Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008132.1 Hibiscus syriacus cultivar Beakdansim tig00110687_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: 357788
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
File 2 of 2
Found at i:285634 original size:21 final size:22
Alignment explanation
Indices: 285608--285686 Score: 85
Period size: 20 Copynumber: 3.7 Consensus size: 22
285598 AGGGTGTCAA
285608 AGTGCATCCATGCACC-CCTAC-
1 AGTGCATCCATGCACCGCC-ACT
285629 AGTGCATCCATGCACCTGCCACT
1 AGTGCATCCATGCACC-GCCACT
* * *
285652 AGTGCATCTATGCA-C-CAAGT
1 AGTGCATCCATGCACCGCCACT
285672 AGTGCATCCATGCAC
1 AGTGCATCCATGCAC
285687 TCTATTTCGA
Statistics
Matches: 50, Mismatches: 4, Indels: 8
0.81 0.06 0.13
Matches are distributed among these distances:
20 16 0.32
21 16 0.32
22 3 0.06
23 15 0.30
ACGTcount: A:0.25, C:0.35, G:0.18, T:0.22
Consensus pattern (22 bp):
AGTGCATCCATGCACCGCCACT
Found at i:285659 original size:23 final size:21
Alignment explanation
Indices: 285608--285667 Score: 77
Period size: 23 Copynumber: 2.8 Consensus size: 21
285598 AGGGTGTCAA
285608 AGTGCATCCATGCACCCCTAC
1 AGTGCATCCATGCACCCCTAC
285629 AGTGCATCCATGCACCTGCC-AC
1 AGTGCATCCATGCACC--CCTAC
*
285651 TAGTGCATCTATGCACC
1 -AGTGCATCCATGCACC
285668 AAGTAGTGCA
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
21 16 0.46
22 2 0.06
23 17 0.49
ACGTcount: A:0.23, C:0.38, G:0.17, T:0.22
Consensus pattern (21 bp):
AGTGCATCCATGCACCCCTAC
Found at i:289631 original size:17 final size:17
Alignment explanation
Indices: 289609--289749 Score: 86
Period size: 17 Copynumber: 8.1 Consensus size: 17
289599 AATTAAGAAT
289609 TAGTTTAATAAATGAAC
1 TAGTTTAATAAATGAAC
* *
289626 TAGTTTGATGAATGAAC
1 TAGTTTAATAAATGAAC
* * *
289643 AAGTTTGATGAATGAAC
1 TAGTTTAATAAATGAAC
* *
289660 TAGTTTAATTAATAAAC
1 TAGTTTAATAAATGAAC
* * * *
289677 TAACTTTATTCAATAAAC
1 T-AGTTTAATAAATGAAC
* *
289695 TAGTTGT-ATGAATGAAG
1 TAGTT-TAATAAATGAAC
* *
289712 TAGTTTACTAAATGATC
1 TAGTTTAATAAATGAAC
* *
289729 TAAATATGAATAAATGAAC
1 T-AGT-TTAATAAATGAAC
289748 TA
1 TA
289750 CCTCTCTAAA
Statistics
Matches: 96, Mismatches: 23, Indels: 9
0.75 0.18 0.07
Matches are distributed among these distances:
16 1 0.01
17 66 0.69
18 18 0.19
19 11 0.11
ACGTcount: A:0.43, C:0.07, G:0.14, T:0.35
Consensus pattern (17 bp):
TAGTTTAATAAATGAAC
Found at i:303330 original size:2 final size:2
Alignment explanation
Indices: 303323--303375 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
303313 CTTTTAAAAC
303323 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
303365 AT AT AT AT AT A
1 AT AT AT AT AT A
303376 CCCTCATCCG
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:303564 original size:24 final size:24
Alignment explanation
Indices: 303536--303642 Score: 79
Period size: 24 Copynumber: 4.5 Consensus size: 24
303526 AAACAGAGAT
*
303536 ATCAGAAATCAAAACATAATTCAG
1 ATCAGAAATCAAAACAGAATTCAG
* * *
303560 ATCAGATATCAGAACAGAATCCAG
1 ATCAGAAATCAAAACAGAATTCAG
* * * * * *
303584 GTTAGGAATCAGAACAGATTTTAG
1 ATCAGAAATCAAAACAGAATTCAG
** * *
303608 ATCAGATGTCAAAACAAAATTCAA
1 ATCAGAAATCAAAACAGAATTCAG
*
303632 ATAAGAAATCA
1 ATCAGAAATCA
303643 GATAAAATAT
Statistics
Matches: 59, Mismatches: 24, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
24 59 1.00
ACGTcount: A:0.50, C:0.15, G:0.14, T:0.21
Consensus pattern (24 bp):
ATCAGAAATCAAAACAGAATTCAG
Found at i:309046 original size:16 final size:15
Alignment explanation
Indices: 309025--309108 Score: 60
Period size: 16 Copynumber: 5.3 Consensus size: 15
309015 ATGATCTAAT
309025 ATGATAAACAAAAATA
1 ATGATAAA-AAAAATA
** **
309041 ATGATATAATGATCTA
1 ATGATA-AAAAAAATA
309057 ATGATAAAAAAAATA
1 ATGATAAAAAAAATA
** **
309072 ATGATATAATGATCTA
1 ATGATA-AAAAAAATA
309088 ATGATAAACAAAAATA
1 ATGATAAA-AAAAATA
309104 ATGAT
1 ATGAT
309109 GATAAACATT
Statistics
Matches: 49, Mismatches: 16, Indels: 6
0.69 0.23 0.08
Matches are distributed among these distances:
15 13 0.27
16 34 0.69
17 2 0.04
ACGTcount: A:0.58, C:0.05, G:0.10, T:0.27
Consensus pattern (15 bp):
ATGATAAAAAAAATA
Found at i:309051 original size:8 final size:8
Alignment explanation
Indices: 309038--309093 Score: 60
Period size: 8 Copynumber: 7.1 Consensus size: 8
309028 ATAAACAAAA
309038 ATAATGAT
1 ATAATGAT
309046 ATAATGAT
1 ATAATGAT
*
309054 CTAATGAT
1 ATAATGAT
** *
309062 A-AAAAAA
1 ATAATGAT
309069 ATAATGAT
1 ATAATGAT
309077 ATAATGAT
1 ATAATGAT
*
309085 CTAATGAT
1 ATAATGAT
309093 A
1 A
309094 AACAAAAATA
Statistics
Matches: 37, Mismatches: 10, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
7 4 0.11
8 33 0.89
ACGTcount: A:0.54, C:0.04, G:0.11, T:0.32
Consensus pattern (8 bp):
ATAATGAT
Found at i:309072 original size:31 final size:32
Alignment explanation
Indices: 309013--309113 Score: 168
Period size: 31 Copynumber: 3.1 Consensus size: 32
309003 AAGATATAAT
309013 TAATGATCTAATATGATAAACAAAAATAATGATA
1 TAATGATCT-A-ATGATAAACAAAAATAATGATA
309047 TAATGATCTAATGATAAA-AAAAATAATGATA
1 TAATGATCTAATGATAAACAAAAATAATGATA
309078 TAATGATCTAATGATAAACAAAAATAATGATGA
1 TAATGATCTAATGATAAACAAAAATAATGAT-A
309111 TAA
1 TAA
309114 ACATTAGTAT
Statistics
Matches: 65, Mismatches: 0, Indels: 5
0.93 0.00 0.07
Matches are distributed among these distances:
31 31 0.48
32 20 0.31
33 5 0.08
34 9 0.14
ACGTcount: A:0.56, C:0.05, G:0.10, T:0.29
Consensus pattern (32 bp):
TAATGATCTAATGATAAACAAAAATAATGATA
Found at i:309782 original size:17 final size:17
Alignment explanation
Indices: 309762--309808 Score: 58
Period size: 17 Copynumber: 2.8 Consensus size: 17
309752 TTATAATCCT
*
309762 ATTATTTCAAAATTATA
1 ATTATTTAAAAATTATA
* *
309779 ATTATATAAAAAATATA
1 ATTATTTAAAAATTATA
*
309796 TTTATTTAAAAAT
1 ATTATTTAAAAAT
309809 ATCAGAAAAT
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (17 bp):
ATTATTTAAAAATTATA
Found at i:309896 original size:18 final size:19
Alignment explanation
Indices: 309861--309896 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
309851 TCGATATATA
309861 TTATAATAATTAAATTTTT
1 TTATAATAATTAAATTTTT
*
309880 TTATAAT-ATTTAATTTT
1 TTATAATAATTAAATTTT
309897 AAAATACCAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (19 bp):
TTATAATAATTAAATTTTT
Found at i:310101 original size:28 final size:28
Alignment explanation
Indices: 310058--310119 Score: 74
Period size: 28 Copynumber: 2.2 Consensus size: 28
310048 ATAAATAAAA
* *
310058 TTAAAACAATAAAAATACAAT-TATATAT
1 TTAAAACAATAAAAATA-AATGAAAATAT
310086 TTAAAAGCAAT-AAAATAAATGAAAATAT
1 TTAAAA-CAATAAAAATAAATGAAAATAT
310114 TTAAAA
1 TTAAAA
310120 TTAGTGACTA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
27 3 0.10
28 23 0.77
29 4 0.13
ACGTcount: A:0.63, C:0.05, G:0.03, T:0.29
Consensus pattern (28 bp):
TTAAAACAATAAAAATAAATGAAAATAT
Found at i:311389 original size:3 final size:3
Alignment explanation
Indices: 311383--311457 Score: 98
Period size: 3 Copynumber: 25.0 Consensus size: 3
311373 ATTATTTTTT
* *
311383 TAA TAA TAA TAA TAA T-A TATA TAA TAA TTA TAA TAA TAA TAA TTA
1 TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA
* *
311428 TAA TAA TAA TAA TTA TAG TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
311458 AAATGGGTAA
Statistics
Matches: 62, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
2 2 0.03
3 57 0.92
4 3 0.05
ACGTcount: A:0.60, C:0.00, G:0.01, T:0.39
Consensus pattern (3 bp):
TAA
Found at i:311818 original size:124 final size:121
Alignment explanation
Indices: 311593--311889 Score: 390
Period size: 124 Copynumber: 2.5 Consensus size: 121
311583 GAGATGTTGA
311593 ATAAA-TTCTTCTCTTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTGCTGG---GGATGAT
1 ATAAACTTCTT-TCTTT-TTCAGATGAGTTCTTCTCATTATGAACTTTCT-CTGGAAAGGATGAT
* * * * *
311654 GTTGACCTATTTCCTTCTGTGATAGAGTCATTCAAAAGGTTGAATAAGCTCTTCTCATT
63 GCTAACCTATCTCCTTCTGTGATAGAATCAATCAAAAGGTTGAATAAGCTCTTCTCATT
*
311713 ATAAACTTCTTCTTTCTTTTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAGGTTGAT
1 ATAAA---CTTCTTTCTTTTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAGGATGAT
* * *
311778 GCTAATCTATCTGCTTCTGTGATAGAATTAATCAAAAGGTTGAATAAGCTCTTCTCATT
63 GCTAACCTATCTCCTTCTGTGATAGAATCAATCAAAAGGTTGAATAAGCTCTTCTCATT
* * *
311837 GTGAACTT-TTTCTTCTTCAGATGAGTTCTTCTCATTATGAAC-TTCTCTGGAAA
1 ATAAACTTCTTTCTTTTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAA
311890 AATTGATCCA
Statistics
Matches: 158, Mismatches: 12, Indels: 15
0.85 0.06 0.08
Matches are distributed among these distances:
119 11 0.07
120 38 0.24
121 7 0.04
122 32 0.20
123 5 0.03
124 65 0.41
ACGTcount: A:0.25, C:0.18, G:0.15, T:0.42
Consensus pattern (121 bp):
ATAAACTTCTTTCTTTTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAGGATGATGCT
AACCTATCTCCTTCTGTGATAGAATCAATCAAAAGGTTGAATAAGCTCTTCTCATT
Found at i:312055 original size:116 final size:112
Alignment explanation
Indices: 311797--312445 Score: 798
Period size: 113 Copynumber: 5.8 Consensus size: 112
311787 TCTGCTTCTG
* * ** *
311797 TGATAGAATT-AATCAAAAGGTTGAATAAGCTCTTCTCATTGTGAAC-T-TT-TT-CTTCTTCAG
1 TGAT-GAATTCAAACAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAG
*
311857 ATGAGTTCTTCTCATTATGAACTTCTCTGGAAAAATTGATCCATCAAG
65 ATGAGTTCTTCTCATTATGAACTTCTCTGGAAAAATTGATCCATCAAA
* ** * *
311905 TGATGGATTTGAGCAAAAAGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGA
1 TGATGAATTCAAACAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTC--A
* ** *
311970 TGATGAGTTCTTCTCATTATGAAC-TCTACATGGCAATGTTAATCCATCAAA
64 -GATGAGTTCTTCTCATTATGAACTTCT-C-TGGAAAAATTGATCCATCAAA
*
312021 TGATGAATTCAAACAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGA
1 TGATGAATTCAAACAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGA
* * * **
312086 TGAGTTATTCTCTTTATGAACTATAC-CTGGCAATGTTGATCCATCAAA
66 TGAGTTCTTCTCATTATGAACT-T-CTCTGGAAAAATTGATCCATCAAA
* * *
312134 TTATGAATTCAAACAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTATTCCTTCTTCAGA
1 TGATGAATTCAAACAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGA
* *
312199 TGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAACTGATCCATCAAT
66 TGAGTTCTTCTCATTATGAAC-TTCTCTGGAAAAATTGATCCATCAAA
*
312247 TGATGAATTCAAACAAAAGGTTGAACAAATTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGA
1 TGATGAATTCAAACAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGA
* *
312312 TGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAACTGATCCATCGAA
66 TGAGTTCTTCTCATTATGAAC-TTCTCTGGAAAAATTGATCCATCAAA
* ** * *
312360 TGATGGATTTGAGCAAAAAGTTGAACAAATTCTTCTCATTATGAA--T-TTCTT-CTTCTTCAGA
1 TGATGAATTCAAACAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGA
312421 TGACGAGTTCTTCTCATTATGAACT
66 T---GAGTTCTTCTCATTATGAACT
312446 CTACCTGGCA
Statistics
Matches: 480, Mismatches: 43, Indels: 33
0.86 0.08 0.06
Matches are distributed among these distances:
107 4 0.01
108 33 0.07
109 12 0.03
110 7 0.01
111 4 0.01
112 28 0.06
113 287 0.60
114 7 0.01
115 25 0.05
116 73 0.15
ACGTcount: A:0.31, C:0.18, G:0.13, T:0.38
Consensus pattern (112 bp):
TGATGAATTCAAACAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGA
TGAGTTCTTCTCATTATGAACTTCTCTGGAAAAATTGATCCATCAAA
Found at i:312267 original size:226 final size:224
Alignment explanation
Indices: 311797--312578 Score: 890
Period size: 226 Copynumber: 3.6 Consensus size: 224
311787 TCTGCTTCTG
* * ** * *
311797 TGATAGAATT-AATCAAAAGGTTGAATAAGCTCTTCTCATTGTGAA--CTT-TTTCTTCTTCAGA
1 TGAT-GAATTCAAACAAAAGGTTGAACAAATTCTTCTCATTATGAATTCTTCTTCCTTCTTCAGA
*
311858 TGAGTTCTTCTCATTATGAACTTCTCTGGAAAAATTGATCCATCAAGTGATGGATTTGAGCAAAA
65 TGAGTTCTTCTCATTATGAACTTCTCTGGAAAAATTGATCCATCAAATGATGGATTTGAGCAAAA
*
311923 AGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGATGAGTTCTTCTCATT
130 AGTTGAACAAATTCTTCTCATTATGAATTTCTT-TTCCTTCTTC--A-GATGAGTTCTTCTCATT
* ***
311988 ATGAAC-TCTACATGGCAATGTTAATCCATCAAA
191 ATGAACTTCTACATGGAAAAACTAATCCATCAAA
312021 TGATGAATTCAAACAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGA
1 TGATGAATTCAAACAAAAGGTTGAACAAATTCTTCTCATTATGAA-TTCTTCTTCCTTCTTCAGA
* * * ** * * ** *
312086 TGAGTTATTCTCTTTATGAACTATAC-CTGGCAATGTTGATCCATCAAATTATGAATTCAAACAA
65 TGAGTTCTTCTCATTATGAACT-T-CTCTGGAAAAATTGATCCATCAAATGATGGATTTGAGCAA
*
312150 AAGGTTGAACAAATTCTTCTCATTATGAATTTCTTATTCCTTCTTCAGATGAGTTCTTCTCATTA
128 AAAGTTGAACAAATTCTTCTCATTATGAATTTCTT-TTCCTTCTTCAGATGAGTTCTTCTCATTA
* *
312215 TGAACTTTCT-C-TGGAAAAACTGATCCATCAAT
192 TGAAC-TTCTACATGGAAAAACTAATCCATCAAA
*
312247 TGATGAATTCAAACAAAAGGTTGAACAAATTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGA
1 TGATGAATTCAAACAAAAGGTTGAACAAATTCTTCTCATTATGAA-TTCTTCTTCCTTCTTCAGA
* *
312312 TGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAACTGATCCATCGAATGATGGATTTGAGCAAA
65 TGAGTTCTTCTCATTATGAAC-TTCTCTGGAAAAATTGATCCATCAAATGATGGATTTGAGCAAA
312377 AAGTTGAACAAATTCTTCTCATTATGAATTTC--TT-CTTCTTCAGATGACGAGTTCTTCTCATT
129 AAGTTGAACAAATTCTTCTCATTATGAATTTCTTTTCCTTCTTCAGAT---GAGTTCTTCTCATT
*
312439 ATGAAC-TCTACCTGG--------------C-AA
191 ATGAACTTCTACATGGAAAAACTAATCCATCAAA
*
312457 TGTTG-A-TC---CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGA
1 TGATGAATTCAAACAAAAGGTTGAACAAATTCTTCTCATTATGAA-TTCTTCTTCCTTCTTCAGA
* * *
312517 TAAGTTCTTCTCATTATGAACTTTCTCTGGAAAAACTGATCCATCAAGTGATGGATTTGAGC
65 TGAGTTCTTCTCATTATGAAC-TTCTCTGGAAAAATTGATCCATCAAATGATGGATTTGAGC
312579 TTTGCTAAAA
Statistics
Matches: 495, Mismatches: 47, Indels: 51
0.83 0.08 0.09
Matches are distributed among these distances:
205 110 0.22
208 2 0.00
209 1 0.00
210 5 0.01
211 1 0.00
222 11 0.02
223 10 0.02
224 35 0.07
225 24 0.05
226 181 0.37
227 6 0.01
228 35 0.07
229 73 0.15
230 1 0.00
ACGTcount: A:0.30, C:0.19, G:0.13, T:0.38
Consensus pattern (224 bp):
TGATGAATTCAAACAAAAGGTTGAACAAATTCTTCTCATTATGAATTCTTCTTCCTTCTTCAGAT
GAGTTCTTCTCATTATGAACTTCTCTGGAAAAATTGATCCATCAAATGATGGATTTGAGCAAAAA
GTTGAACAAATTCTTCTCATTATGAATTTCTTTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
CTTCTACATGGAAAAACTAATCCATCAAA
Found at i:313649 original size:93 final size:93
Alignment explanation
Indices: 313310--313649 Score: 547
Period size: 93 Copynumber: 3.7 Consensus size: 93
313300 TGGTTCTATG
* * * *
313310 GTTCCTACCGAACCAGATCAAATAACTCAAA-AATCACTTCCAAAAGATGCTATGAGCACATTCA
1 GTTCATACCAAACCAGATCAGATAACTCAAAGAA-CACTTCCAAAAGATGCTATGAGCACACTCA
* *
313374 TCTTCCAAATTCAATAATTGGTTTTTGGG
65 TCTTCCAAATTCAATGATTGGTTTTTGGT
* *
313403 GTTCATACCAAACCAGATTAGATAACTCAAAGAACACTTCCAAAAGATGCTATGAGCACATTCAT
1 GTTCATACCAAACCAGATCAGATAACTCAAAGAACACTTCCAAAAGATGCTATGAGCACACTCAT
313468 CTTCCAAATTCAATGATTGGTTTTTGGT
66 CTTCCAAATTCAATGATTGGTTTTTGGT
* *
313496 GTTCATACCAAACCGGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACACTCAT
1 GTTCATACCAAACCAGATCAGATAACTCAAAGAACACTTCCAAAAGATGCTATGAGCACACTCAT
*
313561 CTTTCAAATTCAATGATTGGTTTTTGGT
66 CTTCCAAATTCAATGATTGGTTTTTGGT
* *
313589 GTTCATACCAAACCAGATCAGATAACACAAAGAACACTTCCAGAAGATGCTATGAGCACAC
1 GTTCATACCAAACCAGATCAGATAACTCAAAGAACACTTCCAAAAGATGCTATGAGCACAC
313650 GGCACTTGTT
Statistics
Matches: 233, Mismatches: 13, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
93 231 0.99
94 2 0.01
ACGTcount: A:0.36, C:0.22, G:0.14, T:0.27
Consensus pattern (93 bp):
GTTCATACCAAACCAGATCAGATAACTCAAAGAACACTTCCAAAAGATGCTATGAGCACACTCAT
CTTCCAAATTCAATGATTGGTTTTTGGT
Found at i:314656 original size:11 final size:11
Alignment explanation
Indices: 314635--314686 Score: 63
Period size: 12 Copynumber: 4.6 Consensus size: 11
314625 TCTTGACCCC
314635 CTTTTTATTTTT
1 CTTTTT-TTTTT
314647 CTTTTTTTTTT
1 CTTTTTTTTTT
314658 C--TTTTTTTT
1 CTTTTTTTTTT
314667 CTTTATTTTTTT
1 CTTT-TTTTTTT
314679 CTTATTTT
1 CTT-TTTT
314687 CTTCAAGCAA
Statistics
Matches: 36, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
9 9 0.25
11 7 0.19
12 19 0.53
13 1 0.03
ACGTcount: A:0.06, C:0.10, G:0.00, T:0.85
Consensus pattern (11 bp):
CTTTTTTTTTT
Found at i:314664 original size:12 final size:12
Alignment explanation
Indices: 314635--314678 Score: 54
Period size: 11 Copynumber: 3.7 Consensus size: 12
314625 TCTTGACCCC
*
314635 CTTTTTATTTTT
1 CTTTTTTTTTTT
314647 C-TTTTTTTTTT
1 CTTTTTTTTTTT
314658 CTTTTTTTTCTTT
1 CTTTTTTTT-TTT
*
314671 ATTTTTTT
1 CTTTTTTT
314679 CTTATTTTCT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
11 10 0.36
12 8 0.29
13 10 0.36
ACGTcount: A:0.05, C:0.09, G:0.00, T:0.86
Consensus pattern (12 bp):
CTTTTTTTTTTT
Found at i:314667 original size:20 final size:22
Alignment explanation
Indices: 314642--314686 Score: 76
Period size: 21 Copynumber: 2.1 Consensus size: 22
314632 CCCCTTTTTA
314642 TTTTTCTTT-TTTTTTTCTT-T
1 TTTTTCTTTATTTTTTTCTTAT
314662 TTTTTCTTTATTTTTTTCTTAT
1 TTTTTCTTTATTTTTTTCTTAT
314684 TTT
1 TTT
314687 CTTCAAGCAA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
20 9 0.39
21 10 0.43
22 4 0.17
ACGTcount: A:0.04, C:0.09, G:0.00, T:0.87
Consensus pattern (22 bp):
TTTTTCTTTATTTTTTTCTTAT
Found at i:314687 original size:20 final size:20
Alignment explanation
Indices: 314638--314689 Score: 70
Period size: 20 Copynumber: 2.5 Consensus size: 20
314628 TGACCCCCTT
314638 TTTATTTTTCTTTTTTTTTTC
1 TTTA-TTTTCTTTTTTTTTTC
*
314659 TTTTTTTTCTTTATTTTTTTC
1 TTTATTTTCTTT-TTTTTTTC
314680 -TTATTTTCTT
1 TTTATTTTCTT
314690 CAAGCAAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
20 17 0.61
21 11 0.39
ACGTcount: A:0.06, C:0.10, G:0.00, T:0.85
Consensus pattern (20 bp):
TTTATTTTCTTTTTTTTTTC
Found at i:322047 original size:15 final size:15
Alignment explanation
Indices: 322024--322055 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
322014 TGAAATGAAT
322024 AATGAATGTATGCAA
1 AATGAATGTATGCAA
*
322039 AATGTATGTATGCAA
1 AATGAATGTATGCAA
322054 AA
1 AA
322056 AGGTATTAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.47, C:0.06, G:0.19, T:0.28
Consensus pattern (15 bp):
AATGAATGTATGCAA
Found at i:325781 original size:17 final size:16
Alignment explanation
Indices: 325761--325807 Score: 53
Period size: 14 Copynumber: 3.0 Consensus size: 16
325751 TTATAATCCT
325761 ATTATTTCAAAATTATA
1 ATTATTT-AAAATTATA
*
325778 ATTATATAAAA-TAT-
1 ATTATTTAAAATTATA
*
325792 ATTATTTAAAAATATA
1 ATTATTTAAAATTATA
325808 TATATATATA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
14 10 0.38
15 6 0.23
16 4 0.15
17 6 0.23
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (16 bp):
ATTATTTAAAATTATA
Found at i:325803 original size:15 final size:15
Alignment explanation
Indices: 325760--325808 Score: 55
Period size: 15 Copynumber: 3.2 Consensus size: 15
325750 TTTATAATCC
*
325760 TATTATTTCAAAAT-
1 TATTATTTAAAAATA
*
325774 TATAATTATATAAAATA
1 TATTATT-TA-AAAATA
325791 TATTATTTAAAAATA
1 TATTATTTAAAAATA
325806 TAT
1 TAT
325809 ATATATATAT
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
14 6 0.21
15 10 0.34
16 7 0.24
17 6 0.21
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (15 bp):
TATTATTTAAAAATA
Found at i:326048 original size:28 final size:28
Alignment explanation
Indices: 326005--326066 Score: 74
Period size: 28 Copynumber: 2.2 Consensus size: 28
325995 ATAAATAAAA
* *
326005 TTAAAACAATAAAAATACAAT-TATATAT
1 TTAAAACAATAAAAATA-AATGAAAATAT
326033 TTAAAAGCAAT-AAAATAAATGAAAATAT
1 TTAAAA-CAATAAAAATAAATGAAAATAT
326061 TTAAAA
1 TTAAAA
326067 TTAGTGACTA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
27 3 0.10
28 23 0.77
29 4 0.13
ACGTcount: A:0.63, C:0.05, G:0.03, T:0.29
Consensus pattern (28 bp):
TTAAAACAATAAAAATAAATGAAAATAT
Found at i:327215 original size:3 final size:3
Alignment explanation
Indices: 327209--327276 Score: 82
Period size: 3 Copynumber: 22.0 Consensus size: 3
327199 ATTATTTTTT
* *
327209 TAA TAA TAA TAA TATA TATA TAA TAA TTA TAA TAA TTA TAA TAA TAA
1 TAA TAA TAA TAA TA-A TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA
* *
327256 TAA TTA TAG TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA
327277 AAATGGGTAA
Statistics
Matches: 56, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
3 49 0.88
4 7 0.12
ACGTcount: A:0.59, C:0.00, G:0.01, T:0.40
Consensus pattern (3 bp):
TAA
Found at i:327637 original size:124 final size:121
Alignment explanation
Indices: 327417--327708 Score: 378
Period size: 124 Copynumber: 2.4 Consensus size: 121
327407 GTTGAATAAA
* * *
327417 TTCTTCTCTTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTGTTGG---GGATGATGTTGAC
1 TTCTT-TCTTT-TTCAGATGAGTTCTTCTCATTATGAACTTTCT-CTGGAAAGGATGATGCTAAC
* * * *
327479 CTATTTCCTTCTGTGATAGAGTCATTCAAAAGGTTGAATAAGCTCTTCTCATTATGAACTTC
63 CTATCTCCTTCTGTGATAGAATCATGCAAAAGGTTGAATAAGCTCTTCTCAGTATGAA---C
* *
327541 TTCTTTCTTTTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAGGTTGATGCTAATCTA
1 TTCTTTCTTTTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAGGATGATGCTAACCTA
* * *
327606 TCTGCTTCTGTGATAGAATTATGCAAAAGGTTGAATAAGCTCTTCTCAGTGTGAAC
66 TCTCCTTCTGTGATAGAATCATGCAAAAGGTTGAATAAGCTCTTCTCAGTATGAAC
*
327662 TT-TTTCTTCTTCAGATGAGTTCTTCTCATTATGAAC-TTCTCTGGAAA
1 TTCTTTCTTTTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAA
327709 AACTGATCCA
Statistics
Matches: 152, Mismatches: 13, Indels: 11
0.86 0.07 0.06
Matches are distributed among these distances:
119 11 0.07
120 33 0.22
121 6 0.04
122 32 0.21
123 5 0.03
124 65 0.43
ACGTcount: A:0.23, C:0.18, G:0.17, T:0.42
Consensus pattern (121 bp):
TTCTTTCTTTTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAGGATGATGCTAACCTA
TCTCCTTCTGTGATAGAATCATGCAAAAGGTTGAATAAGCTCTTCTCAGTATGAAC
Found at i:327886 original size:16 final size:16
Alignment explanation
Indices: 327867--327917 Score: 50
Period size: 16 Copynumber: 3.1 Consensus size: 16
327857 AGGTTGAACA
327867 AATTCTTCTCATTATG
1 AATTCTTCTCATTATG
*
327883 AATTTCTTCTTCA-GATG
1 AA-TTCTTC-TCATTATG
* *
327900 AGTTCTTCTCTTTATG
1 AATTCTTCTCATTATG
327916 AA
1 AA
327918 CTATACCTGG
Statistics
Matches: 27, Mismatches: 5, Indels: 6
0.71 0.13 0.16
Matches are distributed among these distances:
15 2 0.07
16 12 0.44
17 10 0.37
18 3 0.11
ACGTcount: A:0.24, C:0.18, G:0.10, T:0.49
Consensus pattern (16 bp):
AATTCTTCTCATTATG
Found at i:328080 original size:113 final size:113
Alignment explanation
Indices: 327629--328257 Score: 765
Period size: 113 Copynumber: 5.7 Consensus size: 113
327619 TAGAATTATG
* ** * *
327629 CAAAAGGTTGAATAAGCTCTTCTCAGTGTGAAC-T-TT-TT-CTTCTTCAGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
* * ** *
327690 TTATGAAC-TTCTCTGGAAAAACTGATCCATCAAGTGATGGATTTGAG
66 TTATGAACTTTCTCTGGAAAAACTGATCCATCAAATGATGAATTCAAA
* *
327737 CAAAAAGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTATTCAGATGATGAGTTCTTC
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTC--A-GATGAGTTCTTC
* *** *
327802 TCATTATGAAC--TCTACATGGGAATGTTAATCCATCAAATGATGAATTCAAA
63 TCATTATGAACTTTCT-C-TGGAAAAACTGATCCATCAAATGATGAATTCAAA
*
327853 CAAAAGGTTGAACAAATTCTTCTCATTATGAA-----T-TT-CTTCTTCAGATGAGTTCTTCTCT
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
* * ***
327911 TTATGAACTATAC-CTGGCAATGTTGATCCATCAAATGATGAATTCAAA
66 TTATGAACT-TTCTCTGGAAAAACTGATCCATCAAATGATGAATTCAAA
*
327959 CAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
328024 TTATGAACTTTCTCTGGAAAAACTGATCCATCAAATGATGAATTCAAA
66 TTATGAACTTTCTCTGGAAAAACTGATCCATCAAATGATGAATTCAAA
*
328072 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGTGTTCTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
* ** *
328137 TTATGAACTTTCTCTGGAAAAACTGATCCATCAAATGATGGATTTGAG
66 TTATGAACTTTCTCTGGAAAAACTGATCCATCAAATGATGAATTCAAA
* *
328185 CAAAAAGTTAAACAAATTCTTCTCATTATGAA--T-TTCTT-CTTCTTCAGATGACGAGTTCTTC
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGAT---GAGTTCTTC
328246 TCATTATGAACT
63 TCATTATGAACT
328258 CTACCTGGCA
Statistics
Matches: 460, Mismatches: 38, Indels: 42
0.85 0.07 0.08
Matches are distributed among these distances:
106 86 0.19
107 2 0.00
108 27 0.06
109 19 0.04
110 9 0.02
111 5 0.01
112 30 0.07
113 199 0.43
114 4 0.01
115 24 0.05
116 55 0.12
ACGTcount: A:0.31, C:0.19, G:0.13, T:0.37
Consensus pattern (113 bp):
CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
TTATGAACTTTCTCTGGAAAAACTGATCCATCAAATGATGAATTCAAA
Found at i:329453 original size:93 final size:93
Alignment explanation
Indices: 329114--329453 Score: 545
Period size: 93 Copynumber: 3.7 Consensus size: 93
329104 TGGTTCTATG
* * * * * *
329114 GTTCCTACCGAACCAGATCAAATAACTCAAAGAATACTTCCAAAAGATGTTATGAGCACATTCAT
1 GTTCATACCAAACCAGATCAGATAACTCAAAGAACACTTCCAAAAGATGCTATGAGCACACTCAT
* *
329179 CTTCCAAATTCAATAATTGGTTTTTGGG
66 CTTCCAAATTCAATGATTGGTTTTTGGT
* * *
329207 GTTCATACCAAACCAGATTAGATAACTCAAAAAACACTTCCAAAAGATGCTATGAGCACATTCAT
1 GTTCATACCAAACCAGATCAGATAACTCAAAGAACACTTCCAAAAGATGCTATGAGCACACTCAT
329272 CTTCCAAATTCAATGATTGGTTTTTGGT
66 CTTCCAAATTCAATGATTGGTTTTTGGT
* *
329300 GTTCATACCAAACCAGATCAGATAACTCAAAGAACATTTCCAGAAGATGCTATGAGCACACTCAT
1 GTTCATACCAAACCAGATCAGATAACTCAAAGAACACTTCCAAAAGATGCTATGAGCACACTCAT
*
329365 CTTTCAAATTCAATGATTGGTTTTTGGT
66 CTTCCAAATTCAATGATTGGTTTTTGGT
*
329393 GTTCATACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACAC
1 GTTCATACCAAACCAGATCAGATAACTCAAAGAACACTTCCAAAAGATGCTATGAGCACAC
329454 GACACTTGTT
Statistics
Matches: 231, Mismatches: 16, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
93 231 1.00
ACGTcount: A:0.36, C:0.21, G:0.14, T:0.28
Consensus pattern (93 bp):
GTTCATACCAAACCAGATCAGATAACTCAAAGAACACTTCCAAAAGATGCTATGAGCACACTCAT
CTTCCAAATTCAATGATTGGTTTTTGGT
Found at i:341766 original size:18 final size:19
Alignment explanation
Indices: 341731--341766 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
341721 TCGATATATA
341731 TTATAATAATTAAATTTTT
1 TTATAATAATTAAATTTTT
*
341750 TTATAAT-ATTTAATTTT
1 TTATAATAATTAAATTTT
341767 AAAATACCAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (19 bp):
TTATAATAATTAAATTTTT
Found at i:343282 original size:3 final size:3
Alignment explanation
Indices: 343276--343347 Score: 92
Period size: 3 Copynumber: 24.0 Consensus size: 3
343266 TTATTATTTT
* *
343276 TAA TAA TAA TAA T-A TATA TAA TAA TTA TAA TAA TAA TAA TTA TAA
1 TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA
* *
343321 TAA TAA TAA TTA TAG TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA
343348 AAATGGGTAA
Statistics
Matches: 59, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
2 2 0.03
3 54 0.92
4 3 0.05
ACGTcount: A:0.60, C:0.00, G:0.01, T:0.39
Consensus pattern (3 bp):
TAA
Found at i:345455 original size:12 final size:12
Alignment explanation
Indices: 345440--345505 Score: 89
Period size: 12 Copynumber: 5.6 Consensus size: 12
345430 GTTATTTAAA
345440 CGGGTATTGGGC
1 CGGGTATTGGGC
*
345452 CGGGTATTGGGT
1 CGGGTATTGGGC
*
345464 CGGGTATTGGGT
1 CGGGTATTGGGC
345476 C-GGTATTGGGC
1 CGGGTATTGGGC
* *
345487 CGGGAATCGGGC
1 CGGGTATTGGGC
345499 CGGGTAT
1 CGGGTAT
345506 ATATATATTT
Statistics
Matches: 48, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
11 10 0.21
12 38 0.79
ACGTcount: A:0.11, C:0.15, G:0.48, T:0.26
Consensus pattern (12 bp):
CGGGTATTGGGC
Found at i:345467 original size:24 final size:24
Alignment explanation
Indices: 345440--345505 Score: 89
Period size: 23 Copynumber: 2.8 Consensus size: 24
345430 GTTATTTAAA
*
345440 CGGGTATTGGGCCGGGTATTGGGT
1 CGGGTATTGGGCCGGGTATTGGGC
*
345464 CGGGTATTGGGTC-GGTATTGGGC
1 CGGGTATTGGGCCGGGTATTGGGC
* *
345487 CGGGAATCGGGCCGGGTAT
1 CGGGTATTGGGCCGGGTAT
345506 ATATATATTT
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
23 19 0.53
24 17 0.47
ACGTcount: A:0.11, C:0.15, G:0.48, T:0.26
Consensus pattern (24 bp):
CGGGTATTGGGCCGGGTATTGGGC
Found at i:345654 original size:13 final size:13
Alignment explanation
Indices: 345598--345641 Score: 72
Period size: 13 Copynumber: 3.5 Consensus size: 13
345588 TTTAATATTT
*
345598 ATCGGGTCGGGT-
1 ATCGGGGCGGGTA
345610 ATCGGGGCGGGTA
1 ATCGGGGCGGGTA
345623 ATCGGGGCGGGTA
1 ATCGGGGCGGGTA
345636 ATCGGG
1 ATCGGG
345642 TAATCGGGGC
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
12 11 0.37
13 19 0.63
ACGTcount: A:0.14, C:0.16, G:0.52, T:0.18
Consensus pattern (13 bp):
ATCGGGGCGGGTA
Found at i:345675 original size:6 final size:6
Alignment explanation
Indices: 345664--345692 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
345654 GATTACCAAA
345664 CCCGTC CCCGTC CCCGTC CCCGTC CCCGT
1 CCCGTC CCCGTC CCCGTC CCCGTC CCCGT
345693 TTAAAATAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.00, C:0.66, G:0.17, T:0.17
Consensus pattern (6 bp):
CCCGTC
Found at i:345721 original size:6 final size:6
Alignment explanation
Indices: 345710--345734 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
345700 AAATGGGTTT
345710 TCCCCG TCCCCG TCCCCG TCCCCG T
1 TCCCCG TCCCCG TCCCCG TCCCCG T
345735 TTATCATCCC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.00, C:0.64, G:0.16, T:0.20
Consensus pattern (6 bp):
TCCCCG
Found at i:347482 original size:17 final size:17
Alignment explanation
Indices: 347462--347506 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 17
347452 GCATGCATTG
*
347462 CATTTATGAATGTATTT
1 CATTTATGAATGTAGTT
*
347479 CATTTAGGGAA-GTAGTT
1 CATTTA-TGAATGTAGTT
347496 CATTTATGAAT
1 CATTTATGAAT
347507 CGAGTTATTT
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
16 3 0.13
17 17 0.74
18 3 0.13
ACGTcount: A:0.31, C:0.07, G:0.18, T:0.44
Consensus pattern (17 bp):
CATTTATGAATGTAGTT
Found at i:347929 original size:15 final size:15
Alignment explanation
Indices: 347909--347941 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
347899 TCCAATAACA
347909 CAAGACATTCATATT
1 CAAGACATTCATATT
347924 CAAGACATTCATATT
1 CAAGACATTCATATT
347939 CAA
1 CAA
347942 TCGGACATCG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.42, C:0.21, G:0.06, T:0.30
Consensus pattern (15 bp):
CAAGACATTCATATT
Found at i:349236 original size:19 final size:18
Alignment explanation
Indices: 349158--349255 Score: 87
Period size: 18 Copynumber: 5.5 Consensus size: 18
349148 AAATTGGTTT
* * *
349158 TAAAATAAAATATTAGAA
1 TAAAATAAAAGATCAGGA
* *
349176 TAAAATAAAAGATAAAGA
1 TAAAATAAAAGATCAGGA
349194 TAAAATATATAA-AT-A--A
1 TAAAATA-A-AAGATCAGGA
*
349210 TGAAATAAAAGATCAGGA
1 TAAAATAAAAGATCAGGA
349228 TAAAAATAAAAGATCAGGA
1 T-AAAATAAAAGATCAGGA
349247 TAAAATAAA
1 TAAAATAAA
349256 TAATTAATTA
Statistics
Matches: 67, Mismatches: 6, Indels: 14
0.77 0.07 0.16
Matches are distributed among these distances:
14 2 0.03
15 3 0.04
16 8 0.12
18 32 0.48
19 20 0.30
20 2 0.03
ACGTcount: A:0.66, C:0.02, G:0.10, T:0.21
Consensus pattern (18 bp):
TAAAATAAAAGATCAGGA
Found at i:349249 original size:53 final size:52
Alignment explanation
Indices: 349160--349263 Score: 136
Period size: 53 Copynumber: 2.0 Consensus size: 52
349150 ATTGGTTTTA
* * *
349160 AAATAAAATATTAGAATAAAATAAAAGATAAAGATAAAATATATAAATAATG
1 AAATAAAAGATCAGAATAAAATAAAAGATAAAGATAAAATAAATAAATAATG
* * * *
349212 AAATAAAAGATCAGGATAAAAATAAAAGATCAGGATAAAATAAATAATTAAT
1 AAATAAAAGATCAGAAT-AAAATAAAAGATAAAGATAAAATAAATAAATAAT
349264 TAAACTTAAA
Statistics
Matches: 44, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
52 14 0.32
53 30 0.68
ACGTcount: A:0.65, C:0.02, G:0.10, T:0.23
Consensus pattern (52 bp):
AAATAAAAGATCAGAATAAAATAAAAGATAAAGATAAAATAAATAAATAATG
Found at i:350950 original size:6 final size:5
Alignment explanation
Indices: 350907--350936 Score: 51
Period size: 5 Copynumber: 5.8 Consensus size: 5
350897 AAATATTCCA
350907 AAAAT AAAAT AAAAT AAAAT AAAACT AAAA
1 AAAAT AAAAT AAAAT AAAAT AAAA-T AAAA
350937 ATATAAACAT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 19 0.79
6 5 0.21
ACGTcount: A:0.80, C:0.03, G:0.00, T:0.17
Consensus pattern (5 bp):
AAAAT
Found at i:350973 original size:17 final size:17
Alignment explanation
Indices: 350951--350987 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
350941 AAACATAAAC
350951 TTCTTTTTTCATTT-TTT
1 TTCTTTTTTC-TTTCTTT
350968 TTCTTTTTTCTTTCTTT
1 TTCTTTTTTCTTTCTTT
350985 TTC
1 TTC
350988 ACCATTTCTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 3 0.16
17 16 0.84
ACGTcount: A:0.03, C:0.16, G:0.00, T:0.81
Consensus pattern (17 bp):
TTCTTTTTTCTTTCTTT
Found at i:351006 original size:30 final size:30
Alignment explanation
Indices: 350960--351016 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
350950 CTTCTTTTTT
350960 CATTTTTTTTCTTTTTTCTTTCTTTTTCAC
1 CATTTTTTTTCTTTTTTCTTTCTTTTTCAC
*
350990 CATTTCTTTTTC-TTTTTCTTTTTTTTT
1 CATTT-TTTTTCTTTTTTCTTTCTTTTT
351017 AATTTTTGGG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
30 19 0.76
31 6 0.24
ACGTcount: A:0.05, C:0.18, G:0.00, T:0.77
Consensus pattern (30 bp):
CATTTTTTTTCTTTTTTCTTTCTTTTTCAC
Found at i:352270 original size:44 final size:44
Alignment explanation
Indices: 352211--352307 Score: 140
Period size: 44 Copynumber: 2.2 Consensus size: 44
352201 TTCAATGTGT
** * *
352211 ATCGATGCAGTCTTTAAAGAAGAAACATCAAATGCAATTGGTGC
1 ATCGATGCACCCTTTAAAGAAGAAACATCAAATACAATTGGTAC
**
352255 ATCGATGCACCCTTTAAAGAAGAAACATTGAATACAATTGGTAC
1 ATCGATGCACCCTTTAAAGAAGAAACATCAAATACAATTGGTAC
352299 ATCGATGCA
1 ATCGATGCA
352308 TAAGGAGTGC
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
44 47 1.00
ACGTcount: A:0.39, C:0.18, G:0.19, T:0.25
Consensus pattern (44 bp):
ATCGATGCACCCTTTAAAGAAGAAACATCAAATACAATTGGTAC
Found at i:352322 original size:19 final size:19
Alignment explanation
Indices: 352298--352342 Score: 90
Period size: 19 Copynumber: 2.4 Consensus size: 19
352288 ACAATTGGTA
352298 CATCGATGCATAAGGAGTG
1 CATCGATGCATAAGGAGTG
352317 CATCGATGCATAAGGAGTG
1 CATCGATGCATAAGGAGTG
352336 CATCGAT
1 CATCGAT
352343 ACACCACCTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.31, C:0.18, G:0.29, T:0.22
Consensus pattern (19 bp):
CATCGATGCATAAGGAGTG
Found at i:352365 original size:83 final size:82
Alignment explanation
Indices: 352251--352409 Score: 178
Period size: 83 Copynumber: 1.9 Consensus size: 82
352241 AATGCAATTG
* * ** *
352251 GTGCATCGATGCACCCTTTAAAGAAGAAACATTGAATACAATTGGTACATCGATGCATAAGG-AG
1 GTGCATCGATACACCCCTTAAAGAAGAAACATCCAAGACAATTGGTACATCGATGCAT-AGGTAG
352315 TGCATCGATGCATAAGGA
65 TGCATCGATGCATAAGGA
* *** * *
352333 GTGCATCGATACACCACCTTAAA-ATGAAAACATCCAAGGTGATTGGTATATCGATGCATGGGTA
1 GTGCATCGATACACC-CCTTAAAGAAG-AAACATCCAAGACAATTGGTACATCGATGCATAGGTA
352397 GTGCATCGATGCA
64 GTGCATCGATGCA
352410 CATGTTAAAG
Statistics
Matches: 63, Mismatches: 11, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
82 18 0.29
83 45 0.71
ACGTcount: A:0.35, C:0.18, G:0.23, T:0.24
Consensus pattern (82 bp):
GTGCATCGATACACCCCTTAAAGAAGAAACATCCAAGACAATTGGTACATCGATGCATAGGTAGT
GCATCGATGCATAAGGA
Found at i:354077 original size:23 final size:23
Alignment explanation
Indices: 354009--354066 Score: 98
Period size: 23 Copynumber: 2.5 Consensus size: 23
353999 ACATTTTATA
*
354009 TGGCACTTCGATGCAATTCTACG
1 TGGCACTTCGGTGCAATTCTACG
*
354032 CGGCACTTCGGTGCAATTCTACG
1 TGGCACTTCGGTGCAATTCTACG
354055 TGGCACTTCGGT
1 TGGCACTTCGGT
354067 ACATTTATAC
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.17, C:0.28, G:0.26, T:0.29
Consensus pattern (23 bp):
TGGCACTTCGGTGCAATTCTACG
Found at i:357545 original size:20 final size:23
Alignment explanation
Indices: 357500--357553 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 23
357490 GCATAGGTAG
357500 TGCATCGATGCACATGTTAAAGAA
1 TGCATCGATGCACATGTT-AAGAA
357524 TGCATCGATGCAC-TG-T-AGAA
1 TGCATCGATGCACATGTTAAGAA
*
357544 TGTATCGATG
1 TGCATCGATG
357554 TACTTCAAAG
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
20 13 0.45
22 1 0.03
23 2 0.07
24 13 0.45
ACGTcount: A:0.31, C:0.17, G:0.24, T:0.28
Consensus pattern (23 bp):
TGCATCGATGCACATGTTAAGAA
Done.