Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009140.1 Hibiscus syriacus cultivar Beakdansim tig00112647_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: 511116
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 3
Found at i:410348 original size:12 final size:12
Alignment explanation
Indices: 410327--410361 Score: 61
Period size: 12 Copynumber: 2.9 Consensus size: 12
410317 TTAAGCATAT
410327 TATTATTATTAC
1 TATTATTATTAC
*
410339 TATTACTATTAC
1 TATTATTATTAC
410351 TATTATTATTA
1 TATTATTATTA
410362 TTAAATAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.34, C:0.09, G:0.00, T:0.57
Consensus pattern (12 bp):
TATTATTATTAC
Found at i:410776 original size:13 final size:14
Alignment explanation
Indices: 410758--410790 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
410748 CCTCACCTGC
410758 AAAAGAAGA-AAAA
1 AAAAGAAGAGAAAA
*
410771 AAAAGAATAGAAAA
1 AAAAGAAGAGAAAA
410785 AAAAGA
1 AAAAGA
410791 GGACAACTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 8 0.44
14 10 0.56
ACGTcount: A:0.82, C:0.00, G:0.15, T:0.03
Consensus pattern (14 bp):
AAAAGAAGAGAAAA
Found at i:411639 original size:43 final size:42
Alignment explanation
Indices: 411589--411678 Score: 119
Period size: 43 Copynumber: 2.1 Consensus size: 42
411579 TTCATTTTGT
411589 TTTTATTACT-TTCAATATGTTTAAATTATTGCTTTAATTATTA
1 TTTTATTACTATTCAATAT-TTT-AATTATTGCTTTAATTATTA
* **
411632 TTTTATTATTAATTTTATATTTTAATTATTGCTTTAATTATTA
1 TTTTATTACT-ATTCAATATTTTAATTATTGCTTTAATTATTA
411675 TTTT
1 TTTT
411679 TATCTTAGTC
Statistics
Matches: 42, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
43 33 0.79
44 3 0.07
45 6 0.14
ACGTcount: A:0.29, C:0.04, G:0.03, T:0.63
Consensus pattern (42 bp):
TTTTATTACTATTCAATATTTTAATTATTGCTTTAATTATTA
Found at i:411657 original size:31 final size:32
Alignment explanation
Indices: 411621--411681 Score: 88
Period size: 32 Copynumber: 1.9 Consensus size: 32
411611 AAATTATTGC
*
411621 TTTAATTATT-ATTTTATTATTAATTTTATAT
1 TTTAATTATTGATTTAATTATTAATTTTATAT
* *
411652 TTTAATTATTGCTTTAATTATTATTTTTAT
1 TTTAATTATTGATTTAATTATTAATTTTAT
411682 CTTAGTCTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
31 10 0.38
32 16 0.62
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.67
Consensus pattern (32 bp):
TTTAATTATTGATTTAATTATTAATTTTATAT
Found at i:412123 original size:23 final size:21
Alignment explanation
Indices: 412091--412132 Score: 57
Period size: 23 Copynumber: 1.9 Consensus size: 21
412081 CATTTTCTAA
*
412091 TATTTCTAAATAATTAAATATCT
1 TATTTATAAAT-A-TAAATATCT
412114 TATTTATAAATATAAATAT
1 TATTTATAAATATAAATAT
412133 TTTCTTAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 7 0.39
22 1 0.06
23 10 0.56
ACGTcount: A:0.48, C:0.05, G:0.00, T:0.48
Consensus pattern (21 bp):
TATTTATAAATATAAATATCT
Found at i:416557 original size:18 final size:17
Alignment explanation
Indices: 416510--416557 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 17
416500 TTTTTAAGAC
416510 TAATTATAATATTAGTA
1 TAATTATAATATTAGTA
*
416527 TAAATATATATATTA-TGA
1 TAATTATA-ATATTAGT-A
416545 TAATTTATAATAT
1 TAA-TTATAATAT
416558 AATTTTAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
17 8 0.31
18 14 0.54
19 4 0.15
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (17 bp):
TAATTATAATATTAGTA
Found at i:417697 original size:45 final size:47
Alignment explanation
Indices: 417611--417698 Score: 117
Period size: 45 Copynumber: 1.9 Consensus size: 47
417601 TATTATTTTA
* * * * *
417611 TTTTCTAAATAAATGCATGTGAACTAGAAATCATGTGGTTAGGTTAT
1 TTTTCCAAACAAATGCATGTGAACTAAAAAGCATGAGGTTAGGTTAT
417658 TTTTCCAAACAAA-GCATG-GAACTAAAAAGCATGAGGTTAGG
1 TTTTCCAAACAAATGCATGTGAACTAAAAAGCATGAGGTTAGG
417699 ATATGATTTG
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
45 20 0.56
46 5 0.14
47 11 0.31
ACGTcount: A:0.38, C:0.11, G:0.20, T:0.31
Consensus pattern (47 bp):
TTTTCCAAACAAATGCATGTGAACTAAAAAGCATGAGGTTAGGTTAT
Found at i:423007 original size:23 final size:23
Alignment explanation
Indices: 422977--423020 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
422967 TGCTGTAAGG
422977 ATGATAGATTCTCTTTTCAAATA
1 ATGATAGATTCTCTTTTCAAATA
*
423000 ATGATAGATTCTTTTTTCAAA
1 ATGATAGATTCTCTTTTCAAA
423021 GACAGAAAGC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.34, C:0.11, G:0.09, T:0.45
Consensus pattern (23 bp):
ATGATAGATTCTCTTTTCAAATA
Found at i:423686 original size:20 final size:20
Alignment explanation
Indices: 423661--423702 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
423651 ATTTCCACGA
423661 ATTTGTAGAA-CCTTCGGGTC
1 ATTTGTA-AATCCTTCGGGTC
*
423681 ATTTGTAAATCCTTTGGGTC
1 ATTTGTAAATCCTTCGGGTC
423701 AT
1 AT
423703 CTATCAGTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 2 0.10
20 18 0.90
ACGTcount: A:0.21, C:0.17, G:0.21, T:0.40
Consensus pattern (20 bp):
ATTTGTAAATCCTTCGGGTC
Found at i:425742 original size:2 final size:2
Alignment explanation
Indices: 425730--425766 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
425720 ATAATATTAG
*
425730 TA TA AA 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 T
425767 TATGATAATT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:432513 original size:18 final size:18
Alignment explanation
Indices: 432490--432524 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
432480 TTTTAGTATT
432490 AATATTTTATTTTATTTA
1 AATATTTTATTTTATTTA
432508 AATATTTTATTTTATTT
1 AATATTTTATTTTATTT
432525 TTATTATGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (18 bp):
AATATTTTATTTTATTTA
Found at i:434308 original size:17 final size:17
Alignment explanation
Indices: 434271--434322 Score: 56
Period size: 17 Copynumber: 3.2 Consensus size: 17
434261 ATATTTTGTA
*
434271 TTTAATTTATTTAAGCA-
1 TTTAATTTATTTAA-TAT
434288 TTTAATTTATTTAATAT
1 TTTAATTTATTTAATAT
*
434305 TTT-ATTTAATTAAT-T
1 TTTAATTTATTTAATAT
434320 TTT
1 TTT
434323 TTGCAGATAT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
15 4 0.12
16 11 0.34
17 17 0.53
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (17 bp):
TTTAATTTATTTAATAT
Found at i:438447 original size:14 final size:15
Alignment explanation
Indices: 438428--438456 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
438418 CACGTTATCT
438428 ATTTATTA-TTTTAA
1 ATTTATTAGTTTTAA
438442 ATTTATTAGTTTTAA
1 ATTTATTAGTTTTAA
438457 GAAAATCTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.62
Consensus pattern (15 bp):
ATTTATTAGTTTTAA
Found at i:439686 original size:16 final size:15
Alignment explanation
Indices: 439667--439725 Score: 68
Period size: 15 Copynumber: 4.0 Consensus size: 15
439657 AATATAATTA
439667 ATAATATATATTATTT
1 ATAATATA-ATTATTT
*
439683 ATAATATACTTATTT
1 ATAATATAATTATTT
*
439698 -TAATA-AATAATTT
1 ATAATATAATTATTT
*
439711 ATAATATGATTATTT
1 ATAATATAATTATTT
439726 CAATAGAATA
Statistics
Matches: 36, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
13 6 0.17
14 10 0.28
15 12 0.33
16 8 0.22
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.53
Consensus pattern (15 bp):
ATAATATAATTATTT
Found at i:439689 original size:14 final size:14
Alignment explanation
Indices: 439672--439725 Score: 65
Period size: 14 Copynumber: 3.8 Consensus size: 14
439662 AATTAATAAT
439672 ATATATTATTTATA
1 ATATATTATTTATA
439686 ATATACTTATTT-TA
1 ATATA-TTATTTATA
* *
439700 ATAAATAATTTATA
1 ATATATTATTTATA
439714 ATATGATTATTT
1 ATAT-ATTATTT
439726 CAATAGAATA
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
13 5 0.15
14 16 0.48
15 12 0.36
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.54
Consensus pattern (14 bp):
ATATATTATTTATA
Found at i:439710 original size:28 final size:29
Alignment explanation
Indices: 439679--439735 Score: 82
Period size: 28 Copynumber: 2.0 Consensus size: 29
439669 AATATATATT
*
439679 ATTTATAATAT-ACTTATTTTAATA-AATA
1 ATTTATAATATGA-TTATTTCAATAGAATA
439707 ATTTATAATATGATTATTTCAATAGAATA
1 ATTTATAATATGATTATTTCAATAGAATA
439736 TACTAATCTT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
28 21 0.81
29 5 0.19
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.47
Consensus pattern (29 bp):
ATTTATAATATGATTATTTCAATAGAATA
Found at i:439804 original size:15 final size:15
Alignment explanation
Indices: 439769--439810 Score: 59
Period size: 14 Copynumber: 2.9 Consensus size: 15
439759 AAAATTGTAG
**
439769 AAATAATATTTTAAT
1 AAATAATATTGAAAT
439784 -AATAATATTGAAAT
1 AAATAATATTGAAAT
439798 AAATAATATTGAA
1 AAATAATATTGAA
439811 TAGATTATTC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
14 12 0.50
15 12 0.50
ACGTcount: A:0.57, C:0.00, G:0.05, T:0.38
Consensus pattern (15 bp):
AAATAATATTGAAAT
Found at i:449926 original size:13 final size:13
Alignment explanation
Indices: 449908--449933 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
449898 AAAAATTAAA
449908 ATGGTTCAGAGAT
1 ATGGTTCAGAGAT
449921 ATGGTTCAGAGAT
1 ATGGTTCAGAGAT
449934 GATATATCTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.08, G:0.31, T:0.31
Consensus pattern (13 bp):
ATGGTTCAGAGAT
Found at i:456540 original size:246 final size:243
Alignment explanation
Indices: 456093--457311 Score: 1654
Period size: 246 Copynumber: 5.0 Consensus size: 243
456083 TCTTGATCCA
456093 AAAGCAACCCCGTTGACATCTACAGGGGGTAAAGAAATCTCACTAGGAGATGCTAAATGGCCATT
1 AAAGCAACCCCGTTGACATCTACAGGGGGTAAAGAAATCTCAC-AGGAGATGCTAAATGGCCATT
456158 TTCAAAATCTCCAATCTTTGGATTGGAAGCAGTAGGAAGAGCACTTCCGTCCTCGACATGAATAT
65 TTCAAAATCTCCAATCTTTGGATTGGAAGCAGTAGGAAGAGCACTTCCGTCCT-GACATGAATAT
* * * * * *
456223 GTGAAATGCCAACAGAATCTGTCTTTTCAGATATCTGTTCATCTGAACCATTATGTATTCCCCGA
129 GCGAAATGCCAACAGAACCAGTCTTTTGAGATATCTGTTCATCTGAAACATCATGTATTCCCCGA
* * * *
456288 GTCTTAGAATCTTCCATCAGTTTACCCTGACTATCTTTCTCCGTTTCACC
194 GTCTTAGAATCTTCCATCAGTCTACCCTGATTATCTTTCTCAGTTTCATC
* * *
456338 GAAAGAAACCCCGTTGACATCTACAGGGGGTAAAGAAATCTCAGCAGGAGATGTTAAACGGCCAT
1 -AAAGCAACCCCGTTGACATCTACAGGGGGTAAAGAAATCTCA-CAGGAGATGCTAAATGGCCAT
* * *
456403 CTACAAAATCTCCGATCTTTGGATTGGAAGCAGTAGGAAGAGCACTTCCGTCCTGAACATGAATA
64 TTTCAAAATCTCCAATCTTTGGATTGGAAGCAGTAGGAAGAGCACTTCCGTCCTG-ACATGAATA
* * *
456468 TGCGAAATGCCAACAGAACCAGTCTTTTGAGATATCTGCTCATCTGAAACGTCATGTA-TCCCCC
128 TGCGAAATGCCAACAGAACCAGTCTTTTGAGATATCTGTTCATCTGAAACATCATGTATTCCCCG
* *
456532 ACGTCTTAGAATCTTCCATCAGTCTACCCTGGTTATCTTTCTCAGTTTGATC
193 A-GTCTTAGAATCTTCCATCAGTCTACCCTGATTATCTTTCTCAGTTTCATC
* * * *
456584 AACAGCAACCCCGTTGACATCTACAAGGGTTAAAGAAATCTCACTAGGAAATGTTAAATGGCCAT
1 AA-AGCAACCCCGTTGACATCTACAGGGGGTAAAGAAATCTCAC-AGGAGATGCTAAATGGCCAT
* * *
456649 TTTCAAAATCTCCAATCGTTGGATTGGAAGCAGTAGGAAGAGCACTTCGGTCCTCGACATGTATA
64 TTTCAAAATCTCCAATCTTTGGATTGGAAGCAGTAGGAAGAGCACTTCCGTCCT-GACATGAATA
* * * *
456714 TGCGAAATGCTAACAGAACCGGTCTTTTGAGATATCTGTTCATCTGAAACTTCATGTATTCCCTG
128 TGCGAAATGCCAACAGAACCAGTCTTTTGAGATATCTGTTCATCTGAAACATCATGTATTCCCCG
* **
456779 AGTCTTAGAATCTTCCATCAGTCTACCCTGATTATCTTTCTCGGTACCATC
193 AGTCTTAGAATCTTCCATCAGTCTACCCTGATTATCTTTCTCAGTTTCATC
* *
456830 AAAACCAACCCCGTTGACATCTACAGGGGGTAAAGAAATCTCAGCAGGAGATGCTAAATGGTCAT
1 -AAAGCAACCCCGTTGACATCTACAGGGGGTAAAGAAATCTCA-CAGGAGATGCTAAATGGCCAT
* * *
456895 TTTCAAAATCTCCAATCTTTGGTTTGGAAGTAGTAGGAAGAGCACTTCCGT-C-GACATGCATAT
64 TTTCAAAATCTCCAATCTTTGGATTGGAAGCAGTAGGAAGAGCACTTCCGTCCTGACATGAATAT
* * * *
456958 GTGAAATGCCAACAGAACCATTCTTTTGAGATATTTGTTCATCTG-AAC--CAT-CA-T----GA
129 GCGAAATGCCAACAGAACCAGTCTTTTGAGATATCTGTTCATCTGAAACATCATGTATTCCCCGA
* * ** * *
457014 GTCTT-GTATTCTTCCTTCAGGATAGCCTGATTATCTTTCTCAGTTTGATC
194 GTCTTAG-AATCTTCCATCAGTCTACCCTGATTATCTTTCTCAGTTTCATC
* *
457064 AACAGCAACCCCGTTGACATCTACAGGGGGTGAAGAAATCTCTCCAGGAGATGCTAAATGGCCAT
1 AA-AGCAACCCCGTTGACATCTACAGGGGGTAAAGAAATCTC-ACAGGAGATGCTAAATGGCCAT
* * * *
457129 TTTCAAAATCTTCAATCTTTGGATTGGAAGCAGTAGAAAGAGCACATCCGTCCTCAACATGAATA
64 TTTCAAAATCTCCAATCTTTGGATTGGAAGCAGTAGGAAGAGCACTTCCGTCCT-GACATGAATA
* * *
457194 TGCGAAATGCCAACAGAACCAGTCTTTTGAGATATCTGTTTATCTGAACCATCCTGTATTCCCCG
128 TGCGAAATGCCAACAGAACCAGTCTTTTGAGATATCTGTTCATCTGAAACATCATGTATTCCCCG
* * *
457259 AGTCATATAATCTTCCATCAGTCTACCCTGATTATCTTTCTCAGTTTGATC
193 AGTCTTAGAATCTTCCATCAGTCTACCCTGATTATCTTTCTCAGTTTCATC
457310 AA
1 AA
457312 TTTCAGTTGA
Statistics
Matches: 854, Mismatches: 94, Indels: 50
0.86 0.09 0.05
Matches are distributed among these distances:
233 3 0.00
234 144 0.17
235 1 0.00
237 50 0.06
238 3 0.00
239 1 0.00
240 5 0.01
241 1 0.00
242 4 0.00
243 50 0.06
245 11 0.01
246 571 0.67
247 10 0.01
ACGTcount: A:0.29, C:0.23, G:0.18, T:0.29
Consensus pattern (243 bp):
AAAGCAACCCCGTTGACATCTACAGGGGGTAAAGAAATCTCACAGGAGATGCTAAATGGCCATTT
TCAAAATCTCCAATCTTTGGATTGGAAGCAGTAGGAAGAGCACTTCCGTCCTGACATGAATATGC
GAAATGCCAACAGAACCAGTCTTTTGAGATATCTGTTCATCTGAAACATCATGTATTCCCCGAGT
CTTAGAATCTTCCATCAGTCTACCCTGATTATCTTTCTCAGTTTCATC
Found at i:458919 original size:20 final size:21
Alignment explanation
Indices: 458883--458926 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
458873 TCGATCGATA
*
458883 TTCTTTATTATC-CTTTTATT
1 TTCTTTATTATCATTTTTATT
458903 TTCTTATATTA-CATTTTTATT
1 TTCTT-TATTATCATTTTTATT
458924 TTC
1 TTC
458927 AATAAGTATG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 6 0.29
21 15 0.71
ACGTcount: A:0.18, C:0.14, G:0.00, T:0.68
Consensus pattern (21 bp):
TTCTTTATTATCATTTTTATT
Found at i:460275 original size:42 final size:42
Alignment explanation
Indices: 460199--460295 Score: 122
Period size: 42 Copynumber: 2.3 Consensus size: 42
460189 GTTAAAAGTT
* * * * *
460199 ATGATTTTTAGCGGCATTTTTTTATAAACTCCGCTAAAGGTG
1 ATGATATTTAGCGACATTTTGTTACAAACACCGCTAAAGGTG
* * *
460241 ATGGTATTTAGCGACGTTTTGTTACAAACACCGCTAAAGGTT
1 ATGATATTTAGCGACATTTTGTTACAAACACCGCTAAAGGTG
460283 ATGATATTTAGCG
1 ATGATATTTAGCG
460296 GCGCTTTTTC
Statistics
Matches: 46, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
42 46 1.00
ACGTcount: A:0.28, C:0.14, G:0.21, T:0.37
Consensus pattern (42 bp):
ATGATATTTAGCGACATTTTGTTACAAACACCGCTAAAGGTG
Found at i:460681 original size:21 final size:21
Alignment explanation
Indices: 460655--460713 Score: 100
Period size: 21 Copynumber: 2.8 Consensus size: 21
460645 ATTATCCAAT
*
460655 AAACTTGACATCCATAACAAC
1 AAACTTGAAATCCATAACAAC
*
460676 AAACTTGAAATCCATAACAAG
1 AAACTTGAAATCCATAACAAC
460697 AAACTTGAAATCCATAA
1 AAACTTGAAATCCATAA
460714 TAATAAATCA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.51, C:0.22, G:0.07, T:0.20
Consensus pattern (21 bp):
AAACTTGAAATCCATAACAAC
Found at i:467317 original size:42 final size:40
Alignment explanation
Indices: 467270--467389 Score: 123
Period size: 42 Copynumber: 2.9 Consensus size: 40
467260 AATTGGTAAG
*
467270 TCCTTCGGGCCATCAGTAAGTCTTTCGAGAATGATGATTAAA
1 TCCTTCGGGCCATCA-TAAGACTTTCGAGAATGATGA-TAAA
* * * * *
467312 TCCTTCAGGTCATCTATAAGCCTTTTCGAGAAAGATGATAAG
1 TCCTTCGGGCCATC-ATAAGAC-TTTCGAGAATGATGATAAA
* *
467354 TCCTTCGGGCCATCCATAAGACCTTCGAGCATGATG
1 TCCTTCGGGCCAT-CATAAGACTTTCGAGAATGATG
467390 TTTTCACATG
Statistics
Matches: 64, Mismatches: 11, Indels: 7
0.78 0.13 0.09
Matches are distributed among these distances:
41 11 0.17
42 37 0.58
43 16 0.25
ACGTcount: A:0.28, C:0.23, G:0.21, T:0.29
Consensus pattern (40 bp):
TCCTTCGGGCCATCATAAGACTTTCGAGAATGATGATAAA
Found at i:467633 original size:41 final size:42
Alignment explanation
Indices: 467527--467638 Score: 138
Period size: 42 Copynumber: 2.7 Consensus size: 42
467517 CAAAAATTGG
* *
467527 TAAGTCCTTCGGGCCAT-CAGTAGGCCTTTCAAGCATGATGAT
1 TAAGTCCTTCGGGCCATCCA-TAAGCCTTTCAAGCAAGATGAT
* * * *
467569 TAAATCCTTCGGGTCATCTATAAGCCTTTCGAGCAAGATGA-
1 TAAGTCCTTCGGGCCATCCATAAGCCTTTCAAGCAAGATGAT
467610 TAAGTCCTTCGGGCCATCCATAAGACCTT
1 TAAGTCCTTCGGGCCATCCATAAG-CCTT
467639 CGGTCAGGAT
Statistics
Matches: 59, Mismatches: 9, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
41 21 0.36
42 37 0.63
43 1 0.02
ACGTcount: A:0.26, C:0.25, G:0.21, T:0.29
Consensus pattern (42 bp):
TAAGTCCTTCGGGCCATCCATAAGCCTTTCAAGCAAGATGAT
Found at i:467780 original size:255 final size:253
Alignment explanation
Indices: 466758--467799 Score: 1482
Period size: 255 Copynumber: 4.1 Consensus size: 253
466748 TTCTTACTTA
* * *
466758 GTAAGTCCTTCGGGCTATTAGTAAGTCTTTCTAACATGATGATTAAA-CCTTTCGGGTCATCTAT
1 GTAAGTCCTTCGGGCCATCAGTAAGCCTTTC-AACATGATGATTAAATCC-TTCGGGTCATCTAT
* ** * * * *
466822 AAGCCTTTCGGGCAAGACAATAAGTCCTTCGAGCCATCCATAAGGCTTTTGGGTAGGTTGTTTTC
64 AAGCCTTTCGAGCAAGATGATAAGTCCTTCGAGCCATCCATAAGAC-CTTCGGTAGGATGTTTTC
* * *
466887 ACATGTTTTTCGAAAAATGCGAAAACGATTTCCAAAGTTTATCATTTAAATCTGAAAATTGAAAA
128 ACATGTTTTTCGAAAAATGAGAAAACGATTTCCAAAGTTTCTCATTTAAATCTGAAAATTGAAAT
* **
466952 TTTTGAAAAGTAAGAAAACGATTTCCAAAGTTTCCGACCTAGTAAACTATTTCCAAAATTG
193 TTTTGAAAAGTAAGAAAATGATTTCCAAAGTTTCTTACCTAGTAAACTATTTCCAAAATTG
* * ** * *
467013 GTATGTCATTCGGGCCATCAACAAGTCTTTTGAACATGATGATTAAATCCTTCGGGTCATCTATA
1 GTAAGTCCTTCGGGCCATCAGTAAG-CCTTTCAACATGATGATTAAATCCTTCGGGTCATCTATA
*
467078 AGCCTTTCGAGCAAGATGAT-AGTCCTTCGAGCCATTCATAAGACCTTCGGGTAGGAT-TTTTCA
65 AGCCTTTCGAGCAAGATGATAAGTCCTTCGAGCCATCCATAAGACCTTC-GGTAGGATGTTTTCA
** *
467141 CATGTTTTTCGAAAAATGAGAAAACTTTTTCTAAAGTTTCTCATTTAAATCTG-AAATTGAAATT
129 CATGTTTTTCGAAAAATGAGAAAACGATTTCCAAAGTTTCTCATTTAAATCTGAAAATTGAAATT
* *
467205 TTTTAAAAGTAAGAAAATGATTTCCAAAGTTTCTTACCTAGTAAACTATTTCTAAAATTG
194 TTTGAAAAGTAAGAAAATGATTTCCAAAGTTTCTTACCTAGTAAACTATTTCCAAAATTG
* *
467265 GTAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGA-ATGATGATTAAATCCTTCAGGTCATCTAT
1 GTAAGTCCTTCGGGCCATCAGTAAGCCTTTC-A-ACATGATGATTAAATCCTTCGGGTCATCTAT
* * * *
467329 AAGCCTTTTCGAGAAAGATGATAAGTCCTTCGGGCCATCCATAAGACCTTCGAGCATGATGTTTT
64 AAGCC-TTTCGAGCAAGATGATAAGTCCTTCGAGCCATCCATAAGACCTTCG-GTAGGATGTTTT
** ** * *
467394 CACATGTTTTTCGAAAAAAAAACAAGAAAATAAATTTCTAAAGTTTCTCATTTAAATCTAAAAAT
127 CACATGTTTTTCG----AAAAATGAGAAAA-CGATTTCCAAAGTTTCTCATTTAAATCTGAAAAT
* * *
467459 TGAAATTTTTGAAAAGTAAGAAAATGATCTCCAAAGTTTCTTACCTAGTAAACTATTGCAAAAAT
187 TGAAATTTTTGAAAAGTAAGAAAATGATTTCCAAAGTTTCTTACCTAGTAAACTATTTCCAAAAT
467524 TG
252 TG
*
467526 GTAAGTCCTTCGGGCCATCAGTAGGCCTTTCAAGCATGATGATTAAATCCTTCGGGTCATCTATA
1 GTAAGTCCTTCGGGCCATCAGTAAGCCTTTCAA-CATGATGATTAAATCCTTCGGGTCATCTATA
*
467591 AGCCTTTCGAGCAAGATGATAAGTCCTTCGGGCCATCCATAAGACCTTCGGTCAGGATGTTTTCA
65 AGCCTTTCGAGCAAGATGATAAGTCCTTCGAGCCATCCATAAGACCTTCGGT-AGGATGTTTTCA
* *
467656 CATGTTTTTCGAAAAATGAGAAAACGATTTCCAAAATTTCTCATTTAAATTTGAAAATTGAAATT
129 CATGTTTTTCGAAAAATGAGAAAACGATTTCCAAAGTTTCTCATTTAAATCTGAAAATTGAAATT
467721 TTTGAAAAGTAAGAAAATGATTTCCAAAGTTTCTTACCTAGTAAACTATTTCCAAAATTG
194 TTTGAAAAGTAAGAAAATGATTTCCAAAGTTTCTTACCTAGTAAACTATTTCCAAAATTG
467781 GTAAGTCCTTCGGGCCATC
1 GTAAGTCCTTCGGGCCATC
467800 TATTAGTCTT
Statistics
Matches: 701, Mismatches: 68, Indels: 36
0.87 0.08 0.04
Matches are distributed among these distances:
251 3 0.00
252 120 0.17
253 73 0.10
254 60 0.09
255 194 0.28
256 16 0.02
259 13 0.02
260 93 0.13
261 129 0.18
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Consensus pattern (253 bp):
GTAAGTCCTTCGGGCCATCAGTAAGCCTTTCAACATGATGATTAAATCCTTCGGGTCATCTATAA
GCCTTTCGAGCAAGATGATAAGTCCTTCGAGCCATCCATAAGACCTTCGGTAGGATGTTTTCACA
TGTTTTTCGAAAAATGAGAAAACGATTTCCAAAGTTTCTCATTTAAATCTGAAAATTGAAATTTT
TGAAAAGTAAGAAAATGATTTCCAAAGTTTCTTACCTAGTAAACTATTTCCAAAATTG
Found at i:468086 original size:3 final size:3
Alignment explanation
Indices: 468080--468115 Score: 65
Period size: 3 Copynumber: 12.3 Consensus size: 3
468070 TTAATAATAA
468080 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T-T TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
468116 TTCAGAAAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 30 0.94
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TAT
Found at i:468650 original size:31 final size:30
Alignment explanation
Indices: 468613--468685 Score: 130
Period size: 31 Copynumber: 2.4 Consensus size: 30
468603 GGGGAAATCG
468613 GAGAGAAAAAAGGAGGGGTCTTTGCTTTTC
1 GAGAGAAAAAAGGAGGGGTCTTTGCTTTTC
468643 AGAGAGAAAAAAGGAGGGGTCTTTGCTTTTC
1 -GAGAGAAAAAAGGAGGGGTCTTTGCTTTTC
468674 G-GAGAAAAAAGG
1 GAGAGAAAAAAGG
468686 GAAAAGTCGA
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
29 11 0.26
30 1 0.02
31 30 0.71
ACGTcount: A:0.36, C:0.08, G:0.34, T:0.22
Consensus pattern (30 bp):
GAGAGAAAAAAGGAGGGGTCTTTGCTTTTC
Found at i:469749 original size:2 final size:2
Alignment explanation
Indices: 469737--469779 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
469727 TTATTTCATT
469737 TA TA T- 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
469778 TA
1 TA
469780 CATGTGTGCG
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 39 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:470713 original size:131 final size:131
Alignment explanation
Indices: 470473--470723 Score: 378
Period size: 131 Copynumber: 1.9 Consensus size: 131
470463 AGTAACACCT
* *
470473 GAATTAATATTAAATTTTAGGACGAAATACTAATATCTTTTCATTTCGGTTGGAGTAATAAATGA
1 GAATCAATATTAAATTTTAGGACGAAATACTAATATCTTTTCATTTCGATTGGAGTAATAAATGA
* * * * *
470538 CTGCTTTAAAGCATGAGATGTCATTTATTCCCGATTGTATATAATTAGATATTATCGTTTTCTAT
66 CTGCTTTAAAGCATGAGAGGCCATTTATTCCCGATTGGAAATAATTAAATATTATCGTTTTCTAT
470603 C
131 C
* * *
470604 GAATCAATATTGAATTTTAGGATGAAATAGTAATATCTCTTT-ATTTCGATTGGAGTAATAAATG
1 GAATCAATATTAAATTTTAGGACGAAATACTAATATCT-TTTCATTTCGATTGGAGTAATAAATG
* *
470668 ACTGCTTTAAGGCATGAGAGGCCATTTATTCTCGATTGGAAATAATTAAATATTAT
65 ACTGCTTTAAAGCATGAGAGGCCATTTATTCCCGATTGGAAATAATTAAATATTAT
470724 TATTTTTCCT
Statistics
Matches: 107, Mismatches: 12, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
131 104 0.97
132 3 0.03
ACGTcount: A:0.34, C:0.10, G:0.16, T:0.39
Consensus pattern (131 bp):
GAATCAATATTAAATTTTAGGACGAAATACTAATATCTTTTCATTTCGATTGGAGTAATAAATGA
CTGCTTTAAAGCATGAGAGGCCATTTATTCCCGATTGGAAATAATTAAATATTATCGTTTTCTAT
C
Found at i:471313 original size:15 final size:14
Alignment explanation
Indices: 471279--471312 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
471269 GAGACGATAT
*
471279 CTTTTAAAAAATCA
1 CTTTTTAAAAATCA
471293 CTTTTTAAAAATCA
1 CTTTTTAAAAATCA
*
471307 ATTTTT
1 CTTTTT
471313 TTTAAAGAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.41, C:0.12, G:0.00, T:0.47
Consensus pattern (14 bp):
CTTTTTAAAAATCA
Found at i:474111 original size:11 final size:10
Alignment explanation
Indices: 474097--474155 Score: 55
Period size: 11 Copynumber: 5.4 Consensus size: 10
474087 TTTATGTGAC
474097 TAATATGAAAA
1 TAATAT-AAAA
474108 TAATAATAAAA
1 TAAT-ATAAAA
474119 TAATATAAAA
1 TAATATAAAA
*
474129 GTAATAACAAAA
1 -TAAT-ATAAAA
*
474141 TAATAAATAAA
1 TAATATA-AAA
474152 TAAT
1 TAAT
474156 GATTAAAAAG
Statistics
Matches: 42, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
10 8 0.19
11 27 0.64
12 7 0.17
ACGTcount: A:0.68, C:0.02, G:0.03, T:0.27
Consensus pattern (10 bp):
TAATATAAAA
Found at i:474155 original size:22 final size:22
Alignment explanation
Indices: 474097--474155 Score: 75
Period size: 22 Copynumber: 2.7 Consensus size: 22
474087 TTTATGTGAC
* *
474097 TAATATGAAAATAATAATAAAA
1 TAATATAAAAATAATAACAAAA
*
474119 TAATATAAAAGTAATAACAAAA
1 TAATATAAAAATAATAACAAAA
474141 TAATA-AATAAATAAT
1 TAATATAA-AAATAAT
474156 GATTAAAAAG
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
21 2 0.06
22 30 0.94
ACGTcount: A:0.68, C:0.02, G:0.03, T:0.27
Consensus pattern (22 bp):
TAATATAAAAATAATAACAAAA
Found at i:475448 original size:3 final size:3
Alignment explanation
Indices: 475440--475469 Score: 51
Period size: 3 Copynumber: 9.7 Consensus size: 3
475430 ATTATTTATT
475440 TAA TAA TAA TAA TATA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TA-A TAA TAA TAA TAA TA
475470 TATGAAAATG
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 23 0.88
4 3 0.12
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:475461 original size:16 final size:16
Alignment explanation
Indices: 475440--475472 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
475430 ATTATTTATT
475440 TAATAATAATAATATA
1 TAATAATAATAATATA
475456 TAATAATAATAATATA
1 TAATAATAATAATATA
475472 T
1 T
475473 GAAAATGAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (16 bp):
TAATAATAATAATATA
Found at i:475923 original size:112 final size:112
Alignment explanation
Indices: 475790--476199 Score: 590
Period size: 112 Copynumber: 3.7 Consensus size: 112
475780 TAGAGTTATG
* ** *
475790 CAAAAGGTTGAACAAGCTCTTCTCCTTATGAACTTCTTCTTCTTCTTCAGATAAGTTCTTCTCAT
1 CAAAAAGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCTTCTTCAGATAAGTTCTTCTCAT
475855 TATGAACTTTCTCTGGAAAAGTTGATCCATCGAGTGATGAATTCAAA
66 TATGAACTTTCTCTGGAAAAGTTGATCCATCGAGTGATGAATTCAAA
* **
475902 CAAAAAGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCATTCTTCAGACGAGTTCTTCTCA
1 CAAAAAGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTC-TTCTTCAGATAAGTTCTTCTCA
* * * * * *
475967 TTATGAACTCTAC-CTGGCAATGTTGATCCATCAAATGATGAATTTAAA
65 TTATGAACT-TTCTCTGGAAAAGTTGATCCATCGAGTGATGAATTCAAA
* * *
476015 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTCCTTCTTCAGATGAGTTCTTCTCAT
1 CAAAAAGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCTTCTTCAGATAAGTTCTTCTCAT
**
476080 TATGAACTTTCTCTGGAAAAACTGATCCATCGAGTGATGAATTCAAA
66 TATGAACTTTCTCTGGAAAAGTTGATCCATCGAGTGATGAATTCAAA
* * *
476127 C-AAAAGTTGAACAAATTCTTCTCATTATAAATTTCTTCTTTCTTCTTCAAATAAGTTCTTCTCA
1 CAAAAAGTTGAACAAATTCTTCTCATTATGAACTTCTTC-TTCTTCTTCAGATAAGTTCTTCTCA
476191 TTATGAACT
65 TTATGAACT
476200 CTAACTGGCA
Statistics
Matches: 263, Mismatches: 31, Indels: 8
0.87 0.10 0.03
Matches are distributed among these distances:
111 36 0.14
112 127 0.48
113 98 0.37
114 2 0.01
ACGTcount: A:0.30, C:0.20, G:0.12, T:0.38
Consensus pattern (112 bp):
CAAAAAGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCTTCTTCAGATAAGTTCTTCTCAT
TATGAACTTTCTCTGGAAAAGTTGATCCATCGAGTGATGAATTCAAA
Found at i:476025 original size:225 final size:224
Alignment explanation
Indices: 475790--476220 Score: 711
Period size: 225 Copynumber: 1.9 Consensus size: 224
475780 TAGAGTTATG
* * *
475790 CAAAAGGTTGAACAAGCTCTTCTCCTTATGAACTTCTTCTTCTTCTTCAGATAAGTTCTTCTCAT
1 CAAAAGGTTGAACAAACTCTTCTCATTATGAACTTCTTCTCCTTCTTCAGATAAGTTCTTCTCAT
**
475855 TATGAACTTTCTCTGGAAAAGTTGATCCATCGAGTGATGAATTCAAACAAAAAGTTGAACAAATT
66 TATGAACTTTCTCTGGAAAAACTGATCCATCGAGTGATGAATTCAAAC-AAAAGTTGAACAAATT
* * * *
475920 CTTCTCATTATGAATTTCTTC-TTCATTCTTCAGACGAGTTCTTCTCATTATGAACTCTACCTGG
130 CTTCTCATTATAAATTTCTTCTTTC-TTCTTCAAACAAGTTCTTCTCATTATGAACTCTAACTGG
*
475984 CAATGTTGATCCATCAAATGATGAATTTAAA
194 CAATGCTGATCCATCAAATGATGAATTTAAA
* *
476015 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTCCTTCTTCAGATGAGTTCTTCTCAT
1 CAAAAGGTTGAACAAACTCTTCTCATTATGAACTTCTTCTCCTTCTTCAGATAAGTTCTTCTCAT
476080 TATGAACTTTCTCTGGAAAAACTGATCCATCGAGTGATGAATTCAAACAAAAGTTGAACAAATTC
66 TATGAACTTTCTCTGGAAAAACTGATCCATCGAGTGATGAATTCAAACAAAAGTTGAACAAATTC
*
476145 TTCTCATTATAAATTTCTTCTTTCTTCTTCAAATAAGTTCTTCTCATTATGAACTCTAACTGGCA
131 TTCTCATTATAAATTTCTTCTTTCTTCTTCAAACAAGTTCTTCTCATTATGAACTCTAACTGGCA
*
476210 TTGCTGATCCA
196 ATGCTGATCCA
476221 CCGAAGGTTT
Statistics
Matches: 191, Mismatches: 14, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
224 82 0.43
225 109 0.57
ACGTcount: A:0.30, C:0.20, G:0.12, T:0.37
Consensus pattern (224 bp):
CAAAAGGTTGAACAAACTCTTCTCATTATGAACTTCTTCTCCTTCTTCAGATAAGTTCTTCTCAT
TATGAACTTTCTCTGGAAAAACTGATCCATCGAGTGATGAATTCAAACAAAAGTTGAACAAATTC
TTCTCATTATAAATTTCTTCTTTCTTCTTCAAACAAGTTCTTCTCATTATGAACTCTAACTGGCA
ATGCTGATCCATCAAATGATGAATTTAAA
Found at i:476358 original size:76 final size:76
Alignment explanation
Indices: 476224--476446 Score: 410
Period size: 76 Copynumber: 2.9 Consensus size: 76
476214 TGATCCACCG
* * *
476224 AAGGTTTTGAAAACATCAAAAAGATCCCGAAGGCTTTTTGGAAACATCATGCAATGTAGGACTTA
1 AAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTA
476289 CAGATGACCCT
66 CAGATGACCCT
476300 AAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTA
1 AAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTA
476365 CAGATGACCCT
66 CAGATGACCCT
*
476376 AAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTA
1 AAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTA
476441 CAGATG
66 CAGATG
476447 TAGGAAATAG
Statistics
Matches: 143, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
76 143 1.00
ACGTcount: A:0.35, C:0.21, G:0.20, T:0.24
Consensus pattern (76 bp):
AAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTA
CAGATGACCCT
Found at i:487438 original size:17 final size:16
Alignment explanation
Indices: 487416--487449 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
487406 TAAAAACAGT
487416 AAATAAAAAGATAAATA
1 AAATAAAAAGA-AAATA
*
487433 AAATAAGAAGAAAATA
1 AAATAAAAAGAAAATA
487449 A
1 A
487450 TCCTCACGTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.76, C:0.00, G:0.09, T:0.15
Consensus pattern (16 bp):
AAATAAAAAGAAAATA
Found at i:489090 original size:22 final size:22
Alignment explanation
Indices: 489065--489141 Score: 145
Period size: 22 Copynumber: 3.5 Consensus size: 22
489055 AATAAAGCTT
489065 TCATCTTTGAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
*
489087 TCATCTTTAAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
489109 TCATCTTTGAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
489131 TCATCTTTGAA
1 TCATCTTTGAA
489142 GAGTGTAGAT
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 53 1.00
ACGTcount: A:0.40, C:0.14, G:0.12, T:0.34
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATCTA
Found at i:491826 original size:112 final size:112
Alignment explanation
Indices: 491667--491893 Score: 386
Period size: 112 Copynumber: 2.0 Consensus size: 112
491657 AATCATGCAG
* *
491667 TTCATCTTTCAATTCCAATGATTGGTTCTGGGGTTCCTACCAACAGATCAGATAACTCAAAGAAC
1 TTCATCTTTCAAATCCAATGATTGGTTCTGGGGTTCATACCAACAGATCAGATAACTCAAAGAAC
491732 ACTTCTAGAAGATGCTATTGGGTCACCTTATTTCTACTATGAGCAAA
66 ACTTCTAGAAGATGCTATTGGGTCACCTTATTTCTACTATGAGCAAA
*
491779 TTCATCTTTCAAAT-CAATGATTGGTT-TTGGGTTCATACCAAATCAGATCAGATAACTCAAAGA
1 TTCATCTTTCAAATCCAATGATTGGTTCTGGGGTTCATACC-AA-CAGATCAGATAACTCAAAGA
*
491842 ACACTTCTAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAGCAAA
64 ACACTTCTAGAAGATGCTATTGGGTCACCTTATTTCTACTATGAGCAAA
491891 TTC
1 TTC
491894 GATTGGTTCA
Statistics
Matches: 109, Mismatches: 4, Indels: 4
0.93 0.03 0.03
Matches are distributed among these distances:
110 11 0.10
111 14 0.13
112 84 0.77
ACGTcount: A:0.31, C:0.20, G:0.15, T:0.33
Consensus pattern (112 bp):
TTCATCTTTCAAATCCAATGATTGGTTCTGGGGTTCATACCAACAGATCAGATAACTCAAAGAAC
ACTTCTAGAAGATGCTATTGGGTCACCTTATTTCTACTATGAGCAAA
Found at i:494038 original size:1 final size:1
Alignment explanation
Indices: 494032--494092 Score: 68
Period size: 1 Copynumber: 61.0 Consensus size: 1
494022 TTTCTCCTTC
* * * * * *
494032 TTTTTTTTTTTTTTCTTTTCTTTTTTTTCTTTTTCTTTTTTTTTTTTTTTCTTTCTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
494093 GCTGGATGAG
Statistics
Matches: 48, Mismatches: 12, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
1 48 1.00
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (1 bp):
T
Found at i:494054 original size:20 final size:20
Alignment explanation
Indices: 494029--494090 Score: 99
Period size: 20 Copynumber: 3.1 Consensus size: 20
494019 TAATTTCTCC
494029 TTCTTTTTTTTTTTTTTCTT
1 TTCTTTTTTTTTTTTTTCTT
*
494049 TTCTTTTTTTTCTTTTTCTT
1 TTCTTTTTTTTTTTTTTCTT
494069 TT-TTTTTTTTTTTCTTTCTT
1 TTCTTTTTTTTTTT-TTTCTT
494089 TT
1 TT
494091 TTGCTGGATG
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
19 10 0.26
20 29 0.74
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (20 bp):
TTCTTTTTTTTTTTTTTCTT
Found at i:496851 original size:12 final size:12
Alignment explanation
Indices: 496836--496861 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
496826 AAACATAAAA
496836 AAATGCAAATGT
1 AAATGCAAATGT
496848 AAATGCAAATGT
1 AAATGCAAATGT
496860 AA
1 AA
496862 TATGTGAATG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.54, C:0.08, G:0.15, T:0.23
Consensus pattern (12 bp):
AAATGCAAATGT
Found at i:496955 original size:7 final size:7
Alignment explanation
Indices: 496921--496962 Score: 50
Period size: 7 Copynumber: 6.0 Consensus size: 7
496911 ATAAGAGTAT
496921 AAATGCA
1 AAATGCA
* *
496928 CAATGAA
1 AAATGCA
496935 AAATGCA
1 AAATGCA
496942 AAGATGCA
1 AA-ATGCA
496950 AAATGC-
1 AAATGCA
496956 AAATGCA
1 AAATGCA
496963 TGTATGAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
6 6 0.21
7 16 0.55
8 7 0.24
ACGTcount: A:0.55, C:0.14, G:0.17, T:0.14
Consensus pattern (7 bp):
AAATGCA
Found at i:498513 original size:28 final size:26
Alignment explanation
Indices: 498461--498526 Score: 71
Period size: 28 Copynumber: 2.5 Consensus size: 26
498451 AAATAAAATG
*
498461 AATATTA-AAAAATAATATACATATA
1 AATATTATGAAAATAATATACATATA
*
498486 AATATTATGAAAATAATAAGTATATATA
1 AATATTATGAAAATAAT-A-TACATATA
* *
498514 AAAATTTTGAAAA
1 AATATTATGAAAA
498527 GAAAGAATTA
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
25 7 0.21
26 8 0.24
27 1 0.03
28 18 0.53
ACGTcount: A:0.61, C:0.02, G:0.05, T:0.33
Consensus pattern (26 bp):
AATATTATGAAAATAATATACATATA
Found at i:499389 original size:11 final size:11
Alignment explanation
Indices: 499375--499425 Score: 61
Period size: 11 Copynumber: 4.6 Consensus size: 11
499365 GACTAATATG
499375 AAATAATAATA
1 AAATAATAATA
499386 AAATAAT-ATA
1 AAATAATAATA
*
499396 AAAGTAATAACA
1 AAA-TAATAATA
499408 AAATAATAA-A
1 AAATAATAATA
499418 TAAATAAT
1 -AAATAAT
499426 GATTAAAAAG
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
10 7 0.19
11 24 0.67
12 5 0.14
ACGTcount: A:0.71, C:0.02, G:0.02, T:0.25
Consensus pattern (11 bp):
AAATAATAATA
Found at i:499405 original size:22 final size:21
Alignment explanation
Indices: 499368--499425 Score: 71
Period size: 22 Copynumber: 2.7 Consensus size: 21
499358 TTTATGTGAC
* *
499368 TAATATGAAATAATAATAAAA
1 TAATATAAAATAATAACAAAA
499389 TAATATAAAAGTAATAACAAAA
1 TAATATAAAA-TAATAACAAAA
*
499411 TAATAAATAAATAAT
1 TAATATA-AAATAAT
499426 GATTAAAAAG
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
21 9 0.28
22 20 0.62
23 3 0.09
ACGTcount: A:0.67, C:0.02, G:0.03, T:0.28
Consensus pattern (21 bp):
TAATATAAAATAATAACAAAA
Found at i:500703 original size:3 final size:3
Alignment explanation
Indices: 500695--500741 Score: 53
Period size: 3 Copynumber: 15.7 Consensus size: 3
500685 ATTATTTATT
*
500695 TAA TAA TAA TAAA TATA TAA AAA TAA TAA TAA T-A TAA TAA T-A TAA
1 TAA TAA TAA T-AA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
500740 TA
1 TA
500742 TATGAAAGTG
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
2 4 0.11
3 28 0.74
4 6 0.16
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:500731 original size:8 final size:8
Alignment explanation
Indices: 500697--500741 Score: 58
Period size: 8 Copynumber: 5.8 Consensus size: 8
500687 TATTTATTTA
500697 ATAATAAT
1 ATAATAAT
500705 A-AAT-AT
1 ATAATAAT
*
500711 ATAAAAAT
1 ATAATAAT
500719 AATAATAAT
1 -ATAATAAT
500728 ATAATAAT
1 ATAATAAT
500736 ATAATA
1 ATAATA
500742 TATGAAAGTG
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
6 3 0.09
7 5 0.16
8 17 0.53
9 7 0.22
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (8 bp):
ATAATAAT
Found at i:501878 original size:31 final size:30
Alignment explanation
Indices: 501817--501879 Score: 81
Period size: 31 Copynumber: 2.1 Consensus size: 30
501807 AAGCATTTGT
* *
501817 TGAAAATCAAGGTTGGCACCGAGTGGTGCA
1 TGAAAATCAAGGTTGGCACCGAATGATGCA
* *
501847 TGAAAATCAAAGTTTGGCACTGAATGATGCA
1 TGAAAATC-AAGGTTGGCACCGAATGATGCA
501878 TG
1 TG
501880 GTCAAAAGCA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
30 8 0.29
31 20 0.71
ACGTcount: A:0.33, C:0.14, G:0.29, T:0.24
Consensus pattern (30 bp):
TGAAAATCAAGGTTGGCACCGAATGATGCA
Found at i:504285 original size:30 final size:30
Alignment explanation
Indices: 504249--504308 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
504239 TGAGATATTG
504249 TTGAAAATAAAGGTTGGCACCAAATGGTGC
1 TTGAAAATAAAGGTTGGCACCAAATGGTGC
* * * *
504279 TTGAAAATCAAGTTTGTCACCGAATGGTGC
1 TTGAAAATAAAGGTTGGCACCAAATGGTGC
504309 ATGGTCAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.33, C:0.15, G:0.25, T:0.27
Consensus pattern (30 bp):
TTGAAAATAAAGGTTGGCACCAAATGGTGC
Found at i:510036 original size:16 final size:16
Alignment explanation
Indices: 510015--510056 Score: 75
Period size: 16 Copynumber: 2.6 Consensus size: 16
510005 TTTCGTTGAC
*
510015 ATAGCTTCTATTACGG
1 ATAGCTCCTATTACGG
510031 ATAGCTCCTATTACGG
1 ATAGCTCCTATTACGG
510047 ATAGCTCCTA
1 ATAGCTCCTA
510057 CTATTTCACT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.26, C:0.24, G:0.17, T:0.33
Consensus pattern (16 bp):
ATAGCTCCTATTACGG
Done.