Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr8
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: 19593398
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 1222752 characters in sequence are not A, C, G, or T
File 6 of 50
Found at i:3139764 original size:2 final size:2
Alignment explanation
Indices: 3139759--3139811 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
3139749 GTGTGTGTGT
3139759 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
3139801 GA GA GA GA GA G
1 GA GA GA GA GA G
3139812 GAAGGGTGCA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:3144263 original size:4 final size:4
Alignment explanation
Indices: 3144254--3144292 Score: 78
Period size: 4 Copynumber: 9.8 Consensus size: 4
3144244 GAACAGACAT
3144254 TATG TATG TATG TATG TATG TATG TATG TATG TATG TAT
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TAT
3144293 ATATATATAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 35 1.00
ACGTcount: A:0.26, C:0.00, G:0.23, T:0.51
Consensus pattern (4 bp):
TATG
Found at i:3160581 original size:19 final size:18
Alignment explanation
Indices: 3160557--3160593 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
3160547 TTGAACATTG
*
3160557 AAAACACCTAATAATATA
1 AAAACAACTAATAATATA
3160575 NAAAACAACTAATAATATA
1 -AAAACAACTAATAATATA
3160594 TATATATATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.62, C:0.14, G:0.00, T:0.22
Consensus pattern (18 bp):
AAAACAACTAATAATATA
Found at i:3160596 original size:2 final size:2
Alignment explanation
Indices: 3160589--3160632 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
3160579 ACAACTAATA
3160589 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
3160631 AT
1 AT
3160633 GGCAGTTTTG
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3169741 original size:15 final size:14
Alignment explanation
Indices: 3169721--3169769 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 14
3169711 AAAATAAAAA
3169721 TAAAAATATTTAATT
1 TAAAAA-ATTTAATT
*
3169736 TAAAAAAAATTAATT
1 T-AAAAAATTTAATT
*
3169751 TAAAAAATTAATATT
1 TAAAAAATTTA-ATT
3169766 TAAA
1 TAAA
3169770 TTATACAACA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
14 8 0.28
15 16 0.55
16 5 0.17
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (14 bp):
TAAAAAATTTAATT
Found at i:3169741 original size:16 final size:16
Alignment explanation
Indices: 3169722--3169758 Score: 58
Period size: 15 Copynumber: 2.4 Consensus size: 16
3169712 AAATAAAAAT
*
3169722 AAAAATATTTAATTTA
1 AAAAATAATTAATTTA
3169738 AAAAA-AATTAATTTA
1 AAAAATAATTAATTTA
3169753 AAAAAT
1 AAAAAT
3169759 TAATATTTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
15 14 0.74
16 5 0.26
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (16 bp):
AAAAATAATTAATTTA
Found at i:3173576 original size:15 final size:15
Alignment explanation
Indices: 3173556--3173587 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
3173546 AGGATCCATG
*
3173556 TCATCTTTATCGTCA
1 TCATCTTCATCGTCA
3173571 TCATCTTCATCGTCA
1 TCATCTTCATCGTCA
3173586 TC
1 TC
3173588 GTCATCGTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.19, C:0.31, G:0.06, T:0.44
Consensus pattern (15 bp):
TCATCTTCATCGTCA
Found at i:3173601 original size:15 final size:15
Alignment explanation
Indices: 3173564--3173603 Score: 50
Period size: 12 Copynumber: 2.9 Consensus size: 15
3173554 TGTCATCTTT
*
3173564 ATCGTCATCATCTTC
1 ATCGTCATCATCGTC
3173579 ATCG---TCATCGTC
1 ATCGTCATCATCGTC
3173591 ATCGTCATCATCG
1 ATCGTCATCATCG
3173604 ATTCCACCTT
Statistics
Matches: 21, Mismatches: 1, Indels: 6
0.75 0.04 0.21
Matches are distributed among these distances:
12 11 0.52
15 10 0.48
ACGTcount: A:0.20, C:0.33, G:0.12, T:0.35
Consensus pattern (15 bp):
ATCGTCATCATCGTC
Found at i:3174757 original size:19 final size:19
Alignment explanation
Indices: 3174725--3174762 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
3174715 ATAATAATTT
*
3174725 ATTTAAATTATTTTCAATA
1 ATTTAAATTATTTTAAATA
3174744 ATTTAAACTT-TTTTAAATA
1 ATTTAAA-TTATTTTAAATA
3174763 TTATATCTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 15 0.88
20 2 0.12
ACGTcount: A:0.42, C:0.05, G:0.00, T:0.53
Consensus pattern (19 bp):
ATTTAAATTATTTTAAATA
Found at i:3193056 original size:3 final size:3
Alignment explanation
Indices: 3193041--3193090 Score: 57
Period size: 3 Copynumber: 17.0 Consensus size: 3
3193031 GGGGACAAAG
* * * *
3193041 AGA AGA AGC AGA AGA AGG AGA AGG AGA AGG AGA AGA AGA AGA A-A AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
3193088 AGA
1 AGA
3193091 CGTATCTCTC
Statistics
Matches: 38, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
2 2 0.05
3 36 0.95
ACGTcount: A:0.60, C:0.02, G:0.38, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:3194845 original size:2 final size:2
Alignment explanation
Indices: 3194838--3194874 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
3194828 GTGTTAAGGT
3194838 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
3194875 GTTACCATAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:3203129 original size:30 final size:30
Alignment explanation
Indices: 3203093--3203151 Score: 109
Period size: 30 Copynumber: 2.0 Consensus size: 30
3203083 ATTTCATATA
3203093 GAGGAAAAGGATTTCCCTCGTACCACAAAG
1 GAGGAAAAGGATTTCCCTCGTACCACAAAG
*
3203123 GAGGAAAAGGGTTTCCCTCGTACCACAAA
1 GAGGAAAAGGATTTCCCTCGTACCACAAA
3203152 AGCGCATAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.36, C:0.24, G:0.24, T:0.17
Consensus pattern (30 bp):
GAGGAAAAGGATTTCCCTCGTACCACAAAG
Found at i:3216977 original size:92 final size:92
Alignment explanation
Indices: 3216818--3217001 Score: 262
Period size: 92 Copynumber: 2.0 Consensus size: 92
3216808 GTATCATTGT
* * *
3216818 GTATCTCATAAATCAAAAAAGTAAACAGAACAATCTATATTTGACAAATTTTAATTCTGTCACTA
1 GTATCTCATAAATCAAAAAAGTAAACAGAACAATCTAGATTTGACAAATCTTAATTCTATCACTA
3216883 TAATTTATCTGATATGTCAATTATCGC
66 TAATTTATCTGATATGTCAATTATCGC
* * * * * *
3216910 GTATCTCATGAATCAAAACAGTAAACACG-ACAATTTAGATTTGACAAATCTTACTTCTATTATT
1 GTATCTCATAAATCAAAAAAGTAAACA-GAACAATCTAGATTTGACAAATCTTAATTCTATCACT
*
3216974 ATAATTTATTTGATATGTCAATTATCGC
65 ATAATTTATCTGATATGTCAATTATCGC
3217002 ATTGATTATG
Statistics
Matches: 81, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
92 80 0.99
93 1 0.01
ACGTcount: A:0.39, C:0.15, G:0.09, T:0.37
Consensus pattern (92 bp):
GTATCTCATAAATCAAAAAAGTAAACAGAACAATCTAGATTTGACAAATCTTAATTCTATCACTA
TAATTTATCTGATATGTCAATTATCGC
Found at i:3217853 original size:21 final size:21
Alignment explanation
Indices: 3217829--3217870 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
3217819 AACTCCCTCT
* *
3217829 ACACCTTCCTCCATCAATCCC
1 ACACCATCATCCATCAATCCC
3217850 ACACCATCATCCATCAATCCC
1 ACACCATCATCCATCAATCCC
3217871 CCCCATTTCC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.29, C:0.50, G:0.00, T:0.21
Consensus pattern (21 bp):
ACACCATCATCCATCAATCCC
Found at i:3222979 original size:2 final size:2
Alignment explanation
Indices: 3222968--3223002 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
3222958 AATTAAAGTA
3222968 AT AT -T 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
3223003 CACAAAGTCA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:3238242 original size:3 final size:3
Alignment explanation
Indices: 3238236--3238270 Score: 63
Period size: 3 Copynumber: 12.0 Consensus size: 3
3238226 AGTAGAGGAG
3238236 AGA AGA AGA AGA AGA AGA AGA AGA AGA AG- AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
3238271 GAGTGAAACG
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 29 0.94
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:3239455 original size:2 final size:2
Alignment explanation
Indices: 3239448--3239476 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
3239438 AATAGTAGTT
3239448 TA TA 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 TA TA T
3239477 GCATTTGTTA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3244768 original size:15 final size:15
Alignment explanation
Indices: 3244745--3244775 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
3244735 AAACCTTTCA
3244745 GGCAACTTTATTTAT
1 GGCAACTTTATTTAT
*
3244760 GGCAGCTTTATTTAT
1 GGCAACTTTATTTAT
3244775 G
1 G
3244776 TCTTTTTTTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.23, C:0.13, G:0.19, T:0.45
Consensus pattern (15 bp):
GGCAACTTTATTTAT
Found at i:3252886 original size:43 final size:43
Alignment explanation
Indices: 3252822--3252904 Score: 148
Period size: 43 Copynumber: 1.9 Consensus size: 43
3252812 ATAACCTCCA
*
3252822 AAGAAAAGGGTACCCCGTGAAAGGGCACTACTCAAAAACTAGC
1 AAGAAAAGGGTACCCCATGAAAGGGCACTACTCAAAAACTAGC
*
3252865 AAGAAAAGGTTACCCCATGAAAGGGCACTACTCAAAAACT
1 AAGAAAAGGGTACCCCATGAAAGGGCACTACTCAAAAACT
3252905 TGGGTACAAC
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 38 1.00
ACGTcount: A:0.43, C:0.23, G:0.20, T:0.13
Consensus pattern (43 bp):
AAGAAAAGGGTACCCCATGAAAGGGCACTACTCAAAAACTAGC
Found at i:3255236 original size:15 final size:16
Alignment explanation
Indices: 3255218--3255247 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
3255208 TTTTTATGTG
3255218 GATTTT-ATTTTTAAT
1 GATTTTAATTTTTAAT
3255233 GATTTTAATTTTTAA
1 GATTTTAATTTTTAA
3255248 AAACTAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.30, C:0.00, G:0.07, T:0.63
Consensus pattern (16 bp):
GATTTTAATTTTTAAT
Found at i:3256347 original size:21 final size:22
Alignment explanation
Indices: 3256290--3256348 Score: 59
Period size: 21 Copynumber: 2.7 Consensus size: 22
3256280 CAAAATGAAT
*
3256290 TGTACATAATAATT-GAGTAACA
1 TGTACATAAT-ATTATAGTAACA
* **
3256312 TGTACATCACCTTATAGTAA-A
1 TGTACATAATATTATAGTAACA
3256333 TGTACATAATATTATA
1 TGTACATAATATTATA
3256349 ATAATTGTGA
Statistics
Matches: 29, Mismatches: 7, Indels: 3
0.74 0.18 0.08
Matches are distributed among these distances:
21 16 0.55
22 13 0.45
ACGTcount: A:0.42, C:0.12, G:0.10, T:0.36
Consensus pattern (22 bp):
TGTACATAATATTATAGTAACA
Found at i:3261626 original size:5 final size:5
Alignment explanation
Indices: 3261616--3261641 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
3261606 TGCATGCATG
3261616 TAAAA TAAAA TAAAA TAAAA TAAAA T
1 TAAAA TAAAA TAAAA TAAAA TAAAA T
3261642 TCCTCATTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (5 bp):
TAAAA
Found at i:3277779 original size:42 final size:43
Alignment explanation
Indices: 3277733--3277816 Score: 127
Period size: 44 Copynumber: 2.0 Consensus size: 43
3277723 GAGTAAACAA
3277733 AACCATA-AAAAAGATATTACAAGC-AATAAAAACCAAGAGGTC
1 AACCATAGAAAAAGATATTACAAGCGAA-AAAAACCAAGAGGTC
*
3277775 AACCATAGTAAAAGGATATTACAAGCGAAAAAAACCAAGAGG
1 AACCATAG-AAAAAGATATTACAAGCGAAAAAAACCAAGAGG
3277817 GAAAAAATTT
Statistics
Matches: 38, Mismatches: 1, Indels: 4
0.88 0.02 0.09
Matches are distributed among these distances:
42 7 0.18
44 29 0.76
45 2 0.05
ACGTcount: A:0.56, C:0.15, G:0.15, T:0.13
Consensus pattern (43 bp):
AACCATAGAAAAAGATATTACAAGCGAAAAAAACCAAGAGGTC
Found at i:3286317 original size:19 final size:19
Alignment explanation
Indices: 3286293--3286331 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
3286283 ACATGCTTAT
3286293 GTTTTTTGCATTTGTTGCA
1 GTTTTTTGCATTTGTTGCA
3286312 GTTTTTTGCATTTGTTGCA
1 GTTTTTTGCATTTGTTGCA
3286331 G
1 G
3286332 CTTGTTGCGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.10, C:0.10, G:0.23, T:0.56
Consensus pattern (19 bp):
GTTTTTTGCATTTGTTGCA
Found at i:3286336 original size:10 final size:10
Alignment explanation
Indices: 3286293--3286343 Score: 54
Period size: 9 Copynumber: 5.4 Consensus size: 10
3286283 ACATGCTTAT
*
3286293 GTTTTTTGCA
1 GTTTGTTGCA
3286303 -TTTGTTGCA
1 GTTTGTTGCA
*
3286312 GTTTTTTGCA
1 GTTTGTTGCA
3286322 -TTTGTTGCA
1 GTTTGTTGCA
*
3286331 GCTTGTTGC-
1 GTTTGTTGCA
3286340 GTTT
1 GTTT
3286344 CACAAAATTG
Statistics
Matches: 34, Mismatches: 5, Indels: 5
0.77 0.11 0.11
Matches are distributed among these distances:
9 19 0.56
10 15 0.44
ACGTcount: A:0.08, C:0.12, G:0.24, T:0.57
Consensus pattern (10 bp):
GTTTGTTGCA
Found at i:3286339 original size:19 final size:19
Alignment explanation
Indices: 3286298--3286339 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
3286288 CTTATGTTTT
* *
3286298 TTGCATTTGTTGCAGTTTT
1 TTGCATTTGTTGCAGCTTG
3286317 TTGCATTTGTTGCAGCTTG
1 TTGCATTTGTTGCAGCTTG
3286336 TTGC
1 TTGC
3286340 GTTTCACAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.10, C:0.14, G:0.24, T:0.52
Consensus pattern (19 bp):
TTGCATTTGTTGCAGCTTG
Found at i:3287050 original size:26 final size:26
Alignment explanation
Indices: 3286997--3287062 Score: 73
Period size: 26 Copynumber: 2.6 Consensus size: 26
3286987 ACCAACTCGA
* * **
3286997 AGAAATAAGGAATAGTCAAACGCCAG
1 AGAAATAAGGAAGAGTAAAAAACCAG
3287023 AGAAATAAGGAAGAGTAAAAAA-C-G
1 AGAAATAAGGAAGAGTAAAAAACCAG
*
3287047 AGAGATAAGGAAGAGT
1 AGAAATAAGGAAGAGT
3287063 TAGACAGGAA
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
24 16 0.46
25 1 0.03
26 18 0.51
ACGTcount: A:0.55, C:0.08, G:0.27, T:0.11
Consensus pattern (26 bp):
AGAAATAAGGAAGAGTAAAAAACCAG
Found at i:3287227 original size:34 final size:34
Alignment explanation
Indices: 3287184--3287251 Score: 136
Period size: 34 Copynumber: 2.0 Consensus size: 34
3287174 TCAATTGAAG
3287184 AAAATTGAAACATCCTACTTTTATATATATTATA
1 AAAATTGAAACATCCTACTTTTATATATATTATA
3287218 AAAATTGAAACATCCTACTTTTATATATATTATA
1 AAAATTGAAACATCCTACTTTTATATATATTATA
3287252 GTTATTTATG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.44, C:0.12, G:0.03, T:0.41
Consensus pattern (34 bp):
AAAATTGAAACATCCTACTTTTATATATATTATA
Found at i:3305082 original size:2 final size:2
Alignment explanation
Indices: 3305077--3305104 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
3305067 CCAAAAAAAA
3305077 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
3305105 GCTATTAGTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3308020 original size:20 final size:22
Alignment explanation
Indices: 3307995--3308035 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
3307985 TTCTTGTTTT
3307995 TAAC-AAAAAAT-AATTAAAAA
1 TAACAAAAAAATCAATTAAAAA
3308015 TAACAAAAAAATCAATTAAAA
1 TAACAAAAAAATCAATTAAAA
3308036 GTAGTCTAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 4 0.21
21 7 0.37
22 8 0.42
ACGTcount: A:0.73, C:0.07, G:0.00, T:0.20
Consensus pattern (22 bp):
TAACAAAAAAATCAATTAAAAA
Found at i:3311792 original size:264 final size:266
Alignment explanation
Indices: 3311305--3311826 Score: 660
Period size: 264 Copynumber: 2.0 Consensus size: 266
3311295 GGCTATATTT
* * * *
3311305 CCCTTAGTCATCTCCTTTCTCAAGCCCCACGCTTCTCACATTCTCTCTCCTGCCCGTTGCCAAGC
1 CCCTTAGTAATCTCCTTTCTCAAGCCCCACGCCTCCCACATTCTCTCTCCTACCCGTTGCCAAGC
* * * *
3311370 CAAAGGTCGCTATCCTTCTCTACACATCACCATCGTTGAGCCGCCGCTACTTCAGTCGAACAACC
66 CAAA-GTCGCTATCCTTCTCAACACACCACCATCGTTGAGCCGCCACTACTTCAGTCGAAAAACC
* ** *
3311435 GCCTTTACGGTTAAAACTTCTTCAATACAACAACATTCCCCGACAAACGCCGGCGACGAGCCACA
130 ACCTCCACGGTTAAAACTTCTTCAATACAACAACATTCCCCGACAAACGCCAGCGACGAGCCACA
* * * * * *
3311500 AAACGCTTCTGATCTCACATTTCAACAAACCATTGAAAGACTCTAGGTTCCAAGAGCTACTACCT
195 AAACGCTTCTGATCGCACATTCCAACAAACCACTCAAAGACTCCAGGTTCCAAGAACTACTACCT
3311565 CGCCTTC
260 CGCCTTC
* * *
3311572 CCCTTAGTAATCTCCTTTCTCAAGCCCCACGCCTCCCACGTTTTCTCTCCTACGCGTCT-CCAAG
1 CCCTTAGTAATCTCCTTTCTCAAGCCCCACGCCTCCCACATTCTCTCTCCTACCCGT-TGCCAAG
* * * *
3311636 CCGAA-T-GCTATCCTTCTCAACGCACCACCA-CTGTTGAGCCGCCACTGCTTCAGTTGAAAAAC
65 CCAAAGTCGCTATCCTTCTCAACACACCACCATC-GTTGAGCCGCCACTACTTCAGTCGAAAAAC
* * * * * * * *
3311698 CACCTCCGCGGTTAACACTTCTTTAATTCAACAATATTCCTCGACAAACGCCAGCGATGAGCCGC
129 CACCTCCACGGTTAAAACTTCTTCAATACAACAACATTCCCCGACAAACGCCAGCGACGAGCC-A
3311763 CAAAA-GCTTCT-ATTCGCACATTCCAACAAACCACTCAAAGACTCCAGGTTCCAAGAACTACTA
193 CAAAACGCTTCTGA-TCGCACATTCCAACAAACCACTCAAAGACTCCAGGTTCCAAGAACTACTA
3311826 C
257 C
3311827 TACTGCTACT
Statistics
Matches: 218, Mismatches: 33, Indels: 11
0.83 0.13 0.04
Matches are distributed among these distances:
263 2 0.01
264 150 0.69
265 6 0.03
267 59 0.27
268 1 0.00
ACGTcount: A:0.26, C:0.36, G:0.13, T:0.24
Consensus pattern (266 bp):
CCCTTAGTAATCTCCTTTCTCAAGCCCCACGCCTCCCACATTCTCTCTCCTACCCGTTGCCAAGC
CAAAGTCGCTATCCTTCTCAACACACCACCATCGTTGAGCCGCCACTACTTCAGTCGAAAAACCA
CCTCCACGGTTAAAACTTCTTCAATACAACAACATTCCCCGACAAACGCCAGCGACGAGCCACAA
AACGCTTCTGATCGCACATTCCAACAAACCACTCAAAGACTCCAGGTTCCAAGAACTACTACCTC
GCCTTC
Found at i:3315149 original size:30 final size:33
Alignment explanation
Indices: 3315108--3315173 Score: 84
Period size: 30 Copynumber: 2.1 Consensus size: 33
3315098 TAAGCATGTG
*
3315108 GCATTCCTATTA-TATAT-TAAGGTA-TATGGT
1 GCATTCCTATTATTAAATCTAAGGTATTATGGT
* *
3315138 GCATTCTTATTATTAAATCTAAGGTATTTTGGT
1 GCATTCCTATTATTAAATCTAAGGTATTATGGT
3315171 GCA
1 GCA
3315174 AAATAAATAT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
30 11 0.37
31 4 0.13
32 7 0.23
33 8 0.27
ACGTcount: A:0.29, C:0.11, G:0.17, T:0.44
Consensus pattern (33 bp):
GCATTCCTATTATTAAATCTAAGGTATTATGGT
Found at i:3315191 original size:26 final size:26
Alignment explanation
Indices: 3315162--3315216 Score: 92
Period size: 26 Copynumber: 2.1 Consensus size: 26
3315152 AAATCTAAGG
3315162 TATTTTGGTGCAAAATAAATATTTAA
1 TATTTTGGTGCAAAATAAATATTTAA
* *
3315188 TATTTTGGTGCAAACTATATATTTAA
1 TATTTTGGTGCAAAATAAATATTTAA
3315214 TAT
1 TAT
3315217 ATTTAAAATG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.38, C:0.05, G:0.11, T:0.45
Consensus pattern (26 bp):
TATTTTGGTGCAAAATAAATATTTAA
Found at i:3315363 original size:657 final size:659
Alignment explanation
Indices: 3313347--3316887 Score: 3553
Period size: 657 Copynumber: 5.4 Consensus size: 659
3313337 ATTTTTTGAA
* * * * **
3313347 ACTCATAATGGATTTGAG-TGGTTA-CTTAAGGTGAAAACCACTTTGTGTTGTTTGGAGAAAAAA
1 ACTCATGATGGATTTG-GTTGGTTACCTTAAGGTGAGAACCACTTTGTGGTGTTTGCAG-AAGTA
* * * * * *
3313410 AATAAATTTTAAGGGTGTGG-TATGTGGCATTTTTATTATAAATTAA-GTATAATGGTGCCAATA
64 AATAAACTATAA-GGTGTGGACATGTGACATTTCTATTATATATTAAGGTATAATGGTGCCAATA
* * * ** ** * *
3313473 TGTGAATCTTATAT-TGTT-T-TATGGTGCGTTCCTATAATTTA--ATCAAAGGTATTATGGTTC
128 TGTAAATCTAATATCT-TTGTATATGGTGCATT-CT-TGTTTTACCATTGAAGGTATAATGGTGC
* * * * ** * * * * *
3313533 AAAATACATA-ATGATATATTTGTTATGGCATTCTTAATGTGTAATAAAGACACAATGGTGCTTA
190 GAAATAGATATTTAATATATTTGACATGACATTCCTATTGTGAAATAAAGGCACAATGGTGCTTA
* ** * * * *
3313597 TGT-AACATAGACTTTATGTAATAATTTGACATTTCAATTGTACATTAATGAACAATGATGTCAA
255 TGTGAACATATACTTTATGTGTTAATTTGACATTTCGATTGTACATTAAGGTACAATGGTGTCAA
* * * * *
3313661 TTGAGAATTTTGTTTTTTTAATCATGACCATATGAAATTGTTTTATACTTACGATAGATTTGGTT
320 TTGAGAATTTCGTTTTTTTAATCATGACCACATGAAATTGTTTCATACTTATGATGGATTTGGTT
* * * *
3313726 GGTTAGTGACCTTAAAGGTGAGAACTACTTTGTGGTGTTTGAGAAATA-AAAAATTGTAAAGTGT
385 GGTTAGTTACCTTAAAGGTGAGAACTACTTTGTGGTGTTTGAAAAATAGAAAAAAT-TAAGGTGT
* * * *
3313790 AAGCATGTGGCATTCCTATTATACATAAATGTATAATGGTGCCAATATGTGAAT-CTAGCAT-TT
449 AAGCATGTGGCATTCCTATTATATATTAAGGTATAATGGTGCCAATATGTGAATATTAGCATCTT
3313853 TGGTATATGGTGCATTCTTATTATTTAATCCAAGATATTTTGGTGCAAACTATATATTTAATATA
514 TGGTATATGGTGCATTCTTATTA-TT--T-CAAG-TATTTTGGTGCAAA-TATATATTTAATATA
* * * *
3313918 TTTGAAGTGGCATTCCTATTGTGTAATAAAGGCACAATGGTGCTTATATGAACATATAGTATCAA
573 TTTAAAGTGGCATTCCTATTGTGTAATAAAAGCACAATGGTGCTTATATGAATATATAATATCAA
*
3313983 TTGACAATTCCTTTTGTTTCAT
638 TTGAGAATTCCTTTTGTTTCAT
* * * * *
3314005 ACTCATGATGGTTTTGGTTGATTACCTTAAGATGAGAACCACTTTGTGGTGTTTGAAGAAGCAAA
1 ACTCATGATGGATTTGGTTGGTTACCTTAAGGTGAGAACCACTTTGTGGTGTTTGCAGAAGTAAA
* * * * * * *
3314070 TAAACTATAAGGTATGGGCATGTGACATTTCTATTATACATTAAGGCATAATGGTGTCATTATAT
66 TAAACTATAAGGTGTGGACATGTGACATTTCTATTATATATTAAGGTATAATGGTGCCAATATGT
* * * * * *
3314135 AAATCTAACATCTTTGTATATAGTGCATTCTTGTTTTACCATCG-AGGGATAGTGGTGGGAAATA
131 AAATCTAATATCTTTGTATATGGTGCATTCTTGTTTTACCATTGAAGGTATAATGGTGCGAAATA
* * *
3314199 GATATTTAATATATTTGACATGGCATTCCTATTGTGCAATAAAGGCACAATGGTGGTTATGTGAA
196 GATATTTAATATATTTGACATGACATTCCTATTGTGAAATAAAGGCACAATGGTGCTTATGTGAA
* * * * * *
3314264 CATATATCTTTATGTGTTTATTAGACATTCCAATTGTACATTACGGTATAATGGTGTCTATATTG
261 CATATA-CTTTATGTGTTAATTTGACATTTCGATTGTACATTAAGGTACAATGGTGTC-A-ATTG
* * * *
3314329 AGAATTTTGTTTTCTTAATCATGACCACATGGAATTGTTTCATACTTATGTTGGATTTGGTTGGT
323 AGAATTTCGTTTTTTTAATCATGACCACATGAAATTGTTTCATACTTATGATGGATTTGGTTGGT
* *
3314394 TAGTTACCTTAAAGGTGAGAACTACTTTGTGGTG--T------TAG--------GA-GAGTAAGC
388 TAGTTACCTTAAAGGTGAGAACTACTTTGTGGTGTTTGAAAAATAGAAAAAATTAAGGTGTAAGC
* * ** *
3314442 ATATAGCATTCCTATTATATATTAAGGTATAATGGTATCAATATGTGAAT-TTAGCATC-TTAGT
453 ATGTGGCATTCCTATTATATATTAAGGTATAATGGTGCCAATATGTGAATATTAGCATCTTTGGT
*
3314505 ATATGGTGCATTCTTATTATTTAATCTATGGTATTTTGGTGC--A-ATATA-TTAATATATTTAA
518 ATATGGTGCATTCTTATTA-TT--TC-A-AGTATTTTGGTGCAAATATATATTTAATATATTTAA
*
3314566 AGTGGCATTCCTATTGTGTAA-AAAAGGCACAATGGTACTTATATGAATATATAATATCAATTGA
578 AGTGGCATTCCTATTGTGTAATAAAA-GCACAATGGTGCTTATATGAATATATAATATCAATTGA
3314630 GAATTCCTTTTGTTTCAT
642 GAATTCCTTTTGTTTCAT
* * * * * * * *
3314648 ACTTATGATGGATATGGTTGTTTACCTTAAAGTGAAAACTACTTCGTGGTATTTGCAGAAGTAAA
1 ACTCATGATGGATTTGGTTGGTTACCTTAAGGTGAGAACCACTTTGTGGTGTTTGCAGAAGTAAA
* * *
3314713 TAAACTATTAGGTGTGGACATGTGACATTTTTATTATATATTAAGGTATAATGTTGCCAATATGT
66 TAAACTATAAGGTGTGGACATGTGACATTTCTATTATATATTAAGGTATAATGGTGCCAATATGT
* * * * *
3314778 AAATATAATGTTTTTGTATATGGTGTATTCTTGTTTTACCATTGAAGGTATAATTGTGCGAAATA
131 AAATCTAATATCTTTGTATATGGTGCATTCTTGTTTTACCATTGAAGGTATAATGGTGCGAAATA
* * *
3314843 GATATTTAATATATTTGACATGACATTCCTATTGTGAAATAAAGACACAATGGTGCTTATTTGAG
196 GATATTTAATATATTTGACATGACATTCCTATTGTGAAATAAAGGCACAATGGTGCTTATGTGAA
* * **
3314908 CATATACATTTATGTGTTAATTTGACATTCCGATTGCATGTTAAGGTACAATGGTGTCAATTGAG
261 CATATAC-TTTATGTGTTAATTTGACATTTCGATTGTACATTAAGGTACAATGGTGTCAATTGAG
* * * *
3314973 AATTTCGTTTTTTTTAATCGTGACCATATGGAATTGTTTCATATTTATGATGGATTTGGTTGGTT
325 AATTTCG-TTTTTTTAATCATGACCACATGAAATTGTTTCATACTTATGATGGATTTGGTTGGTT
* *
3315038 AGTTACCTTAAAGGTGAGAACTTCATTGTGGTGTTTGAAAAATAGAAAAACATTAAGGTGTAAGC
389 AGTTACCTTAAAGGTGAGAACTACTTTGTGGTGTTTGAAAAATAGAAAAA-ATTAAGGTGTAAGC
* * * * **
3315103 ATGTGGCATTCCTATTATATATTAAGGTAT-ATGGTG-C-AT-TCTTATTATTA-AATCTAAGGT
453 ATGTGGCATTCCTATTATATATTAAGGTATAATGGTGCCAATATGTGAATATTAGCATCTTTGGT
* *** * * *
3315163 ATTTTGGTGCAAAATAAATATTT-AA-TATTTTGGTGCAAACTATATATTTAATATATTTAAAAT
518 A-TATGGTGCATTCTTATTATTTCAAGTATTTTGGTGCAAA-TATATATTTAATATATTTAAAGT
* * *
3315226 GACATTCCTATTGTGTAATAAAAGCACAATGATGCTTATATGAATATATAATATTAATTGAGAAT
581 GGCATTCCTATTGTGTAATAAAAGCACAATGGTGCTTATATGAATATATAATATCAATTGAGAAT
*
3315291 TCCTGTTGTTTCAT
646 TCCTTTTGTTTCAT
* * * ** * *
3315305 ACTTATGATGGATTTGGTTGTTTACCTTAAGGTGAGAACCACTTTATAATATTTGCAGAGGTAAA
1 ACTCATGATGGATTTGGTTGGTTACCTTAAGGTGAGAACCACTTTGTGGTGTTTGCAGAAGTAAA
* * * * * *
3315370 TAAACTATAAGGTGTAGACATGTGGCA-TTCGTATTATATATTAAGATATAGTGGTACCGATATG
66 TAAACTATAAGGTGTGGACATGTGACATTTC-TATTATATATTAAGGTATAATGGTGCCAATATG
* * ** * *
3315434 TAAATCTAATATCTTTGTATATGGTACTTTCTTGTTTTAGTATTAAAGGTATAATGGTGCTAAAT
130 TAAATCTAATATCTTTGTATATGGTGCATTCTTGTTTTACCATTGAAGGTATAATGGTGCGAAAT
* ** *
3315499 AGATATTTAATATATTTGACATGACACTCCTATCATGAAATAAAGGCACAATGGTGCTTATTTGA
195 AGATATTTAATATATTTGACATGACATTCCTATTGTGAAATAAAGGCACAATGGTGCTTATGTGA
* * * * * *
3315564 GCATATATCTTTATGTTTTAATTTGACATTTGGATTGCACATTAAGGTAGAATGGCGTCAATTGA
260 ACATATA-CTTTATGTGTTAATTTGACATTTCGATTGTACATTAAGGTACAATGGTGTCAATTGA
* * *
3315629 AAATTTCATTTTTTTTAATCATGACCACATAAAATTGTTTCATACTTATGATGGA--T--TTGGT
324 GAATTTC-GTTTTTTTAATCATGACCACATGAAATTGTTTCATACTTATGATGGATTTGGTTGGT
* * **
3315690 TAGTTA-CTTGAAAGGTGAGAACTTCTTTGTGGTGTTTGGAGAAATAGAAAACCTTTAAGGTGTA
388 TAGTTACCTT-AAAGGTGAGAACTACTTTGTGGTGTTT-GAAAAATAGAAAA-AATTAAGGTGTA
* * * * * **
3315754 GGCATATGGCATTTCTATTATATATTAAGGCATAATGGTGCCAATATATGAATA-TAATAT-TTT
450 AGCATGTGGCATTCCTATTATATATTAAGGTATAATGGTGCCAATATGTGAATATTAGCATCTTT
* * *
3315817 GGTATATGGTGCATTATTGTTATTTAATCTAAGGTATTTTGGTGC-AA-A-ATA---AATATATC
515 GGTATATGGTGCATTCTTATTA-TT--TC-AA-GTATTTTGGTGCAAATATATATTTAATATATT
* * * * *
3315876 TGAAGTGACATTCCTATTGTGTAAT-AAAGCACAATGGTGCTTATGTGAATATGTAATATTAATT
575 TAAAGTGGCATTCCTATTGTGTAATAAAAGCACAATGGTGCTTATATGAATATATAATATCAATT
* * *
3315940 GTGAATTCTTTTTGTTTTAT
640 GAGAATTCCTTTTGTTTCAT
* * *
3315960 ACTCATGATGAATTTGGTTGGTTACCTTAAGATGAGAA-CACTTTGTGGTGTTTGGAGAAGTAAA
1 ACTCATGATGGATTTGGTTGGTTACCTTAAGGTGAGAACCACTTTGTGGTGTTTGCAGAAGTAAA
* * * * * * ** *
3316024 GAAATTATAAGGTGTAGATATGT-AGCA-TTCATATTATATATTAACGTATAATAGTATCGATAT
66 TAAACTATAAGGTGTGGACATGTGA-CATTTC-TATTATATATTAAGGTATAATGGTGCCAATAT
* * * * **
3316087 GTAAATTTAACATCTTTGGATATGATGCATTCTTGTTTTACCATTGAAGGTATAACAGTGCGAAA
129 GTAAATCTAATATCTTTGTATATGGTGCATTCTTGTTTTACCATTGAAGGTATAATGGTGCGAAA
** * * * *
3316152 TAGATATTTAATATATTTGATTTAACATTCCTATTGTGCAATAAAGGCATAATGGTCCTTATGTG
194 TAGATATTTAATATATTTGACATGACATTCCTATTGTGAAATAAAGGCACAATGGTGCTTATGTG
* * * * * ** *
3316217 AACATATGTCTTTATATGTTAATTTGACATTTTGATTATACATTAAGGTATAATAATATCAATTG
259 AACATAT-ACTTTATGTGTTAATTTGACATTTCGATTGTACATTAAGGTACAATGGTGTCAATTG
* * * * *
3316282 AAAATTTC-ATTTTTTAATCATGACCACATGAAACTGTTTTACACTTATGATGGATTTGGTTGGT
323 AGAATTTCGTTTTTTTAATCATGACCACATGAAATTGTTTCATACTTATGATGGATTTGGTTGGT
* * ** * *
3316346 TAGTTACCTTAAAGGTGATAACTACTTTGTTGTGTTCAAAAAAATAAAAAAAATTAAGGTGTAGG
388 TAGTTACCTTAAAGGTGAGAACTACTTTGTGGTGTT-TGAAAAATAGAAAAAATTAAGGTGTAAG
* * * ** *
3316411 CATGTGACATTCTTATTATATATCAATATATAATAGTGCCAATATGTGAAT-TTAGCATC-TTGG
452 CATGTGGCATTCCTATTATATATTAAGGTATAATGGTGCCAATATGTGAATATTAGCATCTTTGG
*
3316474 TATATGGTG-ATTCTTATTATTTAATCCAAAGTATTTTGGTGCAAAATAGATATTTAATATATTT
517 TATATGGTGCATTCTTATTA-TT--T-C-AAGTATTTTGGTGC-AAATATATATTTAATATATTT
* * * **
3316538 AAAGTGGCATTCCTATTGTGTAATAAAAGAACAGTGGTGCTTATGTGAACT-TATTGTATCAATT
576 AAAGTGGCATTCCTATTGTGTAATAAAAGCACAATGGTGCTTATATGAA-TATATAATATCAATT
*
3316602 AAGAATTCCTTTTGTTTCAT
640 GAGAATTCCTTTTGTTTCAT
** * * * ** *
3316622 ACTCAACATGGATTTGGTTGGTTACCTTAACGTGAGAATCATTTTGAAGTGTTTAG-GGAAGTAA
1 ACTCATGATGGATTTGGTTGGTTACCTTAAGGTGAGAACCACTTTGTGGTGTTT-GCAGAAGTAA
* * * * *
3316686 ATAAACTATAAGATGTGGATATGTGATATTTCTATTATACATTAAGGTATAATGGTGTCAATATG
65 ATAAACTATAAGGTGTGGACATGTGACATTTCTATTATATATTAAGGTATAATGGTGCCAATATG
* * * * **
3316751 TGAATCTAATATCTTGGTATATGGTGCATTCTTATTATTTA--ATTCAAGGTATTTTGGTG-GAA
130 TAAATCTAATATCTTTGTATATGGTGCATTCTT-GT-TTTACCATTGAAGGTATAATGGTGCGAA
* * * *
3316813 GATAGATATTTAAT-TAATTT-AAAGTGGCATTCCTATTAT-ATAATAAAGGCACAATGGTACTT
193 -ATAGATATTTAATAT-ATTTGACA-TGACATTCCTATTGTGA-AATAAAGGCACAATGGTGCTT
*
3316875 ATGTGAATATATA
254 ATGTGAACATATA
3316888 GTATCAATTA
Statistics
Matches: 2411, Mismatches: 375, Indels: 190
0.81 0.13 0.06
Matches are distributed among these distances:
642 15 0.01
643 315 0.13
644 128 0.05
645 1 0.00
646 1 0.00
647 1 0.00
648 97 0.04
649 2 0.00
651 3 0.00
652 55 0.02
653 37 0.02
654 320 0.13
655 166 0.07
656 97 0.04
657 441 0.18
658 79 0.03
659 77 0.03
660 28 0.01
661 127 0.05
662 94 0.04
663 221 0.09
664 7 0.00
665 99 0.04
ACGTcount: A:0.33, C:0.10, G:0.18, T:0.40
Consensus pattern (659 bp):
ACTCATGATGGATTTGGTTGGTTACCTTAAGGTGAGAACCACTTTGTGGTGTTTGCAGAAGTAAA
TAAACTATAAGGTGTGGACATGTGACATTTCTATTATATATTAAGGTATAATGGTGCCAATATGT
AAATCTAATATCTTTGTATATGGTGCATTCTTGTTTTACCATTGAAGGTATAATGGTGCGAAATA
GATATTTAATATATTTGACATGACATTCCTATTGTGAAATAAAGGCACAATGGTGCTTATGTGAA
CATATACTTTATGTGTTAATTTGACATTTCGATTGTACATTAAGGTACAATGGTGTCAATTGAGA
ATTTCGTTTTTTTAATCATGACCACATGAAATTGTTTCATACTTATGATGGATTTGGTTGGTTAG
TTACCTTAAAGGTGAGAACTACTTTGTGGTGTTTGAAAAATAGAAAAAATTAAGGTGTAAGCATG
TGGCATTCCTATTATATATTAAGGTATAATGGTGCCAATATGTGAATATTAGCATCTTTGGTATA
TGGTGCATTCTTATTATTTCAAGTATTTTGGTGCAAATATATATTTAATATATTTAAAGTGGCAT
TCCTATTGTGTAATAAAAGCACAATGGTGCTTATATGAATATATAATATCAATTGAGAATTCCTT
TTGTTTCAT
Found at i:3316878 original size:295 final size:295
Alignment explanation
Indices: 3316421--3317127 Score: 865
Period size: 295 Copynumber: 2.4 Consensus size: 295
3316411 CATGTGACAT
* * ** * * **
3316421 TCTTATTATATATCAATATATAATAGTGCCAATATGTGAATTTAGCATCTTGGTATATGGTG-AT
1 TCTTATTATACATTAAGGTATAATAGTGACAATATGTGAATCTAATATCTTGGTATATGGTGCAT
3316485 TCTTATTATTTAATCCAAAGTATTTTGGTGCAAAATAGATATTTAATATATTTAAAGTGGCATTC
66 TCTTATTATTTAATCCAAAGTATTTTGGTGCAAAATAGATATTTAATATATTTAAAGTGGCATTC
* * * * *
3316550 CTATTGTGTAATAAAAGAACAGTGGTGCTTATGTGAACT-TATTGTATCAATTAAGAATTCCTTT
131 CTATTATATAATAAAAGAACAATGGTACTTATGTGAA-TATATAGTATCAATTAAGAATTCCTTT
* * *
3316614 TGTTTCATACTCAACATGGATTTGGTTGGTTACCTTAACGTGAGAATCATTTTGAAGTGTTTAGG
195 TGTTTCATACTCAACATGGATTTGGTTGATTACCTTAACGTGAGAACCATTTTGAAGTGTTTAGA
*
3316679 GAAGTAA-ATAAACTATAAGATGTGGATATG-TG-ATA
260 GAAGTAAGA-AAACTATAAGATGTGGACATGTTGTA-A
* * *
3316714 TTTCTATTATACATTAAGGTATAATGGTGTCAATATGTGAATCTAATATCTTGGTATATGGTGCA
1 TCT-TATTATACATTAAGGTATAATAGTGACAATATGTGAATCTAATATCTTGGTATATGGTGCA
* * * *
3316779 TTCTTATTATTTAATTCAAGGTATTTTGGTGGAAGATAGATATTTAAT-TAATTTAAAGTGGCAT
65 TTCTTATTATTTAATCCAAAGTATTTTGGTGCAAAATAGATATTTAATAT-ATTTAAAGTGGCAT
* * *
3316843 TCCTATTATATAATAAAGGCACAATGGTACTTATGTGAATATATAGTATCAATTAAGAATTCTTT
129 TCCTATTATATAATAAAAGAACAATGGTACTTATGTGAATATATAGTATCAATTAAGAATTCCTT
* ** * **
3316908 TTGTTTCATGCTCATGATGGATTTGGTTGATTACCTTAATGTGAGAACCATTTTGTGGTGTTTAG
194 TTGTTTCATACTCAACATGGATTTGGTTGATTACCTTAACGTGAGAACCATTTTGAAGTGTTTAG
* * *
3316973 AGAAGTAAGAAAACTTTAAGGTGTGGGCATGTTGTAA
259 AGAAGTAAGAAAACTATAAGATGTGGACATGTTGTAA
* * **
3317010 TCTTATTATACATTAAGGTATAATAGTGACAATATGTAAATCTAATATATTTATATATGGTGCAT
1 TCTTATTATACATTAAGGTATAATAGTGACAATATGTGAATCTAATATCTTGGTATATGGTGCAT
* * ** * *
3317075 T-TT-TGT-TTTACCATCGAAGGTATAATAGTGCGAAATAGATATTTAATATATTT
66 TCTTAT-TATTTA--ATCCAAAGTATTTTGGTGCAAAATAGATATTTAATATATTT
3317128 GACATGACAT
Statistics
Matches: 353, Mismatches: 50, Indels: 20
0.83 0.12 0.05
Matches are distributed among these distances:
293 7 0.02
294 55 0.16
295 283 0.80
296 7 0.02
297 1 0.00
ACGTcount: A:0.33, C:0.09, G:0.18, T:0.40
Consensus pattern (295 bp):
TCTTATTATACATTAAGGTATAATAGTGACAATATGTGAATCTAATATCTTGGTATATGGTGCAT
TCTTATTATTTAATCCAAAGTATTTTGGTGCAAAATAGATATTTAATATATTTAAAGTGGCATTC
CTATTATATAATAAAAGAACAATGGTACTTATGTGAATATATAGTATCAATTAAGAATTCCTTTT
GTTTCATACTCAACATGGATTTGGTTGATTACCTTAACGTGAGAACCATTTTGAAGTGTTTAGAG
AAGTAAGAAAACTATAAGATGTGGACATGTTGTAA
Found at i:3330575 original size:51 final size:51
Alignment explanation
Indices: 3330499--3330606 Score: 207
Period size: 51 Copynumber: 2.1 Consensus size: 51
3330489 ACTCATTAAC
3330499 GGCATGTTTCATCTTTGATGCCAACAGCATCATCATGTCTCCAGATTCGAT
1 GGCATGTTTCATCTTTGATGCCAACAGCATCATCATGTCTCCAGATTCGAT
3330550 GGCATGTTTCATCTTTGATGCCAACAGCATCATCATGTCTCCAGATTCGAT
1 GGCATGTTTCATCTTTGATGCCAACAGCATCATCATGTCTCCAGATTCGAT
*
3330601 GCCATG
1 GGCATG
3330607 ATCACCGCTT
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 56 1.00
ACGTcount: A:0.23, C:0.26, G:0.19, T:0.32
Consensus pattern (51 bp):
GGCATGTTTCATCTTTGATGCCAACAGCATCATCATGTCTCCAGATTCGAT
Found at i:3346783 original size:42 final size:42
Alignment explanation
Indices: 3346621--3346798 Score: 155
Period size: 42 Copynumber: 4.2 Consensus size: 42
3346611 GAAGCAACAG
* ** *
3346621 GACCTTGCTGAGACAGATTTTGGGCAGGAACAGAAGTAAT-T
1 GACCTTGTTGAGACAGATTTTGGGCTTGAACAGAAGCAATGT
* * * * * * **
3346662 GGACCTTTTTGAGGCTGGTTATGAGC-TGAAACAGAAGTGATAG-
1 -GACCTTGTTGAGACAGATTTTGGGCTTG-AACAGAAGCAAT-GT
* *
3346705 GACCTTGTTGTGACTGATTTTGGGCTTGAACAGAAGCAATGT
1 GACCTTGTTGAGACAGATTTTGGGCTTGAACAGAAGCAATGT
* *
3346747 GACCTTGTTGAGGCAGATTTTGGGCTTGGACAGAAGCAATGT
1 GACCTTGTTGAGACAGATTTTGGGCTTGAACAGAAGCAATGT
*
3346789 TACCTTGTTG
1 GACCTTGTTG
3346799 GAACTGGCTT
Statistics
Matches: 109, Mismatches: 22, Indels: 10
0.77 0.16 0.07
Matches are distributed among these distances:
41 2 0.02
42 105 0.96
43 2 0.02
ACGTcount: A:0.26, C:0.14, G:0.30, T:0.30
Consensus pattern (42 bp):
GACCTTGTTGAGACAGATTTTGGGCTTGAACAGAAGCAATGT
Found at i:3358175 original size:21 final size:21
Alignment explanation
Indices: 3358130--3358191 Score: 67
Period size: 21 Copynumber: 3.0 Consensus size: 21
3358120 AATAATTATA
*
3358130 AAAATAAT-TATAATA-AAAT
1 AAAATAATATATAACATAAAT
3358149 AAAATAATA-ATAACATCAAAT
1 AAAATAATATATAACAT-AAAT
* *
3358170 ATAATAATATTTAACATAAAT
1 AAAATAATATATAACATAAAT
3358191 A
1 A
3358192 CATAAAATTC
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
19 13 0.36
21 17 0.47
22 6 0.17
ACGTcount: A:0.65, C:0.05, G:0.00, T:0.31
Consensus pattern (21 bp):
AAAATAATATATAACATAAAT
Found at i:3359553 original size:16 final size:16
Alignment explanation
Indices: 3359509--3359557 Score: 59
Period size: 16 Copynumber: 3.2 Consensus size: 16
3359499 AAGTATTATT
3359509 ATTTAAATTTTAAAAA
1 ATTTAAATTTTAAAAA
*
3359525 A--T-AATTTCCAAAAA
1 ATTTAAATTT-TAAAAA
3359539 ATTTAAATTTTAAAAA
1 ATTTAAATTTTAAAAA
3359555 ATT
1 ATT
3359558 ACTCAAAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 8
0.73 0.05 0.22
Matches are distributed among these distances:
13 5 0.19
14 7 0.26
16 10 0.37
17 5 0.19
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.41
Consensus pattern (16 bp):
ATTTAAATTTTAAAAA
Found at i:3359565 original size:27 final size:30
Alignment explanation
Indices: 3359509--3359573 Score: 91
Period size: 30 Copynumber: 2.3 Consensus size: 30
3359499 AAGTATTATT
*
3359509 ATTTAAATTTTAAAAAATAATTTCCAAAAA
1 ATTTAAATTTTAAAAAATAATCTCCAAAAA
*
3359539 ATTTAAATTTTAAAAAATTA-CT-C-AAAA
1 ATTTAAATTTTAAAAAATAATCTCCAAAAA
3359566 ATTTAAAT
1 ATTTAAAT
3359574 CTAACTTCAC
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
27 12 0.36
28 1 0.03
29 1 0.03
30 19 0.58
ACGTcount: A:0.55, C:0.06, G:0.00, T:0.38
Consensus pattern (30 bp):
ATTTAAATTTTAAAAAATAATCTCCAAAAA
Found at i:3360120 original size:25 final size:25
Alignment explanation
Indices: 3360092--3360151 Score: 84
Period size: 25 Copynumber: 2.4 Consensus size: 25
3360082 CTAAGTTAGT
* *
3360092 AAGCTTTTCAAATCATGAAAATTGA
1 AAGCTTATCAAATCATGAAAACTGA
*
3360117 AAGCTTATCAAATCATGAAGACTGA
1 AAGCTTATCAAATCATGAAAACTGA
*
3360142 AAGCTAATCA
1 AAGCTTATCA
3360152 TTGATTCATA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 31 1.00
ACGTcount: A:0.45, C:0.15, G:0.13, T:0.27
Consensus pattern (25 bp):
AAGCTTATCAAATCATGAAAACTGA
Found at i:3360644 original size:19 final size:18
Alignment explanation
Indices: 3360606--3360645 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
3360596 TAACAATTTT
*
3360606 AATTTTTTAAATAATCAA
1 AATTTTTTAAATAATAAA
*
3360624 AATTATTTTAAATACTAAA
1 AATT-TTTTAAATAATAAA
3360643 AAT
1 AAT
3360646 GTTTGAAAAG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 4 0.21
19 15 0.79
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (18 bp):
AATTTTTTAAATAATAAA
Found at i:3369731 original size:27 final size:28
Alignment explanation
Indices: 3369701--3369793 Score: 80
Period size: 29 Copynumber: 3.2 Consensus size: 28
3369691 AAGTATTAAA
* *
3369701 GTGTAACAA-AATGTTTTTGAATATGAC
1 GTGTAACAACAATTTTTTTCAATATGAC
* * *
3369728 GTGTAAAAATAATATTTTTTCAATATGGC
1 GTGTAACAACAAT-TTTTTTCAATATGAC
* *
3369757 GTATAACAACAATTTTTTTTCTCAATATGGC
1 GTGTAACAACAA--TTTTTT-TCAATATGAC
3369788 GTGTAA
1 GTGTAA
3369794 TAACCTAACC
Statistics
Matches: 53, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
27 8 0.15
28 3 0.06
29 21 0.40
30 5 0.09
31 16 0.30
ACGTcount: A:0.35, C:0.10, G:0.15, T:0.40
Consensus pattern (28 bp):
GTGTAACAACAATTTTTTTCAATATGAC
Found at i:3369753 original size:29 final size:30
Alignment explanation
Indices: 3369714--3369793 Score: 90
Period size: 29 Copynumber: 2.7 Consensus size: 30
3369704 TAACAAAATG
* * *
3369714 TTTTTGAATATGACGTGTAAAAATAA-TAT
1 TTTTTCAATATGGCGTGTAAAAACAATTAT
* * *
3369743 TTTTTCAATATGGCGTATAACAACAATTTT
1 TTTTTCAATATGGCGTGTAAAAACAATTAT
3369773 TTTTCTCAATATGGCGTGTAA
1 TTTT-TCAATATGGCGTGTAA
3369794 TAACCTAACC
Statistics
Matches: 42, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
29 21 0.50
30 6 0.14
31 15 0.36
ACGTcount: A:0.34, C:0.10, G:0.14, T:0.42
Consensus pattern (30 bp):
TTTTTCAATATGGCGTGTAAAAACAATTAT
Found at i:3369881 original size:21 final size:21
Alignment explanation
Indices: 3369827--3369882 Score: 87
Period size: 21 Copynumber: 2.7 Consensus size: 21
3369817 TGTTTTTGTA
3369827 CATAACGTGTAACAACCTAAC
1 CATAACGTGTAACAACCTAAC
*
3369848 CATAGA-GTATAACAACCTAAC
1 CATA-ACGTGTAACAACCTAAC
3369869 CATAACGTGTAACA
1 CATAACGTGTAACA
3369883 TGTTTTTGTA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
20 1 0.03
21 29 0.94
22 1 0.03
ACGTcount: A:0.45, C:0.25, G:0.11, T:0.20
Consensus pattern (21 bp):
CATAACGTGTAACAACCTAAC
Found at i:3397979 original size:71 final size:71
Alignment explanation
Indices: 3397863--3398007 Score: 254
Period size: 71 Copynumber: 2.0 Consensus size: 71
3397853 TTTGGAACGC
3397863 AATTGTTAATTTGCTGAAGGCAATATAATACAACCTCGTGACAAAGCAAAGTATCCCAAAAATAA
1 AATTGTTAATTTGCTGAAGGCAATATAATACAACCTCGTGACAAAGCAAAGTATCCCAAAAATAA
3397928 GCCGAT
66 GCCGAT
* * *
3397934 AATTGTTAATTTGCTGAAGGCAATATGATACAACCTTGTGACAAAGCAAAGTATCCCAAAAATAT
1 AATTGTTAATTTGCTGAAGGCAATATAATACAACCTCGTGACAAAGCAAAGTATCCCAAAAATAA
*
3397999 GCTGAT
66 GCCGAT
3398005 AAT
1 AAT
3398008 ATAGCTAAAC
Statistics
Matches: 70, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
71 70 1.00
ACGTcount: A:0.41, C:0.17, G:0.16, T:0.26
Consensus pattern (71 bp):
AATTGTTAATTTGCTGAAGGCAATATAATACAACCTCGTGACAAAGCAAAGTATCCCAAAAATAA
GCCGAT
Found at i:3404086 original size:37 final size:37
Alignment explanation
Indices: 3404001--3404086 Score: 88
Period size: 37 Copynumber: 2.3 Consensus size: 37
3403991 ATTAAAACTC
*
3404001 ATAAAATATAATTTTTATATATTAATTTAAAAATAATT
1 ATAAAA-AAAATTTTTATATATTAATTTAAAAATAATT
* *
3404039 A-AAATTAAAATTTTTA-ATAATTAATTT-AATATAATTT
1 ATAAA-AAAAATTTTTATAT-ATTAATTTAAAAATAA-TT
3404076 ATAAAAAAAAT
1 ATAAAAAAAAT
3404087 ATCAACTGTA
Statistics
Matches: 40, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
36 8 0.20
37 28 0.70
38 4 0.10
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (37 bp):
ATAAAAAAAATTTTTATATATTAATTTAAAAATAATT
Found at i:3406462 original size:2 final size:2
Alignment explanation
Indices: 3406455--3406485 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
3406445 GGACCTAGCC
*
3406455 AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3406486 AACTTAAAAC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:3407434 original size:20 final size:20
Alignment explanation
Indices: 3407409--3407448 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
3407399 TGTTATTTAT
* *
3407409 TTTTTTCTTCTTAATATAGC
1 TTTTTTATTCATAATATAGC
*
3407429 TTTTTTATTGATAATATAGC
1 TTTTTTATTCATAATATAGC
3407449 ATGAGAAAAA
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:0.25, C:0.10, G:0.07, T:0.57
Consensus pattern (20 bp):
TTTTTTATTCATAATATAGC
Found at i:3408413 original size:2 final size:2
Alignment explanation
Indices: 3408406--3408433 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
3408396 GCTACAAAGA
3408406 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
3408434 GTTTTACGAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3435389 original size:89 final size:89
Alignment explanation
Indices: 3435238--3435415 Score: 356
Period size: 89 Copynumber: 2.0 Consensus size: 89
3435228 AGATGGAATA
3435238 TTAGCAAGGTAGGGAACCATCAGTTTTTTTATTTGAGCTGTATTGCTTATATCTCTTACACCAAT
1 TTAGCAAGGTAGGGAACCATCAGTTTTTTTATTTGAGCTGTATTGCTTATATCTCTTACACCAAT
3435303 CTGCTTTCTTCTTGTTTATTTTTG
66 CTGCTTTCTTCTTGTTTATTTTTG
3435327 TTAGCAAGGTAGGGAACCATCAGTTTTTTTATTTGAGCTGTATTGCTTATATCTCTTACACCAAT
1 TTAGCAAGGTAGGGAACCATCAGTTTTTTTATTTGAGCTGTATTGCTTATATCTCTTACACCAAT
3435392 CTGCTTTCTTCTTGTTTATTTTTG
66 CTGCTTTCTTCTTGTTTATTTTTG
3435416 CTGGCCATAG
Statistics
Matches: 89, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
89 89 1.00
ACGTcount: A:0.20, C:0.17, G:0.16, T:0.47
Consensus pattern (89 bp):
TTAGCAAGGTAGGGAACCATCAGTTTTTTTATTTGAGCTGTATTGCTTATATCTCTTACACCAAT
CTGCTTTCTTCTTGTTTATTTTTG
Found at i:3462508 original size:34 final size:34
Alignment explanation
Indices: 3462470--3462539 Score: 131
Period size: 34 Copynumber: 2.1 Consensus size: 34
3462460 GCTCTACACT
3462470 TTTCTTATATAACTTGGCTTATAATAGAGGCCCC
1 TTTCTTATATAACTTGGCTTATAATAGAGGCCCC
*
3462504 TTTCTTATATAACTTGGCTTATAATATAGGCCCC
1 TTTCTTATATAACTTGGCTTATAATAGAGGCCCC
3462538 TT
1 TT
3462540 AACTATTTTA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.26, C:0.20, G:0.13, T:0.41
Consensus pattern (34 bp):
TTTCTTATATAACTTGGCTTATAATAGAGGCCCC
Found at i:3470693 original size:274 final size:273
Alignment explanation
Indices: 3470203--3470738 Score: 1063
Period size: 274 Copynumber: 2.0 Consensus size: 273
3470193 AACCATGGCT
3470203 TTAATATACTCATTATAATGTTGCACTGAGTCCCTCCAAGCTTAACATCAACTTCAGCTCTAACA
1 TTAATATACTCATTATAATGTTGCACTGAGTCCCTCCAAGCTTAACATCAACTTCAGCTCTAACA
3470268 AGTGAGATTGGCTGAAAAGCAACAGCATTAGAAAGAATAAGCTACTAAACCAACCCAATAAAATT
66 AGTGAGATTGGCTGAAAAGCAACAGCATTAGAAAGAATAAGCTACTAAACCAACCCAATAAAATT
3470333 ATAAATGTGGCACCCACACTATGTTTAACAGGTCCATATGTCTCTAAAAATATACATCAACCAAA
131 ATAAATGTGGCACCCACACTATGTTTAACAGGTCCATATGTCTCTAAAAATATACATCAACCAAA
3470398 CAAAAGCAAAATAACCTGGTACGAAAACTAGATAGAAATGAGATGGGAAAAAAAGCTTCCTTGTT
196 CAAAAGCAAAATAACCTGGTACGAAAACTAGATAGAAATGAGATGGGAAAAAAAGCTTCCTTGTT
3470463 CCAACAAAGGGTG
261 CCAACAAAGGGTG
3470476 TNTAATATACTCATTATAATGTTGCACTGAGTCCCTCCAAGCTTAACATCAACTTCAGCTCTAAC
1 T-TAATATACTCATTATAATGTTGCACTGAGTCCCTCCAAGCTTAACATCAACTTCAGCTCTAAC
3470541 AAGTGAGATTGGCTGAAAAGCAACAGCATTAGAAAGAATAAGCTACTAAACCAACCCAATAAAAT
65 AAGTGAGATTGGCTGAAAAGCAACAGCATTAGAAAGAATAAGCTACTAAACCAACCCAATAAAAT
3470606 TATAAATGTGGCACCCACACTATGTTTAACAGGTCCATATGTCTCTAAAAATATACATCAACCAA
130 TATAAATGTGGCACCCACACTATGTTTAACAGGTCCATATGTCTCTAAAAATATACATCAACCAA
3470671 ACAAAAGCAAAATAACCTGGTACGAAAACTAGATAGAAATGAGATGGGAAAAAAAGCTTCCTTGT
195 ACAAAAGCAAAATAACCTGGTACGAAAACTAGATAGAAATGAGATGGGAAAAAAAGCTTCCTTGT
3470736 TCC
260 TCC
3470739 CAAACAAAAG
Statistics
Matches: 262, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
273 1 0.00
274 261 1.00
ACGTcount: A:0.41, C:0.20, G:0.15, T:0.24
Consensus pattern (273 bp):
TTAATATACTCATTATAATGTTGCACTGAGTCCCTCCAAGCTTAACATCAACTTCAGCTCTAACA
AGTGAGATTGGCTGAAAAGCAACAGCATTAGAAAGAATAAGCTACTAAACCAACCCAATAAAATT
ATAAATGTGGCACCCACACTATGTTTAACAGGTCCATATGTCTCTAAAAATATACATCAACCAAA
CAAAAGCAAAATAACCTGGTACGAAAACTAGATAGAAATGAGATGGGAAAAAAAGCTTCCTTGTT
CCAACAAAGGGTG
Found at i:3479474 original size:6 final size:6
Alignment explanation
Indices: 3479463--3479489 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
3479453 AGGATAATTG
3479463 TTTCTT TTTCTT TTTCTT TTTCTT TTT
1 TTTCTT TTTCTT TTTCTT TTTCTT TTT
3479490 TTGGTTGTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (6 bp):
TTTCTT
Found at i:3507411 original size:15 final size:15
Alignment explanation
Indices: 3507391--3507428 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
3507381 TTCTAATACT
3507391 TCATCATCAAACTCA
1 TCATCATCAAACTCA
*
3507406 TCATCATCAATCTCA
1 TCATCATCAAACTCA
*
3507421 TGATCATC
1 TCATCATC
3507429 TTGATCTGTG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.34, C:0.32, G:0.03, T:0.32
Consensus pattern (15 bp):
TCATCATCAAACTCA
Found at i:3516454 original size:17 final size:15
Alignment explanation
Indices: 3516432--3516466 Score: 52
Period size: 17 Copynumber: 2.2 Consensus size: 15
3516422 AAAATAGAGA
3516432 GGGGAGGGGAGGGGGAG
1 GGGGAGGGG-GGGGG-G
3516449 GGGGAGGGGGGGGGG
1 GGGGAGGGGGGGGGG
3516464 GGG
1 GGG
3516467 CTTGCTCAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 4 0.22
16 5 0.28
17 9 0.50
ACGTcount: A:0.11, C:0.00, G:0.89, T:0.00
Consensus pattern (15 bp):
GGGGAGGGGGGGGGG
Found at i:3516466 original size:6 final size:6
Alignment explanation
Indices: 3516432--3516463 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
3516422 AAAATAGAGA
3516432 GGGGA- GGGGAG GGGGAG GGGGAG GGGG-G GGGG
1 GGGGAG GGGGAG GGGGAG GGGGAG GGGGAG GGGG
3516464 GGGCTTGCTC
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 10 0.38
6 16 0.62
ACGTcount: A:0.12, C:0.00, G:0.88, T:0.00
Consensus pattern (6 bp):
GGGGAG
Found at i:3518124 original size:17 final size:16
Alignment explanation
Indices: 3518099--3518132 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
3518089 AATTTTATTT
3518099 TAAAATTTTAAATAATA
1 TAAAATTTTAAA-AATA
*
3518116 TAAATTTTTAAAAATA
1 TAAAATTTTAAAAATA
3518132 T
1 T
3518133 TTTATTAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (16 bp):
TAAAATTTTAAAAATA
Found at i:3521158 original size:30 final size:30
Alignment explanation
Indices: 3521122--3521190 Score: 93
Period size: 30 Copynumber: 2.3 Consensus size: 30
3521112 GATCAATCAG
3521122 GTTTTTATACCTTTATTTTGAACCAAATAA
1 GTTTTTATACCTTTATTTTGAACCAAATAA
** * *
3521152 GTTTTTATATTTTTATTTTTAATCAAATAA
1 GTTTTTATACCTTTATTTTGAACCAAATAA
*
3521182 GTCTTTATA
1 GTTTTTATA
3521191 ATTAATGATT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.32, C:0.09, G:0.06, T:0.54
Consensus pattern (30 bp):
GTTTTTATACCTTTATTTTGAACCAAATAA
Found at i:3521992 original size:17 final size:17
Alignment explanation
Indices: 3521970--3522021 Score: 61
Period size: 17 Copynumber: 3.1 Consensus size: 17
3521960 TAAAAATAAA
3521970 AAAAATAAATATTATGT
1 AAAAATAAATATTATGT
* **
3521987 AAAAATAAA-ATAAAAT
1 AAAAATAAATATTATGT
*
3522003 AAAAATAATTATTATGT
1 AAAAATAAATATTATGT
3522020 AA
1 AA
3522022 TTTGATATGA
Statistics
Matches: 27, Mismatches: 7, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
16 12 0.44
17 15 0.56
ACGTcount: A:0.65, C:0.00, G:0.04, T:0.31
Consensus pattern (17 bp):
AAAAATAAATATTATGT
Found at i:3522328 original size:29 final size:30
Alignment explanation
Indices: 3522287--3522352 Score: 84
Period size: 30 Copynumber: 2.3 Consensus size: 30
3522277 ACTAATACTT
*
3522287 TTTTTAT-TTTTTATTAT-ATTC-AATCAAA
1 TTTTTATATTTTTATTATAAATCGAAT-AAA
*
3522315 TTTTTATATTTTTATTTTAAATCGAATAAA
1 TTTTTATATTTTTATTATAAATCGAATAAA
3522345 TTTTTATA
1 TTTTTATA
3522353 ATTAATGATT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
28 7 0.21
29 9 0.27
30 14 0.42
31 3 0.09
ACGTcount: A:0.33, C:0.05, G:0.02, T:0.61
Consensus pattern (30 bp):
TTTTTATATTTTTATTATAAATCGAATAAA
Found at i:3522750 original size:23 final size:22
Alignment explanation
Indices: 3522690--3522752 Score: 74
Period size: 24 Copynumber: 2.8 Consensus size: 22
3522680 TAAATTAATT
*
3522690 AATTTTTAAATTTA-AAATATT
1 AATTTTTAAATTTATAAATATA
*
3522711 AATTTTTATAATATATAATATATA
1 AATTTTTA-AATTTATAA-ATATA
*
3522735 AATTTTCAAATTTATAAA
1 AATTTTTAAATTTATAAA
3522753 AAATATTTTA
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
21 8 0.23
22 6 0.17
23 10 0.29
24 11 0.31
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (22 bp):
AATTTTTAAATTTATAAATATA
Found at i:3533196 original size:1 final size:1
Alignment explanation
Indices: 3533190--3533217 Score: 56
Period size: 1 Copynumber: 28.0 Consensus size: 1
3533180 NNNNNNNNNN
3533190 GGGGGGGGGGGGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGGGGG
3533218 TGTTTAATCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:0.00, C:0.00, G:1.00, T:0.00
Consensus pattern (1 bp):
G
Found at i:3572146 original size:21 final size:23
Alignment explanation
Indices: 3572110--3572154 Score: 67
Period size: 21 Copynumber: 2.0 Consensus size: 23
3572100 CTTATAATAT
3572110 ATTAATATATATAATATTTACTA
1 ATTAATATATATAATATTTACTA
*
3572133 ATTAATATA-A-AATATTTCCTA
1 ATTAATATATATAATATTTACTA
3572154 A
1 A
3572155 AGCAAATATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 11 0.52
22 1 0.05
23 9 0.43
ACGTcount: A:0.49, C:0.07, G:0.00, T:0.44
Consensus pattern (23 bp):
ATTAATATATATAATATTTACTA
Found at i:3577053 original size:2 final size:2
Alignment explanation
Indices: 3577046--3577071 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3577036 AAGGGTGTCA
3577046 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
3577072 TTCAACAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3579304 original size:28 final size:28
Alignment explanation
Indices: 3579264--3579323 Score: 93
Period size: 28 Copynumber: 2.1 Consensus size: 28
3579254 GTTGATGCAT
*
3579264 AATCTCTCTACCTAAAGAGCAGGATTCA
1 AATCTCCCTACCTAAAGAGCAGGATTCA
* *
3579292 AATCTCCCTACCTAAAGAGTAGGGTTCA
1 AATCTCCCTACCTAAAGAGCAGGATTCA
3579320 AATC
1 AATC
3579324 CCCCCTCCTC
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.35, C:0.25, G:0.15, T:0.25
Consensus pattern (28 bp):
AATCTCCCTACCTAAAGAGCAGGATTCA
Found at i:3589917 original size:2 final size:2
Alignment explanation
Indices: 3589910--3589937 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
3589900 TACAGCAGCT
3589910 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3589938 CATGTTAACC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3594537 original size:2 final size:2
Alignment explanation
Indices: 3594530--3594596 Score: 98
Period size: 2 Copynumber: 32.0 Consensus size: 2
3594520 TGCAGCAGCC
*
3594530 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA NGA CTA CTA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA -TA -TA TA
3594573 TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA
3594597 ATGTTAACCC
Statistics
Matches: 61, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
2 56 0.92
3 5 0.08
ACGTcount: A:0.48, C:0.03, G:0.01, T:0.46
Consensus pattern (2 bp):
TA
Found at i:3606291 original size:50 final size:50
Alignment explanation
Indices: 3606230--3606328 Score: 171
Period size: 50 Copynumber: 2.0 Consensus size: 50
3606220 GAAAATAAAC
* *
3606230 TCATACCCTTACATTAATGTAGGAAAGAAAGCAAAGGAAACATTAATAAT
1 TCATACCCTTACATTAATGTAGGAAAGAAAGAAAAGGAAACATCAATAAT
*
3606280 TCATACCCTTACATTAATGTAGGAGAGAAAGAAAAGGAAACATCAATAA
1 TCATACCCTTACATTAATGTAGGAAAGAAAGAAAAGGAAACATCAATAA
3606329 GTTGCCTGGA
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
50 46 1.00
ACGTcount: A:0.48, C:0.14, G:0.15, T:0.22
Consensus pattern (50 bp):
TCATACCCTTACATTAATGTAGGAAAGAAAGAAAAGGAAACATCAATAAT
Found at i:3614296 original size:13 final size:13
Alignment explanation
Indices: 3614278--3614305 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
3614268 TATAAAGTAA
3614278 AGTTCTTAATTGG
1 AGTTCTTAATTGG
3614291 AGTTCTTAATTGG
1 AGTTCTTAATTGG
3614304 AG
1 AG
3614306 AGAAAGAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.25, C:0.07, G:0.25, T:0.43
Consensus pattern (13 bp):
AGTTCTTAATTGG
Found at i:3615787 original size:6 final size:6
Alignment explanation
Indices: 3615776--3615818 Score: 79
Period size: 6 Copynumber: 7.3 Consensus size: 6
3615766 AATTCGAAGG
3615776 AAAGCA AAAGCA AAAGCA AAAGCA AAAGC- AAAGCA AAAGCA AA
1 AAAGCA AAAGCA AAAGCA AAAGCA AAAGCA AAAGCA AAAGCA AA
3615819 GTAGAAAGTT
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
5 5 0.14
6 31 0.86
ACGTcount: A:0.67, C:0.16, G:0.16, T:0.00
Consensus pattern (6 bp):
AAAGCA
Found at i:3615826 original size:23 final size:25
Alignment explanation
Indices: 3615777--3615826 Score: 70
Period size: 23 Copynumber: 2.1 Consensus size: 25
3615767 ATTCGAAGGA
3615777 AAGCAAAAGCAAAAGCAAAAGCA-A
1 AAGCAAAAGCAAAAGCAAAAGCAGA
*
3615801 AAGC-AAAGCAAAAGC-AAAGTAGA
1 AAGCAAAAGCAAAAGCAAAAGCAGA
3615824 AAG
1 AAG
3615827 TTCCGTGCCA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
22 5 0.21
23 15 0.62
24 4 0.17
ACGTcount: A:0.64, C:0.14, G:0.20, T:0.02
Consensus pattern (25 bp):
AAGCAAAAGCAAAAGCAAAAGCAGA
Found at i:3619172 original size:14 final size:15
Alignment explanation
Indices: 3619135--3619174 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
3619125 CCATTCTCAT
* *
3619135 TGAAGGCTTAGCTTA
1 TGAAGGCTTTGCTAA
3619150 TGAAGGCTTTGCTAA
1 TGAAGGCTTTGCTAA
3619165 TG-AGGCTTTG
1 TGAAGGCTTTG
3619175 GAGTTACTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 8 0.35
15 15 0.65
ACGTcount: A:0.23, C:0.12, G:0.30, T:0.35
Consensus pattern (15 bp):
TGAAGGCTTTGCTAA
Found at i:3632876 original size:30 final size:30
Alignment explanation
Indices: 3632842--3632903 Score: 90
Period size: 30 Copynumber: 2.1 Consensus size: 30
3632832 AATTATTAGT
* *
3632842 TATAAAGAC-TTATTAGACTTAAAATGAAAA
1 TATAAAAACTTTATTAG-CTTAAAATAAAAA
3632872 TATAAAAACTTTATTAGCTTAAAATAAAAA
1 TATAAAAACTTTATTAGCTTAAAATAAAAA
3632902 TA
1 TA
3632904 CAAGAGTTTG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
30 22 0.76
31 7 0.24
ACGTcount: A:0.55, C:0.06, G:0.06, T:0.32
Consensus pattern (30 bp):
TATAAAAACTTTATTAGCTTAAAATAAAAA
Found at i:3668443 original size:97 final size:95
Alignment explanation
Indices: 3668293--3668484 Score: 366
Period size: 97 Copynumber: 2.0 Consensus size: 95
3668283 TATAGTTTTC
3668293 TTTGTATATATATATATATATAGAGAGAGAGAGAGAGAGAAAGAGGCAATCGTGACAAATATTTT
1 TTTGTATATATATATATATATAGAGAGAGAGAGAGAGAGAAAGAGGCAATCGTGACAAATATTTT
3668358 AAGGCAATGAATAAATAAAGAATAATGCAT
66 AAGGCAATGAATAAATAAAGAATAATGCAT
3668388 NTTTGTTATATATATATATATATAGAGAGAGAGAGAGAGAGAAAGAGGCAATCGTGACAAATATT
1 -TTTG-TATATATATATATATATAGAGAGAGAGAGAGAGAGAAAGAGGCAATCGTGACAAATATT
3668453 TTAAGGCAATGAATAAATAAAGAATAATGCAT
64 TTAAGGCAATGAATAAATAAAGAATAATGCAT
3668485 CAGTTGAATG
Statistics
Matches: 95, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
96 4 0.04
97 91 0.96
ACGTcount: A:0.47, C:0.05, G:0.21, T:0.27
Consensus pattern (95 bp):
TTTGTATATATATATATATATAGAGAGAGAGAGAGAGAGAAAGAGGCAATCGTGACAAATATTTT
AAGGCAATGAATAAATAAAGAATAATGCAT
Found at i:3668704 original size:28 final size:28
Alignment explanation
Indices: 3668645--3668705 Score: 86
Period size: 28 Copynumber: 2.2 Consensus size: 28
3668635 ATTTAATTAT
* * * *
3668645 TTATTTTTTTAGTTATTTTAGAGATTAT
1 TTATTTTTTTAATTATTTTAAAGAATAG
3668673 TTATTTTTTTAATTATTTTAAAGAATAG
1 TTATTTTTTTAATTATTTTAAAGAATAG
3668701 TTATT
1 TTATT
3668706 GTGACAGAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.30, C:0.00, G:0.08, T:0.62
Consensus pattern (28 bp):
TTATTTTTTTAATTATTTTAAAGAATAG
Found at i:3671888 original size:14 final size:14
Alignment explanation
Indices: 3671871--3671926 Score: 51
Period size: 14 Copynumber: 4.1 Consensus size: 14
3671861 AAAATATTAA
*
3671871 TAATTTTTTAATTT
1 TAATTTTATAATTT
* *
3671885 TAA-TTTAAAATAT
1 TAATTTTATAATTT
*
3671898 TAATTTTATAAGTT
1 TAATTTTATAATTT
* *
3671912 TAAGTTTGTAATTT
1 TAATTTTATAATTT
3671926 T
1 T
3671927 TAAAAATAAA
Statistics
Matches: 32, Mismatches: 9, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
13 10 0.31
14 22 0.69
ACGTcount: A:0.36, C:0.00, G:0.05, T:0.59
Consensus pattern (14 bp):
TAATTTTATAATTT
Found at i:3701712 original size:2 final size:2
Alignment explanation
Indices: 3701701--3701729 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
3701691 AGAACTGATA
3701701 AT AT -T 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
3701730 TCGAAGTGCA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:3705009 original size:11 final size:11
Alignment explanation
Indices: 3704983--3705017 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
3704973 TCAAAAATAG
*
3704983 AATATTATAGAA
1 AATATT-TAAAA
3704995 AATATTTAAAA
1 AATATTTAAAA
3705006 AATATTTAAAA
1 AATATTTAAAA
3705017 A
1 A
3705018 GATGAGAGAC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
11 16 0.73
12 6 0.27
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (11 bp):
AATATTTAAAA
Found at i:3734975 original size:2 final size:2
Alignment explanation
Indices: 3734968--3735009 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
3734958 AATAAACTAG
3734968 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
3735010 TATTTTTCAT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3738823 original size:19 final size:18
Alignment explanation
Indices: 3738793--3738829 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
3738783 CTGCTCTTTA
*
3738793 AATTAAAAATTATATACT
1 AATTAAAAATTAAATACT
3738811 AATTAATAAATTAAATACT
1 AATTAA-AAATTAAATACT
3738830 CAGATATCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.38
Consensus pattern (18 bp):
AATTAAAAATTAAATACT
Found at i:3740736 original size:3 final size:3
Alignment explanation
Indices: 3740728--3740752 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
3740718 TATGGGTGCA
3740728 TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT T
3740753 TGGCTTAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:3765918 original size:14 final size:14
Alignment explanation
Indices: 3765899--3765934 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
3765889 CAGCTAAAAA
*
3765899 TGTGCATGCCTGTG
1 TGTGCATGCCTGTC
*
3765913 TGTGCATGCGTGTC
1 TGTGCATGCCTGTC
3765927 TGTGCATG
1 TGTGCATG
3765935 TGTGAGTGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.08, C:0.19, G:0.36, T:0.36
Consensus pattern (14 bp):
TGTGCATGCCTGTC
Found at i:3765980 original size:2 final size:2
Alignment explanation
Indices: 3765970--3765999 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
3765960 GTGTGTGTGT
*
3765970 GA GA AA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
3766000 TCTCAAGCTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00
Consensus pattern (2 bp):
GA
Found at i:3778117 original size:32 final size:33
Alignment explanation
Indices: 3778059--3778122 Score: 78
Period size: 32 Copynumber: 2.0 Consensus size: 33
3778049 AAAAGAAGCA
*
3778059 AAATTAAAACGTCCATATATATATAAA-AAATT
1 AAATTAAAACGTACATATATATATAAATAAATT
* *
3778091 AAATTAAATCGTACATA-ATTTCATAAATAAAT
1 AAATTAAAACGTACATATATAT-ATAAATAAAT
3778123 AAAGATAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
31 3 0.11
32 20 0.74
33 4 0.15
ACGTcount: A:0.55, C:0.09, G:0.03, T:0.33
Consensus pattern (33 bp):
AAATTAAAACGTACATATATATATAAATAAATT
Found at i:3786889 original size:18 final size:18
Alignment explanation
Indices: 3786847--3786889 Score: 54
Period size: 16 Copynumber: 2.5 Consensus size: 18
3786837 AATTATAAAA
*
3786847 ATAATTATATTATATTAT
1 ATAATTATATTAAATTAT
*
3786865 AT-A-TATATTAAATTTT
1 ATAATTATATTAAATTAT
3786881 ATAATTATA
1 ATAATTATA
3786890 ATAATATAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 4
0.78 0.07 0.15
Matches are distributed among these distances:
16 13 0.62
17 2 0.10
18 6 0.29
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
ATAATTATATTAAATTAT
Found at i:3786896 original size:26 final size:24
Alignment explanation
Indices: 3786836--3786897 Score: 60
Period size: 23 Copynumber: 2.7 Consensus size: 24
3786826 GATTAAAATG
*
3786836 TAATTATAAAAATA-ATTATATTA
1 TAATTATAATAATATATTATATTA
*
3786859 T-ATTAT-AT-ATATATTAAATTTTA
1 TAATTATAATAATATATT--ATATTA
3786882 TAATTATAATAATATA
1 TAATTATAATAATATA
3786898 GAAAATTAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 9
0.74 0.05 0.21
Matches are distributed among these distances:
20 3 0.10
21 4 0.13
22 5 0.16
23 7 0.23
24 5 0.16
25 2 0.06
26 5 0.16
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (24 bp):
TAATTATAATAATATATTATATTA
Found at i:3800064 original size:2 final size:2
Alignment explanation
Indices: 3800057--3800097 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
3800047 TACAACCCTA
3800057 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C- CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
3800098 TTTTCTATGG
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 37 0.97
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:3805504 original size:3 final size:3
Alignment explanation
Indices: 3805496--3805523 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
3805486 GTGAGCGACT
3805496 ATG ATG ATG ATG ATG ATG ATG ATG ATG A
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG A
3805524 CGACGACGAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.36, C:0.00, G:0.32, T:0.32
Consensus pattern (3 bp):
ATG
Found at i:3817026 original size:17 final size:16
Alignment explanation
Indices: 3816965--3817028 Score: 60
Period size: 18 Copynumber: 3.9 Consensus size: 16
3816955 GTCAAAAAAA
3816965 ATAAATTAATAATTTT
1 ATAAATTAATAATTTT
*
3816981 AGTTAATTTAATAATTTT
1 A--TAAATTAATAATTTT
* *
3816999 ATATATT--TAATTAT
1 ATAAATTAATAATTTT
3817013 ATAAAATTAATAATTT
1 AT-AAATTAATAATTT
3817029 AGTTACCAAT
Statistics
Matches: 37, Mismatches: 6, Indels: 9
0.71 0.12 0.17
Matches are distributed among these distances:
14 8 0.22
15 4 0.11
16 5 0.14
17 5 0.14
18 15 0.41
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.52
Consensus pattern (16 bp):
ATAAATTAATAATTTT
Found at i:3817356 original size:28 final size:28
Alignment explanation
Indices: 3817325--3817384 Score: 86
Period size: 28 Copynumber: 2.1 Consensus size: 28
3817315 AATTGAAATT
3817325 TTATTTATGTTT-GATATAATTTATTTAC
1 TTATTTATGTTTAG-TATAATTTATTTAC
* *
3817353 TTATTTATGTTTAGTGTAATTTATTTAT
1 TTATTTATGTTTAGTATAATTTATTTAC
3817381 TTAT
1 TTAT
3817385 AATATATTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
28 28 0.97
29 1 0.03
ACGTcount: A:0.27, C:0.02, G:0.08, T:0.63
Consensus pattern (28 bp):
TTATTTATGTTTAGTATAATTTATTTAC
Found at i:3826054 original size:23 final size:23
Alignment explanation
Indices: 3825990--3826079 Score: 65
Period size: 23 Copynumber: 3.7 Consensus size: 23
3825980 TTTGTAAAAT
* *
3825990 TTAAAATATTAATATTTTATATATAA
1 TTAAACTATTAATA--TTATAT-TGA
3826016 TTTAAACATAATTAATATTA-ATATGA
1 -TTAAAC-T-ATTAATATTATAT-TGA
* *
3826042 TTAAACTATTAATATTTTATTTA
1 TTAAACTATTAATATTATATTGA
*
3826065 TTAAATTATTAATAT
1 TTAAACTATTAATAT
3826080 ATTAAAATTT
Statistics
Matches: 55, Mismatches: 5, Indels: 10
0.79 0.07 0.14
Matches are distributed among these distances:
23 25 0.45
24 3 0.05
25 6 0.11
26 5 0.09
27 8 0.15
28 1 0.02
29 7 0.13
ACGTcount: A:0.47, C:0.02, G:0.01, T:0.50
Consensus pattern (23 bp):
TTAAACTATTAATATTATATTGA
Found at i:3826083 original size:31 final size:32
Alignment explanation
Indices: 3826031--3826091 Score: 81
Period size: 31 Copynumber: 1.9 Consensus size: 32
3826021 ACATAATTAA
*
3826031 TATTAATATGATTAAACTATTAATATTTTATT
1 TATTAATATGATTAAACTATTAAAATTTTATT
*
3826063 TATTAA-ATTATTAATA-TATTAAAATTTTA
1 TATTAATATGATTAA-ACTATTAAAATTTTA
3826092 ATGAGTATAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
31 19 0.73
32 7 0.27
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52
Consensus pattern (32 bp):
TATTAATATGATTAAACTATTAAAATTTTATT
Found at i:3826092 original size:16 final size:16
Alignment explanation
Indices: 3826048--3826093 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
3826038 ATGATTAAAC
* *
3826048 TATTAATATTTT-ATT
1 TATTAAAATTTTAATA
3826063 TATT-AAATTATTAATA
1 TATTAAAATT-TTAATA
3826079 TATTAAAATTTTAAT
1 TATTAAAATTTTAAT
3826094 GAGTATAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
14 4 0.15
15 6 0.23
16 11 0.42
17 5 0.19
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (16 bp):
TATTAAAATTTTAATA
Found at i:3826211 original size:25 final size:25
Alignment explanation
Indices: 3826167--3826214 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
3826157 GATTATTAAT
3826167 TAAAATATTAATAATCAAATTATAC
1 TAAAATATTAATAATCAAATTATAC
* * *
3826192 TAAAATATTGATATTTAAATTAT
1 TAAAATATTAATAATCAAATTAT
3826215 TAATTATTAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.52, C:0.04, G:0.02, T:0.42
Consensus pattern (25 bp):
TAAAATATTAATAATCAAATTATAC
Found at i:3826421 original size:5 final size:5
Alignment explanation
Indices: 3826413--3826455 Score: 61
Period size: 5 Copynumber: 8.4 Consensus size: 5
3826403 TTATATAATA
3826413 TTTAT TTTAT TTTATT TTTAT TTTAT TTTAT TTT-T ATTTAT TT
1 TTTAT TTTAT TTTA-T TTTAT TTTAT TTTAT TTTAT -TTTAT TT
3826456 CACGAATTAA
Statistics
Matches: 35, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
4 1 0.03
5 28 0.80
6 6 0.17
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTAT
Found at i:3826432 original size:16 final size:16
Alignment explanation
Indices: 3826413--3826455 Score: 79
Period size: 16 Copynumber: 2.8 Consensus size: 16
3826403 TTATATAATA
3826413 TTTATTTTATTTTATT
1 TTTATTTTATTTTATT
3826429 TTTATTTTATTTTATT
1 TTTATTTTATTTTATT
3826445 TTTA-TTTATTT
1 TTTATTTTATTT
3826456 CACGAATTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 7 0.26
16 20 0.74
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (16 bp):
TTTATTTTATTTTATT
Found at i:3836219 original size:2 final size:2
Alignment explanation
Indices: 3836212--3836248 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
3836202 TCATGTCTAG
3836212 TA TA TA TA TA TA 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 TA TA TA TA TA TA T
3836249 TTTAAAGGCA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3846620 original size:6 final size:6
Alignment explanation
Indices: 3846609--3846643 Score: 54
Period size: 6 Copynumber: 6.0 Consensus size: 6
3846599 GGAGCCAGGC
*
3846609 AAATAT AAATAT AAATAT ATATAT -AATAT AAATAT
1 AAATAT AAATAT AAATAT AAATAT AAATAT AAATAT
3846644 TTTTCTATAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
5 4 0.15
6 22 0.85
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (6 bp):
AAATAT
Found at i:3868573 original size:2 final size:2
Alignment explanation
Indices: 3868562--3868594 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
3868552 GTAAGGAGAT
3868562 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3868595 ATGTTGCATG
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:3869949 original size:24 final size:24
Alignment explanation
Indices: 3869899--3869949 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
3869889 GTTACACGCT
* * *
3869899 ATGTACAAAAATATGTGACACGTC
1 ATGTACAAAAACATGTGACAAGCC
*
3869923 ATGTACAAAAACCTGTGACAAGCC
1 ATGTACAAAAACATGTGACAAGCC
3869947 ATG
1 ATG
3869950 ATTAGCGTGT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.41, C:0.20, G:0.18, T:0.22
Consensus pattern (24 bp):
ATGTACAAAAACATGTGACAAGCC
Found at i:3869959 original size:69 final size:69
Alignment explanation
Indices: 3869842--3870063 Score: 266
Period size: 69 Copynumber: 3.2 Consensus size: 69
3869832 ACACGCTATG
* * * *
3869842 ATGTTACACGTCATGTATAAAAACCTGTGACAAACCATGGTTAACGTGTTACACGCTATGTACAA
1 ATGTGACAAGTCATGTATAAAAACCTGTGACAAGCCATGGTTAGCGTGTTACACGCTATGTACAA
3869907 AAAT
66 AAAT
* * * * * *
3869911 ATGTGACACGTCATGTACAAAAACCTGTGACAAGCCATGATTAGCGTGTTGCACG-TCAAGTATA
1 ATGTGACAAGTCATGTATAAAAACCTGTGACAAGCCATGGTTAGCGTGTTACACGCT-ATGTACA
*
3869975 AAAAC
65 AAAAT
* * * * * *
3869980 ATGTGACAAGCCAAGTATAAAAACTTGTGACAAGCTATGGTTAGCTTGTTACACGCCATGTACAA
1 ATGTGACAAGTCATGTATAAAAACCTGTGACAAGCCATGGTTAGCGTGTTACACGCTATGTACAA
3870045 AAAT
66 AAAT
*
3870049 CTGTGACAAGTCATG
1 ATGTGACAAGTCATG
3870064 GTTAGGTTGT
Statistics
Matches: 126, Mismatches: 25, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
68 1 0.01
69 125 0.99
ACGTcount: A:0.36, C:0.19, G:0.19, T:0.26
Consensus pattern (69 bp):
ATGTGACAAGTCATGTATAAAAACCTGTGACAAGCCATGGTTAGCGTGTTACACGCTATGTACAA
AAAT
Found at i:3869994 original size:24 final size:24
Alignment explanation
Indices: 3869967--3870014 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
3869957 TGTTGCACGT
3869967 CAAGTATAAAAACATGTGACAAGC
1 CAAGTATAAAAACATGTGACAAGC
*
3869991 CAAGTATAAAAACTTGTGACAAGC
1 CAAGTATAAAAACATGTGACAAGC
3870015 TATGGTTAGC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.48, C:0.17, G:0.17, T:0.19
Consensus pattern (24 bp):
CAAGTATAAAAACATGTGACAAGC
Found at i:3870138 original size:24 final size:25
Alignment explanation
Indices: 3870102--3870175 Score: 78
Period size: 26 Copynumber: 2.9 Consensus size: 25
3870092 AAAATACTGT
*
3870102 TGTTACACTCCATGTAAAAAAAT-A
1 TGTTACACGCCATGTAAAAAAATGA
* *
3870126 TGTTACACGCCATGGTTAAAAAATGT
1 TGTTACACGCCAT-GTAAAAAAATGA
*
3870152 TATTACACGCCATGTTGAAAAAAA
1 TGTTACACGCCATG-T-AAAAAAA
3870176 AATATTATTG
Statistics
Matches: 41, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
24 12 0.29
25 10 0.24
26 13 0.32
27 6 0.15
ACGTcount: A:0.42, C:0.16, G:0.14, T:0.28
Consensus pattern (25 bp):
TGTTACACGCCATGTAAAAAAATGA
Found at i:3870145 original size:26 final size:26
Alignment explanation
Indices: 3870102--3870207 Score: 83
Period size: 32 Copynumber: 3.9 Consensus size: 26
3870092 AAAATACTGT
*
3870102 TGTTACACTCCATG-TAAAAAAAT-A
1 TGTTACACGCCATGTTAAAAAAATGA
*
3870126 TGTTACACGCCATGGTT-AAAAAATGT
1 TGTTACACGCCAT-GTTAAAAAAATGA
* *
3870152 TATTACACGCCATGTTGAAAAAAAAATATTA
1 TGTTACACGCCATGTT----AAAAAA-ATGA
*
3870183 TTGTTACACGACATGTTAAAAAAAT
1 -TGTTACACGCCATGTTAAAAAAAT
3870208 ATTGTTGTTA
Statistics
Matches: 65, Mismatches: 7, Indels: 17
0.73 0.08 0.19
Matches are distributed among these distances:
24 12 0.18
25 11 0.17
26 13 0.20
27 2 0.03
28 6 0.09
30 5 0.08
31 2 0.03
32 14 0.22
ACGTcount: A:0.43, C:0.14, G:0.12, T:0.30
Consensus pattern (26 bp):
TGTTACACGCCATGTTAAAAAAATGA
Found at i:3870203 original size:29 final size:28
Alignment explanation
Indices: 3870090--3870247 Score: 107
Period size: 29 Copynumber: 5.7 Consensus size: 28
3870080 TCATGTTGAA
* * **
3870090 AAAAAATACTGTTGTTACACTCCATG-T
1 AAAAAATATTATTGTTACACGACATGTT
*
3870117 AAAAAA-A-TA-TGTTACACGCCATGGTT
1 AAAAAATATTATTGTTACACGACAT-GTT
* *
3870143 AAAAAATGTTA---TTACACGCCATGTT
1 AAAAAATATTATTGTTACACGACATGTT
3870168 GAAAAAAAAATATTATTGTTACACGACATGTT
1 ----AAAAAATATTATTGTTACACGACATGTT
* *
3870200 AAAAAAATATTGTTGTTACACGACATATT
1 -AAAAAATATTATTGTTACACGACATGTT
* *
3870229 CAAAAACATT-TTGTTACAC
1 AAAAAATATTATTGTTACAC
3870248 TTTAATGCCT
Statistics
Matches: 111, Mismatches: 9, Indels: 22
0.78 0.06 0.15
Matches are distributed among these distances:
24 12 0.11
25 5 0.05
26 19 0.17
27 15 0.14
28 10 0.09
29 37 0.33
32 13 0.12
ACGTcount: A:0.42, C:0.15, G:0.11, T:0.32
Consensus pattern (28 bp):
AAAAAATATTATTGTTACACGACATGTT
Found at i:3870210 original size:26 final size:27
Alignment explanation
Indices: 3870070--3870247 Score: 98
Period size: 29 Copynumber: 6.3 Consensus size: 27
3870060 CATGGTTAGG
3870070 TTGTTACAC-ATCATGTTGAAAAAAAATA
1 TTGTTACACGA-CATGTT-AAAAAAAATA
**
3870098 CTGTTGTTACACTCCATG-T-AAAAAAATA
1 ---TTGTTACACGACATGTTAAAAAAAATA
* *
3870126 -TGTTACACGCCATGGTT--AAAAAATG
1 TTGTTACACGACAT-GTTAAAAAAAATA
* *
3870151 TTATTACACGCCATGTTGAAAAAAAAATATTA
1 TTGTTACACGACATGTT---AAAAAAA-A-TA
*
3870183 TTGTTACACGACATGTTAAAAAAATATTG
1 TTGTTACACGACATGTTAAAAAAA-A-TA
* * * *
3870212 TTGTTACACGACATATTCAAAAACATT
1 TTGTTACACGACATGTTAAAAAAAATA
3870239 TTGTTACAC
1 TTGTTACAC
3870248 TTTAATGCCT
Statistics
Matches: 124, Mismatches: 12, Indels: 26
0.77 0.07 0.16
Matches are distributed among these distances:
24 12 0.10
25 11 0.09
26 13 0.10
27 10 0.08
28 10 0.08
29 32 0.26
30 6 0.05
31 14 0.11
32 16 0.13
ACGTcount: A:0.41, C:0.15, G:0.12, T:0.33
Consensus pattern (27 bp):
TTGTTACACGACATGTTAAAAAAAATA
Found at i:3879690 original size:2 final size:2
Alignment explanation
Indices: 3879685--3879780 Score: 72
Period size: 2 Copynumber: 48.0 Consensus size: 2
3879675 ACATTCTATT
3879685 TA TA TA TA TA TA T- TA TA TA TA TA TA TA TA TA TA T- TA TA T-
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * * * *
3879724 TA TA TT TA CCA GTA TC TA AA TA TA NTA TA TA TA TA TA TT TA CA
1 TA TA TA TA -TA -TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA
* *
3879767 CA CA TA TA TA TA TA
1 TA TA TA TA TA TA TA
3879781 GTATGCAAGT
Statistics
Matches: 76, Mismatches: 13, Indels: 10
0.77 0.13 0.10
Matches are distributed among these distances:
1 3 0.04
2 69 0.91
3 4 0.05
ACGTcount: A:0.45, C:0.06, G:0.01, T:0.47
Consensus pattern (2 bp):
TA
Found at i:3889190 original size:18 final size:18
Alignment explanation
Indices: 3889157--3889191 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
3889147 TAAGAGAGGG
3889157 AAGAGAAATGGATGCAAA
1 AAGAGAAATGGATGCAAA
3889175 AAGACGAAATGG-TGCAA
1 AAGA-GAAATGGATGCAA
3889192 CTTTAACAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.51, C:0.09, G:0.29, T:0.11
Consensus pattern (18 bp):
AAGAGAAATGGATGCAAA
Found at i:3889730 original size:45 final size:45
Alignment explanation
Indices: 3889679--3889827 Score: 190
Period size: 45 Copynumber: 3.3 Consensus size: 45
3889669 ACGTTTTGAC
* * *
3889679 GTTACACGCCATATACAAAAATATGTTACACGCCATGATTAGGTT
1 GTTACACGCCATGTACAAAAACATGTGACACGCCATGATTAGGTT
* * *
3889724 ATTACACGTCATGTACAAAAACATGTGACACGTCATGATTAGGTT
1 GTTACACGCCATGTACAAAAACATGTGACACGCCATGATTAGGTT
* * * * *
3889769 GTTACACACCATGTACAGAAACATGTGACACTCCATGGTTAAGTT
1 GTTACACGCCATGTACAAAAACATGTGACACGCCATGATTAGGTT
*
3889814 GTTACACGTCATGT
1 GTTACACGCCATGT
3889828 TGAAATAATA
Statistics
Matches: 88, Mismatches: 16, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
45 88 1.00
ACGTcount: A:0.34, C:0.20, G:0.17, T:0.29
Consensus pattern (45 bp):
GTTACACGCCATGTACAAAAACATGTGACACGCCATGATTAGGTT
Found at i:3889941 original size:29 final size:29
Alignment explanation
Indices: 3889891--3889950 Score: 68
Period size: 29 Copynumber: 2.1 Consensus size: 29
3889881 TTAAAAAATG
*
3889891 TTGTTACACACCATGTTAAAAAA-ATATTA
1 TTGTTACACACCATATTAAAAAACAT-TTA
** *
3889920 TTGTTACACGTCATATTCAAAAACATTTA
1 TTGTTACACACCATATTAAAAAACATTTA
3889949 TT
1 TT
3889951 ACACTTTAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
29 24 0.92
30 2 0.08
ACGTcount: A:0.40, C:0.15, G:0.07, T:0.38
Consensus pattern (29 bp):
TTGTTACACACCATATTAAAAAACATTTA
Found at i:3908421 original size:18 final size:16
Alignment explanation
Indices: 3908398--3908432 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
3908388 TACAGCTACG
3908398 TTTTGTGTTTATATTTTT
1 TTTTGT-TTTA-ATTTTT
3908416 TTTTGTTTTAATTTTT
1 TTTTGTTTTAATTTTT
3908432 T
1 T
3908433 CAATATAACG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.41
17 4 0.24
18 6 0.35
ACGTcount: A:0.11, C:0.00, G:0.09, T:0.80
Consensus pattern (16 bp):
TTTTGTTTTAATTTTT
Found at i:3914055 original size:17 final size:18
Alignment explanation
Indices: 3914028--3914061 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
3914018 TATTTTTTAT
3914028 TATTTTATTATATTTAAA
1 TATTTTATTATATTTAAA
*
3914046 TATTTT-TTATTTTTAA
1 TATTTTATTATATTTAA
3914062 TTAAATAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (18 bp):
TATTTTATTATATTTAAA
Found at i:3914105 original size:22 final size:20
Alignment explanation
Indices: 3914075--3914121 Score: 58
Period size: 22 Copynumber: 2.2 Consensus size: 20
3914065 AATAATTTTT
* *
3914075 TTATAAATTAATATAAAATTAA
1 TTATTAATTAAT-TAAAAAT-A
3914097 TTATTAATTAATTAAAAATA
1 TTATTAATTAATTAAAAATA
3914117 TTATT
1 TTATT
3914122 TTTTATATTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 6 0.26
21 6 0.26
22 11 0.48
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (20 bp):
TTATTAATTAATTAAAAATA
Found at i:3914274 original size:14 final size:14
Alignment explanation
Indices: 3914255--3914281 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
3914245 CAAGTAATAT
3914255 TTTAATTAATAGTA
1 TTTAATTAATAGTA
3914269 TTTAATTAATAGT
1 TTTAATTAATAGT
3914282 TGATCATTAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.52
Consensus pattern (14 bp):
TTTAATTAATAGTA
Found at i:3931207 original size:3 final size:3
Alignment explanation
Indices: 3931194--3931235 Score: 50
Period size: 3 Copynumber: 14.3 Consensus size: 3
3931184 AACTCGACGA
* * *
3931194 TCT TC- TCT TCT TCT TCT TCT TCT TCT GCT TCC GCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
3931236 GTTATTGTTG
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
2 2 0.06
3 30 0.94
ACGTcount: A:0.00, C:0.36, G:0.05, T:0.60
Consensus pattern (3 bp):
TCT
Found at i:3933436 original size:21 final size:22
Alignment explanation
Indices: 3933394--3933440 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
3933384 TATTAATTAT
* *
3933394 AAAATTTATTTAAATTAAAATA
1 AAAATTTAATCAAATTAAAATA
*
3933416 AAAATTTAATCAAA-TATAATA
1 AAAATTTAATCAAATTAAAATA
3933437 AAAA
1 AAAA
3933441 AAGTAAAATT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 10 0.45
22 12 0.55
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (22 bp):
AAAATTTAATCAAATTAAAATA
Found at i:3946258 original size:2 final size:2
Alignment explanation
Indices: 3946251--3946280 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
3946241 AAAGTGTATG
3946251 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3946281 ATAAAAAAAA
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:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3946324 original size:2 final size:2
Alignment explanation
Indices: 3946312--3946348 Score: 65
Period size: 2 Copynumber: 18.0 Consensus size: 2
3946302 ACCAACTAAG
3946312 TA TA GTA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3946349 AATAAAAAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 32 0.94
3 2 0.06
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
TA
Found at i:3950218 original size:27 final size:25
Alignment explanation
Indices: 3950176--3950227 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 25
3950166 GATTTTAAAA
*
3950176 TTTAAAAAAATGAATTAATTAAATT
1 TTTAAAAAAATAAATTAATTAAATT
*
3950201 TTTAAAAAAATTAAAATTAATTGAATT
1 TTTAAAAAAA-T-AAATTAATTAAATT
3950228 ATAATAAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
25 10 0.43
26 1 0.04
27 12 0.52
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.40
Consensus pattern (25 bp):
TTTAAAAAAATAAATTAATTAAATT
Done.