Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold103
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: 2633873
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 16636 characters in sequence are not A, C, G, or T
File 5 of 21
Found at i:483613 original size:25 final size:25
Alignment explanation
Indices: 483584--483647 Score: 69
Period size: 23 Copynumber: 2.5 Consensus size: 25
483574 ATAAATTTTG
*
483584 ATATATTTATTTATTTATACCATATT
1 ATATA-TTATTTATTGATACCATATT
*
483610 -TATATTATTT-TTGATATCATATT
1 ATATATTATTTATTGATACCATATT
483633 ATATAATTATATTAT
1 ATAT-ATTAT-TTAT
483648 ATTCAAAAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
23 11 0.34
24 9 0.28
25 9 0.28
26 2 0.06
27 1 0.03
ACGTcount: A:0.36, C:0.05, G:0.02, T:0.58
Consensus pattern (25 bp):
ATATATTATTTATTGATACCATATT
Found at i:483670 original size:30 final size:30
Alignment explanation
Indices: 483636--483696 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 30
483626 TCATATTATA
*
483636 TAATTATATTATATTCAAA-AATTTTAAATT
1 TAATTA-ATAATATTCAAATAATTTTAAATT
* *
483666 TAATTAATAATATTTAAATAATTTTTAATT
1 TAATTAATAATATTCAAATAATTTTAAATT
483696 T
1 T
483697 TATATCACAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
29 10 0.37
30 17 0.63
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (30 bp):
TAATTAATAATATTCAAATAATTTTAAATT
Found at i:484223 original size:17 final size:18
Alignment explanation
Indices: 484201--484237 Score: 67
Period size: 17 Copynumber: 2.1 Consensus size: 18
484191 ATATTATGTA
484201 AATATAATATAAA-AAAT
1 AATATAATATAAATAAAT
484218 AATATAATATAAATAAAT
1 AATATAATATAAATAAAT
484236 AA
1 AA
484238 ATATCTTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 13 0.68
18 6 0.32
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (18 bp):
AATATAATATAAATAAAT
Found at i:484240 original size:14 final size:15
Alignment explanation
Indices: 484199--484241 Score: 52
Period size: 17 Copynumber: 2.8 Consensus size: 15
484189 TAATATTATG
484199 TAAATATAATATAAAA
1 TAAATATAATAT-AAA
*
484215 AATAATATAATATAAA
1 TA-AATATAATATAAA
484231 TAAATA-AATAT
1 TAAATATAATAT
484242 CTTAAAATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
14 5 0.21
15 4 0.17
16 5 0.21
17 10 0.42
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (15 bp):
TAAATATAATATAAA
Found at i:484256 original size:33 final size:33
Alignment explanation
Indices: 484219--484296 Score: 104
Period size: 32 Copynumber: 2.4 Consensus size: 33
484209 ATAAAAAATA
484219 ATATAATATAAATAAATAAATATCTTAAAATTT
1 ATATAATATAAATAAATAAATATCTTAAAATTT
** * *
484252 ATATAATAT-AATTTATTAATATGTTAAAATTT
1 ATATAATATAAATAAATAAATATCTTAAAATTT
484284 ATATAAATATAAA
1 ATAT-AATATAAA
484297 ATAATTATAA
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
32 23 0.59
33 14 0.36
34 2 0.05
ACGTcount: A:0.55, C:0.01, G:0.01, T:0.42
Consensus pattern (33 bp):
ATATAATATAAATAAATAAATATCTTAAAATTT
Found at i:484718 original size:16 final size:16
Alignment explanation
Indices: 484693--484723 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
484683 AATAATTATC
484693 TTTTACAATTAAAATA
1 TTTTACAATTAAAATA
*
484709 TTTTATAATTAAAAT
1 TTTTACAATTAAAAT
484724 TAATAAAATA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (16 bp):
TTTTACAATTAAAATA
Found at i:492345 original size:2 final size:2
Alignment explanation
Indices: 492338--492365 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
492328 CAATAGGAAT
492338 CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA
492366 AAGGGGGGGG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:494923 original size:18 final size:18
Alignment explanation
Indices: 494897--494991 Score: 77
Period size: 18 Copynumber: 5.3 Consensus size: 18
494887 TTTTATTTTA
* *
494897 ATTTTAATAATATTAAAT
1 ATTTAAATAATTTTAAAT
**
494915 ATTTAAATATATTTTATTT
1 ATTTAAATA-ATTTTAAAT
* *
494934 ATATAAATATTTTTAAAT
1 ATTTAAATAATTTTAAAT
494952 ATTTAAAT-ATTTATAAA-
1 ATTTAAATAATTT-TAAAT
* * *
494969 ATATAAAAAATTTTATAT
1 ATTTAAATAATTTTAAAT
494987 ATTTA
1 ATTTA
494992 CAAGAATTAA
Statistics
Matches: 59, Mismatches: 14, Indels: 8
0.73 0.17 0.10
Matches are distributed among these distances:
17 12 0.20
18 33 0.56
19 14 0.24
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (18 bp):
ATTTAAATAATTTTAAAT
Found at i:494958 original size:37 final size:39
Alignment explanation
Indices: 494874--494961 Score: 110
Period size: 37 Copynumber: 2.3 Consensus size: 39
494864 TTTAAGATTT
* * *
494874 AATATTTAAAT-TTTTTTATTTTAATTTTAATAATATTA
1 AATATTTAAATATATTTTATTTTAATATAAATAATATTA
* *
494912 AATATTTAAATATATTTTA-TTT-ATATAAATATTTTTA
1 AATATTTAAATATATTTTATTTTAATATAAATAATATTA
494949 AATATTTAAATAT
1 AATATTTAAATAT
494962 TTATAAAATA
Statistics
Matches: 44, Mismatches: 5, Indels: 3
0.85 0.10 0.06
Matches are distributed among these distances:
37 24 0.55
38 14 0.32
39 6 0.14
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (39 bp):
AATATTTAAATATATTTTATTTTAATATAAATAATATTA
Found at i:494973 original size:35 final size:37
Alignment explanation
Indices: 494909--494991 Score: 98
Period size: 35 Copynumber: 2.3 Consensus size: 37
494899 TTTAATAATA
* ** * *
494909 TTAAATATTTAAATATATTTTATTTATATAAATATTT
1 TTAAATATTTAAATATATTATATAAATATAAAAAATT
494946 TTAAATATTTAAATAT-TTATA-AAATATAAAAAATT
1 TTAAATATTTAAATATATTATATAAATATAAAAAATT
*
494981 TTATATATTTA
1 TTAAATATTTA
494992 CAAGAATTAA
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
35 20 0.50
36 4 0.10
37 16 0.40
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (37 bp):
TTAAATATTTAAATATATTATATAAATATAAAAAATT
Found at i:495002 original size:27 final size:28
Alignment explanation
Indices: 494948--495002 Score: 69
Period size: 27 Copynumber: 2.0 Consensus size: 28
494938 AAATATTTTT
*
494948 AAATATTTAAATATTTATAAAATATAAA
1 AAATATTTAAATATTTACAAAATATAAA
*
494976 AAAT-TTTATATATTTACAAGAAT-TAAA
1 AAATATTTAAATATTTACAA-AATATAAA
495003 GTCTTGATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
27 17 0.71
28 7 0.29
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (28 bp):
AAATATTTAAATATTTACAAAATATAAA
Found at i:495074 original size:17 final size:16
Alignment explanation
Indices: 495036--495078 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 16
495026 ATAAAAATTG
495036 ATATTTAATAAATTTAA
1 ATATTTAATAAA-TTAA
495053 ATATTTAATAAA-TAA
1 ATATTTAATAAATTAA
495068 TATTATTTAAT
1 -A-TATTTAAT
495079 TTAAATTTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
15 3 0.12
16 1 0.04
17 20 0.83
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (16 bp):
ATATTTAATAAATTAA
Found at i:495143 original size:21 final size:20
Alignment explanation
Indices: 495118--495157 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
495108 CAAGTAAATA
495118 ATAAATCAGATAAAATTTAAT
1 ATAAATCA-ATAAAATTTAAT
*
495139 ATAAATTAATAAAATTTAA
1 ATAAATCAATAAAATTTAA
495158 ATTTTTAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.60, C:0.03, G:0.03, T:0.35
Consensus pattern (20 bp):
ATAAATCAATAAAATTTAAT
Found at i:495380 original size:3 final size:3
Alignment explanation
Indices: 495372--495400 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
495362 ACCTTTCATA
495372 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
495401 ATAAATAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:496063 original size:40 final size:39
Alignment explanation
Indices: 496012--496095 Score: 98
Period size: 41 Copynumber: 2.1 Consensus size: 39
496002 ATTTAATTAA
* *
496012 AAAATTATATAAAAATAAATA-TAATATTAAATATTAAATATT
1 AAAATTATA-AAATAT-AATACT-ATATTAAATAAT-AATATT
496054 AAAATTATAAAATATAATACGTATATTAAATAATAATATT
1 AAAATTATAAAATATAATAC-TATATTAAATAATAATATT
496094 AA
1 AA
496096 TTATATTTAC
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
40 12 0.32
41 16 0.42
42 10 0.26
ACGTcount: A:0.61, C:0.01, G:0.01, T:0.37
Consensus pattern (39 bp):
AAAATTATAAAATATAATACTATATTAAATAATAATATT
Found at i:497093 original size:17 final size:16
Alignment explanation
Indices: 497072--497120 Score: 55
Period size: 16 Copynumber: 2.9 Consensus size: 16
497062 AATTTGTTAC
497072 TATATTTTATTTTTAT
1 TATATTTTATTTTTAT
497088 TGATA-TTTATTTGTTAT
1 T-ATATTTTATTT-TTAT
*
497105 TATACTTTTAGTTTTA
1 TATA-TTTTATTTTTA
497121 GATTAAGTGT
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
16 11 0.39
17 11 0.39
18 6 0.21
ACGTcount: A:0.24, C:0.02, G:0.06, T:0.67
Consensus pattern (16 bp):
TATATTTTATTTTTAT
Found at i:503279 original size:26 final size:26
Alignment explanation
Indices: 503250--503311 Score: 97
Period size: 26 Copynumber: 2.4 Consensus size: 26
503240 TCATGTAAGT
*
503250 AAATGCAAGCCAAACTTGGAAAAATG
1 AAATGCAAGCCAAACTTGCAAAAATG
* *
503276 AAATGCAAGTCAAACTTGCAAAAATT
1 AAATGCAAGCCAAACTTGCAAAAATG
503302 AAATGCAAGC
1 AAATGCAAGC
503312 TTGCTCTTGA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 32 1.00
ACGTcount: A:0.50, C:0.16, G:0.16, T:0.18
Consensus pattern (26 bp):
AAATGCAAGCCAAACTTGCAAAAATG
Found at i:503959 original size:2 final size:2
Alignment explanation
Indices: 503952--503980 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
503942 GCTCTAAGCA
503952 AT 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 AT A
503981 CACACACACG
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:507364 original size:15 final size:16
Alignment explanation
Indices: 507344--507373 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
507334 AATTTAAAAA
507344 TTAAATATAT-TTATG
1 TTAAATATATATTATG
507359 TTAAATATATATTAT
1 TTAAATATATATTAT
507374 TAATTTAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.53
Consensus pattern (16 bp):
TTAAATATATATTATG
Found at i:507554 original size:18 final size:18
Alignment explanation
Indices: 507533--507595 Score: 58
Period size: 18 Copynumber: 3.5 Consensus size: 18
507523 TTTTATTAGT
507533 TTATTTATATTTAAAATA
1 TTATTTATATTTAAAATA
*
507551 TTATTTA-ATAATAAAATA
1 TTATTTATAT-TTAAAATA
* *
507569 ATATTTTTAATTTAAAAT-
1 TTATTTAT-ATTTAAAATA
*
507587 TTAATTATA
1 TTATTTATA
507596 AAATATATAA
Statistics
Matches: 35, Mismatches: 7, Indels: 7
0.71 0.14 0.14
Matches are distributed among these distances:
17 3 0.09
18 24 0.69
19 6 0.17
20 2 0.06
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (18 bp):
TTATTTATATTTAAAATA
Found at i:508181 original size:16 final size:14
Alignment explanation
Indices: 508145--508188 Score: 61
Period size: 14 Copynumber: 3.0 Consensus size: 14
508135 AATGTTCTAC
508145 AAAATTTTAATTTA
1 AAAATTTTAATTTA
*
508159 AATATTTTAATAATTA
1 AAAATTTTAAT--TTA
508175 AAAATTTTAATTTA
1 AAAATTTTAATTTA
508189 TTTAAAATAA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
14 13 0.50
16 13 0.50
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
AAAATTTTAATTTA
Found at i:509974 original size:2 final size:2
Alignment explanation
Indices: 509953--509992 Score: 55
Period size: 2 Copynumber: 20.5 Consensus size: 2
509943 CCACTAATTC
* *
509953 TA TA TC TA TA TA CA TA -A TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
509993 CAAATTTCAA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:510663 original size:231 final size:231
Alignment explanation
Indices: 510233--510696 Score: 707
Period size: 231 Copynumber: 2.0 Consensus size: 231
510223 AAATTTGATC
* *
510233 TAACTTGATTTGAAAACAAAATTAATAACTTAAAACCAAATAACTCGAATCCAAAATGATGTAAA
1 TAACCTGATTTGAAAAAAAAATTAATAACTTAAAACCAAATAACTCGAATCCAAAATGATGTAAA
* * *
510298 CCAGAAATGATCTAGATAATTAATCCAAAATACTCCAAGCCAAAATAACTGAACCAATAAATTGG
66 CCAGAAATGACCTAGATAATTAATCCAAAATACTCCAAACCAAAATAACTGAACCAATAAATTGA
* * *
510363 ATTGTTAAACATGATTGACTAAAATTCAATTAATTCAAGTGTTAAGTTCGAAATGACACAAGCCA
131 ATTGTTAAACATGATTGACCAAAATTCAATTAATTCAAGTGTTAAGTTCAAAATGACACAAGACA
510428 AATTAACTCGAGTATTAAACTCGAAATGACCTAAAT
196 AATTAACTCGAGTATTAAACTCGAAATGACCTAAAT
* ** *
510464 TAACCTGATTT-AATAAAAAAATTAATAACTTGAAATTAACTAACTCGAATCCAAAATGATGTAA
1 TAACCTGATTTGAA-AAAAAAATTAATAACTTAAAACCAAATAACTCGAATCCAAAATGATGTAA
* * * *
510528 ACTAGAAATGACCTAGATAATTAATCTAAAATAGTTCAAACCAAAATAACTGAACCCAATAAATT
65 ACCAGAAATGACCTAGATAATTAATCCAAAATACTCCAAACCAAAATAACTGAA-CCAATAAATT
* * * *
510593 GAATTGTTAAGCATGATTGACCAGAATTTAATTAATTCAAGTGTT-AGTTCAAAATGATACAAGA
129 GAATTGTTAAACATGATTGACCAAAATTCAATTAATTCAAGTGTTAAGTTCAAAATGACACAAGA
*
510657 CAAATTAACTCGAGTATTAGACTCGAAATGACCTAAAT
194 CAAATTAACTCGAGTATTAAACTCGAAATGACCTAAAT
510695 TA
1 TA
510697 GATTTAACTT
Statistics
Matches: 210, Mismatches: 21, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
230 2 0.01
231 158 0.75
232 50 0.24
ACGTcount: A:0.47, C:0.15, G:0.11, T:0.28
Consensus pattern (231 bp):
TAACCTGATTTGAAAAAAAAATTAATAACTTAAAACCAAATAACTCGAATCCAAAATGATGTAAA
CCAGAAATGACCTAGATAATTAATCCAAAATACTCCAAACCAAAATAACTGAACCAATAAATTGA
ATTGTTAAACATGATTGACCAAAATTCAATTAATTCAAGTGTTAAGTTCAAAATGACACAAGACA
AATTAACTCGAGTATTAAACTCGAAATGACCTAAAT
Found at i:511466 original size:12 final size:12
Alignment explanation
Indices: 511449--511477 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
511439 TTTTGACATC
511449 AATTAATTAAAA
1 AATTAATTAAAA
511461 AATTAATTAAAA
1 AATTAATTAAAA
511473 AATTA
1 AATTA
511478 TTACTATTAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (12 bp):
AATTAATTAAAA
Found at i:512753 original size:34 final size:34
Alignment explanation
Indices: 512683--512753 Score: 83
Period size: 34 Copynumber: 2.1 Consensus size: 34
512673 ATAATTTTAA
* *
512683 TTATTATTTAATAATAATATAATTTATTTATATT
1 TTATTATTTAATAATAATATAATTTAATAATATT
*
512717 TTATTATTTGAT-ATAAATATAATTTTAATAAT-TT
1 TTATTATTTAATAAT-AATATAA-TTTAATAATATT
512751 TTA
1 TTA
512754 ATAATTATTA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
33 2 0.06
34 23 0.72
35 7 0.22
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.58
Consensus pattern (34 bp):
TTATTATTTAATAATAATATAATTTAATAATATT
Found at i:512887 original size:21 final size:22
Alignment explanation
Indices: 512858--512899 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
512848 TATTTTATCA
*
512858 TTAATTTTTATTATTAAAATAT
1 TTAATTTTTATAATTAAAATAT
*
512880 TTAA-TTTTATAATTACAATA
1 TTAATTTTTATAATTAAAATA
512900 ACTAAATCCA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (22 bp):
TTAATTTTTATAATTAAAATAT
Found at i:513764 original size:14 final size:15
Alignment explanation
Indices: 513745--513778 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
513735 ATTATAATTT
513745 ATTTT-ATAAATATA
1 ATTTTAATAAATATA
513759 ATTTTAATAAATATA
1 ATTTTAATAAATATA
513774 ATTTT
1 ATTTT
513779 TTAGTATATA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 5 0.26
15 14 0.74
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
ATTTTAATAAATATA
Found at i:513888 original size:20 final size:21
Alignment explanation
Indices: 513852--513907 Score: 64
Period size: 21 Copynumber: 2.7 Consensus size: 21
513842 TATATGTACC
513852 AAAAATATATAAA-AAT-ATTTT
1 AAAAA-ATA-AAATAATAATTTT
513873 AAAAAATAAAATAATAATTTT
1 AAAAAATAAAATAATAATTTT
*
513894 AAAAGAT-AAATAAT
1 AAAAAATAAAATAAT
513908 GTAGTGCGAA
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
19 3 0.09
20 13 0.41
21 16 0.50
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (21 bp):
AAAAAATAAAATAATAATTTT
Found at i:523375 original size:22 final size:23
Alignment explanation
Indices: 523349--523398 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 23
523339 ATTTTTCTAC
523349 ATTAT-AATATAAATATA-ATTAT
1 ATTATAAATATAAATATATA-TAT
*
523371 ATTATACAATATGAATATATATAT
1 ATTATA-AATATAAATATATATAT
523395 ATTA
1 ATTA
523399 AATTTTATAT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
22 5 0.21
24 18 0.75
25 1 0.04
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (23 bp):
ATTATAAATATAAATATATATAT
Found at i:523440 original size:20 final size:20
Alignment explanation
Indices: 523417--523463 Score: 71
Period size: 19 Copynumber: 2.4 Consensus size: 20
523407 ATAAAATAAA
523417 TTATTAACATATA-AAAATTT
1 TTATTAA-ATATATAAAATTT
523437 TTA-TAAATATATAAAATTT
1 TTATTAAATATATAAAATTT
523456 TTATTAAA
1 TTATTAAA
523464 AATAGCATAA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
18 5 0.20
19 13 0.52
20 7 0.28
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (20 bp):
TTATTAAATATATAAAATTT
Found at i:523798 original size:23 final size:23
Alignment explanation
Indices: 523751--523806 Score: 69
Period size: 23 Copynumber: 2.4 Consensus size: 23
523741 AATATATCAT
* *
523751 AAATATAATATAAAAAATAATTA
1 AAATATTATATAAAAAATAAATA
523774 AAATATTATATAATAAAA-AAATA
1 AAATATTATATAA-AAAATAAATA
523797 AATATATTAT
1 AA-ATATTAT
523807 GAATACACTA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
23 18 0.62
24 11 0.38
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (23 bp):
AAATATTATATAAAAAATAAATA
Found at i:523811 original size:23 final size:23
Alignment explanation
Indices: 523749--523811 Score: 60
Period size: 23 Copynumber: 2.7 Consensus size: 23
523739 TAAATATATC
*
523749 ATAAATATAATATAA-AAAATAA
1 ATAAATATATTATAATAAAATAA
*
523771 TTAAA-ATATTATATAATAAAA-AA
1 ATAAATATA-T-TATAATAAAATAA
523794 ATAAATATATTATGAATA
1 ATAAATATATTAT-AATA
523812 CACTAATATC
Statistics
Matches: 33, Mismatches: 3, Indels: 9
0.73 0.07 0.20
Matches are distributed among these distances:
21 3 0.09
22 7 0.21
23 16 0.48
24 7 0.21
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (23 bp):
ATAAATATATTATAATAAAATAA
Found at i:524503 original size:28 final size:27
Alignment explanation
Indices: 524450--524503 Score: 65
Period size: 28 Copynumber: 2.0 Consensus size: 27
524440 TATTAAAAAA
* *
524450 TTATTTTATATTAAAATTTTTATATTT
1 TTATTTTAAATTAAAATTATTATATTT
524477 TTATTATTAAATTAAAAATTATT-TATT
1 TTATT-TTAAATT-AAAATTATTATATT
524504 AAATAATAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
27 5 0.22
28 10 0.43
29 8 0.35
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (27 bp):
TTATTTTAAATTAAAATTATTATATTT
Found at i:524518 original size:18 final size:19
Alignment explanation
Indices: 524480--524519 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
524470 TATATTTTTA
*
524480 TTATTAAATTAAAAATTAT
1 TTATTAAATTAAAAATAAT
*
524499 TTATTAAA-TAATAATAAT
1 TTATTAAATTAAAAATAAT
524517 TTA
1 TTA
524520 AATAAAATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 11 0.58
19 8 0.42
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (19 bp):
TTATTAAATTAAAAATAAT
Found at i:524596 original size:17 final size:15
Alignment explanation
Indices: 524563--524608 Score: 56
Period size: 16 Copynumber: 2.9 Consensus size: 15
524553 TAAAACTTAT
524563 TAATTTAAAATAATC
1 TAATTTAAAATAATC
*
524578 TAATTTATAAATAGGTC
1 TAATTTA-AAATA-ATC
*
524595 TAATTTAAATTAAT
1 TAATTTAAAATAAT
524609 TTCATTAGAT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
15 8 0.31
16 9 0.35
17 9 0.35
ACGTcount: A:0.48, C:0.04, G:0.04, T:0.43
Consensus pattern (15 bp):
TAATTTAAAATAATC
Found at i:524951 original size:3 final size:3
Alignment explanation
Indices: 524943--524982 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
524933 AAAGAACATT
524943 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
524983 GCGTCTGGTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:528088 original size:37 final size:36
Alignment explanation
Indices: 528035--528133 Score: 135
Period size: 37 Copynumber: 2.7 Consensus size: 36
528025 TTTATTTTTC
* *
528035 GTGGATTGACATTGCCACCCAAATTCTAACAATCATA
1 GTGGATTGGCA-TGCCACCCAAATACTAACAATCATA
*
528072 GTGGATTGGCACTGCCACTCAAATACTAACAATCATA
1 GTGGATTGGCA-TGCCACCCAAATACTAACAATCATA
*
528109 GTGGATTGGTCAAGCCACCCAAATA
1 GTGGATTGG-CATGCCACCCAAATA
528134 TTACTTTTCG
Statistics
Matches: 55, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
37 53 0.96
38 2 0.04
ACGTcount: A:0.34, C:0.24, G:0.17, T:0.24
Consensus pattern (36 bp):
GTGGATTGGCATGCCACCCAAATACTAACAATCATA
Found at i:530246 original size:27 final size:27
Alignment explanation
Indices: 530208--530276 Score: 120
Period size: 27 Copynumber: 2.6 Consensus size: 27
530198 GGTTAAAAAC
530208 GGGGTTGGAGTGTCCCCTCGAAGGAAT
1 GGGGTTGGAGTGTCCCCTCGAAGGAAT
* *
530235 GGGGTTGGAGTGTTCCCTCGGAGGAAT
1 GGGGTTGGAGTGTCCCCTCGAAGGAAT
530262 GGGGTTGGAGTGTCC
1 GGGGTTGGAGTGTCC
530277 TCGACAATGA
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 39 1.00
ACGTcount: A:0.14, C:0.16, G:0.45, T:0.25
Consensus pattern (27 bp):
GGGGTTGGAGTGTCCCCTCGAAGGAAT
Found at i:532670 original size:21 final size:20
Alignment explanation
Indices: 532644--532682 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
532634 GTTGGGACCT
*
532644 TGTATCGATGCATTCTAGAAA
1 TGTATCGATACATT-TAGAAA
532665 TGTATCGATACATTTAGA
1 TGTATCGATACATTTAGA
532683 CAAAATGTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.33, C:0.13, G:0.18, T:0.36
Consensus pattern (20 bp):
TGTATCGATACATTTAGAAA
Found at i:536418 original size:37 final size:37
Alignment explanation
Indices: 536365--536446 Score: 110
Period size: 37 Copynumber: 2.2 Consensus size: 37
536355 TTTATTTTTC
* * *
536365 GTGGATTGGCGCTGCCACCCAAATTCTAACAATCATA
1 GTGGATTGGCACTGCCACCCAAATACTAACAATCACA
* *
536402 GTGGATTGGCATTGCCATCCAAATACTAACAATCACA
1 GTGGATTGGCACTGCCACCCAAATACTAACAATCACA
*
536439 GGGGATTG
1 GTGGATTG
536447 ACCAAGCCAC
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
37 39 1.00
ACGTcount: A:0.30, C:0.23, G:0.22, T:0.24
Consensus pattern (37 bp):
GTGGATTGGCACTGCCACCCAAATACTAACAATCACA
Found at i:536462 original size:37 final size:37
Alignment explanation
Indices: 536378--536463 Score: 86
Period size: 37 Copynumber: 2.3 Consensus size: 37
536368 GATTGGCGCT
* * * * * *
536378 GCCACCCAAATTCTAACAATCATAGTGGATTGGCATT
1 GCCACTCAAATACTAACAATCACAGGGGATTGCCATA
536415 GCCA-TCCAAATACTAACAATCACAGGGGATTGACCA-A
1 GCCACT-CAAATACTAACAATCACAGGGGATTG-CCATA
536452 GCCACTCAAATA
1 GCCACTCAAATA
536464 TTACTTTTCA
Statistics
Matches: 40, Mismatches: 6, Indels: 6
0.77 0.12 0.12
Matches are distributed among these distances:
37 37 0.93
38 3 0.08
ACGTcount: A:0.37, C:0.27, G:0.15, T:0.21
Consensus pattern (37 bp):
GCCACTCAAATACTAACAATCACAGGGGATTGCCATA
Found at i:537865 original size:20 final size:19
Alignment explanation
Indices: 537836--537873 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
537826 TTTATATAGA
537836 TTAAAATTTAAATAAATTT
1 TTAAAATTTAAATAAATTT
*
537855 TTAATAATTTAAATCAATT
1 TTAA-AATTTAAATAAATT
537874 CGATTTAATC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (19 bp):
TTAAAATTTAAATAAATTT
Found at i:537921 original size:24 final size:26
Alignment explanation
Indices: 537892--537940 Score: 75
Period size: 24 Copynumber: 2.0 Consensus size: 26
537882 TCTTAATTAT
537892 AATTTAATAATAAAAA-AT-TATTTA
1 AATTTAATAATAAAAATATATATTTA
*
537916 AATTTAATTATAAAAATATATATTT
1 AATTTAATAATAAAAATATATATTT
537941 TTATATAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 15 0.68
25 2 0.09
26 5 0.23
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (26 bp):
AATTTAATAATAAAAATATATATTTA
Found at i:537964 original size:18 final size:21
Alignment explanation
Indices: 537918--537964 Score: 57
Period size: 18 Copynumber: 2.4 Consensus size: 21
537908 ATTATTTAAA
537918 TTTAATTATAAAAATATATATT
1 TTTAA-TATAAAAATATATATT
537940 TTT-ATAT-AAAATA-AT-TT
1 TTTAATATAAAAATATATATT
537957 TTTAATAT
1 TTTAATAT
537965 TATTTAAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
17 5 0.21
18 6 0.25
19 6 0.25
20 3 0.12
21 1 0.04
22 3 0.12
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (21 bp):
TTTAATATAAAAATATATATT
Found at i:538256 original size:13 final size:13
Alignment explanation
Indices: 538238--538262 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
538228 TTATTTTTTA
538238 ATATTTATTATAG
1 ATATTTATTATAG
538251 ATATTTATTATA
1 ATATTTATTATA
538263 ATTAATTATG
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:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (13 bp):
ATATTTATTATAG
Found at i:540971 original size:3 final size:3
Alignment explanation
Indices: 540963--540997 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
540953 ACTGCAATAT
540963 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
540998 TGATATAAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:542629 original size:19 final size:21
Alignment explanation
Indices: 542586--542629 Score: 60
Period size: 19 Copynumber: 2.3 Consensus size: 21
542576 TATCATGTTA
542586 TAAT-TTTATTTAAAATATTT
1 TAATATTTATTTAAAATATTT
542606 T-ATATTTATTT-AAAT-TTT
1 TAATATTTATTTAAAATATTT
542624 TAATAT
1 TAATAT
542630 ATTAATAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
18 4 0.18
19 10 0.45
20 8 0.36
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (21 bp):
TAATATTTATTTAAAATATTT
Found at i:542639 original size:18 final size:17
Alignment explanation
Indices: 542618--542673 Score: 55
Period size: 18 Copynumber: 3.3 Consensus size: 17
542608 TATTTATTTA
542618 AATTTTTAATATATTAAT
1 AATTTTT-ATATATTAAT
542636 AA--TTTATAT-TTATAT
1 AATTTTTATATATTA-AT
*
542651 AAATTTTGATATATTAAT
1 -AATTTTTATATATTAAT
542669 AATTT
1 AATTT
542674 ATATTATATA
Statistics
Matches: 32, Mismatches: 1, Indels: 11
0.73 0.02 0.25
Matches are distributed among these distances:
14 3 0.09
15 6 0.19
16 5 0.16
17 5 0.16
18 10 0.31
19 3 0.09
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (17 bp):
AATTTTTATATATTAAT
Found at i:542641 original size:16 final size:16
Alignment explanation
Indices: 542622--542674 Score: 56
Period size: 16 Copynumber: 3.2 Consensus size: 16
542612 TATTTAAATT
542622 TTTAATATATTAATAA
1 TTTAATATATTAATAA
542638 TTT-ATAT-TTATATAAA
1 TTTAATATATTA-AT-AA
*
542654 TTTTGATATATTAATAA
1 -TTTAATATATTAATAA
542671 TTTA
1 TTTA
542675 TATTATATAA
Statistics
Matches: 31, Mismatches: 1, Indels: 10
0.74 0.02 0.24
Matches are distributed among these distances:
14 3 0.10
15 6 0.19
16 8 0.26
17 5 0.16
18 6 0.19
19 3 0.10
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (16 bp):
TTTAATATATTAATAA
Found at i:542687 original size:15 final size:15
Alignment explanation
Indices: 542627--542688 Score: 51
Period size: 15 Copynumber: 4.1 Consensus size: 15
542617 AAATTTTTAA
542627 TATATTA-AT-AATT
1 TATATTATATAAATT
542640 TATATTTATATAAATT
1 TATA-TTATATAAATT
542656 T-TGA-TATATTAATAATT
1 TAT-ATTATA-T-A-AATT
542673 TATATTATATAAATT
1 TATATTATATAAATT
542688 T
1 T
542689 TAAAATATTT
Statistics
Matches: 40, Mismatches: 0, Indels: 16
0.71 0.00 0.29
Matches are distributed among these distances:
13 4 0.10
14 7 0.17
15 9 0.22
16 8 0.20
17 7 0.17
18 5 0.12
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.55
Consensus pattern (15 bp):
TATATTATATAAATT
Found at i:542710 original size:33 final size:33
Alignment explanation
Indices: 542599--542697 Score: 146
Period size: 33 Copynumber: 3.0 Consensus size: 33
542589 TTTTATTTAA
* *
542599 AATATTTTATATTTATTTAAATTTTTAATATATT
1 AATAATTTATATTTATATAAA-TTTTAATATATT
*
542633 AATAATTTATATTTATATAAATTTTGATATATT
1 AATAATTTATATTTATATAAATTTTAATATATT
*
542666 AATAATTTATA-TTATATAAATTTTAAAATATT
1 AATAATTTATATTTATATAAATTTTAATATATT
542698 TCTATTTTTA
Statistics
Matches: 60, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
32 19 0.32
33 22 0.37
34 19 0.32
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.56
Consensus pattern (33 bp):
AATAATTTATATTTATATAAATTTTAATATATT
Found at i:542734 original size:19 final size:19
Alignment explanation
Indices: 542692--542739 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
542682 TAAATTTTAA
*
542692 AATATTTCTATTTTTATAT
1 AATATTTATATTTTTATAT
*
542711 CATATTTATATTTTT-TATT
1 AATATTTATATTTTTATA-T
542730 AATATTTATA
1 AATATTTATA
542740 CTTATAATTA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
18 2 0.08
19 23 0.92
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.62
Consensus pattern (19 bp):
AATATTTATATTTTTATAT
Found at i:542893 original size:22 final size:22
Alignment explanation
Indices: 542863--542904 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
542853 GAAAAATACA
542863 TTTTATTTTATTTTGTCATTCC
1 TTTTATTTTATTTTGTCATTCC
* * *
542885 TTTTTTTTTTTTTTTTCATT
1 TTTTATTTTATTTTGTCATT
542905 TAGTTCTTCT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.10, C:0.10, G:0.02, T:0.79
Consensus pattern (22 bp):
TTTTATTTTATTTTGTCATTCC
Found at i:543049 original size:21 final size:20
Alignment explanation
Indices: 543024--543065 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
543014 ATTTTATGAA
543024 TATTTGATATTTGTATATATT
1 TATTTGATATTTGTAT-TATT
* *
543045 TATTTTATATTTTTATTATT
1 TATTTGATATTTGTATTATT
543065 T
1 T
543066 TCATATTATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 5 0.26
21 14 0.74
ACGTcount: A:0.26, C:0.00, G:0.05, T:0.69
Consensus pattern (20 bp):
TATTTGATATTTGTATTATT
Found at i:543122 original size:14 final size:14
Alignment explanation
Indices: 543103--543132 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
543093 TTATTTTTAT
*
543103 TTTATTTTAAATAA
1 TTTATTTTAAAAAA
543117 TTTATTTTAAAAAA
1 TTTATTTTAAAAAA
543131 TT
1 TT
543133 AATCTCACAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (14 bp):
TTTATTTTAAAAAA
Found at i:543867 original size:19 final size:19
Alignment explanation
Indices: 543843--543903 Score: 106
Period size: 19 Copynumber: 3.3 Consensus size: 19
543833 TTAATGATAA
543843 TTTTTTTTAAGTTTTCCTT
1 TTTTTTTTAAGTTTTCCTT
543862 TTTTTTTTAAGTTTTCCTT
1 TTTTTTTTAAGTTTTCCTT
*
543881 TTTTTTTTAA-TTTTCATT
1 TTTTTTTTAAGTTTTCCTT
543899 TTTTT
1 TTTTT
543904 CTTTTAATTT
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
18 12 0.29
19 29 0.71
ACGTcount: A:0.11, C:0.08, G:0.03, T:0.77
Consensus pattern (19 bp):
TTTTTTTTAAGTTTTCCTT
Found at i:543868 original size:20 final size:18
Alignment explanation
Indices: 543843--543914 Score: 99
Period size: 19 Copynumber: 3.8 Consensus size: 18
543833 TTAATGATAA
543843 TTTTTTTTAAGTTTTCCTT
1 TTTTTTTTAA-TTTTCCTT
543862 TTTTTTTTAAGTTTTCCTT
1 TTTTTTTTAA-TTTTCCTT
*
543881 TTTTTTTTAATTTTCATTT
1 TTTTTTTTAATTTTC-CTT
543900 TTTTCTTTTAATTTT
1 TTTT-TTTTAATTTT
543915 AAATTGATCC
Statistics
Matches: 50, Mismatches: 1, Indels: 3
0.93 0.02 0.06
Matches are distributed among these distances:
18 5 0.10
19 35 0.70
20 10 0.20
ACGTcount: A:0.12, C:0.08, G:0.03, T:0.76
Consensus pattern (18 bp):
TTTTTTTTAATTTTCCTT
Found at i:544232 original size:26 final size:25
Alignment explanation
Indices: 544187--544252 Score: 73
Period size: 26 Copynumber: 2.6 Consensus size: 25
544177 TTTTTTAAAA
*
544187 AAATTAA-TAAATAATTATTTAGTA-
1 AAATTAATTAAA-AATAATTTAGTAT
*
544211 AAATTTAATTTAAAAATAATTTATTAT
1 AAA-TTAA-TTAAAAATAATTTAGTAT
544238 AAATTAATTAAAAAT
1 AAATTAATTAAAAAT
544253 TTAAAAAACC
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
24 3 0.08
25 12 0.33
26 14 0.39
27 7 0.19
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (25 bp):
AAATTAATTAAAAATAATTTAGTAT
Found at i:550928 original size:15 final size:15
Alignment explanation
Indices: 550905--550940 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
550895 TTAAATATGA
* *
550905 TATTAATTTAATTTT
1 TATTTATTTAAATTT
550920 TATTTATTTAAATTT
1 TATTTATTTAAATTT
550935 TATTTA
1 TATTTA
550941 AATTTATTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (15 bp):
TATTTATTTAAATTT
Found at i:550939 original size:21 final size:21
Alignment explanation
Indices: 550891--550948 Score: 55
Period size: 21 Copynumber: 2.7 Consensus size: 21
550881 GCGATTGAGG
*
550891 TAATTTAAATATGATATT-AATT
1 TAATTTAAAT-TTAT-TTAAATT
**
550913 TAATTTTTATTTATTTAAATT
1 TAATTTAAATTTATTTAAATT
*
550934 TTATTTAAATTTATT
1 TAATTTAAATTTATT
550949 AATAATTATA
Statistics
Matches: 29, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
20 2 0.07
21 19 0.66
22 8 0.28
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (21 bp):
TAATTTAAATTTATTTAAATT
Found at i:550982 original size:14 final size:14
Alignment explanation
Indices: 550891--550993 Score: 54
Period size: 14 Copynumber: 7.1 Consensus size: 14
550881 GCGATTGAGG
550891 TAATTTAAATATGATAT
1 TAATTTAAAT-T-AT-T
*
550908 TAATTTAATTTTTATT
1 TAATTTAA--ATTATT
550924 T-ATTTAAA-T-TT
1 TAATTTAAATTATT
550935 T-ATTTAAATTTATT
1 TAATTTAAA-TTATT
**
550949 AATAATTATAAA-TAGA
1 --TAATT-TAAATTATT
550965 TAATTTAAATTATT
1 TAATTTAAATTATT
*
550979 TAATTTATATTATT
1 TAATTTAAATTATT
550993 T
1 T
550994 TTTAATATAT
Statistics
Matches: 69, Mismatches: 7, Indels: 23
0.70 0.07 0.23
Matches are distributed among these distances:
11 10 0.14
12 1 0.01
13 5 0.07
14 23 0.33
15 6 0.09
16 5 0.07
17 13 0.19
18 5 0.07
19 1 0.01
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (14 bp):
TAATTTAAATTATT
Found at i:551096 original size:12 final size:13
Alignment explanation
Indices: 551068--551097 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
551058 AATATAATTG
551068 TAATATTTTATTA
1 TAATATTTTATTA
551081 TAATATTTTA-TA
1 TAATATTTTATTA
551093 TAATA
1 TAATA
551098 AAAATTATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 7 0.41
13 10 0.59
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (13 bp):
TAATATTTTATTA
Found at i:551146 original size:16 final size:16
Alignment explanation
Indices: 551069--551146 Score: 58
Period size: 16 Copynumber: 4.9 Consensus size: 16
551059 ATATAATTGT
551069 AATATTTTAT-T-AT-
1 AATATTTTATATAATA
551082 AATATTTTATATAATAAA
1 AATATTTTATATAAT--A
*
551100 AATTATTTAATATAA-A
1 AA-TATTTTATATAATA
*
551116 AATATATTA-ATTAATA
1 AATATTTTATA-TAATA
*
551132 TATATTTTATATAAT
1 AATATTTTATATAAT
551147 TATAAAATAA
Statistics
Matches: 51, Mismatches: 5, Indels: 15
0.72 0.07 0.21
Matches are distributed among these distances:
13 10 0.20
14 2 0.04
15 10 0.20
16 15 0.29
17 1 0.02
18 2 0.04
19 11 0.22
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
AATATTTTATATAATA
Found at i:551577 original size:25 final size:28
Alignment explanation
Indices: 551548--551600 Score: 76
Period size: 27 Copynumber: 2.0 Consensus size: 28
551538 GTAAAGTGTA
551548 TAAAATA-ATA-ATTTTATA-TAAATTT
1 TAAAATATATATATTTTATATTAAATTT
*
551573 TAAAATATGTATATTTTATATTAAATTT
1 TAAAATATATATATTTTATATTAAATTT
551601 ATATTATTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
25 7 0.29
26 2 0.08
27 8 0.33
28 7 0.29
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (28 bp):
TAAAATATATATATTTTATATTAAATTT
Found at i:554984 original size:28 final size:28
Alignment explanation
Indices: 554932--554985 Score: 67
Period size: 28 Copynumber: 1.9 Consensus size: 28
554922 ATTTACATAA
*
554932 TTATATTAAAATCTAATTTATTTATTAT
1 TTATATTAAAATCTAATTTAATTATTAT
554960 TTATATT-AAAT-TAATATATAATTATT
1 TTATATTAAAATCTAAT-T-TAATTATT
554986 TAAATTTGAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
26 4 0.17
27 5 0.22
28 14 0.61
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.56
Consensus pattern (28 bp):
TTATATTAAAATCTAATTTAATTATTAT
Found at i:555008 original size:25 final size:24
Alignment explanation
Indices: 554904--555008 Score: 58
Period size: 25 Copynumber: 4.3 Consensus size: 24
554894 ATAGTTTTTT
* * *
554904 TATAATATTTAAATTTAAATTTACA
1 TATATTATTTAAA-TTAAATTAATA
554929 TA-ATTATATTAAAATCT-AATT--TA
1 TATATTAT-TT-AAAT-TAAATTAATA
* *
554952 TTTATTATTTATATTAAATTAATA
1 TATATTATTTAAATTAAATTAATA
*
554976 TATAATTATTTAAATTTGAATTAA-A
1 TAT-ATTATTTAAA-TTAAATTAATA
555001 TAATATTA
1 T-ATATTA
555009 GTCATTGAAT
Statistics
Matches: 63, Mismatches: 7, Indels: 20
0.70 0.08 0.22
Matches are distributed among these distances:
21 1 0.02
22 7 0.11
23 4 0.06
24 13 0.21
25 24 0.38
26 14 0.22
ACGTcount: A:0.47, C:0.02, G:0.01, T:0.50
Consensus pattern (24 bp):
TATATTATTTAAATTAAATTAATA
Found at i:555335 original size:3 final size:3
Alignment explanation
Indices: 555329--555359 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
555319 ATCATCATCT
555329 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
555360 ATGATATACA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:559097 original size:12 final size:13
Alignment explanation
Indices: 559080--559108 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
559070 AGGGTTGAAT
559080 TGGAAGTGGAAA-
1 TGGAAGTGGAAAG
559092 TGGAAGTGGAAAG
1 TGGAAGTGGAAAG
559105 TGGA
1 TGGA
559109 TGAGTTGTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.38, C:0.00, G:0.45, T:0.17
Consensus pattern (13 bp):
TGGAAGTGGAAAG
Found at i:560240 original size:22 final size:22
Alignment explanation
Indices: 560209--560250 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
560199 CAATCTGTAA
560209 TATATCAATACAAAAAAAAGCT
1 TATATCAATACAAAAAAAAGCT
* *
560231 TATATGAATACAATAAAAAG
1 TATATCAATACAAAAAAAAG
560251 TTTCAAAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.60, C:0.10, G:0.07, T:0.24
Consensus pattern (22 bp):
TATATCAATACAAAAAAAAGCT
Found at i:560470 original size:21 final size:20
Alignment explanation
Indices: 560428--560470 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
560418 AAAACTTTTG
*
560428 AAATATTTTAACATCTTTTA
1 AAATATTTTAACATCATTTA
560448 AAATATTTTCAA-ATTCATTTA
1 AAATATTTT-AACA-TCATTTA
560469 AA
1 AA
560471 GAAAAATATT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 10 0.50
21 10 0.50
ACGTcount: A:0.44, C:0.09, G:0.00, T:0.47
Consensus pattern (20 bp):
AAATATTTTAACATCATTTA
Found at i:566365 original size:6 final size:6
Alignment explanation
Indices: 566356--566383 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
566346 GAATTTGAAA
566356 ATTTGG ATTTGG ATTTGG ATTTGG ATTT
1 ATTTGG ATTTGG ATTTGG ATTTGG ATTT
566384 CATCTGTTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.18, C:0.00, G:0.29, T:0.54
Consensus pattern (6 bp):
ATTTGG
Found at i:566788 original size:6 final size:6
Alignment explanation
Indices: 566777--566812 Score: 72
Period size: 6 Copynumber: 6.0 Consensus size: 6
566767 CAAAATGAAC
566777 TCCAAA TCCAAA TCCAAA TCCAAA TCCAAA TCCAAA
1 TCCAAA TCCAAA TCCAAA TCCAAA TCCAAA TCCAAA
566813 ATTTCAAATT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.50, C:0.33, G:0.00, T:0.17
Consensus pattern (6 bp):
TCCAAA
Found at i:567385 original size:3 final size:3
Alignment explanation
Indices: 567377--567435 Score: 82
Period size: 3 Copynumber: 19.7 Consensus size: 3
567367 TGAGCTTGTG
* * *
567377 TTA TTA TTA TTA TTG TTG TTA TTA TTA TTA TTA TTA TTA TTA TTG TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
567425 TTG TTA TTA TT
1 TTA TTA TTA TT
567436 TCCTATGACT
Statistics
Matches: 50, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 50 1.00
ACGTcount: A:0.25, C:0.00, G:0.07, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:567398 original size:15 final size:15
Alignment explanation
Indices: 567375--567435 Score: 95
Period size: 15 Copynumber: 4.1 Consensus size: 15
567365 GGTGAGCTTG
567375 TGTTATTATTATTAT
1 TGTTATTATTATTAT
*
567390 TGTTGTTATTATTAT
1 TGTTATTATTATTAT
*
567405 TATTATTATTATTAT
1 TGTTATTATTATTAT
*
567420 TGTTATTGTTATTAT
1 TGTTATTATTATTAT
567435 T
1 T
567436 TCCTATGACT
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 41 1.00
ACGTcount: A:0.25, C:0.00, G:0.08, T:0.67
Consensus pattern (15 bp):
TGTTATTATTATTAT
Found at i:570718 original size:16 final size:15
Alignment explanation
Indices: 570697--570731 Score: 52
Period size: 16 Copynumber: 2.3 Consensus size: 15
570687 TTTTATTTTG
570697 ATATTAATATGTATTA
1 ATATTAATAT-TATTA
*
570713 ATATTAATATTTTTA
1 ATATTAATATTATTA
570728 ATAT
1 ATAT
570732 ATTATTTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 8 0.44
16 10 0.56
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (15 bp):
ATATTAATATTATTA
Found at i:570735 original size:17 final size:16
Alignment explanation
Indices: 570713--570778 Score: 68
Period size: 14 Copynumber: 4.2 Consensus size: 16
570703 ATATGTATTA
*
570713 ATATTAATATTTTTAAT
1 ATATT-ATATTTTAAAT
570730 ATA-T-TATTTTAAAT
1 ATATTATATTTTAAAT
570744 ATATTGATATTTTAAA-
1 ATATT-ATATTTTAAAT
*
570760 ATA-TATTTTTTAAAT
1 ATATTATATTTTAAAT
570775 ATAT
1 ATAT
570779 ATAATTTATT
Statistics
Matches: 42, Mismatches: 2, Indels: 11
0.76 0.04 0.20
Matches are distributed among these distances:
14 21 0.50
15 5 0.12
16 4 0.10
17 12 0.29
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (16 bp):
ATATTATATTTTAAAT
Found at i:570754 original size:31 final size:31
Alignment explanation
Indices: 570713--570783 Score: 99
Period size: 31 Copynumber: 2.3 Consensus size: 31
570703 ATATGTATTA
*
570713 ATATTAATATTTT-TAATATATTATTTTAAAT
1 ATATTAATATTTTAAAATATATT-TTTTAAAT
*
570744 ATATTGATATTTTAAAATATATTTTTTAAAT
1 ATATTAATATTTTAAAATATATTTTTTAAAT
570775 ATATATAAT
1 ATAT-TAAT
570784 TTATTTTCAA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
31 24 0.69
32 11 0.31
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.55
Consensus pattern (31 bp):
ATATTAATATTTTAAAATATATTTTTTAAAT
Found at i:570785 original size:18 final size:17
Alignment explanation
Indices: 570728--570781 Score: 53
Period size: 17 Copynumber: 3.3 Consensus size: 17
570718 AATATTTTTA
570728 ATATATTATTTTAAATAT
1 ATATATT-TTTTAAATAT
*
570746 AT-TGATATTTT-AA-A-
1 ATAT-ATTTTTTAAATAT
570760 ATATATTTTTTAAATAT
1 ATATATTTTTTAAATAT
570777 ATATA
1 ATATA
570782 ATTTATTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 11
0.69 0.05 0.26
Matches are distributed among these distances:
14 8 0.28
15 4 0.14
16 3 0.10
17 10 0.34
18 4 0.14
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (17 bp):
ATATATTTTTTAAATAT
Found at i:570872 original size:26 final size:27
Alignment explanation
Indices: 570843--570904 Score: 67
Period size: 26 Copynumber: 2.3 Consensus size: 27
570833 TAAATATTTA
570843 ATATTATATTTAA-AGTAATT-ATAATT-
1 ATATTATATTTAATA-T-ATTAATAATTC
* *
570869 ATATAAAATTTAATATATTAATAATTC
1 ATATTATATTTAATATATTAATAATTC
570896 ATATTATAT
1 ATATTATAT
570905 AACTTTTAAG
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
25 3 0.10
26 18 0.62
27 8 0.28
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (27 bp):
ATATTATATTTAATATATTAATAATTC
Found at i:570894 original size:16 final size:17
Alignment explanation
Indices: 570858--570906 Score: 52
Period size: 16 Copynumber: 3.0 Consensus size: 17
570848 ATATTTAAAG
570858 TAATTATAATTATATAA
1 TAATTATAATTATATAA
570875 -AATT-TAA-TATATTAA
1 TAATTATAATTATA-TAA
570890 TAATTCAT-ATTATATAA
1 TAATT-ATAATTATATAA
570907 CTTTTAAGAC
Statistics
Matches: 27, Mismatches: 0, Indels: 10
0.73 0.00 0.27
Matches are distributed among these distances:
14 4 0.15
15 6 0.22
16 8 0.30
17 4 0.15
18 5 0.19
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (17 bp):
TAATTATAATTATATAA
Found at i:571041 original size:18 final size:18
Alignment explanation
Indices: 571003--571037 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
570993 TATTTTTATT
*
571003 TAAATTTTAATTATAAAA
1 TAAATATTAATTATAAAA
571021 TAAATATTAA-TATAAAA
1 TAAATATTAATTATAAAA
571038 ATAATTTTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (18 bp):
TAAATATTAATTATAAAA
Found at i:571047 original size:17 final size:18
Alignment explanation
Indices: 571003--571047 Score: 58
Period size: 17 Copynumber: 2.6 Consensus size: 18
570993 TATTTTTATT
571003 TAAATTTTAATTATAAAA
1 TAAATTTTAATTATAAAA
*
571021 TAAATATTAA-TATAAAA
1 TAAATTTTAATTATAAAA
571038 -ATAATTTTAA
1 TA-AATTTTAA
571048 AAATTTTGTA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
16 1 0.04
17 14 0.58
18 9 0.38
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (18 bp):
TAAATTTTAATTATAAAA
Found at i:579798 original size:2 final size:2
Alignment explanation
Indices: 579793--579826 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
579783 ATTTTTTAGG
*
579793 TA TA TA TA TA CA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
579827 GCCTTCTTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:580015 original size:6 final size:6
Alignment explanation
Indices: 580004--580046 Score: 52
Period size: 6 Copynumber: 7.3 Consensus size: 6
579994 TTAAAAAATA
* * *
580004 TATATT TATATT AATATT TATATA TAT-TT TATAAT TATATT TA
1 TATATT TATATT TATATT TATATT TATATT TATATT TATATT TA
580047 AATAAAAATA
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
5 4 0.13
6 26 0.87
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (6 bp):
TATATT
Found at i:584062 original size:19 final size:19
Alignment explanation
Indices: 584034--584073 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
584024 TATAACTTAT
584034 AAGCACTAAACATAATTAC
1 AAGCACTAAACATAATTAC
* *
584053 AAGCATTAAACATAGTTAC
1 AAGCACTAAACATAATTAC
584072 AA
1 AA
584074 ATACAAGCGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.53, C:0.17, G:0.07, T:0.23
Consensus pattern (19 bp):
AAGCACTAAACATAATTAC
Found at i:586473 original size:2 final size:2
Alignment explanation
Indices: 586468--586493 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
586458 ACACACACAC
586468 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
586494 CTTCGACATG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:587274 original size:28 final size:29
Alignment explanation
Indices: 587230--587284 Score: 69
Period size: 28 Copynumber: 1.9 Consensus size: 29
587220 TTAATTGAAC
*
587230 TGATTAAACTGAATTTAA-TCAATTTTTT
1 TGATTAAACTGAATTTAACTAAATTTTTT
*
587258 TGATTAAA-TTAATTTTAACTAAATTTT
1 TGATTAAACTGAA-TTTAACTAAATTTT
587285 ACTTTTTCCT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
27 3 0.13
28 13 0.57
29 7 0.30
ACGTcount: A:0.38, C:0.05, G:0.05, T:0.51
Consensus pattern (29 bp):
TGATTAAACTGAATTTAACTAAATTTTTT
Found at i:588027 original size:6 final size:6
Alignment explanation
Indices: 588016--588054 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
588006 CGCATTGTCG
* * *
588016 TTCATA TTCATA TTCATA TTCGTA TTCGTA TTCGTA TTC
1 TTCATA TTCATA TTCATA TTCATA TTCATA TTCATA TTC
588055 TTCATCAATA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.23, C:0.18, G:0.08, T:0.51
Consensus pattern (6 bp):
TTCATA
Found at i:588033 original size:12 final size:12
Alignment explanation
Indices: 588016--588054 Score: 60
Period size: 12 Copynumber: 3.2 Consensus size: 12
588006 CGCATTGTCG
*
588016 TTCATATTCATA
1 TTCATATTCGTA
588028 TTCATATTCGTA
1 TTCATATTCGTA
*
588040 TTCGTATTCGTA
1 TTCATATTCGTA
588052 TTC
1 TTC
588055 TTCATCAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.23, C:0.18, G:0.08, T:0.51
Consensus pattern (12 bp):
TTCATATTCGTA
Found at i:588499 original size:2 final size:2
Alignment explanation
Indices: 588492--588526 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
588482 TTTAAAATCT
588492 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
588527 GGTTTCTATG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:592581 original size:2 final size:2
Alignment explanation
Indices: 592574--592604 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
592564 AGCCAAGGAC
592574 AT AT 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 AT AT A
592605 AGCCAAAAGG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:594482 original size:19 final size:17
Alignment explanation
Indices: 594456--594508 Score: 67
Period size: 15 Copynumber: 3.2 Consensus size: 17
594446 TATAAAAAAT
594456 AATATAAAATTATATAA
1 AATATAAAATTATATAA
594473 ATATATTAAAATT-TATAA
1 A-ATA-TAAAATTATATAA
594491 AATAT-AAATTAT-TAA
1 AATATAAAATTATATAA
594506 AAT
1 AAT
594509 TTTATTTATA
Statistics
Matches: 33, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
15 11 0.33
16 2 0.06
17 4 0.12
18 9 0.27
19 7 0.21
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (17 bp):
AATATAAAATTATATAA
Found at i:594712 original size:17 final size:18
Alignment explanation
Indices: 594683--594718 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
594673 AAAATTTTAT
*
594683 TTTAAAAATATTCACATA
1 TTTAAAAATATTCAAATA
594701 TTTAAAAA-ATTCAAATA
1 TTTAAAAATATTCAAATA
594718 T
1 T
594719 AAAATAATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 9 0.53
18 8 0.47
ACGTcount: A:0.53, C:0.08, G:0.00, T:0.39
Consensus pattern (18 bp):
TTTAAAAATATTCAAATA
Found at i:595837 original size:12 final size:12
Alignment explanation
Indices: 595796--595835 Score: 52
Period size: 10 Copynumber: 3.7 Consensus size: 12
595786 AAAACTATTT
595796 TAATATTTAAAA
1 TAATATTTAAAA
595808 TAATA--TAAAA
1 TAATATTTAAAA
595818 TAAT-TTT-AAA
1 TAATATTTAAAA
595828 TAATATTT
1 TAATATTT
595836 TATTATTTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 7
0.78 0.00 0.22
Matches are distributed among these distances:
10 16 0.64
11 4 0.16
12 5 0.20
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (12 bp):
TAATATTTAAAA
Found at i:595843 original size:20 final size:20
Alignment explanation
Indices: 595782--595843 Score: 54
Period size: 20 Copynumber: 3.1 Consensus size: 20
595772 TTTAAGTTAA
*
595782 TTTAAA-AACTATTTTAATAT
1 TTTAAATAA-TATTTTATTAT
* *** *
595802 TTAAAATAATATAAAATAAT
1 TTTAAATAATATTTTATTAT
595822 TTTAAATAATATTTTATTAT
1 TTTAAATAATATTTTATTAT
595842 TT
1 TT
595844 AAAACGTAAT
Statistics
Matches: 30, Mismatches: 11, Indels: 2
0.70 0.26 0.05
Matches are distributed among these distances:
20 28 0.93
21 2 0.07
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (20 bp):
TTTAAATAATATTTTATTAT
Found at i:597651 original size:15 final size:15
Alignment explanation
Indices: 597633--597676 Score: 56
Period size: 14 Copynumber: 2.9 Consensus size: 15
597623 TTAATCTAAA
597633 AAAATTATAAATATT
1 AAAATTATAAATATT
597648 AAAATT-TAAA-ATTT
1 AAAATTATAAATA-TT
597662 AAAATTATTAAATAT
1 AAAATTA-TAAATAT
597677 ATTTTTTAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 7
0.78 0.00 0.22
Matches are distributed among these distances:
13 1 0.04
14 12 0.48
15 6 0.24
16 5 0.20
17 1 0.04
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (15 bp):
AAAATTATAAATATT
Found at i:597657 original size:14 final size:15
Alignment explanation
Indices: 597633--597674 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
597623 TTAATCTAAA
597633 AAAATTAT-AAATATT
1 AAAATTATAAAAT-TT
597648 AAAATT-TAAAATTT
1 AAAATTATAAAATTT
*
597662 AAAATTATTAAAT
1 AAAATTATAAAAT
597675 ATATTTTTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
14 9 0.38
15 15 0.62
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (15 bp):
AAAATTATAAAATTT
Found at i:598348 original size:8 final size:8
Alignment explanation
Indices: 598335--598380 Score: 53
Period size: 8 Copynumber: 6.0 Consensus size: 8
598325 TTAGTGGCAG
598335 TTTATAAA
1 TTTATAAA
598343 TTTATAAA
1 TTTATAAA
*
598351 TTT-TTAA
1 TTTATAAA
598358 TTTATTAAA
1 TTTA-TAAA
598367 --TATAAA
1 TTTATAAA
598373 TTTATAAA
1 TTTATAAA
598381 AAATATAATA
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
6 4 0.12
7 8 0.25
8 17 0.53
9 3 0.09
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (8 bp):
TTTATAAA
Found at i:598361 original size:15 final size:14
Alignment explanation
Indices: 598337--598380 Score: 52
Period size: 15 Copynumber: 3.0 Consensus size: 14
598327 AGTGGCAGTT
598337 TATAAATTTATAAA
1 TATAAATTTATAAA
* *
598351 TTTTTAATTTATTAAA
1 -TATAAATTTA-TAAA
598367 TATAAATTTATAAA
1 TATAAATTTATAAA
598381 AAATATAATA
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
14 4 0.17
15 16 0.67
16 4 0.17
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
TATAAATTTATAAA
Found at i:599643 original size:11 final size:12
Alignment explanation
Indices: 599623--599675 Score: 54
Period size: 11 Copynumber: 4.2 Consensus size: 12
599613 ATATGGTATA
599623 AAAAATTAATAT
1 AAAAATTAATAT
599635 AAAAA-TAATAT
1 AAAAATTAATAT
*
599646 AAATTATTAATAT
1 AAA-AATTAATAT
*
599659 ATTAAAATTTATAT
1 A--AAAATTAATAT
599673 AAA
1 AAA
599676 TATATATTAT
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
11 9 0.26
12 8 0.24
13 7 0.21
14 8 0.24
15 2 0.06
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (12 bp):
AAAAATTAATAT
Found at i:599672 original size:27 final size:27
Alignment explanation
Indices: 599627--599709 Score: 70
Period size: 27 Copynumber: 3.2 Consensus size: 27
599617 GGTATAAAAA
*
599627 ATTAATATA--AAAA-TAATATAAATT
1 ATTAATATATTAAAATTTATATAAATT
599651 ATTAATATATTAAAATTTATATAAA-T
1 ATTAATATATTAAAATTTATATAAATT
* *
599677 ATATATTAT-TTTAAATTTAATATAATATT
1 AT-TAATATATTAAAATTT-ATATAA-ATT
599706 -TTAA
1 ATTAA
599710 ATAATATAAA
Statistics
Matches: 48, Mismatches: 4, Indels: 11
0.76 0.06 0.17
Matches are distributed among these distances:
24 9 0.19
26 15 0.31
27 21 0.44
28 2 0.04
29 1 0.02
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (27 bp):
ATTAATATATTAAAATTTATATAAATT
Found at i:599736 original size:55 final size:54
Alignment explanation
Indices: 599640--599752 Score: 133
Period size: 55 Copynumber: 2.1 Consensus size: 54
599630 AATATAAAAA
* * *
599640 TAATATAAATTATTAATATATTAAAATTTATATAAATATATATTATT-TTAAATT
1 TAATATAAATTATTAATATAATAAAATTGATATAAATATATA-AATTATTAAATT
*
599694 TAATATAATATT-TTAA-ATAATATAAATATGATATTAATATATAAATTATTAAATT
1 TAATATAA-ATTATTAATATAATA-AAAT-TGATATAAATATATAAATTATTAAATT
599749 TAAT
1 TAAT
599753 TTTAATAAAC
Statistics
Matches: 51, Mismatches: 4, Indels: 7
0.82 0.06 0.11
Matches are distributed among these distances:
53 5 0.10
54 19 0.37
55 27 0.53
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.48
Consensus pattern (54 bp):
TAATATAAATTATTAATATAATAAAATTGATATAAATATATAAATTATTAAATT
Found at i:601030 original size:5 final size:5
Alignment explanation
Indices: 601012--601051 Score: 53
Period size: 5 Copynumber: 8.0 Consensus size: 5
601002 AAGAAAGTAA
* * *
601012 GAAAG GAACG GAAAA GAAAG GAAAG GAAAG GGAAG GAAAG
1 GAAAG GAAAG GAAAG GAAAG GAAAG GAAAG GAAAG GAAAG
601052 TGATGGGAAG
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
5 29 1.00
ACGTcount: A:0.57, C:0.03, G:0.40, T:0.00
Consensus pattern (5 bp):
GAAAG
Found at i:601521 original size:21 final size:19
Alignment explanation
Indices: 601482--601549 Score: 64
Period size: 19 Copynumber: 3.5 Consensus size: 19
601472 TAAATTTTGA
* * *
601482 TATATTTATGTAATTATAT
1 TATATTTATTTTATCATAT
*
601501 CATATTTATTTTATCTAATAT
1 TATATTTATTTTATC--ATAT
* *
601522 TTTAATTATTTTATCATAT
1 TATATTTATTTTATCATAT
601541 TATATTTAT
1 TATATTTAT
601550 ATCGTATTTT
Statistics
Matches: 38, Mismatches: 9, Indels: 4
0.75 0.18 0.08
Matches are distributed among these distances:
19 22 0.58
21 16 0.42
ACGTcount: A:0.34, C:0.04, G:0.01, T:0.60
Consensus pattern (19 bp):
TATATTTATTTTATCATAT
Found at i:601537 original size:35 final size:32
Alignment explanation
Indices: 601493--601576 Score: 91
Period size: 35 Copynumber: 2.5 Consensus size: 32
601483 ATATTTATGT
*
601493 AATTATATCATATTTATTT-TATCTAATATTTTA
1 AATTTTATCATATTTATTTATATC--ATATTTTA
*
601526 ATTATTTTATCATATTATATTTATATCGTATTTTA
1 A--ATTTTATCATATT-TATTTATATCATATTTTA
601561 AATTTTA-CATATTTAT
1 AATTTTATCATATTTAT
601577 CATACTAATT
Statistics
Matches: 45, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
31 3 0.07
32 6 0.13
33 7 0.16
35 20 0.44
36 5 0.11
37 4 0.09
ACGTcount: A:0.35, C:0.06, G:0.01, T:0.58
Consensus pattern (32 bp):
AATTTTATCATATTTATTTATATCATATTTTA
Found at i:601543 original size:45 final size:42
Alignment explanation
Indices: 601446--601545 Score: 100
Period size: 45 Copynumber: 2.4 Consensus size: 42
601436 TTATATAAAC
*
601446 TTTA-CATATTA-ATAATTTATTTTATATAAATTTTGATATA
1 TTTATCATATTATATAATTTATTTTATATAAATTTTAATATA
* *
601486 TTTAT-GTAATTATATCATATTTATTTTATCTAATATTTTAAT-TA
1 TTTATCAT-ATTATAT-A-ATTTATTTTATATAA-ATTTTAATATA
601530 TTTTATCATATTATAT
1 -TTTATCATATTATAT
601546 TTATATCGTA
Statistics
Matches: 48, Mismatches: 4, Indels: 11
0.76 0.06 0.17
Matches are distributed among these distances:
40 5 0.10
41 4 0.08
42 2 0.04
43 1 0.02
44 16 0.33
45 19 0.40
46 1 0.02
ACGTcount: A:0.36, C:0.04, G:0.02, T:0.58
Consensus pattern (42 bp):
TTTATCATATTATATAATTTATTTTATATAAATTTTAATATA
Found at i:602253 original size:3 final size:3
Alignment explanation
Indices: 602245--602273 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
602235 GTGGGGCCTT
602245 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
602274 TTTTGCCAGC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:602442 original size:15 final size:16
Alignment explanation
Indices: 602422--602481 Score: 60
Period size: 15 Copynumber: 4.1 Consensus size: 16
602412 ATATATCTAT
602422 ATATTAAAT-TAATTA
1 ATATTAAATATAATTA
602437 ATATTAAATATAATT-
1 ATATTAAATATAATTA
*
602452 ATA-TAAATATGA-T-
1 ATATTAAATATAATTA
602465 ATATATAAA-ATAATTA
1 ATAT-TAAATATAATTA
602481 A
1 A
602482 AAGATAATAT
Statistics
Matches: 38, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
13 4 0.11
14 11 0.29
15 17 0.45
16 6 0.16
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.42
Consensus pattern (16 bp):
ATATTAAATATAATTA
Found at i:602469 original size:13 final size:13
Alignment explanation
Indices: 602435--602587 Score: 56
Period size: 14 Copynumber: 11.7 Consensus size: 13
602425 TTAAATTAAT
602435 TAATAT-TAAATA
1 TAATATATAAATA
602447 TAATTATATAAATA
1 TAA-TATATAAATA
602461 TGATATATATAAA-A
1 T-A-ATATATAAATA
*
602475 TAAT-TA-AAAGA
1 TAATATATAAATA
*
602486 TAATATCATATATA
1 TAATAT-ATAAATA
* * *
602500 TATTTTA-AAATT
1 TAATATATAAATA
602512 TATATAATATAAAGTA
1 TA-AT-ATATAAA-TA
602528 TTAATATATTAAAT-
1 -TAATATA-TAAATA
**
602542 TTTTATATAAA-A
1 TAATATATAAATA
*
602554 T-AT-TTTAAATA
1 TAATATATAAATA
602565 TAAT-TATAATATTA
1 TAATATATAA-A-TA
*
602579 TAAAATATA
1 TAATATATA
602588 CGAATACAAT
Statistics
Matches: 106, Mismatches: 15, Indels: 37
0.67 0.09 0.23
Matches are distributed among these distances:
10 8 0.08
11 10 0.09
12 22 0.21
13 13 0.12
14 23 0.22
15 20 0.19
16 8 0.08
17 2 0.02
ACGTcount: A:0.54, C:0.01, G:0.02, T:0.44
Consensus pattern (13 bp):
TAATATATAAATA
Found at i:602706 original size:28 final size:29
Alignment explanation
Indices: 602659--602719 Score: 74
Period size: 28 Copynumber: 2.2 Consensus size: 29
602649 ATATTATGTG
602659 ATAT-AAAAATAATTAAAATATAATAT-A
1 ATATAAAAAATAATTAAAATATAATATAA
* *
602686 ATATAAAAAATAA-TATGAATATGATATAA
1 ATATAAAAAATAATTA-AAATATAATATAA
602715 ATATA
1 ATATA
602720 TTAATATATT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
27 6 0.21
28 17 0.59
29 6 0.21
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (29 bp):
ATATAAAAAATAATTAAAATATAATATAA
Found at i:602732 original size:17 final size:17
Alignment explanation
Indices: 602674--602829 Score: 71
Period size: 17 Copynumber: 9.4 Consensus size: 17
602664 AAAATAATTA
**
602674 AAATATAATATAATATAAA
1 AAATAT-AT-TAATATATT
*
602693 AAATAATATGAATATGATAT
1 AAAT-ATATTAATAT-AT-T
602713 AAATATATTAATATATT
1 AAATATATTAATATATT
* *
602730 AAAAATATATAA-AAATT
1 AAATATAT-TAATATATT
*
602747 AAAT-TATTAATAAATT
1 AAATATATTAATATATT
602763 AAA-AT-TT-ATATA--
1 AAATATATTAATATATT
* *
602775 AATTA-ATTAATATTTT
1 AAATATATTAATATATT
* *
602791 AAATATAATAATAATAAT
1 AAATATATTAAT-ATATT
**
602809 AAAT-TAAAAATATA-T
1 AAATATATTAATATATT
602824 AAATAT
1 AAATAT
602830 GGTAAAAAAT
Statistics
Matches: 108, Mismatches: 15, Indels: 31
0.70 0.10 0.20
Matches are distributed among these distances:
12 2 0.02
13 3 0.03
14 8 0.07
15 10 0.09
16 20 0.19
17 26 0.24
18 17 0.16
19 16 0.15
20 6 0.06
ACGTcount: A:0.60, C:0.00, G:0.01, T:0.38
Consensus pattern (17 bp):
AAATATATTAATATATT
Found at i:602736 original size:11 final size:10
Alignment explanation
Indices: 602659--602745 Score: 58
Period size: 9 Copynumber: 9.0 Consensus size: 10
602649 ATATTATGTG
602659 ATATAAAAAT
1 ATATAAAAAT
*
602669 A-ATTAAAAT
1 ATATAAAAAT
*
602678 ATA-ATATAAT
1 ATATA-AAAAT
602688 ATA-AAAAAT
1 ATATAAAAAT
**
602697 A-ATATGAAT
1 ATATAAAAAT
*
602706 ATGATATAAAT
1 AT-ATAAAAAT
* *
602717 ATATTAATAT
1 ATATAAAAAT
602727 AT-TAAAAAT
1 ATATAAAAAT
602736 ATATAAAAAT
1 ATATAAAAAT
602746 TAAATTATTA
Statistics
Matches: 59, Mismatches: 12, Indels: 12
0.71 0.14 0.14
Matches are distributed among these distances:
8 1 0.02
9 25 0.42
10 24 0.41
11 9 0.15
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.34
Consensus pattern (10 bp):
ATATAAAAAT
Found at i:602747 original size:25 final size:28
Alignment explanation
Indices: 602709--602786 Score: 78
Period size: 27 Copynumber: 2.9 Consensus size: 28
602699 TATGAATATG
602709 ATATAAATATATT-AATATATTAA-AAAT
1 ATATAAATATATTAAAT-TATTAATAAAT
602736 ATATAAA-A-ATTAAATTATTAATAAAT
1 ATATAAATATATTAAATTATTAATAAAT
*
602762 -TA-AAATTTATATAAATTAATTAATA
1 ATATAAATATAT-TAAATT-ATTAATA
602787 TTTTAAATAT
Statistics
Matches: 44, Mismatches: 1, Indels: 11
0.79 0.02 0.20
Matches are distributed among these distances:
24 3 0.07
25 11 0.25
26 10 0.23
27 13 0.30
28 7 0.16
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (28 bp):
ATATAAATATATTAAATTATTAATAAAT
Found at i:602778 original size:27 final size:27
Alignment explanation
Indices: 602746--602827 Score: 84
Period size: 27 Copynumber: 3.2 Consensus size: 27
602736 ATATAAAAAT
*
602746 TAAATTATTAATAAATTAAAATTTATA
1 TAAATTATTAATAAATTAAAATATATA
* *
602773 TAAATTAATTAAT-ATTTTAAATATA-A
1 TAAATT-ATTAATAAATTAAAATATATA
*
602799 T-AA-TAATAATAAATTAAAA-ATATA
1 TAAATTATTAATAAATTAAAATATATA
602823 TAAAT
1 TAAAT
602828 ATGGTAAAAA
Statistics
Matches: 44, Mismatches: 6, Indels: 11
0.72 0.10 0.18
Matches are distributed among these distances:
23 8 0.18
24 9 0.20
25 4 0.09
26 2 0.05
27 15 0.34
28 6 0.14
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (27 bp):
TAAATTATTAATAAATTAAAATATATA
Found at i:606721 original size:13 final size:13
Alignment explanation
Indices: 606703--606727 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
606693 ATTTAAATTC
606703 AAATATAAATATT
1 AAATATAAATATT
606716 AAATATAAATAT
1 AAATATAAATAT
606728 ATTTTAATAT
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:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (13 bp):
AAATATAAATATT
Found at i:606748 original size:15 final size:15
Alignment explanation
Indices: 606711--606750 Score: 62
Period size: 16 Copynumber: 2.6 Consensus size: 15
606701 TCAAATATAA
*
606711 ATATTAAATATAAAT
1 ATATTTAATATAAAT
606726 ATATTTTAATATAAAT
1 ATA-TTTAATATAAAT
606742 ATATTTAAT
1 ATATTTAAT
606751 TTATTTTAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 9 0.39
16 14 0.61
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
ATATTTAATATAAAT
Found at i:606786 original size:16 final size:16
Alignment explanation
Indices: 606746--606789 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
606736 ATAAATATAT
606746 TTAATT-TATTTTAAA
1 TTAATTATATTTTAAA
*
606761 TTATTTATATATTTAAA
1 TTAATTATAT-TTTAAA
606778 -TAATTATATTTT
1 TTAATTATATTTT
606790 TTTAATTTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
15 8 0.32
16 11 0.44
17 6 0.24
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
TTAATTATATTTTAAA
Found at i:606793 original size:18 final size:17
Alignment explanation
Indices: 606737--606794 Score: 53
Period size: 18 Copynumber: 3.2 Consensus size: 17
606727 TATTTTAATA
606737 TAAATATATTTAATTTATTT
1 TAAATA-ATTT-ATTT-TTT
* * *
606757 TAAATTATTTATATATT
1 TAAATAATTTATTTTTT
606774 TAAATAATTATATTTTTT
1 TAAATAATT-TATTTTTT
606792 TAA
1 TAA
606795 TTTAAATAAA
Statistics
Matches: 31, Mismatches: 6, Indels: 4
0.76 0.15 0.10
Matches are distributed among these distances:
17 10 0.32
18 12 0.39
19 4 0.13
20 5 0.16
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (17 bp):
TAAATAATTTATTTTTT
Found at i:606818 original size:13 final size:13
Alignment explanation
Indices: 606800--606834 Score: 54
Period size: 13 Copynumber: 2.7 Consensus size: 13
606790 TTTAATTTAA
606800 ATAAATATTAAAT-
1 ATAAATATT-AATC
606813 ATAAATATTAATC
1 ATAAATATTAATC
606826 ATAAATATT
1 ATAAATATT
606835 TAAAAAAGTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 3 0.14
13 18 0.86
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (13 bp):
ATAAATATTAATC
Found at i:608261 original size:58 final size:58
Alignment explanation
Indices: 608166--608279 Score: 192
Period size: 58 Copynumber: 2.0 Consensus size: 58
608156 TCTATTTTAC
* *
608166 TATTTAAAAATAATATTAAAAAATTTAATTTTTTATATTAATATTTATAGTTAAATAT
1 TATTCAAAAATAATATTAAAAAATTTAATTTTTTATATTAATATTTATAATTAAATAT
* *
608224 TATTCAAAAATAATATTAAAAGATTTAATTTTTTATATTAGTATTTATAATTAAAT
1 TATTCAAAAATAATATTAAAAAATTTAATTTTTTATATTAATATTTATAATTAAAT
608280 TTAAATTAAA
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
58 52 1.00
ACGTcount: A:0.47, C:0.01, G:0.03, T:0.49
Consensus pattern (58 bp):
TATTCAAAAATAATATTAAAAAATTTAATTTTTTATATTAATATTTATAATTAAATAT
Done.