Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr06 132263754
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: 132263754
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 372 characters in sequence are not A, C, G, or T
File 420 of 433
Found at i:128708453 original size:21 final size:20
Alignment explanation
Indices: 128708373--128708459 Score: 61
Period size: 21 Copynumber: 4.0 Consensus size: 20
128708363 CTTATTTTAT
128708373 TAAATAAAAAAAT-TTAAAAA
1 TAAATAAAAAAATATT-AAAA
128708393 TATAATAAATCAAATATATTTAAAA
1 TA-AATAAA--AAA-ATA-TTAAAA
*
128708418 -ATATTAAAATAAATATTAAAA
1 TA-AATAAAA-AAATATTAAAA
*
128708439 TAAATAAAAATAATACTAAAA
1 TAAATAAAAA-AATATTAAAA
128708460 CAATTCTTAA
Statistics
Matches: 55, Mismatches: 3, Indels: 17
0.73 0.04 0.23
Matches are distributed among these distances:
20 3 0.05
21 27 0.49
22 5 0.09
23 5 0.09
24 9 0.16
25 4 0.07
26 2 0.04
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (20 bp):
TAAATAAAAAAATATTAAAA
Found at i:128711884 original size:41 final size:39
Alignment explanation
Indices: 128711818--128711894 Score: 100
Period size: 41 Copynumber: 1.9 Consensus size: 39
128711808 TCACTTACAT
* **
128711818 AATTTTAATTAATAATAAAATTATTTTTTAATATTTTTA
1 AATTTTAAATAATAATAAAATTATTTTCAAATATTTTTA
*
128711857 AATTTTGAAATAATATATAATATTATTTTCAAATATTT
1 AATTTT-AAATAATA-ATAAAATTATTTTCAAATATTT
128711895 AATATTTTAT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
39 6 0.19
40 7 0.22
41 19 0.59
ACGTcount: A:0.44, C:0.01, G:0.01, T:0.53
Consensus pattern (39 bp):
AATTTTAAATAATAATAAAATTATTTTCAAATATTTTTA
Found at i:128711902 original size:40 final size:39
Alignment explanation
Indices: 128711818--128711903 Score: 95
Period size: 40 Copynumber: 2.2 Consensus size: 39
128711808 TCACTTACAT
* * *
128711818 AATTTTAATTAATAATAAAATTATTTTTTAATATTTTTA
1 AATTTTAAATAATAATAAAATTATTTTTCAATATATTTA
*
128711857 AATTTTGAAATAATATATAATATTA-TTTTCAA-ATATTTA
1 AATTTT-AAATAATA-ATAAAATTATTTTTCAATATATTTA
128711896 ATATTTTA
1 A-ATTTTA
128711904 TAAAATTAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
39 14 0.35
40 18 0.45
41 8 0.20
ACGTcount: A:0.44, C:0.01, G:0.01, T:0.53
Consensus pattern (39 bp):
AATTTTAAATAATAATAAAATTATTTTTCAATATATTTA
Found at i:128711918 original size:15 final size:16
Alignment explanation
Indices: 128711893--128711930 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 16
128711883 TTTCAAATAT
128711893 TTAATATTTT-ATAAAA
1 TTAATATTTTAAT-AAA
128711909 TTAA-ATTTTAATAAA
1 TTAATATTTTAATAAA
128711924 TTAATAT
1 TTAATAT
128711931 GATGTTTTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
15 12 0.60
16 8 0.40
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
TTAATATTTTAATAAA
Found at i:128738197 original size:26 final size:26
Alignment explanation
Indices: 128738167--128738219 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
128738157 AGAGTTTAAA
128738167 AGCTATGCATGCAACAGAAAGAAGAC
1 AGCTATGCATGCAACAGAAAGAAGAC
128738193 AGCTATGCATGCAACAGAAAGAAGAC
1 AGCTATGCATGCAACAGAAAGAAGAC
128738219 A
1 A
128738220 AAAAAGCTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.47, C:0.19, G:0.23, T:0.11
Consensus pattern (26 bp):
AGCTATGCATGCAACAGAAAGAAGAC
Found at i:128746801 original size:13 final size:13
Alignment explanation
Indices: 128746783--128746809 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
128746773 ACTGATTAAA
128746783 GGAAATTTACCGT
1 GGAAATTTACCGT
128746796 GGAAATTTACCGT
1 GGAAATTTACCGT
128746809 G
1 G
128746810 AACCAGAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.26, T:0.30
Consensus pattern (13 bp):
GGAAATTTACCGT
Found at i:128751136 original size:3 final size:3
Alignment explanation
Indices: 128751128--128751152 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
128751118 TGAATAGTCA
128751128 CAG CAG CAG CAG CAG CAG CAG CAG C
1 CAG CAG CAG CAG CAG CAG CAG CAG C
128751153 TTCTCCATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.36, G:0.32, T:0.00
Consensus pattern (3 bp):
CAG
Found at i:128753501 original size:17 final size:17
Alignment explanation
Indices: 128753479--128753514 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
128753469 GGATTTAAAT
*
128753479 TAATTTAAATATTTGTA
1 TAATTTAAATATTTATA
*
128753496 TAATTTATATATTTATA
1 TAATTTAAATATTTATA
128753513 TA
1 TA
128753515 TTTGTATTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.56
Consensus pattern (17 bp):
TAATTTAAATATTTATA
Found at i:128755469 original size:4 final size:4
Alignment explanation
Indices: 128755452--128755492 Score: 73
Period size: 4 Copynumber: 10.2 Consensus size: 4
128755442 GTTAGAATGA
*
128755452 ACAT ACAT ATAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT A
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT A
128755493 TACATATGTG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
4 35 1.00
ACGTcount: A:0.51, C:0.22, G:0.00, T:0.27
Consensus pattern (4 bp):
ACAT
Found at i:128759109 original size:20 final size:20
Alignment explanation
Indices: 128759081--128759118 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
128759071 TGCTTTGGGT
128759081 GAGAA-TTTTGCTGGCATGTG
1 GAGAATTTTTG-TGGCATGTG
*
128759101 GAGAGTTTTTGTGGCATG
1 GAGAATTTTTGTGGCATG
128759119 AATCTTGGGC
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 11 0.69
21 5 0.31
ACGTcount: A:0.18, C:0.08, G:0.37, T:0.37
Consensus pattern (20 bp):
GAGAATTTTTGTGGCATGTG
Found at i:128767429 original size:20 final size:22
Alignment explanation
Indices: 128767376--128767440 Score: 75
Period size: 22 Copynumber: 3.0 Consensus size: 22
128767366 ATAATAATAT
128767376 TAATTAAA-TCGAATTCAATTAA
1 TAATTAAATTC-AATTCAATTAA
*
128767398 TAATTTAATTC-ATT-AATTAA
1 TAATTAAATTCAATTCAATTAA
128767418 T-ATTAAATTTCAATTCAATTAA
1 TAATTAAA-TTCAATTCAATTAA
128767440 T
1 T
128767441 TCAGTTCGGA
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
19 5 0.14
20 10 0.27
21 6 0.16
22 14 0.38
23 2 0.05
ACGTcount: A:0.46, C:0.08, G:0.02, T:0.45
Consensus pattern (22 bp):
TAATTAAATTCAATTCAATTAA
Found at i:128776900 original size:35 final size:34
Alignment explanation
Indices: 128776835--128776901 Score: 80
Period size: 35 Copynumber: 1.9 Consensus size: 34
128776825 CATGATAGTG
* **
128776835 AAATAATAATAGTAATAATGTTAATAAAGATACA
1 AAATAATAATAGTAAAAATGCCAATAAAGATACA
* *
128776869 AAATGATAATAAGTAAAAATGCCAATGAAGATA
1 AAATAATAAT-AGTAAAAATGCCAATAAAGATA
128776902 ATAAAAAAAA
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
34 9 0.33
35 18 0.67
ACGTcount: A:0.58, C:0.04, G:0.12, T:0.25
Consensus pattern (34 bp):
AAATAATAATAGTAAAAATGCCAATAAAGATACA
Found at i:128776985 original size:12 final size:12
Alignment explanation
Indices: 128776941--128776988 Score: 51
Period size: 12 Copynumber: 3.8 Consensus size: 12
128776931 TGTTCATGCG
*
128776941 TAAATATAAAGA
1 TAAATATAAACA
**
128776953 TAGGTATAATACA
1 TAAATATAA-ACA
128776966 TAAAATATAAACA
1 T-AAATATAAACA
128776979 TAAATATAAA
1 TAAATATAAA
128776989 GAGAGAAATA
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
12 16 0.55
13 7 0.24
14 6 0.21
ACGTcount: A:0.62, C:0.04, G:0.06, T:0.27
Consensus pattern (12 bp):
TAAATATAAACA
Found at i:128777567 original size:13 final size:13
Alignment explanation
Indices: 128777551--128777593 Score: 61
Period size: 14 Copynumber: 3.3 Consensus size: 13
128777541 AGATATATTC
*
128777551 AAAAATAGAAAA-
1 AAAAAAAGAAAAG
128777563 AAAAAAAGAAGAAG
1 AAAAAAAGAA-AAG
128777577 AAAAAAAGAAAAG
1 AAAAAAAGAAAAG
128777590 AAAA
1 AAAA
128777594 CCTTAGCCCG
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
12 9 0.32
13 9 0.32
14 10 0.36
ACGTcount: A:0.84, C:0.00, G:0.14, T:0.02
Consensus pattern (13 bp):
AAAAAAAGAAAAG
Found at i:128777568 original size:14 final size:14
Alignment explanation
Indices: 128777551--128777593 Score: 50
Period size: 16 Copynumber: 2.9 Consensus size: 14
128777541 AGATATATTC
*
128777551 AAAAATAGAAAAAA
1 AAAAAAAGAAAAAA
128777565 AAAAAGAAGAAGAAAA
1 AAAAA-AAGAA-AAAA
128777581 AAAGAAAAGAAAA
1 AAA-AAAAGAAAA
128777594 CCTTAGCCCG
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
14 5 0.20
15 6 0.24
16 12 0.48
17 2 0.08
ACGTcount: A:0.84, C:0.00, G:0.14, T:0.02
Consensus pattern (14 bp):
AAAAAAAGAAAAAA
Found at i:128777931 original size:12 final size:12
Alignment explanation
Indices: 128777914--128777938 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
128777904 TTGGGTTAGT
128777914 GTTTTGGGCTAA
1 GTTTTGGGCTAA
128777926 GTTTTGGGCTAA
1 GTTTTGGGCTAA
128777938 G
1 G
128777939 GGTTTTGGGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.08, G:0.36, T:0.40
Consensus pattern (12 bp):
GTTTTGGGCTAA
Found at i:128778475 original size:42 final size:44
Alignment explanation
Indices: 128778368--128778487 Score: 138
Period size: 42 Copynumber: 2.8 Consensus size: 44
128778358 TATTTGATTT
* * *
128778368 TCAACCTGTTACCCTACTGCTTAGGGGGTTAAGGCTTGTCATCA
1 TCAACCTGTTACCCTACTGCTTAGGGGTTTAAGGCTTGTAAACA
** * * *
128778412 TTGATCTGTTTCCCTACTGCTTAGGGGTTT-A-GATCTGTAAAC-
1 TCAACCTGTTACCCTACTGCTTAGGGGTTTAAGGCT-TGTAAACA
128778454 TCAACCTGTTACCCTACTGCTTAGGGGTTTAAGG
1 TCAACCTGTTACCCTACTGCTTAGGGGTTTAAGG
128778488 TTTGAAAATT
Statistics
Matches: 61, Mismatches: 12, Indels: 6
0.77 0.15 0.08
Matches are distributed among these distances:
42 28 0.46
43 7 0.11
44 26 0.43
ACGTcount: A:0.20, C:0.23, G:0.23, T:0.35
Consensus pattern (44 bp):
TCAACCTGTTACCCTACTGCTTAGGGGTTTAAGGCTTGTAAACA
Found at i:128778539 original size:86 final size:86
Alignment explanation
Indices: 128778367--128778579 Score: 223
Period size: 86 Copynumber: 2.5 Consensus size: 86
128778357 ATATTTGATT
** * *
128778367 TTCAACCTGTTACCCTACTGCTTAGGGGGTTAAGGCTTGTCATCATTGATCTGTTTCCCTACTGC
1 TTCAACCTGTTACCCTACTGCTTAGGGGGTTAAGGCTTGAAAT-ATTGATCTGTTACCCTACTAC
** * *
128778432 TTAGGGGTTTAGATCTGTAAAC
65 TTAGGGAATAAGATCTATAAAC
* * * * *
128778454 -TCAACCTGTTACCCTACTGCTTAGGGGTTTAAGGTTTGAAA-ATTTGGTTTGTTACCCTATTAC
1 TTCAACCTGTTACCCTACTGCTTAGGGGGTTAAGGCTTGAAATA-TTGATCTGTTACCCTACTAC
*
128778517 TTAGGGCAATAATATCTATAAAC
65 TTAGGG-AATAAGATCTATAAAC
* * * *
128778540 TTCAGCTTGTTATCCTACTGCTTAGGGGGTTAAAGCTTGA
1 TTCAACCTGTTACCCTACTGCTTAGGGGGTTAAGGCTTGA
128778580 TGGTTTGAAT
Statistics
Matches: 103, Mismatches: 20, Indels: 6
0.80 0.16 0.05
Matches are distributed among these distances:
84 1 0.01
85 21 0.20
86 48 0.47
87 33 0.32
ACGTcount: A:0.23, C:0.19, G:0.21, T:0.37
Consensus pattern (86 bp):
TTCAACCTGTTACCCTACTGCTTAGGGGGTTAAGGCTTGAAATATTGATCTGTTACCCTACTACT
TAGGGAATAAGATCTATAAAC
Found at i:128784081 original size:13 final size:13
Alignment explanation
Indices: 128784063--128784091 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
128784053 GAAAATTGAA
128784063 GTTATCGACCTTG
1 GTTATCGACCTTG
128784076 GTTATCGACCTTG
1 GTTATCGACCTTG
128784089 GTT
1 GTT
128784092 GGCTTACGGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.14, C:0.21, G:0.24, T:0.41
Consensus pattern (13 bp):
GTTATCGACCTTG
Found at i:128791508 original size:43 final size:43
Alignment explanation
Indices: 128791451--128791600 Score: 140
Period size: 43 Copynumber: 3.5 Consensus size: 43
128791441 GATATTATTG
* * * * *
128791451 CCCTAAGTAATAGGGTAACAAACCAAATTTTCAAACCTTAAAC
1 CCCTAAGCAGTAGGGTAACAGATCAAATTTACAAACCTTAAAC
* ** * * *
128791494 CCCTAAGCAGTAGGGTAACAGGTTGAGTTTACAGATC-TAAAC
1 CCCTAAGCAGTAGGGTAACAGATCAAATTTACAAACCTTAAAC
* * * * *
128791536 CCCTAAGCAGTAGGGAAACAGATCAATAATGACAAGCCTTAACC
1 CCCTAAGCAGTAGGGTAACAGATCAA-ATTTACAAACCTTAAAC
128791580 CCCTAAGCAGTAGGGTAACAG
1 CCCTAAGCAGTAGGGTAACAG
128791601 GTTGAAAATC
Statistics
Matches: 82, Mismatches: 23, Indels: 3
0.76 0.21 0.03
Matches are distributed among these distances:
42 27 0.33
43 31 0.38
44 24 0.29
ACGTcount: A:0.39, C:0.23, G:0.19, T:0.20
Consensus pattern (43 bp):
CCCTAAGCAGTAGGGTAACAGATCAAATTTACAAACCTTAAAC
Found at i:128792951 original size:3 final size:3
Alignment explanation
Indices: 128792820--128792942 Score: 52
Period size: 3 Copynumber: 39.3 Consensus size: 3
128792810 TTATTTGCGC
* * * * *
128792820 TAT TAT TAG TAT TTT TCAT GTAT ATAT TA- TAT TGT TGT TAT TAT TAC
1 TAT TAT TAT TAT TAT T-AT -TAT -TAT TAT TAT TAT TAT TAT TAT TAT
* * * * *
128792867 TAT TAT TAAA TAT TCT TAT TAT TAC TAT TAT TTT TAT TCCT T-T TAT
1 TAT TAT T-AT TAT TAT TAT TAT TAT TAT TAT TAT TAT T-AT TAT TAT
* * *
128792913 TAT TGTT TAT TAT CAA TATT TAT TAT TAT T
1 TAT T-AT TAT TAT TAT TA-T TAT TAT TAT T
128792943 GCTATTATTG
Statistics
Matches: 88, Mismatches: 24, Indels: 16
0.69 0.19 0.12
Matches are distributed among these distances:
2 4 0.05
3 69 0.78
4 14 0.16
5 1 0.01
ACGTcount: A:0.28, C:0.06, G:0.04, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:128793015 original size:12 final size:12
Alignment explanation
Indices: 128793000--128793047 Score: 51
Period size: 12 Copynumber: 3.8 Consensus size: 12
128792990 TATTTCTCTC
128793000 TTTATATTTATG
1 TTTATATTTATG
128793012 TTTATATTTTATG
1 TTTATA-TTTATG
** *
128793025 TATTATACCTATC
1 T-TTATATTTATG
128793038 TTTATATTTA
1 TTTATATTTA
128793048 CGCATGAACA
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
12 13 0.45
13 11 0.38
14 5 0.17
ACGTcount: A:0.27, C:0.06, G:0.04, T:0.62
Consensus pattern (12 bp):
TTTATATTTATG
Found at i:128793239 original size:21 final size:21
Alignment explanation
Indices: 128793215--128793255 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
128793205 TAACGTGCTA
* *
128793215 TTATTACTATTATTTTTATTT
1 TTATTACCATTATTGTTATTT
128793236 TTATTACCATTATTGTTATT
1 TTATTACCATTATTGTTATT
128793256 GTAATTATAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.24, C:0.07, G:0.02, T:0.66
Consensus pattern (21 bp):
TTATTACCATTATTGTTATTT
Found at i:128793262 original size:21 final size:21
Alignment explanation
Indices: 128793217--128793262 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
128793207 ACGTGCTATT
* * * *
128793217 ATTACTATTATTTTTATTTTT
1 ATTACCATTATTGTTATTGTA
128793238 ATTACCATTATTGTTATTGTA
1 ATTACCATTATTGTTATTGTA
128793259 ATTA
1 ATTA
128793263 TATCTATATG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.28, C:0.07, G:0.04, T:0.61
Consensus pattern (21 bp):
ATTACCATTATTGTTATTGTA
Found at i:128794199 original size:13 final size:13
Alignment explanation
Indices: 128794183--128794242 Score: 59
Period size: 13 Copynumber: 4.7 Consensus size: 13
128794173 ACCACCCTTT
128794183 TTGGCCACCCACC
1 TTGGCCACCCACC
*
128794196 TTGGCCACCTA-C
1 TTGGCCACCCACC
** ***
128794208 TCCGCCACCCTTG
1 TTGGCCACCCACC
128794221 TTGGCCACCCACC
1 TTGGCCACCCACC
128794234 TTGGCCACC
1 TTGGCCACC
128794243 TACACCACTA
Statistics
Matches: 35, Mismatches: 11, Indels: 2
0.73 0.23 0.04
Matches are distributed among these distances:
12 8 0.23
13 27 0.77
ACGTcount: A:0.13, C:0.50, G:0.17, T:0.20
Consensus pattern (13 bp):
TTGGCCACCCACC
Found at i:128794216 original size:38 final size:38
Alignment explanation
Indices: 128794162--128794250 Score: 151
Period size: 38 Copynumber: 2.3 Consensus size: 38
128794152 AACCCTAATC
*
128794162 CCACCTACTCCACCACCCTTTTTGGCCACCCACCTTGG
1 CCACCTACTCCACCACCCTTGTTGGCCACCCACCTTGG
*
128794200 CCACCTACTCCGCCACCCTTGTTGGCCACCCACCTTGG
1 CCACCTACTCCACCACCCTTGTTGGCCACCCACCTTGG
*
128794238 CCACCTACACCAC
1 CCACCTACTCCAC
128794251 TATGCCACCA
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
38 47 1.00
ACGTcount: A:0.17, C:0.52, G:0.11, T:0.20
Consensus pattern (38 bp):
CCACCTACTCCACCACCCTTGTTGGCCACCCACCTTGG
Found at i:128794420 original size:17 final size:16
Alignment explanation
Indices: 128794393--128794426 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
128794383 GGCTAAGGTT
128794393 TTCTTTTCTTTTCTTC
1 TTCTTTTCTTTTCTTC
*
128794409 TTCTTCTTCTTTTTTTC
1 TTCTT-TTCTTTTCTTC
128794426 T
1 T
128794427 ATTTTTGAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (16 bp):
TTCTTTTCTTTTCTTC
Found at i:128794486 original size:12 final size:12
Alignment explanation
Indices: 128794466--128794499 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
128794456 ATATTAGAAT
*
128794466 ATATCAAAAAAA
1 ATATAAAAAAAA
*
128794478 ATTTAAAAAAAA
1 ATATAAAAAAAA
128794490 ATATAAAAAA
1 ATATAAAAAA
128794500 GCGTACCTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.76, C:0.03, G:0.00, T:0.21
Consensus pattern (12 bp):
ATATAAAAAAAA
Found at i:128794852 original size:12 final size:12
Alignment explanation
Indices: 128794835--128794859 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
128794825 TTGGGTTAGT
128794835 GTTTTGGGCTAA
1 GTTTTGGGCTAA
128794847 GTTTTGGGCTAA
1 GTTTTGGGCTAA
128794859 G
1 G
128794860 GGTTTTGGGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.08, G:0.36, T:0.40
Consensus pattern (12 bp):
GTTTTGGGCTAA
Found at i:128804965 original size:12 final size:12
Alignment explanation
Indices: 128804925--128804957 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
128804915 TCAATTTCTT
*
128804925 TCTTTTT-AATC
1 TCTTTTTCAATA
128804936 TCTTTTTCAATA
1 TCTTTTTCAATA
128804948 TCTTTTTCAA
1 TCTTTTTCAA
128804958 CTTCTTTTCA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
11 7 0.35
12 13 0.65
ACGTcount: A:0.21, C:0.18, G:0.00, T:0.61
Consensus pattern (12 bp):
TCTTTTTCAATA
Found at i:128805025 original size:18 final size:18
Alignment explanation
Indices: 128804979--128805031 Score: 52
Period size: 18 Copynumber: 2.9 Consensus size: 18
128804969 TCTCAAATTT
* *
128804979 ATTTTCGTTCTCTTTTTC
1 ATTTTCATTTTCTTTTTC
* *
128804997 AATCTCATTTTCTTTTTC
1 ATTTTCATTTTCTTTTTC
*
128805015 ATTTTCTTTTTGCTTTT
1 ATTTTCATTTT-CTTTT
128805032 CAAAGGCTTT
Statistics
Matches: 27, Mismatches: 7, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
18 22 0.81
19 5 0.19
ACGTcount: A:0.09, C:0.19, G:0.04, T:0.68
Consensus pattern (18 bp):
ATTTTCATTTTCTTTTTC
Found at i:128805032 original size:12 final size:12
Alignment explanation
Indices: 128805001--128805025 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
128804991 TTTTTCAATC
128805001 TCATTTTCTTTT
1 TCATTTTCTTTT
128805013 TCATTTTCTTTT
1 TCATTTTCTTTT
128805025 T
1 T
128805026 GCTTTTCAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.08, C:0.16, G:0.00, T:0.76
Consensus pattern (12 bp):
TCATTTTCTTTT
Found at i:128811705 original size:22 final size:22
Alignment explanation
Indices: 128811680--128811721 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
128811670 AGATAATTAC
* *
128811680 AATAACAATAATGGTAATAAAA
1 AATAAAAATAATAGTAATAAAA
128811702 AATAAAAATAATAGTAATAA
1 AATAAAAATAATAGTAATAA
128811722 TAGCACGTTA
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:0.67, C:0.02, G:0.07, T:0.24
Consensus pattern (22 bp):
AATAAAAATAATAGTAATAAAA
Found at i:128811847 original size:35 final size:34
Alignment explanation
Indices: 128811782--128811848 Score: 80
Period size: 35 Copynumber: 1.9 Consensus size: 34
128811772 CATGATAGTG
* **
128811782 AAATAATAATAGTAATAATGTTAATAAAGATACA
1 AAATAATAATAGTAAAAATGCCAATAAAGATACA
* *
128811816 AAATGATAATAAGTAAAAATGCCAATGAAGATA
1 AAATAATAAT-AGTAAAAATGCCAATAAAGATA
128811849 ATAAAAAAAA
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
34 9 0.33
35 18 0.67
ACGTcount: A:0.58, C:0.04, G:0.12, T:0.25
Consensus pattern (34 bp):
AAATAATAATAGTAAAAATGCCAATAAAGATACA
Found at i:128811933 original size:12 final size:12
Alignment explanation
Indices: 128811889--128811936 Score: 51
Period size: 12 Copynumber: 3.8 Consensus size: 12
128811879 TGTTCATGCG
*
128811889 TAAATATAAAGA
1 TAAATATAAACA
**
128811901 TAGGTATAATACA
1 TAAATATAA-ACA
128811914 TAAAATATAAACA
1 T-AAATATAAACA
128811927 TAAATATAAA
1 TAAATATAAA
128811937 GGAGAAATAA
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
12 16 0.55
13 7 0.24
14 6 0.21
ACGTcount: A:0.62, C:0.04, G:0.06, T:0.27
Consensus pattern (12 bp):
TAAATATAAACA
Found at i:128813865 original size:42 final size:44
Alignment explanation
Indices: 128813811--128813930 Score: 138
Period size: 44 Copynumber: 2.8 Consensus size: 44
128813801 AATTTTCAAA
* *
128813811 CCTTAAACCCCTAAGCAGTAGGGTAACAGGTTGA-GTTTAC-AG
1 CCTTAAACCCCTAAGCAGTAGGGTAACAGGTTGATGATGACAAG
* * * **
128813853 -ATCTAAACCCCTAAGCAGTAGGGAAACAGATCAATGATGACAAG
1 CCT-TAAACCCCTAAGCAGTAGGGTAACAGGTTGATGATGACAAG
*
128813897 CCTTAACCCCCTAAGCAGTAGGGTAACAGGTTGA
1 CCTTAAACCCCTAAGCAGTAGGGTAACAGGTTGA
128813931 AAATCAAATA
Statistics
Matches: 61, Mismatches: 13, Indels: 6
0.76 0.16 0.08
Matches are distributed among these distances:
41 1 0.02
42 27 0.44
43 4 0.07
44 28 0.46
45 1 0.02
ACGTcount: A:0.35, C:0.23, G:0.23, T:0.20
Consensus pattern (44 bp):
CCTTAAACCCCTAAGCAGTAGGGTAACAGGTTGATGATGACAAG
Found at i:128814465 original size:13 final size:13
Alignment explanation
Indices: 128814449--128814508 Score: 50
Period size: 13 Copynumber: 4.7 Consensus size: 13
128814439 ACCACCCTTG
128814449 TTGGCCACCCACC
1 TTGGCCACCCACC
*
128814462 TTGGCCACCTA-C
1 TTGGCCACCCACC
*** ***
128814474 TCCACCACCCTTG
1 TTGGCCACCCACC
128814487 TTGGCCACCCACC
1 TTGGCCACCCACC
128814500 TTGGCCACC
1 TTGGCCACC
128814509 TACACCACTA
Statistics
Matches: 33, Mismatches: 13, Indels: 2
0.69 0.27 0.04
Matches are distributed among these distances:
12 7 0.21
13 26 0.79
ACGTcount: A:0.15, C:0.50, G:0.15, T:0.20
Consensus pattern (13 bp):
TTGGCCACCCACC
Found at i:128814479 original size:38 final size:38
Alignment explanation
Indices: 128814428--128814516 Score: 169
Period size: 38 Copynumber: 2.3 Consensus size: 38
128814418 AACCCTAATC
128814428 CCACCTACTCCACCACCCTTGTTGGCCACCCACCTTGG
1 CCACCTACTCCACCACCCTTGTTGGCCACCCACCTTGG
128814466 CCACCTACTCCACCACCCTTGTTGGCCACCCACCTTGG
1 CCACCTACTCCACCACCCTTGTTGGCCACCCACCTTGG
*
128814504 CCACCTACACCAC
1 CCACCTACTCCAC
128814517 TATGCCACCA
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
38 50 1.00
ACGTcount: A:0.18, C:0.52, G:0.11, T:0.19
Consensus pattern (38 bp):
CCACCTACTCCACCACCCTTGTTGGCCACCCACCTTGG
Found at i:128815175 original size:3 final size:3
Alignment explanation
Indices: 128815169--128815291 Score: 52
Period size: 3 Copynumber: 39.3 Consensus size: 3
128815159 TTATTTGCGC
* * * * *
128815169 TAT TAT TAG TAT TTT TCAT GTAT ATAT TA- TAT TGT TGT TAT TAT TAC
1 TAT TAT TAT TAT TAT T-AT -TAT -TAT TAT TAT TAT TAT TAT TAT TAT
* * * * *
128815216 TAT TAT TAAA TAT TCT TAT TAT TAC TAT TAT TTT TAT TCCT T-T TAT
1 TAT TAT T-AT TAT TAT TAT TAT TAT TAT TAT TAT TAT T-AT TAT TAT
* * *
128815262 TAT TGTT TAT TAT CAA TATT TAT TAT TAT T
1 TAT T-AT TAT TAT TAT TA-T TAT TAT TAT T
128815292 GCTCTTATTG
Statistics
Matches: 88, Mismatches: 24, Indels: 16
0.69 0.19 0.12
Matches are distributed among these distances:
2 4 0.05
3 69 0.78
4 14 0.16
5 1 0.01
ACGTcount: A:0.28, C:0.06, G:0.04, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:128815364 original size:12 final size:12
Alignment explanation
Indices: 128815349--128815396 Score: 51
Period size: 12 Copynumber: 3.8 Consensus size: 12
128815339 TATTTCTCTC
128815349 TTTATATTTATG
1 TTTATATTTATG
128815361 TTTATATTTTATG
1 TTTATA-TTTATG
** *
128815374 TATTATACCTATC
1 T-TTATATTTATG
128815387 TTTATATTTA
1 TTTATATTTA
128815397 CGCATGAACA
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
12 13 0.45
13 11 0.38
14 5 0.17
ACGTcount: A:0.27, C:0.06, G:0.04, T:0.62
Consensus pattern (12 bp):
TTTATATTTATG
Found at i:128815589 original size:21 final size:21
Alignment explanation
Indices: 128815565--128815605 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
128815555 TAACGTGCTA
* *
128815565 TTATTACTATTATTTTTATTT
1 TTATTACCATTATTGTTATTT
128815586 TTATTACCATTATTGTTATT
1 TTATTACCATTATTGTTATT
128815606 GTAATTATAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.24, C:0.07, G:0.02, T:0.66
Consensus pattern (21 bp):
TTATTACCATTATTGTTATTT
Found at i:128815612 original size:21 final size:21
Alignment explanation
Indices: 128815567--128815612 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
128815557 ACGTGCTATT
* * * *
128815567 ATTACTATTATTTTTATTTTT
1 ATTACCATTATTGTTATTGTA
128815588 ATTACCATTATTGTTATTGTA
1 ATTACCATTATTGTTATTGTA
128815609 ATTA
1 ATTA
128815613 TATCTATATG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.28, C:0.07, G:0.04, T:0.61
Consensus pattern (21 bp):
ATTACCATTATTGTTATTGTA
Found at i:128816565 original size:38 final size:38
Alignment explanation
Indices: 128816514--128816602 Score: 142
Period size: 38 Copynumber: 2.3 Consensus size: 38
128816504 AACCCTAATC
*
128816514 CCACCTACTCCACCACCCTTGTTGGCCACCCACCTTTG
1 CCACCTACTCCACCACCCTTGTTGGCCACCCACCTTGG
*
128816552 CCACCTACTCCACCACCTTTGTTGGCCACCCACCTTGG
1 CCACCTACTCCACCACCCTTGTTGGCCACCCACCTTGG
* *
128816590 CCACTTACACCAC
1 CCACCTACTCCAC
128816603 TATGCCACCA
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
38 47 1.00
ACGTcount: A:0.18, C:0.49, G:0.10, T:0.22
Consensus pattern (38 bp):
CCACCTACTCCACCACCCTTGTTGGCCACCCACCTTGG
Found at i:128835675 original size:15 final size:15
Alignment explanation
Indices: 128835655--128835684 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
128835645 GTTAGAAGAT
128835655 TTAAATTAAAATCTG
1 TTAAATTAAAATCTG
128835670 TTAAATTAAAATCTG
1 TTAAATTAAAATCTG
128835685 ACTTACCCGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.47, C:0.07, G:0.07, T:0.40
Consensus pattern (15 bp):
TTAAATTAAAATCTG
Found at i:128836715 original size:22 final size:22
Alignment explanation
Indices: 128836672--128836715 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
128836662 TTTAAGAAAA
128836672 CTATACTGAATAATTAAAATAT
1 CTATACTGAATAATTAAAATAT
128836694 CTATACTGAATAATTAAAATAT
1 CTATACTGAATAATTAAAATAT
128836716 TACATTGTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.50, C:0.09, G:0.05, T:0.36
Consensus pattern (22 bp):
CTATACTGAATAATTAAAATAT
Found at i:128840220 original size:19 final size:19
Alignment explanation
Indices: 128840197--128840245 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
128840187 AAAATTTGTA
128840197 AAAAATTAGAAAAAA-ATT
1 AAAAATTAGAAAAAATATT
*
128840215 ATAAAAATA-AAAAAATATT
1 A-AAAATTAGAAAAAATATT
*
128840234 AAATATTAGAAA
1 AAAAATTAGAAA
128840246 TATTAAAATT
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
18 12 0.48
19 13 0.52
ACGTcount: A:0.71, C:0.00, G:0.04, T:0.24
Consensus pattern (19 bp):
AAAAATTAGAAAAAATATT
Found at i:128840262 original size:21 final size:20
Alignment explanation
Indices: 128840236--128840275 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
128840226 AAAATATTAA
128840236 ATATTAGAAATATTAAAATTG
1 ATATTA-AAATATTAAAATTG
**
128840257 ATATTAACTTATTAAAATT
1 ATATTAAAATATTAAAATT
128840276 ATAAAATATA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.50, C:0.03, G:0.05, T:0.42
Consensus pattern (20 bp):
ATATTAAAATATTAAAATTG
Found at i:128840274 original size:28 final size:28
Alignment explanation
Indices: 128840229--128840282 Score: 67
Period size: 28 Copynumber: 1.9 Consensus size: 28
128840219 AAATAAAAAA
128840229 ATATTAAATATTAGAAA-TATTAAAATTG
1 ATATTAAATATTAGAAATTA-TAAAATTG
*
128840257 ATATTAACTTATTA-AAATTATAAAAT
1 ATATTAA-ATATTAGAAATTATAAAAT
128840283 ATAAAAAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
28 16 0.70
29 7 0.30
ACGTcount: A:0.54, C:0.02, G:0.04, T:0.41
Consensus pattern (28 bp):
ATATTAAATATTAGAAATTATAAAATTG
Found at i:128840292 original size:17 final size:17
Alignment explanation
Indices: 128840270--128840328 Score: 64
Period size: 19 Copynumber: 3.2 Consensus size: 17
128840260 TTAACTTATT
128840270 AAAATTATAAAATATAA
1 AAAATTATAAAATATAA
128840287 AAAATTATAAATATTATAA
1 AAAATTATAAA-A-TATAA
* *
128840306 TAAATCTAATAAATTATAA
1 AAAAT-T-ATAAAATATAA
128840325 AAAA
1 AAAA
128840329 AAATTATGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
17 11 0.31
18 1 0.03
19 17 0.49
20 1 0.03
21 5 0.14
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (17 bp):
AAAATTATAAAATATAA
Found at i:128840466 original size:30 final size:30
Alignment explanation
Indices: 128840393--128840467 Score: 73
Period size: 30 Copynumber: 2.5 Consensus size: 30
128840383 TAGAGTTCTT
*
128840393 AAAATAATACAAA-TTGTAAAAGAATATTA
1 AAAATAATACAAACTTATAAAAGAATATTA
* * * *
128840422 AAATTGATATAAACTTATAAAA-ATTATTTA
1 AAAATAATACAAACTTATAAAAGAATA-TTA
*
128840452 AAAATCATACAAACTT
1 AAAATAATACAAACTT
128840468 GAACTGGACT
Statistics
Matches: 36, Mismatches: 8, Indels: 3
0.77 0.17 0.06
Matches are distributed among these distances:
29 13 0.36
30 23 0.64
ACGTcount: A:0.57, C:0.07, G:0.04, T:0.32
Consensus pattern (30 bp):
AAAATAATACAAACTTATAAAAGAATATTA
Found at i:128840979 original size:21 final size:21
Alignment explanation
Indices: 128840951--128840996 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
128840941 TTTTGATGAC
128840951 TTTTATACAATTTT-AATAAG
1 TTTTATACAATTTTAAATAAG
* *
128840971 TTTTAATACCATTTTAAATATG
1 TTTT-ATACAATTTTAAATAAG
128840993 TTTT
1 TTTT
128840997 TTCATCTAGA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 4 0.18
21 9 0.41
22 9 0.41
ACGTcount: A:0.35, C:0.07, G:0.04, T:0.54
Consensus pattern (21 bp):
TTTTATACAATTTTAAATAAG
Found at i:128844463 original size:17 final size:17
Alignment explanation
Indices: 128844441--128844476 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
128844431 GATTATACAT
128844441 GGATAGAGAAATAGAAG
1 GGATAGAGAAATAGAAG
128844458 GGATAGAGAAATAGAAG
1 GGATAGAGAAATAGAAG
128844475 GG
1 GG
128844477 TGAAAAGTAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.50, C:0.00, G:0.39, T:0.11
Consensus pattern (17 bp):
GGATAGAGAAATAGAAG
Found at i:128846886 original size:15 final size:15
Alignment explanation
Indices: 128846862--128846895 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
128846852 ATGATAATGG
*
128846862 TGTTTCTTTTTTTTT
1 TGTTTCTTTTTTTTA
*
128846877 TGTTTTTTTTTTTTA
1 TGTTTCTTTTTTTTA
128846892 TGTT
1 TGTT
128846896 CATTAGGGGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.03, C:0.03, G:0.09, T:0.85
Consensus pattern (15 bp):
TGTTTCTTTTTTTTA
Found at i:128857599 original size:18 final size:20
Alignment explanation
Indices: 128857566--128857609 Score: 65
Period size: 18 Copynumber: 2.3 Consensus size: 20
128857556 AAAAAAATCA
*
128857566 ATAAATTGATTTTAAAATTT
1 ATAAATTGATTTTAAAAATT
128857586 ATAAATT-A-TTTAAAAATT
1 ATAAATTGATTTTAAAAATT
128857604 ATAAAT
1 ATAAAT
128857610 AAAATTATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 15 0.65
19 1 0.04
20 7 0.30
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.45
Consensus pattern (20 bp):
ATAAATTGATTTTAAAAATT
Found at i:128857786 original size:21 final size:21
Alignment explanation
Indices: 128857751--128857806 Score: 60
Period size: 21 Copynumber: 2.6 Consensus size: 21
128857741 ATTTATAACT
* *
128857751 TTTTTAATAAATTTTGTATATAG
1 TTTTT-AT-AATTTTGTAAATAA
*
128857774 TTTTTATAATTTTTTAAATAA
1 TTTTTATAATTTTGTAAATAA
128857795 TTTTTA-AATTTT
1 TTTTTATAATTTT
128857807 AAAAGGGGTC
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
20 6 0.20
21 17 0.57
22 2 0.07
23 5 0.17
ACGTcount: A:0.34, C:0.00, G:0.04, T:0.62
Consensus pattern (21 bp):
TTTTTATAATTTTGTAAATAA
Found at i:128858741 original size:20 final size:20
Alignment explanation
Indices: 128858697--128858754 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 20
128858687 ACCTACATAA
* * *
128858697 AAAATAATAAAAATTATATT
1 AAAATAATAAAAATAACATG
128858717 AAAATAATAAAAATAACATG
1 AAAATAATAAAAATAACATG
*
128858737 CAAATAA-AAAATATAACA
1 AAAATAATAAAA-ATAACA
128858755 AAAACATATA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
19 4 0.12
20 29 0.88
ACGTcount: A:0.69, C:0.05, G:0.02, T:0.24
Consensus pattern (20 bp):
AAAATAATAAAAATAACATG
Found at i:128864632 original size:115 final size:116
Alignment explanation
Indices: 128864282--128864633 Score: 463
Period size: 117 Copynumber: 3.0 Consensus size: 116
128864272 TATAAATAAA
*
128864282 TATAACAACTTTTGCCTTTTAAAAAAAATTATTATTCGATTTTGGCCCTTCCCTCTTAAACTATA
1 TATAACAACTTTTGCCTTTT-AAAAAAATTATTATTCGATTTTGG-CCTTCCCTCTTAAACAATA
* * * * * * *
128864347 TTCTAGTTTTTTTTTTTGTCCTTGGACAGACTTATCTTTAGGTCATTTCAAAATTT
64 TTCTAG---CTTTATTCGTCCTTAGAAAGACTCATCTTTAGGTCATTTCAAAATCT
* * *
128864403 TATAATAATTTTTGCCTTTTAAAAAAATTATTATTCGATTTTGGCTCTCCCCTCTTAAACAATAT
1 TATAACAACTTTTGCCTTTTAAAAAAATTATTATTCGATTTTGGC-CTTCCCTCTTAAACAATAT
* * *
128864468 TCTAGCTTTGTTCGTCCTTAAAAAGACTCATCTTTAGGTCATTTTAAAATCT
65 TCTAGCTTTATTCGTCCTTAGAAAGACTCATCTTTAGGTCATTTCAAAATCT
** * *
128864520 TATAACAACTTTTAACTTTTAAAAAAGTTATTATTCGACTTTGGCCTTCCC-CTTAAACAATATT
1 TATAACAACTTTTGCCTTTTAAAAAAATTATTATTCGATTTTGGCCTTCCCTCTTAAACAATATT
* *
128864584 CTAGCTTTATTCATCATTAGAAAGACTCATCTTTAGGTCATTTCAAAATC
66 CTAGCTTTATTCGTCCTTAGAAAGACTCATCTTTAGGTCATTTCAAAATC
128864634 GGGGCTTCTA
Statistics
Matches: 205, Mismatches: 25, Indels: 8
0.86 0.11 0.03
Matches are distributed among these distances:
115 58 0.28
116 5 0.02
117 77 0.38
119 1 0.00
120 46 0.22
121 18 0.09
ACGTcount: A:0.30, C:0.18, G:0.09, T:0.43
Consensus pattern (116 bp):
TATAACAACTTTTGCCTTTTAAAAAAATTATTATTCGATTTTGGCCTTCCCTCTTAAACAATATT
CTAGCTTTATTCGTCCTTAGAAAGACTCATCTTTAGGTCATTTCAAAATCT
Found at i:128864986 original size:16 final size:18
Alignment explanation
Indices: 128864967--128865017 Score: 52
Period size: 19 Copynumber: 2.9 Consensus size: 18
128864957 TATGAAAAAT
128864967 ATTTTATCT-TTTTTT-A
1 ATTTTATCTATTTTTTGA
*
128864983 ATTTTATTTATTTTTTGA
1 ATTTTATCTATTTTTTGA
* *
128865001 ATTAATATTTATTTTTT
1 ATT-TTATCTATTTTTT
128865018 AATAAAAGAG
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
16 8 0.27
17 6 0.20
18 4 0.13
19 12 0.40
ACGTcount: A:0.24, C:0.02, G:0.02, T:0.73
Consensus pattern (18 bp):
ATTTTATCTATTTTTTGA
Found at i:128865709 original size:33 final size:33
Alignment explanation
Indices: 128865667--128865731 Score: 121
Period size: 33 Copynumber: 2.0 Consensus size: 33
128865657 GTTTTTGTAA
*
128865667 TAAGATTAATGGTTAGATCAATTAGGCCACCAG
1 TAAGATTAATGGTTAGATCAATTAGGCAACCAG
128865700 TAAGATTAATGGTTAGATCAATTAGGCAACCA
1 TAAGATTAATGGTTAGATCAATTAGGCAACCA
128865732 TTATCAATTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.38, C:0.14, G:0.20, T:0.28
Consensus pattern (33 bp):
TAAGATTAATGGTTAGATCAATTAGGCAACCAG
Found at i:128885068 original size:23 final size:23
Alignment explanation
Indices: 128885042--128885089 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
128885032 TCTTTTAATA
*
128885042 TTTATATTT-TTATTAATTTAAAT
1 TTTAT-TTTATTATTAAGTTAAAT
*
128885065 TTTATTTTATTTTTAAGTTAAAT
1 TTTATTTTATTATTAAGTTAAAT
128885088 TT
1 TT
128885090 GAAAAGAGTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 3 0.14
23 19 0.86
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (23 bp):
TTTATTTTATTATTAAGTTAAAT
Found at i:128890916 original size:3 final size:3
Alignment explanation
Indices: 128890908--128890940 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
128890898 TGGTGTCGTT
128890908 TTA TTA TTA -TA TTA TTA TT- TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
128890941 GAATATTAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
2 4 0.14
3 24 0.86
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (3 bp):
TTA
Found at i:128890924 original size:11 final size:11
Alignment explanation
Indices: 128890908--128890939 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
128890898 TGGTGTCGTT
128890908 TTATTATTATA
1 TTATTATTATA
*
128890919 TTATTATTTTA
1 TTATTATTATA
128890930 TTATTATTAT
1 TTATTATTAT
128890940 TGAATATTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (11 bp):
TTATTATTATA
Found at i:128890952 original size:25 final size:22
Alignment explanation
Indices: 128890908--128890957 Score: 64
Period size: 22 Copynumber: 2.1 Consensus size: 22
128890898 TGGTGTCGTT
*
128890908 TTATTATTATATTATTATTTTA
1 TTATTATTATAATATTATTTTA
128890930 TTATTATTATTGAATATTAATTTTA
1 TTATTATTA-T-AATATT-ATTTTA
128890955 TTA
1 TTA
128890958 CTAATTTAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
22 9 0.38
23 1 0.04
24 5 0.21
25 9 0.38
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (22 bp):
TTATTATTATAATATTATTTTA
Found at i:128891594 original size:42 final size:42
Alignment explanation
Indices: 128891547--128891637 Score: 148
Period size: 42 Copynumber: 2.2 Consensus size: 42
128891537 TTAAGCATAA
*
128891547 ATAATTTAAA-ATTTTTTATTCTATATTTAATTTCCATAAAAT
1 ATAATTTAAACA-TTTTTATTATATATTTAATTTCCATAAAAT
*
128891589 ATAATTTAAACATTTTTATTATATATTTAATTTTCATAAAAT
1 ATAATTTAAACATTTTTATTATATATTTAATTTCCATAAAAT
128891631 ATAATTT
1 ATAATTT
128891638 TCAATCCGGC
Statistics
Matches: 46, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
42 45 0.98
43 1 0.02
ACGTcount: A:0.42, C:0.05, G:0.00, T:0.53
Consensus pattern (42 bp):
ATAATTTAAACATTTTTATTATATATTTAATTTCCATAAAAT
Found at i:128909554 original size:13 final size:13
Alignment explanation
Indices: 128909536--128909563 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
128909526 ATATGTGTTA
128909536 ATATATTTATCAC
1 ATATATTTATCAC
128909549 ATATATTTATCAC
1 ATATATTTATCAC
128909562 AT
1 AT
128909564 TAAATTTTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.39, C:0.14, G:0.00, T:0.46
Consensus pattern (13 bp):
ATATATTTATCAC
Found at i:128909637 original size:21 final size:20
Alignment explanation
Indices: 128909613--128909664 Score: 50
Period size: 20 Copynumber: 2.5 Consensus size: 20
128909603 ATCTTTTATC
* * *
128909613 AAAATTAAATTTTAAATTTA
1 AAAAATAAATTTTAAAATGA
**
128909633 AAAAATAAAAATTAAAATGA
1 AAAAATAAATTTTAAAATGA
128909653 AAAAACTAAATT
1 AAAAA-TAAATT
128909665 CACTAATTAA
Statistics
Matches: 24, Mismatches: 7, Indels: 1
0.75 0.22 0.03
Matches are distributed among these distances:
20 20 0.83
21 4 0.17
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (20 bp):
AAAAATAAATTTTAAAATGA
Found at i:128910778 original size:31 final size:31
Alignment explanation
Indices: 128910743--128910808 Score: 80
Period size: 31 Copynumber: 2.1 Consensus size: 31
128910733 ATTATATCAA
* *
128910743 ACTTTTTT-ATCCAATTAGATACCTGAATTTG
1 ACTTTTTTGATCAAATT-GATACATGAATTTG
* *
128910774 ACTTTTTTGTTCAAATTGATGCATGAATTTG
1 ACTTTTTTGATCAAATTGATACATGAATTTG
128910805 ACTT
1 ACTT
128910809 CATAGTTCAA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
31 24 0.80
32 6 0.20
ACGTcount: A:0.27, C:0.14, G:0.12, T:0.47
Consensus pattern (31 bp):
ACTTTTTTGATCAAATTGATACATGAATTTG
Found at i:128911008 original size:61 final size:61
Alignment explanation
Indices: 128910835--128911023 Score: 168
Period size: 61 Copynumber: 3.1 Consensus size: 61
128910825 TAAAATAACT
* * * * * *
128910835 AAGTA-CTAATTTGGATAAAAAAAGCAAGTTTAAGTATCAATTTGAACC-AATAAGCCAAGTTT
1 AAGTACCTAATTT-GACAAAAAAA-AAACTTTAAGTACCAATTTGAACCTTA-AAGCCAAGTTC
* * * * * * * * ** *
128910897 AGGTATCTAATTAGAC-CAAAATAAATTTTAGGTACCAAATTGAAGGTTAAAGCCAAATTC
1 AAGTACCTAATTTGACAAAAAAAAAACTTTAAGTACCAATTTGAACCTTAAAGCCAAGTTC
*
128910957 AAGTACCTAATTTGACAAAAAAAAAACTTTAAGTACCAATTTGAACCTTAAAGCCAAGTCC
1 AAGTACCTAATTTGACAAAAAAAAAACTTTAAGTACCAATTTGAACCTTAAAGCCAAGTTC
128911018 AAGTAC
1 AAGTAC
128911024 TGAAATGTAT
Statistics
Matches: 97, Mismatches: 27, Indels: 7
0.74 0.21 0.05
Matches are distributed among these distances:
60 39 0.40
61 46 0.47
62 6 0.06
63 6 0.06
ACGTcount: A:0.45, C:0.15, G:0.13, T:0.27
Consensus pattern (61 bp):
AAGTACCTAATTTGACAAAAAAAAAACTTTAAGTACCAATTTGAACCTTAAAGCCAAGTTC
Found at i:128911911 original size:12 final size:12
Alignment explanation
Indices: 128911894--128911943 Score: 50
Period size: 12 Copynumber: 4.3 Consensus size: 12
128911884 TTAAACTGGA
128911894 TTTAATGATTTT
1 TTTAATGATTTT
* *
128911906 TTTAAT-A-ATA
1 TTTAATGATTTT
128911916 TTTAATGATTTT
1 TTTAATGATTTT
* *
128911928 TTTAATAATTAT
1 TTTAATGATTTT
128911940 TTTA
1 TTTA
128911944 TTTTAACTAT
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
10 7 0.23
11 2 0.07
12 21 0.70
ACGTcount: A:0.34, C:0.00, G:0.04, T:0.62
Consensus pattern (12 bp):
TTTAATGATTTT
Found at i:128911918 original size:22 final size:23
Alignment explanation
Indices: 128911893--128911941 Score: 91
Period size: 22 Copynumber: 2.2 Consensus size: 23
128911883 GTTAAACTGG
128911893 ATTTAATGATTTTTTTAATAA-T
1 ATTTAATGATTTTTTTAATAATT
128911915 ATTTAATGATTTTTTTAATAATT
1 ATTTAATGATTTTTTTAATAATT
128911938 ATTT
1 ATTT
128911942 TATTTTAACT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
22 21 0.81
23 5 0.19
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.61
Consensus pattern (23 bp):
ATTTAATGATTTTTTTAATAATT
Found at i:128913851 original size:15 final size:16
Alignment explanation
Indices: 128913833--128913862 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
128913823 ATTTATCTTG
128913833 ATTTTTAA-TTCATTC
1 ATTTTTAATTTCATTC
128913848 ATTTTTAATTTCATT
1 ATTTTTAATTTCATT
128913863 TGATGCGGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.27, C:0.10, G:0.00, T:0.63
Consensus pattern (16 bp):
ATTTTTAATTTCATTC
Found at i:128919681 original size:2 final size:2
Alignment explanation
Indices: 128919674--128919698 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
128919664 GTCTGCACTC
128919674 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 A
128919699 GGTAAAAGCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:128927608 original size:18 final size:17
Alignment explanation
Indices: 128927585--128927629 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 17
128927575 TGGTTAATTT
128927585 AATTAAAAAAATTATTAA
1 AATTAAAAAAA-TATTAA
*
128927603 AATTAATTAAAATATTAA
1 AATTAA-AAAAATATTAA
*
128927621 AAATAAAAA
1 AATTAAAAA
128927630 TTATAGTTCA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
17 2 0.09
18 17 0.74
19 4 0.17
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (17 bp):
AATTAAAAAAATATTAA
Found at i:128934076 original size:36 final size:36
Alignment explanation
Indices: 128934029--128934097 Score: 138
Period size: 36 Copynumber: 1.9 Consensus size: 36
128934019 TACTTGATCC
128934029 GAAAAATAGACCTAAAATTTTATTTAAATTTTATCT
1 GAAAAATAGACCTAAAATTTTATTTAAATTTTATCT
128934065 GAAAAATAGACCTAAAATTTTATTTAAATTTTA
1 GAAAAATAGACCTAAAATTTTATTTAAATTTTA
128934098 CCCAGATCAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.46, C:0.07, G:0.06, T:0.41
Consensus pattern (36 bp):
GAAAAATAGACCTAAAATTTTATTTAAATTTTATCT
Found at i:128934528 original size:16 final size:16
Alignment explanation
Indices: 128934499--128934532 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
128934489 AGGCAAAAAA
128934499 TTCTAATTCAAAGTGG
1 TTCTAATTCAAAGTGG
128934515 TTCTCAATTC-AAGTGG
1 TTCT-AATTCAAAGTGG
128934531 TT
1 TT
128934533 AATTAAACTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 12 0.71
17 5 0.29
ACGTcount: A:0.26, C:0.15, G:0.18, T:0.41
Consensus pattern (16 bp):
TTCTAATTCAAAGTGG
Found at i:128945684 original size:16 final size:16
Alignment explanation
Indices: 128945665--128945701 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
128945655 AACCTAACCC
128945665 AAAAAAAAA-AACAAAG
1 AAAAAAAAAGAA-AAAG
128945681 AAAAAAAAAGAAAAAG
1 AAAAAAAAAGAAAAAG
128945697 AAAAA
1 AAAAA
128945702 CCTACCCTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 18 0.90
17 2 0.10
ACGTcount: A:0.89, C:0.03, G:0.08, T:0.00
Consensus pattern (16 bp):
AAAAAAAAAGAAAAAG
Found at i:128945716 original size:16 final size:15
Alignment explanation
Indices: 128945697--128945731 Score: 54
Period size: 15 Copynumber: 2.3 Consensus size: 15
128945687 AAAGAAAAAG
128945697 AAAAACCT-ACCCTAA
1 AAAAACCTAACCC-AA
128945712 AAAAACCTAACCCAA
1 AAAAACCTAACCCAA
128945727 AAAAA
1 AAAAA
128945732 AAAAAGAAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 15 0.79
16 4 0.21
ACGTcount: A:0.63, C:0.29, G:0.00, T:0.09
Consensus pattern (15 bp):
AAAAACCTAACCCAA
Found at i:128945732 original size:16 final size:15
Alignment explanation
Indices: 128945697--128945732 Score: 54
Period size: 16 Copynumber: 2.3 Consensus size: 15
128945687 AAAGAAAAAG
*
128945697 AAAAACCTACCCTAA
1 AAAAACCTACCCAAA
128945712 AAAAACCTAACCCAAA
1 AAAAACCT-ACCCAAA
128945728 AAAAA
1 AAAAA
128945733 AAAAGAAGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 8 0.42
16 11 0.58
ACGTcount: A:0.64, C:0.28, G:0.00, T:0.08
Consensus pattern (15 bp):
AAAAACCTACCCAAA
Found at i:128947851 original size:42 final size:42
Alignment explanation
Indices: 128947788--128947941 Score: 204
Period size: 42 Copynumber: 3.7 Consensus size: 42
128947778 CTTCGTTTTC
** *
128947788 TCGATGCCATAGTTCAACTATGGTCTTACACATCTTCACATAA
1 TCGATGCCATAGCCCAACTATGGTCTTACACATATTCACAT-A
* *
128947831 T-GATGCCATAGCCCAGCTATGGTCTTACACATATTCATATA
1 TCGATGCCATAGCCCAACTATGGTCTTACACATATTCACATA
*
128947872 TCGATGCCATAGCCCAACTATGGTCTTACACGTGA-TCACATA
1 TCGATGCCATAGCCCAACTATGGTCTTACACAT-ATTCACATA
**
128947914 TCGATGCCATAGCCCAGTTATGGTCTTA
1 TCGATGCCATAGCCCAACTATGGTCTTA
128947942 TACGAATCAC
Statistics
Matches: 99, Mismatches: 10, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
41 2 0.02
42 95 0.96
43 2 0.02
ACGTcount: A:0.28, C:0.26, G:0.16, T:0.31
Consensus pattern (42 bp):
TCGATGCCATAGCCCAACTATGGTCTTACACATATTCACATA
Found at i:128947929 original size:84 final size:84
Alignment explanation
Indices: 128947788--128947941 Score: 238
Period size: 84 Copynumber: 1.8 Consensus size: 84
128947778 CTTCGTTTTC
** *
128947788 TCGATGCCATAGTTCAACTATGGTCTTACACATCTTCACATAATGATGCCATAGCCCAGCTATGG
1 TCGATGCCATAGCCCAACTATGGTCTTACACATCATCACATAATGATGCCATAGCCCAGCTATGG
128947853 TCTTACACATATTCATATA
66 TCTTACACATATTCATATA
* * *
128947872 TCGATGCCATAGCCCAACTATGGTCTTACACGTGATCACAT-ATCGATGCCATAGCCCAGTTATG
1 TCGATGCCATAGCCCAACTATGGTCTTACACATCATCACATAAT-GATGCCATAGCCCAGCTATG
128947936 GTCTTA
65 GTCTTA
128947942 TACGAATCAC
Statistics
Matches: 63, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
83 2 0.03
84 61 0.97
ACGTcount: A:0.28, C:0.26, G:0.16, T:0.31
Consensus pattern (84 bp):
TCGATGCCATAGCCCAACTATGGTCTTACACATCATCACATAATGATGCCATAGCCCAGCTATGG
TCTTACACATATTCATATA
Found at i:128948091 original size:31 final size:31
Alignment explanation
Indices: 128948056--128948173 Score: 182
Period size: 31 Copynumber: 3.8 Consensus size: 31
128948046 CTTGTCACTT
* * *
128948056 GTAGCCGAAGATACCACTATTCACTGATTAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
*
128948087 GTAGCCGGAGCTACCACTTTTCACTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
* *
128948118 GTAGTCGGAGCTACCACTTTTCACTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
128948149 GTAGCCGAAGCTACCACTTTTCACT
1 GTAGCCGAAGCTACCACTTTTCACT
128948174 TGTCATTTGT
Statistics
Matches: 80, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 80 1.00
ACGTcount: A:0.25, C:0.27, G:0.20, T:0.27
Consensus pattern (31 bp):
GTAGCCGAAGCTACCACTTTTCACTGATCAG
Found at i:128952412 original size:25 final size:27
Alignment explanation
Indices: 128952375--128952427 Score: 74
Period size: 26 Copynumber: 2.0 Consensus size: 27
128952365 TCAAACATGC
128952375 ATTTAGGTCAATTTAAC-CCTAGGGGT
1 ATTTAGGTCAATTTAACTCCTAGGGGT
* *
128952401 ATTTCGGT-AATTTATCTCCTAGGGGT
1 ATTTAGGTCAATTTAACTCCTAGGGGT
128952427 A
1 A
128952428 AAACTGTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 7 0.29
26 17 0.71
ACGTcount: A:0.25, C:0.15, G:0.23, T:0.38
Consensus pattern (27 bp):
ATTTAGGTCAATTTAACTCCTAGGGGT
Found at i:128953975 original size:26 final size:26
Alignment explanation
Indices: 128953906--128954039 Score: 227
Period size: 26 Copynumber: 5.2 Consensus size: 26
128953896 CATGAAATTC
* *
128953906 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGGAACATTTACCTAACCTA
*
128953932 TTATCAT-GAACATTTACCTAACCCA
1 TTATCATGGAACATTTACCTAACCTA
128953957 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGGAACATTTACCTAACCTA
128953983 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGGAACATTTACCTAACCTA
128954009 TTATCAT-GAACATTTACCTAACCTA
1 TTATCATGGAACATTTACCTAACCTA
128954034 TTATCA
1 TTATCA
128954040 ATTTGTATCA
Statistics
Matches: 105, Mismatches: 2, Indels: 3
0.95 0.02 0.03
Matches are distributed among these distances:
25 48 0.46
26 57 0.54
ACGTcount: A:0.36, C:0.25, G:0.05, T:0.34
Consensus pattern (26 bp):
TTATCATGGAACATTTACCTAACCTA
Found at i:128953986 original size:51 final size:52
Alignment explanation
Indices: 128953906--128954039 Score: 227
Period size: 51 Copynumber: 2.6 Consensus size: 52
128953896 CATGAAATTC
* *
128953906 TTATCATGAAACATTTACCTAACCCATTATCAT-GAACATTTACCTAACCCA
1 TTATCATGGAACATTTACCTAACCTATTATCATGGAACATTTACCTAACCCA
*
128953957 TTATCATGGAACATTTACCTAACCTATTATCATGGAACATTTACCTAACCTA
1 TTATCATGGAACATTTACCTAACCTATTATCATGGAACATTTACCTAACCCA
128954009 TTATCAT-GAACATTTACCTAACCTATTATCA
1 TTATCATGGAACATTTACCTAACCTATTATCA
128954040 ATTTGTATCA
Statistics
Matches: 79, Mismatches: 3, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
51 55 0.70
52 24 0.30
ACGTcount: A:0.36, C:0.25, G:0.05, T:0.34
Consensus pattern (52 bp):
TTATCATGGAACATTTACCTAACCTATTATCATGGAACATTTACCTAACCCA
Found at i:128958181 original size:25 final size:27
Alignment explanation
Indices: 128958144--128958196 Score: 74
Period size: 26 Copynumber: 2.0 Consensus size: 27
128958134 TCAAACATGC
128958144 ATTTAGGTCAATTTAAC-CCTAGGGGT
1 ATTTAGGTCAATTTAACTCCTAGGGGT
* *
128958170 ATTTCGGT-AATTTATCTCCTAGGGGT
1 ATTTAGGTCAATTTAACTCCTAGGGGT
128958196 A
1 A
128958197 AAACTGTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 7 0.29
26 17 0.71
ACGTcount: A:0.25, C:0.15, G:0.23, T:0.38
Consensus pattern (27 bp):
ATTTAGGTCAATTTAACTCCTAGGGGT
Found at i:128959745 original size:26 final size:26
Alignment explanation
Indices: 128959676--128959809 Score: 227
Period size: 26 Copynumber: 5.2 Consensus size: 26
128959666 CATGAAATTC
* *
128959676 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGGAACATTTACCTAACCTA
*
128959702 TTATCAT-GAACATTTACCTAACCCA
1 TTATCATGGAACATTTACCTAACCTA
128959727 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGGAACATTTACCTAACCTA
128959753 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGGAACATTTACCTAACCTA
128959779 TTATCAT-GAACATTTACCTAACCTA
1 TTATCATGGAACATTTACCTAACCTA
128959804 TTATCA
1 TTATCA
128959810 ATTTGTATCA
Statistics
Matches: 105, Mismatches: 2, Indels: 3
0.95 0.02 0.03
Matches are distributed among these distances:
25 48 0.46
26 57 0.54
ACGTcount: A:0.36, C:0.25, G:0.05, T:0.34
Consensus pattern (26 bp):
TTATCATGGAACATTTACCTAACCTA
Found at i:128959756 original size:51 final size:52
Alignment explanation
Indices: 128959676--128959809 Score: 227
Period size: 51 Copynumber: 2.6 Consensus size: 52
128959666 CATGAAATTC
* *
128959676 TTATCATGAAACATTTACCTAACCCATTATCAT-GAACATTTACCTAACCCA
1 TTATCATGGAACATTTACCTAACCTATTATCATGGAACATTTACCTAACCCA
*
128959727 TTATCATGGAACATTTACCTAACCTATTATCATGGAACATTTACCTAACCTA
1 TTATCATGGAACATTTACCTAACCTATTATCATGGAACATTTACCTAACCCA
128959779 TTATCAT-GAACATTTACCTAACCTATTATCA
1 TTATCATGGAACATTTACCTAACCTATTATCA
128959810 ATTTGTATCA
Statistics
Matches: 79, Mismatches: 3, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
51 55 0.70
52 24 0.30
ACGTcount: A:0.36, C:0.25, G:0.05, T:0.34
Consensus pattern (52 bp):
TTATCATGGAACATTTACCTAACCTATTATCATGGAACATTTACCTAACCCA
Found at i:128961440 original size:18 final size:19
Alignment explanation
Indices: 128961417--128961455 Score: 71
Period size: 18 Copynumber: 2.1 Consensus size: 19
128961407 CACCTATAGT
128961417 AAATATGTACTT-AAAGAA
1 AAATATGTACTTAAAAGAA
128961435 AAATATGTACTTAAAAGAA
1 AAATATGTACTTAAAAGAA
128961454 AA
1 AA
128961456 GACAAATAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 12 0.60
19 8 0.40
ACGTcount: A:0.59, C:0.05, G:0.10, T:0.26
Consensus pattern (19 bp):
AAATATGTACTTAAAAGAA
Found at i:128966180 original size:6 final size:6
Alignment explanation
Indices: 128966171--128966201 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
128966161 AAACATAAAA
128966171 ACATAT ACATAT ACATAT ACATAT ACATAT A
1 ACATAT ACATAT ACATAT ACATAT ACATAT A
128966202 TGCATTACAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.52, C:0.16, G:0.00, T:0.32
Consensus pattern (6 bp):
ACATAT
Found at i:128967599 original size:2 final size:2
Alignment explanation
Indices: 128967592--128967617 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
128967582 ATCATTTTAT
128967592 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
128967618 AATTGGATGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:128968758 original size:24 final size:25
Alignment explanation
Indices: 128968726--128968798 Score: 80
Period size: 25 Copynumber: 2.9 Consensus size: 25
128968716 TATTTCTTAT
128968726 TTAA-ATTATTAAATATAATTAAAA
1 TTAATATTATTAAATATAATTAAAA
*
128968750 -TAATATTATTTAAA-ATAATAAAAAA
1 TTAATATTA-TTAAATATAAT-TAAAA
*
128968775 TTAATATAATTAAATAATAATTAA
1 TTAATATTATTAAAT-ATAATTAA
128968799 TATACTTAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
23 3 0.08
24 9 0.22
25 14 0.35
26 9 0.22
27 5 0.12
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (25 bp):
TTAATATTATTAAATATAATTAAAA
Found at i:128968910 original size:15 final size:15
Alignment explanation
Indices: 128968890--128968920 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
128968880 TGAAAATGAC
128968890 TCTAAAAAGGCCAAA
1 TCTAAAAAGGCCAAA
*
128968905 TCTAAAAATGCCAAA
1 TCTAAAAAGGCCAAA
128968920 T
1 T
128968921 TAACATTTAT
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:0.52, C:0.19, G:0.10, T:0.19
Consensus pattern (15 bp):
TCTAAAAAGGCCAAA
Found at i:128969793 original size:19 final size:20
Alignment explanation
Indices: 128969771--128969812 Score: 50
Period size: 19 Copynumber: 2.1 Consensus size: 20
128969761 AAATAATTTT
*
128969771 AATAATTTTTAT-TTTTAAA
1 AATAATTTATATGTTTTAAA
* *
128969790 AATAGTTTATATGTTTTTAA
1 AATAATTTATATGTTTTAAA
128969810 AAT
1 AAT
128969813 TTAAAAAATT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
19 10 0.53
20 9 0.47
ACGTcount: A:0.40, C:0.00, G:0.05, T:0.55
Consensus pattern (20 bp):
AATAATTTATATGTTTTAAA
Found at i:128970524 original size:60 final size:60
Alignment explanation
Indices: 128970431--128970551 Score: 224
Period size: 60 Copynumber: 2.0 Consensus size: 60
128970421 CTTAGTATAA
* *
128970431 TACCTTGTTTTGATTGTATCACACTATGTATCATTTGATAACCGAATAGATCCCCTATCT
1 TACCTTGTTTTGACTGTATCACACTATGTATCATTTAATAACCGAATAGATCCCCTATCT
128970491 TACCTTGTTTTGACTGTATCACACTATGTATCATTTAATAACCGAATAGATCCCCTATCT
1 TACCTTGTTTTGACTGTATCACACTATGTATCATTTAATAACCGAATAGATCCCCTATCT
128970551 T
1 T
128970552 TGGTTCAAAT
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
60 59 1.00
ACGTcount: A:0.27, C:0.22, G:0.11, T:0.40
Consensus pattern (60 bp):
TACCTTGTTTTGACTGTATCACACTATGTATCATTTAATAACCGAATAGATCCCCTATCT
Found at i:128971817 original size:16 final size:16
Alignment explanation
Indices: 128971796--128971828 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
128971786 AAAACAGATA
128971796 TGCAAAGTACCAAAAC
1 TGCAAAGTACCAAAAC
128971812 TGCAAAGTACCAAAAC
1 TGCAAAGTACCAAAAC
128971828 T
1 T
128971829 AACTAATGAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.48, C:0.24, G:0.12, T:0.15
Consensus pattern (16 bp):
TGCAAAGTACCAAAAC
Found at i:128975779 original size:15 final size:15
Alignment explanation
Indices: 128975759--128975821 Score: 53
Period size: 14 Copynumber: 4.4 Consensus size: 15
128975749 TCTTATATGT
128975759 TTATATTACATTTTA
1 TTATATTACATTTTA
128975774 TTATA-TA-ATCTTTA
1 TTATATTACAT-TTTA
* *
128975788 TTATGTTTCA-TTT-
1 TTATATTACATTTTA
* *
128975801 TTATATTACTTTTTT
1 TTATATTACATTTTA
128975816 TTATAT
1 TTATAT
128975822 AAATGTTATG
Statistics
Matches: 38, Mismatches: 5, Indels: 10
0.72 0.09 0.19
Matches are distributed among these distances:
13 9 0.24
14 16 0.42
15 12 0.32
16 1 0.03
ACGTcount: A:0.27, C:0.06, G:0.02, T:0.65
Consensus pattern (15 bp):
TTATATTACATTTTA
Found at i:128975870 original size:15 final size:15
Alignment explanation
Indices: 128975850--128975890 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
128975840 GTATCGTAAA
*
128975850 TTATATTATTTATGT
1 TTATATTATTTATAT
*
128975865 TTATATTATATATAT
1 TTATATTATTTATAT
*
128975880 ATATATTATTT
1 TTATATTATTT
128975891 TAAAAATATA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.63
Consensus pattern (15 bp):
TTATATTATTTATAT
Found at i:128975899 original size:24 final size:22
Alignment explanation
Indices: 128975874--128975916 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
128975864 TTTATATTAT
*
128975874 ATATATATATATTATT-TTAAAA
1 ATATAAAT-TATTATTATTAAAA
128975896 ATATAAATTATTATTATTAAA
1 ATATAAATTATTATTATTAAA
128975917 TCATTTTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 7 0.37
22 12 0.63
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (22 bp):
ATATAAATTATTATTATTAAAA
Found at i:128976056 original size:14 final size:15
Alignment explanation
Indices: 128976032--128976087 Score: 51
Period size: 15 Copynumber: 3.7 Consensus size: 15
128976022 ACTCTCAAAC
128976032 TAATATATTATTATA
1 TAATATATTATTATA
*
128976047 TAAT-TATTATTATTTT
1 TAATATATTATTA--TA
* *
128976063 TATTATGTTATTATA
1 TAATATATTATTATA
*
128976078 TTATATATTA
1 TAATATATTA
128976088 GATACTATTT
Statistics
Matches: 31, Mismatches: 7, Indels: 6
0.70 0.16 0.14
Matches are distributed among these distances:
14 8 0.26
15 12 0.39
16 4 0.13
17 7 0.23
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.61
Consensus pattern (15 bp):
TAATATATTATTATA
Found at i:128976075 original size:8 final size:8
Alignment explanation
Indices: 128976035--128976087 Score: 58
Period size: 8 Copynumber: 6.9 Consensus size: 8
128976025 CTCAAACTAA
128976035 TATATTAT
1 TATATTAT
*
128976043 TATATAAT
1 TATATTAT
128976051 TATTATTAT
1 TA-TATTAT
128976060 T-T-TTAT
1 TATATTAT
*
128976066 TATGTTAT
1 TATATTAT
128976074 TATATTA-
1 TATATTAT
128976081 TATATTA
1 TATATTA
128976088 GATACTATTT
Statistics
Matches: 39, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
6 5 0.13
7 9 0.23
8 19 0.49
9 6 0.15
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (8 bp):
TATATTAT
Found at i:128976383 original size:16 final size:17
Alignment explanation
Indices: 128976362--128976395 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
128976352 CATTTTTTTG
*
128976362 CTTTATAT-GTATTATT
1 CTTTATATCGTAGTATT
128976378 CTTTATATCGTAGTATT
1 CTTTATATCGTAGTATT
128976395 C
1 C
128976396 ATTTTTATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.24, C:0.12, G:0.09, T:0.56
Consensus pattern (17 bp):
CTTTATATCGTAGTATT
Found at i:128988003 original size:119 final size:119
Alignment explanation
Indices: 128987787--128988016 Score: 354
Period size: 119 Copynumber: 1.9 Consensus size: 119
128987777 TTGAAGACAA
* *
128987787 CAGATCTAGACTTCAGACATTTATGCTGAAGCAGATCCAAGATGATTTGGTATTCTTGTGTTTAC
1 CAGATCTAGACTTCAGACATTTATACTGAAGCAGATCCAAGATGATTTGATATTCTTGTGTTTAC
* * *
128987852 AAGAAACAAATCGAGAACATAGCATATTTGACTCTCAGATGTTCTCAAATATAG
66 AAGAAACAAATCGAGAACATAGCAGATATGACTCTCAAATGTTCTCAAATATAG
**
128987906 CAGATCTA-ACTTTCAGATGTTTATACTGAAGCAGATCCAAGATGATTTGATATTCTTGTGTTTA
1 CAGATCTAGAC-TTCAGACATTTATACTGAAGCAGATCCAAGATGATTTGATATTCTTGTGTTTA
* * *
128987970 CAAGGAACAAATCGAGGACATTGCAGATATGACTCTCAAATGTTCTC
65 CAAGAAACAAATCGAGAACATAGCAGATATGACTCTCAAATGTTCTC
128988017 CAACAGACTC
Statistics
Matches: 100, Mismatches: 10, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
118 2 0.02
119 98 0.98
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Consensus pattern (119 bp):
CAGATCTAGACTTCAGACATTTATACTGAAGCAGATCCAAGATGATTTGATATTCTTGTGTTTAC
AAGAAACAAATCGAGAACATAGCAGATATGACTCTCAAATGTTCTCAAATATAG
Found at i:128988055 original size:83 final size:83
Alignment explanation
Indices: 128987960--128988625 Score: 1046
Period size: 83 Copynumber: 8.0 Consensus size: 83
128987950 ATTTGATATT
* *
128987960 CTTGTGTTTACAAGGAACAAATCGAGGACATTGCAGATATGACTCTCAAATGTTCTCCAACAGAC
1 CTTGTGCTTACAAGGAACAAATCGAGGACATTGCAGATATGACTCTCAAATGTTCTCAAACAGAC
*
128988025 TCAAGATGGTTTGGTATC
66 TCAAGATGGTTTGGCATC
* * *
128988043 CTTGTGCTTACAAGGAACAAATCAAGGACATTGCAGATATGACTCTTAAATGTTCTCCAACAGAC
1 CTTGTGCTTACAAGGAACAAATCGAGGACATTGCAGATATGACTCTCAAATGTTCTCAAACAGAC
128988108 TCAAGATGGTTTGGCATC
66 TCAAGATGGTTTGGCATC
* * * *
128988126 CTTGTGCTCACAAGGAACAAATCGAAGACATTGCAGATATAACTCTCAAATGTTCTCAAATAGAC
1 CTTGTGCTTACAAGGAACAAATCGAGGACATTGCAGATATGACTCTCAAATGTTCTCAAACAGAC
*
128988191 TCAAGATGGTTTGGTATC
66 TCAAGATGGTTTGGCATC
* *
128988209 CTTGTGCTTACAAGGAACAAATCAAGGACATTGCAGATATGACTCTCAAATGTTCTCCAACAGAC
1 CTTGTGCTTACAAGGAACAAATCGAGGACATTGCAGATATGACTCTCAAATGTTCTCAAACAGAC
128988274 TCAAGATGGTTTGGCATC
66 TCAAGATGGTTTGGCATC
* * * *
128988292 CTTGTGCTTACAAGGAACAAATCGAAGACATTGTAGATATGATTCTCAAATGTTCTCAAATAGAC
1 CTTGTGCTTACAAGGAACAAATCGAGGACATTGCAGATATGACTCTCAAATGTTCTCAAACAGAC
*
128988357 TCAAGATGGTTTGGTATC
66 TCAAGATGGTTTGGCATC
* *
128988375 CTTGTGCTTATAAGGAACAAATCGAGGACATTGCAGATATGACTCTCAAATATTCTCAAACAGAC
1 CTTGTGCTTACAAGGAACAAATCGAGGACATTGCAGATATGACTCTCAAATGTTCTCAAACAGAC
*
128988440 TCAAGATGATTTGGCATC
66 TCAAGATGGTTTGGCATC
128988458 CTTGTGCTTACAAGGAACAAATCGAGGACATTGCAGATATGACTCTCAAATGTTCTCAAACAGAC
1 CTTGTGCTTACAAGGAACAAATCGAGGACATTGCAGATATGACTCTCAAATGTTCTCAAACAGAC
**
128988523 TCAAGATAATTTGGCATC
66 TCAAGATGGTTTGGCATC
* * * * *
128988541 CTTGTGCTTACAAGGAACAAATCGAGGACGTAGTAGAGATGACTCTCGAATGTTCTCAAAACAGA
1 CTTGTGCTTACAAGGAACAAATCGAGGACATTGCAGATATGACTCTCAAATGTTCTC-AAACAGA
*
128988606 CTCAA-ACTGATTTGGCATC
65 CTCAAGA-TGGTTTGGCATC
128988625 C
1 C
128988626 CCACAAATTG
Statistics
Matches: 538, Mismatches: 43, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
83 514 0.96
84 24 0.04
ACGTcount: A:0.33, C:0.20, G:0.19, T:0.28
Consensus pattern (83 bp):
CTTGTGCTTACAAGGAACAAATCGAGGACATTGCAGATATGACTCTCAAATGTTCTCAAACAGAC
TCAAGATGGTTTGGCATC
Found at i:128990530 original size:26 final size:26
Alignment explanation
Indices: 128990494--128990629 Score: 236
Period size: 26 Copynumber: 5.2 Consensus size: 26
128990484 TGATACAAAT
128990494 TGATAATAGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTTCA
*
128990520 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTTCA
*
128990546 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTTCA
*
128990572 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTTCA
*
128990598 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTTCA
128990624 TGATAA
1 TGATAA
128990630 GAATTTCATG
Statistics
Matches: 107, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 107 1.00
ACGTcount: A:0.34, C:0.05, G:0.24, T:0.37
Consensus pattern (26 bp):
TGATAATAGGTTAGGTAAATGTTTCA
Found at i:128993620 original size:46 final size:42
Alignment explanation
Indices: 128993570--128993665 Score: 102
Period size: 42 Copynumber: 2.2 Consensus size: 42
128993560 ATGTGTTACT
* *
128993570 TTATATTATATCTATTATTTTTCTTATATGTTTATATTACATTTTA
1 TTATATAATATCTATTATGTTTC--AT-T-TTTATATTACATTTTA
* * * *
128993616 TTATATAATCTTTATTATGTTTCATTTTTATATTACTTTTTT
1 TTATATAATATCTATTATGTTTCATTTTTATATTACATTTTA
128993658 TTATATAA
1 TTATATAA
128993666 ATGTTATGTA
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
42 22 0.50
43 1 0.02
44 2 0.05
46 19 0.43
ACGTcount: A:0.28, C:0.06, G:0.02, T:0.64
Consensus pattern (42 bp):
TTATATAATATCTATTATGTTTCATTTTTATATTACATTTTA
Found at i:128993621 original size:15 final size:15
Alignment explanation
Indices: 128993601--128993663 Score: 53
Period size: 14 Copynumber: 4.4 Consensus size: 15
128993591 TCTTATATGT
128993601 TTATATTACATTTTA
1 TTATATTACATTTTA
128993616 TTATA-TA-ATCTTTA
1 TTATATTACAT-TTTA
* *
128993630 TTATGTTTCA-TTT-
1 TTATATTACATTTTA
* *
128993643 TTATATTACTTTTTT
1 TTATATTACATTTTA
128993658 TTATAT
1 TTATAT
128993664 AAATGTTATG
Statistics
Matches: 38, Mismatches: 5, Indels: 10
0.72 0.09 0.19
Matches are distributed among these distances:
13 9 0.24
14 16 0.42
15 12 0.32
16 1 0.03
ACGTcount: A:0.27, C:0.06, G:0.02, T:0.65
Consensus pattern (15 bp):
TTATATTACATTTTA
Found at i:128994233 original size:16 final size:17
Alignment explanation
Indices: 128994212--128994245 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
128994202 CATTTTTTTG
*
128994212 CTTTATAT-GTATTATT
1 CTTTATATCGTAGTATT
128994228 CTTTATATCGTAGTATT
1 CTTTATATCGTAGTATT
128994245 C
1 C
128994246 ATTTTTTATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.24, C:0.12, G:0.09, T:0.56
Consensus pattern (17 bp):
CTTTATATCGTAGTATT
Found at i:128998007 original size:8 final size:8
Alignment explanation
Indices: 128997994--128998018 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
128997984 TCGGTCTGTA
128997994 TATTTTAT
1 TATTTTAT
128998002 TATTTTAT
1 TATTTTAT
128998010 TATTTTAT
1 TATTTTAT
128998018 T
1 T
128998019 CTCTCATCGC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (8 bp):
TATTTTAT
Found at i:128998545 original size:16 final size:15
Alignment explanation
Indices: 128998522--128998553 Score: 55
Period size: 16 Copynumber: 2.1 Consensus size: 15
128998512 TTTTATTTTT
128998522 ATTAAATTATATTAA
1 ATTAAATTATATTAA
128998537 ATTATAATTATATTAA
1 ATTA-AATTATATTAA
128998553 A
1 A
128998554 AATATGATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.25
16 12 0.75
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
ATTAAATTATATTAA
Found at i:128999145 original size:15 final size:15
Alignment explanation
Indices: 128999116--128999144 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
128999106 ATTTAATTTC
128999116 AGTACTTAAATTTTT
1 AGTACTTAAATTTTT
128999131 AGTACTT-AATTTTT
1 AGTACTTAAATTTTT
128999145 TTTAATTTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.31, C:0.07, G:0.07, T:0.55
Consensus pattern (15 bp):
AGTACTTAAATTTTT
Found at i:129003161 original size:37 final size:37
Alignment explanation
Indices: 129003115--129003188 Score: 148
Period size: 37 Copynumber: 2.0 Consensus size: 37
129003105 TTGCTATAAT
129003115 TTTTATATTTATACTTATTTTTATTTAAGAGATTAAC
1 TTTTATATTTATACTTATTTTTATTTAAGAGATTAAC
129003152 TTTTATATTTATACTTATTTTTATTTAAGAGATTAAC
1 TTTTATATTTATACTTATTTTTATTTAAGAGATTAAC
129003189 CAAAAAAATT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.32, C:0.05, G:0.05, T:0.57
Consensus pattern (37 bp):
TTTTATATTTATACTTATTTTTATTTAAGAGATTAAC
Found at i:129003815 original size:16 final size:16
Alignment explanation
Indices: 129003794--129003878 Score: 58
Period size: 16 Copynumber: 5.7 Consensus size: 16
129003784 CATTAAGCCC
129003794 CCCAAAAAAAACCTAA
1 CCCAAAAAAAACCTAA
*
129003810 CCCAAAAAAAAAC-AA
1 CCCAAAAAAAACCTAA
** **
129003825 -AGAAAAAAAA-AGAA
1 CCCAAAAAAAACCTAA
129003839 ---AAAGAAAAACCT-A
1 CCCAAA-AAAAACCTAA
*
129003852 CCCCAAAAAAACCTAA
1 CCCAAAAAAAACCTAA
129003868 CCCAAAAAAAA
1 CCCAAAAAAAA
129003879 AAAAAGAAGA
Statistics
Matches: 54, Mismatches: 8, Indels: 14
0.71 0.11 0.18
Matches are distributed among these distances:
12 3 0.06
13 6 0.11
14 10 0.19
15 10 0.19
16 25 0.46
ACGTcount: A:0.69, C:0.24, G:0.04, T:0.04
Consensus pattern (16 bp):
CCCAAAAAAAACCTAA
Found at i:129003861 original size:15 final size:15
Alignment explanation
Indices: 129003843--129003877 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
129003833 AAAGAAAAAG
*
129003843 AAAAACCTACCCCAA
1 AAAAACCTAACCCAA
129003858 AAAAACCTAACCCAA
1 AAAAACCTAACCCAA
129003873 AAAAA
1 AAAAA
129003878 AAAAAAGAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.63, C:0.31, G:0.00, T:0.06
Consensus pattern (15 bp):
AAAAACCTAACCCAA
Found at i:129004644 original size:11 final size:11
Alignment explanation
Indices: 129004626--129004655 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
129004616 GTGTATATTG
129004626 TATATATTATA
1 TATATATTATA
*
129004637 TTTATATTATA
1 TATATATTATA
129004648 TATATATT
1 TATATATT
129004656 CTTAATGTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (11 bp):
TATATATTATA
Found at i:129006859 original size:12 final size:12
Alignment explanation
Indices: 129006842--129006877 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
129006832 ATTCATTTGA
129006842 CATTCATGCATT
1 CATTCATGCATT
129006854 CATTCATGCATT
1 CATTCATGCATT
* *
129006866 TATTCATACATT
1 CATTCATGCATT
129006878 GCATATCCCA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.28, C:0.22, G:0.06, T:0.44
Consensus pattern (12 bp):
CATTCATGCATT
Found at i:129012305 original size:70 final size:69
Alignment explanation
Indices: 129012186--129012608 Score: 403
Period size: 71 Copynumber: 6.2 Consensus size: 69
129012176 GAGTTAAGCC
*
129012186 TTTT-AATTTTTGTTTTTCAAAATCAACTCATATTGCTAGAGGTGAGTTGAGCCTCGGGGCACGC
1 TTTTCAATTTTTG-TTTT--AAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGGCACGC
129012250 TGAGGTA
63 TGAGGTA
* * ** * *
129012257 TTTTCAATTTTTGTGTTTTAATCAACTCATATTGCGAGAGATGAGTTGAGCCTCAAGACACGTTG
1 TTTTCAATTTTTGT-TTTAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGGCACGCTG
129012322 AGGTA
65 AGGTA
* *
129012327 TTTTTAATTTTTGTTTTCAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCT
1 TTTTCAATTTTTGTTTT--AAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGGCACGCT
129012392 GAGGTA
64 GAGGTA
* * * ** * * *
129012398 TTTTTAGTTTATGTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCT---------TTTA
1 TTTTCAATTTTTGTTTTAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGGCACGCTGA
129012454 ---A
66 GGTA
*** ** *
129012455 TTTTTGTTTTTCA----AAATCAACTCATATTGCTAGAGGTGAGTTGAGCCTCGGGGCACGCTGA
1 TTTTCAATTTTTGTTTTAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGGCACGCTGA
129012516 GGTA
66 GGTA
* * *
129012520 TTTTCAATTTTTGTGTTTTAATTTCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACGC
1 TTTTCAA-TTTT-TGTTTTAA-ATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGGCACGC
129012585 TGAGGTA
63 TGAGGTA
*
129012592 TTTTCAATTTCTGTTTT
1 TTTTCAATTTTTGTTTT
129012609 CAATTTACGT
Statistics
Matches: 285, Mismatches: 44, Indels: 47
0.76 0.12 0.12
Matches are distributed among these distances:
53 31 0.11
57 9 0.03
60 2 0.01
62 2 0.01
65 5 0.02
66 4 0.01
69 34 0.12
70 64 0.22
71 70 0.25
72 64 0.22
ACGTcount: A:0.24, C:0.14, G:0.22, T:0.39
Consensus pattern (69 bp):
TTTTCAATTTTTGTTTTAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGGCACGCTGA
GGTA
Found at i:129012494 original size:122 final size:124
Alignment explanation
Indices: 129012328--129012574 Score: 392
Period size: 122 Copynumber: 2.0 Consensus size: 124
129012318 GTTGAGGTAT
129012328 TTTTAATTTTTGTTTTCAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCTG
1 TTTTAATTTTTGTTTTCAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCTG
* *
129012393 AGGTATTTT-TA-GTTTATGTTTTAAATT-GACTCATATTGCGAGAGGTGAGTTAAGCC
66 AGGTATTTTCAATGTTTATGTTTTAAATTCAACTCATATTGCGAGAGGTGAGTTAAGCC
* *
129012449 TTTTAATTTTTGTTTTTCAAAATCAACTCATATTGCTAGAGGTGAGTTGAGCCTCGGGGCACGCT
1 TTTTAATTTTTG-TTTTCAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCT
* * * *
129012514 GAGGTATTTTCAATTTTTGTGTTTTAATTTCAACTCATATTGCGAGAGGTGAGTTGAGCC
65 GAGGTATTTTCAATGTTTATGTTTTAAATTCAACTCATATTGCGAGAGGTGAGTTAAGCC
129012574 T
1 T
129012575 CAGGTCACGC
Statistics
Matches: 114, Mismatches: 8, Indels: 4
0.90 0.06 0.03
Matches are distributed among these distances:
121 12 0.11
122 60 0.53
123 1 0.01
124 13 0.11
125 28 0.25
ACGTcount: A:0.24, C:0.14, G:0.23, T:0.39
Consensus pattern (124 bp):
TTTTAATTTTTGTTTTCAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCTG
AGGTATTTTCAATGTTTATGTTTTAAATTCAACTCATATTGCGAGAGGTGAGTTAAGCC
Found at i:129012539 original size:263 final size:257
Alignment explanation
Indices: 129012019--129012611 Score: 1042
Period size: 263 Copynumber: 2.3 Consensus size: 257
129012009 TTTCAAGGAA
*
129012019 AATCAACTCATATTGCGAGAGATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAATTGTTGT
1 AATCAACTCATATTGCGAGAGATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAATTTTTGT
129012084 TTTCAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGACACGCTGAGGTATTTTTAGT
66 TTTCAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGACACGCTGAGGTATTTTTAGT
129012149 TTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTCAAAATCAACT
131 TTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTCAAAATCAACT
129012214 CATATTGCTAGAGGTGAGTTGAGCCTCGGGGCACGCTGAGGTATTTTCAATTTTTGTGTTTT
196 CATATTGCTAGAGGTGAGTTGAGCCTCGGGGCACGCTGAGGTATTTTCAATTTTTGTGTTTT
129012276 AATCAACTCATATTGCGAGAGATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAATTTTTGT
1 AATCAACTCATATTGCGAGAGATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAATTTTTGT
*
129012341 TTTCAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCTGAGGTATTTTTAGT
66 TTTCAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGACACGCTGAGGTA---TT--T
129012406 TTATGTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTCAAAA
126 TTA-GTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTCAAAA
129012471 TCAACTCATATTGCTAGAGGTGAGTTGAGCCTCGGGGCACGCTGAGGTATTTTCAATTTTTGTGT
190 TCAACTCATATTGCTAGAGGTGAGTTGAGCCTCGGGGCACGCTGAGGTATTTTCAATTTTTGTGT
129012536 TTT
255 TTT
* * * * * *
129012539 AATTTCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACGCTGAGGTATTTTCAATTTCT
1 AA--TCAACTCATATTGCGAGAGATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAATTTTT
129012604 GTTTTCAA
64 GTTTTCAA
129012612 TTTACGTTGT
Statistics
Matches: 320, Mismatches: 8, Indels: 8
0.95 0.02 0.02
Matches are distributed among these distances:
257 120 0.38
260 2 0.01
262 4 0.01
263 131 0.41
265 63 0.20
ACGTcount: A:0.26, C:0.15, G:0.23, T:0.37
Consensus pattern (257 bp):
AATCAACTCATATTGCGAGAGATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAATTTTTGT
TTTCAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGACACGCTGAGGTATTTTTAGT
TTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTCAAAATCAACT
CATATTGCTAGAGGTGAGTTGAGCCTCGGGGCACGCTGAGGTATTTTCAATTTTTGTGTTTT
Found at i:129012570 original size:72 final size:71
Alignment explanation
Indices: 129012449--129012614 Score: 244
Period size: 72 Copynumber: 2.3 Consensus size: 71
129012439 GAGTTAAGCC
** * *
129012449 TTTT-AATTTTTGTTTTTCAAAATCAACTCATATTGCTAGAGGTGAGTTGAGCCTCGGGGCACGC
1 TTTTCAATTTTTGTTTTT-AATTTCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACGC
129012513 TGAGGTA
65 TGAGGTA
*
129012520 TTTTCAATTTTTGTGTTTTAATTTCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACGC
1 TTTTCAATTTTTGT-TTTTAATTTCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACGC
129012585 TGAGGTA
65 TGAGGTA
* *
129012592 TTTTCAATTTCTGTTTTCAATTT
1 TTTTCAATTTTTGTTTTTAATTT
129012615 ACGTTGTTCA
Statistics
Matches: 86, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
71 12 0.14
72 70 0.81
73 4 0.05
ACGTcount: A:0.22, C:0.15, G:0.21, T:0.42
Consensus pattern (71 bp):
TTTTCAATTTTTGTTTTTAATTTCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACGCT
GAGGTA
Found at i:129012945 original size:74 final size:76
Alignment explanation
Indices: 129012839--129012983 Score: 224
Period size: 74 Copynumber: 1.9 Consensus size: 76
129012829 TTTTTACCTT
*
129012839 TCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAG--GACACG-CTGAGGTAATTT
1 TCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGATCACACGTC-GAGGTAATTT
129012901 CAATTTCTGTTG
65 CAATTTCTGTTG
* * *
129012913 TCAAAAAAGTCAACTCGTATTGCGAGAGGTGAGTTGAGCCTCAGATCACACGTCGAGGTATTTTC
1 TCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGATCACACGTCGAGGTAATTTC
129012978 AATTTC
66 AATTTC
129012984 CATTTTTCAA
Statistics
Matches: 64, Mismatches: 4, Indels: 4
0.89 0.06 0.06
Matches are distributed among these distances:
74 42 0.66
76 21 0.33
77 1 0.02
ACGTcount: A:0.30, C:0.19, G:0.23, T:0.28
Consensus pattern (76 bp):
TCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGATCACACGTCGAGGTAATTTC
AATTTCTGTTG
Done.