Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032246.1 Gossypioides kirkii chromosome KI_03
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: 42061019
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2000 characters in sequence are not A, C, G, or T
File 20 of 135
Found at i:5416961 original size:27 final size:27
Alignment explanation
Indices: 5416928--5416981 Score: 99
Period size: 27 Copynumber: 2.0 Consensus size: 27
5416918 ACAAACAAAT
5416928 GTCTCTAAAATAATAACAAAATTAACA
1 GTCTCTAAAATAATAACAAAATTAACA
*
5416955 GTCTCTAAAATAATAATAAAATTAACA
1 GTCTCTAAAATAATAACAAAATTAACA
5416982 ATAAAATAAG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.56, C:0.13, G:0.04, T:0.28
Consensus pattern (27 bp):
GTCTCTAAAATAATAACAAAATTAACA
Found at i:5417507 original size:10 final size:10
Alignment explanation
Indices: 5417479--5417521 Score: 52
Period size: 10 Copynumber: 4.3 Consensus size: 10
5417469 TGTTGGTAAG
5417479 AATTAT-TAA
1 AATTATATAA
*
5417488 AATTAAATAA
1 AATTATATAA
*
5417498 TATTATATAA
1 AATTATATAA
5417508 AATATATATAA
1 AAT-TATATAA
5417519 AAT
1 AAT
5417522 ACCAAATATC
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
9 5 0.18
10 13 0.46
11 10 0.36
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (10 bp):
AATTATATAA
Found at i:5424130 original size:18 final size:18
Alignment explanation
Indices: 5424094--5424131 Score: 51
Period size: 17 Copynumber: 2.1 Consensus size: 18
5424084 TCTATTAAAT
5424094 TTAATTATAAAATTTATA
1 TTAATTATAAAATTTATA
*
5424112 TTAA-TATAAATTTTAATA
1 TTAATTATAAAATTT-ATA
5424130 TT
1 TT
5424132 TTGACATTGA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 9 0.50
18 9 0.50
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
TTAATTATAAAATTTATA
Found at i:5424550 original size:31 final size:33
Alignment explanation
Indices: 5424482--5424566 Score: 88
Period size: 31 Copynumber: 2.6 Consensus size: 33
5424472 ATAATTATAT
*
5424482 TTAAATATTTAAAATATAATTTATATAATCTAA
1 TTAAATATTTAAAATATAATTAATATAATCTAA
* *
5424515 TTAAAT-TTTATAA-ATAATTAATATAAAT-TAC
1 TTAAATATTTAAAATATAATTAATAT-AATCTAA
5424546 TTAAAAATATTTAAAAT-TAAT
1 TT--AAATATTTAAAATATAAT
5424567 ATTTTCTATA
Statistics
Matches: 43, Mismatches: 4, Indels: 9
0.77 0.07 0.16
Matches are distributed among these distances:
31 14 0.33
32 9 0.21
33 10 0.23
34 10 0.23
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (33 bp):
TTAAATATTTAAAATATAATTAATATAATCTAA
Found at i:5425908 original size:22 final size:22
Alignment explanation
Indices: 5425876--5425924 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
5425866 AATTTTAGTT
*
5425876 ATTTTATTTTTTGAATTTGTAA
1 ATTTTAATTTTTGAATTTGTAA
* *
5425898 ATTTTAATTTTTGTATTTTTAA
1 ATTTTAATTTTTGAATTTGTAA
5425920 ATTTT
1 ATTTT
5425925 GAAAATTTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.27, C:0.00, G:0.06, T:0.67
Consensus pattern (22 bp):
ATTTTAATTTTTGAATTTGTAA
Found at i:5425910 original size:16 final size:16
Alignment explanation
Indices: 5425891--5425936 Score: 58
Period size: 15 Copynumber: 2.9 Consensus size: 16
5425881 ATTTTTTGAA
5425891 TTTGTAAATTTTAATT
1 TTTGTAAATTTTAATT
* *
5425907 TTTGT-ATTTTTAAAT
1 TTTGTAAATTTTAATT
*
5425922 TTTGAAAATTTTAAT
1 TTTGTAAATTTTAAT
5425937 CTTGGCCCAA
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
15 12 0.50
16 12 0.50
ACGTcount: A:0.33, C:0.00, G:0.07, T:0.61
Consensus pattern (16 bp):
TTTGTAAATTTTAATT
Found at i:5425915 original size:31 final size:31
Alignment explanation
Indices: 5425866--5425936 Score: 83
Period size: 31 Copynumber: 2.3 Consensus size: 31
5425856 TTATTTGATT
* * *
5425866 AATTTTAGTTATTTTATTTTTTGAA-TTTGTA
1 AATTTTAATTATTTTA-TTTTTAAATTTTGAA
5425897 AATTTTAATT-TTTGTATTTTTAAATTTTGAA
1 AATTTTAATTATTT-TATTTTTAAATTTTGAA
5425928 AATTTTAAT
1 AATTTTAAT
5425937 CTTGGCCCAA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
30 10 0.29
31 25 0.71
ACGTcount: A:0.31, C:0.00, G:0.07, T:0.62
Consensus pattern (31 bp):
AATTTTAATTATTTTATTTTTAAATTTTGAA
Found at i:5429182 original size:21 final size:21
Alignment explanation
Indices: 5429156--5429221 Score: 60
Period size: 26 Copynumber: 2.9 Consensus size: 21
5429146 ATAAACAATA
5429156 TAATGATTCTGCCTTTTAACT
1 TAATGATTCTGCCTTTTAACT
*
5429177 TAATGAGTAAACATTGCCTTTTAACT
1 TAATGA-T--TC--TGCCTTTTAACT
* *
5429203 TAATGATTTTGACTTTTAA
1 TAATGATTCTGCCTTTTAA
5429222 TTTTAAAAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 10
0.72 0.08 0.20
Matches are distributed among these distances:
21 15 0.42
22 1 0.03
24 1 0.03
25 1 0.03
26 18 0.50
ACGTcount: A:0.30, C:0.14, G:0.11, T:0.45
Consensus pattern (21 bp):
TAATGATTCTGCCTTTTAACT
Found at i:5429685 original size:5 final size:5
Alignment explanation
Indices: 5429675--5429702 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
5429665 TTAACGCCTA
5429675 CTCTC CTCTC CTCTC CTCTC CTCTC CTC
1 CTCTC CTCTC CTCTC CTCTC CTCTC CTC
5429703 ACTCTCTTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.00, C:0.61, G:0.00, T:0.39
Consensus pattern (5 bp):
CTCTC
Found at i:5439633 original size:9 final size:10
Alignment explanation
Indices: 5439610--5439635 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
5439600 AAAAAATTAT
5439610 TTTTTAAATA
1 TTTTTAAATA
5439620 TTTTTAAATA
1 TTTTTAAATA
5439630 TTTTTA
1 TTTTTA
5439636 TCGTACACTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (10 bp):
TTTTTAAATA
Found at i:5445757 original size:54 final size:53
Alignment explanation
Indices: 5445615--5445774 Score: 187
Period size: 54 Copynumber: 3.0 Consensus size: 53
5445605 TCTTCATCGA
** * ** * *
5445615 AGAAAAAAATGAAGAGCCAAAGGACCTTGAGGCTAATGCATCGATTAAAAGGG
1 AGAAAAAAATGAAGAATCAGAGGACCTTGAGGCTGTTGCACCGATTAAAGGGG
* * *
5445668 AGAAAAAAAATGAAAAATCAGAGAACCTTGAGGCTGTTGCACCGACTAAAGGGG
1 AG-AAAAAAATGAAGAATCAGAGGACCTTGAGGCTGTTGCACCGATTAAAGGGG
*
5445722 AGAAATAAAATGAAGAATCAGAGGACCTTGAGGCTGCTT-CACCGTTTAAAGGG
1 AGAAA-AAAATGAAGAATCAGAGGACCTTGAGGCTG-TTGCACCGATTAAAGGG
5445775 AAGGAGAAAA
Statistics
Matches: 90, Mismatches: 14, Indels: 5
0.83 0.13 0.05
Matches are distributed among these distances:
53 5 0.06
54 83 0.92
55 2 0.02
ACGTcount: A:0.42, C:0.14, G:0.26, T:0.17
Consensus pattern (53 bp):
AGAAAAAAATGAAGAATCAGAGGACCTTGAGGCTGTTGCACCGATTAAAGGGG
Found at i:5450514 original size:95 final size:94
Alignment explanation
Indices: 5450341--5450524 Score: 210
Period size: 95 Copynumber: 1.9 Consensus size: 94
5450331 TAAAGATTAA
* * * * *
5450341 AACTATCCATAGCTTCTCTGCAACCCATAAATAGGAAGATAATATGTTTCAACGTACTCAAACCC
1 AACTATCCATAGCCTCTCTCCAACCCATAAAAAAGAAGATAATATGTTTCAACGAACTCAAACCC
*
5450406 ACATCCTTTTGTATTGGCAACAATGCCTAC
66 ACAT-CTTTTGTATTGACAACAATGCCTAC
* * * * *
5450436 AACTATCCATAGCCTCTC-CCTAATCCATAAAAAAGAGGATAATGTGTTTCAGCGAACTCGAACC
1 AACTATCCATAGCCTCTCTCC-AACCCATAAAAAAGAAGATAATATGTTTCAACGAACTCAAACC
*
5450500 CACGT-TTTCCTGTATTGACAACAAT
65 CACATCTTT--TGTATTGACAACAAT
5450525 AATTATGCCA
Statistics
Matches: 74, Mismatches: 12, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
93 3 0.04
94 1 0.01
95 70 0.95
ACGTcount: A:0.34, C:0.26, G:0.12, T:0.28
Consensus pattern (94 bp):
AACTATCCATAGCCTCTCTCCAACCCATAAAAAAGAAGATAATATGTTTCAACGAACTCAAACCC
ACATCTTTTGTATTGACAACAATGCCTAC
Found at i:5451370 original size:8 final size:9
Alignment explanation
Indices: 5451355--5451381 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
5451345 ATAAAATCTA
5451355 TAAAAAAAT
1 TAAAAAAAT
5451364 TAAAAAAAT
1 TAAAAAAAT
5451373 TAAAAAAAT
1 TAAAAAAAT
5451382 CCATATATGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (9 bp):
TAAAAAAAT
Found at i:5454781 original size:20 final size:20
Alignment explanation
Indices: 5454739--5454781 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
5454729 CAAAATCTTG
* * * *
5454739 AACTTTAAACTCGAACTCTA
1 AACTCTAAACCCGAACCCAA
5454759 AACTCTAAACCCGAACCCAA
1 AACTCTAAACCCGAACCCAA
5454779 AAC
1 AAC
5454782 CTTGAATTTC
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.44, C:0.33, G:0.05, T:0.19
Consensus pattern (20 bp):
AACTCTAAACCCGAACCCAA
Found at i:5460016 original size:6 final size:6
Alignment explanation
Indices: 5460005--5460045 Score: 82
Period size: 6 Copynumber: 6.8 Consensus size: 6
5459995 ACACTTGAAA
5460005 ACCCAC ACCCAC ACCCAC ACCCAC ACCCAC ACCCAC ACCCA
1 ACCCAC ACCCAC ACCCAC ACCCAC ACCCAC ACCCAC ACCCA
5460046 ATACAGTACA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 35 1.00
ACGTcount: A:0.34, C:0.66, G:0.00, T:0.00
Consensus pattern (6 bp):
ACCCAC
Found at i:5460688 original size:6 final size:6
Alignment explanation
Indices: 5460666--5460704 Score: 51
Period size: 6 Copynumber: 6.3 Consensus size: 6
5460656 ACATACATAC
* *
5460666 ATACAT CATATAT ATACAT ATACAT ATACAT ATATAT AT
1 ATACAT -ATACAT ATACAT ATACAT ATACAT ATACAT AT
5460705 TTGTAAGTGG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
6 24 0.83
7 5 0.17
ACGTcount: A:0.49, C:0.13, G:0.00, T:0.38
Consensus pattern (6 bp):
ATACAT
Found at i:5460694 original size:12 final size:12
Alignment explanation
Indices: 5460655--5460704 Score: 64
Period size: 12 Copynumber: 4.1 Consensus size: 12
5460645 GATCATGACT
* *
5460655 TACATACATACA
1 TACATATATATA
5460667 TACATCATATATA
1 TACAT-ATATATA
*
5460680 TACATATACATA
1 TACATATATATA
5460692 TACATATATATA
1 TACATATATATA
5460704 T
1 T
5460705 TTGTAAGTGG
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
12 23 0.70
13 10 0.30
ACGTcount: A:0.48, C:0.16, G:0.00, T:0.36
Consensus pattern (12 bp):
TACATATATATA
Found at i:5465534 original size:15 final size:15
Alignment explanation
Indices: 5465509--5465554 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
5465499 AACCTATTTT
5465509 TAATATT-TATATTA
1 TAATATTATATATTA
*
5465523 TAATATTATATATTT
1 TAATATTATATATTA
*
5465538 TAA-ATTTATATAATA
1 TAATA-TTATATATTA
5465553 TA
1 TA
5465555 TAAAAATAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
14 8 0.30
15 19 0.70
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (15 bp):
TAATATTATATATTA
Found at i:5471500 original size:19 final size:18
Alignment explanation
Indices: 5471461--5471496 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
5471451 AAAATAATAA
5471461 AAATTTGATATAATCTTT
1 AAATTTGATATAATCTTT
5471479 AAATTTGATATAATCTTT
1 AAATTTGATATAATCTTT
5471497 TAAAAATTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.39, C:0.06, G:0.06, T:0.50
Consensus pattern (18 bp):
AAATTTGATATAATCTTT
Found at i:5472424 original size:21 final size:21
Alignment explanation
Indices: 5472395--5472434 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
5472385 TGGATCTTGG
* *
5472395 ATTTTTTTATAATTTTTAAAT
1 ATTTGTTTACAATTTTTAAAT
*
5472416 ATTTGTTTACATTTTTTAA
1 ATTTGTTTACAATTTTTAA
5472435 TTTTTTCAGT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.30, C:0.03, G:0.03, T:0.65
Consensus pattern (21 bp):
ATTTGTTTACAATTTTTAAAT
Found at i:5472493 original size:21 final size:18
Alignment explanation
Indices: 5472454--5472498 Score: 54
Period size: 21 Copynumber: 2.3 Consensus size: 18
5472444 TTATTTACTT
*
5472454 TTTTTATAATTTTAAATA
1 TTTTTACAATTTTAAATA
5472472 TTTTTACAATTTTTATAGATA
1 TTTTTACAA-TTTTA-A-ATA
5472493 TTTTTA
1 TTTTTA
5472499 ATGATTTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 8 0.35
19 5 0.22
20 1 0.04
21 9 0.39
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.62
Consensus pattern (18 bp):
TTTTTACAATTTTAAATA
Found at i:5472526 original size:9 final size:9
Alignment explanation
Indices: 5472397--5472527 Score: 61
Period size: 10 Copynumber: 13.7 Consensus size: 9
5472387 GATCTTGGAT
5472397 TTTTTTATAA
1 TTTTTTA-AA
*
5472407 TTTTTAAATA
1 TTTTTTAA-A
*
5472417 TTTGTTTACA
1 TTT-TTTAAA
5472427 TTTTTT-AA
1 TTTTTTAAA
* *
5472435 TTTTTTCAG
1 TTTTTTAAA
* **
5472444 TTATTTACT
1 TTTTTTAAA
5472453 TTTTTTATAA
1 TTTTTTA-AA
5472463 --TTTTAAA
1 TTTTTTAAA
5472470 TATTTTTACAA
1 T-TTTTTA-AA
*
5472481 TTTTTATAGA
1 TTTTT-TAAA
5472491 TATTTTTAATGA
1 T-TTTTTAA--A
5472503 TTTTTTAACA
1 TTTTTTAA-A
*
5472513 ATTTTTAAA
1 TTTTTTAAA
5472522 TTTTTT
1 TTTTTT
5472528 TTGTCCTTGA
Statistics
Matches: 92, Mismatches: 17, Indels: 25
0.69 0.13 0.19
Matches are distributed among these distances:
7 2 0.02
8 12 0.13
9 22 0.24
10 35 0.38
11 19 0.21
12 2 0.02
ACGTcount: A:0.29, C:0.04, G:0.03, T:0.64
Consensus pattern (9 bp):
TTTTTTAAA
Found at i:5473342 original size:16 final size:16
Alignment explanation
Indices: 5473323--5473353 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
5473313 ATTTAAATTT
*
5473323 TTTTAAATTTATAAAA
1 TTTTAAATTGATAAAA
5473339 TTTTAAATTGATAAA
1 TTTTAAATTGATAAA
5473354 GATAAAATTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (16 bp):
TTTTAAATTGATAAAA
Found at i:5473520 original size:9 final size:9
Alignment explanation
Indices: 5473506--5473531 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
5473496 CTAGCTCCAT
5473506 GATGAAGAA
1 GATGAAGAA
5473515 GATGAAGAA
1 GATGAAGAA
5473524 GATGAAGA
1 GATGAAGA
5473532 TTCGCCATTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.54, C:0.00, G:0.35, T:0.12
Consensus pattern (9 bp):
GATGAAGAA
Found at i:5475305 original size:206 final size:214
Alignment explanation
Indices: 5474995--5475491 Score: 501
Period size: 206 Copynumber: 2.4 Consensus size: 214
5474985 GAAAAAAGGG
* * * * * * * * * *
5474995 TAAATAAATATAGCTTGCCAACTGAATTTATCAATTTGA-TGATCAGGTTCTTGGTTTACAGTCC
1 TAAATAAACACAGCTTACCAACTGAATTTAACAATTT-ATTAATCAAGTTCATGGTTCAGAGTAC
* * * * *
5475059 AACATTGACGCTTTA--TG-TG---TTGGTCCTTACTGATTTTGACATCTGCTATGTGTTGATAC
65 AACATCGATGCTTTATGTGTTGATCTTGGTCCTTACTGAATTTGACAGCAGCTATGTGTTGATAC
* * *
5475118 GAGAGAGTTC-TTGCTCGAG-TTTACGTGGGAGGGAAAT-AGGTTCT-GGCAAAACGGTACTCGA
130 GAGAGAGTGCATTG-TCGAGATTT-CCTGGGA-GGAAATAAGGTT-TAGGCAAAAAGGTACTCGA
5475179 ATTGTATT-AC-CAG-G-GAA-AA
191 ATTGTATTAACACAGAGAGAAGAA
* * * * *
5475198 -CAATAAACCCAG-TTGCCAACTGAATTTAACAATTTATTGATCAAGTTCATGGTTCAGAGTA-G
1 TAAATAAACACAGCTTACCAACTGAATTTAACAATTTATTAATCAAGTTCATGGTTCAGAGTACA
* *
5475260 ACATCGGTGCTTTATGTGTTGATCTTGGTCCTTACTGAATTTGACAGCAGTTATGTGTTGATACG
66 ACATCGATGCTTTATGTGTTGATCTTGGTCCTTACTGAATTTGACAGCAGCTATGTGTTGATACG
* * *
5475325 AGAGAGTGCATTGTTGAGATTTCCTGGGAGGCAATAAGGTTTAGGCAAAAAGGTACTCGAGTTGT
131 AGAGAGTGCATTGTCGAGATTTCCTGGGAGGAAATAAGGTTTAGGCAAAAAGGTACTCGAATTGT
*
5475390 ATTAACAGAGAAAAGAGAAGAA
196 ATTAACACAG---AGAGAAGAA
* * *
5475412 TAAATAAACATAGCTTACCAACTGAATTTTACAATTTATTAATCAGGTTCATGGTTCAGAGTACA
1 TAAATAAACACAGCTTACCAACTGAATTTAACAATTTATTAATCAAGTTCATGGTTCAGAGTACA
5475477 ACATCGATGCTTTAT
66 ACATCGATGCTTTAT
5475492 CGGTTGGTCC
Statistics
Matches: 238, Mismatches: 34, Indels: 30
0.79 0.11 0.10
Matches are distributed among these distances:
200 12 0.05
201 41 0.17
202 10 0.04
203 2 0.01
205 6 0.03
206 83 0.35
207 8 0.03
208 2 0.01
212 1 0.00
213 3 0.01
214 2 0.01
215 9 0.04
216 45 0.19
217 14 0.06
ACGTcount: A:0.31, C:0.15, G:0.22, T:0.33
Consensus pattern (214 bp):
TAAATAAACACAGCTTACCAACTGAATTTAACAATTTATTAATCAAGTTCATGGTTCAGAGTACA
ACATCGATGCTTTATGTGTTGATCTTGGTCCTTACTGAATTTGACAGCAGCTATGTGTTGATACG
AGAGAGTGCATTGTCGAGATTTCCTGGGAGGAAATAAGGTTTAGGCAAAAAGGTACTCGAATTGT
ATTAACACAGAGAGAAGAA
Found at i:5475585 original size:216 final size:211
Alignment explanation
Indices: 5474995--5475943 Score: 757
Period size: 219 Copynumber: 4.4 Consensus size: 211
5474985 GAAAAAAGGG
* * * * * *
5474995 TAAATAAATATAGCTTGCCAACTGAATTTATCAATTTGA-TGATCAGGTTCTTGGTTTACAGTCC
1 TAAATAAACATAGCTTACCAACTGAATTTAACAATTT-ATTGATCAGGTTCATGGTTCAGAGT-C
* * * * **
5475059 AACATTGACGCTTTATGTGTTGGTCCTTACTGATTTTGACATCTGCTATGTGTTGATACGAGAGA
64 AACATCGATGCTTTATGTGTTGGTCCTTACTGAATTTGACAGCTATTATGTGTTGATACGAGAGA
* * * * * * * * * *
5475124 GTTC-TTGCTCGAGTTTACGTGGGAGG-GA-AA-TAGGTTCT-GGCAAAACGGTACTCGAATTGT
129 GTGCATCG-T-AAGATTACCTGGGGGGAGAGAATTAAGTT-TAGGCAAAATGATACTCGAGTTGT
5475184 ATTACCA-G----G-GAA-AA
191 ATTACCAGGAAAAGAGAAGAA
* ** * *
5475198 -CAATAAACCCAG-TTGCCAACTGAATTTAACAATTTATTGATCAAGTTCATGGTTCAGAGT-AG
1 TAAATAAACATAGCTTACCAACTGAATTTAACAATTTATTGATCAGGTTCATGGTTCAGAGTCA-
*
5475260 ACATCGGTGCTTTATGTGTTGATCTTGGTCCTTACTGAATTTGACAGC-AGTTATGTGTTGATAC
65 ACATCGATGCTTTA--TG-TG---TTGGTCCTTACTGAATTTGACAGCTA-TTATGTGTTGATAC
* * * * *
5475324 GAGAGAGTGCATTGTTGAGATTTCCT---GGGAG-GCAA-TAAGGTTTAGGCAAAAAGGTACTCG
123 GAGAGAGTGCATCG-TAAGATTACCTGGGGGGAGAG-AATTAA-GTTTAGGCAAAATGATACTCG
*
5475384 AGTTGTATTAACAGAGAAAAGAGAAGAA
185 AGTTGTATTACCAG-GAAAAGAGAAGAA
* *
5475412 TAAATAAACATAGCTTACCAACTGAATTTTACAATTTATTAATCAGGTTCATGGTTCAGAGTACA
1 TAAATAAACATAGCTTACCAACTGAATTTAACAATTTATTGATCAGGTTCATGGTTCAGAGT-CA
* * * * *
5475477 ACATCGATGCTTTATCG-GTTGGTCCTTACTGAATTTAACTGCTATTTTGTGTTGATGCAAGAGA
65 ACATCGATGCTTTAT-GTGTTGGTCCTTACTGAATTTGACAGCTATTATGTGTTGATACGAGAGA
* *
5475541 CTGCATACGTAAGATTACCTGGCGGGGGAGAGAATTAAGTTTAGGCAAAATGATACCTGGA-TTG
129 GTGCAT-CGTAAGATTACCT-G-GGGGGAGAGAATTAAGTTTAGGCAAAATGATA-CTCGAGTTG
*
5475605 TATTACCAGGAAAAGAAAAAAATAGAA
190 TATTACCAGGAAAAG----AGA-AGAA
* * * *
5475632 TAAATGAACATAGCTT-GCGACTGAATTTTAACATTTTATTGA-CAGGTTCATGGTTCAGAGTCT
1 TAAATAAACATAGCTTACCAACTGAA-TTTAACAATTTATTGATCAGGTTCATGGTTCAGAGTC-
* * * * *
5475695 AACATCTATGCTTTATGCGTTGTTCCTTACTGAACTTGACAGCTGTTATGTGTTGATACGAGAGA
64 AACATCGATGCTTTATGTGTTGGTCCTTACTGAATTTGACAGCTATTATGTGTTGATACGAGAGA
* * * * * *
5475760 GTGAATCCTTAAGATTACCTGGGAGGAAATTAAGTTTTAAGTTTAGGCAAAATGATAC-CCAGAT
129 GTGCAT-CGTAAGATTACCTGGGGGGAGA-GAA---TTAAGTTTAGGCAAAATGATACTCGAG-T
* *
5475824 TGTATTTCCAGGAAAAAAGCAAGAA
188 TGTATTACCAGGAAAAGAG-AAGAA
* * *
5475849 TAGATAAGCATA-CTTACCAACTGAATTGTAACATTTTATTGATCAGGTTCATGGTTCAGAGTCA
1 TAAATAAACATAGCTTACCAACTGAATT-TAACAATTTATTGATCAGGTTCATGGTTCAGAGTCA
* *
5475913 GACATTGATGCTTTATGTGTCGGTCCTTACT
65 -ACATCGATGCTTTATGTGTTGGTCCTTACT
5475944 TTGCCACCAT
Statistics
Matches: 604, Mismatches: 85, Indels: 99
0.77 0.11 0.13
Matches are distributed among these distances:
199 1 0.00
200 12 0.02
201 41 0.07
202 10 0.02
203 4 0.01
204 1 0.00
205 5 0.01
206 80 0.13
207 4 0.01
208 1 0.00
211 53 0.09
212 3 0.00
213 3 0.00
214 3 0.00
215 16 0.03
216 83 0.14
217 63 0.10
218 52 0.09
219 99 0.16
220 33 0.05
221 37 0.06
ACGTcount: A:0.31, C:0.15, G:0.22, T:0.32
Consensus pattern (211 bp):
TAAATAAACATAGCTTACCAACTGAATTTAACAATTTATTGATCAGGTTCATGGTTCAGAGTCAA
CATCGATGCTTTATGTGTTGGTCCTTACTGAATTTGACAGCTATTATGTGTTGATACGAGAGAGT
GCATCGTAAGATTACCTGGGGGGAGAGAATTAAGTTTAGGCAAAATGATACTCGAGTTGTATTAC
CAGGAAAAGAGAAGAA
Found at i:5480207 original size:16 final size:16
Alignment explanation
Indices: 5480186--5480216 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
5480176 TTTTGTATTA
*
5480186 TTTTAATATTAAATAT
1 TTTTAAAATTAAATAT
5480202 TTTTAAAATTAAATA
1 TTTTAAAATTAAATA
5480217 ACATTAATAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
TTTTAAAATTAAATAT
Found at i:5481492 original size:15 final size:15
Alignment explanation
Indices: 5481468--5481500 Score: 50
Period size: 14 Copynumber: 2.2 Consensus size: 15
5481458 TAATATTTAA
5481468 AAAATATAAAAT-AT
1 AAAATATAAAATAAT
5481482 AAAATATTAAAATAAT
1 AAAATA-TAAAATAAT
5481498 AAA
1 AAA
5481501 TTTTTCTGCT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 6 0.35
15 6 0.35
16 5 0.29
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (15 bp):
AAAATATAAAATAAT
Found at i:5488465 original size:21 final size:21
Alignment explanation
Indices: 5488441--5488480 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
5488431 AAACACTGAA
5488441 TTAA-AAAAATAAACAAAAAAT
1 TTAAGAAAAA-AAACAAAAAAT
*
5488462 TTAAGAAAAAAAACGAAAA
1 TTAAGAAAAAAAACAAAAA
5488481 CAAAGATTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.75, C:0.05, G:0.05, T:0.15
Consensus pattern (21 bp):
TTAAGAAAAAAAACAAAAAAT
Found at i:5490705 original size:18 final size:17
Alignment explanation
Indices: 5490682--5490745 Score: 60
Period size: 17 Copynumber: 3.7 Consensus size: 17
5490672 ATAGATGATG
5490682 ATATGAATTGTAATATGT
1 ATATGAATTG-AATATGT
*
5490700 ATATG-ATTGAAAATGGT
1 ATATGAATTGAATAT-GT
* *
5490717 ATATGTATTG-ATTTGT
1 ATATGAATTGAATATGT
5490733 ATATGAAATTGAA
1 ATATG-AATTGAA
5490746 CATTAGTATC
Statistics
Matches: 38, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
16 11 0.29
17 17 0.45
18 10 0.26
ACGTcount: A:0.39, C:0.00, G:0.19, T:0.42
Consensus pattern (17 bp):
ATATGAATTGAATATGT
Found at i:5493632 original size:25 final size:24
Alignment explanation
Indices: 5493604--5493656 Score: 61
Period size: 25 Copynumber: 2.2 Consensus size: 24
5493594 TTGTAAAGCT
5493604 ATTTTTATAAATGTTATATACTATA
1 ATTTTTATAAATGTTATATACT-TA
* * * *
5493629 ATTTTTTTAATTTTTATTTACTTA
1 ATTTTTATAAATGTTATATACTTA
5493653 ATTT
1 ATTT
5493657 ATGCATTATA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
24 6 0.25
25 18 0.75
ACGTcount: A:0.32, C:0.04, G:0.02, T:0.62
Consensus pattern (24 bp):
ATTTTTATAAATGTTATATACTTA
Found at i:5498681 original size:15 final size:15
Alignment explanation
Indices: 5498647--5498709 Score: 51
Period size: 14 Copynumber: 4.3 Consensus size: 15
5498637 TTAAGTTGAT
*
5498647 TATATAAA-AAAAAT
1 TATATAAATAAAAAA
5498661 TA-ATAAATAAAAAA
1 TATATAAATAAAAAA
**
5498675 TATATAACATTAGTAAA
1 TATATAA-A-TAAAAAA
*
5498692 TAT-TAAATTAAAAA
1 TATATAAATAAAAAA
5498706 TATA
1 TATA
5498710 AATATTTTTA
Statistics
Matches: 38, Mismatches: 6, Indels: 9
0.72 0.11 0.17
Matches are distributed among these distances:
13 5 0.13
14 16 0.42
15 5 0.13
16 4 0.11
17 8 0.21
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.32
Consensus pattern (15 bp):
TATATAAATAAAAAA
Found at i:5504406 original size:18 final size:19
Alignment explanation
Indices: 5504376--5504425 Score: 84
Period size: 19 Copynumber: 2.6 Consensus size: 19
5504366 TAACTTATAT
5504376 ATTTTTTAGAAATTTTTAAA
1 ATTTTTTA-AAATTTTTAAA
5504396 A-TTTTTAAAATTTTTAAA
1 ATTTTTTAAAATTTTTAAA
5504414 ATTTTTTAAAAT
1 ATTTTTTAAAAT
5504426 ATATAACTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
18 12 0.41
19 16 0.55
20 1 0.03
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (19 bp):
ATTTTTTAAAATTTTTAAA
Found at i:5504420 original size:10 final size:9
Alignment explanation
Indices: 5504378--5504425 Score: 78
Period size: 9 Copynumber: 5.1 Consensus size: 9
5504368 ACTTATATAT
5504378 TTTTTAGAAA
1 TTTTTA-AAA
5504388 TTTTTAAAA
1 TTTTTAAAA
5504397 TTTTTAAAA
1 TTTTTAAAA
5504406 TTTTTAAAA
1 TTTTTAAAA
5504415 TTTTTTAAAA
1 -TTTTTAAAA
5504425 T
1 T
5504426 ATATAACTTT
Statistics
Matches: 37, Mismatches: 0, Indels: 3
0.93 0.00 0.08
Matches are distributed among these distances:
9 22 0.59
10 15 0.41
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (9 bp):
TTTTTAAAA
Found at i:5510397 original size:2 final size:2
Alignment explanation
Indices: 5510390--5510459 Score: 131
Period size: 2 Copynumber: 35.0 Consensus size: 2
5510380 CCAAATTCAC
5510390 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
5510432 AT GT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5510460 TTCCAAATTC
Statistics
Matches: 66, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 66 1.00
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5512633 original size:23 final size:23
Alignment explanation
Indices: 5512602--5512645 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
5512592 ATTAAAAACA
5512602 TTTTTATAATTTAT-TTTTTACT
1 TTTTTATAATTTATATTTTTACT
*
5512624 TTTTTAATAATTTTTATTTTTA
1 TTTTT-ATAATTTATATTTTTA
5512646 AAAAATATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 5 0.26
23 8 0.42
24 6 0.32
ACGTcount: A:0.25, C:0.02, G:0.00, T:0.73
Consensus pattern (23 bp):
TTTTTATAATTTATATTTTTACT
Found at i:5512652 original size:20 final size:21
Alignment explanation
Indices: 5512629--5512669 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
5512619 TTACTTTTTT
5512629 AATAATTTTT-ATTTTTAAAA
1 AATAATTTTTAATTTTTAAAA
*
5512649 AATATTTTTTGAATTTTTAAA
1 AATAATTTTT-AATTTTTAAA
5512670 TTAAAAATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 9 0.50
22 9 0.50
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.56
Consensus pattern (21 bp):
AATAATTTTTAATTTTTAAAA
Found at i:5516677 original size:21 final size:21
Alignment explanation
Indices: 5516651--5516691 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
5516641 CAACTACAAT
*
5516651 GGTATCATTATATCCACCTTG
1 GGTATCATGATATCCACCTTG
5516672 GGTATCATGATATCCACCTT
1 GGTATCATGATATCCACCTT
5516692 CCGAGAGGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.24, C:0.24, G:0.15, T:0.37
Consensus pattern (21 bp):
GGTATCATGATATCCACCTTG
Found at i:5521349 original size:30 final size:32
Alignment explanation
Indices: 5521313--5521377 Score: 89
Period size: 30 Copynumber: 2.1 Consensus size: 32
5521303 TGCATTTCAC
*
5521313 TTTTAAAAATAATAATA-AT-TTAATTTAATT
1 TTTTAAAAATAATAATATATAATAATTTAATT
*
5521343 TTTTAAAAATTATAATATATAAATAATTTAATT
1 TTTTAAAAATAATAATATAT-AATAATTTAATT
5521376 TT
1 TT
5521378 GACCTTTAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
30 16 0.53
31 2 0.07
33 12 0.40
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (32 bp):
TTTTAAAAATAATAATATATAATAATTTAATT
Found at i:5524436 original size:16 final size:16
Alignment explanation
Indices: 5524415--5524481 Score: 82
Period size: 16 Copynumber: 4.2 Consensus size: 16
5524405 GGTTTATTGG
5524415 AATGGAATAGAACTGT
1 AATGGAATAGAACTGT
**
5524431 AATGGAATAGAGTTGT
1 AATGGAATAGAACTGT
*
5524447 AATGGAATA-AAGTTGT
1 AATGGAATAGAA-CTGT
*
5524463 AATGGAATAGAGCTGT
1 AATGGAATAGAACTGT
5524479 AAT
1 AAT
5524482 CAGTAATTCA
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
15 1 0.02
16 42 0.95
17 1 0.02
ACGTcount: A:0.42, C:0.03, G:0.27, T:0.28
Consensus pattern (16 bp):
AATGGAATAGAACTGT
Found at i:5524464 original size:32 final size:32
Alignment explanation
Indices: 5524415--5524481 Score: 100
Period size: 32 Copynumber: 2.1 Consensus size: 32
5524405 GGTTTATTGG
*
5524415 AATGGAATAGAACTGTAATGGAATAGAGTTGT
1 AATGGAATAGAACTGTAATGGAATAGAGCTGT
*
5524447 AATGGAATA-AAGTTGTAATGGAATAGAGCTGT
1 AATGGAATAGAA-CTGTAATGGAATAGAGCTGT
5524479 AAT
1 AAT
5524482 CAGTAATTCA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
31 2 0.06
32 30 0.94
ACGTcount: A:0.42, C:0.03, G:0.27, T:0.28
Consensus pattern (32 bp):
AATGGAATAGAACTGTAATGGAATAGAGCTGT
Found at i:5537069 original size:53 final size:53
Alignment explanation
Indices: 5537006--5537112 Score: 178
Period size: 53 Copynumber: 2.0 Consensus size: 53
5536996 ACCATTTAAG
* * *
5537006 TTCATATATTTATTAACATTTAGAAGAAGGAAAACGACATCGTTTCAGTCCTT
1 TTCATATATTTATTAACAATTAGAAGAAGAAAAACGACATCGTTTCAGCCCTT
*
5537059 TTCATATATTTATTAACAATTAGAAGAAGAAAAACGGCATCGTTTCAGCCCTT
1 TTCATATATTTATTAACAATTAGAAGAAGAAAAACGACATCGTTTCAGCCCTT
5537112 T
1 T
5537113 AGACGAAGGA
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
53 50 1.00
ACGTcount: A:0.36, C:0.16, G:0.13, T:0.35
Consensus pattern (53 bp):
TTCATATATTTATTAACAATTAGAAGAAGAAAAACGACATCGTTTCAGCCCTT
Found at i:5540092 original size:13 final size:13
Alignment explanation
Indices: 5540074--5540122 Score: 57
Period size: 13 Copynumber: 3.8 Consensus size: 13
5540064 TAAACCAAGT
5540074 TTTTCAAAAGTAC
1 TTTTCAAAAGTAC
*
5540087 TTTTCAAAA-TCATT
1 TTTTCAAAAGT-A-C
5540101 TTTTC-AAAGTAC
1 TTTTCAAAAGTAC
5540113 TTTTCAAAAG
1 TTTTCAAAAG
5540123 CAGTGCTAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
12 6 0.20
13 18 0.60
14 6 0.20
ACGTcount: A:0.37, C:0.14, G:0.06, T:0.43
Consensus pattern (13 bp):
TTTTCAAAAGTAC
Found at i:5546353 original size:20 final size:20
Alignment explanation
Indices: 5546328--5546369 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
5546318 TTCGATCAAT
*
5546328 CCATCAAATAAGATCCCAAC
1 CCATCAAATAAGATCCAAAC
5546348 CCATCAAATAAGATCCAAAC
1 CCATCAAATAAGATCCAAAC
5546368 CC
1 CC
5546370 TAACAGCGGC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.45, C:0.36, G:0.05, T:0.14
Consensus pattern (20 bp):
CCATCAAATAAGATCCAAAC
Found at i:5547955 original size:13 final size:13
Alignment explanation
Indices: 5547937--5547961 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5547927 CAAAAATATA
5547937 GTTTAGATATTTT
1 GTTTAGATATTTT
5547950 GTTTAGATATTT
1 GTTTAGATATTT
5547962 ATTTCTTTTT
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:0.24, C:0.00, G:0.16, T:0.60
Consensus pattern (13 bp):
GTTTAGATATTTT
Found at i:5554940 original size:48 final size:46
Alignment explanation
Indices: 5554866--5554995 Score: 132
Period size: 48 Copynumber: 3.0 Consensus size: 46
5554856 ATTCAAAAAA
*
5554866 AATA-TAATACAA-AAAATATTAAAATATTATTATTTACAAAATATT
1 AATATTAAAACAATAAAATATTAAAATATTATTATTTA-AAAATATT
* * * *
5554911 TATATTAAATATAATAAAATATTAAAATATT-TAATTT---TATATT
1 AATATTAAA-ACAATAAAATATTAAAATATTATTATTTAAAAATATT
*
5554954 AATATTAAAACAATAAAATA--AAAGTATTATTATTTAAAAATA
1 AATATTAAAACAATAAAATATTAAAATATTATTATTTAAAAATA
5554996 ATATGAACCA
Statistics
Matches: 68, Mismatches: 10, Indels: 15
0.73 0.11 0.16
Matches are distributed among these distances:
40 7 0.10
41 5 0.07
42 10 0.15
43 13 0.19
44 3 0.04
45 3 0.04
46 3 0.04
47 8 0.12
48 16 0.24
ACGTcount: A:0.57, C:0.02, G:0.01, T:0.40
Consensus pattern (46 bp):
AATATTAAAACAATAAAATATTAAAATATTATTATTTAAAAATATT
Found at i:5558427 original size:11 final size:11
Alignment explanation
Indices: 5558383--5558444 Score: 52
Period size: 11 Copynumber: 5.6 Consensus size: 11
5558373 TCAAAGTCAA
*
5558383 GGTCAACGGTA
1 GGTCAACGGTC
**
5558394 GGTCAAAAGTC
1 GGTCAACGGTC
* **
5558405 GATCAATAGTC
1 GGTCAACGGTC
5558416 GGTCAACGGTC
1 GGTCAACGGTC
*
5558427 GGTCAATGGTC
1 GGTCAACGGTC
*
5558438 GATCAAC
1 GGTCAAC
5558445 AGTTTGACTT
Statistics
Matches: 40, Mismatches: 11, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
11 40 1.00
ACGTcount: A:0.29, C:0.21, G:0.29, T:0.21
Consensus pattern (11 bp):
GGTCAACGGTC
Found at i:5558427 original size:22 final size:22
Alignment explanation
Indices: 5558402--5558444 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
5558392 TAGGTCAAAA
*
5558402 GTCGATCAATAGTCGGTCAACG
1 GTCGATCAATAGTCGATCAACG
* *
5558424 GTCGGTCAATGGTCGATCAAC
1 GTCGATCAATAGTCGATCAAC
5558445 AGTTTGACTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.26, C:0.23, G:0.28, T:0.23
Consensus pattern (22 bp):
GTCGATCAATAGTCGATCAACG
Found at i:5558503 original size:16 final size:15
Alignment explanation
Indices: 5558464--5558520 Score: 53
Period size: 16 Copynumber: 3.7 Consensus size: 15
5558454 TGGTTTGGGT
*
5558464 TTGGACTTGGTTCAA
1 TTGGATTTGGTTCAA
*
5558479 TTGGATTTGGTTCACT
1 TTGGATTTGGTTCA-A
*
5558495 TTGGGTTTGGTTTTCAA
1 TTGGATTTGG--TTCAA
5558512 TTGG-TTTGG
1 TTGGATTTGG
5558521 CTTAAAGGTT
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
15 13 0.37
16 14 0.40
17 4 0.11
18 4 0.11
ACGTcount: A:0.12, C:0.09, G:0.30, T:0.49
Consensus pattern (15 bp):
TTGGATTTGGTTCAA
Found at i:5559726 original size:24 final size:24
Alignment explanation
Indices: 5559699--5559757 Score: 109
Period size: 24 Copynumber: 2.5 Consensus size: 24
5559689 TTTAGCCAAC
5559699 ACGAGCCCAGAATGATTAGCTCTT
1 ACGAGCCCAGAATGATTAGCTCTT
*
5559723 ACGAGCCCGGAATGATTAGCTCTT
1 ACGAGCCCAGAATGATTAGCTCTT
5559747 ACGAGCCCAGA
1 ACGAGCCCAGA
5559758 CAGAGTTTAA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.29, C:0.27, G:0.24, T:0.20
Consensus pattern (24 bp):
ACGAGCCCAGAATGATTAGCTCTT
Found at i:5587427 original size:20 final size:20
Alignment explanation
Indices: 5587399--5587438 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
5587389 CTCTAATCAG
*
5587399 AATCTCTAAAAATCAGCTAT
1 AATCCCTAAAAATCAGCTAT
* *
5587419 AATCCCTAAAGATTAGCTAT
1 AATCCCTAAAAATCAGCTAT
5587439 TCAATGCTGT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.42, C:0.20, G:0.07, T:0.30
Consensus pattern (20 bp):
AATCCCTAAAAATCAGCTAT
Found at i:5589096 original size:71 final size:71
Alignment explanation
Indices: 5588979--5589123 Score: 209
Period size: 71 Copynumber: 2.0 Consensus size: 71
5588969 TTCCATCTTA
** *
5588979 GATCAGTGATAGCTTCTCTCCAATCGTGTAGAACAGACATAAAGAACAAAAACAAAGCAAAAACT
1 GATCAGTGATAGCTTCTCTCCAATCCCGTAGAACAAACATAAAGAACAAAAACAAAGCAAAAACT
*
5589044 CTATGG
66 CTATAG
* ** **
5589050 GATCAGTGATAGCTTCTCTCCAATCCCGTGGAACAAACATTGAGAACAAGGACAAAGCAAAAACT
1 GATCAGTGATAGCTTCTCTCCAATCCCGTAGAACAAACATAAAGAACAAAAACAAAGCAAAAACT
5589115 CTATAG
66 CTATAG
5589121 GAT
1 GAT
5589124 GGGGATAAAG
Statistics
Matches: 65, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
71 65 1.00
ACGTcount: A:0.41, C:0.21, G:0.18, T:0.20
Consensus pattern (71 bp):
GATCAGTGATAGCTTCTCTCCAATCCCGTAGAACAAACATAAAGAACAAAAACAAAGCAAAAACT
CTATAG
Found at i:5591784 original size:163 final size:164
Alignment explanation
Indices: 5591514--5592000 Score: 850
Period size: 164 Copynumber: 3.0 Consensus size: 164
5591504 TGCAATTCAC
*
5591514 AAGCCTTGATAAACAACAAGCAAGACCTTGACCAAGCAAGGTAATTACATCCATCAAGCTTCACA
1 AAGCCTTGATAAACAACAAGCAAGACCTTGACCAAGCAAGGTAATTACGTCCATCAAGCTTCACA
*
5591579 GGACTAATTTGTAACAAGGGATTATCGGATACAATCATGAGCTTCTCATCCTTCGACAAAATACT
66 GGACTAATTTGTAACAAGGGATTATCGGATACAATCATGAGCTTCTCATCCTTCGACATAATACT
5591644 -AAAAAAAAACTAGTACCCAAAAAACTGCTCCAG
131 AAAAAAAAAACTAGTACCCAAAAAACTGCTCCAG
* *
5591677 AAGCCTTGATAAGCAACAAGCAAGACTTTGACCAAGCAAGGTAATTACGTCCATCAAGCTTCACA
1 AAGCCTTGATAAACAACAAGCAAGACCTTGACCAAGCAAGGTAATTACGTCCATCAAGCTTCACA
* *
5591742 GGACTAATTTGTAATAAAGGATTATCGGATACAATCATGAGCTTCTCATCCTTCGACATAATACT
66 GGACTAATTTGTAACAAGGGATTATCGGATACAATCATGAGCTTCTCATCCTTCGACATAATACT
*
5591807 AAAAAAAAAACTAATACCCAAAAAACTGCTCCAG
131 AAAAAAAAAACTAGTACCCAAAAAACTGCTCCAG
* *
5591841 AAACCTTGATAAACAACAAGCAAGACCTTGACCAAGCAAGGTAATTATGTCCATCAAGCTTCACA
1 AAGCCTTGATAAACAACAAGCAAGACCTTGACCAAGCAAGGTAATTACGTCCATCAAGCTTCACA
** * *
5591906 GGACTAATTTGTAACGTGGGATTATTGGATACAATCATGAGCTTCTCATCCTTCGACATAATAGT
66 GGACTAATTTGTAACAAGGGATTATCGGATACAATCATGAGCTTCTCATCCTTCGACATAATACT
5591971 AAAAAAAAAACTAGTACCCAAAAAACTGCT
131 AAAAAAAAAACTAGTACCCAAAAAACTGCT
5592001 TGGAAAAATT
Statistics
Matches: 305, Mismatches: 18, Indels: 1
0.94 0.06 0.00
Matches are distributed among these distances:
163 124 0.41
164 181 0.59
ACGTcount: A:0.41, C:0.22, G:0.14, T:0.23
Consensus pattern (164 bp):
AAGCCTTGATAAACAACAAGCAAGACCTTGACCAAGCAAGGTAATTACGTCCATCAAGCTTCACA
GGACTAATTTGTAACAAGGGATTATCGGATACAATCATGAGCTTCTCATCCTTCGACATAATACT
AAAAAAAAAACTAGTACCCAAAAAACTGCTCCAG
Found at i:5597321 original size:82 final size:80
Alignment explanation
Indices: 5597192--5597347 Score: 206
Period size: 82 Copynumber: 1.9 Consensus size: 80
5597182 TACTATCATG
* *
5597192 ACAAACCAGGTATAAACACTTGTGAACCCTATCTCAGAACGGCTTGATAATA-CTAATGCATGCA
1 ACAAACCAGGAATAAACACTTGGGAACCCTATCTCAGAACGGCTTGATAATACCT-ATGCATGCA
5597256 CAGTGCAAGAGTTACT
65 CAGTGCAAGAGTTACT
* * * * * *
5597272 ACAAACCAAGGAATCAACACTTGGGAAACCGTATTTGAGAACTGTTTGATAATACCTATGCATGC
1 ACAAACC-AGGAATAAACACTTGGG-AACCCTATCTCAGAACGGCTTGATAATACCTATGCATGC
5597337 ACAGTGCAAGA
64 ACAGTGCAAGA
5597348 ATTTCCATTC
Statistics
Matches: 65, Mismatches: 8, Indels: 4
0.84 0.10 0.05
Matches are distributed among these distances:
80 7 0.11
81 14 0.22
82 42 0.65
83 2 0.03
ACGTcount: A:0.37, C:0.21, G:0.19, T:0.23
Consensus pattern (80 bp):
ACAAACCAGGAATAAACACTTGGGAACCCTATCTCAGAACGGCTTGATAATACCTATGCATGCAC
AGTGCAAGAGTTACT
Found at i:5601059 original size:33 final size:33
Alignment explanation
Indices: 5601017--5601104 Score: 167
Period size: 33 Copynumber: 2.7 Consensus size: 33
5601007 GAAATGAATG
*
5601017 ATATTAATGTTGTTAATAAAAAAGACTTTAGTA
1 ATATTAATGTTGTTAATAAAAAAGACTTGAGTA
5601050 ATATTAATGTTGTTAATAAAAAAGACTTGAGTA
1 ATATTAATGTTGTTAATAAAAAAGACTTGAGTA
5601083 ATATTAATGTTGTTAATAAAAA
1 ATATTAATGTTGTTAATAAAAA
5601105 GGAGTATGAA
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 54 1.00
ACGTcount: A:0.47, C:0.02, G:0.12, T:0.39
Consensus pattern (33 bp):
ATATTAATGTTGTTAATAAAAAAGACTTGAGTA
Found at i:5606118 original size:19 final size:20
Alignment explanation
Indices: 5606090--5606128 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
5606080 TTTAAGTTTC
*
5606090 TTTTATATGTTTTTGTTAAT
1 TTTTATATGTTGTTGTTAAT
5606110 TTTTA-ATGTTGTTGTTAAT
1 TTTTATATGTTGTTGTTAAT
5606129 AAATTATTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 13 0.72
20 5 0.28
ACGTcount: A:0.21, C:0.00, G:0.13, T:0.67
Consensus pattern (20 bp):
TTTTATATGTTGTTGTTAAT
Found at i:5606711 original size:25 final size:26
Alignment explanation
Indices: 5606663--5606712 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 26
5606653 CTTTTTCTTT
* *
5606663 TCTTTTCATTTTTAGATTAGGTTTTC
1 TCTTTTCATTTTTAGACTAAGTTTTC
*
5606689 TCTTTTC-TTTTTAGGCTAAGTTTT
1 TCTTTTCATTTTTAGACTAAGTTTT
5606713 TTTGTTTACT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
25 14 0.67
26 7 0.33
ACGTcount: A:0.14, C:0.12, G:0.12, T:0.62
Consensus pattern (26 bp):
TCTTTTCATTTTTAGACTAAGTTTTC
Found at i:5618021 original size:18 final size:18
Alignment explanation
Indices: 5617998--5618032 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
5617988 ATGTTTGTAT
*
5617998 CTCAAAAGTGTTTTTTAC
1 CTCAAAAGTGCTTTTTAC
5618016 CTCAAAAGTGCTTTTTA
1 CTCAAAAGTGCTTTTTA
5618033 GAAGCATTGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.29, C:0.17, G:0.11, T:0.43
Consensus pattern (18 bp):
CTCAAAAGTGCTTTTTAC
Found at i:5627450 original size:20 final size:21
Alignment explanation
Indices: 5627421--5627460 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
5627411 GAAAAATAAA
* *
5627421 ATGGAGAAATTAAAATTATAC
1 ATGGAGAAATAAAAAGTATAC
5627442 ATGGA-AAATAAAAAGTATA
1 ATGGAGAAATAAAAAGTATA
5627461 GGGACCTCCG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.57, C:0.03, G:0.15, T:0.25
Consensus pattern (21 bp):
ATGGAGAAATAAAAAGTATAC
Found at i:5630350 original size:69 final size:65
Alignment explanation
Indices: 5630268--5630398 Score: 190
Period size: 69 Copynumber: 2.0 Consensus size: 65
5630258 ATAAACTTTG
* *
5630268 GAACAAGATTATACTTGTATGAAACACAATGATATCAAGTACACGATGCTATAAGCAATAAAAGT
1 GAACAAGATTATACTTGGAGGAAACACAATGATAT--AGTACA--ATGCTATAAGCAATAAAAGT
5630333 GTTT
62 GTTT
* *
5630337 GAACAAGATTATACTTGGAGGAAACACAATGATATAGTACAATGTTATAAGCAATATAAGTG
1 GAACAAGATTATACTTGGAGGAAACACAATGATATAGTACAATGCTATAAGCAATAAAAGTG
5630399 AGCTTTTATT
Statistics
Matches: 58, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
65 19 0.33
67 6 0.10
69 33 0.57
ACGTcount: A:0.44, C:0.11, G:0.18, T:0.27
Consensus pattern (65 bp):
GAACAAGATTATACTTGGAGGAAACACAATGATATAGTACAATGCTATAAGCAATAAAAGTGTTT
Found at i:5639421 original size:28 final size:27
Alignment explanation
Indices: 5639373--5639426 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 27
5639363 GTTCAAAAAA
5639373 TATTATATAAATATATAATAAATGTAAT
1 TATTATATAAATATATAATAAA-GTAAT
5639401 TATTATATTTAAA-ATAT-ATAAAGTAA
1 TATTATA--TAAATATATAATAAAGTAA
5639427 ACTATATCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
27 4 0.17
28 12 0.50
29 4 0.17
30 4 0.17
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.43
Consensus pattern (27 bp):
TATTATATAAATATATAATAAAGTAAT
Found at i:5640659 original size:56 final size:56
Alignment explanation
Indices: 5640556--5640664 Score: 155
Period size: 56 Copynumber: 1.9 Consensus size: 56
5640546 TTTAGGTTTG
* **
5640556 CTTTACTTCTTTTGTTTTTGATATTATAAGACAATGGTCAAGTTTCAGTTTTACTA
1 CTTTACTTCTTTTGTTTTTGATATTATAAGACAATGATCAAACTTCAGTTTTACTA
* ** *
5640612 CTTTGCTTCTTTTGTTTTTGATATTATAAGACGGTGATTAAACTTCAGTTTTA
1 CTTTACTTCTTTTGTTTTTGATATTATAAGACAATGATCAAACTTCAGTTTTA
5640665 ATCTTTATAC
Statistics
Matches: 46, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
56 46 1.00
ACGTcount: A:0.24, C:0.12, G:0.14, T:0.50
Consensus pattern (56 bp):
CTTTACTTCTTTTGTTTTTGATATTATAAGACAATGATCAAACTTCAGTTTTACTA
Found at i:5646981 original size:11 final size:11
Alignment explanation
Indices: 5646965--5647014 Score: 57
Period size: 11 Copynumber: 4.5 Consensus size: 11
5646955 TAATGTTATA
5646965 AAAAATTATTT
1 AAAAATTATTT
*
5646976 AAAAA-TATGT
1 AAAAATTATTT
*
5646986 AAAAATAACATTT
1 AAAAAT--TATTT
5646999 AAAAATTATTT
1 AAAAATTATTT
5647010 AAAAA
1 AAAAA
5647015 ACATGTCGAA
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
10 9 0.28
11 14 0.44
13 9 0.28
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.34
Consensus pattern (11 bp):
AAAAATTATTT
Found at i:5647027 original size:34 final size:34
Alignment explanation
Indices: 5646965--5647036 Score: 83
Period size: 34 Copynumber: 2.1 Consensus size: 34
5646955 TAATGTTATA
* * *
5646965 AAAAATTATTTAAAAATATGTAAAAATAACATTT
1 AAAAATTATTTAAAAACATGTAAAAATAAAACTT
**
5646999 AAAAATTATTTAAAAAACATGT-CGAATAAAACTT
1 AAAAATTATTT-AAAAACATGTAAAAATAAAACTT
5647033 AAAA
1 AAAA
5647037 TTCAATCCTA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
34 23 0.72
35 9 0.28
ACGTcount: A:0.60, C:0.06, G:0.04, T:0.31
Consensus pattern (34 bp):
AAAAATTATTTAAAAACATGTAAAAATAAAACTT
Found at i:5647957 original size:4 final size:4
Alignment explanation
Indices: 5647929--5647978 Score: 55
Period size: 4 Copynumber: 11.5 Consensus size: 4
5647919 CAAACGGGAG
*
5647929 AGAA GAGAA GAGAA GAGAGA AGAA AGAA AGAA AGAA AGAA AGAG AGAA
1 AGAA -AGAA -AGAA -AGA-A AGAA AGAA AGAA AGAA AGAA AGAA AGAA
5647977 AG
1 AG
5647979 GTAATTTTTT
Statistics
Matches: 42, Mismatches: 2, Indels: 3
0.89 0.04 0.06
Matches are distributed among these distances:
4 25 0.60
5 16 0.38
6 1 0.02
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (4 bp):
AGAA
Found at i:5649634 original size:51 final size:51
Alignment explanation
Indices: 5649518--5649654 Score: 152
Period size: 51 Copynumber: 2.6 Consensus size: 51
5649508 ATTTCACTTA
* *
5649518 ATACTCACGATTACATATAGTCATCGGATCCCTTGTTCCGTATAGGAATTCAT
1 ATACTCACGATGACAT-TAGTCATCGGA-CCCTTATTCCGTATAGGAATTCAT
* * *
5649571 ATACTCATGATGACATTGAGTCATCGGACCTTTAATT-CGT-TATGAATTCAT
1 ATACTCACGATGACATT-AGTCATCGGACCCTT-ATTCCGTATAGGAATTCAT
* *
5649622 TTACTCACGATGACACTTAGTCATTGGACCCTT
1 ATACTCACGATGACA-TTAGTCATCGGACCCTT
5649655 TCGTTTATAG
Statistics
Matches: 72, Mismatches: 9, Indels: 8
0.81 0.10 0.09
Matches are distributed among these distances:
51 36 0.50
52 10 0.14
53 26 0.36
ACGTcount: A:0.28, C:0.22, G:0.15, T:0.35
Consensus pattern (51 bp):
ATACTCACGATGACATTAGTCATCGGACCCTTATTCCGTATAGGAATTCAT
Found at i:5653725 original size:43 final size:43
Alignment explanation
Indices: 5653678--5653794 Score: 154
Period size: 38 Copynumber: 2.8 Consensus size: 43
5653668 ATGTCAAGAA
* *
5653678 ATTAATAAGAGTCAAGTAATATAATTTAGTAACATGCAAACAT
1 ATTAACAAGAATCAAGTAATATAATTTAGTAACATGCAAACAT
*
5653721 ATTAACACGAATCAAGT-A-AT-A--TAGTAACATGCAAACAT
1 ATTAACAAGAATCAAGTAATATAATTTAGTAACATGCAAACAT
* *
5653759 ATTAACATGAATCAAGTAATATAATTTAATAACATG
1 ATTAACAAGAATCAAGTAATATAATTTAGTAACATG
5653795 TCAATGAATA
Statistics
Matches: 64, Mismatches: 5, Indels: 10
0.81 0.06 0.13
Matches are distributed among these distances:
38 33 0.52
39 1 0.02
40 3 0.05
41 3 0.05
42 1 0.02
43 23 0.36
ACGTcount: A:0.50, C:0.11, G:0.10, T:0.29
Consensus pattern (43 bp):
ATTAACAAGAATCAAGTAATATAATTTAGTAACATGCAAACAT
Found at i:5654489 original size:42 final size:42
Alignment explanation
Indices: 5654430--5654517 Score: 167
Period size: 42 Copynumber: 2.1 Consensus size: 42
5654420 CCGATGACCG
5654430 CTAAACCATTGATTGGGAGCCCAAGTTGCAGTGCAACATCCT
1 CTAAACCATTGATTGGGAGCCCAAGTTGCAGTGCAACATCCT
*
5654472 CTAAACCATTGATTGGGAGCCCAAGTTGTAGTGCAACATCCT
1 CTAAACCATTGATTGGGAGCCCAAGTTGCAGTGCAACATCCT
5654514 CTAA
1 CTAA
5654518 CATCACTGTG
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 45 1.00
ACGTcount: A:0.30, C:0.25, G:0.20, T:0.25
Consensus pattern (42 bp):
CTAAACCATTGATTGGGAGCCCAAGTTGCAGTGCAACATCCT
Found at i:5655079 original size:45 final size:47
Alignment explanation
Indices: 5654994--5655115 Score: 178
Period size: 45 Copynumber: 2.6 Consensus size: 47
5654984 ACCAATATAA
* *
5654994 TACAAAAATAATAATTAAATACCAAAAT-GAGTTATTTACCAAAATGG
1 TACAAAAA-AATATTTATATACCAAAATAGAGTTATTTACCAAAATGG
*
5655041 TAC-AAAAAATATTTATATATCAAAATAGA-TTATTTACCAAAATGG
1 TACAAAAAAATATTTATATACCAAAATAGAGTTATTTACCAAAATGG
5655086 TACAAAATAAATATTTATATACCAAAATAG
1 TACAAAA-AAATATTTATATACCAAAATAG
5655116 TATCCACACC
Statistics
Matches: 68, Mismatches: 4, Indels: 6
0.87 0.05 0.08
Matches are distributed among these distances:
45 35 0.51
46 9 0.13
47 24 0.35
ACGTcount: A:0.53, C:0.10, G:0.07, T:0.30
Consensus pattern (47 bp):
TACAAAAAAATATTTATATACCAAAATAGAGTTATTTACCAAAATGG
Found at i:5655301 original size:20 final size:20
Alignment explanation
Indices: 5655276--5655356 Score: 74
Period size: 20 Copynumber: 3.9 Consensus size: 20
5655266 TTTTTACTAC
5655276 TACTAACAAAATAAATTACT
1 TACTAACAAAATAAATTACT
** * *
5655296 TACTAACTTACT-TATTAACT
1 TACTAACAAAATAAATT-ACT
5655316 ACTACTAACAAAATAAAATTACT
1 --TACTAACAAAAT-AAATTACT
*
5655339 TACTAACAAATTAAATTA
1 TACTAACAAAATAAATTA
5655357 AATTAAATTA
Statistics
Matches: 47, Mismatches: 9, Indels: 10
0.71 0.14 0.15
Matches are distributed among these distances:
19 3 0.06
20 18 0.38
21 11 0.23
22 9 0.19
23 3 0.06
24 3 0.06
ACGTcount: A:0.51, C:0.16, G:0.00, T:0.33
Consensus pattern (20 bp):
TACTAACAAAATAAATTACT
Found at i:5655352 original size:39 final size:40
Alignment explanation
Indices: 5655271--5655352 Score: 114
Period size: 42 Copynumber: 2.0 Consensus size: 40
5655261 TTACATTTTT
*
5655271 ACTACTACTAACAAAATAAATTACTTACTAACTTACTTATTA
1 ACTACTACTAACAAAATAAATTACTTACTAAC-TAC-AATTA
5655313 ACTACTACTAACAAAATAAAATTACTTACTAAC-A-AATTA
1 ACTACTACTAACAAAAT-AAATTACTTACTAACTACAATTA
5655352 A
1 A
5655353 ATTAAATTAA
Statistics
Matches: 38, Mismatches: 1, Indels: 5
0.86 0.02 0.11
Matches are distributed among these distances:
39 5 0.13
41 1 0.03
42 17 0.45
43 15 0.39
ACGTcount: A:0.50, C:0.18, G:0.00, T:0.32
Consensus pattern (40 bp):
ACTACTACTAACAAAATAAATTACTTACTAACTACAATTA
Found at i:5655356 original size:5 final size:5
Alignment explanation
Indices: 5655346--5655373 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
5655336 ACTTACTAAC
5655346 AAATT AAATT AAATT AAATT AAATT AAA
1 AAATT AAATT AAATT AAATT AAATT AAA
5655374 AATAACCAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (5 bp):
AAATT
Found at i:5655445 original size:12 final size:11
Alignment explanation
Indices: 5655426--5655459 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
5655416 AACTAAATAA
5655426 AAAAATTAAAT
1 AAAAATTAAAT
*
5655437 AACAAATTAATT
1 AA-AAATTAAAT
5655449 AAAAATTAAAT
1 AAAAATTAAAT
5655460 TAAACAAAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
11 10 0.50
12 10 0.50
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (11 bp):
AAAAATTAAAT
Found at i:5655460 original size:12 final size:12
Alignment explanation
Indices: 5655426--5655463 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
5655416 AACTAAATAA
5655426 AAAAATTAAA-T
1 AAAAATTAAATT
5655437 AACAAATT-AATT
1 AA-AAATTAAATT
5655449 AAAAATTAAATT
1 AAAAATTAAATT
5655461 AAA
1 AAA
5655464 CAAAACAAGT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
11 9 0.38
12 15 0.62
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (12 bp):
AAAAATTAAATT
Found at i:5658043 original size:24 final size:23
Alignment explanation
Indices: 5658016--5658063 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 23
5658006 TAAATGAATG
* *
5658016 ATAAAAAATATTTTTTATAAAAAA
1 ATAAAAAAT-TATTATATAAAAAA
5658040 ATAAAAAATTATTATATAAAAAA
1 ATAAAAAATTATTATATAAAAAA
5658063 A
1 A
5658064 AAACAATGAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 13 0.59
24 9 0.41
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (23 bp):
ATAAAAAATTATTATATAAAAAA
Found at i:5658064 original size:24 final size:24
Alignment explanation
Indices: 5658016--5658065 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 24
5658006 TAAATGAATG
* *
5658016 ATAAAAAATATTTTTTATAAAAAA
1 ATAAAAAATATTATATATAAAAAA
*
5658040 ATAAAAAATTATTATATAAAAAAAA
1 ATAAAAAA-TATTATATATAAAAAA
5658065 A
1 A
5658066 ACAATGATTG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
24 8 0.36
25 14 0.64
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (24 bp):
ATAAAAAATATTATATATAAAAAA
Found at i:5658200 original size:10 final size:10
Alignment explanation
Indices: 5658185--5658244 Score: 72
Period size: 10 Copynumber: 6.1 Consensus size: 10
5658175 TATTATTACC
5658185 ATTTTTAATA
1 ATTTTTAATA
*
5658195 ATTTTT-AGA
1 ATTTTTAATA
5658204 ATTTTTAATA
1 ATTTTTAATA
5658214 ATTATTT-ATA
1 ATT-TTTAATA
5658224 ATTATTTAAT-
1 ATT-TTTAATA
5658234 ATTTTTAATA
1 ATTTTTAATA
5658244 A
1 A
5658245 AGGTAAGTAT
Statistics
Matches: 44, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
9 14 0.32
10 25 0.57
11 5 0.11
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (10 bp):
ATTTTTAATA
Found at i:5658207 original size:19 final size:19
Alignment explanation
Indices: 5658185--5658240 Score: 78
Period size: 19 Copynumber: 2.9 Consensus size: 19
5658175 TATTATTACC
5658185 ATTTTTAATAATTTTTAGA
1 ATTTTTAATAATTTTTAGA
*
5658204 ATTTTTAATAATTATTTATA
1 ATTTTTAATAATT-TTTAGA
5658224 ATTATTTAAT-ATTTTTA
1 ATT-TTTAATAATTTTTA
5658241 ATAAAGGTAA
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
19 17 0.50
20 11 0.32
21 6 0.18
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.61
Consensus pattern (19 bp):
ATTTTTAATAATTTTTAGA
Found at i:5659012 original size:24 final size:22
Alignment explanation
Indices: 5658949--5659012 Score: 65
Period size: 24 Copynumber: 2.7 Consensus size: 22
5658939 TGTAACTCAT
5658949 TATTAATATTTTAATATAATAAA
1 TATTAATATTTTAA-ATAATAAA
* *
5658972 AATTTAAATATTTTAAATAATTAA
1 TA-TT-AATATTTTAAATAATAAA
5658996 TATTAATTATTTATAAA
1 TATTAA-TATTT-TAAA
5659013 ATTTAATTTG
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
22 2 0.06
23 8 0.24
24 14 0.41
25 10 0.29
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
TATTAATATTTTAAATAATAAA
Found at i:5668872 original size:23 final size:23
Alignment explanation
Indices: 5668846--5668890 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
5668836 ATTTTCGAAT
**
5668846 TTCGAATTATTCGAATCGAGTTA
1 TTCGAATTAAACGAATCGAGTTA
*
5668869 TTCGAGTTAAACGAATCGAGTT
1 TTCGAATTAAACGAATCGAGTT
5668891 GAATTTTTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.31, C:0.13, G:0.20, T:0.36
Consensus pattern (23 bp):
TTCGAATTAAACGAATCGAGTTA
Found at i:5669163 original size:58 final size:58
Alignment explanation
Indices: 5669099--5669220 Score: 176
Period size: 58 Copynumber: 2.1 Consensus size: 58
5669089 AAACCCATCA
* *
5669099 ATAAACTAAA-CCTAAATATTTTTAAACCCAAATATAATTTCATTCTTCAAA-AATACTC
1 ATAAACTAAATCC-AAATATTTTTAAACCCAAATATAATTTCATTCCT-AAATAACACTC
* *
5669157 ATAAACTAAATCCAAATATTTTTAAACTCAAATATAATTTTATTCCTAAATAACACTC
1 ATAAACTAAATCCAAATATTTTTAAACCCAAATATAATTTCATTCCTAAATAACACTC
5669215 ATAAAC
1 ATAAAC
5669221 AACTCCTTTT
Statistics
Matches: 58, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
57 3 0.05
58 53 0.91
59 2 0.03
ACGTcount: A:0.48, C:0.18, G:0.00, T:0.34
Consensus pattern (58 bp):
ATAAACTAAATCCAAATATTTTTAAACCCAAATATAATTTCATTCCTAAATAACACTC
Found at i:5674363 original size:58 final size:58
Alignment explanation
Indices: 5674249--5674363 Score: 187
Period size: 58 Copynumber: 2.0 Consensus size: 58
5674239 ATCAACAAAC
* *
5674249 TAAACCCAAATATTTTTAAACTCAAATATAATTTCATTCTTCAAAAATACTTATAAAT
1 TAAACCCAAATATTTTTAAACTCAAATATAATTTCATTCTTCAAAAACACTCATAAAT
*
5674307 TAAACCCAAATATTTTTAAACTCAAATATAATTTTATTCTT-AAATAACACTCATAAA
1 TAAACCCAAATATTTTTAAACTCAAATATAATTTCATTCTTCAAA-AACACTCATAAA
5674364 CAACTCCTTT
Statistics
Matches: 53, Mismatches: 3, Indels: 2
0.91 0.05 0.03
Matches are distributed among these distances:
57 3 0.06
58 50 0.94
ACGTcount: A:0.47, C:0.16, G:0.00, T:0.37
Consensus pattern (58 bp):
TAAACCCAAATATTTTTAAACTCAAATATAATTTCATTCTTCAAAAACACTCATAAAT
Found at i:5680885 original size:4 final size:4
Alignment explanation
Indices: 5680876--5680901 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
5680866 AAGCTCATTT
5680876 TACC TACC TACC TACC TACC TACC TA
1 TACC TACC TACC TACC TACC TACC TA
5680902 AACATCCATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.27, C:0.46, G:0.00, T:0.27
Consensus pattern (4 bp):
TACC
Found at i:5681796 original size:41 final size:38
Alignment explanation
Indices: 5681712--5681797 Score: 109
Period size: 41 Copynumber: 2.2 Consensus size: 38
5681702 TTTTATTTCA
5681712 TTTATTTTAAGTTTTTTTTATTTTTAATTAATAAATAT
1 TTTATTTTAAGTTTTTTTTATTTTTAATTAATAAATAT
* * * *
5681750 ATTATTTTCAATTTTTTATTTATTTTTTAATTAATAACTCT
1 TTTATTTT-AAGTTTTT-TTTA-TTTTTAATTAATAAATAT
5681791 TTTATTT
1 TTTATTT
5681798 ATATAAATAA
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
38 7 0.17
39 7 0.17
40 4 0.10
41 22 0.55
ACGTcount: A:0.29, C:0.03, G:0.01, T:0.66
Consensus pattern (38 bp):
TTTATTTTAAGTTTTTTTTATTTTTAATTAATAAATAT
Found at i:5681848 original size:22 final size:22
Alignment explanation
Indices: 5681808--5681916 Score: 81
Period size: 20 Copynumber: 5.2 Consensus size: 22
5681798 ATATAAATAA
*
5681808 AATAATAAATATGTA-ATTATAT
1 AATAA-AAATATATATATTATAT
5681830 AATAAAAATATATATATTATTAT
1 AATAAAAATATATATATTA-TAT
** *
5681853 GTTAAAAATAT-TAT-TAAT-T
1 AATAAAAATATATATATTATAT
* *
5681872 AAT-AATATTTATAT-TTATAT
1 AATAAAAATATATATATTATAT
*
5681892 AA-ATAAATATATA-ATTATAT
1 AATAAAAATATATATATTATAT
5681912 AATAA
1 AATAA
5681917 GTATATTTTT
Statistics
Matches: 67, Mismatches: 13, Indels: 15
0.71 0.14 0.16
Matches are distributed among these distances:
18 5 0.07
19 8 0.12
20 19 0.28
21 11 0.16
22 12 0.18
23 12 0.18
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (22 bp):
AATAAAAATATATATATTATAT
Found at i:5681878 original size:16 final size:17
Alignment explanation
Indices: 5681843--5681880 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
5681833 AAAAATATAT
*
5681843 ATATTATTATGTTAAAA
1 ATATTATTATATTAAAA
*
5681860 ATATTATTA-ATTAATA
1 ATATTATTATATTAAAA
5681876 ATATT
1 ATATT
5681881 TATATTTATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 10 0.53
17 9 0.47
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (17 bp):
ATATTATTATATTAAAA
Found at i:5681922 original size:37 final size:38
Alignment explanation
Indices: 5681858--5681929 Score: 94
Period size: 37 Copynumber: 1.9 Consensus size: 38
5681848 ATTATGTTAA
**
5681858 AAATATTATTAATTAATAATATTTATATTTATATAAAT
1 AAATATTATTAATTAATAATAAGTATATTTATATAAAT
*
5681896 AAATA-TA-TAATTATATAATAAGTATATTTTTATA
1 AAATATTATTAATTA-ATAATAAGTATATTTATATA
5681930 TCTATTTTAT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
36 6 0.20
37 19 0.63
38 5 0.17
ACGTcount: A:0.50, C:0.00, G:0.01, T:0.49
Consensus pattern (38 bp):
AAATATTATTAATTAATAATAAGTATATTTATATAAAT
Found at i:5681941 original size:25 final size:26
Alignment explanation
Indices: 5681913--5681968 Score: 71
Period size: 25 Copynumber: 2.2 Consensus size: 26
5681903 TAATTATATA
*
5681913 ATAAGTATATTT-TTATATCTATTTT-
1 ATAAATATATTTATT-TATCTATTTTG
*
5681938 ATAAATATATTTATTTATTTATTTTG
1 ATAAATATATTTATTTATCTATTTTG
5681964 ATAAA
1 ATAAA
5681969 AAAAGGCCTA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
25 20 0.74
26 7 0.26
ACGTcount: A:0.38, C:0.02, G:0.04, T:0.57
Consensus pattern (26 bp):
ATAAATATATTTATTTATCTATTTTG
Found at i:5683690 original size:29 final size:30
Alignment explanation
Indices: 5683633--5683709 Score: 84
Period size: 31 Copynumber: 2.5 Consensus size: 30
5683623 TCAAAATTAT
*
5683633 ACATGAACTTTAATTTGATGTGCAATTATAT
1 ACATGAACTTTAATTTGA-GTGCAATTATAC
* * * *
5683664 GCATGAACTTTGATTTG-GTGTAGTTATAC
1 ACATGAACTTTAATTTGAGTGCAATTATAC
5683693 ACATGAAACTTTAATTT
1 ACATG-AACTTTAATTT
5683710 TGATTTAATT
Statistics
Matches: 38, Mismatches: 7, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
29 13 0.34
30 10 0.26
31 15 0.39
ACGTcount: A:0.32, C:0.10, G:0.16, T:0.42
Consensus pattern (30 bp):
ACATGAACTTTAATTTGAGTGCAATTATAC
Found at i:5684005 original size:6 final size:6
Alignment explanation
Indices: 5683994--5684021 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
5683984 ACGTTCAGAA
5683994 AATTAC AATTAC AATTAC AATTAC AATT
1 AATTAC AATTAC AATTAC AATTAC AATT
5684022 CTTTATAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.50, C:0.14, G:0.00, T:0.36
Consensus pattern (6 bp):
AATTAC
Found at i:5684618 original size:16 final size:16
Alignment explanation
Indices: 5684597--5684646 Score: 61
Period size: 16 Copynumber: 3.2 Consensus size: 16
5684587 ATATTTAGTC
5684597 ATATAATAAATTATTA
1 ATATAATAAATTATTA
*
5684613 ATATAATTAATTATT-
1 ATATAATAAATTATTA
5684628 -T-TAATAAATTATTTA
1 ATATAATAAATTA-TTA
5684643 ATAT
1 ATAT
5684647 TTCAATTTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
13 9 0.32
14 3 0.11
16 15 0.54
17 1 0.04
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
ATATAATAAATTATTA
Found at i:5684653 original size:29 final size:29
Alignment explanation
Indices: 5684600--5684666 Score: 77
Period size: 29 Copynumber: 2.3 Consensus size: 29
5684590 TTTAGTCATA
5684600 TAATAAATTATTAATATAATTAA-TTATTT
1 TAATAAATTATTAATAT-ATTAATTTATTT
5684629 TAATAAATTATTTAATAT-TTCAATTTTATTT
1 TAATAAATTA-TTAATATATT-AA-TTTATTT
5684660 TAA-AAAT
1 TAATAAAT
5684667 AAATTTAAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
28 2 0.06
29 12 0.35
30 11 0.32
31 9 0.26
ACGTcount: A:0.46, C:0.01, G:0.00, T:0.52
Consensus pattern (29 bp):
TAATAAATTATTAATATATTAATTTATTT
Found at i:5695683 original size:45 final size:46
Alignment explanation
Indices: 5695622--5695725 Score: 124
Period size: 45 Copynumber: 2.3 Consensus size: 46
5695612 AAGTGCTGGG
* *
5695622 GAAACAATAAGCACACACAATGC-AATCCAGTAGGCACACACA-GTGC
1 GAAACAGTAAGCACACACAACGCAAAT-CAGTAGGCACACA-AGGTGC
* * *
5695668 -AAACAGTAGGCACACATAGCGCAAATCAGTAGGCACACAAGGTGC
1 GAAACAGTAAGCACACACAACGCAAATCAGTAGGCACACAAGGTGC
5695713 GAAACAGTAAGCA
1 GAAACAGTAAGCA
5695726 TGCTAGCATT
Statistics
Matches: 49, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
44 1 0.02
45 34 0.69
46 14 0.29
ACGTcount: A:0.43, C:0.25, G:0.21, T:0.11
Consensus pattern (46 bp):
GAAACAGTAAGCACACACAACGCAAATCAGTAGGCACACAAGGTGC
Found at i:5695720 original size:23 final size:22
Alignment explanation
Indices: 5695623--5695721 Score: 101
Period size: 23 Copynumber: 4.4 Consensus size: 22
5695613 AGTGCTGGGG
* * *
5695623 AAACAATAAGCACACACAATGC
1 AAACAGTAGGCACACACAGTGC
*
5695645 AATCCAGTAGGCACACACAGTGC
1 AA-ACAGTAGGCACACACAGTGC
* *
5695668 AAACAGTAGGCACACATAGCGC
1 AAACAGTAGGCACACACAGTGC
5695690 AAATCAGTAGGCACACA-AGGTGC
1 AAA-CAGTAGGCACACACA-GTGC
5695713 GAAACAGTA
1 -AAACAGTA
5695722 AGCATGCTAG
Statistics
Matches: 65, Mismatches: 8, Indels: 7
0.81 0.10 0.09
Matches are distributed among these distances:
22 23 0.35
23 39 0.60
24 3 0.05
ACGTcount: A:0.43, C:0.25, G:0.20, T:0.11
Consensus pattern (22 bp):
AAACAGTAGGCACACACAGTGC
Found at i:5702319 original size:23 final size:22
Alignment explanation
Indices: 5702220--5702346 Score: 96
Period size: 23 Copynumber: 5.5 Consensus size: 22
5702210 CGAAGTACTT
*
5702220 AACAGTAAGCACACAAGTGTTGGGGA
1 AACAGTAAGCACACAA--G-T-GCGA
*
5702246 AACAATAAGCACACACAGTGC-A
1 AACAGTAAGCACACA-AGTGCGA
* * * *
5702268 ATCAGTAGGCGCACATAGCGC-A
1 AACAGTAAGCACACA-AGTGCGA
*
5702290 AATCAGTAGGCACACAAGGTGCGA
1 AA-CAGTAAGCACACAA-GTGCGA
5702314 AACAGTAAGCACACAAAGTGCGA
1 AACAGTAAGCACAC-AAGTGCGA
5702337 AACAGTAAGC
1 AACAGTAAGC
5702347 GCGCTAGTGT
Statistics
Matches: 84, Mismatches: 12, Indels: 13
0.77 0.11 0.12
Matches are distributed among these distances:
22 19 0.23
23 43 0.51
24 6 0.07
25 1 0.01
26 14 0.17
27 1 0.01
ACGTcount: A:0.42, C:0.22, G:0.24, T:0.12
Consensus pattern (22 bp):
AACAGTAAGCACACAAGTGCGA
Found at i:5708015 original size:12 final size:12
Alignment explanation
Indices: 5707998--5708022 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
5707988 GCAACAAGAA
5707998 ATTTCAAAATAT
1 ATTTCAAAATAT
5708010 ATTTCAAAATAT
1 ATTTCAAAATAT
5708022 A
1 A
5708023 ACAGAAAATT
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:0.52, C:0.08, G:0.00, T:0.40
Consensus pattern (12 bp):
ATTTCAAAATAT
Found at i:5708597 original size:63 final size:62
Alignment explanation
Indices: 5708498--5708730 Score: 349
Period size: 63 Copynumber: 3.7 Consensus size: 62
5708488 ATTTTCGAAA
* *
5708498 CAGGAGGAGAATCAAATGCCTGCTTTGCAACATCCTTCTGCTCAATGTTCTGTTCATTGGAAG
1 CAGGAGGAGAATCAAATGCCCGCTTTGCAACATCCTTCTGCTCAA-GTTCTGTTCGTTGGAAG
* * *
5708561 CAGGAGGAGAATCAAATGCCCACTTCGCAACATCCTTCTGCACCAAGTTCTGTTCGTTGGAAG
1 CAGGAGGAGAATCAAATGCCCGCTTTGCAACATCCTTCTGC-TCAAGTTCTGTTCGTTGGAAG
* * * *
5708624 GAGGAGGAGAATCAAATGCTCGCTTTGCAACATCCTTCTGTTGCAAGTTATGTTCGTTGGAAG
1 CAGGAGGAGAATCAAATGCCCGCTTTGCAACATCCTTCTGCT-CAAGTTCTGTTCGTTGGAAG
*
5708687 CAGGAGGAGAATCAAATGCCCGCTTTGCAACATCCTTCCGCTCA
1 CAGGAGGAGAATCAAATGCCCGCTTTGCAACATCCTTCTGCTCA
5708731 TAGCTGTGAC
Statistics
Matches: 152, Mismatches: 16, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
62 2 0.01
63 147 0.97
64 3 0.02
ACGTcount: A:0.26, C:0.24, G:0.23, T:0.27
Consensus pattern (62 bp):
CAGGAGGAGAATCAAATGCCCGCTTTGCAACATCCTTCTGCTCAAGTTCTGTTCGTTGGAAG
Found at i:5708815 original size:24 final size:24
Alignment explanation
Indices: 5708788--5708834 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
5708778 GCTCCGCCCT
*
5708788 CGACCAGGACTACGGCTGTAGCTA
1 CGACAAGGACTACGGCTGTAGCTA
*
5708812 CGACAAGGGCTACGGCTGTAGCT
1 CGACAAGGACTACGGCTGTAGCT
5708835 GCGGCTACGA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.23, C:0.28, G:0.32, T:0.17
Consensus pattern (24 bp):
CGACAAGGACTACGGCTGTAGCTA
Found at i:5709222 original size:18 final size:18
Alignment explanation
Indices: 5709201--5709258 Score: 52
Period size: 18 Copynumber: 3.4 Consensus size: 18
5709191 TATCCCTCAT
5709201 ACCACCACGACCGCCAAA
1 ACCACCACGACCGCCAAA
* **
5709219 ACCACCATC--CC-TC-GT
1 ACCACCA-CGACCGCCAAA
5709234 ACCACCACGACCGCCAAA
1 ACCACCACGACCGCCAAA
5709252 ACCACCA
1 ACCACCA
5709259 TCTCTCATAC
Statistics
Matches: 29, Mismatches: 6, Indels: 10
0.64 0.13 0.22
Matches are distributed among these distances:
14 1 0.03
15 7 0.24
16 3 0.10
17 3 0.10
18 14 0.48
19 1 0.03
ACGTcount: A:0.34, C:0.52, G:0.09, T:0.05
Consensus pattern (18 bp):
ACCACCACGACCGCCAAA
Found at i:5709311 original size:33 final size:33
Alignment explanation
Indices: 5709176--5709308 Score: 176
Period size: 33 Copynumber: 4.0 Consensus size: 33
5709166 CTCCCTCCAG
* *
5709176 GACCACCAAAGCCACTATCCCTCATACCACCAC
1 GACCACCAAAACCACCATCCCTCATACCACCAC
* *
5709209 GACCGCCAAAACCACCATCCCTCGTACCACCAC
1 GACCACCAAAACCACCATCCCTCATACCACCAC
* *
5709242 GACCGCCAAAACCACCATCTCTCATACCACCAC
1 GACCACCAAAACCACCATCCCTCATACCACCAC
* * * *
5709275 GGCCACCAAAGCCTCCATCCCTCATTCCACCAC
1 GACCACCAAAACCACCATCCCTCATACCACCAC
5709308 G
1 G
5709309 GCCTCCAGAA
Statistics
Matches: 88, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 88 1.00
ACGTcount: A:0.30, C:0.50, G:0.08, T:0.12
Consensus pattern (33 bp):
GACCACCAAAACCACCATCCCTCATACCACCAC
Found at i:5717877 original size:6 final size:7
Alignment explanation
Indices: 5717852--5717876 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
5717842 TAAAATTTTG
5717852 AAAAATT
1 AAAAATT
5717859 AAAAATT
1 AAAAATT
5717866 AAAAATT
1 AAAAATT
5717873 AAAA
1 AAAA
5717877 TCATTTTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (7 bp):
AAAAATT
Found at i:5717893 original size:30 final size:27
Alignment explanation
Indices: 5717818--5717893 Score: 73
Period size: 29 Copynumber: 2.6 Consensus size: 27
5717808 TATTTTTTTC
5717818 ATATTTTAAATAAAAACATAAAAATAAA
1 ATATTTTAAATAAAAA-ATAAAAATAAA
* *
5717846 AT-TTTGAAAAATTAAAAATTAAAAATTAAA
1 ATATTT--TAAA-TAAAAAATAAAAA-TAAA
5717876 ATCATTTTAAATAAAAAA
1 AT-ATTTTAAATAAAAAA
5717894 AATCCCCAAT
Statistics
Matches: 38, Mismatches: 4, Indels: 11
0.72 0.08 0.21
Matches are distributed among these distances:
27 3 0.08
28 2 0.05
29 15 0.39
30 15 0.39
32 3 0.08
ACGTcount: A:0.64, C:0.03, G:0.01, T:0.32
Consensus pattern (27 bp):
ATATTTTAAATAAAAAATAAAAATAAA
Found at i:5719287 original size:23 final size:22
Alignment explanation
Indices: 5719261--5719305 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 22
5719251 ATGTTTATAA
*
5719261 TTAATAAATATATATTTTTATTT
1 TTAATAAATAAAT-TTTTTATTT
*
5719284 TTAATTAATAAATTTTTTATTT
1 TTAATAAATAAATTTTTTATTT
5719306 ATAAAATCAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 9 0.45
23 11 0.55
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (22 bp):
TTAATAAATAAATTTTTTATTT
Found at i:5720115 original size:6 final size:6
Alignment explanation
Indices: 5720104--5720131 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
5720094 GGTACTTCTA
5720104 TTAAAT TTAAAT TTAAAT TTAAAT TTAA
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAA
5720132 GTCTCTATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (6 bp):
TTAAAT
Found at i:5721848 original size:26 final size:24
Alignment explanation
Indices: 5721802--5721863 Score: 61
Period size: 26 Copynumber: 2.4 Consensus size: 24
5721792 TCCATATTTT
* *
5721802 ATTTTATTTTATTTTAATATTTAATA
1 ATTTTA-TATATTTTAATATTGAA-A
*
5721828 ATTTTATATATTTTATTTATTGAAA
1 ATTTTATATATTTTA-ATATTGAAA
5721853 ATTTTTATATA
1 A-TTTTATATA
5721864 GTATCTTAAC
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
25 10 0.32
26 21 0.68
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (24 bp):
ATTTTATATATTTTAATATTGAAA
Found at i:5721966 original size:18 final size:17
Alignment explanation
Indices: 5721940--5721976 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 17
5721930 TATATGTTTT
*
5721940 AAATTACATAATATATAA
1 AAATAACATAATATA-AA
5721958 AAATAACATAATATAAA
1 AAATAACATAATATAAA
5721975 AA
1 AA
5721977 GGTCGGGTCA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 4 0.22
18 14 0.78
ACGTcount: A:0.68, C:0.05, G:0.00, T:0.27
Consensus pattern (17 bp):
AAATAACATAATATAAA
Found at i:5722679 original size:45 final size:45
Alignment explanation
Indices: 5722629--5722714 Score: 172
Period size: 45 Copynumber: 1.9 Consensus size: 45
5722619 AACTTTTTTG
5722629 ATCAATTTATTATGAATTTAAAATTTATGTCTAACTTAATAATAA
1 ATCAATTTATTATGAATTTAAAATTTATGTCTAACTTAATAATAA
5722674 ATCAATTTATTATGAATTTAAAATTTATGTCTAACTTAATA
1 ATCAATTTATTATGAATTTAAAATTTATGTCTAACTTAATA
5722715 TTATTATGGG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 41 1.00
ACGTcount: A:0.43, C:0.07, G:0.05, T:0.45
Consensus pattern (45 bp):
ATCAATTTATTATGAATTTAAAATTTATGTCTAACTTAATAATAA
Found at i:5723733 original size:58 final size:58
Alignment explanation
Indices: 5723635--5723755 Score: 163
Period size: 58 Copynumber: 2.1 Consensus size: 58
5723625 CCTCTGCCTC
* ** *
5723635 TTCCACTTTTATTTTTTATTTATTTATTTTTTTCTCAACCAATAAATTGCTATACATT
1 TTCCACTTTTATTTTTTATTTATTTATTTGTAGCTCAACCAATAAATTGCTATACAAT
* * *
5723693 TTCCACTTTTATTTTTT-TATTATTTCTTTGTAGCTTAACCAATAAATTGCTGTACAAT
1 TTCCACTTTTATTTTTTAT-TTATTTATTTGTAGCTCAACCAATAAATTGCTATACAAT
5723751 TTCCA
1 TTCCA
5723756 TTAAGACCAA
Statistics
Matches: 55, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
57 1 0.02
58 54 0.98
ACGTcount: A:0.26, C:0.17, G:0.04, T:0.54
Consensus pattern (58 bp):
TTCCACTTTTATTTTTTATTTATTTATTTGTAGCTCAACCAATAAATTGCTATACAAT
Found at i:5728164 original size:37 final size:37
Alignment explanation
Indices: 5728117--5728192 Score: 134
Period size: 37 Copynumber: 2.1 Consensus size: 37
5728107 ACAAATGGCC
*
5728117 ACAAGTATGTTTTCTGGTTCAAATATCAGTGAAGTAG
1 ACAAGGATGTTTTCTGGTTCAAATATCAGTGAAGTAG
*
5728154 ACAAGGATGTTTTCTGGTTCAAATATCGGTGAAGTAG
1 ACAAGGATGTTTTCTGGTTCAAATATCAGTGAAGTAG
5728191 AC
1 AC
5728193 GAGGGGGGAA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.32, C:0.12, G:0.24, T:0.33
Consensus pattern (37 bp):
ACAAGGATGTTTTCTGGTTCAAATATCAGTGAAGTAG
Found at i:5731685 original size:21 final size:21
Alignment explanation
Indices: 5731650--5731701 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
5731640 AAATTATTGT
5731650 TTTTCAAATTATTTAATTTAAA
1 TTTTCAAATTATTT-ATTTAAA
* *
5731672 TTTT-AAATTTTTTATTTAAT
1 TTTTCAAATTATTTATTTAAA
*
5731692 TTTTCGAATT
1 TTTTCAAATT
5731702 GAATTTTTAT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
20 10 0.38
21 12 0.46
22 4 0.15
ACGTcount: A:0.33, C:0.04, G:0.02, T:0.62
Consensus pattern (21 bp):
TTTTCAAATTATTTATTTAAA
Found at i:5745496 original size:6 final size:7
Alignment explanation
Indices: 5745478--5745508 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
5745468 CAACAGTAGA
5745478 AGGGGGG
1 AGGGGGG
5745485 AGGGGGG
1 AGGGGGG
5745492 AGGGGGG
1 AGGGGGG
5745499 AGGGGGG
1 AGGGGGG
5745506 AGG
1 AGG
5745509 TGTAGGATGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.16, C:0.00, G:0.84, T:0.00
Consensus pattern (7 bp):
AGGGGGG
Found at i:5748736 original size:20 final size:21
Alignment explanation
Indices: 5748699--5748737 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
5748689 TTTTTAACAT
* *
5748699 AAATTTTTTAACTTTTATCCA
1 AAATTTTATAACTATTATCCA
5748720 AAATTTTATAA-TATTATC
1 AAATTTTATAACTATTATC
5748738 TCAGACTCAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 6 0.38
21 10 0.62
ACGTcount: A:0.38, C:0.10, G:0.00, T:0.51
Consensus pattern (21 bp):
AAATTTTATAACTATTATCCA
Found at i:5754696 original size:23 final size:23
Alignment explanation
Indices: 5754652--5754701 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
5754642 CAATCTTTCC
5754652 ATTTCTATTAAAAATTTGTATAA
1 ATTTCTATTAAAAATTTGTATAA
* *
5754675 ATTTCATATT-AAATTTTTTATAA
1 ATTTC-TATTAAAAATTTGTATAA
5754698 ATTT
1 ATTT
5754702 AATCTGCCAC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 20 0.83
24 4 0.17
ACGTcount: A:0.40, C:0.04, G:0.02, T:0.54
Consensus pattern (23 bp):
ATTTCTATTAAAAATTTGTATAA
Found at i:5761222 original size:2 final size:2
Alignment explanation
Indices: 5761217--5761246 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
5761207 GTGCGTCTGT
5761217 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
5761247 TGGAACCATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:5764702 original size:3 final size:3
Alignment explanation
Indices: 5764694--5764719 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
5764684 ACCTTTTACC
5764694 TCA TCA TCA TCA TCA TCA TCA TCA TC
1 TCA TCA TCA TCA TCA TCA TCA TCA TC
5764720 GAGAACAACG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.35, G:0.00, T:0.35
Consensus pattern (3 bp):
TCA
Found at i:5767214 original size:90 final size:90
Alignment explanation
Indices: 5767061--5767234 Score: 206
Period size: 90 Copynumber: 1.9 Consensus size: 90
5767051 TATATATAAA
* * ** * *
5767061 AATATATTGCAAGTCTAATAAGGGCAGGTTTAGATGGGCGGTATGGTGCGTTTAGCTTATTTTTA
1 AATATATTACAAGTCTAATAAAGGCAGGTTTAGATACGCGGTACGGTGCATTTAGCTTATTTTTA
* *
5767126 TCTCATGTTACAGTATCTATATATC
66 TCTCATATTACAATATCTATATATC
* * * *
5767151 AATATATTACGAGTCTAA-AAAGGCGGGTTTGGATACGCGGTACGGTGTATTTAGCTTATTTTTT
1 AATATATTACAAGTCTAATAAAGGCAGGTTTAGATACGCGGTACGGTGCATTTAGCTTA-TTTTT
* *
5767215 GTGTCATATTACAATATCTA
65 ATCTCATATTACAATATCTA
5767235 ATTTCACTGT
Statistics
Matches: 69, Mismatches: 14, Indels: 2
0.81 0.16 0.02
Matches are distributed among these distances:
89 32 0.46
90 37 0.54
ACGTcount: A:0.28, C:0.12, G:0.22, T:0.39
Consensus pattern (90 bp):
AATATATTACAAGTCTAATAAAGGCAGGTTTAGATACGCGGTACGGTGCATTTAGCTTATTTTTA
TCTCATATTACAATATCTATATATC
Found at i:5769165 original size:24 final size:24
Alignment explanation
Indices: 5769132--5769198 Score: 98
Period size: 24 Copynumber: 2.8 Consensus size: 24
5769122 AGAAATAATC
* *
5769132 TTTCAGTTAAACTTTGTTTAATTG
1 TTTCAATTAAACTCTGTTTAATTG
*
5769156 TTTCAATTAAACTCTGTTTATTTG
1 TTTCAATTAAACTCTGTTTAATTG
*
5769180 TTTCACTTAAACTCTGTTT
1 TTTCAATTAAACTCTGTTT
5769199 GAGTCAAACT
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 39 1.00
ACGTcount: A:0.24, C:0.13, G:0.09, T:0.54
Consensus pattern (24 bp):
TTTCAATTAAACTCTGTTTAATTG
Found at i:5771154 original size:24 final size:24
Alignment explanation
Indices: 5771126--5771188 Score: 80
Period size: 20 Copynumber: 2.8 Consensus size: 24
5771116 AGAAATAATC
*
5771126 TTTCAGTTAAACTCTGTTTAATTG
1 TTTCAATTAAACTCTGTTTAATTG
*
5771150 TTTCAATT----TCTGTTTATTTG
1 TTTCAATTAAACTCTGTTTAATTG
5771170 TTTCAATTAAACTCTGTTT
1 TTTCAATTAAACTCTGTTT
5771189 GAGTCAAACT
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
20 19 0.58
24 14 0.42
ACGTcount: A:0.22, C:0.13, G:0.10, T:0.56
Consensus pattern (24 bp):
TTTCAATTAAACTCTGTTTAATTG
Found at i:5773371 original size:18 final size:18
Alignment explanation
Indices: 5773348--5773395 Score: 60
Period size: 18 Copynumber: 2.7 Consensus size: 18
5773338 ACAATTTATA
5773348 TCACTTTCAATTCCAATT
1 TCACTTTCAATTCCAATT
* * * *
5773366 TCACTTTTACTTTCACTT
1 TCACTTTCAATTCCAATT
5773384 TCACTTTCAATT
1 TCACTTTCAATT
5773396 TTTATCACAA
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.23, C:0.27, G:0.00, T:0.50
Consensus pattern (18 bp):
TCACTTTCAATTCCAATT
Found at i:5773377 original size:6 final size:6
Alignment explanation
Indices: 5773348--5773392 Score: 54
Period size: 6 Copynumber: 7.5 Consensus size: 6
5773338 ACAATTTATA
* * * *
5773348 TCACTT TCAATT CCAATT TCACTT TTACTT TCACTT TCACTT TCA
1 TCACTT TCACTT TCACTT TCACTT TCACTT TCACTT TCACTT TCA
5773393 ATTTTTATCA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.22, C:0.29, G:0.00, T:0.49
Consensus pattern (6 bp):
TCACTT
Done.