Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008150.1 Hibiscus syriacus cultivar Beakdansim tig00110716_pilon, whole genome shotgun sequence
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: 3012591
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 14
Found at i:279938 original size:14 final size:14
Alignment explanation
Indices: 279919--279962 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
279909 GCAATAATGT
279919 ATATTATAAAAATA
1 ATATTATAAAAATA
*
279933 ATATTAATCAAAAGT-
1 ATATT-AT-AAAAATA
279948 ATATTATAAAAATA
1 ATATTATAAAAATA
279962 A
1 A
279963 AAGGGACGAA
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
13 5 0.20
14 8 0.32
15 7 0.28
16 5 0.20
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.34
Consensus pattern (14 bp):
ATATTATAAAAATA
Found at i:281999 original size:26 final size:27
Alignment explanation
Indices: 281970--282024 Score: 87
Period size: 26 Copynumber: 2.1 Consensus size: 27
281960 ATAATAATAA
281970 TTATTATTATTATTAAAT-ATATT-TAT
1 TTATTATTATTATT-AATGATATTATAT
281996 TTATTATTATTATTAATGATATTATAT
1 TTATTATTATTATTAATGATATTATAT
282023 TT
1 TT
282025 TTGTTACAGG
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
25 3 0.11
26 19 0.70
27 5 0.19
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (27 bp):
TTATTATTATTATTAATGATATTATAT
Found at i:285240 original size:21 final size:22
Alignment explanation
Indices: 285216--285257 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
285206 AATAAAAAAT
285216 ATTA-TTATTAACATATTTAAA
1 ATTATTTATTAACATATTTAAA
* *
285237 ATTATTTATTAATATTTTTAA
1 ATTATTTATTAACATATTTAA
285258 TAATATAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (22 bp):
ATTATTTATTAACATATTTAAA
Found at i:285282 original size:25 final size:26
Alignment explanation
Indices: 285246--285318 Score: 82
Period size: 25 Copynumber: 2.9 Consensus size: 26
285236 AATTATTTAT
*
285246 TAATATTTTTAATAAT-ATAATAT-AA
1 TAATATTATTAATAATAAT-ATATCAA
285271 TAATATTATTAAT-ATAATATATCAA
1 TAATATTATTAATAATAATATATCAA
*
285296 TTATATTA-TAATAATAATGATAT
1 TAATATTATTAATAATAAT-ATAT
285319 GTTATATTCT
Statistics
Matches: 42, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
24 10 0.24
25 28 0.67
26 4 0.10
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.47
Consensus pattern (26 bp):
TAATATTATTAATAATAATATATCAA
Found at i:285664 original size:21 final size:22
Alignment explanation
Indices: 285638--285678 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
285628 TTATTCTAAT
285638 ATTTTTAAAAT-AATAATATTA
1 ATTTTTAAAATAAATAATATTA
*
285659 ATTTTTATAATAAATAATAT
1 ATTTTTAAAATAAATAATAT
285679 ATTTATTATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (22 bp):
ATTTTTAAAATAAATAATATTA
Found at i:285687 original size:21 final size:19
Alignment explanation
Indices: 285636--285688 Score: 61
Period size: 21 Copynumber: 2.6 Consensus size: 19
285626 AATTATTCTA
*
285636 ATATTTTTAAAATAATAAT
1 ATATTTTTATAATAATAAT
285655 ATTAATTTTTATAATAAATAAT
1 A-T-ATTTTTATAAT-AATAAT
285677 ATATTTATTATA
1 ATATTT-TTATA
285689 TTTTACATTT
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
19 1 0.03
20 5 0.17
21 16 0.55
22 7 0.24
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (19 bp):
ATATTTTTATAATAATAAT
Found at i:287770 original size:27 final size:27
Alignment explanation
Indices: 287740--287796 Score: 114
Period size: 27 Copynumber: 2.1 Consensus size: 27
287730 AGAGTTTCAC
287740 TATTTGAGTTATACAAATATCATTATA
1 TATTTGAGTTATACAAATATCATTATA
287767 TATTTGAGTTATACAAATATCATTATA
1 TATTTGAGTTATACAAATATCATTATA
287794 TAT
1 TAT
287797 GTAGGTTGAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.40, C:0.07, G:0.07, T:0.46
Consensus pattern (27 bp):
TATTTGAGTTATACAAATATCATTATA
Found at i:291153 original size:15 final size:15
Alignment explanation
Indices: 291114--291156 Score: 77
Period size: 15 Copynumber: 2.9 Consensus size: 15
291104 CAATTGATCC
*
291114 AAAATAAAAAGCTTG
1 AAAATAAAAGGCTTG
291129 AAAATAAAAGGCTTG
1 AAAATAAAAGGCTTG
291144 AAAATAAAAGGCT
1 AAAATAAAAGGCT
291157 AAATAACAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.58, C:0.07, G:0.16, T:0.19
Consensus pattern (15 bp):
AAAATAAAAGGCTTG
Found at i:291215 original size:43 final size:43
Alignment explanation
Indices: 291164--291253 Score: 171
Period size: 43 Copynumber: 2.1 Consensus size: 43
291154 GCTAAATAAC
291164 AAAGAGAATAAAAAACGATATTGGCCAAAAGTAAATGGGCTAA
1 AAAGAGAATAAAAAACGATATTGGCCAAAAGTAAATGGGCTAA
*
291207 AAAGAGAATAAAAAACGATATTGGCCGAAAGTAAATGGGCTAA
1 AAAGAGAATAAAAAACGATATTGGCCAAAAGTAAATGGGCTAA
291250 AAAG
1 AAAG
291254 GATAGGCTAG
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 46 1.00
ACGTcount: A:0.53, C:0.09, G:0.22, T:0.16
Consensus pattern (43 bp):
AAAGAGAATAAAAAACGATATTGGCCAAAAGTAAATGGGCTAA
Found at i:298282 original size:20 final size:20
Alignment explanation
Indices: 298257--298312 Score: 103
Period size: 20 Copynumber: 2.8 Consensus size: 20
298247 ATCTTCATTT
*
298257 AAATCATTTATTTTCATCAA
1 AAATCATGTATTTTCATCAA
298277 AAATCATGTATTTTCATCAA
1 AAATCATGTATTTTCATCAA
298297 AAATCATGTATTTTCA
1 AAATCATGTATTTTCA
298313 AAGGGGTTTC
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.39, C:0.14, G:0.04, T:0.43
Consensus pattern (20 bp):
AAATCATGTATTTTCATCAA
Found at i:298982 original size:23 final size:23
Alignment explanation
Indices: 298956--299000 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
298946 AAATCCAGCA
*
298956 AAGAAAATCAAAGCACTTAAAAT
1 AAGAAAATCAAAGCACTCAAAAT
* *
298979 AAGAAATTGAAAGCACTCAAAA
1 AAGAAAATCAAAGCACTCAAAA
299001 AGGAAGAAAA
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:0.60, C:0.13, G:0.11, T:0.16
Consensus pattern (23 bp):
AAGAAAATCAAAGCACTCAAAAT
Found at i:299021 original size:10 final size:10
Alignment explanation
Indices: 298997--299035 Score: 51
Period size: 10 Copynumber: 3.9 Consensus size: 10
298987 GAAAGCACTC
* *
298997 AAAAAGGAAG
1 AAAAAGAAAA
299007 AAAAAGAAAA
1 AAAAAGAAAA
*
299017 GAAAAGAAAA
1 AAAAAGAAAA
299027 AAAAAGAAA
1 AAAAAGAAA
299036 GTTGAAGCAC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
10 25 1.00
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (10 bp):
AAAAAGAAAA
Found at i:303661 original size:21 final size:21
Alignment explanation
Indices: 303610--303662 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 21
303600 ATTATGACTA
303610 TCGCAATGCGATTTTCCAATT
1 TCGCAATGCGATTTTCCAATT
**
303631 TCGCGTTGCGATTTTCCCAA-T
1 TCGCAATGCGATTTT-CCAATT
303652 TCGCAATGCGA
1 TCGCAATGCGA
303663 ATAAGTAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 23 0.85
22 4 0.15
ACGTcount: A:0.21, C:0.26, G:0.19, T:0.34
Consensus pattern (21 bp):
TCGCAATGCGATTTTCCAATT
Found at i:303677 original size:20 final size:21
Alignment explanation
Indices: 303652--303703 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
303642 TTTTCCCAAT
*
303652 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
303672 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
303693 TCGCAATGCGA
1 TCGCAATGCGA
303704 TACTGACTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 11 0.42
21 15 0.58
ACGTcount: A:0.38, C:0.19, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:303716 original size:41 final size:41
Alignment explanation
Indices: 303689--303826 Score: 163
Period size: 41 Copynumber: 3.4 Consensus size: 41
303679 GCGAATTGGG
*
303689 AAAATCGCAATGCGATACTGACTATCGCAACGCGATAATAC
1 AAAATCGCAAAGCGATACTGACTATCGCAACGCGATAATAC
* *
303730 AAAATCGCAAAGCGATACTGACTTTCGCAACGCGATACTTAC
1 AAAATCGCAAAGCGATACTGACTATCGCAACGCGATA-ATAC
** * * *
303772 --TTTCGCAACGCGATACTGACTTTCGCAACGAGATAATAC
1 AAAATCGCAAAGCGATACTGACTATCGCAACGCGATAATAC
* *
303811 ATAATCGCAATGCGAT
1 AAAATCGCAAAGCGAT
303827 TTTCAAAGCG
Statistics
Matches: 83, Mismatches: 11, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
39 3 0.04
40 31 0.37
41 46 0.55
42 3 0.04
ACGTcount: A:0.36, C:0.25, G:0.17, T:0.22
Consensus pattern (41 bp):
AAAATCGCAAAGCGATACTGACTATCGCAACGCGATAATAC
Found at i:303717 original size:20 final size:20
Alignment explanation
Indices: 303692--303806 Score: 124
Period size: 20 Copynumber: 5.7 Consensus size: 20
303682 AATTGGGAAA
*
303692 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
303712 ATCGCAACGCGATAAT-ACAAA
1 ATCGCAACGCGATACTGAC--T
*
303733 ATCGCAAAGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
303753 TTCGCAACGCGATACTTACT
1 ATCGCAACGCGATACTGACT
*
303773 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
303793 TTCGCAACGAGATA
1 ATCGCAACGCGATA
303807 ATACATAATC
Statistics
Matches: 81, Mismatches: 11, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
19 2 0.02
20 63 0.78
21 14 0.17
22 2 0.02
ACGTcount: A:0.33, C:0.26, G:0.18, T:0.23
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:305692 original size:18 final size:18
Alignment explanation
Indices: 305666--305713 Score: 87
Period size: 18 Copynumber: 2.7 Consensus size: 18
305656 CCCACTTCGG
305666 GAGCCATCACCTCACCCA
1 GAGCCATCACCTCACCCA
*
305684 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
305702 GAGCCATCACCT
1 GAGCCATCACCT
305714 GATCGACCCG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.27, C:0.46, G:0.12, T:0.15
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:306279 original size:20 final size:20
Alignment explanation
Indices: 306254--306299 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
306244 TAGTTTACTT
306254 TCGCAACACGAAAATGACTA
1 TCGCAACACGAAAATGACTA
* * *
306274 TCGCAACGCGGAAATGGCTA
1 TCGCAACACGAAAATGACTA
306294 TCGCAA
1 TCGCAA
306300 TGCAAAATGA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.37, C:0.26, G:0.22, T:0.15
Consensus pattern (20 bp):
TCGCAACACGAAAATGACTA
Found at i:306335 original size:33 final size:33
Alignment explanation
Indices: 306293--306383 Score: 137
Period size: 33 Copynumber: 2.8 Consensus size: 33
306283 GGAAATGGCT
* *
306293 ATCGCAATGCAAAATGAAAATCGCAATGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
* *
306326 ATCGCAATGCGAAATGAAAATCGAAACGACTAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
*
306359 ATCGCAACGCGAAATGAAAATCGCA
1 ATCGCAATGCGAAATGAAAATCGCA
306384 TTGCGATTTT
Statistics
Matches: 52, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 52 1.00
ACGTcount: A:0.48, C:0.20, G:0.18, T:0.14
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:306347 original size:19 final size:19
Alignment explanation
Indices: 306293--306389 Score: 70
Period size: 19 Copynumber: 5.6 Consensus size: 19
306283 GGAAATGGCT
*
306293 ATCGCAATGCAAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
306312 ATCGCAAT--G--A-CAAA
1 ATCGCAATGCGAAATGAAA
306326 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
* *
306345 ATCG-AA-ACG-ACT--AA
1 ATCGCAATGCGAAATGAAA
*
306359 ATCGCAACGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
306378 ATCGCATTGCGA
1 ATCGCAATGCGA
306390 TTTTGTCGTT
Statistics
Matches: 59, Mismatches: 9, Indels: 20
0.67 0.10 0.23
Matches are distributed among these distances:
14 17 0.29
15 3 0.05
16 5 0.08
17 4 0.07
18 3 0.05
19 27 0.46
ACGTcount: A:0.46, C:0.20, G:0.19, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:306403 original size:14 final size:14
Alignment explanation
Indices: 306384--306440 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
306374 GAAAATCGCA
306384 TTGCGATTTTGTCG
1 TTGCGATTTTGTCG
*
306398 TTGCGATTTTCATTTCG
1 TTGCGA-TTT--TGTCG
306415 CATTGCGATTTTGTCG
1 --TTGCGATTTTGTCG
306431 TTGCGATTTT
1 TTGCGATTTT
306441 CATTTCGCAT
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 16 0.44
15 3 0.08
16 4 0.11
17 4 0.11
18 3 0.08
19 6 0.17
ACGTcount: A:0.11, C:0.16, G:0.23, T:0.51
Consensus pattern (14 bp):
TTGCGATTTTGTCG
Found at i:306421 original size:33 final size:33
Alignment explanation
Indices: 306379--306459 Score: 153
Period size: 33 Copynumber: 2.5 Consensus size: 33
306369 GAAATGAAAA
306379 TCGCATTGCGATTTTGTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTGTCGTTGCGATTTTCATT
306412 TCGCATTGCGATTTTGTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTGTCGTTGCGATTTTCATT
*
306445 TCGCATTACGATTTT
1 TCGCATTGCGATTTT
306460 CATTTCGCGT
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 47 1.00
ACGTcount: A:0.14, C:0.19, G:0.20, T:0.48
Consensus pattern (33 bp):
TCGCATTGCGATTTTGTCGTTGCGATTTTCATT
Found at i:306422 original size:19 final size:19
Alignment explanation
Indices: 306398--306475 Score: 94
Period size: 19 Copynumber: 4.4 Consensus size: 19
306388 GATTTTGTCG
306398 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
306417 TTGCGA-TTT--TGTCG--
1 TTGCGATTTTCATTTCGCA
306431 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
* *
306450 TTACGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCA
306469 TTGCGAT
1 TTGCGAT
306476 AGCCATTTTC
Statistics
Matches: 49, Mismatches: 5, Indels: 10
0.77 0.08 0.16
Matches are distributed among these distances:
14 6 0.12
15 3 0.06
16 4 0.08
17 4 0.08
18 3 0.06
19 29 0.59
ACGTcount: A:0.14, C:0.19, G:0.19, T:0.47
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:306487 original size:20 final size:20
Alignment explanation
Indices: 306462--306514 Score: 97
Period size: 20 Copynumber: 2.6 Consensus size: 20
306452 ACGATTTTCA
306462 TTTCGCGTTGCGATAGCCAT
1 TTTCGCGTTGCGATAGCCAT
*
306482 TTTCGCGTTGCGATAGTCAT
1 TTTCGCGTTGCGATAGCCAT
306502 TTTCGCGTTGCGA
1 TTTCGCGTTGCGA
306515 AAGTAAGTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.13, C:0.23, G:0.26, T:0.38
Consensus pattern (20 bp):
TTTCGCGTTGCGATAGCCAT
Found at i:306525 original size:20 final size:20
Alignment explanation
Indices: 306462--306540 Score: 95
Period size: 20 Copynumber: 4.0 Consensus size: 20
306452 ACGATTTTCA
* **
306462 TTTCGCGTTGCGATAGCCAT
1 TTTCGCGTTGCGAAAGTAAT
* *
306482 TTTCGCGTTGCGATAGTCAT
1 TTTCGCGTTGCGAAAGTAAT
*
306502 TTTCGCGTTGCGAAAGTAAG
1 TTTCGCGTTGCGAAAGTAAT
*
306522 TTTCGTGTTGCGAAAGTAA
1 TTTCGCGTTGCGAAAGTAA
306541 ACTATTCTTC
Statistics
Matches: 54, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 54 1.00
ACGTcount: A:0.20, C:0.18, G:0.27, T:0.35
Consensus pattern (20 bp):
TTTCGCGTTGCGAAAGTAAT
Found at i:306968 original size:41 final size:42
Alignment explanation
Indices: 306878--306968 Score: 121
Period size: 41 Copynumber: 2.2 Consensus size: 42
306868 CCCGACTCAC
* * *
306878 CTGTCATCCCTTAAGAGTCCCCTCCAATCATTCAAGAGGCCC
1 CTGTCATCCCTCAAGAGTCCCCTCCAACCATTCAAGAGGCCA
* * *
306920 CTATCATCCCTCAAGAGTCCCC-CCCACCTTTCAAGAGGCCA
1 CTGTCATCCCTCAAGAGTCCCCTCCAACCATTCAAGAGGCCA
306961 CTGTCATC
1 CTGTCATC
306969 GTTGAAGAGG
Statistics
Matches: 42, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
41 22 0.52
42 20 0.48
ACGTcount: A:0.23, C:0.41, G:0.13, T:0.23
Consensus pattern (42 bp):
CTGTCATCCCTCAAGAGTCCCCTCCAACCATTCAAGAGGCCA
Found at i:306977 original size:41 final size:41
Alignment explanation
Indices: 306881--306998 Score: 119
Period size: 42 Copynumber: 2.8 Consensus size: 41
306871 GACTCACCTG
* * * *
306881 TCATCCCTTAAGAGTCCCCTCCAATCATTCAAGAGGCCCCTA
1 TCATCCCTCAAGAGTCCCC-CCCACCATTCAAGAGGCCACTA
* *
306923 TCATCCCTCAAGAGTCCCCCCCACCTTTCAAGAGGCCACTG
1 TCATCCCTCAAGAGTCCCCCCCACCATTCAAGAGGCCACTA
** * * *
306964 TCATCGTTGAAGAGGTCCCTCCCACCATTCCAGAG
1 TCATCCCTCAAGA-GTCCCCCCCACCATTCAAGAG
306999 CCCGATTCAC
Statistics
Matches: 63, Mismatches: 12, Indels: 2
0.82 0.16 0.03
Matches are distributed among these distances:
41 27 0.43
42 36 0.57
ACGTcount: A:0.24, C:0.39, G:0.15, T:0.22
Consensus pattern (41 bp):
TCATCCCTCAAGAGTCCCCCCCACCATTCAAGAGGCCACTA
Found at i:308412 original size:14 final size:14
Alignment explanation
Indices: 308378--308416 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
308368 TTGATTGTTT
308378 AATTGATTTGTAAA
1 AATTGATTTGTAAA
*
308392 AAATGATTTGTAAA
1 AATTGATTTGTAAA
**
308406 TGTTGATTTGT
1 AATTGATTTGT
308417 TTAATTGATG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.36, C:0.00, G:0.18, T:0.46
Consensus pattern (14 bp):
AATTGATTTGTAAA
Found at i:308537 original size:20 final size:20
Alignment explanation
Indices: 308512--308550 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
308502 ATGTTGAAGG
308512 CAAAACAGACTATCGCAACA
1 CAAAACAGACTATCGCAACA
*
308532 CAAAACTGACTATCGCAAC
1 CAAAACAGACTATCGCAAC
308551 GAGAGAATCG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.46, C:0.31, G:0.10, T:0.13
Consensus pattern (20 bp):
CAAAACAGACTATCGCAACA
Found at i:308584 original size:19 final size:19
Alignment explanation
Indices: 308556--308658 Score: 135
Period size: 19 Copynumber: 5.7 Consensus size: 19
308546 GCAACGAGAG
308556 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
308575 AATCGTAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
308594 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
* *
308613 AATCGCAACGAGAAATGAA
1 AATCGCAATGCGAAATGAA
*
308632 AATCACAA--CG--A-GAA
1 AATCGCAATGCGAAATGAA
308646 AATCGCAATGCGA
1 AATCGCAATGCGA
308659 TTTTCATTTC
Statistics
Matches: 74, Mismatches: 7, Indels: 8
0.83 0.08 0.09
Matches are distributed among these distances:
14 10 0.14
15 1 0.01
16 2 0.03
17 1 0.01
19 60 0.81
ACGTcount: A:0.49, C:0.17, G:0.20, T:0.15
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:308702 original size:20 final size:20
Alignment explanation
Indices: 308677--308732 Score: 94
Period size: 20 Copynumber: 2.8 Consensus size: 20
308667 TCGCATTGCG
*
308677 ATTTTCTCGTTGCGATAGCC
1 ATTTTCGCGTTGCGATAGCC
*
308697 ATTTTCGCGTTGCGATAGTC
1 ATTTTCGCGTTGCGATAGCC
308717 ATTTTCGCGTTGCGAT
1 ATTTTCGCGTTGCGAT
308733 TTCCCCGTTG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.14, C:0.21, G:0.23, T:0.41
Consensus pattern (20 bp):
ATTTTCGCGTTGCGATAGCC
Found at i:311027 original size:12 final size:12
Alignment explanation
Indices: 311010--311034 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
311000 TCTTCGGGGA
311010 CTTTTTCTTCTT
1 CTTTTTCTTCTT
311022 CTTTTTCTTCTT
1 CTTTTTCTTCTT
311034 C
1 C
311035 AGGATTATAT
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:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:312104 original size:21 final size:21
Alignment explanation
Indices: 312061--312115 Score: 94
Period size: 21 Copynumber: 2.7 Consensus size: 21
312051 CGAAAGTCAG
*
312061 TATCGCGTTGCGA-TTTGTAT
1 TATCGCGTTGCGATTTTATAT
312081 TATCGCGTTGCGATTTTATAT
1 TATCGCGTTGCGATTTTATAT
312102 TATCGCGTTGCGAT
1 TATCGCGTTGCGAT
312116 AGTCAGTATC
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
20 13 0.39
21 20 0.61
ACGTcount: A:0.16, C:0.16, G:0.24, T:0.44
Consensus pattern (21 bp):
TATCGCGTTGCGATTTTATAT
Found at i:312135 original size:20 final size:20
Alignment explanation
Indices: 312007--312135 Score: 134
Period size: 20 Copynumber: 6.4 Consensus size: 20
311997 GTATTATTTT
* *
312007 GTTGCGAAAGTCAGAATCGC
1 GTTGCGATAGTCAGTATCGC
*
312027 GTTGCGAAAGTCAGTATCGC
1 GTTGCGATAGTCAGTATCGC
*
312047 GTTGCGAAAGTCAGTATCGC
1 GTTGCGATAGTCAGTATCGC
* *
312067 GTTGCGATTTGT-ATTATCGC
1 GTTGCGA-TAGTCAGTATCGC
** * *
312087 GTTGCGATTTTATATTATCGC
1 GTTGCGATAGT-CAGTATCGC
312108 GTTGCGATAGTCAGTATCGC
1 GTTGCGATAGTCAGTATCGC
*
312128 ATTGCGAT
1 GTTGCGAT
312136 TTTCCAAATT
Statistics
Matches: 96, Mismatches: 10, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
19 3 0.03
20 74 0.77
21 19 0.20
ACGTcount: A:0.22, C:0.18, G:0.27, T:0.33
Consensus pattern (20 bp):
GTTGCGATAGTCAGTATCGC
Found at i:312149 original size:41 final size:41
Alignment explanation
Indices: 312022--312156 Score: 134
Period size: 41 Copynumber: 3.3 Consensus size: 41
312012 GAAAGTCAGA
* *** *
312022 ATCGCGTTGCGAAAGTCAGTATCGCGTTGCGAAAGTC-AGT
1 ATCGCGTTGCGATAGTCAGTATCGCGTTGCGATTTTCAAAT
* * *
312062 ATCGCGTTGCGATTTGT-ATTATCGCGTTGCGATTTT-ATATT
1 ATCGCGTTGCGA-TAGTCAGTATCGCGTTGCGATTTTCA-AAT
*
312103 ATCGCGTTGCGATAGTCAGTATCGCATTGCGATTTTCCAAAT
1 ATCGCGTTGCGATAGTCAGTATCGCGTTGCGATTTT-CAAAT
312145 -TCGCGTTGCGAT
1 ATCGCGTTGCGAT
312157 TTACTTATTT
Statistics
Matches: 78, Mismatches: 11, Indels: 11
0.78 0.11 0.11
Matches are distributed among these distances:
40 30 0.38
41 45 0.58
42 2 0.03
43 1 0.01
ACGTcount: A:0.21, C:0.19, G:0.25, T:0.35
Consensus pattern (41 bp):
ATCGCGTTGCGATAGTCAGTATCGCGTTGCGATTTTCAAAT
Found at i:312175 original size:61 final size:61
Alignment explanation
Indices: 312041--312158 Score: 150
Period size: 61 Copynumber: 1.9 Consensus size: 61
312031 CGAAAGTCAG
* * *
312041 TATCGCGTTGCGAAAGTCAGTATCGCGTTGCGATTTGTATTATCGCGTTGCGATTTTATAT
1 TATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTGTAATATCGCGTTGCGATTTTATAT
* *
312102 TATCGCGTTGCGATAGTCAGTATCGCATTGCGATTT-TCCAA-ATTCGCGTTGCGATTT
1 TATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTGT--AATA-TCGCGTTGCGATTT
312159 ACTTATTTGC
Statistics
Matches: 51, Mismatches: 3, Indels: 5
0.86 0.05 0.08
Matches are distributed among these distances:
60 1 0.02
61 35 0.69
62 15 0.29
ACGTcount: A:0.19, C:0.19, G:0.24, T:0.38
Consensus pattern (61 bp):
TATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTGTAATATCGCGTTGCGATTTTATAT
Found at i:312217 original size:21 final size:22
Alignment explanation
Indices: 312167--312217 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 22
312157 TTACTTATTT
*
312167 GCATTGCG-AATTGGGAAAATC
1 GCATTGCGAAATTGAGAAAATC
**
312188 GCAACGCGAAATT-AGAAAATC
1 GCATTGCGAAATTGAGAAAATC
312209 GCATTGCGA
1 GCATTGCGA
312218 TAGTCATAAT
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.37, C:0.18, G:0.25, T:0.20
Consensus pattern (22 bp):
GCATTGCGAAATTGAGAAAATC
Found at i:312610 original size:19 final size:19
Alignment explanation
Indices: 312586--312624 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
312576 GTTTGTGATA
312586 TATATTTTAATAAAATATT
1 TATATTTTAATAAAATATT
* *
312605 TATATTTTGATAAGATATT
1 TATATTTTAATAAAATATT
312624 T
1 T
312625 GACGTGGTTC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (19 bp):
TATATTTTAATAAAATATT
Found at i:312653 original size:2 final size:2
Alignment explanation
Indices: 312646--312680 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
312636 TGCACTTTTG
312646 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
312681 ATTATAATAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:318295 original size:14 final size:14
Alignment explanation
Indices: 318276--318302 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
318266 ACTTAGCATA
318276 TTTAAAAATAAAGC
1 TTTAAAAATAAAGC
318290 TTTAAAAATAAAG
1 TTTAAAAATAAAG
318303 TAAAAACCGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.59, C:0.04, G:0.07, T:0.30
Consensus pattern (14 bp):
TTTAAAAATAAAGC
Found at i:319400 original size:11 final size:12
Alignment explanation
Indices: 319378--319406 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
319368 TGTTTTCCAT
319378 TTTTTTCATGTC
1 TTTTTTCATGTC
319390 TTTTTTC-TGTC
1 TTTTTTCATGTC
319401 TTTTTT
1 TTTTTT
319407 TCGAACAACA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 10 0.59
12 7 0.41
ACGTcount: A:0.03, C:0.14, G:0.07, T:0.76
Consensus pattern (12 bp):
TTTTTTCATGTC
Found at i:319407 original size:12 final size:13
Alignment explanation
Indices: 319377--319408 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
319367 TTGTTTTCCA
319377 TTTTTTTCATGTC
1 TTTTTTTCATGTC
319390 -TTTTTTC-TGTC
1 TTTTTTTCATGTC
319401 TTTTTTTC
1 TTTTTTTC
319409 GAACAACATC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 4 0.22
12 14 0.78
ACGTcount: A:0.03, C:0.16, G:0.06, T:0.75
Consensus pattern (13 bp):
TTTTTTTCATGTC
Found at i:319832 original size:147 final size:146
Alignment explanation
Indices: 319652--319944 Score: 532
Period size: 147 Copynumber: 2.0 Consensus size: 146
319642 CTAAGTGCCC
319652 AAATCATTTTAAGCATCATGTTCATGTGTAATCTCGACAGTATTTAAAATGCAGGTTCTAGAATA
1 AAATCATTTTAAGCATCATGTTCATGTGTAATCTCGACAGTATTTAAAATGCAGGTTCTAGAATA
*
319717 CAAATGTCAAATTCGACACACTCAAATGAAATCAAAAATAATATGCTCGTAAAGGCTCAAATCTC
66 CAAATGTCAAATTCGACACACTCAAATGAAAGCAAAAATAATATGCTCGTAAAGGCTCAAATCTC
319782 ACCAAATTGTTTTCAT
131 ACCAAATTGTTTTCAT
*
319798 AAATCATTTTTAAGCATCATGTTCATGTGTAATCTCGACAGTATTTAAAATGCAGGTTCTATAAT
1 AAATCA-TTTTAAGCATCATGTTCATGTGTAATCTCGACAGTATTTAAAATGCAGGTTCTAGAAT
* * *
319863 ACAAATGTCAAATTCGACACACTCAAATGAAAGCGAAAATTATATTCTCGTAAAGGCTCAAATCT
65 ACAAATGTCAAATTCGACACACTCAAATGAAAGCAAAAATAATATGCTCGTAAAGGCTCAAATCT
319928 CACCAAATTGTTTTCAT
130 CACCAAATTGTTTTCAT
319945 GCATTGAGCT
Statistics
Matches: 141, Mismatches: 5, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
146 6 0.04
147 135 0.96
ACGTcount: A:0.38, C:0.18, G:0.12, T:0.32
Consensus pattern (146 bp):
AAATCATTTTAAGCATCATGTTCATGTGTAATCTCGACAGTATTTAAAATGCAGGTTCTAGAATA
CAAATGTCAAATTCGACACACTCAAATGAAAGCAAAAATAATATGCTCGTAAAGGCTCAAATCTC
ACCAAATTGTTTTCAT
Found at i:320371 original size:19 final size:20
Alignment explanation
Indices: 320328--320379 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
320318 GGGAGTCAAC
*
320328 GGTATCGATACCGTCAGAGG
1 GGTATCGATACCATCAGAGG
**
320348 GGTATCGATACCATTTGA-G
1 GGTATCGATACCATCAGAGG
320367 GGTATC-ATACCAT
1 GGTATCGATACCAT
320380 ATTTCGATTA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
18 7 0.24
19 7 0.24
20 15 0.52
ACGTcount: A:0.27, C:0.19, G:0.27, T:0.27
Consensus pattern (20 bp):
GGTATCGATACCATCAGAGG
Found at i:327470 original size:2 final size:2
Alignment explanation
Indices: 327463--327512 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
327453 ATTTAAACAA
327463 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
327505 AT AT AT AT
1 AT AT AT AT
327513 GACTAAGATT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:329066 original size:3 final size:3
Alignment explanation
Indices: 329058--329115 Score: 71
Period size: 3 Copynumber: 19.0 Consensus size: 3
329048 TTAATTTATT
* * * *
329058 TAA TAA TAA TAA TAA CAA TAA TAT TTA TAA TAA TAA TAA TAA TAA CAAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA -TAA
329107 TAA TAA TAA
1 TAA TAA TAA
329116 AAGTAAACTG
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
3 44 0.96
4 2 0.04
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:329736 original size:76 final size:76
Alignment explanation
Indices: 329259--329709 Score: 839
Period size: 76 Copynumber: 5.9 Consensus size: 76
329249 ATTCTGCCCA
* * *
329259 GAGGTTTTAAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACATA
1 GAGGGTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTA
329324 CAGATGACCCT
66 CAGATGACCCT
*
329335 GAGGGTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAGACATCATGCACTGCAGGACTTA
1 GAGGGTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTA
329400 CAGATGACCCT
66 CAGATGACCCT
* *
329411 GAGGGTTTGAAAACGTCAAAAAGCTCCCGAAGGCTTTTTGGAGACATCATGCACTGCAGGACTTA
1 GAGGGTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTA
329476 CAGATGACCCT
66 CAGATGACCCT
329487 GAGGGTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTA
1 GAGGGTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTA
329552 CAGATGACCCT
66 CAGATGACCCT
*
329563 GAGGGTTTGAAAACATCAAAAAGCTCCCGAAGTCTTTTTGGAAACATCATGCACTGCAGGACTTA
1 GAGGGTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTA
329628 CAGATGACCCT
66 CAGATGACCCT
329639 GAGGGTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTA
1 GAGGGTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTA
329704 CAGATG
66 CAGATG
329710 TGGGAAATAG
Statistics
Matches: 366, Mismatches: 9, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
76 366 1.00
ACGTcount: A:0.33, C:0.22, G:0.23, T:0.23
Consensus pattern (76 bp):
GAGGGTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTA
CAGATGACCCT
Found at i:329962 original size:185 final size:185
Alignment explanation
Indices: 329650--330205 Score: 1076
Period size: 185 Copynumber: 3.0 Consensus size: 185
329640 AGGGTTTGAA
329650 AACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGTGGGA
1 AACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGTGGGA
*
329715 AATAGTTTACTAAGTAAAAAAACTAAGGAAATTGTTTTCTTACTTTTCAACAATTTCATTTTTAG
66 AATAGTTTACTAAGTAAAAAAACTAAGGAAATCGTTTTCTTACTTTTCAACAATTTCATTTTTAG
*
329780 AAAAGATTGAATGAGAAACTATGAAAATCGTTTTCACATTATTTTTCAAAGTAAC
131 AAAAGATTGAATGAGAAACTATGAAAATCGTTTTCTCATTATTTTTCAAAGTAAC
329835 AACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGTGGGA
1 AACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGTGGGA
329900 AATAGTTTACTAAGTAAAAAAACTAAGGAAATCGTTTTCTTACTTTTCAACAATTTCATTTTTAG
66 AATAGTTTACTAAGTAAAAAAACTAAGGAAATCGTTTTCTTACTTTTCAACAATTTCATTTTTAG
329965 AAAAGATTGAATGAGAAACTATGAAAATCGTTTTCTCATTATTTTTCAAAGTAAC
131 AAAAGATTGAATGAGAAACTATGAAAATCGTTTTCTCATTATTTTTCAAAGTAAC
330020 AACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGTGGGA
1 AACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGTGGGA
330085 AATAGTTTACTAAGTAAAAAAACTAAGGAAATCGTTTTCTTACTTTTCAACAATTTCATTTTTAG
66 AATAGTTTACTAAGTAAAAAAACTAAGGAAATCGTTTTCTTACTTTTCAACAATTTCATTTTTAG
* *
330150 AAAAGATTGAATGAGAAACTATGGAAATCGTTTTCTCATTATTTTTCAAAATAAC
131 AAAAGATTGAATGAGAAACTATGAAAATCGTTTTCTCATTATTTTTCAAAGTAAC
330205 A
1 A
330206 TGTTGATTGG
Statistics
Matches: 367, Mismatches: 4, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
185 367 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.32
Consensus pattern (185 bp):
AACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGTGGGA
AATAGTTTACTAAGTAAAAAAACTAAGGAAATCGTTTTCTTACTTTTCAACAATTTCATTTTTAG
AAAAGATTGAATGAGAAACTATGAAAATCGTTTTCTCATTATTTTTCAAAGTAAC
Found at i:330355 original size:164 final size:167
Alignment explanation
Indices: 330082--330405 Score: 564
Period size: 165 Copynumber: 2.0 Consensus size: 167
330072 TACAGATGTG
*
330082 GGAAATAGTTTACTAAGTAAAAAAACTAAGGAAATCGTTTTCTTACTTTTCAACAATTTCATTTT
1 GGAAATAGTTTACTAAGTAAAAAAACTAAGAAAATCGTTTTCTTACTTTTCAACAATTTCATTTT
** *
330147 TAGAAAAGATTGAATGAGAAACTATGGAAATCGTTTTCTCATTAT-TTTTCAAAATAACATGTTG
66 TAGAAAAGATAAAATGAGAAACTATGGAAATCGTTTTCTCATTATGTTTTCAAAATAACATATTG
*
330211 ATTGGGTAACATGCCCCAATCTCAAGATAAGGCTGTT
131 ATTGGGTAACATGCCCCAACCTCAAGATAAGGCTGTT
330248 GGAAATAGTTTACTAAG-AAAAAAACTAAGAAAATCGTTTTCTTACTTTTCAACAATTTCA-TTT
1 GGAAATAGTTTACTAAGTAAAAAAACTAAGAAAATCGTTTTCTTACTTTTCAACAATTTCATTTT
**
330311 TAGAAAAGATAAAATGAGAAACTATGGAAATCGTTTTCTCATTATGTTTTTGAAATAACATATTG
66 TAGAAAAGATAAAATGAGAAACTATGGAAATCGTTTTCTCATTATGTTTTCAAAATAACATATTG
330376 ATTGGGTAACATGCCCCAACCTCAAGATAA
131 ATTGGGTAACATGCCCCAACCTCAAGATAA
330406 TGCTCATTCT
Statistics
Matches: 150, Mismatches: 7, Indels: 3
0.94 0.04 0.02
Matches are distributed among these distances:
164 46 0.31
165 87 0.58
166 17 0.11
ACGTcount: A:0.39, C:0.13, G:0.14, T:0.34
Consensus pattern (167 bp):
GGAAATAGTTTACTAAGTAAAAAAACTAAGAAAATCGTTTTCTTACTTTTCAACAATTTCATTTT
TAGAAAAGATAAAATGAGAAACTATGGAAATCGTTTTCTCATTATGTTTTCAAAATAACATATTG
ATTGGGTAACATGCCCCAACCTCAAGATAAGGCTGTT
Found at i:330936 original size:22 final size:23
Alignment explanation
Indices: 330908--330964 Score: 100
Period size: 22 Copynumber: 2.6 Consensus size: 23
330898 CATAAAGCTT
330908 TCATCTTTGAA-AAGAGAATCTA
1 TCATCTTTGAAGAAGAGAATCTA
330930 TCATCTTT-AAGAAGAGAATCTA
1 TCATCTTTGAAGAAGAGAATCTA
330952 TCATCTTTGAAGA
1 TCATCTTTGAAGA
330965 GTGTAGATGT
Statistics
Matches: 33, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
21 2 0.06
22 27 0.82
23 4 0.12
ACGTcount: A:0.39, C:0.14, G:0.14, T:0.33
Consensus pattern (23 bp):
TCATCTTTGAAGAAGAGAATCTA
Found at i:335003 original size:9 final size:9
Alignment explanation
Indices: 334989--335013 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
334979 AATCATAAAC
334989 AATGAATTT
1 AATGAATTT
334998 AATGAATTT
1 AATGAATTT
335007 AATGAAT
1 AATGAAT
335014 ATCAAATAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.48, C:0.00, G:0.12, T:0.40
Consensus pattern (9 bp):
AATGAATTT
Found at i:338490 original size:14 final size:14
Alignment explanation
Indices: 338471--338509 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
338461 ATAAAGTATG
338471 AATGCAAAATGAAA
1 AATGCAAAATGAAA
*
338485 AATGCAAAGATGCAA
1 AATGCAAA-ATGAAA
338500 AATG-AAAATG
1 AATGCAAAATG
338510 CATATATGAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
13 3 0.13
14 11 0.48
15 9 0.39
ACGTcount: A:0.59, C:0.08, G:0.18, T:0.15
Consensus pattern (14 bp):
AATGCAAAATGAAA
Found at i:340732 original size:2 final size:2
Alignment explanation
Indices: 340725--340763 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
340715 TTTAAACAAA
340725 AT AT AT AT AT AT -T 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
340764 GACTAAGATT
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:342316 original size:3 final size:3
Alignment explanation
Indices: 342308--342362 Score: 74
Period size: 3 Copynumber: 18.0 Consensus size: 3
342298 TTATTTTATT
* * *
342308 TAA TAA TAA TAA TAA CAA TAA TAA TAT TTA TAA TAA TAA TAA TTAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA -TAA
342354 TAA TAA TAA
1 TAA TAA TAA
342363 AAGTAAACTG
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
3 42 0.93
4 3 0.07
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:360976 original size:23 final size:22
Alignment explanation
Indices: 360950--360993 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
360940 GGTCGGGTCT
* *
360950 GATCGGGTAAGCGAGTCAGGTTG
1 GATCGAGTAAACGAGTC-GGTTG
360973 GATCGAGTAAACGAGTCGGTT
1 GATCGAGTAAACGAGTCGGTT
360994 CAACCCATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 4 0.21
23 15 0.79
ACGTcount: A:0.25, C:0.14, G:0.39, T:0.23
Consensus pattern (22 bp):
GATCGAGTAAACGAGTCGGTTG
Found at i:362583 original size:14 final size:14
Alignment explanation
Indices: 362564--362592 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
362554 GATTTCAGTT
362564 GACTAAAAGGAGTA
1 GACTAAAAGGAGTA
362578 GACTAAAAGGAGTA
1 GACTAAAAGGAGTA
362592 G
1 G
362593 TGCGTGATCG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.48, C:0.07, G:0.31, T:0.14
Consensus pattern (14 bp):
GACTAAAAGGAGTA
Found at i:363573 original size:29 final size:29
Alignment explanation
Indices: 363513--363573 Score: 70
Period size: 29 Copynumber: 2.1 Consensus size: 29
363503 AAACACCAGG
* * *
363513 TTAGTGACCAAATTATAAAATTTTATAAT
1 TTAGTGACCAAAGTAGAAAATTTTAAAAT
*
363542 TTAGTGACTAAAGTAGAAAA-TTTAAAAGT
1 TTAGTGACCAAAGTAGAAAATTTTAAAA-T
363571 TTA
1 TTA
363574 AGAGCTTACA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
28 6 0.22
29 21 0.78
ACGTcount: A:0.46, C:0.05, G:0.11, T:0.38
Consensus pattern (29 bp):
TTAGTGACCAAAGTAGAAAATTTTAAAAT
Found at i:366019 original size:15 final size:16
Alignment explanation
Indices: 365991--366023 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
365981 AGTTATAAAT
365991 ATTAGGTTTAATTTTA
1 ATTAGGTTTAATTTTA
*
366007 ATTA-GTTTCATTTTA
1 ATTAGGTTTAATTTTA
366022 AT
1 AT
366024 ATGCATGTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.30, C:0.03, G:0.09, T:0.58
Consensus pattern (16 bp):
ATTAGGTTTAATTTTA
Found at i:370983 original size:30 final size:30
Alignment explanation
Indices: 370949--371011 Score: 90
Period size: 30 Copynumber: 2.1 Consensus size: 30
370939 GTTATATGAG
* * * *
370949 CTATGTGATAAAGGTGTGGAAATGATGTGT
1 CTATGTGATAAAAGTATGGAAATAATATGT
370979 CTATGTGATAAAAGTATGGAAATAATATGT
1 CTATGTGATAAAAGTATGGAAATAATATGT
371009 CTA
1 CTA
371012 CGCGATATGA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.37, C:0.05, G:0.25, T:0.33
Consensus pattern (30 bp):
CTATGTGATAAAAGTATGGAAATAATATGT
Found at i:371282 original size:23 final size:23
Alignment explanation
Indices: 371252--371361 Score: 134
Period size: 23 Copynumber: 4.7 Consensus size: 23
371242 GACATATTAT
*
371252 ATGGCACTACGGTGCAATTCTAC
1 ATGGCACTTCGGTGCAATTCTAC
371275 ATGGCACTTCGGTGCAATTCTAC
1 ATGGCACTTCGGTGCAATTCTAC
* *
371298 ATGGCACTTCGGTGCATTTTTAC
1 ATGGCACTTCGGTGCAATTCTAC
* *
371321 GCTGTC-CTTC-GTGACAAATTCTAC
1 -ATGGCACTTCGGTG-C-AATTCTAC
371345 ATGGCACTTCGGTGCAA
1 ATGGCACTTCGGTGCAA
371362 ATTTATACGA
Statistics
Matches: 73, Mismatches: 9, Indels: 10
0.79 0.10 0.11
Matches are distributed among these distances:
22 3 0.04
23 53 0.73
24 14 0.19
25 3 0.04
ACGTcount: A:0.22, C:0.25, G:0.22, T:0.31
Consensus pattern (23 bp):
ATGGCACTTCGGTGCAATTCTAC
Found at i:371998 original size:20 final size:20
Alignment explanation
Indices: 371973--372013 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 20
371963 CGAAATTTTT
371973 ATGCATC-AGTGCACTGTAGC
1 ATGCATCGA-TGCACTGTAGC
371993 ATGCATCGATGCACTGTAGC
1 ATGCATCGATGCACTGTAGC
372013 A
1 A
372014 CTGTAGCACA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 19 0.95
21 1 0.05
ACGTcount: A:0.27, C:0.24, G:0.24, T:0.24
Consensus pattern (20 bp):
ATGCATCGATGCACTGTAGC
Found at i:378144 original size:30 final size:30
Alignment explanation
Indices: 378110--378169 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
378100 GTTATATGAG
* *
378110 CTATGTGATAAAGGTATGGAAATGATATGT
1 CTATGTGATAAAAGTATGGAAATAATATGT
378140 CTATGTGATAAAAGTATGGAAATAATATGT
1 CTATGTGATAAAAGTATGGAAATAATATGT
378170 TTACGCAATA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.40, C:0.03, G:0.23, T:0.33
Consensus pattern (30 bp):
CTATGTGATAAAAGTATGGAAATAATATGT
Found at i:378455 original size:23 final size:23
Alignment explanation
Indices: 378413--378498 Score: 77
Period size: 23 Copynumber: 3.7 Consensus size: 23
378403 ACATATTATA
* **
378413 TGGCACTACGGTTTAATTCTACG
1 TGGCACTTCGGTGCAATTCTACG
*
378436 TGGCACTTCGGTGCATTTCTACG
1 TGGCACTTCGGTGCAATTCTACG
* *
378459 CTGTC-CTTCGG-GACAAATTCTAAG
1 -TGGCACTTCGGTG-C-AATTCTACG
378483 TGGCACTTCGGTGCAA
1 TGGCACTTCGGTGCAA
378499 ATTTATACGA
Statistics
Matches: 50, Mismatches: 8, Indels: 10
0.74 0.12 0.15
Matches are distributed among these distances:
22 1 0.02
23 31 0.62
24 17 0.34
25 1 0.02
ACGTcount: A:0.20, C:0.24, G:0.24, T:0.31
Consensus pattern (23 bp):
TGGCACTTCGGTGCAATTCTACG
Found at i:386989 original size:21 final size:21
Alignment explanation
Indices: 386965--387047 Score: 98
Period size: 21 Copynumber: 4.0 Consensus size: 21
386955 TTTTACTTGA
386965 AGAATAAAAGAAAA-AAAAAAG
1 AGAA-AAAAGAAAAGAAAAAAG
* *
386986 AGAAAAAAGGAAAGAGAAAAG
1 AGAAAAAAGAAAAGAAAAAAG
*
387007 A-AAAAAAGAAAGAGGAAAAAG
1 AGAAAAAAGAAA-AGAAAAAAG
*
387028 AGAAAAGAGAAAAGAAAAAA
1 AGAAAAAAGAAAAGAAAAAA
387048 ATAAAAATGA
Statistics
Matches: 52, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
20 17 0.33
21 26 0.50
22 9 0.17
ACGTcount: A:0.77, C:0.00, G:0.22, T:0.01
Consensus pattern (21 bp):
AGAAAAAAGAAAAGAAAAAAG
Found at i:386991 original size:7 final size:7
Alignment explanation
Indices: 386970--387046 Score: 67
Period size: 7 Copynumber: 11.6 Consensus size: 7
386960 CTTGAAGAAT
386970 AAAAGA-
1 AAAAGAG
386976 AAAA-A-
1 AAAAGAG
386981 AAAAGAG
1 AAAAGAG
*
386988 AAAAAAG
1 AAAAGAG
*
386995 GAAAGAG
1 AAAAGAG
387002 AAAAGA-
1 AAAAGAG
*
387008 AAAAAAG
1 AAAAGAG
387015 -AAAGAGG
1 AAAAGA-G
387022 AAAAAGAG
1 -AAAAGAG
387030 AAAAGAG
1 AAAAGAG
387037 AAAAGA-
1 AAAAGAG
387043 AAAA
1 AAAA
387047 AATAAAAATG
Statistics
Matches: 59, Mismatches: 6, Indels: 12
0.77 0.08 0.16
Matches are distributed among these distances:
5 5 0.08
6 18 0.31
7 30 0.51
8 1 0.02
9 5 0.08
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (7 bp):
AAAAGAG
Found at i:386999 original size:14 final size:14
Alignment explanation
Indices: 386970--387047 Score: 60
Period size: 13 Copynumber: 5.8 Consensus size: 14
386960 CTTGAAGAAT
386970 AAAAGAAAAAA--A
1 AAAAGAAAAAAGGA
386982 AAAGAGAAAAAAGGA
1 AAA-AGAAAAAAGGA
*
386997 AAGAGAAAAGAA--A
1 AAAAGAAAA-AAGGA
*
387010 AAAAG-AAAGAGGA
1 AAAAGAAAAAAGGA
*
387023 AAAAGAGAAAA-GA
1 AAAAGAAAAAAGGA
387036 GAAAAGAAAAAA
1 -AAAAGAAAAAA
387048 ATAAAAATGA
Statistics
Matches: 52, Mismatches: 6, Indels: 14
0.72 0.08 0.19
Matches are distributed among these distances:
11 1 0.02
12 6 0.12
13 21 0.40
14 19 0.37
15 5 0.10
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (14 bp):
AAAAGAAAAAAGGA
Found at i:387014 original size:40 final size:40
Alignment explanation
Indices: 386964--387054 Score: 105
Period size: 40 Copynumber: 2.2 Consensus size: 40
386954 ATTTTACTTG
*
386964 AAGAATAAAAGAAA-A-AAAAAAGAGAAAAAAGGAAAGAGAA
1 AAGAAAAAAAGAAAGAGAAAAAAGAGAAAAAA-GAAA-AGAA
* *
387004 AAGAAAAAAAGAAAGAGGAAAAAGAGAAAAGAGAAAAGAA
1 AAGAAAAAAAGAAAGAGAAAAAAGAGAAAAAAGAAAAGAA
*
387044 AAAAATAAAAA
1 AAGAA-AAAAA
387055 TGAGGTCTCA
Statistics
Matches: 44, Mismatches: 4, Indels: 5
0.83 0.08 0.09
Matches are distributed among these distances:
40 21 0.48
41 10 0.23
42 13 0.30
ACGTcount: A:0.78, C:0.00, G:0.20, T:0.02
Consensus pattern (40 bp):
AAGAAAAAAAGAAAGAGAAAAAAGAGAAAAAAGAAAAGAA
Found at i:387019 original size:33 final size:34
Alignment explanation
Indices: 386970--387048 Score: 126
Period size: 35 Copynumber: 2.4 Consensus size: 34
386960 CTTGAAGAAT
*
386970 AAAAGAAAAAAAAAAGA-GAAAAA-AGGAAAGAG
1 AAAAGAAAAAAAAAAGAGGAAAAAGAGAAAAGAG
387002 AAAAGAAAAAAAGAAAGAGGAAAAAGAGAAAAGAG
1 AAAAGAAAAAAA-AAAGAGGAAAAAGAGAAAAGAG
387037 AAAAGAAAAAAA
1 AAAAGAAAAAAA
387049 TAAAAATGAG
Statistics
Matches: 43, Mismatches: 1, Indels: 3
0.91 0.02 0.06
Matches are distributed among these distances:
32 12 0.28
33 5 0.12
34 6 0.14
35 20 0.47
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (34 bp):
AAAAGAAAAAAAAAAGAGGAAAAAGAGAAAAGAG
Found at i:387054 original size:28 final size:28
Alignment explanation
Indices: 386963--387044 Score: 82
Period size: 27 Copynumber: 3.0 Consensus size: 28
386953 TATTTTACTT
386963 GAAGAATAAA-AGAAAA-AAAAAAGAGAAA
1 GAAGAA-AAAGAGAAAAGAAAAAA-AGAAA
* *
386991 AAAG-GAAAGAGAAAAGAAAAAAAGAAA
1 GAAGAAAAAGAGAAAAGAAAAAAAGAAA
* *
387018 GAGGAAAAAGAGAAAAG-AGAAAAGAAA
1 GAAGAAAAAGAGAAAAGAAAAAAAGAAA
387045 AAAATAAAAA
Statistics
Matches: 45, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
26 3 0.07
27 22 0.49
28 20 0.44
ACGTcount: A:0.76, C:0.00, G:0.23, T:0.01
Consensus pattern (28 bp):
GAAGAAAAAGAGAAAAGAAAAAAAGAAA
Found at i:389630 original size:14 final size:14
Alignment explanation
Indices: 389613--389649 Score: 74
Period size: 14 Copynumber: 2.6 Consensus size: 14
389603 GTGATACATG
389613 ATATGTGATAAGAA
1 ATATGTGATAAGAA
389627 ATATGTGATAAGAA
1 ATATGTGATAAGAA
389641 ATATGTGAT
1 ATATGTGAT
389650 TATAAGAGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.46, C:0.00, G:0.22, T:0.32
Consensus pattern (14 bp):
ATATGTGATAAGAA
Found at i:390765 original size:21 final size:21
Alignment explanation
Indices: 390740--390792 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
390730 GTCGAGGGAT
* *
390740 TATATTAGGTCCTTCGAGACA
1 TATATGAGGTCCTACGAGACA
*
390761 TATATGAGGTCCTACGGGACA
1 TATATGAGGTCCTACGAGACA
* *
390782 TACAAGAGGTC
1 TATATGAGGTC
390793 ATTCGTGATA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.30, C:0.19, G:0.25, T:0.26
Consensus pattern (21 bp):
TATATGAGGTCCTACGAGACA
Found at i:393795 original size:30 final size:30
Alignment explanation
Indices: 393759--393824 Score: 87
Period size: 30 Copynumber: 2.2 Consensus size: 30
393749 AGAATTTGGA
* *
393759 TCCAAATTTAATCAAAATTTCACTTTGGTC
1 TCCAAATTTAATCAAAATTTCAATTTAGTC
* *
393789 TCCAAATTTAGTTAAAATTTCAATTTAGTC
1 TCCAAATTTAATCAAAATTTCAATTTAGTC
*
393819 CCCAAA
1 TCCAAA
393825 ATAAATTTTA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.36, C:0.20, G:0.06, T:0.38
Consensus pattern (30 bp):
TCCAAATTTAATCAAAATTTCAATTTAGTC
Found at i:398107 original size:11 final size:11
Alignment explanation
Indices: 398088--398126 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
398078 TTATTTAATA
*
398088 GACCTGTTTTG
1 GACCCGTTTTG
398099 GACCCGTTTTG
1 GACCCGTTTTG
**
398110 GACTTGTTTTG
1 GACCCGTTTTG
398121 GACCCG
1 GACCCG
398127 GATTTGTTGG
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.10, C:0.23, G:0.28, T:0.38
Consensus pattern (11 bp):
GACCCGTTTTG
Found at i:400901 original size:25 final size:25
Alignment explanation
Indices: 400871--400919 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
400861 TAGTGCTGAT
* *
400871 GTGGTGGTCTATGGTGTCTAGTGAG
1 GTGGTGATCCATGGTGTCTAGTGAG
400896 GTGGTGATCCATGGTGTCTAGTGA
1 GTGGTGATCCATGGTGTCTAGTGA
400920 CGTGATTGAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.14, C:0.10, G:0.41, T:0.35
Consensus pattern (25 bp):
GTGGTGATCCATGGTGTCTAGTGAG
Found at i:401058 original size:16 final size:16
Alignment explanation
Indices: 401045--401077 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
401035 ACAAATATAC
401045 AAAAAATAAAATATTA
1 AAAAAATAAAATATTA
401061 AAAAAATAAAA-ATTA
1 AAAAAATAAAATATTA
401076 AA
1 AA
401078 TTACTAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (16 bp):
AAAAAATAAAATATTA
Found at i:401072 original size:24 final size:24
Alignment explanation
Indices: 401027--401072 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
401017 AATTTTAAAC
* *
401027 TAAAATATACAAATATACAAAAAA
1 TAAAATATAAAAAAATACAAAAAA
401051 TAAAATATTAAAAAAATA-AAAA
1 TAAAATA-TAAAAAAATACAAAA
401073 TTAAATTACT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
24 11 0.58
25 8 0.42
ACGTcount: A:0.74, C:0.04, G:0.00, T:0.22
Consensus pattern (24 bp):
TAAAATATAAAAAAATACAAAAAA
Found at i:401078 original size:22 final size:23
Alignment explanation
Indices: 401046--401097 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 23
401036 CAAATATACA
*
401046 AAAAATAAAA-TATTAAAAAAAT
1 AAAAATAAAATTACTAAAAAAAT
* **
401068 AAAAATTAAATTACTAAAAAGTT
1 AAAAATAAAATTACTAAAAAAAT
401091 AAAAATA
1 AAAAATA
401098 TATATTCATT
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
22 9 0.38
23 15 0.62
ACGTcount: A:0.71, C:0.02, G:0.02, T:0.25
Consensus pattern (23 bp):
AAAAATAAAATTACTAAAAAAAT
Found at i:401163 original size:2 final size:2
Alignment explanation
Indices: 401156--401184 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
401146 CTGAATTTAA
401156 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
401185 ATTTTTTAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:401421 original size:20 final size:19
Alignment explanation
Indices: 401384--401423 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
401374 AAAAATACTC
*
401384 TTTTTTAATTGTATAATTA
1 TTTTTTAATTGTAAAATTA
*
401403 TTTTTTATATTTTAAAATTA
1 TTTTTTA-ATTGTAAAATTA
401423 T
1 T
401424 ATAGTTTTAC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 7 0.39
20 11 0.61
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.65
Consensus pattern (19 bp):
TTTTTTAATTGTAAAATTA
Found at i:401731 original size:16 final size:16
Alignment explanation
Indices: 401712--401744 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
401702 TATTATTATA
401712 TTTTAT-TTTTATAATT
1 TTTTATATTTTA-AATT
401728 TTTTATATTTTAAATT
1 TTTTATATTTTAAATT
401744 T
1 T
401745 AAATATGTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (16 bp):
TTTTATATTTTAAATT
Found at i:401755 original size:23 final size:23
Alignment explanation
Indices: 401707--401760 Score: 58
Period size: 23 Copynumber: 2.4 Consensus size: 23
401697 CATTTTATTA
** *
401707 TTATATTTTATTTTTATAATTTT
1 TTATATTTTAAATTTATAATTGT
401730 TTATATTTTAAATTTA-AATATGT
1 TTATATTTTAAATTTATAAT-TGT
401753 TTA-ATTTT
1 TTATATTTT
401761 TAAAAAAATA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
22 8 0.30
23 19 0.70
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (23 bp):
TTATATTTTAAATTTATAATTGT
Found at i:402844 original size:7 final size:7
Alignment explanation
Indices: 402834--402858 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
402824 TAAATCTTTC
402834 ATATTAT
1 ATATTAT
402841 ATATTAT
1 ATATTAT
402848 ATATTAT
1 ATATTAT
402855 ATAT
1 ATAT
402859 AGAAGCGTCA
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:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (7 bp):
ATATTAT
Found at i:403128 original size:17 final size:16
Alignment explanation
Indices: 403086--403128 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 16
403076 TAAGTTATGC
*
403086 TTAGAA-ATAAGATTA
1 TTAGAATATAAAATTA
403101 TTAGAATATAAAATTA
1 TTAGAATATAAAATTA
*
403117 TTTGATATATAA
1 TTAGA-ATATAA
403129 TTGAGAATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
15 6 0.25
16 12 0.50
17 6 0.25
ACGTcount: A:0.51, C:0.00, G:0.09, T:0.40
Consensus pattern (16 bp):
TTAGAATATAAAATTA
Found at i:407460 original size:23 final size:22
Alignment explanation
Indices: 407397--407460 Score: 83
Period size: 22 Copynumber: 2.8 Consensus size: 22
407387 TGAATTTTGC
*
407397 AGCTGCCAATTTGGACTTCAACA
1 AGCT-CCAATTTGGACTTTAACA
*
407420 AGCTCTAATTTGGACTTTAACA
1 AGCTCCAATTTGGACTTTAACA
*
407442 AGCTACCAATTTAGACTTT
1 AGCT-CCAATTTGGACTTT
407461 TTTTTAACAA
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
22 20 0.56
23 16 0.44
ACGTcount: A:0.31, C:0.22, G:0.14, T:0.33
Consensus pattern (22 bp):
AGCTCCAATTTGGACTTTAACA
Found at i:408195 original size:22 final size:22
Alignment explanation
Indices: 408170--408250 Score: 126
Period size: 22 Copynumber: 3.6 Consensus size: 22
408160 TTTGCAGTTG
*
408170 CCAATTTGGACTTCAACAAGCT
1 CCAATTTGGACTTTAACAAGCT
408192 CCAATTTGGACTTTAACAAGCT
1 CCAATTTGGACTTTAACAAGCT
*
408214 CCAATCTGGACTTTAACAAGCT
1 CCAATTTGGACTTTAACAAGCT
*
408236 GCCAATTTAGACTTT
1 -CCAATTTGGACTTT
408251 TTTTAACAAT
Statistics
Matches: 54, Mismatches: 4, Indels: 1
0.92 0.07 0.02
Matches are distributed among these distances:
22 42 0.78
23 12 0.22
ACGTcount: A:0.31, C:0.25, G:0.14, T:0.31
Consensus pattern (22 bp):
CCAATTTGGACTTTAACAAGCT
Found at i:412812 original size:23 final size:22
Alignment explanation
Indices: 412757--412814 Score: 89
Period size: 22 Copynumber: 2.6 Consensus size: 22
412747 CCGAATTGCT
*
412757 CAATTTGGACTTCAATAAGCTC
1 CAATTTGGACTTTAATAAGCTC
412779 CAATTTGGACTTTAATAAGCTGC
1 CAATTTGGACTTTAATAAGCT-C
*
412802 CAATTTAGACTTT
1 CAATTTGGACTTT
412815 TTTTAACACT
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
22 20 0.61
23 13 0.39
ACGTcount: A:0.31, C:0.19, G:0.14, T:0.36
Consensus pattern (22 bp):
CAATTTGGACTTTAATAAGCTC
Found at i:423523 original size:56 final size:57
Alignment explanation
Indices: 423408--423524 Score: 164
Period size: 56 Copynumber: 2.1 Consensus size: 57
423398 TAAGTTTTAT
* * * * **
423408 TTTAATTTATTTAATTTAATATATTTCAACTCCAATAAGTGAGTGACACGTGTTGCC
1 TTTAATTTATTTAATTTAAGACATTTCAACTCCAATAAGAGAGTGACACATGTCCCC
*
423465 TTTAATTTATTTAATTT-AGACATTTCAACTCCAATAAGAGAGTGACATATGTCCCC
1 TTTAATTTATTTAATTTAAGACATTTCAACTCCAATAAGAGAGTGACACATGTCCCC
423521 TTTA
1 TTTA
423525 TTTGGTGTCA
Statistics
Matches: 53, Mismatches: 7, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
56 36 0.68
57 17 0.32
ACGTcount: A:0.32, C:0.15, G:0.11, T:0.41
Consensus pattern (57 bp):
TTTAATTTATTTAATTTAAGACATTTCAACTCCAATAAGAGAGTGACACATGTCCCC
Found at i:429889 original size:14 final size:14
Alignment explanation
Indices: 429838--429880 Score: 63
Period size: 14 Copynumber: 3.2 Consensus size: 14
429828 TTTAGCCCCA
429838 AATT-TATTT-TTT
1 AATTATATTTATTT
*
429850 AATTATAGTTATTT
1 AATTATATTTATTT
429864 AATTATATTTATTT
1 AATTATATTTATTT
429878 AAT
1 AAT
429881 ATGTTTTATC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
12 4 0.15
13 4 0.15
14 19 0.70
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (14 bp):
AATTATATTTATTT
Found at i:433985 original size:24 final size:24
Alignment explanation
Indices: 433958--434016 Score: 66
Period size: 24 Copynumber: 2.4 Consensus size: 24
433948 GTAGTTAAAA
*
433958 TAAGAGTAAAATATATTT-TTAAGT
1 TAAGA-TAAAATATATTTAATAAGT
* *
433982 TAAGAATAAAATTTATTTAATAATT
1 TAAG-ATAAAATATATTTAATAAGT
434007 TAAGATAAAA
1 TAAGATAAAA
434017 ATAAAATATT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
24 21 0.70
25 9 0.30
ACGTcount: A:0.53, C:0.00, G:0.08, T:0.39
Consensus pattern (24 bp):
TAAGATAAAATATATTTAATAAGT
Found at i:434058 original size:18 final size:18
Alignment explanation
Indices: 434037--434071 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
434027 TTTTTGAAAG
*
434037 TTAAGATTTGAATTTAAT
1 TTAAGATATGAATTTAAT
*
434055 TTAATATATGAATTTAA
1 TTAAGATATGAATTTAA
434072 GTTGAGAGAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.43, C:0.00, G:0.09, T:0.49
Consensus pattern (18 bp):
TTAAGATATGAATTTAAT
Found at i:441271 original size:19 final size:19
Alignment explanation
Indices: 441249--441303 Score: 58
Period size: 19 Copynumber: 2.8 Consensus size: 19
441239 ATCACTCTAA
441249 TTTATTTTATTAATATTTT
1 TTTATTTTATTAATATTTT
***
441268 TTTATGAAATTAA-ATTTTT
1 TTTATTTTATTAATA-TTTT
441287 TATTATTTTATTAATAT
1 T-TTATTTTATTAATAT
441304 ATAATTAAAA
Statistics
Matches: 27, Mismatches: 6, Indels: 5
0.71 0.16 0.13
Matches are distributed among these distances:
18 1 0.04
19 15 0.56
20 10 0.37
21 1 0.04
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (19 bp):
TTTATTTTATTAATATTTT
Found at i:442001 original size:24 final size:24
Alignment explanation
Indices: 441950--442008 Score: 66
Period size: 24 Copynumber: 2.5 Consensus size: 24
441940 GTTCGACAAT
*
441950 ATGTTCGTTTA-ATATTCGCGAAC
1 ATGTTCGTTTATATATTCACGAAC
* *
441973 ATGTTCGTTTATATGTTCATGAAC
1 ATGTTCGTTTATATATTCACGAAC
* *
441997 GTGTTCATTTAT
1 ATGTTCGTTTAT
442009 CGTTTACGAA
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
23 11 0.37
24 19 0.63
ACGTcount: A:0.24, C:0.14, G:0.17, T:0.46
Consensus pattern (24 bp):
ATGTTCGTTTATATATTCACGAAC
Found at i:442553 original size:2 final size:2
Alignment explanation
Indices: 442546--442570 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
442536 ATCATTATCG
442546 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
442571 TTAGATTGGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:446919 original size:21 final size:20
Alignment explanation
Indices: 446871--446920 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
446861 GGGTCTACGC
*
446871 GGTCCTTTGGGACATATATA
1 GGTCCTTTGGAACATATATA
** *
446891 TATCCTTTGGAACATCTATGA
1 GGTCCTTTGGAACATATAT-A
446912 GGTCCTTTG
1 GGTCCTTTG
446921 AGACACATAC
Statistics
Matches: 23, Mismatches: 6, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
20 15 0.65
21 8 0.35
ACGTcount: A:0.22, C:0.18, G:0.22, T:0.38
Consensus pattern (20 bp):
GGTCCTTTGGAACATATATA
Found at i:450814 original size:33 final size:33
Alignment explanation
Indices: 450763--450840 Score: 88
Period size: 33 Copynumber: 2.4 Consensus size: 33
450753 ATGTAAAAAA
*
450763 ATAT-TGTATAATAAAAGAAAACAGTGTATATGT
1 ATATATGTATAATAAAAGAAAA-AGTGAATATGT
* *
450796 ATATATGTATAGT-AAAGAAAATGTGAATATGT
1 ATATATGTATAATAAAAGAAAAAGTGAATATGT
*
450828 ATTATATATATAA
1 A-TATATGTATAA
450841 ACAATTTTTT
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
32 10 0.26
33 21 0.55
34 7 0.18
ACGTcount: A:0.49, C:0.01, G:0.14, T:0.36
Consensus pattern (33 bp):
ATATATGTATAATAAAAGAAAAAGTGAATATGT
Found at i:452197 original size:55 final size:55
Alignment explanation
Indices: 452118--452486 Score: 449
Period size: 55 Copynumber: 6.6 Consensus size: 55
452108 ATCAATACAA
* * * * ** *
452118 AAATTTATACACTTCGTATGAATTTCCT-AGTTTTGTACATAAACTGCCCATATAG
1 AAATTCATCCACTTAGTATGAATTTCTTAAGTTTTACACATAAAGTGCCCATA-AG
* * *
452173 AAATTCATCCACTTAGTATCAATTTCTTAAGTTTTTACACATAAAGTTCCCATACGG
1 AAATTCATCCACTTAGTATGAATTTCTTAAG-TTTTACACATAAAGTGCCCATA-AG
* *
452230 AAATTCATCCACTTAGTATGAATTTCTTAAG-TTTACACATAAAGTGCTCATACAT
1 AAATTCATCCACTTAGTATGAATTTCTTAAGTTTTACACATAAAGTGCCCATA-AG
* * * *
452285 AAATTCATCAACTTAGTATGAATTTCTTATGTTTTTGCACATAAAGTGCCCATACG
1 AAATTCATCCACTTAGTATGAATTTCTTAAG-TTTTACACATAAAGTGCCCATAAG
* *
452341 AAAATTCATCCACTTAGTATGAATTTATTAAG-TTTACACATAAAGTGCCCATACG
1 -AAATTCATCCACTTAGTATGAATTTCTTAAGTTTTACACATAAAGTGCCCATAAG
* * *
452396 AAAATTCATCTACTTAGTATGAATTTATTAAG-TTTACACATAAAGTGCCCATATGG
1 -AAATTCATCCACTTAGTATGAATTTCTTAAGTTTTACACATAAAGTGCCCATA-AG
452452 AAATTCATCCACTTAGTATGAATTTCTTAAGTTTT
1 AAATTCATCCACTTAGTATGAATTTCTTAAGTTTT
452487 TGCACACTTG
Statistics
Matches: 277, Mismatches: 30, Indels: 13
0.87 0.09 0.04
Matches are distributed among these distances:
55 175 0.63
56 6 0.02
57 96 0.35
ACGTcount: A:0.35, C:0.18, G:0.11, T:0.37
Consensus pattern (55 bp):
AAATTCATCCACTTAGTATGAATTTCTTAAGTTTTACACATAAAGTGCCCATAAG
Found at i:452319 original size:112 final size:111
Alignment explanation
Indices: 452118--452485 Score: 508
Period size: 112 Copynumber: 3.3 Consensus size: 111
452108 ATCAATACAA
* * * * ** * *
452118 AAATTTATACACTTCGTATGAATTTCCT-AGTTTTGTACATAAACTGCCCATATAGAAATTCATC
1 AAATTCATCCACTTAGTATGAATTTCTTAAG-TTTACACATAAAGTGCCCATACA-AAATTCATC
* * *
452182 CACTTAGTATCAATTTCTTAAGTTTTTACACATAAAGTTCCCATACGG
64 AACTTAGTATGAATTTCTTAAGTTTTTACACATAAAGTGCCCATACGG
*
452230 AAATTCATCCACTTAGTATGAATTTCTTAAGTTTACACATAAAGTGCTCATACATAAATTCATCA
1 AAATTCATCCACTTAGTATGAATTTCTTAAGTTTACACATAAAGTGCCCATACA-AAATTCATCA
* * *
452295 ACTTAGTATGAATTTCTTATGTTTTTGCACATAAAGTGCCCATACGA
65 ACTTAGTATGAATTTCTTAAGTTTTTACACATAAAGTGCCCATACGG
* *
452342 AAATTCATCCACTTAGTATGAATTTATTAAGTTTACACATAAAGTGCCCATACGAAAATTCATCT
1 AAATTCATCCACTTAGTATGAATTTCTTAAGTTTACACATAAAGTGCCCATAC-AAAATTCATCA
* *
452407 ACTTAGTATGAATTTATTAAG--TTTACACATAAAGTGCCCATATGG
65 ACTTAGTATGAATTTCTTAAGTTTTTACACATAAAGTGCCCATACGG
452452 AAATTCATCCACTTAGTATGAATTTCTTAAGTTT
1 AAATTCATCCACTTAGTATGAATTTCTTAAGTTT
452486 TTGCACACTT
Statistics
Matches: 229, Mismatches: 25, Indels: 6
0.88 0.10 0.02
Matches are distributed among these distances:
110 54 0.24
112 172 0.75
113 3 0.01
ACGTcount: A:0.35, C:0.18, G:0.11, T:0.37
Consensus pattern (111 bp):
AAATTCATCCACTTAGTATGAATTTCTTAAGTTTACACATAAAGTGCCCATACAAAATTCATCAA
CTTAGTATGAATTTCTTAAGTTTTTACACATAAAGTGCCCATACGG
Found at i:452413 original size:167 final size:167
Alignment explanation
Indices: 452128--452492 Score: 529
Period size: 167 Copynumber: 2.2 Consensus size: 167
452118 AAATTTATAC
* * * *
452128 ACTTCGTATGAATTTCCTAG-TTTTGTACATAAACTGCCCATATAGAAATTCATCCACTTAGTAT
1 ACTTAGTATGAATTTCTTAGTTTTTGCACATAAACTGCCCATAGAGAAATTCATCCACTTAGTAT
* * * *
452192 CAATTTCTTAAGTTTTTACACATAAAGTTCCCATACGGAAATTCATCCACTTAGTATGAATTTCT
66 CAATTTATTAAG-TTTTACACATAAAGTGCCCATACGAAAATTCATCCACTTAGTATGAATTTAT
* *
452257 TAAGTTTACACATAAAGTGCTCATACATAAATTCATCA
130 TAAGTTTACACATAAAGTGCCCATACAGAAATTCATCA
*
452295 ACTTAGTATGAATTTCTTATGTTTTTGCACATAAAGTGCCCATACGA-AAATTCATCCACTTAGT
1 ACTTAGTATGAATTTCTTA-GTTTTTGCACATAAACTGCCCATA-GAGAAATTCATCCACTTAGT
* *
452359 ATGAATTTATTAAG-TTTACACATAAAGTGCCCATACGAAAATTCATCTACTTAGTATGAATTTA
64 ATCAATTTATTAAGTTTTACACATAAAGTGCCCATACGAAAATTCATCCACTTAGTATGAATTTA
** *
452423 TTAAGTTTACACATAAAGTGCCCATATGGAAATTCATCC
129 TTAAGTTTACACATAAAGTGCCCATACAGAAATTCATCA
452462 ACTTAGTATGAATTTCTTAAGTTTTTGCACA
1 ACTTAGTATGAATTTCTT-AGTTTTTGCACA
452493 CTTGGTGCCA
Statistics
Matches: 178, Mismatches: 16, Indels: 8
0.88 0.08 0.04
Matches are distributed among these distances:
167 126 0.71
168 2 0.01
169 49 0.28
170 1 0.01
ACGTcount: A:0.34, C:0.18, G:0.11, T:0.37
Consensus pattern (167 bp):
ACTTAGTATGAATTTCTTAGTTTTTGCACATAAACTGCCCATAGAGAAATTCATCCACTTAGTAT
CAATTTATTAAGTTTTACACATAAAGTGCCCATACGAAAATTCATCCACTTAGTATGAATTTATT
AAGTTTACACATAAAGTGCCCATACAGAAATTCATCA
Found at i:452948 original size:18 final size:20
Alignment explanation
Indices: 452906--452953 Score: 64
Period size: 18 Copynumber: 2.5 Consensus size: 20
452896 TGTTTTAATG
* *
452906 GTATCGATACCTTCCTTATA
1 GTATCGATACCTCCCTTACA
452926 GTATCGATACC-CCCTT-CA
1 GTATCGATACCTCCCTTACA
452944 GTATCGATAC
1 GTATCGATAC
452954 TGATTACATT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
18 11 0.42
19 4 0.15
20 11 0.42
ACGTcount: A:0.25, C:0.29, G:0.12, T:0.33
Consensus pattern (20 bp):
GTATCGATACCTCCCTTACA
Found at i:456359 original size:23 final size:23
Alignment explanation
Indices: 456342--456389 Score: 87
Period size: 23 Copynumber: 2.1 Consensus size: 23
456332 CCTTCGGGAT
456342 AACTCTACGTGGCACTTCGGTGC
1 AACTCTACGTGGCACTTCGGTGC
*
456365 AACTCTACGTGGCACTTTGGTGC
1 AACTCTACGTGGCACTTCGGTGC
456388 AA
1 AA
456390 ATTATGTGAG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.21, C:0.27, G:0.25, T:0.27
Consensus pattern (23 bp):
AACTCTACGTGGCACTTCGGTGC
Found at i:461485 original size:21 final size:20
Alignment explanation
Indices: 461456--461495 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
461446 ATAAACCGGA
*
461456 TGAACAATATCGATACTGAT
1 TGAACAATATAGATACTGAT
461476 TGAATCAATATAGATACTGA
1 TGAA-CAATATAGATACTGA
461496 GGTGGTGATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.42, C:0.12, G:0.15, T:0.30
Consensus pattern (20 bp):
TGAACAATATAGATACTGAT
Found at i:462212 original size:28 final size:28
Alignment explanation
Indices: 462170--462223 Score: 81
Period size: 28 Copynumber: 1.9 Consensus size: 28
462160 TATATATGAT
* * *
462170 AATGTGCTAAGTGAAAAGGTTCTACGTG
1 AATGTGATAAATGAAAAAGTTCTACGTG
462198 AATGTGATAAATGAAAAAGTTCTACG
1 AATGTGATAAATGAAAAAGTTCTACG
462224 CGAAGATACC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.39, C:0.09, G:0.24, T:0.28
Consensus pattern (28 bp):
AATGTGATAAATGAAAAAGTTCTACGTG
Found at i:462388 original size:21 final size:22
Alignment explanation
Indices: 462364--462448 Score: 82
Period size: 23 Copynumber: 3.8 Consensus size: 22
462354 AGATGAGGGT
* *
462364 TCTACATGGTCCTTCGGATA-A
1 TCTACGTGGTCCTTCGGACATA
* *
462385 TCTATGTGGTCCTTCGGGACATT
1 TCTACGTGGTCCTTC-GGACATA
*
462408 TCTACGTGGTCCTTCGGGACAAA
1 TCTACGTGGTCCTTC-GGACATA
*
462431 TTCTACGCGGTCCTTCGG
1 -TCTACGTGGTCCTTCGG
462449 GACAAAACTA
Statistics
Matches: 53, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
21 13 0.25
22 4 0.08
23 22 0.42
24 14 0.26
ACGTcount: A:0.16, C:0.26, G:0.25, T:0.33
Consensus pattern (22 bp):
TCTACGTGGTCCTTCGGACATA
Found at i:462416 original size:23 final size:22
Alignment explanation
Indices: 462363--462452 Score: 101
Period size: 24 Copynumber: 4.0 Consensus size: 22
462353 GAGATGAGGG
* *
462363 TTCTACATGGTCCTTC-GGATA
1 TTCTACGTGGTCCTTCGGGACA
* *
462384 ATCTATGTGGTCCTTCGGGACA
1 TTCTACGTGGTCCTTCGGGACA
462406 TTTCTACGTGGTCCTTCGGGACAAA
1 -TTCTACGTGGTCCTTCGGGAC--A
*
462431 TTCTACGCGGTCCTTCGGGACA
1 TTCTACGTGGTCCTTCGGGACA
462453 AAACTATGTG
Statistics
Matches: 58, Mismatches: 7, Indels: 7
0.81 0.10 0.10
Matches are distributed among these distances:
21 13 0.22
22 5 0.09
23 19 0.33
24 20 0.34
25 1 0.02
ACGTcount: A:0.18, C:0.26, G:0.24, T:0.32
Consensus pattern (22 bp):
TTCTACGTGGTCCTTCGGGACA
Found at i:462822 original size:21 final size:21
Alignment explanation
Indices: 462775--462822 Score: 51
Period size: 21 Copynumber: 2.3 Consensus size: 21
462765 AGATTTGTGG
**
462775 TGTTTTGTAAAATTAAACATT
1 TGTTTTGTAAAATTAAACAAA
* * *
462796 TCTTTTGTAAATTTATACAAA
1 TGTTTTGTAAAATTAAACAAA
462817 TGTTTT
1 TGTTTT
462823 ATTGTTTTAT
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.33, C:0.06, G:0.08, T:0.52
Consensus pattern (21 bp):
TGTTTTGTAAAATTAAACAAA
Found at i:466315 original size:216 final size:216
Alignment explanation
Indices: 465941--466372 Score: 828
Period size: 216 Copynumber: 2.0 Consensus size: 216
465931 GATCTGAGCA
*
465941 CTGTAGACTTTCCAACATCATCATAACATCGTTCAATCATAAATTCGCATCCATCGGACCTTCAT
1 CTGTAGACTTTCCAACATCATCATAACATCGTTCAATCATAAATTCACATCCATCGGACCTTCAT
466006 CTTCTTCTCCCTGAACTCAGGAGCTCCTAAACTTCTTAACTCCTTAGGAATTAACATTCGCGGAG
66 CTTCTTCTCCCTGAACTCAGGAGCTCCTAAACTTCTTAACTCCTTAGGAATTAACATTCGCGGAG
* *
466071 CTGGAGGAGCAGGGGGAGGTGGAGGAGGATGAAACCTTGTCAAAATAGTATCAAGAGCTTGCATG
131 CTGGAGGAGCAGAGGGAGGCGGAGGAGGATGAAACCTTGTCAAAATAGTATCAAGAGCTTGCATG
466136 AAAGCTCCAAACTCCGATATT
196 AAAGCTCCAAACTCCGATATT
466157 CTGTAGACTTTCCAACATCATCATAACATCGTTCAATCATAAATTCACATCCATCGGACCTTCAT
1 CTGTAGACTTTCCAACATCATCATAACATCGTTCAATCATAAATTCACATCCATCGGACCTTCAT
*
466222 CTTCTTCTCCCTGAACTCAGGAGCTCCTAAACTTCTTAACTCCTTAGGAGTTAACATTCGCGGAG
66 CTTCTTCTCCCTGAACTCAGGAGCTCCTAAACTTCTTAACTCCTTAGGAATTAACATTCGCGGAG
466287 CTGGAGGAGCAGAGGGAGGCGGAGGAGGATGAAACCTTGTCAAAATAGTATCAAGAGCTTGCATG
131 CTGGAGGAGCAGAGGGAGGCGGAGGAGGATGAAACCTTGTCAAAATAGTATCAAGAGCTTGCATG
466352 AAAGCTCCAAACTCCGATATT
196 AAAGCTCCAAACTCCGATATT
466373 GGCATACCCT
Statistics
Matches: 212, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
216 212 1.00
ACGTcount: A:0.30, C:0.24, G:0.20, T:0.26
Consensus pattern (216 bp):
CTGTAGACTTTCCAACATCATCATAACATCGTTCAATCATAAATTCACATCCATCGGACCTTCAT
CTTCTTCTCCCTGAACTCAGGAGCTCCTAAACTTCTTAACTCCTTAGGAATTAACATTCGCGGAG
CTGGAGGAGCAGAGGGAGGCGGAGGAGGATGAAACCTTGTCAAAATAGTATCAAGAGCTTGCATG
AAAGCTCCAAACTCCGATATT
Found at i:467301 original size:55 final size:55
Alignment explanation
Indices: 467248--467880 Score: 808
Period size: 55 Copynumber: 11.6 Consensus size: 55
467238 ACCAATACAA
* * * ** *
467248 AAATTTATACACTTAGTATGAATTTCCT-AGTTTTGTACATAAAGTGCCCATACAG
1 AAATTCATCCACTTAGTATGAATTTCTTAAG-TTTACACATAAAGTGCCCATACGG
* ** *
467303 AAATTCATCCACTTAGTATGAATTCCTTAAGTTTACACATAAAGTTTCCATACGA
1 AAATTCATCCACTTAGTATGAATTTCTTAAGTTTACACATAAAGTGCCCATACGG
** *
467358 AAATTCATTTACTTAGTATGAATTTCTTAAGTTTACACATAAAGTGCCCATACAG
1 AAATTCATCCACTTAGTATGAATTTCTTAAGTTTACACATAAAGTGCCCATACGG
*
467413 AAATTCATCCACTTAGTATGAATTTCTTAAGTTTTTACACATAAAGTGCCCATATGG
1 AAATTCATCCACTTAGTATGAATTTCTTAAG--TTTACACATAAAGTGCCCATACGG
* *
467470 AAATTCATCCACTTAGTATGAATTTCTTAAGTTTACATATAAAGTGCTCATACGG
1 AAATTCATCCACTTAGTATGAATTTCTTAAGTTTACACATAAAGTGCCCATACGG
* *
467525 -AATCCATCCACTTAGTATGAATTTCTTAAGTTTACACATAAAGTGCTCATACGG
1 AAATTCATCCACTTAGTATGAATTTCTTAAGTTTACACATAAAGTGCCCATACGG
* **
467579 --A---A---A--T-GTATGAATTTCTTAAGTTTTTGCACATAAAGTGCCCATACAT
1 AAATTCATCCACTTAGTATGAATTTCTTAAG--TTTACACATAAAGTGCCCATACGG
* * *
467625 AAATTCATCCATTTAGTATGAATTTCTTAAGTTTACACATAAAGTGTCCATACAG
1 AAATTCATCCACTTAGTATGAATTTCTTAAGTTTACACATAAAGTGCCCATACGG
* * *
467680 AAATTCATCCACTTAGTATGAATTTTTTAAGTTTTTGCACATAAAGTGCCCATATGG
1 AAATTCATCCACTTAGTATGAATTTCTTAAG--TTTACACATAAAGTGCCCATACGG
* *
467737 AAATTCATCTACTTAGTATGAATTTCTTAAGTTTACAC-TGAAAGTGCCCATATGG
1 AAATTCATCCACTTAGTATGAATTTCTTAAGTTTACACAT-AAAGTGCCCATACGG
* *
467792 GAATTCATCCACTTAGTATGAATTTCTTAAGTTTACACATAAAGTGCCCATATGG
1 AAATTCATCCACTTAGTATGAATTTCTTAAGTTTACACATAAAGTGCCCATACGG
*
467847 AAATTCATCCACTTAGTATGAATTTATTAAGTTT
1 AAATTCATCCACTTAGTATGAATTTCTTAAGTTT
467881 TTGTACACTT
Statistics
Matches: 512, Mismatches: 46, Indels: 40
0.86 0.08 0.07
Matches are distributed among these distances:
44 16 0.03
45 1 0.00
46 20 0.04
47 1 0.00
48 1 0.00
50 1 0.00
51 1 0.00
53 1 0.00
54 54 0.11
55 294 0.57
56 4 0.01
57 118 0.23
ACGTcount: A:0.34, C:0.17, G:0.12, T:0.36
Consensus pattern (55 bp):
AAATTCATCCACTTAGTATGAATTTCTTAAGTTTACACATAAAGTGCCCATACGG
Found at i:467504 original size:112 final size:111
Alignment explanation
Indices: 467248--467880 Score: 814
Period size: 112 Copynumber: 5.8 Consensus size: 111
467238 ACCAATACAA
* * * **
467248 AAATTTATACACTTAGTATGAATTTCCT-AGTTTTGTACATAAAGTGCCCATACAGAAATTCATC
1 AAATTCATCCACTTAGTATGAATTTCTTAAGTTTTACACATAAAGTGCCCATACAGAAATTCATC
* ** *
467312 CACTTAGTATGAATTCCTTAAGTTTACACATAAAGTTTCCATACGA
66 CACTTAGTATGAATTTCTTAAGTTTACACATAAAGTGCCCATACGG
**
467358 AAATTCATTTACTTAGTATGAATTTCTTAAG-TTTACACATAAAGTGCCCATACAGAAATTCATC
1 AAATTCATCCACTTAGTATGAATTTCTTAAGTTTTACACATAAAGTGCCCATACAGAAATTCATC
*
467422 CACTTAGTATGAATTTCTTAAGTTTTTACACATAAAGTGCCCATATGG
66 CACTTAGTATGAATTTCTTAAG--TTTACACATAAAGTGCCCATACGG
* * * *
467470 AAATTCATCCACTTAGTATGAATTTCTTAAG-TTTACATATAAAGTGCTCATAC-GGAATCCATC
1 AAATTCATCCACTTAGTATGAATTTCTTAAGTTTTACACATAAAGTGCCCATACAGAAATTCATC
*
467533 CACTTAGTATGAATTTCTTAAGTTTACACATAAAGTGCTCATACGG
66 CACTTAGTATGAATTTCTTAAGTTTACACATAAAGTGCCCATACGG
* *
467579 --A---A---A--T-GTATGAATTTCTTAAGTTTTTGCACATAAAGTGCCCATACATAAATTCAT
1 AAATTCATCCACTTAGTATGAATTTCTTAAG-TTTTACACATAAAGTGCCCATACAGAAATTCAT
* * *
467633 CCATTTAGTATGAATTTCTTAAGTTTACACATAAAGTGTCCATACAG
65 CCACTTAGTATGAATTTCTTAAGTTTACACATAAAGTGCCCATACGG
* * **
467680 AAATTCATCCACTTAGTATGAATTTTTTAAGTTTTTGCACATAAAGTGCCCATATGGAAATTCAT
1 AAATTCATCCACTTAGTATGAATTTCTTAAG-TTTTACACATAAAGTGCCCATACAGAAATTCAT
* *
467745 CTACTTAGTATGAATTTCTTAAGTTTACAC-TGAAAGTGCCCATATGG
65 CCACTTAGTATGAATTTCTTAAGTTTACACAT-AAAGTGCCCATACGG
* **
467792 GAATTCATCCACTTAGTATGAATTTCTTAAG-TTTACACATAAAGTGCCCATATGGAAATTCATC
1 AAATTCATCCACTTAGTATGAATTTCTTAAGTTTTACACATAAAGTGCCCATACAGAAATTCATC
*
467856 CACTTAGTATGAATTTATTAAGTTT
66 CACTTAGTATGAATTTCTTAAGTTT
467881 TTGTACACTT
Statistics
Matches: 462, Mismatches: 43, Indels: 36
0.85 0.08 0.07
Matches are distributed among these distances:
98 16 0.03
99 1 0.00
100 19 0.04
101 50 0.11
103 1 0.00
104 1 0.00
106 1 0.00
107 1 0.00
109 23 0.05
110 131 0.28
111 34 0.07
112 184 0.40
ACGTcount: A:0.34, C:0.17, G:0.12, T:0.36
Consensus pattern (111 bp):
AAATTCATCCACTTAGTATGAATTTCTTAAGTTTTACACATAAAGTGCCCATACAGAAATTCATC
CACTTAGTATGAATTTCTTAAGTTTACACATAAAGTGCCCATACGG
Found at i:468245 original size:20 final size:20
Alignment explanation
Indices: 468220--468269 Score: 100
Period size: 20 Copynumber: 2.5 Consensus size: 20
468210 TGGCTCTTTA
468220 GTATCGATACCCTTACCATG
1 GTATCGATACCCTTACCATG
468240 GTATCGATACCCTTACCATG
1 GTATCGATACCCTTACCATG
468260 GTATCGATAC
1 GTATCGATAC
468270 TACTATACTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.26, C:0.28, G:0.16, T:0.30
Consensus pattern (20 bp):
GTATCGATACCCTTACCATG
Found at i:475633 original size:26 final size:24
Alignment explanation
Indices: 475573--475633 Score: 58
Period size: 23 Copynumber: 2.6 Consensus size: 24
475563 TTTTAATCAA
475573 AAAAT-TA-ATTATTAAAATATTT
1 AAAATATATATTATTAAAATATTT
*
475595 AAAATATAT-TTATTAATAT-TTCT
1 AAAATATATATTATTAAAATATT-T
475618 AATAATATAATATTAT
1 AA-AATAT-ATATTAT
475634 ATTTTTAATA
Statistics
Matches: 32, Mismatches: 1, Indels: 8
0.78 0.02 0.20
Matches are distributed among these distances:
22 7 0.22
23 14 0.44
24 5 0.16
25 2 0.06
26 4 0.12
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.48
Consensus pattern (24 bp):
AAAATATATATTATTAAAATATTT
Found at i:475634 original size:8 final size:8
Alignment explanation
Indices: 475617--475696 Score: 53
Period size: 8 Copynumber: 10.5 Consensus size: 8
475607 TTAATATTTC
*
475617 TAATAATA
1 TAATATTA
475625 TAATATTA
1 TAATATTA
*
475633 T-AT-TTT
1 TAATATTA
475639 TAATATTA
1 TAATATTA
**
475647 TAATAAAA
1 TAATATTA
475655 TAATCA--A
1 TAAT-ATTA
*
475662 TTATATTA
1 TAATATTA
*
475670 TAATAATA
1 TAATATTA
*
475678 TAATATAA
1 TAATATTA
475686 T-ATATTA
1 TAATATTA
475693 TAAT
1 TAAT
475697 TCTATTTTAA
Statistics
Matches: 55, Mismatches: 11, Indels: 12
0.71 0.14 0.15
Matches are distributed among these distances:
6 4 0.07
7 14 0.25
8 36 0.65
9 1 0.02
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.46
Consensus pattern (8 bp):
TAATATTA
Found at i:475635 original size:22 final size:23
Alignment explanation
Indices: 475605--475651 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 23
475595 AAAATATATT
475605 TATTAATATTTCTAATAATATAA
1 TATTAATATTTCTAATAATATAA
* *
475628 TATT-ATATTTTTAATATTATAA
1 TATTAATATTTCTAATAATATAA
475650 TA
1 TA
475652 AAATAATCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 18 0.82
23 4 0.18
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (23 bp):
TATTAATATTTCTAATAATATAA
Found at i:475670 original size:23 final size:23
Alignment explanation
Indices: 475641--475696 Score: 78
Period size: 23 Copynumber: 2.4 Consensus size: 23
475631 TATATTTTTA
*
475641 ATATTATAATAAAATAATCA-ATT
1 ATATTATAATAAAATAAT-ATAAT
*
475664 ATATTATAATAATATAATATAAT
1 ATATTATAATAAAATAATATAAT
475687 ATATTATAAT
1 ATATTATAAT
475697 TCTATTTTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
22 1 0.03
23 29 0.97
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (23 bp):
ATATTATAATAAAATAATATAAT
Found at i:475855 original size:23 final size:22
Alignment explanation
Indices: 475808--475880 Score: 65
Period size: 23 Copynumber: 3.1 Consensus size: 22
475798 TATATATTTG
*
475808 ATATTAATATAATAATCTAATAAT
1 ATATTAATA-AATAATTTAA-AAT
*
475832 ATTTTAATAAATACATTTAAAAT
1 ATATTAATAAATA-ATTTAAAAT
* * *
475855 ATACTAATTAATATTTTTAAAAT
1 ATATTAATAAATA-ATTTAAAAT
475878 ATA
1 ATA
475881 ATATAAAACT
Statistics
Matches: 41, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
23 28 0.68
24 13 0.32
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.44
Consensus pattern (22 bp):
ATATTAATAAATAATTTAAAAT
Found at i:476169 original size:13 final size:14
Alignment explanation
Indices: 476153--476183 Score: 55
Period size: 13 Copynumber: 2.3 Consensus size: 14
476143 AGTTTTCTAG
476153 AAAATATTTTTC-A
1 AAAATATTTTTCGA
476166 AAAATATTTTTCGA
1 AAAATATTTTTCGA
476180 AAAA
1 AAAA
476184 CGTTTTCAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 12 0.71
14 5 0.29
ACGTcount: A:0.52, C:0.06, G:0.03, T:0.39
Consensus pattern (14 bp):
AAAATATTTTTCGA
Found at i:485772 original size:19 final size:20
Alignment explanation
Indices: 485744--485781 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
485734 ATATGTATAT
485744 ATATCCATGAT-TTTGATTG
1 ATATCCATGATATTTGATTG
*
485763 ATATCTATGATATTTGATT
1 ATATCCATGATATTTGATT
485782 TGACGAGTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.29, C:0.08, G:0.13, T:0.50
Consensus pattern (20 bp):
ATATCCATGATATTTGATTG
Found at i:486459 original size:4 final size:4
Alignment explanation
Indices: 486450--486489 Score: 80
Period size: 4 Copynumber: 10.0 Consensus size: 4
486440 AGTCGCATAT
486450 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC
486490 AGCCTTTTGA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 36 1.00
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (4 bp):
TTTC
Found at i:488766 original size:25 final size:23
Alignment explanation
Indices: 488738--488783 Score: 74
Period size: 25 Copynumber: 1.9 Consensus size: 23
488728 ATTTTTTTTT
488738 ATTTTTTTATTTTACTTTTATTTCC
1 ATTTTTTTA-TTTA-TTTTATTTCC
488763 ATTTTTTTATTTATTTTATTT
1 ATTTTTTTATTTATTTTATTT
488784 TTTATTCACC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
23 8 0.38
24 4 0.19
25 9 0.43
ACGTcount: A:0.17, C:0.07, G:0.00, T:0.76
Consensus pattern (23 bp):
ATTTTTTTATTTATTTTATTTCC
Found at i:488803 original size:30 final size:29
Alignment explanation
Indices: 488743--488803 Score: 70
Period size: 29 Copynumber: 2.1 Consensus size: 29
488733 TTTTTATTTT
*
488743 TTTATTTTACTTTTATTTCCATTTTTTTA
1 TTTATTTTACTTTTATTTCCATTTTCTTA
* *
488772 TTTATTTTA-TTTTTTATTCACCTTTTCTTA
1 TTTATTTTACTTTTAT-TTC-CATTTTCTTA
488802 TT
1 TT
488804 ACTTATCAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
28 5 0.19
29 12 0.44
30 10 0.37
ACGTcount: A:0.16, C:0.11, G:0.00, T:0.72
Consensus pattern (29 bp):
TTTATTTTACTTTTATTTCCATTTTCTTA
Found at i:496405 original size:14 final size:14
Alignment explanation
Indices: 496388--496483 Score: 75
Period size: 14 Copynumber: 6.7 Consensus size: 14
496378 ATATCATATA
496388 TCATATTATATAGT
1 TCATATTATATAGT
* ** *
496402 TCATAGTCCATAAT
1 TCATATTATATAGT
496416 TGCATATTATATAGT
1 T-CATATTATATAGT
* *
496431 TCATATTAAATAAT
1 TCATATTATATAGT
*
496445 TGCATATCATATAGT
1 T-CATATTATATAGT
* *
496460 CCATATTAAATAGT
1 TCATATTATATAGT
* *
496474 ACGTATTATA
1 TCATATTATA
496484 GTCCATTATA
Statistics
Matches: 61, Mismatches: 19, Indels: 4
0.73 0.23 0.05
Matches are distributed among these distances:
14 41 0.67
15 20 0.33
ACGTcount: A:0.39, C:0.11, G:0.08, T:0.42
Consensus pattern (14 bp):
TCATATTATATAGT
Done.