Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012833.1 Corchorus olitorius cultivar O-4 contig12866, 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: 87294
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.31
Found at i:4075 original size:15 final size:15
Alignment explanation
Indices: 4055--4084 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
4045 CACAAGAAGA
4055 AGAAACCCCACAATT
1 AGAAACCCCACAATT
4070 AGAAACCCCACAATT
1 AGAAACCCCACAATT
4085 CTCACTCTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.47, C:0.33, G:0.07, T:0.13
Consensus pattern (15 bp):
AGAAACCCCACAATT
Found at i:4532 original size:22 final size:22
Alignment explanation
Indices: 4504--4547 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
4494 TTTTTTCAGA
4504 GATAAATCAAATTGGAAAATGG
1 GATAAATCAAATTGGAAAATGG
*
4526 GATAAATCAATTTGGAAAATGG
1 GATAAATCAAATTGGAAAATGG
4548 TGACACTGAC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.48, C:0.05, G:0.23, T:0.25
Consensus pattern (22 bp):
GATAAATCAAATTGGAAAATGG
Found at i:13002 original size:44 final size:44
Alignment explanation
Indices: 12944--13060 Score: 119
Period size: 44 Copynumber: 2.7 Consensus size: 44
12934 AAACCAAATT
* ** *
12944 TTCATA-GGATGGTTATTAAATTTTCATACCGTAATTACCAAAAC
1 TTCATATGGA-GGTTATCAAAACTTCATAACGTAATTACCAAAAC
* * * *
12988 TTCATATGGAGGTTATCAAAACTTCATAATGTAGTTATCAAAAT
1 TTCATATGGAGGTTATCAAAACTTCATAACGTAATTACCAAAAC
* * *
13032 TTCATATAGAGGTTACCAAAATTTCATAA
1 TTCATATGGAGGTTATCAAAACTTCATAA
13061 AAATGTTATC
Statistics
Matches: 61, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
44 58 0.95
45 3 0.05
ACGTcount: A:0.38, C:0.14, G:0.12, T:0.36
Consensus pattern (44 bp):
TTCATATGGAGGTTATCAAAACTTCATAACGTAATTACCAAAAC
Found at i:13007 original size:22 final size:22
Alignment explanation
Indices: 12982--13059 Score: 95
Period size: 22 Copynumber: 3.5 Consensus size: 22
12972 CCGTAATTAC
12982 CAAAACTTCATATGGAGGTTAT
1 CAAAACTTCATATGGAGGTTAT
*
13004 CAAAACTTCATAATGTA-GTTAT
1 CAAAACTTCAT-ATGGAGGTTAT
* * *
13026 CAAAATTTCATATAGAGGTTAC
1 CAAAACTTCATATGGAGGTTAT
*
13048 CAAAATTTCATA
1 CAAAACTTCATA
13060 AAAATGTTAT
Statistics
Matches: 49, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
21 3 0.06
22 42 0.86
23 4 0.08
ACGTcount: A:0.41, C:0.14, G:0.12, T:0.33
Consensus pattern (22 bp):
CAAAACTTCATATGGAGGTTAT
Found at i:13068 original size:22 final size:22
Alignment explanation
Indices: 12997--13091 Score: 84
Period size: 22 Copynumber: 4.3 Consensus size: 22
12987 CTTCATATGG
* **
12997 AGGTTATCAAAACTTCATAATGT
1 AGGTTATCAAAATTTCATAA-AA
* *
13020 A-GTTATCAAAATTTCATATAG
1 AGGTTATCAAAATTTCATAAAA
*
13041 AGGTTACCAAAATTTCATAAAA
1 AGGTTATCAAAATTTCATAAAA
* * **
13063 ATGTTATCAAAATTTAATACGA
1 AGGTTATCAAAATTTCATAAAA
13085 AGGTTAT
1 AGGTTAT
13092 TGAAATTTTA
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
21 1 0.02
22 56 0.97
23 1 0.02
ACGTcount: A:0.43, C:0.11, G:0.12, T:0.35
Consensus pattern (22 bp):
AGGTTATCAAAATTTCATAAAA
Found at i:13069 original size:44 final size:44
Alignment explanation
Indices: 12982--13077 Score: 122
Period size: 44 Copynumber: 2.2 Consensus size: 44
12972 CCGTAATTAC
* * * **
12982 CAAAACTTCATATGGAGGTTATCAAAACTTCATAATGTAGTTAT
1 CAAAATTTCATATAGAGGTTACCAAAACTTCATAAAATAGTTAT
*
13026 CAAAATTTCATATAGAGGTTACCAAAATTTCATAAAA-ATGTTAT
1 CAAAATTTCATATAGAGGTTACCAAAACTTCATAAAATA-GTTAT
13070 CAAAATTT
1 CAAAATTT
13078 AATACGAAGG
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
43 1 0.02
44 44 0.98
ACGTcount: A:0.43, C:0.12, G:0.10, T:0.34
Consensus pattern (44 bp):
CAAAATTTCATATAGAGGTTACCAAAACTTCATAAAATAGTTAT
Found at i:13179 original size:19 final size:20
Alignment explanation
Indices: 13151--13208 Score: 73
Period size: 19 Copynumber: 2.9 Consensus size: 20
13141 TTCATAGGGA
*
13151 GGGAGATTATCAAAATTT-C
1 GGGAGGTTATCAAAATTTAC
*
13170 GGGAGGTTATGAAAATGTTAC
1 GGGAGGTTATCAAAAT-TTAC
13191 GGAGAGGTTATCAAAATT
1 GG-GAGGTTATCAAAATT
13209 ACATATAAAG
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
19 14 0.42
20 2 0.06
21 4 0.12
22 13 0.39
ACGTcount: A:0.36, C:0.07, G:0.28, T:0.29
Consensus pattern (20 bp):
GGGAGGTTATCAAAATTTAC
Found at i:13272 original size:22 final size:22
Alignment explanation
Indices: 13254--13638 Score: 325
Period size: 22 Copynumber: 17.5 Consensus size: 22
13244 GAAGTTAGCG
* *
13254 AAATTTCATAGTGTGGTTATCA
1 AAATTTCATAGTGAGGTTACCA
* *
13276 AAATTTTATGAG-GAGGTTATCA
1 AAATTTCAT-AGTGAGGTTACCA
* *
13298 AAATTTTCATAGTGCGATTACCA
1 AAA-TTTCATAGTGAGGTTACCA
** * * *
13321 ATTTTTTATTGTGA--TTATCA
1 AAATTTCATAGTGAGGTTACCA
* *
13341 AAATTTCACATTGAGGTTACCA
1 AAATTTCATAGTGAGGTTACCA
*
13363 AAATTTCATAGGGAGGTTACCA
1 AAATTTCATAGTGAGGTTACCA
* * * * **
13385 AAATTTTATTGGGAGATTACTG
1 AAATTTCATAGTGAGGTTACCA
* *
13407 AAATTTCATAGTGAGGTAACCG
1 AAATTTCATAGTGAGGTTACCA
* * *
13429 AAATTTAATAGTGGGGTTAACA
1 AAATTTCATAGTGAGGTTACCA
* *
13451 AAATTTCATCG-GGGGTTACCA
1 AAATTTCATAGTGAGGTTACCA
* *
13472 AAATTTCATAGGGAGGTTGCCA
1 AAATTTCATAGTGAGGTTACCA
* *
13494 TAAGTTTTATAGTG-GAGTTACCA
1 -AAATTTCATAGTGAG-GTTACCA
* *
13517 AAATTTCAT-GGGAACGTTACCA
1 AAATTTCATAGTG-AGGTTACCA
* * *
13539 AAATTTCATAGTCAAGTTACCG
1 AAATTTCATAGTGAGGTTACCA
*
13561 AAATTTCATAGTGAGGTCACCA
1 AAATTTCATAGTGAGGTTACCA
*
13583 AAATTTCATAGTCAGGTTACCA
1 AAATTTCATAGTGAGGTTACCA
13605 AAATTTCATA-TGGAGGTTACCA
1 AAATTTCATAGT-GAGGTTACCA
13627 AAATTTCATAGT
1 AAATTTCATAGT
13639 AATTAAGAAA
Statistics
Matches: 287, Mismatches: 63, Indels: 25
0.77 0.17 0.07
Matches are distributed among these distances:
20 13 0.05
21 22 0.08
22 219 0.76
23 33 0.11
ACGTcount: A:0.35, C:0.13, G:0.19, T:0.34
Consensus pattern (22 bp):
AAATTTCATAGTGAGGTTACCA
Found at i:18914 original size:22 final size:23
Alignment explanation
Indices: 18889--18987 Score: 98
Period size: 22 Copynumber: 4.5 Consensus size: 23
18879 GAAAGTTATT
*
18889 AAAATTTCATACTGTA-ATTACC
1 AAAATTTCATACTGTAGGTTACC
* * *
18911 AAAACTTCATA-TGGAGGTTATC
1 AAAATTTCATACTGTAGGTTACC
* * *
18933 AAAACTTCATAATGTA-GTTATC
1 AAAATTTCATACTGTAGGTTACC
*
18955 AAAATTTCATACAG-AGGTTACC
1 AAAATTTCATACTGTAGGTTACC
18977 AAAATTTCATA
1 AAAATTTCATA
18988 AAAGTACTAT
Statistics
Matches: 65, Mismatches: 9, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
21 4 0.06
22 58 0.89
23 3 0.05
ACGTcount: A:0.41, C:0.15, G:0.10, T:0.33
Consensus pattern (23 bp):
AAAATTTCATACTGTAGGTTACC
Found at i:18914 original size:44 final size:43
Alignment explanation
Indices: 18864--19019 Score: 109
Period size: 44 Copynumber: 3.5 Consensus size: 43
18854 TGACAATTAA
* * *
18864 ACCAAAATTACATA-GGAAAGTTATTAAAATTTCATACTGTAATT
1 ACCAAAATT-CATATGG-AAGTTATCAAAACTTCATAATGTAATT
* *
18908 ACCAAAACTTCATATGGAGGTTATCAAAACTTCATAATGTAGTT
1 ACCAAAA-TTCATATGGAAGTTATCAAAACTTCATAATGTAATT
* ** * * * * *
18952 ATCAAAATTTCATACAGAGGTTACCAAAATTTCATAAAAGT-ACT
1 ACCAAAA-TTCATATGGAAGTTATCAAAACTTCAT-AATGTAATT
* *
18996 ATCAAAATTTCATATGAAAGTTAT
1 ACCAAAA-TTCATATGGAAGTTAT
19020 TGAAATTTTA
Statistics
Matches: 90, Mismatches: 19, Indels: 6
0.78 0.17 0.05
Matches are distributed among these distances:
44 82 0.91
45 8 0.09
ACGTcount: A:0.44, C:0.13, G:0.10, T:0.33
Consensus pattern (43 bp):
ACCAAAATTCATATGGAAGTTATCAAAACTTCATAATGTAATT
Found at i:19001 original size:22 final size:21
Alignment explanation
Indices: 18929--19009 Score: 67
Period size: 22 Copynumber: 3.7 Consensus size: 21
18919 ATATGGAGGT
* *
18929 TATCAAAACTTCAT-AATGTA
1 TATCAAAATTTCATAAAAGTA
*
18949 GTTATCAAAATTTCATACAGAGGT-
1 --TATCAAAATTTCATA-A-AAGTA
*
18973 TACCAAAATTTCATAAAAGTA
1 TATCAAAATTTCATAAAAGTA
18994 CTATCAAAATTTCATA
1 -TATCAAAATTTCATA
19010 TGAAAGTTAT
Statistics
Matches: 49, Mismatches: 5, Indels: 10
0.77 0.08 0.16
Matches are distributed among these distances:
20 3 0.06
21 1 0.02
22 41 0.84
24 1 0.02
25 3 0.06
ACGTcount: A:0.44, C:0.15, G:0.07, T:0.33
Consensus pattern (21 bp):
TATCAAAATTTCATAAAAGTA
Found at i:19026 original size:66 final size:65
Alignment explanation
Indices: 18866--19027 Score: 159
Period size: 66 Copynumber: 2.5 Consensus size: 65
18856 ACAATTAAAC
* * * * *
18866 CAAAATTACATAGGAAAGTTATTAAAATTTCATACTGTAATTACCAAAACTTCATATGGAGGTTA
1 CAAAATTTCATATGAAAGTTATTAAAATTTCATACAGTAATTACCAAAACTTCATA-GAAAGTTA
18931 T
65 T
* * * * *
18932 CAAAACTTCATAATG-TAGTTATCAAAATTTCATACAG-AGGTTACCAAAATTTCATA-AAAGTA
1 CAAAATTTCAT-ATGAAAGTTATTAAAATTTCATACAGTA-ATTACCAAAACTTCATAGAAAGT-
18994 CTAT
63 -TAT
*
18998 CAAAATTTCATATGAAAGTTATTGAAATTT
1 CAAAATTTCATATGAAAGTTATTAAAATTT
19028 TATAGCGTGA
Statistics
Matches: 77, Mismatches: 14, Indels: 10
0.76 0.14 0.10
Matches are distributed among these distances:
64 3 0.04
65 4 0.05
66 68 0.88
67 2 0.03
ACGTcount: A:0.43, C:0.12, G:0.10, T:0.34
Consensus pattern (65 bp):
CAAAATTTCATATGAAAGTTATTAAAATTTCATACAGTAATTACCAAAACTTCATAGAAAGTTAT
Found at i:19232 original size:22 final size:22
Alignment explanation
Indices: 19207--19432 Score: 145
Period size: 22 Copynumber: 10.3 Consensus size: 22
19197 GAAGTTAGCG
*
19207 AAATTTCATGGTGTGGTTATCA
1 AAATTTCATAGTGTGGTTATCA
* *
19229 AAATTTTATGAG-GAGGTTATCA
1 AAATTTCAT-AGTGTGGTTATCA
* *
19251 AAATTTTCATAGTGCGATTA-C-
1 AAA-TTTCATAGTGTGGTTATCA
* ** * *
19272 CAATTTTTTAATGTGATTATCA
1 AAATTTCATAGTGTGGTTATCA
* * * *
19294 AAATTTCACACTGAGCTTATCA
1 AAATTTCATAGTGTGGTTATCA
* *
19316 AAACTTCATTGTGTGGTTATCA
1 AAATTTCATAGTGTGGTTATCA
* *
19338 GAATTTCACAGTGTGGTTATCA
1 AAATTTCATAGTGTGGTTATCA
* * *
19360 AATTTTCATAAG-GAGGTTATCG
1 AAATTTCAT-AGTGTGGTTATCA
* * *
19382 AAATTTCACAATGAGGTTATCA
1 AAATTTCATAGTGTGGTTATCA
* **
19404 AATTTTCGCAGTGTGGTTATCA
1 AAATTTCATAGTGTGGTTATCA
*
19426 ATATTTC
1 AAATTTC
19433 TACGTTGGAG
Statistics
Matches: 154, Mismatches: 43, Indels: 14
0.73 0.20 0.07
Matches are distributed among these distances:
20 12 0.08
21 4 0.03
22 125 0.81
23 13 0.08
ACGTcount: A:0.31, C:0.12, G:0.17, T:0.39
Consensus pattern (22 bp):
AAATTTCATAGTGTGGTTATCA
Found at i:24494 original size:31 final size:30
Alignment explanation
Indices: 24459--24533 Score: 98
Period size: 29 Copynumber: 2.5 Consensus size: 30
24449 ATCTGAGAGC
* * *
24459 TCCCTGTACTGCACAAAAATGTTCAATTTCG
1 TCCCTGTACT-CACAAAAACGATCAATTTAG
*
24490 TCCCTGTACTCA-AAAAGCGATCAATTTAG
1 TCCCTGTACTCACAAAAACGATCAATTTAG
24519 TCCCTGTACTCACAA
1 TCCCTGTACTCACAA
24534 GATTGGGTGA
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
29 25 0.64
30 4 0.10
31 10 0.26
ACGTcount: A:0.31, C:0.28, G:0.12, T:0.29
Consensus pattern (30 bp):
TCCCTGTACTCACAAAAACGATCAATTTAG
Found at i:28936 original size:64 final size:64
Alignment explanation
Indices: 28835--28963 Score: 240
Period size: 64 Copynumber: 2.0 Consensus size: 64
28825 AAACACTCAA
*
28835 ATTCCTTTAAAAAATAAAAGAGCCCTCACACCAGCAATTATGCAAATGAACAGTTGTTCAACTT
1 ATTCCTTTAAAAAATAAAAGAGCCCTCACACCAGCAATTATACAAATGAACAGTTGTTCAACTT
*
28899 ATTCCTTTAAAAAATAGAAGAGCCCTCACACCAGCAATTATACAAATGAACAGTTGTTCAACTT
1 ATTCCTTTAAAAAATAAAAGAGCCCTCACACCAGCAATTATACAAATGAACAGTTGTTCAACTT
28963 A
1 A
28964 CACAGAACGA
Statistics
Matches: 63, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
64 63 1.00
ACGTcount: A:0.41, C:0.22, G:0.11, T:0.26
Consensus pattern (64 bp):
ATTCCTTTAAAAAATAAAAGAGCCCTCACACCAGCAATTATACAAATGAACAGTTGTTCAACTT
Found at i:42460 original size:197 final size:199
Alignment explanation
Indices: 42125--42522 Score: 764
Period size: 197 Copynumber: 2.0 Consensus size: 199
42115 AACACGCTGT
42125 TAAGCTTAGAAACCCGTGAATACTCATTAAGAGGCTATAACAATGTATCAAGCAGAATAAAAAGA
1 TAAGCTTAGAAACCCGTGAATACTCATTAAGAGGCTATAACAATGTATCAAGCAGAATAAAAAGA
42190 AAAAACGCCTTAATTACATGCCTAAAACTAATTCAAACCCAGCATAAACTTCCTATTCTATTTCC
66 AAAAACGCCTTAATTACATGCCTAAAACTAATTCAAACCCAGCATAAACTTCCTATTCTATTTCC
42255 ACATAGTCAAGCTTC-AAA-AAGAAGAAGAAAACATATAAAAATACTCATAAGAAAGGAACTCAC
131 ACATAGTCAAGCTTCAAAAGAAGAAGAAGAAAACATATAAAAATACTCATAAGAAAGGAACTCAC
42318 GTCC
196 GTCC
42322 TAAGCTTAGAAACCCGTGAATACTCATTAAGAGGCTATAACAATGTATCAAGCAGAATAAAAAGA
1 TAAGCTTAGAAACCCGTGAATACTCATTAAGAGGCTATAACAATGTATCAAGCAGAATAAAAAGA
*
42387 AAAAACGCCTTAATTACATGCCTAAAACTAATTCAAACCCAGCATAAACTTCCTATTCTATTTCT
66 AAAAACGCCTTAATTACATGCCTAAAACTAATTCAAACCCAGCATAAACTTCCTATTCTATTTCC
42452 ACATAGTCAAGCTTCAAAAAGAAGAAGAAGAAAACATATAAAAATACTCATAAGAAAGGAACTCA
131 ACATAGTCAAGCTTC-AAAAGAAGAAGAAGAAAACATATAAAAATACTCATAAGAAAGGAACTCA
42517 CGTCC
195 CGTCC
42522 T
1 T
42523 GAGCCATTTG
Statistics
Matches: 197, Mismatches: 1, Indels: 3
0.98 0.00 0.01
Matches are distributed among these distances:
197 144 0.73
199 3 0.02
200 50 0.25
ACGTcount: A:0.46, C:0.20, G:0.12, T:0.23
Consensus pattern (199 bp):
TAAGCTTAGAAACCCGTGAATACTCATTAAGAGGCTATAACAATGTATCAAGCAGAATAAAAAGA
AAAAACGCCTTAATTACATGCCTAAAACTAATTCAAACCCAGCATAAACTTCCTATTCTATTTCC
ACATAGTCAAGCTTCAAAAGAAGAAGAAGAAAACATATAAAAATACTCATAAGAAAGGAACTCAC
GTCC
Found at i:45587 original size:34 final size:34
Alignment explanation
Indices: 45548--45613 Score: 123
Period size: 34 Copynumber: 1.9 Consensus size: 34
45538 TGCTGATCCA
*
45548 TAGAGCATCCCTCTTCCTTTGATGAATCTTATTT
1 TAGAGCATCCCTCTTCCTTTGATAAATCTTATTT
45582 TAGAGCATCCCTCTTCCTTTGATAAATCTTAT
1 TAGAGCATCCCTCTTCCTTTGATAAATCTTAT
45614 CTTTGTTTGG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.23, C:0.24, G:0.11, T:0.42
Consensus pattern (34 bp):
TAGAGCATCCCTCTTCCTTTGATAAATCTTATTT
Found at i:49443 original size:25 final size:25
Alignment explanation
Indices: 49415--49474 Score: 102
Period size: 25 Copynumber: 2.4 Consensus size: 25
49405 GTTCAAAACA
49415 TAAATAATATAAGGGAATTTAAAAG
1 TAAATAATATAAGGGAATTTAAAAG
*
49440 TAAATAATATAGGGGAATTTAAAAG
1 TAAATAATATAAGGGAATTTAAAAG
*
49465 TGAATAATAT
1 TAAATAATAT
49475 GAACAAATAT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
25 33 1.00
ACGTcount: A:0.53, C:0.00, G:0.17, T:0.30
Consensus pattern (25 bp):
TAAATAATATAAGGGAATTTAAAAG
Found at i:50798 original size:2 final size:2
Alignment explanation
Indices: 50791--50960 Score: 97
Period size: 2 Copynumber: 87.0 Consensus size: 2
50781 ATTAAGGTAT
* *
50791 TA TA TA TA -A GA TA TA TT TA TGA TA TGA TA TA TA TA TA TA TA -A
1 TA TA TA TA TA TA TA TA TA TA T-A TA T-A TA TA TA TA TA TA TA TA
* * * * *
50833 TA TA TA TA AA AA AA TA TA TT TA TGA TA TA TA TA -A AA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA TA TA TA TA TA TA
* * * *
50875 TA -A TA TA TA TA -A AA TA TA TT TA GGA TA TA TA TA -A AA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA
* * * *
50915 TA TA -A TA TA TA TA -A AA TA TA TT TA GGA TA TA TA TA -A AA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA
50955 TA TA TA
1 TA TA TA
50961 ATAAATTATT
Statistics
Matches: 134, Mismatches: 20, Indels: 28
0.74 0.11 0.15
Matches are distributed among these distances:
1 9 0.07
2 117 0.87
3 8 0.06
ACGTcount: A:0.54, C:0.00, G:0.05, T:0.42
Consensus pattern (2 bp):
TA
Found at i:50835 original size:11 final size:11
Alignment explanation
Indices: 50791--50963 Score: 135
Period size: 11 Copynumber: 16.0 Consensus size: 11
50781 ATTAAGGTAT
*
50791 TATATATAAGA
1 TATATATAATA
*
50802 TATAT-TTATGA
1 TATATATAAT-A
50813 TATGATAT-ATA
1 TAT-ATATAATA
50824 TATATATAATA
1 TATATATAATA
*
50835 TATATA-AAAA
1 TATATATAATA
* *
50845 AATATATTTATGA
1 TATATA-TAAT-A
*
50858 TATATATAAAA
1 TATATATAATA
50869 TATATATAATA
1 TATATATAATA
50880 TATATA-AA-A
1 TATATATAATA
* **
50889 TATATTTAGGA
1 TATATATAATA
*
50900 TATATATAAAA
1 TATATATAATA
50911 TATATATAATA
1 TATATATAATA
50922 TATATA-AA-A
1 TATATATAATA
* **
50931 TATATTTAGGA
1 TATATATAATA
*
50942 TATATATAAAA
1 TATATATAATA
50953 TATATATAATA
1 TATATATAATA
50964 AATTATTTTA
Statistics
Matches: 129, Mismatches: 22, Indels: 22
0.75 0.13 0.13
Matches are distributed among these distances:
9 12 0.09
10 20 0.16
11 83 0.64
12 7 0.05
13 7 0.05
ACGTcount: A:0.54, C:0.00, G:0.05, T:0.42
Consensus pattern (11 bp):
TATATATAATA
Found at i:50863 original size:42 final size:40
Alignment explanation
Indices: 50791--50963 Score: 220
Period size: 42 Copynumber: 4.0 Consensus size: 40
50781 ATTAAGGTAT
* *
50791 TATATATAAGATATATTTATGATATGATATATATATATATAA
1 TATATATAAAATATATTTAGGATAT-ATATA-ATATATATAA
*
50833 TATATATAAAAAAATATATTTATGATATATATAAAATATATATAA
1 TATATAT---AAAATATATTTAGGATATATAT--AATATATATAA
50878 TATATATAAAATATATTTAGGATATATATAAAATATATATAA
1 TATATATAAAATATATTTAGGATATATAT--AATATATATAA
50920 TATATATAAAATATATTTAGGATATATATAAAATATATATAA
1 TATATATAAAATATATTTAGGATATATAT--AATATATATAA
50962 TA
1 TA
50964 AATTATTTTA
Statistics
Matches: 124, Mismatches: 2, Indels: 10
0.91 0.01 0.07
Matches are distributed among these distances:
42 85 0.69
44 4 0.03
45 34 0.27
46 1 0.01
ACGTcount: A:0.54, C:0.00, G:0.05, T:0.42
Consensus pattern (40 bp):
TATATATAAAATATATTTAGGATATATATAATATATATAA
Found at i:65239 original size:15 final size:14
Alignment explanation
Indices: 65216--65261 Score: 53
Period size: 14 Copynumber: 3.4 Consensus size: 14
65206 ATATTCTTTT
65216 AAAAA-GATTTTACA
1 AAAAATGATTTT-CA
65230 AAAAATGATTTCTC-
1 AAAAATGATTT-TCA
65244 AAAAATG-TTTTCA
1 AAAAATGATTTTCA
65257 AAAAA
1 AAAAA
65262 ATTGTTTTCA
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
12 2 0.07
13 8 0.28
14 12 0.41
15 6 0.21
16 1 0.03
ACGTcount: A:0.54, C:0.09, G:0.07, T:0.30
Consensus pattern (14 bp):
AAAAATGATTTTCA
Found at i:65261 original size:14 final size:14
Alignment explanation
Indices: 65229--65271 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
65219 AAGATTTTAC
* *
65229 AAAAAATGATTTCT
1 AAAAAATGTTTTCA
*
65243 CAAAAATGTTTTCA
1 AAAAAATGTTTTCA
65257 AAAAAATTGTTTTCA
1 AAAAAA-TGTTTTCA
65272 CGAGTGATGC
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
14 16 0.67
15 8 0.33
ACGTcount: A:0.47, C:0.09, G:0.07, T:0.37
Consensus pattern (14 bp):
AAAAAATGTTTTCA
Found at i:65582 original size:14 final size:14
Alignment explanation
Indices: 65565--65597 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
65555 AAAGATGGAG
*
65565 GAAAAAAGGAAAAA
1 GAAAAAAAGAAAAA
65579 GAAAAAAAGAAAAA
1 GAAAAAAAGAAAAA
65593 GAAAA
1 GAAAA
65598 GAAAAATTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (14 bp):
GAAAAAAAGAAAAA
Found at i:66841 original size:8 final size:8
Alignment explanation
Indices: 66825--67462 Score: 51
Period size: 8 Copynumber: 81.8 Consensus size: 8
66815 TTCAATTAGC
66825 TTCAATTT
1 TTCAATTT
*
66833 TTTAATTT
1 TTCAATTT
*
66841 TTCAATTA
1 TTCAATTT
* **
66849 TCCAATGC
1 TTCAATTT
* *
66857 TCCAATTC
1 TTCAATTT
*
66865 TTCAATTA
1 TTCAATTT
* *
66873 TCCAATTC
1 TTCAATTT
*
66881 TTCAATTC
1 TTCAATTT
*
66889 TTCAA--A
1 TTCAATTT
*
66895 TTCAATTC
1 TTCAATTT
**
66903 TTCAACAT
1 TTCAATTT
**
66911 TTCAATAC
1 TTCAATTT
*
66919 TTCAATTC
1 TTCAATTT
**
66927 TTCAATGC
1 TTCAATTT
66935 TTCAA--T
1 TTCAATTT
66941 TTCAATATAT
1 TTCAAT-T-T
66951 GGTTCAA--T
1 --TTCAATTT
**
66959 TTCAATAC
1 TTCAATTT
*
66967 TTCAATTC
1 TTCAATTT
*
66975 TTCAA--A
1 TTCAATTT
*
66981 TTCAATTC
1 TTCAATTT
**
66989 TTCAATGC
1 TTCAATTT
*
66997 TTCAATAT
1 TTCAATTT
**
67005 TTCAATGG
1 TTCAATTT
67013 TTCAA--T
1 TTCAATTT
**
67019 TTCAATAC
1 TTCAATTT
*
67027 TTCAATTC
1 TTCAATTT
*
67035 TTCAA--A
1 TTCAATTT
*
67041 TTCAATTC
1 TTCAATTT
*
67049 TTCAATAT
1 TTCAATTT
67057 TTCAA--T
1 TTCAATTT
*
67063 TTCAATTC
1 TTCAATTT
*
67071 TTCAA--A
1 TTCAATTT
*
67077 TTCAATTC
1 TTCAATTT
**
67085 TTCAATGC
1 TTCAATTT
67093 TTCAA--T
1 TTCAATTT
*
67099 TTCAATAT
1 TTCAATTT
**
67107 TTCAATAC
1 TTCAATTT
67115 TTCAA--T
1 TTCAATTT
*
67121 TTCAATTC
1 TTCAATTT
**
67129 TTCAATGC
1 TTCAATTT
67137 TTCAATTT
1 TTCAATTT
67145 CAATTCCAATTT
1 ---TT-CAATTT
* *
67157 CTCAA--A
1 TTCAATTT
*
67163 TTCAAATT
1 TTCAATTT
*
67171 TTCAATGT
1 TTCAATTT
67179 TTCAA--T
1 TTCAATTT
*
67185 TTCAATAT
1 TTCAATTT
**
67193 TTCAATGC
1 TTCAATTT
67201 TTCAATTT
1 TTCAATTT
67209 CAATTCCAATTT
1 ---TT-CAATTT
* *
67221 CTCAA--G
1 TTCAATTT
*
67227 TTCAATTC
1 TTCAATTT
*
67235 TTCAATGT
1 TTCAATTT
67243 TTCAA--T
1 TTCAATTT
*
67249 TTCAATAT
1 TTCAATTT
**
67257 TTCAATGC
1 TTCAATTT
67265 TTCAATTT
1 TTCAATTT
67273 CAATTCCAATTT
1 ---TT-CAATTT
* *
67285 CTCAA--G
1 TTCAATTT
*
67291 TTCAATTC
1 TTCAATTT
*
67299 TTCAATGT
1 TTCAATTT
67307 TTCAA--T
1 TTCAATTT
*
67313 TTCAATAT
1 TTCAATTT
**
67321 TTCAATGC
1 TTCAATTT
67329 TTCAATTT
1 TTCAATTT
67337 CAATTCCAATTT
1 ---TT-CAATTT
* *
67349 CTCAA--A
1 TTCAATTT
*
67355 TTCAATTC
1 TTCAATTT
*
67363 TTCAATGT
1 TTCAATTT
67371 TTCAATTT
1 TTCAATTT
67379 CAATTCCAATTT
1 ---TT-CAATTT
* *
67391 CTCAA--A
1 TTCAATTT
*
67397 TTCAATTC
1 TTCAATTT
*
67405 TTCAATGT
1 TTCAATTT
67413 TTCAA--T
1 TTCAATTT
*
67419 TTCAATAT
1 TTCAATTT
*
67427 TTCAATTC
1 TTCAATTT
*
67435 TTCAA--A
1 TTCAATTT
*
67441 TTCAATTC
1 TTCAATTT
*
67449 TTCAATGT
1 TTCAATTT
67457 TTCAAT
1 TTCAAT
67463 ATGTCAATGC
Statistics
Matches: 468, Mismatches: 98, Indels: 128
0.67 0.14 0.18
Matches are distributed among these distances:
6 100 0.21
8 317 0.68
9 5 0.01
10 1 0.00
11 10 0.02
12 35 0.07
ACGTcount: A:0.31, C:0.20, G:0.03, T:0.45
Consensus pattern (8 bp):
TTCAATTT
Found at i:66863 original size:24 final size:24
Alignment explanation
Indices: 66836--66893 Score: 89
Period size: 24 Copynumber: 2.4 Consensus size: 24
66826 TCAATTTTTT
*
66836 AATTTTTCAATTATCCAATGCTCC
1 AATTCTTCAATTATCCAATGCTCC
* *
66860 AATTCTTCAATTATCCAATTCTTC
1 AATTCTTCAATTATCCAATGCTCC
66884 AATTCTTCAA
1 AATTCTTCAA
66894 ATTCAATTCT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.31, C:0.24, G:0.02, T:0.43
Consensus pattern (24 bp):
AATTCTTCAATTATCCAATGCTCC
Found at i:66887 original size:16 final size:16
Alignment explanation
Indices: 66857--66887 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
66847 TATCCAATGC
66857 TCCAATTCTTCAATTA
1 TCCAATTCTTCAATTA
66873 TCCAATTCTTCAATT
1 TCCAATTCTTCAATT
66888 CTTCAAATTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.29, C:0.26, G:0.00, T:0.45
Consensus pattern (16 bp):
TCCAATTCTTCAATTA
Found at i:66900 original size:14 final size:14
Alignment explanation
Indices: 66881--67453 Score: 123
Period size: 14 Copynumber: 38.9 Consensus size: 14
66871 TATCCAATTC
66881 TTCAATTCTTCAAA
1 TTCAATTCTTCAAA
66895 TTCAATTCTTCAACA
1 TTCAATTCTTCAA-A
* *
66910 TTTCAATACTTCAATTC
1 -TTCAATTCTTCAA--A
* *
66927 TTCAATGCTTCAAT
1 TTCAATTCTTCAAA
* **
66941 TTCAA-T-AT-ATGG
1 TTCAATTCTTCA-AA
66953 TTCAA-T-TTCAATA
1 TTCAATTCTTCAA-A
66966 CTTCAATTCTTCAAA
1 -TTCAATTCTTCAAA
*
66981 TTCAATTCTTCAATGC
1 TTCAATTCTTCAA--A
*
66997 TTCAATAT-TTCAATGG
1 TTCAAT-TCTTCAA--A
67013 TTCAA-T-TTCAATA
1 TTCAATTCTTCAA-A
67026 CTTCAATTCTTCAAA
1 -TTCAATTCTTCAAA
67041 TTCAATTCTTC-AA
1 TTCAATTCTTCAAA
*
67054 -T--A-T-TTCAAT
1 TTCAATTCTTCAAA
67063 TTCAATTCTTCAAA
1 TTCAATTCTTCAAA
*
67077 TTCAATTCTTCAATGC
1 TTCAATTCTTCAA--A
67093 TTCAA-T-TTCAATA
1 TTCAATTCTTCAA-A
* *
67106 TTTCAATACTTCAAT
1 -TTCAATTCTTCAAA
*
67121 TTCAATTCTTCAATGC
1 TTCAATTCTTCAA--A
67137 TTCAA-T-TTC-AA
1 TTCAATTCTTCAAA
67148 TTCCAATT-TCTCAAA
1 TT-CAATTCT-TCAAA
*
67163 TTCAAATT-TTCAATGT
1 TTC-AATTCTTCAA--A
67179 TTCAA-T-TTCAATA
1 TTCAATTCTTCAA-A
* *
67192 TTTCAATGCTTCAAT
1 -TTCAATTCTTCAAA
*
67207 TTCAATTCCAATTTCTCAAG
1 TTCAATT-C----T-TCAAA
*
67227 TTCAATTCTTCAATGT
1 TTCAATTCTTCAA--A
67243 TTCAA-T-TTCAATA
1 TTCAATTCTTCAA-A
* *
67256 TTTCAATGCTTCAAT
1 -TTCAATTCTTCAAA
*
67271 TTCAATTCCAATTTCTCAAG
1 TTCAATT-C----T-TCAAA
*
67291 TTCAATTCTTCAATGT
1 TTCAATTCTTCAA--A
67307 TTCAA-T-TTCAATA
1 TTCAATTCTTCAA-A
* *
67320 TTTCAATGCTTCAAT
1 -TTCAATTCTTCAAA
67335 TTCAATTCCAATTTCTCAAA
1 TTCAATT-C----T-TCAAA
*
67355 TTCAATTCTTCAATGT
1 TTCAATTCTTCAA--A
67371 TTCAA-T-TTC-AA
1 TTCAATTCTTCAAA
67382 TTCCAATT-TCTCAAA
1 TT-CAATTCT-TCAAA
*
67397 TTCAATTCTTCAATGT
1 TTCAATTCTTCAA--A
67413 TTCAA-T-TTCAATA
1 TTCAATTCTTCAA-A
67426 TTTCAATTCTTCAAA
1 -TTCAATTCTTCAAA
67441 TTCAATTCTTCAA
1 TTCAATTCTTCAA
67454 TGTTTCAATA
Statistics
Matches: 429, Mismatches: 52, Indels: 156
0.67 0.08 0.24
Matches are distributed among these distances:
8 3 0.01
9 2 0.00
10 2 0.00
11 5 0.01
12 16 0.04
13 10 0.02
14 206 0.48
15 35 0.08
16 110 0.26
17 1 0.00
19 6 0.01
20 33 0.08
ACGTcount: A:0.32, C:0.20, G:0.03, T:0.45
Consensus pattern (14 bp):
TTCAATTCTTCAAA
Found at i:66903 original size:22 final size:22
Alignment explanation
Indices: 66859--67694 Score: 375
Period size: 22 Copynumber: 37.5 Consensus size: 22
66849 TCCAATGCTC
*
66859 CAATTCTTCAATTATCCAATTCTT
1 CAATTCTTCAA--ATTCAATTCTT
66883 CAATTCTTCAAATTCAATTCTT
1 CAATTCTTCAAATTCAATTCTT
*
66905 CAACAT-TTCAATACTTCAATTCTT
1 CAA-TTCTTCAA-A-TTCAATTCTT
* * *
66929 CAATGCTTCAATTTCAATATATGGTT
1 CAATTCTTCAAATTC-A-AT-T-CTT
66955 CAA-T-TTCAATACTTCAATTCTT
1 CAATTCTTCAA-A-TTCAATTCTT
*
66977 CAAATTCAATTC---TTCAATGCTT
1 C-AATTC--TTCAAATTCAATTCTT
*
66999 CAATAT-TTCAATGGTTCAA-T-TT
1 CAAT-TCTTCAA--ATTCAATTCTT
*
67021 CAATACTTC-AATTC--TTCAAATT
1 CAATTCTTCAAATTCAATTC---TT
67043 CAATTCTTCAATATTTCAA-T-TT
1 CAATTCTTCAA-A-TTCAATTCTT
67065 CAATTCTTCAAATTCAATTCTT
1 CAATTCTTCAAATTCAATTCTT
* *
67087 CAATGCTTCAATTTCAATAT-TT
1 CAATTCTTCAAATTCAAT-TCTT
* *
67109 CAATACTTCAATTTCAATTCTT
1 CAATTCTTCAAATTCAATTCTT
* *
67131 CAATGCTTCAATTTCAATTC--
1 CAATTCTTCAAATTCAATTCTT
67151 CAATT-TCTCAAATTCAAATT-TT
1 CAATTCT-TCAAATTC-AATTCTT
*
67173 CAATGT-TTCAATTTCAATAT-TT
1 CAAT-TCTTCAAATTCAAT-TCTT
* *
67195 CAATGCTTCAATTTCAATTC--
1 CAATTCTTCAAATTCAATTCTT
*
67215 CAATT-TCTCAAGTTCAATTCTT
1 CAATTCT-TCAAATTCAATTCTT
*
67237 CAATGT-TTCAATTTCAATAT-TT
1 CAAT-TCTTCAAATTCAAT-TCTT
* *
67259 CAATGCTTCAATTTCAATTC--
1 CAATTCTTCAAATTCAATTCTT
*
67279 CAATT-TCTCAAGTTCAATTCTT
1 CAATTCT-TCAAATTCAATTCTT
*
67301 CAATGT-TTCAATTTCAATAT-TT
1 CAAT-TCTTCAAATTCAAT-TCTT
* *
67323 CAATGCTTCAATTTCAATTC--
1 CAATTCTTCAAATTCAATTCTT
67343 CAATT-TCTCAAATTCAATTCTT
1 CAATTCT-TCAAATTCAATTCTT
*
67365 CAATGT-TTCAATTTCAATTC--
1 CAAT-TCTTCAAATTCAATTCTT
67385 CAATT-TCTCAAATTCAATTCTT
1 CAATTCT-TCAAATTCAATTCTT
*
67407 CAATGT-TTCAATTTCAATAT-TT
1 CAAT-TCTTCAAATTCAAT-TCTT
67429 CAATTCTTCAAATTCAATTCTT
1 CAATTCTTCAAATTCAATTCTT
*
67451 CAATGT-TTCAATATGTCAATGCTT
1 CAAT-TCTTCAA-AT-TCAATTCTT
* *
67475 C-AGT-TTCAAATTCAATTCCT
1 CAATTCTTCAAATTCAATTCTT
* * *
67495 CAATGCTTCAATTTCAGTAT-TT
1 CAATTCTTCAAATTCAAT-TCTT
* *
67517 CAATGT-TTCAATTCTTCAATGCTT
1 CAAT-TCTTCAA--ATTCAATTCTT
*
67541 CAATGTC-TCAATTTCAA-T-TT
1 CAAT-TCTTCAAATTCAATTCTT
*
67561 CAA-TCATTCAATGATTCAATTCTC
1 CAATTC-TTCAA--ATTCAATTCTT
*
67585 CAATTCTTCAATTATTCAATGCTT
1 CAATTCTTCAA--ATTCAATTCTT
* * *
67609 CAGTTCTTCAATGCTTCAACTCTT
1 CAATTCTTCAA--ATTCAATTCTT
* *
67633 CAATTATTCAGATGCTTCAATTCTT
1 CAATTCTTCA-A--ATTCAATTCTT
* *
67658 CAAATTATTCAAGCGCTTCAATTCTT
1 C-AATTCTTCAA---ATTCAATTCTT
*
67684 CAATTATTCAA
1 CAATTCTTCAA
67695 TGCATCAATT
Statistics
Matches: 657, Mismatches: 65, Indels: 179
0.73 0.07 0.20
Matches are distributed among these distances:
18 3 0.00
19 12 0.02
20 97 0.15
21 22 0.03
22 313 0.48
23 27 0.04
24 117 0.18
25 32 0.05
26 31 0.05
27 3 0.00
ACGTcount: A:0.31, C:0.21, G:0.04, T:0.44
Consensus pattern (22 bp):
CAATTCTTCAAATTCAATTCTT
Found at i:66971 original size:64 final size:61
Alignment explanation
Indices: 66910--67510 Score: 425
Period size: 64 Copynumber: 9.5 Consensus size: 61
66900 TTCTTCAACA
* *
66910 TTTCAATACTTCAATTCTTCAATGCTTCAATTTCAATAT-ATGGTTCAATTTCAATACTTCAAT
1 TTTCAA-A-TTCAATTCTTCAATGTTTCAATTTCAATATAATGCTTCAATTTCAATA-TTCAAT
* * *
66973 TCTTCAAATTCAATTCTTCAATGCTTCAATATT---T-CAATGGTTCAATTTCAATACTTCAAT
1 T-TTCAAATTCAATTCTTCAATGTTTCAAT-TTCAATATAATGCTTCAATTTCAATA-TTCAAT
* * *
67033 TCTTCAAATTCAATTCTTCAATATTTCAATTTC-A-AT--T-CTTCAAATTCAATTCTTCAAT
1 T-TTCAAATTCAATTCTTCAATGTTTCAATTTCAATATAATGCTTCAATTTCAA-TATTCAAT
* * ** * *
67091 GCTTCAATTTCAATAT-TTCAATACTTCAATTTCAATTCTTCAATGCTTCAATTTCAAT-TCCAA
1 -TTTCAAATTCAAT-TCTTCAATGTTTCAATTTCAA-T-AT-AATGCTTCAATTTCAATATTCAA
67154 T
61 T
*
67155 TTCTCAAATTCAAATT-TTCAATGTTTCAATTTCAATATTTCAATGCTTCAATTTCAAT-TCCAA
1 TT-TCAAATTC-AATTCTTCAATGTTTCAATTTCAATA--T-AATGCTTCAATTTCAATATTCAA
67218 T
61 T
* *
67219 TTCTCAAGTTCAATTCTTCAATGTTTCAATTTCAATATTTCAATGCTTCAATTTCAAT-TCCAAT
1 TT-TCAAATTCAATTCTTCAATGTTTCAATTTCAATA--T-AATGCTTCAATTTCAATATTCAAT
* *
67283 TTCTCAAGTTCAATTCTTCAATGTTTCAATTTCAATATTTCAATGCTTCAATTTCAAT-TCCAAT
1 TT-TCAAATTCAATTCTTCAATGTTTCAATTTCAATA--T-AATGCTTCAATTTCAATATTCAAT
* * *
67347 TTCTCAAATTCAATTCTTCAATGTTTCAATTTCAAT-TCCAAT-TTCTCAAATTCAATTCTTCAA
1 TT-TCAAATTCAATTCTTCAATGTTTCAATTTCAATAT--AATGCT-TCAATTTCAA-TATTCAA
67410 T
61 T
* * * * *
67411 GTTTCAATTTCAATAT-TTCAAT-TCTTCAAATTCAATTCTTCAATGTTTCAATATGTCAATGCT
1 -TTTCAAATTCAAT-TCTTCAATGT-TTCAATTTCAA-T-AT-AATGCTTCAAT-T-TCAAT-AT
*
67474 TC-AG
57 TCAAT
* *
67478 TTTCAAATTCAATTCCTCAATGCTTCAATTTCA
1 TTTCAAATTCAATTCTTCAATGTTTCAATTTCA
67511 GTATTTCAAT
Statistics
Matches: 469, Mismatches: 31, Indels: 73
0.82 0.05 0.13
Matches are distributed among these distances:
58 43 0.09
59 6 0.01
60 53 0.11
61 2 0.00
62 36 0.08
63 12 0.03
64 248 0.53
65 10 0.02
66 45 0.10
67 6 0.01
68 8 0.02
ACGTcount: A:0.31, C:0.20, G:0.04, T:0.45
Consensus pattern (61 bp):
TTTCAAATTCAATTCTTCAATGTTTCAATTTCAATATAATGCTTCAATTTCAATATTCAAT
Found at i:67505 original size:8 final size:8
Alignment explanation
Indices: 67494--67703 Score: 96
Period size: 8 Copynumber: 26.6 Consensus size: 8
67484 ATTCAATTCC
67494 TCAATGCT
1 TCAATGCT
67502 TCAAT--T
1 TCAATGCT
* **
67508 TCAGTATT
1 TCAATGCT
*
67516 TCAATGTT
1 TCAATGCT
*
67524 TCAATTCT
1 TCAATGCT
67532 TCAATGCT
1 TCAATGCT
67540 TCAATG-T
1 TCAATGCT
67547 CTCAAT--T
1 -TCAATGCT
67554 TCAAT--T
1 TCAATGCT
67560 TCAAT-CAT
1 TCAATGC-T
*
67568 TCAATGAT
1 TCAATGCT
*
67576 TCAATTCT
1 TCAATGCT
* *
67584 CCAATTCT
1 TCAATGCT
**
67592 TCAATTAT
1 TCAATGCT
67600 TCAATGCT
1 TCAATGCT
* *
67608 TCAGTTCT
1 TCAATGCT
67616 TCAATGCT
1 TCAATGCT
67624 TCAACT-CT
1 TCAA-TGCT
**
67632 TCAATTAT
1 TCAATGCT
67640 TCAGATGCT
1 TCA-ATGCT
*
67649 TCAATTCT
1 TCAATGCT
**
67657 TCAAATTAT
1 TC-AATGCT
*
67666 TCAAGCGCT
1 TCAA-TGCT
*
67675 TCAATTCT
1 TCAATGCT
**
67683 TCAATTAT
1 TCAATGCT
*
67691 TCAATGCA
1 TCAATGCT
67699 TCAAT
1 TCAAT
67704 TTACTTCAAA
Statistics
Matches: 159, Mismatches: 32, Indels: 22
0.75 0.15 0.10
Matches are distributed among these distances:
6 16 0.10
7 3 0.02
8 121 0.76
9 19 0.12
ACGTcount: A:0.29, C:0.22, G:0.07, T:0.42
Consensus pattern (8 bp):
TCAATGCT
Found at i:67675 original size:26 final size:26
Alignment explanation
Indices: 67621--67694 Score: 107
Period size: 25 Copynumber: 2.9 Consensus size: 26
67611 GTTCTTCAAT
* *
67621 GCTTCAACTCTTCAATTATTC-AGAT
1 GCTTCAATTCTTCAATTATTCAAGAC
67646 GCTTCAATTCTTCAAATTATTCAAG-C
1 GCTTCAATTCTTC-AATTATTCAAGAC
67672 GCTTCAATTCTTCAATTATTCAA
1 GCTTCAATTCTTCAATTATTCAA
67695 TGCATCAATT
Statistics
Matches: 45, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
25 22 0.49
26 21 0.47
27 2 0.04
ACGTcount: A:0.30, C:0.23, G:0.07, T:0.41
Consensus pattern (26 bp):
GCTTCAATTCTTCAATTATTCAAGAC
Found at i:68336 original size:2 final size:2
Alignment explanation
Indices: 68331--68359 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
68321 TTTTTTGCAA
68331 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 A
68360 AACACACCAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:69880 original size:35 final size:35
Alignment explanation
Indices: 69807--69906 Score: 138
Period size: 35 Copynumber: 3.0 Consensus size: 35
69797 AAACCGAAGG
* *
69807 CCAAATCGATCGGACGGTGATA--CC-TGA--AGA
1 CCAAACCGATCGGACGGTGATATTCCGAGATCAGA
69837 CCAAACCGATCGGACGGTGATATTCCGAGATCAGA
1 CCAAACCGATCGGACGGTGATATTCCGAGATCAGA
*
69872 CCAAACCGATCGGACAGTGATATTCCGAGATCAGA
1 CCAAACCGATCGGACGGTGATATTCCGAGATCAGA
69907 GAGCAAGAGT
Statistics
Matches: 62, Mismatches: 3, Indels: 5
0.89 0.04 0.07
Matches are distributed among these distances:
30 21 0.34
32 2 0.03
33 2 0.03
35 37 0.60
ACGTcount: A:0.33, C:0.25, G:0.25, T:0.17
Consensus pattern (35 bp):
CCAAACCGATCGGACGGTGATATTCCGAGATCAGA
Found at i:71931 original size:68 final size:68
Alignment explanation
Indices: 71632--72162 Score: 573
Period size: 68 Copynumber: 7.9 Consensus size: 68
71622 AATAAAGTTT
* * *
71632 TATTTTCTCTTTCCAGAAATACCCTTTTGGTCGAAGGGTCATTTTCGTC-TTTTGCATTTAAGTT
1 TATTTTCTATTTCCAAAAATACCCTTTCGGTCGAAGGGTCATTTTCGTCTTTTTGCATTTAAGTT
71696 TAG
66 TAG
* * * * * *
71699 CATTTTCAAATTTCC-AAAGTACTCTTTCGGTCGAAGGGTCATTTTCGTCTTTTTACATTCAAGT
1 TATTTTC-TATTTCCAAAAATACCCTTTCGGTCGAAGGGTCATTTTCGTCTTTTTGCATTTAAGT
* *
71763 TCAA
65 TTAG
* *
71767 TATTTTC-ATTTCCAAAAATACCCTTTCGGT-GAAAGGGTCATTTTCGCCTTTTTCGCATCTAAG
1 TATTTTCTATTTCCAAAAATACCCTTTCGGTCG-AAGGGTCATTTTCGTCTTTTT-GCATTTAAG
*
71830 TTTTG
64 TTTAG
* *
71835 TGTTTTCTATTTCCAAAAATACCATTTCGGTCGAAGGGTCATTTTCGTCTTTTTGCATTTAAGTT
1 TATTTTCTATTTCCAAAAATACCCTTTCGGTCGAAGGGTCATTTTCGTCTTTTTGCATTTAAGTT
*
71900 TGG
66 TAG
* * *
71903 TGTTTTCTCTTTCTAAAAATACCCTTTCGGTCGAAGGGTCATTTTCGT-TTTTTCGCATTTAAGT
1 TATTTTCTATTTCCAAAAATACCCTTTCGGTCGAAGGGTCATTTTCGTCTTTTT-GCATTTAAGT
71967 TTAG
65 TTAG
* * **
71971 CATTTTCT-TCTTCCAAAAATACCCTTTCGGTCGAAGGGTCATTTTCGTCTTCTTGCACCTAAGT
1 TATTTTCTAT-TTCCAAAAATACCCTTTCGGTCGAAGGGTCATTTTCGTCTTTTTGCATTTAAGT
72035 TTAG
65 TTAG
* * * * ** * *
72039 TACTTTCTTTTTCCAAAAATGCCCTTTCGGTCGAAGGGTCAATTTCAAC-CTTTCCATGTCTAAG
1 TATTTTCTATTTCCAAAAATACCCTTTCGGTCGAAGGGTCATTTTCGTCTTTTTGCAT-T-TAAG
72103 -TTAG
64 TTTAG
* * * *
72107 --TTTACT-TTTCCCAAAATACCCTTTCGGTCAAAGGGTCAATTTT-GTCATTCTTGCAT
1 TATTTTCTATTTCCAAAAATACCCTTTCGGTCGAAGGGTC-ATTTTCGTC-TTTTTGCAT
72163 ATGACTTTAC
Statistics
Matches: 390, Mismatches: 58, Indels: 32
0.81 0.12 0.07
Matches are distributed among these distances:
65 29 0.07
66 15 0.04
67 85 0.22
68 209 0.54
69 51 0.13
70 1 0.00
ACGTcount: A:0.22, C:0.21, G:0.15, T:0.43
Consensus pattern (68 bp):
TATTTTCTATTTCCAAAAATACCCTTTCGGTCGAAGGGTCATTTTCGTCTTTTTGCATTTAAGTT
TAG
Found at i:72346 original size:6 final size:6
Alignment explanation
Indices: 72335--72374 Score: 62
Period size: 6 Copynumber: 6.3 Consensus size: 6
72325 AAAATACAAA
72335 AAGATT AAGATT AAGATT AAGATT AAGCATTT AAGATT AA
1 AAGATT AAGATT AAGATT AAGATT AAG-A-TT AAGATT AA
72375 AAGCAACCAA
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
6 25 0.78
7 2 0.06
8 5 0.16
ACGTcount: A:0.50, C:0.03, G:0.15, T:0.33
Consensus pattern (6 bp):
AAGATT
Found at i:77092 original size:42 final size:43
Alignment explanation
Indices: 77047--77130 Score: 132
Period size: 45 Copynumber: 1.9 Consensus size: 43
77037 CTAAATTGTA
*
77047 CTCCATCTCTAGGTAATTCATCAAAATAAAGCTAATATTCTACTC
1 CTCCATCTCTAGATAATTCATCAAAATAAAGCTAATATTCTA--C
*
77092 CTCCATCTCTAGATAATTCATCAAAATAAAGCTCATATT
1 CTCCATCTCTAGATAATTCATCAAAATAAAGCTAATATT
77131 ATTTGTTGTT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
45 37 1.00
ACGTcount: A:0.37, C:0.24, G:0.06, T:0.33
Consensus pattern (43 bp):
CTCCATCTCTAGATAATTCATCAAAATAAAGCTAATATTCTAC
Found at i:77462 original size:13 final size:13
Alignment explanation
Indices: 77419--77473 Score: 69
Period size: 13 Copynumber: 4.3 Consensus size: 13
77409 AAATATACTA
77419 AATATAAGCAACT
1 AATATAAGCAACT
* *
77432 AATAGAA--ACCT
1 AATATAAGCAACT
77443 CAATATAAGCAACT
1 -AATATAAGCAACT
77457 AATATAAGCAACT
1 AATATAAGCAACT
77470 AATA
1 AATA
77474 GAAACCTCAA
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
11 3 0.09
12 6 0.17
13 23 0.66
14 3 0.09
ACGTcount: A:0.55, C:0.16, G:0.07, T:0.22
Consensus pattern (13 bp):
AATATAAGCAACT
Found at i:79699 original size:26 final size:26
Alignment explanation
Indices: 79663--79712 Score: 100
Period size: 26 Copynumber: 1.9 Consensus size: 26
79653 AGTTTCTTGA
79663 CCTAGAATGATGCGCCTATATAGTGG
1 CCTAGAATGATGCGCCTATATAGTGG
79689 CCTAGAATGATGCGCCTATATAGT
1 CCTAGAATGATGCGCCTATATAGT
79713 ATCATATTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.28, C:0.20, G:0.24, T:0.28
Consensus pattern (26 bp):
CCTAGAATGATGCGCCTATATAGTGG
Done.