Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold165
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: 1947055
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.31
Warning! 52078 characters in sequence are not A, C, G, or T
File 5 of 11
Found at i:989143 original size:21 final size:22
Alignment explanation
Indices: 989104--989146 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
989094 ATGATTTTGA
* *
989104 TGAAAAATGAAGTATTTTGAAG
1 TGAAAAATGAAGAAATTTGAAG
989126 TGAAAAAT-AAGAAATTTGAAG
1 TGAAAAATGAAGAAATTTGAAG
989147 AAGATTTGAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 11 0.58
22 8 0.42
ACGTcount: A:0.51, C:0.00, G:0.21, T:0.28
Consensus pattern (22 bp):
TGAAAAATGAAGAAATTTGAAG
Found at i:989387 original size:18 final size:20
Alignment explanation
Indices: 989346--989398 Score: 58
Period size: 20 Copynumber: 2.7 Consensus size: 20
989336 CTATAGACCC
989346 TAATTCACATCAAACAAGTA
1 TAATTCACATCAAACAAGTA
989366 TAATTCA-AT-AACACAA-TA
1 TAATTCACATCAA-ACAAGTA
*
989384 TAATTAAACATCAAA
1 TAATT-CACATCAAA
989399 TTCATCCAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 8
0.76 0.03 0.22
Matches are distributed among these distances:
18 9 0.32
19 7 0.25
20 10 0.36
21 2 0.07
ACGTcount: A:0.55, C:0.17, G:0.02, T:0.26
Consensus pattern (20 bp):
TAATTCACATCAAACAAGTA
Found at i:993769 original size:3 final size:3
Alignment explanation
Indices: 993761--993800 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
993751 TCCGAGTCAC
993761 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT C
1 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT C
993801 GTCTTTGATG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.33, C:0.35, G:0.00, T:0.33
Consensus pattern (3 bp):
CAT
Found at i:995672 original size:12 final size:12
Alignment explanation
Indices: 995655--995679 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
995645 CAATTTTTTG
995655 TGTATCGATACA
1 TGTATCGATACA
995667 TGTATCGATACA
1 TGTATCGATACA
995679 T
1 T
995680 ACTTGCTGTA
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (12 bp):
TGTATCGATACA
Found at i:996428 original size:21 final size:21
Alignment explanation
Indices: 996387--996430 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
996377 TTCCCCTTTA
* *
996387 TCTCCCCCGTTTATTAATAAT
1 TCTCCCCCGTTAATCAATAAT
996408 TCTCCCCC-TTAATCAAGTAAT
1 TCTCCCCCGTTAATCAA-TAAT
996429 TC
1 TC
996431 ATATCAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.25, C:0.32, G:0.05, T:0.39
Consensus pattern (21 bp):
TCTCCCCCGTTAATCAATAAT
Found at i:998261 original size:13 final size:13
Alignment explanation
Indices: 998243--998268 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
998233 ATAATCACCC
998243 TGTATCGATACAA
1 TGTATCGATACAA
998256 TGTATCGATACAA
1 TGTATCGATACAA
998269 AGAAAAATGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1000363 original size:15 final size:15
Alignment explanation
Indices: 1000343--1000373 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1000333 ATTTCGTTTG
*
1000343 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
1000358 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
1000373 G
1 G
1000374 GACATTTTTA
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:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:1002223 original size:21 final size:20
Alignment explanation
Indices: 1002173--1002223 Score: 52
Period size: 21 Copynumber: 2.5 Consensus size: 20
1002163 ATGCAAGTTT
*
1002173 TCATT-TTTC-TTAGCTAAC
1 TCATTATTTCATTAGCCAAC
1002191 TCATTATGTTCATTAGCCAAC
1 TCATTAT-TTCATTAGCCAAC
*
1002212 TTCTTTATTTCA
1 -TCATTATTTCA
1002224 ACTTGCAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
18 5 0.19
19 1 0.04
20 3 0.11
21 12 0.44
22 6 0.22
ACGTcount: A:0.24, C:0.22, G:0.06, T:0.49
Consensus pattern (20 bp):
TCATTATTTCATTAGCCAAC
Found at i:1004457 original size:13 final size:13
Alignment explanation
Indices: 1004439--1004464 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1004429 CATTTTTTTG
1004439 TGTATCGATACAT
1 TGTATCGATACAT
1004452 TGTATCGATACAT
1 TGTATCGATACAT
1004465 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1005295 original size:20 final size:20
Alignment explanation
Indices: 1005270--1005324 Score: 101
Period size: 20 Copynumber: 2.8 Consensus size: 20
1005260 TCATGTAGCT
1005270 ATGTATCGATACAATTCATA
1 ATGTATCGATACAATTCATA
*
1005290 ATGTATCGATACAATTCATC
1 ATGTATCGATACAATTCATA
1005310 ATGTATCGATACAAT
1 ATGTATCGATACAAT
1005325 GTGCCATGTA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.38, C:0.16, G:0.11, T:0.35
Consensus pattern (20 bp):
ATGTATCGATACAATTCATA
Found at i:1005332 original size:20 final size:19
Alignment explanation
Indices: 1005270--1005343 Score: 87
Period size: 20 Copynumber: 3.7 Consensus size: 19
1005260 TCATGTAGCT
*
1005270 ATGTATCGATACAATTCATA
1 ATGTATCGATACAATTCA-C
1005290 ATGTATCGATACAATTCATC
1 ATGTATCGATACAATTCA-C
1005310 ATGTATCGATACAATGTGC-C
1 ATGTATCGATACAAT-T-CAC
*
1005330 ATGTATTGATACAA
1 ATGTATCGATACAA
1005344 ACAGTGGTAG
Statistics
Matches: 50, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
20 48 0.96
21 1 0.02
22 1 0.02
ACGTcount: A:0.36, C:0.16, G:0.14, T:0.34
Consensus pattern (19 bp):
ATGTATCGATACAATTCAC
Found at i:1008611 original size:20 final size:20
Alignment explanation
Indices: 1008554--1008605 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
1008544 GTCAAAACCC
1008554 TTAAAAGTATCGATACACAA
1 TTAAAAGTATCGATACACAA
1008574 TTAAAAGTATCGATACACAA
1 TTAAAAGTATCGATACACAA
*
1008594 TTCAAAGTATCG
1 TTAAAAGTATCG
1008606 GCACACCAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.46, C:0.15, G:0.12, T:0.27
Consensus pattern (20 bp):
TTAAAAGTATCGATACACAA
Found at i:1010389 original size:15 final size:15
Alignment explanation
Indices: 1010369--1010399 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1010359 TAAAAATGTC
*
1010369 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
1010384 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
1010399 C
1 C
1010400 CAAACGAAAT
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:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:1012498 original size:13 final size:13
Alignment explanation
Indices: 1012480--1012517 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
1012470 CATTTTTCTT
1012480 TGTATCGATACAA
1 TGTATCGATACAA
*
1012493 TGTATCGATACAC
1 TGTATCGATACAA
1012506 TGTATCGATACA
1 TGTATCGATACA
1012518 GGGGGATTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1012681 original size:20 final size:20
Alignment explanation
Indices: 1012638--1012683 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
1012628 AAATCTTTTG
1012638 CAAAATACTTGTTTTTCACTT
1 CAAAATACTTGTTTTTCAC-T
*
1012659 CAAATTACTTCGTTTTTCA-T
1 CAAAATACTT-GTTTTTCACT
1012679 CAAAA
1 CAAAA
1012684 CCAGCATCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 5 0.23
21 9 0.41
22 8 0.36
ACGTcount: A:0.33, C:0.20, G:0.04, T:0.43
Consensus pattern (20 bp):
CAAAATACTTGTTTTTCACT
Found at i:1015092 original size:13 final size:13
Alignment explanation
Indices: 1015074--1015099 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1015064 TACACAAAGT
1015074 ATGTATCGATACA
1 ATGTATCGATACA
1015087 ATGTATCGATACA
1 ATGTATCGATACA
1015100 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1015099 original size:32 final size:33
Alignment explanation
Indices: 1015056--1015119 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
1015046 TAGCCAAACT
**
1015056 TGTATCAATACACAAAGTA-TGTATCGATACAA
1 TGTATCAATACACAAAAAATTGTATCGATACAA
*
1015088 TGTATCGATACACAAAAAATTGTATCGATACA
1 TGTATCAATACACAAAAAATTGTATCGATACA
1015120 TTGGCTTGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 16 0.57
33 12 0.43
ACGTcount: A:0.44, C:0.16, G:0.12, T:0.28
Consensus pattern (33 bp):
TGTATCAATACACAAAAAATTGTATCGATACAA
Found at i:1015184 original size:20 final size:21
Alignment explanation
Indices: 1015154--1015192 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 21
1015144 CTATATTTTC
1015154 AAATATGTATCGATACATTAA
1 AAATATGTATCGATACATTAA
1015175 AAAT-TGTATCGATACATT
1 AAATATGTATCGATACATT
1015193 TACACGGGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.44, C:0.10, G:0.10, T:0.36
Consensus pattern (21 bp):
AAATATGTATCGATACATTAA
Found at i:1023150 original size:32 final size:30
Alignment explanation
Indices: 1023114--1023172 Score: 75
Period size: 32 Copynumber: 1.9 Consensus size: 30
1023104 AAAATCAAAT
1023114 ACAAAGAGCT-TAGAAAAATAATAACAATATGA
1 ACAAA-AGCTCTAGAAAAAT-ATAA-AATATGA
*
1023146 ACAAAAGCTCTTGAAAAATATAAAATA
1 ACAAAAGCTCTAGAAAAATATAAAATA
1023173 CTTTGATCTA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
30 4 0.16
31 8 0.32
32 13 0.52
ACGTcount: A:0.59, C:0.10, G:0.10, T:0.20
Consensus pattern (30 bp):
ACAAAAGCTCTAGAAAAATATAAAATATGA
Found at i:1023471 original size:13 final size:13
Alignment explanation
Indices: 1023453--1023478 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1023443 ATATTTTTTG
1023453 TGTATCGATACAT
1 TGTATCGATACAT
1023466 TGTATCGATACAT
1 TGTATCGATACAT
1023479 ATTTTGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1023489 original size:32 final size:33
Alignment explanation
Indices: 1023432--1023496 Score: 114
Period size: 32 Copynumber: 2.0 Consensus size: 33
1023422 TACAAGCCAA
1023432 TGTATCGATACATATTTTTTGTGTATCGATACAT
1 TGTATCGATACATA-TTTTTGTGTATCGATACAT
1023466 TGTATCGATACATA-TTTTGTGTATCGATACA
1 TGTATCGATACATATTTTTGTGTATCGATACA
1023497 AGTTTGGCTA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
32 17 0.55
34 14 0.45
ACGTcount: A:0.28, C:0.12, G:0.15, T:0.45
Consensus pattern (33 bp):
TGTATCGATACATATTTTTGTGTATCGATACAT
Found at i:1023490 original size:19 final size:19
Alignment explanation
Indices: 1023432--1023496 Score: 70
Period size: 19 Copynumber: 3.6 Consensus size: 19
1023422 TACAAGCCAA
1023432 TGTATCGATACATATTTTTTG
1 TGTATCGATACATA--TTTTG
1023453 TGTATCGATAC--A---T-
1 TGTATCGATACATATTTTG
1023466 TGTATCGATACATATTTTG
1 TGTATCGATACATATTTTG
1023485 TGTATCGATACA
1 TGTATCGATACA
1023497 AGTTTGGCTA
Statistics
Matches: 38, Mismatches: 0, Indels: 14
0.73 0.00 0.27
Matches are distributed among these distances:
13 11 0.29
14 1 0.03
15 1 0.03
18 1 0.03
19 13 0.34
21 11 0.29
ACGTcount: A:0.28, C:0.12, G:0.15, T:0.45
Consensus pattern (19 bp):
TGTATCGATACATATTTTG
Found at i:1025578 original size:21 final size:20
Alignment explanation
Indices: 1025549--1025591 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
1025539 GACTAGTGTG
* *
1025549 GGGACTGCCCGGTTGTGACCT
1 GGGACTG-CCGGTCGCGACCT
*
1025570 GGGAGTGCCGGTCGCGACCT
1 GGGACTGCCGGTCGCGACCT
1025590 GG
1 GG
1025592 TGGTGCTGCC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 13 0.68
21 6 0.32
ACGTcount: A:0.09, C:0.28, G:0.44, T:0.19
Consensus pattern (20 bp):
GGGACTGCCGGTCGCGACCT
Found at i:1026042 original size:13 final size:13
Alignment explanation
Indices: 1026024--1026048 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1026014 ATAATCCCCC
1026024 TGTATCGATACAG
1 TGTATCGATACAG
1026037 TGTATCGATACA
1 TGTATCGATACA
1026049 AAGAAAAATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.20, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAG
Found at i:1029877 original size:15 final size:15
Alignment explanation
Indices: 1029857--1029887 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1029847 ATTTCGTTTG
*
1029857 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
1029872 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
1029887 G
1 G
1029888 GACATTTTTA
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:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:1033650 original size:32 final size:30
Alignment explanation
Indices: 1033614--1033672 Score: 75
Period size: 32 Copynumber: 1.9 Consensus size: 30
1033604 GAAATCAAAT
1033614 ACAAAGAGCT-TAGAAAAATAATAACAATATGA
1 ACAAA-AGCTCTAGAAAAAT-ATAA-AATATGA
*
1033646 ACAAAAGCTCTTGAAAAATATAAAATA
1 ACAAAAGCTCTAGAAAAATATAAAATA
1033673 CTTTGATCTA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
30 4 0.16
31 8 0.32
32 13 0.52
ACGTcount: A:0.59, C:0.10, G:0.10, T:0.20
Consensus pattern (30 bp):
ACAAAAGCTCTAGAAAAATATAAAATATGA
Found at i:1033971 original size:13 final size:13
Alignment explanation
Indices: 1033953--1034010 Score: 62
Period size: 13 Copynumber: 4.0 Consensus size: 13
1033943 ATATTTTTTG
1033953 TGTATCGATACAT
1 TGTATCGATACAT
1033966 TGTATCGATACATATTTT
1 TGTATCGATAC--A---T
1033984 GTGTATCGATACAT
1 -TGTATCGATACAT
1033998 TGTATCGATACAT
1 TGTATCGATACAT
1034011 ATTTTGTGTA
Statistics
Matches: 39, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 24 0.62
14 1 0.03
15 1 0.03
17 1 0.03
18 1 0.03
19 11 0.28
ACGTcount: A:0.29, C:0.14, G:0.16, T:0.41
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1033989 original size:32 final size:32
Alignment explanation
Indices: 1033934--1034028 Score: 172
Period size: 32 Copynumber: 2.9 Consensus size: 32
1033924 CAAGCCAATC
1033934 TATCGATACATATTTTTTGTGTATCGATACATTG
1 TATCGATACATA--TTTTGTGTATCGATACATTG
1033968 TATCGATACATATTTTGTGTATCGATACATTG
1 TATCGATACATATTTTGTGTATCGATACATTG
1034000 TATCGATACATATTTTGTGTATCGATACA
1 TATCGATACATATTTTGTGTATCGATACA
1034029 AGTTTGGCTA
Statistics
Matches: 61, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
32 49 0.80
34 12 0.20
ACGTcount: A:0.28, C:0.13, G:0.15, T:0.44
Consensus pattern (32 bp):
TATCGATACATATTTTGTGTATCGATACATTG
Found at i:1033990 original size:19 final size:19
Alignment explanation
Indices: 1033934--1034028 Score: 88
Period size: 19 Copynumber: 5.5 Consensus size: 19
1033924 CAAGCCAATC
1033934 TATCGATACATATTTTTTGTG
1 TATCGATACATA--TTTTGTG
1033955 TATCGATAC--A---T-TG
1 TATCGATACATATTTTGTG
1033968 TATCGATACATATTTTGTG
1 TATCGATACATATTTTGTG
1033987 TATCGATAC--A---T-TG
1 TATCGATACATATTTTGTG
1034000 TATCGATACATATTTTGTG
1 TATCGATACATATTTTGTG
1034019 TATCGATACA
1 TATCGATACA
1034029 AGTTTGGCTA
Statistics
Matches: 62, Mismatches: 0, Indels: 26
0.70 0.00 0.30
Matches are distributed among these distances:
13 22 0.35
14 2 0.03
15 2 0.03
17 1 0.02
18 2 0.03
19 24 0.39
21 9 0.15
ACGTcount: A:0.28, C:0.13, G:0.15, T:0.44
Consensus pattern (19 bp):
TATCGATACATATTTTGTG
Found at i:1034815 original size:13 final size:13
Alignment explanation
Indices: 1034797--1034822 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1034787 AACCCTTGAA
1034797 TGTATCGATACAT
1 TGTATCGATACAT
1034810 TGTATCGATACAT
1 TGTATCGATACAT
1034823 GTTTATTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1038806 original size:260 final size:261
Alignment explanation
Indices: 1038343--1038878 Score: 1024
Period size: 260 Copynumber: 2.1 Consensus size: 261
1038333 AAAAAAAGGG
1038343 AGAAGGGGTCG-AAAAAAAAAAAAGAAAGGAAGAGGCTTTCAAAAAAAACCAAAGTGGGTTTTCC
1 AGAAGGGGTCGAAAAAAAAAAAAAGAAAGGAAGAGGCTTTCAAAAAAAACCAAAGTGGGTTTTCC
1038407 GATTGAGGAGGTTCTGGTCATTGTTTGGAAAATCCGAACGGTGAGAAAGAAGTTCACACTAAGGG
66 GATTGAGGAGGTTCTGGTCATTGTTTGGAAAATCCGAACGGTGAGAAAGAAGTTCACACTAAGGG
1038472 TAAGAACATACTAGATTTTGGGAGCGATCCGACGGTAGACGGTGACCGAATTTGAGGTATAAGAT
131 TAAGAACATACTAGATTTTGGGAGCGATCCGACGGTAGACGGTGACCGAATTTGAGGTATAAGAT
*
1038537 TCGAATTTCTCTTGTAGATCTAGAAAAATCTAAAAAGAATTAGAAAAATCTAATTCCGGATTTGA
196 TCAAATTTCTCTTGTAGATCTAGAAAAATCTAAAAAGAATTAGAAAAATCTAATTCCGGATTTGA
1038602 A
261 A
1038603 AGAAGGGGTCGAAAAAAAAAAAAAGAAAGGAAGAGGCTTTC-AAAAAAACCAAAGTGGGTTTTCC
1 AGAAGGGGTCGAAAAAAAAAAAAAGAAAGGAAGAGGCTTTCAAAAAAAACCAAAGTGGGTTTTCC
1038667 GATTGAGGAGGTTCTGGTCATTGTTTGGAAAATCCGAACGGTGAGAAAGAAGTTCACACTAAGGG
66 GATTGAGGAGGTTCTGGTCATTGTTTGGAAAATCCGAACGGTGAGAAAGAAGTTCACACTAAGGG
1038732 TAAGAACATACTAGATTTTGGGAGCGATCCGACGGTAGACGGTGACCGAATTTGAGGTATAAGAT
131 TAAGAACATACTAGATTTTGGGAGCGATCCGACGGTAGACGGTGACCGAATTTGAGGTATAAGAT
1038797 TCAAATTTCTCTTGTAGATCTAGAAAAATCTAAAAAGAATTAGAAAAATCTAATTCCGGATTTGA
196 TCAAATTTCTCTTGTAGATCTAGAAAAATCTAAAAAGAATTAGAAAAATCTAATTCCGGATTTGA
1038862 A
261 A
1038863 A-AGAGGAGGTCGAAAA
1 AGA-AGG-GGTCGAAAA
1038879 GAGTCTAGAA
Statistics
Matches: 272, Mismatches: 1, Indels: 5
0.98 0.00 0.02
Matches are distributed among these distances:
259 1 0.00
260 233 0.86
261 38 0.14
ACGTcount: A:0.39, C:0.12, G:0.25, T:0.23
Consensus pattern (261 bp):
AGAAGGGGTCGAAAAAAAAAAAAAGAAAGGAAGAGGCTTTCAAAAAAAACCAAAGTGGGTTTTCC
GATTGAGGAGGTTCTGGTCATTGTTTGGAAAATCCGAACGGTGAGAAAGAAGTTCACACTAAGGG
TAAGAACATACTAGATTTTGGGAGCGATCCGACGGTAGACGGTGACCGAATTTGAGGTATAAGAT
TCAAATTTCTCTTGTAGATCTAGAAAAATCTAAAAAGAATTAGAAAAATCTAATTCCGGATTTGA
A
Found at i:1039032 original size:24 final size:24
Alignment explanation
Indices: 1039005--1039064 Score: 59
Period size: 24 Copynumber: 2.5 Consensus size: 24
1038995 GTTATGGGTT
*
1039005 GAAAAAAAAAAG-TTAAGTAAAAAA
1 GAAAAAAAAAAGATGAAG-AAAAAA
* * *
1039029 GAAAGAAAGAAGATGAAGAAGAAA
1 GAAAAAAAAAAGATGAAGAAAAAA
1039053 GAAAGAAAAAAA
1 GAAA-AAAAAAA
1039065 AAAAAGAGAA
Statistics
Matches: 28, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
24 19 0.68
25 9 0.32
ACGTcount: A:0.73, C:0.00, G:0.20, T:0.07
Consensus pattern (24 bp):
GAAAAAAAAAAGATGAAGAAAAAA
Found at i:1039460 original size:12 final size:12
Alignment explanation
Indices: 1039443--1039471 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
1039433 TTATTTTATT
1039443 TATATGTATATA
1 TATATGTATATA
1039455 TATATGTATATA
1 TATATGTATATA
1039467 TATAT
1 TATAT
1039472 ATTTTAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.52
Consensus pattern (12 bp):
TATATGTATATA
Found at i:1040996 original size:12 final size:12
Alignment explanation
Indices: 1040979--1041003 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1040969 AATTTTCTTT
1040979 TACTTGTCATTA
1 TACTTGTCATTA
1040991 TACTTGTCATTA
1 TACTTGTCATTA
1041003 T
1 T
1041004 GATGATTATT
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:0.24, C:0.16, G:0.08, T:0.52
Consensus pattern (12 bp):
TACTTGTCATTA
Found at i:1045514 original size:36 final size:35
Alignment explanation
Indices: 1045434--1045514 Score: 85
Period size: 36 Copynumber: 2.3 Consensus size: 35
1045424 TCAAAATGAC
* *
1045434 AAAAAAAAAAGTCAAAAGCAAAAGCACAAAAAATG
1 AAAACAAAAAGTCAAAAGCAAAAGCACAAAAAAGG
* *
1045469 AAAAGAAAAAGTGCAAAAGCAAAA-TA-AAAAAAGGG
1 AAAACAAAAAGT-CAAAAGCAAAAGCACAAAAAA-GG
1045504 AACAACAAAAA
1 AA-AACAAAAA
1045515 TAAAAAAAAC
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
34 6 0.15
35 15 0.38
36 18 0.46
ACGTcount: A:0.72, C:0.10, G:0.14, T:0.05
Consensus pattern (35 bp):
AAAACAAAAAGTCAAAAGCAAAAGCACAAAAAAGG
Found at i:1046900 original size:28 final size:28
Alignment explanation
Indices: 1046819--1047216 Score: 525
Period size: 28 Copynumber: 14.4 Consensus size: 28
1046809 GACCTTTTCA
* * * *
1046819 AAGTCCACGACTCAGTGGCATTTTCTTTT
1 AAGTCCACAACTCCGTGGCA-CTCCTTTT
* *
1046848 AAAGTCCACAACTCTGTGGCA-TCTTTTT
1 -AAGTCCACAACTCCGTGGCACTCCTTTT
1046876 AAGTCCACAACTCCGTGGCACT-CTTTT
1 AAGTCCACAACTCCGTGGCACTCCTTTT
1046903 AAGTCCACAACTCCGTGGCA-TCCCTTTT
1 AAGTCCACAACTCCGTGGCACT-CCTTTT
1046931 AAGTCCACAACTCCGTGGCAC-CCTTTT
1 AAGTCCACAACTCCGTGGCACTCCTTTT
1046958 AAAGTCCACAACTCCGTGGCAC-CCTTTTT
1 -AAGTCCACAACTCCGTGGCACTCC-TTTT
*
1046987 AAGTCCACAACTCCGTGGTA-TCCCTTTT
1 AAGTCCACAACTCCGTGGCACT-CCTTTT
*
1047015 AAGTCCACAACTCCGTGGTAC-CCTTTT
1 AAGTCCACAACTCCGTGGCACTCCTTTT
1047042 AAGTCCACAACTCCGTGGCAC-CCTTTT
1 AAGTCCACAACTCCGTGGCACTCCTTTT
1047069 AAGTCCACAACTCCGTGGCA-TCCTTTTT
1 AAGTCCACAACTCCGTGGCACTCC-TTTT
1047097 AAGTCCACAACTCCGTGGCAC-CCTTTT
1 AAGTCCACAACTCCGTGGCACTCCTTTT
1047124 AAGTCCACAACTCCGTGGCAC-CCTTTT
1 AAGTCCACAACTCCGTGGCACTCCTTTT
1047151 AAGTCCACAACTCCGTGGCA-TCCCTTTT
1 AAGTCCACAACTCCGTGGCACT-CCTTTT
* **
1047179 AAGTTCACAACTTTGTGGCAC-CCTTTTT
1 AAGTCCACAACTCCGTGGCACTCC-TTTT
1047207 AAGTCCACAA
1 AAGTCCACAA
1047217 GGCGGTGGCA
Statistics
Matches: 340, Mismatches: 12, Indels: 34
0.88 0.03 0.09
Matches are distributed among these distances:
26 1 0.00
27 156 0.46
28 159 0.47
29 6 0.02
30 18 0.05
ACGTcount: A:0.23, C:0.33, G:0.15, T:0.30
Consensus pattern (28 bp):
AAGTCCACAACTCCGTGGCACTCCTTTT
Found at i:1046958 original size:82 final size:82
Alignment explanation
Indices: 1046819--1047216 Score: 625
Period size: 82 Copynumber: 4.8 Consensus size: 82
1046809 GACCTTTTCA
* * ** * * *
1046819 AAGTCCACGACTCAGTGGCATTTTCTTTTAAAGTCCACAACTCTGTGGCATCTTTTTAAGTCCAC
1 AAGTCCACAACTCCGTGGCA-TCCCTTTT-AAGTCCACAACTCCGTGGCACCCTTTTAAGTCCAC
*
1046884 AACTCCGTGGCACTCTTTT
64 AACTCCGTGGCACCCTTTT
1046903 AAGTCCACAACTCCGTGGCATCCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAAGTCCACA
1 AAGTCCACAACTCCGTGGCATCCCTTTTAAGTCCACAACTCCGTGGCACCCTTTT-AAGTCCACA
1046968 ACTCCGTGGCACCCTTTTT
65 ACTCCGTGGCACCC-TTTT
* *
1046987 AAGTCCACAACTCCGTGGTATCCCTTTTAAGTCCACAACTCCGTGGTACCCTTTTAAGTCCACAA
1 AAGTCCACAACTCCGTGGCATCCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAA
1047052 CTCCGTGGCACCCTTTT
66 CTCCGTGGCACCCTTTT
*
1047069 AAGTCCACAACTCCGTGGCATCCTTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAA
1 AAGTCCACAACTCCGTGGCATCCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAA
1047134 CTCCGTGGCACCCTTTT
66 CTCCGTGGCACCCTTTT
* **
1047151 AAGTCCACAACTCCGTGGCATCCCTTTTAAGTTCACAACTTTGTGGCACCCTTTTTAAGTCCACA
1 AAGTCCACAACTCCGTGGCATCCCTTTTAAGTCCACAACTCCGTGGCACCC-TTTTAAGTCCACA
1047216 A
65 A
1047217 GGCGGTGGCA
Statistics
Matches: 294, Mismatches: 17, Indels: 7
0.92 0.05 0.02
Matches are distributed among these distances:
82 154 0.52
83 65 0.22
84 75 0.26
ACGTcount: A:0.23, C:0.33, G:0.15, T:0.30
Consensus pattern (82 bp):
AAGTCCACAACTCCGTGGCATCCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAA
CTCCGTGGCACCCTTTT
Found at i:1047226 original size:28 final size:27
Alignment explanation
Indices: 1046843--1047216 Score: 586
Period size: 27 Copynumber: 13.6 Consensus size: 27
1046833 GTGGCATTTT
* *
1046843 CTTTTAAAGTCCACAACTCTGTGGCATC
1 CTTTT-AAGTCCACAACTCCGTGGCACC
* *
1046871 TTTTTAAGTCCACAACTCCGTGGCACT
1 CTTTTAAGTCCACAACTCCGTGGCACC
1046898 CTTTTAAGTCCACAACTCCGTGGCATCC
1 CTTTTAAGTCCACAACTCCGTGGCA-CC
1046926 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
1046953 CTTTTAAAGTCCACAACTCCGTGGCACC
1 CTTTT-AAGTCCACAACTCCGTGGCACC
*
1046981 CTTTTTAAGTCCACAACTCCGTGGTATCC
1 C-TTTTAAGTCCACAACTCCGTGGCA-CC
*
1047010 CTTTTAAGTCCACAACTCCGTGGTACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
1047037 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
1047064 CTTTTAAGTCCACAACTCCGTGGCATCC
1 CTTTTAAGTCCACAACTCCGTGGCA-CC
*
1047092 TTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
1047119 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
1047146 CTTTTAAGTCCACAACTCCGTGGCATCC
1 CTTTTAAGTCCACAACTCCGTGGCA-CC
* **
1047174 CTTTTAAGTTCACAACTTTGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
1047201 CTTTTTAAGTCCACAA
1 C-TTTTAAGTCCACAA
1047217 GGCGGTGGCA
Statistics
Matches: 325, Mismatches: 14, Indels: 14
0.92 0.04 0.04
Matches are distributed among these distances:
27 159 0.49
28 159 0.49
29 7 0.02
ACGTcount: A:0.23, C:0.33, G:0.14, T:0.30
Consensus pattern (27 bp):
CTTTTAAGTCCACAACTCCGTGGCACC
Found at i:1047255 original size:30 final size:29
Alignment explanation
Indices: 1047221--1047302 Score: 105
Period size: 29 Copynumber: 2.8 Consensus size: 29
1047211 CCACAAGGCG
*
1047221 GTGGCATTCCCTTCTAAAGCCCACAAGTTA
1 GTGGCA-TCCTTTCTAAAGCCCACAAGTTA
*
1047251 GTGGCA-CCTTTTTCAAAGCCCACAAGTTA
1 GTGGCATCCTTTCT-AAAGCCCACAAGTTA
*
1047280 GTGGCATCTTTTC-AAAGCCCACA
1 GTGGCATCCTTTCTAAAGCCCACA
1047303 CAAGTCGGTG
Statistics
Matches: 46, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
28 15 0.33
29 21 0.46
30 10 0.22
ACGTcount: A:0.27, C:0.29, G:0.17, T:0.27
Consensus pattern (29 bp):
GTGGCATCCTTTCTAAAGCCCACAAGTTA
Found at i:1047330 original size:32 final size:32
Alignment explanation
Indices: 1047289--1047935 Score: 1159
Period size: 32 Copynumber: 20.2 Consensus size: 32
1047279 AGTGGCATCT
1047289 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
*
1047321 TTTCAAAGCCCACACAAGTCGGTGGCAACCCT
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
1047353 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
1047385 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
*
1047417 TTTCAAAGCCCTCACAAGTCGGTGGCAACCCA
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
1047449 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
1047481 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
1047513 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
1047545 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
*
1047577 TTCCAAAGCCCACACAAGTCGGTGGCAACCCA
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
1047609 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
*
1047641 TTTCAAAGCCCTCACAAGTCGGTGGCAACCCA
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
1047673 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
1047705 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
1047737 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
1047769 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
*
1047801 TTCCAAAGCCCACACAAGTCGGTGGCAACCCA
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
* *
1047833 TTTCAAAGCCCACACAAGTCGGTGGCGACCCT
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
* *
1047865 TTTCAAAGCCCACACAAGTCGATGGTAACCCA
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
* ** * * *
1047897 TTTAAAAGCCCATGCAAGTCAGTGGCACCCCT
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
1047929 TTTCAAA
1 TTTCAAA
1047936 TCGCCATTTT
Statistics
Matches: 590, Mismatches: 25, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
32 590 1.00
ACGTcount: A:0.31, C:0.34, G:0.19, T:0.17
Consensus pattern (32 bp):
TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
Found at i:1049228 original size:260 final size:261
Alignment explanation
Indices: 1048766--1049302 Score: 1024
Period size: 260 Copynumber: 2.1 Consensus size: 261
1048756 AAAAAAAGGG
1048766 AGAAGGGGTCGAAAAAAAAAAAAGAAAGGAAGAGGCTTTCAAAAAAAAACCAAAGTGGGTTTTCC
1 AGAAGGGGTCGAAAAAAAAAAAAGAAAGGAAGAGGCTTTCAAAAAAAAACCAAAGTGGGTTTTCC
1048831 GATTGAGGAGGTTCTGGTCATTGTTTGGAAAATCCGAACGGTGAGAAAGAAGTTCACACTAAGGG
66 GATTGAGGAGGTTCTGGTCATTGTTTGGAAAATCCGAACGGTGAGAAAGAAGTTCACACTAAGGG
*
1048896 TAAGAACATACTAGATTTTGGGAGCGATTCGACGGTAGACGGTGACCGAATTTGAGGTATAAGAT
131 TAAGAACATACTAGATTTTGGGAGCGATCCGACGGTAGACGGTGACCGAATTTGAGGTATAAGAT
1048961 TCGAATTTCTCTTGTAGATCTAGAAAAATCTAAAAAGAATTAGAAAAATCTAATTCCGGATTTGA
196 TCGAATTTCTCTTGTAGATCTAGAAAAATCTAAAAAGAATTAGAAAAATCTAATTCCGGATTTGA
1049026 A
261 A
1049027 AGAAGGGGTCGAAAAAAAAAAAAGAAAGGAAGAGGCTTTC-AAAAAAAACCAAAGTGGGTTTTCC
1 AGAAGGGGTCGAAAAAAAAAAAAGAAAGGAAGAGGCTTTCAAAAAAAAACCAAAGTGGGTTTTCC
1049091 GATTGAGGAGGTTCTGGTCATTGTTTGGAAAATCCGAACGGTGAGAAAGAAGTTCACACTAAGGG
66 GATTGAGGAGGTTCTGGTCATTGTTTGGAAAATCCGAACGGTGAGAAAGAAGTTCACACTAAGGG
*
1049156 TAAGAACATACTAGATTTTGGGAGCGATCCGACGGTAGACGGTTACCGAATTTGAGGTATAAGAT
131 TAAGAACATACTAGATTTTGGGAGCGATCCGACGGTAGACGGTGACCGAATTTGAGGTATAAGAT
1049221 TCGAATTTCTCTTGTAGATCTAGAAAAATCTAAAAAGAATTAGAAAAATCTAATTCCGGATTTGA
196 TCGAATTTCTCTTGTAGATCTAGAAAAATCTAAAAAGAATTAGAAAAATCTAATTCCGGATTTGA
1049286 A
261 A
1049287 A-AGAGGAGGTCGAAAA
1 AGA-AGG-GGTCGAAAA
1049303 GAGTCTAGAA
Statistics
Matches: 272, Mismatches: 2, Indels: 4
0.98 0.01 0.01
Matches are distributed among these distances:
259 1 0.00
260 222 0.82
261 49 0.18
ACGTcount: A:0.39, C:0.12, G:0.25, T:0.24
Consensus pattern (261 bp):
AGAAGGGGTCGAAAAAAAAAAAAGAAAGGAAGAGGCTTTCAAAAAAAAACCAAAGTGGGTTTTCC
GATTGAGGAGGTTCTGGTCATTGTTTGGAAAATCCGAACGGTGAGAAAGAAGTTCACACTAAGGG
TAAGAACATACTAGATTTTGGGAGCGATCCGACGGTAGACGGTGACCGAATTTGAGGTATAAGAT
TCGAATTTCTCTTGTAGATCTAGAAAAATCTAAAAAGAATTAGAAAAATCTAATTCCGGATTTGA
A
Found at i:1049456 original size:24 final size:24
Alignment explanation
Indices: 1049429--1049488 Score: 59
Period size: 24 Copynumber: 2.5 Consensus size: 24
1049419 GTTATGGGTT
*
1049429 GAAAAAAAAAAG-TTAAGTAAAAAA
1 GAAAAAAAAAAGATGAAG-AAAAAA
* * *
1049453 GAAAGAAAGAAGATGAAGAAGAAA
1 GAAAAAAAAAAGATGAAGAAAAAA
1049477 GAAAGAAAAAAA
1 GAAA-AAAAAAA
1049489 AAAAAGAGAA
Statistics
Matches: 28, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
24 19 0.68
25 9 0.32
ACGTcount: A:0.73, C:0.00, G:0.20, T:0.07
Consensus pattern (24 bp):
GAAAAAAAAAAGATGAAGAAAAAA
Found at i:1049884 original size:12 final size:12
Alignment explanation
Indices: 1049867--1049895 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
1049857 TTATTTTATT
1049867 TATATGTATATA
1 TATATGTATATA
1049879 TATATGTATATA
1 TATATGTATATA
1049891 TATAT
1 TATAT
1049896 ATTTTAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.52
Consensus pattern (12 bp):
TATATGTATATA
Found at i:1051420 original size:12 final size:12
Alignment explanation
Indices: 1051403--1051427 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1051393 AATTTTCTTT
1051403 TACTTGTCATTA
1 TACTTGTCATTA
1051415 TACTTGTCATTA
1 TACTTGTCATTA
1051427 T
1 T
1051428 GATGATTATT
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:0.24, C:0.16, G:0.08, T:0.52
Consensus pattern (12 bp):
TACTTGTCATTA
Found at i:1055350 original size:13 final size:13
Alignment explanation
Indices: 1055332--1055370 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
1055322 ACAATATTCT
1055332 TTGTATCGATACA
1 TTGTATCGATACA
*
1055345 TTGTATCGATATA
1 TTGTATCGATACA
1055358 TTGTATCGATACA
1 TTGTATCGATACA
1055371 AGGGTTACTA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.31, C:0.13, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:1057996 original size:13 final size:13
Alignment explanation
Indices: 1057978--1058002 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1057968 TATGGCACAT
1057978 TGTATCGATACAA
1 TGTATCGATACAA
1057991 TGTATCGATACA
1 TGTATCGATACA
1058003 TGATAAATTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1066100 original size:21 final size:21
Alignment explanation
Indices: 1066076--1066132 Score: 105
Period size: 21 Copynumber: 2.7 Consensus size: 21
1066066 AAATTATCCA
1066076 AATGTATCGATACATTTGTAG
1 AATGTATCGATACATTTGTAG
*
1066097 AATGTATCGATACATTTGTGG
1 AATGTATCGATACATTTGTAG
1066118 AATGTATCGATACAT
1 AATGTATCGATACAT
1066133 CCTACAAATG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.33, C:0.11, G:0.19, T:0.37
Consensus pattern (21 bp):
AATGTATCGATACATTTGTAG
Found at i:1066212 original size:19 final size:19
Alignment explanation
Indices: 1066188--1066255 Score: 85
Period size: 19 Copynumber: 3.9 Consensus size: 19
1066178 AATTCAACAA
1066188 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
1066207 TTTGTATCGATAC--AA--
1 TTTGTATCGATACATAAGT
1066222 --TGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
*
1066239 ATTGTATCGATACATAA
1 TTTGTATCGATACATAA
1066256 TTAGCTACTG
Statistics
Matches: 43, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
13 11 0.26
15 2 0.05
17 2 0.05
19 28 0.65
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:1066227 original size:13 final size:13
Alignment explanation
Indices: 1066209--1066233 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1066199 ACATAAGTTT
1066209 TGTATCGATACAA
1 TGTATCGATACAA
1066222 TGTATCGATACA
1 TGTATCGATACA
1066234 TAAGTATTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1066231 original size:32 final size:32
Alignment explanation
Indices: 1066190--1066252 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
1066180 TTCAACAATT
*
1066190 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTATTGTATCGATACAA
1066222 TGTATCGATACATAAGTATTGTATCGATACA
1 TGTATCGATACATAAGTATTGTATCGATACA
1066253 TAATTAGCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAGTATTGTATCGATACAA
Found at i:1066313 original size:13 final size:13
Alignment explanation
Indices: 1066295--1066320 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1066285 CATTTTTCTG
1066295 TGTATCGATACAT
1 TGTATCGATACAT
1066308 TGTATCGATACAT
1 TGTATCGATACAT
1066321 GGATCTTTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1066317 original size:33 final size:33
Alignment explanation
Indices: 1066275--1066341 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
1066265 GCCAAGGAAA
***
1066275 TGTATCGATACATTTTTCTGTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
*
1066308 TGTATCGATACATGGATCTTTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
1066341 T
1 T
1066342 TGGAAATTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.25, C:0.15, G:0.16, T:0.43
Consensus pattern (33 bp):
TGTATCGATACATGGATCTGTGTATCGATACAT
Found at i:1068812 original size:27 final size:28
Alignment explanation
Indices: 1068782--1068857 Score: 109
Period size: 27 Copynumber: 2.8 Consensus size: 28
1068772 AATTTTCACA
1068782 ATCGGGGATACTCCAACCCCGTTA-ATC
1 ATCGGGGATACTCCAACCCCGTTATATC
*
1068809 ATCGGGGATACTCCAACCCCGTTATTTC
1 ATCGGGGATACTCCAACCCCGTTATATC
***
1068837 CGAGGGGATACTCCAACCCCG
1 ATCGGGGATACTCCAACCCCG
1068858 ACTTTATTTC
Statistics
Matches: 44, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
27 24 0.55
28 20 0.45
ACGTcount: A:0.24, C:0.34, G:0.21, T:0.21
Consensus pattern (28 bp):
ATCGGGGATACTCCAACCCCGTTATATC
Found at i:1068965 original size:52 final size:51
Alignment explanation
Indices: 1068674--1069061 Score: 241
Period size: 52 Copynumber: 7.4 Consensus size: 51
1068664 CTCAATTCTC
* * * *
1068674 CACAATCGGGGATATTCCAACTCCGATTTTATTT-TCAAGACACTAA-TTTT
1 CACAATCGGGGATACTCCAACCCCGATTTTATTTCT-AAAACACCAATTTTT
* * * *
1068724 CTATAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAAACACCAAATTTT
1 C-ACAATCGGGGATACTCCAACCCCGATTTTATTT-C-TAAAACACCAATTTTT
* * ** **
1068778 CACAATCGGGGATACTCCAACCCCG-TTAATCATCGGGGATACTCCAAC-CCCGTTATTT
1 CACAATCGGGGATACTCCAACCCCGATT--TTAT------TTCTAAAACACCAATT-TTT
* * * * ***
1068836 C-CGA--GGGGATACTCCAACCCCGACTTTATTTCCAAAATATTGATTTTT
1 CACAATCGGGGATACTCCAACCCCGATTTTATTTCTAAAACACCAATTTTT
* * * * * *
1068884 CATAATCGGGGATATTCCAATCCCGGTTTTATTGCTAAAACACTAATTTTT
1 CACAATCGGGGATACTCCAACCCCGATTTTATTTCTAAAACACCAATTTTT
* * * *
1068935 CCACAATCGGGGATACTCCAACCCCGGTTTTATTTTTGAAACACCAATTTTC
1 -CACAATCGGGGATACTCCAACCCCGATTTTATTTCTAAAACACCAATTTTT
** * * *
1068987 CTTTAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAATACCAATTTTT
1 C-ACAATCGGGGATACTCCAACCCCGATTTTATTT-CTAAAACACCAATTTTT
* *
1069040 CACAGTCGAGGATACTCCAACC
1 CACAATCGGGGATACTCCAACC
1069062 TTGTTATTTC
Statistics
Matches: 256, Mismatches: 60, Indels: 42
0.72 0.17 0.12
Matches are distributed among these distances:
48 8 0.03
49 3 0.01
50 1 0.00
51 67 0.26
52 90 0.35
53 43 0.17
54 11 0.04
55 18 0.07
56 1 0.00
57 5 0.02
58 7 0.03
59 1 0.00
60 1 0.00
ACGTcount: A:0.29, C:0.26, G:0.13, T:0.32
Consensus pattern (51 bp):
CACAATCGGGGATACTCCAACCCCGATTTTATTTCTAAAACACCAATTTTT
Found at i:1069081 original size:28 final size:28
Alignment explanation
Indices: 1069049--1069120 Score: 90
Period size: 28 Copynumber: 2.6 Consensus size: 28
1069039 TCACAGTCGA
** * **
1069049 GGATACTCCAACCTTGTTATTTCATCGG
1 GGATACTCCAACCCCGTTACTTCAGAGG
*
1069077 GGATACTCCAACCCCGTTACTTCCGAGG
1 GGATACTCCAACCCCGTTACTTCAGAGG
1069105 GGATACTCCAACCCCG
1 GGATACTCCAACCCCG
1069121 GCTTTATTCC
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 38 1.00
ACGTcount: A:0.22, C:0.33, G:0.19, T:0.25
Consensus pattern (28 bp):
GGATACTCCAACCCCGTTACTTCAGAGG
Found at i:1069138 original size:263 final size:262
Alignment explanation
Indices: 1068672--1069171 Score: 779
Period size: 263 Copynumber: 1.9 Consensus size: 262
1068662 TTCTCAATTC
* * *
1068672 TCCACAATCGGGGATATTCCAACTCCGATTTTATTTTCAAGACACTAATTTTCTATAATCGGGGA
1 TCCACAATCGGGGATACTCCAACCCCGATTTTATTTTCAAGACACCAATTTTCTATAATCGGGGA
*
1068737 TACTCCAACTCCGATTTTATTTCCAAAAAACACCAAATTTTCACAATCGGGGATACTCCAACCCC
66 TACTCCAACTCCGATTTTATTTCCAAAAAACACCAAATTTTCACAATCGAGGATACTCCAACCCC
* *
1068802 GTTAATCATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGACTTTATTT
131 GTTAATCATCGGGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCCAACCCCGACTTTATTC
* * *
1068867 CCAAAATATTGATTTTTCATAATCGGGGATATTCCAATCCCGGTTTTATTGCTAAAACACTAATT
196 CCAAAATATTGATTTCTCATAATCGGGGATACTCCAACCCCGGTTTTATTGCTAAAACACTAATT
1068932 TT
261 TT
* * *
1068934 TCCACAATCGGGGATACTCCAACCCCGGTTTTATTTTTGAA-ACACCAATTTTCCTTTAATCGGG
1 TCCACAATCGGGGATACTCCAACCCCGATTTTA-TTTTCAAGACACCAATTTT-CTATAATCGGG
* * *
1068998 GATACTCCAACTCCGATTTTATTTCC-AAAAATACCAATTTTTCACAGTCGAGGATACTCCAACC
64 GATACTCCAACTCCGATTTTATTTCCAAAAAACACCAAATTTTCACAATCGAGGATACTCCAACC
** * *
1069062 TTGTTATTTCATCGGGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCCAACCCCGGCTTTA
129 CCGTTA-ATCATCGGGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCCAACCCCGACTTTA
*
1069127 TTCCCAAAATATTGATTTCTCATAATTGGGGATACTCCAACCCCG
193 TTCCCAAAATATTGATTTCTCATAATCGGGGATACTCCAACCCCG
1069172 TTATTTTCGA
Statistics
Matches: 215, Mismatches: 20, Indels: 5
0.90 0.08 0.02
Matches are distributed among these distances:
262 78 0.36
263 137 0.64
ACGTcount: A:0.28, C:0.27, G:0.14, T:0.31
Consensus pattern (262 bp):
TCCACAATCGGGGATACTCCAACCCCGATTTTATTTTCAAGACACCAATTTTCTATAATCGGGGA
TACTCCAACTCCGATTTTATTTCCAAAAAACACCAAATTTTCACAATCGAGGATACTCCAACCCC
GTTAATCATCGGGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCCAACCCCGACTTTATTC
CCAAAATATTGATTTCTCATAATCGGGGATACTCCAACCCCGGTTTTATTGCTAAAACACTAATT
TT
Found at i:1069253 original size:78 final size:78
Alignment explanation
Indices: 1069074--1069277 Score: 239
Period size: 78 Copynumber: 2.6 Consensus size: 78
1069064 GTTATTTCAT
* * *
1069074 CGGGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCCAACCCCGGCTTTATTCCCAAAATAT
1 CGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCC-GATTTATTCCCAAAATAT
* * *
1069139 TGATTTCTCATAAT
65 CGATTTCTCACAAC
* * * ** *
1069153 TGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAATCCCGATTTTTTTTC-TAATGAT
1 CGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGATTTATTCCCAAAAT-AT
1069217 CGATTTCTCACAAC
65 CGATTTCTCACAAC
* * * *
1069231 CGGGGATACTCCAGCCCCGTTATTTTCAAGGGAACACTCCAACCCCG
1 CGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCG
1069278 TTATTATCTC
Statistics
Matches: 106, Mismatches: 18, Indels: 3
0.83 0.14 0.02
Matches are distributed among these distances:
77 3 0.03
78 61 0.58
79 42 0.40
ACGTcount: A:0.24, C:0.30, G:0.18, T:0.28
Consensus pattern (78 bp):
CGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGATTTATTCCCAAAATATC
GATTTCTCACAAC
Found at i:1081692 original size:8 final size:8
Alignment explanation
Indices: 1081679--1081745 Score: 59
Period size: 8 Copynumber: 8.6 Consensus size: 8
1081669 CTTTTCTTCA
1081679 AAAAAAAG
1 AAAAAAAG
1081687 -AAAAAAG
1 AAAAAAAG
*
1081694 CAAAAAA-
1 AAAAAAAG
*
1081701 AAAAAAAC
1 AAAAAAAG
*
1081709 AAAAAAAC
1 AAAAAAAG
1081717 AAAACAAAG
1 AAAA-AAAG
*
1081726 AAAAAGAG
1 AAAAAAAG
*
1081734 -AGAAAAG
1 AAAAAAAG
1081741 AAAAA
1 AAAAA
1081746 GAACCTGCTT
Statistics
Matches: 49, Mismatches: 6, Indels: 8
0.78 0.10 0.13
Matches are distributed among these distances:
7 18 0.37
8 24 0.49
9 7 0.14
ACGTcount: A:0.84, C:0.06, G:0.10, T:0.00
Consensus pattern (8 bp):
AAAAAAAG
Found at i:1081704 original size:14 final size:13
Alignment explanation
Indices: 1081680--1081730 Score: 57
Period size: 13 Copynumber: 3.6 Consensus size: 13
1081670 TTTTCTTCAA
1081680 AAAAAAGAAAAAAGC
1 AAAAAA-AAAAAA-C
1081695 AAAAAAAAAAAAAC
1 -AAAAAAAAAAAAC
*
1081709 AAAAAAACAAAAC
1 AAAAAAAAAAAAC
1081722 AAAGAAAAA
1 AAA-AAAAA
1081731 GAGAGAAAAG
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
13 15 0.47
14 5 0.16
15 6 0.19
16 6 0.19
ACGTcount: A:0.86, C:0.08, G:0.06, T:0.00
Consensus pattern (13 bp):
AAAAAAAAAAAAC
Found at i:1082792 original size:55 final size:54
Alignment explanation
Indices: 1082710--1083292 Score: 738
Period size: 55 Copynumber: 10.4 Consensus size: 54
1082700 CTCCTTCCGC
1082710 TTTTCAGTCC-CAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA
1 TTTTCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA
1082763 TTTTCCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA
1 TTTT-CAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA
*
1082818 TTTTTCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAATTTGGTGGCA
1 -TTTTCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA
* * *
1082873 TTTTCCAGTCCTCAAAGAGCAGGACACCTTTTAAAGCCTACACAGGTTGGTGGCA
1 TTTT-CAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA
* * *
1082928 TTTTTCAGTCCTCAAAAAGCAGGATGCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCA
1 -TTTTCAGTCCTCAAAGAGCAGGA--C----ACCTTTCAAAGCCCACACAAGTTGGTGGCA
*
1082989 CCTTTCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA
1 -TTTTCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA
* * * *
1083044 TTTCCAGTCCTCAAAGGGCAGGACACCTTTTAAAGCCCACACAGGTTGGTGGCA
1 TTTTCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA
* *
1083098 TTTTTCAGTCCTCAAAGAGCAGGATGCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCA
1 -TTTTCAGTCCTCAAAGAGCAGGA--C----ACCTTTCAAAGCCCACACAAGTTGGTGGCA
* *
1083159 CCTTTCAGTCCCCAAAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCA
1 -TTTTCAGTCCTCAAAGAGCAGGACACCT-TTCAAAGCCCACACAAGTTGGTGGCA
* * * *
1083214 CCTTTCAGTCCTCAAAAAGCAGGACGCCTTTCAAAGCCCACACGAGTTGGTGGCA
1 -TTTTCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA
* * * *
1083269 CTTTTTACTCCTCAATGAGAAGGA
1 -TTTTCAGTCCTCAAAGAGCAGGA
1083293 TACACTTTAT
Statistics
Matches: 468, Mismatches: 42, Indels: 38
0.85 0.08 0.07
Matches are distributed among these distances:
53 4 0.01
54 61 0.13
55 296 0.63
56 10 0.02
57 2 0.00
59 2 0.00
61 93 0.20
ACGTcount: A:0.28, C:0.27, G:0.20, T:0.25
Consensus pattern (54 bp):
TTTTCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA
Found at i:1083128 original size:170 final size:171
Alignment explanation
Indices: 1082709--1083293 Score: 870
Period size: 170 Copynumber: 3.5 Consensus size: 171
1082699 TCTCCTTCCG
* * *
1082709 CTTTTCAGTCC-CAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTC
1 CTTTCCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAGGTTGGTGGCATTTTTCAGTC
* * **
1082773 CTCAAAGAGCAGGA--C----ACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTTCAGTCCTCA
66 CTCAAAGAGCAGGATGCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCA
*
1082832 AAGAGCAGGACACCTTTCAAAGCCCACACAATTTGGTGGCA
131 AAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA
* * *
1082873 TTTTCCAGTCCTCAAAGAGCAGGACACCTTTTAAAGCCTACACAGGTTGGTGGCATTTTTCAGTC
1 CTTTCCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAGGTTGGTGGCATTTTTCAGTC
*
1082938 CTCAAAAAGCAGGATGCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCA
66 CTCAAAGAGCAGGATGCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCA
1083003 AAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA
131 AAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA
* *
1083044 -TTTCCAGTCCTCAAAGGGCAGGACACCTTTTAAAGCCCACACAGGTTGGTGGCATTTTTCAGTC
1 CTTTCCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAGGTTGGTGGCATTTTTCAGTC
*
1083108 CTCAAAGAGCAGGATGCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCCCA
66 CTCAAAGAGCAGGATGCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCA
1083173 AAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCA
131 AAGAGCAGGACACCT-TTCAAAGCCCACACAAGTTGGTGGCA
* *
1083214 CCTTT-CAGTCCTCAAAAAGCAGGACGCCTTTCAAAGCCCACAC-GAGTTGGTGGCACTTTTT-A
1 -CTTTCCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAG-GTTGGTGGCA-TTTTTCA
* * *
1083276 CTCCTCAATGAGAAGGAT
63 GTCCTCAAAGAGCAGGAT
1083294 ACACTTTATT
Statistics
Matches: 386, Mismatches: 23, Indels: 17
0.91 0.05 0.04
Matches are distributed among these distances:
164 9 0.02
165 62 0.16
167 1 0.00
170 164 0.42
171 142 0.37
172 8 0.02
ACGTcount: A:0.28, C:0.28, G:0.20, T:0.25
Consensus pattern (171 bp):
CTTTCCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAGGTTGGTGGCATTTTTCAGTC
CTCAAAGAGCAGGATGCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCA
AAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA
Found at i:1083201 original size:225 final size:220
Alignment explanation
Indices: 1082711--1083273 Score: 783
Period size: 225 Copynumber: 2.5 Consensus size: 220
1082701 TCCTTCCGCT
*
1082711 TTTCAGT-CCCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA-TTTTCCAGTCC
1 TTTCAGTCCCCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCACCTTT-CAGTCC
*
1082774 TCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTTCAGTCCTCAAAGAGCA
65 TCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCA
*
1082839 GGACACCTTTCAAAGCCCACACAATTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACACCTTT
130 GGACACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACACCTTT
* * **
1082904 TAAAGCCTACACAGGTTGGTGGCATT
195 TAAAGCCCACACAAGTTGGTGGCACC
* * * *
1082930 TTTCAGTCCTCAAAAAGCAGGATGCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCACCTTTC
1 TTTCAGTCCCCAAAGAGCAGGA--C----ACCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTC
1082995 AGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA-TTTCCAGTCCTCAAA
60 AGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAA
* * * *
1083059 GGGCAGGACACCTTTTAAAGCCCACACAGGTTGGTGGCATTTTTCAGTCCTCAAAGAGCAGGATG
125 GAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGA--
**
1083124 CTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCACC
188 C---ACCTTTT-AAAGCCCACACAAGTTGGTGGCACC
1083161 TTTCAGTCCCCAAAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCACCTTTCAGTCC
1 TTTCAGTCCCCAAAGAGCAGGACACCT-TTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCC
* * *
1083225 TCAAAAAGCAGGACGCCTTTCAAAGCCCACACGAGTTGGTGGCACTTTT
65 TCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA-TTTT
1083274 TACTCCTCAA
Statistics
Matches: 303, Mismatches: 24, Indels: 26
0.86 0.07 0.07
Matches are distributed among these distances:
219 7 0.02
220 12 0.04
222 1 0.00
225 149 0.49
226 80 0.26
227 7 0.02
229 1 0.00
230 5 0.02
231 41 0.14
ACGTcount: A:0.28, C:0.28, G:0.20, T:0.25
Consensus pattern (220 bp):
TTTCAGTCCCCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCT
CAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAG
GACACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACACCTTTT
AAAGCCCACACAAGTTGGTGGCACC
Found at i:1083216 original size:29 final size:28
Alignment explanation
Indices: 1083136--1083218 Score: 75
Period size: 27 Copynumber: 3.0 Consensus size: 28
1083126 TTTTCTTTTC
1083136 AAAGCCCACACAAGTTGGTGGCACCTTT
1 AAAGCCCACACAAGTTGGTGGCACCTTT
* * **
1083164 -CAGTCCC-CA-AAG-AGCAGGACACCTCTT
1 AAAG-CCCACACAAGTTGGTGG-CACCT-TT
1083191 AAAGCCCACACAAGTTGGTGGCACCTTT
1 AAAGCCCACACAAGTTGGTGGCACCTTT
1083219 CAGTCCTCAA
Statistics
Matches: 40, Mismatches: 8, Indels: 14
0.65 0.13 0.23
Matches are distributed among these distances:
25 3 0.08
26 8 0.20
27 9 0.22
28 9 0.22
29 8 0.20
30 3 0.08
ACGTcount: A:0.29, C:0.31, G:0.20, T:0.19
Consensus pattern (28 bp):
AAAGCCCACACAAGTTGGTGGCACCTTT
Found at i:1084076 original size:21 final size:21
Alignment explanation
Indices: 1084052--1084108 Score: 105
Period size: 21 Copynumber: 2.7 Consensus size: 21
1084042 AAATTATCCA
1084052 AATGTATCGATACATTTGTAG
1 AATGTATCGATACATTTGTAG
*
1084073 AATGTATCGATACATTTGTGG
1 AATGTATCGATACATTTGTAG
1084094 AATGTATCGATACAT
1 AATGTATCGATACAT
1084109 CCTACAAATG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.33, C:0.11, G:0.19, T:0.37
Consensus pattern (21 bp):
AATGTATCGATACATTTGTAG
Found at i:1084188 original size:19 final size:19
Alignment explanation
Indices: 1084164--1084231 Score: 85
Period size: 19 Copynumber: 3.9 Consensus size: 19
1084154 AATTCAACAA
1084164 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
1084183 TTTGTATCGATAC--AA--
1 TTTGTATCGATACATAAGT
1084198 --TGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
*
1084215 ATTGTATCGATACATAA
1 TTTGTATCGATACATAA
1084232 TTAGCTACTA
Statistics
Matches: 43, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
13 11 0.26
15 2 0.05
17 2 0.05
19 28 0.65
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:1084203 original size:13 final size:13
Alignment explanation
Indices: 1084185--1084209 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1084175 ACATAAGTTT
1084185 TGTATCGATACAA
1 TGTATCGATACAA
1084198 TGTATCGATACA
1 TGTATCGATACA
1084210 TAAGTATTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1084207 original size:32 final size:32
Alignment explanation
Indices: 1084166--1084228 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
1084156 TTCAACAATT
*
1084166 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTATTGTATCGATACAA
1084198 TGTATCGATACATAAGTATTGTATCGATACA
1 TGTATCGATACATAAGTATTGTATCGATACA
1084229 TAATTAGCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAGTATTGTATCGATACAA
Found at i:1084289 original size:13 final size:13
Alignment explanation
Indices: 1084271--1084296 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1084261 CATTTTTCTG
1084271 TGTATCGATACAT
1 TGTATCGATACAT
1084284 TGTATCGATACAT
1 TGTATCGATACAT
1084297 GGATCTTTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1084293 original size:33 final size:33
Alignment explanation
Indices: 1084251--1084317 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
1084241 ACCAAGGAAA
***
1084251 TGTATCGATACATTTTTCTGTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
*
1084284 TGTATCGATACATGGATCTTTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
1084317 T
1 T
1084318 TGGAAATTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.25, C:0.15, G:0.16, T:0.43
Consensus pattern (33 bp):
TGTATCGATACATGGATCTGTGTATCGATACAT
Found at i:1086679 original size:51 final size:52
Alignment explanation
Indices: 1086620--1087006 Score: 215
Period size: 52 Copynumber: 7.4 Consensus size: 52
1086610 CTCAATTCTC
* * * *
1086620 CACAATCGGGGATATTCCAACTCCGATTTTATTTTC-AAGACA-CTAATTTT
1 CACAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAACACCAAATTTT
*
1086670 CTATAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAAACACCAAATTTT
1 C-ACAATCGGGGATACTCCAACTCCGATTTTATTTCC-AAAAACACCAAATTTT
* * * *** * * *
1086724 CACAATCGGGGATACTCCAACCCCG--TTAATCATCGGGGATACTCCAACCCCGTTATTT
1 CACAATCGGGGATACTCCAACTCCGATTTTAT-TTC-CAAAAACACCAA-----AT-TTT
* * * * *** *
1086782 C-CGA--GGGGATACTCCAACCCCGACTTTATTTCC-AAAATATTGATTTTT
1 CACAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAACACCAAATTTT
* * * * * *
1086830 CATAATCGGGGATATTCCAA-TCCCAGTTTTA-TTGCTAAAACACCAATTTTT
1 CACAATCGGGGATACTCCAACTCCGA-TTTTATTTCCAAAAACACCAAATTTT
* * * *
1086881 CCACAATCGGGGATACTCCAACCCCGGTTTTATTTTC-GAAACACC-AATTTT
1 -CACAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAACACCAAATTTT
* * *
1086932 C-CTTTAATCGGGGATACTCTAACTCCGATTTTATTTCCAAAAATACCAATTTTT
1 CAC---AATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAACACCAAATTTT
* *
1086986 CACAGTCGAGGATACTCCAAC
1 CACAATCGGGGATACTCCAAC
1087007 CTTGTTATTT
Statistics
Matches: 254, Mismatches: 55, Indels: 54
0.70 0.15 0.15
Matches are distributed among these distances:
48 4 0.02
49 4 0.02
50 8 0.03
51 68 0.27
52 83 0.33
53 38 0.15
54 17 0.07
55 19 0.07
56 2 0.01
57 7 0.03
58 4 0.02
ACGTcount: A:0.30, C:0.26, G:0.13, T:0.32
Consensus pattern (52 bp):
CACAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAACACCAAATTTT
Found at i:1086758 original size:27 final size:28
Alignment explanation
Indices: 1086728--1086803 Score: 109
Period size: 27 Copynumber: 2.8 Consensus size: 28
1086718 AATTTTCACA
1086728 ATCGGGGATACTCCAACCCCGTTA-ATC
1 ATCGGGGATACTCCAACCCCGTTATATC
*
1086755 ATCGGGGATACTCCAACCCCGTTATTTC
1 ATCGGGGATACTCCAACCCCGTTATATC
***
1086783 CGAGGGGATACTCCAACCCCG
1 ATCGGGGATACTCCAACCCCG
1086804 ACTTTATTTC
Statistics
Matches: 44, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
27 24 0.55
28 20 0.45
ACGTcount: A:0.24, C:0.34, G:0.21, T:0.21
Consensus pattern (28 bp):
ATCGGGGATACTCCAACCCCGTTATATC
Found at i:1087041 original size:28 final size:28
Alignment explanation
Indices: 1086993--1087066 Score: 89
Period size: 28 Copynumber: 2.6 Consensus size: 28
1086983 TTTCACAGTC
**
1086993 GAGGATACTCCAACCTTGTTA-TTTC-A
1 GAGGATACTCCAACCCCGTTACTTTCGA
*
1087019 TCGGGGATACTCCAACCCCGTTACTTTCGA
1 --GAGGATACTCCAACCCCGTTACTTTCGA
1087049 GAGGATACTCCAACCCCG
1 GAGGATACTCCAACCCCG
1087067 GCTTTATTCC
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
28 35 0.88
29 4 0.10
30 1 0.03
ACGTcount: A:0.24, C:0.31, G:0.19, T:0.26
Consensus pattern (28 bp):
GAGGATACTCCAACCCCGTTACTTTCGA
Found at i:1087084 original size:263 final size:262
Alignment explanation
Indices: 1086618--1087112 Score: 762
Period size: 263 Copynumber: 1.9 Consensus size: 262
1086608 TTCTCAATTC
* * *
1086618 TCCACAATCGGGGATATTCCAACTCCGATTTTATTTTCAAGACACTAATTTTCTATAATCGGGGA
1 TCCACAATCGGGGATACTCCAACCCCGATTTTATTTTCAAGACACCAATTTTCTATAATCGGGGA
*
1086683 TACTCCAACTCCGATTTTATTTCCAAAAAACACCAAATTTTCACAATCGGGGATACTCCAACCCC
66 TACTCCAACTCCGATTTTATTTCCAAAAAACACCAAATTTTCACAATCGAGGATACTCCAACCCC
* *
1086748 GTTAATCATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGACTTTATTT
131 GTTAATCATCGGGGATACTCCAACCCCGTTATTTCCGAGAGGATACTCCAACCCCGACTTTATTC
* *
1086813 CCAAAATATTGATTTTTCATAATCGGGGATATTCCAATCCCAGTTTTATTGCTAAAACACCAATT
196 CCAAAATATTGATTTCTCATAATCGGGGATACTCCAATCCCAGTTTTATTGCTAAAACACCAATT
1086878 TT
261 TT
* *
1086880 TCCACAATCGGGGATACTCCAACCCCGGTTTTATTTTCGAA-ACACCAATTTTCCTTTAATCGGG
1 TCCACAATCGGGGATACTCCAACCCCGATTTTATTTTC-AAGACACCAATTTT-CTATAATCGGG
* * * *
1086944 GATACTCTAACTCCGATTTTATTTCC-AAAAATACCAATTTTTCACAGTCGAGGATACTCCAACC
64 GATACTCCAACTCCGATTTTATTTCCAAAAAACACCAAATTTTCACAATCGAGGATACTCCAACC
** * *
1087008 TTGTTATTTCATCGGGGATACTCCAACCCCGTTACTTT-CGAGAGGATACTCCAACCCCGGCTTT
129 CCGTTA-ATCATCGGGGATACTCCAACCCCGTTA-TTTCCGAGAGGATACTCCAACCCCGACTTT
*
1087072 ATTCCCAAAATATTGATTTCTCATAATTGGGGATACTCCAA
192 ATTCCCAAAATATTGATTTCTCATAATCGGGGATACTCCAA
1087113 CCCCGTTATT
Statistics
Matches: 210, Mismatches: 19, Indels: 7
0.89 0.08 0.03
Matches are distributed among these distances:
262 83 0.40
263 124 0.59
264 3 0.01
ACGTcount: A:0.29, C:0.26, G:0.14, T:0.32
Consensus pattern (262 bp):
TCCACAATCGGGGATACTCCAACCCCGATTTTATTTTCAAGACACCAATTTTCTATAATCGGGGA
TACTCCAACTCCGATTTTATTTCCAAAAAACACCAAATTTTCACAATCGAGGATACTCCAACCCC
GTTAATCATCGGGGATACTCCAACCCCGTTATTTCCGAGAGGATACTCCAACCCCGACTTTATTC
CCAAAATATTGATTTCTCATAATCGGGGATACTCCAATCCCAGTTTTATTGCTAAAACACCAATT
TT
Found at i:1087199 original size:78 final size:78
Alignment explanation
Indices: 1087018--1087223 Score: 252
Period size: 78 Copynumber: 2.6 Consensus size: 78
1087008 TTGTTATTTC
* * *
1087018 ATCGGGGATACTCCAACCCCGTTACTTTCGAGAGGATACTCCAACCCCGGCTTTATTCCCAAAAT
1 ATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCC-GATTTATTCCCAAAAT
* *
1087083 ATTGATTTCTCATA
65 ATCGATTTCTCACA
* * * ** *
1087097 ATTGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAATCCCGATTTTTTTTC-TAATC
1 ATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGATTTATTCCCAAAAT-
1087161 ATCGATTTCTCACA
65 ATCGATTTCTCACA
* * * *
1087175 ATCGGGGATACTCCAGCCCCGTTATTTTCAAGGGAACACTCCAACCCCG
1 ATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCG
1087224 TTATTATCTC
Statistics
Matches: 109, Mismatches: 17, Indels: 3
0.84 0.13 0.02
Matches are distributed among these distances:
77 3 0.03
78 62 0.57
79 44 0.40
ACGTcount: A:0.25, C:0.29, G:0.17, T:0.30
Consensus pattern (78 bp):
ATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGATTTATTCCCAAAATA
TCGATTTCTCACA
Found at i:1090479 original size:3 final size:3
Alignment explanation
Indices: 1090464--1090501 Score: 58
Period size: 3 Copynumber: 12.7 Consensus size: 3
1090454 AACCGTCAAA
* *
1090464 GAT GAT GAA GAT GAT GAT GAT GAT GAT GAT AAT GAT GA
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GA
1090502 GGTTGACTCG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.39, C:0.00, G:0.32, T:0.29
Consensus pattern (3 bp):
GAT
Found at i:1096277 original size:20 final size:19
Alignment explanation
Indices: 1096252--1096324 Score: 76
Period size: 20 Copynumber: 3.7 Consensus size: 19
1096242 TTTCCAGTTT
**
1096252 CATGTATCGATACAATTGTC
1 CATGTATCGATACAA-TGAA
*
1096272 CATGTATCAATACAATGAA
1 CATGTATCGATACAATGAA
*
1096291 CATGTATCGATACAAAGCATA
1 CATGTATCGATACAATG-A-A
1096312 -ATGTATCGATACA
1 CATGTATCGATACA
1096325 TCTGGGTGTG
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
19 17 0.37
20 28 0.61
21 1 0.02
ACGTcount: A:0.40, C:0.18, G:0.14, T:0.29
Consensus pattern (19 bp):
CATGTATCGATACAATGAA
Found at i:1096296 original size:19 final size:20
Alignment explanation
Indices: 1096252--1096305 Score: 74
Period size: 19 Copynumber: 2.8 Consensus size: 20
1096242 TTTCCAGTTT
**
1096252 CATGTATCGATACAATTGTC
1 CATGTATCGATACAATTGAA
*
1096272 CATGTATCAATACAA-TGAA
1 CATGTATCGATACAATTGAA
1096291 CATGTATCGATACAA
1 CATGTATCGATACAA
1096306 AGCATAATGT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
19 16 0.53
20 14 0.47
ACGTcount: A:0.39, C:0.19, G:0.13, T:0.30
Consensus pattern (20 bp):
CATGTATCGATACAATTGAA
Found at i:1098632 original size:22 final size:21
Alignment explanation
Indices: 1098597--1098646 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
1098587 TTTGTGGATG
*
1098597 ATTTTG-A-TGAAAAATGAAGT
1 ATTTTGAAGTGAAAAAT-AAGA
1098617 ATTTTGAAGTGAAAAATAAGA
1 ATTTTGAAGTGAAAAATAAGA
*
1098638 AATTTGAAG
1 ATTTTGAAG
1098647 AAGATTTGAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
20 6 0.23
21 12 0.46
22 8 0.31
ACGTcount: A:0.48, C:0.00, G:0.20, T:0.32
Consensus pattern (21 bp):
ATTTTGAAGTGAAAAATAAGA
Found at i:1098643 original size:21 final size:22
Alignment explanation
Indices: 1098604--1098646 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
1098594 ATGATTTTGA
* *
1098604 TGAAAAATGAAGTATTTTGAAG
1 TGAAAAATGAAGAAATTTGAAG
1098626 TGAAAAAT-AAGAAATTTGAAG
1 TGAAAAATGAAGAAATTTGAAG
1098647 AAGATTTGAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 11 0.58
22 8 0.42
ACGTcount: A:0.51, C:0.00, G:0.21, T:0.28
Consensus pattern (22 bp):
TGAAAAATGAAGAAATTTGAAG
Found at i:1102584 original size:20 final size:19
Alignment explanation
Indices: 1102561--1102655 Score: 100
Period size: 20 Copynumber: 4.8 Consensus size: 19
1102551 AAAAAGACAG
1102561 AATGTATCGATACATTGAA
1 AATGTATCGATACATTGAA
* *
1102580 GAATGTATCGATATATTCGTA
1 -AATGTATCGATACATT-GAA
* *
1102601 CATGTATCGATACATTCATA
1 AATGTATCGATACATTGA-A
* *
1102621 CATGTATCGATACATTAAAA
1 AATGTATCGATACATT-GAA
1102641 AATGTATCGATACAT
1 AATGTATCGATACAT
1102656 CTAGGTAAAA
Statistics
Matches: 64, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
20 61 0.95
21 3 0.05
ACGTcount: A:0.39, C:0.14, G:0.14, T:0.34
Consensus pattern (19 bp):
AATGTATCGATACATTGAA
Found at i:1102626 original size:40 final size:40
Alignment explanation
Indices: 1102561--1102655 Score: 111
Period size: 40 Copynumber: 2.4 Consensus size: 40
1102551 AAAAAGACAG
* * ***
1102561 AATGTATCGATACATTGAAGAATGTATCGATATATTCGTA
1 AATGTATCGATACATTCAAGAATGTATCGATACATTAAAA
* *
1102601 CATGTATCGATACATTCATA-CATGTATCGATACATTAAAA
1 AATGTATCGATACATTCA-AGAATGTATCGATACATTAAAA
1102641 AATGTATCGATACAT
1 AATGTATCGATACAT
1102656 CTAGGTAAAA
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
40 45 0.98
41 1 0.02
ACGTcount: A:0.39, C:0.14, G:0.14, T:0.34
Consensus pattern (40 bp):
AATGTATCGATACATTCAAGAATGTATCGATACATTAAAA
Found at i:1102715 original size:40 final size:40
Alignment explanation
Indices: 1102670--1102799 Score: 125
Period size: 40 Copynumber: 3.5 Consensus size: 40
1102660 GTAAAAAGAC
*
1102670 AAAATGTATCGATGCATTCATACATGTATCGATACATTGA
1 AAAATGTATCGATACATTCATACATGTATCGATACATTGA
* ** **
1102710 AAAATGTATCAATACA-TC-T--GGGTA---A-A-AAAGA
1 AAAATGTATCGATACATTCATACATGTATCGATACATTGA
*
1102741 TATAATGTATCGATACATTCATACATGTATCGATACATTGA
1 -AAAATGTATCGATACATTCATACATGTATCGATACATTGA
1102782 AAAATGTATCGATACATT
1 AAAATGTATCGATACATT
1102800 TAGGTAAAAA
Statistics
Matches: 67, Mismatches: 13, Indels: 20
0.67 0.13 0.20
Matches are distributed among these distances:
31 3 0.04
32 15 0.22
33 3 0.04
34 1 0.01
36 6 0.09
38 1 0.01
39 3 0.04
40 32 0.48
41 3 0.04
ACGTcount: A:0.42, C:0.13, G:0.14, T:0.32
Consensus pattern (40 bp):
AAAATGTATCGATACATTCATACATGTATCGATACATTGA
Found at i:1102716 original size:20 final size:20
Alignment explanation
Indices: 1102670--1102799 Score: 80
Period size: 20 Copynumber: 5.9 Consensus size: 20
1102660 GTAAAAAGAC
* *
1102670 AAAATGTATCGATGCATTCA
1 AAAATGTATCGATACATTGA
* *
1102690 TACATGTATCGATACATTGA
1 AAAATGTATCGATACATTGA
*
1102710 AAAATGTATCAATACATCTGGGTAAAA
1 AAAATGTATCGATACAT-T--G----A
*
1102737 AAGATATAATGTATCGATACATTCA
1 AA-A-AT---GTATCGATACATTGA
* *
1102762 TACATGTATCGATACATTGA
1 AAAATGTATCGATACATTGA
1102782 AAAATGTATCGATACATT
1 AAAATGTATCGATACATT
1102800 TAGGTAAAAA
Statistics
Matches: 84, Mismatches: 14, Indels: 24
0.69 0.11 0.20
Matches are distributed among these distances:
20 60 0.71
21 1 0.01
23 3 0.04
25 2 0.02
27 3 0.04
28 1 0.01
29 2 0.02
31 1 0.01
32 11 0.13
ACGTcount: A:0.42, C:0.13, G:0.14, T:0.32
Consensus pattern (20 bp):
AAAATGTATCGATACATTGA
Found at i:1102717 original size:111 final size:111
Alignment explanation
Indices: 1102511--1102726 Score: 265
Period size: 111 Copynumber: 1.9 Consensus size: 111
1102501 TTTTAACTAG
*** * * *
1102511 ATGTATCGATACAATATTCAATATATCGATACATTTGGGTAAAAAGACAGAATGTATCGATACAT
1 ATGTATCGATACAATAAAAAATATATCGATACATCTAGGTAAAAAGACAAAATGTATCGATACAT
* * * * *
1102576 TGAAGAATGTATCGATATATTCGTACATGTATCGATACATTCATAC
66 TCAAGAATGTATCGATACATTCGAAAATGTATCAATACATTCATAC
* * *
1102622 ATGTATCGATACATTAAAAAATGTATCGATACATCTAGGTAAAAAGACAAAATGTATCGATGCAT
1 ATGTATCGATACAATAAAAAATATATCGATACATCTAGGTAAAAAGACAAAATGTATCGATACAT
*
1102687 TCATA-CATGTATCGATACATT-GAAAAATGTATCAATACAT
66 TCA-AGAATGTATCGATACATTCG-AAAATGTATCAATACAT
1102727 CTGGGTAAAA
Statistics
Matches: 88, Mismatches: 15, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
110 1 0.01
111 86 0.98
112 1 0.01
ACGTcount: A:0.41, C:0.13, G:0.14, T:0.31
Consensus pattern (111 bp):
ATGTATCGATACAATAAAAAATATATCGATACATCTAGGTAAAAAGACAAAATGTATCGATACAT
TCAAGAATGTATCGATACATTCGAAAATGTATCAATACATTCATAC
Found at i:1102760 original size:72 final size:72
Alignment explanation
Indices: 1102602--1102809 Score: 346
Period size: 72 Copynumber: 2.9 Consensus size: 72
1102592 ATATTCGTAC
*
1102602 ATGTATCGATACATTCATACATGTATCGATACATTAAAAAATGTATCGATACATCTAGGT-AAAA
1 ATGTATCGATACATTCATACATGTATCGATACATTGAAAAATGTATCGATACATCTAGGTAAAAA
1102666 AGACAAA
66 AGACAAA
* * *
1102673 ATGTATCGATGCATTCATACATGTATCGATACATTGAAAAATGTATCAATACATCTGGGTAAAAA
1 ATGTATCGATACATTCATACATGTATCGATACATTGAAAAATGTATCGATACATCTAGGTAAAAA
* *
1102738 AGATATA
66 AGACAAA
*
1102745 ATGTATCGATACATTCATACATGTATCGATACATTGAAAAATGTATCGATACATTTAGGTAAAAA
1 ATGTATCGATACATTCATACATGTATCGATACATTGAAAAATGTATCGATACATCTAGGTAAAAA
1102810 TGTGACTTTT
Statistics
Matches: 126, Mismatches: 10, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
71 56 0.44
72 70 0.56
ACGTcount: A:0.43, C:0.13, G:0.14, T:0.30
Consensus pattern (72 bp):
ATGTATCGATACATTCATACATGTATCGATACATTGAAAAATGTATCGATACATCTAGGTAAAAA
AGACAAA
Found at i:1103713 original size:32 final size:32
Alignment explanation
Indices: 1103676--1103756 Score: 96
Period size: 32 Copynumber: 2.6 Consensus size: 32
1103666 GGTGCCATTA
1103676 ACTTGTATGGGCTTTGAAAAGAGT-TACCACCG
1 ACTTGT-TGGGCTTTGAAAAGAGTATACCACCG
* * *
1103708 ACTTGTGTGGGCTTTG-AAAGGGTATGCCACTG
1 ACTTGT-TGGGCTTTGAAAAGAGTATACCACCG
1103740 ACTTG-TGGGCTTTGAAA
1 ACTTGTTGGGCTTTGAAA
1103757 GGGTGCCACT
Statistics
Matches: 43, Mismatches: 4, Indels: 5
0.83 0.08 0.10
Matches are distributed among these distances:
30 9 0.21
31 8 0.19
32 26 0.60
ACGTcount: A:0.23, C:0.16, G:0.30, T:0.31
Consensus pattern (32 bp):
ACTTGTTGGGCTTTGAAAAGAGTATACCACCG
Found at i:1103772 original size:28 final size:28
Alignment explanation
Indices: 1103713--1103896 Score: 208
Period size: 28 Copynumber: 6.5 Consensus size: 28
1103703 CACCGACTTG
*
1103713 TGTGGGCTTTGAAAGGGTATGCCACTGACT
1 TGTGGGCTTTGAAAGGG--TGCCACTAACT
1103743 TGTGGGCTTTGAAAGGGTGCCACTAACT
1 TGTGGGCTTTGAAAGGGTGCCACTAACT
* * * * *
1103771 TGTAGTCTTT-AAAGGGGTACCATTGACT
1 TGTGGGCTTTGAAA-GGGTGCCACTAACT
1103799 TGTGGGCTTTGAAAGGGTGCCACTAACT
1 TGTGGGCTTTGAAAGGGTGCCACTAACT
* * *
1103827 TGTAGGCTTTGAAAGTGTGCCACTAATT
1 TGTGGGCTTTGAAAGGGTGCCACTAACT
* * *
1103855 TATAGGGCTTTGAAAGGATGCCACTAACC
1 TGT-GGGCTTTGAAAGGGTGCCACTAACT
*
1103884 TATGGGCTTTGAA
1 TGTGGGCTTTGAA
1103897 GAGATGAACG
Statistics
Matches: 131, Mismatches: 20, Indels: 8
0.82 0.13 0.05
Matches are distributed among these distances:
27 3 0.02
28 85 0.65
29 26 0.20
30 17 0.13
ACGTcount: A:0.24, C:0.16, G:0.29, T:0.31
Consensus pattern (28 bp):
TGTGGGCTTTGAAAGGGTGCCACTAACT
Found at i:1105192 original size:13 final size:13
Alignment explanation
Indices: 1105167--1105208 Score: 52
Period size: 12 Copynumber: 3.3 Consensus size: 13
1105157 ATTTTTTCTA
*
1105167 TTTTT-TTGTTTT
1 TTTTTCTTGGTTT
1105179 TTTTTCTTGG-TT
1 TTTTTCTTGGTTT
1105191 TTTTTCTTGGCTTT
1 TTTTTCTTGG-TTT
1105205 TTTT
1 TTTT
1105209 GTTCTTTTTG
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
12 17 0.65
13 3 0.12
14 6 0.23
ACGTcount: A:0.00, C:0.07, G:0.12, T:0.81
Consensus pattern (13 bp):
TTTTTCTTGGTTT
Found at i:1105196 original size:12 final size:13
Alignment explanation
Indices: 1105177--1105208 Score: 57
Period size: 12 Copynumber: 2.5 Consensus size: 13
1105167 TTTTTTTGTT
1105177 TTTTTTTCTTGG-
1 TTTTTTTCTTGGC
1105189 TTTTTTTCTTGGC
1 TTTTTTTCTTGGC
1105202 TTTTTTT
1 TTTTTTT
1105209 GTTCTTTTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 12 0.63
13 7 0.37
ACGTcount: A:0.00, C:0.09, G:0.12, T:0.78
Consensus pattern (13 bp):
TTTTTTTCTTGGC
Found at i:1149804 original size:19 final size:19
Alignment explanation
Indices: 1149779--1149835 Score: 62
Period size: 19 Copynumber: 2.9 Consensus size: 19
1149769 AGGTAAAAGA
1149779 CAGAATGTATCGATACATT
1 CAGAATGTATCGATACATT
* *
1149798 GAGAATGCATCG-TAACATT
1 CAGAATGTATCGAT-ACATT
*
1149817 CATACATGTATCGATACAT
1 CAGA-ATGTATCGATACAT
1149836 CTGGGTAAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 5
0.75 0.12 0.12
Matches are distributed among these distances:
18 1 0.03
19 17 0.57
20 11 0.37
21 1 0.03
ACGTcount: A:0.37, C:0.18, G:0.16, T:0.30
Consensus pattern (19 bp):
CAGAATGTATCGATACATT
Found at i:1149929 original size:51 final size:52
Alignment explanation
Indices: 1149799--1149939 Score: 157
Period size: 51 Copynumber: 2.8 Consensus size: 52
1149789 CGATACATTG
* * * *
1149799 AGAATGCATCG-TAACATTCATACATGTATCGATACATCTGGGTAAAAAGAC
1 AGAATGTATCGATTACATTCATACATGTATCGATACATTTGGGAAAAAAGAC
* * *
1149850 ATAATGTATCGATTACA-TGA-AAATTGTATCGATACATTTGGGAAAAAAAGAC
1 AGAATGTATCGATTACATTCATACA-TGTATCGATACATTTGGG-AAAAAAGAC
*
1149902 AGAATG-ATCGA-TGCATTCATACATGTATCGATACATTT
1 AGAATGTATCGATTACATTCATACATGTATCGATACATTT
1149940 TTCAATGTAT
Statistics
Matches: 74, Mismatches: 11, Indels: 10
0.78 0.12 0.11
Matches are distributed among these distances:
50 5 0.07
51 50 0.68
52 19 0.26
ACGTcount: A:0.40, C:0.14, G:0.17, T:0.29
Consensus pattern (52 bp):
AGAATGTATCGATTACATTCATACATGTATCGATACATTTGGGAAAAAAGAC
Found at i:1154515 original size:21 final size:18
Alignment explanation
Indices: 1154491--1154549 Score: 55
Period size: 19 Copynumber: 3.1 Consensus size: 18
1154481 TTTCAACAAT
1154491 TTGTATCGATACAACCAGTAA
1 TTGTATCGATACAA--AGT-A
* *
1154512 TTGTATTGATACATAAGTG
1 TTGTATCGATACA-AAGTA
*
1154531 TTGTATCGATACAATGTA
1 TTGTATCGATACAAAGTA
1154549 T
1 T
1154550 CGCTACAAAG
Statistics
Matches: 32, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
18 4 0.12
19 12 0.38
20 3 0.09
21 12 0.38
22 1 0.03
ACGTcount: A:0.34, C:0.12, G:0.17, T:0.37
Consensus pattern (18 bp):
TTGTATCGATACAAAGTA
Found at i:1158673 original size:13 final size:13
Alignment explanation
Indices: 1158655--1158680 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1158645 TACAAAAAAT
1158655 ATGTATCGATACA
1 ATGTATCGATACA
1158668 ATGTATCGATACA
1 ATGTATCGATACA
1158681 CAAAAAAATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1158673 original size:32 final size:34
Alignment explanation
Indices: 1158637--1158701 Score: 107
Period size: 32 Copynumber: 2.0 Consensus size: 34
1158627 TAGCCAAACT
*
1158637 TGTATCGATACA-AAAAATA-TGTATCGATACAA
1 TGTATCGATACACAAAAAAATTGTATCGATACAA
1158669 TGTATCGATACACAAAAAAATTGTATCGATACA
1 TGTATCGATACACAAAAAAATTGTATCGATACA
1158702 TTGGCTTGTA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
32 12 0.40
33 6 0.20
34 12 0.40
ACGTcount: A:0.46, C:0.14, G:0.12, T:0.28
Consensus pattern (34 bp):
TGTATCGATACACAAAAAAATTGTATCGATACAA
Found at i:1160915 original size:21 final size:21
Alignment explanation
Indices: 1160882--1160931 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 21
1160872 TTGCAAGTTG
*
1160882 AAATAAAGAAGTTGGCTAATGA
1 AAATAAAGAAGTTAGCTAA-GA
*
1160904 AAATAATG-AGTTAGCTAAGAA
1 AAATAAAGAAGTTAGCTAAG-A
1160925 AAATAAA
1 AAATAAA
1160932 AACTTGCATA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
20 1 0.04
21 16 0.67
22 7 0.29
ACGTcount: A:0.56, C:0.04, G:0.18, T:0.22
Consensus pattern (21 bp):
AAATAAAGAAGTTAGCTAAGA
Found at i:1162749 original size:15 final size:15
Alignment explanation
Indices: 1162729--1162759 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1162719 TAAAAATATC
*
1162729 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
1162744 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
1162759 C
1 C
1162760 CAAACGAAAT
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:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:1164848 original size:13 final size:13
Alignment explanation
Indices: 1164830--1164867 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
1164820 CATTTTTCTT
1164830 TGTATCGATACAA
1 TGTATCGATACAA
*
1164843 TGTATCGATACAC
1 TGTATCGATACAA
1164856 TGTATCGATACA
1 TGTATCGATACA
1164868 GGGGGATTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1165022 original size:20 final size:20
Alignment explanation
Indices: 1164979--1165024 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
1164969 AAATCTTTTG
1164979 CAAAATACTTGTTTTTCACTT
1 CAAAATACTTGTTTTTCAC-T
*
1165000 CAAATTACTTCGTTTTTCA-T
1 CAAAATACTT-GTTTTTCACT
1165020 CAAAA
1 CAAAA
1165025 CCAGCATCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 5 0.23
21 9 0.41
22 8 0.36
ACGTcount: A:0.33, C:0.20, G:0.04, T:0.43
Consensus pattern (20 bp):
CAAAATACTTGTTTTTCACT
Found at i:1167401 original size:13 final size:13
Alignment explanation
Indices: 1167383--1167408 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1167373 TACACAAAAT
1167383 ATGTATCGATACA
1 ATGTATCGATACA
1167396 ATGTATCGATACA
1 ATGTATCGATACA
1167409 CAAAAAAATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1167406 original size:32 final size:34
Alignment explanation
Indices: 1167365--1167429 Score: 107
Period size: 32 Copynumber: 2.0 Consensus size: 34
1167355 TAGCCAAACT
*
1167365 TGTATCGATACAC-AAAATA-TGTATCGATACAA
1 TGTATCGATACACAAAAAAATTGTATCGATACAA
1167397 TGTATCGATACACAAAAAAATTGTATCGATACA
1 TGTATCGATACACAAAAAAATTGTATCGATACA
1167430 TTGGCTTGTA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
32 13 0.43
33 5 0.17
34 12 0.40
ACGTcount: A:0.45, C:0.15, G:0.12, T:0.28
Consensus pattern (34 bp):
TGTATCGATACACAAAAAAATTGTATCGATACAA
Found at i:1178090 original size:19 final size:20
Alignment explanation
Indices: 1178054--1178091 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
1178044 AATCTTGGAT
*
1178054 AAAAAATATGAATATTTAAG
1 AAAAAATATCAATATTTAAG
*
1178074 AAAAAAT-TCAATTTTTAA
1 AAAAAATATCAATATTTAA
1178092 ATATTTTCTT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 9 0.56
20 7 0.44
ACGTcount: A:0.58, C:0.03, G:0.05, T:0.34
Consensus pattern (20 bp):
AAAAAATATCAATATTTAAG
Found at i:1179062 original size:165 final size:155
Alignment explanation
Indices: 1178698--1179070 Score: 417
Period size: 157 Copynumber: 2.3 Consensus size: 155
1178688 CTACTTTGTG
** * * * *
1178698 AATTTTTTCAGAAGGGTTTTTCTTAATTTTTAATTTTGAAAATTCATCAAATATCATTATTTATT
1 AATTTTTT-AGAAGGGTTTTTCTTGGTTTTCAATTTTTAAAATTCATCAAACATCATTATTTACT
* * * ** *
1178763 TTATATTAATTTAGTTTTTTAAAAATTCATTCATTTTTATTTTTTTCCTTGAAGCTTCTTTTTTT
65 TCATATTAATTCAGTTTTTTAAAAATTCATTCATTTTTATTTTTTTCCTTGAAACTTCCCTTTTC
* *
1178828 CTAAAATACGGTGTTTTCTACTCCGTA
130 CGAAAATAC-GTGTTTTCTACACCGTA
* * *
1178855 AATTTTTTCGAAGGGCTTTTTCCTGGTTTTCAGTTTTTAAAATTCATCAAACATCATTATTTACT
1 AATTTTTTAGAAGGG-TTTTTCTTGGTTTTCAATTTTTAAAATTCATCAAACATCATTATTTACT
1178920 TCATATTAATTCAG-TTTTTAAAAATTCATTCATTTTCATTCATTTTTGTTTTTTTCCTTGAAAC
65 TCATATTAATTCAGTTTTTTAAAAATTCATTCA-TTT--TT-A------TTTTTTTCCTTGAAAC
1178984 TTCCCTTTTCCGAAACATA-GTGTTTTCTACACCGTA
120 TTCCCTTTTCCGAAA-ATACGTGTTTTCTACACCGTA
* * *
1179020 AATTTTTTTGAAGGGATTTTTCTTGGTTTACAATTTTTAAAATTCTTCAAA
1 AATTTTTTAGAAGGG-TTTTTCTTGGTTTTCAATTTTTAAAATTCATCAAA
1179071 TATTATCATT
Statistics
Matches: 181, Mismatches: 23, Indels: 16
0.82 0.10 0.07
Matches are distributed among these distances:
156 24 0.13
157 64 0.35
159 2 0.01
160 1 0.01
165 61 0.34
166 26 0.14
167 3 0.02
ACGTcount: A:0.27, C:0.13, G:0.09, T:0.51
Consensus pattern (155 bp):
AATTTTTTAGAAGGGTTTTTCTTGGTTTTCAATTTTTAAAATTCATCAAACATCATTATTTACTT
CATATTAATTCAGTTTTTTAAAAATTCATTCATTTTTATTTTTTTCCTTGAAACTTCCCTTTTCC
GAAAATACGTGTTTTCTACACCGTA
Found at i:1179101 original size:165 final size:165
Alignment explanation
Indices: 1178788--1179140 Score: 419
Period size: 165 Copynumber: 2.1 Consensus size: 165
1178778 TTTTTAAAAA
* * ** * * *
1178788 TTCATTCATTTTTATTTTTTTCCTTGAAGCTTCTTTTTTTCTAAAATACGGTGTTTTCTACTCCG
1 TTCATTCATTTTTGTTTTTTTCCTTGAAACTTCCCTTTTCCGAAAATAC-GTGTTTTCTACACCG
* * * *
1178853 TAAATTTTTTCGAAGGGCTTTTTCCTGGTTTTCAGTTTTTAAAATTCATCAAACATCATTATTTA
65 TAAATTTTTTCGAAGGGATTTTTCCTGGTTTACAATTTTTAAAATTCATCAAACATCATCATTTA
* * *
1178918 CTTCATATTAATTCAGTTTTTAA-AAATTCATT-CATT
130 CTCCACATTAAATCAG-TTTTAAGAAATTC-TTCCATT
1178954 TTCATTCATTTTTGTTTTTTTCCTTGAAACTTCCCTTTTCCGAAACATA-GTGTTTTCTACACCG
1 TTCATTCATTTTTGTTTTTTTCCTTGAAACTTCCCTTTTCCGAAA-ATACGTGTTTTCTACACCG
* * * * *
1179018 TAAATTTTTTTGAAGGGATTTTTCTTGGTTTACAATTTTTAAAATTCTTCAAATATTATCATTTG
65 TAAATTTTTTCGAAGGGATTTTTCCTGGTTTACAATTTTTAAAATTCATCAAACATCATCATTT-
*
1179083 A-TCCACGTTAAATCAGTTTTAAGAAATTCTTCCATT
129 ACTCCACATTAAATCAGTTTTAAGAAATTCTTCCATT
* *
1179119 TTCA-TGAGTTTTTGATTTTTTC
1 TTCATTCA-TTTTTGTTTTTTTC
1179141 ATTTAAATTC
Statistics
Matches: 160, Mismatches: 22, Indels: 11
0.83 0.11 0.06
Matches are distributed among these distances:
164 10 0.06
165 107 0.67
166 40 0.25
167 3 0.02
ACGTcount: A:0.25, C:0.16, G:0.09, T:0.50
Consensus pattern (165 bp):
TTCATTCATTTTTGTTTTTTTCCTTGAAACTTCCCTTTTCCGAAAATACGTGTTTTCTACACCGT
AAATTTTTTCGAAGGGATTTTTCCTGGTTTACAATTTTTAAAATTCATCAAACATCATCATTTAC
TCCACATTAAATCAGTTTTAAGAAATTCTTCCATT
Found at i:1180367 original size:19 final size:20
Alignment explanation
Indices: 1180324--1180376 Score: 72
Period size: 19 Copynumber: 2.7 Consensus size: 20
1180314 CACACCCAAA
* * *
1180324 TGTATCAATACATTATGCTT
1 TGTATCGATACATGATGCAT
1180344 TGTATCGATACATGAT-CAT
1 TGTATCGATACATGATGCAT
1180363 TGTATCGATACATG
1 TGTATCGATACATG
1180377 GACAATTGTA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 16 0.53
20 14 0.47
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.40
Consensus pattern (20 bp):
TGTATCGATACATGATGCAT
Found at i:1181150 original size:20 final size:20
Alignment explanation
Indices: 1181125--1181175 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 20
1181115 GTTACAAGCA
*
1181125 ATGTATCGATACAATT-CATC
1 ATGTATCGATAC-ATTGCACC
*
1181145 ATGTATCGATACATTGTACC
1 ATGTATCGATACATTGCACC
1181165 ATGTATCGATA
1 ATGTATCGATA
1181176 TAAACAGTGG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 3 0.11
20 25 0.89
ACGTcount: A:0.33, C:0.18, G:0.14, T:0.35
Consensus pattern (20 bp):
ATGTATCGATACATTGCACC
Found at i:1181637 original size:13 final size:13
Alignment explanation
Indices: 1181619--1181651 Score: 66
Period size: 13 Copynumber: 2.5 Consensus size: 13
1181609 CGATACATGG
1181619 TACATTGTATCGA
1 TACATTGTATCGA
1181632 TACATTGTATCGA
1 TACATTGTATCGA
1181645 TACATTG
1 TACATTG
1181652 CTTGTAAAGG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.39
Consensus pattern (13 bp):
TACATTGTATCGA
Found at i:1187687 original size:13 final size:13
Alignment explanation
Indices: 1187671--1187723 Score: 64
Period size: 13 Copynumber: 4.5 Consensus size: 13
1187661 CGATACATGG
1187671 TACATTGTATCGA
1 TACATTGTATCGA
1187684 TACATTGTATCGA
1 TACATTGTATCGA
1187697 TACA-TG-AT-G-
1 TACATTGTATCGA
1187706 -A-ATTGTATCGA
1 TACATTGTATCGA
1187717 TACATTG
1 TACATTG
1187724 CTTGTAACGG
Statistics
Matches: 34, Mismatches: 0, Indels: 12
0.74 0.00 0.26
Matches are distributed among these distances:
7 1 0.03
8 3 0.09
9 2 0.06
10 2 0.06
11 2 0.06
12 3 0.09
13 21 0.62
ACGTcount: A:0.32, C:0.13, G:0.17, T:0.38
Consensus pattern (13 bp):
TACATTGTATCGA
Found at i:1187698 original size:33 final size:33
Alignment explanation
Indices: 1187655--1187723 Score: 104
Period size: 33 Copynumber: 2.1 Consensus size: 33
1187645 CTACCACTGT
*
1187655 TTGTACCGATACATGGT-ACATTGTATCGATACA
1 TTGTACCGATACATGATGA-ATTGTATCGATACA
*
1187688 TTGTATCGATACATGATGAATTGTATCGATACA
1 TTGTACCGATACATGATGAATTGTATCGATACA
1187721 TTG
1 TTG
1187724 CTTGTAACGG
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
33 32 0.97
34 1 0.03
ACGTcount: A:0.30, C:0.14, G:0.19, T:0.36
Consensus pattern (33 bp):
TTGTACCGATACATGATGAATTGTATCGATACA
Found at i:1189376 original size:21 final size:20
Alignment explanation
Indices: 1189348--1189386 Score: 69
Period size: 21 Copynumber: 1.9 Consensus size: 20
1189338 TACTGCCAAG
1189348 GAAATGTATCGATACATTAA
1 GAAATGTATCGATACATTAA
1189368 GAAAGTGTATCGATACATT
1 GAAA-TGTATCGATACATT
1189387 GTATCGTTAC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.41, C:0.10, G:0.18, T:0.31
Consensus pattern (20 bp):
GAAATGTATCGATACATTAA
Found at i:1191818 original size:51 final size:51
Alignment explanation
Indices: 1191758--1191858 Score: 145
Period size: 51 Copynumber: 2.0 Consensus size: 51
1191748 TTTCTCAATT
*
1191758 TTTCATAATCGGGGATAC-TCAAAC-CCTAGTTTTATTTTC-AAAACACCAAG
1 TTTCATAATCGGGGATACTTC-AACTCCGA-TTTTATTTTCAAAAACACCAAG
1191808 TTTCTATAATCGGGGATACTTCAACTCCGATTTTATTTTCAAAAACACCAA
1 TTTC-ATAATCGGGGATACTTCAACTCCGATTTTATTTTCAAAAACACCAA
1191859 TTTTTCACAA
Statistics
Matches: 46, Mismatches: 1, Indels: 6
0.87 0.02 0.11
Matches are distributed among these distances:
50 4 0.09
51 27 0.59
52 15 0.33
ACGTcount: A:0.34, C:0.22, G:0.11, T:0.34
Consensus pattern (51 bp):
TTTCATAATCGGGGATACTTCAACTCCGATTTTATTTTCAAAAACACCAAG
Found at i:1191895 original size:24 final size:25
Alignment explanation
Indices: 1191867--1191918 Score: 61
Period size: 27 Copynumber: 2.0 Consensus size: 25
1191857 AATTTTTCAC
1191867 AATCA-AGGACACTCCAACCCCGTT
1 AATCACAGGACACTCCAACCCCGTT
* *
1191891 AATCATCGGGGATACTCCAACCCCGTT
1 AATCA-C-AGGACACTCCAACCCCGTT
1191918 A
1 A
1191919 TTTCCAAGGG
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
24 5 0.22
27 18 0.78
ACGTcount: A:0.31, C:0.35, G:0.15, T:0.19
Consensus pattern (25 bp):
AATCACAGGACACTCCAACCCCGTT
Found at i:1192038 original size:79 final size:79
Alignment explanation
Indices: 1191895--1192051 Score: 210
Period size: 79 Copynumber: 2.0 Consensus size: 79
1191885 CCCGTTAATC
* * *
1191895 ATCGGGGATACTCCAACCCCGTTATTTCCAAGGGGATACTCTAACCCTGGTTTTATTTCTAAAAT
1 ATCGGGGATACTCCAACCCCGTTATTTCCAAGGGGATACTCCAACCC-GGTTTTATCTCCAAAAT
*
1191960 ATT-GATTTCTCACA
65 ATTAAATTTCTCACA
***
1191974 ATCGGGGATACTCCAACCCCGTTATTTTTTAGGGGATACTCCAACACC-GTTATTATCTCCAAAA
1 ATCGGGGATACTCCAACCCCGTTATTTCCAAGGGGATACTCCAAC-CCGGTT-TTATCTCCAAAA
1192038 TATTAAATTTCTCA
64 TATTAAATTTCTCA
1192052 TCGGGAGATG
Statistics
Matches: 68, Mismatches: 7, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
78 3 0.04
79 55 0.81
80 10 0.15
ACGTcount: A:0.28, C:0.24, G:0.14, T:0.34
Consensus pattern (79 bp):
ATCGGGGATACTCCAACCCCGTTATTTCCAAGGGGATACTCCAACCCGGTTTTATCTCCAAAATA
TTAAATTTCTCACA
Found at i:1193892 original size:308 final size:309
Alignment explanation
Indices: 1193364--1193949 Score: 824
Period size: 308 Copynumber: 1.9 Consensus size: 309
1193354 TAGAATCGAG
* * *
1193364 TCCTAGGTTATCACCATGTCCACTTTTATGCCGAAGGTAGGTATTTAGGATAGGTTCACCATTTT
1 TCCTAGGTCATCACCAGGTCCACTTTTATGCCGAAGGTAGGCATTTAGGATAGGTTCACCATTTT
* * * ** * *
1193429 TATAGCCTTTTTAAGTCTTTTAGGGTTGTCGAGATACTTTCACGTCGAAGATATCTTTTAGGAAC
66 TATAACCTTTTTAAGTCCTTTAAGGTTACCAAGATACTTTCACGTCGAAGATATCTTTAAGGAAC
* * * * *
1193494 AGTTTTGGTAATTTTCTATAACCATCTCCTAGGTCATTACCGGGTCCGCTTTTATGCCGAAGATG
131 AGTTTTCGTAATTTTCTAGAACAATCTCCTAGGTCATCACCGGGTCCGCTTTTATGCCAAAGATG
*
1193559 GGCATTTAGGATAGGTTCATCCCATTTCTAGCATTTTTAAGTCTTTTAGAGGTATCGAGATACTT
196 GGCATTTAGGATAGGTTCATCCCATTTCTAGCATTTCTAAGTCTTTTAGAGGTATCGAGATACTT
*
1193624 TCACGTCGATGATATCCCCAAGGGGCATTTTTATAATTTTATAACCAAC
261 TCACGTCGAAGATATCCCCAAGGGGCATTTTTATAATTTTATAACCAAC
* * * *
1193673 TCCTAGGTCATCACCGGGTCCACTTTTATGCTGAAGGTAGGCATTTAGGATGGGTTCATCCGTTT
1 TCCTAGGTCATCACCAGGTCCACTTTTATGCCGAAGGTAGGCATTTAGGATAGGTTCA-CCATTT
* *
1193738 TTCTAATCTTTTTAAGTCCTTTAAGG-TACCAAGATACTTTCACGTCGAATG-TATCTTATAAGG
65 TTATAACCTTTTTAAGTCCTTTAAGGTTACCAAGATACTTTCACGTCGAA-GATATCTT-TAAGG
* *
1193801 -ACA-TTTTCGTAATTCTT-TAGAATGAAT-TCCTAGGTCATCACCGGGTTCGCTTTTATGCCAA
128 AACAGTTTTCGTAATT-TTCTAGAA-CAATCTCCTAGGTCATCACCGGGTCCGCTTTTATGCCAA
* * * *
1193862 AGGTGGGCATTTAGGATAGGTTCATCCCATTTCTAGCCTTTCTAAGTTTTTTAGAGGTATCGGGA
191 AGATGGGCATTTAGGATAGGTTCATCCCATTTCTAGCATTTCTAAGTCTTTTAGAGGTATCGAGA
1193927 TACTTTCACGTCGAAGATATCCC
256 TACTTTCACGTCGAAGATATCCC
1193950 TTAGAGGCAT
Statistics
Matches: 243, Mismatches: 29, Indels: 11
0.86 0.10 0.04
Matches are distributed among these distances:
308 127 0.52
309 85 0.35
310 31 0.13
ACGTcount: A:0.24, C:0.19, G:0.20, T:0.37
Consensus pattern (309 bp):
TCCTAGGTCATCACCAGGTCCACTTTTATGCCGAAGGTAGGCATTTAGGATAGGTTCACCATTTT
TATAACCTTTTTAAGTCCTTTAAGGTTACCAAGATACTTTCACGTCGAAGATATCTTTAAGGAAC
AGTTTTCGTAATTTTCTAGAACAATCTCCTAGGTCATCACCGGGTCCGCTTTTATGCCAAAGATG
GGCATTTAGGATAGGTTCATCCCATTTCTAGCATTTCTAAGTCTTTTAGAGGTATCGAGATACTT
TCACGTCGAAGATATCCCCAAGGGGCATTTTTATAATTTTATAACCAAC
Found at i:1195480 original size:13 final size:13
Alignment explanation
Indices: 1195462--1195488 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1195452 ACATTATGCT
1195462 TTGTATCGATACA
1 TTGTATCGATACA
1195475 TTGTATCGATACA
1 TTGTATCGATACA
1195488 T
1 T
1195489 GTTCATTGTA
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:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:1198209 original size:21 final size:21
Alignment explanation
Indices: 1198168--1198211 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
1198158 CTCCCCTTTA
* *
1198168 TCTCCCCCGTTTATTAATAAT
1 TCTCCCCCGTTAATCAATAAT
1198189 TCTCCCCC-TTAATCAAGTAAT
1 TCTCCCCCGTTAATCAA-TAAT
1198210 TC
1 TC
1198212 ATATCAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.25, C:0.32, G:0.05, T:0.39
Consensus pattern (21 bp):
TCTCCCCCGTTAATCAATAAT
Found at i:1202124 original size:15 final size:15
Alignment explanation
Indices: 1202104--1202134 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1202094 ATTTCGTTTG
*
1202104 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
1202119 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
1202134 G
1 G
1202135 GACATTTTTA
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:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:1203984 original size:21 final size:21
Alignment explanation
Indices: 1203938--1203982 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
1203928 AAGTTTTCAT
1203938 TTTTC-TTAGCTAACTCATTA
1 TTTTCATTAGCTAACTCATTA
*
1203958 TTTTCATTAGCTAACTTCTTTA
1 TTTTCATTAGCTAAC-TCATTA
1203980 TTT
1 TTT
1203983 CAACTTGCAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 5 0.23
21 9 0.41
22 8 0.36
ACGTcount: A:0.22, C:0.18, G:0.04, T:0.56
Consensus pattern (21 bp):
TTTTCATTAGCTAACTCATTA
Found at i:1217471 original size:1 final size:1
Alignment explanation
Indices: 1217461--1217518 Score: 62
Period size: 1 Copynumber: 58.0 Consensus size: 1
1217451 TGGCAATTGG
* * * * * *
1217461 AAAAAGAAAAAAACAAAACAAAAAAAAAGAAAAAGAAAAAAAAAAAACAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1217519 GTGAAGATTT
Statistics
Matches: 45, Mismatches: 12, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
1 45 1.00
ACGTcount: A:0.90, C:0.05, G:0.05, T:0.00
Consensus pattern (1 bp):
A
Found at i:1217525 original size:29 final size:29
Alignment explanation
Indices: 1217460--1217517 Score: 107
Period size: 29 Copynumber: 2.0 Consensus size: 29
1217450 ATGGCAATTG
*
1217460 GAAAAAGAAAAAAACAAAACAAAAAAAAA
1 GAAAAAGAAAAAAAAAAAACAAAAAAAAA
1217489 GAAAAAGAAAAAAAAAAAACAAAAAAAAA
1 GAAAAAGAAAAAAAAAAAACAAAAAAAAA
1217518 AGTGAAGATT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.88, C:0.05, G:0.07, T:0.00
Consensus pattern (29 bp):
GAAAAAGAAAAAAAAAAAACAAAAAAAAA
Found at i:1223441 original size:22 final size:22
Alignment explanation
Indices: 1223416--1223463 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
1223406 GACAAAGAGG
* *
1223416 GAGAGATGCTTTGATTATGGGA
1 GAGAAATGCTTTAATTATGGGA
* *
1223438 GAGAAATTCTTTAATTATGGGG
1 GAGAAATGCTTTAATTATGGGA
1223460 GAGA
1 GAGA
1223464 CAAATGAAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.31, C:0.04, G:0.33, T:0.31
Consensus pattern (22 bp):
GAGAAATGCTTTAATTATGGGA
Done.