Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007782.1 Hibiscus syriacus cultivar Beakdansim tig00110065_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: 3900615
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 19
Found at i:405521 original size:26 final size:26
Alignment explanation
Indices: 405485--405538 Score: 72
Period size: 26 Copynumber: 2.1 Consensus size: 26
405475 CTTATTCCAG
* **
405485 TAGCTGGTTTGATCAACTAATTTGAT
1 TAGCTGATTTGAGAAACTAATTTGAT
*
405511 TAGCTGATTTGAGAAACTGATTTGAT
1 TAGCTGATTTGAGAAACTAATTTGAT
405537 TA
1 TA
405539 ACTGTTTATA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.30, C:0.09, G:0.20, T:0.41
Consensus pattern (26 bp):
TAGCTGATTTGAGAAACTAATTTGAT
Found at i:424740 original size:23 final size:23
Alignment explanation
Indices: 424714--424777 Score: 92
Period size: 23 Copynumber: 2.8 Consensus size: 23
424704 AGCTCATATA
424714 AATTGCACCGAAGTGCCACGTAG
1 AATTGCACCGAAGTGCCACGTAG
* * *
424737 AATTGTACCGTAGTGCCGCGTAG
1 AATTGCACCGAAGTGCCACGTAG
*
424760 AAATGCACCGAAGTGCCA
1 AATTGCACCGAAGTGCCA
424778 TATAAGGTTG
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.30, C:0.25, G:0.27, T:0.19
Consensus pattern (23 bp):
AATTGCACCGAAGTGCCACGTAG
Found at i:429661 original size:23 final size:23
Alignment explanation
Indices: 429634--429687 Score: 72
Period size: 23 Copynumber: 2.3 Consensus size: 23
429624 AGTTGTACCA
*
429634 AAGTGCCACATAGAATTGCACCG
1 AAGTGCCACATAGAAATGCACCG
* * *
429657 TAGTGCCGCGTAGAAATGCACCG
1 AAGTGCCACATAGAAATGCACCG
429680 AAGTGCCA
1 AAGTGCCA
429688 TATAAGGTTG
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.31, C:0.26, G:0.26, T:0.17
Consensus pattern (23 bp):
AAGTGCCACATAGAAATGCACCG
Found at i:435960 original size:18 final size:18
Alignment explanation
Indices: 435937--435971 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
435927 TTTAATAAGT
435937 TATTTTAAAAATTTCAAG
1 TATTTTAAAAATTTCAAG
*
435955 TATTTTAATAATTTCAA
1 TATTTTAAAAATTTCAA
435972 TTTAAGAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.43, C:0.06, G:0.03, T:0.49
Consensus pattern (18 bp):
TATTTTAAAAATTTCAAG
Found at i:446338 original size:39 final size:39
Alignment explanation
Indices: 446284--446362 Score: 124
Period size: 39 Copynumber: 2.0 Consensus size: 39
446274 AAATTGTAGC
*
446284 CATAATGTTGATTCTGGTGAGAA-GAGTTACTCTAGTTTG
1 CATAATGTTGATTCTGGTGA-AAGGAGATACTCTAGTTTG
*
446323 CATAATGTTGATTCTGGTGAAAGGAGATACTTTAGTTTG
1 CATAATGTTGATTCTGGTGAAAGGAGATACTCTAGTTTG
446362 C
1 C
446363 GTGCTGCACC
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
38 2 0.05
39 35 0.95
ACGTcount: A:0.27, C:0.10, G:0.25, T:0.38
Consensus pattern (39 bp):
CATAATGTTGATTCTGGTGAAAGGAGATACTCTAGTTTG
Found at i:452022 original size:37 final size:37
Alignment explanation
Indices: 451972--452047 Score: 134
Period size: 37 Copynumber: 2.1 Consensus size: 37
451962 TTTATTTAGA
451972 TTATTAGTTGTTTTAAAGCTAATTTAGTTGCATGTAG
1 TTATTAGTTGTTTTAAAGCTAATTTAGTTGCATGTAG
* *
452009 TTATTAGTTGTTTTAAAGTTTATTTAGTTGCATGTAG
1 TTATTAGTTGTTTTAAAGCTAATTTAGTTGCATGTAG
452046 TT
1 TT
452048 TATTTAATTG
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.25, C:0.04, G:0.18, T:0.53
Consensus pattern (37 bp):
TTATTAGTTGTTTTAAAGCTAATTTAGTTGCATGTAG
Found at i:452037 original size:20 final size:19
Alignment explanation
Indices: 451975--452038 Score: 53
Period size: 20 Copynumber: 3.4 Consensus size: 19
451965 ATTTAGATTA
*
451975 TTAGTTGTTTTAAAGCTAAT
1 TTAGTTGTTTTAAAG-TTAT
* *
451995 TTAGTTGCATGT--AGTTA-
1 TTAGTTG-TTTTAAAGTTAT
452012 TTAGTTGTTTTAAAGTTTAT
1 TTAGTTGTTTTAAAG-TTAT
452032 TTAGTTG
1 TTAGTTG
452039 CATGTAGTTT
Statistics
Matches: 34, Mismatches: 5, Indels: 10
0.69 0.10 0.20
Matches are distributed among these distances:
16 2 0.06
17 7 0.21
18 4 0.12
19 5 0.15
20 14 0.41
21 2 0.06
ACGTcount: A:0.25, C:0.03, G:0.19, T:0.53
Consensus pattern (19 bp):
TTAGTTGTTTTAAAGTTAT
Found at i:452047 original size:19 final size:19
Alignment explanation
Indices: 451993--452064 Score: 78
Period size: 19 Copynumber: 3.8 Consensus size: 19
451983 TTTAAAGCTA
451993 ATTTAGTTGCATGTAG-TT
1 ATTTAGTTGCATGTAGTTT
* *
452011 A-TTAGTTG-TTTTAAAGTTT
1 ATTTAGTTGCATGT--AGTTT
452030 ATTTAGTTGCATGTAGTTT
1 ATTTAGTTGCATGTAGTTT
*
452049 ATTTAATTGCATGTAG
1 ATTTAGTTGCATGTAG
452065 CCATTTGCAT
Statistics
Matches: 44, Mismatches: 5, Indels: 9
0.76 0.09 0.16
Matches are distributed among these distances:
16 2 0.05
17 7 0.16
18 3 0.07
19 23 0.52
20 7 0.16
21 2 0.05
ACGTcount: A:0.25, C:0.04, G:0.19, T:0.51
Consensus pattern (19 bp):
ATTTAGTTGCATGTAGTTT
Found at i:452074 original size:14 final size:14
Alignment explanation
Indices: 452055--452084 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
452045 GTTTATTTAA
452055 TTGCATGTAGCCAT
1 TTGCATGTAGCCAT
452069 TTGCATGTAGCCAT
1 TTGCATGTAGCCAT
452083 TT
1 TT
452085 AGTTGCATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.20, C:0.20, G:0.20, T:0.40
Consensus pattern (14 bp):
TTGCATGTAGCCAT
Found at i:456603 original size:39 final size:39
Alignment explanation
Indices: 456549--456627 Score: 124
Period size: 39 Copynumber: 2.0 Consensus size: 39
456539 AAATTGTAGC
*
456549 CATAATGTTGATTCTGGTGAGAA-GAGTTACTCTAGTTTG
1 CATAATGTTGATTCTGGTGA-AAGGAGATACTCTAGTTTG
*
456588 CATAATGTTGATTCTGGTGAAAGGAGATACTTTAGTTTG
1 CATAATGTTGATTCTGGTGAAAGGAGATACTCTAGTTTG
456627 C
1 C
456628 GTGCTGCACC
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
38 2 0.05
39 35 0.95
ACGTcount: A:0.27, C:0.10, G:0.25, T:0.38
Consensus pattern (39 bp):
CATAATGTTGATTCTGGTGAAAGGAGATACTCTAGTTTG
Found at i:462294 original size:37 final size:37
Alignment explanation
Indices: 462244--462319 Score: 134
Period size: 37 Copynumber: 2.1 Consensus size: 37
462234 TTTATTTAGA
462244 TTATTAGTTGTTTTAAAGCTAATTTAGTTGCATGTAG
1 TTATTAGTTGTTTTAAAGCTAATTTAGTTGCATGTAG
* *
462281 TTATTAGTTGTTTTAAAGTTTATTTAGTTGCATGTAG
1 TTATTAGTTGTTTTAAAGCTAATTTAGTTGCATGTAG
462318 TT
1 TT
462320 TATTTAATTG
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.25, C:0.04, G:0.18, T:0.53
Consensus pattern (37 bp):
TTATTAGTTGTTTTAAAGCTAATTTAGTTGCATGTAG
Found at i:462309 original size:20 final size:19
Alignment explanation
Indices: 462247--462310 Score: 53
Period size: 20 Copynumber: 3.4 Consensus size: 19
462237 ATTTAGATTA
*
462247 TTAGTTGTTTTAAAGCTAAT
1 TTAGTTGTTTTAAAG-TTAT
* *
462267 TTAGTTGCATGT--AGTTA-
1 TTAGTTG-TTTTAAAGTTAT
462284 TTAGTTGTTTTAAAGTTTAT
1 TTAGTTGTTTTAAAG-TTAT
462304 TTAGTTG
1 TTAGTTG
462311 CATGTAGTTT
Statistics
Matches: 34, Mismatches: 5, Indels: 10
0.69 0.10 0.20
Matches are distributed among these distances:
16 2 0.06
17 7 0.21
18 4 0.12
19 5 0.15
20 14 0.41
21 2 0.06
ACGTcount: A:0.25, C:0.03, G:0.19, T:0.53
Consensus pattern (19 bp):
TTAGTTGTTTTAAAGTTAT
Found at i:462319 original size:19 final size:18
Alignment explanation
Indices: 462265--462350 Score: 77
Period size: 19 Copynumber: 4.7 Consensus size: 18
462255 TTTAAAGCTA
462265 ATTTAGTTGCATGTAGTT
1 ATTTAGTTGCATGTAGTT
* *
462283 A-TTAGTTG-TTTTAAAGTTT
1 ATTTAGTTGCATGT--AG-TT
462302 ATTTAGTTGCATGTAGTTT
1 ATTTAGTTGCATGTAG-TT
* **
462321 ATTTAATTGCATGTAGCC
1 ATTTAGTTGCATGTAGTT
462339 ATTTAGTTGCAT
1 ATTTAGTTGCAT
462351 ATGGTGGTGT
Statistics
Matches: 55, Mismatches: 8, Indels: 10
0.75 0.11 0.14
Matches are distributed among these distances:
16 2 0.04
17 7 0.13
18 14 0.25
19 23 0.42
20 7 0.13
21 2 0.04
ACGTcount: A:0.24, C:0.07, G:0.19, T:0.50
Consensus pattern (18 bp):
ATTTAGTTGCATGTAGTT
Found at i:467439 original size:194 final size:194
Alignment explanation
Indices: 467108--467490 Score: 543
Period size: 194 Copynumber: 2.0 Consensus size: 194
467098 ATTGAAATTT
* * *
467108 GTATCGATACTTTTCTAAGTATATGCACCAAATTATCGATACTTTAGGAATTTAAAAAAATTGCA
1 GTATCGATACTTTTATAAGTATATGCACCAAAGTATCGATACTTCAGGAATTTAAAAAAATTGCA
* * * *
467173 ATAATAACACCTATAAAGTATCAATACTTTATAAACATGTATCAATACATGACTATATAACATGT
66 ATAATAACACCTATAAAGTATCAATACTTTAGAAACATGTATCAATACATAACAATATAACAAGT
*
467238 AAAAATATGACAAAACCAGTTTCAATAT-AACAAAATCAGTAAAGCGCTACCAGATATGTTGAAG
131 AAAAATATGACAAAACCAGTTTCAATATGAA-AAAACCAGTAAAGCGCTACCAGATATGTTGAAG
* * * * *
467302 GTATCGATACTTTTATAAGTATATGTATCATAGTATCGATACTTCAGGAATTTAAAAGAATTGTA
1 GTATCGATACTTTTATAAGTATATGCACCAAAGTATCGATACTTCAGGAATTTAAAAAAATTGCA
* *** * *
467367 ATAGTAGTGCCTATAAAGTATCGATACTTTAGAAACATGTATCGATACATAACAATATAACAAGT
66 ATAATAACACCTATAAAGTATCAATACTTTAGAAACATGTATCAATACATAACAATATAACAAGT
* * * *
467432 TAAAATATGACAAAACCGGTTTCAATATGAAAAAACCGGTAAAGCGCTACCGGATATGT
131 AAAAATATGACAAAACCAGTTTCAATATGAAAAAACCAGTAAAGCGCTACCAGATATGT
467491 CAAACTTCAA
Statistics
Matches: 165, Mismatches: 23, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
194 163 0.99
195 2 0.01
ACGTcount: A:0.43, C:0.14, G:0.13, T:0.30
Consensus pattern (194 bp):
GTATCGATACTTTTATAAGTATATGCACCAAAGTATCGATACTTCAGGAATTTAAAAAAATTGCA
ATAATAACACCTATAAAGTATCAATACTTTAGAAACATGTATCAATACATAACAATATAACAAGT
AAAAATATGACAAAACCAGTTTCAATATGAAAAAACCAGTAAAGCGCTACCAGATATGTTGAAG
Found at i:467526 original size:194 final size:194
Alignment explanation
Indices: 467109--467539 Score: 494
Period size: 194 Copynumber: 2.2 Consensus size: 194
467099 TTGAAATTTG
* * * * * * * *
467109 TATCGATACTTTTCTAAGTATATGCACCAAATTATCGATACTTTAGGAATTTAAAAAAATTGCAA
1 TATCGATACTTTTATAAGTAAACGTATCATAGTATCGATACTTCAGGAATTTAAAAAAATTGCAA
* * * *
467174 TAATAACACCTATAAAGTATCAATACTTTATAAACATGTATCAATACATGACTATATAACATGTA
66 TAATAACACCTATAAAGTATCAATACTTTAGAAACATGTATCAATACATAACAATATAACAAGTA
* * **
467239 AAAATATGACAAAACCAGTTTCAATATAACAAAATCAGTAAAGCGCTACCAGATATGTTGAAGG
131 AAAATATGACAAAACCAGTTTCAATATAACAAAACCAGTAAAGCGCTACCAGATATGTTCAAAC
* * * *
467303 TATCGATACTTTTATAAGTATATGTATCATAGTATCGATACTTCAGGAATTTAAAAGAATTGTAA
1 TATCGATACTTTTATAAGTAAACGTATCATAGTATCGATACTTCAGGAATTTAAAAAAATTGCAA
* *** * * *
467368 TAGTAGTGCCTATAAAGTATCGATACTTTAGAAACATGTATCGATACATAACAATATAACAAGTT
66 TAATAACACCTATAAAGTATCAATACTTTAGAAACATGTATCAATACATAACAATATAACAAGTA
* * *
467433 AAAATATGACAAAACCGGTTTCAATATGAA-AAAACCGGTAAAGCGCTACCGGATATG-TCAAAC
131 AAAATATGACAAAACCAGTTTCAATAT-AACAAAACCAGTAAAGCGCTACCAGATATGTTCAAAC
* *
467496 T-TC-A-ACCTTTTATATTGTTAAAACGTATCATATTATCGATACTT
1 TATCGATA-CTTTTATA-AG-T-AAACGTATCATAGTATCGATACTT
467540 TAAAGGAAAA
Statistics
Matches: 202, Mismatches: 30, Indels: 10
0.83 0.12 0.04
Matches are distributed among these distances:
190 1 0.00
191 9 0.04
192 3 0.01
193 5 0.02
194 182 0.90
195 2 0.01
ACGTcount: A:0.42, C:0.15, G:0.12, T:0.31
Consensus pattern (194 bp):
TATCGATACTTTTATAAGTAAACGTATCATAGTATCGATACTTCAGGAATTTAAAAAAATTGCAA
TAATAACACCTATAAAGTATCAATACTTTAGAAACATGTATCAATACATAACAATATAACAAGTA
AAAATATGACAAAACCAGTTTCAATATAACAAAACCAGTAAAGCGCTACCAGATATGTTCAAAC
Found at i:468197 original size:229 final size:225
Alignment explanation
Indices: 467800--468259 Score: 613
Period size: 229 Copynumber: 2.0 Consensus size: 225
467790 ATACGTTGTC
* * * * *
467800 GAAACCCTAGTTTTTTATTATTACAATAATCGAAAATAGGGGTTTTATGGGTTTTAGGTTTTCGA
1 GAAACCCTAGTTTTTTAGTATTACAATAATCGAAAATAGGGGGTTTATGAGTTTGAGGATTTCGA
* *
467865 AGTAAAAAAAGCATTTGTGACCGATTACAGGAATAAAGTGATATTCTAGGTAGAAAATAAATATC
66 AGTAAAAAAAGCATTTGGGACCGATTACAGGAATAAAGTGATATTATAGGTAGAAAATAAATATC
* * * *
467930 GATACTTTTATAAAATATTGTAGGTAGAAAATGATATTGTAGGTTGTATAAATCTACTGATACTT
131 AATACTTGTACAAAATATTATAGGTAGAAAATGATATTGTAGGTTGTATAAATCTACTGATACTT
*
467995 GTAGTAGAGATTATTCTC-ATTCGTTTGAAG
196 GTAGTAGAGAGTATTC-CGATTCGTTTGAAG
* *
468025 GAAACCCTAGTTTTTTAGTATTACAGTAATC-ATAAATAGGGATTAGGGTTTATGAGTTTGGGGA
1 GAAACCCTAGTTTTTTAGTATTACAATAATCGA-AAATA-GG----GGGTTTATGAGTTTGAGGA
* * * * *
468089 TTTCGAAG-CAAAGAAGGATTTGGGACCGATTAGAGTTAA-AAAGTGATATTATAGGTAGAAAAT
60 TTTCGAAGTAAAAAAAGCATTTGGGACCGATTACAG-GAATAAAGTGATATTATAGGTAGAAAAT
* * *
468152 AAATATCAATACTTGTACATAATATTATAGGTAGAAAATGATATTGTAGGTTGTATAAATGTATT
124 AAATATCAATACTTGTACAAAATATTATAGGTAGAAAATGATATTGTAGGTTGTATAAATCTACT
*
468217 GATACTTGTAGTAGAGAGTATTCCGATTCTTTTGAAG
189 GATACTTGTAGTAGAGAGTATTCCGATTCGTTTGAAG
468254 GAAACC
1 GAAACC
468260 ATTTTACTAT
Statistics
Matches: 204, Mismatches: 23, Indels: 12
0.85 0.10 0.05
Matches are distributed among these distances:
224 1 0.00
225 34 0.17
226 2 0.01
228 1 0.00
229 142 0.70
230 24 0.12
ACGTcount: A:0.36, C:0.08, G:0.21, T:0.35
Consensus pattern (225 bp):
GAAACCCTAGTTTTTTAGTATTACAATAATCGAAAATAGGGGGTTTATGAGTTTGAGGATTTCGA
AGTAAAAAAAGCATTTGGGACCGATTACAGGAATAAAGTGATATTATAGGTAGAAAATAAATATC
AATACTTGTACAAAATATTATAGGTAGAAAATGATATTGTAGGTTGTATAAATCTACTGATACTT
GTAGTAGAGAGTATTCCGATTCGTTTGAAG
Found at i:469851 original size:21 final size:21
Alignment explanation
Indices: 469827--469870 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
469817 CAGAAGAGGA
* *
469827 AGAGGAGGAAGAGGAGAAGGT
1 AGAGAAGGAAGAAGAGAAGGT
469848 AGAGAAGGAAGAAGAGAAGGT
1 AGAGAAGGAAGAAGAGAAGGT
469869 AG
1 AG
469871 TAGGGGGATG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.48, C:0.00, G:0.48, T:0.05
Consensus pattern (21 bp):
AGAGAAGGAAGAAGAGAAGGT
Found at i:471839 original size:212 final size:212
Alignment explanation
Indices: 471472--471895 Score: 839
Period size: 212 Copynumber: 2.0 Consensus size: 212
471462 GGTCAACGTA
471472 TGATTTGGTAAGTGGAATGAAAAATTAGTTTGCAGTTAAAATGTTAAAAGTCGTAGATTGAATGT
1 TGATTTGGTAAGTGGAATGAAAAATTAGTTTGCAGTTAAAATGTTAAAAGTCGTAGATTGAATGT
471537 TGTGGTTAACATACTGACAATTTTAATATAGGTTGGAAAATTGGATCATATGAGAATATTAAACG
66 TGTGGTTAACATACTGACAATTTTAATATAGGTTGGAAAATTGGATCATATGAGAATATTAAACG
*
471602 ATCTCATAAGCCACTATCAAAATACACGGAGAGATGTGGTGACAATGGCTTCCATCAGACACATG
131 ATCTCATAAACCACTATCAAAATACACGGAGAGATGTGGTGACAATGGCTTCCATCAGACACATG
471667 TACGATTTTGTAAATTT
196 TACGATTTTGTAAATTT
471684 TGATTTGGTAAGTGGAATGAAAAATTAGTTTGCAGTTAAAATGTTAAAAGTCGTAGATTGAATGT
1 TGATTTGGTAAGTGGAATGAAAAATTAGTTTGCAGTTAAAATGTTAAAAGTCGTAGATTGAATGT
471749 TGTGGTTAACATACTGACAATTTTAATATAGGTTGGAAAATTGGATCATATGAGAATATTAAACG
66 TGTGGTTAACATACTGACAATTTTAATATAGGTTGGAAAATTGGATCATATGAGAATATTAAACG
471814 ATCTCATAAACCACTATCAAAATACACGGAGAGATGTGGTGACAATGGCTTCCATCAGACACATG
131 ATCTCATAAACCACTATCAAAATACACGGAGAGATGTGGTGACAATGGCTTCCATCAGACACATG
471879 TACGATTTTGTAAATTT
196 TACGATTTTGTAAATTT
471896 CTTTTATGGT
Statistics
Matches: 211, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
212 211 1.00
ACGTcount: A:0.37, C:0.11, G:0.21, T:0.32
Consensus pattern (212 bp):
TGATTTGGTAAGTGGAATGAAAAATTAGTTTGCAGTTAAAATGTTAAAAGTCGTAGATTGAATGT
TGTGGTTAACATACTGACAATTTTAATATAGGTTGGAAAATTGGATCATATGAGAATATTAAACG
ATCTCATAAACCACTATCAAAATACACGGAGAGATGTGGTGACAATGGCTTCCATCAGACACATG
TACGATTTTGTAAATTT
Found at i:472339 original size:2 final size:2
Alignment explanation
Indices: 472332--472391 Score: 120
Period size: 2 Copynumber: 30.0 Consensus size: 2
472322 TTATTATGCC
472332 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
472374 AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT
472392 TATTTAATAG
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 58 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:472664 original size:6 final size:6
Alignment explanation
Indices: 472649--472685 Score: 53
Period size: 6 Copynumber: 6.7 Consensus size: 6
472639 TAATAAAATC
472649 ATTT-T ATTTCT ATTTCT ATTTCT ATTTC- ATTT-T ATTT
1 ATTTCT ATTTCT ATTTCT ATTTCT ATTTCT ATTTCT ATTT
472686 ATTTTTTATT
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
5 12 0.40
6 18 0.60
ACGTcount: A:0.19, C:0.11, G:0.00, T:0.70
Consensus pattern (6 bp):
ATTTCT
Found at i:475109 original size:21 final size:21
Alignment explanation
Indices: 475062--475113 Score: 77
Period size: 21 Copynumber: 2.5 Consensus size: 21
475052 GCTAAATAAA
* *
475062 GATGACGACATTACAGATGAT
1 GATGATGACGTTACAGATGAT
*
475083 GATGATGACGTTATAGATGAT
1 GATGATGACGTTACAGATGAT
475104 GATGATGACG
1 GATGATGACG
475114 ATGAAGATCC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.35, C:0.10, G:0.29, T:0.27
Consensus pattern (21 bp):
GATGATGACGTTACAGATGAT
Found at i:475121 original size:21 final size:21
Alignment explanation
Indices: 475076--475121 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
475066 ACGACATTAC
*
475076 AGATGATGATGATGACGTTAT
1 AGATGATGATGATGACGTGAT
475097 AGATGATGATGATGACGATGA-
1 AGATGATGATGATGACG-TGAT
475118 AGAT
1 AGAT
475122 CCAAACAAGT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 21 0.91
22 2 0.09
ACGTcount: A:0.37, C:0.04, G:0.30, T:0.28
Consensus pattern (21 bp):
AGATGATGATGATGACGTGAT
Found at i:476260 original size:15 final size:15
Alignment explanation
Indices: 476240--476269 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
476230 AGACAAAAAA
476240 AACATTGTTATGTAT
1 AACATTGTTATGTAT
*
476255 AACATTGTTTTGTAT
1 AACATTGTTATGTAT
476270 GCATATTTGG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.30, C:0.07, G:0.13, T:0.50
Consensus pattern (15 bp):
AACATTGTTATGTAT
Found at i:476553 original size:30 final size:30
Alignment explanation
Indices: 476519--476631 Score: 127
Period size: 30 Copynumber: 3.8 Consensus size: 30
476509 TGCAGTTTTC
* *
476519 AATTTTAATTTTAATTTTAATTTTAATTTG
1 AATTTTAATTTCAATTTCAATTTTAATTTG
* * *
476549 AATTTCATTTTCAATTTTAATTTTAATTTG
1 AATTTTAATTTCAATTTCAATTTTAATTTG
* * * *
476579 AGTTTCAATTTCAATATCAATTTTAATTCG
1 AATTTTAATTTCAATTTCAATTTTAATTTG
* *
476609 AGTTTGAATTTCAATTTCAATTT
1 AATTTTAATTTCAATTTCAATTT
476632 CGGCTCCACT
Statistics
Matches: 73, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 73 1.00
ACGTcount: A:0.32, C:0.07, G:0.05, T:0.56
Consensus pattern (30 bp):
AATTTTAATTTCAATTTCAATTTTAATTTG
Found at i:476615 original size:36 final size:36
Alignment explanation
Indices: 476515--476629 Score: 122
Period size: 36 Copynumber: 3.2 Consensus size: 36
476505 TTTATGCAGT
* * ** * *
476515 TTTCAATTTTAATTTTAATTTTAATTTTAATTTGAA
1 TTTCAATATCAATTTTAATTCGAATTTGAATTTCAA
* * ** *
476551 TTTCATTTTCAATTTTAATTTTAATTTGAGTTTCAA
1 TTTCAATATCAATTTTAATTCGAATTTGAATTTCAA
*
476587 TTTCAATATCAATTTTAATTCGAGTTTGAATTTCAA
1 TTTCAATATCAATTTTAATTCGAATTTGAATTTCAA
476623 TTTCAAT
1 TTTCAAT
476630 TTCGGCTCCA
Statistics
Matches: 68, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
36 68 1.00
ACGTcount: A:0.31, C:0.08, G:0.05, T:0.56
Consensus pattern (36 bp):
TTTCAATATCAATTTTAATTCGAATTTGAATTTCAA
Found at i:476624 original size:6 final size:6
Alignment explanation
Indices: 476515--476632 Score: 94
Period size: 6 Copynumber: 19.7 Consensus size: 6
476505 TTTATGCAGT
* * * * * *
476515 TTTCAA TTTTAA TTTTAA TTTTAA TTTTAA TTTGAA TTTCAT TTTCAA
1 TTTCAA TTTCAA TTTCAA TTTCAA TTTCAA TTTCAA TTTCAA TTTCAA
* * * * * * *
476563 TTTTAA TTTTAA TTTGAG TTTCAA TTTCAA TATCAA TTTTAA -TTCGAG
1 TTTCAA TTTCAA TTTCAA TTTCAA TTTCAA TTTCAA TTTCAA TTTC-AA
*
476611 TTTGAA TTTCAA TTTCAA TTTC
1 TTTCAA TTTCAA TTTCAA TTTC
476633 GGCTCCACTA
Statistics
Matches: 92, Mismatches: 18, Indels: 4
0.81 0.16 0.04
Matches are distributed among these distances:
5 2 0.02
6 88 0.96
7 2 0.02
ACGTcount: A:0.31, C:0.08, G:0.05, T:0.56
Consensus pattern (6 bp):
TTTCAA
Found at i:478495 original size:20 final size:20
Alignment explanation
Indices: 478450--478495 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 20
478440 GTTAACATAA
*
478450 AGTATCGATACTTTTTGTAT
1 AGTATCGATACTTTTTGTAC
*
478470 ATGTATCGATACTTTTTGTCC
1 A-GTATCGATACTTTTTGTAC
478491 AGTAT
1 AGTAT
478496 GCTTCCCAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 5 0.22
21 18 0.78
ACGTcount: A:0.24, C:0.13, G:0.15, T:0.48
Consensus pattern (20 bp):
AGTATCGATACTTTTTGTAC
Found at i:479055 original size:448 final size:448
Alignment explanation
Indices: 478087--479130 Score: 1497
Period size: 448 Copynumber: 2.3 Consensus size: 448
478077 TACCTAAGAA
* * * * * *
478087 ACATGTATCAATACATGACAATATAACAAGTTGAAAATTGAAAAAACCGATTTCAATATGCCAAT
1 ACATGTATCGATACATGACAATATAACAGGTTGAAAATTGATAAAACCGGTTTCAATATGACAAA
* * *
478152 ACCGGTAAAGAGATACCAGTTTACAAAAAAAAAAAACGAAACGTCTCGAAAGTATCGATACCTTA
66 ACAGGTAAA-AGATACCGGTTTAC----AAAAAAAACGAAACGTCTCGAAAGTATCGATACATTA
* * * * *
478217 CAAAAAAGTATCGAGACTTAAGTAAGGGTAATGGTATCGATTAAATATAAATAACTTAACATGTT
126 CAAAAAAGTATCGATACTTAAATAAGGGTAATGATATCGATTAAATATAAAAAACTTAACAGGTT
* *
478282 CAAAATTAACAAAACTGGTTTCCATAATTACACCTATAAAGTATCGATATACGTATGAGAAGTAT
191 CAAAATTAACAAAACTGGTTTCCATAATTACACCTATAAAGTATCGATACACGTACGAGAAGTAT
* *
478347 TGATTCTTAAAACTTTGAAAAGGATTACTTTAAAGTAATAGGTAAATTTACTATTTAAGCGGTAA
256 CGATTCTTAAAACTTCGAAAAGGATTACTTTAAAGTAATAGGTAAATTTACTATTTAAGCGGTAA
* * *
478412 AAATATACCGGTTTAATGAAAAAAATATGTTAACATAAAGTATCGATACTTTTTGTATATGTATC
321 AAATATACCAGTTTAATGAAAAAAATACGTTAACATAAAGTATCAATACTTTTTGTATATGTATC
* * * **
478477 GATACTTTTTGTCCAGTATGCTTCCCAAACTAAATGCACGCAGAAAGTATCAATACCTAATAC
386 GATACTTTTTGTCCAATATACTTCCCAAACTAAATGCACACAGAAAGTATCAATAAATAATAC
* * *
478540 ACATGTATCGATACATGACAATATAAC-GCTTGAAAATTGATAAAATCAGTTTCAATATGACAAA
1 ACATGTATCGATACATGACAATATAACAGGTTGAAAATTGATAAAACCGGTTTCAATATGACAAA
* *
478604 ACAGGTAAAAGATACCGGTTTACAAAAAAAATGAAACGTCTCGAAAGTATCAATACATTACAAAA
66 ACAGGTAAAAGATACCGGTTTACAAAAAAAACGAAACGTCTCGAAAGTATCGATACATTACAAAA
* *
478669 AAGTATTGATACTTAAATAAGGGTAATGATATCGATTAAATATAAAAAAACTTAATAGGTTCAAA
131 AAGTATCGATACTTAAATAAGGGTAATGATATCGATTAAATAT-AAAAAACTTAACAGGTTCAAA
* *
478734 ATTGACAAAA-TCGGTTTCCATAATTGCACCTATAAAGTATCGATACACGTACGAGAAGTATCGA
195 ATTAACAAAACT-GGTTTCCATAATTACACCTATAAAGTATCGATACACGTACGAGAAGTATCGA
* *
478798 TTCTTAAAACTTCGAAATGGATTACTTTAAAGTAATAGGTAAATTTA-TAATTTAAGCTGTAAAA
259 TTCTTAAAACTTCGAAAAGGATTACTTTAAAGTAATAGGTAAATTTACT-ATTTAAGCGGTAAAA
* * *
478862 ATATACCAGTTTACTG-ACAAAATACGTTAATATAAAGTATCAATACTTTTTGTATATGTATCGA
323 ATATACCAGTTTAATGAAAAAAATACGTTAACATAAAGTATCAATACTTTTTGTATATGTATCGA
* *
478926 TACTTTTTGTCCAATATACTTCCCAAACTAGATGCACACAGAAAGTATCGATAAATAATAC
388 TACTTTTTGTCCAATATACTTCCCAAACTAAATGCACACAGAAAGTATCAATAAATAATAC
* *
478987 ACATGTATCGATACATGACAATATAACAGGTTGAAAATTGATAAAACCGGTTTTAATATGATAAA
1 ACATGTATCGATACATGACAATATAACAGGTTGAAAATTGATAAAACCGGTTTCAATATGACAAA
* * * * * *
479052 ACAGGTAAAAAGATACCGATCTAC-ACAAAAACGAAACATCTCAAAAATATCGATACCA-TACAA
66 ACAGGT-AAAAGATACCGGTTTACAAAAAAAACGAAACGTCTCGAAAGTATCGATA-CATTACAA
*
479115 AAAAATATCGATACTT
129 AAAAGTATCGATACTT
479131 CAGTAAGAAT
Statistics
Matches: 528, Mismatches: 57, Indels: 17
0.88 0.09 0.03
Matches are distributed among these distances:
447 205 0.39
448 230 0.44
449 17 0.03
451 13 0.02
452 37 0.07
453 26 0.05
ACGTcount: A:0.44, C:0.14, G:0.13, T:0.29
Consensus pattern (448 bp):
ACATGTATCGATACATGACAATATAACAGGTTGAAAATTGATAAAACCGGTTTCAATATGACAAA
ACAGGTAAAAGATACCGGTTTACAAAAAAAACGAAACGTCTCGAAAGTATCGATACATTACAAAA
AAGTATCGATACTTAAATAAGGGTAATGATATCGATTAAATATAAAAAACTTAACAGGTTCAAAA
TTAACAAAACTGGTTTCCATAATTACACCTATAAAGTATCGATACACGTACGAGAAGTATCGATT
CTTAAAACTTCGAAAAGGATTACTTTAAAGTAATAGGTAAATTTACTATTTAAGCGGTAAAAATA
TACCAGTTTAATGAAAAAAATACGTTAACATAAAGTATCAATACTTTTTGTATATGTATCGATAC
TTTTTGTCCAATATACTTCCCAAACTAAATGCACACAGAAAGTATCAATAAATAATAC
Found at i:481170 original size:2 final size:2
Alignment explanation
Indices: 481165--481230 Score: 132
Period size: 2 Copynumber: 33.0 Consensus size: 2
481155 AAACACACAA
481165 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
481207 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
481231 TCCATACTTA
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 64 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:481729 original size:225 final size:220
Alignment explanation
Indices: 481353--482027 Score: 802
Period size: 225 Copynumber: 3.1 Consensus size: 220
481343 TAACAAATCA
* *
481353 AGTAATTAACTGGTTATGTTATCGTCGGATTCATAAGGCTCCATTAGCTTAAACTTTGGTAACAT
1 AGTAATTAACCGGTTATGTTATCGTCGGATTCATAAGGCTCCATCAGCTTAAACTTTGGTAA-AT
* *
481418 ATTAGGCGTTACCTAATATGTTGATAATACTGATAACAAATTAAGTAATTAACCTATTTTGTTAT
65 TTTAGGCGTTACCTAATATGTTGATAATACTAATAACAAATTAAGTAATTAACCTATTTTGTTAT
481483 CGTCGGATTTCCAAAGCCCCATAAGCTTTTAGAAGGCGCTGTCTATTACGTTACATAAGTACTAC
130 CGTCGGATTTCCAAAGCCCCATAAGCTTTTAGAAGGCGCTG-CTATTACGTTACATAAGT-CTAC
481548 ATAATATGTTATTATGCTTGATAATGTTTCC
193 AT-ATATGTT-TTATG-TTGATAATGTTTCC
* * * *
481579 AGTAATTAACAGGTTATGTTATCGTTGGATTCCTAAGGC-CCATCAGCTCAAACTTTGGTAATAT
1 AGTAATTAACCGGTTATGTTATCGTCGGATTCATAAGGCTCCATCAGCTTAAACTTTGGTAA-AT
* * * *
481643 TTTAGACGTTACCTAATATGTTGATAATAATAATAACAAATTAAGTAATTAATCAATTTTGTTAT
65 TTTAGGCGTTACCTAATATGTTGATAATACTAATAACAAATTAAGTAATTAACCTATTTTGTTAT
* * * * *
481708 TGTCAGATTTCCAAAGCCCCATCAA-CTTTTAGAA-G-AC-GC---TAC-CTA-ATATGT-T--A
130 CGTCGGATTTCCAAAGCCCCAT-AAGCTTTTAGAAGGCGCTGCTATTACGTTACATAAGTCTACA
* *
481761 T-TATG------CTTGATAATATTTCC
194 TATATGTTTTATGTTGATAATGTTTCC
* *
481781 AGTAATTAACCGGTTATGTTGTCGTCGGATTCTTAAGGGCTCCATCAGCTTAAACTTTGGTACAA
1 AGTAATTAACCGGTTATGTTATCGTCGGATTCATAA-GGCTCCATCAGCTTAAACTTTGGTA-AA
*
481846 -TTTAGGCGTTACCTAATATGCTT-ATAATACTAATAAAAAATTAAGTAATTAACCTATTTTGTT
64 TTTTAGGCGTTACCTAATATG-TTGATAATACTAATAACAAATTAAGTAATTAACCTATTTTGTT
* * * * *
481909 ATCGTCGGATTTCCAAAG-CCCATCAGCTTTAAAAAGGCGCTACCTATTACGTTACATAAGCGCT
128 ATCGTCGGATTTCCAAAGCCCCATAAGCTTTTAGAAGGCGCT-GCTATTACGTTACATAAG-TCT
*
481973 ACCTTATATGTTTTATGATTGATAATGTTTCC
191 A-CATATATGTTTTATG-TTGATAATGTTTCC
482005 AGTAATTAACCGGTTATGTTATC
1 AGTAATTAACCGGTTATGTTATC
482028 TTCTATAATT
Statistics
Matches: 378, Mismatches: 43, Indels: 58
0.79 0.09 0.12
Matches are distributed among these distances:
201 1 0.00
202 57 0.15
203 75 0.20
204 24 0.06
205 1 0.00
206 1 0.00
209 3 0.01
210 6 0.02
211 4 0.01
212 2 0.01
213 1 0.00
214 1 0.00
216 6 0.02
217 6 0.02
218 3 0.01
221 1 0.00
222 1 0.00
223 1 0.00
224 36 0.10
225 110 0.29
226 38 0.10
ACGTcount: A:0.32, C:0.16, G:0.15, T:0.37
Consensus pattern (220 bp):
AGTAATTAACCGGTTATGTTATCGTCGGATTCATAAGGCTCCATCAGCTTAAACTTTGGTAAATT
TTAGGCGTTACCTAATATGTTGATAATACTAATAACAAATTAAGTAATTAACCTATTTTGTTATC
GTCGGATTTCCAAAGCCCCATAAGCTTTTAGAAGGCGCTGCTATTACGTTACATAAGTCTACATA
TATGTTTTATGTTGATAATGTTTCC
Found at i:481933 original size:202 final size:202
Alignment explanation
Indices: 481544--481954 Score: 596
Period size: 202 Copynumber: 2.0 Consensus size: 202
481534 TACATAAGTA
* * *
481544 CTACATAATATGTTATTATGCTTGATAATGTTTCCAGTAATTAACAGGTTATGTTATCGTTGGAT
1 CTACCTAATATGTTATTATGCTTGATAATATTTCCAGTAATTAACAGGTTATGTTATCGTCGGAT
481609 TCCTAAGGCCCATCAGCTCAAACTTTGGTAATATTTTAGACGTTACCTAATATGTTGATAATAAT
66 TCCTAAGGCCCATCAGCTCAAACTTTGGTAATATTTTAGACGTTACCTAATATGTTGATAATAAT
* * * *
481674 AATAACAAATTAAGTAATTAATCAATTTTGTTATTGTCAGATTTCCAAAGCCCCATCAACTTTTA
131 AATAAAAAATTAAGTAATTAACCAATTTTGTTATCGTCAGATTTCCAAAGCCCCATCAACTTTAA
*
481739 GAAGACG
196 AAAGACG
* *
481746 CTACCTAATATGTTATTATGCTTGATAATATTTCCAGTAATTAACCGGTTATGTTGTCGTCGGAT
1 CTACCTAATATGTTATTATGCTTGATAATATTTCCAGTAATTAACAGGTTATGTTATCGTCGGAT
* * *
481811 TCTTAAGGGCTCCATCAGCTTAAACTTTGGTACA-A-TTTAGGCGTTACCTAATATGCTT-ATAA
66 TCCTAA-GGC-CCATCAGCTCAAACTTTGGTA-ATATTTTAGACGTTACCTAATATG-TTGATAA
* * * *
481873 TACTAATAAAAAATTAAGTAATTAACCTATTTTGTTATCGTCGGATTTCCAAAG-CCCATCAGCT
127 TAATAATAAAAAATTAAGTAATTAACCAATTTTGTTATCGTCAGATTTCCAAAGCCCCATCAACT
*
481937 TTAAAAAGGCG
192 TTAAAAAGACG
481948 CTACCTA
1 CTACCTA
481955 TTACGTTACA
Statistics
Matches: 187, Mismatches: 18, Indels: 8
0.88 0.08 0.04
Matches are distributed among these distances:
202 89 0.48
203 74 0.40
204 23 0.12
205 1 0.01
ACGTcount: A:0.32, C:0.17, G:0.14, T:0.36
Consensus pattern (202 bp):
CTACCTAATATGTTATTATGCTTGATAATATTTCCAGTAATTAACAGGTTATGTTATCGTCGGAT
TCCTAAGGCCCATCAGCTCAAACTTTGGTAATATTTTAGACGTTACCTAATATGTTGATAATAAT
AATAAAAAATTAAGTAATTAACCAATTTTGTTATCGTCAGATTTCCAAAGCCCCATCAACTTTAA
AAAGACG
Found at i:483144 original size:22 final size:20
Alignment explanation
Indices: 483095--483148 Score: 56
Period size: 22 Copynumber: 2.6 Consensus size: 20
483085 TGATGTTGTT
*
483095 TTATTTTAATTTACTCACTG
1 TTATTTTAATTTACTCACTA
*
483115 TTAATTTATGATTTAGCT-ACTA
1 TT-ATTT-TAATTTA-CTCACTA
483137 TTATTTTAATTT
1 TTATTTTAATTT
483149 TTACATTTTG
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
20 7 0.25
21 8 0.29
22 11 0.39
23 2 0.07
ACGTcount: A:0.28, C:0.09, G:0.06, T:0.57
Consensus pattern (20 bp):
TTATTTTAATTTACTCACTA
Found at i:488310 original size:35 final size:35
Alignment explanation
Indices: 488197--488312 Score: 111
Period size: 29 Copynumber: 3.5 Consensus size: 35
488187 CACTAAAGGC
** *
488197 AGTTTCCCTTGAAACAAGTTTTGTCTCTCTTGAGAT
1 AGTTTCCCTTGAAACAA-AATTGTCTCCCTTGAGAT
* *
488233 AATTTCCCTTGAAACAAAA-----T-CGTTGA-AT
1 AGTTTCCCTTGAAACAAAATTGTCTCCCTTGAGAT
488261 ATGTTTCCCTTGAAACAAAATTGTCTCCCTTGAGAT
1 A-GTTTCCCTTGAAACAAAATTGTCTCCCTTGAGAT
*
488297 AGTTTCCCATGAAACA
1 AGTTTCCCTTGAAACA
488313 GAAGATTTTG
Statistics
Matches: 64, Mismatches: 8, Indels: 17
0.72 0.09 0.19
Matches are distributed among these distances:
28 3 0.05
29 21 0.33
30 1 0.02
34 1 0.02
35 19 0.30
36 19 0.30
ACGTcount: A:0.30, C:0.21, G:0.14, T:0.35
Consensus pattern (35 bp):
AGTTTCCCTTGAAACAAAATTGTCTCCCTTGAGAT
Found at i:488401 original size:76 final size:77
Alignment explanation
Indices: 488314--488488 Score: 184
Period size: 76 Copynumber: 2.4 Consensus size: 77
488304 CATGAAACAG
* * * * *
488314 AAGATTTTGTCTCGTTTGAGACAGTTTTTACTCGAAACAAGAAGATTT-ATTTCACTCAAGATTG
1 AAGATTTTGTCTCGCTTAAGACAGTTTTTACTCAAAACAAG-ACATTTCATTTCACTCAAGATTC
488378 TTTTTCTTAAAAC
65 TTTTTCTTAAAAC
* * * *
488391 AAGA-TTTGTCTTGCTTAAGACAGTTTTTACTTAAAAGAAGACATTTCTTTTCACTCAAGATTC-
1 AAGATTTTGTCTCGCTTAAGACAGTTTTTACTCAAAACAAGACATTTCATTTCACTCAAGATTCT
*
488454 --TT-TT-AAAG
66 TTTTCTTAAAAC
* *
488462 AAGATTTTGTCTCGCTTGAGATAGTTT
1 AAGATTTTGTCTCGCTTAAGACAGTTT
488489 CCCTCGAAAC
Statistics
Matches: 83, Mismatches: 13, Indels: 9
0.79 0.12 0.09
Matches are distributed among these distances:
71 7 0.08
72 21 0.25
73 2 0.02
75 5 0.06
76 44 0.53
77 4 0.05
ACGTcount: A:0.30, C:0.14, G:0.15, T:0.41
Consensus pattern (77 bp):
AAGATTTTGTCTCGCTTAAGACAGTTTTTACTCAAAACAAGACATTTCATTTCACTCAAGATTCT
TTTTCTTAAAAC
Found at i:488407 original size:21 final size:20
Alignment explanation
Indices: 488370--488408 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
488360 TTATTTCACT
* *
488370 CAAGATTGTTTTTCTTAAAA
1 CAAGATTGTCTTGCTTAAAA
488390 CAAGATTTGTCTTGCTTAA
1 CAAGA-TTGTCTTGCTTAA
488409 GACAGTTTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 5 0.31
21 11 0.69
ACGTcount: A:0.31, C:0.13, G:0.13, T:0.44
Consensus pattern (20 bp):
CAAGATTGTCTTGCTTAAAA
Found at i:488516 original size:39 final size:39
Alignment explanation
Indices: 488460--488840 Score: 483
Period size: 39 Copynumber: 10.0 Consensus size: 39
488450 ATTCTTTTAA
488460 AGAAGATTTTGTCTCGCTTGAGATAGTTTCCCTCGAAAC
1 AGAAGATTTTGTCTCGCTTGAGATAGTTTCCCTCGAAAC
* * * *
488499 ATAAGATTTTATCTCGCTTGAGATAGTTTCGCTCAAAAC
1 AGAAGATTTTGTCTCGCTTGAGATAGTTTCCCTCGAAAC
* *
488538 AGAAGATTTTATCTCGCTTGAGATAGTTTCCCTTGAAAC
1 AGAAGATTTTGTCTCGCTTGAGATAGTTTCCCTCGAAAC
* * *
488577 AGAATATTTTGTCTCACTTGAGATAGTTTCCCTCAAAAC
1 AGAAGATTTTGTCTCGCTTGAGATAGTTTCCCTCGAAAC
* *
488616 ATAAGATTTTGTCTCGCTTGAGATAATTTCCCTCGAAAC
1 AGAAGATTTTGTCTCGCTTGAGATAGTTTCCCTCGAAAC
* *
488655 AGAAGATTTTATCTCGCTTGAGATAGTTTCTCTCGAAAC
1 AGAAGATTTTGTCTCGCTTGAGATAGTTTCCCTCGAAAC
* * ** *
488694 AAAATATTTTGTCTTACTTGAGATAGTTTCCCTCAAAAC
1 AGAAGATTTTGTCTCGCTTGAGATAGTTTCCCTCGAAAC
488733 AGAAGATTTTGTCT--C-------AGTTTCCCTCGAAAC
1 AGAAGATTTTGTCTCGCTTGAGATAGTTTCCCTCGAAAC
488763 AGAAGATTTTGTCTCGCTTGAGATAGTTTCCCTCGAAAC
1 AGAAGATTTTGTCTCGCTTGAGATAGTTTCCCTCGAAAC
* * * * * *
488802 ATAAAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAAC
1 AGAAGATTTTGTCTCGCTTGAGATAGTTTCCCTCGAAAC
488841 GATTTTTTTC
Statistics
Matches: 295, Mismatches: 38, Indels: 18
0.84 0.11 0.05
Matches are distributed among these distances:
30 28 0.09
32 1 0.00
37 1 0.00
39 265 0.90
ACGTcount: A:0.29, C:0.19, G:0.16, T:0.36
Consensus pattern (39 bp):
AGAAGATTTTGTCTCGCTTGAGATAGTTTCCCTCGAAAC
Found at i:488754 original size:30 final size:30
Alignment explanation
Indices: 488718--488777 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
488708 TACTTGAGAT
488718 AGTTTCCCTCAAAACAGAAGATTTTGTCTC
1 AGTTTCCCTCAAAACAGAAGATTTTGTCTC
*
488748 AGTTTCCCTCGAAACAGAAGATTTTGTCTC
1 AGTTTCCCTCAAAACAGAAGATTTTGTCTC
488778 GCTTGAGATA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.28, C:0.23, G:0.15, T:0.33
Consensus pattern (30 bp):
AGTTTCCCTCAAAACAGAAGATTTTGTCTC
Found at i:488790 original size:69 final size:69
Alignment explanation
Indices: 488679--488816 Score: 204
Period size: 69 Copynumber: 2.0 Consensus size: 69
488669 CGCTTGAGAT
* * * *
488679 AGTTTCTCTCGAAACAAAATATTTTGTCTTACTTGAGATAGTTTCCCTCAAAACAGAAGATTTTG
1 AGTTTCCCTCGAAACAAAAGATTTTGTCTCACTTGAGATAGTTTCCCTCAAAACAGAAAATTTTG
488744 TCTC
66 TCTC
* * * *
488748 AGTTTCCCTCGAAACAGAAGATTTTGTCTCGCTTGAGATAGTTTCCCTCGAAACATAAAATTTTG
1 AGTTTCCCTCGAAACAAAAGATTTTGTCTCACTTGAGATAGTTTCCCTCAAAACAGAAAATTTTG
488813 TCTC
66 TCTC
488817 TCTTGAGACA
Statistics
Matches: 61, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
69 61 1.00
ACGTcount: A:0.29, C:0.20, G:0.14, T:0.36
Consensus pattern (69 bp):
AGTTTCCCTCGAAACAAAAGATTTTGTCTCACTTGAGATAGTTTCCCTCAAAACAGAAAATTTTG
TCTC
Found at i:488860 original size:36 final size:36
Alignment explanation
Indices: 488808--489014 Score: 239
Period size: 36 Copynumber: 5.9 Consensus size: 36
488798 AAACATAAAA
*
488808 TTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACGAT
1 TTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACGAG
* * *
488844 TTTTTTCTCTCTTGAGACAATTTCTCTTGAAACGAA
1 TTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACGAG
*
488880 TTTTGTCTCTCTTTAGACAG-------TGAAACGAG
1 TTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACGAG
* * *
488909 TTTTGTCTCCCTTGAGACATTTTCTCTTGAAACAAG
1 TTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACGAG
* *
488945 TTTTGTCTCTCTTGAGACAATTTCTCTTGAAACAAAG
1 TTTTGTCTCTCTTGAGACAGTTTCTCTTGAAAC-GAG
* * *
488982 TTTTGTCTCTCTAGAGACAGTTTCCCTCGAAAC
1 TTTTGTCTCTCTTGAGACAGTTTCTCTTGAAAC
489015 AAATCTCACT
Statistics
Matches: 146, Mismatches: 17, Indels: 15
0.82 0.10 0.08
Matches are distributed among these distances:
29 25 0.17
36 89 0.61
37 32 0.22
ACGTcount: A:0.23, C:0.21, G:0.15, T:0.41
Consensus pattern (36 bp):
TTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACGAG
Found at i:488891 original size:21 final size:20
Alignment explanation
Indices: 488830--488892 Score: 55
Period size: 21 Copynumber: 3.3 Consensus size: 20
488820 TGAGACAGTT
*
488830 TCTCTTGAAACGATTTTTTTC
1 TCTCTTGAAACGA-ATTTTTC
*
488851 TCTCTTGAGAC-AA---TT-
1 TCTCTTGAAACGAATTTTTC
488866 TCTCTTGAAACGAATTTTGTC
1 TCTCTTGAAACGAATTTT-TC
488887 TCTCTT
1 TCTCTT
488893 TAGACAGTGA
Statistics
Matches: 33, Mismatches: 3, Indels: 12
0.69 0.06 0.25
Matches are distributed among these distances:
15 10 0.30
16 4 0.12
19 1 0.03
20 2 0.06
21 16 0.48
ACGTcount: A:0.21, C:0.21, G:0.11, T:0.48
Consensus pattern (20 bp):
TCTCTTGAAACGAATTTTTC
Found at i:488913 original size:29 final size:29
Alignment explanation
Indices: 488871--488927 Score: 87
Period size: 29 Copynumber: 2.0 Consensus size: 29
488861 CAATTTCTCT
* *
488871 TGAAACGAATTTTGTCTCTCTTTAGACAG
1 TGAAACGAATTTTGTCTCCCTTGAGACAG
*
488900 TGAAACGAGTTTTGTCTCCCTTGAGACA
1 TGAAACGAATTTTGTCTCCCTTGAGACA
488928 TTTTCTCTTG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.26, C:0.19, G:0.19, T:0.35
Consensus pattern (29 bp):
TGAAACGAATTTTGTCTCCCTTGAGACAG
Found at i:488924 original size:101 final size:102
Alignment explanation
Indices: 488808--489002 Score: 311
Period size: 101 Copynumber: 1.9 Consensus size: 102
488798 AAACATAAAA
* * * *
488808 TTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACGATTTTTTTCTCTCTTGAGACAATTTCTCTTG
1 TTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACAAGTTTTGTCTCTCTTGAGACAATTTCTCTTG
* **
488873 AAACGAA-TTTTGTCTCTCTTTAGACAGTGAAACGAG
66 AAACAAAGTTTTGTCTCTCTAGAGACAGTGAAACGAG
*
488909 TTTTGTCTCCCTTGAGACATTTTCTCTTGAAACAAGTTTTGTCTCTCTTGAGACAATTTCTCTTG
1 TTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACAAGTTTTGTCTCTCTTGAGACAATTTCTCTTG
488974 AAACAAAGTTTTGTCTCTCTAGAGACAGT
66 AAACAAAGTTTTGTCTCTCTAGAGACAGT
489003 TTCCCTCGAA
Statistics
Matches: 85, Mismatches: 8, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
101 66 0.78
102 19 0.22
ACGTcount: A:0.23, C:0.19, G:0.15, T:0.42
Consensus pattern (102 bp):
TTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACAAGTTTTGTCTCTCTTGAGACAATTTCTCTTG
AAACAAAGTTTTGTCTCTCTAGAGACAGTGAAACGAG
Found at i:488927 original size:65 final size:65
Alignment explanation
Indices: 488835--488963 Score: 197
Period size: 65 Copynumber: 2.0 Consensus size: 65
488825 CAGTTTCTCT
* * * *
488835 TGAAACGATTTTTTTCTCTCTTGAGACAATTTCTCTTGAAACGAA-TTTTGTCTCTCTTTAGACA
1 TGAAACGAGTTTTGTCTCCCTTGAGACAATTTCTCTTGAAAC-AAGTTTTGTCTCTCTTGAGACA
488899 G
65 G
*
488900 TGAAACGAGTTTTGTCTCCCTTGAGACATTTTCTCTTGAAACAAGTTTTGTCTCTCTTGAGACA
1 TGAAACGAGTTTTGTCTCCCTTGAGACAATTTCTCTTGAAACAAGTTTTGTCTCTCTTGAGACA
488964 ATTTCTCTTG
Statistics
Matches: 58, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
64 2 0.03
65 56 0.97
ACGTcount: A:0.24, C:0.19, G:0.16, T:0.41
Consensus pattern (65 bp):
TGAAACGAGTTTTGTCTCCCTTGAGACAATTTCTCTTGAAACAAGTTTTGTCTCTCTTGAGACAG
Found at i:488992 original size:37 final size:37
Alignment explanation
Indices: 488907--489017 Score: 161
Period size: 37 Copynumber: 3.0 Consensus size: 37
488897 CAGTGAAACG
* *
488907 AGTTTTGTCTCCCTTGAGACATTTTCTCTTGAAAC-A
1 AGTTTTGTCTCTCTTGAGACAATTTCTCTTGAAACAA
488943 AGTTTTGTCTCTCTTGAGACAATTTCTCTTGAAACAA
1 AGTTTTGTCTCTCTTGAGACAATTTCTCTTGAAACAA
* * * *
488980 AGTTTTGTCTCTCTAGAGACAGTTTCCCTCGAAACAA
1 AGTTTTGTCTCTCTTGAGACAATTTCTCTTGAAACAA
489017 A
1 A
489018 TCTCACTTGA
Statistics
Matches: 68, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
36 33 0.49
37 35 0.51
ACGTcount: A:0.26, C:0.22, G:0.14, T:0.38
Consensus pattern (37 bp):
AGTTTTGTCTCTCTTGAGACAATTTCTCTTGAAACAA
Found at i:489451 original size:41 final size:41
Alignment explanation
Indices: 489406--489598 Score: 147
Period size: 41 Copynumber: 4.6 Consensus size: 41
489396 TTCGTTTGAT
*
489406 TCCATCACAGAAGGAGGTGGATCGACATTTGTTCGGTCAAA
1 TCCATCACAGAAGGAGGTGGATCGACATTTGTTCGCTCAAA
* * * ** ***
489447 TCCATCGCAGAAGGAGTTGGATCAACATCAACTT-TTTACTCGTT
1 TCCATCACAGAAGGAGGTGGATCGACAT----TTGTTCGCTCAAA
* * ** * *
489491 TCTATCACAGAAGGAGGTAGATCAGCACCAACAT-TTCGCTCGAT
1 TCCATCACAGAAGGAGGTGGATC-G-A-C-ATTTGTTCGCTCAAA
*
489535 TCCATCACAGAAGGAGGTGGATCGATATTTGTTCGCTCAAA
1 TCCATCACAGAAGGAGGTGGATCGACATTTGTTCGCTCAAA
*
489576 TCCATCACAGAAGGAGTTGGATC
1 TCCATCACAGAAGGAGGTGGATC
489599 AGCGTCAACT
Statistics
Matches: 116, Mismatches: 27, Indels: 18
0.72 0.17 0.11
Matches are distributed among these distances:
40 2 0.02
41 55 0.47
42 1 0.01
43 1 0.01
44 52 0.45
45 2 0.02
46 1 0.01
47 1 0.01
48 1 0.01
ACGTcount: A:0.30, C:0.22, G:0.23, T:0.26
Consensus pattern (41 bp):
TCCATCACAGAAGGAGGTGGATCGACATTTGTTCGCTCAAA
Found at i:489503 original size:44 final size:44
Alignment explanation
Indices: 489447--489789 Score: 138
Period size: 44 Copynumber: 7.5 Consensus size: 44
489437 TTCGGTCAAA
* * * * * *
489447 TCCATCGCAGAAGGAGTTGGATCAACATCAACTTTTTACTCGTT
1 TCCATCACAGAAGGAGGTGGATCAACACCAACATTTCACTCGAT
* * * *
489491 TCTATCACAGAAGGAGGTAGATCAGCACCAACATTTCGCTCGAT
1 TCCATCACAGAAGGAGGTGGATCAACACCAACATTTCACTCGAT
* * ** * * *
489535 TCCATCACAGAAGGAGGTGGATC--GA--TATTTGTTCGCTCAAA
1 TCCATCACAGAAGGAGGTGGATCAACACCAACAT-TTCACTCGAT
* * ** * *
489576 TCCATCACAGAAGGAGTTGGATCAGCGTCAAC-TTTTAGCTTGAT
1 TCCATCACAGAAGGAGGTGGATCAACACCAACATTTCA-CTCGAT
** * * * ** * **
489620 TTTATCACAGAAGGAGGTAGATCAACATCGATGTATCGTTCGATT
1 TCCATCACAGAAGGAGGTGGATCAACACCAACATTTCACTCGA-T
* * *
489665 TCCATCACAGAACGAGAAGGAGGTAGATCAGCACCAACATTTCAGTCGATT
1 TCCAT--C---AC-AGAAGGAGGTGGATCAACACCAACATTTCACTCGA-T
* * *
489716 TCCATCACAGAAGGAGAAGGAGGTAGATCATCACCAACATTTCGCTCGATT
1 TCCATCAC------AGAAGGAGGTGGATCAACACCAACATTTCACTCGA-T
*
489767 TCCATCACAGAAGCAGGTGGATC
1 TCCATCACAGAAGGAGGTGGATC
489790 GACATTTTTA
Statistics
Matches: 224, Mismatches: 56, Indels: 37
0.71 0.18 0.12
Matches are distributed among these distances:
40 2 0.01
41 30 0.13
42 1 0.00
43 2 0.01
44 86 0.38
45 20 0.09
46 2 0.01
47 1 0.00
49 1 0.00
50 2 0.01
51 77 0.34
ACGTcount: A:0.31, C:0.22, G:0.22, T:0.25
Consensus pattern (44 bp):
TCCATCACAGAAGGAGGTGGATCAACACCAACATTTCACTCGAT
Found at i:489575 original size:129 final size:129
Alignment explanation
Indices: 489345--490447 Score: 829
Period size: 129 Copynumber: 8.2 Consensus size: 129
489335 AAGAGATTAT
* * * * * *
489345 TCAACTGTTTGCTCGATTCTATCACAGAAGAAGGTATATCAGCACCAACATTTCGTTTGATTCCA
1 TCAACT-TTTACTCGATTCTATCACAGAAGGAGGTAGATCAGCACCGACATCTCGTTCGATTCCA
* * * *
489410 TCACAGAAGGAGGTGGATCGACATT-TGTTCGGTCAAATCCATCGCAGAAGGAGTTGGATCAACA
65 TCACAGAAGGAGGTGGATCGATATTATTTTCGCTCAAATCCATCGCAGAAGGAGTTGGATCAACG
* * * *
489474 TCAACTTTTTACTCGTTTCTATCACAGAAGGAGGTAGATCAGCACCAACATTTCGCTCGATTCCA
1 TCAAC-TTTTACTCGATTCTATCACAGAAGGAGGTAGATCAGCACCGACATCTCGTTCGATTCCA
* * *
489539 TCACAGAAGGAGGTGGATCGATATT-TGTTCGCTCAAATCCATCACAGAAGGAGTTGGATCAGCG
65 TCACAGAAGGAGGTGGATCGATATTATTTTCGCTCAAATCCATCGCAGAAGGAGTTGGATCAACG
* * * * ** *
489603 TCAACTTTTAGCTTGATTTTATCACAGAAGGAGGTAGATCAACATCGATGTATCGTTCGATTTCC
1 TCAACTTTTA-CTCGATTCTATCACAGAAGGAGGTAGATCAGCACCGACATCTCGTTCGA-TTCC
* * ** ** *
489668 ATCACAGAACGAGAAGGAGGTAGATCAGCACCAACA-TTTCAG-TCGATTTCCATCACAGAAGGA
64 AT--C---AC-AGAAGGAGGTGGATC-G-A-TATTATTTTC-GCTC-AAATCCATCGCAGAAGGA
** *
489731 GAAGGAGGT-AGATCA
118 GTTGGA--TCA-A-CG
** * * * ***** * * *
489746 TCACCAACATTTCGCTCGATTTCCATCACAGAAGCAGGTGGATC-GACATTTTTATTTTCGCTCA
1 T---CAAC-TTTTACTCGA-TTCTATCACAGAAGGAGGTAGATCAG-CACCGACA-TCTCGTTCG
* ** * * *
489810 AATCCATCGTAGAAGGAGTTAGATCAGAGTCGATATTTTTATTTTCGATCAAATCCATTGCAGAA
59 ATTCCATCACAGAAGGAG---G-T-GGA-TCGATA---TTATTTTCGCTCAAATCCATCGCAGAA
*
489875 GGAGTTGGATCAACA
115 GGAGTTGGATCAACG
* * * * **
489890 TCAACTTTTAGCT-TATTCTATCACAGAAAGTGGTAGATCAACACCGGTATCTCGTTCGATTCCA
1 TCAACTTTTA-CTCGATTCTATCACAGAAGGAGGTAGATCAGCACCGACATCTCGTTCGATTCCA
* * * *
489954 TTACAAAAGGAGGTGGATTGACATTTTTATTTTCGCTCAAATCCATCGCAGAAGGAGTTGGATCA
65 TCACAGAAGGAGGTGGATCG--A-TATTATTTTCGCTCAAATCCATCGCAGAAGGAGTTGGATCA
* *
490019 TCT
127 ACG
* * * * *
490022 TCAACTTTTTTTGCGCGGTTCTATCACAGAAGGAGGTAGATCAGCACCAACATCTCATTCGATTC
1 TCAAC---TTTTACTCGATTCTATCACAGAAGGAGGTAGATCAGCACCGACATCTCGTTCGATTC
* *
490087 CATCACAGAAGGAGGTGGATCAATATTTTTATTTCGCTCAAATCCATCGCAGAAGGAGTTGGATC
63 CATCACAGAAGGAGGTGGATCGATA-TTAT-TTTCGCTCAAATCCATCGCAGAAGGAGTTGGATC
*
490152 AGCG
126 AACG
* * * * * **
490156 TCAACTTTTAGCTTGATTCTATTACAGAAAGAGGTAGATCAACATCGGTATCTCGTTCGATTCCA
1 TCAACTTTTA-CTCGATTCTATCACAGAAGGAGGTAGATCAGCACCGACATCTCGTTCGATTCCA
* * * *
490221 TCACAGAAGGAGGTGGATCGACATTTTTATTTTTGGTCAAATCCATCGCATAAGGAGTTGGAT-A
65 TCACAGAAGGAGGTGGATCG--A-TATTATTTTCGCTCAAATCCATCGCAGAAGGAGTTGGATCA
490285 AGCG
127 A-CG
* *
490289 TCAACTTTTAGCTCGATTCTATCACAGAAGGAGGTAGATCAGCATCGACATATCGTTCGATTTCC
1 TCAACTTTTA-CTCGATTCTATCACAGAAGGAGGTAGATCAGCACCGACATCTCGTTCGA-TTCC
* *
490354 ATCACAGAAGGAGGTGGATCGATATTTTTATTTTCCCTCAAATCCATCGCATAAGGAGTTGGATC
64 ATCACAGAAGGAGGTGGATCGATA---TTATTTTCGCTCAAATCCATCGCAGAAGGAGTTGGATC
*
490419 AGCG
126 AACG
*
490423 TCAACTTCTTGCTCGATTC-ATCACA
1 TCAACTT-TTACTCGATTCTATCACA
490448 AATAGAGTTA
Statistics
Matches: 776, Mismatches: 138, Indels: 116
0.75 0.13 0.11
Matches are distributed among these distances:
128 5 0.01
129 160 0.21
130 7 0.01
131 5 0.01
132 111 0.14
133 97 0.12
134 124 0.16
135 70 0.09
136 14 0.02
137 1 0.00
138 20 0.03
139 29 0.04
140 25 0.03
141 15 0.02
142 1 0.00
143 2 0.00
144 5 0.01
145 5 0.01
146 13 0.02
147 54 0.07
148 13 0.02
ACGTcount: A:0.30, C:0.20, G:0.21, T:0.29
Consensus pattern (129 bp):
TCAACTTTTACTCGATTCTATCACAGAAGGAGGTAGATCAGCACCGACATCTCGTTCGATTCCAT
CACAGAAGGAGGTGGATCGATATTATTTTCGCTCAAATCCATCGCAGAAGGAGTTGGATCAACG
Found at i:489584 original size:85 final size:88
Alignment explanation
Indices: 489494--489731 Score: 223
Period size: 85 Copynumber: 2.6 Consensus size: 88
489484 ACTCGTTTCT
* *
489494 ATCACAGAAGGAGGTAGATCAGCACCAACATTTCGCTCGATTCCATCACAGAAGGAGGTGGATCG
1 ATCACAGAAGGAGGTAGATCAGCACCAACATTTCGCTCGATTCCATCACAGAAGGAGGTAGATCA
* *
489559 ATAT-TTGT-TCGCTC-AAATCC
66 ACATCATGTATCGCTCGAAATCC
* * ** * * * **
489579 ATCACAGAAGGAGTTGGATCAGCGTCAACTTTTAGCTTGATTTTATCACAGAAGGAGGTAGATCA
1 ATCACAGAAGGAGGTAGATCAGCACCAACATTTCGCTCGATTCCATCACAGAAGGAGGTAGATCA
* **
489644 ACATCGATGTATCGTTCGATTTCC
66 ACATC-ATGTATCGCTCGAAATCC
489668 ATCACAGAACGAGAAGGAGGTAGATCAGCACCAACATTTCAG-TCGATTTCCATCACAGAAGGAG
1 AT--C---AC-AGAAGGAGGTAGATCAGCACCAACATTTC-GCTCGA-TTCCATCACAGAAGGAG
489732 AAGGAGGTAG
Statistics
Matches: 116, Mismatches: 25, Indels: 13
0.75 0.16 0.08
Matches are distributed among these distances:
85 57 0.49
87 3 0.03
88 5 0.04
89 6 0.05
91 1 0.01
94 2 0.02
95 26 0.22
96 16 0.14
ACGTcount: A:0.32, C:0.21, G:0.23, T:0.24
Consensus pattern (88 bp):
ATCACAGAAGGAGGTAGATCAGCACCAACATTTCGCTCGATTCCATCACAGAAGGAGGTAGATCA
ACATCATGTATCGCTCGAAATCC
Found at i:489779 original size:51 final size:51
Alignment explanation
Indices: 489659--489779 Score: 208
Period size: 51 Copynumber: 2.4 Consensus size: 51
489649 GATGTATCGT
*
489659 TCGATTTCCATCACAGAACGAGAAGGAGGTAGATCAGCACCAACATTTCAG
1 TCGATTTCCATCACAGAAGGAGAAGGAGGTAGATCAGCACCAACATTTCAG
*
489710 TCGATTTCCATCACAGAAGGAGAAGGAGGTAGATCATCACCAACATTTC-G
1 TCGATTTCCATCACAGAAGGAGAAGGAGGTAGATCAGCACCAACATTTCAG
489760 CTCGATTTCCATCACAGAAG
1 -TCGATTTCCATCACAGAAG
489780 CAGGTGGATC
Statistics
Matches: 67, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
50 1 0.01
51 66 0.99
ACGTcount: A:0.34, C:0.24, G:0.21, T:0.21
Consensus pattern (51 bp):
TCGATTTCCATCACAGAAGGAGAAGGAGGTAGATCAGCACCAACATTTCAG
Found at i:489851 original size:51 final size:51
Alignment explanation
Indices: 489788--489886 Score: 153
Period size: 51 Copynumber: 1.9 Consensus size: 51
489778 AGCAGGTGGA
* *
489788 TCGACATTTTTATTTTCGCTCAAATCCATCGTAGAAGGAGTTAGATCAGAG
1 TCGACATTTTTATTTTCGATCAAATCCATCGCAGAAGGAGTTAGATCAGAG
* * *
489839 TCGATATTTTTATTTTCGATCAAATCCATTGCAGAAGGAGTTGGATCA
1 TCGACATTTTTATTTTCGATCAAATCCATCGCAGAAGGAGTTAGATCA
489887 ACATCAACTT
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
51 43 1.00
ACGTcount: A:0.29, C:0.16, G:0.19, T:0.35
Consensus pattern (51 bp):
TCGACATTTTTATTTTCGATCAAATCCATCGCAGAAGGAGTTAGATCAGAG
Found at i:490211 original size:267 final size:266
Alignment explanation
Indices: 489345--490447 Score: 1097
Period size: 267 Copynumber: 4.1 Consensus size: 266
489335 AAGAGATTAT
* * * * *** * *
489345 TCAACTGTTT-GCTCGATTCTATCACAG-AAGAAGGTATATCAGCACCAACATTTCGTTTGATTC
1 TCAACT-TTTAGCTTGATTCTATCACAGAAAG-AGGTAGATCAACATCGGTATCTCGTTCGATTC
* *
489408 CATCACAGAAGGAGGTGGATCGACA---TT-TGTTCGGTCAAATCCATCGCAGAAGGAGTTGGAT
64 CATCACAAAAGGAGGTGGATCGACATTTTTATTTTCGGTCAAATCCATCGCAGAAGGAGTTGGAT
* *
489469 CAACATCAACTTTTTACTCGTTTCTATCACAGAAGGAGGTAGATCAGCACCAACATTTCGCTCGA
129 CATCATCAACTTTTTGCTCGTTTCTATCACAGAAGGAGGTAGATCAGCACCAACATTTCGCTCGA
* *
489534 TTCCATCACAGAAGGAGGTGGATCGATA---TT-TGTTCGCTCAAATCCATCACAGAAGGAGTTG
194 TTCCATCACAGAAGGAGGTGGATCGATATTTTTATTTTCGCTCAAATCCATCGCAGAAGGAGTTG
489595 GATCAGCG
259 GATCAGCG
* * * * *
489603 TCAACTTTTAGCTTGATTTTATCACAGAAGGAGGTAGATCAACATCGATGTATCGTTCGATTTCC
1 TCAACTTTTAGCTTGATTCTATCACAGAAAGAGGTAGATCAACATCGGTATCTCGTTCGA-TTCC
* ***** * ** *
489668 ATCACAGAACGAGAAGGAGGTAGATC-AGCACCAACA-TTTCAGTCGATTTCCATCACAGAAGGA
65 ATCAC---A--A-AAGGAGGTGGATCGA-CATTTTTATTTTCGGTC-AAATCCAT--C----GCA
* * * * * * * * *
489731 GAAGGAGGTAGATCATCACCAACATTTCGCTCGATTTCCATCACAGAAGCAGGTGGATC-GACAT
116 GAAGGAGTTGGATCATCATCAACTTTTTGCTCG-TTTCTATCACAGAAGGAGGTAGATCAG-CAC
**** * * ** * *
489795 TTTTATTTTCGCTCAAATCCATCGTAGAAGGAGTTAGATCAGAGTCGATATTTTTATTTTCGATC
179 CAACA-TTTCGCTCGATTCCATCACAGAAGGAG---G-T-GGA-TCGATATTTTTATTTTCGCTC
* * *
489860 AAATCCATTGCAGAAGGAGTTGGATCAACA
237 AAATCCATCGCAGAAGGAGTTGGATCAGCG
* *
489890 TCAACTTTTAGCTT-ATTCTATCACAGAAAGTGGTAGATCAACACCGGTATCTCGTTCGATTCCA
1 TCAACTTTTAGCTTGATTCTATCACAGAAAGAGGTAGATCAACATCGGTATCTCGTTCGATTCCA
* * *
489954 TTACAAAAGGAGGTGGATTGACATTTTTATTTTCGCTCAAATCCATCGCAGAAGGAGTTGGATCA
66 TCACAAAAGGAGGTGGATCGACATTTTTATTTTCGGTCAAATCCATCGCAGAAGGAGTTGGATCA
* * * * **
490019 TCTTCAACTTTTTTTGCGCGGTTCTATCACAGAAGGAGGTAGATCAGCACCAACATCTCATTCGA
131 TCATCAAC--TTTTTGCTCGTTTCTATCACAGAAGGAGGTAGATCAGCACCAACATTTCGCTCGA
*
490084 TTCCATCACAGAAGGAGGTGGATCAATATTTTTA-TTTCGCTCAAATCCATCGCAGAAGGAGTTG
194 TTCCATCACAGAAGGAGGTGGATCGATATTTTTATTTTCGCTCAAATCCATCGCAGAAGGAGTTG
490148 GATCAGCG
259 GATCAGCG
*
490156 TCAACTTTTAGCTTGATTCTATTACAGAAAGAGGTAGATCAACATCGGTATCTCGTTCGATTCCA
1 TCAACTTTTAGCTTGATTCTATCACAGAAAGAGGTAGATCAACATCGGTATCTCGTTCGATTCCA
* * * *
490221 TCACAGAAGGAGGTGGATCGACATTTTTATTTTTGGTCAAATCCATCGCATAAGGAGTTGGATAA
66 TCACAAAAGGAGGTGGATCGACATTTTTATTTTCGGTCAAATCCATCGCAGAAGGAGTTGGATCA
* * * * * * * *
490286 GCGTCAACTTTTAGCTCGATTCTATCACAGAAGGAGGTAGATCAGCATCGACATATCGTTCGATT
131 TCATCAACTTTTTGCTCGTTTCTATCACAGAAGGAGGTAGATCAGCACCAACATTTCGCTCGA-T
* *
490351 TCCATCACAGAAGGAGGTGGATCGATATTTTTATTTTCCCTCAAATCCATCGCATAAGGAGTTGG
195 TCCATCACAGAAGGAGGTGGATCGATATTTTTATTTTCGCTCAAATCCATCGCAGAAGGAGTTGG
490416 ATCAGCG
260 ATCAGCG
*
490423 TCAACTTCTT-GCTCGATTC-ATCACA
1 TCAACTT-TTAGCTTGATTCTATCACA
490448 AATAGAGTTA
Statistics
Matches: 683, Mismatches: 119, Indels: 78
0.78 0.14 0.09
Matches are distributed among these distances:
257 3 0.00
258 42 0.06
259 11 0.02
262 1 0.00
264 1 0.00
265 62 0.09
266 86 0.13
267 173 0.25
268 10 0.01
269 7 0.01
270 1 0.00
271 1 0.00
273 41 0.06
274 24 0.04
275 37 0.05
276 25 0.04
277 24 0.04
279 20 0.03
280 9 0.01
281 1 0.00
282 3 0.00
283 6 0.01
285 8 0.01
286 40 0.06
287 47 0.07
ACGTcount: A:0.30, C:0.20, G:0.21, T:0.29
Consensus pattern (266 bp):
TCAACTTTTAGCTTGATTCTATCACAGAAAGAGGTAGATCAACATCGGTATCTCGTTCGATTCCA
TCACAAAAGGAGGTGGATCGACATTTTTATTTTCGGTCAAATCCATCGCAGAAGGAGTTGGATCA
TCATCAACTTTTTGCTCGTTTCTATCACAGAAGGAGGTAGATCAGCACCAACATTTCGCTCGATT
CCATCACAGAAGGAGGTGGATCGATATTTTTATTTTCGCTCAAATCCATCGCAGAAGGAGTTGGA
TCAGCG
Found at i:495990 original size:18 final size:18
Alignment explanation
Indices: 495964--495998 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
495954 CTTATTTTAA
* *
495964 ATAAGGTTTAAGGAATTG
1 ATAAAGTTTAAAGAATTG
495982 ATAAAGTTTAAAGAATT
1 ATAAAGTTTAAAGAATT
495999 TATTTTGAGG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.46, C:0.00, G:0.20, T:0.34
Consensus pattern (18 bp):
ATAAAGTTTAAAGAATTG
Found at i:496066 original size:18 final size:18
Alignment explanation
Indices: 496043--496078 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
496033 CCCTTAAAAG
*
496043 CAATTCCTTAAACTTTAT
1 CAATTCCTTAAACCTTAT
496061 CAATTCCTTAAACCTTAT
1 CAATTCCTTAAACCTTAT
496079 TTCTCCCTCC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.33, C:0.25, G:0.00, T:0.42
Consensus pattern (18 bp):
CAATTCCTTAAACCTTAT
Found at i:501901 original size:5 final size:6
Alignment explanation
Indices: 501883--501907 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
501873 ATCTTTAGGA
501883 TTATTT TTATTT TTATTT TTATTT T
1 TTATTT TTATTT TTATTT TTATTT T
501908 GTTTATCTCT
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:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (6 bp):
TTATTT
Found at i:507177 original size:27 final size:27
Alignment explanation
Indices: 507136--507199 Score: 103
Period size: 27 Copynumber: 2.4 Consensus size: 27
507126 GTCTGACGTG
* *
507136 GCAG-TTTCTAGAAGGTTCAGTTAGCA
1 GCAGTTTTCTACAAGGTTCAGTCAGCA
507162 GCAGTTTTCTACAAGGTTCAGTCAGCA
1 GCAGTTTTCTACAAGGTTCAGTCAGCA
507189 GCAGTTTTCTA
1 GCAGTTTTCTA
507200 GAAGATCGGG
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
26 4 0.11
27 31 0.89
ACGTcount: A:0.25, C:0.19, G:0.23, T:0.33
Consensus pattern (27 bp):
GCAGTTTTCTACAAGGTTCAGTCAGCA
Found at i:512159 original size:2 final size:2
Alignment explanation
Indices: 512152--512190 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
512142 TTACATTGTG
512152 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
512191 TCTCATTTCC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:512369 original size:30 final size:30
Alignment explanation
Indices: 512313--512369 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 30
512303 GCATATTTTC
* **
512313 AAATATCAGGGACCAAAATGGTATATAAAT
1 AAATATCAAGGACCAAAATGACATATAAAT
512343 AAATATCAAGGACCAAAATGACATATA
1 AAATATCAAGGACCAAAATGACATATA
512370 CAAAATACTT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.53, C:0.12, G:0.14, T:0.21
Consensus pattern (30 bp):
AAATATCAAGGACCAAAATGACATATAAAT
Found at i:512658 original size:3 final size:3
Alignment explanation
Indices: 512652--512695 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
512642 GAGTTTTATT
512652 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
512696 TTAATTGAAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:514378 original size:35 final size:34
Alignment explanation
Indices: 514329--514416 Score: 115
Period size: 35 Copynumber: 2.5 Consensus size: 34
514319 TTGATAATAT
514329 AAAAAGAAAAATAGTTTGATTGTAAAA-AACAAAAG
1 AAAAA-AAAAATAGTTTGATTGTAAAATAA-AAAAG
514364 AAAGAAAAAAATAGTTTGATTGTAAAATTAAAAAAG
1 AAA-AAAAAAATAGTTTGATTGTAAAA-TAAAAAAG
* *
514400 AAAAGAAAATTAGTTTG
1 AAAAAAAAAATAGTTTG
514417 TGTCAGGTTT
Statistics
Matches: 48, Mismatches: 2, Indels: 6
0.86 0.04 0.11
Matches are distributed among these distances:
35 36 0.75
36 10 0.21
37 2 0.04
ACGTcount: A:0.60, C:0.01, G:0.15, T:0.24
Consensus pattern (34 bp):
AAAAAAAAAATAGTTTGATTGTAAAATAAAAAAG
Found at i:514478 original size:22 final size:19
Alignment explanation
Indices: 514453--514496 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 19
514443 TATATTTTTA
514453 ATTTTCTACATATTAATTATTC
1 ATTTT-TACATATT--TTATTC
514475 A-TTTTACATATTTTATTC
1 ATTTTTACATATTTTATTC
514493 ATTT
1 ATTT
514497 ATATATGTGC
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
18 7 0.33
19 2 0.10
20 8 0.38
21 3 0.14
22 1 0.05
ACGTcount: A:0.30, C:0.11, G:0.00, T:0.59
Consensus pattern (19 bp):
ATTTTTACATATTTTATTC
Found at i:514492 original size:18 final size:19
Alignment explanation
Indices: 514459--514496 Score: 60
Period size: 18 Copynumber: 2.0 Consensus size: 19
514449 TTTAATTTTC
514459 TACATATTAATTATTCATTT
1 TACATATT-ATTATTCATTT
514479 TACATATT-TTATTCATTT
1 TACATATTATTATTCATTT
514497 ATATATGTGC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 10 0.56
20 8 0.44
ACGTcount: A:0.32, C:0.11, G:0.00, T:0.58
Consensus pattern (19 bp):
TACATATTATTATTCATTT
Found at i:515440 original size:13 final size:13
Alignment explanation
Indices: 515424--515448 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
515414 AGTTAAGACC
515424 ATTTGATGAAAAG
1 ATTTGATGAAAAG
515437 ATTTGATGAAAA
1 ATTTGATGAAAA
515449 ACTAATAGAT
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:0.00, G:0.20, T:0.32
Consensus pattern (13 bp):
ATTTGATGAAAAG
Found at i:515533 original size:34 final size:35
Alignment explanation
Indices: 515490--515557 Score: 111
Period size: 35 Copynumber: 2.0 Consensus size: 35
515480 TAAACCAATA
* *
515490 AATAAGTCTATTCA-CAGGTGATATGACTTATTAT
1 AATAAGTCTATTCACCAAGTGATATAACTTATTAT
515524 AATAAGTCTATTCACCAAGTGATATAACTTATTA
1 AATAAGTCTATTCACCAAGTGATATAACTTATTA
515558 GAACTAACAT
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 14 0.45
35 17 0.55
ACGTcount: A:0.38, C:0.13, G:0.12, T:0.37
Consensus pattern (35 bp):
AATAAGTCTATTCACCAAGTGATATAACTTATTAT
Found at i:520595 original size:113 final size:113
Alignment explanation
Indices: 520466--520692 Score: 418
Period size: 113 Copynumber: 2.0 Consensus size: 113
520456 TAATTAACAA
*
520466 AATAAAAATAAAGTACAAATTATAGAAGATTTAAAACCTAGAAGTGTAAAATATAAACAGTGGAA
1 AATAAAAATAAAGTACAAATTATAGAAGATTTAAAACCTAGAAGTATAAAATATAAACAGTGGAA
*
520531 AGGGAGAGGGTTTGTATGCAATTTGACCATTTAAATTAAAACAAAAGT
66 AGGGAGAGGGTTTGCATGCAATTTGACCATTTAAATTAAAACAAAAGT
* *
520579 AATAAAAATAAAGTACAAATTATAGAATATTTAAAACCTAGAAGTATAAAATCTAAACAGTGGAA
1 AATAAAAATAAAGTACAAATTATAGAAGATTTAAAACCTAGAAGTATAAAATATAAACAGTGGAA
520644 AGGGAGAGGGTTTGCATGCAATTTGACCATTTAAATTAAAACAAAAGT
66 AGGGAGAGGGTTTGCATGCAATTTGACCATTTAAATTAAAACAAAAGT
520692 A
1 A
520693 CGGGGGTGGG
Statistics
Matches: 110, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
113 110 1.00
ACGTcount: A:0.50, C:0.08, G:0.17, T:0.26
Consensus pattern (113 bp):
AATAAAAATAAAGTACAAATTATAGAAGATTTAAAACCTAGAAGTATAAAATATAAACAGTGGAA
AGGGAGAGGGTTTGCATGCAATTTGACCATTTAAATTAAAACAAAAGT
Found at i:521247 original size:21 final size:21
Alignment explanation
Indices: 521221--521266 Score: 83
Period size: 21 Copynumber: 2.2 Consensus size: 21
521211 CGCCTGACAG
521221 CAACCTTAAGTTATACATAAA
1 CAACCTTAAGTTATACATAAA
*
521242 CAACCTTAAGTTATACATAAG
1 CAACCTTAAGTTATACATAAA
521263 CAAC
1 CAAC
521267 AAACATAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.46, C:0.22, G:0.07, T:0.26
Consensus pattern (21 bp):
CAACCTTAAGTTATACATAAA
Found at i:532983 original size:3 final size:3
Alignment explanation
Indices: 532975--533045 Score: 142
Period size: 3 Copynumber: 23.7 Consensus size: 3
532965 GTTAATGAAC
532975 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
533023 ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT AT
533046 AAAATATTTT
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 68 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:535343 original size:20 final size:19
Alignment explanation
Indices: 535306--535381 Score: 73
Period size: 20 Copynumber: 3.9 Consensus size: 19
535296 ATTAAAAATG
* *
535306 AATATATTAATA-AAATTT
1 AATATATAAATATATATTT
* *
535324 AATATATAATTAATGTATTT
1 AATATATAAAT-ATATATTT
535344 AATATACTAAATATATATTAT
1 AATATA-TAAATATATATT-T
*
535365 AATATATATATATATAT
1 AATATATAAATATATAT
535382 ACAATAATAT
Statistics
Matches: 47, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
18 9 0.19
19 1 0.02
20 26 0.55
21 11 0.23
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.46
Consensus pattern (19 bp):
AATATATAAATATATATTT
Found at i:535361 original size:2 final size:2
Alignment explanation
Indices: 535354--535482 Score: 93
Period size: 2 Copynumber: 69.0 Consensus size: 2
535344 AATATACTAA
*
535354 AT AT AT AT -T AT A- AT AT AT AT AT AT AT AT AC A- 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
* * *
535392 AT ACT AT AT A- AT AA AC AT AT -T AT AT AC A- AT AT AT ACT AT AT
1 AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT
* *
535433 A- AT AA AC AT AT -T AT AT AT -T AT AT AT A- AT AT AT ACT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT
535472 AT AT -T AT AT AT
1 AT AT AT AT AT AT
535483 TTATTTTTCT
Statistics
Matches: 104, Mismatches: 8, Indels: 30
0.73 0.06 0.21
Matches are distributed among these distances:
1 12 0.12
2 86 0.83
3 6 0.06
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.43
Consensus pattern (2 bp):
AT
Found at i:535400 original size:39 final size:37
Alignment explanation
Indices: 535345--535482 Score: 125
Period size: 36 Copynumber: 3.9 Consensus size: 37
535335 AATGTATTTA
535345 ATATAC-TAA-ATATA-TAT-TATAATATATATATAT
1 ATATACATAATATATACTATATATAATATATATATAT
* *
535378 ATATACAATAATATATAC--TATATAATAAACATAT-T
1 ATATAC-ATAATATATACTATATATAATATATATATAT
*
535413 ATATAC--AATATATACTATATAATAA-ACATATTATAT
1 ATATACATAATATATACTATAT-ATAATATATA-TATAT
* *
535449 ATTATATATAATATATACTATATATATTATATAT
1 A-TATACATAATATATACTATATATAATATATAT
535483 TTATTTTTCT
Statistics
Matches: 84, Mismatches: 7, Indels: 23
0.74 0.06 0.20
Matches are distributed among these distances:
32 9 0.11
33 6 0.07
34 6 0.07
35 18 0.21
36 19 0.23
37 4 0.05
38 4 0.05
39 18 0.21
ACGTcount: A:0.51, C:0.06, G:0.00, T:0.43
Consensus pattern (37 bp):
ATATACATAATATATACTATATATAATATATATATAT
Found at i:535415 original size:23 final size:25
Alignment explanation
Indices: 535363--535475 Score: 89
Period size: 23 Copynumber: 4.8 Consensus size: 25
535353 AATATATATT
535363 ATAATATATA-TATATATAT--ACA
1 ATAATATATACTATATATATAAACA
535385 ATAATATATACTATATA-ATAAAC-
1 ATAATATATACTATATATATAAACA
* * * *
535408 ATATTATATACAATATATACTATATA
1 ATAATATATACTATATATA-TAAACA
* * * *
535434 ATAA-ACATATTATATAT-TATA-T
1 ATAATATATACTATATATATAAACA
535456 ATAATATATACTATATATAT
1 ATAATATATACTATATATAT
535476 TATATATTTA
Statistics
Matches: 72, Mismatches: 11, Indels: 14
0.74 0.11 0.14
Matches are distributed among these distances:
22 16 0.22
23 36 0.50
24 4 0.06
25 13 0.18
26 3 0.04
ACGTcount: A:0.52, C:0.06, G:0.00, T:0.42
Consensus pattern (25 bp):
ATAATATATACTATATATATAAACA
Found at i:535423 original size:32 final size:32
Alignment explanation
Indices: 535353--535481 Score: 136
Period size: 32 Copynumber: 4.0 Consensus size: 32
535343 TAATATACTA
* *
535353 AATATATA-T-TATAATATATATATATATATAC
1 AATATATACTATATAATAAACATAT-TATATAC
535384 AATAATATATACTATATAATAAACATATTATATAC
1 ---AATATATACTATATAATAAACATATTATATAC
*
535419 AATATATACTATATAATAAACATATTATATAT
1 AATATATACTATATAATAAACATATTATATAC
* * * * *
535451 TATATATAATATATACTATATATATTATATA
1 AATATATACTATATAATAAACATATTATATA
535482 TTTATTTTTC
Statistics
Matches: 85, Mismatches: 8, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
32 57 0.67
34 8 0.09
35 8 0.09
36 12 0.14
ACGTcount: A:0.52, C:0.05, G:0.00, T:0.43
Consensus pattern (32 bp):
AATATATACTATATAATAAACATATTATATAC
Found at i:535479 original size:7 final size:7
Alignment explanation
Indices: 535440--535483 Score: 52
Period size: 7 Copynumber: 5.7 Consensus size: 7
535430 TATAATAAAC
535440 ATATTAT
1 ATATTAT
535447 ATATTAT
1 ATATTAT
535454 ATATAATAT
1 ATAT--TAT
535463 ATACTATAT
1 ATA-T-TAT
535472 ATATTAT
1 ATATTAT
535479 ATATT
1 ATATT
535484 TATTTTTCTT
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
7 19 0.56
8 1 0.03
9 13 0.38
10 1 0.03
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.52
Consensus pattern (7 bp):
ATATTAT
Found at i:535538 original size:16 final size:18
Alignment explanation
Indices: 535500--535540 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
535490 TCTTAAAAAC
*
535500 TATATTTTCGAAATATTA
1 TATATTTTCAAAATATTA
*
535518 TATATTTTCAAAATATAA
1 TATATTTTCAAAATATTA
535536 TATAT
1 TATAT
535541 GCATATATAG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.44, C:0.05, G:0.02, T:0.49
Consensus pattern (18 bp):
TATATTTTCAAAATATTA
Found at i:536578 original size:19 final size:19
Alignment explanation
Indices: 536556--536600 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 19
536546 TATATAATAT
536556 TTTTATAAAATATTTTACC
1 TTTTATAAAATATTTTACC
* * **
536575 TTTTGTTAAATATTTTTTC
1 TTTTATAAAATATTTTACC
536594 TTTTATA
1 TTTTATA
536601 TTTTTTTCGT
Statistics
Matches: 20, Mismatches: 6, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.29, C:0.07, G:0.02, T:0.62
Consensus pattern (19 bp):
TTTTATAAAATATTTTACC
Found at i:542326 original size:16 final size:16
Alignment explanation
Indices: 542274--542328 Score: 65
Period size: 16 Copynumber: 3.4 Consensus size: 16
542264 AAACTCGACC
542274 AAACCCAAACACAAATA
1 AAACCCAAAC-CAAATA
* * **
542291 AAACCCTAACCCAACC
1 AAACCCAAACCAAATA
542307 AAACCCAAACCAAATA
1 AAACCCAAACCAAATA
542323 AAACCC
1 AAACCC
542329 CAAAACCTAA
Statistics
Matches: 30, Mismatches: 8, Indels: 1
0.77 0.21 0.03
Matches are distributed among these distances:
16 21 0.70
17 9 0.30
ACGTcount: A:0.56, C:0.38, G:0.00, T:0.05
Consensus pattern (16 bp):
AAACCCAAACCAAATA
Found at i:542753 original size:2 final size:2
Alignment explanation
Indices: 542746--542793 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
542736 ATCTCTGTAA
542746 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
542788 AT AT AT
1 AT AT AT
542794 TTCTTTTCGA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:544971 original size:19 final size:19
Alignment explanation
Indices: 544949--544990 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
544939 AAACTTGGTA
544949 TTTTTATAAAAATAAAATG
1 TTTTTATAAAAATAAAATG
* * *
544968 TTTTTATTAAAATCACATG
1 TTTTTATAAAAATAAAATG
544987 TTTT
1 TTTT
544991 CACGATGTCC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.40, C:0.05, G:0.05, T:0.50
Consensus pattern (19 bp):
TTTTTATAAAAATAAAATG
Found at i:546287 original size:20 final size:20
Alignment explanation
Indices: 546263--546333 Score: 65
Period size: 20 Copynumber: 3.5 Consensus size: 20
546253 TCAATTCATT
546263 TTTGCATTTGCATCTCGCAT-
1 TTTGCATTTGCATCT-GCATC
* *
546283 TTTGCACTCT-CATTTTTGCATC
1 TTTGCA-TTTGCA--TCTGCATC
*
546305 TTTGCATTTGCATGTGCATC
1 TTTGCATTTGCATCTGCATC
546325 TTTGCATTT
1 TTTGCATTT
546334 TTACATTAGT
Statistics
Matches: 42, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
20 24 0.57
21 8 0.19
22 10 0.24
ACGTcount: A:0.14, C:0.23, G:0.14, T:0.49
Consensus pattern (20 bp):
TTTGCATTTGCATCTGCATC
Found at i:546288 original size:14 final size:14
Alignment explanation
Indices: 546269--546331 Score: 51
Period size: 14 Copynumber: 4.5 Consensus size: 14
546259 CATTTTTGCA
546269 TTTGCATCTCGCAT
1 TTTGCATCTCGCAT
*
546283 TTTGCA-CTCTCATT
1 TTTGCATCTCGCA-T
*
546297 TTTGCATCTTTGCA-
1 TTTGCATC-TCGCAT
*
546311 TTTGCATGT-GCAT
1 TTTGCATCTCGCAT
546324 CTTTGCAT
1 -TTTGCAT
546332 TTTTACATTA
Statistics
Matches: 40, Mismatches: 4, Indels: 10
0.74 0.07 0.19
Matches are distributed among these distances:
12 3 0.08
13 6 0.15
14 27 0.68
15 1 0.03
16 3 0.08
ACGTcount: A:0.14, C:0.24, G:0.14, T:0.48
Consensus pattern (14 bp):
TTTGCATCTCGCAT
Found at i:547706 original size:37 final size:38
Alignment explanation
Indices: 547647--547733 Score: 97
Period size: 37 Copynumber: 2.3 Consensus size: 38
547637 ACACAGAGAT
* * * *
547647 AAAAAG-AAGAGATATAGCAAAAAAATAAAAAATGAGA
1 AAAAAGAAAGAAATATAGAAAAAAAATAAAAAATAAAA
* * *
547684 GAAAAGAAAGAAATA-AGAAAAAAAGTAAAAAGTAAAA
1 AAAAAGAAAGAAATATAGAAAAAAAATAAAAAATAAAA
547721 AAAAAGAAAGAAA
1 AAAAAGAAAGAAA
547734 ATCTATCAAA
Statistics
Matches: 41, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
37 34 0.83
38 7 0.17
ACGTcount: A:0.75, C:0.01, G:0.16, T:0.08
Consensus pattern (38 bp):
AAAAAGAAAGAAATATAGAAAAAAAATAAAAAATAAAA
Found at i:549850 original size:57 final size:54
Alignment explanation
Indices: 549648--549848 Score: 255
Period size: 54 Copynumber: 3.7 Consensus size: 54
549638 GACGAATTTG
* *
549648 AAAGAAGCTAAGCCTGATTTTCAGGGGTTTCTTGATGTTTTCAAAAGAATTTTG
1 AAAGAAGCTAAGCCTAATTTTCAGGGGTTTCTTGATGTTTTCAAAAGAATTTTT
* * *
549702 AAAGAAGCTAAGCTTAATTTTTAGGGGTTTCTTGATGTTTTCAAAAAGCATTTTT
1 AAAGAAGCTAAGCCTAATTTTCAGGGGTTTCTTGATGTTTTC-AAAAGAATTTTT
** *
549757 AGAA-AA--TAAGTATAATTTTCAGGGGTTTCTTGATGATTATTTCCAAAGAATTTTT
1 A-AAGAAGCTAAGCCTAATTTTCAGGGGTTTCTTGATG--T-TTTCAAAAGAATTTTT
*
549812 AAAGAAGCTAAGCCTAATTTTTAGGGGTTTCTTGATG
1 AAAGAAGCTAAGCCTAATTTTCAGGGGTTTCTTGATG
549849 ATAATTGTAA
Statistics
Matches: 126, Mismatches: 13, Indels: 13
0.83 0.09 0.09
Matches are distributed among these distances:
53 26 0.21
54 41 0.33
55 27 0.21
56 6 0.05
57 26 0.21
ACGTcount: A:0.31, C:0.09, G:0.20, T:0.39
Consensus pattern (54 bp):
AAAGAAGCTAAGCCTAATTTTCAGGGGTTTCTTGATGTTTTCAAAAGAATTTTT
Found at i:549891 original size:58 final size:55
Alignment explanation
Indices: 549649--549907 Score: 196
Period size: 58 Copynumber: 4.7 Consensus size: 55
549639 ACGAATTTGA
* * * * *
549649 AAGAAGCTAAGCCTGATTTTCAGGGGTTTCTTGATG-T-TTT-CA-AAAGAATTTT
1 AAGAAACTAAGCTTAATTTTTAGGGGTTTCTTGATGATATTTAAAGAAAG-ATTTT
* *
549701 GAAAGAAGCTAAGCTTAATTTTTAGGGGTTTCTTGATG-T-TTTCAA-AAAGCATTTT
1 --AAGAAACTAAGCTTAATTTTTAGGGGTTTCTTGATGATATTTAAAGAAAG-ATTTT
* * * *
549756 TAGAAAATAAG-TATAATTTTCAGGGGTTTCTTGATGATTATTTCCAAAG-AA-TTTTT
1 AAGAAACTAAGCT-TAATTTTTAGGGGTTTCTTGATGA-TATTT--AAAGAAAGATTTT
* *
549812 AAAGAAGCTAAGCCTAATTTTTAGGGGTTTCTTGATGATAATTGTAAATGAAAGATTTT
1 -AAGAAACTAAGCTTAATTTTTAGGGGTTTCTTGATGAT-ATT-TAAA-GAAAGATTTT
* * *
549871 AAGAAACTAAGCTTTATTTTTAAGGGTATCTTGATGA
1 AAGAAACTAAGCTTAATTTTTAGGGGTTTCTTGATGA
549908 GTAAGTCCTT
Statistics
Matches: 168, Mismatches: 22, Indels: 26
0.78 0.10 0.12
Matches are distributed among these distances:
52 1 0.01
53 30 0.18
54 37 0.22
55 11 0.07
56 11 0.07
57 35 0.21
58 39 0.23
59 4 0.02
ACGTcount: A:0.33, C:0.08, G:0.19, T:0.39
Consensus pattern (55 bp):
AAGAAACTAAGCTTAATTTTTAGGGGTTTCTTGATGATATTTAAAGAAAGATTTT
Found at i:550015 original size:41 final size:41
Alignment explanation
Indices: 549903--550031 Score: 134
Period size: 42 Copynumber: 3.1 Consensus size: 41
549893 AGGGTATCTT
* **
549903 GATGAGTAAGTCCTTCGGGCCAT-CAGTAAGTTTTTCGAGCTT
1 GATGA-TAAGTCCTTCGGGCCATCCA-TAAGTCTTTCGAGCAA
* * * *
549945 GATGCTTAAATCCTTCGGGTCATCTATAAGTCTTTCGAGCAA
1 GATG-ATAAGTCCTTCGGGCCATCCATAAGTCTTTCGAGCAA
* * *
549987 GATGATAAGTCCTTTGGGCCATCCATAAGACCTTCGAGCAA
1 GATGATAAGTCCTTCGGGCCATCCATAAGTCTTTCGAGCAA
550028 GATG
1 GATG
550032 TTTTTAACAT
Statistics
Matches: 71, Mismatches: 14, Indels: 5
0.79 0.16 0.06
Matches are distributed among these distances:
41 34 0.48
42 36 0.51
43 1 0.01
ACGTcount: A:0.26, C:0.21, G:0.23, T:0.30
Consensus pattern (41 bp):
GATGATAAGTCCTTCGGGCCATCCATAAGTCTTTCGAGCAA
Found at i:550301 original size:41 final size:42
Alignment explanation
Indices: 550196--550293 Score: 135
Period size: 42 Copynumber: 2.4 Consensus size: 42
550186 AAATCAGCAA
* * *
550196 AAGTCCTTCAGGCCATCAATAAGTCTTTCGAGAATGATGTTT
1 AAGTCCTTCGGGCCATCAATAAGTCTTTCGAGAAAGATGATT
* * *
550238 AAATCCTTCGGGTCATCTATAAGTCTTTCGAGAAAGATGATT
1 AAGTCCTTCGGGCCATCAATAAGTCTTTCGAGAAAGATGATT
550280 -AGTCCTTCGGGCCA
1 AAGTCCTTCGGGCCA
550294 CCCATAAGAC
Statistics
Matches: 48, Mismatches: 8, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
41 12 0.25
42 36 0.75
ACGTcount: A:0.28, C:0.20, G:0.20, T:0.32
Consensus pattern (42 bp):
AAGTCCTTCGGGCCATCAATAAGTCTTTCGAGAAAGATGATT
Found at i:551082 original size:96 final size:96
Alignment explanation
Indices: 550957--551165 Score: 337
Period size: 96 Copynumber: 2.2 Consensus size: 96
550947 AGGGAAAAGA
* * *
550957 AGTTTATAATGAGAAGAGCTTGTTAAACCTATCGCTTGATTCATGGTATTTCAAATCAATGACGC
1 AGTTCATAATGAGAAGAGCTTGTTAAACCTATCGCTCGATTCATGGTATTTCAAATCAACGACGC
551022 CTCACTTGAGGGATTAACATTTCAAATGGAG
66 CTCACTTGAGGGATTAACATTTCAAATGGAG
* * *
551053 AGTTCATAATGAGAAGAGCTTGTTCAACCTATCGCTCGATTCATGGTATTTCGAATCAGCGACGC
1 AGTTCATAATGAGAAGAGCTTGTTAAACCTATCGCTCGATTCATGGTATTTCAAATCAACGACGC
* * *
551118 CTCGCTTGTGGGATTAACATTTTAAATGGAG
66 CTCACTTGAGGGATTAACATTTCAAATGGAG
551149 AGTTCATAATGAGAAGA
1 AGTTCATAATGAGAAGA
551166 ACTCATCCGA
Statistics
Matches: 104, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
96 104 1.00
ACGTcount: A:0.31, C:0.16, G:0.22, T:0.31
Consensus pattern (96 bp):
AGTTCATAATGAGAAGAGCTTGTTAAACCTATCGCTCGATTCATGGTATTTCAAATCAACGACGC
CTCACTTGAGGGATTAACATTTCAAATGGAG
Found at i:551293 original size:134 final size:135
Alignment explanation
Indices: 551053--551390 Score: 462
Period size: 134 Copynumber: 2.5 Consensus size: 135
551043 TCAAATGGAG
* *** *
551053 AGTTCATAATGAGAAGAGCTTGTTCAACCTATCGCTCGATTCATGGTATTTCGAATCAGCGACGC
1 AGTTCATAATGAGAAGAACTTGTTCAACCTATCGCTCGATTCATAACACTTCGAATCAGCGACGC
* * * *
551118 CTCGCTTGTGGGATTAACATTTTAAATGGAGAGTTCATAATGAGAAGAACTCATCC-GAGAGGGA
66 CTCGCTTGAGGGATTAACATTTCAAATGGAGAGTTCATAATGAGAAGAACTCATCCAAAGACGGA
*
551182 GAATA
131 GAAGA
* * * * * * *
551187 AGTTCATAATGAGAAGATCTTGTTCTACATATTGCTCGATTCACAACACTTCGAATCAGTGACAC
1 AGTTCATAATGAGAAGAACTTGTTCAACCTATCGCTCGATTCATAACACTTCGAATCAGCGACGC
* ** *
551252 CTCGCTTGAGGGATTGACATTTCCGATTGAGAGTTCATAATGAGAAGAACTCATCCAAAAGACGG
66 CTCGCTTGAGGGATTAACATTTCAAATGGAGAGTTCATAATGAGAAGAACTCATCC-AAAGACGG
551317 AGAAGA
130 AGAAGA
*
551323 AGTTCATAATGAGAAGAACTTGTTCAACCTATCGCTAGATTCATAACACTTCGAATCAGCGACGC
1 AGTTCATAATGAGAAGAACTTGTTCAACCTATCGCTCGATTCATAACACTTCGAATCAGCGACGC
551388 CTC
66 CTC
551391 ACTTTGTAGA
Statistics
Matches: 174, Mismatches: 28, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
134 104 0.60
136 70 0.40
ACGTcount: A:0.33, C:0.20, G:0.21, T:0.27
Consensus pattern (135 bp):
AGTTCATAATGAGAAGAACTTGTTCAACCTATCGCTCGATTCATAACACTTCGAATCAGCGACGC
CTCGCTTGAGGGATTAACATTTCAAATGGAGAGTTCATAATGAGAAGAACTCATCCAAAGACGGA
GAAGA
Found at i:551586 original size:18 final size:18
Alignment explanation
Indices: 551563--551613 Score: 52
Period size: 18 Copynumber: 2.9 Consensus size: 18
551553 TATTATTTTA
551563 CAACCAAACCCTAAAACC
1 CAACCAAACCCTAAAACC
*
551581 CAACCAAGCCC--AAACC
1 CAACCAAACCCTAAAACC
**
551597 CAAATAAAACCCTAAAA
1 C-AACCAAACCCTAAAA
551614 TATGGCAAAG
Statistics
Matches: 26, Mismatches: 4, Indels: 5
0.74 0.11 0.14
Matches are distributed among these distances:
16 6 0.23
17 7 0.27
18 10 0.38
19 3 0.12
ACGTcount: A:0.53, C:0.39, G:0.02, T:0.06
Consensus pattern (18 bp):
CAACCAAACCCTAAAACC
Found at i:554745 original size:5 final size:5
Alignment explanation
Indices: 554731--554857 Score: 70
Period size: 5 Copynumber: 25.2 Consensus size: 5
554721 AAAAATAAAA
* * * *
554731 AATATT AATAA AATAT AATAT AATAT ATAAAT AATAT -ATTT AATAT ACTA-
1 AATA-T AATAT AATAT AATAT AATAT A-ATAT AATAT AATAT AATAT AATAT
* *
554781 AATAT ATATTAT ATTAT ATTAT AATAT -ATAT -ATAT ATATAT ACA-AT
1 AATAT A-A-TAT AATAT AATAT AATAT AATAT AATAT A-ATAT A-ATAT
*
554827 AATAT -ATACT -ATAT AATAT ACATAT TATAT A
1 AATAT AATA-T AATAT AATAT A-ATAT AATAT A
554858 TTTATTTTTC
Statistics
Matches: 97, Mismatches: 13, Indels: 23
0.73 0.10 0.17
Matches are distributed among these distances:
4 19 0.20
5 55 0.57
6 19 0.20
7 4 0.04
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (5 bp):
AATAT
Found at i:554764 original size:16 final size:16
Alignment explanation
Indices: 554745--554858 Score: 60
Period size: 19 Copynumber: 6.9 Consensus size: 16
554735 TTAATAAAAT
554745 ATAATATAATATATAA
1 ATAATATAATATATAA
554761 ATAATAT-AT-T-T-A
1 ATAATATAATATATAA
*
554773 AT-ATACTAA-ATATAT
1 ATAATA-TAATATATAA
* *
554788 ATTATATTATATTATAA
1 ATAATATAATA-TATAA
554805 TATATATATATATATATACA
1 -ATA-ATATA-ATATATA-A
554825 ATAATATATACTATATAA
1 ATAATATA-A-TATATAA
*
554843 TATACATATTATATAT
1 -ATA-ATATAATATAT
554859 TTATTTTTCT
Statistics
Matches: 77, Mismatches: 6, Indels: 28
0.69 0.05 0.25
Matches are distributed among these distances:
11 3 0.04
12 4 0.05
13 3 0.04
14 2 0.03
15 6 0.08
16 11 0.14
17 4 0.05
18 15 0.19
19 21 0.27
20 8 0.10
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.45
Consensus pattern (16 bp):
ATAATATAATATATAA
Found at i:554769 original size:2 final size:2
Alignment explanation
Indices: 554743--554959 Score: 167
Period size: 2 Copynumber: 114.0 Consensus size: 2
554733 TATTAATAAA
* * *
554743 AT AT A- AT AT A- AT AT AT AA AT A- AT AT AT TT A- AT AT ACT AA
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT
554782 AT AT AT AT -T AT AT -T AT AT -T AT A- AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
554820 AT AC A- AT A- AT AT AT ACT AT AT A- AT AT AC AT AT -T AT AT AT
1 AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT
* * * * * * * *
554859 TT AT TT TT CT -T AA AA ACT AT AT AG AT -T GT A- AT AT AT AT AT
1 AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT
554899 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
554941 AT AT AT AT ACT TT AT AT AT
1 AT AT AT AT A-T AT AT AT AT
554960 TAAAACTATT
Statistics
Matches: 176, Mismatches: 20, Indels: 38
0.75 0.09 0.16
Matches are distributed among these distances:
1 15 0.09
2 155 0.88
3 6 0.03
ACGTcount: A:0.48, C:0.03, G:0.01, T:0.47
Consensus pattern (2 bp):
AT
Found at i:554776 original size:20 final size:21
Alignment explanation
Indices: 554742--554833 Score: 68
Period size: 21 Copynumber: 4.4 Consensus size: 21
554732 ATATTAATAA
*
554742 AATATA-ATATAATATA-TA-
1 AATATATATTTAATATACTAC
554760 AATAATATATTTAATATACTA-
1 AAT-ATATATTTAATATACTAC
* * *
554781 AATATATATTATATTATATTAT
1 AATATATATT-TAATATACTAC
*
554803 AATATATATATATATATA-TAC
1 AATATATATTTA-ATATACTAC
554824 AATAATATAT
1 AAT-ATATAT
554834 ACTATATAAT
Statistics
Matches: 61, Mismatches: 6, Indels: 10
0.79 0.08 0.13
Matches are distributed among these distances:
18 3 0.05
19 3 0.05
20 16 0.26
21 20 0.33
22 19 0.31
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (21 bp):
AATATATATTTAATATACTAC
Found at i:573371 original size:17 final size:17
Alignment explanation
Indices: 573344--573382 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
573334 AAATAACAAT
573344 TAATT-TAAATAATATC
1 TAATTATAAATAATATC
573360 TAATTATAAATAATATC
1 TAATTATAAATAATATC
573377 TAATTA
1 TAATTA
573383 ATTTAATTCA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 5 0.23
17 17 0.77
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (17 bp):
TAATTATAAATAATATC
Found at i:575300 original size:18 final size:21
Alignment explanation
Indices: 575255--575300 Score: 55
Period size: 20 Copynumber: 2.4 Consensus size: 21
575245 CCCCTATTGG
*
575255 GAGTATCAATACTACCCACTT
1 GAGTATCGATACTACCCACTT
575276 G-GTATCGATACT-CCC-C-T
1 GAGTATCGATACTACCCACTT
575293 GAGTATCG
1 GAGTATCG
575301 GTACCAAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
17 2 0.09
18 7 0.30
19 3 0.13
20 10 0.43
21 1 0.04
ACGTcount: A:0.26, C:0.28, G:0.17, T:0.28
Consensus pattern (21 bp):
GAGTATCGATACTACCCACTT
Found at i:584292 original size:16 final size:17
Alignment explanation
Indices: 584261--584293 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
584251 GGATCACCAA
584261 AAAATTTATCATTTTAAT
1 AAAATTTA-CATTTTAAT
584279 AAAATTTA-ATTTTAA
1 AAAATTTACATTTTAA
584294 ATATTATTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
18 8 0.53
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (17 bp):
AAAATTTACATTTTAAT
Found at i:585589 original size:219 final size:224
Alignment explanation
Indices: 585335--585781 Score: 825
Period size: 219 Copynumber: 2.0 Consensus size: 224
585325 ACTCACCTTT
585335 GGAAATTTATTAGTGTAAAATAGAATAAATTAGGGTTATGGTAAACAAAGTTTAAAAAAATTAAA
1 GGAAATTTATTAGTGTAAAATAGAATAAATTAGGGTTATGGTAAACAAAGTTTAAAAAAATTAAA
585400 TTAAGTATAATCTGGGGAAAAAAGGCAAAAGGGTCACGCGTTTC-A-AT-AAAAATCCATAC-AA
66 TTAAGTATAATCTGGGGAAAAAAGGCAAAAGGGTCACGCGTTTCAACATAAAAAATCCATACAAA
585461 TAAATTAAGAATAAAAGAGAAAGAAGAG-AAATTTAAAGTTCAGATGAAAT-AAAAGATATTAAA
131 TAAATTAAGAATAAAAGAGAAAGAAGAGAAAATTTAAAGTTCAGATGAAATAAAAAGATATTAAA
585524 GTGAAAAAATTAATATGAATAAAAAAATAG
196 GTGAAAAAATTAATATGAAT-AAAAAATAG
585554 GGAAATTTATTAGTGTAAAATAGAATAAATTAGGGTTATGGTAAACAAAGTTTAAAAAAATTAAA
1 GGAAATTTATTAGTGTAAAATAGAATAAATTAGGGTTATGGTAAACAAAGTTTAAAAAAATTAAA
585619 TTAAGTATAATCTGGGGAAAAAAGGCAAAAGGGTCACGCGTTTCAACATAAAAAATCCATACAAA
66 TTAAGTATAATCTGGGGAAAAAAGGCAAAAGGGTCACGCGTTTCAACATAAAAAATCCATACAAA
*
585684 TAAATTAAGAATAAAATAGAAAGAAGAGACAAATTTAAAGTTCAGATGAAATAAAAAGATATTAA
131 TAAATTAAGAATAAAAGAGAAAGAAGAGA-AAATTTAAAGTTCAGATGAAATAAAAAGATATTAA
585749 AGTGAAAAAATTAATATGAATAAAAAATAG
195 AGTGAAAAAATTAATATGAATAAAAAATAG
585779 GGA
1 GGA
585782 CTAAAATTTA
Statistics
Matches: 220, Mismatches: 1, Indels: 8
0.96 0.00 0.03
Matches are distributed among these distances:
219 109 0.50
220 1 0.00
221 2 0.01
222 12 0.05
223 29 0.13
225 34 0.15
226 33 0.15
ACGTcount: A:0.53, C:0.05, G:0.17, T:0.24
Consensus pattern (224 bp):
GGAAATTTATTAGTGTAAAATAGAATAAATTAGGGTTATGGTAAACAAAGTTTAAAAAAATTAAA
TTAAGTATAATCTGGGGAAAAAAGGCAAAAGGGTCACGCGTTTCAACATAAAAAATCCATACAAA
TAAATTAAGAATAAAAGAGAAAGAAGAGAAAATTTAAAGTTCAGATGAAATAAAAAGATATTAAA
GTGAAAAAATTAATATGAATAAAAAATAG
Found at i:587403 original size:31 final size:31
Alignment explanation
Indices: 587367--587425 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
587357 AACTTAAAAG
* *
587367 AATTTTGCAATACTGAAATTTAAATAATTTT
1 AATTTTACAATAATGAAATTTAAATAATTTT
*
587398 AATTTTATAATAATGAAATTTAAATAAT
1 AATTTTACAATAATGAAATTTAAATAAT
587426 CCATAAACTA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.47, C:0.03, G:0.05, T:0.44
Consensus pattern (31 bp):
AATTTTACAATAATGAAATTTAAATAATTTT
Found at i:587474 original size:22 final size:22
Alignment explanation
Indices: 587449--587989 Score: 804
Period size: 22 Copynumber: 24.6 Consensus size: 22
587439 TAATAATTTT
*
587449 TTTTAAAATAAATCAATTCATA
1 TTTTAAAATAAATCAATCCATA
587471 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
**
587493 TTTTAAAATAAAAT-TTTCCATA
1 TTTTAAAAT-AAATCAATCCATA
587515 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
587537 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
**
587559 TTTTAAAATAAAAT-TTTCCATA
1 TTTTAAAAT-AAATCAATCCATA
587581 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
587603 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
**
587625 TTTTAAAATAAAAT-TTTCCATA
1 TTTTAAAAT-AAATCAATCCATA
587647 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
587669 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
*
587691 TTTTAAAATAAATCAATCAATA
1 TTTTAAAATAAATCAATCCATA
* **
587713 ATTTAAAATAAAAT-TTTCCATA
1 TTTTAAAAT-AAATCAATCCATA
**
587735 TTTTAAAATTAAAT-TTTCCATA
1 TTTTAAAA-TAAATCAATCCATA
587757 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
587779 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
587801 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
***
587823 TTTTAAAATAAATTTTTCCATA
1 TTTTAAAATAAATCAATCCATA
587845 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
587867 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
587889 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
* *** *
587911 TTTTAAAATAATTTTTTTCATA
1 TTTTAAAATAAATCAATCCATA
587933 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
*
587955 TTTTAAAATAATTCAATCCATA
1 TTTTAAAATAAATCAATCCATA
587977 TTTTAAAATAAAT
1 TTTTAAAATAAAT
587990 TTTAAAATAG
Statistics
Matches: 471, Mismatches: 39, Indels: 18
0.89 0.07 0.03
Matches are distributed among these distances:
21 17 0.04
22 437 0.93
23 17 0.04
ACGTcount: A:0.48, C:0.11, G:0.00, T:0.40
Consensus pattern (22 bp):
TTTTAAAATAAATCAATCCATA
Found at i:588006 original size:11 final size:12
Alignment explanation
Indices: 587976--588015 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
587966 TTCAATCCAT
587976 ATTTTAAAATAA
1 ATTTTAAAATAA
*
587988 ATTTTAAAATAG
1 ATTTTAAAATAA
588000 A-TTT-AAAT-A
1 ATTTTAAAATAA
588009 ATTTTAA
1 ATTTTAA
588016 TTTCTTTGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
9 1 0.04
10 7 0.29
11 4 0.17
12 12 0.50
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.45
Consensus pattern (12 bp):
ATTTTAAAATAA
Found at i:588992 original size:21 final size:20
Alignment explanation
Indices: 588956--588999 Score: 54
Period size: 19 Copynumber: 2.1 Consensus size: 20
588946 GTGTGTATAT
588956 ATATATATTTAATTAT-TTA
1 ATATATATTTAATTATATTA
*
588975 ATATATACTTTATGTTATATTA
1 ATATATA-TTTA-ATTATATTA
588997 ATA
1 ATA
589000 CTACACAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 7 0.33
20 4 0.19
21 4 0.19
22 6 0.29
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.55
Consensus pattern (20 bp):
ATATATATTTAATTATATTA
Found at i:589651 original size:2 final size:2
Alignment explanation
Indices: 589626--589708 Score: 90
Period size: 2 Copynumber: 44.5 Consensus size: 2
589616 TATATTTTAA
589626 AT AT -T AT A- AT AT A- AT AT GAT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT -AT AT AT AT AT AT AT AT AT AT AT
* *
589666 AT AT AT -T AT A- AT AT AT AT AT AT A- AC AT AA AT AT AT AT -T
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
589704 AT AT A
1 AT AT A
589709 ATAAAATACA
Statistics
Matches: 70, Mismatches: 3, Indels: 16
0.79 0.03 0.18
Matches are distributed among these distances:
1 7 0.10
2 61 0.87
3 2 0.03
ACGTcount: A:0.52, C:0.01, G:0.01, T:0.46
Consensus pattern (2 bp):
AT
Found at i:590225 original size:2 final size:2
Alignment explanation
Indices: 590214--590274 Score: 108
Period size: 2 Copynumber: 31.5 Consensus size: 2
590204 CTAAATTTTC
590214 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
590255 TA TA T- TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA T
590275 TAAGTTGCTT
Statistics
Matches: 57, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
1 2 0.04
2 55 0.96
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:590359 original size:18 final size:18
Alignment explanation
Indices: 590336--590372 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
590326 ATCATGGTTA
590336 TATGTTATAACACGCCAT
1 TATGTTATAACACGCCAT
590354 TATGTTATAACACGCCAT
1 TATGTTATAACACGCCAT
590372 T
1 T
590373 TATATATGCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.32, C:0.22, G:0.11, T:0.35
Consensus pattern (18 bp):
TATGTTATAACACGCCAT
Found at i:593311 original size:2 final size:2
Alignment explanation
Indices: 593256--593291 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
593246 GAACTAGGGC
593256 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
593292 CACACACGCA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:594156 original size:29 final size:30
Alignment explanation
Indices: 594086--594145 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 30
594076 CAATTTAAGG
*
594086 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1 CAAAAT-GTTTTTGGACTTGAATTAAATTTA
594117 CAAAATGTTTTTGGACTT-AATTAAATTTA
1 CAAAATGTTTTTGGACTTGAATTAAATTTA
594146 TTCAAAGTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 10 0.36
30 12 0.43
31 6 0.21
ACGTcount: A:0.35, C:0.07, G:0.15, T:0.43
Consensus pattern (30 bp):
CAAAATGTTTTTGGACTTGAATTAAATTTA
Found at i:594251 original size:21 final size:21
Alignment explanation
Indices: 594225--594282 Score: 116
Period size: 21 Copynumber: 2.8 Consensus size: 21
594215 AGGGTGTCAA
594225 AGTGCATCCATGCACCCCTGC
1 AGTGCATCCATGCACCCCTGC
594246 AGTGCATCCATGCACCCCTGC
1 AGTGCATCCATGCACCCCTGC
594267 AGTGCATCCATGCACC
1 AGTGCATCCATGCACC
594283 TGCACTAATG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 37 1.00
ACGTcount: A:0.21, C:0.41, G:0.19, T:0.19
Consensus pattern (21 bp):
AGTGCATCCATGCACCCCTGC
Found at i:594401 original size:20 final size:20
Alignment explanation
Indices: 594336--594409 Score: 78
Period size: 20 Copynumber: 3.6 Consensus size: 20
594326 AATGCAATTA
*
594336 GTGCATCGATGCATCCT-TCT
1 GTGCATCGATGCATCATGT-T
* * *
594356 ATGCATCGATGCATCAAGGAT
1 GTGCATCGATGCATC-ATGTT
594377 GTGCATCGATGCATCATGTT
1 GTGCATCGATGCATCATGTT
*
594397 GTGCATCCATGCA
1 GTGCATCGATGCA
594410 CGAAGGCTGC
Statistics
Matches: 44, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
20 29 0.66
21 15 0.34
ACGTcount: A:0.23, C:0.24, G:0.23, T:0.30
Consensus pattern (20 bp):
GTGCATCGATGCATCATGTT
Found at i:594550 original size:20 final size:22
Alignment explanation
Indices: 594512--594551 Score: 66
Period size: 20 Copynumber: 1.9 Consensus size: 22
594502 TTTGAGTAGA
594512 AAAATCATCCCCAAACGGCTCC
1 AAAATCATCCCCAAACGGCTCC
594534 AAAA-CATCCCC-AACGGCT
1 AAAATCATCCCCAAACGGCT
594552 ATATACAACA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 7 0.39
21 7 0.39
22 4 0.22
ACGTcount: A:0.38, C:0.40, G:0.10, T:0.12
Consensus pattern (22 bp):
AAAATCATCCCCAAACGGCTCC
Found at i:596115 original size:146 final size:142
Alignment explanation
Indices: 595907--596206 Score: 507
Period size: 144 Copynumber: 2.1 Consensus size: 142
595897 CGAAGTGCCC
*
595907 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATCCTTAGAATCA
1 CGTAAAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATCCTTAGAATCA
595972 TATACATATACTATGGATCAAGTATGTGTC-TTCAAGACTTCACACAGGTTCCAAAGGATATACA
66 TATAC--ATACTA-GGATCAAGTATGTGTCTTTCAAGACTTCACACAGGTTCCAAA-G-TATACA
596036 TATGTCCTAAAGAACCG
126 TATGTCCTAAAGAACCG
596053 CGTAAAATTGCACCGTAGTGCCATATAAT-A-GTCCATAAGGACCACATAGAATTCCTTAAGAAT
1 CGTAAAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAA-TCCTT-AGAAT
596116 CATATACATACTAGGATCAAGTATGTGTCTTTCAAGACTTCACACAGGTTCCAAAGTATACATAT
64 CATATACATACTAGGATCAAGTATGTGTCTTTCAAGACTTCACACAGGTTCCAAAGTATACATAT
596181 GTCCTAAAGAACCG
129 GTCCTAAAGAACCG
596195 CGTAAAATTGCA
1 CGTAAAATTGCA
596207 ATGTCCTAAA
Statistics
Matches: 150, Mismatches: 1, Indels: 10
0.93 0.01 0.06
Matches are distributed among these distances:
142 35 0.23
143 17 0.11
144 52 0.35
145 6 0.04
146 40 0.27
ACGTcount: A:0.37, C:0.21, G:0.16, T:0.27
Consensus pattern (142 bp):
CGTAAAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATCCTTAGAATCA
TATACATACTAGGATCAAGTATGTGTCTTTCAAGACTTCACACAGGTTCCAAAGTATACATATGT
CCTAAAGAACCG
Found at i:596219 original size:28 final size:28
Alignment explanation
Indices: 596179--596234 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
596169 AAGTATACAT
596179 ATGTCCTAAAGAACCGCGTAAAATTGCA
1 ATGTCCTAAAGAACCGCGTAAAATTGCA
596207 ATGTCCTAAAGAACCGCGTAAAATTGCA
1 ATGTCCTAAAGAACCGCGTAAAATTGCA
596235 CCGTAGTGCC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.39, C:0.21, G:0.18, T:0.21
Consensus pattern (28 bp):
ATGTCCTAAAGAACCGCGTAAAATTGCA
Found at i:596339 original size:170 final size:172
Alignment explanation
Indices: 596037--596370 Score: 588
Period size: 170 Copynumber: 2.0 Consensus size: 172
596027 GGATATACAT
596037 ATGTCCTAAAGAACCGCGTAAAATTGCACCGTAGTGCCATATAATAGTCCATAAGGACCACATAG
1 ATGTCCTAAAGAACCGCGTAAAATTGCACCGTAGTGCCATATAATAGTCCATAAGGACCACATAG
* *
596102 AATTCCTTAAGAATCATATACATACTAGGATCAAGTATGTGTCTTTCAAGACTTCACACAGGTTC
66 AATTCCTTAAGAATCATACACATACTAGGATCAAGTATGTGTCTTTCAAGACTTCACACAAGTTC
596167 CAAA-G-TATACATATGTCCTAAAGAACCGCGTAAAATTGCA
131 CAAAGGATATACATATGTCCTAAAGAACCGCGTAAAATTGCA
596207 ATGTCCTAAAGAACCGCGTAAAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACAT
1 ATGTCCTAAAGAACCGCGTAAAATTGCACCGTAGTGCCATATAAT-A-GTCCATAAGGACCACAT
596272 AGAATTCC-TAAGAATCATACA-ATACT-GGATCAAGTATGTGTCTTTCAAGACTTCACACACAG
64 AGAATTCCTTAAGAATCATACACATACTAGGATCAAGTATGTGTCTTTCAAGACTTCACACA-AG
596334 TTCCAAAGGATATACATATGTCCTAAAGAACCGCGTA
128 TTCCAAAGGATATACATATGTCCTAAAGAACCGCGTA
596371 GACCCTCTAC
Statistics
Matches: 157, Mismatches: 2, Indels: 8
0.94 0.01 0.05
Matches are distributed among these distances:
169 33 0.21
170 58 0.37
171 14 0.09
172 52 0.33
ACGTcount: A:0.37, C:0.22, G:0.16, T:0.25
Consensus pattern (172 bp):
ATGTCCTAAAGAACCGCGTAAAATTGCACCGTAGTGCCATATAATAGTCCATAAGGACCACATAG
AATTCCTTAAGAATCATACACATACTAGGATCAAGTATGTGTCTTTCAAGACTTCACACAAGTTC
CAAAGGATATACATATGTCCTAAAGAACCGCGTAAAATTGCA
Found at i:597171 original size:65 final size:64
Alignment explanation
Indices: 597008--597178 Score: 200
Period size: 63 Copynumber: 2.6 Consensus size: 64
596998 TTTTTCTCAT
* * * *
597008 GGGGGAATCGGTTCCCCCCCTGGGGGTATCGATTCCCCTAAAGCATTCTGGAATTTCCTATCGAT
1 GGGGGTATCGGTT--CCCCATGGGGGTATCGATTCCCCT-AAGCATTCTGGAAATTCATATCGAT
597073 GA
63 GA
* * *
597075 GGGGGTATCGGTTCCCCATGGGGGTATCGATTCCTCT-AGCATTCTGGAAATTCATTTCGTTGA
1 GGGGGTATCGGTTCCCCATGGGGGTATCGATTCCCCTAAGCATTCTGGAAATTCATATCGATGA
* * *
597138 GGGGGTATCGGTTCCCCTTGAATGGGTACCGATTCCCCTAA
1 GGGGGTATCGGTTCCCCATG--GGGGTATCGATTCCCCTAA
597179 CCAGAAATCC
Statistics
Matches: 90, Mismatches: 11, Indels: 7
0.83 0.10 0.06
Matches are distributed among these distances:
63 41 0.46
65 36 0.40
66 1 0.01
67 12 0.13
ACGTcount: A:0.18, C:0.25, G:0.28, T:0.29
Consensus pattern (64 bp):
GGGGGTATCGGTTCCCCATGGGGGTATCGATTCCCCTAAGCATTCTGGAAATTCATATCGATGA
Found at i:603128 original size:23 final size:23
Alignment explanation
Indices: 603102--603146 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
603092 CACCACAGCT
*
603102 CGTATAAATGCACCGAAGTGCCC
1 CGTAGAAATGCACCGAAGTGCCC
* *
603125 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAAATGCACCGAAGTGCC
603147 ATATAATAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.27, C:0.29, G:0.24, T:0.20
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCC
Found at i:603400 original size:149 final size:149
Alignment explanation
Indices: 603125--603575 Score: 884
Period size: 149 Copynumber: 3.0 Consensus size: 149
603115 CGAAGTGCCC
*
603125 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCCTTAAGAAT
1 CGTAAAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCCTTAAGAAT
603190 CATATACATATACTATGGATCAAGTATGTGTCTTTCAAGACTTCACACAGGTTCCAAAGGATATA
66 CATATACATATACTATGGATCAAGTATGTGTCTTTCAAGACTTCACACAGGTTCCAAAGGATATA
603255 CATATGTCCTAAAGAACCG
131 CATATGTCCTAAAGAACCG
603274 CGTAAAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCCTTAAGAAT
1 CGTAAAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCCTTAAGAAT
603339 CATATACATATACTATGGATCAAGTATGTGTCTTTCAAGACTTCACACAGGTTCCAAAGGATATA
66 CATATACATATACTATGGATCAAGTATGTGTCTTTCAAGACTTCACACAGGTTCCAAAGGATATA
*
603404 CATATATCCTAAAGAACCG
131 CATATGTCCTAAAGAACCG
603423 CGTAAAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCCTTAAGAAT
1 CGTAAAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCCTTAAGAAT
603488 CATATACATATACTATGGATCAAGTATGTGTCTTTCAAGACTTCACACAGGTTCCAAAGGATATA
66 CATATACATATACTATGGATCAAGTATGTGTCTTTCAAGACTTCACACAGGTTCCAAAGGATATA
603553 CATATGTCCTAAAGAACCG
131 CATATGTCCTAAAGAACCG
603572 CGTA
1 CGTA
603576 GACCCTCTAC
Statistics
Matches: 299, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
149 299 1.00
ACGTcount: A:0.37, C:0.20, G:0.16, T:0.27
Consensus pattern (149 bp):
CGTAAAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCCTTAAGAAT
CATATACATATACTATGGATCAAGTATGTGTCTTTCAAGACTTCACACAGGTTCCAAAGGATATA
CATATGTCCTAAAGAACCG
Found at i:604127 original size:19 final size:20
Alignment explanation
Indices: 604090--604127 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
604080 TTTTTTCTCA
*
604090 TGGGGGAATCGGTTCCCCCC
1 TGGGGGAATCGATTCCCCCC
*
604110 TGGGGGTATCGATTCCCC
1 TGGGGGAATCGATTCCCC
604128 TAAAGCATTC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.11, C:0.32, G:0.34, T:0.24
Consensus pattern (20 bp):
TGGGGGAATCGATTCCCCCC
Found at i:604262 original size:67 final size:67
Alignment explanation
Indices: 604091--604240 Score: 221
Period size: 67 Copynumber: 2.3 Consensus size: 67
604081 TTTTTCTCAT
* * * *
604091 GGGGGAATCGGTTCCCCCCTGGGGGTATCGATTCCCCTAAAGCATTCTGGAATTTCCTATACGAT
1 GGGGGTATCGGTTCCCCCATGGGGGTATCGATTCCCCTAAAGCATTCTGGAAATTCATATACGAT
604156 GA
66 GA
** * *
604158 GGGGGTATCGGTTCCCCCATGGGGGTATCGATTCCCCTCTAGCATTCTGGAAATTCAT-TTCGTT
1 GGGGGTATCGGTTCCCCCATGGGGGTATCGATTCCCCTAAAGCATTCTGGAAATTCATATACGAT
604222 GA
66 GA
604224 GGGGGTATCGGTTCCCC
1 GGGGGTATCGGTTCCCC
604241 TTGAATGGGT
Statistics
Matches: 75, Mismatches: 8, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
66 23 0.31
67 52 0.69
ACGTcount: A:0.17, C:0.25, G:0.29, T:0.29
Consensus pattern (67 bp):
GGGGGTATCGGTTCCCCCATGGGGGTATCGATTCCCCTAAAGCATTCTGGAAATTCATATACGAT
GA
Found at i:605378 original size:19 final size:20
Alignment explanation
Indices: 605354--605401 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
605344 AATGATTTTC
*
605354 TTTTGAAAACAAAAAT-AGA
1 TTTTGAAAACAAAAATGAAA
* *
605373 TTTTGAAAGCCAAAATGAAA
1 TTTTGAAAACAAAAATGAAA
605393 TTTTGAAAA
1 TTTTGAAAA
605402 AGGATTTAGA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.52, C:0.06, G:0.12, T:0.29
Consensus pattern (20 bp):
TTTTGAAAACAAAAATGAAA
Found at i:606662 original size:34 final size:30
Alignment explanation
Indices: 606624--606692 Score: 95
Period size: 30 Copynumber: 2.2 Consensus size: 30
606614 TTGATATAAC
606624 AATTTAAGGCAAAATGGTTTTTGGACTTGAATTG
1 AATTTAA--CAAAAT-GTTTTTGGACTT-AATTG
606658 AATTT-ACAAAATGTTTTTGGACTTAATTG
1 AATTTAACAAAATGTTTTTGGACTTAATTG
606687 AATTTA
1 AATTTA
606693 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:606703 original size:29 final size:30
Alignment explanation
Indices: 606633--606692 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 30
606623 CAATTTAAGG
606633 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1 CAAAAT-GTTTTTGGACTTGAATTGAATTTA
606664 CAAAATGTTTTTGGACTT-AATTGAATTTA
1 CAAAATGTTTTTGGACTTGAATTGAATTTA
606693 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:606798 original size:21 final size:21
Alignment explanation
Indices: 606772--606829 Score: 107
Period size: 21 Copynumber: 2.8 Consensus size: 21
606762 AGGGTGTCAA
606772 AGTGCATCCATGCACCCCTGC
1 AGTGCATCCATGCACCCCTGC
*
606793 AGTGCATCCATGCATCCCTGC
1 AGTGCATCCATGCACCCCTGC
606814 AGTGCATCCATGCACC
1 AGTGCATCCATGCACC
606830 TGCACTAATG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.21, C:0.40, G:0.19, T:0.21
Consensus pattern (21 bp):
AGTGCATCCATGCACCCCTGC
Found at i:606946 original size:20 final size:20
Alignment explanation
Indices: 606883--606955 Score: 94
Period size: 20 Copynumber: 3.6 Consensus size: 20
606873 AATGCAATTA
* **
606883 GTGCATCGATGCATCCTTCT
1 GTGCATCGATGCATCATGAT
*
606903 GTGCATCGATGCATCAAGGAT
1 GTGCATCGATGCATC-ATGAT
606924 GTGCATCGATGCATCATGAT
1 GTGCATCGATGCATCATGAT
606944 GTGCATC-ATGCA
1 GTGCATCGATGCA
606956 CGAAGGCTGC
Statistics
Matches: 47, Mismatches: 5, Indels: 3
0.85 0.09 0.05
Matches are distributed among these distances:
19 5 0.11
20 26 0.55
21 16 0.34
ACGTcount: A:0.23, C:0.23, G:0.25, T:0.29
Consensus pattern (20 bp):
GTGCATCGATGCATCATGAT
Done.