Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008610.1 Hibiscus syriacus cultivar Beakdansim tig00111566_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: 2108335
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 11
Found at i:187112 original size:41 final size:41
Alignment explanation
Indices: 187020--187114 Score: 111
Period size: 41 Copynumber: 2.3 Consensus size: 41
187010 GAAAGTCAAA
* * ** *
187020 ATCGCGTTGCGAAAGTCAGTATCGCGTTGCGATTTTGTATT
1 ATCGCGTTGCGATAGTCAGTATCGCATTGCGATTTTCCAAT
* *
187061 ATCGCATTGCGATAGTTAGTATCGCATTGCGATTTTCCCAAT
1 ATCGCGTTGCGATAGTCAGTATCGCATTGCGATTTT-CCAAT
187103 -TCGCGTTGCGAT
1 ATCGCGTTGCGAT
187115 TTACTTATTC
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
41 43 0.96
42 2 0.04
ACGTcount: A:0.20, C:0.20, G:0.24, T:0.36
Consensus pattern (41 bp):
ATCGCGTTGCGATAGTCAGTATCGCATTGCGATTTTCCAAT
Found at i:192736 original size:21 final size:21
Alignment explanation
Indices: 192712--192802 Score: 103
Period size: 21 Copynumber: 4.3 Consensus size: 21
192702 TGACTCGTAT
192712 GACCACATATATGTTCCAAAG
1 GACCACATATATGTTCCAAAG
*
192733 GACCAAATATATG-TCCAAGAAG
1 GACCACATATATGTTCC-A-AAG
**
192755 GACTTCATATATGTTCCAAAG
1 GACCACATATATGTTCCAAAG
* * *
192776 GATCACATATATGTCCCGAAG
1 GACCACATATATGTTCCAAAG
192797 GACCAC
1 GACCAC
192803 GTAGAACCCT
Statistics
Matches: 57, Mismatches: 10, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
20 3 0.05
21 37 0.65
22 14 0.25
23 3 0.05
ACGTcount: A:0.37, C:0.23, G:0.16, T:0.23
Consensus pattern (21 bp):
GACCACATATATGTTCCAAAG
Found at i:192771 original size:43 final size:42
Alignment explanation
Indices: 192717--192799 Score: 130
Period size: 43 Copynumber: 2.0 Consensus size: 42
192707 CGTATGACCA
192717 CATATATGTTCCAAAGGACCAAATATATGTCCAAGAAGGACTT
1 CATATATGTTCCAAAGGACCAAATATATGTCC-AGAAGGACTT
* * *
192760 CATATATGTTCCAAAGGATCACATATATGTCCCGAAGGAC
1 CATATATGTTCCAAAGGACCAAATATATGTCCAGAAGGAC
192800 CACGTAGAAC
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
42 7 0.19
43 30 0.81
ACGTcount: A:0.37, C:0.20, G:0.17, T:0.25
Consensus pattern (42 bp):
CATATATGTTCCAAAGGACCAAATATATGTCCAGAAGGACTT
Found at i:198021 original size:31 final size:31
Alignment explanation
Indices: 197968--198042 Score: 87
Period size: 31 Copynumber: 2.4 Consensus size: 31
197958 CAACGAAGTG
*** *
197968 ATCATTTTGTTACAATTTGATAATATTAGTA
1 ATCATTTTGTTACAAACCGATAACATTAGTA
*
197999 ATCATTTTGTTACAAACCGATAACATTAGTG
1 ATCATTTTGTTACAAACCGATAACATTAGTA
* *
198030 ATCAATCTGTTAC
1 ATCATTTTGTTAC
198043 TTTTGAAACT
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 37 1.00
ACGTcount: A:0.35, C:0.13, G:0.11, T:0.41
Consensus pattern (31 bp):
ATCATTTTGTTACAAACCGATAACATTAGTA
Found at i:200196 original size:2 final size:2
Alignment explanation
Indices: 200189--200225 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
200179 TTAAGAGCGG
200189 AT AT AT 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 AT AT AT A
200226 ATAACATAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:202283 original size:21 final size:21
Alignment explanation
Indices: 202239--202288 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
202229 GTTTCCAGAT
202239 TCGCAACGCGAACATCGACAA
1 TCGCAACGCGAACATCGACAA
* * * *
202260 TCGCTACGCGAACTTGGACTA
1 TCGCAACGCGAACATCGACAA
202281 TCGCAACG
1 TCGCAACG
202289 AATTTATTCT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.30, C:0.32, G:0.22, T:0.16
Consensus pattern (21 bp):
TCGCAACGCGAACATCGACAA
Found at i:202330 original size:21 final size:21
Alignment explanation
Indices: 202304--202447 Score: 152
Period size: 21 Copynumber: 6.8 Consensus size: 21
202294 ATTCTAAGTT
*
202304 CGTTGCGATAGTCGAAGTTCG
1 CGTTGCGATAGTCCAAGTTCG
*
202325 CGTTGCGATTTATTCCAAGTTCG
1 CGTTGCGA--TAGTCCAAGTTCG
202348 CGTTGCGATAGTCCAAGTTCG
1 CGTTGCGATAGTCCAAGTTCG
*
202369 CGTTGCGATTTATTCCAAGTT--
1 CGTTGCGA--TAGTCCAAGTTCG
*
202390 CGTTGCGATAGTCGAAGTTCG
1 CGTTGCGATAGTCCAAGTTCG
* *
202411 CGTTTCGATTTATTCCAAGTT--
1 CGTTGCGA--TAGTCCAAGTTCG
202432 CGTTGCGATAGTCCAA
1 CGTTGCGATAGTCCAA
202448 AATCGCAACG
Statistics
Matches: 104, Mismatches: 11, Indels: 18
0.78 0.08 0.14
Matches are distributed among these distances:
19 16 0.15
21 50 0.48
23 38 0.37
ACGTcount: A:0.19, C:0.21, G:0.25, T:0.35
Consensus pattern (21 bp):
CGTTGCGATAGTCCAAGTTCG
Found at i:202408 original size:42 final size:42
Alignment explanation
Indices: 202290--202444 Score: 265
Period size: 42 Copynumber: 3.6 Consensus size: 42
202280 ATCGCAACGA
*
202290 ATTTATTCTAAGTTCGTTGCGATAGTCGAAGTTCGCGTTGCG
1 ATTTATTCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTTGCG
*
202332 ATTTATTCCAAGTTCGCGTTGCGATAGTCCAAGTTCGCGTTGCG
1 ATTTATTCCAAGTT--CGTTGCGATAGTCGAAGTTCGCGTTGCG
*
202376 ATTTATTCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTTTCG
1 ATTTATTCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTTGCG
202418 ATTTATTCCAAGTTCGTTGCGATAGTC
1 ATTTATTCCAAGTTCGTTGCGATAGTC
202445 CAAAATCGCA
Statistics
Matches: 107, Mismatches: 4, Indels: 4
0.93 0.03 0.03
Matches are distributed among these distances:
42 66 0.62
44 41 0.38
ACGTcount: A:0.19, C:0.19, G:0.24, T:0.37
Consensus pattern (42 bp):
ATTTATTCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTTGCG
Found at i:203340 original size:21 final size:21
Alignment explanation
Indices: 203310--203373 Score: 87
Period size: 21 Copynumber: 3.1 Consensus size: 21
203300 ATCAGTCGTT
203310 ACGAATTTGGAATAAATCGCA
1 ACGAATTTGGAATAAATCGCA
* *
203331 ACGAACTTGGACT--ATCGCA
1 ACGAATTTGGAATAAATCGCA
*
203350 ACGAATTTGTAATAAATCGCA
1 ACGAATTTGGAATAAATCGCA
203371 ACG
1 ACG
203374 CGAACTTCGA
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
19 16 0.44
21 20 0.56
ACGTcount: A:0.39, C:0.19, G:0.19, T:0.23
Consensus pattern (21 bp):
ACGAATTTGGAATAAATCGCA
Found at i:203365 original size:40 final size:41
Alignment explanation
Indices: 203310--203394 Score: 127
Period size: 40 Copynumber: 2.1 Consensus size: 41
203300 ATCAGTCGTT
*
203310 ACGAATTTGGAATAAATCGCAA-CGAACTTGGACTATCGCA
1 ACGAATTTGGAATAAATCGCAACCGAACTTCGACTATCGCA
* *
203350 ACGAATTTGTAATAAATCGCAACGCGAACTTCGACTGTCGCA
1 ACGAATTTGGAATAAATCGCAAC-CGAACTTCGACTATCGCA
203392 ACG
1 ACG
203395 CGAACTTCGA
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
40 21 0.52
42 19 0.47
ACGTcount: A:0.35, C:0.22, G:0.20, T:0.22
Consensus pattern (41 bp):
ACGAATTTGGAATAAATCGCAACCGAACTTCGACTATCGCA
Found at i:203390 original size:21 final size:21
Alignment explanation
Indices: 203365--203419 Score: 92
Period size: 21 Copynumber: 2.6 Consensus size: 21
203355 TTTGTAATAA
203365 ATCGCAACGCGAACTTCGACT
1 ATCGCAACGCGAACTTCGACT
*
203386 GTCGCAACGCGAACTTCGACT
1 ATCGCAACGCGAACTTCGACT
*
203407 ATCGCAATGCGAA
1 ATCGCAACGCGAA
203420 TATGTAAATC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.29, C:0.31, G:0.22, T:0.18
Consensus pattern (21 bp):
ATCGCAACGCGAACTTCGACT
Found at i:209798 original size:65 final size:65
Alignment explanation
Indices: 209727--209854 Score: 177
Period size: 65 Copynumber: 2.0 Consensus size: 65
209717 CATTAATTGC
** *
209727 ATTCGATGTTTCAAAAAAGCCTGGAGTGCATCGATGCATG-ATATGTTCATCGGTACACAAAATC
1 ATTCGATGTTTCAAAAAAGCCAAGAGTGCATCGATGCATGCAT-TGTGCATCGGTACACAAAATC
209791 A
65 A
* ** *
209792 ATTCGATGTTTCAAAACATTCAAGAGTGCATCGATGCATGCCTTGTGCATCGGTACACAAAAT
1 ATTCGATGTTTCAAAAAAGCCAAGAGTGCATCGATGCATGCATTGTGCATCGGTACACAAAAT
209855 GCACTCGGAA
Statistics
Matches: 55, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
65 54 0.98
66 1 0.02
ACGTcount: A:0.33, C:0.20, G:0.20, T:0.28
Consensus pattern (65 bp):
ATTCGATGTTTCAAAAAAGCCAAGAGTGCATCGATGCATGCATTGTGCATCGGTACACAAAATCA
Found at i:210538 original size:2 final size:2
Alignment explanation
Indices: 210531--210562 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
210521 AACAAACTGA
*
210531 AT AT AT AT AT GT 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
210563 TAAGTTCAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:218502 original size:65 final size:65
Alignment explanation
Indices: 218402--218559 Score: 158
Period size: 65 Copynumber: 2.4 Consensus size: 65
218392 GTACACTAGG
* ** * * * * * * *
218402 AGTGCATCGATGCATTAATTGCATTCGGTGTTTCAAAATAGCCTAGAGTGCATTGATGCATG-GT
1 AGTGCATCGATACACAAAATGCATTCGATGATTCAAAACAGCCAAGAGTGCATCGATGCATGCCT
* * **
218466 ATGTGCATTGGTACACAAAAT-CAATTCGATGATTCAAAACATTCAAGAGTGCATCGATGCATGC
1 A-GTGCATCGATACACAAAATGC-ATTCGATGATTCAAAACAGCCAAGAGTGCATCGATGCATGC
218530 CT
64 CT
218532 AGTGCATCGATACACAAAATGCATTCGA
1 AGTGCATCGATACACAAAATGCATTCGA
218560 AATTCAATTT
Statistics
Matches: 74, Mismatches: 16, Indels: 7
0.76 0.16 0.07
Matches are distributed among these distances:
64 2 0.03
65 69 0.93
66 3 0.04
ACGTcount: A:0.32, C:0.18, G:0.21, T:0.28
Consensus pattern (65 bp):
AGTGCATCGATACACAAAATGCATTCGATGATTCAAAACAGCCAAGAGTGCATCGATGCATGCCT
Found at i:219609 original size:16 final size:16
Alignment explanation
Indices: 219573--219608 Score: 56
Period size: 15 Copynumber: 2.3 Consensus size: 16
219563 GGGACTGAAA
*
219573 TAAAATGCAACAAAAT
1 TAAAAGGCAACAAAAT
219589 TAAAAGGCAA-AAAAT
1 TAAAAGGCAACAAAAT
219604 TAAAA
1 TAAAA
219609 ATGTTGGAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 10 0.53
16 9 0.47
ACGTcount: A:0.67, C:0.08, G:0.08, T:0.17
Consensus pattern (16 bp):
TAAAAGGCAACAAAAT
Found at i:219890 original size:32 final size:31
Alignment explanation
Indices: 219829--219917 Score: 99
Period size: 31 Copynumber: 2.8 Consensus size: 31
219819 ACAATAAAAA
*
219829 AAATAAAAAGTTAGTATGTTAGTAAGAACAAAT
1 AAATAAAAA-TTAGAATGTTAGTAAGAAC-AAT
**
219862 AAATAAAAATTAGAATGTTAGTTCGAACAAT
1 AAATAAAAATTAGAATGTTAGTAAGAACAAT
* *
219893 AAA-ATAAAAGTAGAATGCTAGTAAG
1 AAATA-AAAATTAGAATGTTAGTAAG
219918 TTAGTGATTA
Statistics
Matches: 48, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
30 1 0.02
31 22 0.46
32 16 0.33
33 9 0.19
ACGTcount: A:0.54, C:0.04, G:0.16, T:0.26
Consensus pattern (31 bp):
AAATAAAAATTAGAATGTTAGTAAGAACAAT
Found at i:219907 original size:31 final size:31
Alignment explanation
Indices: 219826--219917 Score: 105
Period size: 32 Copynumber: 2.9 Consensus size: 31
219816 ATAACAATAA
*
219826 AAAAAATAAAAAGTTAGTATGTTAGTAAGAAC
1 AAAAAATAAAAAG-TAGAATGTTAGTAAGAAC
* **
219858 AAATAAATAAAAATTAGAATGTTAGTTCGAAC
1 AAA-AAATAAAAAGTAGAATGTTAGTAAGAAC
*
219890 AATAAAAT-AAAAGTAGAATGCTAGTAAG
1 AA-AAAATAAAAAGTAGAATGTTAGTAAG
219918 TTAGTGATTA
Statistics
Matches: 50, Mismatches: 8, Indels: 5
0.79 0.13 0.08
Matches are distributed among these distances:
31 16 0.32
32 24 0.48
33 10 0.20
ACGTcount: A:0.55, C:0.04, G:0.15, T:0.25
Consensus pattern (31 bp):
AAAAAATAAAAAGTAGAATGTTAGTAAGAAC
Found at i:224436 original size:16 final size:16
Alignment explanation
Indices: 224415--224447 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
224405 AACATTTATG
224415 TTTCAGTTCTATGAAA
1 TTTCAGTTCTATGAAA
224431 TTTCAGTTCTATGAAA
1 TTTCAGTTCTATGAAA
224447 T
1 T
224448 CTTCCGTTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.30, C:0.12, G:0.12, T:0.45
Consensus pattern (16 bp):
TTTCAGTTCTATGAAA
Found at i:229606 original size:6 final size:6
Alignment explanation
Indices: 229597--229675 Score: 51
Period size: 6 Copynumber: 12.8 Consensus size: 6
229587 TATTTATATC
229597 AAAAAT AAAAAT -AAAAT AAAAAT AGCACAAGAT -AAAAT -AAAAT -AAAAT
1 AAAAAT AAAAAT AAAAAT AAAAAT A--A-AA-AT AAAAAT AAAAAT AAAAAT
*
229645 AAAAAGAT AAAAAT AAAGCA- AAAAAT AAAAA
1 -AAAA-AT AAAAAT AAA-AAT AAAAAT AAAAA
229676 AAGAAGACTA
Statistics
Matches: 61, Mismatches: 2, Indels: 20
0.73 0.02 0.24
Matches are distributed among these distances:
5 18 0.30
6 27 0.44
7 9 0.15
8 3 0.05
9 2 0.03
10 2 0.03
ACGTcount: A:0.77, C:0.04, G:0.05, T:0.14
Consensus pattern (6 bp):
AAAAAT
Found at i:229675 original size:18 final size:18
Alignment explanation
Indices: 229597--229675 Score: 63
Period size: 19 Copynumber: 4.3 Consensus size: 18
229587 TATTTATATC
*
229597 AAAAATAAAA-ATAAAAT
1 AAAAATAAAACAAAAAAT
**
229614 AAAAATAGCACAAGATAAA-
1 AAAAATAAAACAA-A-AAAT
*
229633 ATAAAATAAAATAAAAAGAT
1 A-AAAATAAAACAAAAA-AT
*
229653 AAAAATAAAGCAAAAAAT
1 AAAAATAAAACAAAAAAT
229671 AAAAA
1 AAAAA
229676 AAGAAGACTA
Statistics
Matches: 48, Mismatches: 8, Indels: 11
0.72 0.12 0.16
Matches are distributed among these distances:
17 8 0.17
18 10 0.21
19 17 0.35
20 13 0.27
ACGTcount: A:0.77, C:0.04, G:0.05, T:0.14
Consensus pattern (18 bp):
AAAAATAAAACAAAAAAT
Found at i:230446 original size:34 final size:33
Alignment explanation
Indices: 230394--230463 Score: 95
Period size: 34 Copynumber: 2.1 Consensus size: 33
230384 TTAGTTTGTG
** *
230394 CAATAAAATAAAGTGTTAGTAAGTTAGTAATAA
1 CAATAAAATAAAAAGTTAGTAAGTTAGTAAGAA
*
230427 CAATAAAAATAAAAAGTTAGTATGTTAGTAAGAA
1 CAAT-AAAATAAAAAGTTAGTAAGTTAGTAAGAA
230461 CAA
1 CAA
230464 ATAATGTTAG
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
33 4 0.12
34 28 0.88
ACGTcount: A:0.54, C:0.04, G:0.14, T:0.27
Consensus pattern (33 bp):
CAATAAAATAAAAAGTTAGTAAGTTAGTAAGAA
Found at i:230472 original size:19 final size:19
Alignment explanation
Indices: 230448--230486 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
230438 AAAAGTTAGT
230448 ATGTTAGTAAGAACAAATA
1 ATGTTAGTAAGAACAAATA
*
230467 ATGTTAGTAGGAACAAATA
1 ATGTTAGTAAGAACAAATA
230486 A
1 A
230487 ATAAAATTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.51, C:0.05, G:0.18, T:0.26
Consensus pattern (19 bp):
ATGTTAGTAAGAACAAATA
Found at i:230502 original size:32 final size:32
Alignment explanation
Indices: 230466--230539 Score: 96
Period size: 32 Copynumber: 2.3 Consensus size: 32
230456 AAGAACAAAT
* *
230466 AATGTTAGTAGGAACAA-ATAAATAAAATTTAG
1 AATGTTAGTACGAACAATA-AAATAAAAGTTAG
* *
230498 AATGTTATTTCGAACAATAAAATAAAAGTTAG
1 AATGTTAGTACGAACAATAAAATAAAAGTTAG
230530 AATGTTAGTA
1 AATGTTAGTA
230540 AGTTAGTGAC
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
32 34 0.97
33 1 0.03
ACGTcount: A:0.50, C:0.04, G:0.15, T:0.31
Consensus pattern (32 bp):
AATGTTAGTACGAACAATAAAATAAAAGTTAG
Found at i:236208 original size:3 final size:3
Alignment explanation
Indices: 236200--236224 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
236190 TTTGGAATGA
236200 AAC AAC AAC AAC AAC AAC AAC AAC A
1 AAC AAC AAC AAC AAC AAC AAC AAC A
236225 CCCTATTCCC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.32, G:0.00, T:0.00
Consensus pattern (3 bp):
AAC
Found at i:237397 original size:20 final size:19
Alignment explanation
Indices: 237329--237394 Score: 105
Period size: 19 Copynumber: 3.4 Consensus size: 19
237319 AAACCCCAAA
*
237329 TTCCTTTTCGATCTCAAAT
1 TTCCTTTTCGATCTCGAAT
*
237348 TTCCTTTTTTGATCTCGAAT
1 TTCC-TTTTCGATCTCGAAT
237368 TTCCTTTTCGATCTCGAAT
1 TTCCTTTTCGATCTCGAAT
237387 TTCCTTTT
1 TTCCTTTT
237395 TCGCTCCTCT
Statistics
Matches: 43, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
19 26 0.60
20 17 0.40
ACGTcount: A:0.15, C:0.24, G:0.08, T:0.53
Consensus pattern (19 bp):
TTCCTTTTCGATCTCGAAT
Found at i:239865 original size:26 final size:26
Alignment explanation
Indices: 239836--239887 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
239826 CCCTTCCAGG
239836 GAATCCTATCTCTAAAAGTGAGAATA
1 GAATCCTATCTCTAAAAGTGAGAATA
239862 GAATCCTATCTCTAAAAGTGAGAATA
1 GAATCCTATCTCTAAAAGTGAGAATA
239888 TATATATTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.42, C:0.15, G:0.15, T:0.27
Consensus pattern (26 bp):
GAATCCTATCTCTAAAAGTGAGAATA
Found at i:242285 original size:21 final size:21
Alignment explanation
Indices: 242259--242318 Score: 84
Period size: 21 Copynumber: 2.9 Consensus size: 21
242249 TCAAAACCTG
* *
242259 CTGAAAATCCTATAGCCACTA
1 CTGAAAATCCTACAACCACTA
*
242280 CTGAAAATCCTACAACCACTG
1 CTGAAAATCCTACAACCACTA
*
242301 CTGAAATTCCTACAACCA
1 CTGAAAATCCTACAACCA
242319 TTGTAGTTCC
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.38, C:0.32, G:0.08, T:0.22
Consensus pattern (21 bp):
CTGAAAATCCTACAACCACTA
Found at i:245400 original size:2 final size:2
Alignment explanation
Indices: 245393--245430 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
245383 ATTCTAATCC
245393 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
245431 GCTCTCATAG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:258804 original size:3 final size:3
Alignment explanation
Indices: 258784--258826 Score: 50
Period size: 3 Copynumber: 14.3 Consensus size: 3
258774 TCTACAAAAA
* * * *
258784 TAT TAA TAT TAA TAT TAT TAT TAT TAT TAT TAA CAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
258827 TTACAACTTT
Statistics
Matches: 32, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (3 bp):
TAT
Found at i:266194 original size:34 final size:34
Alignment explanation
Indices: 266150--266216 Score: 107
Period size: 34 Copynumber: 2.0 Consensus size: 34
266140 TGATGGTGTT
266150 TTTCTAAAAACAAATTTTGTCTCACTTGAGACAA
1 TTTCTAAAAACAAATTTTGTCTCACTTGAGACAA
* **
266184 TTTCTCAAAACAAATTTTGTCTTGCTTGAGACA
1 TTTCTAAAAACAAATTTTGTCTCACTTGAGACA
266217 TTTTTCCTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.34, C:0.18, G:0.10, T:0.37
Consensus pattern (34 bp):
TTTCTAAAAACAAATTTTGTCTCACTTGAGACAA
Found at i:266650 original size:70 final size:68
Alignment explanation
Indices: 266568--266799 Score: 272
Period size: 70 Copynumber: 3.4 Consensus size: 68
266558 AATTTATAAT
* * * *
266568 CTTTGAGTTTGTTT-TCTTGAAACAAAAT-TTTGTCTCCTTCGAGACAGTTTCTTATGAAACAAC
1 CTTTGAGATTGTTTCCCTTGAAAC-AAATCTTT-T-TCCTT-GAGACCGTTTCTCATGAAACAAC
266631 AACCAAA
62 AACCAAA
* * * *
266638 CTTTGAGATTGTTTACCTTGAAACAAATCTTATTTTCGTTGAAACCGTTTCTCATGAAACAATAA
1 CTTTGAGATTGTTTCCCTTGAAACAAATC-T-TTTTCCTTGAGACCGTTTCTCATGAAACAACAA
266703 CCAAA
64 CCAAA
* *
266708 CTTTGAGATTGTTTCTCTTGAAACAAATCTATTTTCCTTGAGACCGTTTCTCATGAAACAACAAT
1 CTTTGAGATTGTTTCCCTTGAAACAAATCT-TTTTCCTTGAGACCGTTTCTCATGAAACAACAAC
*
266773 C-AT
65 CAAA
*
266776 CTTTGAGATCGTTTCCCTTGAAAC
1 CTTTGAGATTGTTTCCCTTGAAAC
266800 GAATTAAATC
Statistics
Matches: 142, Mismatches: 16, Indels: 10
0.85 0.10 0.06
Matches are distributed among these distances:
68 23 0.16
69 33 0.23
70 70 0.49
71 12 0.08
72 2 0.01
73 2 0.01
ACGTcount: A:0.31, C:0.20, G:0.12, T:0.37
Consensus pattern (68 bp):
CTTTGAGATTGTTTCCCTTGAAACAAATCTTTTTCCTTGAGACCGTTTCTCATGAAACAACAACC
AAA
Found at i:266789 original size:33 final size:35
Alignment explanation
Indices: 266638--266832 Score: 125
Period size: 33 Copynumber: 5.7 Consensus size: 35
266628 AACAACCAAA
* * **
266638 CTTTGAGATTGTTTAC-CTTGAAACAAATCTTATTTT
1 CTTTGAGATCGTTT-CTCTTGAAACAAATC-AATCAT
* * * * * *
266674 CGTTGAAACCGTTTCTCATGAAAC-AAT-AACCAAA
1 CTTTGAGATCGTTTCTCTTGAAACAAATCAATC-AT
* * **
266708 CTTTGAGATTGTTTCTCTTGAAACAAATCTATTTT
1 CTTTGAGATCGTTTCTCTTGAAACAAATCAATCAT
* * *
266743 CCTTGAGACCGTTTCTCATGAAAC-AA-CAATCAT
1 CTTTGAGATCGTTTCTCTTGAAACAAATCAATCAT
* * *
266776 CTTTGAGATCGTTTCCCTTGAAACGAATTAA--AT
1 CTTTGAGATCGTTTCTCTTGAAACAAATCAATCAT
*
266809 CTTTGAGAACGTTTCTCTTGAAAC
1 CTTTGAGATCGTTTCTCTTGAAAC
266833 GAATTAAATC
Statistics
Matches: 119, Mismatches: 34, Indels: 15
0.71 0.20 0.09
Matches are distributed among these distances:
33 49 0.41
34 23 0.19
35 29 0.24
36 18 0.15
ACGTcount: A:0.31, C:0.19, G:0.13, T:0.37
Consensus pattern (35 bp):
CTTTGAGATCGTTTCTCTTGAAACAAATCAATCAT
Found at i:266833 original size:33 final size:33
Alignment explanation
Indices: 266676--266864 Score: 143
Period size: 33 Copynumber: 5.6 Consensus size: 33
266666 CTTATTTTCG
* * * *
266676 TTGAAACCGTTTCTCATGAAAC-AATAACCAAACT
1 TTGAGACCGTTTCTCTTGAAACGAATTA--AATCT
** * ** *
266710 TTGAGATTGTTTCTCTTGAAACAAATCTATTTTCC
1 TTGAGACCGTTTCTCTTGAAACGAAT-TA-AATCT
* *
266745 TTGAGACCGTTTCTCATGAAAC-AA-CAATCATCT
1 TTGAGACCGTTTCTCTTGAAACGAATTAA--ATCT
* *
266778 TTGAGATCGTTTCCCTTGAAACGAATTAAATCT
1 TTGAGACCGTTTCTCTTGAAACGAATTAAATCT
*
266811 TTGAGAACGTTTCTCTTGAAACGAATTAAATCT
1 TTGAGACCGTTTCTCTTGAAACGAATTAAATCT
*
266844 TTAAG-CCTGTTTCTCTTGAAA
1 TTGAGACC-GTTTCTCTTGAAA
266865 GAAAACCATC
Statistics
Matches: 123, Mismatches: 25, Indels: 15
0.75 0.15 0.09
Matches are distributed among these distances:
32 2 0.02
33 73 0.59
34 22 0.18
35 25 0.20
36 1 0.01
ACGTcount: A:0.32, C:0.20, G:0.13, T:0.36
Consensus pattern (33 bp):
TTGAGACCGTTTCTCTTGAAACGAATTAAATCT
Found at i:266845 original size:66 final size:67
Alignment explanation
Indices: 266614--266832 Score: 201
Period size: 70 Copynumber: 3.2 Consensus size: 67
266604 CTTCGAGACA
* * * * ** *
266614 GTTTCTTATGAAACAACAACCAAACTTTGAGATTGTTTACCTTGAAACAAATCTTATTTTCGTTG
1 GTTTCTCATGAAACAACAA-C-ATCTTTGAGATCGTTTCCCTTGAAACAAATC-TATAATCCTTG
266679 A-AACC
63 AGAA-C
* * * * **
266684 GTTTCTCATGAAACAATAACCAAACTTTGAGATTGTTTCTCTTGAAACAAATCTATTTTCCTTGA
1 GTTTCTCATGAAACAACAA-C-ATCTTTGAGATCGTTTCCCTTGAAACAAATCTATAATCCTTGA
*
266749 GACC
64 GAAC
* *
266753 GTTTCTCATGAAACAACAATCATCTTTGAGATCGTTTCCCTTGAAACGAAT-TA-AATCTTTGAG
1 GTTTCTCATGAAACAACAA-CATCTTTGAGATCGTTTCCCTTGAAACAAATCTATAATCCTTGAG
266816 AAC
65 AAC
*
266819 GTTTCTCTTGAAAC
1 GTTTCTCATGAAAC
266833 GAATTAAATC
Statistics
Matches: 131, Mismatches: 17, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
66 22 0.17
67 2 0.02
68 26 0.20
69 31 0.24
70 50 0.38
ACGTcount: A:0.32, C:0.20, G:0.12, T:0.36
Consensus pattern (67 bp):
GTTTCTCATGAAACAACAACATCTTTGAGATCGTTTCCCTTGAAACAAATCTATAATCCTTGAGA
AC
Found at i:267299 original size:43 final size:43
Alignment explanation
Indices: 267251--267346 Score: 129
Period size: 43 Copynumber: 2.2 Consensus size: 43
267241 CCAAAACTCT
* * * *
267251 TCATCACGTATGAGCTGTGTCAACCCTAGATAACCAGCCATCC
1 TCATCACGTAGGAGCTGTATCAAACCTAGATAACCAACCATCC
* *
267294 TCATCACGTAGGAGTTGTATCAAACCTTGATAACCAACCATCC
1 TCATCACGTAGGAGCTGTATCAAACCTAGATAACCAACCATCC
*
267337 TCATCGCGTA
1 TCATCACGTA
267347 AGAACCGAGT
Statistics
Matches: 46, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
43 46 1.00
ACGTcount: A:0.29, C:0.30, G:0.16, T:0.25
Consensus pattern (43 bp):
TCATCACGTAGGAGCTGTATCAAACCTAGATAACCAACCATCC
Found at i:268473 original size:16 final size:16
Alignment explanation
Indices: 268452--268482 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
268442 CCCATAGTGG
268452 GAGAGTTTTCTCTCTT
1 GAGAGTTTTCTCTCTT
268468 GAGAGTTTTCTCTCT
1 GAGAGTTTTCTCTCT
268483 GTGAAATGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.13, C:0.19, G:0.19, T:0.48
Consensus pattern (16 bp):
GAGAGTTTTCTCTCTT
Found at i:273440 original size:16 final size:16
Alignment explanation
Indices: 273408--273441 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
273398 TCTTATAAAA
* *
273408 TTGTTTTCTTTCGTTT
1 TTGTTTTCTTCCCTTT
273424 TTGTTTTCTTCCCTTT
1 TTGTTTTCTTCCCTTT
273440 TT
1 TT
273442 TATTTATTTG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.00, C:0.18, G:0.09, T:0.74
Consensus pattern (16 bp):
TTGTTTTCTTCCCTTT
Found at i:281461 original size:87 final size:87
Alignment explanation
Indices: 281315--281507 Score: 305
Period size: 87 Copynumber: 2.2 Consensus size: 87
281305 CGAGATCGAC
* * *
281315 TCAACTTCACGATGAAAGAGTCATCAGCAACCTAGCTCAACTCAACAACGAGGAACTATTTTTTA
1 TCAACTTCACGATGAAAGAGTCATCAGCAACCTAGCCCAACTCAACAACAAGGAACTATTTTTCA
281380 ACCAAGGTCTTCAAGTCAAATT
66 ACCAAGGTCTTCAAGTCAAATT
* * * * * *
281402 TCAACTTCATGATGAAGGATTCATCCGTAACCTAGCCCAACTCAACAGCAAGGAACTATTTTTCA
1 TCAACTTCACGATGAAAGAGTCATCAGCAACCTAGCCCAACTCAACAACAAGGAACTATTTTTCA
281467 ACCAAGGTCTTCAAGTCAAATT
66 ACCAAGGTCTTCAAGTCAAATT
281489 TCAACTTCACGATGAAAGA
1 TCAACTTCACGATGAAAGA
281508 TATTGGACTA
Statistics
Matches: 95, Mismatches: 11, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
87 95 1.00
ACGTcount: A:0.36, C:0.24, G:0.14, T:0.25
Consensus pattern (87 bp):
TCAACTTCACGATGAAAGAGTCATCAGCAACCTAGCCCAACTCAACAACAAGGAACTATTTTTCA
ACCAAGGTCTTCAAGTCAAATT
Found at i:282378 original size:5 final size:5
Alignment explanation
Indices: 282359--282420 Score: 51
Period size: 5 Copynumber: 13.0 Consensus size: 5
282349 GAGACTTTTA
* * * *
282359 ATTAT ATAAT A-TAT ATTAT AGT-T ATTAT ATTAT ATTAC ATTAT -TTCTT
1 ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATT-AT
282407 ATTAT ATTAT -TTAT
1 ATTAT ATTAT ATTAT
282421 TAAAAATTTA
Statistics
Matches: 45, Mismatches: 8, Indels: 9
0.73 0.13 0.15
Matches are distributed among these distances:
4 12 0.27
5 31 0.69
6 2 0.04
ACGTcount: A:0.37, C:0.03, G:0.02, T:0.58
Consensus pattern (5 bp):
ATTAT
Found at i:285633 original size:23 final size:23
Alignment explanation
Indices: 285602--285646 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
285592 TTTATTTAAT
*
285602 TTTTTATTTAGTAT-TAGTTTATA
1 TTTTAATTT-GTATATAGTTTATA
*
285625 TTTTAATTTGTATATTGTTTAT
1 TTTTAATTTGTATATAGTTTAT
285647 TTAATTAGGG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 4 0.21
23 15 0.79
ACGTcount: A:0.24, C:0.00, G:0.09, T:0.67
Consensus pattern (23 bp):
TTTTAATTTGTATATAGTTTATA
Found at i:299092 original size:13 final size:13
Alignment explanation
Indices: 299055--299113 Score: 64
Period size: 14 Copynumber: 4.3 Consensus size: 13
299045 ATATTTTTAT
299055 TATTTAATTGTTTG
1 TATTTAA-TGTTTG
* *
299069 AATTGTAATGTTAG
1 TATT-TAATGTTTG
299083 TATTTAATGTTTG
1 TATTTAATGTTTG
*
299096 TATTTAATTGTTTT
1 TATTTAA-TGTTTG
299110 TATT
1 TATT
299114 ATTTAGTTTG
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
13 15 0.39
14 20 0.53
15 3 0.08
ACGTcount: A:0.25, C:0.00, G:0.14, T:0.61
Consensus pattern (13 bp):
TATTTAATGTTTG
Found at i:301205 original size:77 final size:77
Alignment explanation
Indices: 301078--301229 Score: 304
Period size: 77 Copynumber: 2.0 Consensus size: 77
301068 CACATTTTGG
301078 TAATCATCTAAAGGATTTTTTTTACAAAAAAAATTAGGTCAGTTCCCCAATCCAGGGCCAAGACA
1 TAATCATCTAAAGGATTTTTTTTACAAAAAAAATTAGGTCAGTTCCCCAATCCAGGGCCAAGACA
301143 TACGTAAGGCTT
66 TACGTAAGGCTT
301155 TAATCATCTAAAGGATTTTTTTTACAAAAAAAATTAGGTCAGTTCCCCAATCCAGGGCCAAGACA
1 TAATCATCTAAAGGATTTTTTTTACAAAAAAAATTAGGTCAGTTCCCCAATCCAGGGCCAAGACA
301220 TACGTAAGGC
66 TACGTAAGGC
301230 CAATTGTGAA
Statistics
Matches: 75, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
77 75 1.00
ACGTcount: A:0.37, C:0.20, G:0.16, T:0.28
Consensus pattern (77 bp):
TAATCATCTAAAGGATTTTTTTTACAAAAAAAATTAGGTCAGTTCCCCAATCCAGGGCCAAGACA
TACGTAAGGCTT
Found at i:302678 original size:15 final size:15
Alignment explanation
Indices: 302658--302709 Score: 61
Period size: 15 Copynumber: 3.5 Consensus size: 15
302648 TCCAGTCACC
302658 GAGTCAACTCGATTT
1 GAGTCAACTCGATTT
* **
302673 GAGTCAAC-CCATCC
1 GAGTCAACTCGATTT
302687 GAGTCAACTCGATTT
1 GAGTCAACTCGATTT
*
302702 GACTCAAC
1 GAGTCAAC
302710 CCGTCTAACT
Statistics
Matches: 29, Mismatches: 7, Indels: 2
0.76 0.18 0.05
Matches are distributed among these distances:
14 11 0.38
15 18 0.62
ACGTcount: A:0.29, C:0.29, G:0.17, T:0.25
Consensus pattern (15 bp):
GAGTCAACTCGATTT
Found at i:302698 original size:29 final size:29
Alignment explanation
Indices: 302656--302739 Score: 107
Period size: 29 Copynumber: 2.9 Consensus size: 29
302646 GATCCAGTCA
302656 CCGAGTCAACTCGATTTGAGTCAACCCAT
1 CCGAGTCAACTCGATTTGAGTCAACCCAT
* *
302685 CCGAGTCAACTCGATTTGACTCAACCCGT
1 CCGAGTCAACTCGATTTGAGTCAACCCAT
** * *
302714 CTAACTCAACTCG-TCTGAGTCAACCC
1 CCGAGTCAACTCGATTTGAGTCAACCC
302740 GTTGAATTTG
Statistics
Matches: 48, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
28 11 0.23
29 37 0.77
ACGTcount: A:0.26, C:0.35, G:0.15, T:0.24
Consensus pattern (29 bp):
CCGAGTCAACTCGATTTGAGTCAACCCAT
Found at i:302722 original size:14 final size:14
Alignment explanation
Indices: 302703--302741 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
302693 ACTCGATTTG
302703 ACTCAACCCGTCTA
1 ACTCAACCCGTCTA
* *
302717 ACTCAACTCGTCTG
1 ACTCAACCCGTCTA
*
302731 AGTCAACCCGT
1 ACTCAACCCGT
302742 TGAATTTGAC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.26, C:0.38, G:0.13, T:0.23
Consensus pattern (14 bp):
ACTCAACCCGTCTA
Found at i:307185 original size:15 final size:14
Alignment explanation
Indices: 307162--307237 Score: 64
Period size: 14 Copynumber: 5.4 Consensus size: 14
307152 TCCAGTCACC
*
307162 GAGTCAACTCGATCT
1 GAGTTAACTCG-TCT
*
307177 GAGTTAACTCGTCC
1 GAGTTAACTCGTCT
*
307191 GAGATAACTCTGTCT
1 GAGTTAACTC-GTCT
* *
307206 GAGTGAACTCGTCC
1 GAGTTAACTCGTCT
* *
307220 GAGTCAACCCG-CT
1 GAGTTAACTCGTCT
307233 GAGTT
1 GAGTT
307238 TGACCGTTAA
Statistics
Matches: 49, Mismatches: 11, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
13 5 0.10
14 23 0.47
15 21 0.43
ACGTcount: A:0.24, C:0.26, G:0.24, T:0.26
Consensus pattern (14 bp):
GAGTTAACTCGTCT
Found at i:307193 original size:29 final size:29
Alignment explanation
Indices: 307160--307227 Score: 95
Period size: 29 Copynumber: 2.3 Consensus size: 29
307150 GGTCCAGTCA
*
307160 CCGAGTCAACTC-GATCTGAGTTAACTCGT
1 CCGAGTCAACTCTG-TCTGAGTGAACTCGT
307189 CCGAGAT-AACTCTGTCTGAGTGAACTCGT
1 CCGAG-TCAACTCTGTCTGAGTGAACTCGT
307218 CCGAGTCAAC
1 CCGAGTCAAC
307228 CCGCTGAGTT
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
28 1 0.03
29 32 0.91
30 2 0.06
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (29 bp):
CCGAGTCAACTCTGTCTGAGTGAACTCGT
Found at i:307200 original size:14 final size:13
Alignment explanation
Indices: 307160--307223 Score: 56
Period size: 15 Copynumber: 4.5 Consensus size: 13
307150 GGTCCAGTCA
307160 CCGAGTCAACTCGAT
1 CCGAGT-AACTCG-T
*
307175 CTGAGTTAACTCGT
1 CCGAG-TAACTCGT
307189 CCGAGATAACTCTGT
1 CCGAG-TAACTC-GT
*
307204 CTGAGTGAACTCGT
1 CCGAGT-AACTCGT
307218 CCGAGT
1 CCGAGT
307224 CAACCCGCTG
Statistics
Matches: 41, Mismatches: 5, Indels: 7
0.77 0.09 0.13
Matches are distributed among these distances:
14 19 0.46
15 21 0.51
16 1 0.02
ACGTcount: A:0.23, C:0.27, G:0.23, T:0.27
Consensus pattern (13 bp):
CCGAGTAACTCGT
Found at i:310753 original size:23 final size:24
Alignment explanation
Indices: 310723--310771 Score: 91
Period size: 23 Copynumber: 2.1 Consensus size: 24
310713 CCTCGTAGCC
310723 AAGGTCAATTGATTCCAC-AGGAT
1 AAGGTCAATTGATTCCACAAGGAT
310746 AAGGTCAATTGATTCCACAAGGAT
1 AAGGTCAATTGATTCCACAAGGAT
310770 AA
1 AA
310772 TTCTGTTCAA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 18 0.72
24 7 0.28
ACGTcount: A:0.39, C:0.16, G:0.20, T:0.24
Consensus pattern (24 bp):
AAGGTCAATTGATTCCACAAGGAT
Found at i:315717 original size:19 final size:20
Alignment explanation
Indices: 315672--315722 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
315662 CTCCTACTGG
315672 GAGTATCGATACTCTACCCC
1 GAGTATCGATACTCTACCCC
* *
315692 CAGTATCGATACTCT-CCGC
1 GAGTATCGATACTCTACCCC
315711 GAGTATCGATAC
1 GAGTATCGATAC
315723 CAAAATTGGA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 14 0.50
20 14 0.50
ACGTcount: A:0.25, C:0.31, G:0.18, T:0.25
Consensus pattern (20 bp):
GAGTATCGATACTCTACCCC
Found at i:318575 original size:29 final size:30
Alignment explanation
Indices: 318521--318585 Score: 73
Period size: 29 Copynumber: 2.2 Consensus size: 30
318511 AATCATTTAC
318521 GATATTAAACTTTCCAAATTTATAT-AA-TG
1 GATATTAAACTTT-CAAATTTATATAAATTG
*
318550 GATATTAAACTTT-AAATTTTCTTATAAATTG
1 GATATTAAACTTTCAAA-TTT-ATATAAATTG
318581 GATAT
1 GATAT
318586 GACAAATTTA
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
27 3 0.10
28 3 0.10
29 16 0.52
30 2 0.06
31 7 0.23
ACGTcount: A:0.40, C:0.08, G:0.08, T:0.45
Consensus pattern (30 bp):
GATATTAAACTTTCAAATTTATATAAATTG
Found at i:322143 original size:22 final size:20
Alignment explanation
Indices: 322095--322145 Score: 57
Period size: 21 Copynumber: 2.5 Consensus size: 20
322085 AGTTCAAAAT
322095 ATTTTTTTATTTTTTATTAA
1 ATTTTTTTATTTTTTATTAA
* **
322115 ATATTTTTGATATTTTTATTTC
1 AT-TTTTTTAT-TTTTTATTAA
322137 ATTTTTTTA
1 ATTTTTTTA
322146 AATAATTATA
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
20 2 0.08
21 13 0.52
22 10 0.40
ACGTcount: A:0.24, C:0.02, G:0.02, T:0.73
Consensus pattern (20 bp):
ATTTTTTTATTTTTTATTAA
Found at i:326786 original size:14 final size:14
Alignment explanation
Indices: 326767--326797 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
326757 GATATTGCCC
326767 CTCCAGTATCGATA
1 CTCCAGTATCGATA
326781 CTCCAGTATCGATA
1 CTCCAGTATCGATA
326795 CTC
1 CTC
326798 AGGGTGACAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.26, C:0.32, G:0.13, T:0.29
Consensus pattern (14 bp):
CTCCAGTATCGATA
Found at i:326818 original size:55 final size:53
Alignment explanation
Indices: 326731--326834 Score: 156
Period size: 55 Copynumber: 1.9 Consensus size: 53
326721 TTAGGCTAGA
*
326731 AGTATCGATACTGCCAGGGGAGTATCGATATTGCCCCTCCAGTATCGATACTCC
1 AGTATCGATACT-CCAGGGGAGTATCAATATTGCCCCTCCAGTATCGATACTCC
326785 AGTATCGATACT-CAGGGTGACAGTATCAATATTGCCCCTCCAGTATCGAT
1 AGTATCGATACTCCAGGG-G--AGTATCAATATTGCCCCTCCAGTATCGAT
326835 TCTCAGAGTG
Statistics
Matches: 46, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
52 5 0.11
53 1 0.02
54 12 0.26
55 28 0.61
ACGTcount: A:0.26, C:0.26, G:0.21, T:0.27
Consensus pattern (53 bp):
AGTATCGATACTCCAGGGGAGTATCAATATTGCCCCTCCAGTATCGATACTCC
Found at i:326840 original size:41 final size:41
Alignment explanation
Indices: 326781--326859 Score: 122
Period size: 41 Copynumber: 1.9 Consensus size: 41
326771 AGTATCGATA
* *
326781 CTCCAGTATCGATACTCAGGGTGACAGTATCAATATTGCCC
1 CTCCAGTATCGATACTCAGAGTGACAATATCAATATTGCCC
* *
326822 CTCCAGTATCGATTCTCAGAGTGACAATATCGATATTG
1 CTCCAGTATCGATACTCAGAGTGACAATATCAATATTG
326860 GACCTCAATT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 34 1.00
ACGTcount: A:0.28, C:0.24, G:0.19, T:0.29
Consensus pattern (41 bp):
CTCCAGTATCGATACTCAGAGTGACAATATCAATATTGCCC
Found at i:334570 original size:23 final size:24
Alignment explanation
Indices: 334538--334599 Score: 90
Period size: 23 Copynumber: 2.6 Consensus size: 24
334528 TTCATTTAAC
*
334538 GTTCGCGAACTTGTTTGTAT-AAT
1 GTTCGCGAACATGTTTGTATAAAT
* *
334561 GTTCGTGAACATGTTTGTTTAAAT
1 GTTCGCGAACATGTTTGTATAAAT
334585 GTTCGCGAACATGTT
1 GTTCGCGAACATGTT
334600 AGTTTAGCAT
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
23 17 0.50
24 17 0.50
ACGTcount: A:0.23, C:0.13, G:0.23, T:0.42
Consensus pattern (24 bp):
GTTCGCGAACATGTTTGTATAAAT
Found at i:334594 original size:24 final size:24
Alignment explanation
Indices: 334538--334605 Score: 93
Period size: 24 Copynumber: 2.9 Consensus size: 24
334528 TTCATTTAAC
* *
334538 GTTCGCGAACTTGTTTGTAT-AAT
1 GTTCGCGAACATGTTTGTTTAAAT
*
334561 GTTCGTGAACATGTTTGTTTAAAT
1 GTTCGCGAACATGTTTGTTTAAAT
*
334585 GTTCGCGAACATGTTAGTTTA
1 GTTCGCGAACATGTTTGTTTA
334606 GCATTCGTGA
Statistics
Matches: 39, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
23 17 0.44
24 22 0.56
ACGTcount: A:0.24, C:0.12, G:0.22, T:0.43
Consensus pattern (24 bp):
GTTCGCGAACATGTTTGTTTAAAT
Found at i:334617 original size:23 final size:23
Alignment explanation
Indices: 334532--334622 Score: 76
Period size: 23 Copynumber: 3.9 Consensus size: 23
334522 TGTTCGTTCA
* * * *
334532 TTTAACGTTCGCGAACTTGTTTG
1 TTTAAAGTTCGTGAACATGTTAG
* * *
334555 TATAATGTTCGTGAACATGTTTG
1 TTTAAAGTTCGTGAACATGTTAG
*
334578 TTTAAATGTTCGCGAACATGTTAG
1 TTTAAA-GTTCGTGAACATGTTAG
*
334602 TTTAGCA-TTCGTGAACATGTT
1 TTTA-AAGTTCGTGAACATGTT
334623 CATGTAGCGT
Statistics
Matches: 56, Mismatches: 10, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
23 36 0.64
24 19 0.34
25 1 0.02
ACGTcount: A:0.24, C:0.13, G:0.21, T:0.42
Consensus pattern (23 bp):
TTTAAAGTTCGTGAACATGTTAG
Found at i:334630 original size:23 final size:23
Alignment explanation
Indices: 334586--334630 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
334576 TGTTTAAATG
*
334586 TTCGCGAACATGTTAGTTTAGCA
1 TTCGCGAACATGTTAGTGTAGCA
*
334609 TTCGTGAACATGTTCA-TGTAGC
1 TTCGCGAACATGTT-AGTGTAGC
334631 GTTCATTTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 18 0.95
24 1 0.05
ACGTcount: A:0.24, C:0.18, G:0.22, T:0.36
Consensus pattern (23 bp):
TTCGCGAACATGTTAGTGTAGCA
Found at i:334668 original size:23 final size:23
Alignment explanation
Indices: 334636--334691 Score: 76
Period size: 23 Copynumber: 2.4 Consensus size: 23
334626 GTAGCGTTCA
*
334636 TTTAACGTTTATGAACATATTCG
1 TTTAACGTTTATGAACATATCCG
* *
334659 TTTAATGTTTATGAACATGTCCG
1 TTTAACGTTTATGAACATATCCG
*
334682 TTTAGCGTTT
1 TTTAACGTTT
334692 GTTTAATGTT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.25, C:0.12, G:0.16, T:0.46
Consensus pattern (23 bp):
TTTAACGTTTATGAACATATCCG
Found at i:337076 original size:12 final size:12
Alignment explanation
Indices: 337059--337107 Score: 71
Period size: 12 Copynumber: 4.0 Consensus size: 12
337049 TTTTAATATT
*
337059 TATCGGGTCGGG
1 TATCGGGCCGGG
337071 TATCGGGCCGGG
1 TATCGGGCCGGG
337083 TATCGGGCCGGG
1 TATCGGGCCGGG
*
337095 TAATCGGGGCGGG
1 T-ATCGGGCCGGG
337108 GATTACCAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
12 24 0.71
13 10 0.29
ACGTcount: A:0.10, C:0.20, G:0.51, T:0.18
Consensus pattern (12 bp):
TATCGGGCCGGG
Found at i:338726 original size:4 final size:4
Alignment explanation
Indices: 338717--338741 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
338707 CATGAAACAC
338717 AATA AATA AATA AATA AATA AATA A
1 AATA AATA AATA AATA AATA AATA A
338742 GGCATAACGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AATA
Found at i:339041 original size:54 final size:55
Alignment explanation
Indices: 338974--339166 Score: 297
Period size: 54 Copynumber: 3.6 Consensus size: 55
338964 CTCTATTTTT
* *
338974 TAGATATATTCGATTTCGGG-CCCTATTTTTATGCTTCTTAATAGCAACAACTGA
1 TAGATATATTCGATTTCGGGCCCCTATTTTTATGCTTATTAATGGCAACAACTGA
* *
339028 TAGATATACTCGATTTCGGGCCCCTA-TTTTATGTTTATTAATGGCAACAACTGA
1 TAGATATATTCGATTTCGGGCCCCTATTTTTATGCTTATTAATGGCAACAACTGA
339082 T--ATATATTCGATTTCGGGACCCCTATTTTTATGCTTATTAATGGCAACAACTGA
1 TAGATATATTCGATTTCGGG-CCCCTATTTTTATGCTTATTAATGGCAACAACTGA
339136 TAGATATATTCGA-TTCGGGACCCCTATTTTT
1 TAGATATATTCGATTTCGGG-CCCCTATTTTT
339167 GGGGCCCTGC
Statistics
Matches: 128, Mismatches: 6, Indels: 9
0.90 0.04 0.06
Matches are distributed among these distances:
52 16 0.12
53 6 0.05
54 73 0.57
55 23 0.18
56 10 0.08
ACGTcount: A:0.27, C:0.19, G:0.16, T:0.39
Consensus pattern (55 bp):
TAGATATATTCGATTTCGGGCCCCTATTTTTATGCTTATTAATGGCAACAACTGA
Found at i:339370 original size:31 final size:31
Alignment explanation
Indices: 339205--339370 Score: 81
Period size: 31 Copynumber: 5.4 Consensus size: 31
339195 CCCTGGTTAT
* * * *
339205 ATGTCCGAAGTGATGATATGAAAAGTTTCA-
1 ATGTCCAAAGTGATGATGTGACAAGTGTCAC
* *
339235 AGTGTCCAAAGTGATGATGTTACATA-TGACAC
1 A-TGTCCAAAGTGATGATGTGACA-AGTGTCAC
* * * *
339267 ATGTCTAAAGTGATGATATAACACA-TGTTAC
1 ATGTCCAAAGTGATGATGTGACA-AGTGTCAC
* * * ** * *
339298 GTGTCC-AAGTGATAATGTGTCTCGT-ACTAT
1 ATGTCCAAAGTGATGATGTGACAAGTGTC-AC
* **
339328 ATATCTGAAGTGATGATGTGACAAGTGTCAC
1 ATGTCCAAAGTGATGATGTGACAAGTGTCAC
339359 ATGTCCAAAGTG
1 ATGTCCAAAGTG
339371 TTGTTATAGA
Statistics
Matches: 94, Mismatches: 35, Indels: 13
0.66 0.25 0.09
Matches are distributed among these distances:
30 17 0.18
31 74 0.79
32 3 0.03
ACGTcount: A:0.33, C:0.14, G:0.22, T:0.31
Consensus pattern (31 bp):
ATGTCCAAAGTGATGATGTGACAAGTGTCAC
Found at i:343737 original size:16 final size:16
Alignment explanation
Indices: 343707--343745 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
343697 TCATATATGC
*
343707 TAGTTTTATAAATGAA
1 TAGTATTATAAATGAA
* *
343723 TATTATTATATATGAA
1 TAGTATTATAAATGAA
343739 TAGTATT
1 TAGTATT
343746 TTATTAAATC
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.41, C:0.00, G:0.10, T:0.49
Consensus pattern (16 bp):
TAGTATTATAAATGAA
Found at i:346401 original size:23 final size:23
Alignment explanation
Indices: 346367--346423 Score: 71
Period size: 23 Copynumber: 2.5 Consensus size: 23
346357 TGTGGCATGT
*
346367 TCTCTG-TCTTTATGGCATGTTTA
1 TCTCTGCT-TTTATGACATGTTTA
*
346390 TCTCTGCTTTTATGACATGTTTT
1 TCTCTGCTTTTATGACATGTTTA
*
346413 TCTCTACTTTT
1 TCTCTGCTTTT
346424 TGGTAGCTTA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
23 29 0.97
24 1 0.03
ACGTcount: A:0.12, C:0.19, G:0.12, T:0.56
Consensus pattern (23 bp):
TCTCTGCTTTTATGACATGTTTA
Found at i:353908 original size:55 final size:54
Alignment explanation
Indices: 353842--354079 Score: 244
Period size: 55 Copynumber: 4.3 Consensus size: 54
353832 CTGAATTAGC
* * * * * *
353842 GATTGAGCACCTCTGTGCATAAATCGAAAGCTAACACCTCTGTGTAGCTAAAACG
1 GATTGAGCACCTATGTGCTTCAACCGAAA-CTGACACCTCTGTGTAGCTAAAACT
* * * *
353897 GATTGAGCACCTTTGTGCTTCAACCGAGAACTGACACCTCTGTGCAGTTAAAAAT
1 GATTGAGCACCTATGTGCTTCAACCGA-AACTGACACCTCTGTGTAGCTAAAACT
* * * * *
353952 GACTGAGCACCTATGTACTTCAGCCGAGAGCTGACACCTCTGTATAGCTAAAACT
1 GATTGAGCACCTATGTGCTTCAACCGA-AACTGACACCTCTGTGTAGCTAAAACT
* * * * *
354007 GATTGAGCACCTCTGTGCTTCAATCTAGAAA-TGATACCTCTGTGTAGCTAAGATT
1 GATTGAGCACCTATGTGCTTCAA-C-CGAAACTGACACCTCTGTGTAGCTAAAACT
354062 GATTGAGCACCTATGTGC
1 GATTGAGCACCTATGTGC
354080 AGCTAAGATT
Statistics
Matches: 151, Mismatches: 29, Indels: 6
0.81 0.16 0.03
Matches are distributed among these distances:
55 145 0.96
56 4 0.03
57 2 0.01
ACGTcount: A:0.29, C:0.24, G:0.21, T:0.27
Consensus pattern (54 bp):
GATTGAGCACCTATGTGCTTCAACCGAAACTGACACCTCTGTGTAGCTAAAACT
Found at i:354000 original size:110 final size:110
Alignment explanation
Indices: 353870--354077 Score: 299
Period size: 110 Copynumber: 1.9 Consensus size: 110
353860 ATAAATCGAA
* * *
353870 AGCTAACACCTCTGTGTAGCTAAAACGGATTGAGCACCTTTGTGCTTCAACCGAGAACTGACACC
1 AGCTAACACCTCTGTATAGCTAAAACGGATTGAGCACCTCTGTGCTTCAACCGAGAAATGACACC
*
353935 TCTGTGCAGTTAAAAATGACTGAGCACCTATGTACTTCAGCCGAG
66 TCTGTGCAGCTAAAAATGACTGAGCACCTATGTACTTCAGCCGAG
* * * * *
353980 AGCTGACACCTCTGTATAGCTAAAACTGATTGAGCACCTCTGTGCTTCAATCTAGAAATGATACC
1 AGCTAACACCTCTGTATAGCTAAAACGGATTGAGCACCTCTGTGCTTCAACCGAGAAATGACACC
* * * *
354045 TCTGTGTAGCTAAGATTGATTGAGCACCTATGT
66 TCTGTGCAGCTAAAAATGACTGAGCACCTATGT
354078 GCAGCTAAGA
Statistics
Matches: 85, Mismatches: 13, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
110 85 1.00
ACGTcount: A:0.29, C:0.24, G:0.20, T:0.27
Consensus pattern (110 bp):
AGCTAACACCTCTGTATAGCTAAAACGGATTGAGCACCTCTGTGCTTCAACCGAGAAATGACACC
TCTGTGCAGCTAAAAATGACTGAGCACCTATGTACTTCAGCCGAG
Found at i:354153 original size:26 final size:28
Alignment explanation
Indices: 354042--354161 Score: 163
Period size: 28 Copynumber: 4.4 Consensus size: 28
354032 TAGAAATGAT
*
354042 ACCTCTGTGTAGCTAAGATTGATTGAGC
1 ACCTCTGTGCAGCTAAGATTGATTGAGC
*
354070 ACCTATGTGCAGCTAAGATTGATTGAGC
1 ACCTCTGTGCAGCTAAGATTGATTGAGC
* *
354098 ATCTCTATGCAGCTAAGATTGATTGAGC
1 ACCTCTGTGCAGCTAAGATTGATTGAGC
* *
354126 ACCTCTGTGTA-TTAAGA-TGATTGAGC
1 ACCTCTGTGCAGCTAAGATTGATTGAGC
*
354152 ACATCTGTGC
1 ACCTCTGTGC
354162 TACAATCTAA
Statistics
Matches: 81, Mismatches: 11, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
26 17 0.21
27 5 0.06
28 59 0.73
ACGTcount: A:0.27, C:0.18, G:0.23, T:0.32
Consensus pattern (28 bp):
ACCTCTGTGCAGCTAAGATTGATTGAGC
Found at i:364102 original size:31 final size:31
Alignment explanation
Indices: 364045--364103 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 31
364035 AATTATTTGA
* * *
364045 AATATTTGTTATTATGGTTTCGTTTTTTCTT
1 AATATTTATTATTATGGCTTCATTTTTTCTT
364076 AATATTTATTATTATGAGCTT-ATTTTTT
1 AATATTTATTATTATG-GCTTCATTTTTT
364104 AATATTTGTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
31 21 0.88
32 3 0.12
ACGTcount: A:0.22, C:0.05, G:0.10, T:0.63
Consensus pattern (31 bp):
AATATTTATTATTATGGCTTCATTTTTTCTT
Found at i:364222 original size:28 final size:29
Alignment explanation
Indices: 364177--364254 Score: 79
Period size: 28 Copynumber: 2.7 Consensus size: 29
364167 TGCCAATATT
* *
364177 TTTTCTAACATTTGTTATTAAAG-GTCTAA
1 TTTT-TAATATTTGTTATTAAAGTGTCCAA
* *
364206 TTTTTAATATTTATTA-TCAAGTGTCCAA
1 TTTTTAATATTTGTTATTAAAGTGTCCAA
364234 TTTATTCAATATTTGTTATTA
1 TTT-TT-AATATTTGTTATTA
364255 GGGGCATACT
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
27 4 0.10
28 18 0.46
29 6 0.15
30 10 0.26
31 1 0.03
ACGTcount: A:0.31, C:0.09, G:0.08, T:0.53
Consensus pattern (29 bp):
TTTTTAATATTTGTTATTAAAGTGTCCAA
Found at i:366231 original size:55 final size:55
Alignment explanation
Indices: 366157--366267 Score: 188
Period size: 55 Copynumber: 2.0 Consensus size: 55
366147 TTTCACTAAC
*
366157 ATTTTTATTTAATAGTATATTAAAATATATTAGAGTGAGGTAATACCCTCAATCA
1 ATTTTTATTTAACAGTATATTAAAATATATTAGAGTGAGGTAATACCCTCAATCA
*
366212 ATTTTTATTTAACCA-TATATTAAAGTATATTAGAGTGAGGTAATACCCTCAATCA
1 ATTTTTATTTAA-CAGTATATTAAAATATATTAGAGTGAGGTAATACCCTCAATCA
366267 A
1 A
366268 GTGCCATAGC
Statistics
Matches: 53, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
55 52 0.98
56 1 0.02
ACGTcount: A:0.40, C:0.11, G:0.11, T:0.39
Consensus pattern (55 bp):
ATTTTTATTTAACAGTATATTAAAATATATTAGAGTGAGGTAATACCCTCAATCA
Found at i:367694 original size:11 final size:11
Alignment explanation
Indices: 367678--367707 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
367668 TTATTTTTTA
367678 TTATATTATAT
1 TTATATTATAT
367689 TTATATTATAT
1 TTATATTATAT
367700 TTA-ATTAT
1 TTATATTAT
367708 TTGAATAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 5 0.26
11 14 0.74
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (11 bp):
TTATATTATAT
Found at i:367697 original size:16 final size:15
Alignment explanation
Indices: 367667--367700 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
367657 ATAAGGTAAA
*
367667 ATTATTTTTTATTAT
1 ATTATTTTATATTAT
367682 ATTATATTTATATTAT
1 ATTAT-TTTATATTAT
367698 ATT
1 ATT
367701 TAATTATTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 5 0.29
16 12 0.71
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (15 bp):
ATTATTTTATATTAT
Found at i:370552 original size:17 final size:18
Alignment explanation
Indices: 370519--370554 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
370509 AGAAAACGAT
370519 ACAACTCAAACAATAAAA
1 ACAACTCAAACAATAAAA
*
370537 ACAACT-AAATAATAAAA
1 ACAACTCAAACAATAAAA
370554 A
1 A
370555 TATTTCAAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 11 0.65
18 6 0.35
ACGTcount: A:0.69, C:0.17, G:0.00, T:0.14
Consensus pattern (18 bp):
ACAACTCAAACAATAAAA
Found at i:370590 original size:26 final size:26
Alignment explanation
Indices: 370532--370590 Score: 91
Period size: 26 Copynumber: 2.3 Consensus size: 26
370522 ACTCAAACAA
370532 TAAAAACAACTAAATAATAAAAATAT
1 TAAAAACAACTAAATAATAAAAATAT
** *
370558 TTCAAACAATTAAATAATAAAAATAT
1 TAAAAACAACTAAATAATAAAAATAT
370584 TAAAAAC
1 TAAAAAC
370591 CCAAATAAAT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.66, C:0.08, G:0.00, T:0.25
Consensus pattern (26 bp):
TAAAAACAACTAAATAATAAAAATAT
Found at i:372914 original size:18 final size:19
Alignment explanation
Indices: 372891--372939 Score: 55
Period size: 18 Copynumber: 2.5 Consensus size: 19
372881 TAAAATTAGT
372891 ATAATAAAATTGAATAA-A
1 ATAATAAAATTGAATAATA
* *
372909 ATAATAAATTATTGATTAATT
1 ATAATAAA--ATTGAATAATA
372930 ATAATAAAAT
1 ATAATAAAAT
372940 AAAAATATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
18 8 0.31
19 2 0.08
20 8 0.31
21 8 0.31
ACGTcount: A:0.59, C:0.00, G:0.04, T:0.37
Consensus pattern (19 bp):
ATAATAAAATTGAATAATA
Found at i:373937 original size:19 final size:19
Alignment explanation
Indices: 373913--373958 Score: 83
Period size: 19 Copynumber: 2.4 Consensus size: 19
373903 AATTCAAGTT
373913 CAAATCGAGGTGTAATATG
1 CAAATCGAGGTGTAATATG
373932 CAAATCGAGGTGTAATATG
1 CAAATCGAGGTGTAATATG
*
373951 CAACTCGA
1 CAAATCGA
373959 ATAACTCAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.37, C:0.15, G:0.24, T:0.24
Consensus pattern (19 bp):
CAAATCGAGGTGTAATATG
Found at i:377609 original size:26 final size:26
Alignment explanation
Indices: 377556--377609 Score: 65
Period size: 26 Copynumber: 2.1 Consensus size: 26
377546 GCCAACTCTG
*
377556 TTATCATACCATGATAATTATGACAT
1 TTATCATACCATGATAATTATGAAAT
**
377582 TTATCATATGATGA-AATTATGAGAAT
1 TTATCATACCATGATAATTATGA-AAT
377608 TT
1 TT
377610 CATAGAAATG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 8 0.33
26 16 0.67
ACGTcount: A:0.39, C:0.09, G:0.11, T:0.41
Consensus pattern (26 bp):
TTATCATACCATGATAATTATGAAAT
Found at i:384571 original size:26 final size:27
Alignment explanation
Indices: 384526--384577 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 27
384516 AAAAATAAAT
384526 AAATTAAATTAAAATGAAGA-AAAAAC
1 AAATTAAATTAAAATGAAGATAAAAAC
*
384552 AAATTAAA-TAAAATATAAGATAAAAA
1 AAATTAAATTAAAAT-GAAGATAAAAA
384578 AAGCAAAGAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
25 6 0.26
26 12 0.52
27 5 0.22
ACGTcount: A:0.71, C:0.02, G:0.06, T:0.21
Consensus pattern (27 bp):
AAATTAAATTAAAATGAAGATAAAAAC
Found at i:384687 original size:9 final size:9
Alignment explanation
Indices: 384606--384737 Score: 51
Period size: 9 Copynumber: 14.4 Consensus size: 9
384596 AAGTAATATA
384606 AAAAATATAT
1 AAAAATA-AT
*
384616 AAAAA-AAG
1 AAAAATAAT
* *
384624 AAAAAGAAG
1 AAAAATAAT
384633 AAAAA-ATAT
1 AAAAATA-AT
*
384642 ATAAATAA-
1 AAAAATAAT
384650 AATAAATAA-
1 AA-AAATAAT
*
384659 AATAATAAT
1 AAAAATAAT
* *
384668 -AAAACAGT
1 AAAAATAAT
384676 AAAAATAAT
1 AAAAATAAT
384685 AAATATATAA-
1 AAA-A-ATAAT
*
384695 AATAAAAAAT
1 AA-AAATAAT
*
384705 AAAAATAGT
1 AAAAATAAT
*
384714 AAATATATAT
1 AAAAATA-AT
*
384724 ATAAATTAAT
1 A-AAAATAAT
384734 AAAA
1 AAAA
384738 TGGATAATAA
Statistics
Matches: 93, Mismatches: 17, Indels: 25
0.69 0.13 0.19
Matches are distributed among these distances:
8 18 0.19
9 49 0.53
10 17 0.18
11 9 0.10
ACGTcount: A:0.73, C:0.01, G:0.04, T:0.23
Consensus pattern (9 bp):
AAAAATAAT
Found at i:384705 original size:20 final size:19
Alignment explanation
Indices: 384633--384711 Score: 54
Period size: 20 Copynumber: 3.8 Consensus size: 19
384623 GAAAAAGAAG
*
384633 AAAAAATATATAAATAAAAT
1 AAAAAATAAAT-AATAAAAT
384653 AAATAAA-ATAATAATAAAACAGT
1 AAA-AAATA-AATAAT-AAA-A-T
384676 AAAAATAATAAATATATAAAAT
1 -AAAA-AATAAATA-ATAAAAT
384698 AAAAAATAAA-AATA
1 AAAAAATAAATAATA
384712 GTAAATATAT
Statistics
Matches: 49, Mismatches: 1, Indels: 20
0.70 0.01 0.29
Matches are distributed among these distances:
18 3 0.06
19 1 0.02
20 13 0.27
21 12 0.24
22 2 0.04
23 3 0.06
24 12 0.24
25 3 0.06
ACGTcount: A:0.75, C:0.01, G:0.01, T:0.23
Consensus pattern (19 bp):
AAAAAATAAATAATAAAAT
Found at i:384810 original size:20 final size:19
Alignment explanation
Indices: 384785--384831 Score: 51
Period size: 19 Copynumber: 2.4 Consensus size: 19
384775 CTAAAAAAAT
384785 AAAAATATATACTAAA-GTAA
1 AAAAATATATA--AAATGTAA
**
384805 AAAAATGCATAAAATGTAA
1 AAAAATATATAAAATGTAA
384824 AAAAATAT
1 AAAAATAT
384832 TACATGAAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 3
0.76 0.14 0.10
Matches are distributed among these distances:
18 3 0.14
19 10 0.45
20 9 0.41
ACGTcount: A:0.66, C:0.04, G:0.06, T:0.23
Consensus pattern (19 bp):
AAAAATATATAAAATGTAA
Found at i:385371 original size:37 final size:37
Alignment explanation
Indices: 385319--385465 Score: 249
Period size: 37 Copynumber: 4.0 Consensus size: 37
385309 GCTTGTGGAA
* * *
385319 CCTATTTTCATGAGTTTGAATCATAGTAAAACTCTAT
1 CCTATTTTTAGGAGTTTGAATCCTAGTAAAACTCTAT
385356 CCTATTTTTAGGAGTTTGAATCCTAGTAAAACTCTAT
1 CCTATTTTTAGGAGTTTGAATCCTAGTAAAACTCTAT
*
385393 CATATTTTTAGGAGTTTGAATCCTAGTAAAACTCTAT
1 CCTATTTTTAGGAGTTTGAATCCTAGTAAAACTCTAT
*
385430 CCTATTTTTAGGAGTTTGAATCCTACTAAAACTCTA
1 CCTATTTTTAGGAGTTTGAATCCTAGTAAAACTCTA
385466 ACATTTGTTT
Statistics
Matches: 104, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 104 1.00
ACGTcount: A:0.31, C:0.16, G:0.12, T:0.40
Consensus pattern (37 bp):
CCTATTTTTAGGAGTTTGAATCCTAGTAAAACTCTAT
Found at i:386148 original size:34 final size:34
Alignment explanation
Indices: 386072--386185 Score: 174
Period size: 34 Copynumber: 3.3 Consensus size: 34
386062 AAGGTCTTGG
*
386072 GTTTCAAGAGAAACATTTTCAAAGGTTTTTTTTTTGT
1 GTTTCAAGAGAAACAATTTCAAAGG---TTTTTTTGT
386109 GTTTCAAGAGAAACAATTTCAAAGGTTTTTTTGT
1 GTTTCAAGAGAAACAATTTCAAAGGTTTTTTTGT
* *
386143 ATTTCAAGAGAAACAATTTCAAAGGTTTTTTCGT
1 GTTTCAAGAGAAACAATTTCAAAGGTTTTTTTGT
386177 GTTTCAAGA
1 GTTTCAAGA
386186 TAAATTGTCT
Statistics
Matches: 73, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
34 49 0.67
37 24 0.33
ACGTcount: A:0.32, C:0.10, G:0.17, T:0.42
Consensus pattern (34 bp):
GTTTCAAGAGAAACAATTTCAAAGGTTTTTTTGT
Found at i:386329 original size:37 final size:36
Alignment explanation
Indices: 386243--386349 Score: 187
Period size: 37 Copynumber: 2.9 Consensus size: 36
386233 CAAAGATTGG
386243 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
* *
386279 TGTTTCAACGGAAACTGTCTCAAGAGAGACAAGATTT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAA-AATT
386316 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
386350 CTTGGAAATT
Statistics
Matches: 66, Mismatches: 4, Indels: 2
0.92 0.06 0.03
Matches are distributed among these distances:
36 32 0.48
37 34 0.52
ACGTcount: A:0.38, C:0.15, G:0.22, T:0.24
Consensus pattern (36 bp):
TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
Found at i:387666 original size:33 final size:32
Alignment explanation
Indices: 387562--387656 Score: 136
Period size: 32 Copynumber: 2.9 Consensus size: 32
387552 ATTCCCAAAG
*
387562 ATGCCCCAATATTTGATGTTGAATCTCAAAAA
1 ATGCCCCAACATTTGATGTTGAATCTCAAAAA
* *
387594 ATACCCCAACATTTGATGTTAAATCTCAAAAA
1 ATGCCCCAACATTTGATGTTGAATCTCAAAAA
* *
387626 ATGCCTCAGCATTTGATGTTGAATCTTCAAA
1 ATGCCCCAACATTTGATGTTGAATC-TCAAA
387657 GATGCCCTCA
Statistics
Matches: 55, Mismatches: 7, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
32 50 0.91
33 5 0.09
ACGTcount: A:0.37, C:0.20, G:0.12, T:0.32
Consensus pattern (32 bp):
ATGCCCCAACATTTGATGTTGAATCTCAAAAA
Found at i:388754 original size:27 final size:28
Alignment explanation
Indices: 388704--388777 Score: 91
Period size: 29 Copynumber: 2.6 Consensus size: 28
388694 TTGTCTTTTT
388704 TTTTCTTCAATTTT-TCTTTGTTTTTTCTC
1 TTTTCTT--ATTTTCTCTTTGTTTTTTCTC
388733 -TTT-TTATTTTCTCTTTGCTTTTTTCTC
1 TTTTCTTATTTTCTCTTTG-TTTTTTCTC
*
388760 TTTTCTTTTTTTCTCTTT
1 TTTTCTTATTTTCTCTTT
388778 TTGTTCTTGA
Statistics
Matches: 40, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
25 5 0.12
26 6 0.15
27 11 0.28
28 6 0.15
29 12 0.30
ACGTcount: A:0.04, C:0.18, G:0.03, T:0.76
Consensus pattern (28 bp):
TTTTCTTATTTTCTCTTTGTTTTTTCTC
Found at i:388756 original size:14 final size:13
Alignment explanation
Indices: 388714--388777 Score: 69
Period size: 13 Copynumber: 4.8 Consensus size: 13
388704 TTTTCTTCAA
388714 TTTT-TCTTTGTT
1 TTTTCTCTTTGTT
388726 TTTTCTCTTT-TT
1 TTTTCTCTTTGTT
388738 ATTTTCTCTTTGCTT
1 -TTTTCTCTTTG-TT
*
388753 TTTTCTCTTTTCTTT
1 TTTTCTC-TTT-GTT
388768 TTTTCTCTTT
1 TTTTCTCTTT
388778 TTGTTCTTGA
Statistics
Matches: 45, Mismatches: 1, Indels: 10
0.80 0.02 0.18
Matches are distributed among these distances:
12 6 0.13
13 15 0.33
14 10 0.22
15 14 0.31
ACGTcount: A:0.02, C:0.17, G:0.03, T:0.78
Consensus pattern (13 bp):
TTTTCTCTTTGTT
Found at i:388765 original size:7 final size:7
Alignment explanation
Indices: 388726--388778 Score: 54
Period size: 7 Copynumber: 7.6 Consensus size: 7
388716 TTTCTTTGTT
388726 TTTTCTC
1 TTTTCTC
*
388733 TTTT-TA
1 TTTTCTC
388739 TTTTCTC
1 TTTTCTC
* *
388746 TTTGCTT
1 TTTTCTC
388753 TTTTCTC
1 TTTTCTC
*
388760 TTTTCTTT
1 TTTTC-TC
388768 TTTTCTC
1 TTTTCTC
388775 TTTT
1 TTTT
388779 TGTTCTTGAT
Statistics
Matches: 36, Mismatches: 8, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
6 5 0.14
7 25 0.69
8 6 0.17
ACGTcount: A:0.02, C:0.19, G:0.02, T:0.77
Consensus pattern (7 bp):
TTTTCTC
Found at i:388771 original size:15 final size:15
Alignment explanation
Indices: 388724--388778 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 15
388714 TTTTTCTTTG
388724 TTTTTTCTC-TTT-T
1 TTTTTTCTCTTTTCT
* *
388737 TATTTTCTCTTTGC-
1 TTTTTTCTCTTTTCT
388751 TTTTTTCTCTTTTCT
1 TTTTTTCTCTTTTCT
388766 TTTTTTCTCTTTT
1 TTTTTTCTCTTTT
388779 TGTTCTTGAT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
13 8 0.23
14 14 0.40
15 13 0.37
ACGTcount: A:0.02, C:0.18, G:0.02, T:0.78
Consensus pattern (15 bp):
TTTTTTCTCTTTTCT
Found at i:389119 original size:16 final size:16
Alignment explanation
Indices: 389100--389133 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
389090 GTAATTAATG
389100 CATGATAGAATTATTT
1 CATGATAGAATTATTT
389116 CATGATAGAATTATTT
1 CATGATAGAATTATTT
389132 CA
1 CA
389134 AGTGAATTCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.38, C:0.09, G:0.12, T:0.41
Consensus pattern (16 bp):
CATGATAGAATTATTT
Found at i:389428 original size:23 final size:22
Alignment explanation
Indices: 389397--389445 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 22
389387 AAACTTGGTC
*
389397 TTTTTGGT-AATAACCATGAGTTA
1 TTTTGGGTAAATAACCA--AGTTA
*
389420 TTTTGGGTAAATAATCAAGTTA
1 TTTTGGGTAAATAACCAAGTTA
389442 TTTT
1 TTTT
389446 ATTTTGGGGT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
22 9 0.39
23 7 0.30
24 7 0.30
ACGTcount: A:0.31, C:0.06, G:0.16, T:0.47
Consensus pattern (22 bp):
TTTTGGGTAAATAACCAAGTTA
Found at i:391920 original size:27 final size:27
Alignment explanation
Indices: 391877--391979 Score: 90
Period size: 27 Copynumber: 3.8 Consensus size: 27
391867 ATTAAAATGA
391877 ATAAAAACAAAT-TAAATAAAAGATAAG
1 ATAAAAA-AAATATAAATAAAAGATAAG
* *
391904 ATAAAAAAAGATA-AAATAGTAAG-TAAT
1 ATAAAAAAA-ATATAAATA-AAAGATAAG
*
391931 ATAAAAAAATATATAAA-AAAAGAAAAAG
1 ATAAAAAAA-ATATAAATAAAAG-ATAAG
391959 A-AGAAAAAAATATAAATAAAA
1 ATA-AAAAAAATATAAATAAAA
391980 CATATAAATA
Statistics
Matches: 62, Mismatches: 6, Indels: 15
0.75 0.07 0.18
Matches are distributed among these distances:
26 5 0.08
27 38 0.61
28 19 0.31
ACGTcount: A:0.74, C:0.01, G:0.08, T:0.17
Consensus pattern (27 bp):
ATAAAAAAAATATAAATAAAAGATAAG
Found at i:391951 original size:13 final size:13
Alignment explanation
Indices: 391929--392005 Score: 52
Period size: 13 Copynumber: 5.9 Consensus size: 13
391919 ATAGTAAGTA
391929 ATAT-AAAAAAAT
1 ATATAAAAAAAAT
*
391941 ATATAAAAAAAGAA
1 ATATAAAAAAA-AT
* *
391955 AAAGAAGAAAAAA-
1 ATATAA-AAAAAAT
* *
391968 ATATAAATAAAAC
1 ATATAAAAAAAAT
*
391981 ATATAAATAAAAT
1 ATATAAAAAAAAT
391994 A-ATAATAAAAAA
1 ATATAA-AAAAAA
392006 GTAAAAATAA
Statistics
Matches: 52, Mismatches: 8, Indels: 9
0.75 0.12 0.13
Matches are distributed among these distances:
12 13 0.25
13 28 0.54
14 6 0.12
15 5 0.10
ACGTcount: A:0.77, C:0.01, G:0.04, T:0.18
Consensus pattern (13 bp):
ATATAAAAAAAAT
Found at i:392723 original size:37 final size:37
Alignment explanation
Indices: 392673--392817 Score: 263
Period size: 37 Copynumber: 3.9 Consensus size: 37
392663 TTGTGGAACC
392673 TATTTTTAGGAGTTTGAATCATAGTAAAACTCTATCA
1 TATTTTTAGGAGTTTGAATCATAGTAAAACTCTATCA
*
392710 TATTTTTAGGAGTTTGAATCATAGTAAAACTCTATCC
1 TATTTTTAGGAGTTTGAATCATAGTAAAACTCTATCA
392747 TATTTTTAGGAGTTTGAATCATAGTAAAACTCTATCA
1 TATTTTTAGGAGTTTGAATCATAGTAAAACTCTATCA
* *
392784 TATTTTTAGGAGTTTGAATCCTACTAAAACTCTA
1 TATTTTTAGGAGTTTGAATCATAGTAAAACTCTA
392818 ACGTTTGTTT
Statistics
Matches: 104, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
37 104 1.00
ACGTcount: A:0.34, C:0.12, G:0.13, T:0.41
Consensus pattern (37 bp):
TATTTTTAGGAGTTTGAATCATAGTAAAACTCTATCA
Found at i:394023 original size:15 final size:15
Alignment explanation
Indices: 394005--394066 Score: 76
Period size: 15 Copynumber: 4.3 Consensus size: 15
393995 ATACAAAAAT
394005 ATATTATATATATTG
1 ATATTATATATATTG
394020 ATATTAT-T-TATT-
1 ATATTATATATATTG
* *
394032 ATAATATAATATATTT
1 ATATTAT-ATATATTG
394048 ATATTATATATATTG
1 ATATTATATATATTG
394063 ATAT
1 ATAT
394067 AATTTATTAT
Statistics
Matches: 40, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
12 6 0.15
13 4 0.10
14 2 0.05
15 22 0.55
16 6 0.15
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (15 bp):
ATATTATATATATTG
Found at i:394056 original size:43 final size:43
Alignment explanation
Indices: 394004--394094 Score: 173
Period size: 43 Copynumber: 2.1 Consensus size: 43
393994 TATACAAAAA
*
394004 TATATTATATATATTGATATTATTTATTATAATATAATATATT
1 TATATTATATATATTGATATAATTTATTATAATATAATATATT
394047 TATATTATATATATTGATATAATTTATTATAATATAATATATT
1 TATATTATATATATTGATATAATTTATTATAATATAATATATT
394090 TATAT
1 TATAT
394095 GATTTATTCT
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 47 1.00
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (43 bp):
TATATTATATATATTGATATAATTTATTATAATATAATATATT
Found at i:394066 original size:28 final size:28
Alignment explanation
Indices: 394012--394094 Score: 80
Period size: 28 Copynumber: 3.0 Consensus size: 28
394002 AATATATTAT
* *
394012 ATATATTGATATTATTTAT-TATAATATA
1 ATATATTTATATTATATATAT-TAATATA
*
394040 ATATATTTATATTATATATATTGATATA
1 ATATATTTATATTATATATATTAATATA
* * *
394068 ATTTA-TTATAATATAATATATTTATAT
1 ATATATTTATATTAT-ATATATTAATAT
394095 GATTTATTCT
Statistics
Matches: 47, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
27 8 0.17
28 38 0.81
29 1 0.02
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.54
Consensus pattern (28 bp):
ATATATTTATATTATATATATTAATATA
Found at i:394081 original size:15 final size:14
Alignment explanation
Indices: 394002--394094 Score: 60
Period size: 15 Copynumber: 7.0 Consensus size: 14
393992 CATATACAAA
394002 AATATATTATATAT
1 AATATATTATATAT
*
394016 ATTGATATTAT-T-T
1 AAT-ATATTATATAT
394029 -AT-TA-TA-ATAT
1 AATATATTATATAT
394039 AATATATT-TATATT
1 AATATATTATATA-T
*
394053 ATATATATT-GATAT
1 A-ATATATTATATAT
*
394067 AATTTATTATAATAT
1 AATATATTAT-ATAT
394082 AATATATT-TATAT
1 AATATATTATATAT
394095 GATTTATTCT
Statistics
Matches: 62, Mismatches: 6, Indels: 23
0.68 0.07 0.25
Matches are distributed among these distances:
9 3 0.05
10 3 0.05
11 2 0.03
12 3 0.05
13 15 0.24
14 8 0.13
15 28 0.45
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (14 bp):
AATATATTATATAT
Found at i:394099 original size:28 final size:27
Alignment explanation
Indices: 394035--394102 Score: 82
Period size: 28 Copynumber: 2.4 Consensus size: 27
394025 ATTTATTATA
* *
394035 ATATAATATATTTATATTATATATATTG
1 ATATAATTTA-TTATAATATATATATTG
*
394063 ATATAATTTATTATAATATAATATATTT
1 ATATAATTTATTATAATAT-ATATATTG
*
394091 ATATGATTTATT
1 ATATAATTTATT
394103 CTATAGAAAT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
27 8 0.23
28 27 0.77
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (27 bp):
ATATAATTTATTATAATATATATATTG
Found at i:394101 original size:9 final size:8
Alignment explanation
Indices: 394003--394101 Score: 56
Period size: 9 Copynumber: 11.2 Consensus size: 8
393993 ATATACAAAA
394003 ATATATTAT
1 ATATATT-T
*
394012 ATATATTG
1 ATATATTT
394020 ATATTATTT
1 ATA-TATTT
*
394029 ATTATAATATA
1 A-TAT-AT-TT
394040 ATATATTT
1 ATATATTT
*
394048 ATAT-TAT
1 ATATATTT
*
394055 ATATATTG
1 ATATATTT
394063 ATATAATTT
1 ATAT-ATTT
*
394072 ATTATAATATA
1 A-TAT-AT-TT
394083 ATATATTT
1 ATATATTT
394091 ATATGATTT
1 ATAT-ATTT
394100 AT
1 AT
394102 TCTATAGAAA
Statistics
Matches: 71, Mismatches: 10, Indels: 18
0.72 0.10 0.18
Matches are distributed among these distances:
7 6 0.08
8 18 0.25
9 27 0.38
10 16 0.23
11 4 0.06
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (8 bp):
ATATATTT
Found at i:394113 original size:28 final size:28
Alignment explanation
Indices: 394055--394119 Score: 69
Period size: 28 Copynumber: 2.3 Consensus size: 28
394045 TTTATATTAT
*
394055 ATATATTGATATAATTTATTATAATATA
1 ATATATTGATATAATTTATTATAATAAA
* * *
394083 ATATATTTATATGATTTATTCT-ATAGAA
1 ATATATTGATATAATTTATTATAATA-AA
394111 ATATCATTG
1 ATAT-ATTG
394120 GGTTATGATA
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
27 3 0.10
28 24 0.80
29 3 0.10
ACGTcount: A:0.42, C:0.03, G:0.06, T:0.49
Consensus pattern (28 bp):
ATATATTGATATAATTTATTATAATAAA
Found at i:395548 original size:25 final size:26
Alignment explanation
Indices: 395509--395565 Score: 73
Period size: 25 Copynumber: 2.2 Consensus size: 26
395499 TTCAAAAACT
*
395509 TTCATATTTCATTTTTTAC-TTTCATA
1 TTCATATTTCA-TTTTCACATTTCATA
*
395535 TTCATA-TTCATTTTCACATTTCATT
1 TTCATATTTCATTTTCACATTTCATA
395560 TTCATA
1 TTCATA
395566 GCCCAATGTA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
24 6 0.21
25 16 0.57
26 6 0.21
ACGTcount: A:0.25, C:0.18, G:0.00, T:0.58
Consensus pattern (26 bp):
TTCATATTTCATTTTCACATTTCATA
Found at i:395550 original size:12 final size:13
Alignment explanation
Indices: 395508--395565 Score: 66
Period size: 13 Copynumber: 4.5 Consensus size: 13
395498 TTTCAAAAAC
395508 TTTCATATTTCAT
1 TTTCATATTTCAT
*
395521 TTT-TTACTTTCAT
1 TTTCATA-TTTCAT
*
395534 ATTCATA-TTCAT
1 TTTCATATTTCAT
*
395546 TTTCACATTTCAT
1 TTTCATATTTCAT
395559 TTTCATA
1 TTTCATA
395566 GCCCAATGTA
Statistics
Matches: 36, Mismatches: 6, Indels: 6
0.75 0.12 0.12
Matches are distributed among these distances:
12 12 0.33
13 22 0.61
14 2 0.06
ACGTcount: A:0.24, C:0.17, G:0.00, T:0.59
Consensus pattern (13 bp):
TTTCATATTTCAT
Found at i:397238 original size:10 final size:10
Alignment explanation
Indices: 397223--397247 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
397213 TAATCACAAC
397223 ATCAAATTCA
1 ATCAAATTCA
397233 ATCAAATTCA
1 ATCAAATTCA
397243 ATCAA
1 ATCAA
397248 CCTTTATAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.52, C:0.20, G:0.00, T:0.28
Consensus pattern (10 bp):
ATCAAATTCA
Found at i:399560 original size:13 final size:13
Alignment explanation
Indices: 399542--399573 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
399532 CTAAACTTAA
399542 TGGTTTTATTATT
1 TGGTTTTATTATT
399555 TGGTTTTATTATT
1 TGGTTTTATTATT
399568 TGGTTT
1 TGGTTT
399574 CTCATTTAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.12, C:0.00, G:0.19, T:0.69
Consensus pattern (13 bp):
TGGTTTTATTATT
Found at i:405419 original size:21 final size:23
Alignment explanation
Indices: 405394--405437 Score: 65
Period size: 21 Copynumber: 2.0 Consensus size: 23
405384 ATTTAACAAA
405394 AAGGGGGAG-AAGTTTT-AAAGT
1 AAGGGGGAGTAAGTTTTCAAAGT
*
405415 AAGGGGGAGTAATTTTTCAAAGT
1 AAGGGGGAGTAAGTTTTCAAAGT
405438 TGATTTCAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 9 0.45
22 6 0.30
23 5 0.25
ACGTcount: A:0.36, C:0.02, G:0.34, T:0.27
Consensus pattern (23 bp):
AAGGGGGAGTAAGTTTTCAAAGT
Found at i:405920 original size:64 final size:63
Alignment explanation
Indices: 405794--405948 Score: 233
Period size: 64 Copynumber: 2.4 Consensus size: 63
405784 CACTCACCAT
*
405794 ATCGAATGCATTTTATGCATCAATGCACTACCATGCATCGATGCACTCAGGTTTTATGAAAAC
1 ATCGAATGCATTTTATGCATCAATGCACAACCATGCATCGATGCACTCAGGTTTTATGAAAAC
* *
405857 ATCGAATGCATTTTATGAATCGATGCACAAACCATGCATCGATGCACTCAGGCTTGTT-T-AAAA
1 ATCGAATGCATTTTATGCATCAATGCAC-AACCATGCATCGATGCACTCAGG-TT-TTATGAAAA
405920 C
63 C
*
405921 ATCGAAAGCATTTTATGCATCAATGCAC
1 ATCGAATGCATTTTATGCATCAATGCAC
405949 TCTTAGTGTA
Statistics
Matches: 83, Mismatches: 6, Indels: 5
0.88 0.06 0.05
Matches are distributed among these distances:
63 26 0.31
64 52 0.63
65 3 0.04
66 2 0.02
ACGTcount: A:0.33, C:0.22, G:0.16, T:0.29
Consensus pattern (63 bp):
ATCGAATGCATTTTATGCATCAATGCACAACCATGCATCGATGCACTCAGGTTTTATGAAAAC
Found at i:409055 original size:37 final size:37
Alignment explanation
Indices: 409005--409079 Score: 141
Period size: 37 Copynumber: 2.0 Consensus size: 37
408995 AACTTTCTCT
409005 CCACGATAATTCTTTCTTCAGGATGACTATATTGCTG
1 CCACGATAATTCTTTCTTCAGGATGACTATATTGCTG
*
409042 CCACGATAATTCTTTCTTCGGGATGACTATATTGCTG
1 CCACGATAATTCTTTCTTCAGGATGACTATATTGCTG
409079 C
1 C
409080 TACTTGCTCC
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.23, C:0.23, G:0.17, T:0.37
Consensus pattern (37 bp):
CCACGATAATTCTTTCTTCAGGATGACTATATTGCTG
Found at i:414147 original size:21 final size:22
Alignment explanation
Indices: 414108--414148 Score: 59
Period size: 21 Copynumber: 1.9 Consensus size: 22
414098 ATAAATCATC
414108 CATAAAATTTCATAGTTTAAAA
1 CATAAAATTTCATAGTTTAAAA
414130 CATAAACATTT-A-AGTTTAA
1 CATAAA-ATTTCATAGTTTAA
414149 CAAAAGAGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 7 0.39
22 7 0.39
23 4 0.22
ACGTcount: A:0.49, C:0.10, G:0.05, T:0.37
Consensus pattern (22 bp):
CATAAAATTTCATAGTTTAAAA
Found at i:414508 original size:22 final size:22
Alignment explanation
Indices: 414482--414535 Score: 72
Period size: 22 Copynumber: 2.5 Consensus size: 22
414472 CCATCAAATA
* *
414482 ACTAAAGTGCCACATCACTGGT
1 ACTAAAGTGCCACAGCACTGAT
*
414504 ACTAAAGTGCCTCAGCACTGAT
1 ACTAAAGTGCCACAGCACTGAT
*
414526 ACGAAAGTGC
1 ACTAAAGTGC
414536 ATTATATCTA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.33, C:0.26, G:0.20, T:0.20
Consensus pattern (22 bp):
ACTAAAGTGCCACAGCACTGAT
Found at i:416463 original size:30 final size:30
Alignment explanation
Indices: 416427--416500 Score: 139
Period size: 30 Copynumber: 2.5 Consensus size: 30
416417 TTCCTACAGA
*
416427 TTTCAAATTGGTCCCTTAACCTTTCTATGC
1 TTTCAAATTGGTCCCTTAACCTTTCCATGC
416457 TTTCAAATTGGTCCCTTAACCTTTCCATGC
1 TTTCAAATTGGTCCCTTAACCTTTCCATGC
416487 TTTCAAATTGGTCC
1 TTTCAAATTGGTCC
416501 AAACAACATT
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
30 43 1.00
ACGTcount: A:0.20, C:0.27, G:0.11, T:0.42
Consensus pattern (30 bp):
TTTCAAATTGGTCCCTTAACCTTTCCATGC
Found at i:422501 original size:104 final size:103
Alignment explanation
Indices: 422302--422521 Score: 287
Period size: 104 Copynumber: 2.1 Consensus size: 103
422292 TGACATTCTA
* * * *
422302 TTCGACACAATTATCAATATAAATTGTGATGAATTTTTTGGCACTAAAAATATACTTTGTGACCA
1 TTCGACACTATTATCAATAGAAATTGTGATAAATTTTTTGACACTAAAAATATACTTTGTGACCA
* *
422367 TCAATATTATCACATTAAGTATTTTTAGTGACCAAATG
66 CCAATATTATCACACTAAGTATTTTTAGTGACCAAATG
* * * * * * *
422405 TTCGATACTATTATCAATAGAAATTGTGATAAATTTATTTGACAGTGAACATATATTTTGTGGCG
1 TTCGACACTATTATCAATAGAAATTGTGATAAATTT-TTTGACACTAAAAATATACTTTGTGACC
* * *
422470 ACCAATCTTGTCACACTAAGTGTTTTTAGTGACCAAATG
65 ACCAATATTATCACACTAAGTATTTTTAGTGACCAAATG
422509 TTCGACACTATTA
1 TTCGACACTATTA
422522 GGAATAACTC
Statistics
Matches: 99, Mismatches: 17, Indels: 1
0.85 0.15 0.01
Matches are distributed among these distances:
103 32 0.32
104 67 0.68
ACGTcount: A:0.35, C:0.14, G:0.14, T:0.38
Consensus pattern (103 bp):
TTCGACACTATTATCAATAGAAATTGTGATAAATTTTTTGACACTAAAAATATACTTTGTGACCA
CCAATATTATCACACTAAGTATTTTTAGTGACCAAATG
Found at i:422947 original size:14 final size:14
Alignment explanation
Indices: 422928--422960 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
422918 TTCTAGAAGA
*
422928 TCCAGTTAGCAGCG
1 TCCAGTCAGCAGCG
422942 TCCAGTCAGCAGCG
1 TCCAGTCAGCAGCG
422956 TCCAG
1 TCCAG
422961 AAAATGAATG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.21, C:0.33, G:0.27, T:0.18
Consensus pattern (14 bp):
TCCAGTCAGCAGCG
Found at i:423721 original size:13 final size:12
Alignment explanation
Indices: 423701--423735 Score: 52
Period size: 12 Copynumber: 2.8 Consensus size: 12
423691 CATATTGCAT
423701 TTTCTTTTAAAA
1 TTTCTTTTAAAA
*
423713 TTTCTTTTTAAA
1 TTTCTTTTAAAA
423725 TTTCGTTTTAA
1 TTTC-TTTTAA
423736 TCTTCTTTGA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
12 15 0.75
13 5 0.25
ACGTcount: A:0.26, C:0.09, G:0.03, T:0.63
Consensus pattern (12 bp):
TTTCTTTTAAAA
Found at i:424181 original size:15 final size:17
Alignment explanation
Indices: 424149--424186 Score: 53
Period size: 15 Copynumber: 2.3 Consensus size: 17
424139 ACGCAACCCT
424149 TTTTTTTATTTTGTTCAA
1 TTTTTTTA-TTTGTTCAA
424167 TTTTTTTA-TTG-TCAA
1 TTTTTTTATTTGTTCAA
424182 TTTTT
1 TTTTT
424187 ATTTTTTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
15 9 0.45
16 3 0.15
18 8 0.40
ACGTcount: A:0.16, C:0.05, G:0.05, T:0.74
Consensus pattern (17 bp):
TTTTTTTATTTGTTCAA
Found at i:424201 original size:15 final size:15
Alignment explanation
Indices: 424181--424222 Score: 57
Period size: 15 Copynumber: 2.7 Consensus size: 15
424171 TTTATTGTCA
*
424181 ATTTTTATTTTTTTTT
1 ATTTTT-TTTGTTTTT
424197 ATTTTTTTTGTTTTT
1 ATTTTTTTTGTTTTT
424212 ATTTTTCTTTG
1 ATTTTT-TTTG
424223 AATTTTTAGG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
15 14 0.58
16 10 0.42
ACGTcount: A:0.10, C:0.02, G:0.05, T:0.83
Consensus pattern (15 bp):
ATTTTTTTTGTTTTT
Found at i:424228 original size:25 final size:25
Alignment explanation
Indices: 424182--424229 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
424172 TTATTGTCAA
* *
424182 TTTTTATTTTTTTTTATTTTTTTTG
1 TTTTTATTTTTTTTGATATTTTTTG
424207 TTTTTATTTTTCTTTGA-ATTTTT
1 TTTTTATTTTT-TTTGATATTTTT
424230 AGGTACCTCG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
25 16 0.80
26 4 0.20
ACGTcount: A:0.10, C:0.02, G:0.04, T:0.83
Consensus pattern (25 bp):
TTTTTATTTTTTTTGATATTTTTTG
Found at i:424632 original size:7 final size:8
Alignment explanation
Indices: 424617--424648 Score: 55
Period size: 8 Copynumber: 3.9 Consensus size: 8
424607 GAACAATGAG
424617 AGAAAAAA
1 AGAAAAAA
424625 AGAAAAAA
1 AGAAAAAA
424633 AGAAAAAA
1 AGAAAAAA
424641 AGAGAAAA
1 AGA-AAAA
424649 GGATAAAGCT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 19 0.83
9 4 0.17
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (8 bp):
AGAAAAAA
Done.