Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015120.1 Kokia drynarioides strain JFW-HI SEQ_130164, 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: 618428
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.33
Warning! 267 characters in sequence are not A, C, G, or T
File 3 of 3
Found at i:588493 original size:199 final size:199
Alignment explanation
Indices: 588210--588626 Score: 541
Period size: 199 Copynumber: 2.1 Consensus size: 199
588200 CGATCCTTCA
** * * *
588210 CATCACGTCTTCTAAGGTATTGGGTTTGCCTGTTGCGACCTCAACCTTTCCCTTCAAATCTTCAT
1 CATCACGTCTTCTAAGGTACCGAGTTCGCCTATTGCGACCTCAACCTTTCCCTTCAAATCTTCAT
* * * * *
588275 GGTATCGGGTTCATCGTTGCAACTTCAACCTTTCCCATCACGTCTTTTAAGGTATCAGGTTTACC
66 GGTACCGAGTTCATCGTTGCAACCTCAACCTCTCCCATCACGTCTTTTAAGGTATCAGGTTCACC
* * * *
588340 GTTACGACCTCAACCCTTT-CCTTTATATCATCATAGTACT-TGGTTCACCGTTACGGCCTCAAC
131 GTTACGACCTCAA-CCTTTCCCTTCAAATCATCATAGTA-TGGGGTTCACCATTACGGCCTCAAC
588403 CTTTCC
194 CTTTCC
* *
588409 CATCACGTCTTCTAAGGTACCGAGTTCGCCTATTGCGGCCTCAACCTTTCCCTTCAAATTTTCAT
1 CATCACGTCTTCTAAGGTACCGAGTTCGCCTATTGCGACCTCAACCTTTCCCTTCAAATCTTCAT
** ** *
588474 GGTACCGAGTTTGTCGTTGCGGCCTCAACCTCTCCCATCACGTCTTTTAAGGTATCGGGTTCACC
66 GGTACCGAGTTCATCGTTGCAACCTCAACCTCTCCCATCACGTCTTTTAAGGTATCAGGTTCACC
* * * * * *
588539 GTTGCGACCTCAACCTTTCCCTTCAAATCTTCATGGTATGGGGTTCGCTATTGCGGCCTCAACCT
131 GTTACGACCTCAACCTTTCCCTTCAAATCATCATAGTATGGGGTTCACCATTACGGCCTCAACCT
588604 TTCC
196 TTCC
* *
588608 CATCATGTATTCTAAGGTA
1 CATCACGTCTTCTAAGGTA
588627 TCTATTTGCC
Statistics
Matches: 187, Mismatches: 29, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
198 6 0.03
199 181 0.97
ACGTcount: A:0.19, C:0.30, G:0.17, T:0.34
Consensus pattern (199 bp):
CATCACGTCTTCTAAGGTACCGAGTTCGCCTATTGCGACCTCAACCTTTCCCTTCAAATCTTCAT
GGTACCGAGTTCATCGTTGCAACCTCAACCTCTCCCATCACGTCTTTTAAGGTATCAGGTTCACC
GTTACGACCTCAACCTTTCCCTTCAAATCATCATAGTATGGGGTTCACCATTACGGCCTCAACCT
TTCC
Found at i:588936 original size:148 final size:148
Alignment explanation
Indices: 588382--589004 Score: 411
Period size: 148 Copynumber: 4.2 Consensus size: 148
588372 ATAGTACTTG
* * ** * * * *
588382 GTTCACCGTTACGGCCTCAACCTTTCCCATCACGTCTTCTAAGGTACC-GAGTTCGCCTATTGCG
1 GTTCGCCGTTGCGGCCTCAACCTTTCCCATCATATCTAC-AAGATACCAG-GTTCG-CTATTACA
* * * * * * * * *
588446 GCCTCAACCTTTCCCTTCAAATTTTC-ATGGTA-CCGAGTTTG-TCGTTGCGGCCTCAACCTCTC
63 ACCTCAACCTTTCCCATCAAATCTTCTAAGGTATCGGA-TTCGCT-GTTGCGACCTCAACATTTC
* ** * * * *
588508 CCATCACGTCTTTTAAGGTATCGG
126 CCTTCAAATC-TTCATGGTAACGA
* * * * * * * *** * **
588532 GTTCACCGTTGCGACCTCAACCTTTCCCTTCAAATCTTCATGGTATGGGGTTCGCTATTGCGGCC
1 GTTCGCCGTTGCGGCCTCAACCTTTCCCATCATATCTACAAGATACCAGGTTCGCTATTACAACC
** * * * * * * *
588597 TCAACCTTTCCCATCATGTATTCTAAGGTATC-TATTTGCCGTTG-TAGTCTTAACATTTCCCTT
66 TCAACCTTTCCCATCAAATCTTCTAAGGTATCGGATTCGCTGTTGCGA-CCTCAACATTTCCCTT
* *
588660 TAAATCTTCATGGTAACGG
130 CAAATCTTCATGGTAACGA
* * * * **
588679 GTTCGCCGTTGCGGCCTCAACCCTTT-CCTTCATATCTTCATGATACCAGGTTCGTTATTATGAC
1 GTTCGCCGTTGCGGCCTCAA-CCTTTCCCATCATATCTACAAGATACCAGGTTCGCTATTACAAC
* * * * *
588743 CTCAACCTTTCCCATCACATCTTCTAAGGTATCGGATTTGTTGTTGTGGCCTCAACATTTCCCTT
65 CTCAACCTTTCCCATCAAATCTTCTAAGGTATCGGATTCGCTGTTGCGACCTCAACATTTCCCTT
*
588808 CAAATCTTCATGGTATCGA
130 CAAATCTTCATGGTAACGA
* * * *
588827 GTTCGCCGTTGCGGCCTCAACCTTTCCCATGATATCTACTAAGGTATCGGGTTCGCTATTACAAC
1 GTTCGCCGTTGCGGCCTCAACCTTTCCCATCATATCTAC-AAGATACCAGGTTCGCTATTACAAC
* * * * * *
588892 CTCAACCTTTCTCTTTAAATCTTC-ATGGTAAT-GGGTTCGCTGTTGCGACCTCAACCCTTT-CC
65 CTCAACCTTTCCCATCAAATCTTCTAAGGT-ATCGGATTCGCTGTTGCGACCTCAA-CATTTCCC
* * *
588954 GTCATATCTTCATGGTACCGA
128 TTCAAATCTTCATGGTAACGA
*
588975 GTTCGCCGTTGCAGCCTCAACCTTTCCCAT
1 GTTCGCCGTTGCGGCCTCAACCTTTCCCAT
589005 TACATCTTTT
Statistics
Matches: 384, Mismatches: 77, Indels: 26
0.79 0.16 0.05
Matches are distributed among these distances:
147 92 0.24
148 196 0.51
149 60 0.16
150 36 0.09
ACGTcount: A:0.19, C:0.30, G:0.17, T:0.35
Consensus pattern (148 bp):
GTTCGCCGTTGCGGCCTCAACCTTTCCCATCATATCTACAAGATACCAGGTTCGCTATTACAACC
TCAACCTTTCCCATCAAATCTTCTAAGGTATCGGATTCGCTGTTGCGACCTCAACATTTCCCTTC
AAATCTTCATGGTAACGA
Found at i:589180 original size:50 final size:50
Alignment explanation
Indices: 589094--589479 Score: 304
Period size: 50 Copynumber: 7.8 Consensus size: 50
589084 TTCCTTCATA
* * * *
589094 TTCGCTGTTGCGGCCTCAACCTTTCCCATTATATCTTCTAAGGTACC-AGG
1 TTCGCCGTTGCGGCCTCAACCTTTCCTATCAAATCTTCTAAGGTACCGA-G
* *
589144 TTCGTCGTTGCGGCCTCAACCTTTCCTATCACATCTTCTAAGGTACCGAG
1 TTCGCCGTTGCGGCCTCAACCTTTCCTATCAAATCTTCTAAGGTACCGAG
* * * * *
589194 TTCACCTATTACGGCCTCAATCTTTCCCT-TCAAATCTTC-ATGGTACCGAG
1 TTCGCC-GTTGCGGCCTCAACCTTT-CCTATCAAATCTTCTAAGGTACCGAG
* * * * * *
589244 TTTGCCGTTGCGACCTTAGCCTTTCCCT-TCAAATCTTC-ATGGTACTGAG
1 TTCGCCGTTGCGGCCTCAACCTTT-CCTATCAAATCTTCTAAGGTACCGAG
* * * ** *
589293 TTCACCGTTGCGACCTCAACCTTTCCCATCATGTCTTCTAAGGTA-CTAGG
1 TTCGCCGTTGCGGCCTCAACCTTTCCTATCAAATCTTCTAAGGTACCGA-G
* * * * * *
589343 TTCACCGTTGTGACCTCAACCTTTCCCT-TAAAATCTT-TATGGTACCGGG
1 TTCGCCGTTGCGGCCTCAACCTTT-CCTATCAAATCTTCTAAGGTACCGAG
* * * * ***
589392 CTCGCCGTTGTGGCTTCAACATTT-CTCATCGCGTCTTCTAAGGTACCGAG
1 TTCGCCGTTGCGGCCTCAACCTTTCCT-ATCAAATCTTCTAAGGTACCGAG
* *
589442 TTCGCCGTTGCGGCCTCAACCTTTCCCACCAAATCTTC
1 TTCGCCGTTGCGGCCTCAACCTTTCCTATCAAATCTTC
589480 ATGTTTTCTT
Statistics
Matches: 265, Mismatches: 59, Indels: 24
0.76 0.17 0.07
Matches are distributed among these distances:
47 2 0.01
48 2 0.01
49 96 0.36
50 134 0.51
51 28 0.11
52 3 0.01
ACGTcount: A:0.18, C:0.32, G:0.17, T:0.33
Consensus pattern (50 bp):
TTCGCCGTTGCGGCCTCAACCTTTCCTATCAAATCTTCTAAGGTACCGAG
Found at i:589351 original size:99 final size:99
Alignment explanation
Indices: 589100--589482 Score: 369
Period size: 99 Copynumber: 3.9 Consensus size: 99
589090 CATATTCGCT
* * *
589100 GTTGCGGCCTCAACCTTTCCCATTATATCTTCTAAGGTACCAG-GTTCGTCGTTGCGGCCTCAAC
1 GTTGCGGCCTCAACCTTTCCCATCATATCTTCTAAGGTA-CAGAGTTCGCCGTTGCGACCTCAAC
* *
589164 CTTT-CCTATCACATCTTCTAAGGTACCGAGTTCACC
65 CTTTCCCT-TCAAATCTTC-ATGGTACCGAGTTCACC
* * * * * * * * * *
589200 TATTACGGCCTCAATCTTTCCCTTCAAATCTTC-ATGGTACCGAGTTTGCCGTTGCGACCTTAGC
1 -GTTGCGGCCTCAACCTTTCCCATCATATCTTCTAAGGTACAGAGTTCGCCGTTGCGACCTCAAC
*
589264 CTTTCCCTTCAAATCTTCATGGTACTGAGTTCACC
65 CTTTCCCTTCAAATCTTCATGGTACCGAGTTCACC
* * * *
589299 GTTGCGACCTCAACCTTTCCCATCATGTCTTCTAAGGTACTAG-GTTCACCGTTGTGACCTCAAC
1 GTTGCGGCCTCAACCTTTCCCATCATATCTTCTAAGGTAC-AGAGTTCGCCGTTGCGACCTCAAC
* * * * *
589363 CTTTCCCTTAAAATCTTTATGGTACCGGGCTCGCC
65 CTTTCCCTTCAAATCTTCATGGTACCGAGTTCACC
* * * * *** * *
589398 GTTGTGGCTTCAACATTTCTCATCGCGTCTTCTAAGGTACCGAGTTCGCCGTTGCGGCCTCAACC
1 GTTGCGGCCTCAACCTTTCCCATCATATCTTCTAAGGTACAGAGTTCGCCGTTGCGACCTCAACC
**
589463 TTTCCCACCAAATCTTCATG
66 TTTCCCTTCAAATCTTCATG
589483 TTTTCTTGAT
Statistics
Matches: 226, Mismatches: 51, Indels: 12
0.78 0.18 0.04
Matches are distributed among these distances:
98 26 0.12
99 136 0.60
100 35 0.15
101 29 0.13
ACGTcount: A:0.19, C:0.31, G:0.17, T:0.33
Consensus pattern (99 bp):
GTTGCGGCCTCAACCTTTCCCATCATATCTTCTAAGGTACAGAGTTCGCCGTTGCGACCTCAACC
TTTCCCTTCAAATCTTCATGGTACCGAGTTCACC
Found at i:589479 original size:149 final size:150
Alignment explanation
Indices: 589095--589479 Score: 384
Period size: 149 Copynumber: 2.6 Consensus size: 150
589085 TCCTTCATAT
* * * * * * *
589095 TCGCTGTTGCGGCCTCAACCTTTCCCATTATATCTTCTAAGGTACC-AGGTTCGTCGTTGCGGCC
1 TCGCCGTTGCGACCTTAACATTTCCCATCAAATCTTCTAAGGTACCGA-GTTCGCCGTTGCGGCC
* * * * *
589159 TCAACCTTTCCTATCACATCTTCTAAGGTACCGAGTTCACCTATTACGGCCTCAATCTTTCCCTT
65 TCAACCTTTCCCATCAAATCTTCTAAGGTACAGAGTTCACCTATTACGACCTCAACCTTTCCCTT
* *
589224 CAAATCTTCATGGTACCGAGT
130 AAAATCTTCATGGTACCGAGC
* * * * * * * *
589245 TTGCCGTTGCGACCTTAGCCTTTCCCTTCAAATCTTC-ATGGTACTGAGTTCACCGTTGCGACCT
1 TCGCCGTTGCGACCTTAACATTTCCCATCAAATCTTCTAAGGTACCGAGTTCGCCGTTGCGGCCT
** * **
589309 CAACCTTTCCCATCATGTCTTCTAAGGTACTAG-GTTCACC-GTTGTGACCTCAACCTTTCCCTT
66 CAACCTTTCCCATCAAATCTTCTAAGGTAC-AGAGTTCACCTATTACGACCTCAACCTTTCCCTT
* *
589372 AAAATCTTTATGGTACCGGGC
130 AAAATCTTCATGGTACCGAGC
* * * ***
589393 TCGCCGTTGTG-GCTTCAACATTTCTCATCGCGTCTTCTAAGGTACCGAGTTCGCCGTTGCGGCC
1 TCGCCGTTGCGACCTT-AACATTTCCCATCAAATCTTCTAAGGTACCGAGTTCGCCGTTGCGGCC
*
589457 TCAACCTTTCCCACCAAATCTTC
65 TCAACCTTTCCCATCAAATCTTC
589480 ATGTTTTCTT
Statistics
Matches: 188, Mismatches: 43, Indels: 9
0.78 0.18 0.04
Matches are distributed among these distances:
147 3 0.02
148 58 0.31
149 96 0.51
150 31 0.16
ACGTcount: A:0.18, C:0.32, G:0.17, T:0.33
Consensus pattern (150 bp):
TCGCCGTTGCGACCTTAACATTTCCCATCAAATCTTCTAAGGTACCGAGTTCGCCGTTGCGGCCT
CAACCTTTCCCATCAAATCTTCTAAGGTACAGAGTTCACCTATTACGACCTCAACCTTTCCCTTA
AAATCTTCATGGTACCGAGC
Found at i:590435 original size:6 final size:6
Alignment explanation
Indices: 590426--590492 Score: 50
Period size: 6 Copynumber: 11.3 Consensus size: 6
590416 CAACCTCTCC
* * *
590426 TTTTCT TTTTCT TTTT-T TTTTCCT TCTT-T TCTTCT TTTTCT TATTTAT
1 TTTTCT TTTTCT TTTTCT TTTT-CT TTTTCT TTTTCT TTTTCT T-TTTCT
* *
590474 TTTTAT TTTT-A TTTTCT TT
1 TTTTCT TTTTCT TTTTCT TT
590493 CTTTTTTTAT
Statistics
Matches: 51, Mismatches: 5, Indels: 10
0.77 0.08 0.15
Matches are distributed among these distances:
5 14 0.27
6 28 0.55
7 9 0.18
ACGTcount: A:0.06, C:0.13, G:0.00, T:0.81
Consensus pattern (6 bp):
TTTTCT
Found at i:590453 original size:21 final size:21
Alignment explanation
Indices: 590427--590513 Score: 79
Period size: 21 Copynumber: 4.1 Consensus size: 21
590417 AACCTCTCCT
590427 TTTCTTTTTCTTTTTTTTTTC
1 TTTCTTTTTCTTTTTTTTTTC
* * *
590448 CTTC-TTTTCTTCTTTTTCTTA
1 TTTCTTTTTCTT-TTTTTTTTC
* * *
590469 TTTATTTTTATTTTTATTTTC
1 TTTCTTTTTCTTTTTTTTTTC
*
590490 TTTCTTTTT-TTATTTATTTTC
1 TTTCTTTTTCTT-TTTTTTTTC
590511 TTT
1 TTT
590514 ATCGGATCCG
Statistics
Matches: 53, Mismatches: 10, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
20 9 0.17
21 38 0.72
22 6 0.11
ACGTcount: A:0.07, C:0.13, G:0.00, T:0.80
Consensus pattern (21 bp):
TTTCTTTTTCTTTTTTTTTTC
Found at i:594836 original size:18 final size:17
Alignment explanation
Indices: 594813--594858 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 17
594803 TCATTTTAAG
594813 TTTAAATTTACTTAAAAA
1 TTTAAATTTA-TTAAAAA
* *
594831 TTTAAATTTATTATATA
1 TTTAAATTTATTAAAAA
594848 TTTAAAGTTTA
1 TTTAAA-TTTA
594859 AATCTATTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 11 0.44
18 14 0.56
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.52
Consensus pattern (17 bp):
TTTAAATTTATTAAAAA
Found at i:594852 original size:17 final size:17
Alignment explanation
Indices: 594795--594871 Score: 59
Period size: 17 Copynumber: 4.5 Consensus size: 17
594785 GCCCAACAGG
* *
594795 ATTTAAATTCATTTTA-
1 ATTTAAATTTATTATAT
* *
594811 AGTTTAAATTTACTTAAAA
1 A-TTTAAATTTA-TTATAT
594830 ATTTAAATTTATTATAT
1 ATTTAAATTTATTATAT
* *
594847 ATTTAAAGTTTA-AATCT
1 ATTTAAA-TTTATTATAT
594864 ATTTAAAT
1 ATTTAAAT
594872 CAAGTTCAAT
Statistics
Matches: 50, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
16 2 0.04
17 30 0.60
18 17 0.34
19 1 0.02
ACGTcount: A:0.43, C:0.04, G:0.03, T:0.51
Consensus pattern (17 bp):
ATTTAAATTTATTATAT
Found at i:595566 original size:21 final size:21
Alignment explanation
Indices: 595542--595593 Score: 54
Period size: 21 Copynumber: 2.6 Consensus size: 21
595532 ATAACTGTTT
595542 TAATAATAACAACAATAATAA
1 TAATAATAACAACAATAATAA
* ** *
595563 TAATATTAATGACATTAATAA
1 TAATAATAACAACAATAATAA
595584 TAA-AA-AACAA
1 TAATAATAACAA
595594 TTTTCTTAAT
Statistics
Matches: 24, Mismatches: 7, Indels: 2
0.73 0.21 0.06
Matches are distributed among these distances:
19 3 0.12
20 1 0.04
21 20 0.83
ACGTcount: A:0.63, C:0.08, G:0.02, T:0.27
Consensus pattern (21 bp):
TAATAATAACAACAATAATAA
Found at i:595655 original size:24 final size:24
Alignment explanation
Indices: 595610--595655 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
595600 TAATAATCAT
**
595610 TAATAATAATAAATGTTTTTATGA
1 TAATAATAATAAATGTAATTATGA
595634 TAATAATAATAATAT-TAATTAT
1 TAATAATAATAA-ATGTAATTAT
595656 TTTAATAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
24 17 0.89
25 2 0.11
ACGTcount: A:0.50, C:0.00, G:0.04, T:0.46
Consensus pattern (24 bp):
TAATAATAATAAATGTAATTATGA
Found at i:596714 original size:59 final size:58
Alignment explanation
Indices: 596614--596896 Score: 279
Period size: 59 Copynumber: 4.9 Consensus size: 58
596604 AAGGTCTCTA
* * * * *
596614 AACTGTCCAAAAATTTCGTTTTTACCCCCGAACTTCCAAAAATCCCATTTTTACTCCCG
1 AACT-TCCAAAAATTCCATTTTTACCCTCAAACTTCCAAAAATTCCATTTTTACTCCCG
* * * *
596673 AACTTCCTAAAATTCCATTTTTGACCCTGAAACTTCCAAAAATTTCATTTTTACCCCCG
1 AACTTCCAAAAATTCCATTTTT-ACCCTCAAACTTCCAAAAATTCCATTTTTACTCCCG
* * * * **
596732 AACTTCCAAAAATCCCATTTTTACCCTCAAACTTCCCAAAATTTCATTTATGAGCT-CAA
1 AACTTCCAAAAATTCCATTTTTACCCTCAAACTTCCAAAAATTCCATTT-TTA-CTCCCG
* * * *
596791 AACTTCCAAAAATTCCATTTTTACCCTCAAAGTTCCCAAAATTACATTTTGA--CCCG
1 AACTTCCAAAAATTCCATTTTTACCCTCAAACTTCCAAAAATTCCATTTTTACTCCCG
* * * *
596847 AAACTT-CTAAAATTTCATTTTTACCCT-AAGCTTTCAAAAATTCCATTTTT
1 -AACTTCCAAAAATTCCATTTTTACCCTCAAACTTCCAAAAATTCCATTTTT
596897 GACCCTAAAA
Statistics
Matches: 189, Mismatches: 30, Indels: 14
0.81 0.13 0.06
Matches are distributed among these distances:
55 17 0.09
56 20 0.11
57 5 0.03
58 43 0.23
59 103 0.54
60 1 0.01
ACGTcount: A:0.33, C:0.28, G:0.05, T:0.35
Consensus pattern (58 bp):
AACTTCCAAAAATTCCATTTTTACCCTCAAACTTCCAAAAATTCCATTTTTACTCCCG
Found at i:596773 original size:88 final size:86
Alignment explanation
Indices: 596611--596925 Score: 348
Period size: 88 Copynumber: 3.6 Consensus size: 86
596601 CTGAAGGTCT
* * * *
596611 CTAAACTGTCCAAAAATTTCGTTTTTACCCCCGAACTTCCAAAAATCCCATTTTTACTCCCGAAC
1 CTAAACT-TCCAAAAATTCCATTTTTACCCCCAAACTTCCAAAAATCCCATTTTTAC-CCCAAAC
*
596676 TTCCTAAAATTCCATTTTTGACC
64 TTCCTAAAATTTCATTTTTGACC
* *
596699 CTGAAACTTCCAAAAATTTCATTTTTACCCCCGAACTTCCAAAAATCCCATTTTTACCCTCAAAC
1 CT-AAACTTCCAAAAATTCCATTTTTACCCCCAAACTTCCAAAAATCCCATTTTTACCC-CAAAC
* * *
596764 TTCCCAAAATTTCATTTATGAGCT
64 TTCCTAAAATTTCATTTTTGA-CC
* * * * ** * *
596788 CAAAACTTCCAAAAATTCCATTTTTACCCTCAAAGTTCCCAAAATTACATTTTGACCCGAAACTT
1 CTAAACTTCCAAAAATTCCATTTTTACCCCCAAACTTCCAAAAATCCCATTTTTACCCCAAACTT
596853 -CTAAAATTTCATTTTT-ACC
66 CCTAAAATTTCATTTTTGACC
* * **
596872 CTAAGCTTTCAAAAATTCCATTTTTGACCCTAAAACTTCCAAAAATACCC-TTTT
1 CTAAACTTCCAAAAATTCCATTTTT-ACCCCCAAACTTCCAAAAAT-CCCATTTT
596926 ACCATTTGAA
Statistics
Matches: 195, Mismatches: 27, Indels: 13
0.83 0.11 0.06
Matches are distributed among these distances:
84 23 0.12
85 22 0.11
86 15 0.08
87 8 0.04
88 120 0.62
89 7 0.04
ACGTcount: A:0.33, C:0.28, G:0.04, T:0.34
Consensus pattern (86 bp):
CTAAACTTCCAAAAATTCCATTTTTACCCCCAAACTTCCAAAAATCCCATTTTTACCCCAAACTT
CCTAAAATTTCATTTTTGACC
Found at i:596925 original size:29 final size:29
Alignment explanation
Indices: 596613--596917 Score: 251
Period size: 29 Copynumber: 10.5 Consensus size: 29
596603 GAAGGTCTCT
* * * *
596613 AAACTGTCCAAAAATTTCGTTTTTACCCCC
1 AAACT-TCCAAAAATTCCATTTTGACCCTC
* * *
596643 GAACTTCCAAAAATCCCATTTTTACTCC-C
1 AAACTTCCAAAAATTCCATTTTGAC-CCTC
* * *
596672 GAACTTCCTAAAATTCCATTTTTGACCCTG
1 AAACTTCCAAAAATTCCA-TTTTGACCCTC
* * *
596702 AAACTTCCAAAAATTTCATTTTTACCCCC
1 AAACTTCCAAAAATTCCATTTTGACCCTC
* * *
596731 GAACTTCCAAAAATCCCATTTTTACCCTC
1 AAACTTCCAAAAATTCCATTTTGACCCTC
* * *
596760 AAACTTCCCAAAATTTCATTTATGA-GCTC
1 AAACTTCCAAAAATTCCATTT-TGACCCTC
*
596789 AAAACTTCCAAAAATTCCATTTTTACCCTC
1 -AAACTTCCAAAAATTCCATTTTGACCCTC
* * * *
596819 AAAGTTCCCAAAATTACATTTTGACCC-G
1 AAACTTCCAAAAATTCCATTTTGACCCTC
* * *
596847 AAACTT-CTAAAATTTCATTTTTACCCT-
1 AAACTTCCAAAAATTCCATTTTGACCCTC
* * *
596874 AAGCTTTCAAAAATTCCATTTTTGACCCTA
1 AAACTTCCAAAAATTCCA-TTTTGACCCTC
596904 AAACTTCCAAAAAT
1 AAACTTCCAAAAAT
596918 ACCCTTTTAC
Statistics
Matches: 222, Mismatches: 43, Indels: 20
0.78 0.15 0.07
Matches are distributed among these distances:
27 22 0.10
28 14 0.06
29 123 0.55
30 63 0.28
ACGTcount: A:0.34, C:0.28, G:0.05, T:0.34
Consensus pattern (29 bp):
AAACTTCCAAAAATTCCATTTTGACCCTC
Found at i:597351 original size:96 final size:96
Alignment explanation
Indices: 597251--597442 Score: 246
Period size: 96 Copynumber: 2.0 Consensus size: 96
597241 AAGACTTTAA
* * *
597251 AATCGAGGTAATA-TTCTTTTAT-TTCGAGTTTTGAAA-ATTTCTGCCTTAACTTACTAGGTGCA
1 AATCGAGGTAATATTTC-GTTATCTTCGA-TTCTGAAATATTAC-GCCTTAACTTACTAGGTGCA
** *
597313 ATTTTTCTTCAAATTGAAATAATCGAATACCCTT
63 ACCTTTCTTCAAATCGAAATAATCGAATACCCTT
* *
597347 AATCGGGGTAATGTTTCGTTATCTTCGATTCTGAAATATTACGCCTTAACTTACTAGGTGCAACC
1 AATCGAGGTAATATTTCGTTATCTTCGATTCTGAAATATTACGCCTTAACTTACTAGGTGCAACC
* *
597412 TTTCTTCAAATCGAGATAATCGAATATCCTT
66 TTTCTTCAAATCGAAATAATCGAATACCCTT
597443 TTCCCANNNN
Statistics
Matches: 83, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
96 71 0.86
97 12 0.14
ACGTcount: A:0.29, C:0.18, G:0.14, T:0.39
Consensus pattern (96 bp):
AATCGAGGTAATATTTCGTTATCTTCGATTCTGAAATATTACGCCTTAACTTACTAGGTGCAACC
TTTCTTCAAATCGAAATAATCGAATACCCTT
Found at i:609009 original size:75 final size:75
Alignment explanation
Indices: 608886--609061 Score: 262
Period size: 75 Copynumber: 2.3 Consensus size: 75
608876 ATGCAGTCAT
* * * * * * *
608886 CTTCCTGATGAGATACCGAGAAGAAGACCGAATCAATGAAACGAGGCTCGATGTGAGCAAATCTT
1 CTTCCTGATGAGATACTGAGAAGTAGACCAAATCAATGAAACAAGGCTCAAAGCGAGCAAATCTT
*
608951 CAAACCCTAG
66 CAAACCCCAG
608961 CTTCCTGATGAGATACTGAGAAGTAGACCAAATCAATGAAACAAGGCTCAAAGCGAGCAAATCTT
1 CTTCCTGATGAGATACTGAGAAGTAGACCAAATCAATGAAACAAGGCTCAAAGCGAGCAAATCTT
*
609026 CTAACCCCAG
66 CAAACCCCAG
*
609036 CTTCCTGATGAGACACTGAGAAGTAG
1 CTTCCTGATGAGATACTGAGAAGTAG
609062 GTCGAAGTAA
Statistics
Matches: 91, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
75 91 1.00
ACGTcount: A:0.36, C:0.23, G:0.22, T:0.19
Consensus pattern (75 bp):
CTTCCTGATGAGATACTGAGAAGTAGACCAAATCAATGAAACAAGGCTCAAAGCGAGCAAATCTT
CAAACCCCAG
Found at i:609267 original size:201 final size:202
Alignment explanation
Indices: 608961--609498 Score: 571
Period size: 201 Copynumber: 2.6 Consensus size: 202
608951 CAAACCCTAG
* * *
608961 CTTCCTGATGAGATACTGAGAAGTAGACCAAATCAATGAAACAAGGCTCAAAGCGAGCAAATCTT
1 CTTCCTGATGAGATACAGAGAAGAAGACCAAATC------A-AAGGCTCAAAGTGAGCAAATCTT
* * * *
609026 CTAACCCCAGCTTCCTGATGAGACACTGAGAAGTAGGTCGAAGTAATAAAAAGGTTAGCTTCCTG
59 CGAACCCCAGCTTCATGATGAGATACTGAGAAGCAGGTCGAAGTAATAAAAAGGTTAGCTTCCTG
* * *
609091 ACGAGATACTGAGAAGT-GTACCAAATTCGTCTTCCTGATGAGGTACAGAGAAGCGAATTAAAAC
124 ACGAAATACTGAGAAGTCG-ACCAAATTCGTCTTCCTGATGAGATACAGAGAAACGAATTAAAAC
** ***
609155 AAGTGAGGTGGTCAT
188 AAACGACACGGTCAT
* * * * * * *
609170 CTTCTTGATGAGATACAGAGAAGTATACGAACTC-GAGGCTCAACGTGAGCAAATCTTCGAACCC
1 CTTCCTGATGAGATACAGAGAAGAAGACCAAATCAAAGGCTCAAAGTGAGCAAATCTTCGAACCC
* * * * * *
609234 CAACTTCTTTATGAGATACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGCTTCCTGATGAAAT
66 CAGCTTCATGATGAGATACTGAGAAGCAGGTCGAAGTAATAAAAAGGTTAGCTTCCTGACGAAAT
* * * *
609299 ATTGAGAAGTCGACCAAATTCGTCTTCCTGGTGAGATACAGAGAAACGGATTGAAACAAACGACA
131 ACTGAGAAGTCGACCAAATTCGTCTTCCTGATGAGATACAGAGAAACGAATTAAAACAAACGACA
609364 CGGTCAT
196 CGGTCAT
* * * *
609371 CTTCCTGATGAGGTACTGAGAAGAAGACCAAATCAAACCCGCACTCGATA-TGAGCAAATCTTCG
1 CTTCCTGATGAGATACAGAGAAGAAGACCAAATCAAA---G-GCTC-AAAGTGAGCAAATCTTCG
* * *
609435 AACCCCAGCTTCATGATGAGATATTAAGAAGCAGGTCGAAGTAATAAAACA-GTTAGCTCCCTGA
61 AACCCCAGCTTCATGATGAGATACTGAGAAGCAGGTCGAAGTAATAAAA-AGGTTAGCTTCCTGA
609499 TGAAGTACGG
Statistics
Matches: 273, Mismatches: 48, Indels: 19
0.80 0.14 0.06
Matches are distributed among these distances:
201 168 0.62
202 2 0.01
205 1 0.00
206 72 0.26
207 1 0.00
209 29 0.11
ACGTcount: A:0.36, C:0.20, G:0.22, T:0.22
Consensus pattern (202 bp):
CTTCCTGATGAGATACAGAGAAGAAGACCAAATCAAAGGCTCAAAGTGAGCAAATCTTCGAACCC
CAGCTTCATGATGAGATACTGAGAAGCAGGTCGAAGTAATAAAAAGGTTAGCTTCCTGACGAAAT
ACTGAGAAGTCGACCAAATTCGTCTTCCTGATGAGATACAGAGAAACGAATTAAAACAAACGACA
CGGTCAT
Found at i:609582 original size:206 final size:206
Alignment explanation
Indices: 609215--609588 Score: 453
Period size: 206 Copynumber: 1.8 Consensus size: 206
609205 AGGCTCAACG
* * * **
609215 TGAGCAAATCTTCGAACCCCAACTTCTTTATGAGATACTGAGAAGCAGGTCGAAGCAATAAAATG
1 TGAGCAAATCTTCGAACCCCAACTTCATGATGAGATACTAAGAAGCAGGTCGAAGCAATAAAACA
* ** ** * ** * *
609280 GTTAGCTTCCTGATGAAATATTGAGAAGTCGACCAAATTCGTCTTCCTGGTGAGATACAGAGAAA
66 GTTAGCTCCCTGATGAAATACGGAGAAGTCGACCAAAACCATCTTCCTAATGAAACACAGAGAAA
***
609345 CGGATTGAAACAAACGACACGGTCATCTTCCTGATGAGGTACTGAGAAGAAGACCAAATCAAACC
131 CGGACCAAAACAAACGACACGGTCATCTTCCTGATGAGGTACTGAGAAGAAGACCAAATCAAACC
609410 CGCACTCGATA
196 CGCACTCGATA
* * *
609421 TGAGCAAATCTTCGAACCCCAGCTTCATGATGAGATATTAAGAAGCAGGTCGAAGTAATAAAACA
1 TGAGCAAATCTTCGAACCCCAACTTCATGATGAGATACTAAGAAGCAGGTCGAAGCAATAAAACA
* *
609486 GTTAGCTCCCTGATGAAGTACGGGGAAGT-GAACCAAAACCATCTTCCTAATGAAACACAGAGAA
66 GTTAGCTCCCTGATGAAATACGGAGAAGTCG-ACCAAAACCATCTTCCTAATGAAACACAGAGAA
** * ** * * *
609550 GTGGACCAAAACCAGTGATATGGTCGTCTTCCTGATGAG
130 ACGGACCAAAACAAACGACACGGTCATCTTCCTGATGAG
609589 ATGCTAAAAG
Statistics
Matches: 136, Mismatches: 31, Indels: 2
0.80 0.18 0.01
Matches are distributed among these distances:
205 1 0.01
206 135 0.99
ACGTcount: A:0.36, C:0.21, G:0.22, T:0.22
Consensus pattern (206 bp):
TGAGCAAATCTTCGAACCCCAACTTCATGATGAGATACTAAGAAGCAGGTCGAAGCAATAAAACA
GTTAGCTCCCTGATGAAATACGGAGAAGTCGACCAAAACCATCTTCCTAATGAAACACAGAGAAA
CGGACCAAAACAAACGACACGGTCATCTTCCTGATGAGGTACTGAGAAGAAGACCAAATCAAACC
CGCACTCGATA
Found at i:609985 original size:18 final size:17
Alignment explanation
Indices: 609927--610007 Score: 83
Period size: 17 Copynumber: 4.6 Consensus size: 17
609917 GCCCAACAGG
* *
609927 ATTTAAATTCATTTTAAA
1 ATTTAAATTTA-TTAAAA
**
609945 A-TTAAATTTATTTTAA
1 ATTTAAATTTATTAAAA
*
609961 GTTTAAATTTACTTAAAA
1 ATTTAAATTTA-TTAAAA
609979 ATTTAAATTTATTAAAA
1 ATTTAAATTTATTAAAA
609996 ATTTAAAGTTTA
1 ATTTAAA-TTTA
610008 AATCTATTTA
Statistics
Matches: 54, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
16 5 0.09
17 30 0.56
18 19 0.35
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.49
Consensus pattern (17 bp):
ATTTAAATTTATTAAAA
Found at i:610673 original size:10 final size:10
Alignment explanation
Indices: 610658--610688 Score: 55
Period size: 10 Copynumber: 3.2 Consensus size: 10
610648 TCAAAACATT
610658 TTAATAACTA
1 TTAATAACTA
610668 TTAATAA-TA
1 TTAATAACTA
610677 TTAATAACTA
1 TTAATAACTA
610687 TT
1 TT
610689 TTAATAATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
9 9 0.45
10 11 0.55
ACGTcount: A:0.48, C:0.06, G:0.00, T:0.45
Consensus pattern (10 bp):
TTAATAACTA
Found at i:610801 original size:6 final size:6
Alignment explanation
Indices: 610792--610868 Score: 63
Period size: 6 Copynumber: 13.3 Consensus size: 6
610782 TCATTTTGGG
* * * * *
610792 TTTAAA TTT-AG TTTAAG TTTAAA -TTAAG TTTAAA -TTAAG TTTAAT
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
*
610837 TTTAAA TTT-AA TTTGAA TTTAAAA TTTAAA TT
1 TTTAAA TTTAAA TTTAAA TTT-AAA TTTAAA TT
610869 AATTGAAAAG
Statistics
Matches: 58, Mismatches: 8, Indels: 10
0.76 0.11 0.13
Matches are distributed among these distances:
5 17 0.29
6 36 0.62
7 5 0.09
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.52
Consensus pattern (6 bp):
TTTAAA
Found at i:610807 original size:11 final size:11
Alignment explanation
Indices: 610804--610835 Score: 64
Period size: 11 Copynumber: 2.9 Consensus size: 11
610794 TAAATTTAGT
610804 TTAAGTTTAAA
1 TTAAGTTTAAA
610815 TTAAGTTTAAA
1 TTAAGTTTAAA
610826 TTAAGTTTAA
1 TTAAGTTTAA
610836 TTTTAAATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.44, C:0.00, G:0.09, T:0.47
Consensus pattern (11 bp):
TTAAGTTTAAA
Found at i:610823 original size:22 final size:22
Alignment explanation
Indices: 610793--610847 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 22
610783 CATTTTGGGT
**
610793 TTAAATTTAGTTTAAGTTTAAA
1 TTAAATTTAAATTAAGTTTAAA
* *
610815 TTAAGTTTAAATTAAGTTTAATT
1 TTAAATTTAAATTAAGTTTAA-A
610838 TTAAATTTAA
1 TTAAATTTAA
610848 TTTGAATTTA
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
22 18 0.67
23 9 0.33
ACGTcount: A:0.42, C:0.00, G:0.07, T:0.51
Consensus pattern (22 bp):
TTAAATTTAAATTAAGTTTAAA
Found at i:610835 original size:17 final size:17
Alignment explanation
Indices: 610791--610824 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
610781 TTCATTTTGG
*
610791 GTTTAAATTTAGTTTAA
1 GTTTAAATTAAGTTTAA
610808 GTTTAAATTAAGTTTAA
1 GTTTAAATTAAGTTTAA
610825 ATTAAGTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.38, C:0.00, G:0.12, T:0.50
Consensus pattern (17 bp):
GTTTAAATTAAGTTTAA
Found at i:610877 original size:17 final size:18
Alignment explanation
Indices: 610840--610877 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
610830 GTTTAATTTT
* *
610840 AAATTTAATTTGAATTTA
1 AAATTTAAATTGAATTGA
610858 AAATTTAAATT-AATTGA
1 AAATTTAAATTGAATTGA
610875 AAA
1 AAA
610878 GGTCCAGTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 8 0.44
18 10 0.56
ACGTcount: A:0.53, C:0.00, G:0.05, T:0.42
Consensus pattern (18 bp):
AAATTTAAATTGAATTGA
Found at i:612797 original size:29 final size:29
Alignment explanation
Indices: 612729--613037 Score: 229
Period size: 30 Copynumber: 10.6 Consensus size: 29
612719 ACTATCTAAG
**
612729 AATTCCATTTTTACCCCCGAACTTCCAAAAA
1 AATTCCATTTTTACCCCAAAACTTCC--AAA
*
612760 AATT---TTTTTAACCCCAAAACTTCTAAA
1 AATTCCATTTTT-ACCCCAAAACTTCCAAA
* *
612787 AATTCCATTTTTAACCTC-GAACTTCCAAA
1 AATTCCATTTTT-ACCCCAAAACTTCCAAA
*
612816 AATTCCATTTTTACCCTC-GAACTTCCAAA
1 AATTCCATTTTTACCC-CAAAACTTCCAAA
**
612845 AACCCCATTTTTGACCCCAAAACTTCCAAA
1 AATTCCATTTTT-ACCCCAAAACTTCCAAA
* * *
612875 AA-TCTTATTTTTGACCTCGAAACTTCCAAA
1 AATTC-CATTTTT-ACCCCAAAACTTCCAAA
* * *
612905 AATCCCATTTTTGCCCTC-AAACTTCAAAA
1 AATTCCATTTTTACCC-CAAAACTTCCAAA
* * ** * *
612934 AATCCCATTTTTGAACTGAAAACCTCTAAA
1 AATTCCATTTTT-ACCCCAAAACTTCCAAA
** *
612964 AATTCCATTTTTA-CCCTGAACTTTCAAA
1 AATTCCATTTTTACCCCAAAACTTCCAAA
* *
612992 AATGCCATTTTTAACCCCAAAACTTCCAAG
1 AATTCCATTTTT-ACCCCAAAACTTCCAAA
*
613022 AATTTCATTTTTACCC
1 AATTCCATTTTTACCC
613038 TCGAACCTCC
Statistics
Matches: 224, Mismatches: 40, Indels: 30
0.76 0.14 0.10
Matches are distributed among these distances:
27 7 0.03
28 27 0.12
29 86 0.38
30 99 0.44
31 5 0.02
ACGTcount: A:0.35, C:0.28, G:0.04, T:0.33
Consensus pattern (29 bp):
AATTCCATTTTTACCCCAAAACTTCCAAA
Found at i:612877 original size:59 final size:59
Alignment explanation
Indices: 612776--613073 Score: 214
Period size: 59 Copynumber: 5.1 Consensus size: 59
612766 TTTAACCCCA
* ** ** *
612776 AAACTTCTAAAAATTCCATTTTTAACCTCGAACTTCCAAAAATTCCATTTTT-ACCCTCG
1 AAACTTCCAAAAACCCCATTTTTGCCCTCAAACTTCCAAAAATTCCATTTTTGA-CCTCG
*
612835 -AACTTCCAAAAACCCCATTTTTGACCC-CAAAACTTCCAAAAA-TCTTATTTTTGACCTCG
1 AAACTTCCAAAAACCCCATTTTTG-CCCTC-AAACTTCCAAAAATTC-CATTTTTGACCTCG
* * * *
612894 AAACTTCCAAAAATCCCATTTTTGCCCTCAAACTTCAAAAAATCCCATTTTTGAACT-G
1 AAACTTCCAAAAACCCCATTTTTGCCCTCAAACTTCCAAAAATTCCATTTTTGACCTCG
* * ** * * * * * * *
612952 AAAACCTCTAAAAATTCCATTTTTACCCT-GAACTTTCAAAAATGCCATTTTTAACCCCA
1 -AAACTTCCAAAAACCCCATTTTTGCCCTCAAACTTCCAAAAATTCCATTTTTGACCTCG
* *** * * * * *
613011 AAACTTCCAAGAATTTCATTTTTACCCTCGAACCTCC-AAAATCTCTATTTTCGACCTCG
1 AAACTTCCAAAAACCCCATTTTTGCCCTCAAACTTCCAAAAAT-TCCATTTTTGACCTCG
613070 AAAC
1 AAAC
613074 CTTAAAAATT
Statistics
Matches: 192, Mismatches: 36, Indels: 22
0.77 0.14 0.09
Matches are distributed among these distances:
58 73 0.38
59 94 0.49
60 25 0.13
ACGTcount: A:0.35, C:0.29, G:0.05, T:0.32
Consensus pattern (59 bp):
AAACTTCCAAAAACCCCATTTTTGCCCTCAAACTTCCAAAAATTCCATTTTTGACCTCG
Found at i:613048 original size:29 final size:29
Alignment explanation
Indices: 612729--613051 Score: 245
Period size: 29 Copynumber: 11.0 Consensus size: 29
612719 ACTATCTAAG
*
612729 AATTCCATTTTTACCCCCGAACTTCCAAAAA
1 AATTCCATTTTTACCCTCGAACTTCC--AAA
* *
612760 AATT---TTTTTAACCC-CAAAACTTCTAAA
1 AATTCCATTTTT-ACCCTC-GAACTTCCAAA
*
612787 AATTCCATTTTTAACCTCGAACTTCCAAA
1 AATTCCATTTTTACCCTCGAACTTCCAAA
612816 AATTCCATTTTTACCCTCGAACTTCCAAA
1 AATTCCATTTTTACCCTCGAACTTCCAAA
** *
612845 AACCCCATTTTTGACCC-CAAAACTTCCAAA
1 AATTCCATTTTT-ACCCTC-GAACTTCCAAA
*
612875 AA-TCTTATTTTTGA-CCTCGAAACTTCCAAA
1 AATTC-CATTTTT-ACCCTCG-AACTTCCAAA
* * * *
612905 AATCCCATTTTTGCCCTCAAACTTCAAAA
1 AATTCCATTTTTACCCTCGAACTTCCAAA
* * * *
612934 AATCCCATTTTTGA-ACT-GAAAACCTCTAAA
1 AATTCCATTTTT-ACCCTCG--AACTTCCAAA
*
612964 AATTCCATTTTTACCCT-GAACTTTCAAA
1 AATTCCATTTTTACCCTCGAACTTCCAAA
* * *
612992 AATGCCATTTTTAACCC-CAAAACTTCCAAG
1 AATTCCATTTTT-ACCCTC-GAACTTCCAAA
* *
613022 AATTTCATTTTTACCCTCGAACCTCCAAA
1 AATTCCATTTTTACCCTCGAACTTCCAAA
613051 A
1 A
613052 TCTCTATTTT
Statistics
Matches: 235, Mismatches: 36, Indels: 44
0.75 0.11 0.14
Matches are distributed among these distances:
27 7 0.03
28 24 0.10
29 105 0.45
30 94 0.40
31 5 0.02
ACGTcount: A:0.35, C:0.28, G:0.04, T:0.32
Consensus pattern (29 bp):
AATTCCATTTTTACCCTCGAACTTCCAAA
Found at i:614022 original size:18 final size:18
Alignment explanation
Indices: 613999--614044 Score: 92
Period size: 18 Copynumber: 2.6 Consensus size: 18
613989 CGACTCCTAT
613999 TAATTTTCGATTTTAAAA
1 TAATTTTCGATTTTAAAA
614017 TAATTTTCGATTTTAAAA
1 TAATTTTCGATTTTAAAA
614035 TAATTTTCGA
1 TAATTTTCGA
614045 AACTCGTCGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.37, C:0.07, G:0.07, T:0.50
Consensus pattern (18 bp):
TAATTTTCGATTTTAAAA
Found at i:615182 original size:29 final size:28
Alignment explanation
Indices: 615137--615378 Score: 211
Period size: 29 Copynumber: 8.3 Consensus size: 28
615127 CCCTAAATTG
*
615137 TCCAAAAATTC-TGTTTTGACCCCCGAACT
1 TCCAAAAATTCAT-TTTT-ACCCCCAAACT
* *
615166 TCCAAAAATCTCATTTTTACTCCCGAACT
1 TCCAAAAAT-TCATTTTTACCCCCAAACT
**
615195 TCTC-AAAATTCCATTTTTAACCCTAAAACT
1 TC-CAAAAATT-CATTTTT-ACCCCCAAACT
* *
615225 TCCAAAAATTCATTTTTACCCTCGAACT
1 TCCAAAAATTCATTTTTACCCCCAAACT
*
615253 TCCAAAAATTCCATTTTTACCCTCAAACT
1 TCCAAAAATT-CATTTTTACCCCCAAACT
* * * *
615282 TCCCAACATTCCATTTTGACCCCAAAACT
1 TCCAAAAATT-CATTTTTACCCCCAAACT
* *
615311 TCCAAAAATTCCAATTTTACCCTCAAGA-T
1 TCCAAAAATT-CATTTTTACCCCCAA-ACT
**
615340 TCCAAAAATTCCATTTTTAACCCTAAAACT
1 TCCAAAAATT-CATTTTT-ACCCCCAAACT
615370 TCCAAAAAT
1 TCCAAAAAT
615379 ACCCTTTTAC
Statistics
Matches: 182, Mismatches: 21, Indels: 19
0.82 0.09 0.09
Matches are distributed among these distances:
28 20 0.11
29 121 0.66
30 40 0.22
31 1 0.01
ACGTcount: A:0.35, C:0.30, G:0.03, T:0.33
Consensus pattern (28 bp):
TCCAAAAATTCATTTTTACCCCCAAACT
Found at i:615251 original size:58 final size:57
Alignment explanation
Indices: 615162--615378 Score: 244
Period size: 58 Copynumber: 3.7 Consensus size: 57
615152 TTGACCCCCG
*
615162 AACTTCCAAAAA-TCTCATTTTTACTCCCGAACTTCTC-AAAATTCCATTTTTAACCCTAA
1 AACTTCCAAAAATTC-CATTTTTAC-CCCAAACTTC-CAAAAATTCCATTTTT-ACCCTAA
* *
615221 AACTTCCAAAAATT-CATTTTTACCCTCGAACTTCCAAAAATTCCATTTTTACCCTCA
1 AACTTCCAAAAATTCCATTTTTACCC-CAAACTTCCAAAAATTCCATTTTTACCCTAA
* * * *
615278 AACTTCCCAACATTCCATTTTGACCCCAAAACTTCCAAAAATTCCAATTTTACCCTCAA
1 AACTTCCAAAAATTCCATTTTTACCCC-AAACTTCCAAAAATTCCATTTTTACCCT-AA
* *
615337 GA-TTCCAAAAATTCCATTTTTAACCCTAAAACTTCCAAAAAT
1 AACTTCCAAAAATTCCATTTTT-ACCC-CAAACTTCCAAAAAT
615379 ACCCTTTTAC
Statistics
Matches: 138, Mismatches: 12, Indels: 16
0.83 0.07 0.10
Matches are distributed among these distances:
57 22 0.16
58 83 0.60
59 32 0.23
60 1 0.01
ACGTcount: A:0.36, C:0.29, G:0.02, T:0.33
Consensus pattern (57 bp):
AACTTCCAAAAATTCCATTTTTACCCCAAACTTCCAAAAATTCCATTTTTACCCTAA
Found at i:615282 original size:87 final size:85
Alignment explanation
Indices: 615137--615376 Score: 290
Period size: 87 Copynumber: 2.8 Consensus size: 85
615127 CCCTAAATTG
* *
615137 TCCAAAAATTC-TGTTTTGACCCCCGAACTTCCAAAAA-TCTCATTTTTACTCC-CGAACTTCTC
1 TCCAAAAATTCAT-TTTT-ACCCTCGAACTTCCAAAAATTC-CATTTTTAC-CCTCAAACTTC-C
*
615199 AAAATTCCATTTTTAACCCTAAAACT
61 AAAATTCCA-TTTTAACCCCAAAACT
*
615225 TCCAAAAATTCATTTTTACCCTCGAACTTCCAAAAATTCCATTTTTACCCTCAAACTTCCCAACA
1 TCCAAAAATTCATTTTTACCCTCGAACTTCCAAAAATTCCATTTTTACCCTCAAACTT-CCAAAA
*
615290 TTCCATTTTGACCCCAAAACT
65 TTCCATTTTAACCCCAAAACT
* * *
615311 TCCAAAAATTCCAATTTTACCCTC-AAGATTCCAAAAATTCCATTTTTAACCCTAAAACTTCCAA
1 TCCAAAAATT-CATTTTTACCCTCGAA-CTTCCAAAAATTCCATTTTT-ACCCTCAAACTTCCAA
615375 AA
63 AA
615377 ATACCCTTTT
Statistics
Matches: 136, Mismatches: 9, Indels: 15
0.85 0.06 0.09
Matches are distributed among these distances:
86 28 0.21
87 78 0.57
88 29 0.21
89 1 0.01
ACGTcount: A:0.35, C:0.30, G:0.03, T:0.33
Consensus pattern (85 bp):
TCCAAAAATTCATTTTTACCCTCGAACTTCCAAAAATTCCATTTTTACCCTCAAACTTCCAAAAT
TCCATTTTAACCCCAAAACT
Found at i:615386 original size:29 final size:29
Alignment explanation
Indices: 615191--615423 Score: 215
Period size: 29 Copynumber: 8.0 Consensus size: 29
615181 TTTACTCCCG
615191 AACTTCTC-AAAATTCCATTTTTAACCCTAA
1 AACTTC-CAAAAATTCCA-TTTTAACCCTAA
* **
615221 AACTTCCAAAAATT-CATTTTTACCCTCG
1 AACTTCCAAAAATTCCATTTTAACCCTAA
* *
615249 AACTTCCAAAAATTCCATTTTTACCCTCA
1 AACTTCCAAAAATTCCATTTTAACCCTAA
* * * *
615278 AACTTCCCAACATTCCATTTTGACCCCAA
1 AACTTCCAAAAATTCCATTTTAACCCTAA
615307 AACTTCCAAAAATTCCAATTTT-ACCCTCAA
1 AACTTCCAAAAATTCC-ATTTTAACCCT-AA
*
615337 GA-TTCCAAAAATTCCATTTTTAACCCTAA
1 AACTTCCAAAAATTCCA-TTTTAACCCTAA
* * * **
615366 AACTTCCAAAAATACCCTTTTACCCCTCG
1 AACTTCCAAAAATTCCATTTTAACCCTAA
* *
615395 AA-TGTCTAAAAAGTCCATTTTTAACCCTA
1 AACT-TCCAAAAATTCCA-TTTTAACCCTA
615424 GATTTTCCCA
Statistics
Matches: 169, Mismatches: 25, Indels: 18
0.80 0.12 0.08
Matches are distributed among these distances:
28 25 0.15
29 98 0.58
30 46 0.27
ACGTcount: A:0.35, C:0.30, G:0.03, T:0.33
Consensus pattern (29 bp):
AACTTCCAAAAATTCCATTTTAACCCTAA
Found at i:615387 original size:58 final size:58
Alignment explanation
Indices: 615191--615423 Score: 242
Period size: 58 Copynumber: 4.0 Consensus size: 58
615181 TTTACTCCCG
* * **
615191 AACTTCTC-AAAATTCCATTTTTAACCCTAAAACTTCCAAAAATT-CATTTTT-ACCCTCG
1 AACTTC-CAAAAATTCCAATTTT-ACCCTCAAA-TTCCAAAAATTCCATTTTTAACCCTAA
* * * * *
615249 AACTTCCAAAAATTCCATTTTTACCCTCAAACTTCCCAACATTCCA-TTTTGACCCCAA
1 AACTTCCAAAAATTCCAATTTTACCCTCAAA-TTCCAAAAATTCCATTTTTAACCCTAA
615307 AACTTCCAAAAATTCCAATTTTACCCTCAAGATTCCAAAAATTCCATTTTTAACCCTAA
1 AACTTCCAAAAATTCCAATTTTACCCTCAA-ATTCCAAAAATTCCATTTTTAACCCTAA
* * * * *
615366 AACTTCCAAAAATACC-CTTTTACCCCTCGAATGTCTAAAAAGTCCATTTTTAACCCTA
1 AACTTCCAAAAATTCCAATTTTA-CCCTCAAAT-TCCAAAAATTCCATTTTTAACCCTA
615424 GATTTTCCCA
Statistics
Matches: 152, Mismatches: 16, Indels: 13
0.84 0.09 0.07
Matches are distributed among these distances:
57 23 0.15
58 74 0.49
59 55 0.36
ACGTcount: A:0.35, C:0.30, G:0.03, T:0.33
Consensus pattern (58 bp):
AACTTCCAAAAATTCCAATTTTACCCTCAAATTCCAAAAATTCCATTTTTAACCCTAA
Found at i:616955 original size:29 final size:29
Alignment explanation
Indices: 616923--617053 Score: 142
Period size: 28 Copynumber: 4.6 Consensus size: 29
616913 TTTTGGAGAA
* *
616923 TTTAGGGTTAAAATATAATTTTAGAAAAG
1 TTTAGGGTTAAAATATAATTTTGGGAAAG
*
616952 TTTAGGG-TAAAATGTAATTTTGGGAAAG
1 TTTAGGGTTAAAATATAATTTTGGGAAAG
* *
616980 CTTGAGGGTTAAAATGTAATTTTGGGAAAG
1 -TTTAGGGTTAAAATATAATTTTGGGAAAG
* *
617010 TTT-GATGTTAAAATATGATTTTGGG-AAG
1 TTTAG-GGTTAAAATATAATTTTGGGAAAG
* *
617038 TTTGGGGTCAAAATAT
1 TTTAGGGTTAAAATAT
617054 GACTTTAGGA
Statistics
Matches: 88, Mismatches: 10, Indels: 9
0.82 0.09 0.08
Matches are distributed among these distances:
28 34 0.39
29 33 0.38
30 21 0.24
ACGTcount: A:0.36, C:0.02, G:0.25, T:0.37
Consensus pattern (29 bp):
TTTAGGGTTAAAATATAATTTTGGGAAAG
Found at i:617000 original size:58 final size:59
Alignment explanation
Indices: 616926--617053 Score: 154
Period size: 58 Copynumber: 2.2 Consensus size: 59
616916 TGGAGAATTT
*
616926 AGGGTTAAAATATAATTTTAGAAAAGTTT-AGGGTAAAATGTAATTTTGGGAAAGCTTG
1 AGGGTTAAAATATAATTTTAGAAAAGTTTGAGGGTAAAATATAATTTTGGGAAAGCTTG
* * * * * * *
616984 AGGGTTAAAATGTAATTTTGGGAAAGTTTGATGTTAAAATATGATTTTGGG-AAGTTTG
1 AGGGTTAAAATATAATTTTAGAAAAGTTTGAGGGTAAAATATAATTTTGGGAAAGCTTG
*
617042 -GGGTCAAAATAT
1 AGGGTTAAAATAT
617054 GACTTTAGGA
Statistics
Matches: 59, Mismatches: 10, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
57 10 0.17
58 32 0.54
59 17 0.29
ACGTcount: A:0.37, C:0.02, G:0.26, T:0.36
Consensus pattern (59 bp):
AGGGTTAAAATATAATTTTAGAAAAGTTTGAGGGTAAAATATAATTTTGGGAAAGCTTG
Found at i:618018 original size:16 final size:15
Alignment explanation
Indices: 617993--618027 Score: 52
Period size: 16 Copynumber: 2.3 Consensus size: 15
617983 ATATTTTCTT
617993 TTTAAATTAAAATAAA
1 TTTAAATTAAAAT-AA
*
618009 TTTAATTTAAAATAA
1 TTTAAATTAAAATAA
618024 TTTA
1 TTTA
618028 TTTCTGAGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 6 0.33
16 12 0.67
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (15 bp):
TTTAAATTAAAATAA
Done.