matches are distributed among these distances:
26 19 0.32
27 11 0.19
28 8 0.14
29 10 0.17
31 4 0.07
32 7 0.12
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (26 bp):
TTTAATAAAATAATAATTAAATATAA
Found at i:265584 original size:29 final size:29
Alignment explanation
Indices: 265502--265581 Score: 83
Period size: 29 Copynumber: 2.8 Consensus size: 29
265492 TTTAATTATA
*
265502 TTTTAACATAATTATTATTAAAT-ACAAT
1 TTTTAAAATAATTATTATTAAATAACAAT
* * *
265530 TTAATAAAATAATAATTAATTTAATAAC-AT
1 TT-TTAAAATAATTATT-ATTAAATAACAAT
*
265560 TTTTAATATAATTATTATTAAA
1 TTTTAAAATAATTATTATTAAA
265582 ATATGAATTA
Statistics
Matches: 41, Mismatches: 8, Indels: 6
0.75 0.15 0.11
Matches are distributed among these distances:
28 7 0.17
29 22 0.54
30 10 0.24
31 2 0.05
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (29 bp):
TTTTAAAATAATTATTATTAAATAACAAT
Found at i:271681 original size:20 final size:20
Alignment explanation
Indices: 271617--271682 Score: 64
Period size: 20 Copynumber: 3.2 Consensus size: 20
271607 AATAATTAAC
271617 TAAAAATCAAATAAA-AAATAT
1 TAAAAAT-AAATAAACAAA-AT
* * *
271638 TAGAAATAAATCGAACACAA-
1 TAAAAATAAAT-AAACAAAAT
271658 TAAAAATAAATAAACAAAAT
1 TAAAAATAAATAAACAAAAT
271678 TAAAA
1 TAAAA
271683 TGGAGTAGAG
Statistics
Matches: 36, Mismatches: 6, Indels: 7
0.73 0.12 0.14
Matches are distributed among these distances:
19 6 0.17
20 19 0.53
21 9 0.25
22 2 0.06
ACGTcount: A:0.70, C:0.08, G:0.03, T:0.20
Consensus pattern (20 bp):
TAAAAATAAATAAACAAAAT
Found at i:280684 original size:85 final size:85
Alignment explanation
Indices: 280585--280757 Score: 346
Period size: 85 Copynumber: 2.0 Consensus size: 85
280575 GACCAGGAGT
280585 TATTTAGTGCATTAGAATTGTCTTACAACAAAGGGGATGTTATATTGGCTTACTAAAGGGTAAAA
1 TATTTAGTGCATTAGAATTGTCTTACAACAAAGGGGATGTTATATTGGCTTACTAAAGGGTAAAA
280650 ACACAATTTATCTTTGGTAA
66 ACACAATTTATCTTTGGTAA
280670 TATTTAGTGCATTAGAATTGTCTTACAACAAAGGGGATGTTATATTGGCTTACTAAAGGGTAAAA
1 TATTTAGTGCATTAGAATTGTCTTACAACAAAGGGGATGTTATATTGGCTTACTAAAGGGTAAAA
280735 ACACAATTTATCTTTGGTAA
66 ACACAATTTATCTTTGGTAA
280755 TAT
1 TAT
280758 CTTTTTACCT
Statistics
Matches: 88, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
85 88 1.00
ACGTcount: A:0.35, C:0.10, G:0.18, T:0.36
Consensus pattern (85 bp):
TATTTAGTGCATTAGAATTGTCTTACAACAAAGGGGATGTTATATTGGCTTACTAAAGGGTAAAA
ACACAATTTATCTTTGGTAA
Found at i:286323 original size:2 final size:2
Alignment explanation
Indices: 286316--286363 Score: 71
Period size: 2 Copynumber: 24.5 Consensus size: 2
286306 AAACATGCAC
* *
286316 AT AT AT AT AT AC AC AT AT AT AT AT AT AT AT AT AT AT 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
286357 AT AT AT A
1 AT AT AT A
286364 ATAGACCATG
Statistics
Matches: 43, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
1 1 0.02
2 42 0.98
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:286716 original size:2 final size:2
Alignment explanation
Indices: 286709--286738 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
286699 GCATTTTATG
*
286709 TA TA TA TA TA TA TA TA TA TA TA TA CA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
286739 AACACGTATT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:291866 original size:5 final size:6
Alignment explanation
Indices: 291829--291865 Score: 60
Period size: 6 Copynumber: 6.5 Consensus size: 6
291819 ACTTTTGCTA
291829 AAAATT AAAATT AAAATT AAAATT -AAATT -AAATT AAA
1 AAAATT AAAATT AAAATT AAAATT AAAATT AAAATT AAA
291866 TAAGAAGTTC
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
5 10 0.33
6 20 0.67
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (6 bp):
AAAATT
Found at i:292589 original size:15 final size:16
Alignment explanation
Indices: 292567--292598 Score: 55
Period size: 16 Copynumber: 1.9 Consensus size: 16
292557 GATACCTATA
292567 TATATATATATTTTATT
1 TATATAT-TATTTTATT
292584 TATATATTATTTTAT
1 TATATATTATTTTAT
292599 GGTTTACAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (16 bp):
TATATATTATTTTATT
Found at i:293574 original size:179 final size:181
Alignment explanation
Indices: 293350--293680 Score: 416
Period size: 185 Copynumber: 1.8 Consensus size: 181
293340 TTACATCCAA
* * * *
293350 TTAATTAGAGAAAAAGTTAAAAATAAGAGCATTCAAATAATTACTTTTG-TTTCA-AT-CTATAC
1 TTAAATAGAGAAAAAATTAAAAATAAGAACATTCAAATAATTACTTTTGTTTTAATATACTATAC
* * * * * * * *
293412 TGTTATTTAAGAGTTTGATTGAGTTGGTGATACTCATTAATTAGATTCCAACTCAATTTTAAATT
66 TATTATTCAAGAGCTTGATTGAGTTGGTGACAATCAATAACTAAATTCCAACTCAATTTTAAATT
* *
293477 ACCAAAATTCCATTATTTTTATAAAGCGTCTAATATTAATTTGAGGATATT
131 AACAAAACTCCATTATTTTTATAAAGCGTCTAATATTAATTTGAGGATATT
* * *
293528 TTAAATAGAGAAAAAATTAAAAAATAATAATATTCAAATAATTACTTTTGTTTTAATTTATAATT
1 TTAAATAGAGAAAAAATT-AAAAATAAGAACATTCAAATAATTACTTTTGTTTTAA--TAT-ACT
* * *
293593 ATACTATTATTCAAGAGCTTGATTGAGTTTGTGACAATCAATAACTAAATTTCAACTCGATTTTA
62 ATACTATTATTCAAGAGCTTGATTGAGTTGGTGACAATCAATAACTAAATTCCAACTCAATTTTA
*
293658 AATTAATAAAACTCCATTATTTT
127 AATTAACAAAACTCCATTATTTT
293681 AGGTAAAATA
Statistics
Matches: 125, Mismatches: 21, Indels: 7
0.82 0.14 0.05
Matches are distributed among these distances:
178 16 0.13
179 28 0.22
180 4 0.03
183 2 0.02
185 75 0.60
ACGTcount: A:0.40, C:0.10, G:0.10, T:0.40
Consensus pattern (181 bp):
TTAAATAGAGAAAAAATTAAAAATAAGAACATTCAAATAATTACTTTTGTTTTAATATACTATAC
TATTATTCAAGAGCTTGATTGAGTTGGTGACAATCAATAACTAAATTCCAACTCAATTTTAAATT
AACAAAACTCCATTATTTTTATAAAGCGTCTAATATTAATTTGAGGATATT
Done.