Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr8
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: 70076365
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 3341059 characters in sequence are not A, C, G, or T
File 125 of 210
Found at i:41936507 original size:13 final size:13
Alignment explanation
Indices: 41936489--41936513 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
41936479 TTTTAGTTTT
41936489 ATTGGGTTGGGTA
1 ATTGGGTTGGGTA
41936502 ATTGGGTTGGGT
1 ATTGGGTTGGGT
41936514 TGGATAATTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.12, C:0.00, G:0.48, T:0.40
Consensus pattern (13 bp):
ATTGGGTTGGGTA
Found at i:41937553 original size:13 final size:13
Alignment explanation
Indices: 41937531--41937564 Score: 61
Period size: 12 Copynumber: 2.7 Consensus size: 13
41937521 ATTTGACTCG
41937531 TAAATATTTTT-A
1 TAAATATTTTTAA
41937543 TAAATATTTTTAA
1 TAAATATTTTTAA
41937556 TAAATATTT
1 TAAATATTT
41937565 ATGAAGCTAG
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 11 0.52
13 10 0.48
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
TAAATATTTTTAA
Found at i:41937951 original size:158 final size:158
Alignment explanation
Indices: 41937663--41937979 Score: 634
Period size: 158 Copynumber: 2.0 Consensus size: 158
41937653 AGGGTGAAAG
41937663 TTGAATTATAGATTAAAGAATAATTAAAGGAACTAAAGAAGCAATATTATCATTGTTTCTTTAAG
1 TTGAATTATAGATTAAAGAATAATTAAAGGAACTAAAGAAGCAATATTATCATTGTTTCTTTAAG
41937728 TGGGATGGTTAGTGATATATATTATATGTAAATTTAATTTATATATTATATTATAATATGAAATC
66 TGGGATGGTTAGTGATATATATTATATGTAAATTTAATTTATATATTATATTATAATATGAAATC
41937793 TTAATTGTTAAGTATATATATTATATAA
131 TTAATTGTTAAGTATATATATTATATAA
41937821 TTGAATTATAGATTAAAGAATAATTAAAGGAACTAAAGAAGCAATATTATCATTGTTTCTTTAAG
1 TTGAATTATAGATTAAAGAATAATTAAAGGAACTAAAGAAGCAATATTATCATTGTTTCTTTAAG
41937886 TGGGATGGTTAGTGATATATATTATATGTAAATTTAATTTATATATTATATTATAATATGAAATC
66 TGGGATGGTTAGTGATATATATTATATGTAAATTTAATTTATATATTATATTATAATATGAAATC
41937951 TTAATTGTTAAGTATATATATTATATAA
131 TTAATTGTTAAGTATATATATTATATAA
41937979 T
1 T
41937980 ATTAAAACAA
Statistics
Matches: 159, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
158 159 1.00
ACGTcount: A:0.42, C:0.03, G:0.13, T:0.43
Consensus pattern (158 bp):
TTGAATTATAGATTAAAGAATAATTAAAGGAACTAAAGAAGCAATATTATCATTGTTTCTTTAAG
TGGGATGGTTAGTGATATATATTATATGTAAATTTAATTTATATATTATATTATAATATGAAATC
TTAATTGTTAAGTATATATATTATATAA
Found at i:41941675 original size:22 final size:22
Alignment explanation
Indices: 41941647--41941779 Score: 108
Period size: 22 Copynumber: 6.0 Consensus size: 22
41941637 TACACCACAC
*
41941647 CAGTAGGCACCATAGTGTAAAT
1 CAGTAGGCACCATAGTGCAAAT
*
41941669 CAGTAGGCACCAAAGTGC-AAT
1 CAGTAGGCACCATAGTGCAAAT
* *
41941690 ACAGTAGGCACCGTAGTACAAAT
1 -CAGTAGGCACCATAGTGCAAAT
** * *
41941713 CAAAAGGCACTATAGTACAGAAT
1 CAGTAGGCACCATAGTGCA-AAT
* **
41941736 -AGTAGACACTGTAGTGCAAAT
1 CAGTAGGCACCATAGTGCAAAT
* * *
41941757 CAGTAGGCATCAAATTGCAAAT
1 CAGTAGGCACCATAGTGCAAAT
41941779 C
1 C
41941780 CCATACACGC
Statistics
Matches: 87, Mismatches: 20, Indels: 8
0.76 0.17 0.07
Matches are distributed among these distances:
21 6 0.07
22 75 0.86
23 6 0.07
ACGTcount: A:0.40, C:0.20, G:0.21, T:0.20
Consensus pattern (22 bp):
CAGTAGGCACCATAGTGCAAAT
Found at i:41941713 original size:44 final size:43
Alignment explanation
Indices: 41941647--41941777 Score: 127
Period size: 44 Copynumber: 3.0 Consensus size: 43
41941637 TACACCACAC
* *
41941647 CAGTAGGCACCATAGTGTAAATCAGTAGGCACCAAAGTGCAATA
1 CAGTAGGCACCGTAGTGCAAATCAGTAGGCACCAAAGTGCAA-A
* ** * * *
41941691 CAGTAGGCACCGTAGTACAAATCAAAAGGCACTATAGTACAGAA
1 CAGTAGGCACCGTAGTGCAAATCAGTAGGCACCAAAGTGCA-AA
* * * * *
41941735 TAGTAGACACTGTAGTGCAAATCAGTAGGCATCAAATTGCAAA
1 CAGTAGGCACCGTAGTGCAAATCAGTAGGCACCAAAGTGCAAA
41941778 TCCCATACAC
Statistics
Matches: 67, Mismatches: 19, Indels: 3
0.75 0.21 0.03
Matches are distributed among these distances:
43 2 0.03
44 64 0.96
45 1 0.01
ACGTcount: A:0.40, C:0.19, G:0.21, T:0.19
Consensus pattern (43 bp):
CAGTAGGCACCGTAGTGCAAATCAGTAGGCACCAAAGTGCAAA
Found at i:41942834 original size:215 final size:215
Alignment explanation
Indices: 41942463--41942892 Score: 844
Period size: 215 Copynumber: 2.0 Consensus size: 215
41942453 TATTAATAAA
41942463 TAATATTTACCTACTCGAATCTCAAAAAATGGAGTTCTAAAACTATTATTTTCGATACTACTGAA
1 TAATATTTACCTACTCGAATCTCAAAAAATGGAGTTCTAAAACTATTATTTTCGATACTACTGAA
41942528 AACGAGCTGCTATATTATCAATTTAAATAAAGTAAGTTATTTAAATGCTTTAATGGAAACTTGCG
66 AACGAGCTGCTATATTATCAATTTAAATAAAGTAAGTTATTTAAATGCTTTAATGGAAACTTGCG
41942593 GTGGGCATTATCAAATGTCACTCAACTCA-TTCAACACATTTTGACTCAACAAAAATATTATAAA
131 GTGGGCATTATCAAATGTCACTCAACTCATTTCAACACA-TTTGACTCAACAAAAATATTATAAA
41942657 TATATTTTTATATTAATATTT
195 TATATTTTTATATTAATATTT
41942678 TAATATTTACCTACTCGAATCTCAAAAAATGGAGTTCTAAAACTATTATTTTCGATACTACTGAA
1 TAATATTTACCTACTCGAATCTCAAAAAATGGAGTTCTAAAACTATTATTTTCGATACTACTGAA
41942743 AACGAGCTGCTATATTATCAATTTAAATAAAGTAAGTTATTTAAATGCTTTAATGGAAACTTGCG
66 AACGAGCTGCTATATTATCAATTTAAATAAAGTAAGTTATTTAAATGCTTTAATGGAAACTTGCG
41942808 GTGGGCATTATCAAATGTCACTCAACTCATTTCAACACATTTGACTCAACAAAAATATTATAAAT
131 GTGGGCATTATCAAATGTCACTCAACTCATTTCAACACATTTGACTCAACAAAAATATTATAAAT
41942873 ATATTTTTATATTAATATTT
196 ATATTTTTATATTAATATTT
41942893 ATATATTATT
Statistics
Matches: 214, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
215 205 0.96
216 9 0.04
ACGTcount: A:0.39, C:0.14, G:0.10, T:0.37
Consensus pattern (215 bp):
TAATATTTACCTACTCGAATCTCAAAAAATGGAGTTCTAAAACTATTATTTTCGATACTACTGAA
AACGAGCTGCTATATTATCAATTTAAATAAAGTAAGTTATTTAAATGCTTTAATGGAAACTTGCG
GTGGGCATTATCAAATGTCACTCAACTCATTTCAACACATTTGACTCAACAAAAATATTATAAAT
ATATTTTTATATTAATATTT
Found at i:41945567 original size:33 final size:34
Alignment explanation
Indices: 41945525--41945593 Score: 113
Period size: 33 Copynumber: 2.1 Consensus size: 34
41945515 TTCCACAAAC
41945525 AACTTTTAAAAATTGCACGTCTCT-CTTTTTTAA
1 AACTTTTAAAAATTGCACGTCTCTACTTTTTTAA
* *
41945558 AACTTTTAAAAATTGCACGTGTCTATTTTTTTAA
1 AACTTTTAAAAATTGCACGTCTCTACTTTTTTAA
41945592 AA
1 AA
41945594 ATATTTTACT
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
33 23 0.70
34 10 0.30
ACGTcount: A:0.33, C:0.14, G:0.07, T:0.45
Consensus pattern (34 bp):
AACTTTTAAAAATTGCACGTCTCTACTTTTTTAA
Found at i:41945759 original size:14 final size:13
Alignment explanation
Indices: 41945736--41945765 Score: 51
Period size: 14 Copynumber: 2.2 Consensus size: 13
41945726 AACAATTACA
41945736 ATTTAGAAAATTT
1 ATTTAGAAAATTT
41945749 ATTTAAGAAAATTT
1 ATTT-AGAAAATTT
41945763 ATT
1 ATT
41945766 CAATATAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 4 0.25
14 12 0.75
ACGTcount: A:0.47, C:0.00, G:0.07, T:0.47
Consensus pattern (13 bp):
ATTTAGAAAATTT
Found at i:41947570 original size:19 final size:18
Alignment explanation
Indices: 41947548--41947596 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 18
41947538 CTATTTCCTA
*
41947548 AAATAAATATTATTTAATC
1 AAATAAATATT-CTTAATC
* *
41947567 AAATTAATATTCTTAATT
1 AAATAAATATTCTTAATC
41947585 AAATAAAT-TTCT
1 AAATAAATATTCT
41947597 CAACTCAATT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
17 4 0.15
18 12 0.46
19 10 0.38
ACGTcount: A:0.49, C:0.06, G:0.00, T:0.45
Consensus pattern (18 bp):
AAATAAATATTCTTAATC
Found at i:41950955 original size:2 final size:2
Alignment explanation
Indices: 41950950--41950976 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
41950940 TATATATATA
41950950 TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG T
41950977 TAGTCAATGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:41951605 original size:41 final size:41
Alignment explanation
Indices: 41951560--41952272 Score: 1284
Period size: 41 Copynumber: 17.4 Consensus size: 41
41951550 GACTTTAAGT
* * * *
41951560 CTAGCAGGCTACGTGCCGGTGATCTGAACCAGGTTATGAAC
1 CTAGCAGGCTAAGTGCCGGTGATCTAAATCAGGTTATAAAC
* * *
41951601 CTAGCAGGCTAAGTGTCGATGATCTGAATCAGGTTATAAAC
1 CTAGCAGGCTAAGTGCCGGTGATCTAAATCAGGTTATAAAC
* * * *
41951642 CTAGCAGGCTACGTGTCGGTGATCTGAA-CTAGGTTATGAAC
1 CTAGCAGGCTAAGTGCCGGTGATCTAAATC-AGGTTATAAAC
41951683 CTAGCAGGCTAAGTGCCGGTGATCTAAATCAGGTTATAAAC
1 CTAGCAGGCTAAGTGCCGGTGATCTAAATCAGGTTATAAAC
41951724 CTAGCAGGCTAAGTGCCGGTGATCTAAATCAGGTTATAAAC
1 CTAGCAGGCTAAGTGCCGGTGATCTAAATCAGGTTATAAAC
41951765 CTAGCAGGCTAAGTGCCGGTGATCTAAATCAGGTTATAAAC
1 CTAGCAGGCTAAGTGCCGGTGATCTAAATCAGGTTATAAAC
41951806 CTAGCAGGCTAAGTGCCGGTGATCTAAATCAGGTTATAAAC
1 CTAGCAGGCTAAGTGCCGGTGATCTAAATCAGGTTATAAAC
41951847 CTAGCAGGCTAAGTGCCGGTGATCTAAATCAGGTTATAAAC
1 CTAGCAGGCTAAGTGCCGGTGATCTAAATCAGGTTATAAAC
41951888 CTAGCAGGCTAAGTGCCGGTGATCTAAATCAGGTTATAAAC
1 CTAGCAGGCTAAGTGCCGGTGATCTAAATCAGGTTATAAAC
41951929 CTAGCAGGCTAAGTGCCGGTGATCTAAATCAGGTTATAAAC
1 CTAGCAGGCTAAGTGCCGGTGATCTAAATCAGGTTATAAAC
41951970 CTAGCAGGCTAAGTGCCGGTGATCTAAATCAGGTTATAAAC
1 CTAGCAGGCTAAGTGCCGGTGATCTAAATCAGGTTATAAAC
41952011 CTAGCAGGCTAAGTGCCGGTGATCTAAATCAGGTTATAAAC
1 CTAGCAGGCTAAGTGCCGGTGATCTAAATCAGGTTATAAAC
41952052 CTAGCAGGCTAAGTGCCGGTGATCTAAATCAGGTTATAAAC
1 CTAGCAGGCTAAGTGCCGGTGATCTAAATCAGGTTATAAAC
41952093 CTAGCAGGCTAAGTGCCGGTGATCTAAATCAGGTTATAAAC
1 CTAGCAGGCTAAGTGCCGGTGATCTAAATCAGGTTATAAAC
41952134 CTAGCAGGCTAAGTGCCGGTGATCTAAATCAGGTTATAAAC
1 CTAGCAGGCTAAGTGCCGGTGATCTAAATCAGGTTATAAAC
41952175 CTAGCAGGCTAAGTGCCGGTGATCTAAATCAGGTTATAAAC
1 CTAGCAGGCTAAGTGCCGGTGATCTAAATCAGGTTATAAAC
* * *
41952216 CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGCTATAAGC
1 CTAGCAGGCTAAGTGCCGGTGATCTAAATCAGGTTATAAAC
41952257 CTAGCAGGCTAAGTGC
1 CTAGCAGGCTAAGTGC
41952273 TAGTGAATAT
Statistics
Matches: 655, Mismatches: 15, Indels: 4
0.97 0.02 0.01
Matches are distributed among these distances:
40 1 0.00
41 653 1.00
42 1 0.00
ACGTcount: A:0.30, C:0.20, G:0.25, T:0.24
Consensus pattern (41 bp):
CTAGCAGGCTAAGTGCCGGTGATCTAAATCAGGTTATAAAC
Found at i:41953963 original size:12 final size:12
Alignment explanation
Indices: 41953946--41953974 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
41953936 CTCGTGCACC
41953946 TGCCAGAGCATA
1 TGCCAGAGCATA
41953958 TGCCAGAGCATA
1 TGCCAGAGCATA
41953970 TGCCA
1 TGCCA
41953975 TCTGTGCTCG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.31, C:0.28, G:0.24, T:0.17
Consensus pattern (12 bp):
TGCCAGAGCATA
Found at i:41962852 original size:19 final size:18
Alignment explanation
Indices: 41962810--41962854 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 18
41962800 ATTTTATTTT
41962810 TTATTTTTTAATTTCATA
1 TTATTTTTTAATTTCATA
*
41962828 TAATTTTTTAAATTTTC-TA
1 TTATTTTTT-AA-TTTCATA
41962847 TTATTTTT
1 TTATTTTT
41962855 GAATAATTTG
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
18 8 0.35
19 11 0.48
20 4 0.17
ACGTcount: A:0.27, C:0.04, G:0.00, T:0.69
Consensus pattern (18 bp):
TTATTTTTTAATTTCATA
Found at i:41962900 original size:17 final size:18
Alignment explanation
Indices: 41962880--41962928 Score: 57
Period size: 18 Copynumber: 2.7 Consensus size: 18
41962870 TTTTTTTGTA
41962880 ATTTTATATTTTTCCA-T
1 ATTTTATATTTTTCCACT
*
41962897 ATTTTATAATTTTTGCACT
1 ATTTTAT-ATTTTTCCACT
41962916 -TTTCTATATTTTT
1 ATTT-TATATTTTT
41962929 ATAACATTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
17 7 0.25
18 17 0.61
19 4 0.14
ACGTcount: A:0.22, C:0.10, G:0.02, T:0.65
Consensus pattern (18 bp):
ATTTTATATTTTTCCACT
Found at i:41965323 original size:20 final size:18
Alignment explanation
Indices: 41965300--41965384 Score: 61
Period size: 18 Copynumber: 4.7 Consensus size: 18
41965290 AAGAAACTAG
*
41965300 AAAATTATTAAAGTTATTAT
1 AAAATTA-TAAAATT-TTAT
41965320 AAAATTATAAAATTTTAT
1 AAAATTATAAAATTTTAT
*
41965338 -AAA-TAAAAAATTCTT-T
1 AAAATTATAAAATT-TTAT
**
41965354 AAAA-TATTAAAAAGTTAT
1 AAAATTA-TAAAATTTTAT
41965372 AAAATTTATAAAA
1 AAAA-TTATAAAA
41965385 AAATAAATTG
Statistics
Matches: 54, Mismatches: 5, Indels: 13
0.75 0.07 0.18
Matches are distributed among these distances:
16 9 0.17
17 12 0.22
18 13 0.24
19 11 0.20
20 9 0.17
ACGTcount: A:0.58, C:0.01, G:0.02, T:0.39
Consensus pattern (18 bp):
AAAATTATAAAATTTTAT
Found at i:41965803 original size:18 final size:20
Alignment explanation
Indices: 41965780--41965817 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
41965770 CAAAAAAGTG
41965780 TAGTAA-TTT-TTAAATTTT
1 TAGTAAGTTTGTTAAATTTT
41965798 TAGTAAGTTTGTTAAATTTT
1 TAGTAAGTTTGTTAAATTTT
41965818 ATATATTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 6 0.33
19 3 0.17
20 9 0.50
ACGTcount: A:0.32, C:0.00, G:0.11, T:0.58
Consensus pattern (20 bp):
TAGTAAGTTTGTTAAATTTT
Found at i:41966326 original size:2 final size:2
Alignment explanation
Indices: 41966319--41966355 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
41966309 TGAAAAACAT
41966319 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
41966356 ATGTTTTATA
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:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:41976369 original size:48 final size:49
Alignment explanation
Indices: 41976275--41976371 Score: 142
Period size: 49 Copynumber: 2.0 Consensus size: 49
41976265 TGAGGGAATT
* * * *
41976275 CTGTTGAATCTTTTATCGTTGCAAGATTAGGCTGACTTAGGTGTTTTTA
1 CTGTTGAATCTGTTATCATTGCAAGATTAGGCTAACTTAGGCGTTTTTA
*
41976324 CTGTTGAATCTGTTATCATTGCGAG-TTAGGCTAACTTAGGCGTTTTTA
1 CTGTTGAATCTGTTATCATTGCAAGATTAGGCTAACTTAGGCGTTTTTA
41976372 AGCAAAGAAA
Statistics
Matches: 43, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
48 21 0.49
49 22 0.51
ACGTcount: A:0.21, C:0.13, G:0.23, T:0.43
Consensus pattern (49 bp):
CTGTTGAATCTGTTATCATTGCAAGATTAGGCTAACTTAGGCGTTTTTA
Found at i:41981469 original size:48 final size:49
Alignment explanation
Indices: 41981374--41981470 Score: 126
Period size: 48 Copynumber: 2.0 Consensus size: 49
41981364 TGAAGGAATT
* * * **
41981374 CTGTTGAATCCTTTATCGTTGCACGATTAGGCTGACTTAGGTGTTTTTA
1 CTGTTGAATCCGTTATCATTGCACGATTAGGCTAACTTAGGCATTTTTA
41981423 CTGTTGAATCCGTTATCATTG--CGAGTTAGGCTAACTTAGGCATTTTTA
1 CTGTTGAATCCGTTATCATTGCACGA-TTAGGCTAACTTAGGCATTTTTA
41981471 AGCAAAGAAA
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
47 3 0.07
48 20 0.48
49 19 0.45
ACGTcount: A:0.21, C:0.16, G:0.22, T:0.41
Consensus pattern (49 bp):
CTGTTGAATCCGTTATCATTGCACGATTAGGCTAACTTAGGCATTTTTA
Found at i:41988046 original size:10 final size:11
Alignment explanation
Indices: 41988020--41988045 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
41988010 GAAAATGTTT
41988020 AAAAACTTCAA
1 AAAAACTTCAA
41988031 AAAAACTTCAA
1 AAAAACTTCAA
41988042 AAAA
1 AAAA
41988046 CAGGCTGAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.69, C:0.15, G:0.00, T:0.15
Consensus pattern (11 bp):
AAAAACTTCAA
Found at i:41998334 original size:24 final size:24
Alignment explanation
Indices: 41998307--41998388 Score: 78
Period size: 24 Copynumber: 3.4 Consensus size: 24
41998297 GTCATTAGGG
*
41998307 TTACCGATTTCAGCTCATATGAGC
1 TTACCGATTTCAGCTCATAAGAGC
*
41998331 TTACC-ATTATTCAGCTCAGAAGAGC
1 TTACCGA-T-TTCAGCTCATAAGAGC
**
41998356 TTACCG-TTTACAGCTTGTAAGAGC
1 TTACCGATTT-CAGCTCATAAGAGC
*
41998380 ATACCGATT
1 TTACCGATT
41998389 CAGAGCTCGT
Statistics
Matches: 47, Mismatches: 6, Indels: 9
0.76 0.10 0.15
Matches are distributed among these distances:
23 3 0.06
24 23 0.49
25 21 0.45
ACGTcount: A:0.28, C:0.23, G:0.17, T:0.32
Consensus pattern (24 bp):
TTACCGATTTCAGCTCATAAGAGC
Found at i:42001676 original size:39 final size:39
Alignment explanation
Indices: 42001641--42001766 Score: 139
Period size: 39 Copynumber: 3.2 Consensus size: 39
42001631 CCTTTAAATT
42001641 TTAAAAAATAAAAAAAATTAATAAAAATATTTTTAAAAA
1 TTAAAAAATAAAAAAAATTAATAAAAATATTTTTAAAAA
* *** * * **
42001680 TTAAAAAA-ACATAAAAAA-TATTTTTTATTAATTTTAAATT
1 TTAAAAAATA-A-AAAAAATTA-ATAAAAATATTTTTAAAAA
42001720 TTAAAAAATAAAAAAAATTAATAAAAATATTTTTAAAAA
1 TTAAAAAATAAAAAAAATTAATAAAAATATTTTTAAAAA
42001759 TTAAAAAA
1 TTAAAAAA
42001767 ACATAAAAAA
Statistics
Matches: 66, Mismatches: 16, Indels: 10
0.72 0.17 0.11
Matches are distributed among these distances:
38 1 0.02
39 36 0.55
40 28 0.42
41 1 0.02
ACGTcount: A:0.64, C:0.01, G:0.00, T:0.35
Consensus pattern (39 bp):
TTAAAAAATAAAAAAAATTAATAAAAATATTTTTAAAAA
Found at i:42001706 original size:31 final size:32
Alignment explanation
Indices: 42001639--42001704 Score: 93
Period size: 32 Copynumber: 2.1 Consensus size: 32
42001629 ATCCTTTAAA
42001639 TTTTAAAAAATAAAAAAAATTAATAAAAATAT
1 TTTTAAAAAATAAAAAAAATTAATAAAAATAT
*
42001671 TTTTAAAAATTAAAAAAACA-T-A-AAAAATAT
1 TTTTAAAAAATAAAAAAA-ATTAATAAAAATAT
42001701 TTTT
1 TTTT
42001705 TATTAATTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
30 12 0.38
31 1 0.03
32 18 0.56
33 1 0.03
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.35
Consensus pattern (32 bp):
TTTTAAAAAATAAAAAAAATTAATAAAAATAT
Found at i:42001710 original size:49 final size:49
Alignment explanation
Indices: 42001657--42001753 Score: 110
Period size: 49 Copynumber: 2.0 Consensus size: 49
42001647 AATAAAAAAA
*
42001657 ATTAATAAAAATATTTTTAAAAATTAAAAAAACA-T-A-AAAAATATTTTTT
1 ATTAATAAAAA-A-TTTTAAAAAATAAAAAAA-ATTAATAAAAATATTTTTT
***
42001706 ATTAATTTTAAATTTTAAAAAATAAAAAAAATTAATAAAAATATTTTT
1 ATTAATAAAAAATTTTAAAAAATAAAAAAAATTAATAAAAATATTTTT
42001754 AAAAATTAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
46 1 0.02
47 18 0.44
48 2 0.05
49 20 0.49
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.40
Consensus pattern (49 bp):
ATTAATAAAAAATTTTAAAAAATAAAAAAAATTAATAAAAATATTTTTT
Found at i:42001724 original size:79 final size:79
Alignment explanation
Indices: 42001633--42001807 Score: 350
Period size: 79 Copynumber: 2.2 Consensus size: 79
42001623 GTCATTATCC
42001633 TTTAAATTTTAAAAAATAAAAAAAATTAATAAAAATATTTTTAAAAATTAAAAAAACATAAAAAA
1 TTTAAATTTTAAAAAATAAAAAAAATTAATAAAAATATTTTTAAAAATTAAAAAAACATAAAAAA
42001698 TATTTTTTATTAAT
66 TATTTTTTATTAAT
42001712 TTTAAATTTTAAAAAATAAAAAAAATTAATAAAAATATTTTTAAAAATTAAAAAAACATAAAAAA
1 TTTAAATTTTAAAAAATAAAAAAAATTAATAAAAATATTTTTAAAAATTAAAAAAACATAAAAAA
42001777 TATTTTTTATTAAT
66 TATTTTTTATTAAT
42001791 TTTAAATTTTAAAAAAT
1 TTTAAATTTTAAAAAAT
42001808 TAATTAATTG
Statistics
Matches: 96, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
79 96 1.00
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.39
Consensus pattern (79 bp):
TTTAAATTTTAAAAAATAAAAAAAATTAATAAAAATATTTTTAAAAATTAAAAAAACATAAAAAA
TATTTTTTATTAAT
Found at i:42001785 original size:31 final size:32
Alignment explanation
Indices: 42001718--42001783 Score: 93
Period size: 32 Copynumber: 2.1 Consensus size: 32
42001708 TAATTTTAAA
42001718 TTTTAAAAAATAAAAAAAATTAATAAAAATAT
1 TTTTAAAAAATAAAAAAAATTAATAAAAATAT
*
42001750 TTTTAAAAATTAAAAAAACA-T-A-AAAAATAT
1 TTTTAAAAAATAAAAAAA-ATTAATAAAAATAT
42001780 TTTT
1 TTTT
42001784 TATTAATTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
30 12 0.38
31 1 0.03
32 18 0.56
33 1 0.03
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.35
Consensus pattern (32 bp):
TTTTAAAAAATAAAAAAAATTAATAAAAATAT
Found at i:42001794 original size:40 final size:40
Alignment explanation
Indices: 42001671--42001806 Score: 143
Period size: 40 Copynumber: 3.4 Consensus size: 40
42001661 ATAAAAATAT
42001671 TTTTAAAAATTAAAAAAACATAAAAAATATTTTTTATTAA
1 TTTTAAAAATTAAAAAAACATAAAAAATATTTTTTATTAA
** * *** * *
42001711 TTTTAAATTTTAAAAAATA-A-AAAAAAT-TAATAAAAATAT
1 TTTTAAAAATTAAAAAA-ACATAAAAAATAT-TTTTTATTAA
42001750 TTTTAAAAATTAAAAAAACATAAAAAATATTTTTTATTAA
1 TTTTAAAAATTAAAAAAACATAAAAAATATTTTTTATTAA
**
42001790 TTTTAAATTTTAAAAAA
1 TTTTAAAAATTAAAAAA
42001807 TTAATTAATT
Statistics
Matches: 73, Mismatches: 18, Indels: 10
0.72 0.18 0.10
Matches are distributed among these distances:
38 2 0.03
39 27 0.37
40 42 0.58
41 2 0.03
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.40
Consensus pattern (40 bp):
TTTTAAAAATTAAAAAAACATAAAAAATATTTTTTATTAA
Found at i:42009099 original size:32 final size:32
Alignment explanation
Indices: 42009062--42009125 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
42009052 CTACTAAGAC
42009062 ACCTGCATTTTTCCCCTTTGACAATCCTCCAA
1 ACCTGCATTTTTCCCCTTTGACAATCCTCCAA
42009094 ACCTGCATTTTTCCCCTTTGACAATCCTCCAA
1 ACCTGCATTTTTCCCCTTTGACAATCCTCCAA
42009126 TGTACTTCTC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.22, C:0.38, G:0.06, T:0.34
Consensus pattern (32 bp):
ACCTGCATTTTTCCCCTTTGACAATCCTCCAA
Found at i:42011262 original size:5 final size:5
Alignment explanation
Indices: 42011252--42011276 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
42011242 TGGGGCCTGA
42011252 GCCCG GCCCG GCCCG GCCCG GCCCG
1 GCCCG GCCCG GCCCG GCCCG GCCCG
42011277 TTTTAATTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.00, C:0.60, G:0.40, T:0.00
Consensus pattern (5 bp):
GCCCG
Found at i:42011346 original size:16 final size:16
Alignment explanation
Indices: 42011309--42011348 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
42011299 TTGATAAAAT
* *
42011309 TAAAACTAATTGTTAT
1 TAAAATTAATTGTTAG
42011325 TAAAATTAATTGTTAG
1 TAAAATTAATTGTTAG
42011341 TAAAATTA
1 TAAAATTA
42011349 TCAAATTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.47, C:0.03, G:0.07, T:0.42
Consensus pattern (16 bp):
TAAAATTAATTGTTAG
Found at i:42011554 original size:2 final size:2
Alignment explanation
Indices: 42011547--42011572 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
42011537 TAAACATAAA
42011547 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
42011573 TTTAAACATA
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:42012752 original size:24 final size:24
Alignment explanation
Indices: 42012710--42012755 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
42012700 CTTGAAACCA
* * *
42012710 TTTCCACAGCTCTTTTCTTCACCC
1 TTTCCACAACTCCTCTCTTCACCC
42012734 TTTCCACAACTCCTCTCTTCAC
1 TTTCCACAACTCCTCTCTTCAC
42012756 TCTCTTCACC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.15, C:0.43, G:0.02, T:0.39
Consensus pattern (24 bp):
TTTCCACAACTCCTCTCTTCACCC
Found at i:42012797 original size:14 final size:14
Alignment explanation
Indices: 42012778--42012807 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
42012768 ATCGATTGCA
42012778 GCCTCATCATCTCT
1 GCCTCATCATCTCT
*
42012792 GCCTCATCTTCTCT
1 GCCTCATCATCTCT
42012806 GC
1 GC
42012808 TAATTTTGCT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.10, C:0.43, G:0.10, T:0.37
Consensus pattern (14 bp):
GCCTCATCATCTCT
Found at i:42013290 original size:27 final size:27
Alignment explanation
Indices: 42013234--42013291 Score: 91
Period size: 27 Copynumber: 2.1 Consensus size: 27
42013224 AAAATTGCAG
*
42013234 CCTTAACACCAATACAGTAGCATCTTA
1 CCTTAACACCAATACAGTAACATCTTA
42013261 CCTTAACACCAATACAGTAACAT-TTGA
1 CCTTAACACCAATACAGTAACATCTT-A
42013288 CCTT
1 CCTT
42013292 CAAAGCTTTA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
26 2 0.07
27 27 0.93
ACGTcount: A:0.36, C:0.29, G:0.07, T:0.28
Consensus pattern (27 bp):
CCTTAACACCAATACAGTAACATCTTA
Found at i:42014666 original size:17 final size:15
Alignment explanation
Indices: 42014632--42014674 Score: 59
Period size: 17 Copynumber: 2.7 Consensus size: 15
42014622 AATAGCATGG
*
42014632 CATTTGTTTTTGAAA
1 CATTTGTTTTTCAAA
42014647 CATTTGTTTCATTCAAA
1 CATTTGTTT--TTCAAA
42014664 CATTTGTTTTT
1 CATTTGTTTTT
42014675 ATATATACAC
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
15 11 0.44
17 14 0.56
ACGTcount: A:0.23, C:0.12, G:0.09, T:0.56
Consensus pattern (15 bp):
CATTTGTTTTTCAAA
Found at i:42015604 original size:15 final size:15
Alignment explanation
Indices: 42015584--42015614 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
42015574 AAAATATTAA
*
42015584 CATCATCAGTCACAT
1 CATCATCAATCACAT
42015599 CATCATCAATCACAT
1 CATCATCAATCACAT
42015614 C
1 C
42015615 CTTGGCTTTA
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:0.35, C:0.35, G:0.03, T:0.26
Consensus pattern (15 bp):
CATCATCAATCACAT
Found at i:42015799 original size:20 final size:20
Alignment explanation
Indices: 42015735--42015811 Score: 77
Period size: 20 Copynumber: 3.9 Consensus size: 20
42015725 AAATCATTGC
*
42015735 AATATATGTAAAAATAATTT
1 AATATATGTAAAAACAATTT
* ** *
42015755 AA-A-ATATAAAAATTTATTA
1 AATATATGTAAAAA-CAATTT
42015774 ATATATATGTAAAAACAATTT
1 A-ATATATGTAAAAACAATTT
42015795 AATATATGTAAAAACAA
1 AATATATGTAAAAACAA
42015812 CTTTTCCGAA
Statistics
Matches: 46, Mismatches: 7, Indels: 8
0.75 0.11 0.13
Matches are distributed among these distances:
18 8 0.17
19 6 0.13
20 19 0.41
21 5 0.11
22 8 0.17
ACGTcount: A:0.58, C:0.03, G:0.04, T:0.35
Consensus pattern (20 bp):
AATATATGTAAAAACAATTT
Found at i:42015923 original size:20 final size:20
Alignment explanation
Indices: 42015898--42015937 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
42015888 AATATTTTCC
*
42015898 AGTAAATCATTTTACAGAAA
1 AGTAAAACATTTTACAGAAA
*
42015918 AGTAAAACATTTTCCAGAAA
1 AGTAAAACATTTTACAGAAA
42015938 TCATTTTCCG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.50, C:0.12, G:0.10, T:0.28
Consensus pattern (20 bp):
AGTAAAACATTTTACAGAAA
Found at i:42015944 original size:14 final size:14
Alignment explanation
Indices: 42015921--42015958 Score: 58
Period size: 14 Copynumber: 2.7 Consensus size: 14
42015911 ACAGAAAAGT
42015921 AAAACATTTTCCAG
1 AAAACATTTTCCAG
* *
42015935 AAATCATTTTCCGG
1 AAAACATTTTCCAG
42015949 AAAACATTTT
1 AAAACATTTT
42015959 ACTCCCAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.39, C:0.18, G:0.08, T:0.34
Consensus pattern (14 bp):
AAAACATTTTCCAG
Found at i:42021584 original size:31 final size:31
Alignment explanation
Indices: 42021548--42021610 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
42021538 AGGGGCTATT
42021548 GGATGGATGATTATCGACATAAAAGGGTTAA
1 GGATGGATGATTATCGACATAAAAGGGTTAA
42021579 GGATGGATGATTATCGACATAAAAGGGTTAA
1 GGATGGATGATTATCGACATAAAAGGGTTAA
42021610 G
1 G
42021611 TCCCTCAAGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.38, C:0.06, G:0.30, T:0.25
Consensus pattern (31 bp):
GGATGGATGATTATCGACATAAAAGGGTTAA
Found at i:42023851 original size:10 final size:10
Alignment explanation
Indices: 42023836--42023860 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
42023826 CTCATATTCG
42023836 GTAAAAAGAT
1 GTAAAAAGAT
42023846 GTAAAAAGAT
1 GTAAAAAGAT
42023856 GTAAA
1 GTAAA
42023861 CCTTCCAGCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.60, C:0.00, G:0.20, T:0.20
Consensus pattern (10 bp):
GTAAAAAGAT
Found at i:42025946 original size:13 final size:13
Alignment explanation
Indices: 42025928--42025969 Score: 54
Period size: 13 Copynumber: 3.5 Consensus size: 13
42025918 AATTTTAAAT
42025928 TATTTAGTGATAA
1 TATTTAGTGATAA
*
42025941 TATTTA--GA-AT
1 TATTTAGTGATAA
42025951 TATTTAGTGATAA
1 TATTTAGTGATAA
42025964 TATTTA
1 TATTTA
42025970 TGAAAAATCT
Statistics
Matches: 24, Mismatches: 2, Indels: 6
0.75 0.06 0.19
Matches are distributed among these distances:
10 7 0.29
11 2 0.08
12 2 0.08
13 13 0.54
ACGTcount: A:0.38, C:0.00, G:0.12, T:0.50
Consensus pattern (13 bp):
TATTTAGTGATAA
Found at i:42025969 original size:23 final size:22
Alignment explanation
Indices: 42025921--42025969 Score: 89
Period size: 23 Copynumber: 2.2 Consensus size: 22
42025911 ATTTTTAAAT
42025921 TTTAAATTATTTAGTGATAATA
1 TTTAAATTATTTAGTGATAATA
42025943 TTTAGAATTATTTAGTGATAATA
1 TTTA-AATTATTTAGTGATAATA
42025966 TTTA
1 TTTA
42025970 TGAAAAATCT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
22 4 0.15
23 22 0.85
ACGTcount: A:0.39, C:0.00, G:0.10, T:0.51
Consensus pattern (22 bp):
TTTAAATTATTTAGTGATAATA
Found at i:42028823 original size:130 final size:130
Alignment explanation
Indices: 42028581--42028845 Score: 505
Period size: 130 Copynumber: 2.0 Consensus size: 130
42028571 AAAATGGATA
42028581 AAAAAGTTAACATTTATTAATTTTACTGATGTGGCATATACATGGATTACCACATGGATACATAA
1 AAAAAGTTAACATTTATTAATTTTACTGATGTGGCATATACATGGATTACCACATGGATACATAA
*
42028646 CATGCCGTGAAAACAATTAAGTAATATTTTAAAATTTTAAAGAAATAAAAATTATTTAAATTATT
66 CATGCCGTGAAAACAATTAAGTAAAATTTTAAAATTTTAAAGAAATAAAAATTATTTAAATTATT
42028711 ATAAAAGTT-ACATTTATTAATTTTACTGATGTGGCATATACATGGATTACCACATGGATACATA
1 A-AAAAGTTAACATTTATTAATTTTACTGATGTGGCATATACATGGATTACCACATGGATACATA
42028775 ACATGCCGTGAAAACAATTAAGTAAAATTTTAAAATTTTAAAGAAATAAAAATTATTTAAATTAT
65 ACATGCCGTGAAAACAATTAAGTAAAATTTTAAAATTTTAAAGAAATAAAAATTATTTAAATTAT
42028840 T
130 T
42028841 AAAAA
1 AAAAA
42028846 TTATAAAAAT
Statistics
Matches: 133, Mismatches: 1, Indels: 3
0.97 0.01 0.02
Matches are distributed among these distances:
129 4 0.03
130 122 0.92
131 7 0.05
ACGTcount: A:0.46, C:0.09, G:0.11, T:0.35
Consensus pattern (130 bp):
AAAAAGTTAACATTTATTAATTTTACTGATGTGGCATATACATGGATTACCACATGGATACATAA
CATGCCGTGAAAACAATTAAGTAAAATTTTAAAATTTTAAAGAAATAAAAATTATTTAAATTATT
Found at i:42028833 original size:19 final size:19
Alignment explanation
Indices: 42028811--42028849 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
42028801 ATTTTAAAAT
42028811 TTTAAAGAAATAAAAATTA
1 TTTAAAGAAATAAAAATTA
** *
42028830 TTTAAATTATTAAAAATTA
1 TTTAAAGAAATAAAAATTA
42028849 T
1 T
42028850 AAAAATATTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (19 bp):
TTTAAAGAAATAAAAATTA
Found at i:42028835 original size:27 final size:26
Alignment explanation
Indices: 42028798--42028859 Score: 67
Period size: 27 Copynumber: 2.3 Consensus size: 26
42028788 ACAATTAAGT
42028798 AAAAT-TTTAAAATT-TTAAAGAA-ATA
1 AAAATATTT-AAATTATTAAA-AATATA
42028823 AAAATTATTTAAATTATTAAAAATTATA
1 AAAA-TATTTAAATTATTAAAAA-TATA
42028851 AAAATATTT
1 AAAATATTT
42028860 TTATTTTTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
25 4 0.12
26 8 0.25
27 13 0.41
28 7 0.22
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (26 bp):
AAAATATTTAAATTATTAAAAATATA
Found at i:42030904 original size:30 final size:30
Alignment explanation
Indices: 42030868--42030938 Score: 124
Period size: 30 Copynumber: 2.4 Consensus size: 30
42030858 GCTGCAAGGG
* *
42030868 TCACACGGCCATGTGGCCGGACTGTGTGAT
1 TCACACGGCCATGTGGCCAGACCGTGTGAT
42030898 TCACACGGCCATGTGGCCAGACCGTGTGAT
1 TCACACGGCCATGTGGCCAGACCGTGTGAT
42030928 TCACACGGCCA
1 TCACACGGCCA
42030939 AGAGACACAC
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 39 1.00
ACGTcount: A:0.20, C:0.31, G:0.30, T:0.20
Consensus pattern (30 bp):
TCACACGGCCATGTGGCCAGACCGTGTGAT
Found at i:42032154 original size:25 final size:25
Alignment explanation
Indices: 42032095--42032207 Score: 95
Period size: 25 Copynumber: 4.5 Consensus size: 25
42032085 GTACATATAT
* * * *
42032095 GCTCATATGAGCTATGAATCGGTAT
1 GCTCATACGAGCTAAGAATCAGTAA
* *
42032120 GTTC-TCACGAGCTATGAATCAGTAA
1 GCTCAT-ACGAGCTAAGAATCAGTAA
* *
42032145 ACTCATACGAGTTAAGAATCAGTAA
1 GCTCATACGAGCTAAGAATCAGTAA
* **
42032170 GCTC-TCACGAGCTACGAATTGGTAA
1 GCTCAT-ACGAGCTAAGAATCAGTAA
42032195 GCTCATACGAGCT
1 GCTCATACGAGCT
42032208 GTGGTGTGTC
Statistics
Matches: 71, Mismatches: 13, Indels: 8
0.77 0.14 0.09
Matches are distributed among these distances:
24 2 0.03
25 67 0.94
26 2 0.03
ACGTcount: A:0.32, C:0.20, G:0.21, T:0.27
Consensus pattern (25 bp):
GCTCATACGAGCTAAGAATCAGTAA
Found at i:42033338 original size:14 final size:14
Alignment explanation
Indices: 42033319--42033358 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
42033309 AACGGGTCCA
42033319 GTAAAATGTTTTCC
1 GTAAAATGTTTTCC
* *
42033333 GTAAAATGATTTCT
1 GTAAAATGTTTTCC
*
42033347 GGAAAATGTTTT
1 GTAAAATGTTTT
42033359 ACTTTTCTGT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.42
Consensus pattern (14 bp):
GTAAAATGTTTTCC
Found at i:42033367 original size:20 final size:20
Alignment explanation
Indices: 42033342--42033381 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
42033332 CGTAAAATGA
*
42033342 TTTCTGGAAAATGTTTTACT
1 TTTCTGGAAAATGATTTACT
*
42033362 TTTCTGTAAAATGATTTACT
1 TTTCTGGAAAATGATTTACT
42033382 GGAANNNNNN
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.28, C:0.10, G:0.12, T:0.50
Consensus pattern (20 bp):
TTTCTGGAAAATGATTTACT
Found at i:42034646 original size:25 final size:25
Alignment explanation
Indices: 42034587--42034699 Score: 95
Period size: 25 Copynumber: 4.5 Consensus size: 25
42034577 GTACATATAT
* * * *
42034587 GCTCATATGAGCTATGAATCGGTAT
1 GCTCATACGAGCTAAGAATCAGTAA
* *
42034612 GTTC-TCACGAGCTATGAATCAGTAA
1 GCTCAT-ACGAGCTAAGAATCAGTAA
* *
42034637 ACTCATACGAGTTAAGAATCAGTAA
1 GCTCATACGAGCTAAGAATCAGTAA
* **
42034662 GCTC-TCACGAGCTACGAATTGGTAA
1 GCTCAT-ACGAGCTAAGAATCAGTAA
42034687 GCTCATACGAGCT
1 GCTCATACGAGCT
42034700 GTGGTGTGTC
Statistics
Matches: 71, Mismatches: 13, Indels: 8
0.77 0.14 0.09
Matches are distributed among these distances:
24 2 0.03
25 67 0.94
26 2 0.03
ACGTcount: A:0.32, C:0.20, G:0.21, T:0.27
Consensus pattern (25 bp):
GCTCATACGAGCTAAGAATCAGTAA
Found at i:42037020 original size:17 final size:17
Alignment explanation
Indices: 42037000--42037033 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
42036990 ATATATTTCT
* *
42037000 TTTTTAAATTTTTTTAA
1 TTTTAAAATATTTTTAA
42037017 TTTTAAAATATTTTTAA
1 TTTTAAAATATTTTTAA
42037034 AATACTTTTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (17 bp):
TTTTAAAATATTTTTAA
Found at i:42037064 original size:21 final size:21
Alignment explanation
Indices: 42037026--42037065 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
42037016 ATTTTAAAAT
**
42037026 ATTTTTAAAATACTTTTTTTA
1 ATTTTTAAAATAAATTTTTTA
*
42037047 ATTTTTACAATAAATTTTT
1 ATTTTTAAAATAAATTTTT
42037066 GGTATTTATT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.35, C:0.05, G:0.00, T:0.60
Consensus pattern (21 bp):
ATTTTTAAAATAAATTTTTTA
Found at i:42040060 original size:34 final size:34
Alignment explanation
Indices: 42040017--42040084 Score: 127
Period size: 34 Copynumber: 2.0 Consensus size: 34
42040007 TTACTGACGA
*
42040017 TTGTATTTTGTTTGGTGATGCGATAAAAAGAGGG
1 TTGTATTTTGTTTGGTGATGCGACAAAAAGAGGG
42040051 TTGTATTTTGTTTGGTGATGCGACAAAAAGAGGG
1 TTGTATTTTGTTTGGTGATGCGACAAAAAGAGGG
42040085 GCACATACTT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.26, C:0.04, G:0.32, T:0.37
Consensus pattern (34 bp):
TTGTATTTTGTTTGGTGATGCGACAAAAAGAGGG
Found at i:42042955 original size:31 final size:31
Alignment explanation
Indices: 42042886--42042955 Score: 77
Period size: 31 Copynumber: 2.3 Consensus size: 31
42042876 TTTAAGCCCC
* * * *
42042886 TCAAAATTTTTAAAAGTTCTAATTTAAATCT
1 TCAAAAATATTAAAACTTCTAATTAAAATCT
** *
42042917 TTTAAAATATTAAAACTTTTAATTAAAATCT
1 TCAAAAATATTAAAACTTCTAATTAAAATCT
42042948 TCAAAAAT
1 TCAAAAAT
42042956 TTATGTAAAA
Statistics
Matches: 30, Mismatches: 9, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.47, C:0.09, G:0.01, T:0.43
Consensus pattern (31 bp):
TCAAAAATATTAAAACTTCTAATTAAAATCT
Found at i:42048970 original size:41 final size:41
Alignment explanation
Indices: 42048883--42048998 Score: 135
Period size: 41 Copynumber: 2.8 Consensus size: 41
42048873 AATGCTCTAT
* * ** *
42048883 CCTTTAGCGACGTTTTTGAAGAAGCGCCGGC-ATTGCTCTGG
1 CCTTTAGCGGCGTTTTTGAAGAAGCGCC-GCTAATGCTAAGA
*
42048924 CCTTTAGCGGCATTTTTGAAGAAGCGCCGCTAATGCTAAGA
1 CCTTTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGCTAAGA
* * *
42048965 TCTTTAGCAGCGTTTTTGAAAAAGCGCCGCTAAT
1 CCTTTAGCGGCGTTTTTGAAGAAGCGCCGCTAAT
42048999 ATATTTTTTA
Statistics
Matches: 64, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
40 2 0.03
41 62 0.97
ACGTcount: A:0.23, C:0.22, G:0.25, T:0.29
Consensus pattern (41 bp):
CCTTTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGCTAAGA
Found at i:42049634 original size:14 final size:15
Alignment explanation
Indices: 42049607--42049639 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
42049597 AAGGTTTATA
42049607 GATTATGAAATTAGG
1 GATTATGAAATTAGG
42049622 GATTATG-AATTAGG
1 GATTATGAAATTAGG
42049636 GATT
1 GATT
42049640 CTAATTTAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 11 0.61
15 7 0.39
ACGTcount: A:0.36, C:0.00, G:0.27, T:0.36
Consensus pattern (15 bp):
GATTATGAAATTAGG
Found at i:42049693 original size:7 final size:7
Alignment explanation
Indices: 42049670--42049703 Score: 50
Period size: 7 Copynumber: 4.9 Consensus size: 7
42049660 TAAGGTTTAT
42049670 GGGTTAG
1 GGGTTAG
* *
42049677 AGGCTAG
1 GGGTTAG
42049684 GGGTTAG
1 GGGTTAG
42049691 GGGTTAG
1 GGGTTAG
42049698 GGGTTA
1 GGGTTA
42049704 AGATCAATTA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.18, C:0.03, G:0.53, T:0.26
Consensus pattern (7 bp):
GGGTTAG
Found at i:42049731 original size:15 final size:16
Alignment explanation
Indices: 42049711--42049742 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
42049701 TTAAGATCAA
42049711 TTATGGATTT-AGGGT
1 TTATGGATTTAAGGGT
42049726 TTATGGATTTAAGGGT
1 TTATGGATTTAAGGGT
42049742 T
1 T
42049743 AGAGGTTAGG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.62
16 6 0.38
ACGTcount: A:0.22, C:0.00, G:0.31, T:0.47
Consensus pattern (16 bp):
TTATGGATTTAAGGGT
Found at i:42049815 original size:7 final size:7
Alignment explanation
Indices: 42049803--42049914 Score: 54
Period size: 7 Copynumber: 16.4 Consensus size: 7
42049793 TAAATAATGT
42049803 TTAGGGG
1 TTAGGGG
*
42049810 TTAGGGA
1 TTAGGGG
**
42049817 TTCTGGG
1 TTAGGGG
42049824 TT--GGG
1 TTAGGGG
*
42049829 TTAGGGT
1 TTAGGGG
*
42049836 TTAGGGA
1 TTAGGGG
*
42049843 TTAGGGAT
1 TTAGGG-G
42049851 TTA-GGG
1 TTAGGGG
42049857 TT--GGG
1 TTAGGGG
**
42049862 TTAGGAT
1 TTAGGGG
* *
42049869 TTAAGGT
1 TTAGGGG
*
42049876 TTAAGGG
1 TTAGGGG
42049883 TTAGGGG
1 TTAGGGG
*
42049890 TTAGAGG
1 TTAGGGG
*
42049897 TTAGAGGT
1 TTAG-GGG
42049905 TTAGGGG
1 TTAGGGG
42049912 TTA
1 TTA
42049915 AGAGTTAAAG
Statistics
Matches: 81, Mismatches: 18, Indels: 12
0.73 0.16 0.11
Matches are distributed among these distances:
5 10 0.12
6 2 0.02
7 61 0.75
8 8 0.10
ACGTcount: A:0.20, C:0.01, G:0.44, T:0.36
Consensus pattern (7 bp):
TTAGGGG
Found at i:42049847 original size:33 final size:33
Alignment explanation
Indices: 42049801--42049910 Score: 109
Period size: 33 Copynumber: 3.2 Consensus size: 33
42049791 ATTAAATAAT
*
42049801 GTTTAGGGGTTAGGGATTCT-GGGTTGGGTTAGG
1 GTTTAGGGATTAGGGATT-TAGGGTTGGGTTAGG
42049834 GTTTAGGGATTAGGGATTTAGGGTTGGGTTAGG
1 GTTTAGGGATTAGGGATTTAGGGTTGGGTTAGG
* * *
42049867 ATTTAAGGTTTAAGGG--TTAGGGGTTAGAGGTTAGAG
1 GTTTAGGGATT-AGGGATTTA-GGGTT-G-GGTTAG-G
42049903 GTTTAGGG
1 GTTTAGGG
42049911 GTTAAGAGTT
Statistics
Matches: 65, Mismatches: 6, Indels: 9
0.81 0.08 0.11
Matches are distributed among these distances:
32 4 0.06
33 43 0.66
34 5 0.08
35 6 0.09
36 7 0.11
ACGTcount: A:0.19, C:0.01, G:0.45, T:0.35
Consensus pattern (33 bp):
GTTTAGGGATTAGGGATTTAGGGTTGGGTTAGG
Found at i:42049848 original size:14 final size:13
Alignment explanation
Indices: 42049826--42049910 Score: 75
Period size: 14 Copynumber: 6.2 Consensus size: 13
42049816 ATTCTGGGTT
42049826 GGGTTAGGGTTTA
1 GGGTTAGGGTTTA
42049839 GGGATTAGGGATTTA
1 GGG-TTAGGG-TTTA
42049854 GGGTT-GGG-TTA
1 GGGTTAGGGTTTA
* *
42049865 GGATTTAAGGTTTAA
1 GG-GTTAGGGTTT-A
*
42049880 GGGTTAGGGGTTA
1 GGGTTAGGGTTTA
42049893 GAGGTTAGAGGTTTA
1 G-GGTTAG-GGTTTA
42049908 GGG
1 GGG
42049911 GTTAAGAGTT
Statistics
Matches: 58, Mismatches: 6, Indels: 15
0.73 0.08 0.19
Matches are distributed among these distances:
11 5 0.09
12 2 0.03
13 10 0.17
14 25 0.43
15 16 0.28
ACGTcount: A:0.21, C:0.00, G:0.45, T:0.34
Consensus pattern (13 bp):
GGGTTAGGGTTTA
Found at i:42049855 original size:15 final size:14
Alignment explanation
Indices: 42049803--42049910 Score: 63
Period size: 14 Copynumber: 7.9 Consensus size: 14
42049793 TAAATAATGT
*
42049803 TTAGGGGTTAGGGA
1 TTAGGGTTTAGGGA
*
42049817 TTCTGGG-TT-GGG-
1 TT-AGGGTTTAGGGA
42049829 TTAGGGTTTAGGGA
1 TTAGGGTTTAGGGA
42049843 TTAGGGATTTAGGG-
1 TTAGGG-TTTAGGGA
42049857 TT-GGG-TTA-GGA
1 TTAGGGTTTAGGGA
*
42049868 TTTAAGGTTTAAGGG-
1 -TTAGGGTTT-AGGGA
*
42049883 TTAGGGGTTAGAGG-
1 TTAGGGTTTAG-GGA
42049897 TTAGAGGTTTAGGG
1 TTAG-GGTTTAGGG
42049911 GTTAAGAGTT
Statistics
Matches: 75, Mismatches: 6, Indels: 26
0.70 0.06 0.24
Matches are distributed among these distances:
10 2 0.03
11 6 0.08
12 6 0.08
13 13 0.17
14 29 0.39
15 17 0.23
16 2 0.03
ACGTcount: A:0.19, C:0.01, G:0.44, T:0.35
Consensus pattern (14 bp):
TTAGGGTTTAGGGA
Found at i:42049921 original size:22 final size:22
Alignment explanation
Indices: 42049883--42049930 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
42049873 GGTTTAAGGG
* *
42049883 TTAGGGGTTAGAGGTTAGAGGT
1 TTAGGGGTTAGAGGTTAAAGAT
42049905 TTAGGGGTTA-AGAGTTAAAGAT
1 TTAGGGGTTAGAG-GTTAAAGAT
42049927 TTAG
1 TTAG
42049931 AGTTTAGGGT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 2 0.09
22 21 0.91
ACGTcount: A:0.29, C:0.00, G:0.38, T:0.33
Consensus pattern (22 bp):
TTAGGGGTTAGAGGTTAAAGAT
Found at i:42049921 original size:29 final size:30
Alignment explanation
Indices: 42049872--42049939 Score: 77
Period size: 29 Copynumber: 2.3 Consensus size: 30
42049862 TTAGGATTTA
* * * *
42049872 AGGTTTAAGGGTTAGGGGTTAGAG-GTTAG
1 AGGTTTAGGGGTTAAGAGTTAAAGAGTTAG
*
42049901 AGGTTTAGGGGTTAAGAGTTAAAGATTTAG
1 AGGTTTAGGGGTTAAGAGTTAAAGAGTTAG
42049931 A-GTTTAGGG
1 AGGTTTAGGG
42049940 TTTCATGGGT
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
29 28 0.85
30 5 0.15
ACGTcount: A:0.28, C:0.00, G:0.40, T:0.32
Consensus pattern (30 bp):
AGGTTTAGGGGTTAAGAGTTAAAGAGTTAG
Found at i:42050285 original size:24 final size:24
Alignment explanation
Indices: 42050253--42050306 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 24
42050243 GGGAAAAGTA
* *
42050253 AGTTC-TTTCTGTATGTGTTGAAC
1 AGTTCATTTCTGCATGTATTGAAC
* *
42050276 GGTTCATTTCTGCATGTATTTAAC
1 AGTTCATTTCTGCATGTATTGAAC
42050300 AGTTCAT
1 AGTTCAT
42050307 CTTTCATCAG
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
23 4 0.16
24 21 0.84
ACGTcount: A:0.20, C:0.15, G:0.19, T:0.46
Consensus pattern (24 bp):
AGTTCATTTCTGCATGTATTGAAC
Found at i:42052041 original size:42 final size:43
Alignment explanation
Indices: 42051979--42052162 Score: 289
Period size: 43 Copynumber: 4.3 Consensus size: 43
42051969 AGGTTATGTT
* * * * *
42051979 TTTAGCGGCGTTTTTGGGAAAAGTGCCGCTAAAGGTCATGGTA
1 TTTAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAGGTCTTGGTC
*
42052022 TTTAGCGGTGTTTGTGGAAAAAGCGCCGCTAAAGGTCTTGGTC
1 TTTAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAGGTCTTGGTC
42052065 TTTAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAGGTCTTGGTC
1 TTTAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAGGTCTTGGTC
* *
42052108 TTTAGCGGCGATTGTGG-AAAAGCGCCACTAAAGGTCTTGGTC
1 TTTAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAGGTCTTGGTC
42052150 TTTAGCGGCGTTT
1 TTTAGCGGCGTTT
42052163 TTTCTCTAAA
Statistics
Matches: 131, Mismatches: 10, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
42 36 0.27
43 95 0.73
ACGTcount: A:0.21, C:0.17, G:0.32, T:0.30
Consensus pattern (43 bp):
TTTAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAGGTCTTGGTC
Found at i:42052291 original size:22 final size:22
Alignment explanation
Indices: 42052257--42052299 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
42052247 TAGCTGCGCT
*
42052257 AAAAAGCGCCGCTAAAGGCCTA
1 AAAAAGCGCCGCTAAAAGCCTA
* *
42052279 AAAAAGTGTCGCTAAAAGCCT
1 AAAAAGCGCCGCTAAAAGCCT
42052300 GTTTTGGTGT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.42, C:0.23, G:0.21, T:0.14
Consensus pattern (22 bp):
AAAAAGCGCCGCTAAAAGCCTA
Found at i:42054228 original size:18 final size:18
Alignment explanation
Indices: 42054201--42054247 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
42054191 GAACTCAAAT
* * *
42054201 GATGCAAGCTTATTGAAA
1 GATGCGAGCTCATCGAAA
42054219 GATGCGAGCTCATCGAAA
1 GATGCGAGCTCATCGAAA
*
42054237 GTTGCGAGCTC
1 GATGCGAGCTC
42054248 TCCCAAAGAC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.30, C:0.19, G:0.28, T:0.23
Consensus pattern (18 bp):
GATGCGAGCTCATCGAAA
Found at i:42056724 original size:73 final size:73
Alignment explanation
Indices: 42056605--42056750 Score: 283
Period size: 73 Copynumber: 2.0 Consensus size: 73
42056595 TTTTTTAAAC
*
42056605 CTTATTAAACTCCATCTATTTGATATTAATTAGAATAAGGTGTTTCAATCTTACTACACTCCTAT
1 CTTATTAAACTCCATCTATTTGATATTAATTAGAATAAGGTATTTCAATCTTACTACACTCCTAT
42056670 TAGAATAT
66 TAGAATAT
42056678 CTTATTAAACTCCATCTATTTGATATTAATTAGAATAAGGTATTTCAATCTTACTACACTCCTAT
1 CTTATTAAACTCCATCTATTTGATATTAATTAGAATAAGGTATTTCAATCTTACTACACTCCTAT
42056743 TAGAATAT
66 TAGAATAT
42056751 GGTTTTACGA
Statistics
Matches: 72, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
73 72 1.00
ACGTcount: A:0.35, C:0.16, G:0.08, T:0.41
Consensus pattern (73 bp):
CTTATTAAACTCCATCTATTTGATATTAATTAGAATAAGGTATTTCAATCTTACTACACTCCTAT
TAGAATAT
Found at i:42063160 original size:85 final size:85
Alignment explanation
Indices: 42063017--42063187 Score: 288
Period size: 85 Copynumber: 2.0 Consensus size: 85
42063007 AATATAACCG
*
42063017 ACATTATACCTCGAATCTAACATTGTCATAAATTTATTACCAAAGTAGTCTTACATTCCTTGAAC
1 ACATTATACCTCAAATCTAACATTGTCATAAATTTATTACCAAAGTAGTCTTACATTCCTTGAAC
42063082 CAAATGCACTCCAATAGTAA
66 CAAATGCACTCCAATAGTAA
* * *
42063102 ACATTATCCCTCAAATCTAACATTGTCATAATTTTGTTACCAAAGTAGTCTTACATTCCTTGAAC
1 ACATTATACCTCAAATCTAACATTGTCATAAATTTATTACCAAAGTAGTCTTACATTCCTTGAAC
* *
42063167 CAAATGTACTCTAATAGTAA
66 CAAATGCACTCCAATAGTAA
42063187 A
1 A
42063188 ATGGTCCCTA
Statistics
Matches: 80, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
85 80 1.00
ACGTcount: A:0.37, C:0.22, G:0.08, T:0.33
Consensus pattern (85 bp):
ACATTATACCTCAAATCTAACATTGTCATAAATTTATTACCAAAGTAGTCTTACATTCCTTGAAC
CAAATGCACTCCAATAGTAA
Found at i:42071690 original size:2 final size:2
Alignment explanation
Indices: 42071683--42071711 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
42071673 TAAAATGCAT
42071683 TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
42071712 AAAAAACTAT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:42073397 original size:44 final size:44
Alignment explanation
Indices: 42073298--42073456 Score: 161
Period size: 44 Copynumber: 3.7 Consensus size: 44
42073288 TAGTTCTGTT
* * *
42073298 TGCTCCACTGCAACTTCAGGGAGATAAGACTAGAT-GC---GATC
1 TGCTCCACTGCAACTTCAGGGAGATAAGATTAG-TGGCTTTAACC
* * *
42073339 TGC-CCTCTGCAACTTCAGAGAGATAAGATCT-GTGGTTTTAATCC
1 TGCTCCACTGCAACTTCAGGGAGATAAGAT-TAGTGGCTTTAA-CC
* * *
42073383 -GTTCCACTGCAACTTCAGGGAGATAGGATTATTGGCTTTAACC
1 TGCTCCACTGCAACTTCAGGGAGATAAGATTAGTGGCTTTAACC
42073426 TGCTCCACTGCAACTTCAGGGAGATAAGATT
1 TGCTCCACTGCAACTTCAGGGAGATAAGATT
42073457 CGCCATCTTC
Statistics
Matches: 95, Mismatches: 14, Indels: 15
0.77 0.11 0.12
Matches are distributed among these distances:
39 1 0.01
40 25 0.26
41 4 0.04
43 5 0.05
44 60 0.63
ACGTcount: A:0.27, C:0.23, G:0.23, T:0.28
Consensus pattern (44 bp):
TGCTCCACTGCAACTTCAGGGAGATAAGATTAGTGGCTTTAACC
Found at i:42073445 original size:128 final size:128
Alignment explanation
Indices: 42073217--42073454 Score: 327
Period size: 128 Copynumber: 1.9 Consensus size: 128
42073207 ATTTGCTCTA
* * * **
42073217 CTGCAGCTTCAGATAGATGAGATCTGTGGTTCTAATCCACTCCGTTGCAACTTCAAGGAGATAGG
1 CTGCAACTTCAGAGAGATAAGATCTGTGGTTCTAATCCACTCCACTGCAACTTCAAGGAGATAGG
***
42073282 ATTAGTTAGTTCTGTTTGCTCCACTGCAACTTCAGGGAGATAAGACTAGATGCGATCTGCCCT
66 ATTAGTTAGTTCTACCTGCTCCACTGCAACTTCAGGGAGATAAGACTAGATGCGATCTGCCCT
* ** *
42073345 CTGCAACTTCAGAGAGATAAGATCTGTGGTTTTAATCCGTTCCACTGCAACTTCAGGGAGATAGG
1 CTGCAACTTCAGAGAGATAAGATCTGTGGTTCTAATCCACTCCACTGCAACTTCAAGGAGATAGG
*
42073410 ATTA-TTGGCTT-TAACCTGCTCCACTGCAACTTCAGGGAGATAAGA
66 ATTAGTTAG-TTCT-ACCTGCTCCACTGCAACTTCAGGGAGATAAGA
42073455 TTCGCCATCT
Statistics
Matches: 95, Mismatches: 13, Indels: 4
0.85 0.12 0.04
Matches are distributed among these distances:
127 4 0.04
128 91 0.96
ACGTcount: A:0.26, C:0.21, G:0.23, T:0.29
Consensus pattern (128 bp):
CTGCAACTTCAGAGAGATAAGATCTGTGGTTCTAATCCACTCCACTGCAACTTCAAGGAGATAGG
ATTAGTTAGTTCTACCTGCTCCACTGCAACTTCAGGGAGATAAGACTAGATGCGATCTGCCCT
Found at i:42073600 original size:44 final size:45
Alignment explanation
Indices: 42073551--42073865 Score: 121
Period size: 44 Copynumber: 7.2 Consensus size: 45
42073541 CGCTGCCTAA
*
42073551 GGAGATAAGATCTGTAAT-CTTCAATCTATTCCACTGTTGCCCAG
1 GGAGATAAGATCTGTAATGCTTCAATCTACTCCACTGTTGCCCAG
* * * **
42073595 GGAGAT-AGA-AT-TACTGGCTTCAATGTACTCCACTGTAACCTCAG
1 GGAGATAAGATCTGTAAT-GCTTCAATCTACTCCACTGTTGCC-CAG
* * * ** * * * ** **
42073639 GGAGGTAAAATCCGCCATCCTT-GATCTGCTCCACTACTGCTTAG
1 GGAGATAAGATCTGTAATGCTTCAATCTACTCCACTGTTGCCCAG
* *
42073683 GGAGATAAGATCTGTAAT-CTTCAATCTATTCCACTGTTGCCCAT
1 GGAGATAAGATCTGTAATGCTTCAATCTACTCCACTGTTGCCCAG
* * * * ** *
42073727 AGAGAT-AGA-AT-TACTGGCTTCAATGTACTCCACTGTAACCTCAA
1 GGAGATAAGATCTGTAAT-GCTTCAATCTACTCCACTGTTGCC-CAG
* * * * ** * * * * ** **
42073771 TGAGGTAAAATCCGCCATCCTT-GATCTGCTACACTACTGCTTAG
1 GGAGATAAGATCTGTAATGCTTCAATCTACTCCACTGTTGCCCAG
* * *
42073815 GGAGATAAGATCTGTAAT-CTTCAATCTATTCCACTATTGCCCAT
1 GGAGATAAGATCTGTAATGCTTCAATCTACTCCACTGTTGCCCAG
42073859 GGAGATA
1 GGAGATA
42073866 GAATTACTGG
Statistics
Matches: 179, Mismatches: 78, Indels: 28
0.63 0.27 0.10
Matches are distributed among these distances:
41 6 0.03
42 2 0.01
43 50 0.28
44 88 0.49
45 25 0.14
46 6 0.03
47 2 0.01
ACGTcount: A:0.28, C:0.24, G:0.18, T:0.30
Consensus pattern (45 bp):
GGAGATAAGATCTGTAATGCTTCAATCTACTCCACTGTTGCCCAG
Found at i:42073788 original size:132 final size:132
Alignment explanation
Indices: 42073551--42073921 Score: 670
Period size: 132 Copynumber: 2.8 Consensus size: 132
42073541 CGCTGCCTAA
*
42073551 GGAGATAAGATCTGTAATCTTCAATCTATTCCACTGTTGCCCAGGGAGATAGAATTACTGGCTTC
1 GGAGATAAGATCTGTAATCTTCAATCTATTCCACTGTTGCCCATGGAGATAGAATTACTGGCTTC
*
42073616 AATGTACTCCACTGTAACCTCAGGGAGGTAAAATCCGCCATCCTTGATCTGCTCCACTACTGCTT
66 AATGTACTCCACTGTAACCTCAGGGAGGTAAAATCCGCCATCCTTGATCTGCTACACTACTGCTT
42073681 AG
131 AG
*
42073683 GGAGATAAGATCTGTAATCTTCAATCTATTCCACTGTTGCCCATAGAGATAGAATTACTGGCTTC
1 GGAGATAAGATCTGTAATCTTCAATCTATTCCACTGTTGCCCATGGAGATAGAATTACTGGCTTC
**
42073748 AATGTACTCCACTGTAACCTCAATGAGGTAAAATCCGCCATCCTTGATCTGCTACACTACTGCTT
66 AATGTACTCCACTGTAACCTCAGGGAGGTAAAATCCGCCATCCTTGATCTGCTACACTACTGCTT
42073813 AG
131 AG
*
42073815 GGAGATAAGATCTGTAATCTTCAATCTATTCCACTATTGCCCATGGAGATAGAATTACTGGCTTC
1 GGAGATAAGATCTGTAATCTTCAATCTATTCCACTGTTGCCCATGGAGATAGAATTACTGGCTTC
* *
42073880 TATGTACTCCACTGTAACCTCAGGGAGGTAAAATCTGCCATC
66 AATGTACTCCACTGTAACCTCAGGGAGGTAAAATCCGCCATC
42073922 AACCTACTCC
Statistics
Matches: 228, Mismatches: 11, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
132 228 1.00
ACGTcount: A:0.28, C:0.24, G:0.18, T:0.30
Consensus pattern (132 bp):
GGAGATAAGATCTGTAATCTTCAATCTATTCCACTGTTGCCCATGGAGATAGAATTACTGGCTTC
AATGTACTCCACTGTAACCTCAGGGAGGTAAAATCCGCCATCCTTGATCTGCTACACTACTGCTT
AG
Found at i:42078180 original size:19 final size:20
Alignment explanation
Indices: 42078152--42078197 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 20
42078142 TAATTGTGTT
* *
42078152 TAATGCAATGCATATG-ATG
1 TAATGAAATGCAAATGCATG
42078171 TAATGAAATGCAAATGCATG
1 TAATGAAATGCAAATGCATG
*
42078191 AAATGAA
1 TAATGAA
42078198 TGCGAAAAGA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 14 0.61
20 9 0.39
ACGTcount: A:0.46, C:0.09, G:0.20, T:0.26
Consensus pattern (20 bp):
TAATGAAATGCAAATGCATG
Found at i:42078249 original size:13 final size:13
Alignment explanation
Indices: 42078231--42078256 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
42078221 GTTCAATTTT
42078231 TTTACTAGAAAAC
1 TTTACTAGAAAAC
42078244 TTTACTAGAAAAC
1 TTTACTAGAAAAC
42078257 AAATCTCTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.15, G:0.08, T:0.31
Consensus pattern (13 bp):
TTTACTAGAAAAC
Found at i:42080409 original size:2 final size:2
Alignment explanation
Indices: 42080402--42080430 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
42080392 TAAAATGCAT
42080402 TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
42080431 AAAAAACTAT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:42081799 original size:41 final size:39
Alignment explanation
Indices: 42081671--42081810 Score: 142
Period size: 41 Copynumber: 3.6 Consensus size: 39
42081661 ACACACTAGT
*
42081671 TTGACACCCAGTGCCTCATC-AGATAATTCGAAGCAATAAA
1 TTGACACCCAGTGCCTCATCGA-ATAATCCGAAG-AATAAA
* * ** * *
42081711 TTGACACCCAGTGTCTTATCGGCTAAACC-AA-AGTAAA
1 TTGACACCCAGTGCCTCATCGAATAATCCGAAGAATAAA
42081748 TTGACACCCAGTGCCTCATCGAATTAATCCGAAGTAATAAA
1 TTGACACCCAGTGCCTCATCGAA-TAATCCGAAG-AATAAA
* *
42081789 TTGACGCCCAGTGTCTCATCGA
1 TTGACACCCAGTGCCTCATCGA
42081811 CTCGAAGTCG
Statistics
Matches: 80, Mismatches: 15, Indels: 9
0.77 0.14 0.09
Matches are distributed among these distances:
37 24 0.30
38 5 0.06
39 4 0.05
40 22 0.28
41 25 0.31
ACGTcount: A:0.34, C:0.26, G:0.16, T:0.24
Consensus pattern (39 bp):
TTGACACCCAGTGCCTCATCGAATAATCCGAAGAATAAA
Found at i:42083979 original size:2 final size:2
Alignment explanation
Indices: 42083974--42084004 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
42083964 ACTATCACGT
42083974 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
42084005 TCACTAGAAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:42088338 original size:29 final size:30
Alignment explanation
Indices: 42088306--42088372 Score: 84
Period size: 30 Copynumber: 2.3 Consensus size: 30
42088296 AAACTCCAAA
42088306 TCCTCTTTACTTTCCC-CAAAAACTTTTAC
1 TCCTCTTTACTTTCCCTCAAAAACTTTTAC
* * *
42088335 TCCTAC-TCACTTTCCCTCCAAACCTTTTAC
1 TCCT-CTTTACTTTCCCTCAAAAACTTTTAC
42088365 TCCTCTTT
1 TCCTCTTT
42088373 CATCCCACCC
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
29 14 0.45
30 17 0.55
ACGTcount: A:0.19, C:0.39, G:0.00, T:0.42
Consensus pattern (30 bp):
TCCTCTTTACTTTCCCTCAAAAACTTTTAC
Found at i:42090498 original size:43 final size:43
Alignment explanation
Indices: 42090444--42090567 Score: 167
Period size: 43 Copynumber: 2.9 Consensus size: 43
42090434 TGTAGCTACG
42090444 GCTATTGGCATCGATTTGAGATTTCGTGTAAGACCATAGCTGA
1 GCTATTGGCATCGATTTGAGATTTCGTGTAAGACCATAGCTGA
* * *
42090487 GCTATTGGCATCTATTTTAGATTTCGTGTAAGACCATAGCTGG
1 GCTATTGGCATCGATTTGAGATTTCGTGTAAGACCATAGCTGA
* ** * *
42090530 GCTATTGGAATCGATACGAGATTCCCATGTAAGACCAT
1 GCTATTGGCATCGATTTGAGATT-TCGTGTAAGACCAT
42090568 GTCTGAGACA
Statistics
Matches: 70, Mismatches: 10, Indels: 1
0.86 0.12 0.01
Matches are distributed among these distances:
43 58 0.83
44 12 0.17
ACGTcount: A:0.27, C:0.18, G:0.23, T:0.32
Consensus pattern (43 bp):
GCTATTGGCATCGATTTGAGATTTCGTGTAAGACCATAGCTGA
Found at i:42091780 original size:41 final size:39
Alignment explanation
Indices: 42091652--42091791 Score: 142
Period size: 41 Copynumber: 3.6 Consensus size: 39
42091642 ACACACTAGT
*
42091652 TTGACACCCAGTGCCTCATC-AGATAATTCGAAGCAATAAA
1 TTGACACCCAGTGCCTCATCGA-ATAATCCGAAG-AATAAA
* * ** * *
42091692 TTGACACCCAGTGTCTTATCGGCTAAACC-AA-AGTAAA
1 TTGACACCCAGTGCCTCATCGAATAATCCGAAGAATAAA
42091729 TTGACACCCAGTGCCTCATCGAATTAATCCGAAGTAATAAA
1 TTGACACCCAGTGCCTCATCGAA-TAATCCGAAG-AATAAA
* *
42091770 TTGACGCCCAGTGTCTCATCGA
1 TTGACACCCAGTGCCTCATCGA
42091792 CTCGAAGTCG
Statistics
Matches: 80, Mismatches: 15, Indels: 9
0.77 0.14 0.09
Matches are distributed among these distances:
37 24 0.30
38 5 0.06
39 4 0.05
40 22 0.28
41 25 0.31
ACGTcount: A:0.34, C:0.26, G:0.16, T:0.24
Consensus pattern (39 bp):
TTGACACCCAGTGCCTCATCGAATAATCCGAAGAATAAA
Found at i:42092675 original size:4 final size:4
Alignment explanation
Indices: 42092666--42092726 Score: 50
Period size: 4 Copynumber: 13.8 Consensus size: 4
42092656 CCCTTTTCTT
* *
42092666 TTTC TTTC TTTC TTTC TTTTC TAATTC GTTTGGC TTTC TCTG TTTC TTTC
1 TTTC TTTC TTTC TTTC -TTTC T--TTC -TTT--C TTTC TTTC TTTC TTTC
42092716 TTTC TTTC TTT
1 TTTC TTTC TTT
42092727 TTTATTATAA
Statistics
Matches: 47, Mismatches: 4, Indels: 12
0.75 0.06 0.19
Matches are distributed among these distances:
4 33 0.70
5 6 0.13
6 6 0.13
7 2 0.04
ACGTcount: A:0.03, C:0.21, G:0.07, T:0.69
Consensus pattern (4 bp):
TTTC
Found at i:42094253 original size:2 final size:2
Alignment explanation
Indices: 42094248--42094278 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
42094238 ACTATCACGT
42094248 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
42094279 TCACTAGAAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:42098612 original size:29 final size:30
Alignment explanation
Indices: 42098580--42098646 Score: 84
Period size: 30 Copynumber: 2.3 Consensus size: 30
42098570 AAACTCCAAA
42098580 TCCTCTTTACTTTCCC-CAAAAACTTTTAC
1 TCCTCTTTACTTTCCCTCAAAAACTTTTAC
* * *
42098609 TCCTAC-TCACTTTCCCTCCAAACCTTTTAC
1 TCCT-CTTTACTTTCCCTCAAAAACTTTTAC
42098639 TCCTCTTT
1 TCCTCTTT
42098647 CATCCCACCC
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
29 14 0.45
30 17 0.55
ACGTcount: A:0.19, C:0.39, G:0.00, T:0.42
Consensus pattern (30 bp):
TCCTCTTTACTTTCCCTCAAAAACTTTTAC
Found at i:42100772 original size:43 final size:43
Alignment explanation
Indices: 42100718--42100841 Score: 167
Period size: 43 Copynumber: 2.9 Consensus size: 43
42100708 TGTAGCTACG
42100718 GCTATTGGCATCGATTTGAGATTTCGTGTAAGACCATAGCTGA
1 GCTATTGGCATCGATTTGAGATTTCGTGTAAGACCATAGCTGA
* * *
42100761 GCTATTGGCATCTATTTTAGATTTCGTGTAAGACCATAGCTGG
1 GCTATTGGCATCGATTTGAGATTTCGTGTAAGACCATAGCTGA
* ** * *
42100804 GCTATTGGAATCGATACGAGATTCCCATGTAAGACCAT
1 GCTATTGGCATCGATTTGAGATT-TCGTGTAAGACCAT
42100842 GTCTGAGACA
Statistics
Matches: 70, Mismatches: 10, Indels: 1
0.86 0.12 0.01
Matches are distributed among these distances:
43 58 0.83
44 12 0.17
ACGTcount: A:0.27, C:0.18, G:0.23, T:0.32
Consensus pattern (43 bp):
GCTATTGGCATCGATTTGAGATTTCGTGTAAGACCATAGCTGA
Found at i:42113512 original size:21 final size:21
Alignment explanation
Indices: 42113488--42113530 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
42113478 ACAAGCTAAA
**
42113488 AAATCTCCCTAGGACTTAATC
1 AAATCTCCCTAAAACTTAATC
42113509 AAATCTCCCTAAAACTTAATC
1 AAATCTCCCTAAAACTTAATC
42113530 A
1 A
42113531 TAATATAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.40, C:0.28, G:0.05, T:0.28
Consensus pattern (21 bp):
AAATCTCCCTAAAACTTAATC
Found at i:42115154 original size:6 final size:6
Alignment explanation
Indices: 42115143--42115175 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
42115133 GCTTTGCTTC
42115143 TTGGAG TTGGAG TTGGAG TTGGAG TTGGAG TTG
1 TTGGAG TTGGAG TTGGAG TTGGAG TTGGAG TTG
42115176 AGGGTAATTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.15, C:0.00, G:0.48, T:0.36
Consensus pattern (6 bp):
TTGGAG
Found at i:42115236 original size:6 final size:7
Alignment explanation
Indices: 42115221--42115245 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
42115211 GAATTGTACA
42115221 TTTTCTT
1 TTTTCTT
42115228 TTTTCTT
1 TTTTCTT
42115235 TTTTCTT
1 TTTTCTT
42115242 TTTT
1 TTTT
42115246 TAATATTCAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (7 bp):
TTTTCTT
Found at i:42131341 original size:12 final size:12
Alignment explanation
Indices: 42131311--42131343 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
42131301 TATATATTTT
42131311 AAAATT-ATATA
1 AAAATTAATATA
42131322 AAAA-TAATATA
1 AAAATTAATATA
42131333 AAAATTAATAT
1 AAAATTAATAT
42131344 GGGTGGGCCG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
10 1 0.05
11 13 0.65
12 6 0.30
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (12 bp):
AAAATTAATATA
Found at i:42133925 original size:13 final size:11
Alignment explanation
Indices: 42133890--42133917 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
42133880 TTACTTTAAG
42133890 TTTTTTTTGTT
1 TTTTTTTTGTT
42133901 TTTTTTTTGTT
1 TTTTTTTTGTT
42133912 TTTTTT
1 TTTTTT
42133918 CATTGTTTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.00, C:0.00, G:0.07, T:0.93
Consensus pattern (11 bp):
TTTTTTTTGTT
Found at i:42141889 original size:42 final size:42
Alignment explanation
Indices: 42141833--42141914 Score: 119
Period size: 42 Copynumber: 2.0 Consensus size: 42
42141823 ACACAATAAC
42141833 AATAATAATAGTTTTATACTCAAAATAATACTAACTAACAAT
1 AATAATAATAGTTTTATACTCAAAATAATACTAACTAACAAT
* * * * *
42141875 AATAATATTAGTTTTTTACTGACAATAATACTAAGTAACA
1 AATAATAATAGTTTTATACTCAAAATAATACTAACTAACA
42141915 TCTAAACCCT
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 35 1.00
ACGTcount: A:0.49, C:0.11, G:0.05, T:0.35
Consensus pattern (42 bp):
AATAATAATAGTTTTATACTCAAAATAATACTAACTAACAAT
Found at i:42142094 original size:10 final size:10
Alignment explanation
Indices: 42142066--42142101 Score: 54
Period size: 10 Copynumber: 3.5 Consensus size: 10
42142056 AAAATACCTT
42142066 TTTTTCTCTTC
1 TTTTTCTC-TC
*
42142077 TCTTTCTCTC
1 TTTTTCTCTC
42142087 TTTTTCTCTC
1 TTTTTCTCTC
42142097 TTTTT
1 TTTTT
42142102 TCGGCGCCAC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
10 16 0.70
11 7 0.30
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (10 bp):
TTTTTCTCTC
Found at i:42143277 original size:30 final size:30
Alignment explanation
Indices: 42143242--42143306 Score: 103
Period size: 30 Copynumber: 2.2 Consensus size: 30
42143232 TGGCAAAAAA
*
42143242 CTCTCAAATTTCTCCCTAAATTTCTTAAAG
1 CTCTCAAATTTCTCCCTAAATTTCTCAAAG
**
42143272 CTCTCAAATTTCTCTTTAAATTTCTCAAAG
1 CTCTCAAATTTCTCCCTAAATTTCTCAAAG
42143302 CTCTC
1 CTCTC
42143307 TTTAATTAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.28, C:0.28, G:0.03, T:0.42
Consensus pattern (30 bp):
CTCTCAAATTTCTCCCTAAATTTCTCAAAG
Found at i:42143290 original size:21 final size:21
Alignment explanation
Indices: 42143266--42143311 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
42143256 CCTAAATTTC
**
42143266 TTAAAGCTCTCAAATTTCTCT
1 TTAAAGCTCTCAAAGCTCTCT
**
42143287 TTAAATTTCTCAAAGCTCTCT
1 TTAAAGCTCTCAAAGCTCTCT
42143308 TTAA
1 TTAA
42143312 TTAATTATTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.30, C:0.22, G:0.04, T:0.43
Consensus pattern (21 bp):
TTAAAGCTCTCAAAGCTCTCT
Found at i:42143502 original size:20 final size:19
Alignment explanation
Indices: 42143460--42143507 Score: 51
Period size: 20 Copynumber: 2.5 Consensus size: 19
42143450 GTAAGGATTC
*
42143460 ATTTAAATTTTTTAATATT
1 ATTTAAATTTTTTAATATA
* *
42143479 ATTTAATATTTTTTCATGTA
1 ATTTAA-ATTTTTTAATATA
*
42143499 ATTTTAATT
1 ATTTAAATT
42143508 AATTTGTATT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
19 9 0.38
20 15 0.62
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.62
Consensus pattern (19 bp):
ATTTAAATTTTTTAATATA
Found at i:42144820 original size:150 final size:150
Alignment explanation
Indices: 42144537--42144828 Score: 449
Period size: 150 Copynumber: 1.9 Consensus size: 150
42144527 AGGATTCGAC
* * * *
42144537 AATTCGGGTAGTAATTCCGGATGAATTCTTTCAAAATTCAAACATTTGGCATGTTAATGTCCCAT
1 AATTCGGGCAGTAATTCCGGATAAATTCTTTCAAAATCCAAACATTTGGCATGTTAAGGTCCCAT
* * * *
42144602 TGCTCAACTATGCTACTGTCGAGATGCACCAGACGGATAAAGTGTTGCGACAATTTGGATTCCAA
66 TGCTCAACTATGCTACTGTCGAGATACACCAGACAGATAAAGTGTTACGACAATTTAGATTCCAA
*
42144667 CAACGGATTCCCATTGGTCG
131 CAACCGATTCCCATTGGTCG
* *
42144687 AATTTGGGCAGTAATTCCGGATAAATTCTTTCAAAATCCGAACATTTGGCATGTTAAGGTCCCAT
1 AATTCGGGCAGTAATTCCGGATAAATTCTTTCAAAATCCAAACATTTGGCATGTTAAGGTCCCAT
* * * *
42144752 TGGTCAACTATGCTACTGTTGAGATACACCAGACAGATAAAGTGTTACGACAATTTAGATTTCGA
66 TGCTCAACTATGCTACTGTCGAGATACACCAGACAGATAAAGTGTTACGACAATTTAGATTCCAA
42144817 CAACCGATTCCC
131 CAACCGATTCCC
42144829 GAGGCACCTG
Statistics
Matches: 127, Mismatches: 15, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
150 127 1.00
ACGTcount: A:0.30, C:0.21, G:0.20, T:0.30
Consensus pattern (150 bp):
AATTCGGGCAGTAATTCCGGATAAATTCTTTCAAAATCCAAACATTTGGCATGTTAAGGTCCCAT
TGCTCAACTATGCTACTGTCGAGATACACCAGACAGATAAAGTGTTACGACAATTTAGATTCCAA
CAACCGATTCCCATTGGTCG
Found at i:42145655 original size:24 final size:25
Alignment explanation
Indices: 42145628--42145674 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
42145618 CATTTAATAA
*
42145628 AATA-AAAATTGTTTTTAATATTTT
1 AATAGAAAATTATTTTTAATATTTT
* *
42145652 AATAGTAAATTATTTTTATTATT
1 AATAGAAAATTATTTTTAATATT
42145675 ATGTATATAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 4 0.21
25 15 0.79
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.55
Consensus pattern (25 bp):
AATAGAAAATTATTTTTAATATTTT
Found at i:42146023 original size:150 final size:150
Alignment explanation
Indices: 42145740--42146031 Score: 449
Period size: 150 Copynumber: 1.9 Consensus size: 150
42145730 AGGATTCGAC
* * * *
42145740 AATTCGGGTAGTAATTCCGGATGAATTCTTTCAAAATTCAAACATTTGGCATGTTAATGTCCCAT
1 AATTCGGGCAGTAATTCCGGATAAATTCTTTCAAAATCCAAACATTTGGCATGTTAAGGTCCCAT
* * * *
42145805 TGCTCAACTATGCTACTGTCGAGATGCACCAGACGGATAAAGTGTTGCGACAATTTGGATTCCAA
66 TGCTCAACTATGCTACTGTCGAGATACACCAGACAGATAAAGTGTTACGACAATTTAGATTCCAA
*
42145870 CAACGGATTCCCATTGGTCG
131 CAACCGATTCCCATTGGTCG
* *
42145890 AATTTGGGCAGTAATTCCGGATAAATTCTTTCAAAATCCGAACATTTGGCATGTTAAGGTCCCAT
1 AATTCGGGCAGTAATTCCGGATAAATTCTTTCAAAATCCAAACATTTGGCATGTTAAGGTCCCAT
* * * *
42145955 TGGTCAACTATGCTACTGTTGAGATACACCAGACAGATAAAGTGTTACGACAATTTAGATTTCGA
66 TGCTCAACTATGCTACTGTCGAGATACACCAGACAGATAAAGTGTTACGACAATTTAGATTCCAA
42146020 CAACCGATTCCC
131 CAACCGATTCCC
42146032 GAGGCACCTG
Statistics
Matches: 127, Mismatches: 15, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
150 127 1.00
ACGTcount: A:0.30, C:0.21, G:0.20, T:0.30
Consensus pattern (150 bp):
AATTCGGGCAGTAATTCCGGATAAATTCTTTCAAAATCCAAACATTTGGCATGTTAAGGTCCCAT
TGCTCAACTATGCTACTGTCGAGATACACCAGACAGATAAAGTGTTACGACAATTTAGATTCCAA
CAACCGATTCCCATTGGTCG
Found at i:42146858 original size:24 final size:24
Alignment explanation
Indices: 42146831--42146886 Score: 69
Period size: 25 Copynumber: 2.3 Consensus size: 24
42146821 CATTTAATAA
*
42146831 AATAAAAATTGTTTTTA-ATATTTT
1 AATAAAAATTATTTTTATAT-TTTT
*
42146855 AATAGTAAATTATTTTTATATTTTT
1 AATA-AAAATTATTTTTATATTTTT
42146880 AATAAAA
1 AATAAAA
42146887 TAGAAGTTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
24 6 0.22
25 19 0.70
26 2 0.07
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.52
Consensus pattern (24 bp):
AATAAAAATTATTTTTATATTTTT
Found at i:42146870 original size:25 final size:25
Alignment explanation
Indices: 42146836--42146883 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
42146826 AATAAAATAA
*
42146836 AAATTGTTTTTA-ATATTTTAATAGT
1 AAATTATTTTTATAT-TTTTAATAGT
42146861 AAATTATTTTTATATTTTTAATA
1 AAATTATTTTTATATTTTTAATA
42146884 AAATAGAAGT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 19 0.90
26 2 0.10
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (25 bp):
AAATTATTTTTATATTTTTAATAGT
Found at i:42150171 original size:124 final size:124
Alignment explanation
Indices: 42149932--42150198 Score: 394
Period size: 124 Copynumber: 2.1 Consensus size: 124
42149922 GGCTAAACAT
* * * * *
42149932 GAACTACTATAGAAAAATAGCGTCGACGTGGGAGCTTTTTTCATCAATTTTATTGACAGTGCATC
1 GAACTACTGTAGAAAAA-AGCGTCCACGTGGGAACCTTTTTCATCAATTTTACTGACAGTGCATC
* * *
42149997 CTGCTTGAAGCGTTTTTGACACTATTTGTTCAGAAACATCTTCTCAAAATTATTTTTTCAG
65 CTGCTTGAAGCATTTTTCACACTATTTGTTCAGAAACATATTCTCAAAATTA-TTTTTCAG
*
42150058 GAACTACTGTAGAAAAAAGCGTCCACGT-GGAACCTTTTTCAAT-AATTTTGCTGACAGTGCATC
1 GAACTACTGTAGAAAAAAGCGTCCACGTGGGAACCTTTTTC-ATCAATTTTACTGACAGTGCATC
* *
42150121 CTGCTTGAAGCATTTTTCACACTATTTGTTCAGAACCGTATTCTCAAAATTATTTTTCAG
65 CTGCTTGAAGCATTTTTCACACTATTTGTTCAGAAACATATTCTCAAAATTATTTTTCAG
42150181 GAACTACTGTAGAAAAAA
1 GAACTACTGTAGAAAAAA
42150199 ATAAAATCCT
Statistics
Matches: 129, Mismatches: 11, Indels: 5
0.89 0.08 0.03
Matches are distributed among these distances:
123 26 0.20
124 75 0.58
125 12 0.09
126 16 0.12
ACGTcount: A:0.31, C:0.18, G:0.16, T:0.35
Consensus pattern (124 bp):
GAACTACTGTAGAAAAAAGCGTCCACGTGGGAACCTTTTTCATCAATTTTACTGACAGTGCATCC
TGCTTGAAGCATTTTTCACACTATTTGTTCAGAAACATATTCTCAAAATTATTTTTCAG
Found at i:42150359 original size:21 final size:21
Alignment explanation
Indices: 42150330--42150402 Score: 60
Period size: 21 Copynumber: 3.5 Consensus size: 21
42150320 TAAAATTCCT
42150330 AAAACCCTAAATTATTTTAAC
1 AAAACCCTAAATTATTTTAAC
* * **
42150351 AAAATCCTAAACT-TTACAA-
1 AAAACCCTAAATTATTTTAAC
*
42150370 ATCCAACCCTAAATTATTTTAAC
1 A--AAACCCTAAATTATTTTAAC
*
42150393 AAAATCCTAA
1 AAAACCCTAA
42150403 CCCTAAAAAC
Statistics
Matches: 37, Mismatches: 11, Indels: 8
0.66 0.20 0.14
Matches are distributed among these distances:
19 1 0.03
20 4 0.11
21 27 0.73
22 4 0.11
23 1 0.03
ACGTcount: A:0.48, C:0.22, G:0.00, T:0.30
Consensus pattern (21 bp):
AAAACCCTAAATTATTTTAAC
Found at i:42151102 original size:13 final size:12
Alignment explanation
Indices: 42151064--42151093 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
42151054 ATATATAATT
42151064 AAAATTGTTAAA
1 AAAATTGTTAAA
42151076 AAAATTGTTAAA
1 AAAATTGTTAAA
42151088 AAAATT
1 AAAATT
42151094 AAGTAAAAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.60, C:0.00, G:0.07, T:0.33
Consensus pattern (12 bp):
AAAATTGTTAAA
Found at i:42153225 original size:102 final size:103
Alignment explanation
Indices: 42153095--42153302 Score: 409
Period size: 102 Copynumber: 2.0 Consensus size: 103
42153085 ATATATATAT
42153095 TATGTTTTTAGTTTATCATATAACATGTCATTGTCTGAATTGTGTGTATGGAGTTTTTAAATTTC
1 TATGTTTTTAGTTTATCATATAACATGTCATTGTCTGAATTGTGTGTATGGAGTTTTTAAATTTC
42153160 ATTGGACACTAGTATAACATATCAAATAATTTTTCTTA
66 ATTGGACACTAGTATAACATATCAAATAATTTTTCTTA
42153198 TATGTTTTTAG-TTATCATATAACATGTCATTGTCTGAATTGTGTGTATGGAGTTTTTAAATTTC
1 TATGTTTTTAGTTTATCATATAACATGTCATTGTCTGAATTGTGTGTATGGAGTTTTTAAATTTC
42153262 ATTGGACACTAGTATAACATATCAAATAATTTTTCTTA
66 ATTGGACACTAGTATAACATATCAAATAATTTTTCTTA
42153300 TAT
1 TAT
42153303 ATTAAGATGA
Statistics
Matches: 105, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
102 94 0.90
103 11 0.10
ACGTcount: A:0.30, C:0.10, G:0.13, T:0.47
Consensus pattern (103 bp):
TATGTTTTTAGTTTATCATATAACATGTCATTGTCTGAATTGTGTGTATGGAGTTTTTAAATTTC
ATTGGACACTAGTATAACATATCAAATAATTTTTCTTA
Found at i:42157900 original size:57 final size:57
Alignment explanation
Indices: 42157830--42157960 Score: 156
Period size: 57 Copynumber: 2.3 Consensus size: 57
42157820 AAACAATCTG
* * * * *
42157830 ATATGGCATTGAAATGAATAATGTGAAATTGGTATAAACTTAT-AATTTGATAATTGA
1 ATATGACATTGAAATGAATAAGGTGAAATTAGCATAAACTTATGAA-TTGATAATAGA
* * * *
42157887 ATATGACATTGAAATGAATTAGGTGAAATTAGCATGATCTTATGAATTGATGATAGA
1 ATATGACATTGAAATGAATAAGGTGAAATTAGCATAAACTTATGAATTGATAATAGA
*
42157944 ATATGACATTGAGATGA
1 ATATGACATTGAAATGA
42157961 GTTACGTGAA
Statistics
Matches: 63, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
57 61 0.97
58 2 0.03
ACGTcount: A:0.41, C:0.05, G:0.20, T:0.34
Consensus pattern (57 bp):
ATATGACATTGAAATGAATAAGGTGAAATTAGCATAAACTTATGAATTGATAATAGA
Found at i:42163438 original size:57 final size:57
Alignment explanation
Indices: 42163368--42163498 Score: 156
Period size: 57 Copynumber: 2.3 Consensus size: 57
42163358 AAACAATCTG
* * * * *
42163368 ATATGGCATTGAAATGAATAATGTGAAATTGGTATAAACTTAT-AATTTGATAATTGA
1 ATATGACATTGAAATGAATAAGGTGAAATTAGCATAAACTTATGAA-TTGATAATAGA
* * * *
42163425 ATATGACATTGAAATGAATTAGGTGAAATTAGCATGATCTTATGAATTGATGATAGA
1 ATATGACATTGAAATGAATAAGGTGAAATTAGCATAAACTTATGAATTGATAATAGA
*
42163482 ATATGACATTGAGATGA
1 ATATGACATTGAAATGA
42163499 GTTACGTGAA
Statistics
Matches: 63, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
57 61 0.97
58 2 0.03
ACGTcount: A:0.41, C:0.05, G:0.20, T:0.34
Consensus pattern (57 bp):
ATATGACATTGAAATGAATAAGGTGAAATTAGCATAAACTTATGAATTGATAATAGA
Found at i:42164426 original size:2 final size:2
Alignment explanation
Indices: 42164419--42164445 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
42164409 ACCACCAATT
42164419 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
42164446 GCATTCGTCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:42164877 original size:21 final size:21
Alignment explanation
Indices: 42164853--42164902 Score: 68
Period size: 21 Copynumber: 2.4 Consensus size: 21
42164843 TGCTCATCAA
42164853 ACTTATTTATCAAATATATAT
1 ACTTATTTATCAAATATATAT
*
42164874 ACTTGATCT-TCAAATATATAT
1 ACTT-ATTTATCAAATATATAT
42164895 A-TTATTTA
1 ACTTATTTA
42164903 CATATCACGT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
19 3 0.12
20 2 0.08
21 17 0.68
22 3 0.12
ACGTcount: A:0.40, C:0.10, G:0.02, T:0.48
Consensus pattern (21 bp):
ACTTATTTATCAAATATATAT
Found at i:42165078 original size:41 final size:40
Alignment explanation
Indices: 42164988--42165107 Score: 132
Period size: 41 Copynumber: 2.9 Consensus size: 40
42164978 TGATTTAATA
* * * * * *
42164988 CACCGGCTTTTAGCCTGCTAGACTTATAGTCCGAATAATTT
1 CACCGGCATTAAGCCTGCTAGAC-AATAGTCTGAATTATAT
*
42165029 CACTGGCATTAAGCCTGCTAGACAATGAGTCTGAATTATAT
1 CACCGGCATTAAGCCTGCTAGACAAT-AGTCTGAATTATAT
* *
42165070 CACCGGCATCAAGCCTGCTAGATAATAAGTCTGAATTA
1 CACCGGCATTAAGCCTGCTAGACAAT-AGTCTGAATTA
42165108 CATTCGATCA
Statistics
Matches: 67, Mismatches: 11, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
40 2 0.03
41 65 0.97
ACGTcount: A:0.30, C:0.23, G:0.18, T:0.29
Consensus pattern (40 bp):
CACCGGCATTAAGCCTGCTAGACAATAGTCTGAATTATAT
Found at i:42167902 original size:19 final size:17
Alignment explanation
Indices: 42167853--42167911 Score: 55
Period size: 19 Copynumber: 3.2 Consensus size: 17
42167843 TTTAATACAA
*
42167853 TTTTAAGAAATTTTTTAT
1 TTTTAA-AAATTTTTAAT
*
42167871 TTTATAAACATTTATTAAT
1 TTT-TAAAAATTT-TTAAT
42167890 TTTTAATAAATTTTGTAAT
1 TTTTAA-AAATTTT-TAAT
42167909 TTT
1 TTT
42167912 GATAATTTTC
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
18 12 0.35
19 22 0.65
ACGTcount: A:0.36, C:0.02, G:0.03, T:0.59
Consensus pattern (17 bp):
TTTTAAAAATTTTTAAT
Found at i:42167972 original size:18 final size:18
Alignment explanation
Indices: 42167907--42167972 Score: 53
Period size: 18 Copynumber: 3.6 Consensus size: 18
42167897 AAATTTTGTA
*
42167907 ATTTTGATAATTTTCTATTTT
1 ATTTT-ATAATTTT-T-TTAT
**
42167928 A-TTTATAATTTTTAAAT
1 ATTTTATAATTTTTTTAT
* *
42167945 AATTTCTAATTTTTTTAT
1 ATTTTATAATTTTTTTAT
42167963 ATTTTATAAT
1 ATTTTATAAT
42167973 ACTTAATGAT
Statistics
Matches: 36, Mismatches: 8, Indels: 5
0.73 0.16 0.10
Matches are distributed among these distances:
17 2 0.06
18 22 0.61
19 8 0.22
20 3 0.08
21 1 0.03
ACGTcount: A:0.32, C:0.03, G:0.02, T:0.64
Consensus pattern (18 bp):
ATTTTATAATTTTTTTAT
Found at i:42168072 original size:30 final size:29
Alignment explanation
Indices: 42168036--42168109 Score: 103
Period size: 30 Copynumber: 2.5 Consensus size: 29
42168026 TGAAATAATC
*
42168036 AATTAAGCCCTAGTAAAATAATAAAAAATT
1 AATTAAGCCCTA-CAAAATAATAAAAAATT
* *
42168066 AATTAAGTCCTCACAAAATAATAAAAATTT
1 AATTAAGCCCT-ACAAAATAATAAAAAATT
42168096 AATTAAGCCCTACA
1 AATTAAGCCCTACA
42168110 TATCATTTTT
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
29 3 0.08
30 35 0.90
31 1 0.03
ACGTcount: A:0.53, C:0.15, G:0.05, T:0.27
Consensus pattern (29 bp):
AATTAAGCCCTACAAAATAATAAAAAATT
Found at i:42181105 original size:16 final size:17
Alignment explanation
Indices: 42181084--42181118 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
42181074 TGTTTTAATA
42181084 TTTTTGAAATAA-ATTT
1 TTTTTGAAATAATATTT
*
42181100 TTTTTGAAGTAATATTT
1 TTTTTGAAATAATATTT
42181117 TT
1 TT
42181119 GAAATTATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 11 0.65
17 6 0.35
ACGTcount: A:0.31, C:0.00, G:0.09, T:0.60
Consensus pattern (17 bp):
TTTTTGAAATAATATTT
Found at i:42184922 original size:5 final size:5
Alignment explanation
Indices: 42184912--42184948 Score: 65
Period size: 5 Copynumber: 7.2 Consensus size: 5
42184902 TTCAAGGTTA
42184912 TTTAT TTTAT TTTAT TTTCAT TTTAT TTTAT TTTAT T
1 TTTAT TTTAT TTTAT TTT-AT TTTAT TTTAT TTTAT T
42184949 CTCTTTATTT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
5 26 0.84
6 5 0.16
ACGTcount: A:0.19, C:0.03, G:0.00, T:0.78
Consensus pattern (5 bp):
TTTAT
Found at i:42184936 original size:16 final size:16
Alignment explanation
Indices: 42184915--42184945 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
42184905 AAGGTTATTT
42184915 ATTTTATTTTATTTTC
1 ATTTTATTTTATTTTC
42184931 ATTTTATTTTATTTT
1 ATTTTATTTTATTTT
42184946 ATTCTCTTTA
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:0.19, C:0.03, G:0.00, T:0.77
Consensus pattern (16 bp):
ATTTTATTTTATTTTC
Found at i:42185879 original size:15 final size:15
Alignment explanation
Indices: 42185859--42185898 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
42185849 TAATTTTTAG
**
42185859 ATTATTATTAGTATT
1 ATTATTATTACCATT
*
42185874 ATTATTAATACCATT
1 ATTATTATTACCATT
42185889 ATTATTATTA
1 ATTATTATTA
42185899 TTCTTAAATT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.38, C:0.05, G:0.03, T:0.55
Consensus pattern (15 bp):
ATTATTATTACCATT
Found at i:42187105 original size:30 final size:30
Alignment explanation
Indices: 42187069--42187127 Score: 118
Period size: 30 Copynumber: 2.0 Consensus size: 30
42187059 GATAGTGGAT
42187069 CGCTTTTGGGATACATCCATACCTATGTCA
1 CGCTTTTGGGATACATCCATACCTATGTCA
42187099 CGCTTTTGGGATACATCCATACCTATGTC
1 CGCTTTTGGGATACATCCATACCTATGTC
42187128 TTTGTGAGAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.22, C:0.27, G:0.17, T:0.34
Consensus pattern (30 bp):
CGCTTTTGGGATACATCCATACCTATGTCA
Done.