Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009055.1 Hibiscus syriacus cultivar Beakdansim tig00112470_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: 451578
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 3
Found at i:130693 original size:19 final size:19
Alignment explanation
Indices: 130671--130707 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
130661 ATCACTGAGA
130671 TTATTTTCTCTAAAATAAG
1 TTATTTTCTCTAAAATAAG
*
130690 TTATTTTCTTTAAAATAA
1 TTATTTTCTCTAAAATAA
130708 ACAAAAAATG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.38, C:0.08, G:0.03, T:0.51
Consensus pattern (19 bp):
TTATTTTCTCTAAAATAAG
Found at i:139562 original size:153 final size:154
Alignment explanation
Indices: 139284--139595 Score: 617
Period size: 153 Copynumber: 2.0 Consensus size: 154
139274 CAGTTGCTTA
139284 AACTTGATGATTGGGATTTGATAGTCGTTTGAGATTTTGTGATCGAATTTTATCATATCACAATT
1 AACTTGATGATTGGGATTTGATAGTCGTTTGAGATTTTGTGATCGAATTTTATCATATCACAATT
139349 AACAAGTTAACGTTCAGCTCAGAATATCATTTATTTTTTAATGGAAAATGACGAGTTTGAAACAT
66 AACAAGTTAACGTTCAGCTCAGAATATCATTTATTTTTTAATGGAAAATGACGAGTTTGAAACAT
139414 AATAAATAGCC-GTGATATTTTGT
131 AATAAATAGCCGGTGATATTTTGT
139437 AACTTGATGATTGGGATTTGATAGTCGTTTGAGATTTTGTGATCGAATTTTATCATATCACAATT
1 AACTTGATGATTGGGATTTGATAGTCGTTTGAGATTTTGTGATCGAATTTTATCATATCACAATT
139502 AACAAGTTAACGTTCAGCTCAGAATATCATTTATTTTTTAATGGAAAATGACGAGTTTGAAACAT
66 AACAAGTTAACGTTCAGCTCAGAATATCATTTATTTTTTAATGGAAAATGACGAGTTTGAAACAT
139567 AATAAATAGCCGGTGATATTTTGT
131 AATAAATAGCCGGTGATATTTTGT
139591 AACTT
1 AACTT
139596 TTAATAGTCG
Statistics
Matches: 158, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
153 141 0.89
154 17 0.11
ACGTcount: A:0.33, C:0.11, G:0.18, T:0.38
Consensus pattern (154 bp):
AACTTGATGATTGGGATTTGATAGTCGTTTGAGATTTTGTGATCGAATTTTATCATATCACAATT
AACAAGTTAACGTTCAGCTCAGAATATCATTTATTTTTTAATGGAAAATGACGAGTTTGAAACAT
AATAAATAGCCGGTGATATTTTGT
Found at i:140016 original size:23 final size:22
Alignment explanation
Indices: 139972--140016 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
139962 CGGTAAAATA
139972 TTACCTAAAACATTATTTTTTT
1 TTACCTAAAACATTATTTTTTT
*
139994 TTACCTAAAACATTAATTTTTT
1 TTACCTAAAACATTATTTTTTT
140016 T
1 T
140017 CAATATTTCC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.33, C:0.13, G:0.00, T:0.53
Consensus pattern (22 bp):
TTACCTAAAACATTATTTTTTT
Found at i:140257 original size:31 final size:31
Alignment explanation
Indices: 140222--140284 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
140212 TGTATCCATC
140222 GTAAATTCAATTCAAGTCCAAAAACCATTTT
1 GTAAATTCAATTCAAGTCCAAAAACCATTTT
140253 GTAAATTCAATTCAAGTCCAAAAACCATTTT
1 GTAAATTCAATTCAAGTCCAAAAACCATTTT
140284 G
1 G
140285 CCTTAAATTG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.41, C:0.19, G:0.08, T:0.32
Consensus pattern (31 bp):
GTAAATTCAATTCAAGTCCAAAAACCATTTT
Found at i:140819 original size:34 final size:32
Alignment explanation
Indices: 140776--140845 Score: 95
Period size: 34 Copynumber: 2.1 Consensus size: 32
140766 TTTTGTAAAG
* *
140776 GGGAAAGGTTCTAGCTTAGCCCGTATAAAAGCTA
1 GGGAAAGGTTCTAGCTTAACCCGGA-AAAA-CTA
*
140810 GGGAAAGGTTCTAGTTTAACCCGGAAAAACTA
1 GGGAAAGGTTCTAGCTTAACCCGGAAAAACTA
140842 GGGA
1 GGGA
140846 GTTGTAAGGT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 7 0.21
33 4 0.12
34 22 0.67
ACGTcount: A:0.34, C:0.16, G:0.29, T:0.21
Consensus pattern (32 bp):
GGGAAAGGTTCTAGCTTAACCCGGAAAAACTA
Found at i:141379 original size:31 final size:31
Alignment explanation
Indices: 141281--141371 Score: 168
Period size: 31 Copynumber: 3.0 Consensus size: 31
141271 CAATTTAAGG
141281 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1 CAAAATGGTTTTTGGACTTGAATTGAATTTA
141312 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1 CAAAATGGTTTTTGGACTTGAATTGAATTTA
141343 CAAAAT-GTTTTTGGACTT-AATTGAATTTA
1 CAAAATGGTTTTTGGACTTGAATTGAATTTA
141372 TTCAAAATTT
Statistics
Matches: 60, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
29 11 0.18
30 12 0.20
31 37 0.62
ACGTcount: A:0.33, C:0.07, G:0.18, T:0.43
Consensus pattern (31 bp):
CAAAATGGTTTTTGGACTTGAATTGAATTTA
Found at i:141463 original size:19 final size:19
Alignment explanation
Indices: 141436--141485 Score: 82
Period size: 19 Copynumber: 2.6 Consensus size: 19
141426 AATGTTTTTA
* *
141436 TGAATAGTAATTTACTATT
1 TGAACAGTAAATTACTATT
141455 TGAACAGTAAATTACTATT
1 TGAACAGTAAATTACTATT
141474 TGAACAGTAAAT
1 TGAACAGTAAAT
141486 CACTCTAAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.42, C:0.08, G:0.12, T:0.38
Consensus pattern (19 bp):
TGAACAGTAAATTACTATT
Found at i:143451 original size:15 final size:15
Alignment explanation
Indices: 143433--143465 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
143423 AAATTCTAAA
143433 TATTTAAATAAAAAT
1 TATTTAAATAAAAAT
*
143448 TATTTATATAAAAAT
1 TATTTAAATAAAAAT
143463 TAT
1 TAT
143466 ATTTGTTGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
TATTTAAATAAAAAT
Found at i:144274 original size:2 final size:2
Alignment explanation
Indices: 144267--144291 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
144257 TGTGTCGAAC
144267 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 A
144292 CGGAGATGCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:146688 original size:31 final size:33
Alignment explanation
Indices: 146653--146726 Score: 116
Period size: 33 Copynumber: 2.3 Consensus size: 33
146643 AAAACATAAT
*
146653 ATATGATCACTTT-G-ATTTTTATTTAATTAAG
1 ATATGGTCACTTTAGTATTTTTATTTAATTAAG
*
146684 ATATGGTCACTTTAGTTTTTTTATTTAATTAAG
1 ATATGGTCACTTTAGTATTTTTATTTAATTAAG
146717 ATATGGTCAC
1 ATATGGTCAC
146727 CCCGAGTTAA
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
31 12 0.31
32 1 0.03
33 26 0.67
ACGTcount: A:0.30, C:0.08, G:0.12, T:0.50
Consensus pattern (33 bp):
ATATGGTCACTTTAGTATTTTTATTTAATTAAG
Found at i:147176 original size:39 final size:39
Alignment explanation
Indices: 147070--147178 Score: 116
Period size: 39 Copynumber: 2.8 Consensus size: 39
147060 TTATTTGTAA
*
147070 TTCTCAAATTATTTCAC-TATAACATTCTAAAATCCTAAT
1 TTCTTAAATTATTTCACAT-TAACATTCTAAAATCCTAAT
* * * *
147109 TTCTTAAATT-TTGACACCA-TAATATTCTAAATTCTTAAT
1 TTCTTAAATTATT-TCA-CATTAACATTCTAAAATCCTAAT
*
147148 TTCTTAAATTATTTCACATTAACGTTCTAAA
1 TTCTTAAATTATTTCACATTAACATTCTAAA
147179 CTGTTTTTTA
Statistics
Matches: 57, Mismatches: 8, Indels: 10
0.76 0.11 0.13
Matches are distributed among these distances:
38 4 0.07
39 50 0.88
40 3 0.05
ACGTcount: A:0.37, C:0.17, G:0.02, T:0.44
Consensus pattern (39 bp):
TTCTTAAATTATTTCACATTAACATTCTAAAATCCTAAT
Found at i:147715 original size:32 final size:32
Alignment explanation
Indices: 147674--147743 Score: 122
Period size: 32 Copynumber: 2.2 Consensus size: 32
147664 ATAAAAACGA
147674 AAAATGATCATATATTTTTTGAAATCAATAATC
1 AAAA-GATCATATATTTTTTGAAATCAATAATC
*
147707 AAAAGATCATATATTTTTTTAAATCAATAATC
1 AAAAGATCATATATTTTTTGAAATCAATAATC
147739 AAAAG
1 AAAAG
147744 TGGATAAAAT
Statistics
Matches: 36, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
32 32 0.89
33 4 0.11
ACGTcount: A:0.49, C:0.09, G:0.06, T:0.37
Consensus pattern (32 bp):
AAAAGATCATATATTTTTTGAAATCAATAATC
Found at i:152831 original size:20 final size:20
Alignment explanation
Indices: 152802--152843 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
152792 TTTTGATAAC
*
152802 TTACGTTTTTTTATCATTGT
1 TTACGGTTTTTTATCATTGT
* *
152822 TTACGGTTTTTTGTCGTTGT
1 TTACGGTTTTTTATCATTGT
152842 TT
1 TT
152844 TTGTTTATCT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.10, C:0.10, G:0.17, T:0.64
Consensus pattern (20 bp):
TTACGGTTTTTTATCATTGT
Found at i:161259 original size:18 final size:17
Alignment explanation
Indices: 161214--161250 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
161204 CGGACTTATG
* *
161214 TCCGTAGCCGACCGTAC
1 TCCGTATCCGACCCTAC
161231 TCCGTATCCGACCCTAC
1 TCCGTATCCGACCCTAC
161248 TCC
1 TCC
161251 TTGATCCGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.16, C:0.46, G:0.16, T:0.22
Consensus pattern (17 bp):
TCCGTATCCGACCCTAC
Found at i:165226 original size:12 final size:12
Alignment explanation
Indices: 165201--165270 Score: 70
Period size: 12 Copynumber: 5.8 Consensus size: 12
165191 ACGGAGATAT
* *
165201 CAGAAATCAAAA
1 CAGAATTCAGAA
165213 CAGAATTCAGAA
1 CAGAATTCAGAA
165225 CAG-ATATCAGAA
1 CAGAAT-TCAGAA
* *
165237 CAGAATCCAGAT
1 CAGAATTCAGAA
* *
165249 CAGAAATCATAA
1 CAGAATTCAGAA
165261 CAGAATTCAG
1 CAGAATTCAG
165271 GTCATATATC
Statistics
Matches: 46, Mismatches: 10, Indels: 4
0.77 0.17 0.07
Matches are distributed among these distances:
11 2 0.04
12 42 0.91
13 2 0.04
ACGTcount: A:0.51, C:0.19, G:0.14, T:0.16
Consensus pattern (12 bp):
CAGAATTCAGAA
Found at i:165228 original size:24 final size:24
Alignment explanation
Indices: 165201--165270 Score: 95
Period size: 24 Copynumber: 2.9 Consensus size: 24
165191 ACGGAGATAT
165201 CAGAAATCAAAACAGAATTCAGAA
1 CAGAAATCAAAACAGAATTCAGAA
* * * *
165225 CAGATATCAGAACAGAATCCAGAT
1 CAGAAATCAAAACAGAATTCAGAA
*
165249 CAGAAATCATAACAGAATTCAG
1 CAGAAATCAAAACAGAATTCAG
165271 GTCATATATC
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 39 1.00
ACGTcount: A:0.51, C:0.19, G:0.14, T:0.16
Consensus pattern (24 bp):
CAGAAATCAAAACAGAATTCAGAA
Found at i:165281 original size:24 final size:24
Alignment explanation
Indices: 165199--165281 Score: 94
Period size: 24 Copynumber: 3.5 Consensus size: 24
165189 AAACGGAGAT
*
165199 ATCAGAAATCAAAACAGAATTCAG
1 ATCAGATATCAAAACAGAATTCAG
* * *
165223 AACAGATATCAGAACAGAATCCAG
1 ATCAGATATCAAAACAGAATTCAG
* *
165247 ATCAGAAATCATAACAGAATTCAG
1 ATCAGATATCAAAACAGAATTCAG
* *
165271 GTCATATATCA
1 ATCAGATATCA
165282 GATAAAATAT
Statistics
Matches: 48, Mismatches: 11, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 48 1.00
ACGTcount: A:0.49, C:0.18, G:0.13, T:0.19
Consensus pattern (24 bp):
ATCAGATATCAAAACAGAATTCAG
Found at i:169469 original size:12 final size:12
Alignment explanation
Indices: 169444--169501 Score: 62
Period size: 12 Copynumber: 4.8 Consensus size: 12
169434 ACGGAAATAT
* *
169444 CAGAAATCAAAA
1 CAGAATTCAGAA
169456 CAGAATTCAGAA
1 CAGAATTCAGAA
* *
169468 CAGAATCCAGAT
1 CAGAATTCAGAA
* *
169480 CAGAAATCATAA
1 CAGAATTCAGAA
169492 CAGAATTCAG
1 CAGAATTCAG
169502 GTCATATATC
Statistics
Matches: 36, Mismatches: 10, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
12 36 1.00
ACGTcount: A:0.52, C:0.19, G:0.14, T:0.16
Consensus pattern (12 bp):
CAGAATTCAGAA
Found at i:172273 original size:18 final size:18
Alignment explanation
Indices: 172252--172290 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
172242 GGTCAACGCC
172252 GGTCAACGGGTCAGGTCG
1 GGTCAACGGGTCAGGTCG
* *
172270 GGTCAACGTGTCGGGTCG
1 GGTCAACGGGTCAGGTCG
172288 GGT
1 GGT
172291 TGTGACCGGC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.13, C:0.21, G:0.46, T:0.21
Consensus pattern (18 bp):
GGTCAACGGGTCAGGTCG
Found at i:182889 original size:37 final size:39
Alignment explanation
Indices: 182821--182968 Score: 163
Period size: 39 Copynumber: 4.0 Consensus size: 39
182811 AATGCTAAGA
182821 TAAAAA-ATA-TTTT-AATATATTTTAAATATATAAAAC
1 TAAAAATATATTTTTCAATATATTTTAAATATATAAAAC
182857 TAAAAATATATTTTTCAATATATTTTAAATATATAAAAC
1 TAAAAATATATTTTTCAATATATTTTAAATATATAAAAC
* * * *
182896 TAAAAATATATTTTTACAATTTTAATGTT-AATGT-TAAGA-
1 TAAAAATATATTTTT-CAA-TAT-ATTTTAAATATATAAAAC
182935 T-AAAATATA--TTT-AATATATTTTAAATATATAAAA
1 TAAAAATATATTTTTCAATATATTTTAAATATATAAAA
182969 ATGTGAATTA
Statistics
Matches: 96, Mismatches: 8, Indels: 18
0.79 0.07 0.15
Matches are distributed among these distances:
32 4 0.04
33 6 0.06
34 6 0.06
36 9 0.09
37 3 0.03
38 12 0.12
39 39 0.41
40 7 0.07
41 6 0.06
42 4 0.04
ACGTcount: A:0.51, C:0.03, G:0.02, T:0.44
Consensus pattern (39 bp):
TAAAAATATATTTTTCAATATATTTTAAATATATAAAAC
Found at i:183236 original size:20 final size:21
Alignment explanation
Indices: 183211--183262 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
183201 TTTTCCTAAT
*
183211 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
183231 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
183252 TCGCAATGCGA
1 TCGCAATGCGA
183263 TACTTACTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 11 0.42
21 15 0.58
ACGTcount: A:0.38, C:0.19, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:183275 original size:41 final size:41
Alignment explanation
Indices: 183248--183325 Score: 120
Period size: 41 Copynumber: 1.9 Consensus size: 41
183238 GCGAATTGGG
* * *
183248 AAAATCGCAATGCGATACTTACTATCGCAATGCGATAATAC
1 AAAATCGCAACGAGATACTTACTATCGCAACGCGATAATAC
*
183289 AAAATCGCAACGAGATACTTACTTTCGCAACGCGATA
1 AAAATCGCAACGAGATACTTACTATCGCAACGCGATA
183326 CTGACTTTCG
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 33 1.00
ACGTcount: A:0.38, C:0.23, G:0.15, T:0.23
Consensus pattern (41 bp):
AAAATCGCAACGAGATACTTACTATCGCAACGCGATAATAC
Found at i:183276 original size:20 final size:20
Alignment explanation
Indices: 183251--183344 Score: 91
Period size: 20 Copynumber: 4.7 Consensus size: 20
183241 AATTGGGAAA
*
183251 ATCGCAATGCGATACTTACT
1 ATCGCAACGCGATACTTACT
* * *
183271 ATCGCAATGCGATA-ATACAAA
1 ATCGCAACGCGATACTTAC--T
*
183292 ATCGCAACGAGATACTTACT
1 ATCGCAACGCGATACTTACT
* *
183312 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTTACT
*
183332 TTCGCAACGCGAT
1 ATCGCAACGCGAT
183345 TTACATAGCG
Statistics
Matches: 62, Mismatches: 9, Indels: 6
0.81 0.12 0.08
Matches are distributed among these distances:
19 3 0.05
20 44 0.71
21 12 0.19
22 3 0.05
ACGTcount: A:0.33, C:0.26, G:0.17, T:0.24
Consensus pattern (20 bp):
ATCGCAACGCGATACTTACT
Found at i:184296 original size:42 final size:42
Alignment explanation
Indices: 184236--184358 Score: 122
Period size: 42 Copynumber: 2.9 Consensus size: 42
184226 GCCCGACTCG
* * *
184236 CCTATCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCC
1 CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
* * *
184278 CCTATCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCC
1 CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
* * ** * *
184320 ACTGTCATCGTTGAAGAGGTCC-CTCCCACCATTCAAGAG
1 CCTATCATCCCTCAAGA-GTCCACTCCCACCGTTCAAGAG
184359 CCCGATTCAC
Statistics
Matches: 66, Mismatches: 14, Indels: 2
0.80 0.17 0.02
Matches are distributed among these distances:
42 62 0.94
43 4 0.06
ACGTcount: A:0.23, C:0.37, G:0.18, T:0.23
Consensus pattern (42 bp):
CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
Found at i:184316 original size:21 final size:21
Alignment explanation
Indices: 184292--184358 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
184282 TCATTCCTCG
184292 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
184313 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
184334 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
184355 AGAG
1 AGAG
184359 CCCGATTCAC
Statistics
Matches: 32, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.24, C:0.36, G:0.21, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:185736 original size:14 final size:14
Alignment explanation
Indices: 185717--185752 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
185707 ATTGTTTAAT
185717 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
185731 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
185745 TGATTTGT
1 TGATTTGT
185753 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:185914 original size:34 final size:33
Alignment explanation
Indices: 185860--185924 Score: 112
Period size: 34 Copynumber: 1.9 Consensus size: 33
185850 AAAAAGTACT
*
185860 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
185893 ATCGCAACGCGAAAATGAAAATCGCAACGAGA
1 ATCGCAACGCG-AAATGAAAATCGCAACGAGA
185925 AATTAAATTC
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
33 10 0.33
34 20 0.67
ACGTcount: A:0.46, C:0.20, G:0.23, T:0.11
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
Found at i:185954 original size:19 final size:19
Alignment explanation
Indices: 185932--186082 Score: 71
Period size: 19 Copynumber: 8.7 Consensus size: 19
185922 AGAAATTAAA
185932 TTCGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
185951 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
* *
185966 -CCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* *
185984 TTCGCATTGCGA-----AA
1 TTCGCGTTGCGATTTTCAT
*
185998 TTAGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
186017 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
* *
186032 -CCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* ** *
186050 TTCGCATTGCGATAGTAAT
1 TTCGCGTTGCGATTTTCAT
186069 TTCCGCGTTGCGAT
1 TT-CGCGTTGCGAT
186083 GGACATTAAG
Statistics
Matches: 93, Mismatches: 23, Indels: 31
0.63 0.16 0.21
Matches are distributed among these distances:
14 27 0.29
16 6 0.06
17 6 0.06
19 44 0.47
20 10 0.11
ACGTcount: A:0.15, C:0.23, G:0.21, T:0.41
Consensus pattern (19 bp):
TTCGCGTTGCGATTTTCAT
Found at i:185978 original size:33 final size:33
Alignment explanation
Indices: 185936--186062 Score: 204
Period size: 33 Copynumber: 3.8 Consensus size: 33
185926 ATTAAATTCG
185936 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
**
185969 CGTTGCGATTTTCATTTCGCATTGCGAAATT--AG
1 CGTTGCGATTTTCATTTCGCATTGCG--ATTCCCT
186002 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
186035 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
186063 AGTAATTTCC
Statistics
Matches: 86, Mismatches: 4, Indels: 8
0.88 0.04 0.08
Matches are distributed among these distances:
31 3 0.03
33 80 0.93
35 3 0.03
ACGTcount: A:0.15, C:0.24, G:0.20, T:0.42
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
Found at i:186025 original size:66 final size:66
Alignment explanation
Indices: 185929--186061 Score: 257
Period size: 66 Copynumber: 2.0 Consensus size: 66
185919 ACGAGAAATT
*
185929 AAATTCGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
1 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
185994 G
66 G
185995 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
1 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
186060 G
66 G
186061 A
1 A
186062 TAGTAATTTC
Statistics
Matches: 66, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
66 66 1.00
ACGTcount: A:0.17, C:0.23, G:0.20, T:0.41
Consensus pattern (66 bp):
AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
G
Found at i:186881 original size:20 final size:20
Alignment explanation
Indices: 186853--186945 Score: 80
Period size: 20 Copynumber: 4.6 Consensus size: 20
186843 CGCTATGTAA
* *
186853 ATCGTGTTGCGAAAGTCAGT
1 ATCGCGTTGCGAAAGTAAGT
186873 ATCGCGTTGCGAAAGTAAGT
1 ATCGCGTTGCGAAAGTAAGT
* ** *
186893 ATCTCGTTGCGATTTTGT-ATT
1 ATCGCGTTGCGA--AAGTAAGT
* *
186914 ATCGCATTGCGATAGTAAGT
1 ATCGCGTTGCGAAAGTAAGT
*
186934 ATCGCATTGCGA
1 ATCGCGTTGCGA
186946 TTTTCCCAAT
Statistics
Matches: 60, Mismatches: 10, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
19 3 0.05
20 43 0.72
21 12 0.20
22 2 0.03
ACGTcount: A:0.25, C:0.16, G:0.26, T:0.33
Consensus pattern (20 bp):
ATCGCGTTGCGAAAGTAAGT
Found at i:186964 original size:21 final size:21
Alignment explanation
Indices: 186935--187027 Score: 100
Period size: 20 Copynumber: 4.5 Consensus size: 21
186925 ATAGTAAGTA
186935 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
* * **
186956 TCGCGTTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTCCCAAT
186976 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
* * **
186997 TCGCGTTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTCCCAAT
187017 TCGCATTGCGA
1 TCGCATTGCGA
187028 ATTGGGAAAA
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 32 0.55
21 26 0.45
ACGTcount: A:0.17, C:0.25, G:0.18, T:0.40
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCCAAT
Found at i:186965 original size:41 final size:41
Alignment explanation
Indices: 186874--187008 Score: 148
Period size: 41 Copynumber: 3.3 Consensus size: 41
186864 AAAGTCAGTA
* * * ** *
186874 TCGCGTTGCGAAAGTAAGTATCTCGTTGCGATTTT-GTATT
1 TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
*
186914 ATCGCATTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
1 -TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
* **
186956 TCGCGTTGCGAT-TTACTTATTCGCATTGCGATTTTCCCAAT
1 TCGCGTTGCGATAGTAAGTA-TCGCATTGCGATTTTCCCAAT
186997 TCGCGTTGCGAT
1 TCGCGTTGCGAT
187009 TTACTTATTC
Statistics
Matches: 81, Mismatches: 11, Indels: 4
0.84 0.11 0.04
Matches are distributed among these distances:
40 4 0.05
41 75 0.93
42 2 0.02
ACGTcount: A:0.20, C:0.21, G:0.21, T:0.38
Consensus pattern (41 bp):
TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
Found at i:187009 original size:41 final size:41
Alignment explanation
Indices: 186935--187027 Score: 186
Period size: 41 Copynumber: 2.3 Consensus size: 41
186925 ATAGTAAGTA
186935 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
186976 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
187017 TCGCATTGCGA
1 TCGCATTGCGA
187028 ATTGGGAAAA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.17, C:0.25, G:0.18, T:0.40
Consensus pattern (41 bp):
TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
Found at i:202731 original size:36 final size:36
Alignment explanation
Indices: 202682--202756 Score: 105
Period size: 36 Copynumber: 2.1 Consensus size: 36
202672 GCGCCGGCGC
* *
202682 AGGTGGTGCAGGAGGACTAACACTAATGGGGGTAGG
1 AGGTGGTGCAGGAGGACTAACACTAATCGGGGCAGG
* * *
202718 AGGTGGTGGAGGAGGACTAGCTCTAATCGGGGCAGG
1 AGGTGGTGCAGGAGGACTAACACTAATCGGGGCAGG
202754 AGG
1 AGG
202757 CTCCGGGGGA
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.25, C:0.12, G:0.47, T:0.16
Consensus pattern (36 bp):
AGGTGGTGCAGGAGGACTAACACTAATCGGGGCAGG
Found at i:207279 original size:28 final size:28
Alignment explanation
Indices: 207247--207390 Score: 88
Period size: 28 Copynumber: 5.2 Consensus size: 28
207237 AATAAATTAT
207247 TTAATAATCATTTTATAAATTTTAATAA
1 TTAATAATCATTTTATAAATTTTAATAA
* ** * **
207275 TTAATAA-AATTAACAAAACAACGTTATATAA
1 TTAATAATCATT--TTATA-AATTTTA-ATAA
207306 TTAAATAATCATTTTATAAA-TTT--TAA
1 TT-AATAATCATTTTATAAATTTTAATAA
*
207332 -TAAT--T-ATTTTATAATTTTTAATAA
1 TTAATAATCATTTTATAAATTTTAATAA
* * *
207356 TCAATAATTATTTTATAATTTTTAATAA
1 TTAATAATCATTTTATAAATTTTAATAA
*
207384 TAAATAA
1 TTAATAA
207391 ACTTAATAAA
Statistics
Matches: 89, Mismatches: 14, Indels: 26
0.69 0.11 0.20
Matches are distributed among these distances:
21 9 0.10
22 4 0.04
24 6 0.07
25 4 0.04
26 3 0.03
27 4 0.04
28 32 0.36
29 4 0.04
30 7 0.08
31 8 0.09
32 5 0.06
33 3 0.03
ACGTcount: A:0.49, C:0.04, G:0.01, T:0.47
Consensus pattern (28 bp):
TTAATAATCATTTTATAAATTTTAATAA
Found at i:207333 original size:21 final size:21
Alignment explanation
Indices: 207309--207358 Score: 82
Period size: 21 Copynumber: 2.4 Consensus size: 21
207299 TATATAATTA
207309 AATAATCATTTTATAAATTTT
1 AATAATCATTTTATAAATTTT
* *
207330 AATAATTATTTTATAATTTTT
1 AATAATCATTTTATAAATTTT
207351 AATAATCA
1 AATAATCA
207359 ATAATTATTT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.44, C:0.04, G:0.00, T:0.52
Consensus pattern (21 bp):
AATAATCATTTTATAAATTTT
Found at i:207719 original size:21 final size:19
Alignment explanation
Indices: 207699--207852 Score: 94
Period size: 21 Copynumber: 7.5 Consensus size: 19
207689 TAGAAGTTCG
207699 CGTTGCGATTTTCCAAATT
1 CGTTGCGATTTTCCAAATT
**
207718 CGTTGCGATAGT-CAAAGTT
1 CGTTGCGATTTTCCAAA-TT
207737 CGCGTTGCGATTTATTCCAAATT
1 --CGTTGCGA-TT-TTCCAAATT
** *
207760 CGTTGCGATAGTCCAAGTT
1 CGTTGCGATTTTCCAAATT
*
207779 CGCGTTGCGATTTATTCCAAGTT
1 --CGTTGCGA-TT-TTCCAAATT
** * *
207802 CGTTGCGATAGTCGAAGTT
1 CGTTGCGATTTTCCAAATT
207821 CGCGTTGCGATTTATTCCAAATT
1 --CGTTGCGA-TT-TTCCAAATT
207844 CGTTGCGAT
1 CGTTGCGAT
207853 AATCCAAAAT
Statistics
Matches: 105, Mismatches: 16, Indels: 27
0.71 0.11 0.18
Matches are distributed among these distances:
18 4 0.04
19 26 0.25
20 3 0.03
21 48 0.46
22 3 0.03
23 17 0.16
24 4 0.04
ACGTcount: A:0.21, C:0.20, G:0.23, T:0.36
Consensus pattern (19 bp):
CGTTGCGATTTTCCAAATT
Found at i:207768 original size:42 final size:42
Alignment explanation
Indices: 207680--207853 Score: 291
Period size: 42 Copynumber: 4.2 Consensus size: 42
207670 GACTATCGCA
207680 TTGCGATAGT-AGAAGTTCGCGTTGCGA-TT-TTCCAAATTCG
1 TTGCGATAGTCA-AAGTTCGCGTTGCGATTTATTCCAAATTCG
207720 TTGCGATAGTCAAAGTTCGCGTTGCGATTTATTCCAAATTCG
1 TTGCGATAGTCAAAGTTCGCGTTGCGATTTATTCCAAATTCG
* *
207762 TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAGTTCG
1 TTGCGATAGTCAAAGTTCGCGTTGCGATTTATTCCAAATTCG
*
207804 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCG
1 TTGCGATAGTCAAAGTTCGCGTTGCGATTTATTCCAAATTCG
207846 TTGCGATA
1 TTGCGATA
207854 ATCCAAAATC
Statistics
Matches: 127, Mismatches: 4, Indels: 4
0.94 0.03 0.03
Matches are distributed among these distances:
40 25 0.20
41 3 0.02
42 99 0.78
ACGTcount: A:0.22, C:0.19, G:0.24, T:0.36
Consensus pattern (42 bp):
TTGCGATAGTCAAAGTTCGCGTTGCGATTTATTCCAAATTCG
Found at i:208631 original size:21 final size:21
Alignment explanation
Indices: 208607--208676 Score: 63
Period size: 21 Copynumber: 3.4 Consensus size: 21
208597 TTTTGAATAA
208607 ATCGCAACGCGAACTTCGACT
1 ATCGCAACGCGAACTTCGACT
* * ** **
208628 ATCGCAA--CTAATTTAAAAA
1 ATCGCAACGCGAACTTCGACT
208647 ATCGCAACGCGAACTTCGACT
1 ATCGCAACGCGAACTTCGACT
*
208668 ATCACAACG
1 ATCGCAACG
208677 AATTTGAAAA
Statistics
Matches: 34, Mismatches: 13, Indels: 4
0.67 0.25 0.08
Matches are distributed among these distances:
19 13 0.38
21 21 0.62
ACGTcount: A:0.37, C:0.29, G:0.14, T:0.20
Consensus pattern (21 bp):
ATCGCAACGCGAACTTCGACT
Found at i:208660 original size:40 final size:40
Alignment explanation
Indices: 208548--208754 Score: 245
Period size: 40 Copynumber: 5.1 Consensus size: 40
208538 CAATACCATC
* **
208548 CAACGAATTTGAAATAAATAGCAACGTAAACTT-GAACTATCG
1 CAACGAATTT-AAA-AAATCGCAACGCGAACTTCG-ACTATCG
* *
208590 TAACGAATTTTGAATAAATCGCAACGCGAACTTCGACTATCG
1 CAACGAA-TTT-AAAAAATCGCAACGCGAACTTCGACTATCG
* *
208632 CAACTAATTTAAAAAATCGCAACGCGAACTTCGACTATCA
1 CAACGAATTTAAAAAATCGCAACGCGAACTTCGACTATCG
* * * *
208672 CAACGAATTTGAAAAATCGTAATGCGAACTTCAACTATCG
1 CAACGAATTTAAAAAATCGCAACGCGAACTTCGACTATCG
* *
208712 CAACGAATTTAAAAAATCACAACGCGAACTTCGAGTATCG
1 CAACGAATTTAAAAAATCGCAACGCGAACTTCGACTATCG
208752 CAA
1 CAA
208755 TGCGAATATA
Statistics
Matches: 142, Mismatches: 21, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
40 99 0.70
41 3 0.02
42 33 0.23
43 7 0.05
ACGTcount: A:0.42, C:0.21, G:0.14, T:0.23
Consensus pattern (40 bp):
CAACGAATTTAAAAAATCGCAACGCGAACTTCGACTATCG
Found at i:210676 original size:15 final size:15
Alignment explanation
Indices: 210656--210689 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
210646 TTTAATCGTT
*
210656 AATTAAATTATTTAA
1 AATTAAATTAATTAA
210671 AATTAAATTAATTAA
1 AATTAAATTAATTAA
210686 AATT
1 AATT
210690 TTAAAATATT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (15 bp):
AATTAAATTAATTAA
Found at i:223681 original size:30 final size:26
Alignment explanation
Indices: 223611--223665 Score: 101
Period size: 26 Copynumber: 2.1 Consensus size: 26
223601 ATTAAAATGA
223611 TTTCATTTTGATCTTTAGTTAAATAAT
1 TTTCATTTTGAT-TTTAGTTAAATAAT
223638 TTTCATTTTGATTTTAGTTAAATAAT
1 TTTCATTTTGATTTTAGTTAAATAAT
223664 TT
1 TT
223666 GATTCTTCTG
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
26 16 0.57
27 12 0.43
ACGTcount: A:0.29, C:0.05, G:0.07, T:0.58
Consensus pattern (26 bp):
TTTCATTTTGATTTTAGTTAAATAAT
Found at i:231318 original size:30 final size:30
Alignment explanation
Indices: 231282--231354 Score: 119
Period size: 30 Copynumber: 2.4 Consensus size: 30
231272 TCCAAATGAC
*
231282 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGATAA
231312 CTATCCAGAGGTCATAAAGATCCTCGATAA
1 CTATCCAGAGGTCATAAAGATCCTCGATAA
* *
231342 CTGTCCATAGGTC
1 CTATCCAGAGGTC
231355 CCGAAGAACC
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 40 1.00
ACGTcount: A:0.32, C:0.25, G:0.19, T:0.25
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCCTCGATAA
Found at i:231428 original size:31 final size:31
Alignment explanation
Indices: 231340--231432 Score: 91
Period size: 31 Copynumber: 3.0 Consensus size: 31
231330 GATCCTCGAT
* * *
231340 AACTGTCCATAGGTCCCGAAGAACCTAGGTA
1 AACTGTCCATATGTCTCGAAGAACATAGGTA
* **
231371 AACTATCCATATGT-TCCTTAGAACATAGGTA
1 AACTGTCCATATGTCT-CGAAGAACATAGGTA
*
231402 TACTGTCCATATGTCTCGAA-AGACATAGGTA
1 AACTGTCCATATGTCTCGAAGA-ACATAGGTA
231433 GTTCTTTGAC
Statistics
Matches: 49, Mismatches: 10, Indels: 6
0.75 0.15 0.09
Matches are distributed among these distances:
30 1 0.02
31 47 0.96
32 1 0.02
ACGTcount: A:0.33, C:0.22, G:0.18, T:0.27
Consensus pattern (31 bp):
AACTGTCCATATGTCTCGAAGAACATAGGTA
Found at i:235403 original size:30 final size:30
Alignment explanation
Indices: 235301--235392 Score: 175
Period size: 30 Copynumber: 3.1 Consensus size: 30
235291 TCCAAATGAC
*
235301 CTATCCAGAGGTCATAAAGATCCTCAGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
235331 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
235361 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
235391 CT
1 CT
235393 GTTCATAGGT
Statistics
Matches: 61, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
30 61 1.00
ACGTcount: A:0.34, C:0.24, G:0.18, T:0.24
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCCTCGGTAA
Found at i:235420 original size:60 final size:61
Alignment explanation
Indices: 235301--235428 Score: 168
Period size: 60 Copynumber: 2.1 Consensus size: 61
235291 TCCAAATGAC
* * *
235301 CTATCCAGAGGTCATAAAGATCCTCAGTAACTATCCAGAGGTCATAAAGATCCTCGGT-AA
1 CTATCCAGAGGTCATAAAGATCCTCAGTAACTATCCAGAGGTCACAAAGAACCTAGGTAAA
* * * * * *
235361 CTATCCAGAGGTCATAAAGATCCTCGGTAACTGTTCATAGGTCCCGAAGAACCTAGGTAAA
1 CTATCCAGAGGTCATAAAGATCCTCAGTAACTATCCAGAGGTCACAAAGAACCTAGGTAAA
235422 CTATCCA
1 CTATCCA
235429 TATGTTCCTT
Statistics
Matches: 58, Mismatches: 9, Indels: 1
0.85 0.13 0.01
Matches are distributed among these distances:
60 49 0.84
61 9 0.16
ACGTcount: A:0.34, C:0.24, G:0.19, T:0.23
Consensus pattern (61 bp):
CTATCCAGAGGTCATAAAGATCCTCAGTAACTATCCAGAGGTCACAAAGAACCTAGGTAAA
Found at i:238705 original size:18 final size:19
Alignment explanation
Indices: 238664--238706 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 19
238654 GTAAACTATG
* *
238664 TGATAAGTGATAAGTGACA
1 TGATATGTGATAAATGACA
238683 T-ATATGTGATAAATGA-A
1 TGATATGTGATAAATGACA
238700 TGATATG
1 TGATATG
238707 AAAAGTGAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
17 2 0.10
18 18 0.86
19 1 0.05
ACGTcount: A:0.42, C:0.02, G:0.23, T:0.33
Consensus pattern (19 bp):
TGATATGTGATAAATGACA
Found at i:239526 original size:31 final size:30
Alignment explanation
Indices: 239439--239563 Score: 126
Period size: 31 Copynumber: 4.0 Consensus size: 30
239429 AGAGTCGAGG
239439 GTATACCTATGTTCTACGGAACATATGGACA
1 GTATACCTATGTTCTACGG-ACATATGGACA
* *
239470 GAATTACCTATG-TCTTTCGAGACATATGGACA
1 GTA-TACCTATGTTC-TACG-GACATATGGACA
*
239502 GTATACCTATGTTCTAAGGTACATATGGACA
1 GTATACCTATGTTCTACGG-ACATATGGACA
* * * *
239533 GTTTACCTAGGTTCTTCGGAACCTATGGACA
1 GTATACCTATGTTCTACGG-ACATATGGACA
239564 ATTGCCAAGG
Statistics
Matches: 78, Mismatches: 11, Indels: 10
0.79 0.11 0.10
Matches are distributed among these distances:
30 1 0.01
31 50 0.64
32 26 0.33
33 1 0.01
ACGTcount: A:0.30, C:0.19, G:0.20, T:0.31
Consensus pattern (30 bp):
GTATACCTATGTTCTACGGACATATGGACA
Found at i:240438 original size:23 final size:27
Alignment explanation
Indices: 240412--240462 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 27
240402 GATGATAATC
240412 ATAAAAAC-AT-TTATTT-T-CATTCA
1 ATAAAAACAATGTTATTTATACATTCA
240435 ATAAAAACAATGTTATTTATACATTCA
1 ATAAAAACAATGTTATTTATACATTCA
240462 A
1 A
240463 ATTGATTTGC
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
23 8 0.33
24 2 0.08
25 6 0.25
26 1 0.04
27 7 0.29
ACGTcount: A:0.47, C:0.12, G:0.02, T:0.39
Consensus pattern (27 bp):
ATAAAAACAATGTTATTTATACATTCA
Found at i:242613 original size:2 final size:2
Alignment explanation
Indices: 242608--242636 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
242598 ACTAAAAAAT
242608 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
242637 TAACCAAAGT
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:243202 original size:22 final size:22
Alignment explanation
Indices: 243158--243209 Score: 63
Period size: 21 Copynumber: 2.3 Consensus size: 22
243148 AATATAATAA
243158 TATATTTTTTATTTTTAGTAATT
1 TATA-TTTTTATTTTTAGTAATT
243181 TA-ATTTTTATTTTT-GATAAATT
1 TATATTTTTATTTTTAG-T-AATT
243203 TATATTT
1 TATATTT
243210 ACTTTTTTGA
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
20 1 0.04
21 12 0.46
22 7 0.27
23 6 0.23
ACGTcount: A:0.29, C:0.00, G:0.04, T:0.67
Consensus pattern (22 bp):
TATATTTTTATTTTTAGTAATT
Found at i:243210 original size:21 final size:21
Alignment explanation
Indices: 243165--243216 Score: 54
Period size: 21 Copynumber: 2.4 Consensus size: 21
243155 TAATATATTT
*
243165 TTTATTTTTAGTAATTTAATT
1 TTTATTTTTAGTAATTTAATA
243186 TTTATTTTT-GATAAATTT-ATA
1 TTTATTTTTAG-T-AATTTAATA
243207 TTTACTTTTT
1 TTTA-TTTTT
243217 TGAATAACTT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
20 1 0.04
21 16 0.59
22 10 0.37
ACGTcount: A:0.27, C:0.02, G:0.04, T:0.67
Consensus pattern (21 bp):
TTTATTTTTAGTAATTTAATA
Found at i:247005 original size:37 final size:37
Alignment explanation
Indices: 246955--247027 Score: 137
Period size: 37 Copynumber: 2.0 Consensus size: 37
246945 GTTAGTTTGT
246955 TCAATTCAACTCAACTCGTTATCGTCACTACATGTAC
1 TCAATTCAACTCAACTCGTTATCGTCACTACATGTAC
*
246992 TCAATTCAACTCAACTTGTTATCGTCACTACATGTA
1 TCAATTCAACTCAACTCGTTATCGTCACTACATGTA
247028 ACTTATTTAG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.30, C:0.27, G:0.08, T:0.34
Consensus pattern (37 bp):
TCAATTCAACTCAACTCGTTATCGTCACTACATGTAC
Found at i:247079 original size:22 final size:21
Alignment explanation
Indices: 247054--247099 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 21
247044 AGGATCTAGG
*
247054 TTTTAAAATTTAGAATTTAATA
1 TTTTAAAATTAAGAATTTAA-A
**
247076 TTTTATGATTAAGAATTTAAA
1 TTTTAAAATTAAGAATTTAAA
247097 TTT
1 TTT
247100 CAGGCTTAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 4 0.19
22 17 0.81
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.52
Consensus pattern (21 bp):
TTTTAAAATTAAGAATTTAAA
Found at i:250306 original size:17 final size:18
Alignment explanation
Indices: 250284--250317 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
250274 TCAAAATTAA
250284 AATCAAAATTT-ATTTAT
1 AATCAAAATTTCATTTAT
*
250301 AATCAAGATTTCATTTA
1 AATCAAAATTTCATTTA
250318 ATTTAATTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.44, C:0.09, G:0.03, T:0.44
Consensus pattern (18 bp):
AATCAAAATTTCATTTAT
Found at i:250321 original size:5 final size:5
Alignment explanation
Indices: 250308--250338 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
250298 TATAATCAAG
*
250308 ATTTC ATTTA ATTTA ATTTA ATTTA ATTTA A
1 ATTTA ATTTA ATTTA ATTTA ATTTA ATTTA A
250339 CTGATTGAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (5 bp):
ATTTA
Found at i:250755 original size:139 final size:138
Alignment explanation
Indices: 250495--250771 Score: 457
Period size: 139 Copynumber: 2.0 Consensus size: 138
250485 AAACCATAAC
*
250495 TGATGTACTCTGTGGCCAAGGCTGACCCGCCTCTCTCTCCTCCACCCATTTAATATCCTGCCACC
1 TGATGTACTCTGTGGCCAAGGCTGACCCGCCTCTCTCTCCTCCACCCATTTAATATCCGGCCACC
* * *
250560 GGTGTTTCAATGAGTGACTCCTCCCCTGAAATCGACTCCGATTTCACCCATTCGAATTCGGAACA
66 GGTGTTTCAATGAATGACGCCTCCCCTAAAATCGACTCCGATTTCACCCATTCGAATTCGGAACA
250625 CATGAAAT
131 CATGAAAT
* *
250633 TGATGTACTTTTGTGGCCAAGGCTGACCCGCCTCTCTCTCCTCCACCCATTTAATATTCGGCCAC
1 TGATGTAC-TCTGTGGCCAAGGCTGACCCGCCTCTCTCTCCTCCACCCATTTAATATCCGGCCAC
* *
250698 CGGTGTTTCGATGAATGACGCCTCCCTTAAAATCGACAT-CGATTTCACCCATTCGAATTCGGAA
65 CGGTGTTTCAATGAATGACGCCTCCCCTAAAATCGAC-TCCGATTTCACCCATTCGAATTCGGAA
250762 CACATGAAAT
129 CACATGAAAT
250772 CGCAGTTTCA
Statistics
Matches: 129, Mismatches: 8, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
138 8 0.06
139 120 0.93
140 1 0.01
ACGTcount: A:0.23, C:0.32, G:0.17, T:0.28
Consensus pattern (138 bp):
TGATGTACTCTGTGGCCAAGGCTGACCCGCCTCTCTCTCCTCCACCCATTTAATATCCGGCCACC
GGTGTTTCAATGAATGACGCCTCCCCTAAAATCGACTCCGATTTCACCCATTCGAATTCGGAACA
CATGAAAT
Found at i:255008 original size:14 final size:14
Alignment explanation
Indices: 254989--255038 Score: 52
Period size: 14 Copynumber: 3.7 Consensus size: 14
254979 TTTTTAAAAA
*
254989 ATAATTAAAATTTT
1 ATAATTAAAATATT
255003 ATAATTAAAATATT
1 ATAATTAAAATATT
*
255017 AT--TTATAAA-GTT
1 ATAATTA-AAATATT
255029 ATAATTAAAA
1 ATAATTAAAA
255039 AAATACTTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
12 7 0.23
13 6 0.19
14 18 0.58
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (14 bp):
ATAATTAAAATATT
Found at i:256486 original size:13 final size:13
Alignment explanation
Indices: 256468--256495 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
256458 ACTAAGACAC
256468 TTGAGGGGATTTT
1 TTGAGGGGATTTT
256481 TTGAGGGGATTTT
1 TTGAGGGGATTTT
256494 TT
1 TT
256496 AGTGTTTACC
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:0.14, C:0.00, G:0.36, T:0.50
Consensus pattern (13 bp):
TTGAGGGGATTTT
Found at i:262483 original size:13 final size:13
Alignment explanation
Indices: 262465--262500 Score: 72
Period size: 13 Copynumber: 2.8 Consensus size: 13
262455 GAGGTTGGTG
262465 TTATTTTCAATTT
1 TTATTTTCAATTT
262478 TTATTTTCAATTT
1 TTATTTTCAATTT
262491 TTATTTTCAA
1 TTATTTTCAA
262501 CGAATAAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.25, C:0.08, G:0.00, T:0.67
Consensus pattern (13 bp):
TTATTTTCAATTT
Found at i:266640 original size:31 final size:31
Alignment explanation
Indices: 266605--266663 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
266595 AACGAAAGTG
*
266605 ATCATATCTTAGTTAAATAAAAACAAAAATC
1 ATCATATCTTAATTAAATAAAAACAAAAATC
* *
266636 ATCATATCTTAATTGAATAAAAATAAAA
1 ATCATATCTTAATTAAATAAAAACAAAA
266664 GTTACGACAT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.56, C:0.10, G:0.03, T:0.31
Consensus pattern (31 bp):
ATCATATCTTAATTAAATAAAAACAAAAATC
Found at i:267934 original size:15 final size:16
Alignment explanation
Indices: 267914--267946 Score: 59
Period size: 15 Copynumber: 2.1 Consensus size: 16
267904 CATCAGTATG
267914 TTGGGATTTGG-TTTT
1 TTGGGATTTGGATTTT
267929 TTGGGATTTGGATTTT
1 TTGGGATTTGGATTTT
267945 TT
1 TT
267947 TTGTAATTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.65
16 6 0.35
ACGTcount: A:0.09, C:0.00, G:0.30, T:0.61
Consensus pattern (16 bp):
TTGGGATTTGGATTTT
Found at i:271162 original size:9 final size:9
Alignment explanation
Indices: 271148--271173 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
271138 CATATTTTTA
271148 ATAAAAAAT
1 ATAAAAAAT
271157 ATAAAAAAT
1 ATAAAAAAT
271166 ATAAAAAA
1 ATAAAAAA
271174 AAACTTTTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (9 bp):
ATAAAAAAT
Found at i:273423 original size:82 final size:83
Alignment explanation
Indices: 273311--273477 Score: 246
Period size: 82 Copynumber: 2.0 Consensus size: 83
273301 TCTTAGCATT
* * * *
273311 GTTAAAATAGTTAAGTGATATGATTGATAAAAATAAAAGATCGATAATTAAACTAAAATCC-CTT
1 GTTAAAATAATTAAGTGACATGATTGATAAAAATAAAAGATCAATAATCAAACTAAAATCCTCTT
273375 ATAATTAAGTGGTTATAA
66 ATAATTAAGTGGTTATAA
* *
273393 GTTAAAATAATTAAGTGACATGTTTGATAAAAATAAAAGATCAATAATCAGACTAAAATCCTCTT
1 GTTAAAATAATTAAGTGACATGATTGATAAAAATAAAAGATCAATAATCAAACTAAAATCCTCTT
* * *
273458 ATTATTTAGTTGTTATAA
66 ATAATTAAGTGGTTATAA
273476 GT
1 GT
273478 GTATTTTGCC
Statistics
Matches: 75, Mismatches: 9, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
82 55 0.73
83 20 0.27
ACGTcount: A:0.46, C:0.07, G:0.13, T:0.35
Consensus pattern (83 bp):
GTTAAAATAATTAAGTGACATGATTGATAAAAATAAAAGATCAATAATCAAACTAAAATCCTCTT
ATAATTAAGTGGTTATAA
Found at i:280468 original size:54 final size:54
Alignment explanation
Indices: 280407--280516 Score: 211
Period size: 54 Copynumber: 2.0 Consensus size: 54
280397 AAAAGCATGA
*
280407 GGCGGTGGACCTGATTGGTGGTTGTGATGTGGTGGTGGTGGAGGAGGAGGTGGT
1 GGCGGTGGACCTGATTGGTGGTTGTGATGTGGTGGTGGTGGAGGAGGAGGAGGT
280461 GGCGGTGGACCTGATTGGTGGTTGTGATGTGGTGGTGGTGGAGGAGGAGGAGGT
1 GGCGGTGGACCTGATTGGTGGTTGTGATGTGGTGGTGGTGGAGGAGGAGGAGGT
280515 GG
1 GG
280517 TGGCGGAGGC
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
54 55 1.00
ACGTcount: A:0.12, C:0.05, G:0.56, T:0.26
Consensus pattern (54 bp):
GGCGGTGGACCTGATTGGTGGTTGTGATGTGGTGGTGGTGGAGGAGGAGGAGGT
Found at i:282328 original size:31 final size:31
Alignment explanation
Indices: 282293--282379 Score: 120
Period size: 32 Copynumber: 2.8 Consensus size: 31
282283 AAATATGATT
* * *
282293 CTAAAAAATAAGTGGATGACCAAAATAGAAA
1 CTAAATAATAGGTGGATGACCAAAATAAAAA
*
282324 CTAAATAATAGGTGTATGACCAAAAATAAAAA
1 CTAAATAATAGGTGGATGACC-AAAATAAAAA
*
282356 CTAAATAATAGGTGGATGATCAAA
1 CTAAATAATAGGTGGATGACCAAA
282380 TAAGTAATTT
Statistics
Matches: 49, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
31 21 0.43
32 28 0.57
ACGTcount: A:0.54, C:0.09, G:0.16, T:0.21
Consensus pattern (31 bp):
CTAAATAATAGGTGGATGACCAAAATAAAAA
Found at i:292992 original size:28 final size:28
Alignment explanation
Indices: 292952--293024 Score: 137
Period size: 28 Copynumber: 2.6 Consensus size: 28
292942 TCTACTGAGT
292952 TTAACGAGCAAAGAGTCGAGTAGCGAGC
1 TTAACGAGCAAAGAGTCGAGTAGCGAGC
292980 TTAACGAGCAAAGAGTCGAGTAGCGAGC
1 TTAACGAGCAAAGAGTCGAGTAGCGAGC
*
293008 TTAACGAGCAACGAGTC
1 TTAACGAGCAAAGAGTC
293025 AAGCAAAAAA
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
28 44 1.00
ACGTcount: A:0.36, C:0.19, G:0.30, T:0.15
Consensus pattern (28 bp):
TTAACGAGCAAAGAGTCGAGTAGCGAGC
Found at i:293651 original size:33 final size:33
Alignment explanation
Indices: 293614--293719 Score: 142
Period size: 33 Copynumber: 3.2 Consensus size: 33
293604 CGCTCGCTCT
*
293614 GATGCCCTCGCATAGCTCGCTCAGCT-GCTCTCG
1 GATGCCCTCGCATAGCTCGCTCAGATGGC-CTCG
* *
293647 GATGCCCTCGCATAGCTCGGTCGGATGGCCTCG
1 GATGCCCTCGCATAGCTCGCTCAGATGGCCTCG
* * *
293680 GATGCTCTCGCATAGCTCGGTCGGATGGCCTCG
1 GATGCCCTCGCATAGCTCGCTCAGATGGCCTCG
293713 GATGCCC
1 GATGCCC
293720 AGCGTGTTAG
Statistics
Matches: 67, Mismatches: 5, Indels: 2
0.91 0.07 0.03
Matches are distributed among these distances:
33 65 0.97
34 2 0.03
ACGTcount: A:0.12, C:0.35, G:0.30, T:0.23
Consensus pattern (33 bp):
GATGCCCTCGCATAGCTCGCTCAGATGGCCTCG
Found at i:293793 original size:29 final size:29
Alignment explanation
Indices: 293756--293813 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
293746 GCAATCTCTT
* *
293756 GTAGCTCGCCGGGAAGACATGGCGACCTA
1 GTAGCTCGCCCGGAAGACATGACGACCTA
* *
293785 GTAGGTCGCCCGGAAGGCATGACGACCTA
1 GTAGCTCGCCCGGAAGACATGACGACCTA
293814 CGATCAACAC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.24, C:0.28, G:0.34, T:0.14
Consensus pattern (29 bp):
GTAGCTCGCCCGGAAGACATGACGACCTA
Found at i:303529 original size:3 final size:3
Alignment explanation
Indices: 303501--303551 Score: 63
Period size: 3 Copynumber: 17.3 Consensus size: 3
303491 TTTATAAAAA
303501 TAT T-T TAT TA- TAT TA- TATT TATT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TA-T TA-T TAT TAT TAT TAT TAT TAT TAT
303545 TAT TAT T
1 TAT TAT T
303552 TTTTAGTTTT
Statistics
Matches: 44, Mismatches: 0, Indels: 8
0.85 0.00 0.15
Matches are distributed among these distances:
2 6 0.14
3 32 0.73
4 6 0.14
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TAT
Found at i:303646 original size:33 final size:33
Alignment explanation
Indices: 303609--303677 Score: 111
Period size: 33 Copynumber: 2.1 Consensus size: 33
303599 TTCAAAAAAT
*
303609 AAATCAACGTATTTGAATCATATTGAAACACTA
1 AAATCAACGTATTTGAATCATATTAAAACACTA
* *
303642 AAATCAACGTATTTGAGTCTTATTAAAACACTA
1 AAATCAACGTATTTGAATCATATTAAAACACTA
303675 AAA
1 AAA
303678 CTGAAGCATT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.46, C:0.14, G:0.09, T:0.30
Consensus pattern (33 bp):
AAATCAACGTATTTGAATCATATTAAAACACTA
Found at i:303689 original size:33 final size:33
Alignment explanation
Indices: 303609--303694 Score: 102
Period size: 33 Copynumber: 2.6 Consensus size: 33
303599 TTCAAAAAAT
* * * *
303609 AAATCAACGTATTTGAATCATATTGAAACACTA
1 AAATCAACGCATTTGAGTCTTATTAAAACACTA
*
303642 AAATCAACGTATTTGAGTCTTATTAAAACACTA
1 AAATCAACGCATTTGAGTCTTATTAAAACACTA
*
303675 AAACTGAA-GCATTTGAGTCT
1 AAA-TCAACGCATTTGAGTCT
303695 AAGTAGGACT
Statistics
Matches: 47, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
33 44 0.94
34 3 0.06
ACGTcount: A:0.42, C:0.15, G:0.12, T:0.31
Consensus pattern (33 bp):
AAATCAACGCATTTGAGTCTTATTAAAACACTA
Found at i:304366 original size:2 final size:2
Alignment explanation
Indices: 304359--304392 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
304349 TGTTTTATTA
304359 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
304393 TATTTTTTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:304406 original size:9 final size:9
Alignment explanation
Indices: 304392--304544 Score: 65
Period size: 9 Copynumber: 15.8 Consensus size: 9
304382 TATATATATA
304392 TTATTTTTT
1 TTATTTTTT
304401 TTATTTTTAT
1 TTATTTTT-T
304411 TTATTTATTT
1 TTATTT-TTT
*
304421 ATATTTTTT
1 TTATTTTTT
* *
304430 CT-TTTTCT
1 TTATTTTTT
304438 TTATTTTTT
1 TTATTTTTT
*
304447 AATATTTTTT
1 -TTATTTTTT
** *
304457 ACATATTTAT
1 TTAT-TTTTT
*
304467 TTATTTATT
1 TTATTTTTT
*
304476 TTACTTACTATT
1 TTA-TT--TTTT
304488 TTATCTTTATT
1 TTAT-TTT-TT
*
304499 TTCTTTATTT
1 TTATTT-TTT
*
304509 TATATTATCTT
1 T-TATT-TTTT
**
304520 TTATTTAAT
1 TTATTTTTT
304529 TTATTTTTT
1 TTATTTTTT
*
304538 TCATTTT
1 TTATTTT
304545 AATTCAATTT
Statistics
Matches: 110, Mismatches: 21, Indels: 26
0.70 0.13 0.17
Matches are distributed among these distances:
8 6 0.05
9 41 0.37
10 39 0.35
11 15 0.14
12 9 0.08
ACGTcount: A:0.20, C:0.06, G:0.00, T:0.74
Consensus pattern (9 bp):
TTATTTTTT
Found at i:304469 original size:4 final size:4
Alignment explanation
Indices: 304406--304566 Score: 52
Period size: 4 Copynumber: 39.8 Consensus size: 4
304396 TTTTTTTATT
* *
304406 TTTA TTTA TTTA TTTA TATT- TTT- TCTT- TTTC TTTA TTT- TTTA -ATA
1 TTTA TTTA TTTA TTTA T-TTA TTTA T-TTA TTTA TTTA TTTA TTTA TTTA
** * * * *
304451 TTT- TTTA CATA TTTA TTTA TTTA TTTTA CTTA -CTA TTT- TATC TTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA -TTTA TTTA TTTA TTTA TTTA TTTA
* * *
304497 TTTTC TTTA TTTTA TATTA TCT- TTTA TTTAA TTTA TTTT TTTCA TTTTAA
1 -TTTA TTTA -TTTA T-TTA TTTA TTTA TTT-A TTTA TTTA TTT-A -TTT-A
*
304547 TTCAA TTTA TTTA TTTA TTT
1 TT-TA TTTA TTTA TTTA TTT
304567 CTTACATTTT
Statistics
Matches: 118, Mismatches: 22, Indels: 34
0.68 0.13 0.20
Matches are distributed among these distances:
3 19 0.16
4 69 0.58
5 26 0.22
6 4 0.03
ACGTcount: A:0.22, C:0.06, G:0.00, T:0.71
Consensus pattern (4 bp):
TTTA
Found at i:304522 original size:32 final size:32
Alignment explanation
Indices: 304432--304566 Score: 82
Period size: 32 Copynumber: 4.1 Consensus size: 32
304422 TATTTTTTCT
* * *
304432 TTTTCTTTATTTTTTAATATTTTTTACATATTTA
1 TTTTCTTTATTTTATATTATATTTT--ATATTTA
* * *
304466 -TTTATTTATTTTA-CTTACTATTTTATCTTTA
1 TTTTCTTTATTTTATATTA-TATTTTATATTTA
*
304497 TTTTCTTTATTTTATATTATCTTTTATTTAATTTA
1 TTTTCTTTATTTTATATTATATTTTA--T-ATTTA
*
304532 TTTT-TTTCATTTTA-ATTCA-ATTTATTTATTTA
1 TTTTCTTT-ATTTTATATT-ATATTT-TATATTTA
304564 TTT
1 TTT
304567 CTTACATTTT
Statistics
Matches: 80, Mismatches: 12, Indels: 20
0.71 0.11 0.18
Matches are distributed among these distances:
31 6 0.08
32 28 0.35
33 20 0.25
34 10 0.12
35 16 0.20
ACGTcount: A:0.23, C:0.07, G:0.00, T:0.70
Consensus pattern (32 bp):
TTTTCTTTATTTTATATTATATTTTATATTTA
Found at i:304554 original size:24 final size:22
Alignment explanation
Indices: 304518--304566 Score: 62
Period size: 24 Copynumber: 2.1 Consensus size: 22
304508 TTATATTATC
* *
304518 TTTTATTTAATTTATTTTTTTCA
1 TTTTATTCAATTTATTTATTT-A
304541 TTTTAATTCAATTTATTTATTTA
1 TTTT-ATTCAATTTATTTATTTA
304564 TTT
1 TTT
304567 CTTACATTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 8 0.35
24 15 0.65
ACGTcount: A:0.24, C:0.04, G:0.00, T:0.71
Consensus pattern (22 bp):
TTTTATTCAATTTATTTATTTA
Found at i:304556 original size:65 final size:65
Alignment explanation
Indices: 304432--304556 Score: 146
Period size: 65 Copynumber: 1.9 Consensus size: 65
304422 TATTTTTTCT
* * * *
304432 TTTTCTTTATTTTTTAATATTTTTTACATATTTATTTATTTATTTTACTTACTATTTTATCTTTA
1 TTTTCTTTATTTTATAATATCTTTTACATATTTATTTATTTATTTTAATTACTAATTTATCTTTA
* ** *
304497 TTTTCTTTATTTTATATTATCTTTTATTTAATTTATTTTTTTCATTTTAATT-C-AATTTAT
1 TTTTCTTTATTTTATAATATCTTTTACAT-ATTTATTTATTT-ATTTTAATTACTAATTTAT
304557 TTATTTATTT
Statistics
Matches: 50, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
65 30 0.60
66 12 0.24
67 8 0.16
ACGTcount: A:0.23, C:0.07, G:0.00, T:0.70
Consensus pattern (65 bp):
TTTTCTTTATTTTATAATATCTTTTACATATTTATTTATTTATTTTAATTACTAATTTATCTTTA
Found at i:305282 original size:3 final size:3
Alignment explanation
Indices: 305274--305303 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
305264 AATGATAGAA
305274 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
305304 TATTATTATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:305308 original size:3 final size:3
Alignment explanation
Indices: 305302--305370 Score: 138
Period size: 3 Copynumber: 23.0 Consensus size: 3
305292 AATAATAATA
305302 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
305350 ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT
305371 TAAGGGACTT
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 66 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:306570 original size:14 final size:14
Alignment explanation
Indices: 306553--306580 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
306543 AACATTTATG
306553 TATTAATATATTAA
1 TATTAATATATTAA
306567 TATTAATATATTAA
1 TATTAATATATTAA
306581 GATTTCATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
TATTAATATATTAA
Found at i:306889 original size:31 final size:31
Alignment explanation
Indices: 306851--306921 Score: 99
Period size: 31 Copynumber: 2.3 Consensus size: 31
306841 AGGTGAATAG
* *
306851 ATAATATTTTAAAAAATGTTTTAATGTCTAA
1 ATAATATTTCAAAAAATATTTTAATGTCTAA
*
306882 ATAATATTTCAAAAAATATTTTAATGTTTAA
1 ATAATATTTCAAAAAATATTTTAATGTCTAA
*
306913 AGAAT-TTTC
1 ATAATATTTC
306922 CGTTAAAAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
30 4 0.11
31 32 0.89
ACGTcount: A:0.45, C:0.04, G:0.06, T:0.45
Consensus pattern (31 bp):
ATAATATTTCAAAAAATATTTTAATGTCTAA
Found at i:307048 original size:13 final size:14
Alignment explanation
Indices: 307018--307047 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
307008 TTTTTAAATG
307018 AAATATTATTTAAA
1 AAATATTATTTAAA
*
307032 AAATATTTTTTAAA
1 AAATATTATTTAAA
307046 AA
1 AA
307048 TTTGGGCGTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (14 bp):
AAATATTATTTAAA
Found at i:313825 original size:14 final size:14
Alignment explanation
Indices: 313806--313832 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
313796 CCATTAGGTT
313806 CCTTCCACCATCCA
1 CCTTCCACCATCCA
313820 CCTTCCACCATCC
1 CCTTCCACCATCC
313833 TCGCCGCCAC
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:0.19, C:0.59, G:0.00, T:0.22
Consensus pattern (14 bp):
CCTTCCACCATCCA
Found at i:315601 original size:29 final size:29
Alignment explanation
Indices: 315552--315621 Score: 90
Period size: 29 Copynumber: 2.4 Consensus size: 29
315542 CTGACATTAG
*
315552 TTAT-AATTGAGTAATTTGGTTGTAATAA
1 TTATAAATTGAGTAATATGGTTGTAATAA
*
315580 TTGATAAATTGAGT-ATATGGTTGTTATAA
1 TT-ATAAATTGAGTAATATGGTTGTAATAA
*
315609 TTATAAATAGAGT
1 TTATAAATTGAGT
315622 GACTAGGGAT
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
28 12 0.32
29 17 0.46
30 8 0.22
ACGTcount: A:0.37, C:0.00, G:0.19, T:0.44
Consensus pattern (29 bp):
TTATAAATTGAGTAATATGGTTGTAATAA
Found at i:318302 original size:18 final size:17
Alignment explanation
Indices: 318265--318311 Score: 58
Period size: 18 Copynumber: 2.7 Consensus size: 17
318255 TATGGAATTG
*
318265 GATTCCAATTCCTGACA
1 GATTCCAATTCCTCACA
*
318282 GATTTCAATTCCTTCACA
1 GATTCCAATTCC-TCACA
*
318300 GATTCTAATTCC
1 GATTCCAATTCC
318312 AACAGAAATA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
17 11 0.44
18 14 0.56
ACGTcount: A:0.28, C:0.28, G:0.09, T:0.36
Consensus pattern (17 bp):
GATTCCAATTCCTCACA
Found at i:323058 original size:14 final size:14
Alignment explanation
Indices: 323039--323075 Score: 60
Period size: 12 Copynumber: 2.8 Consensus size: 14
323029 TCATATATAA
323039 ATTTTTAAAAAAAT
1 ATTTTTAAAAAAAT
323053 ATTTTT--AAAAAT
1 ATTTTTAAAAAAAT
323065 ATTTTTAAAAA
1 ATTTTTAAAAA
323076 CTGGACATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
12 12 0.57
14 9 0.43
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (14 bp):
ATTTTTAAAAAAAT
Found at i:323219 original size:25 final size:24
Alignment explanation
Indices: 323191--323244 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
323181 CCTAAATTAA
323191 TTTTAAATATAGTTTAAGTATTTAT
1 TTTTAAATAT-GTTTAAGTATTTAT
*
323216 TTTTATATATGTTTAAGTATTTAT
1 TTTTAAATATGTTTAAGTATTTAT
323240 TTTTA
1 TTTTA
323245 TATAAAGTAA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
24 19 0.68
25 9 0.32
ACGTcount: A:0.31, C:0.00, G:0.07, T:0.61
Consensus pattern (24 bp):
TTTTAAATATGTTTAAGTATTTAT
Found at i:338608 original size:28 final size:30
Alignment explanation
Indices: 338552--338610 Score: 77
Period size: 31 Copynumber: 2.0 Consensus size: 30
338542 ATATAAAAGT
* *
338552 AAAACAAAAAGCAACATTTTCTTCCTATCAA
1 AAAAAAAAAAGCAACA-TTTCTTCATATCAA
338583 AAAAAAAAAAGCAACA-TT-TTCATATCAA
1 AAAAAAAAAAGCAACATTTCTTCATATCAA
338611 TTGCTTTATT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
28 9 0.35
29 2 0.08
31 15 0.58
ACGTcount: A:0.54, C:0.19, G:0.03, T:0.24
Consensus pattern (30 bp):
AAAAAAAAAAGCAACATTTCTTCATATCAA
Found at i:340657 original size:40 final size:39
Alignment explanation
Indices: 340626--340733 Score: 113
Period size: 33 Copynumber: 2.9 Consensus size: 39
340616 TCGGGTCGGA
*
340626 ATTTTTTAAAGTTTGATATTCGAGTCGGGTTCGGATCAAG
1 ATTTTTT-AAGTGTGATATTCGAGTCGGGTTCGGATCAAG
*
340666 ATTTTTTAAGTGTGATATTCGGGTCGGG-TC-G---AA-
1 ATTTTTTAAGTGTGATATTCGAGTCGGGTTCGGATCAAG
* *
340699 TTTTTTTAAGTGTGATATTCG-GATCGAGTTCGGAT
1 ATTTTTTAAGTGTGATATTCGAG-TCGGGTTCGGAT
340734 TTAGGGTGAA
Statistics
Matches: 59, Mismatches: 4, Indels: 13
0.78 0.05 0.17
Matches are distributed among these distances:
32 1 0.02
33 24 0.41
34 4 0.07
35 1 0.02
37 1 0.02
38 2 0.03
39 19 0.32
40 7 0.12
ACGTcount: A:0.22, C:0.09, G:0.27, T:0.42
Consensus pattern (39 bp):
ATTTTTTAAGTGTGATATTCGAGTCGGGTTCGGATCAAG
Found at i:340709 original size:33 final size:34
Alignment explanation
Indices: 340616--340720 Score: 122
Period size: 39 Copynumber: 3.0 Consensus size: 34
340606 AAAATTGGGT
* * *
340616 TCGGGTCGGAATTTTTTAAAGTTTGATATTCGAG
1 TCGGGTCGGAATTTTTTTAAGTGTGATATTCGGG
*
340650 TCGGGTTCGGATCAAGATTTTTTAAGTGTGATATTCGGG
1 TCGGG-TCGG---AA-TTTTTTTAAGTGTGATATTCGGG
340689 TCGGGTC-GAATTTTTTTAAGTGTGATATTCGG
1 TCGGGTCGGAATTTTTTTAAGTGTGATATTCGG
340721 ATCGAGTTCG
Statistics
Matches: 61, Mismatches: 5, Indels: 11
0.79 0.06 0.14
Matches are distributed among these distances:
33 21 0.34
34 7 0.11
35 4 0.07
37 1 0.02
38 4 0.07
39 24 0.39
ACGTcount: A:0.21, C:0.10, G:0.29, T:0.41
Consensus pattern (34 bp):
TCGGGTCGGAATTTTTTTAAGTGTGATATTCGGG
Found at i:343029 original size:29 final size:29
Alignment explanation
Indices: 342974--343030 Score: 69
Period size: 29 Copynumber: 2.0 Consensus size: 29
342964 ACCGGGTAAC
* * * **
342974 TATTTTGTAGCTTTTAATAGTTGATGGAT
1 TATTTTATAACTTTTAATACTCAATGGAT
343003 TATTTTATAACTTTTAATACTCAATGGA
1 TATTTTATAACTTTTAATACTCAATGGA
343031 CTCGATAAAA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.30, C:0.07, G:0.14, T:0.49
Consensus pattern (29 bp):
TATTTTATAACTTTTAATACTCAATGGAT
Found at i:343916 original size:28 final size:27
Alignment explanation
Indices: 343875--343953 Score: 90
Period size: 26 Copynumber: 2.9 Consensus size: 27
343865 ACTCGCGTTT
343875 GAACAATATTATTTACACGTGTGAGTTC
1 GAACAAT-TTATTTACACGTGTGAGTTC
* *
343903 GAACAATTTCATTTACAC--GTAATTTC
1 GAACAATTT-ATTTACACGTGTGAGTTC
*
343929 GAACAATTTTACTTACACGTGTGAG
1 GAACAA-TTTATTTACACGTGTGAG
343954 CTTATCCAAA
Statistics
Matches: 42, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
26 19 0.45
27 5 0.12
28 18 0.43
ACGTcount: A:0.33, C:0.16, G:0.15, T:0.35
Consensus pattern (27 bp):
GAACAATTTATTTACACGTGTGAGTTC
Found at i:345480 original size:84 final size:84
Alignment explanation
Indices: 345385--345553 Score: 329
Period size: 84 Copynumber: 2.0 Consensus size: 84
345375 ACAATCTTCC
345385 GGAGTATATATCCCACAATCTGATTGTACACCTCACTCAAATGCCAAGAAAGAAGCCTAAAATGT
1 GGAGTATATATCCCACAATCTGATTGTACACCTCACTCAAATGCCAAGAAAGAAGCCTAAAATGT
345450 TCGATACTAAAACAAAATA
66 TCGATACTAAAACAAAATA
345469 GGAGTATATATCCCACAATCTGATTGTACACCTCACTCAAATGCCAAGAAAGAAGCCTAAAATGT
1 GGAGTATATATCCCACAATCTGATTGTACACCTCACTCAAATGCCAAGAAAGAAGCCTAAAATGT
*
345534 TCGCTACTAAAACAAAATA
66 TCGATACTAAAACAAAATA
345553 G
1 G
345554 AAGGGAAAAA
Statistics
Matches: 84, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
84 84 1.00
ACGTcount: A:0.42, C:0.22, G:0.14, T:0.22
Consensus pattern (84 bp):
GGAGTATATATCCCACAATCTGATTGTACACCTCACTCAAATGCCAAGAAAGAAGCCTAAAATGT
TCGATACTAAAACAAAATA
Found at i:363544 original size:22 final size:22
Alignment explanation
Indices: 363496--363560 Score: 78
Period size: 22 Copynumber: 3.0 Consensus size: 22
363486 CGAGAAAGAA
*
363496 AAACGTACCACAAAGATAGAAT
1 AAACGTACCACAAAGATAAAAT
* *
363518 TAACGTACCACAAAGGTAAAAT
1 AAACGTACCACAAAGATAAAAT
**
363540 AAACGTGTCACAAA-ATAAAAT
1 AAACGTACCACAAAGATAAAAT
363561 TATTCTTATT
Statistics
Matches: 36, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
21 6 0.17
22 30 0.83
ACGTcount: A:0.54, C:0.17, G:0.12, T:0.17
Consensus pattern (22 bp):
AAACGTACCACAAAGATAAAAT
Found at i:372471 original size:2 final size:2
Alignment explanation
Indices: 372416--372455 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
372406 TATTTATTTA
372416 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
372456 TAAAAATACA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:391389 original size:36 final size:35
Alignment explanation
Indices: 391325--391394 Score: 95
Period size: 36 Copynumber: 2.0 Consensus size: 35
391315 CTTAAAGTAC
*
391325 TTTTATAAATATTGTGATAAATTCATAAAATTTAAT
1 TTTTATAAATATTGTAATAAATTCAT-AAATTTAAT
* * *
391361 TTTTATAAATATTTTAATATATTGATAAATTTAA
1 TTTTATAAATATTGTAATAAATTCATAAATTTAA
391395 ATAATTTTAA
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
35 8 0.27
36 22 0.73
ACGTcount: A:0.44, C:0.01, G:0.04, T:0.50
Consensus pattern (35 bp):
TTTTATAAATATTGTAATAAATTCATAAATTTAAT
Found at i:391663 original size:60 final size:60
Alignment explanation
Indices: 391585--391762 Score: 179
Period size: 59 Copynumber: 3.0 Consensus size: 60
391575 ACATCACAAT
* * *
391585 CTATGA-CCTCATTTTAAATTGGTCCTTAAACTTTTAAATATTTCAATTTCATCCCTAAA
1 CTATGATCTTCATTCTAAATTGGTCCTTAAACTTTTAAATATTTCAATTTAATCCCTAAA
** * * *
391644 CTATGAT-TATCATTCTAAATTACTCCTCAAACTTTTAACAT-TTT-ATTTTTATACCC-AAA
1 CTATGATCT-TCATTCTAAATTGGTCCTTAAACTTTTAA-ATATTTCAATTTAAT-CCCTAAA
* * *
391703 CTATGATCTTCATTCTAAATTGGTCCCTAAACTTTTTTAATATTGCAATTTAAT-CCTAAA
1 CTATGATCTTCATTCTAAATTGGTCCTTAAAC-TTTTAAATATTTCAATTTAATCCCTAAA
391763 TTATATGTGT
Statistics
Matches: 95, Mismatches: 15, Indels: 17
0.75 0.12 0.13
Matches are distributed among these distances:
59 45 0.47
60 42 0.44
61 8 0.08
ACGTcount: A:0.33, C:0.20, G:0.04, T:0.43
Consensus pattern (60 bp):
CTATGATCTTCATTCTAAATTGGTCCTTAAACTTTTAAATATTTCAATTTAATCCCTAAA
Found at i:393671 original size:26 final size:26
Alignment explanation
Indices: 393642--393728 Score: 63
Period size: 28 Copynumber: 3.2 Consensus size: 26
393632 AGCACTCAAA
393642 AAATATTATTTTATACATTTAATATT
1 AAATATTATTTTATACATTTAATATT
* *
393668 AAAT-TAATATTTATATCATTTTAAT-TA
1 AAATATTAT-TTTATA-CA-TTTAATATT
* *
393695 AAATATTAATTATTAAAATATTTAATA-T
1 AAATATT-ATT-TT-ATACATTTAATATT
393723 AAATAT
1 AAATAT
393729 AATATAATTT
Statistics
Matches: 47, Mismatches: 6, Indels: 14
0.70 0.09 0.21
Matches are distributed among these distances:
25 3 0.06
26 10 0.21
27 7 0.15
28 20 0.43
29 5 0.11
30 2 0.04
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.49
Consensus pattern (26 bp):
AAATATTATTTTATACATTTAATATT
Found at i:393711 original size:15 final size:15
Alignment explanation
Indices: 393691--393754 Score: 53
Period size: 15 Copynumber: 4.1 Consensus size: 15
393681 TATCATTTTA
393691 ATTAAAATATTAATT
1 ATTAAAATATTAATT
393706 ATTAAAATATTTAA-T
1 ATTAAAATA-TTAATT
393721 A-TAAATATAATATAATT
1 ATTAAA-AT-AT-TAATT
393738 -TTAATAATATTATATT
1 ATTAA-AATATTA-ATT
393754 A
1 A
393755 ATATATACTC
Statistics
Matches: 40, Mismatches: 0, Indels: 16
0.71 0.00 0.29
Matches are distributed among these distances:
14 4 0.10
15 16 0.40
16 13 0.32
17 6 0.15
18 1 0.03
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
ATTAAAATATTAATT
Found at i:393717 original size:29 final size:33
Alignment explanation
Indices: 393685--393748 Score: 77
Period size: 32 Copynumber: 2.1 Consensus size: 33
393675 TATTTATATC
393685 ATTTTAAT-TAAA-AT-AT-TAATTATTAA-AAT
1 ATTTTAATATAAATATAATATAATT-TTAATAAT
393714 A-TTTAATATAAATATAATATAATTTTAATAAT
1 ATTTTAATATAAATATAATATAATTTTAATAAT
393746 ATT
1 ATT
393749 ATATTAATAT
Statistics
Matches: 29, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
28 6 0.21
29 5 0.17
30 2 0.07
31 6 0.21
32 9 0.31
33 1 0.03
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (33 bp):
ATTTTAATATAAATATAATATAATTTTAATAAT
Found at i:393744 original size:14 final size:14
Alignment explanation
Indices: 393727--393901 Score: 53
Period size: 13 Copynumber: 13.4 Consensus size: 14
393717 TAATATAAAT
*
393727 ATAATATAATTTTA
1 ATAATATAATATTA
*
393741 ATAATATTATATTA
1 ATAATATAATATTA
*
393755 AT-ATATACTCA-T-
1 ATAATATAAT-ATTA
*
393767 AT-ATATATTA-TA
1 ATAATATAATATTA
393779 ATAATATATGATATT-
1 ATAATATA--ATATTA
* * *
393794 ATATTTTAA-ATAA
1 ATAATATAATATTA
* *
393807 ATTAT-TAATATTT
1 ATAATATAATATTA
* *
393820 AT-ATATTAT-TTT
1 ATAATATAATATTA
393832 ATAATATAATATTA
1 ATAATATAATATTA
*
393846 TTAA-AT--TATTA
1 ATAATATAATATTA
393857 ATAATGAGTAATATTA
1 ATAAT-A-TAATATTA
*
393873 AT-TTAT-ATATT-
1 ATAATATAATATTA
393884 -TAATATCAATA-TA
1 ATAATAT-AATATTA
393897 ATAAT
1 ATAAT
393902 TTAGTATTAT
Statistics
Matches: 120, Mismatches: 20, Indels: 42
0.66 0.11 0.23
Matches are distributed among these distances:
10 1 0.01
11 13 0.11
12 28 0.23
13 35 0.29
14 26 0.22
15 9 0.08
16 8 0.07
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (14 bp):
ATAATATAATATTA
Found at i:394227 original size:29 final size:30
Alignment explanation
Indices: 394181--394258 Score: 95
Period size: 29 Copynumber: 2.6 Consensus size: 30
394171 TCTGAAAAAT
*
394181 ATAATTCATTTTATGTAAAACAATTTT-AG
1 ATAATTCATTTTACGTAAAACAATTTTCAG
* * * *
394210 GTAATTCATTTTACGTAAAATATTTTTCAT
1 ATAATTCATTTTACGTAAAACAATTTTCAG
*
394240 ATAATTTATTTTACGTAAA
1 ATAATTCATTTTACGTAAA
394259 TTATTTTTCA
Statistics
Matches: 41, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
29 23 0.56
30 18 0.44
ACGTcount: A:0.38, C:0.08, G:0.06, T:0.47
Consensus pattern (30 bp):
ATAATTCATTTTACGTAAAACAATTTTCAG
Found at i:394234 original size:14 final size:14
Alignment explanation
Indices: 394203--394265 Score: 56
Period size: 14 Copynumber: 4.4 Consensus size: 14
394193 ATGTAAAACA
*
394203 ATTTTAGGT-AATT
1 ATTTTACGTAAATT
*
394216 CATTTTACGTAAAAT
1 -ATTTTACGTAAATT
* *
394231 ATTTTTCATATAATTT
1 ATTTTACGTA-AA-TT
394247 ATTTTACGTAAATT
1 ATTTTACGTAAATT
394261 ATTTT
1 ATTTT
394266 TCAGAAAATT
Statistics
Matches: 39, Mismatches: 7, Indels: 6
0.75 0.13 0.12
Matches are distributed among these distances:
14 23 0.59
15 7 0.18
16 9 0.23
ACGTcount: A:0.33, C:0.06, G:0.06, T:0.54
Consensus pattern (14 bp):
ATTTTACGTAAATT
Found at i:394251 original size:30 final size:30
Alignment explanation
Indices: 394179--394268 Score: 110
Period size: 30 Copynumber: 3.0 Consensus size: 30
394169 TTTCTGAAAA
* * *
394179 ATATAATTCATTTTATGTAAAACAATTTT-
1 ATATAATTCATTTTACGTAAAATATTTTTC
**
394208 AGGTAATTCATTTTACGTAAAATATTTTTC
1 ATATAATTCATTTTACGTAAAATATTTTTC
* *
394238 ATATAATTTATTTTACGTAAATTATTTTTC
1 ATATAATTCATTTTACGTAAAATATTTTTC
394268 A
1 A
394269 GAAAATTAAT
Statistics
Matches: 51, Mismatches: 9, Indels: 1
0.84 0.15 0.02
Matches are distributed among these distances:
29 24 0.47
30 27 0.53
ACGTcount: A:0.37, C:0.08, G:0.06, T:0.50
Consensus pattern (30 bp):
ATATAATTCATTTTACGTAAAATATTTTTC
Found at i:399876 original size:20 final size:20
Alignment explanation
Indices: 399851--399890 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
399841 AAAAAAATAT
399851 TTCTGCATAAGGACAGCTGG
1 TTCTGCATAAGGACAGCTGG
399871 TTCTGCATAAGGACAGCTGG
1 TTCTGCATAAGGACAGCTGG
399891 CACTGGACAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.25, C:0.20, G:0.30, T:0.25
Consensus pattern (20 bp):
TTCTGCATAAGGACAGCTGG
Found at i:403555 original size:15 final size:16
Alignment explanation
Indices: 403535--403567 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
403525 TCAATTTAAG
*
403535 TATCG-ATTTTATTTT
1 TATCGAATTTTATATT
403550 TATCGAATTTTATATT
1 TATCGAATTTTATATT
403566 TA
1 TA
403568 AATTTAAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 5 0.31
16 11 0.69
ACGTcount: A:0.27, C:0.06, G:0.06, T:0.61
Consensus pattern (16 bp):
TATCGAATTTTATATT
Found at i:404347 original size:17 final size:17
Alignment explanation
Indices: 404300--404468 Score: 160
Period size: 17 Copynumber: 9.7 Consensus size: 17
404290 ATTCTAAATG
* *
404300 TTTACAGTTATCATACA
1 TTTACAGTTATCAGATA
*
404317 TTTCACCGTTATCAGATA
1 TTT-ACAGTTATCAGATA
*
404335 TTTACAATTATCAGATGA
1 TTTACAGTTATCAGAT-A
**
404353 TTTTTAGTTATCAGATA
1 TTTACAGTTATCAGATA
*
404370 TTTACAGTTATTAGATGA
1 TTTACAGTTATCAGAT-A
**
404388 TTTTTAGTTATCAGATA
1 TTTACAGTTATCAGATA
*
404405 TTTACAGATATCAGATGA
1 TTTACAGTTATCAGAT-A
*
404423 -TTACAGTTATTAGATA
1 TTTACAGTTATCAGATA
* *
404439 TTTACAGATATCAGATGT
1 TTTACAGTTATCAGAT-A
*
404457 TTTATAGTTATC
1 TTTACAGTTATC
404469 GGACATAGAT
Statistics
Matches: 122, Mismatches: 24, Indels: 11
0.78 0.15 0.07
Matches are distributed among these distances:
16 1 0.01
17 68 0.56
18 53 0.43
ACGTcount: A:0.33, C:0.11, G:0.12, T:0.44
Consensus pattern (17 bp):
TTTACAGTTATCAGATA
Found at i:404363 original size:35 final size:35
Alignment explanation
Indices: 404324--404468 Score: 206
Period size: 35 Copynumber: 4.2 Consensus size: 35
404314 ACATTTCACC
404324 GTTATCAGATATTTACA-ATTATCAGATGATTTTTA
1 GTTATCAGATATTTACAGA-TATCAGATGATTTTTA
* *
404359 GTTATCAGATATTTACAGTTATTAGATGATTTTTA
1 GTTATCAGATATTTACAGATATCAGATGATTTTTA
**
404394 GTTATCAGATATTTACAGATATCAGATGA-TTACA
1 GTTATCAGATATTTACAGATATCAGATGATTTTTA
*
404428 GTTATTAGATATTTACAGATATCAGATG-TTTTATA
1 GTTATCAGATATTTACAGATATCAGATGATTTT-TA
404463 GTTATC
1 GTTATC
404469 GGACATAGAT
Statistics
Matches: 97, Mismatches: 10, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
34 32 0.33
35 65 0.67
ACGTcount: A:0.34, C:0.08, G:0.14, T:0.44
Consensus pattern (35 bp):
GTTATCAGATATTTACAGATATCAGATGATTTTTA
Found at i:404418 original size:52 final size:52
Alignment explanation
Indices: 404324--404460 Score: 143
Period size: 52 Copynumber: 2.6 Consensus size: 52
404314 ACATTTCACC
* ** * ** *
404324 GTTATCAGATATTTACAATTATCAGATGATTTTTAGTTATCAGAT-ATTTACA
1 GTTATTAGATATTTTTAGTTATCAGATGATTTACAGATATCAGATGA-TTACA
404376 GTTATTAGATGATTTTTAGTTATCAGAT-ATTTACAGATATCAGATGATTACA
1 GTTATTAGAT-ATTTTTAGTTATCAGATGATTTACAGATATCAGATGATTACA
** * *
404428 GTTATTAGATATTTACAGATATCAGATGTTTTA
1 GTTATTAGATATTTTTAGTTATCAGATGATTTA
404461 TAGTTATCGG
Statistics
Matches: 71, Mismatches: 11, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
51 14 0.20
52 42 0.59
53 15 0.21
ACGTcount: A:0.34, C:0.08, G:0.14, T:0.44
Consensus pattern (52 bp):
GTTATTAGATATTTTTAGTTATCAGATGATTTACAGATATCAGATGATTACA
Found at i:406731 original size:32 final size:32
Alignment explanation
Indices: 406692--406777 Score: 145
Period size: 32 Copynumber: 2.7 Consensus size: 32
406682 AGCTTGCGAG
* *
406692 TTTTCGAGTCGAGTTGAACTCATATTTCAGAA
1 TTTTCGAGTAGAGTCGAACTCATATTTCAGAA
406724 TTTTCGAGTAGAGTCGAACTCATATTTCAGAA
1 TTTTCGAGTAGAGTCGAACTCATATTTCAGAA
*
406756 TTTTCGAGTAGAGTCGACCTCA
1 TTTTCGAGTAGAGTCGAACTCA
406778 GCAATACTTG
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 51 1.00
ACGTcount: A:0.28, C:0.17, G:0.20, T:0.35
Consensus pattern (32 bp):
TTTTCGAGTAGAGTCGAACTCATATTTCAGAA
Found at i:407611 original size:23 final size:23
Alignment explanation
Indices: 407576--407631 Score: 94
Period size: 23 Copynumber: 2.4 Consensus size: 23
407566 GATATGTTTG
*
407576 TAATGTTTGGACTTAAAATCATTT
1 TAATG-TTGGACTTAAAAGCATTT
407600 TAATGTTGGACTTAAAAGCATTT
1 TAATGTTGGACTTAAAAGCATTT
407623 TAATGTTGG
1 TAATGTTGG
407632 GTTTTAACAT
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
23 26 0.84
24 5 0.16
ACGTcount: A:0.32, C:0.07, G:0.18, T:0.43
Consensus pattern (23 bp):
TAATGTTGGACTTAAAAGCATTT
Found at i:407922 original size:2 final size:2
Alignment explanation
Indices: 407915--407945 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
407905 AGGACTACAA
407915 AT 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 AT A
407946 GAACTATGCC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:409031 original size:14 final size:14
Alignment explanation
Indices: 409012--409049 Score: 67
Period size: 14 Copynumber: 2.7 Consensus size: 14
409002 CGCTGGGCAT
409012 CCGAGGCCATCCGA
1 CCGAGGCCATCCGA
409026 CCGAGGCCATCCGA
1 CCGAGGCCATCCGA
*
409040 CCGATGCCAT
1 CCGAGGCCAT
409050 TCGAGAGCAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.21, C:0.42, G:0.26, T:0.11
Consensus pattern (14 bp):
CCGAGGCCATCCGA
Found at i:409066 original size:34 final size:33
Alignment explanation
Indices: 409026--409098 Score: 101
Period size: 33 Copynumber: 2.2 Consensus size: 33
409016 GGCCATCCGA
* *
409026 CCGAGGCCATCCGACCGATGCCATTCGAGAGCAT
1 CCGAGGCCATCCGAACGA-GCCATGCGAGAGCAT
* *
409060 CCGAGGCCATCCGAACGAGCTATGCGAGGGCAT
1 CCGAGGCCATCCGAACGAGCCATGCGAGAGCAT
409093 CCGAGG
1 CCGAGG
409099 GTAACCGAGC
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
33 18 0.51
34 17 0.49
ACGTcount: A:0.23, C:0.33, G:0.32, T:0.12
Consensus pattern (33 bp):
CCGAGGCCATCCGAACGAGCCATGCGAGAGCAT
Found at i:409117 original size:33 final size:33
Alignment explanation
Indices: 409051--409144 Score: 98
Period size: 33 Copynumber: 2.8 Consensus size: 33
409041 CGATGCCATT
* * * *
409051 CGAGAGCATCCGAGGCCATCCGAACGAGCTATG
1 CGAGGGCATCCGAGGGCAACCGAGCGAGCTATG
* *
409084 CGAGGGCATCCGAGGGTAACCGAGCGAGTTATG
1 CGAGGGCATCCGAGGGCAACCGAGCGAGCTATG
* * * *
409117 CAAGGGAATCTGAGGGCAGCCGAGCGAG
1 CGAGGGCATCCGAGGGCAACCGAGCGAG
409145 GGTAGGTCGC
Statistics
Matches: 50, Mismatches: 11, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
33 50 1.00
ACGTcount: A:0.27, C:0.24, G:0.37, T:0.12
Consensus pattern (33 bp):
CGAGGGCATCCGAGGGCAACCGAGCGAGCTATG
Found at i:409293 original size:29 final size:29
Alignment explanation
Indices: 409251--409334 Score: 107
Period size: 29 Copynumber: 2.9 Consensus size: 29
409241 GAGCAAGGGT
* *
409251 AGGTCGCCCAGAGTGTATGACGACCTACA
1 AGGTCGCCCGGAGTGCATGACGACCTACA
* *
409280 AGGTCGCCCGGAGTGCATGGCGACCTATA
1 AGGTCGCCCGGAGTGCATGACGACCTACA
*
409309 AGGTCGCCCGGAAG-ACATGACGACCT
1 AGGTCGCCCGG-AGTGCATGACGACCT
409335 CCGGCCAACA
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
29 46 0.96
30 2 0.04
ACGTcount: A:0.25, C:0.29, G:0.31, T:0.15
Consensus pattern (29 bp):
AGGTCGCCCGGAGTGCATGACGACCTACA
Found at i:410905 original size:18 final size:19
Alignment explanation
Indices: 410865--410902 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 19
410855 TGGTTCACGA
410865 AATGTAAGATTACCAGTGGG
1 AATGTAAGATTACCAG-GGG
410885 AATGTAAGATTACCAGGG
1 AATGTAAGATTACCAGGG
410903 AATAGGATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 2 0.11
20 16 0.89
ACGTcount: A:0.37, C:0.11, G:0.29, T:0.24
Consensus pattern (19 bp):
AATGTAAGATTACCAGGGG
Found at i:411131 original size:37 final size:38
Alignment explanation
Indices: 411050--411131 Score: 98
Period size: 37 Copynumber: 2.2 Consensus size: 38
411040 TAATAAGTTG
* *
411050 TAAAATATTTATATATTTTCTTTAAAAAATTTAAATTCA
1 TAAAA-ATTTATATATTTTCTTTAAAAAATTGAAAATCA
*
411089 T-AAAATTTATATAATTTT-TTTACAAAATTGAAAAT-A
1 TAAAAATTTATAT-ATTTTCTTTAAAAAATTGAAAATCA
411125 TAAAAAT
1 TAAAAAT
411132 GTTTAATGAA
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
36 2 0.05
37 27 0.71
38 8 0.21
39 1 0.03
ACGTcount: A:0.50, C:0.04, G:0.01, T:0.45
Consensus pattern (38 bp):
TAAAAATTTATATATTTTCTTTAAAAAATTGAAAATCA
Done.