Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008301.1 Hibiscus syriacus cultivar Beakdansim tig00110987_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: 3376434
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 18 of 18
Found at i:3331912 original size:47 final size:47
Alignment explanation
Indices: 3331851--3331954 Score: 199
Period size: 47 Copynumber: 2.2 Consensus size: 47
3331841 ATAATAAAAT
*
3331851 AATACATATACAAAATACAACTTATATTAAATAAGTGGGAAAATAAA
1 AATACATATACAAAATACAACTTAGATTAAATAAGTGGGAAAATAAA
3331898 AATACATATACAAAATACAACTTAGATTAAATAAGTGGGAAAATAAA
1 AATACATATACAAAATACAACTTAGATTAAATAAGTGGGAAAATAAA
3331945 AATACATATA
1 AATACATATA
3331955 AAATTAAATT
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 56 1.00
ACGTcount: A:0.58, C:0.09, G:0.09, T:0.25
Consensus pattern (47 bp):
AATACATATACAAAATACAACTTAGATTAAATAAGTGGGAAAATAAA
Found at i:3334498 original size:6 final size:6
Alignment explanation
Indices: 3334487--3334518 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
3334477 TTTCTTATTA
3334487 AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AA
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AA
3334519 GAGAAGAGTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:3335312 original size:60 final size:60
Alignment explanation
Indices: 3335145--3335313 Score: 162
Period size: 60 Copynumber: 2.8 Consensus size: 60
3335135 TAACTGTAAC
* * * * * * *
3335145 ATTCATCCCCAAACTATGACTCTTATTCCAATTTGATTCCT-AAACTTTTGAATATTTTAA
1 ATTCATCCTCAAACTATGACTCTTATTCTAAATT-AGTCCTCAAACTTTTAAAAATTCTAA
* * * * * * *
3335205 TTTCATACCT-AAACTATGATTCTCATTTTAAATTGGTCCCCACACTTTTAAAAATTCTAA
1 ATTCAT-CCTCAAACTATGACTCTTATTCTAAATTAGTCCTCAAACTTTTAAAAATTCTAA
* *
3335265 ATTCATCCTCAAACTATGACCCTTATTCTAAATTAGTCTTCAAACTTTT
1 ATTCATCCTCAAACTATGACTCTTATTCTAAATTAGTCCTCAAACTTTT
3335314 GAACATTCCA
Statistics
Matches: 83, Mismatches: 23, Indels: 6
0.74 0.21 0.05
Matches are distributed among these distances:
59 6 0.07
60 75 0.90
61 2 0.02
ACGTcount: A:0.32, C:0.22, G:0.05, T:0.41
Consensus pattern (60 bp):
ATTCATCCTCAAACTATGACTCTTATTCTAAATTAGTCCTCAAACTTTTAAAAATTCTAA
Found at i:3335888 original size:29 final size:29
Alignment explanation
Indices: 3335847--3335914 Score: 93
Period size: 29 Copynumber: 2.4 Consensus size: 29
3335837 TTGACTATTT
* *
3335847 AAGGGGCAAATTGTACTATAAATAAATTA
1 AAGGGGCATATTGTACTATAAATAAACTA
* *
3335876 AAGGGGCATATTGTATTATAAATACACTA
1 AAGGGGCATATTGTACTATAAATAAACTA
3335905 AAGGGG-ATAT
1 AAGGGGCATAT
3335915 AGGCCATATA
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
28 4 0.11
29 31 0.89
ACGTcount: A:0.44, C:0.07, G:0.21, T:0.28
Consensus pattern (29 bp):
AAGGGGCATATTGTACTATAAATAAACTA
Found at i:3336443 original size:3 final size:3
Alignment explanation
Indices: 3336437--3336497 Score: 106
Period size: 3 Copynumber: 20.3 Consensus size: 3
3336427 TTAATAATAA
3336437 TAT TAT TA- TAT ATAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
3336482 TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT T
3336498 CAGGTTACAA
Statistics
Matches: 56, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.04
3 51 0.91
4 3 0.05
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:3338233 original size:27 final size:27
Alignment explanation
Indices: 3338203--3338262 Score: 111
Period size: 27 Copynumber: 2.2 Consensus size: 27
3338193 TAAAGTATAA
3338203 GAAAGTTACTTTCGATAAATTTAAAAC
1 GAAAGTTACTTTCGATAAATTTAAAAC
*
3338230 GAAAGTTACTTTCGATAAATTTAAAAT
1 GAAAGTTACTTTCGATAAATTTAAAAC
3338257 GAAAGT
1 GAAAGT
3338263 ATATCCTATT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.45, C:0.08, G:0.13, T:0.33
Consensus pattern (27 bp):
GAAAGTTACTTTCGATAAATTTAAAAC
Found at i:3338880 original size:131 final size:132
Alignment explanation
Indices: 3338542--3338896 Score: 412
Period size: 130 Copynumber: 2.7 Consensus size: 132
3338532 CGATATAGAG
* * * * *
3338542 AATAATAATATCTT-TTCATTTCGGTTGGACTAATAAATGATTGCTTTAAGGTATGAAAAGTTAT
1 AATAGTAATAT-TTCTTCATTTCGATTGGAGTAATAAATGATTGCTTTAAGGTATGAAAGGTCAT
* * * * * * *
3338606 TTATTCTCGATAGGAAATAATTCGATATTACCGTTTTCTCTCTAATCAATATTGATTTTTTAAGA
65 TTATTCTCGATTGGAAACAATTAGATATTACCGTTTCCACTCGAATCAATATTGATATTTTAAGA
3338671 CAA
130 CAA
* * * * *
3338674 AATAGTGATATCTCTTCATTTTGATTGGAG--ATAAATGATTGCTTTAAGATATGAGAGGTCATT
1 AATAGTAATATTTCTTCATTTCGATTGGAGTAATAAATGATTGCTTTAAGGTATGAAAGGTCATT
* * * *
3338737 CATTCTTGATTGGAAACCATTAGATATTACCGTTTCCACTCGAATCGATATTGA-ATTTTAAGAC
66 TATTCTCGATTGGAAACAATTAGATATTACCGTTTCCACTCGAATCAATATTGATATTTTAAGAC
*
3338801 GA
131 AA
* ** *
3338803 AATAGTAATATTTCTTCATTTCGATTGGAGTAATAAATGACTATTTTAAGGCATGAAAGGTCATT
1 AATAGTAATATTTCTTCATTTCGATTGGAGTAATAAATGATTGCTTTAAGGTATGAAAGGTCATT
* * *
3338868 TATACTCGATTGGAAATAATTAAATATTA
66 TATTCTCGATTGGAAACAATTAGATATTA
3338897 TAATTTTCTC
Statistics
Matches: 183, Mismatches: 37, Indels: 7
0.81 0.16 0.03
Matches are distributed among these distances:
129 37 0.20
130 73 0.40
131 51 0.28
132 22 0.12
ACGTcount: A:0.34, C:0.11, G:0.15, T:0.39
Consensus pattern (132 bp):
AATAGTAATATTTCTTCATTTCGATTGGAGTAATAAATGATTGCTTTAAGGTATGAAAGGTCATT
TATTCTCGATTGGAAACAATTAGATATTACCGTTTCCACTCGAATCAATATTGATATTTTAAGAC
AA
Found at i:3345592 original size:233 final size:231
Alignment explanation
Indices: 3345128--3345856 Score: 784
Period size: 233 Copynumber: 3.1 Consensus size: 231
3345118 TTTCTTACTT
* * * * * * * *
3345128 AGTAAGTCCTTTGGGCCATTAGTAAGTCTTTTGAGCATGATGATTAAATCCTTCGGGCAATCCAT
1 AGTAAATCCTTCGGGTCATTTGTAAGTCTTTCGAGCAAGATGA-TAAGTCCTTCGGGCCATCCAT
* * *
3345193 AAGAACTTCAAGG-AGGATGTTTTCAGAAGTTTTTCGAAAAATGAGAAAAATTTATCATTTAAAT
65 AAG-ACTTC-GGGCAGGATGTTTTCACATG-TTTTCGAAAAATGAGAAAAATTTATCATTTAAAT
* * *
3345257 CTGAAAATTGAATTTTTTGAAAAGTAAGGAAAGTTTCTTACCTAGTAAACTATTTCCAAAATTAG
127 ATGAAAATTGAATTTTTTGAAAAGTAAGAAAAGTTTATTACCTAGTAAACTATTTCCAAAATTAG
* *
3345322 TAAGTCCTTTGGGCCATCAGTAAGTCTTTCTAGCATGATG
192 TAAGTCCTTCGGGACATCAGTAAGTCTTTCTAGCATGATG
* *
3345362 ATTAAATCCTTCGGGTCATTTGTAAGTCTTTCGAGCAAGATGATAAGTCATTCGGGCCA-CTCAT
1 AGTAAATCCTTCGGGTCATTTGTAAGTCTTTCGAGCAAGATGATAAGTCCTTCGGGCCATC-CAT
* * * *
3345426 AAGACCATCGGGCAGGATGTTTTCACATGTCTTGCGAAAAATGAGAAAAATTTCTCATTTAAATT
65 AAGA-CTTCGGGCAGGATGTTTTCACATGT-TTTCGAAAAATGAGAAAAATTTATCATTTAAATA
* *
3345491 TTAAAATTGAATTTTTTGAAAAGTAAGAAAAGTTTATTACCTAGTAAACTA-TTCCTAAAATTGG
128 TGAAAATTGAATTTTTTGAAAAGTAAGAAAAGTTTATTACCTAGTAAACTATTTCC-AAAATTAG
3345555 TAAGTCCTTCGGGACATCAGTAAGTCTTT-TGAGCATGATG
192 TAAGTCCTTCGGGACATCAGTAAGTCTTTCT-AGCATGATG
* * ** * * *
3345595 AGTAAATCCTTCGGGTCATCTATAAACCTTTCGAGCAAGATGATAAGACCTTCAGGCCATCCAGA
1 AGTAAATCCTTCGGGTCATTTGTAAGTCTTTCGAGCAAGATGATAAGTCCTTCGGGCCATCCATA
* * * * *
3345660 AGACTTTGGGCAGGAAGTTTTCACATGTTTCTCAAAAAATGAGAAAAAATTATCATTTTAATATG
66 AGACTTCGGGCAGGATGTTTTCACATGTTT-TCGAAAAATGAGAAAAATTTATCATTTAAATATG
* * * *
3345725 AGAATTGAAATTTTTAAAAAGTAAGAAAATAATTTCCAAATCTTCTTACCTAGTAAACTATTTCC
130 AAAATTGAATTTTTTGAAAAGTAAG-AAA-AGTTT----A-----TTACCTAGTAAACTATTTCC
* * * * * * * *
3345790 AAAATTTGTAAGTCTTTTGGGCCATCGGTAAGTATTT-TGTGGATGATG
184 AAAATTAGTAAGTCCTTCGGGACATCAGTAAGTCTTTCT-AGCATGATG
*
3345838 AGTAAATCCTTCGAGTCAT
1 AGTAAATCCTTCGGGTCAT
3345857 CTATAAGCCT
Statistics
Matches: 420, Mismatches: 55, Indels: 31
0.83 0.11 0.06
Matches are distributed among these distances:
231 2 0.00
232 81 0.19
233 218 0.52
234 41 0.10
238 1 0.00
243 73 0.17
244 4 0.01
ACGTcount: A:0.34, C:0.15, G:0.18, T:0.33
Consensus pattern (231 bp):
AGTAAATCCTTCGGGTCATTTGTAAGTCTTTCGAGCAAGATGATAAGTCCTTCGGGCCATCCATA
AGACTTCGGGCAGGATGTTTTCACATGTTTTCGAAAAATGAGAAAAATTTATCATTTAAATATGA
AAATTGAATTTTTTGAAAAGTAAGAAAAGTTTATTACCTAGTAAACTATTTCCAAAATTAGTAAG
TCCTTCGGGACATCAGTAAGTCTTTCTAGCATGATG
Found at i:3345631 original size:42 final size:42
Alignment explanation
Indices: 3345554--3345637 Score: 98
Period size: 42 Copynumber: 2.0 Consensus size: 42
3345544 CCTAAAATTG
* ** * *
3345554 GTAAGTCCTTCGGGACATCAGTAAGTCTTTTGAGCATGATGA
1 GTAAATCCTTCGGGACATCAGTAAACCTTTCGAGCAAGATGA
*
3345596 GTAAATCCTTCGGGTCATCTA-TAAACCTTTCGAGCAAGATGA
1 GTAAATCCTTCGGGACATC-AGTAAACCTTTCGAGCAAGATGA
3345638 TAAGACCTTC
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
42 34 0.97
43 1 0.03
ACGTcount: A:0.29, C:0.19, G:0.23, T:0.30
Consensus pattern (42 bp):
GTAAATCCTTCGGGACATCAGTAAACCTTTCGAGCAAGATGA
Found at i:3348313 original size:17 final size:17
Alignment explanation
Indices: 3348293--3348340 Score: 60
Period size: 18 Copynumber: 2.8 Consensus size: 17
3348283 ATGAATATAC
* *
3348293 ATCAGAAACTAAATTTA
1 ATCAAAAACTAAATTGA
*
3348310 ATCAAAAAACCAAATTGA
1 ATC-AAAAACTAAATTGA
3348328 ATCAAAAACTAAA
1 ATCAAAAACTAAA
3348341 ACACTGAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
17 12 0.46
18 14 0.54
ACGTcount: A:0.60, C:0.15, G:0.04, T:0.21
Consensus pattern (17 bp):
ATCAAAAACTAAATTGA
Found at i:3351862 original size:27 final size:27
Alignment explanation
Indices: 3351805--3351862 Score: 64
Period size: 27 Copynumber: 2.1 Consensus size: 27
3351795 TAATATAGTC
* * * *
3351805 ATTTTACACTTCAATGGTATTTTGGTC
1 ATTTTACACTTCAAGGGAATTATGGTA
3351832 ATTTTACACTTCAAGGGAAATTAT-GTA
1 ATTTTACACTTCAAGGG-AATTATGGTA
3351859 ATTT
1 ATTT
3351863 CATACTAAGG
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
27 22 0.85
28 4 0.15
ACGTcount: A:0.29, C:0.12, G:0.14, T:0.45
Consensus pattern (27 bp):
ATTTTACACTTCAAGGGAATTATGGTA
Found at i:3352316 original size:19 final size:19
Alignment explanation
Indices: 3352257--3352321 Score: 78
Period size: 19 Copynumber: 3.4 Consensus size: 19
3352247 ACCGGTCAAT
** *
3352257 GGTCAGGTCAAAGAAAATG
1 GGTCAGGTCAAAGTTAACG
*
3352276 GGTCAGGTCAAAGTTAAGG
1 GGTCAGGTCAAAGTTAACG
3352295 GGTCAGGTCAAA-TTCAACG
1 GGTCAGGTCAAAGTT-AACG
3352314 GGTCAGGT
1 GGTCAGGT
3352322 TGGGTTGACT
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
18 2 0.05
19 39 0.95
ACGTcount: A:0.32, C:0.14, G:0.34, T:0.20
Consensus pattern (19 bp):
GGTCAGGTCAAAGTTAACG
Found at i:3355057 original size:8 final size:7
Alignment explanation
Indices: 3355022--3355056 Score: 52
Period size: 7 Copynumber: 4.9 Consensus size: 7
3355012 TCTTTTTTTA
3355022 AAAAAAT
1 AAAAAAT
3355029 AAAAAAT
1 AAAAAAT
*
3355036 GAAAAAT
1 AAAAAAT
3355043 GAAAAAAT
1 -AAAAAAT
3355051 AAAAAA
1 AAAAAA
3355057 AAAGAAGGTA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
7 19 0.76
8 6 0.24
ACGTcount: A:0.83, C:0.00, G:0.06, T:0.11
Consensus pattern (7 bp):
AAAAAAT
Found at i:3356473 original size:131 final size:131
Alignment explanation
Indices: 3356164--3356511 Score: 357
Period size: 131 Copynumber: 2.7 Consensus size: 131
3356154 CGATATAGAG
* ** ** * *
3356164 AATAGT-ATCATCTTTTCATTTTGGTTGGAGTAATAAATGACGGCTTTAAGGCATGAGAGGTAAT
1 AATAGTAAT-ATCTCTTCATTTTACTTGGAGTAATAAATGAATGCTTTAAGGCATGAGAAGTCAT
* * ** * * * *
3356228 TT-TTCTCGATTGGAAATAATTCGTTATTACTGTTTTCTCTCGAATGAATATTGATTTTTAAGAC
65 TTATTCTCAATTGGAAATAATTAGAAATTACTGTTTACACTCGAATCAATATTGAATTTTAAGAC
*
3356292 AT
130 AA
* * ** * * * *
3356294 AATAGTGATATCTCTTCATTTTGAC-TGCAACAATATATGATTGCTTTAAGGTATGAGATGTCAT
1 AATAGTAATATCTCTTCATTTT-ACTTGGAGTAATAAATGAATGCTTTAAGGCATGAGAAGTCAT
3356358 TTATTCTCAATTGGAAA-ACATTAGAAATTACTGTTTACACTCGAATCAATATTGAATTTTAAGA
65 TTATTCTCAATTGGAAATA-ATTAGAAATTACTGTTTACACTCGAATCAATATTGAATTTTAAGA
3356422 CAA
129 CAA
* * *
3356425 AATTGTAATATCTCTTCA-TTTATCTTGGAGTAATAAATGAATGTTTTAAGGCATGA-AAGAACA
1 AATAGTAATATCTCTTCATTTTA-CTTGGAGTAATAAATGAATGCTTTAAGGCATGAGAAG-TCA
*
3356488 TTTATACTCAATTGGAAATAATTA
64 TTTATTCTCAATTGGAAATAATTA
3356512 AATATTATCA
Statistics
Matches: 177, Mismatches: 33, Indels: 15
0.79 0.15 0.07
Matches are distributed among these distances:
129 1 0.01
130 57 0.32
131 118 0.67
132 1 0.01
ACGTcount: A:0.34, C:0.11, G:0.16, T:0.39
Consensus pattern (131 bp):
AATAGTAATATCTCTTCATTTTACTTGGAGTAATAAATGAATGCTTTAAGGCATGAGAAGTCATT
TATTCTCAATTGGAAATAATTAGAAATTACTGTTTACACTCGAATCAATATTGAATTTTAAGACA
A
Found at i:3359400 original size:21 final size:21
Alignment explanation
Indices: 3359375--3359423 Score: 89
Period size: 21 Copynumber: 2.3 Consensus size: 21
3359365 GATAGTCTTT
*
3359375 CTTAAAATCAAAACGCTTTCA
1 CTTAAAATCAAAACACTTTCA
3359396 CTTAAAATCAAAACACTTTCA
1 CTTAAAATCAAAACACTTTCA
3359417 CTTAAAA
1 CTTAAAA
3359424 AATAGATTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.47, C:0.22, G:0.02, T:0.29
Consensus pattern (21 bp):
CTTAAAATCAAAACACTTTCA
Found at i:3363134 original size:2 final size:2
Alignment explanation
Indices: 3363123--3363159 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
3363113 CAACCCTAAA
3363123 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3363160 ATACAAAACA
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 2 0.06
2 31 0.94
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:3364126 original size:24 final size:24
Alignment explanation
Indices: 3364094--3364141 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
3364084 TATTCTTGCT
3364094 CTTTGTTTCAATTGAGTGTGCCTA
1 CTTTGTTTCAATTGAGTGTGCCTA
3364118 CTTTGTTTCAATTGAGTGTGCCTA
1 CTTTGTTTCAATTGAGTGTGCCTA
3364142 ACTAATTGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.17, C:0.17, G:0.21, T:0.46
Consensus pattern (24 bp):
CTTTGTTTCAATTGAGTGTGCCTA
Found at i:3365660 original size:11 final size:11
Alignment explanation
Indices: 3365638--3365674 Score: 56
Period size: 11 Copynumber: 3.3 Consensus size: 11
3365628 TTTTATAAAT
3365638 TTTTACTTTTTC
1 TTTTA-TTTTTC
3365650 TTTTATTTTTC
1 TTTTATTTTTC
*
3365661 ATTTATTTTTC
1 TTTTATTTTTC
3365672 TTT
1 TTT
3365675 AAAAGTTTTC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
11 18 0.78
12 5 0.22
ACGTcount: A:0.11, C:0.11, G:0.00, T:0.78
Consensus pattern (11 bp):
TTTTATTTTTC
Found at i:3367338 original size:2 final size:2
Alignment explanation
Indices: 3367316--3367365 Score: 75
Period size: 2 Copynumber: 25.5 Consensus size: 2
3367306 AATAAATTAA
* *
3367316 AT AT TT AT AT -T AT AT AA 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
3367357 AT AT AT AT A
1 AT AT AT AT A
3367366 ATTACTTGAA
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
1 1 0.02
2 42 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3368306 original size:15 final size:16
Alignment explanation
Indices: 3368286--3368318 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
3368276 AAATTATGTT
3368286 TATAAAAGT-AATTTA
1 TATAAAAGTAAATTTA
*
3368301 TATAAAATTAAATTTA
1 TATAAAAGTAAATTTA
3368317 TA
1 TA
3368319 AATTAGATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (16 bp):
TATAAAAGTAAATTTA
Found at i:3368518 original size:29 final size:28
Alignment explanation
Indices: 3368476--3368585 Score: 91
Period size: 29 Copynumber: 3.7 Consensus size: 28
3368466 AAATAGTGAC
3368476 TAAAATA-AATAAAATTAAAACTATAGTAT
1 TAAAATATAA-AAAATTAAAACT-TAGTAT
3368505 TAAAATATAAAAAATATAAAACTT-GTAGT
1 TAAAATATAAAAAAT-TAAAACTTAGTA-T
*
3368534 TAAAAATAAATAAAAGTATTAAAA-TTAGTGAT
1 T-AAAAT--ATAAAA-AATTAAAACTTAGT-AT
* *
3368566 TAAATTATAAAATATTAAAA
1 TAAAATATAAAAAATTAAAA
3368586 TCAAATGCAC
Statistics
Matches: 70, Mismatches: 2, Indels: 19
0.77 0.02 0.21
Matches are distributed among these distances:
28 11 0.16
29 21 0.30
30 14 0.20
31 6 0.09
32 15 0.21
33 3 0.04
ACGTcount: A:0.61, C:0.02, G:0.05, T:0.32
Consensus pattern (28 bp):
TAAAATATAAAAAATTAAAACTTAGTAT
Found at i:3368543 original size:28 final size:30
Alignment explanation
Indices: 3368477--3368548 Score: 89
Period size: 30 Copynumber: 2.4 Consensus size: 30
3368467 AATAGTGACT
3368477 AAAATAAATAAAATTAAAACTATAGTATT-
1 AAAATAAATAAAATTAAAACTATAGTATTA
3368506 AAAATATAA-AAAATATAAAACT-T-GTAGTTA
1 AAAATA-AATAAAAT-TAAAACTATAGTA-TTA
3368536 AAAATAAATAAAA
1 AAAATAAATAAAA
3368549 GTATTAAAAT
Statistics
Matches: 38, Mismatches: 0, Indels: 9
0.81 0.00 0.19
Matches are distributed among these distances:
28 3 0.08
29 16 0.42
30 19 0.50
ACGTcount: A:0.65, C:0.03, G:0.04, T:0.28
Consensus pattern (30 bp):
AAAATAAATAAAATTAAAACTATAGTATTA
Found at i:3369708 original size:3 final size:3
Alignment explanation
Indices: 3369690--3369754 Score: 73
Period size: 3 Copynumber: 22.0 Consensus size: 3
3369680 AGTATTTATT
* *
3369690 TAA TAAA TAT TAA TAA TAA TAA TAA TAA TAA TGTA TAA TAA TAA TAA
1 TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA
3369737 T-A TAA -AA -AA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA
3369755 AAACAAACTA
Statistics
Matches: 54, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
2 6 0.11
3 43 0.80
4 5 0.09
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:3370073 original size:45 final size:45
Alignment explanation
Indices: 3370009--3370583 Score: 839
Period size: 45 Copynumber: 12.8 Consensus size: 45
3369999 TAAAATCTCA
* * ** *
3370009 TTTGAAAACATCCCGCACTGTAA-GTCTTATGGATGACCCGAAGGC
1 TTTGAAAACATCCTGCACTG-AAGGGCTTACAGATGACCCGAAGGT
* * *
3370054 TTTGAAAACATCATGCACTGAAGAGCTTACAGATGACCTGAAGGT
1 TTTGAAAACATCCTGCACTGAAGGGCTTACAGATGACCCGAAGGT
* * * *
3370099 TTTGAAAACATCATGCACTGAAGGTCTTACAGATGACCCGGAGGC
1 TTTGAAAACATCCTGCACTGAAGGGCTTACAGATGACCCGAAGGT
*
3370144 TTTGAAAACATCCTGCCCTGAAGGGCTTACAGATGACCCGAAGGT
1 TTTGAAAACATCCTGCACTGAAGGGCTTACAGATGACCCGAAGGT
* * * *
3370189 TTTGAAAACATCATGAACTGAAGGGCTTACTA-ATGACCCAAAGCT
1 TTTGAAAACATCCTGCACTGAAGGGCTTAC-AGATGACCCGAAGGT
* *
3370234 TTTGAAAACATCCTGCACTGAAAGGCTTATAGATGACCCGAAGGT
1 TTTGAAAACATCCTGCACTGAAGGGCTTACAGATGACCCGAAGGT
* *
3370279 TTTGAAAACATCCTGCACTGAAGGGCTTACAGATAACCCGAAGGC
1 TTTGAAAACATCCTGCACTGAAGGGCTTACAGATGACCCGAAGGT
* **
3370324 TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACATGAAGGT
1 TTTGAAAACATCCTGCACTGAAGGGCTTACAGATGACCCGAAGGT
* * * *
3370369 TTTGAAAACATCATGCACTGAAGGTCTTACAGATGACCCGGAGGC
1 TTTGAAAACATCCTGCACTGAAGGGCTTACAGATGACCCGAAGGT
3370414 TTTGAAAACATCCTGCACTGAAGGGCTTACAGATGACCCGAAGGT
1 TTTGAAAACATCCTGCACTGAAGGGCTTACAGATGACCCGAAGGT
*
3370459 TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGT
1 TTTGAAAACATCCTGCACTGAAGGGCTTACAGATGACCCGAAGGT
* *
3370504 TTTGAAAACATCCTGCACTAAAGGGCTTATAGATGACCCGAAGGT
1 TTTGAAAACATCCTGCACTGAAGGGCTTACAGATGACCCGAAGGT
3370549 TTTGAAAACATCCTGCACTGAAGGGCTTACAGATG
1 TTTGAAAACATCCTGCACTGAAGGGCTTACAGATG
3370584 TGGGAAATAG
Statistics
Matches: 474, Mismatches: 53, Indels: 6
0.89 0.10 0.01
Matches are distributed among these distances:
44 3 0.01
45 470 0.99
46 1 0.00
ACGTcount: A:0.33, C:0.21, G:0.23, T:0.23
Consensus pattern (45 bp):
TTTGAAAACATCCTGCACTGAAGGGCTTACAGATGACCCGAAGGT
Found at i:3371735 original size:54 final size:54
Alignment explanation
Indices: 3371653--3371814 Score: 279
Period size: 54 Copynumber: 3.0 Consensus size: 54
3371643 AGAATAACTG
* *
3371653 GTTCGTAAAACATTTGATAACACATTCATTCTTTATTGTGGCTTCTGCCCAGAT
1 GTTCGTAAAGCATTTGACAACACATTCATTCTTTATTGTGGCTTCTGCCCAGAT
3371707 GTTCGTAAAGCATTTGACAACACATTCATTCTTTATTGTGGCTTCTGCCCAGAT
1 GTTCGTAAAGCATTTGACAACACATTCATTCTTTATTGTGGCTTCTGCCCAGAT
* **
3371761 GTTCGTAAAGCATTTGACAACACATTCATCCTTTCCTGTGGCTTCTGCCCAGAT
1 GTTCGTAAAGCATTTGACAACACATTCATTCTTTATTGTGGCTTCTGCCCAGAT
3371815 TTCTCAATCA
Statistics
Matches: 103, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
54 103 1.00
ACGTcount: A:0.24, C:0.23, G:0.16, T:0.36
Consensus pattern (54 bp):
GTTCGTAAAGCATTTGACAACACATTCATTCTTTATTGTGGCTTCTGCCCAGAT
Done.