Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D02
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: 70731513
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1900000 characters in sequence are not A, C, G, or T
File 150 of 222
Found at i:48408872 original size:16 final size:18
Alignment explanation
Indices: 48408837--48408873 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
48408827 CAATTCTTTT
*
48408837 ATTTTTTTTATTTTAGTA
1 ATTTTTATTATTTTAGTA
48408855 ATTTTTATT-TTTTA-TA
1 ATTTTTATTATTTTAGTA
48408871 ATT
1 ATT
48408874 CTATTAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
16 5 0.28
17 5 0.28
18 8 0.44
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.73
Consensus pattern (18 bp):
ATTTTTATTATTTTAGTA
Found at i:48415054 original size:28 final size:28
Alignment explanation
Indices: 48415015--48415079 Score: 94
Period size: 28 Copynumber: 2.3 Consensus size: 28
48415005 ACATTCTAAT
* *
48415015 TTTTCGTTTGTTTGATTCTGATAAGTTA
1 TTTTAGTTTGTTTGATTCTAATAAGTTA
* *
48415043 TTTTAGTTTGTTTGATTCTAATAGGTTC
1 TTTTAGTTTGTTTGATTCTAATAAGTTA
48415071 TTTTAGTTT
1 TTTTAGTTT
48415080 ATGAGTAGAG
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 33 1.00
ACGTcount: A:0.17, C:0.06, G:0.17, T:0.60
Consensus pattern (28 bp):
TTTTAGTTTGTTTGATTCTAATAAGTTA
Found at i:48418263 original size:5 final size:5
Alignment explanation
Indices: 48418236--48418284 Score: 64
Period size: 5 Copynumber: 10.0 Consensus size: 5
48418226 TATTTTTAGT
* **
48418236 TTTTA -TTTA TTTTA GTTCC TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA
48418285 GTATGCATTT
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
4 4 0.11
5 33 0.89
ACGTcount: A:0.18, C:0.04, G:0.02, T:0.76
Consensus pattern (5 bp):
TTTTA
Found at i:48421769 original size:23 final size:22
Alignment explanation
Indices: 48421693--48421811 Score: 121
Period size: 23 Copynumber: 5.2 Consensus size: 22
48421683 ATAAGATATA
48421693 ATTTGTGATGCCTTTTGTGGCAT
1 ATTTGTGATGCC-TTTGTGGCAT
* *
48421716 ATTCTATGATGCATTTGTGGCAT
1 ATT-TGTGATGCCTTTGTGGCAT
**
48421739 ATGTTGTGATGCCTTTGTGGTGT
1 AT-TTGTGATGCCTTTGTGGCAT
* *
48421762 ATTATGTGATGCCTTCGTGGCGT
1 ATT-TGTGATGCCTTTGTGGCAT
* *
48421785 ATTTTGTGAAGCCCTTGTGGCAT
1 A-TTTGTGATGCCTTTGTGGCAT
48421808 ATTT
1 ATTT
48421812 TGTAACACCC
Statistics
Matches: 80, Mismatches: 12, Indels: 9
0.79 0.12 0.09
Matches are distributed among these distances:
22 4 0.05
23 66 0.82
24 10 0.12
ACGTcount: A:0.15, C:0.13, G:0.27, T:0.45
Consensus pattern (22 bp):
ATTTGTGATGCCTTTGTGGCAT
Found at i:48421822 original size:23 final size:23
Alignment explanation
Indices: 48421773--48421824 Score: 61
Period size: 23 Copynumber: 2.2 Consensus size: 23
48421763 TTATGTGATG
* *
48421773 CCTTCGTGGCGTATTTTGTGAAGC
1 CCTT-GTGGCATATTTTGTGAAAC
48421797 CCTTGTGGCATATTTTGT-AACAC
1 CCTTGTGGCATATTTTGTGAA-AC
48421820 CCTTG
1 CCTTG
48421825 AGGTAAAATC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
22 2 0.08
23 19 0.76
24 4 0.16
ACGTcount: A:0.15, C:0.23, G:0.23, T:0.38
Consensus pattern (23 bp):
CCTTGTGGCATATTTTGTGAAAC
Found at i:48427689 original size:3 final size:3
Alignment explanation
Indices: 48427681--48427717 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
48427671 CAGGAAATGC
48427681 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
48427718 TGAGATTTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:48428359 original size:16 final size:16
Alignment explanation
Indices: 48428335--48428388 Score: 90
Period size: 16 Copynumber: 3.4 Consensus size: 16
48428325 TTTGGTTCGC
* *
48428335 TGTATTGGATTAGAGG
1 TGTAATGGAATAGAGG
48428351 TGTAATGGAATAGAGG
1 TGTAATGGAATAGAGG
48428367 TGTAATGGAATAGAGG
1 TGTAATGGAATAGAGG
48428383 TGTAAT
1 TGTAAT
48428389 AGCAAATCAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 36 1.00
ACGTcount: A:0.33, C:0.00, G:0.35, T:0.31
Consensus pattern (16 bp):
TGTAATGGAATAGAGG
Found at i:48428472 original size:39 final size:43
Alignment explanation
Indices: 48428367--48428476 Score: 131
Period size: 45 Copynumber: 2.6 Consensus size: 43
48428357 GGAATAGAGG
48428367 TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTTGAA
1 TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTT--A
* * *
48428412 TGTAATGGAATAGAGGCGTAATAG-TAATCTTA-TGTTTGG-T-
1 TGTAATGGAATAGAGGTGTAATAGCAAATC-AACTGTTTGGTTA
48428452 TG-AATGGAATAGAGGTGTAATAGCA
1 TGTAATGGAATAGAGGTGTAATAGCA
48428477 TAATGGAAAA
Statistics
Matches: 58, Mismatches: 5, Indels: 9
0.81 0.07 0.12
Matches are distributed among these distances:
39 20 0.34
40 2 0.03
43 1 0.02
44 11 0.19
45 24 0.41
ACGTcount: A:0.35, C:0.05, G:0.28, T:0.32
Consensus pattern (43 bp):
TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTTA
Found at i:48428760 original size:16 final size:16
Alignment explanation
Indices: 48428716--48428762 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
48428706 TACTATAAAA
*
48428716 TATAATTTAACATA-AT
1 TATAA-TTAAAATATAT
*
48428732 TATTATT-AAATATAT
1 TATAATTAAAATATAT
48428747 TATAATTAAAATATAT
1 TATAATTAAAATATAT
48428763 AATTTAGTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
14 4 0.15
15 10 0.38
16 12 0.46
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (16 bp):
TATAATTAAAATATAT
Found at i:48428834 original size:120 final size:121
Alignment explanation
Indices: 48428600--48429135 Score: 861
Period size: 120 Copynumber: 4.5 Consensus size: 121
48428590 ATTTAATTAT
* * *
48428600 ATTTAAACATAATAATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATA
1 ATTTGAACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATA
*
48428665 ATCAATA-TCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATA
66 ATCAATATTCTTATATGAATTTACTAAAATCATAATATATGATACTATAAAATATA
* * *
48428720 ATTT-AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAGTAAAATTCTTAAAA
1 ATTTGAACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATA
* * *
48428784 ATTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGATA
66 ATCAATATTCTTATATGAATTTACTAAAATCATAATATATGATACTATAAAATATA
48428840 ATTT-AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATA
1 ATTTGAACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATA
*
48428904 ATCAAAATTCTTATATGAATTTACTAAAATCATAATATATGATACTATAAAATATA
66 ATCAATATTCTTATATGAATTTACTAAAATCATAATATATGATACTATAAAATATA
* *
48428960 ATTTGAA-TTAATTAATATTAAA-ATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATA
1 ATTTGAACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATA
*
48429023 ATCAACATTCTTATATGAATTTACTAAAATCATAATATATGATACTATAAAATATA
66 ATCAATATTCTTATATGAATTTACTAAAATCATAATATATGATACTATAAAATATA
* * *
48429079 ATTTGAA-GTAATTAATATTCAAA-ATATTTTAATTAAAATATATGATTTAATAAAATT
1 ATTTGAACATAATTATTATT-AAATATATTTTAATTAAAATATATAATTTAATAAAATT
48429136 TAAAATAATT
Statistics
Matches: 396, Mismatches: 17, Indels: 6
0.95 0.04 0.01
Matches are distributed among these distances:
119 177 0.45
120 217 0.55
121 2 0.01
ACGTcount: A:0.50, C:0.06, G:0.03, T:0.42
Consensus pattern (121 bp):
ATTTGAACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATA
ATCAATATTCTTATATGAATTTACTAAAATCATAATATATGATACTATAAAATATA
Found at i:48428882 original size:18 final size:17
Alignment explanation
Indices: 48428861--48428895 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
48428851 TTATTATTAA
*
48428861 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
48428879 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
48428896 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:48428912 original size:16 final size:15
Alignment explanation
Indices: 48428887--48428916 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
48428877 ATATATAATT
48428887 TAATAAAATTCTTAA
1 TAATAAAATTCTTAA
48428902 TAATCAAAATTCTTA
1 TAAT-AAAATTCTTA
48428917 TATGAATTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.50, C:0.10, G:0.00, T:0.40
Consensus pattern (15 bp):
TAATAAAATTCTTAA
Found at i:48429035 original size:239 final size:240
Alignment explanation
Indices: 48428600--48429135 Score: 857
Period size: 239 Copynumber: 2.2 Consensus size: 240
48428590 ATTTAATTAT
* *
48428600 ATTTAAACATAATAATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATA
1 ATTTAAACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATA
* *
48428665 ATCAATATCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATAATTTAACATA
66 ATCAAAATCTTATATGAATTTACTAAAATCATAATATATGATACTATAAAATATAATTTAACATA
* * * *
48428730 ATTATTATTAAATATATTATAATTAAAATATATAATTTAGTAAAATTCTTAAAAATTAATATTCT
131 ATTAATATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAAAAATCAACATTCT
*
48428795 TATATGAATTTACTCAAATCATAATATATGATACTATAAAAGATA
196 TATATGAATTTACTAAAATCATAATATATGATACTATAAAAGATA
48428840 ATTT-AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATA
1 ATTTAAACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATA
*
48428904 ATCAAAATTCTTATATGAATTTACTAAAATCATAATATATGATACTATAAAATATAATTTGAA-T
66 ATCAAAA-TCTTATATGAATTTACTAAAATCATAATATATGATACTATAAAATATAATTT-AACA
* *
48428968 TAATTAATATTAAA-ATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATCAACATT
129 TAATTAATATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAAAAATCAACATT
*
48429032 CTTATATGAATTTACTAAAATCATAATATATGATACTATAAAATATA
194 CTTATATGAATTTACTAAAATCATAATATATGATACTATAAAAGATA
* * * *
48429079 ATTTGAA-GTAATTAATATTCAAA-ATATTTTAATTAAAATATATGATTTAATAAAATT
1 ATTTAAACATAATTATTATT-AAATATATTTTAATTAAAATATATAATTTAATAAAATT
48429136 TAAAATAATT
Statistics
Matches: 276, Mismatches: 16, Indels: 9
0.92 0.05 0.03
Matches are distributed among these distances:
239 201 0.73
240 73 0.26
241 2 0.01
ACGTcount: A:0.50, C:0.06, G:0.03, T:0.42
Consensus pattern (240 bp):
ATTTAAACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATA
ATCAAAATCTTATATGAATTTACTAAAATCATAATATATGATACTATAAAATATAATTTAACATA
ATTAATATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAAAAATCAACATTCT
TATATGAATTTACTAAAATCATAATATATGATACTATAAAAGATA
Found at i:48429186 original size:47 final size:46
Alignment explanation
Indices: 48429117--48429284 Score: 134
Period size: 47 Copynumber: 3.7 Consensus size: 46
48429107 TTAATTAAAA
*
48429117 TATATG-ATTTAATAAAATTTAAAATAATTATAACTAATAAATTTTCT
1 TATATGAATTT-ATATAATTTAAAATAATTATAA-TAATAAATTTTCT
* * * *
48429164 TATATGAATTTGTATAATTTAAAAAAATTAT--TATTAAATATAAT-T
1 TATATGAATTTATATAATTTAAAATAATTATAATAATAAAT-T-TTCT
* * * *
48429209 TA-AT-AATAATATATAATTTCATAA-AATTCGTGATAATAAATTTTCT
1 TATATGAAT-TTATATAATTT-AAAATAATT-ATAATAATAAATTTTCT
*
48429255 TATATGAATTTATACAATTTAAAATAATTA
1 TATATGAATTTATATAATTTAAAATAATTA
48429285 ATATTCAATA
Statistics
Matches: 94, Mismatches: 15, Indels: 25
0.70 0.11 0.19
Matches are distributed among these distances:
43 3 0.03
44 22 0.23
45 9 0.10
46 8 0.09
47 45 0.48
48 7 0.07
ACGTcount: A:0.48, C:0.04, G:0.04, T:0.45
Consensus pattern (46 bp):
TATATGAATTTATATAATTTAAAATAATTATAATAATAAATTTTCT
Found at i:48443333 original size:19 final size:18
Alignment explanation
Indices: 48443284--48443333 Score: 55
Period size: 19 Copynumber: 2.6 Consensus size: 18
48443274 ATTCGGGACC
48443284 AATTTGAAACAAATTGAAA
1 AATTTGAAA-AAATTGAAA
* *
48443303 AATTTAGGAAAAATATGCAA
1 AATTT-GAAAAAAT-TGAAA
48443323 AATTTGAAAAA
1 AATTTGAAAAA
48443334 TAGGGGTCAC
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
19 14 0.54
20 12 0.46
ACGTcount: A:0.58, C:0.04, G:0.12, T:0.26
Consensus pattern (18 bp):
AATTTGAAAAAATTGAAA
Found at i:48450683 original size:37 final size:37
Alignment explanation
Indices: 48450629--48450702 Score: 130
Period size: 37 Copynumber: 2.0 Consensus size: 37
48450619 ACATTCCCAT
*
48450629 TGCCTATGGTTGTAGGTAAACTTGTCTGGTAATTGTA
1 TGCCTATGGTTGCAGGTAAACTTGTCTGGTAATTGTA
*
48450666 TGCCTGTGGTTGCAGGTAAACTTGTCTGGTAATTGTA
1 TGCCTATGGTTGCAGGTAAACTTGTCTGGTAATTGTA
48450703 GTGCTAAGTA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.20, C:0.12, G:0.28, T:0.39
Consensus pattern (37 bp):
TGCCTATGGTTGCAGGTAAACTTGTCTGGTAATTGTA
Found at i:48451714 original size:27 final size:28
Alignment explanation
Indices: 48451684--48451743 Score: 70
Period size: 28 Copynumber: 2.2 Consensus size: 28
48451674 AATTTATAAA
*
48451684 ATTTTAA-AT-TAATAATGATAAAATTAC
1 ATTTTAATATCTAA-AATAATAAAATTAC
* *
48451711 ATTTTAATCTCTAAAATAATAAAATTAT
1 ATTTTAATATCTAAAATAATAAAATTAC
48451739 ATTTT
1 ATTTT
48451744 TACAATAATA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
27 7 0.25
28 18 0.64
29 3 0.11
ACGTcount: A:0.48, C:0.05, G:0.02, T:0.45
Consensus pattern (28 bp):
ATTTTAATATCTAAAATAATAAAATTAC
Found at i:48452045 original size:18 final size:18
Alignment explanation
Indices: 48452014--48452051 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
48452004 AAGCAATTTC
*
48452014 TTTTCTTTT-TTTTTCTT
1 TTTTCTTTTCTTTTGCTT
48452031 TTTTACTTTTCTTTTGCTT
1 TTTT-CTTTTCTTTTGCTT
48452050 TT
1 TT
48452052 ATGGAAATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 4 0.22
18 5 0.28
19 9 0.50
ACGTcount: A:0.03, C:0.13, G:0.03, T:0.82
Consensus pattern (18 bp):
TTTTCTTTTCTTTTGCTT
Found at i:48456208 original size:29 final size:29
Alignment explanation
Indices: 48456171--48456250 Score: 151
Period size: 29 Copynumber: 2.8 Consensus size: 29
48456161 TTTTTAACCG
*
48456171 TTAATCGAACCGAAATTTTTTCAAAAAAA
1 TTAACCGAACCGAAATTTTTTCAAAAAAA
48456200 TTAACCGAACCGAAATTTTTTCAAAAAAA
1 TTAACCGAACCGAAATTTTTTCAAAAAAA
48456229 TTAACCGAACCGAAATTTTTTC
1 TTAACCGAACCGAAATTTTTTC
48456251 GGTTAATTCG
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
29 50 1.00
ACGTcount: A:0.44, C:0.17, G:0.07, T:0.31
Consensus pattern (29 bp):
TTAACCGAACCGAAATTTTTTCAAAAAAA
Found at i:48456327 original size:9 final size:9
Alignment explanation
Indices: 48456313--48456390 Score: 102
Period size: 9 Copynumber: 8.7 Consensus size: 9
48456303 TTTGGTTAAA
48456313 AATTAACCG
1 AATTAACCG
*
48456322 AATTAACCA
1 AATTAACCG
48456331 AATTAACCG
1 AATTAACCG
* *
48456340 AATTACCCA
1 AATTAACCG
48456349 AATTAACCG
1 AATTAACCG
*
48456358 AATTACCCG
1 AATTAACCG
*
48456367 AATTACCCG
1 AATTAACCG
*
48456376 AATTAACCT
1 AATTAACCG
48456385 AATTAA
1 AATTAA
48456391 ATCATACATA
Statistics
Matches: 60, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
9 60 1.00
ACGTcount: A:0.45, C:0.24, G:0.06, T:0.24
Consensus pattern (9 bp):
AATTAACCG
Found at i:48456335 original size:18 final size:18
Alignment explanation
Indices: 48456312--48456390 Score: 113
Period size: 18 Copynumber: 4.4 Consensus size: 18
48456302 TTTTGGTTAA
48456312 AAATTAACCGAATTAACC
1 AAATTAACCGAATTAACC
*
48456330 AAATTAACCGAATTACCC
1 AAATTAACCGAATTAACC
*
48456348 AAATTAACCGAATTACCC
1 AAATTAACCGAATTAACC
* *
48456366 GAATTACCCGAATTAACC
1 AAATTAACCGAATTAACC
*
48456384 TAATTAA
1 AAATTAA
48456391 ATCATACATA
Statistics
Matches: 55, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 55 1.00
ACGTcount: A:0.46, C:0.24, G:0.06, T:0.24
Consensus pattern (18 bp):
AAATTAACCGAATTAACC
Found at i:48456462 original size:20 final size:20
Alignment explanation
Indices: 48456433--48456476 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
48456423 TATATTTTAG
48456433 TTTTAGTTTTAGTT-TTAGAA
1 TTTTAGTTTTAGTTATTA-AA
* *
48456453 TTTTATTTTTATTTATTAAA
1 TTTTAGTTTTAGTTATTAAA
48456473 TTTT
1 TTTT
48456477 TTGTAATTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 18 0.86
21 3 0.14
ACGTcount: A:0.25, C:0.00, G:0.07, T:0.68
Consensus pattern (20 bp):
TTTTAGTTTTAGTTATTAAA
Found at i:48458625 original size:13 final size:14
Alignment explanation
Indices: 48458590--48458627 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
48458580 CCAGAAAAGT
48458590 AAGTCATTTTCTAG
1 AAGTCATTTTCTAG
* *
48458604 AAATCATTTTC-CG
1 AAGTCATTTTCTAG
48458617 AAGTCATTTTC
1 AAGTCATTTTC
48458628 AGTAAAACAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
13 11 0.52
14 10 0.48
ACGTcount: A:0.29, C:0.18, G:0.11, T:0.42
Consensus pattern (14 bp):
AAGTCATTTTCTAG
Found at i:48479107 original size:15 final size:14
Alignment explanation
Indices: 48479080--48479110 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
48479070 GGGCTCATAA
48479080 AAAAATAATAAACC
1 AAAAATAATAAACC
*
48479094 AAAAATAATAAAAC
1 AAAAATAATAAACC
48479108 AAA
1 AAA
48479111 GTCCAAAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.77, C:0.10, G:0.00, T:0.13
Consensus pattern (14 bp):
AAAAATAATAAACC
Found at i:48479241 original size:19 final size:19
Alignment explanation
Indices: 48479212--48479265 Score: 90
Period size: 19 Copynumber: 2.8 Consensus size: 19
48479202 AATTTTCAAG
*
48479212 GATATACAATCTTAGATAT
1 GATATGCAATCTTAGATAT
*
48479231 GATATGTAATCTTAGATAT
1 GATATGCAATCTTAGATAT
48479250 GATATGCAATCTTAGA
1 GATATGCAATCTTAGA
48479266 AGATATGATT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 32 1.00
ACGTcount: A:0.39, C:0.09, G:0.15, T:0.37
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:48479291 original size:22 final size:22
Alignment explanation
Indices: 48479244--48479288 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 22
48479234 ATGTAATCTT
*
48479244 AGATATGATATGCAATCTTAGA
1 AGATATGATATGCAATATTAGA
* *
48479266 AGATATGATTTTGTAATATTAGA
1 AGATATGA-TATGCAATATTAGA
48479289 GATTTAATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 8 0.42
23 11 0.58
ACGTcount: A:0.40, C:0.04, G:0.18, T:0.38
Consensus pattern (22 bp):
AGATATGATATGCAATATTAGA
Found at i:48479516 original size:23 final size:23
Alignment explanation
Indices: 48479472--48479516 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
48479462 TCTTATTTTG
* *
48479472 TTGATTTGTGTATAATTTATTTA
1 TTGATTTGTATATAATTGATTTA
**
48479495 TTGATTTGTATATTGTTGATTT
1 TTGATTTGTATATAATTGATTT
48479517 CAAATCTCTT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.22, C:0.00, G:0.16, T:0.62
Consensus pattern (23 bp):
TTGATTTGTATATAATTGATTTA
Found at i:48479562 original size:15 final size:16
Alignment explanation
Indices: 48479536--48479568 Score: 59
Period size: 15 Copynumber: 2.1 Consensus size: 16
48479526 TTTTTCCTTA
48479536 TTATTCATTTTCAAAT
1 TTATTCATTTTCAAAT
48479552 TTATT-ATTTTCAAAT
1 TTATTCATTTTCAAAT
48479567 TT
1 TT
48479569 GTTTACATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 12 0.71
16 5 0.29
ACGTcount: A:0.30, C:0.09, G:0.00, T:0.61
Consensus pattern (16 bp):
TTATTCATTTTCAAAT
Found at i:48484933 original size:14 final size:15
Alignment explanation
Indices: 48484907--48484939 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
48484897 TCCCAAGTTG
48484907 GGAAGGACCTTATGT
1 GGAAGGACCTTATGT
*
48484922 GGAAGG-CCTTATTT
1 GGAAGGACCTTATGT
48484936 GGAA
1 GGAA
48484940 AAGCGCCGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 11 0.65
15 6 0.35
ACGTcount: A:0.27, C:0.12, G:0.33, T:0.27
Consensus pattern (15 bp):
GGAAGGACCTTATGT
Found at i:48486409 original size:88 final size:88
Alignment explanation
Indices: 48486260--48486738 Score: 681
Period size: 88 Copynumber: 5.4 Consensus size: 88
48486250 GTGAAGATAA
* * *
48486260 CAGATCTTGCCTTCCTGCACCGATAGCGAAGCAGATCGAAGACACCAACCTTGCTTCCCTGGGTT
1 CAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTT
* *
48486325 GTAGCAGG-CCAGGTTAAAAATAG
66 GCAGC-GGAGCAGGTTAAAAATAG
* * * *
48486348 CAGATCTTACATTCCTGCACCGACAGCGAAACAGATCGAAGACACTAGCCTTGCCTCCCTGGGTT
1 CAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTT
48486413 GCAGCGGAGCAGGTTAAAAATAG
66 GCAGCGGAGCAGGTTAAAAATAG
* * *
48486436 CAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGTCTTGCCACCCTAGGTT
1 CAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTT
48486501 GCAGCGGAGCAGGTTAAAAATAG
66 GCAGCGGAGCAGGTTAAAAATAG
* * * * * * * *
48486524 GAGATCTTGCCTTCCTACACCGACAGCAAAGCAGATCAAAGACACTAGACTTGCCTCCCTAGTTT
1 CAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTT
*
48486589 GTAGCGGAGCAGGTTAAAAATAG
66 GCAGCGGAGCAGGTTAAAAATAG
* * * *
48486612 CAAATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAACCTTTCCTCCCTGGATT
1 CAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTT
48486677 GCAGCGGAGCAGGTTAAAAATAG
66 GCAGCGGAGCAGGTTAAAAATAG
* * * *
48486700 CAGATCTTGCCTTCTTGCACCGGCAGCAAAGCAAATCGA
1 CAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGA
48486739 TGACTCCATC
Statistics
Matches: 348, Mismatches: 42, Indels: 2
0.89 0.11 0.01
Matches are distributed among these distances:
87 2 0.01
88 346 0.99
ACGTcount: A:0.29, C:0.28, G:0.23, T:0.20
Consensus pattern (88 bp):
CAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTT
GCAGCGGAGCAGGTTAAAAATAG
Found at i:48486447 original size:44 final size:44
Alignment explanation
Indices: 48486397--48486711 Score: 172
Period size: 44 Copynumber: 7.2 Consensus size: 44
48486387 AGACACTAGC
*
48486397 CTTGCCTCCCTGGGTTGCAGCGGAGCAGGTTAAAAATAGCAGAT
1 CTTGCCTCCCTGGATTGCAGCGGAGCAGGTTAAAAATAGCAGAT
* * ** * * ** * * *
48486441 CTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAG-T
1 CTTGCCTCCCTGGATTG-CAGCGGAGCAGGTTAAAAATAGCAGAT
* *
48486485 CTTGCCACCCTAGG-TTGCAGCGGAGCAGGTTAAAAATAGGAGAT
1 CTTGCCTCCCT-GGATTGCAGCGGAGCAGGTTAAAAATAGCAGAT
* ** ** ** * * * *
48486529 CTTGCCTTCCTACACCGACAGCAAAGCAGATCAAAGACA-CTAGA-
1 CTTGCCTCCCTGGATTG-CAGCGGAGCAGGTTAAAAATAGC-AGAT
* * * *
48486573 CTTGCCTCCCTAGTTTGTAGCGGAGCAGGTTAAAAATAGCAAAT
1 CTTGCCTCCCTGGATTGCAGCGGAGCAGGTTAAAAATAGCAGAT
* * ** * * ** * * * *
48486617 CTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCA-AC
1 CTTGCCTCCCTGGATTG-CAGCGGAGCAGGTTAAAAATAGCAGAT
*
48486661 CTTTCCTCCCTGGATTGCAGCGGAGCAGGTTAAAAATAGCAGAT
1 CTTGCCTCCCTGGATTGCAGCGGAGCAGGTTAAAAATAGCAGAT
48486705 CTTGCCT
1 CTTGCCT
48486712 TCTTGCACCG
Statistics
Matches: 181, Mismatches: 80, Indels: 20
0.64 0.28 0.07
Matches are distributed among these distances:
43 50 0.28
44 78 0.43
45 53 0.29
ACGTcount: A:0.29, C:0.27, G:0.23, T:0.21
Consensus pattern (44 bp):
CTTGCCTCCCTGGATTGCAGCGGAGCAGGTTAAAAATAGCAGAT
Found at i:48486815 original size:44 final size:44
Alignment explanation
Indices: 48486749--48486914 Score: 246
Period size: 44 Copynumber: 3.8 Consensus size: 44
48486739 TGACTCCATC
*
48486749 CCTATCTCCCTGGTCAGTAGTGGAATAGGTTGAAGATTGT-AAGT
1 CCTATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGTGAA-T
*
48486793 CCTATCTCCCTGGTCAGCAGTGGAATAGGTTGAAAATTGTGAAT
1 CCTATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGTGAAT
*
48486837 CCTATCTCCTTGGTCAGCAGTGGAATAGGTTGAAGATTGTGAAT
1 CCTATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGTGAAT
* * *
48486881 CCCATCTCCCTGAG-CAACAGTGGAGTAGGTTGAA
1 CCTATCTCCCTG-GTCAGCAGTGGAATAGGTTGAA
48486915 AATACCAGAT
Statistics
Matches: 112, Mismatches: 8, Indels: 4
0.90 0.06 0.03
Matches are distributed among these distances:
44 109 0.97
45 3 0.03
ACGTcount: A:0.26, C:0.19, G:0.27, T:0.29
Consensus pattern (44 bp):
CCTATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGTGAAT
Found at i:48487030 original size:50 final size:50
Alignment explanation
Indices: 48486976--48487073 Score: 124
Period size: 50 Copynumber: 2.0 Consensus size: 50
48486966 AGTCTTATCG
* *
48486976 CCTTGACGTTGCAATGGAAAAGATTGAAGCCACAATGGTGAATCTTATTT
1 CCTTGACGTTGCAACGGAAAAGATTGAAGCCACAACGGTGAATCTTATTT
* * * ** *
48487026 CCTTGGCGTTGTAGCGGAGCAGATTGAAGCCACGACGGTGAATCTTAT
1 CCTTGACGTTGCAACGGAAAAGATTGAAGCCACAACGGTGAATCTTAT
48487074 CTCCCTGGTG
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
50 40 1.00
ACGTcount: A:0.28, C:0.18, G:0.27, T:0.28
Consensus pattern (50 bp):
CCTTGACGTTGCAACGGAAAAGATTGAAGCCACAACGGTGAATCTTATTT
Found at i:48487333 original size:44 final size:43
Alignment explanation
Indices: 48487278--48487748 Score: 233
Period size: 44 Copynumber: 10.9 Consensus size: 43
48487268 GAAGATGGCG
*
48487278 AATCTTATCTCCCTGAAGTTGCAGTGGGGCAGATTAAAGCCAAT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAG-CAAT
* * * * *
48487322 AATCCTATCTCCCTGAAGTCGCAGTGAAGCGGATTAAAATCACA-
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATT-AAAGCA-AT
* * * * * *
48487366 GATCTTATCTCTCTGAAGTTGCAG-AGAGTAGA-T--CGCATCT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCA-AT
* * * *
48487406 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACT-AAGTAAGC
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCAA-T
* * * * * *
48487449 AAGCCTTATC-CTCCT-AAATTGTAGT-GAGGCAAACTGAAGATGGC--G
1 AA-TCTTATCTC-CCTGAAGTTGCAGTGGA-GCAGA-TTAA-A--GCAAT
*
48487494 AATCTTATCTCCCTGAAGTTGTAGTGGAGCAGATTAAAGCCAAT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAG-CAAT
* ** *
48487538 AATCCTATCTCCCTGAAGTTGCAGTGGAGTGGATTAAAATCACA-
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATT-AAAGCA-AT
* * *
48487582 GATCTTATCTCTCTGAAGTTGCAG-AGAGCAGATT---GC-AT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCAAT
** * * *
48487620 CGGGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACCT-AAGAAAGCG
1 --AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGA-TTAAAGCAA--T
* * * *
48487667 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTCAAGAAAT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCAAT
* * *
48487710 CAAGTCTTATC-CCCTGAAATTGCAGTGGGGCAGACTAAA
1 -AA-TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAA
48487749 TAAACAAATT
Statistics
Matches: 326, Mismatches: 65, Indels: 72
0.70 0.14 0.16
Matches are distributed among these distances:
37 1 0.00
39 3 0.01
40 43 0.13
41 14 0.04
42 6 0.02
43 28 0.09
44 156 0.48
45 71 0.22
46 3 0.01
48 1 0.00
ACGTcount: A:0.30, C:0.21, G:0.23, T:0.26
Consensus pattern (43 bp):
AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCAAT
Found at i:48487639 original size:40 final size:44
Alignment explanation
Indices: 48487623--48487747 Score: 189
Period size: 45 Copynumber: 2.8 Consensus size: 44
48487613 ATTGCATCGG
48487623 GTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACCTAAGAAAGCGA
1 GTCTTATCTCCCTGAAGTTGCAGTGGAGCAGA-CTAAGAAAGCGA
* *
48487668 GTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTCAAGAAATCAA
1 GTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACT-AAGAAAGCGA
* *
48487713 GTCTTATC-CCCTGAAATTGCAGTGGGGCAGACTAA
1 GTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAA
48487748 ATAAACAAAT
Statistics
Matches: 75, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
43 2 0.03
44 25 0.33
45 48 0.64
ACGTcount: A:0.29, C:0.22, G:0.25, T:0.24
Consensus pattern (44 bp):
GTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGAAAGCGA
Found at i:48487639 original size:216 final size:217
Alignment explanation
Indices: 48487265--48487675 Score: 707
Period size: 216 Copynumber: 1.9 Consensus size: 217
48487255 AATTTAAAAG
*
48487265 ACTGAAGATGGCGAATCTTATCTCCCTGAAGTTGCAGTGGGGCAGATTAAAGCCAATAATCCTAT
1 ACTGAAGATGGCGAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAATAATCCTAT
*
48487330 CTCCCTGAAGTCGCAGTGAAGCGGATTAAAATCACAGATCTTATCTCTCTGAAGTTGCAGAGAGT
66 CTCCCTGAAGTCGCAGTGAAGCGGATTAAAATCACAGATCTTATCTCTCTGAAGTTGCAGAGAGC
* *
48487395 AGATCGCATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGA-CTAAGTAAGCAAGCCTTATC
131 AGATCGCATCGAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACCTAAGAAAGCAAGCCTTATC
48487459 CTCCTAAATTGTAGTGAGGCAA
196 CTCCTAAATTGTAGTGAGGCAA
*
48487481 ACTGAAGATGGCGAATCTTATCTCCCTGAAGTTGTAGTGGAGCAGATTAAAGCCAATAATCCTAT
1 ACTGAAGATGGCGAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAATAATCCTAT
* * *
48487546 CTCCCTGAAGTTGCAGTGGAGTGGATTAAAATCACAGATCTTATCTCTCTGAAGTTGCAGAGAGC
66 CTCCCTGAAGTCGCAGTGAAGCGGATTAAAATCACAGATCTTATCTCTCTGAAGTTGCAGAGAGC
* * * *
48487611 AGATTGCATCGGGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACCTAAGAAAGCGAGTCTTATC
131 AGATCGCATCGAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACCTAAGAAAGCAAGCCTTATC
48487676 TCCCTGAAGT
Statistics
Matches: 182, Mismatches: 12, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
216 165 0.91
217 17 0.09
ACGTcount: A:0.29, C:0.21, G:0.23, T:0.27
Consensus pattern (217 bp):
ACTGAAGATGGCGAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAATAATCCTAT
CTCCCTGAAGTCGCAGTGAAGCGGATTAAAATCACAGATCTTATCTCTCTGAAGTTGCAGAGAGC
AGATCGCATCGAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACCTAAGAAAGCAAGCCTTATC
CTCCTAAATTGTAGTGAGGCAA
Found at i:48487674 original size:45 final size:44
Alignment explanation
Indices: 48487406--48487747 Score: 251
Period size: 44 Copynumber: 7.8 Consensus size: 44
48487396 GATCGCATCT
* *
48487406 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCA
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGAAAGCG
* * * * **
48487450 AGCCTTATC-CTCCT-AAATTGTAGT-GAGGCAAACTGAAGATGGCG
1 AGTCTTATCTC-CCTGAAGTTGCAGTGGA-GCAGACT-AAGAAAGCG
* * * * *
48487494 AATCTTATCTCCCTGAAGTTGTAGTGGAGCAGATTAAAGCCAA--T
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACT-AAG-AAAGCG
* * ** *
48487538 AATCCTATCTCCCTGAAGTTGCAGTGGAGTGGATTAA-AATCA-C-
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGAA--AGCG
* * * * *
48487581 AGATCTTATCTCTCTGAAGTTGCAG-AGAGCAGA-T-TG-CATCG
1 AG-TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGAAAGCG
*
48487622 GGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACCTAAGAAAGCG
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGA-CTAAGAAAGCG
* *
48487667 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTCAAGAAATCA
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACT-AAGAAAGCG
* *
48487712 AGTCTTATC-CCCTGAAATTGCAGTGGGGCAGACTAA
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAA
48487748 ATAAACAAAT
Statistics
Matches: 236, Mismatches: 42, Indels: 41
0.74 0.13 0.13
Matches are distributed among these distances:
39 1 0.00
40 22 0.09
41 9 0.04
42 3 0.01
43 27 0.11
44 103 0.44
45 69 0.29
46 2 0.01
ACGTcount: A:0.29, C:0.21, G:0.24, T:0.26
Consensus pattern (44 bp):
AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGAAAGCG
Found at i:48487781 original size:44 final size:45
Alignment explanation
Indices: 48487623--48487783 Score: 152
Period size: 45 Copynumber: 3.6 Consensus size: 45
48487613 ATTGCATCGG
* * * *
48487623 GTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACCT-AAGAAAGCGA
1 GTCTCATCTCCCTAAAGTTGCAGTGGAGCAGA-CTAAAGAAATCAA
* * *
48487668 GTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTCAAGAAATCAA
1 GTCTCATCTCCCTAAAGTTGCAGTGGAGCAGACTAAAGAAATCAA
* * *
48487713 GTCTTATC-CCCTGAAA-TTGCAGTGGGGCAGACTAAATAAA-CAA
1 GTCTCATCTCCCT-AAAGTTGCAGTGGAGCAGACTAAAGAAATCAA
* *
48487756 AT-TCCATCTCCCTAAAGTTGTAGTGGAG
1 GTCT-CATCTCCCTAAAGTTGCAGTGGAG
48487784 TGGATTAGAA
Statistics
Matches: 101, Mismatches: 10, Indels: 11
0.83 0.08 0.09
Matches are distributed among these distances:
42 1 0.01
43 10 0.10
44 40 0.40
45 50 0.50
ACGTcount: A:0.30, C:0.22, G:0.23, T:0.25
Consensus pattern (45 bp):
GTCTCATCTCCCTAAAGTTGCAGTGGAGCAGACTAAAGAAATCAA
Found at i:48488190 original size:15 final size:14
Alignment explanation
Indices: 48488163--48488193 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
48488153 GGGCTCATAA
48488163 AAAAATAATAAACC
1 AAAAATAATAAACC
*
48488177 AAAAATAATAAAAC
1 AAAAATAATAAACC
48488191 AAA
1 AAA
48488194 GTCCAAAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.77, C:0.10, G:0.00, T:0.13
Consensus pattern (14 bp):
AAAAATAATAAACC
Found at i:48488324 original size:19 final size:19
Alignment explanation
Indices: 48488295--48488348 Score: 90
Period size: 19 Copynumber: 2.8 Consensus size: 19
48488285 AATTTTCAAG
*
48488295 GATATACAATCTTAGATAT
1 GATATGCAATCTTAGATAT
*
48488314 GATATGTAATCTTAGATAT
1 GATATGCAATCTTAGATAT
48488333 GATATGCAATCTTAGA
1 GATATGCAATCTTAGA
48488349 AGATATGATT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 32 1.00
ACGTcount: A:0.39, C:0.09, G:0.15, T:0.37
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:48488374 original size:22 final size:22
Alignment explanation
Indices: 48488327--48488371 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 22
48488317 ATGTAATCTT
*
48488327 AGATATGATATGCAATCTTAGA
1 AGATATGATATGCAATATTAGA
* *
48488349 AGATATGATTTTGTAATATTAGA
1 AGATATGA-TATGCAATATTAGA
48488372 GATTTAATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 8 0.42
23 11 0.58
ACGTcount: A:0.40, C:0.04, G:0.18, T:0.38
Consensus pattern (22 bp):
AGATATGATATGCAATATTAGA
Found at i:48488597 original size:23 final size:23
Alignment explanation
Indices: 48488553--48488597 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
48488543 TCTTATTTTG
* *
48488553 TTGATTTGTGTATAATTTATTTA
1 TTGATTTGTATATAATTGATTTA
**
48488576 TTGATTTGTATATTGTTGATTT
1 TTGATTTGTATATAATTGATTT
48488598 CAAATCTCTT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.22, C:0.00, G:0.16, T:0.62
Consensus pattern (23 bp):
TTGATTTGTATATAATTGATTTA
Found at i:48488642 original size:15 final size:16
Alignment explanation
Indices: 48488616--48488648 Score: 59
Period size: 15 Copynumber: 2.1 Consensus size: 16
48488606 TTTTTCCTTA
48488616 TTATTCATTTTCAAAT
1 TTATTCATTTTCAAAT
48488632 TTATT-ATTTTCAAAT
1 TTATTCATTTTCAAAT
48488647 TT
1 TT
48488649 GTTTACATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 12 0.71
16 5 0.29
ACGTcount: A:0.30, C:0.09, G:0.00, T:0.61
Consensus pattern (16 bp):
TTATTCATTTTCAAAT
Found at i:48490445 original size:20 final size:21
Alignment explanation
Indices: 48490420--48490469 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 21
48490410 TAAAAGTAAC
*
48490420 ATACAAATGAA-AGTATAGAT
1 ATACAAATGAATAATATAGAT
48490440 ATACAAAT-AATAATATAGAT
1 ATACAAATGAATAATATAGAT
*
48490460 ATATAAATGA
1 ATACAAATGA
48490470 TGAAAGTAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
19 2 0.08
20 23 0.88
21 1 0.04
ACGTcount: A:0.58, C:0.04, G:0.10, T:0.28
Consensus pattern (21 bp):
ATACAAATGAATAATATAGAT
Found at i:48497007 original size:19 final size:20
Alignment explanation
Indices: 48496977--48497015 Score: 71
Period size: 19 Copynumber: 2.0 Consensus size: 20
48496967 TTTCTTCCCA
48496977 TTTTCTTCTTTCTTTCATTT
1 TTTTCTTCTTTCTTTCATTT
48496997 TTTTCTT-TTTCTTTCATTT
1 TTTTCTTCTTTCTTTCATTT
48497016 GGTTTTCTAC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 12 0.63
20 7 0.37
ACGTcount: A:0.05, C:0.18, G:0.00, T:0.77
Consensus pattern (20 bp):
TTTTCTTCTTTCTTTCATTT
Found at i:48501630 original size:17 final size:18
Alignment explanation
Indices: 48501601--48501635 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
48501591 TTTTTACTCG
*
48501601 GTTTTTGATAATTTTTAC
1 GTTTTTGATAATTGTTAC
48501619 GTTTTTGA-AATTGTTAC
1 GTTTTTGATAATTGTTAC
48501636 TTCAAATACT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.23, C:0.06, G:0.14, T:0.57
Consensus pattern (18 bp):
GTTTTTGATAATTGTTAC
Found at i:48502418 original size:44 final size:43
Alignment explanation
Indices: 48502354--48502484 Score: 142
Period size: 43 Copynumber: 3.0 Consensus size: 43
48502344 ACATAGAATT
* *
48502354 TCGATATGAGATTTCGTGTAAGACCACATCTGGGACGATGGCA
1 TCGATTTGAGATTTCGTGTAAGACCACGTCTGGGACGATGGCA
48502397 TCGATTTGAGACTTTCGTGTAAGACC-CTGTCTGGGAC-AGTGGCA
1 TCGATTTGAGA-TTTCGTGTAAGACCAC-GTCTGGGACGA-TGGCA
* * * * *
48502441 TCGATATT-TGATTACATGTAAGACCATGTCTGGGACGTTGGCA
1 TCGAT-TTGAGATTTCGTGTAAGACCACGTCTGGGACGATGGCA
48502484 T
1 T
48502485 TGTACGAGCT
Statistics
Matches: 75, Mismatches: 7, Indels: 12
0.80 0.07 0.13
Matches are distributed among these distances:
43 39 0.52
44 34 0.45
45 2 0.03
ACGTcount: A:0.24, C:0.18, G:0.27, T:0.30
Consensus pattern (43 bp):
TCGATTTGAGATTTCGTGTAAGACCACGTCTGGGACGATGGCA
Found at i:48504470 original size:38 final size:41
Alignment explanation
Indices: 48504426--48504513 Score: 101
Period size: 43 Copynumber: 2.2 Consensus size: 41
48504416 TAATATTAAT
*
48504426 TTAATAT-AATACTTA-T-CAAGATAAATATTAGATTAAAC
1 TTAATATAAATACTTACTACAAGATAAATATTAAATTAAAC
* * *
48504464 TTAATATTAAATATTTATCTACAAGATAAATATTAAATTTAAT
1 TTAATA-TAAATACTTA-CTACAAGATAAATATTAAATTAAAC
48504507 TTAATAT
1 TTAATAT
48504514 TAAGATAATC
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
38 6 0.15
39 1 0.02
40 7 0.17
42 2 0.05
43 25 0.61
ACGTcount: A:0.49, C:0.06, G:0.03, T:0.42
Consensus pattern (41 bp):
TTAATATAAATACTTACTACAAGATAAATATTAAATTAAAC
Found at i:48526457 original size:17 final size:20
Alignment explanation
Indices: 48526417--48526457 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
48526407 ACTTAAGAAG
*
48526417 TCTTCATGACTCACCTCTCT
1 TCTTTATGACTCACCTCTCT
48526437 TCTTTATGACTCACCTCTCT
1 TCTTTATGACTCACCTCTCT
48526457 T
1 T
48526458 TCCTAGTATC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.15, C:0.37, G:0.05, T:0.44
Consensus pattern (20 bp):
TCTTTATGACTCACCTCTCT
Found at i:48533810 original size:48 final size:49
Alignment explanation
Indices: 48533737--48533830 Score: 129
Period size: 48 Copynumber: 1.9 Consensus size: 49
48533727 AATATACCAA
* *
48533737 TATTTGAAAAAAAAATTGGTTCTGGCCATGTA-ATGGCCGGCACCAGAGC
1 TATTTGAAAAAAAAATTGGTGCTGGCCA-GTAGATGGCCAGCACCAGAGC
* *
48533786 TATTT-AAAAAAAATTTGGTGCTGGCCAGTAGATGGCTAGCACCAG
1 TATTTGAAAAAAAAATTGGTGCTGGCCAGTAGATGGCCAGCACCAG
48533831 GTACATATTT
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
47 3 0.08
48 32 0.80
49 5 0.12
ACGTcount: A:0.33, C:0.17, G:0.24, T:0.26
Consensus pattern (49 bp):
TATTTGAAAAAAAAATTGGTGCTGGCCAGTAGATGGCCAGCACCAGAGC
Found at i:48536110 original size:90 final size:90
Alignment explanation
Indices: 48535762--48536087 Score: 456
Period size: 90 Copynumber: 3.6 Consensus size: 90
48535752 ATTCTAGAAT
* * * * * * *
48535762 ATTAATACACAAAAATATAAAATTCAAAC-AAAAATAATACACACTAAATTAAATTTAGACACCC
1 ATTAATACACGAAAATTTTAAATTCAAACTATATATAATACAGACTAAATTAAATTTAAACACCC
48535826 AACAAACTACAAACAGATGGGTAAA
66 AACAAACTACAAACAGATGGGTAAA
* * ** *
48535851 ATTAATACATGAAAATTTTAAATTCTAACTATATATAATATGGGCTAAATTAAATTTAAACACCC
1 ATTAATACACGAAAATTTTAAATTCAAACTATATATAATACAGACTAAATTAAATTTAAACACCC
* *
48535916 AACAAACTAAAAACAGATGGATAAA
66 AACAAACTACAAACAGATGGGTAAA
* * * *
48535941 ATTAGTGCACGAAATTTTTAAATTCAAACTATATATAACACAGACTAAATTAAATTTAAACACCC
1 ATTAATACACGAAAATTTTAAATTCAAACTATATATAATACAGACTAAATTAAATTTAAACACCC
48536006 AACAAACTACAAACAGATGGGTAAA
66 AACAAACTACAAACAGATGGGTAAA
* * *
48536031 ATTAATACACGAAAATTTTAAATTCAAACTACATATAATACGGGCTAAATTAAATTT
1 ATTAATACACGAAAATTTTAAATTCAAACTATATATAATACAGACTAAATTAAATTT
48536088 GGAGATACAA
Statistics
Matches: 204, Mismatches: 32, Indels: 1
0.86 0.14 0.00
Matches are distributed among these distances:
89 24 0.12
90 180 0.88
ACGTcount: A:0.52, C:0.15, G:0.07, T:0.26
Consensus pattern (90 bp):
ATTAATACACGAAAATTTTAAATTCAAACTATATATAATACAGACTAAATTAAATTTAAACACCC
AACAAACTACAAACAGATGGGTAAA
Found at i:48536175 original size:180 final size:177
Alignment explanation
Indices: 48535719--48536178 Score: 530
Period size: 180 Copynumber: 2.6 Consensus size: 177
48535709 AGTACACAAC
* * * *
48535719 AAATGAAATTTACAGATACAATAAAATACAAACATTCT-AGAATATTAATACACAAAAATATAAA
1 AAATTAAATTTAAAGATACAAAAAAATACAAACATTCTAAGAA-ATTAATACACGAAAATATAAA
* *
48535783 ATTCAAAC-AAAAATAATACACACTAAATTAAATTTAGACACCCAACAAACTACAAACAGATGGG
65 ATTCAAACTAAATATAA-ACA-ACTAAATTAAATTTAAACACCCAACAAACTACAAACAGATGGG
* * * *
48535847 TAAAATTAATACATGAAAATTTTAAATTCTAACTATATATAATATGGGCT
128 TAAAATTAATACACGAAAATTTTAAATTCAAACTACATATAATACGGGCT
* ** * * * * ** * * * * *
48535897 AAATTAAATTTAAACACCCAACAAACTAAAAACAGATGGATA-AAATTAGTGCACGAAATTTTTA
1 AAATTAAATTTAAAGATACAAAAAAATACAAACA-TTCTA-AGAAATTAATACACGAAAATATAA
*
48535961 AATTCAAACTATATATAACACAGACTAAATTAAATTTAAACACCCAACAAACTACAAACAGATGG
64 AATTCAAACTAAATATAA-ACA-ACTAAATTAAATTTAAACACCCAACAAACTACAAACAGATGG
48536026 GTAAAATTAATACACGAAAATTTTAAATTCAAACTACATATAATACGGGCT
127 GTAAAATTAATACACGAAAATTTTAAATTCAAACTACATATAATACGGGCT
**
48536077 AAATTAAATTTGGAGATACAAAAAAATACAAACATTCTAAGAAATTAATACACGAAAATATAAAA
1 AAATTAAATTTAAAGATACAAAAAAATACAAACATTCTAAGAAATTAATACACGAAAATATAAAA
* * * *
48536142 ATGAAACCTTAAATCCTAAACAACTACATTAAATTTA
66 TTCAAA-C-TAAAT-ATAAACAACTAAATTAAATTTA
48536179 CATATATAAA
Statistics
Matches: 227, Mismatches: 47, Indels: 14
0.79 0.16 0.05
Matches are distributed among these distances:
178 27 0.12
179 49 0.22
180 140 0.62
181 8 0.04
182 3 0.01
ACGTcount: A:0.53, C:0.14, G:0.07, T:0.26
Consensus pattern (177 bp):
AAATTAAATTTAAAGATACAAAAAAATACAAACATTCTAAGAAATTAATACACGAAAATATAAAA
TTCAAACTAAATATAAACAACTAAATTAAATTTAAACACCCAACAAACTACAAACAGATGGGTAA
AATTAATACACGAAAATTTTAAATTCAAACTACATATAATACGGGCT
Found at i:48537414 original size:12 final size:12
Alignment explanation
Indices: 48537397--48537442 Score: 58
Period size: 12 Copynumber: 3.7 Consensus size: 12
48537387 AATATAATAG
48537397 TTAATTTTAGTT
1 TTAATTTTAGTT
48537409 TTAATTTTAAGTTT
1 TTAATTTT-AG-TT
48537423 TTAATTTTTAGTT
1 TTAA-TTTTAGTT
48537436 TT-ATTTT
1 TTAATTTT
48537443 TCACTTTCCC
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
11 4 0.13
12 9 0.29
13 6 0.19
14 8 0.26
15 4 0.13
ACGTcount: A:0.24, C:0.00, G:0.07, T:0.70
Consensus pattern (12 bp):
TTAATTTTAGTT
Found at i:48537426 original size:14 final size:13
Alignment explanation
Indices: 48537397--48537437 Score: 57
Period size: 14 Copynumber: 3.1 Consensus size: 13
48537387 AATATAATAG
48537397 TTAATTTTAG-TT
1 TTAATTTTAGTTT
48537409 TTAATTTTAAGTTT
1 TTAATTTT-AGTTT
48537423 TTAATTTTTAGTTT
1 TTAA-TTTTAGTTT
48537437 T
1 T
48537438 ATTTTTCACT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
12 8 0.31
13 2 0.08
14 12 0.46
15 4 0.15
ACGTcount: A:0.24, C:0.00, G:0.07, T:0.68
Consensus pattern (13 bp):
TTAATTTTAGTTT
Found at i:48538793 original size:23 final size:24
Alignment explanation
Indices: 48538746--48538791 Score: 76
Period size: 24 Copynumber: 1.9 Consensus size: 24
48538736 AAAAAATATT
48538746 AAATATATATATTTTTTATTTTTA
1 AAATATATATATTTTTTATTTTTA
48538770 AAATATA-ATAGTTTTTTATTTT
1 AAATATATATA-TTTTTTATTTT
48538792 AAGTTTATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
23 3 0.14
24 18 0.86
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (24 bp):
AAATATATATATTTTTTATTTTTA
Found at i:48538921 original size:59 final size:59
Alignment explanation
Indices: 48538858--48539027 Score: 313
Period size: 59 Copynumber: 2.9 Consensus size: 59
48538848 TCAAGTTTGT
*
48538858 TTTACTAATCAAATGTTAGATTTTGTTACAACAATTAATACAATTAATAATTTGATAAA
1 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATAATTTGATAAA
48538917 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATAATTTGATAAA
1 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATAATTTGATAAA
* *
48538976 TTTACTAATCAAATGTTAGATTTTATTATAACAATTAATACAATTAACAATT
1 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATAATT
48539028 AATAATTTGA
Statistics
Matches: 108, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
59 108 1.00
ACGTcount: A:0.45, C:0.09, G:0.05, T:0.41
Consensus pattern (59 bp):
TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATAATTTGATAAA
Found at i:48539059 original size:16 final size:16
Alignment explanation
Indices: 48539038--48539079 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
48539028 AATAATTTGA
*
48539038 TAATTTTACTAACAAT
1 TAATTTTAATAACAAT
48539054 TAATTTTAATAACAAT
1 TAATTTTAATAACAAT
*
48539070 TAGTTTTAAT
1 TAATTTTAAT
48539080 TTTATTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.43, C:0.07, G:0.02, T:0.48
Consensus pattern (16 bp):
TAATTTTAATAACAAT
Found at i:48539078 original size:22 final size:23
Alignment explanation
Indices: 48539053--48539114 Score: 72
Period size: 23 Copynumber: 2.7 Consensus size: 23
48539043 TTACTAACAA
* *
48539053 TTAATTTTAAT-AACAATTAGTT
1 TTAATTTTAATAAAAAAATAGTT
* *
48539075 TTAATTTTATTAAAAAAATATTT
1 TTAATTTTAATAAAAAAATAGTT
*
48539098 TTAATTTTAATTAAAAA
1 TTAATTTTAATAAAAAA
48539115 CGGGCCGGGC
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
22 10 0.30
23 23 0.70
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.50
Consensus pattern (23 bp):
TTAATTTTAATAAAAAAATAGTT
Found at i:48552351 original size:15 final size:16
Alignment explanation
Indices: 48552321--48552354 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
48552311 AAAATATATT
48552321 TTTATCATTTTAATAA
1 TTTATCATTTTAATAA
*
48552337 TTTAT-ATTTTTATAA
1 TTTATCATTTTAATAA
48552352 TTT
1 TTT
48552355 TTAAATGATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 12 0.71
16 5 0.29
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (16 bp):
TTTATCATTTTAATAA
Found at i:48554389 original size:18 final size:17
Alignment explanation
Indices: 48554368--48554402 Score: 61
Period size: 18 Copynumber: 2.0 Consensus size: 17
48554358 TTTTTAAAAA
48554368 TATTTTAAAATACTTTTT
1 TATTTTAAAATA-TTTTT
48554386 TATTTTAAAATATTTTT
1 TATTTTAAAATATTTTT
48554403 AAAATACTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 5 0.29
18 12 0.71
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (17 bp):
TATTTTAAAATATTTTT
Found at i:48554416 original size:30 final size:30
Alignment explanation
Indices: 48554351--48554415 Score: 107
Period size: 29 Copynumber: 2.2 Consensus size: 30
48554341 TAAATATATA
48554351 TTTTTTATTTTTAAAAATATTTTAAAATAC
1 TTTTTTATTTTTAAAAATATTTTAAAATAC
48554381 TTTTTTA-TTTT-AAAATATTTTTAAAATAC
1 TTTTTTATTTTTAAAAATA-TTTTAAAATAC
48554410 TTTTTT
1 TTTTTT
48554416 TTAATTTTCT
Statistics
Matches: 34, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
28 6 0.18
29 21 0.62
30 7 0.21
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (30 bp):
TTTTTTATTTTTAAAAATATTTTAAAATAC
Found at i:48557265 original size:71 final size:71
Alignment explanation
Indices: 48557149--48557290 Score: 230
Period size: 71 Copynumber: 2.0 Consensus size: 71
48557139 TCTCAGATTT
* * * * *
48557149 AAAAAAGGGATCATGCCCAATAAGTTAGGACACGATCTTTTCTTAATTCCTGAGATTGTTTAAAA
1 AAAAAAAGGATCACGCCCAATAAGTTAGGACACGATCTCTTCTTAATTCCCGAGATCGTTTAAAA
48557214 CTTGAG
66 CTTGAG
*
48557220 AAAAAAAGGATCACGCCCAGTAAGTTAGGACACGATCTCTTCTTAATTCCCGAGATCGTTTAAAA
1 AAAAAAAGGATCACGCCCAATAAGTTAGGACACGATCTCTTCTTAATTCCCGAGATCGTTTAAAA
48557285 CTTGAG
66 CTTGAG
48557291 TTTGAAAAGA
Statistics
Matches: 65, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
71 65 1.00
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.28
Consensus pattern (71 bp):
AAAAAAAGGATCACGCCCAATAAGTTAGGACACGATCTCTTCTTAATTCCCGAGATCGTTTAAAA
CTTGAG
Found at i:48560339 original size:19 final size:19
Alignment explanation
Indices: 48560296--48560333 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
48560286 ATTTTTAAAA
48560296 TATAAAT-TTTAGAATTTT
1 TATAAATATTTAGAATTTT
48560314 TATAAATATTTAGAATTTT
1 TATAAATATTTAGAATTTT
48560333 T
1 T
48560334 GAAAATTATT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 7 0.37
19 12 0.63
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.55
Consensus pattern (19 bp):
TATAAATATTTAGAATTTT
Found at i:48562337 original size:21 final size:21
Alignment explanation
Indices: 48562311--48562353 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
48562301 TTTTGCCTAA
*
48562311 AATATGAATTGGATTGAATTG
1 AATATGAATTGGATTAAATTG
*
48562332 AATATGAATTGTATTAAATTG
1 AATATGAATTGGATTAAATTG
48562353 A
1 A
48562354 GTTAAATTTA
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:0.42, C:0.00, G:0.19, T:0.40
Consensus pattern (21 bp):
AATATGAATTGGATTAAATTG
Found at i:48563104 original size:31 final size:31
Alignment explanation
Indices: 48563060--48563121 Score: 72
Period size: 31 Copynumber: 2.0 Consensus size: 31
48563050 TACTTAAATT
*
48563060 TTAAGTTAAAAGATATTTAT-TAGATAAATAA
1 TTAAATTAAAAGATATTTATGT-GATAAATAA
* * *
48563091 TTAAATTATAAGATTTTTGTGTGATAAATAA
1 TTAAATTAAAAGATATTTATGTGATAAATAA
48563122 AATAAATGAT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
31 25 0.96
32 1 0.04
ACGTcount: A:0.47, C:0.00, G:0.11, T:0.42
Consensus pattern (31 bp):
TTAAATTAAAAGATATTTATGTGATAAATAA
Found at i:48563480 original size:11 final size:11
Alignment explanation
Indices: 48563466--48563496 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
48563456 ATACGAAAAT
48563466 AAGAAGAAAGA
1 AAGAAGAAAGA
48563477 AAGAAGAAAGA
1 AAGAAGAAAGA
48563488 AAGAA-AAAG
1 AAGAAGAAAG
48563497 GAGAAACTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 4 0.20
11 16 0.80
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (11 bp):
AAGAAGAAAGA
Found at i:48563849 original size:22 final size:24
Alignment explanation
Indices: 48563821--48563864 Score: 74
Period size: 23 Copynumber: 1.9 Consensus size: 24
48563811 TATGACAAGA
48563821 AATTAAG-TAGAAAAG-AAGTATG
1 AATTAAGTTAGAAAAGTAAGTATG
48563843 AATTAAGTTAGAAAAGTAAGTA
1 AATTAAGTTAGAAAAGTAAGTA
48563865 AACTTAGTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 7 0.35
23 8 0.40
24 5 0.25
ACGTcount: A:0.55, C:0.00, G:0.20, T:0.25
Consensus pattern (24 bp):
AATTAAGTTAGAAAAGTAAGTATG
Found at i:48566828 original size:21 final size:19
Alignment explanation
Indices: 48566795--48566833 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 19
48566785 TGGTTTTGGT
*
48566795 TTGGTTAAAATGTTTTAAG
1 TTGGTTAAAATGTGTTAAG
48566814 TTGGTTGATAAATGTGTTAA
1 TTGGTT-A-AAATGTGTTAA
48566834 AATGTTGATG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 6 0.35
20 1 0.06
21 10 0.59
ACGTcount: A:0.31, C:0.00, G:0.23, T:0.46
Consensus pattern (19 bp):
TTGGTTAAAATGTGTTAAG
Found at i:48568480 original size:49 final size:49
Alignment explanation
Indices: 48568427--48568543 Score: 207
Period size: 49 Copynumber: 2.4 Consensus size: 49
48568417 ATTTGGTAGC
*
48568427 AGGGTTTTGTTATTACCTTCCGTGAGTCTCCCCCTATGCATCTAGGAAA
1 AGGGTTTTGTTATTACCTTCCGTGAGCCTCCCCCTATGCATCTAGGAAA
48568476 AGGGTTTTGTTATTACCTTCCGTGAGCCTCCCCCTATGCATCTAGGAAA
1 AGGGTTTTGTTATTACCTTCCGTGAGCCTCCCCCTATGCATCTAGGAAA
* *
48568525 AGAGTTTTATTATTACCTT
1 AGGGTTTTGTTATTACCTT
48568544 TCATAAGCCT
Statistics
Matches: 65, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
49 65 1.00
ACGTcount: A:0.21, C:0.23, G:0.19, T:0.37
Consensus pattern (49 bp):
AGGGTTTTGTTATTACCTTCCGTGAGCCTCCCCCTATGCATCTAGGAAA
Found at i:48575850 original size:30 final size:30
Alignment explanation
Indices: 48575816--48576228 Score: 517
Period size: 30 Copynumber: 13.8 Consensus size: 30
48575806 ATGTATTCAT
*
48575816 ATACAAATCAATTCGGCAATGCATATCCAA
1 ATACAAATCAATTCGGCAATGTATATCCAA
48575846 ATACAAATCAATTCGGCAATGTATATCCAA
1 ATACAAATCAATTCGGCAATGTATATCCAA
* * * * *
48575876 ATACAAATCAATTCAGAAATGAATATCTAT
1 ATACAAATCAATTCGGCAATGTATATCCAA
** *
48575906 ATACAAATCAATTCAACAATATATATCCAA
1 ATACAAATCAATTCGGCAATGTATATCCAA
* * *
48575936 ATACGAATCAATTCGGTAATGTATATCCGA
1 ATACAAATCAATTCGGCAATGTATATCCAA
*
48575966 ATACAAATCAATTCAGCAATGTATAT-CAA
1 ATACAAATCAATTCGGCAATGTATATCCAA
* *
48575995 TATACCAATCAATTCGACAATGTATATCCAA
1 -ATACAAATCAATTCGGCAATGTATATCCAA
* * *
48576026 ATACAAATCAATTCGGTAATGTATATCTAT
1 ATACAAATCAATTCGGCAATGTATATCCAA
48576056 ATACAAATCAATTCGGCAATGTATATCCAA
1 ATACAAATCAATTCGGCAATGTATATCCAA
* *
48576086 ATACGAATCAATTTGGCAATGTATATCCAA
1 ATACAAATCAATTCGGCAATGTATATCCAA
* * * * *
48576116 ATATAAATCAATTCGGCATTGTAGATCTAT
1 ATACAAATCAATTCGGCAATGTATATCCAA
* *
48576146 ATACCAATCAATTCGGCAATGTATAT--AT
1 ATACAAATCAATTCGGCAATGTATATCCAA
* *
48576174 ATACAAATCAATTCTGTAATGTATATCCAA
1 ATACAAATCAATTCGGCAATGTATATCCAA
* *
48576204 ATACGAATTAATTCGGCAATGTATA
1 ATACAAATCAATTCGGCAATGTATA
48576229 AAACATATAC
Statistics
Matches: 325, Mismatches: 54, Indels: 8
0.84 0.14 0.02
Matches are distributed among these distances:
28 25 0.08
29 2 0.01
30 295 0.91
31 3 0.01
ACGTcount: A:0.43, C:0.17, G:0.10, T:0.30
Consensus pattern (30 bp):
ATACAAATCAATTCGGCAATGTATATCCAA
Found at i:48577317 original size:20 final size:21
Alignment explanation
Indices: 48577292--48577333 Score: 61
Period size: 20 Copynumber: 2.0 Consensus size: 21
48577282 TGTTGAATTG
48577292 TGTATT-TTGGAATGTT-CAAA
1 TGTATTCTT-GAATGTTACAAA
48577312 TGTATTCTTGAATGTTACAAA
1 TGTATTCTTGAATGTTACAAA
48577333 T
1 T
48577334 TGGTACAAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 13 0.65
21 7 0.35
ACGTcount: A:0.31, C:0.07, G:0.17, T:0.45
Consensus pattern (21 bp):
TGTATTCTTGAATGTTACAAA
Found at i:48592700 original size:10 final size:10
Alignment explanation
Indices: 48592680--48592780 Score: 52
Period size: 9 Copynumber: 9.9 Consensus size: 10
48592670 GCCCATTTTT
48592680 ATTTT-AAAA
1 ATTTTAAAAA
48592689 ATTTTAAAAA
1 ATTTTAAAAA
*
48592699 A-TTAAAAAA
1 ATTTTAAAAA
*
48592708 AGTATTTTAAAA
1 A-T-TTTAAAAA
48592720 ATATTT-AAAA
1 AT-TTTAAAAA
48592730 ATATTT--AAA
1 AT-TTTAAAAA
*
48592739 A-TTAAAAAA
1 ATTTTAAAAA
*
48592748 ATTTAAAAAAA
1 ATTT-TAAAAA
48592759 GTATTTTAAAAA
1 --ATTTTAAAAA
48592771 TATTTTAAAA
1 -ATTTTAAAA
48592781 TTAAAAAATT
Statistics
Matches: 77, Mismatches: 5, Indels: 18
0.77 0.05 0.18
Matches are distributed among these distances:
7 2 0.03
9 21 0.27
10 17 0.22
11 21 0.27
12 12 0.16
13 4 0.05
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (10 bp):
ATTTTAAAAA
Found at i:48592717 original size:31 final size:33
Alignment explanation
Indices: 48592679--48592739 Score: 99
Period size: 31 Copynumber: 1.9 Consensus size: 33
48592669 GGCCCATTTT
48592679 TATTTTAAAAAT-TTTAAAAA-ATTAAAAAAAG
1 TATTTTAAAAATATTTAAAAATATTAAAAAAAG
*
48592710 TATTTTAAAAATATTTAAAAATATTTAAAA
1 TATTTTAAAAATATTTAAAAATATTAAAAA
48592740 TTAAAAAAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
31 12 0.44
32 8 0.30
33 7 0.26
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (33 bp):
TATTTTAAAAATATTTAAAAATATTAAAAAAAG
Found at i:48592719 original size:11 final size:10
Alignment explanation
Indices: 48592682--48592781 Score: 68
Period size: 10 Copynumber: 9.9 Consensus size: 10
48592672 CCATTTTTAT
48592682 TTTAAAAAT-
1 TTTAAAAATA
48592691 TTTAAAAA-A
1 TTTAAAAATA
*
48592700 TTAAAAAAAGTA
1 TT-TAAAAA-TA
48592712 TTTTAAAAATA
1 -TTTAAAAATA
48592723 TTTAAAAATA
1 TTTAAAAATA
48592733 TTT--AAA-A
1 TTTAAAAATA
*
48592740 -TTAAAAAAA
1 TTTAAAAATA
48592749 TTTAAAAAAAGTA
1 TTT--AAAAA-TA
48592762 TTTTAAAAATA
1 -TTTAAAAATA
*
48592773 TTTTAAAAT
1 TTTAAAAAT
48592782 TAAAAAATTA
Statistics
Matches: 74, Mismatches: 4, Indels: 25
0.72 0.04 0.24
Matches are distributed among these distances:
6 2 0.03
7 1 0.01
8 6 0.08
9 11 0.15
10 28 0.38
11 4 0.05
12 16 0.22
13 3 0.04
14 3 0.04
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (10 bp):
TTTAAAAATA
Found at i:48592745 original size:16 final size:16
Alignment explanation
Indices: 48592724--48592755 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
48592714 TTAAAAATAT
*
48592724 TTAAAAATATTTAAAA
1 TTAAAAAAATTTAAAA
48592740 TTAAAAAAATTTAAAA
1 TTAAAAAAATTTAAAA
48592756 AAAGTATTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (16 bp):
TTAAAAAAATTTAAAA
Found at i:48592747 original size:40 final size:41
Alignment explanation
Indices: 48592679--48592870 Score: 243
Period size: 40 Copynumber: 4.8 Consensus size: 41
48592669 GGCCCATTTT
* **
48592679 TATTTTAAAAAT-TTTAAAAAATTAAAAAAAGTATTTTAAAAA-
1 TATTTTAAAAATATTT-TAAAATTAAAAAAA-T-TTAAAAAAAG
48592721 TA-TTTAAAAATA-TTTAAAATTAAAAAAATTTAAAAAAAG
1 TATTTTAAAAATATTTTAAAATTAAAAAAATTTAAAAAAAG
*
48592760 TATTTTAAAAATATTTTAAAATT-AAAAAATTAAAAAAAAG
1 TATTTTAAAAATATTTTAAAATTAAAAAAATTTAAAAAAAG
*
48592800 TATTTTAAAAATATTTTAAAATTAAAAAAA-ATAAAAAAAG
1 TATTTTAAAAATATTTTAAAATTAAAAAAATTTAAAAAAAG
* * *
48592840 TATGTAAAAAATATTTTAAAATAAAAAAAAT
1 TATTTTAAAAATATTTTAAAATTAAAAAAAT
48592871 AAATATATTT
Statistics
Matches: 135, Mismatches: 9, Indels: 13
0.86 0.06 0.08
Matches are distributed among these distances:
38 7 0.05
39 3 0.02
40 97 0.72
41 26 0.19
42 2 0.01
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (41 bp):
TATTTTAAAAATATTTTAAAATTAAAAAAATTTAAAAAAAG
Found at i:48592757 original size:9 final size:9
Alignment explanation
Indices: 48592682--48592757 Score: 57
Period size: 9 Copynumber: 8.0 Consensus size: 9
48592672 CCATTTTTAT
*
48592682 TTTAAAAAT
1 TTTAAAAAA
48592691 TTTAAAAAA
1 TTTAAAAAA
*
48592700 TTAAAAAAAGTA
1 TT-TAAAAA--A
48592712 TTTTAAAAATA
1 -TTTAAAAA-A
48592723 TTTAAAAATA
1 TTTAAAAA-A
48592733 TTT--AAAA
1 TTTAAAAAA
*
48592740 TTAAAAAAA
1 TTTAAAAAA
48592749 TTTAAAAAA
1 TTTAAAAAA
48592758 AGTATTTTAA
Statistics
Matches: 56, Mismatches: 5, Indels: 12
0.77 0.07 0.16
Matches are distributed among these distances:
7 3 0.05
8 3 0.05
9 22 0.39
10 18 0.32
11 2 0.04
12 6 0.11
13 2 0.04
ACGTcount: A:0.63, C:0.00, G:0.01, T:0.36
Consensus pattern (9 bp):
TTTAAAAAA
Found at i:48592798 original size:50 final size:50
Alignment explanation
Indices: 48592684--48592797 Score: 169
Period size: 50 Copynumber: 2.3 Consensus size: 50
48592674 ATTTTTATTT
* *
48592684 TAAAAATTTTAAAAAA-TTAAAAAAAGTATTTTAAAAATATTTAAAAATA
1 TAAAAAATTAAAAAAATTTAAAAAAAGTATTTTAAAAATATTTAAAAATA
** *
48592733 TTTAAAATTAAAAAAATTTAAAAAAAGTATTTTAAAAATATTTTAAAAT-
1 TAAAAAATTAAAAAAATTTAAAAAAAGTATTTTAAAAATATTTAAAAATA
48592782 TAAAAAATTAAAAAAA
1 TAAAAAATTAAAAAAA
48592798 AGTATTTTAA
Statistics
Matches: 57, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
49 26 0.46
50 31 0.54
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (50 bp):
TAAAAAATTAAAAAAATTTAAAAAAAGTATTTTAAAAATATTTAAAAATA
Found at i:48599870 original size:24 final size:24
Alignment explanation
Indices: 48599843--48599889 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
48599833 ATTGAAATGG
48599843 ATTG-ATTTAGTATATGA-TGAATTT
1 ATTGAATTTA-TAT-TGATTGAATTT
48599867 ATTGAATTTATATTGATTGAATT
1 ATTGAATTTATATTGATTGAATT
48599890 GGTATATATA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
23 3 0.14
24 13 0.62
25 5 0.24
ACGTcount: A:0.34, C:0.00, G:0.15, T:0.51
Consensus pattern (24 bp):
ATTGAATTTATATTGATTGAATTT
Found at i:48601428 original size:13 final size:13
Alignment explanation
Indices: 48601410--48601448 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
48601400 ACCGTGTGCC
48601410 TCACATGGCTGTG
1 TCACATGGCTGTG
*
48601423 TCACATGCCTGTG
1 TCACATGGCTGTG
*
48601436 TCCCA-GGCTGTG
1 TCACATGGCTGTG
48601448 T
1 T
48601449 GAACCCAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
12 7 0.30
13 16 0.70
ACGTcount: A:0.13, C:0.28, G:0.28, T:0.31
Consensus pattern (13 bp):
TCACATGGCTGTG
Found at i:48606620 original size:56 final size:56
Alignment explanation
Indices: 48606534--48606653 Score: 231
Period size: 56 Copynumber: 2.1 Consensus size: 56
48606524 ACAAGGGATG
48606534 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
*
48606590 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAGAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
48606646 ATGGGCAA
1 ATGGGCAA
48606654 TAAACTAATA
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 63 1.00
ACGTcount: A:0.45, C:0.09, G:0.23, T:0.23
Consensus pattern (56 bp):
ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
Found at i:48607899 original size:40 final size:40
Alignment explanation
Indices: 48607816--48608001 Score: 243
Period size: 40 Copynumber: 4.7 Consensus size: 40
48607806 TCGAATGATG
* * * *
48607816 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
* *
48607856 TCCGGACTAAGAT-CCGAAGGCATTGGTGCGAGTTACTAAA
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
*
48607896 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
48607936 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
*
48607977 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
48608002 AATGAGTAGC
Statistics
Matches: 131, Mismatches: 11, Indels: 8
0.87 0.07 0.05
Matches are distributed among these distances:
39 1 0.01
40 121 0.92
41 9 0.07
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:48608019 original size:80 final size:79
Alignment explanation
Indices: 48607816--48608024 Score: 210
Period size: 80 Copynumber: 2.6 Consensus size: 79
48607806 TCGAATGATG
** * * * * *
48607816 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGAT-CCGAAGGCAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGAAC-GAGTTACTAAATCCGG-TTAAG-TCCCGAAGGCAT
48607879 TGGTGCGAGTTACTAAA
63 TGGTGCGAGTTACTAAA
* ** *
48607896 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCATTT
1 TCCGGGCTAAGTCCCGAAGGCATTTGAACGAGTTACTAAATCC-GGTTAAGTCCCGAAGGCATTG
48607961 GTGCGAGTTACTATAA
65 GTGCGAGTTACTA-AA
* * *
48607977 -CCGGGCTATGTCCCGAAGGCATTTGAATGAG-TAGCTATATCCGGTTAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGAACGAGTTA-CTAAATCCGGTTAA
48608025 ATTTCGAAGG
Statistics
Matches: 111, Mismatches: 13, Indels: 11
0.82 0.10 0.08
Matches are distributed among these distances:
79 9 0.08
80 91 0.82
81 11 0.10
ACGTcount: A:0.25, C:0.21, G:0.27, T:0.26
Consensus pattern (79 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGAACGAGTTACTAAATCCGGTTAAGTCCCGAAGGCATTGG
TGCGAGTTACTAAA
Found at i:48627201 original size:21 final size:21
Alignment explanation
Indices: 48627161--48627201 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
48627151 CTTATTTATA
**
48627161 TTTTAATTAATCATGTTTTAG
1 TTTTAATTAATCATAATTTAG
*
48627182 TTTTAATTAATCTTAATTTA
1 TTTTAATTAATCATAATTTA
48627202 CTTAATTAAG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.32, C:0.05, G:0.05, T:0.59
Consensus pattern (21 bp):
TTTTAATTAATCATAATTTAG
Found at i:48632427 original size:21 final size:21
Alignment explanation
Indices: 48632403--48632449 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
48632393 AGATATTGTG
*
48632403 ATACCCAAAGTGGATATCGCT
1 ATACCCAAAATGGATATCGCT
*
48632424 ATACCCAAAATGGATATCGTT
1 ATACCCAAAATGGATATCGCT
48632445 ATACC
1 ATACC
48632450 ACTGTAGGTG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.36, C:0.23, G:0.15, T:0.26
Consensus pattern (21 bp):
ATACCCAAAATGGATATCGCT
Found at i:48638728 original size:15 final size:16
Alignment explanation
Indices: 48638699--48638728 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
48638689 CAAACATGCT
48638699 TTAACACATTATCAAA
1 TTAACACATTATCAAA
48638715 TTAACACA-TATCAA
1 TTAACACATTATCAA
48638729 CAAGGCACCA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.50, C:0.20, G:0.00, T:0.30
Consensus pattern (16 bp):
TTAACACATTATCAAA
Found at i:48639214 original size:20 final size:19
Alignment explanation
Indices: 48639176--48639218 Score: 59
Period size: 20 Copynumber: 2.2 Consensus size: 19
48639166 CTCTTTCAAA
* *
48639176 ATTTCTTATTTTCATTTGC
1 ATTTCTTACTTTCAATTGC
48639195 ATTTCATTACTTTCAATTGC
1 ATTTC-TTACTTTCAATTGC
48639215 ATTT
1 ATTT
48639219 ACTTCTTTAG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 5 0.24
20 16 0.76
ACGTcount: A:0.21, C:0.16, G:0.05, T:0.58
Consensus pattern (19 bp):
ATTTCTTACTTTCAATTGC
Found at i:48643920 original size:11 final size:11
Alignment explanation
Indices: 48643906--48643941 Score: 56
Period size: 11 Copynumber: 3.4 Consensus size: 11
48643896 TAGAAAACTG
48643906 TAAAGAAAAAC
1 TAAAGAAAAAC
*
48643917 TAAAGAAAACC
1 TAAAGAAAAAC
48643928 TAAAG-AAAAC
1 TAAAGAAAAAC
48643938 TAAA
1 TAAA
48643942 CCTAAAACTA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
10 8 0.35
11 15 0.65
ACGTcount: A:0.69, C:0.11, G:0.08, T:0.11
Consensus pattern (11 bp):
TAAAGAAAAAC
Found at i:48643952 original size:22 final size:22
Alignment explanation
Indices: 48643897--48643941 Score: 65
Period size: 21 Copynumber: 2.0 Consensus size: 22
48643887 AAAAACTCCT
*
48643897 AGAAAACTGTAAAGAAAAACTAA
1 AGAAAAC-CTAAAGAAAAACTAA
48643920 AGAAAACCTAAAG-AAAACTAA
1 AGAAAACCTAAAGAAAAACTAA
48643941 A
1 A
48643942 CCTAAAACTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 9 0.43
22 5 0.24
23 7 0.33
ACGTcount: A:0.67, C:0.11, G:0.11, T:0.11
Consensus pattern (22 bp):
AGAAAACCTAAAGAAAAACTAA
Found at i:48647133 original size:37 final size:37
Alignment explanation
Indices: 48647083--48647161 Score: 122
Period size: 37 Copynumber: 2.1 Consensus size: 37
48647073 TTATTACAAA
* * *
48647083 GTCTTACCCGGACATAATCTCCACACGAAGTTATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
*
48647120 GTCTTACCCGGACAAAATCCCCACACGTAGTCATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
48647157 GTCTT
1 GTCTT
48647162 TAGAGCTCGG
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.25, C:0.32, G:0.19, T:0.24
Consensus pattern (37 bp):
GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
Found at i:48647358 original size:47 final size:47
Alignment explanation
Indices: 48647280--48648038 Score: 1250
Period size: 47 Copynumber: 16.0 Consensus size: 47
48647270 CCCTTCGGGA
* * * * * *
48647280 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
48647327 CCTGTCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
48647374 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
48647421 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
48647470 CCTATCACATATATATACACTTTCACATTCATCAAATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
48647519 CCTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
48647568 CTTATCACATATATACATTTTCACATTCATCACATCGGCCA-TACGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTA-GGC
* *
48647615 TTTATCACATATATACTCTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
48647662 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
48647709 CTTATCACATATATACACTTTCACATTCATCCCATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
48647756 CTTATCACATATATACACTTTCACATTCATCGCATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
48647803 CTTATCACATATATACACTTTCACATTCATCGCATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
48647850 CTTATCACATATATACACTTTCACATTCATCGCATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
48647897 CTTATCACATATATACACTTTCACATTAATCGCATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
48647944 CTTATCACATATATACACTTTCACATTCATCGCATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
48647991 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
48648038 C
1 C
48648039 ATACTATCAT
Statistics
Matches: 681, Mismatches: 27, Indels: 8
0.95 0.04 0.01
Matches are distributed among these distances:
46 2 0.00
47 536 0.79
48 2 0.00
49 141 0.21
ACGTcount: A:0.29, C:0.30, G:0.09, T:0.32
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:48651466 original size:40 final size:40
Alignment explanation
Indices: 48651440--48651705 Score: 399
Period size: 40 Copynumber: 6.7 Consensus size: 40
48651430 TGATTACTCT
* * * *
48651440 TCGGGACCTAGCCCGGATATAACACCAGCACGAATGCTCT
1 TCGGGACTTAGCCCGGATATATCACTAGCACGAATGCTCC
* * * * * *
48651480 TCGAGG-TTTAGCACAGATATATTACTAGCACAAATGCTCT
1 TCG-GGACTTAGCCCGGATATATCACTAGCACGAATGCTCC
* *
48651520 TCGGAACTTAGCCCGGATACATCACTAGCACGAATGCTCC
1 TCGGGACTTAGCCCGGATATATCACTAGCACGAATGCTCC
*
48651560 TCGGGACTTAGCCCGGATATATCACTAGCATGAATGCTCC
1 TCGGGACTTAGCCCGGATATATCACTAGCACGAATGCTCC
48651600 TCGGGACTTAGCCCGGATATATCACTAGCACGAATGCTCC
1 TCGGGACTTAGCCCGGATATATCACTAGCACGAATGCTCC
48651640 TCGGGACTTAGCCCGGATATATCACTAGCACGAATGCTCC
1 TCGGGACTTAGCCCGGATATATCACTAGCACGAATGCTCC
48651680 TCGGGACTTAGCCCGGATATATCACT
1 TCGGGACTTAGCCCGGATATATCACT
48651706 CTCAATTCTC
Statistics
Matches: 204, Mismatches: 20, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
39 1 0.00
40 201 0.99
41 2 0.01
ACGTcount: A:0.27, C:0.29, G:0.21, T:0.23
Consensus pattern (40 bp):
TCGGGACTTAGCCCGGATATATCACTAGCACGAATGCTCC
Found at i:48652969 original size:37 final size:37
Alignment explanation
Indices: 48652919--48652997 Score: 122
Period size: 37 Copynumber: 2.1 Consensus size: 37
48652909 TTATTACGAA
* * *
48652919 GTCTTACCCGGACATAATCTCCACACGAAGTTATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
*
48652956 GTCTTACCCGGACAAAATCCCCACACGTAGTCATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
48652993 GTCTT
1 GTCTT
48652998 TAGAGCTCGG
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.25, C:0.32, G:0.19, T:0.24
Consensus pattern (37 bp):
GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
Found at i:48653203 original size:47 final size:47
Alignment explanation
Indices: 48653116--48653962 Score: 1446
Period size: 47 Copynumber: 18.0 Consensus size: 47
48653106 CCCTTCAGGA
* * * * * * * *
48653116 CTTATCACATTTATACACTTTCACATCCACCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCGCATCGGCCATTAGGC
* * *
48653163 CCTGTCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCGCATCGGCCATTAGGC
*
48653210 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCGCATCGGCCATTAGGC
*
48653257 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCGCATCGGCCATTAGGC
* *
48653306 CCTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCGCATCGGCCATTAGGC
48653353 CTTATCACATATATACACTTTCACATTCATCGCATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCGCATCGGCCATTAGGC
48653400 CTTATCACATATATACACTTTCACATTCATCG--TCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCGCATCGGCCATTAGGC
48653445 CTTATCACATATATACACTTTCACATTCATCGCATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCGCATCGGCCATTAGGC
*
48653492 CTTATCACGTATATACACTTTCACATTCATCGCATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCGCATCGGCCATTAGGC
* *
48653539 CTTATCACGTATATACACTTTCACATTCATCGTATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCGCATCGGCCATTAGGC
*
48653586 CTTATCACATATATACACTTTCACATTCATCGCATCGGCCATTAGAC
1 CTTATCACATATATACACTTTCACATTCATCGCATCGGCCATTAGGC
48653633 CTTATCACATATATACACTTTCACATTCATCGCATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCGCATCGGCCATTAGGC
48653680 CTTATCACATATATACACTTTCACATTCATCGCATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCGCATCGGCCATTAGGC
* *
48653727 CTTATCACATATATACACTTTCACATTCATCGCATCGTCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCGCATCGGCCATTAGGC
48653774 CTTATCACATATATACACTTTCACATTCATCGCATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCGCATCGGCCATTAGGC
*
48653821 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCGCATCGGCCATTAGGC
*
48653868 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCGCATCGGCCATTAGGC
*
48653915 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCGCATCGGCCATTAGGC
48653962 C
1 C
48653963 ATATGTCATT
Statistics
Matches: 771, Mismatches: 25, Indels: 8
0.96 0.03 0.01
Matches are distributed among these distances:
45 45 0.06
47 680 0.88
49 46 0.06
ACGTcount: A:0.28, C:0.30, G:0.10, T:0.32
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCGCATCGGCCATTAGGC
Found at i:48658681 original size:56 final size:57
Alignment explanation
Indices: 48658587--48658771 Score: 219
Period size: 57 Copynumber: 3.3 Consensus size: 57
48658577 TTGCATGCTA
* * * *
48658587 TCATAAATTGAATTAAAGCTGTTGTTTGAGTGCATCAAATTGAGCATTTCCTTACTG
1 TCATAAATTGAATTAAAGCTGTTATTTTAGTGTATCAAATTGAGCATTTCCATACTG
* * * * *
48658644 TCTTAAATTGAA-TCAAGCTGTTATTTTAGTGTTTCAAATTGAGCATTTTCATGCTG
1 TCATAAATTGAATTAAAGCTGTTATTTTAGTGTATCAAATTGAGCATTTCCATACTG
* * * **
48658700 TCATAAATTGAATTAAAGTTGCTATTTTAGTGTATCAAATTGAGCATTTTCATGTTG
1 TCATAAATTGAATTAAAGCTGTTATTTTAGTGTATCAAATTGAGCATTTCCATACTG
* *
48658757 TCTTAAATTAAATTA
1 TCATAAATTGAATTA
48658772 GCCTAATGTT
Statistics
Matches: 110, Mismatches: 17, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
56 47 0.43
57 63 0.57
ACGTcount: A:0.31, C:0.11, G:0.15, T:0.43
Consensus pattern (57 bp):
TCATAAATTGAATTAAAGCTGTTATTTTAGTGTATCAAATTGAGCATTTCCATACTG
Found at i:48658747 original size:57 final size:57
Alignment explanation
Indices: 48658580--48658834 Score: 250
Period size: 56 Copynumber: 4.5 Consensus size: 57
48658570 TTACTGTTTG
* * * * *
48658580 CATGCTATCATAAATTGAATTAAAGCTGTTGTTTGAGTGCATCAAATTGAGCATTTC
1 CATGCTGTCATAAATTGAATTAAAGCTGTTATTTTAGTGTATCAAATTGAGCATTTT
* * * * *
48658637 CTTACTGTCTTAAATTGAA-TCAAGCTGTTATTTTAGTGTTTCAAATTGAGCATTTT
1 CATGCTGTCATAAATTGAATTAAAGCTGTTATTTTAGTGTATCAAATTGAGCATTTT
* *
48658693 CATGCTGTCATAAATTGAATTAAAGTTGCTATTTTAGTGTATCAAATTGAGCATTTT
1 CATGCTGTCATAAATTGAATTAAAGCTGTTATTTTAGTGTATCAAATTGAGCATTTT
* * * ** * * * *
48658750 CATGTTGTCTTAAATTAAATT--AGCCTAATGTTTTAATGTTTCAAATTGAGTATTATT
1 CATGCTGTCATAAATTGAATTAAAG-CTGTTATTTTAGTGTATCAAATTGAGCATT-TT
* *
48658807 -ATGCTGTCCTAAATTAAATTAAAG-TGTT
1 CATGCTGTCATAAATTGAATTAAAGCTGTT
48658835 GCTTCAGTGT
Statistics
Matches: 162, Mismatches: 31, Indels: 11
0.79 0.15 0.05
Matches are distributed among these distances:
55 2 0.01
56 90 0.56
57 68 0.42
58 2 0.01
ACGTcount: A:0.31, C:0.11, G:0.15, T:0.43
Consensus pattern (57 bp):
CATGCTGTCATAAATTGAATTAAAGCTGTTATTTTAGTGTATCAAATTGAGCATTTT
Found at i:48658784 original size:113 final size:114
Alignment explanation
Indices: 48658580--48658831 Score: 303
Period size: 113 Copynumber: 2.2 Consensus size: 114
48658570 TTACTGTTTG
* * * * *
48658580 CATGCTATCATAAATTGAATTAAAGCTGTTGTTTGAGTGCATCAAATTGAGCATTTCCTTACTGT
1 CATGCTGTCATAAATTGAATTAAAGTTGCTATTTGAGTGCATCAAATTGAGCATTTCCATACTGT
* ** *
48658645 CTTAAATTGAATCAAGCTGTTATTTTAGTGTTTCAAATTGAGCATT-TT
66 CTTAAATTAAATCAAGCTAATATTTTAATGTTTCAAATTGAGCATTATT
* * * **
48658693 CATGCTGTCATAAATTGAATTAAAGTTGCTATTTTAGTGTATCAAATTGAGCATTTTCATGTTGT
1 CATGCTGTCATAAATTGAATTAAAGTTGCTATTTGAGTGCATCAAATTGAGCATTTCCATACTGT
* * *
48658758 CTTAAATTAAAT-TAGCCTAATGTTTTAATGTTTCAAATTGAGTATTATT
66 CTTAAATTAAATCAAG-CTAATATTTTAATGTTTCAAATTGAGCATTATT
* *
48658807 -ATGCTGTCCTAAATTAAATTAAAGT
1 CATGCTGTCATAAATTGAATTAAAGT
48658832 GTTGCTTCAG
Statistics
Matches: 118, Mismatches: 19, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
112 2 0.02
113 114 0.97
114 2 0.02
ACGTcount: A:0.31, C:0.12, G:0.15, T:0.42
Consensus pattern (114 bp):
CATGCTGTCATAAATTGAATTAAAGTTGCTATTTGAGTGCATCAAATTGAGCATTTCCATACTGT
CTTAAATTAAATCAAGCTAATATTTTAATGTTTCAAATTGAGCATTATT
Found at i:48658850 original size:56 final size:56
Alignment explanation
Indices: 48658580--48658867 Score: 213
Period size: 56 Copynumber: 5.1 Consensus size: 56
48658570 TTACTGTTTG
* * * * ** *
48658580 CATGCTATCATAAATTGAATTAAAGCTGTTGTTTGAGTGCATCAAATTGAGCATTTC
1 CATGCTGTCATAAATTAAATTAAAG-TGATGTTTTAGTGTTTCAAATTGAGCATTTT
* * * * * * *
48658637 CTTACTGTCTTAAATTGAA-TCAAGCTGTTATTTTAGTGTTTCAAATTGAGCATTTT
1 CATGCTGTCATAAATTAAATTAAAG-TGATGTTTTAGTGTTTCAAATTGAGCATTTT
* * * *
48658693 CATGCTGTCATAAATTGAATTAAAGTTGCTATTTTAGTGTATCAAATTGAGCATTTT
1 CATGCTGTCATAAATTAAATTAAAG-TGATGTTTTAGTGTTTCAAATTGAGCATTTT
* * *** * * *
48658750 CATGTTGTCTTAAATTAAATTAGCCTAATGTTTTAATGTTTCAAATTGAGTATTATT
1 CATGCTGTCATAAATTAAATTAAAGTGATGTTTTAGTGTTTCAAATTGAGCATT-TT
* * * * * * *
48658807 -ATGCTGTCCTAAATTAAATTAAAGTGTTGCTTCAGTGTCTCAAAGTAAGCATTATT
1 CATGCTGTCATAAATTAAATTAAAGTGATGTTTTAGTGTTTCAAATTGAGCATT-TT
48658863 -ATGCT
1 CATGCT
48658868 ATTGAAAAAT
Statistics
Matches: 186, Mismatches: 43, Indels: 5
0.79 0.18 0.02
Matches are distributed among these distances:
56 117 0.63
57 69 0.37
ACGTcount: A:0.31, C:0.12, G:0.15, T:0.42
Consensus pattern (56 bp):
CATGCTGTCATAAATTAAATTAAAGTGATGTTTTAGTGTTTCAAATTGAGCATTTT
Found at i:48659723 original size:113 final size:113
Alignment explanation
Indices: 48659522--48659751 Score: 433
Period size: 113 Copynumber: 2.0 Consensus size: 113
48659512 GAAAAGTAAG
48659522 AATATTCATTATATTGATAAAGTACACCACATTCTCTTTTGGCTTATGTGCCTCCAATGTGATGA
1 AATATTCATTATATTGATAAAGTACACCACATTCTCTTTTGGCTTATGTGCCTCCAATGTGATGA
*
48659587 AAAATATAAGGAAATCAATAGTAAAATCTTGTTAAATGGTTTTCTTGA
66 AAAATATAAGGAAATCAAGAGTAAAATCTTGTTAAATGGTTTTCTTGA
*
48659635 AATATTCATTATATTGATAAAGTACACTACATTCTCTTTTGGCTTATGTGCCTCCAATGTGATGA
1 AATATTCATTATATTGATAAAGTACACCACATTCTCTTTTGGCTTATGTGCCTCCAATGTGATGA
*
48659700 AAATTATAAGGAAATCAAGAGTAAAATCTTGTTAAATGGTTTTCTTGA
66 AAAATATAAGGAAATCAAGAGTAAAATCTTGTTAAATGGTTTTCTTGA
48659748 AATA
1 AATA
48659752 CGTTAATAAT
Statistics
Matches: 114, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
113 114 1.00
ACGTcount: A:0.36, C:0.13, G:0.14, T:0.37
Consensus pattern (113 bp):
AATATTCATTATATTGATAAAGTACACCACATTCTCTTTTGGCTTATGTGCCTCCAATGTGATGA
AAAATATAAGGAAATCAAGAGTAAAATCTTGTTAAATGGTTTTCTTGA
Found at i:48661667 original size:102 final size:102
Alignment explanation
Indices: 48661491--48661694 Score: 408
Period size: 102 Copynumber: 2.0 Consensus size: 102
48661481 GGATATCGCG
48661491 ATATCCCTTGTTTTTGGACCCCTCACCTTCGAGTCTGTTTGAGGTATCGCGATACCCAACCTTGG
1 ATATCCCTTGTTTTTGGACCCCTCACCTTCGAGTCTGTTTGAGGTATCGCGATACCCAACCTTGG
48661556 GTATCGCGATATCACTATGTAAAACCAAAATTTTTTA
66 GTATCGCGATATCACTATGTAAAACCAAAATTTTTTA
48661593 ATATCCCTTGTTTTTGGACCCCTCACCTTCGAGTCTGTTTGAGGTATCGCGATACCCAACCTTGG
1 ATATCCCTTGTTTTTGGACCCCTCACCTTCGAGTCTGTTTGAGGTATCGCGATACCCAACCTTGG
48661658 GTATCGCGATATCACTATGTAAAACCAAAATTTTTTA
66 GTATCGCGATATCACTATGTAAAACCAAAATTTTTTA
48661695 GTTTTGAAAT
Statistics
Matches: 102, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
102 102 1.00
ACGTcount: A:0.25, C:0.25, G:0.17, T:0.34
Consensus pattern (102 bp):
ATATCCCTTGTTTTTGGACCCCTCACCTTCGAGTCTGTTTGAGGTATCGCGATACCCAACCTTGG
GTATCGCGATATCACTATGTAAAACCAAAATTTTTTA
Found at i:48669845 original size:18 final size:17
Alignment explanation
Indices: 48669812--48669843 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
48669802 CAATCAAACA
48669812 TTTTTTTTTGCTTTTTC
1 TTTTTTTTTGCTTTTTC
48669829 TTTTTTTTTG-TTTTT
1 TTTTTTTTTGCTTTTT
48669844 TTAGAACAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.00, C:0.06, G:0.06, T:0.88
Consensus pattern (17 bp):
TTTTTTTTTGCTTTTTC
Found at i:48672671 original size:25 final size:26
Alignment explanation
Indices: 48672643--48672692 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 26
48672633 AAAATCTACT
48672643 CTAAAAAGGAAAAAGAAAA-CCTAAA
1 CTAAAAAGGAAAAAGAAAATCCTAAA
* *
48672668 CTAAAAATGAAAAGGAAAATCCTAA
1 CTAAAAAGGAAAAAGAAAATCCTAA
48672693 CCCTAACCTA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 17 0.77
26 5 0.23
ACGTcount: A:0.64, C:0.12, G:0.12, T:0.12
Consensus pattern (26 bp):
CTAAAAAGGAAAAAGAAAATCCTAAA
Found at i:48676730 original size:29 final size:29
Alignment explanation
Indices: 48676688--48676746 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
48676678 CTTTTCTTAG
48676688 CCATAGCACATTGGATAATAATTAATGTT
1 CCATAGCACATTGGATAATAATTAATGTT
48676717 CCATAGCACATTGGATAATAATTAATGTT
1 CCATAGCACATTGGATAATAATTAATGTT
48676746 C
1 C
48676747 AAAAGAAACT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.37, C:0.15, G:0.14, T:0.34
Consensus pattern (29 bp):
CCATAGCACATTGGATAATAATTAATGTT
Found at i:48686023 original size:16 final size:16
Alignment explanation
Indices: 48686002--48686035 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
48685992 TTTCTTCCCC
48686002 AACTAAAAGTATAAAG
1 AACTAAAAGTATAAAG
48686018 AACTAAAAGTATAAAG
1 AACTAAAAGTATAAAG
48686034 AA
1 AA
48686036 ACCATAAGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.65, C:0.06, G:0.12, T:0.18
Consensus pattern (16 bp):
AACTAAAAGTATAAAG
Found at i:48687134 original size:26 final size:29
Alignment explanation
Indices: 48687086--48687141 Score: 82
Period size: 26 Copynumber: 2.0 Consensus size: 29
48687076 GATGTTGGTG
48687086 ATATTTTAAATAATATATATTAATAATAA
1 ATATTTTAAATAATATATATTAATAATAA
*
48687115 ATATTTT-GATAATAT-T-TTAATAATAA
1 ATATTTTAAATAATATATATTAATAATAA
48687141 A
1 A
48687142 ATGATATTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
26 11 0.42
27 1 0.04
28 7 0.27
29 7 0.27
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (29 bp):
ATATTTTAAATAATATATATTAATAATAA
Found at i:48690027 original size:43 final size:43
Alignment explanation
Indices: 48689955--48690117 Score: 222
Period size: 43 Copynumber: 3.8 Consensus size: 43
48689945 GCGTCGCTAA
* * * *
48689955 CTTTTGCGGCGCTTTTACCATAAACGCCGCTAAAGACCAGTAC
1 CTTTAGCGACGCTTTTCCCACAAACGCCGCTAAAGACCAGTAC
* *
48689998 CTTTAGC-AGCACTTTTCCCACAAACGCCGCTATAGACCA-TGAC
1 CTTTAGCGA-CGCTTTTCCCACAAACGCCGCTAAAGACCAGT-AC
48690041 CTTTAGCGACGCTTTTCCCACAAACGCCGCTAAAGACCAGTAC
1 CTTTAGCGACGCTTTTCCCACAAACGCCGCTAAAGACCAGTAC
* *
48690084 CTTTAGCGACGCTTTTCACAAAAACGCCGCTAAA
1 CTTTAGCGACGCTTTTCCCACAAACGCCGCTAAA
48690118 AACTTATCTT
Statistics
Matches: 106, Mismatches: 10, Indels: 8
0.85 0.08 0.06
Matches are distributed among these distances:
42 1 0.01
43 103 0.97
44 2 0.02
ACGTcount: A:0.28, C:0.33, G:0.16, T:0.23
Consensus pattern (43 bp):
CTTTAGCGACGCTTTTCCCACAAACGCCGCTAAAGACCAGTAC
Found at i:48690436 original size:43 final size:43
Alignment explanation
Indices: 48690388--48690482 Score: 145
Period size: 43 Copynumber: 2.2 Consensus size: 43
48690378 ACATATGCAA
* * * *
48690388 GGTAATAAAATATACAATGCATTTTCTTAATCAAGTAAATCTT
1 GGTAATAAAAGATACAATACATTTACTTAATCAAGGAAATCTT
*
48690431 GGTAATAAAAGATATAATACATTTACTTAATCAAGGAAATCTT
1 GGTAATAAAAGATACAATACATTTACTTAATCAAGGAAATCTT
48690474 GGTAATAAA
1 GGTAATAAA
48690483 GTATCCTGAA
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
43 47 1.00
ACGTcount: A:0.45, C:0.09, G:0.12, T:0.34
Consensus pattern (43 bp):
GGTAATAAAAGATACAATACATTTACTTAATCAAGGAAATCTT
Found at i:48694751 original size:27 final size:27
Alignment explanation
Indices: 48694719--48694772 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
48694709 CATTCTTTTC
48694719 TCTTGTTTACATTCCCTTAATTAATTT
1 TCTTGTTTACATTCCCTTAATTAATTT
48694746 TCTTGTTTACATTCCCTTAATTAATTT
1 TCTTGTTTACATTCCCTTAATTAATTT
48694773 CAACATGTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.22, C:0.19, G:0.04, T:0.56
Consensus pattern (27 bp):
TCTTGTTTACATTCCCTTAATTAATTT
Found at i:48695418 original size:7 final size:7
Alignment explanation
Indices: 48695374--48695405 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
48695364 TACTAACTCT
48695374 TAACCCC
1 TAACCCC
48695381 TAACCCC
1 TAACCCC
48695388 TAACCCC
1 TAACCCC
*
48695395 AAACCCC
1 TAACCCC
48695402 TAAC
1 TAAC
48695406 TACTAACCTC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.34, C:0.53, G:0.00, T:0.12
Consensus pattern (7 bp):
TAACCCC
Found at i:48695487 original size:7 final size:7
Alignment explanation
Indices: 48695462--48695501 Score: 55
Period size: 7 Copynumber: 5.9 Consensus size: 7
48695452 TTGATTTAAA
48695462 CCCTAA-
1 CCCTAAC
* *
48695468 CCCGAAT
1 CCCTAAC
48695475 CCCTAAC
1 CCCTAAC
48695482 CCCTAAC
1 CCCTAAC
48695489 CCCTAAC
1 CCCTAAC
48695496 CCCTAA
1 CCCTAA
48695502 ATCACAACCC
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
6 5 0.17
7 25 0.83
ACGTcount: A:0.30, C:0.53, G:0.03, T:0.15
Consensus pattern (7 bp):
CCCTAAC
Found at i:48695914 original size:19 final size:20
Alignment explanation
Indices: 48695888--48695933 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
48695878 ATAGAATTTT
48695888 AATT-AATA-TAAATAAACA
1 AATTAAATAGTAAATAAACA
* *
48695906 AATTAAATAGTAATTAGACA
1 AATTAAATAGTAAATAAACA
*
48695926 AATAAAAT
1 AATTAAAT
48695934 GTTTTTGCGG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
18 4 0.17
19 4 0.17
20 15 0.65
ACGTcount: A:0.63, C:0.04, G:0.04, T:0.28
Consensus pattern (20 bp):
AATTAAATAGTAAATAAACA
Found at i:48695997 original size:41 final size:41
Alignment explanation
Indices: 48695940--48696050 Score: 177
Period size: 41 Copynumber: 2.7 Consensus size: 41
48695930 AAATGTTTTT
*
48695940 GCGGCGCTTTTCCAAAAACGCCGCTAAAGACCAGAGCATTA
1 GCGGCGCTTTTCCAAAAACGCCGCTAAAGACCAGAGAATTA
* *
48695981 GCGGCGCTTCTCCAAAAACGCCGCTAAAGACCCGAGAATTA
1 GCGGCGCTTTTCCAAAAACGCCGCTAAAGACCAGAGAATTA
**
48696022 GCGGCGCTTTTATAAAAACGCCGCTAAAG
1 GCGGCGCTTTTCCAAAAACGCCGCTAAAG
48696051 CCCCAAAAGG
Statistics
Matches: 64, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
41 64 1.00
ACGTcount: A:0.32, C:0.29, G:0.23, T:0.17
Consensus pattern (41 bp):
GCGGCGCTTTTCCAAAAACGCCGCTAAAGACCAGAGAATTA
Found at i:48701238 original size:16 final size:16
Alignment explanation
Indices: 48701187--48701229 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
48701177 ATTAAAATGT
*
48701187 ATAATATATAACATATAA
1 ATAATATTTAA-A-ATAA
*
48701205 GTAATATTTAAAATAA
1 ATAATATTTAAAATAA
48701221 ATAATATTT
1 ATAATATTT
48701230 TATAAAAATT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
16 12 0.55
17 1 0.05
18 9 0.41
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (16 bp):
ATAATATTTAAAATAA
Found at i:48701958 original size:44 final size:46
Alignment explanation
Indices: 48701908--48702006 Score: 130
Period size: 52 Copynumber: 2.1 Consensus size: 46
48701898 TACAAGATAG
48701908 AAAATTATTTT-AAG-ACATTTGGAAATTTAAAATGACATATATAT
1 AAAATTATTTTAAAGAACATTTGGAAATTTAAAATGACATATATAT
48701952 AAAATTATTTTAAAAGAACTTAACATTTGGAAATTTAAAATGACATATATAT
1 AAAATTATTTT-AAAG-----AACATTTGGAAATTTAAAATGACATATATAT
48702004 AAA
1 AAA
48702007 TATATGATAA
Statistics
Matches: 47, Mismatches: 0, Indels: 8
0.85 0.00 0.15
Matches are distributed among these distances:
44 11 0.23
46 3 0.06
52 33 0.70
ACGTcount: A:0.51, C:0.05, G:0.08, T:0.36
Consensus pattern (46 bp):
AAAATTATTTTAAAGAACATTTGGAAATTTAAAATGACATATATAT
Found at i:48702970 original size:124 final size:124
Alignment explanation
Indices: 48702833--48703086 Score: 499
Period size: 124 Copynumber: 2.0 Consensus size: 124
48702823 ACATAATTAG
48702833 AAGGTTTCTAAAGTTACTTTGAAGTTTAGTTAATGAATTCTCAAGTTTTAATGAATTTTCATCAT
1 AAGGTTTCTAAAGTTACTTTGAAGTTTAGTTAATGAATTCTCAAGTTTTAATGAATTTTCATCAT
*
48702898 AATGGCCAAAACTTGTAAAAAAATTTGAAACCTTGAAACATGTAGTTTTGTATAGTTTA
66 AATGGCCAAAACTTGTAAAAAAATTTGAAACCTAGAAACATGTAGTTTTGTATAGTTTA
48702957 AAGGTTTCTAAAGTTACTTTGAAGTTTAGTTAATGAATTCTCAAGTTTTAATGAATTTTCATCAT
1 AAGGTTTCTAAAGTTACTTTGAAGTTTAGTTAATGAATTCTCAAGTTTTAATGAATTTTCATCAT
48703022 AATGGCCAAAACTTGTAAAAAAATTTGAAACCTAGAAACATGTAGTTTTGTATAGTTTA
66 AATGGCCAAAACTTGTAAAAAAATTTGAAACCTAGAAACATGTAGTTTTGTATAGTTTA
48703081 AAGGTT
1 AAGGTT
48703087 GAGAATTAGT
Statistics
Matches: 129, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
124 129 1.00
ACGTcount: A:0.37, C:0.09, G:0.15, T:0.39
Consensus pattern (124 bp):
AAGGTTTCTAAAGTTACTTTGAAGTTTAGTTAATGAATTCTCAAGTTTTAATGAATTTTCATCAT
AATGGCCAAAACTTGTAAAAAAATTTGAAACCTAGAAACATGTAGTTTTGTATAGTTTA
Found at i:48716784 original size:29 final size:29
Alignment explanation
Indices: 48716742--48716797 Score: 69
Period size: 29 Copynumber: 1.9 Consensus size: 29
48716732 AAATTTTGTT
* *
48716742 CTTTTGTTTGATG-ATTGTGATACTATTCC
1 CTTTTGGTTAATGAATT-TGATACTATTCC
*
48716771 CTTTTGGTTAATGAATTTGATTCTATT
1 CTTTTGGTTAATGAATTTGATACTATT
48716798 TTATCCCCCT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
29 20 0.87
30 3 0.13
ACGTcount: A:0.20, C:0.11, G:0.16, T:0.54
Consensus pattern (29 bp):
CTTTTGGTTAATGAATTTGATACTATTCC
Found at i:48750947 original size:20 final size:20
Alignment explanation
Indices: 48750919--48750956 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
48750909 AACTATCATG
*
48750919 TTTTCTTTATTTTATTAACC
1 TTTTATTTATTTTATTAACC
48750939 TTTTATTTATTTTATTAA
1 TTTTATTTATTTTATTAA
48750957 TAAAATAACA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.24, C:0.08, G:0.00, T:0.68
Consensus pattern (20 bp):
TTTTATTTATTTTATTAACC
Found at i:48754106 original size:47 final size:47
Alignment explanation
Indices: 48754035--48754382 Score: 516
Period size: 47 Copynumber: 7.4 Consensus size: 47
48754025 CCCTTCGGGA
* * * *
48754035 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* * * * *
48754082 CCTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
*
48754129 CCTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* * *
48754176 CTTATCACATATATACACTTTCACATTCATCACATCGACCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* *
48754223 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
*
48754270 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGAC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* *
48754319 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
48754366 CTTATCACATATATACA
1 CTTATCACATATATACA
48754383 GGCCTTATCA
Statistics
Matches: 283, Mismatches: 16, Indels: 4
0.93 0.05 0.01
Matches are distributed among these distances:
47 239 0.84
49 44 0.16
ACGTcount: A:0.29, C:0.31, G:0.08, T:0.32
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
Found at i:48754160 original size:25 final size:25
Alignment explanation
Indices: 48754132--48754210 Score: 76
Period size: 25 Copynumber: 3.3 Consensus size: 25
48754122 ACTCGGCCCT
48754132 ATCACATATATACACTTTCACATTC
1 ATCACATATATACACTTTCACATTC
** * * *
48754157 ATCACAT-T-GGC-CATTCGGCCTT-
1 ATCACATATATACACTTTC-ACATTC
48754179 ATCACATATATACACTTTCACATTC
1 ATCACATATATACACTTTCACATTC
48754204 ATCACAT
1 ATCACAT
48754211 CGACCATTAG
Statistics
Matches: 39, Mismatches: 10, Indels: 10
0.66 0.17 0.17
Matches are distributed among these distances:
22 11 0.28
23 5 0.13
24 5 0.13
25 18 0.46
ACGTcount: A:0.32, C:0.29, G:0.05, T:0.34
Consensus pattern (25 bp):
ATCACATATATACACTTTCACATTC
Found at i:48754342 original size:143 final size:141
Alignment explanation
Indices: 48754035--48754382 Score: 534
Period size: 143 Copynumber: 2.5 Consensus size: 141
48754025 CCCTTCGGGA
* * * * * * * *
48754035 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGCCCTATCACATTTATACAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
* * *
48754100 TTTCACATCCATCACGTTGGCCACTCGGCCCTATCACATATATACACTTTCACATTCATCACATT
66 TTTCACATCCATCACATCGGCCACTAGGCCCTATCACATATATACACTTTCACATTCATCACATT
*
48754165 GGCCATTCGGC
131 GGCCATTCGAC
*
48754176 CTTATCACATATATACACTTTCACATTCATCACATCGACCATTAGGCCTTATCACATATATACAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
* * *
48754241 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACACTTTCACATTCATCACA
66 TTTCACATCCATCACATCGGCCACTAGGCCCTATCAC--ATATATACACTTTCACATTCATCACA
48754306 TTGGCCATTCGAC
129 TTGGCCATTCGAC
48754319 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACA
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACA
48754383 GGCCTTATCA
Statistics
Matches: 188, Mismatches: 17, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
141 87 0.46
143 101 0.54
ACGTcount: A:0.29, C:0.31, G:0.08, T:0.32
Consensus pattern (141 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
TTTCACATCCATCACATCGGCCACTAGGCCCTATCACATATATACACTTTCACATTCATCACATT
GGCCATTCGAC
Done.