Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015275.1 Kokia drynarioides strain JFW-HI SEQ_130320, 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: 493191
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.33
Warning! 391 characters in sequence are not A, C, G, or T
File 2 of 2
Found at i:363378 original size:23 final size:23
Alignment explanation
Indices: 363341--363424 Score: 75
Period size: 23 Copynumber: 3.7 Consensus size: 23
363331 ATTTATTTTA
**
363341 TTATTTAAAAATAATAAAATATT
1 TTATTTAAATTTAATAAAATATT
363364 TTATTTAAATTTAATTATAAATA--
1 TTATTTAAATTTAA-TA-AAATATT
* * *
363387 -TATATACATGTTAATATAATATT
1 TTATTTAAAT-TTAATAAAATATT
363410 TTATTTAAATTTAAT
1 TTATTTAAATTTAAT
363425 TATAAAAATA
Statistics
Matches: 48, Mismatches: 7, Indels: 12
0.72 0.10 0.18
Matches are distributed among these distances:
21 4 0.08
22 9 0.19
23 21 0.44
24 9 0.19
25 5 0.10
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.50
Consensus pattern (23 bp):
TTATTTAAATTTAATAAAATATT
Found at i:363580 original size:31 final size:31
Alignment explanation
Indices: 363544--363604 Score: 77
Period size: 31 Copynumber: 2.0 Consensus size: 31
363534 ATGATCATTA
* * *
363544 AATTATTCGAAAGTTTTTGTTTAAGTTACTG
1 AATTATTCGAAAATTATTATTTAAGTTACTG
* *
363575 AATTATTTGAAAATTATTATTTCAGTTACT
1 AATTATTCGAAAATTATTATTTAAGTTACT
363605 TGGTTGTTAA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.33, C:0.07, G:0.11, T:0.49
Consensus pattern (31 bp):
AATTATTCGAAAATTATTATTTAAGTTACTG
Found at i:364026 original size:17 final size:17
Alignment explanation
Indices: 363990--364025 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
363980 TTACTAATAA
*
363990 TTTAGTATCATCCCTAT
1 TTTAATATCATCCCTAT
364007 TTTAATATCATCCCT-T
1 TTTAATATCATCCCTAT
364023 TTT
1 TTT
364026 TGTGGAGTCC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 4 0.22
17 14 0.78
ACGTcount: A:0.22, C:0.22, G:0.03, T:0.53
Consensus pattern (17 bp):
TTTAATATCATCCCTAT
Found at i:365265 original size:169 final size:167
Alignment explanation
Indices: 364825--365283 Score: 525
Period size: 169 Copynumber: 2.7 Consensus size: 167
364815 CATGTTTAGA
* * *
364825 GCTAAATTGCCGTATGATATAATTTAGGTTACTTGTGTGAGTTCTATAACAATACGGTTTTATGA
1 GCTAAATTGCCCTAT-ATATAATTTAGTTTACTTGTGTGAGTTCTATAACAATACGGTTTTACGA
* ** **
364890 GAACCCCGATGAGCTTCACCT-GCAGTCGGAATGTTGTCTCATAGTCTTTTGTTACTTGCATGCT
65 GAA-CCCGATGAGCTTCA-CTGGCGGTCGGAATGTCATCTCATAGTCTTTCATTACTTGCATGCT
*
364954 TCATTATTTTTGTCATTGTGTAATCACAAGGAGATTTGGT
128 TCATCATTTTTGTCATTGTGTAATCACAAGGAGATTTGGT
* * *
364994 GCTAAATTGCCGTAT-GATAATTTA-TGTTACTTGTGTGAGTTCTATAACAATACAGTTTTACGA
1 GCTAAATTGCCCTATATATAATTTAGT-TTACTTGTGTGAGTTCTATAACAATACGGTTTTACGA
** ** * * *
365057 GAATCCTTATGAGCTTCAAC-GATGGTTGGAAACGTCATCTCGTAGTCTTTCATTACTTGCATGC
65 GAA-CCCGATGAGCTTC-ACTGGCGGTCGG-AATGTCATCTCATAGTCTTTCATTACTTGCATGC
* * *
365121 TTCATCATTTTTGTCATTTGTGTGATTATAAGGAGATTTGGT
127 TTCATCATTTTTGTCA-TTGTGTAATCACAAGGAGATTTGGT
* * * *
365163 GCTAAATTGCCCTCTATATAGTTTAGTTTACTTGTGTGAGTTCTATAACGATATGGTTTTACGAG
1 GCTAAATTGCCCTATATATAATTTAGTTTACTTGTGTGAGTTCTATAACAATACGGTTTTACGAG
* * *
365228 -AGCCGAATAAGCTTCACTGGCGGTCGAGAATGTCATCTCTTAGTC-TTCATTACTTG
66 AACCCG-ATGAGCTTCACTGGCGGTCG-GAATGTCATCTCATAGTCTTTCATTACTTG
365284 TTTGCTTACC
Statistics
Matches: 243, Mismatches: 37, Indels: 21
0.81 0.12 0.07
Matches are distributed among these distances:
167 62 0.26
168 58 0.24
169 79 0.33
170 43 0.18
171 1 0.00
ACGTcount: A:0.25, C:0.16, G:0.20, T:0.39
Consensus pattern (167 bp):
GCTAAATTGCCCTATATATAATTTAGTTTACTTGTGTGAGTTCTATAACAATACGGTTTTACGAG
AACCCGATGAGCTTCACTGGCGGTCGGAATGTCATCTCATAGTCTTTCATTACTTGCATGCTTCA
TCATTTTTGTCATTGTGTAATCACAAGGAGATTTGGT
Found at i:367080 original size:28 final size:26
Alignment explanation
Indices: 367007--367091 Score: 91
Period size: 27 Copynumber: 3.1 Consensus size: 26
366997 AATTTCTGTA
*
367007 TTTTTTTTTTTAA-TTTGAAATTTAG
1 TTTTTTTTTTTAATTTTAAAATTTAG
* *
367032 TCTTTGTATTTTTATTTTTAAAAATTTAG
1 T-TTT-TTTTTTTAATTTT-AAAATTTAG
367061 TTTTTTTTTTTAGATTTTAAAATTTAAG
1 TTTTTTTTTTTA-ATTTTAAAATTT-AG
367089 TTT
1 TTT
367092 AACTATTAAA
Statistics
Matches: 49, Mismatches: 5, Indels: 9
0.78 0.08 0.14
Matches are distributed among these distances:
25 1 0.02
26 3 0.06
27 21 0.43
28 15 0.31
29 9 0.18
ACGTcount: A:0.26, C:0.01, G:0.07, T:0.66
Consensus pattern (26 bp):
TTTTTTTTTTTAATTTTAAAATTTAG
Found at i:370354 original size:2 final size:2
Alignment explanation
Indices: 370347--370373 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
370337 ATGATACATC
370347 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
370374 AACATCAACT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:371548 original size:14 final size:15
Alignment explanation
Indices: 371523--371554 Score: 57
Period size: 14 Copynumber: 2.2 Consensus size: 15
371513 GATAAAAATC
371523 AAATTATAATATATT
1 AAATTATAATATATT
371538 AAATTAT-ATATATT
1 AAATTATAATATATT
371552 AAA
1 AAA
371555 AAAACTAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.59
15 7 0.41
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (15 bp):
AAATTATAATATATT
Found at i:371595 original size:40 final size:44
Alignment explanation
Indices: 371515--371597 Score: 102
Period size: 45 Copynumber: 2.0 Consensus size: 44
371505 AGTAAATTGA
* * *
371515 TAAAAATCAAATTATAATATATTAAATTATATATATTAAAAAAAC
1 TAAAAATCAAATTATAATATA-TAAATGATATAGACTAAAAAAAC
371560 TAAAAATCAAATTATAATA-A-AAATGA-A-AGACTAAAAAA
1 TAAAAATCAAATTATAATATATAAATGATATAGACTAAAAAA
371598 TATTAAATTA
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
40 9 0.26
41 1 0.03
42 5 0.14
44 1 0.03
45 19 0.54
ACGTcount: A:0.64, C:0.05, G:0.02, T:0.29
Consensus pattern (44 bp):
TAAAAATCAAATTATAATATATAAATGATATAGACTAAAAAAAC
Found at i:377728 original size:46 final size:46
Alignment explanation
Indices: 377675--377766 Score: 157
Period size: 46 Copynumber: 2.0 Consensus size: 46
377665 TCATCATATC
* *
377675 TTAATAGAATTCAAATTTAGAGATTAAATCGGAAAAAGTTTCAAAA
1 TTAATAGAAATCAAATTTAGAGATTAAATCGGAAAAAGTTTAAAAA
*
377721 TTAATAGAAATCAAATTTAGGGATTAAATCGGAAAAAGTTTAAAAA
1 TTAATAGAAATCAAATTTAGAGATTAAATCGGAAAAAGTTTAAAAA
377767 ATCCAGGATT
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:0.51, C:0.05, G:0.14, T:0.29
Consensus pattern (46 bp):
TTAATAGAAATCAAATTTAGAGATTAAATCGGAAAAAGTTTAAAAA
Found at i:382786 original size:8 final size:7
Alignment explanation
Indices: 382760--382804 Score: 81
Period size: 7 Copynumber: 6.3 Consensus size: 7
382750 TATTTTATTT
382760 TTTTTTC
1 TTTTTTC
382767 TTTTTTTC
1 -TTTTTTC
382775 TTTTTTC
1 TTTTTTC
382782 TTTTTTC
1 TTTTTTC
382789 TTTTTTC
1 TTTTTTC
382796 TTTTTTC
1 TTTTTTC
382803 TT
1 TT
382805 CTCTTTACCT
Statistics
Matches: 37, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
7 30 0.81
8 7 0.19
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (7 bp):
TTTTTTC
Found at i:383100 original size:14 final size:15
Alignment explanation
Indices: 383083--383132 Score: 50
Period size: 15 Copynumber: 3.5 Consensus size: 15
383073 ATTTTGCGGA
383083 TTTTTTT-TTACTT-
1 TTTTTTTGTTACTTG
*
383096 TTTTTTGGTTACTTG
1 TTTTTTTGTTACTTG
** *
383111 TTTTTTTCATATTTG
1 TTTTTTTGTTACTTG
383126 TTTTTTT
1 TTTTTTT
383133 AATTGAAATA
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
13 6 0.20
14 6 0.20
15 18 0.60
ACGTcount: A:0.08, C:0.06, G:0.08, T:0.78
Consensus pattern (15 bp):
TTTTTTTGTTACTTG
Found at i:383474 original size:18 final size:18
Alignment explanation
Indices: 383453--383488 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
383443 GGATATTATA
383453 TAATTCTTGTT-TTATTTT
1 TAATT-TTGTTATTATTTT
383471 TAATTTTGTTATTATTTT
1 TAATTTTGTTATTATTTT
383489 AGAGATATTC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.29
18 12 0.71
ACGTcount: A:0.19, C:0.03, G:0.06, T:0.72
Consensus pattern (18 bp):
TAATTTTGTTATTATTTT
Found at i:391063 original size:9 final size:9
Alignment explanation
Indices: 390951--391088 Score: 56
Period size: 10 Copynumber: 15.0 Consensus size: 9
390941 ATGTTAAAAA
*
390951 AAAAATGAT
1 AAAAATTAT
390960 AAAAA-TAT
1 AAAAATTAT
390968 -AAAA-TAT
1 AAAAATTAT
* *
390975 AAAAGTGATT
1 AAAAATTA-T
*
390985 AAAATTTATTT
1 AAAAATTA--T
390996 AAAATATT-T
1 AAAA-ATTAT
*
391005 AAAAGTTAT
1 AAAAATTAT
*
391014 TAAAATTA-
1 AAAAATTAT
*
391022 AAAAA-TAA
1 AAAAATTAT
*
391030 ATAAAATTTT
1 A-AAAATTAT
391040 ATAAAATCGTA-
1 A-AAAAT--TAT
391051 AAAAATTAT
1 AAAAATTAT
*
391060 AAAAATAAAT
1 AAAAAT-TAT
391070 AAAAATTTAT
1 AAAAA-TTAT
391080 AAAAATTAT
1 AAAAATTAT
391089 CATGTCTTTC
Statistics
Matches: 100, Mismatches: 15, Indels: 28
0.70 0.10 0.20
Matches are distributed among these distances:
7 9 0.09
8 14 0.14
9 32 0.32
10 34 0.34
11 8 0.08
12 3 0.03
ACGTcount: A:0.62, C:0.01, G:0.04, T:0.33
Consensus pattern (9 bp):
AAAAATTAT
Found at i:391072 original size:20 final size:20
Alignment explanation
Indices: 391015--391085 Score: 76
Period size: 20 Copynumber: 3.7 Consensus size: 20
391005 AAAAGTTATT
391015 AAAATTA-AAAAATAAATAA
1 AAAATTATAAAAATAAATAA
** **
391034 AATTTTAT-AAAAT-CGTAA
1 AAAATTATAAAAATAAATAA
391052 AAAATTATAAAAATAAATAA
1 AAAATTATAAAAATAAATAA
*
391072 AAATTTATAAAAAT
1 AAAATTATAAAAAT
391086 TATCATGTCT
Statistics
Matches: 40, Mismatches: 9, Indels: 5
0.74 0.17 0.09
Matches are distributed among these distances:
18 9 0.22
19 15 0.38
20 16 0.40
ACGTcount: A:0.68, C:0.01, G:0.01, T:0.30
Consensus pattern (20 bp):
AAAATTATAAAAATAAATAA
Found at i:393794 original size:333 final size:333
Alignment explanation
Indices: 392958--394283 Score: 1442
Period size: 333 Copynumber: 4.0 Consensus size: 333
392948 TTGGATTCGG
* * * *
392958 GTGAGTTCAAAAAAGGTATTTTC--TGTGTTAAGATGATCTCTGGAAGATCAT-TTCCTATACTC
1 GTGAGTTCAAAAAGGGTATTTTCTATGTATTAAAAGGATCTCTGGAAGATCATATTCCTATACTC
* * * *
393020 GTGTTCAAGTTAGAGGTGTC--TGAGTTAGAACTAGCTCATGTGTAGCATCAACACTATATAGGT
66 GTGTTCAGGTTAGAGGTGTCTATGAGTTGGACCAAGCTCATGTGTAGCATCAACACTATATAGGT
* * * * * *
393083 TTCATATTTTGGCCAAGTTCATTCTCGAGCCTAATATTTTTGTATAAATCTTCCCAAATACCGGG
131 CTCATATTTTGGCCAAGTTCATTCT-TAGCTTAATATTTTTGTTTAAACCTTCCCAAATACCAGG
* * * * **
393148 TGGGGTTCTGCCCATGGGTCCTTGGACAGGTCTAGTTCAAGTATGTGTCAGACATGATTACCGCA
195 TGGGCTT-TGCTCATGGGTCCTTGGACAAGTCTAGTTCAAGTATGTGTCAGACACGATTACTTCA
* * *
393213 AGAAAAGCAAGGGGAAGTGATAGCTTTTTGGCTTCGGGTGCTAAGGTACTTGGATTTGCGTGTGA
259 AGAAAAGCAA-GGGAAGTGTTAGCTTTTTGGCTTC-GGTGCTATGGTACTTGGATTTGGGTGTGA
393278 GTGTGCACACAA
322 GTGTGCACACAA
* * * * * * ** *
393290 GCGTGTTCAAAAAGAGTGTATCTTCTATGTAGTAATAGGATCTCTGGAAGATCATACTGTTATAT
1 GTGAGTTCAAAAAG-G-GTATTTTCTATGTATTAAAAGGATCTCTGGAAGATCATATTCCTATAC
* *
393355 TCGTGTTCAGGTCT-GAGGTGTCTATGAGATGGACCAAGCTCATGTGTAGCATCAACACTACATA
64 TCGTGTTCAGGT-TAGAGGTGTCTATGAGTTGGACCAAGCTCATGTGTAGCATCAACACTATATA
* *
393419 GGTCTCATATTTTGGCCAAGTTGATTCTTAGACTTTATATTTTTGTTTAAACCTTCCCAAATACC
128 GGTCTCATATTTTGGCCAAGTTCATTCTTAG-CTTAATATTTTTGTTTAAACCTTCCCAAATACC
* *
393484 AGGTGGAGCTTTGCTCATGGGTCTTTGGACAAGTCTAGTACAAGTATGTGTCAGACACGA-TAC-
192 AGGTGG-GCTTTGCTCATGGGTCCTTGGACAAGTCTAGTTCAAGTATGTGTCAGACACGATTACT
* * * * * * *
393547 TGAAGAAAAG-AGGGGAAGTGTTAACTTTTTGGCTTCAGGAGATATGGTTCTTGGGTTTGGGTGT
256 TCAAGAAAAGCAAGGGAAGTGTTAGCTTTTTGGCTTC-GGTGCTATGGTACTTGGATTTGGGTGT
*
393611 GAGTGTGTACACAA
320 GAGTGTGCACACAA
* * * *
393625 GTGAGGTCAAAAAGGGTATTTTCTATGTATTAAAAAGATCTTTGGAAGATCATATTCCTATACTT
1 GTGAGTTCAAAAAGGGTATTTTCTATGTATTAAAAGGATCTCTGGAAGATCATATTCCTATACTC
** ** **
393690 GTGTTTGGGTTAGAGGTGTCTATGAGTTGGACCTGGCTCATGTGTAGCATCAACGTTATATAGGT
66 GTGTTCAGGTTAGAGGTGTCTATGAGTTGGACCAAGCTCATGTGTAGCATCAACACTATATAGGT
* *** * * * * *
393755 CTCATGTTTCCACCAAGTTCATTCTCAAGCTTGATATTTTTGTTTAAACCTTCTCGAATACTAGG
131 CTCATATTTTGGCCAAGTTCATTCT-TAGCTTAATATTTTTGTTTAAACCTTCCCAAATACCAGG
* * * *
393820 TAGGGCTTTGGTCATGGGTCCTTGGA-AAGGTCTAGTTCAAGTAGGTGTCAAACACAATTACTTC
195 T-GGGCTTTGCTCATGGGTCCTTGGACAA-GTCTAGTTCAAGTATGTGTCAGACACGATTACTTC
* ** *
393884 AAGAAAAGCAAAGGGAAGTGTTAGCTTTTTGGCTTCGAGTGCTATGGTGCTTGGATTCAGGTGTC
258 AAGAAAAGC-AAGGGAAGTGTTAGCTTTTTGGCTTCG-GTGCTATGGTACTTGGATTTGGGTGTG
* **
393949 AATGTGCACACGG
321 AGTGTGCACACAA
* ** **
393962 GTGTGTTC-GCAAGGGTATTTTCTATGTATTAAAAGGAT-T-T-TTAGAT-ATATTCCTATACTC
1 GTGAGTTCAAAAAGGGTATTTTCTATGTATTAAAAGGATCTCTGGAAGATCATATTCCTATACTC
* * * * * * * * *
394022 GTGTTCAGATTAAAGGTATTTATAAGTTGGACCAAACTCATATGTAACATCAACAGTATATAGGT
66 GTGTTCAGGTTAGAGGTGTCTATGAGTTGGACCAAGCTCATGTGTAGCATCAACACTATATAGGT
* * * * *
394087 CTCATATTTTGGCCAAGTTCATTATTGGGTCTAATATTTTTGTCTAAACCTTCCCAAATATCA-G
131 CTCATATTTTGGCCAAGTTCATTCTTAGCT-TAATATTTTTGTTTAAACCTTCCCAAATACCAGG
* * ** *
394151 TGGGGCTTTGCACATAGGTCCTTGGACAAGTCTAGTTCAAGTATGTGTTGGGCACGATTACTTCA
195 T-GGGCTTTGCTCATGGGTCCTTGGACAAGTCTAGTTCAAGTATGTGTCAGACACGATTACTTCA
* * **
394216 AGAAAAGCAAGGGAAGTGTTAGCTTTTTGGCTTTGGGTGCTATGGTGCTTGGATTCAGGTGTGAG
259 AGAAAAGCAAGGGAAGTGTTAGCTTTTTGGC-TTCGGTGCTATGGTACTTGGATTTGGGTGTGAG
394281 TGT
323 TGT
394284 TCAAAAAGGG
Statistics
Matches: 827, Mismatches: 145, Indels: 46
0.81 0.14 0.05
Matches are distributed among these distances:
330 53 0.06
331 66 0.08
332 126 0.15
333 197 0.24
334 16 0.02
335 77 0.09
336 53 0.06
337 91 0.11
338 6 0.01
339 139 0.17
340 3 0.00
ACGTcount: A:0.26, C:0.15, G:0.24, T:0.34
Consensus pattern (333 bp):
GTGAGTTCAAAAAGGGTATTTTCTATGTATTAAAAGGATCTCTGGAAGATCATATTCCTATACTC
GTGTTCAGGTTAGAGGTGTCTATGAGTTGGACCAAGCTCATGTGTAGCATCAACACTATATAGGT
CTCATATTTTGGCCAAGTTCATTCTTAGCTTAATATTTTTGTTTAAACCTTCCCAAATACCAGGT
GGGCTTTGCTCATGGGTCCTTGGACAAGTCTAGTTCAAGTATGTGTCAGACACGATTACTTCAAG
AAAAGCAAGGGAAGTGTTAGCTTTTTGGCTTCGGTGCTATGGTACTTGGATTTGGGTGTGAGTGT
GCACACAA
Found at i:401893 original size:5 final size:5
Alignment explanation
Indices: 401885--401910 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
401875 AAAATAAAAA
401885 TATAT TATAT TATAT TATAT TATAT T
1 TATAT TATAT TATAT TATAT TATAT T
401911 TAAAAAATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (5 bp):
TATAT
Found at i:402610 original size:27 final size:27
Alignment explanation
Indices: 402572--402627 Score: 103
Period size: 27 Copynumber: 2.1 Consensus size: 27
402562 TGAAAGTAAC
*
402572 ATTACTGATGAAGGTAATAGAGTGTAT
1 ATTACTAATGAAGGTAATAGAGTGTAT
402599 ATTACTAATGAAGGTAATAGAGTGTAT
1 ATTACTAATGAAGGTAATAGAGTGTAT
402626 AT
1 AT
402628 AATAAAATTA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.39, C:0.04, G:0.23, T:0.34
Consensus pattern (27 bp):
ATTACTAATGAAGGTAATAGAGTGTAT
Found at i:405884 original size:30 final size:30
Alignment explanation
Indices: 405848--405906 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 30
405838 ACCGAACATC
405848 GAAAACATTATATGAGATACCAGAAGCATT
1 GAAAACATTATATGAGATACCAGAAGCATT
* *
405878 GAAAACATTATATGAGGTATCAGAAGCAT
1 GAAAACATTATATGAGATACCAGAAGCAT
405907 GGACTACAAC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.46, C:0.12, G:0.19, T:0.24
Consensus pattern (30 bp):
GAAAACATTATATGAGATACCAGAAGCATT
Found at i:405949 original size:47 final size:47
Alignment explanation
Indices: 405879--406034 Score: 224
Period size: 47 Copynumber: 3.3 Consensus size: 47
405869 AGAAGCATTG
*
405879 AAAACATTATATGAGGTATCAGAAGCATGGACTACAACCGAACATCA
1 AAAACATTATATGAGGTACCAGAAGCATGGACTACAACCGAACATCA
* * *
405926 AAAACATTGTATAAGGTACCAGAAGCATGGACTACAACCGAACATCG
1 AAAACATTATATGAGGTACCAGAAGCATGGACTACAACCGAACATCA
* * *
405973 AAAACATTATATGAGGTACTAGAAGCATGGACTACAACCAAACA-CTG
1 AAAACATTATATGAGGTACCAGAAGCATGGACTACAACCGAACATC-A
*
406020 AAAACATTTTATGAG
1 AAAACATTATATGAG
406035 ATCAACAGAA
Statistics
Matches: 99, Mismatches: 9, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
46 1 0.01
47 98 0.99
ACGTcount: A:0.44, C:0.19, G:0.17, T:0.20
Consensus pattern (47 bp):
AAAACATTATATGAGGTACCAGAAGCATGGACTACAACCGAACATCA
Found at i:409368 original size:30 final size:29
Alignment explanation
Indices: 409303--409373 Score: 81
Period size: 29 Copynumber: 2.4 Consensus size: 29
409293 TTAACCCTCC
*
409303 AAAAATGGATAATTATATTTTTGTCCCTT
1 AAAAATGGAAAATTATATTTTTGTCCCTT
* *
409332 ATAAATGGTAAAATTATA-TTTTGTCTTCTT
1 AAAAATGG-AAAATTATATTTTTGTC-CCTT
*
409362 AAAAATGAAAAA
1 AAAAATGGAAAA
409374 AAAAATTTAA
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
29 18 0.51
30 17 0.49
ACGTcount: A:0.42, C:0.07, G:0.10, T:0.41
Consensus pattern (29 bp):
AAAAATGGAAAATTATATTTTTGTCCCTT
Found at i:414978 original size:307 final size:307
Alignment explanation
Indices: 414398--414993 Score: 788
Period size: 307 Copynumber: 1.9 Consensus size: 307
414388 GAATTGGCAA
* *
414398 AGATTAGATTATCAAGCAACATCAGCAAATACTTCTACTCTCTTATTACCAGAAAGCTAATAGCC
1 AGATTAGATTATCAAGCAACATCAGCAAATACTTCTACTCCCTTACTACCAGAAAGCTAATAGCC
*** *
414463 ATAACACAAATCAAATCAATCCATTCACTGATTAAAATTCAATTTCTCTCATTTATCATCGCAAA
66 ATAACACAAATCAAATCAATCCATTCACTGATTAAAATTCAAGACCTCTCATTTATCATCACAAA
* * * *
414528 CTCATGCGTGAGTATCGAATACATGTATGTGACCAACACGAGTATGTTCAATTTTTCCAAGATTT
131 CTCAAGCATGAGTATCGAATACAAGTATGTGACCAACACGAGTATGTTCAATTTTTCCAAGATTC
** * *
414593 TTGTGTATTTCCTGAGATGTATAGCACACAGATACTTCAAGAAAAATGAATAAATATGAAAAAAG
196 TTGCATATTTACTGAGATGAATAGCACACAGATACTTCAAGAAAAATGAATAAATATGAAAAAAG
414658 AAAAAACAGCAGCATTTACTAAAAATAACCATCCATTACACTAGGAT
261 AAAAAACAGCAGCATTTACTAAAAATAACCATCCATTACACTAGGAT
* * * * *
414705 AGATTAGATTATCAAGCAATATCAGTAAATATTTCTATTCCCTTACTACCAGAAAGCTAATTGCC
1 AGATTAGATTATCAAGCAACATCAGCAAATACTTCTACTCCCTTACTACCAGAAAGCTAATAGCC
* *
414770 ATAACATAAATCAAATCAACTATCCATCCACTCACTGATTAAATTTCAAGACCTCTCATTTATCA
66 ATAACACAAATCAAATC-A--ATCCAT----TCACTGATTAAAATTCAAGACCTCTCATTTATCA
* * *
414835 TCACAAACTCAAGCATGA-TCATGGAATACAAGTAT-TTACCGACACGA-TATGTTC-ATTTTTC
124 TCACAAACTCAAGCATGAGT-ATCGAATACAAGTATGTGACCAACACGAGTATGTTCAATTTTTC
* ** * *
414896 CAAGATTCTTGCATATTTACTGAGATGAATTGCACACAGATACTTCAAGAAAGCT-ATTATATAT
188 CAAGATTCTTGCATATTTACTGAGATGAATAGCACACAGATACTTCAAGAAAAATGAATAAATAT
*
414960 GAAAAAAAAAAAAGCAGCAGCAGCATTTACTAAA
253 GAAAAAAGAAAAA--A-CAGCAGCATTTACTAAA
414994 GCGAGTATGT
Statistics
Matches: 248, Mismatches: 30, Indels: 16
0.84 0.10 0.05
Matches are distributed among these distances:
307 74 0.30
308 1 0.00
310 25 0.10
311 54 0.22
312 8 0.03
313 28 0.11
314 58 0.23
ACGTcount: A:0.40, C:0.20, G:0.11, T:0.29
Consensus pattern (307 bp):
AGATTAGATTATCAAGCAACATCAGCAAATACTTCTACTCCCTTACTACCAGAAAGCTAATAGCC
ATAACACAAATCAAATCAATCCATTCACTGATTAAAATTCAAGACCTCTCATTTATCATCACAAA
CTCAAGCATGAGTATCGAATACAAGTATGTGACCAACACGAGTATGTTCAATTTTTCCAAGATTC
TTGCATATTTACTGAGATGAATAGCACACAGATACTTCAAGAAAAATGAATAAATATGAAAAAAG
AAAAAACAGCAGCATTTACTAAAAATAACCATCCATTACACTAGGAT
Found at i:419291 original size:26 final size:28
Alignment explanation
Indices: 419262--419322 Score: 74
Period size: 26 Copynumber: 2.2 Consensus size: 28
419252 TTAAGATGAC
419262 AATATAAAAAATT-TT-AATAAATAAAA-
1 AATATAAAAAATTATTAAAT-AATAAAAT
* *
419288 AATATATAAAATTATTAAATATTAAAAT
1 AATATAAAAAATTATTAAATAATAAAAT
419316 AATATAA
1 AATATAA
419323 TATAAATATT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
26 12 0.41
27 8 0.28
28 9 0.31
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (28 bp):
AATATAAAAAATTATTAAATAATAAAAT
Found at i:419338 original size:32 final size:29
Alignment explanation
Indices: 419269--419355 Score: 90
Period size: 32 Copynumber: 3.0 Consensus size: 29
419259 GACAATATAA
*
419269 AAAATT-TTAATAAAT-AAAAAAT-ATAT
1 AAAATTATTAAAAAATAAAAAAATAATAT
* *
419295 AAAATTATTAAATATTAAAATAATATAATAT
1 AAAATTATTAAAAAATAAAA-AA-ATAATAT
*
419326 AAATATTTTTAAAAAATAAAAAAATAATAT
1 AAA-ATTATTAAAAAATAAAAAAATAATAT
419356 GAGCAGGCTT
Statistics
Matches: 49, Mismatches: 6, Indels: 8
0.78 0.10 0.13
Matches are distributed among these distances:
26 6 0.12
27 6 0.12
28 3 0.06
29 2 0.04
30 9 0.18
31 9 0.18
32 14 0.29
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (29 bp):
AAAATTATTAAAAAATAAAAAAATAATAT
Found at i:423109 original size:23 final size:22
Alignment explanation
Indices: 423075--423117 Score: 52
Period size: 23 Copynumber: 1.9 Consensus size: 22
423065 TTGTATTAAC
423075 TTACAAAGTTAA-ACTAAAAACG
1 TTACAAAGTTAACA-TAAAAACG
*
423097 TTACTAAATTTAACATAAAAA
1 TTAC-AAAGTTAACATAAAAA
423118 ACTATAAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 4 0.22
23 13 0.72
24 1 0.06
ACGTcount: A:0.56, C:0.12, G:0.05, T:0.28
Consensus pattern (22 bp):
TTACAAAGTTAACATAAAAACG
Found at i:423736 original size:31 final size:29
Alignment explanation
Indices: 423627--423738 Score: 98
Period size: 31 Copynumber: 3.7 Consensus size: 29
423617 ATGATTAAAT
* * *
423627 CAAAATCAAAGTTTCAAGTATACATTTGAA
1 CAAAATCAAAG-TTCATGTATACAATTGCA
* * * *
423657 CCAAAATCAGAGTTCACGTGTATAATTGCA
1 -CAAAATCAAAGTTCATGTATACAATTGCA
* * *
423687 CCAAATTAAATTTCATGTATACAATTGCA
1 CAAAATCAAAGTTCATGTATACAATTGCA
423716 CATTAAATCAAAGTTCATGTATA
1 CA--AAATCAAAGTTCATGTATA
423739 ATTTTGAGAT
Statistics
Matches: 63, Mismatches: 16, Indels: 4
0.76 0.19 0.05
Matches are distributed among these distances:
29 23 0.37
30 13 0.21
31 27 0.43
ACGTcount: A:0.42, C:0.16, G:0.11, T:0.31
Consensus pattern (29 bp):
CAAAATCAAAGTTCATGTATACAATTGCA
Found at i:428046 original size:41 final size:44
Alignment explanation
Indices: 427975--428056 Score: 107
Period size: 42 Copynumber: 1.9 Consensus size: 44
427965 CCATAGTATT
* * *
427975 ATTCATAAATTTAGAATTTAATTTTTATATT-TTTATTTTTAGG
1 ATTCATAAATTTAGAATCTAATTTTAATATTATTAATTTTTAGG
*
428018 ATTCA-AAATTTAG-GTCTAATTTTAATATTATTAATTTTT
1 ATTCATAAATTTAGAATCTAATTTTAATATTATTAATTTTT
428057 TTGTTAAATT
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
41 13 0.38
42 16 0.47
43 5 0.15
ACGTcount: A:0.34, C:0.04, G:0.06, T:0.56
Consensus pattern (44 bp):
ATTCATAAATTTAGAATCTAATTTTAATATTATTAATTTTTAGG
Found at i:430016 original size:20 final size:20
Alignment explanation
Indices: 429980--430018 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
429970 TTGAGGTGAG
429980 TTTTCTTTTTCTTTTAAATGT
1 TTTTCTTTTTC-TTTAAATGT
430001 TTTTCATTTTTC-TTAAAT
1 TTTTC-TTTTTCTTTAAAT
430019 TAAATAATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
20 6 0.35
21 5 0.29
22 6 0.35
ACGTcount: A:0.18, C:0.10, G:0.03, T:0.69
Consensus pattern (20 bp):
TTTTCTTTTTCTTTAAATGT
Found at i:430470 original size:31 final size:29
Alignment explanation
Indices: 430430--430504 Score: 80
Period size: 30 Copynumber: 2.4 Consensus size: 29
430420 AAATTTTAAA
*
430430 TAAATAATGATAAAATTAT-ATTTTGATCTTTT
1 TAAA-AATGATAAAATT-TGA-TTTAAT-TTTT
430462 TAAAAATGATAAAAATTTGATTTAATTTTT
1 TAAAAATGAT-AAAATTTGATTTAATTTTT
*
430492 TAAAAATTATAAA
1 TAAAAATGATAAA
430505 GATACATATT
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
29 3 0.08
30 13 0.33
31 12 0.31
32 11 0.28
ACGTcount: A:0.48, C:0.01, G:0.05, T:0.45
Consensus pattern (29 bp):
TAAAAATGATAAAATTTGATTTAATTTTT
Found at i:437338 original size:24 final size:24
Alignment explanation
Indices: 437277--437339 Score: 90
Period size: 24 Copynumber: 2.6 Consensus size: 24
437267 TAGAGTAATA
* *
437277 AGAGTTTGACTCAAACAAATAAAC
1 AGAGTTTAACTGAAACAAATAAAC
* *
437301 AGAGTTTAATTGAAACAATTAAAC
1 AGAGTTTAACTGAAACAAATAAAC
437325 AGAGTTTAACTGAAA
1 AGAGTTTAACTGAAA
437340 GATTATTTCC
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.49, C:0.11, G:0.14, T:0.25
Consensus pattern (24 bp):
AGAGTTTAACTGAAACAAATAAAC
Found at i:439276 original size:24 final size:24
Alignment explanation
Indices: 439216--439279 Score: 83
Period size: 24 Copynumber: 2.7 Consensus size: 24
439206 CTAGAGTAAT
* * *
439216 AAGAGTTTGACTCAAATAAATAAA
1 AAGAGTTTAACTGAAACAAATAAA
*
439240 CAGAGTTTAACTGAAACAAATAAA
1 AAGAGTTTAACTGAAACAAATAAA
*
439264 AATAGTTTAACTGAAA
1 AAGAGTTTAACTGAAA
439280 GGTTATTTTT
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.53, C:0.09, G:0.12, T:0.25
Consensus pattern (24 bp):
AAGAGTTTAACTGAAACAAATAAA
Found at i:440051 original size:34 final size:35
Alignment explanation
Indices: 440002--440067 Score: 98
Period size: 34 Copynumber: 1.9 Consensus size: 35
439992 GATTTAAAAA
**
440002 TTGTTTTACGGTTTAT-AAAATTAATTTTTCATAT
1 TTGTTTTACAATTTATAAAAATTAATTTTTCATAT
*
440036 TTGTTTTACAATTTATAAAAATTCATTTTTCA
1 TTGTTTTACAATTTATAAAAATTAATTTTTCA
440068 AAACTTATTG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 14 0.50
35 14 0.50
ACGTcount: A:0.32, C:0.08, G:0.06, T:0.55
Consensus pattern (35 bp):
TTGTTTTACAATTTATAAAAATTAATTTTTCATAT
Found at i:441553 original size:118 final size:117
Alignment explanation
Indices: 441391--441626 Score: 275
Period size: 118 Copynumber: 2.0 Consensus size: 117
441381 AGAGATCTAC
* ** *
441391 GGGGTGCAAGTTCATTAAGTTGGGAGTGTCTTGGTTGGTAGAGATACAATC-TTATCTTAATGTT
1 GGGGTGCAAGTTCATAAAGTTGGGAGCATCTTGGTTGGTAGAGATACAA-CAGTATCTTAATGTT
* *
441455 -AGAGTTTTGTCCCTCGAC-TT-CATTGAGAGCTTGAGTAT-CTTAAGAGGCTTGCAA
65 GAG-GTTTTGTCCCCCAACTTTGCA--GAGAGCTTGAGT-TCCTTAAGAGG-TTGCAA
** * * * *
441509 GGGGTGCGGGTTCATAAAGTTGGGAGCATCTTGGTTGGTGGAGATACGACAGTGTCTTATTGTTG
1 GGGGTGCAAGTTCATAAAGTTGGGAGCATCTTGGTTGGTAGAGATACAACAGTATCTTAATGTTG
441574 AGGTTTTGTCCCCCAACTTTGCAGAGAGCTTGAGTTCCTTAAGAGGTTGCAA
66 AGGTTTTGTCCCCCAACTTTGCAGAGAGCTTGAGTTCCTTAAGAGGTTGCAA
441626 G
1 G
441627 TGATACTGAT
Statistics
Matches: 101, Mismatches: 12, Indels: 11
0.81 0.10 0.09
Matches are distributed among these distances:
117 9 0.09
118 86 0.85
119 4 0.04
120 2 0.02
ACGTcount: A:0.22, C:0.14, G:0.30, T:0.33
Consensus pattern (117 bp):
GGGGTGCAAGTTCATAAAGTTGGGAGCATCTTGGTTGGTAGAGATACAACAGTATCTTAATGTTG
AGGTTTTGTCCCCCAACTTTGCAGAGAGCTTGAGTTCCTTAAGAGGTTGCAA
Found at i:443236 original size:21 final size:21
Alignment explanation
Indices: 443212--443274 Score: 54
Period size: 21 Copynumber: 2.9 Consensus size: 21
443202 TCTGACTTTT
* *
443212 AAATTAAAAATTTAAGATTCG
1 AAATTAAAAATTTAAAATTCA
** *
443233 AAATTCGAAATTTAAAATTTA
1 AAATTAAAAATTTAAAATTCA
*
443254 AAATAAAAAATTATTAAAATT
1 AAATTAAAAA-T-TTAAAATT
443275 ATGTACGCGA
Statistics
Matches: 32, Mismatches: 8, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
21 23 0.72
22 1 0.03
23 8 0.25
ACGTcount: A:0.57, C:0.03, G:0.05, T:0.35
Consensus pattern (21 bp):
AAATTAAAAATTTAAAATTCA
Found at i:461165 original size:12 final size:11
Alignment explanation
Indices: 461138--461164 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
461128 TGGCCTTCCC
461138 TTTTTCTTTTT
1 TTTTTCTTTTT
461149 TTTTTCTTTTT
1 TTTTTCTTTTT
461160 TTTTT
1 TTTTT
461165 TACGTAATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.00, C:0.07, G:0.00, T:0.93
Consensus pattern (11 bp):
TTTTTCTTTTT
Found at i:466851 original size:20 final size:19
Alignment explanation
Indices: 466805--466852 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 19
466795 AAAAAAAAAA
466805 ATTATATTAATATTTTTTTT
1 ATTAT-TTAATATTTTTTTT
*
466825 ATATATTTATTATTTATTTTT
1 AT-TATTTAATATTT-TTTTT
466846 ATTATTT
1 ATTATTT
466853 TTAAATAGTA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
20 15 0.60
21 10 0.40
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (19 bp):
ATTATTTAATATTTTTTTT
Found at i:467837 original size:20 final size:20
Alignment explanation
Indices: 467812--467850 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
467802 TTTCATGCTT
467812 TTTTTTTTGAAT-TTTTATAC
1 TTTTTTTT-AATATTTTATAC
467832 TTTTTTTTAATATTTTATA
1 TTTTTTTTAATATTTTATA
467851 AAACTTAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 3 0.17
20 15 0.83
ACGTcount: A:0.23, C:0.03, G:0.03, T:0.72
Consensus pattern (20 bp):
TTTTTTTTAATATTTTATAC
Found at i:469891 original size:11 final size:11
Alignment explanation
Indices: 469875--469900 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
469865 CCATCTCTTT
469875 TTTTTTTTTTG
1 TTTTTTTTTTG
469886 TTTTTTTTTTG
1 TTTTTTTTTTG
469897 TTTT
1 TTTT
469901 GGTCATAAGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.00, C:0.00, G:0.08, T:0.92
Consensus pattern (11 bp):
TTTTTTTTTTG
Found at i:471241 original size:2 final size:2
Alignment explanation
Indices: 471234--471265 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
471224 TTATTATTTC
471234 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
471266 TTACGTAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:473377 original size:22 final size:21
Alignment explanation
Indices: 473327--473393 Score: 57
Period size: 22 Copynumber: 3.0 Consensus size: 21
473317 TGAAAACATA
473327 ATTTTTATTATTTATTA-A-ATT
1 ATTTTTA-TATTT-TTAGAGATT
473348 ATAATTTTATATTTTTGAGAGATT
1 AT--TTTTATATTTTT-AGAGATT
* *
473372 ATTTTTTTATTTTTAGGGATT
1 ATTTTTATATTTTTAGAGATT
473393 A
1 A
473394 ACGTATAATT
Statistics
Matches: 39, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
21 11 0.28
22 17 0.44
23 6 0.15
24 5 0.13
ACGTcount: A:0.30, C:0.00, G:0.09, T:0.61
Consensus pattern (21 bp):
ATTTTTATATTTTTAGAGATT
Found at i:485418 original size:13 final size:13
Alignment explanation
Indices: 485400--485424 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
485390 CACGATGTGT
485400 TTGATTTATTGCC
1 TTGATTTATTGCC
485413 TTGATTTATTGC
1 TTGATTTATTGC
485425 GTTCTTCACT
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:0.16, C:0.12, G:0.16, T:0.56
Consensus pattern (13 bp):
TTGATTTATTGCC
Found at i:489312 original size:25 final size:25
Alignment explanation
Indices: 489257--489332 Score: 84
Period size: 25 Copynumber: 3.0 Consensus size: 25
489247 AAAGATAATA
* *
489257 ATAAATTTAAATAATAAAAGATAAATT
1 ATAAATTT-AATTATAAAA-ATATATT
*
489284 -TAAATTTAATTATAAGAATATATT
1 ATAAATTTAATTATAAAAATATATT
489308 ATAAATATTAA-TATAAAAATATATT
1 ATAAAT-TTAATTATAAAAATATATT
489333 TTGAACAAAG
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
24 6 0.14
25 26 0.60
26 11 0.26
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (25 bp):
ATAAATTTAATTATAAAAATATATT
Found at i:490754 original size:16 final size:16
Alignment explanation
Indices: 490733--490767 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
490723 GCCGTTTGAG
490733 TCGGGTATTACTAAGC
1 TCGGGTATTACTAAGC
490749 TCGGGTATTACTAAGC
1 TCGGGTATTACTAAGC
490765 TCG
1 TCG
490768 AATTTAGCTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.23, C:0.20, G:0.26, T:0.31
Consensus pattern (16 bp):
TCGGGTATTACTAAGC
Done.