Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold105
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: 2918491
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.33
Warning! 41655 characters in sequence are not A, C, G, or T
File 16 of 16
Found at i:2777452 original size:87 final size:86
Alignment explanation
Indices: 2777242--2777489 Score: 460
Period size: 87 Copynumber: 2.9 Consensus size: 86
2777232 CAAGTCAAGC
2777242 AAGAGTTAACAAGTCAAGCTATCGCAAACTATAGCCAATGCTAAGCCATTTTAGCTTTGCTTGTG
1 AAGAGTTAACAAGTCAAGCTATCGCAAACTATAGCCAATGCTAAG-CATTTTAGCTTTGCTTGTG
2777307 AACTATGTAATATCTACTATAG
65 AACTATGTAATATCTACTATAG
2777329 AAGAGTTAACAAGTCAAGCTATCGCAAACTATAGCCAATGCTAAGCATTTTAGCTTTGCTTGTGA
1 AAGAGTTAACAAGTCAAGCTATCGCAAACTATAGCCAATGCTAAGCATTTTAGCTTTGCTTGTGA
2777394 ACTATGTAATATCTACTATAG
66 ACTATGTAATATCTACTATAG
* *
2777415 AAGAGTTAACAAGTCAAGCTATCGCAAACTGTAAGCCAATGCTAAACATTTTAGCTTTGCTTGTG
1 AAGAGTTAACAAGTCAAGCTATCGCAAACTAT-AGCCAATGCTAAGCATTTTAGCTTTGCTTGTG
2777480 AACTATGTAA
65 AACTATGTAA
2777490 ACACACATAC
Statistics
Matches: 158, Mismatches: 2, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
86 72 0.46
87 86 0.54
ACGTcount: A:0.35, C:0.18, G:0.17, T:0.31
Consensus pattern (86 bp):
AAGAGTTAACAAGTCAAGCTATCGCAAACTATAGCCAATGCTAAGCATTTTAGCTTTGCTTGTGA
ACTATGTAATATCTACTATAG
Found at i:2779488 original size:102 final size:102
Alignment explanation
Indices: 2779307--2779495 Score: 274
Period size: 102 Copynumber: 1.9 Consensus size: 102
2779297 TATGAATGTC
* * *
2779307 CTGCAACCAGACATATTTGAGACACTAGTCATTATCTTGTAGGAAATAGAATAAGCCAACATACC
1 CTGCAACCAAACATACTTGAGACACTAATCATTATCTTGTAGGAAATAGAATAAGCCAACATACC
*
2779372 GACAGACTATTTTAACCAAAATGTTTGAAAAAATATA
66 AACAGACTATTTTAACCAAAATGTTTGAAAAAATATA
* * *
2779409 CTGCAACCAAACATACTTGAGACACTAATCATTATCTTAG-AGGAAATAGAATAAGCTAAGATGC
1 CTGCAACCAAACATACTTGAGACACTAATCATTATCTT-GTAGGAAATAGAATAAGCCAACATAC
*
2779473 CAATAGACT-TATTTAACCAAAAT
65 CAACAGACTAT-TTTAACCAAAAT
2779496 ATACTGACAA
Statistics
Matches: 77, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
101 1 0.01
102 75 0.97
103 1 0.01
ACGTcount: A:0.43, C:0.18, G:0.13, T:0.26
Consensus pattern (102 bp):
CTGCAACCAAACATACTTGAGACACTAATCATTATCTTGTAGGAAATAGAATAAGCCAACATACC
AACAGACTATTTTAACCAAAATGTTTGAAAAAATATA
Found at i:2783212 original size:27 final size:27
Alignment explanation
Indices: 2783182--2783236 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
2783172 TGGAACAGTA
2783182 TCCTCTACTTTCCAAGCAAAACAAGCT
1 TCCTCTACTTTCCAAGCAAAACAAGCT
2783209 TCCTCTACTTTCCAAGCAAAACAAGCT
1 TCCTCTACTTTCCAAGCAAAACAAGCT
2783236 T
1 T
2783237 ATATCATTAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.33, C:0.33, G:0.07, T:0.27
Consensus pattern (27 bp):
TCCTCTACTTTCCAAGCAAAACAAGCT
Found at i:2785381 original size:25 final size:25
Alignment explanation
Indices: 2785351--2785403 Score: 106
Period size: 25 Copynumber: 2.1 Consensus size: 25
2785341 AAACCAACTG
2785351 TGATGAAAGAAGTAAGCAGTAAAAA
1 TGATGAAAGAAGTAAGCAGTAAAAA
2785376 TGATGAAAGAAGTAAGCAGTAAAAA
1 TGATGAAAGAAGTAAGCAGTAAAAA
2785401 TGA
1 TGA
2785404 ACAATGAGCC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.55, C:0.04, G:0.25, T:0.17
Consensus pattern (25 bp):
TGATGAAAGAAGTAAGCAGTAAAAA
Found at i:2785513 original size:27 final size:27
Alignment explanation
Indices: 2785483--2785567 Score: 152
Period size: 27 Copynumber: 3.1 Consensus size: 27
2785473 CAAGAATGTC
*
2785483 TGAATAATTCTATATCTATAATGACAG
1 TGAATAATTCTATATGTATAATGACAG
2785510 TGAATAATTCTATATGTATAATGACAG
1 TGAATAATTCTATATGTATAATGACAG
*
2785537 TGAATAATTCTATATGTATAATGACAA
1 TGAATAATTCTATATGTATAATGACAG
2785564 TGAA
1 TGAA
2785568 CACGATTTGA
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 56 1.00
ACGTcount: A:0.42, C:0.08, G:0.13, T:0.36
Consensus pattern (27 bp):
TGAATAATTCTATATGTATAATGACAG
Found at i:2786674 original size:2 final size:2
Alignment explanation
Indices: 2786669--2786698 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
2786659 CTTTTTTTTT
*
2786669 TA TA TA CA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2786699 CATTACAAGT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:2786976 original size:34 final size:34
Alignment explanation
Indices: 2786933--2787002 Score: 122
Period size: 34 Copynumber: 2.1 Consensus size: 34
2786923 TTTTGCGCTT
**
2786933 ATTGCCCACTAAGTTAAATCGGTTTTTCAAATTA
1 ATTGCCCACTAAGTTAAATCAATTTTTCAAATTA
2786967 ATTGCCCACTAAGTTAAATCAATTTTTCAAATTA
1 ATTGCCCACTAAGTTAAATCAATTTTTCAAATTA
2787001 AT
1 AT
2787003 AGCACGTGAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.36, C:0.17, G:0.09, T:0.39
Consensus pattern (34 bp):
ATTGCCCACTAAGTTAAATCAATTTTTCAAATTA
Found at i:2787541 original size:2 final size:2
Alignment explanation
Indices: 2787534--2787570 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
2787524 AATAAAGTAA
2787534 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
2787571 GATTTTACAA
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:2801758 original size:228 final size:230
Alignment explanation
Indices: 2801332--2802028 Score: 1060
Period size: 228 Copynumber: 3.0 Consensus size: 230
2801322 GCAAAACCCA
* *
2801332 TTGCTTCATTGTCTACCACTTGGCCTATTTAACAAACTACAAGAAGGCAAGCAGAATGCATTATA
1 TTGCTTCATTGTCTTCCACTTGGCCTA--T-ACAAACTACAAGAAGGCAAGCAGAATACATTATA
*
2801397 AAAAAGAAACCATTTAAAATTAAAAT-AAAACAGAAATCCGGAACACCAAGGCCAAATCCAGCAC
63 AAAAAGAAACCTTTTAAAATTAAAATAAAAAC-GAAATCCGGAACACCAAGGCCAAATCCAGCAC
* * * *
2801461 CTTGCCTACTCACTCTAAATCAATTGGCTTAATAAAAAGAATTGCTTGGAAATGGACGAATCATT
127 CTTGCCTACTTACTCTAAATCAATTGGGTTCATAAAAAGAATAGCTTGGAAATGGACGAATCATT
*
2801526 CCAAAAAACTCTTTCACCAGTATCCTTTCTAGAACCGGT
192 CCAAAAAACTCTTTCACCAGTATCCTTTCTAGAACTGGT
* * *
2801565 TTGCTTCATTGTCTTCCACTTGGCCTAT-CTAACTACAAGGAGGCAAGCAGAATACATTACAAAA
1 TTGCTTCATTGTCTTCCACTTGGCCTATACAAACTACAAGAAGGCAAGCAGAATACATTATAAAA
*
2801629 AAGAAACCTTTTAAAATTAAAATAAAAACGAAATCCGGAGCACCAAGGCC-AATCCAGCACCTTG
66 AAGAAACCTTTTAAAATTAAAATAAAAACGAAATCCGGAACACCAAGGCCAAATCCAGCACCTTG
2801693 CCTACTTACTCTAAATCAATTGGGTTCATAAAAAGAATAGCTTGGAAATGGACGAATCATTCCAA
131 CCTACTTACTCTAAATCAATTGGGTTCATAAAAAGAATAGCTTGGAAATGGACGAATCATTCCAA
*
2801758 AAAACTCTTTCACCAGGATCCTTTCTAGAACTGGT
196 AAAACTCTTTCACCAGTATCCTTTCTAGAACTGGT
*
2801793 TTGCTTCATTGTCATCCACTTGGCCTATCGGACAAACTACAAGAAGGCAAGCAGAATACATTATA
1 TTGCTTCATTGTCTTCCACTTGGCCTAT---ACAAACTACAAGAAGGCAAGCAGAATACATTATA
* * * *
2801858 AAAAAGAAACCTTTTAAAACTAAAATAAAAAAGAAATCCAGAACACCAAGGCCAAATCCATCACC
63 AAAAAGAAACCTTTTAAAATTAAAATAAAAACGAAATCCGGAACACCAAGGCCAAATCCAGCACC
* *
2801923 TTGCCTACTTACTCTAAATCAATTGGGTTCATAAAAAGAACAGCTTGGAAAAATGGACAAATCAT
128 TTGCCTACTTACTCTAAATCAATTGGGTTCATAAAAAGAATAGCTTGG--AAATGGACGAATCAT
** * *
2801988 T-CAGAAATCCTCTTTCACCAGTTTCCTTGCTAGAACTGGT
191 TCCA-AAAAACTCTTTCACCAGTATCCTTTCTAGAACTGGT
2802028 T
1 T
2802029 GTCAATGCCT
Statistics
Matches: 426, Mismatches: 29, Indels: 16
0.90 0.06 0.03
Matches are distributed among these distances:
228 135 0.32
229 74 0.17
230 5 0.01
231 1 0.00
232 79 0.19
233 83 0.19
234 2 0.00
235 47 0.11
ACGTcount: A:0.39, C:0.22, G:0.14, T:0.25
Consensus pattern (230 bp):
TTGCTTCATTGTCTTCCACTTGGCCTATACAAACTACAAGAAGGCAAGCAGAATACATTATAAAA
AAGAAACCTTTTAAAATTAAAATAAAAACGAAATCCGGAACACCAAGGCCAAATCCAGCACCTTG
CCTACTTACTCTAAATCAATTGGGTTCATAAAAAGAATAGCTTGGAAATGGACGAATCATTCCAA
AAAACTCTTTCACCAGTATCCTTTCTAGAACTGGT
Found at i:2809612 original size:12 final size:12
Alignment explanation
Indices: 2809595--2809619 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2809585 TCATATAAAC
2809595 ATCTTTGACTAA
1 ATCTTTGACTAA
2809607 ATCTTTGACTAA
1 ATCTTTGACTAA
2809619 A
1 A
2809620 GTATAAGGCT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.36, C:0.16, G:0.08, T:0.40
Consensus pattern (12 bp):
ATCTTTGACTAA
Found at i:2810741 original size:22 final size:22
Alignment explanation
Indices: 2810716--2810761 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 22
2810706 TACTCCAAAT
*
2810716 TTATTTAAATATAAATAAAAAA
1 TTATTTAAATAAAAATAAAAAA
** *
2810738 TTATTTTGATAAAAATTAAAAA
1 TTATTTAAATAAAAATAAAAAA
2810760 TT
1 TT
2810762 TAAAACAATT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (22 bp):
TTATTTAAATAAAAATAAAAAA
Found at i:2810766 original size:29 final size:29
Alignment explanation
Indices: 2810740--2810795 Score: 87
Period size: 29 Copynumber: 1.9 Consensus size: 29
2810730 ATAAAAAATT
2810740 ATTTT-GATAAAAATTAAAAATTTAAAACA
1 ATTTTAGATAAAAATT-AAAATTTAAAACA
*
2810769 ATTTTAGATAGAAATTAAAATTTAAAA
1 ATTTTAGATAAAAATTAAAATTTAAAA
2810796 ATTTATTTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
29 16 0.64
30 9 0.36
ACGTcount: A:0.57, C:0.02, G:0.05, T:0.36
Consensus pattern (29 bp):
ATTTTAGATAAAAATTAAAATTTAAAACA
Found at i:2846321 original size:12 final size:12
Alignment explanation
Indices: 2846304--2846328 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2846294 TCATATAAAC
2846304 ATCTTTGACTAA
1 ATCTTTGACTAA
2846316 ATCTTTGACTAA
1 ATCTTTGACTAA
2846328 A
1 A
2846329 GTATAAGGCT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.36, C:0.16, G:0.08, T:0.40
Consensus pattern (12 bp):
ATCTTTGACTAA
Found at i:2847679 original size:23 final size:26
Alignment explanation
Indices: 2847648--2847699 Score: 65
Period size: 24 Copynumber: 2.1 Consensus size: 26
2847638 ATCTTATTTC
2847648 AAATAAAATTT-TTAAAAGTTTA-AA
1 AAATAAAATTTATTAAAAGTTTATAA
* *
2847672 AAAT-AAATTTATTCAAATTTTATAA
1 AAATAAAATTTATTAAAAGTTTATAA
2847697 AAA
1 AAA
2847700 GTTTTTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 6 0.25
24 13 0.54
25 5 0.21
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.38
Consensus pattern (26 bp):
AAATAAAATTTATTAAAAGTTTATAA
Found at i:2848508 original size:28 final size:28
Alignment explanation
Indices: 2848466--2848520 Score: 85
Period size: 28 Copynumber: 2.0 Consensus size: 28
2848456 CATATCCACG
2848466 TAAATGATATAATTTAAAAAATAATAAA
1 TAAATGATATAATTTAAAAAATAATAAA
*
2848494 TAAATGA-ATATATTTAAAAAATGATAA
1 TAAATGATATA-ATTTAAAAAATAATAA
2848521 TTCTTTTGAT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
27 3 0.12
28 22 0.88
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.33
Consensus pattern (28 bp):
TAAATGATATAATTTAAAAAATAATAAA
Found at i:2848823 original size:20 final size:20
Alignment explanation
Indices: 2848798--2848840 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
2848788 CCAAGATTAA
2848798 CATACTATTAGAATCATAAC
1 CATACTATTAGAATCATAAC
2848818 CATACTATTAGAATCATAAC
1 CATACTATTAGAATCATAAC
2848838 CAT
1 CAT
2848841 TACTGTCGCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.44, C:0.21, G:0.05, T:0.30
Consensus pattern (20 bp):
CATACTATTAGAATCATAAC
Found at i:2849869 original size:28 final size:27
Alignment explanation
Indices: 2849808--2849881 Score: 69
Period size: 28 Copynumber: 2.7 Consensus size: 27
2849798 TTTTGGAGAT
*
2849808 AATAACGGGGTTGGAGTGTCCCCACGGA
1 AATAACGGGGTTGGAGT-ACCCCACGGA
**
2849836 GGTAACGGGGTTGGAGTACCCC-CGATGA
1 AATAACGGGGTTGGAGTACCCCACG--GA
* *
2849864 AATAACGAGATTGGAGTA
1 AATAACGGGGTTGGAGTA
2849882 TCCTCGATTG
Statistics
Matches: 37, Mismatches: 7, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
26 2 0.05
27 4 0.11
28 31 0.84
ACGTcount: A:0.28, C:0.18, G:0.35, T:0.19
Consensus pattern (27 bp):
AATAACGGGGTTGGAGTACCCCACGGA
Found at i:2850005 original size:52 final size:52
Alignment explanation
Indices: 2849874--2850046 Score: 163
Period size: 52 Copynumber: 3.3 Consensus size: 52
2849864 AATAACGAGA
* * * * **
2849874 TTGGAGTATCCTCGATTGTGAAAAAATTGGTGTTTTTGGAAATAAAATCGAAG
1 TTGGAGTATCCCCGATTGTGGAAAAATTGGTG-TTTTGAAAATAAAACCGGGG
* * **
2849927 CTGGAGTATCCCTGATTAAAGG-AAAATTGGTGTTTTGAAAATAAAACCGGGG
1 TTGGAGTATCCCCGATT-GTGGAAAAATTGGTGTTTTGAAAATAAAACCGGGG
* * * **
2849979 TTGGAGTATCCCCAATTGTGGAAAAATTAGTGTTTT-AGCAAT-AAACTAGGG
1 TTGGAGTATCCCCGATTGTGGAAAAATTGGTGTTTTGA-AAATAAAACCGGGG
2850030 TTGGAGTATCCCCGATT
1 TTGGAGTATCCCCGATT
2850047 ATGAGAAATC
Statistics
Matches: 97, Mismatches: 20, Indels: 8
0.78 0.16 0.06
Matches are distributed among these distances:
51 26 0.27
52 46 0.47
53 24 0.25
54 1 0.01
ACGTcount: A:0.32, C:0.12, G:0.25, T:0.31
Consensus pattern (52 bp):
TTGGAGTATCCCCGATTGTGGAAAAATTGGTGTTTTGAAAATAAAACCGGGG
Found at i:2850035 original size:51 final size:51
Alignment explanation
Indices: 2849976--2850093 Score: 141
Period size: 51 Copynumber: 2.3 Consensus size: 51
2849966 AATAAAACCG
* * * * *
2849976 GGGTTGGAGTATCCCCAATTGTGGAAAAATTAGTGTTTT-AGCAATAAA-CTA
1 GGGTTGGAGTATCCCCAATTAT-GAAAAATCAATATTTTAAG-AATAAAGCAA
* *
2850027 GGGTTGGAGTATCCCCGATTATGAGAAATCAATATTTTAAGAATAAAGCAA
1 GGGTTGGAGTATCCCCAATTATGAAAAATCAATATTTTAAGAATAAAGCAA
2850078 GGGTTGGAGTATCCCC
1 GGGTTGGAGTATCCCC
2850094 TCGGAAATAA
Statistics
Matches: 58, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
50 18 0.31
51 40 0.69
ACGTcount: A:0.33, C:0.14, G:0.25, T:0.29
Consensus pattern (51 bp):
GGGTTGGAGTATCCCCAATTATGAAAAATCAATATTTTAAGAATAAAGCAA
Found at i:2852663 original size:33 final size:33
Alignment explanation
Indices: 2852605--2852671 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 33
2852595 AAAATTTTCA
***
2852605 AATGTATCGATACAAAGATCCATGTATCAATAC
1 AATGTATCGATACAAAGAAAAATGTATCAATAC
* *
2852638 AATGTATCGATACACAGAAAAATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCAATAC
2852671 A
1 A
2852672 TTTCCTTGGC
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.45, C:0.16, G:0.13, T:0.25
Consensus pattern (33 bp):
AATGTATCGATACAAAGAAAAATGTATCAATAC
Found at i:2853908 original size:61 final size:60
Alignment explanation
Indices: 2853460--2854118 Score: 733
Period size: 55 Copynumber: 11.3 Consensus size: 60
2853450 ACAAACTGTA
* * *
2853460 TCCTGCTCTTTGAGAACTGAAAGGTGCCACCAACTTGTGTGGACTTT--AAG---AGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCG
* *
2853515 TCCTGCTCTTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTT--AAG---AGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCG
* * *
2853570 TCCTGCTTTTTGGGGACTGAAAGGTGCCACCAACTTGTGTGGG-TTT---TGAAAAGG-G
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCG
* *
2853625 TCCTGCTCTTTGGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTTAAAAGAAAAAGCG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGC-TTTAAAAGAAAAGGCG
* * * * *
2853686 TCCCGCTCTTTGAGGACTG-AAGGTGCCACTAACTTGGGTGAGCTTTAAAAGAAAAAGCG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCG
* * *
2853745 TCCCGCTCTTTGAGGACT-AAAGGTGCCACCAACTTGTGTGGGTTTTAAAAGAAAATGCG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCG
* * *
2853804 TCCCGCTCTTTGAGGACTG-AAGGTGCCACCAACTTGGGTGGGCTTTAAAAGGAGAAGGCG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAA-GAAAAGGCG
* * *
2853864 TCCTGCTCTTTGAGGACTGGGAA-GTGCCACCAACTTGTGTGGGCTTTAAAAGGAGAAGACG
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTAAAA-GAAAAGGCG
* * *
2853925 TCCTGCTCTTTAAGGACTGGGAA-GTGCCACCAACTTGTGTGGGTTTTAAAAG----GG-G
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCG
* * * * *
2853980 TCCTGCTCTTTG-GAGACGGAAAGATGCCACCAAGTTGTGTAGGCTTTGAAAGAAAAGGCG
1 TCCTGCTCTTTGAG-GACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCG
* ** *
2854040 TCCCGCTCTTTGAGGACTGAAAAATGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCA
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAA-GAAAAGGCG
2854101 TCCTGCTCTTTGAGGACT
1 TCCTGCTCTTTGAGGACT
2854119 AAAAAGCGGA
Statistics
Matches: 533, Mismatches: 46, Indels: 44
0.86 0.07 0.07
Matches are distributed among these distances:
53 1 0.00
54 11 0.02
55 164 0.31
56 8 0.02
57 3 0.01
59 118 0.22
60 96 0.18
61 130 0.24
62 2 0.00
ACGTcount: A:0.25, C:0.20, G:0.29, T:0.26
Consensus pattern (60 bp):
TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCG
Found at i:2855145 original size:14 final size:14
Alignment explanation
Indices: 2855087--2855148 Score: 56
Period size: 14 Copynumber: 4.4 Consensus size: 14
2855077 AAGCAGGTTC
2855087 TTTTTTTTTT-CTCT
1 TTTTTTTTTTGCT-T
* *
2855101 CTTTTTCTTTG-TT
1 TTTTTTTTTTGCTT
* *
2855114 TTGTTTCTTTTGTTT
1 TT-TTTTTTTTGCTT
2855129 TTTTTTTTTTGCTT
1 TTTTTTTTTTGCTT
2855143 TTTTTT
1 TTTTTT
2855149 AAAGAGAAGG
Statistics
Matches: 38, Mismatches: 7, Indels: 6
0.75 0.14 0.12
Matches are distributed among these distances:
13 2 0.05
14 32 0.84
15 4 0.11
ACGTcount: A:0.00, C:0.10, G:0.06, T:0.84
Consensus pattern (14 bp):
TTTTTTTTTTGCTT
Found at i:2861613 original size:2 final size:2
Alignment explanation
Indices: 2861600--2861649 Score: 91
Period size: 2 Copynumber: 25.0 Consensus size: 2
2861590 CTTTAATGAG
*
2861600 TA TA TG TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2861642 TA TA TA TA
1 TA TA TA TA
2861650 AAAGCACTAA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2862792 original size:35 final size:35
Alignment explanation
Indices: 2862746--2862817 Score: 126
Period size: 35 Copynumber: 2.1 Consensus size: 35
2862736 AACAAGCAAT
*
2862746 AGAGCGTGTGATCAGTCAAACACAAAAAAAAGAAC
1 AGAGCGAGTGATCAGTCAAACACAAAAAAAAGAAC
*
2862781 AGAGCGAGTGATGAGTCAAACACAAAAAAAAGAAC
1 AGAGCGAGTGATCAGTCAAACACAAAAAAAAGAAC
2862816 AG
1 AG
2862818 CGTTCCAACC
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.53, C:0.15, G:0.22, T:0.10
Consensus pattern (35 bp):
AGAGCGAGTGATCAGTCAAACACAAAAAAAAGAAC
Found at i:2863107 original size:6 final size:6
Alignment explanation
Indices: 2863098--2863122 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
2863088 CAACAAGCAC
2863098 AACTGT AACTGT AACTGT AACTGT A
1 AACTGT AACTGT AACTGT AACTGT A
2863123 TAAGGATACC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (6 bp):
AACTGT
Found at i:2866061 original size:67 final size:67
Alignment explanation
Indices: 2865982--2866116 Score: 243
Period size: 67 Copynumber: 2.0 Consensus size: 67
2865972 GTCTCTTAAG
* *
2865982 ATAATGAACTATAGATAACCAAGAAACAAAGCAGTTTAACTGTTAAACACGGGCATAGCTCCCTT
1 ATAATGAACTATAGATAACCAAGAAACAAAGCAGTTTAACTGTTAAACACAGACATAGCTCCCTT
2866047 TA
66 TA
*
2866049 ATAATGAACTATAGATAACCAAGAAACAAAGCAGTTTAACTGTTTAACACAGACATAGCTCCCTT
1 ATAATGAACTATAGATAACCAAGAAACAAAGCAGTTTAACTGTTAAACACAGACATAGCTCCCTT
2866114 TA
66 TA
2866116 A
1 A
2866117 AAGAATATTG
Statistics
Matches: 65, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
67 65 1.00
ACGTcount: A:0.43, C:0.19, G:0.13, T:0.24
Consensus pattern (67 bp):
ATAATGAACTATAGATAACCAAGAAACAAAGCAGTTTAACTGTTAAACACAGACATAGCTCCCTT
TA
Found at i:2868433 original size:2 final size:2
Alignment explanation
Indices: 2868426--2868462 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
2868416 ACACAAACAC
2868426 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT G
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT G
2868463 ACAAGCCAAC
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:0.00, C:0.00, G:0.51, T:0.49
Consensus pattern (2 bp):
GT
Found at i:2869043 original size:67 final size:67
Alignment explanation
Indices: 2868960--2869094 Score: 261
Period size: 67 Copynumber: 2.0 Consensus size: 67
2868950 ATCTCTTAAG
*
2868960 ATAATGAACTATAGATAACCAAGAAACAAAGCAGTTTAACTGTTAAACACGGGCATAGCTCCCTT
1 ATAATGAACTATAGATAACCAAGAAACAAAGCAGTTTAACTGTTAAACACGGACATAGCTCCCTT
2869025 TA
66 TA
2869027 ATAATGAACTATAGATAACCAAGAAACAAAGCAGTTTAACTGTTAAACACGGACATAGCTCCCTT
1 ATAATGAACTATAGATAACCAAGAAACAAAGCAGTTTAACTGTTAAACACGGACATAGCTCCCTT
2869092 TA
66 TA
2869094 A
1 A
2869095 AGGAATATTT
Statistics
Matches: 67, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
67 67 1.00
ACGTcount: A:0.43, C:0.19, G:0.14, T:0.24
Consensus pattern (67 bp):
ATAATGAACTATAGATAACCAAGAAACAAAGCAGTTTAACTGTTAAACACGGACATAGCTCCCTT
TA
Found at i:2871178 original size:27 final size:27
Alignment explanation
Indices: 2871148--2871204 Score: 105
Period size: 27 Copynumber: 2.1 Consensus size: 27
2871138 AAGAATGTCC
*
2871148 GAATAATTCTATATCTATAATGACAGT
1 GAATAATTCTATATCTATAATGACAAT
2871175 GAATAATTCTATATCTATAATGACAAT
1 GAATAATTCTATATCTATAATGACAAT
2871202 GAA
1 GAA
2871205 CAATGAACAC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.44, C:0.11, G:0.11, T:0.35
Consensus pattern (27 bp):
GAATAATTCTATATCTATAATGACAAT
Found at i:2872002 original size:13 final size:14
Alignment explanation
Indices: 2871972--2872007 Score: 56
Period size: 13 Copynumber: 2.6 Consensus size: 14
2871962 CAAAACTCAT
2871972 TCTAAAAGCCCAAC
1 TCTAAAAGCCCAAC
*
2871986 TCTAATAGCCC-AC
1 TCTAAAAGCCCAAC
2871999 TCTAAAAGC
1 TCTAAAAGC
2872008 TAACCTTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
13 10 0.50
14 10 0.50
ACGTcount: A:0.39, C:0.33, G:0.08, T:0.19
Consensus pattern (14 bp):
TCTAAAAGCCCAAC
Found at i:2876230 original size:2 final size:2
Alignment explanation
Indices: 2876219--2876247 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
2876209 GAAATAGAAT
2876219 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2876248 AAAAACTTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:2878233 original size:67 final size:67
Alignment explanation
Indices: 2878154--2878288 Score: 270
Period size: 67 Copynumber: 2.0 Consensus size: 67
2878144 GTCTCTTAAG
2878154 ATAATGAACTATAGATAACCAAGAAACAAAGCAGTTTAACTGTTAAACACGGGCATAGCTCCCTT
1 ATAATGAACTATAGATAACCAAGAAACAAAGCAGTTTAACTGTTAAACACGGGCATAGCTCCCTT
2878219 TA
66 TA
2878221 ATAATGAACTATAGATAACCAAGAAACAAAGCAGTTTAACTGTTAAACACGGGCATAGCTCCCTT
1 ATAATGAACTATAGATAACCAAGAAACAAAGCAGTTTAACTGTTAAACACGGGCATAGCTCCCTT
2878286 TA
66 TA
2878288 A
1 A
2878289 AAGAATATTG
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
67 68 1.00
ACGTcount: A:0.42, C:0.19, G:0.15, T:0.24
Consensus pattern (67 bp):
ATAATGAACTATAGATAACCAAGAAACAAAGCAGTTTAACTGTTAAACACGGGCATAGCTCCCTT
TA
Found at i:2878919 original size:23 final size:23
Alignment explanation
Indices: 2878893--2878952 Score: 95
Period size: 23 Copynumber: 2.6 Consensus size: 23
2878883 AACAAAGATC
2878893 GAAAAAGATGAAAAGAAATAATT
1 GAAAAAGATGAAAAGAAATAATT
*
2878916 GAAAAAGATGCAAAGAAATAATT
1 GAAAAAGATGAAAAGAAATAATT
2878939 GAAAACAGA-GAAAA
1 GAAAA-AGATGAAAA
2878953 TCATAAAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
23 31 0.91
24 3 0.09
ACGTcount: A:0.65, C:0.03, G:0.18, T:0.13
Consensus pattern (23 bp):
GAAAAAGATGAAAAGAAATAATT
Found at i:2880250 original size:27 final size:27
Alignment explanation
Indices: 2880220--2880277 Score: 107
Period size: 27 Copynumber: 2.1 Consensus size: 27
2880210 CAAGAATGTC
*
2880220 TGAATAATTCTATATCTATAATGACAG
1 TGAATAATTCTATATCTATAATGACAA
2880247 TGAATAATTCTATATCTATAATGACAA
1 TGAATAATTCTATATCTATAATGACAA
2880274 TGAA
1 TGAA
2880278 CAATGAACAC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.43, C:0.10, G:0.10, T:0.36
Consensus pattern (27 bp):
TGAATAATTCTATATCTATAATGACAA
Found at i:2881136 original size:13 final size:13
Alignment explanation
Indices: 2881118--2881164 Score: 51
Period size: 13 Copynumber: 3.5 Consensus size: 13
2881108 TCTAAAAGCT
2881118 AACCCATCTCTT-A
1 AACCCA-CTCTTAA
2881131 AACCCAGCTCTTCAA
1 AACCCA-CTCTT-AA
*
2881146 AACCCACTCTAAA
1 AACCCACTCTTAA
2881159 AACCCA
1 AACCCA
2881165 ACCCAAAGTT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
13 19 0.63
14 4 0.13
15 7 0.23
ACGTcount: A:0.38, C:0.40, G:0.02, T:0.19
Consensus pattern (13 bp):
AACCCACTCTTAA
Found at i:2881257 original size:3 final size:3
Alignment explanation
Indices: 2881240--2881275 Score: 58
Period size: 3 Copynumber: 12.7 Consensus size: 3
2881230 TATAATTGGA
2881240 ATT A-T ATT A-T ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
2881276 AATAAAAATA
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
2 4 0.13
3 27 0.87
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:2885239 original size:227 final size:230
Alignment explanation
Indices: 2884834--2885524 Score: 1039
Period size: 227 Copynumber: 3.0 Consensus size: 230
2884824 GCAAAACCCA
* *
2884834 TTGCTTCATTGTCTACCACTTGGCCTATTTAACAAACTACAAGAAGGCAAGCAGAATGCATTATA
1 TTGCTTCATTGTCTTCCACTTGGCCTA--T-ACAAACTACAAGAAGGCAAGCAGAATACATTATA
2884899 AAAAAGAAACCTTTTAAAATTAAAAT-AAAACAGAAATCCGGAACACCAAGGCCAAATCCAGCAC
63 AAAAAGAAACCTTTTAAAATTAAAATAAAAAC-GAAATCCGGAACACCAAGGCCAAATCCAGCAC
* * * * *
2884963 CTTGCCTACTCACTCTAAATCAATTGGCTTAATAAAAAGATTTGCTTGGAAATGGACGAATCATT
127 CTTGCCTACTTACTCTAAATCAATTGGGTTCATAAAAAGAATAGCTTGGAAATGGACGAATCATT
2885028 CAAAAAAACTCTTTCACCAGTATCCTTTCTAGAACCGAT
192 CAAAAAAACTCTTTCACCAGTATCCTTTCTAGAACCGAT
* * *
2885067 TTGCTTCATTGTCTTCCACTTGGCCTAT-CTAACTACAAGGAGGCAAGCAGAATACATTACAAAA
1 TTGCTTCATTGTCTTCCACTTGGCCTATACAAACTACAAGAAGGCAAGCAGAATACATTATAAAA
*
2885131 AAGGAACCTTTT-AAATTAAAATAAAAACGAAATCCGGAACACCAAGGCC-AATCCAGCACCTTG
66 AAGAAACCTTTTAAAATTAAAATAAAAACGAAATCCGGAACACCAAGGCCAAATCCAGCACCTTG
2885194 CCTACTTACTCTAAATCAATTGGGTTCATAAAAAGAATAGCTTGGAAATGGACGAATCATTCAAA
131 CCTACTTACTCTAAATCAATTGGGTTCATAAAAAGAATAGCTTGGAAATGGACGAATCATTCAAA
* * * *
2885259 AAAACTCTTTCAACAGAATCCTTTCTAGAACTGGT
196 AAAACTCTTTCACCAGTATCCTTTCTAGAACCGAT
*
2885294 TTGCTTCATTGTCATCCACTTGGCCTATCGAACAAACTACAAGAAGGCAAGCAGAATACATTATA
1 TTGCTTCATTGTCTTCCACTTGGCCTAT---ACAAACTACAAGAAGGCAAGCAGAATACATTATA
* * *
2885359 AAAAAGAAACCTTTTAAAATTAAAATAAAAAAGAAATCCAGAACACCAAGGCCAAATCCATCACC
63 AAAAAGAAACCTTTTAAAATTAAAATAAAAACGAAATCCGGAACACCAAGGCCAAATCCAGCACC
* *
2885424 TTGCCTACTTACTCTAAATCAATTGGGTTCATAAAAAGAACAGCTTGGAAAAATGGACAAATCAT
128 TTGCCTACTTACTCTAAATCAATTGGGTTCATAAAAAGAATAGCTTGG--AAATGGACGAATCAT
* ** * *
2885489 TCAGAAATCCTCTTTCACCAGTTTCCTTGCTAGAAC
191 TCAAAAAAACTCTTTCACCAGTATCCTTTCTAGAAC
2885525 TGGTTGTCAA
Statistics
Matches: 417, Mismatches: 32, Indels: 16
0.90 0.07 0.03
Matches are distributed among these distances:
227 132 0.32
228 31 0.07
229 48 0.12
231 45 0.11
232 35 0.08
233 83 0.20
235 43 0.10
ACGTcount: A:0.40, C:0.22, G:0.13, T:0.25
Consensus pattern (230 bp):
TTGCTTCATTGTCTTCCACTTGGCCTATACAAACTACAAGAAGGCAAGCAGAATACATTATAAAA
AAGAAACCTTTTAAAATTAAAATAAAAACGAAATCCGGAACACCAAGGCCAAATCCAGCACCTTG
CCTACTTACTCTAAATCAATTGGGTTCATAAAAAGAATAGCTTGGAAATGGACGAATCATTCAAA
AAAACTCTTTCACCAGTATCCTTTCTAGAACCGAT
Found at i:2891121 original size:2 final size:2
Alignment explanation
Indices: 2891114--2891139 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2891104 GAACAGAAAA
2891114 AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC
2891140 TTGTCCAGTT
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:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:2893508 original size:2 final size:2
Alignment explanation
Indices: 2893497--2893529 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
2893487 GAAATAGAAT
2893497 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2893530 AAGAACTTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:2895020 original size:18 final size:19
Alignment explanation
Indices: 2894993--2895034 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 19
2894983 AACCTTGAGA
* *
2894993 AAAATTAAGTGAACC-AAG
1 AAAATCAAGTAAACCAAAG
2895011 AAAATCAAGTAAACCAAAG
1 AAAATCAAGTAAACCAAAG
2895030 AAAAT
1 AAAAT
2895035 AAAGCATTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 13 0.62
19 8 0.38
ACGTcount: A:0.62, C:0.12, G:0.12, T:0.14
Consensus pattern (19 bp):
AAAATCAAGTAAACCAAAG
Found at i:2896197 original size:230 final size:229
Alignment explanation
Indices: 2895788--2896487 Score: 1026
Period size: 232 Copynumber: 3.0 Consensus size: 229
2895778 GCAGAATCCA
* * *
2895788 TTGCTTCACTGTCTACCACTTGGCCTATTTAACAAACTACAAGAAGGCAAGCAGAATGCATTATA
1 TTGCTTCATTGTCTTCCACTTGGCCTA--T-ACAAACTACAAGAAGGCAAGCAGAATACATTA-A
* * *
2895853 AAAAAAGAAACCTTTTAAAATTAAACTGAAAAAGAAATCCGGAAAACCAAGGCCAAATCCAGCAC
62 AAAAAAGAAACCTTTTAAAATTAAAAT-AAAAAGAAATCCAGAACACCAAGGCCAAATCCAGCAC
* * *
2895918 CTTGCCTACTTACTCTAAATCAATTGGGTTCATAAAAGGAATTGCTTGGAAATGGACTAATCATT
126 CTTGCCTACTTACTCTAAATCAATTGGGTTCATAAAAAGAATAGCTTGGAAATGGACAAATCATT
2895983 CAAAAAAAAACTCTTTCACCAGTATCCTTTCTAGAACTGGT
191 C--AAAAAAACTCTTTCACCAGTATCCTTTCTAGAACTGGT
* * * *
2896024 TTGCTTCATTGTCTTCCACTTGGCCTAT-CTAACTAAAAGAAGCCAAGCAGAATACATTACAAAA
1 TTGCTTCATTGTCTTCCACTTGGCCTATACAAACTACAAGAAGGCAAGCAGAATACATTAAAAAA
2896088 AAGAAACCTTTTAAAATTAAAATAAAAACGAAATCCAGAACACCAAGGCC-AATCCAGCACCTTG
66 AAGAAACCTTTTAAAATTAAAATAAAAA-GAAATCCAGAACACCAAGGCCAAATCCAGCACCTTG
*
2896152 CCTACTTACTCTAAATCAATTGGGTTCATAAAAAGAATAGCTTGGAAATGGACGAATCATTCAAA
130 CCTACTTACTCTAAATCAATTGGGTTCATAAAAAGAATAGCTTGGAAATGGACAAATCATTCAAA
*
2896217 AAAACTCTTTCACCAGCATCCTTTCTAGAACTGGT
195 AAAACTCTTTCACCAGTATCCTTTCTAGAACTGGT
* *
2896252 TTGCTTCATTGTCATCCACTTGGCCTATCGAACAAACTACAAGAAGGCAAGCAGAATACATTATA
1 TTGCTTCATTGTCTTCCACTTGGCCTAT---ACAAACTACAAGAAGGCAAGCAGAATACATTAAA
* * *
2896317 ACAAAGAAACATTTTAAAATTAAAATAAAAAAGAAATCCAGAACACCAAGGCCAAATCCATCACC
63 AAAAAGAAACCTTTTAAAATTAAAAT-AAAAAGAAATCCAGAACACCAAGGCCAAATCCAGCACC
*
2896382 TTGCCTACTTACTCTAAATCAATTGGGTTCATAAAAAGAACAGCTTGGAAAAATGGACAAATCAT
127 TTGCCTACTTACTCTAAATCAATTGGGTTCATAAAAAGAATAGCTTGG--AAATGGACAAATCAT
* ** * *
2896447 TCAGAAATCCTCTTTCACCAGTTTCCTTGCTAGAACTGGT
190 TCAAAAAAACTCTTTCACCAGTATCCTTTCTAGAACTGGT
2896487 T
1 T
2896488 GTCAAGGCCT
Statistics
Matches: 425, Mismatches: 30, Indels: 19
0.90 0.06 0.04
Matches are distributed among these distances:
228 64 0.15
230 78 0.18
231 45 0.11
232 101 0.24
233 62 0.15
234 1 0.00
235 49 0.12
236 25 0.06
ACGTcount: A:0.40, C:0.22, G:0.13, T:0.26
Consensus pattern (229 bp):
TTGCTTCATTGTCTTCCACTTGGCCTATACAAACTACAAGAAGGCAAGCAGAATACATTAAAAAA
AAGAAACCTTTTAAAATTAAAATAAAAAGAAATCCAGAACACCAAGGCCAAATCCAGCACCTTGC
CTACTTACTCTAAATCAATTGGGTTCATAAAAAGAATAGCTTGGAAATGGACAAATCATTCAAAA
AAACTCTTTCACCAGTATCCTTTCTAGAACTGGT
Found at i:2904063 original size:12 final size:12
Alignment explanation
Indices: 2904046--2904072 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
2904036 GGTCATATAA
2904046 AAATCTTTGACT
1 AAATCTTTGACT
2904058 AAATCTTTGACT
1 AAATCTTTGACT
2904070 AAA
1 AAA
2904073 GTATAAGGCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.41, C:0.15, G:0.07, T:0.37
Consensus pattern (12 bp):
AAATCTTTGACT
Found at i:2904262 original size:3 final size:3
Alignment explanation
Indices: 2904256--2904301 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
2904246 TTTTTTTTTA
2904256 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
2904302 TTGCTAATAT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:2905246 original size:17 final size:17
Alignment explanation
Indices: 2905200--2905246 Score: 60
Period size: 17 Copynumber: 2.8 Consensus size: 17
2905190 CGTATTTTTA
2905200 TATTTAAATTAAAATTT
1 TATTTAAATTAAAATTT
* *
2905217 TAATTATATTAAAA-TT
1 TATTTAAATTAAAATTT
2905233 TATTTAAATATAAA
1 TATTTAAAT-TAAA
2905247 TAAAGAAATT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
16 9 0.36
17 16 0.64
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (17 bp):
TATTTAAATTAAAATTT
Found at i:2905349 original size:28 final size:29
Alignment explanation
Indices: 2905287--2905355 Score: 86
Period size: 29 Copynumber: 2.3 Consensus size: 29
2905277 TTAAAACAAT
* *
2905287 TTTAGATAGAAATTAAAATTTTAAAATTTA
1 TTTA-ATATAAATTAAAATTATAAAATTTA
*
2905317 TTTAATATAAATTAAAATTAT-CAATTTA
1 TTTAATATAAATTAAAATTATAAAATTTA
2905345 TTTAAATATAA
1 TTT-AATATAA
2905356 TCACAAACTT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
28 9 0.26
29 22 0.63
30 4 0.11
ACGTcount: A:0.51, C:0.01, G:0.03, T:0.45
Consensus pattern (29 bp):
TTTAATATAAATTAAAATTATAAAATTTA
Found at i:2905455 original size:28 final size:28
Alignment explanation
Indices: 2905423--2905543 Score: 92
Period size: 28 Copynumber: 4.3 Consensus size: 28
2905413 ATCTTGCTTC
2905423 AGGTAAAATGTAAATTTTTTTATTTATA
1 AGGTAAAATGTAAATTTTTTTATTTATA
*
2905451 AGGTAAAA--T-AATTTTTTAAGTTTTATA
1 AGGTAAAATGTAAATTTTTTTA--TTTATA
* * *
2905478 A-G-AAATTTTAAGAAATTTTATTATCTTA-A
1 AGGTAAAATGT---AAATTTTTTTAT-TTATA
**
2905507 ATTTAAAATGTAAATTTTTTTATTTATA
1 AGGTAAAATGTAAATTTTTTTATTTATA
2905535 AGGTAAAAT
1 AGGTAAAAT
2905544 AATTTTTTAA
Statistics
Matches: 71, Mismatches: 10, Indels: 24
0.68 0.10 0.23
Matches are distributed among these distances:
25 12 0.17
26 2 0.03
27 11 0.15
28 27 0.38
29 3 0.04
30 3 0.04
31 13 0.18
ACGTcount: A:0.42, C:0.01, G:0.09, T:0.48
Consensus pattern (28 bp):
AGGTAAAATGTAAATTTTTTTATTTATA
Found at i:2905832 original size:3 final size:3
Alignment explanation
Indices: 2905818--2905851 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
2905808 TTCATTTTAA
*
2905818 TAT TAA TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
2905852 CCTTTTATAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:2905859 original size:15 final size:16
Alignment explanation
Indices: 2905824--2905867 Score: 56
Period size: 15 Copynumber: 2.9 Consensus size: 16
2905814 TTAATATTAA
2905824 TATTATTATTATT-AT
1 TATTATTATTATTCAT
*
2905839 TATTATTATTATTCCT
1 TATTATTATTATTCAT
*
2905855 T-TTATAATTATTC
1 TATTATTATTATTC
2905868 TTTCAATTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
15 24 0.92
16 2 0.08
ACGTcount: A:0.30, C:0.07, G:0.00, T:0.64
Consensus pattern (16 bp):
TATTATTATTATTCAT
Found at i:2906287 original size:145 final size:140
Alignment explanation
Indices: 2906110--2906503 Score: 492
Period size: 129 Copynumber: 2.8 Consensus size: 140
2906100 TTCTTAATTA
* * *
2906110 AAAAAAAATTATTTAGAAA-AAAAATACCATAAGCAAGAAGGATAATCGAGAAAGATTAAAAACT
1 AAAAAAAATTGTTTAGAAAGAGAAATGCCATAAGCAAGAAGGATAATCGAGAAAGATTAAAAACT
2906174 TAAATGAACGTACTCATTTCTACTTAATCTCTTTTCTAAAATTAAAGAGCCAATCACTTGTC-TG
66 TAAATGAACGTACTC-TTTCT-CTTAATCTC--TTC-AAAATTAAAGAGCCAATCACTTG-CATG
*
2906238 GGATCATTCACATAAT
125 AGATCATTCACATAAT
* ** *
2906254 AAAAATAATTGTTTAGAAAGAGAAATGCCATAAGCAAGAAAAATAATCGAGAAGGATTAAAAACT
1 AAAAAAAATTGTTTAGAAAGAGAAATGCCATAAGCAAGAAGGATAATCGAGAAAGATTAAAAACT
* *
2906319 TAAATGATCGTACTC-TT-TC-----C-C--C-AAATTAAGGAGCCAATCACTTGCATGAGATCA
66 TAAATGAACGTACTCTTTCTCTTAATCTCTTCAAAATTAAAGAGCCAATCACTTGCATGAGATCA
2906373 TTCACATAAT
131 TTCACATAAT
2906383 AAAAAAAATTGTTTAGAAAGAGAAATGCCATAAGCAA-AAGGATAATCGAGAAAGATTAAAAACT
1 AAAAAAAATTGTTTAGAAAGAGAAATGCCATAAGCAAGAAGGATAATCGAGAAAGATTAAAAACT
*
2906447 TAAATGAACGTACTCGTTTCTGCTTAATCTCTAATCCAAAATTAAAAAGCCAATCAC
66 TAAATGAACGTACTC-TTTCT-CTTAATCTCT--T-CAAAATTAAAGAGCCAATCAC
2906504 AAGATCATTA
Statistics
Matches: 215, Mismatches: 17, Indels: 36
0.80 0.06 0.13
Matches are distributed among these distances:
128 39 0.18
129 74 0.34
130 2 0.01
131 2 0.01
132 1 0.00
135 1 0.00
136 1 0.00
137 1 0.00
138 1 0.00
141 1 0.00
142 1 0.00
143 3 0.01
144 34 0.16
145 54 0.25
ACGTcount: A:0.46, C:0.15, G:0.13, T:0.26
Consensus pattern (140 bp):
AAAAAAAATTGTTTAGAAAGAGAAATGCCATAAGCAAGAAGGATAATCGAGAAAGATTAAAAACT
TAAATGAACGTACTCTTTCTCTTAATCTCTTCAAAATTAAAGAGCCAATCACTTGCATGAGATCA
TTCACATAAT
Done.