Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007516.1 Hibiscus syriacus cultivar Beakdansim tig00020920_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: 111407
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Found at i:5309 original size:21 final size:21
Alignment explanation
Indices: 5279--5322 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
5269 AATATAAATT
*
5279 GTGTAGCGATGCACTGCTACA
1 GTGTACCGATGCACTGCTACA
*
5300 GTGTACCGATTCACTGCTACA
1 GTGTACCGATGCACTGCTACA
5321 GT
1 GT
5323 AACTTCAGCT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.23, C:0.25, G:0.25, T:0.27
Consensus pattern (21 bp):
GTGTACCGATGCACTGCTACA
Found at i:6059 original size:31 final size:31
Alignment explanation
Indices: 6024--6133 Score: 186
Period size: 31 Copynumber: 3.6 Consensus size: 31
6014 CCATAGATTT
*
6024 CGAAGAACCTAGGTAAACAATCCATATGTCC
1 CGAAGAACATAGGTAAACAATCCATATGTCC
*
6055 CGAAGAACATAGGTAAACAGTCCATATGTCC
1 CGAAGAACATAGGTAAACAATCCATATGTCC
*
6086 CGAAGAACATAGGTAAACAATCCATATATCC
1 CGAAGAACATAGGTAAACAATCCATATGTCC
6117 C-AAGAACATAGGTAAAC
1 CGAAGAACATAGGTAAAC
6134 CTCGACCCTT
Statistics
Matches: 75, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
30 16 0.21
31 59 0.79
ACGTcount: A:0.43, C:0.23, G:0.16, T:0.18
Consensus pattern (31 bp):
CGAAGAACATAGGTAAACAATCCATATGTCC
Found at i:7164 original size:3 final size:3
Alignment explanation
Indices: 7156--7211 Score: 60
Period size: 3 Copynumber: 19.0 Consensus size: 3
7146 ATGAAAAAGT
* * **
7156 ATA ATA ATA ATA ATA ATT ATA ATA AGA ATA ATA ATA A-A GCA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
*
7203 ATA TTA ATA
1 ATA ATA ATA
7212 TTATCAGGAC
Statistics
Matches: 43, Mismatches: 9, Indels: 2
0.80 0.17 0.04
Matches are distributed among these distances:
2 1 0.02
3 42 0.98
ACGTcount: A:0.62, C:0.02, G:0.04, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:7853 original size:132 final size:134
Alignment explanation
Indices: 7394--7955 Score: 515
Period size: 132 Copynumber: 4.2 Consensus size: 134
7384 GTAAACGTTA
* *
7394 ATTCATTCCACTGTTCATAAGGGAAGATTGAATCGA-GACAGACTTGTTCCACTGCTACTCAGGG
1 ATTCATTCCACTGTTCTTCAGGGAAGATTGAATCGACGA-AGACTTGTTCCACTGCTACTCAGGG
* * * * *
7458 AAGATCAAATTCGAAAAGAAAGAGGGATATGTTCCGCTACTTCTTGAGGGAAATTTAGATCTAAA
65 AAGATCAAA-TCTAGAA-AAAGAGGGATATGTTCCGCTACTTCTTGAGGGAAAATCAGATCTAGA
7523 AATGATT-
128 AAT-ATTG
* * * * * *
7530 ATTCATTACA-TGTTCTTTAGGGAAGATTGAATCTACGCAGACTTG--CTACTACTACTCAGGGA
1 ATTCATTCCACTGTTCTTCAGGGAAGATTGAATCGACGAAGACTTGTTCCACTGCTACTCAGGGA
* * * * ** * * * *
7592 AGATCAAATATGGAAAAAGATGGATTTGTTATGTTGCTTCTTGAGGGAAAATCAAATCTGGAAAT
66 AGATCAAATCTAGAAAAAGAGGGATATGTTCCGCTACTTCTTGAGGGAAAATCAGATCTAGAAAT
*
7657 GTTG
131 ATTG
* * * * * *
7661 ATTCATTCCACTATTCTTCACGGAATATTGAATTGAGGCAAG-CTTGTTCCATTGCTACTCAGGG
1 ATTCATTCCACTGTTCTTCAGGGAAGATTGAATCGACG-AAGACTTGTTCCACTGCTACTCAGGG
* * * * * **
7725 AAAATCAAATCTAGAAAAAGAGGGATTTGTTTCGCTACTTCTTGA-GGAAAAT-A-ATTTTGGGG
65 AAGATCAAATCTAGAAAAAGAGGGATATGTTCCGCTACTTCTTGAGGGAAAATCAGA-TCTAGAA
*
7787 ACATTG
129 ATATTG
*
7793 ATTTATTCCACTGTTCTTCAGGGAAGATTGAATCGA-GAATGACTTGTTCCACTGCTACTCAGGG
1 ATTCATTCCACTGTTCTTCAGGGAAGATTGAATCGACGAA-GACTTGTTCCACTGCTACTCAGGG
* * * * * * **
7857 AAGATC-AATTTGGAAAGAGAGGGGATATGTTCCGTTATTTCTTCA-GGAAAATCAGATCTAGGG
65 AAGATCAAATCTAGAAAAAGA-GGGATATGTTCCGCTACTTCTTGAGGGAAAATCAGATCTAGAA
*
7920 ATGTTG
129 ATATTG
7926 ATTCATTCCACTGTT-TT-AGGG-AGATTGAAT
1 ATTCATTCCACTGTTCTTCAGGGAAGATTGAAT
7956 TGAGTTTGAT
Statistics
Matches: 346, Mismatches: 68, Indels: 30
0.78 0.15 0.07
Matches are distributed among these distances:
130 13 0.04
131 66 0.19
132 121 0.35
133 56 0.16
134 51 0.15
135 29 0.08
136 10 0.03
ACGTcount: A:0.31, C:0.15, G:0.22, T:0.31
Consensus pattern (134 bp):
ATTCATTCCACTGTTCTTCAGGGAAGATTGAATCGACGAAGACTTGTTCCACTGCTACTCAGGGA
AGATCAAATCTAGAAAAAGAGGGATATGTTCCGCTACTTCTTGAGGGAAAATCAGATCTAGAAAT
ATTG
Found at i:7934 original size:265 final size:267
Alignment explanation
Indices: 7394--7937 Score: 588
Period size: 265 Copynumber: 2.0 Consensus size: 267
7384 GTAAACGTTA
* *
7394 ATTCATTCCACTGTTCATAAGGGAAGATTGAATCGAGACAGACTTGTTCCACTGCTACTCAGGGA
1 ATTCATTCCACTATTCATAACGGAAGATTGAATCGAGACAGACTTGTTCCACTGCTACTCAGGGA
* *
7459 AGATCAAATTCGAAAAGAAAGAGGGATATGTTCCGCTACTTCTTGAGGGAAATTTAGATCTAAAA
66 AAATCAAATTCGAAAAGAAAGAGGGATATGTTCCGCTACTTCTTGAGGGAAATATAGATCTAAAA
* * * * *
7524 ATGATTATTCATTACATGTTCTTTAGGGAAGATTGAATCTACGCAGACTTGCTACTACTACTCAG
131 ATCATTATTCATTACATGTTCTTCAGGGAAGATTGAATCGACGAAGACTTGCCACTACTACTCAG
* * * * *
7589 GGAAGATCAAATATGGAAAAAGATGGATTTGTTATGTTGCTTCTTGAGGGAAAATCAAATCTGGA
196 GGAAGATCAAATATGGAAAAAGAGGGATATGTTACGTTACTTCTTCAGGGAAAATCAAATCTGGA
7654 AATGTTG
261 AATGTTG
* * * * * *
7661 ATTCATTCCACTATTCTTCACGGAATATTGAATTGAGGCA-AGCTTGTTCCATTGCTACTCAGGG
1 ATTCATTCCACTATTCATAACGGAAGATTGAATCGAGACAGA-CTTGTTCCACTGCTACTCAGGG
* * * * * **
7725 AAAATCAAA-TCTAGAA-AAAGAGGGATTTGTTTCGCTACTTCTTGA-GGAAA-ATA-ATTTTGG
65 AAAATCAAATTCGAAAAGAAAGAGGGATATGTTCCGCTACTTCTTGAGGGAAATATAGA-TCTAA
** * * *
7785 GGA-CATTGATTTATTCCACTGTTCTTCAGGGAAGATTGAATCGA-GAATGACTTGTTCCACTGC
129 AAATCATT-ATTCATTACA-TGTTCTTCAGGGAAGATTGAATCGACGAA-GACTTG--CCACTAC
* * * *
7848 TACTCAGGGAAGATC-AATTTGGAAAGAGAGGGGATATGTTCCGTTATTTCTTCA-GGAAAATCA
189 TACTCAGGGAAGATCAAATATGGAAAAAGA-GGGATATGTTACGTTACTTCTTCAGGGAAAATCA
* *
7911 GATCTAGG-GATGTTG
253 AATCT-GGAAATGTTG
7926 ATTCATTCCACT
1 ATTCATTCCACT
7938 GTTTTAGGGA
Statistics
Matches: 230, Mismatches: 38, Indels: 20
0.80 0.13 0.07
Matches are distributed among these distances:
262 4 0.02
263 15 0.07
264 34 0.15
265 70 0.30
266 45 0.20
267 62 0.27
ACGTcount: A:0.32, C:0.15, G:0.22, T:0.31
Consensus pattern (267 bp):
ATTCATTCCACTATTCATAACGGAAGATTGAATCGAGACAGACTTGTTCCACTGCTACTCAGGGA
AAATCAAATTCGAAAAGAAAGAGGGATATGTTCCGCTACTTCTTGAGGGAAATATAGATCTAAAA
ATCATTATTCATTACATGTTCTTCAGGGAAGATTGAATCGACGAAGACTTGCCACTACTACTCAG
GGAAGATCAAATATGGAAAAAGAGGGATATGTTACGTTACTTCTTCAGGGAAAATCAAATCTGGA
AATGTTG
Found at i:9228 original size:13 final size:13
Alignment explanation
Indices: 9197--9270 Score: 71
Period size: 13 Copynumber: 5.7 Consensus size: 13
9187 TTGAACCCCC
*
9197 TTTTTGTTTATTCT
1 TTTTTCTTT-TTCT
*
9211 CTTTTCTTTTTCT
1 TTTTTCTTTTTCT
*
9224 TTTTTCTTTCT-T
1 TTTTTCTTTTTCT
*
9236 TTTTTC-TTTTAT
1 TTTTTCTTTTTCT
*
9248 TTTTTCATTTTCT
1 TTTTTCTTTTTCT
9261 TTATTTCTTT
1 TT-TTTCTTT
9271 AGGAGATGTA
Statistics
Matches: 50, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
11 3 0.06
12 14 0.28
13 20 0.40
14 13 0.26
ACGTcount: A:0.05, C:0.14, G:0.01, T:0.80
Consensus pattern (13 bp):
TTTTTCTTTTTCT
Found at i:9235 original size:17 final size:17
Alignment explanation
Indices: 9213--9270 Score: 62
Period size: 18 Copynumber: 3.2 Consensus size: 17
9203 TTTATTCTCT
9213 TTTCTTTTTCTTTTTTC
1 TTTCTTTTTCTTTTTTC
*
9230 TTTCTTTTTTTCTTTTATTT
1 TTTC--TTTTTCTTTT-TTC
*
9250 TTTCATTTTCTTTATTTC
1 TTTCTTTTTCTTT-TTTC
9268 TTT
1 TTT
9271 AGGAGATGTA
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
17 4 0.12
18 13 0.38
19 11 0.32
20 6 0.18
ACGTcount: A:0.05, C:0.14, G:0.00, T:0.81
Consensus pattern (17 bp):
TTTCTTTTTCTTTTTTC
Found at i:9238 original size:12 final size:13
Alignment explanation
Indices: 9212--9253 Score: 52
Period size: 12 Copynumber: 3.4 Consensus size: 13
9202 GTTTATTCTC
* *
9212 TTTTCTTTTTCTT
1 TTTTCTTTCTATT
9225 TTTTCTTTCT-TT
1 TTTTCTTTCTATT
9237 TTTTCTTT-TATT
1 TTTTCTTTCTATT
9249 TTTTC
1 TTTTC
9254 ATTTTCTTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
11 1 0.04
12 17 0.63
13 9 0.33
ACGTcount: A:0.02, C:0.14, G:0.00, T:0.83
Consensus pattern (13 bp):
TTTTCTTTCTATT
Found at i:31279 original size:131 final size:132
Alignment explanation
Indices: 31036--31405 Score: 431
Period size: 132 Copynumber: 2.8 Consensus size: 132
31026 ATAATTTTAA
* * * * *
31036 GAGAGAAAACGATAATATCTAATTATTTTCAATTGAGAATAAATGGCATATCATGCCTTAAAACA
1 GAGAGAAAACGATAATATCTAATTATTTTCAATCGAGAATAAATGACCTCTCATGCCTTAAAGCA
* * * * **
31101 -ATCATTTATTACCCCAATTGAAATGAAGAGATGTCACTATTTCGTCTT-AAAATTCAATATTGA
66 TA-CATTTATTACTCCAATCGAAATAAAGAGATATCACTATTTCGTCTTAAAAAAACAATATTGA
*
31164 TTC
130 CTC
** * *
31167 GATTGAAAATGATAATATCTAATGATTTTCAATCGAGAATAAATGACCTCTCATGCCTTAAAGCA
1 GAGAGAAAACGATAATATCTAATTATTTTCAATCGAGAATAAATGACCTCTCATGCCTTAAAGCA
* *
31232 TACATATATTACTCCGATCGAAATAAAGAGATATCACTA-TTCTGTCTTAAAAAAACAATATTGA
66 TACATTTATTACTCCAATCGAAATAAAGAGATATCACTATTTC-GTCTTAAAAAAACAATATTGA
31296 CTC
130 CTC
* ** * * * *
31299 GAGAGAAAACGGTAATATCTGCTTATTTCCAATCGAGAATAAATGATCTCTCATTCCCTAAAGCA
1 GAGAGAAAACGATAATATCTAATTATTTTCAATCGAGAATAAATGACCTCTCATGCCTTAAAGCA
* * ** *
31364 TTCATTTATTACTCCAATCGAAATGATTAGATATTACTATTT
66 TACATTTATTACTCCAATCGAAATAAAGAGATATCACTATTT
31406 TCAATATCGA
Statistics
Matches: 199, Mismatches: 36, Indels: 6
0.83 0.15 0.02
Matches are distributed among these distances:
130 3 0.02
131 92 0.46
132 102 0.51
133 2 0.01
ACGTcount: A:0.39, C:0.16, G:0.12, T:0.33
Consensus pattern (132 bp):
GAGAGAAAACGATAATATCTAATTATTTTCAATCGAGAATAAATGACCTCTCATGCCTTAAAGCA
TACATTTATTACTCCAATCGAAATAAAGAGATATCACTATTTCGTCTTAAAAAAACAATATTGAC
TC
Found at i:32046 original size:29 final size:28
Alignment explanation
Indices: 32006--32073 Score: 84
Period size: 29 Copynumber: 2.4 Consensus size: 28
31996 ACAAAGAATA
32006 AAAATAAATAAAA-CATAGGGACTAAATT
1 AAAATAAATAAAATCATAGGGAC-AAATT
** *
32034 AAAATAAACTAAAATTGTATGGACAAATT
1 AAAATAAA-TAAAATCATAGGGACAAATT
32063 AAAATAAATAA
1 AAAATAAATAA
32074 GAAAATAGAT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
28 11 0.31
29 18 0.51
30 6 0.17
ACGTcount: A:0.62, C:0.06, G:0.09, T:0.24
Consensus pattern (28 bp):
AAAATAAATAAAATCATAGGGACAAATT
Found at i:37056 original size:3 final size:3
Alignment explanation
Indices: 37048--37090 Score: 59
Period size: 3 Copynumber: 13.7 Consensus size: 3
37038 TCCCGACATT
*
37048 TTA TTA TTA TTA TTA TTA TTA TTAA TTA TAA TTA TTTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA -TTA TTA TT
37091 GTTGTTTTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
3 30 0.83
4 6 0.17
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:38534 original size:29 final size:29
Alignment explanation
Indices: 38492--38549 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
38482 TCGAACCCGA
* *
38492 ATGTGTTTTTATTTATTTTAATTT-GTCC
1 ATGTGTTTTAATTTATTGTAATTTAGTCC
*
38520 ATGTAGTTTTAATTTGTTGTAATTTAGTCC
1 ATGT-GTTTTAATTTATTGTAATTTAGTCC
38550 CCATGTTTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 4 0.16
29 17 0.68
30 4 0.16
ACGTcount: A:0.21, C:0.07, G:0.14, T:0.59
Consensus pattern (29 bp):
ATGTGTTTTAATTTATTGTAATTTAGTCC
Found at i:39312 original size:131 final size:131
Alignment explanation
Indices: 39052--39312 Score: 310
Period size: 131 Copynumber: 2.0 Consensus size: 131
39042 TCGATAACGA
* * *
39052 GAATAGTAATATATTTTCATTTCAGTTGGAGTAATAAATGACTGCTCTAAGGCATGAGAGGTCAT
1 GAATAGTAATATATCTTCATTTCAGTTGGAGCAATAAATGACTACTCTAAGGCATGAGAGGTCAT
* * * * *
39117 TTATTCTCTATTGGAAATAATTTGATACTGTCATTTTCTCTCGAATTAATATCAATTTTCAAGAT
66 TTATTCTCGATTGGAAATAATTAGATACTATCATTTTCACTCGAATCAATATCAATTTTCAAGAT
39182 G
131 G
* * * * * *
39183 GAATAGTGATATCTCTTCATTTC-GATTGGAGCAATAAATGACTATTTTAATGTATGAGAGGTCA
1 GAATAGTAATATATCTTCATTTCAG-TTGGAGCAATAAATGACTACTCTAAGGCATGAGAGGTCA
* * * * * *
39247 TTTATTCTCGATTGGAAATCATTAGATATTATCGTTTTCACTTGAATCGATATTGAATTTT-AAG
65 TTTATTCTCGATTGGAAATAATTAGATACTATCATTTTCACTCGAATCAATA-TCAATTTTCAAG
39311 AT
129 AT
39313 ATATTATTCT
Statistics
Matches: 108, Mismatches: 20, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
130 1 0.01
131 100 0.93
132 7 0.06
ACGTcount: A:0.32, C:0.11, G:0.16, T:0.40
Consensus pattern (131 bp):
GAATAGTAATATATCTTCATTTCAGTTGGAGCAATAAATGACTACTCTAAGGCATGAGAGGTCAT
TTATTCTCGATTGGAAATAATTAGATACTATCATTTTCACTCGAATCAATATCAATTTTCAAGAT
G
Found at i:42408 original size:21 final size:21
Alignment explanation
Indices: 42375--42415 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
42365 TGTAACAAAA
*
42375 GTTGTTAAGAGTTGGTTAAGT
1 GTTGTTAAGAGTTAGTTAAGT
**
42396 GTTGTTACTAGTTAGTTAAG
1 GTTGTTAAGAGTTAGTTAAG
42416 GGAAGTTGTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.24, C:0.02, G:0.29, T:0.44
Consensus pattern (21 bp):
GTTGTTAAGAGTTAGTTAAGT
Found at i:45595 original size:27 final size:27
Alignment explanation
Indices: 45564--45720 Score: 244
Period size: 27 Copynumber: 5.9 Consensus size: 27
45554 ACACTCTACC
*
45564 CCACCTGGGAATGTTACTGAAGAATCA
1 CCACCTGGGAATGTTGCTGAAGAATCA
*
45591 CCACCT-GGAATGTTGTTGAAGAATCA
1 CCACCTGGGAATGTTGCTGAAGAATCA
*
45617 CCACCTGGGAATGTTGCTGAAGAGTCA
1 CCACCTGGGAATGTTGCTGAAGAATCA
*
45644 CCACCTGGGAATGTTGCTGAAGAGTCA
1 CCACCTGGGAATGTTGCTGAAGAATCA
* *
45671 CCACTTGGGAATGTTACTGAAGAATCA
1 CCACCTGGGAATGTTGCTGAAGAATCA
*
45698 CCACCTGAGAATGTTGCTGAAGA
1 CCACCTGGGAATGTTGCTGAAGA
45721 GTTGATTTCA
Statistics
Matches: 119, Mismatches: 10, Indels: 2
0.91 0.08 0.02
Matches are distributed among these distances:
26 24 0.20
27 95 0.80
ACGTcount: A:0.30, C:0.21, G:0.25, T:0.24
Consensus pattern (27 bp):
CCACCTGGGAATGTTGCTGAAGAATCA
Found at i:50300 original size:2 final size:2
Alignment explanation
Indices: 50293--50334 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
50283 TAATACTCTT
50293 TA TA 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 TA TA
50335 CTTATTTTAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:53034 original size:2 final size:2
Alignment explanation
Indices: 53027--53074 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
53017 CATTGGTATC
53027 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
53069 AT AT AT
1 AT AT AT
53075 TGATTAACTA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:56336 original size:27 final size:27
Alignment explanation
Indices: 56298--56372 Score: 141
Period size: 27 Copynumber: 2.8 Consensus size: 27
56288 TATAGAATTT
*
56298 CCCCTGAAGAGTAAAATGACCAAAATG
1 CCCCTAAAGAGTAAAATGACCAAAATG
56325 CCCCTAAAGAGTAAAATGACCAAAATG
1 CCCCTAAAGAGTAAAATGACCAAAATG
56352 CCCCTAAAGAGTAAAATGACC
1 CCCCTAAAGAGTAAAATGACC
56373 TAAAGTATCT
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
27 47 1.00
ACGTcount: A:0.45, C:0.24, G:0.16, T:0.15
Consensus pattern (27 bp):
CCCCTAAAGAGTAAAATGACCAAAATG
Found at i:58834 original size:20 final size:20
Alignment explanation
Indices: 58776--58836 Score: 86
Period size: 20 Copynumber: 3.0 Consensus size: 20
58766 CCGTTAGACA
* *
58776 GGGGGAATCGGTACCCCTTG
1 GGGGGAATCTGTACCCCCTG
* *
58796 GGGGGAATCTGTTCTCCCTG
1 GGGGGAATCTGTACCCCCTG
58816 GGGGGAATCTGTACCCCCTG
1 GGGGGAATCTGTACCCCCTG
58836 G
1 G
58837 ACAATCTGAT
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.13, C:0.26, G:0.38, T:0.23
Consensus pattern (20 bp):
GGGGGAATCTGTACCCCCTG
Found at i:61586 original size:23 final size:23
Alignment explanation
Indices: 61552--61611 Score: 84
Period size: 23 Copynumber: 2.6 Consensus size: 23
61542 CATTTTATAT
*
61552 GGCACTTTGGTGCAATTCTACGC
1 GGCACTTCGGTGCAATTCTACGC
* * *
61575 GGCACTTCGGTGTAATTCTATGT
1 GGCACTTCGGTGCAATTCTACGC
61598 GGCACTTCGGTGCA
1 GGCACTTCGGTGCA
61612 TTTATACGAG
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.17, C:0.23, G:0.28, T:0.32
Consensus pattern (23 bp):
GGCACTTCGGTGCAATTCTACGC
Found at i:66956 original size:23 final size:23
Alignment explanation
Indices: 66911--66956 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
66901 ACATTTTATA
*
66911 TGGCACTTCGGTGCAATTCTACG
1 TGGCACTTCGGTGCAATTATACG
*
66934 TGGCACTTCGGTGCATTTATACG
1 TGGCACTTCGGTGCAATTATACG
66957 AGCTGTGGTC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.17, C:0.24, G:0.26, T:0.33
Consensus pattern (23 bp):
TGGCACTTCGGTGCAATTATACG
Found at i:68426 original size:15 final size:15
Alignment explanation
Indices: 68406--68435 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
68396 ATAAGAATTC
68406 ATAATGTTGTACCCT
1 ATAATGTTGTACCCT
68421 ATAATGTTGTACCCT
1 ATAATGTTGTACCCT
68436 CACGTGTTTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.27, C:0.20, G:0.13, T:0.40
Consensus pattern (15 bp):
ATAATGTTGTACCCT
Found at i:68877 original size:25 final size:25
Alignment explanation
Indices: 68849--68907 Score: 109
Period size: 25 Copynumber: 2.4 Consensus size: 25
68839 AAAGCTTTGG
68849 TGATTAAAATGATATATTTCTTTAA
1 TGATTAAAATGATATATTTCTTTAA
68874 TGATTAAAATGATATATTTCTTTAA
1 TGATTAAAATGATATATTTCTTTAA
*
68899 TGATGAAAA
1 TGATTAAAA
68908 CATCAACAAT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 33 1.00
ACGTcount: A:0.42, C:0.03, G:0.10, T:0.44
Consensus pattern (25 bp):
TGATTAAAATGATATATTTCTTTAA
Found at i:69629 original size:41 final size:41
Alignment explanation
Indices: 69577--69886 Score: 164
Period size: 41 Copynumber: 7.6 Consensus size: 41
69567 CGTTTTTTGA
* * *
69577 ACAAACGCCGCTATATACTCGTACTTTAGTGGTGTTTTTAT
1 ACAAACACCGCTAAAGACTCGTACTTTAGTGGTGTTTTTAT
* * **
69618 ATAAACACCGCTAAAGACT-ATA-TATTAGTGGCATTTTTAT
1 ACAAACACCGCTAAAGACTCGTACT-TTAGTGGTGTTTTTAT
* **** * * *
69658 GCAAATGTTGCTATAGACTCGTACATTAATGGTGTTTTT-T
1 ACAAACACCGCTAAAGACTCGTACTTTAGTGGTGTTTTTAT
* * * *** * * * *
69698 GAATAAACGCC-ATAATTTCTCAGCACATTAGCGGCG--TTTAT
1 --ACAAACACCGCTAAAGACTC-GTACTTTAGTGGTGTTTTTAT
*
69739 ACAAACACCGCTAAAGACTTGTACTTTAGTGGTGTTTTTAT
1 ACAAACACCGCTAAAGACTCGTACTTTAGTGGTGTTTTTAT
* ** * * *
69780 GCAAACACAACTAAAGACTCATACTTTAGTGATATTTTTTAT
1 ACAAACACCGCTAAAGACTCGTACTTTAGTGGT-GTTTTTAT
* * * * * *
69822 ACAAACGCCGCTAAAGATTCATTCTTTAGTGGCGTTTTTAG
1 ACAAACACCGCTAAAGACTCGTACTTTAGTGGTGTTTTTAT
* * *
69863 ATAAACACCACTATAGACTCGTAC
1 ACAAACACCGCTAAAGACTCGTAC
69887 ATTGAAAGCT
Statistics
Matches: 190, Mismatches: 68, Indels: 22
0.68 0.24 0.08
Matches are distributed among these distances:
39 18 0.09
40 37 0.19
41 89 0.47
42 46 0.24
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.35
Consensus pattern (41 bp):
ACAAACACCGCTAAAGACTCGTACTTTAGTGGTGTTTTTAT
Found at i:69901 original size:83 final size:83
Alignment explanation
Indices: 69734--69903 Score: 182
Period size: 83 Copynumber: 2.0 Consensus size: 83
69724 ATTAGCGGCG
* *
69734 TTTATACAAACACCGCTAAAGACTTGTACTTTAGTGGTGTTTTTATGCAAACACAACTAAAGACT
1 TTTATACAAACACCGCTAAAGACTTATACTTTAGTGGCGTTTTTATGCAAACACAACTAAAGACT
* **
69799 CATACTTTAGTGATATTT
66 CATACTTGAAAGATATTT
* * * * *
69817 TTTATACAAACGCCGCTAAAGA-TTCATTCTTTAGTGGCGTTTTTA-GATAAACACCACTATAGA
1 TTTATACAAACACCGCTAAAGACTT-ATACTTTAGTGGCGTTTTTATG-CAAACACAACTAAAGA
* * *
69880 CTCGTACATTGAAAGCTTTTT
64 CTCATAC-TTGAAAGATATTT
69901 TTT
1 TTT
69904 GGATAAACAC
Statistics
Matches: 71, Mismatches: 13, Indels: 5
0.80 0.15 0.06
Matches are distributed among these distances:
82 3 0.04
83 57 0.80
84 11 0.15
ACGTcount: A:0.32, C:0.18, G:0.14, T:0.37
Consensus pattern (83 bp):
TTTATACAAACACCGCTAAAGACTTATACTTTAGTGGCGTTTTTATGCAAACACAACTAAAGACT
CATACTTGAAAGATATTT
Found at i:80998 original size:17 final size:17
Alignment explanation
Indices: 80978--81010 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
80968 CTCACTAACC
*
80978 CTTTTATTTTTTGTTCT
1 CTTTTATTTTGTGTTCT
80995 CTTTTATTTTGTGTTC
1 CTTTTATTTTGTGTTC
81011 ATCGTTTGCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.06, C:0.12, G:0.09, T:0.73
Consensus pattern (17 bp):
CTTTTATTTTGTGTTCT
Found at i:81655 original size:19 final size:19
Alignment explanation
Indices: 81621--81665 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
81611 ATTTAGACAT
81621 TTTGCA-TTTCTTATTTTC
1 TTTGCATTTTCTTATTTTC
*
81639 TTTGCATTTTGTTATTTTC
1 TTTGCATTTTCTTATTTTC
81658 TTTGCATT
1 TTTGCATT
81666 CACATTAACT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
18 6 0.24
19 19 0.76
ACGTcount: A:0.11, C:0.13, G:0.09, T:0.67
Consensus pattern (19 bp):
TTTGCATTTTCTTATTTTC
Found at i:85500 original size:165 final size:164
Alignment explanation
Indices: 85054--85621 Score: 929
Period size: 164 Copynumber: 3.5 Consensus size: 164
85044 TTTAAGACAA
* * * * *
85054 CATTTGCATCATAACTCAAGGCAAGAAGGGTTATCTGCCAACAAAGACCTTCGAGTTCGACTACA
1 CATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGCCACCAAAGACCTTCGAGTTCGACTACG
* *
85119 CTCAGCTCTAAGGCACATCATTTTCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCC
66 CTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCC
*
85184 CCGAGTTCGATTATACTCAGCTTCGAGGGCATAT
131 CCGAGTTCGATTACACTCAGCTTCGAGGGCATAT
* *
85218 CATTTACAGTATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAGACCTTCGAGTTCGACTACG
1 CATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGCCACCAAAGACCTTCGAGTTCGACTACG
* *
85283 CTCAGCTCCAAGGCACATCATTTGCAGTATAGCTTAAGTCGAGAAAGGCTATCTGCCAAAGACCC
66 CTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCC
85348 CCGAGTTCGATTACACTCAGCTTCGAGGGCATAT
131 CCGAGTTCGATTACACTCAGCTTCGAGGGCATAT
* * * *
85382 CATTTACAGCATAACTTAAGTCTAGAAGGGTTGTGTGCCAACCAAAGACCTTCGAGTTCGACTAC
1 CATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGCC-ACCAAAGACCTTCGAGTTCGACTAC
*
85447 GCTCAGCTCCAAGGCACATCATTTGCAACATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACC
65 GCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACC
85512 CCCGAGTTCGATTACACTCAGCTTCGAGGGCATAT
130 CCCGAGTTCGATTACACTCAGCTTCGAGGGCATAT
* * * *
85547 CATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAATACCTTCAAGTTCAACTACG
1 CATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGCCACCAAAGACCTTCGAGTTCGACTACG
*
85612 CTCAACTCCA
66 CTCAGCTCCA
85622 GACAACGCAA
Statistics
Matches: 373, Mismatches: 30, Indels: 2
0.92 0.07 0.00
Matches are distributed among these distances:
164 217 0.58
165 156 0.42
ACGTcount: A:0.30, C:0.26, G:0.20, T:0.24
Consensus pattern (164 bp):
CATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGCCACCAAAGACCTTCGAGTTCGACTACG
CTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCC
CCGAGTTCGATTACACTCAGCTTCGAGGGCATAT
Found at i:85780 original size:106 final size:106
Alignment explanation
Indices: 85616--86549 Score: 1268
Period size: 106 Copynumber: 9.0 Consensus size: 106
85606 ACTACGCTCA
* *
85616 ACTCCAGACAACGCAAGTTCAACCTCATGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* *
85681 AATTTCAGAGCCAATTTCAACTTCACAGCGAAAGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* *
85722 ACTCCAGACAACGTAAGTTCAACTTCATGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* *
85787 AATTTCAGAGCCAATTTCAACTTCACAGCGAAAGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
85828 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
*
85893 AATTTCGGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
*
85934 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* * * *
85999 AATTTTAGAGCCAATTTCAACTTCACAGCGAAGTATATTGA
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
*
86040 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTC-A-ATA-AA-----C
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
86097 AATTTC----CCAATTTCAACTTCACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* *** ** *
86134 ACTCAAGACAGTACAAGTTCAACTTCACGACGAAGGGACCGCTGACTGTCAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
*
86199 AATTTCAGAGCCAATTTCAACTTCACAACGAAAGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* *
86240 ACTCCAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTC-A-ATA-AA-----C
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* *
86297 AATTTC----CCAATTTCAACTTCACAACGAAGGGTATTGC
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* *** * * ** * *
86334 ACTCAAGACAGTACAAGTTCAACTTCACGACGAAGGGGCGGCTGACTGTCAACAAACAGCTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
86399 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * *
86440 ACTCCAAACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* * * * * ** *
86505 AGTTCCAGAACCAGTTTCAACTGCACAGTGGAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
86546 ACTC
1 ACTC
86550 GGAACAATAC
Statistics
Matches: 739, Mismatches: 65, Indels: 48
0.87 0.08 0.06
Matches are distributed among these distances:
94 143 0.19
95 2 0.00
96 4 0.01
97 3 0.00
98 13 0.02
102 14 0.02
103 4 0.01
104 4 0.01
105 2 0.00
106 550 0.74
ACGTcount: A:0.34, C:0.26, G:0.18, T:0.22
Consensus pattern (106 bp):
ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
Found at i:86153 original size:200 final size:200
Alignment explanation
Indices: 85616--86505 Score: 1219
Period size: 200 Copynumber: 4.3 Consensus size: 200
85606 ACTACGCTCA
* *
85616 ACTCCAGACAACGCAAGTTCAACCTCATGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTC-A-AAA-AA-----C
* * *
85681 AATTTCAGAGCCAATTTCAACTTCACAGCGAAAGATATTGGACTCCAGACA--ACGTAAGTTCAA
58 AATTTC----CCAATTTCAACTTCACAACGAAGGATATTGGACTCAAGACAGTAC--AAGTTCAA
* **
85744 CTTCATGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCAATTTCAACT
117 CTTCACGACGAAGGGACCGCTGACTGTCAACAAACAACTTCCCAATTTCAGAGCCAATTTCAACT
*
85809 TCACAGCGAAAGATATTGG
182 TCACAACGAAAGATATTGG
85828 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTC-A-AAA-AA-----C
* ***
85893 AATTTCGGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACT
58 AATTTC----CCAATTTCAACTTCACAACGAAGGATATTGGACTCAAGACAGTACAAGTTCAACT
** * *
85958 TCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAATTTTAGAGCCAATTTCAACTTC
119 TCACGACGAAGGGACCGCTGACTGTCAACAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTC
* *
86023 ACAGCG-AAGTATATTGA
184 ACAACGAAAG-ATATTGG
*
86040 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAAAAAACAATTTCCC
86105 AATTTCAACTTCACAACGAAGGATATTGGACTCAAGACAGTACAAGTTCAACTTCACGACGAAGG
66 AATTTCAACTTCACAACGAAGGATATTGGACTCAAGACAGTACAAGTTCAACTTCACGACGAAGG
*
86170 GACCGCTGACTGTCAACAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAAGAT
131 GACCGCTGACTGTCAACAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAACGAAAGAT
86235 ATTGG
196 ATTGG
* *
86240 ACTCCAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAAAAAACAATTTCCC
* *
86305 AATTTCAACTTCACAACGAAGGGTATTGCACTCAAGACAGTACAAGTTCAACTTCACGACGAAGG
66 AATTTCAACTTCACAACGAAGGATATTGGACTCAAGACAGTACAAGTTCAACTTCACGACGAAGG
* * * * *
86370 GGCGGCTGACTGTCAACAAACAGCTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGAT
131 GACCGCTGACTGTCAACAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAACGAAAGAT
86435 ATTGG
196 ATTGG
* * *
86440 ACTCCAAACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAAAAAACAATTTCCC
86505 A
66 A
86506 GTTCCAGAAC
Statistics
Matches: 643, Mismatches: 31, Indels: 20
0.93 0.04 0.03
Matches are distributed among these distances:
200 379 0.59
201 3 0.00
204 7 0.01
209 2 0.00
210 2 0.00
211 4 0.01
212 245 0.38
214 1 0.00
ACGTcount: A:0.34, C:0.26, G:0.18, T:0.22
Consensus pattern (200 bp):
ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAAAAAACAATTTCCC
AATTTCAACTTCACAACGAAGGATATTGGACTCAAGACAGTACAAGTTCAACTTCACGACGAAGG
GACCGCTGACTGTCAACAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAACGAAAGAT
ATTGG
Found at i:86212 original size:306 final size:306
Alignment explanation
Indices: 85616--86549 Score: 1176
Period size: 306 Copynumber: 3.0 Consensus size: 306
85606 ACTACGCTCA
* * *
85616 ACTCCAGACAACGCAAGTTCAACCTCATGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCC
* *
85681 AATTTCAGAGCCAATTTCAACTTCACAGCGAAAGATATTGGACTCCAGACAACGTAAGTTCAACT
66 AATTT-AGAGCCAATTTCAACTTCACAGCG-AAGATATTGAACTCCAGACAACGCAAGTTCAACT
*
85746 TCATGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTC
129 TCACGACGAAGGGACCGCTGGTTGTC-A-AAA-AA----CCAATTTC--A-CCAATTTCAACTTC
* * * *
85811 ACAGCGAAAGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTG
184 ACAACGAAGGATATTGGACTCAAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTG
*
85876 TCAACAAACAACTTCCCAATTTCGGAGCCAATTTCAACTTCACAACGAAGGATATTGG
249 TCAACAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
85934 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCC
85999 AATTTTAGAGCCAATTTCAACTTCACAGCGAAGTATATTGAACTCCAGACAACGCAAGTTCAACT
66 AA-TTTAGAGCCAATTTCAACTTCACAGCGAAG-ATATTGAACTCCAGACAACGCAAGTTCAACT
*
86064 TCACGACGAAGGGACCGCTGGTTGTCAATAAA-CAATTTC-CCAATTTCAACTTCACAACGAAGG
129 TCACGACGAAGGGACCGCTGGTTGTCAAAAAACCAATTTCACCAATTTCAACTTCACAACGAAGG
** **
86127 ATATTGGACTCAAGACAGTACAAGTTCAACTTCACGACGAAGGGACCGCTGACTGTCAACAAACA
194 ATATTGGACTCAAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACA
* *
86192 ACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAAGATATTGG
259 ACTTCCCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* *
86240 ACTCCAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTT--C
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCC
* * * * ***
86303 ---------CCAATTTCAACTTCACAACGAAGGGTATTGCACTCAAGACAGTACAAGTTCAACTT
66 AATTTAGAGCCAATTTCAACTTCACAGCGAA-GATATTGAACTCCAGACAACGCAAGTTCAACTT
* * **
86359 CACGACGAAGGGGCGGCTGACTGTCAACAAACAGCTTCTCAATTTCAGAGCCAATTTCAACTTCA
130 CACGACGAAGGGACCGCTGGTTGTCAA-AAA-A----C-CAATTTC--A-CCAATTTCAACTTCA
86424 CAACGAAGGATATTGGACTCCAA-ACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTG
185 CAACGAAGGATATTGGACT-CAAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTG
* * * * * * ** *
86488 TCAACAAACAATTTCCCAGTTCCAGAACCAGTTTCAACTGCACAGTGGAGGATATTGG
249 TCAACAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
86546 ACTC
1 ACTC
86550 GGAACAATAC
Statistics
Matches: 553, Mismatches: 47, Indels: 44
0.86 0.07 0.07
Matches are distributed among these distances:
294 70 0.13
295 3 0.01
296 1 0.00
302 7 0.01
304 1 0.00
306 308 0.56
307 3 0.01
310 7 0.01
315 2 0.00
316 2 0.00
317 4 0.01
318 142 0.26
319 3 0.01
ACGTcount: A:0.34, C:0.26, G:0.18, T:0.22
Consensus pattern (306 bp):
ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCC
AATTTAGAGCCAATTTCAACTTCACAGCGAAGATATTGAACTCCAGACAACGCAAGTTCAACTTC
ACGACGAAGGGACCGCTGGTTGTCAAAAAACCAATTTCACCAATTTCAACTTCACAACGAAGGAT
ATTGGACTCAAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAAC
TTCCCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
Found at i:87824 original size:21 final size:21
Alignment explanation
Indices: 87798--87842 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
87788 GATTTCTGGG
* *
87798 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
87819 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
87840 CAA
1 CAA
87843 ACGAACAAGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:89406 original size:22 final size:22
Alignment explanation
Indices: 89378--89444 Score: 125
Period size: 22 Copynumber: 3.0 Consensus size: 22
89368 TTATGGACAT
89378 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
89400 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
*
89422 AATTCTATGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
89444 A
1 A
89445 TTTATACGAG
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
22 44 1.00
ACGTcount: A:0.19, C:0.25, G:0.27, T:0.28
Consensus pattern (22 bp):
AATTCTACGGGCACTTCGGTGC
Found at i:89656 original size:16 final size:17
Alignment explanation
Indices: 89635--89668 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
89625 TATATGATAA
89635 TATGTGAATG-ATGAAT
1 TATGTGAATGTATGAAT
*
89651 TATGTGTATGTATGAAT
1 TATGTGAATGTATGAAT
89668 T
1 T
89669 TACTGCGATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.32, C:0.00, G:0.24, T:0.44
Consensus pattern (17 bp):
TATGTGAATGTATGAAT
Found at i:92729 original size:21 final size:21
Alignment explanation
Indices: 92703--92747 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
92693 GATTTCTGGG
* *
92703 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
92724 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
92745 CAA
1 CAA
92748 ACGAACAAGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:94367 original size:22 final size:22
Alignment explanation
Indices: 94293--94359 Score: 134
Period size: 22 Copynumber: 3.0 Consensus size: 22
94283 TTATGGACAT
94293 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
94315 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
94337 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
94359 A
1 A
94360 TTTATACGAG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 45 1.00
ACGTcount: A:0.19, C:0.27, G:0.27, T:0.27
Consensus pattern (22 bp):
AATTCTACGGGCACTTCGGTGC
Found at i:94571 original size:16 final size:17
Alignment explanation
Indices: 94550--94583 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
94540 TATATGATAA
94550 TATGTGAATG-ATGAAT
1 TATGTGAATGTATGAAT
*
94566 TATGTGTATGTATGAAT
1 TATGTGAATGTATGAAT
94583 T
1 T
94584 TACTGCGATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.32, C:0.00, G:0.24, T:0.44
Consensus pattern (17 bp):
TATGTGAATGTATGAAT
Found at i:101215 original size:3 final size:3
Alignment explanation
Indices: 101204--101267 Score: 89
Period size: 3 Copynumber: 22.0 Consensus size: 3
101194 TTTTTTTCCG
*
101204 TTA TT- TTA TTA TTA TTA TTA TTA TTA TTA TCA TTA -TA TTA TTA TT-
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
101249 TTA TTA TTA TTTA TTA TTA
1 TTA TTA TTA -TTA TTA TTA
101268 CAATTTTTGC
Statistics
Matches: 55, Mismatches: 2, Indels: 8
0.85 0.03 0.12
Matches are distributed among these distances:
2 6 0.11
3 46 0.84
4 3 0.05
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:101431 original size:25 final size:25
Alignment explanation
Indices: 101403--101520 Score: 220
Period size: 25 Copynumber: 4.8 Consensus size: 25
101393 ACCCATCAGA
101403 TTAGGGTTTCAAACCCTAAATCAAT
1 TTAGGGTTTCAAACCCTAAATCAAT
*
101428 TTAGGGTTTCAAACCCTAAATCAGT
1 TTAGGGTTTCAAACCCTAAATCAAT
101453 TTAGGGTTTCAAACCCTAAATCAAT
1 TTAGGGTTTCAAACCCTAAATCAAT
101478 TTAGGGTTTCAAACCCTAAATCAAT
1 TTAGGGTTTCAAACCCTAAATCAAT
101503 TTAGGGTTTC-AACCCTAA
1 TTAGGGTTTCAAACCCTAA
101521 TCCCCTTCCA
Statistics
Matches: 91, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
24 8 0.09
25 83 0.91
ACGTcount: A:0.34, C:0.20, G:0.14, T:0.32
Consensus pattern (25 bp):
TTAGGGTTTCAAACCCTAAATCAAT
Found at i:103127 original size:15 final size:16
Alignment explanation
Indices: 103104--103137 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
103094 TAGAAATTAT
*
103104 TTTTATTGTTATTTTA
1 TTTTATTGTTAATTTA
103120 TTTT-TTGTTAATTTA
1 TTTTATTGTTAATTTA
103135 TTT
1 TTT
103138 GATGTTCATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 13 0.76
16 4 0.24
ACGTcount: A:0.18, C:0.00, G:0.06, T:0.76
Consensus pattern (16 bp):
TTTTATTGTTAATTTA
Done.