Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D10
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: 67973905
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.32
Warning! 1760000 characters in sequence are not A, C, G, or T
File 67 of 228
Found at i:20059856 original size:286 final size:286
Alignment explanation
Indices: 20058778--20059957 Score: 2077
Period size: 285 Copynumber: 4.1 Consensus size: 286
20058768 TCTTCGTGTG
20058778 TTTTATTACTTTAAAAAATATCATAATTTCTAATTTTATAAATTTATTAATTTAGTGTGTTTTTA
1 TTTTATTACTTTAAAAAATATCATAATTTCTAATTTTATAAATTTATTAATTTAGTGTGTTTTTA
* ***
20058843 AAATTAATTTAGTGTAAAAAAAACCATTATTCCCGCCATTTGCTCGTATTATTTTCACAAATTTT
66 AAATTAATTTAGTGT-AAAAAAACCCTTATTCCCGCCATTTGCTCGTATTATTTTCGTGAATTTT
*
20058908 ATTACTTTCAATAACATAATTTTATTTTCGTATTTTATTATTTTATATTATTTCAATACATTTTG
130 ATTACTTTCAATAAAATAATTTTATTTTCGTATTTTATTATTTTATATTATTTCAATACATTTTG
*
20058973 TTTCAAATATTCGTATTAATTATTTCTGAATTTTTAAAAAATTTTGTAAAACACTCTTACCTCGG
195 TTTCAAATATTTGTATTAATTATTTCTGAATTTTTAAAAAATTTTGTAAAACACTCTTACCTCGG
*
20059038 CC-TTTTTTCGTATTTTTTTCTCCGCA
260 CCATTTCTTCGTATTTTTTTCTCCGCA
*
20059064 TTTAATTACTTTAAAAAATATCATAATTTCTAATTTTATAAATTTATTAATTTAGTGTGTTTTTA
1 TTTTATTACTTTAAAAAATATCATAATTTCTAATTTTATAAATTTATTAATTTAGTGTGTTTTTA
20059129 AAATTAATTTAGTGTAAAAAAACCCTTATTCCCGCCATTTGCTCGTATTATTTTC-TCGAATTTT
66 AAATTAATTTAGTGTAAAAAAACCCTTATTCCCGCCATTTGCTCGTATTATTTTCGT-GAATTTT
20059193 ATTACTTTCAATAAAATAATTTTATTTTCGTATTGTT-TTATTTTATATTATTTCAATACATTTT
130 ATTACTTTCAATAAAATAATTTTATTTTCGTATT-TTATTATTTTATATTATTTCAATACATTTT
20059257 GTTTCAAATATTT-T-TTAATTATTTCTGAATTTTTAAAAAATTTTGTAAAACACTCTTACCTCG
194 GTTTCAAATATTTGTATTAATTATTTCTGAATTTTTAAAAAATTTTGTAAAACACTCTTACCTCG
* *
20059320 GCCATTTTTTCGTATTTTTTTCTCCTCA
259 GCCATTTCTTCGTATTTTTTTCTCCGCA
* *
20059348 TTTTATTACTTTAAAAATTATCATAATTTCTAATTTTATAAATTTATTAATTTAGTGTGTTTTTT
1 TTTTATTACTTTAAAAAATATCATAATTTCTAATTTTATAAATTTATTAATTTAGTGTGTTTTTA
* *
20059413 AAATTAATTTAGTGTAAAAAAACTCTTATTCCCGCCATTTGCTCGTATTATGTTCGTGAATTTTA
66 AAATTAATTTAGTGTAAAAAAACCCTTATTCCCGCCATTTGCTCGTATTATTTTCGTGAATTTTA
* *
20059478 TTACTTT-AATAAAATAATTTTATTTGCGTATTTTATTATTTTATATTATTTCAGTACATTTTGT
131 TTACTTTCAATAAAATAATTTTATTTTCGTATTTTATTATTTTATATTATTTCAATACATTTTGT
*
20059542 TTCAAATATTTGTATTAATTATTTCTGAATTTTTTAAAAATTTTGTAAAACACTCTTACCTCGGC
196 TTCAAATATTTGTATTAATTATTTCTGAATTTTTAAAAAATTTTGTAAAACACTCTTACCTCGGC
*
20059607 CATTTCTTCGTATTTTTTTCTCCTCA
261 CATTTCTTCGTATTTTTTTCTCCGCA
*
20059633 TTTTATTACTTTAAAAAATATCATAATTTCTAATTTTATAAATTTATTAATTTAGTGTATTTTTA
1 TTTTATTACTTTAAAAAATATCATAATTTCTAATTTTATAAATTTATTAATTTAGTGTGTTTTTA
20059698 AAATTAATTTAGTGTAAAAAAACCCTTATTCCCGCCATTTGCTCGTATTATTTTCGTGAATTTTA
66 AAATTAATTTAGTGTAAAAAAACCCTTATTCCCGCCATTTGCTCGTATTATTTTCGTGAATTTTA
* * *
20059763 TTACTTTCAATAAAATAATTTTATTTTTGTATTTTACTATTTTATAGTATTTCAATACATTTTGT
131 TTACTTTCAATAAAATAATTTTATTTTCGTATTTTATTATTTTATATTATTTCAATACATTTTGT
20059828 TTCAAATATTTGTATTAATTATTTCTGAATTTTTAAAAAA-TTTGTAAAACACTCTTACCTCGGC
196 TTCAAATATTTGTATTAATTATTTCTGAATTTTTAAAAAATTTTGTAAAACACTCTTACCTCGGC
20059892 CATTTCTTCGTATTTTTTTCTCCGCA
261 CATTTCTTCGTATTTTTTTCTCCGCA
*
20059918 TTTTATTACTTTAAAAAATTTCATAATTTCTAATTTTATA
1 TTTTATTACTTTAAAAAATATCATAATTTCTAATTTTATA
20059958 TTTTTACTTT
Statistics
Matches: 857, Mismatches: 29, Indels: 17
0.95 0.03 0.02
Matches are distributed among these distances:
282 2 0.00
283 115 0.13
284 155 0.18
285 413 0.48
286 172 0.20
ACGTcount: A:0.31, C:0.12, G:0.06, T:0.51
Consensus pattern (286 bp):
TTTTATTACTTTAAAAAATATCATAATTTCTAATTTTATAAATTTATTAATTTAGTGTGTTTTTA
AAATTAATTTAGTGTAAAAAAACCCTTATTCCCGCCATTTGCTCGTATTATTTTCGTGAATTTTA
TTACTTTCAATAAAATAATTTTATTTTCGTATTTTATTATTTTATATTATTTCAATACATTTTGT
TTCAAATATTTGTATTAATTATTTCTGAATTTTTAAAAAATTTTGTAAAACACTCTTACCTCGGC
CATTTCTTCGTATTTTTTTCTCCGCA
Found at i:20060243 original size:22 final size:23
Alignment explanation
Indices: 20060200--20060245 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
20060190 CATGAATTTT
* *
20060200 TTCATAAATTTTGTCATGCTAAA
1 TTCATAAAATTTATCATGCTAAA
20060223 TTCATAAAATTTAT-ATGCTAAA
1 TTCATAAAATTTATCATGCTAAA
20060245 T
1 T
20060246 AACATAATAG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 9 0.43
23 12 0.57
ACGTcount: A:0.39, C:0.11, G:0.07, T:0.43
Consensus pattern (23 bp):
TTCATAAAATTTATCATGCTAAA
Found at i:20060387 original size:19 final size:19
Alignment explanation
Indices: 20060363--20060432 Score: 56
Period size: 19 Copynumber: 3.5 Consensus size: 19
20060353 CCTTCCTCCC
20060363 CTCTTCTTCTTTTTTTTTT
1 CTCTTCTTCTTTTTTTTTT
*
20060382 CTCTTCTCCTTTCCTTTTCTTT
1 CTCTTCTTCTTT--TTTT-TTT
20060404 C-CTTCATT-TTCTTTCTTTTT
1 CTCTTC-TTCTT-TTT-TTTTT
20060424 -TCTTCTTCT
1 CTCTTCTTCT
20060433 CATTTCCTTT
Statistics
Matches: 41, Mismatches: 2, Indels: 15
0.71 0.03 0.26
Matches are distributed among these distances:
19 13 0.32
20 10 0.24
21 12 0.29
22 6 0.15
ACGTcount: A:0.01, C:0.29, G:0.00, T:0.70
Consensus pattern (19 bp):
CTCTTCTTCTTTTTTTTTT
Found at i:20060439 original size:44 final size:44
Alignment explanation
Indices: 20060369--20060477 Score: 166
Period size: 44 Copynumber: 2.5 Consensus size: 44
20060359 TCCCCTCTTC
* *
20060369 TTCTTTTTTTTTTC-TCTTCTCCTTTCCTTTTCTTTCCTTCATT
1 TTCTTTCTTTTTTCTTCTTCTCATTTCCTTTTCTTTCCTTCATT
*
20060412 TTCTTTCTTTTTTCTTCTTCTCATTTCCTTTTCTTTCCTTCTTT
1 TTCTTTCTTTTTTCTTCTTCTCATTTCCTTTTCTTTCCTTCATT
*
20060456 TTCTCTCTTTCTTTCTTCTTCT
1 TTCTTTCTTT-TTTCTTCTTCT
20060478 TTCCCTCTCC
Statistics
Matches: 60, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
43 13 0.22
44 36 0.60
45 11 0.18
ACGTcount: A:0.02, C:0.28, G:0.00, T:0.70
Consensus pattern (44 bp):
TTCTTTCTTTTTTCTTCTTCTCATTTCCTTTTCTTTCCTTCATT
Found at i:20060452 original size:24 final size:23
Alignment explanation
Indices: 20060383--20060477 Score: 80
Period size: 22 Copynumber: 4.3 Consensus size: 23
20060373 TTTTTTTTTC
20060383 TCTTCTCCTTTCCTTTTCTTTCCT
1 TCTTCT-CTTTCCTTTTCTTTCCT
*
20060407 TCATTTTCTTT-C-TTT-TTT-CT
1 TC-TTCTCTTTCCTTTTCTTTCCT
20060427 TCTTCTCATTTCCTTTTCTTTCCT
1 TCTTCTC-TTTCCTTTTCTTTCCT
20060451 TC-T-T-TTTCTCTCTTTCTTT-CT
1 TCTTCTCTTTC-CT-TTTCTTTCCT
20060472 TCTTCT
1 TCTTCT
20060478 TTCCCTCTCC
Statistics
Matches: 59, Mismatches: 2, Indels: 21
0.72 0.02 0.26
Matches are distributed among these distances:
19 4 0.07
20 11 0.19
21 10 0.17
22 15 0.25
23 6 0.10
24 10 0.17
25 3 0.05
ACGTcount: A:0.02, C:0.31, G:0.00, T:0.67
Consensus pattern (23 bp):
TCTTCTCTTTCCTTTTCTTTCCT
Found at i:20060466 original size:18 final size:18
Alignment explanation
Indices: 20060443--20060477 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
20060433 CATTTCCTTT
*
20060443 TCTTTCCTTCTTTTTCTC
1 TCTTTCCTTCTTCTTCTC
*
20060461 TCTTTCTTTCTTCTTCT
1 TCTTTCCTTCTTCTTCT
20060478 TTCCCTCTCC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (18 bp):
TCTTTCCTTCTTCTTCTC
Found at i:20061204 original size:10 final size:10
Alignment explanation
Indices: 20061189--20061233 Score: 72
Period size: 10 Copynumber: 4.5 Consensus size: 10
20061179 TGAAGAGGAG
20061189 AAGAAGAGAA
1 AAGAAGAGAA
20061199 AAGAAGAGAA
1 AAGAAGAGAA
* *
20061209 GAGACGAGAA
1 AAGAAGAGAA
20061219 AAGAAGAGAA
1 AAGAAGAGAA
20061229 AAGAA
1 AAGAA
20061234 AAGAGAGGGT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
10 31 1.00
ACGTcount: A:0.67, C:0.02, G:0.31, T:0.00
Consensus pattern (10 bp):
AAGAAGAGAA
Found at i:20061210 original size:15 final size:15
Alignment explanation
Indices: 20061189--20061237 Score: 71
Period size: 15 Copynumber: 3.3 Consensus size: 15
20061179 TGAAGAGGAG
20061189 AAGAAGAGAAAAGAA
1 AAGAAGAGAAAAGAA
* **
20061204 GAGAAGAGACGAGAA
1 AAGAAGAGAAAAGAA
20061219 AAGAAGAGAAAAGAA
1 AAGAAGAGAAAAGAA
20061234 AAGA
1 AAGA
20061238 GAGGGTTCGG
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
15 28 1.00
ACGTcount: A:0.67, C:0.02, G:0.31, T:0.00
Consensus pattern (15 bp):
AAGAAGAGAAAAGAA
Found at i:20061219 original size:20 final size:18
Alignment explanation
Indices: 20061181--20061232 Score: 70
Period size: 20 Copynumber: 2.8 Consensus size: 18
20061171 CACTGGAATG
*
20061181 AAGAGGAGAAGAAGAGAA
1 AAGAAGAGAAGAAGAGAA
20061199 AAGAAGAGAAGAGACGAGAA
1 AAGAAGAGAAGA-A-GAGAA
20061219 AAGAAGAGAA-AAGA
1 AAGAAGAGAAGAAGA
20061233 AAAGAGAGGG
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
17 2 0.06
18 12 0.39
19 2 0.06
20 15 0.48
ACGTcount: A:0.63, C:0.02, G:0.35, T:0.00
Consensus pattern (18 bp):
AAGAAGAGAAGAAGAGAA
Found at i:20079584 original size:48 final size:49
Alignment explanation
Indices: 20079462--20079631 Score: 227
Period size: 48 Copynumber: 3.5 Consensus size: 49
20079452 ACAAGTATCA
* *
20079462 TCATACGAGCT-ATGAATCGGTATGCTCTTACGAGCTATAAATCGGTAAGC
1 TCATACGAGCTGA-GAATCGGTAAGCTCTCACGAGCTAT-AATCGGTAAGC
* * *
20079512 TCTTACGAGCTGAGAATCGATAAGCTCTCACGAGCTGTAATCGGTAAGC
1 TCATACGAGCTGAGAATCGGTAAGCTCTCACGAGCTATAATCGGTAAGC
* * * *
20079561 TC-TACGAGCTGAGAATCAGTAAGCTATCACGAGCTACAATCGGTAAGA
1 TCATACGAGCTGAGAATCGGTAAGCTCTCACGAGCTATAATCGGTAAGC
20079609 TCATACGAGCTGAGAATCGGTAA
1 TCATACGAGCTGAGAATCGGTAA
20079632 TCCCTAATGA
Statistics
Matches: 106, Mismatches: 12, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
48 42 0.40
49 32 0.30
50 31 0.29
51 1 0.01
ACGTcount: A:0.32, C:0.21, G:0.24, T:0.24
Consensus pattern (49 bp):
TCATACGAGCTGAGAATCGGTAAGCTCTCACGAGCTATAATCGGTAAGC
Found at i:20079593 original size:73 final size:73
Alignment explanation
Indices: 20079461--20079631 Score: 186
Period size: 73 Copynumber: 2.3 Consensus size: 73
20079451 TACAAGTATC
* * * * * *
20079461 ATCATACGAGCTATGAATCGGTATGCTCTTACGAGCTATAAATCGGTAAGCTCTTACGAGCTGAG
1 ATCATACGAGCTGT-AATCGGTAAGCTCTTACGAGCTATAAATCAGTAAGCTATCACGAGCT-AC
20079526 AATCGATAAG
64 AATCGATAAG
* *
20079536 CTC-TCACGAGCTGTAATCGGTAAGCTC-TACGAGCTGA-GAATCAGTAAGCTATCACGAGCTAC
1 ATCAT-ACGAGCTGTAATCGGTAAGCTCTTACGAGCT-ATAAATCAGTAAGCTATCACGAGCTAC
*
20079598 AATCGGTAAG
64 AATCGATAAG
*
20079608 ATCATACGAGCTGAGAATCGGTAA
1 ATCATACGAGCTG-TAATCGGTAA
20079632 TCCCTAATGA
Statistics
Matches: 81, Mismatches: 11, Indels: 10
0.79 0.11 0.10
Matches are distributed among these distances:
72 20 0.25
73 37 0.46
74 14 0.17
75 10 0.12
ACGTcount: A:0.32, C:0.20, G:0.23, T:0.24
Consensus pattern (73 bp):
ATCATACGAGCTGTAATCGGTAAGCTCTTACGAGCTATAAATCAGTAAGCTATCACGAGCTACAA
TCGATAAG
Found at i:20079631 original size:25 final size:25
Alignment explanation
Indices: 20079462--20079631 Score: 174
Period size: 25 Copynumber: 6.9 Consensus size: 25
20079452 ACAAGTATCA
*
20079462 TCATACGAGCT-ATGAATCGGTATGC
1 TCATACGAGCTGA-GAATCGGTAAGC
* *
20079487 TCTTACGAGCT-ATAAATCGGTAAGC
1 TCATACGAGCTGA-GAATCGGTAAGC
* *
20079512 TCTTACGAGCTGAGAATCGATAAGC
1 TCATACGAGCTGAGAATCGGTAAGC
*
20079537 TC-TCACGAGCTG-TAATCGGTAAGC
1 TCAT-ACGAGCTGAGAATCGGTAAGC
*
20079561 TC-TACGAGCTGAGAATCAGTAAGC
1 TCATACGAGCTGAGAATCGGTAAGC
* *
20079585 T-ATCACGAGCT-ACAATCGGTAAGA
1 TCAT-ACGAGCTGAGAATCGGTAAGC
20079609 TCATACGAGCTGAGAATCGGTAA
1 TCATACGAGCTGAGAATCGGTAA
20079632 TCCCTAATGA
Statistics
Matches: 125, Mismatches: 13, Indels: 14
0.82 0.09 0.09
Matches are distributed among these distances:
23 8 0.06
24 44 0.35
25 72 0.58
26 1 0.01
ACGTcount: A:0.32, C:0.21, G:0.24, T:0.24
Consensus pattern (25 bp):
TCATACGAGCTGAGAATCGGTAAGC
Found at i:20100467 original size:40 final size:40
Alignment explanation
Indices: 20100411--20100519 Score: 121
Period size: 40 Copynumber: 2.7 Consensus size: 40
20100401 GAAATTTCCA
* * * * ** *
20100411 AAGTATAAACAAGGGCACGTAAGTGTAATTAGGGGTATCG
1 AAGTACAAACAGGGGCACGTAAGTGCAATCAAAGGTACCG
*
20100451 AAGTACAAACAGGGGCACG-ATTGTGCAATCAAAGGTACCG
1 AAGTACAAACAGGGGCACGTA-AGTGCAATCAAAGGTACCG
*
20100491 AAGTACAAATAGGGGCACGTAAGTGCAAT
1 AAGTACAAACAGGGGCACGTAAGTGCAAT
20100520 AAGAATAATT
Statistics
Matches: 57, Mismatches: 10, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
39 1 0.02
40 55 0.96
41 1 0.02
ACGTcount: A:0.39, C:0.15, G:0.28, T:0.18
Consensus pattern (40 bp):
AAGTACAAACAGGGGCACGTAAGTGCAATCAAAGGTACCG
Found at i:20102890 original size:50 final size:51
Alignment explanation
Indices: 20102826--20102956 Score: 165
Period size: 51 Copynumber: 2.6 Consensus size: 51
20102816 TCAATACACC
* * * * * ** *
20102826 TAGTAGCATTCACATAGTACTACAAACGTGATCAA-GCTTTTTGGTTCACG
1 TAGTAGCCTACACATAGTACTACACACGTGACCAATGCCTTGCGGTTCACA
20102876 TAGTAGCCTACACATAGTACTACACACGTGACCAATGCCTTGCGGTTCACA
1 TAGTAGCCTACACATAGTACTACACACGTGACCAATGCCTTGCGGTTCACA
* *
20102927 TAGTAGCCTGCACTTAGTACTACACACGTG
1 TAGTAGCCTACACATAGTACTACACACGTG
20102957 TTCGTAGACA
Statistics
Matches: 70, Mismatches: 10, Indels: 1
0.86 0.12 0.01
Matches are distributed among these distances:
50 31 0.44
51 39 0.56
ACGTcount: A:0.29, C:0.25, G:0.18, T:0.27
Consensus pattern (51 bp):
TAGTAGCCTACACATAGTACTACACACGTGACCAATGCCTTGCGGTTCACA
Found at i:20110389 original size:50 final size:50
Alignment explanation
Indices: 20110330--20110508 Score: 186
Period size: 50 Copynumber: 3.6 Consensus size: 50
20110320 TCATTCGATA
* *
20110330 CACGTAGTAGCCTTCACATAGTACTACACACGTGATCAAGCTTTTCGGTT
1 CACGTAGTAGCCTGCACATAGTACTACACACGTGACCAAGCTTTTCGGTT
* *
20110380 CACGTAGTAGCCTACACATAG---TACACACGTGACCAAGGCTTTCCGGTT
1 CACGTAGTAGCCTGCACATAGTACTACACACGTGACCAA-GCTTTTCGGTT
* * * *** * *
20110428 CACATAGTAG-CTGCACTTAGTACTACACATGTGACCATTATTTATCGATA
1 CACGTAGTAGCCTGCACATAGTACTACACACGTGACCAAGCTTT-TCGGTT
* *
20110478 CAGGTAGTAGCCTGCACTTAGTACTACACAC
1 CACGTAGTAGCCTGCACATAGTACTACACAC
20110509 ATGTTCGCAG
Statistics
Matches: 107, Mismatches: 16, Indels: 11
0.80 0.12 0.08
Matches are distributed among these distances:
47 22 0.21
48 19 0.18
49 3 0.03
50 44 0.41
51 19 0.18
ACGTcount: A:0.28, C:0.26, G:0.18, T:0.27
Consensus pattern (50 bp):
CACGTAGTAGCCTGCACATAGTACTACACACGTGACCAAGCTTTTCGGTT
Found at i:20110449 original size:47 final size:47
Alignment explanation
Indices: 20110334--20110464 Score: 138
Period size: 47 Copynumber: 2.7 Consensus size: 47
20110324 TCGATACACG
* * * *
20110334 TAGTAGCCTTCACATAGTACTACACACGTGATCAAGCTTTTCGGTTCACG
1 TAGTAGCCTACACATAG---TACACACGTGACCAAGCTTTCCGGTTCACA
20110384 TAGTAGCCTACACATAGTACACACGTGACCAAGGCTTTCCGGTTCACA
1 TAGTAGCCTACACATAGTACACACGTGACCAA-GCTTTCCGGTTCACA
* *
20110432 TAGTAG-CTGCACTTAGTACTACACATGTGACCA
1 TAGTAGCCTACACATAGTAC-ACAC--GTGACCA
20110465 TTATTTATCG
Statistics
Matches: 71, Mismatches: 6, Indels: 8
0.84 0.07 0.09
Matches are distributed among these distances:
47 25 0.35
48 23 0.32
50 23 0.32
ACGTcount: A:0.28, C:0.27, G:0.18, T:0.27
Consensus pattern (47 bp):
TAGTAGCCTACACATAGTACACACGTGACCAAGCTTTCCGGTTCACA
Found at i:20122020 original size:73 final size:74
Alignment explanation
Indices: 20121893--20122034 Score: 214
Period size: 73 Copynumber: 1.9 Consensus size: 74
20121883 AAGTTCTCCA
*
20121893 AAGCTAACATTAGTACCATACTTGCTCAAGGGTCATCTTTTCATTTATTATCTTTATTTATGTTG
1 AAGCTAACATTAGTACCATACTTGCCCAAGGGTCATCTTTTCATTTATTATCTTTATTTATGTTG
20121958 CTTGTCCTC
66 CTTGTCCTC
* * * * * *
20121967 AAGC-AACATTCGTACCATACTTGCCCAGGGGTTATCTTTTCATTTATTGTCTTTGTTTGTGTTG
1 AAGCTAACATTAGTACCATACTTGCCCAAGGGTCATCTTTTCATTTATTATCTTTATTTATGTTG
20122031 CTTG
66 CTTG
20122035 AGGACAAGAA
Statistics
Matches: 61, Mismatches: 7, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
73 57 0.93
74 4 0.07
ACGTcount: A:0.20, C:0.20, G:0.15, T:0.44
Consensus pattern (74 bp):
AAGCTAACATTAGTACCATACTTGCCCAAGGGTCATCTTTTCATTTATTATCTTTATTTATGTTG
CTTGTCCTC
Found at i:20124519 original size:25 final size:25
Alignment explanation
Indices: 20124457--20124570 Score: 94
Period size: 24 Copynumber: 4.6 Consensus size: 25
20124447 CAATTCTCAG
20124457 CTCGTATGAGCTTACCAATTGCAAA
1 CTCGTATGAGCTTACCAATTGCAAA
* * *
20124482 -TTGTAAGAGCTTACTAATT-CAGAA
1 CTCGTATGAGCTTACCAATTGCA-AA
* * *
20124506 CTCGTATGAGCTTACCGATTG-TAG
1 CTCGTATGAGCTTACCAATTGCAAA
* *
20124530 CTCGTGA-GAGCTTACCAATT-CTCAG
1 CTCGT-ATGAGCTTACCAATTGC-AAA
20124555 CTCGTATGAGCTTACC
1 CTCGTATGAGCTTACC
20124571 GATTTATAGC
Statistics
Matches: 71, Mismatches: 11, Indels: 14
0.74 0.11 0.15
Matches are distributed among these distances:
23 2 0.03
24 37 0.52
25 32 0.45
ACGTcount: A:0.27, C:0.23, G:0.19, T:0.31
Consensus pattern (25 bp):
CTCGTATGAGCTTACCAATTGCAAA
Found at i:20124571 original size:49 final size:49
Alignment explanation
Indices: 20124443--20124590 Score: 188
Period size: 49 Copynumber: 3.0 Consensus size: 49
20124433 TCATTAGGGA
* * ** * *
20124443 TTACCAATTCTCAGCTCGTATGAGCTTACCAATTGCAAATTGTAAGAGC
1 TTACCAATTCTCAGCTCGTATGAGCTTACCGATTGTAGCTCGTGAGAGC
* ** *
20124492 TTACTAATTCAGAACTCGTATGAGCTTACCGATTGTAGCTCGTGAGAGC
1 TTACCAATTCTCAGCTCGTATGAGCTTACCGATTGTAGCTCGTGAGAGC
*
20124541 TTACCAATTCTCAGCTCGTATGAGCTTACCGATTTATAGCTCGTGAGAGC
1 TTACCAATTCTCAGCTCGTATGAGCTTACCGA-TTGTAGCTCGTGAGAGC
20124591 ATACTGATTC
Statistics
Matches: 83, Mismatches: 15, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
49 67 0.81
50 16 0.19
ACGTcount: A:0.27, C:0.22, G:0.20, T:0.31
Consensus pattern (49 bp):
TTACCAATTCTCAGCTCGTATGAGCTTACCGATTGTAGCTCGTGAGAGC
Found at i:20124581 original size:25 final size:25
Alignment explanation
Indices: 20124506--20124615 Score: 102
Period size: 25 Copynumber: 4.4 Consensus size: 25
20124496 TAATTCAGAA
*
20124506 CTCGTATGAGCTTACCGA-TTGTAG
1 CTCGTATGAGCTTACCGATTTATAG
* *
20124530 CTCGTGA-GAGCTTACCAATTCT-CAG
1 CTCGT-ATGAGCTTACCGATT-TATAG
20124555 CTCGTATGAGCTTACCGATTTATAG
1 CTCGTATGAGCTTACCGATTTATAG
* * *
20124580 CTCGTGA-GAGCATACTGATTCATAG
1 CTCGT-ATGAGCTTACCGATTTATAG
*
20124605 CTTGTATGAGC
1 CTCGTATGAGC
20124616 ATACATCTAA
Statistics
Matches: 71, Mismatches: 8, Indels: 13
0.77 0.09 0.14
Matches are distributed among these distances:
24 18 0.25
25 51 0.72
26 2 0.03
ACGTcount: A:0.24, C:0.22, G:0.23, T:0.32
Consensus pattern (25 bp):
CTCGTATGAGCTTACCGATTTATAG
Found at i:20124806 original size:30 final size:29
Alignment explanation
Indices: 20124767--20124828 Score: 74
Period size: 31 Copynumber: 2.1 Consensus size: 29
20124757 TACATGAAAT
20124767 ACATGGAAATG-ATATTACATGATATATTGAA
1 ACATGGAAATGAATA-TACATG-TATA-TGAA
20124798 ACAT-GAAATGAATGATACATGTATATGAA
1 ACATGGAAATGAAT-ATACATGTATATGAA
20124827 AC
1 AC
20124829 TTGCTTAGTG
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
29 6 0.21
30 10 0.34
31 12 0.41
32 1 0.03
ACGTcount: A:0.47, C:0.08, G:0.16, T:0.29
Consensus pattern (29 bp):
ACATGGAAATGAATATACATGTATATGAA
Found at i:20133183 original size:7 final size:7
Alignment explanation
Indices: 20133173--20133213 Score: 73
Period size: 7 Copynumber: 5.9 Consensus size: 7
20133163 ATATGTGTAT
*
20133173 TGTGATA
1 TGTGACA
20133180 TGTGACA
1 TGTGACA
20133187 TGTGACA
1 TGTGACA
20133194 TGTGACA
1 TGTGACA
20133201 TGTGACA
1 TGTGACA
20133208 TGTGAC
1 TGTGAC
20133214 CATTACGTAA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
7 33 1.00
ACGTcount: A:0.27, C:0.12, G:0.29, T:0.32
Consensus pattern (7 bp):
TGTGACA
Found at i:20157924 original size:15 final size:15
Alignment explanation
Indices: 20157901--20157937 Score: 65
Period size: 15 Copynumber: 2.5 Consensus size: 15
20157891 GACAAACCAC
*
20157901 AAAAGCACACAATCA
1 AAAATCACACAATCA
20157916 AAAATCACACAATCA
1 AAAATCACACAATCA
20157931 AAAATCA
1 AAAATCA
20157938 ACCATTGACT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.62, C:0.24, G:0.03, T:0.11
Consensus pattern (15 bp):
AAAATCACACAATCA
Found at i:20162518 original size:21 final size:22
Alignment explanation
Indices: 20162494--20162535 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
20162484 TTCATGTAAC
*
20162494 TAAATTGTATATT-TGTATGTT
1 TAAATTGAATATTGTGTATGTT
*
20162515 TAAATTGAATGTTGTGTATGT
1 TAAATTGAATATTGTGTATGT
20162536 GTGTTGTGTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.29, C:0.00, G:0.19, T:0.52
Consensus pattern (22 bp):
TAAATTGAATATTGTGTATGTT
Found at i:20162866 original size:26 final size:26
Alignment explanation
Indices: 20162837--20162893 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 26
20162827 CCTGATATAT
*
20162837 GGCTCTTCATGAGCTTCCCAATTAAA
1 GGCTCTTCATGAGATTCCCAATTAAA
** * *
20162863 GGCTCTTTGTGAGATTCCTAATTAAT
1 GGCTCTTCATGAGATTCCCAATTAAA
20162889 GGCTC
1 GGCTC
20162894 GCCAGAGCTT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.23, C:0.23, G:0.19, T:0.35
Consensus pattern (26 bp):
GGCTCTTCATGAGATTCCCAATTAAA
Found at i:20162914 original size:23 final size:23
Alignment explanation
Indices: 20162887--20162934 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
20162877 TTCCTAATTA
* *
20162887 ATGGCTCGCCAGAGCTTCTCGAT
1 ATGGCTCACCAGAACTTCTCGAT
**
20162910 ATGGCTCACTTGAACTTCTCGAT
1 ATGGCTCACCAGAACTTCTCGAT
20162933 AT
1 AT
20162935 ATGGCTATCA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.21, C:0.27, G:0.21, T:0.31
Consensus pattern (23 bp):
ATGGCTCACCAGAACTTCTCGAT
Found at i:20162973 original size:25 final size:25
Alignment explanation
Indices: 20162835--20163016 Score: 76
Period size: 25 Copynumber: 7.4 Consensus size: 25
20162825 GTCCTGATAT
*
20162835 ATGGCTCTTCATGAGCTTCCCAATTA
1 ATGGCTCTTCA-GAGCTTCCCGATTA
* ** * **
20162861 AAGGCTCTTTGTGAGATTCCTAATTA
1 ATGGCTC-TTCAGAGCTTCCCGATTA
** *
20162887 ATGGCTCGCCAGAGCTTCTCGA-T-
1 ATGGCTCTTCAGAGCTTCCCGATTA
* *
20162910 ATGGCTCACTT--GAACTTCTCGA-TA
1 ATGGCT--CTTCAGAGCTTCCCGATTA
*
20162934 TATGGCT-ATCAAGAGCTTCCCGATTA
1 -ATGGCTCTTC-AGAGCTTCCCGATTA
*
20162960 ATGGCTCTTCAGAGCTACCCG-TTA
1 ATGGCTCTTCAGAGCTTCCCGATTA
* * * *
20162984 TTGGCTC-ACATGACCTTCCTGATT-
1 ATGGCTCTTCA-GAGCTTCCCGATTA
20163008 ATGGCTCTT
1 ATGGCTCTT
20163017 ATATGCTTCC
Statistics
Matches: 114, Mismatches: 29, Indels: 27
0.67 0.17 0.16
Matches are distributed among these distances:
22 1 0.01
23 19 0.17
24 23 0.20
25 41 0.36
26 28 0.25
27 2 0.02
ACGTcount: A:0.22, C:0.25, G:0.19, T:0.34
Consensus pattern (25 bp):
ATGGCTCTTCAGAGCTTCCCGATTA
Found at i:20163073 original size:25 final size:25
Alignment explanation
Indices: 20162908--20163131 Score: 120
Period size: 25 Copynumber: 8.9 Consensus size: 25
20162898 GAGCTTCTCG
* * * *
20162908 ATATGGCTCACTTGAACTTCTCGAT
1 ATATGGCTCACATGAGCTTCCCGTT
*
20162933 ATATGGCT-ATCAAGAGCTTCCCGATT
1 ATATGGCTCA-CATGAGCTTCCCG-TT
* *
20162959 A-ATGGCTCTTCA-GAGCTACCCGTT
1 ATATGGCTC-ACATGAGCTTCCCGTT
* * *
20162983 AT-TGGCTCACATGACCTTCCTGAT
1 ATATGGCTCACATGAGCTTCCCGTT
**
20163007 -TATGGCTCTTAT-ATGCTTCCCGTT
1 ATATGGCTCACATGA-GCTTCCCGTT
** * ** *
20163031 ATACAGCCCGGATAAGCTTCCCGTT
1 ATATGGCTCACATGAGCTTCCCGTT
* * *
20163056 ACATGGCTCATATGAGCTTCCCTTT
1 ATATGGCTCACATGAGCTTCCCGTT
* *
20163081 ATATGGCTCGAGAGAGAGCTTCCCGTT
1 ATATGGCTC-ACA-TGAGCTTCCCGTT
20163108 -TATGTGCTCACATGAGCATTCCCG
1 ATATG-GCTCACATGAGC-TTCCCG
20163132 AATATGAATT
Statistics
Matches: 149, Mismatches: 36, Indels: 27
0.70 0.17 0.13
Matches are distributed among these distances:
23 4 0.03
24 33 0.22
25 78 0.52
26 19 0.13
27 15 0.10
ACGTcount: A:0.21, C:0.27, G:0.20, T:0.32
Consensus pattern (25 bp):
ATATGGCTCACATGAGCTTCCCGTT
Found at i:20174997 original size:13 final size:13
Alignment explanation
Indices: 20174951--20175127 Score: 84
Period size: 13 Copynumber: 13.4 Consensus size: 13
20174941 TCCAATGTTC
20174951 CATTTCATAT-AT
1 CATTTCATATAAT
20174963 CAATTTCCATATAATT
1 C-ATTT-CATATAA-T
*
20174979 GA-TTCATATAAT
1 CATTTCATATAAT
20174991 CATTTCATAT-AT
1 CATTTCATATAAT
*
20175003 CTATTTCCATTTAA-
1 C-ATTT-CATATAAT
*
20175017 CTAATTCATATAA-
1 C-ATTTCATATAAT
20175030 CTATTTCATAT-AT
1 C-ATTTCATATAAT
* *
20175043 CTATTCCGTATAATT
1 C-ATTTCATATAA-T
* *
20175058 GA-TTCATATAAC
1 CATTTCATATAAT
20175070 CATTTCATAT-AT
1 CATTTCATATAAT
20175082 CTATTTTCATATAACT
1 C-A-TTTCATATAA-T
* *
20175098 GA-TTCATATAAA
1 CATTTCATATAAT
* *
20175110 CATTTCATTTATT
1 CATTTCATATAAT
20175123 CATTT
1 CATTT
20175128 TTCATCCAAT
Statistics
Matches: 128, Mismatches: 20, Indels: 33
0.71 0.11 0.18
Matches are distributed among these distances:
12 11 0.09
13 83 0.65
14 26 0.20
15 6 0.05
16 2 0.02
ACGTcount: A:0.34, C:0.16, G:0.02, T:0.47
Consensus pattern (13 bp):
CATTTCATATAAT
Found at i:20175062 original size:79 final size:80
Alignment explanation
Indices: 20174951--20175117 Score: 257
Period size: 79 Copynumber: 2.1 Consensus size: 80
20174941 TCCAATGTTC
* *
20174951 CATTTCATATATCAATTTCCATATAATTGATTCATATAATCATTTCATATATCTATTTCCATTTA
1 CATTTCATATATCAATTTCCATATAATTGATTCATATAACCATTTCATATATCTATTTCCATATA
20175016 ACTAATTCATAT-AA
66 ACTAATTCATATAAA
* * *
20175030 CTATTTCATATATCTA-TTCCGTATAATTGATTCATATAACCATTTCATATATCTATTTTCATAT
1 C-ATTTCATATATCAATTTCCATATAATTGATTCATATAACCATTTCATATATCTATTTCCATAT
*
20175094 AACTGATTCATATAAA
65 AACTAATTCATATAAA
20175110 CATTTCAT
1 CATTTCAT
20175118 TTATTCATTT
Statistics
Matches: 80, Mismatches: 6, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
79 64 0.80
80 16 0.20
ACGTcount: A:0.35, C:0.17, G:0.02, T:0.46
Consensus pattern (80 bp):
CATTTCATATATCAATTTCCATATAATTGATTCATATAACCATTTCATATATCTATTTCCATATA
ACTAATTCATATAAA
Found at i:20175128 original size:40 final size:40
Alignment explanation
Indices: 20174951--20175117 Score: 230
Period size: 40 Copynumber: 4.2 Consensus size: 40
20174941 TCCAATGTTC
* * *
20174951 CATTTCATATATCAATTTCCATATAATTGATTCATATAAT
1 CATTTCATATATCTATTTCCATATAACTGATTCATATAAA
* *
20174991 CATTTCATATATCTATTTCCATTTAACTAATTCATAT-AA
1 CATTTCATATATCTATTTCCATATAACTGATTCATATAAA
* * *
20175030 CTATTTCATATATCTA-TTCCGTATAATTGATTCATATAAC
1 C-ATTTCATATATCTATTTCCATATAACTGATTCATATAAA
*
20175070 CATTTCATATATCTATTTTCATATAACTGATTCATATAAA
1 CATTTCATATATCTATTTCCATATAACTGATTCATATAAA
20175110 CATTTCAT
1 CATTTCAT
20175118 TTATTCATTT
Statistics
Matches: 110, Mismatches: 14, Indels: 6
0.85 0.11 0.05
Matches are distributed among these distances:
39 33 0.30
40 77 0.70
ACGTcount: A:0.35, C:0.17, G:0.02, T:0.46
Consensus pattern (40 bp):
CATTTCATATATCTATTTCCATATAACTGATTCATATAAA
Found at i:20175235 original size:26 final size:25
Alignment explanation
Indices: 20175173--20175236 Score: 83
Period size: 25 Copynumber: 2.5 Consensus size: 25
20175163 CGCAGGAATG
* *
20175173 ATGCTCACACAAGCTGTAACTGTAT
1 ATGCTCACACAAGCTGTAAATGGAT
*
20175198 ATGCTCACACAAGCTGTAAAATGGGT
1 ATGCTCACACAAGCTGT-AAATGGAT
*
20175224 CTGCTCACACAAG
1 ATGCTCACACAAG
20175237 ATGTGGGTCA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
25 17 0.50
26 17 0.50
ACGTcount: A:0.33, C:0.25, G:0.19, T:0.23
Consensus pattern (25 bp):
ATGCTCACACAAGCTGTAAATGGAT
Found at i:20176334 original size:17 final size:18
Alignment explanation
Indices: 20176308--20176341 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
20176298 TAACATTTGA
20176308 TTATTATAAAA-ATAAAC
1 TTATTATAAAACATAAAC
*
20176325 TTATTTTAAAACATAAA
1 TTATTATAAAACATAAA
20176342 AATACCTATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.38
Consensus pattern (18 bp):
TTATTATAAAACATAAAC
Found at i:20183762 original size:31 final size:32
Alignment explanation
Indices: 20183727--20183786 Score: 77
Period size: 31 Copynumber: 1.9 Consensus size: 32
20183717 AAAAACACTT
*
20183727 AATAGCCTAGTAACTTAAAT-AAAATTTTTCA
1 AATAGCCTAGTAACATAAATGAAAATTTTTCA
** *
20183758 AATAGTTTAGTGACATAAATGAAAATTTT
1 AATAGCCTAGTAACATAAATGAAAATTTT
20183787 CTAATAAATC
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
31 16 0.67
32 8 0.33
ACGTcount: A:0.45, C:0.08, G:0.10, T:0.37
Consensus pattern (32 bp):
AATAGCCTAGTAACATAAATGAAAATTTTTCA
Found at i:20189098 original size:16 final size:17
Alignment explanation
Indices: 20189077--20189109 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
20189067 CATATTAAAG
20189077 CATATAAATTT-AAAAC
1 CATATAAATTTGAAAAC
*
20189093 CATATATATTTGAAAAC
1 CATATAAATTTGAAAAC
20189110 TAAACTTGAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.52, C:0.12, G:0.03, T:0.33
Consensus pattern (17 bp):
CATATAAATTTGAAAAC
Found at i:20189220 original size:20 final size:19
Alignment explanation
Indices: 20189163--20189229 Score: 64
Period size: 20 Copynumber: 3.5 Consensus size: 19
20189153 TATTTAGAAA
*
20189163 TTTTTTAAATTTTT-TACT
1 TTTTTTAAATTTTTATAAT
* * * *
20189181 TTCTTTACATATTTAGAAT
1 TTTTTTAAATTTTTATAAT
20189200 TTTTTTAAAATTTTTATAAT
1 TTTTTT-AAATTTTTATAAT
*
20189220 TTTTTAAAAT
1 TTTTTTAAAT
20189230 ATATCAATTT
Statistics
Matches: 37, Mismatches: 10, Indels: 3
0.74 0.20 0.06
Matches are distributed among these distances:
18 11 0.30
19 11 0.30
20 15 0.41
ACGTcount: A:0.31, C:0.04, G:0.01, T:0.63
Consensus pattern (19 bp):
TTTTTTAAATTTTTATAAT
Found at i:20189223 original size:10 final size:9
Alignment explanation
Indices: 20189160--20189227 Score: 50
Period size: 9 Copynumber: 7.3 Consensus size: 9
20189150 TATTATTTAG
20189160 AAATTTTTT
1 AAATTTTTT
20189169 AAATTTTTT
1 AAATTTTTT
*
20189178 -ACTTTCTTT
1 AAATTT-TTT
* *
20189187 ACA-TATTT
1 AAATTTTTT
20189195 AGAATTTTTTT
1 A-AA-TTTTTT
*
20189206 AAAATTTTT
1 AAATTTTTT
20189215 ATAATTTTTT
1 A-AATTTTTT
20189225 AAA
1 AAA
20189228 ATATATCAAT
Statistics
Matches: 45, Mismatches: 8, Indels: 12
0.69 0.12 0.18
Matches are distributed among these distances:
8 8 0.18
9 22 0.49
10 10 0.22
11 5 0.11
ACGTcount: A:0.34, C:0.04, G:0.01, T:0.60
Consensus pattern (9 bp):
AAATTTTTT
Found at i:20189266 original size:19 final size:20
Alignment explanation
Indices: 20189236--20189286 Score: 77
Period size: 20 Copynumber: 2.5 Consensus size: 20
20189226 AAATATATCA
*
20189236 ATTTTAGAATTTTTATAAA-T
1 ATTTT-GAATTTTTAAAAATT
20189256 ATTTTGAATTTTTAAAAATT
1 ATTTTGAATTTTTAAAAATT
20189276 ATTTTGAATTT
1 ATTTTGAATTT
20189287 GTTTTTTGTA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 12 0.41
20 17 0.59
ACGTcount: A:0.37, C:0.00, G:0.06, T:0.57
Consensus pattern (20 bp):
ATTTTGAATTTTTAAAAATT
Found at i:20189398 original size:18 final size:18
Alignment explanation
Indices: 20189372--20189406 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
20189362 CAATCTATTA
*
20189372 TTTGAGTTATTCGAATTT
1 TTTGAGTTATGCGAATTT
*
20189390 TTTGTGTTATGCGAATT
1 TTTGAGTTATGCGAATT
20189407 GTATAATTCA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.20, C:0.06, G:0.20, T:0.54
Consensus pattern (18 bp):
TTTGAGTTATGCGAATTT
Found at i:20190941 original size:3 final size:3
Alignment explanation
Indices: 20190933--20190977 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
20190923 GGGGAAGGTT
20190933 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
20190978 TACCTCCCGA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:20193324 original size:23 final size:25
Alignment explanation
Indices: 20193280--20193333 Score: 67
Period size: 24 Copynumber: 2.2 Consensus size: 25
20193270 AATAAATGGA
20193280 AAAAAAATTAAAATAACATAAAA-G
1 AAAAAAATTAAAATAACATAAAACG
** *
20193304 AAAAAAATT-AAATTGCTTAAAACG
1 AAAAAAATTAAAATAACATAAAACG
20193328 AAAAAA
1 AAAAAA
20193334 TATGGGGATC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
23 10 0.38
24 16 0.62
ACGTcount: A:0.70, C:0.06, G:0.06, T:0.19
Consensus pattern (25 bp):
AAAAAAATTAAAATAACATAAAACG
Found at i:20196058 original size:27 final size:27
Alignment explanation
Indices: 20196028--20196081 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
20196018 ATACAGATTT
*
20196028 GCCACCAAGGAGACCCATTCAGAGTAC
1 GCCACAAAGGAGACCCATTCAGAGTAC
* * *
20196055 GCCACAAAGGTGATCCATTCCGAGTAC
1 GCCACAAAGGAGACCCATTCAGAGTAC
20196082 ACCATGAAGG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.31, C:0.31, G:0.22, T:0.15
Consensus pattern (27 bp):
GCCACAAAGGAGACCCATTCAGAGTAC
Found at i:20196091 original size:27 final size:27
Alignment explanation
Indices: 20196042--20196095 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
20196032 CCAAGGAGAC
*
20196042 CCATTCAGAGTACGCCACAAAGGTGAT
1 CCATTCAGAGTACACCACAAAGGTGAT
* **
20196069 CCATTCCGAGTACACCATGAAGGTGAT
1 CCATTCAGAGTACACCACAAAGGTGAT
20196096 TTATTTAGAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.31, C:0.26, G:0.22, T:0.20
Consensus pattern (27 bp):
CCATTCAGAGTACACCACAAAGGTGAT
Found at i:20197508 original size:38 final size:37
Alignment explanation
Indices: 20197457--20197639 Score: 195
Period size: 38 Copynumber: 4.8 Consensus size: 37
20197447 TGAATTATAT
*
20197457 TGTTATTCAAGCTTTGTGCCTAGCAAGCTTTGTGCCGG
1 TGTTATTC-AGCTTTGTGCCTAGCAAGCTTAGTGCCGG
* *
20197495 TGTTATTCGAGCTTTGTGCCTAGCAGGCTTAGTGCCGA
1 TGTTATTC-AGCTTTGTGCCTAGCAAGCTTAGTGCCGG
* **
20197533 TGTTATTCAGGCTTTTTGCCTAGCAAGCTTAGTGGAGG
1 TGTTATTCA-GCTTTGTGCCTAGCAAGCTTAGTGCCGG
* * * *
20197571 TGTTATTCAGACTTTATGCCTAACAGGCTTAGTGTCGG
1 TGTTATTCAG-CTTTGTGCCTAGCAAGCTTAGTGCCGG
* * * *
20197609 TGTTATTTAGGCTTAGTGCCTAACAGGCTTA
1 TGTTATTCA-GCTTTGTGCCTAGCAAGCTTA
20197640 TTACCAGTGT
Statistics
Matches: 125, Mismatches: 17, Indels: 6
0.84 0.11 0.04
Matches are distributed among these distances:
37 2 0.02
38 122 0.98
39 1 0.01
ACGTcount: A:0.19, C:0.19, G:0.26, T:0.37
Consensus pattern (37 bp):
TGTTATTCAGCTTTGTGCCTAGCAAGCTTAGTGCCGG
Found at i:20197591 original size:76 final size:76
Alignment explanation
Indices: 20197457--20197639 Score: 233
Period size: 76 Copynumber: 2.4 Consensus size: 76
20197447 TGAATTATAT
* * * * *
20197457 TGTTATTCAAGCTTTGTGCCTAGCAAGCTTTGTGCCGGTGTTATTCGAGCTTTGTGCCTAGCAGG
1 TGTTATTCAGGCTTTGTGCCTAGCAAGCTTAGTGCAGGTGTTATTCGAGCTTTATGCCTAACAGG
20197522 CTTAGTGCCGA
66 CTTAGTGCCGA
* *
20197533 TGTTATTCAGGCTTTTTGCCTAGCAAGCTTAGTGGAGGTGTTATTC-AGACTTTATGCCTAACAG
1 TGTTATTCAGGCTTTGTGCCTAGCAAGCTTAGTGCAGGTGTTATTCGAG-CTTTATGCCTAACAG
* *
20197597 GCTTAGTGTCGG
65 GCTTAGTGCCGA
* * * *
20197609 TGTTATTTAGGCTTAGTGCCTAACAGGCTTA
1 TGTTATTCAGGCTTTGTGCCTAGCAAGCTTA
20197640 TTACCAGTGT
Statistics
Matches: 92, Mismatches: 14, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
75 2 0.02
76 90 0.98
ACGTcount: A:0.19, C:0.19, G:0.26, T:0.37
Consensus pattern (76 bp):
TGTTATTCAGGCTTTGTGCCTAGCAAGCTTAGTGCAGGTGTTATTCGAGCTTTATGCCTAACAGG
CTTAGTGCCGA
Found at i:20201749 original size:39 final size:39
Alignment explanation
Indices: 20201695--20201775 Score: 162
Period size: 39 Copynumber: 2.1 Consensus size: 39
20201685 ATGTAATCGA
20201695 TTTGTTCATCTTTAAAGCTTTACTTGAACTATTGTTTTC
1 TTTGTTCATCTTTAAAGCTTTACTTGAACTATTGTTTTC
20201734 TTTGTTCATCTTTAAAGCTTTACTTGAACTATTGTTTTC
1 TTTGTTCATCTTTAAAGCTTTACTTGAACTATTGTTTTC
20201773 TTT
1 TTT
20201776 TCCCTTTAGT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 42 1.00
ACGTcount: A:0.20, C:0.15, G:0.10, T:0.56
Consensus pattern (39 bp):
TTTGTTCATCTTTAAAGCTTTACTTGAACTATTGTTTTC
Found at i:20202168 original size:29 final size:29
Alignment explanation
Indices: 20202088--20202567 Score: 827
Period size: 29 Copynumber: 16.2 Consensus size: 29
20202078 GAATAAACCG
20202088 AATACACTACATATATTTTTTTATTTTTAA
1 AATACACTACATATA-TTTTTTATTTTTAA
20202118 AATACACTACATATATATTTTTATTTTTAA
1 AATACACTACATATAT-TTTTTATTTTTAA
20202148 AATACACTACATATATTTTTTATTTTTAA
1 AATACACTACATATATTTTTTATTTTTAA
20202177 AATACACTACATATA-TTTTTATTTTTAA
1 AATACACTACATATATTTTTTATTTTTAA
20202205 AATACACTACATATATATTTTTTATTTTTAA
1 AATACACTAC--ATATATTTTTTATTTTTAA
*
20202236 AATACAGTACATATATTTTTTTATTTTTAA
1 AATACACTACATATA-TTTTTTATTTTTAA
20202266 AATACACTACATATATTTTTTATTTTTAA
1 AATACACTACATATATTTTTTATTTTTAA
20202295 AATACACTACATATATTTTTTATTTTTAA
1 AATACACTACATATATTTTTTATTTTTAA
* **
20202324 AATAAACTACGCATATTTTTTATTTTTAA
1 AATACACTACATATATTTTTTATTTTTAA
20202353 AATACACTACATATATTTTTTATTTTTAA
1 AATACACTACATATATTTTTTATTTTTAA
20202382 AATACACTACATATATTTTTTATTTTTAA
1 AATACACTACATATATTTTTTATTTTTAA
20202411 AATACACTACATATATTTCTTTATTTTTAA
1 AATACACTACATATATTT-TTTATTTTTAA
20202441 AATACACTACATATATTTTTTTTATTTTTAA
1 AATACACTACATATA--TTTTTTATTTTTAA
20202472 AATACACTACATATATTTTTTATTTTTAA
1 AATACACTACATATATTTTTTATTTTTAA
20202501 AATACACTACATATATTTTTTTATTTTTAA
1 AATACACTACATATA-TTTTTTATTTTTAA
20202531 AATACACTACATATATTTTTTTATTTTTAA
1 AATACACTACATATA-TTTTTTATTTTTAA
20202561 AATACAC
1 AATACAC
20202568 AAATACAATG
Statistics
Matches: 433, Mismatches: 8, Indels: 18
0.94 0.02 0.04
Matches are distributed among these distances:
28 23 0.05
29 205 0.47
30 154 0.36
31 48 0.11
32 3 0.01
ACGTcount: A:0.38, C:0.10, G:0.00, T:0.51
Consensus pattern (29 bp):
AATACACTACATATATTTTTTATTTTTAA
Found at i:20202183 original size:59 final size:58
Alignment explanation
Indices: 20202088--20202567 Score: 827
Period size: 59 Copynumber: 8.1 Consensus size: 58
20202078 GAATAAACCG
20202088 AATACACTACATATATTTTTTTATTTTTAAAATACACTACATATATATTTTTATTTTTAA
1 AATACACTACATATA-TTTTTTATTTTTAAAATACACTACATATAT-TTTTTATTTTTAA
20202148 AATACACTACATATATTTTTTATTTTTAAAATACACTACATATA-TTTTTATTTTTAA
1 AATACACTACATATATTTTTTATTTTTAAAATACACTACATATATTTTTTATTTTTAA
*
20202205 AATACACTACATATATATTTTTTATTTTTAAAATACAGTACATATATTTTTTTATTTTTAA
1 AATACACTAC--ATATATTTTTTATTTTTAAAATACACTACATATA-TTTTTTATTTTTAA
20202266 AATACACTACATATATTTTTTATTTTTAAAATACACTACATATATTTTTTATTTTTAA
1 AATACACTACATATATTTTTTATTTTTAAAATACACTACATATATTTTTTATTTTTAA
* **
20202324 AATAAACTACGCATATTTTTTATTTTTAAAATACACTACATATATTTTTTATTTTTAA
1 AATACACTACATATATTTTTTATTTTTAAAATACACTACATATATTTTTTATTTTTAA
20202382 AATACACTACATATATTTTTTATTTTTAAAATACACTACATATATTTCTTTATTTTTAA
1 AATACACTACATATATTTTTTATTTTTAAAATACACTACATATATTT-TTTATTTTTAA
20202441 AATACACTACATATATTTTTTTTATTTTTAAAATACACTACATATATTTTTTATTTTTAA
1 AATACACTACATATA--TTTTTTATTTTTAAAATACACTACATATATTTTTTATTTTTAA
20202501 AATACACTACATATATTTTTTTATTTTTAAAATACACTACATATATTTTTTTATTTTTAA
1 AATACACTACATATA-TTTTTTATTTTTAAAATACACTACATATA-TTTTTTATTTTTAA
20202561 AATACAC
1 AATACAC
20202568 AAATACAATG
Statistics
Matches: 404, Mismatches: 8, Indels: 16
0.94 0.02 0.04
Matches are distributed among these distances:
57 23 0.06
58 113 0.28
59 151 0.37
60 62 0.15
61 55 0.14
ACGTcount: A:0.38, C:0.10, G:0.00, T:0.51
Consensus pattern (58 bp):
AATACACTACATATATTTTTTATTTTTAAAATACACTACATATATTTTTTATTTTTAA
Found at i:20205499 original size:18 final size:18
Alignment explanation
Indices: 20205476--20205510 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
20205466 GCTTCGAGGG
20205476 AAAACTATTTTAAATAAA
1 AAAACTATTTTAAATAAA
*
20205494 AAAACTGTTTTAAATAA
1 AAAACTATTTTAAATAA
20205511 TAAATATACC
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:0.57, C:0.06, G:0.03, T:0.34
Consensus pattern (18 bp):
AAAACTATTTTAAATAAA
Found at i:20205737 original size:21 final size:21
Alignment explanation
Indices: 20205701--20205785 Score: 98
Period size: 21 Copynumber: 4.0 Consensus size: 21
20205691 CCAAGAACAA
*
20205701 AGCAAAAAAGAGGGGAGAAACC
1 AGCAAAAACGA-GGGAGAAACC
*
20205723 AGCAAAAACGAGGGACAAACC
1 AGCAAAAACGAGGGAGAAACC
* * *
20205744 AGTAAGAACAAGGGAGAAACC
1 AGCAAAAACGAGGGAGAAACC
*
20205765 AGCAAGAACGAGGGAAGAAAC
1 AGCAAAAACGAGGG-AGAAAC
20205786 TGTTGTTTTG
Statistics
Matches: 54, Mismatches: 8, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
21 38 0.70
22 16 0.30
ACGTcount: A:0.53, C:0.16, G:0.29, T:0.01
Consensus pattern (21 bp):
AGCAAAAACGAGGGAGAAACC
Found at i:20209587 original size:87 final size:86
Alignment explanation
Indices: 20209473--20209717 Score: 348
Period size: 87 Copynumber: 2.8 Consensus size: 86
20209463 AAGATTGAGA
* * *
20209473 TATTATTCTTAATGAATTCATAGCCCAAAGTTTGGGTAGTCCTATTGAGACAGACTTGATGAATT
1 TATTACTCTTAATGAACTCATATCCCAAAGTTTGGGT-GTCCTATTGAGACAGACTTGATGAATT
20209538 CACCGACATGTAAGGTTGAGTT
65 CACCGACATGTAAGGTTGAGTT
*
20209560 TCTTACTCTTAATGAACTCATATCCCAAAGTTTGGGTGATCCTATTGAGACAGACTTGATGAATT
1 TATTACTCTTAATGAACTCATATCCCAAAGTTTGGGTG-TCCTATTGAGACAGACTTGATGAATT
* * *
20209625 CACTGACGTGTGAGGTTGAGTT
65 CACCGACATGTAAGGTTGAGTT
* * * *
20209647 TATTACTCTTAATGAGCTCATATTCTAAAGTTTGGGTGGT-CTAATTGAGACGGACTTGATGAAT
1 TATTACTCTTAATGAACTCATATCCCAAAGTTTGGGT-GTCCT-ATTGAGACAGACTTGATGAAT
20209711 TCACCGA
64 TCACCGA
20209718 ATTTAAATTT
Statistics
Matches: 142, Mismatches: 13, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
86 3 0.02
87 138 0.97
88 1 0.01
ACGTcount: A:0.28, C:0.16, G:0.21, T:0.35
Consensus pattern (86 bp):
TATTACTCTTAATGAACTCATATCCCAAAGTTTGGGTGTCCTATTGAGACAGACTTGATGAATTC
ACCGACATGTAAGGTTGAGTT
Found at i:20211875 original size:7 final size:7
Alignment explanation
Indices: 20211863--20211895 Score: 66
Period size: 7 Copynumber: 4.7 Consensus size: 7
20211853 CAATTTTCAA
20211863 CATCTTG
1 CATCTTG
20211870 CATCTTG
1 CATCTTG
20211877 CATCTTG
1 CATCTTG
20211884 CATCTTG
1 CATCTTG
20211891 CATCT
1 CATCT
20211896 CTCTTTTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.15, C:0.30, G:0.12, T:0.42
Consensus pattern (7 bp):
CATCTTG
Found at i:20217539 original size:4 final size:4
Alignment explanation
Indices: 20217525--20217554 Score: 51
Period size: 4 Copynumber: 7.2 Consensus size: 4
20217515 ACAGTACTAA
20217525 ACAT AACAT ACAT ACAT ACAT ACAT ACAT A
1 ACAT -ACAT ACAT ACAT ACAT ACAT ACAT A
20217555 AACATTAATA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
4 21 0.84
5 4 0.16
ACGTcount: A:0.53, C:0.23, G:0.00, T:0.23
Consensus pattern (4 bp):
ACAT
Found at i:20218326 original size:29 final size:28
Alignment explanation
Indices: 20218278--20218335 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 28
20218268 ACTAAACCAG
* * *
20218278 TGGGCAAAAAAAAGTTTAGGTATCAATC
1 TGGGCAAAAAAAACTATAGGTACCAATC
20218306 TGGGACAAAAAAAACTATAGGTACCAATC
1 TGGG-CAAAAAAAACTATAGGTACCAATC
20218335 T
1 T
20218336 AGGAGAAGTG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
28 4 0.15
29 22 0.85
ACGTcount: A:0.45, C:0.14, G:0.19, T:0.22
Consensus pattern (28 bp):
TGGGCAAAAAAAACTATAGGTACCAATC
Found at i:20221241 original size:28 final size:27
Alignment explanation
Indices: 20221179--20221230 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
20221169 GGTAATAGAT
*
20221179 ATTTTTAATTATAAAAATGCAATACGC
1 ATTTTTAATTATAAAAATGCAAGACGC
*
20221206 ATTTTTAATTATAAAAATGTAAGAC
1 ATTTTTAATTATAAAAATGCAAGAC
20221231 ATTCTTTTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.46, C:0.08, G:0.08, T:0.38
Consensus pattern (27 bp):
ATTTTTAATTATAAAAATGCAAGACGC
Found at i:20221518 original size:24 final size:25
Alignment explanation
Indices: 20221491--20221539 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
20221481 GTAAATTTTT
20221491 AATTAA-AAATATTTTGTTGA-ATAA
1 AATTAATAAATATTTT-TTGACATAA
*
20221515 AATTAATATATATTTTTTGACATAA
1 AATTAATAAATATTTTTTGACATAA
20221540 TTAATATATA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
24 10 0.45
25 12 0.55
ACGTcount: A:0.47, C:0.02, G:0.06, T:0.45
Consensus pattern (25 bp):
AATTAATAAATATTTTTTGACATAA
Found at i:20221541 original size:23 final size:23
Alignment explanation
Indices: 20221490--20221549 Score: 70
Period size: 23 Copynumber: 2.6 Consensus size: 23
20221480 GGTAAATTTT
*
20221490 TAATTAA-AAATATTTTGTTGAA
1 TAATTAATATATATTTTGTTGAA
20221512 TAAAATTAATATATATTTT-TTGACA
1 T--AATTAATATATATTTTGTTGA-A
20221537 TAATTAATATATA
1 TAATTAATATATA
20221550 AATTTATATA
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
22 1 0.03
23 12 0.36
24 10 0.30
25 10 0.30
ACGTcount: A:0.47, C:0.02, G:0.05, T:0.47
Consensus pattern (23 bp):
TAATTAATATATATTTTGTTGAA
Found at i:20234478 original size:7 final size:7
Alignment explanation
Indices: 20234466--20234508 Score: 86
Period size: 7 Copynumber: 6.1 Consensus size: 7
20234456 AGAGGAATAG
20234466 AAATAAA
1 AAATAAA
20234473 AAATAAA
1 AAATAAA
20234480 AAATAAA
1 AAATAAA
20234487 AAATAAA
1 AAATAAA
20234494 AAATAAA
1 AAATAAA
20234501 AAATAAA
1 AAATAAA
20234508 A
1 A
20234509 TAAAATGTAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 36 1.00
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (7 bp):
AAATAAA
Found at i:20234519 original size:12 final size:12
Alignment explanation
Indices: 20234461--20234513 Score: 61
Period size: 14 Copynumber: 4.0 Consensus size: 12
20234451 AAAATAGAGG
20234461 AATAGAAATAAAA
1 AATA-AAATAAAA
20234474 AATAAAAAATAAAA
1 AAT--AAAATAAAA
20234488 AATAAAAAATAAAA
1 AAT--AAAATAAAA
20234502 AATAAAATAAAA
1 AATAAAATAAAA
20234514 TGTAAAGAAC
Statistics
Matches: 38, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
12 9 0.24
13 3 0.08
14 25 0.66
15 1 0.03
ACGTcount: A:0.83, C:0.00, G:0.02, T:0.15
Consensus pattern (12 bp):
AATAAAATAAAA
Found at i:20235635 original size:44 final size:44
Alignment explanation
Indices: 20235572--20235661 Score: 128
Period size: 44 Copynumber: 2.0 Consensus size: 44
20235562 AACTCTATTT
* *
20235572 TTAGTTTACCACTTAAACTCTGATTAGTGTAAGTTATTTTAATA
1 TTAGTTTACCACTTAAACTCTGATCAGTATAAGTTATTTTAATA
* *
20235616 TTAGTTT-CTCACTTAAACTCTGATCGGTATAGGTTATTTTAATA
1 TTAGTTTAC-CACTTAAACTCTGATCAGTATAAGTTATTTTAATA
20235660 TT
1 TT
20235662 CTTTAACCTA
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
43 1 0.02
44 40 0.98
ACGTcount: A:0.29, C:0.12, G:0.12, T:0.47
Consensus pattern (44 bp):
TTAGTTTACCACTTAAACTCTGATCAGTATAAGTTATTTTAATA
Found at i:20237670 original size:3 final size:3
Alignment explanation
Indices: 20237662--20237698 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
20237652 CATACTTGTT
20237662 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T
20237699 GCAACTCTGT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:20243074 original size:16 final size:16
Alignment explanation
Indices: 20243045--20243106 Score: 72
Period size: 16 Copynumber: 3.9 Consensus size: 16
20243035 ACTGGAATTG
* *
20243045 AATAGGGTTATAATGA
1 AATAGAGTTGTAATGA
*
20243061 AATATAGTTGTAATAGA
1 AATAGAGTTGTAAT-GA
*
20243078 AA-AGAGTTATAATGA
1 AATAGAGTTGTAATGA
20243093 AATAGAGTTGTAAT
1 AATAGAGTTGTAAT
20243107 CAGTAATTCA
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
15 4 0.11
16 30 0.79
17 4 0.11
ACGTcount: A:0.47, C:0.00, G:0.21, T:0.32
Consensus pattern (16 bp):
AATAGAGTTGTAATGA
Found at i:20248615 original size:23 final size:23
Alignment explanation
Indices: 20248589--20248687 Score: 135
Period size: 23 Copynumber: 4.3 Consensus size: 23
20248579 ATAAGTGCAA
20248589 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
20248612 CACTGAAATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
* *
20248635 CACTGTTATGTAGCTGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
* * * *
20248658 CACTGAAACGTAACTGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
20248681 CACTGAT
1 CACTGAT
20248688 CAATAACACT
Statistics
Matches: 67, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 67 1.00
ACGTcount: A:0.32, C:0.25, G:0.20, T:0.22
Consensus pattern (23 bp):
CACTGATATGTAGCCGAAGCTAC
Found at i:20248656 original size:46 final size:46
Alignment explanation
Indices: 20248589--20248687 Score: 153
Period size: 46 Copynumber: 2.2 Consensus size: 46
20248579 ATAAGTGCAA
* *
20248589 CACTGATATGTAGCCGAAGCTACCACTGAAATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTACCACTGAAACGTAACCGAAGCTAC
* * *
20248635 CACTGTTATGTAGCTGAAGCTACCACTGAAACGTAACTGAAGCTAC
1 CACTGATATGTAGCCGAAGCTACCACTGAAACGTAACCGAAGCTAC
20248681 CACTGAT
1 CACTGAT
20248688 CAATAACACT
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
46 47 1.00
ACGTcount: A:0.32, C:0.25, G:0.20, T:0.22
Consensus pattern (46 bp):
CACTGATATGTAGCCGAAGCTACCACTGAAACGTAACCGAAGCTAC
Found at i:20255110 original size:17 final size:17
Alignment explanation
Indices: 20255088--20255122 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
20255078 AATAGGAAAA
*
20255088 GTAATCTTAGAAGATAT
1 GTAATCTGAGAAGATAT
*
20255105 GTAATCTGATAAGATAT
1 GTAATCTGAGAAGATAT
20255122 G
1 G
20255123 ATTTTGTAAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.40, C:0.06, G:0.20, T:0.34
Consensus pattern (17 bp):
GTAATCTGAGAAGATAT
Found at i:20257421 original size:22 final size:23
Alignment explanation
Indices: 20257368--20257423 Score: 69
Period size: 22 Copynumber: 2.5 Consensus size: 23
20257358 TTCAATTAAA
* * *
20257368 ATTAAAATTAAAATTATTTTTTT
1 ATTAAAATTAAAACTATATTGTT
*
20257391 AATAAAATTAAAACTA-ATTGTT
1 ATTAAAATTAAAACTATATTGTT
20257413 ATTAAAATTAA
1 ATTAAAATTAA
20257424 TTGTTAGTAA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
22 14 0.50
23 14 0.50
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (23 bp):
ATTAAAATTAAAACTATATTGTT
Found at i:20257436 original size:16 final size:16
Alignment explanation
Indices: 20257399--20257438 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
20257389 TTAATAAAAT
* *
20257399 TAAAACTAATTGTTAT
1 TAAAATTAATTGTTAG
20257415 TAAAATTAATTGTTAG
1 TAAAATTAATTGTTAG
20257431 TAAAATTA
1 TAAAATTA
20257439 TCAAATTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.47, C:0.03, G:0.07, T:0.42
Consensus pattern (16 bp):
TAAAATTAATTGTTAG
Found at i:20257517 original size:59 final size:59
Alignment explanation
Indices: 20257449--20257588 Score: 271
Period size: 59 Copynumber: 2.4 Consensus size: 59
20257439 TCAAATTATT
*
20257449 AATTGTTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAATTTATCA
1 AATTATTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAATTTATCA
20257508 AATTATTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAATTTATCA
1 AATTATTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAATTTATCA
20257567 AATTATTAATTGTATTAATTGT
1 AATTATTAATTGTATTAATTGT
20257589 ATTAATTGTT
Statistics
Matches: 80, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
59 80 1.00
ACGTcount: A:0.39, C:0.04, G:0.09, T:0.47
Consensus pattern (59 bp):
AATTATTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAATTTATCA
Found at i:20257582 original size:9 final size:9
Alignment explanation
Indices: 20257570--20257597 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
20257560 TTTATCAAAT
20257570 TATTAATTG
1 TATTAATTG
20257579 TATTAATTG
1 TATTAATTG
20257588 TATTAATTG
1 TATTAATTG
20257597 T
1 T
20257598 TGTAACAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.11, T:0.57
Consensus pattern (9 bp):
TATTAATTG
Found at i:20258306 original size:12 final size:12
Alignment explanation
Indices: 20258289--20258356 Score: 54
Period size: 12 Copynumber: 6.0 Consensus size: 12
20258279 ATTCAATATC
20258289 AATTTCTTTCAA
1 AATTTCTTTCAA
*
20258301 AATTTCTCTC--
1 AATTTCTTTCAA
*
20258311 AATTCCTTTCAA
1 AATTTCTTTCAA
*
20258323 AATTTCTCTC--
1 AATTTCTTTCAA
* *
20258333 AATTCCCTTCAA
1 AATTTCTTTCAA
*
20258345 AATTTCTATCAA
1 AATTTCTTTCAA
20258357 TTTCCTTCCA
Statistics
Matches: 41, Mismatches: 11, Indels: 8
0.68 0.18 0.13
Matches are distributed among these distances:
10 15 0.37
12 26 0.63
ACGTcount: A:0.31, C:0.25, G:0.00, T:0.44
Consensus pattern (12 bp):
AATTTCTTTCAA
Found at i:20258312 original size:22 final size:22
Alignment explanation
Indices: 20258287--20258378 Score: 132
Period size: 22 Copynumber: 4.2 Consensus size: 22
20258277 AAATTCAATA
*
20258287 TCAATTTCTTTCAAAATTTCTC
1 TCAATTCCTTTCAAAATTTCTC
20258309 TCAATTCCTTTCAAAATTTCTC
1 TCAATTCCTTTCAAAATTTCTC
* *
20258331 TCAATTCCCTTCAAAATTTCTA
1 TCAATTCCTTTCAAAATTTCTC
*
20258353 TCAATTTCCTTCCAAAA-TTCTC
1 TCAA-TTCCTTTCAAAATTTCTC
20258375 TCAA
1 TCAA
20258379 ACTCTCAAAT
Statistics
Matches: 63, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
22 53 0.84
23 10 0.16
ACGTcount: A:0.29, C:0.27, G:0.00, T:0.43
Consensus pattern (22 bp):
TCAATTCCTTTCAAAATTTCTC
Found at i:20258394 original size:52 final size:51
Alignment explanation
Indices: 20258328--20258430 Score: 129
Period size: 52 Copynumber: 2.0 Consensus size: 51
20258318 TTCAAAATTT
* * *
20258328 CTCTCAATTCCCTT-CAAAATTTCTATCAATTTCCTTCCAAAATTCTCTCAAA
1 CTCTCAATTCCCTTCCAAAA-TCCTATCAATTTCCTTCAAAAAATCTC-CAAA
*
20258380 CTCTCAAATT-CCTTCCAAAATCCTCTCAATTTCCTTCAAAAAATCTCCAAA
1 CTCTC-AATTCCCTTCCAAAATCCTATCAATTTCCTTCAAAAAATCTCCAAA
20258431 TCCATATTAA
Statistics
Matches: 45, Mismatches: 4, Indels: 5
0.83 0.07 0.09
Matches are distributed among these distances:
51 4 0.09
52 32 0.71
53 9 0.20
ACGTcount: A:0.33, C:0.32, G:0.00, T:0.35
Consensus pattern (51 bp):
CTCTCAATTCCCTTCCAAAATCCTATCAATTTCCTTCAAAAAATCTCCAAA
Found at i:20258419 original size:21 final size:22
Alignment explanation
Indices: 20258380--20258421 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
20258370 TTCTCTCAAA
20258380 CTCTCAAATTCCTTCCAAAATC
1 CTCTCAAATTCCTTCCAAAATC
* *
20258402 CTCTCAATTTCCTTCAAAAA
1 CTCTCAAATTCCTTCCAAAA
20258422 ATCTCCAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (22 bp):
CTCTCAAATTCCTTCCAAAATC
Found at i:20258503 original size:26 final size:27
Alignment explanation
Indices: 20258464--20258515 Score: 88
Period size: 26 Copynumber: 2.0 Consensus size: 27
20258454 TTAAATTTCA
20258464 TTTTTAAGAAAATTTTAAAATTTTTAT
1 TTTTTAAGAAAATTTTAAAATTTTTAT
*
20258491 TTTTTAA-ATAATTTTAAAATTTTTA
1 TTTTTAAGAAAATTTTAAAATTTTTA
20258516 ATATTTTCAA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
26 17 0.71
27 7 0.29
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (27 bp):
TTTTTAAGAAAATTTTAAAATTTTTAT
Found at i:20258513 original size:25 final size:25
Alignment explanation
Indices: 20258456--20258513 Score: 73
Period size: 26 Copynumber: 2.3 Consensus size: 25
20258446 TTTTTCCATT
*
20258456 AAATTTCATTTTTAAGAAAATTTTA
1 AAATTTTATTTTTAAGAAAATTTTA
*
20258481 AAATTTTTATTTTTTAA-ATAATTTTA
1 AAA-TTTTA-TTTTTAAGAAAATTTTA
20258507 AAATTTT
1 AAATTTT
20258514 TAATATTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
25 7 0.24
26 15 0.52
27 7 0.24
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.55
Consensus pattern (25 bp):
AAATTTTATTTTTAAGAAAATTTTA
Found at i:20258633 original size:23 final size:23
Alignment explanation
Indices: 20258607--20258664 Score: 57
Period size: 22 Copynumber: 2.6 Consensus size: 23
20258597 AAATTTAAAT
20258607 TTTA-AAATTTTTAAGATATTTTA
1 TTTATAAATTTTT-AGATATTTTA
**
20258630 TTTATGTATTTTTAGATA-TTTA
1 TTTATAAATTTTTAGATATTTTA
* *
20258652 TTAATATATTTTT
1 TTTATAAATTTTT
20258665 TGTTATAAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
22 15 0.50
23 9 0.30
24 6 0.20
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.62
Consensus pattern (23 bp):
TTTATAAATTTTTAGATATTTTA
Found at i:20258661 original size:22 final size:24
Alignment explanation
Indices: 20258613--20258664 Score: 72
Period size: 22 Copynumber: 2.2 Consensus size: 24
20258603 AAATTTTAAA
* *
20258613 ATTTTTAAGATATTTTATTTATGT
1 ATTTTTAAGATATTTTATTAATAT
20258637 ATTTTT-AGATA-TTTATTAATAT
1 ATTTTTAAGATATTTTATTAATAT
20258659 ATTTTT
1 ATTTTT
20258665 TGTTATAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
22 15 0.58
23 5 0.19
24 6 0.23
ACGTcount: A:0.31, C:0.00, G:0.06, T:0.63
Consensus pattern (24 bp):
ATTTTTAAGATATTTTATTAATAT
Found at i:20258665 original size:23 final size:24
Alignment explanation
Indices: 20258613--20258665 Score: 65
Period size: 23 Copynumber: 2.3 Consensus size: 24
20258603 AAATTTTAAA
* * *
20258613 ATTTTTAAGATATTTTATTTATGT
1 ATTTTTTAGATATTTTATTAATAT
20258637 A-TTTTTAGATA-TTTATTAATAT
1 ATTTTTTAGATATTTTATTAATAT
20258659 ATTTTTT
1 ATTTTTT
20258666 GTTATAAAAG
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
22 10 0.40
23 14 0.56
24 1 0.04
ACGTcount: A:0.30, C:0.00, G:0.06, T:0.64
Consensus pattern (24 bp):
ATTTTTTAGATATTTTATTAATAT
Found at i:20260855 original size:28 final size:28
Alignment explanation
Indices: 20260813--20262447 Score: 1466
Period size: 28 Copynumber: 59.6 Consensus size: 28
20260803 CTTAATTAAA
*
20260813 AACCTTAATTTAATTAAATTAAAAACCCT
1 AACC-TAACTTAATTAAATTAAAAACCCT
*
20260842 AACCTAACCTAATTAAATTAAAAACCCT
1 AACCTAACTTAATTAAATTAAAAACCCT
* **
20260870 AATCTTATTTTAATTAAATTAAAAACCCT
1 AA-CCTAACTTAATTAAATTAAAAACCCT
* * *
20260899 AACCTAACCTACTTAAATTAAAAACTCT
1 AACCTAACTTAATTAAATTAAAAACCCT
**
20260927 AACCTTATTTTAATTAAATTAAAAACCCT
1 AACC-TAACTTAATTAAATTAAAAACCCT
*
20260956 AACC---C-TACTT-AATTAAAAACCCT
1 AACCTAACTTAATTAAATTAAAAACCCT
20260979 -A---A--TTAATTAAATTAAAAACCCT
1 AACCTAACTTAATTAAATTAAAAACCCT
* *
20261001 AACCTTATTTAATTAAATTAAAAACCCT
1 AACCTAACTTAATTAAATTAAAAACCCT
*****
20261029 AACCCT-ACTTAATTAAAACCCTAA-CCT
1 AA-CCTAACTTAATTAAATTAAAAACCCT
*
20261056 AACCTAACCTAATT-AATTAAAAACCCT
1 AACCTAACTTAATTAAATTAAAAACCCT
*
20261083 AACCTAATTTAATTAAATTAAAAACCCT
1 AACCTAACTTAATTAAATTAAAAACCCT
* *
20261111 AACCTAACCTACTTAAATTAAAAACCCT
1 AACCTAACTTAATTAAATTAAAAACCCT
* *
20261139 AACCTAACCTAATTAAATTAAAAACTCT
1 AACCTAACTTAATTAAATTAAAAACCCT
* * *
20261167 AACCTTATTTAATTAAACTAAAAACCCT
1 AACCTAACTTAATTAAATTAAAAACCCT
*
20261195 AACCTTA-TTAATTAAATTAAAAACCCT
1 AACCTAACTTAATTAAATTAAAAACCCT
*
20261222 AAACCCT-ACTTAATTAAA--AACCCTAA-CCT
1 -AA-CCTAACTTAATTAAATTAA---AAACCCT
* *
20261251 AACCTAACCTAATTTAATTAAAAACCCT
1 AACCTAACTTAATTAAATTAAAAACCCT
*
20261279 AACCTAATTTAATTAAATTAAAAACCCT
1 AACCTAACTTAATTAAATTAAAAACCCT
* *
20261307 AACCTAACCTAATTTAATTAAAAACCCT
1 AACCTAACTTAATTAAATTAAAAACCCT
*
20261335 AACCTAATTTAATTAAATT-AAAACCCT
1 AACCTAACTTAATTAAATTAAAAACCCT
* *
20261362 AACCTTATTTAATTAAATTAAAAACCCT
1 AACCTAACTTAATTAAATTAAAAACCCT
*
20261390 AAACCCT-ACTTAATTAAA--AACCCTAACCCT
1 -AA-CCTAACTTAATTAAATTAA---AAACCCT
* *
20261420 AACCTAACCTAATTTAATTAAAAACCCT
1 AACCTAACTTAATTAAATTAAAAACCCT
*
20261448 AACCTAATTTAATTAAATTAAAAACCCT
1 AACCTAACTTAATTAAATTAAAAACCCT
* *
20261476 AACCTTATTTAATTAAATTAAAAACCCT
1 AACCTAACTTAATTAAATTAAAAACCCT
*
20261504 AAACCCT-ACTTAATTAAA--AACCCTAACCCT
1 -AA-CCTAACTTAATTAAATTAA---AAACCCT
* * *
20261534 AACCTAACCTAATTTAATTTAAAACCCT
1 AACCTAACTTAATTAAATTAAAAACCCT
*
20261562 AACCTAATTTAATTAAATTAAAAACCCT
1 AACCTAACTTAATTAAATTAAAAACCCT
*
20261590 AAACCCT-ACTTAATTAAA--AACCCTAACCCT
1 -AA-CCTAACTTAATTAAATTAA---AAACCCT
*
20261620 AACCTAACCTAATTAAATTAAAAACCCT
1 AACCTAACTTAATTAAATTAAAAACCCT
*
20261648 AACCTAATTTAATTAAATTAAAAACCCT
1 AACCTAACTTAATTAAATTAAAAACCCT
* *
20261676 AACCTAACCTAATTTAATTAAAAACCCT
1 AACCTAACTTAATTAAATTAAAAACCCT
*
20261704 AACCTAATTTAATTAAATTAAAAACCCT
1 AACCTAACTTAATTAAATTAAAAACCCT
*
20261732 AACC---C-TACTT-AATTAAAAACCCT
1 AACCTAACTTAATTAAATTAAAAACCCT
*
20261755 AA--T---TTAATTAAATTAAAAATCCT
1 AACCTAACTTAATTAAATTAAAAACCCT
* *
20261778 AACCTTATTTAATTAAATTAAAAACCCT
1 AACCTAACTTAATTAAATTAAAAACCCT
*
20261806 AAACCCT-ACTTAATTAAA--AACCCTAACCCT
1 -AA-CCTAACTTAATTAAATTAA---AAACCCT
* *
20261836 AACCTAACCTAATTTAATTAAAAACCCT
1 AACCTAACTTAATTAAATTAAAAACCCT
*
20261864 AACCTAATTTAATTAAATTAAAAACCCT
1 AACCTAACTTAATTAAATTAAAAACCCT
20261892 AACCTAA--T--TT-AATTAAAAACCCT
1 AACCTAACTTAATTAAATTAAAAACCCT
20261915 AACCTAA--T--TT-AATTAAAAACCCT
1 AACCTAACTTAATTAAATTAAAAACCCT
20261938 AACCT-AC----TTAAATTAAAAACCCT
1 AACCTAACTTAATTAAATTAAAAACCCT
*
20261961 AACCTAATTTAATTAAATTAAAAACCCT
1 AACCTAACTTAATTAAATTAAAAACCCT
* *
20261989 AACCTTATTTAATTAAATTAAAAACCCT
1 AACCTAACTTAATTAAATTAAAAACCCT
*
20262017 AAACCCT-ACTTAATTAAA--AACCCTAACCCT
1 -AA-CCTAACTTAATTAAATTAA---AAACCCT
* * * * *
20262047 AACCTAACCTAACCTAATTTAATTTAAAACCC
1 AACCTAACTTAA-TTAAATTAA---AAACCCT
* * ** *
20262079 TAACCTAATTTAATTAAATTAAAAACCCT
1 AACCTAACTT-AATTAAATTAAAAACCCT
* *
20262108 AACCTAACCTAATTTAATTAAAAACCCT
1 AACCTAACTTAATTAAATTAAAAACCCT
*
20262136 AACCTAATTTAATTAAATTAAAAACCCT
1 AACCTAACTTAATTAAATTAAAAACCCT
* *
20262164 AACCTTATTTAATTAAATTAAAAACCCT
1 AACCTAACTTAATTAAATTAAAAACCCT
*
20262192 AAACCCT-ACTTAATTAAA--AACCCTAACCCT
1 -AA-CCTAACTTAATTAAATTAA---AAACCCT
* *
20262222 AACCTAACCTAATTTAATTAAAAACCCT
1 AACCTAACTTAATTAAATTAAAAACCCT
*
20262250 AACCTAATTTAATTAAATTAAAAACCCT
1 AACCTAACTTAATTAAATTAAAAACCCT
* *
20262278 AACCTTATTTAATTAAATTAAAAACCCT
1 AACCTAACTTAATTAAATTAAAAACCCT
20262306 AACCTAA--T--TT-AATTAAAAACCCT
1 AACCTAACTTAATTAAATTAAAAACCCT
20262329 AACCT-AC----TTAAATTAAAAACCCT
1 AACCTAACTTAATTAAATTAAAAACCCT
* * *
20262352 AACCTTATTTAATTAAATTAAAAACTCT
1 AACCTAACTTAATTAAATTAAAAACCCT
*
20262380 AACC---C-T-ACTAAATTAAAAACCCT
1 AACCTAACTTAATTAAATTAAAAACCCT
* *
20262403 AACCTAATTTAATTAAATTAAAAACGCT
1 AACCTAACTTAATTAAATTAAAAACCCT
*
20262431 AACCCT-ATTTAATTAAA
1 AA-CCTAACTTAATTAAA
20262448 AACCCTAATT
Statistics
Matches: 1346, Mismatches: 156, Indels: 209
0.79 0.09 0.12
Matches are distributed among these distances:
21 4 0.00
22 24 0.02
23 157 0.12
24 15 0.01
25 1 0.00
26 9 0.01
27 92 0.07
28 739 0.55
29 216 0.16
30 61 0.05
31 9 0.01
32 17 0.01
33 2 0.00
ACGTcount: A:0.47, C:0.23, G:0.00, T:0.30
Consensus pattern (28 bp):
AACCTAACTTAATTAAATTAAAAACCCT
Found at i:20260978 original size:17 final size:17
Alignment explanation
Indices: 20260956--20260989 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
20260946 TAAAAACCCT
*
20260956 AACCCTACTTAATTAAA
1 AACCCTAATTAATTAAA
20260973 AACCCTAATTAATTAAA
1 AACCCTAATTAATTAAA
20260990 TTAAAAACCC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.50, C:0.21, G:0.00, T:0.29
Consensus pattern (17 bp):
AACCCTAATTAATTAAA
Found at i:20261280 original size:23 final size:23
Alignment explanation
Indices: 20261253--20261378 Score: 117
Period size: 23 Copynumber: 4.9 Consensus size: 23
20261243 CCTAACCTAA
20261253 CCTAACCTAATTTAATTAAAAAC
1 CCTAACCTAATTTAATTAAAAAC
20261276 CCTAACCTAATTTAATTAAATTAAAAACCC
1 CCTAACCTAA--T--TT-AATTAAAAA--C
20261306 TAACCTAACCTAATTTAATTAAAAAC
1 ---CCTAACCTAATTTAATTAAAAAC
20261332 CCTAACCTAATTTAATTAAATTAAAAC
1 CCTAACCTAATTTAATT--A--AAAAC
*
20261359 CCTAACCTTATTTAATTAAA
1 CCTAACCTAATTTAATTAAA
20261379 TTAAAAACCC
Statistics
Matches: 88, Mismatches: 1, Indels: 28
0.75 0.01 0.24
Matches are distributed among these distances:
23 29 0.33
25 3 0.03
26 1 0.01
27 23 0.26
28 18 0.20
29 2 0.02
30 1 0.01
31 1 0.01
33 10 0.11
ACGTcount: A:0.47, C:0.21, G:0.00, T:0.33
Consensus pattern (23 bp):
CCTAACCTAATTTAATTAAAAAC
Found at i:20261387 original size:22 final size:24
Alignment explanation
Indices: 20261312--20261384 Score: 69
Period size: 27 Copynumber: 3.0 Consensus size: 24
20261302 ACCCTAACCT
**
20261312 AACCTAATTTAATTAAA--AACCC
1 AACCTAATTTAATTAAATTAAAAC
20261334 TAACCTAATTTAATTAAATTAAAACCC
1 -AACCTAATTTAATTAAATTAAAA--C
*
20261361 TAACCTTATTTAATTAAATTAAAA
1 -AACCTAATTTAATTAAATTAAAA
20261385 ACCCTAAACC
Statistics
Matches: 43, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
23 17 0.40
25 2 0.05
27 24 0.56
ACGTcount: A:0.49, C:0.16, G:0.00, T:0.34
Consensus pattern (24 bp):
AACCTAATTTAATTAAATTAAAAC
Found at i:20261754 original size:17 final size:18
Alignment explanation
Indices: 20261732--20261766 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
20261722 TAAAAACCCT
20261732 AACCCT-ACTTAATTAAA
1 AACCCTAACTTAATTAAA
*
20261749 AACCCTAATTTAATTAAA
1 AACCCTAACTTAATTAAA
20261767 TTAAAAATCC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.49, C:0.20, G:0.00, T:0.31
Consensus pattern (18 bp):
AACCCTAACTTAATTAAA
Found at i:20261969 original size:18 final size:19
Alignment explanation
Indices: 20261879--20261969 Score: 67
Period size: 23 Copynumber: 4.2 Consensus size: 19
20261869 AATTTAATTA
20261879 AATTAAAAACCCTAACCTAATTT
1 AATTAAAAACCCTAACC----TT
20261902 AATTAAAAACCCTAACCTAATTT
1 AATTAAAAACCCTAACC----TT
20261925 AATTAAAAACCCTAACCTACTT
1 AATTAAAAACCCTAA-C--CTT
20261947 AAATTAAAAACCCTAACC-T
1 -AATTAAAAACCCTAACCTT
20261966 AATT
1 AATT
20261970 TAATTAAATT
Statistics
Matches: 64, Mismatches: 0, Indels: 13
0.83 0.00 0.17
Matches are distributed among these distances:
18 4 0.06
19 1 0.02
20 1 0.02
22 3 0.05
23 53 0.83
24 1 0.02
26 1 0.02
ACGTcount: A:0.48, C:0.23, G:0.00, T:0.29
Consensus pattern (19 bp):
AATTAAAAACCCTAACCTT
Found at i:20262251 original size:23 final size:23
Alignment explanation
Indices: 20262224--20262455 Score: 180
Period size: 23 Copynumber: 9.2 Consensus size: 23
20262214 CTAACCCTAA
20262224 CCTAACCTAATTTAATTAAAAAC
1 CCTAACCTAATTTAATTAAAAAC
20262247 CCTAACCTAATTTAATTAAATTAAAAAC
1 CCTAACCTAA--T--TT-AATTAAAAAC
*
20262275 CCTAACCTTATTTAATTAAATTAAAAAC
1 CCTAACC-----TAATTTAATTAAAAAC
20262303 CCTAACCTAATTTAATTAAAAAC
1 CCTAACCTAATTTAATTAAAAAC
* *
20262326 CCTAACCTACTTAAATTAAAAAC
1 CCTAACCTAATTTAATTAAAAAC
*
20262349 CCTAACCTTATTTAATTAAATTAAAAAC
1 CCTAACC-----TAATTTAATTAAAAAC
* * *
20262377 TCTAACCCT-ACTAAATTAAAAAC
1 CCTAA-CCTAATTTAATTAAAAAC
20262400 CCTAACCTAATTTAATTAAATTAAAAAC
1 CCTAACCTAA--T--TT-AATTAAAAAC
*
20262428 GCTAACCCT-ATTTAATTAAAAAC
1 CCTAA-CCTAATTTAATTAAAAAC
20262451 CCTAA
1 CCTAA
20262456 TTAAATTGTA
Statistics
Matches: 174, Mismatches: 12, Indels: 46
0.75 0.05 0.20
Matches are distributed among these distances:
22 3 0.02
23 85 0.49
24 3 0.02
25 1 0.01
26 1 0.01
27 3 0.02
28 68 0.39
29 6 0.03
31 1 0.01
33 3 0.02
ACGTcount: A:0.47, C:0.21, G:0.00, T:0.31
Consensus pattern (23 bp):
CCTAACCTAATTTAATTAAAAAC
Found at i:20265842 original size:124 final size:124
Alignment explanation
Indices: 20265622--20265901 Score: 370
Period size: 124 Copynumber: 2.3 Consensus size: 124
20265612 CCACGAGGGC
20265622 GCGATTTGACACTATTTGCTCAGAAACGTCAAAAAAAATTATTTCCTACATGACCAACTGTAGCG
1 GCGATTTGACACTATTTGCTCAGAAACGTCAAAAAAAATTATTTCCTACATGACCAACTGTAGCG
* * * * * **
20265687 AAATCGCGTCCACGAGGGCTCGATTTCACAATTTCTTCTCATATAGCATCCTGGTATCA
66 AAATCGCGTCCACGAGGCCACGATTTCACAATTTCTTCTCAAATAACATCCTAGTAGAA
* *
20265746 GCGATTTTATACTATTT-CTCAGAAAACGTCAAAAAAAAATTATTT-CTCACATGACC-ACTGTA
1 GCGATTTGACACTATTTGCTCAG-AAACGTC-AAAAAAAATTATTTCCT-ACATGACCAACTGTA
* *
20265808 GCGAAATCGCGTCCACGAGGCCACTATTTCACAATTTCTTCTTAAATAACATCCTAGTAGAA
63 GCGAAATCGCGTCCACGAGGCCACGATTTCACAATTTCTTCTCAAATAACATCCTAGTAGAA
** *
20265870 GCGATTTCCCACTATTTAAC-CAGAAACGTCAA
1 GCGATTTGACACTATTT-GCTCAGAAACGTCAA
20265902 CTCGAAAAAA
Statistics
Matches: 137, Mismatches: 14, Indels: 11
0.85 0.09 0.07
Matches are distributed among these distances:
123 7 0.05
124 104 0.76
125 25 0.18
126 1 0.01
ACGTcount: A:0.33, C:0.24, G:0.14, T:0.29
Consensus pattern (124 bp):
GCGATTTGACACTATTTGCTCAGAAACGTCAAAAAAAATTATTTCCTACATGACCAACTGTAGCG
AAATCGCGTCCACGAGGCCACGATTTCACAATTTCTTCTCAAATAACATCCTAGTAGAA
Found at i:20266596 original size:17 final size:18
Alignment explanation
Indices: 20266574--20266607 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
20266564 AATCTCTTCT
20266574 TTTTTAG-TTTTACTTTA
1 TTTTTAGTTTTTACTTTA
20266591 TTTTTAGTTTTTACTTT
1 TTTTTAGTTTTTACTTT
20266608 TAAAAGTAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.15, C:0.06, G:0.06, T:0.74
Consensus pattern (18 bp):
TTTTTAGTTTTTACTTTA
Found at i:20266789 original size:28 final size:28
Alignment explanation
Indices: 20266749--20266816 Score: 100
Period size: 28 Copynumber: 2.4 Consensus size: 28
20266739 ATTGATATAA
* *
20266749 CTTTTAAGTTTGAGATGCAATTAGATTG
1 CTTTGAAGTTTGAGATGCAATTAGAATG
*
20266777 CTTTGAAGTTTGAGATGTAATTAGAATG
1 CTTTGAAGTTTGAGATGCAATTAGAATG
*
20266805 TTTTGAAGTTTG
1 CTTTGAAGTTTG
20266817 TGAACCAATT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 36 1.00
ACGTcount: A:0.28, C:0.04, G:0.24, T:0.44
Consensus pattern (28 bp):
CTTTGAAGTTTGAGATGCAATTAGAATG
Found at i:20266826 original size:28 final size:28
Alignment explanation
Indices: 20266749--20266826 Score: 75
Period size: 28 Copynumber: 2.8 Consensus size: 28
20266739 ATTGATATAA
* ** *
20266749 CTTTTAAGTTTGAGATGCAATTAGATTG
1 CTTTGAAGTTTGAGAACCAATTAGAATG
***
20266777 CTTTGAAGTTTGAGATGTAATTAGAATG
1 CTTTGAAGTTTGAGAACCAATTAGAATG
* *
20266805 TTTTGAAGTTTGTGAACCAATT
1 CTTTGAAGTTTGAGAACCAATT
20266827 TAAAATGATA
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
28 42 1.00
ACGTcount: A:0.29, C:0.06, G:0.22, T:0.42
Consensus pattern (28 bp):
CTTTGAAGTTTGAGAACCAATTAGAATG
Found at i:20267299 original size:16 final size:16
Alignment explanation
Indices: 20267259--20267293 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
20267249 ATTAAAATAT
*
20267259 AATAAA-ATATTAAAA
1 AATAAATATTTTAAAA
20267274 AATAAATATTTTAAAA
1 AATAAATATTTTAAAA
20267290 AATA
1 AATA
20267294 CTTATTAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 6 0.33
16 12 0.67
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (16 bp):
AATAAATATTTTAAAA
Found at i:20285675 original size:40 final size:40
Alignment explanation
Indices: 20285599--20285677 Score: 97
Period size: 40 Copynumber: 2.0 Consensus size: 40
20285589 TATACTTTTT
* * *
20285599 TTAGCACTACGGTGCTTTTGACGGCACATTCGTGCTCCTA
1 TTAGCACTACAGTGCTCTTGACAGCACATTCGTGCTCCTA
* *
20285639 TTAGCACTACAGTGCTCTTGATAGCATATT-GATGCTCCT
1 TTAGCACTACAGTGCTCTTGACAGCACATTCG-TGCTCCT
20285678 CTTTCCTTTA
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
39 1 0.03
40 32 0.97
ACGTcount: A:0.20, C:0.25, G:0.20, T:0.34
Consensus pattern (40 bp):
TTAGCACTACAGTGCTCTTGACAGCACATTCGTGCTCCTA
Found at i:20285903 original size:17 final size:17
Alignment explanation
Indices: 20285881--20285916 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 17
20285871 CTTGGGCTGA
20285881 ATTGATTGAA-ATGTTAT
1 ATTGATT-AACATGTTAT
20285898 ATTGATTAACATGTTAT
1 ATTGATTAACATGTTAT
20285915 AT
1 AT
20285917 GGTTTTACGA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 2 0.11
17 16 0.89
ACGTcount: A:0.36, C:0.03, G:0.14, T:0.47
Consensus pattern (17 bp):
ATTGATTAACATGTTAT
Found at i:20287417 original size:15 final size:15
Alignment explanation
Indices: 20287397--20287427 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
20287387 AATGGCATGA
*
20287397 TTGAATAAGTTGAAT
1 TTGAATAAATTGAAT
20287412 TTGAATAAATTGAAT
1 TTGAATAAATTGAAT
20287427 T
1 T
20287428 GATATCTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.42, C:0.00, G:0.16, T:0.42
Consensus pattern (15 bp):
TTGAATAAATTGAAT
Found at i:20304522 original size:42 final size:41
Alignment explanation
Indices: 20304420--20304605 Score: 160
Period size: 42 Copynumber: 4.5 Consensus size: 41
20304410 CGAAGGCTGT
* * * * **
20304420 ACTGAAGCACATAAGTGCTAAACAGAAACCTGTAAGGGTTAA
1 ACTGAAGCTCAGAAGAGCTGAACAGAAACCCATAAGGGTT-A
* * *
20304462 ACGGAAGCTCATAGGAGCTGAACAGAAACCCATAAGGGTTA
1 ACTGAAGCTCAGAAGAGCTGAACAGAAACCCATAAGGGTTA
* * *
20304503 ATCTGAAGCTCAGAAGAGCT-AAAATAAAACCCATTAGGGTTA
1 A-CTGAAGCTCAGAAGAGCTGAACA-GAAACCCATAAGGGTTA
* * * * *
20304545 AGCTGAAGCTCAAAAGAGCTGAACTGAAACTCATATGAGTTA
1 A-CTGAAGCTCAGAAGAGCTGAACAGAAACCCATAAGGGTTA
20304587 ACTGAAGCTCATG-AGAGCT
1 ACTGAAGCTCA-GAAGAGCT
20304606 AAATGGAAAG
Statistics
Matches: 117, Mismatches: 23, Indels: 9
0.79 0.15 0.06
Matches are distributed among these distances:
41 21 0.18
42 94 0.80
43 2 0.02
ACGTcount: A:0.40, C:0.18, G:0.23, T:0.19
Consensus pattern (41 bp):
ACTGAAGCTCAGAAGAGCTGAACAGAAACCCATAAGGGTTA
Found at i:20304564 original size:84 final size:83
Alignment explanation
Indices: 20304454--20304608 Score: 213
Period size: 84 Copynumber: 1.9 Consensus size: 83
20304444 GAAACCTGTA
* * *
20304454 AGGGTTAAACGGAAGCTCATAGGAGCTGAACAGAAACCCATAAGGGTTAATCTGAAGCTCA-GAA
1 AGGGTTAAACGGAAGCTCAAAAGAGCTGAACAGAAACCCATAAGAGTTAA-CTGAAGCTCATG-A
20304518 GAGCTAAAATAAAACCCATT
64 GAGCTAAAATAAAACCCATT
* * * * *
20304538 AGGGTTAAGCTGAAGCTCAAAAGAGCTGAACTGAAACTCATATGAGTTAACTGAAGCTCATGAGA
1 AGGGTTAAACGGAAGCTCAAAAGAGCTGAACAGAAACCCATAAGAGTTAACTGAAGCTCATGAGA
20304603 GCTAAA
66 GCTAAA
20304609 TGGAAAGCAA
Statistics
Matches: 62, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
83 19 0.31
84 43 0.69
ACGTcount: A:0.41, C:0.17, G:0.23, T:0.19
Consensus pattern (83 bp):
AGGGTTAAACGGAAGCTCAAAAGAGCTGAACAGAAACCCATAAGAGTTAACTGAAGCTCATGAGA
GCTAAAATAAAACCCATT
Found at i:20304968 original size:15 final size:15
Alignment explanation
Indices: 20304948--20304982 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
20304938 ACAAACCCAC
*
20304948 CAGAACAGGATAGAG
1 CAGAACAGGATAGAA
*
20304963 CAGAACATGATAGAA
1 CAGAACAGGATAGAA
20304978 CAGAA
1 CAGAA
20304983 TAGAGCAGAG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.51, C:0.14, G:0.26, T:0.09
Consensus pattern (15 bp):
CAGAACAGGATAGAA
Found at i:20306896 original size:13 final size:13
Alignment explanation
Indices: 20306878--20306903 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
20306868 ACCTGAAAGC
20306878 AATTTAATTCATA
1 AATTTAATTCATA
20306891 AATTTAATTCATA
1 AATTTAATTCATA
20306904 TTAGGACACA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.08, G:0.00, T:0.46
Consensus pattern (13 bp):
AATTTAATTCATA
Found at i:20313753 original size:31 final size:30
Alignment explanation
Indices: 20313711--20313801 Score: 96
Period size: 31 Copynumber: 2.9 Consensus size: 30
20313701 ACCAAAACTT
20313711 TATTTTAAAAATTAAAACAAAAATTTTAAAAA-
1 TATTTT-AAAATT-AAA-AAAAATTTTAAAAAG
* *
20313743 TATTTTAAAATT-TAAAAAATTTAAAAAAAAG
1 TATTTTAAAATTAAAAAAAATTT--TAAAAAG
*
20313774 TATTTTAAAATGAAAAAAAATTTTAAAA
1 TATTTTAAAATTAAAAAAAATTTTAAAA
20313802 TAAAAATATT
Statistics
Matches: 50, Mismatches: 5, Indels: 10
0.77 0.08 0.15
Matches are distributed among these distances:
28 8 0.16
29 1 0.02
30 9 0.18
31 17 0.34
32 15 0.30
ACGTcount: A:0.62, C:0.01, G:0.02, T:0.35
Consensus pattern (30 bp):
TATTTTAAAATTAAAAAAAATTTTAAAAAG
Found at i:20313758 original size:18 final size:17
Alignment explanation
Indices: 20313736--20313812 Score: 74
Period size: 18 Copynumber: 4.7 Consensus size: 17
20313726 AACAAAAATT
20313736 TTAAAAATATTTTAAAA
1 TTAAAAATATTTTAAAA
20313753 TTTAAAAA-A-TTTAAAA
1 -TTAAAAATATTTTAAAA
*
20313769 --AAAAGTATTTTAAAA
1 TTAAAAATATTTTAAAA
* *
20313784 TGAAAAAAAATTTTAAAA
1 T-TAAAAATATTTTAAAA
20313802 -TAAAAATATTT
1 TTAAAAATATTT
20313813 ATTATATTCA
Statistics
Matches: 49, Mismatches: 5, Indels: 12
0.74 0.08 0.18
Matches are distributed among these distances:
13 4 0.08
14 1 0.02
15 7 0.14
16 16 0.33
17 1 0.02
18 20 0.41
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (17 bp):
TTAAAAATATTTTAAAA
Found at i:20313771 original size:10 final size:9
Alignment explanation
Indices: 20313729--20313770 Score: 50
Period size: 9 Copynumber: 4.7 Consensus size: 9
20313719 AAATTAAAAC
*
20313729 AAAAATTTT
1 AAAAAATTT
20313738 AAAAATATTT
1 AAAAA-ATTT
*
20313748 -TAAAATTT
1 AAAAAATTT
20313756 AAAAAATTT
1 AAAAAATTT
20313765 AAAAAA
1 AAAAAA
20313771 AAGTATTTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
8 4 0.14
9 21 0.75
10 3 0.11
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (9 bp):
AAAAAATTT
Found at i:20315528 original size:37 final size:38
Alignment explanation
Indices: 20315477--20315552 Score: 145
Period size: 37 Copynumber: 2.0 Consensus size: 38
20315467 AATATATCAC
20315477 ATAGTTTTTTCTAGATAATTCGTCCCAAGGACTTTACA
1 ATAGTTTTTTCTAGATAATTCGTCCCAAGGACTTTACA
20315515 ATAG-TTTTTCTAGATAATTCGTCCCAAGGACTTTACA
1 ATAGTTTTTTCTAGATAATTCGTCCCAAGGACTTTACA
20315552 A
1 A
20315553 ATAATTTGTC
Statistics
Matches: 38, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
37 34 0.89
38 4 0.11
ACGTcount: A:0.30, C:0.18, G:0.13, T:0.38
Consensus pattern (38 bp):
ATAGTTTTTTCTAGATAATTCGTCCCAAGGACTTTACA
Found at i:20316627 original size:16 final size:16
Alignment explanation
Indices: 20316603--20316634 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
20316593 CAAAACTCTA
*
20316603 GGGCTTAGTCTTTCTT
1 GGGCGTAGTCTTTCTT
20316619 GGGCGTAGTCTTTCTT
1 GGGCGTAGTCTTTCTT
20316635 CACTTGAAGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.06, C:0.19, G:0.28, T:0.47
Consensus pattern (16 bp):
GGGCGTAGTCTTTCTT
Found at i:20318314 original size:28 final size:29
Alignment explanation
Indices: 20318283--20318344 Score: 92
Period size: 28 Copynumber: 2.2 Consensus size: 29
20318273 TATTTGTTAT
20318283 TTTTTTA-TTTAAAATATTTTGAAAATAC
1 TTTTTTATTTTAAAATATTTTGAAAATAC
* *
20318311 -TTTTAATTTTAAAATATTTTTAAAATAC
1 TTTTTTATTTTAAAATATTTTGAAAATAC
20318339 TTTTTT
1 TTTTTT
20318345 TTATTTTTTA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
27 5 0.17
28 20 0.69
29 4 0.14
ACGTcount: A:0.37, C:0.03, G:0.02, T:0.58
Consensus pattern (29 bp):
TTTTTTATTTTAAAATATTTTGAAAATAC
Found at i:20318326 original size:17 final size:18
Alignment explanation
Indices: 20318298--20318333 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
20318288 TATTTAAAAT
20318298 ATTTTGAAAATACTTTTA
1 ATTTTGAAAATACTTTTA
*
20318316 ATTTT-AAAATATTTTTA
1 ATTTTGAAAATACTTTTA
20318333 A
1 A
20318334 AATACTTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 12 0.71
18 5 0.29
ACGTcount: A:0.42, C:0.03, G:0.03, T:0.53
Consensus pattern (18 bp):
ATTTTGAAAATACTTTTA
Found at i:20318333 original size:39 final size:39
Alignment explanation
Indices: 20318290--20318381 Score: 123
Period size: 39 Copynumber: 2.4 Consensus size: 39
20318280 TATTTTTTTA
20318290 TTTAAAATA-TTTTGAAAATACTTTTAATTTTAAAATATT
1 TTTAAAATACTTTTGAAAAT-CTTTTAATTTTAAAATATT
**** *
20318329 TTTAAAATACTTTTTTTTATTTTTTAATTTTAAAATATT
1 TTTAAAATACTTTTGAAAATCTTTTAATTTTAAAATATT
20318368 TTTAAAATACTTTT
1 TTTAAAATACTTTT
20318382 TTTATTTTTT
Statistics
Matches: 47, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
39 41 0.87
40 6 0.13
ACGTcount: A:0.38, C:0.03, G:0.01, T:0.58
Consensus pattern (39 bp):
TTTAAAATACTTTTGAAAATCTTTTAATTTTAAAATATT
Found at i:20318382 original size:39 final size:40
Alignment explanation
Indices: 20318311--20318405 Score: 165
Period size: 39 Copynumber: 2.4 Consensus size: 40
20318301 TTGAAAATAC
20318311 TTTTAATTTTAAAATATTTTTAAAATACTTTTTTT-TATT
1 TTTTAATTTTAAAATATTTTTAAAATACTTTTTTTATATT
*
20318350 TTTTAATTTTAAAATATTTTTAAAATACTTTTTTTATTTT
1 TTTTAATTTTAAAATATTTTTAAAATACTTTTTTTATATT
*
20318390 TTTTATTTTTAAAATA
1 TTTTAATTTTAAAATA
20318406 AATTTTTGGT
Statistics
Matches: 53, Mismatches: 2, Indels: 1
0.95 0.04 0.02
Matches are distributed among these distances:
39 35 0.66
40 18 0.34
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (40 bp):
TTTTAATTTTAAAATATTTTTAAAATACTTTTTTTATATT
Found at i:20321399 original size:27 final size:27
Alignment explanation
Indices: 20321346--20321422 Score: 68
Period size: 27 Copynumber: 2.9 Consensus size: 27
20321336 CCCTCCACAA
* * *
20321346 TTCACCACAAAGGC-ATTCATTTGATA-
1 TTCAACACAAAGGCTCTTC-TTTCATAT
*
20321372 TTCAAACACGAAGGCTCTTCTTTCATAT
1 TTC-AACACAAAGGCTCTTCTTTCATAT
* *
20321400 TTCACCACAAAGGCTTTTCTTTC
1 TTCAACACAAAGGCTCTTCTTTC
20321423 CTGTCGTGTT
Statistics
Matches: 41, Mismatches: 7, Indels: 5
0.77 0.13 0.09
Matches are distributed among these distances:
26 3 0.07
27 32 0.78
28 6 0.15
ACGTcount: A:0.29, C:0.26, G:0.10, T:0.35
Consensus pattern (27 bp):
TTCAACACAAAGGCTCTTCTTTCATAT
Found at i:20340320 original size:17 final size:17
Alignment explanation
Indices: 20340302--20340334 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
20340292 TTTTTATTAT
*
20340302 TTTTTAAAT-TTTTTAA
1 TTTTAAAATATTTTTAA
20340318 TTTTAAAATATTTTTAA
1 TTTTAAAATATTTTTAA
20340335 AATACTTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (17 bp):
TTTTAAAATATTTTTAA
Found at i:20340332 original size:11 final size:11
Alignment explanation
Indices: 20340318--20340407 Score: 57
Period size: 11 Copynumber: 8.5 Consensus size: 11
20340308 AATTTTTTAA
20340318 TTTTAAAATAT
1 TTTTAAAATAT
20340329 TTTTAAAATACT
1 TTTTAAAATA-T
* *
20340341 TTTT-TATTAT
1 TTTTAAAATAT
*
20340351 TTTT----TAA
1 TTTTAAAATAT
20340358 TTTTAAAATAT
1 TTTTAAAATAT
20340369 TTTTAAAATACT
1 TTTTAAAATA-T
**
20340381 TTTTTTAAT-T
1 TTTTAAAATAT
*
20340391 TTTTAAATAAAT
1 TTTTAAA-ATAT
20340403 TTTTA
1 TTTTA
20340408 GTATTTATTA
Statistics
Matches: 62, Mismatches: 9, Indels: 15
0.72 0.10 0.17
Matches are distributed among these distances:
7 6 0.10
10 11 0.18
11 26 0.42
12 19 0.31
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (11 bp):
TTTTAAAATAT
Found at i:20340353 original size:40 final size:40
Alignment explanation
Indices: 20340301--20340396 Score: 169
Period size: 40 Copynumber: 2.5 Consensus size: 40
20340291 TTTTTTATTA
20340301 TTTTTTA-AATTTTTTAATTTTAAAATATTTTTAAAATAC
1 TTTTTTATAATTTTTTAATTTTAAAATATTTTTAAAATAC
*
20340340 TTTTTTATTATTTTTTAATTTTAAAATATTTTTAAAATAC
1 TTTTTTATAATTTTTTAATTTTAAAATATTTTTAAAATAC
20340380 TTTTTT-TAATTTTTTAA
1 TTTTTTATAATTTTTTAA
20340397 ATAAATTTTT
Statistics
Matches: 54, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
39 17 0.31
40 37 0.69
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (40 bp):
TTTTTTATAATTTTTTAATTTTAAAATATTTTTAAAATAC
Found at i:20340383 original size:29 final size:29
Alignment explanation
Indices: 20340329--20340384 Score: 69
Period size: 29 Copynumber: 1.9 Consensus size: 29
20340319 TTTAAAATAT
* * *
20340329 TTTTAAAATACTTTTTTATTATTTTTTAA
1 TTTTAAAATACTTTTTAAATACTTTTTAA
20340358 TTTTAAAATA-TTTTTAAAATACTTTTT
1 TTTTAAAATACTTTTT-AAATACTTTTT
20340385 TTAATTTTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
28 5 0.22
29 18 0.78
ACGTcount: A:0.34, C:0.04, G:0.00, T:0.62
Consensus pattern (29 bp):
TTTTAAAATACTTTTTAAATACTTTTTAA
Found at i:20340405 original size:21 final size:21
Alignment explanation
Indices: 20340367--20340406 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
20340357 ATTTTAAAAT
**
20340367 ATTTTTAAAATACTTTTTTTA
1 ATTTTTAAAATAAATTTTTTA
*
20340388 ATTTTTTAAATAAATTTTT
1 ATTTTTAAAATAAATTTTT
20340407 AGTATTTATT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (21 bp):
ATTTTTAAAATAAATTTTTTA
Found at i:20351029 original size:15 final size:14
Alignment explanation
Indices: 20350998--20351044 Score: 51
Period size: 13 Copynumber: 3.4 Consensus size: 14
20350988 ATATTTTTCT
* *
20350998 TTATTTTTATTTTC
1 TTATTTTTATATAC
20351012 TTAGTTTTTATATAC
1 TTA-TTTTTATATAC
*
20351027 TTA-TTATATATAC
1 TTATTTTTATATAC
20351040 TTATT
1 TTATT
20351045 CATTTTATTT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
13 12 0.43
14 4 0.14
15 12 0.43
ACGTcount: A:0.26, C:0.06, G:0.02, T:0.66
Consensus pattern (14 bp):
TTATTTTTATATAC
Found at i:20351248 original size:12 final size:12
Alignment explanation
Indices: 20351231--20351259 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
20351221 TATGCATACC
20351231 TACATATTTTAA
1 TACATATTTTAA
20351243 TACATATTTTAA
1 TACATATTTTAA
20351255 TACAT
1 TACAT
20351260 TCATTTTCTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.41, C:0.10, G:0.00, T:0.48
Consensus pattern (12 bp):
TACATATTTTAA
Found at i:20351384 original size:18 final size:19
Alignment explanation
Indices: 20351348--20351386 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
20351338 TTTTATATGC
* *
20351348 ATATTGTACATATATACAT
1 ATATTGTACATACACACAT
20351367 ATATT-TACATACACACAT
1 ATATTGTACATACACACAT
20351385 AT
1 AT
20351387 TTCATGATAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 13 0.72
19 5 0.28
ACGTcount: A:0.44, C:0.15, G:0.03, T:0.38
Consensus pattern (19 bp):
ATATTGTACATACACACAT
Found at i:20356066 original size:24 final size:21
Alignment explanation
Indices: 20356011--20356066 Score: 58
Period size: 22 Copynumber: 2.5 Consensus size: 21
20356001 GCAACACATA
*
20356011 ATATTTTATATATAAAATATT
1 ATATTTTAAATATAAAATATT
*
20356032 ATAATTATAAATATAAAAATTCATT
1 AT-ATTTTAAATAT-AAAA-T-ATT
20356057 ATATTTTAAA
1 ATATTTTAAA
20356067 CTTTTTTATT
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
21 2 0.07
22 9 0.32
23 4 0.14
24 8 0.29
25 5 0.18
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (21 bp):
ATATTTTAAATATAAAATATT
Found at i:20356124 original size:5 final size:5
Alignment explanation
Indices: 20356073--20356154 Score: 91
Period size: 5 Copynumber: 16.6 Consensus size: 5
20356063 TAAACTTTTT
* *
20356073 TATTA TA-TA TATT- TATTA T-TTA TCTATA TATTAAA TATTC T-TTA
1 TATTA TATTA TATTA TATTA TATTA TAT-TA TATT--A TATTA TATTA
20356117 TATTA TATTA TATTA TATTA TATTA TATTA TATTA TAT
1 TATTA TATTA TATTA TATTA TATTA TATTA TATTA TAT
20356155 GTTATATTGA
Statistics
Matches: 67, Mismatches: 3, Indels: 14
0.80 0.04 0.17
Matches are distributed among these distances:
4 15 0.22
5 43 0.64
6 4 0.06
7 5 0.07
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (5 bp):
TATTA
Found at i:20356248 original size:17 final size:17
Alignment explanation
Indices: 20356226--20356264 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
20356216 CTACCTCCAT
* *
20356226 TTTTATTTTTTAGTTTA
1 TTTTATATTTTAGTATA
20356243 TTTTATATTTTAGTATA
1 TTTTATATTTTAGTATA
20356260 TTTTA
1 TTTTA
20356265 CATCTAAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.23, C:0.00, G:0.05, T:0.72
Consensus pattern (17 bp):
TTTTATATTTTAGTATA
Found at i:20358465 original size:43 final size:43
Alignment explanation
Indices: 20358403--20358501 Score: 137
Period size: 43 Copynumber: 2.3 Consensus size: 43
20358393 TCTTTCACAT
*
20358403 AAACGCCGCAAAAGAACATGACCTTTAGCGGCG-CTTTTATCAC
1 AAACGCCGCTAAAGAACATGACCTTTAGCGGCGCCTTTT-TCAC
* * *
20358446 AAACACCGCTAAAGAACATGACTTTTAGTGGCGCCTTTTTCAC
1 AAACGCCGCTAAAGAACATGACCTTTAGCGGCGCCTTTTTCAC
*
20358489 AAACGCTGCTAAA
1 AAACGCCGCTAAA
20358502 AGCATCGTTC
Statistics
Matches: 49, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
43 44 0.90
44 5 0.10
ACGTcount: A:0.33, C:0.26, G:0.17, T:0.23
Consensus pattern (43 bp):
AAACGCCGCTAAAGAACATGACCTTTAGCGGCGCCTTTTTCAC
Found at i:20364329 original size:9 final size:9
Alignment explanation
Indices: 20364277--20364346 Score: 65
Period size: 9 Copynumber: 8.0 Consensus size: 9
20364267 CAAGTATAAA
*
20364277 TAAGTTCTG
1 TAAGTTATG
20364286 TAAGTTATG
1 TAAGTTATG
* * *
20364295 ATATGATATA
1 -TAAGTTATG
*
20364305 T-ATTTATG
1 TAAGTTATG
20364313 T-A-TTATG
1 TAAGTTATG
20364320 TAAGTTATG
1 TAAGTTATG
20364329 TAAGTTATG
1 TAAGTTATG
20364338 TAAGTTATG
1 TAAGTTATG
20364347 ATATGATATA
Statistics
Matches: 50, Mismatches: 8, Indels: 6
0.78 0.12 0.09
Matches are distributed among these distances:
7 6 0.12
8 6 0.12
9 32 0.64
10 6 0.12
ACGTcount: A:0.33, C:0.01, G:0.19, T:0.47
Consensus pattern (9 bp):
TAAGTTATG
Done.