Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A11
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: 114316535
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 4920000 characters in sequence are not A, C, G, or T
File 29 of 356
Found at i:9819749 original size:28 final size:29
Alignment explanation
Indices: 9819717--9819829 Score: 176
Period size: 29 Copynumber: 4.0 Consensus size: 29
9819707 AACACACCAG
** *
9819717 TATAATCC-TCCAAAACACACCAGTGTCA
1 TATAATCCATCCAAAACACACCAGAATAA
*
9819745 TATAATCC-TCCCAAACACACCAGAATAA
1 TATAATCCATCCAAAACACACCAGAATAA
9819773 TATAATCCATCCAAAACACACCAGAATAA
1 TATAATCCATCCAAAACACACCAGAATAA
9819802 TATAATCCATCCAAAACACACCAGAATA
1 TATAATCCATCCAAAACACACCAGAATA
9819830 GCACAAAGTG
Statistics
Matches: 79, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
28 32 0.41
29 47 0.59
ACGTcount: A:0.47, C:0.30, G:0.04, T:0.19
Consensus pattern (29 bp):
TATAATCCATCCAAAACACACCAGAATAA
Found at i:9819789 original size:57 final size:57
Alignment explanation
Indices: 9819717--9819829 Score: 174
Period size: 57 Copynumber: 2.0 Consensus size: 57
9819707 AACACACCAG
** * *
9819717 TATAATCCTCCAAAACACACCAGTGTCATATAATCC-TCCCAAACACACCAGAATAA
1 TATAATCCTCCAAAACACACCAGAATAATATAATCCATCCAAAACACACCAGAATAA
9819773 TATAATCCATCCAAAACACACCAGAATAATATAATCCATCCAAAACACACCAGAATA
1 TATAATCC-TCCAAAACACACCAGAATAATATAATCCATCCAAAACACACCAGAATA
9819830 GCACAAAGTG
Statistics
Matches: 51, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
56 8 0.16
57 25 0.49
58 18 0.35
ACGTcount: A:0.47, C:0.30, G:0.04, T:0.19
Consensus pattern (57 bp):
TATAATCCTCCAAAACACACCAGAATAATATAATCCATCCAAAACACACCAGAATAA
Found at i:9822864 original size:40 final size:38
Alignment explanation
Indices: 9822798--9822930 Score: 92
Period size: 40 Copynumber: 3.4 Consensus size: 38
9822788 TAGAATGGCA
* * *
9822798 CCCAGTGCCTCATCGGATAGTTCGAAGCAATATAGTGAC
1 CCCAGTGCCTCATCGGCTAG-CCGAAGAAATATAGTGAC
* * *
9822837 GCCCAGTGTCTCATCGGCCTAGCCGAAGTAAA-GTGGT-A-
1 -CCCAGTGCCTCATCGG-CTAGCCGAAG-AAATATAGTGAC
* * *
9822875 CCCAGTACCTCATCGAATCTATCCGAAGAAATATAGTGAC
1 CCCAGTGCCTCATCG--GCTAGCCGAAGAAATATAGTGAC
*
9822915 ACCCAGTGTCTCATCG
1 -CCCAGTGCCTCATCG
9822931 ACTCGAGGTT
Statistics
Matches: 71, Mismatches: 14, Indels: 15
0.71 0.14 0.15
Matches are distributed among these distances:
37 16 0.23
38 12 0.17
39 2 0.03
40 23 0.32
41 18 0.25
ACGTcount: A:0.28, C:0.28, G:0.22, T:0.23
Consensus pattern (38 bp):
CCCAGTGCCTCATCGGCTAGCCGAAGAAATATAGTGAC
Found at i:9823850 original size:20 final size:21
Alignment explanation
Indices: 9823827--9823871 Score: 74
Period size: 20 Copynumber: 2.2 Consensus size: 21
9823817 AATTATTTAT
*
9823827 TTAATAAATATCT-TTTATAA
1 TTAATAAATATCTATTAATAA
9823847 TTAATAAATATCTATTAATAA
1 TTAATAAATATCTATTAATAA
9823868 TTAA
1 TTAA
9823872 ATACATATAT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 13 0.57
21 10 0.43
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (21 bp):
TTAATAAATATCTATTAATAA
Found at i:9824426 original size:28 final size:29
Alignment explanation
Indices: 9824377--9824440 Score: 71
Period size: 28 Copynumber: 2.3 Consensus size: 29
9824367 TTATAATATA
* *
9824377 ATTA-TAATAAATTAATTTAATATCA-TTT
1 ATTATTAATAAATTAAATAAATAT-ATTTT
9824405 ATTATTAATAAA-TAAATAAATATATTTT
1 ATTATTAATAAATTAAATAAATATATTTT
*
9824433 ATAATTAA
1 ATTATTAA
9824441 AATCTAAGTA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
27 1 0.03
28 23 0.74
29 7 0.23
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.47
Consensus pattern (29 bp):
ATTATTAATAAATTAAATAAATATATTTT
Found at i:9827167 original size:24 final size:22
Alignment explanation
Indices: 9827144--9827186 Score: 68
Period size: 23 Copynumber: 1.9 Consensus size: 22
9827134 TTTATAATAT
9827144 TTCGGGTGTGTTTGGGCTGGATA
1 TTCGGGTGTGTTTGGG-TGGATA
*
9827167 TTCTGGTGTGTTTGGGTGGA
1 TTCGGGTGTGTTTGGGTGGA
9827187 ATCCGCGTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 4 0.21
23 15 0.79
ACGTcount: A:0.07, C:0.07, G:0.44, T:0.42
Consensus pattern (22 bp):
TTCGGGTGTGTTTGGGTGGATA
Found at i:9833061 original size:21 final size:22
Alignment explanation
Indices: 9833037--9833085 Score: 59
Period size: 21 Copynumber: 2.3 Consensus size: 22
9833027 CTAGATTTAT
9833037 TTTTTATTTCATT-TTTTCAA-G
1 TTTTTATTT-ATTATTTTCAATG
9833058 TTTTT-TTTATTAATTTTCAATG
1 TTTTTATTTATT-ATTTTCAATG
9833080 TTTTTA
1 TTTTTA
9833086 ATTAATAAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
19 3 0.12
20 3 0.12
21 12 0.50
22 6 0.25
ACGTcount: A:0.20, C:0.06, G:0.04, T:0.69
Consensus pattern (22 bp):
TTTTTATTTATTATTTTCAATG
Found at i:9833089 original size:20 final size:21
Alignment explanation
Indices: 9833050--9833091 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
9833040 TTATTTCATT
* *
9833050 TTTTCAAGTTTTTTTTATTAA
1 TTTTCAAGTGTTTTTAATTAA
9833071 TTTTCAA-TGTTTTTAATTAA
1 TTTTCAAGTGTTTTTAATTAA
9833091 T
1 T
9833092 AAACATGTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 12 0.63
21 7 0.37
ACGTcount: A:0.26, C:0.05, G:0.05, T:0.64
Consensus pattern (21 bp):
TTTTCAAGTGTTTTTAATTAA
Found at i:9838531 original size:65 final size:66
Alignment explanation
Indices: 9838462--9838590 Score: 165
Period size: 66 Copynumber: 2.0 Consensus size: 66
9838452 TGGTACAGGT
* **
9838462 TGAAAAGGTTATGTACACTTTGTGTGTATA-C-TTGGA-AAGGTTAGGTATACTTTGTGTATACC
1 TGAAAAGGTTAGGTACAC-TT-TGTGTATACCATTGGACAAGGAAAGGTATACTTTGTGTATACC
9838524 ATA
64 ATA
* * *
9838527 TGAAAAGGTTAGGTATACTTTGTGTATACCATTTGACAAGGAAAGGTATACTTTGTGTGTACCA
1 TGAAAAGGTTAGGTACACTTTGTGTATACCATTGGACAAGGAAAGGTATACTTTGTGTATACCA
9838591 CTCGGAAAGA
Statistics
Matches: 55, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
63 8 0.15
64 3 0.05
65 20 0.36
66 24 0.44
ACGTcount: A:0.30, C:0.10, G:0.23, T:0.36
Consensus pattern (66 bp):
TGAAAAGGTTAGGTACACTTTGTGTATACCATTGGACAAGGAAAGGTATACTTTGTGTATACCAT
A
Found at i:9838538 original size:33 final size:32
Alignment explanation
Indices: 9838461--9838590 Score: 147
Period size: 33 Copynumber: 4.0 Consensus size: 32
9838451 ATGGTACAGG
* *
9838461 TTGAAAAGGTTATGTACACTTTGTGTGTATA-C-
1 TTGAAAAGGTTAGGTATAC-TT-TGTGTATACCA
*
9838493 TTGGAAAGGTTAGGTATACTTTGTGTATACCA
1 TTGAAAAGGTTAGGTATACTTTGTGTATACCA
9838525 TATGAAAAGGTTAGGTATACTTTGTGTATACCA
1 T-TGAAAAGGTTAGGTATACTTTGTGTATACCA
* ** *
9838558 TTTGACAAGGAAAGGTATACTTTGTGTGTACCA
1 -TTGAAAAGGTTAGGTATACTTTGTGTATACCA
9838591 CTCGGAAAGA
Statistics
Matches: 86, Mismatches: 8, Indels: 7
0.85 0.08 0.07
Matches are distributed among these distances:
30 8 0.09
31 3 0.03
32 17 0.20
33 57 0.66
34 1 0.01
ACGTcount: A:0.30, C:0.10, G:0.23, T:0.37
Consensus pattern (32 bp):
TTGAAAAGGTTAGGTATACTTTGTGTATACCA
Found at i:9850866 original size:19 final size:19
Alignment explanation
Indices: 9850842--9850883 Score: 84
Period size: 19 Copynumber: 2.2 Consensus size: 19
9850832 CCTAGCTATA
9850842 CGCTCAAGCGCACTTTATC
1 CGCTCAAGCGCACTTTATC
9850861 CGCTCAAGCGCACTTTATC
1 CGCTCAAGCGCACTTTATC
9850880 CGCT
1 CGCT
9850884 TATTTAAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.19, C:0.38, G:0.17, T:0.26
Consensus pattern (19 bp):
CGCTCAAGCGCACTTTATC
Found at i:9854609 original size:2 final size:2
Alignment explanation
Indices: 9854596--9854642 Score: 76
Period size: 2 Copynumber: 23.5 Consensus size: 2
9854586 TCATAAATTA
* *
9854596 AG AG AG AC AG AG AG AT AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
9854638 AG AG A
1 AG AG A
9854643 TCATACCTTT
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.02, G:0.45, T:0.02
Consensus pattern (2 bp):
AG
Found at i:9859811 original size:30 final size:30
Alignment explanation
Indices: 9859777--9859842 Score: 87
Period size: 30 Copynumber: 2.2 Consensus size: 30
9859767 TTTACACTTT
** * *
9859777 AATTTTAATTTGATTTTTTTTTTAATTTTA
1 AATTTTAATTAAATATTTTTATTAATTTTA
*
9859807 AATTTTAATTAAATATTTTTATTATTTTTA
1 AATTTTAATTAAATATTTTTATTAATTTTA
9859837 AATTTT
1 AATTTT
9859843 TATGAGGTAA
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:0.32, C:0.00, G:0.02, T:0.67
Consensus pattern (30 bp):
AATTTTAATTAAATATTTTTATTAATTTTA
Found at i:9865851 original size:27 final size:26
Alignment explanation
Indices: 9865821--9865901 Score: 71
Period size: 27 Copynumber: 3.2 Consensus size: 26
9865811 TTAATTTAAG
*
9865821 AAAAAATTCAAATCGAGTTAAGATAAT
1 AAAAAATT-AAATTGAGTTAAGATAAT
* **
9865848 -AAAAA-T-AATTTA-TTAACTTAACT
1 AAAAAATTAAATTGAGTTAAGATAA-T
9865871 AAAAAATTTAAATTGAGTTAAGATAAT
1 AAAAAA-TTAAATTGAGTTAAGATAAT
9865898 AAAA
1 AAAA
9865902 TATAACTTAT
Statistics
Matches: 41, Mismatches: 7, Indels: 12
0.68 0.12 0.20
Matches are distributed among these distances:
22 7 0.17
23 5 0.12
24 5 0.12
25 1 0.02
26 6 0.15
27 10 0.24
28 7 0.17
ACGTcount: A:0.57, C:0.05, G:0.07, T:0.31
Consensus pattern (26 bp):
AAAAAATTAAATTGAGTTAAGATAAT
Found at i:9865889 original size:50 final size:51
Alignment explanation
Indices: 9865821--9865923 Score: 172
Period size: 50 Copynumber: 2.0 Consensus size: 51
9865811 TTAATTTAAG
*
9865821 AAAAAATTCAAATCGAGTTAAGATAATAAAA-ATAATTTATTAACTTAACT
1 AAAAAATTCAAATCGAGTTAAGATAATAAAATATAACTTATTAACTTAACT
* *
9865871 AAAAAATTTAAATTGAGTTAAGATAATAAAATATAACTTATTAACTTAACT
1 AAAAAATTCAAATCGAGTTAAGATAATAAAATATAACTTATTAACTTAACT
9865922 AA
1 AA
9865924 CTCAAAATTT
Statistics
Matches: 49, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
50 29 0.59
51 20 0.41
ACGTcount: A:0.54, C:0.07, G:0.06, T:0.33
Consensus pattern (51 bp):
AAAAAATTCAAATCGAGTTAAGATAATAAAATATAACTTATTAACTTAACT
Found at i:9873173 original size:21 final size:17
Alignment explanation
Indices: 9873130--9873169 Score: 62
Period size: 17 Copynumber: 2.2 Consensus size: 17
9873120 CATGGGAAGG
9873130 AAGAAAGAAAAAGAGAA
1 AAGAAAGAAAAAGAGAA
9873147 AAGAAAGAAGAAAGAAGAA
1 AAGAAAGAA-AAAG-AGAA
9873166 AAGA
1 AAGA
9873170 GAAAATTAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 9 0.43
18 4 0.19
19 8 0.38
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (17 bp):
AAGAAAGAAAAAGAGAA
Found at i:9874022 original size:7 final size:7
Alignment explanation
Indices: 9874012--9874101 Score: 58
Period size: 7 Copynumber: 12.0 Consensus size: 7
9874002 TTATATAAAA
9874012 TATATAT
1 TATATAT
9874019 TATATAT
1 TATATAT
9874026 TATATTAACT
1 TATA-T-A-T
9874036 TA-ATAT
1 TATATAT
*
9874042 TTTAGTAT
1 TATA-TAT
9874050 TAATATAT
1 T-ATATAT
*
9874058 AATATAT
1 TATATAT
9874065 TATATTAT
1 TATA-TAT
9874073 TATAT-T
1 TATATAT
*
9874079 ATATATAA
1 -TATATAT
9874087 TATAATAT
1 TAT-ATAT
*
9874095 AATATAT
1 TATATAT
9874102 AAAACATAAA
Statistics
Matches: 66, Mismatches: 7, Indels: 20
0.71 0.08 0.22
Matches are distributed among these distances:
6 3 0.05
7 35 0.53
8 21 0.32
9 4 0.06
10 3 0.05
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.52
Consensus pattern (7 bp):
TATATAT
Found at i:9875253 original size:22 final size:22
Alignment explanation
Indices: 9875224--9875280 Score: 71
Period size: 22 Copynumber: 2.6 Consensus size: 22
9875214 TAGCACGTTA
9875224 AGTGCTCTCTGTTTAGCACATCT
1 AGTGCTCTCTGTTTAGCAC-TCT
* * *
9875247 -GTGCTCTCTATATAGCACTTT
1 AGTGCTCTCTGTTTAGCACTCT
9875268 AGTGCTCTCTGTT
1 AGTGCTCTCTGTT
9875281 CGTTTGTGCA
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
21 2 0.07
22 26 0.93
ACGTcount: A:0.16, C:0.25, G:0.18, T:0.42
Consensus pattern (22 bp):
AGTGCTCTCTGTTTAGCACTCT
Found at i:9876652 original size:6 final size:6
Alignment explanation
Indices: 9876641--9876667 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
9876631 TGTGTACCGC
9876641 TACTGT TACTGT TACTGT TACTGT TAC
1 TACTGT TACTGT TACTGT TACTGT TAC
9876668 CCTTACGGTT
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:0.19, C:0.19, G:0.15, T:0.48
Consensus pattern (6 bp):
TACTGT
Found at i:9879458 original size:65 final size:65
Alignment explanation
Indices: 9879341--9879469 Score: 174
Period size: 65 Copynumber: 2.0 Consensus size: 65
9879331 GGGTTTTCAA
* * *
9879341 TTCACTTTTCAACAACAATCAATATTCAATTATCACAATATTTATATAAATCTCAATTCAATATT
1 TTCACATTTCAACAACAATCAATATTCAATAATCACAATATTCATATAAATCTCAATTCAATATT
*
9879406 TTCACATTTCAACAACAATTAATAGTTTC-ATCAATCACAA-ATTCATAT-AATCTCAATTCAAT
1 TTCACATTTCAACAACAATCAATA--TTCAAT-AATCACAATATTCATATAAATCTCAATTCAAT
9879468 AT
63 AT
9879470 CAAGATAATA
Statistics
Matches: 57, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
65 38 0.67
66 9 0.16
67 10 0.18
ACGTcount: A:0.42, C:0.19, G:0.01, T:0.38
Consensus pattern (65 bp):
TTCACATTTCAACAACAATCAATATTCAATAATCACAATATTCATATAAATCTCAATTCAATATT
Found at i:9881379 original size:41 final size:41
Alignment explanation
Indices: 9881325--9881405 Score: 162
Period size: 41 Copynumber: 2.0 Consensus size: 41
9881315 TTGAAAATCG
9881325 ATAACACTAACAATTTTCAACCACCATTGCAAGTAAAAAAA
1 ATAACACTAACAATTTTCAACCACCATTGCAAGTAAAAAAA
9881366 ATAACACTAACAATTTTCAACCACCATTGCAAGTAAAAAA
1 ATAACACTAACAATTTTCAACCACCATTGCAAGTAAAAAA
9881406 CCTGTTTTTT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 40 1.00
ACGTcount: A:0.51, C:0.22, G:0.05, T:0.22
Consensus pattern (41 bp):
ATAACACTAACAATTTTCAACCACCATTGCAAGTAAAAAAA
Found at i:9882156 original size:22 final size:22
Alignment explanation
Indices: 9882113--9882156 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
9882103 TAAATCTAAT
*
9882113 ATAAAATTATATTTAATTAAAA
1 ATAAAATTATATTTAATAAAAA
*
9882135 ATAAAATTA-ATTTTTATAAAAA
1 ATAAAATTATA-TTTAATAAAAA
9882157 TACATTCTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 1 0.05
22 18 0.95
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (22 bp):
ATAAAATTATATTTAATAAAAA
Found at i:9883021 original size:25 final size:25
Alignment explanation
Indices: 9882983--9883037 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 25
9882973 AAATTACAAA
* * *
9882983 AAAAAATTAAAAAAATTATTTTTTT
1 AAAATATTAAAAAAATTAATATTTT
* *
9883008 AAAATATTAGAAAATTTAATATTTT
1 AAAATATTAAAAAAATTAATATTTT
9883033 AAAAT
1 AAAAT
9883038 TTTATAAATT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (25 bp):
AAAATATTAAAAAAATTAATATTTT
Found at i:9895453 original size:3 final size:3
Alignment explanation
Indices: 9895445--9895490 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
9895435 GTTGGGCAGT
9895445 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A
9895491 TGGCAAGAGG
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:9900356 original size:36 final size:36
Alignment explanation
Indices: 9900268--9900371 Score: 111
Period size: 36 Copynumber: 2.9 Consensus size: 36
9900258 AATGTATTGG
* *
9900268 ATAACTAACTGCCACTGAATAATTGACTGTTACTAA
1 ATAACTGACTGCTACTGAATAATTGACTGTTACTAA
* * *
9900304 ATAACTGACTGCTACTGAGTAATTGACTGTTATTGA
1 ATAACTGACTGCTACTGAATAATTGACTGTTACTAA
* * * *
9900340 ATAATTTA-TCGTTACTGAATAACTGACTGTTA
1 ATAACTGACT-GCTACTGAATAATTGACTGTTA
9900372 AAGAGTGACT
Statistics
Matches: 57, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
35 1 0.02
36 56 0.98
ACGTcount: A:0.35, C:0.15, G:0.14, T:0.36
Consensus pattern (36 bp):
ATAACTGACTGCTACTGAATAATTGACTGTTACTAA
Found at i:9900371 original size:18 final size:18
Alignment explanation
Indices: 9900281--9900371 Score: 103
Period size: 18 Copynumber: 5.1 Consensus size: 18
9900271 ACTAACTGCC
9900281 ACTGAATAATTGACTGTT
1 ACTGAATAATTGACTGTT
* * *
9900299 ACTAAATAACTGACTGCT
1 ACTGAATAATTGACTGTT
*
9900317 ACTGAGTAATTGACTGTT
1 ACTGAATAATTGACTGTT
* *
9900335 ATTGAATAATTTA-TCGTT
1 ACTGAATAATTGACT-GTT
*
9900353 ACTGAATAACTGACTGTT
1 ACTGAATAATTGACTGTT
9900371 A
1 A
9900372 AAGAGTGACT
Statistics
Matches: 58, Mismatches: 13, Indels: 4
0.77 0.17 0.05
Matches are distributed among these distances:
17 1 0.02
18 56 0.97
19 1 0.02
ACGTcount: A:0.34, C:0.13, G:0.15, T:0.37
Consensus pattern (18 bp):
ACTGAATAATTGACTGTT
Found at i:9913917 original size:25 final size:25
Alignment explanation
Indices: 9913883--9913932 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
9913873 TAACCAAAGA
*
9913883 AATCCAATTCATTGCATATTCATAT
1 AATCCAATTCACTGCATATTCATAT
*
9913908 AATCTAATTCACTGCATATTCATAT
1 AATCCAATTCACTGCATATTCATAT
9913933 TCATACACTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.36, C:0.20, G:0.04, T:0.40
Consensus pattern (25 bp):
AATCCAATTCACTGCATATTCATAT
Found at i:9915778 original size:10 final size:10
Alignment explanation
Indices: 9915746--9915806 Score: 52
Period size: 10 Copynumber: 6.0 Consensus size: 10
9915736 GATTTTAGTT
*
9915746 TTTATTTATA
1 TTTAATTATA
*
9915756 ATTAATTATTA
1 TTTAATTA-TA
9915767 TTTAATTATA
1 TTTAATTATA
* *
9915777 TTTAAATAAA
1 TTTAATTATA
9915787 TTT-ATTACTA
1 TTTAATTA-TA
*
9915797 TTTATTTATA
1 TTTAATTATA
9915807 ATGAGGACTT
Statistics
Matches: 40, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
9 3 0.08
10 25 0.62
11 12 0.30
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (10 bp):
TTTAATTATA
Found at i:9920091 original size:33 final size:35
Alignment explanation
Indices: 9920053--9920149 Score: 98
Period size: 33 Copynumber: 2.8 Consensus size: 35
9920043 ATAGTTATAT
9920053 TTAAATATTTAAAATATATTTTATATATT-C-TAA
1 TTAAATATTTAAAATATATTTTATATATTGCTTAA
* *
9920086 TTAAAT-TTTATAAATA-ATTAATATTTATTGCTTAA
1 TTAAATATTTA-AAATATATT-TTATATATTGCTTAA
9920121 --AAATATTTAAAATTTATATTTTATATATT
1 TTAAATATTTAAAA--TATATTTTATATATT
9920150 AAAATATTAA
Statistics
Matches: 52, Mismatches: 4, Indels: 14
0.74 0.06 0.20
Matches are distributed among these distances:
32 7 0.13
33 25 0.48
34 5 0.10
35 12 0.23
36 3 0.06
ACGTcount: A:0.44, C:0.02, G:0.01, T:0.53
Consensus pattern (35 bp):
TTAAATATTTAAAATATATTTTATATATTGCTTAA
Found at i:9920751 original size:33 final size:36
Alignment explanation
Indices: 9920714--9920788 Score: 86
Period size: 33 Copynumber: 2.2 Consensus size: 36
9920704 AAAAAACATA
* * *
9920714 ATTTAATT-TAATATAAAATTATTTTAA-ATGAT-T
1 ATTTAATTATAATACAAAATCATTTTAATATAATGT
*
9920747 ATTT-ATTATATTACAAAATCATTTTAATATAATGT
1 ATTTAATTATAATACAAAATCATTTTAATATAATGT
9920782 ATTTAAT
1 ATTTAAT
9920789 ACTCATTTTT
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
32 3 0.09
33 20 0.59
34 4 0.12
35 5 0.15
36 2 0.06
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.51
Consensus pattern (36 bp):
ATTTAATTATAATACAAAATCATTTTAATATAATGT
Found at i:9923396 original size:24 final size:24
Alignment explanation
Indices: 9923355--9923400 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
9923345 ATATTATTTT
9923355 TTTTATAATTTTAGAATATTTATA
1 TTTTATAATTTTAGAATATTTATA
*
9923379 TTTT-TAATTGTTATAATATTTA
1 TTTTATAATT-TTAGAATATTTA
9923401 ACAATTTTTG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 5 0.25
24 15 0.75
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.61
Consensus pattern (24 bp):
TTTTATAATTTTAGAATATTTATA
Found at i:9926753 original size:18 final size:19
Alignment explanation
Indices: 9926720--9926756 Score: 58
Period size: 18 Copynumber: 1.9 Consensus size: 19
9926710 ACAAAATAAT
9926720 TAATTTACATTATTTTTTTC
1 TAATTTACA-TATTTTTTTC
9926740 TAATTTAC-TATTTTTTT
1 TAATTTACATATTTTTTT
9926757 AATAAAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 9 0.53
20 8 0.47
ACGTcount: A:0.24, C:0.08, G:0.00, T:0.68
Consensus pattern (19 bp):
TAATTTACATATTTTTTTC
Found at i:9934391 original size:50 final size:50
Alignment explanation
Indices: 9934267--9934565 Score: 384
Period size: 50 Copynumber: 5.8 Consensus size: 50
9934257 GATAATAACA
* * ** *
9934267 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCGTGAT-GG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGA-CCTCTCGT-CTCGG
* * *
9934318 TGCCCATGCCATGTCCCAGACATGGTCTTATAGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCGTCTCGG
* *
9934368 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCGTCTCGG
*
9934418 TGCCCATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCGTCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCGTCTCGG
* *
9934468 TGCCCATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATGATCTTAAGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTC--G-TC-T-CGG
* *
9934523 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 -TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCT
9934566 TTACCCAAAT
Statistics
Matches: 221, Mismatches: 20, Indels: 9
0.88 0.08 0.04
Matches are distributed among these distances:
49 1 0.00
50 142 0.64
51 33 0.15
52 1 0.00
53 2 0.01
54 1 0.00
55 2 0.01
56 39 0.18
ACGTcount: A:0.20, C:0.30, G:0.24, T:0.26
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCGTCTCGG
Found at i:9934681 original size:13 final size:13
Alignment explanation
Indices: 9934660--9934691 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
9934650 GCTTGGATCA
*
9934660 TCATCAAATAAAT
1 TCATAAAATAAAT
9934673 TCATAAAATAAAT
1 TCATAAAATAAAT
9934686 TCATAA
1 TCATAA
9934692 TTGCTGGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.31
Consensus pattern (13 bp):
TCATAAAATAAAT
Found at i:9934938 original size:30 final size:30
Alignment explanation
Indices: 9934903--9934960 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
9934893 CCTCGACTCT
*
9934903 AACTTTTTCAAAATTACAATTTTGCCCCTA
1 AACTTTTACAAAATTACAATTTTGCCCCTA
* *
9934933 AACTTTTACATAATTACATTTTTGCCCC
1 AACTTTTACAAAATTACAATTTTGCCCC
9934961 AAGGCGCGGA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.31, C:0.24, G:0.03, T:0.41
Consensus pattern (30 bp):
AACTTTTACAAAATTACAATTTTGCCCCTA
Found at i:9936990 original size:5 final size:5
Alignment explanation
Indices: 9936980--9937008 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
9936970 TGTGTGGTTC
9936980 TTTAT TTTAT TTTAT TTTAT TTTAT TTTA
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTTA
9937009 CAACATAACA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (5 bp):
TTTAT
Found at i:9941027 original size:13 final size:13
Alignment explanation
Indices: 9941011--9941035 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
9941001 ATACTTAAGT
9941011 ATAATATAATAAA
1 ATAATATAATAAA
9941024 ATAATATAATAA
1 ATAATATAATAA
9941036 TACATAAAGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (13 bp):
ATAATATAATAAA
Found at i:9941590 original size:44 final size:42
Alignment explanation
Indices: 9941524--9941631 Score: 101
Period size: 42 Copynumber: 2.5 Consensus size: 42
9941514 GACTTCGAGT
** * * *
9941524 CGATGAGGCACT-ATGTGTCGTATTATTATTGCTTCAGATATATC
1 CGATGAGGCACTGA-GTACCGTATTATT-TTACTTC-GACATAGC
* * *
9941568 CGATGAGGTACTGAGTACCGTATTGTTTTACTTCGACATGGC
1 CGATGAGGCACTGAGTACCGTATTATTTTACTTCGACATAGC
*
9941610 CGATGAGGCACTGAGTGCCGTA
1 CGATGAGGCACTGAGTACCGTA
9941632 CTGGTGCGTT
Statistics
Matches: 53, Mismatches: 10, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
42 25 0.47
43 6 0.11
44 21 0.40
45 1 0.02
ACGTcount: A:0.23, C:0.19, G:0.26, T:0.32
Consensus pattern (42 bp):
CGATGAGGCACTGAGTACCGTATTATTTTACTTCGACATAGC
Found at i:9950417 original size:10 final size:10
Alignment explanation
Indices: 9950402--9950426 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
9950392 ACTCTATTAC
9950402 TCAAAAAATA
1 TCAAAAAATA
9950412 TCAAAAAATA
1 TCAAAAAATA
9950422 TCAAA
1 TCAAA
9950427 TTAGTTTTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.68, C:0.12, G:0.00, T:0.20
Consensus pattern (10 bp):
TCAAAAAATA
Found at i:9956451 original size:16 final size:17
Alignment explanation
Indices: 9956424--9956463 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
9956414 CCCTTTTCTT
*
9956424 TCTCTCTTTTTCGTCTG
1 TCTCTCTGTTTCGTCTG
*
9956441 T-TCTCTGTTTCTTCTG
1 TCTCTCTGTTTCGTCTG
9956457 TCTCTCT
1 TCTCTCT
9956464 TTTATTTCCT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
16 14 0.70
17 6 0.30
ACGTcount: A:0.00, C:0.30, G:0.10, T:0.60
Consensus pattern (17 bp):
TCTCTCTGTTTCGTCTG
Found at i:9958754 original size:16 final size:16
Alignment explanation
Indices: 9958735--9958775 Score: 68
Period size: 16 Copynumber: 2.7 Consensus size: 16
9958725 TTTATAATAA
9958735 TAATTATTATTATTTT
1 TAATTATTATTATTTT
9958751 TAATTATTATTATTTT
1 TAATTATTATTATTTT
9958767 T--TTATTATT
1 TAATTATTATT
9958776 TTTCGTCATG
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.32
16 17 0.68
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (16 bp):
TAATTATTATTATTTT
Found at i:9958754 original size:19 final size:18
Alignment explanation
Indices: 9958732--9958770 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 18
9958722 ATATTTATAA
9958732 TAATAATTATTATTATTTT
1 TAATAATTATTATT-TTTT
*
9958751 TAATTATTATTATTTTTT
1 TAATAATTATTATTTTTT
9958769 TA
1 TA
9958771 TTATTTTTCG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 6 0.32
19 13 0.68
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (18 bp):
TAATAATTATTATTTTTT
Found at i:9958758 original size:10 final size:9
Alignment explanation
Indices: 9958741--9958778 Score: 51
Period size: 9 Copynumber: 4.2 Consensus size: 9
9958731 ATAATAATTA
9958741 TTATTATTT
1 TTATTATTT
*
9958750 TTAATTATTA
1 TT-ATTATTT
9958760 TTATT-TTT
1 TTATTATTT
9958768 TTATTATTT
1 TTATTATTT
9958777 TT
1 TT
9958779 CGTCATGTGT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
8 7 0.28
9 10 0.40
10 8 0.32
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (9 bp):
TTATTATTT
Found at i:9960496 original size:8 final size:8
Alignment explanation
Indices: 9960480--9960509 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
9960470 CTAAGAAATA
9960480 GAAAGTTG
1 GAAAGTTG
*
9960488 GAAAATTG
1 GAAAGTTG
9960496 GAAAGTTG
1 GAAAGTTG
9960504 GAAAGT
1 GAAAGT
9960510 GTAATTGGGG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.43, C:0.00, G:0.33, T:0.23
Consensus pattern (8 bp):
GAAAGTTG
Found at i:9975994 original size:45 final size:45
Alignment explanation
Indices: 9975944--9976050 Score: 128
Period size: 45 Copynumber: 2.4 Consensus size: 45
9975934 CGACTACGGT
*
9975944 TACTGTTACCGTTACTGTTACCA-ATTC-GACACTTTGTGTGTCGAA
1 TACTGTTACAGTTACTGTTA-CAGATTCAG-CACTTTGTGTGTCGAA
* * *
9975989 TACTGTTACAATTACTGTTATAGATTCAGCACTTTGTGTGTTGAA
1 TACTGTTACAGTTACTGTTACAGATTCAGCACTTTGTGTGTCGAA
* *
9976034 TATTGTTACTGTTACTG
1 TACTGTTACAGTTACTG
9976051 CTACTGCTAC
Statistics
Matches: 53, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
44 1 0.02
45 51 0.96
46 1 0.02
ACGTcount: A:0.23, C:0.17, G:0.18, T:0.42
Consensus pattern (45 bp):
TACTGTTACAGTTACTGTTACAGATTCAGCACTTTGTGTGTCGAA
Found at i:9982565 original size:12 final size:12
Alignment explanation
Indices: 9982550--9982593 Score: 61
Period size: 12 Copynumber: 3.6 Consensus size: 12
9982540 AAAACAGGGG
9982550 AGAAAAAGAGAA
1 AGAAAAAGAGAA
*
9982562 AGAAAAAGGGAA
1 AGAAAAAGAGAA
*
9982574 AGAAAAAGAAAA
1 AGAAAAAGAGAA
9982586 AGGAAAAA
1 A-GAAAAA
9982594 CTAGAGATTT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
12 22 0.79
13 6 0.21
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (12 bp):
AGAAAAAGAGAA
Found at i:9982569 original size:6 final size:6
Alignment explanation
Indices: 9982550--9982593 Score: 52
Period size: 6 Copynumber: 7.2 Consensus size: 6
9982540 AAAACAGGGG
* **
9982550 AGAAAA AGAGAA AGAAAA AGGGAA AGAAAA AGAAAA AGGAAAA A
1 AGAAAA AGAAAA AGAAAA AGAAAA AGAAAA AGAAAA A-GAAAA A
9982594 CTAGAGATTT
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
6 25 0.81
7 6 0.19
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (6 bp):
AGAAAA
Found at i:9982581 original size:18 final size:18
Alignment explanation
Indices: 9982554--9982588 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
9982544 CAGGGGAGAA
*
9982554 AAAGAGAAAGAAAAAGGG
1 AAAGAAAAAGAAAAAGGG
9982572 AAAGAAAAAGAAAAAGG
1 AAAGAAAAAGAAAAAGG
9982589 AAAAACTAGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (18 bp):
AAAGAAAAAGAAAAAGGG
Found at i:9983198 original size:45 final size:45
Alignment explanation
Indices: 9983148--9983251 Score: 163
Period size: 45 Copynumber: 2.3 Consensus size: 45
9983138 CTACTGTTAT
* *
9983148 TGTTACCGTTACTGTTACCGATTCAACACTTTGTGTGTCGAATAC
1 TGTTACCGTTACTGTTACAGATTCAACACTTTGTCTGTCGAATAC
* *
9983193 TGTTACCGTTATTGTTACAGATTCAACACTTTGTCTGTTGAATAC
1 TGTTACCGTTACTGTTACAGATTCAACACTTTGTCTGTCGAATAC
*
9983238 TGTTACTGTTACTG
1 TGTTACCGTTACTG
9983252 CTACTGCTAC
Statistics
Matches: 53, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
45 53 1.00
ACGTcount: A:0.22, C:0.19, G:0.17, T:0.41
Consensus pattern (45 bp):
TGTTACCGTTACTGTTACAGATTCAACACTTTGTCTGTCGAATAC
Found at i:9983266 original size:18 final size:18
Alignment explanation
Indices: 9983235--9983269 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
9983225 GTCTGTTGAA
* *
9983235 TACTGTTACTGTTACTGC
1 TACTGCTACCGTTACTGC
9983253 TACTGCTACCGTTACTG
1 TACTGCTACCGTTACTG
9983270 ATTACTGATT
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:0.17, C:0.26, G:0.17, T:0.40
Consensus pattern (18 bp):
TACTGCTACCGTTACTGC
Found at i:9984020 original size:14 final size:14
Alignment explanation
Indices: 9984001--9984027 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
9983991 CGAAATTTAT
9984001 AAAATAATAATAAA
1 AAAATAATAATAAA
9984015 AAAATAATAATAA
1 AAAATAATAATAA
9984028 TAAATTGGAG
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:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (14 bp):
AAAATAATAATAAA
Found at i:10003984 original size:3 final size:3
Alignment explanation
Indices: 10003976--10004001 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
10003966 GTAGAAGACC
10003976 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
10004002 ATGAAAAGAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:10017459 original size:21 final size:21
Alignment explanation
Indices: 10017435--10017477 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
10017425 TTCTTCTTTT
10017435 TTTTTTTTTTTCATCTCATGG
1 TTTTTTTTTTTCATCTCATGG
10017456 TTTTTTTTTTTCATCTCATGG
1 TTTTTTTTTTTCATCTCATGG
10017477 T
1 T
10017478 CTTCTTCATC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.09, C:0.14, G:0.09, T:0.67
Consensus pattern (21 bp):
TTTTTTTTTTTCATCTCATGG
Found at i:10022334 original size:23 final size:23
Alignment explanation
Indices: 10022308--10022368 Score: 59
Period size: 29 Copynumber: 2.4 Consensus size: 23
10022298 TGTTATCATG
10022308 AGAAAAAATAGGATTATATTGAA
1 AGAAAAAATAGGATTATATTGAA
10022331 AGAACAAATTTATATAGGATTATATTGAA
1 AG-A-AAA---A-ATAGGATTATATTGAA
*
10022360 AGAACAAAT
1 AGAAAAAAT
10022369 TTATCTCAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 12
0.70 0.02 0.27
Matches are distributed among these distances:
23 4 0.13
24 2 0.06
25 3 0.10
27 2 0.06
28 2 0.06
29 18 0.58
ACGTcount: A:0.54, C:0.03, G:0.15, T:0.28
Consensus pattern (23 bp):
AGAAAAAATAGGATTATATTGAA
Found at i:10022357 original size:29 final size:29
Alignment explanation
Indices: 10022315--10022372 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
10022305 ATGAGAAAAA
10022315 ATAGGATTATATTGAAAGAACAAATTTAT
1 ATAGGATTATATTGAAAGAACAAATTTAT
10022344 ATAGGATTATATTGAAAGAACAAATTTAT
1 ATAGGATTATATTGAAAGAACAAATTTAT
10022373 CTCAAAGAGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.48, C:0.03, G:0.14, T:0.34
Consensus pattern (29 bp):
ATAGGATTATATTGAAAGAACAAATTTAT
Found at i:10022568 original size:30 final size:30
Alignment explanation
Indices: 10022532--10022594 Score: 117
Period size: 30 Copynumber: 2.1 Consensus size: 30
10022522 ATTAATAGGA
*
10022532 GAAAAATTAAAACTTAATTTTAAATCATTT
1 GAAAAATTAAAACTTAATCTTAAATCATTT
10022562 GAAAAATTAAAACTTAATCTTAAATCATTT
1 GAAAAATTAAAACTTAATCTTAAATCATTT
10022592 GAA
1 GAA
10022595 CCCTAATTAT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.51, C:0.08, G:0.05, T:0.37
Consensus pattern (30 bp):
GAAAAATTAAAACTTAATCTTAAATCATTT
Found at i:10027941 original size:43 final size:43
Alignment explanation
Indices: 10027845--10027946 Score: 98
Period size: 43 Copynumber: 2.4 Consensus size: 43
10027835 TGAGATTACG
* ** ** *
10027845 TGTAAGACCATGTCTGAGACATTGGCATCGTTAATCGATTTCG
1 TGTAAGACCATGTCTGAGACAGTGGCATCAATAATCGATAACA
* * *
10027888 TATAAAACCATGTCTGAGACAGTGGCATCAATATAT-GGTAACA
1 TGTAAGACCATGTCTGAGACAGTGGCATCAATA-ATCGATAACA
*
10027931 TGTAAGACCATATCTG
1 TGTAAGACCATGTCTG
10027947 GGATATGGCA
Statistics
Matches: 46, Mismatches: 12, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
43 44 0.96
44 2 0.04
ACGTcount: A:0.32, C:0.18, G:0.21, T:0.29
Consensus pattern (43 bp):
TGTAAGACCATGTCTGAGACAGTGGCATCAATAATCGATAACA
Found at i:10034011 original size:24 final size:24
Alignment explanation
Indices: 10033965--10034011 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
10033955 CGTTCTGTAT
* **
10033965 CAAAGGATGAATTGATGGTAAATG
1 CAAAGGATGAATTGACGAAAAATG
*
10033989 CAAAGGATGAATTGGCGAAAAAT
1 CAAAGGATGAATTGACGAAAAAT
10034012 TACCCAAGTA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.45, C:0.06, G:0.28, T:0.21
Consensus pattern (24 bp):
CAAAGGATGAATTGACGAAAAATG
Found at i:10034153 original size:42 final size:41
Alignment explanation
Indices: 10034107--10034216 Score: 103
Period size: 42 Copynumber: 2.6 Consensus size: 41
10034097 ATAAGTTTCT
**
10034107 GTTTAACCTAAATGGGTTTCTGTTTAGCTCATACGAGCTTCA
1 GTTTAACCT-AATGGGTTTCCATTTAGCTCATACGAGCTTCA
* * * *
10034149 GTTTAACCCTTATGGGTTTCCATTTAGCTCCTATGAGCTTCC
1 GTTTAA-CCTAATGGGTTTCCATTTAGCTCATACGAGCTTCA
* * * *
10034191 GTTCAACCCTTATGAGTTTCTATTTA
1 GTTTAA-CCTAATGGGTTTCCATTTA
10034217 ACACTTAGGT
Statistics
Matches: 58, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
42 55 0.95
43 3 0.05
ACGTcount: A:0.21, C:0.22, G:0.16, T:0.41
Consensus pattern (41 bp):
GTTTAACCTAATGGGTTTCCATTTAGCTCATACGAGCTTCA
Found at i:10034231 original size:42 final size:42
Alignment explanation
Indices: 10034141--10034234 Score: 107
Period size: 42 Copynumber: 2.2 Consensus size: 42
10034131 TAGCTCATAC
* * * * * *
10034141 GAGCTTCAGTTTAACCCTTATGGGTTTCCATTTAGCTCCTAT
1 GAGCTTCCGTTCAACCCTTATGAGTTTCCATTTAACACCTAG
* *
10034183 GAGCTTCCGTTCAACCCTTATGAGTTTCTATTTAACACTTAG
1 GAGCTTCCGTTCAACCCTTATGAGTTTCCATTTAACACCTAG
*
10034225 GTGCTTCCGT
1 GAGCTTCCGT
10034235 GTAGCCTTCG
Statistics
Matches: 43, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.19, C:0.24, G:0.17, T:0.39
Consensus pattern (42 bp):
GAGCTTCCGTTCAACCCTTATGAGTTTCCATTTAACACCTAG
Found at i:10040946 original size:25 final size:25
Alignment explanation
Indices: 10040905--10040965 Score: 63
Period size: 25 Copynumber: 2.4 Consensus size: 25
10040895 CCACAGAATT
* *
10040905 TTTTTTATTTATT-TTTTTTCAT-AT
1 TTTTTT-TTTGTTCTTTTTTCATCAC
*
10040929 TTTATTTTTTGTTCTTTTTTTATCAC
1 TTT-TTTTTTGTTCTTTTTTCATCAC
10040955 TTTTTTTTTGT
1 TTTTTTTTTGT
10040966 GGGAAATATT
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
24 8 0.26
25 19 0.61
26 4 0.13
ACGTcount: A:0.11, C:0.07, G:0.03, T:0.79
Consensus pattern (25 bp):
TTTTTTTTTGTTCTTTTTTCATCAC
Found at i:10048305 original size:34 final size:34
Alignment explanation
Indices: 10048262--10048328 Score: 134
Period size: 34 Copynumber: 2.0 Consensus size: 34
10048252 ATATTGTCCC
10048262 TTAATTGGACTATAGAAGCTCAATATGAACTGTT
1 TTAATTGGACTATAGAAGCTCAATATGAACTGTT
10048296 TTAATTGGACTATAGAAGCTCAATATGAACTGT
1 TTAATTGGACTATAGAAGCTCAATATGAACTGT
10048329 AAAATCAAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.36, C:0.12, G:0.18, T:0.34
Consensus pattern (34 bp):
TTAATTGGACTATAGAAGCTCAATATGAACTGTT
Found at i:10049913 original size:19 final size:20
Alignment explanation
Indices: 10049879--10049917 Score: 62
Period size: 19 Copynumber: 1.9 Consensus size: 20
10049869 TCAGAGGATA
10049879 AATAATTTAAATTTTATCAAC
1 AATAATTT-AATTTTATCAAC
10049900 AATAATTT-ATTTTATCAA
1 AATAATTTAATTTTATCAA
10049918 TGAACTTTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 10 0.56
21 8 0.44
ACGTcount: A:0.46, C:0.08, G:0.00, T:0.46
Consensus pattern (20 bp):
AATAATTTAATTTTATCAAC
Found at i:10054091 original size:21 final size:19
Alignment explanation
Indices: 10054048--10054099 Score: 52
Period size: 19 Copynumber: 2.6 Consensus size: 19
10054038 AAAGTTACAA
*
10054048 TTTATTAAAAATTAGAAATTTT
1 TTTA-TAAAAATTAGAAA--AT
10054070 TTTATAAAAATT-GTAAAAT
1 TTTATAAAAATTAG-AAAAT
10054089 TTTATAAAAAT
1 TTTATAAAAAT
10054100 CATAAAAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
19 12 0.43
20 1 0.04
21 11 0.39
22 4 0.14
ACGTcount: A:0.50, C:0.00, G:0.04, T:0.46
Consensus pattern (19 bp):
TTTATAAAAATTAGAAAAT
Found at i:10054105 original size:19 final size:19
Alignment explanation
Indices: 10054069--10054106 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
10054059 TTAGAAATTT
**
10054069 TTTTATAAAAATTGTAAAA
1 TTTTATAAAAATCATAAAA
10054088 TTTTATAAAAATCATAAAA
1 TTTTATAAAAATCATAAAA
10054107 AAATTAATGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.55, C:0.03, G:0.03, T:0.39
Consensus pattern (19 bp):
TTTTATAAAAATCATAAAA
Found at i:10054369 original size:11 final size:11
Alignment explanation
Indices: 10054353--10054378 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
10054343 ATATTTTATA
10054353 TTTTTCCTAAT
1 TTTTTCCTAAT
10054364 TTTTTCCTAAT
1 TTTTTCCTAAT
10054375 TTTT
1 TTTT
10054379 AATATTTTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.15, C:0.15, G:0.00, T:0.69
Consensus pattern (11 bp):
TTTTTCCTAAT
Found at i:10054384 original size:37 final size:36
Alignment explanation
Indices: 10054323--10054393 Score: 99
Period size: 37 Copynumber: 1.9 Consensus size: 36
10054313 TAAACTTTTA
10054323 TAATTTTTTCATATTTCTATATATTTTATATTTTTCC
1 TAATTTTTTCATATTTCTATATATTTT-TATTTTTCC
* *
10054360 TAATTTTTTCCTAATTTTTA-ATATTTTTATTTTT
1 TAATTTTTTCAT-ATTTCTATATATTTTTATTTTT
10054394 ATTAAAATTT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
36 7 0.23
37 18 0.58
38 6 0.19
ACGTcount: A:0.24, C:0.08, G:0.00, T:0.68
Consensus pattern (36 bp):
TAATTTTTTCATATTTCTATATATTTTTATTTTTCC
Found at i:10054447 original size:17 final size:17
Alignment explanation
Indices: 10054410--10054447 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
10054400 ATTTAATAAT
*
10054410 ATTTATATTTTTTATTG
1 ATTTATATTTTTTATTA
10054427 ATTTAT-TTTTTTATATA
1 ATTTATATTTTTTAT-TA
10054444 ATTT
1 ATTT
10054448 TTTATAAAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 8 0.42
17 11 0.58
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.71
Consensus pattern (17 bp):
ATTTATATTTTTTATTA
Found at i:10054590 original size:88 final size:87
Alignment explanation
Indices: 10054453--10054668 Score: 238
Period size: 88 Copynumber: 2.4 Consensus size: 87
10054443 AATTTTTTAT
* * *
10054453 AAAAGCAGGGGCTTAATTTATTTTTTTTGAAAAAGTTTGAGAGTATTTTTAATGTATTTTAAAAT
1 AAAAGTAGGGGCTTAA-TTATTTTTTTT--AAAAGTTTGAGAGTATTTTTAATGCATTTTAAAAG
* * *
10054518 TTCAAATACCCAATTGAGTGCAAAA
63 TTCAAATACCCAAATAAGTACAAAA
* *
10054543 AAATAGTAGGGGCTTAATTATTTTTTTTAAAGGTTTGAGAGCT-TTTTTTATGCATTTTAAAAGT
1 AAA-AGTAGGGGCTTAATTATTTTTTTTAAAAGTTTGAGAG-TATTTTTAATGCATTTTAAAAGT
* *
10054607 TCAAGTACGCAAATAAGTACAAAA
64 TCAAATACCCAAATAAGTACAAAA
* * *
10054631 AAAAGTAGAGACTTAATT-TCTTTTTTTAATATGTTTGA
1 AAAAGTAGGGGCTTAATTAT-TTTTTTTAA-AAGTTTGA
10054669 AGGTTTGCAC
Statistics
Matches: 109, Mismatches: 13, Indels: 10
0.83 0.10 0.08
Matches are distributed among these distances:
86 1 0.01
87 22 0.20
88 59 0.54
89 1 0.01
90 14 0.13
91 12 0.11
ACGTcount: A:0.37, C:0.07, G:0.16, T:0.40
Consensus pattern (87 bp):
AAAAGTAGGGGCTTAATTATTTTTTTTAAAAGTTTGAGAGTATTTTTAATGCATTTTAAAAGTTC
AAATACCCAAATAAGTACAAAA
Found at i:10059153 original size:21 final size:21
Alignment explanation
Indices: 10059127--10059170 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
10059117 ACTATTTAAA
*
10059127 ACCCTTTATTAAATTAGTCTT
1 ACCCTTTATTAAAATAGTCTT
*
10059148 ACCCTTTATTAAAATAGTGTT
1 ACCCTTTATTAAAATAGTCTT
10059169 AC
1 AC
10059171 AAGTTAACCA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.32, C:0.18, G:0.07, T:0.43
Consensus pattern (21 bp):
ACCCTTTATTAAAATAGTCTT
Found at i:10063381 original size:57 final size:60
Alignment explanation
Indices: 10063232--10063384 Score: 154
Period size: 60 Copynumber: 2.6 Consensus size: 60
10063222 AAAAGTCAAA
* * * * * **
10063232 TTTAAGTATCAATTTAAACAAAGAAACTTAGTTCAAATGCTTAATTGAATCAAAATAAAC
1 TTTAAGTACCAATTTGAACCATGAAACTAAGTTCAAACACTTAATTGAATCAAAATAAAC
* * * *
10063292 TTTAAGTACCAAATTGAACC-TTAAAGTCAAGTTCAAACACTTACTT-AGA-CAAAA-AAAC
1 TTTAAGTACCAATTTGAACCATGAAACT-AAGTTCAAACACTTAATTGA-ATCAAAATAAAC
10063350 -TTAAGTACCAATTTGAACCATGAAACTAAGTTCAA
1 TTTAAGTACCAATTTGAACCATGAAACTAAGTTCAA
10063385 GTAGCAAAGT
Statistics
Matches: 76, Mismatches: 14, Indels: 9
0.77 0.14 0.09
Matches are distributed among these distances:
57 26 0.34
58 9 0.12
59 10 0.13
60 31 0.41
ACGTcount: A:0.46, C:0.16, G:0.09, T:0.29
Consensus pattern (60 bp):
TTTAAGTACCAATTTGAACCATGAAACTAAGTTCAAACACTTAATTGAATCAAAATAAAC
Found at i:10067376 original size:13 final size:13
Alignment explanation
Indices: 10067358--10067389 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
10067348 AAAGGTACGC
*
10067358 TTTTTTATATATT
1 TTTTTTAAATATT
10067371 TTTTTTAAATATT
1 TTTTTTAAATATT
10067384 TTTTTT
1 TTTTTT
10067390 TTGATATAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (13 bp):
TTTTTTAAATATT
Found at i:10067745 original size:38 final size:38
Alignment explanation
Indices: 10067697--10067783 Score: 156
Period size: 38 Copynumber: 2.3 Consensus size: 38
10067687 TGGTGGCATA
*
10067697 GTGGTGTAGGTGACCAAGGTGGGTGGCCAACAAGGGTG
1 GTGGAGTAGGTGACCAAGGTGGGTGGCCAACAAGGGTG
*
10067735 GTGGAGTAGGTGGCCAAGGTGGGTGGCCAACAAGGGTG
1 GTGGAGTAGGTGACCAAGGTGGGTGGCCAACAAGGGTG
10067773 GTGGAGTAGGT
1 GTGGAGTAGGT
10067784 AGGATTAGGG
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
38 47 1.00
ACGTcount: A:0.21, C:0.11, G:0.49, T:0.18
Consensus pattern (38 bp):
GTGGAGTAGGTGACCAAGGTGGGTGGCCAACAAGGGTG
Found at i:10067847 original size:12 final size:12
Alignment explanation
Indices: 10067830--10067854 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
10067820 TTGGGTTAGT
10067830 GTTTTGGGCTAA
1 GTTTTGGGCTAA
10067842 GTTTTGGGCTAA
1 GTTTTGGGCTAA
10067854 G
1 G
10067855 GGTTTGTATT
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:0.16, C:0.08, G:0.36, T:0.40
Consensus pattern (12 bp):
GTTTTGGGCTAA
Found at i:10068381 original size:42 final size:41
Alignment explanation
Indices: 10068326--10068476 Score: 117
Period size: 43 Copynumber: 3.5 Consensus size: 41
10068316 CATCATTGAT
* *
10068326 CTGTTTCCTTACTGCTTAGGGGTTTAGATCTATAAACTCAAC
1 CTGTTACCCTACTGCTTAGGGGTTTAGATCTATAAACTC-AC
* * * **
10068368 CTGTTACCCTACTGCTTAGGGGTTTAAGGTTTGA-AAATTTGGC
1 CTGTTACCCTACTGCTTAGGGGTTT-AGATCT-ATAAA-CTCAC
* * * *
10068411 TTGTTACCCTATTGCTTA-GGGTAATAATATCTATAAACTTCAC
1 CTGTTACCCTACTGCTTAGGGGT--TTAGATCTATAAAC-TCAC
10068454 CTTGTTACCCTACTGCTTAGGGG
1 C-TGTTACCCTACTGCTTAGGGG
10068477 GTTAAAGCTT
Statistics
Matches: 82, Mismatches: 18, Indels: 15
0.71 0.16 0.13
Matches are distributed among these distances:
42 28 0.34
43 32 0.39
44 19 0.23
45 3 0.04
ACGTcount: A:0.23, C:0.20, G:0.19, T:0.38
Consensus pattern (41 bp):
CTGTTACCCTACTGCTTAGGGGTTTAGATCTATAAACTCAC
Found at i:10091468 original size:3 final size:3
Alignment explanation
Indices: 10091460--10091510 Score: 50
Period size: 3 Copynumber: 16.0 Consensus size: 3
10091450 AATAGGGGTG
*
10091460 ATA ATA ATA ATA ATA ATA ATA CA-A ACA ATA ATA CATA TATA TATA ATA
1 ATA ATA ATA ATA ATA ATA ATA -ATA ATA ATA ATA -ATA -ATA -ATA ATA
10091508 ATA
1 ATA
10091511 GTAGTCAGAA
Statistics
Matches: 43, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
2 1 0.02
3 31 0.72
4 11 0.26
ACGTcount: A:0.63, C:0.06, G:0.00, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:10091609 original size:12 final size:12
Alignment explanation
Indices: 10091585--10091615 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
10091575 GAGGGTATAT
10091585 ATAATAT-AATA
1 ATAATATAAATA
10091596 ATAATATAAATA
1 ATAATATAAATA
10091608 ATAATATA
1 ATAATATA
10091616 TACATGAGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 7 0.37
12 12 0.63
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (12 bp):
ATAATATAAATA
Found at i:10094588 original size:23 final size:23
Alignment explanation
Indices: 10094537--10094590 Score: 65
Period size: 23 Copynumber: 2.3 Consensus size: 23
10094527 AAATAATTTG
*
10094537 AATTTCAAGTTAATTGAATCGAGT
1 AATTT-AAGTTAATTGAATCAAGT
*
10094561 TATTTAAGTTAATTCGAAT-AAGT
1 AATTTAAGTTAATT-GAATCAAGT
10094584 AATTTAA
1 AATTTAA
10094591 ATTTCGAGTT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
23 18 0.69
24 8 0.31
ACGTcount: A:0.41, C:0.06, G:0.13, T:0.41
Consensus pattern (23 bp):
AATTTAAGTTAATTGAATCAAGT
Found at i:10094771 original size:19 final size:21
Alignment explanation
Indices: 10094736--10094781 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
10094726 AAAAATAAAA
10094736 TAAAATAATTTTCAAAAATT-
1 TAAAATAATTTTCAAAAATTC
10094756 TAAAAT-ATTTAT-AAAAATTC
1 TAAAATAATTT-TCAAAAATTC
10094776 TAAAAT
1 TAAAAT
10094782 TTATATTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 11 0.46
20 13 0.54
ACGTcount: A:0.57, C:0.04, G:0.00, T:0.39
Consensus pattern (21 bp):
TAAAATAATTTTCAAAAATTC
Found at i:10101563 original size:209 final size:210
Alignment explanation
Indices: 10101193--10101677 Score: 821
Period size: 209 Copynumber: 2.3 Consensus size: 210
10101183 TTCGACAAAA
* **
10101193 GTACCATTTAGAATTATACTTTTGAATCATCTTTTGCATCAAGTGAATTATATGCCCATTTACAT
1 GTACCATTTAGAATTATACTTTTGAATCATCTTTTGCATCAAGTGAATTATATG--AATAAACAT
10101258 GCAGAATTTACATGCATCAACAACATTAATGATATACCTCATTACATGCAGAATTTACAGTATTT
64 GC-------ACATGCATCAACAACATTAATGATATACCTCATTACATGCAGAATTTACAGTATTT
10101323 AAGCTCCTTAGAATTATACTTTTGAATCATCTTTTGCATCAAGTGAATTATATGCCCATTTAGAA
122 AAGCTCCTTAGAATTATACTTTTGAATCATCTTTTGCATCAAGTGAATTATATGCCCATTTAGAA
10101388 TTTAATGCCAGAAAATGAAACAAT
187 TTTAATGCCAGAAAATGAAACAAT
10101412 GTACCATTTAGAATTATACTTTTGAATCATCTTTTGCATCAAGTGAATTATATGAATAAACACTG
1 GTACCATTTAGAATTATACTTTTGAATCATCTTTTGCATCAAGTGAATTATATGAATAAACA-TG
*
10101477 C-CGT-CATCAACAACATTAATGATATACCTCATTACATGCAGAATTTACAGTATTTAAGCTCCT
65 CACATGCATCAACAACATTAATGATATACCTCATTACATGCAGAATTTACAGTATTTAAGCTCCT
10101540 TAGAATTATACTTTTGAATCATCTTTTGCATCAAGTGAATTATATGCCCATTTAGAATTTAATGC
130 TAGAATTATACTTTTGAATCATCTTTTGCATCAAGTGAATTATATGCCCATTTAGAATTTAATGC
10101605 CAGAAAATGAAACAAT
195 CAGAAAATGAAACAAT
*
10101621 GTACCATTTAGAATTATACTTTTGAATCATCTTTTGCATCAAGTGGATTATATGAAT
1 GTACCATTTAGAATTATACTTTTGAATCATCTTTTGCATCAAGTGAATTATATGAAT
10101678 TATGATTACC
Statistics
Matches: 260, Mismatches: 5, Indels: 12
0.94 0.02 0.04
Matches are distributed among these distances:
209 196 0.75
210 2 0.01
217 5 0.02
218 3 0.01
219 54 0.21
ACGTcount: A:0.35, C:0.16, G:0.12, T:0.36
Consensus pattern (210 bp):
GTACCATTTAGAATTATACTTTTGAATCATCTTTTGCATCAAGTGAATTATATGAATAAACATGC
ACATGCATCAACAACATTAATGATATACCTCATTACATGCAGAATTTACAGTATTTAAGCTCCTT
AGAATTATACTTTTGAATCATCTTTTGCATCAAGTGAATTATATGCCCATTTAGAATTTAATGCC
AGAAAATGAAACAAT
Found at i:10107397 original size:7 final size:7
Alignment explanation
Indices: 10107385--10107482 Score: 54
Period size: 7 Copynumber: 13.4 Consensus size: 7
10107375 AGTTAACTCC
*
10107385 TAAACCT
1 TAAACCA
*
10107392 TAAACCC
1 TAAACCA
10107399 TAAACCA
1 TAAACCA
* * *
10107406 TATATCT
1 TAAACCA
10107413 TAAACCA
1 TAAACCA
10107420 TAGTTAACTCA
1 TA---AAC-CA
10107431 TAAA-CA
1 TAAACCA
*
10107437 TTAAACCC
1 -TAAACCA
10107445 TAAACCA
1 TAAACCA
* * *
10107452 TATATCT
1 TAAACCA
10107459 TAAACCA
1 TAAACCA
10107466 TAAACCA
1 TAAACCA
*
10107473 TAAACTA
1 TAAACCA
10107480 TAA
1 TAA
10107483 TGATAATTAA
Statistics
Matches: 68, Mismatches: 17, Indels: 12
0.70 0.18 0.12
Matches are distributed among these distances:
6 2 0.03
7 56 0.82
8 3 0.04
10 3 0.04
11 4 0.06
ACGTcount: A:0.48, C:0.24, G:0.01, T:0.27
Consensus pattern (7 bp):
TAAACCA
Found at i:10107402 original size:72 final size:70
Alignment explanation
Indices: 10107307--10107442 Score: 159
Period size: 72 Copynumber: 1.9 Consensus size: 70
10107297 CCTTAAACTC
* * ** *
10107307 TAACCCTAACCCCTAACCCCTAAATTATA-ATCCTTAAACCCATAATTCA-TCATAAACATTGAA
1 TAACCCTAAACCCTAAACCCTAAACCATATAT-CTTAAA-CCATAATTAACTCATAAACATT-AA
10107370 ACAATAGT
63 ACAATAGT
* *
10107378 TAACTCCTAAACCTTAAACCCTAAACCATATATCTTAAACCATAGTTAACTCATAAACATTAAAC
1 TAAC-CCTAAACCCTAAACCCTAAACCATATATCTTAAACCATAATTAACTCATAAACATTAAAC
10107443 CCTAAACCAT
Statistics
Matches: 55, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
71 16 0.29
72 37 0.67
73 2 0.04
ACGTcount: A:0.43, C:0.27, G:0.02, T:0.27
Consensus pattern (70 bp):
TAACCCTAAACCCTAAACCCTAAACCATATATCTTAAACCATAATTAACTCATAAACATTAAACA
ATAGT
Found at i:10107416 original size:21 final size:21
Alignment explanation
Indices: 10107390--10107474 Score: 91
Period size: 21 Copynumber: 3.9 Consensus size: 21
10107380 ACTCCTAAAC
*
10107390 CTTAAACCCTAAACCATATAT
1 CTTAAACCATAAACCATATAT
*
10107411 CTTAAACCATAGTTAACTCATA-AA
1 CTTAAACCATA---AAC-CATATAT
*
10107435 CATTAAACCCTAAACCATATAT
1 C-TTAAACCATAAACCATATAT
10107457 CTTAAACCATAAACCATA
1 CTTAAACCATAAACCATA
10107475 AACTATAATG
Statistics
Matches: 53, Mismatches: 5, Indels: 12
0.76 0.07 0.17
Matches are distributed among these distances:
21 30 0.57
22 5 0.09
24 5 0.09
25 13 0.25
ACGTcount: A:0.46, C:0.26, G:0.01, T:0.27
Consensus pattern (21 bp):
CTTAAACCATAAACCATATAT
Found at i:10107425 original size:46 final size:46
Alignment explanation
Indices: 10107368--10107467 Score: 173
Period size: 46 Copynumber: 2.2 Consensus size: 46
10107358 ATAAACATTG
* * *
10107368 AAACAATAGTTAACTCCTAAACCTTAAACCCTAAACCATATATCTT
1 AAACCATAGTTAACTCATAAACATTAAACCCTAAACCATATATCTT
10107414 AAACCATAGTTAACTCATAAACATTAAACCCTAAACCATATATCTT
1 AAACCATAGTTAACTCATAAACATTAAACCCTAAACCATATATCTT
10107460 AAACCATA
1 AAACCATA
10107468 AACCATAAAC
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
46 51 1.00
ACGTcount: A:0.46, C:0.25, G:0.02, T:0.27
Consensus pattern (46 bp):
AAACCATAGTTAACTCATAAACATTAAACCCTAAACCATATATCTT
Found at i:10107701 original size:41 final size:40
Alignment explanation
Indices: 10107640--10107724 Score: 134
Period size: 41 Copynumber: 2.1 Consensus size: 40
10107630 GTTATATGAC
10107640 TTTTAGCGACGTTTTGCCAAAAGCGCCGCTAATGCTCTGGT
1 TTTTAGCGACGTTTTGCCAAAAGCGCCGCTAATGCT-TGGT
* * *
10107681 TTTTAGCGGCGTTTTTCCAAAAGCGCCGCTAATGCTTTGT
1 TTTTAGCGACGTTTTGCCAAAAGCGCCGCTAATGCTTGGT
10107721 TTTT
1 TTTT
10107725 CTATTGCTAT
Statistics
Matches: 41, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
40 7 0.17
41 34 0.83
ACGTcount: A:0.18, C:0.22, G:0.22, T:0.38
Consensus pattern (40 bp):
TTTTAGCGACGTTTTGCCAAAAGCGCCGCTAATGCTTGGT
Found at i:10116106 original size:14 final size:14
Alignment explanation
Indices: 10116087--10116113 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
10116077 TTGGTAACCT
10116087 GTAAAAGCTTTTCC
1 GTAAAAGCTTTTCC
10116101 GTAAAAGCTTTTC
1 GTAAAAGCTTTTC
10116114 AAGCTTTTCT
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:0.30, C:0.19, G:0.15, T:0.37
Consensus pattern (14 bp):
GTAAAAGCTTTTCC
Found at i:10116276 original size:6 final size:6
Alignment explanation
Indices: 10116265--10116296 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
10116255 CTTCTCCCAT
10116265 TTCCCC TTCCCC TTCCCC TTCCCC TTCCCC TT
1 TTCCCC TTCCCC TTCCCC TTCCCC TTCCCC TT
10116297 GGGTTGCAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.00, C:0.62, G:0.00, T:0.38
Consensus pattern (6 bp):
TTCCCC
Found at i:10118151 original size:27 final size:27
Alignment explanation
Indices: 10118113--10118179 Score: 89
Period size: 27 Copynumber: 2.5 Consensus size: 27
10118103 GGCGCGAGAG
* * *
10118113 AAAGGCACAAATGGTTGTGCCTATCTC
1 AAAGGCGCAAATGGTTGTACCTATCCC
10118140 AAAGGCGCAAATGGTTGTACCTATCCC
1 AAAGGCGCAAATGGTTGTACCTATCCC
**
10118167 GGAGGCGCAAATG
1 AAAGGCGCAAATG
10118180 ATAGGGCCCA
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.30, C:0.22, G:0.27, T:0.21
Consensus pattern (27 bp):
AAAGGCGCAAATGGTTGTACCTATCCC
Found at i:10124872 original size:59 final size:60
Alignment explanation
Indices: 10124784--10124900 Score: 182
Period size: 59 Copynumber: 2.0 Consensus size: 60
10124774 ATACTAAACT
* * * *
10124784 AAACACAACAATTTATAACTTAATCCTAAATTACTAATAAATTAATTTTAAAATAATTCC
1 AAACAAAAAAATTTATAACATAATCCTAAATTACTAACAAATTAATTTTAAAATAATTCC
*
10124844 AAACAAAAAAATTT-TAACATAATCCTAAATTTCTAACAAATTAATTTTAAAATAATT
1 AAACAAAAAAATTTATAACATAATCCTAAATTACTAACAAATTAATTTTAAAATAATT
10124901 ATAAAAAACA
Statistics
Matches: 52, Mismatches: 5, Indels: 1
0.90 0.09 0.02
Matches are distributed among these distances:
59 40 0.77
60 12 0.23
ACGTcount: A:0.52, C:0.13, G:0.00, T:0.35
Consensus pattern (60 bp):
AAACAAAAAAATTTATAACATAATCCTAAATTACTAACAAATTAATTTTAAAATAATTCC
Found at i:10125089 original size:21 final size:22
Alignment explanation
Indices: 10125064--10125120 Score: 73
Period size: 21 Copynumber: 2.7 Consensus size: 22
10125054 TACATTACTT
10125064 TTTTTTTCTTTCTTC-TTCTTC
1 TTTTTTTCTTTCTTCTTTCTTC
* *
10125085 TTTTTTTC-TTCTCCTTTCTTT
1 TTTTTTTCTTTCTTCTTTCTTC
*
10125106 TTTTTTTCTCTCTTC
1 TTTTTTTCTTTCTTC
10125121 CGGTGTGTGG
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
20 5 0.17
21 21 0.70
22 4 0.13
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (22 bp):
TTTTTTTCTTTCTTCTTTCTTC
Found at i:10125090 original size:20 final size:20
Alignment explanation
Indices: 10125061--10125111 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 20
10125051 AAATACATTA
10125061 CTTTTTTTTTCTTTCTTC-TT
1 CTTTTTTTTTC-TTCTTCTTT
*
10125081 CTTCTTTTTTTCTTCTCCTTT
1 CTT-TTTTTTTCTTCTTCTTT
10125102 CTTTTTTTTT
1 CTTTTTTTTT
10125112 TCTCTCTTCC
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
20 15 0.54
21 13 0.46
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (20 bp):
CTTTTTTTTTCTTCTTCTTT
Found at i:10125103 original size:18 final size:17
Alignment explanation
Indices: 10125067--10125120 Score: 63
Period size: 18 Copynumber: 3.0 Consensus size: 17
10125057 ATTACTTTTT
*
10125067 TTTTCTTTCTTCTTCTTC
1 TTTT-TTTCTTCTCCTTC
10125085 TTTTTTTCTTCTCCTTTC
1 TTTTTTTCTTCTCC-TTC
*
10125103 TTTTTTTTTTCTCTCTTC
1 TTTTTTTCTTCTC-CTTC
10125121 CGGTGTGTGG
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
17 9 0.28
18 22 0.69
19 1 0.03
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (17 bp):
TTTTTTTCTTCTCCTTC
Found at i:10125689 original size:30 final size:30
Alignment explanation
Indices: 10125644--10125705 Score: 97
Period size: 30 Copynumber: 2.1 Consensus size: 30
10125634 CTTAACAAGC
*
10125644 AAATACCTCTAAAATAATAATAAAATTAAT
1 AAATACCTCTAAAATAATAACAAAATTAAT
* *
10125674 AAATGCCTTTAAAATAATAACAAAATTAAT
1 AAATACCTCTAAAATAATAACAAAATTAAT
10125704 AA
1 AA
10125706 TAAAATAAGT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.60, C:0.10, G:0.02, T:0.29
Consensus pattern (30 bp):
AAATACCTCTAAAATAATAACAAAATTAAT
Found at i:10130998 original size:19 final size:20
Alignment explanation
Indices: 10130964--10131001 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
10130954 AATCCTTATA
10130964 CTAAATTAACCTTAATTAAG
1 CTAAATTAACCTTAATTAAG
*
10130984 CTAAATTTA-CTTAATTAA
1 CTAAATTAACCTTAATTAA
10131002 AATCTAATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.45, C:0.13, G:0.03, T:0.39
Consensus pattern (20 bp):
CTAAATTAACCTTAATTAAG
Found at i:10141486 original size:19 final size:20
Alignment explanation
Indices: 10141462--10141505 Score: 72
Period size: 19 Copynumber: 2.2 Consensus size: 20
10141452 TCCAAACACT
*
10141462 AGAAAAGTAAATTATTTT-C
1 AGAAAAGTAAATCATTTTCC
10141481 AGAAAAGTAAATCATTTTCC
1 AGAAAAGTAAATCATTTTCC
10141501 AGAAA
1 AGAAA
10141506 TAATTTTTCG
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 17 0.74
20 6 0.26
ACGTcount: A:0.50, C:0.09, G:0.11, T:0.30
Consensus pattern (20 bp):
AGAAAAGTAAATCATTTTCC
Found at i:10142584 original size:13 final size:13
Alignment explanation
Indices: 10142566--10142620 Score: 65
Period size: 13 Copynumber: 4.2 Consensus size: 13
10142556 CTAGTTTGGC
10142566 AATGCTTTTGAAA
1 AATGCTTTTGAAA
* *
10142579 AATGCTGTGGAAA
1 AATGCTTTTGAAA
* *
10142592 AGTGCTTTTGAGA
1 AATGCTTTTGAAA
*
10142605 AGTGCTTTTGAAA
1 AATGCTTTTGAAA
10142618 AAT
1 AAT
10142621 TTAATTTAAA
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
13 34 1.00
ACGTcount: A:0.35, C:0.07, G:0.24, T:0.35
Consensus pattern (13 bp):
AATGCTTTTGAAA
Found at i:10142878 original size:12 final size:12
Alignment explanation
Indices: 10142861--10142893 Score: 66
Period size: 12 Copynumber: 2.8 Consensus size: 12
10142851 AGGGGAGGAC
10142861 TTGGGGATTACT
1 TTGGGGATTACT
10142873 TTGGGGATTACT
1 TTGGGGATTACT
10142885 TTGGGGATT
1 TTGGGGATT
10142894 CCTACTTCAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.15, C:0.06, G:0.36, T:0.42
Consensus pattern (12 bp):
TTGGGGATTACT
Found at i:10143394 original size:15 final size:14
Alignment explanation
Indices: 10143338--10143454 Score: 69
Period size: 15 Copynumber: 8.1 Consensus size: 14
10143328 TTATTATGTT
*
10143338 TCTATTTATATTTA
1 TCTATTTTTATTTA
*
10143352 T-T-TTATTATTCTAA
1 TCTATTTTTATT-T-A
*
10143366 TACTATTATTATTTA
1 T-CTATTTTTATTTA
10143381 TCTAATTTTTATTTA
1 TCT-ATTTTTATTTA
* *
10143396 TCTATTTATATTTC
1 TCTATTTTTATTTA
* *
10143410 TACTATTATTATATA
1 T-CTATTTTTATTTA
10143425 TCTATTTATTATATT-
1 TCTATTT-TTAT-TTA
* *
10143440 TTTATTTCTATTTA
1 TCTATTTTTATTTA
10143454 T
1 T
10143455 ATACTAATAT
Statistics
Matches: 80, Mismatches: 13, Indels: 20
0.71 0.12 0.18
Matches are distributed among these distances:
12 6 0.08
13 4 0.05
14 24 0.30
15 35 0.44
16 3 0.04
17 8 0.10
ACGTcount: A:0.28, C:0.08, G:0.00, T:0.64
Consensus pattern (14 bp):
TCTATTTTTATTTA
Found at i:10143445 original size:29 final size:29
Alignment explanation
Indices: 10143323--10143433 Score: 100
Period size: 29 Copynumber: 3.8 Consensus size: 29
10143313 ATATTATTGC
* *
10143323 TATTATTATTATGTTTCTATTTATATTTA
1 TATTATTATTATATATCTATTTATATTTA
* *
10143352 TTTTATTATTCTA-ATACTA-TTATTATTTA
1 TATTATTATTATATAT-CTATTTA-TATTTA
* * * * *
10143381 TCTAATTTTTATTTATCTATTTATATTTC
1 TATTATTATTATATATCTATTTATATTTA
*
10143410 TACTATTATTATATATCTATTTAT
1 TATTATTATTATATATCTATTTAT
10143434 TATATTTTTA
Statistics
Matches: 63, Mismatches: 15, Indels: 8
0.73 0.17 0.09
Matches are distributed among these distances:
28 4 0.06
29 54 0.86
30 5 0.08
ACGTcount: A:0.29, C:0.07, G:0.01, T:0.63
Consensus pattern (29 bp):
TATTATTATTATATATCTATTTATATTTA
Found at i:10143452 original size:58 final size:58
Alignment explanation
Indices: 10143338--10143454 Score: 132
Period size: 58 Copynumber: 2.0 Consensus size: 58
10143328 TTATTATGTT
** * *
10143338 TCTATTTATATTTATTTTATTATTCTAATACTATTATTATTTATCTAATTTTTATTTA
1 TCTATTTATATTTATACTATTATTATAATACTATTATTATTTATCTAATTTCTATTTA
* *
10143396 TCTATTTATATTTCTACTATTATTAT-ATATCTATTTATTATATT-T-TTATTTCTATTTA
1 TCTATTTATATTTATACTATTATTATAATA-CTA-TTATTAT-TTATCTAATTTCTATTTA
10143454 T
1 T
10143455 ATACTAATAT
Statistics
Matches: 50, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
57 3 0.06
58 37 0.74
59 8 0.16
60 2 0.04
ACGTcount: A:0.28, C:0.08, G:0.00, T:0.64
Consensus pattern (58 bp):
TCTATTTATATTTATACTATTATTATAATACTATTATTATTTATCTAATTTCTATTTA
Found at i:10143490 original size:52 final size:54
Alignment explanation
Indices: 10143369--10143490 Score: 125
Period size: 52 Copynumber: 2.4 Consensus size: 54
10143359 ATTCTAATAC
* * *
10143369 TATTATTATTTATC-TA-ATTTTTATTTATCTATTTATATTTCTACTATTATTA
1 TATTATTATTTTTCTTATATTTTTATTTATCTATTTATATTACTAATATTATTA
* *
10143421 TA-TATCTA--TTTATTATATTTTTA-TT-TCTATTTATA-TACTAATATTATTT
1 TATTAT-TATTTTTCTTATATTTTTATTTATCTATTTATATTACTAATATTATTA
10143470 TCATTATTATTTTTCTTATAT
1 T-ATTATTATTTTTCTTATAT
10143491 ATGTTTTTCT
Statistics
Matches: 57, Mismatches: 6, Indels: 14
0.74 0.08 0.18
Matches are distributed among these distances:
49 12 0.21
50 15 0.26
51 10 0.18
52 20 0.35
ACGTcount: A:0.29, C:0.07, G:0.00, T:0.64
Consensus pattern (54 bp):
TATTATTATTTTTCTTATATTTTTATTTATCTATTTATATTACTAATATTATTA
Found at i:10144805 original size:22 final size:21
Alignment explanation
Indices: 10144770--10144810 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
10144760 TTGTAATTAG
*
10144770 TATTTTTAAAAATATTTTTTT
1 TATTTTTAAAAATAATTTTTT
*
10144791 TATTTTTAATTAATAATTTT
1 TATTTTTAA-AAATAATTTT
10144811 AACACATTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 9 0.53
22 8 0.47
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (21 bp):
TATTTTTAAAAATAATTTTTT
Found at i:10145820 original size:3 final size:3
Alignment explanation
Indices: 10145814--10145838 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
10145804 GAGACGAAGA
10145814 AGG AGG AGG AGG AGG AGG AGG AGG A
1 AGG AGG AGG AGG AGG AGG AGG AGG A
10145839 AAACGATGAA
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:0.36, C:0.00, G:0.64, T:0.00
Consensus pattern (3 bp):
AGG
Found at i:10158008 original size:19 final size:19
Alignment explanation
Indices: 10157971--10158009 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
10157961 AGCAGACCAG
* *
10157971 GAAAAAAAAGGTAAGAAGA
1 GAAAAAAAAGGAAAAAAGA
*
10157990 GAAAAAAAATGAAAAAAGA
1 GAAAAAAAAGGAAAAAAGA
10158009 G
1 G
10158010 GGGTCCATTC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.72, C:0.00, G:0.23, T:0.05
Consensus pattern (19 bp):
GAAAAAAAAGGAAAAAAGA
Found at i:10162551 original size:21 final size:21
Alignment explanation
Indices: 10162522--10162562 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
10162512 ATCTGCTCAA
* *
10162522 ACTCCACCTGTTTTGGAGTAC
1 ACTCCACCTGCTGTGGAGTAC
*
10162543 ACTCTACCTGCTGTGGAGTA
1 ACTCCACCTGCTGTGGAGTA
10162563 TTGCTCGTCT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.20, C:0.27, G:0.22, T:0.32
Consensus pattern (21 bp):
ACTCCACCTGCTGTGGAGTAC
Found at i:10166894 original size:31 final size:31
Alignment explanation
Indices: 10166859--10166934 Score: 91
Period size: 31 Copynumber: 2.5 Consensus size: 31
10166849 TAGCCAAATG
* *
10166859 AATTTGAAACA-TGCAAAGATTAAAATTGATT
1 AATTTGAAA-AGTACAAAGAATAAAATTGATT
**
10166890 AATTTGAAAAGTACATGGAATAAAATTGATT
1 AATTTGAAAAGTACAAAGAATAAAATTGATT
*
10166921 AATTTAAAAAGTAC
1 AATTTGAAAAGTAC
10166935 GTAGACTAAA
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
30 1 0.03
31 38 0.97
ACGTcount: A:0.50, C:0.05, G:0.13, T:0.32
Consensus pattern (31 bp):
AATTTGAAAAGTACAAAGAATAAAATTGATT
Found at i:10169661 original size:46 final size:46
Alignment explanation
Indices: 10169591--10169726 Score: 184
Period size: 46 Copynumber: 3.0 Consensus size: 46
10169581 TTCGACATTA
* * * ** * *
10169591 TGCCATAGTATCTTTCAACTATGGTTTTACTAGTTTTC-TGTCATGT
1 TGCCATGGTATCTTTCAACCATGGTCTTAC-ACATTTCATATCAGGT
10169637 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
*
10169683 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATTTCAG
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAG
10169727 AGAGCACACT
Statistics
Matches: 81, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
45 5 0.06
46 76 0.94
ACGTcount: A:0.22, C:0.22, G:0.15, T:0.41
Consensus pattern (46 bp):
TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
Found at i:10191957 original size:21 final size:21
Alignment explanation
Indices: 10191932--10191972 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
10191922 CATTGATTTA
10191932 GTAAATTAGTTTATGAAATTC
1 GTAAATTAGTTTATGAAATTC
10191953 GTAAATTAGTTTATGAAATT
1 GTAAATTAGTTTATGAAATT
10191973 AGAATATGCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.39, C:0.02, G:0.15, T:0.44
Consensus pattern (21 bp):
GTAAATTAGTTTATGAAATTC
Found at i:10192676 original size:39 final size:39
Alignment explanation
Indices: 10192617--10192693 Score: 136
Period size: 39 Copynumber: 2.0 Consensus size: 39
10192607 TGCATGATAT
10192617 TTGGAAACATATCCGAACTTGAGGTCCGCAAGCTACGTG
1 TTGGAAACATATCCGAACTTGAGGTCCGCAAGCTACGTG
* *
10192656 TTGGAAACATATCCGGACTTGAGGTCCGCAGGCTACGT
1 TTGGAAACATATCCGAACTTGAGGTCCGCAAGCTACGT
10192694 ACTGGAATAT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 36 1.00
ACGTcount: A:0.26, C:0.23, G:0.27, T:0.23
Consensus pattern (39 bp):
TTGGAAACATATCCGAACTTGAGGTCCGCAAGCTACGTG
Found at i:10192700 original size:39 final size:39
Alignment explanation
Indices: 10192618--10192709 Score: 132
Period size: 39 Copynumber: 2.4 Consensus size: 39
10192608 GCATGATATT
* **
10192618 TGGAAACATATCCGAACTTGAGGTCCGCAAGCTACGTGT
1 TGGAAACATATCCGGACTTGAGGTCCGCAAGCTACGTAC
*
10192657 TGGAAACATATCCGGACTTGAGGTCCGCAGGCTACGTAC
1 TGGAAACATATCCGGACTTGAGGTCCGCAAGCTACGTAC
*
10192696 TGG-AATATATCCGG
1 TGGAAACATATCCGG
10192710 GCCTAAAGTC
Statistics
Matches: 48, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
38 10 0.21
39 38 0.79
ACGTcount: A:0.27, C:0.23, G:0.27, T:0.23
Consensus pattern (39 bp):
TGGAAACATATCCGGACTTGAGGTCCGCAAGCTACGTAC
Found at i:10194353 original size:13 final size:13
Alignment explanation
Indices: 10194335--10194361 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
10194325 GCTCGGCAGG
10194335 GACACGCCCGTGT
1 GACACGCCCGTGT
10194348 GACACGCCCGTGT
1 GACACGCCCGTGT
10194361 G
1 G
10194362 CAATTACTTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.15, C:0.37, G:0.33, T:0.15
Consensus pattern (13 bp):
GACACGCCCGTGT
Found at i:10195920 original size:12 final size:13
Alignment explanation
Indices: 10195893--10195930 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
10195883 ACAAAATATT
10195893 AAATTTATTCATA
1 AAATTTATTCATA
*
10195906 AAATTTATTTA-A
1 AAATTTATTCATA
10195918 AAATTTTATTCAT
1 AAA-TTTATTCAT
10195931 TTTCACAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
12 4 0.19
13 17 0.81
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (13 bp):
AAATTTATTCATA
Found at i:10200925 original size:20 final size:18
Alignment explanation
Indices: 10200886--10200937 Score: 59
Period size: 21 Copynumber: 2.7 Consensus size: 18
10200876 TCTTCTGACC
10200886 AAAATAAAAATATATCAA
1 AAAATAAAAATATATCAA
*
10200904 AAAACTAAAAAGTATAATAAA
1 AAAA-TAAAAA-TAT-ATCAA
10200925 AAAATAATAAATA
1 AAAATAA-AAATA
10200938 AAAATTTACA
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
18 4 0.14
19 6 0.21
20 8 0.28
21 11 0.38
ACGTcount: A:0.73, C:0.04, G:0.02, T:0.21
Consensus pattern (18 bp):
AAAATAAAAATATATCAA
Found at i:10220032 original size:21 final size:21
Alignment explanation
Indices: 10220006--10220081 Score: 71
Period size: 21 Copynumber: 3.6 Consensus size: 21
10219996 TCGAACTTTT
*
10220006 TATTTAACTCTTACAAGCTTC
1 TATTTAACTCTTACGAGCTTC
* * *
10220027 TATTTAACTCATACGTGTTTC
1 TATTTAACTCTTACGAGCTTC
* * *
10220048 TGTTTAGCTCTTATGAGCTTC
1 TATTTAACTCTTACGAGCTTC
* *
10220069 TGTTCAACTCTTA
1 TATTTAACTCTTA
10220082 AGAGTTTTTG
Statistics
Matches: 43, Mismatches: 12, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
21 43 1.00
ACGTcount: A:0.22, C:0.21, G:0.11, T:0.46
Consensus pattern (21 bp):
TATTTAACTCTTACGAGCTTC
Found at i:10220093 original size:21 final size:21
Alignment explanation
Indices: 10220045--10220112 Score: 59
Period size: 21 Copynumber: 3.3 Consensus size: 21
10220035 TCATACGTGT
* * *
10220045 TTCTGTTTAGCTCTTATGAGC
1 TTCTGTTCAACTCTTAAGAGC
*
10220066 TTCTGTTCAACTCTTAAGAGT
1 TTCTGTTCAACTCTTAAGAGC
* * *
10220087 TTTTGTTC-A-GCTTATGAGC
1 TTCTGTTCAACTCTTAAGAGC
10220106 TTCTGTT
1 TTCTGTT
10220113 AATGATGTAC
Statistics
Matches: 38, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
19 13 0.34
20 1 0.03
21 24 0.63
ACGTcount: A:0.16, C:0.18, G:0.18, T:0.49
Consensus pattern (21 bp):
TTCTGTTCAACTCTTAAGAGC
Found at i:10220112 original size:19 final size:21
Alignment explanation
Indices: 10220057--10220112 Score: 62
Period size: 21 Copynumber: 2.8 Consensus size: 21
10220047 CTGTTTAGCT
*
10220057 CTTATGAGCTTCTGTTCAACT
1 CTTATGAGCTTCTGTTCAACG
* * *
10220078 CTTAAGAGTTTTTGTTC-A-G
1 CTTATGAGCTTCTGTTCAACG
10220097 CTTATGAGCTTCTGTT
1 CTTATGAGCTTCTGTT
10220113 AATGATGTAC
Statistics
Matches: 28, Mismatches: 7, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
19 13 0.46
20 1 0.04
21 14 0.50
ACGTcount: A:0.18, C:0.18, G:0.18, T:0.46
Consensus pattern (21 bp):
CTTATGAGCTTCTGTTCAACG
Found at i:10222692 original size:3 final size:3
Alignment explanation
Indices: 10222684--10222709 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
10222674 TAATTAAATT
10222684 TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TT
10222710 TTGGTTTTGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:10224222 original size:11 final size:11
Alignment explanation
Indices: 10224206--10224230 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
10224196 TCAAACCCCA
10224206 AAAAAAAAAAG
1 AAAAAAAAAAG
10224217 AAAAAAAAAAG
1 AAAAAAAAAAG
10224228 AAA
1 AAA
10224231 GATATTTTGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (11 bp):
AAAAAAAAAAG
Found at i:10228471 original size:24 final size:24
Alignment explanation
Indices: 10228440--10228492 Score: 97
Period size: 24 Copynumber: 2.2 Consensus size: 24
10228430 AAATTAGATC
10228440 TCTATTTCTTTTATAATTCTTATA
1 TCTATTTCTTTTATAATTCTTATA
10228464 TCTATTTCTTTTATAATTCTTATA
1 TCTATTTCTTTTATAATTCTTATA
*
10228488 CCTAT
1 TCTAT
10228493 AAATAAAGGC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.25, C:0.15, G:0.00, T:0.60
Consensus pattern (24 bp):
TCTATTTCTTTTATAATTCTTATA
Found at i:10229651 original size:15 final size:15
Alignment explanation
Indices: 10229631--10229682 Score: 50
Period size: 15 Copynumber: 3.2 Consensus size: 15
10229621 ATTACAAAAC
10229631 ATTTATTATTAATAT
1 ATTTATTATTAATAT
*
10229646 ATTTATAATTATAATAAAT
1 ATTTATTA-T-TAAT--AT
*
10229665 ATTTATTATTAAAAT
1 ATTTATTATTAATAT
10229680 ATT
1 ATT
10229683 AATATTGAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 8
0.73 0.07 0.20
Matches are distributed among these distances:
15 12 0.40
16 1 0.03
17 7 0.23
18 1 0.03
19 9 0.30
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (15 bp):
ATTTATTATTAATAT
Done.