Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007104.1 Hibiscus syriacus cultivar Beakdansim tig00018567_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: 49773
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33
Found at i:2702 original size:59 final size:59
Alignment explanation
Indices: 2639--2773 Score: 166
Period size: 59 Copynumber: 2.3 Consensus size: 59
2629 ATAGTCGTGT
** * *
2639 GACCATTTTGTAACTTTTAATAGTTGATGGACTCAACAAAGCAACATCCTAAAGTC-AGG
1 GACCATTTTGTAACTTTTAATAGTCAATAGACTCAACAAAGCAA-ACCCTAAAGTCGAGG
* * * *
2698 GACCATTTTGTAACTTTTTATAGTCAATAGACTCAACAAAGTAAACCCTATAGTCGATG
1 GACCATTTTGTAACTTTTAATAGTCAATAGACTCAACAAAGCAAACCCTAAAGTCGAGG
2757 GACCATTTTTGT-ACTTT
1 GACCA-TTTTGTAACTTT
2774 ACCCAAAAAA
Statistics
Matches: 66, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
58 9 0.14
59 51 0.77
60 6 0.09
ACGTcount: A:0.33, C:0.19, G:0.15, T:0.33
Consensus pattern (59 bp):
GACCATTTTGTAACTTTTAATAGTCAATAGACTCAACAAAGCAAACCCTAAAGTCGAGG
Found at i:12134 original size:42 final size:41
Alignment explanation
Indices: 12048--12336 Score: 384
Period size: 42 Copynumber: 6.8 Consensus size: 41
12038 CTATACACCA
* * *
12048 GTAAGGCTTAACCTGTGCACAAAGCAGA-GGAGCCTAGGAAAACT
1 GTAAGGCTT-ACCT-TGCACACAGCAAAGGGA-CCT-GGTAAACT
* * *
12092 GTAAGGTTTATCCTTGCACACAACAAAGGGACCTGTTAAACT
1 GTAAGGCTTA-CCTTGCACACAGCAAAGGGACCTGGTAAACT
*
12134 GTAAGGCTTACCTTCGGACACAGCAAAGGGACCTAGG-AAACT
1 GTAAGGCTTACCTT-GCACACAGCAAAGGGACCT-GGTAAACT
12176 GTAAGGCTTACCCTTGCACACAGCAAAGGGACCTGGTAAACT
1 GTAAGGCTTA-CCTTGCACACAGCAAAGGGACCTGGTAAACT
* *
12218 GTAAGGCTTACCTTCGCACACAACAAAGGGACCTGGGAAACT
1 GTAAGGCTTACCTT-GCACACAGCAAAGGGACCTGGTAAACT
12260 GTAAGGCTTACCCTTGCACACAGCAAAGGGACCTGGTAAACT
1 GTAAGGCTTA-CCTTGCACACAGCAAAGGGACCTGGTAAACT
12302 GTAAGGCTTACCTTTGCACACAGCAAAGGGACCTG
1 GTAAGGCTTACC-TTGCACACAGCAAAGGGACCTG
12337 ATAATACTTC
Statistics
Matches: 221, Mismatches: 15, Indels: 20
0.86 0.06 0.08
Matches are distributed among these distances:
41 12 0.05
42 172 0.78
43 23 0.10
44 14 0.06
ACGTcount: A:0.33, C:0.24, G:0.24, T:0.19
Consensus pattern (41 bp):
GTAAGGCTTACCTTGCACACAGCAAAGGGACCTGGTAAACT
Found at i:12191 original size:84 final size:84
Alignment explanation
Indices: 12048--12335 Score: 436
Period size: 84 Copynumber: 3.4 Consensus size: 84
12038 CTATACACCA
* * * *
12048 GTAAGGCTTAACCTGT-GCACAAAGCAGA-GGAGCCTAGGAAAACTGTAAGGTTTATCCTTGCAC
1 GTAAGGCTT-ACCT-TCGCACACAGCAAAGGGA-CCTAGG-AAACTGTAAGGCTTACCCTTGCAC
* *
12111 ACAACAAAGGGACCTGTTAAACT
62 ACAGCAAAGGGACCTGGTAAACT
*
12134 GTAAGGCTTACCTTCGGACACAGCAAAGGGACCTAGGAAACTGTAAGGCTTACCCTTGCACACAG
1 GTAAGGCTTACCTTCGCACACAGCAAAGGGACCTAGGAAACTGTAAGGCTTACCCTTGCACACAG
12199 CAAAGGGACCTGGTAAACT
66 CAAAGGGACCTGGTAAACT
* *
12218 GTAAGGCTTACCTTCGCACACAACAAAGGGACCTGGGAAACTGTAAGGCTTACCCTTGCACACAG
1 GTAAGGCTTACCTTCGCACACAGCAAAGGGACCTAGGAAACTGTAAGGCTTACCCTTGCACACAG
12283 CAAAGGGACCTGGTAAACT
66 CAAAGGGACCTGGTAAACT
*
12302 GTAAGGCTTACCTTTGCACACAGCAAAGGGACCT
1 GTAAGGCTTACCTTCGCACACAGCAAAGGGACCT
12336 GATAATACTT
Statistics
Matches: 188, Mismatches: 12, Indels: 6
0.91 0.06 0.03
Matches are distributed among these distances:
84 157 0.84
85 19 0.10
86 12 0.06
ACGTcount: A:0.33, C:0.24, G:0.24, T:0.19
Consensus pattern (84 bp):
GTAAGGCTTACCTTCGCACACAGCAAAGGGACCTAGGAAACTGTAAGGCTTACCCTTGCACACAG
CAAAGGGACCTGGTAAACT
Found at i:13224 original size:29 final size:29
Alignment explanation
Indices: 13192--13258 Score: 100
Period size: 28 Copynumber: 2.3 Consensus size: 29
13182 CATTTTACAC
*
13192 AAATAGCACCCTTTTTAAAATAATTACCA
1 AAATAGCACCCTTTTCAAAATAATTACCA
* *
13221 AAATAGCA-CCTTTTCGAATTAATTACCA
1 AAATAGCACCCTTTTCAAAATAATTACCA
13249 AAATAGCACC
1 AAATAGCACC
13259 AATTTCGAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
28 25 0.74
29 9 0.26
ACGTcount: A:0.43, C:0.22, G:0.06, T:0.28
Consensus pattern (29 bp):
AAATAGCACCCTTTTCAAAATAATTACCA
Found at i:13348 original size:78 final size:78
Alignment explanation
Indices: 13213--13359 Score: 231
Period size: 78 Copynumber: 1.9 Consensus size: 78
13203 TTTTTAAAAT
* *** *
13213 AATTACCAAAATAGCACCTTTTCGAATTAATTACCAAAATAGCACCAATTTCGAATTAATTCCCA
1 AATTACCAAAATAGCACCATTTCGAATTAATTACCAAAATAGCACCAAAACCAAATTAATTCCCA
13278 GAATTTCACAAAC
66 GAATTTCACAAAC
* *
13291 AATTACCAAAATAGCACCATTTCGAATTAATTCCCAGAATAGCACCAAAACCAAATTAATTCCCA
1 AATTACCAAAATAGCACCATTTCGAATTAATTACCAAAATAGCACCAAAACCAAATTAATTCCCA
13356 GAAT
66 GAAT
13360 AGCATCAGTC
Statistics
Matches: 62, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
78 62 1.00
ACGTcount: A:0.44, C:0.24, G:0.07, T:0.26
Consensus pattern (78 bp):
AATTACCAAAATAGCACCATTTCGAATTAATTACCAAAATAGCACCAAAACCAAATTAATTCCCA
GAATTTCACAAAC
Found at i:13444 original size:31 final size:31
Alignment explanation
Indices: 13374--13451 Score: 79
Period size: 31 Copynumber: 2.5 Consensus size: 31
13364 TCAGTCAACG
* ** *
13374 GTCAAC-GGTCGGGTTAACGGGTAGGGTCGG
1 GTCAACGGGTCGGGTCAACGAATAGGGTCGA
*
13404 GT-AGTCGGGTCGGGTCAACGAATAGGGTCGA
1 GTCA-ACGGGTCGGGTCAACGAATAGGGTCGA
*
13435 GTCAACGGGTCTGGTCA
1 GTCAACGGGTCGGGTCA
13452 TAACCGGTCA
Statistics
Matches: 38, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
29 1 0.03
30 3 0.08
31 33 0.87
32 1 0.03
ACGTcount: A:0.19, C:0.18, G:0.42, T:0.21
Consensus pattern (31 bp):
GTCAACGGGTCGGGTCAACGAATAGGGTCGA
Found at i:19131 original size:42 final size:41
Alignment explanation
Indices: 19040--19370 Score: 457
Period size: 42 Copynumber: 7.8 Consensus size: 41
19030 CTATACACCA
* * *
19040 GTAAGGCTTAACCTGTGCACAAAGCAGA-GGAGCCTAGGAAAACT
1 GTAAGGCTT-ACCT-TGCACACAGCAAAGGGA-CCT-GGGAAACT
*
19084 GTAAGGTTTATCCTTGCACACAGCAAAGGGACCTGGGAAACT
1 GTAAGGCTTA-CCTTGCACACAGCAAAGGGACCTGGGAAACT
*
19126 GTAAGGCTTACCCTTGCACACAGCAAAGGGACCTGGTAAACT
1 GTAAGGCTTA-CCTTGCACACAGCAAAGGGACCTGGGAAACT
* *
19168 GTAAGGCTTACATTCGCACACAACAAAGGGACCTGGGAAACT
1 GTAAGGCTTACCTT-GCACACAGCAAAGGGACCTGGGAAACT
* *
19210 ATAAGGCTTACCCTTGCACACAGCAAAGGGACCTGGTAAACT
1 GTAAGGCTTA-CCTTGCACACAGCAAAGGGACCTGGGAAACT
*
19252 GTAAGGCTTACCTTCGCACACAGCGAAGGGACCTGGGAAACT
1 GTAAGGCTTACCTT-GCACACAGCAAAGGGACCTGGGAAACT
*
19294 GTAAGGCTTACCCTTGCACACAGCAAAGGGACCTGGTAAACT
1 GTAAGGCTTA-CCTTGCACACAGCAAAGGGACCTGGGAAACT
19336 GTAAGGCTTACCTTCGCACACAGCAAAGGGACCTG
1 GTAAGGCTTACCTT-GCACACAGCAAAGGGACCTG
19371 ATAATACTTC
Statistics
Matches: 261, Mismatches: 19, Indels: 16
0.88 0.06 0.05
Matches are distributed among these distances:
41 11 0.04
42 214 0.82
43 22 0.08
44 14 0.05
ACGTcount: A:0.32, C:0.25, G:0.25, T:0.18
Consensus pattern (41 bp):
GTAAGGCTTACCTTGCACACAGCAAAGGGACCTGGGAAACT
Found at i:19187 original size:84 final size:84
Alignment explanation
Indices: 19040--19370 Score: 531
Period size: 84 Copynumber: 3.9 Consensus size: 84
19030 CTATACACCA
* * * * *
19040 GTAAGGCTTAACCTGTGCACAAAGCAGA-GGAGCCTAGGAAAACTGTAAGGTTTATCCTT-GCAC
1 GTAAGGCTTACCCT-TGCACACAGCAAAGGGA-CCT-GGTAAACTGTAAGGCTTA-CCTTCGCAC
19103 ACAGCAAAGGGACCTGGGAAACT
62 ACAGCAAAGGGACCTGGGAAACT
* *
19126 GTAAGGCTTACCCTTGCACACAGCAAAGGGACCTGGTAAACTGTAAGGCTTACATTCGCACACAA
1 GTAAGGCTTACCCTTGCACACAGCAAAGGGACCTGGTAAACTGTAAGGCTTACCTTCGCACACAG
19191 CAAAGGGACCTGGGAAACT
66 CAAAGGGACCTGGGAAACT
*
19210 ATAAGGCTTACCCTTGCACACAGCAAAGGGACCTGGTAAACTGTAAGGCTTACCTTCGCACACAG
1 GTAAGGCTTACCCTTGCACACAGCAAAGGGACCTGGTAAACTGTAAGGCTTACCTTCGCACACAG
*
19275 CGAAGGGACCTGGGAAACT
66 CAAAGGGACCTGGGAAACT
19294 GTAAGGCTTACCCTTGCACACAGCAAAGGGACCTGGTAAACTGTAAGGCTTACCTTCGCACACAG
1 GTAAGGCTTACCCTTGCACACAGCAAAGGGACCTGGTAAACTGTAAGGCTTACCTTCGCACACAG
19359 CAAAGGGACCTG
66 CAAAGGGACCTG
19371 ATAATACTTC
Statistics
Matches: 230, Mismatches: 13, Indels: 6
0.92 0.05 0.02
Matches are distributed among these distances:
83 3 0.01
84 197 0.86
85 14 0.06
86 16 0.07
ACGTcount: A:0.32, C:0.25, G:0.25, T:0.18
Consensus pattern (84 bp):
GTAAGGCTTACCCTTGCACACAGCAAAGGGACCTGGTAAACTGTAAGGCTTACCTTCGCACACAG
CAAAGGGACCTGGGAAACT
Found at i:20262 original size:29 final size:29
Alignment explanation
Indices: 20226--20378 Score: 141
Period size: 29 Copynumber: 5.3 Consensus size: 29
20216 CATTTTACAC
**
20226 AAATAGCACCCTTTTTAAAATAATTACCA
1 AAATAGCACCCTTTTCGAAATAATTACCA
*
20255 AAATAGCACCCTTTTCGAATTAATTACCA
1 AAATAGCACCCTTTTCGAAATAATTACCA
** * *
20284 AAATAGCACCAATTTCGAATTAATTCCCA
1 AAATAGCACCCTTTTCGAAATAATTACCA
* * * *
20313 GAATATCACCTTTTTCTAAA-AA-TACCA
1 AAATAGCACCCTTTTCGAAATAATTACCA
* *
20340 AAATAGCA-CCTATTTCGAATTAATTCCCA
1 AAATAGCACCCT-TTTCGAAATAATTACCA
* *
20369 GAATAACACC
1 AAATAGCACC
20379 AAAACTGAAT
Statistics
Matches: 99, Mismatches: 21, Indels: 7
0.78 0.17 0.06
Matches are distributed among these distances:
26 2 0.02
27 16 0.16
28 4 0.04
29 76 0.77
30 1 0.01
ACGTcount: A:0.41, C:0.24, G:0.06, T:0.29
Consensus pattern (29 bp):
AAATAGCACCCTTTTCGAAATAATTACCA
Found at i:20393 original size:85 final size:85
Alignment explanation
Indices: 20227--20407 Score: 224
Period size: 85 Copynumber: 2.1 Consensus size: 85
20217 ATTTTACACA
* *
20227 AATAGCACCCTTTTT-AAAATAATTACCAAAATAGCACCCTTTTCGAATTAATTACCAAAATAGC
1 AATAGCA-CCTTTTTCTAAA-AA-TACCAAAATAGCACCCTTTTCGAATTAATTACCAAAATAAC
**
20291 ACCAATTTCGAATTAATTCCCAG
63 ACCAAACTCGAATTAATTCCCAG
* * *
20314 AATATCACCTTTTTCTAAAAATACCAAAATAGCA-CCTATTTCGAATTAATTCCCAGAATAACAC
1 AATAGCACCTTTTTCTAAAAATACCAAAATAGCACCCT-TTTCGAATTAATTACCAAAATAACAC
*
20378 CAAAACT-GAATTAATTCCTAG
65 C-AAACTCGAATTAATTCCCAG
20399 AATAGCACC
1 AATAGCACC
20408 GGTCAACGGT
Statistics
Matches: 82, Mismatches: 9, Indels: 8
0.83 0.09 0.08
Matches are distributed among these distances:
84 3 0.04
85 58 0.71
86 12 0.15
87 9 0.11
ACGTcount: A:0.41, C:0.23, G:0.07, T:0.29
Consensus pattern (85 bp):
AATAGCACCTTTTTCTAAAAATACCAAAATAGCACCCTTTTCGAATTAATTACCAAAATAACACC
AAACTCGAATTAATTCCCAG
Found at i:20465 original size:18 final size:18
Alignment explanation
Indices: 20422--20466 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
20412 AACGGTCAAC
20422 GGTCGGGTCGGGTCAATG
1 GGTCGGGTCGGGTCAATG
* *
20440 GGTAGGGTCGGGTC-GTCG
1 GGTCGGGTCGGGTCAAT-G
20458 GGTCGGGTC
1 GGTCGGGTC
20467 AACCGGTTTC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
17 1 0.04
18 22 0.96
ACGTcount: A:0.07, C:0.18, G:0.53, T:0.22
Consensus pattern (18 bp):
GGTCGGGTCGGGTCAATG
Found at i:23199 original size:49 final size:49
Alignment explanation
Indices: 23143--23243 Score: 202
Period size: 49 Copynumber: 2.1 Consensus size: 49
23133 TATAATTGGT
23143 ACAAGTTGAAGGGTTGATAGTGGAGATAAATATTTATGGAATTCGATGA
1 ACAAGTTGAAGGGTTGATAGTGGAGATAAATATTTATGGAATTCGATGA
23192 ACAAGTTGAAGGGTTGATAGTGGAGATAAATATTTATGGAATTCGATGA
1 ACAAGTTGAAGGGTTGATAGTGGAGATAAATATTTATGGAATTCGATGA
23241 ACA
1 ACA
23244 TGTAGTTTGA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 52 1.00
ACGTcount: A:0.38, C:0.05, G:0.28, T:0.30
Consensus pattern (49 bp):
ACAAGTTGAAGGGTTGATAGTGGAGATAAATATTTATGGAATTCGATGA
Found at i:23279 original size:29 final size:29
Alignment explanation
Indices: 23246--23308 Score: 99
Period size: 29 Copynumber: 2.2 Consensus size: 29
23236 GATGAACATG
* **
23246 TAGTTTGAGATTATGATGGAAGTACGATT
1 TAGTTTGAGATTACGACAGAAGTACGATT
23275 TAGTTTGAGATTACGACAGAAGTACGATT
1 TAGTTTGAGATTACGACAGAAGTACGATT
23304 TAGTT
1 TAGTT
23309 GTATATCGAT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.32, C:0.06, G:0.25, T:0.37
Consensus pattern (29 bp):
TAGTTTGAGATTACGACAGAAGTACGATT
Found at i:26214 original size:30 final size:30
Alignment explanation
Indices: 26009--26197 Score: 317
Period size: 30 Copynumber: 6.3 Consensus size: 30
25999 GAAGGACCTA
* * *
26009 TCCAGAGGTCACAAAGA-CCCCGGTAAGTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
26038 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
*
26068 TCCAGAGGTCATAAATATCCTCGGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
26098 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
*
26128 TCCAGAGGTCATAAAGATCATCGGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
26158 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
*
26188 TCCATAGGTC
1 TCCAGAGGTC
26198 CCGAAGAACC
Statistics
Matches: 151, Mismatches: 8, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
29 16 0.11
30 135 0.89
ACGTcount: A:0.30, C:0.24, G:0.23, T:0.23
Consensus pattern (30 bp):
TCCAGAGGTCATAAAGATCCTCGGTAACTG
Found at i:27566 original size:21 final size:21
Alignment explanation
Indices: 27542--27586 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
27532 CCATGTTCAT
* * *
27542 TTGAGGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
27563 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
27584 TTG
1 TTG
27587 CCCAGAAATC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.13, C:0.24, G:0.31, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:30372 original size:2 final size:2
Alignment explanation
Indices: 30365--30394 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
30355 TGCACCTTTC
*
30365 AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
30395 CCACGCGTAC
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):
AT
Found at i:30871 original size:30 final size:30
Alignment explanation
Indices: 30666--30854 Score: 344
Period size: 30 Copynumber: 6.3 Consensus size: 30
30656 GAAGGACCTA
* *
30666 TCCAGAGGTCACAAAGA-CCCCGGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
30695 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
30725 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
30755 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
30785 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
30815 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
*
30845 TCCATAGGTC
1 TCCAGAGGTC
30855 CCGAAGAACC
Statistics
Matches: 156, Mismatches: 3, Indels: 1
0.98 0.02 0.01
Matches are distributed among these distances:
29 16 0.10
30 140 0.90
ACGTcount: A:0.30, C:0.25, G:0.23, T:0.22
Consensus pattern (30 bp):
TCCAGAGGTCATAAAGATCCTCGGTAACTG
Found at i:32222 original size:21 final size:21
Alignment explanation
Indices: 32198--32242 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
32188 CCATGTTCGT
* * *
32198 TTGAGGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
32219 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
32240 TTG
1 TTG
32243 CCCAGAAATC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.13, C:0.24, G:0.31, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:39449 original size:3 final size:3
Alignment explanation
Indices: 39441--39476 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
39431 TATATGACTA
39441 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
39477 TAAATATAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:39497 original size:14 final size:13
Alignment explanation
Indices: 39439--39513 Score: 60
Period size: 15 Copynumber: 5.3 Consensus size: 13
39429 TTTATATGAC
39439 TAAATAATAATAATAA
1 TAAA-AATAA-AAT-A
*
39455 TAATAATAATAATAA
1 TAAAAATAA-AAT-A
* *
39470 TAATAATTAAATA
1 TAAAAATAAAATA
39483 TAAAAATAAACATA
1 TAAAAATAAA-ATA
*
39497 TAAAATTAAAATA
1 TAAAAATAAAATA
39510 TAAA
1 TAAA
39514 TAAACAATGA
Statistics
Matches: 53, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
13 16 0.30
14 15 0.28
15 19 0.36
16 3 0.06
ACGTcount: A:0.68, C:0.01, G:0.00, T:0.31
Consensus pattern (13 bp):
TAAAAATAAAATA
Found at i:39514 original size:25 final size:27
Alignment explanation
Indices: 39469--39519 Score: 79
Period size: 25 Copynumber: 2.0 Consensus size: 27
39459 AATAATAATA
39469 ATAATAATTAAATATAAAAATAAACAT
1 ATAATAATTAAATATAAAAATAAACAT
*
39496 ATAA-AATTAAA-ATATAAATAAACA
1 ATAATAATTAAATATAAAAATAAACA
39520 ATGACTGAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 12 0.52
26 7 0.30
27 4 0.17
ACGTcount: A:0.69, C:0.04, G:0.00, T:0.27
Consensus pattern (27 bp):
ATAATAATTAAATATAAAAATAAACAT
Found at i:40902 original size:3 final size:3
Alignment explanation
Indices: 40894--41004 Score: 98
Period size: 3 Copynumber: 36.3 Consensus size: 3
40884 TGTAATTATT
* * *
40894 TAA TAA TAA TAA TAA GATA TAA TGTA TAA TAT TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TA-A TAA T-AA TAA TAA TAA TAA TAA TAA TAA
** * * * *
40941 TTT TAA TAA TAA TAA TAA TAA TAA TAC T-A TAT TAA TAT TGA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
40988 TAA TAA TTAA AAA TAA T
1 TAA TAA -TAA TAA TAA T
41005 TTTAAAAGAA
Statistics
Matches: 84, Mismatches: 20, Indels: 8
0.75 0.18 0.07
Matches are distributed among these distances:
2 1 0.01
3 76 0.90
4 7 0.08
ACGTcount: A:0.58, C:0.01, G:0.03, T:0.39
Consensus pattern (3 bp):
TAA
Found at i:42009 original size:24 final size:24
Alignment explanation
Indices: 41982--42031 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
41972 TGGTGGTTGA
*
41982 TTTAATGGT-TGTTTGAACTTTATT
1 TTTAATGGTATATTT-AACTTTATT
*
42006 TTTAATGGTATATTTAAGTTTATT
1 TTTAATGGTATATTTAACTTTATT
42030 TT
1 TT
42032 GGTTCTTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 19 0.83
25 4 0.17
ACGTcount: A:0.24, C:0.02, G:0.14, T:0.60
Consensus pattern (24 bp):
TTTAATGGTATATTTAACTTTATT
Found at i:46507 original size:16 final size:18
Alignment explanation
Indices: 46488--46524 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 18
46478 AAAATTTAAG
*
46488 TTTTTCTTT-ATTTT-TA
1 TTTTTATTTCATTTTCTA
46504 TTTTTATTTCATTTTCTA
1 TTTTTATTTCATTTTCTA
46522 TTT
1 TTT
46525 AATTTTTGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
16 8 0.44
17 5 0.28
18 5 0.28
ACGTcount: A:0.14, C:0.08, G:0.00, T:0.78
Consensus pattern (18 bp):
TTTTTATTTCATTTTCTA
Found at i:46856 original size:20 final size:20
Alignment explanation
Indices: 46814--46864 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
46804 TAACTTTTTC
* *
46814 TTTTCTATTTCTTTATTAAT
1 TTTTCTTTTTCATTATTAAT
46834 TTTTCTTTTTCATT-TTAACT
1 TTTTCTTTTTCATTATTAA-T
*
46854 TTTACTTTTTC
1 TTTTCTTTTTC
46865 TCTTTCTTCA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
19 4 0.15
20 23 0.85
ACGTcount: A:0.16, C:0.14, G:0.00, T:0.71
Consensus pattern (20 bp):
TTTTCTTTTTCATTATTAAT
Done.