Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011306.1 Kokia drynarioides strain JFW-HI SEQ_126286, 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: 547520
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 344 characters in sequence are not A, C, G, or T
File 2 of 2
Found at i:327376 original size:17 final size:17
Alignment explanation
Indices: 327354--327388 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
327344 TTTTGAGAGC
327354 ATAAAATA-AAAGATAAA
1 ATAAAATAGAAA-ATAAA
327371 ATAAAATAGAAAATAAA
1 ATAAAATAGAAAATAAA
327388 A
1 A
327389 ACAAAAGTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 14 0.82
18 3 0.18
ACGTcount: A:0.77, C:0.00, G:0.06, T:0.17
Consensus pattern (17 bp):
ATAAAATAGAAAATAAA
Found at i:328609 original size:39 final size:39
Alignment explanation
Indices: 328555--328636 Score: 155
Period size: 39 Copynumber: 2.1 Consensus size: 39
328545 CCTAATCTTT
328555 ATGTATGCACGGATCTAAGGAAAGGAAAGAAAGTTAAAA
1 ATGTATGCACGGATCTAAGGAAAGGAAAGAAAGTTAAAA
*
328594 ATGTATGCTCGGATCTAAGGAAAGGAAAGAAAGTTAAAA
1 ATGTATGCACGGATCTAAGGAAAGGAAAGAAAGTTAAAA
328633 ATGT
1 ATGT
328637 CAGTTAGATG
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 42 1.00
ACGTcount: A:0.46, C:0.07, G:0.26, T:0.21
Consensus pattern (39 bp):
ATGTATGCACGGATCTAAGGAAAGGAAAGAAAGTTAAAA
Found at i:329454 original size:27 final size:26
Alignment explanation
Indices: 329417--329580 Score: 154
Period size: 27 Copynumber: 6.2 Consensus size: 26
329407 CATTACCATA
* *
329417 AATGTGGAAGTTCGCAAGGACTATAT
1 AATGTGGAAGTACGCAAGGACTATCT
*
329443 AATGTGGAAAGT-CTGTC-AGAACTATCT
1 AATGTGG-AAGTAC-G-CAAGGACTATCT
*
329470 AATGTGGAAGTACACAAGGACTATCT
1 AATGTGGAAGTACGCAAGGACTATCT
* * *
329496 AATGTAAGAGGTCCGTCAA-GACTATCT
1 AATGT-GGAAGTACG-CAAGGACTATCT
* *
329523 AATGTGGAAGTACACAATGACTATCT
1 AATGTGGAAGTACGCAAGGACTATCT
* *
329549 AATGTGAGAAGTCCGCCAGGACTATCT
1 AATGTG-GAAGTACGCAAGGACTATCT
329576 AATGT
1 AATGT
329581 AGAGAGTCTA
Statistics
Matches: 113, Mismatches: 16, Indels: 17
0.77 0.11 0.12
Matches are distributed among these distances:
25 4 0.04
26 45 0.40
27 60 0.53
28 4 0.04
ACGTcount: A:0.35, C:0.16, G:0.23, T:0.26
Consensus pattern (26 bp):
AATGTGGAAGTACGCAAGGACTATCT
Found at i:329499 original size:53 final size:52
Alignment explanation
Indices: 329417--329580 Score: 206
Period size: 53 Copynumber: 3.1 Consensus size: 52
329407 CATTACCATA
* * * *
329417 AATGTGGAAGTTCGCAAGGACTATATAATGTGGAAAGTCTGTCAGAACTATCT
1 AATGTGGAAGTACACAAGGACTATCTAATGT-GAAAGTCCGTCAGAACTATCT
329470 AATGTGGAAGTACACAAGGACTATCTAATGT-AAGAGGTCCGTCA-AGACTATCT
1 AATGTGGAAGTACACAAGGACTATCTAATGTGAA-A-GTCCGTCAGA-ACTATCT
* * *
329523 AATGTGGAAGTACACAATGACTATCTAATGTGAGAAGTCCGCCAGGACTATCT
1 AATGTGGAAGTACACAAGGACTATCTAATGTGA-AAGTCCGTCAGAACTATCT
329576 AATGT
1 AATGT
329581 AGAGAGTCTA
Statistics
Matches: 98, Mismatches: 7, Indels: 12
0.84 0.06 0.10
Matches are distributed among these distances:
51 2 0.02
52 2 0.02
53 91 0.93
54 2 0.02
55 1 0.01
ACGTcount: A:0.35, C:0.16, G:0.23, T:0.26
Consensus pattern (52 bp):
AATGTGGAAGTACACAAGGACTATCTAATGTGAAAGTCCGTCAGAACTATCT
Found at i:329598 original size:27 final size:26
Alignment explanation
Indices: 329435--329602 Score: 107
Period size: 27 Copynumber: 6.3 Consensus size: 26
329425 AGTTCGCAAG
* * *
329435 GACTATATAATGTGGAAAGTCTGTC-A
1 GACTATCTAATGTGGAGAGTC-ATCAA
329461 GAACTATCTAATGTGGA-AGTACA-CAA
1 G-ACTATCTAATGTGGAGAGT-CATCAA
* *
329487 GGACTATCTAATGT-AAGAGGTCCGTCAA
1 -GACTATCTAATGTGGAGA-GT-CATCAA
329515 GACTATCTAATGTGGA-AGTACA-CAA
1 GACTATCTAATGTGGAGAGT-CATCAA
** *
329540 TGACTATCTAATGT-GAGAAGTCCGCCAG
1 -GACTATCTAATGTGGAG-AGT-CATCAA
*
329568 GACTATCTAATGTAGAGAGTCTATCAA
1 GACTATCTAATGTGGAGAGTC-ATCAA
329595 GACTATCT
1 GACTATCT
329603 GTTGGGTGAA
Statistics
Matches: 114, Mismatches: 14, Indels: 27
0.74 0.09 0.17
Matches are distributed among these distances:
25 7 0.06
26 35 0.31
27 63 0.55
28 9 0.08
ACGTcount: A:0.35, C:0.17, G:0.21, T:0.27
Consensus pattern (26 bp):
GACTATCTAATGTGGAGAGTCATCAA
Found at i:331210 original size:306 final size:306
Alignment explanation
Indices: 330652--331247 Score: 1084
Period size: 306 Copynumber: 1.9 Consensus size: 306
330642 CTATATAAAT
* * *
330652 AACCTATCTTTGTCGTCGAAATAGGGTTACAGAGCATTATGTTACATATCGATACAATTAAAATC
1 AACCCATCTTTGTCGTCGAAATAAGGTTACAGAGCATTATGTTACATATCAATACAATTAAAATC
* *
330717 ATTAAACCATTCATTTAGTATTAGTTTTTTTAAACAGATTGGTTAATAAAACATATTCATTGATT
66 ATTAAACCATTCATTTAGTATTAGTTTTTTTAAACAAATTGGTTAATAAAACAAATTCATTGATT
330782 ACATTAATATACTTTGTATAATTGTCCTCATATGGTTTTTACACGTAAAGCAAAATGAAAGCAAA
131 ACATTAATATACTTTGTATAATTGTCCTCATATGGTTTTTACACGTAAAGCAAAATGAAAGCAAA
330847 TTTTGCTAATTGGTTGTCTAATATTTAAATTAATCCTAAGTGGTATCACGTGGTCGGATCATAAT
196 TTTTGCTAATTGGTTGTCTAATATTTAAATTAATCCTAAGTGGTATCACGTGGTCGGATCATAAT
*
330912 ACGGAAAGACAATTTATATTAGTATACGAAGTCATGTAACACCCCG
261 ACGGAAAGACAAGTTATATTAGTATACGAAGTCATGTAACACCCCG
* * * *
330958 AACCCATCTTTGTTGTCGGAATAAGGTTACAGAGTATTTTGTTACATATCAATACAATTAAAATC
1 AACCCATCTTTGTCGTCGAAATAAGGTTACAGAGCATTATGTTACATATCAATACAATTAAAATC
* *
331023 ATTAAACCATTCATTTAGTATTAGTTTTTTTGAACAAATTGGTTAATAAAATAAATTCATTGATT
66 ATTAAACCATTCATTTAGTATTAGTTTTTTTAAACAAATTGGTTAATAAAACAAATTCATTGATT
331088 ACATTAATATACTTTGTATAATTGTCCTCATATGGTTTTTACACGTAAAGCAAAATGAAAGCAAA
131 ACATTAATATACTTTGTATAATTGTCCTCATATGGTTTTTACACGTAAAGCAAAATGAAAGCAAA
331153 TTTTGCTAATTGGTTGTCTAATATTTAAATTAATCCTAAGTGGTATCACGTGGTCGGATCATAAT
196 TTTTGCTAATTGGTTGTCTAATATTTAAATTAATCCTAAGTGGTATCACGTGGTCGGATCATAAT
331218 ACGGAAAGACAAGTTATATTAGTATACGAA
261 ACGGAAAGACAAGTTATATTAGTATACGAA
331248 CCTAAACATG
Statistics
Matches: 278, Mismatches: 12, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
306 278 1.00
ACGTcount: A:0.36, C:0.13, G:0.14, T:0.37
Consensus pattern (306 bp):
AACCCATCTTTGTCGTCGAAATAAGGTTACAGAGCATTATGTTACATATCAATACAATTAAAATC
ATTAAACCATTCATTTAGTATTAGTTTTTTTAAACAAATTGGTTAATAAAACAAATTCATTGATT
ACATTAATATACTTTGTATAATTGTCCTCATATGGTTTTTACACGTAAAGCAAAATGAAAGCAAA
TTTTGCTAATTGGTTGTCTAATATTTAAATTAATCCTAAGTGGTATCACGTGGTCGGATCATAAT
ACGGAAAGACAAGTTATATTAGTATACGAAGTCATGTAACACCCCG
Found at i:333126 original size:5 final size:5
Alignment explanation
Indices: 333116--333154 Score: 51
Period size: 5 Copynumber: 7.8 Consensus size: 5
333106 ATTACCGCGA
* * *
333116 GGATT GGATT GCATT GCATT GCATT GGATT GGATT GGAT
1 GGATT GGATT GGATT GGATT GGATT GGATT GGATT GGAT
333155 GGGTATGAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
5 32 1.00
ACGTcount: A:0.21, C:0.08, G:0.33, T:0.38
Consensus pattern (5 bp):
GGATT
Found at i:338732 original size:2 final size:2
Alignment explanation
Indices: 338725--338753 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
338715 TTGTTTTGAA
338725 TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
338754 TTACTATGAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:346455 original size:24 final size:24
Alignment explanation
Indices: 346396--346456 Score: 77
Period size: 24 Copynumber: 2.5 Consensus size: 24
346386 GACTAATAAT
* *
346396 AGTTTAACTCAAACAACTAAACAA
1 AGTTTAACTGAAACAAATAAACAA
* *
346420 AGTTTAATTGAAACAAATAAACAG
1 AGTTTAACTGAAACAAATAAACAA
*
346444 AGTTTAGCTGAAA
1 AGTTTAACTGAAA
346457 GATTATTTCT
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.51, C:0.13, G:0.11, T:0.25
Consensus pattern (24 bp):
AGTTTAACTGAAACAAATAAACAA
Found at i:358635 original size:20 final size:20
Alignment explanation
Indices: 358593--358635 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
358583 GCTTTCACAA
* *
358593 TTAAGCTTAATTAACCTCTT
1 TTAACCTTAATTAACCTCAT
358613 TTAACCTTAATTAATCCT-AT
1 TTAACCTTAATTAA-CCTCAT
358633 TTA
1 TTA
358636 TATTCAATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 17 0.85
21 3 0.15
ACGTcount: A:0.33, C:0.19, G:0.02, T:0.47
Consensus pattern (20 bp):
TTAACCTTAATTAACCTCAT
Found at i:366762 original size:45 final size:44
Alignment explanation
Indices: 366687--366804 Score: 133
Period size: 44 Copynumber: 2.8 Consensus size: 44
366677 ACAAACCAAT
*
366687 AAAACTTTTTATTTTCTACCAAAATTTTACT-TTCAAAAACCCTC
1 AAAACTTTTTATTTTCTACCAAAATTTTACTACT-AAAAACCCTC
*
366731 AAAACTTTTTATTTT-TCCCCAAAATTTTTACTACTAAAAACCCTC
1 AAAACTTTTTATTTTCT-ACCAAAA-TTTTACTACTAAAAACCCTC
366776 AAAA---TTT-TTTTCT-CCAAAACTTTTACTAC
1 AAAACTTTTTATTTTCTACCAAAA-TTTTACTAC
366805 CTCCCACTTT
Statistics
Matches: 67, Mismatches: 3, Indels: 12
0.82 0.04 0.15
Matches are distributed among these distances:
40 15 0.22
41 4 0.06
42 4 0.06
43 1 0.01
44 21 0.31
45 21 0.31
46 1 0.01
ACGTcount: A:0.36, C:0.23, G:0.00, T:0.42
Consensus pattern (44 bp):
AAAACTTTTTATTTTCTACCAAAATTTTACTACTAAAAACCCTC
Found at i:366784 original size:44 final size:42
Alignment explanation
Indices: 366650--366785 Score: 139
Period size: 44 Copynumber: 3.1 Consensus size: 42
366640 TGCTCTCTCG
* * *
366650 TTTACTTTCCCCAAAAATTTTACTCGTACAAACCAAT-AAAACTT
1 TTTATTTTCCCC-AAAATTTTACTC-TAAAAACC-CTCAAAACTT
* *
366694 TTTATTTTCTACCAAAATTTTACTTTCAAAAACCCTCAAAACTT
1 TTTATTTTC-CCCAAAATTTTACTCT-AAAAACCCTCAAAACTT
*
366738 TTTATTTTTCCCCAAAATTTTTACTACTAAAAACCCTCAAAATTT
1 TTTA-TTTTCCCCAAAA-TTTTACT-CTAAAAACCCTCAAAACTT
366783 TTT
1 TTT
366786 TCTCCAAAAC
Statistics
Matches: 78, Mismatches: 8, Indels: 11
0.80 0.08 0.11
Matches are distributed among these distances:
43 2 0.03
44 42 0.54
45 33 0.42
46 1 0.01
ACGTcount: A:0.36, C:0.23, G:0.01, T:0.40
Consensus pattern (42 bp):
TTTATTTTCCCCAAAATTTTACTCTAAAAACCCTCAAAACTT
Found at i:368428 original size:93 final size:95
Alignment explanation
Indices: 368301--368473 Score: 221
Period size: 96 Copynumber: 1.8 Consensus size: 95
368291 CAATAAAATG
* * *
368301 ACATAAAAATAAATAACAACAAGATAAATAAATAA-AA-AAATTAAGTG-CTAAAAGAAACAAAC
1 ACATAAAAATAAATAACAACAAAATAAATAAATAACAATAAATTAAATGTC-AAAAAAAAC-AAC
368363 -AAATATAAATAATAAAAATAATTGGGATTAA
64 TAAATATAAATAATAAAAATAATTGGGATTAA
* * *
368394 ACATGAAAATAAATGACAA-ATAAATTAATAAATAATCAATAAATTAAATGTCAAAAAAAACAAC
1 ACATAAAAATAAATAACAACA-AAATAAATAAATAA-CAATAAATTAAATGTCAAAAAAAACAAC
368458 TAAATATAAATAATAA
64 TAAATATAAATAATAA
368474 TAAAAAAGAA
Statistics
Matches: 68, Mismatches: 6, Indels: 9
0.82 0.07 0.11
Matches are distributed among these distances:
92 1 0.01
93 29 0.43
95 5 0.07
96 32 0.47
97 1 0.01
ACGTcount: A:0.65, C:0.07, G:0.06, T:0.22
Consensus pattern (95 bp):
ACATAAAAATAAATAACAACAAAATAAATAAATAACAATAAATTAAATGTCAAAAAAAACAACTA
AATATAAATAATAAAAATAATTGGGATTAA
Found at i:371961 original size:33 final size:33
Alignment explanation
Indices: 371895--371966 Score: 92
Period size: 33 Copynumber: 2.2 Consensus size: 33
371885 TGAACAGTGA
* *
371895 TCACATTTGGCGAGCTCACAATAAATGACGAGC
1 TCACATTTGGCGAGCTCACAAGAAAGGACGAGC
* *
371928 TCACATTTGGCGAGTTCATAAGAAGAGGA-GAGC
1 TCACATTTGGCGAGCTCACAAGAA-AGGACGAGC
371961 TCACAT
1 TCACAT
371967 AAAGTGGCAA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
33 31 0.91
34 3 0.09
ACGTcount: A:0.33, C:0.21, G:0.24, T:0.22
Consensus pattern (33 bp):
TCACATTTGGCGAGCTCACAAGAAAGGACGAGC
Found at i:372072 original size:28 final size:28
Alignment explanation
Indices: 372041--372113 Score: 101
Period size: 28 Copynumber: 2.6 Consensus size: 28
372031 GAACTTGTAT
*
372041 AGTGAAACTGCGAAGTGCGAGCTGTCAC
1 AGTGAAACTGCGAAGTGCGAGCTGGCAC
* *
372069 AGTGAATCTACGAAGTGCGAGCTGGCAC
1 AGTGAAACTGCGAAGTGCGAGCTGGCAC
* *
372097 AATAAAACTGCGAAGTG
1 AGTGAAACTGCGAAGTG
372114 TGAACTCTTA
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
28 38 1.00
ACGTcount: A:0.33, C:0.19, G:0.30, T:0.18
Consensus pattern (28 bp):
AGTGAAACTGCGAAGTGCGAGCTGGCAC
Found at i:373752 original size:30 final size:30
Alignment explanation
Indices: 373690--373752 Score: 99
Period size: 30 Copynumber: 2.1 Consensus size: 30
373680 TCTTATTTTA
* *
373690 TTGTTAATTTTGTTATTATTTTAGAAGTAT
1 TTGTTAATTTTGTTACTATTTTAGAAGCAT
*
373720 TTGTTAATTTTGTTACTATTTTAGAGGCAT
1 TTGTTAATTTTGTTACTATTTTAGAAGCAT
373750 TTG
1 TTG
373753 CTTGTTAAGT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.24, C:0.03, G:0.16, T:0.57
Consensus pattern (30 bp):
TTGTTAATTTTGTTACTATTTTAGAAGCAT
Found at i:375964 original size:18 final size:17
Alignment explanation
Indices: 375941--375976 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
375931 AGAGCTCATA
375941 GGTGAGCTCCCAGTCTTT
1 GGTGAGCTCCCAGT-TTT
*
375959 GGTGAGCTCGCAGTTTT
1 GGTGAGCTCCCAGTTTT
375976 G
1 G
375977 CAATCACAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 4 0.24
18 13 0.76
ACGTcount: A:0.11, C:0.22, G:0.33, T:0.33
Consensus pattern (17 bp):
GGTGAGCTCCCAGTTTT
Found at i:380075 original size:29 final size:30
Alignment explanation
Indices: 380032--380092 Score: 72
Period size: 29 Copynumber: 2.0 Consensus size: 30
380022 TGAATGACAC
*
380032 AATAAAATAAAATAACATGATCAT-GATAATA
1 AATAAAAT-AAATAACATAATCATAG-TAATA
*
380063 AATAAAAT-AATAATATAATCATAGTAATA
1 AATAAAATAAATAACATAATCATAGTAATA
380092 A
1 A
380093 TGATAACAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
29 18 0.67
30 1 0.04
31 8 0.30
ACGTcount: A:0.62, C:0.05, G:0.05, T:0.28
Consensus pattern (30 bp):
AATAAAATAAATAACATAATCATAGTAATA
Found at i:380517 original size:4 final size:4
Alignment explanation
Indices: 380508--380556 Score: 64
Period size: 4 Copynumber: 12.0 Consensus size: 4
380498 TTAGGCATAA
*
380508 AAAT AAAT AAAT -AAT AAAT AAAT AAAT AAATT AAAT CAAT AAATT AAAT
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA-T AAAT AAAT AAA-T AAAT
380557 GCCAAAATAA
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
3 3 0.08
4 29 0.73
5 8 0.20
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (4 bp):
AAAT
Found at i:380564 original size:13 final size:13
Alignment explanation
Indices: 380509--380556 Score: 66
Period size: 13 Copynumber: 3.9 Consensus size: 13
380499 TAGGCATAAA
380509 AATAAA-TAAAT-
1 AATAAATTAAATC
*
380520 AATAAA-TAAATA
1 AATAAATTAAATC
380532 AATAAATTAAATC
1 AATAAATTAAATC
380545 AATAAATTAAAT
1 AATAAATTAAAT
380557 GCCAAAATAA
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
11 11 0.32
12 6 0.18
13 17 0.50
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (13 bp):
AATAAATTAAATC
Found at i:380838 original size:24 final size:24
Alignment explanation
Indices: 380786--380838 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
380776 TGTTTTGAAT
380786 TTTCTTTGAATATATCTAAAAAAA
1 TTTCTTTGAATATATCTAAAAAAA
* * *
380810 ATTCTTTGAATGT-TGTATAAAAAA
1 TTTCTTTGAATATATCTA-AAAAAA
380834 TTTCT
1 TTTCT
380839 GAATCTTATT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
23 3 0.12
24 21 0.88
ACGTcount: A:0.40, C:0.08, G:0.08, T:0.45
Consensus pattern (24 bp):
TTTCTTTGAATATATCTAAAAAAA
Found at i:381505 original size:50 final size:50
Alignment explanation
Indices: 381429--381612 Score: 160
Period size: 50 Copynumber: 3.7 Consensus size: 50
381419 CTACAACTTC
* * *
381429 AGGGGTATAAGATTCA-CCTTCACGGCTTTAGT-TTGCCTCTCTATAGCTTT
1 AGGGGTATAAGATTCATCGTT-GCGGCTTTAATCTTGCC-CTCTATAGCTTT
* * * *
381479 AGGGGTATAAGATTTATCGTTGCGGCTTTAATCTTTCCCTCTTTAGTTTT
1 AGGGGTATAAGATTCATCGTTGCGGCTTTAATCTTGCCCTCTATAGCTTT
* * * * * *
381529 AGGGGTGTAAGATTCATCGTAGCAGCTTTAAT-TTATCCCTCT-TCGATTTT
1 AGGGGTATAAGATTCATCGTTGCGGCTTTAATCTT-GCCCTCTATAG-CTTT
* * *
381579 AGGGGTGTAAGATTCACCGTTACGGCTTTAATCT
1 AGGGGTATAAGATTCATCGTTGCGGCTTTAATCT
381613 ATCTCTCTTC
Statistics
Matches: 113, Mismatches: 16, Indels: 9
0.82 0.12 0.07
Matches are distributed among these distances:
49 4 0.04
50 101 0.89
51 8 0.07
ACGTcount: A:0.21, C:0.18, G:0.21, T:0.40
Consensus pattern (50 bp):
AGGGGTATAAGATTCATCGTTGCGGCTTTAATCTTGCCCTCTATAGCTTT
Found at i:382038 original size:49 final size:49
Alignment explanation
Indices: 381476--382030 Score: 451
Period size: 49 Copynumber: 11.3 Consensus size: 49
381466 TCTCTATAGC
* * * * **
381476 TTTAGGGGTATAAGATTTATCGTTGCGGCTTTAATCTTTCCCTCTTTAGT
1 TTTA-GGGTGTAAGATTCACCGTTACGGCTTTAATCTTTCCCTCTTCGGT
* * *
381526 TTTAGGGGTGTAAGATTCATCG-TAGCAGCTTTAAT-TTATCCCTCTTCGAT
1 TTTA-GGGTGTAAGATTCACCGTTA-CGGCTTTAATCTT-TCCCTCTTCGGT
* * *
381576 TTTAGGGGTGTAAGATTCACCGTTACGGCTTTAATCTATCTCTCTTCGAT
1 TTTA-GGGTGTAAGATTCACCGTTACGGCTTTAATCTTTCCCTCTTCGGT
* * * ** * *
381626 TTTAAGGTGTAAGATTCACTGTTACGACTGCAATCTGTCCCTCTTCAGT
1 TTTAGGGTGTAAGATTCACCGTTACGGCTTTAATCTTTCCCTCTTCGGT
* * * * *
381675 TTTAAGGTGTAAGATTCACCGTTATGACTTTAATCTAT--C-CTTCAGT
1 TTTAGGGTGTAAGATTCACCGTTACGGCTTTAATCTTTCCCTCTTCGGT
** * * * *
381721 TTTAGGGTGTAAGATTCGTCGCTACGACTTTAAT-TTGTCCCTC-TCCGA
1 TTTAGGGTGTAAGATTCACCGTTACGGCTTTAATCTT-TCCCTCTTCGGT
* ** ** * * *
381769 TTTAAGGTGTAAGATTCATTGTTGTGGCTTTAATCTATCCTTCTTTGGT
1 TTTAGGGTGTAAGATTCACCGTTACGGCTTTAATCTTTCCCTCTTCGGT
* * * **
381818 TTTAGGATGTAAGATTCACCATTACTGCTTTAAT-TTGTCCCTCTTCAAT
1 TTTAGGGTGTAAGATTCACCGTTACGGCTTTAATCTT-TCCCTCTTCGGT
* * * * * * *
381867 TTTAGGGTGTAATATTCACCATTAAGACTTTAATATTTCCCTCTTTGAT
1 TTTAGGGTGTAAGATTCACCGTTACGGCTTTAATCTTTCCCTCTTCGGT
* ** * * *
381916 TTTAAGGTGTAAGATTTTCCGTTGCGGCTTTAATCTTTCCCTTTTCGAT
1 TTTAGGGTGTAAGATTCACCGTTACGGCTTTAATCTTTCCCTCTTCGGT
* * * *
381965 TTTAGGTTGTAAGATTCACCGTTGCGGTTTTAATCTTTCCCTCTTTGGT
1 TTTAGGGTGTAAGATTCACCGTTACGGCTTTAATCTTTCCCTCTTCGGT
382014 TTTAGGGTGTAAGATTC
1 TTTAGGGTGTAAGATTC
382031 GTTGTTGCAT
Statistics
Matches: 408, Mismatches: 85, Indels: 25
0.79 0.16 0.05
Matches are distributed among these distances:
45 1 0.00
46 37 0.09
47 1 0.00
48 37 0.09
49 244 0.60
50 85 0.21
51 3 0.01
ACGTcount: A:0.21, C:0.18, G:0.18, T:0.43
Consensus pattern (49 bp):
TTTAGGGTGTAAGATTCACCGTTACGGCTTTAATCTTTCCCTCTTCGGT
Found at i:382038 original size:98 final size:97
Alignment explanation
Indices: 381486--382030 Score: 503
Period size: 98 Copynumber: 5.6 Consensus size: 97
381476 TTTAGGGGTA
* * * * *
381486 TAAGATTTATCGTTGCGGCTTTAATCTTTCCCTCTTTAGTTTTAGGGGTGTAAGATTCATCG-TA
1 TAAGATTCACCGTTACGGCTTTAATCTATCCCTCTTTGGTTTTA-GGGTGTAAGATTCATCGTTA
* *
381550 GCAGCTTTAATTTATCCCTCTTCGATTTTAGGGGTG
65 -CGGCTTTAATTTGTCCCTCTTCGATTTTA--GGTG
* * * *
381586 TAAGATTCACCGTTACGGCTTTAATCTATCTCTCTTCGATTTTAAGGTGTAAGATTCA-CTGTTA
1 TAAGATTCACCGTTACGGCTTTAATCTATCCCTCTTTGGTTTTAGGGTGTAAGATTCATC-GTTA
* ** *
381650 CGACTGCAATCTGTCCCTCTTC-AGTTTTAAGGTG
65 CGGCTTTAATTTGTCCCTCTTCGA-TTTT-AGGTG
* * ** * *
381684 TAAGATTCACCGTTATGACTTTAATCTAT--C-CTTCAGTTTTAGGGTGTAAGATTCGTCGCTAC
1 TAAGATTCACCGTTACGGCTTTAATCTATCCCTCTTTGGTTTTAGGGTGTAAGATTCATCGTTAC
* * *
381746 GACTTTAATTTGTCCCTCTCCGATTTAAGGTG
66 GGCTTTAATTTGTCCCTCTTCGATTTTAGGTG
** ** * * * *
381778 TAAGATTCATTGTTGTGGCTTTAATCTATCCTTCTTTGGTTTTAGGATGTAAGATTCACCATTAC
1 TAAGATTCACCGTTACGGCTTTAATCTATCCCTCTTTGGTTTTAGGGTGTAAGATTCATCGTTAC
* *
381843 TGCTTTAATTTGTCCCTCTTCAATTTTAGGGTG
66 GGCTTTAATTTGTCCCTCTTCGATTTTA-GGTG
* * * * * * * * * *
381876 TAATATTCACCATTAAGACTTTAATATTTCCCTCTTTGATTTTAAGGTGTAAGATT-TTCCGTTG
1 TAAGATTCACCGTTACGGCTTTAATCTATCCCTCTTTGGTTTTAGGGTGTAAGATTCAT-CGTTA
*
381940 CGGCTTTAATCTT-TCCCTTTTCGATTTTAGGTTG
65 CGGCTTTAAT-TTGTCCCTCTTCGATTTTAGG-TG
* * *
381974 TAAGATTCACCGTTGCGGTTTTAATCTTTCCCTCTTTGGTTTTAGGGTGTAAGATTC
1 TAAGATTCACCGTTACGGCTTTAATCTATCCCTCTTTGGTTTTAGGGTGTAAGATTC
382031 GTTGTTGCAT
Statistics
Matches: 358, Mismatches: 73, Indels: 29
0.78 0.16 0.06
Matches are distributed among these distances:
94 30 0.08
95 45 0.13
96 3 0.01
97 50 0.14
98 155 0.43
99 36 0.10
100 39 0.11
ACGTcount: A:0.21, C:0.18, G:0.18, T:0.43
Consensus pattern (97 bp):
TAAGATTCACCGTTACGGCTTTAATCTATCCCTCTTTGGTTTTAGGGTGTAAGATTCATCGTTAC
GGCTTTAATTTGTCCCTCTTCGATTTTAGGTG
Found at i:391148 original size:14 final size:16
Alignment explanation
Indices: 391121--391161 Score: 55
Period size: 19 Copynumber: 2.4 Consensus size: 16
391111 CCTTTGGTCG
391121 AATGAAATGCAATGCATGT
1 AATGAAATGCAATGC---T
391140 AATGAAATGCAATGCT
1 AATGAAATGCAATGCT
391156 AATGAA
1 AATGAA
391162 TGCGTACACA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.32
19 15 0.68
ACGTcount: A:0.46, C:0.10, G:0.20, T:0.24
Consensus pattern (16 bp):
AATGAAATGCAATGCT
Found at i:411586 original size:21 final size:21
Alignment explanation
Indices: 411562--411612 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
411552 GTAATAGTTT
*
411562 TACCGATACAAGT-GTAACTTC
1 TACCGATACAAGTCAT-ACTTC
* *
411583 TACCGAAACAAGTCATGCTTC
1 TACCGATACAAGTCATACTTC
411604 TACCGATAC
1 TACCGATAC
411613 TAAAAACTCC
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
21 24 0.96
22 1 0.04
ACGTcount: A:0.33, C:0.27, G:0.14, T:0.25
Consensus pattern (21 bp):
TACCGATACAAGTCATACTTC
Found at i:416584 original size:19 final size:18
Alignment explanation
Indices: 416560--416625 Score: 51
Period size: 19 Copynumber: 3.4 Consensus size: 18
416550 TTAGACATGA
416560 AAATAAATGAGAAATAAAT
1 AAATAAATGA-AAATAAAT
** *
416579 AAATAAACAAAAAATCAAT
1 AAATAAA-TGAAAATAAAT
*
416598 AATTAAATGCCAAAATAAAT
1 AAATAAATG--AAAATAAAT
*
416618 AACTAAAT
1 AAATAAAT
416626 ATAAAATAAT
Statistics
Matches: 36, Mismatches: 8, Indels: 5
0.73 0.16 0.10
Matches are distributed among these distances:
19 20 0.56
20 16 0.44
ACGTcount: A:0.67, C:0.08, G:0.05, T:0.21
Consensus pattern (18 bp):
AAATAAATGAAAATAAAT
Found at i:416771 original size:18 final size:18
Alignment explanation
Indices: 416748--416784 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
416738 AAAAAACTAG
416748 ATCTATATTTATTTTTTT
1 ATCTATATTTATTTTTTT
*
416766 ATCTATATTTGTTTTTTT
1 ATCTATATTTATTTTTTT
416784 A
1 A
416785 GTTTCAAAGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.22, C:0.05, G:0.03, T:0.70
Consensus pattern (18 bp):
ATCTATATTTATTTTTTT
Found at i:418437 original size:15 final size:12
Alignment explanation
Indices: 418401--418430 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
418391 ACAATATCAT
418401 AATAATCCTAAC
1 AATAATCCTAAC
418413 AATAATCCTAAC
1 AATAATCCTAAC
418425 AATAAT
1 AATAAT
418431 GTTCCTATGC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.53, C:0.20, G:0.00, T:0.27
Consensus pattern (12 bp):
AATAATCCTAAC
Found at i:421754 original size:24 final size:23
Alignment explanation
Indices: 421685--421754 Score: 68
Period size: 23 Copynumber: 3.0 Consensus size: 23
421675 TTCATTTAAC
* *
421685 TTAATTGAGCATGTGCACGAACA
1 TTAATTGAACATGTTCACGAACA
** **
421708 TTAAACGAACATGTTCATAAACA
1 TTAATTGAACATGTTCACGAACA
*
421731 TATAATTGAACATATTCACGAACA
1 T-TAATTGAACATGTTCACGAACA
421755 ATGTTAATGA
Statistics
Matches: 35, Mismatches: 11, Indels: 1
0.74 0.23 0.02
Matches are distributed among these distances:
23 18 0.51
24 17 0.49
ACGTcount: A:0.43, C:0.17, G:0.13, T:0.27
Consensus pattern (23 bp):
TTAATTGAACATGTTCACGAACA
Found at i:421861 original size:12 final size:11
Alignment explanation
Indices: 421844--421890 Score: 58
Period size: 12 Copynumber: 4.0 Consensus size: 11
421834 ATCATTAATA
421844 AATAAACGAGTC
1 AATAAACGAG-C
421856 AATAAACGAGC
1 AATAAACGAGC
*
421867 TTATAAACGAGAC
1 -AATAAACGAG-C
421880 AATAAACGAGC
1 AATAAACGAGC
421891 TTGTTCGTTA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
11 2 0.06
12 28 0.90
13 1 0.03
ACGTcount: A:0.51, C:0.17, G:0.17, T:0.15
Consensus pattern (11 bp):
AATAAACGAGC
Found at i:421872 original size:24 final size:24
Alignment explanation
Indices: 421845--421892 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
421835 TCATTAATAA
*
421845 ATAAACGAGTCAATAAACGAGCTT
1 ATAAACGAGACAATAAACGAGCTT
421869 ATAAACGAGACAATAAACGAGCTT
1 ATAAACGAGACAATAAACGAGCTT
421893 GTTCGTTAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.48, C:0.17, G:0.17, T:0.19
Consensus pattern (24 bp):
ATAAACGAGACAATAAACGAGCTT
Found at i:427727 original size:23 final size:24
Alignment explanation
Indices: 427701--427763 Score: 83
Period size: 24 Copynumber: 2.7 Consensus size: 24
427691 AATTTAGTCA
*
427701 AACATGTTCACAAACAT-TAAATG
1 AACATGTTCACGAACATATAAATG
* *
427724 AACATGTTCATGAACATATAACTG
1 AACATGTTCACGAACATATAAATG
*
427748 AACATGTCCACGAACA
1 AACATGTTCACGAACA
427764 ATATTGATAA
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
23 15 0.44
24 19 0.56
ACGTcount: A:0.44, C:0.21, G:0.11, T:0.24
Consensus pattern (24 bp):
AACATGTTCACGAACATATAAATG
Found at i:432294 original size:20 final size:20
Alignment explanation
Indices: 432269--432320 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 20
432259 AGTCTTCAAG
*
432269 GTATCGGTAGAACTGTAGTT
1 GTATCGGTAGAACTGGAGTT
*
432289 GTATCGGTAGAAGTGGAGTT
1 GTATCGGTAGAACTGGAGTT
* *
432309 CTACCGGTAGAA
1 GTATCGGTAGAA
432321 GTCTCACTGG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.27, C:0.12, G:0.33, T:0.29
Consensus pattern (20 bp):
GTATCGGTAGAACTGGAGTT
Found at i:434350 original size:194 final size:194
Alignment explanation
Indices: 434006--434399 Score: 698
Period size: 194 Copynumber: 2.0 Consensus size: 194
433996 AGCTTTGATT
* * *
434006 CCTTGACTTTATTCGTTCCTTCATGGGTGACCTCAAGCTTGTCCCATATTTCTTTGGCATCGTTG
1 CCTTCACTCTATTCGTTCCTTCATGGGTGACCTCAAGATTGTCCCATATTTCTTTGGCATCGTTG
*
434071 CATGAGGAGACTCTATTGTGCTCATTTTCACCAAGAGCACAAAATAGAGTGTGCATAGCTTTTGC
66 CACGAGGAGACTCTATTGTGCTCATTTTCACCAAGAGCACAAAATAGAGTGTGCATAGCTTTTGC
*
434136 ATTAAGTCACACCGTCTTGATGTCATTTGCATCCTATTCATTCTCCTCCTTTAGAACACTAACA
131 ATTAAGTCACACCGTCTTGATGTCATTTGCATCCCATTCATTCTCCTCCTTTAGAACACTAACA
*
434200 CCTTCACTCTATTCGTTCCTTCATGGGTGACCTCAAGATTGTCTCATATTTCTTTGGCATCGTTG
1 CCTTCACTCTATTCGTTCCTTCATGGGTGACCTCAAGATTGTCCCATATTTCTTTGGCATCGTTG
434265 CACGAGGAGACTCTATTGTGCTCATTTTCACCAAGAGCACAAAATAGAGTGTGCATAGCTTTTGC
66 CACGAGGAGACTCTATTGTGCTCATTTTCACCAAGAGCACAAAATAGAGTGTGCATAGCTTTTGC
** * *
434330 ATTAAGTTGCACCTTCTTGATGTCATTTGCATCCCATTCATTCTCCTCCTTTGGAACACTAACA
131 ATTAAGTCACACCGTCTTGATGTCATTTGCATCCCATTCATTCTCCTCCTTTAGAACACTAACA
434394 CCTTCA
1 CCTTCA
434400 ACTATCTTCA
Statistics
Matches: 190, Mismatches: 10, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
194 190 1.00
ACGTcount: A:0.23, C:0.25, G:0.16, T:0.36
Consensus pattern (194 bp):
CCTTCACTCTATTCGTTCCTTCATGGGTGACCTCAAGATTGTCCCATATTTCTTTGGCATCGTTG
CACGAGGAGACTCTATTGTGCTCATTTTCACCAAGAGCACAAAATAGAGTGTGCATAGCTTTTGC
ATTAAGTCACACCGTCTTGATGTCATTTGCATCCCATTCATTCTCCTCCTTTAGAACACTAACA
Found at i:435325 original size:20 final size:19
Alignment explanation
Indices: 435296--435336 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
435286 TGCAGTCTGT
* *
435296 AACTTAGTTGTTTCGGTAG
1 AACTTAGTTGTATCAGTAG
435315 AACTATAGTTGTATCAGTAG
1 AACT-TAGTTGTATCAGTAG
435335 AA
1 AA
435337 GAGGAGTACT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 4 0.21
20 15 0.79
ACGTcount: A:0.32, C:0.10, G:0.22, T:0.37
Consensus pattern (19 bp):
AACTTAGTTGTATCAGTAG
Found at i:435572 original size:20 final size:20
Alignment explanation
Indices: 435547--435591 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
435537 TTGAAGGTAT
* *
435547 CGGTAGAACTGTAGTTGTAC
1 CGGTAGAACTGGAGTTCTAC
*
435567 CGGTAGAAGTGGAGTTCTAC
1 CGGTAGAACTGGAGTTCTAC
435587 CGGTA
1 CGGTA
435592 AAAGTCTCAC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.24, C:0.16, G:0.33, T:0.27
Consensus pattern (20 bp):
CGGTAGAACTGGAGTTCTAC
Found at i:435596 original size:20 final size:20
Alignment explanation
Indices: 435559--435596 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
435549 GTAGAACTGT
* *
435559 AGTTGTACCGGTAGAAGTGG
1 AGTTCTACCGGTAAAAGTGG
435579 AGTTCTACCGGTAAAAGT
1 AGTTCTACCGGTAAAAGT
435597 CTCACTGGAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.29, C:0.13, G:0.32, T:0.26
Consensus pattern (20 bp):
AGTTCTACCGGTAAAAGTGG
Found at i:440626 original size:21 final size:21
Alignment explanation
Indices: 440602--440645 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
440592 TTCTACTAAA
*
440602 ACAAATGATAGTTCTACCGAT
1 ACAAATGATACTTCTACCGAT
**
440623 ACAAATTTTACTTCTACCGAT
1 ACAAATGATACTTCTACCGAT
440644 AC
1 AC
440646 TAAAAACTCT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.36, C:0.23, G:0.09, T:0.32
Consensus pattern (21 bp):
ACAAATGATACTTCTACCGAT
Found at i:441395 original size:43 final size:41
Alignment explanation
Indices: 441335--441525 Score: 188
Period size: 41 Copynumber: 4.6 Consensus size: 41
441325 TATGCTCTAA
** *
441335 CGAGTCATAAGTCTTCCTTTTTAACATATTCTCACGCTCATTT
1 CGAGTCACGAGTCTTCC-TTTTAACATATTCTCATGCTCA-TT
* * * *
441378 CGAGTCACGAGTCTTCC-TTTAACACATTCTCATTCTTATCC
1 CGAGTCACGAGTCTTCCTTTTAACATATTCTCATGCTCAT-T
* * * *
441419 CGAGACATGAGTCTTCC-TTTAATATTTTCTCATGCTCATT
1 CGAGTCACGAGTCTTCCTTTTAACATATTCTCATGCTCATT
* *
441459 CTGAGTCACGAGTCTTCCTTTTATATAAATTCTCATGCTCATT
1 C-GAGTCACGAGTCTTCCTTTTA-ACATATTCTCATGCTCATT
*
441502 CTGAGTCACGAGTCTTCCATTTAA
1 C-GAGTCACGAGTCTTCCTTTTAA
441526 ACATCAAGTT
Statistics
Matches: 124, Mismatches: 20, Indels: 9
0.81 0.13 0.06
Matches are distributed among these distances:
40 2 0.02
41 63 0.51
42 5 0.04
43 54 0.44
ACGTcount: A:0.23, C:0.26, G:0.12, T:0.40
Consensus pattern (41 bp):
CGAGTCACGAGTCTTCCTTTTAACATATTCTCATGCTCATT
Found at i:447987 original size:40 final size:43
Alignment explanation
Indices: 447943--448054 Score: 119
Period size: 41 Copynumber: 2.7 Consensus size: 43
447933 AAATTCATGT
* *
447943 GTCTTCCTTTTTAACA-A-TCTTATGCTC-TATCGAGTCA-TAA
1 GTCTTCCTTTTTAACATATTCTCATGCTCATATCAAGTCACT-A
* *
447983 GTCTTCCCTTTTAACATATTCTCATGCTCATTTCAAGTCACTA
1 GTCTTCCTTTTTAACATATTCTCATGCTCATATCAAGTCACTA
* *
448026 GTCTTCC--TTTAACACATTCTCATTCTCAT
1 GTCTTCCTTTTTAACATATTCTCATGCTCAT
448055 CTTCCTTTAA
Statistics
Matches: 62, Mismatches: 6, Indels: 7
0.83 0.08 0.09
Matches are distributed among these distances:
40 15 0.24
41 21 0.34
42 9 0.15
43 16 0.26
44 1 0.02
ACGTcount: A:0.23, C:0.27, G:0.07, T:0.43
Consensus pattern (43 bp):
GTCTTCCTTTTTAACATATTCTCATGCTCATATCAAGTCACTA
Found at i:448080 original size:27 final size:27
Alignment explanation
Indices: 448027--448081 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 27
448017 AAGTCACTAG
**
448027 TCTTCCTTTAACACATTCTCATTCTCA
1 TCTTCCTTTAACACATTCTCAAGCTCA
* **
448054 TCTTCCTTTAATATTTTCTCAAGCTCA
1 TCTTCCTTTAACACATTCTCAAGCTCA
448081 T
1 T
448082 TCCGAGTCAT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.22, C:0.29, G:0.02, T:0.47
Consensus pattern (27 bp):
TCTTCCTTTAACACATTCTCAAGCTCA
Found at i:448123 original size:43 final size:43
Alignment explanation
Indices: 448069--448191 Score: 192
Period size: 43 Copynumber: 2.9 Consensus size: 43
448059 CTTTAATATT
* *
448069 TTCTCAAGCTCATTCCGAGTCATGAGTCTTCCTTTTATATAAA
1 TTCTCATGCTCATTCCGAGTCACGAGTCTTCCTTTTATATAAA
* *
448112 TTCTCATGCTCAGTACGAGTCACGAGTCTTCCTTTTATATAAA
1 TTCTCATGCTCATTCCGAGTCACGAGTCTTCCTTTTATATAAA
* *
448155 TTCTCATGCTCATTCCGAGTCACAAGTCTTCCATTTA
1 TTCTCATGCTCATTCCGAGTCACGAGTCTTCCTTTTA
448192 AACATCAACT
Statistics
Matches: 72, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
43 72 1.00
ACGTcount: A:0.24, C:0.25, G:0.12, T:0.38
Consensus pattern (43 bp):
TTCTCATGCTCATTCCGAGTCACGAGTCTTCCTTTTATATAAA
Found at i:451261 original size:23 final size:23
Alignment explanation
Indices: 451232--451492 Score: 290
Period size: 23 Copynumber: 11.3 Consensus size: 23
451222 CTTATATATG
451232 TGCTTAAATATTAATATGATTTA
1 TGCTTAAATATTAATATGATTTA
* *
451255 TGATTAAATATTATTGA-GATTTA
1 TGCTTAAATATTAAT-ATGATTTA
*
451278 TGCTTAAATATTAATGTGATTTA
1 TGCTTAAATATTAATATGATTTA
* *
451301 TGCTTAAATATTAATGTGATTTG
1 TGCTTAAATATTAATATGATTTA
* * * *
451324 CGCATAAATATTAATGTGATTTG
1 TGCTTAAATATTAATATGATTTA
* * *
451347 TACTCAAATATTAATATGATTTG
1 TGCTTAAATATTAATATGATTTA
*
451370 TGCTTAAATATTAATATGATTTG
1 TGCTTAAATATTAATATGATTTA
* *
451393 TGCTCAAATATTAATGTGATTTA
1 TGCTTAAATATTAATATGATTTA
* * *
451416 TGCTTAAATATTAATGTTATTTG
1 TGCTTAAATATTAATATGATTTA
*
451439 TGCTTAAATATTATTATGATTTA
1 TGCTTAAATATTAATATGATTTA
* * ** *
451462 TGATTAAATATCAACGTGATTTG
1 TGCTTAAATATTAATATGATTTA
451485 TGCTTAAA
1 TGCTTAAA
451493 GAATTAAAAT
Statistics
Matches: 204, Mismatches: 32, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
23 203 1.00
24 1 0.00
ACGTcount: A:0.35, C:0.06, G:0.13, T:0.46
Consensus pattern (23 bp):
TGCTTAAATATTAATATGATTTA
Found at i:451345 original size:69 final size:69
Alignment explanation
Indices: 451230--451492 Score: 348
Period size: 69 Copynumber: 3.8 Consensus size: 69
451220 TTCTTATATA
* *
451230 TGTGCTTAAATATTAATATGATTTATGATTAAATATTATTGAGATTTATGCTTAAATATTAATGT
1 TGTGCTTAAATATTAATATGATTTATGATTAAATATTAATGTGATTTATGCTTAAATATTAATGT
451295 GATT
66 GATT
* * ** * * * *
451299 TATGCTTAAATATTAATGTGATTTGCGCA-TAAATATTAATGTGATTTGTACTCAAATATTAATA
1 TGTGCTTAAATATTAATATGATTTATG-ATTAAATATTAATGTGATTTATGCTTAAATATTAATG
451363 TGATT
65 TGATT
* * *
451368 TGTGCTTAAATATTAATATGATTTGTGCTCAAATATTAATGTGATTTATGCTTAAATATTAATGT
1 TGTGCTTAAATATTAATATGATTTATGATTAAATATTAATGTGATTTATGCTTAAATATTAATGT
*
451433 TATT
66 GATT
* * * *
451437 TGTGCTTAAATATTATTATGATTTATGATTAAATATCAACGTGATTTGTGCTTAAA
1 TGTGCTTAAATATTAATATGATTTATGATTAAATATTAATGTGATTTATGCTTAAA
451493 GAATTAAAAT
Statistics
Matches: 165, Mismatches: 27, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
69 164 0.99
70 1 0.01
ACGTcount: A:0.35, C:0.06, G:0.13, T:0.46
Consensus pattern (69 bp):
TGTGCTTAAATATTAATATGATTTATGATTAAATATTAATGTGATTTATGCTTAAATATTAATGT
GATT
Found at i:460446 original size:13 final size:13
Alignment explanation
Indices: 460428--460452 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
460418 GCCAAAGTGT
460428 ATTACATGATTTA
1 ATTACATGATTTA
460441 ATTACATGATTT
1 ATTACATGATTT
460453 GATGAGAAAT
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:0.36, C:0.08, G:0.08, T:0.48
Consensus pattern (13 bp):
ATTACATGATTTA
Found at i:480206 original size:37 final size:37
Alignment explanation
Indices: 480151--480223 Score: 128
Period size: 37 Copynumber: 2.0 Consensus size: 37
480141 AACGCAACGA
*
480151 GATGGTCCAACAACCTATCATGCAGGTTGAGCTCTTT
1 GATGCTCCAACAACCTATCATGCAGGTTGAGCTCTTT
*
480188 GATGCTCCAACAACCTATCATGGAGGTTGAGCTCTT
1 GATGCTCCAACAACCTATCATGCAGGTTGAGCTCTT
480224 CGATCCTAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.25, C:0.25, G:0.22, T:0.29
Consensus pattern (37 bp):
GATGCTCCAACAACCTATCATGCAGGTTGAGCTCTTT
Found at i:480416 original size:248 final size:248
Alignment explanation
Indices: 479978--480439 Score: 753
Period size: 248 Copynumber: 1.9 Consensus size: 248
479968 AATGCTTTCA
* *
479978 ATCCTAAAGCATTGCCACGATGCTCCTTATGAAGGTCATTTTGGTGGTGTTAGGACTGCTGCAAA
1 ATCCTAAAGCATTGCCACGATGCTCCTTATGAAGGCCATTTTGGTGGTGTTAGGACTACTGCAAA
*
480043 GGTCCTACAATCAGGATATTTCTGGCCTATATTATTTCGAGATGCCTACAATTTTGCTCAACAAT
66 GGTCCTACAATCAGGATATTTCTGGCCTATATTATTTCGAGATGCCTACAATTTTGCTCAAAAAT
* * * *
480108 ATGACAAATGTCAACGCACTAATTTCATATCTCAACGCAACGAGATGGTCCAACAACCTATCATG
131 ATGACAAATGTCAACACACCAATTCCATATCTCAACGCAACGAGATGCTCCAACAACCTATCATG
480173 CAGGTTGAGCTCTTTGATGCTCCAACAACCTATCATGGAGGTTGAGCTCTTCG
196 CAGGTTGAGCTCTTTGATGCTCCAACAACCTATCATGGAGGTTGAGCTCTTCG
*
480226 ATCCTAAAGCATTGCCATGATGCTCCTTATGAAGGCCATTTTGGTGGTGTTAGGACTACTGCAAA
1 ATCCTAAAGCATTGCCACGATGCTCCTTATGAAGGCCATTTTGGTGGTGTTAGGACTACTGCAAA
* * *
480291 GGTCCTACAATCAGGATCTTTCTGGCCTATATTATTTTGAGATGCCTATAATTTTGCTCAAAAAT
66 GGTCCTACAATCAGGATATTTCTGGCCTATATTATTTCGAGATGCCTACAATTTTGCTCAAAAAT
* * * * * * *
480356 GTGACAAATGTCAACATACCAATTCCCTATTTCGATGCAACGAGATGCTTCAACAACCTATCATG
131 ATGACAAATGTCAACACACCAATTCCATATCTCAACGCAACGAGATGCTCCAACAACCTATCATG
*
480421 GAGGTTGAGCTCTTTGATG
196 CAGGTTGAGCTCTTTGATG
480440 TTTGGGGTAT
Statistics
Matches: 195, Mismatches: 19, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
248 195 1.00
ACGTcount: A:0.28, C:0.22, G:0.19, T:0.31
Consensus pattern (248 bp):
ATCCTAAAGCATTGCCACGATGCTCCTTATGAAGGCCATTTTGGTGGTGTTAGGACTACTGCAAA
GGTCCTACAATCAGGATATTTCTGGCCTATATTATTTCGAGATGCCTACAATTTTGCTCAAAAAT
ATGACAAATGTCAACACACCAATTCCATATCTCAACGCAACGAGATGCTCCAACAACCTATCATG
CAGGTTGAGCTCTTTGATGCTCCAACAACCTATCATGGAGGTTGAGCTCTTCG
Found at i:491856 original size:19 final size:20
Alignment explanation
Indices: 491824--491865 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
491814 AAATTTAAAA
*
491824 TTTAACCAATTCAAAATCAT
1 TTTAACCAAATCAAAATCAT
*
491844 TTTAA-CAAATCAAAATGAT
1 TTTAACCAAATCAAAATCAT
491863 TTT
1 TTT
491866 CAAACAAGTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 15 0.75
20 5 0.25
ACGTcount: A:0.45, C:0.14, G:0.02, T:0.38
Consensus pattern (20 bp):
TTTAACCAAATCAAAATCAT
Found at i:494043 original size:28 final size:29
Alignment explanation
Indices: 494001--494073 Score: 105
Period size: 28 Copynumber: 2.6 Consensus size: 29
493991 TCACCAATAT
*
494001 TCTTCCACTTAGACTATCCACAACTTT-G
1 TCTTGCACTTAGACTATCCACAACTTTAG
* *
494029 TCTTGCACTTGGACTATCCACCACTTTAG
1 TCTTGCACTTAGACTATCCACAACTTTAG
494058 -CTTGCACTTAGACTAT
1 TCTTGCACTTAGACTAT
494074 TCGACACTTG
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
28 39 0.98
29 1 0.03
ACGTcount: A:0.23, C:0.30, G:0.11, T:0.36
Consensus pattern (29 bp):
TCTTGCACTTAGACTATCCACAACTTTAG
Found at i:494081 original size:28 final size:27
Alignment explanation
Indices: 494001--494082 Score: 94
Period size: 28 Copynumber: 2.9 Consensus size: 27
493991 TCACCAATAT
*
494001 TCTTCCACTTAGACTATCCACAACTTTG
1 TCTTGCACTTAGACTATCCAC-ACTTTG
*
494029 TCTTGCACTTGGACTATCCACCACTTTAG
1 TCTTGCACTTAGACTATCCA-CACTTT-G
*
494058 -CTTGCACTTAGACTATTCGACACTT
1 TCTTGCACTTAGACTA-TCCACACTT
494083 GTTCGAGCTG
Statistics
Matches: 47, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
28 42 0.89
29 5 0.11
ACGTcount: A:0.23, C:0.30, G:0.11, T:0.35
Consensus pattern (27 bp):
TCTTGCACTTAGACTATCCACACTTTG
Found at i:514606 original size:17 final size:18
Alignment explanation
Indices: 514584--514618 Score: 63
Period size: 17 Copynumber: 2.0 Consensus size: 18
514574 ATTTTGTAAT
514584 AGCTTTTAAACAT-CATA
1 AGCTTTTAAACATACATA
514601 AGCTTTTAAACATACATA
1 AGCTTTTAAACATACATA
514619 CTCATATCTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 13 0.76
18 4 0.24
ACGTcount: A:0.43, C:0.17, G:0.06, T:0.34
Consensus pattern (18 bp):
AGCTTTTAAACATACATA
Found at i:519512 original size:43 final size:43
Alignment explanation
Indices: 519451--519539 Score: 169
Period size: 43 Copynumber: 2.1 Consensus size: 43
519441 ATTCGTTCAA
*
519451 TGTAAGAATTTATTACCAATTGAAAATGTTGAGGTTGCTAGGT
1 TGTAAGAATTTATTACCAATTGAAAATATTGAGGTTGCTAGGT
519494 TGTAAGAATTTATTACCAATTGAAAATATTGAGGTTGCTAGGT
1 TGTAAGAATTTATTACCAATTGAAAATATTGAGGTTGCTAGGT
519537 TGT
1 TGT
519540 TACTCGTGCA
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 45 1.00
ACGTcount: A:0.33, C:0.07, G:0.22, T:0.38
Consensus pattern (43 bp):
TGTAAGAATTTATTACCAATTGAAAATATTGAGGTTGCTAGGT
Found at i:521277 original size:23 final size:23
Alignment explanation
Indices: 521247--521292 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
521237 AGCTAAAAGG
521247 TAAATATATCAAAAGCACAATAA
1 TAAATATATCAAAAGCACAATAA
521270 TAAATATATCAAAAGCACAATAA
1 TAAATATATCAAAAGCACAATAA
521293 AGAATTGACA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.61, C:0.13, G:0.04, T:0.22
Consensus pattern (23 bp):
TAAATATATCAAAAGCACAATAA
Found at i:522142 original size:18 final size:18
Alignment explanation
Indices: 522109--522143 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
522099 TTCTAAGAAA
*
522109 CACTTTTGGGACAAAAAT
1 CACTTTTGAGACAAAAAT
*
522127 CACTTTTGAGATAAAAA
1 CACTTTTGAGACAAAAA
522144 CATTGCTAAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.43, C:0.14, G:0.14, T:0.29
Consensus pattern (18 bp):
CACTTTTGAGACAAAAAT
Found at i:526393 original size:17 final size:18
Alignment explanation
Indices: 526371--526409 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
526361 AAAAATAAAG
* *
526371 AAAATAATATATT-TTAA
1 AAAATAAAAAATTATTAA
526388 AAAATAAAAAATTATTAA
1 AAAATAAAAAATTATTAA
526406 AAAA
1 AAAA
526410 AGTAATGGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 11 0.58
18 8 0.42
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (18 bp):
AAAATAAAAAATTATTAA
Found at i:526410 original size:20 final size:21
Alignment explanation
Indices: 526336--526408 Score: 60
Period size: 20 Copynumber: 3.4 Consensus size: 21
526326 TTATACGTCA
* *
526336 TATTAATAAATAAATATAAGAT
1 TATTAA-AAATAAATAAAAAAT
*
526358 TA-TAAAAATAAAGAAAATAAT
1 TATTAAAAATAAATAAAA-AAT
**
526379 ATATTTTAAA-AAATAAAAAAT
1 -TATTAAAAATAAATAAAAAAT
526400 TATTAAAAA
1 TATTAAAAA
526409 AAGTAATGGA
Statistics
Matches: 40, Mismatches: 8, Indels: 8
0.71 0.14 0.14
Matches are distributed among these distances:
20 17 0.43
21 8 0.20
22 11 0.28
23 4 0.10
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.32
Consensus pattern (21 bp):
TATTAAAAATAAATAAAAAAT
Found at i:535395 original size:56 final size:56
Alignment explanation
Indices: 535261--535459 Score: 199
Period size: 56 Copynumber: 3.6 Consensus size: 56
535251 AGCTCGAATC
* * * *
535261 TGCTTACGTCTC-GATTAGAGCATAATGCTATTATAGCTCGGGTAGAGTTTTGGACA
1 TGCTTATGTCTCAG-TTAGAGCATAATGTTATTATAGCTTGGGTAGAGCTTTGGACA
* * * *
535317 TGCTTATGTAT-AGGTTAAAGCGTAATGTTATTATAGCTTGGGTATAGCTTTGGACA
1 TGCTTATGTCTCA-GTTAGAGCATAATGTTATTATAGCTTGGGTAGAGCTTTGGACA
* * * * * *
535373 TGTTTATATCTCAGTTAGAGCGTGAA-GTTATTATAGCTTAGGTAGAGCTCTGG-CT
1 TGCTTATGTCTCAGTTAGAGCAT-AATGTTATTATAGCTTGGGTAGAGCTTTGGACA
* *
535428 TGCTTATGTCTCGGTTAGAGCATAAGGTTATT
1 TGCTTATGTCTCAGTTAGAGCATAATGTTATT
535460 TCAGCTCAGA
Statistics
Matches: 118, Mismatches: 20, Indels: 11
0.79 0.13 0.07
Matches are distributed among these distances:
54 2 0.02
55 26 0.22
56 86 0.73
57 4 0.03
ACGTcount: A:0.25, C:0.13, G:0.25, T:0.38
Consensus pattern (56 bp):
TGCTTATGTCTCAGTTAGAGCATAATGTTATTATAGCTTGGGTAGAGCTTTGGACA
Found at i:537243 original size:56 final size:56
Alignment explanation
Indices: 537176--537358 Score: 183
Period size: 56 Copynumber: 3.3 Consensus size: 56
537166 TCTGCTTATG
* *
537176 TCTCGGTTAGAGCGTAATGCTATTATAGCT-TGAGAAGAGTTTTGGACATGTTTACA
1 TCTCGGTTAGAGCGTAATGCTATTATAGCTCTG-GAAGAGCTTTGGACATGCTTACA
* * **
537232 TCTCGGTTAGAGCGTAATGCTCTTATAGCTCTGGTAGAGCTTTGGACATGCTTATG
1 TCTCGGTTAGAGCGTAATGCTATTATAGCTCTGGAAGAGCTTTGGACATGCTTACA
* * * * * * * ** *
537288 TCTCAGTTAGAGCGTAAAGTTGTTATAGCTCGGGTAGAGCTCT--AGTTTCTTACA
1 TCTCGGTTAGAGCGTAATGCTATTATAGCTCTGGAAGAGCTTTGGACATGCTTACA
*
537342 TCTCGGTTAGAGAGTAA
1 TCTCGGTTAGAGCGTAA
537359 GGTTATTTCA
Statistics
Matches: 107, Mismatches: 19, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
54 21 0.20
56 84 0.79
57 2 0.02
ACGTcount: A:0.24, C:0.15, G:0.26, T:0.35
Consensus pattern (56 bp):
TCTCGGTTAGAGCGTAATGCTATTATAGCTCTGGAAGAGCTTTGGACATGCTTACA
Found at i:547453 original size:15 final size:15
Alignment explanation
Indices: 547430--547474 Score: 54
Period size: 15 Copynumber: 3.0 Consensus size: 15
547420 TTTTTGACAT
547430 AAATAATACAAAAAA
1 AAATAATACAAAAAA
* **
547445 AAATTATACACCAAA
1 AAATAATACAAAAAA
*
547460 ATATAATACAAAAAA
1 AAATAATACAAAAAA
547475 TAAAATTAAT
Statistics
Matches: 23, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.71, C:0.11, G:0.00, T:0.18
Consensus pattern (15 bp):
AAATAATACAAAAAA
Done.