Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012152.1 Kokia drynarioides strain JFW-HI SEQ_127151, 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: 458257
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 84 characters in sequence are not A, C, G, or T
File 2 of 2
Found at i:388749 original size:16 final size:17
Alignment explanation
Indices: 388728--388761 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
388718 TTTAAAACCC
*
388728 TAAATA-CTAACCATTA
1 TAAATATCTAAACATTA
388744 TAAATATCTAAACATTA
1 TAAATATCTAAACATTA
388761 T
1 T
388762 TCTAACTCAT
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:0.50, C:0.15, G:0.00, T:0.35
Consensus pattern (17 bp):
TAAATATCTAAACATTA
Found at i:392055 original size:16 final size:16
Alignment explanation
Indices: 392034--392067 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
392024 CTGCAACTAC
392034 AACAATGTCATGACAA
1 AACAATGTCATGACAA
* *
392050 AACAATGTTATGGCAA
1 AACAATGTCATGACAA
392066 AA
1 AA
392068 TATAAAAATG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.15, G:0.15, T:0.21
Consensus pattern (16 bp):
AACAATGTCATGACAA
Found at i:398829 original size:28 final size:28
Alignment explanation
Indices: 398798--398887 Score: 69
Period size: 28 Copynumber: 3.2 Consensus size: 28
398788 ACATCTTGGT
*
398798 TAGAGCGTAATCCCATGTACAGCTCGGG
1 TAGAGCGTAATACCATGTACAGCTCGGG
* ** *
398826 TAGAGCTGTTATTTGC-T-TAC-GTCTCGGT
1 TAGAGC-G-TAATACCATGTACAG-CTCGGG
* *
398854 TAGAGCGTAATACCATGTACAACTCGAG
1 TAGAGCGTAATACCATGTACAGCTCGGG
398882 TAGAGC
1 TAGAGC
398888 TATGATTTGC
Statistics
Matches: 46, Mismatches: 10, Indels: 12
0.68 0.15 0.18
Matches are distributed among these distances:
26 4 0.09
27 3 0.07
28 33 0.72
29 2 0.04
30 4 0.09
ACGTcount: A:0.26, C:0.21, G:0.26, T:0.28
Consensus pattern (28 bp):
TAGAGCGTAATACCATGTACAGCTCGGG
Found at i:398957 original size:56 final size:56
Alignment explanation
Indices: 398670--398962 Score: 343
Period size: 56 Copynumber: 5.2 Consensus size: 56
398660 AGGTTATGGA
* *
398670 TTGCTTATGTCTCAGTTAGAGCGTAATGCCTTGTACAACTCGGGTAGAGCTATGAT
1 TTGCTTACGTCTCAGTTAGAGCGTAATGCCATGTACAACTCGGGTAGAGCTATGAT
* * * * * * * *
398726 TTGCTTACATTTCAATTAAAGCATAATGTCATGTACAGCTCGAGTAGAGCTATGAT
1 TTGCTTACGTCTCAGTTAGAGCGTAATGCCATGTACAACTCGGGTAGAGCTATGAT
* ** * * * *
398782 TTGCTTACATCTTGGTTAGAGCGTAATCCCATGTACAGCTCGGGTAGAGCTGTTAT
1 TTGCTTACGTCTCAGTTAGAGCGTAATGCCATGTACAACTCGGGTAGAGCTATGAT
* * *
398838 TTGCTTACGTCTCGGTTAGAGCGTAATACCATGTACAACTCGAGTAGAGCTATGAT
1 TTGCTTACGTCTCAGTTAGAGCGTAATGCCATGTACAACTCGGGTAGAGCTATGAT
* ** * *
398894 TTGCTTATGTCTCAGTTAGAGATTAAGGCCATGTACAACTCGGGTAGAACTATGAT
1 TTGCTTACGTCTCAGTTAGAGCGTAATGCCATGTACAACTCGGGTAGAGCTATGAT
* *
398950 TTTCTTATGTCTC
1 TTGCTTACGTCTC
398963 GATTGGAGCG
Statistics
Matches: 200, Mismatches: 37, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
56 200 1.00
ACGTcount: A:0.26, C:0.18, G:0.22, T:0.34
Consensus pattern (56 bp):
TTGCTTACGTCTCAGTTAGAGCGTAATGCCATGTACAACTCGGGTAGAGCTATGAT
Found at i:398962 original size:112 final size:112
Alignment explanation
Indices: 398670--398972 Score: 381
Period size: 112 Copynumber: 2.7 Consensus size: 112
398660 AGGTTATGGA
* *
398670 TTGCTTATGTCTCAGTTAGAGCGTAATGCCTTGTACAACTCGGGTAGAGCTATGATTTGCTTACA
1 TTGCTTATGTCTCAGTTAGAGCGTAATGCCATGTACAACTCGGGTAGAGCTATGATTTGCTTACG
* * * * ** *
398735 TTTCAATTAAAGCATAATGTCATGTACAGCTCGAGTAGAGCTATGAT
66 TCTCGATTAGAGCGTAATACCATGTACAACTCGAGTAGAGCTATGAT
** ** * * * *
398782 TTGCTTACATCTTGGTTAGAGCGTAATCCCATGTACAGCTCGGGTAGAGCTGTTATTTGCTTACG
1 TTGCTTATGTCTCAGTTAGAGCGTAATGCCATGTACAACTCGGGTAGAGCTATGATTTGCTTACG
*
398847 TCTCGGTTAGAGCGTAATACCATGTACAACTCGAGTAGAGCTATGAT
66 TCTCGATTAGAGCGTAATACCATGTACAACTCGAGTAGAGCTATGAT
** * * * *
398894 TTGCTTATGTCTCAGTTAGAGATTAAGGCCATGTACAACTCGGGTAGAACTATGATTTTCTTATG
1 TTGCTTATGTCTCAGTTAGAGCGTAATGCCATGTACAACTCGGGTAGAGCTATGATTTGCTTACG
*
398959 TCTCGATTGGAGCG
66 TCTCGATTAGAGCG
398973 AAAGGCCATG
Statistics
Matches: 157, Mismatches: 34, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
112 157 1.00
ACGTcount: A:0.25, C:0.18, G:0.23, T:0.34
Consensus pattern (112 bp):
TTGCTTATGTCTCAGTTAGAGCGTAATGCCATGTACAACTCGGGTAGAGCTATGATTTGCTTACG
TCTCGATTAGAGCGTAATACCATGTACAACTCGAGTAGAGCTATGAT
Found at i:412334 original size:25 final size:25
Alignment explanation
Indices: 412279--412332 Score: 65
Period size: 25 Copynumber: 2.1 Consensus size: 25
412269 ACAAAAGTAT
* *
412279 TAAATTAACCCAATTATTTAATAAT
1 TAAATAAACCCAATTATTTAATAAA
412304 TAAATAAACCCAAGTTA-TTAATGAAA
1 TAAATAAACCCAA-TTATTTAAT-AAA
412330 TAA
1 TAA
412333 TATATATTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 17 0.68
26 8 0.32
ACGTcount: A:0.52, C:0.11, G:0.04, T:0.33
Consensus pattern (25 bp):
TAAATAAACCCAATTATTTAATAAA
Found at i:415498 original size:217 final size:218
Alignment explanation
Indices: 415123--415560 Score: 671
Period size: 217 Copynumber: 2.0 Consensus size: 218
415113 ATGGTGACTA
* * *
415123 TTGAACTTGTTGATTGAAACCAAGAGGTTGATTTGATCTATGTTGCATGTAATTGTTGTTCGGTC
1 TTGAACTTATTGATTGAAACCAAGAGGTTGATTTAATCTATGTTGCATGTAATTGTTCTTCGGTC
* *** * *
415188 CACCTCCTTGGTAATAGATTGGTGGCTGAGCTGCAACATGATTTAAGTTGTTAGTAGTAAATTGT
66 CACCTCCTTGGTAATAGATTGGTGGCTGAGCTACAACATGATTTAAAACGTTAGTAGTAAACTAT
*
415253 TTCAACATTGAAGAGATAGAGGATACTTGAGGTGAGAGTGAAGCGAGGGCACCTA-TTCATGCAC
131 TTCAACATTGAAGAGATAGAGGATACTTGAGGTGAGAGTAAAGCGAGGGCACCTACTTCATGCAC
* *
415317 TCCGGCTACTTGTCTTCTTGAAG
196 TCCAGCTACTTGTCTTCTTAAAG
415340 TTGAACTTATTGATTGAAACCAAGAGGTTGATTTAATCTATGTTGCATGTAATTGTTCTTCGGTC
1 TTGAACTTATTGATTGAAACCAAGAGGTTGATTTAATCTATGTTGCATGTAATTGTTCTTCGGTC
* *
415405 CACCTCCTTGGTAGTGGATTGGTGGCTGAGCTACAACATGATTTAAAACGTTAGTAGTAAACTAT
66 CACCTCCTTGGTAATAGATTGGTGGCTGAGCTACAACATGATTTAAAACGTTAGTAGTAAACTAT
* * * * * *
415470 TTCAACATTTAAGAGATAGATGATACTTGAGTTGAGAGTAAAGTGAGTGCATCTACTTCATGCAC
131 TTCAACATTGAAGAGATAGAGGATACTTGAGGTGAGAGTAAAGCGAGGGCACCTACTTCATGCAC
* *
415535 TCTATCTACTTGTCTTCTTAAAG
196 TCCAGCTACTTGTCTTCTTAAAG
415558 TTG
1 TTG
415561 TTTGATTTGT
Statistics
Matches: 198, Mismatches: 22, Indels: 1
0.90 0.10 0.00
Matches are distributed among these distances:
217 167 0.84
218 31 0.16
ACGTcount: A:0.27, C:0.15, G:0.23, T:0.35
Consensus pattern (218 bp):
TTGAACTTATTGATTGAAACCAAGAGGTTGATTTAATCTATGTTGCATGTAATTGTTCTTCGGTC
CACCTCCTTGGTAATAGATTGGTGGCTGAGCTACAACATGATTTAAAACGTTAGTAGTAAACTAT
TTCAACATTGAAGAGATAGAGGATACTTGAGGTGAGAGTAAAGCGAGGGCACCTACTTCATGCAC
TCCAGCTACTTGTCTTCTTAAAG
Found at i:416406 original size:5 final size:5
Alignment explanation
Indices: 416396--416457 Score: 51
Period size: 5 Copynumber: 12.8 Consensus size: 5
416386 TAGCCACATG
* * *
416396 AAAAT AAAAT AAAA- AAAAT -AATT AGATAGT AAAAT TAAA- AAAAT -AAAT
1 AAAAT AAAAT AAAAT AAAAT AAAAT A-A-AAT AAAAT AAAAT AAAAT AAAAT
416444 AAAAT AAAAT AAAA
1 AAAAT AAAAT AAAA
416458 ACCAATTTAC
Statistics
Matches: 46, Mismatches: 5, Indels: 12
0.73 0.08 0.19
Matches are distributed among these distances:
4 14 0.30
5 27 0.59
6 2 0.04
7 3 0.07
ACGTcount: A:0.76, C:0.00, G:0.03, T:0.21
Consensus pattern (5 bp):
AAAAT
Found at i:416415 original size:9 final size:10
Alignment explanation
Indices: 416396--416457 Score: 51
Period size: 9 Copynumber: 6.4 Consensus size: 10
416386 TAGCCACATG
416396 AAAATAAAAT
1 AAAATAAAAT
416406 AAAA-AAAAT
1 AAAATAAAAT
* *
416415 -AATTAGATAGT
1 AAAATA-A-AAT
*
416426 AAAATTAAA-
1 AAAATAAAAT
416435 AAAAT-AAAT
1 AAAATAAAAT
416444 AAAATAAAAT
1 AAAATAAAAT
416454 AAAA
1 AAAA
416458 ACCAATTTAC
Statistics
Matches: 41, Mismatches: 5, Indels: 12
0.71 0.09 0.21
Matches are distributed among these distances:
8 5 0.12
9 16 0.39
10 14 0.34
11 3 0.07
12 3 0.07
ACGTcount: A:0.76, C:0.00, G:0.03, T:0.21
Consensus pattern (10 bp):
AAAATAAAAT
Found at i:416428 original size:25 final size:23
Alignment explanation
Indices: 416396--416458 Score: 81
Period size: 25 Copynumber: 2.7 Consensus size: 23
416386 TAGCCACATG
*
416396 AAAATAAAATAAAAAAAATAATT
1 AAAATAAAATAAAAAAAATAAAT
* *
416419 AGATAGTAAAATTAAAAAAATAAAT
1 A-A-AATAAAATAAAAAAAATAAAT
416444 AAAATAAAATAAAAA
1 AAAATAAAATAAAAA
416459 CCAATTTACA
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
23 12 0.36
24 2 0.06
25 19 0.58
ACGTcount: A:0.76, C:0.00, G:0.03, T:0.21
Consensus pattern (23 bp):
AAAATAAAATAAAAAAAATAAAT
Found at i:418033 original size:34 final size:34
Alignment explanation
Indices: 417990--418057 Score: 136
Period size: 34 Copynumber: 2.0 Consensus size: 34
417980 TCTTAGCAAA
417990 ATAGGGAAATTAGATGGGTGGAAAAGAATGAAAG
1 ATAGGGAAATTAGATGGGTGGAAAAGAATGAAAG
418024 ATAGGGAAATTAGATGGGTGGAAAAGAATGAAAG
1 ATAGGGAAATTAGATGGGTGGAAAAGAATGAAAG
418058 TTAGAAAGAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.47, C:0.00, G:0.35, T:0.18
Consensus pattern (34 bp):
ATAGGGAAATTAGATGGGTGGAAAAGAATGAAAG
Found at i:419542 original size:97 final size:100
Alignment explanation
Indices: 419439--419625 Score: 242
Period size: 97 Copynumber: 1.9 Consensus size: 100
419429 TAATAAACGA
* *
419439 CATGAAAATAAAT-A-ATAACAAGATAAATAAA-TAAAAAT-AA-AAATTAAATACTAAAATAAA
1 CATGAAAATAAATGACA-AACAA-ATAAA-AAACAAAAAATCAATAAATTAAATACAAAAATAAA
*
419499 CAAAC-AAATATAAACAATAAAAATAATTGAGATTAGG
63 AAAACTAAATATAAACAATAAAAATAATTGAGATTAGG
* *
419536 CATGAAAATAAATGACAAATAAATAAAAAACAAAAAATCAATAAATTAAATGCAAAAATAAAAAA
1 CATGAAAATAAATGACAAACAAATAAAAAACAAAAAATCAATAAATTAAATACAAAAATAAAAAA
* *
419601 ACTAAATATAAATAATAATAATAAT
66 ACTAAATATAAACAATAAAAATAAT
419626 AAAGAAGATG
Statistics
Matches: 77, Mismatches: 7, Indels: 9
0.83 0.08 0.10
Matches are distributed among these distances:
96 3 0.04
97 24 0.31
98 7 0.09
99 23 0.30
100 20 0.26
ACGTcount: A:0.67, C:0.06, G:0.05, T:0.21
Consensus pattern (100 bp):
CATGAAAATAAATGACAAACAAATAAAAAACAAAAAATCAATAAATTAAATACAAAAATAAAAAA
ACTAAATATAAACAATAAAAATAATTGAGATTAGG
Found at i:419606 original size:21 final size:21
Alignment explanation
Indices: 419568--419607 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
419558 ATAAAAAACA
* * *
419568 AAAAATCAATAAATTAAATGC
1 AAAAATAAAAAAACTAAATGC
419589 AAAAATAAAAAAACTAAAT
1 AAAAATAAAAAAACTAAAT
419608 ATAAATAATA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.70, C:0.07, G:0.03, T:0.20
Consensus pattern (21 bp):
AAAAATAAAAAAACTAAATGC
Found at i:419845 original size:26 final size:25
Alignment explanation
Indices: 419810--419861 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 25
419800 GTTTTGAATT
* *
419810 TTCTTCGAATGTATGTCTCAAAAAAA
1 TTCTTCGAATGT-TGTATAAAAAAAA
*
419836 TTCTTTGAATGTTGTATAAAAAAAA
1 TTCTTCGAATGTTGTATAAAAAAAA
419861 T
1 T
419862 CTCTAAATCT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
25 12 0.52
26 11 0.48
ACGTcount: A:0.40, C:0.10, G:0.12, T:0.38
Consensus pattern (25 bp):
TTCTTCGAATGTTGTATAAAAAAAA
Found at i:420388 original size:45 final size:45
Alignment explanation
Indices: 420309--420873 Score: 552
Period size: 45 Copynumber: 12.6 Consensus size: 45
420299 GATTTAGCGA
*
420309 TAAAAGATTGGATTTGGTGACTTCAATCTT-CCCCTCTAGATTAGGGG
1 TAAAAGATTGGA--TGGTGGCTTCAAT-TTGCCCCTCTAGATTAGGGG
* * *
420356 TAAAAGATTGGATGGTGGCTTCAATTTGCCCCTTTGGATTAAGGG
1 TAAAAGATTGGATGGTGGCTTCAATTTGCCCCTCTAGATTAGGGG
* * * * *
420401 TAAAAGACTGAATGGTGGCTTCAATCTGCCCTTCTGGATTA-GGG
1 TAAAAGATTGGATGGTGGCTTCAATTTGCCCCTCTAGATTAGGGG
* * * *
420445 TAAAGGATTGGATGGTTGCTTCAATCCT-CCCCTCTAGATTAGAGG
1 TAAAAGATTGGATGGTGGCTTCAAT-TTGCCCCTCTAGATTAGGGG
* *
420490 TAAAAGACTGGATTGTGGCTTCAATTTGCCCCT-TAGATTAGGGG
1 TAAAAGATTGGATGGTGGCTTCAATTTGCCCCTCTAGATTAGGGG
* * * * * *
420534 TAAAGGACTGGATGGCT-GCTTCAATCTACCCCTTTGGATTAGGGG
1 TAAAAGATTGGATGG-TGGCTTCAATTTGCCCCTCTAGATTAGGGG
* * * *
420579 TAAAAGACTGGATGGTGGCTTTAATTTGCCCCTCTGGATTAAGGG
1 TAAAAGATTGGATGGTGGCTTCAATTTGCCCCTCTAGATTAGGGG
* ** * *
420624 TAAAAGATTGGATGATTACTTCAATTTGCCCTTCTAGATTAGGAG
1 TAAAAGATTGGATGGTGGCTTCAATTTGCCCCTCTAGATTAGGGG
* * *
420669 TAAAAGATTTGATGGTGGCTTCAATCTGCCCCTCTAGATTAAGGG
1 TAAAAGATTGGATGGTGGCTTCAATTTGCCCCTCTAGATTAGGGG
* * * * * * *
420714 TAAAAGACTGGATAGTGACTTCAATTTACCTCTCTACATTAAGGG
1 TAAAAGATTGGATGGTGGCTTCAATTTGCCCCTCTAGATTAGGGG
* * * *
420759 T-AAAGATTGGATGGTGGCTTCAATCTACCCCTATAGATTAGAGG
1 TAAAAGATTGGATGGTGGCTTCAATTTGCCCCTCTAGATTAGGGG
* * * **
420803 T-AAAGATTGGATGATGACTTCAATCTATCCCTCTAGATTAGGGG
1 TAAAAGATTGGATGGTGGCTTCAATTTGCCCCTCTAGATTAGGGG
* *
420847 TAAAATATT-GATGTGGTGACTTCAATT
1 TAAAAGATTGGA--TGGTGGCTTCAATT
420874 CGTTTAGTTT
Statistics
Matches: 433, Mismatches: 75, Indels: 21
0.82 0.14 0.04
Matches are distributed among these distances:
44 152 0.35
45 257 0.59
46 12 0.03
47 12 0.03
ACGTcount: A:0.27, C:0.16, G:0.25, T:0.32
Consensus pattern (45 bp):
TAAAAGATTGGATGGTGGCTTCAATTTGCCCCTCTAGATTAGGGG
Found at i:420466 original size:89 final size:89
Alignment explanation
Indices: 420309--420851 Score: 537
Period size: 89 Copynumber: 6.1 Consensus size: 89
420299 GATTTAGCGA
* * * *
420309 TAAAAGATTGGATTTGGTGACTTCAATCTTCCCCTCTAGATTAGGGGTAAAAGATTGGATGGTGG
1 TAAAAGACTGGA--TGGTGGCTTCAATCTGCCCCTCTAGATTA-GGGTAAAAGATTGGATGGTTG
* *
420374 CTTCAATTTGCCCCTTTGGATTAAGGG
63 CTTCAATTTACCCCTTTAGATTAAGGG
* * * *
420401 TAAAAGACTGAATGGTGGCTTCAATCTGCCCTTCTGGATTAGGGTAAAGGATTGGATGGTTGCTT
1 TAAAAGACTGGATGGTGGCTTCAATCTGCCCCTCTAGATTAGGGTAAAAGATTGGATGGTTGCTT
* *
420466 CAATCCT-CCCCTCTAGATT-AGAGG
66 CAAT-TTACCCCTTTAGATTAAG-GG
* * * * *
420490 TAAAAGACTGGATTGTGGCTTCAATTTGCCCCT-TAGATTAGGGGTAAAGGACTGGATGGCTGCT
1 TAAAAGACTGGATGGTGGCTTCAATCTGCCCCTCTAGATTA-GGGTAAAAGATTGGATGGTTGCT
* * *
420554 TCAATCTACCCCTTTGGATTAGGGG
65 TCAATTTACCCCTTTAGATTAAGGG
* * * * *
420579 TAAAAGACTGGATGGTGGCTTTAATTTGCCCCTCTGGATTAAGGGTAAAAGATTGGATGATTACT
1 TAAAAGACTGGATGGTGGCTTCAATCTGCCCCTCTAGATT-AGGGTAAAAGATTGGATGGTTGCT
*
420644 TCAATTT-GCCCTTCTAGATT-AGGAG
65 TCAATTTACCCCTT-TAGATTAAGG-G
* * * *
420669 TAAAAGATTTGATGGTGGCTTCAATCTGCCCCTCTAGATTAAGGGTAAAAGACTGGATAG-TGAC
1 TAAAAGACTGGATGGTGGCTTCAATCTGCCCCTCTAGATT-AGGGTAAAAGATTGGATGGTTG-C
* * *
420733 TTCAATTTACCTCTCTACATTAAGGG
64 TTCAATTTACCCCTTTAGATTAAGGG
* * * *
420759 T-AAAGATTGGATGGTGGCTTCAATCTACCCCTATAGATTAGAGGT-AAAGATTGGAT-GATGAC
1 TAAAAGACTGGATGGTGGCTTCAATCTGCCCCTCTAGATTAG-GGTAAAAGATTGGATGGTTG-C
* * * *
420821 TTCAATCTATCCCTCTAGATTAGGGG
64 TTCAATTTACCCCTTTAGATTAAGGG
420847 TAAAA
1 TAAAA
420852 TATTGATGTG
Statistics
Matches: 381, Mismatches: 55, Indels: 33
0.81 0.12 0.07
Matches are distributed among these distances:
87 1 0.00
88 48 0.13
89 185 0.49
90 130 0.34
91 7 0.02
92 10 0.03
ACGTcount: A:0.27, C:0.17, G:0.25, T:0.31
Consensus pattern (89 bp):
TAAAAGACTGGATGGTGGCTTCAATCTGCCCCTCTAGATTAGGGTAAAAGATTGGATGGTTGCTT
CAATTTACCCCTTTAGATTAAGGG
Found at i:420479 original size:134 final size:133
Alignment explanation
Indices: 420284--420873 Score: 544
Period size: 134 Copynumber: 4.4 Consensus size: 133
420274 TGTTGTAACG
* * *
420284 TCAATCTGCCC-CCTGGATTTAGCGATAAAAGATTGGATTTGGTGACTTCAATCTT-CCCCTCTA
1 TCAATCTGCCCTTCTGGA-TTAG-GGTAAAAGACTGGA--TGGTGACTTCAAT-TTACCCCTCTA
* *
420347 GATTAGGGGTAAAAGATTGGATGGTGGCTTCAATTTGCCCCTTTGGATTAAGGGTAAAAGACTGA
61 GATTAAGGGTAAAAGATTGGATGGTGGCTTCAATTTGCCCCTTTAGATTAAGGGTAAAAGACTG-
420412 ATGGTGGCT
125 ATGGTGGCT
* * *
420421 TCAATCTGCCCTTCTGGATTAGGGTAAAGGATTGGATGGTTG-CTTCAATCCT-CCCCTCTAGAT
1 TCAATCTGCCCTTCTGGATTAGGGTAAAAGACTGGATGG-TGACTTCAAT-TTACCCCTCTAGAT
* * * *
420484 T-AGAGGTAAAAGACTGGATTGTGGCTTCAATTTGCCCC-TTAGATTAGGGGTAAAGGACTGGAT
64 TAAG-GGTAAAAGATTGGATGGTGGCTTCAATTTGCCCCTTTAGATTAAGGGTAAAAGACT-GAT
420547 GGCT-GCT
127 GG-TGGCT
* * * * *
420554 TCAATCTACCCCTT-TGGATTAGGGGTAAAAGACTGGATGGTGGCTTTAATTTGCCCCTCTGGAT
1 TCAATCT-GCCCTTCTGGATTA-GGGTAAAAGACTGGATGGTGACTTCAATTTACCCCTCTAGAT
* ** *
420618 TAAGGGTAAAAGATTGGATGATTACTTCAATTTG-CCCTTCTAGATT-AGGAGTAAAAGATTTGA
64 TAAGGGTAAAAGATTGGATGGTGGCTTCAATTTGCCCCTT-TAGATTAAGG-GTAAAAGA-CTGA
420681 TGGTGGCT
126 TGGTGGCT
* * * * *
420689 TCAATCTGCCCCTCTAGATTAAGGGTAAAAGACTGGATAGTGACTTCAATTTACCTCTCTACATT
1 TCAATCTGCCCTTCTGGATT-AGGGTAAAAGACTGGATGGTGACTTCAATTTACCCCTCTAGATT
* * * *
420754 AAGGGT-AAAGATTGGATGGTGGCTTCAATCTACCCCTATAGATT-AGAGGT-AAAGATTGGATG
65 AAGGGTAAAAGATTGGATGGTGGCTTCAATTTGCCCCTTTAGATTAAG-GGTAAAAGACT-GATG
* *
420816 ATGACT
128 GTGGCT
* * * *
420822 TCAATCTATCCC-TCTAGATTAGGGGTAAAATA-TTGATGTGGTGACTTCAATT
1 TCAATCT-GCCCTTCTGGATTA-GGGTAAAAGACTGGA--TGGTGACTTCAATT
420874 CGTTTAGTTT
Statistics
Matches: 383, Mismatches: 46, Indels: 51
0.80 0.10 0.11
Matches are distributed among these distances:
132 6 0.02
133 83 0.22
134 176 0.46
135 84 0.22
136 14 0.04
137 15 0.04
138 5 0.01
ACGTcount: A:0.27, C:0.17, G:0.24, T:0.32
Consensus pattern (133 bp):
TCAATCTGCCCTTCTGGATTAGGGTAAAAGACTGGATGGTGACTTCAATTTACCCCTCTAGATTA
AGGGTAAAAGATTGGATGGTGGCTTCAATTTGCCCCTTTAGATTAAGGGTAAAAGACTGATGGTG
GCT
Found at i:421000 original size:49 final size:49
Alignment explanation
Indices: 420947--421362 Score: 341
Period size: 49 Copynumber: 8.5 Consensus size: 49
420937 TCCGCTATTG
* * **
420947 CGGCTTCAACCTATCCCTCTTTAATTTTAAGGTGTAAGATCTGTCGTTA
1 CGGCTTCAATCTATCCCTCTTCAATTTTAAGGTGTAAGATCCATCGTTA
* * *
420996 CGGCTTCAATCTATCCCTCTTCAGTTTTAAGGTGTAAGATCCGTCGTTG
1 CGGCTTCAATCTATCCCTCTTCAATTTTAAGGTGTAAGATCCATCGTTA
* * * * * * * * *
421045 CGACTTTAGTCTTTTCCTCTTCAATTTTAGGGTGTTAGGTCCACCGTTA
1 CGGCTTCAATCTATCCCTCTTCAATTTTAAGGTGTAAGATCCATCGTTA
* * * *
421094 CGACTTCAATTTATCCCTCTTCGATTTTAAGGTGTAAGATCCATTGTTA
1 CGGCTTCAATCTATCCCTCTTCAATTTTAAGGTGTAAGATCCATCGTTA
* * * * * * *
421143 TGACTTCAATCTTTCCCTTTTCAATTTT-AGCGTGTTAGGTCCATCGTTG
1 CGGCTTCAATCTATCCCTCTTCAATTTTAAG-GTGTAAGATCCATCGTTA
* * * *
421192 CAGCTTCAACCTATCCCTCTTCAGTTTTAAGGTGTAAGATCCACCGTTA
1 CGGCTTCAATCTATCCCTCTTCAATTTTAAGGTGTAAGATCCATCGTTA
* * * * * * * ** *
421241 TGGCTTCAATCTTTCCCACTTCGATTTTAGGGTGTTAGAT-TAGTAATTG
1 CGGCTTCAATCTATCCCTCTTCAATTTTAAGGTGTAAGATCCA-TCGTTA
* * * * * * * *
421290 CGGCTTTAATCTATCCTTCTTTAATTTTAAGGCGTTAGGTCCGTCGTTG
1 CGGCTTCAATCTATCCCTCTTCAATTTTAAGGTGTAAGATCCATCGTTA
* *
421339 CGGCTTCAACCTATCCTTCTTCAA
1 CGGCTTCAATCTATCCCTCTTCAA
421363 ACTCTATGAT
Statistics
Matches: 284, Mismatches: 79, Indels: 8
0.77 0.21 0.02
Matches are distributed among these distances:
48 3 0.01
49 279 0.98
50 2 0.01
ACGTcount: A:0.20, C:0.23, G:0.17, T:0.40
Consensus pattern (49 bp):
CGGCTTCAATCTATCCCTCTTCAATTTTAAGGTGTAAGATCCATCGTTA
Found at i:421192 original size:147 final size:148
Alignment explanation
Indices: 420950--421362 Score: 379
Period size: 147 Copynumber: 2.8 Consensus size: 148
420940 GCTATTGCGG
* ** ** *
420950 CTTCAA-CCTATCCCTCTTTAATTTTAAGGTGTAAGATCTGTCGTTACGGCTTCAATCTATCCCT
1 CTTCAATCTTATCCCTCTTCGATTTTAAGGTGTAAGATCCATCGTTACGACTTCAATCTATCCCT
* * * ** * * *
421014 CTTCAGTTTTAAGGTGTAAGATCCGTCGTTGC-GACTTTAGTCTTTTCCTCTTCAATTTTAGGGT
66 CTTCAATTTTAAGGTGTAAGATCCATCGTTGCAG-CTTCAACCTATCCCTCTTCAATTTTAAGGT
* *
421078 GTTAGGTCCACCGTTACGA
130 GTAAGATCCACCGTTACGA
* * *
421097 CTTCAAT-TTATCCCTCTTCGATTTTAAGGTGTAAGATCCATTGTTATGACTTCAATCTTTCCCT
1 CTTCAATCTTATCCCTCTTCGATTTTAAGGTGTAAGATCCATCGTTACGACTTCAATCTATCCCT
* * * *
421161 TTTCAATTTT-AGCGTGTTAGGTCCATCGTTGCAGCTTCAACCTATCCCTCTTCAGTTTTAAGGT
66 CTTCAATTTTAAG-GTGTAAGATCCATCGTTGCAGCTTCAACCTATCCCTCTTCAATTTTAAGGT
* *
421225 GTAAGATCCACCGTTATGG
130 GTAAGATCCACCGTTACGA
* * * * ** * * * *
421244 CTTCAATCTT-TCCCACTTCGATTTTAGGGTGTTAGAT-TAGTAATTGCGGCTTTAATCTATCCT
1 CTTCAATCTTATCCCTCTTCGATTTTAAGGTGTAAGATCCA-TCGTTACGACTTCAATCTATCCC
* * * * * * *
421307 TCTTTAATTTTAAGGCGTTAGGTCCGTCGTTGCGGCTTCAACCTATCCTTCTTCAA
65 TCTTCAATTTTAAGGTGTAAGATCCATCGTTGCAGCTTCAACCTATCCCTCTTCAA
421363 ACTCTATGAT
Statistics
Matches: 216, Mismatches: 44, Indels: 12
0.79 0.16 0.04
Matches are distributed among these distances:
146 3 0.01
147 208 0.96
148 5 0.02
ACGTcount: A:0.20, C:0.23, G:0.17, T:0.40
Consensus pattern (148 bp):
CTTCAATCTTATCCCTCTTCGATTTTAAGGTGTAAGATCCATCGTTACGACTTCAATCTATCCCT
CTTCAATTTTAAGGTGTAAGATCCATCGTTGCAGCTTCAACCTATCCCTCTTCAATTTTAAGGTG
TAAGATCCACCGTTACGA
Found at i:421305 original size:98 final size:98
Alignment explanation
Indices: 420950--421278 Score: 390
Period size: 98 Copynumber: 3.4 Consensus size: 98
420940 GCTATTGCGG
* * * * * * ** *
420950 CTTCAACCTATCCCTCTTTAATTTTAAGGTGTAAGATCTGTCGTTACGGCTTCAATCTATCCCTC
1 CTTCAATCTTTCCCTCTTCAATTTTAGGGTGTTAGGTCCATCGTTGCGGCTTCAATCTATCCCTC
* **
421015 TTCAGTTTTAAGGTGTAAGATCCGTCGTTGCGA
66 TTCAGTTTTAAGGTGTAAGATCCATCGTTATGA
* * * * * * *
421048 CTTTAGTCTTTTCCTCTTCAATTTTAGGGTGTTAGGTCCACCGTTACGACTTCAATTTATCCCTC
1 CTTCAATCTTTCCCTCTTCAATTTTAGGGTGTTAGGTCCATCGTTGCGGCTTCAATCTATCCCTC
*
421113 TTC-GATTTTAAGGTGTAAGATCCATTGTTATGA
66 TTCAG-TTTTAAGGTGTAAGATCCATCGTTATGA
* * * *
421146 CTTCAATCTTTCCCTTTTCAATTTTAGCGTGTTAGGTCCATCGTTGCAGCTTCAACCTATCCCTC
1 CTTCAATCTTTCCCTCTTCAATTTTAGGGTGTTAGGTCCATCGTTGCGGCTTCAATCTATCCCTC
* *
421211 TTCAGTTTTAAGGTGTAAGATCCACCGTTATGG
66 TTCAGTTTTAAGGTGTAAGATCCATCGTTATGA
* *
421244 CTTCAATCTTTCCCACTTCGATTTTAGGGTGTTAG
1 CTTCAATCTTTCCCTCTTCAATTTTAGGGTGTTAG
421279 ATTAGTAATT
Statistics
Matches: 193, Mismatches: 36, Indels: 4
0.83 0.15 0.02
Matches are distributed among these distances:
97 1 0.01
98 191 0.99
99 1 0.01
ACGTcount: A:0.20, C:0.23, G:0.17, T:0.40
Consensus pattern (98 bp):
CTTCAATCTTTCCCTCTTCAATTTTAGGGTGTTAGGTCCATCGTTGCGGCTTCAATCTATCCCTC
TTCAGTTTTAAGGTGTAAGATCCATCGTTATGA
Found at i:422395 original size:20 final size:19
Alignment explanation
Indices: 422372--422432 Score: 61
Period size: 19 Copynumber: 3.2 Consensus size: 19
422362 CGACCCCTCC
*
422372 TTTTTTTGTTTTCTTCTCT
1 TTTTTTTTTTTTCTTCTCT
422391 TTTTTTCCTTTTTT-TTCTCT
1 TTTTTT--TTTTTTCTTCTCT
* * *
422411 CTTTTTCTTTTTCTTTTCT
1 TTTTTTTTTTTTCTTCTCT
422430 TTT
1 TTT
422433 ATTCTCTTCT
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
18 5 0.15
19 13 0.38
20 11 0.32
21 5 0.15
ACGTcount: A:0.00, C:0.18, G:0.02, T:0.80
Consensus pattern (19 bp):
TTTTTTTTTTTTCTTCTCT
Found at i:422413 original size:27 final size:26
Alignment explanation
Indices: 422369--422450 Score: 87
Period size: 27 Copynumber: 3.0 Consensus size: 26
422359 TCTCGACCCC
*
422369 TCCTTTTTTTGTTTTCTTCTCTT-TTTT
1 TCCTTTTTTT-TTCTCTTCT-TTCTTTT
422396 TCCTTTTTTTTCTCTCTT-TTTCTTTT
1 TCCTTTTTTTT-TCTCTTCTTTCTTTT
*
422422 TCTTTTCTTTTATTCTCTTCTTTCTTTT
1 TCCTTT-TTTT-TTCTCTTCTTTCTTTT
422450 T
1 T
422451 GCTAGTTCGA
Statistics
Matches: 48, Mismatches: 2, Indels: 9
0.81 0.03 0.15
Matches are distributed among these distances:
25 2 0.04
26 11 0.23
27 25 0.52
28 10 0.21
ACGTcount: A:0.01, C:0.21, G:0.01, T:0.77
Consensus pattern (26 bp):
TCCTTTTTTTTTCTCTTCTTTCTTTT
Found at i:422427 original size:22 final size:22
Alignment explanation
Indices: 422373--422430 Score: 66
Period size: 22 Copynumber: 2.6 Consensus size: 22
422363 GACCCCTCCT
422373 TTTTTTGTTTTCTTCTCTTTTT-
1 TTTTTT-TTTTCTTCTCTTTTTC
422395 TTCCTTTTTTTTC-TCTCTTTTTC
1 TT--TTTTTTTTCTTCTCTTTTTC
*
422418 TTTTTCTTTTCTT
1 TTTTTTTTTTCTT
422431 TTATTCTCTT
Statistics
Matches: 31, Mismatches: 1, Indels: 8
0.77 0.03 0.20
Matches are distributed among these distances:
21 8 0.26
22 12 0.39
23 7 0.23
24 4 0.13
ACGTcount: A:0.00, C:0.19, G:0.02, T:0.79
Consensus pattern (22 bp):
TTTTTTTTTTCTTCTCTTTTTC
Found at i:428495 original size:46 final size:46
Alignment explanation
Indices: 428442--428533 Score: 157
Period size: 46 Copynumber: 2.0 Consensus size: 46
428432 ATCCTTTCAA
* * *
428442 TATACGTGTCAGTTTCAAAAAGAAGAAGAGATGTCATACTTATCCC
1 TATACGTGTCAGCTTCAAAAAGAAAAAGAGATGTCAGACTTATCCC
428488 TATACGTGTCAGCTTCAAAAAGAAAAAGAGATGTCAGACTTATCCC
1 TATACGTGTCAGCTTCAAAAAGAAAAAGAGATGTCAGACTTATCCC
428534 GGCATTGTGC
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
46 43 1.00
ACGTcount: A:0.38, C:0.18, G:0.17, T:0.26
Consensus pattern (46 bp):
TATACGTGTCAGCTTCAAAAAGAAAAAGAGATGTCAGACTTATCCC
Found at i:433292 original size:26 final size:26
Alignment explanation
Indices: 433262--433313 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
433252 ACCATAAATA
*
433262 CAACATACATAAAATAAAATGCAAAG
1 CAACATACATAAAATAAAATGAAAAG
*
433288 CAACATATATAAAATAAAATGAAAAG
1 CAACATACATAAAATAAAATGAAAAG
433314 GATCACAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.63, C:0.12, G:0.08, T:0.17
Consensus pattern (26 bp):
CAACATACATAAAATAAAATGAAAAG
Found at i:434435 original size:44 final size:44
Alignment explanation
Indices: 434387--434472 Score: 102
Period size: 44 Copynumber: 2.0 Consensus size: 44
434377 ACATGTAATT
* * *
434387 AAATAAAAAGAAAAAAT-AAAATTTAATAATAAATAAATAAATAA
1 AAATAAAAACAAAAAATGAAAATTAAATAAAAAAT-AATAAATAA
* * *
434431 AAATAATAACAATAAATGTAAATTAAATAAAAAATAATAAAT
1 AAATAAAAACAAAAAATGAAAATTAAATAAAAAATAATAAAT
434473 GGCATGAAAA
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
44 21 0.60
45 14 0.40
ACGTcount: A:0.72, C:0.01, G:0.02, T:0.24
Consensus pattern (44 bp):
AAATAAAAACAAAAAATGAAAATTAAATAAAAAATAATAAATAA
Found at i:434579 original size:99 final size:99
Alignment explanation
Indices: 434411--434655 Score: 253
Period size: 99 Copynumber: 2.5 Consensus size: 99
434401 AATAAAATTT
*
434411 AATAATAAATAAAT-AAA--TAAAAAT-AATAACAATAAATGTAAATTAAATAAAAAATAA-T-A
1 AATAATAAATAAATAAAATGTAAAAATAAATAAC--TAAATATAAA-T-AAT-AAAAATAATTGA
* * * *
434470 -AAT-GGCATGAAAATAAATAATAACTAAATAAATAAACA
61 GATTAGGTATG-AAATAAATAACAAATAAATAAATAAACA
434508 AA-AA-AAATAAAATAAAATGCT-AAAATAAATAAAC-AAATATAAATAATAAAAATAATTGAGA
1 AATAATAAAT-AAATAAAATG-TAAAAATAAAT-AACTAAATATAAATAATAAAAATAATTGAGA
*
434569 TTAGGTATGAAATAAATAACAAATAAATAAATAAGCA
63 TTAGGTATGAAATAAATAACAAATAAATAAATAAACA
* *
434606 AATAATCAATAAATTAAATGTAAAAATAAATAACTAAATATAAATAATAA
1 AATAATAAATAAATAAAATGTAAAAATAAATAACTAAATATAAATAATAA
434656 TAAAAAAGAA
Statistics
Matches: 125, Mismatches: 8, Indels: 28
0.78 0.05 0.17
Matches are distributed among these distances:
95 12 0.10
96 10 0.08
97 7 0.06
98 41 0.33
99 45 0.36
100 7 0.06
101 3 0.02
ACGTcount: A:0.67, C:0.04, G:0.05, T:0.24
Consensus pattern (99 bp):
AATAATAAATAAATAAAATGTAAAAATAAATAACTAAATATAAATAATAAAAATAATTGAGATTA
GGTATGAAATAAATAACAAATAAATAAATAAACA
Found at i:434617 original size:15 final size:15
Alignment explanation
Indices: 434578--434610 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 15
434568 ATTAGGTATG
434578 AAATAAATAACAAAT
1 AAATAAATAACAAAT
434593 AAATAAATAAGCAAAT
1 AAATAAATAA-CAAAT
434609 AA
1 AA
434611 TCAATAAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.59
16 7 0.41
ACGTcount: A:0.73, C:0.06, G:0.03, T:0.18
Consensus pattern (15 bp):
AAATAAATAACAAAT
Found at i:434635 original size:6 final size:7
Alignment explanation
Indices: 434579--434655 Score: 52
Period size: 8 Copynumber: 10.7 Consensus size: 7
434569 TTAGGTATGA
434579 AATAAAT
1 AATAAAT
*
434586 AACAAAT
1 AATAAAT
434593 AAATAAAT
1 -AATAAAT
*
434601 AAGCAAAT
1 AA-TAAAT
*
434609 AATCAAT
1 AATAAAT
434616 AAATTAAAT
1 -AA-TAAAT
*
434625 -GTAAA-
1 AATAAAT
434630 AATAAAT
1 AATAAAT
434637 AACTAAAT
1 AA-TAAAT
434645 -ATAAAT
1 AATAAAT
434651 AATAA
1 AATAA
434656 TAAAAAAGAA
Statistics
Matches: 54, Mismatches: 8, Indels: 16
0.69 0.10 0.21
Matches are distributed among these distances:
6 13 0.24
7 18 0.33
8 19 0.35
9 4 0.07
ACGTcount: A:0.68, C:0.05, G:0.03, T:0.25
Consensus pattern (7 bp):
AATAAAT
Found at i:434658 original size:20 final size:21
Alignment explanation
Indices: 434580--434655 Score: 64
Period size: 20 Copynumber: 3.5 Consensus size: 21
434570 TAGGTATGAA
* *
434580 ATAAATAACAAATAAATAAAT
1 ATAAATAATAAATAACTAAAT
* * *
434601 AAGCAAATAATCAATAAATTAAAT
1 -A-TAAATAATAAAT-AACTAAAT
*
434625 GTAAA-AATAAATAACTAAAT
1 ATAAATAATAAATAACTAAAT
434645 ATAAATAATAA
1 ATAAATAATAA
434656 TAAAAAAGAA
Statistics
Matches: 42, Mismatches: 9, Indels: 7
0.72 0.16 0.12
Matches are distributed among these distances:
20 11 0.26
21 11 0.26
22 4 0.10
23 9 0.21
24 7 0.17
ACGTcount: A:0.67, C:0.05, G:0.03, T:0.25
Consensus pattern (21 bp):
ATAAATAATAAATAACTAAAT
Found at i:434892 original size:22 final size:24
Alignment explanation
Indices: 434847--434900 Score: 74
Period size: 24 Copynumber: 2.2 Consensus size: 24
434837 GCTTTGAAAT
434847 TTCTTTGAATGTATGTGTAAAAAAA
1 TTCTTTGAATG-ATGTGTAAAAAAA
* *
434872 TTCTTTGAATGTTGTATAAAAAAA
1 TTCTTTGAATGATGTGTAAAAAAA
434896 -TCTTT
1 TTCTTT
434901 AAATCTTATT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
23 5 0.19
24 11 0.41
25 11 0.41
ACGTcount: A:0.37, C:0.06, G:0.13, T:0.44
Consensus pattern (24 bp):
TTCTTTGAATGATGTGTAAAAAAA
Found at i:434896 original size:24 final size:25
Alignment explanation
Indices: 434847--434900 Score: 85
Period size: 25 Copynumber: 2.2 Consensus size: 25
434837 GCTTTGAAAT
*
434847 TTCTTTGAATGTATGTGTAAAAAAA
1 TTCTTTGAATGTATGTATAAAAAAA
434872 TTCTTTGAATGT-TGTATAAAAAAA
1 TTCTTTGAATGTATGTATAAAAAAA
434896 -TCTTT
1 TTCTTT
434901 AAATCTTATT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
23 5 0.18
24 11 0.39
25 12 0.43
ACGTcount: A:0.37, C:0.06, G:0.13, T:0.44
Consensus pattern (25 bp):
TTCTTTGAATGTATGTATAAAAAAA
Found at i:437867 original size:10 final size:10
Alignment explanation
Indices: 437816--437869 Score: 63
Period size: 10 Copynumber: 5.3 Consensus size: 10
437806 ATATATTTCG
437816 TCACATATTAA
1 TCACATA-TAA
*
437827 TCACATATAG
1 TCACATATAA
*
437837 TCACATATAG
1 TCACATATAA
*
437847 TCACGTATAA
1 TCACATATAA
*
437857 TCACATTTAA
1 TCACATATAA
437867 TCA
1 TCA
437870 TAATTTATGA
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
10 31 0.82
11 7 0.18
ACGTcount: A:0.41, C:0.20, G:0.06, T:0.33
Consensus pattern (10 bp):
TCACATATAA
Found at i:438307 original size:36 final size:36
Alignment explanation
Indices: 438267--438355 Score: 117
Period size: 36 Copynumber: 2.5 Consensus size: 36
438257 TATTAGCACA
*
438267 ATATAATTACTGTCACATGGCATGAAAAACATACCC
1 ATATAATTACTGTCACATGACATGAAAAACATACCC
* * *
438303 ATATATTTATTGTCACATGACATGAATAACATACCC
1 ATATAATTACTGTCACATGACATGAAAAACATACCC
*
438339 -TCATAATTACTTTCACA
1 AT-ATAATTACTGTCACA
438356 ACAGTCATCA
Statistics
Matches: 45, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
35 1 0.02
36 44 0.98
ACGTcount: A:0.39, C:0.21, G:0.08, T:0.31
Consensus pattern (36 bp):
ATATAATTACTGTCACATGACATGAAAAACATACCC
Found at i:443176 original size:33 final size:33
Alignment explanation
Indices: 443139--443222 Score: 114
Period size: 33 Copynumber: 2.5 Consensus size: 33
443129 ATATGTCAAT
* *
443139 TTCTCCTTCTCATCATCCTGTCGATCTGTAGGA
1 TTCTCCTTGTCATCATCCTGCCGATCTGTAGGA
* * *
443172 TTCTCATTGTCATCATCCTGCCTATCTGTCGGA
1 TTCTCCTTGTCATCATCCTGCCGATCTGTAGGA
*
443205 TTCTCCTTGTTATCATCC
1 TTCTCCTTGTCATCATCC
443223 CGTGAATCCT
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
33 44 1.00
ACGTcount: A:0.14, C:0.31, G:0.13, T:0.42
Consensus pattern (33 bp):
TTCTCCTTGTCATCATCCTGCCGATCTGTAGGA
Found at i:445828 original size:8 final size:7
Alignment explanation
Indices: 445802--445827 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
445792 TTTGCAATAT
445802 TTTTTAA
1 TTTTTAA
445809 TTTTTAA
1 TTTTTAA
445816 TTTTTAA
1 TTTTTAA
445823 TTTTT
1 TTTTT
445828 TTTATAACTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (7 bp):
TTTTTAA
Found at i:446125 original size:5 final size:5
Alignment explanation
Indices: 446115--446141 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
446105 ATATGACAAG
446115 ATATA ATATA ATATA ATATA ATATA AT
1 ATATA ATATA ATATA ATATA ATATA AT
446142 TATTTTATCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (5 bp):
ATATA
Found at i:447148 original size:17 final size:18
Alignment explanation
Indices: 447126--447165 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
447116 AATATACAAC
*
447126 ATAAAAAAT-TAAAATTT
1 ATAAAAAATATAAAATGT
447143 AT-AAAAATATAAAATGT
1 ATAAAAAATATAAAATGT
447160 ATAAAA
1 ATAAAA
447166 TTTTGTCCAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
16 6 0.30
17 11 0.55
18 3 0.15
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.30
Consensus pattern (18 bp):
ATAAAAAATATAAAATGT
Done.