Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009287.1 Hibiscus syriacus cultivar Beakdansim tig00112980_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: 362425
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
File 2 of 2
Found at i:200129 original size:13 final size:13
Alignment explanation
Indices: 200082--200134 Score: 52
Period size: 14 Copynumber: 3.9 Consensus size: 13
200072 TTGATTGTTT
200082 AATTGATTTGTAA
1 AATTGATTTGTAA
*
200095 AAGATGATTTGTAA
1 AA-TTGATTTGTAA
**
200109 ATATTGATTTGTTT
1 A-ATTGATTTGTAA
*
200123 AATTGATGTGTA
1 AATTGATTTGTA
200135 CATAATTATT
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
13 11 0.34
14 20 0.62
15 1 0.03
ACGTcount: A:0.34, C:0.00, G:0.19, T:0.47
Consensus pattern (13 bp):
AATTGATTTGTAA
Found at i:200316 original size:20 final size:20
Alignment explanation
Indices: 200291--200384 Score: 152
Period size: 20 Copynumber: 4.7 Consensus size: 20
200281 GCGATTCTCT
200291 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTTCCG
200311 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTTCCG
200331 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTTCCG
* * *
200351 CATTACGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTCCG
*
200371 TGTTGCGATAGTCA
1 CGTTGCGATAGTCA
200385 AATGAATGTC
Statistics
Matches: 68, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 68 1.00
ACGTcount: A:0.18, C:0.22, G:0.23, T:0.36
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTCCG
Found at i:203733 original size:20 final size:20
Alignment explanation
Indices: 203710--203755 Score: 67
Period size: 20 Copynumber: 2.3 Consensus size: 20
203700 CAGAATCTCG
*
203710 TTGCGATTTACAG-ATTTGCA
1 TTGCGATTTAC-GTATTCGCA
203730 TTGCGATTTACGTATTCGCA
1 TTGCGATTTACGTATTCGCA
203750 TTGCGA
1 TTGCGA
203756 ATTAGGAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 1 0.04
20 23 0.96
ACGTcount: A:0.22, C:0.17, G:0.22, T:0.39
Consensus pattern (20 bp):
TTGCGATTTACGTATTCGCA
Found at i:203776 original size:21 final size:21
Alignment explanation
Indices: 203752--203797 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
203742 TATTCGCATT
203752 GCGAATTAGGAAAATCGCAAC
1 GCGAATTAGGAAAATCGCAAC
* * *
203773 GCGAATTTGGGAAATCGCAAT
1 GCGAATTAGGAAAATCGCAAC
203794 GCGA
1 GCGA
203798 TAGTCAGAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.37, C:0.17, G:0.28, T:0.17
Consensus pattern (21 bp):
GCGAATTAGGAAAATCGCAAC
Found at i:207544 original size:25 final size:25
Alignment explanation
Indices: 207516--207563 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
207506 AAATAACTGA
*
207516 TACATGTAATAAGCTTAACACATTC
1 TACATATAATAAGCTTAACACATTC
*
207541 TACATATTATAAGCTTAACACAT
1 TACATATAATAAGCTTAACACAT
207564 CCACCGTACC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.42, C:0.19, G:0.06, T:0.33
Consensus pattern (25 bp):
TACATATAATAAGCTTAACACATTC
Found at i:208646 original size:2 final size:2
Alignment explanation
Indices: 208639--208663 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
208629 CATAATTACG
208639 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 T
208664 TGTACACCTA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:213690 original size:13 final size:13
Alignment explanation
Indices: 213672--213700 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
213662 CTGTCATTAA
213672 TAATTTAATAAAG
1 TAATTTAATAAAG
213685 TAATTTAATAAAG
1 TAATTTAATAAAG
213698 TAA
1 TAA
213701 AAACCGTTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.55, C:0.00, G:0.07, T:0.38
Consensus pattern (13 bp):
TAATTTAATAAAG
Found at i:214953 original size:23 final size:23
Alignment explanation
Indices: 214880--214953 Score: 55
Period size: 23 Copynumber: 3.2 Consensus size: 23
214870 CCGTATATGT
*
214880 TATAAAACATGTATTCAAACTCG
1 TATAAAACATGTATTCGAACTCG
* * *
214903 TATATAACGATTTGGT-TTCGTA-T-T
1 TATAAAAC-A--T-GTATTCGAACTCG
214927 TATAAAACATGTATTCGAACTCG
1 TATAAAACATGTATTCGAACTCG
214950 TATA
1 TATA
214954 TATTCATCAA
Statistics
Matches: 37, Mismatches: 7, Indels: 14
0.64 0.12 0.24
Matches are distributed among these distances:
20 2 0.05
21 6 0.16
22 1 0.03
23 12 0.32
24 8 0.22
25 1 0.03
26 5 0.14
27 2 0.05
ACGTcount: A:0.36, C:0.14, G:0.12, T:0.38
Consensus pattern (23 bp):
TATAAAACATGTATTCGAACTCG
Found at i:221574 original size:21 final size:21
Alignment explanation
Indices: 221548--221597 Score: 91
Period size: 21 Copynumber: 2.4 Consensus size: 21
221538 TGCCCTAAAT
221548 CCGAATCCGACTCGACTCGAC
1 CCGAATCCGACTCGACTCGAC
*
221569 CCGAATCTGACTCGACTCGAC
1 CCGAATCCGACTCGACTCGAC
221590 CCGAATCC
1 CCGAATCC
221598 TATTTTTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.24, C:0.42, G:0.18, T:0.16
Consensus pattern (21 bp):
CCGAATCCGACTCGACTCGAC
Found at i:221791 original size:5 final size:5
Alignment explanation
Indices: 221781--221907 Score: 218
Period size: 5 Copynumber: 25.4 Consensus size: 5
221771 TGCCTCAACC
* *
221781 ATTCT ATTCT ATTCT ATTCT ATTCT ATTCT ATTTT ATTCT ATTCT ATTTT
1 ATTCT ATTCT ATTCT ATTCT ATTCT ATTCT ATTCT ATTCT ATTCT ATTCT
* *
221831 ATTTT ATTCT ATTCT ATTCT ATTCT ATTTT ATTCT ATTCT ATTCT ATTCT
1 ATTCT ATTCT ATTCT ATTCT ATTCT ATTCT ATTCT ATTCT ATTCT ATTCT
221881 ATTCT ATTCT ATTCT ATTCT ATTCT AT
1 ATTCT ATTCT ATTCT ATTCT ATTCT AT
221908 CATCACCATC
Statistics
Matches: 116, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
5 116 1.00
ACGTcount: A:0.20, C:0.17, G:0.00, T:0.63
Consensus pattern (5 bp):
ATTCT
Found at i:223977 original size:3 final size:3
Alignment explanation
Indices: 223969--223997 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
223959 ACCTCAACCG
223969 TCA TCA TCA TCA TCA TCA TCA TCA TCA TC
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TC
223998 CAAGCTTCTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.31, C:0.34, G:0.00, T:0.34
Consensus pattern (3 bp):
TCA
Found at i:226107 original size:86 final size:86
Alignment explanation
Indices: 225962--226134 Score: 346
Period size: 86 Copynumber: 2.0 Consensus size: 86
225952 GCCTCTCCCC
225962 CCTTATCTCAAGAAACATGCTTCAACTCCAGCAATGTGACTGCTACAACTTATTTCGATCTATGT
1 CCTTATCTCAAGAAACATGCTTCAACTCCAGCAATGTGACTGCTACAACTTATTTCGATCTATGT
226027 ACTAATTCATATGGTGTTATT
66 ACTAATTCATATGGTGTTATT
226048 CCTTATCTCAAGAAACATGCTTCAACTCCAGCAATGTGACTGCTACAACTTATTTCGATCTATGT
1 CCTTATCTCAAGAAACATGCTTCAACTCCAGCAATGTGACTGCTACAACTTATTTCGATCTATGT
226113 ACTAATTCATATGGTGTTATT
66 ACTAATTCATATGGTGTTATT
226134 C
1 C
226135 GAAAAGTTCG
Statistics
Matches: 87, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
86 87 1.00
ACGTcount: A:0.29, C:0.23, G:0.13, T:0.36
Consensus pattern (86 bp):
CCTTATCTCAAGAAACATGCTTCAACTCCAGCAATGTGACTGCTACAACTTATTTCGATCTATGT
ACTAATTCATATGGTGTTATT
Found at i:233051 original size:34 final size:30
Alignment explanation
Indices: 233013--233081 Score: 95
Period size: 30 Copynumber: 2.2 Consensus size: 30
233003 TTGATATAAC
233013 AATTTAAGGCAAAATGGTTTTTGGACTTGAATTG
1 AATTTAA--CAAAAT-GTTTTTGGACTT-AATTG
233047 AATTT-ACAAAATGTTTTTGGACTTAATTG
1 AATTTAACAAAATGTTTTTGGACTTAATTG
233076 AATTTA
1 AATTTA
233082 TTCAAAGTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
29 10 0.29
30 12 0.35
31 6 0.18
33 1 0.03
34 5 0.15
ACGTcount: A:0.35, C:0.06, G:0.17, T:0.42
Consensus pattern (30 bp):
AATTTAACAAAATGTTTTTGGACTTAATTG
Found at i:233092 original size:29 final size:30
Alignment explanation
Indices: 233022--233081 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 30
233012 CAATTTAAGG
233022 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1 CAAAAT-GTTTTTGGACTTGAATTGAATTTA
233053 CAAAATGTTTTTGGACTT-AATTGAATTTA
1 CAAAATGTTTTTGGACTTGAATTGAATTTA
233082 TTCAAAGTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 11 0.38
30 12 0.41
31 6 0.21
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.43
Consensus pattern (30 bp):
CAAAATGTTTTTGGACTTGAATTGAATTTA
Found at i:233187 original size:21 final size:21
Alignment explanation
Indices: 233161--233214 Score: 99
Period size: 21 Copynumber: 2.6 Consensus size: 21
233151 AGGGTGTCAA
*
233161 AGTGCATCTATGCATCCCTGC
1 AGTGCATCCATGCATCCCTGC
233182 AGTGCATCCATGCATCCCTGC
1 AGTGCATCCATGCATCCCTGC
233203 AGTGCATCCATG
1 AGTGCATCCATG
233215 TATCTGCACT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.20, C:0.33, G:0.20, T:0.26
Consensus pattern (21 bp):
AGTGCATCCATGCATCCCTGC
Found at i:233322 original size:20 final size:21
Alignment explanation
Indices: 233281--233376 Score: 160
Period size: 20 Copynumber: 4.7 Consensus size: 21
233271 ATGCATTTAG
233281 TGCATCGATGCATCCTTGCCA
1 TGCATCGATGCATCCTTGCCA
233302 TGCATCGATGCATCC-TGCCA
1 TGCATCGATGCATCCTTGCCA
*
233322 TGCATCCATGCATCCTTGCCA
1 TGCATCGATGCATCCTTGCCA
233343 TGCATCGATGCAT-CTTGCCA
1 TGCATCGATGCATCCTTGCCA
*
233363 TGCATCCATGCATC
1 TGCATCGATGCATC
233377 AAGGCTGCAA
Statistics
Matches: 70, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
20 38 0.54
21 32 0.46
ACGTcount: A:0.20, C:0.34, G:0.18, T:0.28
Consensus pattern (21 bp):
TGCATCGATGCATCCTTGCCA
Found at i:233333 original size:41 final size:41
Alignment explanation
Indices: 233281--233376 Score: 174
Period size: 41 Copynumber: 2.3 Consensus size: 41
233271 ATGCATTTAG
*
233281 TGCATCGATGCATCCTTGCCATGCATCGATGCATCCTGCCA
1 TGCATCCATGCATCCTTGCCATGCATCGATGCATCCTGCCA
*
233322 TGCATCCATGCATCCTTGCCATGCATCGATGCATCTTGCCA
1 TGCATCCATGCATCCTTGCCATGCATCGATGCATCCTGCCA
233363 TGCATCCATGCATC
1 TGCATCCATGCATC
233377 AAGGCTGCAA
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 53 1.00
ACGTcount: A:0.20, C:0.34, G:0.18, T:0.28
Consensus pattern (41 bp):
TGCATCCATGCATCCTTGCCATGCATCGATGCATCCTGCCA
Found at i:234178 original size:24 final size:23
Alignment explanation
Indices: 234121--234185 Score: 82
Period size: 24 Copynumber: 2.9 Consensus size: 23
234111 TTCCCCTTGA
234121 AGTGCATCGATGCATT-C-T-AC
1 AGTGCATCGATGCATTCCTTAAC
*
234141 AGTGTATCGATGCATTCCTTAAC
1 AGTGCATCGATGCATTCCTTAAC
*
234164 ATGTGCATCGATGCACTCCTTA
1 A-GTGCATCGATGCATTCCTTA
234186 TGCATCGATG
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 15 0.39
21 1 0.03
22 1 0.03
23 3 0.08
24 18 0.47
ACGTcount: A:0.25, C:0.25, G:0.18, T:0.32
Consensus pattern (23 bp):
AGTGCATCGATGCATTCCTTAAC
Found at i:237032 original size:23 final size:23
Alignment explanation
Indices: 237001--237096 Score: 115
Period size: 23 Copynumber: 4.3 Consensus size: 23
236991 AGGGACATTT
*
237001 TATATGGCACTTCGGTGCAATTC
1 TATACGGCACTTCGGTGCAATTC
*
237024 TATACGGCACTTCAGTGCAATTC
1 TATACGGCACTTCGGTGCAATTC
**
237047 TACGCGGCACTTCGGTGCAATTC
1 TATACGGCACTTCGGTGCAATTC
***
237070 TACGTGGCACTTCGGTGC-ATT-
1 TATACGGCACTTCGGTGCAATTC
237091 TATACG
1 TATACG
237097 AACTGTGGTG
Statistics
Matches: 64, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
21 3 0.05
22 3 0.05
23 58 0.91
ACGTcount: A:0.21, C:0.25, G:0.23, T:0.31
Consensus pattern (23 bp):
TATACGGCACTTCGGTGCAATTC
Found at i:237285 original size:28 final size:28
Alignment explanation
Indices: 237232--237285 Score: 65
Period size: 28 Copynumber: 1.9 Consensus size: 28
237222 AATGAATTGT
* * *
237232 ATTATATGATTTATATGATGATATGTGG
1 ATTATATGATTTAAATGATCAAATGTGG
237260 ATTATATGA-TTAAATGAGTCAAATGT
1 ATTATATGATTTAAATGA-TCAAATGT
237286 TGGTTAAATT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
27 7 0.32
28 15 0.68
ACGTcount: A:0.37, C:0.02, G:0.19, T:0.43
Consensus pattern (28 bp):
ATTATATGATTTAAATGATCAAATGTGG
Found at i:240665 original size:19 final size:19
Alignment explanation
Indices: 240641--240692 Score: 104
Period size: 19 Copynumber: 2.7 Consensus size: 19
240631 CCTTAACATG
240641 TGCATCGATGCACTCCTTA
1 TGCATCGATGCACTCCTTA
240660 TGCATCGATGCACTCCTTA
1 TGCATCGATGCACTCCTTA
240679 TGCATCGATGCACT
1 TGCATCGATGCACT
240693 AATTGCATTC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 33 1.00
ACGTcount: A:0.21, C:0.31, G:0.17, T:0.31
Consensus pattern (19 bp):
TGCATCGATGCACTCCTTA
Found at i:241327 original size:55 final size:55
Alignment explanation
Indices: 241268--241386 Score: 229
Period size: 55 Copynumber: 2.2 Consensus size: 55
241258 TTCTCTTGGC
241268 TTCCACGTGAAGAAGAATAAAGGAGAAGAAGAGAACTATAGATAAATCTCTCCCT
1 TTCCACGTGAAGAAGAATAAAGGAGAAGAAGAGAACTATAGATAAATCTCTCCCT
*
241323 TTCCACGTGAAGAAGAATAAAGGAGAAGAAGAGAACTATGGATAAATCTCTCCCT
1 TTCCACGTGAAGAAGAATAAAGGAGAAGAAGAGAACTATAGATAAATCTCTCCCT
241378 TTCCACGTG
1 TTCCACGTG
241387 GTTCCCTTTT
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
55 63 1.00
ACGTcount: A:0.40, C:0.18, G:0.21, T:0.21
Consensus pattern (55 bp):
TTCCACGTGAAGAAGAATAAAGGAGAAGAAGAGAACTATAGATAAATCTCTCCCT
Found at i:246820 original size:86 final size:86
Alignment explanation
Indices: 246675--246860 Score: 372
Period size: 86 Copynumber: 2.2 Consensus size: 86
246665 TATATAACCA
246675 TTTCCATTCGGACTTAATGAATTGTGTAGTTTGGTTGTAGTCAAAGAAGACATACAGATTTAATA
1 TTTCCATTCGGACTTAATGAATTGTGTAGTTTGGTTGTAGTCAAAGAAGACATACAGATTTAATA
246740 AGAAGAAGCAATTCCCTTCCC
66 AGAAGAAGCAATTCCCTTCCC
246761 TTTCCATTCGGACTTAATGAATTGTGTAGTTTGGTTGTAGTCAAAGAAGACATACAGATTTAATA
1 TTTCCATTCGGACTTAATGAATTGTGTAGTTTGGTTGTAGTCAAAGAAGACATACAGATTTAATA
246826 AGAAGAAGCAATTCCCTTCCC
66 AGAAGAAGCAATTCCCTTCCC
246847 TTTCCATTCGGACT
1 TTTCCATTCGGACT
246861 ATGCAATATG
Statistics
Matches: 100, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
86 100 1.00
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.33
Consensus pattern (86 bp):
TTTCCATTCGGACTTAATGAATTGTGTAGTTTGGTTGTAGTCAAAGAAGACATACAGATTTAATA
AGAAGAAGCAATTCCCTTCCC
Found at i:247511 original size:55 final size:55
Alignment explanation
Indices: 247425--247529 Score: 174
Period size: 55 Copynumber: 1.9 Consensus size: 55
247415 CATCTGCACA
* *
247425 ATATCAAATTGCATTAGAATCTAAAATCTTATAACCAAAACTGTAAAAATACTGG
1 ATATCAAATTGCATTAGAATCTAAAAACTTATAACCAAAACTGGAAAAATACTGG
* *
247480 ATATCAGATTGCATTAGAATCTAAAAACTTATAACCGAAACTGGAAAAAT
1 ATATCAAATTGCATTAGAATCTAAAAACTTATAACCAAAACTGGAAAAAT
247530 TTTCTTAGAA
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
55 46 1.00
ACGTcount: A:0.48, C:0.14, G:0.10, T:0.28
Consensus pattern (55 bp):
ATATCAAATTGCATTAGAATCTAAAAACTTATAACCAAAACTGGAAAAATACTGG
Found at i:248566 original size:2 final size:2
Alignment explanation
Indices: 248559--248584 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
248549 ATCTAAAATA
248559 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
248585 GTGTGTGTGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:255571 original size:2 final size:2
Alignment explanation
Indices: 255566--255624 Score: 58
Period size: 2 Copynumber: 32.5 Consensus size: 2
255556 ATATAAAATA
*
255566 AT AT AT AT AT AT AT AT AT AT A- AT -T A- AT AT AA AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
255604 A- AA AT AT -T AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT A
255625 ATCGGGGCGG
Statistics
Matches: 48, Mismatches: 3, Indels: 12
0.76 0.05 0.19
Matches are distributed among these distances:
1 6 0.12
2 42 0.88
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:255592 original size:44 final size:44
Alignment explanation
Indices: 255529--255624 Score: 158
Period size: 44 Copynumber: 2.2 Consensus size: 44
255519 AAACCCGAAA
*
255529 ATAT-TATATATATAATTAATCTAAAAAATATAAAATAATATAT
1 ATATATATATATATAATTAATATAAAAAATATAAAATAATATAT
* *
255572 ATATATATATATATAATTAATATAAATAATATAAAATATTATAT
1 ATATATATATATATAATTAATATAAAAAATATAAAATAATATAT
255616 ATATATATA
1 ATATATATA
255625 ATCGGGGCGG
Statistics
Matches: 49, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
43 4 0.08
44 45 0.92
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.42
Consensus pattern (44 bp):
ATATATATATATATAATTAATATAAAAAATATAAAATAATATAT
Found at i:255596 original size:9 final size:9
Alignment explanation
Indices: 255538--255625 Score: 63
Period size: 9 Copynumber: 9.7 Consensus size: 9
255528 AATATTATAT
*
255538 ATATAATTA
1 ATATAAATA
* *
255547 ATCTAAAAA
1 ATATAAATA
255556 ATATAAAATA
1 ATAT-AAATA
*
255566 ATATATAT-
1 ATATAAATA
*
255574 ATATATAT-
1 ATATAAATA
*
255582 ATATAATTA
1 ATATAAATA
255591 ATATAAATA
1 ATATAAATA
255600 ATATAAAATA
1 ATAT-AAATA
* *
255610 TTATATATA
1 ATATAAATA
255619 TATATAA
1 -ATATAA
255626 TCGGGGCGGG
Statistics
Matches: 62, Mismatches: 13, Indels: 7
0.76 0.16 0.09
Matches are distributed among these distances:
8 14 0.23
9 28 0.45
10 20 0.32
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.40
Consensus pattern (9 bp):
ATATAAATA
Found at i:257051 original size:29 final size:29
Alignment explanation
Indices: 257018--257083 Score: 132
Period size: 29 Copynumber: 2.3 Consensus size: 29
257008 AAATCTCCAA
257018 GAAATGGATCACTAATGAGGAAATCCATC
1 GAAATGGATCACTAATGAGGAAATCCATC
257047 GAAATGGATCACTAATGAGGAAATCCATC
1 GAAATGGATCACTAATGAGGAAATCCATC
257076 GAAATGGA
1 GAAATGGA
257084 AATGTAAGTG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 37 1.00
ACGTcount: A:0.42, C:0.15, G:0.23, T:0.20
Consensus pattern (29 bp):
GAAATGGATCACTAATGAGGAAATCCATC
Found at i:259563 original size:26 final size:26
Alignment explanation
Indices: 259529--259607 Score: 140
Period size: 26 Copynumber: 3.0 Consensus size: 26
259519 TTTAAGAATA
259529 TATTATCCAAATCAAACAATGATAAT
1 TATTATCCAAATCAAACAATGATAAT
*
259555 TATTATCCAAATCAAACAAAGATAAT
1 TATTATCCAAATCAAACAATGATAAT
*
259581 TATTATCTAAATCAAACAATGATAAT
1 TATTATCCAAATCAAACAATGATAAT
259607 T
1 T
259608 TAAATTAATT
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 50 1.00
ACGTcount: A:0.51, C:0.14, G:0.04, T:0.32
Consensus pattern (26 bp):
TATTATCCAAATCAAACAATGATAAT
Found at i:261813 original size:14 final size:14
Alignment explanation
Indices: 261794--261822 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
261784 CAAATATATA
261794 ATAATTTATAGTTT
1 ATAATTTATAGTTT
261808 ATAATTTATAGTTT
1 ATAATTTATAGTTT
261822 A
1 A
261823 AATATTAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.38, C:0.00, G:0.07, T:0.55
Consensus pattern (14 bp):
ATAATTTATAGTTT
Found at i:262026 original size:21 final size:23
Alignment explanation
Indices: 262002--262045 Score: 65
Period size: 21 Copynumber: 2.0 Consensus size: 23
261992 AATAATCTAA
*
262002 ATTAATTTAA-TTTA-AGAATAT
1 ATTAATATAATTTTATAGAATAT
262023 ATTAATATAATTTTATAGAATAT
1 ATTAATATAATTTTATAGAATAT
262046 GATTGGAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 9 0.45
22 4 0.20
23 7 0.35
ACGTcount: A:0.48, C:0.00, G:0.05, T:0.48
Consensus pattern (23 bp):
ATTAATATAATTTTATAGAATAT
Found at i:262535 original size:4 final size:4
Alignment explanation
Indices: 262526--262551 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
262516 ATATATGCAG
262526 AATA AATA AATA AATA AATA AATA AA
1 AATA AATA AATA AATA AATA AATA AA
262552 GGGATAGAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AATA
Found at i:267421 original size:15 final size:17
Alignment explanation
Indices: 267397--267433 Score: 51
Period size: 15 Copynumber: 2.3 Consensus size: 17
267387 TAATATGATC
*
267397 CAAATGTAAAAA-AATT
1 CAAATATAAAAATAATT
267413 -AAATATAAAAATAATT
1 CAAATATAAAAATAATT
267429 CAAAT
1 CAAAT
267434 GCATCGCATA
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
15 10 0.56
16 4 0.22
17 4 0.22
ACGTcount: A:0.65, C:0.05, G:0.03, T:0.27
Consensus pattern (17 bp):
CAAATATAAAAATAATT
Found at i:271837 original size:6 final size:6
Alignment explanation
Indices: 271826--271850 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
271816 TTATAGTTTA
271826 AATATT AATATT AATATT AATATT A
1 AATATT AATATT AATATT AATATT A
271851 TGATTTTGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (6 bp):
AATATT
Found at i:274443 original size:9 final size:9
Alignment explanation
Indices: 274429--274467 Score: 51
Period size: 9 Copynumber: 4.1 Consensus size: 9
274419 TAAATTAATT
274429 TAATTTAAA
1 TAATTTAAA
*
274438 TTATTTAAA
1 TAATTTAAA
274447 TAATATTAGAA
1 TAAT-TTA-AA
274458 TAATTTAAA
1 TAATTTAAA
274467 T
1 T
274468 TATTATGTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
9 14 0.54
10 6 0.23
11 6 0.23
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (9 bp):
TAATTTAAA
Found at i:274492 original size:31 final size:30
Alignment explanation
Indices: 274448--274519 Score: 94
Period size: 31 Copynumber: 2.4 Consensus size: 30
274438 TTATTTAAAT
*
274448 AATATTAGA-ATAATTTAAAT-TATTATGTTA
1 AATATTA-ATATAATTTAAATCTATAAT-TTA
274478 ACATATTAATATAATTTAAATCTATAATTTA
1 A-ATATTAATATAATTTAAATCTATAATTTA
274509 AATATTAATAT
1 AATATTAATAT
274520 TATTATATAG
Statistics
Matches: 38, Mismatches: 1, Indels: 6
0.84 0.02 0.13
Matches are distributed among these distances:
30 12 0.32
31 21 0.55
32 5 0.13
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.46
Consensus pattern (30 bp):
AATATTAATATAATTTAAATCTATAATTTA
Found at i:274503 original size:13 final size:13
Alignment explanation
Indices: 274487--274511 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
274477 AACATATTAA
274487 TATAATTTAAATC
1 TATAATTTAAATC
274500 TATAATTTAAAT
1 TATAATTTAAAT
274512 ATTAATATTA
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:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (13 bp):
TATAATTTAAATC
Found at i:274817 original size:19 final size:20
Alignment explanation
Indices: 274789--274832 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
274779 AATTTAAGAA
*
274789 TAAATTATATAAAAAT-ATT
1 TAAATAATATAAAAATAATT
* *
274808 TAAATAATATTATAATAATT
1 TAAATAATATAAAAATAATT
274828 TAAAT
1 TAAAT
274833 CAATTTTAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 13 0.62
20 8 0.38
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (20 bp):
TAAATAATATAAAAATAATT
Found at i:275158 original size:21 final size:20
Alignment explanation
Indices: 275134--275187 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 20
275124 TTTATAAATT
275134 AATTAATTTAAATTAAGAATA
1 AATTAATTTAAATTAAG-ATA
* *
275155 AATTAATTTAATTTATGATA
1 AATTAATTTAAATTAAGATA
**
275175 TTTTAATTTAAAT
1 AATTAATTTAAAT
275188 AAATAATATT
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
20 13 0.46
21 15 0.54
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (20 bp):
AATTAATTTAAATTAAGATA
Found at i:279002 original size:16 final size:17
Alignment explanation
Indices: 278977--279014 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
278967 TAATCTGATC
*
278977 CAAATGTAAAAAAAATT
1 CAAATATAAAAAAAATT
*
278994 -AAATATAAAAATAATT
1 CAAATATAAAAAAAATT
279010 CAAAT
1 CAAAT
279015 GCATCGCATA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
16 14 0.78
17 4 0.22
ACGTcount: A:0.66, C:0.05, G:0.03, T:0.26
Consensus pattern (17 bp):
CAAATATAAAAAAAATT
Found at i:281167 original size:26 final size:26
Alignment explanation
Indices: 281137--281187 Score: 93
Period size: 26 Copynumber: 2.0 Consensus size: 26
281127 TTAAGAATAA
281137 ATTATCCAAATCAAACAATGATAATC
1 ATTATCCAAATCAAACAATGATAATC
*
281163 ATTATCCAAATGAAACAATGATAAT
1 ATTATCCAAATCAAACAATGATAAT
281188 TTAAATTAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.51, C:0.16, G:0.06, T:0.27
Consensus pattern (26 bp):
ATTATCCAAATCAAACAATGATAATC
Found at i:281246 original size:33 final size:32
Alignment explanation
Indices: 281183--281260 Score: 88
Period size: 33 Copynumber: 2.4 Consensus size: 32
281173 TGAAACAATG
*
281183 ATAATTTAAATTAATTTCATTTAAGAATATTAT
1 ATAATTTAAATTAATGTCATTTAAGAATATT-T
*
281216 ATAATTTAAATTAATGT-ATTCTTATG-ATATTT
1 ATAATTTAAATTAATGTCA-T-TTAAGAATATTT
281248 ATAATTTATAATT
1 ATAATTTA-AATT
281261 TAAATATTTA
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
32 10 0.25
33 26 0.65
34 4 0.10
ACGTcount: A:0.42, C:0.03, G:0.04, T:0.51
Consensus pattern (32 bp):
ATAATTTAAATTAATGTCATTTAAGAATATTT
Found at i:281829 original size:37 final size:36
Alignment explanation
Indices: 281743--281830 Score: 94
Period size: 36 Copynumber: 2.5 Consensus size: 36
281733 TAGAGTGTGT
*
281743 TTTAATTAATATTA-T-AATAATTTAAATTTATTTAA
1 TTTAAATAATATTATTAAATAATTTAAATTTA-TTAA
* *
281778 TTTTAAGAAT-TTATTAATATAATTTTAAATTTA-TAA
1 TTTAAATAATATTATTAA-ATAA-TTTAAATTTATTAA
281814 TTTAAATAATATTATTA
1 TTTAAATAATATTATTA
281831 TATGGGGCAA
Statistics
Matches: 43, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
34 3 0.07
35 8 0.19
36 12 0.28
37 10 0.23
38 10 0.23
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.53
Consensus pattern (36 bp):
TTTAAATAATATTATTAAATAATTTAAATTTATTAA
Found at i:282111 original size:19 final size:19
Alignment explanation
Indices: 282083--282123 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
282073 AATTTATGAA
*
282083 TAAATTATATA-AAAATATT
1 TAAATGATATAGAAAA-ATT
282102 TAAATGATATAGAAAAATT
1 TAAATGATATAGAAAAATT
282121 TAA
1 TAA
282124 TTTAAGAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 16 0.80
20 4 0.20
ACGTcount: A:0.59, C:0.00, G:0.05, T:0.37
Consensus pattern (19 bp):
TAAATGATATAGAAAAATT
Found at i:301126 original size:16 final size:16
Alignment explanation
Indices: 301101--301143 Score: 68
Period size: 16 Copynumber: 2.7 Consensus size: 16
301091 AATCGAATGA
*
301101 TGCCATGTGTCACTGG
1 TGCCACGTGTCACTGG
301117 TGCCACGTGTCACTGG
1 TGCCACGTGTCACTGG
*
301133 TGCCACATGTC
1 TGCCACGTGTC
301144 GTGCACGAGT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.14, C:0.30, G:0.28, T:0.28
Consensus pattern (16 bp):
TGCCACGTGTCACTGG
Found at i:305726 original size:21 final size:21
Alignment explanation
Indices: 305696--305742 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
305686 ATAGCTGGGT
* *
305696 AACTTTTAAGAACTTAAGGTG
1 AACTTGTAAGAACTAAAGGTG
305717 AACTTGTAAGAACTAAAGGTG
1 AACTTGTAAGAACTAAAGGTG
305738 AACTT
1 AACTT
305743 TTATCATTTG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.40, C:0.11, G:0.19, T:0.30
Consensus pattern (21 bp):
AACTTGTAAGAACTAAAGGTG
Found at i:308509 original size:31 final size:31
Alignment explanation
Indices: 308469--308528 Score: 86
Period size: 31 Copynumber: 1.9 Consensus size: 31
308459 ATACAATCCC
308469 TCAACATTTAG-TCTGTTTGCAATATGGTCTT
1 TCAACATTTAGTTC-GTTTGCAATATGGTCTT
* *
308500 TCAATATTTAGTTCGTTTGTAATATGGTC
1 TCAACATTTAGTTCGTTTGCAATATGGTC
308529 CCCGAAGTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
31 24 0.92
32 2 0.08
ACGTcount: A:0.23, C:0.13, G:0.17, T:0.47
Consensus pattern (31 bp):
TCAACATTTAGTTCGTTTGCAATATGGTCTT
Found at i:308862 original size:29 final size:29
Alignment explanation
Indices: 308829--308886 Score: 100
Period size: 29 Copynumber: 2.0 Consensus size: 29
308819 CCGTCCCTAG
308829 TAAACTCTCCATGAGCTCT-TCGCTTCTTT
1 TAAACTCTCCATGAGCTCTGT-GCTTCTTT
308858 TAAACTCTCCATGAGCTCTGTGCTTCTTT
1 TAAACTCTCCATGAGCTCTGTGCTTCTTT
308887 GAAGAAGTAG
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
29 27 0.96
30 1 0.04
ACGTcount: A:0.17, C:0.29, G:0.12, T:0.41
Consensus pattern (29 bp):
TAAACTCTCCATGAGCTCTGTGCTTCTTT
Found at i:310313 original size:20 final size:22
Alignment explanation
Indices: 310285--310344 Score: 72
Period size: 23 Copynumber: 2.8 Consensus size: 22
310275 ACAATAAACC
310285 ATACC-ATTACATTATA-AA-G
1 ATACCTATTACATTATATAACG
310304 ATACCTATTACATTATATAAGCG
1 ATACCTATTACATTATATAA-CG
* *
310327 CTACCTATTACATCATAT
1 ATACCTATTACATTATAT
310345 GTTACCTATT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.14
20 11 0.31
21 2 0.06
23 17 0.49
ACGTcount: A:0.40, C:0.20, G:0.05, T:0.35
Consensus pattern (22 bp):
ATACCTATTACATTATATAACG
Found at i:310783 original size:38 final size:39
Alignment explanation
Indices: 310735--310817 Score: 141
Period size: 38 Copynumber: 2.2 Consensus size: 39
310725 AAGTTGTAGA
*
310735 TTTGATTTCCTTTTGCTTGGCATCATAT-AGATTTGGAT
1 TTTGATTTCCTTTTGCTTGGCACCATATGAGATTTGGAT
*
310773 TTTGATTTCCTTTTGCTTGGCACCATATGAGCTTTGGAT
1 TTTGATTTCCTTTTGCTTGGCACCATATGAGATTTGGAT
310812 TTTGAT
1 TTTGAT
310818 GAGCACCGGA
Statistics
Matches: 42, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
38 27 0.64
39 15 0.36
ACGTcount: A:0.17, C:0.14, G:0.19, T:0.49
Consensus pattern (39 bp):
TTTGATTTCCTTTTGCTTGGCACCATATGAGATTTGGAT
Found at i:311168 original size:20 final size:20
Alignment explanation
Indices: 311122--311175 Score: 56
Period size: 20 Copynumber: 2.6 Consensus size: 20
311112 GATTCTTGAC
311122 AATCGCAATGCGATAGTACA
1 AATCGCAATGCGATAGTACA
* *
311142 AATTCGCATTGCGAT-TTACA
1 AA-TCGCAATGCGATAGTACA
*
311162 GAATCGCAACGCGA
1 -AATCGCAATGCGA
311176 ATATGAAAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
20 15 0.54
21 13 0.46
ACGTcount: A:0.35, C:0.22, G:0.20, T:0.22
Consensus pattern (20 bp):
AATCGCAATGCGATAGTACA
Found at i:311277 original size:20 final size:20
Alignment explanation
Indices: 311163--311411 Score: 245
Period size: 20 Copynumber: 12.4 Consensus size: 20
311153 CGATTTACAG
* ** *
311163 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
311183 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
* *
311203 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
311223 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
311243 AATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
311263 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
311283 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
311303 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* *
311323 AATCGCAACG-ATAATCAGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
311343 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
311363 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
311383 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
311403 AATCACAAC
1 AATCGCAAC
311412 ACTGAAATTT
Statistics
Matches: 198, Mismatches: 25, Indels: 12
0.84 0.11 0.05
Matches are distributed among these distances:
19 2 0.01
20 194 0.98
21 2 0.01
ACGTcount: A:0.38, C:0.26, G:0.18, T:0.19
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:311546 original size:20 final size:22
Alignment explanation
Indices: 311505--311547 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
311495 CTCTCTCCGG
*
311505 CGACATCCGTTCCTATATCCAA
1 CGACATCCGTTCCCATATCCAA
311527 CGACATCC-TTCCCA-ATCCAA
1 CGACATCCGTTCCCATATCCAA
311547 C
1 C
311548 AGGTTTTAGT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 7 0.35
21 5 0.25
22 8 0.40
ACGTcount: A:0.28, C:0.42, G:0.07, T:0.23
Consensus pattern (22 bp):
CGACATCCGTTCCCATATCCAA
Found at i:312110 original size:24 final size:24
Alignment explanation
Indices: 312083--312129 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
312073 GAAATTGGTC
312083 TTGGTCAATATC-CGGACTTTGATA
1 TTGGTCAATA-CACGGACTTTGATA
*
312107 TTGGTCAATACACGGATTTTGAT
1 TTGGTCAATACACGGACTTTGAT
312130 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATACACGGACTTTGATA
Found at i:313587 original size:152 final size:154
Alignment explanation
Indices: 313346--313651 Score: 589
Period size: 152 Copynumber: 2.0 Consensus size: 154
313336 TTTCCCAGAT
313346 GCTTTTCATGGACTTTGTGGTGTTCATTTGGATAGAAATCTAAAATCAAGGTCTGCTGGTATAAA
1 GCTTTTCATGGACTTTGTGGTGTTCATTTGGATAGAAATCTAAAATCAAGGTCTGCTGGTATAAA
313411 AAAGCACAAATGGACATACTGGAAGGCTGTAAAAGCTTATCGGGAAG-GGATTTCAATAAGCATA
66 AAAGCACAAATGGACATACTGGAAGGCTGTAAAAGCTTATCGGGAAGTGGATTTCAATAAGCATA
313475 AAATTGTTTAAGACGTGTTTTGCC
131 AAATTGTTTAAGACGTGTTTTGCC
*
313499 GCTTTTCATGGACTTTGTGGTGTTCA-TTGTATAGAAATCTAAAATCAAGGTCTGCTGGTATAAA
1 GCTTTTCATGGACTTTGTGGTGTTCATTTGGATAGAAATCTAAAATCAAGGTCTGCTGGTATAAA
313563 AAAGCACAAATGGACATACTGGAAGGCTGTAAAAGCTTATCGGGAAGTGGATTTCAATAAGCATA
66 AAAGCACAAATGGACATACTGGAAGGCTGTAAAAGCTTATCGGGAAGTGGATTTCAATAAGCATA
313628 AAATTGTTTAAGACGTGTTTTGCC
131 AAATTGTTTAAGACGTGTTTTGCC
313652 TCAGTGTGCT
Statistics
Matches: 151, Mismatches: 1, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
152 84 0.56
153 67 0.44
ACGTcount: A:0.33, C:0.13, G:0.23, T:0.31
Consensus pattern (154 bp):
GCTTTTCATGGACTTTGTGGTGTTCATTTGGATAGAAATCTAAAATCAAGGTCTGCTGGTATAAA
AAAGCACAAATGGACATACTGGAAGGCTGTAAAAGCTTATCGGGAAGTGGATTTCAATAAGCATA
AAATTGTTTAAGACGTGTTTTGCC
Found at i:314783 original size:19 final size:19
Alignment explanation
Indices: 314747--314902 Score: 190
Period size: 19 Copynumber: 8.7 Consensus size: 19
314737 GCAACGAGAG
314747 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
314767 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
314786 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
314800 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
314819 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
314838 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
314852 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
314872 AATCGC-ATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
314890 AATCGCATTGCGA
1 AATCGCAATGCGA
314903 TTCTCTCGTT
Statistics
Matches: 119, Mismatches: 5, Indels: 25
0.80 0.03 0.17
Matches are distributed among these distances:
14 20 0.17
15 2 0.02
16 3 0.03
17 5 0.04
18 15 0.13
19 55 0.46
20 19 0.16
ACGTcount: A:0.44, C:0.17, G:0.24, T:0.15
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:314837 original size:52 final size:53
Alignment explanation
Indices: 314726--314896 Score: 328
Period size: 52 Copynumber: 3.3 Consensus size: 53
314716 TTACAATCGC
314726 AAATGAAAATCGCAACGAGAGAATCGCAATGCGGAAATGAAAATCGCAATGCG
1 AAATGAAAATCGCAACGAGAGAATCGCAATGCGGAAATGAAAATCGCAATGCG
314779 AAATGAAAATCGCAACGAGAGAATCGCAATGC-GAAATGAAAATCGCAATGCG
1 AAATGAAAATCGCAACGAGAGAATCGCAATGCGGAAATGAAAATCGCAATGCG
314831 AAATGAAAATCGCAACGAGAGAATCGCAATGCGGAAATGAAAATCGC-ATGCG
1 AAATGAAAATCGCAACGAGAGAATCGCAATGCGGAAATGAAAATCGCAATGCG
314883 AAATGAAAATCGCA
1 AAATGAAAATCGCA
314897 TTGCGATTCT
Statistics
Matches: 117, Mismatches: 0, Indels: 3
0.98 0.00 0.03
Matches are distributed among these distances:
52 71 0.61
53 46 0.39
ACGTcount: A:0.46, C:0.17, G:0.23, T:0.13
Consensus pattern (53 bp):
AAATGAAAATCGCAACGAGAGAATCGCAATGCGGAAATGAAAATCGCAATGCG
Found at i:314935 original size:19 final size:18
Alignment explanation
Indices: 314892--314996 Score: 109
Period size: 19 Copynumber: 6.1 Consensus size: 18
314882 GAAATGAAAA
*
314892 TCGCATTGCGA-TTC-TC
1 TCGCATTGCGATTTCATT
314908 TCG--TTGCGATTTCATT
1 TCGCATTGCGATTTCATT
314924 TCCGCATTGCGATTTTCATT
1 T-CGCATTGCGA-TTTCATT
*
314944 TCGCATTGCGA-TTC-TC
1 TCGCATTGCGATTTCATT
314960 TCG--TTGCGATTTCATT
1 TCGCATTGCGATTTCATT
314976 TCGCATTGCGATTTTCATT
1 TCGCATTGCGA-TTTCATT
314995 TC
1 TC
314997 AACATAATGC
Statistics
Matches: 75, Mismatches: 3, Indels: 19
0.77 0.03 0.20
Matches are distributed among these distances:
14 12 0.16
15 6 0.08
16 13 0.17
17 5 0.07
18 6 0.08
19 25 0.33
20 8 0.11
ACGTcount: A:0.13, C:0.25, G:0.17, T:0.45
Consensus pattern (18 bp):
TCGCATTGCGATTTCATT
Found at i:314935 original size:52 final size:51
Alignment explanation
Indices: 314874--314986 Score: 156
Period size: 52 Copynumber: 2.2 Consensus size: 51
314864 GAAATGAAAA
314874 TCGCA-TGCGAAATGAAAATCGCATTGCGATTCTCTCGTTGCGATTTCATT
1 TCGCATTGCGAAATGAAAATCGCATTGCGATTCTCTCGTTGCGATTTCATT
** ** **
314924 TCCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTCATT
1 T-CGCATTGCGAAATGAAAATCGCATTGCGATTCTCTCGTTGCGATTTCATT
314976 TCGCATTGCGA
1 TCGCATTGCGA
314987 TTTTCATTTC
Statistics
Matches: 55, Mismatches: 6, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
50 1 0.02
51 14 0.25
52 40 0.73
ACGTcount: A:0.19, C:0.24, G:0.19, T:0.38
Consensus pattern (51 bp):
TCGCATTGCGAAATGAAAATCGCATTGCGATTCTCTCGTTGCGATTTCATT
Found at i:315065 original size:14 final size:14
Alignment explanation
Indices: 315046--315101 Score: 67
Period size: 14 Copynumber: 3.7 Consensus size: 14
315036 TTTCATTTCG
315046 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
315060 CGTTGCGATTTCATTT
1 CGTTGCGA-TTC-TCT
315076 CGCATTGCGATTCTCT
1 CG--TTGCGATTCTCT
315092 CGTTGCGATT
1 CGTTGCGATT
315102 TCATTTCTCT
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
14 16 0.44
15 3 0.08
16 8 0.22
17 3 0.08
18 6 0.17
ACGTcount: A:0.11, C:0.25, G:0.21, T:0.43
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:315076 original size:32 final size:32
Alignment explanation
Indices: 315035--315108 Score: 139
Period size: 32 Copynumber: 2.3 Consensus size: 32
315025 CAACCATTAC
*
315035 ATTTCATTTCGCGTTGCGATTCTCTCGTTGCG
1 ATTTCATTTCGCATTGCGATTCTCTCGTTGCG
315067 ATTTCATTTCGCATTGCGATTCTCTCGTTGCG
1 ATTTCATTTCGCATTGCGATTCTCTCGTTGCG
315099 ATTTCATTTC
1 ATTTCATTTC
315109 TCTCGTTGCG
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
32 41 1.00
ACGTcount: A:0.12, C:0.24, G:0.18, T:0.46
Consensus pattern (32 bp):
ATTTCATTTCGCATTGCGATTCTCTCGTTGCG
Found at i:315111 original size:20 final size:19
Alignment explanation
Indices: 315086--315158 Score: 94
Period size: 20 Copynumber: 3.7 Consensus size: 19
315076 CGCATTGCGA
315086 TTCTCTCGTTGCGATTTCAT
1 TTCTCTCGTTGCGA-TTCAT
*
315106 TTCTCTCGTTGCGACAGTCA-
1 TTCTCTCGTTGCG--ATTCAT
315126 TTCTCTCGTTGCGATTCAT
1 TTCTCTCGTTGCGATTCAT
*
315145 TTATCTCGTTGCGA
1 TTCTCTCGTTGCGA
315159 CTCTTCTGCA
Statistics
Matches: 47, Mismatches: 3, Indels: 7
0.82 0.05 0.12
Matches are distributed among these distances:
18 4 0.09
19 13 0.28
20 26 0.55
21 3 0.06
22 1 0.02
ACGTcount: A:0.12, C:0.26, G:0.18, T:0.44
Consensus pattern (19 bp):
TTCTCTCGTTGCGATTCAT
Found at i:315279 original size:33 final size:33
Alignment explanation
Indices: 315237--315307 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
315227 AATACTAACT
315237 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
* *
315270 TGAAAATCGCAACGAGAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
315303 TGAAA
1 TGAAA
315308 TCTAAGTGAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.48, C:0.17, G:0.24, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
Found at i:315701 original size:20 final size:20
Alignment explanation
Indices: 315676--315867 Score: 244
Period size: 20 Copynumber: 9.6 Consensus size: 20
315666 CTTTAAAAAT
315676 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
315696 CGCGTTGCGATTTACTGATTA
1 CGCGTTGCGATTTACGGA-TA
*
315717 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
315736 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
*
315756 CGCATTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
315776 CGCATTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
315796 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
315816 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
315836 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
315856 CGCGTTGCGATT
1 CGCGTTGCGATT
315868 CTTGAAAATC
Statistics
Matches: 152, Mismatches: 16, Indels: 8
0.86 0.09 0.05
Matches are distributed among these distances:
19 2 0.01
20 147 0.97
21 3 0.02
ACGTcount: A:0.20, C:0.19, G:0.27, T:0.34
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:316662 original size:23 final size:24
Alignment explanation
Indices: 316617--316663 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
316607 ATTATTTTTC
*
316617 CAATAATGTACCCATAACAATGTT
1 CAATAATGTACCCACAACAATGTT
316641 CAATAATGTACCC-CAACAATGTT
1 CAATAATGTACCCACAACAATGTT
316664 TAATTGATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 9 0.41
24 13 0.59
ACGTcount: A:0.40, C:0.23, G:0.09, T:0.28
Consensus pattern (24 bp):
CAATAATGTACCCACAACAATGTT
Found at i:318046 original size:184 final size:179
Alignment explanation
Indices: 317558--318227 Score: 1124
Period size: 179 Copynumber: 3.7 Consensus size: 179
317548 TTAAAATTAC
* *
317558 CGACACTTTTTTAAATGGTATCGACACATTTTTCTTCCAATCTGGACATAAAGTACCGACACAAT
1 CGACACTTTTTTAAATCGTATCG--ACATTTTTCTTCCAATATGGACATAAAGTACCGACACAAT
*
317623 ATTATAAAGTGTCGATATAGG-TGTAGA-CTATTCGCGCATAAACCGGTATATTTATA-CGGTTA
64 ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAACCGGTATATTTATACCGGTTA
* * *
317685 TATTACAAATTATCTATTACATTATAAATCTGGGTTCCGATGTGTAAATGT
129 TATTAAAAATTATCTATTACATTATAATTATGGGTTCCGATGTGTAAATGT
*
317736 CGATACTTTTTTAAATCGTATCGACA-TTTTCTTCCAATATGGACATAAAGTACCG--ACAATAT
1 CGACACTTTTTTAAATCGTATCGACATTTTTCTTCCAATATGGACATAAAGTACCGACACAATAT
317798 TAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCAGCATAAAACCGGTATATTTATACCGGTTA
66 TAAAAAGTGTCGATATAGGTTGTAGACCTATTCGC-GCAT-AAACCGGTATATTTATACCGGTTA
317863 TATTATAAAATTATCTATTACATTATAATTATGGGTTCCGATGTGTAAATGT
129 TATTA-AAAATTATCTATTACATTATAATTATGGGTTCCGATGTGTAAATGT
317915 CGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACCGACACAAT
1 CGACACTTTTTTAAATCGTATCG--ACATTTTTCTTCCAATATGGACATAAAGTACCGACACAAT
317980 ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAAACCGGTATATTTATACCGGT
64 ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCAT--AAACCGGTATATTTATACCGGT
318045 TATATTACAAAATTATCTATTACATTATAATTAT-GGTTCCGATGTGT-AATGT
127 TATATTA-AAAATTATCTATTACATTATAATTATGGGTTCCGATGTGTAAATGT
318097 CGACACTTTTTTAAATCGTATCGACATTTTTCTTCCAATATGGACATAAAGTACCGACACAATAT
1 CGACACTTTTTTAAATCGTATCGACATTTTTCTTCCAATATGGACATAAAGTACCGACACAATAT
318162 T-AAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAACCGGTATATTTATACCGGTTATA
66 TAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAACCGGTATATTTATACCGGTTATA
318226 TT
131 TT
318228 GCAAATTTAC
Statistics
Matches: 471, Mismatches: 9, Indels: 25
0.93 0.02 0.05
Matches are distributed among these distances:
173 25 0.05
174 6 0.01
175 36 0.08
176 7 0.01
177 45 0.10
178 32 0.07
179 102 0.22
180 43 0.09
181 3 0.01
182 57 0.12
183 17 0.04
184 98 0.21
ACGTcount: A:0.33, C:0.16, G:0.15, T:0.35
Consensus pattern (179 bp):
CGACACTTTTTTAAATCGTATCGACATTTTTCTTCCAATATGGACATAAAGTACCGACACAATAT
TAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAACCGGTATATTTATACCGGTTATA
TTAAAAATTATCTATTACATTATAATTATGGGTTCCGATGTGTAAATGT
Found at i:319420 original size:14 final size:14
Alignment explanation
Indices: 319401--319427 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
319391 GACCAAAGGG
319401 CAACACAAAATTGT
1 CAACACAAAATTGT
319415 CAACACAAAATTG
1 CAACACAAAATTG
319428 CATAAATTCA
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:0.52, C:0.22, G:0.07, T:0.19
Consensus pattern (14 bp):
CAACACAAAATTGT
Found at i:319649 original size:3 final size:3
Alignment explanation
Indices: 319634--319684 Score: 66
Period size: 3 Copynumber: 17.0 Consensus size: 3
319624 ACTTGTTTGG
* * * *
319634 ATC ATC TTC ATC ATC ATC ATC ATC ATC GTC ATC ATC ATC GTC ATC TTC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
319682 ATC
1 ATC
319685 GTCAGCTTCA
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.25, C:0.33, G:0.04, T:0.37
Consensus pattern (3 bp):
ATC
Found at i:319651 original size:12 final size:12
Alignment explanation
Indices: 319641--319688 Score: 78
Period size: 12 Copynumber: 4.0 Consensus size: 12
319631 TGGATCATCT
*
319641 TCATCATCATCA
1 TCATCATCGTCA
319653 TCATCATCGTCA
1 TCATCATCGTCA
319665 TCATCATCGTCA
1 TCATCATCGTCA
*
319677 TCTTCATCGTCA
1 TCATCATCGTCA
319689 GCTTCATCTT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 34 1.00
ACGTcount: A:0.25, C:0.33, G:0.06, T:0.35
Consensus pattern (12 bp):
TCATCATCGTCA
Found at i:319657 original size:18 final size:18
Alignment explanation
Indices: 319634--319699 Score: 69
Period size: 18 Copynumber: 3.7 Consensus size: 18
319624 ACTTGTTTGG
* *
319634 ATCATCTTCATCATCATC
1 ATCATCATCTTCATCATC
*
319652 ATCATCATCGTCATCATC
1 ATCATCATCTTCATCATC
* *
319670 ATCGTCATCTTCATCGTC
1 ATCATCATCTTCATCATC
* *
319688 AGCTTCATCTTC
1 ATCATCATCTTC
319700 TGCGACCGCT
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 41 1.00
ACGTcount: A:0.23, C:0.33, G:0.06, T:0.38
Consensus pattern (18 bp):
ATCATCATCTTCATCATC
Found at i:319693 original size:12 final size:12
Alignment explanation
Indices: 319644--319696 Score: 70
Period size: 12 Copynumber: 4.4 Consensus size: 12
319634 ATCATCTTCA
* *
319644 TCATCATCATCA
1 TCATCGTCATCT
*
319656 TCATCGTCATCA
1 TCATCGTCATCT
319668 TCATCGTCATCT
1 TCATCGTCATCT
*
319680 TCATCGTCAGCT
1 TCATCGTCATCT
319692 TCATC
1 TCATC
319697 TTCTGCGACC
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
12 38 1.00
ACGTcount: A:0.23, C:0.34, G:0.08, T:0.36
Consensus pattern (12 bp):
TCATCGTCATCT
Found at i:321820 original size:198 final size:198
Alignment explanation
Indices: 321121--322633 Score: 2747
Period size: 198 Copynumber: 7.7 Consensus size: 198
321111 TTTAAATTAG
321121 TATCGACACAAA-TATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACC-GTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
*
321184 ATTGTACCGGTTAGATTGAAAAATTACATA-TACATTATACTTTTGGGTTCCATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
321248 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGG-AAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
321312 AAA
196 AAA
*
321315 TATCGACACAAACTATATTAGTGTCGACACATTATTTATACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
*
321380 ATTGTACC-GTTAGATTG-AAAATTACATATTACATTATACTTTTGGGTTCCATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
*
321443 CGACACTTTTTATATATGGAT--AGACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGG-AAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
321505 AAA
196 AAA
*
321508 TATCGACACAAACTATATTAGTGTCGACACATTATTTATACATATTCTCTCAT-AAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
321572 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
*
321637 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCATGTTTTCCATTCATTCTGGAAAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
321702 AAA
196 AAA
*
321705 TATCGACACAAACTATATTAGTGTCGACACATTATTTATACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
321770 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGA-GATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
321834 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGG-AAA
321899 AAAA
195 AAAA
321903 TATCGACACAAACTATA-TAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
*
321967 ATTGTACCGG-TATATTGAAAAATTACATATTACATTATACTTTTGGG-TCGATGA-TTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
322029 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
322094 AAA
196 AAA
*
322097 TATCGACAC-AACTATA-TAGTGTCGACACATTA-TTATACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
*
322159 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCCATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
322224 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
322289 AAA
196 AAA
***
322292 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAATAAGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
322357 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
322422 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
*
322487 CAA
196 AAA
322490 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
* *
322555 ATTGTACCGATTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTCGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
322620 CGACACTTTTTATA
131 CGACACTTTTTATA
322634 CTGCTAACTT
Statistics
Matches: 1280, Mismatches: 22, Indels: 30
0.96 0.02 0.02
Matches are distributed among these distances:
192 58 0.05
193 164 0.13
194 111 0.09
195 267 0.21
196 94 0.07
197 202 0.16
198 384 0.30
ACGTcount: A:0.32, C:0.17, G:0.15, T:0.37
Consensus pattern (198 bp):
TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
AAA
Found at i:322290 original size:587 final size:587
Alignment explanation
Indices: 321121--322633 Score: 2758
Period size: 587 Copynumber: 2.6 Consensus size: 587
321111 TTTAAATTAG
321121 TATCGACACAAA-TATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGTATAA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGTATAA
*
321185 TTGTACCGGTTAGATTGAAAAATTACATA-TACATTATACTTTTGGGTTCCATGATTTTGGGATC
66 TTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATC
321249 GACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGG-AAAA
131 GACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAAA
*
321313 AATATCGACACAAACTATATTAGTGTCGACACATTATTTATACATATTCTCTCATAAAACCGGTA
196 AATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTA
*
321378 TAATTGTACCGTTAGATTG-AAAATTACATATTACATTATACTTTTGGGTTCCATGATTTTGGGA
261 TAATTGTACCGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGA-TTTGGGA
*
321442 TCGACACTTTTTATATATGGATAGACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAAA
325 TCGACACTTTTTATATATGGATACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAAA
321507 ATATCGACACAAACTATATTAGTGTCGACACATTATTTATACATATTCTCTCATAAACCGGTATA
390 ATATCGACACAAACTATATTAGTGTCGACACATTATTTATACATATTCTCTCATAAACCGGTATA
*
321572 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
455 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCCATGATTTTGGGAT
321637 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCATGTTTTCCATTCATTCTGGAAAA
520 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCATGTTTTCCATTCATTCTGGAAAA
321702 AAA
585 AAA
*
321705 TATCGACACAAACTATATTAGTGTCGACACATTATTTATACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACC-GTATA
321770 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGA-GATTTTGGGAT
65 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
321834 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
130 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGG-AAA
321899 AAAATATCGACACAAACTATA-TAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGG
194 AAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGG
* *
321963 TATAATTGTACCGGTATATTGAAAAATTACATATTACATTATACTTTTGGG-TCGATGATTTGGG
259 TATAATTGTACCGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTGGG
322027 ATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAA
324 ATCGACACTTTTTATATATGGAT--ACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGG-A
322092 AAAAATATCGACAC-AACTATA-TAGTGTCGACACATTA-TTATACATATTCTCTCATAAAACCG
386 AAAAATATCGACACAAACTATATTAGTGTCGACACATTATTTATACATATTCTCTCAT-AAACCG
322154 GTATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCCATGATTTT
450 GTATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCCATGATTTT
*
322219 GGGATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTG
515 GGGATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCATGTTTTCCATTCATTCTG
322284 GAAAAAAA
580 GAAAAAAA
**
322292 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAATAAGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAA-CCGTATA
322357 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
65 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
322422 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
130 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
*
322487 CAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGT
195 AAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGT
322552 ATAATTGTACCGATTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTCGG
260 ATAATTGTACCG-TTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTT-GG
322617 GATCGACACTTTTTATA
323 GATCGACACTTTTTATA
322634 CTGCTAACTT
Statistics
Matches: 898, Mismatches: 15, Indels: 25
0.96 0.02 0.03
Matches are distributed among these distances:
584 12 0.01
585 45 0.05
586 154 0.17
587 383 0.43
588 224 0.25
589 51 0.06
590 10 0.01
591 19 0.02
ACGTcount: A:0.32, C:0.17, G:0.15, T:0.37
Consensus pattern (587 bp):
TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGTATAA
TTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATC
GACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAAA
AATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTA
TAATTGTACCGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTGGGAT
CGACACTTTTTATATATGGATACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAAAA
TATCGACACAAACTATATTAGTGTCGACACATTATTTATACATATTCTCTCATAAACCGGTATAA
TTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCCATGATTTTGGGATC
GACACTTTTTATATATGGATCGACACTTTATGGGTGCACCATGTTTTCCATTCATTCTGGAAAAA
AA
Found at i:322718 original size:19 final size:19
Alignment explanation
Indices: 322672--322720 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
322662 TTATATTCAC
*
322672 ATACAAAAATATAAATCGT
1 ATACAAAATTATAAATCGT
*
322691 ATACAAAATTATAAATCTT
1 ATACAAAATTATAAATCGT
322710 ATACAAAATTA
1 ATACAAAATTA
322721 ACCCTACATT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.57, C:0.10, G:0.02, T:0.31
Consensus pattern (19 bp):
ATACAAAATTATAAATCGT
Found at i:324547 original size:33 final size:33
Alignment explanation
Indices: 324510--324575 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
324500 CATCTTAATA
* *
324510 TCACCCCTTAACACCCCAACTTCTTTCACCACT
1 TCACCCCTCAACACCCCAACTTCATTCACCACT
* *
324543 TCACCCCTCAACACCTCTACTTCATTCACCACT
1 TCACCCCTCAACACCCCAACTTCATTCACCACT
324576 CCATCTATTT
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:0.24, C:0.48, G:0.00, T:0.27
Consensus pattern (33 bp):
TCACCCCTCAACACCCCAACTTCATTCACCACT
Found at i:326943 original size:20 final size:19
Alignment explanation
Indices: 326889--326934 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 19
326879 TCCGGTATCA
326889 TTTACCGGTTTTATCATTT
1 TTTACCGGTTTTATCATTT
*
326908 TGATACCGGTTTTATCATATT
1 T-TTACCGGTTTTATCAT-TT
326929 TTTACC
1 TTTACC
326935 TGTTATATCG
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
19 1 0.04
20 19 0.83
21 3 0.13
ACGTcount: A:0.20, C:0.17, G:0.11, T:0.52
Consensus pattern (19 bp):
TTTACCGGTTTTATCATTT
Found at i:327588 original size:228 final size:227
Alignment explanation
Indices: 327163--327610 Score: 781
Period size: 229 Copynumber: 2.0 Consensus size: 227
327153 TTAAAACTGC
327163 TTTTAAAGTTATGTAATTTATGTTTCAATTTATTTAATAGTGTTTCATGTTTTCCACTACAATAT
1 TTTTAAAGTTATGTAATTTATGTTTCAATTTATTTAATAGTGTTTCATGTTTTCCACTACAATAT
**
327228 TAATTTAATAATTTAATTTACACAAAATTTTATTTGATTGTTTTGATATTTTATAAAATATTATT
66 TAATTTAATAATTTAATTTACACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATATTATT
* *
327293 TAGAATTTAAATTTAACAATATTAACCAAATATAATAATAAATATGTTTTCAACAGTGAAATAAG
131 TAGAATTTAAATTTAACAATATTAACCAAAGATAATAATAAATATATTTTCAACAGTGAAATAAG
*
327358 TATGAACACTTTTATAAAAATGATATATACTT
196 TATGAACACTTTTATAAAAAGGATATATACTT
*
327390 TTTTGAAAGTTATGTAATTTATGTTTCAATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAAT
1 TTTT-AAAGTTATGTAATTTATGTTTCAATTTATTTAATAGTGTTTCATGTTTTCCA-CTACAAT
*
327455 ATTAATTTAATAATTTCATTTACACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATATTA
64 ATTAATTTAATAATTTAATTTACACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATATTA
* *
327520 TTTAGATTTTAAATTTAACAATATTAACTAAAGATAATAATAAATATATTTTC-ACAGTGAAATA
129 TTTAGAATTTAAATTTAACAATATTAACCAAAGATAATAATAAATATATTTTCAACAGTGAAATA
*
327584 AGTATGGACACTTTTATAAAAAGGATA
194 AGTATGAACACTTTTATAAAAAGGATA
327611 GATAATTTAC
Statistics
Matches: 209, Mismatches: 10, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
227 4 0.02
228 87 0.42
229 118 0.56
ACGTcount: A:0.40, C:0.07, G:0.08, T:0.45
Consensus pattern (227 bp):
TTTTAAAGTTATGTAATTTATGTTTCAATTTATTTAATAGTGTTTCATGTTTTCCACTACAATAT
TAATTTAATAATTTAATTTACACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATATTATT
TAGAATTTAAATTTAACAATATTAACCAAAGATAATAATAAATATATTTTCAACAGTGAAATAAG
TATGAACACTTTTATAAAAAGGATATATACTT
Found at i:330145 original size:31 final size:31
Alignment explanation
Indices: 330070--330147 Score: 138
Period size: 31 Copynumber: 2.5 Consensus size: 31
330060 TAGTTACTTC
*
330070 GGGGACCATATTGAAAACGGACTAAATGTTG
1 GGGGACCATATTGCAAACGGACTAAATGTTG
330101 GGGGACCATATTGCAAACGGACTAAATGTTG
1 GGGGACCATATTGCAAACGGACTAAATGTTG
*
330132 GGGGACTATATTGCAA
1 GGGGACCATATTGCAA
330148 GTTTTAAAAG
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 45 1.00
ACGTcount: A:0.33, C:0.14, G:0.29, T:0.23
Consensus pattern (31 bp):
GGGGACCATATTGCAAACGGACTAAATGTTG
Found at i:332775 original size:27 final size:27
Alignment explanation
Indices: 332745--332798 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
332735 AGATGTCATG
332745 AAAAAAATTAATATTGTAGATTACACT
1 AAAAAAATTAATATTGTAGATTACACT
332772 AAAAAAATTAATATTGTAGATTACACT
1 AAAAAAATTAATATTGTAGATTACACT
332799 CAACAGAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.52, C:0.07, G:0.07, T:0.33
Consensus pattern (27 bp):
AAAAAAATTAATATTGTAGATTACACT
Found at i:333086 original size:20 final size:20
Alignment explanation
Indices: 333034--333071 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
333024 TCAATAGATC
333034 AGATAATAATATGTTAAACA
1 AGATAATAATATGTTAAACA
333054 AGATAATAATATGTTAAA
1 AGATAATAATATGTTAAA
333072 TATAGTTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.55, C:0.03, G:0.11, T:0.32
Consensus pattern (20 bp):
AGATAATAATATGTTAAACA
Found at i:338267 original size:20 final size:20
Alignment explanation
Indices: 338244--338400 Score: 137
Period size: 20 Copynumber: 7.8 Consensus size: 20
338234 ACACATGTTC
338244 CAAATTCGCAACGCGAAAGT
1 CAAATTCGCAACGCGAAAGT
* **
338264 CAAAATCGCAACATGAAAGT
1 CAAATTCGCAACGCGAAAGT
*
338284 TAAATTCGCAACGCGAAAGT
1 CAAATTCGCAACGCGAAAGT
* * *
338304 CAAAATCGCAATGCAAAAGT
1 CAAATTCGCAACGCGAAAGT
338324 CAAATTCGCAACGCGAATAGGT
1 CAAATTCGCAACGCGAA-A-GT
**
338346 -AAA-TCGCAACGATAATATGT
1 CAAATTCGCAACGCGAA-A-GT
338366 -AAA-TCGCAACGCGAATATGT
1 CAAATTCGCAACGCGAA-A-GT
338386 -AAATT-GCAACGCGAA
1 CAAATTCGCAACGCGAA
338401 TATTATTTTC
Statistics
Matches: 115, Mismatches: 19, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
20 108 0.94
21 5 0.04
22 2 0.02
ACGTcount: A:0.43, C:0.20, G:0.18, T:0.18
Consensus pattern (20 bp):
CAAATTCGCAACGCGAAAGT
Found at i:338273 original size:40 final size:39
Alignment explanation
Indices: 338229--338340 Score: 147
Period size: 40 Copynumber: 2.8 Consensus size: 39
338219 AAGTCCAATT
* *
338229 TCGCAACACATGTTCCAAATTCGCAACGCGAAAGTCAAAA
1 TCGCAACAAAAGTT-CAAATTCGCAACGCGAAAGTCAAAA
338269 TCGCAACATGAAAGTT-AAATTCGCAACGCGAAAGTCAAAA
1 TCGCAACA--AAAGTTCAAATTCGCAACGCGAAAGTCAAAA
338309 TCGCAATGCAAAAG-TCAAATTCGCAACGCGAA
1 TCGCAA--CAAAAGTTCAAATTCGCAACGCGAA
338341 TAGGTAAATC
Statistics
Matches: 65, Mismatches: 2, Indels: 10
0.84 0.03 0.13
Matches are distributed among these distances:
39 1 0.02
40 58 0.89
42 6 0.09
ACGTcount: A:0.42, C:0.24, G:0.17, T:0.17
Consensus pattern (39 bp):
TCGCAACAAAAGTTCAAATTCGCAACGCGAAAGTCAAAA
Found at i:338935 original size:20 final size:20
Alignment explanation
Indices: 338912--338958 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
338902 AAACTTAAAT
*
338912 TCGCAACATGAAAATGAAAA
1 TCGCAACACGAAAATGAAAA
*
338932 TCGCAACGCGAAAATGAAAA
1 TCGCAACACGAAAATGAAAA
*
338952 TTGCAAC
1 TCGCAAC
338959 GTTGCGAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.49, C:0.19, G:0.17, T:0.15
Consensus pattern (20 bp):
TCGCAACACGAAAATGAAAA
Found at i:338959 original size:20 final size:21
Alignment explanation
Indices: 338921--338973 Score: 72
Period size: 20 Copynumber: 2.5 Consensus size: 21
338911 TTCGCAACAT
338921 GAAAATGAAAATCGCAAC-GC
1 GAAAATGAAAATCGCAACTGC
*
338941 GAAAATGAAAATTGCAACGTTGC
1 GAAAATGAAAATCGCAAC--TGC
338964 GAAAATGAAA
1 GAAAATGAAA
338974 TTTCCATTGC
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
20 17 0.59
23 12 0.41
ACGTcount: A:0.51, C:0.13, G:0.21, T:0.15
Consensus pattern (21 bp):
GAAAATGAAAATCGCAACTGC
Found at i:340549 original size:21 final size:21
Alignment explanation
Indices: 340523--340577 Score: 101
Period size: 21 Copynumber: 2.6 Consensus size: 21
340513 CTCGACACCC
340523 AGAGCCATCACCTCCACAACA
1 AGAGCCATCACCTCCACAACA
*
340544 AGAGCCATCACCTCCACAACG
1 AGAGCCATCACCTCCACAACA
340565 AGAGCCATCACCT
1 AGAGCCATCACCT
340578 ATTCCATCAC
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:0.42, G:0.13, T:0.11
Consensus pattern (21 bp):
AGAGCCATCACCTCCACAACA
Found at i:341174 original size:21 final size:21
Alignment explanation
Indices: 341148--341266 Score: 132
Period size: 21 Copynumber: 5.7 Consensus size: 21
341138 GATTCACCTG
*
341148 TCATCGTTCAAGAGGCCTCTCA
1 TCATCGTTCAAGAGGCCCCT-A
341170 T-ATCGTTCAAGAGGCCCCTA
1 TCATCGTTCAAGAGGCCCCTA
* * *
341190 TCATCCTTCAAGAGGCCTCTC
1 TCATCGTTCAAGAGGCCCCTA
* *
341211 CCACCGTTCAAGAGGCCCCTA
1 TCATCGTTCAAGAGGCCCCTA
* *
341232 TCATCGTTCAAGAGGTCCCTC
1 TCATCGTTCAAGAGGCCCCTA
* *
341253 CCACCGTTCAAGAG
1 TCATCGTTCAAGAG
341267 CCCAATTCAC
Statistics
Matches: 81, Mismatches: 15, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
20 2 0.02
21 78 0.96
22 1 0.01
ACGTcount: A:0.23, C:0.35, G:0.18, T:0.24
Consensus pattern (21 bp):
TCATCGTTCAAGAGGCCCCTA
Found at i:341207 original size:42 final size:42
Alignment explanation
Indices: 341148--341266 Score: 177
Period size: 42 Copynumber: 2.8 Consensus size: 42
341138 GATTCACCTG
* *
341148 TCATCGTTCAAGAGGCCTCTCATATCGTTCAAGAGGCCCCTA
1 TCATCGTTCAAGAGGCCTCTCACACCGTTCAAGAGGCCCCTA
* *
341190 TCATCCTTCAAGAGGCCTCTCCCACCGTTCAAGAGGCCCCTA
1 TCATCGTTCAAGAGGCCTCTCACACCGTTCAAGAGGCCCCTA
*
341232 TCATCGTTCAAGAGGTCC-CTCCCACCGTTCAAGAG
1 TCATCGTTCAAGAGG-CCTCTCACACCGTTCAAGAG
341267 CCCAATTCAC
Statistics
Matches: 71, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
42 69 0.97
43 2 0.03
ACGTcount: A:0.23, C:0.35, G:0.18, T:0.24
Consensus pattern (42 bp):
TCATCGTTCAAGAGGCCTCTCACACCGTTCAAGAGGCCCCTA
Found at i:342654 original size:13 final size:13
Alignment explanation
Indices: 342616--342655 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
342606 ATTTTTTTGC
342616 TTGTTTAATTGAT
1 TTGTTTAATTGAT
**
342629 TTGTAAAATTTGAT
1 TTGTTTAA-TTGAT
342643 TTGTTTAATTGAT
1 TTGTTTAATTGAT
342656 GAGGAAATAA
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
13 11 0.50
14 11 0.50
ACGTcount: A:0.28, C:0.00, G:0.15, T:0.57
Consensus pattern (13 bp):
TTGTTTAATTGAT
Found at i:342787 original size:20 final size:20
Alignment explanation
Indices: 342762--342810 Score: 89
Period size: 20 Copynumber: 2.5 Consensus size: 20
342752 AAAAAGACCA
342762 GAAAGTCAAAATCGCAACAC
1 GAAAGTCAAAATCGCAACAC
*
342782 GAAAGTCAAAATCGCAACGC
1 GAAAGTCAAAATCGCAACAC
342802 GAAAGTCAA
1 GAAAGTCAA
342811 CGCGATTTTG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.49, C:0.22, G:0.18, T:0.10
Consensus pattern (20 bp):
GAAAGTCAAAATCGCAACAC
Found at i:343077 original size:20 final size:20
Alignment explanation
Indices: 343030--343098 Score: 84
Period size: 20 Copynumber: 3.5 Consensus size: 20
343020 ACACTTTCGC
*
343030 AACGCGAAAATCAAGATCGA
1 AACGCGAAAATCAAAATCGA
*
343050 AACACGAAAATCAAAATCGA
1 AACGCGAAAATCAAAATCGA
* * * *
343070 AATGCGAAAGTCAAATTCGC
1 AACGCGAAAATCAAAATCGA
343090 AACGCGAAA
1 AACGCGAAA
343099 GCCAAATTCA
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 41 1.00
ACGTcount: A:0.51, C:0.20, G:0.17, T:0.12
Consensus pattern (20 bp):
AACGCGAAAATCAAAATCGA
Found at i:343140 original size:20 final size:20
Alignment explanation
Indices: 343115--343191 Score: 93
Period size: 20 Copynumber: 3.9 Consensus size: 20
343105 TTCACGTTGC
343115 GATTTTCGCGTTGCGAATTT
1 GATTTTCGCGTTGCGAATTT
**
343135 GATTTTCGCGTTGCGGTTTT
1 GATTTTCGCGTTGCGAATTT
*
343155 GACTTTT-GCGTTGCAAATTT
1 GA-TTTTCGCGTTGCGAATTT
* *
343175 GAGTTTCGCATTGCGAA
1 GATTTTCGCGTTGCGAA
343192 AGTGTACCTT
Statistics
Matches: 47, Mismatches: 8, Indels: 4
0.80 0.14 0.07
Matches are distributed among these distances:
19 3 0.06
20 40 0.85
21 4 0.09
ACGTcount: A:0.16, C:0.16, G:0.26, T:0.43
Consensus pattern (20 bp):
GATTTTCGCGTTGCGAATTT
Found at i:345855 original size:24 final size:24
Alignment explanation
Indices: 345804--345855 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
345794 ATCTGAGTAT
** *
345804 TGACCAAGATCAAAGTCCGGGTAT
1 TGACCAAGATCAAAGTCCGAATAC
* *
345828 TGACCAAGATCAAATTTCGAATAC
1 TGACCAAGATCAAAGTCCGAATAC
345852 TGAC
1 TGAC
345856 TAGTACTCAC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.37, C:0.21, G:0.19, T:0.23
Consensus pattern (24 bp):
TGACCAAGATCAAAGTCCGAATAC
Found at i:346786 original size:20 final size:20
Alignment explanation
Indices: 346738--346789 Score: 65
Period size: 18 Copynumber: 2.7 Consensus size: 20
346728 TACCCAAAAC
346738 ATTTGTGTTGCGAAAATAAA
1 ATTTGTGTTGCGAAAATAAA
*
346758 A---GCTGTTGCGAAATTAAA
1 ATTTG-TGTTGCGAAAATAAA
346776 ATTTGTGTTGCGAA
1 ATTTGTGTTGCGAA
346790 TTTGAAAATC
Statistics
Matches: 27, Mismatches: 1, Indels: 8
0.75 0.03 0.22
Matches are distributed among these distances:
17 1 0.04
18 15 0.56
20 10 0.37
21 1 0.04
ACGTcount: A:0.35, C:0.08, G:0.23, T:0.35
Consensus pattern (20 bp):
ATTTGTGTTGCGAAAATAAA
Found at i:346825 original size:40 final size:40
Alignment explanation
Indices: 346762--346839 Score: 104
Period size: 40 Copynumber: 1.9 Consensus size: 40
346752 AATAAAAGCT
* * **
346762 GTTGCGAAATTAAAATTTGTGTTGCGAATTT-GAAAATCGA
1 GTTGAGAAATCAAAATTCATGTTGCG-ATTTAGAAAATCGA
346802 GTTGAGAAATCAAAATTCATGTTGCGATTTAGAAAATC
1 GTTGAGAAATCAAAATTCATGTTGCGATTTAGAAAATC
346840 TTGTTGCGAA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
39 4 0.12
40 29 0.88
ACGTcount: A:0.37, C:0.09, G:0.21, T:0.33
Consensus pattern (40 bp):
GTTGAGAAATCAAAATTCATGTTGCGATTTAGAAAATCGA
Found at i:346906 original size:20 final size:20
Alignment explanation
Indices: 346881--347013 Score: 112
Period size: 20 Copynumber: 6.6 Consensus size: 20
346871 CATAAATTCG
346881 CGTTGCGATTTACATATTAT
1 CGTTGCGATTTACATATTAT
* *
346901 CGTTGCGATTTACCTGTTCA-
1 CGTTGCGATTTACATATT-AT
* * **
346921 CGTTGCGAATTT-GATTTTCG
1 CGTTGCG-ATTTACATATTAT
**
346941 CGTTGCGATTTACATATTCG
1 CGTTGCGATTTACATATTAT
*
346961 CGTTACGATTTACATATTAT
1 CGTTGCGATTTACATATTAT
346981 CGTTGCGATTTA-ACTATT-T
1 CGTTGCGATTTACA-TATTAT
347000 GCGTTGCGAATTTA
1 -CGTTGCG-ATTTA
347014 TAAAATTGCC
Statistics
Matches: 94, Mismatches: 12, Indels: 13
0.79 0.10 0.11
Matches are distributed among these distances:
19 6 0.06
20 78 0.83
21 10 0.11
ACGTcount: A:0.21, C:0.17, G:0.19, T:0.43
Consensus pattern (20 bp):
CGTTGCGATTTACATATTAT
Found at i:346985 original size:60 final size:61
Alignment explanation
Indices: 346877--347013 Score: 165
Period size: 60 Copynumber: 2.3 Consensus size: 61
346867 GAAACATAAA
* * * * *
346877 TTCGCGTTGCGATTTACATATTATCGTTGCGATTTACCTGTTCACGTTGCGAATTTGA-T-T
1 TTCGCGTTGCGATTTACATATTAGCGTTACGATTTACATATTCACGTTGCG-ATTTAACTAT
*
346937 TTCGCGTTGCGATTTACATATTCGCGTTACGATTTACATATT-ATCGTTGCGATTTAACTAT
1 TTCGCGTTGCGATTTACATATTAGCGTTACGATTTACATATTCA-CGTTGCGATTTAACTAT
346998 TT-GCGTTGCGAATTTA
1 TTCGCGTTGCG-ATTTA
347014 TAAAATTGCC
Statistics
Matches: 67, Mismatches: 6, Indels: 7
0.84 0.08 0.09
Matches are distributed among these distances:
59 6 0.09
60 53 0.79
61 8 0.12
ACGTcount: A:0.20, C:0.18, G:0.19, T:0.43
Consensus pattern (61 bp):
TTCGCGTTGCGATTTACATATTAGCGTTACGATTTACATATTCACGTTGCGATTTAACTAT
Found at i:347004 original size:40 final size:41
Alignment explanation
Indices: 346876--347013 Score: 158
Period size: 40 Copynumber: 3.4 Consensus size: 41
346866 TGAAACATAA
*
346876 ATTCGCGTTGCG-ATTTACATATTATCGTTGCGATTTACCT
1 ATTCGCGTTGCGAATTTACATATTATCGTTGCGATTTAACT
* * * * **
346916 GTTCACGTTGCGAATTT-GATTTTCGCGTTGCGATTT-ACAT
1 ATTCGCGTTGCGAATTTACATATTATCGTTGCGATTTAAC-T
*
346956 ATTCGCGTTACG-ATTTACATATTATCGTTGCGATTTAACT
1 ATTCGCGTTGCGAATTTACATATTATCGTTGCGATTTAACT
*
346996 ATTTGCGTTGCGAATTTA
1 ATTCGCGTTGCGAATTTA
347014 TAAAATTGCC
Statistics
Matches: 77, Mismatches: 16, Indels: 9
0.75 0.16 0.09
Matches are distributed among these distances:
39 5 0.06
40 61 0.79
41 11 0.14
ACGTcount: A:0.21, C:0.17, G:0.19, T:0.43
Consensus pattern (41 bp):
ATTCGCGTTGCGAATTTACATATTATCGTTGCGATTTAACT
Found at i:353644 original size:11 final size:11
Alignment explanation
Indices: 353628--353657 Score: 53
Period size: 10 Copynumber: 2.8 Consensus size: 11
353618 AAATTCTTTA
353628 AAATAAAAAAG
1 AAATAAAAAAG
353639 AAAT-AAAAAG
1 AAATAAAAAAG
353649 AAATAAAAA
1 AAATAAAAA
353658 TATTCTTTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
10 10 0.56
11 8 0.44
ACGTcount: A:0.83, C:0.00, G:0.07, T:0.10
Consensus pattern (11 bp):
AAATAAAAAAG
Found at i:354141 original size:81 final size:81
Alignment explanation
Indices: 353983--354216 Score: 279
Period size: 81 Copynumber: 3.0 Consensus size: 81
353973 AAATTTCGAG
* * * *
353983 AGAGTTTTACTCAAACTAAAACTCTTTTAATATCT-AA---AAATAGATAATAATA-TTT---TT
1 AGAGTTTTACTCAAACAAAAACTCTTTTAATATCTAAATTTAAAAAAATTATAATATTTTAAATT
* *
354040 TA-AATGATTAAATCTG
66 TATAAT-ATTAAACCTA
* *
354056 AGAGTTTTACTCTAACAAAAACTCTTTTAATATCTAAATTTAAACAAATTATAATATTTTAAATT
1 AGAGTTTTACTCAAACAAAAACTCTTTTAATATCTAAATTTAAAAAAATTATAATATTTTAAATT
354121 TATAATATTAAACCTA
66 TATAATATTAAACCTA
* * *
354137 AGAGTTTTACTCCAACCAAAACTCTTTTAATATATAAATTTAAAAAAATTATAATATCTTTTAAA
1 AGAGTTTTACTCAAACAAAAACTCTTTTAATATCTAAATTTAAAAAAATTATAATA--TTTTAAA
354202 TTTATAATATTAAAC
64 TTTATAATATTAAAC
354217 ACATATTTCC
Statistics
Matches: 139, Mismatches: 11, Indels: 12
0.86 0.07 0.07
Matches are distributed among these distances:
73 33 0.24
74 2 0.01
77 12 0.09
78 3 0.02
81 64 0.46
82 3 0.02
83 22 0.16
ACGTcount: A:0.45, C:0.11, G:0.04, T:0.40
Consensus pattern (81 bp):
AGAGTTTTACTCAAACAAAAACTCTTTTAATATCTAAATTTAAAAAAATTATAATATTTTAAATT
TATAATATTAAACCTA
Found at i:357468 original size:25 final size:25
Alignment explanation
Indices: 357438--357486 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 25
357428 AAGAATATAT
357438 TATCCAAATCAAAAAATGATAATTA
1 TATCCAAATCAAAAAATGATAATTA
*
357463 TATCCAAATCAAACAATGATAATT
1 TATCCAAATCAAAAAATGATAATT
357487 TAAATTAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.53, C:0.14, G:0.04, T:0.29
Consensus pattern (25 bp):
TATCCAAATCAAAAAATGATAATTA
Found at i:357597 original size:30 final size:28
Alignment explanation
Indices: 357561--357623 Score: 81
Period size: 30 Copynumber: 2.2 Consensus size: 28
357551 ATTTATAATT
**
357561 TAAATATTATTATTATATTAATAAATTATA
1 TAAATATTATTATT-TAAGAATAAATTA-A
*
357591 TAAATATTTTTATTTAAGAATAAATTAA
1 TAAATATTATTATTTAAGAATAAATTAA
357619 TAAAT
1 TAAAT
357624 CAGAGTTTGA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
28 6 0.20
29 11 0.37
30 13 0.43
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.48
Consensus pattern (28 bp):
TAAATATTATTATTTAAGAATAAATTAA
Found at i:359678 original size:14 final size:14
Alignment explanation
Indices: 359659--359686 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
359649 CAAATATATA
359659 ATAATTTATAGTTT
1 ATAATTTATAGTTT
359673 ATAATTTATAGTTT
1 ATAATTTATAGTTT
359687 CAATATTAAT
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:0.36, C:0.00, G:0.07, T:0.57
Consensus pattern (14 bp):
ATAATTTATAGTTT
Found at i:362272 original size:16 final size:17
Alignment explanation
Indices: 362243--362277 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
362233 ATTATACCTA
362243 AATTCTTATGATATTAT
1 AATTCTTATGATATTAT
*
362260 AATT-TTATTATATTAT
1 AATTCTTATGATATTAT
362276 AA
1 AA
362278 ACTATAAACC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 13 0.76
17 4 0.24
ACGTcount: A:0.40, C:0.03, G:0.03, T:0.54
Consensus pattern (17 bp):
AATTCTTATGATATTAT
Found at i:362325 original size:9 final size:9
Alignment explanation
Indices: 362312--362378 Score: 55
Period size: 9 Copynumber: 7.3 Consensus size: 9
362302 TAAATTAATT
362312 TAATTTAAA
1 TAATTTAAA
* *
362321 AAATTTATA
1 TAATTTAAA
**
362330 TAATAAAAA
1 TAATTTAAA
362339 T-ATTTAAA
1 TAATTTAAA
362347 TAATATTAGAA
1 TAAT-TTA-AA
362358 TAATTTAAA
1 TAATTTAAA
* *
362367 TTATTTATA
1 TAATTTAAA
362376 TAA
1 TAA
362379 GAACATATTA
Statistics
Matches: 44, Mismatches: 11, Indels: 6
0.72 0.18 0.10
Matches are distributed among these distances:
8 6 0.14
9 26 0.59
10 6 0.14
11 6 0.14
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.43
Consensus pattern (9 bp):
TAATTTAAA
Found at i:362343 original size:17 final size:16
Alignment explanation
Indices: 362317--362351 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
362307 TAATTTAATT
*
362317 TAAAAAATTTATATAA
1 TAAAAAATTTAAATAA
362333 TAAAAATATTTAAATAA
1 TAAAAA-ATTTAAATAA
362350 TA
1 TA
362352 TTAGAATAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 6 0.35
17 11 0.65
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (16 bp):
TAAAAAATTTAAATAA
Found at i:362408 original size:13 final size:13
Alignment explanation
Indices: 362390--362414 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
362380 AACATATTAA
362390 TATAATTTAAATC
1 TATAATTTAAATC
362403 TATAATTTAAAT
1 TATAATTTAAAT
362415 ATCAATATTA
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:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (13 bp):
TATAATTTAAATC
Done.