Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007109.1 Hibiscus syriacus cultivar Beakdansim tig00018575_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: 74863
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
Found at i:1193 original size:21 final size:21
Alignment explanation
Indices: 1156--1195 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1146 TGTCCTTGTA
*
1156 TTCTACTTTAATCATTTTTAC
1 TTCTACTTTAATAATTTTTAC
1177 TTCTACTTTTAA-AATTTTT
1 TTCTAC-TTTAATAATTTTT
1196 GGCCTTGACC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.25, C:0.15, G:0.00, T:0.60
Consensus pattern (21 bp):
TTCTACTTTAATAATTTTTAC
Found at i:2396 original size:35 final size:34
Alignment explanation
Indices: 2329--2424 Score: 102
Period size: 35 Copynumber: 2.8 Consensus size: 34
2319 GCAACACAAT
*
2329 CATCAATTACATTTTAACCCCAAATTCCAAAATA
1 CATCAATTACATTTAAACCCCAAATTCCAAAATA
* * * **
2363 CTTCAATTATATTCTAAACCTCAAATTTTAAAATA
1 CATCAATTACATT-TAAACCCCAAATTCCAAAATA
***
2398 CATCAATTACATACCAACCCCAAATTC
1 CATCAATTACATTTAAACCCCAAATTC
2425 ATAATCCATT
Statistics
Matches: 48, Mismatches: 13, Indels: 2
0.76 0.21 0.03
Matches are distributed among these distances:
34 21 0.44
35 27 0.56
ACGTcount: A:0.43, C:0.26, G:0.00, T:0.31
Consensus pattern (34 bp):
CATCAATTACATTTAAACCCCAAATTCCAAAATA
Found at i:4266 original size:55 final size:55
Alignment explanation
Indices: 4113--4431 Score: 431
Period size: 55 Copynumber: 5.9 Consensus size: 55
4103 ATATGTGTAC
* *
4113 TACAGGCACTATGTGTGCAAATCCACGGAATTCATCATGAGTTGATGAATAATCG
1 TACAGACACTATGTGTGCAAATCCACGGAATTCATCATGAGTTGATGAATAACCG
* * *
4168 TACA-AGCACTA--TGTGCAAATTCACAGAATTCATCATGATTTGATGAATAACCG
1 TACAGA-CACTATGTGTGCAAATCCACGGAATTCATCATGAGTTGATGAATAACCG
*
4221 TACAGACACTATGTGTGCAAATCCACGGAATTTATCATGAGTTGATGAATAACCG
1 TACAGACACTATGTGTGCAAATCCACGGAATTCATCATGAGTTGATGAATAACCG
4276 TACATG-CACTATGTGTGCAAATCCACGGAATTCATCATGAGTTGATGAATAACCG
1 TACA-GACACTATGTGTGCAAATCCACGGAATTCATCATGAGTTGATGAATAACCG
* * *
4331 TACA-AGCACTATGTGTGCAAATCCACAGAATTTATCATGA-TTGATG-ATAAACG
1 TACAGA-CACTATGTGTGCAAATCCACGGAATTCATCATGAGTTGATGAATAACCG
* * *
4384 TACATG-CACGATGTGTGC-AACCCACGGAATTCATCATGAGTTGGTGAA
1 TACA-GACACTATGTGTGCAAATCCACGGAATTCATCATGAGTTGATGAA
4432 CTATCGTATA
Statistics
Matches: 235, Mismatches: 18, Indels: 23
0.85 0.07 0.08
Matches are distributed among these distances:
52 18 0.08
53 73 0.31
54 8 0.03
55 135 0.57
56 1 0.00
ACGTcount: A:0.34, C:0.19, G:0.20, T:0.27
Consensus pattern (55 bp):
TACAGACACTATGTGTGCAAATCCACGGAATTCATCATGAGTTGATGAATAACCG
Found at i:4400 original size:163 final size:162
Alignment explanation
Indices: 4113--4431 Score: 500
Period size: 163 Copynumber: 2.0 Consensus size: 162
4103 ATATGTGTAC
*
4113 TACAGGCACTATGTGTGCAAATCCACGGAATTCATCATGAGTTGATGAATAATCGTACAAGCACT
1 TACAGGCACTATGTGTGCAAATCCACGGAATTCATCATGAGTTGATGAATAACCGTACAAGCACT
* * * *
4178 ATGTGCAAATTCACAGAATTCATCATGATTTGATGAATAACCGTACAGACACTATGTGTGCAAAT
66 ATGTGCAAATCCACAGAATTCATCATGATTTGATGAATAAACGTACAGACACGATGTGTGC-AAC
*
4243 CCACGGAATTTATCATGAGTTGATGAATAACCG
130 CCACGGAATTCATCATGAGTTGATGAATAACCG
*
4276 TACATGCACTATGTGTGCAAATCCACGGAATTCATCATGAGTTGATGAATAACCGTACAAGCACT
1 TACAGGCACTATGTGTGCAAATCCACGGAATTCATCATGAGTTGATGAATAACCGTACAAGCACT
*
4341 ATGTGTGCAAATCCACAGAATTTATCATGA-TTGATG-ATAAACGTACATG-CACGATGTGTGCA
66 A--TGTGCAAATCCACAGAATTCATCATGATTTGATGAATAAACGTACA-GACACGATGTGTGCA
*
4403 ACCCACGGAATTCATCATGAGTTGGTGAA
128 ACCCACGGAATTCATCATGAGTTGATGAA
4432 CTATCGTATA
Statistics
Matches: 144, Mismatches: 9, Indels: 7
0.90 0.06 0.04
Matches are distributed among these distances:
162 27 0.19
163 85 0.59
164 7 0.05
165 25 0.17
ACGTcount: A:0.34, C:0.19, G:0.20, T:0.27
Consensus pattern (162 bp):
TACAGGCACTATGTGTGCAAATCCACGGAATTCATCATGAGTTGATGAATAACCGTACAAGCACT
ATGTGCAAATCCACAGAATTCATCATGATTTGATGAATAAACGTACAGACACGATGTGTGCAACC
CACGGAATTCATCATGAGTTGATGAATAACCG
Found at i:4471 original size:17 final size:17
Alignment explanation
Indices: 4449--4482 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
4439 ATAGCACTAC
4449 GTGTGCATCTTAATAAA
1 GTGTGCATCTTAATAAA
4466 GTGTGCATCTTAATAAA
1 GTGTGCATCTTAATAAA
4483 TGAACATGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.35, C:0.12, G:0.18, T:0.35
Consensus pattern (17 bp):
GTGTGCATCTTAATAAA
Found at i:5546 original size:35 final size:35
Alignment explanation
Indices: 5507--5583 Score: 118
Period size: 35 Copynumber: 2.2 Consensus size: 35
5497 GTTAGGCATA
**
5507 TAATTGAAGTATTTTAGAATTTGAGGTTTAGAATG
1 TAATTGAAACATTTTAGAATTTGAGGTTTAGAATG
* *
5542 TAATTGAAACATTTTGGAATTTGGGGTTTAGAATG
1 TAATTGAAACATTTTAGAATTTGAGGTTTAGAATG
5577 TAATTGA
1 TAATTGA
5584 TGATTGTGTT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.34, C:0.01, G:0.23, T:0.42
Consensus pattern (35 bp):
TAATTGAAACATTTTAGAATTTGAGGTTTAGAATG
Found at i:6390 original size:214 final size:214
Alignment explanation
Indices: 5992--6424 Score: 816
Period size: 216 Copynumber: 2.0 Consensus size: 214
5982 GGCGTTGGCA
5992 GTTAAAAAGGGTAAAATACACAATGGTCAGCCGATTACAGGGTGTTGTTCTGTTGAGTCTCATAA
1 GTTAAAAAGGGTAAAATACACAATGGTCAGCCGATTACAGGGTGTTGTTCTGTTGAGTCTCATAA
6057 TTATTAAAAGTTATAAAATGATTGATCGACCATAAGATGTTATTTTGTTGGATCCCTCAATATTA
66 TTATTAAAAGTTATAAAATGATTGATCGACCATAAGATGTTATTTTGTTGGATCCCTCAATATTA
6122 AAAATTACAAAATGATCATTCGAGTATTTATATGTTCCAAATCGTCATTTTCTGTTAAAAAAAAT
131 AAAATTACAAAATGATCATTCGAGTATTTATATGTTCCAAATCGTCATTTTCTGTT-AAAAAAAT
6187 GATGATCGTCTAAGTTGGAC
195 GATGATCGTCTAAGTTGGAC
6207 GTTAAAAAGGGTAAAATACACAAATGGTCAGCCGATTACAGGGTGTTGTTCTGTTGAGTCTCATA
1 GTTAAAAAGGGTAAAATACAC-AATGGTCAGCCGATTACAGGGTGTTGTTCTGTTGAGTCTCATA
*
6272 ATTATTAAAAGTTATAAAATGATTGATCGACCATAGGATG-T-TTTTGTTGGATCCCTCAATATT
65 ATTATTAAAAGTTATAAAATGATTGATCGACCATAAGATGTTATTTTGTTGGATCCCTCAATATT
6335 AAAAATTACAAAATGATCATTCGAGTATTTATATGTTCCAAATCGTCATTTTCTGTTAAAAAAAT
130 AAAAATTACAAAATGATCATTCGAGTATTTATATGTTCCAAATCGTCATTTTCTGTTAAAAAAAT
*
6400 GATGATCGTCTAAGTTTGAC
195 GATGATCGTCTAAGTTGGAC
6420 GTTAA
1 GTTAA
6425 CATGCTGACT
Statistics
Matches: 215, Mismatches: 2, Indels: 4
0.97 0.01 0.02
Matches are distributed among these distances:
213 32 0.15
214 79 0.37
215 22 0.10
216 82 0.38
ACGTcount: A:0.35, C:0.12, G:0.17, T:0.35
Consensus pattern (214 bp):
GTTAAAAAGGGTAAAATACACAATGGTCAGCCGATTACAGGGTGTTGTTCTGTTGAGTCTCATAA
TTATTAAAAGTTATAAAATGATTGATCGACCATAAGATGTTATTTTGTTGGATCCCTCAATATTA
AAAATTACAAAATGATCATTCGAGTATTTATATGTTCCAAATCGTCATTTTCTGTTAAAAAAATG
ATGATCGTCTAAGTTGGAC
Found at i:7336 original size:23 final size:22
Alignment explanation
Indices: 7288--7336 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
7278 ACAGAATGTC
7288 AAGG-GGGAACCGATACCCCCA
1 AAGGAGGGAACCGATACCCCCA
* *
7309 CAGGAGGGAACCGATTCCCCCTA
1 AAGGAGGGAACCGATACCCCC-A
7332 AAGGA
1 AAGGA
7337 AAATGAATAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
21 3 0.13
22 15 0.65
23 5 0.22
ACGTcount: A:0.33, C:0.31, G:0.29, T:0.08
Consensus pattern (22 bp):
AAGGAGGGAACCGATACCCCCA
Found at i:8890 original size:23 final size:23
Alignment explanation
Indices: 8860--8910 Score: 93
Period size: 23 Copynumber: 2.2 Consensus size: 23
8850 CATTTTATAT
8860 GGCACTTCGGTGCAATTCTACGC
1 GGCACTTCGGTGCAATTCTACGC
*
8883 GGCACTTCGGTGCAATTCTACGT
1 GGCACTTCGGTGCAATTCTACGC
8906 GGCAC
1 GGCAC
8911 AATTCTACGT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.18, C:0.29, G:0.27, T:0.25
Consensus pattern (23 bp):
GGCACTTCGGTGCAATTCTACGC
Found at i:8915 original size:15 final size:15
Alignment explanation
Indices: 8895--8925 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
8885 CACTTCGGTG
8895 CAATTCTACGTGGCA
1 CAATTCTACGTGGCA
8910 CAATTCTACGTGGCA
1 CAATTCTACGTGGCA
8925 C
1 C
8926 TTCGGTGCAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.26, C:0.29, G:0.19, T:0.26
Consensus pattern (15 bp):
CAATTCTACGTGGCA
Found at i:15363 original size:30 final size:29
Alignment explanation
Indices: 15338--15437 Score: 130
Period size: 29 Copynumber: 3.4 Consensus size: 29
15328 GACTAAGATG
*
15338 GTAAAAATATAAAGTTTAGGGA-CTAAAGT
1 GTAAAAATATAAAGTCTAGGGACCT-AAGT
* *
15367 GTAAAAGATCTAAAGTCTAAGGACCTAAGT
1 GTAAAA-ATATAAAGTCTAGGGACCTAAGT
* *
15397 GTAATAATCTAAAGTCTAGGGACCTAAGT
1 GTAAAAATATAAAGTCTAGGGACCTAAGT
15426 GTAAAAATATAA
1 GTAAAAATATAA
15438 TCCTAGAAGG
Statistics
Matches: 62, Mismatches: 7, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
29 38 0.61
30 22 0.35
31 2 0.03
ACGTcount: A:0.46, C:0.09, G:0.19, T:0.26
Consensus pattern (29 bp):
GTAAAAATATAAAGTCTAGGGACCTAAGT
Found at i:15412 original size:29 final size:30
Alignment explanation
Indices: 15325--15431 Score: 114
Period size: 29 Copynumber: 3.6 Consensus size: 30
15315 CCCCTAATTA
* *
15325 AAGGA-CTAAGATGGTAAAA-ATATAAAGTTT
1 AAGGACCTAAG-T-GTAAAAGATCTAAAGTCT
*
15355 AGGGA-CTAAAGTGTAAAAGATCTAAAGTCT
1 AAGGACCT-AAGTGTAAAAGATCTAAAGTCT
*
15385 AAGGACCTAAGTGTAATA-ATCTAAAGTCT
1 AAGGACCTAAGTGTAAAAGATCTAAAGTCT
*
15414 AGGGACCTAAGTGTAAAA
1 AAGGACCTAAGTGTAAAA
15432 ATATAATCCT
Statistics
Matches: 67, Mismatches: 7, Indels: 7
0.83 0.09 0.09
Matches are distributed among these distances:
29 33 0.49
30 29 0.43
31 5 0.07
ACGTcount: A:0.45, C:0.09, G:0.21, T:0.24
Consensus pattern (30 bp):
AAGGACCTAAGTGTAAAAGATCTAAAGTCT
Found at i:17534 original size:17 final size:15
Alignment explanation
Indices: 17498--17528 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
17488 AAATTCTAAA
*
17498 TATTTATATAAAGAT
1 TATTTATATAAAAAT
17513 TATTTATATAAAAAT
1 TATTTATATAAAAAT
17528 T
1 T
17529 CTATTTGTTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (15 bp):
TATTTATATAAAAAT
Found at i:17823 original size:2 final size:2
Alignment explanation
Indices: 17816--17856 Score: 55
Period size: 2 Copynumber: 20.5 Consensus size: 2
17806 AGCAAACTTC
* * *
17816 AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT GT AT GT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
17857 AATAAATGTC
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.44, C:0.00, G:0.07, T:0.49
Consensus pattern (2 bp):
AT
Found at i:21452 original size:17 final size:16
Alignment explanation
Indices: 21432--21490 Score: 57
Period size: 17 Copynumber: 3.6 Consensus size: 16
21422 TAACCCATTA
21432 AAAATCATAACCTCCAC
1 AAAATCATAACC-CCAC
* ***
21449 AAAATCAAAAAGACA-
1 AAAATCATAACCCCAC
21464 AAAATCATAACCCCAC
1 AAAATCATAACCCCAC
21480 AAAAATCATAA
1 -AAAATCATAA
21491 TCATGTTCTC
Statistics
Matches: 32, Mismatches: 8, Indels: 4
0.73 0.18 0.09
Matches are distributed among these distances:
15 11 0.34
16 2 0.06
17 19 0.59
ACGTcount: A:0.59, C:0.25, G:0.02, T:0.14
Consensus pattern (16 bp):
AAAATCATAACCCCAC
Found at i:21453 original size:49 final size:50
Alignment explanation
Indices: 21355--21490 Score: 150
Period size: 49 Copynumber: 2.8 Consensus size: 50
21345 ACCTAAACTC
* * * * * ** *
21355 CAAAAACTCAAAAATTATAACCCCATTGAAAATTATAAGCTTGATAAAAT
1 CAAAAACACAAAAATCATAACCCCATTAAAAATCATAACCTCCACAAAAT
* *
21405 CAAAAACCCAAAAAGCATAA-CCCATTAAAAATCATAACCTCCACAAAAT
1 CAAAAACACAAAAATCATAACCCCATTAAAAATCATAACCTCCACAAAAT
* *
21454 CAAAAAGACAAAAATCATAACCCCA-CAAAAATCATAA
1 CAAAAACACAAAAATCATAACCCCATTAAAAATCATAA
21491 TCATGTTCTC
Statistics
Matches: 72, Mismatches: 13, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
49 51 0.71
50 21 0.29
ACGTcount: A:0.56, C:0.23, G:0.04, T:0.18
Consensus pattern (50 bp):
CAAAAACACAAAAATCATAACCCCATTAAAAATCATAACCTCCACAAAAT
Found at i:22936 original size:18 final size:18
Alignment explanation
Indices: 22910--22953 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
22900 GTCAATGGAG
*
22910 TGTTTATCGGCTTTGCAT
1 TGTTCATCGGCTTTGCAT
22928 TGTTCATCGGCTTTGCAT
1 TGTTCATCGGCTTTGCAT
*
22946 TATTCATC
1 TGTTCATC
22954 CCAAACCTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.14, C:0.20, G:0.18, T:0.48
Consensus pattern (18 bp):
TGTTCATCGGCTTTGCAT
Found at i:25472 original size:15 final size:15
Alignment explanation
Indices: 25434--25542 Score: 92
Period size: 16 Copynumber: 6.9 Consensus size: 15
25424 GAGTATCAGT
25434 GTTATGATTTTGTGGG
1 GTTATGATTTT-TGGG
25450 GTTATGATTTTTGGG
1 GTTATGATTTTTGGG
* *
25465 TTTTTGATTTTTGGAG
1 GTTATGATTTTTGG-G
25481 GTTATGATTTTTGGG
1 GTTATGATTTTTGGG
* * * * *
25496 TTTTTAATCTATGGAG
1 GTTATGATTTTTGG-G
*
25512 CTTATGATTTTCAATGGG
1 GTTATGATTTT---TGGG
25530 GTTATGATTTTTG
1 GTTATGATTTTTG
25543 AGTTTTTTGG
Statistics
Matches: 73, Mismatches: 15, Indels: 11
0.74 0.15 0.11
Matches are distributed among these distances:
15 28 0.38
16 31 0.42
18 11 0.15
19 3 0.04
ACGTcount: A:0.17, C:0.03, G:0.28, T:0.53
Consensus pattern (15 bp):
GTTATGATTTTTGGG
Found at i:25484 original size:31 final size:31
Alignment explanation
Indices: 25438--25522 Score: 118
Period size: 31 Copynumber: 2.7 Consensus size: 31
25428 ATCAGTGTTA
25438 TGATTTTGTGG-GGTTATGATTTTTGGGTTTT
1 TGATTTT-TGGAGGTTATGATTTTTGGGTTTT
25469 TGATTTTTGGAGGTTATGATTTTTGGGTTTT
1 TGATTTTTGGAGGTTATGATTTTTGGGTTTT
* * * *
25500 TAATCTATGGAGCTTATGATTTT
1 TGATTTTTGGAGGTTATGATTTT
25523 CAATGGGGTT
Statistics
Matches: 49, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
30 3 0.06
31 46 0.94
ACGTcount: A:0.15, C:0.02, G:0.27, T:0.55
Consensus pattern (31 bp):
TGATTTTTGGAGGTTATGATTTTTGGGTTTT
Found at i:26665 original size:41 final size:41
Alignment explanation
Indices: 26618--26697 Score: 97
Period size: 41 Copynumber: 1.9 Consensus size: 41
26608 GGTAATAAAA
* * *
26618 TAAAAATAAGAAAAGACAAATAAATAAATAAATAAAATACAC
1 TAAAATTAA-AAAAGAAAAAAAAATAAATAAATAAAATACAC
* * *
26660 TAAAATTAAAAGAGAAAAAAAAATGAATAACTAAAATA
1 TAAAATTAAAAAAGAAAAAAAAATAAATAAATAAAATA
26698 AAAAATACTA
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
41 24 0.75
42 8 0.25
ACGTcount: A:0.71, C:0.05, G:0.06, T:0.17
Consensus pattern (41 bp):
TAAAATTAAAAAAGAAAAAAAAATAAATAAATAAAATACAC
Found at i:26697 original size:46 final size:43
Alignment explanation
Indices: 26625--26755 Score: 129
Period size: 46 Copynumber: 2.9 Consensus size: 43
26615 AAATAAAAAT
* *
26625 AAGAAAAGACAAATAAATAAAT-AAATAAAATACACTAAAATTAAA
1 AAGAAAA-A-AAATGAATAACTAAAATAAAATA-ACTAAAATTAAA
*
26670 AGAGAAAAAAAAATGAATAACTAAAATAAAAAATACTAAAATTAAA
1 A-AG-AAAAAAAATGAATAACTAAAATAAAATA-ACTAAAATTAAA
* * * * *
26716 AAGGAACAAAATGAATAACTAAATTGAAATAATTAAAATT
1 AAGAAAAAAAATGAATAACTAAAATAAAATAACTAAAATT
26756 GATGGATTAA
Statistics
Matches: 73, Mismatches: 10, Indels: 8
0.80 0.11 0.09
Matches are distributed among these distances:
43 8 0.11
44 23 0.32
45 13 0.18
46 25 0.34
47 4 0.05
ACGTcount: A:0.68, C:0.05, G:0.07, T:0.20
Consensus pattern (43 bp):
AAGAAAAAAAATGAATAACTAAAATAAAATAACTAAAATTAAA
Found at i:28728 original size:84 final size:83
Alignment explanation
Indices: 28498--28784 Score: 283
Period size: 84 Copynumber: 3.4 Consensus size: 83
28488 CTGAATGAAA
* * * * * * * *
28498 TCGAACTCGTCAGGTCTTTGGTTGGCAGATAGCCCTTCTCGACTCAAGTTATGCTTTAAATGATG
1 TCGAACTCG-AAGGTCTTTGG-TGACAAATAACCCTTCTAGACTTAAGCTATGCTGTAAATGATG
* * * *
28563 TGCCCTCGAAGCTGAGTGTAA
64 TGCCTTAG-AGCTGAGCGTAG
* * * * * *
28584 TCGAACTCGAGGGTCTTT-G-G-CAGATAGCCCTTCTCGACTTAAGCTATACTGCAAATGATGTG
1 TCGAACTCGAAGGTCTTTGGTGACAAATAACCCTTCTAGACTTAAGCTATGCTGTAAATGATGTG
28646 CCTTAGAGCTGAGCGTAG
66 CCTTAGAGCTGAGCGTAG
* * * *
28664 TCGAACTCAAAGGTCTTTTGGTGACATATAACCCTTCTAGCCTTGAGCTATGCTGTAAATGATGT
1 TCGAACTCGAAGGTC-TTTGGTGACAAATAACCCTTCTAGACTTAAGCTATGCTGTAAATGATGT
*
28729 GCCTTGGAGCTGAGCGTAG
65 GCCTTAGAGCTGAGCGTAG
* * *
28748 TCAAACTCGAAGGTCTTTGTTGACAAATAATCCTTCT
1 TCGAACTCGAAGGTCTTTGGTGACAAATAACCCTTCT
28785 TTGAGTTGGA
Statistics
Matches: 171, Mismatches: 26, Indels: 11
0.82 0.12 0.05
Matches are distributed among these distances:
80 23 0.13
81 44 0.26
82 2 0.01
83 20 0.12
84 66 0.39
85 7 0.04
86 9 0.05
ACGTcount: A:0.24, C:0.22, G:0.24, T:0.31
Consensus pattern (83 bp):
TCGAACTCGAAGGTCTTTGGTGACAAATAACCCTTCTAGACTTAAGCTATGCTGTAAATGATGTG
CCTTAGAGCTGAGCGTAG
Found at i:29586 original size:105 final size:105
Alignment explanation
Indices: 28947--30567 Score: 2553
Period size: 105 Copynumber: 15.4 Consensus size: 105
28937 GCATTGTTCC
* ** * * * * *
28947 GAGTCCAATATCCTCCGCCGTGAAGTTGAAATTGGCTCTGGAA-CTGGGAAATTATTTGTTAACA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAAATC-GAGAAA-TGTTTGTTGACA
29011 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
64 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * * *
29053 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATCGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAAATCGAGAAA-TGTTTGTTGACAA
* *
29118 CCAGCGGTCCCTTCGTCATGAAGTTGGACTTGCGTTGTCTG
65 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * * *
29159 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATCGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAAATCGAGAAA-TGTTTGTTGACAA
29224 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
65 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
29265 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAAATCGAGAAA-TGTTTGTTGACAA
*
29330 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTT
65 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * * *
29371 GAGTCCAATATCTTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAAATCGAGAAA-TGTTTGTTGACAA
* * *
29436 CCAGCGGTCCCTTCGCCGTGAAGTTGAAATTACGTTGTCTG
65 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
29477 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAAATCGAGAAATGTTTGTTGACAAC
* *
29542 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTT
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
29582 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAAATCGAGAAATGTTTGTTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAAATCGAGAAATGTTTGTTGACAAC
29647 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
29687 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAAATCGAGAAATGTTTGTTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAAATCGAGAAATGTTTGTTGACAAC
29752 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
29792 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAAATCGAGAAATGTTTGTTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAAATCGAGAAATGTTTGTTGACAAC
29857 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
29897 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAAATCGAGAAATGTTTGTTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAAATCGAGAAATGTTTGTTGACAAC
29962 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
30002 GAGTCCAATATCCTTTGTTGTGAAGTTGAAATTGACTCTGAAATCGAGAAATGTTTGTTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAAATCGAGAAATGTTTGTTGACAAC
*
30067 CAGCGGTCCCTTCATCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
30107 GAGTCCAATATCCTTCGTTTTGAAGTTGAAATTGACTCTGAAATCGAGAAATGTTTATTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAAATCGAGAAATGTTTGTTGACAAC
* *
30172 CAGCGGTCCCTTCATCGTGAAGTTGAGCTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
30212 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAAATCGAGAAATTGTTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAAATCGAGAAA-TGTTTGTTGACAA
* *
30277 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGCCTG
65 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
30318 TAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAAATCGAGAAATTGTTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAAATCGAGAAA-TGTTTGTTGACAA
* *
30383 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGCCTG
65 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
30424 GAGTCCAATATCCTTCGTGGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAT
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAAATCGAGAAATGTTTGTTGACAAC
* * * * *
30489 CAGCCGCCCCTTCGTCATGAAGTTGAGCTTGTGTTGTCTTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTC-TG
* * * * * *
30530 GA-TTCGAGATCCTTCGTTGAGAAGTTAAAATTTACTCT
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCT
30568 CGAGCAAATT
Statistics
Matches: 1449, Mismatches: 63, Indels: 7
0.95 0.04 0.00
Matches are distributed among these distances:
105 792 0.55
106 657 0.45
ACGTcount: A:0.24, C:0.19, G:0.24, T:0.33
Consensus pattern (105 bp):
GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAAATCGAGAAATGTTTGTTGACAAC
CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:34168 original size:12 final size:12
Alignment explanation
Indices: 34151--34178 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
34141 CTTAGTTGCG
34151 AAAATTTAAATT
1 AAAATTTAAATT
34163 AAAATTTAAATT
1 AAAATTTAAATT
34175 AAAA
1 AAAA
34179 AAAAAAAATC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (12 bp):
AAAATTTAAATT
Found at i:34354 original size:45 final size:44
Alignment explanation
Indices: 34272--34384 Score: 138
Period size: 44 Copynumber: 2.5 Consensus size: 44
34262 AAATAAAAAT
* * *
34272 AAGAAAAGACAAATAAATAAAT-AAATAAAATACACTAAAATTAAA
1 AAGAAAA-A-AAATGAATAACTAAAATAAAAAACACTAAAATTAAA
*
34317 AGAGAAAAAAAATGAATAACTAAAATAAAAAATACTAAAATTAAA
1 A-AGAAAAAAAATGAATAACTAAAATAAAAAACACTAAAATTAAA
* *
34362 AAGGAACAAAATGAATAACTAAA
1 AAGAAAAAAAATGAATAACTAAA
34385 TTGAAATAAA
Statistics
Matches: 60, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
44 30 0.50
45 24 0.40
46 6 0.10
ACGTcount: A:0.70, C:0.06, G:0.07, T:0.17
Consensus pattern (44 bp):
AAGAAAAAAAATGAATAACTAAAATAAAAAACACTAAAATTAAA
Found at i:34375 original size:44 final size:45
Alignment explanation
Indices: 34294--34384 Score: 139
Period size: 45 Copynumber: 2.0 Consensus size: 45
34284 ATAAATAAAT
*
34294 AAATAAAATACACTAAAATTAAAAGAGAAAAAAAATGAATAACTA
1 AAATAAAAAACACTAAAATTAAAAGAGAAAAAAAATGAATAACTA
* * *
34339 AAATAAAAAATACTAAAATTAAAA-AGGAACAAAATGAATAACTA
1 AAATAAAAAACACTAAAATTAAAAGAGAAAAAAAATGAATAACTA
34383 AA
1 AA
34385 TTGAAATAAA
Statistics
Matches: 42, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
44 20 0.48
45 22 0.52
ACGTcount: A:0.69, C:0.07, G:0.07, T:0.18
Consensus pattern (45 bp):
AAATAAAAAACACTAAAATTAAAAGAGAAAAAAAATGAATAACTA
Found at i:34400 original size:44 final size:44
Alignment explanation
Indices: 34307--34402 Score: 124
Period size: 44 Copynumber: 2.2 Consensus size: 44
34297 TAAAATACAC
34307 TAAAATTAAAAGAGAAAAAAAATGAATAACTAAAATAAAAAATA
1 TAAAATTAAAAGAGAAAAAAAATGAATAACTAAAATAAAAAATA
* * *
34351 CTAAAATTAAAA-AGGAACAAAATGAATAACTAAATTGAAATAAAT-
1 -TAAAATTAAAAGAGAAAAAAAATGAATAACTAAAAT-AAA-AAATA
34396 TAAAATT
1 TAAAATT
34403 GATGGATTAA
Statistics
Matches: 46, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
44 28 0.61
45 14 0.30
46 4 0.09
ACGTcount: A:0.67, C:0.04, G:0.07, T:0.22
Consensus pattern (44 bp):
TAAAATTAAAAGAGAAAAAAAATGAATAACTAAAATAAAAAATA
Found at i:36292 original size:2 final size:2
Alignment explanation
Indices: 36285--36322 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
36275 TATTTAAGAG
36285 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
36323 ACAAAATTAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:36795 original size:3 final size:3
Alignment explanation
Indices: 36773--37038 Score: 92
Period size: 3 Copynumber: 83.3 Consensus size: 3
36763 CCAGAAAATA
* * *
36773 TAT TATT TAT TCT TACT TAT TAT TAT AAT ATAT TAT TAT TAT AATT TAT
1 TAT TA-T TAT TAT TA-T TAT TAT TAT TAT -TAT TAT TAT TAT TA-T TAT
* * * * *
36822 TAT TAC TAT TAC TAT TTT TAT TAT ATAT TAT T-T TAT TAA AATT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT -TAT TAT TAT TAT TAT TA-T TAT
* * * * *
36868 TAA TAT TAT ATAT TAT TACA TAT CAT TAT T-T GAT ATAT TAGA TAT TAT
1 TAT TAT TAT -TAT TAT TA-T TAT TAT TAT TAT TAT -TAT TA-T TAT TAT
* * * * *
36916 TGT ATAT TATT TAT TAA TCT TAT ATAT TAT CTAT CAG TA- TAT ATATT
1 TAT -TAT TA-T TAT TAT TAT TAT -TAT TAT -TAT TAT TAT TAT -TA-T
* * *
36963 TGT TAT TAC TA- TAT ATAT TAAT TAT TA- TAT TAT TACA TAT TATT TAT
1 TAT TAT TAT TAT TAT -TAT T-AT TAT TAT TAT TAT TA-T TAT TA-T TAT
* * *
37010 TAG TAT TAT TAT ATAG TAT TCT TAT TAT T
1 TAT TAT TAT TAT -TAT TAT TAT TAT TAT T
37039 CTTTTTAATT
Statistics
Matches: 191, Mismatches: 46, Indels: 52
0.66 0.16 0.18
Matches are distributed among these distances:
2 9 0.05
3 131 0.69
4 50 0.26
5 1 0.01
ACGTcount: A:0.35, C:0.05, G:0.03, T:0.58
Consensus pattern (3 bp):
TAT
Found at i:36806 original size:13 final size:13
Alignment explanation
Indices: 36790--36907 Score: 52
Period size: 13 Copynumber: 9.4 Consensus size: 13
36780 TATTCTTACT
36790 TATTATTATAATA
1 TATTATTATAATA
*
36803 TATTATTATTATA
1 TATTATTATAATA
36816 -ATTTATTAT--TA
1 TA-TTATTATAATA
* * *
36827 CTATTACTAT-TTT
1 -TATTATTATAATA
*
36840 TATTA-TATATTA
1 TATTATTATAATA
* * *
36852 TTTTATTAAAATT
1 TATTATTATAATA
* *
36865 TATTAATATTATA
1 TATTATTATAATA
*
36878 TATTATTA-CATA
1 TATTATTATAATA
*
36890 TCATTATT-TGATA
1 T-ATTATTATAATA
36903 TATTA
1 TATTA
36908 GATATTATTG
Statistics
Matches: 81, Mismatches: 16, Indels: 17
0.71 0.14 0.15
Matches are distributed among these distances:
11 5 0.06
12 26 0.32
13 50 0.62
ACGTcount: A:0.38, C:0.03, G:0.01, T:0.58
Consensus pattern (13 bp):
TATTATTATAATA
Found at i:36808 original size:16 final size:16
Alignment explanation
Indices: 36789--36885 Score: 82
Period size: 16 Copynumber: 6.4 Consensus size: 16
36779 TTATTCTTAC
36789 TTATTATTATAATATA
1 TTATTATTATAATATA
*
36805 TTATTATTATAATTTA
1 TTATTATTATAATATA
*
36821 TTATTACTAT--TACTA
1 TTATTATTATAATA-TA
*
36836 TTTTTATTAT-ATATTA
1 TTATTATTATAATA-TA
36852 TT-TTATTA-AA-AT-
1 TTATTATTATAATATA
* *
36864 TTATTAATATTATATA
1 TTATTATTATAATATA
36880 TTATTA
1 TTATTA
36886 CATATCATTA
Statistics
Matches: 66, Mismatches: 8, Indels: 14
0.75 0.09 0.16
Matches are distributed among these distances:
12 2 0.03
13 6 0.09
14 3 0.05
15 19 0.29
16 36 0.55
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (16 bp):
TTATTATTATAATATA
Found at i:36813 original size:19 final size:19
Alignment explanation
Indices: 36789--37037 Score: 62
Period size: 19 Copynumber: 12.5 Consensus size: 19
36779 TTATTCTTAC
36789 TTATTATTATAATATATTA
1 TTATTATTATAATATATTA
*
36808 TTATTATAATTTATTATTACTATTA
1 TTA-T-T-A-TTA-TAATA-TATTA
* * *
36833 CTATTTTTATTATATATTA
1 TTATTATTATAATATATTA
* *
36852 TT-TTATTAAAATTTATTA
1 TTATTATTATAATATATTA
* * *
36870 ATATTA-TATATTATTACATA
1 TTATTATTATAATA-TA-TTA
* *
36890 TCATTATT-TGATATATTA
1 TTATTATTATAATATATTA
* **
36908 -GA-TATTATTGTATATTA
1 TTATTATTATAATATATTA
* * *
36925 TTTATTAATCTTATATATTA
1 -TTATTATTATAATATATTA
* * *
36945 TCTATCAGTAT-ATATATTTG
1 T-TATTATTATAATATA-TTA
*
36965 TTATTACTAT-ATATATTAA
1 TTATTATTATAATATATT-A
36984 TTATTATATTATTACATATTATTTA
1 TTA-T-TATTA-TA-ATA-TA-TTA
* * *
37009 TTAGTATTATTATATAGTA
1 TTATTATTATAATATATTA
*
37028 TTCTTATTAT
1 TTATTATTAT
37038 TCTTTTTAAT
Statistics
Matches: 166, Mismatches: 40, Indels: 48
0.65 0.16 0.19
Matches are distributed among these distances:
16 4 0.02
17 9 0.05
18 21 0.13
19 48 0.29
20 37 0.22
21 12 0.07
22 3 0.02
23 9 0.05
24 8 0.05
25 13 0.08
26 2 0.01
ACGTcount: A:0.36, C:0.04, G:0.03, T:0.57
Consensus pattern (19 bp):
TTATTATTATAATATATTA
Found at i:37002 original size:22 final size:23
Alignment explanation
Indices: 36977--37020 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 23
36967 ATTACTATAT
36977 ATATTAATTATTA-TATTATTAC
1 ATATTAATTATTAGTATTATTAC
*
36999 ATATTATTTATTAGTATTATTA
1 ATATTAATTATTAGTATTATTA
37021 TATAGTATTC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 12 0.60
23 8 0.40
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.57
Consensus pattern (23 bp):
ATATTAATTATTAGTATTATTAC
Found at i:37034 original size:13 final size:12
Alignment explanation
Indices: 36978--37036 Score: 52
Period size: 13 Copynumber: 4.9 Consensus size: 12
36968 TTACTATATA
36978 TATTAATTATTA-
1 TATT-ATTATTAG
*
36990 TATTATTA-CA-
1 TATTATTATTAG
37000 TATTATTTATTAG
1 TATTA-TTATTAG
37013 TATTATTATATAG
1 TATTATTAT-TAG
*
37026 TATTCTTATTA
1 TATTATTATTA
37037 TTCTTTTTAA
Statistics
Matches: 40, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
10 6 0.15
11 7 0.17
12 11 0.28
13 16 0.40
ACGTcount: A:0.36, C:0.03, G:0.03, T:0.58
Consensus pattern (12 bp):
TATTATTATTAG
Found at i:42821 original size:11 final size:11
Alignment explanation
Indices: 42805--42831 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
42795 ATATTTTAAA
42805 TTATTTATTAT
1 TTATTTATTAT
42816 TTATTTATTAT
1 TTATTTATTAT
42827 TTATT
1 TTATT
42832 AAATTTAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (11 bp):
TTATTTATTAT
Found at i:51609 original size:14 final size:14
Alignment explanation
Indices: 51590--51616 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
51580 CGTCAAATAA
51590 GGATCATAATCTAT
1 GGATCATAATCTAT
51604 GGATCATAATCTA
1 GGATCATAATCTA
51617 AACCCTAACA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.15, G:0.15, T:0.33
Consensus pattern (14 bp):
GGATCATAATCTAT
Found at i:56515 original size:55 final size:55
Alignment explanation
Indices: 56411--56518 Score: 135
Period size: 55 Copynumber: 2.0 Consensus size: 55
56401 AATTAAATGT
* * * * *
56411 TAAATATTATTTAAAAAATACTAATTGAGCGACCAAAACGAAGTCATTAGATACA
1 TAAATATCATTTAAAAAATAATAATTGAACGACCAAAACAAAATCATTAGATACA
* * * *
56466 TAAATATCATTTAAAAAATAATAATTGAATGACTAAAATAAAATTATTAGATA
1 TAAATATCATTTAAAAAATAATAATTGAACGACCAAAACAAAATCATTAGATA
56519 TGTAATTTAC
Statistics
Matches: 44, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
55 44 1.00
ACGTcount: A:0.53, C:0.08, G:0.08, T:0.31
Consensus pattern (55 bp):
TAAATATCATTTAAAAAATAATAATTGAACGACCAAAACAAAATCATTAGATACA
Found at i:60245 original size:24 final size:24
Alignment explanation
Indices: 60218--60265 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
60208 AAATACTTTC
*
60218 GAAAATGAATTAATTTTTTTTAAA
1 GAAAATGAATAAATTTTTTTTAAA
* *
60242 GAAAATTAGTAAATTTTTTTTAAA
1 GAAAATGAATAAATTTTTTTTAAA
60266 ATTTTAAATA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.46, C:0.00, G:0.08, T:0.46
Consensus pattern (24 bp):
GAAAATGAATAAATTTTTTTTAAA
Found at i:60266 original size:20 final size:20
Alignment explanation
Indices: 60243--60288 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
60233 TTTTTTAAAG
*
60243 AAAATTAGTAAAT-TTTTTTT
1 AAAATT-GTAAATATATTTTT
*
60263 AAAATTTTAAATATATTTTT
1 AAAATTGTAAATATATTTTT
60283 AAAATT
1 AAAATT
60289 TAATATTTAC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 5 0.22
20 18 0.78
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (20 bp):
AAAATTGTAAATATATTTTT
Found at i:60359 original size:2 final size:2
Alignment explanation
Indices: 60352--60379 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
60342 TAAAATATCA
60352 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
60380 TACTTTCACG
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:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:67437 original size:15 final size:15
Alignment explanation
Indices: 67417--67496 Score: 99
Period size: 15 Copynumber: 5.4 Consensus size: 15
67407 TCGGAAAATA
*
67417 AATTACTGCAATTTG
1 AATTACTGGAATTTG
67432 AATTACTGGAATTTG
1 AATTACTGGAATTTG
**
67447 AATTACTGGAAAATG
1 AATTACTGGAATTTG
*
67462 AATTATTGGAATTTG
1 AATTACTGGAATTTG
**
67477 AATT-CTGGAAAATG
1 AATTACTGGAATTTG
67491 AATTAC
1 AATTAC
67497 ATTTCTGGAA
Statistics
Matches: 55, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
14 11 0.20
15 44 0.80
ACGTcount: A:0.39, C:0.07, G:0.17, T:0.36
Consensus pattern (15 bp):
AATTACTGGAATTTG
Found at i:67475 original size:45 final size:44
Alignment explanation
Indices: 67409--67496 Score: 122
Period size: 45 Copynumber: 2.0 Consensus size: 44
67399 TTGGTTTTTC
**
67409 GGAAAATAAATTACTGCAATTTGAATTACTGGAATTTGAATTACT
1 GGAAAATAAATTACTGCAATTTGAATT-CTGGAAAATGAATTACT
* * *
67454 GGAAAATGAATTATTGGAATTTGAATTCTGGAAAATGAATTAC
1 GGAAAATAAATTACTGCAATTTGAATTCTGGAAAATGAATTAC
67497 ATTTCTGGAA
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
44 14 0.37
45 24 0.63
ACGTcount: A:0.41, C:0.07, G:0.18, T:0.34
Consensus pattern (44 bp):
GGAAAATAAATTACTGCAATTTGAATTCTGGAAAATGAATTACT
Found at i:67494 original size:29 final size:30
Alignment explanation
Indices: 67430--67496 Score: 118
Period size: 30 Copynumber: 2.3 Consensus size: 30
67420 TACTGCAATT
67430 TGAATTACTGGAATTTGAATTACTGGAAAA
1 TGAATTACTGGAATTTGAATTACTGGAAAA
*
67460 TGAATTATTGGAATTTGAATT-CTGGAAAA
1 TGAATTACTGGAATTTGAATTACTGGAAAA
67489 TGAATTAC
1 TGAATTAC
67497 ATTTCTGGAA
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
29 15 0.43
30 20 0.57
ACGTcount: A:0.39, C:0.06, G:0.19, T:0.36
Consensus pattern (30 bp):
TGAATTACTGGAATTTGAATTACTGGAAAA
Found at i:67502 original size:20 final size:21
Alignment explanation
Indices: 67479--67530 Score: 88
Period size: 20 Copynumber: 2.5 Consensus size: 21
67469 GGAATTTGAA
67479 TTCTGGAAAATGAATT-ACAT
1 TTCTGGAAAATGAATTAACAT
67499 TTCTGGAAAATGAATTACACAT
1 TTCTGGAAAATGAATTA-ACAT
67521 TTCTGGAAAA
1 TTCTGGAAAA
67531 CGTTTTATGA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
20 16 0.53
22 14 0.47
ACGTcount: A:0.40, C:0.12, G:0.15, T:0.33
Consensus pattern (21 bp):
TTCTGGAAAATGAATTAACAT
Found at i:67778 original size:90 final size:85
Alignment explanation
Indices: 67662--67828 Score: 203
Period size: 88 Copynumber: 1.9 Consensus size: 85
67652 TATTATTTTA
* * *
67662 AAATATTAAAATAATTTATTTATTATTAAA-T-ATATTTTTATAATTTTATTAATAAAAATATTA
1 AAATATTAAAATAATTTAATTATTATTAAAGTAATAGTTTTAT-ATTATATTAA-AAAAATATT-
*
67725 ATATTGGTATATTTTAGTGAAATG
63 A-ATTAGTATATTTTAGTGAAATG
* *
67749 AAATATTATAAATTATATTAATTATTTATTAAAGTAATAGTTTTATATTATATTTAAAAAATATT
1 AAATATTA-AAATAAT-TTAATTA-TTATTAAAGTAATAGTTTTATATTATATTAAAAAAATATT
67814 AATTAGTATATTTTA
63 AATTAGTATATTTTA
67829 CTAAAATATT
Statistics
Matches: 69, Mismatches: 6, Indels: 9
0.82 0.07 0.11
Matches are distributed among these distances:
87 8 0.12
88 19 0.28
89 7 0.10
90 17 0.25
91 9 0.13
92 9 0.13
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.50
Consensus pattern (85 bp):
AAATATTAAAATAATTTAATTATTATTAAAGTAATAGTTTTATATTATATTAAAAAAATATTAAT
TAGTATATTTTAGTGAAATG
Found at i:67971 original size:31 final size:30
Alignment explanation
Indices: 67874--68001 Score: 108
Period size: 28 Copynumber: 4.3 Consensus size: 30
67864 CATTATTAAA
* * *
67874 TAAAAAAATTATTA-TATATTAT-TAA-AA
1 TAAAAATATAATTATTATATTATATAATAT
*
67901 TAAAAATATAATATCTTATATTATAT--TAT
1 TAAAAATATAAT-TATTATATTATATAATAT
* *
67930 T-ATAATATAATTGATTATTTTATATAATAT
1 TAAAAATATAATT-ATTATATTATATAATAT
67960 TAAAAATATAA-TATTATATTATTATAAATAT
1 TAAAAATATAATTATTATATTA-TAT-AATAT
67991 TAATAAATATA
1 TAA-AAATATA
68002 TTTTAATAAA
Statistics
Matches: 81, Mismatches: 9, Indels: 17
0.76 0.08 0.16
Matches are distributed among these distances:
27 11 0.14
28 20 0.25
29 18 0.22
30 9 0.11
31 16 0.20
32 7 0.09
ACGTcount: A:0.52, C:0.01, G:0.01, T:0.46
Consensus pattern (30 bp):
TAAAAATATAATTATTATATTATATAATAT
Found at i:67977 original size:22 final size:23
Alignment explanation
Indices: 67952--67995 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
67942 GATTATTTTA
67952 TATAATATTAAAAATA-TAATAT
1 TATAATATTAAAAATATTAATAT
* *
67974 TATATTATTATAAATATTAATA
1 TATAATATTAAAAATATTAATA
67996 AATATATTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (23 bp):
TATAATATTAAAAATATTAATAT
Found at i:68000 original size:22 final size:22
Alignment explanation
Indices: 67957--68017 Score: 54
Period size: 22 Copynumber: 2.8 Consensus size: 22
67947 TTTTATATAA
*
67957 TATTAAAAATATAATATTATAT
1 TATTAAAAATATAATATAATAT
*
67979 TATTATAAATATTAATA-AATAT
1 TATTAAAAATA-TAATATAATAT
* *
68001 ATTTTAATAA-ATAATAT
1 -TATTAAAAATATAATAT
68018 TTTGATGAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
21 5 0.16
22 15 0.48
23 11 0.35
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (22 bp):
TATTAAAAATATAATATAATAT
Found at i:68009 original size:14 final size:15
Alignment explanation
Indices: 67990--68020 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
67980 ATTATAAATA
67990 TTAATAAAT-ATATT
1 TTAATAAATAATATT
68004 TTAATAAATAATATT
1 TTAATAAATAATATT
68019 TT
1 TT
68021 GATGAAAATG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.56
15 7 0.44
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TTAATAAATAATATT
Done.