Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008755.1 Hibiscus syriacus cultivar Beakdansim tig00111847_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: 3030620
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 14
Found at i:226295 original size:105 final size:105
Alignment explanation
Indices: 226108--226569 Score: 744
Period size: 105 Copynumber: 4.3 Consensus size: 105
226098 AGGTTTTACC
* * *
226108 CAGAGCCAATTCCAACTTCACAACCGAAATACGGTTATTGGACTCCAGACAACGTAAGTTCAACT
1 CAGAGCCAATTTCAACTTCACAA-CG--A-A-GGATATTGGACTCCAGACAACGCAAGTTCAACT
226173 TCACGACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
61 TCACGACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
*
226218 CAGAGCCAATTTCAAATTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
226283 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
* *
226323 CAGAGCCAATTTCAACTTAAAAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
226388 ACGAAGGGACCGCTGGTTGTCAACAAACACTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
226428 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* *
226493 ACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAAC-ATTTCTCAATTT
* * ** *
226534 CGGATCCAATTTCAACTTCACGGCGAAGTATATTGG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
226570 CCTCGAAACA
Statistics
Matches: 333, Mismatches: 18, Indels: 6
0.93 0.05 0.02
Matches are distributed among these distances:
105 267 0.80
106 42 0.13
107 1 0.00
109 2 0.01
110 21 0.06
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (105 bp):
CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
Found at i:228214 original size:3 final size:3
Alignment explanation
Indices: 228196--228263 Score: 82
Period size: 3 Copynumber: 20.7 Consensus size: 3
228186 ATATTACGTT
228196 TTA TTA TATA TATA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA T-TA T-TA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
228243 TATA TATA TATA TTA CTTA TT
1 T-TA T-TA T-TA TTA -TTA TT
228264 TCTTTTTACT
Statistics
Matches: 62, Mismatches: 0, Indels: 6
0.91 0.00 0.09
Matches are distributed among these distances:
3 41 0.66
4 21 0.34
ACGTcount: A:0.37, C:0.01, G:0.00, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:228312 original size:23 final size:23
Alignment explanation
Indices: 228286--228350 Score: 60
Period size: 23 Copynumber: 2.8 Consensus size: 23
228276 TTTACCATTT
228286 TTATTTTTATTATTATTTTTATA
1 TTATTTTTATTATTATTTTTATA
** *
228309 TTATCCTTATTATT-TCTATTATA
1 TTATTTTTATTATTAT-TTTTATA
* *
228332 CTATTTTTTTTACTTATTT
1 TTATTTTTATTA-TTATTT
228351 ATGTATATAT
Statistics
Matches: 31, Mismatches: 8, Indels: 5
0.70 0.18 0.11
Matches are distributed among these distances:
22 1 0.03
23 26 0.84
24 3 0.10
25 1 0.03
ACGTcount: A:0.23, C:0.08, G:0.00, T:0.69
Consensus pattern (23 bp):
TTATTTTTATTATTATTTTTATA
Found at i:228489 original size:2 final size:2
Alignment explanation
Indices: 228482--228509 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
228472 TAACTAATAG
228482 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
228510 CATGTTTTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:228750 original size:17 final size:18
Alignment explanation
Indices: 228728--228765 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
228718 TTTTCATATT
*
228728 TTTTTATGTTA-TTACTA
1 TTTTTATGTTACTTAATA
*
228745 TTTTTATTTTACTTAATA
1 TTTTTATGTTACTTAATA
228763 TTT
1 TTT
228766 GTATTTTCAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 10 0.56
18 8 0.44
ACGTcount: A:0.24, C:0.05, G:0.03, T:0.68
Consensus pattern (18 bp):
TTTTTATGTTACTTAATA
Found at i:228764 original size:18 final size:17
Alignment explanation
Indices: 228728--228772 Score: 54
Period size: 18 Copynumber: 2.6 Consensus size: 17
228718 TTTTCATATT
* *
228728 TTTTTATGTTATTACTA
1 TTTTTATTTTATTAATA
228745 TTTTTATTTTACTTAATA
1 TTTTTATTTTA-TTAATA
*
228763 TTTGTATTTT
1 TTTTTATTTT
228773 CATTTGGTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
17 10 0.42
18 14 0.58
ACGTcount: A:0.22, C:0.04, G:0.04, T:0.69
Consensus pattern (17 bp):
TTTTTATTTTATTAATA
Found at i:234588 original size:156 final size:156
Alignment explanation
Indices: 234106--234959 Score: 1037
Period size: 156 Copynumber: 5.4 Consensus size: 156
234096 TTTAGTCCCA
* * * * *
234106 AATTTCATTATTCCTCCAATTCACCCTTTATTTTAAGAT-TGTTTTTATCAAATTTGAACCACAT
1 AATTTCCTTATTTCTTCAATTCA-TCTTTATTTTAAG-TCTATTTTTATCAAATTTGAACCACAT
* * * * *
234170 GCTCCTAAACCATCTTAAAATACATATGTACTTTCAGTTTCTCTTTTTGATAACAAATTTTCTAT
64 GCTCCTAAACCAACTTAGAATACATATCTACTTTCAATTTCTCTTTTAGATAACAAATTTTCTAT
*
234235 TTTTCAATTTAGTCTCTTAATTTTTCAT
129 TTTTCAATTTAGTCCCTTAATTTTTCAT
* * *
234263 -A-TTCATTATTTCTTCAATTCATCCTTTATTTTAAGTCTTTTTTTTTTTATATCAAATTTGAAT
1 AATTTCCTTATTTCTTCAATTCAT-CTTTATTTTAAGTC-----TATTTT-TATCAAATTTGAAC
* * * * * * *
234326 CACATACTCATAAACCATA-TCAGAATACATATTTGCTTTCAA-TTCTATTTTAGATAATAAATT
59 CACATGCTCCTAAACCA-ACTTAGAATACATATCTACTTTCAATTTCTCTTTTAGATAACAAATT
*
234389 TTCTATTTTT-AATTTAGTCCCTCAATTTTTCAT
123 TTCTATTTTTCAATTTAGTCCCTTAATTTTTCAT
* * * * *
234422 AATTTACTTATTTCTTCAATTCATCTTTATTTTAAGTCCATTTTTACCAAATTGGAACCATATGC
1 AATTTCCTTATTTCTTCAATTCATCTTTATTTTAAGTCTATTTTTATCAAATTTGAACCACATGC
*
234487 TCCTAAACCAACTTAGAATACATATCTACTTTCAATTTCTCTTTTTGATAACAAATTTTCTATTT
66 TCCTAAACCAACTTAGAATACATATCTACTTTCAATTTCTCTTTTAGATAACAAATTTTCTATTT
*
234552 TTCAATTTAGTCTCTTAATTTTTCAT
131 TTCAATTTAGTCCCTTAATTTTTCAT
* *
234578 AATTTCCTTATTTCTTCAATTCATCCTTTATTTTAAGTCTTTTTTTATATCAAATTTGAATCACA
1 AATTTCCTTATTTCTTCAATTCAT-CTTTATTTTAAGTC-TATTTT-TATCAAATTTGAACCACA
* * * * * *
234643 TGCTCATAAACCATA-TCAGAATACATATTTGCTTTCAA-TTCTATTTTAGATAATAAATTTTCT
63 TGCTCCTAAACCA-ACTTAGAATACATATCTACTTTCAATTTCTCTTTTAGATAACAAATTTTCT
* *
234706 ATTTTTTAATTTAGTCCCTCAATTTTTCAT
127 ATTTTTCAATTTAGTCCCTTAATTTTTCAT
* * * *
234736 AATTTACTTATTTCTTCATTTCATCTTTATTTTAAGTCCATTTTTACCAAATTTGAACCACATGC
1 AATTTCCTTATTTCTTCAATTCATCTTTATTTTAAGTCTATTTTTATCAAATTTGAACCACATGC
* * *
234801 TCCTAAACCATCTTAGAATACATATCTACTTTCAATTTCTCTTTTCGATAACAAATCTTT-GATT
66 TCCTAAACCAACTTAGAATACATATCTACTTTCAATTTCTCTTTTAGATAACAAAT-TTTCTATT
234865 TTTCAATTTAGTCCCTTAATTTTTCAT
130 TTTCAATTTAGTCCCTTAATTTTTCAT
* *
234892 AATTTCTTTATTTCTTCAATTCATCATTTATTTTAAGTCT-TCTTTTA-CTAAATTTGAATCACA
1 AATTTCCTTATTTCTTCAATTCATC-TTTATTTTAAGTCTAT-TTTTATC-AAATTTGAACCACA
234955 TGCTC
63 TGCTC
234960 ATGTACCATA
Statistics
Matches: 598, Mismatches: 75, Indels: 48
0.83 0.10 0.07
Matches are distributed among these distances:
153 1 0.00
154 46 0.08
155 110 0.18
156 118 0.20
157 67 0.11
158 75 0.13
159 67 0.11
160 49 0.08
161 65 0.11
ACGTcount: A:0.29, C:0.18, G:0.04, T:0.48
Consensus pattern (156 bp):
AATTTCCTTATTTCTTCAATTCATCTTTATTTTAAGTCTATTTTTATCAAATTTGAACCACATGC
TCCTAAACCAACTTAGAATACATATCTACTTTCAATTTCTCTTTTAGATAACAAATTTTCTATTT
TTCAATTTAGTCCCTTAATTTTTCAT
Found at i:234804 original size:314 final size:313
Alignment explanation
Indices: 234147--234961 Score: 1388
Period size: 314 Copynumber: 2.6 Consensus size: 313
234137 TTTAAGATTG
* * * *
234147 TTTTTATCAAATTTGAACCACATGCTCCTAAACCATCTTAAAATACATATGTACTTTCAGTTTCT
1 TTTTTACCAAATTTGAACCACATGCTCCTAAACCATCTTAGAATACATATCTACTTTCAATTTCT
234212 CTTTTTGATAACAAATTTTCTATTTTTCAATTTAGTCTCTTAATTTTTCAT-A-TTCATTATTTC
66 CTTTTTGATAACAAATTTTCTATTTTTCAATTTAGTCTCTTAATTTTTCATAATTTCATTATTTC
*
234275 TTCAATTCATCCTTTATTTTAAGTCTTTTTTTTTTTATATCAAATTTGAATCACATACTCATAAA
131 TTCAATTCATCCTTTATTTTAAGTC----TTTTTTTATATCAAATTTGAATCACATGCTCATAAA
234340 CCATATCAGAATACATATTTGCTTTCAATTCTATTTTAGATAATAAATTTTCTATTTTTAATTTA
192 CCATATCAGAATACATATTTGCTTTCAATTCTATTTTAGATAATAAATTTTCTATTTTTAATTTA
234405 GTCCCTCAATTTTTCATAATTTACTTATTTCTTCAATTCATCTTTATTTTAAGTCCA
257 GTCCCTCAATTTTTCATAATTTACTTATTTCTTCAATTCATCTTTATTTTAAGTCCA
* * *
234462 TTTTTACCAAATTGGAACCATATGCTCCTAAACCAACTTAGAATACATATCTACTTTCAATTTCT
1 TTTTTACCAAATTTGAACCACATGCTCCTAAACCATCTTAGAATACATATCTACTTTCAATTTCT
*
234527 CTTTTTGATAACAAATTTTCTATTTTTCAATTTAGTCTCTTAATTTTTCATAATTTCCTTATTTC
66 CTTTTTGATAACAAATTTTCTATTTTTCAATTTAGTCTCTTAATTTTTCATAATTTCATTATTTC
234592 TTCAATTCATCCTTTATTTTAAGTCTTTTTTTATATCAAATTTGAATCACATGCTCATAAACCAT
131 TTCAATTCATCCTTTATTTTAAGTCTTTTTTTATATCAAATTTGAATCACATGCTCATAAACCAT
234657 ATCAGAATACATATTTGCTTTCAATTCTATTTTAGATAATAAATTTTCTATTTTTTAATTTAGTC
196 ATCAGAATACATATTTGCTTTCAATTCTATTTTAGATAATAAATTTTCTA-TTTTTAATTTAGTC
*
234722 CCTCAATTTTTCATAATTTACTTATTTCTTCATTTCATCTTTATTTTAAGTCCA
260 CCTCAATTTTTCATAATTTACTTATTTCTTCAATTCATCTTTATTTTAAGTCCA
234776 TTTTTACCAAATTTGAACCACATGCTCCTAAACCATCTTAGAATACATATCTACTTTCAATTTCT
1 TTTTTACCAAATTTGAACCACATGCTCCTAAACCATCTTAGAATACATATCTACTTTCAATTTCT
* * * *
234841 CTTTTCGATAACAAATCTTT-GATTTTTCAATTTAGTCCCTTAATTTTTCATAATTTCTTTATTT
66 CTTTTTGATAACAAAT-TTTCTATTTTTCAATTTAGTCTCTTAATTTTTCATAATTTCATTATTT
* * *
234905 CTTCAATTCATCATTTATTTTAAGTCTTCTTTTA-CT-AAATTTGAATCACATGCTCAT
130 CTTCAATTCATCCTTTATTTTAAGTCTTTTTTTATATCAAATTTGAATCACATGCTCAT
234962 GTACCATAAT
Statistics
Matches: 476, Mismatches: 20, Indels: 11
0.94 0.04 0.02
Matches are distributed among these distances:
312 21 0.04
313 90 0.19
314 217 0.46
315 112 0.24
316 1 0.00
317 35 0.07
ACGTcount: A:0.29, C:0.18, G:0.04, T:0.49
Consensus pattern (313 bp):
TTTTTACCAAATTTGAACCACATGCTCCTAAACCATCTTAGAATACATATCTACTTTCAATTTCT
CTTTTTGATAACAAATTTTCTATTTTTCAATTTAGTCTCTTAATTTTTCATAATTTCATTATTTC
TTCAATTCATCCTTTATTTTAAGTCTTTTTTTATATCAAATTTGAATCACATGCTCATAAACCAT
ATCAGAATACATATTTGCTTTCAATTCTATTTTAGATAATAAATTTTCTATTTTTAATTTAGTCC
CTCAATTTTTCATAATTTACTTATTTCTTCAATTCATCTTTATTTTAAGTCCA
Found at i:235757 original size:149 final size:147
Alignment explanation
Indices: 235589--235987 Score: 441
Period size: 149 Copynumber: 2.7 Consensus size: 147
235579 TAAATATTAA
* *
235589 AAAATGAGATTATATTATTTTGTAAGGAGAATCTATAGAAATGCTTC-TAGACTGATACGAAGTG
1 AAAATGAGATAATATTATTTTGTAAGG-GAATCTATAGAAATGCTTCTTA-ACTGATAAGAAGTG
* *
235653 TGTTTCGAAGGATTATTCGTACAAAATAATAT-TTTTTATATATATTTGAGTGAGTTTTAAACAT
64 TGTTTCGAAGGATTATTCGTACAAAATAATATCATTTT-T-TATATTTGAATGAGTTTTAAACAT
235717 ATTAAATATATATAATTTAT-T
127 ATTAAATATATATAATTT-TCT
* * ** * * *
235738 AAAATGAGACAATATTATTTTATAAGGGAAATCTGCAAAAAT-ATCTCTTAACTGGTAAGAAGTG
1 AAAATGAGATAATATTATTTTGTAAGGG-AATCTATAGAAATGCT-TCTTAACTGATAAGAAGTG
* * *
235802 TGTTTCAAAGGATTATTCGTACAAAATAATATCATTTTTTATATTTGAATGATTTTTAAATATAT
64 TGTTTCGAAGGATTATTCGTACAAAATAATATCATTTTTTATATTTGAATGAGTTTTAAACATAT
235867 TAAATATATATAATTTTCT
129 TAAATATATATAATTTTCT
* * * * * * * * *
235886 AAACTTATTG-TAATATTATTTTGTAAATGGAATCTATGGAAATGCCTCTTAACTCACAAAAAAT
1 AAAATGA--GATAATATTATTTTGT-AAGGGAATCTATAGAAATGCTTCTTAACTGATAAGAAGT
*
235950 GTGTTTTCG-AGGATTATTCGTACAAAAGAATATCATTT
63 GTG-TTTCGAAGGATTATTCGTACAAAATAATATCATTT
235988 CAATCCTTAA
Statistics
Matches: 208, Mismatches: 32, Indels: 20
0.80 0.12 0.08
Matches are distributed among these distances:
147 1 0.00
148 47 0.23
149 145 0.70
150 15 0.07
ACGTcount: A:0.39, C:0.08, G:0.13, T:0.40
Consensus pattern (147 bp):
AAAATGAGATAATATTATTTTGTAAGGGAATCTATAGAAATGCTTCTTAACTGATAAGAAGTGTG
TTTCGAAGGATTATTCGTACAAAATAATATCATTTTTTATATTTGAATGAGTTTTAAACATATTA
AATATATATAATTTTCT
Found at i:237910 original size:7 final size:7
Alignment explanation
Indices: 237891--237919 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
237881 TGATGAAGGT
237891 TTTTGCA
1 TTTTGCA
237898 -TTTGCA
1 TTTTGCA
237904 TTTTGCA
1 TTTTGCA
237911 TTTTGCA
1 TTTTGCA
237918 TT
1 TT
237920 GCATTAATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
6 6 0.29
7 15 0.71
ACGTcount: A:0.14, C:0.14, G:0.14, T:0.59
Consensus pattern (7 bp):
TTTTGCA
Found at i:243640 original size:20 final size:20
Alignment explanation
Indices: 243544--243634 Score: 155
Period size: 20 Copynumber: 4.5 Consensus size: 20
243534 ATTATATTCC
**
243544 CTGGTAATCTTTTACCCCCA
1 CTGGTAATCTTTTATTCCCA
243564 CTGGTAATCTTTTATTCCCA
1 CTGGTAATCTTTTATTCCCA
243584 CTGGTAATCTTTTATTCCCA
1 CTGGTAATCTTTTATTCCCA
*
243604 CTGGTAATCTTTTATTCTCA
1 CTGGTAATCTTTTATTCCCA
243624 CTGGTAATCTT
1 CTGGTAATCTT
243635 ACATTCCATG
Statistics
Matches: 68, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 68 1.00
ACGTcount: A:0.20, C:0.25, G:0.11, T:0.44
Consensus pattern (20 bp):
CTGGTAATCTTTTATTCCCA
Found at i:244478 original size:16 final size:16
Alignment explanation
Indices: 244457--244492 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 16
244447 TTAAATATTA
244457 TTTTAAATAATTAC-AT
1 TTTTAAATAA-TACTAT
244473 TTTTAAATAATACTAT
1 TTTTAAATAATACTAT
244489 TTTT
1 TTTT
244493 TCATCTCGTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 3 0.16
16 16 0.84
ACGTcount: A:0.39, C:0.06, G:0.00, T:0.56
Consensus pattern (16 bp):
TTTTAAATAATACTAT
Found at i:244491 original size:15 final size:15
Alignment explanation
Indices: 244450--244491 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 15
244440 ACTAAAGTTA
*
244450 AATATTATTTTAAAT
1 AATACTATTTTAAAT
244465 AATTAC-ATTTTTAAAT
1 AA-TACTA-TTTTAAAT
244481 AATACTATTTT
1 AATACTATTTT
244492 TTCATCTCGT
Statistics
Matches: 23, Mismatches: 1, Indels: 6
0.77 0.03 0.20
Matches are distributed among these distances:
15 10 0.43
16 13 0.57
ACGTcount: A:0.43, C:0.05, G:0.00, T:0.52
Consensus pattern (15 bp):
AATACTATTTTAAAT
Found at i:251930 original size:13 final size:13
Alignment explanation
Indices: 251898--251924 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
251888 TTATTAATAA
251898 AAAATTTGTATTT
1 AAAATTTGTATTT
251911 AAAATTTGTATTT
1 AAAATTTGTATTT
251924 A
1 A
251925 TTATTTTATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.52
Consensus pattern (13 bp):
AAAATTTGTATTT
Found at i:254271 original size:110 final size:111
Alignment explanation
Indices: 254023--254413 Score: 520
Period size: 110 Copynumber: 3.5 Consensus size: 111
254013 CAGATCAATT
*
254023 TTGATAAGACGGGTCTGTTCCAC-ACTTCTTTCAGGGAGATAAGACTCAAAAAAATCTTCGAAAG
1 TTGATAAGACGGGTCTGCTCCACTA-TTCTTTCAGGGAGATAAGACT-AAAAAAATCTTCGAAAG
* * * ** *
254087 ACGAGTCTGCTCCCTCTTCTTTCTCAAGGAGTATA-GACTCAAGAAAAAA
64 ACGGGTCCGCTCCCTCTTCTTT-T-AGGGAGTATAGGACTTGAGAAAAAC
* *
254136 TTGATAAGACGGGTCTGCTCCACTATTCTTTCATGGAGATAAGACTAAAAAAATCTTCAAAAGA-
1 TTGATAAGACGGGTCTGCTCCACTATTCTTTCAGGGAGATAAGACTAAAAAAATCTTCGAAAGAC
254200 GGGTCCGCTCCCTCTTCTTTTAGGGAGTATAGGACTTGAGAAAAAC
66 GGGTCCGCTCCCTCTTCTTTTAGGGAGTATAGGACTTGAGAAAAAC
* * * * *
254246 TTGATAAGATGGGTATGTTCCACTATTCTTTCAGGGAGATAAGACTCAAAAAATCTTCGGAAGAC
1 TTGATAAGACGGGTCTGCTCCACTATTCTTTCAGGGAGATAAGACTAAAAAAATCTTCGAAAGAC
* *
254311 GGGTCCGCTCCCTATTCTTTCAGGG-GTATAGGACTTGAGAAAAAC
66 GGGTCCGCTCCCTCTTCTTTTAGGGAGTATAGGACTTGAGAAAAAC
* * * * * *
254356 TTGATAAGATGAGTCTGCTGCACTCTTCTTTCAAGGAGATAAGACTCAAAAAATCTTC
1 TTGATAAGACGGGTCTGCTCCACTATTCTTTCAGGGAGATAAGACTAAAAAAATCTTC
254414 TGATTCACTC
Statistics
Matches: 251, Mismatches: 24, Indels: 9
0.88 0.08 0.03
Matches are distributed among these distances:
109 9 0.04
110 141 0.56
111 41 0.16
112 17 0.07
113 42 0.17
114 1 0.00
ACGTcount: A:0.32, C:0.19, G:0.20, T:0.28
Consensus pattern (111 bp):
TTGATAAGACGGGTCTGCTCCACTATTCTTTCAGGGAGATAAGACTAAAAAAATCTTCGAAAGAC
GGGTCCGCTCCCTCTTCTTTTAGGGAGTATAGGACTTGAGAAAAAC
Found at i:255724 original size:23 final size:23
Alignment explanation
Indices: 255698--255786 Score: 65
Period size: 23 Copynumber: 3.5 Consensus size: 23
255688 CTTAAACCCC
255698 TTTTTATTTATTTTTTTTATCTT
1 TTTTTATTTATTTTTTTTATCTT
255721 TTTTT-TTT-TTTTCATTTTATCCATT
1 TTTTTATTTATTTT--TTTTAT-C-TT
*
255746 TTTTCTTTTTCATTTTTTCTTCTATTCTT
1 TTTT-TATTT-A-TTTTT-TT-TA-TCTT
255775 TTTTTATTTATT
1 TTTTTATTTATT
255787 CTTCAAACAA
Statistics
Matches: 53, Mismatches: 1, Indels: 21
0.71 0.01 0.28
Matches are distributed among these distances:
21 4 0.08
22 3 0.06
23 11 0.21
24 1 0.02
25 6 0.11
26 3 0.06
27 4 0.08
28 5 0.09
29 8 0.15
30 7 0.13
31 1 0.02
ACGTcount: A:0.11, C:0.10, G:0.00, T:0.79
Consensus pattern (23 bp):
TTTTTATTTATTTTTTTTATCTT
Found at i:255761 original size:14 final size:16
Alignment explanation
Indices: 255727--255766 Score: 57
Period size: 14 Copynumber: 2.6 Consensus size: 16
255717 TCTTTTTTTT
255727 TTTTTTCATTTTATCCA
1 TTTTTTC-TTTTATCCA
255744 TTTTTTCTTTT-T-CA
1 TTTTTTCTTTTATCCA
255758 TTTTTTCTT
1 TTTTTTCTT
255767 CTATTCTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 11 0.48
15 1 0.04
16 4 0.17
17 7 0.30
ACGTcount: A:0.10, C:0.15, G:0.00, T:0.75
Consensus pattern (16 bp):
TTTTTTCTTTTATCCA
Found at i:255786 original size:15 final size:15
Alignment explanation
Indices: 255698--255789 Score: 62
Period size: 15 Copynumber: 6.0 Consensus size: 15
255688 CTTAAACCCC
255698 TTTTTATTTATT-TT
1 TTTTTATTTATTCTT
* * *
255712 TTTTATCTTTTTTTTT
1 TTTT-TATTTATTCTT
* *
255728 TTTTTCATTTTATCCAT
1 TTTTT-A-TTTATTCTT
* *
255745 TTTTTCTTT-TTCAT
1 TTTTTATTTATTCTT
*
255759 TTTTTCTTCTATTCTT
1 TTTTTATT-TATTCTT
255775 TTTTTATTTATTCTT
1 TTTTTATTTATTCTT
255790 CAAACAAAAT
Statistics
Matches: 61, Mismatches: 11, Indels: 11
0.73 0.13 0.13
Matches are distributed among these distances:
14 16 0.26
15 18 0.30
16 17 0.28
17 10 0.16
ACGTcount: A:0.11, C:0.11, G:0.00, T:0.78
Consensus pattern (15 bp):
TTTTTATTTATTCTT
Found at i:263591 original size:23 final size:23
Alignment explanation
Indices: 263556--263620 Score: 94
Period size: 23 Copynumber: 2.8 Consensus size: 23
263546 CAACTCGTAT
*
263556 AAATGCACCGAAGTGCCATGTAG
1 AAATACACCGAAGTGCCATGTAG
* *
263579 AATTACACCGAAGTGCCACGTAG
1 AAATACACCGAAGTGCCATGTAG
*
263602 AAATACACTGAAGTGCCAT
1 AAATACACCGAAGTGCCAT
263621 ATAAAATGTC
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.37, C:0.23, G:0.22, T:0.18
Consensus pattern (23 bp):
AAATACACCGAAGTGCCATGTAG
Found at i:268782 original size:252 final size:252
Alignment explanation
Indices: 268337--268836 Score: 911
Period size: 252 Copynumber: 2.0 Consensus size: 252
268327 GGTATTAACC
268337 TTAATCCAATTATGTAATTATAGGTCGAGTTATACACGTGAGGCTATCATGCAAAAATTAATTAA
1 TTAATCCAATTATGTAATTATAGGTCGAGTTATA-ACGTGAGGCTATCATGCAAAAATTAATTAA
268402 ATGATGCTACATATTTGAATAAATAGTTGAATCTAAAGTATGTATGTTCATGCGAATAAATATAT
65 ATGATGCTACATATTTGAATAAATAGTTGAATCTAAAGTATGTATGTTCATGCGAATAAATATAT
268467 ATACTTTACAAATATGCTAATGAATTCCCAACATTTTAAAATTTTTAAACCTATTATGGTTATAT
130 ATACTTTACAAATATGCTAATGAATTCCCAACATTTTAAAATTTTTAAACCTATTATGGTTATAT
268532 TAA-ATAACATGTGATAAATGACTCTTATGCT-AATCGACTATAACTAAAAATAATATT
195 TAACATAACATGTGATAAATGACTC-TATGCTAAATCGACTATAACTAAAAATAATATT
268589 TTAATCCAATTATGTAATTATAGGTCGAGTTAT-ACGTGAGGCTATCATGCAAAAATTAATTAAA
1 TTAATCCAATTATGTAATTATAGGTCGAGTTATAACGTGAGGCTATCATGCAAAAATTAATTAAA
268653 TGATGCTACATAGTTTGAATAAATAGTTGAATCTAAAGTATGTATGTTCATGCGAATATAACTAT
66 TGATGCTACATA-TTTGAATAAATAGTTGAATCTAAAGTATGTATGTTCATGCGAATA-AA-TAT
268718 ATATTACTTTACAAATATGCTAATG-ATTCCC-ACATTTTAAAATTTTTAAACCTATTATGGTTA
128 ATA-TACTTTACAAATATGCTAATGAATTCCCAACATTTTAAAATTTTTAAACCTATTATGGTTA
268781 TATTAACATAACATGTGATAAATGACTCTATGCTAAATCGACTATAACTAAAAATA
192 TATTAACATAACATGTGATAAATGACTCTATGCTAAATCGACTATAACTAAAAATA
268837 TAATATTTCT
Statistics
Matches: 242, Mismatches: 0, Indels: 11
0.96 0.00 0.04
Matches are distributed among these distances:
250 43 0.18
251 45 0.19
252 79 0.33
253 54 0.22
254 21 0.09
ACGTcount: A:0.40, C:0.12, G:0.12, T:0.36
Consensus pattern (252 bp):
TTAATCCAATTATGTAATTATAGGTCGAGTTATAACGTGAGGCTATCATGCAAAAATTAATTAAA
TGATGCTACATATTTGAATAAATAGTTGAATCTAAAGTATGTATGTTCATGCGAATAAATATATA
TACTTTACAAATATGCTAATGAATTCCCAACATTTTAAAATTTTTAAACCTATTATGGTTATATT
AACATAACATGTGATAAATGACTCTATGCTAAATCGACTATAACTAAAAATAATATT
Found at i:270319 original size:21 final size:21
Alignment explanation
Indices: 270295--270347 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 21
270285 ATAATTATTC
*
270295 TATACTATATATATATTTATA
1 TATACTATATATATATTTAAA
*
270316 TATAAC-CTATATATATTTAAA
1 TAT-ACTATATATATATTTAAA
270337 TA-ACTA-ATATA
1 TATACTATATATA
270348 AAAAATGATA
Statistics
Matches: 27, Mismatches: 3, Indels: 6
0.75 0.08 0.17
Matches are distributed among these distances:
19 7 0.26
21 18 0.67
22 2 0.07
ACGTcount: A:0.47, C:0.08, G:0.00, T:0.45
Consensus pattern (21 bp):
TATACTATATATATATTTAAA
Found at i:273246 original size:16 final size:14
Alignment explanation
Indices: 273214--273240 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
273204 ATAATATATA
273214 TATATAAATTTTAT
1 TATATAAATTTTAT
273228 TATATAAATTTTA
1 TATATAAATTTTA
273241 CCTTATGCTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (14 bp):
TATATAAATTTTAT
Found at i:273468 original size:296 final size:301
Alignment explanation
Indices: 272903--273512 Score: 1107
Period size: 296 Copynumber: 2.1 Consensus size: 301
272893 TATGGTTATA
272903 TATAATATATATA-AAAATTTTATTATTATAATAAATTTACCTTATGCTGATGGTCTTAGTTTTT
1 TATAATATATATATAAAATTTTATTATTATAATAAATTTACCTTATGCTGATGGTCTTAGTTTTT
272967 CCTGTCGTTTCATGGCATTGTCATGAAAGAACCGCCAGGGTAATTAACGTGAAAGAGGGAGAAGA
66 CCTGTCGTTTCATGGCATTGTCATGAAAGAACCGCCAGGGTAATTAACGTGAAAGAGGGAGAAGA
273032 ATTGAAGAAAAAAATTGAAAAGGTGAGAGACACTACAAACATGGTGTCTTCCTTGATCGCATGGA
131 ATTGAAGAAAAAAATTGAAAAGGTGAGAGACACTACAAACATGGTGTCTTCCTTGATCGCATGGA
273097 TTGTTGTTCGACTTCCCTTGGTCGCATGAACCATAGAGCGTCTCCCTAGTACTGTAACAATCACC
196 TTGTTGTTCGACTTCCCTTGGTCGCATGAACCATAGAGCGTCTCCCTAGTACTGTAACAATCACC
273162 CTATTTCAATAAATAATCAC-ACCTACATTTGTATTTCGGAT
261 CTATTTCAATAAATAATCACAACCTACA-TTGTATTTCGGAT
*
273203 TATAATATATATATATAAATTTTATTA-TAT-A-AATTTTACCTTATGCTGATGGTCTTAG-TTT
1 TATAATATATATATA-AAATTTTATTATTATAATAAATTTACCTTATGCTGATGGTCTTAGTTTT
273264 TCCTGTCGTTTCATGGCATTGTCATGAAAGAACCGCCAGGGTAATTAACGTGAAAGA-GG-GAAG
65 TCCTGTCGTTTCATGGCATTGTCATGAAAGAACCGCCAGGGTAATTAACGTGAAAGAGGGAGAAG
273327 AATTGAAGAAAAAAATTGAAAAGGTGAGAGACACTACAAACATGGTGTCTTCCTTGATCGCATGG
130 AATTGAAGAAAAAAATTGAAAAGGTGAGAGACACTACAAACATGGTGTCTTCCTTGATCGCATGG
273392 ATTGTTGTTCGACTTCCCTTGGTCGCATGAACCATAGAGCGTCTCCCCTAGTACTGTAACAATCA
195 ATTGTTGTTCGACTTCCCTTGGTCGCATGAACCATAGAGCGTCT-CCCTAGTACTGTAACAATCA
273457 CCCTA-TTCAATAAATAATCACAACCTACATTGTATTTCGGAT
259 CCCTATTTCAATAAATAATCACAACCTACATTGTATTTCGGAT
273499 TAT-ATA-ATATATAA
1 TATAATATATATATAA
273513 TATTATGCTC
Statistics
Matches: 305, Mismatches: 1, Indels: 15
0.95 0.00 0.05
Matches are distributed among these distances:
293 1 0.00
294 7 0.02
295 3 0.01
296 145 0.48
297 34 0.11
298 60 0.20
299 26 0.09
300 14 0.05
301 4 0.01
302 11 0.04
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Consensus pattern (301 bp):
TATAATATATATATAAAATTTTATTATTATAATAAATTTACCTTATGCTGATGGTCTTAGTTTTT
CCTGTCGTTTCATGGCATTGTCATGAAAGAACCGCCAGGGTAATTAACGTGAAAGAGGGAGAAGA
ATTGAAGAAAAAAATTGAAAAGGTGAGAGACACTACAAACATGGTGTCTTCCTTGATCGCATGGA
TTGTTGTTCGACTTCCCTTGGTCGCATGAACCATAGAGCGTCTCCCTAGTACTGTAACAATCACC
CTATTTCAATAAATAATCACAACCTACATTGTATTTCGGAT
Found at i:284345 original size:11 final size:10
Alignment explanation
Indices: 284321--284351 Score: 53
Period size: 10 Copynumber: 3.0 Consensus size: 10
284311 GAGACTTTAA
284321 AAGAAGAAAG
1 AAGAAGAAAG
284331 AAGAAGAAGAG
1 AAGAAGAA-AG
284342 AAGAAGAAAG
1 AAGAAGAAAG
284352 TTGGGATTGC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 10 0.50
11 10 0.50
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (10 bp):
AAGAAGAAAG
Found at i:284791 original size:21 final size:19
Alignment explanation
Indices: 284765--284805 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
284755 GATATCATAC
284765 TTTCAAATAATAAGAAAAATA
1 TTTCAAA-AA-AAGAAAAATA
*
284786 TTTCAAAAAATGAAAAATA
1 TTTCAAAAAAAGAAAAATA
284805 T
1 T
284806 CTCTTATCTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 10 0.53
20 2 0.11
21 7 0.37
ACGTcount: A:0.61, C:0.05, G:0.05, T:0.29
Consensus pattern (19 bp):
TTTCAAAAAAAGAAAAATA
Found at i:286530 original size:18 final size:18
Alignment explanation
Indices: 286496--286530 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
286486 ACTGAATATT
*
286496 TGTCCCGAATGACCACTA
1 TGTCCCGAAGGACCACTA
*
286514 TGTCCCGAAGGATCACT
1 TGTCCCGAAGGACCACT
286531 CCTTAAGAAC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.26, C:0.31, G:0.20, T:0.23
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:287388 original size:20 final size:20
Alignment explanation
Indices: 287363--287416 Score: 90
Period size: 20 Copynumber: 2.7 Consensus size: 20
287353 CGATACACAG
*
287363 GTATCGGTACACCCCCGAAT
1 GTATCGATACACCCCCGAAT
*
287383 GTATCGATACACCCCTGAAT
1 GTATCGATACACCCCCGAAT
287403 GTATCGATACACCC
1 GTATCGATACACCC
287417 TGTGTTGTTC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.28, C:0.33, G:0.17, T:0.22
Consensus pattern (20 bp):
GTATCGATACACCCCCGAAT
Found at i:291756 original size:22 final size:22
Alignment explanation
Indices: 291728--291786 Score: 82
Period size: 22 Copynumber: 2.6 Consensus size: 22
291718 AGTCGAGGGT
*
291728 TACATAGGTTCTTCAGGACATA
1 TACATAGGTCCTTCAGGACATA
**
291750 TACATAGGTCCTTGGGGACATA
1 TACATAGGTCCTTCAGGACATA
291772 TACATGAGGTCCTTC
1 TACAT-AGGTCCTTC
291787 GAGACAAATT
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
22 24 0.75
23 8 0.25
ACGTcount: A:0.27, C:0.20, G:0.22, T:0.31
Consensus pattern (22 bp):
TACATAGGTCCTTCAGGACATA
Found at i:297950 original size:13 final size:13
Alignment explanation
Indices: 297932--297959 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
297922 AGTATAGGAG
297932 TATCGATACTAGT
1 TATCGATACTAGT
297945 TATCGATACTAGT
1 TATCGATACTAGT
297958 TA
1 TA
297960 AACAATATCG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.32, C:0.14, G:0.14, T:0.39
Consensus pattern (13 bp):
TATCGATACTAGT
Found at i:298051 original size:15 final size:16
Alignment explanation
Indices: 298028--298060 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
298018 TGGGAAGGTA
298028 GTATCGATACCA-AAG
1 GTATCGATACCATAAG
*
298043 GTATTGATACCATAAG
1 GTATCGATACCATAAG
298059 GT
1 GT
298061 TAGTATCGAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 11 0.69
16 5 0.31
ACGTcount: A:0.36, C:0.15, G:0.21, T:0.27
Consensus pattern (16 bp):
GTATCGATACCATAAG
Found at i:298071 original size:20 final size:19
Alignment explanation
Indices: 298022--298075 Score: 71
Period size: 20 Copynumber: 3.0 Consensus size: 19
298012 GATACCTGGG
298022 AAGGTAGTATCGATACCA-
1 AAGGTAGTATCGATACCAT
298040 AAGGTA-T-T-GATACCAT
1 AAGGTAGTATCGATACCAT
298056 AAGGTTAGTATCGATACCAT
1 AAGG-TAGTATCGATACCAT
298076 TTTTGAAATG
Statistics
Matches: 31, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
15 7 0.23
16 5 0.16
17 3 0.10
18 7 0.23
19 1 0.03
20 8 0.26
ACGTcount: A:0.37, C:0.15, G:0.20, T:0.28
Consensus pattern (19 bp):
AAGGTAGTATCGATACCAT
Found at i:298790 original size:23 final size:22
Alignment explanation
Indices: 298758--298800 Score: 77
Period size: 23 Copynumber: 1.9 Consensus size: 22
298748 AGTCGAGGGT
298758 TACATAGGTCCTTCGGGACATA
1 TACATAGGTCCTTCGGGACATA
298780 TACATGAGGTCCTTCGGGACA
1 TACAT-AGGTCCTTCGGGACA
298801 AATTTCATGT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
22 5 0.25
23 15 0.75
ACGTcount: A:0.26, C:0.23, G:0.26, T:0.26
Consensus pattern (22 bp):
TACATAGGTCCTTCGGGACATA
Found at i:301565 original size:3 final size:3
Alignment explanation
Indices: 301557--301584 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
301547 ATTAAAAAAT
301557 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
301585 ATGTCTAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:301826 original size:2 final size:2
Alignment explanation
Indices: 301821--301849 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
301811 TTTCACACAC
301821 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
301850 ATTCATTAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:303377 original size:18 final size:20
Alignment explanation
Indices: 303346--303391 Score: 53
Period size: 18 Copynumber: 2.4 Consensus size: 20
303336 ATACTTTCTG
303346 TTTT-TGGATGATTT-ATGC
1 TTTTATGGATGATTTCATGC
303364 TTTTATGGAT-ATTTCGATGC
1 TTTTATGGATGATTTC-ATGC
303384 TTATTATG
1 TT-TTATG
303392 ATTTTACGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
18 8 0.33
19 5 0.21
20 6 0.25
21 5 0.21
ACGTcount: A:0.20, C:0.07, G:0.20, T:0.54
Consensus pattern (20 bp):
TTTTATGGATGATTTCATGC
Found at i:305208 original size:31 final size:31
Alignment explanation
Indices: 305122--305208 Score: 77
Period size: 31 Copynumber: 2.8 Consensus size: 31
305112 AGTAATGATA
* * * * *
305122 TGACACATATCATGTGTTAAAATATTATGATG
1 TGACACATATTATATGTTAAAA-ATAACGACG
* * *
305154 TGACATATATTGTATATCT-AAAATAACGACG
1 TGACACATATTATATGT-TAAAAATAACGACG
305185 TGACACATATTATATGTTAAAAAT
1 TGACACATATTATATGTTAAAAAT
305209 GACAATGTAA
Statistics
Matches: 42, Mismatches: 11, Indels: 5
0.72 0.19 0.09
Matches are distributed among these distances:
30 1 0.02
31 25 0.60
32 15 0.36
33 1 0.02
ACGTcount: A:0.41, C:0.10, G:0.13, T:0.36
Consensus pattern (31 bp):
TGACACATATTATATGTTAAAAATAACGACG
Found at i:311504 original size:42 final size:42
Alignment explanation
Indices: 311443--311532 Score: 162
Period size: 42 Copynumber: 2.1 Consensus size: 42
311433 TTCCTCCAAC
*
311443 CAAACACTGGAAAACATTTTCCGGAAAACGAATTACGTGAAA
1 CAAACACGGGAAAACATTTTCCGGAAAACGAATTACGTGAAA
*
311485 CAAACACGGGAAAATATTTTCCGGAAAACGAATTACGTGAAA
1 CAAACACGGGAAAACATTTTCCGGAAAACGAATTACGTGAAA
311527 CAAACA
1 CAAACA
311533 TGGAATTTCG
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
42 46 1.00
ACGTcount: A:0.47, C:0.19, G:0.17, T:0.18
Consensus pattern (42 bp):
CAAACACGGGAAAACATTTTCCGGAAAACGAATTACGTGAAA
Found at i:312092 original size:14 final size:14
Alignment explanation
Indices: 312051--312102 Score: 50
Period size: 14 Copynumber: 3.6 Consensus size: 14
312041 CGGAAAACGT
*
312051 TTTCCAGAATTTAA
1 TTTCCAGAATTCAA
* * *
312065 ATTACAGTAATTCAT
1 TTTCCAG-AATTCAA
312080 TTTCCAGAATTCAA
1 TTTCCAGAATTCAA
*
312094 TTTCTAGAA
1 TTTCCAGAA
312103 AACCAATTAC
Statistics
Matches: 29, Mismatches: 8, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
14 19 0.66
15 10 0.34
ACGTcount: A:0.37, C:0.15, G:0.08, T:0.40
Consensus pattern (14 bp):
TTTCCAGAATTCAA
Found at i:313443 original size:22 final size:22
Alignment explanation
Indices: 313418--313459 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
313408 TTTTATCTTA
313418 AAAGTTTACACTTTTAATATCT
1 AAAGTTTACACTTTTAATATCT
*
313440 AAAGTTTATACTTTTAATAT
1 AAAGTTTACACTTTTAATAT
313460 TTATAGTGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.38, C:0.10, G:0.05, T:0.48
Consensus pattern (22 bp):
AAAGTTTACACTTTTAATATCT
Found at i:315061 original size:26 final size:26
Alignment explanation
Indices: 315025--315078 Score: 72
Period size: 26 Copynumber: 2.1 Consensus size: 26
315015 TGATAGCTGA
* *
315025 TAGTTGGTTTGATCAACTGATTTAAT
1 TAGTTGATTTGATAAACTGATTTAAT
* *
315051 TAGTTGATTTGATAAATTGATTTGAT
1 TAGTTGATTTGATAAACTGATTTAAT
315077 TA
1 TA
315079 ACTATTTATA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.30, C:0.04, G:0.19, T:0.48
Consensus pattern (26 bp):
TAGTTGATTTGATAAACTGATTTAAT
Found at i:320305 original size:54 final size:54
Alignment explanation
Indices: 320223--320368 Score: 238
Period size: 54 Copynumber: 2.7 Consensus size: 54
320213 ATCTGATTAA
* * *
320223 ATATGGAGATATGGAAGGAATTAGGATAAATCTTTTTATGAGTTATTTCAAGGG
1 ATATGGAGACATGAAAGGAATTAGGATAAATCTTTTTATGAGTTATTTCAAGAG
*
320277 ATATGGAGACATGAAAGGAATTAGGATAAATCTTTTTATGAGTTATTTTAAGAG
1 ATATGGAGACATGAAAGGAATTAGGATAAATCTTTTTATGAGTTATTTCAAGAG
*
320331 ATATGGAGACATGAAATGAATTAGGATAAATCCTTTTT
1 ATATGGAGACATGAAAGGAATTAGGATAAAT-CTTTTT
320369 GTGAAGTGTT
Statistics
Matches: 86, Mismatches: 5, Indels: 1
0.93 0.05 0.01
Matches are distributed among these distances:
54 80 0.93
55 6 0.07
ACGTcount: A:0.38, C:0.05, G:0.23, T:0.35
Consensus pattern (54 bp):
ATATGGAGACATGAAAGGAATTAGGATAAATCTTTTTATGAGTTATTTCAAGAG
Found at i:320492 original size:23 final size:23
Alignment explanation
Indices: 320464--320518 Score: 60
Period size: 23 Copynumber: 2.4 Consensus size: 23
320454 TGCTTTAAAG
320464 ATGATAGATTT-TATTTTAAAAAA
1 ATGATAGATTTCTATTTT-AAAAA
* * *
320487 ATGATAG-TTTCTCTTTTCAAAG
1 ATGATAGATTTCTATTTTAAAAA
320509 ATGATAGATT
1 ATGATAGATT
320519 ATTTTTTCAA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
22 13 0.48
23 14 0.52
ACGTcount: A:0.38, C:0.05, G:0.13, T:0.44
Consensus pattern (23 bp):
ATGATAGATTTCTATTTTAAAAA
Found at i:320515 original size:22 final size:21
Alignment explanation
Indices: 320460--320531 Score: 65
Period size: 22 Copynumber: 3.2 Consensus size: 21
320450 TACATGCTTT
*
320460 AAAGATGATAGATTTTATTTTAA
1 AAAGATGATAG-TTTTATTTT-C
* *
320483 AAAAATGATAGTTTCTCTTTTC
1 AAAGATGATAGTTT-TATTTTC
320505 AAAGATGATAGATTATT-TTTTC
1 AAAGATGATAG-TT-TTATTTTC
320527 AAAGA
1 AAAGA
320532 AAAAAGCTTT
Statistics
Matches: 42, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
22 23 0.55
23 18 0.43
24 1 0.02
ACGTcount: A:0.40, C:0.06, G:0.12, T:0.42
Consensus pattern (21 bp):
AAAGATGATAGTTTTATTTTC
Found at i:321326 original size:99 final size:99
Alignment explanation
Indices: 321162--321373 Score: 291
Period size: 99 Copynumber: 2.1 Consensus size: 99
321152 AAACCTCCAG
*
321162 GTCATATGTAAAACCTCATGGTAGGATGTTTTCGCATGAAAATGAGAAAGCAAGTTGTAAAGTTT
1 GTCATATGTAAAACCTCAGGGTAGGATGTTTTCGCATGAAAATGAGAAAGCAAGTTGTAAAGTTT
* *
321227 CTCATTTAATGTTCTAGAAAATTATATCCTCCGA
66 CTCATTTAATATTCTAGAAAATTAAATCCTCCGA
* * * ** *
321261 GTCATCTGTGAAACCTCCGGGTAGGATGTTTTCGCATGAAAATGAGAAAGTGA-TTTTCAAAGTT
1 GTCATATGTAAAACCTCAGGGTAGGATGTTTTCGCATGAAAATGAGAAAGCAAGTTGT-AAAGTT
* *
321325 TCTTATTTAATATTCTAGAAAATTAAATCCTCCGG
65 TCTCATTTAATATTCTAGAAAATTAAATCCTCCGA
* *
321360 GTGATTTGTAAAAC
1 GTCATATGTAAAAC
321374 GTCTGGGTCA
Statistics
Matches: 98, Mismatches: 14, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
98 3 0.03
99 95 0.97
ACGTcount: A:0.33, C:0.14, G:0.19, T:0.34
Consensus pattern (99 bp):
GTCATATGTAAAACCTCAGGGTAGGATGTTTTCGCATGAAAATGAGAAAGCAAGTTGTAAAGTTT
CTCATTTAATATTCTAGAAAATTAAATCCTCCGA
Found at i:321568 original size:20 final size:19
Alignment explanation
Indices: 321543--321648 Score: 103
Period size: 20 Copynumber: 5.6 Consensus size: 19
321533 CATCCGGTCT
*
321543 TATTATTATTTTTATTATCA
1 TATTATTATTATTATTAT-A
321563 TATTATTATTATTATTAT-
1 TATTATTATTATTATTATA
*
321581 TATATATAATTATATATTATA
1 TAT-TATTATTAT-TATTATA
321602 CTATTATTA-TATTATTA-A
1 -TATTATTATTATTATTATA
* * *
321620 TATTATTACTACTAATAT-
1 TATTATTATTATTATTATA
321638 TATTATTATTA
1 TATTATTATTA
321649 ATAATAATTA
Statistics
Matches: 74, Mismatches: 6, Indels: 14
0.79 0.06 0.15
Matches are distributed among these distances:
17 8 0.11
18 20 0.27
19 13 0.18
20 26 0.35
21 4 0.05
22 3 0.04
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.58
Consensus pattern (19 bp):
TATTATTATTATTATTATA
Found at i:321661 original size:3 final size:3
Alignment explanation
Indices: 321542--321648 Score: 103
Period size: 3 Copynumber: 36.0 Consensus size: 3
321532 TCATCCGGTC
* *
321542 TTA TTA TTA TTT TTA TTA TCA -TA TTA TTA TTA TTA TTA TTA TATA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA
* * * *
321587 TAA TTA TATA TTA -TA CTA TTA TTA -TA TTA TTA ATA TTA TTA CTA
1 TTA TTA T-TA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* *
321631 CTA ATA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA
321649 ATAATAATTA
Statistics
Matches: 87, Mismatches: 12, Indels: 10
0.80 0.11 0.09
Matches are distributed among these distances:
2 5 0.06
3 76 0.87
4 6 0.07
ACGTcount: A:0.37, C:0.04, G:0.00, T:0.59
Consensus pattern (3 bp):
TTA
Found at i:327446 original size:112 final size:112
Alignment explanation
Indices: 327244--327594 Score: 551
Period size: 112 Copynumber: 3.1 Consensus size: 112
327234 TTGTCGGTTT
*
327244 GTGTCGATACTTTATAAAAATATAT-TGATCCATAACAATATAACAAGTAAAAAAATGACAAAAC
1 GTGTCGATACTTTATAAAAATGTATCT-ATCCATAACAATATAACAAGTAAAAAAATGACAAAAC
327308 CGGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
65 CGGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
* *
327356 GTGTTGATACTTTATAAAAATGTATCTATCCATAACAATATAACATGTAAAAAAATGACAAAACC
1 GTGTCGATACTTTATAAAAATGTATCTATCCATAACAATATAACAAGTAAAAAAATGACAAAACC
327421 GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
66 GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
* * * *
327468 GTGTCGATACTTTATAAAAATGTATCGATCCATAATAATATAACAGGTAAAAATATGACAAAACC
1 GTGTCGATACTTTATAAAAATGTATCTATCCATAACAATATAACAAGTAAAAAAATGACAAAACC
** * * * *
327533 GGTCTCGAAATGACAAAACCGGTAAAGAGCTACCGGATATGTTGATA
66 GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
* *
327580 GTGTCTATATTTTAT
1 GTGTCGATACTTTAT
327595 TATAAGTATC
Statistics
Matches: 222, Mismatches: 16, Indels: 2
0.93 0.07 0.01
Matches are distributed among these distances:
112 221 1.00
113 1 0.00
ACGTcount: A:0.44, C:0.14, G:0.15, T:0.26
Consensus pattern (112 bp):
GTGTCGATACTTTATAAAAATGTATCTATCCATAACAATATAACAAGTAAAAAAATGACAAAACC
GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
Found at i:328403 original size:23 final size:23
Alignment explanation
Indices: 328357--328404 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
328347 AAATAAGTTA
* * *
328357 ATATAAGCGCTGCCTATTACATT
1 ATATAAGCGCTACATAATACATT
*
328380 ATATAAGCGCTACATAATATATT
1 ATATAAGCGCTACATAATACATT
328403 AT
1 AT
328405 TGTACTTGCT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.38, C:0.17, G:0.10, T:0.35
Consensus pattern (23 bp):
ATATAAGCGCTACATAATACATT
Found at i:331642 original size:20 final size:20
Alignment explanation
Indices: 331610--331647 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
331600 TTCCTCATTG
331610 AATTGATTCGAGTCAACTCA
1 AATTGATTCGAGTCAACTCA
331630 AATTAGATT-GAGTCAACT
1 AATT-GATTCGAGTCAACT
331648 GAGATCAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.37, C:0.16, G:0.16, T:0.32
Consensus pattern (20 bp):
AATTGATTCGAGTCAACTCA
Found at i:332818 original size:20 final size:20
Alignment explanation
Indices: 332795--332836 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
332785 CGAAGCAAAT
*
332795 TGAGTCAACCCAAGTCGGTC
1 TGAGTCAACCCAAATCGGTC
332815 TGAGTCAACCCAAATCGGTC
1 TGAGTCAACCCAAATCGGTC
332835 TG
1 TG
332837 GACCGTTGAC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.26, C:0.29, G:0.24, T:0.21
Consensus pattern (20 bp):
TGAGTCAACCCAAATCGGTC
Found at i:338105 original size:27 final size:29
Alignment explanation
Indices: 338046--338106 Score: 74
Period size: 27 Copynumber: 2.2 Consensus size: 29
338036 CTTTATGTCT
* *
338046 TTATTATTATTTTAATTATCCATTATATA
1 TTATTATTATTTTAAATATCCAGTATATA
*
338075 -TATT-TTATTTTAAATA-CTAGTATATA
1 TTATTATTATTTTAAATATCCAGTATATA
338101 TTATTA
1 TTATTA
338107 GGATATATGT
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
26 8 0.30
27 15 0.56
28 4 0.15
ACGTcount: A:0.36, C:0.05, G:0.02, T:0.57
Consensus pattern (29 bp):
TTATTATTATTTTAAATATCCAGTATATA
Found at i:339368 original size:3 final size:3
Alignment explanation
Indices: 339362--339415 Score: 56
Period size: 3 Copynumber: 17.7 Consensus size: 3
339352 GTATTATTTT
* **
339362 TAA TAA TATA TATA TAA TAA TAT TAA TAA TAA TTG TAA T-A TAA TAA
1 TAA TAA TA-A TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
339408 TAA TAA TA
1 TAA TAA TA
339416 TATAGTCTAG
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
2 2 0.05
3 34 0.79
4 7 0.16
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (3 bp):
TAA
Found at i:339381 original size:14 final size:14
Alignment explanation
Indices: 339362--339419 Score: 59
Period size: 14 Copynumber: 4.1 Consensus size: 14
339352 GTATTATTTT
339362 TAATAATATATATA
1 TAATAATATATATA
339376 TAATAATAT-TA-A
1 TAATAATATATATA
*
339388 TAATAAT-TGTAATA
1 TAATAATATAT-ATA
339402 TAATAATAATAATATA
1 TAATAAT-AT-ATATA
339418 TA
1 TA
339420 GTCTAGGACA
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
11 1 0.03
12 9 0.24
13 3 0.08
14 17 0.46
16 6 0.16
17 1 0.03
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (14 bp):
TAATAATATATATA
Found at i:339389 original size:23 final size:21
Alignment explanation
Indices: 339361--339419 Score: 75
Period size: 20 Copynumber: 2.8 Consensus size: 21
339351 TGTATTATTT
339361 TTAATAATATATATATAATAATA
1 TTAATAATA-ATATATAAT-ATA
*
339384 TTAATAATAAT-TGTAATATA
1 TTAATAATAATATATAATATA
*
339404 ATAATAATAATATATA
1 TTAATAATAATATATA
339420 GTCTAGGACA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
20 13 0.41
21 8 0.25
22 2 0.06
23 9 0.28
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (21 bp):
TTAATAATAATATATAATATA
Found at i:339392 original size:26 final size:26
Alignment explanation
Indices: 339362--339415 Score: 74
Period size: 26 Copynumber: 2.1 Consensus size: 26
339352 GTATTATTTT
*
339362 TAATAA-TATATATATAATAATATTAA
1 TAATAATTATA-ATATAATAATAATAA
*
339388 TAATAATTGTAATATAATAATAATAA
1 TAATAATTATAATATAATAATAATAA
339414 TA
1 TA
339416 TATAGTCTAG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 22 0.88
27 3 0.12
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (26 bp):
TAATAATTATAATATAATAATAATAA
Found at i:339592 original size:20 final size:20
Alignment explanation
Indices: 339567--339615 Score: 80
Period size: 20 Copynumber: 2.5 Consensus size: 20
339557 ATCCTACCTT
*
339567 GAGGTTTTACAGATGACCCA
1 GAGGTTTTACAAATGACCCA
*
339587 GAGGTTTTACAAATTACCCA
1 GAGGTTTTACAAATGACCCA
339607 GAGGTTTTA
1 GAGGTTTTA
339616 ATTTTTTAGA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.31, C:0.16, G:0.22, T:0.31
Consensus pattern (20 bp):
GAGGTTTTACAAATGACCCA
Found at i:339709 original size:20 final size:20
Alignment explanation
Indices: 339681--339734 Score: 72
Period size: 20 Copynumber: 2.7 Consensus size: 20
339671 AAAACATCCT
* *
339681 ACCCTGAGGTTTTACAGATG
1 ACCCGGAGGTTTTACAAATG
*
339701 ACCCGGAGGTTTTACAAATT
1 ACCCGGAGGTTTTACAAATG
*
339721 ACCCGAAGGTTTTA
1 ACCCGGAGGTTTTA
339735 ATTTTCTAGA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.28, C:0.20, G:0.22, T:0.30
Consensus pattern (20 bp):
ACCCGGAGGTTTTACAAATG
Found at i:339763 original size:119 final size:119
Alignment explanation
Indices: 339552--339833 Score: 485
Period size: 119 Copynumber: 2.4 Consensus size: 119
339542 TAAAGTAAAA
*
339552 AAAACATCCTACCTTGAGGTTTTACAGATGACCCAGAGGTTTTACAAATTACCCAGAGGTTTTAA
1 AAAACATCCTACCTTGAGGTTTTACAGATGACCCGGAGGTTTTACAAATTACCCAGAGGTTTTAA
* *
339617 TTTTTTAGAACATTAAATGAGAAACTTTGTTTATTACTTTCTCATTTTCATACG
66 TTTTCTAGAACATTAAATGACAAACTTTGTTTATTACTTTCTCATTTTCATACG
*
339671 AAAACATCCTACCCTGAGGTTTTACAGATGACCCGGAGGTTTTACAAATTACCC-GAAGGTTTTA
1 AAAACATCCTACCTTGAGGTTTTACAGATGACCCGGAGGTTTTACAAATTACCCAG-AGGTTTTA
**
339735 ATTTTCTAGAACATTAAATGACAAACTTTGTTTATTACTTTCTCATTTTCATGTG
65 ATTTTCTAGAACATTAAATGACAAACTTTGTTTATTACTTTCTCATTTTCATACG
*
339790 AAAACATCCTACCTTGAGGTTTTACAAATGACCCGGAGGTTTTA
1 AAAACATCCTACCTTGAGGTTTTACAGATGACCCGGAGGTTTTA
339834 ATTTTCTATA
Statistics
Matches: 154, Mismatches: 8, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
118 1 0.01
119 153 0.99
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.36
Consensus pattern (119 bp):
AAAACATCCTACCTTGAGGTTTTACAGATGACCCGGAGGTTTTACAAATTACCCAGAGGTTTTAA
TTTTCTAGAACATTAAATGACAAACTTTGTTTATTACTTTCTCATTTTCATACG
Found at i:339877 original size:99 final size:99
Alignment explanation
Indices: 339701--340150 Score: 513
Period size: 99 Copynumber: 4.3 Consensus size: 99
339691 TTTACAGATG
* * * * *
339701 ACCCGGAGGTTTTACAAATTACCCGAAGGTTTTAATTTTCTAGAACATTAAATGACAAACTTTGT
1 ACCCTGAGGTTTTACAAATGACCCGGAGGTTTTAATTTTCTAGAACATTAAATGAGAAACTTTGG
*
339766 TTATTACTTTCTCATTTTCATGTGAAAACATCCT
66 TTATTACTTTCTCATTTTCATGCGAAAACATCCT
* *
339800 ACCTTGAGGTTTTACAAATGACCCGGAGGTTTTAATTTTCTATAACATTAAATGAGAAACTTTGG
1 ACCCTGAGGTTTTACAAATGACCCGGAGGTTTTAATTTTCTAGAACATTAAATGAGAAACTTTGG
339865 TTATTACTTTCTCATTTTCATGCGAAAACATCCT
66 TTATTACTTTCTCATTTTCATGCGAAAACATCCT
* * * * ** * **
339899 ACCTTGAGGTTTTACAGATGATCCTGAGGTTTTACAAATTACCCGGAGGTTTTAATTTTCTAGAA
1 ACCCTGAGGTTTTACAAATGACCCGGAGGTTTT---AATT-TTC-TA-G----AA-CAT-T--AA
* *
339964 CATTAAATGAGAAACTTTGGTTATTTCTTTCTCATTTTCATGCGAAAACATCAT
52 ------ATGAGAAACTTTGGTTATTACTTTCTCATTTTCATGCGAAAACATCCT
* * *
340018 ACCCTGAGGTTTTACAAATTACCCGGAGGTTTTAATTTTCTATAACATTAAATGAGAAACTTTGT
1 ACCCTGAGGTTTTACAAATGACCCGGAGGTTTTAATTTTCTAGAACATTAAATGAGAAACTTTGG
340083 TTATTACTTTCTCATTTTCATGCGAAAACATCCT
66 TTATTACTTTCTCATTTTCATGCGAAAACATCCT
*
340117 ACCCTGAGGTTTTACAGATGACCCGGAGGTTTTA
1 ACCCTGAGGTTTTACAAATGACCCGGAGGTTTTA
340151 CAAATTACTC
Statistics
Matches: 296, Mismatches: 35, Indels: 40
0.80 0.09 0.11
Matches are distributed among these distances:
99 198 0.67
102 4 0.01
103 1 0.00
104 1 0.00
105 2 0.01
107 1 0.00
108 1 0.00
109 4 0.01
110 1 0.00
111 1 0.00
113 2 0.01
114 1 0.00
115 1 0.00
116 4 0.01
119 74 0.25
ACGTcount: A:0.30, C:0.18, G:0.15, T:0.38
Consensus pattern (99 bp):
ACCCTGAGGTTTTACAAATGACCCGGAGGTTTTAATTTTCTAGAACATTAAATGAGAAACTTTGG
TTATTACTTTCTCATTTTCATGCGAAAACATCCT
Found at i:339947 original size:20 final size:20
Alignment explanation
Indices: 339904--339952 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
339894 ATCCTACCTT
* * *
339904 GAGGTTTTACAGATGATCCT
1 GAGGTTTTACAAATGACCCG
*
339924 GAGGTTTTACAAATTACCCG
1 GAGGTTTTACAAATGACCCG
339944 GAGGTTTTA
1 GAGGTTTTA
339953 ATTTTCTAGA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.27, C:0.14, G:0.24, T:0.35
Consensus pattern (20 bp):
GAGGTTTTACAAATGACCCG
Found at i:339949 original size:119 final size:119
Alignment explanation
Indices: 339804--340051 Score: 415
Period size: 119 Copynumber: 2.1 Consensus size: 119
339794 CATCCTACCT
*
339804 TGAGGTTTTACAAATGACCCGGAGGTTTTAATTTTCTATAACATTAAATGAGAAACTTTGGTTAT
1 TGAGGTTTTACAAATGACCCGGAGGTTTTAATTTTCTAGAACATTAAATGAGAAACTTTGGTTAT
* * * *
339869 TACTTTCTCATTTTCATGCGAAAACATCCTACCTTGAGGTTTTACAGATGATCC
66 TACTTTCTCATTTTCATGCGAAAACATCATACCCTGAGGTTTTACAAATGACCC
*
339923 TGAGGTTTTACAAATTACCCGGAGGTTTTAATTTTCTAGAACATTAAATGAGAAACTTTGGTTAT
1 TGAGGTTTTACAAATGACCCGGAGGTTTTAATTTTCTAGAACATTAAATGAGAAACTTTGGTTAT
* *
339988 TTCTTTCTCATTTTCATGCGAAAACATCATACCCTGAGGTTTTACAAATTACCC
66 TACTTTCTCATTTTCATGCGAAAACATCATACCCTGAGGTTTTACAAATGACCC
*
340042 GGAGGTTTTA
1 TGAGGTTTTA
340052 ATTTTCTATA
Statistics
Matches: 120, Mismatches: 9, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
119 120 1.00
ACGTcount: A:0.29, C:0.17, G:0.16, T:0.38
Consensus pattern (119 bp):
TGAGGTTTTACAAATGACCCGGAGGTTTTAATTTTCTAGAACATTAAATGAGAAACTTTGGTTAT
TACTTTCTCATTTTCATGCGAAAACATCATACCCTGAGGTTTTACAAATGACCC
Found at i:339965 original size:218 final size:218
Alignment explanation
Indices: 339582--340872 Score: 1630
Period size: 218 Copynumber: 5.6 Consensus size: 218
339572 TTTACAGATG
* * * * *
339582 ACCCAGAGGTTTTACAAATTACCCAGAGGTTTTAATTTTTTAGAACATTAAATGAGAAACTTTGT
1 ACCCTGAGGTTTTACAAATGACCCGGAGGTTTTAATTTTCTATAACATTAAATGAGAAACTTTGT
* *
339647 TTATTACTTTCTCATTTTCATACGAAAACATCCTACCCTGAGGTTTTACAGATGACCCGGAGGTT
66 TTATTACTTTCTCATTTTCATGCGAAAACATCCTACCCTGAGGTTTTACAGATGACCCTGAGGTT
* *
339712 TTACAAATTACCCGAAGGTTTTAATTTTCTAGAACATTAAATGACAAACTTTGTTTATTACTTTC
131 TTACAAATTACCCGGAGGTTTTAATTTTCTAGAACATTAAATGAGAAACTTTGTTTATTACTTTC
*
339777 TCATTTTCATGTGAAAACATCCT
196 TCATTTTCATGCGAAAACATCCT
* *
339800 ACCTTGAGGTTTTACAAATGACCCGGAGGTTTTAATTTTCTATAACATTAAATGAGAAACTTTGG
1 ACCCTGAGGTTTTACAAATGACCCGGAGGTTTTAATTTTCTATAACATTAAATGAGAAACTTTGT
* *
339865 TTATTACTTTCTCATTTTCATGCGAAAACATCCTACCTTGAGGTTTTACAGATGATCCTGAGGTT
66 TTATTACTTTCTCATTTTCATGCGAAAACATCCTACCCTGAGGTTTTACAGATGACCCTGAGGTT
* *
339930 TTACAAATTACCCGGAGGTTTTAATTTTCTAGAACATTAAATGAGAAACTTTGGTTATTTCTTTC
131 TTACAAATTACCCGGAGGTTTTAATTTTCTAGAACATTAAATGAGAAACTTTGTTTATTACTTTC
*
339995 TCATTTTCATGCGAAAACATCAT
196 TCATTTTCATGCGAAAACATCCT
*
340018 ACCCTGAGGTTTTACAAATTACCCGGAGGTTTTAATTTTCTATAACATTAAATGAGAAACTTTGT
1 ACCCTGAGGTTTTACAAATGACCCGGAGGTTTTAATTTTCTATAACATTAAATGAGAAACTTTGT
*
340083 TTATTACTTTCTCATTTTCATGCGAAAACATCCTACCCTGAGGTTTTACAGATGACCCGGAGGTT
66 TTATTACTTTCTCATTTTCATGCGAAAACATCCTACCCTGAGGTTTTACAGATGACCCTGAGGTT
* * *
340148 TTACAAATTACTCGAAGGTTTTAATTTTCTAGAACATTAAATGACAAACTTTGTTTATTACTTTC
131 TTACAAATTACCCGGAGGTTTTAATTTTCTAGAACATTAAATGAGAAACTTTGTTTATTACTTTC
*
340213 TCATTTTCATGCGAAAAAAATCCT
196 TCATTTTCATGCG-AAAACATCCT
*
340237 ACCCTGAGGTTTTACAAATGACCCGGAGGATTTACAAATTACCCGGAGGTTTTAATTTTCTAGAA
1 ACCCTGAGGTTTTACAAAT---------G-----------ACCCGGAGGTTTTAATTTTCTATAA
* * * *
340302 CATTAAATGAGAAACTTTGGTTATTACTTTCTCATTTTCATGAGAAAACATCCTACCTTAAGGTT
46 CATTAAATGAGAAACTTTGTTTATTACTTTCTCATTTTCATGCGAAAACATCCTACCCTGAGGTT
*
340367 TTATAGATGACCCTGAGGTTTTACAAATTACCCGGAGGTTTTAATTTTCTAGAACATTAAATGAG
111 TTACAGATGACCCTGAGGTTTTACAAATTACCCGGAGGTTTTAATTTTCTAGAACATTAAATGAG
* * *
340432 AAACTTTGGTTATTACTTTCTCATTTTCAAGCAAAAACATCCT
176 AAACTTTGTTTATTACTTTCTCATTTTCATGCGAAAACATCCT
340475 ACCCTGAGGTTTTACAGATGACCTTGAGGTTTTACAAATTACCCGGAGGTTTTAATTTTCTATAA
1 ACCCTGAGGTTTTACA-A--A---T---G-----------ACCCGGAGGTTTTAATTTTCTATAA
*
340540 CATTAAATGAGAAACTTTGTTTATTACTTTCTCATTTTCATGCGAAAATATCCTACCCTGAGGTT
46 CATTAAATGAGAAACTTTGTTTATTACTTTCTCATTTTCATGCGAAAACATCCTACCCTGAGGTT
*
340605 TTACAGATGACCCTGAGGTTTTACAAATTACCCGGAGGTTTTAATTTTCTATAACATTAAATGAG
111 TTACAGATGACCCTGAGGTTTTACAAATTACCCGGAGGTTTTAATTTTCTAGAACATTAAATGAG
*
340670 AACCTTTGTTTATTACTTTCTCATTTTCATGCGAAAACATCCT
176 AAACTTTGTTTATTACTTTCTCATTTTCATGCGAAAACATCCT
* *
340713 ACCCTGAGGTTTTACAGATGACCCGGAGGATTTACAAATTACCCGGAGGTTTTAATTTTCTAGAA
1 ACCCTGA-G-------G-T-----------TTTACAAATGACCCGGAGGTTTTAATTTTCTATAA
* * *
340778 CATTAAATGAGAAACTTTGATTATTACTTTCTCATTTTTCATGCGAAAATATCCTACCCCGAGGT
46 CATTAAATGAGAAACTTTGTTTATTACTTTCTCA-TTTTCATGCGAAAACATCCTACCCTGAGGT
* *
340843 TTTACAGATGA-CCTGGAAGATTTACAAATT
110 TTTACAGATGACCCT-GAGGTTTTACAAATT
340873 TGTGGAAAAT
Statistics
Matches: 960, Mismatches: 64, Indels: 77
0.87 0.06 0.07
Matches are distributed among these distances:
218 398 0.41
219 27 0.03
238 292 0.30
239 230 0.24
241 1 0.00
244 1 0.00
246 1 0.00
247 1 0.00
252 1 0.00
255 1 0.00
257 1 0.00
258 6 0.01
ACGTcount: A:0.31, C:0.18, G:0.14, T:0.37
Consensus pattern (218 bp):
ACCCTGAGGTTTTACAAATGACCCGGAGGTTTTAATTTTCTATAACATTAAATGAGAAACTTTGT
TTATTACTTTCTCATTTTCATGCGAAAACATCCTACCCTGAGGTTTTACAGATGACCCTGAGGTT
TTACAAATTACCCGGAGGTTTTAATTTTCTAGAACATTAAATGAGAAACTTTGTTTATTACTTTC
TCATTTTCATGCGAAAACATCCT
Found at i:340049 original size:238 final size:238
Alignment explanation
Indices: 339805--340872 Score: 1647
Period size: 238 Copynumber: 4.6 Consensus size: 238
339795 ATCCTACCTT
* *
339805 GAGGTTTTACAAATGACCCGGAGGTTTTAATTTTCTATAACATTAAATGAGAAACTTTGGTTATT
1 GAGGATTTACAAATTACCCGGAGGTTTTAATTTTCTATAACATTAAATGAGAAACTTTGGTTATT
* *
339870 ACTTTCTCATTTTCATGCGAAAACATCCTACCTTGAGGTTTTACAGATGATCCTGAGGTTTTACA
66 ACTTTCTCATTTTCATGCGAAAACATCCTACCCTGAGGTTTTACAGATGACCCTGAGGTTTTACA
*
339935 AATTACCCGGAGGTTTTAATTTTCTAGAACATTAAATGAGAAACTTTGGTTATTTCTTTCTCATT
131 AATTACCCGGAGGTTTTAATTTTCTAGAACATTAAATGAGAAACTTTGGTTATTACTTTCTCATT
*
340000 TTCATGCGAAAACATCATACCCTGA-G-------G-T------
196 TTCATGCGAAAACATCCTACCCTGAGGTTTTACAGATGACCCG
*
340028 -----TTTACAAATTACCCGGAGGTTTTAATTTTCTATAACATTAAATGAGAAACTTTGTTTATT
1 GAGGATTTACAAATTACCCGGAGGTTTTAATTTTCTATAACATTAAATGAGAAACTTTGGTTATT
*
340088 ACTTTCTCATTTTCATGCGAAAACATCCTACCCTGAGGTTTTACAGATGACCCGGAGGTTTTACA
66 ACTTTCTCATTTTCATGCGAAAACATCCTACCCTGAGGTTTTACAGATGACCCTGAGGTTTTACA
* * * *
340153 AATTACTCGAAGGTTTTAATTTTCTAGAACATTAAATGACAAACTTTGTTTATTACTTTCTCATT
131 AATTACCCGGAGGTTTTAATTTTCTAGAACATTAAATGAGAAACTTTGGTTATTACTTTCTCATT
* *
340218 TTCATGCGAAAAAAATCCTACCCTGAGGTTTTACAAATGACCCG
196 TTCATGCG-AAAACATCCTACCCTGAGGTTTTACAGATGACCCG
*
340262 GAGGATTTACAAATTACCCGGAGGTTTTAATTTTCTAGAACATTAAATGAGAAACTTTGGTTATT
1 GAGGATTTACAAATTACCCGGAGGTTTTAATTTTCTATAACATTAAATGAGAAACTTTGGTTATT
* * * *
340327 ACTTTCTCATTTTCATGAGAAAACATCCTACCTTAAGGTTTTATAGATGACCCTGAGGTTTTACA
66 ACTTTCTCATTTTCATGCGAAAACATCCTACCCTGAGGTTTTACAGATGACCCTGAGGTTTTACA
340392 AATTACCCGGAGGTTTTAATTTTCTAGAACATTAAATGAGAAACTTTGGTTATTACTTTCTCATT
131 AATTACCCGGAGGTTTTAATTTTCTAGAACATTAAATGAGAAACTTTGGTTATTACTTTCTCATT
* * **
340457 TTCAAGCAAAAACATCCTACCCTGAGGTTTTACAGATGACCTT
196 TTCATGCGAAAACATCCTACCCTGAGGTTTTACAGATGACCCG
* *
340500 GAGGTTTTACAAATTACCCGGAGGTTTTAATTTTCTATAACATTAAATGAGAAACTTTGTTTATT
1 GAGGATTTACAAATTACCCGGAGGTTTTAATTTTCTATAACATTAAATGAGAAACTTTGGTTATT
*
340565 ACTTTCTCATTTTCATGCGAAAATATCCTACCCTGAGGTTTTACAGATGACCCTGAGGTTTTACA
66 ACTTTCTCATTTTCATGCGAAAACATCCTACCCTGAGGTTTTACAGATGACCCTGAGGTTTTACA
* * *
340630 AATTACCCGGAGGTTTTAATTTTCTATAACATTAAATGAGAACCTTTGTTTATTACTTTCTCATT
131 AATTACCCGGAGGTTTTAATTTTCTAGAACATTAAATGAGAAACTTTGGTTATTACTTTCTCATT
340695 TTCATGCGAAAACATCCTACCCTGAGGTTTTACAGATGACCCG
196 TTCATGCGAAAACATCCTACCCTGAGGTTTTACAGATGACCCG
* *
340738 GAGGATTTACAAATTACCCGGAGGTTTTAATTTTCTAGAACATTAAATGAGAAACTTTGATTATT
1 GAGGATTTACAAATTACCCGGAGGTTTTAATTTTCTATAACATTAAATGAGAAACTTTGGTTATT
* * * *
340803 ACTTTCTCATTTTTCATGCGAAAATATCCTACCCCGAGGTTTTACAGATGA-CCTGGAAGATTTA
66 ACTTTCTCA-TTTTCATGCGAAAACATCCTACCCTGAGGTTTTACAGATGACCCT-GAGGTTTTA
340867 CAAATT
129 CAAATT
340873 TGTGGAAAAT
Statistics
Matches: 771, Mismatches: 51, Indels: 30
0.90 0.06 0.04
Matches are distributed among these distances:
218 188 0.24
219 15 0.02
220 1 0.00
228 1 0.00
238 328 0.43
239 238 0.31
ACGTcount: A:0.31, C:0.17, G:0.15, T:0.37
Consensus pattern (238 bp):
GAGGATTTACAAATTACCCGGAGGTTTTAATTTTCTATAACATTAAATGAGAAACTTTGGTTATT
ACTTTCTCATTTTCATGCGAAAACATCCTACCCTGAGGTTTTACAGATGACCCTGAGGTTTTACA
AATTACCCGGAGGTTTTAATTTTCTAGAACATTAAATGAGAAACTTTGGTTATTACTTTCTCATT
TTCATGCGAAAACATCCTACCCTGAGGTTTTACAGATGACCCG
Found at i:340166 original size:20 final size:20
Alignment explanation
Indices: 340123--340170 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
340113 TCCTACCCTG
* *
340123 AGGTTTTACAGATGACCCGG
1 AGGTTTTACAAATGACCCGA
* *
340143 AGGTTTTACAAATTACTCGA
1 AGGTTTTACAAATGACCCGA
340163 AGGTTTTA
1 AGGTTTTA
340171 ATTTTCTAGA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.29, C:0.15, G:0.23, T:0.33
Consensus pattern (20 bp):
AGGTTTTACAAATGACCCGA
Found at i:340265 original size:20 final size:20
Alignment explanation
Indices: 340237--340290 Score: 81
Period size: 20 Copynumber: 2.7 Consensus size: 20
340227 AAAAAATCCT
*
340237 ACCCTGAGGTTTTACAAATG
1 ACCCGGAGGTTTTACAAATG
* *
340257 ACCCGGAGGATTTACAAATT
1 ACCCGGAGGTTTTACAAATG
340277 ACCCGGAGGTTTTA
1 ACCCGGAGGTTTTA
340291 ATTTTCTAGA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.30, C:0.20, G:0.22, T:0.28
Consensus pattern (20 bp):
ACCCGGAGGTTTTACAAATG
Found at i:340387 original size:20 final size:20
Alignment explanation
Indices: 340362--340409 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
340352 TCCTACCTTA
* * *
340362 AGGTTTTATAGATGACCCTG
1 AGGTTTTACAAATGACCCGG
*
340382 AGGTTTTACAAATTACCCGG
1 AGGTTTTACAAATGACCCGG
340402 AGGTTTTA
1 AGGTTTTA
340410 ATTTTCTAGA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.27, C:0.15, G:0.23, T:0.35
Consensus pattern (20 bp):
AGGTTTTACAAATGACCCGG
Found at i:340426 original size:119 final size:119
Alignment explanation
Indices: 340018--340872 Score: 1415
Period size: 119 Copynumber: 7.2 Consensus size: 119
340008 AAAACATCAT
*
340018 ACCCTGAGGTTTTACAAATTACCCGGAGGTTTTAATTTTCTATAACATTAAATGAGAAACTTTGT
1 ACCCTGAGGTTTTACAAATTACCCGGAGGTTTTAATTTTCTAGAACATTAAATGAGAAACTTTGT
340083 TTATTACTTTCTCATTTTCATGCGAAAACATCCTACCCTGAGGTTTTACAGATG
66 TTATTACTTTCTCATTTTCATGCGAAAACATCCTACCCTGAGGTTTTACAGATG
* * * *
340137 ACCCGGAGGTTTTACAAATTACTCGAAGGTTTTAATTTTCTAGAACATTAAATGACAAACTTTGT
1 ACCCTGAGGTTTTACAAATTACCCGGAGGTTTTAATTTTCTAGAACATTAAATGAGAAACTTTGT
* *
340202 TTATTACTTTCTCATTTTCATGCGAAAAAAATCCTACCCTGAGGTTTTACAAATG
66 TTATTACTTTCTCATTTTCATGCG-AAAACATCCTACCCTGAGGTTTTACAGATG
* * *
340257 ACCCGGAGGATTTACAAATTACCCGGAGGTTTTAATTTTCTAGAACATTAAATGAGAAACTTTGG
1 ACCCTGAGGTTTTACAAATTACCCGGAGGTTTTAATTTTCTAGAACATTAAATGAGAAACTTTGT
* * * *
340322 TTATTACTTTCTCATTTTCATGAGAAAACATCCTACCTTAAGGTTTTATAGATG
66 TTATTACTTTCTCATTTTCATGCGAAAACATCCTACCCTGAGGTTTTACAGATG
*
340376 ACCCTGAGGTTTTACAAATTACCCGGAGGTTTTAATTTTCTAGAACATTAAATGAGAAACTTTGG
1 ACCCTGAGGTTTTACAAATTACCCGGAGGTTTTAATTTTCTAGAACATTAAATGAGAAACTTTGT
* *
340441 TTATTACTTTCTCATTTTCAAGCAAAAACATCCTACCCTGAGGTTTTACAGATG
66 TTATTACTTTCTCATTTTCATGCGAAAACATCCTACCCTGAGGTTTTACAGATG
* *
340495 ACCTTGAGGTTTTACAAATTACCCGGAGGTTTTAATTTTCTATAACATTAAATGAGAAACTTTGT
1 ACCCTGAGGTTTTACAAATTACCCGGAGGTTTTAATTTTCTAGAACATTAAATGAGAAACTTTGT
*
340560 TTATTACTTTCTCATTTTCATGCGAAAATATCCTACCCTGAGGTTTTACAGATG
66 TTATTACTTTCTCATTTTCATGCGAAAACATCCTACCCTGAGGTTTTACAGATG
* *
340614 ACCCTGAGGTTTTACAAATTACCCGGAGGTTTTAATTTTCTATAACATTAAATGAGAACCTTTGT
1 ACCCTGAGGTTTTACAAATTACCCGGAGGTTTTAATTTTCTAGAACATTAAATGAGAAACTTTGT
340679 TTATTACTTTCTCATTTTCATGCGAAAACATCCTACCCTGAGGTTTTACAGATG
66 TTATTACTTTCTCATTTTCATGCGAAAACATCCTACCCTGAGGTTTTACAGATG
* * *
340733 ACCCGGAGGATTTACAAATTACCCGGAGGTTTTAATTTTCTAGAACATTAAATGAGAAACTTTGA
1 ACCCTGAGGTTTTACAAATTACCCGGAGGTTTTAATTTTCTAGAACATTAAATGAGAAACTTTGT
* *
340798 TTATTACTTTCTCATTTTTCATGCGAAAATATCCTACCCCGAGGTTTTACAGATG
66 TTATTACTTTCTCA-TTTTCATGCGAAAACATCCTACCCTGAGGTTTTACAGATG
* *
340853 A-CCTGGAAGATTTACAAATT
1 ACCCT-GAGGTTTTACAAATT
340873 TGTGGAAAAT
Statistics
Matches: 689, Mismatches: 44, Indels: 5
0.93 0.06 0.01
Matches are distributed among these distances:
119 525 0.76
120 164 0.24
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.37
Consensus pattern (119 bp):
ACCCTGAGGTTTTACAAATTACCCGGAGGTTTTAATTTTCTAGAACATTAAATGAGAAACTTTGT
TTATTACTTTCTCATTTTCATGCGAAAACATCCTACCCTGAGGTTTTACAGATG
Found at i:340523 original size:20 final size:20
Alignment explanation
Indices: 340474--340528 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 20
340464 AAAAACATCC
*
340474 TACCCTGAGGTTTTACAGAT
1 TACCCTGAGGTTTTACAAAT
* *
340494 GACCTTGAGGTTTTACAAAT
1 TACCCTGAGGTTTTACAAAT
*
340514 TACCCGGAGGTTTTA
1 TACCCTGAGGTTTTA
340529 ATTTTCTATA
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.25, C:0.18, G:0.22, T:0.35
Consensus pattern (20 bp):
TACCCTGAGGTTTTACAAAT
Found at i:340619 original size:20 final size:20
Alignment explanation
Indices: 340594--340647 Score: 81
Period size: 20 Copynumber: 2.7 Consensus size: 20
340584 AAAATATCCT
*
340594 ACCCTGAGGTTTTACAGATG
1 ACCCTGAGGTTTTACAAATG
*
340614 ACCCTGAGGTTTTACAAATT
1 ACCCTGAGGTTTTACAAATG
*
340634 ACCCGGAGGTTTTA
1 ACCCTGAGGTTTTA
340648 ATTTTCTATA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.26, C:0.20, G:0.22, T:0.31
Consensus pattern (20 bp):
ACCCTGAGGTTTTACAAATG
Found at i:340741 original size:20 final size:20
Alignment explanation
Indices: 340713--340766 Score: 72
Period size: 20 Copynumber: 2.7 Consensus size: 20
340703 AAAACATCCT
* *
340713 ACCCTGAGGTTTTACAGATG
1 ACCCGGAGGTTTTACAAATG
* *
340733 ACCCGGAGGATTTACAAATT
1 ACCCGGAGGTTTTACAAATG
340753 ACCCGGAGGTTTTA
1 ACCCGGAGGTTTTA
340767 ATTTTCTAGA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.28, C:0.20, G:0.24, T:0.28
Consensus pattern (20 bp):
ACCCGGAGGTTTTACAAATG
Found at i:343600 original size:22 final size:22
Alignment explanation
Indices: 343562--343673 Score: 83
Period size: 22 Copynumber: 5.1 Consensus size: 22
343552 TCTTTTCTCT
343562 TTTATTTTTTTATTTTTATTTTTC
1 TTTA-TTTTTTA-TTTTATTTTTC
*
343586 TTTATTTTTTATTTTTATTTTTA
1 TTTATTTTTTA-TTTTATTTTTC
* *
343609 TTT-TTCTTTA-TTT-TTATT-
1 TTTATTTTTTATTTTATTTTTC
*
343627 TTTATTTTTCT-TTTTCTTTTTC
1 TTTATTTTT-TATTTTATTTTTC
* *
343649 TTT-TTATTTTTTTTTCTTTTTC
1 TTTATT-TTTTATTTTATTTTTC
343671 TTT
1 TTT
343674 CCTTTTTCTT
Statistics
Matches: 76, Mismatches: 5, Indels: 16
0.78 0.05 0.16
Matches are distributed among these distances:
18 3 0.04
19 8 0.11
20 7 0.09
21 7 0.09
22 26 0.34
23 21 0.28
24 4 0.05
ACGTcount: A:0.10, C:0.06, G:0.00, T:0.84
Consensus pattern (22 bp):
TTTATTTTTTATTTTATTTTTC
Found at i:343612 original size:28 final size:29
Alignment explanation
Indices: 343568--343673 Score: 155
Period size: 28 Copynumber: 3.7 Consensus size: 29
343558 CTCTTTTATT
343568 TTTTTATTTTTATTTTTCTTTATTTTTTA
1 TTTTTATTTTTATTTTTCTTTATTTTTTA
343597 TTTTTATTTTTATTTTTCTTTA-TTTTTA
1 TTTTTATTTTTATTTTTCTTTATTTTTTA
* *
343625 TTTTTATTTTTCTTTTTCTTTTTCTTTTTA
1 TTTTTATTTTTATTTTTCTTTAT-TTTTTA
*
343655 -TTTT-TTTTTCTTTTTCTTT
1 TTTTTATTTTTATTTTTCTTT
343674 CCTTTTTCTT
Statistics
Matches: 73, Mismatches: 2, Indels: 5
0.91 0.03 0.06
Matches are distributed among these distances:
28 41 0.56
29 26 0.36
30 6 0.08
ACGTcount: A:0.09, C:0.07, G:0.00, T:0.84
Consensus pattern (29 bp):
TTTTTATTTTTATTTTTCTTTATTTTTTA
Found at i:343668 original size:6 final size:6
Alignment explanation
Indices: 343539--343690 Score: 113
Period size: 6 Copynumber: 26.3 Consensus size: 6
343529 CTTGATTCAA
* * * *
343539 TTTCTT CTTC-T TTTCTT TTCTCTT TTATTTT TTTATT TTTATT TTTCTT
1 TTTCTT TTTCTT TTTCTT TT-TCTT TT-TCTT TTTCTT TTTCTT TTTCTT
* * * * * * *
343588 TAT-TT TTTATT TTTATT TTTATT TTTC-- TTTATT TTTATT TTTATT
1 TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT
* *
343633 TTTCTT TTTCTT TTTCTT TTT-AT TTT-TT TTTCTT TTTC-T TTCCTT
1 TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT
343678 TTTC-T TTTCTT TT
1 TTTCTT TTTCTT TT
343691 GGATGAGTAT
Statistics
Matches: 123, Mismatches: 15, Indels: 16
0.80 0.10 0.10
Matches are distributed among these distances:
4 3 0.02
5 25 0.20
6 84 0.68
7 11 0.09
ACGTcount: A:0.07, C:0.11, G:0.00, T:0.82
Consensus pattern (6 bp):
TTTCTT
Found at i:343680 original size:1 final size:1
Alignment explanation
Indices: 343561--343669 Score: 65
Period size: 1 Copynumber: 109.0 Consensus size: 1
343551 TTCTTTTCTC
* * * * * * * * * * *
343561 TTTTATTTTTTTATTTTTATTTTTCTTTATTTTTTATTTTTATTTTTATTTTTCTTTATTTTTAT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* * * * * *
343626 TTTTATTTTTCTTTTTCTTTTTCTTTTTATTTTTTTTTCTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
343670 CTTTCCTTTT
Statistics
Matches: 74, Mismatches: 34, Indels: 0
0.69 0.31 0.00
Matches are distributed among these distances:
1 74 1.00
ACGTcount: A:0.10, C:0.06, G:0.00, T:0.84
Consensus pattern (1 bp):
T
Found at i:343680 original size:22 final size:21
Alignment explanation
Indices: 343540--343690 Score: 81
Period size: 22 Copynumber: 6.8 Consensus size: 21
343530 TTGATTCAAT
* *
343540 TTCTTCTTCTTTTCTTTTCTCTT
1 TTCTTTTTC-TTTCTTTT-TTTT
* *
343563 TTATTTTT-TTAT-TTTTATTT
1 TTCTTTTTCTT-TCTTTTTTTT
* *
343583 TTCTTTATTTTTTATTTTTATTT
1 TTCTTT-TTCTTTCTTTTT-TTT
* *
343606 TTATTTTTCTTTATTTTTATTT
1 TTCTTTTTCTTTCTTTTT-TTT
*
343628 TTATTTTTCTTTTTCTTTTTCTTT
1 TTCTTTTTC--TTTCTTTTT-TTT
* * *
343652 TTATTTTTTTTTCTTTTTCTT
1 TTCTTTTTCTTTCTTTTTTTT
*
343673 TCCTTTTTCTTTTCTTTT
1 TTCTTTTTC-TTTCTTTT
343691 GGATGAGTAT
Statistics
Matches: 105, Mismatches: 15, Indels: 17
0.77 0.11 0.12
Matches are distributed among these distances:
20 7 0.07
21 17 0.16
22 48 0.46
23 14 0.13
24 19 0.18
ACGTcount: A:0.07, C:0.11, G:0.00, T:0.81
Consensus pattern (21 bp):
TTCTTTTTCTTTCTTTTTTTT
Found at i:343680 original size:28 final size:29
Alignment explanation
Indices: 343549--343685 Score: 145
Period size: 28 Copynumber: 4.7 Consensus size: 29
343539 TTTCTTCTTC
*
343549 TTTTCTTTTCTCTTTTATTTTTTTATTTTTAT
1 TTTTC-TTTCT-TTTT-TATTTTTATTTTTAT
*
343581 TTTTCTTTATTTTTTATTTTTATTTTTAT
1 TTTTCTTTCTTTTTTATTTTTATTTTTAT
* *
343610 TTTTCTTT-ATTTTTATTTTTATTTTTCT
1 TTTTCTTTCTTTTTTATTTTTATTTTTAT
* *
343638 TTTTCTTTTTCTTTTTA-TTTT-TTTTTCT
1 TTTTCTTTCT-TTTTTATTTTTATTTTTAT
* *
343666 TTTTCTTTCCTTTTTCTTTT
1 TTTTCTTTCTTTTTTATTTT
343686 CTTTTGGATG
Statistics
Matches: 94, Mismatches: 8, Indels: 10
0.84 0.07 0.09
Matches are distributed among these distances:
27 5 0.05
28 44 0.47
29 26 0.28
30 10 0.11
31 4 0.04
32 5 0.05
ACGTcount: A:0.08, C:0.09, G:0.00, T:0.82
Consensus pattern (29 bp):
TTTTCTTTCTTTTTTATTTTTATTTTTAT
Found at i:351249 original size:27 final size:29
Alignment explanation
Indices: 351190--351250 Score: 74
Period size: 27 Copynumber: 2.2 Consensus size: 29
351180 CTTTATGTCT
* *
351190 TTATTATTATTTTAATTATCCATTATATA
1 TTATTATTATTTTAAATATCCAGTATATA
*
351219 -TATT-TTATTTTAAATAT-TAGTATATA
1 TTATTATTATTTTAAATATCCAGTATATA
351245 TTATTA
1 TTATTA
351251 GGATATATCT
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
26 7 0.26
27 16 0.59
28 4 0.15
ACGTcount: A:0.36, C:0.03, G:0.02, T:0.59
Consensus pattern (29 bp):
TTATTATTATTTTAAATATCCAGTATATA
Found at i:352490 original size:3 final size:3
Alignment explanation
Indices: 352482--352540 Score: 59
Period size: 3 Copynumber: 19.7 Consensus size: 3
352472 GTATTTTTTG
* **
352482 TAA TAA TAA -ATA TATA TAA TAA TAT TAA TAA TAA TTG TAA T-A TAA
1 TAA TAA TAA TA-A TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
352527 TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TA
352541 TATAGTCTCG
Statistics
Matches: 47, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
2 3 0.06
3 39 0.83
4 5 0.11
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (3 bp):
TAA
Found at i:352762 original size:23 final size:23
Alignment explanation
Indices: 352736--352790 Score: 74
Period size: 23 Copynumber: 2.4 Consensus size: 23
352726 TTTTAGAATC
352736 ATATTATTTATTTAATTGAAATA
1 ATATTATTTATTTAATTGAAATA
* * *
352759 ATATTAATTATTTATTTTAAATA
1 ATATTATTTATTTAATTGAAATA
*
352782 ATGTTATTT
1 ATATTATTT
352791 TTAAATTATC
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (23 bp):
ATATTATTTATTTAATTGAAATA
Found at i:352804 original size:15 final size:15
Alignment explanation
Indices: 352764--352805 Score: 50
Period size: 16 Copynumber: 2.8 Consensus size: 15
352754 AAATAATATT
352764 AATTATTTA-TTTTA
1 AATTATTTATTTTTA
*
352778 AATAATGTTATTTTTA
1 AATTAT-TTATTTTTA
*
352794 AATTATCTATTT
1 AATTATTTATTT
352806 AATTTTAAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
14 5 0.22
15 8 0.35
16 10 0.43
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.60
Consensus pattern (15 bp):
AATTATTTATTTTTA
Found at i:352932 original size:14 final size:14
Alignment explanation
Indices: 352892--352932 Score: 55
Period size: 15 Copynumber: 2.9 Consensus size: 14
352882 ATTTAAAATT
*
352892 AAATAGATAATTTA
1 AAATAAATAATTTA
*
352906 AAATAATATAATTTC
1 AAATAA-ATAATTTA
352921 AAATAAATAATT
1 AAATAAATAATT
352933 AATTTTATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
14 11 0.46
15 13 0.54
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.37
Consensus pattern (14 bp):
AAATAAATAATTTA
Found at i:352935 original size:23 final size:23
Alignment explanation
Indices: 352909--352953 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
352899 TAATTTAAAA
*
352909 TAATATAATTTCAAATAAATAAT
1 TAATATAATTTCAAAAAAATAAT
* * *
352932 TAATTTTATTTTAAAAAAATAA
1 TAATATAATTTCAAAAAAATAA
352954 ATAAATATTT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (23 bp):
TAATATAATTTCAAAAAAATAAT
Found at i:356850 original size:3 final size:3
Alignment explanation
Indices: 356833--356878 Score: 67
Period size: 3 Copynumber: 15.7 Consensus size: 3
356823 GAGTTCTAAT
* *
356833 TTA TCA TTA -TA TTA TTA TTA TTA TTA TTA CTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
356879 TTTTATTTTC
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
2 2 0.05
3 36 0.95
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:363215 original size:2 final size:2
Alignment explanation
Indices: 363210--363250 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
363200 TATATTTTAT
363210 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
363251 TTCTTTAATA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:367777 original size:182 final size:182
Alignment explanation
Indices: 367443--367977 Score: 957
Period size: 182 Copynumber: 2.9 Consensus size: 182
367433 ATTAAATCCG
*
367443 TAAAGCTGAGCTATTCCACTAAGGCAATGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGAA
1 TAAAGCTGAGCTATTCCACTAAGGCATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGAA
367508 TAGATTATGTTCAAACTATGACACTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTGCTTT
66 TAGATTATGTTCAAACTATGACACTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTGCTTT
367573 TGTCAGGCCAAAGACTTTGTGATGAGATGAACCCTTCAGTGATTTGTCCCTC
131 TGTCAGGCCAAAGACTTTGTGATGAGATGAACCCTTCAGTGATTTGTCCCTC
367625 TAAAGCTGAGCTATTCCACTAAGGCAGTTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
1 TAAAGCTGAGCTATTCCACTAAGGCA-TTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
*
367690 ATAGATTATGTTCAAACTATGACACTGCTCGGACACTTGGCAATTCAGTGTTTGCTCCACTGC-T
65 ATAGATTATGTTCAAACTATGACACTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTGCTT
*
367754 TTGTCAGGCCAAAGACTTTGTGATGAGACGAACCCTTCAGTGATTTGTCCCTC
130 TTGTCAGGCCAAAGACTTTGTGATGAGATGAACCCTTCAGTGATTTGTCCCTC
367807 TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
1 TAAAGCTGAGCTATTCCACTAAGGC-ATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
** * *
367872 ATAGATTACATTCAAA-TCATGACATTGCTCGGACACTTGGCAATTCGGTGTTTTCTCCACTGCT
65 ATAGATTATGTTCAAACT-ATGACACTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTGCT
*
367936 TTTGTCAGGTCAAAGACTTTGTGATGAGATGAACCCTTCAGT
129 TTTGTCAGGCCAAAGACTTTGTGATGAGATGAACCCTTCAGT
367978 TAAACCTGAT
Statistics
Matches: 339, Mismatches: 10, Indels: 7
0.95 0.03 0.02
Matches are distributed among these distances:
181 1 0.00
182 198 0.58
183 140 0.41
ACGTcount: A:0.27, C:0.21, G:0.22, T:0.30
Consensus pattern (182 bp):
TAAAGCTGAGCTATTCCACTAAGGCATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGAA
TAGATTATGTTCAAACTATGACACTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTGCTTT
TGTCAGGCCAAAGACTTTGTGATGAGATGAACCCTTCAGTGATTTGTCCCTC
Found at i:369210 original size:72 final size:75
Alignment explanation
Indices: 369123--369293 Score: 208
Period size: 72 Copynumber: 2.3 Consensus size: 75
369113 GATGATTATC
* * *
369123 TCACTCAA-ATTTGTTTTTCTTAAAACATA-CTTTGTCTCACTTGAGACTGTTTT-TCTCGAAAG
1 TCACTCAAGA-TTGTTTTTCTTAAAACA-AGATTTGTCTCACTTGAGACCGTTTTCACTCGAAAG
369185 AA-TA-TTCATT
64 AAGTATTTCATT
**
369195 TCACTCAAGATTGTTTTTCTTAAAACAAGATTTGTCTTGCTTGAGACCGTTTTCACTCGAAAGAA
1 TCACTCAAGATTGTTTTTCTTAAAACAAGATTTGTCTCACTTGAGACCGTTTTCACTCGAAAGAA
369260 TGTATTTCATT
66 -GTATTTCATT
** *
369271 TCACTCAAGGCTGTTTTTTTTAA
1 TCACTCAAGATTGTTTTTCTTAA
369294 GAAGATTTTA
Statistics
Matches: 85, Mismatches: 8, Indels: 8
0.84 0.08 0.08
Matches are distributed among these distances:
71 1 0.01
72 45 0.53
73 11 0.13
75 2 0.02
76 26 0.31
ACGTcount: A:0.27, C:0.18, G:0.12, T:0.43
Consensus pattern (75 bp):
TCACTCAAGATTGTTTTTCTTAAAACAAGATTTGTCTCACTTGAGACCGTTTTCACTCGAAAGAA
GTATTTCATT
Found at i:369352 original size:39 final size:39
Alignment explanation
Indices: 369309--369461 Score: 101
Period size: 39 Copynumber: 3.6 Consensus size: 39
369299 TTTTATCTTG
*
369309 CTTGAGATAGTTTCCCTCGAAACAGAAAATTTTGTCTCC
1 CTTGAGACAGTTTCCCTCGAAACAGAAAATTTTGTCTCC
** * *
369348 CTTGAGACAGTTTCTTTTGAAAACATTTCCCTTGAAATTAATTTTTTCTCTC
1 CTTGAGACAGTTTCCCTCG-AAACA--------G-AA--AATTTTGTCTC-C
* *
369400 C-TCAGATAGTTTCCCTCGAAACAGAAAATTTTGTCTCC
1 CTTGAGACAGTTTCCCTCGAAACAGAAAATTTTGTCTCC
* *
369438 CTTGAGACAGTTTCTCTTGAAACA
1 CTTGAGACAGTTTCCCTCGAAACA
369462 TAAACATTGA
Statistics
Matches: 85, Mismatches: 15, Indels: 28
0.66 0.12 0.22
Matches are distributed among these distances:
38 2 0.02
39 43 0.51
40 5 0.06
41 2 0.02
42 1 0.01
48 1 0.01
49 2 0.02
50 5 0.06
51 22 0.26
52 2 0.02
ACGTcount: A:0.27, C:0.22, G:0.13, T:0.37
Consensus pattern (39 bp):
CTTGAGACAGTTTCCCTCGAAACAGAAAATTTTGTCTCC
Found at i:369472 original size:104 final size:104
Alignment explanation
Indices: 369364--369681 Score: 498
Period size: 104 Copynumber: 3.1 Consensus size: 104
369354 ACAGTTTCTT
* * *
369364 TTGAAAACATTTCCCTTGAAATTAATTTTTTCTCTCCTCAGATAGTTTCCCTCGAAACAGAAAAT
1 TTGAAAACATTTCCCTTGAAATGAATTTTTTCTCTCTTGAGATAGTTTCCCTCGAAACAGAAAAT
369429 TTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACA
66 TTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACA
*
369468 TTGAAAACATTTCCCTTGAAATGATTTTTTTCTCTCTTGAGATAGTTTCCCTCGAAACAGAAAAT
1 TTGAAAACATTTCCCTTGAAATGAATTTTTTCTCTCTTGAGATAGTTTCCCTCGAAACAGAAAAT
369533 TTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACA
66 TTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACA
* * * * * *
369572 TTGAAAACATTTCCCTAGAAATGAATTTTATCTCGCTTGAGACAGCTTCCCTTGAAAC-G--AAT
1 TTGAAAACATTTCCCTTGAAATGAATTTTTTCTCTCTTGAGATAGTTTCCCTCGAAACAGAAAAT
** *
369634 TTTGTCTCCCTTGAGACAGTTTCTCTCCAAACATAAACT
66 TTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACA
369673 TTGAAAACA
1 TTGAAAACA
369682 ATTTAACGAA
Statistics
Matches: 200, Mismatches: 14, Indels: 3
0.92 0.06 0.01
Matches are distributed among these distances:
101 48 0.24
103 1 0.00
104 151 0.75
ACGTcount: A:0.31, C:0.22, G:0.12, T:0.36
Consensus pattern (104 bp):
TTGAAAACATTTCCCTTGAAATGAATTTTTTCTCTCTTGAGATAGTTTCCCTCGAAACAGAAAAT
TTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACA
Found at i:369634 original size:36 final size:36
Alignment explanation
Indices: 369582--369652 Score: 106
Period size: 36 Copynumber: 2.0 Consensus size: 36
369572 TTGAAAACAT
* *
369582 TTCCCTAGAAATGAATTTTATCTCGCTTGAGACAGC
1 TTCCCTAGAAACGAATTTTATCTCCCTTGAGACAGC
* *
369618 TTCCCTTGAAACGAATTTTGTCTCCCTTGAGACAG
1 TTCCCTAGAAACGAATTTTATCTCCCTTGAGACAG
369653 TTTCTCTCCA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.25, C:0.24, G:0.17, T:0.34
Consensus pattern (36 bp):
TTCCCTAGAAACGAATTTTATCTCCCTTGAGACAGC
Found at i:370055 original size:105 final size:105
Alignment explanation
Indices: 369856--370429 Score: 845
Period size: 105 Copynumber: 5.5 Consensus size: 105
369846 ATATCGTGAC
* ** * *
369856 ACTCGAGACAACATAAGTTCAACTTCACAACGAAGGGACGGCTGATTGTCAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACAACGAAGGGACCGCTGCTTGTCAAC-AACAACTTCTC
369921 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
65 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* *
369962 ACTCCAGACAACGCAAGTTCAACTTCACAACGAAGGGACTGCTGCTTGTCAAAAACAACTTCTCA
1 ACTCCAGACAACGCAAGTTCAACTTCACAACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCA
* *
370027 ATTTCAGAGCCAATTTAAACTTCGCAACGAAGGATATTGG
66 ATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * *
370067 ACTTCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCA
1 ACTCCAGACAACGCAAGTTCAACTTCACAACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCA
* *
370132 ATCTCAGAGCCAATTTCAACTTCACAACGAAAGATATTGG
66 ATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * *
370172 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGTTGCTTGTCAACAACAACTTCCCA
1 ACTCCAGACAACGCAAGTTCAACTTCACAACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCA
*
370237 ATCTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 ATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * *
370277 ACTCCAGACAACGCAAGTTCAACTCCACGACGAAGGGACCGCTGCTTGTTAACAA-AA-TT-TC-
1 ACTCCAGACAACGCAAGTTCAACTTCACAACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCA
** *
370338 A-TTCAGAGTAAATTTCAACTTCACAGCGAAGGATATTGG
66 ATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * *
370377 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGA-CGACTGGTTGTCAAC
1 ACTCCAGACAACGCAAGTTCAACTTCACAACGAAGGGACCG-CTGCTTGTCAAC
370430 TTCACGACGG
Statistics
Matches: 433, Mismatches: 34, Indels: 8
0.91 0.07 0.02
Matches are distributed among these distances:
99 2 0.00
100 78 0.18
101 1 0.00
102 1 0.00
103 2 0.00
104 2 0.00
105 300 0.69
106 47 0.11
ACGTcount: A:0.35, C:0.26, G:0.18, T:0.22
Consensus pattern (105 bp):
ACTCCAGACAACGCAAGTTCAACTTCACAACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCA
ATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
Found at i:371494 original size:18 final size:17
Alignment explanation
Indices: 371455--371497 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
371445 ATTATATTGA
371455 TATT-TTATTCATTTAT
1 TATTATTATTCATTTAT
*
371471 TTTTATTATTCATGTTAT
1 TATTATTATTCAT-TTAT
371489 TATTATTAT
1 TATTATTAT
371498 ATGTATATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 3 0.13
17 8 0.35
18 12 0.52
ACGTcount: A:0.26, C:0.05, G:0.02, T:0.67
Consensus pattern (17 bp):
TATTATTATTCATTTAT
Found at i:376248 original size:27 final size:28
Alignment explanation
Indices: 376213--376265 Score: 72
Period size: 27 Copynumber: 1.9 Consensus size: 28
376203 TTTATCTTTA
**
376213 TTTTCTATTTTTTATTTTTAGAAAATAG
1 TTTTCTATTTTCAATTTTTAGAAAATAG
*
376241 TTTT-TATTTTCAATTTTTTGAAAAT
1 TTTTCTATTTTCAATTTTTAGAAAAT
376266 TTGGAAATAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 18 0.82
28 4 0.18
ACGTcount: A:0.28, C:0.04, G:0.06, T:0.62
Consensus pattern (28 bp):
TTTTCTATTTTCAATTTTTAGAAAATAG
Found at i:376980 original size:15 final size:16
Alignment explanation
Indices: 376946--376984 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
376936 TCAATAAATT
376946 AAATATAAAATACTACA
1 AAAT-TAAAATACTACA
*
376963 AAATTAAATTACTA-A
1 AAATTAAAATACTACA
376978 AAATTAA
1 AAATTAA
376985 TATAAAGAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 8 0.38
16 9 0.43
17 4 0.19
ACGTcount: A:0.64, C:0.08, G:0.00, T:0.28
Consensus pattern (16 bp):
AAATTAAAATACTACA
Found at i:382348 original size:18 final size:19
Alignment explanation
Indices: 382313--382351 Score: 62
Period size: 20 Copynumber: 2.1 Consensus size: 19
382303 TCATTTAAGG
382313 AGTATCGATACCTAAAGGGT
1 AGTATCGATACC-AAAGGGT
382333 AGTATCGATACC-AAGGGT
1 AGTATCGATACCAAAGGGT
382351 A
1 A
382352 CTGATACCAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 7 0.37
20 12 0.63
ACGTcount: A:0.36, C:0.15, G:0.26, T:0.23
Consensus pattern (19 bp):
AGTATCGATACCAAAGGGT
Found at i:383154 original size:21 final size:21
Alignment explanation
Indices: 383060--383178 Score: 105
Period size: 21 Copynumber: 5.6 Consensus size: 21
383050 TCGAGAGTTC
*
383060 TATGTGGTCCTTTGGGACATA
1 TATGTGGTCCTTTGGAACATA
** *
383081 TATGTAATCTTTTGGAACATA
1 TATGTGGTCCTTTGGAACATA
* * *
383102 TATGTGGTTCGTTGGAACACA
1 TATGTGGTCCTTTGGAACATA
* * *
383123 TATTTGGTCCTTTAGAATATA
1 TATGTGGTCCTTTGGAACATA
*
383144 TATGTGGTCCTTAAGGAGA-ATTA
1 TATGTGGTCCTT-TGGA-ACA-TA
383167 TATGTGGTCCTT
1 TATGTGGTCCTT
383179 CGGGATAAAT
Statistics
Matches: 76, Mismatches: 19, Indels: 4
0.77 0.19 0.04
Matches are distributed among these distances:
21 58 0.76
22 3 0.04
23 15 0.20
ACGTcount: A:0.25, C:0.12, G:0.23, T:0.40
Consensus pattern (21 bp):
TATGTGGTCCTTTGGAACATA
Found at i:383194 original size:24 final size:23
Alignment explanation
Indices: 383142--383196 Score: 65
Period size: 23 Copynumber: 2.3 Consensus size: 23
383132 CTTTAGAATA
*
383142 TATATGTGGTCCTTAAGGAGAAT
1 TATATGTGGTCCTTAAGGAAAAT
**
383165 TATATGTGGTCCTTCGGGATAAAT
1 TATATGTGGTCCTTAAGGA-AAAT
*
383189 TCTATGTG
1 TATATGTG
383197 CCCCTAGTGG
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
23 17 0.63
24 10 0.37
ACGTcount: A:0.25, C:0.11, G:0.25, T:0.38
Consensus pattern (23 bp):
TATATGTGGTCCTTAAGGAAAAT
Found at i:385217 original size:21 final size:21
Alignment explanation
Indices: 385191--385239 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
385181 TTTCCCGAAA
*
385191 GACCTCATGTATGTCCAGAAG
1 GACCTCATATATGTCCAGAAG
* *
385212 GACCTCGTATATGTCCCGAAG
1 GACCTCATATATGTCCAGAAG
385233 GACCTCA
1 GACCTCA
385240 AATAACCCTC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.27, C:0.29, G:0.22, T:0.22
Consensus pattern (21 bp):
GACCTCATATATGTCCAGAAG
Found at i:385821 original size:20 final size:20
Alignment explanation
Indices: 385796--385866 Score: 101
Period size: 20 Copynumber: 3.5 Consensus size: 20
385786 ATTTCAAAAT
385796 GGTATCGATACATGCCTTAG
1 GGTATCGATACATGCCTTAG
385816 GGTATCGATACATGCCTTAG
1 GGTATCGATACATGCCTTAG
*
385836 GGTATCGATA-ATACCTTTTA-
1 GGTATCGATACATGCC--TTAG
385856 GGTATCGATAC
1 GGTATCGATAC
385867 CCGTTGAATA
Statistics
Matches: 47, Mismatches: 1, Indels: 5
0.89 0.02 0.09
Matches are distributed among these distances:
19 4 0.09
20 40 0.85
21 3 0.06
ACGTcount: A:0.27, C:0.18, G:0.23, T:0.32
Consensus pattern (20 bp):
GGTATCGATACATGCCTTAG
Found at i:388992 original size:21 final size:21
Alignment explanation
Indices: 388966--389018 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
388956 TTTCCCGAAA
*
388966 GACCTCATGTATGTCCAGAAG
1 GACCTCATATATGTCCAGAAG
* *
388987 GACCTCGTATATGTCCCGAAG
1 GACCTCATATATGTCCAGAAG
389008 GACCTCATATA
1 GACCTCATATA
389019 ACCCTCGACT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.28, C:0.26, G:0.21, T:0.25
Consensus pattern (21 bp):
GACCTCATATATGTCCAGAAG
Found at i:389602 original size:20 final size:20
Alignment explanation
Indices: 389577--389647 Score: 101
Period size: 20 Copynumber: 3.5 Consensus size: 20
389567 ATTTCAAAAT
389577 GGTATCGATACATGCCTTAG
1 GGTATCGATACATGCCTTAG
389597 GGTATCGATACATGCCTTAG
1 GGTATCGATACATGCCTTAG
*
389617 GGTATCGATA-ATACCTTTTA-
1 GGTATCGATACATGCC--TTAG
389637 GGTATCGATAC
1 GGTATCGATAC
389648 CCGTTGAATA
Statistics
Matches: 47, Mismatches: 1, Indels: 5
0.89 0.02 0.09
Matches are distributed among these distances:
19 4 0.09
20 40 0.85
21 3 0.06
ACGTcount: A:0.27, C:0.18, G:0.23, T:0.32
Consensus pattern (20 bp):
GGTATCGATACATGCCTTAG
Found at i:395347 original size:21 final size:21
Alignment explanation
Indices: 395321--395379 Score: 82
Period size: 21 Copynumber: 2.8 Consensus size: 21
395311 AAAATTTGTT
* *
395321 CCGAAGGACCTCATGTATGTG
1 CCGAAGGACCTCATATATGTC
*
395342 CCGAAGGACCTCGTATATGTC
1 CCGAAGGACCTCATATATGTC
*
395363 CCGAATGACCTCATATA
1 CCGAAGGACCTCATATA
395380 ACCCTCGACT
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.27, C:0.27, G:0.22, T:0.24
Consensus pattern (21 bp):
CCGAAGGACCTCATATATGTC
Found at i:397743 original size:86 final size:88
Alignment explanation
Indices: 397612--397782 Score: 274
Period size: 86 Copynumber: 2.0 Consensus size: 88
397602 CATAAAGCTA
** *
397612 TCCAAAAATGTTATGCATTTGAAAAAAATTGATATCAATTTTTAGAGATATATCATTTGCAATAA
1 TCCAAAAATGTTATGCATTT-AAAAAAATTGATATCAATAGTTAGAGAGATATCATTTGCAATAA
397677 ATCACAAGCATAAACATTTATACT
65 ATCACAAGCATAAACATTTATACT
*
397701 TCCAAAAATGTTATGCA-TT-AAAAAATTGATATCAATAGTTAGAGAGATATCATTTGCAATGAA
1 TCCAAAAATGTTATGCATTTAAAAAAATTGATATCAATAGTTAGAGAGATATCATTTGCAATAAA
*
397764 TCACATGCATAAACATTTA
66 TCACAAGCATAAACATTTA
397783 AATTAAGGTA
Statistics
Matches: 77, Mismatches: 5, Indels: 3
0.91 0.06 0.04
Matches are distributed among these distances:
86 58 0.75
88 2 0.03
89 17 0.22
ACGTcount: A:0.44, C:0.12, G:0.11, T:0.33
Consensus pattern (88 bp):
TCCAAAAATGTTATGCATTTAAAAAAATTGATATCAATAGTTAGAGAGATATCATTTGCAATAAA
TCACAAGCATAAACATTTATACT
Found at i:399717 original size:54 final size:53
Alignment explanation
Indices: 399658--399987 Score: 407
Period size: 54 Copynumber: 6.2 Consensus size: 53
399648 TACTATAGAT
* **
399658 ACTAAGTGTGTAACCCACTGAATTCATCATATGTTGATGAATGGTCGTATAGGC
1 ACTAAGTGTGTAACCCAC-GAATTCATCATATGTTGATGAACGACCGTATAGGC
* *
399712 ACTAAGTGTGCAACCCACATAATTCATCATATGTTGATGAACGACCGTATAGGC
1 ACTAAGTGTGTAACCCAC-GAATTCATCATATGTTGATGAACGACCGTATAGGC
* * *
399766 ACTAAGTGTGCAACCCACAAAATTCATCGTATGTTGATGAACGACCGTATAGGC
1 ACTAAGTGTGTAACCCAC-GAATTCATCATATGTTGATGAACGACCGTATAGGC
399820 ACTAAGTGTGTAACCCACGAAATTCATCATATGTTGATGAACGACCGTATAGGC
1 ACTAAGTGTGTAACCCACG-AATTCATCATATGTTGATGAACGACCGTATAGGC
* *
399874 ACTAAGTGTGTAACCCACGAAATTCATCATATGTT-ATTGAACGACCATATATGC
1 ACTAAGTGTGTAACCCACG-AATTCATCATATGTTGA-TGAACGACCGTATAGGC
* * * * * * *
399928 ACTATGTGTGCAAACCAC--A-TAATTCATATGTTTATGAATGACTGTATAGGC
1 ACTAAGTGTGTAACCCACGAATTCA-TCATATGTTGATGAACGACCGTATAGGC
*
399979 ACTACGTGT
1 ACTAAGTGT
399988 TAATCTCAAC
Statistics
Matches: 250, Mismatches: 22, Indels: 11
0.88 0.08 0.04
Matches are distributed among these distances:
50 2 0.01
51 31 0.12
52 1 0.00
53 1 0.00
54 215 0.86
ACGTcount: A:0.33, C:0.20, G:0.19, T:0.28
Consensus pattern (53 bp):
ACTAAGTGTGTAACCCACGAATTCATCATATGTTGATGAACGACCGTATAGGC
Found at i:399844 original size:108 final size:108
Alignment explanation
Indices: 399658--399987 Score: 454
Period size: 108 Copynumber: 3.1 Consensus size: 108
399648 TACTATAGAT
** * **
399658 ACTAAGTGTGTAACCCACTGAATTCATCATATGTTGATGAATGGTCGTATAGGCACTAAGTGTGC
1 ACTAAGTGTGTAACCCACAAAATTCATCATATGTTGATGAACGACCGTATAGGCACTAAGTGTGC
399723 AACCCACATAATTCATCATATGTTGATGAACGACCGTATAGGC
66 AACCCACATAATTCATCATATGTTGATGAACGACCGTATAGGC
* * *
399766 ACTAAGTGTGCAACCCACAAAATTCATCGTATGTTGATGAACGACCGTATAGGCACTAAGTGTGT
1 ACTAAGTGTGTAACCCACAAAATTCATCATATGTTGATGAACGACCGTATAGGCACTAAGTGTGC
399831 AACCCACGA-AATTCATCATATGTTGATGAACGACCGTATAGGC
66 AACCCAC-ATAATTCATCATATGTTGATGAACGACCGTATAGGC
* * * *
399874 ACTAAGTGTGTAACCCACGAAATTCATCATATGTT-ATTGAACGACCATATATGCACTATGTGTG
1 ACTAAGTGTGTAACCCACAAAATTCATCATATGTTGA-TGAACGACCGTATAGGCACTAAGTGTG
* * * *
399938 CAAACCACATAA-T--TCATATGTTTATGAATGACTGTATAGGC
65 CAACCCACATAATTCATCATATGTTGATGAACGACCGTATAGGC
*
399979 ACTACGTGT
1 ACTAAGTGT
399988 TAATCTCAAC
Statistics
Matches: 199, Mismatches: 20, Indels: 9
0.87 0.09 0.04
Matches are distributed among these distances:
105 33 0.17
107 3 0.02
108 162 0.81
109 1 0.01
ACGTcount: A:0.33, C:0.20, G:0.19, T:0.28
Consensus pattern (108 bp):
ACTAAGTGTGTAACCCACAAAATTCATCATATGTTGATGAACGACCGTATAGGCACTAAGTGTGC
AACCCACATAATTCATCATATGTTGATGAACGACCGTATAGGC
Found at i:399849 original size:162 final size:159
Alignment explanation
Indices: 399658--399987 Score: 468
Period size: 162 Copynumber: 2.1 Consensus size: 159
399648 TACTATAGAT
* **
399658 ACTAAGTGTGTAACCCACTGAATTCATCATATGTTGATGAATGGTCGTATAGGCACTAAGTGTGC
1 ACTAAGTGTGTAACCCACTGAATTCATCATATGTTGATGAACGACCGTATAGGCACTAAGTGTGC
* *
399723 AACCCAC-ATAATTCATCATATGTTGA-TGAACGACCGTATAGGCACTAAGTGTGCAACCCACAA
66 AACCCACGA-AATTCATCATATGTT-ATTGAACGACCATATAGGCACTAAGTGTGCAAACCACAA
399786 AATTCATCGTATGTTGATGAACGACCGTATAGGC
129 AATTCA---TATGTTGATGAACGACCGTATAGGC
399820 ACTAAGTGTGTAACCCAC-GAAATTCATCATATGTTGATGAACGACCGTATAGGCACTAAGTGTG
1 ACTAAGTGTGTAACCCACTG-AATTCATCATATGTTGATGAACGACCGTATAGGCACTAAGTGTG
* * * *
399884 TAACCCACGAAATTCATCATATGTTATTGAACGACCATATATGCACTATGTGTGCAAACCACATA
65 CAACCCACGAAATTCATCATATGTTATTGAACGACCATATAGGCACTAAGTGTGCAAACCACAAA
* * *
399949 ATTCATATGTTTATGAATGACTGTATAGGC
130 ATTCATATGTTGATGAACGACCGTATAGGC
*
399979 ACTACGTGT
1 ACTAAGTGT
399988 TAATCTCAAC
Statistics
Matches: 152, Mismatches: 13, Indels: 9
0.87 0.07 0.05
Matches are distributed among these distances:
159 30 0.20
161 2 0.01
162 119 0.78
163 1 0.01
ACGTcount: A:0.33, C:0.20, G:0.19, T:0.28
Consensus pattern (159 bp):
ACTAAGTGTGTAACCCACTGAATTCATCATATGTTGATGAACGACCGTATAGGCACTAAGTGTGC
AACCCACGAAATTCATCATATGTTATTGAACGACCATATAGGCACTAAGTGTGCAAACCACAAAA
TTCATATGTTGATGAACGACCGTATAGGC
Found at i:401301 original size:20 final size:18
Alignment explanation
Indices: 401255--401302 Score: 51
Period size: 20 Copynumber: 2.6 Consensus size: 18
401245 GATGTAATTA
**
401255 GTATCGATACTGATGTGG
1 GTATCGATACTGATGAAG
*
401273 GTATTGATACTGTAATGAAG
1 GTATCGATACTG--ATGAAG
401293 GTATCGATAC
1 GTATCGATAC
401303 CATGGATTCC
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
18 11 0.46
20 13 0.54
ACGTcount: A:0.29, C:0.10, G:0.27, T:0.33
Consensus pattern (18 bp):
GTATCGATACTGATGAAG
Found at i:401388 original size:15 final size:14
Alignment explanation
Indices: 401368--401399 Score: 55
Period size: 15 Copynumber: 2.2 Consensus size: 14
401358 TAATATAGAA
401368 GTATCGATACCAGTG
1 GTATCGATACCAG-G
401383 GTATCGATACCAGG
1 GTATCGATACCAGG
401397 GTA
1 GTA
401400 GAGGTACCGA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.24
15 13 0.76
ACGTcount: A:0.28, C:0.19, G:0.28, T:0.25
Consensus pattern (14 bp):
GTATCGATACCAGG
Found at i:401947 original size:162 final size:162
Alignment explanation
Indices: 401746--402185 Score: 603
Period size: 162 Copynumber: 2.7 Consensus size: 162
401736 ATATGTGTAC
* * * * * *
401746 TATAAGCACTAAGTGTACAACCCACGGAATTTGTCATATGATGATGAACGACTGTATAGGCACTA
1 TATAAGCACTAAGTGTGCAACCCACGAAATTTATCATATGTTGATGAACGACCGTATAGGCATTA
* *
401811 AGTGTGCAACCCATAGAATTCATCATATGTTGATGAACGACCGTATAGGCACTAAGTGTGCAACC
66 AGTGTGCAACCCATAGAATTCATCATATGTTGATGAACGACCGTATAGGCACTAACTGTACAACC
* * *
401876 TATAGAATTCATCATATATTGATGAACGACCG
131 CACAAAATTCATCATATATTGATGAACGACCG
* * * * * *
401908 TATAAGCACTAAGTGTGCAACCCACAAAATTCATCATATGTTGATGAACGACCGCACATGTATTA
1 TATAAGCACTAAGTGTGCAACCCACGAAATTTATCATATGTTGATGAACGACCGTATAGGCATTA
** * * *
401973 AGTGTATAATCC-TCAGAATTCATCATATGTTGATGGACGACCGTATAAGCACTAACTGTACAAC
66 AGTGTGCAACCCAT-AGAATTCATCATATGTTGATGAACGACCGTATAGGCACTAACTGTACAAC
402037 CCACAAAATTCATCATATATTGATGAACGACCG
130 CCACAAAATTCATCATATATTGATGAACGACCG
* *
402070 TATAGGCACTAAATGTGCAACCCACGAAATTTATCATATGTTGATGAACGACCGTATAGGCATTA
1 TATAAGCACTAAGTGTGCAACCCACGAAATTTATCATATGTTGATGAACGACCGTATAGGCATTA
* * * **
402135 AGTGTGCAACCCACAAAATTCATCATATATTGATGAACGACTATATAGGCA
66 AGTGTGCAACCCATAGAATTCATCATATGTTGATGAACGACCGTATAGGCA
402186 TTATGTGTAT
Statistics
Matches: 236, Mismatches: 40, Indels: 4
0.84 0.14 0.01
Matches are distributed among these distances:
161 1 0.00
162 235 1.00
ACGTcount: A:0.36, C:0.20, G:0.17, T:0.27
Consensus pattern (162 bp):
TATAAGCACTAAGTGTGCAACCCACGAAATTTATCATATGTTGATGAACGACCGTATAGGCATTA
AGTGTGCAACCCATAGAATTCATCATATGTTGATGAACGACCGTATAGGCACTAACTGTACAACC
CACAAAATTCATCATATATTGATGAACGACCG
Found at i:402211 original size:54 final size:54
Alignment explanation
Indices: 401746--402185 Score: 531
Period size: 54 Copynumber: 8.1 Consensus size: 54
401736 ATATGTGTAC
* * ** ** *
401746 TATAAGCACTAAGTGTACAACCCACGGAATTTGTCATATGA-TGATGAACGACTG
1 TATAGGCACTAAGTGTGCAACCCACAAAATTCATCATAT-ATTGATGAACGACCG
* * *
401800 TATAGGCACTAAGTGTGCAACCCATAGAATTCATCATATGTTGATGAACGACCG
1 TATAGGCACTAAGTGTGCAACCCACAAAATTCATCATATATTGATGAACGACCG
* * *
401854 TATAGGCACTAAGTGTGCAACCTATAGAATTCATCATATATTGATGAACGACCG
1 TATAGGCACTAAGTGTGCAACCCACAAAATTCATCATATATTGATGAACGACCG
* *
401908 TATAAGCACTAAGTGTGCAACCCACAAAATTCATCATATGTTGATGAACGACCG
1 TATAGGCACTAAGTGTGCAACCCACAAAATTCATCATATATTGATGAACGACCG
* * * * * ** * * * * *
401962 CACATGTATTAAGTGTATAATCCTCAGAATTCATCATATGTTGATGGACGACCG
1 TATAGGCACTAAGTGTGCAACCCACAAAATTCATCATATATTGATGAACGACCG
* * *
402016 TATAAGCACTAACTGTACAACCCACAAAATTCATCATATATTGATGAACGACCG
1 TATAGGCACTAAGTGTGCAACCCACAAAATTCATCATATATTGATGAACGACCG
* * * *
402070 TATAGGCACTAAATGTGCAACCCACGAAATTTATCATATGTTGATGAACGACCG
1 TATAGGCACTAAGTGTGCAACCCACAAAATTCATCATATATTGATGAACGACCG
* **
402124 TATAGGCATTAAGTGTGCAACCCACAAAATTCATCATATATTGATGAACGACTA
1 TATAGGCACTAAGTGTGCAACCCACAAAATTCATCATATATTGATGAACGACCG
402178 TATAGGCA
1 TATAGGCA
402186 TTATGTGTAT
Statistics
Matches: 334, Mismatches: 51, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
54 334 1.00
ACGTcount: A:0.36, C:0.20, G:0.17, T:0.27
Consensus pattern (54 bp):
TATAGGCACTAAGTGTGCAACCCACAAAATTCATCATATATTGATGAACGACCG
Found at i:402768 original size:20 final size:19
Alignment explanation
Indices: 402743--402789 Score: 60
Period size: 20 Copynumber: 2.5 Consensus size: 19
402733 CCAAAATCCT
* *
402743 TTTTCAAAATTTCATTTTG
1 TTTTCAAAATCTAATTTTG
402762 ATTTTCAAAATCTAATTTTG
1 -TTTTCAAAATCTAATTTTG
402782 TTTT-AAAA
1 TTTTCAAAA
402790 AGAAATTCAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 4 0.16
19 4 0.16
20 17 0.68
ACGTcount: A:0.34, C:0.09, G:0.04, T:0.53
Consensus pattern (19 bp):
TTTTCAAAATCTAATTTTG
Found at i:403494 original size:16 final size:16
Alignment explanation
Indices: 403473--403512 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
403463 ATTAGTTTTT
403473 GAGATTAAGGAGTAAA
1 GAGATTAAGGAGTAAA
* *
403489 GAGATTAGGGAGTAAG
1 GAGATTAAGGAGTAAA
403505 GAGATTAA
1 GAGATTAA
403513 AAAGATAGAC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.45, C:0.00, G:0.35, T:0.20
Consensus pattern (16 bp):
GAGATTAAGGAGTAAA
Found at i:421252 original size:38 final size:38
Alignment explanation
Indices: 421195--421271 Score: 138
Period size: 38 Copynumber: 2.0 Consensus size: 38
421185 TGAAAATGTG
421195 ATAAGCATGTGGCATTAACCTATGTGATTATA-GAAAA
1 ATAAGCATGTGGCATTAACCTATGTGATTATATGAAAA
421232 ATAAGCTATGTGGCATTAACCTATGTGATTATATGAAAA
1 ATAAGC-ATGTGGCATTAACCTATGTGATTATATGAAAA
421271 A
1 A
421272 GTGATATAAG
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
37 6 0.16
38 26 0.68
39 6 0.16
ACGTcount: A:0.40, C:0.10, G:0.18, T:0.31
Consensus pattern (38 bp):
ATAAGCATGTGGCATTAACCTATGTGATTATATGAAAA
Found at i:421474 original size:23 final size:23
Alignment explanation
Indices: 421414--421486 Score: 83
Period size: 23 Copynumber: 3.2 Consensus size: 23
421404 GGTTCTACGC
* * **
421414 GGTCCTACGGGACAATTCTACAT
1 GGTCCTTCGGGACATTTCTATGT
*
421437 GGTTCTTCGGGACATTTCTATGT
1 GGTCCTTCGGGACATTTCTATGT
**
421460 GGTCCTTCGGGACATACCTATGT
1 GGTCCTTCGGGACATTTCTATGT
421483 GGTC
1 GGTC
421487 ATCCTTCAAG
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 42 1.00
ACGTcount: A:0.18, C:0.23, G:0.26, T:0.33
Consensus pattern (23 bp):
GGTCCTTCGGGACATTTCTATGT
Found at i:421663 original size:2 final size:2
Alignment explanation
Indices: 421656--421769 Score: 212
Period size: 2 Copynumber: 57.5 Consensus size: 2
421646 ATGAACAGTG
421656 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
421698 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
*
421740 TA TA TA TA TA TA T- TA TA TA TA TA TG TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
421770 GTATGTTTTG
Statistics
Matches: 109, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
1 1 0.01
2 108 0.99
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (2 bp):
TA
Found at i:425120 original size:31 final size:31
Alignment explanation
Indices: 425068--425127 Score: 86
Period size: 31 Copynumber: 1.9 Consensus size: 31
425058 ATTTAGAAAG
*
425068 TTGACAAAGTTTGATTGTTAAATGGTAAACA
1 TTGACAAAGTTTGATGGTTAAATGGTAAACA
*
425099 TTGAGAAAGTTT-ATGGATTAAATGGTAAA
1 TTGACAAAGTTTGATGG-TTAAATGGTAAA
425128 TATGGCATTG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
30 3 0.12
31 23 0.88
ACGTcount: A:0.40, C:0.03, G:0.22, T:0.35
Consensus pattern (31 bp):
TTGACAAAGTTTGATGGTTAAATGGTAAACA
Found at i:426438 original size:2 final size:2
Alignment explanation
Indices: 426431--426459 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
426421 TAAACGTTAT
426431 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
426460 TTGAAGAACG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:430736 original size:13 final size:13
Alignment explanation
Indices: 430718--430742 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
430708 TAATAAAAAT
430718 ATTTTTTTATTTA
1 ATTTTTTTATTTA
430731 ATTTTTTTATTT
1 ATTTTTTTATTT
430743 TGATGTGATA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (13 bp):
ATTTTTTTATTTA
Found at i:431144 original size:24 final size:24
Alignment explanation
Indices: 431069--431154 Score: 118
Period size: 24 Copynumber: 3.6 Consensus size: 24
431059 CGTTTGTGAA
*
431069 CGTTCGGTTATGTTCATTTATGCT
1 CGTTCGGTTATGTTCGTTTATGCT
* *
431093 CGTCCGGTTATGCTCGTTTATGCT
1 CGTTCGGTTATGTTCGTTTATGCT
*
431117 CGTTCGGTTATGTTCGTTTATGTT
1 CGTTCGGTTATGTTCGTTTATGCT
**
431141 CGTTCATTTATGTT
1 CGTTCGGTTATGTT
431155 TAACCCAATC
Statistics
Matches: 54, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 54 1.00
ACGTcount: A:0.10, C:0.17, G:0.22, T:0.50
Consensus pattern (24 bp):
CGTTCGGTTATGTTCGTTTATGCT
Found at i:432254 original size:16 final size:16
Alignment explanation
Indices: 432233--432285 Score: 97
Period size: 16 Copynumber: 3.3 Consensus size: 16
432223 GTCTCCAACG
432233 TTTATGTTCGTGTTCA
1 TTTATGTTCGTGTTCA
*
432249 TTTATGTTCGTGTTCG
1 TTTATGTTCGTGTTCA
432265 TTTATGTTCGTGTTCA
1 TTTATGTTCGTGTTCA
432281 TTTAT
1 TTTAT
432286 TTATTAAATG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 35 1.00
ACGTcount: A:0.11, C:0.11, G:0.19, T:0.58
Consensus pattern (16 bp):
TTTATGTTCGTGTTCA
Found at i:438962 original size:15 final size:16
Alignment explanation
Indices: 438944--438984 Score: 50
Period size: 15 Copynumber: 2.6 Consensus size: 16
438934 ATGATAATAA
438944 TTATATTAATACA-TC
1 TTATATTAATACACTC
438959 TTATATTTAAATACACTC
1 TTATA-TT-AATACACTC
438977 TTA-ATTAA
1 TTATATTAA
438985 AAAAAAAGTC
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
15 7 0.30
16 4 0.17
17 7 0.30
18 5 0.22
ACGTcount: A:0.41, C:0.12, G:0.00, T:0.46
Consensus pattern (16 bp):
TTATATTAATACACTC
Done.