Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr05 ID=Chr05-JGI_221_v2.0
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: 64140413
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 820884 characters in sequence are not A, C, G, or T
File 142 of 208
Found at i:43436496 original size:29 final size:29
Alignment explanation
Indices: 43436444--43436563 Score: 133
Period size: 29 Copynumber: 4.2 Consensus size: 29
43436434 ACTTGCATGC
43436444 ATGCATGCATATTCATGCATGCATGTATGAT
1 ATGCATGCATA--CATGCATGCATGTATGAT
43436475 ATGCATGCATACATGCATGCATGTATGAT
1 ATGCATGCATACATGCATGCATGTATGAT
* *
43436504 ATGCATGCATGCATGTATG-A--TATGA-
1 ATGCATGCATACATGCATGCATGTATGAT
* ** *
43436529 ATACATGCATGTATGCATGTATGTATG-T
1 ATGCATGCATACATGCATGCATGTATGAT
43436557 ATGCATG
1 ATGCATG
43436564 TAGGCATGCA
Statistics
Matches: 79, Mismatches: 6, Indels: 11
0.82 0.06 0.11
Matches are distributed among these distances:
25 16 0.20
26 6 0.08
28 11 0.14
29 35 0.44
31 11 0.14
ACGTcount: A:0.30, C:0.14, G:0.22, T:0.34
Consensus pattern (29 bp):
ATGCATGCATACATGCATGCATGTATGAT
Found at i:43436552 original size:12 final size:12
Alignment explanation
Indices: 43436495--43436955 Score: 548
Period size: 12 Copynumber: 38.2 Consensus size: 12
43436485 ACATGCATGC
*
43436495 ATGTATGATATGC
1 ATGTATG-TATGT
* *
43436508 ATGCATGCATGT
1 ATGTATGTATGT
* **
43436520 ATGATATGAATAC
1 ATG-TATGTATGT
* *
43436533 ATGCATGTATGC
1 ATGTATGTATGT
43436545 ATGTATGTATGT
1 ATGTATGTATGT
* * *
43436557 ATGCATGTAGGC
1 ATGTATGTATGT
* *
43436569 ATGCATATATGCT
1 ATGTATGTATG-T
43436582 -TGTATGTATGT
1 ATGTATGTATGT
43436593 ATGTATGTATGT
1 ATGTATGTATGT
43436605 ATGTATGTATGT
1 ATGTATGTATGT
43436617 ATGTATGTATGT
1 ATGTATGTATGT
43436629 ATGTATGTATGT
1 ATGTATGTATGT
* *
43436641 ATGTATCTTTGT
1 ATGTATGTATGT
*
43436653 ATGTACGTATGT
1 ATGTATGTATGT
* *
43436665 ACGTATGTACGT
1 ATGTATGTATGT
*
43436677 ATATATGTATGT
1 ATGTATGTATGT
* *
43436689 ACGTATGTACGT
1 ATGTATGTATGT
*
43436701 ATGTACGTATGT
1 ATGTATGTATGT
* *
43436713 ACGTATGTACGT
1 ATGTATGTATGT
*
43436725 ATGTATGCATGT
1 ATGTATGTATGT
*
43436737 ATGTATGCATGT
1 ATGTATGTATGT
*
43436749 ATGCATGTATGT
1 ATGTATGTATGT
*
43436761 ATGCATGTATGT
1 ATGTATGTATGT
*
43436773 ATGCATGTATGT
1 ATGTATGTATGT
*
43436785 ATGGATGTATGT
1 ATGTATGTATGT
*
43436797 ATGTATGTATGG
1 ATGTATGTATGT
* *
43436809 ATGCATGTATGG
1 ATGTATGTATGT
43436821 ATGTATGTATGT
1 ATGTATGTATGT
43436833 ATGTATGTATGT
1 ATGTATGTATGT
43436845 ATGTATGTATGT
1 ATGTATGTATGT
43436857 ATGTATGTATGT
1 ATGTATGTATGT
43436869 ATGTATGTATGT
1 ATGTATGTATGT
43436881 ATGTATGTATGT
1 ATGTATGTATGT
43436893 ATGTATGTATGT
1 ATGTATGTATGT
43436905 ATGTATGTATGT
1 ATGTATGTATGT
43436917 AT-TAATGTATGT
1 ATGT-ATGTATGT
* *
43436929 ATGCATGTATGC
1 ATGTATGTATGT
*
43436941 ATGTATGCATGT
1 ATGTATGTATGT
43436953 ATG
1 ATG
43436956 CATGATATTC
Statistics
Matches: 387, Mismatches: 56, Indels: 11
0.85 0.12 0.02
Matches are distributed among these distances:
11 2 0.01
12 371 0.96
13 14 0.04
ACGTcount: A:0.26, C:0.06, G:0.25, T:0.43
Consensus pattern (12 bp):
ATGTATGTATGT
Found at i:43436580 original size:8 final size:8
Alignment explanation
Indices: 43436437--43436959 Score: 301
Period size: 8 Copynumber: 65.8 Consensus size: 8
43436427 TGTCTTAACT
*
43436437 TGCATGCA
1 TGCATGTA
43436445 TGCATGCATA
1 TGCATG--TA
* *
43436455 TTCATGCA
1 TGCATGTA
43436463 TGCATGTA
1 TGCATGTA
43436471 TG-A--TA
1 TGCATGTA
*
43436476 TGCATGCA
1 TGCATGTA
* *
43436484 TACATGCA
1 TGCATGTA
43436492 TGCATGTA
1 TGCATGTA
43436500 TG-A--TA
1 TGCATGTA
*
43436505 TGCATGCA
1 TGCATGTA
43436513 TGCATGTA
1 TGCATGTA
43436521 TG-A--TA
1 TGCATGTA
* **
43436526 TGAATACA
1 TGCATGTA
43436534 TGCATGTA
1 TGCATGTA
43436542 TGCATGTA
1 TGCATGTA
*
43436550 TGTATGTA
1 TGCATGTA
43436558 TGCATGTAGGCA
1 TGCATGT----A
*
43436570 TGCATATA
1 TGCATGTA
*
43436578 TGCTTGTA
1 TGCATGTA
*
43436586 TGTATGTA
1 TGCATGTA
*
43436594 TGTATGTA
1 TGCATGTA
*
43436602 TGTATGTA
1 TGCATGTA
*
43436610 TGTATGTA
1 TGCATGTA
*
43436618 TGTATGTA
1 TGCATGTA
*
43436626 TGTATGTA
1 TGCATGTA
*
43436634 TGTATGTA
1 TGCATGTA
* * *
43436642 TGTATCTT
1 TGCATGTA
*
43436650 TGTATGTA
1 TGCATGTA
* *
43436658 CGTATGTA
1 TGCATGTA
* *
43436666 CGTATGTA
1 TGCATGTA
* * *
43436674 CGTATATA
1 TGCATGTA
*
43436682 TGTATGTA
1 TGCATGTA
* *
43436690 CGTATGTA
1 TGCATGTA
* *
43436698 CGTATGTA
1 TGCATGTA
* *
43436706 CGTATGTA
1 TGCATGTA
* *
43436714 CGTATGTA
1 TGCATGTA
* *
43436722 CGTATGTA
1 TGCATGTA
43436730 TGCATGTA
1 TGCATGTA
* *
43436738 TGTATGCA
1 TGCATGTA
* *
43436746 TGTATGCA
1 TGCATGTA
*
43436754 TGTATGTA
1 TGCATGTA
43436762 TGCATGTA
1 TGCATGTA
* *
43436770 TGTATGCA
1 TGCATGTA
*
43436778 TGTATGTA
1 TGCATGTA
*
43436786 TGGATGTA
1 TGCATGTA
*
43436794 TGTATGTA
1 TGCATGTA
* *
43436802 TGTATGGA
1 TGCATGTA
43436810 TGCATGTA
1 TGCATGTA
*
43436818 TGGATGTA
1 TGCATGTA
*
43436826 TGTATGTA
1 TGCATGTA
*
43436834 TGTATGTA
1 TGCATGTA
*
43436842 TGTATGTA
1 TGCATGTA
*
43436850 TGTATGTA
1 TGCATGTA
*
43436858 TGTATGTA
1 TGCATGTA
*
43436866 TGTATGTA
1 TGCATGTA
*
43436874 TGTATGTA
1 TGCATGTA
*
43436882 TGTATGTA
1 TGCATGTA
*
43436890 TGTATGTA
1 TGCATGTA
*
43436898 TGTATGTA
1 TGCATGTA
*
43436906 TGTATGTA
1 TGCATGTA
*
43436914 TGTAT-TAA
1 TGCATGT-A
*
43436922 TGTATGTA
1 TGCATGTA
43436930 TGCATGTA
1 TGCATGTA
43436938 TGCATGTA
1 TGCATGTA
43436946 TGCATGTA
1 TGCATGTA
43436954 TGCATG
1 TGCATG
43436960 ATATTCCGAA
Statistics
Matches: 450, Mismatches: 48, Indels: 34
0.85 0.09 0.06
Matches are distributed among these distances:
5 12 0.03
6 3 0.01
7 4 0.01
8 417 0.93
9 1 0.00
10 6 0.01
12 7 0.02
ACGTcount: A:0.26, C:0.08, G:0.24, T:0.42
Consensus pattern (8 bp):
TGCATGTA
Found at i:43438071 original size:35 final size:33
Alignment explanation
Indices: 43438008--43438072 Score: 78
Period size: 35 Copynumber: 1.9 Consensus size: 33
43437998 ATATTTTTAT
* *
43438008 TTTTTTTAATTTTAAAGAGTTCTTATTTTTGCA
1 TTTTTTTAATTTTAAAGAGTTATAATTTTTGCA
43438041 TTTTTTTAATTTTTTAAA-AGATTATAATTTTT
1 TTTTTTTAA--TTTTAAAGAG-TTATAATTTTT
43438073 TTAGTTTTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
33 9 0.33
34 2 0.07
35 16 0.59
ACGTcount: A:0.28, C:0.03, G:0.06, T:0.63
Consensus pattern (33 bp):
TTTTTTTAATTTTAAAGAGTTATAATTTTTGCA
Found at i:43454492 original size:22 final size:22
Alignment explanation
Indices: 43454464--43454507 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
43454454 TGTATCAATG
43454464 ATTAAATTTATCCTTCATGATT
1 ATTAAATTTATCCTTCATGATT
43454486 ATTAAATTTATCCTTCATGATT
1 ATTAAATTTATCCTTCATGATT
43454508 TTCAAGATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.32, C:0.14, G:0.05, T:0.50
Consensus pattern (22 bp):
ATTAAATTTATCCTTCATGATT
Found at i:43454804 original size:2 final size:2
Alignment explanation
Indices: 43454797--43454838 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
43454787 TGACTATGAC
*
43454797 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TT TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
43454839 ATTGCATGAA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:43460214 original size:41 final size:41
Alignment explanation
Indices: 43460161--43460487 Score: 426
Period size: 41 Copynumber: 8.0 Consensus size: 41
43460151 CTTTCGGGGC
*
43460161 TTTAGCGGCGTTTTTTAGAAAGCGCCGCTAATGCTCAGGCT
1 TTTAGCGGCGTTTTTCAGAAAGCGCCGCTAATGCTCAGGCT
* *
43460202 TTTAGCGGCGTTTTTGAGAAAGCGCCGCTAATGCCCAGGCT
1 TTTAGCGGCGTTTTTCAGAAAGCGCCGCTAATGCTCAGGCT
**
43460243 TTTAGCGGCGTTTTGGAGAAAGCGCCGCTAATGCTCAGGCT
1 TTTAGCGGCGTTTTTCAGAAAGCGCCGCTAATGCTCAGGCT
* *
43460284 TTTAGCGGCATTTTTGAGAAAGCGCCGCTAATGCTCAGGCT
1 TTTAGCGGCGTTTTTCAGAAAGCGCCGCTAATGCTCAGGCT
* *
43460325 TTTAGCGGCGTTTTTCAAAAAGCACCGCTAATGCTCAGGGCT
1 TTTAGCGGCGTTTTTCAGAAAGCGCCGCTAATGCTCA-GGCT
* * * *
43460367 TTTAGCGGCGTTTTTAAAAAAGCGCCACTAATGCTCGGAGC-
1 TTTAGCGGCGTTTTTCAGAAAGCGCCGCTAATGCTCAG-GCT
* * * *
43460408 TTTAGCGGCATTTTTCAAAAAGCGCCGCTAATGTTCGGGGC-
1 TTTAGCGGCGTTTTTCAGAAAGCGCCGCTAATGCTC-AGGCT
* *
43460449 TTTAGCGGCATTTTCCA-AGAAGCGCCGCTAATGCTCAGG
1 TTTAGCGGCGTTTTTCAGA-AAGCGCCGCTAATGCTCAGG
43460488 ATTTAGTATT
Statistics
Matches: 261, Mismatches: 21, Indels: 9
0.90 0.07 0.03
Matches are distributed among these distances:
40 3 0.01
41 217 0.83
42 41 0.16
ACGTcount: A:0.22, C:0.23, G:0.27, T:0.28
Consensus pattern (41 bp):
TTTAGCGGCGTTTTTCAGAAAGCGCCGCTAATGCTCAGGCT
Found at i:43460430 original size:124 final size:123
Alignment explanation
Indices: 43460157--43460487 Score: 459
Period size: 124 Copynumber: 2.7 Consensus size: 123
43460147 TGACCTTTCG
* * * *
43460157 GGGCTTTAGCGGCGTTTTTTAGAAAGCGCCGCTAATGCTCAGGCTTTTAGCGGCGTTTTTGAGAA
1 GGGCTTTAGCGGCATTTTTCAGAAAGCGCCGCTAATGCTCAGGCTTTTAGCGGCGTTTTTCAAAA
* * * *
43460222 AGCGCCGCTAATGCCCA-GGCTTTTAGCGGCGTTTTGGAGAAAGCGCCGCTAATGCTC
66 AGCGCCGCTAATGCTCAGGGCTTTTAGCGGCGTTTTGAAAAAAGCGCCACTAATGCTC
* *
43460279 AGGCTTTTAGCGGCATTTTTGAGAAAGCGCCGCTAATGCTCAGGCTTTTAGCGGCGTTTTTCAAA
1 GGGC-TTTAGCGGCATTTTTCAGAAAGCGCCGCTAATGCTCAGGCTTTTAGCGGCGTTTTTCAAA
* *
43460344 AAGCACCGCTAATGCTCAGGGCTTTTAGCGGCGTTTTTAAAAAAGCGCCACTAATGCTC
65 AAGCGCCGCTAATGCTCAGGGCTTTTAGCGGCGTTTTGAAAAAAGCGCCACTAATGCTC
* * * * *
43460403 GGAGCTTTAGCGGCATTTTTCAAAAAGCGCCGCTAATGTTCGGGGC-TTTAGCGGCATTTTCCAA
1 GG-GCTTTAGCGGCATTTTTCAGAAAGCGCCGCTAATGCTC-AGGCTTTTAGCGGCGTTTTTCAA
*
43460467 GAAGCGCCGCTAATGCTCAGG
64 AAAGCGCCGCTAATGCTCAGG
43460488 ATTTAGTATT
Statistics
Matches: 185, Mismatches: 20, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
122 3 0.02
123 72 0.39
124 105 0.57
125 5 0.03
ACGTcount: A:0.22, C:0.23, G:0.27, T:0.28
Consensus pattern (123 bp):
GGGCTTTAGCGGCATTTTTCAGAAAGCGCCGCTAATGCTCAGGCTTTTAGCGGCGTTTTTCAAAA
AGCGCCGCTAATGCTCAGGGCTTTTAGCGGCGTTTTGAAAAAAGCGCCACTAATGCTC
Found at i:43460517 original size:20 final size:20
Alignment explanation
Indices: 43460488--43460532 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
43460478 AATGCTCAGG
* *
43460488 ATTTAGTATTTTATCTGTCT
1 ATTTACTATTTAATCTGTCT
* *
43460508 ATTTACTATTTAATTTGTTT
1 ATTTACTATTTAATCTGTCT
43460528 ATTTA
1 ATTTA
43460533 ATTATATTAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.24, C:0.07, G:0.07, T:0.62
Consensus pattern (20 bp):
ATTTACTATTTAATCTGTCT
Found at i:43461192 original size:28 final size:28
Alignment explanation
Indices: 43461134--43461193 Score: 77
Period size: 28 Copynumber: 2.1 Consensus size: 28
43461124 TAAATAAGGT
*
43461134 TTAGGGGTTAGTAGTTAAAGATTAAGGG
1 TTAGGGGTTAGTAGTTAAAGATTAAGAG
* *
43461162 TTAGGGGTTAG-AGGTTAGAGGTTAAGAG
1 TTAGGGGTTAGTA-GTTAAAGATTAAGAG
43461190 TTAG
1 TTAG
43461194 TGATTTAGGG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
27 1 0.04
28 27 0.96
ACGTcount: A:0.30, C:0.00, G:0.38, T:0.32
Consensus pattern (28 bp):
TTAGGGGTTAGTAGTTAAAGATTAAGAG
Found at i:43462238 original size:19 final size:20
Alignment explanation
Indices: 43462214--43462253 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 20
43462204 GCCATTTTAT
43462214 CCCTAAA-TTCCCCCTAAAA
1 CCCTAAATTTCCCCCTAAAA
43462233 CCCTAAATTTTCCCCCTAAAA
1 CCCTAAA-TTTCCCCCTAAAA
43462254 ATAATCACTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 7 0.37
21 12 0.63
ACGTcount: A:0.35, C:0.40, G:0.00, T:0.25
Consensus pattern (20 bp):
CCCTAAATTTCCCCCTAAAA
Found at i:43462647 original size:3 final size:3
Alignment explanation
Indices: 43462639--43462693 Score: 110
Period size: 3 Copynumber: 18.3 Consensus size: 3
43462629 CATTGAGCTG
43462639 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
43462687 TTA TTA T
1 TTA TTA T
43462694 GGTTAATTTT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 52 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:43466690 original size:43 final size:43
Alignment explanation
Indices: 43466596--43466826 Score: 284
Period size: 43 Copynumber: 5.4 Consensus size: 43
43466586 GATATGTTTT
* * * * * *
43466596 TAGCGGCGTTTTTGCGAGAAGCGTCGCTAAAGGT-TTGATCTA
1 TAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGGTCTA
* * *
43466638 TAGCGGCGTTTGTGGGAAAATCGCCACTAAAGGTCATGGCCTA
1 TAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGGTCTA
* * * * *
43466681 TAGCGGCGTTTGTGGGAAAAACGTCGCTAAAGATTATGGTCTT
1 TAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGGTCTA
* *
43466724 TAGCGGCGTTTGTGAGAAAAGCGCCGCTAAAGGTCATGGTCTT
1 TAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGGTCTA
* *
43466767 TAGCGGCGTTTGTGGGAAGAGCGCCGCTAAAGCTCATGGTCTA
1 TAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGGTCTA
*
43466810 TAGCGGAGTTTGTGGGA
1 TAGCGGCGTTTGTGGGA
43466827 TCTTGACTTT
Statistics
Matches: 162, Mismatches: 26, Indels: 1
0.86 0.14 0.01
Matches are distributed among these distances:
42 28 0.17
43 134 0.83
ACGTcount: A:0.23, C:0.17, G:0.33, T:0.27
Consensus pattern (43 bp):
TAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGGTCTA
Found at i:43466823 original size:129 final size:128
Alignment explanation
Indices: 43466594--43466826 Score: 340
Period size: 129 Copynumber: 1.8 Consensus size: 128
43466584 ATGATATGTT
* * * * * *
43466594 TTTAGCGGCGTTTTTGCGAGAAGCGTCGCTAAAGGTTTGATCTATAGCGGCGTTTGTGGGAAAAT
1 TTTAGCGGCGTTTGTGAGAAAAGCGCCGCTAAAGGTATGATCTATAGCGGCGTTTGTGGGAAAAG
* *
43466659 CGCCACTAAAGGTCATGGCCTATAGCGGCGTTTGTGGGAAAAACGTCGCTAAAGATTATGGTC
66 CGCCACTAAAGCTCATGGCCTATAGCGGAGTTTGTGGGAAAAACGTCGCTAAAGATTATGGTC
* * *
43466722 TTTAGCGGCGTTTGTGAGAAAAGCGCCGCTAAAGGTCATGGTCTTTAGCGGCGTTTGTGGGAAGA
1 TTTAGCGGCGTTTGTGAGAAAAGCGCCGCTAAAGGT-ATGATCTATAGCGGCGTTTGTGGGAAAA
* *
43466787 GCGCCGCTAAAGCTCATGGTCTATAGCGGAGTTTGTGGGA
65 GCGCCACTAAAGCTCATGGCCTATAGCGGAGTTTGTGGGA
43466827 TCTTGACTTT
Statistics
Matches: 91, Mismatches: 13, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
128 32 0.35
129 59 0.65
ACGTcount: A:0.23, C:0.17, G:0.33, T:0.27
Consensus pattern (128 bp):
TTTAGCGGCGTTTGTGAGAAAAGCGCCGCTAAAGGTATGATCTATAGCGGCGTTTGTGGGAAAAG
CGCCACTAAAGCTCATGGCCTATAGCGGAGTTTGTGGGAAAAACGTCGCTAAAGATTATGGTC
Found at i:43478094 original size:94 final size:93
Alignment explanation
Indices: 43477956--43478179 Score: 288
Period size: 94 Copynumber: 2.4 Consensus size: 93
43477946 GAAGCTGCAA
* * *
43477956 CTACAAATCCTATACCCCTGAAGTTGCAGTGGGTCAGGTCGAATCTACCATAGCGAATCTTATCT
1 CTACAAATCCTATATCCTTGAAGTTGCAGTGGATC-GGTCGAATCTACCATAGCGAATCTTATCT
** *
43478021 CCTTAAAGTTGCAGTGGAGCAAAATGAAG
65 CCCCAAAGTTGCAGTAGAGCAAAATGAAG
* *
43478050 TTACAAATCCTATATCCTTGAAGTTGCAGTGGATCGGATTGAATCTACCATAGCGAATCTTATCT
1 CTACAAATCCTATATCCTTGAAGTTGCAGTGGATCGG-TCGAATCTACCATAGCGAATCTTATCT
* * *
43478115 CCCCGAAGTTGTAGTAGAGCAAGATGAAG
65 CCCCAAAGTTGCAGTAGAGCAAAATGAAG
* * *
43478144 CTACAAATCTTATAT-CTCTAAAGTTGCAGTGTATCG
1 CTACAAATCCTATATCCT-TGAAGTTGCAGTGGATCG
43478180 AATTAAAGCT
Statistics
Matches: 113, Mismatches: 15, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
93 4 0.04
94 109 0.96
ACGTcount: A:0.31, C:0.21, G:0.20, T:0.29
Consensus pattern (93 bp):
CTACAAATCCTATATCCTTGAAGTTGCAGTGGATCGGTCGAATCTACCATAGCGAATCTTATCTC
CCCAAAGTTGCAGTAGAGCAAAATGAAG
Found at i:43488805 original size:13 final size:13
Alignment explanation
Indices: 43488789--43488819 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
43488779 CAGAGCACTG
*
43488789 TTTCTCTTCCCGA
1 TTTCTCTCCCCGA
43488802 TTTCTCTCCCCGA
1 TTTCTCTCCCCGA
43488815 TTTCT
1 TTTCT
43488820 TGCACCTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.06, C:0.39, G:0.06, T:0.48
Consensus pattern (13 bp):
TTTCTCTCCCCGA
Found at i:43490960 original size:20 final size:20
Alignment explanation
Indices: 43490924--43490962 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
43490914 AATTTTTTAA
*
43490924 AAATATATTTATAATATAAT
1 AAATATATTAATAATATAAT
43490944 AAATATA-TAATACATATAA
1 AAATATATTAATA-ATATAA
43490963 ATTTAAATCA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (20 bp):
AAATATATTAATAATATAAT
Found at i:43494736 original size:26 final size:24
Alignment explanation
Indices: 43494701--43494752 Score: 68
Period size: 26 Copynumber: 2.1 Consensus size: 24
43494691 ACATTTTATG
43494701 AAATTATATTTAATAATAATTATTTT
1 AAATTATATTTAATAAT-A-TATTTT
* *
43494727 AAATTGTATTTAATCATATATTTT
1 AAATTATATTTAATAATATATTTT
43494751 AA
1 AA
43494753 TTAAAATATA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 8 0.33
25 1 0.04
26 15 0.62
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52
Consensus pattern (24 bp):
AAATTATATTTAATAATATATTTT
Found at i:43494859 original size:18 final size:17
Alignment explanation
Indices: 43494831--43494865 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
43494821 ATTATTAAGA
*
43494831 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
43494848 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
43494866 TTAATAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:43494865 original size:16 final size:16
Alignment explanation
Indices: 43494831--43494885 Score: 53
Period size: 16 Copynumber: 3.4 Consensus size: 16
43494821 ATTATTAAGA
43494831 ATTTT-ATTAAATTATAT
1 ATTTTAATTAAA--ATAT
43494848 ATTTTAATTAAAATAT
1 ATTTTAATTAAAATAT
*
43494864 A-TTTAA-TAAAAAAT
1 ATTTTAATTAAAATAT
43494878 ATGTTTAA
1 AT-TTTAA
43494886 ATATGATTAA
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
14 8 0.24
15 5 0.15
16 10 0.29
17 5 0.15
18 6 0.18
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (16 bp):
ATTTTAATTAAAATAT
Found at i:43495015 original size:18 final size:17
Alignment explanation
Indices: 43494987--43495021 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
43494977 AATTATAAGA
*
43494987 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
43495004 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
43495022 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:43495129 original size:156 final size:157
Alignment explanation
Indices: 43494819--43495134 Score: 580
Period size: 156 Copynumber: 2.0 Consensus size: 157
43494809 ATAAGAATAT
43494819 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAAAAAATATGTTT
1 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAAAAAATATGTTT
* *
43494884 AAATATGATTAAATTATTTATTATTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAA
66 AAATATGATTAAAATATTTATTACTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAA
43494949 TAATCATTTACCAAAACAAATTTATGC
131 TAATCATTTACCAAAACAAATTTATGC
* *
43494976 TAATTA-TAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTT
1 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAAAAAATATGTTT
43495040 AAATATGATTAAAATATTTATTACTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAA
66 AAATATGATTAAAATATTTATTACTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAA
*
43495105 TAATCATTTACCAAAACAATTTTATGC
131 TAATCATTTACCAAAACAAATTTATGC
43495132 TAA
1 TAA
43495135 GGGTATTCTA
Statistics
Matches: 154, Mismatches: 5, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
156 148 0.96
157 6 0.04
ACGTcount: A:0.49, C:0.05, G:0.03, T:0.43
Consensus pattern (157 bp):
TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAAAAAATATGTTT
AAATATGATTAAAATATTTATTACTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAA
TAATCATTTACCAAAACAAATTTATGC
Found at i:43495251 original size:44 final size:45
Alignment explanation
Indices: 43495186--43495271 Score: 120
Period size: 44 Copynumber: 1.9 Consensus size: 45
43495176 ACCTCTATTC
* *
43495186 CATTCAACCAAACACAAGATTA-CTATTACGCCTCTATTCCATTA
1 CATTCAACCAAACACAAGATTAGCTATTACACCTCTAATCCATTA
***
43495230 CATTCAACCAAACAGTGGATTAGCTATTACACCTCTAATCCA
1 CATTCAACCAAACACAAGATTAGCTATTACACCTCTAATCCA
43495272 ATATACCTCT
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
44 19 0.53
45 17 0.47
ACGTcount: A:0.36, C:0.29, G:0.07, T:0.28
Consensus pattern (45 bp):
CATTCAACCAAACACAAGATTAGCTATTACACCTCTAATCCATTA
Found at i:43495281 original size:16 final size:16
Alignment explanation
Indices: 43495260--43495290 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
43495250 TAGCTATTAC
43495260 ACCTCTAATCCAATAT
1 ACCTCTAATCCAATAT
43495276 ACCTCTAATCCAATA
1 ACCTCTAATCCAATA
43495291 CAGCGAACCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.39, C:0.32, G:0.00, T:0.29
Consensus pattern (16 bp):
ACCTCTAATCCAATAT
Found at i:43502907 original size:15 final size:15
Alignment explanation
Indices: 43502887--43502916 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
43502877 AAGCCCTAAG
*
43502887 AAAATAGAATTAGAA
1 AAAATAGAAATAGAA
43502902 AAAATAGAAATAGAA
1 AAAATAGAAATAGAA
43502917 TTTTTAGGAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.70, C:0.00, G:0.13, T:0.17
Consensus pattern (15 bp):
AAAATAGAAATAGAA
Found at i:43503377 original size:47 final size:47
Alignment explanation
Indices: 43503323--43503418 Score: 192
Period size: 47 Copynumber: 2.0 Consensus size: 47
43503313 GTAACGATAC
43503323 TTGGAGAAATAATATCGTAGTATTCATTGTAAGTTTTTATATTTTAT
1 TTGGAGAAATAATATCGTAGTATTCATTGTAAGTTTTTATATTTTAT
43503370 TTGGAGAAATAATATCGTAGTATTCATTGTAAGTTTTTATATTTTAT
1 TTGGAGAAATAATATCGTAGTATTCATTGTAAGTTTTTATATTTTAT
43503417 TT
1 TT
43503419 ACAATTTCGT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 49 1.00
ACGTcount: A:0.31, C:0.04, G:0.15, T:0.50
Consensus pattern (47 bp):
TTGGAGAAATAATATCGTAGTATTCATTGTAAGTTTTTATATTTTAT
Found at i:43504617 original size:21 final size:21
Alignment explanation
Indices: 43504576--43504618 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
43504566 ACCCTAAACT
*
43504576 CTCAAAACTTTTTACTTTTCC
1 CTCAAAACTTTTTACTCTTCC
43504597 CTCAAAAC-TTTTACTCCTTCC
1 CTCAAAACTTTTTACT-CTTCC
43504618 C
1 C
43504619 AGTTTCCCCC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 7 0.35
21 13 0.65
ACGTcount: A:0.23, C:0.35, G:0.00, T:0.42
Consensus pattern (21 bp):
CTCAAAACTTTTTACTCTTCC
Found at i:43505463 original size:5 final size:5
Alignment explanation
Indices: 43505453--43505478 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
43505443 AACTCGAACA
43505453 ATTCG ATTCG ATTCG ATTCG ATTCG A
1 ATTCG ATTCG ATTCG ATTCG ATTCG A
43505479 ATTCCATCAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.23, C:0.19, G:0.19, T:0.38
Consensus pattern (5 bp):
ATTCG
Found at i:43516344 original size:103 final size:104
Alignment explanation
Indices: 43516121--43516386 Score: 410
Period size: 103 Copynumber: 2.6 Consensus size: 104
43516111 TGTATATAAA
** * * * *
43516121 AGGGGTTGCTGTGTGCTGATTCCCCGATTTATGGGTGGTGCTATGTGCGTGATCCACCATATCTT
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTACGTGATCCACCATATCTT
**
43516186 TGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
66 TGAAATGAAAAAGGGGGTTGCTATGTGCTGATTCCCCCG
43516225 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTACGAT-ATCCACCATATCT
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTACG-TGATCCACCATATCT
43516289 TTGAAAT-AAAAAGGGGGTTGCTATGTGCTGATTCCCCCG
65 TTGAAATGAAAAAGGGGGTTGCTATGTGCTGATTCCCCCG
* * *
43516328 AGGGGTTGCTAAGTGCTGATTCCCCGATTCAGTGGTGGTGCTAAGTGCGGGATCCACCA
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTACGTGATCCACCA
43516387 ATAACGGCTA
Statistics
Matches: 149, Mismatches: 11, Indels: 5
0.90 0.07 0.03
Matches are distributed among these distances:
103 85 0.57
104 63 0.42
105 1 0.01
ACGTcount: A:0.20, C:0.20, G:0.30, T:0.30
Consensus pattern (104 bp):
AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTACGTGATCCACCATATCTT
TGAAATGAAAAAGGGGGTTGCTATGTGCTGATTCCCCCG
Found at i:43520418 original size:19 final size:19
Alignment explanation
Indices: 43520394--43520430 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
43520384 TGGCCAGTGC
43520394 TGGTCCTAGCATTAGACAA
1 TGGTCCTAGCATTAGACAA
*
43520413 TGGTCCTAGCATTGGACA
1 TGGTCCTAGCATTAGACA
43520431 GGGCTCACTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.27, C:0.22, G:0.24, T:0.27
Consensus pattern (19 bp):
TGGTCCTAGCATTAGACAA
Found at i:43528106 original size:9 final size:9
Alignment explanation
Indices: 43528092--43528119 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
43528082 GTTTCTTTCA
43528092 AAACTACAT
1 AAACTACAT
43528101 AAACTACAT
1 AAACTACAT
43528110 AAACTACAT
1 AAACTACAT
43528119 A
1 A
43528120 TTGCTACTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.57, C:0.21, G:0.00, T:0.21
Consensus pattern (9 bp):
AAACTACAT
Found at i:43529171 original size:23 final size:23
Alignment explanation
Indices: 43529134--43529184 Score: 77
Period size: 23 Copynumber: 2.2 Consensus size: 23
43529124 GTTGTTTCTT
43529134 TGTAATATCCCGAAAATTACTAC
1 TGTAATATCCCGAAAATTACTAC
43529157 TGTAATA-CCCTGAAAATTACTAC
1 TGTAATATCCC-GAAAATTACTAC
*
43529180 AGTAA
1 TGTAA
43529185 GAAAGTAGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
22 3 0.12
23 23 0.88
ACGTcount: A:0.41, C:0.20, G:0.10, T:0.29
Consensus pattern (23 bp):
TGTAATATCCCGAAAATTACTAC
Found at i:43532361 original size:9 final size:9
Alignment explanation
Indices: 43532340--43532373 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
43532330 CTGGTTAGTG
43532340 TTTAAGTTGT
1 TTTAA-TTGT
*
43532350 TTTAATTTT
1 TTTAATTGT
43532359 TTTAATTGT
1 TTTAATTGT
43532368 TTTAAT
1 TTTAAT
43532374 GGTGGGTAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
9 17 0.77
10 5 0.23
ACGTcount: A:0.24, C:0.00, G:0.09, T:0.68
Consensus pattern (9 bp):
TTTAATTGT
Found at i:43532437 original size:18 final size:18
Alignment explanation
Indices: 43532402--43532442 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
43532392 ATTTTCTAAA
*
43532402 CATTTTTTAATTTTAATT
1 CATTTTTTAATTTAAATT
43532420 -ATTTTTTAAGTTTAAATT
1 CATTTTTTAA-TTTAAATT
43532438 CATTT
1 CATTT
43532443 GCTGACGTGT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
17 9 0.45
18 7 0.35
19 4 0.20
ACGTcount: A:0.29, C:0.05, G:0.02, T:0.63
Consensus pattern (18 bp):
CATTTTTTAATTTAAATT
Found at i:43532549 original size:30 final size:30
Alignment explanation
Indices: 43532513--43532571 Score: 109
Period size: 30 Copynumber: 2.0 Consensus size: 30
43532503 ACAAAAAAAT
*
43532513 TCGGTTAACCGACCGCATTCGGTTAATCGG
1 TCGGTTAACCGACCGAATTCGGTTAATCGG
43532543 TCGGTTAACCGACCGAATTCGGTTAATCG
1 TCGGTTAACCGACCGAATTCGGTTAATCG
43532572 ATTGGTAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.22, C:0.25, G:0.25, T:0.27
Consensus pattern (30 bp):
TCGGTTAACCGACCGAATTCGGTTAATCGG
Found at i:43532566 original size:18 final size:18
Alignment explanation
Indices: 43532510--43532568 Score: 58
Period size: 18 Copynumber: 3.6 Consensus size: 18
43532500 AAAACAAAAA
43532510 AATTCGGTTAACCGACCG
1 AATTCGGTTAACCGACCG
* *
43532528 CATTCGGTTAATCG---G
1 AATTCGGTTAACCGACCG
43532543 ---TCGGTTAACCGACCG
1 AATTCGGTTAACCGACCG
43532558 AATTCGGTTAA
1 AATTCGGTTAA
43532569 TCGATTGGTA
Statistics
Matches: 32, Mismatches: 3, Indels: 12
0.68 0.06 0.26
Matches are distributed among these distances:
12 10 0.31
15 2 0.06
18 20 0.62
ACGTcount: A:0.25, C:0.24, G:0.24, T:0.27
Consensus pattern (18 bp):
AATTCGGTTAACCGACCG
Found at i:43532684 original size:17 final size:18
Alignment explanation
Indices: 43532656--43532705 Score: 75
Period size: 17 Copynumber: 2.8 Consensus size: 18
43532646 TAATAAATAA
*
43532656 AATTATCCAACCCAACCC
1 AATTACCCAACCCAACCC
*
43532674 AATTA-CCAACCTAACCC
1 AATTACCCAACCCAACCC
43532691 AATTACCCAACCCAA
1 AATTACCCAACCCAA
43532706 TAAAACTAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
17 16 0.55
18 13 0.45
ACGTcount: A:0.42, C:0.42, G:0.00, T:0.16
Consensus pattern (18 bp):
AATTACCCAACCCAACCC
Found at i:43532740 original size:38 final size:39
Alignment explanation
Indices: 43532687--43532764 Score: 131
Period size: 38 Copynumber: 2.0 Consensus size: 39
43532677 TACCAACCTA
* *
43532687 ACCCAATTACCCAACCCAATAAAACTAAAACTAAAGTCT
1 ACCCAAGTACCCAACCCAATAAAAATAAAACTAAAGTCT
43532726 ACCCAAGTA-CCAACCCAATAAAAATAAAACTAAAGTCT
1 ACCCAAGTACCCAACCCAATAAAAATAAAACTAAAGTCT
43532764 A
1 A
43532765 ACTCTTAAGA
Statistics
Matches: 37, Mismatches: 2, Indels: 1
0.93 0.05 0.03
Matches are distributed among these distances:
38 29 0.78
39 8 0.22
ACGTcount: A:0.51, C:0.28, G:0.04, T:0.17
Consensus pattern (39 bp):
ACCCAAGTACCCAACCCAATAAAAATAAAACTAAAGTCT
Found at i:43532934 original size:37 final size:37
Alignment explanation
Indices: 43532888--43532962 Score: 123
Period size: 37 Copynumber: 2.0 Consensus size: 37
43532878 TGTTAATTTC
*
43532888 AAGAATTATGTAATGTTTTTAATTACGTAGTGATTCA
1 AAGAATTATGTAATATTTTTAATTACGTAGTGATTCA
* *
43532925 AAGACTTATGTAATATTTTTAATTATGTAGTGATTCA
1 AAGAATTATGTAATATTTTTAATTACGTAGTGATTCA
43532962 A
1 A
43532963 TTCAGGTAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.36, C:0.05, G:0.15, T:0.44
Consensus pattern (37 bp):
AAGAATTATGTAATATTTTTAATTACGTAGTGATTCA
Found at i:43540246 original size:15 final size:15
Alignment explanation
Indices: 43540226--43540256 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
43540216 AAAACAACAT
43540226 AACTCTTGACATTTC
1 AACTCTTGACATTTC
*
43540241 AACTCTTGACCTTTC
1 AACTCTTGACATTTC
43540256 A
1 A
43540257 CTTACATAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.26, C:0.29, G:0.06, T:0.39
Consensus pattern (15 bp):
AACTCTTGACATTTC
Found at i:43542868 original size:49 final size:50
Alignment explanation
Indices: 43542781--43542879 Score: 132
Period size: 50 Copynumber: 2.0 Consensus size: 50
43542771 TATCGTTATT
*
43542781 TTTAATTTTAGATTTATTAATGAATATTTTATATTTAAA-ATTTATTTAA
1 TTTAATTTTAGATTTATAAATGAATATTTTATATTTAAATATTTATTTAA
* *
43542830 TTTAATTTTTATATTTATAAAT-AAT-TTTTATATATTAAATATTTTTTTAA
1 TTTAA-TTTTAGATTTATAAATGAATATTTTATAT-TTAAATATTTATTTAA
43542880 AAATATTGAC
Statistics
Matches: 44, Mismatches: 3, Indels: 5
0.85 0.06 0.10
Matches are distributed among these distances:
48 8 0.18
49 13 0.30
50 23 0.52
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (50 bp):
TTTAATTTTAGATTTATAAATGAATATTTTATATTTAAATATTTATTTAA
Found at i:43542878 original size:19 final size:19
Alignment explanation
Indices: 43542832--43542875 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
43542822 TTATTTAATT
*
43542832 TAATTTTTATATTTATAAA
1 TAATTTTTATATATATAAA
43542851 TAATTTTTATATAT-TAAA
1 TAATTTTTATATATATAAA
43542869 T-ATTTTT
1 TAATTTTT
43542876 TTAAAAATAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
17 6 0.25
18 5 0.21
19 13 0.54
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (19 bp):
TAATTTTTATATATATAAA
Found at i:43546577 original size:2 final size:2
Alignment explanation
Indices: 43546570--43546603 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
43546560 GAAATGATGC
*
43546570 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
43546604 GCACATTGTT
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):
AT
Found at i:43548543 original size:16 final size:16
Alignment explanation
Indices: 43548496--43548544 Score: 55
Period size: 16 Copynumber: 3.0 Consensus size: 16
43548486 TTAAAAATTA
43548496 ATAAGAAATGAAAATA-
1 ATAAGAAAT-AAAATAT
* *
43548512 AAAAGAATTAATAATAT
1 ATAAGAAATAA-AATAT
43548529 ATAAGAAATAAAATAT
1 ATAAGAAATAAAATAT
43548545 TTTAAATTTA
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
15 2 0.07
16 16 0.59
17 9 0.33
ACGTcount: A:0.67, C:0.00, G:0.08, T:0.24
Consensus pattern (16 bp):
ATAAGAAATAAAATAT
Found at i:43556019 original size:2 final size:2
Alignment explanation
Indices: 43556012--43556074 Score: 94
Period size: 2 Copynumber: 32.5 Consensus size: 2
43556002 TCTTCTCATA
43556012 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
43556054 AT AT -T AT TT CT AT -T AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT A
43556075 CACGCCACTT
Statistics
Matches: 56, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
1 2 0.04
2 54 0.96
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:43566288 original size:35 final size:35
Alignment explanation
Indices: 43566237--43566305 Score: 129
Period size: 35 Copynumber: 2.0 Consensus size: 35
43566227 CTTATACAAG
43566237 AATATAGTTACAAGGAACACAAATATTATCAATGT
1 AATATAGTTACAAGGAACACAAATATTATCAATGT
*
43566272 AATATAGTTACGAGGAACACAAATATTATCAATG
1 AATATAGTTACAAGGAACACAAATATTATCAATG
43566306 AACTTATACA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.48, C:0.12, G:0.13, T:0.28
Consensus pattern (35 bp):
AATATAGTTACAAGGAACACAAATATTATCAATGT
Found at i:43570406 original size:20 final size:20
Alignment explanation
Indices: 43570381--43570422 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
43570371 ATGGTAAAAG
43570381 AGAAGGTTGAGGAGTATCAA
1 AGAAGGTTGAGGAGTATCAA
*
43570401 AGAAGGTTGAGGAGTATTAA
1 AGAAGGTTGAGGAGTATCAA
43570421 AG
1 AG
43570423 TGGTAAAATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.40, C:0.02, G:0.36, T:0.21
Consensus pattern (20 bp):
AGAAGGTTGAGGAGTATCAA
Found at i:43581699 original size:5 final size:5
Alignment explanation
Indices: 43581689--43581726 Score: 76
Period size: 5 Copynumber: 7.6 Consensus size: 5
43581679 CCATCACCAT
43581689 ATATC ATATC ATATC ATATC ATATC ATATC ATATC ATA
1 ATATC ATATC ATATC ATATC ATATC ATATC ATATC ATA
43581727 AATATCAGAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 33 1.00
ACGTcount: A:0.42, C:0.18, G:0.00, T:0.39
Consensus pattern (5 bp):
ATATC
Found at i:43584741 original size:67 final size:67
Alignment explanation
Indices: 43584620--43585036 Score: 416
Period size: 67 Copynumber: 6.3 Consensus size: 67
43584610 TGGGGGAATG
* * * * * *
43584620 ATGTATAATACCATAGCTCGACTATGGCAACATAAAAAGTCTGTTAGGACATTAAACATGGGGTA
1 ATGTGTAAGACCATAGCTCGACTATGGCAACATAGAGAGTATGTCAGGACATTAAACATGGGGTA
43584685 TA
66 TA
* * *
43584687 ATGTGTAAGACCATAGCTCGACTATGGCAACATAGAGAGTATGTCAGTATATTAAACATGAGGTA
1 ATGTGTAAGACCATAGCTCGACTATGGCAACATAGAGAGTATGTCAGGACATTAAACATGGGGTA
43584752 TA
66 TA
* * * * * * *
43584754 ATGTGTAACACCATAGCTCGACTATGGAAACATAGAGAGTTTGCCAAGACATTAATCATGAGGTA
1 ATGTGTAAGACCATAGCTCGACTATGGCAACATAGAGAGTATGTCAGGACATTAAACATGGGGTA
43584819 TA
66 TA
* * * * * * *
43584821 ATGTGTAAAACCCTAGCTCGGCTATGGCAACATAAAGAGTATAGT-AGGACATTTAATATGGGAT
1 ATGTGTAAGACCATAGCTCGACTATGGCAACATAGAGAGTAT-GTCAGGACATTAAACATGGGGT
*
43584885 ATG
65 ATA
* * * * * *
43584888 ATATGTAAGACCATAGCTCGACTATGGCAACGTA-A-A--AAGTCCATGACATTAAACGTGGGAT
1 ATGTGTAAGACCATAGCTCGACTATGGCAACATAGAGAGTATGT-CAGGACATTAAACATGGGGT
*
43584949 ATG
65 ATA
* * * **
43584952 ATATGTAAAACCATAGCTCGATTATGGCAACATAGAGA--ATCCACTAGGACATTAAACATGGGG
1 ATGTGTAAGACCATAGCTCGACTATGGCAACATAGAGAGTAT-GTC-AGGACATTAAACATGGGG
*
43585015 TATG
64 TATA
43585019 ATGTGTAAGACCATAGCT
1 ATGTGTAAGACCATAGCT
43585037 TGGCTATGAT
Statistics
Matches: 291, Mismatches: 52, Indels: 14
0.82 0.15 0.04
Matches are distributed among these distances:
62 2 0.01
63 1 0.00
64 49 0.17
65 2 0.01
66 4 0.01
67 232 0.80
68 1 0.00
ACGTcount: A:0.37, C:0.15, G:0.22, T:0.26
Consensus pattern (67 bp):
ATGTGTAAGACCATAGCTCGACTATGGCAACATAGAGAGTATGTCAGGACATTAAACATGGGGTA
TA
Found at i:43584895 original size:134 final size:132
Alignment explanation
Indices: 43584617--43585067 Score: 471
Period size: 134 Copynumber: 3.4 Consensus size: 132
43584607 TAATGGGGGA
* * * ** *
43584617 ATGATGTATAATACCATAGCTCGACTATGGCAACATAAAAAGTCTGTTAGGACATTAAACATGGG
1 ATGATGTGTAAGACCATAGCTCGACTATGGAAACATAAAAAGTCTGCCAAGACATTAAACAT-GG
* * *
43584682 GTATAATGTGTAAGACCATAGCTCGACTATGGCAACATAGAGAGTAT-GTCAGTATATTAAACAT
65 GTATAATGTGTAAAACCATAGCTCGACTATGGCAACATAGAGAGTATAGT-AGGACATTAAACAT
43584746 GAGGT
129 G-GGT
* * * * * *
43584751 ATAATGTGTAACACCATAGCTCGACTATGGAAACATAGAGAGTTTGCCAAGACATTAATCATGAG
1 ATGATGTGTAAGACCATAGCTCGACTATGGAAACATAAAAAGTCTGCCAAGACATTAAACATG-G
* * * * *
43584816 GTATAATGTGTAAAACCCTAGCTCGGCTATGGCAACATAAAGAGTATAGTAGGACATTTAATATG
65 GTATAATGTGTAAAACCATAGCTCGACTATGGCAACATAGAGAGTATAGTAGGACATTAAACATG
43584881 GGAT
130 GG-T
* * * * *
43584885 ATGATATGTAAGACCATAGCTCGACTATGGCAACGTAAAAAG--T-CCATGACATTAAACGTGGG
1 ATGATGTGTAAGACCATAGCTCGACTATGGAAACATAAAAAGTCTGCCAAGACATTAAACATGGG
* * * * ** *
43584947 ATATGATATGTAAAACCATAGCTCGATTATGGCAACATAGAGAATCCACTAGGACATTAAACATG
66 -TATAATGTGTAAAACCATAGCTCGACTATGGCAACATAGAGAGTATAGTAGGACATTAAACAT-
43585012 GGGT
129 GGGT
* * * *
43585016 ATGATGTGTAAGACCATAGCTTGGCTAT-GATAACATATAGAGTCTGCCAAGA
1 ATGATGTGTAAGACCATAGCTCGACTATGGA-AACATAAAAAGTCTGCCAAGA
43585068 AATAAATGCG
Statistics
Matches: 259, Mismatches: 49, Indels: 18
0.79 0.15 0.06
Matches are distributed among these distances:
130 3 0.01
131 99 0.38
132 4 0.02
133 4 0.02
134 147 0.57
135 2 0.01
ACGTcount: A:0.37, C:0.15, G:0.22, T:0.26
Consensus pattern (132 bp):
ATGATGTGTAAGACCATAGCTCGACTATGGAAACATAAAAAGTCTGCCAAGACATTAAACATGGG
TATAATGTGTAAAACCATAGCTCGACTATGGCAACATAGAGAGTATAGTAGGACATTAAACATGG
GT
Found at i:43594019 original size:13 final size:13
Alignment explanation
Indices: 43593989--43594024 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
43593979 ACTTAAAAAG
43593989 AAACTTAA-G-AA
1 AAACTTAATGAAA
43594000 AAA-TTAATGAAA
1 AAACTTAATGAAA
43594012 AAACTTAATGAAA
1 AAACTTAATGAAA
43594025 TTAGTTTAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
10 4 0.18
11 4 0.18
12 5 0.23
13 9 0.41
ACGTcount: A:0.64, C:0.06, G:0.08, T:0.22
Consensus pattern (13 bp):
AAACTTAATGAAA
Found at i:43599266 original size:25 final size:27
Alignment explanation
Indices: 43599238--43599299 Score: 76
Period size: 26 Copynumber: 2.4 Consensus size: 27
43599228 AATTTTAATG
*
43599238 ATTTTACCCCT-GATAA-TTTTTGACA
1 ATTTTACCCCTCGATAAGATTTTGACA
**
43599263 ATTTTA-CGTTCGATAAGATTTTGACA
1 ATTTTACCCCTCGATAAGATTTTGACA
43599289 ATTTTACCCCT
1 ATTTTACCCCT
43599300 AGAAAAATTT
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
24 2 0.07
25 11 0.38
26 14 0.48
27 2 0.07
ACGTcount: A:0.27, C:0.19, G:0.10, T:0.44
Consensus pattern (27 bp):
ATTTTACCCCTCGATAAGATTTTGACA
Found at i:43599309 original size:26 final size:26
Alignment explanation
Indices: 43599211--43599309 Score: 69
Period size: 25 Copynumber: 3.9 Consensus size: 26
43599201 TTTTTCATCC
* * *
43599211 CAATTTTACTCC-AGTAAAATTTTAA
1 CAATTTTACCCCTAGAAAAATTTTGA
** * *
43599236 TGATTTTACCCCT-GATAATTTTTGA
1 CAATTTTACCCCTAGAAAAATTTTGA
** * *
43599261 CAATTTTA-CGTTCGATAAGATTTTGA
1 CAATTTTACCCCTAGA-AAAATTTTGA
43599287 CAATTTTACCCCTAGAAAAATTT
1 CAATTTTACCCCTAGAAAAATTT
43599310 CAAGAAAAAT
Statistics
Matches: 52, Mismatches: 18, Indels: 7
0.68 0.23 0.09
Matches are distributed among these distances:
24 2 0.04
25 25 0.48
26 21 0.40
27 4 0.08
ACGTcount: A:0.33, C:0.16, G:0.09, T:0.41
Consensus pattern (26 bp):
CAATTTTACCCCTAGAAAAATTTTGA
Found at i:43622912 original size:40 final size:39
Alignment explanation
Indices: 43622850--43623065 Score: 121
Period size: 40 Copynumber: 5.6 Consensus size: 39
43622840 TGGTGAACAA
* * * *
43622850 ATCTTTGTCGATTTACGTGACTAGTGTTAGGCACATCATT
1 ATCTTCGTCGATTTAC-CGACTAGTGCTGGGCACATCATT
* *
43622890 ATCTTCGTCGATTTATCCGACTAGCGCTGGGCGCA--A--
1 ATCTTCGTCGATTTA-CCGACTAGTGCTGGGCACATCATT
* * *
43622926 ATCTTCGTCAATTTACCTTACTAGTACTGGGCACATCATT
1 ATCTTCGTCGATTTACC-GACTAGTGCTGGGCACATCATT
* * * * *
43622966 ATCTTCATCGATTTATTCGACTAGCGCAGGGCGCA--A--
1 ATCTTCGTCGATTTA-CCGACTAGTGCTGGGCACATCATT
*
43623002 ATCTTTGTC-AGTTTACCTGACTA-TAGCTGGGCACATCATT
1 ATCTTCGTCGA-TTTACC-GACTAGT-GCTGGGCACATCATT
* *
43623042 ATATTCGACGGA-TTATCCGACTAG
1 ATCTTCGTC-GATTTA-CCGACTAG
43623066 CGCTAGGCGC
Statistics
Matches: 130, Mismatches: 28, Indels: 35
0.67 0.15 0.18
Matches are distributed among these distances:
35 4 0.03
36 51 0.39
38 4 0.03
40 66 0.51
41 4 0.03
42 1 0.01
ACGTcount: A:0.24, C:0.23, G:0.19, T:0.34
Consensus pattern (39 bp):
ATCTTCGTCGATTTACCGACTAGTGCTGGGCACATCATT
Found at i:43622940 original size:36 final size:36
Alignment explanation
Indices: 43622890--43623101 Score: 115
Period size: 36 Copynumber: 5.7 Consensus size: 36
43622880 GCACATCATT
*
43622890 ATCTTCGTCGATTTATCCGACTAGCGCTGGGCGCAA
1 ATCTTCGTCAATTTATCCGACTAGCGCTGGGCGCAA
* ** *
43622926 ATCTTCGTCAATTTA-CCTTACTAGTACTGGGCACATCA
1 ATCTTCGTCAATTTATCC-GACTAGCGCTGGGCGCA--A
* * * *
43622964 TTATCTTCATCGATTTATTCGACTAGCGCAGGGCGCAA
1 --ATCTTCGTCAATTTATCCGACTAGCGCTGGGCGCAA
* * ** *
43623002 ATCTTTGTCAGTTTA-CCTGACTATAGCTGGGCACATCA
1 ATCTTCGTCAATTTATCC-GACTAGCGCTGGGCGCA--A
* * * *
43623040 TTATATTCGACGGA-TTATCCGACTAGCGCTAGGCGCAA
1 --ATCTTCGTC-AATTTATCCGACTAGCGCTGGGCGCAA
* * *
43623078 ATCTTCGTTAGTTTATCTGACTAG
1 ATCTTCGTCAATTTATCCGACTAG
43623102 TGCTAGGCAC
Statistics
Matches: 125, Mismatches: 37, Indels: 28
0.66 0.19 0.15
Matches are distributed among these distances:
35 3 0.02
36 68 0.54
38 4 0.03
40 47 0.38
41 3 0.02
ACGTcount: A:0.24, C:0.24, G:0.20, T:0.33
Consensus pattern (36 bp):
ATCTTCGTCAATTTATCCGACTAGCGCTGGGCGCAA
Found at i:43622977 original size:76 final size:76
Alignment explanation
Indices: 43622847--43623112 Score: 313
Period size: 76 Copynumber: 3.5 Consensus size: 76
43622837 TTTTGGTGAA
* * * ** *
43622847 CAAATCTTTGTCGATTTACGTGACTAGTGTTAGGCACATCATTATCTTCGTCGATTTATCCGACT
1 CAAATCTTCGTCAATTTACCTGACTAGTACTAGGCACATCATTATCTTCATCGATTTATCCGACT
43622912 AGCGCTGGGCG
66 AGCGCTGGGCG
* * *
43622923 CAAATCTTCGTCAATTTACCTTACTAGTACTGGGCACATCATTATCTTCATCGATTTATTCGACT
1 CAAATCTTCGTCAATTTACCTGACTAGTACTAGGCACATCATTATCTTCATCGATTTATCCGACT
*
43622988 AGCGCAGGGCG
66 AGCGCTGGGCG
* * * *
43622999 CAAATCTTTGTCAGTTTACCTGACTA-TAGCTGGGCACATCATTATATTCGA-CGGA-TTATCCG
1 CAAATCTTCGTCAATTTACCTGACTAGTA-CTAGGCACATCATTATCTTC-ATC-GATTTATCCG
*
43623061 ACTAGCGCTAGGCG
63 ACTAGCGCTGGGCG
* * * *
43623075 CAAATCTTCGTTAGTTTATCTGACTAGTGCTAGGCACA
1 CAAATCTTCGTCAATTTACCTGACTAGTACTAGGCACA
43623113 ACCTCTATAT
Statistics
Matches: 164, Mismatches: 22, Indels: 8
0.85 0.11 0.04
Matches are distributed among these distances:
75 2 0.01
76 158 0.96
77 4 0.02
ACGTcount: A:0.24, C:0.23, G:0.20, T:0.33
Consensus pattern (76 bp):
CAAATCTTCGTCAATTTACCTGACTAGTACTAGGCACATCATTATCTTCATCGATTTATCCGACT
AGCGCTGGGCG
Found at i:43626714 original size:41 final size:41
Alignment explanation
Indices: 43626659--43627010 Score: 342
Period size: 41 Copynumber: 8.6 Consensus size: 41
43626649 CTTTCGGGGC
*
43626659 TTTAGCGGCT-TTTTTGATAAAGCGCCGCTAATGCTCAGAGC-
1 TTTAGCGG-TGTTTTTGAAAAAGCGCCGCTAATGCTCAG-GCT
* *
43626700 TTTAGCGGTGTTTTTTAAAAAGCGCCGCTAATACTC-GAGCT
1 TTTAGCGGTGTTTTTGAAAAAGCGCCGCTAATGCTCAG-GCT
* ** * * *
43626741 TTTAGTGGCATTTTTAAAAAAGCACCTCTAATGCTCAGGCT
1 TTTAGCGGTGTTTTTGAAAAAGCGCCGCTAATGCTCAGGCT
* * *
43626782 TTTAGCAGCGTTTTTAAAAAAGCGCCGCTAATGCTCAGGCT
1 TTTAGCGGTGTTTTTGAAAAAGCGCCGCTAATGCTCAGGCT
* *
43626823 TTTAGCGGCGTTTTTGAATAAGCGCCGCTAATGCTCAGGAC-
1 TTTAGCGGTGTTTTTGAAAAAGCGCCGCTAATGCTCAGG-CT
* * *
43626864 TTTAGTGGTGTTTTTAAAAAAGCGCCGCTAATGATCAGGCT
1 TTTAGCGGTGTTTTTGAAAAAGCGCCGCTAATGCTCAGGCT
* * * * *
43626905 TTTAG-TGTCATTTTTGAAGAAGCACAGCTAATGCTCAGGCT
1 TTTAGCGGT-GTTTTTGAAAAAGCGCCGCTAATGCTCAGGCT
** *
43626946 TTTAGCGGCT-TTTTT-AAAAAGCATCGCTAATGCTCGGGGC-
1 TTTAGCGG-TGTTTTTGAAAAAGCGCCGCTAATGCTC-AGGCT
* *
43626986 TTTAGCAGCGTTTTTGAAAAAGCGC
1 TTTAGCGGTGTTTTTGAAAAAGCGC
43627011 TGCAAAAACA
Statistics
Matches: 261, Mismatches: 39, Indels: 22
0.81 0.12 0.07
Matches are distributed among these distances:
40 37 0.14
41 220 0.84
42 3 0.01
43 1 0.00
ACGTcount: A:0.25, C:0.19, G:0.23, T:0.32
Consensus pattern (41 bp):
TTTAGCGGTGTTTTTGAAAAAGCGCCGCTAATGCTCAGGCT
Found at i:43626763 original size:82 final size:82
Alignment explanation
Indices: 43626659--43627008 Score: 381
Period size: 82 Copynumber: 4.3 Consensus size: 82
43626649 CTTTCGGGGC
* * * *
43626659 TTTAGCGGCTTTTTTGATAAAGCGCCGCTAATGCTCAGAGC-TTTAGCGGTGTTTTTTAAAAAGC
1 TTTAGCGGCATTTTTGAAAAAGCACCGCTAATGCTCAG-GCTTTTAGCGGTGTTTTTAAAAAAGC
43626723 GCCGCTAATACTC-GAGCT
65 GCCGCTAATACTCAG-GCT
* * * * *
43626741 TTTAGTGGCATTTTTAAAAAAGCACCTCTAATGCTCAGGCTTTTAGCAGCGTTTTTAAAAAAGCG
1 TTTAGCGGCATTTTTGAAAAAGCACCGCTAATGCTCAGGCTTTTAGCGGTGTTTTTAAAAAAGCG
*
43626806 CCGCTAATGCTCAGGCT
66 CCGCTAATACTCAGGCT
* * * *
43626823 TTTAGCGGCGTTTTTGAATAAGCGCCGCTAATGCTCAGGAC-TTTAGTGGTGTTTTTAAAAAAGC
1 TTTAGCGGCATTTTTGAAAAAGCACCGCTAATGCTCAGG-CTTTTAGCGGTGTTTTTAAAAAAGC
43626887 GCCGCTAATGA-TCAGGCT
65 GCCGCTAAT-ACTCAGGCT
* * * *
43626905 TTTAGTGTCATTTTTGAAGAAGCACAGCTAATGCTCAGGCTTTTAGCGGCT-TTTTT-AAAAAGC
1 TTTAGCGGCATTTTTGAAAAAGCACCGCTAATGCTCAGGCTTTTAGCGG-TGTTTTTAAAAAAGC
** * *
43626968 ATCGCTAATGCTCGGGGC-
65 GCCGCTAATACTC-AGGCT
* *
43626986 TTTAGCAGCGTTTTTGAAAAAGC
1 TTTAGCGGCATTTTTGAAAAAGC
43627009 GCTGCAAAAA
Statistics
Matches: 224, Mismatches: 36, Indels: 17
0.81 0.13 0.06
Matches are distributed among these distances:
81 37 0.17
82 184 0.82
83 3 0.01
ACGTcount: A:0.25, C:0.19, G:0.23, T:0.33
Consensus pattern (82 bp):
TTTAGCGGCATTTTTGAAAAAGCACCGCTAATGCTCAGGCTTTTAGCGGTGTTTTTAAAAAAGCG
CCGCTAATACTCAGGCT
Found at i:43626804 original size:123 final size:123
Alignment explanation
Indices: 43626659--43627008 Score: 388
Period size: 123 Copynumber: 2.9 Consensus size: 123
43626649 CTTTCGGGGC
* * *
43626659 TTTAGCGGCTTTTTTGATAAAGCGCCGCTAATGCTCAGAGC-TTTAGCGGTGTTTTTTAAAAAGC
1 TTTAGCAGCATTTTTGAAAAAGCGCCGCTAATGCTCAG-GCTTTTAGCGG-GTTTTTTAAAAAGC
* * *
43626723 GCCGCTAATACTCGA-G-CTTTTAGTGGCATTTTTAAAAAAGCACCTCTAATGCTCAGGCT
64 GCCGCTAATGCTCGAGGAC-TTTAGTGGCATTTTTAAAAAAGCACCGCTAATGATCAGGCT
* * * *
43626782 TTTAGCAGCGTTTTTAAAAAAGCGCCGCTAATGCTCAGGCTTTTAGCGGCGTTTTTGAATAAGCG
1 TTTAGCAGCATTTTTGAAAAAGCGCCGCTAATGCTCAGGCTTTTAGCGG-GTTTTTTAAAAAGCG
** *
43626847 CCGCTAATGCTC-AGGACTTTAGTGGTGTTTTTAAAAAAGCGCCGCTAATGATCAGGCT
65 CCGCTAATGCTCGAGGACTTTAGTGGCATTTTTAAAAAAGCACCGCTAATGATCAGGCT
* * * * * *
43626905 TTTAG-TGTCATTTTTGAAGAAGCACAGCTAATGCTCAGGCTTTTAGCGGCTTTTTTAAAAAGCA
1 TTTAGCAG-CATTTTTGAAAAAGCGCCGCTAATGCTCAGGCTTTTAGCGGGTTTTTTAAAAAGCG
* * ** * *
43626969 TCGCTAATGCTCG-GGGCTTTAGCAGCGTTTTTGAAAAAGC
65 CCGCTAATGCTCGAGGACTTTAGTGGCATTTTTAAAAAAGC
43627009 GCTGCAAAAA
Statistics
Matches: 193, Mismatches: 29, Indels: 11
0.83 0.12 0.05
Matches are distributed among these distances:
122 48 0.25
123 144 0.75
124 1 0.01
ACGTcount: A:0.25, C:0.19, G:0.23, T:0.33
Consensus pattern (123 bp):
TTTAGCAGCATTTTTGAAAAAGCGCCGCTAATGCTCAGGCTTTTAGCGGGTTTTTTAAAAAGCGC
CGCTAATGCTCGAGGACTTTAGTGGCATTTTTAAAAAAGCACCGCTAATGATCAGGCT
Found at i:43627439 original size:14 final size:15
Alignment explanation
Indices: 43627411--43627443 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
43627401 AAGGTTTATA
43627411 GATTATGGAATTAGG
1 GATTATGGAATTAGG
43627426 GATTATGG-ATTAGG
1 GATTATGGAATTAGG
43627440 GATT
1 GATT
43627444 CTGGTTTAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 10 0.56
15 8 0.44
ACGTcount: A:0.30, C:0.00, G:0.33, T:0.36
Consensus pattern (15 bp):
GATTATGGAATTAGG
Found at i:43627645 original size:136 final size:137
Alignment explanation
Indices: 43627465--43627739 Score: 288
Period size: 136 Copynumber: 2.0 Consensus size: 137
43627455 GTTGTGACTT
* * * * *
43627465 AGGGGTTAGAGGTTAGAGGTTAAGAGTTAGTGATTTAAGGTTTAGAGATTCGG-GGTCGAGTTA-
1 AGGGGTTAGAGGTTAGAGGTTAAGAGTTAGTGATTTAAGATTTAGAGATTAGGAGATAGAGGTAG
* * *
43627528 GGGTTTAATGTTTAGATTAATTAGTATTTTTTAAAATTTATATATTAATTAAGTTC-TTATATAA
66 GGGTTTAAGGCTTAGATTAATTAGTATTTTTT--AATTTATATATTAAATAAGTTCTTTATATAA
43627592 TTATAAAAG
129 TTATAAAAG
* * * * * * * * *
43627601 AGGGGTTAGGGGTTAGGGGTTTAATATTTA-TGTTTTATGATTTAGGGTTTAGGAGATAGGGGTA
1 AGGGGTTAGAGGTTAGAGG-TTAAGAGTTAGTGATTTAAGATTTAGAGATTAGGAGATAGAGGTA
* * * * *
43627665 GGGGTTTAGGGCTTAGATTATTTGGTATTTTTTAATTTATATATTAAATAATTTCTTTTTATAAT
65 GGGGTTTAAGGCTTAGATTAATTAGTATTTTTTAATTTATATATTAAATAAGTTCTTTATATAAT
*
43627730 TGTAAAAG
130 TATAAAAG
43627738 AG
1 AG
43627740 ATCATTTTAA
Statistics
Matches: 112, Mismatches: 23, Indels: 7
0.79 0.16 0.05
Matches are distributed among these distances:
136 54 0.48
137 31 0.28
138 27 0.24
ACGTcount: A:0.30, C:0.02, G:0.25, T:0.43
Consensus pattern (137 bp):
AGGGGTTAGAGGTTAGAGGTTAAGAGTTAGTGATTTAAGATTTAGAGATTAGGAGATAGAGGTAG
GGGTTTAAGGCTTAGATTAATTAGTATTTTTTAATTTATATATTAAATAAGTTCTTTATATAATT
ATAAAAG
Found at i:43631997 original size:45 final size:44
Alignment explanation
Indices: 43631891--43632038 Score: 169
Period size: 43 Copynumber: 3.4 Consensus size: 44
43631881 TTTAAACGTT
* *
43631891 ATGTT-TTTAGCGGCGTTTTTG-CAAGAAGCGCCGCTAAAGGT-
1 ATGTTCTTTAGCGGCGTTTGTGACAAAAAGCGCCGCTAAAGGTC
* * * *
43631932 TTGATCTATAGCGGCGTTTGTGACAAAAAAACGCCGCTAAAGGTC
1 ATGTTCTTTAGCGGCGTTTGTGAC-AAAAAGCGCCGCTAAAGGTC
* * *
43631977 ATGTTCTTTAGCGGCGTTTGT-ACCAAAAGCACCGCTAAATGTC
1 ATGTTCTTTAGCGGCGTTTGTGACAAAAAGCGCCGCTAAAGGTC
*
43632020 ATGGTCTTTAGCGGCGTTT
1 ATGTTCTTTAGCGGCGTTT
43632039 TTTCACATAA
Statistics
Matches: 89, Mismatches: 14, Indels: 6
0.82 0.13 0.06
Matches are distributed among these distances:
41 3 0.03
42 14 0.16
43 35 0.39
44 19 0.21
45 18 0.20
ACGTcount: A:0.24, C:0.20, G:0.26, T:0.30
Consensus pattern (44 bp):
ATGTTCTTTAGCGGCGTTTGTGACAAAAAGCGCCGCTAAAGGTC
Found at i:43632231 original size:17 final size:17
Alignment explanation
Indices: 43632206--43632238 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
43632196 AATATTTTAT
43632206 TTAAATATAATTATTAA
1 TTAAATATAATTATTAA
*
43632223 TTAATTATAATTATTA
1 TTAAATATAATTATTA
43632239 TAAATAAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (17 bp):
TTAAATATAATTATTAA
Found at i:43633445 original size:30 final size:31
Alignment explanation
Indices: 43633400--43633459 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 31
43633390 AGAGGTGGGA
*
43633400 TGGGAAGGGAATAAAAGTTTTAGAGGAAAAG
1 TGGGAAGGGAATAAAAATTTTAGAGGAAAAG
* * *
43633431 TGGG-AGGGAGTAAAAATTTTGGGGGAAAA
1 TGGGAAGGGAATAAAAATTTTAGAGGAAAA
43633460 TAAAAGGTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 21 0.84
31 4 0.16
ACGTcount: A:0.42, C:0.00, G:0.38, T:0.20
Consensus pattern (31 bp):
TGGGAAGGGAATAAAAATTTTAGAGGAAAAG
Found at i:43634369 original size:20 final size:20
Alignment explanation
Indices: 43634344--43634403 Score: 59
Period size: 20 Copynumber: 3.0 Consensus size: 20
43634334 AATTAGATTT
43634344 ATTTAAAATAAAAATATTAA
1 ATTTAAAATAAAAATATTAA
* *
43634364 ATTTAAATTTAAAAATA-GAA
1 ATTTAAA-ATAAAAATATTAA
* *
43634384 AATTAAAATATCAAATATTA
1 ATTTAAAATA-AAAATATTA
43634404 TTGAAAACAC
Statistics
Matches: 31, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
19 2 0.06
20 20 0.65
21 9 0.29
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.35
Consensus pattern (20 bp):
ATTTAAAATAAAAATATTAA
Found at i:43634386 original size:21 final size:21
Alignment explanation
Indices: 43634344--43634394 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 21
43634334 AATTAGATTT
**
43634344 ATTTAAA-ATAAAAATATTAA
1 ATTTAAATATAAAAATAGAAA
*
43634364 ATTTAAATTTAAAAATAGAAA
1 ATTTAAATATAAAAATAGAAA
*
43634385 ATTAAAATAT
1 ATTTAAATAT
43634395 CAAATATTAT
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 7 0.28
21 18 0.72
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (21 bp):
ATTTAAATATAAAAATAGAAA
Found at i:43638196 original size:25 final size:25
Alignment explanation
Indices: 43638159--43638265 Score: 74
Period size: 25 Copynumber: 4.3 Consensus size: 25
43638149 GACACACCAC
* * * *
43638159 AGCTCGCAAGAGCGTCCCGTTATTT
1 AGCTCTCATGAGCATCCCGTTATAT
*
43638184 AGCTCTTATGAGCATCCCGTTATAT
1 AGCTCTCATGAGCATCCCGTTATAT
* * * *
43638209 GGCTCTCATGAGCTTCCTGATATAT
1 AGCTCTCATGAGCATCCCGTTATAT
* *
43638234 TGCTCTC-TGGAGCTTCCCGATTA-AT
1 AGCTCTCAT-GAGCATCCCG-TTATAT
*
43638259 GGCTCTC
1 AGCTCTC
43638266 TTAAGCTTCT
Statistics
Matches: 66, Mismatches: 14, Indels: 4
0.79 0.17 0.05
Matches are distributed among these distances:
24 1 0.02
25 63 0.95
26 2 0.03
ACGTcount: A:0.19, C:0.27, G:0.21, T:0.34
Consensus pattern (25 bp):
AGCTCTCATGAGCATCCCGTTATAT
Found at i:43638261 original size:50 final size:50
Alignment explanation
Indices: 43638182--43638311 Score: 142
Period size: 50 Copynumber: 2.6 Consensus size: 50
43638172 GTCCCGTTAT
* * *
43638182 TTAGCTCTTATGAGCATCCCG-TTATATGGCTCTCATGAGCTTC-CTGATATA
1 TTAGCTCTAATGAGCTTCCCGATTA-ATGGCTCTCATAAGCTTCTC-GATA-A
* *
43638233 TT-GCTCT-CTGGAGCTTCCCGATTAATGGCTCTCTTAAGCTTCTCGATAA
1 TTAGCTCTAAT-GAGCTTCCCGATTAATGGCTCTCATAAGCTTCTCGATAA
*
43638282 TTAGCTCTAATGAGCTTCTCGATTAATGGC
1 TTAGCTCTAATGAGCTTCCCGATTAATGGC
43638312 CTTCGGAGCT
Statistics
Matches: 68, Mismatches: 6, Indels: 11
0.80 0.07 0.13
Matches are distributed among these distances:
49 4 0.06
50 57 0.84
51 7 0.10
ACGTcount: A:0.21, C:0.24, G:0.18, T:0.37
Consensus pattern (50 bp):
TTAGCTCTAATGAGCTTCCCGATTAATGGCTCTCATAAGCTTCTCGATAA
Found at i:43638266 original size:25 final size:23
Alignment explanation
Indices: 43638192--43638361 Score: 108
Period size: 25 Copynumber: 6.9 Consensus size: 23
43638182 TTAGCTCTTA
* *
43638192 TGAGCATCCCGTTATATGGCTCTC
1 TGAGCTTCCCGATA-ATGGCTCTC
* *
43638216 ATGAGCTTCCTGATATATTGCTCTC
1 -TGAGCTTCCCGATA-ATGGCTCTC
43638241 TGGAGCTTCCCGATTAATGGCTCTC
1 T-GAGCTTCCCGA-TAATGGCTCTC
* * * *
43638266 TTAAGCTTCTCGATAATTAGCTCTAA
1 -TGAGCTTCCCGATAA-TGGCTCT-C
*
43638292 TGAGCTTCTCGATTAATGGC-CTTC
1 TGAGCTTCCCGA-TAATGGCTC-TC
* * * *
43638316 GGAGCTTCCCAATATTGGCTCATA
1 TGAGCTTCCCGATAATGGCTC-TC
43638340 TGAGCTTCCCGATAATTGGCTC
1 TGAGCTTCCCGATAA-TGGCTC
43638362 GCAAGTGTTT
Statistics
Matches: 114, Mismatches: 22, Indels: 18
0.74 0.14 0.12
Matches are distributed among these distances:
23 6 0.05
24 28 0.25
25 74 0.65
26 6 0.05
ACGTcount: A:0.21, C:0.25, G:0.19, T:0.35
Consensus pattern (23 bp):
TGAGCTTCCCGATAATGGCTCTC
Found at i:43640455 original size:56 final size:50
Alignment explanation
Indices: 43640359--43640604 Score: 201
Period size: 49 Copynumber: 4.8 Consensus size: 50
43640349 ATTTGGGTAA
* * * *
43640359 AGAGATCCCATGTAAGACCATGTCTGGGACATGACATTGGCATCATTGAGATTATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCA-C--CGAG---ATG
*
43640415 AGAGGTCTCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
* * * *
43640465 AGAGGTCCCATGTAAGACCATGTCTGGGGCATGGCGTTGGCAGCTATAT-
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
** * * * * * *
43640514 AGAACTCTCATGTAAGACCATATCTGGGATATGGCATTGGCA--GTACAAG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCG-AGATG
* ** * * *
43640563 AAACATCCCATGTAAGACTATGTCTGGGACATAGCTTTGGCA
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCA
43640605 TGTTACATTC
Statistics
Matches: 159, Mismatches: 29, Indels: 11
0.80 0.15 0.06
Matches are distributed among these distances:
48 2 0.01
49 68 0.43
50 47 0.30
53 3 0.02
55 1 0.01
56 38 0.24
ACGTcount: A:0.28, C:0.20, G:0.28, T:0.25
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
Found at i:43640466 original size:50 final size:50
Alignment explanation
Indices: 43640367--43640555 Score: 200
Period size: 50 Copynumber: 3.7 Consensus size: 50
43640357 AAAGAGATCC
* *
43640367 CATGTAAGACCATGTCTGGGACATGACATTGGCATCATTGAGATTATGAGAGGTCT
1 CATGTAAGACCATGTCTGGGACATGGCATTGGCA-C--CGAG---ATGAGAGGTCT
* *
43640423 CATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGGTCC
1 CATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGGTCT
* * * * * **
43640473 CATGTAAGACCATGTCTGGGGCATGGCGTTGGCAGCTATAT-AGAACTCT
1 CATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGGTCT
* *
43640522 CATGTAAGACCATATCTGGGATATGGCATTGGCA
1 CATGTAAGACCATGTCTGGGACATGGCATTGGCA
43640556 GTACAAGAAA
Statistics
Matches: 118, Mismatches: 15, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
49 35 0.30
50 47 0.40
53 3 0.03
55 1 0.01
56 32 0.27
ACGTcount: A:0.26, C:0.19, G:0.29, T:0.25
Consensus pattern (50 bp):
CATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGGTCT
Found at i:43645076 original size:27 final size:27
Alignment explanation
Indices: 43645046--43645114 Score: 102
Period size: 27 Copynumber: 2.6 Consensus size: 27
43645036 GTCTTGAAAG
**
43645046 ACTATCTTGTGTTTACCATCCCATTAA
1 ACTATCTTGTGTTTACCATCCCAGCAA
* *
43645073 ACTATCTCGTGTTTACCGTCCCAGCAA
1 ACTATCTTGTGTTTACCATCCCAGCAA
43645100 ACTATCTTGTGTTTA
1 ACTATCTTGTGTTTA
43645115 GTGTCTCGGT
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 37 1.00
ACGTcount: A:0.23, C:0.26, G:0.12, T:0.39
Consensus pattern (27 bp):
ACTATCTTGTGTTTACCATCCCAGCAA
Found at i:43648183 original size:30 final size:28
Alignment explanation
Indices: 43648117--43648183 Score: 71
Period size: 29 Copynumber: 2.3 Consensus size: 28
43648107 CTTCAAAATG
* * *
43648117 TTAGAATTTAGTCACTGTATTTTTATTT
1 TTAGAATTTAATCACTCTATTTTTAATT
*
43648145 TTAGGAATTTAATCCCTCTACTTTTTAGATT
1 TTA-GAATTTAATCACTCTA-TTTTTA-ATT
43648176 TTAGAATT
1 TTAGAATT
43648184 CAAGTCCAAC
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
28 3 0.09
29 13 0.41
30 11 0.34
31 5 0.16
ACGTcount: A:0.27, C:0.10, G:0.10, T:0.52
Consensus pattern (28 bp):
TTAGAATTTAATCACTCTATTTTTAATT
Found at i:43652611 original size:2 final size:2
Alignment explanation
Indices: 43652604--43652640 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
43652594 GCTTGAAAGC
43652604 AT AT AT 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 AT AT AT A
43652641 AGNNNNNNNN
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:43652804 original size:2 final size:2
Alignment explanation
Indices: 43652755--43652791 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
43652745 GTTAGAAGAC
43652755 AT AT AT 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 AT AT AT A
43652792 AAACGTGTAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:43655493 original size:14 final size:14
Alignment explanation
Indices: 43655456--43655501 Score: 51
Period size: 14 Copynumber: 3.3 Consensus size: 14
43655446 TTATAAATGA
43655456 AATTAGAATTGATTT
1 AATTAGAATT-ATTT
43655471 -ATGTA-AATTATTT
1 AAT-TAGAATTATTT
*
43655484 AATTAGAATTAATT
1 AATTAGAATTATTT
43655498 AATT
1 AATT
43655502 TTTGGAAAAG
Statistics
Matches: 27, Mismatches: 1, Indels: 7
0.77 0.03 0.20
Matches are distributed among these distances:
13 6 0.22
14 19 0.70
15 2 0.07
ACGTcount: A:0.43, C:0.00, G:0.09, T:0.48
Consensus pattern (14 bp):
AATTAGAATTATTT
Found at i:43669380 original size:92 final size:92
Alignment explanation
Indices: 43669223--43669409 Score: 322
Period size: 92 Copynumber: 2.0 Consensus size: 92
43669213 TCCTGGTATG
*
43669223 GAAAAAGCTATAACAATGTATTGTGATAACGGTGCAGCAATAACTAATACCAAGAAAATAAGAAG
1 GAAAAAGCTATAACAATGTATTGTGATAACAGTGCAGCAATAACTAATACCAAGAAAATAAGAAG
43669288 TCACAAGAGGACCAAACATATTGACCA
66 TCACAAGAGGACCAAACATATTGACCA
* * *
43669315 GAAAAAGTTATAACAATGTATTGTGATAACAGTGCTGTAATAACTAATACCAAGGAAAA-AAGAA
1 GAAAAAGCTATAACAATGTATTGTGATAACAGTGCAGCAATAACTAATACCAA-GAAAATAAGAA
43669379 GTCACAAGAGGACCAAACATATTGACCA
65 GTCACAAGAGGACCAAACATATTGACCA
43669407 GAA
1 GAA
43669410 GTATCACTTG
Statistics
Matches: 90, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
92 85 0.94
93 5 0.06
ACGTcount: A:0.48, C:0.15, G:0.18, T:0.19
Consensus pattern (92 bp):
GAAAAAGCTATAACAATGTATTGTGATAACAGTGCAGCAATAACTAATACCAAGAAAATAAGAAG
TCACAAGAGGACCAAACATATTGACCA
Found at i:43669708 original size:15 final size:15
Alignment explanation
Indices: 43669688--43669717 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
43669678 TTCACTATTA
*
43669688 TGTCTTTTGTATTTT
1 TGTCTTTTATATTTT
43669703 TGTCTTTTATATTTT
1 TGTCTTTTATATTTT
43669718 GCATGCACAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.10, C:0.07, G:0.10, T:0.73
Consensus pattern (15 bp):
TGTCTTTTATATTTT
Found at i:43671320 original size:24 final size:25
Alignment explanation
Indices: 43671284--43671333 Score: 59
Period size: 25 Copynumber: 2.0 Consensus size: 25
43671274 TAACTATACC
*
43671284 AAAAATAATATT-ATTTTAATAGTTT
1 AAAAATAATATTAAATTTAATA-TTT
*
43671309 AAAATTAA-ATTAAATTTAATATTT
1 AAAAATAATATTAAATTTAATATTT
43671333 A
1 A
43671334 TCTTAATAGT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
24 7 0.32
25 15 0.68
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (25 bp):
AAAAATAATATTAAATTTAATATTT
Found at i:43671442 original size:17 final size:17
Alignment explanation
Indices: 43671417--43671449 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
43671407 TATTATTTTA
*
43671417 ATTAGATTTAATATTAG
1 ATTAAATTTAATATTAG
43671434 ATTAAATTTAATATTA
1 ATTAAATTTAATATTA
43671450 AAGTGATTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.45, C:0.00, G:0.06, T:0.48
Consensus pattern (17 bp):
ATTAAATTTAATATTAG
Found at i:43671604 original size:23 final size:25
Alignment explanation
Indices: 43671556--43671605 Score: 68
Period size: 23 Copynumber: 2.0 Consensus size: 25
43671546 AGTTGTAGAG
43671556 AGAAAATTCTCTGAAGAGATTATTTT
1 AGAAAATTCTCT-AAGAGATTATTTT
*
43671582 AGAAAATT-TCT-AGAGATTTTTTT
1 AGAAAATTCTCTAAGAGATTATTTT
43671605 A
1 A
43671606 ATTTACAACT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
23 12 0.52
25 3 0.13
26 8 0.35
ACGTcount: A:0.38, C:0.06, G:0.14, T:0.42
Consensus pattern (25 bp):
AGAAAATTCTCTAAGAGATTATTTT
Found at i:43673088 original size:21 final size:21
Alignment explanation
Indices: 43673043--43673094 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 21
43673033 GTATCGATCC
*
43673043 AGTATCGATAGT--TTTCTTAA
1 AGTATCGATA-TAATTTCCTAA
*
43673063 AGTATTGATATAATTTCCTAA
1 AGTATCGATATAATTTCCTAA
*
43673084 GGTATCGATAT
1 AGTATCGATAT
43673095 TCCTACTCCA
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
19 1 0.04
20 9 0.35
21 16 0.62
ACGTcount: A:0.33, C:0.10, G:0.15, T:0.42
Consensus pattern (21 bp):
AGTATCGATATAATTTCCTAA
Found at i:43674108 original size:14 final size:13
Alignment explanation
Indices: 43674082--43674115 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
43674072 TCAACTAGAG
43674082 AATTTAATTAAAA
1 AATTTAATTAAAA
*
43674095 AATTTTATTAAAA
1 AATTTAATTAAAA
43674108 AA-TTAATT
1 AATTTAATT
43674116 TGGAAAATCT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
12 5 0.26
13 14 0.74
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
AATTTAATTAAAA
Found at i:43674319 original size:16 final size:16
Alignment explanation
Indices: 43674295--43674348 Score: 90
Period size: 16 Copynumber: 3.4 Consensus size: 16
43674285 TTTGGTTCGC
* *
43674295 TGTATTGGATTAGAGG
1 TGTAATGGAATAGAGG
43674311 TGTAATGGAATAGAGG
1 TGTAATGGAATAGAGG
43674327 TGTAATGGAATAGAGG
1 TGTAATGGAATAGAGG
43674343 TGTAAT
1 TGTAAT
43674349 AGCAAATCAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 36 1.00
ACGTcount: A:0.33, C:0.00, G:0.35, T:0.31
Consensus pattern (16 bp):
TGTAATGGAATAGAGG
Found at i:43674432 original size:39 final size:43
Alignment explanation
Indices: 43674327--43674436 Score: 129
Period size: 45 Copynumber: 2.6 Consensus size: 43
43674317 GGAATAGAGG
43674327 TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTTGAA
1 TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTT--A
* * ***
43674372 TGTAATGGAATAGAGGCGTAATAG-TAATCTTGTGTTTGG-T-
1 TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTTA
43674412 TG-AATGGAATAGAGGTGTAATAGCA
1 TGTAATGGAATAGAGGTGTAATAGCA
43674437 TAATGGAAAA
Statistics
Matches: 57, Mismatches: 7, Indels: 7
0.80 0.10 0.10
Matches are distributed among these distances:
39 20 0.35
40 2 0.04
43 1 0.02
44 11 0.19
45 23 0.40
ACGTcount: A:0.34, C:0.05, G:0.29, T:0.32
Consensus pattern (43 bp):
TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTTA
Found at i:43674603 original size:18 final size:17
Alignment explanation
Indices: 43674582--43674616 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
43674572 TTATTATTAA
*
43674582 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
43674600 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
43674617 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:43674670 original size:157 final size:157
Alignment explanation
Indices: 43674469--43674785 Score: 589
Period size: 157 Copynumber: 2.0 Consensus size: 157
43674459 TAGAATACCC
*
43674469 TTAGCATAAATTTATTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTA
1 TTAGCAGAAATTTATTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTA
* *
43674534 TTATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTTTAATTAAAA
66 ATATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAA
43674599 TATATAATTTAATAAAATTCTTAATAA
131 TATATAATTTAATAAAATTCTTAATAA
* *
43674626 TTAGCAGAAATTTGTTTTGGTAAATTATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTA
1 TTAGCAGAAATTTATTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTA
43674691 ATATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAA
66 ATATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAA
43674756 TATATAATTTAATAAAATTCTTAATAA
131 TATATAATTTAATAAAATTCTTAATAA
43674783 TTA
1 TTA
43674786 ATATTCTTAT
Statistics
Matches: 155, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
157 155 1.00
ACGTcount: A:0.45, C:0.03, G:0.05, T:0.47
Consensus pattern (157 bp):
TTAGCAGAAATTTATTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTA
ATATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAA
TATATAATTTAATAAAATTCTTAATAA
Found at i:43674756 original size:16 final size:16
Alignment explanation
Indices: 43674719--43674760 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
43674709 TTAATCATAT
*
43674719 TTAAACATA-ATTATTA
1 TTAAA-ATATATTATAA
43674735 TT-AAATATATTATAA
1 TTAAAATATATTATAA
43674750 TTAAAATATAT
1 TTAAAATATAT
43674761 AATTTAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 3 0.13
15 10 0.43
16 10 0.43
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (16 bp):
TTAAAATATATTATAA
Found at i:43674767 original size:14 final size:15
Alignment explanation
Indices: 43674728--43674769 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
43674718 TTTAAACATA
*
43674728 ATTATTATTAAATAT
1 ATTATAATTAAATAT
43674743 ATTATAATTAAA-AT
1 ATTATAATTAAATAT
*
43674757 A-TATAATTTAATA
1 ATTATAATTAAATA
43674770 AAATTCTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 9 0.38
14 4 0.17
15 11 0.46
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATTATAATTAAATAT
Found at i:43674819 original size:61 final size:61
Alignment explanation
Indices: 43674754--43674941 Score: 190
Period size: 61 Copynumber: 3.1 Consensus size: 61
43674744 TTATAATTAA
43674754 AATATATAATTTAATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTCAAATCAT
1 AATATATAATTTAATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTCAAATCAT
* * * * * * * * * * *
43674815 AATATATGATACT-GTAAAA-TATAAATTAA--AATAATTATTAT-TAAATATA-TTATAATTAA
1 AATATATAAT-TTAATAAAATTCTTAA-TAATTAAT-ATTCTTATATGAATTTACTCA-AATCAT
*
43674874 AATATATAATTTAAGAAAATTCTTAATAATTAATATTCTTATATGAATTTACTCAAATCAT
1 AATATATAATTTAATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTCAAATCAT
43674935 AATATAT
1 AATATAT
43674942 GATACTATAA
Statistics
Matches: 94, Mismatches: 23, Indels: 20
0.69 0.17 0.15
Matches are distributed among these distances:
58 3 0.03
59 29 0.31
60 22 0.23
61 37 0.39
62 3 0.03
ACGTcount: A:0.49, C:0.06, G:0.03, T:0.43
Consensus pattern (61 bp):
AATATATAATTTAATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTCAAATCAT
Found at i:43674856 original size:120 final size:120
Alignment explanation
Indices: 43674717--43675012 Score: 499
Period size: 120 Copynumber: 2.5 Consensus size: 120
43674707 ATTTAATCAT
43674717 ATTTAAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATA
1 ATTTAAA-ATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATA
* *
43674782 ATTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTGTAAAATATAA
65 ATTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGA-AA
*
43674839 A-TTAAAATAATTATTATTAAATATATTATAATTAAAATATATAATTTAAGAAAATTCTTAATAA
1 ATTTAAAATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAA
43674903 TTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGAAA
66 TTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGAAA
* * *
43674958 ATTTGAAATAATTAATATTAAATATATT-TAATT-AAATATATGATTTAATAAAATT
1 ATTTAAAATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATT
43675013 TAAAATAATT
Statistics
Matches: 166, Mismatches: 7, Indels: 6
0.93 0.04 0.03
Matches are distributed among these distances:
118 20 0.12
119 8 0.05
120 132 0.80
121 5 0.03
122 1 0.01
ACGTcount: A:0.50, C:0.04, G:0.03, T:0.42
Consensus pattern (120 bp):
ATTTAAAATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAA
TTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGAAA
Found at i:43674859 original size:15 final size:16
Alignment explanation
Indices: 43674838--43674880 Score: 63
Period size: 15 Copynumber: 2.8 Consensus size: 16
43674828 GTAAAATATA
43674838 AATTAAAATA-ATTAT
1 AATTAAAATATATTAT
*
43674853 TATT-AAATATATTAT
1 AATTAAAATATATTAT
43674868 AATTAAAATATAT
1 AATTAAAATATAT
43674881 AATTTAAGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
14 5 0.21
15 11 0.46
16 8 0.33
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (16 bp):
AATTAAAATATATTAT
Found at i:43674940 original size:59 final size:58
Alignment explanation
Indices: 43674757--43674940 Score: 164
Period size: 57 Copynumber: 3.1 Consensus size: 58
43674747 TAATTAAAAT
43674757 ATATAATTTAATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTCAAATCATA
1 ATATAATTTAA-AAAATTCTTAATAATTAATATTCTTATATGAATTTACTCAAATCATA
* ** * * * *
43674816 ATATATGATACTGTAAAATATAAATTAA-AA-TAATTATTATTAAAT-ATATTATAATTAAA--A
1 ATATA--AT--T-TAAAAAAT-TCTTAATAATTAA-TATTCTTATATGA-ATT-TACTCAAATCA
43674876 T-
57 TA
43674877 ATATAATTTAAGAAAATTCTTAATAATTAATATTCTTATATGAATTTACTCAAATCATA
1 ATATAATTTAA-AAAATTCTTAATAATTAATATTCTTATATGAATTTACTCAAATCATA
43674936 ATATA
1 ATATA
43674941 TGATACTATA
Statistics
Matches: 95, Mismatches: 14, Indels: 32
0.67 0.10 0.23
Matches are distributed among these distances:
56 13 0.14
57 19 0.20
58 6 0.06
59 12 0.13
61 7 0.07
62 6 0.06
63 19 0.20
64 13 0.14
ACGTcount: A:0.49, C:0.06, G:0.03, T:0.42
Consensus pattern (58 bp):
ATATAATTTAAAAAATTCTTAATAATTAATATTCTTATATGAATTTACTCAAATCATA
Found at i:43674998 original size:16 final size:17
Alignment explanation
Indices: 43674979--43675011 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
43674969 TTAATATTAA
*
43674979 ATAT-ATTTAATTAAAT
1 ATATGATTTAATAAAAT
43674995 ATATGATTTAATAAAAT
1 ATATGATTTAATAAAAT
43675012 TTAAAATAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (17 bp):
ATATGATTTAATAAAAT
Found at i:43675093 original size:18 final size:19
Alignment explanation
Indices: 43675070--43675106 Score: 67
Period size: 18 Copynumber: 2.0 Consensus size: 19
43675060 TAAAATAATT
43675070 ATTATTACATAT-AATTTA
1 ATTATTACATATAAATTTA
43675088 ATTATTACATATAAATTTA
1 ATTATTACATATAAATTTA
43675107 GTTTAATTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 12 0.67
19 6 0.33
ACGTcount: A:0.46, C:0.05, G:0.00, T:0.49
Consensus pattern (19 bp):
ATTATTACATATAAATTTA
Found at i:43687289 original size:13 final size:13
Alignment explanation
Indices: 43687273--43687323 Score: 66
Period size: 13 Copynumber: 3.9 Consensus size: 13
43687263 TTTAAACCAA
43687273 ACTTTTCAAAAGC
1 ACTTTTCAAAAGC
*
43687286 ACTTTTCAATAGC
1 ACTTTTCAAAAGC
* *
43687299 ACTTTTCCACAGC
1 ACTTTTCAAAAGC
*
43687312 ACTTTTCCAAAG
1 ACTTTTCAAAAG
43687324 TATTGTCAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
13 34 1.00
ACGTcount: A:0.31, C:0.27, G:0.08, T:0.33
Consensus pattern (13 bp):
ACTTTTCAAAAGC
Found at i:43694049 original size:20 final size:21
Alignment explanation
Indices: 43694026--43694065 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
43694016 TAAATAATTT
*
43694026 TTAAAAA-TTGGAAAAAAAAA
1 TTAAAAAGTTAGAAAAAAAAA
43694046 TTAAAAAGTTAGAAAAAAAA
1 TTAAAAAGTTAGAAAAAAAA
43694066 CTAGTAATAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.70, C:0.00, G:0.10, T:0.20
Consensus pattern (21 bp):
TTAAAAAGTTAGAAAAAAAAA
Found at i:43694366 original size:32 final size:32
Alignment explanation
Indices: 43694303--43694376 Score: 82
Period size: 32 Copynumber: 2.3 Consensus size: 32
43694293 ATAAATTTGG
**
43694303 ATAATTTTTTTCAGTTTATTTAAATAATAAAA
1 ATAATTTTTTTCAGTTTAAATAAATAATAAAA
43694335 ATAATTTTATTTCAG-TTAAAT-AATAATTAAAA
1 ATAATTTT-TTTCAGTTTAAATAAATAA-TAAAA
*
43694367 A-AATATTTTT
1 ATAATTTTTTT
43694377 AATTATTCCA
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
30 3 0.08
31 10 0.27
32 18 0.49
33 6 0.16
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.49
Consensus pattern (32 bp):
ATAATTTTTTTCAGTTTAAATAAATAATAAAA
Found at i:43695042 original size:10 final size:9
Alignment explanation
Indices: 43695027--43695084 Score: 53
Period size: 10 Copynumber: 6.0 Consensus size: 9
43695017 TTAAAAAAAA
43695027 TTACAATCTT
1 TTACAAT-TT
43695037 TTACAATTT
1 TTACAATTT
* *
43695046 CTAATAATTT
1 -TTACAATTT
*
43695056 TTATAATTT
1 TTACAATTT
43695065 CTTACAATATT
1 -TTACAAT-TT
43695076 TTACAATTT
1 TTACAATTT
43695085 CTATTTTTTA
Statistics
Matches: 41, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
9 12 0.29
10 27 0.66
11 2 0.05
ACGTcount: A:0.34, C:0.12, G:0.00, T:0.53
Consensus pattern (9 bp):
TTACAATTT
Found at i:43695072 original size:39 final size:38
Alignment explanation
Indices: 43695027--43695133 Score: 121
Period size: 39 Copynumber: 2.8 Consensus size: 38
43695017 TTAAAAAAAA
43695027 TTACAATCTTTTACAATTTCTAATAATTTTTATAATTTC
1 TTACAAT-TTTTACAATTTCTAATAATTTTTATAATTTC
*
43695066 TTACAATATTTTACAATTTCT-AT--TTTTTATAATTTT
1 TTACAAT-TTTTACAATTTCTAATAATTTTTATAATTTC
* * * *
43695102 TTATAATTTTTAAAAATTCTAACATATTTTTA
1 TTACAATTTTTACAATTTCTAATA-ATTTTTA
43695134 ATTTTTGAAT
Statistics
Matches: 58, Mismatches: 6, Indels: 8
0.81 0.08 0.11
Matches are distributed among these distances:
35 11 0.19
36 19 0.33
38 2 0.03
39 26 0.45
ACGTcount: A:0.35, C:0.09, G:0.00, T:0.56
Consensus pattern (38 bp):
TTACAATTTTTACAATTTCTAATAATTTTTATAATTTC
Found at i:43695083 original size:20 final size:19
Alignment explanation
Indices: 43695027--43695133 Score: 76
Period size: 19 Copynumber: 5.6 Consensus size: 19
43695017 TTAAAAAAAA
43695027 TTACAATCTTTTACAATTTC
1 TTACAAT-TTTTACAATTTC
* * *
43695047 TAATAATTTTTATAATTTC
1 TTACAATTTTTACAATTTC
43695066 TTACAATATTTTACAATTTC
1 TTACAAT-TTTTACAATTTC
* * *
43695086 -T--ATTTTTTATAATTTT
1 TTACAATTTTTACAATTTC
* * *
43695102 TTATAATTTTTAAAAATTC
1 TTACAATTTTTACAATTTC
*
43695121 TAACATATTTTTA
1 TTACA-ATTTTTA
43695134 ATTTTTGAAT
Statistics
Matches: 67, Mismatches: 15, Indels: 10
0.73 0.16 0.11
Matches are distributed among these distances:
16 10 0.15
17 3 0.04
19 31 0.46
20 23 0.34
ACGTcount: A:0.35, C:0.09, G:0.00, T:0.56
Consensus pattern (19 bp):
TTACAATTTTTACAATTTC
Found at i:43695101 original size:8 final size:9
Alignment explanation
Indices: 43695035--43695247 Score: 72
Period size: 10 Copynumber: 23.6 Consensus size: 9
43695025 AATTACAATC
*
43695035 TTTTACAAT
1 TTTTATAAT
*
43695044 TTCTAATAAT
1 TT-TTATAAT
43695054 TTTTATAAT
1 TTTTATAAT
*
43695063 TTCTTACAAT
1 TT-TTATAAT
*
43695073 ATTTTACAAT
1 -TTTTATAAT
*
43695083 TTCTAT--T
1 TTTTATAAT
43695090 TTTTATAATT
1 TTTTATAA-T
43695100 TTTTATAAT
1 TTTTATAAT
* *
43695109 TTTTAAAAA
1 TTTTATAAT
*
43695118 TTCTA-ACAT
1 TTTTATA-AT
43695127 ATTTT-TAAT
1 -TTTTATAAT
*
43695136 TTTT-GAAT
1 TTTTATAAT
*
43695144 ATTT-T--T
1 TTTTATAAT
*
43695150 TTTTGTAATT
1 TTTTATAA-T
43695160 TTTATATAAT
1 TTT-TATAAT
43695170 TTTTA-AAT
1 TTTTATAAT
* *
43695178 TTTTAAAAAA
1 TTTT-ATAAT
*
43695188 TTCTA-ACAT
1 TTTTATA-AT
43695197 GTTTT-TAAT
1 -TTTTATAAT
*
43695206 TTTTAAATAT
1 TTTTATA-AT
*
43695216 TTTTGTAAT
1 TTTTATAAT
43695225 TTTTAT-AT
1 TTTTATAAT
*
43695233 TTTTAAAGAT
1 TTTTATA-AT
43695243 TTTTA
1 TTTTA
43695248 GGGTTTTTTT
Statistics
Matches: 155, Mismatches: 26, Indels: 45
0.69 0.12 0.20
Matches are distributed among these distances:
6 4 0.03
7 7 0.05
8 30 0.19
9 44 0.28
10 64 0.41
11 6 0.04
ACGTcount: A:0.33, C:0.05, G:0.02, T:0.60
Consensus pattern (9 bp):
TTTTATAAT
Found at i:43695149 original size:46 final size:47
Alignment explanation
Indices: 43695052--43695149 Score: 105
Period size: 46 Copynumber: 2.1 Consensus size: 47
43695042 ATTTCTAATA
* * * *
43695052 ATTTTTATAATTTCTTACAATATTTTACAATTTCTATTTTTTATAAT
1 ATTTTTATAATTTCTTACAAAATTTAACAATTTCTAATTTTTAGAAT
*
43695099 -TTTTTATAATTT-TTA-AAAATTCTAACATATTTTTAATTTTT-GAAT
1 ATTTTTATAATTTCTTACAAAATT-TAACA-ATTTCTAATTTTTAGAAT
43695144 ATTTTT
1 ATTTTT
43695150 TTTTGTAATT
Statistics
Matches: 43, Mismatches: 5, Indels: 7
0.78 0.09 0.13
Matches are distributed among these distances:
44 5 0.12
45 10 0.23
46 28 0.65
ACGTcount: A:0.33, C:0.06, G:0.01, T:0.60
Consensus pattern (47 bp):
ATTTTTATAATTTCTTACAAAATTTAACAATTTCTAATTTTTAGAAT
Found at i:43695172 original size:23 final size:22
Alignment explanation
Indices: 43695128--43695173 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 22
43695118 TTCTAACATA
*
43695128 TTTTTAATTTTTGAATATTTTT
1 TTTTTAATTTTTGAATAATTTT
43695150 TTTTGTAATTTTT-ATATAATTTT
1 TTTT-TAATTTTTGA-ATAATTTT
43695173 T
1 T
43695174 AAATTTTTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 5 0.24
23 16 0.76
ACGTcount: A:0.24, C:0.00, G:0.04, T:0.72
Consensus pattern (22 bp):
TTTTTAATTTTTGAATAATTTT
Found at i:43695178 original size:19 final size:19
Alignment explanation
Indices: 43695156--43695237 Score: 64
Period size: 19 Copynumber: 4.4 Consensus size: 19
43695146 TTTTTTTTGT
43695156 AATTTTTATATAATTTTTA
1 AATTTTTATATAATTTTTA
* * *
43695175 AATTTTTA-AAAAATTCTA
1 AATTTTTATATAATTTTTA
*
43695193 ACATGTTT-T-TAATTTTTA
1 A-ATTTTTATATAATTTTTA
*
43695211 AATATTTT-TGTAATTTTTA
1 AAT-TTTTATATAATTTTTA
*
43695230 TATTTTTA
1 AATTTTTA
43695238 AAGATTTTTA
Statistics
Matches: 49, Mismatches: 9, Indels: 10
0.72 0.13 0.15
Matches are distributed among these distances:
17 2 0.04
18 23 0.47
19 24 0.49
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.60
Consensus pattern (19 bp):
AATTTTTATATAATTTTTA
Found at i:43695190 original size:70 final size:70
Alignment explanation
Indices: 43695087--43695219 Score: 216
Period size: 70 Copynumber: 1.9 Consensus size: 70
43695077 TACAATTTCT
*
43695087 ATTTTTTATAATTTTTTATAATTTTTAAAAATTCTAACATATTTTTAATTTTTGAATATTTTTTT
1 ATTTTTTATAATTTTTTATAATTTTTAAAAATTCTAACATATTTTTAATTTTTAAATATTTTTTT
43695152 TTGTA
66 TTGTA
*
43695157 ATTTTTATATAA-TTTTTA-AATTTTTAAAAAATTCTAACATGTTTTTAATTTTTAAATATTTTT
1 ATTTTT-TATAATTTTTTATAATTTTT-AAAAATTCTAACATATTTTTAATTTTTAAATATTTTT
43695220 GTAATTTTTA
Statistics
Matches: 59, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
69 7 0.12
70 47 0.80
71 5 0.08
ACGTcount: A:0.34, C:0.03, G:0.02, T:0.61
Consensus pattern (70 bp):
ATTTTTTATAATTTTTTATAATTTTTAAAAATTCTAACATATTTTTAATTTTTAAATATTTTTTT
TTGTA
Found at i:43703027 original size:19 final size:19
Alignment explanation
Indices: 43702992--43703042 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 19
43702982 TTTATAACGT
*
43702992 ATACCAAAATCTTTAA-CAG
1 ATACCAAAAT-TTTAACCAA
43703011 ATACCAAAATTTGTAACCAA
1 ATACCAAAATTT-TAACCAA
43703031 ATACCAAAATTT
1 ATACCAAAATTT
43703043 CTAATGATAC
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
18 2 0.07
19 13 0.45
20 14 0.48
ACGTcount: A:0.49, C:0.20, G:0.04, T:0.27
Consensus pattern (19 bp):
ATACCAAAATTTTAACCAA
Found at i:43706307 original size:42 final size:42
Alignment explanation
Indices: 43706261--43706372 Score: 206
Period size: 42 Copynumber: 2.7 Consensus size: 42
43706251 AATGAATTTA
*
43706261 ATATTTAATTTAATTTAATATTTATCTAGATATTAATATGGG
1 ATATTAAATTTAATTTAATATTTATCTAGATATTAATATGGG
*
43706303 ATATTAAATTTAATTTAATATTTACCTAGATATTAATATGGG
1 ATATTAAATTTAATTTAATATTTATCTAGATATTAATATGGG
43706345 ATATTAAATTTAATTTAATATTTATCTA
1 ATATTAAATTTAATTTAATATTTATCTA
43706373 TATAATATTT
Statistics
Matches: 67, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
42 67 1.00
ACGTcount: A:0.40, C:0.04, G:0.07, T:0.49
Consensus pattern (42 bp):
ATATTAAATTTAATTTAATATTTATCTAGATATTAATATGGG
Found at i:43706394 original size:16 final size:16
Alignment explanation
Indices: 43706354--43706397 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
43706344 GATATTAAAT
43706354 TTAATTTAATA-TTTA
1 TTAATTTAATATTTTA
*
43706369 TCT-ATATAATATTTTA
1 T-TAATTTAATATTTTA
43706385 TTAATTTAATATT
1 TTAATTTAATATT
43706398 AATGTGATTA
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
15 9 0.38
16 15 0.62
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (16 bp):
TTAATTTAATATTTTA
Found at i:43713117 original size:20 final size:20
Alignment explanation
Indices: 43713092--43713133 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
43713082 CAAGTTAAAC
*
43713092 AATATACAAAATAAATATAT
1 AATATACAAAATAAAAATAT
* *
43713112 AATATATAATATAAAAATAT
1 AATATACAAAATAAAAATAT
43713132 AA
1 AA
43713134 AATAAATTGT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (20 bp):
AATATACAAAATAAAAATAT
Found at i:43713133 original size:13 final size:14
Alignment explanation
Indices: 43713092--43713133 Score: 52
Period size: 13 Copynumber: 3.1 Consensus size: 14
43713082 CAAGTTAAAC
43713092 AATATACAAAATA-
1 AATATACAAAATAT
* *
43713105 AATATATAATATAT
1 AATATACAAAATAT
43713119 AATATA-AAAATAT
1 AATATACAAAATAT
43713132 AA
1 AA
43713134 AATAAATTGT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
13 19 0.76
14 6 0.24
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (14 bp):
AATATACAAAATAT
Found at i:43718659 original size:21 final size:21
Alignment explanation
Indices: 43718635--43718676 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
43718625 TATAAATTTT
43718635 AAAAATCAAAATATTATATAA
1 AAAAATCAAAATATTATATAA
* * *
43718656 AAAAATGAAAATTTTTTATAA
1 AAAAATCAAAATATTATATAA
43718677 TATTATATAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.33
Consensus pattern (21 bp):
AAAAATCAAAATATTATATAA
Found at i:43718981 original size:22 final size:19
Alignment explanation
Indices: 43718955--43719003 Score: 62
Period size: 22 Copynumber: 2.4 Consensus size: 19
43718945 ATATTTTGAT
43718955 TTTTTAAAATTTATATTTATA
1 TTTTTAAAATTT-TATTT-TA
*
43718976 TATTTTAGAATTTTATTTTA
1 T-TTTTAAAATTTTATTTTA
43718996 TTTTTAAA
1 TTTTTAAA
43719004 CTTTGTTTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
19 6 0.24
20 3 0.12
21 6 0.24
22 10 0.40
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (19 bp):
TTTTTAAAATTTTATTTTA
Found at i:43720271 original size:16 final size:16
Alignment explanation
Indices: 43720238--43720274 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
43720228 AATCATAATC
*
43720238 TAATATAATTATTATT
1 TAATATAATAATTATT
*
43720254 TAATATAATAATTTTT
1 TAATATAATAATTATT
43720270 TAATA
1 TAATA
43720275 AAAATAAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (16 bp):
TAATATAATAATTATT
Found at i:43725937 original size:27 final size:26
Alignment explanation
Indices: 43725855--43725940 Score: 73
Period size: 27 Copynumber: 3.2 Consensus size: 26
43725845 ATTTAAAGAT
* *
43725855 ATATGATAAAAATTTTAAAAATTCAAAA
1 ATAT-ATAAAAATTATAAAAA-TAAAAA
* * * *
43725883 ATATATAGAAATTATAAAAGTTATAA
1 ATATATAAAAATTATAAAAATAAAAA
* *
43725909 ATTTATCAAAAATTGTAAAAATAAAAA
1 ATATAT-AAAAATTATAAAAATAAAAA
43725936 ATATA
1 ATATA
43725941 ATCAATTACC
Statistics
Matches: 45, Mismatches: 12, Indels: 3
0.75 0.20 0.05
Matches are distributed among these distances:
26 9 0.20
27 32 0.71
28 4 0.09
ACGTcount: A:0.60, C:0.02, G:0.05, T:0.33
Consensus pattern (26 bp):
ATATATAAAAATTATAAAAATAAAAA
Found at i:43727883 original size:2 final size:2
Alignment explanation
Indices: 43727876--43727901 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
43727866 TAACAAGTAA
43727876 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
43727902 TTGTTGTTAT
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:43729279 original size:117 final size:113
Alignment explanation
Indices: 43729030--43729347 Score: 381
Period size: 117 Copynumber: 2.8 Consensus size: 113
43729020 TGTGTGTGTA
* * * * * * *
43729030 TTTTATTAAGTTTAAGTTTGTATTAAAAGTATGATTTGTTTGTTTTATTATTGTTTTTATGATAC
1 TTTTATTAGGTTTAAGTTTGTATTAAAGGTATGATTAGTTTGTTTTATTAATGTTTTTGTGGTAT
* *
43729095 CTTATATCA-GTTTTATGTATTTAA-GACAAATAATTTTTTTATTGTG
66 CTTATATCAGGTTTTTTGTATTTAAGGACAAAGAATTTTTTTATTGTG
* * * *
43729141 TTTTATTAGCTTTAAGTTTGTATTAACGGCATGATTAGTTTGTTTTGTTAATGTTTTTGTGGTAT
1 TTTTATTAGGTTTAAGTTTGTATTAAAGGTATGATTAGTTTGTTTTATTAATGTTTTTGTGGTAT
** * *
43729206 CTTATATCAGGTTTTTTTGTATTTAAGGGGAAGGACATTTTTTTTTGCTGTG
66 CTTATATCAGG-TTTTTTGTATTTAAGGACAAAGA-ATTTTTTTAT--TGTG
* * * **
43729258 TTTTATTAGGTTTAAGTTTGTATTAAAGGTATGCTTAATCTGTTTTATTAATGTTTTTGAAGTAT
1 TTTTATTAGGTTTAAGTTTGTATTAAAGGTATGATTAGTTTGTTTTATTAATGTTTTTGTGGTAT
43729323 CTTATATC-GGTTTTTTGTATTTAAG
66 CTTATATCAGGTTTTTTGTATTTAAG
43729348 ATATGAACAT
Statistics
Matches: 175, Mismatches: 26, Indels: 8
0.84 0.12 0.04
Matches are distributed among these distances:
111 63 0.36
112 1 0.01
113 13 0.07
114 4 0.02
115 24 0.14
116 2 0.01
117 68 0.39
ACGTcount: A:0.24, C:0.05, G:0.17, T:0.54
Consensus pattern (113 bp):
TTTTATTAGGTTTAAGTTTGTATTAAAGGTATGATTAGTTTGTTTTATTAATGTTTTTGTGGTAT
CTTATATCAGGTTTTTTGTATTTAAGGACAAAGAATTTTTTTATTGTG
Found at i:43730230 original size:15 final size:16
Alignment explanation
Indices: 43730202--43730251 Score: 54
Period size: 17 Copynumber: 3.2 Consensus size: 16
43730192 TATAATTTAA
43730202 AAATAAATA--ATTTT
1 AAATAAATATTATTTT
43730216 AAAT-AAT-TTATTTTT
1 AAATAAATATTA-TTTT
43730231 AATATAAATATTATTTT
1 AA-ATAAATATTATTTT
43730248 AAAT
1 AAAT
43730252 TTTTTAGTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 10
0.75 0.00 0.25
Matches are distributed among these distances:
13 3 0.10
14 5 0.17
15 6 0.20
16 4 0.13
17 9 0.30
18 3 0.10
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
AAATAAATATTATTTT
Found at i:43732977 original size:14 final size:14
Alignment explanation
Indices: 43732958--43732984 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
43732948 CCAATTTATT
43732958 AATGAAATATTAAA
1 AATGAAATATTAAA
43732972 AATGAAATATTAA
1 AATGAAATATTAA
43732985 TATAAATTTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.63, C:0.00, G:0.07, T:0.30
Consensus pattern (14 bp):
AATGAAATATTAAA
Found at i:43737332 original size:18 final size:18
Alignment explanation
Indices: 43737311--43737353 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
43737301 CATTCGTTTC
43737311 CAAAACATTATTC-ATTT
1 CAAAACATTATTCAATTT
* *
43737328 ACAAATCGTTATTCAATTT
1 -CAAAACATTATTCAATTT
43737347 CAAAACA
1 CAAAACA
43737354 CTTTTTTTTG
Statistics
Matches: 20, Mismatches: 4, Indels: 2
0.77 0.15 0.08
Matches are distributed among these distances:
18 16 0.80
19 4 0.20
ACGTcount: A:0.44, C:0.19, G:0.02, T:0.35
Consensus pattern (18 bp):
CAAAACATTATTCAATTT
Done.