Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_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: 113101708
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2797742 characters in sequence are not A, C, G, or T
File 30 of 352
Found at i:9634241 original size:40 final size:38
Alignment explanation
Indices: 9634175--9634307 Score: 92
Period size: 40 Copynumber: 3.4 Consensus size: 38
9634165 CAGAATGGCA
* * *
9634175 CCCAGTGCCTCATCGGATAGTTCGAAGCAATATAGTGAC
1 CCCAGTGCCTCATCGGCTAG-CCGAAGAAATATAGTGAC
* * *
9634214 GCCCAGTGTCTCATCGGCCTAGCCGAAGTAAA-GTGGT-A-
1 -CCCAGTGCCTCATCGG-CTAGCCGAAG-AAATATAGTGAC
* * *
9634252 CCCAGTACCTCATCGAATCTATCCGAAGAAATATAGTGAC
1 CCCAGTGCCTCATCG--GCTAGCCGAAGAAATATAGTGAC
*
9634292 ACCCAGTGTCTCATCG
1 -CCCAGTGCCTCATCG
9634308 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:9635230 original size:20 final size:21
Alignment explanation
Indices: 9635207--9635251 Score: 74
Period size: 20 Copynumber: 2.2 Consensus size: 21
9635197 AATTATTTAT
*
9635207 TTAATAAATATCT-TTTATAA
1 TTAATAAATATCTATTAATAA
9635227 TTAATAAATATCTATTAATAA
1 TTAATAAATATCTATTAATAA
9635248 TTAA
1 TTAA
9635252 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:9635825 original size:29 final size:33
Alignment explanation
Indices: 9635738--9635825 Score: 80
Period size: 34 Copynumber: 2.8 Consensus size: 33
9635728 TATTTATCAT
*
9635738 ATAAATATC-TTATAATATAATTATAATAAATTAA
1 ATAAATATCATT-TATTATAATTA-AATAAATTAA
* *
9635772 TTTAATATCATTTATTATTAA-TAAATAAA-TAA
1 ATAAATATCATTTATTA-TAATTAAATAAATTAA
9635804 ATAAATAT-A-TT-TTATAATTAAA
1 ATAAATATCATTTATTATAATTAAA
9635826 ATCTAAGTAA
Statistics
Matches: 46, Mismatches: 5, Indels: 11
0.74 0.08 0.18
Matches are distributed among these distances:
28 3 0.07
29 7 0.15
30 2 0.04
31 1 0.02
32 9 0.20
33 6 0.13
34 13 0.28
35 5 0.11
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.44
Consensus pattern (33 bp):
ATAAATATCATTTATTATAATTAAATAAATTAA
Found at i:9644455 original size:21 final size:22
Alignment explanation
Indices: 9644431--9644479 Score: 59
Period size: 21 Copynumber: 2.3 Consensus size: 22
9644421 CTAGATTTAT
9644431 TTTTTATTTCATT-TTTTCAA-G
1 TTTTTATTT-ATTATTTTCAATG
9644452 TTTTT-TTTATTAATTTTCAATG
1 TTTTTATTTATT-ATTTTCAATG
9644474 TTTTTA
1 TTTTTA
9644480 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:9644483 original size:20 final size:21
Alignment explanation
Indices: 9644444--9644485 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
9644434 TTATTTCATT
* *
9644444 TTTTCAAGTTTTTTTTATTAA
1 TTTTCAAGTGTTTTTAATTAA
9644465 TTTTCAA-TGTTTTTAATTAA
1 TTTTCAAGTGTTTTTAATTAA
9644485 T
1 T
9644486 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:9649616 original size:65 final size:66
Alignment explanation
Indices: 9649547--9649675 Score: 165
Period size: 66 Copynumber: 2.0 Consensus size: 66
9649537 TGGTACAGGT
* **
9649547 TGAAAAGGTTATGTACACTTTGTGTGTATA-C-TTGGA-AAGGTTAGGTATACTTTGTGTATACC
1 TGAAAAGGTTAGGTACAC-TT-TGTGTATACCATTGGACAAGGAAAGGTATACTTTGTGTATACC
9649609 ATA
64 ATA
* * *
9649612 TGAAAAGGTTAGGTATACTTTGTGTATACCATTTGACAAGGAAAGGTATACTTTGTGTGTACCA
1 TGAAAAGGTTAGGTACACTTTGTGTATACCATTGGACAAGGAAAGGTATACTTTGTGTATACCA
9649676 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:9649623 original size:33 final size:32
Alignment explanation
Indices: 9649546--9649675 Score: 147
Period size: 33 Copynumber: 4.0 Consensus size: 32
9649536 ATGGTACAGG
* *
9649546 TTGAAAAGGTTATGTACACTTTGTGTGTATA-C-
1 TTGAAAAGGTTAGGTATAC-TT-TGTGTATACCA
*
9649578 TTGGAAAGGTTAGGTATACTTTGTGTATACCA
1 TTGAAAAGGTTAGGTATACTTTGTGTATACCA
9649610 TATGAAAAGGTTAGGTATACTTTGTGTATACCA
1 T-TGAAAAGGTTAGGTATACTTTGTGTATACCA
* ** *
9649643 TTTGACAAGGAAAGGTATACTTTGTGTGTACCA
1 -TTGAAAAGGTTAGGTATACTTTGTGTATACCA
9649676 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:9651845 original size:24 final size:23
Alignment explanation
Indices: 9651797--9651846 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
9651787 ACAAAGAAAA
*
9651797 TAAAAATAAAAAAGGAACAATTT
1 TAAAAATAAAAAAGGAACAAATT
* *
9651820 TAAATATAAAAAAGGGACTAAATT
1 TAAAAATAAAAAAGGAAC-AAATT
9651844 TAA
1 TAA
9651847 GGGAAAAATA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
23 16 0.70
24 7 0.30
ACGTcount: A:0.62, C:0.04, G:0.10, T:0.24
Consensus pattern (23 bp):
TAAAAATAAAAAAGGAACAAATT
Found at i:9657387 original size:16 final size:17
Alignment explanation
Indices: 9657356--9657387 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
9657346 GCAAGCAATT
9657356 TTTTAAAATATTTATTC
1 TTTTAAAATATTTATTC
9657373 TTTTAAAAT-TTTATT
1 TTTTAAAATATTTATT
9657388 ATATCCGAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.62
Consensus pattern (17 bp):
TTTTAAAATATTTATTC
Found at i:9661946 original size:19 final size:19
Alignment explanation
Indices: 9661922--9661963 Score: 84
Period size: 19 Copynumber: 2.2 Consensus size: 19
9661912 CCTAGCTATA
9661922 CGCTCAAGCGCACTTTATC
1 CGCTCAAGCGCACTTTATC
9661941 CGCTCAAGCGCACTTTATC
1 CGCTCAAGCGCACTTTATC
9661960 CGCT
1 CGCT
9661964 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:9665690 original size:2 final size:2
Alignment explanation
Indices: 9665677--9665721 Score: 72
Period size: 2 Copynumber: 22.5 Consensus size: 2
9665667 TCATAAATTA
* *
9665677 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
9665719 AG A
1 AG A
9665722 TCATACCTTT
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.02, G:0.44, T:0.02
Consensus pattern (2 bp):
AG
Found at i:9676717 original size:2 final size:2
Alignment explanation
Indices: 9676710--9676739 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
9676700 TTTTCACCAA
9676710 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
9676740 GGTTTCAAAT
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):
AT
Found at i:9676889 original size:27 final size:26
Alignment explanation
Indices: 9676859--9676939 Score: 71
Period size: 27 Copynumber: 3.2 Consensus size: 26
9676849 TTAATTTAAG
*
9676859 AAAAAATTCAAATCGAGTTAAGATAAT
1 AAAAAATT-AAATTGAGTTAAGATAAT
* **
9676886 -AAAAA-T-AATTTA-TTAACTTAACT
1 AAAAAATTAAATTGAGTTAAGATAA-T
9676909 AAAAAATTTAAATTGAGTTAAGATAAT
1 AAAAAA-TTAAATTGAGTTAAGATAAT
9676936 AAAA
1 AAAA
9676940 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:9676927 original size:50 final size:51
Alignment explanation
Indices: 9676859--9676961 Score: 172
Period size: 50 Copynumber: 2.0 Consensus size: 51
9676849 TTAATTTAAG
*
9676859 AAAAAATTCAAATCGAGTTAAGATAATAAAA-ATAATTTATTAACTTAACT
1 AAAAAATTCAAATCGAGTTAAGATAATAAAATATAACTTATTAACTTAACT
* *
9676909 AAAAAATTTAAATTGAGTTAAGATAATAAAATATAACTTATTAACTTAACT
1 AAAAAATTCAAATCGAGTTAAGATAATAAAATATAACTTATTAACTTAACT
9676960 AA
1 AA
9676962 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:9684180 original size:21 final size:17
Alignment explanation
Indices: 9684137--9684176 Score: 62
Period size: 17 Copynumber: 2.2 Consensus size: 17
9684127 CAGGGGAAGG
9684137 AAGAAAGAAAAAGAGAA
1 AAGAAAGAAAAAGAGAA
9684154 AAGAAAGAAGAAAGAAGAA
1 AAGAAAGAA-AAAG-AGAA
9684173 AAGA
1 AAGA
9684177 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:9685027 original size:7 final size:7
Alignment explanation
Indices: 9685017--9685106 Score: 58
Period size: 7 Copynumber: 12.0 Consensus size: 7
9685007 TTATATAAAA
9685017 TATATAT
1 TATATAT
9685024 TATATAT
1 TATATAT
9685031 TATATTAACT
1 TATA-T-A-T
9685041 TA-ATAT
1 TATATAT
*
9685047 TTTAGTAT
1 TATA-TAT
9685055 TAATATAT
1 T-ATATAT
*
9685063 AATATAT
1 TATATAT
9685070 TATATTAT
1 TATA-TAT
9685078 TATAT-T
1 TATATAT
*
9685084 ATATATAA
1 -TATATAT
9685092 TATAATAT
1 TAT-ATAT
*
9685100 AATATAT
1 TATATAT
9685107 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:9686311 original size:22 final size:22
Alignment explanation
Indices: 9686282--9686338 Score: 71
Period size: 22 Copynumber: 2.6 Consensus size: 22
9686272 TAGCACGTTA
9686282 AGTGCTCTCTGTTTAGCACATCT
1 AGTGCTCTCTGTTTAGCAC-TCT
* * *
9686305 -GTGCTCTCTATATAGCACTTT
1 AGTGCTCTCTGTTTAGCACTCT
9686326 AGTGCTCTCTGTT
1 AGTGCTCTCTGTT
9686339 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:9687703 original size:6 final size:6
Alignment explanation
Indices: 9687692--9687718 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
9687682 TGTGTACCGC
9687692 TACTGT TACTGT TACTGT TACTGT TAC
1 TACTGT TACTGT TACTGT TACTGT TAC
9687719 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:9690509 original size:65 final size:65
Alignment explanation
Indices: 9690392--9690520 Score: 167
Period size: 65 Copynumber: 2.0 Consensus size: 65
9690382 AGGTTTTCAA
* *
9690392 TTCACTTTTCAACAACAATCAATATTCAATTATCACAATATTTACATAAATCTCAATTCAATATT
1 TTCACATTTCAACAACAATCAATATTCAATAATCACAATATTTACATAAATCTCAATTCAATATT
*
9690457 TTCACATTTCAACAACAATTAATAGTTTC-ATCAATCACAA-A-TT-CATATAATCTCAATTCAA
1 TTCACATTTCAACAACAATCAATA--TTCAAT-AATCACAATATTTACATA-AATCTCAATTCAA
9690518 TAT
62 TAT
9690521 CAAGATAATA
Statistics
Matches: 57, Mismatches: 3, Indels: 8
0.84 0.04 0.12
Matches are distributed among these distances:
64 4 0.07
65 40 0.70
66 3 0.05
67 10 0.18
ACGTcount: A:0.42, C:0.20, G:0.01, T:0.37
Consensus pattern (65 bp):
TTCACATTTCAACAACAATCAATATTCAATAATCACAATATTTACATAAATCTCAATTCAATATT
Found at i:9693164 original size:22 final size:22
Alignment explanation
Indices: 9693121--9693164 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
9693111 TAAATCTAAT
*
9693121 ATAAAATTATATTTAATTAAAA
1 ATAAAATTATATTTAATAAAAA
*
9693143 ATAAAATTA-ATTTTTATAAAAA
1 ATAAAATTATA-TTTAATAAAAA
9693165 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:9694026 original size:24 final size:25
Alignment explanation
Indices: 9693994--9694047 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 25
9693984 AAATTACAAA
* *
9693994 AAAAAATTAAAAAAATT-ATTTTTT
1 AAAATATTAAAAAAATTAATATTTT
* *
9694018 AAAATATTAGAAAATTTAATATTTT
1 AAAATATTAAAAAAATTAATATTTT
9694043 AAAAT
1 AAAAT
9694048 TTTATAAATT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
24 14 0.56
25 11 0.44
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (25 bp):
AAAATATTAAAAAAATTAATATTTT
Found at i:9705844 original size:16 final size:16
Alignment explanation
Indices: 9705823--9705858 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
9705813 TTATTCATAA
9705823 AAAGAAGATCAAAATT
1 AAAGAAGATCAAAATT
9705839 AAAGAAGATCAAAATT
1 AAAGAAGATCAAAATT
9705855 AAAG
1 AAAG
9705859 GTTTTGATGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.64, C:0.06, G:0.14, T:0.17
Consensus pattern (16 bp):
AAAGAAGATCAAAATT
Found at i:9706536 original size:3 final size:3
Alignment explanation
Indices: 9706528--9706594 Score: 134
Period size: 3 Copynumber: 22.3 Consensus size: 3
9706518 GTTGGGCAGT
9706528 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
9706576 AGA AGA AGA AGA AGA AGA A
1 AGA AGA AGA AGA AGA AGA A
9706595 TGGCAAGAGG
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 64 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:9711462 original size:36 final size:36
Alignment explanation
Indices: 9711374--9711477 Score: 111
Period size: 36 Copynumber: 2.9 Consensus size: 36
9711364 AATGTATTGG
* *
9711374 ATAACTAACTGCCACTGAATAATTGACTGTTACTAA
1 ATAACTGACTGCTACTGAATAATTGACTGTTACTAA
* * *
9711410 ATAACTGACTGCTACTGAGTAATTGACTGTTATTGA
1 ATAACTGACTGCTACTGAATAATTGACTGTTACTAA
* * * *
9711446 ATAATTTA-TCGTTACTGAATAACTGACTGTTA
1 ATAACTGACT-GCTACTGAATAATTGACTGTTA
9711478 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:9711477 original size:18 final size:18
Alignment explanation
Indices: 9711387--9711477 Score: 103
Period size: 18 Copynumber: 5.1 Consensus size: 18
9711377 ACTAACTGCC
9711387 ACTGAATAATTGACTGTT
1 ACTGAATAATTGACTGTT
* * *
9711405 ACTAAATAACTGACTGCT
1 ACTGAATAATTGACTGTT
*
9711423 ACTGAGTAATTGACTGTT
1 ACTGAATAATTGACTGTT
* *
9711441 ATTGAATAATTTA-TCGTT
1 ACTGAATAATTGACT-GTT
*
9711459 ACTGAATAACTGACTGTT
1 ACTGAATAATTGACTGTT
9711477 A
1 A
9711478 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:9725014 original size:25 final size:25
Alignment explanation
Indices: 9724980--9725029 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
9724970 TAACCAAAGA
*
9724980 AATCCAATTCATTGCATATTCATAT
1 AATCCAATTCACTGCATATTCATAT
*
9725005 AATCTAATTCACTGCATATTCATAT
1 AATCCAATTCACTGCATATTCATAT
9725030 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:9726876 original size:10 final size:10
Alignment explanation
Indices: 9726844--9726904 Score: 52
Period size: 10 Copynumber: 6.0 Consensus size: 10
9726834 GATTTTAGTT
*
9726844 TTTATTTATA
1 TTTAATTATA
*
9726854 ATTAATTATTA
1 TTTAATTA-TA
9726865 TTTAATTATA
1 TTTAATTATA
* *
9726875 TTTAAATAAA
1 TTTAATTATA
9726885 TTT-ATTAGTA
1 TTTAATTA-TA
*
9726895 TTTATTTATA
1 TTTAATTATA
9726905 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:0.00, G:0.02, T:0.59
Consensus pattern (10 bp):
TTTAATTATA
Found at i:9731204 original size:33 final size:35
Alignment explanation
Indices: 9731166--9731262 Score: 98
Period size: 33 Copynumber: 2.8 Consensus size: 35
9731156 ATAGTTATAT
9731166 TTAAATATTTAAAATATATTTTATATATT-C-TAA
1 TTAAATATTTAAAATATATTTTATATATTGCTTAA
* *
9731199 TTAAAT-TTTATAAATA-ATTAATATTTATTGCTTAA
1 TTAAATATTTA-AAATATATT-TTATATATTGCTTAA
9731234 --AAATATTTAAAATTTATATTTTATATATT
1 TTAAATATTTAAAA--TATATTTTATATATT
9731263 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:9731864 original size:33 final size:36
Alignment explanation
Indices: 9731827--9731901 Score: 86
Period size: 33 Copynumber: 2.2 Consensus size: 36
9731817 AAAAAACATA
* * *
9731827 ATTTAATT-TAATATAAAATTATTTTAA-ATGAT-T
1 ATTTAATTATAATACAAAATCATTTTAATATAATGT
*
9731860 ATTT-ATTATATTACAAAATCATTTTAATATAATGT
1 ATTTAATTATAATACAAAATCATTTTAATATAATGT
9731895 ATTTAAT
1 ATTTAAT
9731902 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:9733991 original size:41 final size:41
Alignment explanation
Indices: 9733912--9733991 Score: 92
Period size: 41 Copynumber: 2.0 Consensus size: 41
9733902 GTGAACTTTT
* ***
9733912 TTTAAAAATTTTTTATAAGTTAAAATTATTCTTTTATATTA
1 TTTAAAAATTTTTTATAAATTAAAATTATTCAGATATATTA
9733953 TTTAAAAATATTTTTA-AAATTAAAAATTATT-AGATATAT
1 TTTAAAAAT-TTTTTATAAATT-AAAATTATTCAGATATAT
9733992 ATGATTTCTA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
41 18 0.55
42 15 0.45
ACGTcount: A:0.45, C:0.01, G:0.03, T:0.51
Consensus pattern (41 bp):
TTTAAAAATTTTTTATAAATTAAAATTATTCAGATATATTA
Found at i:9734493 original size:24 final size:24
Alignment explanation
Indices: 9734452--9734497 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
9734442 ATATTATTTT
9734452 TTTTATAATTTTAGAATATTTATA
1 TTTTATAATTTTAGAATATTTATA
*
9734476 TTTT-TAATTGTTATAATATTTA
1 TTTTATAATT-TTAGAATATTTA
9734498 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:9737850 original size:18 final size:19
Alignment explanation
Indices: 9737817--9737853 Score: 58
Period size: 18 Copynumber: 1.9 Consensus size: 19
9737807 ACAAAATAAT
9737817 TAATTTACATTATTTTTTTC
1 TAATTTACA-TATTTTTTTC
9737837 TAATTTAC-TATTTTTTT
1 TAATTTACATATTTTTTT
9737854 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:9745484 original size:50 final size:50
Alignment explanation
Indices: 9745360--9745658 Score: 384
Period size: 50 Copynumber: 5.8 Consensus size: 50
9745350 GATAATAACA
* * ** *
9745360 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCGTGAT-GG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGA-CCTCTCGT-CTCGG
* * *
9745411 TGCCCATGCCATGTCCCAGACATGGTCTTATAGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCGTCTCGG
* *
9745461 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCGTCTCGG
*
9745511 TGCCCATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCGTCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCGTCTCGG
* *
9745561 TGCCCATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATGATCTTAAGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTC--G-TC-T-CGG
* *
9745616 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 -TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCT
9745659 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:9745773 original size:13 final size:13
Alignment explanation
Indices: 9745752--9745783 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
9745742 GCTTGGATCA
*
9745752 TCATCAAATAAAT
1 TCATAAAATAAAT
9745765 TCATAAAATAAAT
1 TCATAAAATAAAT
9745778 TCATAA
1 TCATAA
9745784 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:9746030 original size:30 final size:30
Alignment explanation
Indices: 9745995--9746052 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
9745985 CCTCGACTCT
*
9745995 AACTTTTTCAAAATTACAATTTTGCCCCTA
1 AACTTTTACAAAATTACAATTTTGCCCCTA
* *
9746025 AACTTTTACATAATTACATTTTTGCCCC
1 AACTTTTACAAAATTACAATTTTGCCCC
9746053 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:9748081 original size:5 final size:5
Alignment explanation
Indices: 9748071--9748099 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
9748061 TGTGTGGTTC
9748071 TTTAT TTTAT TTTAT TTTAT TTTAT TTTA
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTTA
9748100 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:9752118 original size:13 final size:13
Alignment explanation
Indices: 9752102--9752126 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
9752092 ATACTTAAGT
9752102 ATAATATAATAAA
1 ATAATATAATAAA
9752115 ATAATATAATAA
1 ATAATATAATAA
9752127 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:9752681 original size:44 final size:42
Alignment explanation
Indices: 9752615--9752722 Score: 101
Period size: 42 Copynumber: 2.5 Consensus size: 42
9752605 GACTTCGAGT
** * * *
9752615 CGATGAGGCACT-ATGTGTCGTATTATTATTGCTTCAGATATATC
1 CGATGAGGCACTGA-GTACCGTATTATT-TTACTTC-GACATAGC
* * *
9752659 CGATGAGGTACTGAGTACCGTATTGTTTTACTTCGACATGGC
1 CGATGAGGCACTGAGTACCGTATTATTTTACTTCGACATAGC
*
9752701 CGATGAGGCACTGAGTGCCGTA
1 CGATGAGGCACTGAGTACCGTA
9752723 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:9761508 original size:10 final size:10
Alignment explanation
Indices: 9761493--9761517 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
9761483 ACTCTATTAC
9761493 TCAAAAAATA
1 TCAAAAAATA
9761503 TCAAAAAATA
1 TCAAAAAATA
9761513 TCAAA
1 TCAAA
9761518 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:9767542 original size:16 final size:17
Alignment explanation
Indices: 9767515--9767554 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
9767505 CCCTTTTCTT
*
9767515 TCTCTCTTTTTCGTCTG
1 TCTCTCTGTTTCGTCTG
*
9767532 T-TCTCTGTTTCTTCTG
1 TCTCTCTGTTTCGTCTG
9767548 TCTCTCT
1 TCTCTCT
9767555 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:9769847 original size:16 final size:16
Alignment explanation
Indices: 9769828--9769868 Score: 68
Period size: 16 Copynumber: 2.7 Consensus size: 16
9769818 TTTATAATAA
9769828 TAATTATTATTATTTT
1 TAATTATTATTATTTT
9769844 TAATTATTATTATTTT
1 TAATTATTATTATTTT
9769860 T--TTATTATT
1 TAATTATTATT
9769869 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:9769847 original size:19 final size:18
Alignment explanation
Indices: 9769825--9769863 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 18
9769815 ATATTTATAA
9769825 TAATAATTATTATTATTTT
1 TAATAATTATTATT-TTTT
*
9769844 TAATTATTATTATTTTTT
1 TAATAATTATTATTTTTT
9769862 TA
1 TA
9769864 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:9769851 original size:10 final size:9
Alignment explanation
Indices: 9769834--9769871 Score: 51
Period size: 9 Copynumber: 4.2 Consensus size: 9
9769824 ATAATAATTA
9769834 TTATTATTT
1 TTATTATTT
*
9769843 TTAATTATTA
1 TT-ATTATTT
9769853 TTATT-TTT
1 TTATTATTT
9769861 TTATTATTT
1 TTATTATTT
9769870 TT
1 TT
9769872 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:9771589 original size:8 final size:8
Alignment explanation
Indices: 9771573--9771602 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
9771563 CTAAGAAATA
9771573 GAAAGTTG
1 GAAAGTTG
*
9771581 GAAAATTG
1 GAAAGTTG
9771589 GAAAGTTG
1 GAAAGTTG
9771597 GAAAGT
1 GAAAGT
9771603 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:9787061 original size:45 final size:45
Alignment explanation
Indices: 9787011--9787117 Score: 128
Period size: 45 Copynumber: 2.4 Consensus size: 45
9787001 CGACTACGGT
*
9787011 TACTGTTACCGTTACTGTTACCA-ATTC-GACACTTTGTGTGTCGAA
1 TACTGTTACAGTTACTGTTA-CAGATTCAG-CACTTTGTGTGTCGAA
* * *
9787056 TACTGTTACAATTACTGTTATAGATTCAGCACTTTGTGTGTTGAA
1 TACTGTTACAGTTACTGTTACAGATTCAGCACTTTGTGTGTCGAA
* *
9787101 TATTGTTACTGTTACTG
1 TACTGTTACAGTTACTG
9787118 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:9793631 original size:12 final size:12
Alignment explanation
Indices: 9793616--9793659 Score: 61
Period size: 12 Copynumber: 3.6 Consensus size: 12
9793606 AAAACAGGGG
9793616 AGAAAAAGAGAA
1 AGAAAAAGAGAA
*
9793628 AGAAAAAGGGAA
1 AGAAAAAGAGAA
*
9793640 AGAAAAAGAAAA
1 AGAAAAAGAGAA
9793652 AGGAAAAA
1 A-GAAAAA
9793660 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:9793635 original size:6 final size:6
Alignment explanation
Indices: 9793616--9793659 Score: 52
Period size: 6 Copynumber: 7.2 Consensus size: 6
9793606 AAAACAGGGG
* **
9793616 AGAAAA AGAGAA AGAAAA AGGGAA AGAAAA AGAAAA AGGAAAA A
1 AGAAAA AGAAAA AGAAAA AGAAAA AGAAAA AGAAAA A-GAAAA A
9793660 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:9793647 original size:18 final size:18
Alignment explanation
Indices: 9793620--9793654 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
9793610 CAGGGGAGAA
*
9793620 AAAGAGAAAGAAAAAGGG
1 AAAGAAAAAGAAAAAGGG
9793638 AAAGAAAAAGAAAAAGG
1 AAAGAAAAAGAAAAAGG
9793655 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:9794264 original size:45 final size:45
Alignment explanation
Indices: 9794214--9794317 Score: 163
Period size: 45 Copynumber: 2.3 Consensus size: 45
9794204 CTACTGTTAT
* *
9794214 TGTTACCGTTACTGTTACCGATTCAACACTTTGTGTGTCGAATAC
1 TGTTACCGTTACTGTTACAGATTCAACACTTTGTCTGTCGAATAC
* *
9794259 TGTTACCGTTATTGTTACAGATTCAACACTTTGTCTGTTGAATAC
1 TGTTACCGTTACTGTTACAGATTCAACACTTTGTCTGTCGAATAC
*
9794304 TGTTACTGTTACTG
1 TGTTACCGTTACTG
9794318 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:9794332 original size:18 final size:18
Alignment explanation
Indices: 9794301--9794335 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
9794291 GTCTGTTGAA
* *
9794301 TACTGTTACTGTTACTGC
1 TACTGCTACCGTTACTGC
9794319 TACTGCTACCGTTACTG
1 TACTGCTACCGTTACTG
9794336 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:9795086 original size:14 final size:14
Alignment explanation
Indices: 9795067--9795093 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
9795057 CGAAATTTAT
9795067 AAAATAATAATAAA
1 AAAATAATAATAAA
9795081 AAAATAATAATAA
1 AAAATAATAATAA
9795094 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:9815050 original size:3 final size:3
Alignment explanation
Indices: 9815042--9815067 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
9815032 GTAGAAGACC
9815042 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
9815068 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:9828517 original size:21 final size:21
Alignment explanation
Indices: 9828493--9828535 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
9828483 CCTTCTTCTT
9828493 TTTTTTTTTTTCATCTCATGG
1 TTTTTTTTTTTCATCTCATGG
9828514 TTTTTTTTTTTCATCTCATGG
1 TTTTTTTTTTTCATCTCATGG
9828535 T
1 T
9828536 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:9833393 original size:23 final size:23
Alignment explanation
Indices: 9833367--9833427 Score: 59
Period size: 29 Copynumber: 2.4 Consensus size: 23
9833357 TGTTATCATG
9833367 AGAAAAAATAGGATTATATTGAA
1 AGAAAAAATAGGATTATATTGAA
9833390 AGAACAAATTTATATAGGATTATATTGAA
1 AG-A-AAA---A-ATAGGATTATATTGAA
*
9833419 AGAACAAAT
1 AGAAAAAAT
9833428 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:9833416 original size:29 final size:29
Alignment explanation
Indices: 9833374--9833431 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
9833364 ATGAGAAAAA
9833374 ATAGGATTATATTGAAAGAACAAATTTAT
1 ATAGGATTATATTGAAAGAACAAATTTAT
9833403 ATAGGATTATATTGAAAGAACAAATTTAT
1 ATAGGATTATATTGAAAGAACAAATTTAT
9833432 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:9833627 original size:30 final size:30
Alignment explanation
Indices: 9833591--9833653 Score: 117
Period size: 30 Copynumber: 2.1 Consensus size: 30
9833581 ATTAATAGGA
*
9833591 GAAAAATTAAAACTTAATTTTAAATCATTT
1 GAAAAATTAAAACTTAATCTTAAATCATTT
9833621 GAAAAATTAAAACTTAATCTTAAATCATTT
1 GAAAAATTAAAACTTAATCTTAAATCATTT
9833651 GAA
1 GAA
9833654 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:9839000 original size:43 final size:43
Alignment explanation
Indices: 9838904--9839005 Score: 98
Period size: 43 Copynumber: 2.4 Consensus size: 43
9838894 TGAGATTACG
* ** ** *
9838904 TGTAAGACCATGTCTGAGACATTGGCATCGTTAATCGATTTCG
1 TGTAAGACCATGTCTGAGACAGTGGCATCAATAATCGATAACA
* * *
9838947 TATAAAACCATGTCTGAGACAGTGGCATCAATATAT-GGTAACA
1 TGTAAGACCATGTCTGAGACAGTGGCATCAATA-ATCGATAACA
*
9838990 TGTAAGACCATATCTG
1 TGTAAGACCATGTCTG
9839006 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:9845070 original size:24 final size:24
Alignment explanation
Indices: 9845024--9845070 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
9845014 CGTTCTGTAT
* **
9845024 CAAAGGATGAATTGATGGTAAATG
1 CAAAGGATGAATTGACGAAAAATG
*
9845048 CAAAGGATGAATTGGCGAAAAAT
1 CAAAGGATGAATTGACGAAAAAT
9845071 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:9845212 original size:42 final size:41
Alignment explanation
Indices: 9845166--9845275 Score: 103
Period size: 42 Copynumber: 2.6 Consensus size: 41
9845156 ATAAGTTTCT
**
9845166 GTTTAACCTAAATGGGTTTCTGTTTAGCTCATACGAGCTTCA
1 GTTTAACCT-AATGGGTTTCCATTTAGCTCATACGAGCTTCA
* * * *
9845208 GTTTAACCCTTATGGGTTTCCATTTAGCTCCTATGAGCTTCC
1 GTTTAA-CCTAATGGGTTTCCATTTAGCTCATACGAGCTTCA
* * * *
9845250 GTTCAACCCTTATGAGTTTCTATTTA
1 GTTTAA-CCTAATGGGTTTCCATTTA
9845276 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:9845290 original size:42 final size:42
Alignment explanation
Indices: 9845200--9845293 Score: 107
Period size: 42 Copynumber: 2.2 Consensus size: 42
9845190 TAGCTCATAC
* * * * * *
9845200 GAGCTTCAGTTTAACCCTTATGGGTTTCCATTTAGCTCCTAT
1 GAGCTTCCGTTCAACCCTTATGAGTTTCCATTTAACACCTAG
* *
9845242 GAGCTTCCGTTCAACCCTTATGAGTTTCTATTTAACACTTAG
1 GAGCTTCCGTTCAACCCTTATGAGTTTCCATTTAACACCTAG
*
9845284 GTGCTTCCGT
1 GAGCTTCCGT
9845294 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:9852004 original size:26 final size:26
Alignment explanation
Indices: 9851961--9852024 Score: 69
Period size: 26 Copynumber: 2.5 Consensus size: 26
9851951 ACCCACAGAA
* * *
9851961 TTTTTTTTAT-TTATTTTTTT-TCATA
1 TTTTTTTTTTGTTCTTTTTTTATCA-C
9851986 TTTTATTTTTTGTTCTTTTTTTATCAC
1 TTTT-TTTTTTGTTCTTTTTTTATCAC
9852013 TTTTTTTTTTGT
1 TTTTTTTTTTGT
9852025 GGGAAATATT
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
25 4 0.12
26 13 0.39
27 13 0.39
28 3 0.09
ACGTcount: A:0.11, C:0.06, G:0.03, T:0.80
Consensus pattern (26 bp):
TTTTTTTTTTGTTCTTTTTTTATCAC
Found at i:9859364 original size:34 final size:34
Alignment explanation
Indices: 9859321--9859387 Score: 134
Period size: 34 Copynumber: 2.0 Consensus size: 34
9859311 ATATTGTCCC
9859321 TTAATTGGACTATAGAAGCTCAATATGAACTGTT
1 TTAATTGGACTATAGAAGCTCAATATGAACTGTT
9859355 TTAATTGGACTATAGAAGCTCAATATGAACTGT
1 TTAATTGGACTATAGAAGCTCAATATGAACTGT
9859388 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:9860974 original size:19 final size:20
Alignment explanation
Indices: 9860940--9860978 Score: 62
Period size: 19 Copynumber: 1.9 Consensus size: 20
9860930 TCAGAGGATA
9860940 AATAATTTAAATTTTATCAAC
1 AATAATTT-AATTTTATCAAC
9860961 AATAATTT-ATTTTATCAA
1 AATAATTTAATTTTATCAA
9860979 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:9865146 original size:21 final size:19
Alignment explanation
Indices: 9865103--9865154 Score: 52
Period size: 19 Copynumber: 2.6 Consensus size: 19
9865093 AAAGTTACAA
*
9865103 TTTATTAAAAATTAGAAATTTT
1 TTTA-TAAAAATTAGAAA--AT
9865125 TTTATAAAAATT-GTAAAAT
1 TTTATAAAAATTAG-AAAAT
9865144 TTTATAAAAAT
1 TTTATAAAAAT
9865155 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:9865160 original size:19 final size:19
Alignment explanation
Indices: 9865124--9865161 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
9865114 TTAGAAATTT
**
9865124 TTTTATAAAAATTGTAAAA
1 TTTTATAAAAATCATAAAA
9865143 TTTTATAAAAATCATAAAA
1 TTTTATAAAAATCATAAAA
9865162 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:9865424 original size:11 final size:11
Alignment explanation
Indices: 9865408--9865433 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
9865398 ATATTTTATA
9865408 TTTTTCCTAAT
1 TTTTTCCTAAT
9865419 TTTTTCCTAAT
1 TTTTTCCTAAT
9865430 TTTT
1 TTTT
9865434 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:9865439 original size:37 final size:36
Alignment explanation
Indices: 9865378--9865448 Score: 99
Period size: 37 Copynumber: 1.9 Consensus size: 36
9865368 TAAACTTTTA
9865378 TAATTTTTTCATATTTCTATATATTTTATATTTTTCC
1 TAATTTTTTCATATTTCTATATATTTT-TATTTTTCC
* *
9865415 TAATTTTTTCCTAATTTTTA-ATATTTTTATTTTT
1 TAATTTTTTCAT-ATTTCTATATATTTTTATTTTT
9865449 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:9865502 original size:17 final size:17
Alignment explanation
Indices: 9865465--9865502 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
9865455 ATTTAATAAT
*
9865465 ATTTATATTTTTTATTG
1 ATTTATATTTTTTATTA
9865482 ATTTAT-TTTTTTATATA
1 ATTTATATTTTTTAT-TA
9865499 ATTT
1 ATTT
9865503 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:9865645 original size:88 final size:87
Alignment explanation
Indices: 9865508--9865723 Score: 238
Period size: 88 Copynumber: 2.4 Consensus size: 87
9865498 AATTTTTTAT
* * *
9865508 AAAAGCAGGGGCTTAATTTATTTTTTTTGAAAAAGTTTGAGAGTATTTTTAATGTATTTTAAAAT
1 AAAAGTAGGGGCTTAA-TTATTTTTTTT--AAAAGTTTGAGAGTATTTTTAATGCATTTTAAAAG
* * *
9865573 TTCAAATACCCAATTGAGTGCAAAA
63 TTCAAATACCCAAATAAGTACAAAA
* *
9865598 AAATAGTAGGGGCTTAATTATTTTTTTTAAAGGTTTGAGAGCT-TTTTTTATGCATTTTAAAAGT
1 AAA-AGTAGGGGCTTAATTATTTTTTTTAAAAGTTTGAGAG-TATTTTTAATGCATTTTAAAAGT
* *
9865662 TCAAGTACGCAAATAAGTACAAAA
64 TCAAATACCCAAATAAGTACAAAA
* * *
9865686 AAAAGTAGAGACTTAATT-TCTTTTTTTAATATGTTTGA
1 AAAAGTAGGGGCTTAATTAT-TTTTTTTAA-AAGTTTGA
9865724 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:9869321 original size:2 final size:2
Alignment explanation
Indices: 9869314--9869341 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
9869304 AATAAACACA
9869314 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
9869342 CAAATCTATT
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:9870212 original size:21 final size:21
Alignment explanation
Indices: 9870186--9870229 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
9870176 ACTATTTAAA
*
9870186 ACCCTTTATTAAATTAGTCTT
1 ACCCTTTATTAAAATAGTCTT
*
9870207 ACCCTTTATTAAAATAGTGTT
1 ACCCTTTATTAAAATAGTCTT
9870228 AC
1 AC
9870230 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:9874439 original size:57 final size:60
Alignment explanation
Indices: 9874290--9874442 Score: 154
Period size: 60 Copynumber: 2.6 Consensus size: 60
9874280 AAAAGTCAAA
* * * * * **
9874290 TTTAAGTATCAATTTAAACAAAGAAACTTAGTTCAAATGCTTAATTGAATCAAAATAAAC
1 TTTAAGTACCAATTTGAACCATGAAACTAAGTTCAAACACTTAATTGAATCAAAATAAAC
* * * *
9874350 TTTAAGTACCAAATTGAACC-TTAAAGTCAAGTTCAAACACTTACTT-AGA-CAAAA-AAAC
1 TTTAAGTACCAATTTGAACCATGAAACT-AAGTTCAAACACTTAATTGA-ATCAAAATAAAC
9874408 -TTAAGTACCAATTTGAACCATGAAACTAAGTTCAA
1 TTTAAGTACCAATTTGAACCATGAAACTAAGTTCAA
9874443 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:9877947 original size:12 final size:13
Alignment explanation
Indices: 9877932--9877979 Score: 55
Period size: 12 Copynumber: 3.7 Consensus size: 13
9877922 AATAGGGGTG
9877932 ATAATAATA-ATA
1 ATAATAATACATA
9877944 ATAATAATACA-A
1 ATAATAATACATA
*
9877956 ACAATAATACATA
1 ATAATAATACATA
9877969 TATATATAATA
1 -ATA-ATAATA
9877980 ATCGTAGTCA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
12 20 0.67
13 2 0.07
14 2 0.07
15 6 0.20
ACGTcount: A:0.62, C:0.06, G:0.00, T:0.31
Consensus pattern (13 bp):
ATAATAATACATA
Found at i:9878437 original size:13 final size:13
Alignment explanation
Indices: 9878419--9878450 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
9878409 AAAGGTACGC
*
9878419 TTTTTTATATATT
1 TTTTTTAAATATT
9878432 TTTTTTAAATATT
1 TTTTTTAAATATT
9878445 TTTTTT
1 TTTTTT
9878451 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:9878805 original size:38 final size:38
Alignment explanation
Indices: 9878757--9878843 Score: 156
Period size: 38 Copynumber: 2.3 Consensus size: 38
9878747 TGGTGGCATA
*
9878757 GTGGTGTAGGTGACCAAGGTGGGTGGCCAACAAGGGTG
1 GTGGAGTAGGTGACCAAGGTGGGTGGCCAACAAGGGTG
*
9878795 GTGGAGTAGGTGGCCAAGGTGGGTGGCCAACAAGGGTG
1 GTGGAGTAGGTGACCAAGGTGGGTGGCCAACAAGGGTG
9878833 GTGGAGTAGGT
1 GTGGAGTAGGT
9878844 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:9878907 original size:12 final size:12
Alignment explanation
Indices: 9878890--9878914 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
9878880 TTGGGTTAGT
9878890 GTTTTGGGCTAA
1 GTTTTGGGCTAA
9878902 GTTTTGGGCTAA
1 GTTTTGGGCTAA
9878914 G
1 G
9878915 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:9879441 original size:42 final size:41
Alignment explanation
Indices: 9879386--9879536 Score: 117
Period size: 43 Copynumber: 3.5 Consensus size: 41
9879376 CATCATTGAT
* *
9879386 CTGTTTCCTTACTGCTTAGGGGTTTAGATCTATAAACTCAAC
1 CTGTTACCCTACTGCTTAGGGGTTTAGATCTATAAACTC-AC
* * * **
9879428 CTGTTACCCTACTGCTTAGGGGTTTAAGGTTTGA-AAATTTGGC
1 CTGTTACCCTACTGCTTAGGGGTTT-AGATCT-ATAAA-CTCAC
* * * *
9879471 TTGTTACCCTATTGCTTA-GGGTAATAATATCTATAAACTTCAC
1 CTGTTACCCTACTGCTTAGGGGT--TTAGATCTATAAAC-TCAC
9879514 CTTGTTACCCTACTGCTTAGGGG
1 C-TGTTACCCTACTGCTTAGGGG
9879537 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:9890256 original size:3 final size:3
Alignment explanation
Indices: 9890248--9890298 Score: 50
Period size: 3 Copynumber: 16.0 Consensus size: 3
9890238 AATAGGGGTG
*
9890248 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
9890296 ATA
1 ATA
9890299 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:9890397 original size:12 final size:12
Alignment explanation
Indices: 9890373--9890403 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
9890363 GAGGGTATAT
9890373 ATAATAT-AATA
1 ATAATATAAATA
9890384 ATAATATAAATA
1 ATAATATAAATA
9890396 ATAATATA
1 ATAATATA
9890404 CATGAGAAGT
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:9893374 original size:23 final size:23
Alignment explanation
Indices: 9893323--9893376 Score: 65
Period size: 23 Copynumber: 2.3 Consensus size: 23
9893313 AAATAATTTG
*
9893323 AATTTCAAGTTAATTGAATCGAGT
1 AATTT-AAGTTAATTGAATCAAGT
*
9893347 TATTTAAGTTAATTCGAAT-AAGT
1 AATTTAAGTTAATT-GAATCAAGT
9893370 AATTTAA
1 AATTTAA
9893377 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:9893557 original size:19 final size:21
Alignment explanation
Indices: 9893522--9893567 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
9893512 AAAAATAAAA
9893522 TAAAATAATTTTCAAAAATT-
1 TAAAATAATTTTCAAAAATTC
9893542 TAAAAT-ATTTAT-AAAAATTC
1 TAAAATAATTT-TCAAAAATTC
9893562 TAAAAT
1 TAAAAT
9893568 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:9900350 original size:209 final size:210
Alignment explanation
Indices: 9899980--9900464 Score: 821
Period size: 209 Copynumber: 2.3 Consensus size: 210
9899970 TTCGACAAAA
* **
9899980 GTACCATTTAGAATTATACTTTTGAATCATCTTTTGCATCAAGTGAATTATATGCCCATTTACAT
1 GTACCATTTAGAATTATACTTTTGAATCATCTTTTGCATCAAGTGAATTATATG--AATAAACAT
9900045 GCAGAATTTACATGCATCAACAACATTAATGATATACCTCATTACATGCAGAATTTACAGTATTT
64 GC-------ACATGCATCAACAACATTAATGATATACCTCATTACATGCAGAATTTACAGTATTT
9900110 AAGCTCCTTAGAATTATACTTTTGAATCATCTTTTGCATCAAGTGAATTATATGCCCATTTAGAA
122 AAGCTCCTTAGAATTATACTTTTGAATCATCTTTTGCATCAAGTGAATTATATGCCCATTTAGAA
9900175 TTTAATGCCAGAAAATGAAACAAT
187 TTTAATGCCAGAAAATGAAACAAT
9900199 GTACCATTTAGAATTATACTTTTGAATCATCTTTTGCATCAAGTGAATTATATGAATAAACACTG
1 GTACCATTTAGAATTATACTTTTGAATCATCTTTTGCATCAAGTGAATTATATGAATAAACA-TG
*
9900264 C-CGT-CATCAACAACATTAATGATATACCTCATTACATGCAGAATTTACAGTATTTAAGCTCCT
65 CACATGCATCAACAACATTAATGATATACCTCATTACATGCAGAATTTACAGTATTTAAGCTCCT
9900327 TAGAATTATACTTTTGAATCATCTTTTGCATCAAGTGAATTATATGCCCATTTAGAATTTAATGC
130 TAGAATTATACTTTTGAATCATCTTTTGCATCAAGTGAATTATATGCCCATTTAGAATTTAATGC
9900392 CAGAAAATGAAACAAT
195 CAGAAAATGAAACAAT
*
9900408 GTACCATTTAGAATTATACTTTTGAATCATCTTTTGCATCAAGTGGATTATATGAAT
1 GTACCATTTAGAATTATACTTTTGAATCATCTTTTGCATCAAGTGAATTATATGAAT
9900465 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:9906183 original size:7 final size:7
Alignment explanation
Indices: 9906171--9906268 Score: 54
Period size: 7 Copynumber: 13.4 Consensus size: 7
9906161 AGTTAACTCC
*
9906171 TAAACCT
1 TAAACCA
*
9906178 TAAACCC
1 TAAACCA
9906185 TAAACCA
1 TAAACCA
* * *
9906192 TATATCT
1 TAAACCA
9906199 TAAACCA
1 TAAACCA
9906206 TAGTTAACTCA
1 TA---AAC-CA
9906217 TAAA-CA
1 TAAACCA
*
9906223 TTAAACCC
1 -TAAACCA
9906231 TAAACCA
1 TAAACCA
* * *
9906238 TATATCT
1 TAAACCA
9906245 TAAACCA
1 TAAACCA
9906252 TAAACCA
1 TAAACCA
*
9906259 TAAACTA
1 TAAACCA
9906266 TAA
1 TAA
9906269 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:9906188 original size:72 final size:70
Alignment explanation
Indices: 9906093--9906228 Score: 159
Period size: 72 Copynumber: 1.9 Consensus size: 70
9906083 CCTTAAACTC
* * ** *
9906093 TAACCCTAACCCCTAACCCCTAAATTATA-ATCCTTAAACCCATAATTCA-TCATAAACATTGAA
1 TAACCCTAAACCCTAAACCCTAAACCATATAT-CTTAAA-CCATAATTAACTCATAAACATT-AA
9906156 ACAATAGT
63 ACAATAGT
* *
9906164 TAACTCCTAAACCTTAAACCCTAAACCATATATCTTAAACCATAGTTAACTCATAAACATTAAAC
1 TAAC-CCTAAACCCTAAACCCTAAACCATATATCTTAAACCATAATTAACTCATAAACATTAAAC
9906229 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:9906202 original size:21 final size:21
Alignment explanation
Indices: 9906176--9906260 Score: 91
Period size: 21 Copynumber: 3.9 Consensus size: 21
9906166 ACTCCTAAAC
*
9906176 CTTAAACCCTAAACCATATAT
1 CTTAAACCATAAACCATATAT
*
9906197 CTTAAACCATAGTTAACTCATA-AA
1 CTTAAACCATA---AAC-CATATAT
*
9906221 CATTAAACCCTAAACCATATAT
1 C-TTAAACCATAAACCATATAT
9906243 CTTAAACCATAAACCATA
1 CTTAAACCATAAACCATA
9906261 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:9906211 original size:46 final size:46
Alignment explanation
Indices: 9906154--9906253 Score: 173
Period size: 46 Copynumber: 2.2 Consensus size: 46
9906144 ATAAACATTG
* * *
9906154 AAACAATAGTTAACTCCTAAACCTTAAACCCTAAACCATATATCTT
1 AAACCATAGTTAACTCATAAACATTAAACCCTAAACCATATATCTT
9906200 AAACCATAGTTAACTCATAAACATTAAACCCTAAACCATATATCTT
1 AAACCATAGTTAACTCATAAACATTAAACCCTAAACCATATATCTT
9906246 AAACCATA
1 AAACCATA
9906254 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:9906487 original size:41 final size:40
Alignment explanation
Indices: 9906426--9906510 Score: 134
Period size: 41 Copynumber: 2.1 Consensus size: 40
9906416 GTTATATGAC
9906426 TTTTAGCGACGTTTTGCCAAAAGCGCCGCTAATGCTCTGGT
1 TTTTAGCGACGTTTTGCCAAAAGCGCCGCTAATGCT-TGGT
* * *
9906467 TTTTAGCGGCGTTTTTCCAAAAGCGCCGCTAATGCTTTGT
1 TTTTAGCGACGTTTTGCCAAAAGCGCCGCTAATGCTTGGT
9906507 TTTT
1 TTTT
9906511 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:9914892 original size:14 final size:14
Alignment explanation
Indices: 9914873--9914899 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
9914863 TTGGTAACCT
9914873 GTAAAAGCTTTTCC
1 GTAAAAGCTTTTCC
9914887 GTAAAAGCTTTTC
1 GTAAAAGCTTTTC
9914900 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:9915062 original size:6 final size:6
Alignment explanation
Indices: 9915051--9915082 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
9915041 CTTCTCCCAT
9915051 TTCCCC TTCCCC TTCCCC TTCCCC TTCCCC TT
1 TTCCCC TTCCCC TTCCCC TTCCCC TTCCCC TT
9915083 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:9916937 original size:27 final size:27
Alignment explanation
Indices: 9916899--9916965 Score: 89
Period size: 27 Copynumber: 2.5 Consensus size: 27
9916889 GGCGCGAGAG
* * *
9916899 AAAGGCACAAATGGTTGTGCCTATCTC
1 AAAGGCGCAAATGGTTGTACCTATCCC
9916926 AAAGGCGCAAATGGTTGTACCTATCCC
1 AAAGGCGCAAATGGTTGTACCTATCCC
**
9916953 GGAGGCGCAAATG
1 AAAGGCGCAAATG
9916966 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:9923658 original size:59 final size:60
Alignment explanation
Indices: 9923570--9923686 Score: 182
Period size: 59 Copynumber: 2.0 Consensus size: 60
9923560 ATACTAAACT
* * * *
9923570 AAACACAACAATTTATAACTTAATCCTAAATTACTAATAAATTAATTTTAAAATAATTCC
1 AAACAAAAAAATTTATAACATAATCCTAAATTACTAACAAATTAATTTTAAAATAATTCC
*
9923630 AAACAAAAAAATTT-TAACATAATCCTAAATTTCTAACAAATTAATTTTAAAATAATT
1 AAACAAAAAAATTTATAACATAATCCTAAATTACTAACAAATTAATTTTAAAATAATT
9923687 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:9923875 original size:21 final size:22
Alignment explanation
Indices: 9923850--9923906 Score: 73
Period size: 21 Copynumber: 2.7 Consensus size: 22
9923840 TACATTACTT
9923850 TTTTTTTCTTTCTTC-TTCTTC
1 TTTTTTTCTTTCTTCTTTCTTC
* *
9923871 TTTTTTTC-TTCTCCTTTCTTT
1 TTTTTTTCTTTCTTCTTTCTTC
*
9923892 TTTTTTTCTCTCTTC
1 TTTTTTTCTTTCTTC
9923907 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:9923876 original size:20 final size:20
Alignment explanation
Indices: 9923847--9923897 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 20
9923837 AAATACATTA
9923847 CTTTTTTTTTCTTTCTTC-TT
1 CTTTTTTTTTC-TTCTTCTTT
*
9923867 CTTCTTTTTTTCTTCTCCTTT
1 CTT-TTTTTTTCTTCTTCTTT
9923888 CTTTTTTTTT
1 CTTTTTTTTT
9923898 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:9923889 original size:18 final size:17
Alignment explanation
Indices: 9923853--9923906 Score: 63
Period size: 18 Copynumber: 3.0 Consensus size: 17
9923843 ATTACTTTTT
*
9923853 TTTTCTTTCTTCTTCTTC
1 TTTT-TTTCTTCTCCTTC
9923871 TTTTTTTCTTCTCCTTTC
1 TTTTTTTCTTCTCC-TTC
*
9923889 TTTTTTTTTTCTCTCTTC
1 TTTTTTTCTTCTC-CTTC
9923907 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:9924475 original size:30 final size:30
Alignment explanation
Indices: 9924430--9924491 Score: 97
Period size: 30 Copynumber: 2.1 Consensus size: 30
9924420 CTTAACAAGC
*
9924430 AAATACCTCTAAAATAATAATAAAATTAAT
1 AAATACCTCTAAAATAATAACAAAATTAAT
* *
9924460 AAATGCCTTTAAAATAATAACAAAATTAAT
1 AAATACCTCTAAAATAATAACAAAATTAAT
9924490 AA
1 AA
9924492 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:9929784 original size:19 final size:20
Alignment explanation
Indices: 9929750--9929787 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
9929740 AATCCTTATA
9929750 CTAAATTAACCTTAATTAAG
1 CTAAATTAACCTTAATTAAG
*
9929770 CTAAATTTA-CTTAATTAA
1 CTAAATTAACCTTAATTAA
9929788 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:9940272 original size:19 final size:20
Alignment explanation
Indices: 9940248--9940291 Score: 72
Period size: 19 Copynumber: 2.2 Consensus size: 20
9940238 TCCAAACACT
*
9940248 AGAAAAGTAAATTATTTT-C
1 AGAAAAGTAAATCATTTTCC
9940267 AGAAAAGTAAATCATTTTCC
1 AGAAAAGTAAATCATTTTCC
9940287 AGAAA
1 AGAAA
9940292 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:9941370 original size:13 final size:13
Alignment explanation
Indices: 9941352--9941406 Score: 65
Period size: 13 Copynumber: 4.2 Consensus size: 13
9941342 CTAGTTTGGC
9941352 AATGCTTTTGAAA
1 AATGCTTTTGAAA
* *
9941365 AATGCTGTGGAAA
1 AATGCTTTTGAAA
* *
9941378 AGTGCTTTTGAGA
1 AATGCTTTTGAAA
*
9941391 AGTGCTTTTGAAA
1 AATGCTTTTGAAA
9941404 AAT
1 AAT
9941407 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:9941664 original size:12 final size:12
Alignment explanation
Indices: 9941647--9941679 Score: 66
Period size: 12 Copynumber: 2.8 Consensus size: 12
9941637 AGGGGAGGAC
9941647 TTGGGGATTACT
1 TTGGGGATTACT
9941659 TTGGGGATTACT
1 TTGGGGATTACT
9941671 TTGGGGATT
1 TTGGGGATT
9941680 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:9942180 original size:15 final size:14
Alignment explanation
Indices: 9942124--9942240 Score: 69
Period size: 15 Copynumber: 8.1 Consensus size: 14
9942114 TTATTATGTT
*
9942124 TCTATTTATATTTA
1 TCTATTTTTATTTA
*
9942138 T-T-TTATTATTCTAA
1 TCTATTTTTATT-T-A
*
9942152 TACTATTATTATTTA
1 T-CTATTTTTATTTA
9942167 TCTAATTTTTATTTA
1 TCT-ATTTTTATTTA
* *
9942182 TCTATTTATATTTC
1 TCTATTTTTATTTA
* *
9942196 TACTATTATTATATA
1 T-CTATTTTTATTTA
9942211 TCTATTTATTATATT-
1 TCTATTT-TTAT-TTA
* *
9942226 TTTATTTCTATTTA
1 TCTATTTTTATTTA
9942240 T
1 T
9942241 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:9942231 original size:29 final size:29
Alignment explanation
Indices: 9942109--9942219 Score: 100
Period size: 29 Copynumber: 3.8 Consensus size: 29
9942099 ATATTATTGC
* *
9942109 TATTATTATTATGTTTCTATTTATATTTA
1 TATTATTATTATATATCTATTTATATTTA
* *
9942138 TTTTATTATTCTA-ATACTA-TTATTATTTA
1 TATTATTATTATATAT-CTATTTA-TATTTA
* * * * *
9942167 TCTAATTTTTATTTATCTATTTATATTTC
1 TATTATTATTATATATCTATTTATATTTA
*
9942196 TACTATTATTATATATCTATTTAT
1 TATTATTATTATATATCTATTTAT
9942220 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:9942238 original size:58 final size:58
Alignment explanation
Indices: 9942124--9942240 Score: 132
Period size: 58 Copynumber: 2.0 Consensus size: 58
9942114 TTATTATGTT
** * *
9942124 TCTATTTATATTTATTTTATTATTCTAATACTATTATTATTTATCTAATTTTTATTTA
1 TCTATTTATATTTATACTATTATTATAATACTATTATTATTTATCTAATTTCTATTTA
* *
9942182 TCTATTTATATTTCTACTATTATTAT-ATATCTATTTATTATATT-T-TTATTTCTATTTA
1 TCTATTTATATTTATACTATTATTATAATA-CTA-TTATTAT-TTATCTAATTTCTATTTA
9942240 T
1 T
9942241 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:9942276 original size:52 final size:54
Alignment explanation
Indices: 9942155--9942276 Score: 125
Period size: 52 Copynumber: 2.4 Consensus size: 54
9942145 ATTCTAATAC
* * *
9942155 TATTATTATTTATC-TA-ATTTTTATTTATCTATTTATATTTCTACTATTATTA
1 TATTATTATTTTTCTTATATTTTTATTTATCTATTTATATTACTAATATTATTA
* *
9942207 TA-TATCTA--TTTATTATATTTTTA-TT-TCTATTTATA-TACTAATATTATTT
1 TATTAT-TATTTTTCTTATATTTTTATTTATCTATTTATATTACTAATATTATTA
9942256 TCATTATTATTTTTCTTATAT
1 T-ATTATTATTTTTCTTATAT
9942277 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:9943591 original size:22 final size:21
Alignment explanation
Indices: 9943556--9943596 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
9943546 TTGTAATTAG
*
9943556 TATTTTTAAAAATATTTTTTT
1 TATTTTTAAAAATAATTTTTT
*
9943577 TATTTTTAATTAATAATTTT
1 TATTTTTAA-AAATAATTTT
9943597 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:9944606 original size:3 final size:3
Alignment explanation
Indices: 9944600--9944624 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
9944590 GAGACGAAGA
9944600 AGG AGG AGG AGG AGG AGG AGG AGG A
1 AGG AGG AGG AGG AGG AGG AGG AGG A
9944625 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:9956792 original size:19 final size:19
Alignment explanation
Indices: 9956755--9956793 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
9956745 AGCAGACCAG
* *
9956755 GAAAAAAAAGGTAAGAAGA
1 GAAAAAAAAGGAAAAAAGA
*
9956774 GAAAAAAAATGAAAAAAGA
1 GAAAAAAAAGGAAAAAAGA
9956793 G
1 G
9956794 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:9961329 original size:21 final size:21
Alignment explanation
Indices: 9961303--9961343 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
9961293 ATCTGCTCAA
* *
9961303 ACTCCACCTGTTTTGGAGTAC
1 ACTCCACCTGCTGTGGAGTAC
9961324 ACTCCACCTGCTGTGGAGTA
1 ACTCCACCTGCTGTGGAGTA
9961344 TTGCTCGTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.29, G:0.22, T:0.29
Consensus pattern (21 bp):
ACTCCACCTGCTGTGGAGTAC
Found at i:9965672 original size:31 final size:31
Alignment explanation
Indices: 9965637--9965712 Score: 91
Period size: 31 Copynumber: 2.5 Consensus size: 31
9965627 TAGCCAAATG
* *
9965637 AATTTGAAACA-TGCAAAGATTAAAATTGATT
1 AATTTGAAA-AGTACAAAGAATAAAATTGATT
**
9965668 AATTTGAAAAGTACATGGAATAAAATTGATT
1 AATTTGAAAAGTACAAAGAATAAAATTGATT
*
9965699 AATTTAAAAAGTAC
1 AATTTGAAAAGTAC
9965713 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:9968439 original size:46 final size:46
Alignment explanation
Indices: 9968369--9968504 Score: 184
Period size: 46 Copynumber: 3.0 Consensus size: 46
9968359 TTCGACATTA
* * * ** * *
9968369 TGCCATAGTATCTTTCAACTATGGTTTTACTAGTTTTC-TGTCATGT
1 TGCCATGGTATCTTTCAACCATGGTCTTAC-ACATTTCATATCAGGT
9968415 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
*
9968461 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATTTCAG
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAG
9968505 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:9990738 original size:21 final size:21
Alignment explanation
Indices: 9990713--9990753 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
9990703 CATTGATTTA
9990713 GTAAATTAGTTTATGAAATTC
1 GTAAATTAGTTTATGAAATTC
9990734 GTAAATTAGTTTATGAAATT
1 GTAAATTAGTTTATGAAATT
9990754 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:9991457 original size:39 final size:39
Alignment explanation
Indices: 9991398--9991474 Score: 136
Period size: 39 Copynumber: 2.0 Consensus size: 39
9991388 TGCATGATAT
9991398 TTGGAAACATATCCGAACTTGAGGTCCGCAAGCTACGTG
1 TTGGAAACATATCCGAACTTGAGGTCCGCAAGCTACGTG
* *
9991437 TTGGAAACATATCCGGACTTGAGGTCCGCAGGCTACGT
1 TTGGAAACATATCCGAACTTGAGGTCCGCAAGCTACGT
9991475 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:9991481 original size:39 final size:39
Alignment explanation
Indices: 9991399--9991490 Score: 132
Period size: 39 Copynumber: 2.4 Consensus size: 39
9991389 GCATGATATT
* **
9991399 TGGAAACATATCCGAACTTGAGGTCCGCAAGCTACGTGT
1 TGGAAACATATCCGGACTTGAGGTCCGCAAGCTACGTAC
*
9991438 TGGAAACATATCCGGACTTGAGGTCCGCAGGCTACGTAC
1 TGGAAACATATCCGGACTTGAGGTCCGCAAGCTACGTAC
*
9991477 TGG-AATATATCCGG
1 TGGAAACATATCCGG
9991491 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:9993134 original size:13 final size:13
Alignment explanation
Indices: 9993116--9993142 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
9993106 GCTCGGCAGG
9993116 GACACGCCCGTGT
1 GACACGCCCGTGT
9993129 GACACGCCCGTGT
1 GACACGCCCGTGT
9993142 G
1 G
9993143 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:9994701 original size:12 final size:13
Alignment explanation
Indices: 9994674--9994711 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
9994664 ACAAAATATT
9994674 AAATTTATTCATA
1 AAATTTATTCATA
*
9994687 AAATTTATTTA-A
1 AAATTTATTCATA
9994699 AAATTTTATTCAT
1 AAA-TTTATTCAT
9994712 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:9999697 original size:20 final size:19
Alignment explanation
Indices: 9999668--9999720 Score: 54
Period size: 20 Copynumber: 2.7 Consensus size: 19
9999658 TCTTCTGACC
9999668 AAAATAAAAAATAT-ATCAA
1 AAAATAAAAAATATAAT-AA
*
9999687 AAAACTAAAAAGTATAATAAA
1 AAAA-TAAAAAATATAAT-AA
*
9999708 AAAATAATAAATA
1 AAAATAAAAAATA
9999721 AAAAATTTAC
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
19 4 0.14
20 16 0.57
21 8 0.29
ACGTcount: A:0.74, C:0.04, G:0.02, T:0.21
Consensus pattern (19 bp):
AAAATAAAAAATATAATAA
Found at i:10000538 original size:20 final size:23
Alignment explanation
Indices: 10000505--10000545 Score: 61
Period size: 21 Copynumber: 1.9 Consensus size: 23
10000495 GTATTTCTTT
10000505 TTTTGTTTTAAT-AAATTATTAA
1 TTTTGTTTTAATAAAATTATTAA
10000527 TTTT-TTTT-ATAAAATTATT
1 TTTTGTTTTAATAAAATTATT
10000546 CATAATAATG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 2 0.11
21 12 0.67
22 4 0.22
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.63
Consensus pattern (23 bp):
TTTTGTTTTAATAAAATTATTAA
Found at i:10018813 original size:21 final size:21
Alignment explanation
Indices: 10018787--10018862 Score: 71
Period size: 21 Copynumber: 3.6 Consensus size: 21
10018777 TCGAACTTTT
*
10018787 TATTTAACTCTTACAAGCTTC
1 TATTTAACTCTTACGAGCTTC
* * *
10018808 TATTTAACTCATACGTGTTTC
1 TATTTAACTCTTACGAGCTTC
* * *
10018829 TGTTTAGCTCTTATGAGCTTC
1 TATTTAACTCTTACGAGCTTC
* *
10018850 TGTTCAACTCTTA
1 TATTTAACTCTTA
10018863 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:10018874 original size:21 final size:21
Alignment explanation
Indices: 10018826--10018893 Score: 59
Period size: 21 Copynumber: 3.3 Consensus size: 21
10018816 TCATACGTGT
* * *
10018826 TTCTGTTTAGCTCTTATGAGC
1 TTCTGTTCAACTCTTAAGAGC
*
10018847 TTCTGTTCAACTCTTAAGAGT
1 TTCTGTTCAACTCTTAAGAGC
* * *
10018868 TTTTGTTC-A-GCTTATGAGC
1 TTCTGTTCAACTCTTAAGAGC
10018887 TTCTGTT
1 TTCTGTT
10018894 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:10018893 original size:19 final size:21
Alignment explanation
Indices: 10018838--10018893 Score: 62
Period size: 21 Copynumber: 2.8 Consensus size: 21
10018828 CTGTTTAGCT
*
10018838 CTTATGAGCTTCTGTTCAACT
1 CTTATGAGCTTCTGTTCAACG
* * *
10018859 CTTAAGAGTTTTTGTTC-A-G
1 CTTATGAGCTTCTGTTCAACG
10018878 CTTATGAGCTTCTGTT
1 CTTATGAGCTTCTGTT
10018894 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:10021473 original size:3 final size:3
Alignment explanation
Indices: 10021465--10021490 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
10021455 TAATTAAATT
10021465 TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TT
10021491 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
Done.