Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr09 ID=Chr09-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 70713020
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1142373 characters in sequence are not A, C, G, or T
File 48 of 226
Found at i:20047027 original size:61 final size:61
Alignment explanation
Indices: 20046961--20047151 Score: 207
Period size: 61 Copynumber: 3.2 Consensus size: 61
20046951 ATTTTATAGT
20046961 ATTATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAA
1 ATTATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAA
* * * * * * *
20047022 ATTATATATT-TTAATT-A-T-AATAT-ATTTAATAATAATTATGTTAATTTA-TATTTTA-TAG
1 ATTATATATTATGATTTGAGTAAAT-TCATATAAGAAT-ATTA-ATT-ATTAAGAATTTTATTA-
*
20047080 T
61 A
*
20047081 ATTATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTATTAA
1 ATTATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAA
20047142 ATTATATATT
1 ATTATATATT
20047152 TTAATTATAA
Statistics
Matches: 101, Mismatches: 17, Indels: 24
0.71 0.12 0.17
Matches are distributed among these distances:
57 11 0.11
58 8 0.08
59 19 0.19
60 16 0.16
61 29 0.29
62 7 0.07
63 11 0.11
ACGTcount: A:0.42, C:0.01, G:0.07, T:0.50
Consensus pattern (61 bp):
ATTATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAA
Found at i:20047051 original size:15 final size:15
Alignment explanation
Indices: 20047016--20047067 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
20047006 TTAAGAATTT
*
20047016 TATTAAATTAT-ATA
1 TATTTAATTATAATA
20047030 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
20047044 TATTTAATAATAAT-
1 TATTTAATTATAATA
20047058 TATGTTAATT
1 TAT-TTAATT
20047068 TATATTTTAT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 8 0.25
14 8 0.25
15 16 0.50
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:20047166 original size:16 final size:16
Alignment explanation
Indices: 20047145--20047186 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
20047135 TTATTAAATT
*
20047145 ATATATTTTAATTATA
1 ATATATTTTAATAATA
20047161 ATATA-TTTAATAATA
1 ATATATTTTAATAATA
20047176 AT-TATGTTTAA
1 ATATAT-TTTAA
20047187 ATATGATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 2 0.09
15 11 0.48
16 10 0.43
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (16 bp):
ATATATTTTAATAATA
Found at i:20047171 original size:15 final size:15
Alignment explanation
Indices: 20047136--20047177 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
20047126 TTAAGAATTT
*
20047136 TATTAAATTAT-ATA
1 TATTTAATTATAATA
20047150 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
20047164 TATTTAATAATAAT
1 TATTTAATTATAAT
20047178 TATGTTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 8 0.33
14 5 0.21
15 11 0.46
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:20052059 original size:9 final size:9
Alignment explanation
Indices: 20052037--20052087 Score: 52
Period size: 9 Copynumber: 5.8 Consensus size: 9
20052027 TAAAGTAAAT
*
20052037 AAAAGAAAC
1 AAAAGAAAG
*
20052046 TAAAGAAAG
1 AAAAGAAAG
20052055 AAAAGAAAG
1 AAAAGAAAG
20052064 -AAAG-AAG
1 AAAAGAAAG
*
20052071 TAAAAGAAAC
1 -AAAAGAAAG
20052081 AAAAGAA
1 AAAAGAA
20052088 CAGCAGAAGC
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
7 3 0.09
8 4 0.11
9 26 0.74
10 2 0.06
ACGTcount: A:0.75, C:0.04, G:0.18, T:0.04
Consensus pattern (9 bp):
AAAAGAAAG
Found at i:20053196 original size:45 final size:45
Alignment explanation
Indices: 20053126--20053218 Score: 150
Period size: 45 Copynumber: 2.1 Consensus size: 45
20053116 ATGTGCCGAC
20053126 TACTATTACTGTTACCAATTCGGCACTTTGTGTGTCGAATACTGT
1 TACTATTACTGTTACCAATTCGGCACTTTGTGTGTCGAATACTGT
* * * *
20053171 TACTGTTACTGTTTCCGATTTGGCACTTTGTGTGTCGAATACTGT
1 TACTATTACTGTTACCAATTCGGCACTTTGTGTGTCGAATACTGT
20053216 TAC
1 TAC
20053219 CGATTCGGCA
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
45 44 1.00
ACGTcount: A:0.19, C:0.19, G:0.19, T:0.42
Consensus pattern (45 bp):
TACTATTACTGTTACCAATTCGGCACTTTGTGTGTCGAATACTGT
Found at i:20053222 original size:33 final size:33
Alignment explanation
Indices: 20053177--20053252 Score: 125
Period size: 33 Copynumber: 2.3 Consensus size: 33
20053167 CTGTTACTGT
* * *
20053177 TACTGTTTCCGATTTGGCACTTTGTGTGTCGAA
1 TACTGTTACCGATTCGGCAATTTGTGTGTCGAA
20053210 TACTGTTACCGATTCGGCAATTTGTGTGTCGAA
1 TACTGTTACCGATTCGGCAATTTGTGTGTCGAA
20053243 TACTGTTACC
1 TACTGTTACC
20053253 ATTACTGATT
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 40 1.00
ACGTcount: A:0.18, C:0.20, G:0.22, T:0.39
Consensus pattern (33 bp):
TACTGTTACCGATTCGGCAATTTGTGTGTCGAA
Found at i:20055589 original size:20 final size:20
Alignment explanation
Indices: 20055564--20055604 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
20055554 TTTCTTGTTT
20055564 TTAGGAAGGTTTAATTATTA
1 TTAGGAAGGTTTAATTATTA
20055584 TTAGGAAGGTTTAATTATTA
1 TTAGGAAGGTTTAATTATTA
20055604 T
1 T
20055605 ATAGTGTATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.34, C:0.00, G:0.20, T:0.46
Consensus pattern (20 bp):
TTAGGAAGGTTTAATTATTA
Found at i:20056214 original size:3 final size:3
Alignment explanation
Indices: 20056206--20056233 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
20056196 TGAAAAGGTA
20056206 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
20056234 TTCTCTTGAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:20059576 original size:18 final size:19
Alignment explanation
Indices: 20059542--20059578 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
20059532 ACCAAATTTT
20059542 AAAATTCCAAATATTTATA
1 AAAATTCCAAATATTTATA
20059561 AAAATTCCAAAT-TTTATA
1 AAAATTCCAAATATTTATA
20059579 TCTTTTAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 6 0.33
19 12 0.67
ACGTcount: A:0.51, C:0.11, G:0.00, T:0.38
Consensus pattern (19 bp):
AAAATTCCAAATATTTATA
Found at i:20060801 original size:2 final size:2
Alignment explanation
Indices: 20060794--20060824 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
20060784 AAACCTCATA
20060794 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
20060825 GTCTTCATTG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:20063850 original size:41 final size:40
Alignment explanation
Indices: 20063784--20063915 Score: 205
Period size: 40 Copynumber: 3.3 Consensus size: 40
20063774 AATTTAAAAT
20063784 AAAAATTAAAAAAAGTATTTTAAAAATATTTTAAAATTAA
1 AAAAATTAAAAAAAGTATTTTAAAAATATTTTAAAATTAA
* *
20063824 AAAAATTAAAAAAAGTATTTTAAAAAAATTTTAAAATAAA
1 AAAAATTAAAAAAAGTATTTTAAAAATATTTTAAAATTAA
* *
20063864 AAAAATTAAAAAAAAGTATTTTAAAAGTATTTTAAAGTT-A
1 AAAAATT-AAAAAAAGTATTTTAAAAATATTTTAAAATTAA
20063904 AAAAA-TAAAAAA
1 AAAAATTAAAAAA
20063916 TAAAAATATT
Statistics
Matches: 85, Mismatches: 6, Indels: 4
0.89 0.06 0.04
Matches are distributed among these distances:
38 6 0.07
39 1 0.01
40 51 0.60
41 27 0.32
ACGTcount: A:0.65, C:0.00, G:0.04, T:0.31
Consensus pattern (40 bp):
AAAAATTAAAAAAAGTATTTTAAAAATATTTTAAAATTAA
Found at i:20063889 original size:11 final size:11
Alignment explanation
Indices: 20063875--20063899 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
20063865 AAAATTAAAA
20063875 AAAAGTATTTT
1 AAAAGTATTTT
20063886 AAAAGTATTTT
1 AAAAGTATTTT
20063897 AAA
1 AAA
20063900 GTTAAAAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.52, C:0.00, G:0.08, T:0.40
Consensus pattern (11 bp):
AAAAGTATTTT
Found at i:20068485 original size:23 final size:21
Alignment explanation
Indices: 20068439--20068493 Score: 60
Period size: 23 Copynumber: 2.6 Consensus size: 21
20068429 AAAAAAAGTT
*
20068439 TAATTACAA-TAATAATGATA
1 TAATTACAATTAATAATCATA
20068459 -AATTACAATTAATATATCCATA
1 TAATTACAATTAATA-AT-CATA
*
20068481 TAATTAAAATTAA
1 TAATTACAATTAA
20068494 AATTAATCAT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
19 8 0.28
20 5 0.17
21 2 0.07
22 3 0.10
23 11 0.38
ACGTcount: A:0.55, C:0.07, G:0.02, T:0.36
Consensus pattern (21 bp):
TAATTACAATTAATAATCATA
Found at i:20070794 original size:27 final size:27
Alignment explanation
Indices: 20070754--20070827 Score: 94
Period size: 27 Copynumber: 2.7 Consensus size: 27
20070744 ATTAAAAATG
*
20070754 ACCAAAATGTTATAAAAAAATTTTATTT
1 ACCAAAAT-ATATAAAAAAATTTTATTT
* ***
20070782 ACCAAAATATATATAATTTTTTTATTT
1 ACCAAAATATATAAAAAAATTTTATTT
20070809 ACCAAAATATATAAAAAAA
1 ACCAAAATATATAAAAAAA
20070828 CAAAAAAAAC
Statistics
Matches: 37, Mismatches: 9, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
27 29 0.78
28 8 0.22
ACGTcount: A:0.53, C:0.08, G:0.01, T:0.38
Consensus pattern (27 bp):
ACCAAAATATATAAAAAAATTTTATTT
Found at i:20070925 original size:27 final size:27
Alignment explanation
Indices: 20070884--20070963 Score: 124
Period size: 27 Copynumber: 3.0 Consensus size: 27
20070874 ACTCTCTGAG
* *
20070884 ACAATGGAACACTGTTGGCGGCACCAA
1 ACAAGGGAACCCTGTTGGCGGCACCAA
20070911 ACAAGGGAACCCTGTTGGCGGCACCAA
1 ACAAGGGAACCCTGTTGGCGGCACCAA
**
20070938 ACAAGGGCTCCCTGTTGGCGGCACCA
1 ACAAGGGAACCCTGTTGGCGGCACCA
20070964 CTCATGTTAT
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 49 1.00
ACGTcount: A:0.28, C:0.30, G:0.29, T:0.14
Consensus pattern (27 bp):
ACAAGGGAACCCTGTTGGCGGCACCAA
Found at i:20071258 original size:3 final size:3
Alignment explanation
Indices: 20071250--20071293 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
20071240 AATTTTATAG
20071250 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
20071294 AGATGTTACT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:20071403 original size:12 final size:12
Alignment explanation
Indices: 20071250--20071403 Score: 64
Period size: 12 Copynumber: 12.6 Consensus size: 12
20071240 AATTTTATAG
*
20071250 TATTATTATTAT
1 TATTATTAATAT
*
20071262 TATTATTATTAT
1 TATTATTAATAT
*
20071274 TATTATTATTAT
1 TATTATTAATAT
*
20071286 TATTATTAAGA-
1 TATTATTAATAT
* *
20071297 TGTTACTTAGTAT
1 TATTA-TTAATAT
* *
20071310 TATTGTTAGTA-
1 TATTATTAATAT
* ** *
20071321 AAAAATTAGTAT
1 TATTATTAATAT
*
20071333 TATT-TTTATAGT
1 TATTATTAATA-T
20071345 TAGTTATTAATAAT
1 TA-TTATTAAT-AT
*
20071359 T-TTAGTTAGTAT
1 TATTA-TTAATAT
* *
20071371 TATTTTGTATATAA
1 TATTAT-TA-ATAT
*
20071385 AATTATTAATAT
1 TATTATTAATAT
20071397 TATTATT
1 TATTATT
20071404 GTGTTAGTTA
Statistics
Matches: 106, Mismatches: 25, Indels: 22
0.69 0.16 0.14
Matches are distributed among these distances:
11 15 0.14
12 63 0.59
13 15 0.14
14 12 0.11
15 1 0.01
ACGTcount: A:0.36, C:0.01, G:0.07, T:0.56
Consensus pattern (12 bp):
TATTATTAATAT
Found at i:20072051 original size:18 final size:18
Alignment explanation
Indices: 20072023--20072067 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
20072013 TTGATATGGT
* *
20072023 TGGTGGTGAAGAAGAATG
1 TGGTGGCGAAGAAGAAGG
*
20072041 TGGTTGCGAAGAAGAAGG
1 TGGTGGCGAAGAAGAAGG
20072059 TGGTGGCGA
1 TGGTGGCGA
20072068 TCATTGGGAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.29, C:0.04, G:0.47, T:0.20
Consensus pattern (18 bp):
TGGTGGCGAAGAAGAAGG
Found at i:20074800 original size:27 final size:27
Alignment explanation
Indices: 20074762--20074854 Score: 150
Period size: 27 Copynumber: 3.4 Consensus size: 27
20074752 ATAACACGAG
*
20074762 TGGTGTCGCCAACAGGGAACCCTTGTT
1 TGGTGCCGCCAACAGGGAACCCTTGTT
20074789 TGGTGCCGCCAACAGGGAACCCTTGTT
1 TGGTGCCGCCAACAGGGAACCCTTGTT
** *
20074816 TGGTGCCGCCAACAGGGTTCTCTTGTT
1 TGGTGCCGCCAACAGGGAACCCTTGTT
20074843 TGGTGCCGCCAA
1 TGGTGCCGCCAA
20074855 TAGTGTTCCC
Statistics
Matches: 62, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 62 1.00
ACGTcount: A:0.16, C:0.28, G:0.30, T:0.26
Consensus pattern (27 bp):
TGGTGCCGCCAACAGGGAACCCTTGTT
Found at i:20074862 original size:27 final size:27
Alignment explanation
Indices: 20074762--20074868 Score: 142
Period size: 27 Copynumber: 4.0 Consensus size: 27
20074752 ATAACACGAG
* **
20074762 TGGTGTCGCCAACAGGGAACCCTTGTT
1 TGGTGCCGCCAACAGGGTTCCCTTGTT
**
20074789 TGGTGCCGCCAACAGGGAACCCTTGTT
1 TGGTGCCGCCAACAGGGTTCCCTTGTT
*
20074816 TGGTGCCGCCAACAGGGTTCTCTTGTT
1 TGGTGCCGCCAACAGGGTTCCCTTGTT
* *
20074843 TGGTGCCGCCAATAGTGTTCCCTTGT
1 TGGTGCCGCCAACAGGGTTCCCTTGT
20074869 CCCAGGGAGT
Statistics
Matches: 73, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 73 1.00
ACGTcount: A:0.15, C:0.27, G:0.29, T:0.29
Consensus pattern (27 bp):
TGGTGCCGCCAACAGGGTTCCCTTGTT
Found at i:20074950 original size:27 final size:26
Alignment explanation
Indices: 20074918--20074988 Score: 106
Period size: 27 Copynumber: 2.7 Consensus size: 26
20074908 TTTTTATTTT
20074918 TTTATATATTTTGGTAAATAAAAAAA
1 TTTATATATTTTGGTAAATAAAAAAA
*
20074944 TTATATATATTTTGATAAATAAAAAAA
1 TT-TATATATTTTGGTAAATAAAAAAA
*
20074971 TTTATAACATTTTGGTAA
1 TTTAT-ATATTTTGGTAA
20074989 TTTTTAATTT
Statistics
Matches: 40, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
26 5 0.12
27 35 0.88
ACGTcount: A:0.48, C:0.01, G:0.07, T:0.44
Consensus pattern (26 bp):
TTTATATATTTTGGTAAATAAAAAAA
Found at i:20081797 original size:7 final size:7
Alignment explanation
Indices: 20081787--20081811 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
20081777 AATATTAAAT
20081787 ATAATTA
1 ATAATTA
20081794 ATAATTA
1 ATAATTA
20081801 ATAATTA
1 ATAATTA
20081808 ATAA
1 ATAA
20081812 AAAATATGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (7 bp):
ATAATTA
Found at i:20085276 original size:17 final size:16
Alignment explanation
Indices: 20085244--20085295 Score: 54
Period size: 16 Copynumber: 3.2 Consensus size: 16
20085234 TGGGTTAAGG
20085244 TTTAAATTTAGTTATT
1 TTTAAATTTAGTTATT
*
20085260 TTTAAATTTA-TAATAT
1 TTTAAATTTAGTTAT-T
*
20085276 TTTATAATAT-GTTATT
1 TTTA-AATTTAGTTATT
20085292 TTTA
1 TTTA
20085296 TATATTATAA
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
15 3 0.10
16 20 0.67
17 7 0.23
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.62
Consensus pattern (16 bp):
TTTAAATTTAGTTATT
Found at i:20085342 original size:22 final size:22
Alignment explanation
Indices: 20085289--20085349 Score: 62
Period size: 19 Copynumber: 3.0 Consensus size: 22
20085279 ATAATATGTT
*
20085289 ATTTTTATA-TATTAT--AATA
1 ATTTATATACTATTATAAAATA
20085308 ATTTAT-TAC--TTATAAAATA
1 ATTTATATACTATTATAAAATA
*
20085327 ATTTATATACTATTATAATATA
1 ATTTATATACTATTATAAAATA
20085349 A
1 A
20085350 ACATAAAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
17 4 0.12
18 2 0.06
19 15 0.44
20 3 0.09
22 10 0.29
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (22 bp):
ATTTATATACTATTATAAAATA
Found at i:20085405 original size:26 final size:29
Alignment explanation
Indices: 20085376--20085429 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 29
20085366 AGAAAATTAT
*
20085376 ATATAAAAT-TT-TAA-TAGATTAAAAAC
1 ATATAAAATATTATAATTAAATTAAAAAC
20085402 ATATAAAATATTATAATTAAATTAAAAA
1 ATATAAAATATTATAATTAAATTAAAAA
20085430 TAATAAATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
26 9 0.38
27 2 0.08
28 3 0.12
29 10 0.42
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.35
Consensus pattern (29 bp):
ATATAAAATATTATAATTAAATTAAAAAC
Found at i:20086344 original size:42 final size:42
Alignment explanation
Indices: 20086295--20086387 Score: 134
Period size: 41 Copynumber: 2.2 Consensus size: 42
20086285 ATTAAAATAT
*
20086295 TTATATTAAAAAAACAATATCATAAATATAATAAATATTTTA
1 TTATATTAAAAAAACAATACCATAAATATAATAAATATTTTA
* * *
20086337 TTATATT-AAAAAATAATACCATAAATATAGTAAATGTTTTA
1 TTATATTAAAAAAACAATACCATAAATATAATAAATATTTTA
*
20086378 TTGTATTAAA
1 TTATATTAAA
20086388 TATAATTTTT
Statistics
Matches: 45, Mismatches: 5, Indels: 2
0.87 0.10 0.04
Matches are distributed among these distances:
41 36 0.80
42 9 0.20
ACGTcount: A:0.53, C:0.04, G:0.03, T:0.40
Consensus pattern (42 bp):
TTATATTAAAAAAACAATACCATAAATATAATAAATATTTTA
Found at i:20090936 original size:29 final size:30
Alignment explanation
Indices: 20090904--20090969 Score: 80
Period size: 30 Copynumber: 2.2 Consensus size: 30
20090894 GAAAAGTTTA
** *
20090904 GTGACTAAATTGAA-AAAATTAATAGTTGG
1 GTGACTAAATAAAACAAAATGAATAGTTGG
* *
20090933 GTGACAAAATAAAACAAAATGCATAGTTGG
1 GTGACTAAATAAAACAAAATGAATAGTTGG
20090963 GTGACTA
1 GTGACTA
20090970 TTTTCAAAGT
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
29 11 0.37
30 19 0.63
ACGTcount: A:0.45, C:0.08, G:0.21, T:0.26
Consensus pattern (30 bp):
GTGACTAAATAAAACAAAATGAATAGTTGG
Found at i:20106988 original size:7 final size:7
Alignment explanation
Indices: 20106976--20107009 Score: 50
Period size: 7 Copynumber: 4.9 Consensus size: 7
20106966 AACAAATTTC
*
20106976 ATTTTGG
1 ATTTTGA
20106983 ATTTTGA
1 ATTTTGA
20106990 ATTTTGA
1 ATTTTGA
*
20106997 ATTTTAA
1 ATTTTGA
20107004 ATTTTG
1 ATTTTG
20107010 GTATTAAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.26, C:0.00, G:0.15, T:0.59
Consensus pattern (7 bp):
ATTTTGA
Found at i:20107583 original size:27 final size:28
Alignment explanation
Indices: 20107544--20107598 Score: 78
Period size: 27 Copynumber: 2.0 Consensus size: 28
20107534 TTTTCTTTCC
*
20107544 ATTTCCTCTTTTCTTTTTCTTT-TTTTT
1 ATTTCCTCTTTTCTCTTTCTTTATTTTT
20107571 ATTT-CTCTCTTTCTCTTTCTTTATTTTT
1 ATTTCCTCT-TTTCTCTTTCTTTATTTTT
20107599 TCCTTCACAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
26 4 0.16
27 16 0.64
28 5 0.20
ACGTcount: A:0.05, C:0.20, G:0.00, T:0.75
Consensus pattern (28 bp):
ATTTCCTCTTTTCTCTTTCTTTATTTTT
Found at i:20109871 original size:44 final size:43
Alignment explanation
Indices: 20109811--20109896 Score: 120
Period size: 44 Copynumber: 2.0 Consensus size: 43
20109801 ATTGTAGTAA
* *
20109811 AATAGAAGTTGCGATAATAATATATTTAAAAATAATTACAATTT
1 AATAGAAGTTGCGATAAGAATACATTT-AAAATAATTACAATTT
*
20109855 AATAGAAGTT-CTGATAAGAATACATTTAAAATAATTATAATT
1 AATAGAAGTTGC-GATAAGAATACATTTAAAATAATTACAATT
20109897 CCATTGACAA
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
43 15 0.39
44 23 0.61
ACGTcount: A:0.50, C:0.05, G:0.09, T:0.36
Consensus pattern (43 bp):
AATAGAAGTTGCGATAAGAATACATTTAAAATAATTACAATTT
Found at i:20127829 original size:10 final size:10
Alignment explanation
Indices: 20127814--20127839 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
20127804 AGTAGAAGGG
20127814 ATTGTATGAA
1 ATTGTATGAA
20127824 ATTGTATGAA
1 ATTGTATGAA
20127834 ATTGTA
1 ATTGTA
20127840 ATACTATGTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.38, C:0.00, G:0.19, T:0.42
Consensus pattern (10 bp):
ATTGTATGAA
Found at i:20129437 original size:27 final size:27
Alignment explanation
Indices: 20129407--20129462 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 27
20129397 ATTAAATTTT
20129407 ATAATTTTAAAGAT-TTTTATTTTAAAA
1 ATAA-TTTAAAGATATTTTATTTTAAAA
* * *
20129434 ATAATTTATATATATTTTATTTTTAAA
1 ATAATTTAAAGATATTTTATTTTAAAA
20129461 AT
1 AT
20129463 TTAAAATTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 7 0.28
27 18 0.72
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (27 bp):
ATAATTTAAAGATATTTTATTTTAAAA
Found at i:20149862 original size:22 final size:22
Alignment explanation
Indices: 20149834--20149891 Score: 84
Period size: 22 Copynumber: 2.7 Consensus size: 22
20149824 AAGTAAATAT
20149834 ATATAATAAAATAAAAAAGTAA
1 ATATAATAAAATAAAAAAGTAA
*
20149856 ATATAATAAAATAAATAAGTAA
1 ATATAATAAAATAAAAAAGTAA
20149878 ATGA-AAT-AAATAAA
1 AT-ATAATAAAATAAA
20149892 GAAAAGAAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
21 7 0.21
22 26 0.76
23 1 0.03
ACGTcount: A:0.71, C:0.00, G:0.05, T:0.24
Consensus pattern (22 bp):
ATATAATAAAATAAAAAAGTAA
Found at i:20149873 original size:4 final size:4
Alignment explanation
Indices: 20149827--20149891 Score: 51
Period size: 4 Copynumber: 15.0 Consensus size: 4
20149817 AACATTTAAG
* *
20149827 TAAA TATA TATAA TAAAA TAAA -AAA GTAAA TATAA TAAAA TAAA TAAG
1 TAAA TAAA TA-AA T-AAA TAAA TAAA -TAAA TA-AA T-AAA TAAA TAAA
20149875 TAAA TGAAA TAAA TAAA
1 TAAA T-AAA TAAA TAAA
20149892 GAAAAGAAAA
Statistics
Matches: 50, Mismatches: 4, Indels: 14
0.74 0.06 0.21
Matches are distributed among these distances:
3 3 0.06
4 27 0.54
5 18 0.36
6 2 0.04
ACGTcount: A:0.69, C:0.00, G:0.05, T:0.26
Consensus pattern (4 bp):
TAAA
Found at i:20149889 original size:26 final size:24
Alignment explanation
Indices: 20149823--20149891 Score: 79
Period size: 22 Copynumber: 2.8 Consensus size: 24
20149813 CTTTAACATT
20149823 TAAGTAAATATATATAATAAAATAAA
1 TAAGTAAATA-ATA-AATAAAATAAA
*
20149849 AAAGTAAAT-AT-AATAAAATAAA
1 TAAGTAAATAATAAATAAAATAAA
20149871 TAAGTAAATGAAATAAATAAA
1 TAAGTAAAT--AATAAATAAA
20149892 GAAAAGAAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
22 19 0.51
24 2 0.05
25 2 0.05
26 14 0.38
ACGTcount: A:0.68, C:0.00, G:0.06, T:0.26
Consensus pattern (24 bp):
TAAGTAAATAATAAATAAAATAAA
Found at i:20152070 original size:89 final size:89
Alignment explanation
Indices: 20151967--20152147 Score: 326
Period size: 89 Copynumber: 2.0 Consensus size: 89
20151957 CACTTTAACT
* ** *
20151967 AATAAAAGTGTATTTTAAAAATTCACATGTAAATGTACGTAAAAAGCAAATTAAAAATATATATT
1 AATAAAAGTATATTTTAAAAATTCACATGTAAATGTACAAAAAAAACAAATTAAAAATATATATT
20152032 TATTTTTATTGATATTATACTTTA
66 TATTTTTATTGATATTATACTTTA
20152056 AATAAAAGTATATTTTAAAAATTCACATGTAAATGTACAAAAAAAACAAATTAAAAATATATATT
1 AATAAAAGTATATTTTAAAAATTCACATGTAAATGTACAAAAAAAACAAATTAAAAATATATATT
20152121 TATTTTTATTGATATTATACTTTA
66 TATTTTTATTGATATTATACTTTA
20152145 AAT
1 AAT
20152148 TACATATATG
Statistics
Matches: 88, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
89 88 1.00
ACGTcount: A:0.49, C:0.06, G:0.06, T:0.40
Consensus pattern (89 bp):
AATAAAAGTATATTTTAAAAATTCACATGTAAATGTACAAAAAAAACAAATTAAAAATATATATT
TATTTTTATTGATATTATACTTTA
Found at i:20157028 original size:899 final size:902
Alignment explanation
Indices: 20155287--20157094 Score: 3262
Period size: 899 Copynumber: 2.0 Consensus size: 902
20155277 GTCGATGCCA
*
20155287 ATCAAATTAAGACTCAATCGGCTTTTATATCAATTTTTTAAATATATTTATTACATAATTATTTT
1 ATCAAATTAAGACTCAATCGGCTTTTATATAAATTTTTTAAATATATTTATTACATAATTATTTT
* * * *
20155352 TGTTACCATCATCATAGATAGACTTGATCATGCGCCAGGCCACCCGTCCCTAACCCAGAACTCAG
66 TATTACCATCATCATAGATAGACTTGATCATGAGCCAGACCACCCGTCCCCAACCCAGAACTCAG
20155417 CTTGGTCCAACCCGTCCCCATCATCATTATTTTTTTTGGCCTGCTCCAACCCAAATTGGCCTATA
131 CTTGGTCCAACCCGTCCCCATCATCATTATTTTTTTTGGCCTGCTCCAACCCAAATTGGCCTATA
* * *
20155482 CTTGATCATATATGCTCTTCTTGACATAATTTCTAGAACTATCCATAGCCCCTCTCCAATCCAAT
196 CTTGATCATATATGCTATTCTTGACACAATTTCTAGAACTATCCATAGCCCATCTCCAATCCAAT
*
20155547 CCATAAATAGGAGGATAATACGCTTTAACATACTCAGACTCACGTCCTCCTGCATTGGCAATAAT
261 CCATAAATAGGAGGATAATACGCTTTAACATACTCAAACTCACGTCCTCCTGCATTGGCAATAAT
*
20155612 GTTCATGTCAATCGAGTTATGACTCAATTGACAACTATTTAAGTATAAAGATTTTTTATATATAT
326 GTTCATGTCAATCGAGTTACGACTCAATTGACAACTATTTAAGTATAAAGATTTTTTATATATAT
20155677 AATTTCAATATTTTGGGAAATATTTATTTTAATATTTTTAGTGTATTTGATGTATTATATTTTTT
391 AATTTCAATATTTTGGGAAATATTTATTTTAATATTTTTAGTGTATTTGATGTATTATATTTTTT
* ** * * *
20155742 AAATTTATTTTTATATAAAAAAATTAATACATGCGGGCCAAGTCGAACTCGAATTTAGCAATTTT
456 AAATTTATATAAAAATAAAAAAATTAATACAGGCGGACCAAGTCGAACTCGAATTTAGCAATTTT
20155807 AATTCAGATTGAGCTTGGGCAGAAATTTAAGTTCAATTTTCAAACCGAACCTAAAAATTAAGACT
521 AATTCAGATTGAGCTTGGGCAGAAATTTAAGTTCAATTTTCAAACCGAACCTAAAAATTAAGACT
* * *
20155872 AAAATTTTACATTGACCCAATCTGATCTATGATCAAGTCCAATCATAAATACACCTTAATTTAAT
586 AAAATTTTACATCGACCCAACCTAATCTATGATCAAGTCCAATCATAAATACACCTTAATTTAAT
20155937 ATATCCTATACCCCTAATCCAATATTCTCACTGAAATCCAAATTAGAAGAATTTCCGTTGCTGCA
651 ATATCCTATACCCCTAATCCAATATTCTCACTGAAATCCAAATTAGAAGAATTTCCGTTGCTGCA
*
20156002 AGAATTCATAAGACCGCAACTACCACTGCAGTTGGTACTCGTCCTATCATAGAATAATTAGTTGA
716 AGAATTCATAAGACCGCAACCACCACTGCAGTTGGTACTCGTCCTATCATAGAATAATTAGTTGA
*
20156067 TGGTAACTTTCATTAATTCTAAAAGCGAGATTAAATAATTGTTATGTATTTTTAATTGATGTTTT
781 TGGTAACTTTCATTAATTCTAAAAGCGAGATTAAATAACTGTTATGTATTTTTAATTGATGTTTT
*
20156132 AAAAAAGAACTAAATAAAACATACAATTTTAAAATTTAAAAACTCTTTAGTCAATTT
846 AAAAAAGAACTAAATAAAACATACAATTTTAAAATTTAAAAACTCTTTAGTAAATTT
*
20156189 ATCAAATTAAGACTCAATCGGTTTTTATATAAATTTTTTAAATATATTTATTACATAATTATTTT
1 ATCAAATTAAGACTCAATCGGCTTTTATATAAATTTTTTAAATATATTTATTACATAATTATTTT
*
20156254 TATTACCATCATCATAGATAGACTTGATCATGAGCCAGACCACCTGTCCCCAACCCAGAACTCAG
66 TATTACCATCATCATAGATAGACTTGATCATGAGCCAGACCACCCGTCCCCAACCCAGAACTCAG
* * *
20156319 CTTGGTTCAACCCGT-CCCATCGTCATTA-TTTTTTTGGCCTGGTCCAACCCAAATTGGCCTATA
131 CTTGGTCCAACCCGTCCCCATCATCATTATTTTTTTTGGCCTGCTCCAACCCAAATTGGCCTATA
*
20156382 CTTGATCATATATGCTATTCTTGACACAATTTCTAGAACTATCCATAGCCTATCTCCAATCCAAT
196 CTTGATCATATATGCTATTCTTGACACAATTTCTAGAACTATCCATAGCCCATCTCCAATCCAAT
20156447 CCATAAATAGGAGGATAATACGCTTTAACATACTCAAACTCACGTCCTCCTGCATTGGCAATAAT
261 CCATAAATAGGAGGATAATACGCTTTAACATACTCAAACTCACGTCCTCCTGCATTGGCAATAAT
*
20156512 GTTCATGTCAATCGAGTTACGGCTCAATTGACAACTATTTAAGTATAAAGATTTTTT-TATATAT
326 GTTCATGTCAATCGAGTTACGACTCAATTGACAACTATTTAAGTATAAAGATTTTTTATATATAT
*
20156576 ATTTTCAATATTTTGGGAAATATTTATTTTAATATTTTTAGTGTATTTGATGTATTATATTTTTT
391 AATTTCAATATTTTGGGAAATATTTATTTTAATATTTTTAGTGTATTTGATGTATTATATTTTTT
**
20156641 AAATTTATATAAAAATAAAAATTTTAATACAGGCGGACCAAGTCGAACTCGAATTTAGCAATTTT
456 AAATTTATATAAAAATAAAAAAATTAATACAGGCGGACCAAGTCGAACTCGAATTTAGCAATTTT
* * *
20156706 AATTCGGATTGAGCTTGGGCAGAATTTTAAGTTCAATTTTCAAGCCGAACCTAAAAATTAAGACT
521 AATTCAGATTGAGCTTGGGCAGAAATTTAAGTTCAATTTTCAAACCGAACCTAAAAATTAAGACT
20156771 AAAATTTTACATCGACCCAACCTAATCTATGATCAAGTCCAATCATAAATACACCTTAATTTAAT
586 AAAATTTTACATCGACCCAACCTAATCTATGATCAAGTCCAATCATAAATACACCTTAATTTAAT
*
20156836 ATATCCTATACCCCTAATCCAATATTCTCACTGAAATCCAATTTAGAAGAATTTCCGTTGCTGCA
651 ATATCCTATACCCCTAATCCAATATTCTCACTGAAATCCAAATTAGAAGAATTTCCGTTGCTGCA
20156901 AGAATTCATAAGACCGCAACCACCACTGCAGTTGGTACTCGTCCTATCATAGAATAATTAGTTGA
716 AGAATTCATAAGACCGCAACCACCACTGCAGTTGGTACTCGTCCTATCATAGAATAATTAGTTGA
20156966 TGGTAACTTTCATTAATTCTAAAAGCGAGATTAAATAACTGTTATGTATTTTTAATTGATGTTTT
781 TGGTAACTTTCATTAATTCTAAAAGCGAGATTAAATAACTGTTATGTATTTTTAATTGATGTTTT
*
20157031 AAAAAAGAACTAAATAAAACATACAATTTTAAAATTTAAAAACTCTTTTGTAAATTT
846 AAAAAAGAACTAAATAAAACATACAATTTTAAAATTTAAAAACTCTTTAGTAAATTT
20157088 ATCAAAT
1 ATCAAAT
20157095 AATATTTATA
Statistics
Matches: 869, Mismatches: 37, Indels: 3
0.96 0.04 0.00
Matches are distributed among these distances:
899 506 0.58
900 214 0.25
901 12 0.01
902 137 0.16
ACGTcount: A:0.35, C:0.18, G:0.11, T:0.36
Consensus pattern (902 bp):
ATCAAATTAAGACTCAATCGGCTTTTATATAAATTTTTTAAATATATTTATTACATAATTATTTT
TATTACCATCATCATAGATAGACTTGATCATGAGCCAGACCACCCGTCCCCAACCCAGAACTCAG
CTTGGTCCAACCCGTCCCCATCATCATTATTTTTTTTGGCCTGCTCCAACCCAAATTGGCCTATA
CTTGATCATATATGCTATTCTTGACACAATTTCTAGAACTATCCATAGCCCATCTCCAATCCAAT
CCATAAATAGGAGGATAATACGCTTTAACATACTCAAACTCACGTCCTCCTGCATTGGCAATAAT
GTTCATGTCAATCGAGTTACGACTCAATTGACAACTATTTAAGTATAAAGATTTTTTATATATAT
AATTTCAATATTTTGGGAAATATTTATTTTAATATTTTTAGTGTATTTGATGTATTATATTTTTT
AAATTTATATAAAAATAAAAAAATTAATACAGGCGGACCAAGTCGAACTCGAATTTAGCAATTTT
AATTCAGATTGAGCTTGGGCAGAAATTTAAGTTCAATTTTCAAACCGAACCTAAAAATTAAGACT
AAAATTTTACATCGACCCAACCTAATCTATGATCAAGTCCAATCATAAATACACCTTAATTTAAT
ATATCCTATACCCCTAATCCAATATTCTCACTGAAATCCAAATTAGAAGAATTTCCGTTGCTGCA
AGAATTCATAAGACCGCAACCACCACTGCAGTTGGTACTCGTCCTATCATAGAATAATTAGTTGA
TGGTAACTTTCATTAATTCTAAAAGCGAGATTAAATAACTGTTATGTATTTTTAATTGATGTTTT
AAAAAAGAACTAAATAAAACATACAATTTTAAAATTTAAAAACTCTTTAGTAAATTT
Found at i:20159350 original size:50 final size:50
Alignment explanation
Indices: 20159299--20159398 Score: 155
Period size: 50 Copynumber: 2.0 Consensus size: 50
20159289 AAGATTCAAA
* * *
20159299 TTTTTAGTTCTAGAATCTTCACTTACACAATCAAACTTCCCAATTATAAAT
1 TTTTTA-TTCTAGAATATTCACTTACACAATCAAACCTCCAAATTATAAAT
*
20159350 TTTTTATTCTAGAATATTCACTTACACAGTCAAACCTCCAAATTATAAA
1 TTTTTATTCTAGAATATTCACTTACACAATCAAACCTCCAAATTATAAA
20159399 AAAAAAAATA
Statistics
Matches: 45, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
50 39 0.87
51 6 0.13
ACGTcount: A:0.37, C:0.21, G:0.04, T:0.38
Consensus pattern (50 bp):
TTTTTATTCTAGAATATTCACTTACACAATCAAACCTCCAAATTATAAAT
Found at i:20160699 original size:11 final size:11
Alignment explanation
Indices: 20160680--20160709 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
20160670 TTCATCTAAG
*
20160680 ATTATTAAATT
1 ATTAATAAATT
20160691 ATTAATAAATT
1 ATTAATAAATT
20160702 ATTAATAA
1 ATTAATAA
20160710 CTTCAAAAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (11 bp):
ATTAATAAATT
Found at i:20161101 original size:19 final size:18
Alignment explanation
Indices: 20161077--20161112 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
20161067 AGTCTACTAT
20161077 CTTAAATAAAAACCTTTGA
1 CTTAAATAAAAA-CTTTGA
*
20161096 CTTAAATGAAAACTTTG
1 CTTAAATAAAAACTTTG
20161113 GAATACTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.44, C:0.14, G:0.08, T:0.33
Consensus pattern (18 bp):
CTTAAATAAAAACTTTGA
Found at i:20163743 original size:30 final size:31
Alignment explanation
Indices: 20163707--20163797 Score: 100
Period size: 30 Copynumber: 3.0 Consensus size: 31
20163697 ATATAGTTTT
20163707 TATATTAT-TTATAAAGCTTATAAT-ATAATA
1 TATATTATATTATAAAG-TTATAATAATAATA
20163737 TATATTATATTATAAAGTTATAATAATAATA
1 TATATTATATTATAAAGTTATAATAATAATA
* * * *
20163768 -ATAATA-ATAATAATAATAATAATAATAATA
1 TATATTATATTATAA-AGTTATAATAATAATA
20163798 ATAATAAGAG
Statistics
Matches: 54, Mismatches: 4, Indels: 6
0.84 0.06 0.09
Matches are distributed among these distances:
29 6 0.11
30 34 0.63
31 14 0.26
ACGTcount: A:0.55, C:0.01, G:0.02, T:0.42
Consensus pattern (31 bp):
TATATTATATTATAAAGTTATAATAATAATA
Found at i:20163745 original size:7 final size:7
Alignment explanation
Indices: 20163729--20163803 Score: 55
Period size: 6 Copynumber: 12.1 Consensus size: 7
20163719 AAAGCTTATA
20163729 ATATAAT
1 ATATAAT
20163736 ATAT-AT
1 ATATAAT
*
20163742 -TATATT
1 ATATAAT
20163748 ATA-AAGT
1 ATATAA-T
20163755 -TATAAT
1 ATATAAT
20163761 A-ATAAT
1 ATATAAT
20163767 A-ATAAT
1 ATATAAT
20163773 A-ATAAT
1 ATATAAT
20163779 A-ATAAT
1 ATATAAT
20163785 A-ATAAT
1 ATATAAT
20163791 A-ATAAT
1 ATATAAT
20163797 A-ATAAT
1 ATATAAT
20163803 A
1 A
20163804 AGAGAAGACA
Statistics
Matches: 61, Mismatches: 2, Indels: 11
0.82 0.03 0.15
Matches are distributed among these distances:
5 3 0.05
6 49 0.80
7 9 0.15
ACGTcount: A:0.60, C:0.00, G:0.01, T:0.39
Consensus pattern (7 bp):
ATATAAT
Found at i:20163764 original size:3 final size:3
Alignment explanation
Indices: 20163756--20163804 Score: 98
Period size: 3 Copynumber: 16.3 Consensus size: 3
20163746 TTATAAAGTT
20163756 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
20163804 A
1 A
20163805 GAGAAGACAA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:20164720 original size:41 final size:41
Alignment explanation
Indices: 20164653--20164824 Score: 211
Period size: 41 Copynumber: 4.2 Consensus size: 41
20164643 GTAAGTTCAA
20164653 GCTTTATGCCTAGCAGGCTTTATGCCGGTGAATTATATCAG
1 GCTTTATGCCTAGCAGGCTTTATGCCGGTGAATTATATCAG
* * *
20164694 GCTTTATGCCTAGCAGACTCTGTGCCGGTGAATTATATCAG
1 GCTTTATGCCTAGCAGGCTTTATGCCGGTGAATTATATCAG
* * * * * * *
20164735 ACTTTATGTCTAGCATGCTTTGTGCCGGTGAAATGTATCGG
1 GCTTTATGCCTAGCAGGCTTTATGCCGGTGAATTATATCAG
* **
20164776 GCTTTGTGCCTAGCAGGCTTTATGCCGGTGTTTTATA-CAAG
1 GCTTTATGCCTAGCAGGCTTTATGCCGGTGAATTATATC-AG
20164817 GCTTTATG
1 GCTTTATG
20164825 TTCTATAAAT
Statistics
Matches: 108, Mismatches: 22, Indels: 2
0.82 0.17 0.02
Matches are distributed among these distances:
40 1 0.01
41 107 0.99
ACGTcount: A:0.20, C:0.19, G:0.26, T:0.35
Consensus pattern (41 bp):
GCTTTATGCCTAGCAGGCTTTATGCCGGTGAATTATATCAG
Found at i:20165719 original size:22 final size:22
Alignment explanation
Indices: 20165694--20165792 Score: 67
Period size: 23 Copynumber: 4.4 Consensus size: 22
20165684 GTTTGGTATG
20165694 TATATGCTGCCTATTTGTTGTA
1 TATATGCTGCCTATTTGTTGTA
*
20165716 TATATGCTG-TTAAATTT-TGTGTA
1 TATATGCTGCCT--ATTTGT-TGTA
* * * * * * *
20165739 AAAATGCTGTTCAATTTGGTATG
1 TATATGCTG-CCTATTTGTTGTA
*
20165762 TATATGCTGCCCATTTGTTGTA
1 TATATGCTGCCTATTTGTTGTA
20165784 TATATGCTG
1 TATATGCTG
20165793 TTAAATTTTG
Statistics
Matches: 56, Mismatches: 15, Indels: 12
0.67 0.18 0.14
Matches are distributed among these distances:
21 1 0.02
22 27 0.48
23 28 0.50
ACGTcount: A:0.23, C:0.11, G:0.19, T:0.46
Consensus pattern (22 bp):
TATATGCTGCCTATTTGTTGTA
Found at i:20165738 original size:23 final size:23
Alignment explanation
Indices: 20165707--20165807 Score: 80
Period size: 23 Copynumber: 4.3 Consensus size: 23
20165697 ATGCTGCCTA
20165707 TTTGTTGTATATATGCTGTTAAAT
1 TTTG-TGTATATATGCTGTTAAAT
* * *
20165731 TTTGTGTAAAAATGCTGTTCAAT
1 TTTGTGTATATATGCTGTTAAAT
* * * ***
20165754 TTGGTATGTATATGCTG-CCCA-
1 TTTGTGTATATATGCTGTTAAAT
20165775 TTTGTTGTATATATGCTGTTAAAT
1 TTTG-TGTATATATGCTGTTAAAT
20165799 TTTGGTGTA
1 TTT-GTGTA
20165808 AAAGTGNNNN
Statistics
Matches: 57, Mismatches: 16, Indels: 8
0.70 0.20 0.10
Matches are distributed among these distances:
21 3 0.05
22 13 0.23
23 29 0.51
24 11 0.19
25 1 0.02
ACGTcount: A:0.24, C:0.08, G:0.20, T:0.49
Consensus pattern (23 bp):
TTTGTGTATATATGCTGTTAAAT
Found at i:20165768 original size:68 final size:68
Alignment explanation
Indices: 20165621--20165810 Score: 299
Period size: 68 Copynumber: 2.8 Consensus size: 68
20165611 TATGATGTAT
* * * * *
20165621 TATGTATATGCTGCCCATTTGTTTTATATATACTGTTCAAATTTGGTGTAAAATTGCTGCTCAGT
1 TATGTATATGCTGCCCATTTGTTGTATATATGCTGTT-AAATTTTGTGTAAAAATGCTGCTCAAT
20165686 TTGG
65 TTGG
* *
20165690 TATGTATATGCTGCCTATTTGTTGTATATATGCTGTTAAATTTTGTGTAAAAATGCTGTTCAATT
1 TATGTATATGCTGCCCATTTGTTGTATATATGCTGTTAAATTTTGTGTAAAAATGCTGCTCAATT
20165755 TGG
66 TGG
20165758 TATGTATATGCTGCCCATTTGTTGTATATATGCTGTTAAATTTTGGTGTAAAA
1 TATGTATATGCTGCCCATTTGTTGTATATATGCTGTTAAATTTT-GTGTAAAA
20165811 GTGNNNNNNN
Statistics
Matches: 112, Mismatches: 8, Indels: 2
0.92 0.07 0.02
Matches are distributed among these distances:
68 70 0.62
69 42 0.38
ACGTcount: A:0.25, C:0.11, G:0.19, T:0.46
Consensus pattern (68 bp):
TATGTATATGCTGCCCATTTGTTGTATATATGCTGTTAAATTTTGTGTAAAAATGCTGCTCAATT
TGG
Found at i:20165990 original size:23 final size:23
Alignment explanation
Indices: 20165945--20166009 Score: 71
Period size: 23 Copynumber: 2.8 Consensus size: 23
20165935 CTATTTGCTG
20165945 TATAT-AAGCTGTCCAAATTTTGA
1 TATATAAAGCTGTCCAAA-TTTGA
20165968 TATATAAATGCTGTCCAAA-TTGA
1 TATATAAA-GCTGTCCAAATTTGA
* *
20165991 TGTATAAGAGTTGTCCAAA
1 TATATAA-AGCTGTCCAAA
20166010 CAATGTAGAT
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
23 24 0.65
24 3 0.08
25 10 0.27
ACGTcount: A:0.37, C:0.12, G:0.15, T:0.35
Consensus pattern (23 bp):
TATATAAAGCTGTCCAAATTTGA
Found at i:20165996 original size:25 final size:22
Alignment explanation
Indices: 20165943--20166009 Score: 64
Period size: 25 Copynumber: 2.9 Consensus size: 22
20165933 GTCTATTTGC
*
20165943 TGTATATAAGCTGTCCAAATTT
1 TGTATATAAGCTGTCCAAATTA
20165965 TGATATATAAATGCTGTCCAAATTGA
1 TG-TATAT-AA-GCTGTCCAAATT-A
*
20165991 TGTATA-AGAGTTGTCCAAA
1 TGTATATA-AGCTGTCCAAA
20166010 CAATGTAGAT
Statistics
Matches: 38, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
22 2 0.05
23 15 0.39
24 3 0.08
25 16 0.42
26 2 0.05
ACGTcount: A:0.36, C:0.12, G:0.16, T:0.36
Consensus pattern (22 bp):
TGTATATAAGCTGTCCAAATTA
Found at i:20169912 original size:50 final size:50
Alignment explanation
Indices: 20169853--20170089 Score: 194
Period size: 50 Copynumber: 4.7 Consensus size: 50
20169843 CATTCGATAT
* * *
20169853 ACGTAGTAGCCTTCACATAGTACTACACACGTGATCA-AACTTTCTGGTT-C
1 ACGTAGTAGCCTACACATAGTACTACACACGTGATCATAA-TATC-CGTTAC
* * *
20169903 ACGTAGTAGCCTGCACATCGTACTACACACGTGACCATTAATATCCGTTAC
1 ACGTAGTAGCCTACACATAGTACTACACACGTGATCA-TAATATCCGTTAC
* * *
20169954 ACATAGTAGCCTACACATAGTACTACACACGTGATTCGA-AGCTATCCGATAC
1 ACGTAGTAGCCTACACATAGTACTACACACGTGA-TC-ATA-ATATCCGTTAC
* * * * * * * * * *
20170006 GCATAGTAGCCTGCACATAGTACCACACATGCGACCTTTCAT-TCCGGTAC
1 ACGTAGTAGCCTACACATAGTACTACACACGTGATC-ATAATATCCGTTAC
* *
20170056 ATGTAGTAGTCTACACATAGTACTACACACGTGA
1 ACGTAGTAGCCTACACATAGTACTACACACGTGA
20170090 CCATCACTTT
Statistics
Matches: 150, Mismatches: 30, Indels: 14
0.77 0.15 0.07
Matches are distributed among these distances:
50 70 0.47
51 38 0.25
52 41 0.27
53 1 0.01
ACGTcount: A:0.30, C:0.27, G:0.16, T:0.26
Consensus pattern (50 bp):
ACGTAGTAGCCTACACATAGTACTACACACGTGATCATAATATCCGTTAC
Found at i:20170023 original size:52 final size:50
Alignment explanation
Indices: 20169847--20170034 Score: 184
Period size: 52 Copynumber: 3.7 Consensus size: 50
20169837 TATTATCATT
* * * *
20169847 CGATATACGTAGTAGCCTTCACATAGTACTACACACGTGA-TCAAACTTTC
1 CGATACACATAGTAGCCTGCACATAGTACTACACACGTGATTC-AACTATC
* * * * *
20169897 TGGTTCACGTAGTAGCCTGCACATCGTACTACACACGTGACCATT-AA-TATC
1 CGATACACATAGTAGCCTGCACATAGTACTACACACGTG---ATTCAACTATC
* *
20169948 CGTTACACATAGTAGCCTACACATAGTACTACACACGTGATTCGAAGCTATC
1 CGATACACATAGTAGCCTGCACATAGTACTACACACGTGATTC-AA-CTATC
* *
20170000 CGATACGCATAGTAGCCTGCACATAGTACCACACA
1 CGATACACATAGTAGCCTGCACATAGTACTACACA
20170035 TGCGACCTTT
Statistics
Matches: 113, Mismatches: 17, Indels: 14
0.78 0.12 0.10
Matches are distributed among these distances:
48 3 0.03
50 35 0.31
51 36 0.32
52 37 0.33
53 1 0.01
54 1 0.01
ACGTcount: A:0.31, C:0.28, G:0.16, T:0.25
Consensus pattern (50 bp):
CGATACACATAGTAGCCTGCACATAGTACTACACACGTGATTCAACTATC
Found at i:20175327 original size:20 final size:20
Alignment explanation
Indices: 20175304--20175388 Score: 80
Period size: 20 Copynumber: 4.0 Consensus size: 20
20175294 GCCTGAGTGA
*
20175304 CATTCTGCTAGCCTTTGTGG
1 CATTCTGCTAGCATTTGTGG
*
20175324 CATTCTGCTAGCATTTATGG
1 CATTCTGCTAGCATTTGTGG
* * *
20175344 CGTATTCTGATTTGGCCTTTGTGG
1 C--ATTCTG--CTAGCATTTGTGG
*
20175368 CATTCTGTTAGCATTTGTGG
1 CATTCTGCTAGCATTTGTGG
20175388 C
1 C
20175389 GTATTTTGAT
Statistics
Matches: 53, Mismatches: 8, Indels: 8
0.77 0.12 0.12
Matches are distributed among these distances:
20 31 0.58
22 12 0.23
24 10 0.19
ACGTcount: A:0.13, C:0.20, G:0.25, T:0.42
Consensus pattern (20 bp):
CATTCTGCTAGCATTTGTGG
Found at i:20175366 original size:44 final size:44
Alignment explanation
Indices: 20175314--20175443 Score: 179
Period size: 44 Copynumber: 3.0 Consensus size: 44
20175304 CATTCTGCTA
*
20175314 GCCTTTGTGGCATTCTGCTAGCATTTATGGCGTATTCTGATTTG
1 GCCTTTGTGGCATTCTGCTAGCATTTGTGGCGTATTCTGATTTG
* *
20175358 GCCTTTGTGGCATTCTGTTAGCATTTGTGGCGTATTTTGATTTG
1 GCCTTTGTGGCATTCTGCTAGCATTTGTGGCGTATTCTGATTTG
* * * * * *
20175402 GCCTTTGTGGTATTTTTCTAGCCTTTGTGGTGTACTCTGATT
1 GCCTTTGTGGCATTCTGCTAGCATTTGTGGCGTATTCTGATT
20175444 AGTTACGACA
Statistics
Matches: 75, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
44 75 1.00
ACGTcount: A:0.12, C:0.16, G:0.25, T:0.47
Consensus pattern (44 bp):
GCCTTTGTGGCATTCTGCTAGCATTTGTGGCGTATTCTGATTTG
Found at i:20175409 original size:24 final size:24
Alignment explanation
Indices: 20175341--20175411 Score: 87
Period size: 24 Copynumber: 3.1 Consensus size: 24
20175331 CTAGCATTTA
20175341 TGGCGTATTCTGATTTGGCCTTTG
1 TGGCGTATTCTGATTTGGCCTTTG
* *
20175365 TGGC--ATTCTG--TTAGCATTTG
1 TGGCGTATTCTGATTTGGCCTTTG
*
20175385 TGGCGTATTTTGATTTGGCCTTTG
1 TGGCGTATTCTGATTTGGCCTTTG
20175409 TGG
1 TGG
20175412 TATTTTTCTA
Statistics
Matches: 38, Mismatches: 5, Indels: 8
0.75 0.10 0.16
Matches are distributed among these distances:
20 12 0.32
22 11 0.29
24 15 0.39
ACGTcount: A:0.10, C:0.14, G:0.30, T:0.46
Consensus pattern (24 bp):
TGGCGTATTCTGATTTGGCCTTTG
Found at i:20175417 original size:22 final size:22
Alignment explanation
Indices: 20175345--20175415 Score: 74
Period size: 22 Copynumber: 3.2 Consensus size: 22
20175335 CATTTATGGC
20175345 GTATTCTGATTTGGCCTTTGTG
1 GTATTCTGATTTGGCCTTTGTG
* * *
20175367 GCATTCTG--TTAGCATTTGTGG
1 GTATTCTGATTTGGCCTTTGT-G
*
20175388 CGTATTTTGATTTGGCCTTTGTG
1 -GTATTCTGATTTGGCCTTTGTG
20175411 GTATT
1 GTATT
20175416 TTTCTAGCCT
Statistics
Matches: 38, Mismatches: 7, Indels: 8
0.72 0.13 0.15
Matches are distributed among these distances:
20 9 0.24
21 1 0.03
22 18 0.47
23 1 0.03
24 9 0.24
ACGTcount: A:0.11, C:0.13, G:0.27, T:0.49
Consensus pattern (22 bp):
GTATTCTGATTTGGCCTTTGTG
Found at i:20175883 original size:10 final size:10
Alignment explanation
Indices: 20175868--20175915 Score: 55
Period size: 10 Copynumber: 4.9 Consensus size: 10
20175858 TTATATTAAT
20175868 TAAATTAAAA
1 TAAATTAAAA
20175878 TAAATTAAAA
1 TAAATTAAAA
* *
20175888 TATAAAT-AAT
1 TA-AATTAAAA
20175898 TAAATTAAAA
1 TAAATTAAAA
20175908 T-AATTAAA
1 TAAATTAAA
20175916 CTCGTAAAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
9 10 0.31
10 19 0.59
11 3 0.09
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (10 bp):
TAAATTAAAA
Found at i:20175885 original size:15 final size:14
Alignment explanation
Indices: 20175864--20175915 Score: 77
Period size: 15 Copynumber: 3.6 Consensus size: 14
20175854 TTATTTATAT
20175864 TAATTAAATTAAAA
1 TAATTAAATTAAAA
*
20175878 TAAATTAAAATATAAA
1 T-AATTAAATTA-AAA
20175894 TAATTAAATTAAAA
1 TAATTAAATTAAAA
20175908 TAATTAAA
1 TAATTAAA
20175916 CTCGTAAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
14 12 0.35
15 18 0.53
16 4 0.12
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (14 bp):
TAATTAAATTAAAA
Found at i:20176075 original size:111 final size:111
Alignment explanation
Indices: 20175846--20176280 Score: 358
Period size: 111 Copynumber: 4.0 Consensus size: 111
20175836 ATCACAAGTT
* * * *
20175846 AAAAATAATTATTTATATTAATTAAATTAAAATAAATTAAAATATAAATAATTAAATTAAAATAA
1 AAAAATAATTATTTACATTAATT-GAGTAAAATAAA-T---ATAT-AATTATTAAATTAAAATAA
* * * * ** * *
20175911 TTAAACTCGT-AA-A-AA-TACGTGCGTGAATTAAGAAACTAATGGAAATTTT-
60 ATAAACACATCAATATAAGTGCGCACGTGATTTAAGAAACTAAT--AATTTTTA
* * *
20175960 -AAAATAATTATTTACTTTAATTGAGTAAAATAAATATATAATTGTTAAATTAAAATAAATAGAC
1 AAAAATAATTATTTACATTAATTGAGTAAAATAAATATATAATTATTAAATTAAAATAAATAAAC
*
20176024 ACGAT-AATATAAGTGCGCACGTGATTTAAGAAATTAATAATTTTTA
66 AC-ATCAATATAAGTGCGCACGTGATTTAAGAAACTAATAATTTTTA
* *
20176070 AAAAATAATTATTTACATTAATTGAGTAAAATAAATATATAGTTATTAAATTAAGATAAATAAAC
1 AAAAATAATTATTTACATTAATTGAGTAAAATAAATATATAATTATTAAATTAAAATAAATAAAC
* *
20176135 ACATCAATATACGTGCGCACGTGATTTGAGAAACTAATAATTTTT-
66 ACATCAATATAAGTGCGCACGTGATTTAAGAAACTAATAATTTTTA
*
20176180 -----TAA--A-TTA-ATT-A---AGTAAAATACATATATAATTAATTAAATTAAAATAAATAAA
1 AAAAATAATTATTTACATTAATTGAGTAAAATAAATATATAATT-ATTAAATTAAAATAAATAAA
* * ** * *
20176232 CGCGTCAATGGACA-TGGGCACGTGATTTAAGAAA-TCAATAAATTTTA
65 CACATCAATATA-AGTGCGCACGTGATTTAAGAAACT-AATAATTTTTA
20176279 AA
1 AA
20176281 CATTTAAAAA
Statistics
Matches: 273, Mismatches: 35, Indels: 39
0.79 0.10 0.11
Matches are distributed among these distances:
97 19 0.07
98 54 0.20
100 1 0.00
101 3 0.01
102 3 0.01
103 1 0.00
105 3 0.01
107 22 0.08
108 7 0.03
109 7 0.03
110 4 0.01
111 119 0.44
112 10 0.04
113 20 0.07
ACGTcount: A:0.50, C:0.06, G:0.09, T:0.34
Consensus pattern (111 bp):
AAAAATAATTATTTACATTAATTGAGTAAAATAAATATATAATTATTAAATTAAAATAAATAAAC
ACATCAATATAAGTGCGCACGTGATTTAAGAAACTAATAATTTTTA
Found at i:20176195 original size:97 final size:98
Alignment explanation
Indices: 20176073--20176265 Score: 262
Period size: 98 Copynumber: 2.0 Consensus size: 98
20176063 ATTTTTAAAA
* * * *
20176073 AATAATTATTTACATTAATTGAGTAAAATAAATATATAGTT-ATTAAATTAAGATAAATAAACAC
1 AATAATTATTTAAATTAATTAAGTAAAATAAATATATAATTAATTAAATTAAAATAAATAAACAC
* * *
20176137 ATCAATATACGTGCGCACGTGATTTGAGAAACT
66 ATCAATAGACATGCGCACGTGATTTAAGAAACT
* * *
20176170 AATAATTTTTTAAATTAATTAAGTAAAATACATATATAATTAATTAAATTAAAATAAATAAACGC
1 AATAATTATTTAAATTAATTAAGTAAAATAAATATATAATTAATTAAATTAAAATAAATAAACAC
* * *
20176235 GTCAATGGACATGGGCACGTGATTTAAGAAA
66 ATCAATAGACATGCGCACGTGATTTAAGAAA
20176266 TCAATAAATT
Statistics
Matches: 82, Mismatches: 13, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
97 36 0.44
98 46 0.56
ACGTcount: A:0.48, C:0.08, G:0.11, T:0.33
Consensus pattern (98 bp):
AATAATTATTTAAATTAATTAAGTAAAATAAATATATAATTAATTAAATTAAAATAAATAAACAC
ATCAATAGACATGCGCACGTGATTTAAGAAACT
Found at i:20178890 original size:9 final size:9
Alignment explanation
Indices: 20178878--20178919 Score: 59
Period size: 9 Copynumber: 4.7 Consensus size: 9
20178868 AAATTAATCA
*
20178878 AATTAAACG
1 AATTAACCG
20178887 AATTAACCG
1 AATTAACCG
20178896 AATT-ACCTG
1 AATTAACC-G
20178905 AATTAACCG
1 AATTAACCG
20178914 AATTAA
1 AATTAA
20178920 ATCACTACAT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
8 3 0.10
9 24 0.80
10 3 0.10
ACGTcount: A:0.48, C:0.17, G:0.10, T:0.26
Consensus pattern (9 bp):
AATTAACCG
Found at i:20179082 original size:18 final size:18
Alignment explanation
Indices: 20179056--20179099 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
20179046 AATTTTTGTG
* *
20179056 ATTGTGTTGAGTTGGGTA
1 ATTGGGTTGAGTTGGATA
*
20179074 ATTGGGTTGGGTTGGATA
1 ATTGGGTTGAGTTGGATA
*
20179092 TTTGGGTT
1 ATTGGGTT
20179100 TGGATTAGGT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.14, C:0.00, G:0.41, T:0.45
Consensus pattern (18 bp):
ATTGGGTTGAGTTGGATA
Found at i:20185553 original size:6 final size:6
Alignment explanation
Indices: 20185542--20185569 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
20185532 AAACAAAAGT
20185542 AAACTC AAACTC AAACTC AAACTC AAAC
1 AAACTC AAACTC AAACTC AAACTC AAAC
20185570 AGAAGTAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.54, C:0.32, G:0.00, T:0.14
Consensus pattern (6 bp):
AAACTC
Found at i:20205979 original size:5 final size:5
Alignment explanation
Indices: 20205969--20205994 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
20205959 TAGAGAGATC
20205969 GGTCG GGTCG GGTCG GGTCG GGTCG G
1 GGTCG GGTCG GGTCG GGTCG GGTCG G
20205995 CTCATCTTGG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.00, C:0.19, G:0.62, T:0.19
Consensus pattern (5 bp):
GGTCG
Found at i:20208241 original size:11 final size:11
Alignment explanation
Indices: 20208227--20208267 Score: 64
Period size: 11 Copynumber: 3.7 Consensus size: 11
20208217 CGTTTTGATG
20208227 TTATTTTACTA
1 TTATTTTACTA
*
20208238 TTATTTTGCTA
1 TTATTTTACTA
*
20208249 TTATATTACTA
1 TTATTTTACTA
20208260 TTATTTTA
1 TTATTTTA
20208268 TGGTTATCAT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
11 26 1.00
ACGTcount: A:0.27, C:0.07, G:0.02, T:0.63
Consensus pattern (11 bp):
TTATTTTACTA
Found at i:20208244 original size:22 final size:22
Alignment explanation
Indices: 20208219--20208274 Score: 69
Period size: 22 Copynumber: 2.5 Consensus size: 22
20208209 TTTGTTGCCG
*
20208219 TTTTGATGTTATTTTACTATTA
1 TTTTGATGTTATATTACTATTA
* *
20208241 TTTTGCTATTATATTACTATTA
1 TTTTGATGTTATATTACTATTA
20208263 TTTT-ATGGTTAT
1 TTTTGAT-GTTAT
20208275 CATTTGGATA
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
21 1 0.04
22 27 0.96
ACGTcount: A:0.23, C:0.05, G:0.09, T:0.62
Consensus pattern (22 bp):
TTTTGATGTTATATTACTATTA
Found at i:20214049 original size:2 final size:2
Alignment explanation
Indices: 20214042--20214082 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
20214032 TGTCAGTGAT
20214042 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
20214083 TACAGTGCGG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:20216852 original size:43 final size:43
Alignment explanation
Indices: 20216791--20216879 Score: 169
Period size: 43 Copynumber: 2.1 Consensus size: 43
20216781 TTTTTCTTAT
20216791 TTTGATGGCATTATATATGAACTATGGGAGTAGCATTTAAAAA
1 TTTGATGGCATTATATATGAACTATGGGAGTAGCATTTAAAAA
*
20216834 TTTGATGGCATTATATATGAACTGTGGGAGTAGCATTTAAAAA
1 TTTGATGGCATTATATATGAACTATGGGAGTAGCATTTAAAAA
20216877 TTT
1 TTT
20216880 CTTTTCTTTT
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 45 1.00
ACGTcount: A:0.35, C:0.07, G:0.21, T:0.37
Consensus pattern (43 bp):
TTTGATGGCATTATATATGAACTATGGGAGTAGCATTTAAAAA
Found at i:20220929 original size:17 final size:17
Alignment explanation
Indices: 20220909--20220945 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
20220899 TTTTTATTCC
20220909 TATGA-TATGATTATTAT
1 TATGATTAT-ATTATTAT
20220926 TATGATTATATTATTAT
1 TATGATTATATTATTAT
20220943 TAT
1 TAT
20220946 TGTAGTCCTC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 16 0.84
18 3 0.16
ACGTcount: A:0.35, C:0.00, G:0.08, T:0.57
Consensus pattern (17 bp):
TATGATTATATTATTAT
Found at i:20222552 original size:6 final size:6
Alignment explanation
Indices: 20222541--20222581 Score: 59
Period size: 6 Copynumber: 7.2 Consensus size: 6
20222531 ATTTTATGTT
*
20222541 TCCAAA TCCAAA TCCAAA TCCAAA TCAAAA T-CAAA T-CAAA T
1 TCCAAA TCCAAA TCCAAA TCCAAA TCCAAA TCCAAA TCCAAA T
20222582 AACTCATCTT
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
5 9 0.27
6 24 0.73
ACGTcount: A:0.54, C:0.27, G:0.00, T:0.20
Consensus pattern (6 bp):
TCCAAA
Found at i:20223093 original size:30 final size:31
Alignment explanation
Indices: 20223033--20223112 Score: 105
Period size: 30 Copynumber: 2.7 Consensus size: 31
20223023 CATAAAATAC
* *
20223033 TTTAAA-AACTTAA-AT-ATAAAAAATGGTA
1 TTTAAATAATTTAATATAATAAAAAATGATA
20223061 TTTAAATAATTTAATATAATAAAAAAT-ATA
1 TTTAAATAATTTAATATAATAAAAAATGATA
*
20223091 TTTAAATAATTTAGTATAATAA
1 TTTAAATAATTTAATATAATAA
20223113 TACATAAAAT
Statistics
Matches: 46, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
28 6 0.13
29 6 0.13
30 25 0.54
31 9 0.20
ACGTcount: A:0.56, C:0.01, G:0.04, T:0.39
Consensus pattern (31 bp):
TTTAAATAATTTAATATAATAAAAAATGATA
Found at i:20223497 original size:30 final size:30
Alignment explanation
Indices: 20223463--20223610 Score: 194
Period size: 30 Copynumber: 5.0 Consensus size: 30
20223453 AATTTTTTTG
*
20223463 CATTTTGACTCCTAAACTTT-TCTAAAATTA
1 CATTTTGACCCCTAAACTTTCTC-AAAATTA
*
20223493 CATTTTGACCTCTAAACTTTCTCAAAATTA
1 CATTTTGACCCCTAAACTTTCTCAAAATTA
** *
20223523 CATTTCAACCCCTAAACTTT-T-TAAATTA
1 CATTTTGACCCCTAAACTTTCTCAAAATTA
*
20223551 TATTTTGACCCCTAAACTTTCTCAAAATTA
1 CATTTTGACCCCTAAACTTTCTCAAAATTA
* *
20223581 CATTTTAACTCCTAAACTTTCTCAAAATTA
1 CATTTTGACCCCTAAACTTTCTCAAAATTA
20223611 TACTTTTGCC
Statistics
Matches: 102, Mismatches: 13, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
28 23 0.23
29 2 0.02
30 75 0.74
31 2 0.02
ACGTcount: A:0.34, C:0.23, G:0.02, T:0.41
Consensus pattern (30 bp):
CATTTTGACCCCTAAACTTTCTCAAAATTA
Found at i:20223566 original size:58 final size:59
Alignment explanation
Indices: 20223473--20223622 Score: 214
Period size: 58 Copynumber: 2.5 Consensus size: 59
20223463 CATTTTGACT
* *
20223473 CCTAAACTTTTCTAAAATTACATTTTGACCTCTAAACTTTCTCAAAATTACATTTCAACC
1 CCTAAACTTTTCT-AAATTATATTTTGACCCCTAAACTTTCTCAAAATTACATTTCAACC
* *
20223533 CCTAAACTTTT-TAAATTATATTTTGACCCCTAAACTTTCTCAAAATTACATTTTAACT
1 CCTAAACTTTTCTAAATTATATTTTGACCCCTAAACTTTCTCAAAATTACATTTCAACC
*
20223591 CCTAAACTTTCTCAAAATTATACTTTTG-CCCC
1 CCTAAACTTT-TCTAAATTATA-TTTTGACCCC
20223623 AAAAATTTTT
Statistics
Matches: 82, Mismatches: 5, Indels: 6
0.88 0.05 0.06
Matches are distributed among these distances:
58 52 0.63
59 2 0.02
60 23 0.28
61 5 0.06
ACGTcount: A:0.33, C:0.25, G:0.02, T:0.40
Consensus pattern (59 bp):
CCTAAACTTTTCTAAATTATATTTTGACCCCTAAACTTTCTCAAAATTACATTTCAACC
Found at i:20223632 original size:88 final size:88
Alignment explanation
Indices: 20223464--20223632 Score: 227
Period size: 88 Copynumber: 1.9 Consensus size: 88
20223454 ATTTTTTTGC
* *
20223464 ATTTTGACTCCTAAACTTTTCTAAAATTACATTTTGACCTCTAAACTTTCTCAAAATTACATTTC
1 ATTTTGACCCCTAAACTTTTCTAAAATTACATTTTAACCTCTAAACTTTCTCAAAATTACATTTC
* *
20223529 AACCCCTAAACTTTTTAAATTAT
66 AACCCCAAAAATTTTTAAATTAT
*
20223552 ATTTTGACCCCTAAAC-TTTCTCAAAATTACATTTTAA-CTCCTAAACTTTCTCAAAATTATACT
1 ATTTTGACCCCTAAACTTTTCT-AAAATTACATTTTAACCT-CTAAACTTTCTCAAAATTACA-T
**
20223615 TT-TGCCCCAAAAATTTTT
63 TTCAACCCCAAAAATTTTT
20223633 CTACGTTTAC
Statistics
Matches: 71, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
87 7 0.10
88 61 0.86
89 3 0.04
ACGTcount: A:0.34, C:0.22, G:0.02, T:0.41
Consensus pattern (88 bp):
ATTTTGACCCCTAAACTTTTCTAAAATTACATTTTAACCTCTAAACTTTCTCAAAATTACATTTC
AACCCCAAAAATTTTTAAATTAT
Found at i:20224146 original size:32 final size:32
Alignment explanation
Indices: 20224110--20224170 Score: 104
Period size: 32 Copynumber: 1.9 Consensus size: 32
20224100 AAAAAGCAAA
* *
20224110 AAAAAAAGAGAAAGAAACAAGAAGCAAAAGAG
1 AAAAAAAGAGAAAGAAAAAAGAAGAAAAAGAG
20224142 AAAAAAAGAGAAAGAAAAAAGAAGAAAAA
1 AAAAAAAGAGAAAGAAAAAAGAAGAAAAA
20224171 TGGGTGAAAG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.77, C:0.03, G:0.20, T:0.00
Consensus pattern (32 bp):
AAAAAAAGAGAAAGAAAAAAGAAGAAAAAGAG
Found at i:20224150 original size:10 final size:10
Alignment explanation
Indices: 20224110--20224170 Score: 52
Period size: 11 Copynumber: 5.7 Consensus size: 10
20224100 AAAAAGCAAA
20224110 AAAAAAAGAG
1 AAAAAAAGAG
20224120 AAAGAAACA-AG
1 AAA-AAA-AGAG
*
20224131 AAGCAAAAGAG
1 AA-AAAAAGAG
20224142 AAAAAAAGAG
1 AAAAAAAGAG
*
20224152 AAAGAAAAAAG
1 AAA-AAAAGAG
20224163 AAGAAAAA
1 AA-AAAAA
20224171 TGGGTGAAAG
Statistics
Matches: 42, Mismatches: 3, Indels: 11
0.75 0.05 0.20
Matches are distributed among these distances:
10 14 0.33
11 26 0.62
12 2 0.05
ACGTcount: A:0.77, C:0.03, G:0.20, T:0.00
Consensus pattern (10 bp):
AAAAAAAGAG
Found at i:20224155 original size:16 final size:15
Alignment explanation
Indices: 20224109--20224166 Score: 64
Period size: 16 Copynumber: 3.7 Consensus size: 15
20224099 CAAAAAGCAA
20224109 AAAAAAAAGAGAAAG
1 AAAAAAAAGAGAAAG
*
20224124 AAACAAGAAGCA-AAAG
1 AAA-AAAAAG-AGAAAG
20224140 AGAAAAAAAGAGAAAG
1 A-AAAAAAAGAGAAAG
20224156 AAAAAAGAAGA
1 AAAAAA-AAGA
20224167 AAAATGGGTG
Statistics
Matches: 36, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
15 9 0.25
16 24 0.67
17 3 0.08
ACGTcount: A:0.76, C:0.03, G:0.21, T:0.00
Consensus pattern (15 bp):
AAAAAAAAGAGAAAG
Found at i:20224301 original size:7 final size:7
Alignment explanation
Indices: 20224271--20224359 Score: 69
Period size: 7 Copynumber: 13.0 Consensus size: 7
20224261 GGCTGATCGG
20224271 GAAAGAAA
1 GAAA-AAA
20224279 GAAAAAA
1 GAAAAAA
*
20224286 G-AGAAA
1 GAAAAAA
*
20224292 GAAAAGA
1 GAAAAAA
*
20224299 GAAGAAA
1 GAAAAAA
*
20224306 GAAAGAA
1 GAAAAAA
*
20224313 G-AAGAA
1 GAAAAAA
*
20224319 GAAGAAA
1 GAAAAAA
*
20224326 GAAAGAA
1 GAAAAAA
20224333 GAAAAAA
1 GAAAAAA
20224340 GAAAATAA
1 GAAAA-AA
20224348 -AAAAAA
1 GAAAAAA
20224354 -AAAAAA
1 GAAAAAA
20224360 AAACAGCAAG
Statistics
Matches: 66, Mismatches: 12, Indels: 8
0.77 0.14 0.09
Matches are distributed among these distances:
6 19 0.29
7 41 0.62
8 6 0.09
ACGTcount: A:0.78, C:0.00, G:0.21, T:0.01
Consensus pattern (7 bp):
GAAAAAA
Found at i:20224304 original size:27 final size:25
Alignment explanation
Indices: 20224273--20224362 Score: 87
Period size: 27 Copynumber: 3.5 Consensus size: 25
20224263 CTGATCGGGA
20224273 AAGAAAGAAAAAAGAGAAAGAAAAGAG
1 AAGAAAGAAAAAAGA-AAAGAAAA-AG
*
20224300 AAGAAAGAAAGAAGAAGAAGAAGAAAG
1 AAGAAAGAAAAAAGAA-AAGAA-AAAG
*
20224327 AA-AGAAGAAAAAAGAAAATAAAAA-
1 AAGA-AAGAAAAAAGAAAAGAAAAAG
*
20224351 AA-AAAAAAAAAA
1 AAGAAAGAAAAAA
20224363 CAGCAAGCCA
Statistics
Matches: 56, Mismatches: 4, Indels: 10
0.80 0.06 0.14
Matches are distributed among these distances:
23 8 0.14
24 3 0.05
25 3 0.05
26 6 0.11
27 34 0.61
28 2 0.04
ACGTcount: A:0.79, C:0.00, G:0.20, T:0.01
Consensus pattern (25 bp):
AAGAAAGAAAAAAGAAAAGAAAAAG
Found at i:20224306 original size:14 final size:14
Alignment explanation
Indices: 20224273--20224318 Score: 60
Period size: 13 Copynumber: 3.4 Consensus size: 14
20224263 CTGATCGGGA
*
20224273 AAGAAAGAAAAAAG
1 AAGAAAGAAAAGAG
20224287 -AGAAAGAAAAGAG
1 AAGAAAGAAAAGAG
20224300 AAGAAAG-AAAGAAG
1 AAGAAAGAAAAG-AG
20224314 AAGAA
1 AAGAA
20224319 GAAGAAAGAA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
13 16 0.55
14 13 0.45
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (14 bp):
AAGAAAGAAAAGAG
Found at i:20224306 original size:20 final size:20
Alignment explanation
Indices: 20224271--20224342 Score: 64
Period size: 18 Copynumber: 3.7 Consensus size: 20
20224261 GGCTGATCGG
20224271 GAAAG-AAAGA-AA-AAAGA
1 GAAAGAAAAGAGAAGAAAGA
20224288 GAAAGAAAAGAGAAG-AA-A
1 GAAAGAAAAGAGAAGAAAGA
20224306 GAAAGAAGAAGAAGAAGAAAGA
1 GAAAGAA-AAG-AGAAGAAAGA
* *
20224328 AAGAAGAAAAAAGAA
1 GA-AAGAAAAGAGAA
20224343 AATAAAAAAA
Statistics
Matches: 45, Mismatches: 2, Indels: 12
0.76 0.03 0.20
Matches are distributed among these distances:
17 5 0.11
18 13 0.29
19 7 0.16
20 5 0.11
21 6 0.13
22 4 0.09
23 5 0.11
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (20 bp):
GAAAGAAAAGAGAAGAAAGA
Found at i:20224309 original size:31 final size:34
Alignment explanation
Indices: 20224271--20224343 Score: 100
Period size: 34 Copynumber: 2.2 Consensus size: 34
20224261 GGCTGATCGG
20224271 GAAAGAAAGAA-AA-AAG-AGAAAGAAA-AGAGAA
1 GAAAGAAAGAAGAAGAAGAAGAAAGAAAGA-AGAA
20224302 GAAAGAAAGAAGAAGAAGAAGAAAGAAAGAAGAA
1 GAAAGAAAGAAGAAGAAGAAGAAAGAAAGAAGAA
*
20224336 AAAAGAAA
1 GAAAGAAA
20224344 ATAAAAAAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
31 11 0.30
32 2 0.05
33 3 0.08
34 20 0.54
35 1 0.03
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (34 bp):
GAAAGAAAGAAGAAGAAGAAGAAAGAAAGAAGAA
Found at i:20224975 original size:17 final size:17
Alignment explanation
Indices: 20224953--20225158 Score: 57
Period size: 19 Copynumber: 11.6 Consensus size: 17
20224943 TTTTTTTAAG
20224953 AAAATTCTCGTGTTTCA
1 AAAATTCTCGTGTTTCA
* *
20224970 AAAATT-TCGAGTTTTAAAA
1 AAAATTCTCGTG-TTT--CA
* *
20224989 AAAATTTTAGT-TTTCAAAA
1 AAAATTCTCGTGTTTC---A
*
20225008 AAAAATTCTCGCGTTTCA
1 A-AAATTCTCGTGTTTCA
* *
20225026 CAAA-TCTTCATGTTTTCA
1 AAAATTC-TCGTG-TTTCA
* *
20225044 AAAACTTTTCGTGTTTAA
1 AAAA-TTCTCGTGTTTCA
**
20225062 AAAAAAC-CGTGTTTCA
1 AAAATTCTCGTGTTTCA
* * *
20225078 AAAATTTTCATGTTTTTA
1 AAAATTCTCGTG-TTTCA
* * *
20225096 AAATTTTTTCGTATTTTCA
1 AAA-ATTCTCGT-GTTTCA
*
20225115 AAAA-TCCCGTGTTTC-
1 AAAATTCTCGTGTTTCA
*
20225130 -AAATTTTCGTGTTTTCA
1 AAAATTCTCGTG-TTTCA
20225147 AAAATTTCTCGT
1 AAAA-TTCTCGT
20225159 ATTTAAAATT
Statistics
Matches: 132, Mismatches: 35, Indels: 42
0.63 0.17 0.20
Matches are distributed among these distances:
14 3 0.02
15 5 0.04
16 26 0.20
17 22 0.17
18 30 0.23
19 32 0.24
20 10 0.08
21 4 0.03
ACGTcount: A:0.34, C:0.14, G:0.09, T:0.43
Consensus pattern (17 bp):
AAAATTCTCGTGTTTCA
Found at i:20225000 original size:18 final size:20
Alignment explanation
Indices: 20224969--20225011 Score: 63
Period size: 19 Copynumber: 2.2 Consensus size: 20
20224959 CTCGTGTTTC
20224969 AAAAATTTCGAGTTTT-AAA
1 AAAAATTTCGAGTTTTCAAA
*
20224988 AAAAATTT-TAGTTTTCAAA
1 AAAAATTTCGAGTTTTCAAA
20225007 AAAAA
1 AAAAA
20225012 ATTCTCGCGT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 6 0.27
19 16 0.73
ACGTcount: A:0.53, C:0.05, G:0.07, T:0.35
Consensus pattern (20 bp):
AAAAATTTCGAGTTTTCAAA
Found at i:20225088 original size:52 final size:50
Alignment explanation
Indices: 20225020--20225166 Score: 161
Period size: 52 Copynumber: 2.8 Consensus size: 50
20225010 AAATTCTCGC
* *
20225020 GTTTCACAAATCTTCATGTTTTCAAAAACTTTTCGTGTTTAAAAAAAACCGT
1 GTTTCA-AAATTTTCATGTTTTCAAAAA-TTTTCGTATTTAAAAAAAACCGT
* * * **
20225072 GTTTCAAAAATTTTCATGTTTTTAAAATTTTTTCGTATTTTCAAAAATCCCGT
1 GTTTC-AAAATTTTCATGTTTTCAAAA-ATTTTCGTA-TTTAAAAAAAACCGT
*
20225125 GTTTC-AAATTTTCGTGTTTTCAAAAATTTCTCGTATTTAAAA
1 GTTTCAAAATTTTCATGTTTTCAAAAATTT-TCGTATTTAAAA
20225167 TTTTTTTCAC
Statistics
Matches: 80, Mismatches: 11, Indels: 10
0.79 0.11 0.10
Matches are distributed among these distances:
50 9 0.11
51 23 0.29
52 30 0.38
53 18 0.22
ACGTcount: A:0.32, C:0.14, G:0.09, T:0.45
Consensus pattern (50 bp):
GTTTCAAAATTTTCATGTTTTCAAAAATTTTCGTATTTAAAAAAAACCGT
Found at i:20225305 original size:18 final size:18
Alignment explanation
Indices: 20225284--20225318 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
20225274 GCATTTTAAA
20225284 AAAAATTATCGTGTTTTT
1 AAAAATTATCGTGTTTTT
*
20225302 AAAAATTTTCGTGTTTT
1 AAAAATTATCGTGTTTT
20225319 CAACAATTCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.06, G:0.11, T:0.51
Consensus pattern (18 bp):
AAAAATTATCGTGTTTTT
Found at i:20225318 original size:17 final size:17
Alignment explanation
Indices: 20225284--20225639 Score: 227
Period size: 17 Copynumber: 20.3 Consensus size: 17
20225274 GCATTTTAAA
*
20225284 AAAAATTATCGTGTTTTT
1 AAAAATTTTCGTG-TTTT
20225302 AAAAATTTTCGTGTTTT
1 AAAAATTTTCGTGTTTT
* * * *
20225319 CAACAATTCTCGCGTTTC
1 -AAAAATTTTCGTGTTTT
* *
20225337 ACAAATTTTCGTATTTT
1 AAAAATTTTCGTGTTTT
** * ******
20225354 AAATTTTTTAGAAAAAGA
1 AAAAATTTTCG-TGTTTT
*
20225372 AAAAATCTTCTCGTGTTTC
1 AAAAAT-TT-TCGTGTTTT
*
20225391 AAAAA-TGTCGTGTTTT
1 AAAAATTTTCGTGTTTT
20225407 AAAAATTTTCGTGTTTCT
1 AAAAATTTTCGTGTTT-T
20225425 -AAAA-TTTCTGTGTTTT
1 AAAAATTTTC-GTGTTTT
* *
20225441 AAAAAAATTTCGTGTTTC
1 -AAAAATTTTCGTGTTTT
*
20225459 AAAAAATTTCGTGTTTT
1 AAAAATTTTCGTGTTTT
20225476 AAAAATTTTCGTGTTTCT
1 AAAAATTTTCGTGTTT-T
*
20225494 -AAAATTTCCGTGTTTT
1 AAAAATTTTCGTGTTTT
*
20225510 AAAAATTCTCGTGTTTT
1 AAAAATTTTCGTGTTTT
20225527 CAAAAATTTTCGTGTTTTT
1 -AAAAATTTTCGTG-TTTT
* * *
20225546 AAGAATTTTCTTGTCTCT
1 AAAAATTTTCGTGT-TTT
*
20225564 -AAAATTCTCGTGTTTT
1 AAAAATTTTCGTGTTTT
*
20225580 AAAAAAATTTTCGTGTTCTC
1 --AAAAATTTTCGTGTT-TT
***** *
20225600 AAAAATAAAAATTGTTTC
1 AAAAAT-TTTCGTGTTTT
20225618 AAAAATTTTCGTGTTTT
1 AAAAATTTTCGTGTTTT
20225635 AAAAA
1 AAAAA
20225640 AAATCGTATT
Statistics
Matches: 259, Mismatches: 59, Indels: 41
0.72 0.16 0.11
Matches are distributed among these distances:
16 21 0.08
17 122 0.47
18 81 0.31
19 32 0.12
20 3 0.01
ACGTcount: A:0.33, C:0.11, G:0.11, T:0.46
Consensus pattern (17 bp):
AAAAATTTTCGTGTTTT
Found at i:20225326 original size:18 final size:18
Alignment explanation
Indices: 20225287--20225353 Score: 57
Period size: 18 Copynumber: 3.8 Consensus size: 18
20225277 TTTTAAAAAA
* * *
20225287 AATTATCGTGTTTTTAAA
1 AATTTTCGTGTTTTCAAC
20225305 AATTTTCGTGTTTTCAAC
1 AATTTTCGTGTTTTCAAC
* *
20225323 AATTCTCGCG-TTTC-AC
1 AATTTTCGTGTTTTCAAC
*
20225339 AAATTTTCGTATTTT
1 -AATTTTCGTGTTTT
20225354 AAATTTTTTA
Statistics
Matches: 39, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
16 2 0.05
17 11 0.28
18 26 0.67
ACGTcount: A:0.25, C:0.15, G:0.10, T:0.49
Consensus pattern (18 bp):
AATTTTCGTGTTTTCAAC
Found at i:20225446 original size:35 final size:34
Alignment explanation
Indices: 20225372--20225605 Score: 251
Period size: 35 Copynumber: 6.7 Consensus size: 34
20225362 TAGAAAAAGA
*
20225372 AAAAATCTTCTCGTGTTTCAAAAATGTC-GTGTTTT
1 AAAAAT-TT-TCGTGTTTCAAAAATTTCTGTGTTTT
*
20225407 AAAAATTTTCGTGTTTCTAAAATTTCTGTGTTTT
1 AAAAATTTTCGTGTTTCAAAAATTTCTGTGTTTT
*
20225441 AAAAAAATTTCGTGTTTCAAAAAATTTC-GTGTTTT
1 -AAAAATTTTCGTGTTTC-AAAAATTTCTGTGTTTT
* *
20225476 AAAAATTTTCGTGTTTCTAAAATTTCCGTGTTTT
1 AAAAATTTTCGTGTTTCAAAAATTTCTGTGTTTT
*
20225510 AAAAATTCTCGTGTTTTCAAAAATTT-TCGTGTTTTT
1 AAAAATTTTCGTG-TTTCAAAAATTTCT-GTG-TTTT
* * * *
20225546 AAGAATTTTCTTGTCTCTAAAA-TTCTCGTGTTTT
1 AAAAATTTTCGTGTTTCAAAAATTTCT-GTGTTTT
20225580 AAAAAAATTTTCGTGTTCTCAAAAAT
1 --AAAAATTTTCGTGTT-TCAAAAAT
20225606 AAAAATTGTT
Statistics
Matches: 169, Mismatches: 18, Indels: 21
0.81 0.09 0.10
Matches are distributed among these distances:
33 24 0.14
34 50 0.30
35 55 0.33
36 34 0.20
37 6 0.04
ACGTcount: A:0.30, C:0.12, G:0.12, T:0.47
Consensus pattern (34 bp):
AAAAATTTTCGTGTTTCAAAAATTTCTGTGTTTT
Found at i:20225471 original size:69 final size:69
Alignment explanation
Indices: 20225382--20225604 Score: 310
Period size: 69 Copynumber: 3.2 Consensus size: 69
20225372 AAAAATCTTC
*
20225382 TCGTGTTTC-AAAAATGTCGTGTTTTAAAAATTTTCGTGTTTCTAAAATTTCTGTGTTTTAAAAA
1 TCGTGTTTCAAAAAATTTCGTGTTTTAAAAATTTTCGTGTTTCTAAAATTTCTGTGTTTTAAAAA
20225446 AATT
66 AATT
*
20225450 TCGTGTTTCAAAAAATTTCGTGTTTTAAAAATTTTCGTGTTTCTAAAATTTCCGTGTTTT--AAA
1 TCGTGTTTCAAAAAATTTCGTGTTTTAAAAATTTTCGTGTTTCTAAAATTTCTGTGTTTTAAAAA
20225513 AATT
66 AATT
* * * *
20225517 CTCGTGTTTTCAAAAATTTTCGTGTTTTTAAGAATTTTCTTGTCTCTAAAA-TTCTCGTGTTTTA
1 -TCGTG-TTTCAAAAAATTTCGTG-TTTTAAAAATTTTCGTGTTTCTAAAATTTCT-GTGTTTTA
20225581 AAAAAATTT
62 AAAAAA-TT
20225590 TCGTGTTCTCAAAAA
1 TCGTGTT-TCAAAAA
20225605 TAAAAATTGT
Statistics
Matches: 139, Mismatches: 7, Indels: 14
0.87 0.04 0.09
Matches are distributed among these distances:
67 7 0.05
68 14 0.10
69 67 0.48
70 30 0.22
71 2 0.01
72 17 0.12
73 2 0.01
ACGTcount: A:0.30, C:0.11, G:0.12, T:0.47
Consensus pattern (69 bp):
TCGTGTTTCAAAAAATTTCGTGTTTTAAAAATTTTCGTGTTTCTAAAATTTCTGTGTTTTAAAAA
AATT
Found at i:20228645 original size:18 final size:18
Alignment explanation
Indices: 20228602--20228648 Score: 67
Period size: 18 Copynumber: 2.6 Consensus size: 18
20228592 TGTAATTTTT
*
20228602 ATAATTGGGTTGGGTTGG
1 ATAATTGGGTTGGGTTGA
*
20228620 GTAATTGGGTTGGGTTGA
1 ATAATTGGGTTGGGTTGA
*
20228638 ATACTTGGGTT
1 ATAATTGGGTT
20228649 TGGATTGGGT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.17, C:0.02, G:0.40, T:0.40
Consensus pattern (18 bp):
ATAATTGGGTTGGGTTGA
Found at i:20233331 original size:21 final size:21
Alignment explanation
Indices: 20233303--20233386 Score: 57
Period size: 21 Copynumber: 4.0 Consensus size: 21
20233293 TGAACGGAAG
20233303 ATCC-TAAGAGCTAAACGAAA
1 ATCCATAAGAGCTAAACGAAA
* * * *
20233323 ATCCATAAGGGTTGAACGGAA
1 ATCCATAAGAGCTAAACGAAA
* *
20233344 ACCCATAAG-GATTAAAC-AAA
1 ATCCATAAGAG-CTAAACGAAA
* *
20233364 AGCTCAAAAGAGCTAAACGAAA
1 ATC-CATAAGAGCTAAACGAAA
20233386 A
1 A
20233387 CTCATATGAG
Statistics
Matches: 49, Mismatches: 10, Indels: 8
0.73 0.15 0.12
Matches are distributed among these distances:
20 9 0.18
21 35 0.71
22 5 0.10
ACGTcount: A:0.50, C:0.18, G:0.18, T:0.14
Consensus pattern (21 bp):
ATCCATAAGAGCTAAACGAAA
Found at i:20233360 original size:42 final size:41
Alignment explanation
Indices: 20233265--20233352 Score: 106
Period size: 42 Copynumber: 2.1 Consensus size: 41
20233255 TGGAAGCACA
* * *
20233265 TAAGTGCTAAACAGAAACCCATAAAGGTTGAACGGAAGATCC
1 TAAGAGCTAAACA-AAATCCATAAAGGTTGAACGGAAGACCC
*
20233307 TAAGAGCTAAACGAAAATCCATAAGGGTTGAACGGAA-ACCC
1 TAAGAGCTAAAC-AAAATCCATAAAGGTTGAACGGAAGACCC
20233348 ATAAG
1 -TAAG
20233353 GATTAAACAA
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
41 3 0.08
42 36 0.90
43 1 0.03
ACGTcount: A:0.44, C:0.18, G:0.22, T:0.16
Consensus pattern (41 bp):
TAAGAGCTAAACAAAATCCATAAAGGTTGAACGGAAGACCC
Found at i:20233401 original size:21 final size:21
Alignment explanation
Indices: 20233355--20233410 Score: 51
Period size: 21 Copynumber: 2.7 Consensus size: 21
20233345 CCCATAAGGA
20233355 TTAAACAAAAGCTCAAAAGAG
1 TTAAACAAAAGCTCAAAAGAG
* * *
20233376 CTAAACGAAAA-CTCATATGAG
1 TTAAAC-AAAAGCTCAAAAGAG
* *
20233397 TTAAATAGAAGCTC
1 TTAAACAAAAGCTC
20233411 GTGAGAGTTA
Statistics
Matches: 27, Mismatches: 6, Indels: 4
0.73 0.16 0.11
Matches are distributed among these distances:
20 3 0.11
21 20 0.74
22 4 0.15
ACGTcount: A:0.50, C:0.16, G:0.14, T:0.20
Consensus pattern (21 bp):
TTAAACAAAAGCTCAAAAGAG
Found at i:20233848 original size:21 final size:21
Alignment explanation
Indices: 20233820--20233903 Score: 57
Period size: 21 Copynumber: 4.0 Consensus size: 21
20233810 TGAACGGAAG
20233820 ATCC-TAAGAGCTAAACGAAA
1 ATCCATAAGAGCTAAACGAAA
* * * *
20233840 ATCCATAAGGGTTGAACGGAA
1 ATCCATAAGAGCTAAACGAAA
* *
20233861 ACCCATAAG-GATTAAAC-AAA
1 ATCCATAAGAG-CTAAACGAAA
* *
20233881 AGCTCAAAAGAGCTAAACGAAA
1 ATC-CATAAGAGCTAAACGAAA
20233903 A
1 A
20233904 CTCATATGAG
Statistics
Matches: 49, Mismatches: 10, Indels: 8
0.73 0.15 0.12
Matches are distributed among these distances:
20 9 0.18
21 35 0.71
22 5 0.10
ACGTcount: A:0.50, C:0.18, G:0.18, T:0.14
Consensus pattern (21 bp):
ATCCATAAGAGCTAAACGAAA
Found at i:20233877 original size:42 final size:41
Alignment explanation
Indices: 20233782--20233869 Score: 106
Period size: 42 Copynumber: 2.1 Consensus size: 41
20233772 TGGAAGCACA
* * *
20233782 TAAGTGCTAAACAGAAACCCATAAAGGTTGAACGGAAGATCC
1 TAAGAGCTAAACA-AAATCCATAAAGGTTGAACGGAAGACCC
*
20233824 TAAGAGCTAAACGAAAATCCATAAGGGTTGAACGGAA-ACCC
1 TAAGAGCTAAAC-AAAATCCATAAAGGTTGAACGGAAGACCC
20233865 ATAAG
1 -TAAG
20233870 GATTAAACAA
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
41 3 0.08
42 36 0.90
43 1 0.03
ACGTcount: A:0.44, C:0.18, G:0.22, T:0.16
Consensus pattern (41 bp):
TAAGAGCTAAACAAAATCCATAAAGGTTGAACGGAAGACCC
Found at i:20233918 original size:21 final size:21
Alignment explanation
Indices: 20233872--20233927 Score: 51
Period size: 21 Copynumber: 2.7 Consensus size: 21
20233862 CCCATAAGGA
20233872 TTAAACAAAAGCTCAAAAGAG
1 TTAAACAAAAGCTCAAAAGAG
* * *
20233893 CTAAACGAAAA-CTCATATGAG
1 TTAAAC-AAAAGCTCAAAAGAG
* *
20233914 TTAAATAGAAGCTC
1 TTAAACAAAAGCTC
20233928 GTGAGAGTTA
Statistics
Matches: 27, Mismatches: 6, Indels: 4
0.73 0.16 0.11
Matches are distributed among these distances:
20 3 0.11
21 20 0.74
22 4 0.15
ACGTcount: A:0.50, C:0.16, G:0.14, T:0.20
Consensus pattern (21 bp):
TTAAACAAAAGCTCAAAAGAG
Found at i:20234058 original size:517 final size:517
Alignment explanation
Indices: 20233085--20234120 Score: 2045
Period size: 517 Copynumber: 2.0 Consensus size: 517
20233075 TTTCTTATCG
*
20233085 AAAATTTCATACGTCATTCCTATCATAATGCAGACCATGCAATAATATTAAAATAATTTTTCTTT
1 AAAATTTCATACGTCATTCCTATCATAATGCAAACCATGCAATAATATTAAAATAATTTTTCTTT
20233150 CTTACTCAAATTTGTGGTCCCAAAATCACTGAAAACGGGCTGTTACAAAATCAGAGAACGGCTTA
66 CTTACTCAAATTTGTGGTCCCAAAATCACTGAAAACGGGCTGTTACAAAATCAGAGAACGGCTTA
20233215 CAGATAAAAATACATCATTTTCAAAAGCCCGAAGCCTGAATGGAAGCACATAAGTGCTAAACAGA
131 CAGATAAAAATACATCATTTTCAAAAGCCCGAAGCCTGAATGGAAGCACATAAGTGCTAAACAGA
20233280 AACCCATAAAGGTTGAACGGAAGATCCTAAGAGCTAAACGAAAATCCATAAGGGTTGAACGGAAA
196 AACCCATAAAGGTTGAACGGAAGATCCTAAGAGCTAAACGAAAATCCATAAGGGTTGAACGGAAA
20233345 CCCATAAGGATTAAACAAAAGCTCAAAAGAGCTAAACGAAAACTCATATGAGTTAAATAGAAGCT
261 CCCATAAGGATTAAACAAAAGCTCAAAAGAGCTAAACGAAAACTCATATGAGTTAAATAGAAGCT
20233410 CGTGAGAGTTAAACGGAAAGTAAACACGTAAGTTCGCAACAAATGCTGAACCTCGATTTACTTGG
326 CGTGAGAGTTAAACGGAAAGTAAACACGTAAGTTCGCAACAAATGCTGAACCTCGATTTACTTGG
20233475 GTAATTTGCTGTCACTTTCCTTCAATGCCGTCAATTCATCAATTGCTGAATGTACTCATATCCTG
391 GTAATTTGCTGTCACTTTCCTTCAATGCCGTCAATTCATCAATTGCTGAATGTACTCATATCCTG
*
20233540 CGTTCTATTTAGTTCGAATATTCAATTTAATTTTATAACTTTAACAATATTTCGTTTTCAAC
456 CGTTCTATTTAGTCCGAATATTCAATTTAATTTTATAACTTTAACAATATTTCGTTTTCAAC
20233602 AAAATTTCATACGTCATTCCTATCATAATGCAAACCATGCAATAATATTAAAATAATTTTTCTTT
1 AAAATTTCATACGTCATTCCTATCATAATGCAAACCATGCAATAATATTAAAATAATTTTTCTTT
*
20233667 CTTACTCAGATTTGTGGTCCCAAAATCACTGAAAACGGGCTGTTACAAAATCAGAGAACGGCTTA
66 CTTACTCAAATTTGTGGTCCCAAAATCACTGAAAACGGGCTGTTACAAAATCAGAGAACGGCTTA
20233732 CAGATAAAAATACATCATTTTCAAAAGCCCGAAGCCTGAATGGAAGCACATAAGTGCTAAACAGA
131 CAGATAAAAATACATCATTTTCAAAAGCCCGAAGCCTGAATGGAAGCACATAAGTGCTAAACAGA
20233797 AACCCATAAAGGTTGAACGGAAGATCCTAAGAGCTAAACGAAAATCCATAAGGGTTGAACGGAAA
196 AACCCATAAAGGTTGAACGGAAGATCCTAAGAGCTAAACGAAAATCCATAAGGGTTGAACGGAAA
20233862 CCCATAAGGATTAAACAAAAGCTCAAAAGAGCTAAACGAAAACTCATATGAGTTAAATAGAAGCT
261 CCCATAAGGATTAAACAAAAGCTCAAAAGAGCTAAACGAAAACTCATATGAGTTAAATAGAAGCT
20233927 CGTGAGAGTTAAACGGAAAGTAAACACGTAAGTTCGCAACAAATGCTGAACCTCGATTTACTTGG
326 CGTGAGAGTTAAACGGAAAGTAAACACGTAAGTTCGCAACAAATGCTGAACCTCGATTTACTTGG
20233992 GTAATTTGCTGTCACTTTCCTTCAATGCCGTCAATTCATCAATTGCTGAATGTACTCATATCCTG
391 GTAATTTGCTGTCACTTTCCTTCAATGCCGTCAATTCATCAATTGCTGAATGTACTCATATCCTG
20234057 CGTTCTATTTAGTCCGAATATTCAATTTAATTTTATAACTTTAACAATATTTCGTTTTCAAC
456 CGTTCTATTTAGTCCGAATATTCAATTTAATTTTATAACTTTAACAATATTTCGTTTTCAAC
20234119 AA
1 AA
20234121 TAGAATAAAT
Statistics
Matches: 516, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
517 516 1.00
ACGTcount: A:0.38, C:0.19, G:0.15, T:0.28
Consensus pattern (517 bp):
AAAATTTCATACGTCATTCCTATCATAATGCAAACCATGCAATAATATTAAAATAATTTTTCTTT
CTTACTCAAATTTGTGGTCCCAAAATCACTGAAAACGGGCTGTTACAAAATCAGAGAACGGCTTA
CAGATAAAAATACATCATTTTCAAAAGCCCGAAGCCTGAATGGAAGCACATAAGTGCTAAACAGA
AACCCATAAAGGTTGAACGGAAGATCCTAAGAGCTAAACGAAAATCCATAAGGGTTGAACGGAAA
CCCATAAGGATTAAACAAAAGCTCAAAAGAGCTAAACGAAAACTCATATGAGTTAAATAGAAGCT
CGTGAGAGTTAAACGGAAAGTAAACACGTAAGTTCGCAACAAATGCTGAACCTCGATTTACTTGG
GTAATTTGCTGTCACTTTCCTTCAATGCCGTCAATTCATCAATTGCTGAATGTACTCATATCCTG
CGTTCTATTTAGTCCGAATATTCAATTTAATTTTATAACTTTAACAATATTTCGTTTTCAAC
Found at i:20235711 original size:23 final size:22
Alignment explanation
Indices: 20235666--20235720 Score: 58
Period size: 22 Copynumber: 2.5 Consensus size: 22
20235656 TTATCGATAT
* *
20235666 TTATAAAAATATATTTAATATA
1 TTATATAAATATATTTAAAATA
20235688 TGTATATAAA-ATATTTACAAATA
1 T-TATATAAATATATTTA-AAATA
*
20235711 TCATATAAAT
1 TTATATAAAT
20235721 GATACTAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
22 15 0.56
23 12 0.44
ACGTcount: A:0.53, C:0.04, G:0.02, T:0.42
Consensus pattern (22 bp):
TTATATAAATATATTTAAAATA
Found at i:20237415 original size:34 final size:35
Alignment explanation
Indices: 20237376--20237441 Score: 91
Period size: 34 Copynumber: 1.9 Consensus size: 35
20237366 TAGATATATA
* *
20237376 ATTTTTATATTTGAA-ATAAAT-TTTCATAAAAAAT
1 ATTTTTATATCT-AATATAAATATTACATAAAAAAT
20237410 ATTTTTATATCTAATATAAATATTACATAAAA
1 ATTTTTATATCTAATATAAATATTACATAAAA
20237442 TACATTAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
33 2 0.07
34 17 0.61
35 9 0.32
ACGTcount: A:0.48, C:0.05, G:0.02, T:0.45
Consensus pattern (35 bp):
ATTTTTATATCTAATATAAATATTACATAAAAAAT
Found at i:20238687 original size:17 final size:17
Alignment explanation
Indices: 20238656--20238703 Score: 71
Period size: 17 Copynumber: 2.9 Consensus size: 17
20238646 GAATTTAGAA
*
20238656 GAATTTT-TGAATTAGT
1 GAATTTTGTGATTTAGT
20238672 GAATTTTGTGATTTAGT
1 GAATTTTGTGATTTAGT
*
20238689 GAATTTTGCGATTTA
1 GAATTTTGTGATTTA
20238704 AAAAGAATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
16 7 0.24
17 22 0.76
ACGTcount: A:0.27, C:0.02, G:0.21, T:0.50
Consensus pattern (17 bp):
GAATTTTGTGATTTAGT
Found at i:20241270 original size:5 final size:5
Alignment explanation
Indices: 20241260--20241285 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
20241250 CTCGAAAATT
20241260 TTCGA TTCGA TTCGA TTCGA TTCGA T
1 TTCGA TTCGA TTCGA TTCGA TTCGA T
20241286 CGAATGCTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.19, C:0.19, G:0.19, T:0.42
Consensus pattern (5 bp):
TTCGA
Found at i:20242322 original size:46 final size:45
Alignment explanation
Indices: 20242255--20242482 Score: 366
Period size: 46 Copynumber: 5.0 Consensus size: 45
20242245 CATGACAAAG
* *
20242255 TGTGAAACGTAGGTATGGTATTTCAGTGAAGAAAACCATACTGAGT
1 TGTGAAAAGTAGGTATGGTATTTC-GTAAAGAAAACCATACTGAGT
20242301 TGTGAAAAGTAGGTATGGTATTTCGATAAAGAAAACCATACTGAGT
1 TGTGAAAAGTAGGTATGGTATTTCG-TAAAGAAAACCATACTGAGT
20242347 TGTGAAAAGTAGGTATGGTATTTCGATAAAGAAAACCATACTGAGT
1 TGTGAAAAGTAGGTATGGTATTTCG-TAAAGAAAACCATACTGAGT
* *
20242393 TGTGAAAAGTAGGTATGGTGTTTCAGTAAAGAAAGCCATACTGAGT
1 TGTGAAAAGTAGGTATGGTATTTC-GTAAAGAAAACCATACTGAGT
*
20242439 TGTGAAAAGTAGGTATGGTATTTCCGTGAAGAAAACCATACTGA
1 TGTGAAAAGTAGGTATGGTATTT-CGTAAAGAAAACCATACTGA
20242483 ATTATAGCAA
Statistics
Matches: 172, Mismatches: 7, Indels: 6
0.93 0.04 0.03
Matches are distributed among these distances:
45 1 0.01
46 169 0.98
47 2 0.01
ACGTcount: A:0.37, C:0.10, G:0.25, T:0.28
Consensus pattern (45 bp):
TGTGAAAAGTAGGTATGGTATTTCGTAAAGAAAACCATACTGAGT
Found at i:20249050 original size:26 final size:26
Alignment explanation
Indices: 20249029--20249113 Score: 116
Period size: 26 Copynumber: 3.3 Consensus size: 26
20249019 AAAATTATTG
* * *
20249029 AAATACTCTCAATGGTTAAATTACAA
1 AAATACCCTCAATGGGTAAATTACCA
20249055 AAATACCCTCAATGGGTAAATTACCA
1 AAATACCCTCAATGGGTAAATTACCA
* * *
20249081 AAATACCCTCGATGGGTAAATTATCG
1 AAATACCCTCAATGGGTAAATTACCA
20249107 AAATACC
1 AAATACC
20249114 TCCGAAAGGT
Statistics
Matches: 53, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 53 1.00
ACGTcount: A:0.42, C:0.20, G:0.12, T:0.26
Consensus pattern (26 bp):
AAATACCCTCAATGGGTAAATTACCA
Found at i:20249124 original size:26 final size:26
Alignment explanation
Indices: 20249045--20249124 Score: 74
Period size: 26 Copynumber: 3.1 Consensus size: 26
20249035 TCTCAATGGT
* *
20249045 TAAATTACAAAAATACCCTC-AATGGG
1 TAAATTACCAAAATACCCTCGAA-AGG
**
20249071 TAAATTACCAAAATACCCTCGATGGG
1 TAAATTACCAAAATACCCTCGAAAGG
* *
20249097 TAAATTATCGAAATA-CCTCCGAAAGG
1 TAAATTACCAAAATACCCT-CGAAAGG
20249123 TA
1 TA
20249125 GAATGACCGT
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
25 3 0.07
26 42 0.91
27 1 0.02
ACGTcount: A:0.42, C:0.20, G:0.14, T:0.24
Consensus pattern (26 bp):
TAAATTACCAAAATACCCTCGAAAGG
Found at i:20252649 original size:5 final size:5
Alignment explanation
Indices: 20252639--20252665 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
20252629 TAATTTGATG
20252639 AATAA AATAA AATAA AATAA AATAA AA
1 AATAA AATAA AATAA AATAA AATAA AA
20252666 ACAAAAGCTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AATAA
Found at i:20258164 original size:17 final size:17
Alignment explanation
Indices: 20258142--20258186 Score: 72
Period size: 17 Copynumber: 2.6 Consensus size: 17
20258132 TTTTAATAAT
* *
20258142 TATTTTTATTTTTTGTG
1 TATTTTAATTTTTTATG
20258159 TATTTTAATTTTTTATG
1 TATTTTAATTTTTTATG
20258176 TATTTTAATTT
1 TATTTTAATTT
20258187 ATTTTTAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.20, C:0.00, G:0.07, T:0.73
Consensus pattern (17 bp):
TATTTTAATTTTTTATG
Found at i:20265743 original size:14 final size:14
Alignment explanation
Indices: 20265721--20265763 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
20265711 TGAATAAAGG
* *
20265721 AATACTATAATACT
1 AATAATATAATAAT
20265735 AATAATATAATAAT
1 AATAATATAATAAT
*
20265749 AATAAGATTAATAAT
1 AATAATA-TAATAAT
20265764 CACGTCATAG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
14 18 0.72
15 7 0.28
ACGTcount: A:0.58, C:0.05, G:0.02, T:0.35
Consensus pattern (14 bp):
AATAATATAATAAT
Found at i:20265998 original size:4 final size:4
Alignment explanation
Indices: 20265989--20266030 Score: 59
Period size: 4 Copynumber: 10.8 Consensus size: 4
20265979 ATAAAAATAA
* *
20265989 AAAT AAAT AAGT -AAT AAAT GAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
20266031 ATTTTGTAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
3 2 0.06
4 31 0.94
ACGTcount: A:0.71, C:0.00, G:0.05, T:0.24
Consensus pattern (4 bp):
AAAT
Found at i:20267720 original size:42 final size:42
Alignment explanation
Indices: 20267661--20267744 Score: 98
Period size: 42 Copynumber: 2.0 Consensus size: 42
20267651 CTATATACAC
* * * *
20267661 CACACGGCTTGGACACATGCCCGTGTCCTTGTACGTGTGGTT
1 CACACGGCTAGGACACATGCCCATGTCCTTGCACGTATGGTT
* *
20267703 CACACGGCCTAGG-CACATGTCTATGTCCTTGCACGTATGGTT
1 CACACGG-CTAGGACACATGCCCATGTCCTTGCACGTATGGTT
20267745 TTAAAGCATA
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
42 31 0.89
43 4 0.11
ACGTcount: A:0.17, C:0.29, G:0.26, T:0.29
Consensus pattern (42 bp):
CACACGGCTAGGACACATGCCCATGTCCTTGCACGTATGGTT
Found at i:20269030 original size:2 final size:2
Alignment explanation
Indices: 20269023--20269710 Score: 1349
Period size: 2 Copynumber: 344.0 Consensus size: 2
20269013 ATGTATAAAC
20269023 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
20269065 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
20269107 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
20269149 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
20269191 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
20269233 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
20269275 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
20269317 AT AT AT AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
20269359 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
20269401 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
20269443 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
20269485 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
20269527 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
20269569 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
20269611 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
20269653 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AG AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
20269695 AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT
20269711 GCGCGCACAA
Statistics
Matches: 680, Mismatches: 6, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
2 680 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:20271003 original size:2 final size:2
Alignment explanation
Indices: 20270998--20271054 Score: 105
Period size: 2 Copynumber: 28.5 Consensus size: 2
20270988 ACATACATAC
20270998 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
20271040 AT AT AT AC AT AT AT A
1 AT AT AT AT AT AT AT A
20271055 AGTATAATAA
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:20271066 original size:3 final size:3
Alignment explanation
Indices: 20271058--20271142 Score: 75
Period size: 3 Copynumber: 27.3 Consensus size: 3
20271048 ATATATAAGT
* * *
20271058 ATA ATA ATA TTA ATA TGTA AT- ATA ATA ATAA ATA ATA CTA ATA ATA
1 ATA ATA ATA ATA ATA -ATA ATA ATA ATA AT-A ATA ATA ATA ATA ATA
*
20271104 ATA CAGTA ATA ATA ACA ATA ATA ATA ATTA AT- ATA ATA A
1 ATA -A-TA ATA ATA ATA ATA ATA ATA A-TA ATA ATA ATA A
20271143 ACTTAATGAT
Statistics
Matches: 67, Mismatches: 8, Indels: 14
0.75 0.09 0.16
Matches are distributed among these distances:
2 4 0.06
3 51 0.76
4 10 0.15
5 2 0.03
ACGTcount: A:0.60, C:0.04, G:0.02, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:20271071 original size:6 final size:5
Alignment explanation
Indices: 20270998--20271141 Score: 50
Period size: 6 Copynumber: 26.6 Consensus size: 5
20270988 ACATACATAC
*
20270998 ATAT- ATATA TATATA TATATA TATATA TATATA TATATA TATATA TATACA
1 ATATA ATATA -ATATA -ATATA -ATATA -ATATA -ATATA -ATATA -ATATA
20271049 TATATA AGTAT- A-ATA ATATTA ATATGTA ATATA ATAATA A-ATA ATACTA
1 -ATATA A-TATA ATATA ATA-TA ATA--TA ATATA AT-ATA ATATA ATA-TA
* *
20271098 ATAATA ATACA GTAATA ATA-A CA-ATA ATAATA AT-TA ATATA ATA
1 AT-ATA ATATA AT-ATA ATATA -ATATA AT-ATA ATATA ATATA ATA
20271142 AACTTAATGA
Statistics
Matches: 116, Mismatches: 7, Indels: 33
0.74 0.04 0.21
Matches are distributed among these distances:
3 2 0.02
4 16 0.14
5 19 0.16
6 73 0.63
7 6 0.05
ACGTcount: A:0.56, C:0.03, G:0.02, T:0.40
Consensus pattern (5 bp):
ATATA
Found at i:20271139 original size:12 final size:11
Alignment explanation
Indices: 20271000--20271142 Score: 62
Period size: 14 Copynumber: 11.8 Consensus size: 11
20270990 ATACATACAT
20271000 ATATATATATATA
1 ATATA-ATA-ATA
20271013 TATATATATATATA
1 -ATATA-ATA-ATA
20271027 TATATATATATATA
1 -ATATA-ATA-ATA
20271041 TATATACATATATA
1 -ATATA-ATA-ATA
20271055 AGTATAATAAT-
1 A-TATAATAATA
*
20271066 AT-TAATATGTA
1 ATATAATA-ATA
20271077 ATATAATAATA
1 ATATAATAATA
*
20271088 A-ATAATACT-
1 ATATAATAATA
20271097 A-ATAATAATA
1 ATATAATAATA
*
20271107 CAGTAATAATAACA
1 -A-T-ATAATAATA
20271121 ATAATAATAATTA
1 AT-ATAATAA-TA
20271134 ATATAATAA
1 ATATAATAA
20271143 ACTTAATGAT
Statistics
Matches: 112, Mismatches: 7, Indels: 22
0.79 0.05 0.16
Matches are distributed among these distances:
9 13 0.12
10 9 0.08
11 7 0.06
12 23 0.21
13 8 0.07
14 52 0.46
ACGTcount: A:0.56, C:0.03, G:0.02, T:0.39
Consensus pattern (11 bp):
ATATAATAATA
Found at i:20271713 original size:21 final size:22
Alignment explanation
Indices: 20271680--20271730 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
20271670 TTTTTTTACA
*
20271680 AAAAAAAACAACAG-AAAAATG
1 AAAAAAAACAACAGTAAAAAGG
20271701 AAAACAAAA-AACAGTAAAAAGG
1 AAAA-AAAACAACAGTAAAAAGG
20271723 AAAAAAAA
1 AAAAAAAA
20271731 TGGAGAAATC
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
21 13 0.48
22 14 0.52
ACGTcount: A:0.78, C:0.08, G:0.10, T:0.04
Consensus pattern (22 bp):
AAAAAAAACAACAGTAAAAAGG
Found at i:20272713 original size:50 final size:50
Alignment explanation
Indices: 20272637--20273720 Score: 423
Period size: 50 Copynumber: 21.6 Consensus size: 50
20272627 ACAATGTCGA
* * * * * *
20272637 GGAAACAAGATCCGCCATCGTAGCTTCAACCTGTTCAACTGCACCGCTAA
1 GGAAATAAGATCCGCCGTTGTGGCTTCAATCTGTTCAACTGCACCGCTAG
* * * ** * *
20272687 GGAAATAAGATCCGCCGTTGTGGCTTCAATCTTTTTAATTGTGCTG-TCGG
1 GGAAATAAGATCCGCCGTTGTGGCTTCAATCTGTTCAACTGCACCGCT-AG
* * * * * * *
20272737 GGAAATCAGATCCGTCGTTGTGACTTCAATCATGCTCCACTGCATCGCCAG
1 GGAAATAAGATCCGCCGTTGTGGCTTCAATC-TGTTCAACTGCACCGCTAG
* ** * * * * * * * *
20272788 GGAAGTAAGATATGCCATTGTGGCTTCAATCTTTTTAATTGCGCTGTTGG
1 GGAAATAAGATCCGCCGTTGTGGCTTCAATCTGTTCAACTGCACCGCTAG
** * ** * **
20272838 GGAAACCAGATCCGTCGTTGTGAATTCAATCTGCTCCGCTGCACCGCTA-
1 GGAAATAAGATCCGCCGTTGTGGCTTCAATCTGTTCAACTGCACCGCTAG
* * * * * * *
20272887 GGAAAGTAAGATCCGCCGTTGTGGCTTTAATCTTTTTAATTGCGCTG-TCGG
1 GGAAA-TAAGATCCGCCGTTGTGGCTTCAATCTGTTCAACTGCACCGCT-AG
* * * *
20272938 GGAAACT-AGATCCGCCGTTGTGACTTCAATCTGCTCCACTGCACCGCCAG
1 GGAAA-TAAGATCCGCCGTTGTGGCTTCAATCTGTTCAACTGCACCGCTAG
* * * * * * * *
20272988 GGAAGTAAGATCTGCCGTTGTGGCTTCAATCCT-TTTAATTACGCTG-TCGG
1 GGAAATAAGATCCGCCGTTGTGGCTTCAAT-CTGTTCAACTGCACCGCT-AG
** * * * * * *
20273038 GGAAACT-AGATCCGTTGTCGTGACTTCAATCTGCTCCACTACACCGCCAG
1 GGAAA-TAAGATCCGCCGTTGTGGCTTCAATCTGTTCAACTGCACCGCTAG
* * ** * * *
20273088 AGAAGTAAGATCTACCGTTGTGGCTTCAATCT-TTTAAAT-TA-CGCTATCGG
1 GGAAATAAGATCCGCCGTTGTGGCTTCAATCTGTTCAACTGCACCGCTA---G
** ** * * * * *
20273138 GGAAACCAGATCCGTTGTTGTGACTTCAATCTGCTCCACTACACCGCCAG
1 GGAAATAAGATCCGCCGTTGTGGCTTCAATCTGTTCAACTGCACCGCTAG
* * * * * * * * * * *
20273188 AGAAGTAAGATCTGCCGTTGTGGCTTCAATCTTTTAAATTACGCTGTTGG
1 GGAAATAAGATCCGCCGTTGTGGCTTCAATCTGTTCAACTGCACCGCTAG
** * * * * *
20273238 GGAAACCAGATCCGCCGTTGTGACTTCAATCTGCTCCACTGCACCGCCAC
1 GGAAATAAGATCCGCCGTTGTGGCTTCAATCTGTTCAACTGCACCGCTAG
* * * * * ** * *
20273288 GGAAGTAAGATCTGCCGTTGTGGCTTCAATCCTTTTAAATTGTGCTG-TCG
1 GGAAATAAGATCCGCCGTTGTGGCTTCAAT-CTGTTCAACTGCACCGCTAG
** * * * * * *
20273338 AGGAAACCAGATCTGCCGTTGTGACTTCAATCTGCTCCACTACACCGCCAG
1 -GGAAATAAGATCCGCCGTTGTGGCTTCAATCTGTTCAACTGCACCGCTAG
* * * * * * * *
20273389 GGAAGTAAAATCCGCCGTTGTGGCTTCAATCTTTTTAATTGCGCTG-TCG
1 GGAAATAAGATCCGCCGTTGTGGCTTCAATCTGTTCAACTGCACCGCTAG
** * * * *
20273438 AGGAAACCAGATCCGCCGTTGTGACTTCAATCTGCTCCACTGCACCGCCAG
1 -GGAAATAAGATCCGCCGTTGTGGCTTCAATCTGTTCAACTGCACCGCTAG
* * * * * * * *
20273489 GGAAGTAAGATCCGTCGTTGTGGCTTCAATCTTTTTAATTGCGCTG-TCG
1 GGAAATAAGATCCGCCGTTGTGGCTTCAATCTGTTCAACTGCACCGCTAG
** * * ** * *
20273538 GAGAAACCAGATCCGCCGTTGTGACTTCAATCTGCTCCGCTGCACCACCAG
1 G-GAAATAAGATCCGCCGTTGTGGCTTCAATCTGTTCAACTGCACCGCTAG
** * * * * * *
20273589 GGAAGCATGATCCGCCGTTGTGGCTTCAATCTTTTTAATTGCGCTG-TCAG
1 GGAAATAAGATCCGCCGTTGTGGCTTCAATCTGTTCAACTGCACCGCT-AG
** * * * * * ** *
20273639 GGAAACCAGATCTGTCGTTGTGACTTCAATTTGCTCCGCTGCACCGCCAG
1 GGAAATAAGATCCGCCGTTGTGGCTTCAATCTGTTCAACTGCACCGCTAG
* *
20273689 GGAAGTAAGATCTGCCGTTGTGGCTTCAATCT
1 GGAAATAAGATCCGCCGTTGTGGCTTCAATCT
20273721 TTTAATTGTG
Statistics
Matches: 696, Mismatches: 309, Indels: 58
0.65 0.29 0.05
Matches are distributed among these distances:
47 4 0.01
48 1 0.00
49 17 0.02
50 588 0.84
51 81 0.12
52 1 0.00
53 4 0.01
ACGTcount: A:0.22, C:0.26, G:0.23, T:0.29
Consensus pattern (50 bp):
GGAAATAAGATCCGCCGTTGTGGCTTCAATCTGTTCAACTGCACCGCTAG
Found at i:20272929 original size:100 final size:100
Alignment explanation
Indices: 20272631--20273772 Score: 1631
Period size: 100 Copynumber: 11.4 Consensus size: 100
20272621 CCAATTACAA
* * * * * * * * * *
20272631 TGTCGAGGAAACAAGATCCGCCATCGT-AGCTTCAACCTGTTCAACTGCACCGCTAAGGAAATAA
1 TGTCGGGGAAACCAGATCCGCCGTTGTGA-CTTCAATCTGCTCCACTGCACCGCCAGGGAAGTAA
* *
20272695 GATCCGCCGTTGTGGCTTCAATCTTTTTAATTGTGC
65 GATCTGCCGTTGTGGCTTCAATCTTTTTAATTGCGC
* * *
20272731 TGTCGGGGAAATCAGATCCGTCGTTGTGACTTCAATCATGCTCCACTGCATCGCCAGGGAAGTAA
1 TGTCGGGGAAACCAGATCCGCCGTTGTGACTTCAATC-TGCTCCACTGCACCGCCAGGGAAGTAA
* *
20272796 GATATGCCATTGTGGCTTCAATCTTTTTAATTGCGC
65 GATCTGCCGTTGTGGCTTCAATCTTTTTAATTGCGC
* * * * * *
20272832 TGTTGGGGAAACCAGATCCGTCGTTGTGAATTCAATCTGCTCCGCTGCACCGCTAGGAAAGTAAG
1 TGTCGGGGAAACCAGATCCGCCGTTGTGACTTCAATCTGCTCCACTGCACCGCCAGGGAAGTAAG
* *
20272897 ATCCGCCGTTGTGGCTTTAATCTTTTTAATTGCGC
66 ATCTGCCGTTGTGGCTTCAATCTTTTTAATTGCGC
*
20272932 TGTCGGGGAAACTAGATCCGCCGTTGTGACTTCAATCTGCTCCACTGCACCGCCAGGGAAGTAAG
1 TGTCGGGGAAACCAGATCCGCCGTTGTGACTTCAATCTGCTCCACTGCACCGCCAGGGAAGTAAG
* *
20272997 ATCTGCCGTTGTGGCTTCAATCCTTTTAATTACGC
66 ATCTGCCGTTGTGGCTTCAATCTTTTTAATTGCGC
* ** * * *
20273032 TGTCGGGGAAACTAGATCCGTTGTCGTGACTTCAATCTGCTCCACTACACCGCCAGAGAAGTAAG
1 TGTCGGGGAAACCAGATCCGCCGTTGTGACTTCAATCTGCTCCACTGCACCGCCAGGGAAGTAAG
* * *
20273097 ATCTACCGTTGTGGCTTCAATCTTTTAAATTACGC
66 ATCTGCCGTTGTGGCTTCAATCTTTTTAATTGCGC
* ** * *
20273132 TATCGGGGAAACCAGATCCGTTGTTGTGACTTCAATCTGCTCCACTACACCGCCAGAGAAGTAAG
1 TGTCGGGGAAACCAGATCCGCCGTTGTGACTTCAATCTGCTCCACTGCACCGCCAGGGAAGTAAG
* *
20273197 ATCTGCCGTTGTGGCTTCAATCTTTTAAATTACGC
66 ATCTGCCGTTGTGGCTTCAATCTTTTTAATTGCGC
* *
20273232 TGTTGGGGAAACCAGATCCGCCGTTGTGACTTCAATCTGCTCCACTGCACCGCCACGGAAGTAAG
1 TGTCGGGGAAACCAGATCCGCCGTTGTGACTTCAATCTGCTCCACTGCACCGCCAGGGAAGTAAG
* *
20273297 ATCTGCCGTTGTGGCTTCAATCCTTTTAAATTGTGC
66 ATCTGCCGTTGTGGCTTCAAT-CTTTTTAATTGCGC
* * * *
20273333 TGTCGAGGAAACCAGATCTGCCGTTGTGACTTCAATCTGCTCCACTACACCGCCAGGGAAGTAAA
1 TGTCGGGGAAACCAGATCCGCCGTTGTGACTTCAATCTGCTCCACTGCACCGCCAGGGAAGTAAG
*
20273398 ATCCGCCGTTGTGGCTTCAATCTTTTTAATTGCGC
66 ATCTGCCGTTGTGGCTTCAATCTTTTTAATTGCGC
*
20273433 TGTCGAGGAAACCAGATCCGCCGTTGTGACTTCAATCTGCTCCACTGCACCGCCAGGGAAGTAAG
1 TGTCGGGGAAACCAGATCCGCCGTTGTGACTTCAATCTGCTCCACTGCACCGCCAGGGAAGTAAG
* *
20273498 ATCCGTCGTTGTGGCTTCAATCTTTTTAATTGCGC
66 ATCTGCCGTTGTGGCTTCAATCTTTTTAATTGCGC
* * * * *
20273533 TGTCGGAGAAACCAGATCCGCCGTTGTGACTTCAATCTGCTCCGCTGCACCACCAGGGAAGCATG
1 TGTCGGGGAAACCAGATCCGCCGTTGTGACTTCAATCTGCTCCACTGCACCGCCAGGGAAGTAAG
*
20273598 ATCCGCCGTTGTGGCTTCAATCTTTTTAATTGCGC
66 ATCTGCCGTTGTGGCTTCAATCTTTTTAATTGCGC
* * * * *
20273633 TGTCAGGGAAACCAGATCTGTCGTTGTGACTTCAATTTGCTCCGCTGCACCGCCAGGGAAGTAAG
1 TGTCGGGGAAACCAGATCCGCCGTTGTGACTTCAATCTGCTCCACTGCACCGCCAGGGAAGTAAG
*
20273698 ATCTGCCGTTGTGGCTTCAATC-TTTTAATTGTGC
66 ATCTGCCGTTGTGGCTTCAATCTTTTTAATTGCGC
20273732 TGTCGGGGAAACCAGATCCGCCGTTGTGACTTCAATCTGCT
1 TGTCGGGGAAACCAGATCCGCCGTTGTGACTTCAATCTGCT
20273773 TCGCTATAAC
Statistics
Matches: 945, Mismatches: 94, Indels: 7
0.90 0.09 0.01
Matches are distributed among these distances:
99 48 0.05
100 718 0.76
101 179 0.19
ACGTcount: A:0.22, C:0.26, G:0.23, T:0.29
Consensus pattern (100 bp):
TGTCGGGGAAACCAGATCCGCCGTTGTGACTTCAATCTGCTCCACTGCACCGCCAGGGAAGTAAG
ATCTGCCGTTGTGGCTTCAATCTTTTTAATTGCGC
Found at i:20273609 original size:501 final size:499
Alignment explanation
Indices: 20272692--20273772 Score: 1658
Period size: 501 Copynumber: 2.2 Consensus size: 499
20272682 GCTAAGGAAA
* * *
20272692 TAAGATCCGCCGTTGTGGCTTCAATCTTTTTAATTGTGCTGTCGGGGAAATCAGATCCGTCGTTG
1 TAAGATCTGCCGTTGTGGCTTCAATC-TTTTAATTGTGCTGTCGGGGAAACCAGATCCGCCGTTG
* *
20272757 TGACTTCAATCATGCTCCACTGCATCGCCAGGGAAGTAAGATATGCCATTGTGGCTTCAATCTTT
65 TGACTTCAATC-TGCTCCACTGCACCGCCACGGAAGTAAGATATGCCATTGTGGCTTCAATCTTT
* * * * * * *
20272822 TTAATTGCGCTGTTGGGGAAACCAGATCCGTCGTTGTGAATTCAATCTGCTCCGCTGCACCGCTA
129 TAAATTGCGCTGTCGAGGAAACCAGATCCGCCGTTGTGAATTCAATCTGCTCCACTACACCGCCA
* * * *
20272887 GGAAAGTAAGATCCGCCGTTGTGGCTTTAATCTTTTTAATTGCGCTGTCGGGGAAACTAGATCCG
194 GGAAAGTAAAATCCGCCGTTGTGGCTTCAATCTTTTTAATTGCGCTGTCGAGGAAACCAGATCCG
*
20272952 CCGTTGTGACTTCAATCTGCTCCACTGCACCGCCAGGGAAGTAAGATCTGCCGTTGTGGCTTCAA
259 CCGTTGTGACTTCAATCTGCTCCACTGCACCGCCAGGGAAGTAAGATCCGCCGTTGTGGCTTCAA
* * **
20273017 TCCTTTTAATTACGCTGTCGGGGAAACTAGATCCGTTGTCGTGACTTCAATCTGCTCCACTACAC
324 TCCTTTTAATTACGCTGTCGGAGAAACCAGATCCGCCGTCGTGACTTCAATCTGCTCCACTACAC
* * * *
20273082 CGCCAGAGAAGTAAGATCTACCGTTGTGGCTTCAATCTTTTAAATTACGCTATCGGGGAAACCAG
389 CACCAGAGAAGCAAGATCCACCGTTGTGGCTTCAATCTTTTAAATTACGCTATCAGGGAAACCAG
*
20273147 ATCCGTTGTTGTGACTTCAATCTGCTCCACTACACCGCCAGAGAAG
454 ATCCGTCGTTGTGACTTCAATCTGCTCCACTACACCGCCAGAGAAG
** *
20273193 TAAGATCTGCCGTTGTGGCTTCAATCTTTTAAATTACGCTGTTGGGGAAACCAGATCCGCCGTTG
1 TAAGATCTGCCGTTGTGGCTTCAATCTTTT-AATTGTGCTGTCGGGGAAACCAGATCCGCCGTTG
* *
20273258 TGACTTCAATCTGCTCCACTGCACCGCCACGGAAGTAAGATCTGCCGTTGTGGCTTCAATCCTTT
65 TGACTTCAATCTGCTCCACTGCACCGCCACGGAAGTAAGATATGCCATTGTGGCTTCAAT-CTTT
* * *
20273323 TAAATTGTGCTGTCGAGGAAACCAGATCTGCCGTTGTGACTTCAATCTGCTCCACTACACCGCCA
129 TAAATTGCGCTGTCGAGGAAACCAGATCCGCCGTTGTGAATTCAATCTGCTCCACTACACCGCCA
*
20273388 GGGAAGTAAAATCCGCCGTTGTGGCTTCAATCTTTTTAATTGCGCTGTCGAGGAAACCAGATCCG
194 GGAAAGTAAAATCCGCCGTTGTGGCTTCAATCTTTTTAATTGCGCTGTCGAGGAAACCAGATCCG
*
20273453 CCGTTGTGACTTCAATCTGCTCCACTGCACCGCCAGGGAAGTAAGATCCGTCGTTGTGGCTTCAA
259 CCGTTGTGACTTCAATCTGCTCCACTGCACCGCCAGGGAAGTAAGATCCGCCGTTGTGGCTTCAA
* * * * *
20273518 TCTTTTTAATTGCGCTGTCGGAGAAACCAGATCCGCCGTTGTGACTTCAATCTGCTCCGCTGCAC
324 TCCTTTTAATTACGCTGTCGGAGAAACCAGATCCGCCGTCGTGACTTCAATCTGCTCCACTACAC
* * * * * *
20273583 CACCAGGGAAGCATGATCCGCCGTTGTGGCTTCAATCTTTTTAATTGCGCTGTCAGGGAAACCAG
389 CACCAGAGAAGCAAGATCCACCGTTGTGGCTTCAATCTTTTAAATTACGCTATCAGGGAAACCAG
* * * * *
20273648 ATCTGTCGTTGTGACTTCAATTTGCTCCGCTGCACCGCCAGGGAAG
454 ATCCGTCGTTGTGACTTCAATCTGCTCCACTACACCGCCAGAGAAG
20273694 TAAGATCTGCCGTTGTGGCTTCAATCTTTTAATTGTGCTGTCGGGGAAACCAGATCCGCCGTTGT
1 TAAGATCTGCCGTTGTGGCTTCAATCTTTTAATTGTGCTGTCGGGGAAACCAGATCCGCCGTTGT
20273759 GACTTCAATCTGCT
66 GACTTCAATCTGCT
20273773 TCGCTATAAC
Statistics
Matches: 523, Mismatches: 55, Indels: 5
0.90 0.09 0.01
Matches are distributed among these distances:
500 95 0.18
501 428 0.82
ACGTcount: A:0.22, C:0.25, G:0.23, T:0.29
Consensus pattern (499 bp):
TAAGATCTGCCGTTGTGGCTTCAATCTTTTAATTGTGCTGTCGGGGAAACCAGATCCGCCGTTGT
GACTTCAATCTGCTCCACTGCACCGCCACGGAAGTAAGATATGCCATTGTGGCTTCAATCTTTTA
AATTGCGCTGTCGAGGAAACCAGATCCGCCGTTGTGAATTCAATCTGCTCCACTACACCGCCAGG
AAAGTAAAATCCGCCGTTGTGGCTTCAATCTTTTTAATTGCGCTGTCGAGGAAACCAGATCCGCC
GTTGTGACTTCAATCTGCTCCACTGCACCGCCAGGGAAGTAAGATCCGCCGTTGTGGCTTCAATC
CTTTTAATTACGCTGTCGGAGAAACCAGATCCGCCGTCGTGACTTCAATCTGCTCCACTACACCA
CCAGAGAAGCAAGATCCACCGTTGTGGCTTCAATCTTTTAAATTACGCTATCAGGGAAACCAGAT
CCGTCGTTGTGACTTCAATCTGCTCCACTACACCGCCAGAGAAG
Found at i:20275089 original size:15 final size:15
Alignment explanation
Indices: 20275069--20275115 Score: 60
Period size: 15 Copynumber: 3.1 Consensus size: 15
20275059 CCCTAGCCTC
20275069 TCCATTTTTACTTTT
1 TCCATTTTTACTTTT
20275084 TCCATTTTT-CATTTT
1 TCCATTTTTAC-TTTT
* *
20275099 TCTATTTTTATTTTT
1 TCCATTTTTACTTTT
20275114 TC
1 TC
20275116 ACATCTTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
14 1 0.04
15 27 0.96
ACGTcount: A:0.13, C:0.17, G:0.00, T:0.70
Consensus pattern (15 bp):
TCCATTTTTACTTTT
Done.