Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008477.1 Hibiscus syriacus cultivar Beakdansim tig00111308_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: 371691
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 2
Found at i:221198 original size:20 final size:20
Alignment explanation
Indices: 221161--221198 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
221151 CACATTTTTA
* *
221161 TCTAGATATTTGACAAGAAT
1 TCTAGATATTAGAAAAGAAT
221181 TCTAGATATTAGAAAAGA
1 TCTAGATATTAGAAAAGA
221199 TTATGATTCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.45, C:0.08, G:0.16, T:0.32
Consensus pattern (20 bp):
TCTAGATATTAGAAAAGAAT
Found at i:221400 original size:106 final size:106
Alignment explanation
Indices: 221204--221623 Score: 517
Period size: 105 Copynumber: 3.9 Consensus size: 106
221194 AAAGATTATG
* * *
221204 ATTCACCA-CAAAAGGAGGTGAACCAACATTTCCAAAAGAGTTCATAATGAGAAGAACTTGTCC-
1 ATTCACCAGCAGAAGGAGGTGAACCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCGTCCA
* * *
221267 TAAAGTAGAAAGTTCATAATGAGAAGAACTTGTACTTTTCAA
66 AAAAG-AGAAAGTTCATAATGAGAAGAACTTGTTCCTTTCAA
* * *
221309 ATTCACCAGGAGAAGGAGGTGAACCAACATTTCCAGAACATTTCATAATGAGAAGAACTCGTCCA
1 ATTCACCAGCAGAAGGAGGTGAACCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCGTCCA
*
221374 AAAAGAGAAAATTCATAATGAGAAGAACTTGTTCCTTTCAA
66 AAAAGAGAAAGTTCATAATGAGAAGAACTTGTTCCTTTCAA
* * * *
221415 ATTCACCA-CAGAATGAGGTGAACCAATATTTCCTGAAGAGTTCATAATGAGAAGAACTCGTCCT
1 ATTCACCAGCAGAAGGAGGTGAACCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCGTCCA
*
221479 AAAAGAGAAAGTTCATAATAAGAAGAACTTGTTCCTTTCAA
66 AAAAGAGAAAGTTCATAATGAGAAGAACTTGTTCCTTTCAA
* * * * * * *
221520 GTCCACC-GCAGAAGAAGGTGGATCAACATTTTCAATGAAGAGTTCATAATGAGAAGAACTCATC
1 ATTCACCAGCAGAAGGAGGTGAACCAACA-TTTCCA-GAAGAGTTCATAATGAGAAGAACTCGTC
* *
221584 CAATGAGGAAGA-AGAAGTTTATAATTAGAAGAACTTGTTC
64 CAA--A--AAGAGA-AAGTTCATAATGAGAAGAACTTGTTC
221624 AACCTTGGTT
Statistics
Matches: 273, Mismatches: 32, Indels: 14
0.86 0.10 0.04
Matches are distributed among these distances:
105 116 0.42
106 94 0.34
107 33 0.12
109 1 0.00
110 1 0.00
111 28 0.10
ACGTcount: A:0.41, C:0.16, G:0.19, T:0.24
Consensus pattern (106 bp):
ATTCACCAGCAGAAGGAGGTGAACCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCGTCCA
AAAAGAGAAAGTTCATAATGAGAAGAACTTGTTCCTTTCAA
Found at i:221710 original size:32 final size:32
Alignment explanation
Indices: 221669--221737 Score: 129
Period size: 32 Copynumber: 2.2 Consensus size: 32
221659 TCAACATTTT
221669 CAATGGAGAGTTCATAATGAGAAAAACTCATC
1 CAATGGAGAGTTCATAATGAGAAAAACTCATC
*
221701 CAATGGAGAGTTCATAATGAGAAGAACTCATC
1 CAATGGAGAGTTCATAATGAGAAAAACTCATC
221733 CAATG
1 CAATG
221738 ATAAAGGAGA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 36 1.00
ACGTcount: A:0.42, C:0.16, G:0.20, T:0.22
Consensus pattern (32 bp):
CAATGGAGAGTTCATAATGAGAAAAACTCATC
Found at i:221834 original size:144 final size:146
Alignment explanation
Indices: 221552--221850 Score: 390
Period size: 144 Copynumber: 2.0 Consensus size: 146
221542 TCAACATTTT
* * *
221552 CAATGAAGAGTTCATAATGAGAAGAACTCATCCAATGAGGAAGAAGAAGTTTATAATTAGAAGAA
1 CAATGAAGAGTTCATAATGAGAAGAACTCATCCAATGAGAAAGAAGAAGTTCATAATGAGAAGAA
* * *
221617 CTTGTTCAACCTTGGTTCGATTCCATCACAGAAGGATGTGGATCAACATTTTCAATGGAGAGTTC
66 CTTGTT--ACCTT-GTTCAATCCCATCACAGAAGGAGGTGGATCAACATTTTCAATGGAGAGTTC
*
221682 ATAATGAGAAAAACTCATC
128 AAAATGAGAAAAACTCATC
* * *
221701 CAATGGAGAGTTCATAATGAGAAGAACTCATCCAATGATAAAGGAGAAAGTTCATAATGAGAAGA
1 CAATGAAGAGTTCATAATGAGAAGAACTCATCCAATGAGAAAGAAG-AAGTTCATAATGAGAAGA
* * * *
221766 ACTTGTT-CC-T-TTCAAGTCCCA-CGCAGAATGAGGTGGATTAATATTTTCAATGGAGAGTTCA
65 ACTTGTTACCTTGTTCAA-TCCCATCACAGAAGGAGGTGGATCAACATTTTCAATGGAGAGTTCA
*
221827 AAATGAGAATAACTCATC
129 AAATGAGAAAAACTCATC
221845 CAATGA
1 CAATGA
221851 GGAAGAATAA
Statistics
Matches: 132, Mismatches: 16, Indels: 9
0.84 0.10 0.06
Matches are distributed among these distances:
144 60 0.45
145 4 0.03
146 1 0.01
147 2 0.02
149 42 0.32
150 23 0.17
ACGTcount: A:0.39, C:0.15, G:0.20, T:0.26
Consensus pattern (146 bp):
CAATGAAGAGTTCATAATGAGAAGAACTCATCCAATGAGAAAGAAGAAGTTCATAATGAGAAGAA
CTTGTTACCTTGTTCAATCCCATCACAGAAGGAGGTGGATCAACATTTTCAATGGAGAGTTCAAA
ATGAGAAAAACTCATC
Found at i:221938 original size:117 final size:117
Alignment explanation
Indices: 221701--222234 Score: 776
Period size: 117 Copynumber: 4.6 Consensus size: 117
221691 AAAACTCATC
** *
221701 CAATGGAGAGTTCATAATGAGAAGAACTCATCCAATGATAAAGGAGAAAGTTCATAATGAGAAGA
1 CAATGGAGAGTTCATAATGAGAAGAACTCATCCAATGAGGAAGAAG-AAGTTCATAATGAGAAGA
* * * *
221766 ACTTGTT---CC-T--TTCAAGTCCCA-CGCAGAATGAGGTGGATTAATATTTT
65 ACTTGTTCAACCTTGGTTCAA-TTCCATCACAGAAGGAGGTGGATCAATATTTT
* * *
221813 CAATGGAGAGTTCAAAATGAGAATAACTCATCCAATGAGGAAGAATAAGTTCATAATGAGAAGAA
1 CAATGGAGAGTTCATAATGAGAAGAACTCATCCAATGAGGAAGAAGAAGTTCATAATGAGAAGAA
*
221878 CTTGTTCAACCTTGGTTTAATTCCATCACAGAAGGAGGTGGATCAATATTTT
66 CTTGTTCAACCTTGGTTCAATTCCATCACAGAAGGAGGTGGATCAATATTTT
* *
221930 CAATGGAGAGTTCATAATAAGAAGAACTCATCCAATGAGGATGAAGAAGTTCATAATGAGAAGAA
1 CAATGGAGAGTTCATAATGAGAAGAACTCATCCAATGAGGAAGAAGAAGTTCATAATGAGAAGAA
* *
221995 CTTGTTCAACCTTGGTTCGATTCCATCACAGAAGGAGGTGGATCAACATTTT
66 CTTGTTCAACCTTGGTTCAATTCCATCACAGAAGGAGGTGGATCAATATTTT
* *
222047 TAATGGAGAGTTCATAATGAGAAGAACTTATCCAATGAGGAAGAAGAAGTTCATAATGAGAAGAA
1 CAATGGAGAGTTCATAATGAGAAGAACTCATCCAATGAGGAAGAAGAAGTTCATAATGAGAAGAA
* * ** * *
222112 ATTATTCAACCTTGGTTTGATTCCCTCATAGAAGGAGGTGGATCAATATTTT
66 CTTGTTCAACCTTGGTTCAATTCCATCACAGAAGGAGGTGGATCAATATTTT
* *
222164 TAATGGAGAGTTCATAATGAGAAGAACTCATCCAAAGAGGAAGAAGAAGTTCATAATGAGAAGAA
1 CAATGGAGAGTTCATAATGAGAAGAACTCATCCAATGAGGAAGAAGAAGTTCATAATGAGAAGAA
222229 CTTGTT
66 CTTGTT
222235 TAACATTGCA
Statistics
Matches: 382, Mismatches: 33, Indels: 9
0.90 0.08 0.02
Matches are distributed among these distances:
111 25 0.07
112 40 0.10
114 2 0.01
115 1 0.00
116 4 0.01
117 310 0.81
ACGTcount: A:0.38, C:0.13, G:0.22, T:0.27
Consensus pattern (117 bp):
CAATGGAGAGTTCATAATGAGAAGAACTCATCCAATGAGGAAGAAGAAGTTCATAATGAGAAGAA
CTTGTTCAACCTTGGTTCAATTCCATCACAGAAGGAGGTGGATCAATATTTT
Found at i:221947 original size:261 final size:256
Alignment explanation
Indices: 221451--221966 Score: 811
Period size: 261 Copynumber: 2.0 Consensus size: 256
221441 TATTTCCTGA
*
221451 AGAGTTCATAATGAGAAGAACTCGTCCTAAAAGAGAAAGTTCATAATAAGAAGAACTTGTTCCTT
1 AGAGTTCATAATGAGAAGAACTCATCCTAAAAGAGAAAGTTCATAATAAGAAGAACTTGTTCCTT
*
221516 TCAAGTCCACCGCAGAAGAAGGTGGATCAACATTTTCAATGAAGAGTTCATAATGAGAAGAACTC
66 TCAAGTCCACCGCAGAAGAAGGTGGATCAACATTTTCAATGAAGAGTTCAAAATGAGAAGAACTC
* * *
221581 ATCCAATGAGGAAGAAGAAGTTTATAATTAGAAGAACTTGTTCAACCTTGGTTCGATTCCATCAC
131 ATCCAATGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTGGTTCAATTCCATCAC
* *
221646 AGAAGGATGTGGATCAACATTTTCAATGGAGAGTTCATAATGAGAAAAACTCATCCAATGG
196 AGAAGGAGGTGGATCAACATTTTCAATGGAGAGTTCATAATAAGAAAAACTCATCCAATGG
*
221707 AGAGTTCATAATGAGAAGAACTCATCCAATGATAAAGGAGAAAGTTCATAATGAGAAGAACTTGT
1 AGAGTTCATAATGAGAAGAACTCATCC--T-A-AAA-GAGAAAGTTCATAATAAGAAGAACTTGT
* * *
221772 TCCTTTCAAGTCC-CACGCAGAATG-AGGTGGATTAATATTTTCAATGGAGAGTTCAAAATGAGA
61 TCCTTTCAAGTCCAC-CGCAGAA-GAAGGTGGATCAACATTTTCAATGAAGAGTTCAAAATGAGA
* * *
221835 ATAACTCATCCAATGAGGAAGAATAAGTTCATAATGAGAAGAACTTGTTCAACCTTGGTTTAATT
124 AGAACTCATCCAATGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTGGTTCAATT
* *
221900 CCATCACAGAAGGAGGTGGATCAATATTTTCAATGGAGAGTTCATAATAAGAAGAACTCATCCAA
189 CCATCACAGAAGGAGGTGGATCAACATTTTCAATGGAGAGTTCATAATAAGAAAAACTCATCCAA
221965 TG
254 TG
221967 AGGATGAAGA
Statistics
Matches: 237, Mismatches: 16, Indels: 9
0.90 0.06 0.03
Matches are distributed among these distances:
256 26 0.11
258 1 0.00
259 1 0.00
260 4 0.02
261 204 0.86
262 1 0.00
ACGTcount: A:0.39, C:0.15, G:0.20, T:0.26
Consensus pattern (256 bp):
AGAGTTCATAATGAGAAGAACTCATCCTAAAAGAGAAAGTTCATAATAAGAAGAACTTGTTCCTT
TCAAGTCCACCGCAGAAGAAGGTGGATCAACATTTTCAATGAAGAGTTCAAAATGAGAAGAACTC
ATCCAATGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTGGTTCAATTCCATCAC
AGAAGGAGGTGGATCAACATTTTCAATGGAGAGTTCATAATAAGAAAAACTCATCCAATGG
Found at i:222068 original size:378 final size:361
Alignment explanation
Indices: 221350--222083 Score: 1015
Period size: 378 Copynumber: 2.0 Consensus size: 361
221340 TCCAGAACAT
*
221350 TTCATAATGAGAAGAACTCGTCCAAAAAGAGAAAATTCATAATGAGAAGAACTTGTTCCTTTCAA
1 TTCATAATGAGAAGAACTCATCCAAAAAGAGAAAATTCATAATGAGAAGAACTTGTTCCTTTCAA
* * * *
221415 ATTCACCACAGAATGAGGTGAACCAATATTTCCTGAAGAGTTCATAATGAGAAGAACTCGTCCTA
66 AGTCACCACAGAATGAGGTGAACCAATATTTCATGAAGAGTTCAAAATGAGAAGAACTCATCCTA
*
221480 AAAGAGAAAGTTCATAATAAGAAGAACTTGTTCCTTTCAAGTCCACCGCAGAAGAAGGTGGATCA
131 AAAGAGAAAGTTCATAATAAGAAGAACTTGTTCCTTTCAAGTCCACCACAGAAGAAGGTGGATCA
* * *
221545 ACATTTTCAATGAAGAGTTCATAATGAGAAGAACTCATCCAATGAGGAAGAAGAAGTTTATAATT
196 ACATTTTCAATGAAGAGTTCATAATAAGAAGAACTCATCCAATGAGGAAGAAGAAGTTCATAATG
*
221610 AGAAGAACTTGTTCAACCTTGGTTCGATTCCATCACAGAAGGATGTGGATCAACATTTTCAATGG
261 AGAAGAACTTGTTCAACCTTGGTTCGATTCCATCACAGAAGGAGGTGGATCAACATTTTCAATGG
221675 AGAGTTCATAATGAGAAAAACTCATCCAATGGAGAG
326 AGAGTTCATAATGAGAAAAACTCATCCAATGGAGAG
*
221711 TTCATAATGAGAAGAACTCATCCAATGATAAAGGAGAAAGTTCATAATGAGAAGAACTTGTTCCT
1 TTCATAATGAGAAGAACTCATCC-A--A-AAA-GAGAAAATTCATAATGAGAAGAACTTGTTCCT
* ** * *
221776 TTC-AAGTC-CCACGCAGAATGAGGTGGATTAATATTTTCAATGGAGAGTTCAAAATGAGAATAA
61 TTCAAAGTCACCA--CAGAATGAGGTGAACCAATA-TTTC-ATGAAGAGTTCAAAATGAGAAGAA
* * * *
221839 CTCATCC-AATGAGGAAGAATAAGTTCATAATGAGAAGAACTTGTTCAACCTTGGTTTAATTCCA
122 CTCATCCTAA--AAG-AG-A-AAGTTCATAATAAGAAGAACTTGTT---CC-T--TTCAAGTCCA
* * * *
221903 TCACAGAAGGAGGTGGATCAATATTTTCAATGGAGAGTTCATAATAAGAAGAACTCATCCAATGA
176 CCACAGAAGAAGGTGGATCAACATTTTCAATGAAGAGTTCATAATAAGAAGAACTCATCCAATGA
*
221968 GGATGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTGGTTCGATTCCATCACAGAAGGAGG
241 GGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTGGTTCGATTCCATCACAGAAGGAGG
* * *
222033 TGGATCAACATTTTTAATGGAGAGTTCATAATGAGAAGAACTTATCCAATG
306 TGGATCAACATTTTCAATGGAGAGTTCATAATGAGAAAAACTCATCCAATG
222084 AGGAAGAAGA
Statistics
Matches: 325, Mismatches: 28, Indels: 23
0.86 0.07 0.06
Matches are distributed among these distances:
361 22 0.07
362 1 0.00
364 4 0.01
365 7 0.02
366 51 0.16
367 6 0.02
368 26 0.08
369 2 0.01
370 2 0.01
371 1 0.00
372 24 0.07
375 2 0.01
376 1 0.00
378 176 0.54
ACGTcount: A:0.39, C:0.15, G:0.20, T:0.26
Consensus pattern (361 bp):
TTCATAATGAGAAGAACTCATCCAAAAAGAGAAAATTCATAATGAGAAGAACTTGTTCCTTTCAA
AGTCACCACAGAATGAGGTGAACCAATATTTCATGAAGAGTTCAAAATGAGAAGAACTCATCCTA
AAAGAGAAAGTTCATAATAAGAAGAACTTGTTCCTTTCAAGTCCACCACAGAAGAAGGTGGATCA
ACATTTTCAATGAAGAGTTCATAATAAGAAGAACTCATCCAATGAGGAAGAAGAAGTTCATAATG
AGAAGAACTTGTTCAACCTTGGTTCGATTCCATCACAGAAGGAGGTGGATCAACATTTTCAATGG
AGAGTTCATAATGAGAAAAACTCATCCAATGGAGAG
Found at i:222119 original size:20 final size:20
Alignment explanation
Indices: 222057--222119 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
222047 TAATGGAGAG
*
222057 TTCATAATGAGAAGAACTTA
1 TTCATAATGAGAAGAAATTA
*
222077 -TC-CAATGAGGAAGAAGA--A
1 TTCATAATGA-GAAGAA-ATTA
222095 GTTCATAATGAGAAGAAATTA
1 -TTCATAATGAGAAGAAATTA
222116 TTCA
1 TTCA
222120 ACCTTGGTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 14
0.66 0.06 0.28
Matches are distributed among these distances:
18 6 0.18
19 9 0.27
20 12 0.36
21 6 0.18
ACGTcount: A:0.46, C:0.10, G:0.19, T:0.25
Consensus pattern (20 bp):
TTCATAATGAGAAGAAATTA
Found at i:222463 original size:3 final size:3
Alignment explanation
Indices: 222451--222506 Score: 60
Period size: 3 Copynumber: 18.7 Consensus size: 3
222441 GGCTTAAATA
* * *
222451 TAT T-T TAT TAT TAA TAT TAT TAT TAT TAT CAT TAT TAT TACT AAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT
*
222496 TAT TGT TAT TA
1 TAT TAT TAT TA
222507 ATTTACATGC
Statistics
Matches: 43, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
2 2 0.05
3 39 0.91
4 2 0.05
ACGTcount: A:0.34, C:0.04, G:0.02, T:0.61
Consensus pattern (3 bp):
TAT
Found at i:225948 original size:17 final size:17
Alignment explanation
Indices: 225917--225970 Score: 65
Period size: 16 Copynumber: 3.1 Consensus size: 17
225907 TTAGCAATTT
225917 ATTGAAAAGAAAAAAAAA
1 ATTG-AAAGAAAAAAAAA
*
225935 ATT-AAAGTAAAAAAAA
1 ATTGAAAGAAAAAAAAA
225951 ATTGAAAGGAAATAAAAAA
1 ATTGAAA-GAAA-AAAAAA
225970 A
1 A
225971 AACCCCCGAC
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
16 15 0.48
17 3 0.10
18 6 0.19
19 7 0.23
ACGTcount: A:0.74, C:0.00, G:0.11, T:0.15
Consensus pattern (17 bp):
ATTGAAAGAAAAAAAAA
Found at i:226090 original size:16 final size:17
Alignment explanation
Indices: 226071--226102 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
226061 AAGATGGAAT
226071 AATATTC-AAAAATAAA
1 AATATTCTAAAAATAAA
226087 AATATTCTAAAAATAA
1 AATATTCTAAAAATAA
226103 TTCAAAAGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.66, C:0.06, G:0.00, T:0.28
Consensus pattern (17 bp):
AATATTCTAAAAATAAA
Found at i:226977 original size:170 final size:168
Alignment explanation
Indices: 226581--227101 Score: 515
Period size: 170 Copynumber: 3.1 Consensus size: 168
226571 GAAAAATATA
* * * *
226581 TATGAACAGATAATGTTTCCTTTTGGAGAATTATTCATCCCAACAACTCACATACCTGATGGGAT
1 TATGTACAGATAATGTTTCCTTTTGG-GAACTATTCATCCCAATAACTC-CATGCCTGATGGGAT
* * * * * *
226646 GAGACGCTAAGACATGGCAGAGA-TTCCTTGCAAAAGGTGAAAGCGCTTCTTGTG---GAAAGAG
64 GAGACACTATGACATGGCAAAGATTTCC-TGCAAAAGGTGAAAACGCTTCTTGTGAAAAAAAAAG
* * *
226707 TTATCATTTTTTAGAGATTTTATGCATATTCCAGTCAATTT
128 TTATCATTTTTTAAAGATTCTATGCATATTCCACTCAATTT
* * ** * *
226748 TATGTACAGGTAATGTTCCCCTTCGGGGAACTATTCATCCAAATAACTCCTACGCCTGATGGGAT
1 TATGTACAGATAATGTT-TCCTTTTGGGAACTATTCATCCCAATAACTCC-ATGCCTGATGGGAT
* *
226813 GAGACACTATGACATGACAAAGATTTCCTACAAAAGGTGAAAACGCTTCTTGTGAAAAAAAAACG
64 GAGACACTATGACATGGCAAAGATTTCCTGCAAAAGGTGAAAACGCTTCTTGTGAAAAAAAAA-G
* * * *
226878 -T-TCTTTTTTTCAAAGATTCTCTGCTTATTCCACTTAATTT
128 TTATCATTTTTT-AAAGATTCTATGCATATTCCACTCAATTT
* * * *
226918 TATGTACATATAATGTTTCTCTTTTGGGAACAATTCATCCCAGTAACTCTCATGCCTGATGGAAT
1 TATGTACAGATAATGTTTC-CTTTTGGGAACTATTCATCCCAATAACTC-CATGCCTGATGGGAT
* * *
226983 GAGACACTATGACATGGCATAA-ATTCCCTGCAAAAGGTTAAACCGCTTCTTGTG---AAAAAAG
64 GAGACACTATGACATGGCA-AAGATTTCCTGCAAAAGGTGAAAACGCTTCTTGTGAAAAAAAAAG
* * *
227044 TCT-TCAATTTTTTATAGTGATTCTTTGCATATTTCACTCAATTT
128 T-TATC-ATTTTTTA-A-AGATTCTATGCATATTCCACTCAATTT
*
227088 TATGTACATATAAT
1 TATGTACAGATAAT
227102 ATTTTCCTCA
Statistics
Matches: 292, Mismatches: 46, Indels: 29
0.80 0.13 0.08
Matches are distributed among these distances:
166 2 0.01
167 95 0.33
168 14 0.05
169 16 0.05
170 161 0.55
171 4 0.01
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.34
Consensus pattern (168 bp):
TATGTACAGATAATGTTTCCTTTTGGGAACTATTCATCCCAATAACTCCATGCCTGATGGGATGA
GACACTATGACATGGCAAAGATTTCCTGCAAAAGGTGAAAACGCTTCTTGTGAAAAAAAAAGTTA
TCATTTTTTAAAGATTCTATGCATATTCCACTCAATTT
Found at i:231964 original size:7 final size:7
Alignment explanation
Indices: 231948--231990 Score: 58
Period size: 7 Copynumber: 6.7 Consensus size: 7
231938 TTGAGATTCG
231948 ATTT-AA
1 ATTTAAA
231954 ATTTAAA
1 ATTTAAA
231961 ATTT---
1 ATTTAAA
231965 ATTTAAA
1 ATTTAAA
231972 ATTTAAA
1 ATTTAAA
231979 ATTTAAA
1 ATTTAAA
231986 ATTTA
1 ATTTA
231991 TACCTAAGCA
Statistics
Matches: 33, Mismatches: 0, Indels: 7
0.82 0.00 0.17
Matches are distributed among these distances:
4 4 0.12
6 4 0.12
7 25 0.76
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (7 bp):
ATTTAAA
Found at i:231970 original size:17 final size:18
Alignment explanation
Indices: 231948--231983 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
231938 TTGAGATTCG
231948 ATTT-AAATTTAAAATTT
1 ATTTAAAATTTAAAATTT
231965 ATTTAAAATTTAAAATTT
1 ATTTAAAATTTAAAATTT
231983 A
1 A
231984 AAATTTATAC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 4 0.22
18 14 0.78
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
ATTTAAAATTTAAAATTT
Found at i:234370 original size:45 final size:45
Alignment explanation
Indices: 234309--234421 Score: 147
Period size: 45 Copynumber: 2.5 Consensus size: 45
234299 GAGCGGTAGA
*
234309 AAAAATAACATTTTAGGTAGCGCCCAAAATTAACATTTCCGA-TAG
1 AAAAATAATATTTTAGGTAGCGCCCAAAATTAACATTTCC-ATTAG
* * * *
234354 AAAAATAATATTTTAGGTAGAGTCCAATATTAACATTTTCATTAG
1 AAAAATAATATTTTAGGTAGCGCCCAAAATTAACATTTCCATTAG
* *
234399 AAAAATACTTTTTTAGGTAGCGC
1 AAAAATAATATTTTAGGTAGCGC
234422 TTTACCAAAA
Statistics
Matches: 58, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
44 1 0.02
45 57 0.98
ACGTcount: A:0.41, C:0.13, G:0.13, T:0.33
Consensus pattern (45 bp):
AAAAATAATATTTTAGGTAGCGCCCAAAATTAACATTTCCATTAG
Found at i:234701 original size:45 final size:45
Alignment explanation
Indices: 234646--234755 Score: 134
Period size: 45 Copynumber: 2.5 Consensus size: 45
234636 TGGTAAAGCG
234646 CTACCT-AAACATTATTTTTCTACC-AGAAATATTAATATTGAACA
1 CTACCTAAAACATTATTTTTCTACCGA-AAATATTAATATTGAACA
* * * * **
234690 CTACTTAAAACACTATTTTTTTACCGAAAATATTAATATTGGATG
1 CTACCTAAAACATTATTTTTCTACCGAAAATATTAATATTGAACA
*
234735 CTACCTAAAATATTATTTTTC
1 CTACCTAAAACATTATTTTTC
234756 CAAATTTTTA
Statistics
Matches: 54, Mismatches: 10, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
44 5 0.09
45 48 0.89
46 1 0.02
ACGTcount: A:0.38, C:0.16, G:0.05, T:0.40
Consensus pattern (45 bp):
CTACCTAAAACATTATTTTTCTACCGAAAATATTAATATTGAACA
Found at i:239050 original size:17 final size:18
Alignment explanation
Indices: 239011--239051 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
239001 AAGAGGTTGG
*
239011 ATTTTTAGAGTCTTAGAT
1 ATTTTTAGAGTCTTAGAA
*
239029 TTTTTTAGA-TCTTAGAA
1 ATTTTTAGAGTCTTAGAA
239046 ATTTTT
1 ATTTTT
239052 GGGGTTTTTA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
17 12 0.60
18 8 0.40
ACGTcount: A:0.27, C:0.05, G:0.12, T:0.56
Consensus pattern (18 bp):
ATTTTTAGAGTCTTAGAA
Found at i:239050 original size:18 final size:18
Alignment explanation
Indices: 239012--239051 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
239002 AGAGGTTGGA
*
239012 TTTTTAGAGTCTTAGATT
1 TTTTTAGAGTCTTAGAAT
239030 TTTTTAGA-TCTTAGAAAT
1 TTTTTAGAGTCTTAG-AAT
239048 TTTT
1 TTTT
239052 GGGGTTTTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 6 0.30
18 14 0.70
ACGTcount: A:0.25, C:0.05, G:0.12, T:0.57
Consensus pattern (18 bp):
TTTTTAGAGTCTTAGAAT
Found at i:245712 original size:23 final size:24
Alignment explanation
Indices: 245658--245713 Score: 80
Period size: 24 Copynumber: 2.4 Consensus size: 24
245648 AAAATAATTT
*
245658 TGTCTTTGTGGCACGTTTTTCCTC
1 TGTCTTTGTGACACGTTTTTCCTC
245682 TG-CGTTTGTGACACGTTTTT-CTC
1 TGTC-TTTGTGACACGTTTTTCCTC
245705 TGTCTTTGT
1 TGTCTTTGT
245714 TGTACGCTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
23 11 0.38
24 18 0.62
ACGTcount: A:0.05, C:0.21, G:0.21, T:0.52
Consensus pattern (24 bp):
TGTCTTTGTGACACGTTTTTCCTC
Found at i:246526 original size:21 final size:22
Alignment explanation
Indices: 246477--246526 Score: 68
Period size: 21 Copynumber: 2.4 Consensus size: 22
246467 ATATAGATTT
246477 AAGGAGTATAGATACTCAAACG
1 AAGGAGTATAGATACTCAAACG
* *
246499 AA-TAGTATGGATACTCAAAC-
1 AAGGAGTATAGATACTCAAACG
246519 AAGGAGTA
1 AAGGAGTA
246527 CATGCACTGA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
20 2 0.08
21 20 0.83
22 2 0.08
ACGTcount: A:0.46, C:0.12, G:0.22, T:0.20
Consensus pattern (22 bp):
AAGGAGTATAGATACTCAAACG
Found at i:248330 original size:23 final size:22
Alignment explanation
Indices: 248289--248331 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
248279 TTATATACAA
*
248289 AAGAAAGAATAAACCAAGAATC
1 AAGAAAGAAAAAACCAAGAATC
*
248311 AAGAAAGTAAAAAACTAAGAA
1 AAGAAAG-AAAAAACCAAGAA
248332 AGCTCGTGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 7 0.39
23 11 0.61
ACGTcount: A:0.67, C:0.09, G:0.14, T:0.09
Consensus pattern (22 bp):
AAGAAAGAAAAAACCAAGAATC
Found at i:248758 original size:29 final size:27
Alignment explanation
Indices: 248726--248801 Score: 71
Period size: 30 Copynumber: 2.6 Consensus size: 27
248716 AATTTTGACT
*
248726 AATTATTATTTAAAATTTATTTTTGATAA
1 AATTATTATTTAAAATGTA-TTTT-ATAA
*
248755 AATTATATTTTTAAATATGTATTTTATAA
1 AATTAT-TATTTAAA-ATGTATTTTATAA
*
248784 AATTTAATTGTTTAAAAT
1 AA-TT-ATTATTTAAAAT
248802 ATTTAAAATA
Statistics
Matches: 40, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
29 14 0.35
30 20 0.50
31 6 0.15
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.54
Consensus pattern (27 bp):
AATTATTATTTAAAATGTATTTTATAA
Found at i:248802 original size:31 final size:31
Alignment explanation
Indices: 248729--248804 Score: 81
Period size: 29 Copynumber: 2.5 Consensus size: 31
248719 TTTGACTAAT
248729 TATTATTTAAAAT-TTATTTTTGATAAAATTA
1 TATT-TTTAAAATATTATTTTTGATAAAATTA
248760 TATTTTT-AAATATGTA-TTTT-ATAAAATT-
1 TATTTTTAAAATAT-TATTTTTGATAAAATTA
248788 TAATTGTTTAAAATATT
1 T-ATT-TTTAAAATATT
248805 TAAAATAATC
Statistics
Matches: 40, Mismatches: 0, Indels: 11
0.78 0.00 0.22
Matches are distributed among these distances:
28 1 0.03
29 15 0.38
30 12 0.30
31 12 0.30
ACGTcount: A:0.41, C:0.00, G:0.04, T:0.55
Consensus pattern (31 bp):
TATTTTTAAAATATTATTTTTGATAAAATTA
Found at i:250095 original size:23 final size:23
Alignment explanation
Indices: 250063--250133 Score: 97
Period size: 23 Copynumber: 3.1 Consensus size: 23
250053 AGCCCATCCA
* * *
250063 TTGACTGTTGACCGATGTTAACT
1 TTGACCGTTGACCAACGTTAACT
250086 TTGACCGTTGACCAACGTTAACT
1 TTGACCGTTGACCAACGTTAACT
* *
250109 TTGACCGTTGATCAACGTTGACT
1 TTGACCGTTGACCAACGTTAACT
250132 TT
1 TT
250134 TTCCTAAGAC
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 43 1.00
ACGTcount: A:0.23, C:0.21, G:0.20, T:0.37
Consensus pattern (23 bp):
TTGACCGTTGACCAACGTTAACT
Found at i:252439 original size:24 final size:24
Alignment explanation
Indices: 252412--252479 Score: 68
Period size: 24 Copynumber: 2.8 Consensus size: 24
252402 AGCTCGTATA
252412 AATTTGCACCGAAGTGCCACGTAG
1 AATTTGCACCGAAGTGCCACGTAG
* *
252436 AATTTGTC-CCAAAG-GACCGCGTAG
1 AATTTG-CACCGAAGTG-CCACGTAG
*
252460 AATTTTGCACCGTAGTGCCA
1 AA-TTTGCACCGAAGTGCCA
252480 TAATATTGTC
Statistics
Matches: 34, Mismatches: 5, Indels: 9
0.71 0.10 0.19
Matches are distributed among these distances:
23 1 0.03
24 21 0.62
25 11 0.32
26 1 0.03
ACGTcount: A:0.28, C:0.25, G:0.24, T:0.24
Consensus pattern (24 bp):
AATTTGCACCGAAGTGCCACGTAG
Found at i:252768 original size:30 final size:30
Alignment explanation
Indices: 252723--252781 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 30
252713 ATCGCGTAGA
* *
252723 CATATTATTTCCATACCTTTATCACATAGG
1 CATATCATTTACATACCTTTATCACATAGG
252753 CATATCATTTACATACCTTTATCACATAG
1 CATATCATTTACATACCTTTATCACATAG
252782 CTCATATAAC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.32, C:0.24, G:0.05, T:0.39
Consensus pattern (30 bp):
CATATCATTTACATACCTTTATCACATAGG
Found at i:252836 original size:29 final size:29
Alignment explanation
Indices: 252803--252903 Score: 202
Period size: 29 Copynumber: 3.5 Consensus size: 29
252793 TTTTCTGCAT
252803 ATTCATGTCATGTAATACATATAATATGA
1 ATTCATGTCATGTAATACATATAATATGA
252832 ATTCATGTCATGTAATACATATAATATGA
1 ATTCATGTCATGTAATACATATAATATGA
252861 ATTCATGTCATGTAATACATATAATATGA
1 ATTCATGTCATGTAATACATATAATATGA
252890 ATTCATGTCATGTA
1 ATTCATGTCATGTA
252904 TCATAATATG
Statistics
Matches: 72, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 72 1.00
ACGTcount: A:0.40, C:0.11, G:0.11, T:0.39
Consensus pattern (29 bp):
ATTCATGTCATGTAATACATATAATATGA
Found at i:259921 original size:30 final size:30
Alignment explanation
Indices: 259876--259934 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 30
259866 ATCGCGTAGA
* *
259876 CATATTATTTCCATACCTTTATCACATAGG
1 CATATCATTTACATACCTTTATCACATAGG
259906 CATATCATTTACATACCTTTATCACATAG
1 CATATCATTTACATACCTTTATCACATAG
259935 CTCATATAAC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.32, C:0.24, G:0.05, T:0.39
Consensus pattern (30 bp):
CATATCATTTACATACCTTTATCACATAGG
Found at i:259989 original size:29 final size:29
Alignment explanation
Indices: 259956--260056 Score: 202
Period size: 29 Copynumber: 3.5 Consensus size: 29
259946 TTTTCTGCAT
259956 ATTCATGTCATGTAATACATATAATATGA
1 ATTCATGTCATGTAATACATATAATATGA
259985 ATTCATGTCATGTAATACATATAATATGA
1 ATTCATGTCATGTAATACATATAATATGA
260014 ATTCATGTCATGTAATACATATAATATGA
1 ATTCATGTCATGTAATACATATAATATGA
260043 ATTCATGTCATGTA
1 ATTCATGTCATGTA
260057 TCATAATATG
Statistics
Matches: 72, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 72 1.00
ACGTcount: A:0.40, C:0.11, G:0.11, T:0.39
Consensus pattern (29 bp):
ATTCATGTCATGTAATACATATAATATGA
Found at i:262233 original size:20 final size:20
Alignment explanation
Indices: 262195--262233 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
262185 CTTTGTTTTA
* *
262195 TAATATTTTTATTATAAATC
1 TAATATTTTTATAACAAATC
262215 TAATATTTTTATAACAAAT
1 TAATATTTTTATAACAAAT
262234 AAGATAAGTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.51
Consensus pattern (20 bp):
TAATATTTTTATAACAAATC
Found at i:262375 original size:17 final size:16
Alignment explanation
Indices: 262353--262391 Score: 51
Period size: 17 Copynumber: 2.4 Consensus size: 16
262343 AAATTATCAA
* *
262353 TTTTATTTAAATTAAT
1 TTTTATTGAAAATAAT
262369 TTATTATTGAAAATAAT
1 TT-TTATTGAAAATAAT
262386 TTTTAT
1 TTTTAT
262392 CGTTTAATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
16 6 0.30
17 14 0.70
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (16 bp):
TTTTATTGAAAATAAT
Found at i:265167 original size:23 final size:22
Alignment explanation
Indices: 265141--265187 Score: 76
Period size: 23 Copynumber: 2.1 Consensus size: 22
265131 GTAAGTTAAC
265141 GATTGGTTGATTGGTGATAATTG
1 GATTGGTTGATTGGTGAT-ATTG
*
265164 GATTGGTTTATTGGTGATATTG
1 GATTGGTTGATTGGTGATATTG
265186 GA
1 GA
265188 CTAATTTTGG
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 6 0.26
23 17 0.74
ACGTcount: A:0.21, C:0.00, G:0.34, T:0.45
Consensus pattern (22 bp):
GATTGGTTGATTGGTGATATTG
Found at i:265859 original size:21 final size:22
Alignment explanation
Indices: 265804--265856 Score: 79
Period size: 22 Copynumber: 2.4 Consensus size: 22
265794 GTAGTTTTGG
* * *
265804 TGTGTGCCCCTTTTTTACGAGG
1 TGTGTTCCCCTATTTTACGAGA
265826 TGTGTTCCCCTATTTTACGAGA
1 TGTGTTCCCCTATTTTACGAGA
265848 TGTGTTCCC
1 TGTGTTCCC
265857 TATGTGCTAC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.11, C:0.25, G:0.23, T:0.42
Consensus pattern (22 bp):
TGTGTTCCCCTATTTTACGAGA
Found at i:272569 original size:22 final size:22
Alignment explanation
Indices: 272529--272570 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
272519 CCATTGACCG
*
272529 GTCTGACCGTTGACCTTGATTT
1 GTCTGACCGTTAACCTTGATTT
*
272551 GTCTGACCGTTAACTTTGAT
1 GTCTGACCGTTAACCTTGAT
272571 CGAAAAAGTC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.17, C:0.21, G:0.21, T:0.40
Consensus pattern (22 bp):
GTCTGACCGTTAACCTTGATTT
Found at i:275855 original size:2 final size:2
Alignment explanation
Indices: 275848--275906 Score: 118
Period size: 2 Copynumber: 29.5 Consensus size: 2
275838 TTTTGTCATC
275848 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
275890 TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA T
275907 TGATAGGTAT
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 57 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:276053 original size:25 final size:26
Alignment explanation
Indices: 276025--276073 Score: 64
Period size: 25 Copynumber: 1.9 Consensus size: 26
276015 GGGCCGTTTG
276025 GTTTTAGAATTAGAAAATA-TTTTCT
1 GTTTTAGAATTAGAAAATAGTTTTCT
***
276050 GTTTTATTTTTAGAAAATAGTTTT
1 GTTTTAGAATTAGAAAATAGTTTT
276074 AAAAAATTAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 16 0.80
26 4 0.20
ACGTcount: A:0.33, C:0.02, G:0.12, T:0.53
Consensus pattern (26 bp):
GTTTTAGAATTAGAAAATAGTTTTCT
Found at i:276280 original size:13 final size:14
Alignment explanation
Indices: 276259--276292 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
276249 AATATAAAAT
276259 AATAAAATTGATAA
1 AATAAAATTGATAA
*
276273 AA-AAAATTTATAA
1 AATAAAATTGATAA
276286 AATAAAA
1 AATAAAA
276293 ATTATTTTAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
13 12 0.67
14 6 0.33
ACGTcount: A:0.71, C:0.00, G:0.03, T:0.26
Consensus pattern (14 bp):
AATAAAATTGATAA
Found at i:277561 original size:42 final size:42
Alignment explanation
Indices: 277506--277622 Score: 189
Period size: 42 Copynumber: 2.8 Consensus size: 42
277496 CCTCGAATTT
* * * *
277506 CCGTATTTATTTCACGTAATTCGTTTTTCGGAAAATATTTTC
1 CCGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAACATTTTC
*
277548 CCGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAACGTTTTC
1 CCGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAACATTTTC
277590 CCGTGTTTGTTTCACGTAATTCGTTTTCCGGAA
1 CCGTGTTTGTTTCACGTAATTCGTTTTCCGGAA
277623 TGTAATTCAT
Statistics
Matches: 70, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 70 1.00
ACGTcount: A:0.19, C:0.20, G:0.17, T:0.44
Consensus pattern (42 bp):
CCGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAACATTTTC
Found at i:277832 original size:30 final size:28
Alignment explanation
Indices: 277798--277866 Score: 77
Period size: 29 Copynumber: 2.4 Consensus size: 28
277788 TTCATCAAAA
*
277798 TATTAATTATTAAAATATTTAAAATATATT
1 TATTAA-TATTAAAATA-ATAAAATATATT
* *
277828 TATTAATATTTATAATAATATAATATATT
1 TATTAATA-TTAAAATAATAAAATATATT
277857 T-TTAATATTA
1 TATTAATATTA
277867 TATAAATAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
27 3 0.09
28 6 0.17
29 13 0.37
30 13 0.37
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (28 bp):
TATTAATATTAAAATAATAAAATATATT
Found at i:277853 original size:29 final size:30
Alignment explanation
Indices: 277820--277876 Score: 91
Period size: 29 Copynumber: 1.9 Consensus size: 30
277810 AAATATTTAA
277820 AATATATTTATTAATATT-TAT-AATAATAT
1 AATATATTT-TTAATATTATATAAATAATAT
277849 AATATATTTTTAATATTATATAAATAAT
1 AATATATTTTTAATATTATATAAATAAT
277877 CAATTATATA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
28 8 0.31
29 12 0.46
30 6 0.23
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (30 bp):
AATATATTTTTAATATTATATAAATAATAT
Found at i:277864 original size:49 final size:48
Alignment explanation
Indices: 277811--277928 Score: 109
Period size: 49 Copynumber: 2.4 Consensus size: 48
277801 TAATTATTAA
** * *
277811 AATATTTAAAATATATTTATTA-ATATTTATAATAATATAATATATTTTT
1 AATATTTAAAATATATCAATTATATA-TAAT-ATAAGATAATATATTTTT
*
277860 AATATTATATAAATA-ATCAATTATATATAATATAAGATATTATATTTTT
1 AATATT-TA-AAATATATCAATTATATATAATATAAGATAATATATTTTT
*
277909 -AT-TTTAATAATATATAAATT
1 AATATTTAA-AATATATCAATT
277929 TTTTATATAT
Statistics
Matches: 58, Mismatches: 6, Indels: 12
0.76 0.08 0.16
Matches are distributed among these distances:
45 1 0.02
46 6 0.10
47 8 0.14
48 2 0.03
49 22 0.38
50 11 0.19
51 8 0.14
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.50
Consensus pattern (48 bp):
AATATTTAAAATATATCAATTATATATAATATAAGATAATATATTTTT
Found at i:277869 original size:21 final size:19
Alignment explanation
Indices: 277833--277900 Score: 55
Period size: 19 Copynumber: 3.3 Consensus size: 19
277823 ATATTTATTA
277833 ATATTTATAATAATATAAT
1 ATATTTATAATAATATAAT
*
277852 ATATTTTTAATATTATATAAAT
1 ATATTTATAATA--ATAT-AAT
* *
277874 AATCAATTATATATAATATAAG
1 -AT-ATTTATA-ATAATATAAT
277896 ATATT
1 ATATT
277901 ATATTTTTAT
Statistics
Matches: 38, Mismatches: 5, Indels: 11
0.70 0.09 0.20
Matches are distributed among these distances:
19 11 0.29
20 2 0.05
21 6 0.16
22 5 0.13
23 6 0.16
24 5 0.13
25 3 0.08
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.47
Consensus pattern (19 bp):
ATATTTATAATAATATAAT
Found at i:277961 original size:28 final size:27
Alignment explanation
Indices: 277902--277977 Score: 93
Period size: 28 Copynumber: 2.8 Consensus size: 27
277892 TAAGATATTA
*
277902 TATTTTTAT-TTTAATAATATATAAAT
1 TATTTATATATTTAATAATATATAAAT
*
277928 TTTTTATATATTTAATAATGA-ATAATAT
1 TATTTATATATTTAATAAT-ATATAA-AT
277956 TATTTATATATTTCAATAATAT
1 TATTTATATATTT-AATAATAT
277978 TTTAGTAAAG
Statistics
Matches: 42, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
26 7 0.17
27 13 0.31
28 16 0.38
29 6 0.14
ACGTcount: A:0.42, C:0.01, G:0.01, T:0.55
Consensus pattern (27 bp):
TATTTATATATTTAATAATATATAAAT
Found at i:278221 original size:20 final size:20
Alignment explanation
Indices: 278143--278212 Score: 122
Period size: 20 Copynumber: 3.5 Consensus size: 20
278133 TTTCCAAATG
278143 TTTTCCAGAAATGTAATTCA
1 TTTTCCAGAAATGTAATTCA
278163 TTTTCCAGAAATGTAATTCA
1 TTTTCCAGAAATGTAATTCA
* *
278183 TTTTACAAAAATGTAATTCA
1 TTTTCCAGAAATGTAATTCA
278203 TTTTCCAGAA
1 TTTTCCAGAA
278213 TTCAAATTCC
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 46 1.00
ACGTcount: A:0.37, C:0.14, G:0.09, T:0.40
Consensus pattern (20 bp):
TTTTCCAGAAATGTAATTCA
Found at i:278231 original size:15 final size:15
Alignment explanation
Indices: 278195--278261 Score: 109
Period size: 15 Copynumber: 4.5 Consensus size: 15
278185 TTACAAAAAT
**
278195 GTAATTCATTTTCCA
1 GTAATTCAAATTCCA
278210 G-AATTCAAATTCCA
1 GTAATTCAAATTCCA
278224 GTAATTCAAATTCCA
1 GTAATTCAAATTCCA
278239 GTAATTCAAATTCCA
1 GTAATTCAAATTCCA
278254 GTAATTCA
1 GTAATTCA
278262 TTTTCTGGAA
Statistics
Matches: 49, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
14 12 0.24
15 37 0.76
ACGTcount: A:0.37, C:0.19, G:0.07, T:0.36
Consensus pattern (15 bp):
GTAATTCAAATTCCA
Found at i:280383 original size:18 final size:18
Alignment explanation
Indices: 280343--280384 Score: 59
Period size: 17 Copynumber: 2.3 Consensus size: 18
280333 TACGTCAAAT
280343 GAATCTCTTGACGCTATG
1 GAATCTCTTGACGCTATG
*
280361 TAATC-CTTGACGCTATTG
1 GAATCTCTTGACGCTA-TG
280379 GAATCT
1 GAATCT
280385 AATGAATCTC
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
17 10 0.50
18 10 0.50
ACGTcount: A:0.24, C:0.21, G:0.19, T:0.36
Consensus pattern (18 bp):
GAATCTCTTGACGCTATG
Found at i:282132 original size:182 final size:182
Alignment explanation
Indices: 281858--282574 Score: 838
Period size: 183 Copynumber: 3.8 Consensus size: 182
281848 ATTCCATAGT
* * * * *
281858 AATATTACAAGTAAAAATATGATAAAATC-GGTCTCGAAATGACAAAACCGATAAAACAATATCG
1 AATATAACAAGTAAAAATATGATAAAACCAGGTCTCAAAATGACAAAACCGGTAAAA-AATACCG
* *
281922 GATATGTTGAAAGTGTCGATAATTTAATATAAGTATCGACACTTTTAGAATTTAAAAGAGAATAA
65 GATATGTTGAAAGTGTCGATAATTTAATATAAGTATCGAAACTTTTAGAATTTAAAAGAGAAGAA
*
281987 GTTATAACGCCTATAAAGTGTCGATACTTTAAAAAAATGTATCGATCCATAAC
130 GTTATAGCGCCTATAAAGTGTCGATACTTTAAAAAAATGTATCGATCCATAAC
* * * *
282040 AATATAACAGGTAAAAGTATGACAAAA-CAGGTCTCAAAAATGACAAAACCGGTAAAAAATACCT
1 AATATAACAAGTAAAAATATGATAAAACCAGGTCTC-AAAATGACAAAACCGGTAAAAAATACCG
* * * *
282104 AATATGTTGAAAGTATCGATAATTTAATATAAGTATCGAAATTTTTTGGAATTTAAAAGAGAAGA
65 GATATGTTGAAAGTGTCGATAATTTAATATAAGTATCGAAA-CTTTTAGAATTTAAAAGAGAAGA
**
282169 AGTTATAGCGCCTATAAAGTGTCGATACTTTAAAAAAATGTATCGATTTATAAC
129 AGTTATAGCGCCTATAAAGTGTCGATACTTTAAAAAAATGTATCGATCCATAAC
* * * ***
282223 AATATAACAGGTAAAAATATGATAAAACC-GGTCCCAAAATGACAAATCCGGTAAAGCGCTACCG
1 AATATAACAAGTAAAAATATGATAAAACCAGGTCTCAAAATGACAAAACCGGTAAA-AAATACCG
*
282287 GATATGTTGAAAGTGTCGATAATTTAATATAAGTATCGAAACTTTTTGAATTT-AAA-A-AAGAA
65 GATATGTTGAAAGTGTCGATAATTTAATATAAGTATCGAAACTTTTAGAATTTAAAAGAGAAGAA
* * **
282349 GTTATAGCGCCTAAAAAGTATCGATACTTTATGAAAATGTATCGATCCATAAC
130 GTTATAGCGCCTATAAAGTGTCGATACTTTAAAAAAATGTATCGATCCATAAC
*
282402 AATATAACAACTAAAAATATGATAAAACCA-GTCTCAAAATGACAAAACCGGTCTCAAAATGACA
1 AATATAACAAGTAAAAATATGATAAAACCAGGTCTCAAAATGACAAAACCGG--------T----
* * *
282466 AAACCGATAAAGAACTACCGTATATGTTGAAAGTGTCGATACTTTAATATAAGTATCGACACTTT
54 ------A-AAA-AA-TACCGGATATGTTGAAAGTGTCGATAATTTAATATAAGTATCGAAACTTT
*
282531 T-GAAATTTAAAAGAGAAGAAGTTATAGCGCCTATAAAGTATCGA
110 TAG-AATTTAAAAGAGAAGAAGTTATAGCGCCTATAAAGTGTCGA
282575 CAGTCTTTAA
Statistics
Matches: 458, Mismatches: 46, Indels: 42
0.84 0.08 0.08
Matches are distributed among these distances:
179 98 0.21
180 1 0.00
181 4 0.01
182 101 0.22
183 163 0.36
184 1 0.00
187 1 0.00
197 1 0.00
198 3 0.01
199 53 0.12
200 3 0.01
201 1 0.00
202 28 0.06
ACGTcount: A:0.45, C:0.13, G:0.15, T:0.27
Consensus pattern (182 bp):
AATATAACAAGTAAAAATATGATAAAACCAGGTCTCAAAATGACAAAACCGGTAAAAAATACCGG
ATATGTTGAAAGTGTCGATAATTTAATATAAGTATCGAAACTTTTAGAATTTAAAAGAGAAGAAG
TTATAGCGCCTATAAAGTGTCGATACTTTAAAAAAATGTATCGATCCATAAC
Found at i:282471 original size:20 final size:20
Alignment explanation
Indices: 282420--282471 Score: 86
Period size: 20 Copynumber: 2.6 Consensus size: 20
282410 AACTAAAAAT
* *
282420 ATGATAAAACCAGTCTCAAA
1 ATGACAAAACCGGTCTCAAA
282440 ATGACAAAACCGGTCTCAAA
1 ATGACAAAACCGGTCTCAAA
282460 ATGACAAAACCG
1 ATGACAAAACCG
282472 ATAAAGAACT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.48, C:0.23, G:0.13, T:0.15
Consensus pattern (20 bp):
ATGACAAAACCGGTCTCAAA
Found at i:283070 original size:23 final size:23
Alignment explanation
Indices: 283020--283064 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
283010 TGCCTATTTT
*
283020 ATTATATAAGCGCTACCTATTAC
1 ATTATATAAGCGCTACCTAATAC
*
283043 ATTATATAAGCGTTACCTAATA
1 ATTATATAAGCGCTACCTAATA
283065 TGTTATTGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.38, C:0.18, G:0.09, T:0.36
Consensus pattern (23 bp):
ATTATATAAGCGCTACCTAATAC
Found at i:283084 original size:87 final size:87
Alignment explanation
Indices: 282936--283097 Score: 270
Period size: 87 Copynumber: 1.9 Consensus size: 87
282926 AAATAGGTCA
* *
282936 ATATAAGCGCTATCTATTACAATATATAAGCGCTACCTAATATATTATTGTACTTGGTAATATTT
1 ATATAAGCGCTACCTATTACAATATATAAGCGCTACCTAATATATTATTGTACTTGATAATATTT
283001 CCGGTTAAATGCCTATTTTATT
66 CCGGTTAAATGCCTATTTTATT
* * * *
283023 ATATAAGCGCTACCTATTACATTATATAAGCGTTACCTAATATGTTATTGTGCTTGATAATATTT
1 ATATAAGCGCTACCTATTACAATATATAAGCGCTACCTAATATATTATTGTACTTGATAATATTT
283088 CCGGTTAAAT
66 CCGGTTAAAT
283098 AATATAACAT
Statistics
Matches: 69, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
87 69 1.00
ACGTcount: A:0.32, C:0.15, G:0.12, T:0.41
Consensus pattern (87 bp):
ATATAAGCGCTACCTATTACAATATATAAGCGCTACCTAATATATTATTGTACTTGATAATATTT
CCGGTTAAATGCCTATTTTATT
Found at i:283847 original size:14 final size:14
Alignment explanation
Indices: 283823--283859 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
283813 GTTGTTCATT
283823 TATTACGTTCGTTTA
1 TATT-CGTTCGTTTA
*
283838 TATTCGTTCGTTTG
1 TATTCGTTCGTTTA
283852 TATTCGTT
1 TATTCGTT
283860 TACGTTCGTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
14 17 0.81
15 4 0.19
ACGTcount: A:0.14, C:0.14, G:0.16, T:0.57
Consensus pattern (14 bp):
TATTCGTTCGTTTA
Found at i:284633 original size:87 final size:87
Alignment explanation
Indices: 284487--284736 Score: 446
Period size: 87 Copynumber: 2.9 Consensus size: 87
284477 TATGTTATAT
* *
284487 TATTTAACCGGAAATATTATCAAGTACAATAACATATTAGGTAACGCTTATATAATGTAATAAAT
1 TATTTAACGGGAAATATTATCAAGTACAATAACATATTAGGTAACGCTTATATAATGTAATAGAT
*
284552 AGCGCTTATATGATAAAATAGG
66 AGCGCTTATATAATAAAATAGG
*
284574 TATTTAACGGGAAATATTATCAAGTACAATAACATATTAGGTAACACTTATATAATGTAATAGAT
1 TATTTAACGGGAAATATTATCAAGTACAATAACATATTAGGTAACGCTTATATAATGTAATAGAT
284639 AGCGCTTATATAATAAAATAGG
66 AGCGCTTATATAATAAAATAGG
* *
284661 TATTTAACGGGAAATATTATCAAGTACAATAACATATTAGGTAGCGCTTATATAATGTAATAGGT
1 TATTTAACGGGAAATATTATCAAGTACAATAACATATTAGGTAACGCTTATATAATGTAATAGAT
284726 AGCGCTTATAT
66 AGCGCTTATAT
284737 TGACCTTTTT
Statistics
Matches: 156, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
87 156 1.00
ACGTcount: A:0.42, C:0.10, G:0.15, T:0.33
Consensus pattern (87 bp):
TATTTAACGGGAAATATTATCAAGTACAATAACATATTAGGTAACGCTTATATAATGTAATAGAT
AGCGCTTATATAATAAAATAGG
Found at i:288463 original size:120 final size:120
Alignment explanation
Indices: 288250--288496 Score: 440
Period size: 120 Copynumber: 2.1 Consensus size: 120
288240 TTTTTCTTCC
* *
288250 ATTCTAGACATAAAGTACCGACACAATATTAAAAAGTGTCGACATAGGTTGTAGACCTATTCGCT
1 ATTCTGGACATAAAGTACCGACACAAAATTAAAAAGTGTCGACATAGGTTGTAGACCTATTCGCT
288315 AATAAAACCGGTATACTTATACCGGTTATATTACAAAATTATCTAGTACATTATA
66 AATAAAACCGGTATACTTATACCGGTTATATTACAAAATTATCTAGTACATTATA
*
288370 ATTCTGGACATAAAGTACCGACACAAAATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCT
1 ATTCTGGACATAAAGTACCGACACAAAATTAAAAAGTGTCGACATAGGTTGTAGACCTATTCGCT
* * *
288435 CATAAAACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATA
66 AATAAAACCGGTATACTTATACCGGTTATATTACAAAATTATCTAGTACATTATA
288490 ATTCTGG
1 ATTCTGG
288497 GTTCCGATGT
Statistics
Matches: 121, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
120 121 1.00
ACGTcount: A:0.38, C:0.16, G:0.14, T:0.32
Consensus pattern (120 bp):
ATTCTGGACATAAAGTACCGACACAAAATTAAAAAGTGTCGACATAGGTTGTAGACCTATTCGCT
AATAAAACCGGTATACTTATACCGGTTATATTACAAAATTATCTAGTACATTATA
Found at i:288647 original size:303 final size:303
Alignment explanation
Indices: 288086--288679 Score: 1089
Period size: 303 Copynumber: 2.0 Consensus size: 303
288076 TAAAATTAGT
*
288086 GACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTTA
1 GACACAAAATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTTA
288151 TACCAGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGATGTGTAAATGTCGAC
66 TACCAGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGATGTGTAAATGTCGAC
288216 ACTTTTTGACAAGGTATCAACATATTTTTCTTCCATTCTAGACATAAAGTACCGACACAATATTA
131 ACTTTTTGACAAGGTATCAACATATTTTTCTTCCATTCTAGACATAAAGTACCGACACAATATTA
*
288281 AAAAGTGTCGACATAGGTTGTAGACCTATTCGCTAATAAAACCGGTATACTTATACCGGTTATAT
196 AAAAGTGTCGACATAGGTTATAGACCTATTCGCTAATAAAACCGGTATACTTATACCGGTTATAT
288346 TACAAAATTATCTAGTACATTATAATTCTGGACATAAAGTACC
261 TACAAAATTATCTAGTACATTATAATTCTGGACATAAAGTACC
288389 GACACAAAATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTTA
1 GACACAAAATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTTA
*
288454 TACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGATGTGTAAATGTCGAC
66 TACCAGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGATGTGTAAATGTCGAC
* * *
288519 ACTTTTTGATAAGGTATCGACATATTTTTCTTCCATTCTGGACATAAAGTACCGACACAATATTA
131 ACTTTTTGACAAGGTATCAACATATTTTTCTTCCATTCTAGACATAAAGTACCGACACAATATTA
* * * *
288584 AAAAGTGTCGATATAGGTTATAGACCTATTCGCTCATAAAACCGGTATATTTATACTGGTTATAT
196 AAAAGTGTCGACATAGGTTATAGACCTATTCGCTAATAAAACCGGTATACTTATACCGGTTATAT
*
288649 TACAAAATTATCTATTACATTATAATTCTGG
261 TACAAAATTATCTAGTACATTATAATTCTGG
288680 GTTCCGATGT
Statistics
Matches: 280, Mismatches: 11, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
303 280 1.00
ACGTcount: A:0.35, C:0.16, G:0.14, T:0.35
Consensus pattern (303 bp):
GACACAAAATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTTA
TACCAGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGATGTGTAAATGTCGAC
ACTTTTTGACAAGGTATCAACATATTTTTCTTCCATTCTAGACATAAAGTACCGACACAATATTA
AAAAGTGTCGACATAGGTTATAGACCTATTCGCTAATAAAACCGGTATACTTATACCGGTTATAT
TACAAAATTATCTAGTACATTATAATTCTGGACATAAAGTACC
Found at i:288678 original size:183 final size:182
Alignment explanation
Indices: 288370--288958 Score: 1027
Period size: 183 Copynumber: 3.2 Consensus size: 182
288360 GTACATTATA
*
288370 ATTCTGGACATAAAGTACCGACACAAAATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCT
1 ATTCTGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCT
288435 CATAAAACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTT
66 CATAAAACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTT
* *
288500 CCGATGTGTAAATGTCGACACTTTTTGATAAGGTATCGACATATTTTTCTTCC
131 CCGATGTGTAAAT-TCGACACTTTTTGAAAAGGTATCGACACATTTTTCTTCC
*
288553 ATTCTGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTATAGACCTATTCGCT
1 ATTCTGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCT
*
288618 CATAAAACCGGTATATTTATACTGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTT
66 CATAAAACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTT
*
288683 CCGATGTGTAAATTTCGACACTTTTTGACAAGGTATCGACACATTTTTCTTCC
131 CCGATGTGTAAA-TTCGACACTTTTTGAAAAGGTATCGACACATTTTTCTTCC
*
288736 ATTCTGGACATAAAGTACCGATACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCT
1 ATTCTGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCT
* *
288801 CATAAAACCGGTATATTTATACCGATTATATTACAAAATTATCTATTACATTATAATTATGGGTT
66 CATAAAACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTT
* *
288866 CCGATGTTTTTTCAATT-GACACTTTTTGAAAAGGTATCGACACATTTTTCTTCC
131 CCGATG---TGTAAATTCGACACTTTTTGAAAAGGTATCGACACATTTTTCTTCC
288920 ATTCTGGACATAAAGTACCGACACAATATTAAAAAGTGT
1 ATTCTGGACATAAAGTACCGACACAATATTAAAAAGTGT
288959 GAAAACTTTG
Statistics
Matches: 388, Mismatches: 14, Indels: 7
0.95 0.03 0.02
Matches are distributed among these distances:
183 307 0.79
184 75 0.19
185 2 0.01
186 4 0.01
ACGTcount: A:0.34, C:0.16, G:0.14, T:0.36
Consensus pattern (182 bp):
ATTCTGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCT
CATAAAACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTT
CCGATGTGTAAATTCGACACTTTTTGAAAAGGTATCGACACATTTTTCTTCC
Found at i:290177 original size:3 final size:3
Alignment explanation
Indices: 290169--290225 Score: 60
Period size: 3 Copynumber: 19.0 Consensus size: 3
290159 ACTTGTTTGG
* * * * *
290169 ATC ATC ATC ATC ATC ATC ATC ATC ATC GTC GTC GTC ATC TTC ATC GTC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
*
290217 ATC TTC ATC
1 ATC ATC ATC
290226 GTCAGCTTCA
Statistics
Matches: 46, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.23, C:0.33, G:0.07, T:0.37
Consensus pattern (3 bp):
ATC
Found at i:290226 original size:12 final size:12
Alignment explanation
Indices: 290173--290242 Score: 77
Period size: 12 Copynumber: 5.8 Consensus size: 12
290163 GTTTGGATCA
* *
290173 TCATCATCATCA
1 TCATCGTCATCT
* *
290185 TCATCATCATCG
1 TCATCGTCATCT
*
290197 TCGTCGTCATCT
1 TCATCGTCATCT
290209 TCATCGTCATCT
1 TCATCGTCATCT
*
290221 TCATCGTCAGCT
1 TCATCGTCATCT
*
290233 TCATCTTCAT
1 TCATCGTCAT
290243 TGACCGCTTG
Statistics
Matches: 50, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 50 1.00
ACGTcount: A:0.20, C:0.33, G:0.09, T:0.39
Consensus pattern (12 bp):
TCATCGTCATCT
Found at i:291968 original size:200 final size:200
Alignment explanation
Indices: 291625--292403 Score: 1310
Period size: 200 Copynumber: 3.9 Consensus size: 200
291615 TTTAAATTAG
* * * * *
291625 TATCGACA-AAACATTAAACAGTGTCGATACA-TATTATATACCAATTCTCCCATAAAACCGGTA
1 TATCGACACAAAC-TAAAAAAGTGTCGATACATTATT-TAGACCTATTCTCTCATAAAACCGGTA
* * *
291688 TACTTATACCGGTTAGATTGAAAAATTACCTAATACATTATACTTTTGGGTTTCGATGTTTATGG
64 TACTTGTACCGGTTAGATTGAAAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTATGG
* *
291753 GATCGACACTTTTTATATATGGATCGACACTTTATGGTTACACCCTGTTTGCCATTCATTCTGGA
129 GATCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCATGTTTGCCATTCATTCTGGA
291818 CCAAAAA
194 CCAAAAA
*
291825 TATCGACACAAACTAAAAAAGTGTCGACACATTATTTAGACCTATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTAAAAAAGTGTCGATACATTATTTAGACCTATTCTCTCATAAAACCGGTATA
*
291890 CTTGTACTGGTTAGATTGAAAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTATGGGA
66 CTTGTACCGGTTAGATTGAAAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTATGGGA
*
291955 TCGACACTTTTTATATATGGATCGACACTTTATTGTTGCACCATGTTTGCCATTCATTCTGGACC
131 TCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCATGTTTGCCATTCATTCTGGACC
292020 AAAAA
196 AAAAA
*
292025 TATCGACACAAACTACAAAAGTGTCGATACATTATTTAGACCTATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTAAAAAAGTGTCGATACATTATTTAGACCTATTCTCTCATAAAACCGGTATA
*
292090 CTTGTACCGGTTAGATTGAAAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTATCGGA
66 CTTGTACCGGTTAGATTGAAAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTATGGGA
* * *
292155 TCGACACTTTTTATATATGGATCGACACTTTATTGTTGCACCCTATTTGCCATTCATTCTGGACC
131 TCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCATGTTTGCCATTCATTCTGGACC
292220 AAAAA
196 AAAAA
* * **
292225 TATCGACACAAACTACAAAAGTGTCGATACGTTATTTAGACCTATTCTCTCATAAAACTAGTATA
1 TATCGACACAAACTAAAAAAGTGTCGATACATTATTTAGACCTATTCTCTCATAAAACCGGTATA
* *
292290 CTTGTACCGATTAGATTGAAAAATTACCTATTACATTATACTTTTGGGTTTCGATGTTTATGGGA
66 CTTGTACCGGTTAGATTGAAAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTATGGGA
292355 TCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCATGTTTG
131 TCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCATGTTTG
292404 ACATATTGTA
Statistics
Matches: 549, Mismatches: 28, Indels: 4
0.94 0.05 0.01
Matches are distributed among these distances:
200 541 0.99
201 8 0.01
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.36
Consensus pattern (200 bp):
TATCGACACAAACTAAAAAAGTGTCGATACATTATTTAGACCTATTCTCTCATAAAACCGGTATA
CTTGTACCGGTTAGATTGAAAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTATGGGA
TCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCATGTTTGCCATTCATTCTGGACC
AAAAA
Found at i:292651 original size:18 final size:18
Alignment explanation
Indices: 292628--292688 Score: 59
Period size: 19 Copynumber: 3.3 Consensus size: 18
292618 TCTCATTCAT
*
292628 AATTATATTCACATACAA
1 AATTATAATCACATACAA
**
292646 AATTATAAATCGTATACAA
1 AATTAT-AATCACATACAA
**
292665 AATTATAAATCTTATACAA
1 AATTAT-AATCACATACAA
292684 AATTA
1 AATTA
292689 ACCCTACATT
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
18 6 0.16
19 32 0.84
ACGTcount: A:0.52, C:0.11, G:0.02, T:0.34
Consensus pattern (18 bp):
AATTATAATCACATACAA
Found at i:292664 original size:19 final size:19
Alignment explanation
Indices: 292640--292688 Score: 89
Period size: 19 Copynumber: 2.6 Consensus size: 19
292630 TTATATTCAC
292640 ATACAAAATTATAAATCGT
1 ATACAAAATTATAAATCGT
*
292659 ATACAAAATTATAAATCTT
1 ATACAAAATTATAAATCGT
292678 ATACAAAATTA
1 ATACAAAATTA
292689 ACCCTACATT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.55, C:0.10, G:0.02, T:0.33
Consensus pattern (19 bp):
ATACAAAATTATAAATCGT
Found at i:294520 original size:33 final size:33
Alignment explanation
Indices: 294483--294548 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
294473 CATCTTAATA
* *
294483 TCACCCCTTAACACCCCAACTTCTTTTACCACT
1 TCACCCCTCAACACCCCAACTTCTTTCACCACT
* *
294516 TCACCCCTCAACACCTCTACTTCTTTCACCACT
1 TCACCCCTCAACACCCCAACTTCTTTCACCACT
294549 CCATCTACTT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.23, C:0.47, G:0.00, T:0.30
Consensus pattern (33 bp):
TCACCCCTCAACACCCCAACTTCTTTCACCACT
Found at i:294607 original size:21 final size:21
Alignment explanation
Indices: 294582--294646 Score: 94
Period size: 21 Copynumber: 3.1 Consensus size: 21
294572 CCCCTTATGC
* *
294582 CTCTCAAGTGTATCTTCGACT
1 CTCTCAAGTTTCTCTTCGACT
*
294603 CTCTCAAGTTTCTCTTCGACC
1 CTCTCAAGTTTCTCTTCGACT
*
294624 CTATCAAGTTTCTCTTCGACT
1 CTCTCAAGTTTCTCTTCGACT
294645 CT
1 CT
294647 TGATTATCTT
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 39 1.00
ACGTcount: A:0.17, C:0.32, G:0.11, T:0.40
Consensus pattern (21 bp):
CTCTCAAGTTTCTCTTCGACT
Found at i:296932 original size:20 final size:19
Alignment explanation
Indices: 296877--296923 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
296867 TCCGGTATAG
296877 TTTTACCAGTTTTATCATT
1 TTTTACCAGTTTTATCATT
* *
296896 TTGATACCGGTTTTATCATAT
1 TT-TTACCAGTTTTATCAT-T
296917 TTTTACC
1 TTTTACC
296924 TGTTATATCG
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
19 2 0.09
20 18 0.78
21 3 0.13
ACGTcount: A:0.21, C:0.17, G:0.09, T:0.53
Consensus pattern (19 bp):
TTTTACCAGTTTTATCATT
Found at i:297101 original size:20 final size:19
Alignment explanation
Indices: 297055--297101 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
297045 TCTGGTAACG
297055 TTTTACCGATTTTATCATT
1 TTTTACCGATTTTATCATT
* *
297074 TTGATACCGGTTTTATCATAT
1 TT-TTACCGATTTTATCAT-T
297095 TTTTACC
1 TTTTACC
297102 TGGTATATCG
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
19 2 0.09
20 18 0.78
21 3 0.13
ACGTcount: A:0.21, C:0.17, G:0.09, T:0.53
Consensus pattern (19 bp):
TTTTACCGATTTTATCATT
Found at i:297285 original size:182 final size:181
Alignment explanation
Indices: 296844--297313 Score: 660
Period size: 182 Copynumber: 2.6 Consensus size: 181
296834 CGTACTTACG
* * *
296844 AAAGTATCGACACTTTCAATATATCCGGTATA-GTTTTACCAGTTTTATCATTTTGATACCGGTT
1 AAAGTACCGACACTTTCAATATATCTGGTA-ACGTTTTACCGGTTTTATCATTTTGATACCGGTT
* * *
296908 TTATCATATTTTTACCTGTTATATCGTTGTGGAT--ATA-TTTTTTTTAAAGTATCGACACATTA
65 TTATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTTTAAAAGTATCGACACATTA
*
296970 TAGGCGCTAAAACTGATTCTCTTTTAAATTCACAAAGTGTCGATCCTTATAT
130 TAGGAGCTAAAACTGATTCTCTTTTAAATTCACAAAGTGTCGATCCTTATAT
* *
297022 AAAGTATCGACACTTTCAATATATCTGGTAACGTTTTACCGATTTTATCATTTTGATACCGGTTT
1 AAAGTACCGACACTTTCAATATATCTGGTAACGTTTTACCGGTTTTATCATTTTGATACCGGTTT
* *
297087 TATCATATTTTTACCTGGTATATCGTTTTGGATCGATACATTTTTTAAAAGTATCGACACTTTAT
66 TATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTTTAAAAGTATCGACACATTAT
** *
297152 AGGATTTAAAACTGATTCTCTTTTAAATTCACGAAGTGTCGATCCTTATATT
131 AGGAGCTAAAACTGATTCTCTTTTAAATTCACAAAGTGTCGATCCTTATA-T
* * * * * ** *
297204 AAATTACCGACACTTTAAATGTATCTGGTAGCGCTTTACCGGTTTTATCATTTCAATACCGGCTT
1 AAAGTACCGACACTTTCAATATATCTGGTAACGTTTTACCGGTTTTATCATTTTGATACCGGTTT
* * * *
297269 TGTCATAGTCTTACCTGTTATACCGTTTTGGATCGATACATTTTT
66 TATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTT
297314 AATTTGGATC
Statistics
Matches: 260, Mismatches: 27, Indels: 6
0.89 0.09 0.02
Matches are distributed among these distances:
177 1 0.00
178 91 0.35
180 3 0.01
181 69 0.27
182 96 0.37
ACGTcount: A:0.27, C:0.17, G:0.14, T:0.42
Consensus pattern (181 bp):
AAAGTACCGACACTTTCAATATATCTGGTAACGTTTTACCGGTTTTATCATTTTGATACCGGTTT
TATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTTTAAAAGTATCGACACATTAT
AGGAGCTAAAACTGATTCTCTTTTAAATTCACAAAGTGTCGATCCTTATAT
Found at i:297315 original size:181 final size:180
Alignment explanation
Indices: 296844--297315 Score: 653
Period size: 178 Copynumber: 2.6 Consensus size: 180
296834 CGTACTTACG
* * *
296844 AAAGTATCGACACTTTCAATATATCCGGTATA-GTTTTACCAGTTTTATCATTTTGATACCGGTT
1 AAAGTACCGACACTTTCAATATATCTGGTA-ACGTTTTACCGGTTTTATCATTTTGATACCGGTT
* ** *
296908 TTATCATATTTTTACCTGTTATATCGTTGTGGAT--ATATTTTTTTTAAAGTATCGACACATTAT
65 TTATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTTAAAAGTATCGACACATTAT
*
296971 AGGCGCTAAAACTGATTCTCTTTTAAATTCACAAAGTGTCGATCCTTATAT
130 AGGAGCTAAAACTGATTCTCTTTTAAATTCACAAAGTGTCGATCCTTATAT
* *
297022 AAAGTATCGACACTTTCAATATATCTGGTAACGTTTTACCGATTTTATCATTTTGATACCGGTTT
1 AAAGTACCGACACTTTCAATATATCTGGTAACGTTTTACCGGTTTTATCATTTTGATACCGGTTT
* *
297087 TATCATATTTTTACCTGGTATATCGTTTTGGATCGATACATTTTTTAAAAGTATCGACACTTTAT
66 TATCATATTTTTACCTGTTATATCGTTTTGGATCGATACA-TTTTTAAAAGTATCGACACATTAT
** *
297152 AGGATTTAAAACTGATTCTCTTTTAAATTCACGAAGTGTCGATCCTTATATT
130 AGGAGCTAAAACTGATTCTCTTTTAAATTCACAAAGTGTCGATCCTTATA-T
* * * * * ** *
297204 AAATTACCGACACTTTAAATGTATCTGGTAGCGCTTTACCGGTTTTATCATTTCAATACCGGCTT
1 AAAGTACCGACACTTTCAATATATCTGGTAACGTTTTACCGGTTTTATCATTTTGATACCGGTTT
* * * *
297269 TGTCATAGTCTTACCTGTTATACCGTTTTGGATCGATACATTTTTAA
66 TATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTTAA
297316 TTTGGATCGA
Statistics
Matches: 261, Mismatches: 28, Indels: 7
0.88 0.09 0.02
Matches are distributed among these distances:
177 1 0.00
178 91 0.35
180 3 0.01
181 75 0.29
182 91 0.35
ACGTcount: A:0.28, C:0.17, G:0.14, T:0.42
Consensus pattern (180 bp):
AAAGTACCGACACTTTCAATATATCTGGTAACGTTTTACCGGTTTTATCATTTTGATACCGGTTT
TATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTTAAAAGTATCGACACATTATA
GGAGCTAAAACTGATTCTCTTTTAAATTCACAAAGTGTCGATCCTTATAT
Found at i:297483 original size:11 final size:11
Alignment explanation
Indices: 297467--297491 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
297457 ATCCGGTAAC
297467 ACCGTATATTA
1 ACCGTATATTA
297478 ACCGTATATTA
1 ACCGTATATTA
297489 ACC
1 ACC
297492 CGTCTTTCCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.36, C:0.24, G:0.08, T:0.32
Consensus pattern (11 bp):
ACCGTATATTA
Found at i:304540 original size:23 final size:23
Alignment explanation
Indices: 304487--304541 Score: 76
Period size: 23 Copynumber: 2.4 Consensus size: 23
304477 ATGTAGAAAT
304487 AGAGTTTTTCGATTCTGGTAAAC
1 AGAGTTTTTCGATTCTGGTAAAC
*
304510 AGAATTTTTC-AGTTCTGGTAAAC
1 AGAGTTTTTCGA-TTCTGGTAAAC
*
304533 AGGGTTTTT
1 AGAGTTTTT
304542 TTATTTTGAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
22 1 0.04
23 27 0.96
ACGTcount: A:0.25, C:0.11, G:0.22, T:0.42
Consensus pattern (23 bp):
AGAGTTTTTCGATTCTGGTAAAC
Found at i:306798 original size:12 final size:12
Alignment explanation
Indices: 306781--306814 Score: 52
Period size: 12 Copynumber: 2.8 Consensus size: 12
306771 AATGCGTGTT
306781 ATTTTATCAT-AA
1 ATTTTAT-ATAAA
306793 ATTTTATATAAA
1 ATTTTATATAAA
306805 ATTTTATATA
1 ATTTTATATA
306815 TTAATAGTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 2 0.10
12 19 0.90
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (12 bp):
ATTTTATATAAA
Found at i:308128 original size:21 final size:21
Alignment explanation
Indices: 308104--308158 Score: 101
Period size: 21 Copynumber: 2.6 Consensus size: 21
308094 CATATATACA
*
308104 TTCATATCATATAGTCATATT
1 TTCATATCACATAGTCATATT
308125 TTCATATCACATAGTCATATT
1 TTCATATCACATAGTCATATT
308146 TTCATATCACATA
1 TTCATATCACATA
308159 TATCATGTAA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.35, C:0.18, G:0.04, T:0.44
Consensus pattern (21 bp):
TTCATATCACATAGTCATATT
Found at i:312148 original size:23 final size:23
Alignment explanation
Indices: 312105--312148 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
312095 ACATAGAATT
*
312105 TGTCTCGAAGGACAATGTAGAAA
1 TGTCTCGAAGGACAATATAGAAA
*
312128 TGTCTCGAAGGACTATATAGA
1 TGTCTCGAAGGACAATATAGA
312149 TGTCCCGAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.36, C:0.14, G:0.25, T:0.25
Consensus pattern (23 bp):
TGTCTCGAAGGACAATATAGAAA
Found at i:315927 original size:27 final size:27
Alignment explanation
Indices: 315897--315951 Score: 92
Period size: 27 Copynumber: 2.0 Consensus size: 27
315887 AGGCTAAGAC
* *
315897 ATAATCTCTATTTATTTTTTTGAACAA
1 ATAATCTCTATTTATTTTATTAAACAA
315924 ATAATCTCTATTTATTTTATTAAACAA
1 ATAATCTCTATTTATTTTATTAAACAA
315951 A
1 A
315952 CCTAATAACC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.38, C:0.11, G:0.02, T:0.49
Consensus pattern (27 bp):
ATAATCTCTATTTATTTTATTAAACAA
Found at i:326573 original size:31 final size:31
Alignment explanation
Indices: 326519--326643 Score: 110
Period size: 31 Copynumber: 4.0 Consensus size: 31
326509 GATCCTTGGC
* * *
326519 AACTGTCCATAGGTGCCGA-AGAACCTAGGTA
1 AACTGTCCATATGTTCC-ATAGAACATAGGTA
* *
326550 AACAGTCCATATGTTCCTTAGAACATAGGTA
1 AACTGTCCATATGTTCCATAGAACATAGGTA
* * * *
326581 TATTGTCCATATGTCTCGAAAG-ACATAGGTA
1 AACTGTCCATATGT-TCCATAGAACATAGGTA
* *
326612 ATTCTGTCCATATGTTCCGTAGAACATAGGTA
1 A-ACTGTCCATATGTTCCATAGAACATAGGTA
326644 TACCCTCGAC
Statistics
Matches: 73, Mismatches: 17, Indels: 7
0.75 0.18 0.07
Matches are distributed among these distances:
31 49 0.67
32 24 0.33
ACGTcount: A:0.32, C:0.19, G:0.20, T:0.29
Consensus pattern (31 bp):
AACTGTCCATATGTTCCATAGAACATAGGTA
Found at i:331016 original size:31 final size:31
Alignment explanation
Indices: 330981--331086 Score: 106
Period size: 31 Copynumber: 3.4 Consensus size: 31
330971 TAGGTTCTGA
* * *
330981 AGAACCTAGGTAAACAGTCCATATGTTCCTT
1 AGAACATAGGTAAACTGTCCATATGTTCCAT
* * * *
331012 AGAACATAGGTATATTGTCCATATGTCTCGAA
1 AGAACATAGGTAAACTGTCCATATGT-TCCAT
* *
331044 AG-ACATAGGTAATTCTGTCCATATGTTCCGT
1 AGAACATAGGTAA-ACTGTCCATATGTTCCAT
331075 AGAACATAGGTA
1 AGAACATAGGTA
331087 TACCCTCGAC
Statistics
Matches: 59, Mismatches: 13, Indels: 5
0.77 0.17 0.06
Matches are distributed among these distances:
31 35 0.59
32 24 0.41
ACGTcount: A:0.33, C:0.18, G:0.19, T:0.30
Consensus pattern (31 bp):
AGAACATAGGTAAACTGTCCATATGTTCCAT
Found at i:331082 original size:32 final size:32
Alignment explanation
Indices: 330997--331086 Score: 107
Period size: 32 Copynumber: 2.8 Consensus size: 32
330987 TAGGTAAACA
*
330997 GTCCATATGTTCCTTAGAACATAGGT-ATATT
1 GTCCATATGTTCCGTAGAACATAGGTAATATT
*
331028 GTCCATATG-TCTCG-AAAGACATAGGTAAT-TCT
1 GTCCATATGTTC-CGTAGA-ACATAGGTAATAT-T
331060 GTCCATATGTTCCGTAGAACATAGGTA
1 GTCCATATGTTCCGTAGAACATAGGTA
331087 TACCCTCGAC
Statistics
Matches: 50, Mismatches: 3, Indels: 11
0.78 0.05 0.17
Matches are distributed among these distances:
30 4 0.08
31 19 0.38
32 23 0.46
33 4 0.08
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.33
Consensus pattern (32 bp):
GTCCATATGTTCCGTAGAACATAGGTAATATT
Found at i:334477 original size:13 final size:13
Alignment explanation
Indices: 334459--334483 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
334449 ATATTACGTG
334459 TTTATTAATTTTA
1 TTTATTAATTTTA
334472 TTTATTAATTTT
1 TTTATTAATTTT
334484 TCACATAAAT
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:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (13 bp):
TTTATTAATTTTA
Found at i:342429 original size:20 final size:21
Alignment explanation
Indices: 342392--342430 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
342382 TTTTGCAACG
*
342392 CTTAAAAACGTCGTTATAGGA
1 CTTAAAAACGTCGCTATAGGA
*
342413 CTTAAAAATG-CGCTATAG
1 CTTAAAAACGTCGCTATAG
342431 AACAATTATG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 7 0.44
21 9 0.56
ACGTcount: A:0.38, C:0.15, G:0.18, T:0.28
Consensus pattern (21 bp):
CTTAAAAACGTCGCTATAGGA
Found at i:349040 original size:24 final size:23
Alignment explanation
Indices: 348963--349043 Score: 63
Period size: 28 Copynumber: 3.1 Consensus size: 23
348953 TTAGACAATA
348963 ATAAAATATATATTTTTAAATTAAATT
1 ATAAAA-A-ATATTTTTAAATT-AA-T
*
348990 AGTAATAAAATATATTTAATAATTTAAT
1 A-TAA-AAAATAT-TTT--TAAATTAAT
349018 ATAAAAAATATTTTTAAAGTTAAT
1 ATAAAAAATATTTTTAAA-TTAAT
349042 AT
1 AT
349044 GTATAAAATA
Statistics
Matches: 46, Mismatches: 2, Indels: 15
0.73 0.03 0.24
Matches are distributed among these distances:
23 3 0.07
24 7 0.15
25 3 0.07
26 7 0.15
27 8 0.17
28 9 0.20
29 4 0.09
30 5 0.11
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.44
Consensus pattern (23 bp):
ATAAAAAATATTTTTAAATTAAT
Found at i:349051 original size:26 final size:25
Alignment explanation
Indices: 348972--349055 Score: 66
Period size: 26 Copynumber: 3.2 Consensus size: 25
348962 AATAAAATAT
348972 ATATTTTTAAATTAA-ATTAGTAATAAA
1 ATATTTTTAAATTAATA-T-GT-ATAAA
* *
348999 ATATATTTAATAATTTAATA--TAAAAA
1 ATAT-TTT--TAAATTAATATGTATAAA
349025 ATATTTTTAAAGTTAATATGTATAAA
1 ATATTTTTAAA-TTAATATGTATAAA
349051 ATATT
1 ATATT
349056 ATGAATTTAA
Statistics
Matches: 46, Mismatches: 4, Indels: 15
0.71 0.06 0.23
Matches are distributed among these distances:
23 3 0.07
24 6 0.13
25 3 0.07
26 18 0.39
27 5 0.11
28 3 0.07
30 7 0.15
31 1 0.02
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.45
Consensus pattern (25 bp):
ATATTTTTAAATTAATATGTATAAA
Found at i:350090 original size:31 final size:31
Alignment explanation
Indices: 350030--350135 Score: 115
Period size: 31 Copynumber: 3.4 Consensus size: 31
350020 AAAACATAAG
* *
350030 TTTTGGTCACTCACATTATTGTTTTTATTAAA
1 TTTTAGTCACTTACATTATTG-TTTTATTAAA
* *
350062 TTTT-GATCGCTTACATTATTGTTTTATTAAG
1 TTTTAG-TCACTTACATTATTGTTTTATTAAA
* * *
350093 TTTTAGTCACTTACGTTATCGTTTTATTAAG
1 TTTTAGTCACTTACATTATTGTTTTATTAAA
*
350124 CTTTAGTCACTT
1 TTTTAGTCACTT
350136 CACTTGGATA
Statistics
Matches: 65, Mismatches: 7, Indels: 5
0.84 0.09 0.06
Matches are distributed among these distances:
31 47 0.72
32 18 0.28
ACGTcount: A:0.23, C:0.13, G:0.11, T:0.53
Consensus pattern (31 bp):
TTTTAGTCACTTACATTATTGTTTTATTAAA
Found at i:354203 original size:15 final size:15
Alignment explanation
Indices: 354179--354215 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
354169 AGCCGAAGAT
* *
354179 TCAATTGCATCATCA
1 TCAATAGCATCAACA
354194 TCAATAGCATCAACA
1 TCAATAGCATCAACA
354209 TCAATAG
1 TCAATAG
354216 TTGCAGGCGG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.41, C:0.24, G:0.08, T:0.27
Consensus pattern (15 bp):
TCAATAGCATCAACA
Found at i:355162 original size:21 final size:21
Alignment explanation
Indices: 355136--355184 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
355126 TACCATATTG
*
355136 AGATTAATTACCATAATAGGT
1 AGATTAATTACCATAATAGGA
**
355157 AGATTAATTACCATGGTAGGA
1 AGATTAATTACCATAATAGGA
355178 AGATTAA
1 AGATTAA
355185 GTGTTAGATT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.43, C:0.08, G:0.18, T:0.31
Consensus pattern (21 bp):
AGATTAATTACCATAATAGGA
Found at i:360692 original size:18 final size:19
Alignment explanation
Indices: 360652--360695 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
360642 TTTGGTTCAC
*
360652 GGAATATAAGATTACCAGTG
1 GGAATAAAAGATTACCAG-G
*
360672 GGAATAAAAGATTATCA-G
1 GGAATAAAAGATTACCAGG
360690 GGAATA
1 GGAATA
360696 GGATTATTGA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 7 0.32
20 15 0.68
ACGTcount: A:0.45, C:0.07, G:0.25, T:0.23
Consensus pattern (19 bp):
GGAATAAAAGATTACCAGG
Done.