Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005015.1 Hibiscus syriacus cultivar Beakdansim tig00011258_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 87724
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:363 original size:195 final size:201
Alignment explanation
Indices: 1--434 Score: 569
Period size: 195 Copynumber: 2.2 Consensus size: 201
* *
1 TCCATTCAA-CTCGATGGTGTATCAACTGCATTGTAGCAGCAGGAACTACTTTCCGGGTGAAGTT
1 TCCATT-AAGCTCGAGGGTGTATCAACCGCATTGTAGCAGCAGGAACTACTTTCCGGGTGAAGTT
*
65 TAAACTGAGGTATTTAAGTCGAAAAAAAAGACCCGGGTTGGATGCGATTTAGAAACAATGAACTA
65 TAAACTGAGGTATTTAAGTCGAAAAAAAAGACCCGGGTTGGATGCGATTTAGAAACAAGGAACTA
*
130 TAATCCCAGCCAAATTCACAGCATAGCTCAAGGCGATAAAGGATATCTATCAATGAAGAC-TTCG
130 T-ATCCCAGCCAAATTCACAGCATAGCTCAAGGCGATAAAGGATATCTATCAATGAACACTTTCG
194 AGTTCGAT
194 AGTTCGAT
* * *
202 TCCATTAATCTTGAGGGTGTATCAACCGCA-TGTAGCAAG-AGGAACTACTTT-CGGTTGAAGTT
1 TCCATTAAGCTCGAGGGTGTATCAACCGCATTGTAGC-AGCAGGAACTACTTTCCGGGTGAAGTT
* * * * * * * *
264 TAAACTGAGGTCTTTAAGTC-CAGAAGATGACCCGGTTTGGATGCGATTTAGCAATAAGGAACTA
65 TAAACTGAGGTATTTAAGTCGAAAAAAAAGACCCGGGTTGGATGCGATTTAGAAACAAGGAACTA
* * * * * * *
328 T-TCCC-TCCAAATTCACAGCATAGCTCAATGCGATAAGGGTTATCTCTCAATGACCACTTTTGA
130 TATCCCAGCCAAATTCACAGCATAGCTCAAGGCGATAAAGGATATCTATCAATGAACACTTTCGA
*
391 GTTTGAT
195 GTTCGAT
*
398 TCCATTCAGCTCGAGGGTGTATCAACCGCATTGTAGC
1 TCCATTAAGCTCGAGGGTGTATCAACCGCATTGTAGC
435 TGTACACCCC
Statistics
Matches: 204, Mismatches: 25, Indels: 12
0.85 0.10 0.05
Matches are distributed among these distances:
195 45 0.22
196 41 0.20
197 6 0.03
198 37 0.18
199 29 0.14
200 20 0.10
201 26 0.13
ACGTcount: A:0.31, C:0.20, G:0.22, T:0.28
Consensus pattern (201 bp):
TCCATTAAGCTCGAGGGTGTATCAACCGCATTGTAGCAGCAGGAACTACTTTCCGGGTGAAGTTT
AAACTGAGGTATTTAAGTCGAAAAAAAAGACCCGGGTTGGATGCGATTTAGAAACAAGGAACTAT
ATCCCAGCCAAATTCACAGCATAGCTCAAGGCGATAAAGGATATCTATCAATGAACACTTTCGAG
TTCGAT
Found at i:1126 original size:23 final size:23
Alignment explanation
Indices: 1074--1147 Score: 98
Period size: 23 Copynumber: 3.3 Consensus size: 23
1064 GTCCGAAGGA
*
1074 CCACATA-GTTTGCACCAAAGT-
1 CCACATAGGGTTGCACCAAAGTG
* **
1095 ACACATAGGGTTGCACTGAAGTG
1 CCACATAGGGTTGCACCAAAGTG
1118 CCACATAGGGTTGCACCAAAGTG
1 CCACATAGGGTTGCACCAAAGTG
1141 CCACATA
1 CCACATA
1148 TTTGTCCCAG
Statistics
Matches: 44, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
21 6 0.14
22 11 0.25
23 27 0.61
ACGTcount: A:0.32, C:0.26, G:0.22, T:0.20
Consensus pattern (23 bp):
CCACATAGGGTTGCACCAAAGTG
Found at i:1166 original size:44 final size:43
Alignment explanation
Indices: 1044--1168 Score: 105
Period size: 44 Copynumber: 2.9 Consensus size: 43
1034 ACTCAATTTA
* * *
1044 CACCGAAGTGCCACATAATTGTCCGA-AGGACCACATAGTTTG
1 CACCAAAGTGCCACATAATTGTCCCAGAGGACCACATAGGTTG
* * * *
1086 CACCAAAGT-ACACATAGGGTTG-CACTGAAGTG-CCACATAGGGTTG
1 CACCAAAGTGCCACATA--ATTGTCCCAG-AG-GACCACATA-GGTTG
*
1131 CACCAAAGTGCCACATATTTGTCCCAGAGGACCACATA
1 CACCAAAGTGCCACATAATTGTCCCAGAGGACCACATA
1169 ATTATCCTGA
Statistics
Matches: 63, Mismatches: 11, Indels: 16
0.70 0.12 0.18
Matches are distributed among these distances:
41 6 0.10
42 9 0.14
43 4 0.06
44 21 0.33
45 17 0.27
46 6 0.10
ACGTcount: A:0.32, C:0.26, G:0.22, T:0.20
Consensus pattern (43 bp):
CACCAAAGTGCCACATAATTGTCCCAGAGGACCACATAGGTTG
Found at i:1365 original size:21 final size:21
Alignment explanation
Indices: 1319--1368 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
1309 ATAGAGTATA
*
1319 TTCACATTCACTGGTTCGAAG
1 TTCATATTCACTGGTTCGAAG
* *
1340 ATCATATTCACTTGTTC-AAGG
1 TTCATATTCACTGGTTCGAA-G
1361 TTCATATT
1 TTCATATT
1369 TTCATAACAC
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
20 2 0.08
21 22 0.92
ACGTcount: A:0.26, C:0.20, G:0.14, T:0.40
Consensus pattern (21 bp):
TTCATATTCACTGGTTCGAAG
Found at i:1761 original size:20 final size:20
Alignment explanation
Indices: 1711--1762 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 20
1701 CATGCTTGAA
1711 GGTATCGATACCACCCTAAG
1 GGTATCGATACCACCCTAAG
* * * *
1731 GCTACCAATACCACCCTCAG
1 GGTATCGATACCACCCTAAG
1751 GGTATCGATACC
1 GGTATCGATACC
1763 TACGTATGTA
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.29, C:0.35, G:0.17, T:0.19
Consensus pattern (20 bp):
GGTATCGATACCACCCTAAG
Found at i:8191 original size:21 final size:21
Alignment explanation
Indices: 8162--8211 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
8152 ATAGAGTATA
* *
8162 TTCACATTCACTGGTTCGAA-G
1 TTCATATTCACTGATTC-AAGG
*
8183 TTCATATTCACTTATTCAAGG
1 TTCATATTCACTGATTCAAGG
8204 TTCATATT
1 TTCATATT
8212 TTCATAACAC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 2 0.08
21 23 0.92
ACGTcount: A:0.26, C:0.20, G:0.12, T:0.42
Consensus pattern (21 bp):
TTCATATTCACTGATTCAAGG
Found at i:8574 original size:22 final size:20
Alignment explanation
Indices: 8524--8577 Score: 63
Period size: 22 Copynumber: 2.6 Consensus size: 20
8514 CATACTTAGA
*
8524 GGTATCGGTACCACCCTAAG
1 GGTATCGATACCACCCTAAG
* *
8544 GGTACCGATACCACCCCTCAGG
1 GGTATCGATACCA-CCCT-AAG
8566 GGTATCGATACC
1 GGTATCGATACC
8578 GACGCATGTA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
20 11 0.39
21 4 0.14
22 13 0.46
ACGTcount: A:0.24, C:0.33, G:0.24, T:0.19
Consensus pattern (20 bp):
GGTATCGATACCACCCTAAG
Found at i:8721 original size:22 final size:24
Alignment explanation
Indices: 8689--8745 Score: 68
Period size: 22 Copynumber: 2.5 Consensus size: 24
8679 GATACCCCCT
* *
8689 AAGGTACCGATACCCA-TC-CATC
1 AAGGTATCGATACCCACTCTCAAC
8711 AAGGTATCGATA-CCACTCTCAAC
1 AAGGTATCGATACCCACTCTCAAC
8734 -AGGTATCGATAC
1 AAGGTATCGATAC
8746 ATCCCTTACA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
21 3 0.10
22 24 0.80
23 3 0.10
ACGTcount: A:0.33, C:0.30, G:0.16, T:0.21
Consensus pattern (24 bp):
AAGGTATCGATACCCACTCTCAAC
Found at i:10380 original size:37 final size:36
Alignment explanation
Indices: 10313--10526 Score: 263
Period size: 37 Copynumber: 5.8 Consensus size: 36
10303 AAAAATCAAT
*
10313 TTTTGAAAATATATATACTATATAGTTTTGAAAACA
1 TTTTGAAAATATATATAATATATAGTTTTGAAAACA
*
10349 TTTTGAAAAAATATATAATATATAGTGTTTGAAAACA
1 TTTTGAAAATATATATAATATATAGT-TTTGAAAACA
*
10386 TTTTGAAAATATATATAATATATAGTTTTTGAAACCA
1 TTTTGAAAATATATATAATATATAG-TTTTGAAAACA
**
10423 TTTTTGAAAATATATATAATA-ATAGTTTT-AAAATG
1 -TTTTGAAAATATATATAATATATAGTTTTGAAAACA
* *
10458 TTTTGAAAAAATATATATAATATATAATTTGGAAAACA
1 TTTTG--AAAATATATATAATATATAGTTTTGAAAACA
*
10496 TTTTTTCGAAAATATATACAATAT-TAGTTTT
1 --TTTT-GAAAATATATATAATATATAGTTTT
10527 TTATATTATA
Statistics
Matches: 154, Mismatches: 14, Indels: 18
0.83 0.08 0.10
Matches are distributed among these distances:
34 5 0.03
35 3 0.02
36 43 0.28
37 53 0.34
38 30 0.19
39 15 0.10
40 4 0.03
41 1 0.01
ACGTcount: A:0.45, C:0.04, G:0.08, T:0.43
Consensus pattern (36 bp):
TTTTGAAAATATATATAATATATAGTTTTGAAAACA
Found at i:10392 original size:73 final size:70
Alignment explanation
Indices: 10313--10526 Score: 248
Period size: 75 Copynumber: 2.9 Consensus size: 70
10303 AAAAATCAAT
*
10313 TTTTGAAAATATATATACTATATAGTTTTGAAAACATTTTGAAAAAATATATAATATATAGTGTT
1 TTTTGAAAATATATATAATATATAGTTTTGAAAACATTTTGAAAAAATATATAATA-ATAGT-TT
10378 TGAAAACA
64 T-AAAACA
* *
10386 TTTTGAAAATATATATAATATATAGTTTTTGAAACCATTTTTGAAAATATATATAATAATAGTTT
1 TTTTGAAAATATATATAATATATAG-TTTTGAAAACA-TTTTGAAAAAATATATAATAATAGTTT
**
10451 TAAAATG
64 TAAAACA
* * * * *
10458 TTTTGAAAAAATATATATAATATATAATTTGGAAAACATTTTTTCGAAAATATATACAATATTAG
1 TTTTG--AAAATATATATAATATATAGTTTTGAAAACA--TTTT-GAAAAAATATATAATAATAG
10523 TTTT
61 TTTT
10527 TTATATTATA
Statistics
Matches: 125, Mismatches: 10, Indels: 10
0.86 0.07 0.07
Matches are distributed among these distances:
72 9 0.07
73 36 0.29
74 39 0.31
75 41 0.33
ACGTcount: A:0.45, C:0.04, G:0.08, T:0.43
Consensus pattern (70 bp):
TTTTGAAAATATATATAATATATAGTTTTGAAAACATTTTGAAAAAATATATAATAATAGTTTTA
AAACA
Found at i:11692 original size:24 final size:23
Alignment explanation
Indices: 11656--11716 Score: 59
Period size: 24 Copynumber: 2.6 Consensus size: 23
11646 TTTATTTTAT
*
11656 TTTTATTACTTTTAGAAATTAACA
1 TTTT-TTATTTTTAGAAATTAACA
** **
11680 TTTTTTCATTTTTTTATTTTAACA
1 TTTTTT-ATTTTTAGAAATTAACA
11704 TTTTTTATTTTTA
1 TTTTTTATTTTTA
11717 TCATTTTCTC
Statistics
Matches: 30, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
23 8 0.27
24 22 0.73
ACGTcount: A:0.26, C:0.07, G:0.02, T:0.66
Consensus pattern (23 bp):
TTTTTTATTTTTAGAAATTAACA
Found at i:11698 original size:16 final size:16
Alignment explanation
Indices: 11679--11723 Score: 56
Period size: 15 Copynumber: 2.8 Consensus size: 16
11669 AGAAATTAAC
11679 ATTTTTTCATTTTTTT
1 ATTTTTTCATTTTTTT
**
11695 ATTTTAACA-TTTTTT
1 ATTTTTTCATTTTTTT
11710 ATTTTTATCATTTT
1 ATTTTT-TCATTTT
11724 CTCTTGTAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
15 11 0.48
16 9 0.39
17 3 0.13
ACGTcount: A:0.20, C:0.07, G:0.00, T:0.73
Consensus pattern (16 bp):
ATTTTTTCATTTTTTT
Found at i:11722 original size:24 final size:24
Alignment explanation
Indices: 11674--11723 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
11664 CTTTTAGAAA
*
11674 TTAACATTTTTTCATTTTTTTATT
1 TTAACATTTTTTCATTTTTTCATT
11698 TTAACATTTTTT-ATTTTTATCATT
1 TTAACATTTTTTCATTTTT-TCATT
11722 TT
1 TT
11724 CTCTTGTAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
23 6 0.25
24 18 0.75
ACGTcount: A:0.22, C:0.08, G:0.00, T:0.70
Consensus pattern (24 bp):
TTAACATTTTTTCATTTTTTCATT
Found at i:12979 original size:98 final size:97
Alignment explanation
Indices: 12809--12989 Score: 256
Period size: 98 Copynumber: 1.9 Consensus size: 97
12799 TCATTACTCG
* * * * *
12809 ACCTTGTGGTGACCCGATCCGAGGTAAGACCCACATTATTATTGTTCGGACTATGCTAACCACTA
1 ACCTTGCGGTGACCCGATCCGAGGTAAAACCCACATTATTATGGTTCGGACTATGCTAAACACAA
*
12874 ACTTTTTTTATATTTATTTGCATTATTCGATTCA
66 AC-CTTTTT-TATTTATTTGCATTATTCGATTCA
* * *
12908 ACCTTGCGGTGACCCGATCCG-GGTAAAATCCACATTATTATGGTTCGGACTTTGCTAAATACAA
1 ACCTTGCGGTGACCCGATCCGAGGTAAAACCCACATTATTATGGTTCGGACTATGCTAAACACAA
12972 ACCTTTTTTATTTATTTG
66 ACCTTTTTTATTTATTTG
12990 TTTTTATATA
Statistics
Matches: 73, Mismatches: 9, Indels: 3
0.86 0.11 0.04
Matches are distributed among these distances:
96 10 0.14
97 5 0.07
98 38 0.52
99 20 0.27
ACGTcount: A:0.25, C:0.21, G:0.16, T:0.38
Consensus pattern (97 bp):
ACCTTGCGGTGACCCGATCCGAGGTAAAACCCACATTATTATGGTTCGGACTATGCTAAACACAA
ACCTTTTTTATTTATTTGCATTATTCGATTCA
Found at i:13108 original size:114 final size:114
Alignment explanation
Indices: 12894--13110 Score: 265
Period size: 115 Copynumber: 1.9 Consensus size: 114
12884 TATTTATTTG
12894 CATTATTCGATTCAACCTTGCGGTGACCCGATCCGGGTAAAATCCACATTATTATGGTTCGGACT
1 CATTATTCGATTCAACCTTGCGGTGACCCGATCCGGGTAAAATCCACATTATTATGGTTCGGACT
* * * ** *** * ***
12959 TTGCTAAATACAAACCTTTTTTATTTATTTGTTTTTATATATCCGTTTC
66 CTACTAAACACAAACCGCTAACATTCATAACTTTTTATATATCCGTTTC
* * *
13008 CATTATTCGATTCGACCTTGTGGTGACCCGATCCGGGGTAAGATCCACATTATTATGGTTCGGAC
1 CATTATTCGATTCAACCTTGCGGTGACCCGATCC-GGGTAAAATCCACATTATTATGGTTCGGAC
* *
13073 TCTACTAACCACTAACCGCTAACATTCA-AACTTTTTAT
65 TCTACTAAACACAAACCGCTAACATTCATAACTTTTTAT
13111 TTTTGTTGTC
Statistics
Matches: 85, Mismatches: 17, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
114 39 0.46
115 46 0.54
ACGTcount: A:0.25, C:0.23, G:0.15, T:0.37
Consensus pattern (114 bp):
CATTATTCGATTCAACCTTGCGGTGACCCGATCCGGGTAAAATCCACATTATTATGGTTCGGACT
CTACTAAACACAAACCGCTAACATTCATAACTTTTTATATATCCGTTTC
Found at i:13325 original size:17 final size:17
Alignment explanation
Indices: 13278--13336 Score: 50
Period size: 17 Copynumber: 3.5 Consensus size: 17
13268 TCTGTTTTTT
13278 ATTTTATTTATTTTCTAAC
1 ATTTTATTT-TTTTC-AAC
**
13297 ATTTTA--AATTTCAAC
1 ATTTTATTTTTTTCAAC
**
13312 ATTTTATTTTTTTCTGC
1 ATTTTATTTTTTTCAAC
13329 ATTTTATT
1 ATTTTATT
13337 CCAGTCTTTT
Statistics
Matches: 32, Mismatches: 6, Indels: 6
0.73 0.14 0.14
Matches are distributed among these distances:
15 9 0.28
16 4 0.12
17 13 0.41
19 6 0.19
ACGTcount: A:0.25, C:0.10, G:0.02, T:0.63
Consensus pattern (17 bp):
ATTTTATTTTTTTCAAC
Found at i:13581 original size:2 final size:2
Alignment explanation
Indices: 13574--13623 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
13564 ATTTATGCGC
13574 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
13616 AT AT AT AT
1 AT AT AT AT
13624 TACATATTTT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:13819 original size:14 final size:14
Alignment explanation
Indices: 13802--13838 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
13792 TTTGTTTTGA
*
13802 TTTTTTTTACTTCG
1 TTTTATTTACTTCG
*
13816 TTTTATTTACTTTG
1 TTTTATTTACTTCG
13830 TTTTATTTA
1 TTTTATTTA
13839 TTTTTATCTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.14, C:0.08, G:0.05, T:0.73
Consensus pattern (14 bp):
TTTTATTTACTTCG
Found at i:22392 original size:89 final size:89
Alignment explanation
Indices: 22241--22413 Score: 346
Period size: 89 Copynumber: 1.9 Consensus size: 89
22231 TTGGTTTACT
22241 CTTAAGTTCCATTGGTTTCCCAGTTCCCACAACCGTAAGTCGCCACTTTTCAACCCTTGCAAGCA
1 CTTAAGTTCCATTGGTTTCCCAGTTCCCACAACCGTAAGTCGCCACTTTTCAACCCTTGCAAGCA
22306 CAAAACAGCCATTTCTTTTCAACC
66 CAAAACAGCCATTTCTTTTCAACC
22330 CTTAAGTTCCATTGGTTTCCCAGTTCCCACAACCGTAAGTCGCCACTTTTCAACCCTTGCAAGCA
1 CTTAAGTTCCATTGGTTTCCCAGTTCCCACAACCGTAAGTCGCCACTTTTCAACCCTTGCAAGCA
22395 CAAAACAGCCATTTCTTTT
66 CAAAACAGCCATTTCTTTT
22414 TTTAATATAT
Statistics
Matches: 84, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
89 84 1.00
ACGTcount: A:0.25, C:0.33, G:0.12, T:0.30
Consensus pattern (89 bp):
CTTAAGTTCCATTGGTTTCCCAGTTCCCACAACCGTAAGTCGCCACTTTTCAACCCTTGCAAGCA
CAAAACAGCCATTTCTTTTCAACC
Found at i:29275 original size:22 final size:23
Alignment explanation
Indices: 29248--29305 Score: 68
Period size: 22 Copynumber: 2.6 Consensus size: 23
29238 TTCAAAAAAT
29248 ACATATAATATAT-GATTTTTG-AA
1 ACATATAATATATCG--TTTTGAAA
*
29271 A-ATATATTATATCGTTTTGAAA
1 ACATATAATATATCGTTTTGAAA
29293 ACATATAATATAT
1 ACATATAATATAT
29306 ATGGCTTTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
21 5 0.17
22 13 0.43
23 12 0.40
ACGTcount: A:0.45, C:0.05, G:0.07, T:0.43
Consensus pattern (23 bp):
ACATATAATATATCGTTTTGAAA
Found at i:29290 original size:21 final size:24
Alignment explanation
Indices: 29264--29321 Score: 68
Period size: 25 Copynumber: 2.5 Consensus size: 24
29254 AATATATGAT
29264 TTTTGAAAATAT-AT-TATATCG-
1 TTTTGAAAATATAATATATATCGC
*
29285 TTTTGAAAACATATAATATATATGGC
1 TTTTG-AAA-ATATAATATATATCGC
29311 TTTTGAAAATA
1 TTTTGAAAATA
29322 ATTTTTAAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
21 5 0.16
22 3 0.10
23 4 0.13
24 5 0.16
25 9 0.29
26 5 0.16
ACGTcount: A:0.41, C:0.05, G:0.10, T:0.43
Consensus pattern (24 bp):
TTTTGAAAATATAATATATATCGC
Found at i:29376 original size:88 final size:85
Alignment explanation
Indices: 29230--29392 Score: 213
Period size: 88 Copynumber: 1.9 Consensus size: 85
29220 TAATATATAT
* * *
29230 AAAATAATTTCAAAAAATACATATAATATATGATTTTTGAAAATATATTATATCG-TTTTGAAAA
1 AAAATAATTTCAAAAAATACATATAATATATAATTTTTGAAAACATATTATATAGTTTTTG-AAA
29294 CATATAATATATATGGCTTTTG
65 -ATATAATATATATGGCTTTTG
* * *
29316 AAAATAATTTTTAAAAACATATATA-ATATATATAATTTTTGAAAACATGTTATATAGTTTTTGA
1 AAAATAA-TTTCAAAAA-ATACATATA-ATATATAATTTTTGAAAACATATTATATAGTTTTTGA
29380 AAATATAATATAT
63 AAATATAATATAT
29393 GTTATATAAT
Statistics
Matches: 67, Mismatches: 6, Indels: 7
0.84 0.08 0.09
Matches are distributed among these distances:
86 7 0.10
87 20 0.30
88 35 0.52
89 5 0.07
ACGTcount: A:0.47, C:0.04, G:0.07, T:0.42
Consensus pattern (85 bp):
AAAATAATTTCAAAAAATACATATAATATATAATTTTTGAAAACATATTATATAGTTTTTGAAAA
TATAATATATATGGCTTTTG
Found at i:29391 original size:22 final size:22
Alignment explanation
Indices: 29343--29392 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 22
29333 CATATATAAT
*
29343 ATATATAATTTTTGAAAACATG
1 ATATATAATTTTTGAAAACATA
* * *
29365 TTATATAGTTTTTGAAAATATA
1 ATATATAATTTTTGAAAACATA
29387 ATATAT
1 ATATAT
29393 GTTATATAAT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.44, C:0.02, G:0.08, T:0.46
Consensus pattern (22 bp):
ATATATAATTTTTGAAAACATA
Found at i:29416 original size:30 final size:29
Alignment explanation
Indices: 29362--29421 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 29
29352 TTTTGAAAAC
* **
29362 ATGTTATATAGTTTTTGAAAATATAATAT
1 ATGTTATATAATTTTAAAAAATATAATAT
*
29391 ATGTTATATAATTTTAAATAAATATAGTAT
1 ATGTTATATAATTTTAAA-AAATATAATAT
29421 A
1 A
29422 GTATTATTTA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
29 15 0.58
30 11 0.42
ACGTcount: A:0.45, C:0.00, G:0.08, T:0.47
Consensus pattern (29 bp):
ATGTTATATAATTTTAAAAAATATAATAT
Found at i:29438 original size:5 final size:5
Alignment explanation
Indices: 29426--29480 Score: 76
Period size: 5 Copynumber: 11.2 Consensus size: 5
29416 AGTATAGTAT
* * *
29426 TATT- TATTA TATTA TATTA CATTA CATTA CATTA TATTA TATTA TATTA
1 TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA
29475 TATTA T
1 TATTA T
29481 TATTCGATAT
Statistics
Matches: 48, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
4 4 0.08
5 44 0.92
ACGTcount: A:0.38, C:0.05, G:0.00, T:0.56
Consensus pattern (5 bp):
TATTA
Found at i:31855 original size:23 final size:23
Alignment explanation
Indices: 31829--31873 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
31819 GAACAAAGAC
*
31829 TAAATTGATAGAATTT-TTAAATA
1 TAAAGTGATA-AATTTATTAAATA
*
31852 TAAAGTGTTAAATTTATTAAAT
1 TAAAGTGATAAATTTATTAAAT
31874 TATTTTAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 5 0.26
23 14 0.74
ACGTcount: A:0.47, C:0.00, G:0.09, T:0.44
Consensus pattern (23 bp):
TAAAGTGATAAATTTATTAAATA
Found at i:33010 original size:2 final size:2
Alignment explanation
Indices: 33003--33042 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
32993 GCTTTAATCG
33003 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
33043 TTCTTCGTCT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:33529 original size:18 final size:17
Alignment explanation
Indices: 33491--33534 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
33481 TTTTAACTGC
33491 TTTATATTTTATTAATAA
1 TTTAT-TTTTATTAATAA
* *
33509 TTTTATTTTTATTACTTA
1 -TTTATTTTTATTAATAA
33527 TTTATTTT
1 TTTATTTT
33535 AAAAAAAGTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 8 0.35
18 10 0.43
19 5 0.22
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.70
Consensus pattern (17 bp):
TTTATTTTTATTAATAA
Found at i:34510 original size:24 final size:24
Alignment explanation
Indices: 34483--34535 Score: 79
Period size: 24 Copynumber: 2.2 Consensus size: 24
34473 ATGTGGTACT
*
34483 GATACCAAAGGTAAGAGAGGTATC
1 GATACCAAAGGTAAGAGAAGTATC
* *
34507 GATACCAAATGTAAGAGAAGTGTC
1 GATACCAAAGGTAAGAGAAGTATC
34531 GATAC
1 GATAC
34536 TCTATAGGTA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.42, C:0.13, G:0.26, T:0.19
Consensus pattern (24 bp):
GATACCAAAGGTAAGAGAAGTATC
Found at i:38265 original size:20 final size:20
Alignment explanation
Indices: 38240--38323 Score: 134
Period size: 20 Copynumber: 4.2 Consensus size: 20
38230 CAAGTTGATG
*
38240 ACACTTAAAGAAATGTTAGA
1 ACACTTAAAGAAGTGTTAGA
38260 ACACTTAAAGAAGTGTTAGA
1 ACACTTAAAGAAGTGTTAGA
38280 ACACTTTAAA-AAGTGTTAGA
1 ACAC-TTAAAGAAGTGTTAGA
*
38300 ACACTTAAAGAAGTATTAGA
1 ACACTTAAAGAAGTGTTAGA
38320 ACAC
1 ACAC
38324 CTATCCAAGC
Statistics
Matches: 60, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
19 5 0.08
20 50 0.83
21 5 0.08
ACGTcount: A:0.48, C:0.12, G:0.15, T:0.25
Consensus pattern (20 bp):
ACACTTAAAGAAGTGTTAGA
Found at i:40076 original size:20 final size:20
Alignment explanation
Indices: 40051--40143 Score: 98
Period size: 20 Copynumber: 4.7 Consensus size: 20
40041 TTTGCAACGC
* *
40051 AATTCGTAATGCGATAGTCA
1 AATTCGCAACGCGATAGTCA
* *
40071 AATTCGCAACAC-AAAGTCA
1 AATTCGCAACGCGATAGTCA
*
40090 AATTCACAACGCGATAGTCA
1 AATTCGCAACGCGATAGTCA
* * * *
40110 AATTCGTAACACAAAAGTCA
1 AATTCGCAACGCGATAGTCA
40130 AATTCGCAACGCGA
1 AATTCGCAACGCGA
40144 ATTTAATTTC
Statistics
Matches: 57, Mismatches: 15, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
19 16 0.28
20 41 0.72
ACGTcount: A:0.42, C:0.23, G:0.15, T:0.20
Consensus pattern (20 bp):
AATTCGCAACGCGATAGTCA
Found at i:40105 original size:39 final size:40
Alignment explanation
Indices: 40061--40143 Score: 141
Period size: 39 Copynumber: 2.1 Consensus size: 40
40051 AATTCGTAAT
40061 GCGATAGTCAAATTCGCAACAC-AAAGTCAAATTCACAAC
1 GCGATAGTCAAATTCGCAACACAAAAGTCAAATTCACAAC
* *
40100 GCGATAGTCAAATTCGTAACACAAAAGTCAAATTCGCAAC
1 GCGATAGTCAAATTCGCAACACAAAAGTCAAATTCACAAC
40140 GCGA
1 GCGA
40144 ATTTAATTTC
Statistics
Matches: 41, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
39 21 0.51
40 20 0.49
ACGTcount: A:0.42, C:0.24, G:0.16, T:0.18
Consensus pattern (40 bp):
GCGATAGTCAAATTCGCAACACAAAAGTCAAATTCACAAC
Found at i:40334 original size:14 final size:15
Alignment explanation
Indices: 40315--40352 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
40305 TCCCCATCTC
40315 TAATTTTTTT-TACA
1 TAATTTTTTTCTACA
*
40329 TAATTTTATTTCTATA
1 TAATTTT-TTTCTACA
40345 TAATTTTT
1 TAATTTTT
40353 CAATGATTTC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 7 0.33
15 4 0.19
16 10 0.48
ACGTcount: A:0.29, C:0.05, G:0.00, T:0.66
Consensus pattern (15 bp):
TAATTTTTTTCTACA
Found at i:40864 original size:23 final size:23
Alignment explanation
Indices: 40834--40883 Score: 100
Period size: 23 Copynumber: 2.2 Consensus size: 23
40824 AATCAACTAA
40834 GTTCTTCAACCCAAAATTTAATG
1 GTTCTTCAACCCAAAATTTAATG
40857 GTTCTTCAACCCAAAATTTAATG
1 GTTCTTCAACCCAAAATTTAATG
40880 GTTC
1 GTTC
40884 CACCAGAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.32, C:0.22, G:0.10, T:0.36
Consensus pattern (23 bp):
GTTCTTCAACCCAAAATTTAATG
Found at i:43424 original size:18 final size:18
Alignment explanation
Indices: 43401--43436 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
43391 AAGCAAAAGG
*
43401 AAATCAAAATCGCAATCA
1 AAATCAAAATCCCAATCA
43419 AAATCAAAATCCCAATCA
1 AAATCAAAATCCCAATCA
43437 CAACCGGCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.56, C:0.25, G:0.03, T:0.17
Consensus pattern (18 bp):
AAATCAAAATCCCAATCA
Found at i:43746 original size:20 final size:20
Alignment explanation
Indices: 43721--43759 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
43711 GATCAAAGCG
*
43721 AAAGTCAAATTCGTAACGCA
1 AAAGTCAAATTCGCAACGCA
43741 AAAGTCAAATTCGCAACGC
1 AAAGTCAAATTCGCAACGC
43760 GAAATAAGCG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.44, C:0.23, G:0.15, T:0.18
Consensus pattern (20 bp):
AAAGTCAAATTCGCAACGCA
Found at i:43794 original size:20 final size:20
Alignment explanation
Indices: 43771--43817 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
43761 AAATAAGCGT
*
43771 TGCGATAGTCAAATTCACAA
1 TGCGAAAGTCAAATTCACAA
*
43791 TGCGAAAGTCAAATTCGCAA
1 TGCGAAAGTCAAATTCACAA
43811 TGCGAAA
1 TGCGAAA
43818 TTGCAAATTG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.40, C:0.19, G:0.19, T:0.21
Consensus pattern (20 bp):
TGCGAAAGTCAAATTCACAA
Found at i:45018 original size:61 final size:63
Alignment explanation
Indices: 44883--45023 Score: 205
Period size: 62 Copynumber: 2.2 Consensus size: 63
44873 TTTTAGAAAT
*
44883 AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAAATAATTCTTATTTACACATCAAATT
1 AACAAATCAACTTTTACAAATCAATT--A-AAGCAAAAAAATAAATCTTATTTACACATCAAATT
44948 A
63 A
* * *
44949 AACAAATCAACTTTTACAAATCAATT-AATCAAAAAAATAAATCTTATTTCCTCATC-AATTA
1 AACAAATCAACTTTTACAAATCAATTAAAGCAAAAAAATAAATCTTATTTACACATCAAATTA
45010 AACAAATCAACTTT
1 AACAAATCAACTTT
45024 CAATGTAAAA
Statistics
Matches: 71, Mismatches: 4, Indels: 5
0.89 0.05 0.06
Matches are distributed among these distances:
61 19 0.27
62 26 0.37
66 26 0.37
ACGTcount: A:0.51, C:0.18, G:0.01, T:0.30
Consensus pattern (63 bp):
AACAAATCAACTTTTACAAATCAATTAAAGCAAAAAAATAAATCTTATTTACACATCAAATTA
Found at i:52162 original size:8 final size:8
Alignment explanation
Indices: 52149--52190 Score: 50
Period size: 8 Copynumber: 5.4 Consensus size: 8
52139 TTATTATATT
52149 TTAAAATA
1 TTAAAATA
52157 TTAAAATA
1 TTAAAATA
* * *
52165 AT-ATATT
1 TTAAAATA
52172 TTAAAATA
1 TTAAAATA
52180 TTAAAATA
1 TTAAAATA
52188 TTA
1 TTA
52191 TATTTTATAA
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
7 4 0.15
8 23 0.85
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (8 bp):
TTAAAATA
Found at i:52169 original size:23 final size:23
Alignment explanation
Indices: 52143--52202 Score: 102
Period size: 23 Copynumber: 2.6 Consensus size: 23
52133 AACCATTTAT
52143 TATATTTTAAAATATTAAAATAA
1 TATATTTTAAAATATTAAAATAA
*
52166 TATATTTTAAAATATTAAAATAT
1 TATATTTTAAAATATTAAAATAA
*
52189 TATATTTTATAATA
1 TATATTTTAAAATA
52203 ATTTATTATG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (23 bp):
TATATTTTAAAATATTAAAATAA
Found at i:73600 original size:2 final size:2
Alignment explanation
Indices: 73593--73621 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
73583 GGATTCTAAT
73593 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
73622 GACAATCAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:75875 original size:28 final size:28
Alignment explanation
Indices: 75840--75897 Score: 82
Period size: 28 Copynumber: 2.1 Consensus size: 28
75830 AAGTGTCATT
*
75840 TTAAATGTGTAT-CATTATCTAATATTTA
1 TTAAATGTGTATAC-TTATCTAATATATA
*
75868 TTAAATGTGTATACTTATCTGATATATA
1 TTAAATGTGTATACTTATCTAATATATA
75896 TT
1 TT
75898 GTGTATACAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
28 26 0.96
29 1 0.04
ACGTcount: A:0.34, C:0.07, G:0.09, T:0.50
Consensus pattern (28 bp):
TTAAATGTGTATACTTATCTAATATATA
Found at i:80152 original size:21 final size:21
Alignment explanation
Indices: 80128--80179 Score: 104
Period size: 21 Copynumber: 2.5 Consensus size: 21
80118 ATTGCTGACG
80128 ACGGCGGCTCGAGTGTGCTCA
1 ACGGCGGCTCGAGTGTGCTCA
80149 ACGGCGGCTCGAGTGTGCTCA
1 ACGGCGGCTCGAGTGTGCTCA
80170 ACGGCGGCTC
1 ACGGCGGCTC
80180 ACGCGACTGG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.13, C:0.31, G:0.38, T:0.17
Consensus pattern (21 bp):
ACGGCGGCTCGAGTGTGCTCA
Found at i:80554 original size:3 final size:3
Alignment explanation
Indices: 80532--80590 Score: 73
Period size: 3 Copynumber: 18.7 Consensus size: 3
80522 TAATTGTTAA
* *
80532 AAT AAT TAT AAT AGT AAT AAT AAT AAT AAT AATT AACTT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA-T AA--T AAT AAT AAT
80580 AAT AAT AAT AA
1 AAT AAT AAT AA
80591 AGACCCGAAC
Statistics
Matches: 50, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
3 43 0.86
4 3 0.06
5 4 0.08
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.36
Consensus pattern (3 bp):
AAT
Found at i:81112 original size:133 final size:134
Alignment explanation
Indices: 80832--81180 Score: 445
Period size: 133 Copynumber: 2.6 Consensus size: 134
80822 GGGTGACACG
* * * ** *
80832 GCTCCAACTTGATGAGGAGATCTGGTCGATGGATGACACAATTCCTACATGATGAGAATGATTGA
1 GCTCCTACGTGATGAGGAGATCTGGTCGGTGGATGACACGGTTCCTACATGATGAGAATGACTGA
**
80897 CCATCTTTAGGGATAATGATAACACGGTTCCTACGTGATGAGGATAGATGGTTATCTAAGGTTGA
66 CCATCTTTAGGGATAATGATAACACGGTTCCTACGTGATGAGGATAGAAAGTTATCTAAGGTTGA
80962 CGTT
131 CGTT
* * *
80966 GCTCCTACGTGATGAGGAGATCTGGTCGGTGGATGACACGGTTCCTACGTGATGAGGATGACTGG
1 GCTCCTACGTGATGAGGAGATCTGGTCGGTGGATGACACGGTTCCTACATGATGAGAATGACTGA
* * * *
81031 CCATCTTTA-GGATGATGATAACATGGTTCCTATGTGATGAGGA-CGACAAGTTATCTAAGGTTG
66 CCATCTTTAGGGATAATGATAACACGGTTCCTACGTGATGAGGATAGA-AAGTTATCTAAGGTTG
81094 ACG-T
130 ACGTT
* * * * ** *
81098 GACTCTTACGTGATGAGGATATTTGGTCGGTGGATGACACGGTTCCTACCTGATGATG-GCGGCT
1 G-CTCCTACGTGATGAGGAGATCTGGTCGGTGGATGACACGGTTCCTACATGATGA-GAATGACT
81162 GACCATCTTTAGGGATAAT
64 GACCATCTTTAGGGATAAT
81181 TGGTTTCAAT
Statistics
Matches: 187, Mismatches: 24, Indels: 8
0.85 0.11 0.04
Matches are distributed among these distances:
132 4 0.02
133 111 0.59
134 72 0.39
ACGTcount: A:0.26, C:0.17, G:0.29, T:0.29
Consensus pattern (134 bp):
GCTCCTACGTGATGAGGAGATCTGGTCGGTGGATGACACGGTTCCTACATGATGAGAATGACTGA
CCATCTTTAGGGATAATGATAACACGGTTCCTACGTGATGAGGATAGAAAGTTATCTAAGGTTGA
CGTT
Found at i:81318 original size:65 final size:65
Alignment explanation
Indices: 81183--81523 Score: 370
Period size: 65 Copynumber: 5.2 Consensus size: 65
81173 GGGATAATTG
* * * *
81183 GTTTCAATAGAATCTGTCTCAAGCGAGACAAAAGTTGTTTCAAGGGAAAC-ATACTCAAAGATTT
1 GTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACTAT-CTCAAAG-TTT
81247 TT
64 TT
81249 -TTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGGGAAA-TA-CTCAAAGATTT
1 GTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TTTGTTTCAAGGGAAACTATCTCAAAG-TTT
81311 TT
64 TT
* * * * * *
81313 GTTTCAAGATAAATTATCTCAAGAGAGACAAAATTTTGTTTCTAGGGAAACAATCTCAATTGTTT
1 GTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TTTGTTTCAAGGGAAACTATCTCAA-AGTTT
81378 TT
64 TT
* * * * *
81380 GTTTCAAGAGAAATTGTCTCAAGGGAGACAAAACTTGTTTCGAGGGAAACTATCTCAATGTTTTT
1 GTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACTATCTCAAAGTTTTT
* * * * *
81445 GTTTCAAGAGAAACTATCTCAAG-GTAGACAAAATTTGTTT-GATGGAAACAATCTCAAAGGTGT
1 GTTTCAAGAGAAACTGTCTCAAGAG-AGACAAAATTTGTTTCAAGGGAAACTATCTCAAA-GTTT
81508 TT
64 TT
* *
81510 ATTTCAAGTGAAAC
1 GTTTCAAGAGAAAC
81524 AATTTCCAAA
Statistics
Matches: 241, Mismatches: 26, Indels: 17
0.85 0.09 0.06
Matches are distributed among these distances:
64 29 0.12
65 132 0.55
66 39 0.16
67 40 0.17
68 1 0.00
ACGTcount: A:0.36, C:0.13, G:0.18, T:0.32
Consensus pattern (65 bp):
GTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACTATCTCAAAGTTTTT
Found at i:81446 original size:132 final size:129
Alignment explanation
Indices: 81183--81523 Score: 404
Period size: 132 Copynumber: 2.6 Consensus size: 129
81173 GGGATAATTG
* * * *
81183 GTTTCAATAGAATCTGTCTCAAGCGAGACAAAAGTTGTTTCAAGGGAAAC-ATACTCAAAGATTT
1 GTTTCAAGAGAAACTATCTCAAG-GAGACAAAATTTGTTTCAAGGGAAACAAT-CTCAAAGATTT
81247 TTTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGGGAAATACTCAAAGATTTT
64 TTTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGGGAAATACTCAAAGATTTT
81312 T
129 T
* * * *
81313 GTTTCAAGATAAATTATCTCAAGAGAGACAAAATTTTGTTTCTAGGGAAACAATCTCAATTG-TT
1 GTTTCAAGAGAAACTATCTCAAG-GAGACAAAA-TTTGTTTCAAGGGAAACAATCTCAA-AGATT
* * * *
81377 TTTGTTTCAAGAGAAATTGTCTCAAGGGAGACAAAAC-TTGTTTCGAGGGAAACTATCTCAATG-
63 TTT-TTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGGGAAA-TA-CTCAAAGA
81440 TTTTT
125 TTTTT
* * *
81445 GTTTCAAGAGAAACTATCTCAAGGTAGACAAAATTTGTTT-GATGGAAACAATCTCAAAGGTGTT
1 GTTTCAAGAGAAACTATCTCAAGG-AGACAAAATTTGTTTCAAGGGAAACAATCTCAAAGAT-TT
* *
81509 TATTTCAAGTGAAAC
64 TTTTTCAAGAGAAAC
81524 AATTTCCAAA
Statistics
Matches: 181, Mismatches: 21, Indels: 18
0.82 0.10 0.08
Matches are distributed among these distances:
129 1 0.01
130 54 0.30
131 50 0.28
132 70 0.39
133 6 0.03
ACGTcount: A:0.36, C:0.13, G:0.18, T:0.32
Consensus pattern (129 bp):
GTTTCAAGAGAAACTATCTCAAGGAGACAAAATTTGTTTCAAGGGAAACAATCTCAAAGATTTTT
TTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGGGAAATACTCAAAGATTTTT
Found at i:82191 original size:20 final size:16
Alignment explanation
Indices: 82152--82207 Score: 85
Period size: 16 Copynumber: 3.5 Consensus size: 16
82142 TTCATGTATC
82152 ATGTATGTATGTGTTA
1 ATGTATGTATGTGTTA
82168 ATGTATGTATGTGTTA
1 ATGTATGTATGTGTTA
* * *
82184 ATATATGTATGTATTG
1 ATGTATGTATGTGTTA
82200 ATGTATGT
1 ATGTATGT
82208 TTTCTTGGTG
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 36 1.00
ACGTcount: A:0.27, C:0.00, G:0.23, T:0.50
Consensus pattern (16 bp):
ATGTATGTATGTGTTA
Found at i:85074 original size:20 final size:20
Alignment explanation
Indices: 85049--85103 Score: 101
Period size: 20 Copynumber: 2.8 Consensus size: 20
85039 TTCAAAAGAG
85049 TGCATCGATGCACCAATCCA
1 TGCATCGATGCACCAATCCA
85069 TGCATCGATGCACCAATCCA
1 TGCATCGATGCACCAATCCA
*
85089 TGCATTGATGCACCA
1 TGCATCGATGCACCA
85104 TTGAATAAAT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.29, C:0.33, G:0.16, T:0.22
Consensus pattern (20 bp):
TGCATCGATGCACCAATCCA
Found at i:85186 original size:63 final size:62
Alignment explanation
Indices: 85113--85270 Score: 203
Period size: 63 Copynumber: 2.5 Consensus size: 62
85103 ATTGAATAAA
* * * *
85113 TGAACATCGAATGCATTTTAGCATAGATGCACATACCATGCATTGATGCACTC-AGGTT-TT
1 TGAACATCGAATGCATTTTAGCATCGATGCACAGACCATGCATCGATGCACTCGAGCTTGTT
*
85173 ATGAAAACATCGAATGCATTTTATCATCGATGCACAGACCATGCATCGATGCACTCGAGCTTGTT
1 -TG--AACATCGAATGCATTTTAGCATCGATGCACAGACCATGCATCGATGCACTCGAGCTTGTT
* *
85238 TGAACATCGAATGCACTTCATGCATCGATGCAC
1 TGAACATCGAATGCATTTTA-GCATCGATGCAC
85271 TCTTAGTGCA
Statistics
Matches: 84, Mismatches: 8, Indels: 8
0.84 0.08 0.08
Matches are distributed among these distances:
61 2 0.02
62 16 0.19
63 58 0.69
64 6 0.07
65 2 0.02
ACGTcount: A:0.30, C:0.23, G:0.18, T:0.28
Consensus pattern (62 bp):
TGAACATCGAATGCATTTTAGCATCGATGCACAGACCATGCATCGATGCACTCGAGCTTGTT
Found at i:85270 original size:17 final size:19
Alignment explanation
Indices: 85242--85290 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
85232 CTTGTTTGAA
85242 CATCGAATGCACT-TCA-TG
1 CATCG-ATGCACTCTCAGTG
*
85260 CATCGATGCACTCTTAGTG
1 CATCGATGCACTCTCAGTG
*
85279 CACCGATGCACT
1 CATCGATGCACT
85291 AAGGGTCCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 7 0.26
18 7 0.26
19 13 0.48
ACGTcount: A:0.24, C:0.31, G:0.18, T:0.27
Consensus pattern (19 bp):
CATCGATGCACTCTCAGTG
Found at i:85360 original size:20 final size:21
Alignment explanation
Indices: 85335--85383 Score: 91
Period size: 21 Copynumber: 2.4 Consensus size: 21
85325 CATAGTGTAC
85335 CGATGCACTAG-CTTATGCAT
1 CGATGCACTAGCCTTATGCAT
85355 CGATGCACTAGCCTTATGCAT
1 CGATGCACTAGCCTTATGCAT
85376 CGATGCAC
1 CGATGCAC
85384 CACACGCTCC
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
20 11 0.39
21 17 0.61
ACGTcount: A:0.24, C:0.29, G:0.20, T:0.27
Consensus pattern (21 bp):
CGATGCACTAGCCTTATGCAT
Done.