Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr2
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: 50190067
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Warning! 915496 characters in sequence are not A, C, G, or T
File 66 of 161
Found at i:20438388 original size:21 final size:20
Alignment explanation
Indices: 20438350--20438442 Score: 127
Period size: 21 Copynumber: 4.7 Consensus size: 20
20438340 AATCATATCT
*
20438350 TCTAAGATTACA-TATCATA
1 TCTAAGATTGCATTATCATA
20438369 TCTAAGATTGCATTTATCATA
1 TCTAAGATTGCA-TTATCATA
20438390 TCTAAGATTGCATATATCATA
1 TCTAAGATTGCAT-TATCATA
**
20438411 TCTTGGATTGCA-TATCATA
1 TCTAAGATTGCATTATCATA
20438430 TCTAAGATTGCAT
1 TCTAAGATTGCAT
20438443 ATCCTCAAAA
Statistics
Matches: 65, Mismatches: 5, Indels: 7
0.84 0.06 0.09
Matches are distributed among these distances:
19 28 0.43
20 1 0.02
21 36 0.55
ACGTcount: A:0.34, C:0.15, G:0.11, T:0.40
Consensus pattern (20 bp):
TCTAAGATTGCATTATCATA
Found at i:20438398 original size:40 final size:38
Alignment explanation
Indices: 20438343--20438445 Score: 120
Period size: 40 Copynumber: 2.7 Consensus size: 38
20438333 ATTACAAAAT
20438343 CATATC-T-TCTAAGATTACATATCATATCTAAGATTG
1 CATATCATATCTAAGATTACATATCATATCTAAGATTG
* **
20438379 CATTTATCATATCTAAGATTGCATATATCATATCTTGGATTG
1 CA--TATCATATCTAAGATT--ACATATCATATCTAAGATTG
*
20438421 CATATCATATCTAAGATTGCATATC
1 CATATCATATCTAAGATTACATATC
20438446 CTCAAAAATT
Statistics
Matches: 56, Mismatches: 5, Indels: 10
0.79 0.07 0.14
Matches are distributed among these distances:
36 2 0.04
38 9 0.16
39 1 0.02
40 25 0.45
42 19 0.34
ACGTcount: A:0.34, C:0.17, G:0.10, T:0.40
Consensus pattern (38 bp):
CATATCATATCTAAGATTACATATCATATCTAAGATTG
Found at i:20439299 original size:20 final size:19
Alignment explanation
Indices: 20439276--20439382 Score: 88
Period size: 20 Copynumber: 5.4 Consensus size: 19
20439266 AATACTAACA
20439276 GCTTGTCTGCAATTCTGGTG
1 GCTTGTCTGCAATT-TGGTG
* *
20439296 GCTTGTCTACAATATTGGTA
1 GCTTGTCTGCAAT-TTGGTG
*
20439316 CCTTGTCTGCAATTATGGTG
1 GCTTGTCTGCAATT-TGGTG
** * *
20439336 GCTTGTCCACAATACTGTTG
1 GCTTGTCTGCAAT-TTGGTG
* *
20439356 GTTTATCTGCAATATTGGTG
1 GCTTGTCTGCAAT-TTGGTG
20439376 GCTTGTC
1 GCTTGTC
20439383 CATAAACTGG
Statistics
Matches: 66, Mismatches: 18, Indels: 6
0.73 0.20 0.07
Matches are distributed among these distances:
19 1 0.02
20 64 0.97
21 1 0.02
ACGTcount: A:0.17, C:0.19, G:0.24, T:0.40
Consensus pattern (19 bp):
GCTTGTCTGCAATTTGGTG
Found at i:20439335 original size:80 final size:79
Alignment explanation
Indices: 20439197--20439351 Score: 197
Period size: 80 Copynumber: 1.9 Consensus size: 79
20439187 GTACTGGCAT
* * *
20439197 CTTGTCTGCAACACTGGTGGCTTGTCCACATTATTGGCTGCTTGTTTGCAGCATTGGTGGCTTGT
1 CTTGTCTGCAACACTGGTGGCTTGTCCACAATATTGGCTCCTTGTCTGCA-CATTGGTGGCTTGT
*
20439262 CCATAATACTAACAG
65 CCACAATACTAACAG
** *
20439277 CTTGTCTGCAATTCTGGTGGCTTGTCTACAATATTGG-TACCTTGTCTGCA-ATTATGGTGGCTT
1 CTTGTCTGCAACACTGGTGGCTTGTCCACAATATTGGCT-CCTTGTCTGCACA-T-TGGTGGCTT
20439340 GTCCACAATACT
63 GTCCACAATACT
20439352 GTTGGTTTAT
Statistics
Matches: 65, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
78 1 0.02
79 2 0.03
80 62 0.95
ACGTcount: A:0.19, C:0.22, G:0.23, T:0.37
Consensus pattern (79 bp):
CTTGTCTGCAACACTGGTGGCTTGTCCACAATATTGGCTCCTTGTCTGCACATTGGTGGCTTGTC
CACAATACTAACAG
Found at i:20439365 original size:40 final size:40
Alignment explanation
Indices: 20439251--20439393 Score: 128
Period size: 40 Copynumber: 3.6 Consensus size: 40
20439241 TTTGCAGCAT
* *** * * *
20439251 TGGTGGCTTGTCCATAATACTAACAGCTTGTCTGCAATTC
1 TGGTGGCTTGTCCACAATACTGGTACCTTATCTGCAATTA
* * *
20439291 TGGTGGCTTGTCTACAATATTGGTACCTTGTCTGCAATTA
1 TGGTGGCTTGTCCACAATACTGGTACCTTATCTGCAATTA
* ***
20439331 TGGTGGCTTGTCCACAATACTGTTGGTTTATCTGCAA-TA
1 TGGTGGCTTGTCCACAATACTGGTACCTTATCTGCAATTA
*
20439370 TTGGTGGCTTGTCCATAA-ACTGGT
1 -TGGTGGCTTGTCCACAATACTGGT
20439394 GTGTTATTGG
Statistics
Matches: 85, Mismatches: 17, Indels: 3
0.81 0.16 0.03
Matches are distributed among these distances:
39 7 0.08
40 78 0.92
ACGTcount: A:0.20, C:0.19, G:0.23, T:0.38
Consensus pattern (40 bp):
TGGTGGCTTGTCCACAATACTGGTACCTTATCTGCAATTA
Found at i:20449535 original size:46 final size:46
Alignment explanation
Indices: 20449485--20449660 Score: 216
Period size: 46 Copynumber: 3.8 Consensus size: 46
20449475 TGGTTGAGCA
20449485 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
20449531 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
*
20449576 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
20449624 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
20449661 GCGGGTTACA
Statistics
Matches: 111, Mismatches: 10, Indels: 18
0.80 0.07 0.13
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
45 3 0.03
46 63 0.57
47 29 0.26
48 3 0.03
50 4 0.04
51 2 0.02
ACGTcount: A:0.20, C:0.21, G:0.30, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:20449641 original size:93 final size:93
Alignment explanation
Indices: 20449482--20449653 Score: 317
Period size: 93 Copynumber: 1.8 Consensus size: 93
20449472 GGATGGTTGA
* *
20449482 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
20449547 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
*
20449575 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
20449640 TGAGTCCGAGTTCG
66 TGAGTCCGAGTTCG
20449654 CTTATGGGCG
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 76 1.00
ACGTcount: A:0.21, C:0.22, G:0.30, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:20451528 original size:14 final size:14
Alignment explanation
Indices: 20451509--20451539 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
20451499 ATATGACTCG
20451509 AAAGAAATAGATGT
1 AAAGAAATAGATGT
20451523 AAAGAAATAGATGT
1 AAAGAAATAGATGT
20451537 AAA
1 AAA
20451540 AAAGAGCATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.61, C:0.00, G:0.19, T:0.19
Consensus pattern (14 bp):
AAAGAAATAGATGT
Found at i:20456439 original size:11 final size:10
Alignment explanation
Indices: 20456413--20456437 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
20456403 GATCTCTCAA
20456413 TTTTTAAAAC
1 TTTTTAAAAC
20456423 TTTTTAAAAC
1 TTTTTAAAAC
20456433 TTTTT
1 TTTTT
20456438 TAGATAAAGC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.32, C:0.08, G:0.00, T:0.60
Consensus pattern (10 bp):
TTTTTAAAAC
Found at i:20458853 original size:18 final size:18
Alignment explanation
Indices: 20458830--20458868 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
20458820 TTATAGGTAG
*
20458830 TAATTTTTCAATTGATTT
1 TAATTTTTCAATTGAGTT
*
20458848 TAATTTTTTAATTGAGTT
1 TAATTTTTCAATTGAGTT
20458866 TAA
1 TAA
20458869 AGAGTTTAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.31, C:0.03, G:0.08, T:0.59
Consensus pattern (18 bp):
TAATTTTTCAATTGAGTT
Found at i:20460935 original size:60 final size:61
Alignment explanation
Indices: 20460787--20460960 Score: 224
Period size: 61 Copynumber: 2.9 Consensus size: 61
20460777 CTAGGAAAGA
* * * * *
20460787 GAAAGTCTTTGTGGTGAGTACTGGATATTAAGGAATGCCTTTATGACACAACTCTAGACAG
1 GAAAGCCTTTGTGGCGAGTACTGGATACTAAGAAATGCCTTTATGGCACAACTCTAGACAG
* * * * *
20460848 GAAAGCCTTTGTGGCGAGTAATAGATACTAAGAAATGCCTTTGTGGCATAACTCTGGACA-
1 GAAAGCCTTTGTGGCGAGTACTGGATACTAAGAAATGCCTTTATGGCACAACTCTAGACAG
* * *
20460908 TAAAGCCTTTGTGGCAAGTACTGGATACTAAGCAATGCCTTTATGGCACAACT
1 GAAAGCCTTTGTGGCGAGTACTGGATACTAAGAAATGCCTTTATGGCACAACT
20460961 TCAAGATAAT
Statistics
Matches: 96, Mismatches: 17, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
60 46 0.48
61 50 0.52
ACGTcount: A:0.31, C:0.17, G:0.24, T:0.28
Consensus pattern (61 bp):
GAAAGCCTTTGTGGCGAGTACTGGATACTAAGAAATGCCTTTATGGCACAACTCTAGACAG
Found at i:20461254 original size:10 final size:10
Alignment explanation
Indices: 20461235--20461265 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
20461225 ATTGTCCTCA
20461235 ATGTATAAAC
1 ATGTATAAAC
*
20461245 ATGTACAAAC
1 ATGTATAAAC
20461255 ATGTATAAAC
1 ATGTATAAAC
20461265 A
1 A
20461266 CAAAATAAGC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.52, C:0.13, G:0.10, T:0.26
Consensus pattern (10 bp):
ATGTATAAAC
Found at i:20464258 original size:15 final size:17
Alignment explanation
Indices: 20464238--20464269 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
20464228 GGACATGCCC
20464238 GTGTGTC-CA-GGCCAT
1 GTGTGTCACATGGCCAT
20464253 GTGTGTCACATGGCCAT
1 GTGTGTCACATGGCCAT
20464270 ATCGCTAGGC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 7 0.47
16 2 0.13
17 6 0.40
ACGTcount: A:0.16, C:0.25, G:0.31, T:0.28
Consensus pattern (17 bp):
GTGTGTCACATGGCCAT
Found at i:20469959 original size:15 final size:17
Alignment explanation
Indices: 20469929--20469960 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
20469919 AGTAAACATC
20469929 TTAAATTAATTTTCCTA
1 TTAAATTAATTTTCCTA
20469946 TTAAA-TAA-TTTCCTA
1 TTAAATTAATTTTCCTA
20469961 AACCTAATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 7 0.47
16 3 0.20
17 5 0.33
ACGTcount: A:0.38, C:0.12, G:0.00, T:0.50
Consensus pattern (17 bp):
TTAAATTAATTTTCCTA
Found at i:20472031 original size:28 final size:28
Alignment explanation
Indices: 20472000--20472112 Score: 102
Period size: 29 Copynumber: 3.9 Consensus size: 28
20471990 ATAGAATTTT
* *
20472000 CCACAATGCATTCTTTTAACATAGAT-G
1 CCACAATGCATCCTTTTAACAGAGATAG
*
20472027 ACCACAAAGACATCCTTTTAACAGAGATAG
1 -CCACAATG-CATCCTTTTAACAGAGATAG
* *
20472057 CCACGAATGCATCCTTTTAAAAGAGACAG
1 CCAC-AATGCATCCTTTTAACAGAGATAG
* * * *
20472086 TCACAAAGGCTTCCATTTAACAGAGAT
1 CCAC-AATGCATCCTTTTAACAGAGAT
20472113 CGACACAAAG
Statistics
Matches: 69, Mismatches: 13, Indels: 5
0.79 0.15 0.06
Matches are distributed among these distances:
28 7 0.10
29 58 0.84
30 4 0.06
ACGTcount: A:0.38, C:0.23, G:0.14, T:0.25
Consensus pattern (28 bp):
CCACAATGCATCCTTTTAACAGAGATAG
Found at i:20472119 original size:29 final size:29
Alignment explanation
Indices: 20472012--20472151 Score: 110
Period size: 29 Copynumber: 4.9 Consensus size: 29
20472002 ACAATGCATT
* * *
20472012 CTTTTAACATAGAT-GACCACAAAGACATC
1 CTTTTAACAGAGATCGA-CACAAAGGCTTC
* * * * *
20472041 CTTTTAACAGAGATAGCCACGAATGCATC
1 CTTTTAACAGAGATCGACACAAAGGCTTC
* *
20472070 CTTTTAAAAGAGA-CAGTCACAAAGGCTTC
1 CTTTTAACAGAGATC-GACACAAAGGCTTC
*
20472099 CATTTAACAGAGATCGACACAAAGGCTTC
1 CTTTTAACAGAGATCGACACAAAGGCTTC
* *
20472128 CTTTCAA-AGATATC--CACAAAGGCT
1 CTTTTAACAGAGATCGACACAAAGGCT
20472152 CACTTATATG
Statistics
Matches: 91, Mismatches: 17, Indels: 9
0.78 0.15 0.08
Matches are distributed among these distances:
26 10 0.11
28 6 0.07
29 73 0.80
30 2 0.02
ACGTcount: A:0.38, C:0.24, G:0.15, T:0.24
Consensus pattern (29 bp):
CTTTTAACAGAGATCGACACAAAGGCTTC
Found at i:20494352 original size:12 final size:12
Alignment explanation
Indices: 20494335--20494368 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
20494325 CGGCCCATCC
20494335 ATATTAATTTTT
1 ATATTAATTTTT
*
20494347 ATATTATTTTTT
1 ATATTAATTTTT
20494359 ATA-TAATTTT
1 ATATTAATTTT
20494369 AAAATATATA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
11 6 0.30
12 14 0.70
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (12 bp):
ATATTAATTTTT
Found at i:20494526 original size:30 final size:30
Alignment explanation
Indices: 20494482--20494544 Score: 108
Period size: 30 Copynumber: 2.1 Consensus size: 30
20494472 ACTTAACAAG
*
20494482 CAAATGTCTCTAAAATAATAACAAAATTAA
1 CAAATATCTCTAAAATAATAACAAAATTAA
*
20494512 CAAATATCTTTAAAATAATAACAAAATTAA
1 CAAATATCTCTAAAATAATAACAAAATTAA
20494542 CAA
1 CAA
20494545 TAAAATAAGT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.59, C:0.13, G:0.02, T:0.27
Consensus pattern (30 bp):
CAAATATCTCTAAAATAATAACAAAATTAA
Found at i:20497100 original size:20 final size:19
Alignment explanation
Indices: 20497063--20497101 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
20497053 TATCCGTCTC
* *
20497063 TATATTTTTGTCTATAAAT
1 TATATTTTTATCAATAAAT
20497082 TATATTTTTATCAATTAAAT
1 TATATTTTTATCAA-TAAAT
20497102 ATTAATTAAC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.36, C:0.05, G:0.03, T:0.56
Consensus pattern (19 bp):
TATATTTTTATCAATAAAT
Found at i:20499163 original size:56 final size:56
Alignment explanation
Indices: 20499101--20499212 Score: 179
Period size: 56 Copynumber: 2.0 Consensus size: 56
20499091 GGAGATTTTA
* * * *
20499101 GGAGAGTGGTTTGTAATCATTTAGGTTTAATATTGGGGTTGTAAATATTCATTGGT
1 GGAGAGTGATTTGTAACCATTTAGGTTTAATATTGGGGATGCAAATATTCATTGGT
*
20499157 GGAGAGTGATTTGTAACCATTTGGGTTTAATATTGGGGATGCAAATATTCATTGGT
1 GGAGAGTGATTTGTAACCATTTAGGTTTAATATTGGGGATGCAAATATTCATTGGT
20499213 CAAAGGGTAG
Statistics
Matches: 51, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
56 51 1.00
ACGTcount: A:0.26, C:0.05, G:0.29, T:0.40
Consensus pattern (56 bp):
GGAGAGTGATTTGTAACCATTTAGGTTTAATATTGGGGATGCAAATATTCATTGGT
Found at i:20503375 original size:12 final size:12
Alignment explanation
Indices: 20503358--20503382 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
20503348 ATTGTAAACT
20503358 ACTTATTCTGTA
1 ACTTATTCTGTA
20503370 ACTTATTCTGTA
1 ACTTATTCTGTA
20503382 A
1 A
20503383 ATTACATATC
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:0.28, C:0.16, G:0.08, T:0.48
Consensus pattern (12 bp):
ACTTATTCTGTA
Found at i:20505167 original size:15 final size:15
Alignment explanation
Indices: 20505147--20505175 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
20505137 ATTTTGTGTG
20505147 ATGTTTTATTATAAA
1 ATGTTTTATTATAAA
20505162 ATGTTTTATTATAA
1 ATGTTTTATTATAA
20505176 GATAAATTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.38, C:0.00, G:0.07, T:0.55
Consensus pattern (15 bp):
ATGTTTTATTATAAA
Found at i:20508823 original size:14 final size:14
Alignment explanation
Indices: 20508804--20508833 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
20508794 TGATTGTTTT
20508804 TAATCTAATTTAAC
1 TAATCTAATTTAAC
20508818 TAATCTAATTTAAC
1 TAATCTAATTTAAC
20508832 TA
1 TA
20508834 CGGATGCAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.43, C:0.13, G:0.00, T:0.43
Consensus pattern (14 bp):
TAATCTAATTTAAC
Found at i:20511519 original size:6 final size:6
Alignment explanation
Indices: 20511500--20511539 Score: 62
Period size: 6 Copynumber: 6.7 Consensus size: 6
20511490 ATAAGTCTAA
* *
20511500 AAAAAT AACAAT AAACAT AAAAAT AAAAAT AAAAAT AAAA
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAA
20511540 CAAATAAACT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.80, C:0.05, G:0.00, T:0.15
Consensus pattern (6 bp):
AAAAAT
Found at i:20524345 original size:20 final size:20
Alignment explanation
Indices: 20524316--20524353 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
20524306 TTAAATTAAC
20524316 AACTATTATGCAAATGAAACA
1 AACTATTATGC-AATGAAACA
20524337 AACTA-TATGCAATGAAA
1 AACTATTATGCAATGAAA
20524354 TGGTTTAGCA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 7 0.41
20 5 0.29
21 5 0.29
ACGTcount: A:0.53, C:0.13, G:0.11, T:0.24
Consensus pattern (20 bp):
AACTATTATGCAATGAAACA
Found at i:20532434 original size:19 final size:19
Alignment explanation
Indices: 20532392--20532430 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
20532382 ACAAAAATCA
* *
20532392 TTATTAGGTTTTTATTTTG
1 TTATTAGGTTTTTACTTAG
20532411 TTATTA-GTTTTTACTTAG
1 TTATTAGGTTTTTACTTAG
20532429 TT
1 TT
20532431 TATTTTATGT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 12 0.67
19 6 0.33
ACGTcount: A:0.18, C:0.03, G:0.13, T:0.67
Consensus pattern (19 bp):
TTATTAGGTTTTTACTTAG
Found at i:20542408 original size:19 final size:19
Alignment explanation
Indices: 20542374--20542423 Score: 84
Period size: 19 Copynumber: 2.7 Consensus size: 19
20542364 ATAACAAATA
*
20542374 TAGGAC-TTCAACCATCGG
1 TAGGACATTCAAGCATCGG
20542392 TAGGACATTCAAGCATCGG
1 TAGGACATTCAAGCATCGG
20542411 TAGGACATTCAAG
1 TAGGACATTCAAG
20542424 ACTATCACCT
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
18 6 0.20
19 24 0.80
ACGTcount: A:0.32, C:0.22, G:0.24, T:0.22
Consensus pattern (19 bp):
TAGGACATTCAAGCATCGG
Found at i:20556656 original size:23 final size:23
Alignment explanation
Indices: 20556603--20556657 Score: 74
Period size: 23 Copynumber: 2.4 Consensus size: 23
20556593 AGTCAGAAAA
* * *
20556603 GCTTCCACAGAATAGCCACAAAG
1 GCTTCCATAGAACAACCACAAAG
*
20556626 GCTTCCATAGAACAACCACAAAT
1 GCTTCCATAGAACAACCACAAAG
20556649 GCTTCCATA
1 GCTTCCATA
20556658 AAATCGGTAG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.38, C:0.31, G:0.13, T:0.18
Consensus pattern (23 bp):
GCTTCCATAGAACAACCACAAAG
Found at i:20569340 original size:50 final size:50
Alignment explanation
Indices: 20569236--20569428 Score: 251
Period size: 50 Copynumber: 3.8 Consensus size: 50
20569226 GCTAATAACA
* * * ** *
20569236 TGCCAAAGCAATGTCCCAGACATGGTCTTACATGGGATGTTCTCATATCGG
1 TGCCAATGCCATGTCCTAGACATGGTCTTACATGGGA-CCTCTCATCTCGG
* * **
20569287 TGCCCATGCCATATCCTAGACATGGTCTTACGGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCTAGACATGGTCTTACATGGGACCTCTCATCTCGG
* *
20569337 TGCCAATGCCATGTCCCAGACATGGTCTAACATGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCTAGACATGGTCTTACATGGGACCTCTCATCTCGG
* *
20569387 TGCCAACGCCATGTCCTAGACATGGTCTTACATGAGACCTCT
1 TGCCAATGCCATGTCCTAGACATGGTCTTACATGGGACCTCT
20569429 TTACCCAAAT
Statistics
Matches: 122, Mismatches: 20, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
50 92 0.75
51 30 0.25
ACGTcount: A:0.22, C:0.30, G:0.22, T:0.26
Consensus pattern (50 bp):
TGCCAATGCCATGTCCTAGACATGGTCTTACATGGGACCTCTCATCTCGG
Found at i:20574028 original size:15 final size:15
Alignment explanation
Indices: 20574008--20574038 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
20573998 ATTTTGTGAG
20574008 ACAATGTCAGAATGA
1 ACAATGTCAGAATGA
*
20574023 ACAATGTTAGAATGA
1 ACAATGTCAGAATGA
20574038 A
1 A
20574039 TTCGGGTTCC
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:0.48, C:0.10, G:0.19, T:0.23
Consensus pattern (15 bp):
ACAATGTCAGAATGA
Found at i:20575042 original size:57 final size:57
Alignment explanation
Indices: 20574966--20575079 Score: 167
Period size: 57 Copynumber: 2.0 Consensus size: 57
20574956 GATCCTATCC
* *
20574966 TGATATAGCCCTCCCGAAGAATATGTGTGAAAA-AGATCTAGCCTGGACGGGTGATCT
1 TGATATAGCCCTCCCGAAGAATATGTG-GAAAATAGATCTAGCCCGGACGGGTAATCT
* * *
20575023 TGATATAGCCCTCCTGAAGAATATGTGGAAAATGGATTTAGCCCGGACGGGTAATCT
1 TGATATAGCCCTCCCGAAGAATATGTGGAAAATAGATCTAGCCCGGACGGGTAATCT
20575080 GAATTAGGGT
Statistics
Matches: 51, Mismatches: 5, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
56 5 0.10
57 46 0.90
ACGTcount: A:0.30, C:0.18, G:0.26, T:0.25
Consensus pattern (57 bp):
TGATATAGCCCTCCCGAAGAATATGTGGAAAATAGATCTAGCCCGGACGGGTAATCT
Found at i:20578880 original size:18 final size:16
Alignment explanation
Indices: 20578857--20578892 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 16
20578847 ATAGGGTTTT
20578857 TAAAAGTATATTACAAAA
1 TAAAAGT-TATTA-AAAA
20578875 TAAAAGTTATTAAAAA
1 TAAAAGTTATTAAAAA
20578891 TA
1 TA
20578893 TATTATATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 6 0.33
17 5 0.28
18 7 0.39
ACGTcount: A:0.61, C:0.03, G:0.06, T:0.31
Consensus pattern (16 bp):
TAAAAGTTATTAAAAA
Found at i:20580865 original size:15 final size:16
Alignment explanation
Indices: 20580845--20580875 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
20580835 AATATTGACA
20580845 TGTTTTTATA-ATTGT
1 TGTTTTTATATATTGT
20580860 TGTTTTTATATATTGT
1 TGTTTTTATATATTGT
20580876 GGTGCCTTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.67
16 5 0.33
ACGTcount: A:0.19, C:0.00, G:0.13, T:0.68
Consensus pattern (16 bp):
TGTTTTTATATATTGT
Found at i:20584120 original size:27 final size:26
Alignment explanation
Indices: 20584074--20584135 Score: 67
Period size: 27 Copynumber: 2.3 Consensus size: 26
20584064 AAAATACTAT
20584074 AAAAT-TTAAAAATGATTAAA-TTGTTA
1 AAAATATTAAAAAT-ATTAAACTT-TTA
20584100 CAAAATATTAAAAAT-TCTAAACTTTTA
1 -AAAATATTAAAAATAT-TAAACTTTTA
20584127 AAAATATTA
1 AAAATATTA
20584136 TAACAAAATT
Statistics
Matches: 32, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
26 10 0.31
27 12 0.38
28 10 0.31
ACGTcount: A:0.55, C:0.05, G:0.03, T:0.37
Consensus pattern (26 bp):
AAAATATTAAAAATATTAAACTTTTA
Found at i:20615211 original size:19 final size:20
Alignment explanation
Indices: 20615180--20615217 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
20615170 TTAAATTAAC
20615180 AACTAATATGCAATGAAATA
1 AACTAATATGCAATGAAATA
20615200 AACTAA-ATGCAATGAAAT
1 AACTAATATGCAATGAAAT
20615218 GGTTTAGCAG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 12 0.67
20 6 0.33
ACGTcount: A:0.55, C:0.11, G:0.11, T:0.24
Consensus pattern (20 bp):
AACTAATATGCAATGAAATA
Found at i:20620586 original size:20 final size:20
Alignment explanation
Indices: 20620561--20620601 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
20620551 TCTCGAACTT
20620561 AAGCATTCATAAATTGACTA
1 AAGCATTCATAAATTGACTA
20620581 AAGCATTCATAAATTGACTA
1 AAGCATTCATAAATTGACTA
20620601 A
1 A
20620602 CTAAACCAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.46, C:0.15, G:0.10, T:0.29
Consensus pattern (20 bp):
AAGCATTCATAAATTGACTA
Found at i:20620769 original size:25 final size:25
Alignment explanation
Indices: 20620705--20620769 Score: 62
Period size: 25 Copynumber: 2.6 Consensus size: 25
20620695 AATATACTTT
* * *
20620705 TTATATTTTATATTATTAAATATAT
1 TTATATTTTATTTTATCAAATATAA
20620730 TTATATATATT-TTTTA-CAAATATAA
1 TTATAT-T-TTATTTTATCAAATATAA
20620755 TTATATTTGTATTTT
1 TTATATTT-TATTTT
20620770 TATATGATTT
Statistics
Matches: 33, Mismatches: 3, Indels: 8
0.75 0.07 0.18
Matches are distributed among these distances:
23 1 0.03
24 2 0.06
25 23 0.70
26 5 0.15
27 2 0.06
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.60
Consensus pattern (25 bp):
TTATATTTTATTTTATCAAATATAA
Found at i:20620911 original size:16 final size:16
Alignment explanation
Indices: 20620890--20620927 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
20620880 ATAATTTTAA
*
20620890 CATTTTAA-AAGGCTTG
1 CATTTTAAGAA-GCGTG
20620906 CATTTTAAGAAGCGTG
1 CATTTTAAGAAGCGTG
20620922 CATTTT
1 CATTTT
20620928 TTATTTTCTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 18 0.90
17 2 0.10
ACGTcount: A:0.29, C:0.13, G:0.18, T:0.39
Consensus pattern (16 bp):
CATTTTAAGAAGCGTG
Found at i:20625515 original size:26 final size:27
Alignment explanation
Indices: 20625470--20625526 Score: 71
Period size: 26 Copynumber: 2.1 Consensus size: 27
20625460 TATTTTAAAA
** * *
20625470 TATTTTTAAAATACTTTTTTTATTTTT
1 TATTTTTAAAATACAATTTTTAGTGTT
20625497 TATTTTTAAAATA-AATTTTTAGTGTT
1 TATTTTTAAAATACAATTTTTAGTGTT
20625523 TATT
1 TATT
20625527 AAAAAATGGG
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
26 13 0.50
27 13 0.50
ACGTcount: A:0.30, C:0.02, G:0.04, T:0.65
Consensus pattern (27 bp):
TATTTTTAAAATACAATTTTTAGTGTT
Found at i:20628501 original size:35 final size:35
Alignment explanation
Indices: 20628458--20628527 Score: 140
Period size: 35 Copynumber: 2.0 Consensus size: 35
20628448 ATCCACAAAG
20628458 TTTGATTGTATCCACAAACTAAAGCTTCCAAAATA
1 TTTGATTGTATCCACAAACTAAAGCTTCCAAAATA
20628493 TTTGATTGTATCCACAAACTAAAGCTTCCAAAATA
1 TTTGATTGTATCCACAAACTAAAGCTTCCAAAATA
20628528 AAACAAAGAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.40, C:0.20, G:0.09, T:0.31
Consensus pattern (35 bp):
TTTGATTGTATCCACAAACTAAAGCTTCCAAAATA
Found at i:20634560 original size:24 final size:23
Alignment explanation
Indices: 20634531--20634578 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 23
20634521 GAAAAATATT
* *
20634531 AAATATATATATTTTTTATTTTTA
1 AAATATA-ATAGTTTTTAATTTTA
20634555 AAATATAATAGTTTTTAATTTTA
1 AAATATAATAGTTTTTAATTTTA
20634578 A
1 A
20634579 GTTTATTTAC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 15 0.68
24 7 0.32
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (23 bp):
AAATATAATAGTTTTTAATTTTA
Found at i:20634687 original size:9 final size:9
Alignment explanation
Indices: 20634673--20634700 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
20634663 TTTTGTTACA
20634673 ACAATTAAT
1 ACAATTAAT
20634682 ACAATTAAT
1 ACAATTAAT
20634691 ACAATTAAT
1 ACAATTAAT
20634700 A
1 A
20634701 ATTTGATAAA
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:0.57, C:0.11, G:0.00, T:0.32
Consensus pattern (9 bp):
ACAATTAAT
Found at i:20634722 original size:68 final size:68
Alignment explanation
Indices: 20634643--20634843 Score: 307
Period size: 59 Copynumber: 3.1 Consensus size: 68
20634633 TCAAGTTTGT
*
20634643 TTTACTAATCAAATGTTAGATTTTGTTACAACAATTAATACAATTAATACAATTAATAATTTGAT
1 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATACAATTAATAATTTGAT
20634708 AAA
66 AAA
20634711 TTTACTAATCAAATGTTAGATTTTATT---AC-----A-ACAATTAATACAATTAATAATTTGAT
1 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATACAATTAATAATTTGAT
20634767 AAA
66 AAA
20634770 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATT-A-ACAATTAATAATTTGAT
1 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATACAATTAATAATTTGAT
*
20634833 AAT
66 AAA
20634836 TTTACTAA
1 TTTACTAA
20634844 CAATTAATTT
Statistics
Matches: 122, Mismatches: 2, Indels: 20
0.85 0.01 0.14
Matches are distributed among these distances:
59 56 0.46
60 1 0.01
62 2 0.02
65 2 0.02
66 27 0.22
67 2 0.02
68 32 0.26
ACGTcount: A:0.45, C:0.09, G:0.05, T:0.41
Consensus pattern (68 bp):
TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATACAATTAATAATTTGAT
AAA
Found at i:20634853 original size:16 final size:16
Alignment explanation
Indices: 20634832--20634873 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
20634822 AATAATTTGA
*
20634832 TAATTTTACTAACAAT
1 TAATTTTAATAACAAT
20634848 TAATTTTAATAACAAT
1 TAATTTTAATAACAAT
*
20634864 TAGTTTTAAT
1 TAATTTTAAT
20634874 TTTATTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.43, C:0.07, G:0.02, T:0.48
Consensus pattern (16 bp):
TAATTTTAATAACAAT
Found at i:20634857 original size:22 final size:23
Alignment explanation
Indices: 20634847--20634908 Score: 72
Period size: 23 Copynumber: 2.7 Consensus size: 23
20634837 TTACTAACAA
* * *
20634847 TTAATTTTAAT-AACAATTAGTT
1 TTAATTTTAATAAAAAAATAATT
*
20634869 TTAATTTTATTAAAAAAATAATT
1 TTAATTTTAATAAAAAAATAATT
*
20634892 TTAATTTTAATTAAAAA
1 TTAATTTTAATAAAAAA
20634909 CGGGCCAGGT
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
22 10 0.30
23 23 0.70
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (23 bp):
TTAATTTTAATAAAAAAATAATT
Found at i:20635700 original size:16 final size:16
Alignment explanation
Indices: 20635681--20635714 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
20635671 AAATTAGGAT
20635681 AAAAAAATG-GAAAAAG
1 AAAAAAA-GAGAAAAAG
20635697 AAAAAAAGAGAAAAAG
1 AAAAAAAGAGAAAAAG
20635713 AA
1 AA
20635715 TGATGGTATG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 1 0.06
16 16 0.94
ACGTcount: A:0.79, C:0.00, G:0.18, T:0.03
Consensus pattern (16 bp):
AAAAAAAGAGAAAAAG
Found at i:20644345 original size:40 final size:40
Alignment explanation
Indices: 20644290--20644431 Score: 207
Period size: 40 Copynumber: 3.6 Consensus size: 40
20644280 TATTCGAATG
*
20644290 ATATCCGGGTTAAGTCCCGAAGGCATTTGTGCTAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
* *
20644330 ATATCCGGGCTAAGTCCCGAAGGCTTTTGTGCTATTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
* *
20644370 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG-CT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAG-TGACT
*
20644410 ATATCC-GGCTAAATCCCGAAGG
1 ATATCCGGGCTAAGTCCCGAAGG
20644432 TACTTGGGTT
Statistics
Matches: 92, Mismatches: 9, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
39 14 0.15
40 76 0.83
41 2 0.02
ACGTcount: A:0.23, C:0.23, G:0.27, T:0.27
Consensus pattern (40 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
Found at i:20656809 original size:123 final size:123
Alignment explanation
Indices: 20656535--20656822 Score: 332
Period size: 123 Copynumber: 2.3 Consensus size: 123
20656525 AGTAGCGCCA
* * * * *
20656535 CTAATGCT-GTGGGTTTTAGCAGCATTTTTAAAAAAGCACCGCTAATGCTTGGGATTTTAGTGGC
1 CTAATGCTCG-GGGTTTTACCGGCATTTTTAGAAAAGCGCCGCTAATGCTAGGGATTTTAGTGGC
* * * * * * **
20656599 GTTTTTGATAAAGCGCCGCTAATGCTTGGGGTTTTAGGGGCGTTTATGATTAAGCACCG
65 GTTTTTGATAAAGCGCCACCAATGCTCGGGGCTTTAGCGGCATTTATGAAAAAGCACCG
20656658 CTAATGCTCGGGGTTTTACCGGCATTTTTAGAAAAGCGCCGCTAATGCTCAGGG-TTTTAGTGGC
1 CTAATGCTCGGGGTTTTACCGGCATTTTTAGAAAAGCGCCGCTAATGCT-AGGGATTTTAGTGGC
* *
20656722 GTTTTTAGA-AAAGCGCCACCAATGCTCGGGGCTTTAGCGGCATTTTTTAAAAAGCACCG
65 GTTTTT-GATAAAGCGCCACCAATGCTCGGGGCTTTAGCGGCATTTATGAAAAAGCACCG
* * * * *
20656781 GTAATGCTCGGGTTTTTAGCGTCTTTTTTATG-AAAGCGCCGC
1 CTAATGCTCGGGGTTTTACCGGCATTTTTA-GAAAAGCGCCGC
20656823 AAAAAAATAT
Statistics
Matches: 141, Mismatches: 20, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
123 134 0.95
124 7 0.05
ACGTcount: A:0.22, C:0.18, G:0.27, T:0.33
Consensus pattern (123 bp):
CTAATGCTCGGGGTTTTACCGGCATTTTTAGAAAAGCGCCGCTAATGCTAGGGATTTTAGTGGCG
TTTTTGATAAAGCGCCACCAATGCTCGGGGCTTTAGCGGCATTTATGAAAAAGCACCG
Found at i:20656817 original size:41 final size:40
Alignment explanation
Indices: 20656535--20656822 Score: 229
Period size: 41 Copynumber: 7.0 Consensus size: 40
20656525 AGTAGCGCCA
* * *
20656535 CTAATGCT-GTGGGTTTTAGCAGCATTTTTAAAAAAGCACCG
1 CTAATGCTCG-GGGTTTTAGCGGC-TTTTTTAGAAAGCACCG
* * * * * *
20656576 CTAATGCTTGGGATTTTAGTGGCGTTTTTGATAAAGCGCCG
1 CTAATGCTCGGGGTTTTAGCGGC-TTTTTTAGAAAGCACCG
* * * *
20656617 CTAATGCTTGGGGTTTTAGGGGCGTTTAT-GATTAAGCACCG
1 CTAATGCTCGGGGTTTTAGCGGCTTTTTTAGA--AAGCACCG
* * *
20656658 CTAATGCTCGGGGTTTTACCGGCATTTTTAGAAAAGCGCCG
1 CTAATGCTCGGGGTTTTAGCGGCTTTTTTAG-AAAGCACCG
* * * * *
20656699 CTAATGCTCAGGGTTTTAGTGGCGTTTTTAGAAAAGCGCCA
1 CTAATGCTCGGGGTTTTAGCGGCTTTTTTAG-AAAGCACCG
* * *
20656740 CCAATGCTCGGGGCTTTAGCGGCATTTTTTAAAAAGCACCG
1 CTAATGCTCGGGGTTTTAGCGGC-TTTTTTAGAAAGCACCG
* * * *
20656781 GTAATGCTCGGGTTTTTAGCGTCTTTTTTATGAAAGCGCCG
1 CTAATGCTCGGGGTTTTAGCGGCTTTTTTA-GAAAGCACCG
20656822 C
1 C
20656823 AAAAAAATAT
Statistics
Matches: 199, Mismatches: 41, Indels: 14
0.78 0.16 0.06
Matches are distributed among these distances:
39 1 0.01
40 10 0.05
41 179 0.90
42 8 0.04
43 1 0.01
ACGTcount: A:0.22, C:0.18, G:0.27, T:0.33
Consensus pattern (40 bp):
CTAATGCTCGGGGTTTTAGCGGCTTTTTTAGAAAGCACCG
Found at i:20658599 original size:21 final size:21
Alignment explanation
Indices: 20658573--20658639 Score: 64
Period size: 21 Copynumber: 3.1 Consensus size: 21
20658563 TATTGATTTG
20658573 GGGGTTAGGATTTAAGGTTTA
1 GGGGTTAGGATTTAAGGTTTA
** *
20658594 GGGGTTAGGGGTTAAGATTTAA
1 GGGGTTAGGATTTAAGGTTT-A
**
20658616 GGATTTAGGATTT-AGGATTTA
1 GGGGTTAGGATTTAAGG-TTTA
20658637 GGG
1 GGG
20658640 ATTCTAGGGT
Statistics
Matches: 35, Mismatches: 9, Indels: 4
0.73 0.19 0.08
Matches are distributed among these distances:
21 22 0.63
22 13 0.37
ACGTcount: A:0.25, C:0.00, G:0.39, T:0.36
Consensus pattern (21 bp):
GGGGTTAGGATTTAAGGTTTA
Found at i:20658637 original size:7 final size:7
Alignment explanation
Indices: 20658577--20658638 Score: 54
Period size: 7 Copynumber: 8.7 Consensus size: 7
20658567 GATTTGGGGG
20658577 TTAGGAT
1 TTAGGAT
20658584 TTAAGG-T
1 TT-AGGAT
**
20658591 TTAGGGG
1 TTAGGAT
**
20658598 TTAGGGG
1 TTAGGAT
*
20658605 TTAAGAT
1 TTAGGAT
20658612 TTAAGGAT
1 TT-AGGAT
20658620 TTAGGAT
1 TTAGGAT
20658627 TTAGGAT
1 TTAGGAT
20658634 TTAGG
1 TTAGG
20658639 GATTCTAGGG
Statistics
Matches: 47, Mismatches: 5, Indels: 6
0.81 0.09 0.10
Matches are distributed among these distances:
6 3 0.06
7 35 0.74
8 9 0.19
ACGTcount: A:0.27, C:0.00, G:0.34, T:0.39
Consensus pattern (7 bp):
TTAGGAT
Found at i:20658641 original size:22 final size:22
Alignment explanation
Indices: 20658577--20658647 Score: 65
Period size: 22 Copynumber: 3.2 Consensus size: 22
20658567 GATTTGGGGG
*
20658577 TTAGGATTTAAGG-TTTAGGG-G
1 TTAGGATTT-AGGATTTAGGGAT
** * *
20658598 TTAGGGGTTAAGATTTAAGGAT
1 TTAGGATTTAGGATTTAGGGAT
20658620 TTAGGATTTAGGATTTAGGGAT
1 TTAGGATTTAGGATTTAGGGAT
20658642 TCTAGG
1 T-TAGG
20658648 GTCAGATCAG
Statistics
Matches: 38, Mismatches: 9, Indels: 4
0.75 0.18 0.08
Matches are distributed among these distances:
20 2 0.05
21 13 0.34
22 19 0.50
23 4 0.11
ACGTcount: A:0.27, C:0.01, G:0.34, T:0.38
Consensus pattern (22 bp):
TTAGGATTTAGGATTTAGGGAT
Found at i:20665885 original size:50 final size:50
Alignment explanation
Indices: 20665821--20665918 Score: 160
Period size: 50 Copynumber: 2.0 Consensus size: 50
20665811 ATTTTAATCC
* *
20665821 TTTTCATAATTTCATGACATAGTTCATTCGAATACATACCTTTACTTTCT
1 TTTTCATAACTTCATGACATAGTTCATTCGAACACATACCTTTACTTTCT
* *
20665871 TTTTTATAACTTCATGACATAGTTCATTCGAACACATACCTTTCCTTT
1 TTTTCATAACTTCATGACATAGTTCATTCGAACACATACCTTTACTTT
20665919 TCATGCCCGT
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
50 44 1.00
ACGTcount: A:0.28, C:0.21, G:0.06, T:0.45
Consensus pattern (50 bp):
TTTTCATAACTTCATGACATAGTTCATTCGAACACATACCTTTACTTTCT
Found at i:20666346 original size:45 final size:45
Alignment explanation
Indices: 20666299--20666469 Score: 236
Period size: 45 Copynumber: 3.8 Consensus size: 45
20666289 CCTTTGATTC
* * * * * *
20666299 GTGATGCCATAGCATCTTTCA-ACTATGGACTTACTCAATAGAATC
1 GTGATGCCATAACGTCTTTCAGTC-ATGGTCTTACTCGATAGAATA
* *
20666344 GTGATGTCATAACGTCTTTCAGTCATGGTCTTATTCGATAGAATA
1 GTGATGCCATAACGTCTTTCAGTCATGGTCTTACTCGATAGAATA
*
20666389 GTGATGCCATAACGTTTTTCAGTCATGGTCTTACTCGATAGAATA
1 GTGATGCCATAACGTCTTTCAGTCATGGTCTTACTCGATAGAATA
*
20666434 GTGATGCCATAACGTCTTTCAGTCATAGTCTTACTC
1 GTGATGCCATAACGTCTTTCAGTCATGGTCTTACTC
20666470 ATTTCTAGTA
Statistics
Matches: 112, Mismatches: 13, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
45 111 0.99
46 1 0.01
ACGTcount: A:0.27, C:0.20, G:0.18, T:0.35
Consensus pattern (45 bp):
GTGATGCCATAACGTCTTTCAGTCATGGTCTTACTCGATAGAATA
Found at i:20666507 original size:90 final size:90
Alignment explanation
Indices: 20666299--20666511 Score: 243
Period size: 90 Copynumber: 2.4 Consensus size: 90
20666289 CCTTTGATTC
* * * *
20666299 GTGATGCCATAGCATCTTTCAACTATGGACTTACTCAATAGAATCGTGATGTCATAACGTCTTTC
1 GTGATGCCATAGCGTCTTTCAACTATGGTCTTACTCAATAGAATAGTGATGCCATAACGTCTTTC
* *
20666364 AGTCATGGTCTTATTCGATAGAATA
66 AGTCATAGTCTTACTCGATAGAATA
* * * *
20666389 GTGATGCCATAACGTTTTTC-AGTCATGGTCTTACTCGATAGAATAGTGATGCCATAACGTCTTT
1 GTGATGCCATAGCGTCTTTCAACT-ATGGTCTTACTCAATAGAATAGTGATGCCATAACGTCTTT
***
20666453 CAGTCATAGTCTTACTC-AT-TTCTA
65 CAGTCATAGTCTTACTCGATAGAATA
* *
20666477 GTATGGTGCCATAGTGTCTTTCAACTATGGTCTTA
1 G--TGATGCCATAGCGTCTTTCAACTATGGTCTTA
20666512 ATCATTTTCC
Statistics
Matches: 101, Mismatches: 18, Indels: 8
0.80 0.14 0.06
Matches are distributed among these distances:
88 3 0.03
89 4 0.04
90 92 0.91
91 2 0.02
ACGTcount: A:0.26, C:0.19, G:0.18, T:0.37
Consensus pattern (90 bp):
GTGATGCCATAGCGTCTTTCAACTATGGTCTTACTCAATAGAATAGTGATGCCATAACGTCTTTC
AGTCATAGTCTTACTCGATAGAATA
Found at i:20667983 original size:14 final size:14
Alignment explanation
Indices: 20667964--20667990 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
20667954 TTAGAAATCC
20667964 TTTCTTTTAAAAAA
1 TTTCTTTTAAAAAA
20667978 TTTCTTTTAAAAA
1 TTTCTTTTAAAAA
20667991 GAACTTGCAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.41, C:0.07, G:0.00, T:0.52
Consensus pattern (14 bp):
TTTCTTTTAAAAAA
Found at i:20669053 original size:27 final size:29
Alignment explanation
Indices: 20669023--20669078 Score: 89
Period size: 27 Copynumber: 2.0 Consensus size: 29
20669013 CACCACACAG
20669023 ACTAGTGAAGCCC-AGCTCGCCAA-ACAT
1 ACTAGTGAAGCCCTAGCTCGCCAATACAT
*
20669050 ACTAGTGAAGCCCTAGCTCGTCAATACAT
1 ACTAGTGAAGCCCTAGCTCGCCAATACAT
20669079 TAGCGAACCT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
27 13 0.50
28 9 0.35
29 4 0.15
ACGTcount: A:0.32, C:0.30, G:0.18, T:0.20
Consensus pattern (29 bp):
ACTAGTGAAGCCCTAGCTCGCCAATACAT
Found at i:20670273 original size:12 final size:12
Alignment explanation
Indices: 20670256--20670290 Score: 70
Period size: 12 Copynumber: 2.9 Consensus size: 12
20670246 TTTCTTATTT
20670256 TCATTTCCATTA
1 TCATTTCCATTA
20670268 TCATTTCCATTA
1 TCATTTCCATTA
20670280 TCATTTCCATT
1 TCATTTCCATT
20670291 TTTTGAGAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.23, C:0.26, G:0.00, T:0.51
Consensus pattern (12 bp):
TCATTTCCATTA
Found at i:20679531 original size:50 final size:49
Alignment explanation
Indices: 20679467--20679608 Score: 167
Period size: 50 Copynumber: 2.8 Consensus size: 49
20679457 TTGTACTACC
* * *
20679467 AATGCCATATCCCAGATATAGTCTTACATGGGAGTTCTCATATCGGTGCA
1 AATGCCATGTCCCAGACATAGTCTTACGTGGGA-TTCTCATATCGGTGCA
* * * * *
20679517 CATGCCATGTCCCAGAGATGGTCTTACGGGGGATCTCTCATCTCGGTGCA
1 AATGCCATGTCCCAGACATAGTCTTACGTGGGAT-TCTCATATCGGTGCA
* *
20679567 AACGCCATGTCCCAGACATAGTCTTACGTGGGACCTCTCATA
1 AATGCCATGTCCCAGACATAGTCTTACGTGGGA-TTCTCATA
20679609 ATCTCAATAA
Statistics
Matches: 76, Mismatches: 14, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
49 1 0.01
50 75 0.99
ACGTcount: A:0.24, C:0.27, G:0.23, T:0.27
Consensus pattern (49 bp):
AATGCCATGTCCCAGACATAGTCTTACGTGGGATTCTCATATCGGTGCA
Found at i:20681493 original size:24 final size:24
Alignment explanation
Indices: 20681461--20681508 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
20681451 CGTATAATTT
20681461 AGCAATTGAATGCGAATTAGGCTG
1 AGCAATTGAATGCGAATTAGGCTG
20681485 AGCAATTGAATGCGAATTAGGCTG
1 AGCAATTGAATGCGAATTAGGCTG
20681509 TGTAGTGTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.33, C:0.12, G:0.29, T:0.25
Consensus pattern (24 bp):
AGCAATTGAATGCGAATTAGGCTG
Found at i:20694283 original size:24 final size:24
Alignment explanation
Indices: 20694251--20694296 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
20694241 GAATCAGACA
* *
20694251 TAAAAGTAGATGTAGCCACTAATG
1 TAAAAGTAGAAGTAACCACTAATG
20694275 TAAAAGTAGAAGTAACCACTAA
1 TAAAAGTAGAAGTAACCACTAA
20694297 CATAGAGCTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.48, C:0.13, G:0.17, T:0.22
Consensus pattern (24 bp):
TAAAAGTAGAAGTAACCACTAATG
Found at i:20713358 original size:41 final size:42
Alignment explanation
Indices: 20713305--20713406 Score: 118
Period size: 41 Copynumber: 2.5 Consensus size: 42
20713295 CTTTTACATA
* *** *
20713305 GCCTTT-TTGCATTCTGTTAACCTTTGTGGTACTTTGGTATG
1 GCCTTTGTGGCATTCTGTTAACCTCCATGGTACTTTGATATG
* * *
20713346 G-CTTTGTGGCATTCTATTAGCCTCCATGGTATTTTGATATG
1 GCCTTTGTGGCATTCTGTTAACCTCCATGGTACTTTGATATG
20713387 GCCTTTGTGGCATTCTGTTA
1 GCCTTTGTGGCATTCTGTTA
20713407 GCATCTGTGT
Statistics
Matches: 50, Mismatches: 9, Indels: 3
0.81 0.15 0.05
Matches are distributed among these distances:
40 4 0.08
41 29 0.58
42 17 0.34
ACGTcount: A:0.14, C:0.18, G:0.23, T:0.46
Consensus pattern (42 bp):
GCCTTTGTGGCATTCTGTTAACCTCCATGGTACTTTGATATG
Found at i:20713426 original size:42 final size:42
Alignment explanation
Indices: 20713342--20713441 Score: 112
Period size: 42 Copynumber: 2.4 Consensus size: 42
20713332 GGTACTTTGG
* **
20713342 TATGG-CTTTGTGGCATTCTATTAGCCTCCATGGTATTTTGA
1 TATGGCCTTTGTGGCATTCTATTAGCATCCATGGTATCCTGA
* ** *
20713383 TATGGCCTTTGTGGCATTCTGTTAGCATCTGTGTTATCCTGA
1 TATGGCCTTTGTGGCATTCTATTAGCATCCATGGTATCCTGA
* *
20713425 TATGGCATTTATGGCAT
1 TATGGCCTTTGTGGCAT
20713442 CCTTTATAAA
Statistics
Matches: 49, Mismatches: 9, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
41 5 0.10
42 44 0.90
ACGTcount: A:0.17, C:0.17, G:0.23, T:0.43
Consensus pattern (42 bp):
TATGGCCTTTGTGGCATTCTATTAGCATCCATGGTATCCTGA
Found at i:20715742 original size:22 final size:22
Alignment explanation
Indices: 20715696--20715742 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
20715686 TGAAAAGTAC
* * *
20715696 ATGTGGCATTCTTCCCTGATCT
1 ATGTGGCATGCTTCCCTCATAT
*
20715718 ATGTGGCATGCTTCTCTCATAT
1 ATGTGGCATGCTTCCCTCATAT
20715740 ATG
1 ATG
20715743 CATGAACATA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.17, C:0.23, G:0.19, T:0.40
Consensus pattern (22 bp):
ATGTGGCATGCTTCCCTCATAT
Found at i:20724615 original size:28 final size:28
Alignment explanation
Indices: 20724584--20724639 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
20724574 TTATTTTGAT
20724584 GAAGTGATTAAAAACTAAAATTTAACTA
1 GAAGTGATTAAAAACTAAAATTTAACTA
20724612 GAAGTGATTAAAAACTAAAATTTAACTA
1 GAAGTGATTAAAAACTAAAATTTAACTA
20724640 AGTAAAATAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.54, C:0.07, G:0.11, T:0.29
Consensus pattern (28 bp):
GAAGTGATTAAAAACTAAAATTTAACTA
Found at i:20725851 original size:23 final size:23
Alignment explanation
Indices: 20725807--20725852 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
20725797 TTTAAGCTGA
*
20725807 TTGGGTCAGCATGTTGGACAGTT
1 TTGGGTCAGCATGTTGCACAGTT
*
20725830 TTGGGT-AGCATGTGTGCTCAGTT
1 TTGGGTCAGCATGT-TGCACAGTT
20725853 GGATCAACCT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 7 0.35
23 13 0.65
ACGTcount: A:0.15, C:0.13, G:0.35, T:0.37
Consensus pattern (23 bp):
TTGGGTCAGCATGTTGCACAGTT
Found at i:20726129 original size:22 final size:22
Alignment explanation
Indices: 20726104--20726147 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
20726094 AAAGTAAATC
* *
20726104 AAAATTTATGAAAATTTAATAT
1 AAAATTAATGAAAATTCAATAT
*
20726126 AAAATTAATTAAAATTCAATAT
1 AAAATTAATGAAAATTCAATAT
20726148 GTTCATAATT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (22 bp):
AAAATTAATGAAAATTCAATAT
Found at i:20729903 original size:29 final size:30
Alignment explanation
Indices: 20729845--20729903 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
20729835 TGCCTTTAAA
* *
20729845 AATATTTACAAAAAGAGACAACTAAGTTTT
1 AATATTTACAAAAAGAGACAACAAAATTTT
20729875 AATATTTACAAAAAGAG-CAACAAAATTTT
1 AATATTTACAAAAAGAGACAACAAAATTTT
20729904 GTAAATAATT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 10 0.37
30 17 0.63
ACGTcount: A:0.53, C:0.10, G:0.08, T:0.29
Consensus pattern (30 bp):
AATATTTACAAAAAGAGACAACAAAATTTT
Found at i:20739162 original size:49 final size:49
Alignment explanation
Indices: 20739069--20739164 Score: 115
Period size: 49 Copynumber: 2.0 Consensus size: 49
20739059 TACGGAGGAA
* * ** *
20739069 GTATCTGGCAGTGTATCTGCAATTTCTGTTGGCTTTACCCCAATATTTT
1 GTATCTAGCAGTATATCTGCAATTTCTGTTGGCTCGACCACAATATTTT
20739118 GTATCTAGCAGTATATCTGC-ATTATCTAG-TGGCTCGACCACAATATT
1 GTATCTAGCAGTATATCTGCAATT-TCT-GTTGGCTCGACCACAATATT
20739165 CCGCTTCTGG
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
48 3 0.08
49 36 0.90
50 1 0.03
ACGTcount: A:0.23, C:0.21, G:0.18, T:0.39
Consensus pattern (49 bp):
GTATCTAGCAGTATATCTGCAATTTCTGTTGGCTCGACCACAATATTTT
Found at i:20761031 original size:36 final size:36
Alignment explanation
Indices: 20760991--20761089 Score: 135
Period size: 36 Copynumber: 2.8 Consensus size: 36
20760981 TTTTTAGTGG
* * *
20760991 CATGCTTTACACGAAAATCAGAATATTAGAATATGA
1 CATGCTTAACATGAAAATCAGAATATCAGAATATGA
* * *
20761027 CATGCTTAACATGTAAATTAGAATATCAGAATATGG
1 CATGCTTAACATGAAAATCAGAATATCAGAATATGA
*
20761063 CATGCTTAACATGCAAATCAGAATATC
1 CATGCTTAACATGAAAATCAGAATATC
20761090 GATAATCATA
Statistics
Matches: 55, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
36 55 1.00
ACGTcount: A:0.42, C:0.15, G:0.14, T:0.28
Consensus pattern (36 bp):
CATGCTTAACATGAAAATCAGAATATCAGAATATGA
Found at i:20762156 original size:17 final size:18
Alignment explanation
Indices: 20762136--20762173 Score: 69
Period size: 17 Copynumber: 2.2 Consensus size: 18
20762126 CAATATGTGG
20762136 AATTAATGAATACTT-GA
1 AATTAATGAATACTTGGA
20762153 AATTAATGAATACTTGGA
1 AATTAATGAATACTTGGA
20762171 AAT
1 AAT
20762174 GTTATGGCAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 15 0.75
18 5 0.25
ACGTcount: A:0.47, C:0.05, G:0.13, T:0.34
Consensus pattern (18 bp):
AATTAATGAATACTTGGA
Found at i:20763108 original size:43 final size:43
Alignment explanation
Indices: 20763060--20763144 Score: 118
Period size: 43 Copynumber: 2.0 Consensus size: 43
20763050 AAGGTAAATC
* * * *
20763060 CAACAACCC-ATGTTTATCTTCTTCTCTTTTTAAATTCTTTTTT
1 CAACAACCCAAT-ATTATATTCTCCTCTTTTTAAATTATTTTTT
20763103 CAACAACCCAATATTATATTCTCCTCTTTTTAAATTATTTTT
1 CAACAACCCAATATTATATTCTCCTCTTTTTAAATTATTTTT
20763145 ATAGGATAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
43 35 0.95
44 2 0.05
ACGTcount: A:0.26, C:0.22, G:0.01, T:0.51
Consensus pattern (43 bp):
CAACAACCCAATATTATATTCTCCTCTTTTTAAATTATTTTTT
Found at i:20764315 original size:27 final size:27
Alignment explanation
Indices: 20764273--20764428 Score: 125
Period size: 27 Copynumber: 5.8 Consensus size: 27
20764263 ATTCAAAGTG
*
20764273 CGCCACAAAGCCTATTCTTTTAGAATA
1 CGCCACAAAGGCTATTCTTTTAGAATA
* * *
20764300 CGCCACAAAGGTTATTCTTTCATAATA
1 CGCCACAAAGGCTATTCTTTTAGAATA
* * ** * *
20764327 CGGCATAAAGTTTATTCTTTTAGACTT
1 CGCCACAAAGGCTATTCTTTTAGAATA
** *
20764354 TACCACAAAGGCTATTATTTT-GTAATA
1 CGCCACAAAGGCTATTCTTTTAG-AATA
* * *
20764381 CACCACAAAGGCTATTCTTTTAGACTT
1 CGCCACAAAGGCTATTCTTTTAGAATA
* * *
20764408 CGTCACAAAGGTTATCCTTTT
1 CGCCACAAAGGCTATTCTTTT
20764429 CCGATGTGTT
Statistics
Matches: 99, Mismatches: 28, Indels: 4
0.76 0.21 0.03
Matches are distributed among these distances:
26 1 0.01
27 97 0.98
28 1 0.01
ACGTcount: A:0.31, C:0.21, G:0.12, T:0.36
Consensus pattern (27 bp):
CGCCACAAAGGCTATTCTTTTAGAATA
Found at i:20764415 original size:54 final size:54
Alignment explanation
Indices: 20764275--20764418 Score: 153
Period size: 54 Copynumber: 2.7 Consensus size: 54
20764265 TCAAAGTGCG
* * * * *
20764275 CCACAAAGCCTATTCTTTTAGAATACGCCACAAAGGTTATTCTTTCATAATACG
1 CCACAAAGCCTATTCTTTTAGACTTCGCCACAAAGGCTATTATTTCATAATACA
* * ** ** **
20764329 GCATAAAGTTTATTCTTTTAGACTTTACCACAAAGGCTATTATTTTGTAATACA
1 CCACAAAGCCTATTCTTTTAGACTTCGCCACAAAGGCTATTATTTCATAATACA
* *
20764383 CCACAAAGGCTATTCTTTTAGACTTCGTCACAAAGG
1 CCACAAAGCCTATTCTTTTAGACTTCGCCACAAAGG
20764419 TTATCCTTTT
Statistics
Matches: 70, Mismatches: 20, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
54 70 1.00
ACGTcount: A:0.33, C:0.21, G:0.12, T:0.34
Consensus pattern (54 bp):
CCACAAAGCCTATTCTTTTAGACTTCGCCACAAAGGCTATTATTTCATAATACA
Found at i:20764428 original size:81 final size:81
Alignment explanation
Indices: 20764275--20764428 Score: 184
Period size: 81 Copynumber: 1.9 Consensus size: 81
20764265 TCAAAGTGCG
* * * * * *
20764275 CCACAAAGCCTATTCTTTTAGAATACGCCACAAAGGTTATTCTTTCATAATACGGCATAAAGTTT
1 CCACAAAGCCTATTATTTTAGAATACACCACAAAGGCTATTCTTTCAGAATACGGCACAAAGGTT
*
20764340 ATTCTTTTAGACTTTA
66 ATCCTTTTAGACTTTA
* * * * *
20764356 CCACAAAGGCTATTATTTT-GTAATACACCACAAAGGCTATTCTTTTAGACTTCGTCACAAAGGT
1 CCACAAAGCCTATTATTTTAG-AATACACCACAAAGGCTATTCTTTCAGAATACGGCACAAAGGT
20764420 TATCCTTTT
65 TATCCTTTT
20764429 CCGATGTGTT
Statistics
Matches: 60, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
80 1 0.02
81 59 0.98
ACGTcount: A:0.31, C:0.21, G:0.12, T:0.36
Consensus pattern (81 bp):
CCACAAAGCCTATTATTTTAGAATACACCACAAAGGCTATTCTTTCAGAATACGGCACAAAGGTT
ATCCTTTTAGACTTTA
Found at i:20764757 original size:18 final size:18
Alignment explanation
Indices: 20764736--20764770 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
20764726 TACTCACATC
20764736 ACATAACATAC-TATCCAG
1 ACAT-ACATACATATCCAG
20764754 ACATACATACATATCCA
1 ACATACATACATATCCA
20764771 TATTTCATCA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.46, C:0.29, G:0.03, T:0.23
Consensus pattern (18 bp):
ACATACATACATATCCAG
Found at i:20769122 original size:25 final size:25
Alignment explanation
Indices: 20769088--20769137 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
20769078 CATCGACAAA
20769088 CTCGATGTTTAACTCAAGTATAGGT
1 CTCGATGTTTAACTCAAGTATAGGT
20769113 CTCGATGTTTAACTCAAGTATAGGT
1 CTCGATGTTTAACTCAAGTATAGGT
20769138 GATCCAATAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.28, C:0.16, G:0.20, T:0.36
Consensus pattern (25 bp):
CTCGATGTTTAACTCAAGTATAGGT
Found at i:20773584 original size:31 final size:31
Alignment explanation
Indices: 20773549--20773610 Score: 99
Period size: 31 Copynumber: 2.0 Consensus size: 31
20773539 ACAGACCAGG
20773549 GACTTAAAT-AAAATTTTTTGAATAGTTCAGT
1 GACTTAAATGAAAA-TTTTTGAATAGTTCAGT
*
20773580 GACTTAAATGGAAATTTTTGAATAGTTCAGT
1 GACTTAAATGAAAATTTTTGAATAGTTCAGT
20773611 AACCAAATCG
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
31 26 0.90
32 3 0.10
ACGTcount: A:0.37, C:0.06, G:0.16, T:0.40
Consensus pattern (31 bp):
GACTTAAATGAAAATTTTTGAATAGTTCAGT
Found at i:20783829 original size:11 final size:13
Alignment explanation
Indices: 20783804--20783835 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
20783794 TAGGTTATTA
20783804 ATATTTTAAATTG
1 ATATTTTAAATTG
20783817 AT-TTTTAAA-TG
1 ATATTTTAAATTG
20783828 ATATTTTA
1 ATATTTTA
20783836 TTATTTTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 4 0.22
12 12 0.67
13 2 0.11
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.56
Consensus pattern (13 bp):
ATATTTTAAATTG
Found at i:20786644 original size:25 final size:25
Alignment explanation
Indices: 20786588--20786685 Score: 78
Period size: 25 Copynumber: 3.9 Consensus size: 25
20786578 GGACCCACCA
*
20786588 CAGCTCGTATGAGCTTACCAATT--T
1 CAGCTCGTA-GAGCTTACCGATTGCT
* *
20786612 ACAACTCGTGAGAGTTTACCGATT-CT
1 -CAGCTCGT-AGAGCTTACCGATTGCT
*
20786638 CAGCTCGTATGAGCTTACCG-TTGTT
1 CAGCTCGTA-GAGCTTACCGATTGCT
*
20786663 CAGCTCGAAAGAGCTTACCGATT
1 CAGCTCG-TAGAGCTTACCGATT
20786686 ATGGCTCGTA
Statistics
Matches: 60, Mismatches: 7, Indels: 11
0.77 0.09 0.14
Matches are distributed among these distances:
24 3 0.05
25 52 0.87
26 5 0.08
ACGTcount: A:0.24, C:0.24, G:0.20, T:0.31
Consensus pattern (25 bp):
CAGCTCGTAGAGCTTACCGATTGCT
Found at i:20786681 original size:50 final size:50
Alignment explanation
Indices: 20786588--20786685 Score: 126
Period size: 50 Copynumber: 2.0 Consensus size: 50
20786578 GGACCCACCA
** *
20786588 CAGCTCGTATGAGCTTACCAATTTACAACTCGTGAGAGTTTACCGATTCT
1 CAGCTCGTATGAGCTTACCAATTTACAACTCGAAAGAGCTTACCGATTCT
* * *
20786638 CAGCTCGTATGAGCTTACC-GTTGTTCAGCTCGAAAGAGCTTACCGATT
1 CAGCTCGTATGAGCTTACCAATT-TACAACTCGAAAGAGCTTACCGATT
20786686 ATGGCTCGTA
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
49 2 0.05
50 39 0.95
ACGTcount: A:0.24, C:0.24, G:0.20, T:0.31
Consensus pattern (50 bp):
CAGCTCGTATGAGCTTACCAATTTACAACTCGAAAGAGCTTACCGATTCT
Found at i:20800704 original size:25 final size:25
Alignment explanation
Indices: 20800653--20800706 Score: 74
Period size: 25 Copynumber: 2.2 Consensus size: 25
20800643 AGTTTCTAAA
* *
20800653 AATTTAATTAATATAAAATATTAAT
1 AATTTAATAAATATAAAATAGTAAT
20800678 AATTTAATAAATATAAAA-AGTAGAT
1 AATTTAATAAATATAAAATAGTA-AT
20800703 AATT
1 AATT
20800707 AAATTAAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
24 3 0.12
25 23 0.88
ACGTcount: A:0.57, C:0.00, G:0.04, T:0.39
Consensus pattern (25 bp):
AATTTAATAAATATAAAATAGTAAT
Found at i:20801422 original size:30 final size:30
Alignment explanation
Indices: 20801362--20801423 Score: 81
Period size: 30 Copynumber: 2.1 Consensus size: 30
20801352 GCTTTTTAAA
* * *
20801362 AATATTTACAAAAAGAGGCATCTAATTTTT
1 AATATTTACAAAAAGAGGCACCAAACTTTT
20801392 AATATTTACAAAAAGA-GCAACCAAACTTTT
1 AATATTTACAAAAAGAGGC-ACCAAACTTTT
20801422 AA
1 AA
20801424 AAATAATTCA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
29 2 0.07
30 26 0.93
ACGTcount: A:0.48, C:0.13, G:0.08, T:0.31
Consensus pattern (30 bp):
AATATTTACAAAAAGAGGCACCAAACTTTT
Found at i:20803136 original size:27 final size:27
Alignment explanation
Indices: 20803114--20803315 Score: 253
Period size: 27 Copynumber: 7.5 Consensus size: 27
20803104 AGGGGTATAA
*
20803114 CAGTCATTTTACTCTATAAGGGTATTT
1 CAGTCATTTTACCCTATAAGGGTATTT
**
20803141 CAGTCATTTTACCCTATGGGGGTATTT
1 CAGTCATTTTACCCTATAAGGGTATTT
* * * *
20803168 CGGTCATTCTACCCTATGAGGTTATTT
1 CAGTCATTTTACCCTATAAGGGTATTT
**
20803195 CAGTCATTTTACCCTATGGGGGTATTT
1 CAGTCATTTTACCCTATAAGGGTATTT
*
20803222 C-GTTCATTTTACCTTATAAGGGTATTT
1 CAG-TCATTTTACCCTATAAGGGTATTT
*
20803249 CAGTCATTTTACCCTATAGGGGTATTT
1 CAGTCATTTTACCCTATAAGGGTATTT
**
20803276 CAGTCATTTTACGTTATAAGGGTATTT
1 CAGTCATTTTACCCTATAAGGGTATTT
**
20803303 TGGTCATTTTACC
1 CAGTCATTTTACC
20803316 TATTTTGGAT
Statistics
Matches: 151, Mismatches: 22, Indels: 4
0.85 0.12 0.02
Matches are distributed among these distances:
26 1 0.01
27 149 0.99
28 1 0.01
ACGTcount: A:0.21, C:0.17, G:0.18, T:0.43
Consensus pattern (27 bp):
CAGTCATTTTACCCTATAAGGGTATTT
Found at i:20803149 original size:54 final size:53
Alignment explanation
Indices: 20803087--20803315 Score: 259
Period size: 54 Copynumber: 4.2 Consensus size: 53
20803077 AATGCCATAA
* **
20803087 CAGTCATTTCATCTCCTA-GGGGTATAACAGTCATTTTACTCTATAAGGGTATTT
1 CAGTCATTTTA-C-CCTAGGGGGTATTTCAGTCATTTTACTCTATAAGGGTATTT
* * * * *
20803141 CAGTCATTTTACCCTATGGGGGTATTTCGGTCATTCTACCCTATGAGGTTATTT
1 CAGTCATTTTACCCTA-GGGGGTATTTCAGTCATTTTACTCTATAAGGGTATTT
20803195 CAGTCATTTTACCCTATGGGGGTATTTC-GTTCATTTTAC-CTTATAAGGGTATTT
1 CAGTCATTTTACCCTA-GGGGGTATTTCAG-TCATTTTACTC-TATAAGGGTATTT
*
20803249 CAGTCATTTTACCCTATAGGGGTATTTCAGTCATTTTACGT-TATAAGGGTATTT
1 CAGTCATTTTACCCTA-GGGGGTATTTCAGTCATTTTAC-TCTATAAGGGTATTT
**
20803303 TGGTCATTTTACC
1 CAGTCATTTTACC
20803316 TATTTTGGAT
Statistics
Matches: 154, Mismatches: 14, Indels: 14
0.85 0.08 0.08
Matches are distributed among these distances:
52 4 0.03
53 3 0.02
54 146 0.95
55 1 0.01
ACGTcount: A:0.22, C:0.18, G:0.18, T:0.42
Consensus pattern (53 bp):
CAGTCATTTTACCCTAGGGGGTATTTCAGTCATTTTACTCTATAAGGGTATTT
Found at i:20806882 original size:27 final size:27
Alignment explanation
Indices: 20806840--20806893 Score: 74
Period size: 26 Copynumber: 2.0 Consensus size: 27
20806830 ATGATAAAGA
* *
20806840 TAATGATATATAATAATTTTAAAATAAT
1 TAATGATATAAAATAA-TTAAAAATAAT
20806868 TAATG-TATAAAATAATTAAAAATAAT
1 TAATGATATAAAATAATTAAAAATAAT
20806894 ACACGAAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 10 0.42
27 9 0.38
28 5 0.21
ACGTcount: A:0.57, C:0.00, G:0.04, T:0.39
Consensus pattern (27 bp):
TAATGATATAAAATAATTAAAAATAAT
Found at i:20814015 original size:43 final size:43
Alignment explanation
Indices: 20813941--20814100 Score: 225
Period size: 43 Copynumber: 3.7 Consensus size: 43
20813931 TGTGTTTCCA
* * * *
20813941 GTAAGACCATATCTGGGATA-TGGCATCGATATGAGACTTCGT
1 GTAAGACCATGTCTGGGACATTGGCATCGATATGTGATTTCGT
* *
20813983 GTAAAACCATGTCTGGGACATTGGCATCGATATGTGATTTCAT
1 GTAAGACCATGTCTGGGACATTGGCATCGATATGTGATTTCGT
20814026 GTAAGACCATGTCTGGGACATTGGCATCGATATGTGATTTCGT
1 GTAAGACCATGTCTGGGACATTGGCATCGATATGTGATTTCGT
* *
20814069 GTAAGATCATGGCTGGG-CTATTGGCATCGATA
1 GTAAGACCATGTCTGGGAC-ATTGGCATCGATA
20814101 CAAGATTACA
Statistics
Matches: 106, Mismatches: 10, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
42 18 0.17
43 88 0.83
ACGTcount: A:0.26, C:0.16, G:0.27, T:0.31
Consensus pattern (43 bp):
GTAAGACCATGTCTGGGACATTGGCATCGATATGTGATTTCGT
Found at i:20814085 original size:86 final size:85
Alignment explanation
Indices: 20813941--20814134 Score: 246
Period size: 86 Copynumber: 2.3 Consensus size: 85
20813931 TGTGTTTCCA
* *
20813941 GTAAGACCATATCTGGGATATGGCATCGATATGAGACTTCGTGTAAAACCATGTCTGGGAC-ATT
1 GTAAGACCATATCTGGGACATGGCATCGATATGAGACTTCGTGTAAAACCATGGCTGGG-CTATT
*** *
20814005 GGCATCGATATGTGATTTCAT
65 GGCATCGATACAAGATTACAT
* * * * *
20814026 GTAAGACCATGTCTGGGACATTGGCATCGATATGTGATTTCGTGTAAGATCATGGCTGGGCTATT
1 GTAAGACCATATCTGGGACA-TGGCATCGATATGAGACTTCGTGTAAAACCATGGCTGGGCTATT
20814091 GGCATCGATACAAGATTACAT
65 GGCATCGATACAAGATTACAT
* *
20814112 GAAAGACCATATCTGGGATATGG
1 GTAAGACCATATCTGGGACATGG
20814135 TATTGTTACG
Statistics
Matches: 93, Mismatches: 14, Indels: 4
0.84 0.13 0.04
Matches are distributed among these distances:
85 22 0.24
86 71 0.76
ACGTcount: A:0.28, C:0.16, G:0.26, T:0.29
Consensus pattern (85 bp):
GTAAGACCATATCTGGGACATGGCATCGATATGAGACTTCGTGTAAAACCATGGCTGGGCTATTG
GCATCGATACAAGATTACAT
Found at i:20814128 original size:43 final size:43
Alignment explanation
Indices: 20813943--20814129 Score: 200
Period size: 43 Copynumber: 4.4 Consensus size: 43
20813933 TGTTTCCAGT
* * * *
20813943 AAGACCATATCTGGGATA-TGGCATCGATATGAGACTTCGTGTA
1 AAGACCATGTCTGGGACATTGGCATCGATATGAGATTTCATG-A
* *
20813986 AA-ACCATGTCTGGGACATTGGCATCGATATGTGATTTCATGT
1 AAGACCATGTCTGGGACATTGGCATCGATATGAGATTTCATGA
* * *
20814028 AAGACCATGTCTGGGACATTGGCATCGATATGTGATTTCGTGT
1 AAGACCATGTCTGGGACATTGGCATCGATATGAGATTTCATGA
* * ** *
20814071 AAGATCATGGCTGGG-CTATTGGCATCGATACAAGATTACATGA
1 AAGACCATGTCTGGGAC-ATTGGCATCGATATGAGATTTCATGA
*
20814114 AAGACCATATCTGGGA
1 AAGACCATGTCTGGGA
20814130 TATGGTATTG
Statistics
Matches: 122, Mismatches: 18, Indels: 7
0.83 0.12 0.05
Matches are distributed among these distances:
42 16 0.13
43 106 0.87
ACGTcount: A:0.29, C:0.17, G:0.26, T:0.29
Consensus pattern (43 bp):
AAGACCATGTCTGGGACATTGGCATCGATATGAGATTTCATGA
Found at i:20815899 original size:571 final size:573
Alignment explanation
Indices: 20814812--20815960 Score: 2167
Period size: 571 Copynumber: 2.0 Consensus size: 573
20814802 GATTTTGGCT
*
20814812 ATTGGTGCCTATATGTTTGAAATGTATTGAGCCATGAGATTTGACTTGTTTATAATGTGAGGTTT
1 ATTGATGCCTATATGTTTGAAATGTATTGAGCCATGAGATTTGACTTGTTTATAATGTGAGGTTT
20814877 GATATGTAGATGGCCTTATAATTGGTATGTGATTGTGCTTATGTGGTAAGCTTCAGTAAAGTTAT
66 GATATGTAGATGGCCTTATAATTGGTATGTGATTGTGCTTATGTGGTAAGCTTCAGTAAAGTTAT
*
20814942 TGATGCATTAATGGAAGTGTCCAAATTGATATTCACAATTGATGAATAATGGTATTTATGCATTT
131 TGATGCATTAATGGAAGTGTCCAAATTGATATTCACAATTGATGAATAATGGTATTTATGCAGTT
20815007 GTTTATATTGGTATTGAGAGGTTAGGTTGCAATTGAGATGATGAAAAAGGAATGGAGTATTTTAG
196 GTTTATATTGGTATTGAGAGGTTAGGTTGCAATTGAGATGATGAAAAAGGAATGGAGTATTTTAG
20815072 GTCTAAAAGACATTGATTTACATGCCTTGTTAAATTGGTTTAAATGATGATTGTTTGGCTAAATA
261 GTCTAAAAGACATTGATTTACATGCCTTGTTAAATTGGTTTAAATGATGATTGTTTGGCTAAATA
20815137 ATAAATCATATCGATATTGTATTTTTGTGGTTAGGCAAAAGTTTGTGTATGAATAGATGAAATGG
326 ATAAATCATATCGATATTGTATTTTTGTGGTTAGGCAAAAGTTTGTGTATGAATAGATGAAATGG
20815202 TTGAATTGGTATGGCATGTTTGATGCATGAATTCACAATGTTTAAGCTGCCTATTGTGTATAAAA
391 TTGAATTGGTATGGCATGTTTGATGCATGAATTCACAATGTTTAAGCTGCCTATTGTGTATAAAA
20815267 ATGGTATATTTTGTGCTTATGTAGGGTTGACCCTTATGGGTGGTGAATTGGCCTTGCAAAT-G-G
456 ATGGTATATTTTGTGCTTATGTAGGGTTGACCCTTATGGGTGGTGAATTGGCCTTGCAAATGGTG
20815330 TCCACACGGCTGTTCACACGGGCGTGTGACATCTGTTACTTAGAAAATTCACA
521 TCCACACGGCTGTTCACACGGGCGTGTGACATCTGTTACTTAGAAAATTCACA
20815383 ATTGATGCCTATATGTTTGAAATGTATTGAGCCATGAGATTTGACTTGTTTATAATGTGAGGTTT
1 ATTGATGCCTATATGTTTGAAATGTATTGAGCCATGAGATTTGACTTGTTTATAATGTGAGGTTT
*
20815448 GATATGTAGATGGCCTTATAATTGGTATGTGATTGTGCTTATTTGGTAAGCTTCAGTAAAGTTAT
66 GATATGTAGATGGCCTTATAATTGGTATGTGATTGTGCTTATGTGGTAAGCTTCAGTAAAGTTAT
20815513 TGATGCATTAATGGAAGTGTCCAAATTGATATTCACAATTGATGAATAATGGTATTTATGCAGTT
131 TGATGCATTAATGGAAGTGTCCAAATTGATATTCACAATTGATGAATAATGGTATTTATGCAGTT
20815578 GTTTATATTGGTATTGAGAGGTTAGGTTGCAATTGAGATGATGAAAAAGGAATGGAGTATTTTAG
196 GTTTATATTGGTATTGAGAGGTTAGGTTGCAATTGAGATGATGAAAAAGGAATGGAGTATTTTAG
*
20815643 GTCTAAAAGATATTGATTTACATGCCTTGTTAAATTGGTTTAAATGATGATTGTTTGGCTAAATA
261 GTCTAAAAGACATTGATTTACATGCCTTGTTAAATTGGTTTAAATGATGATTGTTTGGCTAAATA
20815708 ATAAATCATATCGATATTGTATTTTTGTGGTTAGGCAAAAGTTTGTGTATGAATAGATGAAATGG
326 ATAAATCATATCGATATTGTATTTTTGTGGTTAGGCAAAAGTTTGTGTATGAATAGATGAAATGG
20815773 TTGAATTGGTATGGCATGTTTGATGCATGAATTCACAATGTTTAAGCTGCCTATTGTGTATAAAA
391 TTGAATTGGTATGGCATGTTTGATGCATGAATTCACAATGTTTAAGCTGCCTATTGTGTATAAAA
*
20815838 ATGGTATATTTTGTGCTTGTGTAGGGTTGACCCTTATGGGTGGTGAATTGGCCTTGCAAATGGCC
456 ATGGTATATTTTGTGCTTATGTAGGGTTGACCCTTATGGGTGGTGAATTGGCCTTGCAAATGG--
20815903 TATATTCGTCCACACGGCTGTTCACACGGGCGTGTGACATCTGTTACTTAGAAAATTC
519 -----T-GTCCACACGGCTGTTCACACGGGCGTGTGACATCTGTTACTTAGAAAATTC
20815961 TTAAAGCTTC
Statistics
Matches: 563, Mismatches: 5, Indels: 10
0.97 0.01 0.02
Matches are distributed among these distances:
571 511 0.91
572 1 0.00
581 51 0.09
ACGTcount: A:0.29, C:0.09, G:0.24, T:0.38
Consensus pattern (573 bp):
ATTGATGCCTATATGTTTGAAATGTATTGAGCCATGAGATTTGACTTGTTTATAATGTGAGGTTT
GATATGTAGATGGCCTTATAATTGGTATGTGATTGTGCTTATGTGGTAAGCTTCAGTAAAGTTAT
TGATGCATTAATGGAAGTGTCCAAATTGATATTCACAATTGATGAATAATGGTATTTATGCAGTT
GTTTATATTGGTATTGAGAGGTTAGGTTGCAATTGAGATGATGAAAAAGGAATGGAGTATTTTAG
GTCTAAAAGACATTGATTTACATGCCTTGTTAAATTGGTTTAAATGATGATTGTTTGGCTAAATA
ATAAATCATATCGATATTGTATTTTTGTGGTTAGGCAAAAGTTTGTGTATGAATAGATGAAATGG
TTGAATTGGTATGGCATGTTTGATGCATGAATTCACAATGTTTAAGCTGCCTATTGTGTATAAAA
ATGGTATATTTTGTGCTTATGTAGGGTTGACCCTTATGGGTGGTGAATTGGCCTTGCAAATGGTG
TCCACACGGCTGTTCACACGGGCGTGTGACATCTGTTACTTAGAAAATTCACA
Found at i:20816274 original size:20 final size:20
Alignment explanation
Indices: 20816251--20816355 Score: 79
Period size: 20 Copynumber: 5.2 Consensus size: 20
20816241 ATAGCCCTTC
20816251 TGGCATTCTGTTAGCCTTTG
1 TGGCATTCTGTTAGCCTTTG
* *
20816271 TGGCA-TCTGATATGGCATTTG
1 TGGCATTCTG-T-TAGCCTTTG
* *
20816292 TGGCATTATGTTAGCCTTTC
1 TGGCATTCTGTTAGCCTTTG
* *
20816312 TGGCATT-TGATATGGCTTTTG
1 TGGCATTCTG-T-TAGCCTTTG
* * *
20816333 TAGCATTCTGCTAGCCCTTG
1 TGGCATTCTGTTAGCCTTTG
20816353 TGG
1 TGG
20816356 TGTAATCTGT
Statistics
Matches: 64, Mismatches: 15, Indels: 12
0.70 0.16 0.13
Matches are distributed among these distances:
19 6 0.09
20 28 0.44
21 25 0.39
22 5 0.08
ACGTcount: A:0.14, C:0.18, G:0.26, T:0.42
Consensus pattern (20 bp):
TGGCATTCTGTTAGCCTTTG
Found at i:20816304 original size:41 final size:41
Alignment explanation
Indices: 20816251--20816355 Score: 147
Period size: 41 Copynumber: 2.6 Consensus size: 41
20816241 ATAGCCCTTC
20816251 TGGCATTCTGTTAGCCTTTGTGGCATCTGATATGGCATTTG
1 TGGCATTCTGTTAGCCTTTGTGGCATCTGATATGGCATTTG
* * * *
20816292 TGGCATTATGTTAGCCTTTCTGGCATTTGATATGGCTTTTG
1 TGGCATTCTGTTAGCCTTTGTGGCATCTGATATGGCATTTG
* * *
20816333 TAGCATTCTGCTAGCCCTTGTGG
1 TGGCATTCTGTTAGCCTTTGTGG
20816356 TGTAATCTGT
Statistics
Matches: 55, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
41 55 1.00
ACGTcount: A:0.14, C:0.18, G:0.26, T:0.42
Consensus pattern (41 bp):
TGGCATTCTGTTAGCCTTTGTGGCATCTGATATGGCATTTG
Found at i:20816338 original size:21 final size:21
Alignment explanation
Indices: 20816267--20816339 Score: 69
Period size: 21 Copynumber: 3.5 Consensus size: 21
20816257 TCTGTTAGCC
* *
20816267 TTTGTGGCATCTGATATGGCA
1 TTTGTGGCATTTGATATGGCT
* *
20816288 TTTGTGGCATTATG-T-TAGCC
1 TTTGTGGCATT-TGATATGGCT
*
20816308 TTTCTGGCATTTGATATGGCT
1 TTTGTGGCATTTGATATGGCT
*
20816329 TTTGTAGCATT
1 TTTGTGGCATT
20816340 CTGCTAGCCC
Statistics
Matches: 41, Mismatches: 8, Indels: 6
0.75 0.15 0.11
Matches are distributed among these distances:
19 2 0.05
20 14 0.34
21 23 0.56
22 2 0.05
ACGTcount: A:0.16, C:0.14, G:0.25, T:0.45
Consensus pattern (21 bp):
TTTGTGGCATTTGATATGGCT
Found at i:20816849 original size:28 final size:28
Alignment explanation
Indices: 20816809--20816887 Score: 104
Period size: 28 Copynumber: 2.8 Consensus size: 28
20816799 GATTTATCAA
*
20816809 GATTAGCAAAGGTATTCATCAAAAGTAT
1 GATTAGTAAAGGTATTCATCAAAAGTAT
*
20816837 GATTAGTAAAGGTATTCACCAAAAGTAT
1 GATTAGTAAAGGTATTCATCAAAAGTAT
* * *
20816865 GATAAGTAAGCGGTATCCATCAA
1 GATTAGTAA-AGGTATTCATCAA
20816888 GAATAGTGCT
Statistics
Matches: 44, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
28 34 0.77
29 10 0.23
ACGTcount: A:0.42, C:0.13, G:0.19, T:0.27
Consensus pattern (28 bp):
GATTAGTAAAGGTATTCATCAAAAGTAT
Found at i:20824446 original size:41 final size:41
Alignment explanation
Indices: 20824384--20824570 Score: 230
Period size: 41 Copynumber: 4.6 Consensus size: 41
20824374 CCTTTCGGGG
* * * * *
20824384 CTTTAGTGGCGTTTTTAAAAAATCGCTGCTAGTGCTCAGAT
1 CTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCAGAT
* *
20824425 CTTTAGAGGCGTTTTTGAAAAAGCGCCGCTAATGCTCATAT
1 CTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCAGAT
* * * *
20824466 CTTTAGCGGGGTTTTTGAAAAAGCGCTGGTAATGCTCAAAT
1 CTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCAGAT
* * **
20824507 CTTTAGCGGCGTTTTTGGAAAAGCGCCGCTAATGCTCGGGG
1 CTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCAGAT
*
20824548 CTTTAGCGACGTTTTTGAAAAAG
1 CTTTAGCGGCGTTTTTGAAAAAG
20824571 TGTCGCAAAA
Statistics
Matches: 125, Mismatches: 21, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
41 125 1.00
ACGTcount: A:0.25, C:0.18, G:0.26, T:0.32
Consensus pattern (41 bp):
CTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCAGAT
Found at i:20824718 original size:26 final size:26
Alignment explanation
Indices: 20824673--20824723 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
20824663 AAAATGGATA
** *
20824673 AATTTGAAATAATGACACATAGAAAT
1 AATTTGAAATAAAAAAACATAGAAAT
20824699 AATTTGAAATAAAAAAACATAGAAA
1 AATTTGAAATAAAAAAACATAGAAA
20824724 AATATTTGTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.61, C:0.06, G:0.10, T:0.24
Consensus pattern (26 bp):
AATTTGAAATAAAAAAACATAGAAAT
Found at i:20825196 original size:82 final size:85
Alignment explanation
Indices: 20825099--20825291 Score: 230
Period size: 89 Copynumber: 2.3 Consensus size: 85
20825089 AGTTAGGGAT
* * * *
20825099 TTAGGGTTTATGGATTTGGTGTCAGGTTA-GG-G-TTTAGATTAATTAGTGTATTTTAATTTATA
1 TTAGGGGTTAGGGATTTGGGGTCAGGTTAGGGTGATTTAGATTAATTAATGTATTTTAATTTATA
* *
20825161 TATTAAATAATGTTTAGGGG
66 TATTAAATAAGGCTTAGGGG
* * *
20825181 TTAGGGGTTAGGGATTCGGGGTCTGGTTAGGGTTTATGATTTAGATTAATTAATGTTTTTTAATT
1 TTAGGGGTTAGGGATTTGGGGTCAGGTTAGGG----TGATTTAGATTAATTAATGTATTTTAATT
20825246 TATATATTAAATAAGGCTTAGGGG
62 TATATATTAAATAAGGCTTAGGGG
* *
20825270 TTAGGGGTTTGGGGTTTGGGGT
1 TTAGGGGTTAGGGATTTGGGGT
20825292 TAAGAGTTAG
Statistics
Matches: 92, Mismatches: 12, Indels: 7
0.83 0.11 0.06
Matches are distributed among these distances:
82 24 0.26
83 2 0.02
88 1 0.01
89 65 0.71
ACGTcount: A:0.24, C:0.02, G:0.30, T:0.44
Consensus pattern (85 bp):
TTAGGGGTTAGGGATTTGGGGTCAGGTTAGGGTGATTTAGATTAATTAATGTATTTTAATTTATA
TATTAAATAAGGCTTAGGGG
Found at i:20826450 original size:41 final size:41
Alignment explanation
Indices: 20826388--20826574 Score: 230
Period size: 41 Copynumber: 4.6 Consensus size: 41
20826378 CCTTTCGGGG
* * * * *
20826388 CTTTAGTGGCGTTTTTAAAAAATCGCTGCTAGTGCTCAGAT
1 CTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCAGAT
* *
20826429 CTTTAGAGGCGTTTTTGAAAAAGCGCCGCTAATGCTCATAT
1 CTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCAGAT
* * * *
20826470 CTTTAGCGGGGTTTTTGAAAAAGCGCTGGTAATGCTCAAAT
1 CTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCAGAT
* * **
20826511 CTTTAGCGGCGTTTTTGGAAAAGCGCCGCTAATGCTCGGGG
1 CTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCAGAT
*
20826552 CTTTAGCGACGTTTTTGAAAAAG
1 CTTTAGCGGCGTTTTTGAAAAAG
20826575 TGTCGCAAAA
Statistics
Matches: 125, Mismatches: 21, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
41 125 1.00
ACGTcount: A:0.25, C:0.18, G:0.26, T:0.32
Consensus pattern (41 bp):
CTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCAGAT
Found at i:20826722 original size:26 final size:26
Alignment explanation
Indices: 20826677--20826727 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
20826667 AAAATGGATA
** *
20826677 AATTTGAAATAATGACACATAGAAAT
1 AATTTGAAATAAAAAAACATAGAAAT
20826703 AATTTGAAATAAAAAAACATAGAAA
1 AATTTGAAATAAAAAAACATAGAAA
20826728 AATATTTGTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.61, C:0.06, G:0.10, T:0.24
Consensus pattern (26 bp):
AATTTGAAATAAAAAAACATAGAAAT
Found at i:20827442 original size:17 final size:16
Alignment explanation
Indices: 20827409--20827442 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
20827399 ATATTAGATT
*
20827409 TAAAAAAATTAATAAA
1 TAAAAAAATTAACAAA
20827425 TAAAAAAATGTAACAAA
1 TAAAAAAAT-TAACAAA
20827442 T
1 T
20827443 TGATACGGAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.71, C:0.03, G:0.03, T:0.24
Consensus pattern (16 bp):
TAAAAAAATTAACAAA
Found at i:20830484 original size:741 final size:741
Alignment explanation
Indices: 20829062--20830543 Score: 2964
Period size: 741 Copynumber: 2.0 Consensus size: 741
20829052 TATTGTTATA
20829062 AGTGGTGTAAAGGGAAATGGAAATGGTATGGCAATATCGTGGGGTAATCTGCCTCCATCCTTAAA
1 AGTGGTGTAAAGGGAAATGGAAATGGTATGGCAATATCGTGGGGTAATCTGCCTCCATCCTTAAA
20829127 GCCCCCACCTGAGAATGGATATCCACCTCTTCCTTTTGTGGATTGGGGATAAACTCTCTCTCTCT
66 GCCCCCACCTGAGAATGGATATCCACCTCTTCCTTTTGTGGATTGGGGATAAACTCTCTCTCTCT
20829192 ATTGCTCTGTTTCTAGACACCAATTTCCTCATTTAGTTTCTTCATTTGTTAAAGCTGTATCTTCT
131 ATTGCTCTGTTTCTAGACACCAATTTCCTCATTTAGTTTCTTCATTTGTTAAAGCTGTATCTTCT
20829257 TATATTATTATTACATGTTAGATCACCCACTTTCATTTTCCTGTTCTTTCTCCTTTTACATTTCT
196 TATATTATTATTACATGTTAGATCACCCACTTTCATTTTCCTGTTCTTTCTCCTTTTACATTTCT
20829322 TGTCATCATGAGTATGTCAATACCTTGATAATGGGAATTCATTATATTACACAACACAATTGTCT
261 TGTCATCATGAGTATGTCAATACCTTGATAATGGGAATTCATTATATTACACAACACAATTGTCT
20829387 AACAAATCTAAAAGGTGAAGTGTTATGGTTCAATTGATCCTTGGTTCAGTTTAGTTTGCATTATA
326 AACAAATCTAAAAGGTGAAGTGTTATGGTTCAATTGATCCTTGGTTCAGTTTAGTTTGCATTATA
20829452 GGAACAAATGGTAAGAAAGCAAGTGAGAGTATGAATGTTGTATGATTAGGTGGCAGAATTTGAGT
391 GGAACAAATGGTAAGAAAGCAAGTGAGAGTATGAATGTTGTATGATTAGGTGGCAGAATTTGAGT
20829517 AGACACTTCCAAAGTCTATCCGAAAGCTTCAGAGCTTACTGACATTTAGAGATTATTTGATGTTT
456 AGACACTTCCAAAGTCTATCCGAAAGCTTCAGAGCTTACTGACATTTAGAGATTATTTGATGTTT
20829582 CAAAACTTCAAGTGCTTGTCTGATCAACCTCATCTTCGTAGAGGAAATTCAACCTGGTAATTGGA
521 CAAAACTTCAAGTGCTTGTCTGATCAACCTCATCTTCGTAGAGGAAATTCAACCTGGTAATTGGA
20829647 ATTCGCTTCAATTCTTGCACTTCTTTGGTTGCTAAGGCATTGAAATATTTTGTTTAAAGGGATGC
586 ATTCGCTTCAATTCTTGCACTTCTTTGGTTGCTAAGGCATTGAAATATTTTGTTTAAAGGGATGC
20829712 AAAACCTCTCGTCTCTTAAATTTCTGCCTGAGTTGCTGTACAAGTCTGAAATTAGAGGAAATTGC
651 AAAACCTCTCGTCTCTTAAATTTCTGCCTGAGTTGCTGTACAAGTCTGAAATTAGAGGAAATTGC
20829777 AATGTGAGGGATCTCTGTCTGGGTTG
716 AATGTGAGGGATCTCTGTCTGGGTTG
20829803 AGTGGTGTAAAGGGAAATGGAAATGGTATGGCAATATCGTGGGGTAATCTGCCTCCATCCTTAAA
1 AGTGGTGTAAAGGGAAATGGAAATGGTATGGCAATATCGTGGGGTAATCTGCCTCCATCCTTAAA
20829868 GCCCCCACCTGAGAATGGATATCCACCTCTTCCTTTTGTGGATTGGGGATAAACTCTCTCTCTCT
66 GCCCCCACCTGAGAATGGATATCCACCTCTTCCTTTTGTGGATTGGGGATAAACTCTCTCTCTCT
20829933 ATTGCTCTGTTTCTAGACACCAATTTCCTCATTTAGTTTCTTCATTTGTTAAAGCTGTATCTTCT
131 ATTGCTCTGTTTCTAGACACCAATTTCCTCATTTAGTTTCTTCATTTGTTAAAGCTGTATCTTCT
20829998 TATATTATTATTACATGTTAGATCACCCACTTTCATTTTCCTGTTCTTTCTCCTTTTACATTTCT
196 TATATTATTATTACATGTTAGATCACCCACTTTCATTTTCCTGTTCTTTCTCCTTTTACATTTCT
20830063 TGTCATCATGAGTATGTCAATACCTTGATAATGGGAATTCATTATATTACACAACACAATTGTCT
261 TGTCATCATGAGTATGTCAATACCTTGATAATGGGAATTCATTATATTACACAACACAATTGTCT
20830128 AACAAATCTAAAAGGTGAAGTGTTATGGTTCAATTGATCCTTGGTTCAGTTTAGTTTGCATTATA
326 AACAAATCTAAAAGGTGAAGTGTTATGGTTCAATTGATCCTTGGTTCAGTTTAGTTTGCATTATA
20830193 GGAACAAATGGTAAGAAAGCAAGTGAGAGTATGAATGTTGTATGATTAGGTGGCAGAATTTGAGT
391 GGAACAAATGGTAAGAAAGCAAGTGAGAGTATGAATGTTGTATGATTAGGTGGCAGAATTTGAGT
20830258 AGACACTTCCAAAGTCTATCCGAAAGCTTCAGAGCTTACTGACATTTAGAGATTATTTGATGTTT
456 AGACACTTCCAAAGTCTATCCGAAAGCTTCAGAGCTTACTGACATTTAGAGATTATTTGATGTTT
20830323 CAAAACTTCAAGTGCTTGTCTGATCAACCTCATCTTCGTAGAGGAAATTCAACCTGGTAATTGGA
521 CAAAACTTCAAGTGCTTGTCTGATCAACCTCATCTTCGTAGAGGAAATTCAACCTGGTAATTGGA
20830388 ATTCGCTTCAATTCTTGCACTTCTTTGGTTGCTAAGGCATTGAAATATTTTGTTTAAAGGGATGC
586 ATTCGCTTCAATTCTTGCACTTCTTTGGTTGCTAAGGCATTGAAATATTTTGTTTAAAGGGATGC
20830453 AAAACCTCTCGTCTCTTAAATTTCTGCCTGAGTTGCTGTACAAGTCTGAAATTAGAGGAAATTGC
651 AAAACCTCTCGTCTCTTAAATTTCTGCCTGAGTTGCTGTACAAGTCTGAAATTAGAGGAAATTGC
20830518 AATGTGAGGGATCTCTGTCTGGGTTG
716 AATGTGAGGGATCTCTGTCTGGGTTG
20830544 CTCTTACCCA
Statistics
Matches: 741, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
741 741 1.00
ACGTcount: A:0.27, C:0.18, G:0.19, T:0.36
Consensus pattern (741 bp):
AGTGGTGTAAAGGGAAATGGAAATGGTATGGCAATATCGTGGGGTAATCTGCCTCCATCCTTAAA
GCCCCCACCTGAGAATGGATATCCACCTCTTCCTTTTGTGGATTGGGGATAAACTCTCTCTCTCT
ATTGCTCTGTTTCTAGACACCAATTTCCTCATTTAGTTTCTTCATTTGTTAAAGCTGTATCTTCT
TATATTATTATTACATGTTAGATCACCCACTTTCATTTTCCTGTTCTTTCTCCTTTTACATTTCT
TGTCATCATGAGTATGTCAATACCTTGATAATGGGAATTCATTATATTACACAACACAATTGTCT
AACAAATCTAAAAGGTGAAGTGTTATGGTTCAATTGATCCTTGGTTCAGTTTAGTTTGCATTATA
GGAACAAATGGTAAGAAAGCAAGTGAGAGTATGAATGTTGTATGATTAGGTGGCAGAATTTGAGT
AGACACTTCCAAAGTCTATCCGAAAGCTTCAGAGCTTACTGACATTTAGAGATTATTTGATGTTT
CAAAACTTCAAGTGCTTGTCTGATCAACCTCATCTTCGTAGAGGAAATTCAACCTGGTAATTGGA
ATTCGCTTCAATTCTTGCACTTCTTTGGTTGCTAAGGCATTGAAATATTTTGTTTAAAGGGATGC
AAAACCTCTCGTCTCTTAAATTTCTGCCTGAGTTGCTGTACAAGTCTGAAATTAGAGGAAATTGC
AATGTGAGGGATCTCTGTCTGGGTTG
Found at i:20831461 original size:17 final size:17
Alignment explanation
Indices: 20831417--20831466 Score: 73
Period size: 17 Copynumber: 2.9 Consensus size: 17
20831407 ATTGTATTCC
*
20831417 CTAGGCGATACTGTCTG
1 CTAGGCGATACTATCTG
**
20831434 CTAGGTAATACTATCTG
1 CTAGGCGATACTATCTG
20831451 CTAGGCGATACTATCT
1 CTAGGCGATACTATCT
20831467 AGGTAACTAT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
17 28 1.00
ACGTcount: A:0.24, C:0.22, G:0.22, T:0.32
Consensus pattern (17 bp):
CTAGGCGATACTATCTG
Found at i:20832505 original size:2 final size:2
Alignment explanation
Indices: 20832498--20832538 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
20832488 AACAAATATC
20832498 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
20832539 CGAATGCTGC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:20834653 original size:416 final size:416
Alignment explanation
Indices: 20833882--20834714 Score: 1666
Period size: 416 Copynumber: 2.0 Consensus size: 416
20833872 TTTGAGGCAC
20833882 TTGTTTCATAAGATTTTATTTTATTTTAATTAATTTATAAAATTTTATATATTTAGTTTAGAATC
1 TTGTTTCATAAGATTTTATTTTATTTTAATTAATTTATAAAATTTTATATATTTAGTTTAGAATC
20833947 CATTTTGACTATATGTATGTAACATGCTCCAGAATTTTCTAATTTCTTTTAAATGATGTATATTT
66 CATTTTGACTATATGTATGTAACATGCTCCAGAATTTTCTAATTTCTTTTAAATGATGTATATTT
20834012 GGAACAAGTTTATTTTTAGAAGATATATCTAATTCAATTAGAAAAATAAAAATAAATTTTCATTT
131 GGAACAAGTTTATTTTTAGAAGATATATCTAATTCAATTAGAAAAATAAAAATAAATTTTCATTT
20834077 TTTATATATTTTTAGTTTTAAAGTTTTTATCTACTTTTTTTATACAAAATATTTAAATGATTTAC
196 TTTATATATTTTTAGTTTTAAAGTTTTTATCTACTTTTTTTATACAAAATATTTAAATGATTTAC
20834142 AACATATTAATTGATGTATTGATTTTAGCTCTCCATTTATTTTTCACCTCTTTAGTCTTTAAACT
261 AACATATTAATTGATGTATTGATTTTAGCTCTCCATTTATTTTTCACCTCTTTAGTCTTTAAACT
20834207 TACGTTGTTTGTCAAATTGAGGGGTTAATAATAGGATTTTTTTTTAATGGCAGAATGATGGAAAA
326 TACGTTGTTTGTCAAATTGAGGGGTTAATAATAGGATTTTTTTTTAATGGCAGAATGATGGAAAA
20834272 TACTGGGAAGATTTGGTGCTTATTGT
391 TACTGGGAAGATTTGGTGCTTATTGT
20834298 TTGTTTCATAAGATTTTATTTTATTTTAATTAATTTATAAAATTTTATATATTTAGTTTAGAATC
1 TTGTTTCATAAGATTTTATTTTATTTTAATTAATTTATAAAATTTTATATATTTAGTTTAGAATC
20834363 CATTTTGACTATATGTATGTAACATGCTCCAGAATTTTCTAATTTCTTTTAAATGATGTATATTT
66 CATTTTGACTATATGTATGTAACATGCTCCAGAATTTTCTAATTTCTTTTAAATGATGTATATTT
20834428 GGAACAAGTTTATTTTTAGAAGATATATCTAATTCAATTAGAAAAATAAAAATAAATTTTCATTT
131 GGAACAAGTTTATTTTTAGAAGATATATCTAATTCAATTAGAAAAATAAAAATAAATTTTCATTT
20834493 TTTATATATTTTTAGTTTTAAAGTTTTTATCTACTTTTTTTATACAAAATATTTAAATGATTTAC
196 TTTATATATTTTTAGTTTTAAAGTTTTTATCTACTTTTTTTATACAAAATATTTAAATGATTTAC
20834558 AACATATTAATTGATGTATTGATTTTAGCTCTCCATTTATTTTTCACCTCTTTAGTCTTTAAACT
261 AACATATTAATTGATGTATTGATTTTAGCTCTCCATTTATTTTTCACCTCTTTAGTCTTTAAACT
20834623 TACGTTGTTTGTCAAATTGAGGGGTTAATAATAGGATTTTTTTTTAATGGCAGAATGATGGAAAA
326 TACGTTGTTTGTCAAATTGAGGGGTTAATAATAGGATTTTTTTTTAATGGCAGAATGATGGAAAA
20834688 TACTGGGAAGATTTGGTGCTTATTGT
391 TACTGGGAAGATTTGGTGCTTATTGT
20834714 T
1 T
20834715 GAGTCCAACA
Statistics
Matches: 417, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
416 417 1.00
ACGTcount: A:0.32, C:0.08, G:0.12, T:0.48
Consensus pattern (416 bp):
TTGTTTCATAAGATTTTATTTTATTTTAATTAATTTATAAAATTTTATATATTTAGTTTAGAATC
CATTTTGACTATATGTATGTAACATGCTCCAGAATTTTCTAATTTCTTTTAAATGATGTATATTT
GGAACAAGTTTATTTTTAGAAGATATATCTAATTCAATTAGAAAAATAAAAATAAATTTTCATTT
TTTATATATTTTTAGTTTTAAAGTTTTTATCTACTTTTTTTATACAAAATATTTAAATGATTTAC
AACATATTAATTGATGTATTGATTTTAGCTCTCCATTTATTTTTCACCTCTTTAGTCTTTAAACT
TACGTTGTTTGTCAAATTGAGGGGTTAATAATAGGATTTTTTTTTAATGGCAGAATGATGGAAAA
TACTGGGAAGATTTGGTGCTTATTGT
Found at i:20835161 original size:17 final size:17
Alignment explanation
Indices: 20835117--20835165 Score: 71
Period size: 17 Copynumber: 2.9 Consensus size: 17
20835107 ATTGTATTCC
*
20835117 CTAGGCGATACTGTCTG
1 CTAGGCGATACTATCTG
**
20835134 CTAGGTAATACTATCTG
1 CTAGGCGATACTATCTG
20835151 CTAGGCGATACTATC
1 CTAGGCGATACTATC
20835166 CGCCAGACGA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.24, C:0.22, G:0.22, T:0.31
Consensus pattern (17 bp):
CTAGGCGATACTATCTG
Found at i:20839197 original size:43 final size:43
Alignment explanation
Indices: 20839149--20839240 Score: 130
Period size: 43 Copynumber: 2.1 Consensus size: 43
20839139 CCTTTAGCGG
* *
20839149 CGCTAAAGGTCATGTTCTTTAGCAGCGCTTTTATCACAAACGC
1 CGCTAAAGGTCATGTTCTTTAGCAACGCTTTCATCACAAACGC
* * *
20839192 CGCTAAAGTTCATGTTCTTTAGCAATGCTTTCCTCACAAACGC
1 CGCTAAAGGTCATGTTCTTTAGCAACGCTTTCATCACAAACGC
*
20839235 CACTAA
1 CGCTAA
20839241 TTTTGGGATT
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.27, C:0.27, G:0.15, T:0.30
Consensus pattern (43 bp):
CGCTAAAGGTCATGTTCTTTAGCAACGCTTTCATCACAAACGC
Found at i:20841270 original size:9 final size:9
Alignment explanation
Indices: 20841215--20841322 Score: 64
Period size: 9 Copynumber: 12.2 Consensus size: 9
20841205 GAGTTATGTT
*
20841215 TTATGTAAA
1 TTATGTAAG
20841224 TTATGTAAG
1 TTATGTAAG
*
20841233 TTATTTAAG
1 TTATGTAAG
*
20841242 TTATATAAG
1 TTATGTAAG
* **
20841251 -T-TCTATC
1 TTATGTAAG
20841258 TTATGTAAG
1 TTATGTAAG
*
20841267 TTATGTATG
1 TTATGTAAG
*
20841276 CTATGT-A-
1 TTATGTAAG
20841283 TTATGTAAG
1 TTATGTAAG
*
20841292 TTAT-TATG
1 TTATGTAAG
20841300 TTATTATGTAAG
1 ---TTATGTAAG
*
20841312 TTATGCAAG
1 TTATGTAAG
20841321 TT
1 TT
20841323 TATATATAAG
Statistics
Matches: 75, Mismatches: 16, Indels: 16
0.70 0.15 0.15
Matches are distributed among these distances:
7 8 0.11
8 6 0.08
9 54 0.72
11 4 0.05
12 3 0.04
ACGTcount: A:0.31, C:0.04, G:0.16, T:0.49
Consensus pattern (9 bp):
TTATGTAAG
Found at i:20841306 original size:20 final size:23
Alignment explanation
Indices: 20841258--20841316 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 23
20841248 AAGTTCTATC
20841258 TTATGTAAGTTATGTATGCTATGTA
1 TTATGTAAGTTATGTATG--ATGTA
20841283 TTATGTAAGTTAT-TATG-T-TA
1 TTATGTAAGTTATGTATGATGTA
20841303 TTATGTAAGTTATG
1 TTATGTAAGTTATG
20841317 CAAGTTTATA
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
20 15 0.45
21 1 0.03
24 4 0.12
25 13 0.39
ACGTcount: A:0.29, C:0.02, G:0.19, T:0.51
Consensus pattern (23 bp):
TTATGTAAGTTATGTATGATGTA
Found at i:20841738 original size:31 final size:32
Alignment explanation
Indices: 20841702--20841766 Score: 123
Period size: 32 Copynumber: 2.1 Consensus size: 32
20841692 CTTAGATAAT
20841702 TTTAAAGAG-TTTTATTAGGATTCAATTACTC
1 TTTAAAGAGTTTTTATTAGGATTCAATTACTC
20841733 TTTAAAGAGTTTTTATTAGGATTCAATTACTC
1 TTTAAAGAGTTTTTATTAGGATTCAATTACTC
20841765 TT
1 TT
20841767 GTAATTTGCC
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 9 0.27
32 24 0.73
ACGTcount: A:0.31, C:0.09, G:0.12, T:0.48
Consensus pattern (32 bp):
TTTAAAGAGTTTTTATTAGGATTCAATTACTC
Found at i:20842351 original size:14 final size:15
Alignment explanation
Indices: 20842317--20842350 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
20842307 CAGCAAAAAG
20842317 AAAAAGAAAAAGGAA
1 AAAAAGAAAAAGGAA
* *
20842332 AAAAAGAAGAAGCAA
1 AAAAAGAAAAAGGAA
20842347 AAAA
1 AAAA
20842351 GCGTAAAAAA
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:0.79, C:0.03, G:0.18, T:0.00
Consensus pattern (15 bp):
AAAAAGAAAAAGGAA
Found at i:20847952 original size:31 final size:32
Alignment explanation
Indices: 20847916--20847980 Score: 123
Period size: 32 Copynumber: 2.1 Consensus size: 32
20847906 CTTAGATAAT
20847916 TTTAAAGAG-TTTTATTAGGATTCAATTACTC
1 TTTAAAGAGTTTTTATTAGGATTCAATTACTC
20847947 TTTAAAGAGTTTTTATTAGGATTCAATTACTC
1 TTTAAAGAGTTTTTATTAGGATTCAATTACTC
20847979 TT
1 TT
20847981 GTAATTTGCC
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 9 0.27
32 24 0.73
ACGTcount: A:0.31, C:0.09, G:0.12, T:0.48
Consensus pattern (32 bp):
TTTAAAGAGTTTTTATTAGGATTCAATTACTC
Found at i:20850034 original size:13 final size:13
Alignment explanation
Indices: 20850018--20850058 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
20850008 CATTTACTAT
20850018 ATTCATTAAGAAA
1 ATTCATTAAGAAA
20850031 ATTCATTCAA-AAA
1 ATTCATT-AAGAAA
*
20850044 ATTCATTTAGAAA
1 ATTCATTAAGAAA
20850057 AT
1 AT
20850059 CTGGCAAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
12 1 0.04
13 22 0.88
14 2 0.08
ACGTcount: A:0.51, C:0.10, G:0.05, T:0.34
Consensus pattern (13 bp):
ATTCATTAAGAAA
Found at i:20852152 original size:21 final size:21
Alignment explanation
Indices: 20852128--20852172 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
20852118 TTGTAACATG
20852128 TAACCCTTA-ACCCCTAAACCC
1 TAACCCTTATACCCC-AAACCC
* *
20852149 TAACCTTTATATCCCAAACCC
1 TAACCCTTATACCCCAAACCC
20852170 TAA
1 TAA
20852173 ATCCATACCC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.36, C:0.40, G:0.00, T:0.24
Consensus pattern (21 bp):
TAACCCTTATACCCCAAACCC
Found at i:20853359 original size:40 final size:40
Alignment explanation
Indices: 20853302--20853450 Score: 162
Period size: 41 Copynumber: 3.7 Consensus size: 40
20853292 AATTGTTTTT
* *
20853302 GCGGCGCTTCA-ACAAAAATGCCGCTAAAACACCTAGATTA
1 GCGGCGCTTCATA-AAAAACGCCGCTAAAACACCAAGATTA
*
20853342 GCGGCGCTAT-ATAAAAAACGCCGCTAAAACACTCAACATTA
1 GCGGCGCT-TCATAAAAAACGCCGCTAAAACAC-CAAGATTA
* *
20853383 GCGGCGCTTCTTAAAAAACGCCGCTAATA-ACCAGAGCATTA
1 GCGGCGCTTCATAAAAAACGCCGCTAAAACACCA-AG-ATTA
*
20853424 GCGGCGCTTCACT-AAAAACGCCACTAA
1 GCGGCGCTTCA-TAAAAAACGCCGCTAA
20853451 TTTCCCCGAA
Statistics
Matches: 94, Mismatches: 8, Indels: 13
0.82 0.07 0.11
Matches are distributed among these distances:
39 2 0.02
40 31 0.33
41 60 0.64
42 1 0.01
ACGTcount: A:0.37, C:0.28, G:0.17, T:0.17
Consensus pattern (40 bp):
GCGGCGCTTCATAAAAAACGCCGCTAAAACACCAAGATTA
Found at i:20856875 original size:19 final size:19
Alignment explanation
Indices: 20856839--20856887 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
20856829 TGTTTAAAAT
*
20856839 AATATACAATAAATAATTA
1 AATATATAATAAATAATTA
20856858 AATATATAATAAGA-AATTA
1 AATATATAATAA-ATAATTA
*
20856877 ATTA-ATAATAA
1 AATATATAATAA
20856888 TATGAGAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
18 7 0.26
19 19 0.70
20 1 0.04
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (19 bp):
AATATATAATAAATAATTA
Found at i:20862179 original size:19 final size:19
Alignment explanation
Indices: 20862151--20862190 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
20862141 ATTAATTTTG
*
20862151 ATCAAGTAAAGTT-AAATTA
1 ATCAAATAAA-TTAAAATTA
20862170 ATCAAATAAATTAAAATTA
1 ATCAAATAAATTAAAATTA
20862189 AT
1 AT
20862191 ATGATATTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 2 0.11
19 17 0.89
ACGTcount: A:0.57, C:0.05, G:0.05, T:0.33
Consensus pattern (19 bp):
ATCAAATAAATTAAAATTA
Found at i:20865008 original size:25 final size:25
Alignment explanation
Indices: 20864975--20865054 Score: 81
Period size: 25 Copynumber: 3.2 Consensus size: 25
20864965 GCTGTAATTA
*
20864975 GTAAGCTCATATGAGATGAGTAATG
1 GTAAGCTCATACGAGATGAGTAATG
* * * * *
20865000 GTAAACTCATGCGAGCTGAATAACG
1 GTAAGCTCATACGAGATGAGTAATG
*
20865025 GTAAGCTCATACGAGTTGAG-AATTG
1 GTAAGCTCATACGAGATGAGTAA-TG
20865050 GTAAG
1 GTAAG
20865055 GTAAGCTTTC
Statistics
Matches: 43, Mismatches: 11, Indels: 2
0.77 0.20 0.04
Matches are distributed among these distances:
24 2 0.05
25 41 0.95
ACGTcount: A:0.35, C:0.12, G:0.28, T:0.25
Consensus pattern (25 bp):
GTAAGCTCATACGAGATGAGTAATG
Found at i:20868285 original size:128 final size:128
Alignment explanation
Indices: 20868057--20868314 Score: 498
Period size: 128 Copynumber: 2.0 Consensus size: 128
20868047 TGGATTTTCA
*
20868057 ATGATTGGTTGTTCAATACCCAGTTAAGCTTGATGGGTGTTATGTATGATAACTAATCTCTCACC
1 ATGATTGGTTGTTCAACACCCAGTTAAGCTTGATGGGTGTTATGTATGATAACTAATCTCTCACC
20868122 TAAAGTGGAAGATTGAACTACGGGAATCGTGTCCCGAGACAGATCGTTCTCACTAATTGAGTC
66 TAAAGTGGAAGATTGAACTACGGGAATCGTGTCCCGAGACAGATCGTTCTCACTAATTGAGTC
20868185 ATGATTGGTTGTTCAACACCCAGTTAAGCTTGATGGGTGTTATGTATGATAACTAATCTCTCACC
1 ATGATTGGTTGTTCAACACCCAGTTAAGCTTGATGGGTGTTATGTATGATAACTAATCTCTCACC
*
20868250 TAAAGTGGAAGATTGACCTACGGGAATCGTGTCCCGAGACAGATCGTTCTCACTAATTGAGTC
66 TAAAGTGGAAGATTGAACTACGGGAATCGTGTCCCGAGACAGATCGTTCTCACTAATTGAGTC
20868313 AT
1 AT
20868315 TCTCAAGAAA
Statistics
Matches: 128, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
128 128 1.00
ACGTcount: A:0.28, C:0.19, G:0.22, T:0.31
Consensus pattern (128 bp):
ATGATTGGTTGTTCAACACCCAGTTAAGCTTGATGGGTGTTATGTATGATAACTAATCTCTCACC
TAAAGTGGAAGATTGAACTACGGGAATCGTGTCCCGAGACAGATCGTTCTCACTAATTGAGTC
Found at i:20877727 original size:4 final size:4
Alignment explanation
Indices: 20877718--20877757 Score: 80
Period size: 4 Copynumber: 10.0 Consensus size: 4
20877708 TTCGAATTCA
20877718 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
20877758 GATTGTTGCA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 36 1.00
ACGTcount: A:0.50, C:0.25, G:0.00, T:0.25
Consensus pattern (4 bp):
ACAT
Found at i:20880361 original size:14 final size:14
Alignment explanation
Indices: 20880342--20880370 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
20880332 ATTACTCTAT
20880342 TTTCTCTCTCTCTC
1 TTTCTCTCTCTCTC
20880356 TTTCTCTCTCTCTC
1 TTTCTCTCTCTCTC
20880370 T
1 T
20880371 CTTCACTCTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.00, C:0.41, G:0.00, T:0.59
Consensus pattern (14 bp):
TTTCTCTCTCTCTC
Done.